Multiple sequence alignment - TraesCS3D01G539100

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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 TraesCS3D01G539100 chr3D 100.000 4768 0 0 1 4768 611294513 611299280 0.000000e+00 8805.0
1 TraesCS3D01G539100 chr3D 77.234 1511 240 57 2303 3775 611211663 611210219 0.000000e+00 789.0
2 TraesCS3D01G539100 chr3D 76.311 1659 283 62 1907 3542 611218098 611216527 0.000000e+00 785.0
3 TraesCS3D01G539100 chr3D 78.512 954 158 35 2816 3748 611252735 611251808 2.470000e-162 582.0
4 TraesCS3D01G539100 chr3D 77.146 932 180 26 2857 3775 611164038 611163127 1.180000e-140 510.0
5 TraesCS3D01G539100 chr3D 74.194 1147 211 48 1600 2703 611165188 611164084 2.670000e-107 399.0
6 TraesCS3D01G539100 chr3B 89.360 3346 255 53 1457 4768 829037932 829041210 0.000000e+00 4113.0
7 TraesCS3D01G539100 chr3B 86.559 1049 73 26 387 1376 829036876 829037915 0.000000e+00 1094.0
8 TraesCS3D01G539100 chr3B 77.249 1512 241 57 2303 3775 828993303 828991856 0.000000e+00 791.0
9 TraesCS3D01G539100 chr3B 77.940 961 176 29 2804 3748 829014140 829013200 6.920000e-158 568.0
10 TraesCS3D01G539100 chr3B 76.113 921 174 34 2852 3748 828918424 828917526 1.580000e-119 440.0
11 TraesCS3D01G539100 chr3B 83.871 279 37 6 33 310 829036398 829036669 4.730000e-65 259.0
12 TraesCS3D01G539100 chr3B 79.814 322 43 13 2297 2615 829008103 829007801 1.040000e-51 215.0
13 TraesCS3D01G539100 chr3B 76.344 465 70 23 2301 2759 828919016 828918586 3.740000e-51 213.0
14 TraesCS3D01G539100 chr3B 80.224 268 41 6 1934 2192 829014859 829014595 1.750000e-44 191.0
15 TraesCS3D01G539100 chr3B 77.778 207 33 8 1637 1838 829008773 829008575 1.080000e-21 115.0
16 TraesCS3D01G539100 chr3A 89.936 2504 187 34 2283 4768 746187544 746190000 0.000000e+00 3168.0
17 TraesCS3D01G539100 chr3A 91.866 1045 58 14 620 1640 746185645 746186686 0.000000e+00 1434.0
18 TraesCS3D01G539100 chr3A 93.949 661 27 8 1631 2291 746186878 746187525 0.000000e+00 987.0
19 TraesCS3D01G539100 chr3A 75.405 2224 391 108 1600 3748 746089474 746087332 0.000000e+00 933.0
20 TraesCS3D01G539100 chr3A 75.895 1257 216 49 2512 3748 746175831 746174642 3.220000e-156 562.0
21 TraesCS3D01G539100 chr3A 81.081 296 42 10 1934 2220 746176346 746176056 1.730000e-54 224.0
22 TraesCS3D01G539100 chr3A 78.922 204 34 6 1637 1838 746169909 746169713 3.870000e-26 130.0
23 TraesCS3D01G539100 chr7A 79.412 340 55 8 1907 2244 642744176 642743850 4.800000e-55 226.0
24 TraesCS3D01G539100 chr7A 83.140 172 26 3 2307 2477 642743858 642743689 2.300000e-33 154.0
25 TraesCS3D01G539100 chr5D 74.242 462 99 17 4046 4496 442328437 442328889 4.900000e-40 176.0
26 TraesCS3D01G539100 chr5A 73.834 386 87 11 4122 4496 558540181 558540563 1.790000e-29 141.0
27 TraesCS3D01G539100 chrUn 86.667 75 10 0 3698 3772 50913316 50913242 3.060000e-12 84.2
28 TraesCS3D01G539100 chr7D 89.062 64 7 0 3709 3772 18383918 18383855 3.960000e-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 TraesCS3D01G539100 chr3D 611294513 611299280 4767 False 8805.0 8805 100.000000 1 4768 1 chr3D.!!$F1 4767
1 TraesCS3D01G539100 chr3D 611210219 611211663 1444 True 789.0 789 77.234000 2303 3775 1 chr3D.!!$R1 1472
2 TraesCS3D01G539100 chr3D 611216527 611218098 1571 True 785.0 785 76.311000 1907 3542 1 chr3D.!!$R2 1635
3 TraesCS3D01G539100 chr3D 611251808 611252735 927 True 582.0 582 78.512000 2816 3748 1 chr3D.!!$R3 932
4 TraesCS3D01G539100 chr3D 611163127 611165188 2061 True 454.5 510 75.670000 1600 3775 2 chr3D.!!$R4 2175
5 TraesCS3D01G539100 chr3B 829036398 829041210 4812 False 1822.0 4113 86.596667 33 4768 3 chr3B.!!$F1 4735
6 TraesCS3D01G539100 chr3B 828991856 828993303 1447 True 791.0 791 77.249000 2303 3775 1 chr3B.!!$R1 1472
7 TraesCS3D01G539100 chr3B 829013200 829014859 1659 True 379.5 568 79.082000 1934 3748 2 chr3B.!!$R4 1814
8 TraesCS3D01G539100 chr3B 828917526 828919016 1490 True 326.5 440 76.228500 2301 3748 2 chr3B.!!$R2 1447
9 TraesCS3D01G539100 chr3A 746185645 746190000 4355 False 1863.0 3168 91.917000 620 4768 3 chr3A.!!$F1 4148
10 TraesCS3D01G539100 chr3A 746087332 746089474 2142 True 933.0 933 75.405000 1600 3748 1 chr3A.!!$R1 2148
11 TraesCS3D01G539100 chr3A 746174642 746176346 1704 True 393.0 562 78.488000 1934 3748 2 chr3A.!!$R3 1814

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
924 1082 0.034059 AGACCTCACCGAACTTGCTG 59.966 55.0 0.00 0.00 0.00 4.41 F
1703 2117 0.927767 TACAAACAACCCAGGGTGGT 59.072 50.0 13.85 13.85 42.51 4.16 F
2487 2999 0.036294 GTGACCCACCAGCTAAGGAC 60.036 60.0 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2487 2999 1.086696 AATCATCGCGGTTGGAACAG 58.913 50.0 6.13 0.0 42.39 3.16 R
3335 3972 0.968405 GGCACAGAAAAGGCATTGGA 59.032 50.0 0.00 0.0 0.00 3.53 R
