Multiple sequence alignment - TraesCS2B01G547600

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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 TraesCS2B01G547600 chr2B 100.000 7487 0 0 287 7773 744173354 744165868 0.000000e+00 13826.0
1 TraesCS2B01G547600 chr2B 98.413 252 2 2 4635 4885 407872357 407872607 7.160000e-120 442.0
2 TraesCS2B01G547600 chr2B 90.189 265 21 3 4186 4447 588234084 588234346 2.690000e-89 340.0
3 TraesCS2B01G547600 chr2B 100.000 49 0 0 1 49 744173640 744173592 2.990000e-14 91.6
4 TraesCS2B01G547600 chr2D 92.782 4447 192 60 287 4636 609781740 609777326 0.000000e+00 6314.0
5 TraesCS2B01G547600 chr2D 95.552 2900 100 15 4883 7773 609777330 609774451 0.000000e+00 4614.0
6 TraesCS2B01G547600 chr2D 88.742 151 16 1 4883 5032 299891574 299891724 4.790000e-42 183.0
7 TraesCS2B01G547600 chr2A 95.800 3143 92 15 1515 4636 742725398 742722275 0.000000e+00 5036.0
8 TraesCS2B01G547600 chr2A 95.208 2191 74 12 4883 7068 742722279 742720115 0.000000e+00 3435.0
9 TraesCS2B01G547600 chr2A 93.402 682 13 11 7095 7773 742720060 742719408 0.000000e+00 981.0
10 TraesCS2B01G547600 chr2A 90.345 725 42 14 794 1502 742726156 742725444 0.000000e+00 926.0
11 TraesCS2B01G547600 chr2A 87.238 525 31 14 293 790 742726711 742726196 4.070000e-157 566.0
12 TraesCS2B01G547600 chr2A 95.652 46 1 1 1 45 742726829 742726784 1.080000e-08 73.1
13 TraesCS2B01G547600 chr1B 97.683 259 2 3 4627 4884 424542106 424542361 7.160000e-120 442.0
14 TraesCS2B01G547600 chr1B 98.387 248 3 1 4637 4884 448747189 448747435 1.200000e-117 435.0
15 TraesCS2B01G547600 chr1B 89.377 273 26 3 4178 4448 601141812 601141541 2.690000e-89 340.0
16 TraesCS2B01G547600 chr1B 91.549 142 11 1 4883 5023 334894525 334894666 2.210000e-45 195.0
17 TraesCS2B01G547600 chr4B 98.406 251 1 3 4635 4883 449365517 449365268 9.260000e-119 438.0
18 TraesCS2B01G547600 chr4B 90.943 265 19 4 4186 4447 450022436 450022174 1.240000e-92 351.0
19 TraesCS2B01G547600 chr4B 88.530 279 29 2 4175 4451 64389774 64390051 1.250000e-87 335.0
20 TraesCS2B01G547600 chr3A 98.400 250 2 2 4635 4883 724741075 724741323 9.260000e-119 438.0
21 TraesCS2B01G547600 chr3A 90.909 143 11 2 4883 5023 600923098 600923240 2.860000e-44 191.0
22 TraesCS2B01G547600 chr7B 98.394 249 3 1 4635 4883 428833290 428833537 3.330000e-118 436.0
23 TraesCS2B01G547600 chr7B 97.255 255 6 1 4635 4889 623676576 623676829 1.550000e-116 431.0
24 TraesCS2B01G547600 chr6B 98.394 249 2 2 4635 4882 502312964 502312717 3.330000e-118 436.0
25 TraesCS2B01G547600 chr5B 97.255 255 5 2 4631 4884 291075364 291075617 1.550000e-116 431.0
26 TraesCS2B01G547600 chr5B 82.819 227 26 5 7231 7451 61352857 61352638 2.860000e-44 191.0
27 TraesCS2B01G547600 chr4A 91.176 272 21 2 4178 4447 691994660 691994930 4.430000e-97 366.0
28 TraesCS2B01G547600 chr4A 90.345 145 13 1 4883 5026 150653454 150653310 1.030000e-43 189.0
29 TraesCS2B01G547600 chr7A 90.152 264 23 2 4185 4446 411534707 411534969 2.690000e-89 340.0
30 TraesCS2B01G547600 chr1A 88.645 273 28 2 4176 4446 108409129 108409400 5.810000e-86 329.0
31 TraesCS2B01G547600 chrUn 91.549 142 10 2 4883 5023 81477659 81477799 2.210000e-45 195.0
32 TraesCS2B01G547600 chr5A 91.549 142 11 1 4883 5023 320214385 320214244 2.210000e-45 195.0
33 TraesCS2B01G547600 chr5D 90.845 142 12 1 4883 5023 461072743 461072602 1.030000e-43 189.0


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 TraesCS2B01G547600 chr2B 744165868 744173640 7772 True 6958.800000 13826 100.000000 1 7773 2 chr2B.!!$R1 7772
1 TraesCS2B01G547600 chr2D 609774451 609781740 7289 True 5464.000000 6314 94.167000 287 7773 2 chr2D.!!$R1 7486
2 TraesCS2B01G547600 chr2A 742719408 742726829 7421 True 1836.183333 5036 92.940833 1 7773 6 chr2A.!!$R1 7772

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
806 885 0.100325 TGTGTGACGCCTGCTTTTTG 59.900 50.000 0.00 0.00 0.00 2.44 F
807 886 0.100503 GTGTGACGCCTGCTTTTTGT 59.899 50.000 0.00 0.00 0.00 2.83 F
1818 1986 1.134220 TGCCTGGGTTCGGTTATGATC 60.134 52.381 0.00 0.00 0.00 2.92 F
2819 2991 1.140375 GCTTGCTGGCCATGTAAGC 59.860 57.895 28.05 28.05 43.41 3.09 F
4220 4394 0.249826 AAGTTTGCCAATGGTTGCCG 60.250 50.000 0.00 0.00 0.00 5.69 F
4716 4916 0.036388 TCGCTTGCTTAGGGGTCAAG 60.036 55.000 0.00 0.00 39.95 3.02 F
4879 5079 0.106708 CCCTTCTAGCAGCGCCATAA 59.893 55.000 2.29 0.00 0.00 1.90 F
5185 5390 0.259938 ATCCTGATTTGGACCTGGGC 59.740 55.000 0.00 0.00 39.17 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2288 2456 1.348036 AGAAGTACCTGTGGAAGTGGC 59.652 52.381 0.00 0.00 0.00 5.01 R
2765 2937 1.971695 GTAACCAGCACCAGCCCAC 60.972 63.158 0.00 0.00 43.56 4.61 R
3067 3241 2.024176 AGCAATGCCTACAACGTAGG 57.976 50.000 14.64 14.64 37.75 3.18 R
4697 4897 0.036388 CTTGACCCCTAAGCAAGCGA 60.036 55.000 0.00 0.00 33.48 4.93 R
5171 5376 0.684479 GAAGGGCCCAGGTCCAAATC 60.684 60.000 27.56 3.74 43.56 2.17 R
6379 6584 0.462759 ATGCCTCAACCTCGCTAAGC 60.463 55.000 0.00 0.00 0.00 3.09 R
6463 6668 0.889186 ACCGGAATGTGTGCTGAACC 60.889 55.000 9.46 0.00 0.00 3.62 R
7033 7245 0.174389 GCAGTCTCCGCAGATTCTCA 59.826 55.000 0.00 0.00 0.00 3.27 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
39 40 4.840005 CGCCTTCCGCTTCCCCTC 62.840 72.222 0.00 0.00 34.21 4.30
321 322 3.730761 CAGGTGAGCCGCAACAGC 61.731 66.667 10.39 10.39 36.36 4.40
