Multiple sequence alignment - TraesCS1D01G061700

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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 TraesCS1D01G061700 chr1D 100.000 3327 0 0 1 3327 41758926 41755600 0.000000e+00 6144.0
1 TraesCS1D01G061700 chr1D 89.474 171 18 0 1 171 488539992 488540162 2.010000e-52 217.0
2 TraesCS1D01G061700 chr1B 90.953 1857 111 29 850 2651 61943881 61942027 0.000000e+00 2446.0
3 TraesCS1D01G061700 chr1B 89.238 604 29 11 181 772 61944732 61944153 0.000000e+00 723.0
4 TraesCS1D01G061700 chr1B 76.453 327 31 18 2942 3261 61941636 61941349 5.790000e-28 135.0
5 TraesCS1D01G061700 chr1B 96.552 58 2 0 2648 2705 61941925 61941868 2.730000e-16 97.1
6 TraesCS1D01G061700 chr1A 93.673 1296 61 9 849 2124 41759572 41758278 0.000000e+00 1919.0
7 TraesCS1D01G061700 chr1A 89.588 826 34 12 1 813 41760421 41759635 0.000000e+00 1002.0
8 TraesCS1D01G061700 chr1A 83.652 679 52 24 2118 2750 41755224 41754559 4.780000e-163 584.0
9 TraesCS1D01G061700 chr1A 84.814 349 35 9 2942 3277 41754249 41753906 5.320000e-88 335.0
10 TraesCS1D01G061700 chr3D 86.041 788 101 7 1376 2162 10660946 10661725 0.000000e+00 837.0
11 TraesCS1D01G061700 chr3D 80.142 1128 164 40 966 2067 10723549 10724642 0.000000e+00 787.0
12 TraesCS1D01G061700 chr3D 79.252 1070 165 30 1028 2067 10709680 10710722 0.000000e+00 693.0
13 TraesCS1D01G061700 chr3B 79.083 1243 196 37 850 2075 14402703 14401508 0.000000e+00 797.0
14 TraesCS1D01G061700 chr3B 84.000 800 115 10 1365 2161 26532088 26531299 0.000000e+00 756.0
15 TraesCS1D01G061700 chr3B 85.075 670 88 7 1398 2067 15054845 15055502 0.000000e+00 673.0
16 TraesCS1D01G061700 chr3B 87.500 560 68 2 1590 2148 26578115 26577557 0.000000e+00 645.0
17 TraesCS1D01G061700 chr3B 76.273 746 128 31 871 1592 26583964 26583244 5.280000e-93 351.0
18 TraesCS1D01G061700 chr3B 79.899 199 30 7 1076 1268 15054503 15054697 1.610000e-28 137.0
19 TraesCS1D01G061700 chr3A 84.868 793 109 9 1364 2154 17606439 17605656 0.000000e+00 789.0
20 TraesCS1D01G061700 chr7B 89.560 182 19 0 2 183 104749922 104750103 7.180000e-57 231.0
21 TraesCS1D01G061700 chr7A 87.079 178 17 3 4 178 650673597 650673771 2.620000e-46 196.0
22 TraesCS1D01G061700 chr7A 85.714 175 25 0 4 178 650687862 650688036 5.670000e-43 185.0
23 TraesCS1D01G061700 chr2D 85.638 188 25 2 4 189 600325630 600325817 2.620000e-46 196.0
24 TraesCS1D01G061700 chr6D 94.030 67 4 0 1 67 356233090 356233156 5.870000e-18 102.0
25 TraesCS1D01G061700 chr6B 90.141 71 6 1 19 88 537459590 537459660 1.270000e-14 91.6


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 TraesCS1D01G061700 chr1D 41755600 41758926 3326 True 6144.000 6144 100.00000 1 3327 1 chr1D.!!$R1 3326
1 TraesCS1D01G061700 chr1B 61941349 61944732 3383 True 850.275 2446 88.29900 181 3261 4 chr1B.!!$R1 3080
2 TraesCS1D01G061700 chr1A 41753906 41760421 6515 True 960.000 1919 87.93175 1 3277 4 chr1A.!!$R1 3276
3 TraesCS1D01G061700 chr3D 10660946 10661725 779 False 837.000 837 86.04100 1376 2162 1 chr3D.!!$F1 786
4 TraesCS1D01G061700 chr3D 10723549 10724642 1093 False 787.000 787 80.14200 966 2067 1 chr3D.!!$F3 1101
5 TraesCS1D01G061700 chr3D 10709680 10710722 1042 False 693.000 693 79.25200 1028 2067 1 chr3D.!!$F2 1039
6 TraesCS1D01G061700 chr3B 14401508 14402703 1195 True 797.000 797 79.08300 850 2075 1 chr3B.!!$R1 1225
7 TraesCS1D01G061700 chr3B 26531299 26532088 789 True 756.000 756 84.00000 1365 2161 1 chr3B.!!$R2 796
8 TraesCS1D01G061700 chr3B 26577557 26578115 558 True 645.000 645 87.50000 1590 2148 1 chr3B.!!$R3 558
9 TraesCS1D01G061700 chr3B 15054503 15055502 999 False 405.000 673 82.48700 1076 2067 2 chr3B.!!$F1 991
10 TraesCS1D01G061700 chr3B 26583244 26583964 720 True 351.000 351 76.27300 871 1592 1 chr3B.!!$R4 721
11 TraesCS1D01G061700 chr3A 17605656 17606439 783 True 789.000 789 84.86800 1364 2154 1 chr3A.!!$R1 790

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
249 250 0.516877 CGCGTTCTCTGAAATTGCCA 59.483 50.0 0.0 0.0 0.0 4.92 F
1458 1749 0.462581 TGCTCCTCGTGCCATGAATC 60.463 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 2411 2.525629 TGCAGGAGTCGGACCCAA 60.526 61.111 15.16 1.8 0.0 4.12 R
2379 5812 0.039180 TGTAGAGCAAGAGTCGGGGA 59.961 55.000 0.00 0.0 0.0 4.81 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
