Multiple sequence alignment - TraesCS6B01G470300

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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 TraesCS6B01G470300 chr6B 100.000 3191 0 0 1 3191 718481078 718477888 0.000000e+00 5893.0
1 TraesCS6B01G470300 chr6B 75.789 1330 263 40 1000 2308 718594183 718592892 4.520000e-173 617.0
2 TraesCS6B01G470300 chr6B 78.429 802 141 21 1516 2308 718280595 718281373 7.950000e-136 494.0
3 TraesCS6B01G470300 chr6B 78.089 858 130 28 1013 1860 718591611 718590802 1.030000e-134 490.0
4 TraesCS6B01G470300 chr6B 84.038 426 51 14 1883 2299 718596949 718596532 8.300000e-106 394.0
5 TraesCS6B01G470300 chr6B 83.571 420 51 14 1888 2303 708408305 708408710 8.360000e-101 377.0
6 TraesCS6B01G470300 chr6B 84.211 76 9 3 2469 2542 718596432 718596358 1.590000e-08 71.3
7 TraesCS6B01G470300 chrUn 88.911 1479 114 25 865 2321 330579814 330578364 0.000000e+00 1777.0
8 TraesCS6B01G470300 chrUn 90.280 751 53 15 128 872 308513424 308512688 0.000000e+00 965.0
9 TraesCS6B01G470300 chrUn 89.894 752 55 16 128 872 388972528 388971791 0.000000e+00 948.0
10 TraesCS6B01G470300 chrUn 85.983 478 29 15 2608 3083 430774657 430775098 8.010000e-131 477.0
11 TraesCS6B01G470300 chrUn 83.721 473 39 21 2386 2851 330578270 330577829 2.290000e-111 412.0
12 TraesCS6B01G470300 chrUn 72.951 244 53 10 259 494 111009277 111009039 4.420000e-09 73.1
13 TraesCS6B01G470300 chr7B 88.844 1479 117 23 865 2321 726363384 726361932 0.000000e+00 1773.0
14 TraesCS6B01G470300 chr7B 89.747 751 56 16 128 872 726365367 726364632 0.000000e+00 941.0
15 TraesCS6B01G470300 chr7B 86.183 731 55 20 2398 3120 661744957 661744265 0.000000e+00 749.0
16 TraesCS6B01G470300 chr7B 83.688 705 54 27 2386 3083 726361838 726361188 2.720000e-170 608.0
17 TraesCS6B01G470300 chr7B 79.926 807 129 22 1526 2310 713513442 713512647 2.150000e-156 562.0
18 TraesCS6B01G470300 chr7B 94.276 297 13 1 2015 2311 661745250 661744958 4.850000e-123 451.0
19 TraesCS6B01G470300 chr7B 81.378 392 44 11 997 1387 713513931 713513568 3.110000e-75 292.0
20 TraesCS6B01G470300 chr7B 82.246 276 20 13 2812 3086 713508436 713508189 8.970000e-51 211.0
21 TraesCS6B01G470300 chr7B 75.822 426 58 25 261 647 59076307 59076726 1.180000e-39 174.0
22 TraesCS6B01G470300 chr7B 94.118 102 3 3 2296 2394 544134458 544134559 5.510000e-33 152.0
23 TraesCS6B01G470300 chr7B 77.500 240 25 11 263 495 579998172 579997955 2.010000e-22 117.0
24 TraesCS6B01G470300 chr7B 84.722 72 8 2 3011 3079 669903763 669903692 5.710000e-08 69.4
25 TraesCS6B01G470300 chr7A 77.574 1360 215 50 996 2310 712467542 712466228 0.000000e+00 739.0
26 TraesCS6B01G470300 chr7A 77.047 1246 214 44 1077 2293 694044505 694045707 0.000000e+00 651.0
27 TraesCS6B01G470300 chr7A 80.323 681 116 16 1521 2195 635274228 635274896 1.710000e-137 499.0
28 TraesCS6B01G470300 chr7A 81.884 276 20 13 2812 3086 712465813 712465567 4.170000e-49 206.0
29 TraesCS6B01G470300 chr6A 88.303 607 47 9 1209 1800 616794230 616794827 0.000000e+00 706.0
30 TraesCS6B01G470300 chr6A 83.475 587 54 23 2393 2967 616795161 616795716 1.020000e-139 507.0
31 TraesCS6B01G470300 chr6A 100.000 35 0 0 3086 3120 616795941 616795975 7.390000e-07 65.8
32 TraesCS6B01G470300 chr7D 77.229 1256 214 40 1077 2302 602286843 602288056 0.000000e+00 669.0
33 TraesCS6B01G470300 chr7D 78.968 756 137 19 1525 2274 549834904 549835643 2.210000e-136 496.0
34 TraesCS6B01G470300 chr7D 94.949 99 5 0 2306 2404 220083739 220083641 4.260000e-34 156.0
35 TraesCS6B01G470300 chr7D 94.949 99 5 0 2306 2404 220096518 220096420 4.260000e-34 156.0
36 TraesCS6B01G470300 chr1A 75.990 833 153 32 1003 1825 551307381 551308176 1.390000e-103 387.0
37 TraesCS6B01G470300 chr1B 78.622 421 73 12 1408 1827 630741704 630742108 2.440000e-66 263.0
38 TraesCS6B01G470300 chr4B 76.457 429 63 20 263 657 579395015 579394591 6.980000e-47 198.0
39 TraesCS6B01G470300 chr4B 96.875 96 3 0 2300 2395 630098839 630098744 9.160000e-36 161.0
40 TraesCS6B01G470300 chr4B 79.079 239 43 6 261 495 176902562 176902797 1.180000e-34 158.0
41 TraesCS6B01G470300 chr4B 93.204 103 4 2 2295 2396 429605857 429605957 7.130000e-32 148.0
42 TraesCS6B01G470300 chr5D 76.559 401 65 11 265 646 412463732 412463342 3.250000e-45 193.0
43 TraesCS6B01G470300 chr5A 95.960 99 2 2 2310 2406 705822060 705821962 3.290000e-35 159.0
44 TraesCS6B01G470300 chr2A 97.802 91 2 0 2306 2396 750532480 750532390 1.180000e-34 158.0
45 TraesCS6B01G470300 chr3A 94.898 98 5 0 2309 2406 443203673 443203576 1.530000e-33 154.0
46 TraesCS6B01G470300 chr4A 94.118 102 3 3 2296 2396 616405408 616405309 5.510000e-33 152.0