339 340 2.520741 CTCCTCCTCCTCCCTCGC 60.521 72.222 0.00 0.00 0.00 5.03
340 341 4.144727 TCCTCCTCCTCCCTCGCC 62.145 72.222 0.00 0.00 0.00 5.54
352 353 3.212682 CTCGCCTCCTCGCTGCTA 61.213 66.667 0.00 0.00 0.00 3.49
396 402 1.802636 CCGCGTGGAATTTGATGCT 59.197 52.632 10.20 0.00 37.49 3.79
515 539 0.109086 ACGGATTCAGTCAGACAGCG 60.109 55.000 2.66 0.00 0.00 5.18
542 567 2.654079 CCACTTCCGCTCCTCTGCT 61.654 63.158 0.00 0.00 0.00 4.24
655 685 8.595362 AGCCTTTTTGCTTCCTAATAATAGTT 57.405 30.769 0.00 0.00 38.85 2.24
705 742 9.486497 TGTATTAGGATTCTACTACTACTCGTG 57.514 37.037 9.34 0.00 34.58 4.35
738 775 3.565307 TCAGGCTTTCCAATTTGAGTGT 58.435 40.909 0.00 0.00 33.74 3.55
753 790 1.878088 GAGTGTTCCCGTTCCTTTTCC 59.122 52.381 0.00 0.00 0.00 3.13
773 817 1.135972 CGTGTGCCACTACTGCATTTC 60.136 52.381 0.00 0.00 41.46 2.17
797 846 1.953559 ACATCCATATGTGTGACGCC 58.046 50.000 10.52 0.00 44.79 5.68
799 848 1.869132 CATCCATATGTGTGACGCCTG 59.131 52.381 1.24 0.00 0.00 4.85
806 885 0.100325 TGTGTGACGCCTGCTTTTTG 59.900 50.000 0.00 0.00 0.00 2.44
807 886 0.100503 GTGTGACGCCTGCTTTTTGT 59.899 50.000 0.00 0.00 0.00 2.83
809 888 2.017782 TGTGACGCCTGCTTTTTGTTA 58.982 42.857 0.00 0.00 0.00 2.41
877 956 2.258726 GGACTGCGGACGGCTTTTT 61.259 57.895 0.00 0.00 44.05 1.94
881 960 2.429069 GCGGACGGCTTTTTGCAG 60.429 61.111 0.00 0.00 45.15 4.41
883 962 2.908073 CGGACGGCTTTTTGCAGCT 61.908 57.895 0.00 0.00 45.15 4.24
922 1001 5.105797 TGTTGATTGATGGCAGTTATTGGAC 60.106 40.000 0.00 0.00 0.00 4.02
928 1007 1.702401 TGGCAGTTATTGGACCTGTGA 59.298 47.619 0.00 0.00 0.00 3.58
995 1074 5.147162 GTTTGATTGTGGTTAGAAAGCTCG 58.853 41.667 0.00 0.00 0.00 5.03
998 1077 4.870426 TGATTGTGGTTAGAAAGCTCGATC 59.130 41.667 11.48 11.48 40.81 3.69
1033 1112 4.249661 CAGAGAGGACTTTAAGAGGTTGC 58.750 47.826 0.00 0.00 0.00 4.17
1083 1163 6.366061 TGCTATGCGCTTTCATAACTAGTATG 59.634 38.462 9.73 1.06 39.30 2.39
1124 1204 6.544928 AAGTGACAATGTTTTCCTTTTCCT 57.455 33.333 0.00 0.00 0.00 3.36
1126 1206 6.946340 AGTGACAATGTTTTCCTTTTCCTTT 58.054 32.000 0.00 0.00 0.00 3.11
1128 1208 7.549134 AGTGACAATGTTTTCCTTTTCCTTTTC 59.451 33.333 0.00 0.00 0.00 2.29
1129 1209 6.821160 TGACAATGTTTTCCTTTTCCTTTTCC 59.179 34.615 0.00 0.00 0.00 3.13
1130 1210 6.957631 ACAATGTTTTCCTTTTCCTTTTCCT 58.042 32.000 0.00 0.00 0.00 3.36
1131 1211 7.402054 ACAATGTTTTCCTTTTCCTTTTCCTT 58.598 30.769 0.00 0.00 0.00 3.36
1132 1212 7.888021 ACAATGTTTTCCTTTTCCTTTTCCTTT 59.112 29.630 0.00 0.00 0.00 3.11
1133 1213 8.397906 CAATGTTTTCCTTTTCCTTTTCCTTTC 58.602 33.333 0.00 0.00 0.00 2.62
1166 1246 4.997395 TGACTGTCAATTCTTAAGCCTGAC 59.003 41.667 8.27 17.61 37.50 3.51
1256 1358 4.578516 TGGTAATCCTATTGCCGAAACATG 59.421 41.667 0.00 0.00 34.23 3.21
1287 1389 4.881273 GCTGTATAATCCATGTCCACAACA 59.119 41.667 0.00 0.00 43.51 3.33
1302 1404 7.592938 TGTCCACAACAAAATATTCATGAGTC 58.407 34.615 0.00 0.00 34.03 3.36
1539 1700 4.026356 ACAGAGAAGCAGCCAGTATTTT 57.974 40.909 0.00 0.00 0.00 1.82
1629 1790 5.690816 CACTCTATCAGACGCGTTATATGT 58.309 41.667 15.53 10.65 0.00 2.29
1638 1799 7.449827 TCAGACGCGTTATATGTTTTAACTTG 58.550 34.615 15.53 0.00 0.00 3.16
1655 1816 2.093711 ACTTGTCACTGTGCACTGTACA 60.094 45.455 26.34 24.08 0.00 2.90
1818 1986 1.134220 TGCCTGGGTTCGGTTATGATC 60.134 52.381 0.00 0.00 0.00 2.92
2265 2433 8.563949 CGATGCGTTACATTAAAAGTTACTTTG 58.436 33.333 11.35 2.12 39.84 2.77
2288 2456 3.996150 ATGGACTTCTTTGCACTGTTG 57.004 42.857 0.00 0.00 0.00 3.33
2399 2570 4.205588 GCCTTTTCTTTTACGTGAAAACGG 59.794 41.667 6.96 12.38 37.28 4.44
2547 2718 8.023021 ACTATCCTGAACTATGATTACTGCAA 57.977 34.615 0.00 0.00 0.00 4.08
2723 2895 3.069586 TGCTAAGGATATTCCCTGTGACG 59.930 47.826 0.00 0.00 37.19 4.35
2759 2931 4.892934 AGGACAGCTGGTGTTTTTATTGAA 59.107 37.500 19.93 0.00 40.56 2.69
2765 2937 4.085107 GCTGGTGTTTTTATTGAAACTGCG 60.085 41.667 2.68 0.00 39.62 5.18
2819 2991 1.140375 GCTTGCTGGCCATGTAAGC 59.860 57.895 28.05 28.05 43.41 3.09
2876 3048 5.840715 TGTGCATCTTTATCTAGAGAGCAG 58.159 41.667 0.00 0.00 38.77 4.24
2895 3069 5.430886 AGCAGTATCACAATTATCTGTGCA 58.569 37.500 0.00 0.00 45.25 4.57
2925 3099 4.217334 CACTATGATGAGTGCCTCGAGTAT 59.783 45.833 12.31 0.00 40.42 2.12
3021 3195 6.865834 ACTCTTCAGTTATCCTGTCAGATT 57.134 37.500 0.00 0.00 42.19 2.40
3067 3241 6.064846 CACTTGGAGATTGTGCATAATACC 57.935 41.667 18.30 18.30 0.00 2.73
3072 3246 4.929808 GGAGATTGTGCATAATACCCTACG 59.070 45.833 8.83 0.00 0.00 3.51
3199 3373 7.520119 TTGTCTTACGTCATGTTAAGCATAG 57.480 36.000 0.00 0.00 35.74 2.23
3294 3468 4.065088 TGTTGCAGAATGTTGGTACTCTC 58.935 43.478 0.00 0.00 39.31 3.20
3319 3493 3.290308 ACTTCTTATCCATAGAGCGCG 57.710 47.619 0.00 0.00 0.00 6.86
3414 3588 4.743057 TCATGCTAGCAGTGACAAGTAT 57.257 40.909 23.89 0.00 0.00 2.12
3447 3621 8.434392 TGGAGTATGAGTACCCCAATATTTAAC 58.566 37.037 0.00 0.00 35.95 2.01
3448 3622 8.434392 GGAGTATGAGTACCCCAATATTTAACA 58.566 37.037 0.00 0.00 29.60 2.41
3570 3744 1.281867 TGCTTCTGGTGGGGATTACAG 59.718 52.381 0.00 0.00 0.00 2.74
3586 3760 9.516546 GGGGATTACAGAATTTAAGGTAATAGG 57.483 37.037 0.00 0.00 36.77 2.57
3626 3800 8.715998 CCACACATCTGTTCATTATTCTATAGC 58.284 37.037 0.00 0.00 0.00 2.97
4000 4174 1.002792 GGTCTGAAAAGCCAACGTGTC 60.003 52.381 0.00 0.00 0.00 3.67
4182 4356 6.650120 CACCCAACTTTCTAGCTATTTAGGA 58.350 40.000 0.00 0.00 0.00 2.94
