Multiple sequence alignment - TraesCS5D01G159400

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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 TraesCS5D01G159400 chr5D 100.000 3449 0 0 1 3449 247755305 247758753 0.000000e+00 6370.0
1 TraesCS5D01G159400 chr5D 79.570 1116 197 23 178 1281 395922310 395923406 0.000000e+00 769.0
2 TraesCS5D01G159400 chr5D 82.849 344 52 6 2217 2557 395923827 395924166 5.590000e-78 302.0
3 TraesCS5D01G159400 chr5D 83.438 320 42 10 2243 2557 395725587 395725900 1.570000e-73 287.0
4 TraesCS5D01G159400 chr5D 97.619 42 1 0 2637 2678 247757900 247757941 4.770000e-09 73.1
5 TraesCS5D01G159400 chr5D 97.619 42 1 0 2596 2637 247757941 247757982 4.770000e-09 73.1
6 TraesCS5D01G159400 chr5A 92.278 1580 89 13 1080 2637 331755778 331757346 0.000000e+00 2211.0
7 TraesCS5D01G159400 chr5A 92.982 912 55 5 180 1085 331749702 331750610 0.000000e+00 1321.0
8 TraesCS5D01G159400 chr5A 91.564 486 36 5 2966 3449 331757774 331758256 0.000000e+00 665.0
9 TraesCS5D01G159400 chr5A 94.833 329 16 1 2740 3068 331757447 331757774 2.370000e-141 512.0
10 TraesCS5D01G159400 chr5A 95.413 109 5 0 2637 2745 331757305 331757413 1.270000e-39 174.0
11 TraesCS5D01G159400 chr7B 87.821 1207 115 13 183 1380 56993830 56992647 0.000000e+00 1386.0
12 TraesCS5D01G159400 chr7B 88.301 1171 116 9 180 1341 56361689 56362847 0.000000e+00 1384.0
13 TraesCS5D01G159400 chr7B 91.335 427 31 3 2212 2637 56362928 56363349 2.310000e-161 579.0
14 TraesCS5D01G159400 chr7B 91.101 427 32 4 2212 2637 56992593 56992172 1.070000e-159 573.0
15 TraesCS5D01G159400 chr7B 84.689 209 22 5 2740 2948 56992071 56991873 2.100000e-47 200.0
16 TraesCS5D01G159400 chr7B 84.211 209 23 6 2740 2948 56363450 56363648 9.770000e-46 195.0
17 TraesCS5D01G159400 chr7B 91.818 110 9 0 2637 2746 56363308 56363417 1.660000e-33 154.0
18 TraesCS5D01G159400 chr7B 90.909 110 10 0 2637 2746 56992213 56992104 7.710000e-32 148.0
19 TraesCS5D01G159400 chr7D 88.225 1172 112 11 180 1341 100650461 100651616 0.000000e+00 1376.0
20 TraesCS5D01G159400 chr7D 90.398 427 33 4 2212 2637 100651697 100652116 3.890000e-154 555.0
21 TraesCS5D01G159400 chr7D 84.211 209 23 6 2740 2948 100652217 100652415 9.770000e-46 195.0
22 TraesCS5D01G159400 chr7D 91.818 110 9 0 2637 2746 100652075 100652184 1.660000e-33 154.0
23 TraesCS5D01G159400 chr2D 83.636 330 47 6 2232 2558 550251178 550250853 1.560000e-78 303.0
24 TraesCS5D01G159400 chr2D 83.333 330 48 6 2232 2558 549738420 549738095 7.240000e-77 298.0
25 TraesCS5D01G159400 chr2D 92.432 185 10 2 1 181 620917480 620917296 9.490000e-66 261.0
26 TraesCS5D01G159400 chr2D 83.636 110 18 0 2742 2851 551148795 551148686 1.690000e-18 104.0
27 TraesCS5D01G159400 chr2B 83.333 330 48 6 2232 2558 655997303 655996978 7.240000e-77 298.0
28 TraesCS5D01G159400 chr2B 89.848 197 15 3 1 192 743204171 743203975 7.390000e-62 248.0
29 TraesCS5D01G159400 chr2B 80.714 140 23 3 2757 2896 656358758 656358623 4.710000e-19 106.0
30 TraesCS5D01G159400 chr4B 91.753 194 11 3 1 189 577019291 577019484 7.340000e-67 265.0
31 TraesCS5D01G159400 chr7A 91.534 189 12 3 4 188 321633045 321632857 1.230000e-64 257.0
32 TraesCS5D01G159400 chr1B 90.816 196 13 3 1 191 11895387 11895582 1.230000e-64 257.0
33 TraesCS5D01G159400 chr2A 91.935 186 10 3 1 181 599445900 599446085 4.420000e-64 255.0
34 TraesCS5D01G159400 chr2A 89.340 197 16 3 1 192 741021562 741021366 3.440000e-60 243.0
35 TraesCS5D01G159400 chr3D 91.892 185 10 2 1 180 141335243 141335427 1.590000e-63 254.0
36 TraesCS5D01G159400 chr3B 90.957 188 12 3 1 183 187902956 187903143 7.390000e-62 248.0


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 TraesCS5D01G159400 chr5D 247755305 247758753 3448 False 2172.066667 6370 98.412667 1 3449 3 chr5D.!!$F2 3448
1 TraesCS5D01G159400 chr5D 395922310 395924166 1856 False 535.500000 769 81.209500 178 2557 2 chr5D.!!$F3 2379
2 TraesCS5D01G159400 chr5A 331749702 331750610 908 False 1321.000000 1321 92.982000 180 1085 1 chr5A.!!$F1 905
3 TraesCS5D01G159400 chr5A 331755778 331758256 2478 False 890.500000 2211 93.522000 1080 3449 4 chr5A.!!$F2 2369
4 TraesCS5D01G159400 chr7B 56361689 56363648 1959 False 578.000000 1384 88.916250 180 2948 4 chr7B.!!$F1 2768
5 TraesCS5D01G159400 chr7B 56991873 56993830 1957 True 576.750000 1386 88.630000 183 2948 4 chr7B.!!$R1 2765
6 TraesCS5D01G159400 chr7D 100650461 100652415 1954 False 570.000000 1376 88.663000 180 2948 4 chr7D.!!$F1 2768

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
91 92 0.109723 TCTTTGTTTGGGCCGTAGCT 59.890 50.000 0.00 0.00 39.73 3.32 F
94 95 0.397187 TTGTTTGGGCCGTAGCTACA 59.603 50.000 23.21 0.03 39.73 2.74 F
95 96 0.397187 TGTTTGGGCCGTAGCTACAA 59.603 50.000 23.21 7.13 39.73 2.41 F
165 166 0.888736 TCTCCCATTGCAACACACGG 60.889 55.000 0.00 0.00 0.00 4.94 F
173 174 1.142965 GCAACACACGGGCCTTTTT 59.857 52.632 0.84 0.00 0.00 1.94 F
175 176 1.142965 AACACACGGGCCTTTTTGC 59.857 52.632 0.84 0.00 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 2376 0.819259 GGTTCTGCTTCAGTGCACCA 60.819 55.000 14.63 2.59 38.12 4.17 R
2094 2386 5.677344 GCAATTAGCTTAAGGGTTCTGCTTC 60.677 44.000 4.29 0.00 41.15 3.86 R