47 TraesCS6B01G470300 chr4D 74.463 419 74 23 263 655 115467868 115467457 1.980000e-32 150.0


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 TraesCS6B01G470300 chr6B 718477888 718481078 3190 True 5893.000000 5893 100.000000 1 3191 1 chr6B.!!$R1 3190
1 TraesCS6B01G470300 chr6B 718280595 718281373 778 False 494.000000 494 78.429000 1516 2308 1 chr6B.!!$F2 792
2 TraesCS6B01G470300 chr6B 718590802 718596949 6147 True 393.075000 617 80.531750 1000 2542 4 chr6B.!!$R2 1542
3 TraesCS6B01G470300 chrUn 330577829 330579814 1985 True 1094.500000 1777 86.316000 865 2851 2 chrUn.!!$R4 1986
4 TraesCS6B01G470300 chrUn 308512688 308513424 736 True 965.000000 965 90.280000 128 872 1 chrUn.!!$R2 744
5 TraesCS6B01G470300 chrUn 388971791 388972528 737 True 948.000000 948 89.894000 128 872 1 chrUn.!!$R3 744
6 TraesCS6B01G470300 chr7B 726361188 726365367 4179 True 1107.333333 1773 87.426333 128 3083 3 chr7B.!!$R6 2955
7 TraesCS6B01G470300 chr7B 661744265 661745250 985 True 600.000000 749 90.229500 2015 3120 2 chr7B.!!$R4 1105
8 TraesCS6B01G470300 chr7B 713512647 713513931 1284 True 427.000000 562 80.652000 997 2310 2 chr7B.!!$R5 1313
9 TraesCS6B01G470300 chr7A 694044505 694045707 1202 False 651.000000 651 77.047000 1077 2293 1 chr7A.!!$F2 1216
10 TraesCS6B01G470300 chr7A 635274228 635274896 668 False 499.000000 499 80.323000 1521 2195 1 chr7A.!!$F1 674
11 TraesCS6B01G470300 chr7A 712465567 712467542 1975 True 472.500000 739 79.729000 996 3086 2 chr7A.!!$R1 2090
12 TraesCS6B01G470300 chr6A 616794230 616795975 1745 False 426.266667 706 90.592667 1209 3120 3 chr6A.!!$F1 1911
13 TraesCS6B01G470300 chr7D 602286843 602288056 1213 False 669.000000 669 77.229000 1077 2302 1 chr7D.!!$F2 1225
14 TraesCS6B01G470300 chr7D 549834904 549835643 739 False 496.000000 496 78.968000 1525 2274 1 chr7D.!!$F1 749
15 TraesCS6B01G470300 chr1A 551307381 551308176 795 False 387.000000 387 75.990000 1003 1825 1 chr1A.!!$F1 822

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
993 2269 0.461548 TGAGCAGGTAGATTCGCAGG 59.538 55.0 0.0 0.0 0.0 4.85 F
1721 3553 0.102481 ACTAAGGCCGCTGTCATACG 59.898 55.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 3731 1.153647 CAGCCATTGCAGCCACATG 60.154 57.895 0.00 0.0 41.13 3.21 R
3159 6856 0.039618 AAGAATGAACATGGCCGGGT 59.960 50.000 2.18 0.0 0.00 5.28 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
20 21 3.980238 GCTACCATGAATATTCGCTCG 57.020 47.619 10.80 1.28 0.00 5.03
21 22 3.318017 GCTACCATGAATATTCGCTCGT 58.682 45.455 10.80 6.72 0.00 4.18
22 23 3.741344 GCTACCATGAATATTCGCTCGTT 59.259 43.478 10.80 0.00 0.00 3.85
23 24 4.211374 GCTACCATGAATATTCGCTCGTTT 59.789 41.667 10.80 0.00 0.00 3.60
24 25 5.404366 GCTACCATGAATATTCGCTCGTTTA 59.596 40.000 10.80 0.00 0.00 2.01
25 26 5.907197 ACCATGAATATTCGCTCGTTTAG 57.093 39.130 10.80 0.00 0.00 1.85
26 27 5.597806 ACCATGAATATTCGCTCGTTTAGA 58.402 37.500 10.80 0.00 0.00 2.10
27 28 6.046593 ACCATGAATATTCGCTCGTTTAGAA 58.953 36.000 10.80 0.00 0.00 2.10
28 29 6.018994 ACCATGAATATTCGCTCGTTTAGAAC 60.019 38.462 10.80 0.00 0.00 3.01
29 30 6.201044 CCATGAATATTCGCTCGTTTAGAACT 59.799 38.462 10.80 0.00 0.00 3.01
31 32 5.518847 TGAATATTCGCTCGTTTAGAACTGG 59.481 40.000 10.80 0.00 0.00 4.00
32 33 2.074547 TTCGCTCGTTTAGAACTGGG 57.925 50.000 0.00 0.00 0.00 4.45
33 34 1.250328 TCGCTCGTTTAGAACTGGGA 58.750 50.000 0.00 0.00 0.00 4.37
34 35 1.614903 TCGCTCGTTTAGAACTGGGAA 59.385 47.619 0.00 0.00 0.00 3.97
35 36 2.036217 TCGCTCGTTTAGAACTGGGAAA 59.964 45.455 0.00 0.00 0.00 3.13
37 38 3.400255 GCTCGTTTAGAACTGGGAAAGT 58.600 45.455 0.00 0.00 42.60 2.66
51 52 8.477419 AACTGGGAAAGTTCATATTCTTCAAA 57.523 30.769 0.00 0.00 46.60 2.69
52 53 8.477419 ACTGGGAAAGTTCATATTCTTCAAAA 57.523 30.769 0.00 0.00 34.57 2.44
54 55 7.367285 TGGGAAAGTTCATATTCTTCAAAACG 58.633 34.615 0.00 0.00 0.00 3.60
56 57 7.750903 GGGAAAGTTCATATTCTTCAAAACGAG 59.249 37.037 0.00 0.00 0.00 4.18
57 58 7.750903 GGAAAGTTCATATTCTTCAAAACGAGG 59.249 37.037 0.00 0.00 0.00 4.63
59 60 5.123979 AGTTCATATTCTTCAAAACGAGGGC 59.876 40.000 0.00 0.00 0.00 5.19
60 61 4.584874 TCATATTCTTCAAAACGAGGGCA 58.415 39.130 0.00 0.00 0.00 5.36
62 63 5.652014 TCATATTCTTCAAAACGAGGGCATT 59.348 36.000 0.00 0.00 0.00 3.56
63 64 3.641437 TTCTTCAAAACGAGGGCATTG 57.359 42.857 0.00 0.00 0.00 2.82
65 66 3.420893 TCTTCAAAACGAGGGCATTGAT 58.579 40.909 0.00 0.00 32.35 2.57
66 67 3.191162 TCTTCAAAACGAGGGCATTGATG 59.809 43.478 0.00 0.00 32.35 3.07
67 68 2.789213 TCAAAACGAGGGCATTGATGA 58.211 42.857 0.00 0.00 0.00 2.92
69 70 2.489329 CAAAACGAGGGCATTGATGACT 59.511 45.455 0.00 0.00 35.67 3.41
70 71 3.627395 AAACGAGGGCATTGATGACTA 57.373 42.857 0.00 0.00 35.67 2.59
71 72 3.845781 AACGAGGGCATTGATGACTAT 57.154 42.857 0.00 0.00 35.67 2.12
