Multiple sequence alignment - TraesCS5A01G086000

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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 TraesCS5A01G086000 chr5A 100.000 5186 0 0 1 5186 114679200 114684385 0.000000e+00 9577
1 TraesCS5A01G086000 chr5A 80.053 376 67 8 348 721 549796150 549795781 6.620000e-69 272
2 TraesCS5A01G086000 chr5A 91.262 103 7 2 2037 2137 45001819 45001921 7.000000e-29 139
3 TraesCS5A01G086000 chr5B 95.039 2318 76 16 2136 4448 120946891 120949174 0.000000e+00 3607
4 TraesCS5A01G086000 chr5B 96.612 1092 32 3 805 1896 120945683 120946769 0.000000e+00 1807
5 TraesCS5A01G086000 chr5B 89.376 753 53 12 9 755 120936866 120937597 0.000000e+00 922
6 TraesCS5A01G086000 chr5B 84.406 404 55 6 2269 2668 120547738 120548137 1.750000e-104 390
7 TraesCS5A01G086000 chr5B 79.564 597 82 27 3786 4374 120549196 120549760 1.750000e-104 390
8 TraesCS5A01G086000 chr5B 80.175 343 64 4 348 688 496150776 496150436 2.400000e-63 254
9 TraesCS5A01G086000 chr5B 95.276 127 3 1 1932 2055 120946766 120946892 1.140000e-46 198
10 TraesCS5A01G086000 chr5D 94.910 1945 51 22 2511 4448 111945514 111947417 0.000000e+00 3000
11 TraesCS5A01G086000 chr5D 91.920 1349 72 14 734 2055 111943614 111944952 0.000000e+00 1853
12 TraesCS5A01G086000 chr5D 95.238 567 26 1 2136 2702 111944951 111945516 0.000000e+00 896
13 TraesCS5A01G086000 chr5D 92.857 98 5 2 2044 2140 124913562 124913466 1.950000e-29 141
14 TraesCS5A01G086000 chr6D 90.561 731 50 7 4460 5186 60387891 60387176 0.000000e+00 950
15 TraesCS5A01G086000 chr6D 96.512 86 3 0 2056 2141 85039154 85039239 5.410000e-30 143
16 TraesCS5A01G086000 chr6D 96.386 83 3 0 2056 2138 413065850 413065932 2.520000e-28 137
17 TraesCS5A01G086000 chr1D 89.373 734 71 5 4458 5186 455550277 455551008 0.000000e+00 917
18 TraesCS5A01G086000 chr1D 88.844 735 70 9 4457 5185 342499076 342498348 0.000000e+00 893
19 TraesCS5A01G086000 chr3D 88.707 735 76 6 4457 5186 108504570 108505302 0.000000e+00 891
20 TraesCS5A01G086000 chr4D 88.498 739 70 9 4457 5185 488667393 488668126 0.000000e+00 880
21 TraesCS5A01G086000 chr4D 94.505 91 4 1 2048 2137 70112862 70112952 7.000000e-29 139
22 TraesCS5A01G086000 chr2D 88.108 740 76 10 4453 5186 499713926 499714659 0.000000e+00 869
23 TraesCS5A01G086000 chr7D 88.054 745 69 15 4449 5184 185191546 185192279 0.000000e+00 865
24 TraesCS5A01G086000 chr7D 80.371 377 68 6 348 721 120304340 120303967 1.100000e-71 281
25 TraesCS5A01G086000 chr1A 87.978 732 83 4 4457 5186 532737083 532737811 0.000000e+00 859
26 TraesCS5A01G086000 chr1A 79.472 341 67 3 353 691 21465422 21465761 6.710000e-59 239
27 TraesCS5A01G086000 chr2A 87.534 746 78 13 4449 5185 170608341 170609080 0.000000e+00 848
28 TraesCS5A01G086000 chr7A 80.739 379 66 7 345 721 549788840 549789213 6.570000e-74 289
29 TraesCS5A01G086000 chr3A 80.892 314 54 4 409 721 693124757 693124449 5.190000e-60 243
30 TraesCS5A01G086000 chr3A 87.611 113 9 5 2029 2140 183555976 183556084 5.450000e-25 126
31 TraesCS5A01G086000 chr3B 79.370 349 65 5 345 691 820798127 820798470 6.710000e-59 239
32 TraesCS5A01G086000 chr3B 79.060 234 45 4 459 691 791859600 791859370 1.930000e-34 158
33 TraesCS5A01G086000 chr1B 79.646 339 63 5 356 691 623897523 623897188 6.710000e-59 239
34 TraesCS5A01G086000 chr7B 94.565 92 4 1 2048 2138 104073281 104073372 1.950000e-29 141
35 TraesCS5A01G086000 chr6A 92.784 97 4 3 2045 2138 548412799 548412703 2.520000e-28 137
36 TraesCS5A01G086000 chr4B 92.708 96 5 2 2048 2142 629227443 629227349 2.520000e-28 137


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 TraesCS5A01G086000 chr5A 114679200 114684385 5185 False 9577.000000 9577 100.000000 1 5186 1 chr5A.!!$F2 5185
1 TraesCS5A01G086000 chr5B 120945683 120949174 3491 False 1870.666667 3607 95.642333 805 4448 3 chr5B.!!$F3 3643
2 TraesCS5A01G086000 chr5B 120936866 120937597 731 False 922.000000 922 89.376000 9 755 1 chr5B.!!$F1 746
3 TraesCS5A01G086000 chr5B 120547738 120549760 2022 False 390.000000 390 81.985000 2269 4374 2 chr5B.!!$F2 2105
4 TraesCS5A01G086000 chr5D 111943614 111947417 3803 False 1916.333333 3000 94.022667 734 4448 3 chr5D.!!$F1 3714
5 TraesCS5A01G086000 chr6D 60387176 60387891 715 True 950.000000 950 90.561000 4460 5186 1 chr6D.!!$R1 726
