Multiple sequence alignment - TraesCS5D01G479700

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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 TraesCS5D01G479700 chr5D 100.000 2566 0 0 1 2566 517672081 517669516 0.000000e+00 4739
1 TraesCS5D01G479700 chr5D 96.190 105 4 0 1 105 513466149 513466045 3.390000e-39 172
2 TraesCS5D01G479700 chr5D 95.238 105 5 0 1 105 512894316 512894212 1.580000e-37 167
3 TraesCS5D01G479700 chr5D 95.146 103 5 0 1 103 499619241 499619139 2.040000e-36 163
4 TraesCS5D01G479700 chr5A 87.549 1783 116 51 814 2566 645125144 645123438 0.000000e+00 1965
5 TraesCS5D01G479700 chr5A 88.995 209 13 5 447 652 645125672 645125471 1.520000e-62 250
6 TraesCS5D01G479700 chr5A 99.038 104 1 0 1 104 645126162 645126059 1.210000e-43 187
7 TraesCS5D01G479700 chr5B 93.014 1231 54 14 1343 2566 650164582 650163377 0.000000e+00 1768
8 TraesCS5D01G479700 chr5B 87.190 484 32 15 829 1302 650165047 650164584 8.130000e-145 523
9 TraesCS5D01G479700 chr5B 87.744 359 29 11 298 652 152509015 152508668 3.070000e-109 405
10 TraesCS5D01G479700 chr5B 87.151 358 30 12 298 651 87589198 87588853 2.390000e-105 392
11 TraesCS5D01G479700 chr5B 91.803 183 13 1 824 1006 650174112 650173932 1.180000e-63 254
12 TraesCS5D01G479700 chr5B 96.190 105 4 0 1 105 650165489 650165385 3.390000e-39 172
13 TraesCS5D01G479700 chr5B 92.857 112 8 0 1 112 657596212 657596323 2.040000e-36 163
14 TraesCS5D01G479700 chr5B 94.340 106 5 1 1 105 643973670 643973565 7.350000e-36 161
15 TraesCS5D01G479700 chr4D 88.154 363 27 10 1524 1885 446988095 446988442 3.950000e-113 418
16 TraesCS5D01G479700 chr4A 87.772 368 29 9 1519 1885 17268836 17269188 1.420000e-112 416
17 TraesCS5D01G479700 chr2A 87.945 365 28 9 1522 1885 654734806 654734457 1.420000e-112 416
18 TraesCS5D01G479700 chr3A 87.534 369 28 10 1519 1885 157989524 157989876 6.610000e-111 411
19 TraesCS5D01G479700 chrUn 87.744 359 29 11 298 652 328533687 328534034 3.070000e-109 405
20 TraesCS5D01G479700 chrUn 87.744 359 29 11 298 652 375860887 375861234 3.070000e-109 405
21 TraesCS5D01G479700 chr7A 87.228 368 31 9 1519 1885 643995721 643996073 3.070000e-109 405
22 TraesCS5D01G479700 chr1B 87.744 359 29 11 298 652 559437402 559437749 3.070000e-109 405
23 TraesCS5D01G479700 chr1B 87.395 357 33 9 298 652 525126097 525125751 1.430000e-107 399
24 TraesCS5D01G479700 chr1B 86.351 359 29 14 298 652 92301782 92301440 8.670000e-100 374
25 TraesCS5D01G479700 chr2B 87.430 358 32 9 298 652 465516936 465517283 1.430000e-107 399
26 TraesCS5D01G479700 chr2B 86.538 364 35 10 1523 1885 225356707 225356357 3.100000e-104 388
27 TraesCS5D01G479700 chr2B 85.994 357 37 9 298 652 186777580 186777235 1.120000e-98 370
28 TraesCS5D01G479700 chr3B 86.835 357 33 7 298 652 733132850 733133194 1.110000e-103 387
29 TraesCS5D01G479700 chr3B 85.870 368 36 10 1519 1885 755564997 755565349 6.700000e-101 377
30 TraesCS5D01G479700 chr6D 94.286 105 5 1 1 105 434450253 434450356 2.640000e-35 159
31 TraesCS5D01G479700 chr6D 94.231 104 5 1 1 104 434444058 434444160 9.500000e-35 158


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 TraesCS5D01G479700 chr5D 517669516 517672081 2565 True 4739.000000 4739 100.000000 1 2566 1 chr5D.!!$R4 2565
1 TraesCS5D01G479700 chr5A 645123438 645126162 2724 True 800.666667 1965 91.860667 1 2566 3 chr5A.!!$R1 2565
2 TraesCS5D01G479700 chr5B 650163377 650165489 2112 True 821.000000 1768 92.131333 1 2566 3 chr5B.!!$R5 2565

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
780 963 0.10339 TGAAGTCGCCGTCAGTTCAA 59.897 50.0 0.0 0.0 31.55 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 2235 0.037605 GTAGCTGCTGGTACCGTTGT 60.038 55.0 18.95 0.0 40.24 3.32 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
44 45 3.684788 AGAGTGGACGTCATAATTTGTGC 59.315 43.478 18.91 0.00 0.00 4.57
108 109 9.898152 TTTGAAATTAAATCTTGGTCCTTTTGT 57.102 25.926 0.00 0.00 0.00 2.83
109 110 8.885494 TGAAATTAAATCTTGGTCCTTTTGTG 57.115 30.769 0.00 0.00 0.00 3.33
110 111 7.930865 TGAAATTAAATCTTGGTCCTTTTGTGG 59.069 33.333 0.00 0.00 0.00 4.17
111 112 6.994421 ATTAAATCTTGGTCCTTTTGTGGT 57.006 33.333 0.00 0.00 0.00 4.16
112 113 8.485578 AATTAAATCTTGGTCCTTTTGTGGTA 57.514 30.769 0.00 0.00 0.00 3.25
113 114 7.519032 TTAAATCTTGGTCCTTTTGTGGTAG 57.481 36.000 0.00 0.00 0.00 3.18
114 115 4.993705 ATCTTGGTCCTTTTGTGGTAGA 57.006 40.909 0.00 0.00 0.00 2.59
115 116 4.351874 TCTTGGTCCTTTTGTGGTAGAG 57.648 45.455 0.00 0.00 0.00 2.43
