Multiple sequence alignment - TraesCS5B01G437100

Loading Multiple Alignment...

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 TraesCS5B01G437100 chr5B 100.000 5334 0 0 1 5334 610504552 610499219 0.000000e+00 9851.0
1 TraesCS5B01G437100 chr5B 95.432 613 18 3 4358 4960 610306149 610305537 0.000000e+00 968.0
2 TraesCS5B01G437100 chr5B 97.388 268 5 2 4098 4363 610311504 610311237 6.300000e-124 455.0
3 TraesCS5B01G437100 chr5B 88.492 252 10 5 5020 5271 610304879 610304647 2.430000e-73 287.0
4 TraesCS5B01G437100 chr5D 93.259 3130 141 33 1864 4960 494218830 494215738 0.000000e+00 4547.0
5 TraesCS5B01G437100 chr5D 86.233 1046 57 33 384 1378 494220319 494219310 0.000000e+00 1053.0
6 TraesCS5B01G437100 chr5D 86.320 826 83 15 3305 4123 27284145 27284947 0.000000e+00 872.0
7 TraesCS5B01G437100 chr5D 86.136 678 64 18 3451 4123 510553684 510554336 0.000000e+00 704.0
8 TraesCS5B01G437100 chr5D 84.956 678 72 18 3451 4123 445024974 445024322 0.000000e+00 660.0
9 TraesCS5B01G437100 chr5D 87.113 388 37 10 7 386 494220787 494220405 1.370000e-115 427.0
10 TraesCS5B01G437100 chr5D 93.143 175 7 2 5020 5192 494215094 494214923 8.870000e-63 252.0
11 TraesCS5B01G437100 chr5A 93.466 2066 93 26 2924 4960 617208922 617206870 0.000000e+00 3029.0
12 TraesCS5B01G437100 chr5A 92.213 1053 56 10 1848 2888 617209958 617208920 0.000000e+00 1467.0
13 TraesCS5B01G437100 chr5A 84.267 750 88 21 3305 4048 470929930 470930655 0.000000e+00 704.0
14 TraesCS5B01G437100 chr5A 84.319 778 57 27 7 741 617211850 617211095 0.000000e+00 701.0
15 TraesCS5B01G437100 chr5A 86.677 653 42 23 743 1378 617211044 617210420 0.000000e+00 682.0
16 TraesCS5B01G437100 chr5A 85.207 676 73 18 3453 4123 13088188 13087535 0.000000e+00 669.0
17 TraesCS5B01G437100 chr5A 90.506 158 12 3 5020 5175 617206213 617206057 7.000000e-49 206.0
18 TraesCS5B01G437100 chr7B 86.441 826 88 13 3305 4123 228802386 228803194 0.000000e+00 883.0
19 TraesCS5B01G437100 chr2D 86.320 826 84 14 3305 4123 29095699 29094896 0.000000e+00 872.0
20 TraesCS5B01G437100 chr2D 88.764 356 32 5 3770 4125 519514 519861 3.820000e-116 429.0
21 TraesCS5B01G437100 chr7A 85.801 824 90 14 3307 4123 658272487 658273290 0.000000e+00 848.0
22 TraesCS5B01G437100 chr6D 85.714 826 86 22 3305 4123 450188603 450187803 0.000000e+00 843.0
23 TraesCS5B01G437100 chr3B 92.466 584 34 5 1038 1615 235458706 235458127 0.000000e+00 826.0
24 TraesCS5B01G437100 chr3B 91.737 593 25 3 1655 2225 235458128 235457538 0.000000e+00 802.0
25 TraesCS5B01G437100 chr3B 92.105 152 3 2 2323 2474 235444707 235444565 7.000000e-49 206.0
26 TraesCS5B01G437100 chr2B 84.735 773 88 15 3305 4070 134342985 134343734 0.000000e+00 747.0
27 TraesCS5B01G437100 chr7D 85.988 678 66 17 3451 4123 574099723 574099070 0.000000e+00 699.0
28 TraesCS5B01G437100 chr1B 89.535 344 29 4 3774 4117 289694812 289695148 3.820000e-116 429.0
29 TraesCS5B01G437100 chr1B 93.478 46 3 0 232 277 427065781 427065736 9.590000e-08 69.4
30 TraesCS5B01G437100 chr4A 79.819 332 54 10 4622 4943 508274030 508274358 4.160000e-56 230.0
31 TraesCS5B01G437100 chr4A 77.644 331 63 8 4622 4943 508494130 508494458 1.960000e-44 191.0
32 TraesCS5B01G437100 chr6B 95.556 45 2 0 228 272 136103249 136103205 7.410000e-09 73.1
33 TraesCS5B01G437100 chr3D 95.349 43 2 0 229 271 294047980 294047938 9.590000e-08 69.4


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 TraesCS5B01G437100 chr5B 610499219 610504552 5333 True 9851.00 9851 100.0000 1 5334 1 chr5B.!!$R2 5333
1 TraesCS5B01G437100 chr5B 610304647 610306149 1502 True 627.50 968 91.9620 4358 5271 2 chr5B.!!$R3 913
2 TraesCS5B01G437100 chr5D 494214923 494220787 5864 True 1569.75 4547 89.9370 7 5192 4 chr5D.!!$R2 5185
3 TraesCS5B01G437100 chr5D 27284145 27284947 802 False 872.00 872 86.3200 3305 4123 1 chr5D.!!$F1 818
4 TraesCS5B01G437100 chr5D 510553684 510554336 652 False 704.00 704 86.1360 3451 4123 1 chr5D.!!$F2 672
5 TraesCS5B01G437100 chr5D 445024322 445024974 652 True 660.00 660 84.9560 3451 4123 1 chr5D.!!$R1 672
6 TraesCS5B01G437100 chr5A 617206057 617211850 5793 True 1217.00 3029 89.4362 7 5175 5 chr5A.!!$R2 5168
