Multiple sequence alignment - TraesCS4D01G120300

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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 TraesCS4D01G120300 chr4D 100.000 3083 0 0 1 3083 101435328 101438410 0.000000e+00 5694
1 TraesCS4D01G120300 chr4A 93.202 2236 123 12 2 2217 473947627 473945401 0.000000e+00 3260
2 TraesCS4D01G120300 chr4A 88.034 585 41 12 2327 2908 473945399 473944841 0.000000e+00 665
3 TraesCS4D01G120300 chr4A 95.495 111 5 0 2212 2322 717048653 717048763 8.780000e-41 178
4 TraesCS4D01G120300 chr4B 96.284 1507 52 4 710 2215 145370931 145372434 0.000000e+00 2470
5 TraesCS4D01G120300 chr4B 88.271 665 52 8 1 665 145370288 145370926 0.000000e+00 773
6 TraesCS4D01G120300 chr4B 87.829 608 47 13 2327 2908 145372438 145373044 0.000000e+00 688
7 TraesCS4D01G120300 chr6A 78.505 535 106 7 1565 2096 502366779 502367307 2.940000e-90 342
8 TraesCS4D01G120300 chr6D 78.916 498 99 6 1565 2059 361380293 361380787 1.770000e-87 333
9 TraesCS4D01G120300 chr6D 97.753 178 3 1 2906 3082 470655220 470655397 3.860000e-79 305
10 TraesCS4D01G120300 chr6B 78.715 498 100 5 1565 2059 542585795 542586289 8.240000e-86 327
11 TraesCS4D01G120300 chr2D 97.753 178 3 1 2906 3082 373148069 373147892 3.860000e-79 305
12 TraesCS4D01G120300 chr2D 97.740 177 3 1 2906 3081 503882024 503882200 1.390000e-78 303
13 TraesCS4D01G120300 chr2D 97.207 179 4 1 2906 3083 322842696 322842874 5.000000e-78 302
14 TraesCS4D01G120300 chr2D 96.667 180 5 1 2903 3081 458715800 458715979 6.460000e-77 298
15 TraesCS4D01G120300 chr2D 76.190 567 95 25 97 628 352398330 352397769 2.360000e-66 263
16 TraesCS4D01G120300 chr5D 97.740 177 3 1 2906 3081 381906687 381906863 1.390000e-78 303
17 TraesCS4D01G120300 chr5D 95.699 186 6 2 2899 3082 75415147 75415332 6.460000e-77 298
18 TraesCS4D01G120300 chr5D 94.167 120 7 0 2208 2327 339226161 339226042 1.890000e-42 183
19 TraesCS4D01G120300 chr3D 97.740 177 3 1 2906 3081 133998073 133998249 1.390000e-78 303
20 TraesCS4D01G120300 chr3D 94.330 194 7 3 2890 3081 1258462 1258271 8.360000e-76 294
21 TraesCS4D01G120300 chr3B 95.495 111 5 0 2212 2322 639838976 639839086 8.780000e-41 178
22 TraesCS4D01G120300 chr3B 94.595 111 6 0 2215 2325 579888699 579888589 4.090000e-39 172
23 TraesCS4D01G120300 chr3B 92.437 119 8 1 2206 2324 742660459 742660342 5.290000e-38 169
24 TraesCS4D01G120300 chr1B 92.683 123 7 2 2201 2323 22665260 22665380 3.160000e-40 176
25 TraesCS4D01G120300 chr1B 94.595 111 6 0 2212 2322 96621395 96621505 4.090000e-39 172
26 TraesCS4D01G120300 chr7B 93.860 114 7 0 2209 2322 564918744 564918857 4.090000e-39 172
27 TraesCS4D01G120300 chr7B 94.595 111 6 0 2213 2323 583174801 583174911 4.090000e-39 172
28 TraesCS4D01G120300 chr2B 89.256 121 11 2 502 622 233577306 233577424 1.920000e-32 150


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 TraesCS4D01G120300 chr4D 101435328 101438410 3082 False 5694.000000 5694 100.000000 1 3083 1 chr4D.!!$F1 3082
1 TraesCS4D01G120300 chr4A 473944841 473947627 2786 True 1962.500000 3260 90.618000 2 2908 2 chr4A.!!$R1 2906
2 TraesCS4D01G120300 chr4B 145370288 145373044 2756 False 1310.333333 2470 90.794667 1 2908 3 chr4B.!!$F1 2907
3 TraesCS4D01G120300 chr6A 502366779 502367307 528 False 342.000000 342 78.505000 1565 2096 1 chr6A.!!$F1 531
4 TraesCS4D01G120300 chr2D 352397769 352398330 561 True 263.000000 263 76.190000 97 628 1 chr2D.!!$R1 531

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
95 96 0.588252 CTTTAGTGCGTGTGCTTGCT 59.412 50.0 0.0 0.0 43.34 3.91 F
145 146 1.160137 GGCGACAAAGTGAGCTTCAT 58.840 50.0 0.0 0.0 33.01 2.57 F
1563 1617 0.032813 TGTTAGAGGGGTAGGGGTCG 60.033 60.0 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1555 1609 1.750778 GAATGTTACGTCCGACCCCTA 59.249 52.381 0.00 0.00 0.00 3.53 R
1614 1668 2.434185 GGTGATCGTGCCGCAAGA 60.434 61.111 11.52 11.52 43.02 3.02 R
2953 3052 0.035725 CCCGTTTGGTTCCTAGGGAC 60.036 60.000 12.35 12.35 41.26 4.46 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
55 56 0.773644 TCCTCCTTTGCCTTGAGCTT 59.226 50.000 0.00 0.00 44.23 3.74
63 64 1.896220 TGCCTTGAGCTTTTCGACAT 58.104 45.000 0.00 0.00 44.23 3.06
95 96 0.588252 CTTTAGTGCGTGTGCTTGCT 59.412 50.000 0.00 0.00 43.34 3.91
125 126 4.397481 GTAGTTAGCGAAGTACCCCAAT 57.603 45.455 12.18 0.00 36.02 3.16
126 127 3.261981 AGTTAGCGAAGTACCCCAATG 57.738 47.619 0.00 0.00 0.00 2.82
145 146 1.160137 GGCGACAAAGTGAGCTTCAT 58.840 50.000 0.00 0.00 33.01 2.57
194 198 2.697229 TCAATGGTGGCATGAACACAAA 59.303 40.909 18.69 9.55 40.54 2.83
199 203 3.894427 TGGTGGCATGAACACAAACTTAT 59.106 39.130 18.69 0.00 40.54 1.73
