Multiple sequence alignment - TraesCS6B01G160600

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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 TraesCS6B01G160600 chr6B 100.000 4061 0 0 1 4061 164371069 164375129 0.000000e+00 7500.0
1 TraesCS6B01G160600 chr6B 74.074 351 87 3 1997 2344 408211663 408212012 1.520000e-29 141.0
2 TraesCS6B01G160600 chr6B 95.775 71 3 0 3991 4061 62166904 62166834 9.220000e-22 115.0
3 TraesCS6B01G160600 chr6D 92.798 3013 149 27 223 3184 86724073 86727068 0.000000e+00 4300.0
4 TraesCS6B01G160600 chr6D 89.000 500 46 6 3500 3992 86727849 86728346 9.650000e-171 610.0
5 TraesCS6B01G160600 chr6D 94.783 345 17 1 3134 3478 86727064 86727407 1.660000e-148 536.0
6 TraesCS6B01G160600 chr6D 73.043 1610 380 45 1102 2687 264441064 264442643 1.670000e-143 520.0
7 TraesCS6B01G160600 chr6A 88.279 3353 260 56 158 3440 104411209 104407920 0.000000e+00 3892.0
8 TraesCS6B01G160600 chr6A 92.888 1631 106 3 1797 3425 104402166 104400544 0.000000e+00 2361.0
9 TraesCS6B01G160600 chr6A 89.069 1665 157 19 1786 3440 104406629 104404980 0.000000e+00 2043.0
10 TraesCS6B01G160600 chr6A 88.353 498 49 2 3495 3992 104400394 104399906 1.260000e-164 590.0
11 TraesCS6B01G160600 chr6A 71.654 1524 380 44 1109 2608 373066955 373068450 1.380000e-99 374.0
12 TraesCS6B01G160600 chr6A 91.429 70 6 0 3992 4061 529607863 529607794 3.340000e-16 97.1
13 TraesCS6B01G160600 chr3B 71.636 1583 385 48 1138 2703 89354200 89352665 1.070000e-100 377.0
14 TraesCS6B01G160600 chr3B 71.110 1613 395 47 1106 2703 89093117 89094673 8.410000e-87 331.0
15 TraesCS6B01G160600 chrUn 97.143 70 2 0 3992 4061 65588545 65588476 7.130000e-23 119.0
16 TraesCS6B01G160600 chrUn 95.890 73 3 0 3989 4061 402213650 402213722 7.130000e-23 119.0
17 TraesCS6B01G160600 chrUn 98.361 61 1 0 1 61 287034375 287034315 1.540000e-19 108.0
18 TraesCS6B01G160600 chr5B 97.143 70 2 0 3992 4061 313062396 313062465 7.130000e-23 119.0
19 TraesCS6B01G160600 chr5B 95.588 68 3 0 3994 4061 4065387 4065454 4.290000e-20 110.0
20 TraesCS6B01G160600 chr1A 95.890 73 3 0 3989 4061 169574002 169573930 7.130000e-23 119.0
21 TraesCS6B01G160600 chr1A 97.143 70 2 0 3992 4061 464893752 464893683 7.130000e-23 119.0
22 TraesCS6B01G160600 chr2B 95.714 70 3 0 3992 4061 85700931 85701000 3.320000e-21 113.0
23 TraesCS6B01G160600 chr2B 92.857 70 5 0 1 70 251134844 251134775 7.180000e-18 102.0
24 TraesCS6B01G160600 chr1B 98.387 62 1 0 1 62 113928296 113928357 4.290000e-20 110.0
25 TraesCS6B01G160600 chr1B 98.361 61 1 0 1 61 85478099 85478159 1.540000e-19 108.0
26 TraesCS6B01G160600 chr1B 98.361 61 1 0 1 61 590353081 590353141 1.540000e-19 108.0
27 TraesCS6B01G160600 chr1B 98.361 61 1 0 1 61 661634112 661634052 1.540000e-19 108.0
28 TraesCS6B01G160600 chr1B 98.361 61 1 0 1 61 661769456 661769396 1.540000e-19 108.0
29 TraesCS6B01G160600 chr4B 98.361 61 1 0 1 61 33463450 33463390 1.540000e-19 108.0
30 TraesCS6B01G160600 chr4B 98.361 61 1 0 1 61 637847491 637847551 1.540000e-19 108.0
31 TraesCS6B01G160600 chr5A 77.128 188 38 3 3803 3986 509123408 509123594 2.000000e-18 104.0
32 TraesCS6B01G160600 chr2A 94.595 37 2 0 3946 3982 721415504 721415540 1.580000e-04 58.4


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 TraesCS6B01G160600 chr6B 164371069 164375129 4060 False 7500.000000 7500 100.000000 1 4061 1 chr6B.!!$F1 4060
1 TraesCS6B01G160600 chr6D 86724073 86728346 4273 False 1815.333333 4300 92.193667 223 3992 3 chr6D.!!$F2 3769
2 TraesCS6B01G160600 chr6D 264441064 264442643 1579 False 520.000000 520 73.043000 1102 2687 1 chr6D.!!$F1 1585
3 TraesCS6B01G160600 chr6A 104399906 104411209 11303 True 2221.500000 3892 89.647250 158 3992 4 chr6A.!!$R2 3834
4 TraesCS6B01G160600 chr6A 373066955 373068450 1495 False 374.000000 374 71.654000 1109 2608 1 chr6A.!!$F1 1499
5 TraesCS6B01G160600 chr3B 89352665 89354200 1535 True 377.000000 377 71.636000 1138 2703 1 chr3B.!!$R1 1565
6 TraesCS6B01G160600 chr3B 89093117 89094673 1556 False 331.000000 331 71.110000 1106 2703 1 chr3B.!!$F1 1597

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
984 1043 0.109272 TGCCTCGTCGTCACTTCATC 60.109 55.0 0.00 0.0 0.00 2.92 F
1575 1661 0.026027 CTGGCTACTACGACGACGAC 59.974 60.0 15.32 0.0 42.66 4.34 F
1749 1835 0.386476 ACAACTTGTCGACCGTGCTA 59.614 50.0 14.12 0.0 0.00 3.49 F