7 TraesCS5B01G437100 chr5A 470929930 470930655 725 False 704.00 704 84.2670 3305 4048 1 chr5A.!!$F1 743
8 TraesCS5B01G437100 chr5A 13087535 13088188 653 True 669.00 669 85.2070 3453 4123 1 chr5A.!!$R1 670
9 TraesCS5B01G437100 chr7B 228802386 228803194 808 False 883.00 883 86.4410 3305 4123 1 chr7B.!!$F1 818
10 TraesCS5B01G437100 chr2D 29094896 29095699 803 True 872.00 872 86.3200 3305 4123 1 chr2D.!!$R1 818
11 TraesCS5B01G437100 chr7A 658272487 658273290 803 False 848.00 848 85.8010 3307 4123 1 chr7A.!!$F1 816
12 TraesCS5B01G437100 chr6D 450187803 450188603 800 True 843.00 843 85.7140 3305 4123 1 chr6D.!!$R1 818
13 TraesCS5B01G437100 chr3B 235457538 235458706 1168 True 814.00 826 92.1015 1038 2225 2 chr3B.!!$R2 1187
14 TraesCS5B01G437100 chr2B 134342985 134343734 749 False 747.00 747 84.7350 3305 4070 1 chr2B.!!$F1 765
15 TraesCS5B01G437100 chr7D 574099070 574099723 653 True 699.00 699 85.9880 3451 4123 1 chr7D.!!$R1 672

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
972 1169 0.186386 AACGGAACCCAAATCCACCA 59.814 50.0 0.00 0.0 36.74 4.17 F
2080 2375 0.039256 TTGATTCTTTGCCGCACTGC 60.039 50.0 0.00 0.0 0.00 4.40 F
2583 2887 0.096976 GCATTCACACCGATGTTCCG 59.903 55.0 0.00 0.0 36.72 4.30 F
3590 3917 0.968901 AGTGCGACGTCCTTATCCCA 60.969 55.0 10.58 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2457 2761 1.072331 CCACCTTTAGCGCCTCCATAT 59.928 52.381 2.29 0.0 0.0 1.78 R
3593 3920 0.975556 TTATGACTCCTCCCAGCGCA 60.976 55.000 11.47 0.0 0.0 6.09 R
3977 4326 1.077212 CAGGATCAGCACCCCCTTG 60.077 63.158 0.00 0.0 0.0 3.61 R
5295 6265 0.107945 GCTCTGGATCCGCTTCTTGT 60.108 55.000 7.39 0.0 0.0 3.16 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
71 72 8.447854 TGGTTACCCAAATAATTCCACGGAGT 62.448 42.308 0.00 0.00 39.05 3.85
83 84 0.867753 CACGGAGTATCGCAGCTGAC 60.868 60.000 20.43 6.53 41.61 3.51
114 116 2.099921 TGCTTTTTCGCCAAGTTGCTTA 59.900 40.909 0.00 0.00 0.00 3.09
118 120 3.829886 TTTCGCCAAGTTGCTTATGAG 57.170 42.857 0.00 0.00 0.00 2.90
124 126 4.095483 CGCCAAGTTGCTTATGAGATTTCT 59.905 41.667 0.00 0.00 0.00 2.52
125 127 5.338365 GCCAAGTTGCTTATGAGATTTCTG 58.662 41.667 0.00 0.00 0.00 3.02
131 133 7.041107 AGTTGCTTATGAGATTTCTGTCTCTC 58.959 38.462 5.61 0.00 43.96 3.20
150 152 1.149627 ACAGGCCGCCAAAGTACAA 59.850 52.632 13.15 0.00 0.00 2.41
157 159 1.268845 CCGCCAAAGTACAAACACCAC 60.269 52.381 0.00 0.00 0.00 4.16
172 177 3.585862 ACACCACATTTCTACAGTAGCG 58.414 45.455 2.26 0.00 0.00 4.26
175 180 3.007614 ACCACATTTCTACAGTAGCGGTT 59.992 43.478 2.26 0.00 0.00 4.44
180 185 3.308438 TTCTACAGTAGCGGTTTCACC 57.692 47.619 2.26 0.00 34.05 4.02
196 201 1.771854 TCACCCAACTGCTAGACCAAA 59.228 47.619 0.00 0.00 0.00 3.28
202 207 4.764823 CCCAACTGCTAGACCAAATTGTTA 59.235 41.667 0.00 0.00 0.00 2.41
213 218 9.220767 CTAGACCAAATTGTTAAGCTCTAACTT 57.779 33.333 15.26 4.87 0.00 2.66
245 250 6.864151 ATTAAGTACTACTCCCTCCGTTTT 57.136 37.500 0.00 0.00 0.00 2.43
251 256 7.101700 AGTACTACTCCCTCCGTTTTTAAATG 58.898 38.462 0.00 0.00 0.00 2.32
278 283 8.561738 AAGCCTTTTTAGAGATTTCGATACAA 57.438 30.769 0.00 0.00 0.00 2.41
288 300 6.918569 AGAGATTTCGATACAAAGTACATCCG 59.081 38.462 0.00 0.00 0.00 4.18
289 301 6.802608 AGATTTCGATACAAAGTACATCCGA 58.197 36.000 0.00 0.00 0.00 4.55
307 319 6.878923 ACATCCGAAGTAAAATGAGTGAATCA 59.121 34.615 0.00 0.00 43.70 2.57
310 322 6.934645 TCCGAAGTAAAATGAGTGAATCAACT 59.065 34.615 0.00 0.00 42.53 3.16
312 324 7.237173 CGAAGTAAAATGAGTGAATCAACTCC 58.763 38.462 9.27 0.00 45.03 3.85
372 388 9.841880 CCTGTTAAAATCTCTAAAAAGCCTTAC 57.158 33.333 0.00 0.00 0.00 2.34
553 674 7.985184 ACATACATACATACAACCGATTTGAGT 59.015 33.333 3.99 2.93 38.73 3.41
645 767 1.167851 TTCTGGGCATTTTCTCAGCG 58.832 50.000 0.00 0.00 0.00 5.18
654 776 3.631144 CATTTTCTCAGCGAAACAAGCA 58.369 40.909 0.00 0.00 41.13 3.91
708 830 4.160329 TGTTGTCCCTAGAACAGTGATCT 58.840 43.478 8.12 8.12 34.21 2.75
758 929 5.357314 GCTCCTATTAAACAAAAGGGGAGAC 59.643 44.000 9.48 0.00 40.86 3.36
805 982 2.030628 GCTCTTCGATCTGGTAGGCTAC 60.031 54.545 16.40 16.40 0.00 3.58
808 985 2.563261 TCGATCTGGTAGGCTACGAT 57.437 50.000 17.91 15.17 0.00 3.73
819 1002 9.305555 TCTGGTAGGCTACGATTAGTTAATTAT 57.694 33.333 17.91 0.00 0.00 1.28
