Multiple sequence alignment - TraesCS5A01G357500

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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 TraesCS5A01G357500 chr5A 100.000 5290 0 0 672 5961 559579387 559584676 0.000000e+00 9769.0
1 TraesCS5A01G357500 chr5A 86.223 646 75 8 5330 5961 623334137 623333492 0.000000e+00 688.0
2 TraesCS5A01G357500 chr5A 100.000 351 0 0 1 351 559578716 559579066 0.000000e+00 649.0
3 TraesCS5A01G357500 chr5D 88.442 2163 148 39 3203 5331 443313911 443316005 0.000000e+00 2516.0
4 TraesCS5A01G357500 chr5D 93.241 1524 73 11 674 2188 443312036 443313538 0.000000e+00 2217.0
5 TraesCS5A01G357500 chr5D 92.308 962 64 4 4375 5329 443368968 443369926 0.000000e+00 1358.0
6 TraesCS5A01G357500 chr5D 96.460 339 10 2 2872 3210 443313530 443313866 5.220000e-155 558.0
7 TraesCS5A01G357500 chr5D 94.372 231 13 0 4083 4313 443338916 443339146 7.350000e-94 355.0
8 TraesCS5A01G357500 chr5D 88.679 265 7 10 80 341 443311743 443311987 9.710000e-78 302.0
9 TraesCS5A01G357500 chr5D 73.966 411 97 10 5333 5740 509960804 509960401 2.220000e-34 158.0
10 TraesCS5A01G357500 chr5B 93.198 1529 85 11 674 2188 539610527 539612050 0.000000e+00 2230.0
11 TraesCS5A01G357500 chr5B 97.328 1160 28 2 3413 4572 539612527 539613683 0.000000e+00 1967.0
12 TraesCS5A01G357500 chr5B 94.980 757 25 2 4571 5327 539613797 539614540 0.000000e+00 1175.0
13 TraesCS5A01G357500 chr5B 96.165 339 12 1 2872 3210 539612042 539612379 2.430000e-153 553.0
14 TraesCS5A01G357500 chr5B 84.364 275 10 6 79 341 539610220 539610473 7.720000e-59 239.0
15 TraesCS5A01G357500 chr5B 94.059 101 5 1 3203 3302 539612424 539612524 1.030000e-32 152.0
16 TraesCS5A01G357500 chr5B 98.701 77 1 0 1 77 710332797 710332721 2.900000e-28 137.0
17 TraesCS5A01G357500 chr4A 98.251 686 11 1 2187 2871 593358890 593358205 0.000000e+00 1199.0
18 TraesCS5A01G357500 chr4A 96.988 498 15 0 2189 2686 624873142 624872645 0.000000e+00 837.0
19 TraesCS5A01G357500 chr4A 96.988 498 15 0 2189 2686 624896794 624896297 0.000000e+00 837.0
20 TraesCS5A01G357500 chr4A 96.000 500 20 0 2187 2686 8359188 8358689 0.000000e+00 813.0
21 TraesCS5A01G357500 chr4A 97.326 187 5 0 2685 2871 624872445 624872259 9.640000e-83 318.0
22 TraesCS5A01G357500 chr4A 96.296 189 7 0 2685 2873 8358485 8358297 1.610000e-80 311.0
23 TraesCS5A01G357500 chr4A 96.791 187 5 1 2685 2871 624896097 624895912 1.610000e-80 311.0
24 TraesCS5A01G357500 chr4A 82.812 64 10 1 1655 1718 629468674 629468612 8.350000e-04 56.5
25 TraesCS5A01G357500 chr7A 95.992 499 19 1 2188 2686 35656145 35656642 0.000000e+00 809.0
26 TraesCS5A01G357500 chr7A 86.781 643 71 5 5333 5961 28358846 28358204 0.000000e+00 704.0
27 TraesCS5A01G357500 chr7A 95.789 190 8 0 2682 2871 35656840 35657029 2.090000e-79 307.0
28 TraesCS5A01G357500 chr1A 94.902 510 25 1 2178 2686 56445761 56446270 0.000000e+00 797.0
29 TraesCS5A01G357500 chr1A 94.980 498 18 2 2189 2686 569195020 569195510 0.000000e+00 774.0
30 TraesCS5A01G357500 chr1A 76.246 943 130 52 3450 4333 576904292 576905199 1.200000e-111 414.0
31 TraesCS5A01G357500 chr1A 96.257 187 7 0 2685 2871 508553284 508553098 2.090000e-79 307.0
32 TraesCS5A01G357500 chr1A 95.789 190 7 1 2682 2871 570183874 570184062 7.510000e-79 305.0
33 TraesCS5A01G357500 chr1A 95.263 190 9 0 2682 2871 569195706 569195895 9.710000e-78 302.0
34 TraesCS5A01G357500 chr1A 87.121 132 17 0 1737 1868 449326912 449327043 3.720000e-32 150.0
35 TraesCS5A01G357500 chr1A 94.805 77 4 0 1 77 394444116 394444040 2.920000e-23 121.0
36 TraesCS5A01G357500 chr1A 94.805 77 4 0 1 77 394532510 394532434 2.920000e-23 121.0
37 TraesCS5A01G357500 chr7D 95.200 500 23 1 2188 2686 462070376 462069877 0.000000e+00 789.0
38 TraesCS5A01G357500 chr7D 94.378 498 28 0 2189 2686 497542468 497542965 0.000000e+00 765.0
39 TraesCS5A01G357500 chr7D 96.335 191 6 1 2682 2872 462069679 462069490 4.490000e-81 313.0
40 TraesCS5A01G357500 chr7D 84.186 215 31 3 5334 5547 121783114 121782902 7.830000e-49 206.0
41 TraesCS5A01G357500 chr7D 86.047 172 16 3 674 845 24416269 24416106 1.710000e-40 178.0
