Multiple sequence alignment - TraesCS1B01G371400

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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 TraesCS1B01G371400 chr1B 100.000 6213 0 0 1 6213 600969501 600975713 0.000000e+00 11474.0
1 TraesCS1B01G371400 chr1A 97.154 3549 98 2 387 3932 536349439 536345891 0.000000e+00 5991.0
2 TraesCS1B01G371400 chr1A 97.103 794 17 1 4462 5255 536345214 536344427 0.000000e+00 1334.0
3 TraesCS1B01G371400 chr1A 93.743 879 31 12 5358 6213 536344429 536343552 0.000000e+00 1297.0
4 TraesCS1B01G371400 chr1A 96.256 454 10 3 4017 4465 536345901 536345450 0.000000e+00 737.0
5 TraesCS1B01G371400 chr1A 84.674 261 34 4 4540 4796 169552703 169552445 7.990000e-64 255.0
6 TraesCS1B01G371400 chr1A 91.379 58 4 1 5560 5616 536343633 536343576 1.860000e-10 78.7
7 TraesCS1B01G371400 chr1D 94.018 3661 166 29 3 3633 442370145 442373782 0.000000e+00 5498.0
8 TraesCS1B01G371400 chr1D 91.606 1644 66 23 3626 5255 442373858 442375443 0.000000e+00 2206.0
9 TraesCS1B01G371400 chr1D 94.005 884 25 8 5358 6213 442375441 442376324 0.000000e+00 1314.0
10 TraesCS1B01G371400 chr1D 80.269 223 36 7 1 219 269439136 269438918 1.790000e-35 161.0
11 TraesCS1B01G371400 chr6D 85.926 270 30 7 4534 4797 472139049 472139316 1.320000e-71 281.0
12 TraesCS1B01G371400 chr6D 84.848 264 35 4 4538 4797 128074557 128074819 1.720000e-65 261.0
13 TraesCS1B01G371400 chr6D 96.296 108 3 1 3915 4021 467773582 467773475 6.400000e-40 176.0
14 TraesCS1B01G371400 chr5D 86.038 265 32 5 4540 4800 546697715 546697978 4.740000e-71 279.0
15 TraesCS1B01G371400 chr5D 92.241 116 8 1 3922 4036 301216205 301216090 4.980000e-36 163.0
16 TraesCS1B01G371400 chr6A 85.171 263 34 5 4540 4797 456684867 456684605 1.330000e-66 265.0
17 TraesCS1B01G371400 chr6B 84.861 251 34 3 4540 4786 543799909 543800159 3.720000e-62 250.0
18 TraesCS1B01G371400 chr6B 98.000 100 2 0 3921 4020 219879446 219879347 2.300000e-39 174.0
19 TraesCS1B01G371400 chr5A 83.650 263 38 5 4540 4797 465555708 465555446 6.220000e-60 243.0
20 TraesCS1B01G371400 chr3D 81.277 235 35 8 1 230 275452593 275452823 1.380000e-41 182.0
21 TraesCS1B01G371400 chr3D 98.000 100 2 0 3920 4019 613073454 613073355 2.300000e-39 174.0
22 TraesCS1B01G371400 chr7B 99.000 100 1 0 3922 4021 198885208 198885109 4.950000e-41 180.0
23 TraesCS1B01G371400 chr7B 96.296 108 4 0 5256 5363 677755906 677755799 1.780000e-40 178.0
24 TraesCS1B01G371400 chr7B 93.913 115 6 1 5256 5370 675150131 675150244 8.280000e-39 172.0
25 TraesCS1B01G371400 chr5B 97.170 106 3 0 5256 5361 407639456 407639561 4.950000e-41 180.0
26 TraesCS1B01G371400 chr5B 96.296 108 4 0 5256 5363 366475938 366475831 1.780000e-40 178.0
27 TraesCS1B01G371400 chr5B 93.966 116 4 3 3906 4020 625959447 625959560 8.280000e-39 172.0
28 TraesCS1B01G371400 chr2A 81.197 234 35 8 1 230 753279199 753279427 4.950000e-41 180.0
29 TraesCS1B01G371400 chr4B 97.143 105 3 0 5256 5360 467274886 467274990 1.780000e-40 178.0
30 TraesCS1B01G371400 chr4B 98.039 102 2 0 5259 5360 520425958 520425857 1.780000e-40 178.0
31 TraesCS1B01G371400 chr4B 97.143 105 3 0 5256 5360 583528704 583528808 1.780000e-40 178.0
32 TraesCS1B01G371400 chr4B 97.143 105 3 0 5256 5360 663766107 663766211 1.780000e-40 178.0
33 TraesCS1B01G371400 chr4B 95.327 107 4 1 3915 4021 285608357 285608462 1.070000e-37 169.0
34 TraesCS1B01G371400 chr3B 97.143 105 3 0 5256 5360 380680204 380680308 1.780000e-40 178.0
35 TraesCS1B01G371400 chr3B 97.115 104 2 1 3919 4022 479298478 479298376 2.300000e-39 174.0
36 TraesCS1B01G371400 chr3B 79.263 217 38 5 16 228 607219046 607219259 1.810000e-30 145.0
37 TraesCS1B01G371400 chr7D 98.000 100 2 0 3920 4019 41596645 41596546 2.300000e-39 174.0
38 TraesCS1B01G371400 chr7D 81.818 121 22 0 14 134 518040846 518040966 1.100000e-17 102.0
39 TraesCS1B01G371400 chr3A 85.714 91 9 4 8 96 629698917 629699005 6.630000e-15 93.5
40 TraesCS1B01G371400 chr2D 86.301 73 10 0 8 80 140474188 140474260 5.160000e-11 80.5


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 TraesCS1B01G371400 chr1B 600969501 600975713 6212 False 11474.00 11474 100.000000 1 6213 1 chr1B.!!$F1 6212
1 TraesCS1B01G371400 chr1A 536343552 536349439 5887 True 1887.54 5991 95.127000 387 6213 5 chr1A.!!$R2 5826
2 TraesCS1B01G371400 chr1D 442370145 442376324 6179 False 3006.00 5498 93.209667 3 6213 3 chr1D.!!$F1 6210

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
118 119 0.107703 CTATGGCAGGAAACCGAGCA 60.108 55.000 0.00 0.0 32.62 4.26 F
164 165 0.322997 TAAAAGGGTGCATCGTGGGG 60.323 55.000 0.00 0.0 0.00 4.96 F
375 405 1.075536 GAGGCCCTTTTTCCCTCTTCA 59.924 52.381 0.00 0.0 41.50 3.02 F
1041 1074 1.594293 CTGGTGCACCGTCGTTTCT 60.594 57.895 30.07 0.0 39.43 2.52 F