912 1095 6.936279 TGTTCTTATCCTGGTAGAGACAAAG 58.064 40.000 0.00 0.00 0.00 2.77
921 1104 7.060421 TCCTGGTAGAGACAAAGAAAACAAAT 58.940 34.615 0.00 0.00 0.00 2.32
922 1105 7.559897 TCCTGGTAGAGACAAAGAAAACAAATT 59.440 33.333 0.00 0.00 0.00 1.82
923 1106 8.846211 CCTGGTAGAGACAAAGAAAACAAATTA 58.154 33.333 0.00 0.00 0.00 1.40
972 1169 0.186386 AACGGAACCCAAATCCACCA 59.814 50.000 0.00 0.00 36.74 4.17
1037 1234 5.046231 ACCTGAAACTCCTCCATAGTCTTTC 60.046 44.000 0.00 0.00 0.00 2.62
1115 1316 6.675987 ACTCCTACTCGGTAATATAAAAGCG 58.324 40.000 3.62 3.62 37.92 4.68
1116 1317 6.017400 TCCTACTCGGTAATATAAAAGCGG 57.983 41.667 8.75 3.98 37.22 5.52
1117 1318 5.047802 TCCTACTCGGTAATATAAAAGCGGG 60.048 44.000 7.40 7.40 42.55 6.13
1163 1364 4.201763 GCAGAGTTTGATCGTTTCATCTCC 60.202 45.833 13.83 0.00 36.86 3.71
1181 1382 3.084786 CTCCTGTGATTTGGTTTCCTCC 58.915 50.000 0.00 0.00 0.00 4.30
1195 1398 4.201920 GGTTTCCTCCGATTTTACTCATGC 60.202 45.833 0.00 0.00 0.00 4.06
1383 1587 0.549950 AAGGTGATGATCCCAGCCTG 59.450 55.000 9.79 0.00 32.88 4.85
1429 1642 2.022195 TGAATCTAGACGGCTACGCTT 58.978 47.619 0.00 0.00 46.04 4.68
1521 1737 1.192146 ACTGTCACATAGGCCCGTGT 61.192 55.000 15.11 10.53 34.66 4.49
1589 1805 4.142469 GGATTATTTTTCACCTGGACCGTG 60.142 45.833 0.00 0.00 0.00 4.94
1591 1807 2.649531 TTTTTCACCTGGACCGTGAT 57.350 45.000 0.00 0.00 39.86 3.06
1595 1811 2.649531 TCACCTGGACCGTGATTTTT 57.350 45.000 0.00 0.00 35.35 1.94
1652 1868 8.593492 TTATGGATTTGATATCTTCTCGTGTG 57.407 34.615 3.98 0.00 0.00 3.82
1891 2163 2.233271 CAGGTTGAGTGCACAATTCCT 58.767 47.619 21.04 17.22 32.36 3.36
2070 2365 6.041979 ACCAACCATTAAGCACTTGATTCTTT 59.958 34.615 0.00 0.00 0.00 2.52
2080 2375 0.039256 TTGATTCTTTGCCGCACTGC 60.039 50.000 0.00 0.00 0.00 4.40
2112 2407 6.455360 TGAAATGGTCCTTCAGCATAAATC 57.545 37.500 0.00 0.00 42.70 2.17
2148 2443 6.482641 CAGGAATCTGTCAGATAGTTGAATGG 59.517 42.308 15.77 0.00 32.89 3.16
2208 2503 4.560128 TGTCTACTTGCAGTAAAGCAGAG 58.440 43.478 0.00 0.00 46.54 3.35
2211 2506 2.787994 ACTTGCAGTAAAGCAGAGCAT 58.212 42.857 0.00 0.00 46.54 3.79
2356 2659 9.703892 ATCTATGATCATAGTAAGTTCTTGCAC 57.296 33.333 32.15 0.00 41.12 4.57
2357 2660 8.918116 TCTATGATCATAGTAAGTTCTTGCACT 58.082 33.333 32.15 0.90 41.12 4.40
2358 2661 7.783090 ATGATCATAGTAAGTTCTTGCACTG 57.217 36.000 6.36 1.32 0.00 3.66
2359 2662 6.701340 TGATCATAGTAAGTTCTTGCACTGT 58.299 36.000 0.00 0.00 0.00 3.55
2360 2663 6.813649 TGATCATAGTAAGTTCTTGCACTGTC 59.186 38.462 0.00 2.84 0.00 3.51
2361 2664 6.096673 TCATAGTAAGTTCTTGCACTGTCA 57.903 37.500 0.00 0.00 0.00 3.58
2382 2685 5.111989 TCAGCACTGACAAGCTATGATAAC 58.888 41.667 0.00 0.00 39.50 1.89
2457 2761 0.751277 CAGCCGTGGCCAATATTCCA 60.751 55.000 7.24 0.00 43.17 3.53
2511 2815 2.091111 TCCTGGAGACCTGAGCATATCA 60.091 50.000 0.00 0.00 36.21 2.15
2568 2872 9.158233 CAGAAAATTCATGACTTAATTGGCATT 57.842 29.630 0.00 0.00 0.00 3.56
2583 2887 0.096976 GCATTCACACCGATGTTCCG 59.903 55.000 0.00 0.00 36.72 4.30
2592 2896 1.519455 CGATGTTCCGGCTCCTGAC 60.519 63.158 0.00 0.00 0.00 3.51
2623 2927 4.856487 CCAACGCACAGGTTATTTATTGTG 59.144 41.667 0.00 0.00 42.80 3.33
2667 2971 7.840931 TCTCTGCAGAGTATTGTGAGAATTAA 58.159 34.615 36.32 13.94 42.60 1.40
2668 2972 7.761704 TCTCTGCAGAGTATTGTGAGAATTAAC 59.238 37.037 36.32 0.00 42.60 2.01
2685 2989 8.267620 AGAATTAACCATCTGTATCCTGATGA 57.732 34.615 6.72 0.00 45.11 2.92
2687 2991 7.623999 ATTAACCATCTGTATCCTGATGAGT 57.376 36.000 6.72 1.50 45.11 3.41
2703 3007 6.805271 CCTGATGAGTATTCTTTTGCTTGTTG 59.195 38.462 0.00 0.00 0.00 3.33
2704 3008 7.275888 TGATGAGTATTCTTTTGCTTGTTGT 57.724 32.000 0.00 0.00 0.00 3.32
2729 3038 3.640029 GGATTCAGACAATGGCATGGATT 59.360 43.478 9.33 0.00 0.00 3.01
2756 3065 4.974645 TGAGTACTCAAAGTTCCATGGT 57.025 40.909 23.24 0.00 36.53 3.55
2821 3130 7.862274 TCCATCCTGAAACTCTATCATGTAT 57.138 36.000 0.00 0.00 0.00 2.29
2822 3131 8.956446 TCCATCCTGAAACTCTATCATGTATA 57.044 34.615 0.00 0.00 0.00 1.47
2876 3185 3.618351 AGTGGAAGATGCAGGATTTGAG 58.382 45.455 0.00 0.00 0.00 3.02
2880 3189 3.760684 GGAAGATGCAGGATTTGAGTGTT 59.239 43.478 0.00 0.00 0.00 3.32
2897 3206 5.528690 TGAGTGTTGAGAGAAATCTGGTTTG 59.471 40.000 0.00 0.00 0.00 2.93
