Multiple sequence alignment - TraesCS1D01G428100

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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 TraesCS1D01G428100 chr1D 100.000 7825 0 0 1 7825 480431551 480439375 0.000000e+00 14451.0
1 TraesCS1D01G428100 chr1D 78.621 145 18 5 48 179 409495672 409495816 5.030000e-12 84.2
2 TraesCS1D01G428100 chr1D 92.857 42 3 0 138 179 469831044 469831085 2.360000e-05 62.1
3 TraesCS1D01G428100 chr1B 96.319 5895 143 26 1327 7174 668757641 668763508 0.000000e+00 9616.0
4 TraesCS1D01G428100 chr1B 84.078 873 63 38 226 1066 668756166 668756994 0.000000e+00 773.0
5 TraesCS1D01G428100 chr1B 90.182 275 10 4 7568 7825 668765206 668765480 7.520000e-90 342.0
6 TraesCS1D01G428100 chr1B 85.714 210 17 4 3 199 668755723 668755932 7.960000e-50 209.0
7 TraesCS1D01G428100 chr1A 95.544 4152 142 21 2993 7113 576780205 576784344 0.000000e+00 6602.0
8 TraesCS1D01G428100 chr1A 88.473 2030 124 51 231 2221 576777358 576779316 0.000000e+00 2351.0
9 TraesCS1D01G428100 chr1A 95.400 413 18 1 2270 2682 576779308 576779719 0.000000e+00 656.0
10 TraesCS1D01G428100 chr1A 93.818 275 13 4 2678 2949 576779749 576780022 2.030000e-110 411.0
11 TraesCS1D01G428100 chr1A 87.762 286 16 8 7559 7825 576784399 576784684 4.560000e-82 316.0
12 TraesCS1D01G428100 chr1A 86.758 219 16 6 3 208 576774411 576774629 1.700000e-56 231.0
13 TraesCS1D01G428100 chr1A 84.932 219 20 6 3 208 576775648 576775866 7.960000e-50 209.0
14 TraesCS1D01G428100 chr5D 96.092 1791 47 8 5281 7064 433704538 433706312 0.000000e+00 2898.0
15 TraesCS1D01G428100 chr5D 95.987 1794 44 11 5281 7064 513286778 513285003 0.000000e+00 2889.0
16 TraesCS1D01G428100 chr5D 95.980 1791 49 8 5281 7064 431704980 431703206 0.000000e+00 2887.0
17 TraesCS1D01G428100 chr5D 93.737 1900 75 21 5281 7177 513203036 513201178 0.000000e+00 2809.0
18 TraesCS1D01G428100 chr5D 98.111 953 13 2 3571 4518 513287732 513286780 0.000000e+00 1655.0
19 TraesCS1D01G428100 chr5D 98.006 953 14 2 3571 4518 513203990 513203038 0.000000e+00 1650.0
20 TraesCS1D01G428100 chr5D 96.967 956 20 5 3571 4518 431705936 431704982 0.000000e+00 1596.0
21 TraesCS1D01G428100 chr5D 96.327 953 15 4 3571 4518 433703599 433704536 0.000000e+00 1548.0
22 TraesCS1D01G428100 chr5D 91.398 93 3 3 7085 7177 431703211 431703124 1.070000e-23 122.0
23 TraesCS1D01G428100 chr5D 91.398 93 3 3 7085 7177 433706307 433706394 1.070000e-23 122.0
24 TraesCS1D01G428100 chr5D 90.323 93 4 3 7085 7177 513285008 513284921 4.960000e-22 117.0
25 TraesCS1D01G428100 chr5B 95.477 1791 48 9 5281 7064 522367465 522365701 0.000000e+00 2828.0
26 TraesCS1D01G428100 chr5B 95.366 1791 50 9 5281 7064 522911199 522912963 0.000000e+00 2817.0
27 TraesCS1D01G428100 chr5B 98.323 954 11 2 3571 4519 522368419 522367466 0.000000e+00 1668.0
28 TraesCS1D01G428100 chr5B 98.323 954 11 2 3571 4519 522910245 522911198 0.000000e+00 1668.0
29 TraesCS1D01G428100 chr5B 91.398 93 3 3 7085 7177 522365706 522365619 1.070000e-23 122.0
30 TraesCS1D01G428100 chr5B 91.398 93 3 3 7085 7177 522912958 522913045 1.070000e-23 122.0
31 TraesCS1D01G428100 chr7B 84.247 146 13 5 6868 7010 43562818 43562956 4.930000e-27 134.0
32 TraesCS1D01G428100 chr2D 93.846 65 4 0 7496 7560 24487511 24487575 1.800000e-16 99.0
33 TraesCS1D01G428100 chr2D 100.000 28 0 0 7559 7586 24487716 24487743 1.400000e-02 52.8
34 TraesCS1D01G428100 chr2A 93.846 65 4 0 7496 7560 26865379 26865443 1.800000e-16 99.0
35 TraesCS1D01G428100 chr2A 100.000 28 0 0 7559 7586 26865584 26865611 1.400000e-02 52.8
36 TraesCS1D01G428100 chr7D 77.297 185 28 5 8 179 39020189 39020372 6.460000e-16 97.1
37 TraesCS1D01G428100 chr7D 77.907 172 24 9 42 200 104941806 104941636 2.320000e-15 95.3
38 TraesCS1D01G428100 chr7A 81.343 134 12 8 81 203 166493726 166493595 6.460000e-16 97.1
39 TraesCS1D01G428100 chr2B 96.364 55 2 0 7496 7550 39941002 39941056 3.010000e-14 91.6
40 TraesCS1D01G428100 chr4D 95.238 42 2 0 138 179 308471175 308471216 5.070000e-07 67.6
41 TraesCS1D01G428100 chr4B 100.000 36 0 0 144 179 384339500 384339535 5.070000e-07 67.6


