Multiple sequence alignment - TraesCS6B01G426600

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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 TraesCS6B01G426600 chr6B 100.000 5475 0 0 1 5475 694970356 694975830 0.000000e+00 10111.0
1 TraesCS6B01G426600 chr6B 85.827 889 75 26 4617 5474 695051615 695052483 0.000000e+00 896.0
2 TraesCS6B01G426600 chr6B 86.287 474 45 11 247 707 636375988 636375522 1.060000e-136 497.0
3 TraesCS6B01G426600 chr6B 82.510 486 52 20 4617 5086 695123322 695123790 3.970000e-106 396.0
4 TraesCS6B01G426600 chr6B 83.210 405 26 17 1 380 651430599 651430212 3.160000e-87 333.0
5 TraesCS6B01G426600 chr6B 91.971 137 5 4 4335 4471 72153410 72153540 2.600000e-43 187.0
6 TraesCS6B01G426600 chr6B 91.200 125 9 1 5248 5370 589601927 589601803 9.430000e-38 169.0
7 TraesCS6B01G426600 chr6B 87.179 117 15 0 5130 5246 695124091 695124207 3.440000e-27 134.0
8 TraesCS6B01G426600 chr6D 93.421 3739 127 56 732 4423 456787824 456791490 0.000000e+00 5432.0
9 TraesCS6B01G426600 chr6D 89.947 567 26 9 4926 5467 456793996 456794556 0.000000e+00 702.0
10 TraesCS6B01G426600 chr6D 78.603 673 71 34 4622 5243 456806391 456807041 1.440000e-100 377.0
11 TraesCS6B01G426600 chr6D 82.635 334 29 15 4603 4912 456823606 456823934 9.040000e-68 268.0
12 TraesCS6B01G426600 chr6D 83.673 245 21 11 4657 4900 456793773 456793999 4.300000e-51 213.0
13 TraesCS6B01G426600 chr6D 78.093 388 47 18 4151 4534 456792114 456792467 1.550000e-50 211.0
14 TraesCS6B01G426600 chr6D 96.226 106 4 0 5266 5371 394093259 394093154 2.030000e-39 174.0
15 TraesCS6B01G426600 chr6D 91.453 117 10 0 5130 5246 456823982 456824098 1.580000e-35 161.0
16 TraesCS6B01G426600 chr6A 92.374 3737 152 61 766 4423 603403116 603406798 0.000000e+00 5199.0
17 TraesCS6B01G426600 chr6A 91.473 129 11 0 5243 5371 540261708 540261580 1.570000e-40 178.0
18 TraesCS6B01G426600 chr6A 87.368 95 8 1 4210 4300 603407181 603407275 7.500000e-19 106.0
19 TraesCS6B01G426600 chr3B 98.913 736 8 0 1 736 721061579 721060844 0.000000e+00 1315.0
20 TraesCS6B01G426600 chr5B 98.363 733 10 2 1 732 343958189 343958920 0.000000e+00 1286.0
21 TraesCS6B01G426600 chr5B 92.958 142 5 3 4330 4471 352218272 352218408 9.300000e-48 202.0
22 TraesCS6B01G426600 chr2A 83.784 777 57 23 1 728 241084168 241083412 0.000000e+00 673.0
23 TraesCS6B01G426600 chr2A 84.359 390 45 7 4603 4979 209935597 209935983 8.660000e-98 368.0
24 TraesCS6B01G426600 chr2A 74.359 819 153 48 3124 3912 761306776 761307567 4.150000e-76 296.0
25 TraesCS6B01G426600 chr2A 82.143 140 21 4 2920 3057 761306602 761306739 3.470000e-22 117.0
