Multiple sequence alignment - TraesCS4A01G050900

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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 TraesCS4A01G050900 chr4A 100.000 2582 0 0 1 2582 41947669 41945088 0.000000e+00 4769.0
1 TraesCS4A01G050900 chr4A 78.698 169 16 13 2408 2569 685828110 685827955 7.610000e-16 95.3
2 TraesCS4A01G050900 chr4B 92.570 1171 64 11 851 2013 519375494 519376649 0.000000e+00 1659.0
3 TraesCS4A01G050900 chr4B 85.345 232 32 2 51 281 600606812 600606582 3.320000e-59 239.0
4 TraesCS4A01G050900 chr4B 90.400 125 7 2 2013 2132 519376736 519376860 2.660000e-35 159.0
5 TraesCS4A01G050900 chr4B 81.481 216 11 12 576 790 519374528 519374715 1.600000e-32 150.0
6 TraesCS4A01G050900 chr4B 86.260 131 18 0 193 323 519374030 519374160 2.680000e-30 143.0
7 TraesCS4A01G050900 chr4B 91.667 48 2 2 2471 2517 581083264 581083310 5.960000e-07 65.8
8 TraesCS4A01G050900 chr4D 92.358 1060 35 14 839 1884 422535622 422536649 0.000000e+00 1467.0
9 TraesCS4A01G050900 chr4D 94.872 507 15 2 1888 2383 422537033 422537539 0.000000e+00 782.0
10 TraesCS4A01G050900 chr4D 93.820 178 9 2 607 784 422519046 422519221 1.520000e-67 267.0
11 TraesCS4A01G050900 chr4D 96.575 146 5 0 2437 2582 422538144 422538289 2.570000e-60 243.0
12 TraesCS4A01G050900 chrUn 89.736 682 50 14 935 1605 15317397 15318069 0.000000e+00 854.0
13 TraesCS4A01G050900 chrUn 89.161 286 23 5 963 1248 401404056 401404333 1.470000e-92 350.0
14 TraesCS4A01G050900 chr2A 90.615 650 46 9 963 1605 734910359 734909718 0.000000e+00 848.0
15 TraesCS4A01G050900 chr2A 75.851 323 67 11 1242 1557 71447401 71447083 1.240000e-33 154.0
16 TraesCS4A01G050900 chr2A 88.608 79 5 4 2506 2582 619963403 619963327 2.740000e-15 93.5
17 TraesCS4A01G050900 chr2D 90.062 644 55 7 963 1605 601704824 601704189 0.000000e+00 826.0
18 TraesCS4A01G050900 chr2D 78.417 278 30 11 2307 2569 437949966 437949704 1.240000e-33 154.0
19 TraesCS4A01G050900 chr2D 81.290 155 14 7 2417 2569 512183255 512183396 7.550000e-21 111.0
20 TraesCS4A01G050900 chr2D 78.667 150 22 7 2420 2569 512303945 512304084 9.840000e-15 91.6
21 TraesCS4A01G050900 chr5D 84.541 207 21 8 2381 2579 272663413 272663210 7.290000e-46 195.0
22 TraesCS4A01G050900 chr2B 75.649 308 64 11 1242 1542 110140267 110139964 2.680000e-30 143.0
23 TraesCS4A01G050900 chr7D 100.000 51 0 0 2189 2239 546040685 546040635 7.610000e-16 95.3
24 TraesCS4A01G050900 chr7D 80.583 103 15 3 2187 2289 546119411 546119314 9.910000e-10 75.0
25 TraesCS4A01G050900 chr7A 81.731 104 14 3 2187 2290 628837702 628837604 5.920000e-12 82.4
26 TraesCS4A01G050900 chr3B 100.000 33 0 0 2483 2515 787653515 787653483 7.710000e-06 62.1


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 TraesCS4A01G050900 chr4A 41945088 41947669 2581 True 4769.000000 4769 100.000000 1 2582 1 chr4A.!!$R1 2581
1 TraesCS4A01G050900 chr4B 519374030 519376860 2830 False 527.750000 1659 87.677750 193 2132 4 chr4B.!!$F2 1939
2 TraesCS4A01G050900 chr4D 422535622 422538289 2667 False 830.666667 1467 94.601667 839 2582 3 chr4D.!!$F2 1743
3 TraesCS4A01G050900 chrUn 15317397 15318069 672 False 854.000000 854 89.736000 935 1605 1 chrUn.!!$F1 670
4 TraesCS4A01G050900 chr2A 734909718 734910359 641 True 848.000000 848 90.615000 963 1605 1 chr2A.!!$R3 642
5 TraesCS4A01G050900 chr2D 601704189 601704824 635 True 826.000000 826 90.062000 963 1605 1 chr2D.!!$R2 642

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
333 334 0.179056 ATCAAATCCACCCTACGCCG 60.179 55.0 0.0 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2181 3549 0.110238 CGTTTGTCATCCAACGGCTG 60.11 55.0 0.0 0.0 31.2 4.85 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
17 18 2.436646 AAGGAATGCCACGAGCCG 60.437 61.111 0.00 0.00 42.71 5.52
20 21 4.166011 GAATGCCACGAGCCGCAC 62.166 66.667 0.00 0.00 42.71 5.34
22 23 4.783621 ATGCCACGAGCCGCACAT 62.784 61.111 0.00 0.00 42.71 3.21
24 25 4.465512 GCCACGAGCCGCACATTG 62.466 66.667 0.00 0.00 34.35 2.82
25 26 4.465512 CCACGAGCCGCACATTGC 62.466 66.667 0.00 0.00 40.69 3.56
26 27 3.725459 CACGAGCCGCACATTGCA 61.725 61.111 0.00 0.00 45.36 4.08
27 28 3.425713 ACGAGCCGCACATTGCAG 61.426 61.111 0.00 0.00 45.36 4.41
28 29 4.824166 CGAGCCGCACATTGCAGC 62.824 66.667 0.00 0.00 46.51 5.25
32 33 4.465512 CCGCACATTGCAGCCGTC 62.466 66.667 0.00 0.00 45.36 4.79
33 34 3.725459 CGCACATTGCAGCCGTCA 61.725 61.111 0.00 0.00 45.36 4.35
34 35 2.644418 GCACATTGCAGCCGTCAA 59.356 55.556 0.00 0.00 44.26 3.18
