Multiple sequence alignment - TraesCS4A01G001400

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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 TraesCS4A01G001400 chr4A 100.000 2396 0 0 1 2396 1075557 1077952 0.000000e+00 4425.0
1 TraesCS4A01G001400 chr4A 81.421 183 26 7 1042 1220 685826807 685826985 2.480000e-30 143.0
2 TraesCS4A01G001400 chr4B 86.585 1789 97 66 666 2394 1081034 1079329 0.000000e+00 1842.0
3 TraesCS4A01G001400 chr4B 80.645 496 48 30 176 645 1081575 1081102 8.200000e-90 340.0
4 TraesCS4A01G001400 chr4B 88.936 235 14 6 1199 1426 1066444 1066215 1.810000e-71 279.0
5 TraesCS4A01G001400 chr4B 80.328 183 28 7 1042 1220 606755170 606755348 5.370000e-27 132.0
6 TraesCS4A01G001400 chr4B 94.737 38 2 0 1908 1945 1066218 1066181 2.570000e-05 60.2
7 TraesCS4A01G001400 chr4D 81.915 2151 137 119 362 2394 738325 740341 0.000000e+00 1585.0
8 TraesCS4A01G001400 chr4D 82.199 191 24 9 1042 1227 479525195 479525380 3.190000e-34 156.0
9 TraesCS4A01G001400 chr5D 80.952 168 23 8 1006 1171 488901013 488900853 8.990000e-25 124.0
10 TraesCS4A01G001400 chr5D 85.156 128 12 5 1046 1171 519435855 519435733 8.990000e-25 124.0
11 TraesCS4A01G001400 chr5B 80.952 168 23 8 1006 1171 602341234 602341074 8.990000e-25 124.0
12 TraesCS4A01G001400 chr2A 78.409 176 29 7 1048 1220 680357721 680357552 3.260000e-19 106.0
13 TraesCS4A01G001400 chr2D 77.419 186 27 11 1041 1220 538055276 538055100 1.960000e-16 97.1
14 TraesCS4A01G001400 chr6B 76.243 181 36 6 1045 1223 474749458 474749283 3.280000e-14 89.8
15 TraesCS4A01G001400 chr5A 76.243 181 32 8 1046 1222 393917984 393918157 4.240000e-13 86.1


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 TraesCS4A01G001400 chr4A 1075557 1077952 2395 False 4425 4425 100.000 1 2396 1 chr4A.!!$F1 2395
1 TraesCS4A01G001400 chr4B 1079329 1081575 2246 True 1091 1842 83.615 176 2394 2 chr4B.!!$R2 2218
2 TraesCS4A01G001400 chr4D 738325 740341 2016 False 1585 1585 81.915 362 2394 1 chr4D.!!$F1 2032

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
147 148 0.030638 CCGCAAACACCAACCAGAAG 59.969 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 2022 0.105039 GCCAGGAAGTACGAGGATGG 59.895 60.0 0.0 3.65 0.0 3.51 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
24 25 7.158099 GAAGGTTCCACTATAGCAAAAATGT 57.842 36.000 0.00 0.00 0.00 2.71
25 26 6.515272 AGGTTCCACTATAGCAAAAATGTG 57.485 37.500 0.00 0.00 0.00 3.21
26 27 6.245408 AGGTTCCACTATAGCAAAAATGTGA 58.755 36.000 0.00 0.00 0.00 3.58
27 28 6.719370 AGGTTCCACTATAGCAAAAATGTGAA 59.281 34.615 0.00 0.00 0.00 3.18
28 29 7.029563 GGTTCCACTATAGCAAAAATGTGAAG 58.970 38.462 0.00 0.00 0.00 3.02
29 30 7.094377 GGTTCCACTATAGCAAAAATGTGAAGA 60.094 37.037 0.00 0.00 0.00 2.87
30 31 7.994425 TCCACTATAGCAAAAATGTGAAGAA 57.006 32.000 0.00 0.00 0.00 2.52
31 32 8.579850 TCCACTATAGCAAAAATGTGAAGAAT 57.420 30.769 0.00 0.00 0.00 2.40
32 33 9.023962 TCCACTATAGCAAAAATGTGAAGAATT 57.976 29.630 0.00 0.00 0.00 2.17
33 34 9.643693 CCACTATAGCAAAAATGTGAAGAATTT 57.356 29.630 0.00 0.00 0.00 1.82
39 40 8.579682 AGCAAAAATGTGAAGAATTTAGACAC 57.420 30.769 0.00 0.00 0.00 3.67
40 41 8.196771 AGCAAAAATGTGAAGAATTTAGACACA 58.803 29.630 0.00 0.00 43.70 3.72
41 42 8.816144 GCAAAAATGTGAAGAATTTAGACACAA 58.184 29.630 0.00 0.00 43.02 3.33
48 49 9.607988 TGTGAAGAATTTAGACACAAAGTTAGA 57.392 29.630 0.00 0.00 38.28 2.10
54 55 9.600646 GAATTTAGACACAAAGTTAGAAGAAGC 57.399 33.333 0.00 0.00 0.00 3.86
55 56 8.677148 ATTTAGACACAAAGTTAGAAGAAGCA 57.323 30.769 0.00 0.00 0.00 3.91
56 57 8.677148 TTTAGACACAAAGTTAGAAGAAGCAT 57.323 30.769 0.00 0.00 0.00 3.79
57 58 6.551385 AGACACAAAGTTAGAAGAAGCATG 57.449 37.500 0.00 0.00 0.00 4.06
58 59 5.049129 AGACACAAAGTTAGAAGAAGCATGC 60.049 40.000 10.51 10.51 0.00 4.06
59 60 4.022849 ACACAAAGTTAGAAGAAGCATGCC 60.023 41.667 15.66 0.00 0.00 4.40
60 61 3.189287 ACAAAGTTAGAAGAAGCATGCCG 59.811 43.478 15.66 0.00 0.00 5.69
61 62 2.770164 AGTTAGAAGAAGCATGCCGT 57.230 45.000 15.66 1.78 0.00 5.68
62 63 3.887621 AGTTAGAAGAAGCATGCCGTA 57.112 42.857 15.66 0.00 0.00 4.02
63 64 4.202245 AGTTAGAAGAAGCATGCCGTAA 57.798 40.909 15.66 0.67 0.00 3.18
64 65 4.184629 AGTTAGAAGAAGCATGCCGTAAG 58.815 43.478 15.66 0.00 0.00 2.34
65 66 4.081642 AGTTAGAAGAAGCATGCCGTAAGA 60.082 41.667 15.66 0.00 43.02 2.10
66 67 3.334583 AGAAGAAGCATGCCGTAAGAA 57.665 42.857 15.66 0.00 43.02 2.52
67 68 3.674997 AGAAGAAGCATGCCGTAAGAAA 58.325 40.909 15.66 0.00 43.02 2.52
68 69 4.072131 AGAAGAAGCATGCCGTAAGAAAA 58.928 39.130 15.66 0.00 43.02 2.29
69 70 4.154918 AGAAGAAGCATGCCGTAAGAAAAG 59.845 41.667 15.66 0.00 43.02 2.27
70 71 3.674997 AGAAGCATGCCGTAAGAAAAGA 58.325 40.909 15.66 0.00 43.02 2.52
71 72 4.072131 AGAAGCATGCCGTAAGAAAAGAA 58.928 39.130 15.66 0.00 43.02 2.52