42 TraesCS5A01G357500 chr7D 74.138 406 100 5 5334 5737 601876457 601876055 4.780000e-36 163.0
43 TraesCS5A01G357500 chr6A 89.097 642 56 9 5334 5961 616100217 616100858 0.000000e+00 785.0
44 TraesCS5A01G357500 chr3D 87.558 643 65 6 5333 5961 436227391 436228032 0.000000e+00 730.0
45 TraesCS5A01G357500 chr2A 79.448 326 39 13 1886 2188 267189058 267188738 7.830000e-49 206.0
46 TraesCS5A01G357500 chr2A 87.162 148 18 1 1737 1884 472406853 472406999 3.700000e-37 167.0
47 TraesCS5A01G357500 chr2A 86.486 148 19 1 1737 1884 472566424 472566570 1.720000e-35 161.0
48 TraesCS5A01G357500 chr1D 74.696 411 95 9 5331 5737 491942417 491942012 2.210000e-39 174.0
49 TraesCS5A01G357500 chr3A 87.162 148 18 1 1737 1884 397989790 397989936 3.700000e-37 167.0
50 TraesCS5A01G357500 chr3A 98.701 77 1 0 1 77 69629660 69629736 2.900000e-28 137.0
51 TraesCS5A01G357500 chr3A 98.701 77 1 0 1 77 86386594 86386670 2.900000e-28 137.0
52 TraesCS5A01G357500 chr6B 85.987 157 19 3 1737 1891 506054726 506054881 1.330000e-36 165.0
53 TraesCS5A01G357500 chr6B 74.677 387 89 9 5357 5740 617441806 617441426 4.780000e-36 163.0
54 TraesCS5A01G357500 chr3B 85.987 157 19 3 1737 1891 714981132 714981287 1.330000e-36 165.0
55 TraesCS5A01G357500 chr3B 98.701 77 1 0 1 77 19894937 19895013 2.900000e-28 137.0
56 TraesCS5A01G357500 chr3B 98.701 77 1 0 1 77 61901719 61901643 2.900000e-28 137.0
57 TraesCS5A01G357500 chrUn 84.076 157 23 2 1737 1891 41082920 41083076 3.720000e-32 150.0
58 TraesCS5A01G357500 chrUn 98.701 77 1 0 1 77 479190990 479190914 2.900000e-28 137.0
59 TraesCS5A01G357500 chr2B 98.701 77 1 0 1 77 161380454 161380530 2.900000e-28 137.0
60 TraesCS5A01G357500 chr1B 88.298 94 10 1 4872 4964 668974448 668974541 1.760000e-20 111.0


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 TraesCS5A01G357500 chr5A 559578716 559584676 5960 False 5209.000000 9769 100.0000 1 5961 2 chr5A.!!$F1 5960
1 TraesCS5A01G357500 chr5A 623333492 623334137 645 True 688.000000 688 86.2230 5330 5961 1 chr5A.!!$R1 631
2 TraesCS5A01G357500 chr5D 443311743 443316005 4262 False 1398.250000 2516 91.7055 80 5331 4 chr5D.!!$F3 5251
3 TraesCS5A01G357500 chr5D 443368968 443369926 958 False 1358.000000 1358 92.3080 4375 5329 1 chr5D.!!$F2 954
4 TraesCS5A01G357500 chr5B 539610220 539614540 4320 False 1052.666667 2230 93.3490 79 5327 6 chr5B.!!$F1 5248
5 TraesCS5A01G357500 chr4A 593358205 593358890 685 True 1199.000000 1199 98.2510 2187 2871 1 chr4A.!!$R1 684
6 TraesCS5A01G357500 chr4A 624872259 624873142 883 True 577.500000 837 97.1570 2189 2871 2 chr4A.!!$R4 682
7 TraesCS5A01G357500 chr4A 624895912 624896794 882 True 574.000000 837 96.8895 2189 2871 2 chr4A.!!$R5 682
8 TraesCS5A01G357500 chr4A 8358297 8359188 891 True 562.000000 813 96.1480 2187 2873 2 chr4A.!!$R3 686
9 TraesCS5A01G357500 chr7A 28358204 28358846 642 True 704.000000 704 86.7810 5333 5961 1 chr7A.!!$R1 628
10 TraesCS5A01G357500 chr7A 35656145 35657029 884 False 558.000000 809 95.8905 2188 2871 2 chr7A.!!$F1 683
11 TraesCS5A01G357500 chr1A 56445761 56446270 509 False 797.000000 797 94.9020 2178 2686 1 chr1A.!!$F1 508
12 TraesCS5A01G357500 chr1A 569195020 569195895 875 False 538.000000 774 95.1215 2189 2871 2 chr1A.!!$F5 682
13 TraesCS5A01G357500 chr1A 576904292 576905199 907 False 414.000000 414 76.2460 3450 4333 1 chr1A.!!$F4 883
14 TraesCS5A01G357500 chr7D 462069490 462070376 886 True 551.000000 789 95.7675 2188 2872 2 chr7D.!!$R4 684
15 TraesCS5A01G357500 chr6A 616100217 616100858 641 False 785.000000 785 89.0970 5334 5961 1 chr6A.!!$F1 627
16 TraesCS5A01G357500 chr3D 436227391 436228032 641 False 730.000000 730 87.5580 5333 5961 1 chr3D.!!$F1 628

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
22 23 0.036388 ACATCAGGTACCAGCCGTTG 60.036 55.000 15.94 2.09 0.00 4.10 F
857 883 0.108898 CTGTTCCTGCGGAGTCTCTG 60.109 60.000 2.36 4.11 31.21 3.35 F
1378 1412 1.300971 CCACGAGTTCATGCCACCAG 61.301 60.000 0.00 0.00 0.00 4.00 F
2169 2206 0.108585 ACAATGTCCCAAGCGTCTGT 59.891 50.000 0.00 0.00 0.00 3.41 F
2174 2211 3.716006 CCCAAGCGTCTGTGCACG 61.716 66.667 13.13 7.36 42.95 5.34 F
