Multiple sequence alignment - TraesCS3D01G375800

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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 TraesCS3D01G375800 chr3D 100.000 3926 0 0 1 3926 488905846 488901921 0.000000e+00 7251.0
1 TraesCS3D01G375800 chr3D 83.699 730 115 4 2140 2867 488950777 488950050 0.000000e+00 686.0
2 TraesCS3D01G375800 chr3D 84.958 359 54 0 1633 1991 488951340 488950982 8.020000e-97 364.0
3 TraesCS3D01G375800 chr3D 84.545 220 34 0 1231 1450 488951820 488951601 6.610000e-53 219.0
4 TraesCS3D01G375800 chr3A 90.801 2935 139 68 160 3060 632287267 632290104 0.000000e+00 3803.0
5 TraesCS3D01G375800 chr3A 83.288 730 120 2 2141 2869 632040548 632041276 0.000000e+00 671.0
6 TraesCS3D01G375800 chr3A 84.884 344 52 0 1630 1973 632039990 632040333 8.070000e-92 348.0
7 TraesCS3D01G375800 chr3A 84.793 217 33 0 1231 1447 632039497 632039713 6.610000e-53 219.0
8 TraesCS3D01G375800 chr3B 89.076 3140 152 90 1 3067 651499814 651502835 0.000000e+00 3722.0
9 TraesCS3D01G375800 chr3B 83.333 708 114 4 2162 2867 651426585 651427290 0.000000e+00 651.0
10 TraesCS3D01G375800 chr3B 83.851 644 104 0 2162 2805 489350888 489351531 7.210000e-172 614.0
11 TraesCS3D01G375800 chr3B 84.593 344 53 0 1630 1973 651425997 651426340 3.760000e-90 342.0
12 TraesCS3D01G375800 chr3B 83.430 344 57 0 1630 1973 489350300 489350643 1.760000e-83 320.0
13 TraesCS3D01G375800 chr3B 83.871 217 35 0 1231 1447 651425518 651425734 1.430000e-49 207.0
14 TraesCS3D01G375800 chr6D 97.997 749 12 3 3179 3926 456587517 456586771 0.000000e+00 1297.0
15 TraesCS3D01G375800 chr6D 100.000 35 0 0 3144 3178 456587625 456587591 9.110000e-07 65.8
16 TraesCS3D01G375800 chr7D 97.736 751 15 2 3176 3926 39777083 39777831 0.000000e+00 1291.0
17 TraesCS3D01G375800 chr7D 79.710 414 70 11 1633 2036 89312207 89311798 1.790000e-73 287.0
18 TraesCS3D01G375800 chr7D 82.883 222 36 2 1231 1451 89312797 89312577 8.600000e-47 198.0
19 TraesCS3D01G375800 chr7D 100.000 33 0 0 3146 3178 39777020 39777052 1.180000e-05 62.1
20 TraesCS3D01G375800 chr7D 91.111 45 3 1 3134 3178 574686154 574686197 4.240000e-05 60.2
21 TraesCS3D01G375800 chr7A 95.894 755 24 6 3176 3926 618091585 618092336 0.000000e+00 1216.0
22 TraesCS3D01G375800 chr7A 100.000 33 0 0 3146 3178 618091494 618091526 1.180000e-05 62.1
23 TraesCS3D01G375800 chr2B 89.696 757 61 14 3176 3926 212004359 212005104 0.000000e+00 950.0
24 TraesCS3D01G375800 chr2B 84.227 634 100 0 2172 2805 254626822 254626189 5.570000e-173 617.0
25 TraesCS3D01G375800 chr2B 83.871 341 55 0 1633 1973 254627417 254627077 3.780000e-85 326.0
26 TraesCS3D01G375800 chr2A 88.544 742 56 20 3204 3924 3818328 3819061 0.000000e+00 872.0
27 TraesCS3D01G375800 chr2A 88.640 625 50 18 3311 3926 385277798 385278410 0.000000e+00 741.0
28 TraesCS3D01G375800 chr2A 100.000 28 0 0 3151 3178 3818222 3818249 7.000000e-03 52.8
29 TraesCS3D01G375800 chr1B 90.941 574 38 9 3176 3742 658458894 658458328 0.000000e+00 760.0
30 TraesCS3D01G375800 chr1B 90.426 564 40 11 3182 3742 508571814 508571262 0.000000e+00 730.0
31 TraesCS3D01G375800 chr4B 85.438 673 70 20 3267 3926 11631838 11631181 0.000000e+00 675.0
32 TraesCS3D01G375800 chr4B 84.112 642 102 0 2162 2803 46933585 46934226 4.310000e-174 621.0
33 TraesCS3D01G375800 chrUn 87.796 549 44 12 3382 3926 19788354 19787825 4.310000e-174 621.0
34 TraesCS3D01G375800 chr1D 77.394 752 152 18 2127 2869 365082893 365082151 7.790000e-117 431.0
35 TraesCS3D01G375800 chr7B 80.392 408 72 6 1633 2036 40276839 40276436 1.770000e-78 303.0
36 TraesCS3D01G375800 chr7B 82.353 221 39 0 1231 1451 40277432 40277212 4.000000e-45 193.0


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 TraesCS3D01G375800 chr3D 488901921 488905846 3925 True 7251.000000 7251 100.000000 1 3926 1 chr3D.!!$R1 3925
1 TraesCS3D01G375800 chr3D 488950050 488951820 1770 True 423.000000 686 84.400667 1231 2867 3 chr3D.!!$R2 1636
2 TraesCS3D01G375800 chr3A 632287267 632290104 2837 False 3803.000000 3803 90.801000 160 3060 1 chr3A.!!$F1 2900