2912 3221 6.049955 TCTGGTTTGTAGTTATCCCTCTTG 57.950 41.667 0.00 0.00 0.00 3.02
2913 3222 4.585879 TGGTTTGTAGTTATCCCTCTTGC 58.414 43.478 0.00 0.00 0.00 4.01
3054 3363 2.355009 GCAGGCCAGCGTTTTGTG 60.355 61.111 3.62 0.00 0.00 3.33
3174 3486 6.989169 AGTCATGAAGCCTCAATCTATTACAC 59.011 38.462 0.00 0.00 34.49 2.90
3175 3487 5.985530 TCATGAAGCCTCAATCTATTACACG 59.014 40.000 0.00 0.00 34.49 4.49
3233 3546 2.616960 GTCAGTGGATCGCACAATACA 58.383 47.619 14.31 0.00 0.00 2.29
3242 3555 2.993545 TCGCACAATACACACTTTTGC 58.006 42.857 0.00 0.00 0.00 3.68
3336 3659 3.942829 TCTTCACCTACATTTGCAGAGG 58.057 45.455 0.00 0.00 35.05 3.69
3584 3911 1.081376 CGAAGAGTGCGACGTCCTT 60.081 57.895 10.58 6.85 0.00 3.36
3590 3917 0.968901 AGTGCGACGTCCTTATCCCA 60.969 55.000 10.58 0.00 0.00 4.37
3593 3920 2.017559 GCGACGTCCTTATCCCAGCT 62.018 60.000 10.58 0.00 0.00 4.24
3621 3948 6.442541 TGGGAGGAGTCATAAACAAGTAAA 57.557 37.500 0.00 0.00 0.00 2.01
3629 3956 8.504815 GGAGTCATAAACAAGTAAACTTCTTCC 58.495 37.037 0.00 0.00 33.11 3.46
3632 3962 9.052759 GTCATAAACAAGTAAACTTCTTCCTCA 57.947 33.333 0.00 0.00 33.11 3.86
3636 3969 6.441088 ACAAGTAAACTTCTTCCTCATCCT 57.559 37.500 0.00 0.00 33.11 3.24
3654 3989 2.786445 TCCTAGCTCACCTCATCCTACT 59.214 50.000 0.00 0.00 0.00 2.57
3672 4007 7.291411 TCCTACTTTCTATCAGATTACTGCC 57.709 40.000 0.00 0.00 43.17 4.85
3693 4032 6.136857 TGCCCTGAGTTCAGTTATAGTATCT 58.863 40.000 8.23 0.00 42.27 1.98
3697 4036 7.287927 CCCTGAGTTCAGTTATAGTATCTTCCA 59.712 40.741 8.23 0.00 42.27 3.53
3699 4038 8.824756 TGAGTTCAGTTATAGTATCTTCCAGT 57.175 34.615 0.00 0.00 0.00 4.00
3700 4039 9.916360 TGAGTTCAGTTATAGTATCTTCCAGTA 57.084 33.333 0.00 0.00 0.00 2.74
3711 4052 7.923414 AGTATCTTCCAGTATGTTGTTTTCC 57.077 36.000 0.00 0.00 0.00 3.13
3720 4063 8.626526 TCCAGTATGTTGTTTTCCTTTTTCTAC 58.373 33.333 0.00 0.00 0.00 2.59
3729 4072 9.801873 TTGTTTTCCTTTTTCTACATCTGAAAG 57.198 29.630 0.00 0.00 35.27 2.62
3772 4116 9.241919 ACAACATATTGTCTTGACCATGATTTA 57.758 29.630 0.00 0.00 46.46 1.40
3780 4124 8.868522 TGTCTTGACCATGATTTATTCTTCTT 57.131 30.769 0.00 0.00 0.00 2.52
3782 4126 8.401709 GTCTTGACCATGATTTATTCTTCTTCC 58.598 37.037 0.00 0.00 0.00 3.46
3794 4138 1.089920 CTTCTTCCAGGGACAATGCG 58.910 55.000 0.00 0.00 0.00 4.73
3799 4143 1.825191 CCAGGGACAATGCGGATGG 60.825 63.158 0.00 0.00 0.00 3.51
3827 4171 1.599542 GCAAAGTACATCATCGAGGCC 59.400 52.381 0.00 0.00 0.00 5.19
3908 4252 2.869233 ACAAAGCTCGCATTTGTTGT 57.131 40.000 11.16 0.00 46.04 3.32
3919 4268 6.452872 GCTCGCATTTGTTGTCATAATTCAAC 60.453 38.462 0.00 0.00 42.62 3.18
3977 4326 0.955428 TGGTGCAGATTCTGGCGAAC 60.955 55.000 15.28 0.00 31.21 3.95
4307 4660 0.686441 ATGGGATCCCGTCGAAGTCA 60.686 55.000 26.03 5.13 39.42 3.41
4342 4696 1.003866 GTTCAATAATCGAGCCCGTGC 60.004 52.381 0.00 0.00 37.05 5.34
4395 4749 1.805945 GACCGGCAGAACAGTAGCG 60.806 63.158 0.00 0.00 0.00 4.26
4420 4774 3.326880 ACCACCTTCTTCTTGTAATCCGT 59.673 43.478 0.00 0.00 0.00 4.69
5010 5655 1.514553 GTACTGGTACCGCCTGACC 59.485 63.158 7.57 0.00 39.25 4.02
5011 5656 1.077086 TACTGGTACCGCCTGACCA 59.923 57.895 7.57 0.00 43.55 4.02
5013 5658 3.642778 CTGGTACCGCCTGACCACG 62.643 68.421 7.57 0.00 40.87 4.94
5015 5660 2.342650 GGTACCGCCTGACCACGTA 61.343 63.158 0.00 0.00 35.65 3.57
5018 5663 4.814294 CCGCCTGACCACGTAGCC 62.814 72.222 0.00 0.00 0.00 3.93
5185 6155 3.704512 CAGCTACAGTAGTGATGAGCAG 58.295 50.000 19.08 11.60 32.95 4.24
5200 6170 0.743688 AGCAGGTAGAGATCAGTGCG 59.256 55.000 0.00 0.00 36.04 5.34
5227 6197 1.132453 CTAGATGGACGACAACGCAGA 59.868 52.381 0.00 0.00 43.96 4.26
5229 6199 1.066858 AGATGGACGACAACGCAGAAT 60.067 47.619 0.00 0.00 43.96 2.40
5234 6204 2.477375 GGACGACAACGCAGAATAAACA 59.523 45.455 0.00 0.00 43.96 2.83
5235 6205 3.059461 GGACGACAACGCAGAATAAACAA 60.059 43.478 0.00 0.00 43.96 2.83
5236 6206 4.520078 GACGACAACGCAGAATAAACAAA 58.480 39.130 0.00 0.00 43.96 2.83
5237 6207 4.276460 ACGACAACGCAGAATAAACAAAC 58.724 39.130 0.00 0.00 43.96 2.93
5238 6208 4.201832 ACGACAACGCAGAATAAACAAACA 60.202 37.500 0.00 0.00 43.96 2.83
5239 6209 4.144051 CGACAACGCAGAATAAACAAACAC 59.856 41.667 0.00 0.00 0.00 3.32
5240 6210 5.243426 ACAACGCAGAATAAACAAACACT 57.757 34.783 0.00 0.00 0.00 3.55