3385 3683 4.065088 TCAACAGCCACAATCAGAACTAC 58.935 43.478 0.00 0.00 0.00 2.73 F
3730 4047 2.858745 AGGTGGCGTATTTCAACTTGT 58.141 42.857 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1694 1731 1.070134 TGCTTTGCTTCGTCCTACTGT 59.930 47.619 0.00 0.00 0.00 3.55 R
1997 2034 1.961277 GTCGATTAGGCATGCCCCG 60.961 63.158 33.14 27.52 36.58 5.73 R
3211 3456 2.041081 CACCACCTGAACCTGGGAATAA 59.959 50.000 0.00 0.00 0.00 1.40 R
3385 3683 2.002586 CATCACTAAACTGGGACGCAG 58.997 52.381 17.34 17.34 0.00 5.18 R
3408 3706 4.843220 CTGAGAGCAACAGGAAACAAAT 57.157 40.909 0.00 0.00 0.00 2.32 R
4398 4759 1.261619 GCTGAATCCATAAAGGCGACG 59.738 52.381 0.00 0.00 37.29 5.12 R
5558 6072 0.106419 AACCAAGGTTCGCAGGGAAA 60.106 50.000 0.59 0.00 36.14 3.13 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
19 20 2.154854 CATACATCAGGTACCAGCCG 57.845 55.000 15.94 2.95 34.07 5.52
20 21 1.412710 CATACATCAGGTACCAGCCGT 59.587 52.381 15.94 8.99 34.07 5.68
21 22 1.563924 TACATCAGGTACCAGCCGTT 58.436 50.000 15.94 0.00 0.00 4.44
22 23 0.036388 ACATCAGGTACCAGCCGTTG 60.036 55.000 15.94 2.09 0.00 4.10
23 24 0.249120 CATCAGGTACCAGCCGTTGA 59.751 55.000 15.94 8.25 0.00 3.18
24 25 0.981183 ATCAGGTACCAGCCGTTGAA 59.019 50.000 15.94 0.00 0.00 2.69
25 26 0.981183 TCAGGTACCAGCCGTTGAAT 59.019 50.000 15.94 0.00 0.00 2.57
26 27 1.349688 TCAGGTACCAGCCGTTGAATT 59.650 47.619 15.94 0.00 0.00 2.17
27 28 2.159382 CAGGTACCAGCCGTTGAATTT 58.841 47.619 15.94 0.00 0.00 1.82
28 29 2.161609 CAGGTACCAGCCGTTGAATTTC 59.838 50.000 15.94 0.00 0.00 2.17
29 30 2.039879 AGGTACCAGCCGTTGAATTTCT 59.960 45.455 15.94 0.00 0.00 2.52
30 31 2.161609 GGTACCAGCCGTTGAATTTCTG 59.838 50.000 7.15 0.00 0.00 3.02
31 32 1.981256 ACCAGCCGTTGAATTTCTGT 58.019 45.000 0.00 0.00 0.00 3.41
32 33 1.608590 ACCAGCCGTTGAATTTCTGTG 59.391 47.619 0.00 0.00 0.00 3.66
33 34 1.608590 CCAGCCGTTGAATTTCTGTGT 59.391 47.619 0.00 0.00 0.00 3.72
34 35 2.350772 CCAGCCGTTGAATTTCTGTGTC 60.351 50.000 0.00 0.00 0.00 3.67
35 36 1.531149 AGCCGTTGAATTTCTGTGTCG 59.469 47.619 0.00 0.00 0.00 4.35
36 37 1.263217 GCCGTTGAATTTCTGTGTCGT 59.737 47.619 0.00 0.00 0.00 4.34
37 38 2.903678 CCGTTGAATTTCTGTGTCGTG 58.096 47.619 0.00 0.00 0.00 4.35
38 39 2.298300 CGTTGAATTTCTGTGTCGTGC 58.702 47.619 0.00 0.00 0.00 5.34
39 40 2.286125 CGTTGAATTTCTGTGTCGTGCA 60.286 45.455 0.00 0.00 0.00 4.57
40 41 3.606846 CGTTGAATTTCTGTGTCGTGCAT 60.607 43.478 0.00 0.00 0.00 3.96
41 42 3.541071 TGAATTTCTGTGTCGTGCATG 57.459 42.857 0.00 0.00 0.00 4.06
42 43 2.245096 GAATTTCTGTGTCGTGCATGC 58.755 47.619 11.82 11.82 0.00 4.06
43 44 0.166597 ATTTCTGTGTCGTGCATGCG 59.833 50.000 14.09 0.00 0.00 4.73
44 45 1.157257 TTTCTGTGTCGTGCATGCGT 61.157 50.000 14.09 0.00 0.00 5.24
45 46 1.556591 TTCTGTGTCGTGCATGCGTC 61.557 55.000 14.09 7.90 0.00 5.19
46 47 3.339353 CTGTGTCGTGCATGCGTCG 62.339 63.158 22.86 22.86 0.00 5.12
47 48 4.134187 GTGTCGTGCATGCGTCGG 62.134 66.667 26.26 11.67 0.00 4.79
55 56 4.147449 CATGCGTCGGCCAGGAGA 62.147 66.667 2.24 0.00 38.85 3.71
56 57 3.390521 ATGCGTCGGCCAGGAGAA 61.391 61.111 2.24 0.00 38.85 2.87
57 58 2.735772 ATGCGTCGGCCAGGAGAAT 61.736 57.895 2.24 0.00 38.85 2.40
58 59 2.586357 GCGTCGGCCAGGAGAATC 60.586 66.667 2.24 0.00 0.00 2.52
59 60 2.278857 CGTCGGCCAGGAGAATCG 60.279 66.667 2.24 0.00 34.37 3.34
60 61 2.893398 GTCGGCCAGGAGAATCGT 59.107 61.111 2.24 0.00 34.37 3.73
69 70 1.329906 CAGGAGAATCGTGCATGAAGC 59.670 52.381 13.65 7.95 44.53 3.86
70 71 1.065926 AGGAGAATCGTGCATGAAGCA 60.066 47.619 13.65 0.00 45.07 3.91
156 171 6.454848 CGAGTCTGAACTGAACTGAATATTGC 60.455 42.308 0.00 0.00 35.28 3.56
174 189 1.566018 GCTTGTTTCCGTCCAGACCG 61.566 60.000 0.00 0.00 0.00 4.79
175 190 0.949105 CTTGTTTCCGTCCAGACCGG 60.949 60.000 0.00 0.00 46.83 5.28
187 202 2.835895 GACCGGCTCCTCCTCCTC 60.836 72.222 0.00 0.00 0.00 3.71
188 203 3.351885 ACCGGCTCCTCCTCCTCT 61.352 66.667 0.00 0.00 0.00 3.69
211 226 0.479378 TCCTACCAACCCAACCCAAC 59.521 55.000 0.00 0.00 0.00 3.77
215 230 1.383248 CCAACCCAACCCAACCCAA 60.383 57.895 0.00 0.00 0.00 4.12
216 231 1.691195 CCAACCCAACCCAACCCAAC 61.691 60.000 0.00 0.00 0.00 3.77