2791 10264 0.694771 TGAGGCAGCAGATCCAAAGT 59.305 50.0 0.00 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2772 10245 0.694771 ACTTTGGATCTGCTGCCTCA 59.305 50.0 0.00 0.00 0.00 3.86 R
3024 10497 0.464036 GGTCAGATATGGTGCCGACA 59.536 55.0 0.00 0.00 0.00 4.35 R
3045 10518 0.976641 AGTGTCATCTTCCGCCAGAA 59.023 50.0 0.00 0.00 0.00 3.02 R
4016 11963 0.025001 CATTAAACTGGACGAGCGCG 59.975 55.0 8.75 8.75 44.79 6.86 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
27 28 9.998106 ACTAACATTAGTACAAAGTTGAGTCAT 57.002 29.630 2.38 0.00 41.92 3.06
35 36 8.281212 AGTACAAAGTTGAGTCATTTTTGAGT 57.719 30.769 24.96 13.32 33.98 3.41
36 37 8.398665 AGTACAAAGTTGAGTCATTTTTGAGTC 58.601 33.333 24.96 17.22 38.42 3.36
37 38 7.156876 ACAAAGTTGAGTCATTTTTGAGTCA 57.843 32.000 24.96 8.96 43.96 3.41
38 39 7.029563 ACAAAGTTGAGTCATTTTTGAGTCAC 58.970 34.615 24.96 6.53 44.92 3.67
39 40 7.094205 ACAAAGTTGAGTCATTTTTGAGTCACT 60.094 33.333 24.96 8.36 44.92 3.41
40 41 7.396540 AAGTTGAGTCATTTTTGAGTCACTT 57.603 32.000 11.91 13.95 44.92 3.16
41 42 8.506168 AAGTTGAGTCATTTTTGAGTCACTTA 57.494 30.769 11.91 0.00 44.92 2.24
42 43 8.682936 AGTTGAGTCATTTTTGAGTCACTTAT 57.317 30.769 11.91 0.00 44.92 1.73
43 44 9.125026 AGTTGAGTCATTTTTGAGTCACTTATT 57.875 29.630 11.91 0.00 44.92 1.40
44 45 9.736023 GTTGAGTCATTTTTGAGTCACTTATTT 57.264 29.630 11.91 0.00 44.92 1.40
52 53 9.893305 ATTTTTGAGTCACTTATTTTAGAACGG 57.107 29.630 0.00 0.00 0.00 4.44
53 54 8.665643 TTTTGAGTCACTTATTTTAGAACGGA 57.334 30.769 0.00 0.00 0.00 4.69
54 55 7.884816 TTGAGTCACTTATTTTAGAACGGAG 57.115 36.000 0.00 0.00 0.00 4.63
55 56 6.395629 TGAGTCACTTATTTTAGAACGGAGG 58.604 40.000 0.00 0.00 0.00 4.30
56 57 5.731591 AGTCACTTATTTTAGAACGGAGGG 58.268 41.667 0.00 0.00 0.00 4.30
57 58 5.482878 AGTCACTTATTTTAGAACGGAGGGA 59.517 40.000 0.00 0.00 0.00 4.20
58 59 5.811100 GTCACTTATTTTAGAACGGAGGGAG 59.189 44.000 0.00 0.00 0.00 4.30
59 60 5.482878 TCACTTATTTTAGAACGGAGGGAGT 59.517 40.000 0.00 0.00 0.00 3.85
60 61 6.664816 TCACTTATTTTAGAACGGAGGGAGTA 59.335 38.462 0.00 0.00 0.00 2.59
61 62 7.343833 TCACTTATTTTAGAACGGAGGGAGTAT 59.656 37.037 0.00 0.00 0.00 2.12
62 63 8.636213 CACTTATTTTAGAACGGAGGGAGTATA 58.364 37.037 0.00 0.00 0.00 1.47
63 64 9.205513 ACTTATTTTAGAACGGAGGGAGTATAA 57.794 33.333 0.00 0.00 0.00 0.98
64 65 9.694137 CTTATTTTAGAACGGAGGGAGTATAAG 57.306 37.037 0.00 0.00 0.00 1.73
65 66 7.909485 ATTTTAGAACGGAGGGAGTATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
66 67 6.956202 TTTAGAACGGAGGGAGTATAAGAG 57.044 41.667 0.00 0.00 0.00 2.85
67 68 4.792513 AGAACGGAGGGAGTATAAGAGA 57.207 45.455 0.00 0.00 0.00 3.10
68 69 5.126699 AGAACGGAGGGAGTATAAGAGAA 57.873 43.478 0.00 0.00 0.00 2.87
69 70 5.134661 AGAACGGAGGGAGTATAAGAGAAG 58.865 45.833 0.00 0.00 0.00 2.85
70 71 4.792513 ACGGAGGGAGTATAAGAGAAGA 57.207 45.455 0.00 0.00 0.00 2.87
71 72 5.126699 ACGGAGGGAGTATAAGAGAAGAA 57.873 43.478 0.00 0.00 0.00 2.52
72 73 5.134661 ACGGAGGGAGTATAAGAGAAGAAG 58.865 45.833 0.00 0.00 0.00 2.85
73 74 5.104024 ACGGAGGGAGTATAAGAGAAGAAGA 60.104 44.000 0.00 0.00 0.00 2.87
74 75 5.472137 CGGAGGGAGTATAAGAGAAGAAGAG 59.528 48.000 0.00 0.00 0.00 2.85
75 76 5.773176 GGAGGGAGTATAAGAGAAGAAGAGG 59.227 48.000 0.00 0.00 0.00 3.69
76 77 5.711698 AGGGAGTATAAGAGAAGAAGAGGG 58.288 45.833 0.00 0.00 0.00 4.30
77 78 5.437043 AGGGAGTATAAGAGAAGAAGAGGGA 59.563 44.000 0.00 0.00 0.00 4.20
78 79 5.773176 GGGAGTATAAGAGAAGAAGAGGGAG 59.227 48.000 0.00 0.00 0.00 4.30
79 80 6.411086 GGGAGTATAAGAGAAGAAGAGGGAGA 60.411 46.154 0.00 0.00 0.00 3.71
80 81 7.064229 GGAGTATAAGAGAAGAAGAGGGAGAA 58.936 42.308 0.00 0.00 0.00 2.87
81 82 7.728532 GGAGTATAAGAGAAGAAGAGGGAGAAT 59.271 40.741 0.00 0.00 0.00 2.40
82 83 8.706322 AGTATAAGAGAAGAAGAGGGAGAATC 57.294 38.462 0.00 0.00 0.00 2.52
83 84 8.285891 AGTATAAGAGAAGAAGAGGGAGAATCA 58.714 37.037 0.00 0.00 36.25 2.57
84 85 5.937975 AAGAGAAGAAGAGGGAGAATCAG 57.062 43.478 0.00 0.00 36.25 2.90
85 86 4.946646 AGAGAAGAAGAGGGAGAATCAGT 58.053 43.478 0.00 0.00 36.25 3.41
86 87 5.341169 AGAGAAGAAGAGGGAGAATCAGTT 58.659 41.667 0.00 0.00 36.25 3.16
87 88 5.784906 AGAGAAGAAGAGGGAGAATCAGTTT 59.215 40.000 0.00 0.00 36.25 2.66
88 89 6.272090 AGAGAAGAAGAGGGAGAATCAGTTTT 59.728 38.462 0.00 0.00 36.25 2.43
89 90 6.846988 AGAAGAAGAGGGAGAATCAGTTTTT 58.153 36.000 0.00 0.00 36.25 1.94
90 91 6.939730 AGAAGAAGAGGGAGAATCAGTTTTTC 59.060 38.462 0.00 0.00 36.25 2.29