6 TraesCS5A01G086000 chr1D 455550277 455551008 731 False 917.000000 917 89.373000 4458 5186 1 chr1D.!!$F1 728
7 TraesCS5A01G086000 chr1D 342498348 342499076 728 True 893.000000 893 88.844000 4457 5185 1 chr1D.!!$R1 728
8 TraesCS5A01G086000 chr3D 108504570 108505302 732 False 891.000000 891 88.707000 4457 5186 1 chr3D.!!$F1 729
9 TraesCS5A01G086000 chr4D 488667393 488668126 733 False 880.000000 880 88.498000 4457 5185 1 chr4D.!!$F2 728
10 TraesCS5A01G086000 chr2D 499713926 499714659 733 False 869.000000 869 88.108000 4453 5186 1 chr2D.!!$F1 733
11 TraesCS5A01G086000 chr7D 185191546 185192279 733 False 865.000000 865 88.054000 4449 5184 1 chr7D.!!$F1 735
12 TraesCS5A01G086000 chr1A 532737083 532737811 728 False 859.000000 859 87.978000 4457 5186 1 chr1A.!!$F2 729
13 TraesCS5A01G086000 chr2A 170608341 170609080 739 False 848.000000 848 87.534000 4449 5185 1 chr2A.!!$F1 736

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
52 53 0.479815 TGGCATGGGGATTGAGGATC 59.520 55.000 0.00 0.00 0.00 3.36 F
1222 1252 0.318699 GGCGGCTTGTCTTTGGTTTC 60.319 55.000 0.00 0.00 0.00 2.78 F
1897 1931 1.451567 TGCTCGTCCTAGGACCTCG 60.452 63.158 31.78 22.29 41.76 4.63 F
2413 2450 0.546122 TCCATTCTTGATCCCCGTGG 59.454 55.000 0.00 0.00 0.00 4.94 F
2555 2592 0.902531 GGGTCCGTTCTCTCATTGGA 59.097 55.000 0.00 0.00 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 1876 1.092348 GCACGGGGAGGTCAAAATAC 58.908 55.000 0.00 0.0 0.00 1.89 R
2120 2157 0.032615 AGCTACTCCCTCTGTCCCAG 60.033 60.000 0.00 0.0 0.00 4.45 R
3022 3334 1.078214 TGCATGGCAGCACTACCTC 60.078 57.895 7.40 0.0 40.11 3.85 R
4085 4442 0.036388 ATCGCGGTTCCTTGTGATGT 60.036 50.000 6.13 0.0 34.26 3.06 R
4234 4591 0.901827 TTCGCAACTCATAGGGCTGA 59.098 50.000 0.00 0.0 0.00 4.26 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
46 47 1.325355 GTCAGATGGCATGGGGATTG 58.675 55.000 3.81 0.00 0.00 2.67
52 53 0.479815 TGGCATGGGGATTGAGGATC 59.520 55.000 0.00 0.00 0.00 3.36
54 55 1.271817 GGCATGGGGATTGAGGATCTC 60.272 57.143 0.00 0.00 35.02 2.75
122 123 4.142049 TGTTGAAGTTGTGGTTTGAATCCC 60.142 41.667 0.00 0.00 0.00 3.85
142 143 0.899720 CTAACCCTGTTGTCGCCCTA 59.100 55.000 0.00 0.00 0.00 3.53
162 163 4.790962 CGCTGCTGCCCATGAGGT 62.791 66.667 10.24 0.00 38.26 3.85
163 164 2.827642 GCTGCTGCCCATGAGGTC 60.828 66.667 3.85 0.00 38.26 3.85
167 168 1.377202 GCTGCCCATGAGGTCGAAA 60.377 57.895 0.00 0.00 38.26 3.46
175 176 2.086869 CATGAGGTCGAAACAATGCCT 58.913 47.619 0.00 0.00 0.00 4.75
191 192 2.143122 TGCCTTGAAGTACTTTGAGCG 58.857 47.619 10.02 6.47 0.00 5.03
214 215 9.601217 AGCGTTATTAATATATGGGATGTCTTC 57.399 33.333 0.00 0.00 0.00 2.87
220 221 9.759473 ATTAATATATGGGATGTCTTCTTTGGG 57.241 33.333 0.00 0.00 0.00 4.12
221 222 6.786843 ATATATGGGATGTCTTCTTTGGGT 57.213 37.500 0.00 0.00 0.00 4.51
222 223 2.584835 TGGGATGTCTTCTTTGGGTG 57.415 50.000 0.00 0.00 0.00 4.61
223 224 1.780309 TGGGATGTCTTCTTTGGGTGT 59.220 47.619 0.00 0.00 0.00 4.16
224 225 2.162681 GGGATGTCTTCTTTGGGTGTG 58.837 52.381 0.00 0.00 0.00 3.82
225 226 2.489073 GGGATGTCTTCTTTGGGTGTGT 60.489 50.000 0.00 0.00 0.00 3.72
226 227 2.554032 GGATGTCTTCTTTGGGTGTGTG 59.446 50.000 0.00 0.00 0.00 3.82
227 228 2.799126 TGTCTTCTTTGGGTGTGTGT 57.201 45.000 0.00 0.00 0.00 3.72
228 229 2.364632 TGTCTTCTTTGGGTGTGTGTG 58.635 47.619 0.00 0.00 0.00 3.82
229 230 2.290641 TGTCTTCTTTGGGTGTGTGTGT 60.291 45.455 0.00 0.00 0.00 3.72
230 231 2.097466 GTCTTCTTTGGGTGTGTGTGTG 59.903 50.000 0.00 0.00 0.00 3.82
231 232 2.091541 CTTCTTTGGGTGTGTGTGTGT 58.908 47.619 0.00 0.00 0.00 3.72
232 233 1.458398 TCTTTGGGTGTGTGTGTGTG 58.542 50.000 0.00 0.00 0.00 3.82
233 234 1.173043 CTTTGGGTGTGTGTGTGTGT 58.827 50.000 0.00 0.00 0.00 3.72
234 235 0.884514 TTTGGGTGTGTGTGTGTGTG 59.115 50.000 0.00 0.00 0.00 3.82
235 236 0.962855 TTGGGTGTGTGTGTGTGTGG 60.963 55.000 0.00 0.00 0.00 4.17
262 263 4.624015 GGGGGTGTTTAAGTTTGCTAAAC 58.376 43.478 4.26 4.26 41.69 2.01
267 268 6.530887 GGGTGTTTAAGTTTGCTAAACGAAAA 59.469 34.615 0.00 10.41 45.88 2.29
315 316 4.400120 ACTACCCAATTTAAAACCTCGCA 58.600 39.130 0.00 0.00 0.00 5.10
332 333 4.381079 CCTCGCAAGCTTAGAGAAACTACT 60.381 45.833 24.47 0.00 34.13 2.57
349 350 6.870971 AACTACTCAATTTAAAACCTCGCA 57.129 33.333 0.00 0.00 0.00 5.10