75 76 4.100963 ACGAGGGCATTGATGACTATTGTA 59.899 41.667 0.00 0.00 35.67 2.41
76 77 5.221722 ACGAGGGCATTGATGACTATTGTAT 60.222 40.000 0.00 0.00 35.67 2.29
77 78 5.702670 CGAGGGCATTGATGACTATTGTATT 59.297 40.000 0.00 0.00 35.67 1.89
78 79 6.205464 CGAGGGCATTGATGACTATTGTATTT 59.795 38.462 0.00 0.00 35.67 1.40
80 81 8.995027 AGGGCATTGATGACTATTGTATTTAA 57.005 30.769 0.00 0.00 35.67 1.52
81 82 9.420118 AGGGCATTGATGACTATTGTATTTAAA 57.580 29.630 0.00 0.00 35.67 1.52
113 114 8.990163 ATATTAAATTATTGGTCTTGGGACGT 57.010 30.769 0.00 0.00 42.97 4.34
116 117 8.810990 TTAAATTATTGGTCTTGGGACGTATT 57.189 30.769 0.00 0.00 42.97 1.89
118 119 7.712204 AATTATTGGTCTTGGGACGTATTTT 57.288 32.000 0.00 0.00 42.97 1.82
119 120 7.712204 ATTATTGGTCTTGGGACGTATTTTT 57.288 32.000 0.00 0.00 42.97 1.94
160 161 4.124351 CAGCCAGCCCATTGCACG 62.124 66.667 0.00 0.00 44.83 5.34
161 162 4.349503 AGCCAGCCCATTGCACGA 62.350 61.111 0.00 0.00 44.83 4.35
203 204 7.127186 TGAAGGAATATCTAATGACCAGGAACA 59.873 37.037 0.00 0.00 0.00 3.18
231 232 9.219603 TCAACACACAAAATTGAATGGTAAAAA 57.780 25.926 0.00 0.00 29.56 1.94
287 288 6.416750 CGAAAATACAAAGGTGAACTTGGTTC 59.583 38.462 0.00 3.75 40.53 3.62
288 289 5.784578 AATACAAAGGTGAACTTGGTTCC 57.215 39.130 0.00 0.69 40.53 3.62
306 307 1.153978 CATGCGCACCCACATGAAC 60.154 57.895 14.90 0.00 45.23 3.18
315 316 4.485163 GCACCCACATGAACAGTAAATTC 58.515 43.478 0.00 0.00 0.00 2.17
505 509 8.937634 ATAGCTTCAATTTTGCCTAGATTTTG 57.062 30.769 0.00 0.00 0.00 2.44
513 517 7.664552 ATTTTGCCTAGATTTTGATGGATGA 57.335 32.000 0.00 0.00 0.00 2.92
573 578 9.272901 CGGTTGACTACATGTGTTATAAAAATG 57.727 33.333 9.11 0.00 0.00 2.32
660 665 1.747355 CACCAATCTGCATCCCTGAAC 59.253 52.381 0.00 0.00 0.00 3.18
754 760 1.000827 CAATTTTGCAGCCCGTGTACA 60.001 47.619 0.00 0.00 0.00 2.90
794 800 6.144078 CCAAAACATGGTAACCCTAATAGC 57.856 41.667 0.00 0.00 44.85 2.97
795 801 5.891551 CCAAAACATGGTAACCCTAATAGCT 59.108 40.000 0.00 0.00 44.85 3.32
796 802 6.183360 CCAAAACATGGTAACCCTAATAGCTG 60.183 42.308 0.00 0.00 44.85 4.24
798 804 3.716872 ACATGGTAACCCTAATAGCTGCT 59.283 43.478 7.57 7.57 0.00 4.24
813 819 2.573869 GCTCTAGGCACGCACAGA 59.426 61.111 0.00 0.00 41.35 3.41
815 821 1.515088 CTCTAGGCACGCACAGACG 60.515 63.158 0.00 0.00 39.50 4.18
816 822 1.923227 CTCTAGGCACGCACAGACGA 61.923 60.000 0.00 0.00 36.70 4.20
817 823 1.515088 CTAGGCACGCACAGACGAG 60.515 63.158 0.00 0.00 36.70 4.18
818 824 2.874010 CTAGGCACGCACAGACGAGG 62.874 65.000 0.00 0.00 36.70 4.63
861 877 3.898640 GATCGACGACGGCGCAAC 61.899 66.667 20.49 8.25 42.48 4.17
886 2157 1.676014 CGTAGTTTCCAGCTTCCAGGG 60.676 57.143 0.00 0.00 0.00 4.45
887 2158 1.628846 GTAGTTTCCAGCTTCCAGGGA 59.371 52.381 0.00 0.00 0.00 4.20
888 2159 0.695347 AGTTTCCAGCTTCCAGGGAG 59.305 55.000 0.00 0.00 31.19 4.30
889 2160 0.693049 GTTTCCAGCTTCCAGGGAGA 59.307 55.000 0.00 0.00 31.19 3.71
890 2161 1.073923 GTTTCCAGCTTCCAGGGAGAA 59.926 52.381 0.00 0.00 31.19 2.87
896 2167 3.566130 CTTCCAGGGAGAAGCCAAG 57.434 57.895 0.00 0.00 37.08 3.61
953 2224 3.528905 TCCATCCATCCCAACTCTGAAAT 59.471 43.478 0.00 0.00 0.00 2.17
963 2234 3.070018 CAACTCTGAAATCTTGGAGCGT 58.930 45.455 0.00 0.00 0.00 5.07
965 2236 2.300152 ACTCTGAAATCTTGGAGCGTCA 59.700 45.455 0.00 0.00 0.00 4.35
967 2238 3.937706 CTCTGAAATCTTGGAGCGTCAAT 59.062 43.478 0.00 0.00 0.00 2.57
981 2257 1.078918 TCAATGGCGACTGAGCAGG 60.079 57.895 2.20 0.00 39.27 4.85
985 2261 0.684479 ATGGCGACTGAGCAGGTAGA 60.684 55.000 2.20 0.00 39.27 2.59
988 2264 1.537135 GGCGACTGAGCAGGTAGATTC 60.537 57.143 2.20 0.00 39.27 2.52
989 2265 1.862008 GCGACTGAGCAGGTAGATTCG 60.862 57.143 2.20 2.50 37.05 3.34
990 2266 1.846541 GACTGAGCAGGTAGATTCGC 58.153 55.000 2.20 0.00 0.00 4.70
991 2267 1.135139 GACTGAGCAGGTAGATTCGCA 59.865 52.381 2.20 0.00 0.00 5.10
992 2268 1.135915 ACTGAGCAGGTAGATTCGCAG 59.864 52.381 2.20 0.00 33.55 5.18
993 2269 0.461548 TGAGCAGGTAGATTCGCAGG 59.538 55.000 0.00 0.00 0.00 4.85
994 2270 0.461961 GAGCAGGTAGATTCGCAGGT 59.538 55.000 0.00 0.00 0.00 4.00
1117 2889 1.215647 CTGCTGGTCCACGACTACC 59.784 63.158 0.00 0.00 36.24 3.18
1285 3060 1.160137 AGACGATGCCAACAAGAAGC 58.840 50.000 0.00 0.00 0.00 3.86
1389 3179 4.990257 CTGAAACATACAGCTTCAATGGG 58.010 43.478 5.07 0.00 32.33 4.00
1406 3199 2.033194 GGTTTTCTCGGGCCAGACG 61.033 63.158 4.39 0.00 0.00 4.18
1444 3237 3.256631 ACAAGCCCTTGAACAATCATCAC 59.743 43.478 14.46 0.00 42.93 3.06
1476 3272 1.327764 GACGATTCTTTCACCATCCGC 59.672 52.381 0.00 0.00 0.00 5.54
1496 3292 0.461548 TGCGACATCATGGTCTCCTC 59.538 55.000 0.00 0.00 35.63 3.71
1498 3294 1.407936 CGACATCATGGTCTCCTCCT 58.592 55.000 0.00 0.00 35.63 3.69