91 92 6.446909 AGAAGAGGGAGAATCAGTTTTTCT 57.553 37.500 0.00 0.00 36.25 2.52
92 93 6.846988 AGAAGAGGGAGAATCAGTTTTTCTT 58.153 36.000 0.00 0.00 36.25 2.52
93 94 6.939730 AGAAGAGGGAGAATCAGTTTTTCTTC 59.060 38.462 0.00 0.00 38.68 2.87
94 95 6.446909 AGAGGGAGAATCAGTTTTTCTTCT 57.553 37.500 0.00 0.00 36.25 2.85
95 96 6.846988 AGAGGGAGAATCAGTTTTTCTTCTT 58.153 36.000 0.00 0.00 36.25 2.52
96 97 7.293828 AGAGGGAGAATCAGTTTTTCTTCTTT 58.706 34.615 0.00 0.00 36.25 2.52
97 98 8.440771 AGAGGGAGAATCAGTTTTTCTTCTTTA 58.559 33.333 0.00 0.00 36.25 1.85
98 99 8.397575 AGGGAGAATCAGTTTTTCTTCTTTAC 57.602 34.615 0.00 0.00 36.25 2.01
99 100 7.998964 AGGGAGAATCAGTTTTTCTTCTTTACA 59.001 33.333 0.00 0.00 36.25 2.41
100 101 8.797438 GGGAGAATCAGTTTTTCTTCTTTACAT 58.203 33.333 0.00 0.00 36.25 2.29
101 102 9.617975 GGAGAATCAGTTTTTCTTCTTTACATG 57.382 33.333 0.00 0.00 36.25 3.21
107 108 9.173021 TCAGTTTTTCTTCTTTACATGAGTTCA 57.827 29.630 0.00 0.00 0.00 3.18
108 109 9.956720 CAGTTTTTCTTCTTTACATGAGTTCAT 57.043 29.630 0.00 0.00 36.96 2.57
141 142 5.697473 TTTTTGCGATAGACACAAATCCA 57.303 34.783 0.00 0.00 33.62 3.41
142 143 4.678509 TTTGCGATAGACACAAATCCAC 57.321 40.909 0.00 0.00 39.76 4.02
143 144 3.610040 TGCGATAGACACAAATCCACT 57.390 42.857 0.00 0.00 39.76 4.00
144 145 3.937814 TGCGATAGACACAAATCCACTT 58.062 40.909 0.00 0.00 39.76 3.16
145 146 5.079689 TGCGATAGACACAAATCCACTTA 57.920 39.130 0.00 0.00 39.76 2.24
146 147 5.670485 TGCGATAGACACAAATCCACTTAT 58.330 37.500 0.00 0.00 39.76 1.73
147 148 6.811954 TGCGATAGACACAAATCCACTTATA 58.188 36.000 0.00 0.00 39.76 0.98
148 149 6.923508 TGCGATAGACACAAATCCACTTATAG 59.076 38.462 0.00 0.00 39.76 1.31
149 150 7.145985 GCGATAGACACAAATCCACTTATAGA 58.854 38.462 0.00 0.00 39.76 1.98
150 151 7.327275 GCGATAGACACAAATCCACTTATAGAG 59.673 40.741 0.00 0.00 39.76 2.43
151 152 8.568794 CGATAGACACAAATCCACTTATAGAGA 58.431 37.037 0.00 0.00 39.76 3.10
152 153 9.906660 GATAGACACAAATCCACTTATAGAGAG 57.093 37.037 0.00 0.00 0.00 3.20
153 154 7.726033 AGACACAAATCCACTTATAGAGAGT 57.274 36.000 0.00 0.00 0.00 3.24
154 155 7.777095 AGACACAAATCCACTTATAGAGAGTC 58.223 38.462 0.00 0.00 0.00 3.36
155 156 7.397476 AGACACAAATCCACTTATAGAGAGTCA 59.603 37.037 0.00 0.00 0.00 3.41
156 157 7.907389 ACACAAATCCACTTATAGAGAGTCAA 58.093 34.615 0.00 0.00 0.00 3.18
173 174 9.535878 AGAGAGTCAATAGTTAATTTCCGATTC 57.464 33.333 0.00 0.00 0.00 2.52
186 187 6.566197 ATTTCCGATTCTCATGCTTAATCC 57.434 37.500 8.16 0.00 0.00 3.01
193 194 5.965033 TTCTCATGCTTAATCCCTTCTCT 57.035 39.130 0.00 0.00 0.00 3.10
194 195 5.965033 TCTCATGCTTAATCCCTTCTCTT 57.035 39.130 0.00 0.00 0.00 2.85
249 251 8.861033 AATCATTTACATGTACATCAATGCAC 57.139 30.769 17.57 0.00 0.00 4.57
256 258 2.746904 TGTACATCAATGCACCCGAAAG 59.253 45.455 0.00 0.00 0.00 2.62
272 274 4.219033 CCGAAAGAAATCAACCTTTGACG 58.781 43.478 0.00 0.00 43.48 4.35
273 275 4.024387 CCGAAAGAAATCAACCTTTGACGA 60.024 41.667 0.00 0.00 43.48 4.20
305 309 0.229247 CGTTGCACATTGTTTTGCGG 59.771 50.000 0.00 0.00 41.96 5.69
339 344 2.821366 CCAGCTGATGCGACACCC 60.821 66.667 17.39 0.00 45.42 4.61
340 345 2.267006 CAGCTGATGCGACACCCT 59.733 61.111 8.42 0.00 45.42 4.34
341 346 1.517361 CAGCTGATGCGACACCCTA 59.483 57.895 8.42 0.00 45.42 3.53
342 347 0.529337 CAGCTGATGCGACACCCTAG 60.529 60.000 8.42 0.00 45.42 3.02
371 376 9.757227 TGTTTGGATCATCGAAACTAAATTTTT 57.243 25.926 21.64 0.00 42.87 1.94
472 498 2.572191 AATCAATCAACAGCATGCCG 57.428 45.000 15.66 6.75 42.53 5.69
516 545 8.131100 CCAGCAAGTTTATATTGGAATGTAGTG 58.869 37.037 0.00 0.00 0.00 2.74
520 549 8.345565 CAAGTTTATATTGGAATGTAGTGCCTC 58.654 37.037 0.00 0.00 0.00 4.70
761 809 1.747355 CATGTGGCTCACCTTCATTCC 59.253 52.381 0.00 0.00 36.63 3.01
796 844 4.250464 TCCATGTTCAAAGATACACGTCC 58.750 43.478 0.00 0.00 0.00 4.79
885 944 9.689976 CTGAGTCAGATAATTAATACTGTCCAG 57.310 37.037 15.46 13.42 32.44 3.86
906 965 0.521735 GAAACCAGTCCGCCATTGAC 59.478 55.000 0.00 0.00 0.00 3.18
930 989 3.659786 TGTGACTTTCATACAACCTCGG 58.340 45.455 0.00 0.00 0.00 4.63
931 990 3.070446 TGTGACTTTCATACAACCTCGGT 59.930 43.478 0.00 0.00 0.00 4.69
932 991 3.678548 GTGACTTTCATACAACCTCGGTC 59.321 47.826 0.00 0.00 0.00 4.79
933 992 2.921754 GACTTTCATACAACCTCGGTCG 59.078 50.000 0.00 0.00 0.00 4.79
974 1033 0.319555 TTCAGAAAGGTGCCTCGTCG 60.320 55.000 0.00 0.00 0.00 5.12
975 1034 1.006102 CAGAAAGGTGCCTCGTCGT 60.006 57.895 0.00 0.00 0.00 4.34