2170 2464 5.159209 CAGGTGCTCTGCTTTTTCATTTAG 58.841 41.667 0.00 0.00 36.60 1.85 R
2219 2527 8.062065 AGGAGTCAATCTTTTCACTAGACTAG 57.938 38.462 8.00 8.00 35.24 2.57 R
2288 2597 2.045536 CTTGGCCTGCTGACCCTC 60.046 66.667 3.32 0.00 0.00 4.30 R
2456 2766 2.315176 CCATTGGACCCAACAGTTGAA 58.685 47.619 15.36 0.79 38.88 2.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.818534 AATCTATATGCAAGCCGTGTTG 57.181 40.909 0.00 0.00 0.00 3.33
24 25 3.535280 TCTATATGCAAGCCGTGTTGA 57.465 42.857 0.00 0.00 0.00 3.18
25 26 3.867857 TCTATATGCAAGCCGTGTTGAA 58.132 40.909 0.00 0.00 0.00 2.69
26 27 4.257731 TCTATATGCAAGCCGTGTTGAAA 58.742 39.130 0.00 0.00 0.00 2.69
27 28 4.881273 TCTATATGCAAGCCGTGTTGAAAT 59.119 37.500 0.00 0.00 0.00 2.17
28 29 6.052360 TCTATATGCAAGCCGTGTTGAAATA 58.948 36.000 0.00 0.00 0.00 1.40
29 30 2.987413 TGCAAGCCGTGTTGAAATAG 57.013 45.000 0.00 0.00 0.00 1.73
30 31 2.499197 TGCAAGCCGTGTTGAAATAGA 58.501 42.857 0.00 0.00 0.00 1.98
31 32 2.881513 TGCAAGCCGTGTTGAAATAGAA 59.118 40.909 0.00 0.00 0.00 2.10
32 33 3.505680 TGCAAGCCGTGTTGAAATAGAAT 59.494 39.130 0.00 0.00 0.00 2.40
33 34 4.697828 TGCAAGCCGTGTTGAAATAGAATA 59.302 37.500 0.00 0.00 0.00 1.75
34 35 5.028375 GCAAGCCGTGTTGAAATAGAATAC 58.972 41.667 0.00 0.00 0.00 1.89
35 36 5.569413 CAAGCCGTGTTGAAATAGAATACC 58.431 41.667 0.00 0.00 0.00 2.73
36 37 5.099042 AGCCGTGTTGAAATAGAATACCT 57.901 39.130 0.00 0.00 0.00 3.08
37 38 4.876107 AGCCGTGTTGAAATAGAATACCTG 59.124 41.667 0.00 0.00 0.00 4.00
38 39 4.634443 GCCGTGTTGAAATAGAATACCTGT 59.366 41.667 0.00 0.00 0.00 4.00
39 40 5.447279 GCCGTGTTGAAATAGAATACCTGTG 60.447 44.000 0.00 0.00 0.00 3.66
40 41 5.064707 CCGTGTTGAAATAGAATACCTGTGG 59.935 44.000 0.00 0.00 0.00 4.17
41 42 5.872617 CGTGTTGAAATAGAATACCTGTGGA 59.127 40.000 0.00 0.00 0.00 4.02
42 43 6.370442 CGTGTTGAAATAGAATACCTGTGGAA 59.630 38.462 0.00 0.00 0.00 3.53
43 44 7.065803 CGTGTTGAAATAGAATACCTGTGGAAT 59.934 37.037 0.00 0.00 0.00 3.01
44 45 8.398665 GTGTTGAAATAGAATACCTGTGGAATC 58.601 37.037 0.00 0.00 0.00 2.52
45 46 8.328758 TGTTGAAATAGAATACCTGTGGAATCT 58.671 33.333 0.00 0.00 0.00 2.40
46 47 9.178758 GTTGAAATAGAATACCTGTGGAATCTT 57.821 33.333 0.00 0.00 0.00 2.40
47 48 8.737168 TGAAATAGAATACCTGTGGAATCTTG 57.263 34.615 0.00 0.00 0.00 3.02
48 49 8.548025 TGAAATAGAATACCTGTGGAATCTTGA 58.452 33.333 0.00 0.00 0.00 3.02
49 50 9.566432 GAAATAGAATACCTGTGGAATCTTGAT 57.434 33.333 0.00 0.00 0.00 2.57
50 51 8.915057 AATAGAATACCTGTGGAATCTTGATG 57.085 34.615 0.00 0.00 0.00 3.07
51 52 5.128919 AGAATACCTGTGGAATCTTGATGC 58.871 41.667 0.00 0.00 0.00 3.91
52 53 2.885135 ACCTGTGGAATCTTGATGCA 57.115 45.000 0.00 0.00 0.00 3.96
53 54 2.440409 ACCTGTGGAATCTTGATGCAC 58.560 47.619 0.00 0.00 39.31 4.57
54 55 2.040813 ACCTGTGGAATCTTGATGCACT 59.959 45.455 0.00 0.00 39.55 4.40
55 56 3.087031 CCTGTGGAATCTTGATGCACTT 58.913 45.455 0.00 0.00 39.55 3.16
56 57 3.508793 CCTGTGGAATCTTGATGCACTTT 59.491 43.478 0.00 0.00 39.55 2.66
57 58 4.021719 CCTGTGGAATCTTGATGCACTTTT 60.022 41.667 0.00 0.00 39.55 2.27
58 59 4.873817 TGTGGAATCTTGATGCACTTTTG 58.126 39.130 0.00 0.00 39.55 2.44
59 60 4.341806 TGTGGAATCTTGATGCACTTTTGT 59.658 37.500 0.00 0.00 39.55 2.83
60 61 5.534278 TGTGGAATCTTGATGCACTTTTGTA 59.466 36.000 0.00 0.00 39.55 2.41
61 62 6.088824 GTGGAATCTTGATGCACTTTTGTAG 58.911 40.000 0.00 0.00 36.35 2.74
62 63 5.183713 TGGAATCTTGATGCACTTTTGTAGG 59.816 40.000 0.00 0.00 0.00 3.18
63 64 4.708726 ATCTTGATGCACTTTTGTAGGC 57.291 40.909 0.00 0.00 0.00 3.93
64 65 3.754965 TCTTGATGCACTTTTGTAGGCT 58.245 40.909 0.00 0.00 0.00 4.58
65 66 4.905429 TCTTGATGCACTTTTGTAGGCTA 58.095 39.130 0.00 0.00 0.00 3.93
66 67 5.312895 TCTTGATGCACTTTTGTAGGCTAA 58.687 37.500 0.00 0.00 0.00 3.09
67 68 5.412594 TCTTGATGCACTTTTGTAGGCTAAG 59.587 40.000 0.00 0.00 0.00 2.18
68 69 4.905429 TGATGCACTTTTGTAGGCTAAGA 58.095 39.130 0.00 0.00 0.00 2.10
69 70 4.695455 TGATGCACTTTTGTAGGCTAAGAC 59.305 41.667 0.00 0.00 0.00 3.01
70 71 3.408634 TGCACTTTTGTAGGCTAAGACC 58.591 45.455 0.00 0.00 0.00 3.85
71 72 3.181449 TGCACTTTTGTAGGCTAAGACCA 60.181 43.478 0.00 0.00 0.00 4.02
72 73 4.010349 GCACTTTTGTAGGCTAAGACCAT 58.990 43.478 0.00 0.00 0.00 3.55
73 74 4.095036 GCACTTTTGTAGGCTAAGACCATC 59.905 45.833 0.00 0.00 0.00 3.51
74 75 5.491982 CACTTTTGTAGGCTAAGACCATCT 58.508 41.667 0.00 0.00 0.00 2.90
75 76 5.940470 CACTTTTGTAGGCTAAGACCATCTT 59.060 40.000 0.00 0.00 40.35 2.40
76 77 6.431234 CACTTTTGTAGGCTAAGACCATCTTT 59.569 38.462 0.00 0.00 37.89 2.52
77 78 6.431234 ACTTTTGTAGGCTAAGACCATCTTTG 59.569 38.462 0.00 0.00 37.89 2.77
78 79 5.499004 TTGTAGGCTAAGACCATCTTTGT 57.501 39.130 0.00 0.00 37.89 2.83
79 80 5.499004 TGTAGGCTAAGACCATCTTTGTT 57.501 39.130 0.00 0.00 37.89 2.83
80 81 5.876357 TGTAGGCTAAGACCATCTTTGTTT 58.124 37.500 0.00 0.00 37.89 2.83
81 82 5.705441 TGTAGGCTAAGACCATCTTTGTTTG 59.295 40.000 0.00 0.00 37.89 2.93
82 83 4.082125 AGGCTAAGACCATCTTTGTTTGG 58.918 43.478 0.00 0.00 37.89 3.28
83 84 3.193479 GGCTAAGACCATCTTTGTTTGGG 59.807 47.826 0.00 0.00 37.89 4.12
84 85 3.367395 GCTAAGACCATCTTTGTTTGGGC 60.367 47.826 0.00 0.00 41.73 5.36
85 86 1.632589 AGACCATCTTTGTTTGGGCC 58.367 50.000 0.00 0.00 42.45 5.80
86 87 0.243636 GACCATCTTTGTTTGGGCCG 59.756 55.000 0.00 0.00 34.73 6.13