72 73 4.702131 AGAAGCATGCCGTAAGAAAAGAAT 59.298 37.500 15.66 0.00 43.02 2.40
73 74 5.880332 AGAAGCATGCCGTAAGAAAAGAATA 59.120 36.000 15.66 0.00 43.02 1.75
74 75 5.485662 AGCATGCCGTAAGAAAAGAATAC 57.514 39.130 15.66 0.00 43.02 1.89
75 76 4.941263 AGCATGCCGTAAGAAAAGAATACA 59.059 37.500 15.66 0.00 43.02 2.29
76 77 5.028375 GCATGCCGTAAGAAAAGAATACAC 58.972 41.667 6.36 0.00 43.02 2.90
77 78 4.914312 TGCCGTAAGAAAAGAATACACG 57.086 40.909 0.00 0.00 43.02 4.49
78 79 3.123959 TGCCGTAAGAAAAGAATACACGC 59.876 43.478 0.00 0.00 43.02 5.34
79 80 3.370061 GCCGTAAGAAAAGAATACACGCT 59.630 43.478 0.00 0.00 43.02 5.07
80 81 4.724036 GCCGTAAGAAAAGAATACACGCTG 60.724 45.833 0.00 0.00 43.02 5.18
81 82 4.201685 CCGTAAGAAAAGAATACACGCTGG 60.202 45.833 0.00 0.00 43.02 4.85
82 83 4.624024 CGTAAGAAAAGAATACACGCTGGA 59.376 41.667 0.00 0.00 43.02 3.86
83 84 5.291128 CGTAAGAAAAGAATACACGCTGGAT 59.709 40.000 0.00 0.00 43.02 3.41
84 85 6.474427 CGTAAGAAAAGAATACACGCTGGATA 59.526 38.462 0.00 0.00 43.02 2.59
85 86 7.009815 CGTAAGAAAAGAATACACGCTGGATAA 59.990 37.037 0.00 0.00 43.02 1.75
86 87 7.865706 AAGAAAAGAATACACGCTGGATAAT 57.134 32.000 0.00 0.00 0.00 1.28
87 88 8.958119 AAGAAAAGAATACACGCTGGATAATA 57.042 30.769 0.00 0.00 0.00 0.98
88 89 8.958119 AGAAAAGAATACACGCTGGATAATAA 57.042 30.769 0.00 0.00 0.00 1.40
89 90 9.561069 AGAAAAGAATACACGCTGGATAATAAT 57.439 29.630 0.00 0.00 0.00 1.28
90 91 9.813080 GAAAAGAATACACGCTGGATAATAATC 57.187 33.333 0.00 0.00 0.00 1.75
91 92 8.902540 AAAGAATACACGCTGGATAATAATCA 57.097 30.769 0.00 0.00 33.41 2.57
92 93 9.507329 AAAGAATACACGCTGGATAATAATCAT 57.493 29.630 0.00 0.00 33.41 2.45
93 94 8.709386 AGAATACACGCTGGATAATAATCATC 57.291 34.615 0.00 0.00 33.41 2.92
94 95 8.535335 AGAATACACGCTGGATAATAATCATCT 58.465 33.333 0.00 0.00 33.41 2.90
95 96 9.155975 GAATACACGCTGGATAATAATCATCTT 57.844 33.333 0.00 0.00 33.41 2.40
101 102 9.302345 ACGCTGGATAATAATCATCTTATTACG 57.698 33.333 0.81 2.95 31.85 3.18
102 103 9.302345 CGCTGGATAATAATCATCTTATTACGT 57.698 33.333 0.00 0.00 31.85 3.57
115 116 8.582437 TCATCTTATTACGTAAAGTCCATAGGG 58.418 37.037 12.81 0.00 0.00 3.53
116 117 7.902920 TCTTATTACGTAAAGTCCATAGGGT 57.097 36.000 12.81 0.00 34.93 4.34
117 118 7.945134 TCTTATTACGTAAAGTCCATAGGGTC 58.055 38.462 12.81 0.00 34.93 4.46
118 119 5.541953 ATTACGTAAAGTCCATAGGGTCC 57.458 43.478 12.81 0.00 34.93 4.46
119 120 2.823959 ACGTAAAGTCCATAGGGTCCA 58.176 47.619 0.00 0.00 34.93 4.02
120 121 3.175594 ACGTAAAGTCCATAGGGTCCAA 58.824 45.455 0.00 0.00 34.93 3.53
121 122 3.197116 ACGTAAAGTCCATAGGGTCCAAG 59.803 47.826 0.00 0.00 34.93 3.61
122 123 2.808906 AAAGTCCATAGGGTCCAAGC 57.191 50.000 0.00 0.00 34.93 4.01
123 124 0.919710 AAGTCCATAGGGTCCAAGCC 59.080 55.000 0.00 0.00 35.59 4.35
124 125 0.253160 AGTCCATAGGGTCCAAGCCA 60.253 55.000 0.00 0.00 38.48 4.75
125 126 0.846693 GTCCATAGGGTCCAAGCCAT 59.153 55.000 0.00 0.00 38.48 4.40
126 127 1.215423 GTCCATAGGGTCCAAGCCATT 59.785 52.381 0.00 0.00 38.48 3.16
127 128 1.215173 TCCATAGGGTCCAAGCCATTG 59.785 52.381 0.00 0.00 38.48 2.82
128 129 1.035139 CATAGGGTCCAAGCCATTGC 58.965 55.000 0.00 0.00 38.48 3.56
129 130 0.106015 ATAGGGTCCAAGCCATTGCC 60.106 55.000 0.00 0.00 38.48 4.52
130 131 2.550699 TAGGGTCCAAGCCATTGCCG 62.551 60.000 0.00 0.00 38.48 5.69
131 132 4.133796 GGTCCAAGCCATTGCCGC 62.134 66.667 0.00 0.00 38.69 6.53
132 133 3.372730 GTCCAAGCCATTGCCGCA 61.373 61.111 0.00 0.00 38.69 5.69
133 134 2.599875 TCCAAGCCATTGCCGCAA 60.600 55.556 8.55 8.55 38.69 4.85
134 135 2.205843 TCCAAGCCATTGCCGCAAA 61.206 52.632 10.42 0.00 38.69 3.68
135 136 2.028733 CCAAGCCATTGCCGCAAAC 61.029 57.895 10.42 3.03 38.69 2.93
136 137 1.300775 CAAGCCATTGCCGCAAACA 60.301 52.632 10.42 0.00 38.69 2.83
137 138 1.300853 AAGCCATTGCCGCAAACAC 60.301 52.632 10.42 2.29 38.69 3.32
138 139 2.713927 AAGCCATTGCCGCAAACACC 62.714 55.000 10.42 0.00 38.69 4.16
139 140 2.733301 CCATTGCCGCAAACACCA 59.267 55.556 10.42 0.00 0.00 4.17
140 141 1.068753 CCATTGCCGCAAACACCAA 59.931 52.632 10.42 0.00 0.00 3.67
141 142 1.220817 CCATTGCCGCAAACACCAAC 61.221 55.000 10.42 0.00 0.00 3.77
142 143 1.068921 ATTGCCGCAAACACCAACC 59.931 52.632 10.42 0.00 0.00 3.77
143 144 1.680522 ATTGCCGCAAACACCAACCA 61.681 50.000 10.42 0.00 0.00 3.67
144 145 2.027460 GCCGCAAACACCAACCAG 59.973 61.111 0.00 0.00 0.00 4.00
145 146 2.485795 GCCGCAAACACCAACCAGA 61.486 57.895 0.00 0.00 0.00 3.86
146 147 2.010582 GCCGCAAACACCAACCAGAA 62.011 55.000 0.00 0.00 0.00 3.02
147 148 0.030638 CCGCAAACACCAACCAGAAG 59.969 55.000 0.00 0.00 0.00 2.85
148 149 1.021202 CGCAAACACCAACCAGAAGA 58.979 50.000 0.00 0.00 0.00 2.87
149 150 1.002468 CGCAAACACCAACCAGAAGAG 60.002 52.381 0.00 0.00 0.00 2.85
150 151 2.297701 GCAAACACCAACCAGAAGAGA 58.702 47.619 0.00 0.00 0.00 3.10
151 152 2.887152 GCAAACACCAACCAGAAGAGAT 59.113 45.455 0.00 0.00 0.00 2.75