4033 4704 0.172578 TCTAACATCCGGTGTCGCTG 59.827 55.0 0.00 0.0 41.14 5.18 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
21 22 3.307445 CAGGCAGACTGGAGAGGG 58.693 66.667 4.26 0.00 43.70 4.30
22 23 2.040278 AGGCAGACTGGAGAGGGG 59.960 66.667 4.26 0.00 0.00 4.79
23 24 3.086600 GGCAGACTGGAGAGGGGG 61.087 72.222 4.26 0.00 0.00 5.40
24 25 3.791586 GCAGACTGGAGAGGGGGC 61.792 72.222 4.26 0.00 0.00 5.80
25 26 2.284921 CAGACTGGAGAGGGGGCA 60.285 66.667 0.00 0.00 0.00 5.36
26 27 2.284995 AGACTGGAGAGGGGGCAC 60.285 66.667 0.00 0.00 0.00 5.01
27 28 2.607750 GACTGGAGAGGGGGCACA 60.608 66.667 0.00 0.00 0.00 4.57
28 29 2.121963 ACTGGAGAGGGGGCACAA 60.122 61.111 0.00 0.00 0.00 3.33
29 30 2.352805 CTGGAGAGGGGGCACAAC 59.647 66.667 0.00 0.00 0.00 3.32
30 31 3.256960 TGGAGAGGGGGCACAACC 61.257 66.667 0.00 0.00 37.93 3.77
31 32 3.256960 GGAGAGGGGGCACAACCA 61.257 66.667 0.00 0.00 42.05 3.67
49 50 3.793144 CGCAACCTTCAGCCTCGC 61.793 66.667 0.00 0.00 0.00 5.03
63 64 3.300667 CTCGCTGAGTTGCAACCGC 62.301 63.158 25.62 22.36 39.24 5.68
64 65 4.389576 CGCTGAGTTGCAACCGCC 62.390 66.667 25.62 15.34 37.32 6.13
65 66 3.286751 GCTGAGTTGCAACCGCCA 61.287 61.111 25.62 18.76 37.32 5.69
66 67 2.639286 CTGAGTTGCAACCGCCAC 59.361 61.111 25.62 12.48 37.32 5.01
71 72 1.008538 GTTGCAACCGCCACTGAAG 60.009 57.895 19.15 0.00 37.32 3.02
77 78 3.123620 CCGCCACTGAAGAGCTGC 61.124 66.667 0.00 0.00 0.00 5.25
78 79 2.047465 CGCCACTGAAGAGCTGCT 60.047 61.111 0.00 0.00 0.00 4.24
91 92 0.327259 AGCTGCTGAAGATGCCAAGA 59.673 50.000 0.00 0.00 0.00 3.02
92 93 0.733729 GCTGCTGAAGATGCCAAGAG 59.266 55.000 0.00 0.00 0.00 2.85
96 97 1.830279 CTGAAGATGCCAAGAGCCAA 58.170 50.000 0.00 0.00 42.71 4.52
102 103 0.407139 ATGCCAAGAGCCAAGGAACT 59.593 50.000 0.00 0.00 41.34 3.01
107 108 3.882025 GAGCCAAGGAACTGCTCG 58.118 61.111 0.00 0.00 42.96 5.03
108 109 2.359230 AGCCAAGGAACTGCTCGC 60.359 61.111 0.00 0.00 40.86 5.03
110 111 3.121030 CCAAGGAACTGCTCGCCG 61.121 66.667 0.00 0.00 40.86 6.46
137 138 0.257039 ACCATGGTTGGATCTGGAGC 59.743 55.000 13.00 0.00 46.92 4.70
143 144 2.735772 TTGGATCTGGAGCCGGAGC 61.736 63.158 5.05 5.04 40.42 4.70
166 167 0.748729 GAGATCCGTCGGTGAGGAGT 60.749 60.000 11.88 0.00 40.26 3.85
172 173 1.080705 GTCGGTGAGGAGTTGGACG 60.081 63.158 0.00 0.00 0.00 4.79
173 174 2.432628 CGGTGAGGAGTTGGACGC 60.433 66.667 0.00 0.00 0.00 5.19
178 179 4.136978 AGGAGTTGGACGCCTGAT 57.863 55.556 2.46 0.00 46.88 2.90
185 186 0.325296 TTGGACGCCTGATAGGGAGT 60.325 55.000 0.00 0.00 41.87 3.85
189 190 1.881324 GACGCCTGATAGGGAGTAGAC 59.119 57.143 0.00 0.00 39.40 2.59
194 195 1.532007 CTGATAGGGAGTAGACGACGC 59.468 57.143 0.00 0.00 0.00 5.19
197 198 4.549516 GGGAGTAGACGACGCGGC 62.550 72.222 12.47 6.41 33.59 6.53
207 208 3.760035 GACGCGGCTGGGAGAGAA 61.760 66.667 17.67 0.00 0.00 2.87
210 211 1.450312 CGCGGCTGGGAGAGAAAAT 60.450 57.895 2.84 0.00 0.00 1.82
265 267 4.452733 CAACGGACGGCCTCCTCC 62.453 72.222 5.33 9.57 36.80 4.30
279 281 4.760047 CTCCGGTGGCAACGAGGG 62.760 72.222 29.07 13.02 42.51 4.30
283 285 4.280019 GGTGGCAACGAGGGGGTT 62.280 66.667 0.00 0.00 42.51 4.11
284 286 2.751688 GTGGCAACGAGGGGGTTA 59.248 61.111 0.00 0.00 42.51 2.85
285 287 1.376812 GTGGCAACGAGGGGGTTAG 60.377 63.158 0.00 0.00 42.51 2.34
288 290 1.376812 GCAACGAGGGGGTTAGGTG 60.377 63.158 0.00 0.00 0.00 4.00
299 301 2.612746 TTAGGTGGTGGAGGGGCC 60.613 66.667 0.00 0.00 37.10 5.80
327 329 2.256461 CAAGCGTTGCTGGCCTTC 59.744 61.111 3.32 0.00 39.62 3.46
328 330 2.203337 AAGCGTTGCTGGCCTTCA 60.203 55.556 3.32 0.00 39.62 3.02
329 331 2.263741 AAGCGTTGCTGGCCTTCAG 61.264 57.895 3.32 0.00 46.03 3.02
330 332 2.669569 GCGTTGCTGGCCTTCAGA 60.670 61.111 3.32 0.00 46.18 3.27
331 333 2.684843 GCGTTGCTGGCCTTCAGAG 61.685 63.158 3.32 0.00 46.18 3.35
332 334 1.302033 CGTTGCTGGCCTTCAGAGT 60.302 57.895 3.32 0.00 46.18 3.24
333 335 1.294659 CGTTGCTGGCCTTCAGAGTC 61.295 60.000 3.32 0.00 46.18 3.36
334 336 0.250467 GTTGCTGGCCTTCAGAGTCA 60.250 55.000 3.32 0.00 46.18 3.41
335 337 0.250467 TTGCTGGCCTTCAGAGTCAC 60.250 55.000 3.32 0.00 46.18 3.67
336 338 1.376553 GCTGGCCTTCAGAGTCACC 60.377 63.158 3.32 0.00 46.18 4.02
337 339 1.835927 GCTGGCCTTCAGAGTCACCT 61.836 60.000 3.32 0.00 46.18 4.00
338 340 0.036577 CTGGCCTTCAGAGTCACCTG 60.037 60.000 3.32 0.00 46.18 4.00
339 341 1.298014 GGCCTTCAGAGTCACCTGG 59.702 63.158 0.00 0.00 34.99 4.45
340 342 1.298014 GCCTTCAGAGTCACCTGGG 59.702 63.158 0.00 0.00 34.99 4.45
341 343 1.986413 CCTTCAGAGTCACCTGGGG 59.014 63.158 0.00 0.00 34.99 4.96
342 344 1.298014 CTTCAGAGTCACCTGGGGC 59.702 63.158 0.00 0.00 34.99 5.80
343 345 2.513026 CTTCAGAGTCACCTGGGGCG 62.513 65.000 0.00 0.00 34.99 6.13
344 346 4.087892 CAGAGTCACCTGGGGCGG 62.088 72.222 0.00 0.00 0.00 6.13