217 232 1.383386 AACCCAACCCAACCCAACC 60.383 57.895 0.00 0.00 0.00 3.77
218 233 2.525629 CCCAACCCAACCCAACCC 60.526 66.667 0.00 0.00 0.00 4.11
219 234 2.283809 CCAACCCAACCCAACCCA 59.716 61.111 0.00 0.00 0.00 4.51
220 235 1.383248 CCAACCCAACCCAACCCAA 60.383 57.895 0.00 0.00 0.00 4.12
221 236 1.406860 CCAACCCAACCCAACCCAAG 61.407 60.000 0.00 0.00 0.00 3.61
222 237 1.764454 AACCCAACCCAACCCAAGC 60.764 57.895 0.00 0.00 0.00 4.01
223 238 2.922503 CCCAACCCAACCCAAGCC 60.923 66.667 0.00 0.00 0.00 4.35
224 239 2.123077 CCAACCCAACCCAAGCCA 60.123 61.111 0.00 0.00 0.00 4.75
314 333 2.844839 CGATCCCACCCCTCTCCC 60.845 72.222 0.00 0.00 0.00 4.30
722 741 1.983605 CGTACGAGCTTGTTCGATTGT 59.016 47.619 24.26 0.00 43.03 2.71
724 743 3.605056 CGTACGAGCTTGTTCGATTGTTA 59.395 43.478 24.26 0.00 43.03 2.41
725 744 4.488258 CGTACGAGCTTGTTCGATTGTTAC 60.488 45.833 24.26 7.42 43.03 2.50
770 789 1.084370 CCGACCTCCACGATTTCTGC 61.084 60.000 0.00 0.00 0.00 4.26
775 795 4.851114 CCACGATTTCTGCGCGCG 62.851 66.667 28.44 28.44 0.00 6.86
853 876 0.250513 ATTCCTGTTCCTGCGGAGTC 59.749 55.000 2.36 0.00 31.21 3.36
857 883 0.108898 CTGTTCCTGCGGAGTCTCTG 60.109 60.000 2.36 4.11 31.21 3.35
927 956 2.996621 GTGACCCAGTCGAGATTTTCTG 59.003 50.000 0.00 0.00 34.95 3.02
1013 1042 2.673200 GGGAGATGCAGGTCAGCCA 61.673 63.158 0.00 0.00 37.19 4.75
1024 1053 1.554160 AGGTCAGCCACTCATCTCTTG 59.446 52.381 0.00 0.00 37.19 3.02
1068 1097 1.515954 CTAGGGCGTTCCACGATGT 59.484 57.895 0.00 0.00 46.05 3.06
1149 1179 1.416030 GCAACCCAGACCAACCAAAAT 59.584 47.619 0.00 0.00 0.00 1.82
1183 1213 8.866970 AATTCCCAATTCATGCAAACTTTTAT 57.133 26.923 0.00 0.00 0.00 1.40
1184 1214 9.956640 AATTCCCAATTCATGCAAACTTTTATA 57.043 25.926 0.00 0.00 0.00 0.98
1185 1215 8.770438 TTCCCAATTCATGCAAACTTTTATAC 57.230 30.769 0.00 0.00 0.00 1.47
1273 1307 2.231478 TGAGGCTCGACAGTTTTCTAGG 59.769 50.000 10.42 0.00 0.00 3.02
1279 1313 1.797025 GACAGTTTTCTAGGCAGCGT 58.203 50.000 0.00 0.00 0.00 5.07
1280 1314 2.143925 GACAGTTTTCTAGGCAGCGTT 58.856 47.619 0.00 0.00 0.00 4.84
1366 1400 2.960170 GCGTAGACCACCACGAGT 59.040 61.111 0.00 0.00 40.56 4.18
1378 1412 1.300971 CCACGAGTTCATGCCACCAG 61.301 60.000 0.00 0.00 0.00 4.00
1449 1483 3.814283 GCAGGCATGAGAGGAAAGATAAG 59.186 47.826 0.62 0.00 0.00 1.73
1459 1493 4.081198 AGAGGAAAGATAAGTGACAGGCTG 60.081 45.833 14.16 14.16 0.00 4.85
1509 1545 2.921754 GTTAGCAACACTACAGCCTACG 59.078 50.000 0.00 0.00 0.00 3.51
1529 1565 6.483640 CCTACGGATAAAGCAGCTAGAAAATT 59.516 38.462 0.00 0.00 0.00 1.82
1622 1659 1.650912 CTATGTTCTGCGGCCATGC 59.349 57.895 2.24 0.00 0.00 4.06
1728 1765 3.119245 AGCAAAGCATCTTTGGTAGCATG 60.119 43.478 18.69 0.00 38.22 4.06
1801 1838 3.681594 GCTCTTTCGATGACCCCATGTTA 60.682 47.826 0.00 0.00 32.09 2.41
1919 1956 7.821652 TGTTATTTTTCAGAACAAGTGTGTCA 58.178 30.769 0.00 0.00 36.80 3.58
2075 2112 4.818005 ACTTGTCCGTAGTTAAAACCAAGG 59.182 41.667 0.00 1.21 33.99 3.61
2127 2164 3.966543 CCAAAGGACACCCCGGCT 61.967 66.667 0.00 0.00 40.87 5.52
2169 2206 0.108585 ACAATGTCCCAAGCGTCTGT 59.891 50.000 0.00 0.00 0.00 3.41
2174 2211 3.716006 CCCAAGCGTCTGTGCACG 61.716 66.667 13.13 7.36 42.95 5.34
2277 2314 4.559726 TCCCTATTTAACACGGGGTCTAT 58.440 43.478 0.00 0.00 38.31 1.98
2359 2398 4.468153 TGTAAAAAGACAGTTTTGCCCCTT 59.532 37.500 0.00 0.00 33.61 3.95
2892 3137 9.213799 CTCTCAAGAAAGAGTTAAACTATGCTT 57.786 33.333 0.00 0.00 38.38 3.91
2928 3173 6.710597 AGAAGTAAACTATGCTCGGTGATA 57.289 37.500 0.00 0.00 0.00 2.15
2929 3174 7.291411 AGAAGTAAACTATGCTCGGTGATAT 57.709 36.000 0.00 0.00 0.00 1.63
2995 3240 8.250332 AGTCTATGAAGAAGAGATTGAACTCAC 58.750 37.037 0.00 0.00 39.14 3.51
3210 3455 4.892934 ACATGAGGCAGAAGGTTAACAAAA 59.107 37.500 8.10 0.00 0.00 2.44
3211 3456 5.539955 ACATGAGGCAGAAGGTTAACAAAAT 59.460 36.000 8.10 0.00 0.00 1.82
3347 3645 5.631096 GTCTTATTCAGCAGCTTTTTGGAAC 59.369 40.000 0.00 0.00 0.00 3.62
3385 3683 4.065088 TCAACAGCCACAATCAGAACTAC 58.935 43.478 0.00 0.00 0.00 2.73
3408 3706 3.007074 TGCGTCCCAGTTTAGTGATGTTA 59.993 43.478 0.00 0.00 0.00 2.41
3473 3772 8.282592 TCTTAAAACATTCTGACAATGTCTTCG 58.717 33.333 14.97 3.55 39.73 3.79