87 88 0.469144 ACCATCTTTGTTTGGGCCGT 60.469 50.000 0.00 0.00 37.32 5.68
88 89 1.202952 ACCATCTTTGTTTGGGCCGTA 60.203 47.619 0.00 0.00 37.32 4.02
89 90 1.472480 CCATCTTTGTTTGGGCCGTAG 59.528 52.381 0.00 0.00 0.00 3.51
90 91 1.135402 CATCTTTGTTTGGGCCGTAGC 60.135 52.381 0.00 0.00 38.76 3.58
91 92 0.109723 TCTTTGTTTGGGCCGTAGCT 59.890 50.000 0.00 0.00 39.73 3.32
92 93 1.348366 TCTTTGTTTGGGCCGTAGCTA 59.652 47.619 0.00 0.00 39.73 3.32
93 94 1.467342 CTTTGTTTGGGCCGTAGCTAC 59.533 52.381 14.19 14.19 39.73 3.58
94 95 0.397187 TTGTTTGGGCCGTAGCTACA 59.603 50.000 23.21 0.03 39.73 2.74
95 96 0.397187 TGTTTGGGCCGTAGCTACAA 59.603 50.000 23.21 7.13 39.73 2.41
96 97 1.202782 TGTTTGGGCCGTAGCTACAAA 60.203 47.619 23.21 12.61 40.72 2.83
97 98 2.089201 GTTTGGGCCGTAGCTACAAAT 58.911 47.619 23.21 0.00 42.90 2.32
98 99 2.490509 GTTTGGGCCGTAGCTACAAATT 59.509 45.455 23.21 0.00 42.90 1.82
99 100 2.032680 TGGGCCGTAGCTACAAATTC 57.967 50.000 23.21 9.02 39.73 2.17
100 101 1.557832 TGGGCCGTAGCTACAAATTCT 59.442 47.619 23.21 0.00 39.73 2.40
101 102 2.210961 GGGCCGTAGCTACAAATTCTC 58.789 52.381 23.21 3.68 39.73 2.87
102 103 2.419574 GGGCCGTAGCTACAAATTCTCA 60.420 50.000 23.21 0.00 39.73 3.27
103 104 2.866762 GGCCGTAGCTACAAATTCTCAG 59.133 50.000 23.21 3.89 39.73 3.35
104 105 3.430374 GGCCGTAGCTACAAATTCTCAGA 60.430 47.826 23.21 0.00 39.73 3.27
105 106 4.372656 GCCGTAGCTACAAATTCTCAGAT 58.627 43.478 23.21 0.00 35.50 2.90
106 107 4.811557 GCCGTAGCTACAAATTCTCAGATT 59.188 41.667 23.21 0.00 35.50 2.40
107 108 5.983720 GCCGTAGCTACAAATTCTCAGATTA 59.016 40.000 23.21 0.00 35.50 1.75
108 109 6.647067 GCCGTAGCTACAAATTCTCAGATTAT 59.353 38.462 23.21 0.00 35.50 1.28
109 110 7.813148 GCCGTAGCTACAAATTCTCAGATTATA 59.187 37.037 23.21 0.00 35.50 0.98
110 111 9.347934 CCGTAGCTACAAATTCTCAGATTATAG 57.652 37.037 23.21 0.77 0.00 1.31
163 164 3.451141 TTTTCTCCCATTGCAACACAC 57.549 42.857 0.00 0.00 0.00 3.82
164 165 0.950836 TTCTCCCATTGCAACACACG 59.049 50.000 0.00 0.00 0.00 4.49
165 166 0.888736 TCTCCCATTGCAACACACGG 60.889 55.000 0.00 0.00 0.00 4.94
166 167 1.865788 CTCCCATTGCAACACACGGG 61.866 60.000 0.00 7.33 34.81 5.28
167 168 2.049248 CCATTGCAACACACGGGC 60.049 61.111 0.00 0.00 0.00 6.13
168 169 2.049248 CATTGCAACACACGGGCC 60.049 61.111 0.00 0.00 0.00 5.80
169 170 2.203480 ATTGCAACACACGGGCCT 60.203 55.556 0.00 0.00 0.00 5.19
170 171 1.832167 ATTGCAACACACGGGCCTT 60.832 52.632 0.00 0.00 0.00 4.35
171 172 1.398958 ATTGCAACACACGGGCCTTT 61.399 50.000 0.00 0.00 0.00 3.11
172 173 1.608717 TTGCAACACACGGGCCTTTT 61.609 50.000 0.84 0.00 0.00 2.27
173 174 1.142965 GCAACACACGGGCCTTTTT 59.857 52.632 0.84 0.00 0.00 1.94
174 175 1.151172 GCAACACACGGGCCTTTTTG 61.151 55.000 0.84 0.00 0.00 2.44
175 176 1.142965 AACACACGGGCCTTTTTGC 59.857 52.632 0.84 0.00 0.00 3.68
176 177 1.326951 AACACACGGGCCTTTTTGCT 61.327 50.000 0.84 0.00 0.00 3.91
302 303 6.916360 AGAAAAATTTGATGCCCTTCTGTA 57.084 33.333 0.00 0.00 0.00 2.74
324 325 5.543507 ATGGTGTTGATTTAACTGGCAAA 57.456 34.783 0.00 0.00 40.05 3.68
363 364 2.218603 GGTGGTCTCTCAAGCGAAAAA 58.781 47.619 0.00 0.00 0.00 1.94
391 392 2.677836 TGTGTGCAGCCGATATCTTTTC 59.322 45.455 0.34 0.00 0.00 2.29
595 596 3.008594 ACCCCTCGATGTGTTAATTGTCA 59.991 43.478 0.00 0.00 0.00 3.58
631 632 1.811965 TGCGAGAATGTGAATTGGTGG 59.188 47.619 0.00 0.00 0.00 4.61
657 658 3.366121 CACTACGTCTGCATCAGTTGAAG 59.634 47.826 0.00 0.00 32.61 3.02
665 666 1.469251 GCATCAGTTGAAGCATGCTGG 60.469 52.381 23.48 7.16 38.89 4.85
749 752 6.842437 TGCCCTCTCTGTATCATATAGTTC 57.158 41.667 0.00 0.00 0.00 3.01
783 786 6.830324 AGTCATTGGTGCATATATCAACAACT 59.170 34.615 14.08 8.14 43.03 3.16
801 805 5.343249 ACAACTTAAGCTTCTGTGCAAAAG 58.657 37.500 0.00 0.48 34.94 2.27
807 811 5.582689 AAGCTTCTGTGCAAAAGTACTTT 57.417 34.783 15.22 15.22 34.99 2.66
962 980 5.902613 TTTTGAGAGATTGGTTATGCTGG 57.097 39.130 0.00 0.00 0.00 4.85
980 998 3.989817 GCTGGATTTCGAAAAGCATTTGT 59.010 39.130 22.18 2.56 39.02 2.83
981 999 4.143263 GCTGGATTTCGAAAAGCATTTGTG 60.143 41.667 22.18 6.42 39.02 3.33
982 1000 4.942852 TGGATTTCGAAAAGCATTTGTGT 58.057 34.783 15.66 0.00 39.02 3.72
1031 1049 5.840243 TGTATCAGCTCATTTCCAATTGG 57.160 39.130 19.08 19.08 0.00 3.16
1058 1076 9.672673 TCAGTTTTATGAGAGGAAGATTTTAGG 57.327 33.333 0.00 0.00 0.00 2.69
1072 1090 4.700213 AGATTTTAGGTGGTCCAAATGTCG 59.300 41.667 0.00 0.00 35.89 4.35
1140 1158 6.967199 GCAGCTACACTTTTATAAATGTCACC 59.033 38.462 12.48 4.17 0.00 4.02
1230 1248 7.465353 TTTGCATCTGATCCAAAACATCTTA 57.535 32.000 4.31 0.00 0.00 2.10
1261 1282 3.831911 GTCTATGCTGAGCCTATCCTTCT 59.168 47.826 0.23 0.00 0.00 2.85
1262 1283 4.283212 GTCTATGCTGAGCCTATCCTTCTT 59.717 45.833 0.23 0.00 0.00 2.52
1403 1688 9.763837 AGTATTAAGTTTAAGGGGTTTGCTTAT 57.236 29.630 0.00 0.00 0.00 1.73
1409 1694 6.208007 AGTTTAAGGGGTTTGCTTATGTACAC 59.792 38.462 0.00 0.00 0.00 2.90
1443 1728 7.827236 ACAAAATTACGGATCTCAAATCCACTA 59.173 33.333 5.02 0.00 38.08 2.74
1458 1743 5.665916 ATCCACTAAAGAAAAGGGCATTG 57.334 39.130 0.00 0.00 0.00 2.82
1461 1746 4.475944 CACTAAAGAAAAGGGCATTGTCG 58.524 43.478 0.00 0.00 0.00 4.35
1473 1758 5.007682 AGGGCATTGTCGTACTTAAACATT 58.992 37.500 0.00 0.00 0.00 2.71