116 117 3.072476 TCTTGGTCCTTTTGTGGTAGAGG 59.928 47.826 0.00 0.00 0.00 3.69
117 118 1.702957 TGGTCCTTTTGTGGTAGAGGG 59.297 52.381 0.00 0.00 0.00 4.30
118 119 1.703513 GGTCCTTTTGTGGTAGAGGGT 59.296 52.381 0.00 0.00 0.00 4.34
119 120 2.908351 GGTCCTTTTGTGGTAGAGGGTA 59.092 50.000 0.00 0.00 0.00 3.69
120 121 3.055312 GGTCCTTTTGTGGTAGAGGGTAG 60.055 52.174 0.00 0.00 0.00 3.18
121 122 3.836562 GTCCTTTTGTGGTAGAGGGTAGA 59.163 47.826 0.00 0.00 0.00 2.59
122 123 3.836562 TCCTTTTGTGGTAGAGGGTAGAC 59.163 47.826 0.00 0.00 0.00 2.59
123 124 3.368116 CCTTTTGTGGTAGAGGGTAGACG 60.368 52.174 0.00 0.00 0.00 4.18
124 125 2.885135 TTGTGGTAGAGGGTAGACGA 57.115 50.000 0.00 0.00 0.00 4.20
125 126 2.414994 TGTGGTAGAGGGTAGACGAG 57.585 55.000 0.00 0.00 0.00 4.18
126 127 1.632409 TGTGGTAGAGGGTAGACGAGT 59.368 52.381 0.00 0.00 0.00 4.18
127 128 2.840038 TGTGGTAGAGGGTAGACGAGTA 59.160 50.000 0.00 0.00 0.00 2.59
128 129 3.202097 GTGGTAGAGGGTAGACGAGTAC 58.798 54.545 0.00 0.00 0.00 2.73
129 130 2.159043 TGGTAGAGGGTAGACGAGTACG 60.159 54.545 0.00 0.00 45.75 3.67
130 131 1.864082 GTAGAGGGTAGACGAGTACGC 59.136 57.143 0.00 0.00 43.96 4.42
131 132 0.809241 AGAGGGTAGACGAGTACGCG 60.809 60.000 17.76 17.76 43.96 6.01
132 133 2.023882 GGGTAGACGAGTACGCGC 59.976 66.667 19.25 11.60 43.96 6.86
133 134 2.350537 GGTAGACGAGTACGCGCG 60.351 66.667 30.96 30.96 43.96 6.86
134 135 2.350537 GTAGACGAGTACGCGCGG 60.351 66.667 35.22 18.29 42.14 6.46
135 136 4.228097 TAGACGAGTACGCGCGGC 62.228 66.667 35.22 25.27 46.44 6.53
151 152 4.440145 GCCCCTGCCAATCTTTGA 57.560 55.556 0.00 0.00 0.00 2.69
152 153 2.669878 GCCCCTGCCAATCTTTGAA 58.330 52.632 0.00 0.00 0.00 2.69
153 154 0.975887 GCCCCTGCCAATCTTTGAAA 59.024 50.000 0.00 0.00 0.00 2.69
154 155 1.556451 GCCCCTGCCAATCTTTGAAAT 59.444 47.619 0.00 0.00 0.00 2.17
155 156 2.026915 GCCCCTGCCAATCTTTGAAATT 60.027 45.455 0.00 0.00 0.00 1.82
156 157 3.197549 GCCCCTGCCAATCTTTGAAATTA 59.802 43.478 0.00 0.00 0.00 1.40
157 158 4.323409 GCCCCTGCCAATCTTTGAAATTAA 60.323 41.667 0.00 0.00 0.00 1.40
158 159 5.802821 GCCCCTGCCAATCTTTGAAATTAAA 60.803 40.000 0.00 0.00 0.00 1.52
159 160 6.417258 CCCCTGCCAATCTTTGAAATTAAAT 58.583 36.000 0.00 0.00 0.00 1.40
160 161 6.539826 CCCCTGCCAATCTTTGAAATTAAATC 59.460 38.462 0.00 0.00 0.00 2.17
161 162 7.333323 CCCTGCCAATCTTTGAAATTAAATCT 58.667 34.615 0.00 0.00 0.00 2.40
162 163 7.825761 CCCTGCCAATCTTTGAAATTAAATCTT 59.174 33.333 0.00 0.00 0.00 2.40
163 164 9.874205 CCTGCCAATCTTTGAAATTAAATCTTA 57.126 29.630 0.00 0.00 0.00 2.10
177 178 6.721571 TTAAATCTTAGTCCTGTTTCGCTG 57.278 37.500 0.00 0.00 0.00 5.18
190 191 0.315886 TTCGCTGGCTTACGAAGTCA 59.684 50.000 5.87 0.00 43.93 3.41
211 215 5.531287 GTCAGTTTTACAATCCAGTCCTTGT 59.469 40.000 0.00 0.00 38.95 3.16
220 224 2.638480 CCAGTCCTTGTTCTGGTTCA 57.362 50.000 3.38 0.00 44.19 3.18
222 226 3.077359 CCAGTCCTTGTTCTGGTTCATC 58.923 50.000 3.38 0.00 44.19 2.92
223 227 3.244700 CCAGTCCTTGTTCTGGTTCATCT 60.245 47.826 3.38 0.00 44.19 2.90
224 228 3.750130 CAGTCCTTGTTCTGGTTCATCTG 59.250 47.826 0.00 0.00 0.00 2.90
225 229 3.392616 AGTCCTTGTTCTGGTTCATCTGT 59.607 43.478 0.00 0.00 0.00 3.41
226 230 4.137543 GTCCTTGTTCTGGTTCATCTGTT 58.862 43.478 0.00 0.00 0.00 3.16
227 231 4.023707 GTCCTTGTTCTGGTTCATCTGTTG 60.024 45.833 0.00 0.00 0.00 3.33
228 232 3.304928 CCTTGTTCTGGTTCATCTGTTGC 60.305 47.826 0.00 0.00 0.00 4.17
229 233 2.929641 TGTTCTGGTTCATCTGTTGCA 58.070 42.857 0.00 0.00 0.00 4.08
239 243 1.070821 ATCTGTTGCACACATCGACG 58.929 50.000 0.00 0.00 33.76 5.12
247 294 3.770040 CACATCGACGGGGAGCCA 61.770 66.667 0.00 0.00 0.00 4.75
261 308 1.569479 GAGCCAGCAACGTGTTCTCC 61.569 60.000 0.00 0.00 0.00 3.71
286 333 8.721478 CCGAACAGAGAAAAAGAAGATTTCATA 58.279 33.333 2.32 0.00 38.86 2.15
289 343 8.049655 ACAGAGAAAAAGAAGATTTCATAGGC 57.950 34.615 2.32 0.00 38.86 3.93
303 357 2.053244 CATAGGCTGGAGGGTTCTGAT 58.947 52.381 0.00 0.00 0.00 2.90
305 359 0.985490 AGGCTGGAGGGTTCTGATCC 60.985 60.000 0.00 0.00 0.00 3.36
306 360 1.274703 GGCTGGAGGGTTCTGATCCA 61.275 60.000 7.06 2.68 40.80 3.41
307 361 0.620556 GCTGGAGGGTTCTGATCCAA 59.379 55.000 7.06 0.00 42.40 3.53
308 362 1.407989 GCTGGAGGGTTCTGATCCAAG 60.408 57.143 7.06 0.83 42.40 3.61
313 376 3.348119 GAGGGTTCTGATCCAAGTTTCC 58.652 50.000 7.06 0.00 0.00 3.13
314 377 2.041755 AGGGTTCTGATCCAAGTTTCCC 59.958 50.000 7.06 0.00 0.00 3.97
316 379 3.084786 GGTTCTGATCCAAGTTTCCCTG 58.915 50.000 0.00 0.00 0.00 4.45
332 395 1.133253 CTGAGCAACATGAACGGCG 59.867 57.895 4.80 4.80 0.00 6.46