275 280 3.426292 CGACATCGTCAGAGTCTGCTTTA 60.426 47.826 15.72 1.28 32.09 1.85
294 299 7.338710 TGCTTTAAACATAGCTGGAAGAGTAT 58.661 34.615 0.00 0.00 38.22 2.12
319 324 5.517924 TGAGGAGAGAAGAATCAGTCTCAT 58.482 41.667 13.93 5.40 42.34 2.90
323 328 3.966665 AGAGAAGAATCAGTCTCATCCCC 59.033 47.826 13.93 0.00 42.34 4.81
334 339 2.496470 GTCTCATCCCCGGATATGGTAC 59.504 54.545 0.73 4.66 32.93 3.34
380 385 1.675552 GAGCTAGCGAGAAGGAGAGT 58.324 55.000 9.55 0.00 0.00 3.24
394 399 2.829720 AGGAGAGTACAATACACCGCAA 59.170 45.455 0.00 0.00 0.00 4.85
419 424 2.887152 ACAAAGAACTGGAAGCCACATC 59.113 45.455 0.00 0.00 37.60 3.06
530 564 7.101054 TGTATAATCTAGAGCGTGGTTTTGTT 58.899 34.615 0.00 0.00 0.00 2.83
622 657 5.922544 CACATGACACTTTCCCTCATTTTTC 59.077 40.000 0.00 0.00 0.00 2.29
725 773 2.639286 GAACGTGCTGTTGGGCTG 59.361 61.111 0.00 0.00 42.09 4.85
1500 1554 4.640771 AACAACAGGGAGCTCTGAAATA 57.359 40.909 14.64 0.00 38.11 1.40
1535 1589 5.681543 CGTCGAACTTATCAGATCATTTCGA 59.318 40.000 13.10 13.10 40.58 3.71
1555 1609 1.774856 ACAAGCTGTTGTTAGAGGGGT 59.225 47.619 0.00 0.00 45.00 4.95
1563 1617 0.032813 TGTTAGAGGGGTAGGGGTCG 60.033 60.000 0.00 0.00 0.00 4.79
1569 1623 2.275418 GGGTAGGGGTCGGACGTA 59.725 66.667 1.43 0.00 0.00 3.57
1614 1668 1.585267 TTGCCGCGCACAAGATCATT 61.585 50.000 8.75 0.00 38.71 2.57
1767 1821 1.003003 TCATTGCCTGACGTGGATGAA 59.997 47.619 0.00 0.00 0.00 2.57
1868 1922 4.149511 TGATATGCCAAAACATCCTCGA 57.850 40.909 0.00 0.00 0.00 4.04
2217 2271 5.249852 TGGGTGGCAAGTCTAGTTTATTACT 59.750 40.000 0.00 0.00 41.04 2.24
2218 2272 5.816258 GGGTGGCAAGTCTAGTTTATTACTC 59.184 44.000 0.00 0.00 38.33 2.59
2219 2273 5.816258 GGTGGCAAGTCTAGTTTATTACTCC 59.184 44.000 0.00 0.00 38.33 3.85
2220 2274 5.816258 GTGGCAAGTCTAGTTTATTACTCCC 59.184 44.000 0.00 0.00 38.33 4.30
2221 2275 5.724854 TGGCAAGTCTAGTTTATTACTCCCT 59.275 40.000 0.00 0.00 38.33 4.20
2222 2276 6.127140 TGGCAAGTCTAGTTTATTACTCCCTC 60.127 42.308 0.00 0.00 38.33 4.30
2223 2277 6.282167 GCAAGTCTAGTTTATTACTCCCTCC 58.718 44.000 0.00 0.00 38.33 4.30
2224 2278 6.505272 CAAGTCTAGTTTATTACTCCCTCCG 58.495 44.000 0.00 0.00 38.33 4.63
2225 2279 5.764432 AGTCTAGTTTATTACTCCCTCCGT 58.236 41.667 0.00 0.00 38.33 4.69
2226 2280 5.827267 AGTCTAGTTTATTACTCCCTCCGTC 59.173 44.000 0.00 0.00 38.33 4.79
2227 2281 5.009510 GTCTAGTTTATTACTCCCTCCGTCC 59.990 48.000 0.00 0.00 38.33 4.79
2228 2282 3.036819 AGTTTATTACTCCCTCCGTCCC 58.963 50.000 0.00 0.00 28.23 4.46
2229 2283 2.767960 GTTTATTACTCCCTCCGTCCCA 59.232 50.000 0.00 0.00 0.00 4.37
2230 2284 2.852714 TATTACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
2231 2285 1.961133 ATTACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
2232 2286 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
2233 2287 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2234 2288 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2235 2289 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2236 2290 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2237 2291 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2238 2292 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2239 2293 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
2240 2294 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
2241 2295 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
2242 2296 4.081309 CCTCCGTCCCAAAATAAGTGACTA 60.081 45.833 0.00 0.00 0.00 2.59
2243 2297 5.484715 CTCCGTCCCAAAATAAGTGACTAA 58.515 41.667 0.00 0.00 0.00 2.24
2244 2298 5.867330 TCCGTCCCAAAATAAGTGACTAAA 58.133 37.500 0.00 0.00 0.00 1.85
2245 2299 6.297582 TCCGTCCCAAAATAAGTGACTAAAA 58.702 36.000 0.00 0.00 0.00 1.52
2246 2300 6.771749 TCCGTCCCAAAATAAGTGACTAAAAA 59.228 34.615 0.00 0.00 0.00 1.94
2288 2342 9.310716 ACTAACTTTAGTACAAAGTTGAGTCAC 57.689 33.333 27.85 0.00 46.41 3.67
2289 2343 9.530633 CTAACTTTAGTACAAAGTTGAGTCACT 57.469 33.333 27.85 13.98 46.41 3.41
2290 2344 8.788325 AACTTTAGTACAAAGTTGAGTCACTT 57.212 30.769 23.48 0.00 45.58 3.16
2291 2345 8.788325 ACTTTAGTACAAAGTTGAGTCACTTT 57.212 30.769 14.04 12.24 46.00 2.66
2292 2346 9.227777 ACTTTAGTACAAAGTTGAGTCACTTTT 57.772 29.630 14.29 6.60 43.17 2.27
2293 2347 9.490663 CTTTAGTACAAAGTTGAGTCACTTTTG 57.509 33.333 19.55 19.55 43.17 2.44
2294 2348 8.780846 TTAGTACAAAGTTGAGTCACTTTTGA 57.219 30.769 24.60 12.36 43.17 2.69
2295 2349 7.681939 AGTACAAAGTTGAGTCACTTTTGAA 57.318 32.000 24.60 10.32 43.17 2.69
2296 2350 8.281212 AGTACAAAGTTGAGTCACTTTTGAAT 57.719 30.769 24.60 12.65 43.17 2.57
2297 2351 8.398665 AGTACAAAGTTGAGTCACTTTTGAATC 58.601 33.333 24.60 16.72 43.17 2.52
2307 2361 8.647035 GAGTCACTTTTGAATCACTTATTTCG 57.353 34.615 0.00 0.00 44.64 3.46