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 TraesCS1D01G428100 chr1D 480431551 480439375 7824 False 14451.000000 14451 100.000000 1 7825 1 chr1D.!!$F3 7824
1 TraesCS1D01G428100 chr1B 668755723 668765480 9757 False 2735.000000 9616 89.073250 3 7825 4 chr1B.!!$F1 7822
2 TraesCS1D01G428100 chr1A 576774411 576784684 10273 False 1539.428571 6602 90.383857 3 7825 7 chr1A.!!$F1 7822
3 TraesCS1D01G428100 chr5D 513201178 513203990 2812 True 2229.500000 2809 95.871500 3571 7177 2 chr5D.!!$R2 3606
4 TraesCS1D01G428100 chr5D 513284921 513287732 2811 True 1553.666667 2889 94.807000 3571 7177 3 chr5D.!!$R3 3606
5 TraesCS1D01G428100 chr5D 431703124 431705936 2812 True 1535.000000 2887 94.781667 3571 7177 3 chr5D.!!$R1 3606
6 TraesCS1D01G428100 chr5D 433703599 433706394 2795 False 1522.666667 2898 94.605667 3571 7177 3 chr5D.!!$F1 3606
7 TraesCS1D01G428100 chr5B 522365619 522368419 2800 True 1539.333333 2828 95.066000 3571 7177 3 chr5B.!!$R1 3606
8 TraesCS1D01G428100 chr5B 522910245 522913045 2800 False 1535.666667 2817 95.029000 3571 7177 3 chr5B.!!$F1 3606

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
208 2718 0.037232 CGTCAGGGAAGGAACAGACC 60.037 60.000 0.00 0.0 0.00 3.85 F
529 3263 0.665835 TCCACACGCCAACAACAATC 59.334 50.000 0.00 0.0 0.00 2.67 F
1296 4099 0.928229 AATTCGCCTCGTGTATTCGC 59.072 50.000 0.00 0.0 0.00 4.70 F
2015 5224 1.066858 TCTTTGCAGTAAGAGCCGAGG 60.067 52.381 0.00 0.0 30.87 4.63 F
2962 6223 1.227674 GCTGATAACAGAGCGGGGG 60.228 63.158 3.85 0.0 46.03 5.40 F
4164 7571 0.106116 GGGTCTCCCGGACTGTAGAT 60.106 60.000 0.73 0.0 43.97 1.98 F
4899 8313 1.550976 GCAGTACAACCAGAGCCTACT 59.449 52.381 0.00 0.0 0.00 2.57 F
6083 9514 0.106318 ATCTTGCTGCCCTTCATCCC 60.106 55.000 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1369 4571 0.108615 AGGGAGCGTCACGAAATCAG 60.109 55.000 0.00 0.00 0.00 2.90 R
1421 4623 0.794981 CGATAGGATGCTAGCGCGAC 60.795 60.000 18.78 0.04 39.65 5.19 R
3043 6443 2.350134 CAGGGCAGCTCTGAGCAA 59.650 61.111 29.49 0.00 45.56 3.91 R
3547 6949 5.125417 GTGCCATTTGGTAATTTCTCAGCTA 59.875 40.000 0.00 0.00 37.57 3.32 R
4427 7841 3.967332 AAATCAGCATTGGAAACCTGG 57.033 42.857 0.00 0.00 31.60 4.45 R
5198 8613 1.143684 TGAAGCCAGAGCAGGACTTTT 59.856 47.619 0.00 0.00 43.56 2.27 R
6320 9751 0.107831 CAGTCCCGAAACCTCCAACA 59.892 55.000 0.00 0.00 0.00 3.33 R
7547 12301 0.039074 AAGTCGTGCTCGTCAGGAAG 60.039 55.000 8.17 0.00 40.77 3.46 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
26 27 1.985447 GCCGTCGACGTAGATCACCA 61.985 60.000 33.49 0.00 37.74 4.17
60 1298 1.722034 TGAACAACCTCTCCTGCTCT 58.278 50.000 0.00 0.00 0.00 4.09
68 1306 1.674764 CTCTCCTGCTCTGCACCGAT 61.675 60.000 0.00 0.00 33.79 4.18
112 1350 1.452145 GCAAAGCCCGAGGACACAAA 61.452 55.000 0.00 0.00 0.00 2.83
130 1368 2.497792 AATCCGCCACAAGGATGCCA 62.498 55.000 0.00 0.00 46.99 4.92
175 1426 2.158682 CCCAAATCCATCACCGACCATA 60.159 50.000 0.00 0.00 0.00 2.74
208 2718 0.037232 CGTCAGGGAAGGAACAGACC 60.037 60.000 0.00 0.00 0.00 3.85
228 2918 1.795286 CCTGAAGACTTGTCGCACTTC 59.205 52.381 0.00 0.00 39.08 3.01
274 2995 5.230516 ACTTGTTTGTATTTTCGCCGTTTTC 59.769 36.000 0.00 0.00 0.00 2.29
300 3021 8.062448 CGAACCAATAAAGTCGAATAGATTTCC 58.938 37.037 0.00 0.00 0.00 3.13
335 3061 4.334203 TCCGAATAAAAACATCCATGGTCG 59.666 41.667 12.58 9.25 0.00 4.79
339 3065 7.094805 CCGAATAAAAACATCCATGGTCGATAT 60.095 37.037 12.58 0.00 0.00 1.63
353 3082 7.201705 CCATGGTCGATATAGACACGTATGTAT 60.202 40.741 16.50 0.00 42.62 2.29
364 3093 1.521006 ACGTATGTATGCGCATTGTCG 59.479 47.619 30.42 24.66 39.55 4.35
365 3094 1.521006 CGTATGTATGCGCATTGTCGT 59.479 47.619 30.42 20.82 0.00 4.34
371 3100 2.223537 ATGCGCATTGTCGTCTGATA 57.776 45.000 19.28 0.00 0.00 2.15
499 3233 2.492881 ACACGTTGATGGACGGTGTATA 59.507 45.455 2.39 0.00 46.77 1.47
502 3236 4.569162 CACGTTGATGGACGGTGTATATTT 59.431 41.667 2.39 0.00 46.77 1.40
529 3263 0.665835 TCCACACGCCAACAACAATC 59.334 50.000 0.00 0.00 0.00 2.67
581 3319 9.211485 GATGAATGAATTTGGAAAGAAACACAT 57.789 29.630 0.00 0.00 0.00 3.21
614 3358 1.340502 GCAAGGAAGGAAGGAGAAGGG 60.341 57.143 0.00 0.00 0.00 3.95