1747 1780 1.078426 GGGGATCTGGTCACCGTTG 60.078 63.158 0.00 0.0 41.54 4.10 F
3081 3114 1.538950 GAGAAGGGCAGTGAAAGCAAG 59.461 52.381 0.00 0.0 0.00 4.01 F
4019 4141 0.115745 TTTGGGACGGAGGGAGTACT 59.884 55.000 0.00 0.0 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1066 1099 0.033208 AACACCCCGATGGCATCAAT 60.033 50.000 25.88 6.16 37.83 2.57 R
1095 1128 0.250513 GCTTCACCTCGGAGGACAAT 59.749 55.000 30.13 4.96 37.67 2.71 R
1670 1703 2.093235 ACTAGCTTCACTGCTTCATCCC 60.093 50.000 0.00 0.00 43.74 3.85 R
2987 3020 0.107654 GATGGGAAGTGGAGTTCCGG 60.108 60.000 0.00 0.00 46.28 5.14 R
3423 3456 2.009774 GACGTGATGTGGATTTGAGGG 58.990 52.381 0.00 0.00 0.00 4.30 R
4219 4344 1.067821 GGAGATTAGGAGACGGTGCAG 59.932 57.143 0.00 0.00 0.00 4.41 R
5335 5703 0.030369 CCTCCGTCCGGAAATACTCG 59.970 60.000 5.23 3.90 44.66 4.18 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
31 32 0.898320 CGGTGTGAATGAGAGAGGGT 59.102 55.000 0.00 0.00 0.00 4.34
39 40 1.992519 ATGAGAGAGGGTGCCATGGC 61.993 60.000 30.54 30.54 42.35 4.40
62 63 1.003839 GTGAGGTTGGCGTCATCCA 60.004 57.895 18.88 0.00 40.90 3.41
66 67 1.401905 GAGGTTGGCGTCATCCAATTC 59.598 52.381 18.88 4.66 46.64 2.17
74 75 3.561725 GGCGTCATCCAATTCTAAAGGAG 59.438 47.826 0.00 0.00 34.40 3.69
78 79 5.372373 GTCATCCAATTCTAAAGGAGAGGG 58.628 45.833 0.00 0.00 34.93 4.30
79 80 3.933861 TCCAATTCTAAAGGAGAGGGC 57.066 47.619 0.00 0.00 34.93 5.19
80 81 3.464828 TCCAATTCTAAAGGAGAGGGCT 58.535 45.455 0.00 0.00 34.93 5.19
81 82 3.852578 TCCAATTCTAAAGGAGAGGGCTT 59.147 43.478 0.00 0.00 34.93 4.35
82 83 4.080299 TCCAATTCTAAAGGAGAGGGCTTC 60.080 45.833 0.00 0.00 34.93 3.86
83 84 4.080072 CCAATTCTAAAGGAGAGGGCTTCT 60.080 45.833 0.00 0.00 39.43 2.85
95 96 0.729690 GGGCTTCTGCGAGAAATGTC 59.270 55.000 0.00 0.00 40.82 3.06
96 97 1.677217 GGGCTTCTGCGAGAAATGTCT 60.677 52.381 0.00 0.00 40.82 3.41
97 98 2.079925 GGCTTCTGCGAGAAATGTCTT 58.920 47.619 0.00 0.00 40.82 3.01
118 119 0.107703 CTATGGCAGGAAACCGAGCA 60.108 55.000 0.00 0.00 32.62 4.26
119 120 0.107703 TATGGCAGGAAACCGAGCAG 60.108 55.000 0.00 0.00 32.62 4.24
124 125 0.674895 CAGGAAACCGAGCAGGAAGG 60.675 60.000 5.19 0.00 45.00 3.46
125 126 1.377333 GGAAACCGAGCAGGAAGGG 60.377 63.158 5.19 0.00 45.00 3.95
129 130 1.842381 AACCGAGCAGGAAGGGAAGG 61.842 60.000 5.19 0.00 45.00 3.46
139 140 1.900545 GAAGGGAAGGGTCCGACAGG 61.901 65.000 0.00 0.00 46.04 4.00
140 141 3.400054 GGGAAGGGTCCGACAGGG 61.400 72.222 0.00 0.00 46.04 4.45
141 142 2.606826 GGAAGGGTCCGACAGGGT 60.607 66.667 0.00 0.00 38.33 4.34
149 150 2.302733 GGGTCCGACAGGGTAAGTAAAA 59.697 50.000 0.00 0.00 38.33 1.52
150 151 3.593096 GGTCCGACAGGGTAAGTAAAAG 58.407 50.000 0.00 0.00 38.33 2.27
152 153 2.568509 TCCGACAGGGTAAGTAAAAGGG 59.431 50.000 0.00 0.00 38.33 3.95
153 154 2.303890 CCGACAGGGTAAGTAAAAGGGT 59.696 50.000 0.00 0.00 0.00 4.34
154 155 3.332034 CGACAGGGTAAGTAAAAGGGTG 58.668 50.000 0.00 0.00 0.00 4.61
155 156 3.079578 GACAGGGTAAGTAAAAGGGTGC 58.920 50.000 0.00 0.00 0.00 5.01
156 157 2.444010 ACAGGGTAAGTAAAAGGGTGCA 59.556 45.455 0.00 0.00 0.00 4.57
157 158 3.075432 ACAGGGTAAGTAAAAGGGTGCAT 59.925 43.478 0.00 0.00 0.00 3.96
158 159 3.694566 CAGGGTAAGTAAAAGGGTGCATC 59.305 47.826 0.00 0.00 0.00 3.91
160 161 3.340928 GGTAAGTAAAAGGGTGCATCGT 58.659 45.455 0.00 0.00 0.00 3.73
161 162 3.126343 GGTAAGTAAAAGGGTGCATCGTG 59.874 47.826 0.00 0.00 0.00 4.35
164 165 0.322997 TAAAAGGGTGCATCGTGGGG 60.323 55.000 0.00 0.00 0.00 4.96
165 166 2.366153 AAAAGGGTGCATCGTGGGGT 62.366 55.000 0.00 0.00 0.00 4.95
166 167 3.567579 AAGGGTGCATCGTGGGGTG 62.568 63.158 0.00 0.00 0.00 4.61
167 168 4.344865 GGGTGCATCGTGGGGTGT 62.345 66.667 0.00 0.00 0.00 4.16
168 169 2.282180 GGTGCATCGTGGGGTGTT 60.282 61.111 0.00 0.00 0.00 3.32
189 190 3.692257 TTTTTGTTGGGCCCATGTATG 57.308 42.857 29.23 0.00 0.00 2.39
191 192 2.317371 TTGTTGGGCCCATGTATGTT 57.683 45.000 29.23 0.00 0.00 2.71
192 193 1.554836 TGTTGGGCCCATGTATGTTG 58.445 50.000 29.23 0.00 0.00 3.33
193 194 1.076187 TGTTGGGCCCATGTATGTTGA 59.924 47.619 29.23 3.48 0.00 3.18
200 201 4.892934 GGGCCCATGTATGTTGAAGATAAA 59.107 41.667 19.95 0.00 0.00 1.40
230 232 9.520515 ACAGATATTAAGACAACCACATTTTCT 57.479 29.630 0.00 0.00 0.00 2.52
241 243 2.500098 CCACATTTTCTACGAGGGGAGA 59.500 50.000 0.00 0.00 0.00 3.71
243 245 3.447586 CACATTTTCTACGAGGGGAGAGA 59.552 47.826 0.00 0.00 0.00 3.10
244 246 3.702045 ACATTTTCTACGAGGGGAGAGAG 59.298 47.826 0.00 0.00 0.00 3.20
258 275 2.965147 GGAGAGAGGGGATGAGAAAGAG 59.035 54.545 0.00 0.00 0.00 2.85
263 280 4.225573 AGAGGGGATGAGAAAGAGATGAG 58.774 47.826 0.00 0.00 0.00 2.90
267 284 4.379652 GGGATGAGAAAGAGATGAGCTTC 58.620 47.826 0.00 0.00 0.00 3.86
268 285 4.141756 GGGATGAGAAAGAGATGAGCTTCA 60.142 45.833 0.00 0.00 0.00 3.02
270 287 5.294060 GGATGAGAAAGAGATGAGCTTCAAC 59.706 44.000 0.00 0.00 0.00 3.18