35 36 1.443194 GCACATTGCAGCCGTCAAG 60.443 57.895 0.00 0.00 44.26 3.02
36 37 1.443194 CACATTGCAGCCGTCAAGC 60.443 57.895 0.00 0.00 0.00 4.01
37 38 2.180017 CATTGCAGCCGTCAAGCC 59.820 61.111 0.00 0.00 0.00 4.35
38 39 2.282391 ATTGCAGCCGTCAAGCCA 60.282 55.556 0.00 0.00 0.00 4.75
39 40 1.902918 ATTGCAGCCGTCAAGCCAA 60.903 52.632 0.00 0.00 0.00 4.52
40 41 2.146073 ATTGCAGCCGTCAAGCCAAC 62.146 55.000 0.00 0.00 0.00 3.77
41 42 2.980233 GCAGCCGTCAAGCCAACT 60.980 61.111 0.00 0.00 0.00 3.16
42 43 2.970974 GCAGCCGTCAAGCCAACTC 61.971 63.158 0.00 0.00 0.00 3.01
43 44 2.032681 AGCCGTCAAGCCAACTCC 59.967 61.111 0.00 0.00 0.00 3.85
44 45 3.423154 GCCGTCAAGCCAACTCCG 61.423 66.667 0.00 0.00 0.00 4.63
45 46 2.742372 CCGTCAAGCCAACTCCGG 60.742 66.667 0.00 0.00 0.00 5.14
73 74 4.473520 CGCCACCGCCTCCATCTT 62.474 66.667 0.00 0.00 0.00 2.40
74 75 2.514824 GCCACCGCCTCCATCTTC 60.515 66.667 0.00 0.00 0.00 2.87
75 76 2.190578 CCACCGCCTCCATCTTCC 59.809 66.667 0.00 0.00 0.00 3.46
76 77 2.669133 CCACCGCCTCCATCTTCCA 61.669 63.158 0.00 0.00 0.00 3.53
77 78 1.450312 CACCGCCTCCATCTTCCAC 60.450 63.158 0.00 0.00 0.00 4.02
78 79 1.918293 ACCGCCTCCATCTTCCACA 60.918 57.895 0.00 0.00 0.00 4.17
79 80 1.299648 CCGCCTCCATCTTCCACAA 59.700 57.895 0.00 0.00 0.00 3.33
80 81 1.026718 CCGCCTCCATCTTCCACAAC 61.027 60.000 0.00 0.00 0.00 3.32
81 82 1.026718 CGCCTCCATCTTCCACAACC 61.027 60.000 0.00 0.00 0.00 3.77
82 83 1.026718 GCCTCCATCTTCCACAACCG 61.027 60.000 0.00 0.00 0.00 4.44
83 84 1.026718 CCTCCATCTTCCACAACCGC 61.027 60.000 0.00 0.00 0.00 5.68
84 85 1.361668 CTCCATCTTCCACAACCGCG 61.362 60.000 0.00 0.00 0.00 6.46
85 86 1.375396 CCATCTTCCACAACCGCGA 60.375 57.895 8.23 0.00 0.00 5.87
86 87 1.635663 CCATCTTCCACAACCGCGAC 61.636 60.000 8.23 0.00 0.00 5.19
87 88 1.375523 ATCTTCCACAACCGCGACC 60.376 57.895 8.23 0.00 0.00 4.79
88 89 1.827399 ATCTTCCACAACCGCGACCT 61.827 55.000 8.23 0.00 0.00 3.85
89 90 2.280524 TTCCACAACCGCGACCTG 60.281 61.111 8.23 3.81 0.00 4.00
90 91 3.818121 TTCCACAACCGCGACCTGG 62.818 63.158 8.23 6.71 0.00 4.45
91 92 4.308458 CCACAACCGCGACCTGGA 62.308 66.667 8.23 0.00 0.00 3.86
92 93 2.738521 CACAACCGCGACCTGGAG 60.739 66.667 8.23 0.00 0.00 3.86
93 94 4.681978 ACAACCGCGACCTGGAGC 62.682 66.667 8.23 4.67 0.00 4.70
94 95 4.680237 CAACCGCGACCTGGAGCA 62.680 66.667 8.23 0.00 0.00 4.26
95 96 4.379243 AACCGCGACCTGGAGCAG 62.379 66.667 8.23 9.33 0.00 4.24
117 118 4.847516 CGCGACGGAGGCATTCGA 62.848 66.667 5.83 0.00 34.62 3.71
118 119 2.956964 GCGACGGAGGCATTCGAG 60.957 66.667 5.83 0.00 34.62 4.04
119 120 2.278857 CGACGGAGGCATTCGAGG 60.279 66.667 5.83 0.00 34.62 4.63
120 121 2.771639 CGACGGAGGCATTCGAGGA 61.772 63.158 5.83 0.00 34.62 3.71
121 122 1.227002 GACGGAGGCATTCGAGGAC 60.227 63.158 5.83 0.00 0.00 3.85
122 123 2.278857 CGGAGGCATTCGAGGACG 60.279 66.667 0.00 0.00 41.26 4.79
123 124 2.586357 GGAGGCATTCGAGGACGC 60.586 66.667 0.00 0.00 39.58 5.19
124 125 2.956964 GAGGCATTCGAGGACGCG 60.957 66.667 3.53 3.53 39.58 6.01
125 126 3.411418 GAGGCATTCGAGGACGCGA 62.411 63.158 15.93 0.00 39.58 5.87
126 127 3.255379 GGCATTCGAGGACGCGAC 61.255 66.667 15.93 6.56 40.42 5.19
127 128 2.506217 GCATTCGAGGACGCGACA 60.506 61.111 15.93 0.00 40.42 4.35
128 129 1.878522 GCATTCGAGGACGCGACAT 60.879 57.895 15.93 3.25 40.42 3.06
129 130 0.594028 GCATTCGAGGACGCGACATA 60.594 55.000 15.93 0.00 40.42 2.29
130 131 1.121240 CATTCGAGGACGCGACATAC 58.879 55.000 15.93 0.62 40.42 2.39
131 132 1.022735 ATTCGAGGACGCGACATACT 58.977 50.000 15.93 0.00 40.42 2.12
132 133 0.376152 TTCGAGGACGCGACATACTC 59.624 55.000 15.93 5.00 40.42 2.59
133 134 1.367782 CGAGGACGCGACATACTCG 60.368 63.158 15.93 14.97 45.97 4.18
134 135 2.012237 GAGGACGCGACATACTCGA 58.988 57.895 15.93 0.00 46.14 4.04
135 136 0.316032 GAGGACGCGACATACTCGAC 60.316 60.000 15.93 0.00 46.14 4.20
136 137 1.298190 GGACGCGACATACTCGACC 60.298 63.158 15.93 0.00 46.14 4.79
137 138 1.650536 GACGCGACATACTCGACCG 60.651 63.158 15.93 0.00 46.14 4.79
138 139 3.017314 CGCGACATACTCGACCGC 61.017 66.667 0.00 0.00 46.14 5.68
139 140 2.408022 GCGACATACTCGACCGCT 59.592 61.111 0.00 0.00 46.14 5.52
140 141 1.939785 GCGACATACTCGACCGCTG 60.940 63.158 0.00 0.00 46.14 5.18
141 142 1.939785 CGACATACTCGACCGCTGC 60.940 63.158 0.00 0.00 46.14 5.25
142 143 1.138883 GACATACTCGACCGCTGCA 59.861 57.895 0.00 0.00 0.00 4.41
143 144 0.457853 GACATACTCGACCGCTGCAA 60.458 55.000 0.00 0.00 0.00 4.08
144 145 0.458543 ACATACTCGACCGCTGCAAG 60.459 55.000 0.00 0.00 0.00 4.01