634 3378 2.997315 CAGCTGTCGGTGGGAGGA 60.997 66.667 5.25 0.00 35.06 3.71
636 3380 2.680352 GCTGTCGGTGGGAGGAGA 60.680 66.667 0.00 0.00 0.00 3.71
637 3381 2.716017 GCTGTCGGTGGGAGGAGAG 61.716 68.421 0.00 0.00 0.00 3.20
736 3499 2.664851 GGTACGCAGCAGCACACA 60.665 61.111 0.82 0.00 42.27 3.72
737 3500 2.671177 GGTACGCAGCAGCACACAG 61.671 63.158 0.82 0.00 42.27 3.66
738 3501 2.357396 TACGCAGCAGCACACAGG 60.357 61.111 0.82 0.00 42.27 4.00
739 3502 2.866726 TACGCAGCAGCACACAGGA 61.867 57.895 0.82 0.00 42.27 3.86
740 3503 3.720193 CGCAGCAGCACACAGGAC 61.720 66.667 0.82 0.00 42.27 3.85
741 3504 2.281345 GCAGCAGCACACAGGACT 60.281 61.111 0.00 0.00 41.58 3.85
742 3505 2.323580 GCAGCAGCACACAGGACTC 61.324 63.158 0.00 0.00 41.58 3.36
764 3527 2.280079 CCCCTTCCCAATCCAGCC 59.720 66.667 0.00 0.00 0.00 4.85
805 3579 3.118223 GCAATATATACTCCAGCTCCCCC 60.118 52.174 0.00 0.00 0.00 5.40
806 3580 4.366267 CAATATATACTCCAGCTCCCCCT 58.634 47.826 0.00 0.00 0.00 4.79
1294 4097 2.540101 CTGGAATTCGCCTCGTGTATTC 59.460 50.000 0.00 0.00 0.00 1.75
1295 4098 1.521423 GGAATTCGCCTCGTGTATTCG 59.479 52.381 0.00 0.00 0.00 3.34
1296 4099 0.928229 AATTCGCCTCGTGTATTCGC 59.072 50.000 0.00 0.00 0.00 4.70
1326 4504 2.399356 GGTCAGCGCTAGGGTTTGC 61.399 63.158 10.99 4.60 0.00 3.68
1602 4804 1.985473 TTTGCTGTGTGAGGAAGCAT 58.015 45.000 0.00 0.00 45.75 3.79
1750 4956 3.973206 TCGTCCATGGTTGACTTATGT 57.027 42.857 12.58 0.00 0.00 2.29
1905 5114 5.906113 TTGTTCAAAAGAGTGGCAGTTAA 57.094 34.783 0.00 0.00 0.00 2.01
1994 5203 2.388735 AGAGACGATGACAATGGCCTA 58.611 47.619 3.32 0.00 0.00 3.93
2014 5223 2.370281 TCTTTGCAGTAAGAGCCGAG 57.630 50.000 0.00 0.00 30.87 4.63
2015 5224 1.066858 TCTTTGCAGTAAGAGCCGAGG 60.067 52.381 0.00 0.00 30.87 4.63
2023 5232 1.763545 GTAAGAGCCGAGGGGAAGATT 59.236 52.381 0.00 0.00 34.06 2.40
2082 5291 7.821359 GTCCTATGCTCATGCTTTATCTAATGA 59.179 37.037 0.00 0.00 40.48 2.57
2231 5440 5.242838 GGAGGTCAGTACATAGAGAATCCTG 59.757 48.000 0.00 0.00 33.66 3.86
2232 5441 6.019656 AGGTCAGTACATAGAGAATCCTGA 57.980 41.667 0.00 0.00 33.66 3.86
2242 5451 6.822676 ACATAGAGAATCCTGAAGCTTCAAAG 59.177 38.462 28.16 21.83 36.64 2.77
2247 5456 8.105829 AGAGAATCCTGAAGCTTCAAAGAATAA 58.894 33.333 28.16 10.24 36.64 1.40
2248 5457 8.641498 AGAATCCTGAAGCTTCAAAGAATAAA 57.359 30.769 28.16 8.42 36.64 1.40
2254 5463 9.317936 CCTGAAGCTTCAAAGAATAAAAACTTT 57.682 29.630 28.16 0.00 36.64 2.66
2962 6223 1.227674 GCTGATAACAGAGCGGGGG 60.228 63.158 3.85 0.00 46.03 5.40
3012 6412 5.900865 TTCATTGTGCATGCTTGATTCTA 57.099 34.783 20.33 0.00 32.13 2.10
3043 6443 3.580458 CGATTAGGGAGAGATGGACCATT 59.420 47.826 8.78 0.00 0.00 3.16
3104 6504 7.218228 TCTCTGCATTGTACATGTTTGATTT 57.782 32.000 2.30 0.00 0.00 2.17
3828 7230 3.006940 GGCACGGTCTTGAATAATGACA 58.993 45.455 0.00 0.00 32.84 3.58
4164 7571 0.106116 GGGTCTCCCGGACTGTAGAT 60.106 60.000 0.73 0.00 43.97 1.98
4179 7586 6.350612 GGACTGTAGATCTTATGCATACCTCC 60.351 46.154 5.74 0.00 0.00 4.30
4427 7841 2.441750 TGTAATAATCCCAGGCCACCTC 59.558 50.000 5.01 0.00 0.00 3.85
4899 8313 1.550976 GCAGTACAACCAGAGCCTACT 59.449 52.381 0.00 0.00 0.00 2.57
4972 8386 7.256475 CCCTCTCTAACTTCATGGTATATGCTT 60.256 40.741 0.00 0.00 0.00 3.91
5198 8613 6.705381 CCAGTGATTCCAAAATGCAGTTAAAA 59.295 34.615 0.00 0.00 0.00 1.52
5429 8849 4.286032 AGCCACAAGAGGTATGAACACTTA 59.714 41.667 0.00 0.00 0.00 2.24
5443 8863 9.113838 GTATGAACACTTAACTGAATCATGGAT 57.886 33.333 13.12 0.00 0.00 3.41
5449 8869 8.321353 ACACTTAACTGAATCATGGATTAGACA 58.679 33.333 0.00 0.00 31.89 3.41
6083 9514 0.106318 ATCTTGCTGCCCTTCATCCC 60.106 55.000 0.00 0.00 0.00 3.85
6320 9751 1.342819 GCCTCGATGCTCTCCAACTAT 59.657 52.381 5.34 0.00 0.00 2.12
6365 9796 0.785979 GCATGCCTCAAAACTTTGCG 59.214 50.000 6.36 0.00 38.05 4.85
6383 9814 0.597568 CGCTGAACCAAAGCAATCCA 59.402 50.000 0.00 0.00 40.86 3.41
6536 9978 6.698008 TTGTATGATTGCTAACTTCCATGG 57.302 37.500 4.97 4.97 0.00 3.66
6599 10041 2.435938 GGTTCGCGAGGAATGCCA 60.436 61.111 9.59 0.00 36.92 4.92
6838 10289 1.279025 TACTGATTCAGCCCCACCCC 61.279 60.000 13.64 0.00 34.37 4.95
6839 10290 3.346734 TGATTCAGCCCCACCCCC 61.347 66.667 0.00 0.00 0.00 5.40