64 65 1.338020 CTGAAACAGGGGTGAAGTTGC 59.662 52.381 0.00 0.00 0.00 4.17
70 71 2.093711 ACAGGGGTGAAGTTGCAAAAAC 60.094 45.455 0.00 0.00 0.00 2.43
71 72 2.093764 CAGGGGTGAAGTTGCAAAAACA 60.094 45.455 0.00 0.00 0.00 2.83
84 85 5.437289 TGCAAAAACATGAAGTAGGTGAG 57.563 39.130 0.00 0.00 0.00 3.51
102 103 1.988406 GGGTGGCTCCTAACCGTCT 60.988 63.158 5.46 0.00 37.33 4.18
173 174 1.098712 TCAGCCGGGTGAACACAAAC 61.099 55.000 33.02 0.00 0.00 2.93
246 247 5.456192 ACTAATCGCGTTCTCTGAAATTG 57.544 39.130 5.77 0.00 0.00 2.32
247 248 2.813779 ATCGCGTTCTCTGAAATTGC 57.186 45.000 5.77 0.00 0.00 3.56
249 250 0.516877 CGCGTTCTCTGAAATTGCCA 59.483 50.000 0.00 0.00 0.00 4.92
329 331 2.011617 GCCCAGGCCCATATTCCAGT 62.012 60.000 0.00 0.00 34.56 4.00
407 409 3.839432 CTTCCCCGCTCCGTCTCC 61.839 72.222 0.00 0.00 0.00 3.71
422 424 1.456518 CTCCCCGATCAGGCTCAGA 60.457 63.158 0.00 0.00 39.21 3.27
423 425 1.456518 TCCCCGATCAGGCTCAGAG 60.457 63.158 0.00 0.00 39.21 3.35
424 426 2.420890 CCCGATCAGGCTCAGAGC 59.579 66.667 14.69 14.69 41.46 4.09
497 499 4.586841 CGATCAGTATTCTCCCCTCTTTCT 59.413 45.833 0.00 0.00 0.00 2.52
603 609 0.941542 TTGCAGTGGTTAGACAACGC 59.058 50.000 0.00 0.00 35.34 4.84
657 667 1.640917 TCTGGCTTCGTAACCTTCCT 58.359 50.000 0.00 0.00 0.00 3.36
658 668 1.549170 TCTGGCTTCGTAACCTTCCTC 59.451 52.381 0.00 0.00 0.00 3.71
732 743 7.647907 TTTTACGGTTTCTCTGTCAGATTAC 57.352 36.000 2.22 2.21 36.91 1.89
733 744 6.585695 TTACGGTTTCTCTGTCAGATTACT 57.414 37.500 2.22 0.00 36.91 2.24
734 745 5.470047 ACGGTTTCTCTGTCAGATTACTT 57.530 39.130 2.22 0.00 0.00 2.24
735 746 5.230942 ACGGTTTCTCTGTCAGATTACTTG 58.769 41.667 2.22 2.79 0.00 3.16
736 747 4.092091 CGGTTTCTCTGTCAGATTACTTGC 59.908 45.833 2.22 0.00 0.00 4.01
737 748 4.092091 GGTTTCTCTGTCAGATTACTTGCG 59.908 45.833 2.22 0.00 0.00 4.85
738 749 4.521130 TTCTCTGTCAGATTACTTGCGT 57.479 40.909 2.22 0.00 0.00 5.24
739 750 5.638596 TTCTCTGTCAGATTACTTGCGTA 57.361 39.130 2.22 0.00 0.00 4.42
794 840 5.565509 TCAAACAGGAAGCCAACATATGTA 58.434 37.500 9.21 0.00 0.00 2.29
826 872 6.905578 ACAGTTTACTTGTTTAATTAGGGCG 58.094 36.000 0.00 0.00 0.00 6.13
831 877 2.500392 TGTTTAATTAGGGCGCCTGT 57.500 45.000 28.56 16.88 34.61 4.00
847 927 4.794169 CGCCTGTAAGTGTTTAAATTGCT 58.206 39.130 0.00 0.00 0.00 3.91
865 1081 4.734398 TGCTGTTCCATGACTTTTGTTT 57.266 36.364 0.00 0.00 0.00 2.83
889 1105 2.069273 CATCTCGTGGAACAGGTGAAC 58.931 52.381 0.00 0.00 46.87 3.18
929 1145 6.599244 GTGTTGATCAATAGGTTTGGATCTCA 59.401 38.462 12.12 0.00 37.60 3.27
959 1176 5.655488 GTCTGTGATTCTAGCAGTACACAT 58.345 41.667 0.00 0.00 37.56 3.21
976 1193 4.820897 ACACATCAAGAAAGATAGTGCGA 58.179 39.130 0.00 0.00 33.89 5.10
1203 1439 9.020813 GTCTTTGAACTCAACCTTTTATTTCAC 57.979 33.333 0.00 0.00 35.28 3.18
1253 1495 6.624423 AGCGCTTTGATGAATCTATTTTTGT 58.376 32.000 2.64 0.00 0.00 2.83
1335 1579 9.888878 CTATGTTAGCTCAAATAATGGAATGTG 57.111 33.333 0.00 0.00 0.00 3.21
1452 1743 0.829990 TTCATATGCTCCTCGTGCCA 59.170 50.000 0.00 0.00 0.00 4.92
1458 1749 0.462581 TGCTCCTCGTGCCATGAATC 60.463 55.000 0.00 0.00 0.00 2.52
1797 2088 2.100252 GCCTACATGTTCTGCAATGCAT 59.900 45.455 8.91 0.00 38.13 3.96
2108 2411 5.240891 TCAGCAGATCTTGTTTTCGAGAAT 58.759 37.500 0.00 0.00 42.83 2.40
2176 5539 0.933700 AGGAGAAGGAGGAGGAGGAG 59.066 60.000 0.00 0.00 0.00 3.69
2177 5540 0.930726 GGAGAAGGAGGAGGAGGAGA 59.069 60.000 0.00 0.00 0.00 3.71
2179 5542 2.666317 GAGAAGGAGGAGGAGGAGAAG 58.334 57.143 0.00 0.00 0.00 2.85
2205 5583 1.933051 TCATGAGGAAGAGGAGGAGGA 59.067 52.381 0.00 0.00 0.00 3.71
2215 5593 4.186077 AGAGGAGGAGGACGATAATGAA 57.814 45.455 0.00 0.00 0.00 2.57
2260 5668 2.630098 GGACGAGGATGATGATGAGGAA 59.370 50.000 0.00 0.00 0.00 3.36
2273 5681 2.765689 TGAGGAAGAGGAGGAGGATC 57.234 55.000 0.00 0.00 0.00 3.36
2296 5704 3.710677 AGGAGGAAGAGTTGGATGATGAG 59.289 47.826 0.00 0.00 0.00 2.90
2297 5705 3.181456 GGAGGAAGAGTTGGATGATGAGG 60.181 52.174 0.00 0.00 0.00 3.86
2299 5707 3.710677 AGGAAGAGTTGGATGATGAGGAG 59.289 47.826 0.00 0.00 0.00 3.69
2312 5744 0.253868 TGAGGAGGAGGAGGAGGAGA 60.254 60.000 0.00 0.00 0.00 3.71
2351 5784 3.942115 GGATAAACCTTGAAGTCTCAGCC 59.058 47.826 0.00 0.00 35.41 4.85
2379 5812 0.981943 ACCCCGTCTTCGAGGAAATT 59.018 50.000 0.00 0.00 37.10 1.82
2389 5822 0.824759 CGAGGAAATTCCCCGACTCT 59.175 55.000 10.54 0.00 37.19 3.24
2394 5827 2.010497 GAAATTCCCCGACTCTTGCTC 58.990 52.381 0.00 0.00 0.00 4.26