3 TraesCS3D01G375800 chr3A 632039497 632041276 1779 False 412.666667 671 84.321667 1231 2869 3 chr3A.!!$F2 1638
4 TraesCS3D01G375800 chr3B 651499814 651502835 3021 False 3722.000000 3722 89.076000 1 3067 1 chr3B.!!$F1 3066
5 TraesCS3D01G375800 chr3B 489350300 489351531 1231 False 467.000000 614 83.640500 1630 2805 2 chr3B.!!$F2 1175
6 TraesCS3D01G375800 chr3B 651425518 651427290 1772 False 400.000000 651 83.932333 1231 2867 3 chr3B.!!$F3 1636
7 TraesCS3D01G375800 chr6D 456586771 456587625 854 True 681.400000 1297 98.998500 3144 3926 2 chr6D.!!$R1 782
8 TraesCS3D01G375800 chr7D 39777020 39777831 811 False 676.550000 1291 98.868000 3146 3926 2 chr7D.!!$F2 780
9 TraesCS3D01G375800 chr7D 89311798 89312797 999 True 242.500000 287 81.296500 1231 2036 2 chr7D.!!$R1 805
10 TraesCS3D01G375800 chr7A 618091494 618092336 842 False 639.050000 1216 97.947000 3146 3926 2 chr7A.!!$F1 780
11 TraesCS3D01G375800 chr2B 212004359 212005104 745 False 950.000000 950 89.696000 3176 3926 1 chr2B.!!$F1 750
12 TraesCS3D01G375800 chr2B 254626189 254627417 1228 True 471.500000 617 84.049000 1633 2805 2 chr2B.!!$R1 1172
13 TraesCS3D01G375800 chr2A 385277798 385278410 612 False 741.000000 741 88.640000 3311 3926 1 chr2A.!!$F1 615
14 TraesCS3D01G375800 chr2A 3818222 3819061 839 False 462.400000 872 94.272000 3151 3924 2 chr2A.!!$F2 773
15 TraesCS3D01G375800 chr1B 658458328 658458894 566 True 760.000000 760 90.941000 3176 3742 1 chr1B.!!$R2 566
16 TraesCS3D01G375800 chr1B 508571262 508571814 552 True 730.000000 730 90.426000 3182 3742 1 chr1B.!!$R1 560
17 TraesCS3D01G375800 chr4B 11631181 11631838 657 True 675.000000 675 85.438000 3267 3926 1 chr4B.!!$R1 659
18 TraesCS3D01G375800 chr4B 46933585 46934226 641 False 621.000000 621 84.112000 2162 2803 1 chr4B.!!$F1 641
19 TraesCS3D01G375800 chrUn 19787825 19788354 529 True 621.000000 621 87.796000 3382 3926 1 chrUn.!!$R1 544
20 TraesCS3D01G375800 chr1D 365082151 365082893 742 True 431.000000 431 77.394000 2127 2869 1 chr1D.!!$R1 742
21 TraesCS3D01G375800 chr7B 40276436 40277432 996 True 248.000000 303 81.372500 1231 2036 2 chr7B.!!$R1 805

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
899 943 0.169230 CCGTCTCCATCGATCGATCC 59.831 60.0 27.2 11.8 31.62 3.36 F
1523 1700 0.034059 GGCTGGATGAATCGTCGGAT 59.966 55.0 0.0 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 2106 0.456312 CGTTGTCCTGGACGTAGCTC 60.456 60.0 21.15 7.33 34.95 4.09 R
3091 3505 0.880278 GGACGAAGACTTGCTGCACA 60.880 55.0 0.00 0.00 0.00 4.57 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
23 24 2.192263 GACCCAGGAAGGAAGATCAGT 58.808 52.381 0.00 0.00 41.22 3.41
54 56 4.838152 CATGACTCGGTGGGGCGG 62.838 72.222 0.00 0.00 0.00 6.13
64 66 2.528127 TGGGGCGGAAAGTCTCCA 60.528 61.111 0.00 0.00 45.74 3.86
76 78 6.706270 GCGGAAAGTCTCCAATATTCTCATAA 59.294 38.462 0.00 0.00 45.74 1.90
112 115 1.652947 ACTAGGAACCGGGAATGTGT 58.347 50.000 6.32 0.00 0.00 3.72
115 118 0.248289 AGGAACCGGGAATGTGTACG 59.752 55.000 6.32 0.00 0.00 3.67
117 120 1.204467 GGAACCGGGAATGTGTACGTA 59.796 52.381 6.32 0.00 0.00 3.57
119 122 1.838112 ACCGGGAATGTGTACGTAGA 58.162 50.000 6.32 0.00 0.00 2.59
120 123 1.747355 ACCGGGAATGTGTACGTAGAG 59.253 52.381 6.32 0.00 0.00 2.43
121 124 1.066605 CCGGGAATGTGTACGTAGAGG 59.933 57.143 0.00 0.00 0.00 3.69
122 125 2.019249 CGGGAATGTGTACGTAGAGGA 58.981 52.381 0.00 0.00 0.00 3.71
123 126 2.621998 CGGGAATGTGTACGTAGAGGAT 59.378 50.000 0.00 0.00 0.00 3.24
124 127 3.304525 CGGGAATGTGTACGTAGAGGATC 60.305 52.174 0.00 0.00 0.00 3.36
125 128 3.304525 GGGAATGTGTACGTAGAGGATCG 60.305 52.174 0.00 0.00 42.67 3.69
126 129 3.562973 GGAATGTGTACGTAGAGGATCGA 59.437 47.826 0.00 0.00 42.67 3.59
127 130 4.215827 GGAATGTGTACGTAGAGGATCGAT 59.784 45.833 0.00 0.00 42.67 3.59
128 131 4.750952 ATGTGTACGTAGAGGATCGATG 57.249 45.455 0.54 0.00 42.67 3.84
129 132 2.289820 TGTGTACGTAGAGGATCGATGC 59.710 50.000 9.16 9.16 42.67 3.91
130 133 1.529865 TGTACGTAGAGGATCGATGCG 59.470 52.381 11.52 1.39 42.67 4.73
131 134 1.530293 GTACGTAGAGGATCGATGCGT 59.470 52.381 11.52 7.75 42.67 5.24