4212 4386 4.892934 TGGTTTGAGACTAAGTTTGCCAAT 59.107 37.500 0.00 0.00 0.00 3.16
4220 4394 0.249826 AAGTTTGCCAATGGTTGCCG 60.250 50.000 0.00 0.00 0.00 5.69
4227 4401 1.037030 CCAATGGTTGCCGCACCTAT 61.037 55.000 11.65 0.00 37.75 2.57
4234 4408 0.906066 TTGCCGCACCTATGGTTAGA 59.094 50.000 0.00 0.00 31.02 2.10
4271 4461 1.006639 AGGTGGGTGTTTGGTTCAAGT 59.993 47.619 0.00 0.00 0.00 3.16
4272 4462 1.407618 GGTGGGTGTTTGGTTCAAGTC 59.592 52.381 0.00 0.00 0.00 3.01
4273 4463 2.096248 GTGGGTGTTTGGTTCAAGTCA 58.904 47.619 0.00 0.00 0.00 3.41
4274 4464 2.096248 TGGGTGTTTGGTTCAAGTCAC 58.904 47.619 0.00 0.00 33.22 3.67
4275 4465 2.096248 GGGTGTTTGGTTCAAGTCACA 58.904 47.619 14.49 1.90 34.47 3.58
4276 4466 2.159296 GGGTGTTTGGTTCAAGTCACAC 60.159 50.000 14.49 10.62 34.09 3.82
4277 4467 2.159296 GGTGTTTGGTTCAAGTCACACC 60.159 50.000 13.77 13.77 41.95 4.16
4278 4468 2.752903 GTGTTTGGTTCAAGTCACACCT 59.247 45.455 10.58 0.00 30.82 4.00
4279 4469 3.192633 GTGTTTGGTTCAAGTCACACCTT 59.807 43.478 10.58 0.00 30.82 3.50
4280 4470 4.396790 GTGTTTGGTTCAAGTCACACCTTA 59.603 41.667 10.58 0.00 30.82 2.69
4281 4471 4.638421 TGTTTGGTTCAAGTCACACCTTAG 59.362 41.667 0.00 0.00 0.00 2.18
4282 4472 3.485463 TGGTTCAAGTCACACCTTAGG 57.515 47.619 0.00 0.00 0.00 2.69
4283 4473 2.152016 GGTTCAAGTCACACCTTAGGC 58.848 52.381 0.00 0.00 0.00 3.93
4284 4474 2.486548 GGTTCAAGTCACACCTTAGGCA 60.487 50.000 0.00 0.00 0.00 4.75
4285 4475 3.211045 GTTCAAGTCACACCTTAGGCAA 58.789 45.455 0.00 0.00 0.00 4.52
4286 4476 3.126001 TCAAGTCACACCTTAGGCAAG 57.874 47.619 0.00 0.00 0.00 4.01
4318 4508 3.287222 GCCCCACATTACATACACACAT 58.713 45.455 0.00 0.00 0.00 3.21
4369 4559 3.989817 CCAACTTGTGGCTCTTATTTTGC 59.010 43.478 0.00 0.00 41.72 3.68
4485 4677 7.759489 TCCAGCAGTACACTTTTTGATTATT 57.241 32.000 0.00 0.00 0.00 1.40
4510 4702 6.386050 TGGGGTTTATAGAGAACTAAAGGGAG 59.614 42.308 0.00 0.00 32.04 4.30
4614 4814 7.990314 TGCCTTTAACAGAATGCATATACTACA 59.010 33.333 0.00 0.00 42.53 2.74
4638 4838 9.498176 ACACTTTCCGTTTCTAAATATAAGTGT 57.502 29.630 0.00 0.00 44.71 3.55
4655 4855 4.382345 AGTGTTAGAGTACGTAATGGGC 57.618 45.455 0.00 0.00 0.00 5.36
4656 4856 3.131755 AGTGTTAGAGTACGTAATGGGCC 59.868 47.826 0.00 0.00 0.00 5.80
4657 4857 3.131755 GTGTTAGAGTACGTAATGGGCCT 59.868 47.826 4.53 0.00 0.00 5.19
4658 4858 4.339247 GTGTTAGAGTACGTAATGGGCCTA 59.661 45.833 4.53 0.00 0.00 3.93
4659 4859 4.955450 TGTTAGAGTACGTAATGGGCCTAA 59.045 41.667 4.53 0.00 0.00 2.69
4660 4860 5.599656 TGTTAGAGTACGTAATGGGCCTAAT 59.400 40.000 4.53 0.00 0.00 1.73
4661 4861 4.602340 AGAGTACGTAATGGGCCTAATG 57.398 45.455 4.53 0.00 0.00 1.90
4662 4862 3.323979 AGAGTACGTAATGGGCCTAATGG 59.676 47.826 4.53 0.00 0.00 3.16
4663 4863 2.370849 AGTACGTAATGGGCCTAATGGG 59.629 50.000 4.53 0.00 38.36 4.00
4678 4878 3.884037 AATGGGCCCATTAGTCTTAGG 57.116 47.619 42.77 0.00 43.92 2.69
4679 4879 1.518367 TGGGCCCATTAGTCTTAGGG 58.482 55.000 24.45 0.00 44.37 3.53
4680 4880 1.274767 TGGGCCCATTAGTCTTAGGGT 60.275 52.381 24.45 0.00 43.42 4.34
4681 4881 1.850998 GGGCCCATTAGTCTTAGGGTT 59.149 52.381 19.95 0.00 43.42 4.11
4682 4882 3.050835 GGGCCCATTAGTCTTAGGGTTA 58.949 50.000 19.95 0.00 43.42 2.85
4683 4883 3.460712 GGGCCCATTAGTCTTAGGGTTAA 59.539 47.826 19.95 0.00 43.42 2.01
4684 4884 4.105858 GGGCCCATTAGTCTTAGGGTTAAT 59.894 45.833 19.95 0.00 43.42 1.40
4685 4885 5.399842 GGGCCCATTAGTCTTAGGGTTAATT 60.400 44.000 19.95 0.00 43.42 1.40
4686 4886 6.183361 GGGCCCATTAGTCTTAGGGTTAATTA 60.183 42.308 19.95 0.00 43.42 1.40
4687 4887 6.940867 GGCCCATTAGTCTTAGGGTTAATTAG 59.059 42.308 0.00 0.00 43.42 1.73
4688 4888 7.202158 GGCCCATTAGTCTTAGGGTTAATTAGA 60.202 40.741 0.00 0.00 43.42 2.10
4689 4889 7.878644 GCCCATTAGTCTTAGGGTTAATTAGAG 59.121 40.741 0.00 0.00 43.42 2.43
4690 4890 9.155785 CCCATTAGTCTTAGGGTTAATTAGAGA 57.844 37.037 0.00 0.00 36.52 3.10
4696 4896 9.382307 AGTCTTAGGGTTAATTAGAGATAAGGG 57.618 37.037 8.51 0.00 0.00 3.95
4697 4897 9.156940 GTCTTAGGGTTAATTAGAGATAAGGGT 57.843 37.037 8.51 0.00 0.00 4.34
4698 4898 9.377238 TCTTAGGGTTAATTAGAGATAAGGGTC 57.623 37.037 8.51 0.00 0.00 4.46
4699 4899 6.667558 AGGGTTAATTAGAGATAAGGGTCG 57.332 41.667 0.00 0.00 0.00 4.79
4700 4900 5.011840 AGGGTTAATTAGAGATAAGGGTCGC 59.988 44.000 0.00 0.00 0.00 5.19
4701 4901 5.011840 GGGTTAATTAGAGATAAGGGTCGCT 59.988 44.000 0.00 0.00 32.84 4.93
4702 4902 6.464039 GGGTTAATTAGAGATAAGGGTCGCTT 60.464 42.308 7.38 7.38 30.69 4.68
4703 4903 6.424207 GGTTAATTAGAGATAAGGGTCGCTTG 59.576 42.308 12.19 0.00 30.69 4.01
4704 4904 3.454371 TTAGAGATAAGGGTCGCTTGC 57.546 47.619 12.19 4.62 30.69 4.01
4705 4905 1.490574 AGAGATAAGGGTCGCTTGCT 58.509 50.000 12.19 9.05 0.00 3.91
4706 4906 1.834263 AGAGATAAGGGTCGCTTGCTT 59.166 47.619 12.19 0.00 0.00 3.91
4707 4907 3.031736 AGAGATAAGGGTCGCTTGCTTA 58.968 45.455 12.19 0.00 0.00 3.09
4708 4908 3.068873 AGAGATAAGGGTCGCTTGCTTAG 59.931 47.826 12.19 0.00 0.00 2.18
4709 4909 2.103263 AGATAAGGGTCGCTTGCTTAGG 59.897 50.000 12.19 0.00 0.00 2.69
4710 4910 0.539986 TAAGGGTCGCTTGCTTAGGG 59.460 55.000 12.19 0.00 38.13 3.53
4711 4911 2.124695 GGGTCGCTTGCTTAGGGG 60.125 66.667 4.21 0.00 37.41 4.79
4712 4912 2.669240 GGTCGCTTGCTTAGGGGT 59.331 61.111 4.21 0.00 37.41 4.95
4713 4913 1.449778 GGTCGCTTGCTTAGGGGTC 60.450 63.158 4.21 0.00 37.41 4.46
4714 4914 1.295423 GTCGCTTGCTTAGGGGTCA 59.705 57.895 4.21 0.00 37.41 4.02