3730 4047 2.858745 AGGTGGCGTATTTCAACTTGT 58.141 42.857 0.00 0.00 0.00 3.16
3829 4146 9.485206 TGTTCACTTCAAGGTTACTTTCTATAC 57.515 33.333 0.00 0.00 33.81 1.47
4106 4436 6.551601 TGTTGCTAAATCCAAAACTAAAGGGA 59.448 34.615 0.00 0.00 0.00 4.20
4180 4510 9.023962 GGTGAAATATGCCTGGATATATTGAAA 57.976 33.333 13.80 4.63 31.69 2.69
4326 4687 9.702726 ATGAATTCGTTTTAATCACATTACTCG 57.297 29.630 0.04 0.00 0.00 4.18
4344 4705 3.767673 ACTCGCTATTTCCTACTGGTGAA 59.232 43.478 0.00 0.00 34.23 3.18
4398 4759 2.348666 AGCTATGTCGCATGAAAACGTC 59.651 45.455 0.00 0.00 0.00 4.34
4612 5090 7.013823 AGTATCCATGGATAAATGGTGAGAG 57.986 40.000 31.62 0.00 46.24 3.20
4882 5380 3.159472 TGCAATCACAGGCAATCTTCTT 58.841 40.909 0.00 0.00 37.03 2.52
4969 5467 5.509670 GCCAAAGAAAGAGTAATTTGCAGGT 60.510 40.000 0.00 0.00 32.54 4.00
4993 5491 2.289444 GCAAAGGTACACCAGAGCAGTA 60.289 50.000 0.38 0.00 38.89 2.74
5035 5533 4.512571 TGATTCATGCATGTATCAACTCCG 59.487 41.667 33.79 6.27 40.21 4.63
5060 5558 1.860676 TGTCAGGTGTAACTCGTTGC 58.139 50.000 0.00 0.00 36.74 4.17
5084 5594 1.271163 CCCCGTATGAACTTGTGTGGT 60.271 52.381 0.00 0.00 0.00 4.16
5431 5945 1.901464 AAACCACACATGACGCCCC 60.901 57.895 0.00 0.00 0.00 5.80
5433 5947 4.697756 CCACACATGACGCCCCGT 62.698 66.667 0.00 0.00 45.10 5.28
5451 5965 3.168193 CCGTGGCTAAATTTAAAGCGTG 58.832 45.455 6.82 0.61 39.71 5.34
5474 5988 5.069251 TGTCTAGCTAACTTATGAGCTTCCC 59.931 44.000 1.16 0.00 46.99 3.97
5511 6025 7.660208 ACGACCTTCATGAATAAAACTACAAGT 59.340 33.333 8.96 0.00 0.00 3.16
5548 6062 7.012959 ACGAAGTTTGATCTCATTGATGATG 57.987 36.000 0.00 0.00 37.78 3.07
5558 6072 0.826256 ATTGATGATGGCGCCATGCT 60.826 50.000 44.96 30.50 45.43 3.79
5573 6087 0.251341 ATGCTTTCCCTGCGAACCTT 60.251 50.000 0.00 0.00 0.00 3.50
5586 6100 2.076863 CGAACCTTGGTTGATGTCCTC 58.923 52.381 10.04 0.00 0.00 3.71
5599 6113 2.905415 TGTCCTCGACTACCCCTTTA 57.095 50.000 0.00 0.00 33.15 1.85
5608 6122 3.132289 CGACTACCCCTTTAGCATCTGAA 59.868 47.826 0.00 0.00 0.00 3.02
5629 6143 4.764679 AGATATGACAAAACGCTGCAAA 57.235 36.364 0.00 0.00 0.00 3.68
5650 6164 1.442526 GGAGGTCATCCGCAATGCAG 61.443 60.000 5.91 0.00 38.67 4.41
5660 6174 1.676635 GCAATGCAGAGTGCCTCCA 60.677 57.895 0.00 0.00 44.23 3.86
5661 6175 1.654954 GCAATGCAGAGTGCCTCCAG 61.655 60.000 0.00 0.00 44.23 3.86
5738 6252 2.050918 AGCTGCCTAGATAGTTTCCCC 58.949 52.381 0.00 0.00 0.00 4.81
5739 6253 2.050918 GCTGCCTAGATAGTTTCCCCT 58.949 52.381 0.00 0.00 0.00 4.79
5743 6257 3.711704 TGCCTAGATAGTTTCCCCTTGAG 59.288 47.826 0.00 0.00 0.00 3.02
5752 6266 2.046892 CCCCTTGAGTCACGGCAG 60.047 66.667 10.18 0.20 0.00 4.85
5801 6329 4.214971 GCATCAACATGGACCTTAGCATAG 59.785 45.833 0.00 0.00 0.00 2.23
5835 6363 3.311110 GTGGTCGGGTGCTCCTGA 61.311 66.667 12.37 12.37 45.86 3.86
5842 6370 1.351017 TCGGGTGCTCCTGATTCTTTT 59.649 47.619 12.37 0.00 43.49 2.27
5845 6373 3.359950 GGGTGCTCCTGATTCTTTTCAT 58.640 45.455 4.53 0.00 0.00 2.57
5849 6377 5.824624 GGTGCTCCTGATTCTTTTCATATGA 59.175 40.000 0.00 0.00 0.00 2.15
5884 6412 4.585581 CCCTTCCGGTTTTCTTTCCTTTAA 59.414 41.667 0.00 0.00 0.00 1.52
5909 6437 2.783135 TCAAGCTCACCAATGAACCTC 58.217 47.619 0.00 0.00 33.30 3.85
5948 6476 2.681976 CGATTGTGGGCTCTGGAAGATT 60.682 50.000 0.00 0.00 45.62 2.40
5957 6485 3.212685 GCTCTGGAAGATTCCTTCATGG 58.787 50.000 12.65 0.00 45.62 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.412710 ACGGCTGGTACCTGATGTATG 59.587 52.381 21.97 6.84 0.00 2.39
1 2 1.789523 ACGGCTGGTACCTGATGTAT 58.210 50.000 21.97 0.00 0.00 2.29
2 3 1.206132 CAACGGCTGGTACCTGATGTA 59.794 52.381 21.97 0.00 0.00 2.29
4 5 0.249120 TCAACGGCTGGTACCTGATG 59.751 55.000 21.97 14.50 0.00 3.07
6 7 0.981183 ATTCAACGGCTGGTACCTGA 59.019 50.000 21.97 8.98 0.00 3.86
7 8 1.821216 AATTCAACGGCTGGTACCTG 58.179 50.000 14.36 14.26 0.00 4.00
8 9 2.039879 AGAAATTCAACGGCTGGTACCT 59.960 45.455 14.36 0.00 0.00 3.08
9 10 2.161609 CAGAAATTCAACGGCTGGTACC 59.838 50.000 4.43 4.43 0.00 3.34
10 11 2.812011 ACAGAAATTCAACGGCTGGTAC 59.188 45.455 0.00 0.00 0.00 3.34
11 12 2.811431 CACAGAAATTCAACGGCTGGTA 59.189 45.455 0.00 0.00 0.00 3.25
12 13 1.608590 CACAGAAATTCAACGGCTGGT 59.391 47.619 0.00 0.00 0.00 4.00