132 135 0.308068 ACGTAGAGGATCGATGCGTG 59.692 55.000 11.52 3.66 42.67 5.34
133 136 0.999228 CGTAGAGGATCGATGCGTGC 60.999 60.000 11.52 5.88 42.67 5.34
134 137 0.999228 GTAGAGGATCGATGCGTGCG 60.999 60.000 11.52 0.00 42.67 5.34
135 138 1.444917 TAGAGGATCGATGCGTGCGT 61.445 55.000 11.52 0.00 42.67 5.24
136 139 1.008881 GAGGATCGATGCGTGCGTA 60.009 57.895 11.52 0.00 0.00 4.42
137 140 1.269444 GAGGATCGATGCGTGCGTAC 61.269 60.000 11.52 0.00 0.00 3.67
148 151 1.083806 CGTGCGTACATCATGTGCCT 61.084 55.000 0.00 0.00 28.65 4.75
164 167 2.418976 GTGCCTTCTGTCCCGTATTTTC 59.581 50.000 0.00 0.00 0.00 2.29
179 182 6.821665 CCCGTATTTTCCACTAGAATTTCAGA 59.178 38.462 0.00 0.00 33.44 3.27
219 223 3.068873 CCGAGGTCATTTTCTAGCTAGCT 59.931 47.826 23.12 23.12 0.00 3.32
226 230 6.100004 GTCATTTTCTAGCTAGCTACACACA 58.900 40.000 20.67 1.02 0.00 3.72
227 231 6.035112 GTCATTTTCTAGCTAGCTACACACAC 59.965 42.308 20.67 7.82 0.00 3.82
257 265 3.055385 GGTGGAGTACAACATTCCTAGCA 60.055 47.826 0.00 0.00 36.56 3.49
265 273 1.516110 ACATTCCTAGCAGAGGCCAT 58.484 50.000 5.01 0.00 46.25 4.40
309 317 0.875059 CCTGTCCGTTGCTTTTCCTC 59.125 55.000 0.00 0.00 0.00 3.71
346 354 2.282040 AAGCAAGCAAGCGCCTCT 60.282 55.556 2.29 0.00 39.83 3.69
347 355 2.250841 GAAGCAAGCAAGCGCCTCTC 62.251 60.000 2.29 0.00 39.83 3.20
387 399 1.299541 CATCAGTTTCGAATCGGGGG 58.700 55.000 1.76 0.00 0.00 5.40
413 425 4.692475 GGTGCGTGCGGTTAGGGT 62.692 66.667 0.00 0.00 0.00 4.34
414 426 3.116531 GTGCGTGCGGTTAGGGTC 61.117 66.667 0.00 0.00 0.00 4.46
415 427 4.382320 TGCGTGCGGTTAGGGTCC 62.382 66.667 0.00 0.00 0.00 4.46
489 510 4.562425 GCCGCCCATCCGATCCAA 62.562 66.667 0.00 0.00 0.00 3.53
664 692 4.393680 CGTGAAATTTGAAGAACGGGGATA 59.606 41.667 0.00 0.00 0.00 2.59
676 704 9.196139 TGAAGAACGGGGATAAATTTTGATAAT 57.804 29.630 0.00 0.00 0.00 1.28
887 931 4.436998 CAGGGCACGACCGTCTCC 62.437 72.222 0.00 0.00 40.62 3.71
895 939 1.082692 CGACCGTCTCCATCGATCG 60.083 63.158 9.36 9.36 37.96 3.69
896 940 1.496403 CGACCGTCTCCATCGATCGA 61.496 60.000 21.86 21.86 45.58 3.59
897 941 0.875728 GACCGTCTCCATCGATCGAT 59.124 55.000 24.60 24.60 34.81 3.59
898 942 0.875728 ACCGTCTCCATCGATCGATC 59.124 55.000 27.20 15.68 31.62 3.69
899 943 0.169230 CCGTCTCCATCGATCGATCC 59.831 60.000 27.20 11.80 31.62 3.36
900 944 0.875059 CGTCTCCATCGATCGATCCA 59.125 55.000 27.20 15.32 31.62 3.41
901 945 1.470494 CGTCTCCATCGATCGATCCAT 59.530 52.381 27.20 9.87 31.62 3.41
902 946 2.477021 CGTCTCCATCGATCGATCCATC 60.477 54.545 27.20 14.98 31.62 3.51
903 947 2.489722 GTCTCCATCGATCGATCCATCA 59.510 50.000 27.20 8.25 31.62 3.07
904 948 2.751806 TCTCCATCGATCGATCCATCAG 59.248 50.000 27.20 16.97 31.62 2.90
905 949 2.491298 CTCCATCGATCGATCCATCAGT 59.509 50.000 27.20 2.38 31.62 3.41
906 950 2.489722 TCCATCGATCGATCCATCAGTC 59.510 50.000 27.20 0.00 31.62 3.51
907 951 2.416566 CCATCGATCGATCCATCAGTCC 60.417 54.545 27.20 0.00 31.62 3.85
908 952 1.248486 TCGATCGATCCATCAGTCCC 58.752 55.000 19.51 0.00 0.00 4.46
944 992 1.740043 CGAGCTGACATACACCATGCA 60.740 52.381 0.00 0.00 38.29 3.96
971 1019 3.217017 CCTGCTCGCCTACGCCTA 61.217 66.667 0.00 0.00 39.84 3.93
972 1020 2.026301 CTGCTCGCCTACGCCTAC 59.974 66.667 0.00 0.00 39.84 3.18
984 1032 2.202623 GCCTACGCACACTCGGAG 60.203 66.667 2.83 2.83 40.01 4.63
989 1037 1.583495 TACGCACACTCGGAGGACAG 61.583 60.000 10.23 0.00 0.00 3.51
1100 1151 1.202114 GGTGTTCGTCATGGGTACGTA 59.798 52.381 5.47 0.00 41.08 3.57
1127 1178 3.959975 GCGCGCCGATCTCTCTCT 61.960 66.667 23.24 0.00 0.00 3.10
1131 1182 0.869454 GCGCCGATCTCTCTCTTGTG 60.869 60.000 0.00 0.00 0.00 3.33
1203 1256 3.063861 GGTAGGTTTGTTTCGTTTCGTGT 59.936 43.478 0.00 0.00 0.00 4.49
1216 1269 3.241208 CGTTTCGTGTTGCTGTTTTGTTC 60.241 43.478 0.00 0.00 0.00 3.18
1217 1270 2.166741 TCGTGTTGCTGTTTTGTTCG 57.833 45.000 0.00 0.00 0.00 3.95
1456 1628 0.514255 TCGTCGTGGTAAGTCAGTCG 59.486 55.000 0.00 0.00 0.00 4.18
1458 1630 1.063951 GTCGTGGTAAGTCAGTCGCG 61.064 60.000 0.00 0.00 34.89 5.87
1477 1649 0.461961 GACTCCCGACTCCAATCCAG 59.538 60.000 0.00 0.00 0.00 3.86
1498 1675 2.811873 GCCACAAGAGTCCATGACAAGT 60.812 50.000 0.00 0.00 34.60 3.16