4715 4915 0.321298 GTCGCTTGCTTAGGGGTCAA 60.321 55.000 4.21 0.00 37.41 3.18
4716 4916 0.036388 TCGCTTGCTTAGGGGTCAAG 60.036 55.000 0.00 0.00 39.95 3.02
4717 4917 0.321653 CGCTTGCTTAGGGGTCAAGT 60.322 55.000 0.00 0.00 39.36 3.16
4718 4918 1.066430 CGCTTGCTTAGGGGTCAAGTA 60.066 52.381 0.00 0.00 39.36 2.24
4719 4919 2.614481 CGCTTGCTTAGGGGTCAAGTAA 60.614 50.000 0.00 0.00 39.36 2.24
4720 4920 3.010420 GCTTGCTTAGGGGTCAAGTAAG 58.990 50.000 8.11 8.11 44.06 2.34
4721 4921 2.781681 TGCTTAGGGGTCAAGTAAGC 57.218 50.000 6.41 6.41 45.90 3.09
4722 4922 1.280998 TGCTTAGGGGTCAAGTAAGCC 59.719 52.381 10.06 0.00 45.37 4.35
4723 4923 1.560146 GCTTAGGGGTCAAGTAAGCCT 59.440 52.381 2.53 0.00 41.83 4.58
4724 4924 2.026169 GCTTAGGGGTCAAGTAAGCCTT 60.026 50.000 2.53 0.00 41.83 4.35
4736 4936 3.580084 AGCCTTGCTTGGGAGTCA 58.420 55.556 0.00 0.00 33.89 3.41
4737 4937 1.846261 AGCCTTGCTTGGGAGTCAA 59.154 52.632 0.00 0.00 33.89 3.18
4747 4947 4.625607 CTTGGGAGTCAAGTAAACCTCT 57.374 45.455 0.00 0.00 45.81 3.69
4748 4948 4.570930 CTTGGGAGTCAAGTAAACCTCTC 58.429 47.826 0.00 0.00 45.81 3.20
4749 4949 3.858135 TGGGAGTCAAGTAAACCTCTCT 58.142 45.455 0.00 0.00 0.00 3.10
4750 4950 5.006896 TGGGAGTCAAGTAAACCTCTCTA 57.993 43.478 0.00 0.00 0.00 2.43
4751 4951 5.590818 TGGGAGTCAAGTAAACCTCTCTAT 58.409 41.667 0.00 0.00 0.00 1.98
4752 4952 6.738635 TGGGAGTCAAGTAAACCTCTCTATA 58.261 40.000 0.00 0.00 0.00 1.31
4753 4953 7.363031 TGGGAGTCAAGTAAACCTCTCTATAT 58.637 38.462 0.00 0.00 0.00 0.86
4754 4954 8.508601 TGGGAGTCAAGTAAACCTCTCTATATA 58.491 37.037 0.00 0.00 0.00 0.86
4755 4955 9.364653 GGGAGTCAAGTAAACCTCTCTATATAA 57.635 37.037 0.00 0.00 0.00 0.98
4781 4981 9.599056 AAGAGAGGAGATGTATCAATCTAATCA 57.401 33.333 0.00 0.00 37.03 2.57
4782 4982 9.599056 AGAGAGGAGATGTATCAATCTAATCAA 57.401 33.333 0.00 0.00 37.03 2.57
4783 4983 9.859427 GAGAGGAGATGTATCAATCTAATCAAG 57.141 37.037 0.00 0.00 37.03 3.02
4784 4984 8.313292 AGAGGAGATGTATCAATCTAATCAAGC 58.687 37.037 0.00 0.00 37.03 4.01
4785 4985 7.971201 AGGAGATGTATCAATCTAATCAAGCA 58.029 34.615 0.00 0.00 37.03 3.91
4786 4986 8.435187 AGGAGATGTATCAATCTAATCAAGCAA 58.565 33.333 0.00 0.00 37.03 3.91
4787 4987 8.719648 GGAGATGTATCAATCTAATCAAGCAAG 58.280 37.037 0.00 0.00 37.03 4.01
4788 4988 9.486497 GAGATGTATCAATCTAATCAAGCAAGA 57.514 33.333 0.00 0.00 37.03 3.02
4789 4989 9.842775 AGATGTATCAATCTAATCAAGCAAGAA 57.157 29.630 0.00 0.00 35.09 2.52
4799 4999 9.911788 ATCTAATCAAGCAAGAATTAAGAAGGA 57.088 29.630 0.00 0.00 0.00 3.36
4800 5000 9.739276 TCTAATCAAGCAAGAATTAAGAAGGAA 57.261 29.630 0.00 0.00 0.00 3.36
4803 5003 9.866798 AATCAAGCAAGAATTAAGAAGGAAATC 57.133 29.630 0.00 0.00 0.00 2.17
4804 5004 7.830739 TCAAGCAAGAATTAAGAAGGAAATCC 58.169 34.615 0.00 0.00 0.00 3.01
4805 5005 6.782082 AGCAAGAATTAAGAAGGAAATCCC 57.218 37.500 0.00 0.00 36.42 3.85
4817 5017 1.769026 GAAATCCCTTCCCTCTTGCC 58.231 55.000 0.00 0.00 0.00 4.52
4818 5018 1.286257 GAAATCCCTTCCCTCTTGCCT 59.714 52.381 0.00 0.00 0.00 4.75
4819 5019 0.627986 AATCCCTTCCCTCTTGCCTG 59.372 55.000 0.00 0.00 0.00 4.85
4820 5020 1.284841 ATCCCTTCCCTCTTGCCTGG 61.285 60.000 0.00 0.00 0.00 4.45
4821 5021 2.044551 CCTTCCCTCTTGCCTGGC 60.045 66.667 12.87 12.87 0.00 4.85
4822 5022 2.044551 CTTCCCTCTTGCCTGGCC 60.045 66.667 17.53 0.00 0.00 5.36
4823 5023 3.984193 CTTCCCTCTTGCCTGGCCG 62.984 68.421 17.53 7.51 0.00 6.13
4863 5063 4.787280 CCCTCTCACGCCCTCCCT 62.787 72.222 0.00 0.00 0.00 4.20
4864 5064 2.685380 CCTCTCACGCCCTCCCTT 60.685 66.667 0.00 0.00 0.00 3.95
4865 5065 2.726351 CCTCTCACGCCCTCCCTTC 61.726 68.421 0.00 0.00 0.00 3.46
4866 5066 1.684049 CTCTCACGCCCTCCCTTCT 60.684 63.158 0.00 0.00 0.00 2.85
4867 5067 0.395862 CTCTCACGCCCTCCCTTCTA 60.396 60.000 0.00 0.00 0.00 2.10
4868 5068 0.395862 TCTCACGCCCTCCCTTCTAG 60.396 60.000 0.00 0.00 0.00 2.43
4869 5069 2.022240 CTCACGCCCTCCCTTCTAGC 62.022 65.000 0.00 0.00 0.00 3.42
4870 5070 2.038975 ACGCCCTCCCTTCTAGCA 59.961 61.111 0.00 0.00 0.00 3.49
4871 5071 2.060980 ACGCCCTCCCTTCTAGCAG 61.061 63.158 0.00 0.00 0.00 4.24
4872 5072 2.508436 GCCCTCCCTTCTAGCAGC 59.492 66.667 0.00 0.00 0.00 5.25
4873 5073 2.818132 CCCTCCCTTCTAGCAGCG 59.182 66.667 0.00 0.00 0.00 5.18
4874 5074 2.107953 CCTCCCTTCTAGCAGCGC 59.892 66.667 0.00 0.00 0.00 5.92
4875 5075 2.107953 CTCCCTTCTAGCAGCGCC 59.892 66.667 2.29 0.00 0.00 6.53
4876 5076 2.683572 TCCCTTCTAGCAGCGCCA 60.684 61.111 2.29 0.00 0.00 5.69
4877 5077 2.037620 CTCCCTTCTAGCAGCGCCAT 62.038 60.000 2.29 0.00 0.00 4.40
4878 5078 0.759060 TCCCTTCTAGCAGCGCCATA 60.759 55.000 2.29 0.00 0.00 2.74
4879 5079 0.106708 CCCTTCTAGCAGCGCCATAA 59.893 55.000 2.29 0.00 0.00 1.90
4880 5080 1.221414 CCTTCTAGCAGCGCCATAAC 58.779 55.000 2.29 0.00 0.00 1.89
4881 5081 1.473257 CCTTCTAGCAGCGCCATAACA 60.473 52.381 2.29 0.00 0.00 2.41
5103 5308 1.000274 CCAGGAAAGAGGCAAAAACCG 60.000 52.381 0.00 0.00 33.69 4.44
5171 5376 5.888161 AGCTATTTTGTTAACCCTGATCCTG 59.112 40.000 2.48 0.00 0.00 3.86
5185 5390 0.259938 ATCCTGATTTGGACCTGGGC 59.740 55.000 0.00 0.00 39.17 5.36
5221 5426 6.071616 GGGGTGTCAACTTTGCATTCTAATTA 60.072 38.462 0.00 0.00 0.00 1.40
5341 5546 8.007742 AGACTAATGGACCTTCAGTGTATAGAT 58.992 37.037 0.00 0.00 0.00 1.98
5398 5603 8.429641 ACTAGATCTTTTGTGAGTTTACTTCCA 58.570 33.333 0.00 0.00 0.00 3.53