1474 1759 5.123344 AGGGCATTGTCGTACTTAAACATTC 59.877 40.000 0.00 0.00 0.00 2.67
1513 1798 6.399743 TGTTCCATTACTAGCGTTGTTATCA 58.600 36.000 0.00 0.00 0.00 2.15
1515 1800 7.223971 TGTTCCATTACTAGCGTTGTTATCATC 59.776 37.037 0.00 0.00 0.00 2.92
1520 1805 3.704566 ACTAGCGTTGTTATCATCTGGGA 59.295 43.478 0.00 0.00 0.00 4.37
1552 1837 4.528206 ACAAACCAAATCCCAGAAATCTCC 59.472 41.667 0.00 0.00 0.00 3.71
1554 1839 1.678101 CCAAATCCCAGAAATCTCCGC 59.322 52.381 0.00 0.00 0.00 5.54
1618 1906 9.872757 TCGTTTTGAATTTTAGTGTTAGATCAC 57.127 29.630 0.00 0.00 38.46 3.06
1676 1964 3.449018 CCTACTACATGTGGTGCTTCTCT 59.551 47.826 23.66 0.00 0.00 3.10
1688 1976 4.518970 TGGTGCTTCTCTTTCAAATGTACC 59.481 41.667 0.00 0.00 0.00 3.34
1690 1978 4.518970 GTGCTTCTCTTTCAAATGTACCCA 59.481 41.667 0.00 0.00 0.00 4.51
1692 1980 4.379918 GCTTCTCTTTCAAATGTACCCAGC 60.380 45.833 0.00 0.00 0.00 4.85
1705 1993 3.199071 TGTACCCAGCGAATCCTGTAAAT 59.801 43.478 0.00 0.00 0.00 1.40
1709 1997 4.526650 ACCCAGCGAATCCTGTAAATTTTT 59.473 37.500 0.00 0.00 0.00 1.94
1784 2072 9.956720 CAACTAATCTTATTAGCAAAGGAATGG 57.043 33.333 6.59 0.00 0.00 3.16
1785 2073 9.920946 AACTAATCTTATTAGCAAAGGAATGGA 57.079 29.630 6.59 0.00 0.00 3.41
1792 2080 2.636830 AGCAAAGGAATGGATCAGACG 58.363 47.619 0.00 0.00 0.00 4.18
1793 2081 2.026822 AGCAAAGGAATGGATCAGACGT 60.027 45.455 0.00 0.00 0.00 4.34
1810 2098 5.968387 AGACGTTGTCTGTGAAAAACTAG 57.032 39.130 0.00 0.00 41.76 2.57
1811 2099 5.416947 AGACGTTGTCTGTGAAAAACTAGT 58.583 37.500 0.00 0.00 41.76 2.57
1815 2103 5.504010 CGTTGTCTGTGAAAAACTAGTGCAT 60.504 40.000 0.00 0.00 0.00 3.96
1826 2114 5.746307 AAACTAGTGCATGCATACATCTG 57.254 39.130 25.64 12.17 32.87 2.90
1829 2117 4.813161 ACTAGTGCATGCATACATCTGTTC 59.187 41.667 25.64 6.58 32.87 3.18
1836 2124 3.466836 TGCATACATCTGTTCGGAATCC 58.533 45.455 0.00 0.00 0.00 3.01
1857 2148 1.782028 GCCACCACGACCAACAAGAC 61.782 60.000 0.00 0.00 0.00 3.01
1887 2178 3.119495 CGGCCAACTCAATTTTCTTAGGG 60.119 47.826 2.24 0.00 0.00 3.53
1900 2191 3.414759 TCTTAGGGCAGGGTAGATTGA 57.585 47.619 0.00 0.00 0.00 2.57
1911 2202 6.350949 GGCAGGGTAGATTGAAGATAGATCTC 60.351 46.154 0.00 0.00 35.76 2.75
1913 2204 5.949354 AGGGTAGATTGAAGATAGATCTCCG 59.051 44.000 0.00 0.00 35.76 4.63
1938 2229 5.049818 GTGAAGTCACTCCTGAAATTCACAG 60.050 44.000 17.22 5.85 44.98 3.66
1946 2237 8.950210 TCACTCCTGAAATTCACAGAATTATTC 58.050 33.333 12.28 0.00 37.54 1.75
1958 2249 7.169591 TCACAGAATTATTCGTAAAAAGGGGA 58.830 34.615 0.00 0.00 34.02 4.81
1959 2250 7.666388 TCACAGAATTATTCGTAAAAAGGGGAA 59.334 33.333 0.00 0.00 34.02 3.97
1960 2251 8.301002 CACAGAATTATTCGTAAAAAGGGGAAA 58.699 33.333 0.00 0.00 34.02 3.13
1973 2264 4.670896 AAGGGGAAAAATCACACAACAG 57.329 40.909 0.00 0.00 0.00 3.16
1977 2268 4.583073 GGGGAAAAATCACACAACAGTAGT 59.417 41.667 0.00 0.00 0.00 2.73
1979 2270 5.440685 GGAAAAATCACACAACAGTAGTCG 58.559 41.667 0.00 0.00 0.00 4.18
2094 2386 7.644490 TGTTTATTTAACTAAGTGGTGCACTG 58.356 34.615 17.98 3.21 39.48 3.66
2098 2390 1.884235 ACTAAGTGGTGCACTGAAGC 58.116 50.000 17.98 0.00 44.62 3.86
2170 2464 6.879458 TGCTTTAGAAATTTCCTCACTAGTCC 59.121 38.462 14.61 0.00 0.00 3.85
2207 2501 2.360350 CCTGCTGTTGCCCGTCAT 60.360 61.111 0.00 0.00 38.71 3.06
2288 2597 5.163713 GCTTATTCTTTTGTGTAGCCTGGAG 60.164 44.000 0.00 0.00 0.00 3.86
2508 2818 4.636206 GTCTTGGATTTCTTGCCGATAACT 59.364 41.667 0.00 0.00 0.00 2.24
2627 2937 7.645058 AGGTGGATGTTTTATTTGATGTAGG 57.355 36.000 0.00 0.00 0.00 3.18
2628 2938 6.096846 AGGTGGATGTTTTATTTGATGTAGGC 59.903 38.462 0.00 0.00 0.00 3.93
2629 2939 6.127479 GGTGGATGTTTTATTTGATGTAGGCA 60.127 38.462 0.00 0.00 0.00 4.75
2630 2940 6.751888 GTGGATGTTTTATTTGATGTAGGCAC 59.248 38.462 0.00 0.00 0.00 5.01
2631 2941 6.663093 TGGATGTTTTATTTGATGTAGGCACT 59.337 34.615 0.00 0.00 46.37 4.40
2632 2942 6.974622 GGATGTTTTATTTGATGTAGGCACTG 59.025 38.462 0.00 0.00 41.52 3.66
2633 2943 5.708948 TGTTTTATTTGATGTAGGCACTGC 58.291 37.500 0.00 0.00 41.52 4.40
2698 3008 5.279406 CCTTTGGATTGTTGGAAATGCTACA 60.279 40.000 0.00 0.00 0.00 2.74
2788 3176 3.854809 TGCACGTAAAGCAAAAACTTGAC 59.145 39.130 0.00 0.00 39.39 3.18
2797 3185 3.316308 AGCAAAAACTTGACGAGCTTGAT 59.684 39.130 8.31 0.00 0.00 2.57
2896 3284 9.334693 CAGTTTAACTTTAGACATGCTTTCATC 57.665 33.333 0.00 0.00 0.00 2.92
2914 3302 4.769688 TCATCAGTTCGCCTAATTGTGAT 58.230 39.130 0.00 0.00 0.00 3.06
2988 3376 2.915463 GTGAGACTCATGTTTACCGTCG 59.085 50.000 8.73 0.00 0.00 5.12
3008 3497 2.226437 CGGGGACTTCAGTGTTGAATTG 59.774 50.000 0.00 0.00 42.19 2.32
3015 3504 7.246311 GGACTTCAGTGTTGAATTGATATGTG 58.754 38.462 0.00 0.00 42.19 3.21
3035 3524 7.823745 ATGTGTTGGACTATGTTCTCTTTTT 57.176 32.000 0.00 0.00 0.00 1.94
3036 3525 7.026631 TGTGTTGGACTATGTTCTCTTTTTG 57.973 36.000 0.00 0.00 0.00 2.44
3037 3526 6.601613 TGTGTTGGACTATGTTCTCTTTTTGT 59.398 34.615 0.00 0.00 0.00 2.83
3056 3545 4.530710 TGTGTGGTCATGAACTACCTAC 57.469 45.455 12.94 1.53 38.52 3.18
3113 3602 7.695480 TGGTTTATTTGCATTTGCTAGTCTA 57.305 32.000 3.94 0.00 42.66 2.59
3164 3653 9.273016 TGAGAAGTTTGTCCTTAAGATTTACAG 57.727 33.333 3.36 0.00 0.00 2.74
3174 3663 6.445786 TCCTTAAGATTTACAGGGGTATGTGT 59.554 38.462 3.36 0.00 34.56 3.72