334 397 0.319986 TGAGCAACATGAACGGCGTA 60.320 50.000 15.20 0.00 0.00 4.42
346 409 4.496360 TGAACGGCGTATAACATCTGAAA 58.504 39.130 15.20 0.00 0.00 2.69
351 414 4.260212 CGGCGTATAACATCTGAAACTTGG 60.260 45.833 0.00 0.00 0.00 3.61
358 421 1.815003 CATCTGAAACTTGGGCTGTCC 59.185 52.381 0.00 0.00 0.00 4.02
362 427 1.228154 AAACTTGGGCTGTCCGGTC 60.228 57.895 0.00 0.00 38.76 4.79
382 447 4.738740 GGTCGTATATTCTGGTGTTCTTCG 59.261 45.833 0.00 0.00 0.00 3.79
407 472 5.702209 CCTCCCGCTTACAACTAAGTAAAAA 59.298 40.000 0.00 0.00 33.89 1.94
413 478 6.032042 CGCTTACAACTAAGTAAAAATTGGCG 59.968 38.462 0.00 0.00 35.99 5.69
430 495 1.266718 GGCGACAAATTCACTTCTGCA 59.733 47.619 0.00 0.00 0.00 4.41
437 502 5.615289 ACAAATTCACTTCTGCACTACTCT 58.385 37.500 0.00 0.00 0.00 3.24
439 504 6.647067 ACAAATTCACTTCTGCACTACTCTAC 59.353 38.462 0.00 0.00 0.00 2.59
440 505 6.597832 AATTCACTTCTGCACTACTCTACT 57.402 37.500 0.00 0.00 0.00 2.57
443 508 6.051179 TCACTTCTGCACTACTCTACTAGA 57.949 41.667 0.00 0.00 0.00 2.43
446 511 8.433599 TCACTTCTGCACTACTCTACTAGATAT 58.566 37.037 0.00 0.00 0.00 1.63
448 513 9.938280 ACTTCTGCACTACTCTACTAGATATAG 57.062 37.037 0.00 0.00 0.00 1.31
489 669 7.492669 GTCACTGCAGTCTTGAGCTTATTATAA 59.507 37.037 18.64 0.00 0.00 0.98
490 670 7.492669 TCACTGCAGTCTTGAGCTTATTATAAC 59.507 37.037 18.64 0.00 0.00 1.89
491 671 6.763610 ACTGCAGTCTTGAGCTTATTATAACC 59.236 38.462 15.25 0.00 0.00 2.85
492 672 6.889198 TGCAGTCTTGAGCTTATTATAACCT 58.111 36.000 0.00 0.00 0.00 3.50
493 673 6.763135 TGCAGTCTTGAGCTTATTATAACCTG 59.237 38.462 0.00 0.00 0.00 4.00
495 675 7.042389 GCAGTCTTGAGCTTATTATAACCTGTC 60.042 40.741 0.00 0.00 0.00 3.51
497 677 8.200792 AGTCTTGAGCTTATTATAACCTGTCAG 58.799 37.037 0.00 0.00 0.00 3.51
498 678 7.982354 GTCTTGAGCTTATTATAACCTGTCAGT 59.018 37.037 0.00 0.00 0.00 3.41
499 679 8.540388 TCTTGAGCTTATTATAACCTGTCAGTT 58.460 33.333 0.00 0.00 0.00 3.16
500 680 8.718102 TTGAGCTTATTATAACCTGTCAGTTC 57.282 34.615 0.00 0.00 0.00 3.01
501 681 7.847096 TGAGCTTATTATAACCTGTCAGTTCA 58.153 34.615 0.00 0.00 0.00 3.18
503 683 8.079211 AGCTTATTATAACCTGTCAGTTCAGA 57.921 34.615 0.00 0.00 37.61 3.27
504 684 7.982354 AGCTTATTATAACCTGTCAGTTCAGAC 59.018 37.037 0.00 0.00 37.61 3.51
505 685 7.982354 GCTTATTATAACCTGTCAGTTCAGACT 59.018 37.037 0.00 0.00 39.27 3.24
506 686 9.877178 CTTATTATAACCTGTCAGTTCAGACTT 57.123 33.333 0.00 0.00 39.27 3.01
507 687 9.871238 TTATTATAACCTGTCAGTTCAGACTTC 57.129 33.333 0.00 0.00 39.27 3.01
532 712 2.047179 GACAAGCACCCCGAGTCC 60.047 66.667 0.00 0.00 0.00 3.85
549 729 2.106511 AGTCCAGCTTTAGCCTGAAACA 59.893 45.455 0.00 0.00 43.38 2.83
558 738 5.985530 GCTTTAGCCTGAAACAAAGTGAAAT 59.014 36.000 0.00 0.00 31.95 2.17
599 779 3.799281 ATGTGTCACCAACCAAGTTTG 57.201 42.857 0.00 0.00 0.00 2.93
601 781 0.820871 TGTCACCAACCAAGTTTGCC 59.179 50.000 0.00 0.00 0.00 4.52
602 782 0.248866 GTCACCAACCAAGTTTGCCG 60.249 55.000 0.00 0.00 0.00 5.69
610 790 1.586154 CCAAGTTTGCCGGCTACCAG 61.586 60.000 29.70 18.47 0.00 4.00
618 798 1.889530 GCCGGCTACCAGTTCTCTGT 61.890 60.000 22.15 0.00 39.82 3.41
651 831 2.844122 AACAACACTCCGCAAAACTC 57.156 45.000 0.00 0.00 0.00 3.01
652 832 1.745232 ACAACACTCCGCAAAACTCA 58.255 45.000 0.00 0.00 0.00 3.41
653 833 2.297701 ACAACACTCCGCAAAACTCAT 58.702 42.857 0.00 0.00 0.00 2.90
654 834 2.033299 ACAACACTCCGCAAAACTCATG 59.967 45.455 0.00 0.00 0.00 3.07
655 835 1.967319 ACACTCCGCAAAACTCATGT 58.033 45.000 0.00 0.00 0.00 3.21
656 836 1.603802 ACACTCCGCAAAACTCATGTG 59.396 47.619 0.00 0.00 0.00 3.21
657 837 0.593128 ACTCCGCAAAACTCATGTGC 59.407 50.000 0.00 0.00 34.87 4.57
658 838 0.592637 CTCCGCAAAACTCATGTGCA 59.407 50.000 6.13 0.00 38.19 4.57
659 839 1.200716 CTCCGCAAAACTCATGTGCAT 59.799 47.619 6.13 0.00 38.19 3.96
660 840 1.199789 TCCGCAAAACTCATGTGCATC 59.800 47.619 6.13 0.00 38.19 3.91
661 841 1.200716 CCGCAAAACTCATGTGCATCT 59.799 47.619 6.13 0.00 38.19 2.90
662 842 2.247637 CGCAAAACTCATGTGCATCTG 58.752 47.619 6.13 0.00 38.19 2.90
663 843 2.602878 GCAAAACTCATGTGCATCTGG 58.397 47.619 0.00 0.00 38.19 3.86
664 844 2.229543 GCAAAACTCATGTGCATCTGGA 59.770 45.455 0.00 0.00 38.19 3.86
665 845 3.672511 GCAAAACTCATGTGCATCTGGAG 60.673 47.826 0.00 0.00 38.19 3.86
666 846 1.747709 AACTCATGTGCATCTGGAGC 58.252 50.000 0.00 0.00 0.00 4.70
667 847 0.910338 ACTCATGTGCATCTGGAGCT 59.090 50.000 0.00 0.00 0.00 4.09
668 848 1.300481 CTCATGTGCATCTGGAGCTG 58.700 55.000 0.00 0.00 0.00 4.24
669 849 0.107361 TCATGTGCATCTGGAGCTGG 60.107 55.000 0.00 0.00 0.00 4.85