7028 10492 7.327975 TGTCTGTCTGTTTGTTCTTCTTTCTA 58.672 34.615 0.00 0.00 0.00 2.10
7100 10569 4.507710 TCTATCTAACAAAGCAGCACCAG 58.492 43.478 0.00 0.00 0.00 4.00
7141 10610 3.397482 ACATGAGCTCTGTCTGTGTTTC 58.603 45.455 16.19 0.00 0.00 2.78
7183 10652 7.749539 AAAAGTTTACAAAGTGAACGGATTG 57.250 32.000 0.00 0.00 37.17 2.67
7184 10653 6.445357 AAGTTTACAAAGTGAACGGATTGT 57.555 33.333 0.00 0.00 37.17 2.71
7185 10654 5.816919 AGTTTACAAAGTGAACGGATTGTG 58.183 37.500 10.53 0.00 37.17 3.33
7187 10656 6.539464 AGTTTACAAAGTGAACGGATTGTGTA 59.461 34.615 10.53 0.00 37.17 2.90
7189 10658 3.813166 ACAAAGTGAACGGATTGTGTAGG 59.187 43.478 0.00 0.00 34.88 3.18
7191 10660 3.594603 AGTGAACGGATTGTGTAGGAG 57.405 47.619 0.00 0.00 0.00 3.69
7192 10661 3.162666 AGTGAACGGATTGTGTAGGAGA 58.837 45.455 0.00 0.00 0.00 3.71
7193 10662 3.769844 AGTGAACGGATTGTGTAGGAGAT 59.230 43.478 0.00 0.00 0.00 2.75
7195 10664 4.935808 GTGAACGGATTGTGTAGGAGATTT 59.064 41.667 0.00 0.00 0.00 2.17
7198 10667 7.118680 GTGAACGGATTGTGTAGGAGATTTTTA 59.881 37.037 0.00 0.00 0.00 1.52
7199 10668 7.333423 TGAACGGATTGTGTAGGAGATTTTTAG 59.667 37.037 0.00 0.00 0.00 1.85
7200 10669 6.942976 ACGGATTGTGTAGGAGATTTTTAGA 58.057 36.000 0.00 0.00 0.00 2.10
7201 10670 7.565680 ACGGATTGTGTAGGAGATTTTTAGAT 58.434 34.615 0.00 0.00 0.00 1.98
7229 10717 3.457610 AAGTTCACACCATTGCCAAAG 57.542 42.857 0.00 0.00 0.00 2.77
7231 10719 3.561143 AGTTCACACCATTGCCAAAGTA 58.439 40.909 0.00 0.00 0.00 2.24
7234 10722 5.415701 AGTTCACACCATTGCCAAAGTATAG 59.584 40.000 0.00 0.00 0.00 1.31
7255 10743 9.612620 GTATAGTTATGCAATTTATGTTCTGCC 57.387 33.333 0.00 0.00 33.78 4.85
7256 10744 5.581605 AGTTATGCAATTTATGTTCTGCCG 58.418 37.500 0.00 0.00 33.78 5.69
7258 10746 1.135141 TGCAATTTATGTTCTGCCGGC 60.135 47.619 22.73 22.73 33.78 6.13
7260 10748 2.357637 GCAATTTATGTTCTGCCGGCTA 59.642 45.455 29.70 13.50 0.00 3.93
7261 10749 3.548818 GCAATTTATGTTCTGCCGGCTAG 60.549 47.826 29.70 22.27 0.00 3.42
7262 10750 2.325583 TTTATGTTCTGCCGGCTAGG 57.674 50.000 29.70 17.48 44.97 3.02
7274 10795 3.202829 CCGGCTAGGCTAACCAAATAA 57.797 47.619 15.11 0.00 39.06 1.40
7295 10816 1.408969 TTTGGCCCAAGTCAAACTCC 58.591 50.000 0.00 0.00 42.54 3.85
7296 10817 0.821711 TTGGCCCAAGTCAAACTCCG 60.822 55.000 0.00 0.00 33.77 4.63
7297 10818 1.228154 GGCCCAAGTCAAACTCCGT 60.228 57.895 0.00 0.00 0.00 4.69
7298 10819 0.035739 GGCCCAAGTCAAACTCCGTA 59.964 55.000 0.00 0.00 0.00 4.02
7299 10820 1.339727 GGCCCAAGTCAAACTCCGTAT 60.340 52.381 0.00 0.00 0.00 3.06
7300 10821 2.433436 GCCCAAGTCAAACTCCGTATT 58.567 47.619 0.00 0.00 0.00 1.89
7301 10822 3.602483 GCCCAAGTCAAACTCCGTATTA 58.398 45.455 0.00 0.00 0.00 0.98
7302 10823 4.004982 GCCCAAGTCAAACTCCGTATTAA 58.995 43.478 0.00 0.00 0.00 1.40
7303 10824 4.142752 GCCCAAGTCAAACTCCGTATTAAC 60.143 45.833 0.00 0.00 0.00 2.01
7304 10825 4.998672 CCCAAGTCAAACTCCGTATTAACA 59.001 41.667 0.00 0.00 0.00 2.41
7305 10826 5.646360 CCCAAGTCAAACTCCGTATTAACAT 59.354 40.000 0.00 0.00 0.00 2.71
7306 10827 6.183360 CCCAAGTCAAACTCCGTATTAACATC 60.183 42.308 0.00 0.00 0.00 3.06
7307 10828 6.594159 CCAAGTCAAACTCCGTATTAACATCT 59.406 38.462 0.00 0.00 0.00 2.90
7308 10829 7.762615 CCAAGTCAAACTCCGTATTAACATCTA 59.237 37.037 0.00 0.00 0.00 1.98
7313 10834 7.699391 TCAAACTCCGTATTAACATCTAGAACG 59.301 37.037 0.00 0.00 0.00 3.95
7339 10860 8.663911 GTCAAATTAGTCTTGAGAGATTTCCAG 58.336 37.037 0.00 0.00 33.56 3.86
7343 10864 9.660180 AATTAGTCTTGAGAGATTTCCAGTTAC 57.340 33.333 0.00 0.00 33.70 2.50
7349 10870 7.339721 TCTTGAGAGATTTCCAGTTACGAGTAT 59.660 37.037 0.00 0.00 0.00 2.12
7355 10876 7.259161 AGATTTCCAGTTACGAGTATGAGAAC 58.741 38.462 0.00 0.00 0.00 3.01
7374 10920 8.924511 TGAGAACCTAAAGACATGAAAATTCT 57.075 30.769 0.00 0.00 0.00 2.40
7396 10942 4.827304 TTTTTGCTCACACGAATGATCA 57.173 36.364 0.00 0.00 0.00 2.92
7399 10945 2.282407 TGCTCACACGAATGATCATGG 58.718 47.619 9.46 7.21 0.00 3.66
7400 10946 2.093553 TGCTCACACGAATGATCATGGA 60.094 45.455 9.46 0.29 0.00 3.41
7401 10947 2.938451 GCTCACACGAATGATCATGGAA 59.062 45.455 9.46 0.00 0.00 3.53
7402 10948 3.002042 GCTCACACGAATGATCATGGAAG 59.998 47.826 9.46 3.87 0.00 3.46