350 351 7.448748 AACTACTCAATTTAAAACCTCGCAT 57.551 32.000 0.00 0.00 0.00 4.73
351 352 8.556213 AACTACTCAATTTAAAACCTCGCATA 57.444 30.769 0.00 0.00 0.00 3.14
352 353 8.197988 ACTACTCAATTTAAAACCTCGCATAG 57.802 34.615 0.00 0.00 0.00 2.23
354 355 7.073342 ACTCAATTTAAAACCTCGCATAGTC 57.927 36.000 0.00 0.00 0.00 2.59
355 356 6.102006 TCAATTTAAAACCTCGCATAGTCG 57.898 37.500 0.00 0.00 0.00 4.18
375 382 4.250305 GGGCGTGTGGAGGTGTGT 62.250 66.667 0.00 0.00 0.00 3.72
379 386 2.041976 CGTGTGGAGGTGTGTCTCT 58.958 57.895 0.00 0.00 34.39 3.10
381 388 1.200252 CGTGTGGAGGTGTGTCTCTAG 59.800 57.143 0.00 0.00 34.39 2.43
400 407 2.950781 AGCTGGTCTCATAGGATTCGA 58.049 47.619 0.00 0.00 0.00 3.71
403 410 3.671971 GCTGGTCTCATAGGATTCGATCG 60.672 52.174 9.36 9.36 0.00 3.69
427 434 2.957402 TGTCTTTGGTGGATCTGCTT 57.043 45.000 0.00 0.00 0.00 3.91
445 452 2.093658 GCTTAGATCCGGTCTTTGTCCA 60.094 50.000 11.09 0.00 38.42 4.02
462 469 4.264253 TGTCCATCTTCATTCATGTGTCC 58.736 43.478 0.00 0.00 0.00 4.02
499 506 6.760770 CCTTCTGATCTACACCTTTCTTCATC 59.239 42.308 0.00 0.00 0.00 2.92
500 507 5.895928 TCTGATCTACACCTTTCTTCATCG 58.104 41.667 0.00 0.00 0.00 3.84
501 508 5.652452 TCTGATCTACACCTTTCTTCATCGA 59.348 40.000 0.00 0.00 0.00 3.59
555 562 0.878961 GGCCTCAACACGACGACTTT 60.879 55.000 0.00 0.00 0.00 2.66
562 569 2.121116 ACACGACGACTTTCAGACTG 57.879 50.000 0.00 0.00 0.00 3.51
576 583 7.203910 ACTTTCAGACTGTCTACTACAACAAG 58.796 38.462 10.47 6.49 37.74 3.16
583 590 7.491696 AGACTGTCTACTACAACAAGTTTTGTC 59.508 37.037 8.91 0.00 44.59 3.18
584 591 7.328737 ACTGTCTACTACAACAAGTTTTGTCT 58.671 34.615 6.68 0.00 44.59 3.41
591 598 4.331968 ACAACAAGTTTTGTCTGACTCCA 58.668 39.130 9.51 0.00 44.59 3.86
601 608 2.630098 TGTCTGACTCCAGTGAAGAAGG 59.370 50.000 9.51 0.00 41.16 3.46
605 612 1.078848 CTCCAGTGAAGAAGGGGCG 60.079 63.158 0.00 0.00 0.00 6.13
611 618 1.084370 GTGAAGAAGGGGCGATGACG 61.084 60.000 0.00 0.00 42.93 4.35
613 620 2.240162 GAAGAAGGGGCGATGACGGT 62.240 60.000 0.00 0.00 40.15 4.83
614 621 2.511600 GAAGGGGCGATGACGGTG 60.512 66.667 0.00 0.00 40.15 4.94
661 668 4.374399 CTTGTAGTCGTTGTTAGGTGGTT 58.626 43.478 0.00 0.00 0.00 3.67
664 671 5.288804 TGTAGTCGTTGTTAGGTGGTTTAC 58.711 41.667 0.00 0.00 0.00 2.01
669 676 3.747529 CGTTGTTAGGTGGTTTACGGATT 59.252 43.478 0.00 0.00 0.00 3.01
680 687 6.448852 GTGGTTTACGGATTTGGTTGTAATT 58.551 36.000 0.00 0.00 0.00 1.40
681 688 6.924612 GTGGTTTACGGATTTGGTTGTAATTT 59.075 34.615 0.00 0.00 0.00 1.82
760 767 5.378230 AGTGCCATGATTAAAGATGAGGA 57.622 39.130 0.00 0.00 0.00 3.71
761 768 5.759059 AGTGCCATGATTAAAGATGAGGAA 58.241 37.500 0.00 0.00 0.00 3.36
856 875 1.064505 CTTTACCGTCGATGGCTACGA 59.935 52.381 23.85 4.77 41.55 3.43
953 972 4.082523 CCGTCCGCACTCCACCAT 62.083 66.667 0.00 0.00 0.00 3.55
1132 1151 0.528466 CATCAGGTACGCACGCAGAT 60.528 55.000 0.00 0.00 0.00 2.90
1177 1206 3.716006 CCCACACGCACGCTTCTG 61.716 66.667 0.00 0.00 0.00 3.02
1222 1252 0.318699 GGCGGCTTGTCTTTGGTTTC 60.319 55.000 0.00 0.00 0.00 2.78
1283 1313 5.192927 TGTCTAGGGTTTGATGGCTTATTG 58.807 41.667 0.00 0.00 0.00 1.90
1296 1326 7.529555 TGATGGCTTATTGGAGAGGAAATATT 58.470 34.615 0.00 0.00 0.00 1.28
1318 1348 2.513897 GGCTATGGTTCGCGGCTT 60.514 61.111 6.13 0.00 0.00 4.35
1546 1580 8.380742 TGAATCTACTAGTGAAAGATTTCCCT 57.619 34.615 16.79 0.00 39.46 4.20
1660 1694 5.607939 TGGTCTATCATGTATTCAACCGT 57.392 39.130 0.00 0.00 0.00 4.83
1842 1876 4.994852 TGGTGCAGTTACTTTGCTACTTAG 59.005 41.667 0.00 0.00 42.02 2.18
1897 1931 1.451567 TGCTCGTCCTAGGACCTCG 60.452 63.158 31.78 22.29 41.76 4.63
2063 2100 9.747898 TTTGCCATTAATATTATATCCCTTCGT 57.252 29.630 0.00 0.00 0.00 3.85
2064 2101 8.958119 TGCCATTAATATTATATCCCTTCGTC 57.042 34.615 0.00 0.00 0.00 4.20
2065 2102 7.990886 TGCCATTAATATTATATCCCTTCGTCC 59.009 37.037 0.00 0.00 0.00 4.79
2066 2103 7.444487 GCCATTAATATTATATCCCTTCGTCCC 59.556 40.741 0.00 0.00 0.00 4.46
2067 2104 8.491134 CCATTAATATTATATCCCTTCGTCCCA 58.509 37.037 0.00 0.00 0.00 4.37
2068 2105 9.899661 CATTAATATTATATCCCTTCGTCCCAA 57.100 33.333 0.00 0.00 0.00 4.12
2079 2116 8.631480 ATCCCTTCGTCCCAAAATATAATAAC 57.369 34.615 0.00 0.00 0.00 1.89
2080 2117 6.707161 TCCCTTCGTCCCAAAATATAATAACG 59.293 38.462 0.00 0.00 0.00 3.18
2081 2118 6.484308 CCCTTCGTCCCAAAATATAATAACGT 59.516 38.462 0.00 0.00 0.00 3.99