2308 2362 7.584987 AGTCACTTTTGAATCACTTATTTCGG 58.415 34.615 0.00 0.00 31.90 4.30
2309 2363 6.801862 GTCACTTTTGAATCACTTATTTCGGG 59.198 38.462 0.00 0.00 31.90 5.14
2310 2364 6.712998 TCACTTTTGAATCACTTATTTCGGGA 59.287 34.615 0.00 0.00 0.00 5.14
2311 2365 6.801862 CACTTTTGAATCACTTATTTCGGGAC 59.198 38.462 0.00 0.00 0.00 4.46
2383 2437 0.753867 TGCTGAACGTCAGGGTGTTA 59.246 50.000 14.19 0.00 44.43 2.41
2397 2451 1.265905 GGTGTTAAACTGTTCTGGCCG 59.734 52.381 0.00 0.00 0.00 6.13
2461 2515 5.112686 AGCTACTACTTTGCTGCTATTGTC 58.887 41.667 0.00 0.00 35.54 3.18
2476 2530 7.373441 GCTGCTATTGTCGTGTTAATTATGTTC 59.627 37.037 0.00 0.00 0.00 3.18
2477 2531 8.257830 TGCTATTGTCGTGTTAATTATGTTCA 57.742 30.769 0.00 0.00 0.00 3.18
2499 2553 6.112058 TCACTTCAAAACTGAAAATTTGGGG 58.888 36.000 0.00 0.00 37.19 4.96
2506 2560 1.345415 CTGAAAATTTGGGGCAGCAGT 59.655 47.619 0.00 0.00 0.00 4.40
2526 2580 3.887716 AGTTGAGCAAATATCATCTGGCC 59.112 43.478 0.00 0.00 0.00 5.36
2578 2634 9.558396 TCTGTTAAACTTTTACCTTTTCGGATA 57.442 29.630 0.00 0.00 36.31 2.59
2587 2643 7.775397 TTTACCTTTTCGGATACCTATTTCG 57.225 36.000 0.00 0.00 36.31 3.46
2596 2652 5.813672 TCGGATACCTATTTCGGAAAACTTG 59.186 40.000 7.33 0.00 0.00 3.16
2609 2665 5.995282 TCGGAAAACTTGTACAATCTCACAT 59.005 36.000 9.13 0.00 0.00 3.21
2629 2685 8.171164 TCACATATACAACAATTTGGTGAACA 57.829 30.769 20.90 6.09 37.20 3.18
2716 2772 5.906113 TGTTGTGCCTAAAAAGTTCAAGA 57.094 34.783 0.00 0.00 0.00 3.02
2750 2806 9.177608 TGTTATCTGCTTGATAAACAGCTTAAT 57.822 29.630 12.10 0.00 45.82 1.40
2808 2906 8.086143 TCATGCACTAGTACCTAGGTTTTATT 57.914 34.615 22.11 1.09 38.30 1.40
2810 2908 8.827677 CATGCACTAGTACCTAGGTTTTATTTC 58.172 37.037 22.11 6.09 38.30 2.17
2811 2909 7.333323 TGCACTAGTACCTAGGTTTTATTTCC 58.667 38.462 22.11 3.88 38.30 3.13
2813 2911 7.365384 GCACTAGTACCTAGGTTTTATTTCCCT 60.365 40.741 22.11 5.09 38.30 4.20
2814 2912 8.546322 CACTAGTACCTAGGTTTTATTTCCCTT 58.454 37.037 22.11 0.00 38.30 3.95
2815 2913 9.788815 ACTAGTACCTAGGTTTTATTTCCCTTA 57.211 33.333 22.11 0.00 38.30 2.69
2818 2916 8.893560 AGTACCTAGGTTTTATTTCCCTTAACA 58.106 33.333 22.11 0.00 0.00 2.41
2819 2917 9.519191 GTACCTAGGTTTTATTTCCCTTAACAA 57.481 33.333 22.11 0.00 0.00 2.83
2820 2918 8.645814 ACCTAGGTTTTATTTCCCTTAACAAG 57.354 34.615 9.21 0.00 0.00 3.16
2821 2919 7.177921 ACCTAGGTTTTATTTCCCTTAACAAGC 59.822 37.037 9.21 0.00 0.00 4.01
2822 2920 7.396339 CCTAGGTTTTATTTCCCTTAACAAGCT 59.604 37.037 0.00 0.00 0.00 3.74
2823 2921 6.993079 AGGTTTTATTTCCCTTAACAAGCTG 58.007 36.000 0.00 0.00 0.00 4.24
2824 2922 6.553476 AGGTTTTATTTCCCTTAACAAGCTGT 59.447 34.615 0.00 0.00 0.00 4.40
2825 2923 6.645003 GGTTTTATTTCCCTTAACAAGCTGTG 59.355 38.462 0.00 0.00 0.00 3.66
2826 2924 6.969993 TTTATTTCCCTTAACAAGCTGTGT 57.030 33.333 0.00 0.00 44.64 3.72
2850 2949 9.872721 TGTTGACATATTTTCATGTTGCATATT 57.127 25.926 0.00 0.00 39.25 1.28
2889 2988 2.135189 AGGGGTTATAGATTGCTGCCA 58.865 47.619 0.00 0.00 0.00 4.92
2895 2994 6.318900 GGGGTTATAGATTGCTGCCATATTAC 59.681 42.308 0.00 0.00 0.00 1.89
2897 2996 7.611855 GGGTTATAGATTGCTGCCATATTACTT 59.388 37.037 0.00 0.00 0.00 2.24
2908 3007 7.280876 TGCTGCCATATTACTTCAAAGAGTAAG 59.719 37.037 0.00 0.00 43.25 2.34
2909 3008 7.254932 GCTGCCATATTACTTCAAAGAGTAAGG 60.255 40.741 0.00 1.89 43.25 2.69
2910 3009 7.054124 TGCCATATTACTTCAAAGAGTAAGGG 58.946 38.462 0.00 6.25 43.25 3.95
2911 3010 6.486993 GCCATATTACTTCAAAGAGTAAGGGG 59.513 42.308 0.00 5.98 43.25 4.79
2912 3011 6.998673 CCATATTACTTCAAAGAGTAAGGGGG 59.001 42.308 0.00 2.01 43.25 5.40
2913 3012 7.366551 CCATATTACTTCAAAGAGTAAGGGGGT 60.367 40.741 0.00 0.00 43.25 4.95
2914 3013 3.790089 ACTTCAAAGAGTAAGGGGGTG 57.210 47.619 0.00 0.00 0.00 4.61
2915 3014 3.053826 ACTTCAAAGAGTAAGGGGGTGT 58.946 45.455 0.00 0.00 0.00 4.16
2916 3015 3.462205 ACTTCAAAGAGTAAGGGGGTGTT 59.538 43.478 0.00 0.00 0.00 3.32
2917 3016 4.079385 ACTTCAAAGAGTAAGGGGGTGTTT 60.079 41.667 0.00 0.00 0.00 2.83
2918 3017 3.827722 TCAAAGAGTAAGGGGGTGTTTG 58.172 45.455 0.00 0.00 0.00 2.93
2919 3018 2.890945 CAAAGAGTAAGGGGGTGTTTGG 59.109 50.000 0.00 0.00 0.00 3.28
2920 3019 1.829138 AGAGTAAGGGGGTGTTTGGT 58.171 50.000 0.00 0.00 0.00 3.67
2921 3020 2.141067 AGAGTAAGGGGGTGTTTGGTT 58.859 47.619 0.00 0.00 0.00 3.67
2922 3021 2.107726 AGAGTAAGGGGGTGTTTGGTTC 59.892 50.000 0.00 0.00 0.00 3.62
2923 3022 1.854280 AGTAAGGGGGTGTTTGGTTCA 59.146 47.619 0.00 0.00 0.00 3.18
2924 3023 2.158519 AGTAAGGGGGTGTTTGGTTCAG 60.159 50.000 0.00 0.00 0.00 3.02
2925 3024 0.105709 AAGGGGGTGTTTGGTTCAGG 60.106 55.000 0.00 0.00 0.00 3.86
2926 3025 1.533033 GGGGGTGTTTGGTTCAGGG 60.533 63.158 0.00 0.00 0.00 4.45