976 1035 1.009389 CAGAAAGGTGCCTCGTCGTC 61.009 60.000 0.00 0.00 0.00 4.20
977 1036 1.006571 GAAAGGTGCCTCGTCGTCA 60.007 57.895 0.00 0.00 0.00 4.35
983 1042 0.388649 GTGCCTCGTCGTCACTTCAT 60.389 55.000 0.00 0.00 0.00 2.57
984 1043 0.109272 TGCCTCGTCGTCACTTCATC 60.109 55.000 0.00 0.00 0.00 2.92
985 1044 0.109272 GCCTCGTCGTCACTTCATCA 60.109 55.000 0.00 0.00 0.00 3.07
986 1045 1.901538 CCTCGTCGTCACTTCATCAG 58.098 55.000 0.00 0.00 0.00 2.90
987 1046 1.263776 CTCGTCGTCACTTCATCAGC 58.736 55.000 0.00 0.00 0.00 4.26
1009 1068 1.815421 AGTCCACGAATGGCGATGC 60.815 57.895 0.00 0.00 46.80 3.91
1024 1083 1.747709 GATGCTGCACATGTCCTTCT 58.252 50.000 3.57 0.00 39.84 2.85
1032 1091 2.679349 GCACATGTCCTTCTTCCTCCTC 60.679 54.545 0.00 0.00 0.00 3.71
1053 1112 2.685380 CCCTTCCTCTCCGCTGGT 60.685 66.667 0.00 0.00 0.00 4.00
1058 1117 1.067821 CTTCCTCTCCGCTGGTATCAC 59.932 57.143 0.00 0.00 0.00 3.06
1068 1127 1.134371 GCTGGTATCACCCTTCCACTC 60.134 57.143 0.00 0.00 37.50 3.51
1072 1131 2.127708 GTATCACCCTTCCACTCCCAT 58.872 52.381 0.00 0.00 0.00 4.00
1574 1660 1.699656 GCTGGCTACTACGACGACGA 61.700 60.000 15.32 0.00 42.66 4.20
1575 1661 0.026027 CTGGCTACTACGACGACGAC 59.974 60.000 15.32 0.00 42.66 4.34
1576 1662 1.012889 GGCTACTACGACGACGACG 60.013 63.158 17.60 17.60 42.66 5.12
1735 1821 1.152963 GTCAGCACCACCCACAACT 60.153 57.895 0.00 0.00 0.00 3.16
1749 1835 0.386476 ACAACTTGTCGACCGTGCTA 59.614 50.000 14.12 0.00 0.00 3.49
1750 1836 1.000506 ACAACTTGTCGACCGTGCTAT 59.999 47.619 14.12 0.00 0.00 2.97
1857 1943 4.569180 CCTGCCCCGGCGATTGAT 62.569 66.667 9.30 0.00 45.51 2.57
1944 2030 3.051392 GCCAATAGCAAGCGCGGTT 62.051 57.895 19.31 19.31 45.49 4.44
2064 2150 1.523934 CGTTTCGCGTACAAAGACCTT 59.476 47.619 5.77 0.00 35.54 3.50
2100 2186 1.239347 GGTTCAAGGACAAGCACCTC 58.761 55.000 0.00 0.00 36.67 3.85
2619 10092 1.890894 GCCGGAGCTAGTGAGAACA 59.109 57.895 5.05 0.00 35.50 3.18
2650 10123 1.486726 CCCCTCTAACCGATGCTTTCT 59.513 52.381 0.00 0.00 0.00 2.52
2789 10262 1.538047 GTTGAGGCAGCAGATCCAAA 58.462 50.000 0.00 0.00 0.00 3.28
2791 10264 0.694771 TGAGGCAGCAGATCCAAAGT 59.305 50.000 0.00 0.00 0.00 2.66
2800 10273 2.223782 GCAGATCCAAAGTTGCAACACA 60.224 45.455 30.11 9.99 36.59 3.72
3016 10489 2.766263 TCAAGCCCATTCTCATCTACGT 59.234 45.455 0.00 0.00 0.00 3.57
3024 10497 4.023622 CCATTCTCATCTACGTCGATGACT 60.024 45.833 24.29 12.10 43.47 3.41
3045 10518 1.139058 GTCGGCACCATATCTGACCTT 59.861 52.381 0.00 0.00 33.61 3.50
3183 10704 8.321353 TGACATGATAAGTGGATCTTGTTAACT 58.679 33.333 7.22 0.00 41.66 2.24
3185 10706 6.985188 TGATAAGTGGATCTTGTTAACTGC 57.015 37.500 7.22 0.00 37.56 4.40
3363 10884 6.317893 ACAAGGTTTCGAGTTTACTTGACAAT 59.682 34.615 17.98 1.02 38.80 2.71
3387 10908 2.695359 TCTTGTCGGACATGGTTTAGC 58.305 47.619 19.97 0.00 0.00 3.09
3464 10985 2.817665 ACTTAGACCACTACACTCCCC 58.182 52.381 0.00 0.00 0.00 4.81
3478 10999 2.236395 CACTCCCCGGTCTACTTTCAAT 59.764 50.000 0.00 0.00 0.00 2.57
3480 11001 3.270877 CTCCCCGGTCTACTTTCAATTG 58.729 50.000 0.00 0.00 0.00 2.32
3481 11002 2.026636 TCCCCGGTCTACTTTCAATTGG 60.027 50.000 5.42 0.00 0.00 3.16
3482 11003 1.743394 CCCGGTCTACTTTCAATTGGC 59.257 52.381 5.42 0.00 0.00 4.52
3483 11004 1.743394 CCGGTCTACTTTCAATTGGCC 59.257 52.381 5.42 0.00 0.00 5.36
3485 11006 2.618045 CGGTCTACTTTCAATTGGCCCT 60.618 50.000 5.42 0.00 0.00 5.19
3486 11007 3.017442 GGTCTACTTTCAATTGGCCCTC 58.983 50.000 5.42 0.00 0.00 4.30
3488 11009 2.017049 CTACTTTCAATTGGCCCTCCG 58.983 52.381 5.42 0.00 34.14 4.63
3489 11010 1.250840 ACTTTCAATTGGCCCTCCGC 61.251 55.000 5.42 0.00 34.14 5.54
3526 11467 2.266055 CTCCGCCACTCCCAGAAC 59.734 66.667 0.00 0.00 0.00 3.01
3564 11505 3.300388 AGTTAGAGATTGATCCGGCTGA 58.700 45.455 0.00 0.00 0.00 4.26
3664 11606 1.249407 GTGGTGAGGTTCGTCTCTCT 58.751 55.000 0.00 0.00 34.98 3.10
3684 11626 2.813726 CCCAACTCCGGTGTGGACA 61.814 63.158 20.03 0.00 43.74 4.02
3780 11722 0.670546 CGACATGGCCTTGAACGAGT 60.671 55.000 24.48 1.12 0.00 4.18
3828 11770 6.370166 CACATCCTCTAGAAGTGAAAAAGGAC 59.630 42.308 7.98 0.00 45.12 3.85
3837 11779 0.105224 TGAAAAAGGACGAGGACGCA 59.895 50.000 0.00 0.00 43.96 5.24
3839 11781 0.179067 AAAAAGGACGAGGACGCACA 60.179 50.000 0.00 0.00 43.96 4.57
3854 11796 1.079819 CACACCCTCACGCGAGAAT 60.080 57.895 15.93 0.00 42.34 2.40
3914 11856 4.294347 CAAAGAGAAGGAGGAGGATAGGT 58.706 47.826 0.00 0.00 0.00 3.08
