Multiple sequence alignment - TraesCS7D01G076000

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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 TraesCS7D01G076000 chr7D 100.000 3026 0 0 1 3026 45055264 45058289 0.000000e+00 5589.0
1 TraesCS7D01G076000 chr7D 94.204 1294 71 3 943 2236 45220847 45222136 0.000000e+00 1971.0
2 TraesCS7D01G076000 chr7D 92.772 1259 86 4 979 2236 45029815 45028561 0.000000e+00 1816.0
3 TraesCS7D01G076000 chr7D 97.046 948 23 4 1 945 2510852 2511797 0.000000e+00 1591.0
4 TraesCS7D01G076000 chr7D 89.878 573 45 7 2234 2798 45028750 45028183 0.000000e+00 725.0
5 TraesCS7D01G076000 chr7D 89.724 399 38 3 2234 2630 45221947 45222344 9.680000e-140 507.0
6 TraesCS7D01G076000 chr7D 81.481 513 82 7 2395 2906 45105839 45106339 2.810000e-110 409.0
7 TraesCS7D01G076000 chrUn 96.032 1260 48 2 979 2236 330012436 330013695 0.000000e+00 2049.0
8 TraesCS7D01G076000 chrUn 93.774 787 48 1 1450 2236 396475172 396475957 0.000000e+00 1181.0
9 TraesCS7D01G076000 chrUn 93.139 787 53 1 1450 2236 358915193 358915978 0.000000e+00 1153.0
10 TraesCS7D01G076000 chrUn 93.496 738 47 1 1499 2236 252047990 252048726 0.000000e+00 1096.0
11 TraesCS7D01G076000 chrUn 96.244 639 23 1 979 1616 391210850 391211488 0.000000e+00 1046.0
12 TraesCS7D01G076000 chrUn 96.106 642 24 1 979 1619 397187719 397187078 0.000000e+00 1046.0
13 TraesCS7D01G076000 chrUn 88.441 571 53 9 2237 2798 252048538 252049104 0.000000e+00 676.0
14 TraesCS7D01G076000 chrUn 88.441 571 53 9 2237 2798 396475769 396476335 0.000000e+00 676.0
15 TraesCS7D01G076000 chrUn 88.225 569 54 9 2239 2798 358915792 358916356 0.000000e+00 667.0
16 TraesCS7D01G076000 chrUn 93.447 412 25 2 72 482 100598369 100598779 7.170000e-171 610.0
17 TraesCS7D01G076000 chrUn 87.893 413 40 8 2387 2797 245139704 245140108 7.590000e-131 477.0
18 TraesCS7D01G076000 chrUn 87.621 412 43 7 2387 2797 371971214 371970810 3.530000e-129 472.0
19 TraesCS7D01G076000 chrUn 87.192 203 21 5 2237 2435 215474565 215474364 3.040000e-55 226.0
20 TraesCS7D01G076000 chrUn 87.192 203 21 5 2237 2435 330013506 330013707 3.040000e-55 226.0
21 TraesCS7D01G076000 chrUn 87.192 203 21 5 2237 2435 417621972 417621771 3.040000e-55 226.0
22 TraesCS7D01G076000 chr1A 95.635 1260 53 2 979 2236 12639151 12640410 0.000000e+00 2021.0
23 TraesCS7D01G076000 chr1A 93.520 787 50 1 1450 2236 12642349 12643134 0.000000e+00 1170.0
24 TraesCS7D01G076000 chr1A 88.441 571 53 9 2237 2798 12642946 12643512 0.000000e+00 676.0
25 TraesCS7D01G076000 chr7A 92.000 1175 78 8 963 2134 47435921 47437082 0.000000e+00 1635.0
26 TraesCS7D01G076000 chr7A 89.542 153 12 1 509 661 708563553 708563701 1.110000e-44 191.0
27 TraesCS7D01G076000 chr6D 97.780 946 19 2 1 945 38533942 38532998 0.000000e+00 1629.0
28 TraesCS7D01G076000 chr6D 90.501 379 32 3 104 482 435933571 435933197 5.830000e-137 497.0
29 TraesCS7D01G076000 chr6D 87.879 66 8 0 11 76 115321995 115321930 8.990000e-11 78.7
30 TraesCS7D01G076000 chr6B 95.157 413 18 2 71 482 31777313 31776902 0.000000e+00 651.0
31 TraesCS7D01G076000 chr6B 93.956 182 10 1 481 661 31776757 31776576 1.070000e-69 274.0
32 TraesCS7D01G076000 chr6B 96.364 55 2 0 1 55 31777358 31777304 1.160000e-14 91.6
33 TraesCS7D01G076000 chr3A 90.315 413 36 4 72 482 710085680 710085270 3.430000e-149 538.0
34 TraesCS7D01G076000 chr4A 87.864 412 42 6 2387 2797 656771621 656772025 7.590000e-131 477.0
35 TraesCS7D01G076000 chr4A 96.820 283 9 0 663 945 610049204 610049486 9.820000e-130 473.0
36 TraesCS7D01G076000 chr4A 91.503 153 8 3 509 661 665727967 665727820 3.950000e-49 206.0
37 TraesCS7D01G076000 chr5D 83.101 503 72 6 2405 2906 308220701 308220211 2.140000e-121 446.0
38 TraesCS7D01G076000 chr5D 88.525 366 36 5 72 436 22807592 22807952 3.580000e-119 438.0
39 TraesCS7D01G076000 chr4D 87.786 393 33 8 81 473 85862375 85862752 2.140000e-121 446.0
40 TraesCS7D01G076000 chr4D 88.339 283 30 3 663 943 487058917 487058636 1.340000e-88 337.0
41 TraesCS7D01G076000 chr7B 94.346 283 15 1 663 944 230208021 230208303 1.670000e-117 433.0
42 TraesCS7D01G076000 chr7B 93.421 76 5 0 1 76 605369980 605370055 2.470000e-21 113.0
43 TraesCS7D01G076000 chr7B 100.000 37 0 0 72 108 10215071 10215107 5.410000e-08 69.4
44 TraesCS7D01G076000 chr5A 82.505 503 66 13 2405 2906 389724488 389724969 3.610000e-114 422.0
45 TraesCS7D01G076000 chr5B 85.749 407 42 9 72 477 124632603 124632994 1.680000e-112 416.0
46 TraesCS7D01G076000 chr3B 91.519 283 14 3 663 945 719852223 719852495 6.120000e-102 381.0
47 TraesCS7D01G076000 chr3B 88.158 76 9 0 1 76 284472935 284472860 1.160000e-14 91.6
48 TraesCS7D01G076000 chr2A 88.406 276 11 5 663 938 378840139 378839885 2.260000e-81 313.0
49 TraesCS7D01G076000 chr2A 96.875 32 1 0 899 930 2282440 2282409 2.000000e-03 54.7
50 TraesCS7D01G076000 chr2D 94.382 89 5 0 573 661 357276148 357276236 1.460000e-28 137.0
51 TraesCS7D01G076000 chr2D 98.684 76 1 0 545 620 28361747 28361672 5.260000e-28 135.0
52 TraesCS7D01G076000 chr4B 92.105 76 5 1 1 76 610834232 610834306 4.130000e-19 106.0
53 TraesCS7D01G076000 chr2B 88.889 63 5 2 884 945 6539331 6539270 3.230000e-10 76.8


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 TraesCS7D01G076000 chr7D 45055264 45058289 3025 False 5589.000000 5589 100.0000 1 3026 1 chr7D.!!$F2 3025
1 TraesCS7D01G076000 chr7D 2510852 2511797 945 False 1591.000000 1591 97.0460 1 945 1 chr7D.!!$F1 944
