Multiple sequence alignment - TraesCS3B01G110700

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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 TraesCS3B01G110700 chr3B 100.000 3229 0 0 1 3229 76473482 76476710 0.000000e+00 5963.0
1 TraesCS3B01G110700 chr4B 97.439 1679 41 2 304 1980 553872870 553871192 0.000000e+00 2861.0
2 TraesCS3B01G110700 chr4B 98.008 1205 22 1 2027 3229 553871187 553869983 0.000000e+00 2091.0
3 TraesCS3B01G110700 chr4B 92.000 75 5 1 284 357 553872919 553872845 1.580000e-18 104.0
4 TraesCS3B01G110700 chr3A 96.881 1667 51 1 314 1979 701946647 701944981 0.000000e+00 2789.0
5 TraesCS3B01G110700 chr3A 97.268 1208 28 1 2027 3229 701944975 701943768 0.000000e+00 2043.0
6 TraesCS3B01G110700 chr3A 91.139 158 8 5 1 155 60627670 60627824 3.260000e-50 209.0
7 TraesCS3B01G110700 chr3D 96.452 1663 57 2 319 1980 569869880 569868219 0.000000e+00 2743.0
8 TraesCS3B01G110700 chr3D 97.095 1205 32 2 2027 3229 569868214 569867011 0.000000e+00 2028.0
9 TraesCS3B01G110700 chr3D 93.413 167 7 3 7 173 48419739 48419901 8.950000e-61 244.0
10 TraesCS3B01G110700 chr3D 93.939 66 4 0 214 279 48419911 48419976 2.050000e-17 100.0
11 TraesCS3B01G110700 chr3D 96.875 32 1 0 279 310 569869944 569869913 2.000000e-03 54.7
12 TraesCS3B01G110700 chr5A 93.490 1705 108 3 279 1980 512193098 512191394 0.000000e+00 2531.0
13 TraesCS3B01G110700 chr5A 94.855 1205 56 3 2027 3229 512191389 512190189 0.000000e+00 1877.0
14 TraesCS3B01G110700 chr1B 93.541 1672 102 4 315 1980 647062409 647064080 0.000000e+00 2484.0
15 TraesCS3B01G110700 chr1B 96.232 690 24 1 2542 3229 647068558 647069247 0.000000e+00 1129.0
16 TraesCS3B01G110700 chr1B 96.226 530 20 0 2027 2556 647064085 647064614 0.000000e+00 869.0
17 TraesCS3B01G110700 chr7A 91.023 1682 128 8 314 1980 650427791 650429464 0.000000e+00 2248.0
18 TraesCS3B01G110700 chr7A 93.522 1204 73 3 2028 3229 650429470 650430670 0.000000e+00 1786.0
19 TraesCS3B01G110700 chr2B 94.737 1216 52 6 279 1489 551452394 551453602 0.000000e+00 1881.0
20 TraesCS3B01G110700 chr2B 94.040 1057 62 1 924 1980 635333903 635332848 0.000000e+00 1602.0
21 TraesCS3B01G110700 chr2B 93.642 755 42 4 2478 3229 635321120 635320369 0.000000e+00 1123.0
22 TraesCS3B01G110700 chr2B 95.619 662 27 1 2570 3229 551473576 551474237 0.000000e+00 1061.0
23 TraesCS3B01G110700 chr2B 96.903 549 17 0 2027 2575 551462660 551463208 0.000000e+00 920.0
24 TraesCS3B01G110700 chr2B 92.278 518 19 7 1484 1980 551462138 551462655 0.000000e+00 715.0
25 TraesCS3B01G110700 chr2B 91.103 517 44 2 279 793 635334414 635333898 0.000000e+00 699.0
26 TraesCS3B01G110700 chr2B 94.079 456 26 1 2027 2482 635332843 635332389 0.000000e+00 691.0
27 TraesCS3B01G110700 chr2A 80.986 1136 203 11 2025 3149 105535614 105536747 0.000000e+00 889.0
28 TraesCS3B01G110700 chr5D 93.182 44 2 1 174 217 480977537 480977579 2.690000e-06 63.9


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 TraesCS3B01G110700 chr3B 76473482 76476710 3228 False 5963.000000 5963 100.000000 1 3229 1 chr3B.!!$F1 3228
1 TraesCS3B01G110700 chr4B 553869983 553872919 2936 True 1685.333333 2861 95.815667 284 3229 3 chr4B.!!$R1 2945
2 TraesCS3B01G110700 chr3A 701943768 701946647 2879 True 2416.000000 2789 97.074500 314 3229 2 chr3A.!!$R1 2915
3 TraesCS3B01G110700 chr3D 569867011 569869944 2933 True 1608.566667 2743 96.807333 279 3229 3 chr3D.!!$R1 2950
4 TraesCS3B01G110700 chr5A 512190189 512193098 2909 True 2204.000000 2531 94.172500 279 3229 2 chr5A.!!$R1 2950
5 TraesCS3B01G110700 chr1B 647062409 647069247 6838 False 1494.000000 2484 95.333000 315 3229 3 chr1B.!!$F1 2914
6 TraesCS3B01G110700 chr7A 650427791 650430670 2879 False 2017.000000 2248 92.272500 314 3229 2 chr7A.!!$F1 2915
7 TraesCS3B01G110700 chr2B 551452394 551453602 1208 False 1881.000000 1881 94.737000 279 1489 1 chr2B.!!$F1 1210
8 TraesCS3B01G110700 chr2B 635320369 635321120 751 True 1123.000000 1123 93.642000 2478 3229 1 chr2B.!!$R1 751
9 TraesCS3B01G110700 chr2B 551473576 551474237 661 False 1061.000000 1061 95.619000 2570 3229 1 chr2B.!!$F2 659
10 TraesCS3B01G110700 chr2B 635332389 635334414 2025 True 997.333333 1602 93.074000 279 2482 3 chr2B.!!$R2 2203
11 TraesCS3B01G110700 chr2B 551462138 551463208 1070 False 817.500000 920 94.590500 1484 2575 2 chr2B.!!$F3 1091
12 TraesCS3B01G110700 chr2A 105535614 105536747 1133 False 889.000000 889 80.986000 2025 3149 1 chr2A.!!$F1 1124

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
44 45 0.310854 CGCTTGCGAGGAACCTTTTT 59.689 50.0 9.60 0.00 0.00 1.94 F