13 14 1.608590 ACACAGAAATTCAACGGCTGG 59.391 47.619 0.00 0.00 0.00 4.85
14 15 2.662791 CGACACAGAAATTCAACGGCTG 60.663 50.000 0.00 0.00 0.00 4.85
15 16 1.531149 CGACACAGAAATTCAACGGCT 59.469 47.619 0.00 0.00 0.00 5.52
16 17 1.263217 ACGACACAGAAATTCAACGGC 59.737 47.619 0.00 0.00 0.00 5.68
17 18 2.903678 CACGACACAGAAATTCAACGG 58.096 47.619 0.00 0.00 0.00 4.44
18 19 2.286125 TGCACGACACAGAAATTCAACG 60.286 45.455 0.00 0.00 0.00 4.10
19 20 3.332761 TGCACGACACAGAAATTCAAC 57.667 42.857 0.00 0.00 0.00 3.18
20 21 3.852939 GCATGCACGACACAGAAATTCAA 60.853 43.478 14.21 0.00 0.00 2.69
21 22 2.350676 GCATGCACGACACAGAAATTCA 60.351 45.455 14.21 0.00 0.00 2.57
22 23 2.245096 GCATGCACGACACAGAAATTC 58.755 47.619 14.21 0.00 0.00 2.17
23 24 1.400113 CGCATGCACGACACAGAAATT 60.400 47.619 19.57 0.00 34.06 1.82
24 25 0.166597 CGCATGCACGACACAGAAAT 59.833 50.000 19.57 0.00 34.06 2.17
25 26 1.157257 ACGCATGCACGACACAGAAA 61.157 50.000 19.57 0.00 36.70 2.52
26 27 1.556591 GACGCATGCACGACACAGAA 61.557 55.000 19.57 0.00 36.70 3.02
27 28 2.021584 GACGCATGCACGACACAGA 61.022 57.895 19.57 0.00 36.70 3.41
28 29 2.471607 GACGCATGCACGACACAG 59.528 61.111 19.57 0.50 36.70 3.66
29 30 3.402233 CGACGCATGCACGACACA 61.402 61.111 23.55 0.00 36.70 3.72
30 31 4.134187 CCGACGCATGCACGACAC 62.134 66.667 27.57 8.67 36.70 3.67
38 39 2.930385 ATTCTCCTGGCCGACGCATG 62.930 60.000 0.00 0.00 36.38 4.06
39 40 2.650813 GATTCTCCTGGCCGACGCAT 62.651 60.000 0.00 0.00 36.38 4.73
40 41 3.371097 GATTCTCCTGGCCGACGCA 62.371 63.158 0.00 0.00 36.38 5.24
41 42 2.586357 GATTCTCCTGGCCGACGC 60.586 66.667 0.00 0.00 0.00 5.19
42 43 2.278857 CGATTCTCCTGGCCGACG 60.279 66.667 0.00 0.00 0.00 5.12
43 44 1.519455 CACGATTCTCCTGGCCGAC 60.519 63.158 0.00 0.00 0.00 4.79
44 45 2.892640 CACGATTCTCCTGGCCGA 59.107 61.111 0.00 0.00 0.00 5.54
45 46 2.892425 GCACGATTCTCCTGGCCG 60.892 66.667 0.00 0.00 0.00 6.13
46 47 1.153086 ATGCACGATTCTCCTGGCC 60.153 57.895 0.00 0.00 0.00 5.36
47 48 0.462581 TCATGCACGATTCTCCTGGC 60.463 55.000 0.00 0.00 0.00 4.85
48 49 1.938577 CTTCATGCACGATTCTCCTGG 59.061 52.381 0.00 0.00 0.00 4.45
49 50 1.329906 GCTTCATGCACGATTCTCCTG 59.670 52.381 0.00 0.00 42.31 3.86
50 51 1.661341 GCTTCATGCACGATTCTCCT 58.339 50.000 0.00 0.00 42.31 3.69
61 62 1.632422 CACCCGAAATTGCTTCATGC 58.368 50.000 0.00 0.00 43.25 4.06
62 63 1.067706 TGCACCCGAAATTGCTTCATG 60.068 47.619 0.00 0.00 39.62 3.07
63 64 1.203052 CTGCACCCGAAATTGCTTCAT 59.797 47.619 0.00 0.00 39.62 2.57
64 65 0.597568 CTGCACCCGAAATTGCTTCA 59.402 50.000 0.00 0.00 39.62 3.02
65 66 0.881118 TCTGCACCCGAAATTGCTTC 59.119 50.000 0.00 0.00 39.62 3.86
66 67 1.327303 TTCTGCACCCGAAATTGCTT 58.673 45.000 0.00 0.00 39.62 3.91
67 68 1.270550 CTTTCTGCACCCGAAATTGCT 59.729 47.619 0.60 0.00 39.62 3.91
68 69 1.000274 ACTTTCTGCACCCGAAATTGC 60.000 47.619 0.60 0.00 39.33 3.56
69 70 3.052036 CAACTTTCTGCACCCGAAATTG 58.948 45.455 0.60 4.70 30.75 2.32
70 71 2.693074 ACAACTTTCTGCACCCGAAATT 59.307 40.909 0.60 0.00 30.75 1.82
71 72 2.034558 CACAACTTTCTGCACCCGAAAT 59.965 45.455 0.60 0.00 30.75 2.17
72 73 1.403679 CACAACTTTCTGCACCCGAAA 59.596 47.619 0.35 0.35 0.00 3.46
73 74 1.021202 CACAACTTTCTGCACCCGAA 58.979 50.000 0.00 0.00 0.00 4.30
74 75 1.444119 GCACAACTTTCTGCACCCGA 61.444 55.000 0.00 0.00 33.31 5.14
75 76 1.008538 GCACAACTTTCTGCACCCG 60.009 57.895 0.00 0.00 33.31 5.28
76 77 0.031178 CTGCACAACTTTCTGCACCC 59.969 55.000 0.00 0.00 38.49 4.61
77 78 0.595825 GCTGCACAACTTTCTGCACC 60.596 55.000 0.00 0.00 38.49 5.01
119 127 0.028770 CAGACTCGATCAGCCGTCTC 59.971 60.000 0.15 0.00 34.72 3.36
120 128 0.393132 TCAGACTCGATCAGCCGTCT 60.393 55.000 0.00 0.00 37.22 4.18
156 171 2.528797 CGGTCTGGACGGAAACAAG 58.471 57.895 2.74 0.00 34.05 3.16
174 189 0.759060 GAGGAAGAGGAGGAGGAGCC 60.759 65.000 0.00 0.00 0.00 4.70
175 190 0.759060 GGAGGAAGAGGAGGAGGAGC 60.759 65.000 0.00 0.00 0.00 4.70
179 194 1.571457 TGGTAGGAGGAAGAGGAGGAG 59.429 57.143 0.00 0.00 0.00 3.69
187 202 1.004394 GGTTGGGTTGGTAGGAGGAAG 59.996 57.143 0.00 0.00 0.00 3.46
188 203 1.069775 GGTTGGGTTGGTAGGAGGAA 58.930 55.000 0.00 0.00 0.00 3.36