26 TraesCS6B01G426600 chr2A 75.519 241 48 9 3678 3911 761896742 761896506 2.090000e-19 108.0
27 TraesCS6B01G426600 chr4B 92.720 261 12 3 4345 4605 660176153 660176406 2.410000e-98 370.0
28 TraesCS6B01G426600 chr1B 84.359 390 44 8 4603 4979 3842893 3843278 3.120000e-97 366.0
29 TraesCS6B01G426600 chr1D 90.421 261 15 4 4345 4605 414816497 414816247 8.790000e-88 335.0
30 TraesCS6B01G426600 chr1D 90.244 205 18 2 529 732 159867550 159867347 3.250000e-67 267.0
31 TraesCS6B01G426600 chr1D 72.694 813 175 42 3124 3911 6540937 6540147 1.530000e-55 228.0
32 TraesCS6B01G426600 chr1D 95.082 61 3 0 4251 4311 414816555 414816495 4.510000e-16 97.1
33 TraesCS6B01G426600 chr1D 96.552 58 2 0 4251 4308 459935414 459935357 4.510000e-16 97.1
34 TraesCS6B01G426600 chr1D 96.154 52 2 0 4251 4302 418289795 418289744 9.770000e-13 86.1
35 TraesCS6B01G426600 chr2B 74.877 816 154 43 3124 3912 796598490 796597699 1.900000e-84 324.0
36 TraesCS6B01G426600 chr2B 81.560 141 20 6 2920 3057 796598664 796598527 1.610000e-20 111.0
37 TraesCS6B01G426600 chr2D 74.665 821 147 50 3124 3912 637903674 637904465 1.920000e-79 307.0
38 TraesCS6B01G426600 chr2D 83.688 141 17 6 2920 3057 637903500 637903637 1.600000e-25 128.0
39 TraesCS6B01G426600 chr5D 78.557 499 76 26 246 728 542379145 542379628 3.210000e-77 300.0
40 TraesCS6B01G426600 chr5D 95.798 119 4 1 4330 4448 262659187 262659304 2.010000e-44 191.0
41 TraesCS6B01G426600 chr5D 95.798 119 4 1 4330 4448 549242269 549242386 2.010000e-44 191.0
42 TraesCS6B01G426600 chr1A 72.996 811 170 43 3124 3908 7812435 7813222 7.090000e-59 239.0
43 TraesCS6B01G426600 chrUn 97.414 116 2 1 4333 4448 28594761 28594647 4.330000e-46 196.0
44 TraesCS6B01G426600 chr7D 97.414 116 2 1 4333 4448 461077150 461077036 4.330000e-46 196.0
45 TraesCS6B01G426600 chr7D 76.601 406 63 22 1973 2353 511325042 511325440 1.560000e-45 195.0
46 TraesCS6B01G426600 chr7D 94.828 58 3 0 4251 4308 175151312 175151369 2.100000e-14 91.6
47 TraesCS6B01G426600 chr4D 96.639 119 3 1 4330 4448 414532409 414532526 4.330000e-46 196.0
48 TraesCS6B01G426600 chr7A 76.413 407 62 24 1973 2353 583871785 583872183 7.240000e-44 189.0
49 TraesCS6B01G426600 chr7B 77.188 320 55 12 2046 2353 540248530 540248843 2.620000e-38 171.0
50 TraesCS6B01G426600 chr3D 96.610 59 2 0 4251 4309 60481310 60481252 1.260000e-16 99.0


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 TraesCS6B01G426600 chr6B 694970356 694975830 5474 False 10111.0 10111 100.0000 1 5475 1 chr6B.!!$F2 5474
1 TraesCS6B01G426600 chr6B 695051615 695052483 868 False 896.0 896 85.8270 4617 5474 1 chr6B.!!$F3 857