276 277 0.459585 GCACCTGCATGCTGAAATGG 60.460 55.0 24.53 15.18 42.62 3.16 F
277 278 0.459585 CACCTGCATGCTGAAATGGC 60.460 55.0 24.53 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 2041 1.838077 ACGGACCCTATCTTTTCCTGG 59.162 52.381 0.00 0.00 0.00 4.45 R
2183 2282 1.003696 CCTTCCCTGTCTTCAGTTCCC 59.996 57.143 0.00 0.00 39.82 3.97 R
2436 2542 9.175312 TGACTTGTTTCACTACTAGTAGGATAG 57.825 37.037 29.05 17.45 34.91 2.08 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
25 26 8.273643 CACGCTTACATCATTATTGAAAATCC 57.726 34.615 0.00 0.00 34.96 3.01
26 27 7.112009 CACGCTTACATCATTATTGAAAATCCG 59.888 37.037 0.00 0.00 34.96 4.18
27 28 6.086765 CGCTTACATCATTATTGAAAATCCGC 59.913 38.462 0.00 0.00 34.96 5.54
28 29 7.141363 GCTTACATCATTATTGAAAATCCGCT 58.859 34.615 0.00 0.00 34.96 5.52
29 30 7.649306 GCTTACATCATTATTGAAAATCCGCTT 59.351 33.333 0.00 0.00 34.96 4.68
30 31 8.854979 TTACATCATTATTGAAAATCCGCTTG 57.145 30.769 0.00 0.00 34.96 4.01
31 32 5.750067 ACATCATTATTGAAAATCCGCTTGC 59.250 36.000 0.00 0.00 34.96 4.01
32 33 4.350346 TCATTATTGAAAATCCGCTTGCG 58.650 39.130 8.14 8.14 0.00 4.85
33 34 4.095632 TCATTATTGAAAATCCGCTTGCGA 59.904 37.500 16.99 3.25 0.00 5.10
34 35 2.549633 ATTGAAAATCCGCTTGCGAG 57.450 45.000 16.99 6.85 0.00 5.03
35 36 0.521291 TTGAAAATCCGCTTGCGAGG 59.479 50.000 16.99 0.63 0.00 4.63
36 37 0.321210 TGAAAATCCGCTTGCGAGGA 60.321 50.000 16.99 6.51 43.51 3.71
37 38 0.802494 GAAAATCCGCTTGCGAGGAA 59.198 50.000 16.99 0.00 42.60 3.36
38 39 0.521735 AAAATCCGCTTGCGAGGAAC 59.478 50.000 16.99 0.00 42.60 3.62
39 40 1.305930 AAATCCGCTTGCGAGGAACC 61.306 55.000 16.99 0.00 42.60 3.62
40 41 2.185310 AATCCGCTTGCGAGGAACCT 62.185 55.000 16.99 0.00 42.60 3.50
41 42 2.185310 ATCCGCTTGCGAGGAACCTT 62.185 55.000 16.99 0.00 42.60 3.50
42 43 1.966451 CCGCTTGCGAGGAACCTTT 60.966 57.895 16.99 0.00 30.72 3.11
43 44 1.515521 CCGCTTGCGAGGAACCTTTT 61.516 55.000 16.99 0.00 30.72 2.27
44 45 0.310854 CGCTTGCGAGGAACCTTTTT 59.689 50.000 9.60 0.00 0.00 1.94
45 46 1.663161 CGCTTGCGAGGAACCTTTTTC 60.663 52.381 9.60 0.00 0.00 2.29
46 47 1.663161 GCTTGCGAGGAACCTTTTTCG 60.663 52.381 2.37 0.00 36.23 3.46
47 48 1.871039 CTTGCGAGGAACCTTTTTCGA 59.129 47.619 0.00 0.00 35.19 3.71
48 49 1.508632 TGCGAGGAACCTTTTTCGAG 58.491 50.000 4.79 0.00 35.19 4.04
49 50 1.202604 TGCGAGGAACCTTTTTCGAGT 60.203 47.619 4.79 0.00 35.19 4.18
50 51 2.036217 TGCGAGGAACCTTTTTCGAGTA 59.964 45.455 4.79 0.00 35.19 2.59
51 52 2.666994 GCGAGGAACCTTTTTCGAGTAG 59.333 50.000 4.79 0.00 35.19 2.57
52 53 3.860002 GCGAGGAACCTTTTTCGAGTAGT 60.860 47.826 4.79 0.00 35.19 2.73
53 54 4.616835 GCGAGGAACCTTTTTCGAGTAGTA 60.617 45.833 4.79 0.00 35.19 1.82
54 55 5.648572 CGAGGAACCTTTTTCGAGTAGTAT 58.351 41.667 0.00 0.00 35.19 2.12
55 56 6.678900 GCGAGGAACCTTTTTCGAGTAGTATA 60.679 42.308 4.79 0.00 35.19 1.47
56 57 7.424001 CGAGGAACCTTTTTCGAGTAGTATAT 58.576 38.462 0.00 0.00 35.19 0.86
57 58 7.919621 CGAGGAACCTTTTTCGAGTAGTATATT 59.080 37.037 0.00 0.00 35.19 1.28
60 61 9.807649 GGAACCTTTTTCGAGTAGTATATTACA 57.192 33.333 8.00 0.00 0.00 2.41
68 69 8.570096 TTCGAGTAGTATATTACAACATGTGC 57.430 34.615 0.00 0.00 0.00 4.57
69 70 7.708998 TCGAGTAGTATATTACAACATGTGCA 58.291 34.615 0.00 0.00 0.00 4.57
70 71 8.192110 TCGAGTAGTATATTACAACATGTGCAA 58.808 33.333 0.00 0.00 0.00 4.08
71 72 8.978539 CGAGTAGTATATTACAACATGTGCAAT 58.021 33.333 0.00 2.12 0.00 3.56
73 74 9.613428 AGTAGTATATTACAACATGTGCAATGT 57.387 29.630 0.00 2.16 0.00 2.71
74 75 9.650371 GTAGTATATTACAACATGTGCAATGTG 57.350 33.333 10.49 1.67 31.80 3.21
75 76 8.504812 AGTATATTACAACATGTGCAATGTGA 57.495 30.769 10.49 3.64 31.80 3.58
76 77 8.615211 AGTATATTACAACATGTGCAATGTGAG 58.385 33.333 10.49 11.54 31.80 3.51
77 78 5.710513 ATTACAACATGTGCAATGTGAGT 57.289 34.783 10.49 15.12 31.80 3.41
78 79 3.631145 ACAACATGTGCAATGTGAGTC 57.369 42.857 13.05 0.00 31.80 3.36
79 80 2.950975 ACAACATGTGCAATGTGAGTCA 59.049 40.909 13.05 0.00 31.80 3.41
80 81 3.380954 ACAACATGTGCAATGTGAGTCAA 59.619 39.130 13.05 0.00 31.80 3.18
81 82 3.909776 ACATGTGCAATGTGAGTCAAG 57.090 42.857 11.96 0.00 0.00 3.02
82 83 3.216800 ACATGTGCAATGTGAGTCAAGT 58.783 40.909 11.96 0.00 0.00 3.16
83 84 3.251729 ACATGTGCAATGTGAGTCAAGTC 59.748 43.478 11.96 0.00 0.00 3.01
84 85 2.221169 TGTGCAATGTGAGTCAAGTCC 58.779 47.619 0.00 0.00 0.00 3.85
85 86 2.221169 GTGCAATGTGAGTCAAGTCCA 58.779 47.619 0.00 0.00 0.00 4.02
86 87 2.618241 GTGCAATGTGAGTCAAGTCCAA 59.382 45.455 0.00 0.00 0.00 3.53
87 88 2.880268 TGCAATGTGAGTCAAGTCCAAG 59.120 45.455 0.00 0.00 0.00 3.61
88 89 3.141398 GCAATGTGAGTCAAGTCCAAGA 58.859 45.455 0.00 0.00 0.00 3.02