376 378 3.334054 GGGGGCAGGCTTCACTCT 61.334 66.667 0.00 0.00 0.00 3.24
377 379 2.759795 GGGGCAGGCTTCACTCTT 59.240 61.111 0.00 0.00 0.00 2.85
378 380 1.075659 GGGGCAGGCTTCACTCTTT 59.924 57.895 0.00 0.00 0.00 2.52
379 381 0.962855 GGGGCAGGCTTCACTCTTTC 60.963 60.000 0.00 0.00 0.00 2.62
380 382 0.037447 GGGCAGGCTTCACTCTTTCT 59.963 55.000 0.00 0.00 0.00 2.52
381 383 1.447945 GGCAGGCTTCACTCTTTCTC 58.552 55.000 0.00 0.00 0.00 2.87
382 384 1.447945 GCAGGCTTCACTCTTTCTCC 58.552 55.000 0.00 0.00 0.00 3.71
383 385 1.271054 GCAGGCTTCACTCTTTCTCCA 60.271 52.381 0.00 0.00 0.00 3.86
384 386 2.811873 GCAGGCTTCACTCTTTCTCCAA 60.812 50.000 0.00 0.00 0.00 3.53
385 387 2.810852 CAGGCTTCACTCTTTCTCCAAC 59.189 50.000 0.00 0.00 0.00 3.77
391 523 3.583228 TCACTCTTTCTCCAACCACCTA 58.417 45.455 0.00 0.00 0.00 3.08
399 531 5.416271 TTCTCCAACCACCTATGTTAGTC 57.584 43.478 0.00 0.00 0.00 2.59
400 532 3.773119 TCTCCAACCACCTATGTTAGTCC 59.227 47.826 0.00 0.00 0.00 3.85
417 549 1.121378 TCCGTTGGTTGGACAGTGTA 58.879 50.000 0.00 0.00 0.00 2.90
418 550 1.695242 TCCGTTGGTTGGACAGTGTAT 59.305 47.619 0.00 0.00 0.00 2.29
423 561 4.387862 CGTTGGTTGGACAGTGTATAGTTC 59.612 45.833 0.00 0.00 0.00 3.01
466 604 5.713861 AGAAATTTCCCAGAATGAAGAGGTG 59.286 40.000 14.61 0.00 39.69 4.00
476 614 8.971073 CCCAGAATGAAGAGGTGTTATTTTATT 58.029 33.333 0.00 0.00 39.69 1.40
567 715 5.154418 AGTTGAGAATGGAAAATGGGGAAA 58.846 37.500 0.00 0.00 0.00 3.13
584 732 2.100087 GGAAAAGCCCAAAAGACGTTGA 59.900 45.455 0.00 0.00 0.00 3.18
589 737 3.016736 AGCCCAAAAGACGTTGATATGG 58.983 45.455 0.00 0.00 0.00 2.74
594 742 5.523916 CCCAAAAGACGTTGATATGGAGTAG 59.476 44.000 9.15 0.00 0.00 2.57
597 745 7.222224 CCAAAAGACGTTGATATGGAGTAGTAC 59.778 40.741 0.00 0.00 0.00 2.73
599 747 8.743085 AAAGACGTTGATATGGAGTAGTACTA 57.257 34.615 1.88 0.00 0.00 1.82
600 748 7.727331 AGACGTTGATATGGAGTAGTACTAC 57.273 40.000 23.03 23.03 36.35 2.73
603 751 8.517062 ACGTTGATATGGAGTAGTACTACTTT 57.483 34.615 31.14 21.88 45.63 2.66
649 797 2.656560 AGTTGTGCTATCCGTCTGAC 57.343 50.000 0.00 0.00 0.00 3.51
677 825 5.836347 TCTTGATATCCATCGAGTGTCAAG 58.164 41.667 16.22 16.22 41.71 3.02
690 838 4.447054 CGAGTGTCAAGCTTGATATCCATC 59.553 45.833 30.65 20.93 39.73 3.51
691 839 4.375272 AGTGTCAAGCTTGATATCCATCG 58.625 43.478 30.65 0.00 39.73 3.84
870 1028 2.193306 ATTATTTTGCTTCGCGCCAG 57.807 45.000 0.00 0.00 38.05 4.85
915 1073 2.430921 GTGCACGAGACCTCACCG 60.431 66.667 0.00 0.00 0.00 4.94
916 1074 2.596338 TGCACGAGACCTCACCGA 60.596 61.111 0.00 0.00 0.00 4.69
917 1075 2.197605 TGCACGAGACCTCACCGAA 61.198 57.895 0.00 0.00 0.00 4.30
920 1078 0.314302 CACGAGACCTCACCGAACTT 59.686 55.000 0.00 0.00 0.00 2.66
924 1082 0.034059 AGACCTCACCGAACTTGCTG 59.966 55.000 0.00 0.00 0.00 4.41
941 1110 6.095377 ACTTGCTGCAACAATATTTTAGAGC 58.905 36.000 11.69 0.00 0.00 4.09
951 1120 6.624423 ACAATATTTTAGAGCAAGCAACAGG 58.376 36.000 0.00 0.00 0.00 4.00
972 1151 1.790755 GCCGAAACCAAACCATTTCC 58.209 50.000 0.00 0.00 32.25 3.13
973 1152 1.933052 GCCGAAACCAAACCATTTCCG 60.933 52.381 0.00 0.00 32.25 4.30
980 1163 1.732259 CCAAACCATTTCCGTCTCTCG 59.268 52.381 0.00 0.00 39.52 4.04
982 1165 2.080286 AACCATTTCCGTCTCTCGTG 57.920 50.000 0.00 0.00 37.94 4.35
985 1168 1.084370 CATTTCCGTCTCTCGTGCCC 61.084 60.000 0.00 0.00 37.94 5.36
1216 1399 1.376553 GAGAAGGGAGCAGTGTGCC 60.377 63.158 0.00 0.00 46.52 5.01
1221 1404 2.673523 GGAGCAGTGTGCCTGGAT 59.326 61.111 0.00 0.00 46.52 3.41
1320 1510 1.043816 CCGCACTGTCTATCATCCCT 58.956 55.000 0.00 0.00 0.00 4.20
1384 1582 6.062095 CCATCCTTGACCCGTTTTCTTATAT 58.938 40.000 0.00 0.00 0.00 0.86
1392 1590 6.814644 TGACCCGTTTTCTTATATACTGTGTG 59.185 38.462 0.00 0.00 0.00 3.82
1423 1621 8.624367 TTTATTTTTCTTATTCACGTCTCCCA 57.376 30.769 0.00 0.00 0.00 4.37
1472 1670 6.510799 GCTCAAATGTAGTGGATGATCTTTCG 60.511 42.308 0.00 0.00 0.00 3.46
1500 1698 9.893305 AAGATACACTTTTGATAACCGAAAAAG 57.107 29.630 5.76 5.76 43.39 2.27
1516 1714 9.990360 AACCGAAAAAGGTACAATTTTCATAAT 57.010 25.926 23.66 11.59 45.21 1.28
1531 1729 9.801873 AATTTTCATAATCAAAGTATGGTTCGG 57.198 29.630 0.00 0.00 33.39 4.30
1589 1790 6.324819 CAACGAGATGCCTTTTCATTGTTAT 58.675 36.000 0.00 0.00 0.00 1.89
1680 2093 7.962964 TTAGTTGACTGACCTGTCTATTTTG 57.037 36.000 8.20 0.00 37.79 2.44
1703 2117 0.927767 TACAAACAACCCAGGGTGGT 59.072 50.000 13.85 13.85 42.51 4.16
1863 2296 5.934043 TGATGCCTATCTATTTGTTCCATCG 59.066 40.000 0.00 0.00 34.31 3.84
1868 2304 8.590204 TGCCTATCTATTTGTTCCATCGTTATA 58.410 33.333 0.00 0.00 0.00 0.98
1869 2305 9.601217 GCCTATCTATTTGTTCCATCGTTATAT 57.399 33.333 0.00 0.00 0.00 0.86
2074 2527 2.871182 TGGTATCATGTCGCTGTCTC 57.129 50.000 0.00 0.00 0.00 3.36
2102 2555 4.466828 CTTCAAGTAATGTTCTGTTGGCG 58.533 43.478 0.00 0.00 0.00 5.69
2191 2644 6.059484 ACGAACTCATGGAAAAAGGACTTAA 58.941 36.000 0.00 0.00 0.00 1.85