296 313 7.395190 TTGAAGATCACCCTAATCATTTGTG 57.605 36.000 0.00 0.00 0.00 3.33
298 315 6.599244 TGAAGATCACCCTAATCATTTGTGTC 59.401 38.462 0.00 0.00 0.00 3.67
317 334 9.531942 TTTGTGTCATTCAATTATATCCATTGC 57.468 29.630 3.58 0.00 32.49 3.56
322 339 5.726980 TTCAATTATATCCATTGCAGCCC 57.273 39.130 0.00 0.00 32.49 5.19
323 340 4.738685 TCAATTATATCCATTGCAGCCCA 58.261 39.130 0.00 0.00 32.49 5.36
331 361 2.042831 ATTGCAGCCCAGCGTTCTC 61.043 57.895 0.00 0.00 37.31 2.87
341 371 3.679083 GCCCAGCGTTCTCATAGTAAACT 60.679 47.826 0.00 0.00 0.00 2.66
344 374 5.163540 CCCAGCGTTCTCATAGTAAACTAGT 60.164 44.000 0.00 0.00 0.00 2.57
360 390 2.617774 ACTAGTAAGATCGTTCGAGGCC 59.382 50.000 0.00 0.00 0.00 5.19
367 397 1.397343 GATCGTTCGAGGCCCTTTTTC 59.603 52.381 0.00 0.00 0.00 2.29
375 405 1.075536 GAGGCCCTTTTTCCCTCTTCA 59.924 52.381 0.00 0.00 41.50 3.02
404 434 3.371034 TCTCACCAGATCCATCCGTTTA 58.629 45.455 0.00 0.00 0.00 2.01
407 437 5.104527 TCTCACCAGATCCATCCGTTTAAAT 60.105 40.000 0.00 0.00 0.00 1.40
437 467 3.750371 TCCAAACATTGATCAGACGGTT 58.250 40.909 0.00 0.00 0.00 4.44
440 470 4.935205 CCAAACATTGATCAGACGGTTAGA 59.065 41.667 0.00 0.00 0.00 2.10
464 494 4.101741 AGAAGCTCCAACAGTTCTTACAGT 59.898 41.667 0.00 0.00 0.00 3.55
477 507 1.620819 CTTACAGTCAGTGGCTGGAGT 59.379 52.381 27.56 10.43 38.22 3.85
493 523 1.686052 GGAGTAGCCCATCACTCTCTG 59.314 57.143 2.13 0.00 40.83 3.35
557 587 3.822192 CGCGTGGAGATCCCGTCA 61.822 66.667 0.00 0.00 37.93 4.35
772 805 2.049433 GCAGCGTATCGGCCGTAT 60.049 61.111 27.15 19.04 0.00 3.06
1041 1074 1.594293 CTGGTGCACCGTCGTTTCT 60.594 57.895 30.07 0.00 39.43 2.52
1095 1128 2.598787 CGGGGTGTTCAAGGGGCTA 61.599 63.158 0.00 0.00 0.00 3.93
1212 1245 4.235079 TGGATTGGTGATTAAGTCTGGG 57.765 45.455 0.00 0.00 0.00 4.45
1260 1293 5.238432 GGTTGGATTTGTCGATATGTATGCA 59.762 40.000 0.00 0.00 0.00 3.96
1317 1350 3.071023 TCAGTGAAATTCCGGTGAAGAGT 59.929 43.478 0.00 0.00 33.05 3.24
1409 1442 4.277515 GCAGGGATATGCATAGAGTTGA 57.722 45.455 12.79 0.00 45.77 3.18
1414 1447 6.713903 CAGGGATATGCATAGAGTTGACATTT 59.286 38.462 12.79 0.00 0.00 2.32
1670 1703 2.223340 GCTATCACTCAAATGGTTGCCG 60.223 50.000 0.00 0.00 34.50 5.69
1747 1780 1.078426 GGGGATCTGGTCACCGTTG 60.078 63.158 0.00 0.00 41.54 4.10
1881 1914 2.699576 TAGGATCGCTGATGCACGCC 62.700 60.000 11.26 0.00 39.64 5.68
2150 2183 3.955650 TGTTAGTGCTTCCCTAGTGAC 57.044 47.619 0.00 0.00 0.00 3.67
2221 2254 4.069304 CCACACACCTTTTCCGAGAAATA 58.931 43.478 0.81 0.00 0.00 1.40
2337 2370 2.744202 GCGTCCTGATCATTTCACTTGT 59.256 45.455 0.00 0.00 0.00 3.16
2361 2394 2.249557 CTGTTCTCAGTGCATGCGCC 62.250 60.000 26.95 13.22 36.97 6.53
2380 2413 2.563179 GCCGATATAGGAGCAAAGGAGA 59.437 50.000 5.98 0.00 0.00 3.71
2479 2512 5.304686 AGACCTTTATGTCAAGTGTGGAA 57.695 39.130 0.00 0.00 37.73 3.53
2575 2608 7.336679 TGTTGGGTTATATTCAGAACAGATGTG 59.663 37.037 0.00 0.00 0.00 3.21
2700 2733 6.258947 GTGCTATTGATTTAGGGAGACAAGTC 59.741 42.308 0.00 0.00 0.00 3.01
2794 2827 4.494091 AGATCTGACGGTTTGATGGAAT 57.506 40.909 0.00 0.00 0.00 3.01
2883 2916 2.795329 TCAGAACAAAGGGATGGAAGC 58.205 47.619 0.00 0.00 0.00 3.86
2968 3001 6.262944 TGCTGATGTGCGGAATATTTCTATTT 59.737 34.615 0.00 0.00 35.36 1.40
3081 3114 1.538950 GAGAAGGGCAGTGAAAGCAAG 59.461 52.381 0.00 0.00 0.00 4.01
3097 3130 8.017946 GTGAAAGCAAGGTTTTTCTAGATACAG 58.982 37.037 0.00 0.00 35.02 2.74
3293 3326 5.644644 CATTCCTCCTTGACAAGTTATTGC 58.355 41.667 14.03 0.00 40.27 3.56
3423 3456 4.913335 ATGAGTTCATGCATCATTCACC 57.087 40.909 0.00 0.00 34.83 4.02
3606 3640 7.228108 TGCATGGAAGAATAGATCAAGAATGTC 59.772 37.037 0.00 0.00 0.00 3.06
3640 3755 6.679843 AGCACGAAATAGTTAGCTATACCTC 58.320 40.000 0.00 0.00 36.95 3.85
3928 4050 6.940298 TGCATATTGCTTTACTAATACTCCCC 59.060 38.462 0.75 0.00 45.31 4.81
3944 4066 3.991972 CCCCCGTCCCAAAATAAGT 57.008 52.632 0.00 0.00 0.00 2.24
3948 4070 2.290705 CCCCGTCCCAAAATAAGTGACT 60.291 50.000 0.00 0.00 0.00 3.41
3950 4072 3.558321 CCCGTCCCAAAATAAGTGACTCA 60.558 47.826 0.00 0.00 0.00 3.41
3951 4073 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3952 4074 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
3954 4076 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
3955 4077 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
3956 4078 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
3957 4079 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
3958 4080 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
3959 4081 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
3960 4082 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
3968 4090 7.822822 AGTGACTCAACTTTGTACTAACTTTGT 59.177 33.333 0.00 0.00 0.00 2.83
3995 4117 9.310716 ACTAAAGTTAGTACAAAGTTGAGTCAC 57.689 33.333 1.81 0.00 41.92 3.67
3996 4118 9.530633 CTAAAGTTAGTACAAAGTTGAGTCACT 57.469 33.333 0.00 0.00 0.00 3.41