670 850 1.453379 ATGTGCATCTGGAGCTGGC 60.453 57.895 0.00 0.00 0.00 4.85
671 851 2.045634 GTGCATCTGGAGCTGGCA 60.046 61.111 0.00 0.00 0.00 4.92
672 852 2.113433 GTGCATCTGGAGCTGGCAG 61.113 63.158 10.94 10.94 34.78 4.85
673 853 3.210528 GCATCTGGAGCTGGCAGC 61.211 66.667 31.56 31.56 42.84 5.25
688 868 1.151668 GCAGCTGCCGTATATTCTGG 58.848 55.000 28.76 0.00 34.31 3.86
693 873 2.868044 GCTGCCGTATATTCTGGTCCTG 60.868 54.545 0.00 0.00 0.00 3.86
696 876 3.181469 TGCCGTATATTCTGGTCCTGTTC 60.181 47.826 0.00 0.00 0.00 3.18
739 919 3.515602 AGATTTGGCCAGAACTGAACT 57.484 42.857 5.11 0.00 0.00 3.01
744 924 4.431416 TTGGCCAGAACTGAACTTCTAA 57.569 40.909 5.11 0.00 0.00 2.10
747 927 4.134563 GGCCAGAACTGAACTTCTAAACA 58.865 43.478 0.00 0.00 0.00 2.83
751 931 6.426937 GCCAGAACTGAACTTCTAAACATGTA 59.573 38.462 0.00 0.00 0.00 2.29
753 933 7.118390 CCAGAACTGAACTTCTAAACATGTAGG 59.882 40.741 0.00 0.00 0.00 3.18
766 949 9.256228 TCTAAACATGTAGGTAGAGATTGAAGT 57.744 33.333 0.00 0.00 0.00 3.01
768 951 6.137794 ACATGTAGGTAGAGATTGAAGTCG 57.862 41.667 0.00 0.00 0.00 4.18
770 953 3.380637 TGTAGGTAGAGATTGAAGTCGCC 59.619 47.826 0.00 0.00 0.00 5.54
778 961 1.390463 GATTGAAGTCGCCGTCAGTTC 59.610 52.381 0.00 0.00 30.66 3.01
780 963 0.103390 TGAAGTCGCCGTCAGTTCAA 59.897 50.000 0.00 0.00 31.55 2.69
782 965 0.104304 AAGTCGCCGTCAGTTCAAGT 59.896 50.000 0.00 0.00 0.00 3.16
784 967 1.068472 AGTCGCCGTCAGTTCAAGTAG 60.068 52.381 0.00 0.00 0.00 2.57
785 968 1.068748 GTCGCCGTCAGTTCAAGTAGA 60.069 52.381 0.00 0.00 0.00 2.59
786 969 1.199327 TCGCCGTCAGTTCAAGTAGAG 59.801 52.381 0.00 0.00 0.00 2.43
787 970 1.199327 CGCCGTCAGTTCAAGTAGAGA 59.801 52.381 0.00 0.00 0.00 3.10
788 971 2.597520 GCCGTCAGTTCAAGTAGAGAC 58.402 52.381 0.00 0.00 0.00 3.36
789 972 2.030185 GCCGTCAGTTCAAGTAGAGACA 60.030 50.000 0.00 0.00 0.00 3.41
790 973 3.552273 GCCGTCAGTTCAAGTAGAGACAA 60.552 47.826 0.00 0.00 0.00 3.18
791 974 4.230657 CCGTCAGTTCAAGTAGAGACAAG 58.769 47.826 0.00 0.00 0.00 3.16
792 975 3.670991 CGTCAGTTCAAGTAGAGACAAGC 59.329 47.826 0.00 0.00 0.00 4.01
793 976 4.621991 GTCAGTTCAAGTAGAGACAAGCA 58.378 43.478 0.00 0.00 0.00 3.91
794 977 4.446051 GTCAGTTCAAGTAGAGACAAGCAC 59.554 45.833 0.00 0.00 0.00 4.40
808 991 0.553819 AAGCACCCCCACACAGTTTA 59.446 50.000 0.00 0.00 0.00 2.01
839 1221 9.522804 TTTGACCAGTGTAAATGTAAATTCAAC 57.477 29.630 0.00 0.00 0.00 3.18
862 1244 2.304761 ACTTAAATCTGCCACGGAAGGA 59.695 45.455 0.00 0.00 0.00 3.36
870 1252 3.199946 TCTGCCACGGAAGGAAAGATAAT 59.800 43.478 0.00 0.00 0.00 1.28
877 1259 4.586001 ACGGAAGGAAAGATAATACGGCTA 59.414 41.667 0.00 0.00 0.00 3.93
881 1263 5.394224 AGGAAAGATAATACGGCTAGCTC 57.606 43.478 15.72 1.94 0.00 4.09
1006 1390 0.689080 AACAACAACCACCATGGCCA 60.689 50.000 13.04 8.56 42.67 5.36
1008 1392 0.037139 CAACAACCACCATGGCCATG 60.037 55.000 34.82 34.82 42.67 3.66
1028 1412 3.322466 CTCCGGCTCCAGGGTTGT 61.322 66.667 0.00 0.00 0.00 3.32
1030 1414 2.672996 CCGGCTCCAGGGTTGTTG 60.673 66.667 0.00 0.00 0.00 3.33
1032 1416 2.116125 GGCTCCAGGGTTGTTGCT 59.884 61.111 0.00 0.00 0.00 3.91
1033 1417 1.973812 GGCTCCAGGGTTGTTGCTC 60.974 63.158 0.00 0.00 0.00 4.26
1036 1420 2.113139 CCAGGGTTGTTGCTCCGT 59.887 61.111 0.00 0.00 0.00 4.69
1038 1422 1.227823 CAGGGTTGTTGCTCCGTCA 60.228 57.895 0.00 0.00 0.00 4.35
1049 1433 2.282958 TCCGTCACTCCTCGCCTT 60.283 61.111 0.00 0.00 0.00 4.35
1084 1468 2.511600 CCTTCGCTACCCCGCTTG 60.512 66.667 0.00 0.00 0.00 4.01
1086 1470 3.950794 CTTCGCTACCCCGCTTGCA 62.951 63.158 0.00 0.00 0.00 4.08
1087 1471 3.950794 TTCGCTACCCCGCTTGCAG 62.951 63.158 0.00 0.00 0.00 4.41
1090 1474 2.124570 CTACCCCGCTTGCAGCAT 60.125 61.111 0.00 0.00 42.58 3.79
1091 1475 2.124736 TACCCCGCTTGCAGCATC 60.125 61.111 0.00 0.00 42.58 3.91
1092 1476 3.697439 TACCCCGCTTGCAGCATCC 62.697 63.158 0.00 0.00 42.58 3.51
1105 1489 2.203126 CATCCAAGAGAGGCGCCC 60.203 66.667 26.15 15.34 0.00 6.13
1166 1556 0.613777 ACCCACGATTCCTCCTCAAC 59.386 55.000 0.00 0.00 0.00 3.18
1190 1580 8.947055 ACTTCTCTTATGTTGCATTTTGTTTT 57.053 26.923 0.00 0.00 0.00 2.43
1191 1581 8.819974 ACTTCTCTTATGTTGCATTTTGTTTTG 58.180 29.630 0.00 0.00 0.00 2.44
1192 1582 8.939201 TTCTCTTATGTTGCATTTTGTTTTGA 57.061 26.923 0.00 0.00 0.00 2.69
1193 1583 8.578308 TCTCTTATGTTGCATTTTGTTTTGAG 57.422 30.769 0.00 0.00 0.00 3.02
1194 1584 8.196771 TCTCTTATGTTGCATTTTGTTTTGAGT 58.803 29.630 0.00 0.00 0.00 3.41
1196 1586 5.989551 ATGTTGCATTTTGTTTTGAGTCC 57.010 34.783 0.00 0.00 0.00 3.85
1200 1591 7.044181 TGTTGCATTTTGTTTTGAGTCCATAA 58.956 30.769 0.00 0.00 0.00 1.90