2210 2663 5.412594 ACTTAACAATGCTACACAGGTCATG 59.587 40.000 0.00 0.00 0.00 3.07
2487 2999 0.036294 GTGACCCACCAGCTAAGGAC 60.036 60.000 0.00 0.00 0.00 3.85
2540 3055 8.610035 ACTTGAACTAAAGTACCTTTTTCTTCG 58.390 33.333 0.00 0.00 38.62 3.79
2648 3167 7.517259 GCTTCAAAGTTTAAAAGACATGCCTTG 60.517 37.037 12.01 0.00 0.00 3.61
2939 3540 3.408634 ACCGAGGTAGTTTCCATTGTTG 58.591 45.455 0.00 0.00 0.00 3.33
2960 3561 5.336150 TGAGTTTGATTTTCTTGCCACAA 57.664 34.783 0.00 0.00 0.00 3.33
3390 4029 2.010145 TCAGCTTCCGTGTCAATAGC 57.990 50.000 0.00 0.00 0.00 2.97
3427 4066 1.039068 TGGGTGCATTCAAGGTTGTG 58.961 50.000 0.00 0.00 0.00 3.33
3620 4267 3.801114 TCTGTGGTATCTGATTCACCG 57.199 47.619 16.00 12.02 34.94 4.94
3859 4520 4.509600 GTCCATCATAGTGAAAGCTAGTGC 59.490 45.833 0.00 0.00 40.05 4.40
3868 4529 4.702131 AGTGAAAGCTAGTGCCAATTTAGG 59.298 41.667 0.00 0.00 40.80 2.69
3934 4597 6.660887 AAAGTTCACATTTGTGCGAAAAAT 57.339 29.167 5.81 0.00 45.25 1.82
3944 4607 6.761731 TTTGTGCGAAAAATTGAGGTTATG 57.238 33.333 0.00 0.00 0.00 1.90
3963 4626 9.525826 AGGTTATGAATATTTGGAATGGATCTC 57.474 33.333 0.00 0.00 0.00 2.75
3969 4632 1.522900 TTGGAATGGATCTCCCTCCC 58.477 55.000 10.46 2.73 36.61 4.30
3970 4633 0.649992 TGGAATGGATCTCCCTCCCT 59.350 55.000 10.46 0.00 36.61 4.20
3971 4634 1.873049 TGGAATGGATCTCCCTCCCTA 59.127 52.381 10.46 0.00 36.61 3.53
3972 4635 2.252676 TGGAATGGATCTCCCTCCCTAA 59.747 50.000 10.46 0.00 36.61 2.69
3973 4636 3.115803 TGGAATGGATCTCCCTCCCTAAT 60.116 47.826 10.46 0.00 36.61 1.73
4030 4701 1.342672 TTCCCCTTATGTCGCTCCCC 61.343 60.000 0.00 0.00 0.00 4.81
4031 4702 2.070039 CCCCTTATGTCGCTCCCCA 61.070 63.158 0.00 0.00 0.00 4.96
4032 4703 1.447643 CCCTTATGTCGCTCCCCAG 59.552 63.158 0.00 0.00 0.00 4.45
4033 4704 1.227674 CCTTATGTCGCTCCCCAGC 60.228 63.158 0.00 0.00 42.96 4.85
4049 4720 2.742372 GCAGCGACACCGGATGTT 60.742 61.111 9.46 0.00 43.56 2.71
4050 4721 1.447140 GCAGCGACACCGGATGTTA 60.447 57.895 9.46 0.00 43.56 2.41
4056 4727 1.471287 CGACACCGGATGTTAGAGTCA 59.529 52.381 9.46 0.00 43.56 3.41
4061 4732 4.935808 ACACCGGATGTTAGAGTCAATTTC 59.064 41.667 9.46 0.00 38.98 2.17
4064 4735 4.181578 CGGATGTTAGAGTCAATTTCGGT 58.818 43.478 0.00 0.00 0.00 4.69
4072 4743 8.092068 TGTTAGAGTCAATTTCGGTAAATCTCA 58.908 33.333 0.00 0.00 34.12 3.27
4079 4750 6.155565 TCAATTTCGGTAAATCTCAGGTAGGA 59.844 38.462 0.00 0.00 34.12 2.94
4092 4763 1.380112 GTAGGAGGTCCCGAGCTGT 60.380 63.158 0.22 0.00 39.57 4.40
4135 4806 5.903810 ACAAAATACGCAAGGTTTTTACCA 58.096 33.333 0.00 0.00 46.39 3.25
4138 4809 4.776795 ATACGCAAGGTTTTTACCAAGG 57.223 40.909 0.00 0.00 46.39 3.61
4141 4812 3.196039 ACGCAAGGTTTTTACCAAGGTTT 59.804 39.130 0.00 0.00 46.39 3.27
4143 4814 4.678309 CGCAAGGTTTTTACCAAGGTTTGA 60.678 41.667 0.00 0.00 0.00 2.69
4144 4815 5.179533 GCAAGGTTTTTACCAAGGTTTGAA 58.820 37.500 0.00 0.00 0.00 2.69
4152 4823 1.202770 ACCAAGGTTTGAACTCCCTCG 60.203 52.381 0.00 0.00 0.00 4.63
4209 4880 6.899089 TGTATTGATTGTGGATGGAGTACAT 58.101 36.000 0.00 0.00 44.18 2.29
4216 4887 6.465439 TTGTGGATGGAGTACATAGTACAG 57.535 41.667 9.68 0.00 40.72 2.74
4229 4900 6.869206 ACATAGTACAGGTGTTTCTACCAT 57.131 37.500 0.00 0.00 43.37 3.55
4282 4953 5.291905 CCCCCTGTTTCTATAGGTACTTG 57.708 47.826 0.00 0.00 41.75 3.16
4286 4957 4.966805 CCTGTTTCTATAGGTACTTGGGGA 59.033 45.833 0.00 0.00 41.75 4.81
4293 4964 6.103314 TCTATAGGTACTTGGGGATCTAGGA 58.897 44.000 0.00 0.00 41.75 2.94
4306 4977 7.256399 TGGGGATCTAGGATTACAGATATGTT 58.744 38.462 0.00 0.00 31.63 2.71
4315 4986 6.492429 AGGATTACAGATATGTTGGCTACGTA 59.508 38.462 0.00 3.56 32.93 3.57
4321 4992 6.645415 ACAGATATGTTGGCTACGTATTTAGC 59.355 38.462 13.67 0.00 43.36 3.09
4333 5004 2.218759 CGTATTTAGCAGATCGTGGTGC 59.781 50.000 7.00 2.47 37.49 5.01
4370 5041 2.519302 AGTGCGTGCCAAGCCTTT 60.519 55.556 0.00 0.00 0.00 3.11
4418 5098 0.255890 ATGCGGCCCATTAGTGAACT 59.744 50.000 0.00 0.00 0.00 3.01
4464 5144 3.681835 GGCTGGGAGACGACGTGT 61.682 66.667 4.58 0.00 0.00 4.49
4469 5149 0.820482 TGGGAGACGACGTGTTGAGA 60.820 55.000 4.58 0.00 0.00 3.27
4473 5153 0.742505 AGACGACGTGTTGAGAACCA 59.257 50.000 4.58 0.00 0.00 3.67
4474 5154 1.135527 AGACGACGTGTTGAGAACCAA 59.864 47.619 4.58 0.00 0.00 3.67
4499 5179 2.203938 AGGACACCATCACCGGGT 60.204 61.111 6.32 0.00 39.88 5.28
4513 5193 4.489771 GGGTGCGCATGCCCTAGT 62.490 66.667 25.01 0.00 41.63 2.57
4547 5228 2.042435 CCTCCGCCTCCTCCTTCT 60.042 66.667 0.00 0.00 0.00 2.85
4563 5244 4.827087 CTGCCGATGTCGCCTGCT 62.827 66.667 0.00 0.00 38.18 4.24
4567 5248 0.319555 GCCGATGTCGCCTGCTTATA 60.320 55.000 0.00 0.00 38.18 0.98
4570 5251 2.352715 CCGATGTCGCCTGCTTATATGA 60.353 50.000 0.00 0.00 38.18 2.15
4572 5253 2.134201 TGTCGCCTGCTTATATGACG 57.866 50.000 0.00 0.00 0.00 4.35