5241 6211 5.034152 ACAACGCAGAATAAACAAACACTG 58.966 37.500 0.00 0.00 0.00 3.66
5247 6217 6.291060 CGCAGAATAAACAAACACTGAAACAC 60.291 38.462 0.00 0.00 0.00 3.32
5271 6241 2.589720 TGGTGACTCGGAAAGTAGTGA 58.410 47.619 0.00 0.00 38.74 3.41
5272 6242 2.295349 TGGTGACTCGGAAAGTAGTGAC 59.705 50.000 0.00 0.00 38.74 3.67
5273 6243 2.582687 GTGACTCGGAAAGTAGTGACG 58.417 52.381 0.00 0.00 38.74 4.35
5274 6244 1.538512 TGACTCGGAAAGTAGTGACGG 59.461 52.381 0.00 0.00 38.74 4.79
5275 6245 1.808945 GACTCGGAAAGTAGTGACGGA 59.191 52.381 0.00 0.00 38.74 4.69
5276 6246 1.811359 ACTCGGAAAGTAGTGACGGAG 59.189 52.381 0.00 0.00 36.07 4.63
5277 6247 0.524862 TCGGAAAGTAGTGACGGAGC 59.475 55.000 0.00 0.00 0.00 4.70
5278 6248 0.242825 CGGAAAGTAGTGACGGAGCA 59.757 55.000 0.00 0.00 0.00 4.26
5279 6249 1.732732 CGGAAAGTAGTGACGGAGCAG 60.733 57.143 0.00 0.00 0.00 4.24
5280 6250 1.272769 GGAAAGTAGTGACGGAGCAGT 59.727 52.381 0.00 0.00 0.00 4.40
5281 6251 2.597520 GAAAGTAGTGACGGAGCAGTC 58.402 52.381 0.00 0.00 41.30 3.51
5288 6258 2.542020 TGACGGAGCAGTCAATTTCA 57.458 45.000 7.13 0.00 46.81 2.69
5289 6259 2.844946 TGACGGAGCAGTCAATTTCAA 58.155 42.857 7.13 0.00 46.81 2.69
5290 6260 3.210227 TGACGGAGCAGTCAATTTCAAA 58.790 40.909 7.13 0.00 46.81 2.69
5291 6261 3.250762 TGACGGAGCAGTCAATTTCAAAG 59.749 43.478 7.13 0.00 46.81 2.77
5292 6262 2.030805 ACGGAGCAGTCAATTTCAAAGC 60.031 45.455 0.00 0.00 0.00 3.51
5293 6263 2.589014 GGAGCAGTCAATTTCAAAGCG 58.411 47.619 0.00 0.00 0.00 4.68
5294 6264 1.981533 GAGCAGTCAATTTCAAAGCGC 59.018 47.619 0.00 0.00 0.00 5.92
5295 6265 1.337703 AGCAGTCAATTTCAAAGCGCA 59.662 42.857 11.47 0.00 0.00 6.09
5296 6266 1.453148 GCAGTCAATTTCAAAGCGCAC 59.547 47.619 11.47 0.00 0.00 5.34
5297 6267 2.730069 CAGTCAATTTCAAAGCGCACA 58.270 42.857 11.47 0.00 0.00 4.57
5298 6268 3.114809 CAGTCAATTTCAAAGCGCACAA 58.885 40.909 11.47 0.00 0.00 3.33
5299 6269 3.180980 CAGTCAATTTCAAAGCGCACAAG 59.819 43.478 11.47 0.00 0.00 3.16
5300 6270 3.066621 AGTCAATTTCAAAGCGCACAAGA 59.933 39.130 11.47 0.00 0.00 3.02
5301 6271 3.796178 GTCAATTTCAAAGCGCACAAGAA 59.204 39.130 11.47 5.26 0.00 2.52
5302 6272 4.043750 TCAATTTCAAAGCGCACAAGAAG 58.956 39.130 11.47 0.00 0.00 2.85
5303 6273 1.838913 TTTCAAAGCGCACAAGAAGC 58.161 45.000 11.47 0.00 0.00 3.86
5310 6280 4.301505 GCACAAGAAGCGGATCCA 57.698 55.556 13.41 0.00 0.00 3.41
5311 6281 2.093216 GCACAAGAAGCGGATCCAG 58.907 57.895 13.41 5.88 0.00 3.86
5312 6282 0.391661 GCACAAGAAGCGGATCCAGA 60.392 55.000 13.41 0.00 0.00 3.86
5313 6283 1.649664 CACAAGAAGCGGATCCAGAG 58.350 55.000 13.41 0.00 0.00 3.35
5314 6284 0.107945 ACAAGAAGCGGATCCAGAGC 60.108 55.000 13.41 7.32 0.00 4.09
5315 6285 1.142748 AAGAAGCGGATCCAGAGCG 59.857 57.895 13.41 0.00 35.78 5.03
5316 6286 2.914777 AAGAAGCGGATCCAGAGCGC 62.915 60.000 13.41 8.91 35.78 5.92
5317 6287 4.537433 AAGCGGATCCAGAGCGCC 62.537 66.667 13.41 0.00 35.78 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 4.451096 CGATACTCCGTGGAATTATTTGGG 59.549 45.833 0.00 0.00 0.00 4.12
124 126 3.695606 GGCGGCCTGTGAGAGACA 61.696 66.667 12.87 0.00 0.00 3.41
125 127 2.731691 TTTGGCGGCCTGTGAGAGAC 62.732 60.000 21.46 0.00 0.00 3.36
131 133 1.169661 TTGTACTTTGGCGGCCTGTG 61.170 55.000 21.46 11.86 0.00 3.66
138 140 1.402259 TGTGGTGTTTGTACTTTGGCG 59.598 47.619 0.00 0.00 0.00 5.69
150 152 3.994392 CGCTACTGTAGAAATGTGGTGTT 59.006 43.478 18.64 0.00 0.00 3.32
157 159 5.204673 GTGAAACCGCTACTGTAGAAATG 57.795 43.478 18.64 5.58 0.00 2.32
175 180 1.429930 TGGTCTAGCAGTTGGGTGAA 58.570 50.000 0.00 0.00 0.00 3.18
180 185 4.853924 AACAATTTGGTCTAGCAGTTGG 57.146 40.909 0.78 0.00 0.00 3.77
196 201 9.720769 TTACAGCTAAAGTTAGAGCTTAACAAT 57.279 29.630 16.14 9.63 46.99 2.71
202 207 9.945904 ACTTAATTACAGCTAAAGTTAGAGCTT 57.054 29.630 9.04 5.15 46.99 3.74
213 218 9.129532 GAGGGAGTAGTACTTAATTACAGCTAA 57.870 37.037 0.00 0.00 0.00 3.09
251 256 9.095065 TGTATCGAAATCTCTAAAAAGGCTTAC 57.905 33.333 0.00 0.00 0.00 2.34
271 276 7.745022 TTTACTTCGGATGTACTTTGTATCG 57.255 36.000 3.47 0.00 0.00 2.92
278 283 7.383687 TCACTCATTTTACTTCGGATGTACTT 58.616 34.615 3.47 0.00 0.00 2.24
286 298 7.133891 AGTTGATTCACTCATTTTACTTCGG 57.866 36.000 0.00 0.00 32.72 4.30
288 300 7.391833 AGGGAGTTGATTCACTCATTTTACTTC 59.608 37.037 14.20 1.36 44.53 3.01