2 TraesCS7D01G076000 chr7D 45028183 45029815 1632 True 1270.500000 1816 91.3250 979 2798 2 chr7D.!!$R1 1819
3 TraesCS7D01G076000 chr7D 45220847 45222344 1497 False 1239.000000 1971 91.9640 943 2630 2 chr7D.!!$F4 1687
4 TraesCS7D01G076000 chr7D 45105839 45106339 500 False 409.000000 409 81.4810 2395 2906 1 chr7D.!!$F3 511
5 TraesCS7D01G076000 chrUn 330012436 330013707 1271 False 1137.500000 2049 91.6120 979 2435 2 chrUn.!!$F5 1456
6 TraesCS7D01G076000 chrUn 391210850 391211488 638 False 1046.000000 1046 96.2440 979 1616 1 chrUn.!!$F3 637
7 TraesCS7D01G076000 chrUn 397187078 397187719 641 True 1046.000000 1046 96.1060 979 1619 1 chrUn.!!$R3 640
8 TraesCS7D01G076000 chrUn 396475172 396476335 1163 False 928.500000 1181 91.1075 1450 2798 2 chrUn.!!$F7 1348
9 TraesCS7D01G076000 chrUn 358915193 358916356 1163 False 910.000000 1153 90.6820 1450 2798 2 chrUn.!!$F6 1348
10 TraesCS7D01G076000 chrUn 252047990 252049104 1114 False 886.000000 1096 90.9685 1499 2798 2 chrUn.!!$F4 1299
11 TraesCS7D01G076000 chr1A 12639151 12643512 4361 False 1289.000000 2021 92.5320 979 2798 3 chr1A.!!$F1 1819
12 TraesCS7D01G076000 chr7A 47435921 47437082 1161 False 1635.000000 1635 92.0000 963 2134 1 chr7A.!!$F1 1171
13 TraesCS7D01G076000 chr6D 38532998 38533942 944 True 1629.000000 1629 97.7800 1 945 1 chr6D.!!$R1 944
14 TraesCS7D01G076000 chr6B 31776576 31777358 782 True 338.866667 651 95.1590 1 661 3 chr6B.!!$R1 660

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
477 482 0.61326 TTCTGTAATGCCTCGGCTGT 59.387 50.0 9.65 0.0 42.51 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2206 5096 0.03309 TGCATCTCTCTAGCGCATGG 59.967 55.0 11.47 0.0 0.0 3.66 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
334 337 6.856426 GTCAAAGGTTGTAGCATTTTCTGTAC 59.144 38.462 0.00 0.00 0.00 2.90
337 340 5.373222 AGGTTGTAGCATTTTCTGTACACA 58.627 37.500 0.00 0.00 0.00 3.72
473 478 1.656652 CAGGTTCTGTAATGCCTCGG 58.343 55.000 0.00 0.00 0.00 4.63
477 482 0.613260 TTCTGTAATGCCTCGGCTGT 59.387 50.000 9.65 0.00 42.51 4.40
501 652 4.735132 ATGTGTGACGCCGACGGG 62.735 66.667 17.22 8.43 46.04 5.28
718 870 2.255172 CGCTCCGCCTCGTATCTCT 61.255 63.158 0.00 0.00 0.00 3.10
838 990 0.618458 AAGGCAACCATAGCGAAGGA 59.382 50.000 0.00 0.00 37.17 3.36
939 1091 2.586914 GCGCGCCGGGTATAAACT 60.587 61.111 23.24 0.00 0.00 2.66
945 1097 1.328374 CGCCGGGTATAAACTTTTCCG 59.672 52.381 2.18 0.00 37.50 4.30
950 1102 3.685756 CGGGTATAAACTTTTCCGCAAGA 59.314 43.478 0.00 0.00 43.02 3.02
1025 1177 4.785453 CCTCCTCAAGGCCACCGC 62.785 72.222 5.01 0.00 38.67 5.68
1286 1438 1.788203 GCGAAACGTGCACGACATG 60.788 57.895 42.94 28.37 43.02 3.21
1459 1611 1.105167 CCAGATTGATGGCATGCCGT 61.105 55.000 31.62 31.62 39.42 5.68
1474 1626 2.712539 CGTTGCGCTTCACCAACA 59.287 55.556 9.73 0.00 40.93 3.33
1542 1696 2.678836 CTCGATGAACTACGACAGGTCT 59.321 50.000 8.03 0.00 42.02 3.85
1619 1773 0.457853 CCACGAACATCGGACGTCAT 60.458 55.000 18.91 0.00 45.59 3.06
1666 4546 2.749110 GAACGGTGTCTCGCTCAGCA 62.749 60.000 0.00 0.00 33.61 4.41
1962 4842 3.810310 ACCGAGATCATGGAAAGAGAC 57.190 47.619 9.97 0.00 0.00 3.36
1990 4870 0.113776 ACTCTACCTGGGTTCGGTGA 59.886 55.000 0.00 0.00 35.98 4.02
2038 4918 8.943594 AAAAAGGAAGTAGAGAGAAGTAGAGA 57.056 34.615 0.00 0.00 0.00 3.10
2081 4969 9.302345 GGCTTTTAGTTTCTTATTATTCTTGCC 57.698 33.333 0.00 0.00 0.00 4.52
2105 4993 5.065218 CGCTAAATGTAATGCTCCAGTTTCT 59.935 40.000 0.00 0.00 0.00 2.52
2110 4998 7.951530 AATGTAATGCTCCAGTTTCTTTTTG 57.048 32.000 0.00 0.00 0.00 2.44
2157 5047 8.673711 TCCTTATTTTTACGATCAGACCATTTG 58.326 33.333 0.00 0.00 0.00 2.32
2184 5074 2.822561 TGCTTCATTTTAATGTCCGGCA 59.177 40.909 0.00 0.00 37.65 5.69
2185 5075 3.446873 TGCTTCATTTTAATGTCCGGCAT 59.553 39.130 0.00 0.06 40.03 4.40
2186 5076 3.798337 GCTTCATTTTAATGTCCGGCATG 59.202 43.478 11.38 0.00 37.96 4.06
2187 5077 4.439974 GCTTCATTTTAATGTCCGGCATGA 60.440 41.667 11.38 2.41 37.96 3.07
2188 5078 5.737063 GCTTCATTTTAATGTCCGGCATGAT 60.737 40.000 11.38 1.29 37.96 2.45
2189 5079 6.514870 GCTTCATTTTAATGTCCGGCATGATA 60.515 38.462 11.38 0.45 37.96 2.15
2190 5080 6.312399 TCATTTTAATGTCCGGCATGATAC 57.688 37.500 11.38 0.00 37.96 2.24
2191 5081 6.061441 TCATTTTAATGTCCGGCATGATACT 58.939 36.000 11.38 0.05 37.96 2.12
2192 5082 5.749596 TTTTAATGTCCGGCATGATACTG 57.250 39.130 11.38 0.00 37.96 2.74
2193 5083 4.681074 TTAATGTCCGGCATGATACTGA 57.319 40.909 11.38 0.00 37.96 3.41
2194 5084 3.777106 AATGTCCGGCATGATACTGAT 57.223 42.857 11.38 0.00 37.96 2.90
2195 5085 2.531522 TGTCCGGCATGATACTGATG 57.468 50.000 0.00 0.00 0.00 3.07
2196 5086 1.762370 TGTCCGGCATGATACTGATGT 59.238 47.619 0.00 0.00 0.00 3.06
2197 5087 2.224042 TGTCCGGCATGATACTGATGTC 60.224 50.000 0.00 0.00 0.00 3.06
2198 5088 1.000274 TCCGGCATGATACTGATGTCG 60.000 52.381 0.00 0.00 46.15 4.35
2199 5089 1.269778 CCGGCATGATACTGATGTCGT 60.270 52.381 0.00 0.00 45.35 4.34
2200 5090 2.473816 CGGCATGATACTGATGTCGTT 58.526 47.619 0.00 0.00 42.58 3.85
2201 5091 2.866156 CGGCATGATACTGATGTCGTTT 59.134 45.455 0.00 0.00 42.58 3.60
2202 5092 4.048504 CGGCATGATACTGATGTCGTTTA 58.951 43.478 0.00 0.00 42.58 2.01
2203 5093 4.085055 CGGCATGATACTGATGTCGTTTAC 60.085 45.833 0.00 0.00 42.58 2.01
2204 5094 5.050490 GGCATGATACTGATGTCGTTTACT 58.950 41.667 0.00 0.00 0.00 2.24
2205 5095 5.050769 GGCATGATACTGATGTCGTTTACTG 60.051 44.000 0.00 0.00 0.00 2.74