4574 5255 2.052157 GTCGCCTGCTTATATGACGTC 58.948 52.381 9.11 9.11 0.00 4.34
4577 5261 1.419374 CCTGCTTATATGACGTCGCC 58.581 55.000 11.62 0.00 0.00 5.54
4600 5284 0.035458 GCGGTCCCCATCTCCTAATG 59.965 60.000 0.00 0.00 0.00 1.90
4607 5291 2.338809 CCCATCTCCTAATGGTGGCTA 58.661 52.381 2.49 0.00 44.05 3.93
4614 5298 1.271597 CCTAATGGTGGCTAGGGATGC 60.272 57.143 0.00 0.00 32.46 3.91
4617 5301 0.695462 ATGGTGGCTAGGGATGCTCA 60.695 55.000 0.00 0.00 0.00 4.26
4622 5306 3.094062 GCTAGGGATGCTCACGCCA 62.094 63.158 0.00 0.00 34.43 5.69
4667 5351 3.507009 GACGGAGACCTCGTCGGG 61.507 72.222 0.95 0.00 45.53 5.14
4671 5355 1.975407 GGAGACCTCGTCGGGTTCA 60.975 63.158 6.82 0.00 40.06 3.18
4680 5364 0.319211 CGTCGGGTTCAGTGCACTAA 60.319 55.000 21.20 0.57 0.00 2.24
4686 5370 1.202770 GGTTCAGTGCACTAAGGTGGT 60.203 52.381 21.20 0.00 43.18 4.16
4718 5402 0.978146 CCCTTCTCCTCGTGGTGGAT 60.978 60.000 2.99 0.00 32.56 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.391395 CTCTCCAGTCTGCCTGCAAG 60.391 60.000 0.00 0.00 40.06 4.01
4 5 2.365586 CCCCTCTCCAGTCTGCCTG 61.366 68.421 0.00 0.00 41.15 4.85
6 7 3.086600 CCCCCTCTCCAGTCTGCC 61.087 72.222 0.00 0.00 0.00 4.85
8 9 2.284921 TGCCCCCTCTCCAGTCTG 60.285 66.667 0.00 0.00 0.00 3.51
9 10 2.284995 GTGCCCCCTCTCCAGTCT 60.285 66.667 0.00 0.00 0.00 3.24
10 11 2.224159 TTGTGCCCCCTCTCCAGTC 61.224 63.158 0.00 0.00 0.00 3.51
11 12 2.121963 TTGTGCCCCCTCTCCAGT 60.122 61.111 0.00 0.00 0.00 4.00
12 13 2.352805 GTTGTGCCCCCTCTCCAG 59.647 66.667 0.00 0.00 0.00 3.86
13 14 3.256960 GGTTGTGCCCCCTCTCCA 61.257 66.667 0.00 0.00 0.00 3.86
14 15 3.256960 TGGTTGTGCCCCCTCTCC 61.257 66.667 0.00 0.00 36.04 3.71
15 16 2.034221 GTGGTTGTGCCCCCTCTC 59.966 66.667 0.00 0.00 36.04 3.20
16 17 3.953775 CGTGGTTGTGCCCCCTCT 61.954 66.667 0.00 0.00 36.04 3.69
20 21 4.279043 GTTGCGTGGTTGTGCCCC 62.279 66.667 0.00 0.00 36.04 5.80
21 22 4.279043 GGTTGCGTGGTTGTGCCC 62.279 66.667 0.00 0.00 36.04 5.36
22 23 2.677573 GAAGGTTGCGTGGTTGTGCC 62.678 60.000 0.00 0.00 37.90 5.01
23 24 1.299089 GAAGGTTGCGTGGTTGTGC 60.299 57.895 0.00 0.00 0.00 4.57
24 25 0.029300 CTGAAGGTTGCGTGGTTGTG 59.971 55.000 0.00 0.00 0.00 3.33
25 26 1.724582 GCTGAAGGTTGCGTGGTTGT 61.725 55.000 0.00 0.00 0.00 3.32
26 27 1.008538 GCTGAAGGTTGCGTGGTTG 60.009 57.895 0.00 0.00 0.00 3.77
27 28 2.193536 GGCTGAAGGTTGCGTGGTT 61.194 57.895 0.00 0.00 0.00 3.67
28 29 2.594592 GGCTGAAGGTTGCGTGGT 60.595 61.111 0.00 0.00 0.00 4.16
29 30 2.281761 AGGCTGAAGGTTGCGTGG 60.282 61.111 0.00 0.00 0.00 4.94
30 31 2.671177 CGAGGCTGAAGGTTGCGTG 61.671 63.158 0.00 0.00 0.00 5.34
31 32 2.357517 CGAGGCTGAAGGTTGCGT 60.358 61.111 0.00 0.00 0.00 5.24
49 50 2.639286 GTGGCGGTTGCAACTCAG 59.361 61.111 27.64 19.54 42.13 3.35
63 64 1.001746 TCTTCAGCAGCTCTTCAGTGG 59.998 52.381 0.00 0.00 0.00 4.00
64 65 2.452295 TCTTCAGCAGCTCTTCAGTG 57.548 50.000 0.00 0.00 0.00 3.66
65 66 2.936114 GCATCTTCAGCAGCTCTTCAGT 60.936 50.000 0.00 0.00 0.00 3.41
66 67 1.666700 GCATCTTCAGCAGCTCTTCAG 59.333 52.381 0.00 0.00 0.00 3.02
71 72 0.733729 CTTGGCATCTTCAGCAGCTC 59.266 55.000 0.00 0.00 0.00 4.09
77 78 3.564262 TGGCTCTTGGCATCTTCAG 57.436 52.632 0.00 0.00 44.10 3.02
91 92 2.359230 GCGAGCAGTTCCTTGGCT 60.359 61.111 0.00 0.00 41.35 4.75
92 93 3.435186 GGCGAGCAGTTCCTTGGC 61.435 66.667 0.00 0.00 35.04 4.52
107 108 4.067913 CCATGGTGGTTTGCCGGC 62.068 66.667 22.73 22.73 37.67 6.13
137 138 4.637489 CGGATCTCGCAGCTCCGG 62.637 72.222 12.04 0.00 46.32 5.14
143 144 2.278206 CACCGACGGATCTCGCAG 60.278 66.667 23.38 0.00 43.89 5.18
154 155 1.080705 CGTCCAACTCCTCACCGAC 60.081 63.158 0.00 0.00 0.00 4.79
155 156 2.927580 GCGTCCAACTCCTCACCGA 61.928 63.158 0.00 0.00 0.00 4.69
166 167 0.325296 ACTCCCTATCAGGCGTCCAA 60.325 55.000 0.00 0.00 32.73 3.53
172 173 1.881324 GTCGTCTACTCCCTATCAGGC 59.119 57.143 0.00 0.00 32.73 4.85
173 174 2.144730 CGTCGTCTACTCCCTATCAGG 58.855 57.143 0.00 0.00 34.30 3.86
178 179 1.522355 CCGCGTCGTCTACTCCCTA 60.522 63.158 4.92 0.00 0.00 3.53
194 195 3.127030 GTGTTTATTTTCTCTCCCAGCCG 59.873 47.826 0.00 0.00 0.00 5.52
197 198 7.841956 TCTCTAGTGTTTATTTTCTCTCCCAG 58.158 38.462 0.00 0.00 0.00 4.45
198 199 7.792364 TCTCTAGTGTTTATTTTCTCTCCCA 57.208 36.000 0.00 0.00 0.00 4.37
207 208 6.208797 GGGGCAACTTTCTCTAGTGTTTATTT 59.791 38.462 0.00 0.00 0.00 1.40
210 211 4.648651 GGGGCAACTTTCTCTAGTGTTTA 58.351 43.478 0.00 0.00 0.00 2.01
272 274 1.151965 ACCACCTAACCCCCTCGTT 60.152 57.895 0.00 0.00 0.00 3.85
279 281 2.306384 CCCCTCCACCACCTAACCC 61.306 68.421 0.00 0.00 0.00 4.11
280 282 2.980177 GCCCCTCCACCACCTAACC 61.980 68.421 0.00 0.00 0.00 2.85
281 283 2.675371 GCCCCTCCACCACCTAAC 59.325 66.667 0.00 0.00 0.00 2.34
282 284 2.612746 GGCCCCTCCACCACCTAA 60.613 66.667 0.00 0.00 34.01 2.69
288 290 2.675423 GAAAACGGCCCCTCCACC 60.675 66.667 0.00 0.00 34.01 4.61