1598 3427 2.821366 GGTGGGCGCTGATGTGAG 60.821 66.667 7.64 0.00 0.00 3.51
1701 3530 2.276740 CCCATGAAGGAGGGCACC 59.723 66.667 0.00 0.00 42.36 5.01
1721 3553 0.102481 ACTAAGGCCGCTGTCATACG 59.898 55.000 0.00 0.00 0.00 3.06
1776 3608 4.201724 GCCTTGCTTAACTTCATCTACACG 60.202 45.833 0.00 0.00 0.00 4.49
1863 3713 2.554462 GCAAGGACAAGAAAAGGAGACC 59.446 50.000 0.00 0.00 0.00 3.85
1867 3717 3.395941 AGGACAAGAAAAGGAGACCACAT 59.604 43.478 0.00 0.00 0.00 3.21
1870 3720 5.946377 GGACAAGAAAAGGAGACCACATTAT 59.054 40.000 0.00 0.00 0.00 1.28
1871 3721 6.094186 GGACAAGAAAAGGAGACCACATTATC 59.906 42.308 0.00 0.00 0.00 1.75
1872 3722 6.542821 ACAAGAAAAGGAGACCACATTATCA 58.457 36.000 0.00 0.00 0.00 2.15
1873 3723 6.656693 ACAAGAAAAGGAGACCACATTATCAG 59.343 38.462 0.00 0.00 0.00 2.90
1874 3724 6.627087 AGAAAAGGAGACCACATTATCAGA 57.373 37.500 0.00 0.00 0.00 3.27
1875 3725 6.648192 AGAAAAGGAGACCACATTATCAGAG 58.352 40.000 0.00 0.00 0.00 3.35
1877 3727 2.703007 AGGAGACCACATTATCAGAGGC 59.297 50.000 0.00 0.00 0.00 4.70
1878 3728 2.435805 GGAGACCACATTATCAGAGGCA 59.564 50.000 0.00 0.00 0.00 4.75
1879 3729 3.462021 GAGACCACATTATCAGAGGCAC 58.538 50.000 0.00 0.00 0.00 5.01
1881 3731 0.940126 CCACATTATCAGAGGCACGC 59.060 55.000 0.00 0.00 0.00 5.34
1899 3752 1.153647 CATGTGGCTGCAATGGCTG 60.154 57.895 0.50 0.00 41.91 4.85
1941 3794 3.457234 TGACAGATATGATGTCCAACGC 58.543 45.455 12.79 0.00 45.24 4.84
1962 3815 3.144506 CCTCAAGTGCATCTGTGAAAGT 58.855 45.455 0.00 0.00 0.00 2.66
1963 3816 3.058432 CCTCAAGTGCATCTGTGAAAGTG 60.058 47.826 0.00 0.00 0.00 3.16
2020 3873 1.098869 CACTCTTGCTCTAGCCGAGA 58.901 55.000 19.18 12.62 42.62 4.04
2130 3983 2.019984 GGCTGGGATCATGTCTTTGAC 58.980 52.381 0.00 0.00 0.00 3.18
2207 4064 5.701290 GGAACTAACACTTTCTGTATGCAGT 59.299 40.000 10.80 0.00 43.05 4.40
2208 4065 6.872020 GGAACTAACACTTTCTGTATGCAGTA 59.128 38.462 10.80 0.00 43.05 2.74
2209 4066 7.386848 GGAACTAACACTTTCTGTATGCAGTAA 59.613 37.037 10.80 6.69 43.05 2.24
2323 4257 3.972133 TGTCATCTACTCCCTCCGTAAA 58.028 45.455 0.00 0.00 0.00 2.01
2328 4262 6.264970 GTCATCTACTCCCTCCGTAAACTAAT 59.735 42.308 0.00 0.00 0.00 1.73
2330 4264 8.168725 TCATCTACTCCCTCCGTAAACTAATAT 58.831 37.037 0.00 0.00 0.00 1.28
2335 4269 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2336 4270 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2337 4271 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2341 4275 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2429 4385 2.417978 TTGCTGGGCAAACTGTCTG 58.582 52.632 2.28 0.00 45.96 3.51
2532 4532 9.046846 CCCCTATCTAATTGTTGTATCCTCATA 57.953 37.037 0.00 0.00 0.00 2.15
2562 4567 5.970317 TCTCTGTTTATTAGGTGTGTCGA 57.030 39.130 0.00 0.00 0.00 4.20
2603 4608 5.575157 TGTGCCTTCCCTATTATGAAAACA 58.425 37.500 0.00 0.00 0.00 2.83
2605 4610 6.495181 TGTGCCTTCCCTATTATGAAAACAAA 59.505 34.615 0.00 0.00 0.00 2.83
2606 4611 7.015682 TGTGCCTTCCCTATTATGAAAACAAAA 59.984 33.333 0.00 0.00 0.00 2.44
2625 4630 8.719560 AACAAAACCTTATTCTAGCTAGCTAC 57.280 34.615 20.67 0.00 0.00 3.58
2696 4962 3.946606 TCCTGGAATTAAGGGAACGAAC 58.053 45.455 0.00 0.00 35.35 3.95
2713 4979 3.252458 ACGAACCTGGATAACAAAACAGC 59.748 43.478 0.00 0.00 0.00 4.40
2747 5013 4.827692 TGTGGTTACCATGACAGTGATAC 58.172 43.478 7.58 0.00 35.28 2.24
2938 6508 9.897744 ATTAATTCCAGTATATGAACAAATGCG 57.102 29.630 0.00 0.00 0.00 4.73
2974 6544 7.161715 AGCCTGGGTATTAATTAATTCCAGA 57.838 36.000 33.88 21.55 42.25 3.86
3009 6580 9.994432 CATTAATGTTAGCCTCTTTACAGAAAG 57.006 33.333 7.32 0.00 43.05 2.62
3078 6667 4.142138 GGAACACTCACTATGGAGGTACAG 60.142 50.000 0.00 0.00 39.27 2.74
3120 6817 7.897575 ATATCTCAGTTTCTGTGTGTCTTTC 57.102 36.000 0.00 0.00 32.61 2.62
3121 6818 4.112634 TCTCAGTTTCTGTGTGTCTTTCG 58.887 43.478 0.00 0.00 32.61 3.46
3122 6819 2.607635 TCAGTTTCTGTGTGTCTTTCGC 59.392 45.455 0.00 0.00 32.61 4.70
3123 6820 2.609459 CAGTTTCTGTGTGTCTTTCGCT 59.391 45.455 0.00 0.00 0.00 4.93
3124 6821 3.802139 CAGTTTCTGTGTGTCTTTCGCTA 59.198 43.478 0.00 0.00 0.00 4.26
3125 6822 3.802685 AGTTTCTGTGTGTCTTTCGCTAC 59.197 43.478 0.00 0.00 0.00 3.58
3126 6823 3.446310 TTCTGTGTGTCTTTCGCTACA 57.554 42.857 0.00 0.00 0.00 2.74
3127 6824 3.660501 TCTGTGTGTCTTTCGCTACAT 57.339 42.857 0.00 0.00 0.00 2.29
3128 6825 4.776795 TCTGTGTGTCTTTCGCTACATA 57.223 40.909 0.00 0.00 0.00 2.29
3129 6826 4.482386 TCTGTGTGTCTTTCGCTACATAC 58.518 43.478 0.00 0.00 37.98 2.39
3130 6827 3.581755 TGTGTGTCTTTCGCTACATACC 58.418 45.455 0.00 0.00 37.03 2.73
3131 6828 2.928116 GTGTGTCTTTCGCTACATACCC 59.072 50.000 0.00 0.00 33.19 3.69
3132 6829 2.563620 TGTGTCTTTCGCTACATACCCA 59.436 45.455 0.00 0.00 0.00 4.51
3133 6830 2.928116 GTGTCTTTCGCTACATACCCAC 59.072 50.000 0.00 0.00 0.00 4.61