2396 5829 2.160721 ATTCCCCGACTCTTGCTCTA 57.839 50.000 0.00 0.00 0.00 2.43
2401 5834 1.272490 CCCGACTCTTGCTCTACAACA 59.728 52.381 0.00 0.00 33.68 3.33
2463 5896 5.882000 ACACTTTTAGTACCGTCCTTGTTTT 59.118 36.000 0.00 0.00 0.00 2.43
2473 5906 3.317993 CCGTCCTTGTTTTGAGAATTGGT 59.682 43.478 0.00 0.00 0.00 3.67
2483 5916 4.494091 TTGAGAATTGGTCCAGATCCTC 57.506 45.455 0.00 0.00 0.00 3.71
2484 5917 3.729108 TGAGAATTGGTCCAGATCCTCT 58.271 45.455 11.43 3.37 0.00 3.69
2489 5922 2.550277 TGGTCCAGATCCTCTTGCTA 57.450 50.000 0.00 0.00 0.00 3.49
2508 5941 6.038997 TGCTAGGTTTTCTTCTACCTCTTC 57.961 41.667 0.00 0.00 43.58 2.87
2626 6061 6.555812 ACAAAAATAGAGTCGGGAGAAAAC 57.444 37.500 0.00 0.00 42.89 2.43
2627 6062 5.472478 ACAAAAATAGAGTCGGGAGAAAACC 59.528 40.000 0.00 0.00 42.89 3.27
2628 6063 3.908643 AATAGAGTCGGGAGAAAACCC 57.091 47.619 0.00 0.00 45.92 4.11
2700 6251 1.305219 GCGTGGACTTGCTGCCATTA 61.305 55.000 0.00 0.00 36.41 1.90
2711 6264 2.121564 CTGCCATTATGCCGCCTTCG 62.122 60.000 0.00 0.00 0.00 3.79
2712 6265 2.186826 GCCATTATGCCGCCTTCGT 61.187 57.895 0.00 0.00 0.00 3.85
2726 6279 1.337823 CCTTCGTGGTTCTGGTTCGAT 60.338 52.381 0.00 0.00 0.00 3.59
2728 6281 0.963225 TCGTGGTTCTGGTTCGATGA 59.037 50.000 0.00 0.00 0.00 2.92
2740 6293 6.681777 TCTGGTTCGATGATATACATGTCAG 58.318 40.000 0.00 0.00 39.56 3.51
2742 6295 4.627467 GGTTCGATGATATACATGTCAGGC 59.373 45.833 0.00 0.00 39.56 4.85
2746 6299 4.628766 CGATGATATACATGTCAGGCCTTG 59.371 45.833 0.00 0.13 39.56 3.61
2750 6303 0.677731 TACATGTCAGGCCTTGCTGC 60.678 55.000 0.00 0.00 0.00 5.25
2751 6304 1.974875 CATGTCAGGCCTTGCTGCA 60.975 57.895 0.00 0.00 0.00 4.41
2752 6305 1.677966 ATGTCAGGCCTTGCTGCAG 60.678 57.895 10.11 10.11 0.00 4.41
2753 6306 2.033141 GTCAGGCCTTGCTGCAGA 59.967 61.111 20.43 0.00 0.00 4.26
2754 6307 1.378250 GTCAGGCCTTGCTGCAGAT 60.378 57.895 20.43 0.00 0.00 2.90
2755 6308 1.378119 TCAGGCCTTGCTGCAGATG 60.378 57.895 20.43 5.96 0.00 2.90
2756 6309 1.677966 CAGGCCTTGCTGCAGATGT 60.678 57.895 20.43 0.00 0.00 3.06
2757 6310 1.076192 AGGCCTTGCTGCAGATGTT 59.924 52.632 20.43 0.00 0.00 2.71
2759 6312 0.389426 GGCCTTGCTGCAGATGTTTG 60.389 55.000 20.43 0.73 0.00 2.93
2760 6313 0.389426 GCCTTGCTGCAGATGTTTGG 60.389 55.000 20.43 10.71 0.00 3.28
2761 6314 0.963962 CCTTGCTGCAGATGTTTGGT 59.036 50.000 20.43 0.00 0.00 3.67
2762 6315 1.342174 CCTTGCTGCAGATGTTTGGTT 59.658 47.619 20.43 0.00 0.00 3.67
2763 6316 2.557924 CCTTGCTGCAGATGTTTGGTTA 59.442 45.455 20.43 0.00 0.00 2.85
2774 6357 7.828717 TGCAGATGTTTGGTTATCATTTCTCTA 59.171 33.333 0.00 0.00 0.00 2.43
2797 6539 2.897271 TTACATGAATGTGGTGGCCT 57.103 45.000 3.32 0.00 41.89 5.19
2810 6558 0.883833 GTGGCCTGTCAGATGTTTGG 59.116 55.000 3.32 0.00 0.00 3.28
2845 6604 9.546428 AAAAGAAATGAAACCCTCTGTAATTTG 57.454 29.630 0.00 0.00 0.00 2.32
2860 6619 6.014070 TCTGTAATTTGTGGCTGGAGTAGTTA 60.014 38.462 0.00 0.00 0.00 2.24
2862 6621 6.999272 TGTAATTTGTGGCTGGAGTAGTTAAA 59.001 34.615 0.00 0.00 0.00 1.52
2864 6623 3.053831 TGTGGCTGGAGTAGTTAAAGC 57.946 47.619 0.00 0.00 0.00 3.51
2869 6628 3.010420 GCTGGAGTAGTTAAAGCCTTGG 58.990 50.000 0.00 0.00 0.00 3.61
2870 6629 3.559384 GCTGGAGTAGTTAAAGCCTTGGT 60.559 47.826 0.00 0.00 0.00 3.67
2871 6630 4.652822 CTGGAGTAGTTAAAGCCTTGGTT 58.347 43.478 0.00 0.00 0.00 3.67
2872 6631 4.394729 TGGAGTAGTTAAAGCCTTGGTTG 58.605 43.478 0.00 0.00 0.00 3.77
2873 6632 4.141344 TGGAGTAGTTAAAGCCTTGGTTGT 60.141 41.667 0.00 0.00 0.00 3.32
2874 6633 4.825634 GGAGTAGTTAAAGCCTTGGTTGTT 59.174 41.667 0.00 0.00 0.00 2.83
2875 6634 5.278315 GGAGTAGTTAAAGCCTTGGTTGTTG 60.278 44.000 0.00 0.00 0.00 3.33
2876 6635 3.452755 AGTTAAAGCCTTGGTTGTTGC 57.547 42.857 0.00 0.00 0.00 4.17
2877 6636 3.031013 AGTTAAAGCCTTGGTTGTTGCT 58.969 40.909 0.00 0.00 35.08 3.91
2878 6637 3.068165 AGTTAAAGCCTTGGTTGTTGCTC 59.932 43.478 0.00 0.00 32.62 4.26
2879 6638 1.780503 AAAGCCTTGGTTGTTGCTCT 58.219 45.000 0.00 0.00 32.62 4.09
2880 6639 1.322442 AAGCCTTGGTTGTTGCTCTC 58.678 50.000 0.00 0.00 32.62 3.20
2881 6640 0.475906 AGCCTTGGTTGTTGCTCTCT 59.524 50.000 0.00 0.00 0.00 3.10
2882 6641 0.595095 GCCTTGGTTGTTGCTCTCTG 59.405 55.000 0.00 0.00 0.00 3.35
2883 6642 0.595095 CCTTGGTTGTTGCTCTCTGC 59.405 55.000 0.00 0.00 43.25 4.26
2884 6643 1.602311 CTTGGTTGTTGCTCTCTGCT 58.398 50.000 0.00 0.00 43.37 4.24