2 TraesCS6B01G426600 chr6B 695123322 695124207 885 False 265.0 396 84.8445 4617 5246 2 chr6B.!!$F4 629
3 TraesCS6B01G426600 chr6D 456787824 456794556 6732 False 1639.5 5432 86.2835 732 5467 4 chr6D.!!$F2 4735
4 TraesCS6B01G426600 chr6D 456806391 456807041 650 False 377.0 377 78.6030 4622 5243 1 chr6D.!!$F1 621
5 TraesCS6B01G426600 chr6A 603403116 603407275 4159 False 2652.5 5199 89.8710 766 4423 2 chr6A.!!$F1 3657
6 TraesCS6B01G426600 chr3B 721060844 721061579 735 True 1315.0 1315 98.9130 1 736 1 chr3B.!!$R1 735
7 TraesCS6B01G426600 chr5B 343958189 343958920 731 False 1286.0 1286 98.3630 1 732 1 chr5B.!!$F1 731
8 TraesCS6B01G426600 chr2A 241083412 241084168 756 True 673.0 673 83.7840 1 728 1 chr2A.!!$R1 727
9 TraesCS6B01G426600 chr2A 761306602 761307567 965 False 206.5 296 78.2510 2920 3912 2 chr2A.!!$F2 992
10 TraesCS6B01G426600 chr1D 6540147 6540937 790 True 228.0 228 72.6940 3124 3911 1 chr1D.!!$R1 787
11 TraesCS6B01G426600 chr2B 796597699 796598664 965 True 217.5 324 78.2185 2920 3912 2 chr2B.!!$R1 992
12 TraesCS6B01G426600 chr2D 637903500 637904465 965 False 217.5 307 79.1765 2920 3912 2 chr2D.!!$F1 992
13 TraesCS6B01G426600 chr1A 7812435 7813222 787 False 239.0 239 72.9960 3124 3908 1 chr1A.!!$F1 784

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
915 978 0.191064 AACCCACCTCTCACCTCTCA 59.809 55.000 0.00 0.0 0.00 3.27 F
917 980 0.252012 CCCACCTCTCACCTCTCACT 60.252 60.000 0.00 0.0 0.00 3.41 F
1047 1128 0.392998 GCGAGCTTGAATCTTGGGGA 60.393 55.000 4.70 0.0 0.00 4.81 F
1051 1132 0.625849 GCTTGAATCTTGGGGAGGGA 59.374 55.000 0.00 0.0 0.00 4.20 F
1052 1133 1.005924 GCTTGAATCTTGGGGAGGGAA 59.994 52.381 0.00 0.0 0.00 3.97 F
1346 1427 1.578206 GCAACTTCCTCGGCAAGGTC 61.578 60.000 4.46 0.0 46.32 3.85 F
2741 2831 1.889573 GGTGCATCTCCGGCTAAGC 60.890 63.158 0.00 0.0 0.00 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2498 2588 0.664166 GCTCGGCAACCACAAACATG 60.664 55.000 0.00 0.00 0.00 3.21 R
2915 3005 2.202260 TTCGCGACGCAGTACGAG 60.202 61.111 21.35 1.10 46.86 4.18 R
3085 3175 0.099791 CACCGTGGTGTTGTTGTTCC 59.900 55.000 10.94 0.00 40.91 3.62 R
3087 3177 1.939769 GCCACCGTGGTGTTGTTGTT 61.940 55.000 18.95 0.00 44.02 2.83 R
3089 3179 2.118404 AGCCACCGTGGTGTTGTTG 61.118 57.895 18.95 3.37 44.02 3.33 R
3257 3347 0.964860 ACATGTTGCCGGCATTGCTA 60.965 50.000 33.25 12.81 0.00 3.49 R
4501 5583 0.179004 ACCTGGCCGTTTCATCAACA 60.179 50.000 0.00 0.00 34.68 3.33 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
34 36 4.600111 ACTAACAGTTAAACCCCCTCATGA 59.400 41.667 0.00 0.00 0.00 3.07
686 736 2.100252 CGTACGGCTCAGAAAAGGGATA 59.900 50.000 7.57 0.00 0.00 2.59