3134 6831 2.093869 TGTCTTTCGCTACATACCCACC 60.094 50.000 0.00 0.00 0.00 4.61
3135 6832 1.483415 TCTTTCGCTACATACCCACCC 59.517 52.381 0.00 0.00 0.00 4.61
3136 6833 1.208535 CTTTCGCTACATACCCACCCA 59.791 52.381 0.00 0.00 0.00 4.51
3137 6834 1.502690 TTCGCTACATACCCACCCAT 58.497 50.000 0.00 0.00 0.00 4.00
3138 6835 1.502690 TCGCTACATACCCACCCATT 58.497 50.000 0.00 0.00 0.00 3.16
3139 6836 1.841277 TCGCTACATACCCACCCATTT 59.159 47.619 0.00 0.00 0.00 2.32
3140 6837 3.039743 TCGCTACATACCCACCCATTTA 58.960 45.455 0.00 0.00 0.00 1.40
3141 6838 3.649023 TCGCTACATACCCACCCATTTAT 59.351 43.478 0.00 0.00 0.00 1.40
3142 6839 4.103469 TCGCTACATACCCACCCATTTATT 59.897 41.667 0.00 0.00 0.00 1.40
3143 6840 4.825085 CGCTACATACCCACCCATTTATTT 59.175 41.667 0.00 0.00 0.00 1.40
3144 6841 5.300792 CGCTACATACCCACCCATTTATTTT 59.699 40.000 0.00 0.00 0.00 1.82
3145 6842 6.512297 GCTACATACCCACCCATTTATTTTG 58.488 40.000 0.00 0.00 0.00 2.44
3146 6843 6.322712 GCTACATACCCACCCATTTATTTTGA 59.677 38.462 0.00 0.00 0.00 2.69
3147 6844 6.538945 ACATACCCACCCATTTATTTTGAC 57.461 37.500 0.00 0.00 0.00 3.18
3148 6845 6.260663 ACATACCCACCCATTTATTTTGACT 58.739 36.000 0.00 0.00 0.00 3.41
3149 6846 6.154363 ACATACCCACCCATTTATTTTGACTG 59.846 38.462 0.00 0.00 0.00 3.51
3150 6847 4.746466 ACCCACCCATTTATTTTGACTGA 58.254 39.130 0.00 0.00 0.00 3.41
3151 6848 5.341169 ACCCACCCATTTATTTTGACTGAT 58.659 37.500 0.00 0.00 0.00 2.90
3152 6849 6.498538 ACCCACCCATTTATTTTGACTGATA 58.501 36.000 0.00 0.00 0.00 2.15
3153 6850 6.957020 ACCCACCCATTTATTTTGACTGATAA 59.043 34.615 0.00 0.00 0.00 1.75
3154 6851 7.623278 ACCCACCCATTTATTTTGACTGATAAT 59.377 33.333 0.00 0.00 0.00 1.28
3155 6852 8.485392 CCCACCCATTTATTTTGACTGATAATT 58.515 33.333 0.00 0.00 0.00 1.40
3156 6853 9.316730 CCACCCATTTATTTTGACTGATAATTG 57.683 33.333 0.00 0.00 0.00 2.32
3157 6854 8.819974 CACCCATTTATTTTGACTGATAATTGC 58.180 33.333 0.00 0.00 0.00 3.56
3158 6855 8.761689 ACCCATTTATTTTGACTGATAATTGCT 58.238 29.630 0.00 0.00 0.00 3.91
3163 6860 5.811399 TTTTGACTGATAATTGCTACCCG 57.189 39.130 0.00 0.00 0.00 5.28
3164 6861 3.469008 TGACTGATAATTGCTACCCGG 57.531 47.619 0.00 0.00 0.00 5.73
3165 6862 2.143925 GACTGATAATTGCTACCCGGC 58.856 52.381 0.00 0.00 0.00 6.13
3166 6863 1.202770 ACTGATAATTGCTACCCGGCC 60.203 52.381 0.00 0.00 0.00 6.13
3167 6864 0.840617 TGATAATTGCTACCCGGCCA 59.159 50.000 2.24 0.00 0.00 5.36
3168 6865 1.423541 TGATAATTGCTACCCGGCCAT 59.576 47.619 2.24 0.00 0.00 4.40
3169 6866 1.812571 GATAATTGCTACCCGGCCATG 59.187 52.381 2.24 0.00 0.00 3.66
3170 6867 0.548989 TAATTGCTACCCGGCCATGT 59.451 50.000 2.24 0.51 0.00 3.21
3171 6868 0.324275 AATTGCTACCCGGCCATGTT 60.324 50.000 2.24 0.00 0.00 2.71
3172 6869 0.751643 ATTGCTACCCGGCCATGTTC 60.752 55.000 2.24 0.00 0.00 3.18
3173 6870 2.130821 TTGCTACCCGGCCATGTTCA 62.131 55.000 2.24 0.00 0.00 3.18
3174 6871 1.152963 GCTACCCGGCCATGTTCAT 60.153 57.895 2.24 0.00 0.00 2.57
3175 6872 0.751643 GCTACCCGGCCATGTTCATT 60.752 55.000 2.24 0.00 0.00 2.57
3176 6873 1.308998 CTACCCGGCCATGTTCATTC 58.691 55.000 2.24 0.00 0.00 2.67
3177 6874 0.916086 TACCCGGCCATGTTCATTCT 59.084 50.000 2.24 0.00 0.00 2.40
3178 6875 0.039618 ACCCGGCCATGTTCATTCTT 59.960 50.000 2.24 0.00 0.00 2.52
3179 6876 0.457035 CCCGGCCATGTTCATTCTTG 59.543 55.000 2.24 0.00 0.00 3.02
3180 6877 1.176527 CCGGCCATGTTCATTCTTGT 58.823 50.000 2.24 0.00 0.00 3.16
3181 6878 1.545582 CCGGCCATGTTCATTCTTGTT 59.454 47.619 2.24 0.00 0.00 2.83
3182 6879 2.415893 CCGGCCATGTTCATTCTTGTTC 60.416 50.000 2.24 0.00 0.00 3.18
3183 6880 2.489329 CGGCCATGTTCATTCTTGTTCT 59.511 45.455 2.24 0.00 0.00 3.01
3184 6881 3.671433 CGGCCATGTTCATTCTTGTTCTG 60.671 47.826 2.24 0.00 0.00 3.02
3185 6882 3.248266 GCCATGTTCATTCTTGTTCTGC 58.752 45.455 0.00 0.00 0.00 4.26
3186 6883 3.841643 CCATGTTCATTCTTGTTCTGCC 58.158 45.455 0.00 0.00 0.00 4.85
3187 6884 3.367703 CCATGTTCATTCTTGTTCTGCCC 60.368 47.826 0.00 0.00 0.00 5.36
3188 6885 2.238521 TGTTCATTCTTGTTCTGCCCC 58.761 47.619 0.00 0.00 0.00 5.80
3189 6886 2.238521 GTTCATTCTTGTTCTGCCCCA 58.761 47.619 0.00 0.00 0.00 4.96
3190 6887 2.205022 TCATTCTTGTTCTGCCCCAG 57.795 50.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.318017 ACGAGCGAATATTCATGGTAGC 58.682 45.455 15.57 9.07 0.00 3.58
1 2 5.907197 AAACGAGCGAATATTCATGGTAG 57.093 39.130 15.57 8.29 0.00 3.18
2 3 6.741109 TCTAAACGAGCGAATATTCATGGTA 58.259 36.000 15.57 0.00 0.00 3.25
3 4 5.597806 TCTAAACGAGCGAATATTCATGGT 58.402 37.500 15.57 7.69 0.00 3.55
4 5 6.201044 AGTTCTAAACGAGCGAATATTCATGG 59.799 38.462 15.57 7.11 36.23 3.66
5 6 7.059817 CAGTTCTAAACGAGCGAATATTCATG 58.940 38.462 15.57 1.43 36.23 3.07
6 7 6.201044 CCAGTTCTAAACGAGCGAATATTCAT 59.799 38.462 15.57 3.19 36.23 2.57