5399 5604 9.442047 CTAGATCTTTTGTGAGTTTACTTCCAT 57.558 33.333 0.00 0.00 0.00 3.41
5400 5605 8.103948 AGATCTTTTGTGAGTTTACTTCCATG 57.896 34.615 0.00 0.00 0.00 3.66
5401 5606 7.939039 AGATCTTTTGTGAGTTTACTTCCATGA 59.061 33.333 0.00 0.00 0.00 3.07
5568 5773 7.816640 TGTGCTTGATATGTTTAACTTCCTTC 58.183 34.615 0.00 0.00 0.00 3.46
5679 5884 2.479566 TTCTCTTTGCGCTCCTCATT 57.520 45.000 9.73 0.00 0.00 2.57
5705 5910 8.655901 TGGTAACATGCAGGTAGAATGATAATA 58.344 33.333 3.57 0.00 46.17 0.98
5706 5911 9.672673 GGTAACATGCAGGTAGAATGATAATAT 57.327 33.333 3.57 0.00 36.69 1.28
5797 6002 3.457234 TCAATCAGTTGCTATACGCCTG 58.543 45.455 0.00 0.00 38.05 4.85
5911 6116 1.066605 CGGTATAGGTGGTTGGAGACG 59.933 57.143 0.00 0.00 0.00 4.18
6217 6422 7.446319 CCAGTGGATGAGATGCAATTTATTCTA 59.554 37.037 1.68 0.00 30.45 2.10
6244 6449 2.526432 TCCTTGGAGAGTGTGACTACC 58.474 52.381 0.00 0.00 0.00 3.18
6379 6584 1.374758 GTCCAGGACAGTGAAGGCG 60.375 63.158 15.43 0.00 32.09 5.52
6786 6994 3.547413 GCGGACTAACAAAAACAGACCAC 60.547 47.826 0.00 0.00 0.00 4.16
6991 7201 1.250328 CTTTTGATGCCTCTGCCACA 58.750 50.000 0.00 0.00 36.33 4.17
6992 7202 1.822990 CTTTTGATGCCTCTGCCACAT 59.177 47.619 0.00 0.00 36.33 3.21
6993 7203 2.804986 TTTGATGCCTCTGCCACATA 57.195 45.000 0.00 0.00 36.33 2.29
6994 7204 2.804986 TTGATGCCTCTGCCACATAA 57.195 45.000 0.00 0.00 36.33 1.90
6995 7205 3.301794 TTGATGCCTCTGCCACATAAT 57.698 42.857 0.00 0.00 36.33 1.28
7019 7231 0.801251 GTTGCACATCACTGAGCCTC 59.199 55.000 0.00 0.00 38.09 4.70
7026 7238 3.754850 CACATCACTGAGCCTCAAAATCA 59.245 43.478 0.00 0.00 0.00 2.57
7033 7245 2.157738 GAGCCTCAAAATCACAGTGCT 58.842 47.619 0.00 0.00 0.00 4.40
7036 7248 2.095364 GCCTCAAAATCACAGTGCTGAG 60.095 50.000 6.17 11.80 0.00 3.35
7061 7273 0.661552 GCGGAGACTGCGACTACATA 59.338 55.000 21.39 0.00 30.86 2.29
7070 7282 9.472361 GGAGACTGCGACTACATAAAAATATTA 57.528 33.333 0.00 0.00 0.00 0.98
7090 7302 3.959535 ACCGCAATGATGAAATGGTTT 57.040 38.095 0.00 0.00 0.00 3.27
7164 7406 3.390639 AGATCGGCTGAGATTTGGAGAAT 59.609 43.478 0.00 0.00 0.00 2.40
7165 7407 4.590647 AGATCGGCTGAGATTTGGAGAATA 59.409 41.667 0.00 0.00 0.00 1.75
7166 7408 4.753516 TCGGCTGAGATTTGGAGAATAA 57.246 40.909 0.00 0.00 0.00 1.40
7206 7449 3.268595 GGGGGAAAGAGGTTTCAGGATTA 59.731 47.826 0.66 0.00 43.52 1.75
7212 7455 2.572104 AGAGGTTTCAGGATTAAGGCGT 59.428 45.455 0.00 0.00 0.00 5.68
7240 7483 4.640855 ACGGTCGCACCACACTCG 62.641 66.667 6.21 0.00 38.47 4.18
7245 7490 2.801162 CGCACCACACTCGTCTCG 60.801 66.667 0.00 0.00 0.00 4.04
7258 7503 3.138128 TCTCGGCTCGATTGCGGA 61.138 61.111 6.71 6.71 39.41 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
319 320 2.623431 AGGGAGGAGGAGGAGGCT 60.623 66.667 0.00 0.00 0.00 4.58
321 322 2.197324 CGAGGGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 0.00 4.30
384 385 2.557317 CCATGGCAAGCATCAAATTCC 58.443 47.619 0.00 0.00 0.00 3.01
562 587 3.249687 GAGACCACGCCTCCATTTT 57.750 52.632 0.00 0.00 0.00 1.82
643 673 5.148651 AGCGGCCTACAACTATTATTAGG 57.851 43.478 0.00 0.00 35.16 2.69
653 683 0.605589 AAAGTGGAGCGGCCTACAAC 60.606 55.000 0.00 0.00 32.52 3.32
654 684 0.978151 TAAAGTGGAGCGGCCTACAA 59.022 50.000 0.00 0.00 32.52 2.41
655 685 0.248289 GTAAAGTGGAGCGGCCTACA 59.752 55.000 0.00 0.00 37.63 2.74
695 732 7.337480 TGATACATTTAAGGCACGAGTAGTA 57.663 36.000 0.00 0.00 0.00 1.82
696 733 6.216801 TGATACATTTAAGGCACGAGTAGT 57.783 37.500 0.00 0.00 0.00 2.73
725 762 2.649531 ACGGGAACACTCAAATTGGA 57.350 45.000 0.00 0.00 0.00 3.53
738 775 0.180878 ACACGGAAAAGGAACGGGAA 59.819 50.000 0.00 0.00 34.62 3.97
773 817 3.737774 CGTCACACATATGGATGTAGCAG 59.262 47.826 7.80 0.00 44.82 4.24
783 827 1.372582 AAGCAGGCGTCACACATATG 58.627 50.000 0.00 0.00 0.00 1.78
797 846 7.648908 TCACACTGAATGAATAACAAAAAGCAG 59.351 33.333 0.00 0.00 0.00 4.24
799 848 7.928908 TCACACTGAATGAATAACAAAAAGC 57.071 32.000 0.00 0.00 0.00 3.51
806 885 9.844790 TTTGATCAATCACACTGAATGAATAAC 57.155 29.630 9.40 0.00 39.45 1.89
807 886 9.844790 GTTTGATCAATCACACTGAATGAATAA 57.155 29.630 9.40 0.00 39.45 1.40
809 888 7.888424 TGTTTGATCAATCACACTGAATGAAT 58.112 30.769 13.94 0.00 39.45 2.57
881 960 2.481289 ACAGACCCTTTAGCTGAAGC 57.519 50.000 12.62 0.00 42.49 3.86
883 962 4.640771 ATCAACAGACCCTTTAGCTGAA 57.359 40.909 0.00 0.00 33.94 3.02
898 977 5.015515 TCCAATAACTGCCATCAATCAACA 58.984 37.500 0.00 0.00 0.00 3.33
922 1001 0.103937 GGCGAGAGATCCTTCACAGG 59.896 60.000 0.00 0.00 42.50 4.00
928 1007 0.396974 AGAGCTGGCGAGAGATCCTT 60.397 55.000 0.00 0.00 0.00 3.36
995 1074 2.762887 TCTCTGTGTCTGTCCATGGATC 59.237 50.000 19.62 12.25 0.00 3.36
998 1077 1.206610 CCTCTCTGTGTCTGTCCATGG 59.793 57.143 4.97 4.97 0.00 3.66
1033 1112 6.014584 AGGAGTGCCCTTTTAAGTAAAAATGG 60.015 38.462 0.00 3.51 44.85 3.16
1122 1202 1.885887 TGACATGCGGAAAGGAAAAGG 59.114 47.619 0.00 0.00 0.00 3.11
1124 1204 3.057596 GTCATGACATGCGGAAAGGAAAA 60.058 43.478 21.07 0.00 0.00 2.29
1126 1206 2.083774 GTCATGACATGCGGAAAGGAA 58.916 47.619 21.07 0.00 0.00 3.36
1128 1208 1.399440 CAGTCATGACATGCGGAAAGG 59.601 52.381 27.02 0.62 0.00 3.11
1129 1209 2.079158 ACAGTCATGACATGCGGAAAG 58.921 47.619 27.02 7.88 0.00 2.62
1130 1210 2.076100 GACAGTCATGACATGCGGAAA 58.924 47.619 27.02 0.00 0.00 3.13
1131 1211 1.001860 TGACAGTCATGACATGCGGAA 59.998 47.619 27.02 3.80 0.00 4.30
1132 1212 0.607620 TGACAGTCATGACATGCGGA 59.392 50.000 27.02 3.63 0.00 5.54