2927 3026 1.539665 GGGGTGTTTGGTTCAGGGA 59.460 57.895 0.00 0.00 0.00 4.20
2928 3027 0.826256 GGGGTGTTTGGTTCAGGGAC 60.826 60.000 0.00 0.00 0.00 4.46
2929 3028 0.185175 GGGTGTTTGGTTCAGGGACT 59.815 55.000 0.00 0.00 43.88 3.85
2930 3029 1.411074 GGGTGTTTGGTTCAGGGACTT 60.411 52.381 0.00 0.00 34.60 3.01
2931 3030 2.384828 GGTGTTTGGTTCAGGGACTTT 58.615 47.619 0.00 0.00 34.60 2.66
2932 3031 2.764010 GGTGTTTGGTTCAGGGACTTTT 59.236 45.455 0.00 0.00 34.60 2.27
2933 3032 3.196901 GGTGTTTGGTTCAGGGACTTTTT 59.803 43.478 0.00 0.00 34.60 1.94
2934 3033 4.403113 GGTGTTTGGTTCAGGGACTTTTTA 59.597 41.667 0.00 0.00 34.60 1.52
2935 3034 5.451381 GGTGTTTGGTTCAGGGACTTTTTAG 60.451 44.000 0.00 0.00 34.60 1.85
2936 3035 5.358725 GTGTTTGGTTCAGGGACTTTTTAGA 59.641 40.000 0.00 0.00 34.60 2.10
2937 3036 5.358725 TGTTTGGTTCAGGGACTTTTTAGAC 59.641 40.000 0.00 0.00 34.60 2.59
2938 3037 4.094830 TGGTTCAGGGACTTTTTAGACC 57.905 45.455 0.00 0.00 34.60 3.85
2939 3038 3.460340 TGGTTCAGGGACTTTTTAGACCA 59.540 43.478 0.00 0.00 34.60 4.02
2940 3039 4.072839 GGTTCAGGGACTTTTTAGACCAG 58.927 47.826 0.00 0.00 34.60 4.00
2941 3040 4.202430 GGTTCAGGGACTTTTTAGACCAGA 60.202 45.833 0.00 0.00 34.60 3.86
2942 3041 4.891992 TCAGGGACTTTTTAGACCAGAG 57.108 45.455 0.00 0.00 34.60 3.35
2943 3042 4.489737 TCAGGGACTTTTTAGACCAGAGA 58.510 43.478 0.00 0.00 34.60 3.10
2944 3043 4.283722 TCAGGGACTTTTTAGACCAGAGAC 59.716 45.833 0.00 0.00 34.60 3.36
2945 3044 4.284746 CAGGGACTTTTTAGACCAGAGACT 59.715 45.833 0.00 0.00 34.60 3.24
2946 3045 5.480772 CAGGGACTTTTTAGACCAGAGACTA 59.519 44.000 0.00 0.00 34.60 2.59
2947 3046 5.717654 AGGGACTTTTTAGACCAGAGACTAG 59.282 44.000 0.00 0.00 27.25 2.57
2948 3047 5.715753 GGGACTTTTTAGACCAGAGACTAGA 59.284 44.000 0.00 0.00 0.00 2.43
2949 3048 6.210984 GGGACTTTTTAGACCAGAGACTAGAA 59.789 42.308 0.00 0.00 0.00 2.10
2950 3049 7.256225 GGGACTTTTTAGACCAGAGACTAGAAA 60.256 40.741 0.00 0.00 0.00 2.52
2951 3050 8.148999 GGACTTTTTAGACCAGAGACTAGAAAA 58.851 37.037 0.00 0.00 29.00 2.29
2952 3051 9.543783 GACTTTTTAGACCAGAGACTAGAAAAA 57.456 33.333 0.00 0.00 29.00 1.94
2953 3052 9.549078 ACTTTTTAGACCAGAGACTAGAAAAAG 57.451 33.333 12.53 12.53 35.94 2.27
2954 3053 9.549078 CTTTTTAGACCAGAGACTAGAAAAAGT 57.451 33.333 0.00 0.00 31.13 2.66
2955 3054 9.543783 TTTTTAGACCAGAGACTAGAAAAAGTC 57.456 33.333 0.00 0.00 45.20 3.01
2956 3055 5.731957 AGACCAGAGACTAGAAAAAGTCC 57.268 43.478 0.00 0.00 45.86 3.85
2957 3056 4.528987 AGACCAGAGACTAGAAAAAGTCCC 59.471 45.833 0.00 0.00 45.86 4.46
2958 3057 4.494591 ACCAGAGACTAGAAAAAGTCCCT 58.505 43.478 0.00 0.00 45.86 4.20
2959 3058 5.652324 ACCAGAGACTAGAAAAAGTCCCTA 58.348 41.667 0.00 0.00 45.86 3.53
2960 3059 5.717654 ACCAGAGACTAGAAAAAGTCCCTAG 59.282 44.000 0.00 0.00 45.86 3.02
2961 3060 5.128008 CCAGAGACTAGAAAAAGTCCCTAGG 59.872 48.000 0.06 0.06 45.86 3.02
2962 3061 5.952947 CAGAGACTAGAAAAAGTCCCTAGGA 59.047 44.000 11.48 0.00 45.86 2.94
2963 3062 6.437793 CAGAGACTAGAAAAAGTCCCTAGGAA 59.562 42.308 11.48 0.00 45.86 3.36
2964 3063 6.438108 AGAGACTAGAAAAAGTCCCTAGGAAC 59.562 42.308 11.48 0.00 45.86 3.62
2965 3064 5.484644 AGACTAGAAAAAGTCCCTAGGAACC 59.515 44.000 11.48 0.00 45.86 3.62
2966 3065 5.160386 ACTAGAAAAAGTCCCTAGGAACCA 58.840 41.667 11.48 0.00 35.43 3.67
2967 3066 5.609708 ACTAGAAAAAGTCCCTAGGAACCAA 59.390 40.000 11.48 0.00 35.43 3.67
2968 3067 5.397553 AGAAAAAGTCCCTAGGAACCAAA 57.602 39.130 11.48 0.00 31.38 3.28
2969 3068 5.138276 AGAAAAAGTCCCTAGGAACCAAAC 58.862 41.667 11.48 0.00 31.38 2.93
2970 3069 2.853235 AAGTCCCTAGGAACCAAACG 57.147 50.000 11.48 0.00 31.38 3.60
2971 3070 0.981943 AGTCCCTAGGAACCAAACGG 59.018 55.000 11.48 0.00 31.38 4.44
2972 3071 0.035725 GTCCCTAGGAACCAAACGGG 60.036 60.000 11.48 0.00 44.81 5.28
2973 3072 0.178897 TCCCTAGGAACCAAACGGGA 60.179 55.000 11.48 0.00 41.15 5.14
2974 3073 0.252197 CCCTAGGAACCAAACGGGAG 59.748 60.000 11.48 0.00 41.15 4.30
2975 3074 0.252197 CCTAGGAACCAAACGGGAGG 59.748 60.000 1.05 0.00 41.15 4.30
2976 3075 0.252197 CTAGGAACCAAACGGGAGGG 59.748 60.000 0.00 0.00 41.15 4.30
2977 3076 0.178897 TAGGAACCAAACGGGAGGGA 60.179 55.000 0.00 0.00 41.15 4.20
2978 3077 1.303074 GGAACCAAACGGGAGGGAC 60.303 63.158 0.00 0.00 41.15 4.46
2980 3079 0.109913 GAACCAAACGGGAGGGACTT 59.890 55.000 0.00 0.00 41.55 3.01
2981 3080 0.554305 AACCAAACGGGAGGGACTTT 59.446 50.000 0.00 0.00 41.55 2.66
2982 3081 0.554305 ACCAAACGGGAGGGACTTTT 59.446 50.000 0.00 0.00 41.55 2.27
2983 3082 1.063492 ACCAAACGGGAGGGACTTTTT 60.063 47.619 0.00 0.00 41.55 1.94
2984 3083 1.611977 CCAAACGGGAGGGACTTTTTC 59.388 52.381 0.00 0.00 41.55 2.29
2985 3084 2.583143 CAAACGGGAGGGACTTTTTCT 58.417 47.619 0.00 0.00 41.55 2.52