9 10 4.809426 CCCAGTTCTAAACGAGCGAATATT 59.191 41.667 0.00 0.00 36.23 1.28
11 12 3.444742 TCCCAGTTCTAAACGAGCGAATA 59.555 43.478 0.00 0.00 36.23 1.75
12 13 2.232941 TCCCAGTTCTAAACGAGCGAAT 59.767 45.455 0.00 0.00 36.23 3.34
13 14 1.614903 TCCCAGTTCTAAACGAGCGAA 59.385 47.619 0.00 0.00 36.23 4.70
14 15 1.250328 TCCCAGTTCTAAACGAGCGA 58.750 50.000 0.00 0.00 36.23 4.93
16 17 3.400255 ACTTTCCCAGTTCTAAACGAGC 58.600 45.455 0.00 0.00 36.23 5.03
27 28 8.360390 GTTTTGAAGAATATGAACTTTCCCAGT 58.640 33.333 0.00 0.00 37.30 4.00
28 29 7.538678 CGTTTTGAAGAATATGAACTTTCCCAG 59.461 37.037 0.00 0.00 0.00 4.45
29 30 7.229707 TCGTTTTGAAGAATATGAACTTTCCCA 59.770 33.333 0.00 0.00 0.00 4.37
31 32 7.750903 CCTCGTTTTGAAGAATATGAACTTTCC 59.249 37.037 0.00 0.00 0.00 3.13
32 33 7.750903 CCCTCGTTTTGAAGAATATGAACTTTC 59.249 37.037 0.00 0.00 0.00 2.62
33 34 7.593825 CCCTCGTTTTGAAGAATATGAACTTT 58.406 34.615 0.00 0.00 0.00 2.66
34 35 6.349363 GCCCTCGTTTTGAAGAATATGAACTT 60.349 38.462 0.00 0.00 0.00 2.66
35 36 5.123979 GCCCTCGTTTTGAAGAATATGAACT 59.876 40.000 0.00 0.00 0.00 3.01
37 38 5.007034 TGCCCTCGTTTTGAAGAATATGAA 58.993 37.500 0.00 0.00 0.00 2.57
38 39 4.584874 TGCCCTCGTTTTGAAGAATATGA 58.415 39.130 0.00 0.00 0.00 2.15
39 40 4.963276 TGCCCTCGTTTTGAAGAATATG 57.037 40.909 0.00 0.00 0.00 1.78
41 42 5.007034 TCAATGCCCTCGTTTTGAAGAATA 58.993 37.500 0.00 0.00 0.00 1.75
43 44 3.218453 TCAATGCCCTCGTTTTGAAGAA 58.782 40.909 0.00 0.00 0.00 2.52
44 45 2.857483 TCAATGCCCTCGTTTTGAAGA 58.143 42.857 0.00 0.00 0.00 2.87
45 46 3.191162 TCATCAATGCCCTCGTTTTGAAG 59.809 43.478 0.00 0.00 32.35 3.02
46 47 3.057596 GTCATCAATGCCCTCGTTTTGAA 60.058 43.478 0.00 0.00 32.35 2.69
48 49 2.489329 AGTCATCAATGCCCTCGTTTTG 59.511 45.455 0.00 0.00 0.00 2.44
50 51 2.496899 AGTCATCAATGCCCTCGTTT 57.503 45.000 0.00 0.00 0.00 3.60
51 52 3.845781 ATAGTCATCAATGCCCTCGTT 57.154 42.857 0.00 0.00 0.00 3.85
52 53 3.118261 ACAATAGTCATCAATGCCCTCGT 60.118 43.478 0.00 0.00 0.00 4.18
54 55 7.516198 AAATACAATAGTCATCAATGCCCTC 57.484 36.000 0.00 0.00 0.00 4.30
88 89 8.990163 ACGTCCCAAGACCAATAATTTAATAT 57.010 30.769 0.00 0.00 40.12 1.28
90 91 8.990163 ATACGTCCCAAGACCAATAATTTAAT 57.010 30.769 0.00 0.00 40.12 1.40
91 92 8.810990 AATACGTCCCAAGACCAATAATTTAA 57.189 30.769 0.00 0.00 40.12 1.52
92 93 8.810990 AAATACGTCCCAAGACCAATAATTTA 57.189 30.769 0.00 0.00 40.12 1.40
93 94 7.712204 AAATACGTCCCAAGACCAATAATTT 57.288 32.000 0.00 0.00 40.12 1.82
95 96 7.712204 AAAAATACGTCCCAAGACCAATAAT 57.288 32.000 0.00 0.00 40.12 1.28
116 117 4.546829 AGGGTAGCTACGATGACAAAAA 57.453 40.909 17.48 0.00 0.00 1.94
118 119 4.098960 CCTAAGGGTAGCTACGATGACAAA 59.901 45.833 17.48 0.00 0.00 2.83
119 120 3.635373 CCTAAGGGTAGCTACGATGACAA 59.365 47.826 17.48 0.00 0.00 3.18
120 121 3.117776 TCCTAAGGGTAGCTACGATGACA 60.118 47.826 17.48 0.26 0.00 3.58
121 122 3.252944 GTCCTAAGGGTAGCTACGATGAC 59.747 52.174 17.48 12.98 0.00 3.06
124 125 3.488363 CTGTCCTAAGGGTAGCTACGAT 58.512 50.000 17.48 8.60 0.00 3.73
125 126 2.928334 CTGTCCTAAGGGTAGCTACGA 58.072 52.381 17.48 5.37 0.00 3.43
126 127 1.337387 GCTGTCCTAAGGGTAGCTACG 59.663 57.143 17.48 3.40 39.19 3.51
173 174 7.419518 CCTGGTCATTAGATATTCCTTCAGTGT 60.420 40.741 0.00 0.00 0.00 3.55
231 232 7.054124 TCGAGGCCTTTAACATCTTCAATATT 58.946 34.615 6.77 0.00 0.00 1.28
242 243 1.877443 GCACTTTCGAGGCCTTTAACA 59.123 47.619 6.77 0.00 0.00 2.41
243 244 1.136057 CGCACTTTCGAGGCCTTTAAC 60.136 52.381 6.77 0.00 0.00 2.01
287 288 2.341875 TTCATGTGGGTGCGCATGG 61.342 57.895 15.91 0.00 41.83 3.66
288 289 1.153978 GTTCATGTGGGTGCGCATG 60.154 57.895 15.91 6.75 42.62 4.06
347 348 8.108999 TCAAGTTTGATATCCCAAGATTTCAGA 58.891 33.333 0.00 0.00 40.25 3.27
477 478 8.986929 AATCTAGGCAAAATTGAAGCTATACT 57.013 30.769 0.00 0.00 0.00 2.12
605 610 3.298317 GCACGCCTCTTACGAATAGTAG 58.702 50.000 0.00 0.00 36.56 2.57
660 665 5.418310 ACGACAGTAAAATTGAACCACTG 57.582 39.130 0.00 0.00 41.83 3.66
754 760 4.772678 GGCTTTGAGGCCCTCATT 57.227 55.556 15.62 0.00 45.92 2.57
796 802 1.807573 GTCTGTGCGTGCCTAGAGC 60.808 63.158 0.00 0.00 44.14 4.09
798 804 1.923227 CTCGTCTGTGCGTGCCTAGA 61.923 60.000 0.00 0.00 0.00 2.43
828 834 0.601311 GATCCTCCCGGAGATTTGCG 60.601 60.000 16.69 0.00 44.06 4.85
829 835 0.601311 CGATCCTCCCGGAGATTTGC 60.601 60.000 16.69 0.00 44.06 3.68
830 836 1.040646 TCGATCCTCCCGGAGATTTG 58.959 55.000 16.69 6.73 44.06 2.32
831 837 1.041437 GTCGATCCTCCCGGAGATTT 58.959 55.000 16.69 0.00 44.06 2.17
833 839 1.601197 CGTCGATCCTCCCGGAGAT 60.601 63.158 16.69 7.48 44.06 2.75
861 877 0.613777 AAGCTGGAAACTACGAGGGG 59.386 55.000 0.00 0.00 0.00 4.79
953 2224 1.741401 CGCCATTGACGCTCCAAGA 60.741 57.895 0.00 0.00 0.00 3.02