145 146 1.141881 ATACTCGACCGCTGCAAGG 59.858 57.895 6.35 6.35 0.00 3.61
146 147 2.907897 ATACTCGACCGCTGCAAGGC 62.908 60.000 7.72 0.00 0.00 4.35
148 149 4.617520 TCGACCGCTGCAAGGCAA 62.618 61.111 7.72 0.00 38.41 4.52
149 150 4.389576 CGACCGCTGCAAGGCAAC 62.390 66.667 7.72 0.44 38.41 4.17
150 151 4.043200 GACCGCTGCAAGGCAACC 62.043 66.667 7.72 0.00 38.41 3.77
151 152 4.892965 ACCGCTGCAAGGCAACCA 62.893 61.111 7.72 0.00 38.41 3.67
152 153 4.347453 CCGCTGCAAGGCAACCAC 62.347 66.667 0.00 0.00 38.41 4.16
153 154 3.289834 CGCTGCAAGGCAACCACT 61.290 61.111 0.00 0.00 38.41 4.00
154 155 2.647297 GCTGCAAGGCAACCACTC 59.353 61.111 0.00 0.00 38.41 3.51
155 156 2.924105 GCTGCAAGGCAACCACTCC 61.924 63.158 0.00 0.00 38.41 3.85
156 157 1.228367 CTGCAAGGCAACCACTCCT 60.228 57.895 0.00 0.00 38.41 3.69
157 158 1.521450 CTGCAAGGCAACCACTCCTG 61.521 60.000 0.00 0.00 38.41 3.86
158 159 2.270986 GCAAGGCAACCACTCCTGG 61.271 63.158 0.00 0.00 44.26 4.45
159 160 2.116125 AAGGCAACCACTCCTGGC 59.884 61.111 0.00 0.00 42.08 4.85
160 161 3.850098 AAGGCAACCACTCCTGGCG 62.850 63.158 0.00 0.00 42.08 5.69
161 162 4.329545 GGCAACCACTCCTGGCGA 62.330 66.667 0.00 0.00 42.08 5.54
162 163 2.743928 GCAACCACTCCTGGCGAG 60.744 66.667 0.00 0.00 42.08 5.03
163 164 2.743928 CAACCACTCCTGGCGAGC 60.744 66.667 0.00 0.00 43.01 5.03
164 165 2.925170 AACCACTCCTGGCGAGCT 60.925 61.111 0.00 0.00 43.01 4.09
165 166 2.948720 AACCACTCCTGGCGAGCTC 61.949 63.158 2.73 2.73 43.01 4.09
166 167 4.154347 CCACTCCTGGCGAGCTCC 62.154 72.222 8.47 0.47 43.01 4.70
167 168 4.504916 CACTCCTGGCGAGCTCCG 62.505 72.222 8.47 4.62 43.01 4.63
190 191 2.440796 CCGCCATGGCCTCATTGT 60.441 61.111 30.79 0.00 37.98 2.71
191 192 2.777972 CCGCCATGGCCTCATTGTG 61.778 63.158 30.79 13.77 37.98 3.33
192 193 2.497770 GCCATGGCCTCATTGTGC 59.502 61.111 27.24 0.00 34.56 4.57
238 239 2.596776 CTCCTGAAGGATCCACCGT 58.403 57.895 15.82 0.00 44.46 4.83
286 287 4.824515 CCGCCTCCTCCTCTCGGT 62.825 72.222 0.00 0.00 35.75 4.69
288 289 2.043852 GCCTCCTCCTCTCGGTCA 60.044 66.667 0.00 0.00 0.00 4.02
299 300 2.202690 TCGGTCACGCGCCATTAG 60.203 61.111 5.73 0.00 40.69 1.73
300 301 3.925238 CGGTCACGCGCCATTAGC 61.925 66.667 5.73 0.00 38.52 3.09
302 303 2.526120 GGTCACGCGCCATTAGCTC 61.526 63.158 5.73 0.00 40.39 4.09
323 324 2.018727 GCCATGCGCCATCAAATCCA 62.019 55.000 4.18 0.00 0.00 3.41
324 325 0.249155 CCATGCGCCATCAAATCCAC 60.249 55.000 4.18 0.00 0.00 4.02
326 327 1.394266 ATGCGCCATCAAATCCACCC 61.394 55.000 4.18 0.00 0.00 4.61
327 328 1.754234 GCGCCATCAAATCCACCCT 60.754 57.895 0.00 0.00 0.00 4.34
328 329 0.465460 GCGCCATCAAATCCACCCTA 60.465 55.000 0.00 0.00 0.00 3.53
329 330 1.308998 CGCCATCAAATCCACCCTAC 58.691 55.000 0.00 0.00 0.00 3.18
330 331 1.308998 GCCATCAAATCCACCCTACG 58.691 55.000 0.00 0.00 0.00 3.51
331 332 1.308998 CCATCAAATCCACCCTACGC 58.691 55.000 0.00 0.00 0.00 4.42
332 333 1.308998 CATCAAATCCACCCTACGCC 58.691 55.000 0.00 0.00 0.00 5.68
333 334 0.179056 ATCAAATCCACCCTACGCCG 60.179 55.000 0.00 0.00 0.00 6.46
334 335 2.124860 AAATCCACCCTACGCCGC 60.125 61.111 0.00 0.00 0.00 6.53
335 336 3.692370 AAATCCACCCTACGCCGCC 62.692 63.158 0.00 0.00 0.00 6.13
339 340 3.542676 CACCCTACGCCGCCCATA 61.543 66.667 0.00 0.00 0.00 2.74
340 341 2.525877 ACCCTACGCCGCCCATAT 60.526 61.111 0.00 0.00 0.00 1.78
341 342 2.047274 CCCTACGCCGCCCATATG 60.047 66.667 0.00 0.00 0.00 1.78
342 343 2.579657 CCCTACGCCGCCCATATGA 61.580 63.158 3.65 0.00 0.00 2.15
343 344 1.374252 CCTACGCCGCCCATATGAC 60.374 63.158 3.65 0.00 0.00 3.06
344 345 1.733041 CTACGCCGCCCATATGACG 60.733 63.158 3.65 7.68 0.00 4.35
345 346 3.851845 TACGCCGCCCATATGACGC 62.852 63.158 3.65 4.49 0.00 5.19
349 350 4.969196 CGCCCATATGACGCCGCT 62.969 66.667 3.65 0.00 0.00 5.52
350 351 3.044305 GCCCATATGACGCCGCTC 61.044 66.667 3.65 0.00 0.00 5.03
351 352 2.357517 CCCATATGACGCCGCTCC 60.358 66.667 3.65 0.00 0.00 4.70
352 353 2.357517 CCATATGACGCCGCTCCC 60.358 66.667 3.65 0.00 0.00 4.30
353 354 2.357517 CATATGACGCCGCTCCCC 60.358 66.667 0.00 0.00 0.00 4.81
354 355 2.524394 ATATGACGCCGCTCCCCT 60.524 61.111 0.00 0.00 0.00 4.79
355 356 2.872388 ATATGACGCCGCTCCCCTG 61.872 63.158 0.00 0.00 0.00 4.45
432 433 4.101790 CGCCATCACCGCCAACAC 62.102 66.667 0.00 0.00 0.00 3.32
433 434 3.747976 GCCATCACCGCCAACACC 61.748 66.667 0.00 0.00 0.00 4.16
434 435 3.430862 CCATCACCGCCAACACCG 61.431 66.667 0.00 0.00 0.00 4.94
455 456 4.143333 GCGGCAGCGTCTAAGGGA 62.143 66.667 0.00 0.00 0.00 4.20