299 301 1.298041 AACGCTTGCACCGAAAACG 60.298 52.632 12.37 0.00 0.00 3.60
310 312 2.256461 GAAGGCCAGCAACGCTTG 59.744 61.111 5.01 0.00 36.40 4.01
311 313 2.203337 TGAAGGCCAGCAACGCTT 60.203 55.556 5.01 0.00 36.40 4.68
312 314 2.670934 CTGAAGGCCAGCAACGCT 60.671 61.111 5.01 0.00 40.77 5.07
319 321 0.036577 CAGGTGACTCTGAAGGCCAG 60.037 60.000 5.01 0.00 44.27 4.85
322 324 1.298014 CCCAGGTGACTCTGAAGGC 59.702 63.158 3.16 0.00 40.21 4.35
323 325 1.986413 CCCCAGGTGACTCTGAAGG 59.014 63.158 3.16 0.90 40.21 3.46
324 326 1.298014 GCCCCAGGTGACTCTGAAG 59.702 63.158 3.16 0.00 40.21 3.02
325 327 2.583441 CGCCCCAGGTGACTCTGAA 61.583 63.158 3.16 0.00 40.21 3.02
326 328 2.997315 CGCCCCAGGTGACTCTGA 60.997 66.667 3.16 0.00 40.21 3.27
327 329 4.087892 CCGCCCCAGGTGACTCTG 62.088 72.222 0.00 0.00 40.21 3.35
359 361 2.432174 AAAGAGTGAAGCCTGCCCCC 62.432 60.000 0.00 0.00 0.00 5.40
360 362 0.962855 GAAAGAGTGAAGCCTGCCCC 60.963 60.000 0.00 0.00 0.00 5.80
361 363 0.037447 AGAAAGAGTGAAGCCTGCCC 59.963 55.000 0.00 0.00 0.00 5.36
362 364 1.447945 GAGAAAGAGTGAAGCCTGCC 58.552 55.000 0.00 0.00 0.00 4.85
363 365 1.271054 TGGAGAAAGAGTGAAGCCTGC 60.271 52.381 0.00 0.00 0.00 4.85
364 366 2.810852 GTTGGAGAAAGAGTGAAGCCTG 59.189 50.000 0.00 0.00 0.00 4.85
365 367 2.224646 GGTTGGAGAAAGAGTGAAGCCT 60.225 50.000 0.00 0.00 0.00 4.58
366 368 2.155279 GGTTGGAGAAAGAGTGAAGCC 58.845 52.381 0.00 0.00 0.00 4.35
367 369 2.550180 GTGGTTGGAGAAAGAGTGAAGC 59.450 50.000 0.00 0.00 0.00 3.86
368 370 3.142174 GGTGGTTGGAGAAAGAGTGAAG 58.858 50.000 0.00 0.00 0.00 3.02
369 371 2.777692 AGGTGGTTGGAGAAAGAGTGAA 59.222 45.455 0.00 0.00 0.00 3.18
370 372 2.408565 AGGTGGTTGGAGAAAGAGTGA 58.591 47.619 0.00 0.00 0.00 3.41
371 373 2.938956 AGGTGGTTGGAGAAAGAGTG 57.061 50.000 0.00 0.00 0.00 3.51
372 374 3.910627 ACATAGGTGGTTGGAGAAAGAGT 59.089 43.478 0.00 0.00 0.00 3.24
373 375 4.559862 ACATAGGTGGTTGGAGAAAGAG 57.440 45.455 0.00 0.00 0.00 2.85
374 376 4.993705 AACATAGGTGGTTGGAGAAAGA 57.006 40.909 0.00 0.00 0.00 2.52
375 377 5.805728 ACTAACATAGGTGGTTGGAGAAAG 58.194 41.667 0.00 0.00 31.94 2.62
376 378 5.280317 GGACTAACATAGGTGGTTGGAGAAA 60.280 44.000 0.00 0.00 31.94 2.52
377 379 4.224370 GGACTAACATAGGTGGTTGGAGAA 59.776 45.833 0.00 0.00 31.94 2.87
378 380 3.773119 GGACTAACATAGGTGGTTGGAGA 59.227 47.826 0.00 0.00 31.94 3.71
379 381 3.430374 CGGACTAACATAGGTGGTTGGAG 60.430 52.174 0.00 0.00 31.94 3.86
380 382 2.498481 CGGACTAACATAGGTGGTTGGA 59.502 50.000 0.00 0.00 31.94 3.53
381 383 2.235402 ACGGACTAACATAGGTGGTTGG 59.765 50.000 0.00 0.00 33.51 3.77
382 384 3.604875 ACGGACTAACATAGGTGGTTG 57.395 47.619 0.00 0.00 0.00 3.77
383 385 3.307199 CCAACGGACTAACATAGGTGGTT 60.307 47.826 0.00 0.00 0.00 3.67
384 386 2.235402 CCAACGGACTAACATAGGTGGT 59.765 50.000 0.00 0.00 0.00 4.16
385 387 2.235402 ACCAACGGACTAACATAGGTGG 59.765 50.000 0.00 0.00 0.00 4.61
399 531 2.178912 ATACACTGTCCAACCAACGG 57.821 50.000 0.00 0.00 0.00 4.44
400 532 3.921677 ACTATACACTGTCCAACCAACG 58.078 45.455 0.00 0.00 0.00 4.10
411 543 5.940192 TTTGGTGCTTGAACTATACACTG 57.060 39.130 0.00 0.00 0.00 3.66
417 549 6.377996 TCATGCTTATTTGGTGCTTGAACTAT 59.622 34.615 0.00 0.00 37.73 2.12
418 550 5.709631 TCATGCTTATTTGGTGCTTGAACTA 59.290 36.000 0.00 0.00 37.73 2.24
423 561 4.707030 TCTCATGCTTATTTGGTGCTTG 57.293 40.909 0.00 0.00 34.53 4.01
524 662 9.092876 CTCAACTTACAAAATGCCAAGTAAAAA 57.907 29.630 0.00 0.00 29.31 1.94
525 663 8.470805 TCTCAACTTACAAAATGCCAAGTAAAA 58.529 29.630 0.00 0.00 29.31 1.52
526 664 8.001881 TCTCAACTTACAAAATGCCAAGTAAA 57.998 30.769 0.00 0.00 29.31 2.01
527 665 7.575414 TCTCAACTTACAAAATGCCAAGTAA 57.425 32.000 0.00 0.00 29.31 2.24
528 666 7.575414 TTCTCAACTTACAAAATGCCAAGTA 57.425 32.000 0.00 0.00 29.31 2.24
530 668 6.366877 CCATTCTCAACTTACAAAATGCCAAG 59.633 38.462 0.00 0.00 0.00 3.61
531 669 6.041409 TCCATTCTCAACTTACAAAATGCCAA 59.959 34.615 0.00 0.00 0.00 4.52
534 672 7.945033 TTTCCATTCTCAACTTACAAAATGC 57.055 32.000 0.00 0.00 0.00 3.56
537 675 7.930865 CCCATTTTCCATTCTCAACTTACAAAA 59.069 33.333 0.00 0.00 0.00 2.44
538 676 7.441017 CCCATTTTCCATTCTCAACTTACAAA 58.559 34.615 0.00 0.00 0.00 2.83
567 715 3.443681 CCATATCAACGTCTTTTGGGCTT 59.556 43.478 0.00 0.00 0.00 4.35
603 751 8.852135 ACGTCATCCCAACTTCTTTTTATAAAA 58.148 29.630 6.54 6.54 0.00 1.52
606 754 8.316214 ACTACGTCATCCCAACTTCTTTTTATA 58.684 33.333 0.00 0.00 0.00 0.98
607 755 7.166167 ACTACGTCATCCCAACTTCTTTTTAT 58.834 34.615 0.00 0.00 0.00 1.40
608 756 6.527423 ACTACGTCATCCCAACTTCTTTTTA 58.473 36.000 0.00 0.00 0.00 1.52
614 762 3.432252 CACAACTACGTCATCCCAACTTC 59.568 47.826 0.00 0.00 0.00 3.01
616 764 2.870435 GCACAACTACGTCATCCCAACT 60.870 50.000 0.00 0.00 0.00 3.16
617 765 1.463444 GCACAACTACGTCATCCCAAC 59.537 52.381 0.00 0.00 0.00 3.77