289 301 7.234355 AGGGAGTTGATTCACTCATTTTACTT 58.766 34.615 14.20 0.00 44.53 2.24
339 351 8.767478 TTTTAGAGATTTTAACAGGGACTACG 57.233 34.615 0.00 0.00 36.02 3.51
372 388 8.812147 TGTCTGTCAAACAGTACTACTAAATG 57.188 34.615 6.96 0.00 46.03 2.32
381 397 7.170828 TCACAATACATGTCTGTCAAACAGTAC 59.829 37.037 0.00 5.25 46.03 2.73
382 398 7.213678 TCACAATACATGTCTGTCAAACAGTA 58.786 34.615 0.00 0.00 46.03 2.74
553 674 4.635765 GCATGTGGCAACTTCAGATTACTA 59.364 41.667 0.00 0.00 43.97 1.82
579 700 1.074405 TGTTCAAGGAAGCCTCTGCAT 59.926 47.619 0.00 0.00 41.13 3.96
580 701 0.473755 TGTTCAAGGAAGCCTCTGCA 59.526 50.000 0.00 0.00 41.13 4.41
581 702 0.877743 GTGTTCAAGGAAGCCTCTGC 59.122 55.000 0.00 0.00 30.89 4.26
582 703 2.421619 GAGTGTTCAAGGAAGCCTCTG 58.578 52.381 0.00 0.00 30.89 3.35
583 704 1.349357 GGAGTGTTCAAGGAAGCCTCT 59.651 52.381 0.00 0.00 30.89 3.69
584 705 1.349357 AGGAGTGTTCAAGGAAGCCTC 59.651 52.381 0.00 0.00 30.89 4.70
645 767 0.040958 CCGACAGCTGTGCTTGTTTC 60.041 55.000 27.27 5.92 36.40 2.78
741 863 3.479489 GACCGTCTCCCCTTTTGTTTAA 58.521 45.455 0.00 0.00 0.00 1.52
758 929 1.068588 TCTATGCCAAGGAATCGACCG 59.931 52.381 0.00 0.00 34.73 4.79
791 962 5.708877 AACTAATCGTAGCCTACCAGATC 57.291 43.478 0.00 0.00 0.00 2.75
819 1002 3.780294 AGCCCTGTCTGTAATCAATACCA 59.220 43.478 0.00 0.00 33.27 3.25
939 1136 1.604604 TCCGTTCAAAAAGCAGAGGG 58.395 50.000 0.00 0.00 0.00 4.30
972 1169 2.654863 CACACTGAAACTGAACCCCTT 58.345 47.619 0.00 0.00 0.00 3.95
983 1180 6.589907 CGTATGCATATATAGGCACACTGAAA 59.410 38.462 23.65 2.33 46.26 2.69
1054 1251 1.241990 TTAGTGGTGAGAGCGAGCGT 61.242 55.000 0.00 0.00 0.00 5.07
1055 1252 0.798771 GTTAGTGGTGAGAGCGAGCG 60.799 60.000 0.00 0.00 0.00 5.03
1060 1257 2.329379 CGAAGTGTTAGTGGTGAGAGC 58.671 52.381 0.00 0.00 0.00 4.09
1062 1259 1.000506 GGCGAAGTGTTAGTGGTGAGA 59.999 52.381 0.00 0.00 0.00 3.27
1115 1316 4.816925 CGAGAAACCAAAGGATAATCTCCC 59.183 45.833 0.00 0.00 46.27 4.30
1116 1317 4.273724 GCGAGAAACCAAAGGATAATCTCC 59.726 45.833 0.00 0.00 45.33 3.71
1117 1318 4.025647 CGCGAGAAACCAAAGGATAATCTC 60.026 45.833 0.00 0.00 0.00 2.75
1134 1335 0.798389 CGATCAAACTCTGCGCGAGA 60.798 55.000 27.66 18.83 42.62 4.04
1163 1364 2.778299 TCGGAGGAAACCAAATCACAG 58.222 47.619 0.00 0.00 0.00 3.66
1181 1382 2.032550 CCCAGCAGCATGAGTAAAATCG 59.967 50.000 0.00 0.00 39.69 3.34
1195 1398 1.227497 GGATCGAGAAGCCCAGCAG 60.227 63.158 0.00 0.00 0.00 4.24
1318 1522 1.134175 CTCTTCTCGAGCTTGGAGTCC 59.866 57.143 7.81 0.73 31.99 3.85
1379 1583 1.369321 CGAAGGATAGGAGGCAGGC 59.631 63.158 0.00 0.00 0.00 4.85
1383 1587 0.249657 CACAGCGAAGGATAGGAGGC 60.250 60.000 0.00 0.00 0.00 4.70
1429 1642 3.428452 CCCTATAGAACGAACGAACAGCA 60.428 47.826 0.00 0.00 0.00 4.41
1492 1705 5.105752 GCCTATGTGACAGTTCTCAGTAAG 58.894 45.833 0.00 0.00 0.00 2.34
1521 1737 1.075536 GGCAAGGAGGGAGAGGAAAAA 59.924 52.381 0.00 0.00 0.00 1.94
1595 1811 9.280174 CCAGTAATAACCTAACTGAAAACAGAA 57.720 33.333 0.00 0.00 42.59 3.02
1597 1813 8.842358 TCCAGTAATAACCTAACTGAAAACAG 57.158 34.615 3.37 0.00 42.59 3.16
1598 1814 9.802039 AATCCAGTAATAACCTAACTGAAAACA 57.198 29.630 3.37 0.00 42.59 2.83
1627 1843 7.171508 GCACACGAGAAGATATCAAATCCATAA 59.828 37.037 5.32 0.00 0.00 1.90
1629 1845 5.468072 GCACACGAGAAGATATCAAATCCAT 59.532 40.000 5.32 0.00 0.00 3.41
1630 1846 4.811024 GCACACGAGAAGATATCAAATCCA 59.189 41.667 5.32 0.00 0.00 3.41
1639 1855 4.700692 AGTGAAGTAGCACACGAGAAGATA 59.299 41.667 0.00 0.00 41.19 1.98
1642 1858 3.290308 AGTGAAGTAGCACACGAGAAG 57.710 47.619 0.00 0.00 41.19 2.85
1669 1894 2.449464 TCAAGTGATTGCTCAATGGGG 58.551 47.619 0.00 0.00 31.85 4.96
1670 1895 4.730949 AATCAAGTGATTGCTCAATGGG 57.269 40.909 5.74 0.00 42.66 4.00
1671 1896 5.475719 ACAAATCAAGTGATTGCTCAATGG 58.524 37.500 7.29 0.00 43.41 3.16
1673 1898 6.585695 AGACAAATCAAGTGATTGCTCAAT 57.414 33.333 7.29 0.00 43.41 2.57
1891 2163 6.044754 AGGATGCTAATGTCCCATCATCTTTA 59.955 38.462 0.00 0.00 37.64 1.85
2080 2375 1.644786 GGACCATTTCAAGTCGGCGG 61.645 60.000 7.21 0.00 33.66 6.13
2112 2407 2.697751 ACAGATTCCTGAAGGAGATCGG 59.302 50.000 14.17 14.17 46.36 4.18
2148 2443 3.555966 AGGTATGGGCTGAACAATAAGC 58.444 45.455 0.00 0.00 38.76 3.09