1503 1680 6.455647 CACAAGAGTCCATGACAAGTAGTTA 58.544 40.000 0.00 0.00 34.60 2.24
1504 1681 6.587990 CACAAGAGTCCATGACAAGTAGTTAG 59.412 42.308 0.00 0.00 34.60 2.34
1505 1682 5.923733 AGAGTCCATGACAAGTAGTTAGG 57.076 43.478 0.00 0.00 34.60 2.69
1506 1683 4.160626 AGAGTCCATGACAAGTAGTTAGGC 59.839 45.833 0.00 0.00 34.60 3.93
1508 1685 4.081420 AGTCCATGACAAGTAGTTAGGCTG 60.081 45.833 0.00 0.00 34.60 4.85
1511 1688 4.141620 CCATGACAAGTAGTTAGGCTGGAT 60.142 45.833 0.00 0.00 0.00 3.41
1512 1689 4.471904 TGACAAGTAGTTAGGCTGGATG 57.528 45.455 0.00 0.00 0.00 3.51
1513 1690 4.093743 TGACAAGTAGTTAGGCTGGATGA 58.906 43.478 0.00 0.00 0.00 2.92
1514 1691 4.530553 TGACAAGTAGTTAGGCTGGATGAA 59.469 41.667 0.00 0.00 0.00 2.57
1515 1692 5.189736 TGACAAGTAGTTAGGCTGGATGAAT 59.810 40.000 0.00 0.00 0.00 2.57
1516 1693 5.675538 ACAAGTAGTTAGGCTGGATGAATC 58.324 41.667 0.00 0.00 0.00 2.52
1517 1694 4.592485 AGTAGTTAGGCTGGATGAATCG 57.408 45.455 0.00 0.00 0.00 3.34
1518 1695 3.961408 AGTAGTTAGGCTGGATGAATCGT 59.039 43.478 0.00 0.00 0.00 3.73
1519 1696 3.460857 AGTTAGGCTGGATGAATCGTC 57.539 47.619 0.00 0.00 0.00 4.20
1520 1697 2.128035 GTTAGGCTGGATGAATCGTCG 58.872 52.381 0.00 0.00 0.00 5.12
1523 1700 0.034059 GGCTGGATGAATCGTCGGAT 59.966 55.000 0.00 0.00 0.00 4.18
1527 1704 3.190744 GCTGGATGAATCGTCGGATAGTA 59.809 47.826 0.00 0.00 31.01 1.82
2036 2332 5.177511 CACCAAGTATGTACGCTTATCCATG 59.822 44.000 0.00 0.00 0.00 3.66
2037 2333 4.690748 CCAAGTATGTACGCTTATCCATGG 59.309 45.833 4.97 4.97 0.00 3.66
2040 2336 5.297547 AGTATGTACGCTTATCCATGGTTG 58.702 41.667 12.58 1.81 0.00 3.77
2041 2337 3.897141 TGTACGCTTATCCATGGTTGA 57.103 42.857 12.58 0.00 0.00 3.18
2042 2338 4.209307 TGTACGCTTATCCATGGTTGAA 57.791 40.909 12.58 3.70 0.00 2.69
2053 2398 9.177608 CTTATCCATGGTTGAATCTAACTTTGA 57.822 33.333 12.58 0.00 0.00 2.69
2136 2516 0.961358 AGAACTCCGACGAGGACCTG 60.961 60.000 0.00 0.00 45.98 4.00
2901 3296 1.490490 GATTACAGGGGAGGTGATGCA 59.510 52.381 0.00 0.00 0.00 3.96
2904 3299 0.622738 ACAGGGGAGGTGATGCAGAT 60.623 55.000 0.00 0.00 0.00 2.90
2905 3300 0.179026 CAGGGGAGGTGATGCAGATG 60.179 60.000 0.00 0.00 0.00 2.90
2906 3301 1.527844 GGGGAGGTGATGCAGATGC 60.528 63.158 0.00 0.00 42.50 3.91
2907 3302 1.530771 GGGAGGTGATGCAGATGCT 59.469 57.895 6.35 0.00 42.66 3.79
2908 3303 0.818445 GGGAGGTGATGCAGATGCTG 60.818 60.000 6.35 0.00 42.66 4.41
2909 3304 0.179702 GGAGGTGATGCAGATGCTGA 59.820 55.000 6.35 0.00 42.66 4.26
2954 3352 4.650754 ATTCTGGTTAGTACTACGCCAG 57.349 45.455 29.51 29.51 45.82 4.85
2972 3378 1.001293 CAGAGAGGTGTAGCAAGTGCA 59.999 52.381 6.00 0.00 45.16 4.57
2976 3382 3.287222 AGAGGTGTAGCAAGTGCAAAAA 58.713 40.909 6.00 0.00 45.16 1.94
3036 3450 4.477975 AGTGCGCTCGCGGTAGAC 62.478 66.667 9.73 1.92 45.51 2.59
3056 3470 6.590234 AGACTGTCATAAATTTTGGGGTTC 57.410 37.500 10.88 0.00 0.00 3.62
3067 3481 7.581213 AAATTTTGGGGTTCAAATTTTCTCC 57.419 32.000 0.00 0.00 43.95 3.71
3068 3482 5.700402 TTTTGGGGTTCAAATTTTCTCCA 57.300 34.783 3.19 3.19 43.95 3.86
3069 3483 4.953940 TTGGGGTTCAAATTTTCTCCAG 57.046 40.909 6.52 0.00 31.46 3.86
3070 3484 3.922375 TGGGGTTCAAATTTTCTCCAGT 58.078 40.909 3.19 0.00 0.00 4.00
3071 3485 3.895041 TGGGGTTCAAATTTTCTCCAGTC 59.105 43.478 3.19 0.00 0.00 3.51
3072 3486 3.057526 GGGGTTCAAATTTTCTCCAGTCG 60.058 47.826 0.00 0.00 0.00 4.18
3073 3487 3.568430 GGGTTCAAATTTTCTCCAGTCGT 59.432 43.478 0.00 0.00 0.00 4.34
3074 3488 4.758165 GGGTTCAAATTTTCTCCAGTCGTA 59.242 41.667 0.00 0.00 0.00 3.43
3075 3489 5.414765 GGGTTCAAATTTTCTCCAGTCGTAT 59.585 40.000 0.00 0.00 0.00 3.06
3076 3490 6.072119 GGGTTCAAATTTTCTCCAGTCGTATT 60.072 38.462 0.00 0.00 0.00 1.89
3077 3491 7.368059 GGTTCAAATTTTCTCCAGTCGTATTT 58.632 34.615 0.00 0.00 0.00 1.40
3078 3492 8.508875 GGTTCAAATTTTCTCCAGTCGTATTTA 58.491 33.333 0.00 0.00 0.00 1.40
3079 3493 9.543018 GTTCAAATTTTCTCCAGTCGTATTTAG 57.457 33.333 0.00 0.00 0.00 1.85
3080 3494 9.496873 TTCAAATTTTCTCCAGTCGTATTTAGA 57.503 29.630 0.00 0.00 0.00 2.10
3081 3495 8.932791 TCAAATTTTCTCCAGTCGTATTTAGAC 58.067 33.333 0.00 0.00 38.81 2.59