89 90 3.565482 GCAATGTGAGTCAAGTCCAAGAA 59.435 43.478 0.00 0.00 0.00 2.52
90 91 4.036734 GCAATGTGAGTCAAGTCCAAGAAA 59.963 41.667 0.00 0.00 0.00 2.52
91 92 5.450412 GCAATGTGAGTCAAGTCCAAGAAAA 60.450 40.000 0.00 0.00 0.00 2.29
92 93 6.563422 CAATGTGAGTCAAGTCCAAGAAAAA 58.437 36.000 0.00 0.00 0.00 1.94
113 114 6.854091 AAAATAGTTCTAGACTCCGAACCT 57.146 37.500 11.76 5.15 40.18 3.50
114 115 7.951347 AAAATAGTTCTAGACTCCGAACCTA 57.049 36.000 11.76 6.58 40.18 3.08
115 116 7.951347 AAATAGTTCTAGACTCCGAACCTAA 57.049 36.000 11.76 2.52 40.18 2.69
116 117 7.951347 AATAGTTCTAGACTCCGAACCTAAA 57.049 36.000 11.76 0.73 40.18 1.85
117 118 7.951347 ATAGTTCTAGACTCCGAACCTAAAA 57.049 36.000 11.76 0.00 40.18 1.52
118 119 6.661304 AGTTCTAGACTCCGAACCTAAAAA 57.339 37.500 11.76 0.00 40.18 1.94
149 150 2.238245 GTGCAACAATCGAGCTGAAG 57.762 50.000 0.00 0.00 36.32 3.02
150 151 1.135859 GTGCAACAATCGAGCTGAAGG 60.136 52.381 0.00 0.00 36.32 3.46
151 152 1.160137 GCAACAATCGAGCTGAAGGT 58.840 50.000 0.00 0.00 0.00 3.50
152 153 2.289382 TGCAACAATCGAGCTGAAGGTA 60.289 45.455 0.00 0.00 0.00 3.08
153 154 2.349886 GCAACAATCGAGCTGAAGGTAG 59.650 50.000 0.00 0.00 0.00 3.18
154 155 3.849911 CAACAATCGAGCTGAAGGTAGA 58.150 45.455 0.00 0.00 0.00 2.59
155 156 3.791973 ACAATCGAGCTGAAGGTAGAG 57.208 47.619 0.00 0.00 31.23 2.43
156 157 3.357203 ACAATCGAGCTGAAGGTAGAGA 58.643 45.455 0.00 0.00 31.23 3.10
157 158 3.957497 ACAATCGAGCTGAAGGTAGAGAT 59.043 43.478 0.00 0.00 31.23 2.75
158 159 5.133941 ACAATCGAGCTGAAGGTAGAGATA 58.866 41.667 0.00 0.00 31.23 1.98
159 160 5.772672 ACAATCGAGCTGAAGGTAGAGATAT 59.227 40.000 0.00 0.00 31.23 1.63
160 161 6.072175 ACAATCGAGCTGAAGGTAGAGATATC 60.072 42.308 0.00 0.00 31.23 1.63
161 162 5.235850 TCGAGCTGAAGGTAGAGATATCT 57.764 43.478 4.47 4.47 0.00 1.98
162 163 6.361768 TCGAGCTGAAGGTAGAGATATCTA 57.638 41.667 4.89 0.00 0.00 1.98
163 164 6.403049 TCGAGCTGAAGGTAGAGATATCTAG 58.597 44.000 4.89 0.00 0.00 2.43
164 165 5.584649 CGAGCTGAAGGTAGAGATATCTAGG 59.415 48.000 4.89 0.00 0.00 3.02
165 166 6.463053 AGCTGAAGGTAGAGATATCTAGGT 57.537 41.667 4.89 0.00 0.00 3.08
166 167 6.858941 AGCTGAAGGTAGAGATATCTAGGTT 58.141 40.000 4.89 0.00 0.00 3.50
167 168 6.719370 AGCTGAAGGTAGAGATATCTAGGTTG 59.281 42.308 4.89 0.00 0.00 3.77
168 169 6.071616 GCTGAAGGTAGAGATATCTAGGTTGG 60.072 46.154 4.89 0.00 0.00 3.77
169 170 6.315714 TGAAGGTAGAGATATCTAGGTTGGG 58.684 44.000 4.89 0.00 0.00 4.12
170 171 4.679331 AGGTAGAGATATCTAGGTTGGGC 58.321 47.826 4.89 0.00 0.00 5.36
171 172 3.444388 GGTAGAGATATCTAGGTTGGGCG 59.556 52.174 4.89 0.00 0.00 6.13
172 173 3.527507 AGAGATATCTAGGTTGGGCGA 57.472 47.619 4.89 0.00 0.00 5.54
173 174 4.054359 AGAGATATCTAGGTTGGGCGAT 57.946 45.455 4.89 0.00 0.00 4.58
174 175 5.194473 AGAGATATCTAGGTTGGGCGATA 57.806 43.478 4.89 0.00 0.00 2.92
175 176 5.197451 AGAGATATCTAGGTTGGGCGATAG 58.803 45.833 4.89 0.00 0.00 2.08
176 177 4.936802 AGATATCTAGGTTGGGCGATAGT 58.063 43.478 2.53 0.00 39.35 2.12
177 178 4.707448 AGATATCTAGGTTGGGCGATAGTG 59.293 45.833 2.53 0.00 39.35 2.74
178 179 2.447408 TCTAGGTTGGGCGATAGTGA 57.553 50.000 0.00 0.00 39.35 3.41
179 180 2.029623 TCTAGGTTGGGCGATAGTGAC 58.970 52.381 0.00 0.00 39.35 3.67
180 181 1.754803 CTAGGTTGGGCGATAGTGACA 59.245 52.381 0.00 0.00 39.35 3.58
181 182 0.981183 AGGTTGGGCGATAGTGACAA 59.019 50.000 0.00 0.00 39.35 3.18
182 183 1.349688 AGGTTGGGCGATAGTGACAAA 59.650 47.619 0.00 0.00 39.35 2.83
183 184 2.156098 GGTTGGGCGATAGTGACAAAA 58.844 47.619 0.00 0.00 39.35 2.44
184 185 2.554893 GGTTGGGCGATAGTGACAAAAA 59.445 45.455 0.00 0.00 39.35 1.94
205 206 6.727824 AAAAAGGTCTTACATCATGAGACG 57.272 37.500 0.09 0.00 43.37 4.18
206 207 4.392921 AAGGTCTTACATCATGAGACGG 57.607 45.455 0.09 0.00 43.37 4.79
207 208 3.632333 AGGTCTTACATCATGAGACGGA 58.368 45.455 0.09 0.00 43.37 4.69
208 209 3.634448 AGGTCTTACATCATGAGACGGAG 59.366 47.826 0.09 0.00 43.37 4.63
209 210 3.243569 GGTCTTACATCATGAGACGGAGG 60.244 52.174 0.09 0.00 43.37 4.30
210 211 2.959030 TCTTACATCATGAGACGGAGGG 59.041 50.000 0.09 0.00 0.00 4.30
211 212 2.748209 TACATCATGAGACGGAGGGA 57.252 50.000 0.09 0.00 0.00 4.20
212 213 1.407936 ACATCATGAGACGGAGGGAG 58.592 55.000 0.09 0.00 0.00 4.30
213 214 1.342474 ACATCATGAGACGGAGGGAGT 60.342 52.381 0.09 0.00 0.00 3.85
214 215 2.091830 ACATCATGAGACGGAGGGAGTA 60.092 50.000 0.09 0.00 0.00 2.59
215 216 2.350057 TCATGAGACGGAGGGAGTAG 57.650 55.000 0.00 0.00 0.00 2.57
216 217 1.564818 TCATGAGACGGAGGGAGTAGT 59.435 52.381 0.00 0.00 0.00 2.73
217 218 2.025226 TCATGAGACGGAGGGAGTAGTT 60.025 50.000 0.00 0.00 0.00 2.24