152 153 3.304928 GCAAACACCAACCAGAAGAGATG 60.305 47.826 0.00 0.00 0.00 2.90
153 154 3.864789 AACACCAACCAGAAGAGATGT 57.135 42.857 0.00 0.00 0.00 3.06
154 155 3.131709 ACACCAACCAGAAGAGATGTG 57.868 47.619 0.00 0.00 0.00 3.21
155 156 2.439507 ACACCAACCAGAAGAGATGTGT 59.560 45.455 0.00 0.00 0.00 3.72
156 157 3.070018 CACCAACCAGAAGAGATGTGTC 58.930 50.000 0.00 0.00 0.00 3.67
157 158 2.975489 ACCAACCAGAAGAGATGTGTCT 59.025 45.455 0.00 0.00 37.42 3.41
158 159 4.021104 CACCAACCAGAAGAGATGTGTCTA 60.021 45.833 0.00 0.00 33.97 2.59
159 160 4.780021 ACCAACCAGAAGAGATGTGTCTAT 59.220 41.667 0.00 0.00 33.97 1.98
160 161 5.249393 ACCAACCAGAAGAGATGTGTCTATT 59.751 40.000 0.00 0.00 38.55 1.73
202 203 8.840833 ATGTGGGGAATAATTTGTTAAACAAC 57.159 30.769 0.00 0.00 37.90 3.32
206 207 7.815068 TGGGGAATAATTTGTTAAACAACGATG 59.185 33.333 0.00 0.00 37.90 3.84
208 209 7.380320 GGAATAATTTGTTAAACAACGATGCG 58.620 34.615 0.00 0.00 37.90 4.73
225 228 5.756347 ACGATGCGGCTTTATTGATTAAGTA 59.244 36.000 0.00 0.00 0.00 2.24
250 253 5.663795 AAACAATACAGCATATCAGAGCG 57.336 39.130 0.00 0.00 35.48 5.03
278 281 7.437869 AAAAACAAAACAAAAACAACCAACG 57.562 28.000 0.00 0.00 0.00 4.10
279 282 4.135186 ACAAAACAAAAACAACCAACGC 57.865 36.364 0.00 0.00 0.00 4.84
281 284 4.214332 ACAAAACAAAAACAACCAACGCAT 59.786 33.333 0.00 0.00 0.00 4.73
319 330 3.656559 AGAAAATCACACCAAGCAATGC 58.343 40.909 0.00 0.00 0.00 3.56
379 393 3.848272 ACAATCCAACATTTACGGCAG 57.152 42.857 0.00 0.00 0.00 4.85
394 408 1.066002 CGGCAGCCCACATCAATTTAG 59.934 52.381 5.63 0.00 0.00 1.85
430 444 2.907458 CAGAAAACTGGAGGGGGATT 57.093 50.000 0.00 0.00 0.00 3.01
432 446 4.526438 CAGAAAACTGGAGGGGGATTAT 57.474 45.455 0.00 0.00 0.00 1.28
433 447 5.646692 CAGAAAACTGGAGGGGGATTATA 57.353 43.478 0.00 0.00 0.00 0.98
434 448 6.206180 CAGAAAACTGGAGGGGGATTATAT 57.794 41.667 0.00 0.00 0.00 0.86
436 450 5.676811 AGAAAACTGGAGGGGGATTATATGT 59.323 40.000 0.00 0.00 0.00 2.29
438 452 6.449830 AAACTGGAGGGGGATTATATGTAC 57.550 41.667 0.00 0.00 0.00 2.90
439 453 5.101254 ACTGGAGGGGGATTATATGTACA 57.899 43.478 0.00 0.00 0.00 2.90
440 454 5.676125 ACTGGAGGGGGATTATATGTACAT 58.324 41.667 13.93 13.93 0.00 2.29
441 455 5.488919 ACTGGAGGGGGATTATATGTACATG 59.511 44.000 18.81 0.00 0.00 3.21
442 456 5.670899 TGGAGGGGGATTATATGTACATGA 58.329 41.667 18.81 3.40 0.00 3.07
443 457 5.726308 TGGAGGGGGATTATATGTACATGAG 59.274 44.000 18.81 0.00 0.00 2.90
459 473 5.880054 ACATGAGTTTTACAGGCATGTAC 57.120 39.130 11.37 2.41 45.33 2.90
462 482 7.165485 ACATGAGTTTTACAGGCATGTACTAA 58.835 34.615 11.37 5.97 45.33 2.24
484 504 3.830755 AGTACGTATGTGTCCTTTGAGGT 59.169 43.478 0.00 0.00 36.53 3.85
485 505 3.040147 ACGTATGTGTCCTTTGAGGTG 57.960 47.619 0.00 0.00 36.53 4.00
486 506 1.732259 CGTATGTGTCCTTTGAGGTGC 59.268 52.381 0.00 0.00 36.53 5.01
487 507 2.778299 GTATGTGTCCTTTGAGGTGCA 58.222 47.619 0.00 0.00 36.53 4.57
533 568 4.525100 TGTTGTGTCTACATACTAGTGCCA 59.475 41.667 5.39 0.00 36.53 4.92
540 575 7.980099 GTGTCTACATACTAGTGCCAAATACTT 59.020 37.037 5.39 0.00 0.00 2.24
541 576 9.192642 TGTCTACATACTAGTGCCAAATACTTA 57.807 33.333 5.39 0.00 0.00 2.24
550 585 8.647796 ACTAGTGCCAAATACTTATATGTAGCA 58.352 33.333 0.00 5.75 0.00 3.49
552 587 7.279615 AGTGCCAAATACTTATATGTAGCACA 58.720 34.615 25.80 11.34 40.11 4.57
553 588 7.939039 AGTGCCAAATACTTATATGTAGCACAT 59.061 33.333 25.80 16.28 40.11 3.21
566 601 5.876651 TGTAGCACATACATCTGGAGATT 57.123 39.130 0.00 0.00 39.52 2.40
569 604 8.650143 TGTAGCACATACATCTGGAGATTATA 57.350 34.615 0.00 0.00 39.52 0.98
604 644 8.177119 AGAAAGAAACTTTGGTTGTATGCATA 57.823 30.769 1.16 1.16 35.63 3.14
809 915 1.893315 TATCCCTTTCCCACCCTCTG 58.107 55.000 0.00 0.00 0.00 3.35
871 978 2.541346 CCTTCATCACCAACATCGATCG 59.459 50.000 9.36 9.36 0.00 3.69
898 1014 2.028112 CACTTCATTCTCCCTCGTTCCA 60.028 50.000 0.00 0.00 0.00 3.53
915 1031 0.466922 CCATCCAAGCTCCACCATCC 60.467 60.000 0.00 0.00 0.00 3.51
917 1033 1.133575 CATCCAAGCTCCACCATCCAT 60.134 52.381 0.00 0.00 0.00 3.41
929 1045 2.756207 CACCATCCATCACTGATTTGCA 59.244 45.455 0.00 0.00 0.00 4.08
930 1046 2.756760 ACCATCCATCACTGATTTGCAC 59.243 45.455 0.00 0.00 0.00 4.57
935 1062 4.009675 TCCATCACTGATTTGCACTTACC 58.990 43.478 0.00 0.00 0.00 2.85
938 1065 5.295292 CCATCACTGATTTGCACTTACCTAG 59.705 44.000 0.00 0.00 0.00 3.02
946 1073 2.022195 TGCACTTACCTAGCTACTCCG 58.978 52.381 0.00 0.00 0.00 4.63
987 1114 7.703197 GGCTTCTTCATTTCTCACTACTAGTAC 59.297 40.741 0.00 0.00 0.00 2.73
988 1115 7.429920 GCTTCTTCATTTCTCACTACTAGTACG 59.570 40.741 0.00 0.00 0.00 3.67
989 1116 7.918536 TCTTCATTTCTCACTACTAGTACGT 57.081 36.000 0.00 0.00 0.00 3.57
999 1126 8.256605 TCTCACTACTAGTACGTAGTTGAGATT 58.743 37.037 20.34 3.76 45.76 2.40
1017 1144 0.031515 TTATGGAGGGCGGAGAAGGA 60.032 55.000 0.00 0.00 0.00 3.36