1294 1690 2.104792 CACCAGAGAACAGGAACCAGAA 59.895 50.000 0.00 0.00 0.00 3.02
1307 1703 1.512926 ACCAGAACAGTAAGCAAGCG 58.487 50.000 0.00 0.00 0.00 4.68
1308 1704 1.202651 ACCAGAACAGTAAGCAAGCGT 60.203 47.619 0.00 0.00 0.00 5.07
1309 1705 1.195448 CCAGAACAGTAAGCAAGCGTG 59.805 52.381 0.00 0.00 0.00 5.34
1333 1729 2.144730 GTGCATCCATCAGCTCTCATC 58.855 52.381 0.00 0.00 0.00 2.92
1341 1738 6.223351 TCCATCAGCTCTCATCATCATATC 57.777 41.667 0.00 0.00 0.00 1.63
1535 1933 3.211963 GCCATCGCCTTCGCCAAT 61.212 61.111 0.00 0.00 35.26 3.16
1608 2006 2.776913 CCCTTCCGGCGAGAGAGAC 61.777 68.421 9.30 0.00 0.00 3.36
1615 2013 1.357334 GGCGAGAGAGACGATGACC 59.643 63.158 0.00 0.00 0.00 4.02
1656 2054 9.973450 AGAGATTACTGTAAAGCTGTATGTATG 57.027 33.333 4.11 0.00 32.73 2.39
1657 2055 9.751542 GAGATTACTGTAAAGCTGTATGTATGT 57.248 33.333 4.11 0.00 32.73 2.29
1699 2097 5.452255 TCTTTATATAGTGGAGTCACCGGT 58.548 41.667 0.00 0.00 44.64 5.28
1706 2104 0.541063 TGGAGTCACCGGTTGCTCTA 60.541 55.000 25.46 20.38 42.61 2.43
1707 2105 0.108756 GGAGTCACCGGTTGCTCTAC 60.109 60.000 25.46 11.66 32.20 2.59
1708 2106 0.601558 GAGTCACCGGTTGCTCTACA 59.398 55.000 21.61 0.00 0.00 2.74
1709 2107 1.204941 GAGTCACCGGTTGCTCTACAT 59.795 52.381 21.61 0.00 0.00 2.29
1710 2108 2.426024 GAGTCACCGGTTGCTCTACATA 59.574 50.000 21.61 0.00 0.00 2.29
1731 2129 3.014623 ACATTCATGACTGCATCTGGTG 58.985 45.455 12.62 0.00 30.68 4.17
1756 2154 3.251972 GCATATAGAGTGAAAAGCCCTGC 59.748 47.826 0.00 0.00 0.00 4.85
1764 2162 2.545106 GTGAAAAGCCCTGCATTTGTTG 59.455 45.455 0.00 0.00 29.57 3.33
1821 2226 6.024552 TCGATCAAGAATTTGGGGAAAAAG 57.975 37.500 0.00 0.00 34.97 2.27
1825 2230 8.416329 CGATCAAGAATTTGGGGAAAAAGATAT 58.584 33.333 0.00 0.00 34.97 1.63
1845 2250 1.808411 AATGACAACGGTACCAGCAG 58.192 50.000 13.54 0.74 0.00 4.24
1851 2256 0.246635 AACGGTACCAGCAGCTACAG 59.753 55.000 13.54 0.00 0.00 2.74
1885 2290 5.675538 AGGAGGCAAGAATCTACACATAAC 58.324 41.667 0.00 0.00 0.00 1.89
1959 2382 8.927721 CATACATTCTAGCAAGATTCATGAGAG 58.072 37.037 0.00 0.00 0.00 3.20
1980 2403 5.184096 AGAGTCTGCATACCATAGAATACCG 59.816 44.000 0.00 0.00 0.00 4.02
1990 2413 5.548406 ACCATAGAATACCGTTGGCTATTC 58.452 41.667 8.73 8.73 31.86 1.75
2033 2456 2.503356 ACAAAGACATGTTTTTGGGGCA 59.497 40.909 32.91 0.00 38.51 5.36
2067 2490 5.730550 CCCACAGCAGTATACAGTTAAAGA 58.269 41.667 5.50 0.00 0.00 2.52
2079 2502 7.938563 ATACAGTTAAAGATTTTGCGCAAAA 57.061 28.000 40.76 40.76 43.48 2.44
2130 2553 1.664151 CGCGGTTTCCTATCAAACTCC 59.336 52.381 0.00 0.00 36.62 3.85
2136 2559 3.777465 TTCCTATCAAACTCCGACTCG 57.223 47.619 0.00 0.00 0.00 4.18
2189 2612 2.203209 CTTCGCCATGCCCCTACC 60.203 66.667 0.00 0.00 0.00 3.18
2291 2714 3.304324 GCTTCCTTCAGCTTGTTTCTGAC 60.304 47.826 0.00 0.00 39.99 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.732308 GAACGCGTACCCCCTCTAG 59.268 63.158 14.46 0.00 0.00 2.43
105 106 2.040813 ACTCGTCTACCCTCTACCACAA 59.959 50.000 0.00 0.00 0.00 3.33
106 107 1.632409 ACTCGTCTACCCTCTACCACA 59.368 52.381 0.00 0.00 0.00 4.17
107 108 2.416680 ACTCGTCTACCCTCTACCAC 57.583 55.000 0.00 0.00 0.00 4.16
108 109 2.159043 CGTACTCGTCTACCCTCTACCA 60.159 54.545 0.00 0.00 0.00 3.25
109 110 2.478831 CGTACTCGTCTACCCTCTACC 58.521 57.143 0.00 0.00 0.00 3.18
110 111 1.864082 GCGTACTCGTCTACCCTCTAC 59.136 57.143 0.00 0.00 39.49 2.59
111 112 1.536922 CGCGTACTCGTCTACCCTCTA 60.537 57.143 0.00 0.00 39.49 2.43
112 113 0.809241 CGCGTACTCGTCTACCCTCT 60.809 60.000 0.00 0.00 39.49 3.69
113 114 1.640604 CGCGTACTCGTCTACCCTC 59.359 63.158 0.00 0.00 39.49 4.30
114 115 2.467826 GCGCGTACTCGTCTACCCT 61.468 63.158 8.43 0.00 39.49 4.34
115 116 2.023882 GCGCGTACTCGTCTACCC 59.976 66.667 8.43 0.00 39.49 3.69
116 117 2.350537 CGCGCGTACTCGTCTACC 60.351 66.667 24.19 0.00 39.49 3.18
117 118 2.350537 CCGCGCGTACTCGTCTAC 60.351 66.667 29.95 0.00 39.49 2.59
118 119 4.228097 GCCGCGCGTACTCGTCTA 62.228 66.667 29.95 0.00 39.49 2.59
134 135 0.975887 TTTCAAAGATTGGCAGGGGC 59.024 50.000 0.00 0.00 40.13 5.80
135 136 3.986996 AATTTCAAAGATTGGCAGGGG 57.013 42.857 0.00 0.00 0.00 4.79
136 137 7.333323 AGATTTAATTTCAAAGATTGGCAGGG 58.667 34.615 0.00 0.00 0.00 4.45
137 138 8.782339 AAGATTTAATTTCAAAGATTGGCAGG 57.218 30.769 0.00 0.00 0.00 4.85
149 150 8.234546 GCGAAACAGGACTAAGATTTAATTTCA 58.765 33.333 0.00 0.00 0.00 2.69
150 151 8.451748 AGCGAAACAGGACTAAGATTTAATTTC 58.548 33.333 0.00 0.00 0.00 2.17
151 152 8.237267 CAGCGAAACAGGACTAAGATTTAATTT 58.763 33.333 0.00 0.00 0.00 1.82
152 153 7.148239 CCAGCGAAACAGGACTAAGATTTAATT 60.148 37.037 0.00 0.00 0.00 1.40