3997 4119 8.788325 AAAGTTAGTACAAAGTTGAGTCACTT 57.212 30.769 0.00 0.00 38.74 3.16
3998 4120 9.880157 AAAGTTAGTACAAAGTTGAGTCACTTA 57.120 29.630 0.00 0.00 35.87 2.24
4009 4131 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
4010 4132 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
4011 4133 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
4012 4134 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4013 4135 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
4014 4136 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
4015 4137 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
4016 4138 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
4017 4139 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
4018 4140 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
4019 4141 0.115745 TTTGGGACGGAGGGAGTACT 59.884 55.000 0.00 0.00 0.00 2.73
4020 4142 1.002069 TTGGGACGGAGGGAGTACTA 58.998 55.000 0.00 0.00 0.00 1.82
4021 4143 0.257039 TGGGACGGAGGGAGTACTAC 59.743 60.000 0.00 0.00 0.00 2.73
4022 4144 0.467106 GGGACGGAGGGAGTACTACC 60.467 65.000 17.30 17.30 0.00 3.18
4167 4289 7.180408 AGTTGATTCCTACACTAACACCAGTAT 59.820 37.037 0.00 0.00 0.00 2.12
4219 4344 2.615869 CAACTCCTCAAGCTGCTACTC 58.384 52.381 0.90 0.00 0.00 2.59
4341 4468 8.682128 TGTATCTTATTTCAAAATTTGCCGTC 57.318 30.769 0.00 0.00 0.00 4.79
4346 4473 2.025544 TCAAAATTTGCCGTCGAACG 57.974 45.000 0.00 0.00 42.11 3.95
4403 4530 3.659786 TGTAGGTGAGATGTTTTCCGTG 58.340 45.455 0.00 0.00 0.00 4.94
4425 4552 5.801947 GTGGTAATGAAATGAGAACATGCAC 59.198 40.000 0.00 0.00 36.79 4.57
4548 4914 6.841601 TGCAAATAAATGCTATACTCCCTCT 58.158 36.000 0.67 0.00 46.54 3.69
4844 5212 3.074412 TCCTTGTTGAGAATTCTTCCGC 58.926 45.455 9.87 0.00 0.00 5.54
4938 5306 0.533755 GCTGGTCAATCTGCCGCTAT 60.534 55.000 0.00 0.00 0.00 2.97
5089 5457 5.105473 CCCAATTCAGCAACTTCAATCTGAT 60.105 40.000 0.00 0.00 35.74 2.90
5146 5514 5.705609 TCCTTTTATGCTTTTCCACACTC 57.294 39.130 0.00 0.00 0.00 3.51
5147 5515 4.522789 TCCTTTTATGCTTTTCCACACTCC 59.477 41.667 0.00 0.00 0.00 3.85
5148 5516 4.524328 CCTTTTATGCTTTTCCACACTCCT 59.476 41.667 0.00 0.00 0.00 3.69
5149 5517 5.710099 CCTTTTATGCTTTTCCACACTCCTA 59.290 40.000 0.00 0.00 0.00 2.94
5150 5518 6.349363 CCTTTTATGCTTTTCCACACTCCTAC 60.349 42.308 0.00 0.00 0.00 3.18
5151 5519 3.788227 ATGCTTTTCCACACTCCTACA 57.212 42.857 0.00 0.00 0.00 2.74
5202 5570 7.840342 TCTCTCTTATTTGCAGAAGTTCATC 57.160 36.000 5.50 0.00 0.00 2.92
5222 5590 5.521372 TCATCTTCTTGTTGATGTATCAGCG 59.479 40.000 4.61 0.00 40.38 5.18
5257 5625 9.647797 TGGTTTATCTTGCTATATAATGTACCG 57.352 33.333 0.00 0.00 0.00 4.02
5258 5626 9.095065 GGTTTATCTTGCTATATAATGTACCGG 57.905 37.037 0.00 0.00 0.00 5.28
5259 5627 9.865321 GTTTATCTTGCTATATAATGTACCGGA 57.135 33.333 9.46 0.00 0.00 5.14
5264 5632 9.865321 TCTTGCTATATAATGTACCGGAAATAC 57.135 33.333 9.46 0.00 0.00 1.89
5265 5633 9.871238 CTTGCTATATAATGTACCGGAAATACT 57.129 33.333 9.46 0.00 0.00 2.12
5267 5635 9.647797 TGCTATATAATGTACCGGAAATACTTG 57.352 33.333 9.46 0.00 0.00 3.16
5268 5636 9.649167 GCTATATAATGTACCGGAAATACTTGT 57.351 33.333 9.46 0.00 0.00 3.16
5270 5638 8.752766 ATATAATGTACCGGAAATACTTGTCG 57.247 34.615 9.46 0.00 0.00 4.35
5271 5639 3.235157 TGTACCGGAAATACTTGTCGG 57.765 47.619 9.46 0.00 45.42 4.79
5272 5640 2.824936 TGTACCGGAAATACTTGTCGGA 59.175 45.455 9.46 0.00 42.94 4.55
5273 5641 2.667473 ACCGGAAATACTTGTCGGAG 57.333 50.000 9.46 0.00 42.94 4.63
5274 5642 1.206371 ACCGGAAATACTTGTCGGAGG 59.794 52.381 9.46 0.00 42.94 4.30
5275 5643 1.479323 CCGGAAATACTTGTCGGAGGA 59.521 52.381 0.00 0.00 42.94 3.71
5276 5644 2.093869 CCGGAAATACTTGTCGGAGGAA 60.094 50.000 0.00 0.00 42.94 3.36
5277 5645 3.431766 CCGGAAATACTTGTCGGAGGAAT 60.432 47.826 0.00 0.00 42.94 3.01
5278 5646 3.555956 CGGAAATACTTGTCGGAGGAATG 59.444 47.826 0.00 0.00 0.00 2.67
5279 5647 3.877508 GGAAATACTTGTCGGAGGAATGG 59.122 47.826 0.00 0.00 0.00 3.16
5280 5648 4.383770 GGAAATACTTGTCGGAGGAATGGA 60.384 45.833 0.00 0.00 0.00 3.41
5281 5649 5.368989 GAAATACTTGTCGGAGGAATGGAT 58.631 41.667 0.00 0.00 0.00 3.41
5282 5650 2.698855 ACTTGTCGGAGGAATGGATG 57.301 50.000 0.00 0.00 0.00 3.51
5283 5651 1.909302 ACTTGTCGGAGGAATGGATGT 59.091 47.619 0.00 0.00 0.00 3.06
5284 5652 3.104512 ACTTGTCGGAGGAATGGATGTA 58.895 45.455 0.00 0.00 0.00 2.29
5285 5653 3.711704 ACTTGTCGGAGGAATGGATGTAT 59.288 43.478 0.00 0.00 0.00 2.29
5286 5654 4.202264 ACTTGTCGGAGGAATGGATGTATC 60.202 45.833 0.00 0.00 0.00 2.24
5287 5655 3.576861 TGTCGGAGGAATGGATGTATCT 58.423 45.455 0.00 0.00 0.00 1.98
5288 5656 4.736473 TGTCGGAGGAATGGATGTATCTA 58.264 43.478 0.00 0.00 0.00 1.98
5289 5657 4.767409 TGTCGGAGGAATGGATGTATCTAG 59.233 45.833 0.00 0.00 0.00 2.43