2885 6644 2.550855 CCTTGGTTGTTGCTCTCTGCTA 60.551 50.000 0.00 0.00 43.37 3.49
2886 6645 2.928801 TGGTTGTTGCTCTCTGCTAA 57.071 45.000 0.00 0.00 43.37 3.09
2887 6646 3.423539 TGGTTGTTGCTCTCTGCTAAT 57.576 42.857 0.00 0.00 43.37 1.73
2888 6647 4.551702 TGGTTGTTGCTCTCTGCTAATA 57.448 40.909 0.00 0.00 43.37 0.98
2889 6648 5.102953 TGGTTGTTGCTCTCTGCTAATAT 57.897 39.130 0.00 0.00 43.37 1.28
2890 6649 6.233905 TGGTTGTTGCTCTCTGCTAATATA 57.766 37.500 0.00 0.00 43.37 0.86
2891 6650 6.283694 TGGTTGTTGCTCTCTGCTAATATAG 58.716 40.000 0.00 0.00 43.37 1.31
2892 6651 6.127054 TGGTTGTTGCTCTCTGCTAATATAGT 60.127 38.462 0.00 0.00 43.37 2.12
2893 6652 7.069455 TGGTTGTTGCTCTCTGCTAATATAGTA 59.931 37.037 0.00 0.00 43.37 1.82
2894 6653 7.382759 GGTTGTTGCTCTCTGCTAATATAGTAC 59.617 40.741 0.00 0.00 43.37 2.73
2895 6654 7.825331 TGTTGCTCTCTGCTAATATAGTACT 57.175 36.000 0.00 0.00 43.37 2.73
2896 6655 7.877003 TGTTGCTCTCTGCTAATATAGTACTC 58.123 38.462 0.00 0.00 43.37 2.59
2897 6656 7.040340 TGTTGCTCTCTGCTAATATAGTACTCC 60.040 40.741 0.00 0.00 43.37 3.85
2898 6657 6.543735 TGCTCTCTGCTAATATAGTACTCCA 58.456 40.000 0.00 0.00 43.37 3.86
2899 6658 7.178573 TGCTCTCTGCTAATATAGTACTCCAT 58.821 38.462 0.00 0.00 43.37 3.41
2900 6659 7.338196 TGCTCTCTGCTAATATAGTACTCCATC 59.662 40.741 0.00 0.00 43.37 3.51
2901 6660 7.556275 GCTCTCTGCTAATATAGTACTCCATCT 59.444 40.741 0.00 0.00 38.95 2.90
2902 6661 8.800370 TCTCTGCTAATATAGTACTCCATCTG 57.200 38.462 0.00 0.00 0.00 2.90
2903 6662 8.387039 TCTCTGCTAATATAGTACTCCATCTGT 58.613 37.037 0.00 0.00 0.00 3.41
2904 6663 9.674068 CTCTGCTAATATAGTACTCCATCTGTA 57.326 37.037 0.00 0.00 0.00 2.74
2907 6666 9.975218 TGCTAATATAGTACTCCATCTGTATCA 57.025 33.333 0.00 0.00 0.00 2.15
2914 6673 7.789202 AGTACTCCATCTGTATCATTATGCT 57.211 36.000 0.00 0.00 0.00 3.79
2915 6674 8.885693 AGTACTCCATCTGTATCATTATGCTA 57.114 34.615 0.00 0.00 0.00 3.49
2916 6675 8.744652 AGTACTCCATCTGTATCATTATGCTAC 58.255 37.037 0.00 0.00 0.00 3.58
2917 6676 7.544804 ACTCCATCTGTATCATTATGCTACA 57.455 36.000 8.36 8.36 29.64 2.74
2918 6677 7.609960 ACTCCATCTGTATCATTATGCTACAG 58.390 38.462 22.80 22.80 44.20 2.74
2919 6678 6.939622 TCCATCTGTATCATTATGCTACAGG 58.060 40.000 26.04 16.57 43.48 4.00
2920 6679 6.070596 TCCATCTGTATCATTATGCTACAGGG 60.071 42.308 26.04 21.58 43.48 4.45
2921 6680 5.745312 TCTGTATCATTATGCTACAGGGG 57.255 43.478 26.04 10.43 43.48 4.79
2922 6681 5.155161 TCTGTATCATTATGCTACAGGGGT 58.845 41.667 26.04 0.00 43.48 4.95
2923 6682 6.319715 TCTGTATCATTATGCTACAGGGGTA 58.680 40.000 26.04 11.65 43.48 3.69
2924 6683 6.437477 TCTGTATCATTATGCTACAGGGGTAG 59.563 42.308 26.04 9.33 43.48 3.18
2937 6696 5.841957 ACAGGGGTAGTAGTATTTACGTG 57.158 43.478 0.00 0.00 0.00 4.49
2938 6697 4.646492 ACAGGGGTAGTAGTATTTACGTGG 59.354 45.833 0.00 0.00 0.00 4.94
2939 6698 4.646492 CAGGGGTAGTAGTATTTACGTGGT 59.354 45.833 0.00 0.00 0.00 4.16
2940 6699 5.827797 CAGGGGTAGTAGTATTTACGTGGTA 59.172 44.000 0.00 0.00 0.00 3.25
2954 6713 4.483476 ACGTGGTAATTCTGAAGTTTGC 57.517 40.909 0.00 0.00 0.00 3.68
2958 6717 5.399301 CGTGGTAATTCTGAAGTTTGCTTTG 59.601 40.000 0.00 0.00 34.61 2.77
3035 6799 3.847602 CTCAGCGAGAGGCCCCAG 61.848 72.222 0.00 0.00 45.17 4.45
3037 6801 2.759973 CAGCGAGAGGCCCCAGTA 60.760 66.667 0.00 0.00 45.17 2.74
3040 6804 2.494530 GCGAGAGGCCCCAGTAGAG 61.495 68.421 0.00 0.00 34.80 2.43
3061 6825 4.458829 TCGCCGGAGAGGGACCAT 62.459 66.667 5.05 0.00 41.48 3.55
3062 6826 3.470888 CGCCGGAGAGGGACCATT 61.471 66.667 5.05 0.00 41.48 3.16
3064 6828 1.749033 GCCGGAGAGGGACCATTAG 59.251 63.158 5.05 0.00 41.48 1.73
3065 6829 1.759459 GCCGGAGAGGGACCATTAGG 61.759 65.000 5.05 0.00 41.48 2.69
3070 6834 2.119495 GAGAGGGACCATTAGGCTTCA 58.881 52.381 0.00 0.00 39.06 3.02
3077 6841 0.395724 CCATTAGGCTTCACCACCCC 60.396 60.000 0.00 0.00 43.14 4.95
3093 6857 4.504916 CCGTCAGAGGAGCAGCGG 62.505 72.222 0.00 0.00 0.00 5.52
3096 6860 2.049185 GTCAGAGGAGCAGCGGAGA 61.049 63.158 0.00 0.00 0.00 3.71
3112 6887 2.432628 GAAGACGTGTCAGGCCCG 60.433 66.667 0.00 0.00 0.00 6.13
3154 6929 5.556570 GCTGAACTTAACTGAAACTGTCGAC 60.557 44.000 9.11 9.11 0.00 4.20
3166 6941 2.304092 ACTGTCGACTTCCACTGTACA 58.696 47.619 17.92 0.00 0.00 2.90
3167 6942 2.034305 ACTGTCGACTTCCACTGTACAC 59.966 50.000 17.92 0.00 0.00 2.90
3181 6956 1.000607 TGTACACACTTCGGACAGAGC 60.001 52.381 0.00 0.00 0.00 4.09