456 457 2.105128 CGGCAGCGTCTAAGGGAG 59.895 66.667 0.00 0.00 0.00 4.30
457 458 2.202946 GGCAGCGTCTAAGGGAGC 60.203 66.667 0.00 0.00 0.00 4.70
458 459 2.726351 GGCAGCGTCTAAGGGAGCT 61.726 63.158 0.00 0.00 41.07 4.09
459 460 1.227118 GCAGCGTCTAAGGGAGCTC 60.227 63.158 4.71 4.71 37.94 4.09
460 461 1.064946 CAGCGTCTAAGGGAGCTCG 59.935 63.158 7.83 0.00 37.94 5.03
461 462 2.122167 AGCGTCTAAGGGAGCTCGG 61.122 63.158 7.83 0.00 34.48 4.63
462 463 3.121019 CGTCTAAGGGAGCTCGGG 58.879 66.667 7.83 0.00 0.00 5.14
463 464 2.491022 CGTCTAAGGGAGCTCGGGG 61.491 68.421 7.83 0.00 0.00 5.73
464 465 1.381463 GTCTAAGGGAGCTCGGGGT 60.381 63.158 7.83 0.00 0.00 4.95
465 466 1.381327 TCTAAGGGAGCTCGGGGTG 60.381 63.158 7.83 0.00 0.00 4.61
466 467 2.365105 TAAGGGAGCTCGGGGTGG 60.365 66.667 7.83 0.00 0.00 4.61
467 468 3.995809 TAAGGGAGCTCGGGGTGGG 62.996 68.421 7.83 0.00 0.00 4.61
469 470 4.791069 GGGAGCTCGGGGTGGGTA 62.791 72.222 7.83 0.00 0.00 3.69
470 471 3.155167 GGAGCTCGGGGTGGGTAG 61.155 72.222 7.83 0.00 0.00 3.18
471 472 3.155167 GAGCTCGGGGTGGGTAGG 61.155 72.222 0.00 0.00 0.00 3.18
472 473 3.674050 GAGCTCGGGGTGGGTAGGA 62.674 68.421 0.00 0.00 0.00 2.94
473 474 2.686106 GCTCGGGGTGGGTAGGAA 60.686 66.667 0.00 0.00 0.00 3.36
474 475 2.732619 GCTCGGGGTGGGTAGGAAG 61.733 68.421 0.00 0.00 0.00 3.46
475 476 1.305887 CTCGGGGTGGGTAGGAAGT 60.306 63.158 0.00 0.00 0.00 3.01
476 477 0.908180 CTCGGGGTGGGTAGGAAGTT 60.908 60.000 0.00 0.00 0.00 2.66
477 478 1.196104 TCGGGGTGGGTAGGAAGTTG 61.196 60.000 0.00 0.00 0.00 3.16
478 479 1.689412 GGGGTGGGTAGGAAGTTGG 59.311 63.158 0.00 0.00 0.00 3.77
479 480 1.689412 GGGTGGGTAGGAAGTTGGG 59.311 63.158 0.00 0.00 0.00 4.12
480 481 1.138228 GGGTGGGTAGGAAGTTGGGT 61.138 60.000 0.00 0.00 0.00 4.51
481 482 1.660242 GGTGGGTAGGAAGTTGGGTA 58.340 55.000 0.00 0.00 0.00 3.69
482 483 1.280133 GGTGGGTAGGAAGTTGGGTAC 59.720 57.143 0.00 0.00 0.00 3.34
483 484 2.263545 GTGGGTAGGAAGTTGGGTACT 58.736 52.381 0.00 0.00 39.32 2.73
484 485 3.444029 GTGGGTAGGAAGTTGGGTACTA 58.556 50.000 0.00 0.00 35.54 1.82
485 486 3.450096 GTGGGTAGGAAGTTGGGTACTAG 59.550 52.174 0.00 0.00 35.54 2.57
486 487 3.036819 GGGTAGGAAGTTGGGTACTAGG 58.963 54.545 0.00 0.00 35.54 3.02
487 488 3.036819 GGTAGGAAGTTGGGTACTAGGG 58.963 54.545 0.00 0.00 35.54 3.53
488 489 3.567441 GGTAGGAAGTTGGGTACTAGGGT 60.567 52.174 0.00 0.00 35.54 4.34
489 490 3.286871 AGGAAGTTGGGTACTAGGGTT 57.713 47.619 0.00 0.00 35.54 4.11
490 491 3.605879 AGGAAGTTGGGTACTAGGGTTT 58.394 45.455 0.00 0.00 35.54 3.27
491 492 3.586174 AGGAAGTTGGGTACTAGGGTTTC 59.414 47.826 0.00 0.00 35.54 2.78
492 493 3.593096 GAAGTTGGGTACTAGGGTTTCG 58.407 50.000 0.00 0.00 35.54 3.46
493 494 1.277273 AGTTGGGTACTAGGGTTTCGC 59.723 52.381 0.00 0.00 34.56 4.70
494 495 0.614812 TTGGGTACTAGGGTTTCGCC 59.385 55.000 0.00 0.00 0.00 5.54
519 520 4.666532 GTTGCCAGCGCGTGTGAC 62.667 66.667 8.43 0.00 38.08 3.67
551 640 1.265905 GGGGTCGTTGCAAACTACAAG 59.734 52.381 0.00 0.00 46.99 3.16
598 714 5.128499 AGGAAATGACATGACTCTCCTAGTG 59.872 44.000 0.00 0.00 39.07 2.74
604 720 4.541705 ACATGACTCTCCTAGTGCATACT 58.458 43.478 0.00 0.00 39.07 2.12
605 721 4.959210 ACATGACTCTCCTAGTGCATACTT 59.041 41.667 0.00 0.00 39.07 2.24
664 780 3.585862 TGCACGTCAGGATCTTTCTAAC 58.414 45.455 0.00 0.00 0.00 2.34
670 786 7.306866 GCACGTCAGGATCTTTCTAACAATATC 60.307 40.741 0.00 0.00 0.00 1.63
824 940 8.997621 AGAGAAATGTAGCTTGAATACGTAAA 57.002 30.769 0.00 0.00 0.00 2.01
834 950 4.730949 TGAATACGTAAAGCTACTGCCT 57.269 40.909 0.00 0.00 40.80 4.75
836 952 2.953466 TACGTAAAGCTACTGCCTGG 57.047 50.000 0.00 0.00 40.80 4.45
916 1782 1.805945 CAGTTGGCCGACGAGTAGC 60.806 63.158 17.75 0.00 0.00 3.58
950 1816 1.873903 CGGGGCTAATGATCGACCTTG 60.874 57.143 0.00 0.00 0.00 3.61
958 1824 1.153349 GATCGACCTTGGGTGGCTC 60.153 63.158 0.00 0.00 35.25 4.70
1176 2047 1.452145 CCAAACCCACCACCGTTCTG 61.452 60.000 0.00 0.00 0.00 3.02
1293 2164 3.441290 CCGGCCTCGAGAGTCGTT 61.441 66.667 15.71 0.00 41.35 3.85
1326 2197 1.132643 GGATTCTACGTGACAGCGTCT 59.867 52.381 0.00 0.00 44.55 4.18
1503 2374 1.154197 GGTACGTGCTCTGGAAAACC 58.846 55.000 3.01 0.00 0.00 3.27
1586 2464 2.102749 CGCCGGTGCATGAAATGG 59.897 61.111 0.00 0.00 46.86 3.16
1678 2561 6.869695 TGTAGTTACCATCGATATGTGTGTT 58.130 36.000 0.00 0.00 0.00 3.32
1679 2562 6.754675 TGTAGTTACCATCGATATGTGTGTTG 59.245 38.462 0.00 0.00 0.00 3.33
1680 2563 5.730550 AGTTACCATCGATATGTGTGTTGT 58.269 37.500 0.00 0.00 0.00 3.32