2206 5096 5.557136 GCATGATACTGATGTCGTTTACTGC 60.557 44.000 0.00 0.00 0.00 4.40
2207 5097 4.430007 TGATACTGATGTCGTTTACTGCC 58.570 43.478 0.00 0.00 0.00 4.85
2208 5098 2.831685 ACTGATGTCGTTTACTGCCA 57.168 45.000 0.00 0.00 0.00 4.92
2209 5099 3.334583 ACTGATGTCGTTTACTGCCAT 57.665 42.857 0.00 0.00 0.00 4.40
2210 5100 3.002791 ACTGATGTCGTTTACTGCCATG 58.997 45.455 0.00 0.00 0.00 3.66
2211 5101 1.737236 TGATGTCGTTTACTGCCATGC 59.263 47.619 0.00 0.00 0.00 4.06
2212 5102 0.726827 ATGTCGTTTACTGCCATGCG 59.273 50.000 0.00 0.00 0.00 4.73
2213 5103 1.226018 GTCGTTTACTGCCATGCGC 60.226 57.895 0.00 0.00 38.31 6.09
2214 5104 1.375396 TCGTTTACTGCCATGCGCT 60.375 52.632 9.73 0.00 38.78 5.92
2215 5105 0.108567 TCGTTTACTGCCATGCGCTA 60.109 50.000 9.73 0.00 38.78 4.26
2216 5106 0.301687 CGTTTACTGCCATGCGCTAG 59.698 55.000 9.73 0.00 38.78 3.42
2217 5107 1.651987 GTTTACTGCCATGCGCTAGA 58.348 50.000 9.73 0.00 38.78 2.43
2218 5108 1.594862 GTTTACTGCCATGCGCTAGAG 59.405 52.381 9.73 0.00 38.78 2.43
2219 5109 1.111277 TTACTGCCATGCGCTAGAGA 58.889 50.000 9.73 0.00 38.78 3.10
2220 5110 0.670706 TACTGCCATGCGCTAGAGAG 59.329 55.000 9.73 1.59 38.78 3.20
2221 5111 1.039785 ACTGCCATGCGCTAGAGAGA 61.040 55.000 9.73 0.00 38.78 3.10
2222 5112 0.317799 CTGCCATGCGCTAGAGAGAT 59.682 55.000 9.73 0.00 38.78 2.75
2223 5113 0.033090 TGCCATGCGCTAGAGAGATG 59.967 55.000 9.73 1.24 38.78 2.90
2224 5114 1.290491 GCCATGCGCTAGAGAGATGC 61.290 60.000 9.73 0.00 0.00 3.91
2225 5115 0.033090 CCATGCGCTAGAGAGATGCA 59.967 55.000 9.73 0.00 39.15 3.96
2226 5116 1.539712 CCATGCGCTAGAGAGATGCAA 60.540 52.381 9.73 0.00 38.56 4.08
2227 5117 2.207590 CATGCGCTAGAGAGATGCAAA 58.792 47.619 9.73 0.00 38.56 3.68
2228 5118 1.645034 TGCGCTAGAGAGATGCAAAC 58.355 50.000 9.73 0.00 34.01 2.93
2229 5119 1.205655 TGCGCTAGAGAGATGCAAACT 59.794 47.619 9.73 0.00 34.01 2.66
2230 5120 2.275318 GCGCTAGAGAGATGCAAACTT 58.725 47.619 0.00 0.00 0.00 2.66
2231 5121 2.030213 GCGCTAGAGAGATGCAAACTTG 59.970 50.000 0.00 0.00 0.00 3.16
2232 5122 3.515630 CGCTAGAGAGATGCAAACTTGA 58.484 45.455 0.00 0.00 0.00 3.02
2233 5123 3.928992 CGCTAGAGAGATGCAAACTTGAA 59.071 43.478 0.00 0.00 0.00 2.69
2234 5124 4.032672 CGCTAGAGAGATGCAAACTTGAAG 59.967 45.833 0.00 0.00 0.00 3.02
2235 5125 5.174395 GCTAGAGAGATGCAAACTTGAAGA 58.826 41.667 0.00 0.00 0.00 2.87
2236 5126 5.816777 GCTAGAGAGATGCAAACTTGAAGAT 59.183 40.000 0.00 0.00 0.00 2.40
2237 5127 6.983307 GCTAGAGAGATGCAAACTTGAAGATA 59.017 38.462 0.00 0.00 0.00 1.98
2238 5128 7.656948 GCTAGAGAGATGCAAACTTGAAGATAT 59.343 37.037 0.00 0.00 0.00 1.63
2241 5131 8.149647 AGAGAGATGCAAACTTGAAGATATAGG 58.850 37.037 0.00 0.00 0.00 2.57
2242 5132 8.027524 AGAGATGCAAACTTGAAGATATAGGA 57.972 34.615 0.00 0.00 0.00 2.94
2243 5133 8.658619 AGAGATGCAAACTTGAAGATATAGGAT 58.341 33.333 0.00 0.00 0.00 3.24
2244 5134 8.618702 AGATGCAAACTTGAAGATATAGGATG 57.381 34.615 0.00 0.00 0.00 3.51
2245 5135 7.664731 AGATGCAAACTTGAAGATATAGGATGG 59.335 37.037 0.00 0.00 0.00 3.51
2246 5136 6.899089 TGCAAACTTGAAGATATAGGATGGA 58.101 36.000 0.00 0.00 0.00 3.41
2247 5137 7.520798 TGCAAACTTGAAGATATAGGATGGAT 58.479 34.615 0.00 0.00 0.00 3.41
2248 5138 8.000709 TGCAAACTTGAAGATATAGGATGGATT 58.999 33.333 0.00 0.00 0.00 3.01
2249 5139 8.854117 GCAAACTTGAAGATATAGGATGGATTT 58.146 33.333 0.00 0.00 0.00 2.17
2270 5160 9.665264 GGATTTAGTTTCTTATTATTCTTGCGG 57.335 33.333 0.00 0.00 0.00 5.69
2271 5161 9.170584 GATTTAGTTTCTTATTATTCTTGCGGC 57.829 33.333 0.00 0.00 0.00 6.53
2272 5162 7.859325 TTAGTTTCTTATTATTCTTGCGGCT 57.141 32.000 0.00 0.00 0.00 5.52
2273 5163 8.951787 TTAGTTTCTTATTATTCTTGCGGCTA 57.048 30.769 0.00 0.00 0.00 3.93
2274 5164 9.555727 TTAGTTTCTTATTATTCTTGCGGCTAT 57.444 29.630 0.00 0.00 0.00 2.97
2276 5166 9.726438 AGTTTCTTATTATTCTTGCGGCTATAT 57.274 29.630 0.00 0.00 0.00 0.86
2277 5167 9.760660 GTTTCTTATTATTCTTGCGGCTATATG 57.239 33.333 0.00 0.00 0.00 1.78
2278 5168 9.502091 TTTCTTATTATTCTTGCGGCTATATGT 57.498 29.630 0.00 0.00 0.00 2.29
2283 5173 5.551760 ATTCTTGCGGCTATATGTAATGC 57.448 39.130 0.00 0.00 0.00 3.56
2284 5174 4.271696 TCTTGCGGCTATATGTAATGCT 57.728 40.909 0.00 0.00 0.00 3.79
2285 5175 4.245660 TCTTGCGGCTATATGTAATGCTC 58.754 43.478 0.00 0.00 0.00 4.26
2286 5176 2.972625 TGCGGCTATATGTAATGCTCC 58.027 47.619 0.00 0.00 0.00 4.70
2287 5177 2.301583 TGCGGCTATATGTAATGCTCCA 59.698 45.455 0.00 0.00 0.00 3.86
2288 5178 2.932614 GCGGCTATATGTAATGCTCCAG 59.067 50.000 0.00 0.00 0.00 3.86
2289 5179 3.617531 GCGGCTATATGTAATGCTCCAGT 60.618 47.826 0.00 0.00 0.00 4.00
2290 5180 4.569943 CGGCTATATGTAATGCTCCAGTT 58.430 43.478 0.00 0.00 0.00 3.16
2291 5181 4.997395 CGGCTATATGTAATGCTCCAGTTT 59.003 41.667 0.00 0.00 0.00 2.66
2292 5182 5.120830 CGGCTATATGTAATGCTCCAGTTTC 59.879 44.000 0.00 0.00 0.00 2.78
2293 5183 6.234177 GGCTATATGTAATGCTCCAGTTTCT 58.766 40.000 0.00 0.00 0.00 2.52
2294 5184 6.712547 GGCTATATGTAATGCTCCAGTTTCTT 59.287 38.462 0.00 0.00 0.00 2.52
2295 5185 7.229506 GGCTATATGTAATGCTCCAGTTTCTTT 59.770 37.037 0.00 0.00 0.00 2.52
2296 5186 8.624776 GCTATATGTAATGCTCCAGTTTCTTTT 58.375 33.333 0.00 0.00 0.00 2.27
2369 5261 6.826893 TTTTTGCTTCAGTTTAATGTCAGC 57.173 33.333 0.00 0.00 0.00 4.26
2375 5267 5.181245 GCTTCAGTTTAATGTCAGCCAAGTA 59.819 40.000 0.00 0.00 0.00 2.24
2383 5275 1.621317 TGTCAGCCAAGTAACCGATGA 59.379 47.619 0.00 0.00 0.00 2.92
2391 5283 3.247442 CAAGTAACCGATGACGCTTACA 58.753 45.455 0.00 0.00 40.69 2.41