3917 11859 4.055820 AGAGAAGGAGGAGGATAGGTACA 58.944 47.826 0.00 0.00 0.00 2.90
3918 11860 4.672650 AGAGAAGGAGGAGGATAGGTACAT 59.327 45.833 0.00 0.00 0.00 2.29
3931 11873 1.201647 AGGTACATGTCGGACAACTCG 59.798 52.381 15.72 6.78 0.00 4.18
3932 11874 1.200716 GGTACATGTCGGACAACTCGA 59.799 52.381 15.72 0.00 0.00 4.04
3941 11883 1.405526 CGGACAACTCGAATGATGGGT 60.406 52.381 4.99 0.00 0.00 4.51
3942 11884 2.159156 CGGACAACTCGAATGATGGGTA 60.159 50.000 4.99 0.00 0.00 3.69
3984 11931 1.738350 CGTCTTCGAGCTCTACTTCCA 59.262 52.381 12.85 0.00 39.71 3.53
3992 11939 4.082895 TCGAGCTCTACTTCCACAACTAAC 60.083 45.833 12.85 0.00 0.00 2.34
3993 11940 4.082679 CGAGCTCTACTTCCACAACTAACT 60.083 45.833 12.85 0.00 0.00 2.24
3994 11941 5.123502 CGAGCTCTACTTCCACAACTAACTA 59.876 44.000 12.85 0.00 0.00 2.24
3995 11942 6.518208 AGCTCTACTTCCACAACTAACTAG 57.482 41.667 0.00 0.00 0.00 2.57
3996 11943 6.246919 AGCTCTACTTCCACAACTAACTAGA 58.753 40.000 0.00 0.00 0.00 2.43
3997 11944 6.720288 AGCTCTACTTCCACAACTAACTAGAA 59.280 38.462 0.00 0.00 0.00 2.10
3998 11945 6.807720 GCTCTACTTCCACAACTAACTAGAAC 59.192 42.308 0.00 0.00 0.00 3.01
3999 11946 7.523380 GCTCTACTTCCACAACTAACTAGAACA 60.523 40.741 0.00 0.00 0.00 3.18
4000 11947 8.418597 TCTACTTCCACAACTAACTAGAACAT 57.581 34.615 0.00 0.00 0.00 2.71
4001 11948 8.304596 TCTACTTCCACAACTAACTAGAACATG 58.695 37.037 0.00 0.00 0.00 3.21
4002 11949 7.062749 ACTTCCACAACTAACTAGAACATGA 57.937 36.000 0.00 0.00 0.00 3.07
4003 11950 7.680730 ACTTCCACAACTAACTAGAACATGAT 58.319 34.615 0.00 0.00 0.00 2.45
4004 11951 7.604164 ACTTCCACAACTAACTAGAACATGATG 59.396 37.037 0.00 0.00 0.00 3.07
4005 11952 6.406370 TCCACAACTAACTAGAACATGATGG 58.594 40.000 0.00 0.00 0.00 3.51
4006 11953 5.065218 CCACAACTAACTAGAACATGATGGC 59.935 44.000 0.00 0.00 0.00 4.40
4007 11954 4.870426 ACAACTAACTAGAACATGATGGCG 59.130 41.667 0.00 0.00 0.00 5.69
4008 11955 3.458189 ACTAACTAGAACATGATGGCGC 58.542 45.455 0.00 0.00 0.00 6.53
4009 11956 1.290203 AACTAGAACATGATGGCGCG 58.710 50.000 0.00 0.00 0.00 6.86
4010 11957 0.175760 ACTAGAACATGATGGCGCGT 59.824 50.000 8.43 0.00 0.00 6.01
4011 11958 0.578683 CTAGAACATGATGGCGCGTG 59.421 55.000 8.43 0.00 0.00 5.34
4012 11959 0.108377 TAGAACATGATGGCGCGTGT 60.108 50.000 8.43 0.00 39.58 4.49
4013 11960 3.667087 AACATGATGGCGCGTGTT 58.333 50.000 8.43 6.31 41.74 3.32
4014 11961 0.794229 GAACATGATGGCGCGTGTTG 60.794 55.000 18.52 6.49 45.30 3.33
4015 11962 2.577644 CATGATGGCGCGTGTTGC 60.578 61.111 8.43 0.00 41.47 4.17
4032 11979 2.126228 CCGCGCTCGTCCAGTTTA 60.126 61.111 5.56 0.00 0.00 2.01
4033 11980 1.735198 CCGCGCTCGTCCAGTTTAA 60.735 57.895 5.56 0.00 0.00 1.52
4034 11981 1.082117 CCGCGCTCGTCCAGTTTAAT 61.082 55.000 5.56 0.00 0.00 1.40
4035 11982 0.025001 CGCGCTCGTCCAGTTTAATG 59.975 55.000 5.56 0.00 0.00 1.90
4036 11983 0.373716 GCGCTCGTCCAGTTTAATGG 59.626 55.000 0.00 0.00 42.11 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.391006 ACTCAAAAATGACTCAACTTTGTACTA 57.609 29.630 12.53 0.00 0.00 1.82
10 11 8.281212 ACTCAAAAATGACTCAACTTTGTACT 57.719 30.769 12.53 0.48 0.00 2.73
11 12 8.181573 TGACTCAAAAATGACTCAACTTTGTAC 58.818 33.333 12.53 0.00 0.00 2.90
12 13 8.181573 GTGACTCAAAAATGACTCAACTTTGTA 58.818 33.333 12.53 3.94 0.00 2.41
13 14 7.029563 GTGACTCAAAAATGACTCAACTTTGT 58.970 34.615 12.53 0.54 0.00 2.83
14 15 7.253422 AGTGACTCAAAAATGACTCAACTTTG 58.747 34.615 8.79 8.79 0.00 2.77
15 16 7.396540 AGTGACTCAAAAATGACTCAACTTT 57.603 32.000 0.00 0.00 0.00 2.66
16 17 7.396540 AAGTGACTCAAAAATGACTCAACTT 57.603 32.000 0.00 0.00 0.00 2.66
17 18 8.682936 ATAAGTGACTCAAAAATGACTCAACT 57.317 30.769 0.00 0.00 0.00 3.16
18 19 9.736023 AAATAAGTGACTCAAAAATGACTCAAC 57.264 29.630 0.00 0.00 0.00 3.18
26 27 9.893305 CCGTTCTAAAATAAGTGACTCAAAAAT 57.107 29.630 0.00 0.00 0.00 1.82
27 28 9.111613 TCCGTTCTAAAATAAGTGACTCAAAAA 57.888 29.630 0.00 0.00 0.00 1.94
28 29 8.665643 TCCGTTCTAAAATAAGTGACTCAAAA 57.334 30.769 0.00 0.00 0.00 2.44
29 30 7.386848 CCTCCGTTCTAAAATAAGTGACTCAAA 59.613 37.037 0.00 0.00 0.00 2.69
30 31 6.872020 CCTCCGTTCTAAAATAAGTGACTCAA 59.128 38.462 0.00 0.00 0.00 3.02
31 32 6.395629 CCTCCGTTCTAAAATAAGTGACTCA 58.604 40.000 0.00 0.00 0.00 3.41
32 33 5.811100 CCCTCCGTTCTAAAATAAGTGACTC 59.189 44.000 0.00 0.00 0.00 3.36
33 34 5.482878 TCCCTCCGTTCTAAAATAAGTGACT 59.517 40.000 0.00 0.00 0.00 3.41
34 35 5.727434 TCCCTCCGTTCTAAAATAAGTGAC 58.273 41.667 0.00 0.00 0.00 3.67