1681 2564 6.170506 AGTTACCATCGATATGTGTGTTGTT 58.829 36.000 0.00 0.00 0.00 2.83
1682 2565 6.653320 AGTTACCATCGATATGTGTGTTGTTT 59.347 34.615 0.00 0.00 0.00 2.83
1683 2566 5.545658 ACCATCGATATGTGTGTTGTTTC 57.454 39.130 0.00 0.00 0.00 2.78
1684 2567 4.394920 ACCATCGATATGTGTGTTGTTTCC 59.605 41.667 0.00 0.00 0.00 3.13
1685 2568 4.494035 CCATCGATATGTGTGTTGTTTCCG 60.494 45.833 0.00 0.00 0.00 4.30
1701 2584 4.040706 TGTTTCCGGTTTGTGTCCTACTAT 59.959 41.667 0.00 0.00 0.00 2.12
1705 2593 5.623169 TCCGGTTTGTGTCCTACTATTTTT 58.377 37.500 0.00 0.00 0.00 1.94
1745 2634 4.596585 CCCCGGGGCTGTTTGTGT 62.597 66.667 31.01 0.00 0.00 3.72
1866 2757 1.376609 GGGCAATGATCGTGGTGTCC 61.377 60.000 0.00 0.00 0.00 4.02
2058 3426 2.582052 TCCTCACGTTGGAAAAATGCT 58.418 42.857 4.71 0.00 0.00 3.79
2181 3549 6.765512 TGAAAAACTGAATTGGGACCATTTTC 59.234 34.615 13.26 13.26 35.75 2.29
2206 3574 1.600485 GTTGGATGACAAACGAACGGT 59.400 47.619 0.00 0.00 41.58 4.83
2231 3599 1.203523 CTCACGTCTTCTTCCTCCTGG 59.796 57.143 0.00 0.00 0.00 4.45
2383 3752 0.907230 CTAGCCATCCCTCTAGCCCC 60.907 65.000 0.00 0.00 0.00 5.80
2384 3753 2.731801 TAGCCATCCCTCTAGCCCCG 62.732 65.000 0.00 0.00 0.00 5.73
2385 3754 3.631046 CCATCCCTCTAGCCCCGC 61.631 72.222 0.00 0.00 0.00 6.13
2386 3755 3.631046 CATCCCTCTAGCCCCGCC 61.631 72.222 0.00 0.00 0.00 6.13
2387 3756 4.964241 ATCCCTCTAGCCCCGCCC 62.964 72.222 0.00 0.00 0.00 6.13
2399 3768 4.653888 CCGCCCGTGTCCCCTTTT 62.654 66.667 0.00 0.00 0.00 2.27
2400 3769 2.596338 CGCCCGTGTCCCCTTTTT 60.596 61.111 0.00 0.00 0.00 1.94
2448 4368 4.973211 CCCTCACCCTAAACCCTAAGATAA 59.027 45.833 0.00 0.00 0.00 1.75
2449 4369 5.430745 CCCTCACCCTAAACCCTAAGATAAA 59.569 44.000 0.00 0.00 0.00 1.40
2472 4392 1.221021 GGGGTAGCCCTTCGTTGAG 59.779 63.158 23.31 0.00 44.66 3.02
2532 4452 3.428870 GCGAACTCTCAAAAATCGACTGA 59.571 43.478 0.00 0.00 35.65 3.41
2548 4468 4.690748 TCGACTGACCTCAATTTGACATTC 59.309 41.667 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.436646 CGGCTCGTGGCATTCCTT 60.437 61.111 11.75 0.00 44.01 3.36
3 4 4.166011 GTGCGGCTCGTGGCATTC 62.166 66.667 11.75 0.53 41.83 2.67
7 8 4.465512 CAATGTGCGGCTCGTGGC 62.466 66.667 0.00 0.20 40.90 5.01
8 9 4.465512 GCAATGTGCGGCTCGTGG 62.466 66.667 0.00 0.00 31.71 4.94
17 18 1.443194 CTTGACGGCTGCAATGTGC 60.443 57.895 0.50 0.00 45.29 4.57
18 19 1.443194 GCTTGACGGCTGCAATGTG 60.443 57.895 0.50 0.00 0.00 3.21
19 20 2.629656 GGCTTGACGGCTGCAATGT 61.630 57.895 0.50 0.00 34.85 2.71
20 21 2.144833 TTGGCTTGACGGCTGCAATG 62.145 55.000 0.50 0.00 39.32 2.82
21 22 1.902918 TTGGCTTGACGGCTGCAAT 60.903 52.632 0.50 0.00 39.32 3.56
22 23 2.518112 TTGGCTTGACGGCTGCAA 60.518 55.556 0.50 0.00 39.32 4.08
23 24 3.286751 GTTGGCTTGACGGCTGCA 61.287 61.111 0.50 0.00 39.32 4.41
24 25 2.970974 GAGTTGGCTTGACGGCTGC 61.971 63.158 0.00 0.00 39.32 5.25
25 26 2.328099 GGAGTTGGCTTGACGGCTG 61.328 63.158 0.00 0.00 39.32 4.85
26 27 2.032681 GGAGTTGGCTTGACGGCT 59.967 61.111 0.00 0.00 39.32 5.52
27 28 3.423154 CGGAGTTGGCTTGACGGC 61.423 66.667 0.00 0.00 38.97 5.68
28 29 2.742372 CCGGAGTTGGCTTGACGG 60.742 66.667 0.00 0.00 33.18 4.79
56 57 4.473520 AAGATGGAGGCGGTGGCG 62.474 66.667 0.00 0.00 41.24 5.69
57 58 2.514824 GAAGATGGAGGCGGTGGC 60.515 66.667 0.00 0.00 38.90 5.01
58 59 2.190578 GGAAGATGGAGGCGGTGG 59.809 66.667 0.00 0.00 0.00 4.61
59 60 1.450312 GTGGAAGATGGAGGCGGTG 60.450 63.158 0.00 0.00 0.00 4.94
60 61 1.488705 TTGTGGAAGATGGAGGCGGT 61.489 55.000 0.00 0.00 0.00 5.68
61 62 1.026718 GTTGTGGAAGATGGAGGCGG 61.027 60.000 0.00 0.00 0.00 6.13
62 63 1.026718 GGTTGTGGAAGATGGAGGCG 61.027 60.000 0.00 0.00 0.00 5.52
63 64 1.026718 CGGTTGTGGAAGATGGAGGC 61.027 60.000 0.00 0.00 0.00 4.70
64 65 1.026718 GCGGTTGTGGAAGATGGAGG 61.027 60.000 0.00 0.00 0.00 4.30
65 66 1.361668 CGCGGTTGTGGAAGATGGAG 61.362 60.000 0.00 0.00 0.00 3.86
66 67 1.375396 CGCGGTTGTGGAAGATGGA 60.375 57.895 0.00 0.00 0.00 3.41
67 68 1.375396 TCGCGGTTGTGGAAGATGG 60.375 57.895 6.13 0.00 0.00 3.51
68 69 1.635663 GGTCGCGGTTGTGGAAGATG 61.636 60.000 6.13 0.00 0.00 2.90
69 70 1.375523 GGTCGCGGTTGTGGAAGAT 60.376 57.895 6.13 0.00 0.00 2.40
70 71 2.029964 GGTCGCGGTTGTGGAAGA 59.970 61.111 6.13 0.00 0.00 2.87
71 72 2.030562 AGGTCGCGGTTGTGGAAG 59.969 61.111 6.13 0.00 0.00 3.46
72 73 2.280524 CAGGTCGCGGTTGTGGAA 60.281 61.111 6.13 0.00 0.00 3.53
73 74 4.308458 CCAGGTCGCGGTTGTGGA 62.308 66.667 6.13 0.00 0.00 4.02
74 75 4.308458 TCCAGGTCGCGGTTGTGG 62.308 66.667 6.13 8.84 0.00 4.17