3094 3508 9.302345 AGTCGTATTTAGACTGACAATATTGTG 57.698 33.333 25.42 14.23 46.12 3.33
3095 3509 8.056571 GTCGTATTTAGACTGACAATATTGTGC 58.943 37.037 25.42 16.17 37.30 4.57
3096 3510 7.762159 TCGTATTTAGACTGACAATATTGTGCA 59.238 33.333 25.42 19.31 42.43 4.57
3097 3511 8.058328 CGTATTTAGACTGACAATATTGTGCAG 58.942 37.037 27.99 27.99 42.43 4.41
3098 3512 5.801350 TTAGACTGACAATATTGTGCAGC 57.199 39.130 28.76 23.91 42.43 5.25
3099 3513 3.678289 AGACTGACAATATTGTGCAGCA 58.322 40.909 28.76 19.87 42.43 4.41
3100 3514 4.074259 AGACTGACAATATTGTGCAGCAA 58.926 39.130 28.76 11.37 42.43 3.91
3101 3515 4.155462 AGACTGACAATATTGTGCAGCAAG 59.845 41.667 28.76 18.46 42.43 4.01
3102 3516 3.822735 ACTGACAATATTGTGCAGCAAGT 59.177 39.130 28.76 18.88 42.43 3.16
3103 3517 4.083110 ACTGACAATATTGTGCAGCAAGTC 60.083 41.667 28.76 15.03 42.43 3.01
3104 3518 4.074259 TGACAATATTGTGCAGCAAGTCT 58.926 39.130 25.42 0.00 42.43 3.24
3105 3519 4.520111 TGACAATATTGTGCAGCAAGTCTT 59.480 37.500 25.42 0.00 42.43 3.01
3106 3520 5.051891 ACAATATTGTGCAGCAAGTCTTC 57.948 39.130 20.19 0.00 40.86 2.87
3107 3521 4.093514 CAATATTGTGCAGCAAGTCTTCG 58.906 43.478 7.32 0.00 40.86 3.79
3108 3522 1.597742 ATTGTGCAGCAAGTCTTCGT 58.402 45.000 0.00 0.00 40.86 3.85
3109 3523 0.937304 TTGTGCAGCAAGTCTTCGTC 59.063 50.000 0.00 0.00 32.52 4.20
3110 3524 0.880278 TGTGCAGCAAGTCTTCGTCC 60.880 55.000 0.00 0.00 0.00 4.79
3111 3525 1.664649 TGCAGCAAGTCTTCGTCCG 60.665 57.895 0.00 0.00 0.00 4.79
3112 3526 1.372997 GCAGCAAGTCTTCGTCCGA 60.373 57.895 0.00 0.00 0.00 4.55
3113 3527 0.944311 GCAGCAAGTCTTCGTCCGAA 60.944 55.000 1.81 1.81 0.00 4.30
3125 3539 4.514781 TTCGTCCGAAGAGAAATCTGAA 57.485 40.909 0.00 0.00 0.00 3.02
3126 3540 4.720649 TCGTCCGAAGAGAAATCTGAAT 57.279 40.909 0.00 0.00 0.00 2.57
3127 3541 5.073311 TCGTCCGAAGAGAAATCTGAATT 57.927 39.130 0.00 0.00 0.00 2.17
3128 3542 5.479306 TCGTCCGAAGAGAAATCTGAATTT 58.521 37.500 0.00 0.00 37.80 1.82
3188 3675 4.024670 GACTTAGACTTCCTCTGGGCTTA 58.975 47.826 0.00 0.00 0.00 3.09
3348 3849 7.011857 CAGCCTCCTATTGTTTTATGTTCTCTC 59.988 40.741 0.00 0.00 0.00 3.20
3798 4327 1.694150 CCTAGTTATGCCCAGCTGCTA 59.306 52.381 8.66 1.41 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.934579 CGAGTCATGGTGATCAACATCAA 59.065 43.478 23.52 11.91 43.22 2.57
54 56 8.987890 GCTCTTATGAGAATATTGGAGACTTTC 58.012 37.037 9.72 0.00 42.73 2.62
64 66 7.281774 CCACACACTTGCTCTTATGAGAATATT 59.718 37.037 9.72 0.00 42.73 1.28
76 78 0.839946 AGTTCCCACACACTTGCTCT 59.160 50.000 0.00 0.00 0.00 4.09
112 115 1.529865 CACGCATCGATCCTCTACGTA 59.470 52.381 0.00 0.00 0.00 3.57
115 118 0.999228 CGCACGCATCGATCCTCTAC 60.999 60.000 0.00 0.00 0.00 2.59
117 120 1.444917 TACGCACGCATCGATCCTCT 61.445 55.000 0.00 0.00 0.00 3.69
119 122 1.299165 GTACGCACGCATCGATCCT 60.299 57.895 0.00 0.00 0.00 3.24
120 123 0.939577 ATGTACGCACGCATCGATCC 60.940 55.000 0.00 0.00 0.00 3.36
121 124 0.431233 GATGTACGCACGCATCGATC 59.569 55.000 0.00 0.00 33.25 3.69
122 125 0.248866 TGATGTACGCACGCATCGAT 60.249 50.000 0.00 0.00 43.06 3.59
123 126 0.248866 ATGATGTACGCACGCATCGA 60.249 50.000 0.00 0.00 43.06 3.59
124 127 0.111574 CATGATGTACGCACGCATCG 60.112 55.000 0.00 0.00 43.06 3.84
125 128 0.930310 ACATGATGTACGCACGCATC 59.070 50.000 0.00 4.37 41.19 3.91
126 129 0.652071 CACATGATGTACGCACGCAT 59.348 50.000 0.00 0.00 0.00 4.73
127 130 1.965391 GCACATGATGTACGCACGCA 61.965 55.000 0.00 0.00 0.00 5.24
128 131 1.296867 GCACATGATGTACGCACGC 60.297 57.895 0.00 0.00 0.00 5.34
129 132 1.083806 AGGCACATGATGTACGCACG 61.084 55.000 9.64 0.00 0.00 5.34
130 133 1.062587 GAAGGCACATGATGTACGCAC 59.937 52.381 9.64 0.76 0.00 5.34
131 134 1.066215 AGAAGGCACATGATGTACGCA 60.066 47.619 9.64 0.00 0.00 5.24
132 135 1.328680 CAGAAGGCACATGATGTACGC 59.671 52.381 0.00 0.00 0.00 4.42
133 136 2.604914 GACAGAAGGCACATGATGTACG 59.395 50.000 0.00 0.00 0.00 3.67
134 137 2.939103 GGACAGAAGGCACATGATGTAC 59.061 50.000 0.00 0.00 0.00 2.90
135 138 2.092968 GGGACAGAAGGCACATGATGTA 60.093 50.000 0.00 0.00 0.00 2.29
136 139 1.340405 GGGACAGAAGGCACATGATGT 60.340 52.381 0.00 0.00 0.00 3.06