218 219 2.125773 TGAGACGGAGGGAGTAGTTC 57.874 55.000 0.00 0.00 0.00 3.01
219 220 1.634459 TGAGACGGAGGGAGTAGTTCT 59.366 52.381 0.00 0.00 0.00 3.01
220 221 2.018515 GAGACGGAGGGAGTAGTTCTG 58.981 57.143 0.00 0.00 0.00 3.02
221 222 1.634459 AGACGGAGGGAGTAGTTCTGA 59.366 52.381 0.00 0.00 0.00 3.27
222 223 2.242708 AGACGGAGGGAGTAGTTCTGAT 59.757 50.000 0.00 0.00 0.00 2.90
223 224 2.619646 GACGGAGGGAGTAGTTCTGATC 59.380 54.545 0.00 0.00 0.00 2.92
224 225 2.025226 ACGGAGGGAGTAGTTCTGATCA 60.025 50.000 0.00 0.00 0.00 2.92
225 226 3.226777 CGGAGGGAGTAGTTCTGATCAT 58.773 50.000 0.00 0.00 0.00 2.45
226 227 4.141228 ACGGAGGGAGTAGTTCTGATCATA 60.141 45.833 0.00 0.00 0.00 2.15
227 228 4.457603 CGGAGGGAGTAGTTCTGATCATAG 59.542 50.000 0.00 0.00 0.00 2.23
228 229 5.636123 GGAGGGAGTAGTTCTGATCATAGA 58.364 45.833 0.00 0.00 0.00 1.98
229 230 6.071984 GGAGGGAGTAGTTCTGATCATAGAA 58.928 44.000 0.00 0.00 34.46 2.10
251 252 8.678593 AGAACGGATTCTAACTTCTTTTTCTT 57.321 30.769 0.00 0.00 43.70 2.52
252 253 8.775527 AGAACGGATTCTAACTTCTTTTTCTTC 58.224 33.333 0.00 0.00 43.70 2.87
253 254 8.446599 AACGGATTCTAACTTCTTTTTCTTCA 57.553 30.769 0.00 0.00 0.00 3.02
254 255 8.622948 ACGGATTCTAACTTCTTTTTCTTCAT 57.377 30.769 0.00 0.00 0.00 2.57
255 256 9.067986 ACGGATTCTAACTTCTTTTTCTTCATT 57.932 29.630 0.00 0.00 0.00 2.57
261 262 8.784043 TCTAACTTCTTTTTCTTCATTAGCACC 58.216 33.333 0.00 0.00 0.00 5.01
262 263 7.588497 AACTTCTTTTTCTTCATTAGCACCT 57.412 32.000 0.00 0.00 0.00 4.00
263 264 6.974965 ACTTCTTTTTCTTCATTAGCACCTG 58.025 36.000 0.00 0.00 0.00 4.00
264 265 5.376854 TCTTTTTCTTCATTAGCACCTGC 57.623 39.130 0.00 0.00 42.49 4.85
265 266 4.826733 TCTTTTTCTTCATTAGCACCTGCA 59.173 37.500 0.00 0.00 45.16 4.41
266 267 5.477984 TCTTTTTCTTCATTAGCACCTGCAT 59.522 36.000 0.00 0.00 45.16 3.96
267 268 4.707030 TTTCTTCATTAGCACCTGCATG 57.293 40.909 0.00 0.00 45.16 4.06
268 269 2.019249 TCTTCATTAGCACCTGCATGC 58.981 47.619 11.82 11.82 46.50 4.06
275 276 3.044809 GCACCTGCATGCTGAAATG 57.955 52.632 24.53 18.80 42.62 2.32
276 277 0.459585 GCACCTGCATGCTGAAATGG 60.460 55.000 24.53 15.18 42.62 3.16
277 278 0.459585 CACCTGCATGCTGAAATGGC 60.460 55.000 24.53 0.00 0.00 4.40
281 282 1.476891 CTGCATGCTGAAATGGCTTCT 59.523 47.619 20.33 0.00 34.86 2.85
565 640 2.093021 TGGATGTCCGATTGATGCAAGA 60.093 45.455 0.00 0.00 39.43 3.02
612 687 3.133183 TCAGGTGTGCACTACAAGTACAA 59.867 43.478 19.41 0.00 41.89 2.41
629 704 7.285401 ACAAGTACAATTCATCCTCTGTTTTGT 59.715 33.333 0.00 0.00 36.10 2.83
720 797 7.939039 TGACCTGATTGTATGGGAGATAAAATC 59.061 37.037 0.00 0.00 31.82 2.17
750 827 2.180946 TGGGAGATGCCAGTGTAGAT 57.819 50.000 0.00 0.00 38.95 1.98
1092 1169 3.909732 AGTGTGGAAGGAAATTGGACAA 58.090 40.909 0.00 0.00 0.00 3.18
1102 1179 5.066593 AGGAAATTGGACAACAACTCTCTC 58.933 41.667 0.00 0.00 42.94 3.20
1212 1289 6.001460 TGGTGAACTGAAAAGGTTATACAGG 58.999 40.000 0.00 0.00 33.57 4.00
1237 1314 3.184581 CCTTGAGTTCTTTCGTCCTTTCG 59.815 47.826 0.00 0.00 0.00 3.46
1301 1379 4.589216 TTCAGCCCATTCTTGTTCAAAG 57.411 40.909 0.00 0.00 0.00 2.77
1675 1753 1.271871 TGAAGTTTGGTGATGCCCGAT 60.272 47.619 0.00 0.00 36.04 4.18
1707 1785 1.585668 GATCGTGTGCATCTCACTTCG 59.414 52.381 4.63 0.00 45.81 3.79
1816 1894 2.622436 GCTCTGTGTCCAGTTACCATC 58.378 52.381 0.00 0.00 39.82 3.51
1856 1934 9.778741 GGACTACTCACATCATCCAATTAAATA 57.221 33.333 0.00 0.00 0.00 1.40
1942 2041 7.731235 AGGGGTTCTCTTCTTATATTCCTAGAC 59.269 40.741 0.00 0.00 0.00 2.59
1980 2079 3.010696 TCCGTATAGCTGATGGATCCTCT 59.989 47.826 14.23 0.00 0.00 3.69
1982 2081 3.761218 CGTATAGCTGATGGATCCTCTGT 59.239 47.826 14.23 3.63 0.00 3.41
1983 2082 4.219507 CGTATAGCTGATGGATCCTCTGTT 59.780 45.833 14.23 11.74 0.00 3.16
1984 2083 5.279206 CGTATAGCTGATGGATCCTCTGTTT 60.279 44.000 14.23 7.56 0.00 2.83
1985 2084 5.643421 ATAGCTGATGGATCCTCTGTTTT 57.357 39.130 14.23 3.38 0.00 2.43
1986 2085 6.753913 ATAGCTGATGGATCCTCTGTTTTA 57.246 37.500 14.23 7.20 0.00 1.52
1987 2086 5.643421 AGCTGATGGATCCTCTGTTTTAT 57.357 39.130 14.23 0.00 0.00 1.40
1988 2087 6.753913 AGCTGATGGATCCTCTGTTTTATA 57.246 37.500 14.23 0.00 0.00 0.98
1989 2088 7.327064 AGCTGATGGATCCTCTGTTTTATAT 57.673 36.000 14.23 0.00 0.00 0.86
1990 2089 7.166851 AGCTGATGGATCCTCTGTTTTATATG 58.833 38.462 14.23 0.00 0.00 1.78
1991 2090 6.939163 GCTGATGGATCCTCTGTTTTATATGT 59.061 38.462 14.23 0.00 0.00 2.29
1992 2091 7.446625 GCTGATGGATCCTCTGTTTTATATGTT 59.553 37.037 14.23 0.00 0.00 2.71
1993 2092 8.908786 TGATGGATCCTCTGTTTTATATGTTC 57.091 34.615 14.23 0.00 0.00 3.18
1994 2093 7.939039 TGATGGATCCTCTGTTTTATATGTTCC 59.061 37.037 14.23 0.00 0.00 3.62