7403 10949 2.938451 TCACACGAATGATCATGGAAGC 59.062 45.455 9.46 0.00 0.00 3.86
7404 10950 1.935873 ACACGAATGATCATGGAAGCG 59.064 47.619 9.46 10.60 0.00 4.68
7405 10951 1.935873 CACGAATGATCATGGAAGCGT 59.064 47.619 9.46 11.20 0.00 5.07
7406 10952 2.033407 CACGAATGATCATGGAAGCGTC 60.033 50.000 9.46 0.00 0.00 5.19
7407 10953 1.190984 CGAATGATCATGGAAGCGTCG 59.809 52.381 9.46 9.03 0.00 5.12
7408 10954 2.473816 GAATGATCATGGAAGCGTCGA 58.526 47.619 9.46 0.00 0.00 4.20
7409 10955 1.858091 ATGATCATGGAAGCGTCGAC 58.142 50.000 7.59 5.18 0.00 4.20
7410 10956 0.525455 TGATCATGGAAGCGTCGACG 60.525 55.000 32.57 32.57 43.27 5.12
7411 10957 0.525668 GATCATGGAAGCGTCGACGT 60.526 55.000 35.48 19.95 42.22 4.34
7413 10959 2.158959 CATGGAAGCGTCGACGTCC 61.159 63.158 35.48 32.66 42.22 4.79
7415 10961 2.202453 GGAAGCGTCGACGTCCTC 60.202 66.667 35.48 27.03 42.22 3.71
7416 10962 2.688794 GGAAGCGTCGACGTCCTCT 61.689 63.158 35.48 22.60 42.22 3.69
7417 10963 1.512310 GAAGCGTCGACGTCCTCTG 60.512 63.158 35.48 9.81 42.22 3.35
7418 10964 1.909141 GAAGCGTCGACGTCCTCTGA 61.909 60.000 35.48 0.00 42.22 3.27
7432 12109 3.396767 CTGAGGCCTTCAGCTCCA 58.603 61.111 6.77 0.00 46.30 3.86
7440 12117 1.325476 CCTTCAGCTCCAAATGCCCC 61.325 60.000 0.00 0.00 0.00 5.80
7441 12118 1.305213 TTCAGCTCCAAATGCCCCC 60.305 57.895 0.00 0.00 0.00 5.40
7486 12163 2.124942 GCCTCCTCAAAGCTCCCG 60.125 66.667 0.00 0.00 0.00 5.14
7490 12167 4.803908 CCTCAAAGCTCCCGCCCC 62.804 72.222 0.00 0.00 36.60 5.80
7491 12168 3.721706 CTCAAAGCTCCCGCCCCT 61.722 66.667 0.00 0.00 36.60 4.79
7492 12169 3.984193 CTCAAAGCTCCCGCCCCTG 62.984 68.421 0.00 0.00 36.60 4.45
7524 12278 0.250513 GAAGTGCTTCCGGGTGATCT 59.749 55.000 0.00 0.00 33.64 2.75
7581 12366 1.005340 GACTTGAAGATCTGCAGCCG 58.995 55.000 9.47 0.00 0.00 5.52
7629 12422 4.564110 GCACCCGGCTCCATACCC 62.564 72.222 0.00 0.00 40.25 3.69
7802 12618 2.994995 TCGATGGTGGTGTCCGCT 60.995 61.111 0.00 0.00 33.98 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.771356 TACGTCGACGGCAGCTGC 62.771 66.667 37.89 30.88 44.95 5.25
5 6 0.589229 GTGATCTACGTCGACGGCAG 60.589 60.000 37.89 31.63 44.95 4.85
98 1336 2.106683 CGGATTTGTGTCCTCGGGC 61.107 63.158 0.00 0.00 36.07 6.13
112 1350 2.124151 GGCATCCTTGTGGCGGAT 60.124 61.111 0.00 0.00 41.88 4.18
130 1368 1.153289 GTCTGTCCAGGCATGCGAT 60.153 57.895 12.44 0.00 32.23 4.58
135 1373 1.834263 GGAACTAGTCTGTCCAGGCAT 59.166 52.381 7.14 0.00 34.98 4.40
136 1374 1.267121 GGAACTAGTCTGTCCAGGCA 58.733 55.000 7.14 0.00 34.98 4.75
137 1375 0.537653 GGGAACTAGTCTGTCCAGGC 59.462 60.000 13.00 0.00 0.00 4.85
139 1377 4.508662 GATTTGGGAACTAGTCTGTCCAG 58.491 47.826 13.00 0.00 0.00 3.86
142 1393 4.553330 TGGATTTGGGAACTAGTCTGTC 57.447 45.455 0.00 0.00 0.00 3.51
175 1426 0.107456 CTGACGGGGCATTATGCTCT 59.893 55.000 17.16 0.00 45.01 4.09
199 2709 2.104963 ACAAGTCTTCAGGGTCTGTTCC 59.895 50.000 0.00 0.00 32.61 3.62
204 2714 0.318762 GCGACAAGTCTTCAGGGTCT 59.681 55.000 0.00 0.00 0.00 3.85
208 2718 1.795286 GAAGTGCGACAAGTCTTCAGG 59.205 52.381 0.00 0.00 37.04 3.86
228 2918 7.269477 AGTTCAGTTCTTTTTCTTCTCATGG 57.731 36.000 0.00 0.00 0.00 3.66
241 2962 7.220108 GCGAAAATACAAACAAGTTCAGTTCTT 59.780 33.333 0.00 0.00 0.00 2.52
243 2964 6.075046 GGCGAAAATACAAACAAGTTCAGTTC 60.075 38.462 0.00 0.00 0.00 3.01
247 2968 4.201930 ACGGCGAAAATACAAACAAGTTCA 60.202 37.500 16.62 0.00 0.00 3.18
274 2995 8.062448 GGAAATCTATTCGACTTTATTGGTTCG 58.938 37.037 0.00 0.00 0.00 3.95
312 3033 4.334203 CGACCATGGATGTTTTTATTCGGA 59.666 41.667 21.47 0.00 0.00 4.55
313 3034 4.334203 TCGACCATGGATGTTTTTATTCGG 59.666 41.667 21.47 0.00 0.00 4.30
335 3061 5.329493 TGCGCATACATACGTGTCTATATC 58.671 41.667 5.66 0.00 39.77 1.63
339 3065 3.636282 ATGCGCATACATACGTGTCTA 57.364 42.857 24.02 0.00 39.77 2.59
341 3067 2.284150 ACAATGCGCATACATACGTGTC 59.716 45.455 25.61 0.00 39.77 3.67
353 3082 1.134175 TCTATCAGACGACAATGCGCA 59.866 47.619 14.96 14.96 33.86 6.09
364 3093 6.380190 GTGGAATATACACCGTCTATCAGAC 58.620 44.000 0.00 0.00 41.71 3.51
365 3094 5.180680 CGTGGAATATACACCGTCTATCAGA 59.819 44.000 5.24 0.00 35.46 3.27