1020 1147 2.512355 GGAGGGCGGAGAAGGATCC 61.512 68.421 2.48 2.48 35.88 3.36
1026 1153 2.506472 GGAGAAGGATCCGGTGGC 59.494 66.667 5.98 0.00 0.00 5.01
1294 1421 3.267860 CGGCGAGGCAGCAGAATC 61.268 66.667 0.00 0.00 39.27 2.52
1295 1422 2.124983 GGCGAGGCAGCAGAATCA 60.125 61.111 7.25 0.00 39.27 2.57
1296 1423 2.178890 GGCGAGGCAGCAGAATCAG 61.179 63.158 7.25 0.00 39.27 2.90
1401 1538 5.520288 CGACAAATCCAACAAGTAGATCGAT 59.480 40.000 0.00 0.00 0.00 3.59
1402 1539 6.508563 CGACAAATCCAACAAGTAGATCGATG 60.509 42.308 0.54 0.00 0.00 3.84
1424 1561 4.521536 GATCATCCATCCATCCATCCAT 57.478 45.455 0.00 0.00 0.00 3.41
1425 1562 3.732048 TCATCCATCCATCCATCCATG 57.268 47.619 0.00 0.00 0.00 3.66
1523 1660 6.437793 GGATGCAATCTACACTACCTACCTAT 59.562 42.308 0.00 0.00 44.71 2.57
1629 1807 1.485895 TGCATGAGGATTCCATCGACA 59.514 47.619 5.29 0.00 0.00 4.35
1678 1856 2.033407 CGATCGAGTAATTTGCAGCCAG 60.033 50.000 10.26 0.00 0.00 4.85
1683 1861 4.570772 TCGAGTAATTTGCAGCCAGTAATC 59.429 41.667 0.00 0.00 0.00 1.75
1684 1862 4.260784 CGAGTAATTTGCAGCCAGTAATCC 60.261 45.833 0.00 0.00 0.00 3.01
1685 1863 4.599041 AGTAATTTGCAGCCAGTAATCCA 58.401 39.130 0.00 0.00 0.00 3.41
1686 1864 5.016173 AGTAATTTGCAGCCAGTAATCCAA 58.984 37.500 0.00 0.00 0.00 3.53
1687 1865 5.658190 AGTAATTTGCAGCCAGTAATCCAAT 59.342 36.000 0.00 0.00 0.00 3.16
1688 1866 4.660789 ATTTGCAGCCAGTAATCCAATC 57.339 40.909 0.00 0.00 0.00 2.67
1689 1867 1.667236 TGCAGCCAGTAATCCAATCG 58.333 50.000 0.00 0.00 0.00 3.34
1690 1868 1.209261 TGCAGCCAGTAATCCAATCGA 59.791 47.619 0.00 0.00 0.00 3.59
1691 1869 2.158769 TGCAGCCAGTAATCCAATCGAT 60.159 45.455 0.00 0.00 0.00 3.59
1693 1871 3.732212 CAGCCAGTAATCCAATCGATGA 58.268 45.455 0.00 0.00 0.00 2.92
1695 1873 5.482006 CAGCCAGTAATCCAATCGATGATA 58.518 41.667 0.00 0.00 0.00 2.15
1696 1874 6.111382 CAGCCAGTAATCCAATCGATGATAT 58.889 40.000 0.00 0.00 0.00 1.63
1697 1875 6.036844 CAGCCAGTAATCCAATCGATGATATG 59.963 42.308 0.00 0.00 0.00 1.78
1747 1932 4.793216 CGCAATGCCTACATTTTCAGTTAC 59.207 41.667 0.00 0.00 44.21 2.50
1748 1933 5.618863 CGCAATGCCTACATTTTCAGTTACA 60.619 40.000 0.00 0.00 44.21 2.41
1815 2007 7.148457 GCATCGATCATCTCAACATCAACATAT 60.148 37.037 0.00 0.00 0.00 1.78
1871 2064 4.610945 CGAGATTTATTCAATGTTGGGGC 58.389 43.478 0.00 0.00 0.00 5.80
1884 2077 6.598457 TCAATGTTGGGGCATTAAATCAAATG 59.402 34.615 0.00 0.00 37.00 2.32
1915 2108 3.058016 GCTTGTTAGTCACACATGCACAT 60.058 43.478 0.00 0.00 42.23 3.21
1916 2109 4.469552 CTTGTTAGTCACACATGCACATG 58.530 43.478 9.06 9.06 44.15 3.21
1978 2187 4.104897 ACCTACCTGGAAGCTTCTTTCTTT 59.895 41.667 25.05 8.41 39.71 2.52
1979 2188 4.697828 CCTACCTGGAAGCTTCTTTCTTTC 59.302 45.833 25.05 7.94 38.35 2.62
1980 2189 4.170468 ACCTGGAAGCTTCTTTCTTTCA 57.830 40.909 25.05 12.01 0.00 2.69
1981 2190 4.734266 ACCTGGAAGCTTCTTTCTTTCAT 58.266 39.130 25.05 0.00 29.40 2.57
1982 2191 5.143369 ACCTGGAAGCTTCTTTCTTTCATT 58.857 37.500 25.05 1.60 29.40 2.57
1983 2192 5.242615 ACCTGGAAGCTTCTTTCTTTCATTC 59.757 40.000 25.05 5.31 29.40 2.67
2066 2276 6.585695 AGGAATCAAATATGCATGTCATCC 57.414 37.500 10.16 7.86 36.63 3.51
2074 2284 2.941333 CATGTCATCCATCGCCGC 59.059 61.111 0.00 0.00 0.00 6.53
2075 2285 2.281070 ATGTCATCCATCGCCGCC 60.281 61.111 0.00 0.00 0.00 6.13
2076 2286 4.889856 TGTCATCCATCGCCGCCG 62.890 66.667 0.00 0.00 0.00 6.46
2161 2385 1.603172 CCACAGTCTCAACAGTCGACC 60.603 57.143 13.01 0.00 0.00 4.79
2162 2386 1.067060 CACAGTCTCAACAGTCGACCA 59.933 52.381 13.01 0.00 0.00 4.02
2163 2387 1.964223 ACAGTCTCAACAGTCGACCAT 59.036 47.619 13.01 0.00 0.00 3.55
2164 2388 2.288457 ACAGTCTCAACAGTCGACCATG 60.288 50.000 13.01 7.66 0.00 3.66
2254 2508 2.046217 GGAAGTCGGAACCTGCCC 60.046 66.667 0.00 0.00 0.00 5.36
2282 2540 3.687102 CGGCCGTCACCACCAGTA 61.687 66.667 19.50 0.00 0.00 2.74
2283 2541 2.264794 GGCCGTCACCACCAGTAG 59.735 66.667 0.00 0.00 0.00 2.57
2284 2542 2.264794 GCCGTCACCACCAGTAGG 59.735 66.667 0.00 0.00 42.21 3.18
2308 2573 0.546122 TTCACCAACACACCTCTGCT 59.454 50.000 0.00 0.00 0.00 4.24
2309 2574 1.419381 TCACCAACACACCTCTGCTA 58.581 50.000 0.00 0.00 0.00 3.49
2318 2583 1.297664 CACCTCTGCTATTCTGCTGC 58.702 55.000 0.00 0.00 32.95 5.25
2319 2584 1.134461 CACCTCTGCTATTCTGCTGCT 60.134 52.381 0.00 0.00 32.95 4.24
2320 2585 1.134461 ACCTCTGCTATTCTGCTGCTG 60.134 52.381 0.00 0.00 32.95 4.41
2331 2596 1.339291 TCTGCTGCTGGTAGATCATCG 59.661 52.381 6.69 0.00 31.86 3.84
2332 2597 1.339291 CTGCTGCTGGTAGATCATCGA 59.661 52.381 0.00 0.00 0.00 3.59
2333 2598 1.966354 TGCTGCTGGTAGATCATCGAT 59.034 47.619 0.00 0.00 0.00 3.59
2334 2599 2.366590 TGCTGCTGGTAGATCATCGATT 59.633 45.455 0.00 0.00 0.00 3.34
2394 2659 5.221441 TGTCATGTGTAACTGCACTAACTCT 60.221 40.000 0.00 0.00 39.89 3.24