2986 3085 3.497227 CCAAACGGGAGGGACTTTTTCTA 60.497 47.826 0.00 0.00 41.55 2.10
2987 3086 3.413846 AACGGGAGGGACTTTTTCTAC 57.586 47.619 0.00 0.00 41.55 2.59
2988 3087 2.332117 ACGGGAGGGACTTTTTCTACA 58.668 47.619 0.00 0.00 41.55 2.74
2989 3088 2.302157 ACGGGAGGGACTTTTTCTACAG 59.698 50.000 0.00 0.00 41.55 2.74
2990 3089 2.354805 CGGGAGGGACTTTTTCTACAGG 60.355 54.545 0.00 0.00 41.55 4.00
2991 3090 2.026169 GGGAGGGACTTTTTCTACAGGG 60.026 54.545 0.00 0.00 41.55 4.45
2992 3091 2.910977 GGAGGGACTTTTTCTACAGGGA 59.089 50.000 0.00 0.00 41.55 4.20
2993 3092 3.307550 GGAGGGACTTTTTCTACAGGGAC 60.308 52.174 0.00 0.00 41.55 4.46
2994 3093 3.583526 GAGGGACTTTTTCTACAGGGACT 59.416 47.826 0.00 0.00 41.55 3.85
2995 3094 4.759953 AGGGACTTTTTCTACAGGGACTA 58.240 43.478 0.00 0.00 28.08 2.59
2996 3095 4.778427 AGGGACTTTTTCTACAGGGACTAG 59.222 45.833 0.00 0.00 28.08 2.57
2997 3096 4.776308 GGGACTTTTTCTACAGGGACTAGA 59.224 45.833 0.00 0.00 36.02 2.43
2998 3097 5.247792 GGGACTTTTTCTACAGGGACTAGAA 59.752 44.000 0.00 0.00 36.02 2.10
2999 3098 6.239800 GGGACTTTTTCTACAGGGACTAGAAA 60.240 42.308 0.00 0.00 38.08 2.52
3000 3099 7.222161 GGACTTTTTCTACAGGGACTAGAAAA 58.778 38.462 0.00 8.58 43.60 2.29
3004 3103 8.672823 TTTTTCTACAGGGACTAGAAAAAGAC 57.327 34.615 16.61 0.00 46.05 3.01
3005 3104 7.613551 TTTCTACAGGGACTAGAAAAAGACT 57.386 36.000 0.00 0.00 37.31 3.24
3006 3105 6.837471 TCTACAGGGACTAGAAAAAGACTC 57.163 41.667 0.00 0.00 36.02 3.36
3007 3106 6.553857 TCTACAGGGACTAGAAAAAGACTCT 58.446 40.000 0.00 0.00 36.02 3.24
3008 3107 7.011382 TCTACAGGGACTAGAAAAAGACTCTT 58.989 38.462 0.00 0.00 36.02 2.85
3009 3108 6.104146 ACAGGGACTAGAAAAAGACTCTTC 57.896 41.667 0.00 0.00 36.02 2.87
3010 3109 5.841783 ACAGGGACTAGAAAAAGACTCTTCT 59.158 40.000 0.00 5.39 36.02 2.85
3011 3110 7.011382 ACAGGGACTAGAAAAAGACTCTTCTA 58.989 38.462 0.00 6.75 36.02 2.10
3070 3169 4.618920 GTCCTAGGACTTCTGAACCAAA 57.381 45.455 31.12 0.00 41.57 3.28
3071 3170 4.316645 GTCCTAGGACTTCTGAACCAAAC 58.683 47.826 31.12 3.26 41.57 2.93
3072 3171 3.971305 TCCTAGGACTTCTGAACCAAACA 59.029 43.478 7.62 0.00 0.00 2.83
3073 3172 4.065789 CCTAGGACTTCTGAACCAAACAC 58.934 47.826 1.05 0.00 0.00 3.32
3074 3173 2.932261 AGGACTTCTGAACCAAACACC 58.068 47.619 0.58 0.00 0.00 4.16
3075 3174 1.954382 GGACTTCTGAACCAAACACCC 59.046 52.381 0.00 0.00 0.00 4.61
3076 3175 1.954382 GACTTCTGAACCAAACACCCC 59.046 52.381 0.00 0.00 0.00 4.95
3077 3176 1.328279 CTTCTGAACCAAACACCCCC 58.672 55.000 0.00 0.00 0.00 5.40
3078 3177 0.930726 TTCTGAACCAAACACCCCCT 59.069 50.000 0.00 0.00 0.00 4.79
3079 3178 1.822425 TCTGAACCAAACACCCCCTA 58.178 50.000 0.00 0.00 0.00 3.53
3080 3179 2.136863 TCTGAACCAAACACCCCCTAA 58.863 47.619 0.00 0.00 0.00 2.69
3081 3180 2.719705 TCTGAACCAAACACCCCCTAAT 59.280 45.455 0.00 0.00 0.00 1.73
3082 3181 3.141272 TCTGAACCAAACACCCCCTAATT 59.859 43.478 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.695830 ATCTTGTTCCACGCTCCTTTA 57.304 42.857 0.00 0.00 0.00 1.85
55 56 4.318332 AGTCTTTGATGCTCATGTCGAAA 58.682 39.130 0.00 0.00 0.00 3.46
63 64 3.433274 CGCACTAAAGTCTTTGATGCTCA 59.567 43.478 22.89 0.00 34.54 4.26
95 96 0.542467 TCGCTAACTACCCACCACCA 60.542 55.000 0.00 0.00 0.00 4.17
121 122 0.109597 GCTCACTTTGTCGCCATTGG 60.110 55.000 0.00 0.00 0.00 3.16
125 126 0.179059 TGAAGCTCACTTTGTCGCCA 60.179 50.000 0.00 0.00 35.82 5.69
126 127 1.160137 ATGAAGCTCACTTTGTCGCC 58.840 50.000 0.00 0.00 35.82 5.54
137 138 3.555139 CCTCGTCATCTTCAATGAAGCTC 59.445 47.826 17.58 7.15 39.29 4.09
199 203 7.985184 GTGCTAATATGGAAATCACCGGATATA 59.015 37.037 9.46 0.00 32.09 0.86
232 237 1.559831 TGAGATGCGTGCTGATAACG 58.440 50.000 0.00 0.00 43.81 3.18
241 246 0.774685 CGATGTCGATGAGATGCGTG 59.225 55.000 0.00 0.00 43.02 5.34
275 280 6.825721 CCTCAAATACTCTTCCAGCTATGTTT 59.174 38.462 0.00 0.00 0.00 2.83
294 299 5.777223 TGAGACTGATTCTTCTCTCCTCAAA 59.223 40.000 13.63 0.00 39.30 2.69
319 324 2.171027 GTGTTTGTACCATATCCGGGGA 59.829 50.000 0.00 0.00 0.00 4.81
323 328 6.053005 ACCATTAGTGTTTGTACCATATCCG 58.947 40.000 0.00 0.00 0.00 4.18
334 339 7.747888 TCATATTTCACGACCATTAGTGTTTG 58.252 34.615 0.00 0.00 39.25 2.93
347 352 3.304726 CGCTAGCTCCTCATATTTCACGA 60.305 47.826 13.93 0.00 0.00 4.35
380 385 4.895224 TTGTTGTTTGCGGTGTATTGTA 57.105 36.364 0.00 0.00 0.00 2.41
394 399 3.096092 TGGCTTCCAGTTCTTTGTTGTT 58.904 40.909 0.00 0.00 0.00 2.83
419 424 4.662468 TCTTCGATGGAAAGATCTCTGG 57.338 45.455 0.00 0.00 0.00 3.86
497 531 7.155328 CACGCTCTAGATTATACAAAAGGGAT 58.845 38.462 0.00 0.00 0.00 3.85
543 578 3.439129 CGTTAAAACCTTCCATCCCTCAC 59.561 47.826 0.00 0.00 0.00 3.51
672 720 2.223618 GCCAAGGCACGTTTTGACTAAA 60.224 45.455 6.14 0.00 46.34 1.85