371 3100 2.360165 GTCCGTGGAATATACACCGTCT 59.640 50.000 0.00 0.00 35.46 4.18
474 3206 2.739913 CACCGTCCATCAACGTGTTTAT 59.260 45.455 0.00 0.00 41.01 1.40
475 3207 2.136728 CACCGTCCATCAACGTGTTTA 58.863 47.619 0.00 0.00 41.01 2.01
499 3233 0.949105 GCGTGTGGAGTCCGTGAAAT 60.949 55.000 4.30 0.00 0.00 2.17
502 3236 3.986006 GGCGTGTGGAGTCCGTGA 61.986 66.667 4.30 0.00 0.00 4.35
581 3319 0.180642 TCCTTGCCAAACACACGGTA 59.819 50.000 0.00 0.00 0.00 4.02
587 3325 1.341209 CCTTCCTTCCTTGCCAAACAC 59.659 52.381 0.00 0.00 0.00 3.32
724 3487 2.281345 AGTCCTGTGTGCTGCTGC 60.281 61.111 8.89 8.89 40.20 5.25
728 3491 1.517242 GGAAAGAGTCCTGTGTGCTG 58.483 55.000 0.00 0.00 43.98 4.41
730 3493 0.606673 GGGGAAAGAGTCCTGTGTGC 60.607 60.000 0.00 0.00 46.92 4.57
731 3494 0.036875 GGGGGAAAGAGTCCTGTGTG 59.963 60.000 0.00 0.00 46.92 3.82
732 3495 0.104409 AGGGGGAAAGAGTCCTGTGT 60.104 55.000 0.00 0.00 46.92 3.72
733 3496 1.003696 GAAGGGGGAAAGAGTCCTGTG 59.996 57.143 0.00 0.00 46.92 3.66
734 3497 1.363246 GAAGGGGGAAAGAGTCCTGT 58.637 55.000 0.00 0.00 46.92 4.00
735 3498 0.621082 GGAAGGGGGAAAGAGTCCTG 59.379 60.000 0.00 0.00 46.92 3.86
736 3499 0.550393 GGGAAGGGGGAAAGAGTCCT 60.550 60.000 0.00 0.00 46.92 3.85
738 3501 1.073098 TTGGGAAGGGGGAAAGAGTC 58.927 55.000 0.00 0.00 0.00 3.36
739 3502 1.641192 GATTGGGAAGGGGGAAAGAGT 59.359 52.381 0.00 0.00 0.00 3.24
740 3503 1.063642 GGATTGGGAAGGGGGAAAGAG 60.064 57.143 0.00 0.00 0.00 2.85
741 3504 1.007607 GGATTGGGAAGGGGGAAAGA 58.992 55.000 0.00 0.00 0.00 2.52
742 3505 0.709992 TGGATTGGGAAGGGGGAAAG 59.290 55.000 0.00 0.00 0.00 2.62
1269 4072 2.464459 CGAGGCGAATTCCAGGCAC 61.464 63.158 9.09 2.86 35.18 5.01
1294 4097 3.414700 GACCGACAAGGCACTGCG 61.415 66.667 0.00 0.00 46.52 5.18
1295 4098 2.280797 TGACCGACAAGGCACTGC 60.281 61.111 0.00 0.00 46.52 4.40
1296 4099 2.320587 GCTGACCGACAAGGCACTG 61.321 63.158 0.00 0.00 46.52 3.66
1337 4531 3.827784 GACTAGCACGCACGCACG 61.828 66.667 0.00 0.00 39.50 5.34
1338 4532 3.479269 GGACTAGCACGCACGCAC 61.479 66.667 0.00 0.00 0.00 5.34
1369 4571 0.108615 AGGGAGCGTCACGAAATCAG 60.109 55.000 0.00 0.00 0.00 2.90
1421 4623 0.794981 CGATAGGATGCTAGCGCGAC 60.795 60.000 18.78 0.04 39.65 5.19
1518 4720 5.375417 TTGGATCAAACTAACAGCACATG 57.625 39.130 0.00 0.00 0.00 3.21
1519 4721 5.622914 GCATTGGATCAAACTAACAGCACAT 60.623 40.000 0.00 0.00 0.00 3.21
1520 4722 4.321156 GCATTGGATCAAACTAACAGCACA 60.321 41.667 0.00 0.00 0.00 4.57
1521 4723 4.168760 GCATTGGATCAAACTAACAGCAC 58.831 43.478 0.00 0.00 0.00 4.40
1602 4804 3.233980 ACGAGGCACCACAGCTGA 61.234 61.111 23.35 0.00 34.17 4.26
1675 4877 9.726438 ACCAACTATATCCTATTTATGCAACTC 57.274 33.333 0.00 0.00 0.00 3.01
1750 4956 1.896220 CAGCCTTTACACAAGAGCCA 58.104 50.000 0.00 0.00 0.00 4.75
1869 5077 6.847956 TTTTGAACAAAAGGAATGATGCAG 57.152 33.333 8.37 0.00 35.57 4.41
1955 5164 8.039538 TCGTCTCTAGTGAGTTAATAGACTTGA 58.960 37.037 0.00 0.00 40.98 3.02
1994 5203 2.419297 CCTCGGCTCTTACTGCAAAGAT 60.419 50.000 1.38 0.00 35.04 2.40
2023 5232 4.119862 CACAGAAACAAACGAAGAGGAGA 58.880 43.478 0.00 0.00 0.00 3.71
2029 5238 4.811555 TGATCCACAGAAACAAACGAAG 57.188 40.909 0.00 0.00 0.00 3.79
2105 5314 9.366216 CAACATATAGTTAGTTGCTTGTGTAGA 57.634 33.333 0.00 0.00 38.74 2.59
2247 5456 7.290014 ACTGAAGAATATCCCCAACAAAGTTTT 59.710 33.333 0.00 0.00 0.00 2.43
2248 5457 6.782494 ACTGAAGAATATCCCCAACAAAGTTT 59.218 34.615 0.00 0.00 0.00 2.66
2254 5463 3.010027 TGCACTGAAGAATATCCCCAACA 59.990 43.478 0.00 0.00 0.00 3.33
2260 5469 5.521372 GCCAAAAATGCACTGAAGAATATCC 59.479 40.000 0.00 0.00 0.00 2.59
2661 5873 7.907841 TCAGTATTTACATACCCAGCTTCTA 57.092 36.000 0.00 0.00 36.63 2.10
2702 5948 2.946329 TGCAACGAAACTAGGAGCAAAA 59.054 40.909 0.00 0.00 0.00 2.44
2717 5964 3.248602 AGAACTGCTAAAGAAGTGCAACG 59.751 43.478 0.00 0.00 45.86 4.10
2919 6180 2.671130 ACCAAGTGTTGCAACAAAGG 57.329 45.000 32.61 30.91 41.21 3.11
2991 6313 7.571080 TTATAGAATCAAGCATGCACAATGA 57.429 32.000 21.98 17.70 38.72 2.57
3012 6412 7.235606 TCCATCTCTCCCTAATCGTCAAATTAT 59.764 37.037 0.00 0.00 0.00 1.28
3043 6443 2.350134 CAGGGCAGCTCTGAGCAA 59.650 61.111 29.49 0.00 45.56 3.91