3187 6962 1.140589 CTTCGGACAGAGCGATGCT 59.859 57.895 0.00 0.00 43.88 3.79
3256 7034 0.827368 GTTCAGCTACCTCTCCAGGG 59.173 60.000 0.00 0.00 45.53 4.45
3261 7039 1.268283 GCTACCTCTCCAGGGCACTT 61.268 60.000 0.00 0.00 45.53 3.16
3263 7041 1.208293 CTACCTCTCCAGGGCACTTTC 59.792 57.143 0.00 0.00 45.53 2.62
3264 7042 1.078848 CCTCTCCAGGGCACTTTCG 60.079 63.158 0.00 0.00 35.89 3.46
3265 7043 1.674057 CTCTCCAGGGCACTTTCGT 59.326 57.895 0.00 0.00 0.00 3.85
3266 7044 0.035458 CTCTCCAGGGCACTTTCGTT 59.965 55.000 0.00 0.00 0.00 3.85
3268 7046 0.593128 CTCCAGGGCACTTTCGTTTG 59.407 55.000 0.00 0.00 0.00 2.93
3272 7050 1.661509 GGGCACTTTCGTTTGCTGC 60.662 57.895 0.00 0.00 38.85 5.25
3273 7051 1.360192 GGCACTTTCGTTTGCTGCT 59.640 52.632 0.00 0.00 38.85 4.24
3274 7052 0.936297 GGCACTTTCGTTTGCTGCTG 60.936 55.000 0.00 0.00 38.85 4.41
3275 7053 0.248621 GCACTTTCGTTTGCTGCTGT 60.249 50.000 0.00 0.00 35.74 4.40
3276 7054 1.746760 CACTTTCGTTTGCTGCTGTC 58.253 50.000 0.00 0.00 0.00 3.51
3277 7055 0.304705 ACTTTCGTTTGCTGCTGTCG 59.695 50.000 0.00 3.03 0.00 4.35
3278 7056 0.993746 CTTTCGTTTGCTGCTGTCGC 60.994 55.000 0.00 0.00 0.00 5.19
3279 7057 2.387125 TTTCGTTTGCTGCTGTCGCC 62.387 55.000 0.00 0.00 34.43 5.54
3280 7058 3.349006 CGTTTGCTGCTGTCGCCT 61.349 61.111 0.00 0.00 34.43 5.52
3281 7059 2.896801 CGTTTGCTGCTGTCGCCTT 61.897 57.895 0.00 0.00 34.43 4.35
3282 7060 1.081840 GTTTGCTGCTGTCGCCTTC 60.082 57.895 0.00 0.00 34.43 3.46
3283 7061 2.260869 TTTGCTGCTGTCGCCTTCC 61.261 57.895 0.00 0.00 34.43 3.46
3284 7062 4.704833 TGCTGCTGTCGCCTTCCC 62.705 66.667 0.00 0.00 34.43 3.97
3285 7063 4.704833 GCTGCTGTCGCCTTCCCA 62.705 66.667 0.00 0.00 34.43 4.37
3286 7064 2.743928 CTGCTGTCGCCTTCCCAC 60.744 66.667 0.00 0.00 34.43 4.61
3287 7065 3.241530 TGCTGTCGCCTTCCCACT 61.242 61.111 0.00 0.00 34.43 4.00
3288 7066 2.032681 GCTGTCGCCTTCCCACTT 59.967 61.111 0.00 0.00 0.00 3.16
3289 7067 1.600916 GCTGTCGCCTTCCCACTTT 60.601 57.895 0.00 0.00 0.00 2.66
3290 7068 1.172812 GCTGTCGCCTTCCCACTTTT 61.173 55.000 0.00 0.00 0.00 2.27
3291 7069 0.875059 CTGTCGCCTTCCCACTTTTC 59.125 55.000 0.00 0.00 0.00 2.29
3292 7070 0.472471 TGTCGCCTTCCCACTTTTCT 59.528 50.000 0.00 0.00 0.00 2.52
3293 7071 1.133915 TGTCGCCTTCCCACTTTTCTT 60.134 47.619 0.00 0.00 0.00 2.52
3294 7072 1.954382 GTCGCCTTCCCACTTTTCTTT 59.046 47.619 0.00 0.00 0.00 2.52
3295 7073 1.953686 TCGCCTTCCCACTTTTCTTTG 59.046 47.619 0.00 0.00 0.00 2.77
3296 7074 1.602920 CGCCTTCCCACTTTTCTTTGC 60.603 52.381 0.00 0.00 0.00 3.68
3297 7075 1.688735 GCCTTCCCACTTTTCTTTGCT 59.311 47.619 0.00 0.00 0.00 3.91
3298 7076 2.103094 GCCTTCCCACTTTTCTTTGCTT 59.897 45.455 0.00 0.00 0.00 3.91
3299 7077 3.432186 GCCTTCCCACTTTTCTTTGCTTT 60.432 43.478 0.00 0.00 0.00 3.51
3300 7078 4.202212 GCCTTCCCACTTTTCTTTGCTTTA 60.202 41.667 0.00 0.00 0.00 1.85
3301 7079 5.532557 CCTTCCCACTTTTCTTTGCTTTAG 58.467 41.667 0.00 0.00 0.00 1.85
3302 7080 5.069119 CCTTCCCACTTTTCTTTGCTTTAGT 59.931 40.000 0.00 0.00 0.00 2.24
3303 7081 6.406961 CCTTCCCACTTTTCTTTGCTTTAGTT 60.407 38.462 0.00 0.00 0.00 2.24
3304 7082 5.901552 TCCCACTTTTCTTTGCTTTAGTTG 58.098 37.500 0.00 0.00 0.00 3.16
3305 7083 5.049828 CCCACTTTTCTTTGCTTTAGTTGG 58.950 41.667 0.00 0.00 0.00 3.77
3306 7084 5.395214 CCCACTTTTCTTTGCTTTAGTTGGT 60.395 40.000 0.00 0.00 0.00 3.67
3307 7085 6.183360 CCCACTTTTCTTTGCTTTAGTTGGTA 60.183 38.462 0.00 0.00 0.00 3.25
3308 7086 7.262048 CCACTTTTCTTTGCTTTAGTTGGTAA 58.738 34.615 0.00 0.00 0.00 2.85
3309 7087 7.762159 CCACTTTTCTTTGCTTTAGTTGGTAAA 59.238 33.333 0.00 0.00 0.00 2.01
3310 7088 9.145865 CACTTTTCTTTGCTTTAGTTGGTAAAA 57.854 29.630 0.00 0.00 29.93 1.52
3311 7089 9.713713 ACTTTTCTTTGCTTTAGTTGGTAAAAA 57.286 25.926 0.00 0.00 29.93 1.94
3320 7098 9.026074 TGCTTTAGTTGGTAAAAATCTTTTTCG 57.974 29.630 4.03 0.00 40.53 3.46
3321 7099 8.002107 GCTTTAGTTGGTAAAAATCTTTTTCGC 58.998 33.333 4.03 0.48 40.53 4.70
3322 7100 9.244799 CTTTAGTTGGTAAAAATCTTTTTCGCT 57.755 29.630 4.03 1.42 40.53 4.93
3323 7101 8.568732 TTAGTTGGTAAAAATCTTTTTCGCTG 57.431 30.769 4.03 0.00 40.53 5.18
3324 7102 6.569780 AGTTGGTAAAAATCTTTTTCGCTGT 58.430 32.000 4.03 0.00 40.53 4.40
3325 7103 7.708998 AGTTGGTAAAAATCTTTTTCGCTGTA 58.291 30.769 4.03 0.00 40.53 2.74
3326 7104 8.357402 AGTTGGTAAAAATCTTTTTCGCTGTAT 58.643 29.630 4.03 0.00 40.53 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 2.682155 TGTTTTTGCAACTTCACCCC 57.318 45.000 0.00 0.00 0.00 4.95