2395 2660 5.346281 GTCATGTGTAACTGCACTAACTCTC 59.654 44.000 0.00 0.00 39.89 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.029563 CACATTTTTGCTATAGTGGAACCTTC 58.970 38.462 0.84 0.00 37.80 3.46
1 2 6.719370 TCACATTTTTGCTATAGTGGAACCTT 59.281 34.615 0.84 0.00 37.80 3.50
2 3 6.245408 TCACATTTTTGCTATAGTGGAACCT 58.755 36.000 0.84 0.00 37.80 3.50
3 4 6.509418 TCACATTTTTGCTATAGTGGAACC 57.491 37.500 0.84 0.00 37.80 3.62
4 5 7.816640 TCTTCACATTTTTGCTATAGTGGAAC 58.183 34.615 0.84 0.00 0.00 3.62
5 6 7.994425 TCTTCACATTTTTGCTATAGTGGAA 57.006 32.000 0.84 0.00 0.00 3.53
6 7 7.994425 TTCTTCACATTTTTGCTATAGTGGA 57.006 32.000 0.84 0.00 0.00 4.02
7 8 9.643693 AAATTCTTCACATTTTTGCTATAGTGG 57.356 29.630 0.84 0.00 0.00 4.00
13 14 9.677567 GTGTCTAAATTCTTCACATTTTTGCTA 57.322 29.630 0.00 0.00 0.00 3.49
14 15 8.196771 TGTGTCTAAATTCTTCACATTTTTGCT 58.803 29.630 0.00 0.00 34.74 3.91
15 16 8.351495 TGTGTCTAAATTCTTCACATTTTTGC 57.649 30.769 0.00 0.00 34.74 3.68
22 23 9.607988 TCTAACTTTGTGTCTAAATTCTTCACA 57.392 29.630 0.00 0.00 37.27 3.58
28 29 9.600646 GCTTCTTCTAACTTTGTGTCTAAATTC 57.399 33.333 0.00 0.00 0.00 2.17
29 30 9.120538 TGCTTCTTCTAACTTTGTGTCTAAATT 57.879 29.630 0.00 0.00 0.00 1.82
30 31 8.677148 TGCTTCTTCTAACTTTGTGTCTAAAT 57.323 30.769 0.00 0.00 0.00 1.40
31 32 8.559536 CATGCTTCTTCTAACTTTGTGTCTAAA 58.440 33.333 0.00 0.00 0.00 1.85
32 33 7.307989 GCATGCTTCTTCTAACTTTGTGTCTAA 60.308 37.037 11.37 0.00 0.00 2.10
33 34 6.147821 GCATGCTTCTTCTAACTTTGTGTCTA 59.852 38.462 11.37 0.00 0.00 2.59
34 35 5.049129 GCATGCTTCTTCTAACTTTGTGTCT 60.049 40.000 11.37 0.00 0.00 3.41
35 36 5.149977 GCATGCTTCTTCTAACTTTGTGTC 58.850 41.667 11.37 0.00 0.00 3.67
36 37 4.022849 GGCATGCTTCTTCTAACTTTGTGT 60.023 41.667 18.92 0.00 0.00 3.72
37 38 4.479619 GGCATGCTTCTTCTAACTTTGTG 58.520 43.478 18.92 0.00 0.00 3.33
38 39 3.189287 CGGCATGCTTCTTCTAACTTTGT 59.811 43.478 18.92 0.00 0.00 2.83
39 40 3.189287 ACGGCATGCTTCTTCTAACTTTG 59.811 43.478 18.92 0.00 0.00 2.77
40 41 3.412386 ACGGCATGCTTCTTCTAACTTT 58.588 40.909 18.92 0.00 0.00 2.66
41 42 3.059352 ACGGCATGCTTCTTCTAACTT 57.941 42.857 18.92 0.00 0.00 2.66
42 43 2.770164 ACGGCATGCTTCTTCTAACT 57.230 45.000 18.92 0.00 0.00 2.24
43 44 4.181578 TCTTACGGCATGCTTCTTCTAAC 58.818 43.478 18.92 0.00 0.00 2.34
44 45 4.465632 TCTTACGGCATGCTTCTTCTAA 57.534 40.909 18.92 3.84 0.00 2.10
45 46 4.465632 TTCTTACGGCATGCTTCTTCTA 57.534 40.909 18.92 0.00 0.00 2.10
46 47 3.334583 TTCTTACGGCATGCTTCTTCT 57.665 42.857 18.92 0.00 0.00 2.85
47 48 4.154195 TCTTTTCTTACGGCATGCTTCTTC 59.846 41.667 18.92 0.00 0.00 2.87
48 49 4.072131 TCTTTTCTTACGGCATGCTTCTT 58.928 39.130 18.92 1.88 0.00 2.52
49 50 3.674997 TCTTTTCTTACGGCATGCTTCT 58.325 40.909 18.92 2.53 0.00 2.85
50 51 4.419522 TTCTTTTCTTACGGCATGCTTC 57.580 40.909 18.92 0.00 0.00 3.86
51 52 5.414454 TGTATTCTTTTCTTACGGCATGCTT 59.586 36.000 18.92 7.64 0.00 3.91
52 53 4.941263 TGTATTCTTTTCTTACGGCATGCT 59.059 37.500 18.92 0.24 0.00 3.79
53 54 5.028375 GTGTATTCTTTTCTTACGGCATGC 58.972 41.667 9.90 9.90 0.00 4.06
54 55 5.255596 CGTGTATTCTTTTCTTACGGCATG 58.744 41.667 0.00 0.00 0.00 4.06
55 56 4.201783 GCGTGTATTCTTTTCTTACGGCAT 60.202 41.667 0.00 0.00 0.00 4.40
56 57 3.123959 GCGTGTATTCTTTTCTTACGGCA 59.876 43.478 0.00 0.00 0.00 5.69
57 58 3.370061 AGCGTGTATTCTTTTCTTACGGC 59.630 43.478 0.00 0.00 0.00 5.68
58 59 4.201685 CCAGCGTGTATTCTTTTCTTACGG 60.202 45.833 0.00 0.00 0.00 4.02
59 60 4.624024 TCCAGCGTGTATTCTTTTCTTACG 59.376 41.667 0.00 0.00 0.00 3.18
60 61 6.663944 ATCCAGCGTGTATTCTTTTCTTAC 57.336 37.500 0.00 0.00 0.00 2.34
61 62 8.958119 ATTATCCAGCGTGTATTCTTTTCTTA 57.042 30.769 0.00 0.00 0.00 2.10
62 63 7.865706 ATTATCCAGCGTGTATTCTTTTCTT 57.134 32.000 0.00 0.00 0.00 2.52
63 64 8.958119 TTATTATCCAGCGTGTATTCTTTTCT 57.042 30.769 0.00 0.00 0.00 2.52
64 65 9.813080 GATTATTATCCAGCGTGTATTCTTTTC 57.187 33.333 0.00 0.00 0.00 2.29
65 66 9.337396 TGATTATTATCCAGCGTGTATTCTTTT 57.663 29.630 0.00 0.00 0.00 2.27
66 67 8.902540 TGATTATTATCCAGCGTGTATTCTTT 57.097 30.769 0.00 0.00 0.00 2.52
67 68 9.155975 GATGATTATTATCCAGCGTGTATTCTT 57.844 33.333 0.00 0.00 0.00 2.52
68 69 8.535335 AGATGATTATTATCCAGCGTGTATTCT 58.465 33.333 0.00 0.00 0.00 2.40
69 70 8.709386 AGATGATTATTATCCAGCGTGTATTC 57.291 34.615 0.00 0.00 0.00 1.75
75 76 9.302345 CGTAATAAGATGATTATTATCCAGCGT 57.698 33.333 4.01 0.00 31.78 5.07
76 77 9.302345 ACGTAATAAGATGATTATTATCCAGCG 57.698 33.333 0.00 5.21 31.78 5.18
89 90 8.582437 CCCTATGGACTTTACGTAATAAGATGA 58.418 37.037 9.18 0.00 0.00 2.92
90 91 8.365647 ACCCTATGGACTTTACGTAATAAGATG 58.634 37.037 9.18 0.00 34.81 2.90
91 92 8.488308 ACCCTATGGACTTTACGTAATAAGAT 57.512 34.615 9.18 1.38 34.81 2.40
92 93 7.014615 GGACCCTATGGACTTTACGTAATAAGA 59.985 40.741 9.18 0.00 34.81 2.10
93 94 7.150640 GGACCCTATGGACTTTACGTAATAAG 58.849 42.308 9.18 7.15 34.81 1.73