5290 5658 5.010933 GTCGGAGGAATGGATGTATCTAGA 58.989 45.833 0.00 0.00 0.00 2.43
5291 5659 5.010933 TCGGAGGAATGGATGTATCTAGAC 58.989 45.833 0.00 0.00 0.00 2.59
5292 5660 4.142578 CGGAGGAATGGATGTATCTAGACG 60.143 50.000 0.00 0.00 0.00 4.18
5293 5661 4.767928 GGAGGAATGGATGTATCTAGACGT 59.232 45.833 0.00 0.00 0.00 4.34
5294 5662 5.944599 GGAGGAATGGATGTATCTAGACGTA 59.055 44.000 0.00 0.00 0.00 3.57
5295 5663 6.603997 GGAGGAATGGATGTATCTAGACGTAT 59.396 42.308 0.00 0.00 0.00 3.06
5296 5664 7.122948 GGAGGAATGGATGTATCTAGACGTATT 59.877 40.741 0.00 0.00 0.00 1.89
5297 5665 8.423906 AGGAATGGATGTATCTAGACGTATTT 57.576 34.615 0.00 0.00 0.00 1.40
5298 5666 8.871125 AGGAATGGATGTATCTAGACGTATTTT 58.129 33.333 0.00 0.00 0.00 1.82
5332 5700 9.455847 GATACATCTGTTTTTATGCATTTCTCC 57.544 33.333 3.54 0.00 0.00 3.71
5333 5701 6.324819 ACATCTGTTTTTATGCATTTCTCCG 58.675 36.000 3.54 0.00 0.00 4.63
5334 5702 6.150976 ACATCTGTTTTTATGCATTTCTCCGA 59.849 34.615 3.54 0.00 0.00 4.55
5335 5703 5.938322 TCTGTTTTTATGCATTTCTCCGAC 58.062 37.500 3.54 0.00 0.00 4.79
5336 5704 4.717991 TGTTTTTATGCATTTCTCCGACG 58.282 39.130 3.54 0.00 0.00 5.12
5337 5705 4.452795 TGTTTTTATGCATTTCTCCGACGA 59.547 37.500 3.54 0.00 0.00 4.20
5338 5706 4.857871 TTTTATGCATTTCTCCGACGAG 57.142 40.909 3.54 0.00 37.48 4.18
5339 5707 3.520290 TTATGCATTTCTCCGACGAGT 57.480 42.857 3.54 0.00 37.40 4.18
5340 5708 4.642445 TTATGCATTTCTCCGACGAGTA 57.358 40.909 3.54 0.00 37.40 2.59
5341 5709 3.735237 ATGCATTTCTCCGACGAGTAT 57.265 42.857 0.00 0.00 37.40 2.12
5342 5710 3.520290 TGCATTTCTCCGACGAGTATT 57.480 42.857 0.00 0.00 37.40 1.89
5343 5711 3.857052 TGCATTTCTCCGACGAGTATTT 58.143 40.909 0.00 0.00 37.40 1.40
5344 5712 3.863424 TGCATTTCTCCGACGAGTATTTC 59.137 43.478 0.00 0.00 37.40 2.17
5345 5713 3.245519 GCATTTCTCCGACGAGTATTTCC 59.754 47.826 0.00 0.00 37.40 3.13
5346 5714 2.838386 TTCTCCGACGAGTATTTCCG 57.162 50.000 0.00 0.00 37.40 4.30
5347 5715 1.019673 TCTCCGACGAGTATTTCCGG 58.980 55.000 0.00 0.00 41.36 5.14
5348 5716 1.019673 CTCCGACGAGTATTTCCGGA 58.980 55.000 0.00 0.00 45.74 5.14
5349 5717 0.734889 TCCGACGAGTATTTCCGGAC 59.265 55.000 1.83 0.00 43.47 4.79
5350 5718 0.590732 CCGACGAGTATTTCCGGACG 60.591 60.000 1.83 5.89 42.49 4.79
5351 5719 0.590732 CGACGAGTATTTCCGGACGG 60.591 60.000 1.83 3.96 0.00 4.79
5352 5720 0.734889 GACGAGTATTTCCGGACGGA 59.265 55.000 1.83 9.76 43.52 4.69
5353 5721 0.737219 ACGAGTATTTCCGGACGGAG 59.263 55.000 13.64 3.15 46.06 4.63
5354 5722 0.030369 CGAGTATTTCCGGACGGAGG 59.970 60.000 13.64 0.00 46.06 4.30
5355 5723 0.388294 GAGTATTTCCGGACGGAGGG 59.612 60.000 13.64 0.00 46.06 4.30
5356 5724 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
5357 5725 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
5358 5726 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
5359 5727 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
5508 5878 6.889301 AATTCAATGCTCATATGGTACTGG 57.111 37.500 2.13 0.00 0.00 4.00
5512 5882 4.891992 ATGCTCATATGGTACTGGGTAC 57.108 45.455 2.13 0.00 38.19 3.34
5532 5902 3.665190 ACTTGAATTCCTCGTCCAACTC 58.335 45.455 2.27 0.00 0.00 3.01
5854 6249 3.245990 GCAAATTGCAGAAGGTTGTCAAC 59.754 43.478 13.73 7.20 44.26 3.18
5964 6359 4.168760 GTCATGCCTTTATGAACAACAGC 58.831 43.478 0.00 0.00 38.69 4.40
6086 6481 0.819582 AAAGCCGGCCAATCAATCTG 59.180 50.000 26.15 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.772568 TCACACCGCACTTTTTCATG 57.227 45.000 0.00 0.00 0.00 3.07
1 2 3.317711 TCATTCACACCGCACTTTTTCAT 59.682 39.130 0.00 0.00 0.00 2.57
6 7 2.146342 CTCTCATTCACACCGCACTTT 58.854 47.619 0.00 0.00 0.00 2.66
11 12 0.460987 CCCTCTCTCATTCACACCGC 60.461 60.000 0.00 0.00 0.00 5.68
31 32 2.046023 CTCACCTTCGCCATGGCA 60.046 61.111 34.93 19.88 42.06 4.92
39 40 2.027625 GACGCCAACCTCACCTTCG 61.028 63.158 0.00 0.00 0.00 3.79
62 63 4.627498 GCAGAAGCCCTCTCCTTTAGAATT 60.627 45.833 0.00 0.00 31.21 2.17
66 67 1.472376 CGCAGAAGCCCTCTCCTTTAG 60.472 57.143 0.00 0.00 37.52 1.85
74 75 1.012841 CATTTCTCGCAGAAGCCCTC 58.987 55.000 0.11 0.00 35.37 4.30
78 79 2.727298 GCAAGACATTTCTCGCAGAAGC 60.727 50.000 0.00 0.00 35.37 3.86
79 80 2.740981 AGCAAGACATTTCTCGCAGAAG 59.259 45.455 0.00 0.00 33.81 2.85
80 81 2.771089 AGCAAGACATTTCTCGCAGAA 58.229 42.857 0.00 0.00 33.81 3.02
81 82 2.462456 AGCAAGACATTTCTCGCAGA 57.538 45.000 0.00 0.00 33.81 4.26
82 83 3.002042 CCATAGCAAGACATTTCTCGCAG 59.998 47.826 0.00 0.00 33.81 5.18
83 84 2.938451 CCATAGCAAGACATTTCTCGCA 59.062 45.455 0.00 0.00 33.81 5.10
106 107 1.679898 CCTTCCTGCTCGGTTTCCT 59.320 57.895 0.00 0.00 0.00 3.36
118 119 1.612739 GTCGGACCCTTCCCTTCCT 60.613 63.158 0.00 0.00 38.99 3.36
119 120 1.900545 CTGTCGGACCCTTCCCTTCC 61.901 65.000 5.55 0.00 38.99 3.46
124 125 0.906282 TTACCCTGTCGGACCCTTCC 60.906 60.000 5.55 0.00 38.77 3.46
125 126 0.535797 CTTACCCTGTCGGACCCTTC 59.464 60.000 5.55 0.00 34.64 3.46