2082 2119 7.012610 CCCTTCGTCCCAAAATATAATAACGTT 59.987 37.037 5.88 5.88 0.00 3.99
2083 2120 8.400186 CCTTCGTCCCAAAATATAATAACGTTT 58.600 33.333 5.91 0.00 0.00 3.60
2084 2121 9.777575 CTTCGTCCCAAAATATAATAACGTTTT 57.222 29.630 5.91 3.53 0.00 2.43
2110 2147 5.591643 CAGTAGCATAGTGTCAAAAACGT 57.408 39.130 0.00 0.00 37.24 3.99
2111 2148 5.985781 CAGTAGCATAGTGTCAAAAACGTT 58.014 37.500 0.00 0.00 37.24 3.99
2112 2149 6.071463 CAGTAGCATAGTGTCAAAAACGTTC 58.929 40.000 0.00 0.00 37.24 3.95
2113 2150 5.989777 AGTAGCATAGTGTCAAAAACGTTCT 59.010 36.000 0.00 0.00 0.00 3.01
2114 2151 5.751243 AGCATAGTGTCAAAAACGTTCTT 57.249 34.783 0.00 0.00 0.00 2.52
2115 2152 6.854496 AGCATAGTGTCAAAAACGTTCTTA 57.146 33.333 0.00 0.00 0.00 2.10
2116 2153 7.435068 AGCATAGTGTCAAAAACGTTCTTAT 57.565 32.000 0.00 0.00 0.00 1.73
2117 2154 8.542497 AGCATAGTGTCAAAAACGTTCTTATA 57.458 30.769 0.00 0.00 0.00 0.98
2118 2155 9.162764 AGCATAGTGTCAAAAACGTTCTTATAT 57.837 29.630 0.00 0.00 0.00 0.86
2119 2156 9.769093 GCATAGTGTCAAAAACGTTCTTATATT 57.231 29.630 0.00 0.00 0.00 1.28
2123 2160 8.504005 AGTGTCAAAAACGTTCTTATATTCTGG 58.496 33.333 0.00 0.00 0.00 3.86
2124 2161 7.749126 GTGTCAAAAACGTTCTTATATTCTGGG 59.251 37.037 0.00 0.00 0.00 4.45
2125 2162 7.662258 TGTCAAAAACGTTCTTATATTCTGGGA 59.338 33.333 0.00 0.00 0.00 4.37
2126 2163 7.961283 GTCAAAAACGTTCTTATATTCTGGGAC 59.039 37.037 0.00 0.00 0.00 4.46
2127 2164 7.662258 TCAAAAACGTTCTTATATTCTGGGACA 59.338 33.333 0.00 0.00 0.00 4.02
2190 2227 6.068010 TCTCCTAGGAAAGAGTCAGATGATC 58.932 44.000 13.77 0.00 0.00 2.92
2191 2228 5.770919 TCCTAGGAAAGAGTCAGATGATCA 58.229 41.667 9.71 0.00 0.00 2.92
2291 2328 6.462347 CCTTTCCATTCTTAGGTCTCTCTAGC 60.462 46.154 0.00 0.00 0.00 3.42
2349 2386 5.413499 CCTTTTTGTATTTATGCTGCTGCT 58.587 37.500 17.00 5.09 40.48 4.24
2413 2450 0.546122 TCCATTCTTGATCCCCGTGG 59.454 55.000 0.00 0.00 0.00 4.94
2417 2454 2.511600 CTTGATCCCCGTGGCGAC 60.512 66.667 0.00 0.00 0.00 5.19
2555 2592 0.902531 GGGTCCGTTCTCTCATTGGA 59.097 55.000 0.00 0.00 0.00 3.53
2603 2827 1.679944 CGGGGATCTGTGAACTGCAAT 60.680 52.381 0.00 0.00 0.00 3.56
2754 2984 1.676014 GCACAGTAGTCGGCAAAGGAT 60.676 52.381 0.00 0.00 0.00 3.24
3022 3334 4.401022 TCCTTATGAGCTATGCCAATTGG 58.599 43.478 20.81 20.81 38.53 3.16
3062 3374 5.412640 CATGCACAAAAAGAATGGCATCTA 58.587 37.500 0.00 0.00 39.73 1.98
3150 3469 1.133761 AGAGACTCGCCATGGTAGCTA 60.134 52.381 14.67 0.00 0.00 3.32
3228 3547 5.744171 ACTTTGCAAGGAAAAATGGAAGTT 58.256 33.333 16.36 0.00 0.00 2.66
3476 3824 6.071051 GGTATCCTTTTGCCTCTCTATAGGAG 60.071 46.154 0.00 5.69 39.15 3.69
3536 3884 8.747538 AGGTCCATATTACAATTAAAGTGGTC 57.252 34.615 0.00 0.00 31.95 4.02
3691 4044 5.360144 TCTTGCTACTCTGATGGTTACCTAC 59.640 44.000 2.07 0.00 0.00 3.18
3741 4098 6.383147 TCCTTAATCATCTACTTCCTCCGTTT 59.617 38.462 0.00 0.00 0.00 3.60
3755 4112 6.885952 TCCTCCGTTTCAAAATAAATGTCA 57.114 33.333 0.00 0.00 0.00 3.58
3783 4140 5.828299 TTAGTTCCAAATGCGGGAAATAG 57.172 39.130 0.00 0.00 45.47 1.73
3784 4141 3.023832 AGTTCCAAATGCGGGAAATAGG 58.976 45.455 0.00 0.00 45.47 2.57
3834 4191 1.705186 ACAACAGCTCCCTGGTACATT 59.295 47.619 0.00 0.00 43.53 2.71
4085 4442 2.036098 CAGTCCCCATGGCTGCAA 59.964 61.111 6.09 0.00 31.90 4.08
4121 4478 2.630592 GATGGGAAGACGGTCGGCTC 62.631 65.000 0.00 0.00 29.93 4.70
4152 4509 3.075005 GGTGGCCAGCTCTACCGA 61.075 66.667 27.63 0.00 0.00 4.69
4178 4535 1.347707 CTACCTCAGGGTTGCTGACAA 59.652 52.381 0.00 0.00 44.73 3.18
4234 4591 3.181434 TGAACCCAAAGCAGTGAGGTAAT 60.181 43.478 0.00 0.00 0.00 1.89
4263 4620 3.942130 TGAGTTGCGAAGATGAAGAGA 57.058 42.857 0.00 0.00 0.00 3.10
4281 4638 6.929049 TGAAGAGAGAAATTTAGTTGCGAAGA 59.071 34.615 0.00 0.00 0.00 2.87
4395 4758 3.304829 TGCTACTATGTCTGTATGGGCA 58.695 45.455 0.00 0.00 0.00 5.36
4400 4763 2.369983 ATGTCTGTATGGGCAATGGG 57.630 50.000 0.00 0.00 0.00 4.00
4421 4784 5.011329 TGGGATATTACCGCTAACCAGTTAG 59.989 44.000 12.30 12.30 43.98 2.34
4562 4926 7.939039 TGACATAAGTCTTCAGGTCTCAAAAAT 59.061 33.333 0.00 0.00 45.20 1.82
4563 4927 9.436957 GACATAAGTCTTCAGGTCTCAAAAATA 57.563 33.333 0.00 0.00 41.64 1.40
4564 4928 9.442047 ACATAAGTCTTCAGGTCTCAAAAATAG 57.558 33.333 0.00 0.00 0.00 1.73
4565 4929 8.887717 CATAAGTCTTCAGGTCTCAAAAATAGG 58.112 37.037 0.00 0.00 0.00 2.57