3547 6949 5.125417 GTGCCATTTGGTAATTTCTCAGCTA 59.875 40.000 0.00 0.00 37.57 3.32
3828 7230 8.204903 AGATAGCCATCTGTTTTCTCTATCAT 57.795 34.615 0.00 0.00 40.15 2.45
4164 7571 9.120538 GAAATACAAAAGGAGGTATGCATAAGA 57.879 33.333 8.28 0.00 30.95 2.10
4179 7586 6.183360 GGAGCATGCAACATGAAATACAAAAG 60.183 38.462 21.98 0.00 0.00 2.27
4427 7841 3.967332 AAATCAGCATTGGAAACCTGG 57.033 42.857 0.00 0.00 31.60 4.45
5048 8462 9.864034 GTGATATACCAAAATAATCACAACTCG 57.136 33.333 8.47 0.00 37.47 4.18
5198 8613 1.143684 TGAAGCCAGAGCAGGACTTTT 59.856 47.619 0.00 0.00 43.56 2.27
5429 8849 7.667219 AGTTGTTGTCTAATCCATGATTCAGTT 59.333 33.333 0.00 0.00 33.95 3.16
5608 9032 3.311048 GCAGTAAGCAAGAGTTATCCTGC 59.689 47.826 0.00 0.00 42.27 4.85
5766 9196 4.766891 ACAAATGTAAGTGTTGCTAGCCAT 59.233 37.500 13.29 2.52 0.00 4.40
6083 9514 1.202746 GGAAGCCCTCCTTGAGCATAG 60.203 57.143 0.00 0.00 41.61 2.23
6320 9751 0.107831 CAGTCCCGAAACCTCCAACA 59.892 55.000 0.00 0.00 0.00 3.33
6365 9796 2.733227 CGATGGATTGCTTTGGTTCAGC 60.733 50.000 0.00 0.00 37.82 4.26
6383 9814 2.045926 GGAGCTGTGGTTGCCGAT 60.046 61.111 0.00 0.00 0.00 4.18
6516 9958 6.186957 ACAACCATGGAAGTTAGCAATCATA 58.813 36.000 21.47 0.00 0.00 2.15
6517 9959 5.018809 ACAACCATGGAAGTTAGCAATCAT 58.981 37.500 21.47 0.00 0.00 2.45
6518 9960 4.406456 ACAACCATGGAAGTTAGCAATCA 58.594 39.130 21.47 0.00 0.00 2.57
6519 9961 4.702131 AGACAACCATGGAAGTTAGCAATC 59.298 41.667 21.47 2.62 0.00 2.67
6520 9962 4.666512 AGACAACCATGGAAGTTAGCAAT 58.333 39.130 21.47 0.00 0.00 3.56
6521 9963 4.072131 GAGACAACCATGGAAGTTAGCAA 58.928 43.478 21.47 0.00 0.00 3.91
6522 9964 3.327757 AGAGACAACCATGGAAGTTAGCA 59.672 43.478 21.47 0.00 0.00 3.49
6523 9965 3.686726 CAGAGACAACCATGGAAGTTAGC 59.313 47.826 21.47 9.27 0.00 3.09
6536 9978 1.739562 CTCGCCCTGCAGAGACAAC 60.740 63.158 17.39 0.00 33.54 3.32
6599 10041 2.116125 GGGTTGGCAGCAAGAGGT 59.884 61.111 3.14 0.00 0.00 3.85
7100 10569 2.467566 TCCGCCTCCTCAAAAGTTAC 57.532 50.000 0.00 0.00 0.00 2.50
7141 10610 0.667993 TTTTGCCAACTTCGAGCAGG 59.332 50.000 0.00 0.00 37.89 4.85
7177 10646 8.438676 AATCTAAAAATCTCCTACACAATCCG 57.561 34.615 0.00 0.00 0.00 4.18
7198 10667 7.653311 GCAATGGTGTGAACTTTCTAAAAATCT 59.347 33.333 0.00 0.00 0.00 2.40
7199 10668 7.095649 GGCAATGGTGTGAACTTTCTAAAAATC 60.096 37.037 0.00 0.00 0.00 2.17
7200 10669 6.705825 GGCAATGGTGTGAACTTTCTAAAAAT 59.294 34.615 0.00 0.00 0.00 1.82
7201 10670 6.045955 GGCAATGGTGTGAACTTTCTAAAAA 58.954 36.000 0.00 0.00 0.00 1.94
7206 10694 2.665165 TGGCAATGGTGTGAACTTTCT 58.335 42.857 0.00 0.00 0.00 2.52
7208 10696 3.197549 ACTTTGGCAATGGTGTGAACTTT 59.802 39.130 16.35 0.00 0.00 2.66
7229 10717 9.612620 GGCAGAACATAAATTGCATAACTATAC 57.387 33.333 0.00 0.00 38.27 1.47
7231 10719 7.362662 CGGCAGAACATAAATTGCATAACTAT 58.637 34.615 0.00 0.00 38.27 2.12
7234 10722 4.739716 CCGGCAGAACATAAATTGCATAAC 59.260 41.667 0.00 0.00 38.27 1.89
7254 10742 2.922740 TATTTGGTTAGCCTAGCCGG 57.077 50.000 0.00 0.00 35.27 6.13
7255 10743 5.767816 AATTTATTTGGTTAGCCTAGCCG 57.232 39.130 0.00 0.00 35.27 5.52
7268 10789 6.486320 AGTTTGACTTGGGCCAAATTTATTTG 59.514 34.615 21.28 8.36 45.04 2.32
7269 10790 6.600388 AGTTTGACTTGGGCCAAATTTATTT 58.400 32.000 21.28 1.56 35.14 1.40
7274 10795 2.368548 GGAGTTTGACTTGGGCCAAATT 59.631 45.455 21.28 10.22 35.14 1.82
7280 10801 2.109425 ATACGGAGTTTGACTTGGGC 57.891 50.000 0.00 0.00 37.78 5.36
7289 10810 7.542025 ACGTTCTAGATGTTAATACGGAGTTT 58.458 34.615 13.65 0.00 37.78 2.66
7290 10811 7.093322 ACGTTCTAGATGTTAATACGGAGTT 57.907 36.000 13.65 0.00 37.78 3.01
7292 10813 6.722301 TGACGTTCTAGATGTTAATACGGAG 58.278 40.000 13.65 0.00 32.33 4.63
7294 10815 7.745022 TTTGACGTTCTAGATGTTAATACGG 57.255 36.000 13.65 0.00 32.33 4.02
7301 10822 8.926710 CAAGACTAATTTGACGTTCTAGATGTT 58.073 33.333 0.00 0.00 0.00 2.71
7302 10823 8.304596 TCAAGACTAATTTGACGTTCTAGATGT 58.695 33.333 0.00 0.00 30.03 3.06
7303 10824 8.689251 TCAAGACTAATTTGACGTTCTAGATG 57.311 34.615 0.00 0.00 30.03 2.90
7304 10825 8.740906 TCTCAAGACTAATTTGACGTTCTAGAT 58.259 33.333 0.00 0.00 31.66 1.98
7305 10826 8.107399 TCTCAAGACTAATTTGACGTTCTAGA 57.893 34.615 0.00 0.00 31.66 2.43