129 130 3.593096 CTTTTACTTACCCTGTCGGACC 58.407 50.000 5.55 0.00 34.64 4.46
139 140 3.126343 CACGATGCACCCTTTTACTTACC 59.874 47.826 0.00 0.00 0.00 2.85
140 141 3.126343 CCACGATGCACCCTTTTACTTAC 59.874 47.826 0.00 0.00 0.00 2.34
141 142 3.340034 CCACGATGCACCCTTTTACTTA 58.660 45.455 0.00 0.00 0.00 2.24
149 150 4.033776 CACCCCACGATGCACCCT 62.034 66.667 0.00 0.00 0.00 4.34
150 151 3.860930 AACACCCCACGATGCACCC 62.861 63.158 0.00 0.00 0.00 4.61
152 153 0.387565 AAAAACACCCCACGATGCAC 59.612 50.000 0.00 0.00 0.00 4.57
153 154 2.814023 AAAAACACCCCACGATGCA 58.186 47.368 0.00 0.00 0.00 3.96
172 173 1.898472 CAACATACATGGGCCCAACAA 59.102 47.619 32.58 17.57 0.00 2.83
174 175 1.846007 TCAACATACATGGGCCCAAC 58.154 50.000 32.58 0.00 0.00 3.77
211 212 6.425721 CCTCGTAGAAAATGTGGTTGTCTTAA 59.574 38.462 0.00 0.00 35.89 1.85
213 214 4.755123 CCTCGTAGAAAATGTGGTTGTCTT 59.245 41.667 0.00 0.00 35.89 3.01
214 215 4.315803 CCTCGTAGAAAATGTGGTTGTCT 58.684 43.478 0.00 0.00 38.05 3.41
225 227 2.623502 CCCTCTCTCCCCTCGTAGAAAA 60.624 54.545 0.00 0.00 34.09 2.29
230 232 0.701659 ATCCCCTCTCTCCCCTCGTA 60.702 60.000 0.00 0.00 0.00 3.43
231 233 2.015726 ATCCCCTCTCTCCCCTCGT 61.016 63.158 0.00 0.00 0.00 4.18
232 234 1.532794 CATCCCCTCTCTCCCCTCG 60.533 68.421 0.00 0.00 0.00 4.63
241 243 4.225573 CTCATCTCTTTCTCATCCCCTCT 58.774 47.826 0.00 0.00 0.00 3.69
243 245 2.705127 GCTCATCTCTTTCTCATCCCCT 59.295 50.000 0.00 0.00 0.00 4.79
244 246 2.705127 AGCTCATCTCTTTCTCATCCCC 59.295 50.000 0.00 0.00 0.00 4.81
267 284 7.636150 ATGATTAGGGTGATCTTCAAAGTTG 57.364 36.000 0.00 0.00 0.00 3.16
268 285 8.526147 CAAATGATTAGGGTGATCTTCAAAGTT 58.474 33.333 0.00 0.00 0.00 2.66
270 287 7.972277 CACAAATGATTAGGGTGATCTTCAAAG 59.028 37.037 0.00 0.00 0.00 2.77
296 313 6.810182 GGCTGCAATGGATATAATTGAATGAC 59.190 38.462 12.62 3.04 37.22 3.06
298 315 6.103997 GGGCTGCAATGGATATAATTGAATG 58.896 40.000 12.62 5.01 37.22 2.67
313 330 2.034687 AGAACGCTGGGCTGCAAT 59.965 55.556 0.50 0.00 0.00 3.56
314 331 2.669569 GAGAACGCTGGGCTGCAA 60.670 61.111 0.50 0.00 0.00 4.08
316 333 1.153369 TATGAGAACGCTGGGCTGC 60.153 57.895 0.00 0.00 0.00 5.25
317 334 0.176680 ACTATGAGAACGCTGGGCTG 59.823 55.000 0.00 0.00 0.00 4.85
322 339 8.396390 TCTTACTAGTTTACTATGAGAACGCTG 58.604 37.037 0.00 0.00 0.00 5.18
323 340 8.503458 TCTTACTAGTTTACTATGAGAACGCT 57.497 34.615 0.00 0.00 0.00 5.07
331 361 9.583530 CTCGAACGATCTTACTAGTTTACTATG 57.416 37.037 0.00 0.00 0.00 2.23
341 371 1.952296 GGGCCTCGAACGATCTTACTA 59.048 52.381 0.84 0.00 0.00 1.82
344 374 1.481871 AAGGGCCTCGAACGATCTTA 58.518 50.000 6.46 0.00 0.00 2.10
394 424 1.681264 GGCCTGGATTTAAACGGATGG 59.319 52.381 0.00 0.00 0.00 3.51
404 434 0.486879 TGTTTGGAGGGCCTGGATTT 59.513 50.000 12.95 0.00 34.31 2.17
407 437 0.251742 CAATGTTTGGAGGGCCTGGA 60.252 55.000 12.95 0.00 34.31 3.86
437 467 5.552870 AAGAACTGTTGGAGCTTCTTCTA 57.447 39.130 0.00 0.00 31.68 2.10
440 470 5.036117 TGTAAGAACTGTTGGAGCTTCTT 57.964 39.130 0.00 0.00 36.65 2.52
477 507 1.007118 TGGTCAGAGAGTGATGGGCTA 59.993 52.381 0.00 0.00 37.56 3.93
493 523 2.190578 CGAGGGCCCAGATTGGTC 59.809 66.667 27.56 10.00 35.17 4.02
507 537 0.967380 AAAATGGGCTTGGAGGCGAG 60.967 55.000 0.00 0.00 42.43 5.03
772 805 2.104359 ATGGGTCCCACAATGGCCAA 62.104 55.000 14.57 0.00 35.80 4.52
1066 1099 0.033208 AACACCCCGATGGCATCAAT 60.033 50.000 25.88 6.16 37.83 2.57
1095 1128 0.250513 GCTTCACCTCGGAGGACAAT 59.749 55.000 30.13 4.96 37.67 2.71
1203 1236 2.128535 TCAACACCCAACCCAGACTTA 58.871 47.619 0.00 0.00 0.00 2.24
1212 1245 3.005367 CCACAAACCTATCAACACCCAAC 59.995 47.826 0.00 0.00 0.00 3.77
1260 1293 2.354003 GCAGCCTACATTGCCACATTTT 60.354 45.455 0.00 0.00 34.28 1.82
1409 1442 4.151121 TGTCACCACATCCATTGAAATGT 58.849 39.130 2.55 0.43 36.56 2.71
1414 1447 4.011698 CTCAATGTCACCACATCCATTGA 58.988 43.478 11.93 11.93 46.46 2.57
1670 1703 2.093235 ACTAGCTTCACTGCTTCATCCC 60.093 50.000 0.00 0.00 43.74 3.85
1747 1780 8.948631 TCCTCTTTGATATGACAAACATCTAC 57.051 34.615 0.00 0.00 40.07 2.59
1881 1914 6.512415 ACTCTGAAGTTTTGAAGATTGCTTCG 60.512 38.462 0.00 0.00 42.38 3.79
2221 2254 7.096023 CGAGAGCATCGCATTAGTTAAAACTAT 60.096 37.037 3.52 0.00 45.98 2.12
2361 2394 4.321601 CCAGTCTCCTTTGCTCCTATATCG 60.322 50.000 0.00 0.00 0.00 2.92
2700 2733 8.641498 AACCCATCTTTATAATAGAAGCATGG 57.359 34.615 0.00 0.00 34.24 3.66
2794 2827 8.834465 CAAAATTTCTTGAGAGTCTCTTCTTGA 58.166 33.333 20.64 8.83 0.00 3.02
2883 2916 2.095059 CCCAATTTCTTCAAGGTCGCTG 60.095 50.000 0.00 0.00 0.00 5.18
2987 3020 0.107654 GATGGGAAGTGGAGTTCCGG 60.108 60.000 0.00 0.00 46.28 5.14
3081 3114 8.097662 CCCTGATATCCTGTATCTAGAAAAACC 58.902 40.741 0.00 0.00 0.00 3.27
3097 3130 3.181450 CCACCTCTGTTTCCCTGATATCC 60.181 52.174 0.00 0.00 0.00 2.59