633 781 2.430248 TAGGTCAGACGGATAGCACA 57.570 50.000 0.00 0.00 0.00 4.57
643 791 7.032580 CGATGGATATCAAGATTAGGTCAGAC 58.967 42.308 4.83 0.00 32.67 3.51
649 797 6.929625 ACACTCGATGGATATCAAGATTAGG 58.070 40.000 4.83 0.00 32.67 2.69
677 825 2.093764 CCTCTCCCGATGGATATCAAGC 60.094 54.545 4.83 0.00 40.80 4.01
690 838 0.687757 TGGGTTGAGATCCTCTCCCG 60.688 60.000 16.37 0.00 42.73 5.14
691 839 0.833949 GTGGGTTGAGATCCTCTCCC 59.166 60.000 15.38 15.38 42.73 4.30
698 846 2.288825 TGTCTTCACGTGGGTTGAGATC 60.289 50.000 17.00 7.31 0.00 2.75
870 1028 1.139095 CACCCGTCCTCTCGTAAGC 59.861 63.158 0.00 0.00 37.18 3.09
915 1073 7.201384 GCTCTAAAATATTGTTGCAGCAAGTTC 60.201 37.037 20.82 0.00 0.00 3.01
916 1074 6.587608 GCTCTAAAATATTGTTGCAGCAAGTT 59.412 34.615 20.82 14.74 0.00 2.66
917 1075 6.095377 GCTCTAAAATATTGTTGCAGCAAGT 58.905 36.000 20.82 9.76 0.00 3.16
920 1078 5.641783 TGCTCTAAAATATTGTTGCAGCA 57.358 34.783 0.00 0.00 32.06 4.41
924 1082 6.365789 TGTTGCTTGCTCTAAAATATTGTTGC 59.634 34.615 0.00 0.00 0.00 4.17
941 1110 3.192954 TTTCGGCGCCTGTTGCTTG 62.193 57.895 26.68 6.06 38.05 4.01
951 1120 0.598942 AAATGGTTTGGTTTCGGCGC 60.599 50.000 0.00 0.00 0.00 6.53
957 1126 3.562182 AGAGACGGAAATGGTTTGGTTT 58.438 40.909 0.00 0.00 0.00 3.27
1100 1283 3.420606 CGGACAGCAGCAGCAGTG 61.421 66.667 3.31 0.00 40.89 3.66
1236 1419 0.545309 AGCCTCTCTGCAGGTGGTAA 60.545 55.000 15.13 0.00 35.72 2.85
1320 1510 0.679640 GCAACGGGTGATTCATGGGA 60.680 55.000 0.00 0.00 0.00 4.37
1423 1621 8.040727 AGCTTCTTCTTTTGTTTGGTAATTTGT 58.959 29.630 0.00 0.00 0.00 2.83
1472 1670 9.887406 TTTTCGGTTATCAAAAGTGTATCTTTC 57.113 29.630 0.00 0.00 44.50 2.62
1516 1714 5.068723 GTCTCTATCCCGAACCATACTTTGA 59.931 44.000 0.00 0.00 0.00 2.69
1531 1729 2.090377 TAGGGCCCGGGTCTCTATCC 62.090 65.000 27.44 14.15 0.00 2.59
1595 1796 5.645067 TCATGTAGAAGGCATCTTTTGACAG 59.355 40.000 0.00 0.00 39.71 3.51
1597 1798 6.459298 CCATCATGTAGAAGGCATCTTTTGAC 60.459 42.308 0.00 0.00 39.71 3.18
1680 2093 3.006430 CCACCCTGGGTTGTTTGTAATTC 59.994 47.826 17.76 0.00 31.02 2.17
1868 2304 8.177119 TGCAAACAAACAGGAAGATAACTAAT 57.823 30.769 0.00 0.00 0.00 1.73
1869 2305 7.575414 TGCAAACAAACAGGAAGATAACTAA 57.425 32.000 0.00 0.00 0.00 2.24
1870 2306 7.759489 ATGCAAACAAACAGGAAGATAACTA 57.241 32.000 0.00 0.00 0.00 2.24
1871 2307 6.655078 ATGCAAACAAACAGGAAGATAACT 57.345 33.333 0.00 0.00 0.00 2.24
1873 2309 7.967854 CGATTATGCAAACAAACAGGAAGATAA 59.032 33.333 0.00 0.00 0.00 1.75
1874 2310 7.120579 ACGATTATGCAAACAAACAGGAAGATA 59.879 33.333 0.00 0.00 0.00 1.98
1875 2311 6.071952 ACGATTATGCAAACAAACAGGAAGAT 60.072 34.615 0.00 0.00 0.00 2.40
2074 2527 4.024048 ACAGAACATTACTTGAAGCAACGG 60.024 41.667 0.00 0.00 0.00 4.44
2102 2555 4.694509 GTGCTTCCATCCTACATCATCATC 59.305 45.833 0.00 0.00 0.00 2.92
2191 2644 2.086869 GCATGACCTGTGTAGCATTGT 58.913 47.619 0.00 0.00 0.00 2.71
2295 2806 9.565213 CTGAAATGTGTAGAAAAATGAGGAATC 57.435 33.333 0.00 0.00 0.00 2.52
2487 2999 1.086696 AATCATCGCGGTTGGAACAG 58.913 50.000 6.13 0.00 42.39 3.16
2540 3055 7.148000 CCTTTTCCCTGAAATATCCTTTCTGTC 60.148 40.741 0.08 0.00 31.34 3.51
2648 3167 6.919721 TGACCACAAGGCTTGATTATAAAAC 58.080 36.000 32.50 13.37 39.06 2.43
2875 3476 1.202806 TCCTTGGGCAACACTTCTCTG 60.203 52.381 0.00 0.00 39.74 3.35
2939 3540 6.652245 CAATTGTGGCAAGAAAATCAAACTC 58.348 36.000 0.00 0.00 0.00 3.01
2960 3561 6.782986 TGGCATAATCTATTACAGGAGCAAT 58.217 36.000 0.00 0.00 0.00 3.56
3168 3798 5.957842 TTTCGTATCTGTGGCAAAGATTT 57.042 34.783 24.54 5.75 35.92 2.17
3254 3888 4.370049 TGATTTGTGTGGAATTGCAGTTG 58.630 39.130 0.00 0.00 0.00 3.16
3335 3972 0.968405 GGCACAGAAAAGGCATTGGA 59.032 50.000 0.00 0.00 0.00 3.53
3390 4029 1.888512 CCACCATTGTGTTCCTGAAGG 59.111 52.381 0.00 0.00 41.09 3.46
3427 4066 2.050918 CCCCAGTCCTCCTTATCTTCC 58.949 57.143 0.00 0.00 0.00 3.46
3620 4267 9.691362 AAATTGTGATAATCCAAGTAACAACAC 57.309 29.630 0.00 0.00 0.00 3.32
3934 4597 9.659135 ATCCATTCCAAATATTCATAACCTCAA 57.341 29.630 0.00 0.00 0.00 3.02
3944 4607 5.948758 GGAGGGAGATCCATTCCAAATATTC 59.051 44.000 13.82 0.00 39.62 1.75
3963 4626 6.094464 ACGAAACGAATTTTAATTAGGGAGGG 59.906 38.462 0.00 0.00 0.00 4.30
3969 4632 8.702408 TGTGTGACGAAACGAATTTTAATTAG 57.298 30.769 0.00 0.00 0.00 1.73
3970 4633 7.799447 CCTGTGTGACGAAACGAATTTTAATTA 59.201 33.333 0.00 0.00 0.00 1.40
3971 4634 6.635239 CCTGTGTGACGAAACGAATTTTAATT 59.365 34.615 0.00 0.00 0.00 1.40
3972 4635 6.140110 CCTGTGTGACGAAACGAATTTTAAT 58.860 36.000 0.00 0.00 0.00 1.40
3973 4636 5.503498 CCTGTGTGACGAAACGAATTTTAA 58.497 37.500 0.00 0.00 0.00 1.52
4030 4701 3.190849 CATCCGGTGTCGCTGCTG 61.191 66.667 0.00 0.00 34.56 4.41
4031 4702 1.884075 TAACATCCGGTGTCGCTGCT 61.884 55.000 0.00 0.00 41.14 4.24