1995 2094 7.206789 TGGATCCTCTGTTTTATATGTTCCA 57.793 36.000 14.23 0.00 0.00 3.53
1996 2095 7.282585 TGGATCCTCTGTTTTATATGTTCCAG 58.717 38.462 14.23 0.00 0.00 3.86
1997 2096 7.127186 TGGATCCTCTGTTTTATATGTTCCAGA 59.873 37.037 14.23 0.00 0.00 3.86
1998 2097 8.160106 GGATCCTCTGTTTTATATGTTCCAGAT 58.840 37.037 3.84 0.00 0.00 2.90
1999 2098 9.566432 GATCCTCTGTTTTATATGTTCCAGATT 57.434 33.333 0.00 0.00 0.00 2.40
2000 2099 9.927081 ATCCTCTGTTTTATATGTTCCAGATTT 57.073 29.630 0.00 0.00 0.00 2.17
2001 2100 9.753674 TCCTCTGTTTTATATGTTCCAGATTTT 57.246 29.630 0.00 0.00 0.00 1.82
2004 2103 9.527157 TCTGTTTTATATGTTCCAGATTTTCCA 57.473 29.630 0.00 0.00 0.00 3.53
2005 2104 9.793252 CTGTTTTATATGTTCCAGATTTTCCAG 57.207 33.333 0.00 0.00 0.00 3.86
2006 2105 9.308000 TGTTTTATATGTTCCAGATTTTCCAGT 57.692 29.630 0.00 0.00 0.00 4.00
2014 2113 8.348285 TGTTCCAGATTTTCCAGTTTTATAGG 57.652 34.615 0.00 0.00 0.00 2.57
2015 2114 7.947890 TGTTCCAGATTTTCCAGTTTTATAGGT 59.052 33.333 0.00 0.00 0.00 3.08
2016 2115 8.803235 GTTCCAGATTTTCCAGTTTTATAGGTT 58.197 33.333 0.00 0.00 0.00 3.50
2017 2116 8.950007 TCCAGATTTTCCAGTTTTATAGGTTT 57.050 30.769 0.00 0.00 0.00 3.27
2018 2117 9.020731 TCCAGATTTTCCAGTTTTATAGGTTTC 57.979 33.333 0.00 0.00 0.00 2.78
2019 2118 9.025041 CCAGATTTTCCAGTTTTATAGGTTTCT 57.975 33.333 0.00 0.00 0.00 2.52
2111 2210 6.834168 TGTTCCAGATTTTCCAGTAAATCC 57.166 37.500 6.23 0.00 42.72 3.01
2118 2217 7.334090 CAGATTTTCCAGTAAATCCTCTCTCA 58.666 38.462 6.23 0.00 42.72 3.27
2183 2282 4.573201 TGAACCTTACTTTTGTGTCTTCCG 59.427 41.667 0.00 0.00 0.00 4.30
2436 2542 1.680338 CTAAGCATACAAGGGCCACC 58.320 55.000 6.18 0.00 0.00 4.61
2456 2562 6.238981 GCCACCTATCCTACTAGTAGTGAAAC 60.239 46.154 24.84 8.58 0.00 2.78
2787 6856 1.336440 CCAAAATGGTGTCGCTGAACA 59.664 47.619 0.00 0.00 31.35 3.18
3031 7100 7.931275 ACAGAAATTCAGTAGGAAAACTTGAC 58.069 34.615 0.00 0.00 39.39 3.18
3199 7269 3.121929 TGCCATCCTTCTTCCTCTACT 57.878 47.619 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.112009 CGGATTTTCAATAATGATGTAAGCGTG 59.888 37.037 0.00 0.00 34.96 5.34
1 2 7.132213 CGGATTTTCAATAATGATGTAAGCGT 58.868 34.615 0.00 0.00 34.96 5.07
3 4 7.141363 AGCGGATTTTCAATAATGATGTAAGC 58.859 34.615 0.00 0.00 34.96 3.09
4 5 8.961092 CAAGCGGATTTTCAATAATGATGTAAG 58.039 33.333 0.00 0.00 34.96 2.34
5 6 7.434897 GCAAGCGGATTTTCAATAATGATGTAA 59.565 33.333 0.00 0.00 34.96 2.41
6 7 6.917477 GCAAGCGGATTTTCAATAATGATGTA 59.083 34.615 0.00 0.00 34.96 2.29
7 8 5.750067 GCAAGCGGATTTTCAATAATGATGT 59.250 36.000 0.00 0.00 34.96 3.06
8 9 5.108141 CGCAAGCGGATTTTCAATAATGATG 60.108 40.000 6.55 0.00 33.75 3.07
9 10 4.977963 CGCAAGCGGATTTTCAATAATGAT 59.022 37.500 6.55 0.00 33.75 2.45
10 11 4.095632 TCGCAAGCGGATTTTCAATAATGA 59.904 37.500 14.98 0.00 40.25 2.57
11 12 4.350346 TCGCAAGCGGATTTTCAATAATG 58.650 39.130 14.98 0.00 40.25 1.90
12 13 4.601019 CTCGCAAGCGGATTTTCAATAAT 58.399 39.130 14.98 0.00 40.25 1.28
13 14 4.014847 CTCGCAAGCGGATTTTCAATAA 57.985 40.909 14.98 0.00 40.25 1.40
14 15 3.673746 CTCGCAAGCGGATTTTCAATA 57.326 42.857 14.98 0.00 40.25 1.90
15 16 2.549633 CTCGCAAGCGGATTTTCAAT 57.450 45.000 14.98 0.00 40.25 2.57
24 25 1.515521 AAAAGGTTCCTCGCAAGCGG 61.516 55.000 14.98 5.36 45.79 5.52
25 26 0.310854 AAAAAGGTTCCTCGCAAGCG 59.689 50.000 8.36 8.36 41.35 4.68
26 27 1.663161 CGAAAAAGGTTCCTCGCAAGC 60.663 52.381 0.00 0.00 37.18 4.01
27 28 1.871039 TCGAAAAAGGTTCCTCGCAAG 59.129 47.619 0.00 0.00 0.00 4.01
28 29 1.871039 CTCGAAAAAGGTTCCTCGCAA 59.129 47.619 0.00 0.00 0.00 4.85
29 30 1.202604 ACTCGAAAAAGGTTCCTCGCA 60.203 47.619 0.00 0.00 0.00 5.10
30 31 1.509703 ACTCGAAAAAGGTTCCTCGC 58.490 50.000 0.00 0.00 0.00 5.03
31 32 3.910648 ACTACTCGAAAAAGGTTCCTCG 58.089 45.455 0.00 0.00 0.00 4.63
34 35 9.807649 TGTAATATACTACTCGAAAAAGGTTCC 57.192 33.333 0.00 0.00 0.00 3.62
42 43 9.027129 GCACATGTTGTAATATACTACTCGAAA 57.973 33.333 0.00 0.00 35.82 3.46
43 44 8.192110 TGCACATGTTGTAATATACTACTCGAA 58.808 33.333 0.00 0.00 35.82 3.71
44 45 7.708998 TGCACATGTTGTAATATACTACTCGA 58.291 34.615 0.00 0.00 35.82 4.04
45 46 7.924103 TGCACATGTTGTAATATACTACTCG 57.076 36.000 0.00 0.00 35.82 4.18
47 48 9.613428 ACATTGCACATGTTGTAATATACTACT 57.387 29.630 0.00 0.00 38.37 2.57
48 49 9.650371 CACATTGCACATGTTGTAATATACTAC 57.350 33.333 10.56 0.00 38.37 2.73
49 50 9.606631 TCACATTGCACATGTTGTAATATACTA 57.393 29.630 10.56 0.00 38.37 1.82
50 51 8.504812 TCACATTGCACATGTTGTAATATACT 57.495 30.769 10.56 0.00 38.37 2.12
51 52 8.397906 ACTCACATTGCACATGTTGTAATATAC 58.602 33.333 10.56 0.00 38.37 1.47
52 53 8.504812 ACTCACATTGCACATGTTGTAATATA 57.495 30.769 10.56 0.00 38.37 0.86