3293 3326 4.322804 CCAGTAAGTAGTTTTCGTACTGCG 59.677 45.833 11.39 4.45 42.22 5.18
3423 3456 2.009774 GACGTGATGTGGATTTGAGGG 58.990 52.381 0.00 0.00 0.00 4.30
3606 3640 3.924686 ACTATTTCGTGCTAACCTGTTCG 59.075 43.478 0.00 0.00 0.00 3.95
3928 4050 3.007635 GAGTCACTTATTTTGGGACGGG 58.992 50.000 0.00 0.00 33.84 5.28
3942 4064 7.822822 ACAAAGTTAGTACAAAGTTGAGTCACT 59.177 33.333 0.00 0.00 0.00 3.41
3943 4065 7.971455 ACAAAGTTAGTACAAAGTTGAGTCAC 58.029 34.615 0.00 0.00 0.00 3.67
3944 4066 9.090692 GTACAAAGTTAGTACAAAGTTGAGTCA 57.909 33.333 0.00 0.00 41.08 3.41
3972 4094 8.788325 AAGTGACTCAACTTTGTACTAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
3979 4101 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
3980 4102 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
3981 4103 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
3982 4104 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
3983 4105 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
3984 4106 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
3986 4108 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
3987 4109 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3988 4110 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
3989 4111 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
3990 4112 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
3991 4113 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
3992 4114 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
3993 4115 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3994 4116 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3995 4117 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3996 4118 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3997 4119 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3998 4120 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
4021 4143 5.071370 AGTAATGATGTACTACCTCGGAGG 58.929 45.833 22.40 22.40 42.49 4.30
4022 4144 6.439599 CAAGTAATGATGTACTACCTCGGAG 58.560 44.000 0.00 0.00 33.05 4.63
4023 4145 5.221185 GCAAGTAATGATGTACTACCTCGGA 60.221 44.000 0.00 0.00 33.05 4.55
4024 4146 4.982916 GCAAGTAATGATGTACTACCTCGG 59.017 45.833 0.00 0.00 33.05 4.63
4025 4147 5.833082 AGCAAGTAATGATGTACTACCTCG 58.167 41.667 0.00 0.00 33.05 4.63
4167 4289 2.703536 TCCAAGTTGCAGTCCTCTAACA 59.296 45.455 0.00 0.00 0.00 2.41
4219 4344 1.067821 GGAGATTAGGAGACGGTGCAG 59.932 57.143 0.00 0.00 0.00 4.41
4341 4468 4.718858 TGAACCACATTTCTAACGTTCG 57.281 40.909 2.82 0.00 33.87 3.95
4403 4530 5.030295 CGTGCATGTTCTCATTTCATTACC 58.970 41.667 0.00 0.00 31.15 2.85
4425 4552 8.050750 GTCAGTCAGAAATAACAATATCGAACG 58.949 37.037 0.00 0.00 0.00 3.95
4548 4914 8.918202 ATCTATATGCGAAATAAAAAGGACCA 57.082 30.769 0.00 0.00 0.00 4.02
4620 4988 9.950680 GATTTCGTATTGTGAATGTGGATATTT 57.049 29.630 0.00 0.00 0.00 1.40
4844 5212 7.929785 CCAGAAGATTTCATTTAATGGAATGGG 59.070 37.037 15.45 6.14 38.58 4.00
5003 5371 2.225791 CTGGATTCCGCCACGTCTGA 62.226 60.000 0.00 0.00 33.52 3.27
5089 5457 7.667557 AGCACACTGAACTTACAATCTTACTA 58.332 34.615 0.00 0.00 0.00 1.82
5146 5514 4.406003 AGGAAATAGCACTGTAGGTGTAGG 59.594 45.833 0.00 0.00 46.86 3.18
5147 5515 5.599999 AGGAAATAGCACTGTAGGTGTAG 57.400 43.478 0.00 0.00 46.86 2.74
5148 5516 5.730550 CAAGGAAATAGCACTGTAGGTGTA 58.269 41.667 0.00 0.00 46.86 2.90
5149 5517 4.579869 CAAGGAAATAGCACTGTAGGTGT 58.420 43.478 0.00 0.00 46.86 4.16
5151 5519 3.264450 AGCAAGGAAATAGCACTGTAGGT 59.736 43.478 0.00 0.00 0.00 3.08
5202 5570 5.319139 CAACGCTGATACATCAACAAGAAG 58.681 41.667 0.00 0.00 36.18 2.85
5209 5577 4.270808 CACTATGCAACGCTGATACATCAA 59.729 41.667 0.00 0.00 36.18 2.57
5222 5590 5.567138 AGCAAGATAAACCACTATGCAAC 57.433 39.130 0.00 0.00 34.89 4.17
5255 5623 1.479323 TCCTCCGACAAGTATTTCCGG 59.521 52.381 0.00 0.00 41.36 5.14
5256 5624 2.953466 TCCTCCGACAAGTATTTCCG 57.047 50.000 0.00 0.00 0.00 4.30
5257 5625 3.877508 CCATTCCTCCGACAAGTATTTCC 59.122 47.826 0.00 0.00 0.00 3.13
5258 5626 4.766375 TCCATTCCTCCGACAAGTATTTC 58.234 43.478 0.00 0.00 0.00 2.17
5259 5627 4.837093 TCCATTCCTCCGACAAGTATTT 57.163 40.909 0.00 0.00 0.00 1.40
5260 5628 4.164221 ACATCCATTCCTCCGACAAGTATT 59.836 41.667 0.00 0.00 0.00 1.89
5261 5629 3.711704 ACATCCATTCCTCCGACAAGTAT 59.288 43.478 0.00 0.00 0.00 2.12
5262 5630 3.104512 ACATCCATTCCTCCGACAAGTA 58.895 45.455 0.00 0.00 0.00 2.24
5263 5631 1.909302 ACATCCATTCCTCCGACAAGT 59.091 47.619 0.00 0.00 0.00 3.16
5264 5632 2.698855 ACATCCATTCCTCCGACAAG 57.301 50.000 0.00 0.00 0.00 3.16
5265 5633 3.967326 AGATACATCCATTCCTCCGACAA 59.033 43.478 0.00 0.00 0.00 3.18
5266 5634 3.576861 AGATACATCCATTCCTCCGACA 58.423 45.455 0.00 0.00 0.00 4.35
5267 5635 5.010933 TCTAGATACATCCATTCCTCCGAC 58.989 45.833 0.00 0.00 0.00 4.79