75 76 2.738521 CTCCAGGTCGCGGTTGTG 60.739 66.667 6.13 0.00 0.00 3.33
76 77 4.681978 GCTCCAGGTCGCGGTTGT 62.682 66.667 6.13 0.00 0.00 3.32
77 78 4.680237 TGCTCCAGGTCGCGGTTG 62.680 66.667 6.13 2.04 0.00 3.77
78 79 4.379243 CTGCTCCAGGTCGCGGTT 62.379 66.667 6.13 0.00 0.00 4.44
100 101 4.847516 TCGAATGCCTCCGTCGCG 62.848 66.667 0.00 0.00 34.80 5.87
101 102 2.956964 CTCGAATGCCTCCGTCGC 60.957 66.667 0.00 0.00 34.80 5.19
102 103 2.278857 CCTCGAATGCCTCCGTCG 60.279 66.667 0.00 0.00 36.12 5.12
103 104 1.227002 GTCCTCGAATGCCTCCGTC 60.227 63.158 0.00 0.00 0.00 4.79
104 105 2.893398 GTCCTCGAATGCCTCCGT 59.107 61.111 0.00 0.00 0.00 4.69
105 106 2.278857 CGTCCTCGAATGCCTCCG 60.279 66.667 0.00 0.00 39.71 4.63
106 107 2.586357 GCGTCCTCGAATGCCTCC 60.586 66.667 0.00 0.00 39.71 4.30
107 108 2.956964 CGCGTCCTCGAATGCCTC 60.957 66.667 0.00 0.00 39.71 4.70
108 109 3.449227 TCGCGTCCTCGAATGCCT 61.449 61.111 5.77 0.00 39.71 4.75
109 110 3.255379 GTCGCGTCCTCGAATGCC 61.255 66.667 5.77 0.00 40.43 4.40
110 111 0.594028 TATGTCGCGTCCTCGAATGC 60.594 55.000 5.77 0.00 40.43 3.56
111 112 1.121240 GTATGTCGCGTCCTCGAATG 58.879 55.000 5.77 0.00 40.43 2.67
112 113 1.002684 GAGTATGTCGCGTCCTCGAAT 60.003 52.381 5.77 0.00 40.43 3.34
113 114 0.376152 GAGTATGTCGCGTCCTCGAA 59.624 55.000 5.77 0.00 40.43 3.71
114 115 1.759293 CGAGTATGTCGCGTCCTCGA 61.759 60.000 19.46 0.00 45.81 4.04
115 116 1.367782 CGAGTATGTCGCGTCCTCG 60.368 63.158 5.77 10.86 43.03 4.63
116 117 4.591852 CGAGTATGTCGCGTCCTC 57.408 61.111 5.77 1.92 43.03 3.71
124 125 0.457853 TTGCAGCGGTCGAGTATGTC 60.458 55.000 0.00 0.00 0.00 3.06
125 126 0.458543 CTTGCAGCGGTCGAGTATGT 60.459 55.000 0.00 0.00 0.00 2.29
126 127 1.148157 CCTTGCAGCGGTCGAGTATG 61.148 60.000 0.00 0.00 0.00 2.39
127 128 1.141881 CCTTGCAGCGGTCGAGTAT 59.858 57.895 0.00 0.00 0.00 2.12
128 129 2.571757 CCTTGCAGCGGTCGAGTA 59.428 61.111 0.00 0.00 0.00 2.59
131 132 4.617520 TTGCCTTGCAGCGGTCGA 62.618 61.111 6.06 0.00 40.61 4.20
132 133 4.389576 GTTGCCTTGCAGCGGTCG 62.390 66.667 6.06 0.00 40.61 4.79
133 134 4.043200 GGTTGCCTTGCAGCGGTC 62.043 66.667 6.06 0.38 40.59 4.79
134 135 4.892965 TGGTTGCCTTGCAGCGGT 62.893 61.111 6.06 0.00 40.59 5.68
135 136 4.347453 GTGGTTGCCTTGCAGCGG 62.347 66.667 0.01 0.01 40.59 5.52
136 137 3.259425 GAGTGGTTGCCTTGCAGCG 62.259 63.158 0.00 0.00 40.59 5.18
137 138 2.647297 GAGTGGTTGCCTTGCAGC 59.353 61.111 0.00 0.00 40.61 5.25
138 139 1.228367 AGGAGTGGTTGCCTTGCAG 60.228 57.895 0.00 0.00 40.61 4.41
139 140 1.529010 CAGGAGTGGTTGCCTTGCA 60.529 57.895 0.00 0.00 36.47 4.08
140 141 2.270986 CCAGGAGTGGTTGCCTTGC 61.271 63.158 0.00 0.00 39.30 4.01
141 142 2.270986 GCCAGGAGTGGTTGCCTTG 61.271 63.158 0.00 0.00 46.96 3.61
142 143 2.116125 GCCAGGAGTGGTTGCCTT 59.884 61.111 0.00 0.00 46.96 4.35
143 144 4.335647 CGCCAGGAGTGGTTGCCT 62.336 66.667 0.00 0.00 46.96 4.75
144 145 4.329545 TCGCCAGGAGTGGTTGCC 62.330 66.667 0.00 0.00 46.96 4.52
145 146 2.743928 CTCGCCAGGAGTGGTTGC 60.744 66.667 0.00 0.00 46.96 4.17
146 147 2.743928 GCTCGCCAGGAGTGGTTG 60.744 66.667 0.00 0.00 46.96 3.77
147 148 2.925170 AGCTCGCCAGGAGTGGTT 60.925 61.111 0.00 0.00 46.96 3.67
148 149 3.386237 GAGCTCGCCAGGAGTGGT 61.386 66.667 0.00 0.00 46.96 4.16
150 151 4.504916 CGGAGCTCGCCAGGAGTG 62.505 72.222 7.83 0.00 45.03 3.51
173 174 2.440796 ACAATGAGGCCATGGCGG 60.441 61.111 29.90 16.35 43.06 6.13
174 175 2.802792 CACAATGAGGCCATGGCG 59.197 61.111 29.90 17.38 43.06 5.69
175 176 2.497770 GCACAATGAGGCCATGGC 59.502 61.111 29.47 29.47 41.06 4.40
224 225 2.668632 GGCACGGTGGATCCTTCA 59.331 61.111 14.23 0.00 0.00 3.02
238 239 3.838271 GAGGAGATGGTCGCGGCA 61.838 66.667 14.93 0.00 0.00 5.69
305 306 0.249155 GTGGATTTGATGGCGCATGG 60.249 55.000 10.83 0.00 0.00 3.66
307 308 1.394266 GGGTGGATTTGATGGCGCAT 61.394 55.000 10.83 0.00 0.00 4.73
316 317 2.469516 GCGGCGTAGGGTGGATTTG 61.470 63.158 9.37 0.00 0.00 2.32
318 319 4.171103 GGCGGCGTAGGGTGGATT 62.171 66.667 9.37 0.00 0.00 3.01
323 324 2.525877 ATATGGGCGGCGTAGGGT 60.526 61.111 9.37 0.00 0.00 4.34
324 325 2.047274 CATATGGGCGGCGTAGGG 60.047 66.667 9.37 0.00 0.00 3.53
326 327 1.733041 CGTCATATGGGCGGCGTAG 60.733 63.158 9.37 0.00 0.00 3.51
327 328 2.337170 CGTCATATGGGCGGCGTA 59.663 61.111 9.37 0.00 0.00 4.42
333 334 3.044305 GAGCGGCGTCATATGGGC 61.044 66.667 9.37 6.98 0.00 5.36
334 335 2.357517 GGAGCGGCGTCATATGGG 60.358 66.667 9.37 0.00 0.00 4.00
335 336 2.357517 GGGAGCGGCGTCATATGG 60.358 66.667 9.37 0.00 0.00 2.74
336 337 2.357517 GGGGAGCGGCGTCATATG 60.358 66.667 9.37 0.00 0.00 1.78