2208 2503 8.405531 TGTGACTAATTTCCAAAATAGCTATGC 58.594 33.333 7.09 0.00 0.00 3.14
2211 2506 9.905713 AGATGTGACTAATTTCCAAAATAGCTA 57.094 29.630 0.00 0.00 0.00 3.32
2358 2661 8.587071 ATGTTATCATAGCTTGTCAGTGCTGAC 61.587 40.741 21.59 21.59 44.58 3.51
2359 2662 3.900966 ATCATAGCTTGTCAGTGCTGA 57.099 42.857 11.26 0.00 40.08 4.26
2360 2663 4.872124 TGTTATCATAGCTTGTCAGTGCTG 59.128 41.667 11.26 0.00 40.08 4.41
2361 2664 5.089970 TGTTATCATAGCTTGTCAGTGCT 57.910 39.130 0.00 7.43 42.67 4.40
2457 2761 1.072331 CCACCTTTAGCGCCTCCATAT 59.928 52.381 2.29 0.00 0.00 1.78
2511 2815 2.776913 GGTAAGCCGCTCGAGCTCT 61.777 63.158 32.88 25.49 40.49 4.09
2583 2887 2.439156 GTGCCCATGTCAGGAGCC 60.439 66.667 0.00 0.00 0.00 4.70
2589 2893 2.983030 GCGTTGGTGCCCATGTCA 60.983 61.111 0.00 0.00 31.53 3.58
2592 2896 3.271706 CTGTGCGTTGGTGCCCATG 62.272 63.158 0.00 0.00 31.53 3.66
2623 2927 9.467258 TGCAGAGAAATAATAAATATGCAAAGC 57.533 29.630 0.00 0.00 38.13 3.51
2654 2958 8.497745 AGGATACAGATGGTTAATTCTCACAAT 58.502 33.333 0.00 0.00 41.41 2.71
2678 2982 6.506500 ACAAGCAAAAGAATACTCATCAGG 57.493 37.500 0.00 0.00 0.00 3.86
2685 2989 7.759489 TCCATACAACAAGCAAAAGAATACT 57.241 32.000 0.00 0.00 0.00 2.12
2687 2991 8.801299 TGAATCCATACAACAAGCAAAAGAATA 58.199 29.630 0.00 0.00 0.00 1.75
2703 3007 4.022589 CCATGCCATTGTCTGAATCCATAC 60.023 45.833 0.00 0.00 0.00 2.39
2704 3008 4.141205 TCCATGCCATTGTCTGAATCCATA 60.141 41.667 0.00 0.00 0.00 2.74
2729 3038 4.838423 TGGAACTTTGAGTACTCATCCAGA 59.162 41.667 29.71 16.27 39.05 3.86
2846 3155 6.899089 TCCTGCATCTTCCACTTTTCATATA 58.101 36.000 0.00 0.00 0.00 0.86
2848 3157 5.178096 TCCTGCATCTTCCACTTTTCATA 57.822 39.130 0.00 0.00 0.00 2.15
2876 3185 5.757850 ACAAACCAGATTTCTCTCAACAC 57.242 39.130 0.00 0.00 0.00 3.32
2880 3189 8.041323 GGATAACTACAAACCAGATTTCTCTCA 58.959 37.037 0.00 0.00 0.00 3.27
2897 3206 4.423625 ACATGGCAAGAGGGATAACTAC 57.576 45.455 0.00 0.00 0.00 2.73
3194 3506 5.069516 ACTGACGGTCACTTTTTCCTAGTAA 59.930 40.000 6.76 0.00 0.00 2.24
3201 3513 2.557317 TCCACTGACGGTCACTTTTTC 58.443 47.619 6.76 0.00 0.00 2.29
3233 3546 6.458232 TGTAACCATAAAGTGCAAAAGTGT 57.542 33.333 0.00 0.00 0.00 3.55
3242 3555 6.894339 ACTCCCTTTTGTAACCATAAAGTG 57.106 37.500 0.00 0.00 0.00 3.16
3336 3659 3.132824 AGGCAAGCCCAATAATTGCTTAC 59.867 43.478 7.62 0.00 46.61 2.34
3593 3920 0.975556 TTATGACTCCTCCCAGCGCA 60.976 55.000 11.47 0.00 0.00 6.09
3621 3948 3.704061 GTGAGCTAGGATGAGGAAGAAGT 59.296 47.826 0.00 0.00 0.00 3.01
3629 3956 2.562298 GGATGAGGTGAGCTAGGATGAG 59.438 54.545 0.00 0.00 0.00 2.90
3632 3962 3.401002 AGTAGGATGAGGTGAGCTAGGAT 59.599 47.826 0.00 0.00 0.00 3.24
3636 3969 4.873010 AGAAAGTAGGATGAGGTGAGCTA 58.127 43.478 0.00 0.00 0.00 3.32
3654 3989 5.663106 ACTCAGGGCAGTAATCTGATAGAAA 59.337 40.000 0.00 0.00 43.76 2.52
3672 4007 8.356657 CTGGAAGATACTATAACTGAACTCAGG 58.643 40.741 11.31 0.00 42.35 3.86
3693 4032 8.073467 AGAAAAAGGAAAACAACATACTGGAA 57.927 30.769 0.00 0.00 0.00 3.53
3700 4039 8.912988 TCAGATGTAGAAAAAGGAAAACAACAT 58.087 29.630 0.00 0.00 0.00 2.71
3705 4044 7.920682 TGCTTTCAGATGTAGAAAAAGGAAAAC 59.079 33.333 0.00 0.00 34.84 2.43
3708 4049 7.765695 ATGCTTTCAGATGTAGAAAAAGGAA 57.234 32.000 0.00 0.00 34.84 3.36
3709 4050 7.765695 AATGCTTTCAGATGTAGAAAAAGGA 57.234 32.000 0.00 0.00 34.84 3.36
3710 4051 8.822652 AAAATGCTTTCAGATGTAGAAAAAGG 57.177 30.769 0.00 0.00 34.84 3.11
3753 4096 9.471702 AGAAGAATAAATCATGGTCAAGACAAT 57.528 29.630 2.29 0.00 0.00 2.71
3754 4097 8.868522 AGAAGAATAAATCATGGTCAAGACAA 57.131 30.769 2.29 0.00 0.00 3.18
3755 4098 8.868522 AAGAAGAATAAATCATGGTCAAGACA 57.131 30.769 2.29 0.00 0.00 3.41
3756 4099 8.401709 GGAAGAAGAATAAATCATGGTCAAGAC 58.598 37.037 0.00 0.00 0.00 3.01
3772 4116 3.359950 GCATTGTCCCTGGAAGAAGAAT 58.640 45.455 0.00 0.00 34.07 2.40
3780 4124 1.224315 CATCCGCATTGTCCCTGGA 59.776 57.895 0.00 0.00 0.00 3.86
3782 4126 2.484062 GCCATCCGCATTGTCCCTG 61.484 63.158 0.00 0.00 37.47 4.45
3794 4138 3.193267 TGTACTTTGCTTTGATGCCATCC 59.807 43.478 1.49 0.00 0.00 3.51
3799 4143 4.731961 CGATGATGTACTTTGCTTTGATGC 59.268 41.667 0.00 0.00 0.00 3.91
3908 4252 6.424812 CAGTCAGTGTGTGAGTTGAATTATGA 59.575 38.462 0.00 0.00 36.62 2.15