2471 5363 0.616891 ATCCACAGTAACCCGTTCCC 59.383 55.000 0.00 0.00 0.00 3.97
2474 5366 0.321298 CACAGTAACCCGTTCCCCTG 60.321 60.000 0.00 0.00 0.00 4.45
2538 5431 2.429930 CCACCCTGCCGTTCTTGA 59.570 61.111 0.00 0.00 0.00 3.02
2567 5460 4.309950 ACGACAACCCTGACGGCC 62.310 66.667 0.00 0.00 43.62 6.13
2571 5464 4.760047 CAACCCTGACGGCCCTCG 62.760 72.222 0.00 0.00 45.88 4.63
2611 5504 3.506067 CCGTTCTATTCCCACTGCTTTTT 59.494 43.478 0.00 0.00 0.00 1.94
2646 5544 0.326618 CCAGTACCCATCCCTGGTCT 60.327 60.000 0.00 0.00 41.37 3.85
2655 5553 0.031616 ATCCCTGGTCTCCTCTGTCC 60.032 60.000 0.00 0.00 0.00 4.02
2798 5696 4.056125 CCTGTCGGCGCTCACAGA 62.056 66.667 29.47 11.86 42.37 3.41
2799 5697 2.505777 CTGTCGGCGCTCACAGAG 60.506 66.667 25.89 8.28 42.37 3.35
2800 5698 3.274455 CTGTCGGCGCTCACAGAGT 62.274 63.158 25.89 0.00 42.37 3.24
2802 5700 2.983592 TCGGCGCTCACAGAGTCA 60.984 61.111 7.64 0.00 31.39 3.41
2803 5701 2.807045 CGGCGCTCACAGAGTCAC 60.807 66.667 7.64 0.00 31.39 3.67
2804 5702 2.340078 GGCGCTCACAGAGTCACA 59.660 61.111 7.64 0.00 31.39 3.58
2805 5703 1.735920 GGCGCTCACAGAGTCACAG 60.736 63.158 7.64 0.00 31.39 3.66
2806 5704 2.378858 GCGCTCACAGAGTCACAGC 61.379 63.158 0.00 0.00 31.39 4.40
2807 5705 1.735920 CGCTCACAGAGTCACAGCC 60.736 63.158 0.00 0.00 31.39 4.85
2808 5706 1.368950 GCTCACAGAGTCACAGCCA 59.631 57.895 0.00 0.00 31.39 4.75
2809 5707 0.036577 GCTCACAGAGTCACAGCCAT 60.037 55.000 0.00 0.00 31.39 4.40
2848 5746 2.048127 GGACCTGAGCACGGTGAC 60.048 66.667 13.29 5.59 34.19 3.67
2849 5747 2.734591 GACCTGAGCACGGTGACA 59.265 61.111 13.29 9.97 34.19 3.58
2851 5749 0.320771 GACCTGAGCACGGTGACATT 60.321 55.000 13.29 1.68 34.19 2.71
2852 5750 0.603707 ACCTGAGCACGGTGACATTG 60.604 55.000 13.29 7.80 32.41 2.82
2861 5759 3.799755 GTGACATTGCCGGTCCGC 61.800 66.667 5.50 1.95 34.36 5.54
2876 5774 2.699768 CCGCGGGTTGCACATCATT 61.700 57.895 20.10 0.00 46.97 2.57
2885 5783 2.896801 GCACATCATTAGCCGCCCG 61.897 63.158 0.00 0.00 0.00 6.13
2888 5786 1.369692 CATCATTAGCCGCCCGGTA 59.630 57.895 8.66 0.00 37.65 4.02
2890 5788 1.119574 ATCATTAGCCGCCCGGTAGT 61.120 55.000 8.66 0.00 37.65 2.73
2894 5792 3.942377 TAGCCGCCCGGTAGTGTCA 62.942 63.158 8.66 0.00 37.65 3.58
2906 5804 0.826256 TAGTGTCACCGGTCAGCACT 60.826 55.000 27.45 27.45 42.25 4.40
2907 5805 1.664965 GTGTCACCGGTCAGCACTC 60.665 63.158 19.55 7.00 0.00 3.51
2908 5806 2.048127 GTCACCGGTCAGCACTCC 60.048 66.667 2.59 0.00 0.00 3.85
2909 5807 3.311110 TCACCGGTCAGCACTCCC 61.311 66.667 2.59 0.00 0.00 4.30
2910 5808 3.314331 CACCGGTCAGCACTCCCT 61.314 66.667 2.59 0.00 0.00 4.20
2911 5809 2.997897 ACCGGTCAGCACTCCCTC 60.998 66.667 0.00 0.00 0.00 4.30
2912 5810 4.135153 CCGGTCAGCACTCCCTCG 62.135 72.222 0.00 0.00 0.00 4.63
2913 5811 4.803426 CGGTCAGCACTCCCTCGC 62.803 72.222 0.00 0.00 0.00 5.03
2914 5812 3.386237 GGTCAGCACTCCCTCGCT 61.386 66.667 0.00 0.00 39.66 4.93
2915 5813 2.052690 GGTCAGCACTCCCTCGCTA 61.053 63.158 0.00 0.00 36.50 4.26
2916 5814 1.139947 GTCAGCACTCCCTCGCTAC 59.860 63.158 0.00 0.00 36.50 3.58
2917 5815 1.304134 TCAGCACTCCCTCGCTACA 60.304 57.895 0.00 0.00 36.50 2.74
2918 5816 1.140589 CAGCACTCCCTCGCTACAG 59.859 63.158 0.00 0.00 36.50 2.74
2919 5817 2.055042 AGCACTCCCTCGCTACAGG 61.055 63.158 0.00 0.00 36.50 4.00
2920 5818 2.496817 CACTCCCTCGCTACAGGC 59.503 66.667 0.00 0.00 37.64 4.85
2921 5819 2.037367 ACTCCCTCGCTACAGGCA 59.963 61.111 0.00 0.00 41.91 4.75
2922 5820 1.381872 ACTCCCTCGCTACAGGCAT 60.382 57.895 0.00 0.00 41.91 4.40
2923 5821 0.978146 ACTCCCTCGCTACAGGCATT 60.978 55.000 0.00 0.00 41.91 3.56
2924 5822 0.249657 CTCCCTCGCTACAGGCATTC 60.250 60.000 0.00 0.00 41.91 2.67
2925 5823 0.975556 TCCCTCGCTACAGGCATTCA 60.976 55.000 0.00 0.00 41.91 2.57
2926 5824 0.811616 CCCTCGCTACAGGCATTCAC 60.812 60.000 0.00 0.00 41.91 3.18
2927 5825 0.108186 CCTCGCTACAGGCATTCACA 60.108 55.000 0.00 0.00 41.91 3.58
2928 5826 1.675714 CCTCGCTACAGGCATTCACAA 60.676 52.381 0.00 0.00 41.91 3.33
2929 5827 1.394917 CTCGCTACAGGCATTCACAAC 59.605 52.381 0.00 0.00 41.91 3.32
2930 5828 0.447801 CGCTACAGGCATTCACAACC 59.552 55.000 0.00 0.00 41.91 3.77
2931 5829 1.533625 GCTACAGGCATTCACAACCA 58.466 50.000 0.00 0.00 41.35 3.67
2932 5830 2.094675 GCTACAGGCATTCACAACCAT 58.905 47.619 0.00 0.00 41.35 3.55
2933 5831 3.278574 GCTACAGGCATTCACAACCATA 58.721 45.455 0.00 0.00 41.35 2.74
2934 5832 3.885297 GCTACAGGCATTCACAACCATAT 59.115 43.478 0.00 0.00 41.35 1.78
2935 5833 4.261322 GCTACAGGCATTCACAACCATATG 60.261 45.833 0.00 0.00 41.35 1.78
2936 5834 3.966979 ACAGGCATTCACAACCATATGA 58.033 40.909 3.65 0.00 0.00 2.15
2937 5835 4.539726 ACAGGCATTCACAACCATATGAT 58.460 39.130 3.65 0.00 0.00 2.45
2938 5836 4.957954 ACAGGCATTCACAACCATATGATT 59.042 37.500 3.65 0.00 0.00 2.57
2939 5837 6.128486 ACAGGCATTCACAACCATATGATTA 58.872 36.000 3.65 0.00 0.00 1.75
2940 5838 6.263842 ACAGGCATTCACAACCATATGATTAG 59.736 38.462 3.65 0.00 0.00 1.73
2941 5839 5.242393 AGGCATTCACAACCATATGATTAGC 59.758 40.000 3.65 0.00 0.00 3.09
2942 5840 5.242393 GGCATTCACAACCATATGATTAGCT 59.758 40.000 3.65 0.00 0.00 3.32
2943 5841 6.430925 GGCATTCACAACCATATGATTAGCTA 59.569 38.462 3.65 0.00 0.00 3.32
2944 5842 7.301054 GCATTCACAACCATATGATTAGCTAC 58.699 38.462 3.65 0.00 0.00 3.58
2945 5843 7.173907 GCATTCACAACCATATGATTAGCTACT 59.826 37.037 3.65 0.00 0.00 2.57
2946 5844 9.060347 CATTCACAACCATATGATTAGCTACTT 57.940 33.333 3.65 0.00 0.00 2.24