4032 4703 1.421410 CTAACATCCGGTGTCGCTGC 61.421 60.000 0.00 0.00 41.14 5.25
4033 4704 0.172578 TCTAACATCCGGTGTCGCTG 59.827 55.000 0.00 0.00 41.14 5.18
4034 4705 0.456221 CTCTAACATCCGGTGTCGCT 59.544 55.000 0.00 0.00 41.14 4.93
4035 4706 0.172803 ACTCTAACATCCGGTGTCGC 59.827 55.000 0.00 0.00 41.14 5.19
4036 4707 1.471287 TGACTCTAACATCCGGTGTCG 59.529 52.381 0.00 1.21 41.14 4.35
4045 4716 9.099454 GAGATTTACCGAAATTGACTCTAACAT 57.901 33.333 0.00 0.00 35.33 2.71
4049 4720 7.093465 ACCTGAGATTTACCGAAATTGACTCTA 60.093 37.037 0.00 0.00 35.33 2.43
4050 4721 6.109359 CCTGAGATTTACCGAAATTGACTCT 58.891 40.000 0.00 0.00 35.33 3.24
4056 4727 6.408206 CCTCCTACCTGAGATTTACCGAAATT 60.408 42.308 0.00 0.00 35.33 1.82
4061 4732 3.297736 ACCTCCTACCTGAGATTTACCG 58.702 50.000 0.00 0.00 34.11 4.02
4064 4735 3.690438 CGGGACCTCCTACCTGAGATTTA 60.690 52.174 0.00 0.00 34.11 1.40
4072 4743 2.279408 GCTCGGGACCTCCTACCT 59.721 66.667 0.00 0.00 35.95 3.08
4079 4750 2.359967 GGCTAACAGCTCGGGACCT 61.360 63.158 0.00 0.00 41.99 3.85
4092 4763 6.528537 TTGTTACCATCGTACTTAGGCTAA 57.471 37.500 6.80 6.80 0.00 3.09
4116 4787 4.585581 ACCTTGGTAAAAACCTTGCGTATT 59.414 37.500 0.00 0.00 0.00 1.89
4118 4789 3.553904 ACCTTGGTAAAAACCTTGCGTA 58.446 40.909 0.00 0.00 0.00 4.42
4135 4806 2.704065 TCTTCGAGGGAGTTCAAACCTT 59.296 45.455 0.00 0.00 34.02 3.50
4138 4809 3.662247 TCTCTTCGAGGGAGTTCAAAC 57.338 47.619 14.28 0.00 33.06 2.93
4141 4812 5.535406 GGTATTATCTCTTCGAGGGAGTTCA 59.465 44.000 14.28 2.66 33.06 3.18
4143 4814 4.833938 GGGTATTATCTCTTCGAGGGAGTT 59.166 45.833 14.28 10.23 33.06 3.01
4144 4815 4.409187 GGGTATTATCTCTTCGAGGGAGT 58.591 47.826 14.28 7.26 33.06 3.85
4152 4823 7.100409 GCAGAACATAGGGGTATTATCTCTTC 58.900 42.308 0.00 0.00 0.00 2.87
4167 4838 7.933396 TCAATACAATCCAATGCAGAACATAG 58.067 34.615 0.00 0.00 38.34 2.23
4170 4841 6.778834 ATCAATACAATCCAATGCAGAACA 57.221 33.333 0.00 0.00 0.00 3.18
4186 4857 8.150945 ACTATGTACTCCATCCACAATCAATAC 58.849 37.037 0.00 0.00 34.86 1.89
4209 4880 6.250711 TCTCATGGTAGAAACACCTGTACTA 58.749 40.000 0.00 0.00 39.50 1.82
4216 4887 5.491982 AGACAATCTCATGGTAGAAACACC 58.508 41.667 0.00 0.00 39.20 4.16
4229 4900 3.570125 CGTAGAGGCCATAGACAATCTCA 59.430 47.826 5.01 0.00 0.00 3.27
4264 4935 6.555360 AGATCCCCAAGTACCTATAGAAACAG 59.445 42.308 0.00 0.00 0.00 3.16
4265 4936 6.449956 AGATCCCCAAGTACCTATAGAAACA 58.550 40.000 0.00 0.00 0.00 2.83
4270 4941 6.404426 TCCTAGATCCCCAAGTACCTATAG 57.596 45.833 0.00 0.00 0.00 1.31
4280 4951 7.256399 ACATATCTGTAATCCTAGATCCCCAA 58.744 38.462 0.00 0.00 35.42 4.12
4282 4953 7.365117 CCAACATATCTGTAATCCTAGATCCCC 60.365 44.444 0.00 0.00 35.42 4.81
4286 4957 7.805083 AGCCAACATATCTGTAATCCTAGAT 57.195 36.000 0.00 0.00 37.42 1.98
4306 4977 3.317149 ACGATCTGCTAAATACGTAGCCA 59.683 43.478 5.63 0.00 44.98 4.75
4315 4986 2.009774 GTGCACCACGATCTGCTAAAT 58.990 47.619 5.22 0.00 34.29 1.40
4333 5004 4.564372 CACTCCAAGATCAATAGTCGTGTG 59.436 45.833 0.00 0.00 0.00 3.82
4342 5013 1.089920 GCACGCACTCCAAGATCAAT 58.910 50.000 0.00 0.00 0.00 2.57
4343 5014 0.955428 GGCACGCACTCCAAGATCAA 60.955 55.000 0.00 0.00 0.00 2.57
4381 5052 2.419297 GCATCCAGAAGACCTGTACCAG 60.419 54.545 0.00 0.00 41.33 4.00
4383 5054 1.471676 CGCATCCAGAAGACCTGTACC 60.472 57.143 0.00 0.00 41.33 3.34
4386 5066 1.599047 CCGCATCCAGAAGACCTGT 59.401 57.895 0.00 0.00 41.33 4.00
4418 5098 2.445845 CCGAGGAGCCCCATGGTA 60.446 66.667 11.73 0.00 33.88 3.25
4451 5131 0.313043 TTCTCAACACGTCGTCTCCC 59.687 55.000 0.00 0.00 0.00 4.30
4464 5144 3.323979 GTCCTGGACTAGTTGGTTCTCAA 59.676 47.826 19.53 0.00 0.00 3.02
4469 5149 1.697982 GGTGTCCTGGACTAGTTGGTT 59.302 52.381 26.03 0.00 33.15 3.67
4473 5153 2.567615 GTGATGGTGTCCTGGACTAGTT 59.432 50.000 26.03 10.02 33.15 2.24
4474 5154 2.180276 GTGATGGTGTCCTGGACTAGT 58.820 52.381 26.03 10.70 33.15 2.57
4483 5163 2.046314 CACCCGGTGATGGTGTCC 60.046 66.667 12.68 0.00 46.62 4.02
4538 5219 1.667154 CGACATCGGCAGAAGGAGGA 61.667 60.000 0.00 0.00 35.37 3.71
4600 5284 1.147153 GTGAGCATCCCTAGCCACC 59.853 63.158 0.00 0.00 31.41 4.61
4614 5298 2.266554 GAAGATGAAGACTGGCGTGAG 58.733 52.381 0.00 0.00 0.00 3.51
4617 5301 1.205893 GAGGAAGATGAAGACTGGCGT 59.794 52.381 0.00 0.00 0.00 5.68
4622 5306 3.165875 TCAACCGAGGAAGATGAAGACT 58.834 45.455 0.00 0.00 0.00 3.24
4651 5335 3.857309 AACCCGACGAGGTCTCCGT 62.857 63.158 8.23 0.00 40.05 4.69
4662 5346 1.429463 CTTAGTGCACTGAACCCGAC 58.571 55.000 29.57 0.00 0.00 4.79
4667 5351 1.873591 CACCACCTTAGTGCACTGAAC 59.126 52.381 29.57 0.00 43.09 3.18
4671 5355 0.396811 GGTCACCACCTTAGTGCACT 59.603 55.000 25.12 25.12 43.09 4.40
4686 5370 2.472029 GAGAAGGGAAGGATGAGGTCA 58.528 52.381 0.00 0.00 0.00 4.02
4718 5402 2.088423 GACACAACACACCACCAAGAA 58.912 47.619 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.