673 721 1.335496 GCCAAGGCACGTTTTGACTAA 59.665 47.619 6.14 0.00 46.34 2.24
674 722 0.948678 GCCAAGGCACGTTTTGACTA 59.051 50.000 6.14 0.00 46.34 2.59
751 799 2.283821 GCAATGGGACCTGGCCAA 60.284 61.111 7.01 0.00 0.00 4.52
1403 1457 6.760770 GCTATCATCCTTAATGTAGCCTGATC 59.239 42.308 0.00 0.00 38.12 2.92
1500 1554 2.814280 AGTTCGACGATGACACCTTT 57.186 45.000 0.00 0.00 0.00 3.11
1535 1589 1.774856 ACCCCTCTAACAACAGCTTGT 59.225 47.619 0.00 0.00 42.81 3.16
1555 1609 1.750778 GAATGTTACGTCCGACCCCTA 59.249 52.381 0.00 0.00 0.00 3.53
1614 1668 2.434185 GGTGATCGTGCCGCAAGA 60.434 61.111 11.52 11.52 43.02 3.02
1767 1821 5.007034 TCAACGTAATCATCACCACCAAAT 58.993 37.500 0.00 0.00 0.00 2.32
2200 2254 6.096564 ACGGAGGGAGTAATAAACTAGACTTG 59.903 42.308 0.00 0.00 39.07 3.16
2217 2271 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2218 2272 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
2219 2273 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2220 2274 3.939066 AGTCACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 33.84 4.63
2221 2275 5.486735 TTAGTCACTTATTTTGGGACGGA 57.513 39.130 0.00 0.00 33.84 4.69
2222 2276 6.563222 TTTTAGTCACTTATTTTGGGACGG 57.437 37.500 0.00 0.00 33.84 4.79
2262 2316 9.310716 GTGACTCAACTTTGTACTAAAGTTAGT 57.689 33.333 23.56 23.28 45.57 2.24
2263 2317 9.530633 AGTGACTCAACTTTGTACTAAAGTTAG 57.469 33.333 23.56 21.61 45.57 2.34
2264 2318 9.880157 AAGTGACTCAACTTTGTACTAAAGTTA 57.120 29.630 23.56 15.88 45.57 2.24
2265 2319 9.227777 AAAGTGACTCAACTTTGTACTAAAGTT 57.772 29.630 20.78 20.78 46.16 2.66
2266 2320 8.788325 AAAGTGACTCAACTTTGTACTAAAGT 57.212 30.769 14.04 14.04 46.16 2.66
2277 2331 7.396540 AAGTGATTCAAAAGTGACTCAACTT 57.603 32.000 0.00 3.52 42.94 2.66
2278 2332 8.682936 ATAAGTGATTCAAAAGTGACTCAACT 57.317 30.769 0.00 0.00 42.94 3.16
2279 2333 9.736023 AAATAAGTGATTCAAAAGTGACTCAAC 57.264 29.630 0.00 0.00 42.94 3.18
2280 2334 9.950680 GAAATAAGTGATTCAAAAGTGACTCAA 57.049 29.630 0.00 0.00 42.94 3.02
2281 2335 8.282592 CGAAATAAGTGATTCAAAAGTGACTCA 58.717 33.333 0.00 0.00 40.16 3.41
2282 2336 7.746475 CCGAAATAAGTGATTCAAAAGTGACTC 59.254 37.037 0.00 0.00 34.76 3.36
2283 2337 7.308589 CCCGAAATAAGTGATTCAAAAGTGACT 60.309 37.037 0.00 0.00 31.90 3.41
2284 2338 6.801862 CCCGAAATAAGTGATTCAAAAGTGAC 59.198 38.462 0.00 0.00 31.90 3.67
2285 2339 6.712998 TCCCGAAATAAGTGATTCAAAAGTGA 59.287 34.615 0.00 0.00 0.00 3.41
2286 2340 6.801862 GTCCCGAAATAAGTGATTCAAAAGTG 59.198 38.462 0.00 0.00 0.00 3.16
2287 2341 6.348213 CGTCCCGAAATAAGTGATTCAAAAGT 60.348 38.462 0.00 0.00 0.00 2.66
2288 2342 6.021596 CGTCCCGAAATAAGTGATTCAAAAG 58.978 40.000 0.00 0.00 0.00 2.27
2289 2343 5.106475 CCGTCCCGAAATAAGTGATTCAAAA 60.106 40.000 0.00 0.00 0.00 2.44
2290 2344 4.393680 CCGTCCCGAAATAAGTGATTCAAA 59.606 41.667 0.00 0.00 0.00 2.69
2291 2345 3.936453 CCGTCCCGAAATAAGTGATTCAA 59.064 43.478 0.00 0.00 0.00 2.69
2292 2346 3.527533 CCGTCCCGAAATAAGTGATTCA 58.472 45.455 0.00 0.00 0.00 2.57
2293 2347 2.870411 CCCGTCCCGAAATAAGTGATTC 59.130 50.000 0.00 0.00 0.00 2.52
2294 2348 2.420967 CCCCGTCCCGAAATAAGTGATT 60.421 50.000 0.00 0.00 0.00 2.57
2295 2349 1.140252 CCCCGTCCCGAAATAAGTGAT 59.860 52.381 0.00 0.00 0.00 3.06
2296 2350 0.538118 CCCCGTCCCGAAATAAGTGA 59.462 55.000 0.00 0.00 0.00 3.41
2297 2351 0.463116 CCCCCGTCCCGAAATAAGTG 60.463 60.000 0.00 0.00 0.00 3.16
2298 2352 1.909975 CCCCCGTCCCGAAATAAGT 59.090 57.895 0.00 0.00 0.00 2.24
2299 2353 4.870190 CCCCCGTCCCGAAATAAG 57.130 61.111 0.00 0.00 0.00 1.73
2313 2367 4.324267 GTGCACATATATTGTACTCCCCC 58.676 47.826 13.17 0.00 36.57 5.40
2314 2368 4.041691 AGGTGCACATATATTGTACTCCCC 59.958 45.833 20.43 0.00 36.36 4.81
2315 2369 5.228945 AGGTGCACATATATTGTACTCCC 57.771 43.478 20.43 0.00 36.36 4.30
2316 2370 7.067008 ACAAAAGGTGCACATATATTGTACTCC 59.933 37.037 21.20 1.14 36.57 3.85
2317 2371 7.985476 ACAAAAGGTGCACATATATTGTACTC 58.015 34.615 21.20 1.59 36.57 2.59
2318 2372 7.609918 TGACAAAAGGTGCACATATATTGTACT 59.390 33.333 22.05 5.03 36.57 2.73
2319 2373 7.757526 TGACAAAAGGTGCACATATATTGTAC 58.242 34.615 22.05 17.25 36.57 2.90
2320 2374 7.929941 TGACAAAAGGTGCACATATATTGTA 57.070 32.000 22.05 12.58 36.57 2.41
2321 2375 6.832520 TGACAAAAGGTGCACATATATTGT 57.167 33.333 22.13 22.13 39.91 2.71
2322 2376 7.814107 AGTTTGACAAAAGGTGCACATATATTG 59.186 33.333 20.43 18.66 0.00 1.90
2323 2377 7.895759 AGTTTGACAAAAGGTGCACATATATT 58.104 30.769 20.43 5.24 0.00 1.28
2324 2378 7.466746 AGTTTGACAAAAGGTGCACATATAT 57.533 32.000 20.43 0.00 0.00 0.86
2325 2379 6.892658 AGTTTGACAAAAGGTGCACATATA 57.107 33.333 20.43 0.00 0.00 0.86
2383 2437 0.250901 AGATGCGGCCAGAACAGTTT 60.251 50.000 2.24 0.00 0.00 2.66