4609 4985 7.435192 GCAAATAAAATAACAGGATAGCCACAC 59.565 37.037 0.00 0.00 36.29 3.82
4690 5068 2.039216 TCCAAACCGGTTGAAGATAGCA 59.961 45.455 23.08 0.00 39.87 3.49
4691 5069 3.016736 CCAAACCGGTTGAAGATAGCAT 58.983 45.455 23.08 0.00 39.87 3.79
4696 5074 2.009051 CGGTTGAAGATAGCATGTGCA 58.991 47.619 7.83 0.00 45.16 4.57
4706 5084 1.032014 AGCATGTGCAACCGTCTTTT 58.968 45.000 7.83 0.00 45.16 2.27
4711 5089 2.756829 TGTGCAACCGTCTTTTATCGA 58.243 42.857 0.00 0.00 34.36 3.59
4721 5099 6.812998 ACCGTCTTTTATCGAATAGATCCAA 58.187 36.000 0.00 0.00 40.66 3.53
4734 5112 8.899771 TCGAATAGATCCAATAATCATACGCTA 58.100 33.333 0.00 0.00 0.00 4.26
4744 5122 0.106167 TCATACGCTACCTGGCCTCT 60.106 55.000 3.32 0.00 0.00 3.69
4749 5127 2.052690 GCTACCTGGCCTCTGTCGA 61.053 63.158 3.32 0.00 0.00 4.20
4751 5129 0.895530 CTACCTGGCCTCTGTCGAAA 59.104 55.000 3.32 0.00 0.00 3.46
4769 5147 4.037565 TCGAAATGAGTAGCGACCACATAT 59.962 41.667 7.43 0.00 0.00 1.78
4801 5179 0.406361 TGGCCCGGAAAATAACCTGT 59.594 50.000 0.73 0.00 0.00 4.00
4901 5281 3.704566 TCCTACACGGATATGTCTTGCTT 59.295 43.478 0.00 0.00 36.69 3.91
4956 5336 8.914328 TCAAATAACGTGTTGATAGTATTCGA 57.086 30.769 5.69 0.00 0.00 3.71
5060 5441 3.696548 TCATCACGATCACAGAAGCTACT 59.303 43.478 0.00 0.00 0.00 2.57
5062 5443 4.521130 TCACGATCACAGAAGCTACTTT 57.479 40.909 0.00 0.00 0.00 2.66
5063 5444 4.486090 TCACGATCACAGAAGCTACTTTC 58.514 43.478 0.00 0.00 0.00 2.62
5083 5464 3.779444 TCTGTAGATCCTGTCCAGTTGT 58.221 45.455 0.00 0.00 0.00 3.32
5122 5503 9.485206 TGTCCTTAGTTAGAATGACTTGTTTAC 57.515 33.333 0.00 0.00 0.00 2.01
5134 5515 2.352342 ACTTGTTTACGGACAAACCACG 59.648 45.455 6.97 0.00 38.90 4.94
5147 5528 5.738693 GGACAAACCACGTAAACACTTTAAC 59.261 40.000 0.00 0.00 38.79 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.007608 GAGTTAAGGTCATCCGGCAAC 58.992 52.381 0.00 0.00 39.05 4.17
3 4 1.480954 TCAGAGTTAAGGTCATCCGGC 59.519 52.381 0.00 0.00 39.05 6.13
4 5 2.761208 ACTCAGAGTTAAGGTCATCCGG 59.239 50.000 0.00 0.00 39.05 5.14
5 6 4.177026 CAACTCAGAGTTAAGGTCATCCG 58.823 47.826 15.73 0.00 36.03 4.18
6 7 5.153950 ACAACTCAGAGTTAAGGTCATCC 57.846 43.478 15.73 0.00 36.03 3.51
7 8 5.784177 TGACAACTCAGAGTTAAGGTCATC 58.216 41.667 22.33 11.04 36.03 2.92
69 70 1.550869 CCAAATCCAGGGGAAGCAAGT 60.551 52.381 0.00 0.00 34.34 3.16
72 73 0.251742 CACCAAATCCAGGGGAAGCA 60.252 55.000 0.00 0.00 34.34 3.91
105 106 4.149598 GTTAGGGGATTCAAACCACAACT 58.850 43.478 0.00 0.00 32.49 3.16
113 114 3.141272 ACAACAGGGTTAGGGGATTCAAA 59.859 43.478 0.00 0.00 0.00 2.69
122 123 1.376812 GGGCGACAACAGGGTTAGG 60.377 63.158 0.00 0.00 0.00 2.69
142 143 2.282391 TCATGGGCAGCAGCGTTT 60.282 55.556 0.00 0.00 43.41 3.60
162 163 4.385825 AGTACTTCAAGGCATTGTTTCGA 58.614 39.130 11.36 0.00 37.68 3.71
163 164 4.749245 AGTACTTCAAGGCATTGTTTCG 57.251 40.909 11.36 1.12 37.68 3.46
167 168 4.022849 GCTCAAAGTACTTCAAGGCATTGT 60.023 41.667 11.36 0.00 37.68 2.71
214 215 1.135431 CACACACACACACACCCAAAG 60.135 52.381 0.00 0.00 0.00 2.77
218 219 2.118404 CCCACACACACACACACCC 61.118 63.158 0.00 0.00 0.00 4.61
219 220 2.118404 CCCCACACACACACACACC 61.118 63.158 0.00 0.00 0.00 4.16
220 221 2.118404 CCCCCACACACACACACAC 61.118 63.158 0.00 0.00 0.00 3.82
221 222 2.273776 CCCCCACACACACACACA 59.726 61.111 0.00 0.00 0.00 3.72
245 246 8.452534 TCTCTTTTCGTTTAGCAAACTTAAACA 58.547 29.630 8.16 0.00 39.23 2.83
246 247 8.831000 TCTCTTTTCGTTTAGCAAACTTAAAC 57.169 30.769 9.17 3.69 39.23 2.01
247 248 8.126700 CCTCTCTTTTCGTTTAGCAAACTTAAA 58.873 33.333 9.17 7.25 39.23 1.52
258 259 6.755206 TCTGATGAACCTCTCTTTTCGTTTA 58.245 36.000 0.00 0.00 0.00 2.01
262 263 3.616379 GCTCTGATGAACCTCTCTTTTCG 59.384 47.826 0.00 0.00 0.00 3.46
267 268 4.865905 TCTAAGCTCTGATGAACCTCTCT 58.134 43.478 0.00 0.00 0.00 3.10
332 333 5.064198 CCGACTATGCGAGGTTTTAAATTGA 59.936 40.000 0.00 0.00 0.00 2.57
349 350 2.423898 CCACACGCCCTCCGACTAT 61.424 63.158 0.00 0.00 41.02 2.12
350 351 3.066190 CCACACGCCCTCCGACTA 61.066 66.667 0.00 0.00 41.02 2.59
351 352 4.988716 TCCACACGCCCTCCGACT 62.989 66.667 0.00 0.00 41.02 4.18
352 353 4.436998 CTCCACACGCCCTCCGAC 62.437 72.222 0.00 0.00 41.02 4.79
355 356 4.394712 CACCTCCACACGCCCTCC 62.395 72.222 0.00 0.00 0.00 4.30
375 382 5.321102 GAATCCTATGAGACCAGCTAGAGA 58.679 45.833 0.00 0.00 0.00 3.10