64 65 4.827284 ACCCTCACCTACTTCATGTTTTTG 59.173 41.667 0.00 0.00 0.00 2.44
70 71 1.407437 GCCACCCTCACCTACTTCATG 60.407 57.143 0.00 0.00 0.00 3.07
71 72 0.912486 GCCACCCTCACCTACTTCAT 59.088 55.000 0.00 0.00 0.00 2.57
84 85 1.988406 AGACGGTTAGGAGCCACCC 60.988 63.158 0.00 0.00 40.05 4.61
102 103 2.411748 GCGTTCGATCTGTTGTTGATCA 59.588 45.455 0.00 0.00 40.03 2.92
140 141 0.651031 GGCTGATCTTTTCGTACGCC 59.349 55.000 11.24 0.00 0.00 5.68
148 149 1.202879 TGTTCACCCGGCTGATCTTTT 60.203 47.619 0.00 0.00 0.00 2.27
173 174 9.400638 TGTTTCAGCTTTATAATTTGGTAAACG 57.599 29.630 0.00 0.00 0.00 3.60
301 303 3.706373 GGCCTGGGCGTCTTCTCA 61.706 66.667 3.84 0.00 43.06 3.27
329 331 0.322277 AGAGGCGAGAGGTGTACGAA 60.322 55.000 0.00 0.00 0.00 3.85
407 409 2.420890 GCTCTGAGCCTGATCGGG 59.579 66.667 18.80 16.98 34.48 5.14
482 484 2.769095 CTCCGAAGAAAGAGGGGAGAAT 59.231 50.000 0.00 0.00 34.26 2.40
497 499 0.679002 CGGTGACCTCCTACTCCGAA 60.679 60.000 0.00 0.00 42.99 4.30
603 609 2.183555 GAACTACCTGGTCGCCCG 59.816 66.667 0.63 0.00 0.00 6.13
643 653 3.127030 GGCAATTGAGGAAGGTTACGAAG 59.873 47.826 10.34 0.00 0.00 3.79
657 667 1.971167 GTGCGACCCTGGCAATTGA 60.971 57.895 10.34 0.00 42.92 2.57
658 668 1.973281 AGTGCGACCCTGGCAATTG 60.973 57.895 0.00 0.00 42.92 2.32
732 743 2.221749 AGCGACAATGCATATACGCAAG 59.778 45.455 30.37 0.00 46.87 4.01
733 744 2.209273 AGCGACAATGCATATACGCAA 58.791 42.857 30.37 0.00 46.87 4.85
735 746 2.061773 AGAGCGACAATGCATATACGC 58.938 47.619 25.54 25.54 45.03 4.42
736 747 7.645735 AGATATAAGAGCGACAATGCATATACG 59.354 37.037 0.00 7.28 37.31 3.06
737 748 8.864069 AGATATAAGAGCGACAATGCATATAC 57.136 34.615 0.00 0.00 37.31 1.47
738 749 8.686334 TGAGATATAAGAGCGACAATGCATATA 58.314 33.333 0.00 0.00 37.31 0.86
739 750 7.550712 TGAGATATAAGAGCGACAATGCATAT 58.449 34.615 0.00 0.00 37.31 1.78
802 848 6.569035 GCGCCCTAATTAAACAAGTAAACTGT 60.569 38.462 0.00 0.00 0.00 3.55
826 872 5.528870 ACAGCAATTTAAACACTTACAGGC 58.471 37.500 0.00 0.00 0.00 4.85
865 1081 0.320683 CCTGTTCCACGAGATGCACA 60.321 55.000 0.00 0.00 0.00 4.57
889 1105 1.462283 CAACACAATCTCACTGCTCCG 59.538 52.381 0.00 0.00 0.00 4.63
929 1145 2.996621 GCTAGAATCACAGACGCAAACT 59.003 45.455 0.00 0.00 0.00 2.66
959 1176 3.254060 GTGCTCGCACTATCTTTCTTGA 58.746 45.455 14.38 0.00 43.12 3.02
976 1193 2.485302 GCCAACAAAATTCCAAGGTGCT 60.485 45.455 0.00 0.00 0.00 4.40
1005 1223 2.159085 GCTGGAGCTACTACCGTTGATT 60.159 50.000 0.00 0.00 38.21 2.57
1231 1468 9.507280 ACATACAAAAATAGATTCATCAAAGCG 57.493 29.630 0.00 0.00 0.00 4.68
1452 1743 4.141528 GGTCCAGTTGATCCTCAGATTCAT 60.142 45.833 0.00 0.00 30.90 2.57
1458 1749 4.163078 ACTTATGGTCCAGTTGATCCTCAG 59.837 45.833 0.00 0.00 0.00 3.35
1778 2069 3.310501 TCGATGCATTGCAGAACATGTAG 59.689 43.478 17.52 0.00 43.65 2.74
1797 2088 3.746045 AGAAAAAGTAGCTGGTGTCGA 57.254 42.857 0.00 0.00 0.00 4.20
2108 2411 2.525629 TGCAGGAGTCGGACCCAA 60.526 61.111 15.16 1.80 0.00 4.12
2176 5539 3.324556 CCTCTTCCTCATGATCCTCCTTC 59.675 52.174 0.00 0.00 0.00 3.46
2177 5540 3.051496 TCCTCTTCCTCATGATCCTCCTT 60.051 47.826 0.00 0.00 0.00 3.36
2179 5542 2.899256 CTCCTCTTCCTCATGATCCTCC 59.101 54.545 0.00 0.00 0.00 4.30
2205 5583 6.878317 TCATCCAACTCTTCTTCATTATCGT 58.122 36.000 0.00 0.00 0.00 3.73
2215 5593 6.464607 CCTCATGATCATCATCCAACTCTTCT 60.465 42.308 4.86 0.00 34.28 2.85
2260 5668 0.859760 CCTCCTGATCCTCCTCCTCT 59.140 60.000 0.00 0.00 0.00 3.69
2273 5681 3.453717 TCATCATCCAACTCTTCCTCCTG 59.546 47.826 0.00 0.00 0.00 3.86
2296 5704 0.178935 CCATCTCCTCCTCCTCCTCC 60.179 65.000 0.00 0.00 0.00 4.30
2297 5705 0.856982 TCCATCTCCTCCTCCTCCTC 59.143 60.000 0.00 0.00 0.00 3.71
2299 5707 1.148867 TCATCCATCTCCTCCTCCTCC 59.851 57.143 0.00 0.00 0.00 4.30
2312 5744 5.623551 TTATCCTCCTAGTCCTCATCCAT 57.376 43.478 0.00 0.00 0.00 3.41
2364 5797 1.653151 GGGGAATTTCCTCGAAGACG 58.347 55.000 14.95 0.00 36.57 4.18
2379 5812 0.039180 TGTAGAGCAAGAGTCGGGGA 59.961 55.000 0.00 0.00 0.00 4.81
2389 5822 6.211584 AGAGTAGGATCTTTGTTGTAGAGCAA 59.788 38.462 0.00 0.00 29.82 3.91
2394 5827 8.908903 AGTATCAGAGTAGGATCTTTGTTGTAG 58.091 37.037 0.00 0.00 0.00 2.74
2396 5829 7.397476 TCAGTATCAGAGTAGGATCTTTGTTGT 59.603 37.037 0.00 0.00 0.00 3.32
2401 5834 8.805175 CATCATCAGTATCAGAGTAGGATCTTT 58.195 37.037 0.00 0.00 0.00 2.52