3228 3717 5.399013 GTTCCTTTGTACCATAACATGTGC 58.601 41.667 0.00 0.00 0.00 4.57
3232 3721 6.765989 TCCTTTGTACCATAACATGTGCTATC 59.234 38.462 0.00 0.00 0.00 2.08
3233 3722 6.542005 CCTTTGTACCATAACATGTGCTATCA 59.458 38.462 0.00 0.00 0.00 2.15
3234 3723 7.066887 CCTTTGTACCATAACATGTGCTATCAA 59.933 37.037 0.00 0.00 0.00 2.57
3235 3724 6.918892 TGTACCATAACATGTGCTATCAAC 57.081 37.500 0.00 0.00 0.00 3.18
3266 3756 4.102681 ACTTCCTCCGTCCCATAAATAAGG 59.897 45.833 0.00 0.00 0.00 2.69
3269 3759 3.905591 CCTCCGTCCCATAAATAAGGGTA 59.094 47.826 0.97 0.00 45.64 3.69
3276 3766 6.008331 GTCCCATAAATAAGGGTATTGGTCC 58.992 44.000 0.97 0.00 45.64 4.46
3282 3772 0.106719 AAGGGTATTGGTCCATGGCG 60.107 55.000 6.96 0.00 0.00 5.69
3293 3783 1.169661 TCCATGGCGACCAACACAAC 61.170 55.000 6.96 0.00 36.95 3.32
3296 3786 2.898343 GGCGACCAACACAACGGT 60.898 61.111 0.00 0.00 38.56 4.83
3308 3798 4.382345 ACACAACGGTTAGCTATCCTAC 57.618 45.455 16.96 2.32 0.00 3.18
3318 3808 0.966920 GCTATCCTACGCCCTTAGCA 59.033 55.000 0.00 0.00 44.04 3.49
3331 3821 2.365293 CCCTTAGCAAATACAATGCCCC 59.635 50.000 0.00 0.00 44.91 5.80
3343 3833 2.091541 CAATGCCCCGTAAGAACACAT 58.908 47.619 0.00 0.00 43.02 3.21
3357 3847 7.275779 CGTAAGAACACATACAGCTAACTCAAT 59.724 37.037 0.00 0.00 43.02 2.57
3370 3860 7.173907 ACAGCTAACTCAATATATTGCACATCC 59.826 37.037 18.89 7.46 37.68 3.51
3377 3867 6.457355 TCAATATATTGCACATCCATTTGGC 58.543 36.000 18.89 0.00 37.68 4.52
3381 3871 0.971959 TGCACATCCATTTGGCTCCC 60.972 55.000 0.00 0.00 34.44 4.30
3382 3872 2.008268 GCACATCCATTTGGCTCCCG 62.008 60.000 0.00 0.00 34.44 5.14
3398 3888 1.520666 CCGCCTTCGTCCATAGGTT 59.479 57.895 0.00 0.00 33.91 3.50
3400 3890 1.429148 CGCCTTCGTCCATAGGTTGC 61.429 60.000 0.00 0.00 33.91 4.17
3404 3894 2.422597 CTTCGTCCATAGGTTGCACAA 58.577 47.619 0.00 0.00 0.00 3.33
3409 3899 1.176527 CCATAGGTTGCACAACTGGG 58.823 55.000 12.87 6.28 40.94 4.45
3415 3905 0.802494 GTTGCACAACTGGGGTATCG 59.198 55.000 6.27 0.00 38.25 2.92
3425 3915 1.138859 CTGGGGTATCGTGCTTGATGA 59.861 52.381 2.06 0.00 0.00 2.92
3442 3932 1.448013 GAGGCTCGTAACACCCTGC 60.448 63.158 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.052360 TCAACACGGCTTGCATATAGATTTA 58.948 36.000 0.00 0.00 0.00 1.40
1 2 4.881273 TCAACACGGCTTGCATATAGATTT 59.119 37.500 0.00 0.00 0.00 2.17
2 3 4.450976 TCAACACGGCTTGCATATAGATT 58.549 39.130 0.00 0.00 0.00 2.40
3 4 4.071961 TCAACACGGCTTGCATATAGAT 57.928 40.909 0.00 0.00 0.00 1.98
4 5 3.535280 TCAACACGGCTTGCATATAGA 57.465 42.857 0.00 0.00 0.00 1.98
5 6 4.614555 TTTCAACACGGCTTGCATATAG 57.385 40.909 0.00 0.00 0.00 1.31
6 7 6.052360 TCTATTTCAACACGGCTTGCATATA 58.948 36.000 0.00 0.00 0.00 0.86
7 8 4.881273 TCTATTTCAACACGGCTTGCATAT 59.119 37.500 0.00 0.00 0.00 1.78
8 9 4.257731 TCTATTTCAACACGGCTTGCATA 58.742 39.130 0.00 0.00 0.00 3.14
9 10 3.081061 TCTATTTCAACACGGCTTGCAT 58.919 40.909 0.00 0.00 0.00 3.96
10 11 2.499197 TCTATTTCAACACGGCTTGCA 58.501 42.857 0.00 0.00 0.00 4.08
11 12 3.552604 TTCTATTTCAACACGGCTTGC 57.447 42.857 0.00 0.00 0.00 4.01
12 13 5.354234 AGGTATTCTATTTCAACACGGCTTG 59.646 40.000 0.00 0.00 0.00 4.01
13 14 5.354234 CAGGTATTCTATTTCAACACGGCTT 59.646 40.000 0.00 0.00 0.00 4.35
14 15 4.876107 CAGGTATTCTATTTCAACACGGCT 59.124 41.667 0.00 0.00 0.00 5.52
15 16 4.634443 ACAGGTATTCTATTTCAACACGGC 59.366 41.667 0.00 0.00 0.00 5.68
16 17 5.064707 CCACAGGTATTCTATTTCAACACGG 59.935 44.000 0.00 0.00 0.00 4.94
17 18 5.872617 TCCACAGGTATTCTATTTCAACACG 59.127 40.000 0.00 0.00 0.00 4.49
18 19 7.681939 TTCCACAGGTATTCTATTTCAACAC 57.318 36.000 0.00 0.00 0.00 3.32
19 20 8.328758 AGATTCCACAGGTATTCTATTTCAACA 58.671 33.333 0.00 0.00 0.00 3.33
20 21 8.738645 AGATTCCACAGGTATTCTATTTCAAC 57.261 34.615 0.00 0.00 0.00 3.18
21 22 9.177608 CAAGATTCCACAGGTATTCTATTTCAA 57.822 33.333 0.00 0.00 0.00 2.69
22 23 8.548025 TCAAGATTCCACAGGTATTCTATTTCA 58.452 33.333 0.00 0.00 0.00 2.69
23 24 8.964476 TCAAGATTCCACAGGTATTCTATTTC 57.036 34.615 0.00 0.00 0.00 2.17
24 25 9.347240 CATCAAGATTCCACAGGTATTCTATTT 57.653 33.333 0.00 0.00 0.00 1.40
25 26 7.446625 GCATCAAGATTCCACAGGTATTCTATT 59.553 37.037 0.00 0.00 0.00 1.73
26 27 6.939163 GCATCAAGATTCCACAGGTATTCTAT 59.061 38.462 0.00 0.00 0.00 1.98
27 28 6.126796 TGCATCAAGATTCCACAGGTATTCTA 60.127 38.462 0.00 0.00 0.00 2.10
28 29 5.128919 GCATCAAGATTCCACAGGTATTCT 58.871 41.667 0.00 0.00 0.00 2.40
29 30 4.883585 TGCATCAAGATTCCACAGGTATTC 59.116 41.667 0.00 0.00 0.00 1.75
30 31 4.641989 GTGCATCAAGATTCCACAGGTATT 59.358 41.667 0.00 0.00 0.00 1.89
31 32 4.080129 AGTGCATCAAGATTCCACAGGTAT 60.080 41.667 11.09 0.00 0.00 2.73
32 33 3.264193 AGTGCATCAAGATTCCACAGGTA 59.736 43.478 11.09 0.00 0.00 3.08
33 34 2.040813 AGTGCATCAAGATTCCACAGGT 59.959 45.455 11.09 0.00 0.00 4.00
34 35 2.719739 AGTGCATCAAGATTCCACAGG 58.280 47.619 11.09 0.00 0.00 4.00
35 36 4.778534 AAAGTGCATCAAGATTCCACAG 57.221 40.909 11.09 0.00 0.00 3.66
36 37 4.341806 ACAAAAGTGCATCAAGATTCCACA 59.658 37.500 11.09 0.00 0.00 4.17
37 38 4.874970 ACAAAAGTGCATCAAGATTCCAC 58.125 39.130 0.00 3.62 0.00 4.02
38 39 5.183713 CCTACAAAAGTGCATCAAGATTCCA 59.816 40.000 0.00 0.00 0.00 3.53
39 40 5.644644 CCTACAAAAGTGCATCAAGATTCC 58.355 41.667 0.00 0.00 0.00 3.01