379 386 4.100279 TCGAATCCTATGAGACCAGCTA 57.900 45.455 0.00 0.00 0.00 3.32
381 388 3.671971 CGATCGAATCCTATGAGACCAGC 60.672 52.174 10.26 0.00 0.00 4.85
400 407 1.628340 TCCACCAAAGACATCACCGAT 59.372 47.619 0.00 0.00 0.00 4.18
403 410 3.012518 CAGATCCACCAAAGACATCACC 58.987 50.000 0.00 0.00 0.00 4.02
427 434 3.643237 AGATGGACAAAGACCGGATCTA 58.357 45.455 9.46 0.00 36.27 1.98
445 452 5.688814 TCTGAGGACACATGAATGAAGAT 57.311 39.130 0.00 0.00 0.00 2.40
488 495 2.991250 ACCACCATCGATGAAGAAAGG 58.009 47.619 26.86 18.28 0.00 3.11
499 506 1.266718 CCAGAACAACAACCACCATCG 59.733 52.381 0.00 0.00 0.00 3.84
500 507 2.034558 CACCAGAACAACAACCACCATC 59.965 50.000 0.00 0.00 0.00 3.51
501 508 2.031120 CACCAGAACAACAACCACCAT 58.969 47.619 0.00 0.00 0.00 3.55
555 562 6.710597 AACTTGTTGTAGTAGACAGTCTGA 57.289 37.500 13.84 0.00 39.88 3.27
562 569 7.491696 AGTCAGACAAAACTTGTTGTAGTAGAC 59.508 37.037 2.66 0.00 45.52 2.59
576 583 4.442706 TCTTCACTGGAGTCAGACAAAAC 58.557 43.478 2.66 0.00 43.49 2.43
583 590 1.277557 CCCCTTCTTCACTGGAGTCAG 59.722 57.143 0.00 0.00 46.10 3.51
584 591 1.352083 CCCCTTCTTCACTGGAGTCA 58.648 55.000 0.00 0.00 0.00 3.41
591 598 0.250513 GTCATCGCCCCTTCTTCACT 59.749 55.000 0.00 0.00 0.00 3.41
611 618 4.681978 AGCCGAAGACGCACCACC 62.682 66.667 0.00 0.00 38.29 4.61
613 620 3.611674 TGAGCCGAAGACGCACCA 61.612 61.111 0.00 0.00 38.29 4.17
614 621 3.112709 GTGAGCCGAAGACGCACC 61.113 66.667 0.00 0.00 38.29 5.01
732 739 8.158169 TCATCTTTAATCATGGCACTACAATC 57.842 34.615 0.00 0.00 0.00 2.67
785 792 3.119319 AGGTTTCAAATTGGGTGGGTTT 58.881 40.909 0.00 0.00 0.00 3.27
789 796 2.104622 AGCAAGGTTTCAAATTGGGTGG 59.895 45.455 0.00 0.00 0.00 4.61
790 797 3.473923 AGCAAGGTTTCAAATTGGGTG 57.526 42.857 0.00 0.00 0.00 4.61
827 836 1.872679 GACGGTAAAGCTCGCGAGG 60.873 63.158 35.10 19.79 0.00 4.63
953 972 3.511477 AGACTTCTAGAAGCAGGTGGAA 58.489 45.455 28.64 0.00 41.99 3.53
1132 1151 2.428925 GGGGGAGCGTCGATTGGTA 61.429 63.158 0.00 0.00 0.00 3.25
1177 1206 2.728817 CATCCCCGTCGACCTAGC 59.271 66.667 10.58 0.00 0.00 3.42
1222 1252 4.260375 CCTTTATCTCATCAAAACGCGAGG 60.260 45.833 15.93 0.00 0.00 4.63
1318 1348 1.219213 ACTCCATCCAACCCCAACAAA 59.781 47.619 0.00 0.00 0.00 2.83
1369 1399 3.758755 TCTCATTTCACAGCAGTCAGT 57.241 42.857 0.00 0.00 0.00 3.41
1374 1404 4.986034 TGCAAATTTCTCATTTCACAGCAG 59.014 37.500 0.00 0.00 0.00 4.24
1638 1672 5.607939 ACGGTTGAATACATGATAGACCA 57.392 39.130 0.00 0.00 0.00 4.02
1642 1676 8.141835 TGAATCAACGGTTGAATACATGATAG 57.858 34.615 25.64 0.00 43.95 2.08
1842 1876 1.092348 GCACGGGGAGGTCAAAATAC 58.908 55.000 0.00 0.00 0.00 1.89
1897 1931 9.301153 CATAAAACCCAAAATATCAGCAGTTAC 57.699 33.333 0.00 0.00 0.00 2.50
1935 1969 2.037641 TGCCTAGTTCCATGATCCATCG 59.962 50.000 0.00 0.00 0.00 3.84
1979 2013 7.308109 GGTGAATACGTACACTCCAAAATGAAA 60.308 37.037 13.96 0.00 37.22 2.69
2053 2090 9.729281 GTTATTATATTTTGGGACGAAGGGATA 57.271 33.333 0.00 0.00 0.00 2.59
2054 2091 7.389607 CGTTATTATATTTTGGGACGAAGGGAT 59.610 37.037 0.00 0.00 0.00 3.85
2055 2092 6.707161 CGTTATTATATTTTGGGACGAAGGGA 59.293 38.462 0.00 0.00 0.00 4.20
2056 2093 6.484308 ACGTTATTATATTTTGGGACGAAGGG 59.516 38.462 0.00 0.00 33.86 3.95
2057 2094 7.486802 ACGTTATTATATTTTGGGACGAAGG 57.513 36.000 0.00 0.00 33.86 3.46
2058 2095 9.777575 AAAACGTTATTATATTTTGGGACGAAG 57.222 29.630 0.00 0.00 33.86 3.79
2075 2112 9.211485 ACACTATGCTACTGTTAAAAACGTTAT 57.789 29.630 0.00 0.00 0.00 1.89
2076 2113 8.592105 ACACTATGCTACTGTTAAAAACGTTA 57.408 30.769 0.00 0.00 0.00 3.18
2077 2114 7.225145 TGACACTATGCTACTGTTAAAAACGTT 59.775 33.333 0.00 0.00 0.00 3.99
2078 2115 6.702723 TGACACTATGCTACTGTTAAAAACGT 59.297 34.615 0.00 0.00 0.00 3.99
2079 2116 7.112528 TGACACTATGCTACTGTTAAAAACG 57.887 36.000 0.00 0.00 0.00 3.60
2080 2117 9.724839 TTTTGACACTATGCTACTGTTAAAAAC 57.275 29.630 0.00 0.00 33.16 2.43
2082 2119 9.724839 GTTTTTGACACTATGCTACTGTTAAAA 57.275 29.630 0.00 0.00 33.83 1.52
2083 2120 8.065407 CGTTTTTGACACTATGCTACTGTTAAA 58.935 33.333 0.00 0.00 0.00 1.52
2084 2121 7.225145 ACGTTTTTGACACTATGCTACTGTTAA 59.775 33.333 0.00 0.00 0.00 2.01
2085 2122 6.702723 ACGTTTTTGACACTATGCTACTGTTA 59.297 34.615 0.00 0.00 0.00 2.41
2086 2123 5.526111 ACGTTTTTGACACTATGCTACTGTT 59.474 36.000 0.00 0.00 0.00 3.16