35 36 5.482878 ACTCCCTCCGTTCTAAAATAAGTGA 59.517 40.000 0.00 0.00 0.00 3.41
36 37 5.731591 ACTCCCTCCGTTCTAAAATAAGTG 58.268 41.667 0.00 0.00 0.00 3.16
37 38 7.672122 ATACTCCCTCCGTTCTAAAATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
38 39 9.694137 CTTATACTCCCTCCGTTCTAAAATAAG 57.306 37.037 0.00 0.00 0.00 1.73
39 40 9.425248 TCTTATACTCCCTCCGTTCTAAAATAA 57.575 33.333 0.00 0.00 0.00 1.40
40 41 9.075678 CTCTTATACTCCCTCCGTTCTAAAATA 57.924 37.037 0.00 0.00 0.00 1.40
41 42 7.783596 TCTCTTATACTCCCTCCGTTCTAAAAT 59.216 37.037 0.00 0.00 0.00 1.82
42 43 7.121382 TCTCTTATACTCCCTCCGTTCTAAAA 58.879 38.462 0.00 0.00 0.00 1.52
43 44 6.666678 TCTCTTATACTCCCTCCGTTCTAAA 58.333 40.000 0.00 0.00 0.00 1.85
44 45 6.257994 TCTCTTATACTCCCTCCGTTCTAA 57.742 41.667 0.00 0.00 0.00 2.10
45 46 5.901413 TCTCTTATACTCCCTCCGTTCTA 57.099 43.478 0.00 0.00 0.00 2.10
46 47 4.792513 TCTCTTATACTCCCTCCGTTCT 57.207 45.455 0.00 0.00 0.00 3.01
47 48 5.131784 TCTTCTCTTATACTCCCTCCGTTC 58.868 45.833 0.00 0.00 0.00 3.95
48 49 5.126699 TCTTCTCTTATACTCCCTCCGTT 57.873 43.478 0.00 0.00 0.00 4.44
49 50 4.792513 TCTTCTCTTATACTCCCTCCGT 57.207 45.455 0.00 0.00 0.00 4.69
50 51 5.378332 TCTTCTTCTCTTATACTCCCTCCG 58.622 45.833 0.00 0.00 0.00 4.63
51 52 5.773176 CCTCTTCTTCTCTTATACTCCCTCC 59.227 48.000 0.00 0.00 0.00 4.30
52 53 5.773176 CCCTCTTCTTCTCTTATACTCCCTC 59.227 48.000 0.00 0.00 0.00 4.30
53 54 5.437043 TCCCTCTTCTTCTCTTATACTCCCT 59.563 44.000 0.00 0.00 0.00 4.20
54 55 5.707495 TCCCTCTTCTTCTCTTATACTCCC 58.293 45.833 0.00 0.00 0.00 4.30
55 56 6.607019 TCTCCCTCTTCTTCTCTTATACTCC 58.393 44.000 0.00 0.00 0.00 3.85
56 57 8.706322 ATTCTCCCTCTTCTTCTCTTATACTC 57.294 38.462 0.00 0.00 0.00 2.59
57 58 8.285891 TGATTCTCCCTCTTCTTCTCTTATACT 58.714 37.037 0.00 0.00 0.00 2.12
58 59 8.472007 TGATTCTCCCTCTTCTTCTCTTATAC 57.528 38.462 0.00 0.00 0.00 1.47
59 60 8.285891 ACTGATTCTCCCTCTTCTTCTCTTATA 58.714 37.037 0.00 0.00 0.00 0.98
60 61 7.132128 ACTGATTCTCCCTCTTCTTCTCTTAT 58.868 38.462 0.00 0.00 0.00 1.73
61 62 6.498538 ACTGATTCTCCCTCTTCTTCTCTTA 58.501 40.000 0.00 0.00 0.00 2.10
62 63 5.341169 ACTGATTCTCCCTCTTCTTCTCTT 58.659 41.667 0.00 0.00 0.00 2.85
63 64 4.946646 ACTGATTCTCCCTCTTCTTCTCT 58.053 43.478 0.00 0.00 0.00 3.10
64 65 5.675684 AACTGATTCTCCCTCTTCTTCTC 57.324 43.478 0.00 0.00 0.00 2.87
65 66 6.446909 AAAACTGATTCTCCCTCTTCTTCT 57.553 37.500 0.00 0.00 0.00 2.85
66 67 6.939730 AGAAAAACTGATTCTCCCTCTTCTTC 59.060 38.462 0.00 0.00 31.61 2.87
67 68 6.846988 AGAAAAACTGATTCTCCCTCTTCTT 58.153 36.000 0.00 0.00 31.61 2.52
68 69 6.446909 AGAAAAACTGATTCTCCCTCTTCT 57.553 37.500 0.00 0.00 31.61 2.85
69 70 6.939730 AGAAGAAAAACTGATTCTCCCTCTTC 59.060 38.462 0.00 0.00 36.14 2.87
70 71 6.846988 AGAAGAAAAACTGATTCTCCCTCTT 58.153 36.000 0.00 0.00 36.14 2.85
71 72 6.446909 AGAAGAAAAACTGATTCTCCCTCT 57.553 37.500 0.00 0.00 36.14 3.69
72 73 7.517614 AAAGAAGAAAAACTGATTCTCCCTC 57.482 36.000 0.00 0.00 36.14 4.30
73 74 7.998964 TGTAAAGAAGAAAAACTGATTCTCCCT 59.001 33.333 0.00 0.00 36.14 4.20
74 75 8.166422 TGTAAAGAAGAAAAACTGATTCTCCC 57.834 34.615 0.00 0.00 36.14 4.30
75 76 9.617975 CATGTAAAGAAGAAAAACTGATTCTCC 57.382 33.333 0.00 0.00 36.14 3.71
81 82 9.173021 TGAACTCATGTAAAGAAGAAAAACTGA 57.827 29.630 0.00 0.00 0.00 3.41
82 83 9.956720 ATGAACTCATGTAAAGAAGAAAAACTG 57.043 29.630 0.00 0.00 34.83 3.16
122 123 3.937814 AGTGGATTTGTGTCTATCGCAA 58.062 40.909 0.00 0.00 43.56 4.85
123 124 3.610040 AGTGGATTTGTGTCTATCGCA 57.390 42.857 0.00 0.00 34.52 5.10
124 125 7.145985 TCTATAAGTGGATTTGTGTCTATCGC 58.854 38.462 0.00 0.00 0.00 4.58
125 126 8.568794 TCTCTATAAGTGGATTTGTGTCTATCG 58.431 37.037 0.00 0.00 0.00 2.92
126 127 9.906660 CTCTCTATAAGTGGATTTGTGTCTATC 57.093 37.037 0.00 0.00 0.00 2.08
127 128 9.427821 ACTCTCTATAAGTGGATTTGTGTCTAT 57.572 33.333 0.00 0.00 0.00 1.98
128 129 8.824756 ACTCTCTATAAGTGGATTTGTGTCTA 57.175 34.615 0.00 0.00 0.00 2.59
129 130 7.397476 TGACTCTCTATAAGTGGATTTGTGTCT 59.603 37.037 0.00 0.00 0.00 3.41
130 131 7.548097 TGACTCTCTATAAGTGGATTTGTGTC 58.452 38.462 0.00 0.00 0.00 3.67
131 132 7.482169 TGACTCTCTATAAGTGGATTTGTGT 57.518 36.000 0.00 0.00 0.00 3.72
132 133 8.954950 ATTGACTCTCTATAAGTGGATTTGTG 57.045 34.615 0.00 0.00 0.00 3.33
147 148 9.535878 GAATCGGAAATTAACTATTGACTCTCT 57.464 33.333 0.00 0.00 0.00 3.10
148 149 9.535878 AGAATCGGAAATTAACTATTGACTCTC 57.464 33.333 0.00 0.00 0.00 3.20