40 41 5.098211 GCCTACAAAAGTGCATCAAGATTC 58.902 41.667 0.00 0.00 0.00 2.52
41 42 4.768968 AGCCTACAAAAGTGCATCAAGATT 59.231 37.500 0.00 0.00 0.00 2.40
42 43 4.338879 AGCCTACAAAAGTGCATCAAGAT 58.661 39.130 0.00 0.00 0.00 2.40
43 44 3.754965 AGCCTACAAAAGTGCATCAAGA 58.245 40.909 0.00 0.00 0.00 3.02
44 45 5.412594 TCTTAGCCTACAAAAGTGCATCAAG 59.587 40.000 0.00 0.00 0.00 3.02
45 46 5.181245 GTCTTAGCCTACAAAAGTGCATCAA 59.819 40.000 0.00 0.00 0.00 2.57
46 47 4.695455 GTCTTAGCCTACAAAAGTGCATCA 59.305 41.667 0.00 0.00 0.00 3.07
47 48 4.095036 GGTCTTAGCCTACAAAAGTGCATC 59.905 45.833 0.00 0.00 0.00 3.91
48 49 4.010349 GGTCTTAGCCTACAAAAGTGCAT 58.990 43.478 0.00 0.00 0.00 3.96
49 50 3.181449 TGGTCTTAGCCTACAAAAGTGCA 60.181 43.478 0.00 0.00 0.00 4.57
50 51 3.408634 TGGTCTTAGCCTACAAAAGTGC 58.591 45.455 0.00 0.00 0.00 4.40
51 52 5.491982 AGATGGTCTTAGCCTACAAAAGTG 58.508 41.667 0.00 0.00 0.00 3.16
52 53 5.763876 AGATGGTCTTAGCCTACAAAAGT 57.236 39.130 0.00 0.00 0.00 2.66
53 54 6.431234 ACAAAGATGGTCTTAGCCTACAAAAG 59.569 38.462 0.00 0.00 35.27 2.27
54 55 6.303839 ACAAAGATGGTCTTAGCCTACAAAA 58.696 36.000 0.00 0.00 35.27 2.44
55 56 5.876357 ACAAAGATGGTCTTAGCCTACAAA 58.124 37.500 0.00 0.00 35.27 2.83
56 57 5.499004 ACAAAGATGGTCTTAGCCTACAA 57.501 39.130 0.00 0.00 35.27 2.41
57 58 5.499004 AACAAAGATGGTCTTAGCCTACA 57.501 39.130 0.00 0.00 35.27 2.74
58 59 5.123979 CCAAACAAAGATGGTCTTAGCCTAC 59.876 44.000 0.00 0.00 35.27 3.18
59 60 5.253330 CCAAACAAAGATGGTCTTAGCCTA 58.747 41.667 0.00 0.00 35.27 3.93
60 61 4.082125 CCAAACAAAGATGGTCTTAGCCT 58.918 43.478 0.00 0.00 35.27 4.58
61 62 3.193479 CCCAAACAAAGATGGTCTTAGCC 59.807 47.826 0.00 0.00 35.27 3.93
62 63 3.367395 GCCCAAACAAAGATGGTCTTAGC 60.367 47.826 0.00 0.00 35.27 3.09
63 64 3.193479 GGCCCAAACAAAGATGGTCTTAG 59.807 47.826 0.00 0.00 35.27 2.18
64 65 3.161866 GGCCCAAACAAAGATGGTCTTA 58.838 45.455 0.00 0.00 35.27 2.10
65 66 1.970640 GGCCCAAACAAAGATGGTCTT 59.029 47.619 0.00 0.00 38.59 3.01
66 67 1.632589 GGCCCAAACAAAGATGGTCT 58.367 50.000 0.00 0.00 34.79 3.85
67 68 0.243636 CGGCCCAAACAAAGATGGTC 59.756 55.000 0.00 0.00 34.79 4.02
68 69 0.469144 ACGGCCCAAACAAAGATGGT 60.469 50.000 0.00 0.00 34.79 3.55
69 70 1.472480 CTACGGCCCAAACAAAGATGG 59.528 52.381 0.00 0.00 36.42 3.51
70 71 1.135402 GCTACGGCCCAAACAAAGATG 60.135 52.381 0.00 0.00 0.00 2.90
71 72 1.173913 GCTACGGCCCAAACAAAGAT 58.826 50.000 0.00 0.00 0.00 2.40
72 73 0.109723 AGCTACGGCCCAAACAAAGA 59.890 50.000 0.00 0.00 39.73 2.52
73 74 1.467342 GTAGCTACGGCCCAAACAAAG 59.533 52.381 8.40 0.00 39.73 2.77
74 75 1.202782 TGTAGCTACGGCCCAAACAAA 60.203 47.619 18.74 0.00 39.73 2.83
75 76 0.397187 TGTAGCTACGGCCCAAACAA 59.603 50.000 18.74 0.00 39.73 2.83
76 77 0.397187 TTGTAGCTACGGCCCAAACA 59.603 50.000 18.74 0.00 39.73 2.83
77 78 1.525941 TTTGTAGCTACGGCCCAAAC 58.474 50.000 18.74 0.00 35.97 2.93
78 79 2.500392 ATTTGTAGCTACGGCCCAAA 57.500 45.000 18.74 13.07 41.02 3.28
79 80 2.026636 AGAATTTGTAGCTACGGCCCAA 60.027 45.455 18.74 4.59 39.73 4.12
80 81 1.557832 AGAATTTGTAGCTACGGCCCA 59.442 47.619 18.74 0.00 39.73 5.36
81 82 2.210961 GAGAATTTGTAGCTACGGCCC 58.789 52.381 18.74 7.11 39.73 5.80
82 83 2.866762 CTGAGAATTTGTAGCTACGGCC 59.133 50.000 18.74 0.00 39.73 6.13
83 84 3.782046 TCTGAGAATTTGTAGCTACGGC 58.218 45.455 18.74 6.32 39.06 5.68
84 85 9.347934 CTATAATCTGAGAATTTGTAGCTACGG 57.652 37.037 18.74 0.00 0.00 4.02
142 143 3.736433 CGTGTGTTGCAATGGGAGAAAAA 60.736 43.478 0.59 0.00 0.00 1.94
143 144 2.223688 CGTGTGTTGCAATGGGAGAAAA 60.224 45.455 0.59 0.00 0.00 2.29
144 145 1.336440 CGTGTGTTGCAATGGGAGAAA 59.664 47.619 0.59 0.00 0.00 2.52
145 146 0.950836 CGTGTGTTGCAATGGGAGAA 59.049 50.000 0.59 0.00 0.00 2.87
146 147 0.888736 CCGTGTGTTGCAATGGGAGA 60.889 55.000 0.59 0.00 0.00 3.71
147 148 1.580942 CCGTGTGTTGCAATGGGAG 59.419 57.895 0.59 0.00 0.00 4.30
148 149 1.900981 CCCGTGTGTTGCAATGGGA 60.901 57.895 7.55 0.00 43.92 4.37
149 150 2.650196 CCCGTGTGTTGCAATGGG 59.350 61.111 0.59 0.00 38.29 4.00
150 151 2.049248 GCCCGTGTGTTGCAATGG 60.049 61.111 0.59 0.00 0.00 3.16
151 152 2.049248 GGCCCGTGTGTTGCAATG 60.049 61.111 0.59 0.00 0.00 2.82
152 153 1.398958 AAAGGCCCGTGTGTTGCAAT 61.399 50.000 0.59 0.00 0.00 3.56
153 154 1.608717 AAAAGGCCCGTGTGTTGCAA 61.609 50.000 0.00 0.00 0.00 4.08
154 155 1.608717 AAAAAGGCCCGTGTGTTGCA 61.609 50.000 0.00 0.00 0.00 4.08
155 156 1.142965 AAAAAGGCCCGTGTGTTGC 59.857 52.632 0.00 0.00 0.00 4.17
156 157 1.151172 GCAAAAAGGCCCGTGTGTTG 61.151 55.000 0.00 0.00 0.00 3.33
157 158 1.142965 GCAAAAAGGCCCGTGTGTT 59.857 52.632 0.00 0.00 0.00 3.32
158 159 0.466555 TAGCAAAAAGGCCCGTGTGT 60.467 50.000 0.00 0.00 0.00 3.72
159 160 0.240945 CTAGCAAAAAGGCCCGTGTG 59.759 55.000 0.00 0.00 0.00 3.82
160 161 0.179001 ACTAGCAAAAAGGCCCGTGT 60.179 50.000 0.00 0.00 0.00 4.49
161 162 1.816074 TACTAGCAAAAAGGCCCGTG 58.184 50.000 0.00 0.00 0.00 4.94
162 163 2.238898 AGATACTAGCAAAAAGGCCCGT 59.761 45.455 0.00 0.00 0.00 5.28
163 164 2.872858 GAGATACTAGCAAAAAGGCCCG 59.127 50.000 0.00 0.00 0.00 6.13
164 165 4.157849 AGAGATACTAGCAAAAAGGCCC 57.842 45.455 0.00 0.00 0.00 5.80
165 166 7.625828 TTTAAGAGATACTAGCAAAAAGGCC 57.374 36.000 0.00 0.00 0.00 5.19
166 167 8.947115 TCTTTTAAGAGATACTAGCAAAAAGGC 58.053 33.333 0.00 0.00 0.00 4.35