2437 5870 6.160576 ACAAGGACGGTACTAAAAGTGTAA 57.839 37.500 0.00 0.00 0.00 2.41
2438 5871 5.789643 ACAAGGACGGTACTAAAAGTGTA 57.210 39.130 0.00 0.00 0.00 2.90
2439 5872 4.677673 ACAAGGACGGTACTAAAAGTGT 57.322 40.909 0.00 0.00 0.00 3.55
2440 5873 5.996669 AAACAAGGACGGTACTAAAAGTG 57.003 39.130 0.00 0.00 0.00 3.16
2441 5874 6.114767 TCAAAACAAGGACGGTACTAAAAGT 58.885 36.000 0.00 0.00 0.00 2.66
2446 5879 5.534207 TTCTCAAAACAAGGACGGTACTA 57.466 39.130 0.00 0.00 0.00 1.82
2454 5887 4.541705 TGGACCAATTCTCAAAACAAGGA 58.458 39.130 0.00 0.00 0.00 3.36
2483 5916 6.043854 AGAGGTAGAAGAAAACCTAGCAAG 57.956 41.667 0.00 0.00 46.22 4.01
2484 5917 6.270231 AGAAGAGGTAGAAGAAAACCTAGCAA 59.730 38.462 0.00 0.00 46.22 3.91
2508 5941 4.455877 CCACACAAAGCCTAGAAGGTAAAG 59.544 45.833 0.00 0.00 37.80 1.85
2569 6002 8.867112 TTAAGTTATGAATACAGAGCTAACGG 57.133 34.615 0.00 0.00 29.41 4.44
2700 6251 2.746277 GAACCACGAAGGCGGCAT 60.746 61.111 13.08 0.00 43.14 4.40
2711 6264 5.597806 TGTATATCATCGAACCAGAACCAC 58.402 41.667 0.00 0.00 0.00 4.16
2712 6265 5.862678 TGTATATCATCGAACCAGAACCA 57.137 39.130 0.00 0.00 0.00 3.67
2726 6279 3.392285 AGCAAGGCCTGACATGTATATCA 59.608 43.478 5.69 0.00 0.00 2.15
2728 6281 3.748083 CAGCAAGGCCTGACATGTATAT 58.252 45.455 5.69 0.00 34.77 0.86
2740 6293 0.389426 CAAACATCTGCAGCAAGGCC 60.389 55.000 9.47 0.00 0.00 5.19
2742 6295 0.963962 ACCAAACATCTGCAGCAAGG 59.036 50.000 9.47 7.33 0.00 3.61
2746 6299 4.644103 ATGATAACCAAACATCTGCAGC 57.356 40.909 9.47 0.00 0.00 5.25
2750 6303 9.166173 TGTAGAGAAATGATAACCAAACATCTG 57.834 33.333 0.00 0.00 0.00 2.90
2751 6304 9.911788 ATGTAGAGAAATGATAACCAAACATCT 57.088 29.630 0.00 0.00 0.00 2.90
2789 6531 0.478072 AAACATCTGACAGGCCACCA 59.522 50.000 5.01 0.00 0.00 4.17
2810 6558 7.896811 AGGGTTTCATTTCTTTTCCAGATAAC 58.103 34.615 0.00 0.00 0.00 1.89
2860 6619 1.683385 GAGAGCAACAACCAAGGCTTT 59.317 47.619 0.00 0.00 36.59 3.51
2862 6621 0.475906 AGAGAGCAACAACCAAGGCT 59.524 50.000 0.00 0.00 39.75 4.58
2864 6623 0.595095 GCAGAGAGCAACAACCAAGG 59.405 55.000 0.00 0.00 44.79 3.61
2875 6634 7.556275 AGATGGAGTACTATATTAGCAGAGAGC 59.444 40.741 0.00 0.00 46.19 4.09
2876 6635 8.892723 CAGATGGAGTACTATATTAGCAGAGAG 58.107 40.741 0.00 0.00 0.00 3.20
2877 6636 8.387039 ACAGATGGAGTACTATATTAGCAGAGA 58.613 37.037 0.00 0.00 0.00 3.10
2878 6637 8.574251 ACAGATGGAGTACTATATTAGCAGAG 57.426 38.462 0.00 0.00 0.00 3.35
2881 6640 9.975218 TGATACAGATGGAGTACTATATTAGCA 57.025 33.333 0.00 0.00 0.00 3.49
2888 6647 9.486123 AGCATAATGATACAGATGGAGTACTAT 57.514 33.333 0.00 0.00 0.00 2.12
2889 6648 8.885693 AGCATAATGATACAGATGGAGTACTA 57.114 34.615 0.00 0.00 0.00 1.82
2890 6649 7.789202 AGCATAATGATACAGATGGAGTACT 57.211 36.000 0.00 0.00 0.00 2.73
2891 6650 8.523658 TGTAGCATAATGATACAGATGGAGTAC 58.476 37.037 0.00 0.00 43.35 2.73
2892 6651 8.650143 TGTAGCATAATGATACAGATGGAGTA 57.350 34.615 0.00 0.00 43.35 2.59
2893 6652 7.544804 TGTAGCATAATGATACAGATGGAGT 57.455 36.000 0.00 0.00 43.35 3.85
2901 6660 6.082031 ACTACCCCTGTAGCATAATGATACA 58.918 40.000 0.00 0.00 45.62 2.29
2914 6673 5.827797 CCACGTAAATACTACTACCCCTGTA 59.172 44.000 0.00 0.00 0.00 2.74
2915 6674 4.646492 CCACGTAAATACTACTACCCCTGT 59.354 45.833 0.00 0.00 0.00 4.00
2916 6675 4.646492 ACCACGTAAATACTACTACCCCTG 59.354 45.833 0.00 0.00 0.00 4.45
2917 6676 4.871822 ACCACGTAAATACTACTACCCCT 58.128 43.478 0.00 0.00 0.00 4.79
2918 6677 6.709018 TTACCACGTAAATACTACTACCCC 57.291 41.667 0.00 0.00 0.00 4.95
2919 6678 8.633561 AGAATTACCACGTAAATACTACTACCC 58.366 37.037 0.00 0.00 31.56 3.69
2920 6679 9.455847 CAGAATTACCACGTAAATACTACTACC 57.544 37.037 0.00 0.00 31.56 3.18
2923 6682 9.798994 CTTCAGAATTACCACGTAAATACTACT 57.201 33.333 0.00 0.00 31.56 2.57
2924 6683 9.578439 ACTTCAGAATTACCACGTAAATACTAC 57.422 33.333 0.00 0.00 31.56 2.73
2926 6685 9.498176 AAACTTCAGAATTACCACGTAAATACT 57.502 29.630 0.00 0.00 31.56 2.12
2927 6686 9.537848 CAAACTTCAGAATTACCACGTAAATAC 57.462 33.333 0.00 0.00 31.56 1.89
2928 6687 8.231837 GCAAACTTCAGAATTACCACGTAAATA 58.768 33.333 0.00 0.00 31.56 1.40
2929 6688 7.040686 AGCAAACTTCAGAATTACCACGTAAAT 60.041 33.333 0.00 0.00 31.56 1.40
2930 6689 6.261381 AGCAAACTTCAGAATTACCACGTAAA 59.739 34.615 0.00 0.00 31.56 2.01
2931 6690 5.761234 AGCAAACTTCAGAATTACCACGTAA 59.239 36.000 0.00 0.00 32.36 3.18
2932 6691 5.302360 AGCAAACTTCAGAATTACCACGTA 58.698 37.500 0.00 0.00 0.00 3.57