963 2234 1.078918 CCTGCTCAGTCGCCATTGA 60.079 57.895 0.00 0.00 0.00 2.57
965 2236 0.176680 CTACCTGCTCAGTCGCCATT 59.823 55.000 0.00 0.00 0.00 3.16
967 2238 0.684479 ATCTACCTGCTCAGTCGCCA 60.684 55.000 0.00 0.00 0.00 5.69
981 2257 3.068307 ACATGACCTACCTGCGAATCTAC 59.932 47.826 0.00 0.00 0.00 2.59
985 2261 1.202417 CGACATGACCTACCTGCGAAT 60.202 52.381 0.00 0.00 0.00 3.34
988 2264 0.525668 GACGACATGACCTACCTGCG 60.526 60.000 0.00 0.00 0.00 5.18
989 2265 0.525668 CGACGACATGACCTACCTGC 60.526 60.000 0.00 0.00 0.00 4.85
990 2266 0.809385 ACGACGACATGACCTACCTG 59.191 55.000 0.00 0.00 0.00 4.00
991 2267 1.471684 GAACGACGACATGACCTACCT 59.528 52.381 0.00 0.00 0.00 3.08
992 2268 1.792993 CGAACGACGACATGACCTACC 60.793 57.143 0.00 0.00 45.77 3.18
993 2269 1.531912 CGAACGACGACATGACCTAC 58.468 55.000 0.00 0.00 45.77 3.18
994 2270 0.179181 GCGAACGACGACATGACCTA 60.179 55.000 0.00 0.00 45.77 3.08
1102 2874 2.882876 CGGGTAGTCGTGGACCAG 59.117 66.667 0.00 0.00 37.47 4.00
1117 2889 4.093952 CTCTTGCTTGGTGCGCGG 62.094 66.667 8.83 0.00 46.63 6.46
1285 3060 1.880894 CTTCCACCACATGCTGCTG 59.119 57.895 0.00 0.00 0.00 4.41
1389 3179 2.677979 GCGTCTGGCCCGAGAAAAC 61.678 63.158 0.00 0.00 34.80 2.43
1406 3199 3.303406 GCTTGTCTTGTCATGAACTTGC 58.697 45.455 0.00 0.00 0.00 4.01
1444 3237 5.582269 TGAAAGAATCGTCCTTTAGATGCAG 59.418 40.000 0.00 0.00 34.33 4.41
1476 3272 0.463204 AGGAGACCATGATGTCGCAG 59.537 55.000 0.00 0.00 40.26 5.18
1496 3292 2.036256 CCTTGGGGTTGCAGGAGG 59.964 66.667 0.00 0.00 0.00 4.30
1498 3294 2.843545 GTCCTTGGGGTTGCAGGA 59.156 61.111 0.00 0.00 34.10 3.86
1598 3427 3.564027 CGCCGCCGACCTCAAATC 61.564 66.667 0.00 0.00 36.29 2.17
1621 3450 4.269523 ACACCGGTGTGCAGCCAT 62.270 61.111 38.46 12.15 46.86 4.40
1658 3487 3.409026 AGAGTTGTGACATGAAGACCC 57.591 47.619 0.00 0.00 0.00 4.46
1701 3530 1.571919 GTATGACAGCGGCCTTAGTG 58.428 55.000 0.00 0.00 0.00 2.74
1708 3537 0.529773 TTGATCCGTATGACAGCGGC 60.530 55.000 14.27 0.00 46.79 6.53
1721 3553 3.428589 GCTTGCTTCCATGTCTTTGATCC 60.429 47.826 0.00 0.00 0.00 3.36
1834 3684 3.695830 TTCTTGTCCTTGCTCCGTAAT 57.304 42.857 0.00 0.00 0.00 1.89
1863 3713 1.655484 TGCGTGCCTCTGATAATGTG 58.345 50.000 0.00 0.00 0.00 3.21
1867 3717 1.655484 CACATGCGTGCCTCTGATAA 58.345 50.000 5.64 0.00 36.06 1.75
1870 3720 2.046988 CCACATGCGTGCCTCTGA 60.047 61.111 5.64 0.00 42.17 3.27
1871 3721 3.807538 GCCACATGCGTGCCTCTG 61.808 66.667 5.64 0.00 42.17 3.35
1881 3731 1.153647 CAGCCATTGCAGCCACATG 60.154 57.895 0.00 0.00 41.13 3.21
1899 3752 1.766069 CCGCTACCAACAAGTTTTGC 58.234 50.000 0.00 0.00 0.00 3.68
1941 3794 3.058432 CACTTTCACAGATGCACTTGAGG 60.058 47.826 6.30 0.00 0.00 3.86
1962 3815 4.248058 CACATATGTGCTCAGACAACTCA 58.752 43.478 22.27 0.00 39.39 3.41
1963 3816 4.854361 CACATATGTGCTCAGACAACTC 57.146 45.455 22.27 0.00 39.39 3.01
2130 3983 4.080751 TCCTTTAAAACCGAGGGATAGGTG 60.081 45.833 0.00 0.00 41.21 4.00
2208 4065 8.812972 TGAGATCTAACCAAGTTACATGTACTT 58.187 33.333 4.68 9.57 36.31 2.24
2209 4066 8.362464 TGAGATCTAACCAAGTTACATGTACT 57.638 34.615 4.68 3.72 0.00 2.73
2233 4097 1.382522 ATGCATAAGGCCGTCACTTG 58.617 50.000 0.00 0.00 43.89 3.16
2380 4314 8.202137 GCAAATTATACAGTACTCCCTCTGTAA 58.798 37.037 8.67 0.00 45.84 2.41
2381 4315 7.469594 CGCAAATTATACAGTACTCCCTCTGTA 60.470 40.741 7.34 7.34 46.45 2.74
2382 4316 6.583562 GCAAATTATACAGTACTCCCTCTGT 58.416 40.000 0.00 0.00 45.21 3.41
2383 4317 5.692204 CGCAAATTATACAGTACTCCCTCTG 59.308 44.000 0.00 0.00 37.65 3.35
2384 4318 5.363005 ACGCAAATTATACAGTACTCCCTCT 59.637 40.000 0.00 0.00 0.00 3.69
2385 4319 5.598769 ACGCAAATTATACAGTACTCCCTC 58.401 41.667 0.00 0.00 0.00 4.30
2386 4320 5.609533 ACGCAAATTATACAGTACTCCCT 57.390 39.130 0.00 0.00 0.00 4.20
2387 4321 7.958053 AATACGCAAATTATACAGTACTCCC 57.042 36.000 0.00 0.00 0.00 4.30
2388 4322 7.797123 GCAAATACGCAAATTATACAGTACTCC 59.203 37.037 0.00 0.00 0.00 3.85
2389 4323 8.548721 AGCAAATACGCAAATTATACAGTACTC 58.451 33.333 0.00 0.00 0.00 2.59
2390 4324 8.335356 CAGCAAATACGCAAATTATACAGTACT 58.665 33.333 0.00 0.00 0.00 2.73
2391 4325 7.586300 CCAGCAAATACGCAAATTATACAGTAC 59.414 37.037 0.00 0.00 0.00 2.73
2429 4385 2.154462 CAGACCAACCACTCCATCAAC 58.846 52.381 0.00 0.00 0.00 3.18
2567 4572 4.202253 GGGAAGGCACAAAAGAAACATCTT 60.202 41.667 0.00 0.00 0.00 2.40
2569 4574 3.321968 AGGGAAGGCACAAAAGAAACATC 59.678 43.478 0.00 0.00 0.00 3.06
2572 4577 5.468540 AATAGGGAAGGCACAAAAGAAAC 57.531 39.130 0.00 0.00 0.00 2.78
2577 4582 7.015682 TGTTTTCATAATAGGGAAGGCACAAAA 59.984 33.333 0.00 0.00 0.00 2.44
2603 4608 8.541899 AGAGTAGCTAGCTAGAATAAGGTTTT 57.458 34.615 24.78 0.00 0.00 2.43
2605 4610 9.643735 TTTAGAGTAGCTAGCTAGAATAAGGTT 57.356 33.333 24.78 6.06 0.00 3.50