197 198 5.300286 GGGAGGTGAATCCACAAATTCTATG 59.700 44.000 0.00 0.00 44.93 2.23
199 200 4.540099 AGGGAGGTGAATCCACAAATTCTA 59.460 41.667 0.00 0.00 44.93 2.10
302 303 5.543507 TTTGCCAGTTAAATCAACACCAT 57.456 34.783 0.00 0.00 39.81 3.55
324 325 1.977854 CCAAGGCCCCTTTTTAAGCTT 59.022 47.619 3.48 3.48 33.42 3.74
363 364 2.330372 CGGCTGCACACAAGCTGAT 61.330 57.895 0.50 0.00 37.12 2.90
391 392 5.930837 ACTCCATCTAGTTCCTTCTCAAG 57.069 43.478 0.00 0.00 0.00 3.02
657 658 0.737219 CTCCTAGCAAACCAGCATGC 59.263 55.000 10.51 10.51 42.87 4.06
665 666 2.284190 GGCAGTCATCTCCTAGCAAAC 58.716 52.381 0.00 0.00 0.00 2.93
783 786 6.693315 AAGTACTTTTGCACAGAAGCTTAA 57.307 33.333 1.12 0.00 34.99 1.85
906 924 1.538047 TCCAGCTTCTTTGCACATCC 58.462 50.000 0.00 0.00 34.99 3.51
962 980 6.509317 TCAACACAAATGCTTTTCGAAATC 57.491 33.333 12.12 7.51 0.00 2.17
980 998 5.908341 TCATGCGGTACTGTATATTCAACA 58.092 37.500 4.84 0.00 0.00 3.33
981 999 5.983720 ACTCATGCGGTACTGTATATTCAAC 59.016 40.000 4.84 0.00 0.00 3.18
982 1000 6.156748 ACTCATGCGGTACTGTATATTCAA 57.843 37.500 4.84 0.00 0.00 2.69
1058 1076 1.798813 GAGACACGACATTTGGACCAC 59.201 52.381 0.00 0.00 0.00 4.16
1140 1158 3.334583 TCTTTGTCTTCCCTTCCATCG 57.665 47.619 0.00 0.00 0.00 3.84
1230 1248 5.688807 AGGCTCAGCATAGACATACATTTT 58.311 37.500 0.00 0.00 0.00 1.82
1250 1268 5.007430 GCTACGGTTAAAAAGAAGGATAGGC 59.993 44.000 0.00 0.00 0.00 3.93
1261 1282 4.913784 AGGAAGGATGCTACGGTTAAAAA 58.086 39.130 0.00 0.00 0.00 1.94
1262 1283 4.563140 AGGAAGGATGCTACGGTTAAAA 57.437 40.909 0.00 0.00 0.00 1.52
1403 1688 5.472820 CGTAATTTTGTAAAGGGGGTGTACA 59.527 40.000 0.00 0.00 0.00 2.90
1409 1694 5.198207 AGATCCGTAATTTTGTAAAGGGGG 58.802 41.667 0.00 0.00 0.00 5.40
1443 1728 4.142038 AGTACGACAATGCCCTTTTCTTT 58.858 39.130 0.00 0.00 0.00 2.52
1495 1780 6.041637 TCCCAGATGATAACAACGCTAGTAAT 59.958 38.462 0.00 0.00 0.00 1.89
1513 1798 4.044065 TGGTTTGTTAGTTCCATCCCAGAT 59.956 41.667 0.00 0.00 0.00 2.90
1515 1800 3.761897 TGGTTTGTTAGTTCCATCCCAG 58.238 45.455 0.00 0.00 0.00 4.45
1520 1805 5.151454 TGGGATTTGGTTTGTTAGTTCCAT 58.849 37.500 0.00 0.00 0.00 3.41
1554 1839 4.329801 GCCATTAATTTTCTTCGCCAAAGG 59.670 41.667 0.00 0.00 35.54 3.11
1565 1850 9.578439 GATAAGATATGGCTGCCATTAATTTTC 57.422 33.333 36.49 24.86 42.23 2.29
1614 1902 6.420604 CGCCAGTTCAAAATAAAAAGTGTGAT 59.579 34.615 0.00 0.00 0.00 3.06
1618 1906 6.410038 CAACGCCAGTTCAAAATAAAAAGTG 58.590 36.000 0.00 0.00 38.79 3.16
1621 1909 5.661458 TCCAACGCCAGTTCAAAATAAAAA 58.339 33.333 0.00 0.00 38.79 1.94
1676 1964 3.442273 GGATTCGCTGGGTACATTTGAAA 59.558 43.478 0.00 0.00 0.00 2.69
1709 1997 6.985117 AGCATGAAGTAGCAAAAAGATTCAA 58.015 32.000 0.00 0.00 31.14 2.69
1720 2008 5.221521 CCTCTACCATTAGCATGAAGTAGCA 60.222 44.000 0.00 0.00 30.68 3.49
1729 2017 2.774234 ACAGTGCCTCTACCATTAGCAT 59.226 45.455 0.00 0.00 35.62 3.79
1777 2065 2.834549 AGACAACGTCTGATCCATTCCT 59.165 45.455 0.00 0.00 41.76 3.36
1792 2080 5.229921 TGCACTAGTTTTTCACAGACAAC 57.770 39.130 0.00 0.00 0.00 3.32
1793 2081 5.733091 GCATGCACTAGTTTTTCACAGACAA 60.733 40.000 14.21 0.00 0.00 3.18
1810 2098 2.286595 CCGAACAGATGTATGCATGCAC 60.287 50.000 25.37 12.32 35.07 4.57
1811 2099 1.941975 CCGAACAGATGTATGCATGCA 59.058 47.619 25.04 25.04 35.07 3.96
1815 2103 3.466836 GGATTCCGAACAGATGTATGCA 58.533 45.455 0.00 0.00 0.00 3.96
1836 2124 4.920112 TGTTGGTCGTGGTGGCCG 62.920 66.667 0.00 0.00 0.00 6.13
1845 2133 1.676014 GGATCCCTGTCTTGTTGGTCG 60.676 57.143 0.00 0.00 0.00 4.79
1857 2148 2.190578 GAGTTGGCCGGATCCCTG 59.809 66.667 5.05 0.00 0.00 4.45
1887 2178 6.350949 GGAGATCTATCTTCAATCTACCCTGC 60.351 46.154 0.00 0.00 37.25 4.85
1900 2191 4.339814 GTGACTTCACCGGAGATCTATCTT 59.660 45.833 9.46 0.00 40.85 2.40
1913 2204 6.203499 TGTGAATTTCAGGAGTGACTTCACC 61.203 44.000 18.35 0.00 45.13 4.02
1946 2237 5.593010 TGTGTGATTTTTCCCCTTTTTACG 58.407 37.500 0.00 0.00 0.00 3.18
1954 2245 4.583073 ACTACTGTTGTGTGATTTTTCCCC 59.417 41.667 0.00 0.00 0.00 4.81
1958 2249 7.542534 TTACGACTACTGTTGTGTGATTTTT 57.457 32.000 0.00 0.00 40.73 1.94
1959 2250 7.724305 ATTACGACTACTGTTGTGTGATTTT 57.276 32.000 0.00 0.00 40.73 1.82
1960 2251 7.724305 AATTACGACTACTGTTGTGTGATTT 57.276 32.000 0.00 0.00 40.73 2.17
1973 2264 6.589139 AGCCTCACAAAACTAATTACGACTAC 59.411 38.462 0.00 0.00 0.00 2.73
1977 2268 6.870971 AAAGCCTCACAAAACTAATTACGA 57.129 33.333 0.00 0.00 0.00 3.43
1979 2270 9.394477 CTACAAAAGCCTCACAAAACTAATTAC 57.606 33.333 0.00 0.00 0.00 1.89
2073 2364 6.148811 GCTTCAGTGCACCACTTAGTTAAATA 59.851 38.462 14.63 0.00 42.59 1.40
2080 2371 1.802960 CTGCTTCAGTGCACCACTTAG 59.197 52.381 14.63 5.50 42.59 2.18
2085 2376 0.819259 GGTTCTGCTTCAGTGCACCA 60.819 55.000 14.63 2.59 38.12 4.17
2094 2386 5.677344 GCAATTAGCTTAAGGGTTCTGCTTC 60.677 44.000 4.29 0.00 41.15 3.86
2170 2464 5.159209 CAGGTGCTCTGCTTTTTCATTTAG 58.841 41.667 0.00 0.00 36.60 1.85
2219 2527 8.062065 AGGAGTCAATCTTTTCACTAGACTAG 57.938 38.462 8.00 8.00 35.24 2.57
2288 2597 2.045536 CTTGGCCTGCTGACCCTC 60.046 66.667 3.32 0.00 0.00 4.30
2456 2766 2.315176 CCATTGGACCCAACAGTTGAA 58.685 47.619 15.36 0.79 38.88 2.69
2466 2776 1.609783 CTCCACTCCCATTGGACCC 59.390 63.158 3.62 0.00 38.28 4.46