149 150 9.535878 GAGAATCGGAAATTAACTATTGACTCT 57.464 33.333 0.00 0.00 0.00 3.24
150 151 9.314321 TGAGAATCGGAAATTAACTATTGACTC 57.686 33.333 0.00 0.00 38.61 3.36
151 152 9.838339 ATGAGAATCGGAAATTAACTATTGACT 57.162 29.630 0.00 0.00 38.61 3.41
152 153 9.869844 CATGAGAATCGGAAATTAACTATTGAC 57.130 33.333 0.00 0.00 38.61 3.18
153 154 8.559536 GCATGAGAATCGGAAATTAACTATTGA 58.440 33.333 0.00 0.00 38.61 2.57
154 155 8.562892 AGCATGAGAATCGGAAATTAACTATTG 58.437 33.333 0.00 0.00 38.61 1.90
155 156 8.682936 AGCATGAGAATCGGAAATTAACTATT 57.317 30.769 0.00 0.00 38.61 1.73
156 157 8.682936 AAGCATGAGAATCGGAAATTAACTAT 57.317 30.769 0.00 0.00 38.61 2.12
171 172 5.965033 AGAGAAGGGATTAAGCATGAGAA 57.035 39.130 0.00 0.00 0.00 2.87
173 174 6.600822 TCAAAAGAGAAGGGATTAAGCATGAG 59.399 38.462 0.00 0.00 0.00 2.90
186 187 5.397326 GCTAAAGCACATCAAAAGAGAAGG 58.603 41.667 0.00 0.00 41.59 3.46
229 230 4.095632 CGGGTGCATTGATGTACATGTAAA 59.904 41.667 14.43 1.80 43.87 2.01
230 231 3.625313 CGGGTGCATTGATGTACATGTAA 59.375 43.478 14.43 8.75 43.87 2.41
249 251 4.546570 GTCAAAGGTTGATTTCTTTCGGG 58.453 43.478 0.00 0.00 42.47 5.14
339 344 5.352569 AGTTTCGATGATCCAAACAAGCTAG 59.647 40.000 16.02 0.00 33.26 3.42
340 345 5.245531 AGTTTCGATGATCCAAACAAGCTA 58.754 37.500 16.02 0.00 33.26 3.32
341 346 4.074970 AGTTTCGATGATCCAAACAAGCT 58.925 39.130 16.02 0.00 33.26 3.74
342 347 4.425577 AGTTTCGATGATCCAAACAAGC 57.574 40.909 16.02 0.00 33.26 4.01
371 376 5.067273 ACAACTGATGTTTTGGACCGAATA 58.933 37.500 0.00 0.00 40.06 1.75
372 377 3.888930 ACAACTGATGTTTTGGACCGAAT 59.111 39.130 0.00 0.00 40.06 3.34
375 380 2.616376 TGACAACTGATGTTTTGGACCG 59.384 45.455 0.00 0.00 44.12 4.79
405 410 1.063792 TGCCTAATGCCACACCATCAT 60.064 47.619 0.00 0.00 40.16 2.45
429 450 1.686355 AACAATGCCGTCTGGAACAA 58.314 45.000 0.00 0.00 38.70 2.83
431 452 4.434713 AATTAACAATGCCGTCTGGAAC 57.565 40.909 0.00 0.00 37.49 3.62
472 498 1.377333 GTCCCAGCCCTGTACAAGC 60.377 63.158 9.07 9.07 0.00 4.01
595 636 5.180680 GTGTGGGTGTAATAAAAGTCCAGTC 59.819 44.000 0.00 0.00 0.00 3.51
649 693 4.456253 AGCTACCGTGACGACGCG 62.456 66.667 6.54 13.73 44.68 6.01
659 703 1.374252 AACAAGGACGCAGCTACCG 60.374 57.895 4.59 4.59 0.00 4.02
742 786 1.679944 CGGAATGAAGGTGAGCCACAT 60.680 52.381 7.49 0.00 35.86 3.21
833 881 2.026590 GTGTGAACCGACGACCGT 59.973 61.111 0.00 0.00 36.31 4.83
885 944 0.240945 CAATGGCGGACTGGTTTCAC 59.759 55.000 0.00 0.00 0.00 3.18
891 950 1.153369 ATCGTCAATGGCGGACTGG 60.153 57.895 7.59 0.00 33.11 4.00
906 965 4.031765 CGAGGTTGTATGAAAGTCACATCG 59.968 45.833 0.00 0.00 0.00 3.84
930 989 1.328680 TGTAGAATACGTCTCCGCGAC 59.671 52.381 8.23 0.00 46.99 5.19
931 990 1.655484 TGTAGAATACGTCTCCGCGA 58.345 50.000 8.23 0.00 46.99 5.87
932 991 2.107178 GTTGTAGAATACGTCTCCGCG 58.893 52.381 0.00 0.00 46.99 6.46
933 992 3.065095 AGAGTTGTAGAATACGTCTCCGC 59.935 47.826 0.00 0.00 46.99 5.54
942 1001 6.874134 GCACCTTTCTGAAGAGTTGTAGAATA 59.126 38.462 0.00 0.00 34.71 1.75
974 1033 2.999355 GGACTGAAGCTGATGAAGTGAC 59.001 50.000 0.00 0.00 0.00 3.67
975 1034 2.634453 TGGACTGAAGCTGATGAAGTGA 59.366 45.455 0.00 0.00 0.00 3.41
976 1035 2.740981 GTGGACTGAAGCTGATGAAGTG 59.259 50.000 0.00 0.00 0.00 3.16
977 1036 2.611473 CGTGGACTGAAGCTGATGAAGT 60.611 50.000 0.00 0.00 0.00 3.01
983 1042 1.338105 CCATTCGTGGACTGAAGCTGA 60.338 52.381 0.00 0.00 0.00 4.26
984 1043 1.081892 CCATTCGTGGACTGAAGCTG 58.918 55.000 0.00 0.00 0.00 4.24
985 1044 0.674895 GCCATTCGTGGACTGAAGCT 60.675 55.000 0.00 0.00 0.00 3.74
986 1045 1.796796 GCCATTCGTGGACTGAAGC 59.203 57.895 0.00 0.00 0.00 3.86
987 1046 0.389817 TCGCCATTCGTGGACTGAAG 60.390 55.000 0.00 0.00 39.67 3.02
1009 1068 2.354259 GAGGAAGAAGGACATGTGCAG 58.646 52.381 20.21 0.00 0.00 4.41
1024 1083 0.725133 AGGAAGGGGATGAGGAGGAA 59.275 55.000 0.00 0.00 0.00 3.36
1032 1091 1.764054 AGCGGAGAGGAAGGGGATG 60.764 63.158 0.00 0.00 0.00 3.51
1053 1112 2.408565 GATGGGAGTGGAAGGGTGATA 58.591 52.381 0.00 0.00 0.00 2.15
1058 1117 1.972660 GACGGATGGGAGTGGAAGGG 61.973 65.000 0.00 0.00 0.00 3.95
1723 1809 0.463116 GTCGACAAGTTGTGGGTGGT 60.463 55.000 14.57 0.00 0.00 4.16
1735 1821 1.138036 CCGATAGCACGGTCGACAA 59.862 57.895 18.91 0.00 46.70 3.18
1749 1835 1.653115 GATGTACGACGGCTCCGAT 59.347 57.895 15.95 2.79 42.83 4.18
1750 1836 2.816360 CGATGTACGACGGCTCCGA 61.816 63.158 15.95 0.00 45.77 4.55
1944 2030 2.974489 GCCGAAGACGAGGACGACA 61.974 63.158 0.00 0.00 42.66 4.35