5268 5636 5.010933 GTCTAGATACATCCATTCCTCCGA 58.989 45.833 0.00 0.00 0.00 4.55
5269 5637 4.142578 CGTCTAGATACATCCATTCCTCCG 60.143 50.000 0.00 0.00 0.00 4.63
5270 5638 4.767928 ACGTCTAGATACATCCATTCCTCC 59.232 45.833 0.00 0.00 0.00 4.30
5271 5639 5.968528 ACGTCTAGATACATCCATTCCTC 57.031 43.478 0.00 0.00 0.00 3.71
5272 5640 8.423906 AAATACGTCTAGATACATCCATTCCT 57.576 34.615 0.00 0.00 0.00 3.36
5306 5674 9.455847 GGAGAAATGCATAAAAACAGATGTATC 57.544 33.333 0.00 0.00 29.41 2.24
5307 5675 8.131100 CGGAGAAATGCATAAAAACAGATGTAT 58.869 33.333 0.00 0.00 30.71 2.29
5308 5676 7.335673 TCGGAGAAATGCATAAAAACAGATGTA 59.664 33.333 0.00 0.00 0.00 2.29
5309 5677 6.150976 TCGGAGAAATGCATAAAAACAGATGT 59.849 34.615 0.00 0.00 0.00 3.06
5310 5678 6.470235 GTCGGAGAAATGCATAAAAACAGATG 59.530 38.462 0.00 0.00 39.69 2.90
5311 5679 6.555315 GTCGGAGAAATGCATAAAAACAGAT 58.445 36.000 0.00 0.00 39.69 2.90
5312 5680 5.390461 CGTCGGAGAAATGCATAAAAACAGA 60.390 40.000 0.00 0.00 39.69 3.41
5313 5681 4.788100 CGTCGGAGAAATGCATAAAAACAG 59.212 41.667 0.00 0.00 39.69 3.16
5314 5682 4.452795 TCGTCGGAGAAATGCATAAAAACA 59.547 37.500 0.00 0.00 39.69 2.83
5315 5683 4.965062 TCGTCGGAGAAATGCATAAAAAC 58.035 39.130 0.00 0.00 39.69 2.43
5316 5684 4.693566 ACTCGTCGGAGAAATGCATAAAAA 59.306 37.500 0.00 0.00 43.27 1.94
5317 5685 4.250464 ACTCGTCGGAGAAATGCATAAAA 58.750 39.130 0.00 0.00 43.27 1.52
5318 5686 3.857052 ACTCGTCGGAGAAATGCATAAA 58.143 40.909 0.00 0.00 43.27 1.40
5319 5687 3.520290 ACTCGTCGGAGAAATGCATAA 57.480 42.857 0.00 0.00 43.27 1.90
5320 5688 4.848562 ATACTCGTCGGAGAAATGCATA 57.151 40.909 0.00 0.00 43.27 3.14
5321 5689 3.735237 ATACTCGTCGGAGAAATGCAT 57.265 42.857 0.00 0.00 43.27 3.96
5322 5690 3.520290 AATACTCGTCGGAGAAATGCA 57.480 42.857 0.00 0.00 43.27 3.96
5323 5691 3.245519 GGAAATACTCGTCGGAGAAATGC 59.754 47.826 0.00 0.00 43.27 3.56
5324 5692 3.486108 CGGAAATACTCGTCGGAGAAATG 59.514 47.826 0.00 0.00 43.27 2.32
5325 5693 3.490419 CCGGAAATACTCGTCGGAGAAAT 60.490 47.826 0.00 0.00 43.27 2.17
5326 5694 2.159338 CCGGAAATACTCGTCGGAGAAA 60.159 50.000 0.00 0.00 43.27 2.52
5327 5695 1.402968 CCGGAAATACTCGTCGGAGAA 59.597 52.381 0.00 0.00 43.27 2.87
5328 5696 1.019673 CCGGAAATACTCGTCGGAGA 58.980 55.000 0.00 0.00 43.27 3.71
5329 5697 1.019673 TCCGGAAATACTCGTCGGAG 58.980 55.000 0.00 0.00 43.84 4.63
5330 5698 0.734889 GTCCGGAAATACTCGTCGGA 59.265 55.000 5.23 0.00 46.06 4.55
5331 5699 0.590732 CGTCCGGAAATACTCGTCGG 60.591 60.000 5.23 0.00 41.80 4.79
5332 5700 0.590732 CCGTCCGGAAATACTCGTCG 60.591 60.000 5.23 1.25 37.50 5.12
5333 5701 0.734889 TCCGTCCGGAAATACTCGTC 59.265 55.000 5.23 0.00 42.05 4.20
5334 5702 0.737219 CTCCGTCCGGAAATACTCGT 59.263 55.000 5.23 0.00 44.66 4.18
5335 5703 0.030369 CCTCCGTCCGGAAATACTCG 59.970 60.000 5.23 3.90 44.66 4.18
5336 5704 0.388294 CCCTCCGTCCGGAAATACTC 59.612 60.000 5.23 0.00 44.66 2.59
5337 5705 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
5338 5706 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
5339 5707 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
5340 5708 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
5341 5709 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
5342 5710 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
5343 5711 0.982852 TACTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
5344 5712 0.534652 CTACTACTCCCTCCGTCCGG 60.535 65.000 0.00 0.00 0.00 5.14
5345 5713 1.165284 GCTACTACTCCCTCCGTCCG 61.165 65.000 0.00 0.00 0.00 4.79
5346 5714 0.822944 GGCTACTACTCCCTCCGTCC 60.823 65.000 0.00 0.00 0.00 4.79
5347 5715 0.183252 AGGCTACTACTCCCTCCGTC 59.817 60.000 0.00 0.00 0.00 4.79
5348 5716 0.630134 AAGGCTACTACTCCCTCCGT 59.370 55.000 0.00 0.00 0.00 4.69
5349 5717 1.033574 CAAGGCTACTACTCCCTCCG 58.966 60.000 0.00 0.00 0.00 4.63
5350 5718 1.415200 CCAAGGCTACTACTCCCTCC 58.585 60.000 0.00 0.00 0.00 4.30
5351 5719 1.415200 CCCAAGGCTACTACTCCCTC 58.585 60.000 0.00 0.00 0.00 4.30
5352 5720 0.031010 CCCCAAGGCTACTACTCCCT 60.031 60.000 0.00 0.00 0.00 4.20
5353 5721 2.529312 CCCCAAGGCTACTACTCCC 58.471 63.158 0.00 0.00 0.00 4.30
5475 5845 9.923143 CATATGAGCATTGAATTAATGGATGTT 57.077 29.630 0.00 0.00 45.09 2.71
5508 5878 3.604875 TGGACGAGGAATTCAAGTACC 57.395 47.619 7.93 5.64 0.00 3.34
5512 5882 3.003480 GGAGTTGGACGAGGAATTCAAG 58.997 50.000 7.93 0.21 0.00 3.02
5532 5902 0.745468 GGTCTACGAACTAGGGCTGG 59.255 60.000 0.00 0.00 0.00 4.85
5854 6249 4.332543 TGCAGTTTACAGTTGTGACTCTTG 59.667 41.667 0.00 0.00 32.54 3.02
5917 6312 7.068962 ACAAGAGTAAGAGCTATAGGAACCTTC 59.931 40.741 1.04 0.00 0.00 3.46
5975 6370 5.981315 AGTGTTTGATTTGAGCTTGACATTG 59.019 36.000 0.00 0.00 0.00 2.82
6065 6460 0.103026 GATTGATTGGCCGGCTTTCC 59.897 55.000 28.56 10.32 0.00 3.13


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

AutoCloner maintained by Alex Coulton.