137 140 1.386533 GGGACAGAAGGCACATGATG 58.613 55.000 0.00 0.00 0.00 3.07
148 151 4.773674 TCTAGTGGAAAATACGGGACAGAA 59.226 41.667 0.00 0.00 0.00 3.02
164 167 2.420129 CCCCGGTCTGAAATTCTAGTGG 60.420 54.545 0.00 0.00 0.00 4.00
226 230 1.250328 TGTACTCCACCACGATTCGT 58.750 50.000 5.75 5.75 42.36 3.85
227 231 1.990563 GTTGTACTCCACCACGATTCG 59.009 52.381 4.14 4.14 0.00 3.34
253 261 0.396556 TCACGGTATGGCCTCTGCTA 60.397 55.000 3.32 0.00 37.74 3.49
254 262 1.050988 ATCACGGTATGGCCTCTGCT 61.051 55.000 3.32 0.00 37.74 4.24
257 265 1.464376 CGGATCACGGTATGGCCTCT 61.464 60.000 3.32 0.00 39.42 3.69
265 273 0.537653 TTGGCAATCGGATCACGGTA 59.462 50.000 0.00 0.00 44.45 4.02
309 317 5.863397 TGCTTCTGACTTGTGAAAACTTTTG 59.137 36.000 0.00 0.00 0.00 2.44
317 325 2.642427 TGCTTGCTTCTGACTTGTGAA 58.358 42.857 0.00 0.00 0.00 3.18
346 354 1.500474 AACTAGCAGCTGCCATAGGA 58.500 50.000 34.39 12.34 43.38 2.94
347 355 2.548920 GGTAACTAGCAGCTGCCATAGG 60.549 54.545 34.39 20.82 43.38 2.57
408 420 2.203877 AAGTGCACCCGGACCCTA 60.204 61.111 14.63 0.00 33.05 3.53
409 421 3.637273 GAAGTGCACCCGGACCCT 61.637 66.667 14.63 0.00 33.05 4.34
410 422 3.901797 CTGAAGTGCACCCGGACCC 62.902 68.421 14.63 0.00 33.05 4.46
411 423 2.358737 CTGAAGTGCACCCGGACC 60.359 66.667 14.63 0.00 33.05 4.46
412 424 3.050275 GCTGAAGTGCACCCGGAC 61.050 66.667 14.63 4.11 0.00 4.79
413 425 3.555324 TGCTGAAGTGCACCCGGA 61.555 61.111 14.63 0.00 38.12 5.14
590 611 7.773690 AGTACGAATTTATGTCCTGCCTTTTAT 59.226 33.333 0.00 0.00 0.00 1.40
591 612 7.107542 AGTACGAATTTATGTCCTGCCTTTTA 58.892 34.615 0.00 0.00 0.00 1.52
684 712 2.737359 CGTAGCTTCCTGCCGAATTACA 60.737 50.000 0.00 0.00 44.23 2.41
750 791 1.734655 AAGGCACCTCTCCTTTCTCA 58.265 50.000 0.00 0.00 40.87 3.27
782 823 3.555547 TCGATGAACAGCATTTATGACCG 59.444 43.478 0.00 0.00 37.34 4.79
872 916 3.718210 GATGGAGACGGTCGTGCCC 62.718 68.421 0.00 2.51 0.00 5.36
873 917 2.202756 GATGGAGACGGTCGTGCC 60.203 66.667 0.00 6.64 0.00 5.01
874 918 2.337749 ATCGATGGAGACGGTCGTGC 62.338 60.000 0.00 0.00 40.56 5.34
875 919 0.317103 GATCGATGGAGACGGTCGTG 60.317 60.000 0.54 0.00 40.56 4.35
876 920 2.023318 GATCGATGGAGACGGTCGT 58.977 57.895 0.54 0.00 40.56 4.34
877 921 4.924924 GATCGATGGAGACGGTCG 57.075 61.111 0.54 0.00 40.92 4.79
878 922 0.875728 ATCGATCGATGGAGACGGTC 59.124 55.000 28.90 0.00 37.50 4.79
879 923 0.875728 GATCGATCGATGGAGACGGT 59.124 55.000 33.86 8.66 34.60 4.83
880 924 0.169230 GGATCGATCGATGGAGACGG 59.831 60.000 33.86 0.00 34.60 4.79
885 929 2.489722 GACTGATGGATCGATCGATGGA 59.510 50.000 33.86 19.88 34.60 3.41
887 931 2.416566 GGGACTGATGGATCGATCGATG 60.417 54.545 33.86 20.21 34.60 3.84
895 939 0.318762 GTAGGCGGGACTGATGGATC 59.681 60.000 0.00 0.00 0.00 3.36
896 940 0.398522 TGTAGGCGGGACTGATGGAT 60.399 55.000 0.00 0.00 0.00 3.41
897 941 0.398522 ATGTAGGCGGGACTGATGGA 60.399 55.000 0.00 0.00 0.00 3.41
898 942 1.338107 TATGTAGGCGGGACTGATGG 58.662 55.000 0.00 0.00 0.00 3.51
899 943 3.393800 CTTTATGTAGGCGGGACTGATG 58.606 50.000 0.00 0.00 0.00 3.07
900 944 2.224305 GCTTTATGTAGGCGGGACTGAT 60.224 50.000 0.00 0.00 0.00 2.90
901 945 1.138266 GCTTTATGTAGGCGGGACTGA 59.862 52.381 0.00 0.00 0.00 3.41
902 946 1.583054 GCTTTATGTAGGCGGGACTG 58.417 55.000 0.00 0.00 0.00 3.51
903 947 0.104304 CGCTTTATGTAGGCGGGACT 59.896 55.000 0.00 0.00 44.32 3.85
904 948 2.601562 CGCTTTATGTAGGCGGGAC 58.398 57.895 0.00 0.00 44.32 4.46
944 992 3.842923 CGAGCAGGCTCCGGTGAT 61.843 66.667 15.16 0.00 39.77 3.06
969 1017 1.136984 GTCCTCCGAGTGTGCGTAG 59.863 63.158 0.00 0.00 0.00 3.51
970 1018 1.583495 CTGTCCTCCGAGTGTGCGTA 61.583 60.000 0.00 0.00 0.00 4.42
971 1019 2.910479 TGTCCTCCGAGTGTGCGT 60.910 61.111 0.00 0.00 0.00 5.24
972 1020 2.126307 CTGTCCTCCGAGTGTGCG 60.126 66.667 0.00 0.00 0.00 5.34
973 1021 2.433318 GCTGTCCTCCGAGTGTGC 60.433 66.667 0.00 0.00 0.00 4.57
974 1022 2.126307 CGCTGTCCTCCGAGTGTG 60.126 66.667 0.00 0.00 0.00 3.82
1112 1163 0.869454 CACAAGAGAGAGATCGGCGC 60.869 60.000 0.00 0.00 0.00 6.53
1113 1164 0.869454 GCACAAGAGAGAGATCGGCG 60.869 60.000 0.00 0.00 0.00 6.46
1114 1165 0.459489 AGCACAAGAGAGAGATCGGC 59.541 55.000 0.00 0.00 0.00 5.54