2947 5845 8.437360 TTCACAACCATATGATTAGCTACTTG 57.563 34.615 3.65 0.00 0.00 3.16
2948 5846 7.564793 TCACAACCATATGATTAGCTACTTGT 58.435 34.615 3.65 0.00 0.00 3.16
2949 5847 7.710907 TCACAACCATATGATTAGCTACTTGTC 59.289 37.037 3.65 0.00 0.00 3.18
2950 5848 7.712639 CACAACCATATGATTAGCTACTTGTCT 59.287 37.037 3.65 0.00 0.00 3.41
2951 5849 7.712639 ACAACCATATGATTAGCTACTTGTCTG 59.287 37.037 3.65 0.00 0.00 3.51
2952 5850 6.763355 ACCATATGATTAGCTACTTGTCTGG 58.237 40.000 3.65 0.00 0.00 3.86
2953 5851 6.327626 ACCATATGATTAGCTACTTGTCTGGT 59.672 38.462 3.65 0.61 0.00 4.00
2954 5852 7.147479 ACCATATGATTAGCTACTTGTCTGGTT 60.147 37.037 3.65 0.00 0.00 3.67
2955 5853 7.172190 CCATATGATTAGCTACTTGTCTGGTTG 59.828 40.741 3.65 0.00 0.00 3.77
2956 5854 5.483685 TGATTAGCTACTTGTCTGGTTGT 57.516 39.130 0.00 0.00 0.00 3.32
2957 5855 5.237815 TGATTAGCTACTTGTCTGGTTGTG 58.762 41.667 0.00 0.00 0.00 3.33
2958 5856 4.948341 TTAGCTACTTGTCTGGTTGTGA 57.052 40.909 0.00 0.00 0.00 3.58
2959 5857 3.838244 AGCTACTTGTCTGGTTGTGAA 57.162 42.857 0.00 0.00 0.00 3.18
2960 5858 4.357918 AGCTACTTGTCTGGTTGTGAAT 57.642 40.909 0.00 0.00 0.00 2.57
2961 5859 4.067896 AGCTACTTGTCTGGTTGTGAATG 58.932 43.478 0.00 0.00 0.00 2.67
2962 5860 3.365364 GCTACTTGTCTGGTTGTGAATGC 60.365 47.826 0.00 0.00 0.00 3.56
2963 5861 1.956477 ACTTGTCTGGTTGTGAATGCC 59.044 47.619 0.00 0.00 0.00 4.40
2964 5862 2.233271 CTTGTCTGGTTGTGAATGCCT 58.767 47.619 0.00 0.00 0.00 4.75
2965 5863 1.608055 TGTCTGGTTGTGAATGCCTG 58.392 50.000 0.00 0.00 0.00 4.85
2966 5864 0.242017 GTCTGGTTGTGAATGCCTGC 59.758 55.000 0.00 0.00 0.00 4.85
2967 5865 0.178995 TCTGGTTGTGAATGCCTGCA 60.179 50.000 0.00 0.00 0.00 4.41
2968 5866 0.892755 CTGGTTGTGAATGCCTGCAT 59.107 50.000 0.00 0.00 38.46 3.96
2969 5867 0.889994 TGGTTGTGAATGCCTGCATC 59.110 50.000 4.89 0.44 35.31 3.91
2970 5868 1.180029 GGTTGTGAATGCCTGCATCT 58.820 50.000 4.89 0.00 35.31 2.90
2971 5869 1.135199 GGTTGTGAATGCCTGCATCTG 60.135 52.381 4.89 0.00 35.31 2.90
2972 5870 0.528924 TTGTGAATGCCTGCATCTGC 59.471 50.000 4.89 0.00 42.50 4.26
2988 5886 4.691175 CATCTGCATGCACTACTTCTAGT 58.309 43.478 18.46 0.00 33.01 2.57
2989 5887 5.836347 CATCTGCATGCACTACTTCTAGTA 58.164 41.667 18.46 0.00 31.46 1.82
2990 5888 5.250235 TCTGCATGCACTACTTCTAGTAC 57.750 43.478 18.46 0.00 31.46 2.73
2991 5889 4.028852 TGCATGCACTACTTCTAGTACG 57.971 45.455 18.46 0.00 31.46 3.67
2992 5890 3.692593 TGCATGCACTACTTCTAGTACGA 59.307 43.478 18.46 0.00 31.46 3.43
2993 5891 4.201920 TGCATGCACTACTTCTAGTACGAG 60.202 45.833 18.46 0.00 31.46 4.18
2994 5892 4.283678 CATGCACTACTTCTAGTACGAGC 58.716 47.826 0.00 0.00 31.46 5.03
2995 5893 2.350804 TGCACTACTTCTAGTACGAGCG 59.649 50.000 0.00 0.00 31.46 5.03
2996 5894 2.606725 GCACTACTTCTAGTACGAGCGA 59.393 50.000 0.00 0.00 31.46 4.93
2997 5895 3.302610 GCACTACTTCTAGTACGAGCGAG 60.303 52.174 0.00 2.00 31.46 5.03
2998 5896 3.864583 CACTACTTCTAGTACGAGCGAGT 59.135 47.826 13.37 13.37 31.46 4.18
2999 5897 4.329528 CACTACTTCTAGTACGAGCGAGTT 59.670 45.833 13.83 0.08 31.46 3.01
3000 5898 3.743567 ACTTCTAGTACGAGCGAGTTG 57.256 47.619 0.00 0.00 0.00 3.16
3001 5899 3.072944 ACTTCTAGTACGAGCGAGTTGT 58.927 45.455 0.00 0.00 0.00 3.32
3002 5900 3.124976 ACTTCTAGTACGAGCGAGTTGTC 59.875 47.826 0.00 0.00 0.00 3.18
3003 5901 2.691927 TCTAGTACGAGCGAGTTGTCA 58.308 47.619 0.00 0.00 0.00 3.58
3004 5902 3.069289 TCTAGTACGAGCGAGTTGTCAA 58.931 45.455 0.00 0.00 0.00 3.18
3005 5903 3.688185 TCTAGTACGAGCGAGTTGTCAAT 59.312 43.478 0.00 0.00 0.00 2.57
3006 5904 2.596452 AGTACGAGCGAGTTGTCAATG 58.404 47.619 0.00 0.00 0.00 2.82
3007 5905 1.059264 GTACGAGCGAGTTGTCAATGC 59.941 52.381 0.00 0.00 0.00 3.56
3008 5906 1.057822 CGAGCGAGTTGTCAATGCG 59.942 57.895 5.87 5.87 0.00 4.73
3010 5908 2.571611 GCGAGTTGTCAATGCGCG 60.572 61.111 15.85 0.00 38.24 6.86
3011 5909 2.853210 CGAGTTGTCAATGCGCGT 59.147 55.556 8.43 0.00 0.00 6.01
3012 5910 1.507713 CGAGTTGTCAATGCGCGTG 60.508 57.895 8.43 3.19 0.00 5.34
3013 5911 1.859398 GAGTTGTCAATGCGCGTGA 59.141 52.632 8.43 6.13 0.00 4.35
3014 5912 0.234625 GAGTTGTCAATGCGCGTGAA 59.765 50.000 14.44 0.00 0.00 3.18
3015 5913 0.874390 AGTTGTCAATGCGCGTGAAT 59.126 45.000 14.44 0.00 0.00 2.57
3016 5914 1.266718 AGTTGTCAATGCGCGTGAATT 59.733 42.857 14.44 0.00 0.00 2.17
3017 5915 1.643810 GTTGTCAATGCGCGTGAATTC 59.356 47.619 14.44 0.00 0.00 2.17
3018 5916 0.871057 TGTCAATGCGCGTGAATTCA 59.129 45.000 14.44 3.38 0.00 2.57
3019 5917 1.250476 GTCAATGCGCGTGAATTCAC 58.750 50.000 25.68 25.68 43.15 3.18
3020 5918 1.135972 GTCAATGCGCGTGAATTCACT 60.136 47.619 30.45 13.24 44.34 3.41
3021 5919 2.093625 GTCAATGCGCGTGAATTCACTA 59.906 45.455 30.45 17.17 44.34 2.74
3022 5920 2.348362 TCAATGCGCGTGAATTCACTAG 59.652 45.455 30.45 24.54 44.34 2.57
3023 5921 2.293677 ATGCGCGTGAATTCACTAGA 57.706 45.000 30.45 15.41 44.34 2.43
3024 5922 1.629013 TGCGCGTGAATTCACTAGAG 58.371 50.000 30.45 20.43 44.34 2.43
3025 5923 0.299003 GCGCGTGAATTCACTAGAGC 59.701 55.000 30.45 24.91 44.34 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
334 337 1.272490 TCGAGGGAAGCTACAACTGTG 59.728 52.381 0.00 0.00 0.00 3.66
337 340 2.362717 GCTATCGAGGGAAGCTACAACT 59.637 50.000 0.00 0.00 33.40 3.16
473 478 2.798680 CGTCACACATCTACCTACAGC 58.201 52.381 0.00 0.00 0.00 4.40
477 482 0.736636 CGGCGTCACACATCTACCTA 59.263 55.000 0.00 0.00 0.00 3.08
838 990 0.616891 GACCGTGACCCCACCTTATT 59.383 55.000 0.00 0.00 40.12 1.40