708 758 8.770828 GGATAAAGACGAATAATTTTCATCCGA 58.229 33.333 0.00 0.00 0.00 4.55
783 843 1.668101 AAGCGCGACCAAACCCAAAA 61.668 50.000 12.10 0.00 0.00 2.44
818 879 2.104622 CTCAAAAACCACCCAAAGCCAT 59.895 45.455 0.00 0.00 0.00 4.40
906 969 1.845205 AGCAGCAGAACCCACCTCT 60.845 57.895 0.00 0.00 0.00 3.69
908 971 2.061220 CAGCAGAACCCACCTCTCA 58.939 57.895 0.00 0.00 0.00 3.27
910 973 1.003233 GCAGAACCCACCTCTCACC 60.003 63.158 0.00 0.00 0.00 4.02
911 974 1.484444 GCAGAACCCACCTCTCACCT 61.484 60.000 0.00 0.00 0.00 4.00
912 975 0.610687 CAGAACCCACCTCTCACCTC 59.389 60.000 0.00 0.00 0.00 3.85
915 978 0.191064 AACCCACCTCTCACCTCTCA 59.809 55.000 0.00 0.00 0.00 3.27
917 980 0.252012 CCCACCTCTCACCTCTCACT 60.252 60.000 0.00 0.00 0.00 3.41
918 981 1.181786 CCACCTCTCACCTCTCACTC 58.818 60.000 0.00 0.00 0.00 3.51
925 988 1.687493 CACCTCTCACTCCTCCCCC 60.687 68.421 0.00 0.00 0.00 5.40
926 989 1.864559 ACCTCTCACTCCTCCCCCT 60.865 63.158 0.00 0.00 0.00 4.79
996 1077 0.962356 CAGCCGCCCACTCTTTTCAT 60.962 55.000 0.00 0.00 0.00 2.57
1033 1114 1.226547 CTCTGTTCTCCGAGCGAGC 60.227 63.158 0.00 0.00 38.62 5.03
1046 1127 0.393537 AGCGAGCTTGAATCTTGGGG 60.394 55.000 4.70 0.00 0.00 4.96
1047 1128 0.392998 GCGAGCTTGAATCTTGGGGA 60.393 55.000 4.70 0.00 0.00 4.81
1048 1129 1.661341 CGAGCTTGAATCTTGGGGAG 58.339 55.000 0.00 0.00 0.00 4.30
1049 1130 1.745141 CGAGCTTGAATCTTGGGGAGG 60.745 57.143 0.00 0.00 0.00 4.30
1050 1131 0.627986 AGCTTGAATCTTGGGGAGGG 59.372 55.000 0.00 0.00 0.00 4.30
1051 1132 0.625849 GCTTGAATCTTGGGGAGGGA 59.374 55.000 0.00 0.00 0.00 4.20
1052 1133 1.005924 GCTTGAATCTTGGGGAGGGAA 59.994 52.381 0.00 0.00 0.00 3.97
1053 1134 2.557452 GCTTGAATCTTGGGGAGGGAAA 60.557 50.000 0.00 0.00 0.00 3.13
1054 1135 2.899303 TGAATCTTGGGGAGGGAAAC 57.101 50.000 0.00 0.00 0.00 2.78
1346 1427 1.578206 GCAACTTCCTCGGCAAGGTC 61.578 60.000 4.46 0.00 46.32 3.85
1547 1628 4.083862 GTGACTGGCCCCGAGGTC 62.084 72.222 0.00 1.59 38.73 3.85
1793 1883 4.069232 CTCAAGGAGACGCGGCCA 62.069 66.667 9.25 0.00 0.00 5.36
2312 2402 3.718210 CTACGTCGCCCCCAAGCTC 62.718 68.421 0.00 0.00 0.00 4.09
2441 2531 3.417224 CAGATGCTGCGCACACGT 61.417 61.111 5.66 2.29 43.04 4.49
2741 2831 1.889573 GGTGCATCTCCGGCTAAGC 60.890 63.158 0.00 0.00 0.00 3.09
3435 3525 1.183549 GGAGGTCGTGGAGTACATGT 58.816 55.000 2.69 2.69 37.38 3.21
3545 3635 2.738521 CGGTGGTTCGAGCTGGTG 60.739 66.667 0.00 0.00 0.00 4.17
3572 3662 2.126071 CACTACCCGGTGCACTCG 60.126 66.667 17.98 17.67 0.00 4.18
3935 4046 4.717629 TTCTCCGTCGCCTGCGTG 62.718 66.667 11.68 5.57 40.74 5.34
4088 4199 0.976641 CCAAGGCCGATATCCTGCTA 59.023 55.000 10.68 0.00 33.43 3.49