337 338 2.524394 AGGGGAGCGGCGTCATAT 60.524 61.111 9.37 0.00 0.00 1.78
338 339 3.536917 CAGGGGAGCGGCGTCATA 61.537 66.667 9.37 0.00 0.00 2.15
415 416 4.101790 GTGTTGGCGGTGATGGCG 62.102 66.667 0.00 0.00 37.19 5.69
416 417 3.747976 GGTGTTGGCGGTGATGGC 61.748 66.667 0.00 0.00 0.00 4.40
417 418 3.430862 CGGTGTTGGCGGTGATGG 61.431 66.667 0.00 0.00 0.00 3.51
418 419 3.430862 CCGGTGTTGGCGGTGATG 61.431 66.667 0.00 0.00 0.00 3.07
435 436 3.558411 CTTAGACGCTGCCGCTGC 61.558 66.667 11.96 11.96 38.22 5.25
436 437 2.887568 CCTTAGACGCTGCCGCTG 60.888 66.667 0.00 0.00 38.22 5.18
437 438 4.148825 CCCTTAGACGCTGCCGCT 62.149 66.667 0.00 0.00 38.22 5.52
438 439 4.143333 TCCCTTAGACGCTGCCGC 62.143 66.667 0.00 0.00 38.22 6.53
439 440 2.105128 CTCCCTTAGACGCTGCCG 59.895 66.667 0.00 0.00 41.14 5.69
440 441 2.202946 GCTCCCTTAGACGCTGCC 60.203 66.667 0.00 0.00 0.00 4.85
441 442 1.227118 GAGCTCCCTTAGACGCTGC 60.227 63.158 0.87 0.00 31.63 5.25
442 443 1.064946 CGAGCTCCCTTAGACGCTG 59.935 63.158 8.47 0.00 31.63 5.18
443 444 2.122167 CCGAGCTCCCTTAGACGCT 61.122 63.158 8.47 0.00 33.40 5.07
444 445 2.413765 CCGAGCTCCCTTAGACGC 59.586 66.667 8.47 0.00 0.00 5.19
445 446 2.491022 CCCCGAGCTCCCTTAGACG 61.491 68.421 8.47 0.00 0.00 4.18
446 447 1.381463 ACCCCGAGCTCCCTTAGAC 60.381 63.158 8.47 0.00 0.00 2.59
447 448 1.381327 CACCCCGAGCTCCCTTAGA 60.381 63.158 8.47 0.00 0.00 2.10
448 449 2.435693 CCACCCCGAGCTCCCTTAG 61.436 68.421 8.47 0.00 0.00 2.18
449 450 2.365105 CCACCCCGAGCTCCCTTA 60.365 66.667 8.47 0.00 0.00 2.69
452 453 4.791069 TACCCACCCCGAGCTCCC 62.791 72.222 8.47 0.00 0.00 4.30
453 454 3.155167 CTACCCACCCCGAGCTCC 61.155 72.222 8.47 0.00 0.00 4.70
454 455 3.155167 CCTACCCACCCCGAGCTC 61.155 72.222 2.73 2.73 0.00 4.09
455 456 3.248248 TTCCTACCCACCCCGAGCT 62.248 63.158 0.00 0.00 0.00 4.09
456 457 2.686106 TTCCTACCCACCCCGAGC 60.686 66.667 0.00 0.00 0.00 5.03
457 458 0.908180 AACTTCCTACCCACCCCGAG 60.908 60.000 0.00 0.00 0.00 4.63
458 459 1.159184 AACTTCCTACCCACCCCGA 59.841 57.895 0.00 0.00 0.00 5.14
459 460 1.298667 CAACTTCCTACCCACCCCG 59.701 63.158 0.00 0.00 0.00 5.73
460 461 1.689412 CCAACTTCCTACCCACCCC 59.311 63.158 0.00 0.00 0.00 4.95
461 462 1.138228 ACCCAACTTCCTACCCACCC 61.138 60.000 0.00 0.00 0.00 4.61
462 463 1.280133 GTACCCAACTTCCTACCCACC 59.720 57.143 0.00 0.00 0.00 4.61
463 464 2.263545 AGTACCCAACTTCCTACCCAC 58.736 52.381 0.00 0.00 33.35 4.61
464 465 2.727429 AGTACCCAACTTCCTACCCA 57.273 50.000 0.00 0.00 33.35 4.51
465 466 3.036819 CCTAGTACCCAACTTCCTACCC 58.963 54.545 0.00 0.00 39.80 3.69
466 467 3.036819 CCCTAGTACCCAACTTCCTACC 58.963 54.545 0.00 0.00 39.80 3.18
467 468 3.717576 ACCCTAGTACCCAACTTCCTAC 58.282 50.000 0.00 0.00 39.80 3.18
468 469 4.424761 AACCCTAGTACCCAACTTCCTA 57.575 45.455 0.00 0.00 39.80 2.94
469 470 3.286871 AACCCTAGTACCCAACTTCCT 57.713 47.619 0.00 0.00 39.80 3.36
470 471 3.618263 CGAAACCCTAGTACCCAACTTCC 60.618 52.174 0.00 0.00 39.80 3.46
471 472 3.593096 CGAAACCCTAGTACCCAACTTC 58.407 50.000 0.00 0.00 39.80 3.01
472 473 2.289882 GCGAAACCCTAGTACCCAACTT 60.290 50.000 0.00 0.00 39.80 2.66
473 474 1.277273 GCGAAACCCTAGTACCCAACT 59.723 52.381 0.00 0.00 42.62 3.16
474 475 1.676916 GGCGAAACCCTAGTACCCAAC 60.677 57.143 0.00 0.00 0.00 3.77
475 476 0.614812 GGCGAAACCCTAGTACCCAA 59.385 55.000 0.00 0.00 0.00 4.12
476 477 2.289840 GGCGAAACCCTAGTACCCA 58.710 57.895 0.00 0.00 0.00 4.51
502 503 4.666532 GTCACACGCGCTGGCAAC 62.667 66.667 5.73 0.79 39.92 4.17
530 531 0.535553 TGTAGTTTGCAACGACCCCC 60.536 55.000 0.00 0.00 36.35 5.40
531 532 1.265905 CTTGTAGTTTGCAACGACCCC 59.734 52.381 0.00 0.00 36.35 4.95
532 533 1.944709 ACTTGTAGTTTGCAACGACCC 59.055 47.619 0.00 0.00 36.35 4.46
533 534 3.685836 AACTTGTAGTTTGCAACGACC 57.314 42.857 0.00 0.00 34.11 4.79
578 694 3.771479 TGCACTAGGAGAGTCATGTCATT 59.229 43.478 0.00 0.00 35.64 2.57
591 707 9.667107 GGCAATAATTATAAGTATGCACTAGGA 57.333 33.333 16.84 0.00 33.48 2.94
620 736 9.719355 TGCAGTCTTAGTATTGAAGTGAAAATA 57.281 29.630 0.00 0.00 0.00 1.40
628 744 5.688348 GACGTGCAGTCTTAGTATTGAAG 57.312 43.478 0.00 0.00 46.13 3.02
704 820 9.846248 GTGACTGAAACTTGCTGAAAATATAAT 57.154 29.630 0.00 0.00 0.00 1.28
705 821 8.845227 TGTGACTGAAACTTGCTGAAAATATAA 58.155 29.630 0.00 0.00 0.00 0.98
706 822 8.389779 TGTGACTGAAACTTGCTGAAAATATA 57.610 30.769 0.00 0.00 0.00 0.86
707 823 7.275888 TGTGACTGAAACTTGCTGAAAATAT 57.724 32.000 0.00 0.00 0.00 1.28
708 824 6.691754 TGTGACTGAAACTTGCTGAAAATA 57.308 33.333 0.00 0.00 0.00 1.40