153 154 6.316390 CCAGCGAAACAGGACTAAGATTTAAT 59.684 38.462 0.00 0.00 0.00 1.40
154 155 5.642063 CCAGCGAAACAGGACTAAGATTTAA 59.358 40.000 0.00 0.00 0.00 1.52
155 156 5.175859 CCAGCGAAACAGGACTAAGATTTA 58.824 41.667 0.00 0.00 0.00 1.40
156 157 4.003648 CCAGCGAAACAGGACTAAGATTT 58.996 43.478 0.00 0.00 0.00 2.17
157 158 3.600388 CCAGCGAAACAGGACTAAGATT 58.400 45.455 0.00 0.00 0.00 2.40
158 159 2.678190 GCCAGCGAAACAGGACTAAGAT 60.678 50.000 0.00 0.00 0.00 2.40
159 160 1.337823 GCCAGCGAAACAGGACTAAGA 60.338 52.381 0.00 0.00 0.00 2.10
160 161 1.079503 GCCAGCGAAACAGGACTAAG 58.920 55.000 0.00 0.00 0.00 2.18
161 162 0.685097 AGCCAGCGAAACAGGACTAA 59.315 50.000 0.00 0.00 0.00 2.24
162 163 0.685097 AAGCCAGCGAAACAGGACTA 59.315 50.000 0.00 0.00 0.00 2.59
163 164 0.685097 TAAGCCAGCGAAACAGGACT 59.315 50.000 0.00 0.00 0.00 3.85
164 165 0.796927 GTAAGCCAGCGAAACAGGAC 59.203 55.000 0.00 0.00 0.00 3.85
165 166 0.669318 CGTAAGCCAGCGAAACAGGA 60.669 55.000 0.00 0.00 0.00 3.86
166 167 0.669318 TCGTAAGCCAGCGAAACAGG 60.669 55.000 0.00 0.00 33.96 4.00
167 168 1.126846 CTTCGTAAGCCAGCGAAACAG 59.873 52.381 7.92 0.00 44.76 3.16
173 174 0.388649 ACTGACTTCGTAAGCCAGCG 60.389 55.000 9.59 0.00 37.18 5.18
177 178 5.662211 TTGTAAAACTGACTTCGTAAGCC 57.338 39.130 0.00 0.00 37.18 4.35
188 189 5.690865 ACAAGGACTGGATTGTAAAACTGA 58.309 37.500 0.00 0.00 37.85 3.41
190 191 6.263168 CAGAACAAGGACTGGATTGTAAAACT 59.737 38.462 0.00 0.00 38.66 2.66
211 215 2.929641 TGTGCAACAGATGAACCAGAA 58.070 42.857 0.00 0.00 45.67 3.02
224 228 2.677003 CCCCGTCGATGTGTGCAAC 61.677 63.158 3.52 0.00 37.35 4.17
225 229 2.358125 CCCCGTCGATGTGTGCAA 60.358 61.111 3.52 0.00 0.00 4.08
226 230 3.295304 CTCCCCGTCGATGTGTGCA 62.295 63.158 3.52 0.00 0.00 4.57
227 231 2.509336 CTCCCCGTCGATGTGTGC 60.509 66.667 3.52 0.00 0.00 4.57
228 232 2.509336 GCTCCCCGTCGATGTGTG 60.509 66.667 3.52 0.00 0.00 3.82
229 233 3.771160 GGCTCCCCGTCGATGTGT 61.771 66.667 3.52 0.00 0.00 3.72
239 243 4.643387 ACACGTTGCTGGCTCCCC 62.643 66.667 0.00 0.00 0.00 4.81
247 294 0.179094 TGTTCGGAGAACACGTTGCT 60.179 50.000 11.09 0.00 45.90 3.91
261 308 9.752274 CTATGAAATCTTCTTTTTCTCTGTTCG 57.248 33.333 0.00 0.00 34.80 3.95
286 333 0.985490 GGATCAGAACCCTCCAGCCT 60.985 60.000 0.00 0.00 0.00 4.58
289 343 1.912043 ACTTGGATCAGAACCCTCCAG 59.088 52.381 0.00 0.00 40.06 3.86
303 357 1.214175 TGTTGCTCAGGGAAACTTGGA 59.786 47.619 0.00 0.00 38.13 3.53
305 359 2.886523 TCATGTTGCTCAGGGAAACTTG 59.113 45.455 1.05 1.05 38.96 3.16
306 360 3.228188 TCATGTTGCTCAGGGAAACTT 57.772 42.857 0.00 0.00 34.59 2.66
307 361 2.887152 GTTCATGTTGCTCAGGGAAACT 59.113 45.455 0.00 0.00 34.59 2.66
308 362 2.350772 CGTTCATGTTGCTCAGGGAAAC 60.351 50.000 0.00 0.00 34.09 2.78
313 376 1.503542 GCCGTTCATGTTGCTCAGG 59.496 57.895 0.00 0.00 0.00 3.86
314 377 1.133253 CGCCGTTCATGTTGCTCAG 59.867 57.895 0.00 0.00 0.00 3.35
316 379 1.006832 ATACGCCGTTCATGTTGCTC 58.993 50.000 0.00 0.00 0.00 4.26
332 395 5.648092 ACAGCCCAAGTTTCAGATGTTATAC 59.352 40.000 0.00 0.00 0.00 1.47
334 397 4.666512 ACAGCCCAAGTTTCAGATGTTAT 58.333 39.130 0.00 0.00 0.00 1.89
346 409 4.003788 CGACCGGACAGCCCAAGT 62.004 66.667 9.46 0.00 34.14 3.16
351 414 1.612463 AGAATATACGACCGGACAGCC 59.388 52.381 9.46 0.00 0.00 4.85
358 421 4.303086 AGAACACCAGAATATACGACCG 57.697 45.455 0.00 0.00 0.00 4.79
362 427 3.489785 GGCGAAGAACACCAGAATATACG 59.510 47.826 0.00 0.00 0.00 3.06
382 447 1.066358 ACTTAGTTGTAAGCGGGAGGC 60.066 52.381 0.00 0.00 39.58 4.70
407 472 3.612479 GCAGAAGTGAATTTGTCGCCAAT 60.612 43.478 0.00 0.00 37.48 3.16
413 478 5.698545 AGAGTAGTGCAGAAGTGAATTTGTC 59.301 40.000 0.00 0.00 0.00 3.18
446 511 6.382859 TGCAGTGACTTTATTCATCCCTACTA 59.617 38.462 0.00 0.00 0.00 1.82
448 513 5.428253 TGCAGTGACTTTATTCATCCCTAC 58.572 41.667 0.00 0.00 0.00 3.18
460 640 2.158842 AGCTCAAGACTGCAGTGACTTT 60.159 45.455 27.27 10.24 0.00 2.66
489 669 3.068873 GTCTGAAGTCTGAACTGACAGGT 59.931 47.826 7.51 0.00 39.30 4.00
490 670 3.068732 TGTCTGAAGTCTGAACTGACAGG 59.931 47.826 7.51 0.00 39.30 4.00
491 671 4.297510 CTGTCTGAAGTCTGAACTGACAG 58.702 47.826 20.71 20.71 45.85 3.51
492 672 3.954258 TCTGTCTGAAGTCTGAACTGACA 59.046 43.478 12.73 14.35 39.27 3.58
493 673 4.277174 TCTCTGTCTGAAGTCTGAACTGAC 59.723 45.833 4.14 4.14 35.36 3.51
495 675 4.037327 TGTCTCTGTCTGAAGTCTGAACTG 59.963 45.833 0.00 0.00 35.36 3.16
497 677 4.576216 TGTCTCTGTCTGAAGTCTGAAC 57.424 45.455 0.00 0.00 0.00 3.18
498 678 4.500545 GCTTGTCTCTGTCTGAAGTCTGAA 60.501 45.833 0.00 0.00 0.00 3.02