692 711 1.093159 AGCTCGTACGTACCTCCAAG 58.907 55.000 19.67 10.36 0.00 3.61
722 741 3.654178 GCTAATCGCTGGACGGTAA 57.346 52.632 0.00 0.00 43.89 2.85
788 808 4.323569 TGCTACCTAGGGATCTAGATGG 57.676 50.000 14.81 7.23 44.35 3.51
853 876 2.600731 GTCTCGGTGACATGAACAGAG 58.399 52.381 19.36 19.36 44.73 3.35
879 905 6.009115 ACCGGTGCTTATAAACAGAAAAAG 57.991 37.500 6.12 0.00 0.00 2.27
883 909 5.045215 CGATACCGGTGCTTATAAACAGAA 58.955 41.667 19.93 0.00 0.00 3.02
884 910 4.098349 ACGATACCGGTGCTTATAAACAGA 59.902 41.667 19.93 0.00 40.78 3.41
927 956 2.363683 CCAGAAAACAGAGGGCAGATC 58.636 52.381 0.00 0.00 0.00 2.75
996 1025 1.451028 GTGGCTGACCTGCATCTCC 60.451 63.158 0.00 0.00 36.63 3.71
1013 1042 4.955450 ACTGATGCTAGTCAAGAGATGAGT 59.045 41.667 0.00 0.00 44.09 3.41
1024 1053 6.422400 GCCTAACTAAATCACTGATGCTAGTC 59.578 42.308 11.75 1.31 0.00 2.59
1068 1097 2.771943 AGACTGAACTGACAAGGTTGGA 59.228 45.455 0.00 0.00 0.00 3.53
1149 1179 5.933463 GCATGAATTGGGAATTTGACAAGAA 59.067 36.000 0.00 0.00 0.00 2.52
1256 1290 1.996191 CTGCCTAGAAAACTGTCGAGC 59.004 52.381 0.00 0.00 0.00 5.03
1279 1313 9.383519 CTAGTTATTTCTATGTCAAGAGGCAAA 57.616 33.333 0.00 0.00 0.00 3.68
1280 1314 7.987458 CCTAGTTATTTCTATGTCAAGAGGCAA 59.013 37.037 0.00 0.00 0.00 4.52
1288 1322 5.454755 GGGCTGCCTAGTTATTTCTATGTCA 60.455 44.000 19.68 0.00 0.00 3.58
1356 1390 1.302431 TGGCATGAACTCGTGGTGG 60.302 57.895 0.00 0.00 33.60 4.61
1378 1412 1.467920 CCAAGGAACAAGGGATCTGC 58.532 55.000 0.00 0.00 0.00 4.26
1382 1416 1.678970 GCGCCAAGGAACAAGGGAT 60.679 57.895 0.00 0.00 0.00 3.85
1449 1483 3.054878 CAAATCTTTTGCAGCCTGTCAC 58.945 45.455 0.00 0.00 0.00 3.67
1459 1493 6.320944 TCTTTTGTTTTGCCAAATCTTTTGC 58.679 32.000 0.00 0.00 34.50 3.68
1543 1579 8.635765 TTATCTCTTTCTTGCAAACCATAACT 57.364 30.769 0.00 0.00 0.00 2.24
1622 1659 1.720694 AACACCTTTGGACGCCAACG 61.721 55.000 10.30 8.91 43.82 4.10
1694 1731 1.070134 TGCTTTGCTTCGTCCTACTGT 59.930 47.619 0.00 0.00 0.00 3.55
1801 1838 7.775053 TCCCAGCAAAGAAACATAACTAAAT 57.225 32.000 0.00 0.00 0.00 1.40
1919 1956 3.580458 ACTACAAGTCCAGTCTGCAGAAT 59.420 43.478 20.19 15.89 0.00 2.40
1997 2034 1.961277 GTCGATTAGGCATGCCCCG 60.961 63.158 33.14 27.52 36.58 5.73
2064 2101 7.393796 TGACAAGAAGTGTTACCTTGGTTTTAA 59.606 33.333 0.00 0.00 41.96 1.52
2067 2104 5.124936 GTGACAAGAAGTGTTACCTTGGTTT 59.875 40.000 0.00 0.00 41.96 3.27
2068 2105 4.638865 GTGACAAGAAGTGTTACCTTGGTT 59.361 41.667 0.00 0.00 41.96 3.67
2075 2112 4.321217 CGATCGAGTGACAAGAAGTGTTAC 59.679 45.833 10.26 0.00 44.96 2.50
2169 2206 2.481568 CTCTTCTTTCTTCATGCGTGCA 59.518 45.455 0.00 0.00 0.00 4.57
2174 2211 7.600960 AGGAATTTTCTCTTCTTTCTTCATGC 58.399 34.615 0.00 0.00 0.00 4.06
2277 2314 9.421806 CAAAAGTGTCATGAAAGGCATAAAATA 57.578 29.630 0.00 0.00 34.82 1.40
2359 2398 8.491045 TCCAGATGACCAGTTCATATTATACA 57.509 34.615 0.00 0.00 45.67 2.29
2873 3118 7.435068 TCACCAAGCATAGTTTAACTCTTTC 57.565 36.000 0.00 0.00 0.00 2.62
2874 3119 7.665559 TGATCACCAAGCATAGTTTAACTCTTT 59.334 33.333 0.00 0.00 0.00 2.52
2875 3120 7.168219 TGATCACCAAGCATAGTTTAACTCTT 58.832 34.615 0.00 0.00 0.00 2.85
2876 3121 6.711277 TGATCACCAAGCATAGTTTAACTCT 58.289 36.000 0.00 0.00 0.00 3.24
2877 3122 6.457528 GCTGATCACCAAGCATAGTTTAACTC 60.458 42.308 0.00 0.00 0.00 3.01
2878 3123 5.355350 GCTGATCACCAAGCATAGTTTAACT 59.645 40.000 2.32 2.32 0.00 2.24
2879 3124 5.449177 GGCTGATCACCAAGCATAGTTTAAC 60.449 44.000 6.95 0.00 0.00 2.01
2892 3137 4.072131 GTTTACTTCTTGGCTGATCACCA 58.928 43.478 11.56 11.56 34.65 4.17
2928 3173 2.840038 TGTGACTATCCTGTTCTGGCAT 59.160 45.455 0.00 0.00 0.00 4.40
2929 3174 2.256306 TGTGACTATCCTGTTCTGGCA 58.744 47.619 0.00 0.00 0.00 4.92
2995 3240 3.305720 TCTGCACCATTACTACCTAGGG 58.694 50.000 14.81 0.00 0.00 3.53
3108 3353 9.710900 CTATCAATGTTACATAATAGTGCCTCA 57.289 33.333 14.48 0.00 0.00 3.86
3210 3455 2.926329 ACCACCTGAACCTGGGAATAAT 59.074 45.455 0.00 0.00 0.00 1.28
3211 3456 2.041081 CACCACCTGAACCTGGGAATAA 59.959 50.000 0.00 0.00 0.00 1.40
3347 3645 6.479990 TGGCTGTTGAGATCGATACTAATTTG 59.520 38.462 0.00 0.00 0.00 2.32
3385 3683 2.002586 CATCACTAAACTGGGACGCAG 58.997 52.381 17.34 17.34 0.00 5.18