94 95 6.610830 TGGACCCTATGGACTTTACGTAATAA 59.389 38.462 9.18 0.00 34.81 1.40
95 96 6.135454 TGGACCCTATGGACTTTACGTAATA 58.865 40.000 9.18 0.00 34.81 0.98
96 97 4.964262 TGGACCCTATGGACTTTACGTAAT 59.036 41.667 9.18 0.00 34.81 1.89
97 98 4.352009 TGGACCCTATGGACTTTACGTAA 58.648 43.478 3.29 3.29 34.81 3.18
98 99 3.979911 TGGACCCTATGGACTTTACGTA 58.020 45.455 0.00 0.00 34.81 3.57
99 100 2.823959 TGGACCCTATGGACTTTACGT 58.176 47.619 0.00 0.00 34.81 3.57
100 101 3.793559 CTTGGACCCTATGGACTTTACG 58.206 50.000 0.00 0.00 34.81 3.18
101 102 3.542648 GCTTGGACCCTATGGACTTTAC 58.457 50.000 0.00 0.00 34.81 2.01
102 103 2.508300 GGCTTGGACCCTATGGACTTTA 59.492 50.000 0.00 0.00 34.81 1.85
103 104 1.285078 GGCTTGGACCCTATGGACTTT 59.715 52.381 0.00 0.00 34.81 2.66
104 105 0.919710 GGCTTGGACCCTATGGACTT 59.080 55.000 0.00 0.00 34.81 3.01
105 106 0.253160 TGGCTTGGACCCTATGGACT 60.253 55.000 0.00 0.00 34.81 3.85
106 107 0.846693 ATGGCTTGGACCCTATGGAC 59.153 55.000 0.00 0.00 34.81 4.02
107 108 1.215173 CAATGGCTTGGACCCTATGGA 59.785 52.381 0.00 0.00 34.81 3.41
108 109 1.696063 CAATGGCTTGGACCCTATGG 58.304 55.000 0.00 0.00 37.80 2.74
109 110 1.035139 GCAATGGCTTGGACCCTATG 58.965 55.000 0.00 0.00 36.96 2.23
110 111 0.106015 GGCAATGGCTTGGACCCTAT 60.106 55.000 0.00 0.00 40.87 2.57
111 112 1.306296 GGCAATGGCTTGGACCCTA 59.694 57.895 0.00 0.00 40.87 3.53
112 113 2.037847 GGCAATGGCTTGGACCCT 59.962 61.111 0.00 0.00 40.87 4.34
113 114 3.451894 CGGCAATGGCTTGGACCC 61.452 66.667 5.02 0.00 40.87 4.46
114 115 4.133796 GCGGCAATGGCTTGGACC 62.134 66.667 5.02 0.00 40.87 4.46
115 116 2.433231 TTTGCGGCAATGGCTTGGAC 62.433 55.000 17.19 0.00 40.87 4.02
116 117 2.205843 TTTGCGGCAATGGCTTGGA 61.206 52.632 17.19 0.00 40.87 3.53
117 118 2.028733 GTTTGCGGCAATGGCTTGG 61.029 57.895 17.19 0.00 40.87 3.61
118 119 1.300775 TGTTTGCGGCAATGGCTTG 60.301 52.632 17.19 0.00 40.87 4.01
119 120 1.300853 GTGTTTGCGGCAATGGCTT 60.301 52.632 17.19 0.00 40.87 4.35
120 121 2.339712 GTGTTTGCGGCAATGGCT 59.660 55.556 17.19 0.00 40.87 4.75
121 122 2.738139 GGTGTTTGCGGCAATGGC 60.738 61.111 17.19 10.39 40.13 4.40
122 123 1.068753 TTGGTGTTTGCGGCAATGG 59.931 52.632 17.19 0.00 0.00 3.16
123 124 1.220817 GGTTGGTGTTTGCGGCAATG 61.221 55.000 17.19 0.00 0.00 2.82
124 125 1.068921 GGTTGGTGTTTGCGGCAAT 59.931 52.632 17.19 0.00 0.00 3.56
125 126 2.290122 CTGGTTGGTGTTTGCGGCAA 62.290 55.000 12.11 12.11 0.00 4.52
126 127 2.755876 TGGTTGGTGTTTGCGGCA 60.756 55.556 0.00 0.00 0.00 5.69
127 128 2.010582 TTCTGGTTGGTGTTTGCGGC 62.011 55.000 0.00 0.00 0.00 6.53
128 129 0.030638 CTTCTGGTTGGTGTTTGCGG 59.969 55.000 0.00 0.00 0.00 5.69
129 130 1.002468 CTCTTCTGGTTGGTGTTTGCG 60.002 52.381 0.00 0.00 0.00 4.85
130 131 2.297701 TCTCTTCTGGTTGGTGTTTGC 58.702 47.619 0.00 0.00 0.00 3.68
131 132 3.885297 ACATCTCTTCTGGTTGGTGTTTG 59.115 43.478 0.00 0.00 0.00 2.93
132 133 3.885297 CACATCTCTTCTGGTTGGTGTTT 59.115 43.478 0.00 0.00 0.00 2.83
133 134 3.117888 ACACATCTCTTCTGGTTGGTGTT 60.118 43.478 0.00 0.00 34.89 3.32
134 135 2.439507 ACACATCTCTTCTGGTTGGTGT 59.560 45.455 0.00 0.00 33.77 4.16
135 136 3.070018 GACACATCTCTTCTGGTTGGTG 58.930 50.000 0.00 0.00 0.00 4.17
136 137 2.975489 AGACACATCTCTTCTGGTTGGT 59.025 45.455 0.00 0.00 0.00 3.67
137 138 3.692257 AGACACATCTCTTCTGGTTGG 57.308 47.619 0.00 0.00 0.00 3.77
138 139 6.638610 AGAATAGACACATCTCTTCTGGTTG 58.361 40.000 4.64 0.00 43.31 3.77
139 140 6.865834 AGAATAGACACATCTCTTCTGGTT 57.134 37.500 4.64 0.00 43.31 3.67
140 141 8.420222 CAATAGAATAGACACATCTCTTCTGGT 58.580 37.037 12.66 2.60 44.16 4.00
141 142 8.637099 TCAATAGAATAGACACATCTCTTCTGG 58.363 37.037 12.66 5.39 44.16 3.86
182 183 7.462200 CGCATCGTTGTTTAACAAATTATTCCC 60.462 37.037 12.37 0.00 40.15 3.97
183 184 7.380320 CGCATCGTTGTTTAACAAATTATTCC 58.620 34.615 12.37 0.00 40.15 3.01
190 191 2.033550 AGCCGCATCGTTGTTTAACAAA 59.966 40.909 12.37 0.00 40.15 2.83
198 199 2.080693 TCAATAAAGCCGCATCGTTGT 58.919 42.857 0.00 0.00 0.00 3.32
202 203 5.095691 ACTTAATCAATAAAGCCGCATCG 57.904 39.130 0.00 0.00 0.00 3.84
233 236 2.529632 TCCCGCTCTGATATGCTGTAT 58.470 47.619 0.00 0.00 0.00 2.29
259 262 4.133856 TGCGTTGGTTGTTTTTGTTTTG 57.866 36.364 0.00 0.00 0.00 2.44
260 263 6.073222 TGTTATGCGTTGGTTGTTTTTGTTTT 60.073 30.769 0.00 0.00 0.00 2.43
261 264 5.408604 TGTTATGCGTTGGTTGTTTTTGTTT 59.591 32.000 0.00 0.00 0.00 2.83
262 265 4.929808 TGTTATGCGTTGGTTGTTTTTGTT 59.070 33.333 0.00 0.00 0.00 2.83
263 266 4.495422 TGTTATGCGTTGGTTGTTTTTGT 58.505 34.783 0.00 0.00 0.00 2.83
264 267 5.456192 TTGTTATGCGTTGGTTGTTTTTG 57.544 34.783 0.00 0.00 0.00 2.44
265 268 5.869888 TCTTTGTTATGCGTTGGTTGTTTTT 59.130 32.000 0.00 0.00 0.00 1.94
266 269 5.411781 TCTTTGTTATGCGTTGGTTGTTTT 58.588 33.333 0.00 0.00 0.00 2.43