499 679 3.005261 GCTTGTCTCTGTCTGAAGTCTGA 59.995 47.826 0.00 0.00 0.00 3.27
500 680 3.243670 TGCTTGTCTCTGTCTGAAGTCTG 60.244 47.826 0.00 0.00 0.00 3.51
501 681 2.961741 TGCTTGTCTCTGTCTGAAGTCT 59.038 45.455 0.00 0.00 0.00 3.24
503 683 2.224161 GGTGCTTGTCTCTGTCTGAAGT 60.224 50.000 0.00 0.00 0.00 3.01
504 684 2.411904 GGTGCTTGTCTCTGTCTGAAG 58.588 52.381 0.00 0.00 0.00 3.02
505 685 1.070758 GGGTGCTTGTCTCTGTCTGAA 59.929 52.381 0.00 0.00 0.00 3.02
506 686 0.681733 GGGTGCTTGTCTCTGTCTGA 59.318 55.000 0.00 0.00 0.00 3.27
507 687 0.321122 GGGGTGCTTGTCTCTGTCTG 60.321 60.000 0.00 0.00 0.00 3.51
532 712 4.036734 TCACTTTGTTTCAGGCTAAAGCTG 59.963 41.667 6.62 5.32 41.70 4.24
549 729 7.164230 TGTGAAGTTGTTGGTATTTCACTTT 57.836 32.000 14.40 0.00 44.77 2.66
558 738 7.994425 ACATATGATTGTGAAGTTGTTGGTA 57.006 32.000 10.38 0.00 0.00 3.25
580 760 1.203523 GCAAACTTGGTTGGTGACACA 59.796 47.619 8.08 0.00 42.67 3.72
599 779 1.153549 CAGAGAACTGGTAGCCGGC 60.154 63.158 21.89 21.89 40.14 6.13
610 790 2.533266 TTCAGCTCACCACAGAGAAC 57.467 50.000 0.00 0.00 37.87 3.01
643 823 2.229543 TCCAGATGCACATGAGTTTTGC 59.770 45.455 0.00 0.00 36.76 3.68
646 826 2.089980 GCTCCAGATGCACATGAGTTT 58.910 47.619 0.00 0.00 0.00 2.66
651 831 1.725557 GCCAGCTCCAGATGCACATG 61.726 60.000 0.00 0.00 0.00 3.21
652 832 1.453379 GCCAGCTCCAGATGCACAT 60.453 57.895 0.00 0.00 0.00 3.21
653 833 2.045634 GCCAGCTCCAGATGCACA 60.046 61.111 0.00 0.00 0.00 4.57
654 834 2.045634 TGCCAGCTCCAGATGCAC 60.046 61.111 0.00 0.00 0.00 4.57
655 835 2.271173 CTGCCAGCTCCAGATGCA 59.729 61.111 5.18 0.00 32.03 3.96
656 836 3.210528 GCTGCCAGCTCCAGATGC 61.211 66.667 10.04 0.00 38.45 3.91
669 849 1.151668 CCAGAATATACGGCAGCTGC 58.848 55.000 30.88 30.88 41.14 5.25
670 850 2.408050 GACCAGAATATACGGCAGCTG 58.592 52.381 10.11 10.11 0.00 4.24
671 851 1.344763 GGACCAGAATATACGGCAGCT 59.655 52.381 0.00 0.00 0.00 4.24
672 852 1.344763 AGGACCAGAATATACGGCAGC 59.655 52.381 0.00 0.00 0.00 5.25
673 853 2.365617 ACAGGACCAGAATATACGGCAG 59.634 50.000 0.00 0.00 0.00 4.85
674 854 2.394632 ACAGGACCAGAATATACGGCA 58.605 47.619 0.00 0.00 0.00 5.69
675 855 3.181469 TGAACAGGACCAGAATATACGGC 60.181 47.826 0.00 0.00 0.00 5.68
676 856 4.369182 GTGAACAGGACCAGAATATACGG 58.631 47.826 0.00 0.00 0.00 4.02
688 868 9.391006 TGATTGTAATATTAAGGTGAACAGGAC 57.609 33.333 0.00 0.00 0.00 3.85
720 900 3.823304 AGAAGTTCAGTTCTGGCCAAATC 59.177 43.478 7.01 0.00 35.37 2.17
728 908 7.657761 ACCTACATGTTTAGAAGTTCAGTTCTG 59.342 37.037 2.30 0.00 37.36 3.02
744 924 6.565234 CGACTTCAATCTCTACCTACATGTT 58.435 40.000 2.30 0.00 0.00 2.71
747 927 4.038162 GGCGACTTCAATCTCTACCTACAT 59.962 45.833 0.00 0.00 0.00 2.29
751 931 1.405821 CGGCGACTTCAATCTCTACCT 59.594 52.381 0.00 0.00 0.00 3.08
753 933 2.159421 TGACGGCGACTTCAATCTCTAC 60.159 50.000 16.62 0.00 35.42 2.59
766 949 1.199327 CTCTACTTGAACTGACGGCGA 59.801 52.381 16.62 0.00 0.00 5.54
768 951 2.030185 TGTCTCTACTTGAACTGACGGC 60.030 50.000 0.00 0.00 0.00 5.68
770 953 3.670991 GCTTGTCTCTACTTGAACTGACG 59.329 47.826 0.00 0.00 0.00 4.35
778 961 1.339151 GGGGGTGCTTGTCTCTACTTG 60.339 57.143 0.00 0.00 0.00 3.16
780 963 0.178903 TGGGGGTGCTTGTCTCTACT 60.179 55.000 0.00 0.00 0.00 2.57
782 965 0.472925 TGTGGGGGTGCTTGTCTCTA 60.473 55.000 0.00 0.00 0.00 2.43
784 967 1.600916 GTGTGGGGGTGCTTGTCTC 60.601 63.158 0.00 0.00 0.00 3.36
785 968 2.343475 CTGTGTGGGGGTGCTTGTCT 62.343 60.000 0.00 0.00 0.00 3.41
786 969 1.898574 CTGTGTGGGGGTGCTTGTC 60.899 63.158 0.00 0.00 0.00 3.18
787 970 2.195683 CTGTGTGGGGGTGCTTGT 59.804 61.111 0.00 0.00 0.00 3.16
788 971 1.042559 AAACTGTGTGGGGGTGCTTG 61.043 55.000 0.00 0.00 0.00 4.01
789 972 0.553819 TAAACTGTGTGGGGGTGCTT 59.446 50.000 0.00 0.00 0.00 3.91
790 973 0.110486 CTAAACTGTGTGGGGGTGCT 59.890 55.000 0.00 0.00 0.00 4.40
791 974 1.524008 GCTAAACTGTGTGGGGGTGC 61.524 60.000 0.00 0.00 0.00 5.01
792 975 0.179004 TGCTAAACTGTGTGGGGGTG 60.179 55.000 0.00 0.00 0.00 4.61
793 976 0.777446 ATGCTAAACTGTGTGGGGGT 59.223 50.000 0.00 0.00 0.00 4.95
794 977 1.923356 AATGCTAAACTGTGTGGGGG 58.077 50.000 0.00 0.00 0.00 5.40
808 991 5.789643 ACATTTACACTGGTCAAAATGCT 57.210 34.783 12.99 3.85 41.06 3.79
839 1221 3.119849 CCTTCCGTGGCAGATTTAAGTTG 60.120 47.826 0.00 0.00 0.00 3.16
862 1244 4.547532 CACGAGCTAGCCGTATTATCTTT 58.452 43.478 24.32 0.00 38.29 2.52
870 1252 1.878088 CTTATCCACGAGCTAGCCGTA 59.122 52.381 24.32 14.45 38.29 4.02
877 1259 1.478510 CACTCACCTTATCCACGAGCT 59.521 52.381 0.00 0.00 0.00 4.09