939 1091 3.692593 GGCTACCTTAATCTTGCGGAAAA 59.307 43.478 0.00 0.00 0.00 2.29
945 1097 1.950216 GGCTGGCTACCTTAATCTTGC 59.050 52.381 0.00 0.00 0.00 4.01
950 1102 0.179045 CGCTGGCTGGCTACCTTAAT 60.179 55.000 2.00 0.00 0.00 1.40
1025 1177 0.042013 GACGAGTATGACGAGAGCGG 60.042 60.000 0.00 0.00 43.17 5.52
1191 1343 2.203451 AGGATACGGCCGTCGGAT 60.203 61.111 38.01 24.03 46.75 4.18
1203 1355 1.140312 GCCCATTCCACCTCAGGATA 58.860 55.000 0.00 0.00 37.56 2.59
1286 1438 3.365265 CCTCCGTGCCAAACCTGC 61.365 66.667 0.00 0.00 0.00 4.85
1436 1588 0.949397 CATGCCATCAATCTGGTCGG 59.051 55.000 0.00 0.00 38.63 4.79
1459 1611 2.192861 CCCTGTTGGTGAAGCGCAA 61.193 57.895 11.47 0.00 0.00 4.85
1474 1626 2.559668 TGACTTGATCGACGTAAACCCT 59.440 45.455 0.00 0.00 0.00 4.34
1480 1632 0.448990 CCGGTGACTTGATCGACGTA 59.551 55.000 0.00 0.00 0.00 3.57
1542 1696 1.044611 TGGTGACCATCTCGTGTTCA 58.955 50.000 0.00 0.00 0.00 3.18
1619 1773 2.435805 GTCATCCTAGGTTGGAGCATGA 59.564 50.000 17.94 10.72 39.78 3.07
1690 4570 1.920734 TTGCATGGGCCGGTAGATGT 61.921 55.000 1.90 0.00 40.13 3.06
1859 4739 4.194640 GACAGCAAGAAGATGGCTATCAA 58.805 43.478 13.04 0.00 39.06 2.57
1962 4842 0.736325 CCAGGTAGAGTTTGCCGTCG 60.736 60.000 0.00 0.00 36.53 5.12
1990 4870 0.249398 ACGCCGACATAAGGAAGCTT 59.751 50.000 0.00 0.00 0.00 3.74
2038 4918 9.617053 ACTAAAAGCCCTCCTATACATACTATT 57.383 33.333 0.00 0.00 0.00 1.73
2054 4942 9.302345 GCAAGAATAATAAGAAACTAAAAGCCC 57.698 33.333 0.00 0.00 0.00 5.19
2081 4969 4.882671 AACTGGAGCATTACATTTAGCG 57.117 40.909 0.00 0.00 0.00 4.26
2110 4998 8.451908 AAGGATTACAATAGTTTGCCTGATAC 57.548 34.615 0.00 0.00 36.22 2.24
2161 5051 4.241681 GCCGGACATTAAAATGAAGCAAA 58.758 39.130 5.05 0.00 39.67 3.68
2180 5070 2.140065 ACGACATCAGTATCATGCCG 57.860 50.000 0.00 0.00 33.77 5.69
2184 5074 5.050490 GGCAGTAAACGACATCAGTATCAT 58.950 41.667 0.00 0.00 0.00 2.45
2185 5075 4.081917 TGGCAGTAAACGACATCAGTATCA 60.082 41.667 0.00 0.00 0.00 2.15
2186 5076 4.430007 TGGCAGTAAACGACATCAGTATC 58.570 43.478 0.00 0.00 0.00 2.24
2187 5077 4.465632 TGGCAGTAAACGACATCAGTAT 57.534 40.909 0.00 0.00 0.00 2.12
2188 5078 3.945981 TGGCAGTAAACGACATCAGTA 57.054 42.857 0.00 0.00 0.00 2.74
2189 5079 2.831685 TGGCAGTAAACGACATCAGT 57.168 45.000 0.00 0.00 0.00 3.41
2190 5080 2.223112 GCATGGCAGTAAACGACATCAG 60.223 50.000 0.00 0.00 0.00 2.90
2191 5081 1.737236 GCATGGCAGTAAACGACATCA 59.263 47.619 0.00 0.00 0.00 3.07
2192 5082 1.267532 CGCATGGCAGTAAACGACATC 60.268 52.381 0.00 0.00 0.00 3.06
2193 5083 0.726827 CGCATGGCAGTAAACGACAT 59.273 50.000 0.00 0.00 0.00 3.06
2194 5084 1.906994 GCGCATGGCAGTAAACGACA 61.907 55.000 0.30 0.00 42.87 4.35
2195 5085 1.226018 GCGCATGGCAGTAAACGAC 60.226 57.895 0.30 0.00 42.87 4.34
2196 5086 3.173853 GCGCATGGCAGTAAACGA 58.826 55.556 0.30 0.00 42.87 3.85
2205 5095 1.290491 GCATCTCTCTAGCGCATGGC 61.290 60.000 11.47 0.00 44.05 4.40
2206 5096 0.033090 TGCATCTCTCTAGCGCATGG 59.967 55.000 11.47 0.00 0.00 3.66
2207 5097 1.861971 TTGCATCTCTCTAGCGCATG 58.138 50.000 11.47 3.37 32.87 4.06
2208 5098 2.158986 AGTTTGCATCTCTCTAGCGCAT 60.159 45.455 11.47 0.00 32.87 4.73
2209 5099 1.205655 AGTTTGCATCTCTCTAGCGCA 59.794 47.619 11.47 0.00 0.00 6.09
2210 5100 1.933247 AGTTTGCATCTCTCTAGCGC 58.067 50.000 0.00 0.00 0.00 5.92
2211 5101 3.515630 TCAAGTTTGCATCTCTCTAGCG 58.484 45.455 0.00 0.00 0.00 4.26
2212 5102 5.174395 TCTTCAAGTTTGCATCTCTCTAGC 58.826 41.667 0.00 0.00 0.00 3.42
2215 5105 8.149647 CCTATATCTTCAAGTTTGCATCTCTCT 58.850 37.037 0.00 0.00 0.00 3.10
2216 5106 8.147058 TCCTATATCTTCAAGTTTGCATCTCTC 58.853 37.037 0.00 0.00 0.00 3.20
2217 5107 8.027524 TCCTATATCTTCAAGTTTGCATCTCT 57.972 34.615 0.00 0.00 0.00 3.10
2218 5108 8.719648 CATCCTATATCTTCAAGTTTGCATCTC 58.280 37.037 0.00 0.00 0.00 2.75
2219 5109 7.664731 CCATCCTATATCTTCAAGTTTGCATCT 59.335 37.037 0.00 0.00 0.00 2.90
2220 5110 7.663081 TCCATCCTATATCTTCAAGTTTGCATC 59.337 37.037 0.00 0.00 0.00 3.91
2221 5111 7.520798 TCCATCCTATATCTTCAAGTTTGCAT 58.479 34.615 0.00 0.00 0.00 3.96
2222 5112 6.899089 TCCATCCTATATCTTCAAGTTTGCA 58.101 36.000 0.00 0.00 0.00 4.08
2223 5113 7.992754 ATCCATCCTATATCTTCAAGTTTGC 57.007 36.000 0.00 0.00 0.00 3.68
2244 5134 9.665264 CCGCAAGAATAATAAGAAACTAAATCC 57.335 33.333 0.00 0.00 43.02 3.01
2245 5135 9.170584 GCCGCAAGAATAATAAGAAACTAAATC 57.829 33.333 0.00 0.00 43.02 2.17
2246 5136 8.903820 AGCCGCAAGAATAATAAGAAACTAAAT 58.096 29.630 0.00 0.00 43.02 1.40
2247 5137 8.276252 AGCCGCAAGAATAATAAGAAACTAAA 57.724 30.769 0.00 0.00 43.02 1.85
2248 5138 7.859325 AGCCGCAAGAATAATAAGAAACTAA 57.141 32.000 0.00 0.00 43.02 2.24
2250 5140 9.726438 ATATAGCCGCAAGAATAATAAGAAACT 57.274 29.630 0.00 0.00 43.02 2.66
2251 5141 9.760660 CATATAGCCGCAAGAATAATAAGAAAC 57.239 33.333 0.00 0.00 43.02 2.78
2252 5142 9.502091 ACATATAGCCGCAAGAATAATAAGAAA 57.498 29.630 0.00 0.00 43.02 2.52
2257 5147 8.826710 GCATTACATATAGCCGCAAGAATAATA 58.173 33.333 0.00 0.00 43.02 0.98
2258 5148 7.554118 AGCATTACATATAGCCGCAAGAATAAT 59.446 33.333 0.00 0.00 43.02 1.28
2259 5149 6.878923 AGCATTACATATAGCCGCAAGAATAA 59.121 34.615 0.00 0.00 43.02 1.40
2260 5150 6.406370 AGCATTACATATAGCCGCAAGAATA 58.594 36.000 0.00 0.00 43.02 1.75
2261 5151 5.248640 AGCATTACATATAGCCGCAAGAAT 58.751 37.500 0.00 0.00 43.02 2.40
2262 5152 4.641396 AGCATTACATATAGCCGCAAGAA 58.359 39.130 0.00 0.00 43.02 2.52