267 270 5.000012 TCTTTGTTATGCGTTGGTTGTTT 58.000 34.783 0.00 0.00 0.00 2.83
268 271 4.640789 TCTTTGTTATGCGTTGGTTGTT 57.359 36.364 0.00 0.00 0.00 2.83
269 272 4.640789 TTCTTTGTTATGCGTTGGTTGT 57.359 36.364 0.00 0.00 0.00 3.32
270 273 5.957910 TTTTCTTTGTTATGCGTTGGTTG 57.042 34.783 0.00 0.00 0.00 3.77
295 306 5.565439 GCATTGCTTGGTGTGATTTTCTAGT 60.565 40.000 0.16 0.00 0.00 2.57
314 325 1.062258 GCATTGTGACAACGGCATTG 58.938 50.000 16.06 4.77 44.60 2.82
319 330 3.617540 TGTAAAGCATTGTGACAACGG 57.382 42.857 0.00 0.00 0.00 4.44
366 380 0.538516 TGTGGGCTGCCGTAAATGTT 60.539 50.000 13.40 0.00 0.00 2.71
379 393 4.202151 GGTGGATTCTAAATTGATGTGGGC 60.202 45.833 0.00 0.00 0.00 5.36
394 408 2.500229 TCTGGAAAACGTGGTGGATTC 58.500 47.619 0.00 0.00 0.00 2.52
420 434 5.726793 ACTCATGTACATATAATCCCCCTCC 59.273 44.000 8.32 0.00 0.00 4.30
428 442 9.845740 TGCCTGTAAAACTCATGTACATATAAT 57.154 29.630 8.32 0.00 0.00 1.28
430 444 9.271828 CATGCCTGTAAAACTCATGTACATATA 57.728 33.333 8.32 0.00 32.26 0.86
431 445 7.775093 ACATGCCTGTAAAACTCATGTACATAT 59.225 33.333 8.32 0.00 43.88 1.78
432 446 7.109501 ACATGCCTGTAAAACTCATGTACATA 58.890 34.615 8.32 0.00 43.88 2.29
433 447 5.945784 ACATGCCTGTAAAACTCATGTACAT 59.054 36.000 1.41 1.41 43.88 2.29
434 448 5.312895 ACATGCCTGTAAAACTCATGTACA 58.687 37.500 0.00 0.00 43.88 2.90
436 450 6.707290 AGTACATGCCTGTAAAACTCATGTA 58.293 36.000 3.21 8.70 43.88 2.29
438 452 7.334421 ACTTAGTACATGCCTGTAAAACTCATG 59.666 37.037 3.21 0.00 39.51 3.07
439 453 7.394816 ACTTAGTACATGCCTGTAAAACTCAT 58.605 34.615 3.21 0.00 39.51 2.90
440 454 6.765403 ACTTAGTACATGCCTGTAAAACTCA 58.235 36.000 3.21 0.00 39.51 3.41
441 455 7.008992 CGTACTTAGTACATGCCTGTAAAACTC 59.991 40.741 20.62 0.00 39.51 3.01
442 456 6.810182 CGTACTTAGTACATGCCTGTAAAACT 59.190 38.462 20.62 2.69 39.51 2.66
443 457 6.587608 ACGTACTTAGTACATGCCTGTAAAAC 59.412 38.462 20.62 0.00 39.51 2.43
459 473 6.034591 CCTCAAAGGACACATACGTACTTAG 58.965 44.000 0.00 0.00 39.21 2.18
462 482 3.830755 ACCTCAAAGGACACATACGTACT 59.169 43.478 0.00 0.00 37.67 2.73
485 505 6.953691 ACTTATTCAGTTACATGCATGCATGC 60.954 38.462 45.24 38.71 44.56 4.06
486 506 6.416750 CACTTATTCAGTTACATGCATGCATG 59.583 38.462 44.22 44.22 45.67 4.06
487 507 6.095860 ACACTTATTCAGTTACATGCATGCAT 59.904 34.615 27.46 27.46 32.65 3.96
528 562 7.490962 TGTGCTACATATAAGTATTTGGCAC 57.509 36.000 16.90 16.90 46.78 5.01
544 579 5.876651 AATCTCCAGATGTATGTGCTACA 57.123 39.130 0.00 0.00 44.29 2.74
628 668 9.849166 CATTATGCATTGCACTTCATATCATAA 57.151 29.630 14.66 5.07 43.04 1.90
631 671 6.153756 GCATTATGCATTGCACTTCATATCA 58.846 36.000 14.66 0.00 43.04 2.15
632 672 6.627690 GCATTATGCATTGCACTTCATATC 57.372 37.500 14.66 0.00 43.04 1.63
647 687 4.904241 ACTCTTCCTCCTATGCATTATGC 58.096 43.478 10.65 10.65 45.29 3.14
648 688 7.178274 ACTCTACTCTTCCTCCTATGCATTATG 59.822 40.741 3.54 0.00 0.00 1.90
649 689 7.245292 ACTCTACTCTTCCTCCTATGCATTAT 58.755 38.462 3.54 0.00 0.00 1.28
650 690 6.615617 ACTCTACTCTTCCTCCTATGCATTA 58.384 40.000 3.54 0.00 0.00 1.90
659 699 2.953648 GTGCCTACTCTACTCTTCCTCC 59.046 54.545 0.00 0.00 0.00 4.30
769 875 1.562008 TGTCAATATTTGGAGGCGGGA 59.438 47.619 0.00 0.00 0.00 5.14
773 879 5.574188 AGGGATATGTCAATATTTGGAGGC 58.426 41.667 0.00 0.00 0.00 4.70
776 882 7.010160 GGGAAAGGGATATGTCAATATTTGGA 58.990 38.462 0.00 0.00 0.00 3.53
809 915 2.486982 GGAGTCGGAGGGTTTAAAAAGC 59.513 50.000 0.00 0.00 35.75 3.51
845 952 1.993956 TGTTGGTGATGAAGGGTTGG 58.006 50.000 0.00 0.00 0.00 3.77
871 978 3.465871 GAGGGAGAATGAAGTGCTGATC 58.534 50.000 0.00 0.00 0.00 2.92
898 1014 1.144503 GATGGATGGTGGAGCTTGGAT 59.855 52.381 0.00 0.00 0.00 3.41
915 1031 5.220739 GCTAGGTAAGTGCAAATCAGTGATG 60.221 44.000 6.34 0.00 0.00 3.07
917 1033 4.020218 AGCTAGGTAAGTGCAAATCAGTGA 60.020 41.667 0.00 0.00 0.00 3.41
929 1045 2.426381 GTTGCGGAGTAGCTAGGTAAGT 59.574 50.000 2.58 0.00 38.13 2.24
930 1046 2.223758 GGTTGCGGAGTAGCTAGGTAAG 60.224 54.545 2.58 0.00 38.13 2.34
935 1062 1.442148 GGGGTTGCGGAGTAGCTAG 59.558 63.158 0.00 0.00 38.13 3.42
938 1065 3.712907 TGGGGGTTGCGGAGTAGC 61.713 66.667 0.00 0.00 37.71 3.58
987 1114 3.654414 GCCCTCCATAATCTCAACTACG 58.346 50.000 0.00 0.00 0.00 3.51
988 1115 3.555168 CCGCCCTCCATAATCTCAACTAC 60.555 52.174 0.00 0.00 0.00 2.73
989 1116 2.632996 CCGCCCTCCATAATCTCAACTA 59.367 50.000 0.00 0.00 0.00 2.24
999 1126 0.191064 ATCCTTCTCCGCCCTCCATA 59.809 55.000 0.00 0.00 0.00 2.74
1266 1393 2.276743 CTCGCCGACGACGAAGAG 60.277 66.667 7.83 12.42 45.12 2.85
1425 1562 8.466617 ATACAGTAGGTATTATGGATCGATCC 57.533 38.462 33.41 33.41 42.43 3.36
1426 1563 9.121658 TGATACAGTAGGTATTATGGATCGATC 57.878 37.037 17.36 17.36 42.76 3.69
1427 1564 9.647918 ATGATACAGTAGGTATTATGGATCGAT 57.352 33.333 0.00 0.00 42.76 3.59