3977 4326 1.077212 CAGGATCAGCACCCCCTTG 60.077 63.158 0.00 0.00 0.00 3.61
4283 4635 2.134287 CGACGGGATCCCATGGAGT 61.134 63.158 30.42 19.13 34.05 3.85
4307 4660 9.019764 CGATTATTGAACTTTTTGTTGAGTTGT 57.980 29.630 0.00 0.00 39.30 3.32
4342 4696 4.023963 TCGGAGCTTATGTATGAGAGAACG 60.024 45.833 0.00 0.00 0.00 3.95
4395 4749 2.561478 TACAAGAAGAAGGTGGTGCC 57.439 50.000 0.00 0.00 37.58 5.01
4420 4774 1.811558 GCTGTGTTTCACTCTCAGCCA 60.812 52.381 0.00 0.00 43.55 4.75
4499 4860 4.227512 TGCCATGCGATGCTAATAAAAG 57.772 40.909 0.00 0.00 0.00 2.27
4528 4892 1.270550 CAGTTCATGACCTTGTTGGCC 59.729 52.381 0.00 0.00 40.22 5.36
4995 5640 2.264794 GTGGTCAGGCGGTACCAG 59.735 66.667 13.54 6.04 46.19 4.00
4999 5644 2.703798 GCTACGTGGTCAGGCGGTA 61.704 63.158 0.00 0.00 0.00 4.02
5000 5645 4.065281 GCTACGTGGTCAGGCGGT 62.065 66.667 0.00 0.00 0.00 5.68
5005 5650 4.814294 GCCCGGCTACGTGGTCAG 62.814 72.222 3.90 0.00 38.78 3.51
5152 6122 4.498520 TAGCTGCTCCACGCTCGC 62.499 66.667 4.91 0.00 40.11 5.03
5153 6123 2.580867 GTAGCTGCTCCACGCTCG 60.581 66.667 4.91 0.00 40.11 5.03
5185 6155 0.873743 GCTGCGCACTGATCTCTACC 60.874 60.000 5.66 0.00 0.00 3.18
5213 6183 2.477375 TGTTTATTCTGCGTTGTCGTCC 59.523 45.455 0.00 0.00 39.49 4.79
5214 6184 3.781341 TGTTTATTCTGCGTTGTCGTC 57.219 42.857 0.00 0.00 39.49 4.20
5227 6197 8.663911 CCATTTGTGTTTCAGTGTTTGTTTATT 58.336 29.630 0.00 0.00 0.00 1.40
5229 6199 7.116948 CACCATTTGTGTTTCAGTGTTTGTTTA 59.883 33.333 0.00 0.00 40.26 2.01
5234 6204 5.047377 AGTCACCATTTGTGTTTCAGTGTTT 60.047 36.000 0.00 0.00 45.61 2.83
5235 6205 4.462483 AGTCACCATTTGTGTTTCAGTGTT 59.538 37.500 0.00 0.00 45.61 3.32
5236 6206 4.016444 AGTCACCATTTGTGTTTCAGTGT 58.984 39.130 0.00 0.00 45.61 3.55
5237 6207 4.601019 GAGTCACCATTTGTGTTTCAGTG 58.399 43.478 0.00 0.00 45.61 3.66
5238 6208 3.312421 CGAGTCACCATTTGTGTTTCAGT 59.688 43.478 0.00 0.00 45.61 3.41
5239 6209 3.303990 CCGAGTCACCATTTGTGTTTCAG 60.304 47.826 0.00 0.00 45.61 3.02
5240 6210 2.616376 CCGAGTCACCATTTGTGTTTCA 59.384 45.455 0.00 0.00 45.61 2.69
5241 6211 2.875933 TCCGAGTCACCATTTGTGTTTC 59.124 45.455 0.00 0.00 45.61 2.78
5247 6217 4.152402 CACTACTTTCCGAGTCACCATTTG 59.848 45.833 0.00 0.00 39.86 2.32
5271 6241 2.030805 GCTTTGAAATTGACTGCTCCGT 60.031 45.455 0.00 0.00 0.00 4.69
5272 6242 2.589014 GCTTTGAAATTGACTGCTCCG 58.411 47.619 0.00 0.00 0.00 4.63
5273 6243 2.589014 CGCTTTGAAATTGACTGCTCC 58.411 47.619 0.00 0.00 0.00 4.70
5274 6244 1.981533 GCGCTTTGAAATTGACTGCTC 59.018 47.619 0.00 0.00 0.00 4.26
5275 6245 1.337703 TGCGCTTTGAAATTGACTGCT 59.662 42.857 9.73 0.00 0.00 4.24
5276 6246 1.453148 GTGCGCTTTGAAATTGACTGC 59.547 47.619 9.73 0.00 0.00 4.40
5277 6247 2.730069 TGTGCGCTTTGAAATTGACTG 58.270 42.857 9.73 0.00 0.00 3.51
5278 6248 3.066621 TCTTGTGCGCTTTGAAATTGACT 59.933 39.130 9.73 0.00 0.00 3.41
5279 6249 3.371168 TCTTGTGCGCTTTGAAATTGAC 58.629 40.909 9.73 0.00 0.00 3.18
5280 6250 3.706802 TCTTGTGCGCTTTGAAATTGA 57.293 38.095 9.73 0.00 0.00 2.57
5281 6251 3.362304 GCTTCTTGTGCGCTTTGAAATTG 60.362 43.478 9.73 0.00 0.00 2.32
5282 6252 2.796593 GCTTCTTGTGCGCTTTGAAATT 59.203 40.909 9.73 0.00 0.00 1.82
5283 6253 2.397549 GCTTCTTGTGCGCTTTGAAAT 58.602 42.857 9.73 0.00 0.00 2.17
5284 6254 1.838913 GCTTCTTGTGCGCTTTGAAA 58.161 45.000 9.73 0.00 0.00 2.69
5285 6255 0.316937 CGCTTCTTGTGCGCTTTGAA 60.317 50.000 9.73 7.21 46.72 2.69
5286 6256 1.279539 CGCTTCTTGTGCGCTTTGA 59.720 52.632 9.73 0.00 46.72 2.69
5287 6257 3.819393 CGCTTCTTGTGCGCTTTG 58.181 55.556 9.73 0.00 46.72 2.77
5293 6263 0.391661 TCTGGATCCGCTTCTTGTGC 60.392 55.000 7.39 0.00 0.00 4.57
5294 6264 1.649664 CTCTGGATCCGCTTCTTGTG 58.350 55.000 7.39 0.00 0.00 3.33
5295 6265 0.107945 GCTCTGGATCCGCTTCTTGT 60.108 55.000 7.39 0.00 0.00 3.16
5296 6266 1.150567 CGCTCTGGATCCGCTTCTTG 61.151 60.000 7.39 0.00 0.00 3.02
5297 6267 1.142748 CGCTCTGGATCCGCTTCTT 59.857 57.895 7.39 0.00 0.00 2.52
5298 6268 2.811101 CGCTCTGGATCCGCTTCT 59.189 61.111 7.39 0.00 0.00 2.85
5299 6269 2.964389 GCGCTCTGGATCCGCTTC 60.964 66.667 7.39 0.00 43.95 3.86
5300 6270 4.537433 GGCGCTCTGGATCCGCTT 62.537 66.667 7.64 0.00 46.29 4.68


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

AutoCloner maintained by Alex Coulton.