7306 10827 8.237949 TCTCTCAAGACTAATTTGACGTTCTAG 58.762 37.037 0.00 0.00 31.66 2.43
7307 10828 8.107399 TCTCTCAAGACTAATTTGACGTTCTA 57.893 34.615 0.00 0.00 31.66 2.10
7308 10829 6.982852 TCTCTCAAGACTAATTTGACGTTCT 58.017 36.000 0.00 0.00 31.66 3.01
7313 10834 8.553459 TGGAAATCTCTCAAGACTAATTTGAC 57.447 34.615 0.00 0.00 33.32 3.18
7324 10845 5.715070 ACTCGTAACTGGAAATCTCTCAAG 58.285 41.667 0.00 0.00 0.00 3.02
7339 10860 7.533426 TGTCTTTAGGTTCTCATACTCGTAAC 58.467 38.462 0.00 0.00 0.00 2.50
7343 10864 6.796426 TCATGTCTTTAGGTTCTCATACTCG 58.204 40.000 0.00 0.00 0.00 4.18
7349 10870 8.924511 AGAATTTTCATGTCTTTAGGTTCTCA 57.075 30.769 0.00 0.00 0.00 3.27
7377 10923 3.127376 CCATGATCATTCGTGTGAGCAAA 59.873 43.478 5.16 0.00 46.22 3.68
7378 10924 2.679336 CCATGATCATTCGTGTGAGCAA 59.321 45.455 5.16 0.77 46.22 3.91
7380 10926 2.554142 TCCATGATCATTCGTGTGAGC 58.446 47.619 5.16 2.03 37.20 4.26
7381 10927 3.002042 GCTTCCATGATCATTCGTGTGAG 59.998 47.826 5.16 0.00 37.20 3.51
7382 10928 2.938451 GCTTCCATGATCATTCGTGTGA 59.062 45.455 5.16 0.00 37.20 3.58
7383 10929 2.286008 CGCTTCCATGATCATTCGTGTG 60.286 50.000 5.16 0.00 37.20 3.82
7384 10930 1.935873 CGCTTCCATGATCATTCGTGT 59.064 47.619 5.16 0.00 37.20 4.49
7385 10931 1.935873 ACGCTTCCATGATCATTCGTG 59.064 47.619 5.16 4.15 38.41 4.35
7386 10932 2.205074 GACGCTTCCATGATCATTCGT 58.795 47.619 5.16 10.38 0.00 3.85
7387 10933 1.190984 CGACGCTTCCATGATCATTCG 59.809 52.381 5.16 7.37 0.00 3.34
7388 10934 2.219674 GTCGACGCTTCCATGATCATTC 59.780 50.000 5.16 0.00 0.00 2.67
7390 10936 1.858091 GTCGACGCTTCCATGATCAT 58.142 50.000 1.18 1.18 0.00 2.45
7391 10937 0.525455 CGTCGACGCTTCCATGATCA 60.525 55.000 26.59 0.00 0.00 2.92
7392 10938 0.525668 ACGTCGACGCTTCCATGATC 60.526 55.000 35.92 0.00 44.43 2.92
7394 10940 1.154093 GACGTCGACGCTTCCATGA 60.154 57.895 35.92 0.00 44.43 3.07
7395 10941 2.158959 GGACGTCGACGCTTCCATG 61.159 63.158 35.92 9.56 44.43 3.66
7396 10942 2.181021 GGACGTCGACGCTTCCAT 59.819 61.111 35.92 17.12 44.43 3.41
7399 10945 1.512310 CAGAGGACGTCGACGCTTC 60.512 63.158 35.92 29.62 44.43 3.86
7400 10946 1.913451 CTCAGAGGACGTCGACGCTT 61.913 60.000 35.92 24.37 44.43 4.68
7401 10947 2.358369 TCAGAGGACGTCGACGCT 60.358 61.111 35.92 25.81 44.43 5.07
7402 10948 2.098680 CTCAGAGGACGTCGACGC 59.901 66.667 35.92 26.80 44.43 5.19
7403 10949 2.785921 CCTCAGAGGACGTCGACG 59.214 66.667 34.58 34.58 46.33 5.12
7404 10950 2.486042 GCCTCAGAGGACGTCGAC 59.514 66.667 21.89 5.18 37.67 4.20
7405 10951 2.750637 GGCCTCAGAGGACGTCGA 60.751 66.667 21.89 0.00 37.67 4.20
7416 10962 0.700564 ATTTGGAGCTGAAGGCCTCA 59.299 50.000 5.23 5.10 43.05 3.86
7417 10963 1.101331 CATTTGGAGCTGAAGGCCTC 58.899 55.000 5.23 0.00 43.05 4.70
7418 10964 0.969409 GCATTTGGAGCTGAAGGCCT 60.969 55.000 0.00 0.00 43.05 5.19
7491 12168 2.115910 CTTCCTGGTGGCCAAGCA 59.884 61.111 7.24 6.98 30.80 3.91
7492 12169 2.116125 ACTTCCTGGTGGCCAAGC 59.884 61.111 7.24 1.56 30.80 4.01
7495 12172 2.697147 GAAGCACTTCCTGGTGGCCA 62.697 60.000 0.00 0.00 37.65 5.36
7496 12173 1.973812 GAAGCACTTCCTGGTGGCC 60.974 63.158 0.00 0.00 37.65 5.36
7497 12174 3.673599 GAAGCACTTCCTGGTGGC 58.326 61.111 0.00 0.00 37.65 5.01
7547 12301 0.039074 AAGTCGTGCTCGTCAGGAAG 60.039 55.000 8.17 0.00 40.77 3.46
7548 12302 0.318699 CAAGTCGTGCTCGTCAGGAA 60.319 55.000 8.17 0.00 40.77 3.36
7549 12303 1.170290 TCAAGTCGTGCTCGTCAGGA 61.170 55.000 8.17 2.02 37.26 3.86
7551 12305 1.056103 CTTCAAGTCGTGCTCGTCAG 58.944 55.000 8.17 0.39 38.33 3.51
7553 12307 1.914700 GATCTTCAAGTCGTGCTCGTC 59.085 52.381 8.17 2.47 38.33 4.20
7554 12308 1.542030 AGATCTTCAAGTCGTGCTCGT 59.458 47.619 8.17 0.00 38.33 4.18
7555 12309 1.916651 CAGATCTTCAAGTCGTGCTCG 59.083 52.381 0.81 0.81 38.55 5.03
7557 12311 1.001293 TGCAGATCTTCAAGTCGTGCT 59.999 47.619 0.00 0.00 0.00 4.40
7626 12419 3.230976 GGAGATGTTGGAGTTTTTGGGT 58.769 45.455 0.00 0.00 0.00 4.51
7629 12422 2.228822 CCCGGAGATGTTGGAGTTTTTG 59.771 50.000 0.73 0.00 0.00 2.44
7661 12454 3.288484 TGGAGCTCCAGCAGTACG 58.712 61.111 32.00 0.00 42.01 3.67


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

AutoCloner maintained by Alex Coulton.