53 54 7.121020 TGACTCACATTGCACATGTTGTAATAT 59.879 33.333 10.56 0.00 38.37 1.28
54 55 6.429385 TGACTCACATTGCACATGTTGTAATA 59.571 34.615 10.56 0.00 38.37 0.98
55 56 5.241285 TGACTCACATTGCACATGTTGTAAT 59.759 36.000 10.56 0.75 40.86 1.89
56 57 4.578105 TGACTCACATTGCACATGTTGTAA 59.422 37.500 10.56 0.00 33.93 2.41
57 58 4.133078 TGACTCACATTGCACATGTTGTA 58.867 39.130 10.56 0.00 0.00 2.41
58 59 2.950975 TGACTCACATTGCACATGTTGT 59.049 40.909 10.56 11.72 0.00 3.32
59 60 3.629438 TGACTCACATTGCACATGTTG 57.371 42.857 10.56 0.00 0.00 3.33
60 61 3.633525 ACTTGACTCACATTGCACATGTT 59.366 39.130 10.56 0.03 0.00 2.71
61 62 3.216800 ACTTGACTCACATTGCACATGT 58.783 40.909 8.21 8.21 0.00 3.21
62 63 3.365666 GGACTTGACTCACATTGCACATG 60.366 47.826 7.16 7.16 0.00 3.21
63 64 2.816087 GGACTTGACTCACATTGCACAT 59.184 45.455 0.00 0.00 0.00 3.21
64 65 2.221169 GGACTTGACTCACATTGCACA 58.779 47.619 0.00 0.00 0.00 4.57
65 66 2.221169 TGGACTTGACTCACATTGCAC 58.779 47.619 0.00 0.00 0.00 4.57
66 67 2.636647 TGGACTTGACTCACATTGCA 57.363 45.000 0.00 0.00 0.00 4.08
67 68 3.141398 TCTTGGACTTGACTCACATTGC 58.859 45.455 0.00 0.00 0.00 3.56
68 69 5.756195 TTTCTTGGACTTGACTCACATTG 57.244 39.130 0.00 0.00 0.00 2.82
69 70 6.773976 TTTTTCTTGGACTTGACTCACATT 57.226 33.333 0.00 0.00 0.00 2.71
89 90 7.242322 AGGTTCGGAGTCTAGAACTATTTTT 57.758 36.000 22.01 7.39 44.33 1.94
90 91 6.854091 AGGTTCGGAGTCTAGAACTATTTT 57.146 37.500 22.01 8.51 44.33 1.82
91 92 7.951347 TTAGGTTCGGAGTCTAGAACTATTT 57.049 36.000 22.01 13.04 44.33 1.40
92 93 7.951347 TTTAGGTTCGGAGTCTAGAACTATT 57.049 36.000 22.01 14.59 44.33 1.73
93 94 7.951347 TTTTAGGTTCGGAGTCTAGAACTAT 57.049 36.000 22.01 16.42 44.33 2.12
94 95 7.765695 TTTTTAGGTTCGGAGTCTAGAACTA 57.234 36.000 22.01 14.01 44.33 2.24
95 96 6.661304 TTTTTAGGTTCGGAGTCTAGAACT 57.339 37.500 22.01 14.66 44.33 3.01
128 129 1.592064 TCAGCTCGATTGTTGCACAA 58.408 45.000 4.56 4.56 42.95 3.33
129 130 1.532437 CTTCAGCTCGATTGTTGCACA 59.468 47.619 0.00 0.00 0.00 4.57
130 131 1.135859 CCTTCAGCTCGATTGTTGCAC 60.136 52.381 0.00 0.00 0.00 4.57
131 132 1.159285 CCTTCAGCTCGATTGTTGCA 58.841 50.000 0.00 0.00 0.00 4.08
132 133 1.160137 ACCTTCAGCTCGATTGTTGC 58.840 50.000 0.00 0.00 0.00 4.17
133 134 3.849911 TCTACCTTCAGCTCGATTGTTG 58.150 45.455 0.00 0.00 0.00 3.33
134 135 3.764434 TCTCTACCTTCAGCTCGATTGTT 59.236 43.478 0.00 0.00 0.00 2.83
135 136 3.357203 TCTCTACCTTCAGCTCGATTGT 58.643 45.455 0.00 0.00 0.00 2.71
136 137 4.582701 ATCTCTACCTTCAGCTCGATTG 57.417 45.455 0.00 0.00 0.00 2.67
137 138 6.245408 AGATATCTCTACCTTCAGCTCGATT 58.755 40.000 0.00 0.00 0.00 3.34
138 139 5.815581 AGATATCTCTACCTTCAGCTCGAT 58.184 41.667 0.00 0.00 0.00 3.59
139 140 5.235850 AGATATCTCTACCTTCAGCTCGA 57.764 43.478 0.00 0.00 0.00 4.04
140 141 5.584649 CCTAGATATCTCTACCTTCAGCTCG 59.415 48.000 8.95 0.00 32.66 5.03
141 142 6.481643 ACCTAGATATCTCTACCTTCAGCTC 58.518 44.000 8.95 0.00 32.66 4.09
142 143 6.463053 ACCTAGATATCTCTACCTTCAGCT 57.537 41.667 8.95 0.00 32.66 4.24
143 144 6.071616 CCAACCTAGATATCTCTACCTTCAGC 60.072 46.154 8.95 0.00 32.66 4.26
144 145 6.435904 CCCAACCTAGATATCTCTACCTTCAG 59.564 46.154 8.95 0.00 32.66 3.02
145 146 6.315714 CCCAACCTAGATATCTCTACCTTCA 58.684 44.000 8.95 0.00 32.66 3.02
146 147 5.186215 GCCCAACCTAGATATCTCTACCTTC 59.814 48.000 8.95 0.00 32.66 3.46
147 148 5.088026 GCCCAACCTAGATATCTCTACCTT 58.912 45.833 8.95 0.00 32.66 3.50
148 149 4.679331 GCCCAACCTAGATATCTCTACCT 58.321 47.826 8.95 0.00 32.66 3.08
149 150 3.444388 CGCCCAACCTAGATATCTCTACC 59.556 52.174 8.95 0.00 32.66 3.18
150 151 4.333690 TCGCCCAACCTAGATATCTCTAC 58.666 47.826 8.95 0.00 32.66 2.59
151 152 4.652679 TCGCCCAACCTAGATATCTCTA 57.347 45.455 8.95 0.00 32.66 2.43
152 153 3.527507 TCGCCCAACCTAGATATCTCT 57.472 47.619 8.95 0.00 35.39 3.10
153 154 4.951094 ACTATCGCCCAACCTAGATATCTC 59.049 45.833 8.95 0.00 0.00 2.75
154 155 4.707448 CACTATCGCCCAACCTAGATATCT 59.293 45.833 10.73 10.73 0.00 1.98
155 156 4.705507 TCACTATCGCCCAACCTAGATATC 59.294 45.833 0.00 0.00 0.00 1.63
156 157 4.463186 GTCACTATCGCCCAACCTAGATAT 59.537 45.833 0.00 0.00 0.00 1.63
157 158 3.825014 GTCACTATCGCCCAACCTAGATA 59.175 47.826 0.00 0.00 0.00 1.98
158 159 2.628657 GTCACTATCGCCCAACCTAGAT 59.371 50.000 0.00 0.00 0.00 1.98
159 160 2.029623 GTCACTATCGCCCAACCTAGA 58.970 52.381 0.00 0.00 0.00 2.43
160 161 1.754803 TGTCACTATCGCCCAACCTAG 59.245 52.381 0.00 0.00 0.00 3.02
161 162 1.855295 TGTCACTATCGCCCAACCTA 58.145 50.000 0.00 0.00 0.00 3.08
162 163 0.981183 TTGTCACTATCGCCCAACCT 59.019 50.000 0.00 0.00 0.00 3.50
163 164 1.816074 TTTGTCACTATCGCCCAACC 58.184 50.000 0.00 0.00 0.00 3.77