1133 1213 1.441738 TTGACAGTCATGACATGCGG 58.558 50.000 27.02 12.98 31.23 5.69
1166 1246 9.099454 GAGAGAAATTGGTACTACTACAAATGG 57.901 37.037 0.00 0.00 28.29 3.16
1272 1374 7.479352 TGAATATTTTGTTGTGGACATGGAT 57.521 32.000 0.00 0.00 38.26 3.41
1287 1389 8.506083 ACCATAGGAAGGACTCATGAATATTTT 58.494 33.333 0.00 0.00 0.00 1.82
1438 1566 1.608590 ACAAATGACTGGCTTTGTCGG 59.391 47.619 5.58 0.00 40.58 4.79
1629 1790 4.457603 ACAGTGCACAGTGACAAGTTAAAA 59.542 37.500 21.04 0.00 35.75 1.52
1638 1799 3.428870 GTGTATGTACAGTGCACAGTGAC 59.571 47.826 23.60 16.79 36.78 3.67
1818 1986 7.786178 TGAATGATCTTAGTGGATTAAACGG 57.214 36.000 0.00 0.00 0.00 4.44
2265 2433 5.215160 CAACAGTGCAAAGAAGTCCATTAC 58.785 41.667 0.00 0.00 0.00 1.89
2288 2456 1.348036 AGAAGTACCTGTGGAAGTGGC 59.652 52.381 0.00 0.00 0.00 5.01
2355 2524 8.870075 AAGGCTTATTGTTTCAGATAAAGACT 57.130 30.769 0.00 0.00 0.00 3.24
2520 2691 7.287696 TGCAGTAATCATAGTTCAGGATAGTCA 59.712 37.037 0.00 0.00 0.00 3.41
2723 2895 5.221322 ACCAGCTGTCCTTTTCAAATCTTTC 60.221 40.000 13.81 0.00 0.00 2.62
2765 2937 1.971695 GTAACCAGCACCAGCCCAC 60.972 63.158 0.00 0.00 43.56 4.61
2819 2991 9.694520 GATAAACAATACATAGCATAGCAATCG 57.305 33.333 0.00 0.00 0.00 3.34
3021 3195 9.431887 AGTGCTACGAAATCTTTAAACTATCAA 57.568 29.630 0.00 0.00 0.00 2.57
3067 3241 2.024176 AGCAATGCCTACAACGTAGG 57.976 50.000 14.64 14.64 37.75 3.18
3072 3246 6.618287 TGACATATTAGCAATGCCTACAAC 57.382 37.500 0.00 0.00 0.00 3.32
3199 3373 6.308282 CCTACGACAAACTATGTTCAGAGAAC 59.692 42.308 3.05 3.05 44.12 3.01
3294 3468 5.704888 CGCTCTATGGATAAGAAGTACCAG 58.295 45.833 0.00 0.00 35.84 4.00
3319 3493 3.338249 TGACAAGCCAGCAACTATCTTC 58.662 45.455 0.00 0.00 0.00 2.87
3428 3602 6.376018 GCACTTGTTAAATATTGGGGTACTCA 59.624 38.462 0.00 0.00 0.00 3.41
3602 3776 9.836864 TTGCTATAGAATAATGAACAGATGTGT 57.163 29.630 3.21 0.00 39.19 3.72
3626 3800 4.923893 TCTTGTGCACAATGAAAGACTTG 58.076 39.130 31.17 15.92 35.02 3.16
3710 3884 2.420547 CCTGCCATGAGAGAAATTCCGA 60.421 50.000 0.00 0.00 0.00 4.55
4000 4174 8.908786 TCTTATATTCTCACTAGCAATTTGGG 57.091 34.615 0.00 0.00 0.00 4.12
4182 4356 7.277760 GCAAACTTAGTCTCAAACCAAACAAAT 59.722 33.333 0.00 0.00 0.00 2.32
4212 4386 2.045438 CCATAGGTGCGGCAACCA 60.045 61.111 15.61 0.00 43.20 3.67
4220 4394 5.001232 TCAAACTTGTCTAACCATAGGTGC 58.999 41.667 0.00 0.00 35.34 5.01
4271 4461 0.250727 GTGGCTTGCCTAAGGTGTGA 60.251 55.000 13.18 0.00 34.40 3.58
4272 4462 0.537143 TGTGGCTTGCCTAAGGTGTG 60.537 55.000 13.18 0.00 34.40 3.82
4273 4463 0.537371 GTGTGGCTTGCCTAAGGTGT 60.537 55.000 13.18 0.00 34.40 4.16
4274 4464 0.250901 AGTGTGGCTTGCCTAAGGTG 60.251 55.000 13.18 0.00 34.40 4.00
4275 4465 1.279271 CTAGTGTGGCTTGCCTAAGGT 59.721 52.381 13.18 0.00 34.40 3.50
4276 4466 1.407437 CCTAGTGTGGCTTGCCTAAGG 60.407 57.143 13.18 8.19 34.40 2.69
4277 4467 1.407437 CCCTAGTGTGGCTTGCCTAAG 60.407 57.143 13.18 3.40 36.97 2.18
4278 4468 0.618458 CCCTAGTGTGGCTTGCCTAA 59.382 55.000 13.18 0.00 0.00 2.69
4279 4469 1.910580 GCCCTAGTGTGGCTTGCCTA 61.911 60.000 13.18 0.00 45.70 3.93
4280 4470 3.081554 CCCTAGTGTGGCTTGCCT 58.918 61.111 13.18 0.00 0.00 4.75
4281 4471 2.751837 GCCCTAGTGTGGCTTGCC 60.752 66.667 4.43 4.43 45.70 4.52
4318 4508 3.737559 AGGGAATCATGCCACACTTTA 57.262 42.857 0.00 0.00 40.09 1.85
4369 4559 3.944087 AGCTTGCCTAAGGTTAGTTCAG 58.056 45.455 0.00 0.00 41.61 3.02
4485 4677 6.273889 TCCCTTTAGTTCTCTATAAACCCCA 58.726 40.000 0.00 0.00 0.00 4.96
4631 4831 6.462067 GGCCCATTACGTACTCTAACACTTAT 60.462 42.308 0.00 0.00 0.00 1.73
4632 4832 5.163519 GGCCCATTACGTACTCTAACACTTA 60.164 44.000 0.00 0.00 0.00 2.24
4633 4833 4.382362 GGCCCATTACGTACTCTAACACTT 60.382 45.833 0.00 0.00 0.00 3.16
4634 4834 3.131755 GGCCCATTACGTACTCTAACACT 59.868 47.826 0.00 0.00 0.00 3.55
4635 4835 3.131755 AGGCCCATTACGTACTCTAACAC 59.868 47.826 0.00 0.00 0.00 3.32
4636 4836 3.368248 AGGCCCATTACGTACTCTAACA 58.632 45.455 0.00 0.00 0.00 2.41
4637 4837 5.520376 TTAGGCCCATTACGTACTCTAAC 57.480 43.478 0.00 0.00 0.00 2.34
4638 4838 5.011329 CCATTAGGCCCATTACGTACTCTAA 59.989 44.000 0.00 0.00 0.00 2.10
4639 4839 4.525487 CCATTAGGCCCATTACGTACTCTA 59.475 45.833 0.00 0.00 0.00 2.43
4640 4840 3.323979 CCATTAGGCCCATTACGTACTCT 59.676 47.826 0.00 0.00 0.00 3.24
4641 4841 3.556423 CCCATTAGGCCCATTACGTACTC 60.556 52.174 0.00 0.00 0.00 2.59
4642 4842 2.370849 CCCATTAGGCCCATTACGTACT 59.629 50.000 0.00 0.00 0.00 2.73
4643 4843 2.774687 CCCATTAGGCCCATTACGTAC 58.225 52.381 0.00 0.00 0.00 3.67
4657 4857 3.655777 CCCTAAGACTAATGGGCCCATTA 59.344 47.826 41.63 41.63 43.92 1.90
4658 4858 2.447047 CCCTAAGACTAATGGGCCCATT 59.553 50.000 43.64 43.64 46.85 3.16
4659 4859 2.065799 CCCTAAGACTAATGGGCCCAT 58.934 52.381 32.75 32.75 38.46 4.00
4660 4860 1.274767 ACCCTAAGACTAATGGGCCCA 60.275 52.381 30.92 30.92 43.25 5.36
4661 4861 1.519498 ACCCTAAGACTAATGGGCCC 58.481 55.000 17.59 17.59 43.25 5.80
4662 4862 4.783560 TTAACCCTAAGACTAATGGGCC 57.216 45.455 0.00 0.00 43.25 5.80
4663 4863 7.742767 TCTAATTAACCCTAAGACTAATGGGC 58.257 38.462 7.12 0.00 43.25 5.36
4664 4864 9.155785 TCTCTAATTAACCCTAAGACTAATGGG 57.844 37.037 0.00 0.00 44.89 4.00
4670 4870 9.382307 CCCTTATCTCTAATTAACCCTAAGACT 57.618 37.037 0.00 0.00 0.00 3.24
4671 4871 9.156940 ACCCTTATCTCTAATTAACCCTAAGAC 57.843 37.037 0.00 0.00 0.00 3.01