1428 1565 9.121658 GATGATACAGTAGGTATTATGGATCGA 57.878 37.037 0.00 0.00 42.76 3.59
1429 1566 8.353684 GGATGATACAGTAGGTATTATGGATCG 58.646 40.741 0.00 0.00 42.76 3.69
1430 1567 8.643324 GGGATGATACAGTAGGTATTATGGATC 58.357 40.741 0.00 0.00 42.76 3.36
1431 1568 7.287927 CGGGATGATACAGTAGGTATTATGGAT 59.712 40.741 0.00 0.00 42.76 3.41
1432 1569 6.605995 CGGGATGATACAGTAGGTATTATGGA 59.394 42.308 0.00 0.00 42.76 3.41
1433 1570 6.183360 CCGGGATGATACAGTAGGTATTATGG 60.183 46.154 0.00 0.00 42.76 2.74
1434 1571 6.683110 GCCGGGATGATACAGTAGGTATTATG 60.683 46.154 2.18 0.00 42.76 1.90
1523 1660 3.265737 ACCTAATATATGGCCGGAATGCA 59.734 43.478 5.05 0.00 0.00 3.96
1629 1807 6.070767 CCATCAAATATATGGTAGAGGGTCGT 60.071 42.308 0.00 0.00 39.30 4.34
1678 1856 5.745227 ACCCCATATCATCGATTGGATTAC 58.255 41.667 14.24 0.00 31.28 1.89
1683 1861 4.826733 TGAAAACCCCATATCATCGATTGG 59.173 41.667 6.85 6.85 0.00 3.16
1684 1862 5.532406 ACTGAAAACCCCATATCATCGATTG 59.468 40.000 0.00 0.00 0.00 2.67
1685 1863 5.694995 ACTGAAAACCCCATATCATCGATT 58.305 37.500 0.00 0.00 0.00 3.34
1686 1864 5.072329 AGACTGAAAACCCCATATCATCGAT 59.928 40.000 0.00 0.00 0.00 3.59
1687 1865 4.408921 AGACTGAAAACCCCATATCATCGA 59.591 41.667 0.00 0.00 0.00 3.59
1688 1866 4.708177 AGACTGAAAACCCCATATCATCG 58.292 43.478 0.00 0.00 0.00 3.84
1689 1867 5.684704 TGAGACTGAAAACCCCATATCATC 58.315 41.667 0.00 0.00 0.00 2.92
1690 1868 5.715439 TGAGACTGAAAACCCCATATCAT 57.285 39.130 0.00 0.00 0.00 2.45
1691 1869 5.512942 TTGAGACTGAAAACCCCATATCA 57.487 39.130 0.00 0.00 0.00 2.15
1693 1871 6.378280 GTCATTTGAGACTGAAAACCCCATAT 59.622 38.462 0.00 0.00 35.65 1.78
1695 1873 4.524328 GTCATTTGAGACTGAAAACCCCAT 59.476 41.667 0.00 0.00 35.65 4.00
1696 1874 3.888930 GTCATTTGAGACTGAAAACCCCA 59.111 43.478 0.00 0.00 35.65 4.96
1697 1875 3.888930 TGTCATTTGAGACTGAAAACCCC 59.111 43.478 0.00 0.00 39.27 4.95
1747 1932 7.303634 ACAAGTCGGTTAATTAAGCATACTG 57.696 36.000 22.86 19.41 33.00 2.74
1748 1933 9.257651 GATACAAGTCGGTTAATTAAGCATACT 57.742 33.333 23.22 21.01 33.63 2.12
1819 2011 6.145338 AGTACGAGGATGGTTTACAGTATG 57.855 41.667 0.00 0.00 46.00 2.39
1827 2019 2.236395 CCAGGAAGTACGAGGATGGTTT 59.764 50.000 0.00 0.00 0.00 3.27
1830 2022 0.105039 GCCAGGAAGTACGAGGATGG 59.895 60.000 0.00 3.65 0.00 3.51
1831 2023 0.249073 CGCCAGGAAGTACGAGGATG 60.249 60.000 0.00 0.00 0.00 3.51
1871 2064 4.986659 GCTAGCAGGCCATTTGATTTAATG 59.013 41.667 10.63 0.00 35.70 1.90
1884 2077 1.066143 TGACTAACAAGCTAGCAGGCC 60.066 52.381 18.83 0.00 0.00 5.19
1915 2108 1.949525 GCCGGTAATCGAGTACCTACA 59.050 52.381 32.33 0.00 41.33 2.74
1916 2109 1.268079 GGCCGGTAATCGAGTACCTAC 59.732 57.143 32.33 24.74 41.33 3.18
1917 2110 1.609208 GGCCGGTAATCGAGTACCTA 58.391 55.000 32.33 0.00 41.33 3.08
1918 2111 1.111715 GGGCCGGTAATCGAGTACCT 61.112 60.000 32.33 0.00 41.33 3.08
1919 2112 1.365267 GGGCCGGTAATCGAGTACC 59.635 63.158 27.93 27.93 42.43 3.34
2041 2251 7.088905 GGATGACATGCATATTTGATTCCTTC 58.911 38.462 0.00 0.00 37.34 3.46
2164 2388 2.401766 CGGAGTGCATTCTGGGTGC 61.402 63.158 10.11 0.00 42.81 5.01
2254 2508 3.095898 GACGGCCGGAATGAAAGCG 62.096 63.158 31.76 0.00 0.00 4.68
2282 2540 1.473788 GGTGTGTTGGTGAACGTACCT 60.474 52.381 8.89 0.00 41.43 3.08
2283 2541 0.939419 GGTGTGTTGGTGAACGTACC 59.061 55.000 0.20 0.20 41.24 3.34
2284 2542 1.862827 GAGGTGTGTTGGTGAACGTAC 59.137 52.381 0.00 0.00 34.49 3.67
2285 2543 1.758280 AGAGGTGTGTTGGTGAACGTA 59.242 47.619 0.00 0.00 34.49 3.57
2286 2544 0.539986 AGAGGTGTGTTGGTGAACGT 59.460 50.000 0.00 0.00 34.49 3.99
2287 2545 0.937304 CAGAGGTGTGTTGGTGAACG 59.063 55.000 0.00 0.00 34.49 3.95
2288 2546 0.663153 GCAGAGGTGTGTTGGTGAAC 59.337 55.000 0.00 0.00 0.00 3.18
2289 2547 0.546122 AGCAGAGGTGTGTTGGTGAA 59.454 50.000 0.00 0.00 0.00 3.18
2290 2548 1.419381 TAGCAGAGGTGTGTTGGTGA 58.581 50.000 0.00 0.00 0.00 4.02
2293 2551 3.005554 CAGAATAGCAGAGGTGTGTTGG 58.994 50.000 0.00 0.00 0.00 3.77
2296 2561 1.905215 AGCAGAATAGCAGAGGTGTGT 59.095 47.619 0.00 0.00 36.85 3.72
2308 2573 4.321527 CGATGATCTACCAGCAGCAGAATA 60.322 45.833 0.00 0.00 0.00 1.75
2309 2574 3.554544 CGATGATCTACCAGCAGCAGAAT 60.555 47.826 0.00 0.00 0.00 2.40
2318 2583 7.276658 GCAGGTAATTAATCGATGATCTACCAG 59.723 40.741 20.51 16.17 0.00 4.00
2319 2584 7.097192 GCAGGTAATTAATCGATGATCTACCA 58.903 38.462 20.51 0.00 0.00 3.25
2320 2585 6.253727 CGCAGGTAATTAATCGATGATCTACC 59.746 42.308 14.66 14.66 0.00 3.18
2331 2596 1.864711 TCAGCGCGCAGGTAATTAATC 59.135 47.619 35.10 0.00 0.00 1.75
2332 2597 1.948104 TCAGCGCGCAGGTAATTAAT 58.052 45.000 35.10 4.83 0.00 1.40
2333 2598 1.728068 TTCAGCGCGCAGGTAATTAA 58.272 45.000 35.10 11.55 0.00 1.40
2334 2599 1.395608 GTTTCAGCGCGCAGGTAATTA 59.604 47.619 35.10 4.81 0.00 1.40


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

AutoCloner maintained by Alex Coulton.