2933 6692 4.134563 AGCAAACTTCAGAATTACCACGT 58.865 39.130 0.00 0.00 0.00 4.49
2934 6693 4.749245 AGCAAACTTCAGAATTACCACG 57.251 40.909 0.00 0.00 0.00 4.94
2935 6694 6.273071 ACAAAGCAAACTTCAGAATTACCAC 58.727 36.000 0.00 0.00 34.05 4.16
2936 6695 6.463995 ACAAAGCAAACTTCAGAATTACCA 57.536 33.333 0.00 0.00 34.05 3.25
2937 6696 8.865590 TTAACAAAGCAAACTTCAGAATTACC 57.134 30.769 0.00 0.00 34.05 2.85
2938 6697 9.730420 TCTTAACAAAGCAAACTTCAGAATTAC 57.270 29.630 0.00 0.00 34.05 1.89
2940 6699 9.822185 AATCTTAACAAAGCAAACTTCAGAATT 57.178 25.926 0.00 0.00 34.05 2.17
2954 6713 7.973601 AGGCAAACAAACAAATCTTAACAAAG 58.026 30.769 0.00 0.00 0.00 2.77
2958 6717 6.018262 GGGAAGGCAAACAAACAAATCTTAAC 60.018 38.462 0.00 0.00 0.00 2.01
3012 6774 2.498726 CCTCTCGCTGAGAAGGGC 59.501 66.667 9.08 0.00 45.39 5.19
3014 6776 2.498726 GGCCTCTCGCTGAGAAGG 59.501 66.667 0.00 11.93 45.39 3.46
3016 6778 3.077556 GGGGCCTCTCGCTGAGAA 61.078 66.667 0.84 0.00 45.39 2.87
3025 6787 1.075600 GCTCTCTACTGGGGCCTCT 60.076 63.158 3.07 0.00 0.00 3.69
3035 6799 1.503818 CTCTCCGGCGAGCTCTCTAC 61.504 65.000 8.83 0.00 35.94 2.59
3037 6801 2.515991 CTCTCCGGCGAGCTCTCT 60.516 66.667 8.83 0.00 35.94 3.10
3058 6822 0.395724 GGGGTGGTGAAGCCTAATGG 60.396 60.000 0.00 0.00 46.42 3.16
3060 6824 1.205460 ACGGGGTGGTGAAGCCTAAT 61.205 55.000 0.00 0.00 46.42 1.73
3061 6825 1.833787 GACGGGGTGGTGAAGCCTAA 61.834 60.000 0.00 0.00 46.42 2.69
3062 6826 2.203877 ACGGGGTGGTGAAGCCTA 60.204 61.111 0.00 0.00 46.42 3.93
3064 6828 3.901797 CTGACGGGGTGGTGAAGCC 62.902 68.421 0.00 0.00 46.50 4.35
3065 6829 2.358737 CTGACGGGGTGGTGAAGC 60.359 66.667 0.00 0.00 0.00 3.86
3070 6834 2.283966 CTCCTCTGACGGGGTGGT 60.284 66.667 0.00 0.00 0.00 4.16
3077 6841 3.408501 CTCCGCTGCTCCTCTGACG 62.409 68.421 0.00 0.00 0.00 4.35
3093 6857 1.079750 GGGCCTGACACGTCTTCTC 60.080 63.158 0.84 0.00 0.00 2.87
3096 6860 2.915659 TCGGGCCTGACACGTCTT 60.916 61.111 11.27 0.00 0.00 3.01
3112 6887 3.056250 TCAGCAGGTTCAGAGTTGATCTC 60.056 47.826 0.00 0.00 43.05 2.75
3154 6929 2.035449 TCCGAAGTGTGTACAGTGGAAG 59.965 50.000 0.00 0.00 0.00 3.46
3166 6941 0.109086 CATCGCTCTGTCCGAAGTGT 60.109 55.000 0.00 0.00 38.31 3.55
3167 6942 1.416813 GCATCGCTCTGTCCGAAGTG 61.417 60.000 0.00 0.00 38.31 3.16
3181 6956 1.792949 GCCAGATAACGGTTAGCATCG 59.207 52.381 17.38 6.18 0.00 3.84
3187 6962 2.035449 CAGGATCGCCAGATAACGGTTA 59.965 50.000 2.62 2.62 37.19 2.85
3261 7039 2.631428 GCGACAGCAGCAAACGAA 59.369 55.556 8.82 0.00 44.35 3.85
3272 7050 0.875059 GAAAAGTGGGAAGGCGACAG 59.125 55.000 0.00 0.00 0.00 3.51
3273 7051 0.472471 AGAAAAGTGGGAAGGCGACA 59.528 50.000 0.00 0.00 0.00 4.35
3274 7052 1.605753 AAGAAAAGTGGGAAGGCGAC 58.394 50.000 0.00 0.00 0.00 5.19
3275 7053 1.953686 CAAAGAAAAGTGGGAAGGCGA 59.046 47.619 0.00 0.00 0.00 5.54
3276 7054 1.602920 GCAAAGAAAAGTGGGAAGGCG 60.603 52.381 0.00 0.00 0.00 5.52
3277 7055 1.688735 AGCAAAGAAAAGTGGGAAGGC 59.311 47.619 0.00 0.00 0.00 4.35
3278 7056 4.406648 AAAGCAAAGAAAAGTGGGAAGG 57.593 40.909 0.00 0.00 0.00 3.46
3279 7057 6.149129 ACTAAAGCAAAGAAAAGTGGGAAG 57.851 37.500 0.00 0.00 0.00 3.46
3280 7058 6.337356 CAACTAAAGCAAAGAAAAGTGGGAA 58.663 36.000 0.00 0.00 0.00 3.97
3281 7059 5.163457 CCAACTAAAGCAAAGAAAAGTGGGA 60.163 40.000 0.00 0.00 30.81 4.37
3282 7060 5.049828 CCAACTAAAGCAAAGAAAAGTGGG 58.950 41.667 0.00 0.00 0.00 4.61
3283 7061 5.660460 ACCAACTAAAGCAAAGAAAAGTGG 58.340 37.500 0.00 0.00 0.00 4.00
3284 7062 8.696410 TTTACCAACTAAAGCAAAGAAAAGTG 57.304 30.769 0.00 0.00 0.00 3.16
3285 7063 9.713713 TTTTTACCAACTAAAGCAAAGAAAAGT 57.286 25.926 0.00 0.00 0.00 2.66
3294 7072 9.026074 CGAAAAAGATTTTTACCAACTAAAGCA 57.974 29.630 3.39 0.00 40.21 3.91
3295 7073 8.002107 GCGAAAAAGATTTTTACCAACTAAAGC 58.998 33.333 3.39 0.00 40.21 3.51
3296 7074 9.244799 AGCGAAAAAGATTTTTACCAACTAAAG 57.755 29.630 3.39 0.00 40.21 1.85
3297 7075 9.026074 CAGCGAAAAAGATTTTTACCAACTAAA 57.974 29.630 3.39 0.00 40.21 1.85
3298 7076 8.192110 ACAGCGAAAAAGATTTTTACCAACTAA 58.808 29.630 3.39 0.00 40.21 2.24
3299 7077 7.708998 ACAGCGAAAAAGATTTTTACCAACTA 58.291 30.769 3.39 0.00 40.21 2.24
3300 7078 6.569780 ACAGCGAAAAAGATTTTTACCAACT 58.430 32.000 3.39 0.00 40.21 3.16
3301 7079 6.822073 ACAGCGAAAAAGATTTTTACCAAC 57.178 33.333 3.39 0.00 40.21 3.77


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

AutoCloner maintained by Alex Coulton.