4672 4872 9.377238 GACCCTTATCTCTAATTAACCCTAAGA 57.623 37.037 0.00 0.00 0.00 2.10
4673 4873 8.305317 CGACCCTTATCTCTAATTAACCCTAAG 58.695 40.741 0.00 0.00 0.00 2.18
4674 4874 7.256083 GCGACCCTTATCTCTAATTAACCCTAA 60.256 40.741 0.00 0.00 0.00 2.69
4675 4875 6.210185 GCGACCCTTATCTCTAATTAACCCTA 59.790 42.308 0.00 0.00 0.00 3.53
4676 4876 5.011840 GCGACCCTTATCTCTAATTAACCCT 59.988 44.000 0.00 0.00 0.00 4.34
4677 4877 5.011840 AGCGACCCTTATCTCTAATTAACCC 59.988 44.000 0.00 0.00 0.00 4.11
4678 4878 6.099159 AGCGACCCTTATCTCTAATTAACC 57.901 41.667 0.00 0.00 0.00 2.85
4679 4879 6.073711 GCAAGCGACCCTTATCTCTAATTAAC 60.074 42.308 0.00 0.00 31.00 2.01
4680 4880 5.989777 GCAAGCGACCCTTATCTCTAATTAA 59.010 40.000 0.00 0.00 31.00 1.40
4681 4881 5.304614 AGCAAGCGACCCTTATCTCTAATTA 59.695 40.000 0.00 0.00 31.00 1.40
4682 4882 4.101741 AGCAAGCGACCCTTATCTCTAATT 59.898 41.667 0.00 0.00 31.00 1.40
4683 4883 3.643792 AGCAAGCGACCCTTATCTCTAAT 59.356 43.478 0.00 0.00 31.00 1.73
4684 4884 3.031736 AGCAAGCGACCCTTATCTCTAA 58.968 45.455 0.00 0.00 31.00 2.10
4685 4885 2.667470 AGCAAGCGACCCTTATCTCTA 58.333 47.619 0.00 0.00 31.00 2.43
4686 4886 1.490574 AGCAAGCGACCCTTATCTCT 58.509 50.000 0.00 0.00 31.00 3.10
4687 4887 2.317530 AAGCAAGCGACCCTTATCTC 57.682 50.000 0.00 0.00 31.00 2.75
4688 4888 2.103263 CCTAAGCAAGCGACCCTTATCT 59.897 50.000 0.00 0.00 31.00 1.98
4689 4889 2.484889 CCTAAGCAAGCGACCCTTATC 58.515 52.381 0.00 0.00 31.00 1.75
4690 4890 1.141053 CCCTAAGCAAGCGACCCTTAT 59.859 52.381 0.00 0.00 31.00 1.73
4691 4891 0.539986 CCCTAAGCAAGCGACCCTTA 59.460 55.000 0.00 0.00 31.00 2.69
4692 4892 1.299976 CCCTAAGCAAGCGACCCTT 59.700 57.895 0.00 0.00 0.00 3.95
4693 4893 2.670148 CCCCTAAGCAAGCGACCCT 61.670 63.158 0.00 0.00 0.00 4.34
4694 4894 2.124695 CCCCTAAGCAAGCGACCC 60.125 66.667 0.00 0.00 0.00 4.46
4695 4895 1.449778 GACCCCTAAGCAAGCGACC 60.450 63.158 0.00 0.00 0.00 4.79
4696 4896 0.321298 TTGACCCCTAAGCAAGCGAC 60.321 55.000 0.00 0.00 0.00 5.19
4697 4897 0.036388 CTTGACCCCTAAGCAAGCGA 60.036 55.000 0.00 0.00 33.48 4.93
4698 4898 0.321653 ACTTGACCCCTAAGCAAGCG 60.322 55.000 0.00 0.00 41.97 4.68
4699 4899 2.781681 TACTTGACCCCTAAGCAAGC 57.218 50.000 0.00 0.00 41.97 4.01
4700 4900 3.010420 GCTTACTTGACCCCTAAGCAAG 58.990 50.000 0.00 0.00 41.32 4.01
4701 4901 2.290705 GGCTTACTTGACCCCTAAGCAA 60.291 50.000 10.04 0.00 42.79 3.91
4702 4902 1.280998 GGCTTACTTGACCCCTAAGCA 59.719 52.381 10.04 0.00 42.79 3.91
4703 4903 1.560146 AGGCTTACTTGACCCCTAAGC 59.440 52.381 0.00 0.00 41.07 3.09
4719 4919 0.251077 CTTGACTCCCAAGCAAGGCT 60.251 55.000 0.00 0.00 44.90 4.58
4720 4920 2.261215 CTTGACTCCCAAGCAAGGC 58.739 57.895 0.00 0.00 44.90 4.35
4727 4927 4.232091 AGAGAGGTTTACTTGACTCCCAA 58.768 43.478 0.00 0.00 0.00 4.12
4728 4928 3.858135 AGAGAGGTTTACTTGACTCCCA 58.142 45.455 0.00 0.00 0.00 4.37
4729 4929 7.842887 ATATAGAGAGGTTTACTTGACTCCC 57.157 40.000 0.00 0.00 0.00 4.30
4755 4955 9.599056 TGATTAGATTGATACATCTCCTCTCTT 57.401 33.333 0.00 0.00 0.00 2.85
4756 4956 9.599056 TTGATTAGATTGATACATCTCCTCTCT 57.401 33.333 0.00 0.00 0.00 3.10
4757 4957 9.859427 CTTGATTAGATTGATACATCTCCTCTC 57.141 37.037 0.00 0.00 0.00 3.20
4758 4958 8.313292 GCTTGATTAGATTGATACATCTCCTCT 58.687 37.037 0.00 0.00 0.00 3.69
4759 4959 8.093307 TGCTTGATTAGATTGATACATCTCCTC 58.907 37.037 0.00 0.00 0.00 3.71
4760 4960 7.971201 TGCTTGATTAGATTGATACATCTCCT 58.029 34.615 0.00 0.00 0.00 3.69
4761 4961 8.613060 TTGCTTGATTAGATTGATACATCTCC 57.387 34.615 0.00 0.00 0.00 3.71
4762 4962 9.486497 TCTTGCTTGATTAGATTGATACATCTC 57.514 33.333 0.00 0.00 0.00 2.75
4763 4963 9.842775 TTCTTGCTTGATTAGATTGATACATCT 57.157 29.630 0.00 0.00 0.00 2.90
4773 4973 9.911788 TCCTTCTTAATTCTTGCTTGATTAGAT 57.088 29.630 0.00 0.00 0.00 1.98
4774 4974 9.739276 TTCCTTCTTAATTCTTGCTTGATTAGA 57.261 29.630 0.00 0.00 0.00 2.10
4777 4977 9.866798 GATTTCCTTCTTAATTCTTGCTTGATT 57.133 29.630 0.00 0.00 0.00 2.57
4778 4978 8.473219 GGATTTCCTTCTTAATTCTTGCTTGAT 58.527 33.333 0.00 0.00 0.00 2.57
4779 4979 7.093771 GGGATTTCCTTCTTAATTCTTGCTTGA 60.094 37.037 0.00 0.00 35.95 3.02
4780 4980 7.038048 GGGATTTCCTTCTTAATTCTTGCTTG 58.962 38.462 0.00 0.00 35.95 4.01
4781 4981 6.956435 AGGGATTTCCTTCTTAATTCTTGCTT 59.044 34.615 0.00 0.00 45.47 3.91
4782 4982 6.497640 AGGGATTTCCTTCTTAATTCTTGCT 58.502 36.000 0.00 0.00 45.47 3.91
4783 4983 6.782082 AGGGATTTCCTTCTTAATTCTTGC 57.218 37.500 0.00 0.00 45.47 4.01
4798 4998 1.286257 AGGCAAGAGGGAAGGGATTTC 59.714 52.381 0.00 0.00 34.93 2.17
4799 4999 1.006400 CAGGCAAGAGGGAAGGGATTT 59.994 52.381 0.00 0.00 0.00 2.17
4800 5000 0.627986 CAGGCAAGAGGGAAGGGATT 59.372 55.000 0.00 0.00 0.00 3.01
4801 5001 1.284841 CCAGGCAAGAGGGAAGGGAT 61.285 60.000 0.00 0.00 0.00 3.85
4802 5002 1.925455 CCAGGCAAGAGGGAAGGGA 60.925 63.158 0.00 0.00 0.00 4.20
4803 5003 2.679716 CCAGGCAAGAGGGAAGGG 59.320 66.667 0.00 0.00 0.00 3.95
4804 5004 2.044551 GCCAGGCAAGAGGGAAGG 60.045 66.667 6.55 0.00 0.00 3.46
4805 5005 2.044551 GGCCAGGCAAGAGGGAAG 60.045 66.667 15.19 0.00 0.00 3.46
4806 5006 4.033776 CGGCCAGGCAAGAGGGAA 62.034 66.667 15.19 0.00 0.00 3.97
4846 5046 4.787280 AGGGAGGGCGTGAGAGGG 62.787 72.222 0.00 0.00 0.00 4.30
4847 5047 2.685380 AAGGGAGGGCGTGAGAGG 60.685 66.667 0.00 0.00 0.00 3.69
4848 5048 0.395862 TAGAAGGGAGGGCGTGAGAG 60.396 60.000 0.00 0.00 0.00 3.20