2046 2132 3.002553 GGAAAAGGTCTTTGTACGCGAAA 59.997 43.478 15.93 1.38 32.36 3.46
2064 2150 1.727062 ACCCATTTGTGGCATGGAAA 58.273 45.000 6.42 0.00 43.70 3.13
2100 2186 1.676967 GAAGCCTCCTGCACCAAGG 60.677 63.158 0.75 0.75 44.83 3.61
2589 10062 1.604023 CTCCGGCGCTAGGTATCCT 60.604 63.158 18.94 0.00 37.71 3.24
2772 10245 0.694771 ACTTTGGATCTGCTGCCTCA 59.305 50.000 0.00 0.00 0.00 3.86
2789 10262 4.094887 CAGAGTTGTACTTGTGTTGCAACT 59.905 41.667 28.61 11.97 45.01 3.16
2791 10264 4.257731 TCAGAGTTGTACTTGTGTTGCAA 58.742 39.130 0.00 0.00 35.50 4.08
2800 10273 4.800914 GCACACCTCATCAGAGTTGTACTT 60.801 45.833 0.00 0.00 44.55 2.24
3016 10489 1.604147 ATGGTGCCGACAGTCATCGA 61.604 55.000 0.41 0.00 45.13 3.59
3024 10497 0.464036 GGTCAGATATGGTGCCGACA 59.536 55.000 0.00 0.00 0.00 4.35
3045 10518 0.976641 AGTGTCATCTTCCGCCAGAA 59.023 50.000 0.00 0.00 0.00 3.02
3183 10704 3.162147 TGTTAAGGTGCCCTAAATGCA 57.838 42.857 0.00 0.00 36.12 3.96
3185 10706 5.461032 TGTTTGTTAAGGTGCCCTAAATG 57.539 39.130 0.00 0.00 31.13 2.32
3243 10764 9.896645 ATCTGAACTATGATGTGACAGTAAAAT 57.103 29.630 0.00 0.00 31.88 1.82
3251 10772 8.886719 TCATTGAAATCTGAACTATGATGTGAC 58.113 33.333 0.00 0.00 0.00 3.67
3339 10860 5.728351 TGTCAAGTAAACTCGAAACCTTG 57.272 39.130 0.00 0.00 0.00 3.61
3363 10884 5.353123 GCTAAACCATGTCCGACAAGAATAA 59.647 40.000 5.07 0.00 0.00 1.40
3423 10944 6.704512 AGTTGTAGCAACTTTTTGTTTGTG 57.295 33.333 8.53 0.00 36.63 3.33
3432 10953 5.681639 AGTGGTCTAAGTTGTAGCAACTTT 58.318 37.500 25.64 13.88 40.58 2.66
3464 10985 1.743394 GGGCCAATTGAAAGTAGACCG 59.257 52.381 7.12 0.00 0.00 4.79
3483 11004 3.775654 GACTGGGAGTGGCGGAGG 61.776 72.222 0.00 0.00 0.00 4.30
3489 11010 2.124983 CCATGCGACTGGGAGTGG 60.125 66.667 0.00 0.00 32.28 4.00
3540 11481 4.038042 CAGCCGGATCAATCTCTAACTACA 59.962 45.833 5.05 0.00 0.00 2.74
3585 11527 4.185413 GACAGATTCGAGCGCCAA 57.815 55.556 2.29 0.00 0.00 4.52
3664 11606 3.246112 CCACACCGGAGTTGGGGA 61.246 66.667 9.46 0.00 35.34 4.81
3684 11626 2.385803 CTCCCTATAACCCTCACGTGT 58.614 52.381 16.51 0.00 0.00 4.49
3688 11630 1.061579 ACCCCTCCCTATAACCCTCAC 60.062 57.143 0.00 0.00 0.00 3.51
3715 11657 3.499737 CCCATTGCCTCGCACGAC 61.500 66.667 0.00 0.00 38.71 4.34
3718 11660 4.120331 GTGCCCATTGCCTCGCAC 62.120 66.667 0.00 0.00 44.17 5.34
3780 11722 4.262463 GGAGTTGTGGACACAGATGACTTA 60.262 45.833 5.21 0.00 42.94 2.24
3837 11779 0.456221 CTATTCTCGCGTGAGGGTGT 59.544 55.000 24.88 11.36 42.79 4.16
3839 11781 1.134560 GTTCTATTCTCGCGTGAGGGT 59.865 52.381 24.88 15.93 42.79 4.34
3845 11787 1.436336 CCCGGTTCTATTCTCGCGT 59.564 57.895 5.77 0.00 0.00 6.01
3914 11856 3.191791 TCATTCGAGTTGTCCGACATGTA 59.808 43.478 0.00 0.00 35.61 2.29
3917 11859 3.190079 CATCATTCGAGTTGTCCGACAT 58.810 45.455 1.09 0.00 35.61 3.06
3918 11860 2.606108 CATCATTCGAGTTGTCCGACA 58.394 47.619 0.00 0.00 35.61 4.35
3931 11873 0.250338 GCCGGACCTACCCATCATTC 60.250 60.000 5.05 0.00 34.64 2.67
3932 11874 0.694444 AGCCGGACCTACCCATCATT 60.694 55.000 5.05 0.00 34.64 2.57
3941 11883 0.469331 AATGGATCGAGCCGGACCTA 60.469 55.000 16.16 0.00 0.00 3.08
3942 11884 1.338136 AAATGGATCGAGCCGGACCT 61.338 55.000 16.16 0.00 0.00 3.85
3984 11931 4.870426 CGCCATCATGTTCTAGTTAGTTGT 59.130 41.667 0.00 0.00 0.00 3.32
3992 11939 0.578683 CACGCGCCATCATGTTCTAG 59.421 55.000 5.73 0.00 0.00 2.43
3993 11940 0.108377 ACACGCGCCATCATGTTCTA 60.108 50.000 5.73 0.00 0.00 2.10
3994 11941 0.955428 AACACGCGCCATCATGTTCT 60.955 50.000 5.73 0.00 29.30 3.01
3995 11942 0.794229 CAACACGCGCCATCATGTTC 60.794 55.000 5.73 0.00 33.05 3.18
3996 11943 1.209898 CAACACGCGCCATCATGTT 59.790 52.632 5.73 5.19 35.69 2.71
3997 11944 2.869646 CAACACGCGCCATCATGT 59.130 55.556 5.73 0.00 0.00 3.21
3998 11945 2.577644 GCAACACGCGCCATCATG 60.578 61.111 5.73 0.00 0.00 3.07
4015 11962 1.082117 ATTAAACTGGACGAGCGCGG 61.082 55.000 15.86 0.00 43.17 6.46
4016 11963 0.025001 CATTAAACTGGACGAGCGCG 59.975 55.000 8.75 8.75 44.79 6.86
4017 11964 0.373716 CCATTAAACTGGACGAGCGC 59.626 55.000 0.00 0.00 38.69 5.92
4018 11965 2.004583 TCCATTAAACTGGACGAGCG 57.995 50.000 0.00 0.00 40.43 5.03
4019 11966 4.759516 TTTTCCATTAAACTGGACGAGC 57.240 40.909 0.00 0.00 44.97 5.03
4021 11968 9.893634 TCTATAATTTTCCATTAAACTGGACGA 57.106 29.630 0.00 0.00 44.97 4.20


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

AutoCloner maintained by Alex Coulton.