2087 2124 5.054477 ACGTTTTTGACACTATGCTACTGT 58.946 37.500 0.00 0.00 0.00 3.55
2088 2125 5.591643 ACGTTTTTGACACTATGCTACTG 57.408 39.130 0.00 0.00 0.00 2.74
2089 2126 5.989777 AGAACGTTTTTGACACTATGCTACT 59.010 36.000 0.46 0.00 0.00 2.57
2090 2127 6.224420 AGAACGTTTTTGACACTATGCTAC 57.776 37.500 0.46 0.00 0.00 3.58
2091 2128 6.854496 AAGAACGTTTTTGACACTATGCTA 57.146 33.333 0.46 0.00 0.00 3.49
2092 2129 5.751243 AAGAACGTTTTTGACACTATGCT 57.249 34.783 0.46 0.00 0.00 3.79
2093 2130 9.769093 AATATAAGAACGTTTTTGACACTATGC 57.231 29.630 13.87 0.00 0.00 3.14
2097 2134 8.504005 CCAGAATATAAGAACGTTTTTGACACT 58.496 33.333 13.87 4.79 0.00 3.55
2098 2135 7.749126 CCCAGAATATAAGAACGTTTTTGACAC 59.251 37.037 13.87 2.84 0.00 3.67
2099 2136 7.662258 TCCCAGAATATAAGAACGTTTTTGACA 59.338 33.333 13.87 0.01 0.00 3.58
2100 2137 7.961283 GTCCCAGAATATAAGAACGTTTTTGAC 59.039 37.037 13.87 5.89 0.00 3.18
2101 2138 7.662258 TGTCCCAGAATATAAGAACGTTTTTGA 59.338 33.333 13.87 2.81 0.00 2.69
2102 2139 7.812648 TGTCCCAGAATATAAGAACGTTTTTG 58.187 34.615 13.87 0.00 0.00 2.44
2103 2140 7.881232 TCTGTCCCAGAATATAAGAACGTTTTT 59.119 33.333 9.22 9.22 37.57 1.94
2104 2141 7.391620 TCTGTCCCAGAATATAAGAACGTTTT 58.608 34.615 0.46 0.00 37.57 2.43
2105 2142 6.942976 TCTGTCCCAGAATATAAGAACGTTT 58.057 36.000 0.46 0.00 37.57 3.60
2106 2143 6.407074 CCTCTGTCCCAGAATATAAGAACGTT 60.407 42.308 0.00 0.00 40.18 3.99
2107 2144 5.069251 CCTCTGTCCCAGAATATAAGAACGT 59.931 44.000 0.00 0.00 40.18 3.99
2108 2145 5.509840 CCCTCTGTCCCAGAATATAAGAACG 60.510 48.000 0.00 0.00 40.18 3.95
2109 2146 5.602978 TCCCTCTGTCCCAGAATATAAGAAC 59.397 44.000 0.00 0.00 40.18 3.01
2110 2147 5.788430 TCCCTCTGTCCCAGAATATAAGAA 58.212 41.667 0.00 0.00 40.18 2.52
2111 2148 5.103043 ACTCCCTCTGTCCCAGAATATAAGA 60.103 44.000 0.00 0.00 40.18 2.10
2112 2149 5.151454 ACTCCCTCTGTCCCAGAATATAAG 58.849 45.833 0.00 0.00 40.18 1.73
2113 2150 5.157770 ACTCCCTCTGTCCCAGAATATAA 57.842 43.478 0.00 0.00 40.18 0.98
2114 2151 4.834406 ACTCCCTCTGTCCCAGAATATA 57.166 45.455 0.00 0.00 40.18 0.86
2115 2152 3.715648 ACTCCCTCTGTCCCAGAATAT 57.284 47.619 0.00 0.00 40.18 1.28
2116 2153 3.691603 GCTACTCCCTCTGTCCCAGAATA 60.692 52.174 0.00 0.00 40.18 1.75
2117 2154 2.957312 GCTACTCCCTCTGTCCCAGAAT 60.957 54.545 0.00 0.00 40.18 2.40
2118 2155 1.619977 GCTACTCCCTCTGTCCCAGAA 60.620 57.143 0.00 0.00 40.18 3.02
2119 2156 0.033011 GCTACTCCCTCTGTCCCAGA 60.033 60.000 0.00 0.00 38.25 3.86
2120 2157 0.032615 AGCTACTCCCTCTGTCCCAG 60.033 60.000 0.00 0.00 0.00 4.45
2121 2158 0.413832 AAGCTACTCCCTCTGTCCCA 59.586 55.000 0.00 0.00 0.00 4.37
2122 2159 0.827368 CAAGCTACTCCCTCTGTCCC 59.173 60.000 0.00 0.00 0.00 4.46
2123 2160 0.827368 CCAAGCTACTCCCTCTGTCC 59.173 60.000 0.00 0.00 0.00 4.02
2124 2161 1.562783 ACCAAGCTACTCCCTCTGTC 58.437 55.000 0.00 0.00 0.00 3.51
2125 2162 1.625818 CAACCAAGCTACTCCCTCTGT 59.374 52.381 0.00 0.00 0.00 3.41
2126 2163 1.677217 GCAACCAAGCTACTCCCTCTG 60.677 57.143 0.00 0.00 0.00 3.35
2127 2164 0.615850 GCAACCAAGCTACTCCCTCT 59.384 55.000 0.00 0.00 0.00 3.69
2128 2165 0.615850 AGCAACCAAGCTACTCCCTC 59.384 55.000 0.00 0.00 44.50 4.30
2129 2166 1.068121 AAGCAACCAAGCTACTCCCT 58.932 50.000 0.00 0.00 45.89 4.20
2130 2167 1.168714 CAAGCAACCAAGCTACTCCC 58.831 55.000 0.00 0.00 45.89 4.30
2131 2168 1.897560 ACAAGCAACCAAGCTACTCC 58.102 50.000 0.00 0.00 45.89 3.85
2132 2169 2.605580 GCAACAAGCAACCAAGCTACTC 60.606 50.000 0.00 0.00 45.89 2.59
2133 2170 1.338020 GCAACAAGCAACCAAGCTACT 59.662 47.619 0.00 0.00 45.89 2.57
2134 2171 1.770957 GCAACAAGCAACCAAGCTAC 58.229 50.000 0.00 0.00 45.89 3.58
2190 2227 2.948093 GCATGTGCAAACGCCTATG 58.052 52.632 0.00 0.00 41.59 2.23
2266 2303 5.948742 AGAGAGACCTAAGAATGGAAAGG 57.051 43.478 0.00 0.00 35.14 3.11
2291 2328 4.882427 AGTGAATCAAAGCATCAGGATCAG 59.118 41.667 0.00 0.00 0.00 2.90
2349 2386 4.909696 TCCTGAAAAATCGCAAGTCAAA 57.090 36.364 0.00 0.00 39.48 2.69
2417 2454 0.035458 AACTGTCTTTGGCGGAGAGG 59.965 55.000 4.70 0.00 0.00 3.69
2496 2533 1.070786 GGTCCGTCAGCAGGTTCAA 59.929 57.895 0.00 0.00 0.00 2.69
2603 2827 0.103026 CGTCATCGAGCTTGATCCCA 59.897 55.000 13.91 0.00 39.71 4.37
2668 2892 8.084073 TGAGTGAAATTTCCTGATTGCTAAAAG 58.916 33.333 15.48 0.00 0.00 2.27
2754 2984 6.714810 ACTTCATACAGATTGCCTTTAACACA 59.285 34.615 0.00 0.00 0.00 3.72