4849 5049 0.395862 CTAGAAGGGAGGGCGTGAGA 60.396 60.000 0.00 0.00 0.00 3.27
4850 5050 2.022240 GCTAGAAGGGAGGGCGTGAG 62.022 65.000 0.00 0.00 0.00 3.51
4851 5051 2.058595 GCTAGAAGGGAGGGCGTGA 61.059 63.158 0.00 0.00 0.00 4.35
4852 5052 2.303549 CTGCTAGAAGGGAGGGCGTG 62.304 65.000 0.00 0.00 0.00 5.34
4853 5053 2.038975 TGCTAGAAGGGAGGGCGT 59.961 61.111 0.00 0.00 0.00 5.68
4854 5054 2.818132 CTGCTAGAAGGGAGGGCG 59.182 66.667 0.00 0.00 0.00 6.13
4855 5055 2.508436 GCTGCTAGAAGGGAGGGC 59.492 66.667 0.00 0.00 0.00 5.19
4856 5056 2.818132 CGCTGCTAGAAGGGAGGG 59.182 66.667 9.23 0.00 32.03 4.30
4857 5057 2.107953 GCGCTGCTAGAAGGGAGG 59.892 66.667 18.85 0.00 32.03 4.30
4858 5058 2.037620 ATGGCGCTGCTAGAAGGGAG 62.038 60.000 18.85 0.00 32.03 4.30
4859 5059 0.759060 TATGGCGCTGCTAGAAGGGA 60.759 55.000 18.85 0.00 32.03 4.20
4860 5060 0.106708 TTATGGCGCTGCTAGAAGGG 59.893 55.000 10.52 10.52 0.00 3.95
4861 5061 1.221414 GTTATGGCGCTGCTAGAAGG 58.779 55.000 7.64 0.00 0.00 3.46
4862 5062 1.939974 TGTTATGGCGCTGCTAGAAG 58.060 50.000 7.64 0.00 0.00 2.85
4863 5063 2.394930 TTGTTATGGCGCTGCTAGAA 57.605 45.000 7.64 0.00 0.00 2.10
4864 5064 2.620251 ATTGTTATGGCGCTGCTAGA 57.380 45.000 7.64 0.00 0.00 2.43
4865 5065 3.364366 GCTTATTGTTATGGCGCTGCTAG 60.364 47.826 7.64 0.00 0.00 3.42
4866 5066 2.548057 GCTTATTGTTATGGCGCTGCTA 59.452 45.455 7.64 0.00 0.00 3.49
4867 5067 1.334869 GCTTATTGTTATGGCGCTGCT 59.665 47.619 7.64 0.00 0.00 4.24
4868 5068 1.600413 GGCTTATTGTTATGGCGCTGC 60.600 52.381 7.64 0.00 0.00 5.25
4869 5069 1.001378 GGGCTTATTGTTATGGCGCTG 60.001 52.381 7.64 0.00 33.97 5.18
4870 5070 1.133792 AGGGCTTATTGTTATGGCGCT 60.134 47.619 7.64 0.00 40.42 5.92
4871 5071 1.318576 AGGGCTTATTGTTATGGCGC 58.681 50.000 0.00 0.00 36.37 6.53
4872 5072 4.385358 AAAAGGGCTTATTGTTATGGCG 57.615 40.909 0.00 0.00 0.00 5.69
4873 5073 6.709018 TCTAAAAGGGCTTATTGTTATGGC 57.291 37.500 0.00 0.00 0.00 4.40
4948 5152 7.807977 ACATACGGAGCTAAATGAATGAATT 57.192 32.000 0.00 0.00 0.00 2.17
4954 5158 5.506815 CGGACTACATACGGAGCTAAATGAA 60.507 44.000 0.00 0.00 0.00 2.57
4961 5165 2.627515 TACGGACTACATACGGAGCT 57.372 50.000 0.00 0.00 0.00 4.09
4998 5202 6.910259 ACTCCCTCCATTCCTAAATAAAGT 57.090 37.500 0.00 0.00 0.00 2.66
5103 5308 1.273327 CCAGGAAAATGTGAACAGGCC 59.727 52.381 0.00 0.00 0.00 5.19
5158 5363 3.202151 GGTCCAAATCAGGATCAGGGTTA 59.798 47.826 0.00 0.00 40.42 2.85
5171 5376 0.684479 GAAGGGCCCAGGTCCAAATC 60.684 60.000 27.56 3.74 43.56 2.17
5221 5426 4.467769 AGCTGCTCATATAAACCTGCAAT 58.532 39.130 0.00 0.00 0.00 3.56
5392 5597 8.585471 AAAACAATCTATCATGTCATGGAAGT 57.415 30.769 12.90 3.81 0.00 3.01
5568 5773 2.758423 GCCAAGGGTACTGTTAAATGGG 59.242 50.000 0.00 0.00 0.00 4.00
5604 5809 2.634940 CACCTCCCAGGGATATGTACTG 59.365 54.545 9.31 0.00 40.58 2.74
5658 5863 2.479566 TGAGGAGCGCAAAGAGAATT 57.520 45.000 11.47 0.00 0.00 2.17
5679 5884 4.835284 TCATTCTACCTGCATGTTACCA 57.165 40.909 0.00 0.00 0.00 3.25
5705 5910 6.260936 CAGGGTGAAAAGATAGTTTGCGATAT 59.739 38.462 0.00 0.00 0.00 1.63
5706 5911 5.584649 CAGGGTGAAAAGATAGTTTGCGATA 59.415 40.000 0.00 0.00 0.00 2.92
5797 6002 5.040635 CGCTTCTTAACTCTCATCTCTTCC 58.959 45.833 0.00 0.00 0.00 3.46
5911 6116 7.826744 ACCAAATTTTCTTCATCTACTCCTCTC 59.173 37.037 0.00 0.00 0.00 3.20
6217 6422 2.057922 ACACTCTCCAAGGAACCATGT 58.942 47.619 0.00 0.00 0.00 3.21
6244 6449 2.032860 ATCCACTTCGGCCTCCATCG 62.033 60.000 0.00 0.00 33.14 3.84
6379 6584 0.462759 ATGCCTCAACCTCGCTAAGC 60.463 55.000 0.00 0.00 0.00 3.09
6463 6668 0.889186 ACCGGAATGTGTGCTGAACC 60.889 55.000 9.46 0.00 0.00 3.62
6786 6994 2.496899 AGCACAGGTAATTCCCAGTG 57.503 50.000 8.07 8.07 42.16 3.66
6991 7201 7.253422 GCTCAGTGATGTGCAACTTTAATTAT 58.747 34.615 0.00 0.00 38.04 1.28
6992 7202 6.349280 GGCTCAGTGATGTGCAACTTTAATTA 60.349 38.462 5.34 0.00 38.04 1.40
6993 7203 5.464168 GCTCAGTGATGTGCAACTTTAATT 58.536 37.500 0.00 0.00 38.04 1.40
6994 7204 4.082571 GGCTCAGTGATGTGCAACTTTAAT 60.083 41.667 5.34 0.00 38.04 1.40
6995 7205 3.253188 GGCTCAGTGATGTGCAACTTTAA 59.747 43.478 5.34 0.00 38.04 1.52
7019 7231 5.391449 CAGATTCTCAGCACTGTGATTTTG 58.609 41.667 12.86 4.05 33.75 2.44
7026 7238 0.390866 CCGCAGATTCTCAGCACTGT 60.391 55.000 0.00 0.00 33.57 3.55
7033 7245 0.174389 GCAGTCTCCGCAGATTCTCA 59.826 55.000 0.00 0.00 0.00 3.27
7036 7248 1.139734 TCGCAGTCTCCGCAGATTC 59.860 57.895 0.00 0.00 0.00 2.52
7044 7256 7.948278 ATATTTTTATGTAGTCGCAGTCTCC 57.052 36.000 0.00 0.00 0.00 3.71
7061 7273 9.044150 CCATTTCATCATTGCGGTAATATTTTT 57.956 29.630 0.00 0.00 0.00 1.94
7070 7282 3.257873 TCAAACCATTTCATCATTGCGGT 59.742 39.130 0.00 0.00 0.00 5.68
7146 7386 4.446371 ACTTATTCTCCAAATCTCAGCCG 58.554 43.478 0.00 0.00 0.00 5.52
7164 7406 2.637872 CCCTGACCTGACCTGAAACTTA 59.362 50.000 0.00 0.00 0.00 2.24
7165 7407 1.421646 CCCTGACCTGACCTGAAACTT 59.578 52.381 0.00 0.00 0.00 2.66
7166 7408 1.059913 CCCTGACCTGACCTGAAACT 58.940 55.000 0.00 0.00 0.00 2.66
7225 7468 2.733593 GACGAGTGTGGTGCGACC 60.734 66.667 0.00 0.00 39.22 4.79
7226 7469 1.729838 GAGACGAGTGTGGTGCGAC 60.730 63.158 0.00 0.00 0.00 5.19
7240 7483 2.884087 TTCCGCAATCGAGCCGAGAC 62.884 60.000 3.76 0.00 39.91 3.36
7245 7490 2.110734 GAGCATTCCGCAATCGAGCC 62.111 60.000 0.00 0.00 46.13 4.70
7258 7503 2.270205 CGCACCAGGGAGAGCATT 59.730 61.111 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.