164 165 3.907894 TTTTTGTCACTATCGCCCAAC 57.092 42.857 0.00 0.00 0.00 3.77
182 183 5.643777 CCGTCTCATGATGTAAGACCTTTTT 59.356 40.000 8.23 0.00 36.84 1.94
183 184 5.046591 TCCGTCTCATGATGTAAGACCTTTT 60.047 40.000 8.23 0.00 36.84 2.27
184 185 4.466370 TCCGTCTCATGATGTAAGACCTTT 59.534 41.667 8.23 0.00 36.84 3.11
185 186 4.023980 TCCGTCTCATGATGTAAGACCTT 58.976 43.478 8.23 0.00 36.84 3.50
186 187 3.632333 TCCGTCTCATGATGTAAGACCT 58.368 45.455 8.23 0.00 36.84 3.85
187 188 3.243569 CCTCCGTCTCATGATGTAAGACC 60.244 52.174 8.23 0.00 36.84 3.85
188 189 3.243569 CCCTCCGTCTCATGATGTAAGAC 60.244 52.174 0.00 4.65 36.82 3.01
189 190 2.959030 CCCTCCGTCTCATGATGTAAGA 59.041 50.000 0.00 0.00 0.00 2.10
190 191 2.959030 TCCCTCCGTCTCATGATGTAAG 59.041 50.000 0.00 0.00 0.00 2.34
191 192 2.959030 CTCCCTCCGTCTCATGATGTAA 59.041 50.000 0.00 0.00 0.00 2.41
192 193 2.091830 ACTCCCTCCGTCTCATGATGTA 60.092 50.000 0.00 0.00 0.00 2.29
193 194 1.342474 ACTCCCTCCGTCTCATGATGT 60.342 52.381 0.00 0.00 0.00 3.06
194 195 1.407936 ACTCCCTCCGTCTCATGATG 58.592 55.000 0.00 0.00 0.00 3.07
195 196 2.175931 ACTACTCCCTCCGTCTCATGAT 59.824 50.000 0.00 0.00 0.00 2.45
196 197 1.564818 ACTACTCCCTCCGTCTCATGA 59.435 52.381 0.00 0.00 0.00 3.07
197 198 2.060050 ACTACTCCCTCCGTCTCATG 57.940 55.000 0.00 0.00 0.00 3.07
198 199 2.242708 AGAACTACTCCCTCCGTCTCAT 59.757 50.000 0.00 0.00 0.00 2.90
199 200 1.634459 AGAACTACTCCCTCCGTCTCA 59.366 52.381 0.00 0.00 0.00 3.27
200 201 2.018515 CAGAACTACTCCCTCCGTCTC 58.981 57.143 0.00 0.00 0.00 3.36
201 202 1.634459 TCAGAACTACTCCCTCCGTCT 59.366 52.381 0.00 0.00 0.00 4.18
202 203 2.125773 TCAGAACTACTCCCTCCGTC 57.874 55.000 0.00 0.00 0.00 4.79
203 204 2.025226 TGATCAGAACTACTCCCTCCGT 60.025 50.000 0.00 0.00 0.00 4.69
204 205 2.656002 TGATCAGAACTACTCCCTCCG 58.344 52.381 0.00 0.00 0.00 4.63
205 206 5.636123 TCTATGATCAGAACTACTCCCTCC 58.364 45.833 0.09 0.00 0.00 4.30
216 217 8.239038 AGTTAGAATCCGTTCTATGATCAGAA 57.761 34.615 0.09 0.00 44.24 3.02
217 218 7.825331 AGTTAGAATCCGTTCTATGATCAGA 57.175 36.000 0.09 0.00 44.24 3.27
218 219 8.356657 AGAAGTTAGAATCCGTTCTATGATCAG 58.643 37.037 0.09 0.00 44.24 2.90
219 220 8.239038 AGAAGTTAGAATCCGTTCTATGATCA 57.761 34.615 0.00 0.00 44.24 2.92
220 221 9.535878 AAAGAAGTTAGAATCCGTTCTATGATC 57.464 33.333 0.00 0.00 44.24 2.92
221 222 9.892130 AAAAGAAGTTAGAATCCGTTCTATGAT 57.108 29.630 0.00 0.00 44.24 2.45
222 223 9.720769 AAAAAGAAGTTAGAATCCGTTCTATGA 57.279 29.630 0.00 0.00 44.24 2.15
223 224 9.974750 GAAAAAGAAGTTAGAATCCGTTCTATG 57.025 33.333 0.00 0.00 44.24 2.23
224 225 9.945904 AGAAAAAGAAGTTAGAATCCGTTCTAT 57.054 29.630 0.00 0.00 44.24 1.98
225 226 9.774413 AAGAAAAAGAAGTTAGAATCCGTTCTA 57.226 29.630 0.00 0.00 42.79 2.10
226 227 8.678593 AAGAAAAAGAAGTTAGAATCCGTTCT 57.321 30.769 0.00 0.00 46.22 3.01
227 228 8.557029 TGAAGAAAAAGAAGTTAGAATCCGTTC 58.443 33.333 0.00 0.00 34.46 3.95
228 229 8.446599 TGAAGAAAAAGAAGTTAGAATCCGTT 57.553 30.769 0.00 0.00 0.00 4.44
229 230 8.622948 ATGAAGAAAAAGAAGTTAGAATCCGT 57.377 30.769 0.00 0.00 0.00 4.69
235 236 8.784043 GGTGCTAATGAAGAAAAAGAAGTTAGA 58.216 33.333 0.00 0.00 0.00 2.10
236 237 8.787852 AGGTGCTAATGAAGAAAAAGAAGTTAG 58.212 33.333 0.00 0.00 0.00 2.34
237 238 8.567948 CAGGTGCTAATGAAGAAAAAGAAGTTA 58.432 33.333 0.00 0.00 0.00 2.24
238 239 7.428826 CAGGTGCTAATGAAGAAAAAGAAGTT 58.571 34.615 0.00 0.00 0.00 2.66
239 240 6.515696 GCAGGTGCTAATGAAGAAAAAGAAGT 60.516 38.462 0.00 0.00 38.21 3.01
240 241 5.860716 GCAGGTGCTAATGAAGAAAAAGAAG 59.139 40.000 0.00 0.00 38.21 2.85
241 242 5.301551 TGCAGGTGCTAATGAAGAAAAAGAA 59.698 36.000 3.18 0.00 42.66 2.52
242 243 4.826733 TGCAGGTGCTAATGAAGAAAAAGA 59.173 37.500 3.18 0.00 42.66 2.52
243 244 5.125100 TGCAGGTGCTAATGAAGAAAAAG 57.875 39.130 3.18 0.00 42.66 2.27
244 245 5.472148 CATGCAGGTGCTAATGAAGAAAAA 58.528 37.500 3.18 0.00 42.66 1.94
245 246 4.618927 GCATGCAGGTGCTAATGAAGAAAA 60.619 41.667 14.21 0.00 41.82 2.29
246 247 3.119388 GCATGCAGGTGCTAATGAAGAAA 60.119 43.478 14.21 0.00 41.82 2.52
247 248 2.424601 GCATGCAGGTGCTAATGAAGAA 59.575 45.455 14.21 0.00 41.82 2.52
248 249 2.019249 GCATGCAGGTGCTAATGAAGA 58.981 47.619 14.21 0.00 41.82 2.87
249 250 2.486951 GCATGCAGGTGCTAATGAAG 57.513 50.000 14.21 0.00 41.82 3.02
257 258 0.459585 CCATTTCAGCATGCAGGTGC 60.460 55.000 21.98 4.04 45.25 5.01
258 259 0.459585 GCCATTTCAGCATGCAGGTG 60.460 55.000 21.98 9.94 46.98 4.00
259 260 0.613853 AGCCATTTCAGCATGCAGGT 60.614 50.000 21.98 0.00 34.76 4.00
260 261 0.535335 AAGCCATTTCAGCATGCAGG 59.465 50.000 21.98 11.90 34.76 4.85