2263 5153 4.245660 GAGCATTACATATAGCCGCAAGA 58.754 43.478 0.00 0.00 43.02 3.02
2264 5154 3.372206 GGAGCATTACATATAGCCGCAAG 59.628 47.826 0.00 0.00 0.00 4.01
2265 5155 3.244387 TGGAGCATTACATATAGCCGCAA 60.244 43.478 0.00 0.00 0.00 4.85
2266 5156 2.301583 TGGAGCATTACATATAGCCGCA 59.698 45.455 0.00 0.00 0.00 5.69
2267 5157 2.932614 CTGGAGCATTACATATAGCCGC 59.067 50.000 0.00 0.00 0.00 6.53
2268 5158 4.193826 ACTGGAGCATTACATATAGCCG 57.806 45.455 0.00 0.00 0.00 5.52
2269 5159 6.234177 AGAAACTGGAGCATTACATATAGCC 58.766 40.000 0.00 0.00 0.00 3.93
2270 5160 7.736447 AAGAAACTGGAGCATTACATATAGC 57.264 36.000 0.00 0.00 0.00 2.97
2273 5163 8.806146 ACAAAAAGAAACTGGAGCATTACATAT 58.194 29.630 0.00 0.00 0.00 1.78
2274 5164 8.177119 ACAAAAAGAAACTGGAGCATTACATA 57.823 30.769 0.00 0.00 0.00 2.29
2275 5165 7.054491 ACAAAAAGAAACTGGAGCATTACAT 57.946 32.000 0.00 0.00 0.00 2.29
2276 5166 6.463995 ACAAAAAGAAACTGGAGCATTACA 57.536 33.333 0.00 0.00 0.00 2.41
2277 5167 8.296713 TGATACAAAAAGAAACTGGAGCATTAC 58.703 33.333 0.00 0.00 0.00 1.89
2278 5168 8.402798 TGATACAAAAAGAAACTGGAGCATTA 57.597 30.769 0.00 0.00 0.00 1.90
2279 5169 7.288810 TGATACAAAAAGAAACTGGAGCATT 57.711 32.000 0.00 0.00 0.00 3.56
2280 5170 6.071728 CCTGATACAAAAAGAAACTGGAGCAT 60.072 38.462 0.00 0.00 0.00 3.79
2281 5171 5.241506 CCTGATACAAAAAGAAACTGGAGCA 59.758 40.000 0.00 0.00 0.00 4.26
2282 5172 5.703876 CCTGATACAAAAAGAAACTGGAGC 58.296 41.667 0.00 0.00 0.00 4.70
2283 5173 5.241506 TGCCTGATACAAAAAGAAACTGGAG 59.758 40.000 0.00 0.00 0.00 3.86
2284 5174 5.136828 TGCCTGATACAAAAAGAAACTGGA 58.863 37.500 0.00 0.00 0.00 3.86
2285 5175 5.452078 TGCCTGATACAAAAAGAAACTGG 57.548 39.130 0.00 0.00 0.00 4.00
2286 5176 6.980397 AGTTTGCCTGATACAAAAAGAAACTG 59.020 34.615 0.00 0.00 38.64 3.16
2287 5177 7.112452 AGTTTGCCTGATACAAAAAGAAACT 57.888 32.000 0.00 0.00 38.64 2.66
2288 5178 9.476202 AATAGTTTGCCTGATACAAAAAGAAAC 57.524 29.630 0.00 0.00 38.64 2.78
2295 5185 9.249053 TGGATTAAATAGTTTGCCTGATACAAA 57.751 29.630 0.00 0.00 34.74 2.83
2296 5186 8.815565 TGGATTAAATAGTTTGCCTGATACAA 57.184 30.769 0.00 0.00 0.00 2.41
2297 5187 8.995027 ATGGATTAAATAGTTTGCCTGATACA 57.005 30.769 0.00 0.00 0.00 2.29
2357 5249 4.453136 TCGGTTACTTGGCTGACATTAAAC 59.547 41.667 0.00 0.00 0.00 2.01
2369 5261 3.436001 AGCGTCATCGGTTACTTGG 57.564 52.632 0.00 0.00 45.64 3.61
2460 5352 2.751688 GTGCAGGGGAACGGGTTA 59.248 61.111 0.00 0.00 0.00 2.85
2461 5353 4.280019 GGTGCAGGGGAACGGGTT 62.280 66.667 0.00 0.00 0.00 4.11
2471 5363 4.007644 TGAGCGAGGTGGTGCAGG 62.008 66.667 0.00 0.00 0.00 4.85
2526 5419 1.363744 GGAGATGTCAAGAACGGCAG 58.636 55.000 0.00 0.00 0.00 4.85
2538 5431 0.038526 GTTGTCGTCACCGGAGATGT 60.039 55.000 18.94 0.00 33.95 3.06
2567 5460 1.811266 CATGGCGAACTCCACGAGG 60.811 63.158 0.00 0.00 39.25 4.63
2571 5464 0.743345 GGTACCATGGCGAACTCCAC 60.743 60.000 13.04 0.00 39.25 4.02
2611 5504 2.114411 GGGTGGGCTTGAACCGAA 59.886 61.111 0.00 0.00 37.33 4.30
2732 5630 3.482783 GCAGGCTGCTTCGTCGTC 61.483 66.667 31.37 0.00 40.96 4.20
2733 5631 3.596066 ATGCAGGCTGCTTCGTCGT 62.596 57.895 36.50 13.36 45.31 4.34
2734 5632 2.816958 ATGCAGGCTGCTTCGTCG 60.817 61.111 36.50 0.00 45.31 5.12
2803 5701 4.738998 TCCCCAACGGCATGGCTG 62.739 66.667 18.09 13.01 39.26 4.85
2804 5702 3.944250 CTTCCCCAACGGCATGGCT 62.944 63.158 18.09 1.39 39.26 4.75
2805 5703 3.451894 CTTCCCCAACGGCATGGC 61.452 66.667 9.69 9.69 39.26 4.40
2806 5704 2.755469 CCTTCCCCAACGGCATGG 60.755 66.667 0.00 0.00 40.35 3.66
2807 5705 3.451894 GCCTTCCCCAACGGCATG 61.452 66.667 0.00 0.00 43.25 4.06
2808 5706 4.759205 GGCCTTCCCCAACGGCAT 62.759 66.667 0.00 0.00 45.53 4.40
2861 5759 0.381801 GGCTAATGATGTGCAACCCG 59.618 55.000 0.00 0.00 34.36 5.28
2866 5764 1.823470 GGGCGGCTAATGATGTGCA 60.823 57.895 9.56 0.00 0.00 4.57
2868 5766 2.253758 CCGGGCGGCTAATGATGTG 61.254 63.158 9.56 0.00 0.00 3.21
2871 5769 1.119574 ACTACCGGGCGGCTAATGAT 61.120 55.000 9.56 0.00 39.32 2.45
2876 5774 3.142838 GACACTACCGGGCGGCTA 61.143 66.667 9.56 0.00 39.32 3.93
2885 5783 1.080025 GCTGACCGGTGACACTACC 60.080 63.158 14.63 0.00 37.37 3.18
2888 5786 2.088674 GAGTGCTGACCGGTGACACT 62.089 60.000 25.74 25.74 43.93 3.55
2890 5788 2.734591 GAGTGCTGACCGGTGACA 59.265 61.111 14.63 3.10 0.00 3.58
2894 5792 2.997897 GAGGGAGTGCTGACCGGT 60.998 66.667 6.92 6.92 0.00 5.28
2898 5796 1.139947 GTAGCGAGGGAGTGCTGAC 59.860 63.158 0.00 0.00 42.46 3.51
2912 5810 1.533625 TGGTTGTGAATGCCTGTAGC 58.466 50.000 0.00 0.00 44.14 3.58
2913 5811 5.125356 TCATATGGTTGTGAATGCCTGTAG 58.875 41.667 2.13 0.00 0.00 2.74
2914 5812 5.109500 TCATATGGTTGTGAATGCCTGTA 57.891 39.130 2.13 0.00 0.00 2.74
2915 5813 3.966979 TCATATGGTTGTGAATGCCTGT 58.033 40.909 2.13 0.00 0.00 4.00
2916 5814 5.524971 AATCATATGGTTGTGAATGCCTG 57.475 39.130 0.00 0.00 0.00 4.85
2917 5815 5.242393 GCTAATCATATGGTTGTGAATGCCT 59.758 40.000 11.62 0.00 0.00 4.75
2918 5816 5.242393 AGCTAATCATATGGTTGTGAATGCC 59.758 40.000 11.62 0.00 0.00 4.40
2919 5817 6.323203 AGCTAATCATATGGTTGTGAATGC 57.677 37.500 11.62 6.12 0.00 3.56
2920 5818 8.613060 AGTAGCTAATCATATGGTTGTGAATG 57.387 34.615 11.62 0.00 0.00 2.67
2921 5819 9.060347 CAAGTAGCTAATCATATGGTTGTGAAT 57.940 33.333 11.62 0.66 0.00 2.57
2922 5820 8.046708 ACAAGTAGCTAATCATATGGTTGTGAA 58.953 33.333 11.62 0.00 0.00 3.18
2923 5821 7.564793 ACAAGTAGCTAATCATATGGTTGTGA 58.435 34.615 11.62 0.00 0.00 3.58
2924 5822 7.712639 AGACAAGTAGCTAATCATATGGTTGTG 59.287 37.037 11.62 5.47 0.00 3.33