2461 2515 9.445786 AGTTTTGAAGTGAACATAATTAACACG 57.554 29.630 0.00 0.00 36.71 4.49
2476 2530 5.220835 GCCCCAAATTTTCAGTTTTGAAGTG 60.221 40.000 0.00 0.00 43.76 3.16
2477 2531 4.881273 GCCCCAAATTTTCAGTTTTGAAGT 59.119 37.500 0.00 0.00 43.76 3.01
2495 2549 2.925416 TTTGCTCAACTGCTGCCCCA 62.925 55.000 0.00 0.00 0.00 4.96
2499 2553 3.770263 TGATATTTGCTCAACTGCTGC 57.230 42.857 0.00 0.00 0.00 5.25
2506 2560 3.225104 GGGCCAGATGATATTTGCTCAA 58.775 45.455 4.39 0.00 0.00 3.02
2526 2580 3.006859 TGCATGTCCCTCGATAACTATGG 59.993 47.826 0.00 0.00 0.00 2.74
2578 2634 7.664318 AGATTGTACAAGTTTTCCGAAATAGGT 59.336 33.333 14.65 0.00 0.00 3.08
2609 2665 9.823647 AAAATGTGTTCACCAAATTGTTGTATA 57.176 25.926 0.37 0.00 31.08 1.47
2652 2708 5.917541 TTTCAACTACTTAACAGGCTTCG 57.082 39.130 0.00 0.00 0.00 3.79
2681 2737 3.769300 AGGCACAACAAATAGGAATTCCC 59.231 43.478 21.22 3.34 36.42 3.97
2684 2740 8.428852 ACTTTTTAGGCACAACAAATAGGAATT 58.571 29.630 0.00 0.00 0.00 2.17
2752 2808 9.476202 CATCTCGGTATGATACATAACTGAAAA 57.524 33.333 4.83 0.00 0.00 2.29
2772 2828 4.428209 ACTAGTGCATGAAGTTCATCTCG 58.572 43.478 15.60 8.76 34.28 4.04
2816 2914 6.389830 TGAAAATATGTCAACACAGCTTGT 57.610 33.333 0.00 0.00 41.74 3.16
2817 2915 6.864685 ACATGAAAATATGTCAACACAGCTTG 59.135 34.615 0.00 0.00 36.60 4.01
2818 2916 6.985117 ACATGAAAATATGTCAACACAGCTT 58.015 32.000 0.00 0.00 36.60 3.74
2819 2917 6.579666 ACATGAAAATATGTCAACACAGCT 57.420 33.333 0.00 0.00 36.60 4.24
2820 2918 6.400303 GCAACATGAAAATATGTCAACACAGC 60.400 38.462 0.00 0.00 40.24 4.40
2821 2919 6.641723 TGCAACATGAAAATATGTCAACACAG 59.358 34.615 0.00 0.00 40.24 3.66
2822 2920 6.510536 TGCAACATGAAAATATGTCAACACA 58.489 32.000 0.00 0.00 40.24 3.72
2823 2921 7.585286 ATGCAACATGAAAATATGTCAACAC 57.415 32.000 0.00 0.00 40.24 3.32
2824 2922 9.872721 AATATGCAACATGAAAATATGTCAACA 57.127 25.926 0.00 0.00 40.24 3.33
2861 2960 7.665974 GCAGCAATCTATAACCCCTTAATTACT 59.334 37.037 0.00 0.00 0.00 2.24
2889 2988 7.184022 ACACCCCCTTACTCTTTGAAGTAATAT 59.816 37.037 0.00 0.00 40.12 1.28
2895 2994 3.790089 ACACCCCCTTACTCTTTGAAG 57.210 47.619 0.00 0.00 0.00 3.02
2897 2996 3.435890 CCAAACACCCCCTTACTCTTTGA 60.436 47.826 0.00 0.00 0.00 2.69
2908 3007 1.533033 CCCTGAACCAAACACCCCC 60.533 63.158 0.00 0.00 0.00 5.40
2909 3008 0.826256 GTCCCTGAACCAAACACCCC 60.826 60.000 0.00 0.00 0.00 4.95
2910 3009 0.185175 AGTCCCTGAACCAAACACCC 59.815 55.000 0.00 0.00 0.00 4.61
2911 3010 2.067365 AAGTCCCTGAACCAAACACC 57.933 50.000 0.00 0.00 0.00 4.16
2912 3011 4.465632 AAAAAGTCCCTGAACCAAACAC 57.534 40.909 0.00 0.00 0.00 3.32
2913 3012 5.358725 GTCTAAAAAGTCCCTGAACCAAACA 59.641 40.000 0.00 0.00 0.00 2.83
2914 3013 5.221185 GGTCTAAAAAGTCCCTGAACCAAAC 60.221 44.000 0.00 0.00 0.00 2.93
2915 3014 4.891168 GGTCTAAAAAGTCCCTGAACCAAA 59.109 41.667 0.00 0.00 0.00 3.28
2916 3015 4.079672 TGGTCTAAAAAGTCCCTGAACCAA 60.080 41.667 0.00 0.00 0.00 3.67
2917 3016 3.460340 TGGTCTAAAAAGTCCCTGAACCA 59.540 43.478 0.00 0.00 0.00 3.67
2918 3017 4.072839 CTGGTCTAAAAAGTCCCTGAACC 58.927 47.826 0.00 0.00 0.00 3.62
2919 3018 4.969484 TCTGGTCTAAAAAGTCCCTGAAC 58.031 43.478 0.00 0.00 0.00 3.18
2920 3019 4.905456 TCTCTGGTCTAAAAAGTCCCTGAA 59.095 41.667 0.00 0.00 0.00 3.02
2921 3020 4.283722 GTCTCTGGTCTAAAAAGTCCCTGA 59.716 45.833 0.00 0.00 0.00 3.86
2922 3021 4.284746 AGTCTCTGGTCTAAAAAGTCCCTG 59.715 45.833 0.00 0.00 0.00 4.45
2923 3022 4.494591 AGTCTCTGGTCTAAAAAGTCCCT 58.505 43.478 0.00 0.00 0.00 4.20
2924 3023 4.893829 AGTCTCTGGTCTAAAAAGTCCC 57.106 45.455 0.00 0.00 0.00 4.46
2925 3024 6.837471 TCTAGTCTCTGGTCTAAAAAGTCC 57.163 41.667 0.00 0.00 0.00 3.85
2926 3025 9.543783 TTTTTCTAGTCTCTGGTCTAAAAAGTC 57.456 33.333 0.00 0.00 0.00 3.01
2927 3026 9.549078 CTTTTTCTAGTCTCTGGTCTAAAAAGT 57.451 33.333 0.00 0.00 0.00 2.66
2928 3027 9.549078 ACTTTTTCTAGTCTCTGGTCTAAAAAG 57.451 33.333 12.78 12.78 0.00 2.27
2929 3028 9.543783 GACTTTTTCTAGTCTCTGGTCTAAAAA 57.456 33.333 0.00 0.00 41.07 1.94
2930 3029 8.148999 GGACTTTTTCTAGTCTCTGGTCTAAAA 58.851 37.037 0.00 0.00 43.26 1.52
2931 3030 7.256225 GGGACTTTTTCTAGTCTCTGGTCTAAA 60.256 40.741 0.00 0.00 41.50 1.85
2932 3031 6.210984 GGGACTTTTTCTAGTCTCTGGTCTAA 59.789 42.308 0.00 0.00 41.50 2.10
2933 3032 5.715753 GGGACTTTTTCTAGTCTCTGGTCTA 59.284 44.000 0.00 0.00 41.50 2.59
2934 3033 4.528987 GGGACTTTTTCTAGTCTCTGGTCT 59.471 45.833 0.00 0.00 41.50 3.85
2935 3034 4.823157 GGGACTTTTTCTAGTCTCTGGTC 58.177 47.826 0.00 0.00 41.50 4.02
2936 3035 4.893829 GGGACTTTTTCTAGTCTCTGGT 57.106 45.455 0.00 0.00 41.50 4.00
2940 3039 6.351202 GGTTCCTAGGGACTTTTTCTAGTCTC 60.351 46.154 20.08 0.00 44.42 3.36
2941 3040 5.484644 GGTTCCTAGGGACTTTTTCTAGTCT 59.515 44.000 20.08 0.00 43.26 3.24