261 262 1.476891 AGAAGCCATTTCAGCATGCAG 59.523 47.619 21.98 12.90 38.31 4.41
262 263 1.475280 GAGAAGCCATTTCAGCATGCA 59.525 47.619 21.98 0.00 38.31 3.96
263 264 1.533338 CGAGAAGCCATTTCAGCATGC 60.533 52.381 10.51 10.51 38.31 4.06
264 265 1.065102 CCGAGAAGCCATTTCAGCATG 59.935 52.381 0.00 0.00 38.31 4.06
265 266 1.386533 CCGAGAAGCCATTTCAGCAT 58.613 50.000 0.00 0.00 38.31 3.79
266 267 0.677731 CCCGAGAAGCCATTTCAGCA 60.678 55.000 0.00 0.00 38.31 4.41
267 268 0.678048 ACCCGAGAAGCCATTTCAGC 60.678 55.000 0.00 0.00 38.31 4.26
268 269 1.089920 CACCCGAGAAGCCATTTCAG 58.910 55.000 0.00 0.00 38.31 3.02
269 270 0.322456 CCACCCGAGAAGCCATTTCA 60.322 55.000 0.00 0.00 38.31 2.69
270 271 0.035439 TCCACCCGAGAAGCCATTTC 60.035 55.000 0.00 0.00 35.97 2.17
271 272 0.035056 CTCCACCCGAGAAGCCATTT 60.035 55.000 0.00 0.00 41.63 2.32
272 273 1.604378 CTCCACCCGAGAAGCCATT 59.396 57.895 0.00 0.00 41.63 3.16
273 274 3.036429 GCTCCACCCGAGAAGCCAT 62.036 63.158 0.00 0.00 41.63 4.40
274 275 2.798445 TAGCTCCACCCGAGAAGCCA 62.798 60.000 0.00 0.00 41.63 4.75
275 276 2.022240 CTAGCTCCACCCGAGAAGCC 62.022 65.000 0.00 0.00 41.63 4.35
276 277 1.439644 CTAGCTCCACCCGAGAAGC 59.560 63.158 0.00 0.00 41.63 3.86
277 278 1.439644 GCTAGCTCCACCCGAGAAG 59.560 63.158 7.70 0.00 41.63 2.85
612 687 5.829924 ACAGACAACAAAACAGAGGATGAAT 59.170 36.000 0.00 0.00 0.00 2.57
629 704 7.618502 AAACACAACACACTTATACAGACAA 57.381 32.000 0.00 0.00 0.00 3.18
720 797 4.722220 TGGCATCTCCCATCTTATCTTTG 58.278 43.478 0.00 0.00 0.00 2.77
750 827 9.890629 AACTTCTGCATACTCTCACATAATTTA 57.109 29.630 0.00 0.00 0.00 1.40
1092 1169 3.438781 TGTTTGTTTTGCGAGAGAGTTGT 59.561 39.130 0.00 0.00 0.00 3.32
1102 1179 3.306703 ACTTGCATCTTGTTTGTTTTGCG 59.693 39.130 0.00 0.00 32.90 4.85
1212 1289 2.037381 AGGACGAAAGAACTCAAGGTCC 59.963 50.000 0.00 0.00 42.08 4.46
1237 1314 6.183360 GCCAAGTCTTTTGGATCATTAGACTC 60.183 42.308 15.11 4.72 43.39 3.36
1301 1379 2.367241 TGGTTTAGCCCTTCCAAAAAGC 59.633 45.455 0.00 0.00 36.04 3.51
1532 1610 3.135712 TGGCTTTCTCCTGTACTCAAACA 59.864 43.478 0.00 0.00 0.00 2.83
1675 1753 2.416747 CACACGATCTTGCTTCTTCCA 58.583 47.619 0.00 0.00 0.00 3.53
1707 1785 4.437930 GCTGCTGATAATTCACTTGTGGAC 60.438 45.833 0.64 0.00 0.00 4.02
1816 1894 2.834549 AGTAGTCCACACCTTGAGATGG 59.165 50.000 0.00 0.00 0.00 3.51
1919 2018 8.480133 TGGTCTAGGAATATAAGAAGAGAACC 57.520 38.462 0.00 0.00 0.00 3.62
1942 2041 1.838077 ACGGACCCTATCTTTTCCTGG 59.162 52.381 0.00 0.00 0.00 4.45
1980 2079 9.308000 ACTGGAAAATCTGGAACATATAAAACA 57.692 29.630 0.00 0.00 38.20 2.83
1988 2087 8.971073 CCTATAAAACTGGAAAATCTGGAACAT 58.029 33.333 0.00 0.00 38.20 2.71
1989 2088 7.947890 ACCTATAAAACTGGAAAATCTGGAACA 59.052 33.333 0.00 0.00 0.00 3.18
1990 2089 8.349568 ACCTATAAAACTGGAAAATCTGGAAC 57.650 34.615 0.00 0.00 0.00 3.62
1991 2090 8.950007 AACCTATAAAACTGGAAAATCTGGAA 57.050 30.769 0.00 0.00 0.00 3.53
1992 2091 8.950007 AAACCTATAAAACTGGAAAATCTGGA 57.050 30.769 0.00 0.00 0.00 3.86
1993 2092 9.025041 AGAAACCTATAAAACTGGAAAATCTGG 57.975 33.333 0.00 0.00 0.00 3.86
2012 2111 9.643778 TCCCCATTATAGGAATATAAGAAACCT 57.356 33.333 0.00 0.00 35.11 3.50
2013 2112 9.907229 CTCCCCATTATAGGAATATAAGAAACC 57.093 37.037 0.00 0.00 0.00 3.27
2016 2115 9.057911 CCACTCCCCATTATAGGAATATAAGAA 57.942 37.037 0.00 0.00 0.00 2.52
2017 2116 8.414623 TCCACTCCCCATTATAGGAATATAAGA 58.585 37.037 0.00 0.00 0.00 2.10
2018 2117 8.624019 TCCACTCCCCATTATAGGAATATAAG 57.376 38.462 0.00 0.00 0.00 1.73
2019 2118 8.832735 GTTCCACTCCCCATTATAGGAATATAA 58.167 37.037 0.00 0.00 36.23 0.98
2020 2119 8.191110 AGTTCCACTCCCCATTATAGGAATATA 58.809 37.037 0.00 0.00 36.23 0.86
2021 2120 7.031917 AGTTCCACTCCCCATTATAGGAATAT 58.968 38.462 0.00 0.00 36.23 1.28
2022 2121 6.399013 AGTTCCACTCCCCATTATAGGAATA 58.601 40.000 0.00 0.00 36.23 1.75
2023 2122 5.235534 AGTTCCACTCCCCATTATAGGAAT 58.764 41.667 0.00 0.00 36.23 3.01
2024 2123 4.641868 AGTTCCACTCCCCATTATAGGAA 58.358 43.478 0.00 0.00 0.00 3.36
2025 2124 4.295905 AGTTCCACTCCCCATTATAGGA 57.704 45.455 0.00 0.00 0.00 2.94
2111 2210 8.034215 ACTTCATAATTGAACTGACTGAGAGAG 58.966 37.037 0.00 0.00 36.94 3.20
2118 2217 5.482908 AGCGACTTCATAATTGAACTGACT 58.517 37.500 0.00 0.00 36.94 3.41
2183 2282 1.003696 CCTTCCCTGTCTTCAGTTCCC 59.996 57.143 0.00 0.00 39.82 3.97
2436 2542 9.175312 TGACTTGTTTCACTACTAGTAGGATAG 57.825 37.037 29.05 17.45 34.91 2.08
3031 7100 1.855513 TACAACGAACAACACGAGGG 58.144 50.000 0.00 0.00 34.70 4.30
3123 7193 5.621197 TTCACGAAAAGTAACATCCATGG 57.379 39.130 4.97 4.97 0.00 3.66


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

AutoCloner maintained by Alex Coulton.