3408 3706 4.843220 CTGAGAGCAACAGGAAACAAAT 57.157 40.909 0.00 0.00 0.00 2.32
3438 3736 7.123547 TGTCAGAATGTTTTAAGAACCAAGGTT 59.876 33.333 3.73 3.73 38.11 3.50
3439 3737 6.605594 TGTCAGAATGTTTTAAGAACCAAGGT 59.394 34.615 0.00 0.00 37.40 3.50
3473 3772 5.130350 CCTAGCTCTAGATGCCTATAGACC 58.870 50.000 0.00 0.00 35.21 3.85
3730 4047 5.279506 GGATACTGCTCGGGAATTGAGAATA 60.280 44.000 0.00 0.00 35.43 1.75
3829 4146 5.320549 AGCATGTATTTCAAAGAAGGCAG 57.679 39.130 0.00 0.00 0.00 4.85
4002 4322 6.155393 AGGGAATTTCAACAGTACAAACCAAA 59.845 34.615 0.00 0.00 0.00 3.28
4106 4436 9.755804 GAAGAGAAATTGAGGAAACAGAAATTT 57.244 29.630 0.00 0.00 33.98 1.82
4180 4510 1.305465 TGCAGGGCTCCATGCATTT 60.305 52.632 22.37 0.00 46.97 2.32
4249 4610 1.352083 TAAGTGGGCTGTCTGCTTCT 58.648 50.000 1.44 0.00 42.39 2.85
4326 4687 5.086104 TCAGTTCACCAGTAGGAAATAGC 57.914 43.478 0.00 0.00 38.69 2.97
4344 4705 6.205464 CAGTGAGAACATAAACACCAATCAGT 59.795 38.462 0.00 0.00 34.33 3.41
4398 4759 1.261619 GCTGAATCCATAAAGGCGACG 59.738 52.381 0.00 0.00 37.29 5.12
4612 5090 4.667668 GCAGCCGTGATCGATTTGATAATC 60.668 45.833 0.00 0.00 37.47 1.75
4882 5380 1.657751 CTCTGATGTCACCGGAGCGA 61.658 60.000 9.46 0.00 31.17 4.93
4969 5467 1.953686 GCTCTGGTGTACCTTTGCAAA 59.046 47.619 12.14 12.14 36.82 3.68
5035 5533 4.614946 ACGAGTTACACCTGACAACTTAC 58.385 43.478 0.00 0.00 32.79 2.34
5060 5558 4.119862 CACACAAGTTCATACGGGGATAG 58.880 47.826 0.00 0.00 0.00 2.08
5084 5594 5.223449 ACAAGTCGGGTAAGAAAATCAGA 57.777 39.130 0.00 0.00 0.00 3.27
5187 5697 8.287904 TGTTACCAATTCCCTATGAGGATTAT 57.712 34.615 0.00 0.00 37.67 1.28
5197 5707 8.282801 ACCATATACATGTTACCAATTCCCTA 57.717 34.615 2.30 0.00 0.00 3.53
5203 5713 7.147213 TGGAGGAACCATATACATGTTACCAAT 60.147 37.037 2.30 0.00 44.64 3.16
5349 5863 6.261158 GGACTTTGATCAATAAAGACTAGGCC 59.739 42.308 9.40 8.76 38.26 5.19
5355 5869 8.514594 TCATTGTGGACTTTGATCAATAAAGAC 58.485 33.333 9.40 4.40 38.26 3.01
5431 5945 3.817238 ACACGCTTTAAATTTAGCCACG 58.183 40.909 7.25 8.33 33.86 4.94
5433 5947 5.163794 GCTAGACACGCTTTAAATTTAGCCA 60.164 40.000 7.25 0.00 33.86 4.75
5474 5988 7.770801 TTCATGAAGGTCGTGAATGTAATAG 57.229 36.000 3.38 0.00 44.72 1.73
5524 6038 6.037940 CCATCATCAATGAGATCAAACTTCGT 59.962 38.462 0.00 0.00 40.64 3.85
5545 6059 2.414594 GGAAAGCATGGCGCCATC 59.585 61.111 38.60 29.60 44.04 3.51
5548 6062 3.830192 CAGGGAAAGCATGGCGCC 61.830 66.667 22.73 22.73 44.04 6.53
5558 6072 0.106419 AACCAAGGTTCGCAGGGAAA 60.106 50.000 0.59 0.00 36.14 3.13
5573 6087 1.822990 GGTAGTCGAGGACATCAACCA 59.177 52.381 0.00 0.00 34.60 3.67
5586 6100 2.693591 TCAGATGCTAAAGGGGTAGTCG 59.306 50.000 0.00 0.00 0.00 4.18
5599 6113 5.220739 GCGTTTTGTCATATCTTCAGATGCT 60.221 40.000 0.00 0.00 36.05 3.79
5608 6122 4.764679 TTTGCAGCGTTTTGTCATATCT 57.235 36.364 0.00 0.00 0.00 1.98
5629 6143 0.749454 GCATTGCGGATGACCTCCTT 60.749 55.000 4.24 0.00 42.47 3.36
5684 6198 0.527817 CAAGGCGTAGATGACCCGAC 60.528 60.000 0.00 0.00 0.00 4.79
5738 6252 0.946221 GTGGTCTGCCGTGACTCAAG 60.946 60.000 0.00 0.00 37.16 3.02
5739 6253 1.069090 GTGGTCTGCCGTGACTCAA 59.931 57.895 0.00 0.00 37.16 3.02
5743 6257 4.699522 GGGGTGGTCTGCCGTGAC 62.700 72.222 0.00 0.00 37.67 3.67
5752 6266 1.384643 AGGATAGGCAGGGGTGGTC 60.385 63.158 0.00 0.00 0.00 4.02
5766 6294 1.003928 TGTTGATGCAGCTGTGAGGAT 59.996 47.619 16.64 0.00 0.00 3.24
5828 6356 7.447853 AGGATTCATATGAAAAGAATCAGGAGC 59.552 37.037 21.50 0.00 45.82 4.70
5830 6358 9.128404 CAAGGATTCATATGAAAAGAATCAGGA 57.872 33.333 21.50 0.00 45.82 3.86
5835 6363 6.736794 GCGCCAAGGATTCATATGAAAAGAAT 60.737 38.462 21.50 5.24 37.61 2.40
5842 6370 1.545428 GGGCGCCAAGGATTCATATGA 60.545 52.381 30.85 0.00 0.00 2.15
5845 6373 1.150536 GGGGCGCCAAGGATTCATA 59.849 57.895 30.85 0.00 0.00 2.15
5849 6377 2.043953 GAAGGGGCGCCAAGGATT 60.044 61.111 30.85 14.53 0.00 3.01
5873 6401 7.425606 GTGAGCTTGAACAATTAAAGGAAAGA 58.574 34.615 0.00 0.00 0.00 2.52
5884 6412 4.262164 GGTTCATTGGTGAGCTTGAACAAT 60.262 41.667 21.92 14.14 46.12 2.71


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

AutoCloner maintained by Alex Coulton.