2925 5823 7.712639 CAGACAAGTAGCTAATCATATGGTTGT 59.287 37.037 11.62 0.00 0.00 3.32
2926 5824 7.172190 CCAGACAAGTAGCTAATCATATGGTTG 59.828 40.741 11.62 3.03 0.00 3.77
2927 5825 7.147479 ACCAGACAAGTAGCTAATCATATGGTT 60.147 37.037 14.71 6.44 30.97 3.67
2928 5826 6.327626 ACCAGACAAGTAGCTAATCATATGGT 59.672 38.462 14.71 14.71 0.00 3.55
2929 5827 6.763355 ACCAGACAAGTAGCTAATCATATGG 58.237 40.000 13.71 13.71 0.00 2.74
2930 5828 7.712639 ACAACCAGACAAGTAGCTAATCATATG 59.287 37.037 0.00 0.00 0.00 1.78
2931 5829 7.712639 CACAACCAGACAAGTAGCTAATCATAT 59.287 37.037 0.00 0.00 0.00 1.78
2932 5830 7.041721 CACAACCAGACAAGTAGCTAATCATA 58.958 38.462 0.00 0.00 0.00 2.15
2933 5831 5.877012 CACAACCAGACAAGTAGCTAATCAT 59.123 40.000 0.00 0.00 0.00 2.45
2934 5832 5.011635 TCACAACCAGACAAGTAGCTAATCA 59.988 40.000 0.00 0.00 0.00 2.57
2935 5833 5.479306 TCACAACCAGACAAGTAGCTAATC 58.521 41.667 0.00 0.00 0.00 1.75
2936 5834 5.483685 TCACAACCAGACAAGTAGCTAAT 57.516 39.130 0.00 0.00 0.00 1.73
2937 5835 4.948341 TCACAACCAGACAAGTAGCTAA 57.052 40.909 0.00 0.00 0.00 3.09
2938 5836 4.948341 TTCACAACCAGACAAGTAGCTA 57.052 40.909 0.00 0.00 0.00 3.32
2939 5837 3.838244 TTCACAACCAGACAAGTAGCT 57.162 42.857 0.00 0.00 0.00 3.32
2940 5838 3.365364 GCATTCACAACCAGACAAGTAGC 60.365 47.826 0.00 0.00 0.00 3.58
2941 5839 3.189287 GGCATTCACAACCAGACAAGTAG 59.811 47.826 0.00 0.00 0.00 2.57
2942 5840 3.146066 GGCATTCACAACCAGACAAGTA 58.854 45.455 0.00 0.00 0.00 2.24
2943 5841 1.956477 GGCATTCACAACCAGACAAGT 59.044 47.619 0.00 0.00 0.00 3.16
2944 5842 2.030540 CAGGCATTCACAACCAGACAAG 60.031 50.000 0.00 0.00 0.00 3.16
2945 5843 1.955778 CAGGCATTCACAACCAGACAA 59.044 47.619 0.00 0.00 0.00 3.18
2946 5844 1.608055 CAGGCATTCACAACCAGACA 58.392 50.000 0.00 0.00 0.00 3.41
2947 5845 0.242017 GCAGGCATTCACAACCAGAC 59.758 55.000 0.00 0.00 0.00 3.51
2948 5846 0.178995 TGCAGGCATTCACAACCAGA 60.179 50.000 0.00 0.00 0.00 3.86
2949 5847 0.892755 ATGCAGGCATTCACAACCAG 59.107 50.000 0.00 0.00 31.82 4.00
2950 5848 0.889994 GATGCAGGCATTCACAACCA 59.110 50.000 8.34 0.00 36.70 3.67
2951 5849 1.135199 CAGATGCAGGCATTCACAACC 60.135 52.381 8.34 0.00 36.70 3.77
2952 5850 1.734707 GCAGATGCAGGCATTCACAAC 60.735 52.381 8.34 0.00 41.59 3.32
2953 5851 0.528924 GCAGATGCAGGCATTCACAA 59.471 50.000 8.34 0.00 41.59 3.33
2954 5852 2.186155 GCAGATGCAGGCATTCACA 58.814 52.632 8.34 0.00 41.59 3.58
2965 5863 7.710910 GTACTAGAAGTAGTGCATGCAGATGC 61.711 46.154 23.41 16.30 42.34 3.91
2966 5864 4.691175 ACTAGAAGTAGTGCATGCAGATG 58.309 43.478 23.41 6.49 38.14 2.90
2967 5865 5.506483 CGTACTAGAAGTAGTGCATGCAGAT 60.506 44.000 23.41 15.65 40.83 2.90
2968 5866 4.201920 CGTACTAGAAGTAGTGCATGCAGA 60.202 45.833 23.41 9.67 40.83 4.26
2969 5867 4.038361 CGTACTAGAAGTAGTGCATGCAG 58.962 47.826 23.41 8.52 40.83 4.41
2970 5868 3.692593 TCGTACTAGAAGTAGTGCATGCA 59.307 43.478 18.46 18.46 40.83 3.96
2971 5869 4.283678 CTCGTACTAGAAGTAGTGCATGC 58.716 47.826 11.82 11.82 40.83 4.06
2972 5870 4.283678 GCTCGTACTAGAAGTAGTGCATG 58.716 47.826 0.00 0.00 40.83 4.06
2973 5871 3.002451 CGCTCGTACTAGAAGTAGTGCAT 59.998 47.826 0.00 0.00 40.83 3.96
2974 5872 2.350804 CGCTCGTACTAGAAGTAGTGCA 59.649 50.000 0.00 0.00 40.83 4.57
2975 5873 2.606725 TCGCTCGTACTAGAAGTAGTGC 59.393 50.000 0.00 0.00 39.96 4.40
2976 5874 3.864583 ACTCGCTCGTACTAGAAGTAGTG 59.135 47.826 0.00 0.00 39.96 2.74
2977 5875 4.122143 ACTCGCTCGTACTAGAAGTAGT 57.878 45.455 0.00 0.00 42.49 2.73
2978 5876 4.329528 ACAACTCGCTCGTACTAGAAGTAG 59.670 45.833 0.00 0.00 30.12 2.57
2979 5877 4.248859 ACAACTCGCTCGTACTAGAAGTA 58.751 43.478 0.00 0.00 0.00 2.24
2980 5878 3.072944 ACAACTCGCTCGTACTAGAAGT 58.927 45.455 0.00 0.00 0.00 3.01
2981 5879 3.124806 TGACAACTCGCTCGTACTAGAAG 59.875 47.826 0.00 0.00 0.00 2.85
2982 5880 3.069289 TGACAACTCGCTCGTACTAGAA 58.931 45.455 0.00 0.00 0.00 2.10
2983 5881 2.691927 TGACAACTCGCTCGTACTAGA 58.308 47.619 0.00 0.00 0.00 2.43
2984 5882 3.466712 TTGACAACTCGCTCGTACTAG 57.533 47.619 0.00 0.00 0.00 2.57
2985 5883 3.754955 CATTGACAACTCGCTCGTACTA 58.245 45.455 0.00 0.00 0.00 1.82
2986 5884 2.596452 CATTGACAACTCGCTCGTACT 58.404 47.619 0.00 0.00 0.00 2.73
2987 5885 1.059264 GCATTGACAACTCGCTCGTAC 59.941 52.381 0.00 0.00 0.00 3.67
2988 5886 1.346365 GCATTGACAACTCGCTCGTA 58.654 50.000 0.00 0.00 0.00 3.43
2989 5887 1.617755 CGCATTGACAACTCGCTCGT 61.618 55.000 0.00 0.00 0.00 4.18
2990 5888 1.057822 CGCATTGACAACTCGCTCG 59.942 57.895 0.00 0.00 0.00 5.03
2991 5889 1.225854 GCGCATTGACAACTCGCTC 60.226 57.895 21.49 4.94 42.19 5.03
2992 5890 2.863153 GCGCATTGACAACTCGCT 59.137 55.556 21.49 0.00 42.19 4.93
2993 5891 2.571611 CGCGCATTGACAACTCGC 60.572 61.111 19.82 19.82 42.05 5.03
2994 5892 1.507713 CACGCGCATTGACAACTCG 60.508 57.895 5.73 6.56 0.00 4.18
2995 5893 0.234625 TTCACGCGCATTGACAACTC 59.765 50.000 5.73 0.00 0.00 3.01
2996 5894 0.874390 ATTCACGCGCATTGACAACT 59.126 45.000 5.73 0.00 0.00 3.16
2997 5895 1.643810 GAATTCACGCGCATTGACAAC 59.356 47.619 5.73 0.00 0.00 3.32
2998 5896 1.265365 TGAATTCACGCGCATTGACAA 59.735 42.857 5.73 0.00 0.00 3.18
2999 5897 0.871057 TGAATTCACGCGCATTGACA 59.129 45.000 5.73 0.91 0.00 3.58
3000 5898 1.250476 GTGAATTCACGCGCATTGAC 58.750 50.000 22.09 2.86 37.10 3.18
3001 5899 3.674225 GTGAATTCACGCGCATTGA 57.326 47.368 22.09 6.38 37.10 2.57


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

AutoCloner maintained by Alex Coulton.