1115 1166 2.287547 GCTAGCACAAGAGAGAGATCGG 60.288 54.545 10.63 0.00 0.00 4.18
1116 1167 2.357323 TGCTAGCACAAGAGAGAGATCG 59.643 50.000 14.93 0.00 0.00 3.69
1117 1168 3.705604 GTGCTAGCACAAGAGAGAGATC 58.294 50.000 36.93 9.95 45.53 2.75
1118 1169 2.098934 CGTGCTAGCACAAGAGAGAGAT 59.901 50.000 38.95 0.00 46.47 2.75
1119 1170 1.470494 CGTGCTAGCACAAGAGAGAGA 59.530 52.381 38.95 3.74 46.47 3.10
1120 1171 1.201181 ACGTGCTAGCACAAGAGAGAG 59.799 52.381 38.95 25.34 46.47 3.20
1121 1172 1.068264 CACGTGCTAGCACAAGAGAGA 60.068 52.381 38.95 5.06 46.47 3.10
1122 1173 1.344458 CACGTGCTAGCACAAGAGAG 58.656 55.000 38.95 26.59 46.47 3.20
1127 1178 3.041351 CCGCACGTGCTAGCACAA 61.041 61.111 38.95 8.97 46.47 3.33
1131 1182 3.479269 GTCACCGCACGTGCTAGC 61.479 66.667 35.27 18.00 42.69 3.42
1143 1194 2.973180 GAATAGGCTCGGCGGTCACC 62.973 65.000 7.21 3.50 0.00 4.02
1144 1195 1.591863 GAATAGGCTCGGCGGTCAC 60.592 63.158 7.21 0.00 0.00 3.67
1145 1196 2.812499 GAATAGGCTCGGCGGTCA 59.188 61.111 7.21 0.00 0.00 4.02
1146 1197 2.354773 CGAATAGGCTCGGCGGTC 60.355 66.667 7.21 0.00 35.14 4.79
1194 1245 2.246789 ACAAAACAGCAACACGAAACG 58.753 42.857 0.00 0.00 0.00 3.60
1203 1256 0.248825 ATGCGCGAACAAAACAGCAA 60.249 45.000 12.10 0.00 38.15 3.91
1216 1269 4.182315 TCCATTGCTGCATGCGCG 62.182 61.111 22.88 14.30 46.63 6.86
1217 1270 2.071844 ATCTCCATTGCTGCATGCGC 62.072 55.000 22.12 22.12 46.63 6.09
1456 1628 1.227002 GATTGGAGTCGGGAGTCGC 60.227 63.158 0.00 0.00 39.05 5.19
1458 1630 0.461961 CTGGATTGGAGTCGGGAGTC 59.538 60.000 0.00 0.00 0.00 3.36
1477 1649 1.808945 CTTGTCATGGACTCTTGTGGC 59.191 52.381 0.00 0.00 33.15 5.01
1498 1675 3.004419 CGACGATTCATCCAGCCTAACTA 59.996 47.826 0.00 0.00 0.00 2.24
1503 1680 1.043116 TCCGACGATTCATCCAGCCT 61.043 55.000 0.00 0.00 0.00 4.58
1504 1681 0.034059 ATCCGACGATTCATCCAGCC 59.966 55.000 0.00 0.00 0.00 4.85
1505 1682 2.029828 ACTATCCGACGATTCATCCAGC 60.030 50.000 0.00 0.00 0.00 4.85
1506 1683 3.924918 ACTATCCGACGATTCATCCAG 57.075 47.619 0.00 0.00 0.00 3.86
1508 1685 4.008330 TCCTACTATCCGACGATTCATCC 58.992 47.826 0.00 0.00 0.00 3.51
1511 1688 5.067954 TCAATCCTACTATCCGACGATTCA 58.932 41.667 0.00 0.00 0.00 2.57
1512 1689 5.624344 TCAATCCTACTATCCGACGATTC 57.376 43.478 0.00 0.00 0.00 2.52
1513 1690 5.946972 AGATCAATCCTACTATCCGACGATT 59.053 40.000 0.00 0.00 0.00 3.34
1514 1691 5.502079 AGATCAATCCTACTATCCGACGAT 58.498 41.667 0.00 0.00 0.00 3.73
1515 1692 4.907809 AGATCAATCCTACTATCCGACGA 58.092 43.478 0.00 0.00 0.00 4.20
1516 1693 4.095185 GGAGATCAATCCTACTATCCGACG 59.905 50.000 0.00 0.00 36.35 5.12
1517 1694 5.010933 TGGAGATCAATCCTACTATCCGAC 58.989 45.833 0.00 0.00 40.29 4.79
1518 1695 5.256806 TGGAGATCAATCCTACTATCCGA 57.743 43.478 0.00 0.00 40.29 4.55
1519 1696 5.715070 GTTGGAGATCAATCCTACTATCCG 58.285 45.833 7.91 0.00 40.59 4.18
1527 1704 4.161942 CAGACAGAGTTGGAGATCAATCCT 59.838 45.833 0.00 0.00 40.29 3.24
1754 2040 2.303022 CCACCAGTTGAAGAAGGAGCTA 59.697 50.000 0.00 0.00 0.00 3.32
1820 2106 0.456312 CGTTGTCCTGGACGTAGCTC 60.456 60.000 21.15 7.33 34.95 4.09
2036 2332 6.749118 GCACATGATCAAAGTTAGATTCAACC 59.251 38.462 0.00 0.00 0.00 3.77
2037 2333 7.307694 TGCACATGATCAAAGTTAGATTCAAC 58.692 34.615 0.00 0.00 0.00 3.18
2040 2336 7.013083 AGGATGCACATGATCAAAGTTAGATTC 59.987 37.037 0.00 0.00 0.00 2.52
2041 2337 6.832384 AGGATGCACATGATCAAAGTTAGATT 59.168 34.615 0.00 0.00 0.00 2.40
2042 2338 6.363065 AGGATGCACATGATCAAAGTTAGAT 58.637 36.000 0.00 0.00 0.00 1.98
2053 2398 1.483827 ACGTCAGAGGATGCACATGAT 59.516 47.619 0.00 0.00 33.10 2.45
2136 2516 2.363172 GCTCCTCACCTCCTCCACC 61.363 68.421 0.00 0.00 0.00 4.61
2319 2699 2.610859 ACCGGGATGAAGGCCACT 60.611 61.111 6.32 0.00 0.00 4.00
2805 3188 2.360600 AGCTCGAGGACGCAGAGT 60.361 61.111 15.58 0.00 39.58 3.24
2829 3212 2.535331 GCTCGCGAGAAGAAGAAGAAT 58.465 47.619 38.74 0.00 41.32 2.40
2901 3296 3.211865 CACCAATGTAGCATCAGCATCT 58.788 45.455 0.00 0.00 45.49 2.90
2904 3299 2.495155 ACACCAATGTAGCATCAGCA 57.505 45.000 0.00 0.00 45.49 4.41
2905 3300 3.941483 AGTTACACCAATGTAGCATCAGC 59.059 43.478 4.47 0.00 43.11 4.26