2612 2922 5.323371 GGCAGTGCCTACATCAAATAAAA 57.677 39.130 27.48 0.00 46.69 1.52
2642 2952 8.670135 CGTACATCAAATAAAACATCCACCTTA 58.330 33.333 0.00 0.00 0.00 2.69
2643 2953 7.535139 CGTACATCAAATAAAACATCCACCTT 58.465 34.615 0.00 0.00 0.00 3.50
2644 2954 6.404293 GCGTACATCAAATAAAACATCCACCT 60.404 38.462 0.00 0.00 0.00 4.00
2645 2955 5.741982 GCGTACATCAAATAAAACATCCACC 59.258 40.000 0.00 0.00 0.00 4.61
2646 2956 6.250527 GTGCGTACATCAAATAAAACATCCAC 59.749 38.462 0.00 0.00 0.00 4.02
2647 2957 6.150307 AGTGCGTACATCAAATAAAACATCCA 59.850 34.615 6.38 0.00 0.00 3.41
2648 2958 6.468956 CAGTGCGTACATCAAATAAAACATCC 59.531 38.462 6.38 0.00 0.00 3.51
2649 2959 6.021468 GCAGTGCGTACATCAAATAAAACATC 60.021 38.462 6.38 0.00 0.00 3.06
2650 2960 5.799936 GCAGTGCGTACATCAAATAAAACAT 59.200 36.000 6.38 0.00 0.00 2.71
2651 2961 5.150683 GCAGTGCGTACATCAAATAAAACA 58.849 37.500 6.38 0.00 0.00 2.83
2652 2962 4.557301 GGCAGTGCGTACATCAAATAAAAC 59.443 41.667 9.45 0.00 0.00 2.43
2653 2963 4.457603 AGGCAGTGCGTACATCAAATAAAA 59.542 37.500 8.91 0.00 0.00 1.52
2654 2964 4.006989 AGGCAGTGCGTACATCAAATAAA 58.993 39.130 8.91 0.00 0.00 1.40
2655 2965 3.605634 AGGCAGTGCGTACATCAAATAA 58.394 40.909 8.91 0.00 0.00 1.40
2656 2966 3.260475 AGGCAGTGCGTACATCAAATA 57.740 42.857 8.91 0.00 0.00 1.40
2657 2967 2.113860 AGGCAGTGCGTACATCAAAT 57.886 45.000 8.91 0.00 0.00 2.32
2658 2968 1.890876 AAGGCAGTGCGTACATCAAA 58.109 45.000 11.30 0.00 0.00 2.69
2659 2969 1.535028 CAAAGGCAGTGCGTACATCAA 59.465 47.619 11.30 0.00 0.00 2.57
2660 2970 1.155889 CAAAGGCAGTGCGTACATCA 58.844 50.000 11.30 0.00 0.00 3.07
2661 2971 0.447801 CCAAAGGCAGTGCGTACATC 59.552 55.000 11.30 0.00 0.00 3.06
2662 2972 0.036164 TCCAAAGGCAGTGCGTACAT 59.964 50.000 11.30 0.00 0.00 2.29
2663 2973 0.036164 ATCCAAAGGCAGTGCGTACA 59.964 50.000 11.30 0.00 0.00 2.90
2664 2974 1.135689 CAATCCAAAGGCAGTGCGTAC 60.136 52.381 11.30 0.00 0.00 3.67
2665 2975 1.164411 CAATCCAAAGGCAGTGCGTA 58.836 50.000 11.30 0.00 0.00 4.42
2666 2976 0.823356 ACAATCCAAAGGCAGTGCGT 60.823 50.000 9.45 6.79 0.00 5.24
2667 2977 0.314935 AACAATCCAAAGGCAGTGCG 59.685 50.000 9.45 0.00 0.00 5.34
2698 3008 7.548075 CAGACAGTCCCACTTTTATATAACGTT 59.452 37.037 5.88 5.88 0.00 3.99
2788 3176 5.466058 AGCATTAAGAAGATCATCAAGCTCG 59.534 40.000 0.10 0.00 0.00 5.03
2791 3179 6.615264 TCAGCATTAAGAAGATCATCAAGC 57.385 37.500 0.10 0.00 0.00 4.01
2896 3284 6.250819 CAACTTATCACAATTAGGCGAACTG 58.749 40.000 0.00 0.00 0.00 3.16
2914 3302 7.436673 GTGCACATAATTGACAAAACCAACTTA 59.563 33.333 13.17 0.00 0.00 2.24
2988 3376 3.486383 TCAATTCAACACTGAAGTCCCC 58.514 45.455 0.00 0.00 44.68 4.81
3008 3497 8.723942 AAAGAGAACATAGTCCAACACATATC 57.276 34.615 0.00 0.00 0.00 1.63
3015 3504 6.912591 CACACAAAAAGAGAACATAGTCCAAC 59.087 38.462 0.00 0.00 0.00 3.77
3035 3524 3.898741 TGTAGGTAGTTCATGACCACACA 59.101 43.478 0.00 0.00 38.27 3.72
3036 3525 4.530710 TGTAGGTAGTTCATGACCACAC 57.469 45.455 0.00 0.00 38.27 3.82
3037 3526 4.530553 ACATGTAGGTAGTTCATGACCACA 59.469 41.667 0.00 2.37 40.64 4.17
3090 3579 9.586435 AAATAGACTAGCAAATGCAAATAAACC 57.414 29.630 8.28 0.00 45.16 3.27
3132 3621 6.872020 TCTTAAGGACAAACTTCTCAATACCG 59.128 38.462 1.85 0.00 32.02 4.02
3164 3653 6.238925 GCATGGTCTAAAATAACACATACCCC 60.239 42.308 0.00 0.00 0.00 4.95
3174 3663 8.264347 TGACTGACATAGCATGGTCTAAAATAA 58.736 33.333 0.00 0.00 35.11 1.40
3178 3667 5.675684 TGACTGACATAGCATGGTCTAAA 57.324 39.130 0.00 0.00 35.11 1.85
3228 3717 5.919141 CGGAGGAAGTAATAACCGTTGATAG 59.081 44.000 0.00 0.00 36.38 2.08
3235 3724 2.223900 GGGACGGAGGAAGTAATAACCG 60.224 54.545 0.00 0.00 44.77 4.44
3266 3756 2.702847 GTCGCCATGGACCAATACC 58.297 57.895 18.40 0.00 0.00 2.73
3276 3766 1.082169 CGTTGTGTTGGTCGCCATG 60.082 57.895 0.00 0.00 31.53 3.66
3282 3772 1.589803 AGCTAACCGTTGTGTTGGTC 58.410 50.000 0.00 0.00 37.54 4.02
3293 3783 0.243095 GGGCGTAGGATAGCTAACCG 59.757 60.000 13.86 4.37 0.00 4.44
3296 3786 2.824341 GCTAAGGGCGTAGGATAGCTAA 59.176 50.000 0.00 0.00 36.81 3.09
3308 3798 2.543653 GGCATTGTATTTGCTAAGGGCG 60.544 50.000 0.00 0.00 45.43 6.13
3318 3808 4.157105 GTGTTCTTACGGGGCATTGTATTT 59.843 41.667 0.00 0.00 0.00 1.40
3331 3821 6.090783 TGAGTTAGCTGTATGTGTTCTTACG 58.909 40.000 0.00 0.00 0.00 3.18
3343 3833 9.208022 GATGTGCAATATATTGAGTTAGCTGTA 57.792 33.333 26.22 4.12 40.14 2.74
3357 3847 4.523943 GGAGCCAAATGGATGTGCAATATA 59.476 41.667 2.98 0.00 37.39 0.86
3377 3867 1.364171 CTATGGACGAAGGCGGGAG 59.636 63.158 0.00 0.00 43.17 4.30
3381 3871 1.429148 GCAACCTATGGACGAAGGCG 61.429 60.000 0.00 0.00 44.79 5.52
3382 3872 0.392461 TGCAACCTATGGACGAAGGC 60.392 55.000 0.00 0.00 36.24 4.35
3398 3888 0.321210 CACGATACCCCAGTTGTGCA 60.321 55.000 0.00 0.00 0.00 4.57
3400 3890 0.036388 AGCACGATACCCCAGTTGTG 60.036 55.000 0.00 0.00 0.00 3.33
3404 3894 1.134401 CATCAAGCACGATACCCCAGT 60.134 52.381 0.00 0.00 0.00 4.00
3409 3899 1.202580 AGCCTCATCAAGCACGATACC 60.203 52.381 0.00 0.00 0.00 2.73
3415 3905 1.661112 GTTACGAGCCTCATCAAGCAC 59.339 52.381 0.00 0.00 0.00 4.40
3425 3915 2.663196 GCAGGGTGTTACGAGCCT 59.337 61.111 0.00 0.00 45.00 4.58


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

AutoCloner maintained by Alex Coulton.