2984 3296 6.182627 TCATAAGGAATGAAGCACTTGACAT 58.817 36.000 0.00 0.00 41.75 3.06
3022 3334 1.078214 TGCATGGCAGCACTACCTC 60.078 57.895 7.40 0.00 40.11 3.85
3476 3824 7.176165 GCTTTATCCAACCATATTACCCTTACC 59.824 40.741 0.00 0.00 0.00 2.85
3477 3825 7.722285 TGCTTTATCCAACCATATTACCCTTAC 59.278 37.037 0.00 0.00 0.00 2.34
3478 3826 7.817440 TGCTTTATCCAACCATATTACCCTTA 58.183 34.615 0.00 0.00 0.00 2.69
3479 3827 6.678547 TGCTTTATCCAACCATATTACCCTT 58.321 36.000 0.00 0.00 0.00 3.95
3480 3828 6.274322 TGCTTTATCCAACCATATTACCCT 57.726 37.500 0.00 0.00 0.00 4.34
3481 3829 6.969993 TTGCTTTATCCAACCATATTACCC 57.030 37.500 0.00 0.00 0.00 3.69
3482 3830 9.830975 AATTTTGCTTTATCCAACCATATTACC 57.169 29.630 0.00 0.00 0.00 2.85
3691 4044 1.434555 TGAATACCAACCGAACGCTG 58.565 50.000 0.00 0.00 0.00 5.18
3755 4112 3.056179 CCCGCATTTGGAACTAAAACCAT 60.056 43.478 0.00 0.00 36.02 3.55
3783 4140 3.421844 ACACAGGAGAAAACATTAGCCC 58.578 45.455 0.00 0.00 0.00 5.19
3784 4141 4.154918 CAGACACAGGAGAAAACATTAGCC 59.845 45.833 0.00 0.00 0.00 3.93
3834 4191 1.270252 TGTTCAGCAGCATTCGAGACA 60.270 47.619 0.00 0.00 0.00 3.41
4085 4442 0.036388 ATCGCGGTTCCTTGTGATGT 60.036 50.000 6.13 0.00 34.26 3.06
4178 4535 3.261897 AGCAACTCATACAGGCTACTTGT 59.738 43.478 0.00 0.00 32.09 3.16
4234 4591 0.901827 TTCGCAACTCATAGGGCTGA 59.098 50.000 0.00 0.00 0.00 4.26
4263 4620 5.948992 AAGCTCTTCGCAACTAAATTTCT 57.051 34.783 0.00 0.00 42.61 2.52
4289 4646 2.758736 AACAACTTGTTTGCAGCCAA 57.241 40.000 1.00 0.00 37.26 4.52
4395 4758 4.349930 ACTGGTTAGCGGTAATATCCCATT 59.650 41.667 10.69 4.76 0.00 3.16
4421 4784 1.767759 ATGCAGAAACCCTACCATGC 58.232 50.000 0.00 0.00 0.00 4.06
4422 4785 4.097892 GGTAAATGCAGAAACCCTACCATG 59.902 45.833 0.00 0.00 0.00 3.66
4423 4786 4.264172 TGGTAAATGCAGAAACCCTACCAT 60.264 41.667 10.63 0.00 33.98 3.55
4424 4787 3.074687 TGGTAAATGCAGAAACCCTACCA 59.925 43.478 10.63 7.60 35.99 3.25
4425 4788 3.692690 TGGTAAATGCAGAAACCCTACC 58.307 45.455 10.63 5.54 0.00 3.18
4426 4789 5.914898 AATGGTAAATGCAGAAACCCTAC 57.085 39.130 10.63 0.00 0.00 3.18
4427 4790 6.926630 AAAATGGTAAATGCAGAAACCCTA 57.073 33.333 10.63 0.00 0.00 3.53
4428 4791 5.823861 AAAATGGTAAATGCAGAAACCCT 57.176 34.783 10.63 0.12 0.00 4.34
4532 4896 6.042093 TGAGACCTGAAGACTTATGTCAAACT 59.958 38.462 11.02 1.46 45.20 2.66
4536 4900 6.419484 TTTGAGACCTGAAGACTTATGTCA 57.581 37.500 11.02 1.02 45.20 3.58
4537 4901 7.730364 TTTTTGAGACCTGAAGACTTATGTC 57.270 36.000 0.50 0.50 43.22 3.06
4652 5030 5.763204 GGTTTGGATGACGGTCATGTAATAT 59.237 40.000 27.11 2.93 37.20 1.28
4690 5068 3.331150 TCGATAAAAGACGGTTGCACAT 58.669 40.909 0.00 0.00 0.00 3.21
4691 5069 2.756829 TCGATAAAAGACGGTTGCACA 58.243 42.857 0.00 0.00 0.00 4.57
4696 5074 6.812998 TGGATCTATTCGATAAAAGACGGTT 58.187 36.000 0.00 0.00 30.84 4.44
4706 5084 9.678941 GCGTATGATTATTGGATCTATTCGATA 57.321 33.333 0.00 0.00 30.84 2.92
4711 5089 8.982723 AGGTAGCGTATGATTATTGGATCTATT 58.017 33.333 0.00 0.00 0.00 1.73
4721 5099 3.173965 AGGCCAGGTAGCGTATGATTAT 58.826 45.455 5.01 0.00 0.00 1.28
4725 5103 0.106167 AGAGGCCAGGTAGCGTATGA 60.106 55.000 5.01 0.00 0.00 2.15
4734 5112 0.036010 CATTTCGACAGAGGCCAGGT 60.036 55.000 5.01 0.00 0.00 4.00
4749 5127 4.100963 TCCATATGTGGTCGCTACTCATTT 59.899 41.667 8.51 0.00 46.16 2.32
4751 5129 3.230976 TCCATATGTGGTCGCTACTCAT 58.769 45.455 8.51 5.39 46.16 2.90
4769 5147 2.352422 GGCCACTGCACTGATCCA 59.648 61.111 0.00 0.00 40.13 3.41
4834 5212 6.872920 AGTTTGGAACTGCAGAAACAATTTA 58.127 32.000 23.35 4.50 41.01 1.40
4901 5281 5.221461 GGCTAGACGGGATAGATTCAGAAAA 60.221 44.000 0.00 0.00 0.00 2.29
5060 5441 4.593206 ACAACTGGACAGGATCTACAGAAA 59.407 41.667 4.14 0.00 33.57 2.52
5062 5443 3.511540 CACAACTGGACAGGATCTACAGA 59.488 47.826 4.14 0.00 33.57 3.41
5063 5444 3.259374 ACACAACTGGACAGGATCTACAG 59.741 47.826 4.14 0.00 35.40 2.74
5083 5464 5.606348 ACTAAGGACAATTTGGCAAAACA 57.394 34.783 17.70 0.00 0.00 2.83
5122 5503 1.935199 AGTGTTTACGTGGTTTGTCCG 59.065 47.619 0.00 0.00 39.52 4.79
5134 5515 9.577110 AGTGCCTTTAAAAGTTAAAGTGTTTAC 57.423 29.630 15.69 9.13 33.83 2.01
5147 5528 6.337356 TGGAAAGTCAAAGTGCCTTTAAAAG 58.663 36.000 0.63 0.00 31.96 2.27


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

AutoCloner maintained by Alex Coulton.