2906 3301 7.792374 ATAAGTTACACCAATGTAGCATCAG 57.208 36.000 4.47 0.00 43.11 2.90
2907 3302 9.674068 TTAATAAGTTACACCAATGTAGCATCA 57.326 29.630 4.47 0.00 43.11 3.07
2954 3352 2.169832 TTGCACTTGCTACACCTCTC 57.830 50.000 2.33 0.00 42.66 3.20
2955 3353 2.638480 TTTGCACTTGCTACACCTCT 57.362 45.000 2.33 0.00 42.66 3.69
3002 3412 6.051717 AGCGCACTCTATAACAATCTGAAAT 58.948 36.000 11.47 0.00 0.00 2.17
3036 3450 8.620116 AATTTGAACCCCAAAATTTATGACAG 57.380 30.769 0.00 0.00 46.64 3.51
3056 3470 8.936864 AGTCTAAATACGACTGGAGAAAATTTG 58.063 33.333 0.00 0.00 40.07 2.32
3068 3482 9.302345 CACAATATTGTCAGTCTAAATACGACT 57.698 33.333 18.25 0.00 39.73 4.18
3069 3483 8.056571 GCACAATATTGTCAGTCTAAATACGAC 58.943 37.037 18.25 0.00 39.91 4.34
3070 3484 7.762159 TGCACAATATTGTCAGTCTAAATACGA 59.238 33.333 18.25 0.00 39.91 3.43
3071 3485 7.905126 TGCACAATATTGTCAGTCTAAATACG 58.095 34.615 18.25 4.01 39.91 3.06
3072 3486 7.852945 GCTGCACAATATTGTCAGTCTAAATAC 59.147 37.037 28.81 16.91 39.91 1.89
3073 3487 7.552330 TGCTGCACAATATTGTCAGTCTAAATA 59.448 33.333 28.81 15.56 39.91 1.40
3074 3488 6.375174 TGCTGCACAATATTGTCAGTCTAAAT 59.625 34.615 28.81 6.16 39.91 1.40
3075 3489 5.704978 TGCTGCACAATATTGTCAGTCTAAA 59.295 36.000 28.81 17.25 39.91 1.85
3076 3490 5.244755 TGCTGCACAATATTGTCAGTCTAA 58.755 37.500 28.81 18.66 39.91 2.10
3077 3491 4.831107 TGCTGCACAATATTGTCAGTCTA 58.169 39.130 28.81 20.35 39.91 2.59
3078 3492 3.678289 TGCTGCACAATATTGTCAGTCT 58.322 40.909 28.81 8.36 39.91 3.24
3079 3493 4.083110 ACTTGCTGCACAATATTGTCAGTC 60.083 41.667 28.81 24.18 39.91 3.51
3080 3494 3.822735 ACTTGCTGCACAATATTGTCAGT 59.177 39.130 28.81 18.30 39.91 3.41
3081 3495 4.155462 AGACTTGCTGCACAATATTGTCAG 59.845 41.667 26.76 26.76 39.91 3.51
3082 3496 4.074259 AGACTTGCTGCACAATATTGTCA 58.926 39.130 18.25 16.49 39.91 3.58
3083 3497 4.691860 AGACTTGCTGCACAATATTGTC 57.308 40.909 18.25 13.15 39.91 3.18
3084 3498 4.378770 CGAAGACTTGCTGCACAATATTGT 60.379 41.667 15.47 15.47 43.36 2.71
3085 3499 4.093514 CGAAGACTTGCTGCACAATATTG 58.906 43.478 14.01 14.01 37.72 1.90
3086 3500 3.753272 ACGAAGACTTGCTGCACAATATT 59.247 39.130 0.00 0.00 37.72 1.28
3087 3501 3.338249 ACGAAGACTTGCTGCACAATAT 58.662 40.909 0.00 0.00 37.72 1.28
3088 3502 2.736721 GACGAAGACTTGCTGCACAATA 59.263 45.455 0.00 0.00 37.72 1.90
3089 3503 1.532868 GACGAAGACTTGCTGCACAAT 59.467 47.619 0.00 0.00 37.72 2.71
3090 3504 0.937304 GACGAAGACTTGCTGCACAA 59.063 50.000 0.00 0.00 36.62 3.33
3091 3505 0.880278 GGACGAAGACTTGCTGCACA 60.880 55.000 0.00 0.00 0.00 4.57
3092 3506 1.862806 GGACGAAGACTTGCTGCAC 59.137 57.895 0.00 0.00 0.00 4.57
3093 3507 1.664649 CGGACGAAGACTTGCTGCA 60.665 57.895 0.00 0.00 0.00 4.41
3094 3508 0.944311 TTCGGACGAAGACTTGCTGC 60.944 55.000 2.62 0.00 0.00 5.25
3095 3509 3.195041 TTCGGACGAAGACTTGCTG 57.805 52.632 2.62 0.00 0.00 4.41
3103 3517 6.091441 AAATTCAGATTTCTCTTCGGACGAAG 59.909 38.462 24.17 24.17 40.65 3.79
3104 3518 4.514781 TTCAGATTTCTCTTCGGACGAA 57.485 40.909 6.98 6.98 0.00 3.85
3105 3519 4.720649 ATTCAGATTTCTCTTCGGACGA 57.279 40.909 0.00 0.00 0.00 4.20
3106 3520 5.786401 AAATTCAGATTTCTCTTCGGACG 57.214 39.130 0.00 0.00 29.53 4.79
3135 3549 5.472478 GTCCTAGACAAACCCTTCGATTTTT 59.528 40.000 0.00 0.00 32.09 1.94
3136 3550 5.001874 GTCCTAGACAAACCCTTCGATTTT 58.998 41.667 0.00 0.00 32.09 1.82
3137 3551 4.286291 AGTCCTAGACAAACCCTTCGATTT 59.714 41.667 0.00 0.00 34.60 2.17
3138 3552 3.838903 AGTCCTAGACAAACCCTTCGATT 59.161 43.478 0.00 0.00 34.60 3.34
3139 3553 3.442076 AGTCCTAGACAAACCCTTCGAT 58.558 45.455 0.00 0.00 34.60 3.59
3140 3554 2.824341 GAGTCCTAGACAAACCCTTCGA 59.176 50.000 0.00 0.00 34.60 3.71
3141 3555 2.561419 TGAGTCCTAGACAAACCCTTCG 59.439 50.000 0.00 0.00 34.60 3.79
3142 3556 3.579151 ACTGAGTCCTAGACAAACCCTTC 59.421 47.826 0.00 0.00 34.60 3.46
3188 3675 5.148651 AGAAAGCCTCATACACGTTAAGT 57.851 39.130 0.00 0.00 0.00 2.24
3798 4327 1.097547 AAGCAACTGCAAGCGACACT 61.098 50.000 4.22 0.00 45.16 3.55
3845 4374 1.138671 CCAATTTTACAGCGCCCCG 59.861 57.895 2.29 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.