2606 4611 9.292195 CTTTAGAGTAGCTAGCTAGAATAAGGT 57.708 37.037 24.78 6.91 0.00 3.50
2696 4962 3.191371 GGTCAGCTGTTTTGTTATCCAGG 59.809 47.826 14.67 0.00 0.00 4.45
2747 5013 2.918712 ACTGGACCAAGAGTTCACAG 57.081 50.000 0.00 0.00 33.65 3.66
2915 6485 7.283127 ACTCGCATTTGTTCATATACTGGAATT 59.717 33.333 0.00 0.00 0.00 2.17
2938 6508 1.351350 ACCCAGGCTAGGTTTTGACTC 59.649 52.381 0.00 0.00 32.05 3.36
2995 6565 4.543590 TCCTCTGCTTTCTGTAAAGAGG 57.456 45.455 10.19 10.19 44.14 3.69
2996 6566 7.495901 TCATATCCTCTGCTTTCTGTAAAGAG 58.504 38.462 2.15 0.00 44.14 2.85
2997 6567 7.423844 TCATATCCTCTGCTTTCTGTAAAGA 57.576 36.000 2.15 0.00 44.14 2.52
2998 6568 8.674263 AATCATATCCTCTGCTTTCTGTAAAG 57.326 34.615 0.00 0.00 44.21 1.85
3009 6580 5.163281 AGGTGATGAATCATATCCTCTGC 57.837 43.478 11.21 0.00 39.30 4.26
3120 6817 2.341846 AAATGGGTGGGTATGTAGCG 57.658 50.000 0.00 0.00 0.00 4.26
3121 6818 6.322712 TCAAAATAAATGGGTGGGTATGTAGC 59.677 38.462 0.00 0.00 0.00 3.58
3122 6819 7.559897 AGTCAAAATAAATGGGTGGGTATGTAG 59.440 37.037 0.00 0.00 0.00 2.74
3123 6820 7.340743 CAGTCAAAATAAATGGGTGGGTATGTA 59.659 37.037 0.00 0.00 0.00 2.29
3124 6821 6.154363 CAGTCAAAATAAATGGGTGGGTATGT 59.846 38.462 0.00 0.00 0.00 2.29
3125 6822 6.379703 TCAGTCAAAATAAATGGGTGGGTATG 59.620 38.462 0.00 0.00 0.00 2.39
3126 6823 6.498538 TCAGTCAAAATAAATGGGTGGGTAT 58.501 36.000 0.00 0.00 0.00 2.73
3127 6824 5.893500 TCAGTCAAAATAAATGGGTGGGTA 58.106 37.500 0.00 0.00 0.00 3.69
3128 6825 4.746466 TCAGTCAAAATAAATGGGTGGGT 58.254 39.130 0.00 0.00 0.00 4.51
3129 6826 5.937975 ATCAGTCAAAATAAATGGGTGGG 57.062 39.130 0.00 0.00 0.00 4.61
3130 6827 9.316730 CAATTATCAGTCAAAATAAATGGGTGG 57.683 33.333 0.00 0.00 0.00 4.61
3131 6828 8.819974 GCAATTATCAGTCAAAATAAATGGGTG 58.180 33.333 0.00 0.00 0.00 4.61
3132 6829 8.761689 AGCAATTATCAGTCAAAATAAATGGGT 58.238 29.630 0.00 0.00 0.00 4.51
3137 6834 8.402472 CGGGTAGCAATTATCAGTCAAAATAAA 58.598 33.333 0.00 0.00 0.00 1.40
3138 6835 7.012894 CCGGGTAGCAATTATCAGTCAAAATAA 59.987 37.037 0.00 0.00 0.00 1.40
3139 6836 6.485313 CCGGGTAGCAATTATCAGTCAAAATA 59.515 38.462 0.00 0.00 0.00 1.40
3140 6837 5.299279 CCGGGTAGCAATTATCAGTCAAAAT 59.701 40.000 0.00 0.00 0.00 1.82
3141 6838 4.638421 CCGGGTAGCAATTATCAGTCAAAA 59.362 41.667 0.00 0.00 0.00 2.44
3142 6839 4.196193 CCGGGTAGCAATTATCAGTCAAA 58.804 43.478 0.00 0.00 0.00 2.69
3143 6840 3.804036 CCGGGTAGCAATTATCAGTCAA 58.196 45.455 0.00 0.00 0.00 3.18
3144 6841 2.484770 GCCGGGTAGCAATTATCAGTCA 60.485 50.000 2.18 0.00 0.00 3.41
3145 6842 2.143925 GCCGGGTAGCAATTATCAGTC 58.856 52.381 2.18 0.00 0.00 3.51
3146 6843 1.202770 GGCCGGGTAGCAATTATCAGT 60.203 52.381 2.18 0.00 0.00 3.41
3147 6844 1.202758 TGGCCGGGTAGCAATTATCAG 60.203 52.381 2.18 0.00 0.00 2.90
3148 6845 0.840617 TGGCCGGGTAGCAATTATCA 59.159 50.000 2.18 0.00 0.00 2.15
3149 6846 1.812571 CATGGCCGGGTAGCAATTATC 59.187 52.381 2.18 0.00 0.00 1.75
3150 6847 1.144913 ACATGGCCGGGTAGCAATTAT 59.855 47.619 2.18 0.00 0.00 1.28
3151 6848 0.548989 ACATGGCCGGGTAGCAATTA 59.451 50.000 2.18 0.00 0.00 1.40
3152 6849 0.324275 AACATGGCCGGGTAGCAATT 60.324 50.000 2.18 0.00 0.00 2.32
3153 6850 0.751643 GAACATGGCCGGGTAGCAAT 60.752 55.000 2.18 0.00 0.00 3.56
3154 6851 1.377987 GAACATGGCCGGGTAGCAA 60.378 57.895 2.18 0.00 0.00 3.91
3155 6852 1.920734 ATGAACATGGCCGGGTAGCA 61.921 55.000 2.18 1.48 0.00 3.49
3156 6853 0.751643 AATGAACATGGCCGGGTAGC 60.752 55.000 2.18 0.00 0.00 3.58
3157 6854 1.134098 AGAATGAACATGGCCGGGTAG 60.134 52.381 2.18 0.00 0.00 3.18
3158 6855 0.916086 AGAATGAACATGGCCGGGTA 59.084 50.000 2.18 0.00 0.00 3.69
3159 6856 0.039618 AAGAATGAACATGGCCGGGT 59.960 50.000 2.18 0.00 0.00 5.28
3160 6857 0.457035 CAAGAATGAACATGGCCGGG 59.543 55.000 2.18 0.00 0.00 5.73
3161 6858 1.176527 ACAAGAATGAACATGGCCGG 58.823 50.000 0.00 0.00 0.00 6.13
3162 6859 2.489329 AGAACAAGAATGAACATGGCCG 59.511 45.455 0.00 0.00 0.00 6.13
3163 6860 3.841643 CAGAACAAGAATGAACATGGCC 58.158 45.455 0.00 0.00 0.00 5.36
3164 6861 3.248266 GCAGAACAAGAATGAACATGGC 58.752 45.455 0.00 0.00 0.00 4.40
3165 6862 3.367703 GGGCAGAACAAGAATGAACATGG 60.368 47.826 0.00 0.00 0.00 3.66
3166 6863 3.367703 GGGGCAGAACAAGAATGAACATG 60.368 47.826 0.00 0.00 0.00 3.21
3167 6864 2.827921 GGGGCAGAACAAGAATGAACAT 59.172 45.455 0.00 0.00 0.00 2.71
3168 6865 2.238521 GGGGCAGAACAAGAATGAACA 58.761 47.619 0.00 0.00 0.00 3.18
3169 6866 2.229784 CTGGGGCAGAACAAGAATGAAC 59.770 50.000 0.00 0.00 32.44 3.18
3170 6867 2.517959 CTGGGGCAGAACAAGAATGAA 58.482 47.619 0.00 0.00 32.44 2.57
3171 6868 2.205022 CTGGGGCAGAACAAGAATGA 57.795 50.000 0.00 0.00 32.44 2.57


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

AutoCloner maintained by Alex Coulton.