715 831 5.391312 AGTTTTTGTGACTGAAACTTGCT 57.609 34.783 9.84 0.00 39.79 3.91
794 910 8.443160 CGTATTCAAGCTACATTTCTCTCAAAA 58.557 33.333 0.00 0.00 0.00 2.44
795 911 7.602644 ACGTATTCAAGCTACATTTCTCTCAAA 59.397 33.333 0.00 0.00 0.00 2.69
796 912 7.097192 ACGTATTCAAGCTACATTTCTCTCAA 58.903 34.615 0.00 0.00 0.00 3.02
797 913 6.631016 ACGTATTCAAGCTACATTTCTCTCA 58.369 36.000 0.00 0.00 0.00 3.27
798 914 8.630278 TTACGTATTCAAGCTACATTTCTCTC 57.370 34.615 0.00 0.00 0.00 3.20
799 915 8.997621 TTTACGTATTCAAGCTACATTTCTCT 57.002 30.769 0.00 0.00 0.00 3.10
800 916 7.846592 GCTTTACGTATTCAAGCTACATTTCTC 59.153 37.037 18.77 0.00 39.92 2.87
801 917 7.685594 GCTTTACGTATTCAAGCTACATTTCT 58.314 34.615 18.77 0.00 39.92 2.52
802 918 7.878408 GCTTTACGTATTCAAGCTACATTTC 57.122 36.000 18.77 0.00 39.92 2.17
810 926 4.260253 GGCAGTAGCTTTACGTATTCAAGC 60.260 45.833 18.51 18.51 42.81 4.01
811 927 5.005779 CAGGCAGTAGCTTTACGTATTCAAG 59.994 44.000 0.00 0.00 41.70 3.02
812 928 4.868171 CAGGCAGTAGCTTTACGTATTCAA 59.132 41.667 0.00 0.00 41.70 2.69
813 929 4.430007 CAGGCAGTAGCTTTACGTATTCA 58.570 43.478 0.00 0.00 41.70 2.57
814 930 3.802685 CCAGGCAGTAGCTTTACGTATTC 59.197 47.826 0.00 0.00 41.70 1.75
815 931 3.793559 CCAGGCAGTAGCTTTACGTATT 58.206 45.455 0.00 0.00 41.70 1.89
920 1786 0.471401 ATTAGCCCCGAGGGTAGTCC 60.471 60.000 7.48 0.00 46.57 3.85
922 1788 0.263765 TCATTAGCCCCGAGGGTAGT 59.736 55.000 7.48 0.00 46.57 2.73
925 1791 1.472662 CGATCATTAGCCCCGAGGGT 61.473 60.000 7.48 1.48 46.51 4.34
950 1816 3.054655 TCCTTAAATAGTGTGAGCCACCC 60.055 47.826 3.33 0.00 45.74 4.61
958 1824 5.937540 TGTGTCCATGTCCTTAAATAGTGTG 59.062 40.000 0.00 0.00 0.00 3.82
1586 2464 2.866726 AACCCCGCAAACCATGTGC 61.867 57.895 0.00 0.00 38.25 4.57
1678 2561 2.171027 AGTAGGACACAAACCGGAAACA 59.829 45.455 9.46 0.00 0.00 2.83
1679 2562 2.842457 AGTAGGACACAAACCGGAAAC 58.158 47.619 9.46 0.00 0.00 2.78
1680 2563 4.895668 ATAGTAGGACACAAACCGGAAA 57.104 40.909 9.46 0.00 0.00 3.13
1681 2564 4.895668 AATAGTAGGACACAAACCGGAA 57.104 40.909 9.46 0.00 0.00 4.30
1682 2565 4.895668 AAATAGTAGGACACAAACCGGA 57.104 40.909 9.46 0.00 0.00 5.14
1683 2566 5.952526 AAAAATAGTAGGACACAAACCGG 57.047 39.130 0.00 0.00 0.00 5.28
1705 2593 5.708697 GGGTTTTATCCTCCTTTTCGAGAAA 59.291 40.000 0.00 0.00 30.97 2.52
1708 2596 3.945921 GGGGTTTTATCCTCCTTTTCGAG 59.054 47.826 0.00 0.00 0.00 4.04
1745 2634 4.891168 TCAACACAGTGAAGTACAGTAGGA 59.109 41.667 7.81 0.00 0.00 2.94
1866 2757 5.425539 TCTTCCCCAATCAGTTAGGACTTAG 59.574 44.000 0.00 0.00 32.54 2.18
2058 3426 6.741992 AGTCAATAATCAAAATGACGAGCA 57.258 33.333 0.00 0.00 45.21 4.26
2162 3530 3.259123 GCTGAAAATGGTCCCAATTCAGT 59.741 43.478 27.92 3.00 45.40 3.41
2181 3549 0.110238 CGTTTGTCATCCAACGGCTG 60.110 55.000 0.00 0.00 31.20 4.85
2231 3599 4.436584 CCGAGCATGATCTGTTTCTGTTTC 60.437 45.833 9.64 0.00 0.00 2.78
2350 3718 2.654404 CTAGCGGCGCGGTAAGAC 60.654 66.667 27.59 0.00 39.29 3.01
2360 3728 1.882989 CTAGAGGGATGGCTAGCGGC 61.883 65.000 9.00 0.00 40.90 6.53
2361 3729 1.882989 GCTAGAGGGATGGCTAGCGG 61.883 65.000 9.00 0.00 46.82 5.52
2383 3752 2.596338 AAAAAGGGGACACGGGCG 60.596 61.111 0.00 0.00 0.00 6.13
2419 3788 2.598787 TTTAGGGTGAGGGCGGTGG 61.599 63.158 0.00 0.00 0.00 4.61
2420 3789 1.376812 GTTTAGGGTGAGGGCGGTG 60.377 63.158 0.00 0.00 0.00 4.94
2421 3790 2.599757 GGTTTAGGGTGAGGGCGGT 61.600 63.158 0.00 0.00 0.00 5.68
2422 3791 2.271173 GGTTTAGGGTGAGGGCGG 59.729 66.667 0.00 0.00 0.00 6.13
2423 3792 0.979187 TAGGGTTTAGGGTGAGGGCG 60.979 60.000 0.00 0.00 0.00 6.13
2424 3793 1.212195 CTTAGGGTTTAGGGTGAGGGC 59.788 57.143 0.00 0.00 0.00 5.19
2425 3794 2.841795 TCTTAGGGTTTAGGGTGAGGG 58.158 52.381 0.00 0.00 0.00 4.30
2426 3795 6.570654 TTTATCTTAGGGTTTAGGGTGAGG 57.429 41.667 0.00 0.00 0.00 3.86
2429 3798 9.297037 CCATTATTTATCTTAGGGTTTAGGGTG 57.703 37.037 0.00 0.00 0.00 4.61
2430 3799 8.453681 CCCATTATTTATCTTAGGGTTTAGGGT 58.546 37.037 0.00 0.00 0.00 4.34
2431 3800 7.893833 CCCCATTATTTATCTTAGGGTTTAGGG 59.106 40.741 0.00 0.00 32.90 3.53
2432 3801 8.453681 ACCCCATTATTTATCTTAGGGTTTAGG 58.546 37.037 0.00 0.00 44.14 2.69
2435 3804 7.948447 GCTACCCCATTATTTATCTTAGGGTTT 59.052 37.037 2.21 0.00 44.14 3.27
2472 4392 0.544223 GAGGAAGGAGAAGGAAGGGC 59.456 60.000 0.00 0.00 0.00 5.19
2532 4452 4.452455 GTCGACTGAATGTCAAATTGAGGT 59.548 41.667 8.70 0.00 45.60 3.85


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

AutoCloner maintained by Alex Coulton.