881 1263 2.794981 CGTAGCACTCACCTTATCCACG 60.795 54.545 0.00 0.00 0.00 4.94
1011 1395 2.895424 AACAACCCTGGAGCCGGAG 61.895 63.158 5.05 0.00 0.00 4.63
1012 1396 2.852075 AACAACCCTGGAGCCGGA 60.852 61.111 5.05 0.00 0.00 5.14
1013 1397 2.672996 CAACAACCCTGGAGCCGG 60.673 66.667 0.00 0.00 0.00 6.13
1014 1398 3.365265 GCAACAACCCTGGAGCCG 61.365 66.667 0.00 0.00 0.00 5.52
1015 1399 1.973812 GAGCAACAACCCTGGAGCC 60.974 63.158 0.00 0.00 0.00 4.70
1016 1400 1.973812 GGAGCAACAACCCTGGAGC 60.974 63.158 0.00 0.00 0.00 4.70
1017 1401 1.672356 CGGAGCAACAACCCTGGAG 60.672 63.158 0.00 0.00 0.00 3.86
1018 1402 2.391724 GACGGAGCAACAACCCTGGA 62.392 60.000 0.00 0.00 0.00 3.86
1019 1403 1.966451 GACGGAGCAACAACCCTGG 60.966 63.158 0.00 0.00 0.00 4.45
1028 1412 2.962569 CGAGGAGTGACGGAGCAA 59.037 61.111 0.00 0.00 0.00 3.91
1030 1414 4.500116 GGCGAGGAGTGACGGAGC 62.500 72.222 0.00 0.00 0.00 4.70
1032 1416 2.282958 AAGGCGAGGAGTGACGGA 60.283 61.111 0.00 0.00 0.00 4.69
1033 1417 2.182030 GAAGGCGAGGAGTGACGG 59.818 66.667 0.00 0.00 0.00 4.79
1059 1443 2.813908 GTAGCGAAGGTGGTGGCG 60.814 66.667 0.00 0.00 40.22 5.69
1066 1450 3.001406 AAGCGGGGTAGCGAAGGT 61.001 61.111 0.00 0.00 43.00 3.50
1084 1468 2.178890 CGCCTCTCTTGGATGCTGC 61.179 63.158 0.00 0.00 34.20 5.25
1086 1470 2.188994 GCGCCTCTCTTGGATGCT 59.811 61.111 0.00 0.00 34.20 3.79
1087 1471 2.899339 GGCGCCTCTCTTGGATGC 60.899 66.667 22.15 0.00 33.24 3.91
1089 1473 3.854669 CGGGCGCCTCTCTTGGAT 61.855 66.667 28.56 0.00 0.00 3.41
1166 1556 9.033481 TCAAAACAAAATGCAACATAAGAGAAG 57.967 29.630 0.00 0.00 0.00 2.85
1309 1705 0.311165 GAGCTGATGGATGCACATGC 59.689 55.000 0.00 0.00 42.50 4.06
1310 1706 1.874231 GAGAGCTGATGGATGCACATG 59.126 52.381 0.00 0.00 0.00 3.21
1311 1707 1.489230 TGAGAGCTGATGGATGCACAT 59.511 47.619 0.00 0.00 0.00 3.21
1312 1708 0.906775 TGAGAGCTGATGGATGCACA 59.093 50.000 0.00 0.00 0.00 4.57
1313 1709 2.144730 GATGAGAGCTGATGGATGCAC 58.855 52.381 0.00 0.00 0.00 4.57
1318 1714 5.720041 TGATATGATGATGAGAGCTGATGGA 59.280 40.000 0.00 0.00 0.00 3.41
1535 1933 2.192979 GGCGCCTTGATCCATCCA 59.807 61.111 22.15 0.00 0.00 3.41
1608 2006 2.322355 AGAATGGAAGCAGGTCATCG 57.678 50.000 0.00 0.00 0.00 3.84
1615 2013 8.584157 ACAGTAATCTCTATAGAATGGAAGCAG 58.416 37.037 3.57 0.00 34.73 4.24
1699 2097 5.525012 GCAGTCATGAATGTATGTAGAGCAA 59.475 40.000 22.89 0.00 0.00 3.91
1706 2104 4.820173 CCAGATGCAGTCATGAATGTATGT 59.180 41.667 27.51 21.80 32.25 2.29
1707 2105 4.820173 ACCAGATGCAGTCATGAATGTATG 59.180 41.667 27.51 17.11 32.25 2.39
1708 2106 4.820173 CACCAGATGCAGTCATGAATGTAT 59.180 41.667 23.73 23.73 34.62 2.29
1709 2107 4.193865 CACCAGATGCAGTCATGAATGTA 58.806 43.478 22.89 19.65 31.96 2.29
1710 2108 3.014623 CACCAGATGCAGTCATGAATGT 58.985 45.455 22.89 5.51 31.96 2.71
1731 2129 3.251972 GGGCTTTTCACTCTATATGCAGC 59.748 47.826 0.00 0.00 0.00 5.25
1756 2154 4.675510 AGTGTTCACAAGCTCAACAAATG 58.324 39.130 5.74 0.00 31.95 2.32
1764 2162 2.682856 TGTGGAAAGTGTTCACAAGCTC 59.317 45.455 0.00 0.00 35.25 4.09
1809 2207 8.247562 CGTTGTCATTATATCTTTTTCCCCAAA 58.752 33.333 0.00 0.00 0.00 3.28
1821 2226 5.294356 TGCTGGTACCGTTGTCATTATATC 58.706 41.667 7.57 0.00 0.00 1.63
1825 2230 2.933492 GCTGCTGGTACCGTTGTCATTA 60.933 50.000 7.57 0.00 0.00 1.90
1830 2235 0.037605 GTAGCTGCTGGTACCGTTGT 60.038 55.000 18.95 0.00 40.24 3.32
1833 2238 0.611062 TCTGTAGCTGCTGGTACCGT 60.611 55.000 24.46 0.00 44.08 4.83
1845 2250 3.691609 CCTCCTTGGTTGAAATCTGTAGC 59.308 47.826 0.00 0.00 0.00 3.58
1851 2256 3.157087 TCTTGCCTCCTTGGTTGAAATC 58.843 45.455 0.00 0.00 38.35 2.17
1885 2290 3.066621 GTGGCATGTGGTATTGTATGTGG 59.933 47.826 0.00 0.00 0.00 4.17
1959 2382 5.135508 ACGGTATTCTATGGTATGCAGAC 57.864 43.478 1.94 1.94 0.00 3.51
1980 2403 7.475840 CAAGTTTATGAGAAGGAATAGCCAAC 58.524 38.462 0.00 0.00 40.02 3.77
1990 2413 7.615582 TGTTATCTGCAAGTTTATGAGAAGG 57.384 36.000 0.00 0.00 33.76 3.46
2033 2456 0.982852 TGCTGTGGGCTACTGGCTAT 60.983 55.000 16.55 0.00 42.39 2.97
2067 2490 2.593346 TGTGTCCTTTTGCGCAAAAT 57.407 40.000 39.49 0.00 39.29 1.82
2079 2502 1.202855 GGCTGCCATATGATGTGTCCT 60.203 52.381 15.17 0.00 0.00 3.85
2130 2553 2.801162 CCACACTGTCGCGAGTCG 60.801 66.667 10.24 8.54 40.15 4.18
2136 2559 2.607892 GCTTGACCCACACTGTCGC 61.608 63.158 0.00 0.00 35.46 5.19
2291 2714 0.320771 AGTTGGCCGTAAGCAGAGTG 60.321 55.000 0.00 0.00 46.50 3.51
2322 2745 0.885879 CATCAGGAGCAAAGCAGCAA 59.114 50.000 0.00 0.00 36.85 3.91


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

AutoCloner maintained by Alex Coulton.