2942 3041 5.247792 TGGTTCCTAGGGACTTTTTCTAGTC 59.752 44.000 20.08 0.00 43.05 2.59
2943 3042 5.160386 TGGTTCCTAGGGACTTTTTCTAGT 58.840 41.667 20.08 0.00 41.75 2.57
2944 3043 5.757099 TGGTTCCTAGGGACTTTTTCTAG 57.243 43.478 20.08 0.00 41.75 2.43
2945 3044 6.301486 GTTTGGTTCCTAGGGACTTTTTCTA 58.699 40.000 20.08 0.00 41.75 2.10
2946 3045 5.138276 GTTTGGTTCCTAGGGACTTTTTCT 58.862 41.667 20.08 0.00 41.75 2.52
2947 3046 4.023450 CGTTTGGTTCCTAGGGACTTTTTC 60.023 45.833 20.08 3.31 41.75 2.29
2948 3047 3.887110 CGTTTGGTTCCTAGGGACTTTTT 59.113 43.478 20.08 0.00 41.75 1.94
2949 3048 3.483421 CGTTTGGTTCCTAGGGACTTTT 58.517 45.455 20.08 0.00 41.75 2.27
2950 3049 2.224695 CCGTTTGGTTCCTAGGGACTTT 60.225 50.000 20.08 0.00 41.75 2.66
2951 3050 1.350019 CCGTTTGGTTCCTAGGGACTT 59.650 52.381 20.08 0.00 41.75 3.01
2952 3051 0.981943 CCGTTTGGTTCCTAGGGACT 59.018 55.000 20.08 0.00 46.37 3.85
2953 3052 0.035725 CCCGTTTGGTTCCTAGGGAC 60.036 60.000 12.35 12.35 41.26 4.46
2954 3053 0.178897 TCCCGTTTGGTTCCTAGGGA 60.179 55.000 9.46 0.00 44.85 4.20
2955 3054 0.252197 CTCCCGTTTGGTTCCTAGGG 59.748 60.000 9.46 0.00 40.16 3.53
2956 3055 0.252197 CCTCCCGTTTGGTTCCTAGG 59.748 60.000 0.82 0.82 34.77 3.02
2957 3056 0.252197 CCCTCCCGTTTGGTTCCTAG 59.748 60.000 0.00 0.00 34.77 3.02
2958 3057 0.178897 TCCCTCCCGTTTGGTTCCTA 60.179 55.000 0.00 0.00 34.77 2.94
2959 3058 1.462627 TCCCTCCCGTTTGGTTCCT 60.463 57.895 0.00 0.00 34.77 3.36
2960 3059 1.303074 GTCCCTCCCGTTTGGTTCC 60.303 63.158 0.00 0.00 34.77 3.62
2961 3060 0.109913 AAGTCCCTCCCGTTTGGTTC 59.890 55.000 0.00 0.00 34.77 3.62
2962 3061 0.554305 AAAGTCCCTCCCGTTTGGTT 59.446 50.000 0.00 0.00 34.77 3.67
2963 3062 0.554305 AAAAGTCCCTCCCGTTTGGT 59.446 50.000 0.00 0.00 34.77 3.67
2964 3063 1.611977 GAAAAAGTCCCTCCCGTTTGG 59.388 52.381 0.00 0.00 0.00 3.28
2965 3064 2.583143 AGAAAAAGTCCCTCCCGTTTG 58.417 47.619 0.00 0.00 0.00 2.93
2966 3065 3.136992 TGTAGAAAAAGTCCCTCCCGTTT 59.863 43.478 0.00 0.00 0.00 3.60
2967 3066 2.707257 TGTAGAAAAAGTCCCTCCCGTT 59.293 45.455 0.00 0.00 0.00 4.44
2968 3067 2.302157 CTGTAGAAAAAGTCCCTCCCGT 59.698 50.000 0.00 0.00 0.00 5.28
2969 3068 2.354805 CCTGTAGAAAAAGTCCCTCCCG 60.355 54.545 0.00 0.00 0.00 5.14
2970 3069 2.026169 CCCTGTAGAAAAAGTCCCTCCC 60.026 54.545 0.00 0.00 0.00 4.30
2971 3070 2.910977 TCCCTGTAGAAAAAGTCCCTCC 59.089 50.000 0.00 0.00 0.00 4.30
2972 3071 3.583526 AGTCCCTGTAGAAAAAGTCCCTC 59.416 47.826 0.00 0.00 0.00 4.30
2973 3072 3.599348 AGTCCCTGTAGAAAAAGTCCCT 58.401 45.455 0.00 0.00 0.00 4.20
2974 3073 4.776308 TCTAGTCCCTGTAGAAAAAGTCCC 59.224 45.833 0.00 0.00 0.00 4.46
2975 3074 5.997384 TCTAGTCCCTGTAGAAAAAGTCC 57.003 43.478 0.00 0.00 0.00 3.85
2981 3080 7.509659 AGAGTCTTTTTCTAGTCCCTGTAGAAA 59.490 37.037 1.96 1.96 42.24 2.52
2982 3081 7.011382 AGAGTCTTTTTCTAGTCCCTGTAGAA 58.989 38.462 0.00 0.00 35.21 2.10
2983 3082 6.553857 AGAGTCTTTTTCTAGTCCCTGTAGA 58.446 40.000 0.00 0.00 0.00 2.59
2984 3083 6.844097 AGAGTCTTTTTCTAGTCCCTGTAG 57.156 41.667 0.00 0.00 0.00 2.74
2985 3084 7.011382 AGAAGAGTCTTTTTCTAGTCCCTGTA 58.989 38.462 6.88 0.00 32.13 2.74
2986 3085 5.841783 AGAAGAGTCTTTTTCTAGTCCCTGT 59.158 40.000 6.88 0.00 32.13 4.00
2987 3086 6.353404 AGAAGAGTCTTTTTCTAGTCCCTG 57.647 41.667 6.88 0.00 32.13 4.45
2988 3087 7.471890 TCTAGAAGAGTCTTTTTCTAGTCCCT 58.528 38.462 19.83 7.58 46.64 4.20
2989 3088 7.612633 TCTCTAGAAGAGTCTTTTTCTAGTCCC 59.387 40.741 19.83 1.43 46.64 4.46
2990 3089 8.570068 TCTCTAGAAGAGTCTTTTTCTAGTCC 57.430 38.462 19.83 2.02 46.64 3.85
3049 3148 4.202326 TGTTTGGTTCAGAAGTCCTAGGAC 60.202 45.833 31.29 31.29 44.86 3.85
3050 3149 3.971305 TGTTTGGTTCAGAAGTCCTAGGA 59.029 43.478 7.62 7.62 0.00 2.94
3051 3150 4.065789 GTGTTTGGTTCAGAAGTCCTAGG 58.934 47.826 0.82 0.82 0.00 3.02
3052 3151 4.065789 GGTGTTTGGTTCAGAAGTCCTAG 58.934 47.826 0.00 0.00 0.00 3.02
3053 3152 3.181448 GGGTGTTTGGTTCAGAAGTCCTA 60.181 47.826 0.00 0.00 0.00 2.94
3054 3153 2.422945 GGGTGTTTGGTTCAGAAGTCCT 60.423 50.000 0.00 0.00 0.00 3.85
3055 3154 1.954382 GGGTGTTTGGTTCAGAAGTCC 59.046 52.381 0.00 0.00 0.00 3.85
3056 3155 1.954382 GGGGTGTTTGGTTCAGAAGTC 59.046 52.381 0.00 0.00 0.00 3.01
3057 3156 1.411074 GGGGGTGTTTGGTTCAGAAGT 60.411 52.381 0.00 0.00 0.00 3.01
3058 3157 1.133482 AGGGGGTGTTTGGTTCAGAAG 60.133 52.381 0.00 0.00 0.00 2.85
3059 3158 0.930726 AGGGGGTGTTTGGTTCAGAA 59.069 50.000 0.00 0.00 0.00 3.02
3060 3159 1.822425 TAGGGGGTGTTTGGTTCAGA 58.178 50.000 0.00 0.00 0.00 3.27
3061 3160 2.668144 TTAGGGGGTGTTTGGTTCAG 57.332 50.000 0.00 0.00 0.00 3.02
3062 3161 3.621682 AATTAGGGGGTGTTTGGTTCA 57.378 42.857 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.