4094 4205 2.697751 GGCCGATATCCTGCTATGATCT 59.302 50.000 10.68 0.00 0.00 2.75
4095 4206 3.243704 GGCCGATATCCTGCTATGATCTC 60.244 52.174 10.68 0.00 0.00 2.75
4096 4207 3.382865 GCCGATATCCTGCTATGATCTCA 59.617 47.826 0.00 0.00 0.00 3.27
4097 4208 4.142071 GCCGATATCCTGCTATGATCTCAA 60.142 45.833 0.00 0.00 0.00 3.02
4098 4209 5.453057 GCCGATATCCTGCTATGATCTCAAT 60.453 44.000 0.00 0.00 0.00 2.57
4099 4210 6.215121 CCGATATCCTGCTATGATCTCAATC 58.785 44.000 0.00 0.00 0.00 2.67
4103 4214 5.725325 TCCTGCTATGATCTCAATCTCTG 57.275 43.478 0.00 0.00 32.75 3.35
4124 4263 2.669364 CAGCTGCAAAATTGGTGACTC 58.331 47.619 0.00 0.00 0.00 3.36
4131 4272 4.892934 TGCAAAATTGGTGACTCTAACCTT 59.107 37.500 0.00 0.00 38.60 3.50
4133 4274 5.222631 CAAAATTGGTGACTCTAACCTTGC 58.777 41.667 0.00 0.00 38.60 4.01
4170 4311 3.007506 GTGGTTTGGTTATTTTGGAGGGG 59.992 47.826 0.00 0.00 0.00 4.79
4185 4330 0.549950 AGGGGAGTGGATGATGCTTG 59.450 55.000 0.00 0.00 0.00 4.01
4186 4331 0.466922 GGGGAGTGGATGATGCTTGG 60.467 60.000 0.00 0.00 0.00 3.61
4191 4336 1.918262 AGTGGATGATGCTTGGAAGGA 59.082 47.619 0.00 0.00 0.00 3.36
4192 4337 2.309755 AGTGGATGATGCTTGGAAGGAA 59.690 45.455 0.00 0.00 0.00 3.36
4194 4339 3.067742 GTGGATGATGCTTGGAAGGAATG 59.932 47.826 0.00 0.00 0.00 2.67
4199 5277 4.264253 TGATGCTTGGAAGGAATGTAGTG 58.736 43.478 0.00 0.00 0.00 2.74
4217 5295 5.648526 TGTAGTGGCAAGAAACAAACTTGTA 59.351 36.000 0.00 0.00 44.25 2.41
4221 5299 3.740832 GGCAAGAAACAAACTTGTATGCC 59.259 43.478 17.97 17.97 44.25 4.40
4223 5301 5.049828 GCAAGAAACAAACTTGTATGCCTT 58.950 37.500 0.00 0.00 44.25 4.35
4227 5305 5.594317 AGAAACAAACTTGTATGCCTTCTGT 59.406 36.000 5.93 0.00 41.31 3.41
4264 5342 7.012327 TGGTATGCTAGTTGCTTAGCTTAATTG 59.988 37.037 17.64 0.00 44.99 2.32
4281 5363 8.936864 AGCTTAATTGCTGTTAGTGTTAGTTAG 58.063 33.333 0.00 0.00 42.33 2.34
4294 5376 5.105310 AGTGTTAGTTAGTGTATCCTGCTGG 60.105 44.000 2.58 2.58 0.00 4.85
4301 5383 2.106511 AGTGTATCCTGCTGGTTTGTGT 59.893 45.455 9.73 0.00 34.23 3.72
4302 5384 2.226437 GTGTATCCTGCTGGTTTGTGTG 59.774 50.000 9.73 0.00 34.23 3.82
4305 5387 0.751277 TCCTGCTGGTTTGTGTGGTG 60.751 55.000 9.73 0.00 34.23 4.17
4306 5388 1.735360 CTGCTGGTTTGTGTGGTGG 59.265 57.895 0.00 0.00 0.00 4.61
4307 5389 1.000270 TGCTGGTTTGTGTGGTGGT 60.000 52.632 0.00 0.00 0.00 4.16
4308 5390 0.256177 TGCTGGTTTGTGTGGTGGTA 59.744 50.000 0.00 0.00 0.00 3.25
4309 5391 0.951558 GCTGGTTTGTGTGGTGGTAG 59.048 55.000 0.00 0.00 0.00 3.18
4310 5392 0.951558 CTGGTTTGTGTGGTGGTAGC 59.048 55.000 0.00 0.00 0.00 3.58
4311 5393 0.256177 TGGTTTGTGTGGTGGTAGCA 59.744 50.000 0.00 0.00 0.00 3.49
4312 5394 1.341089 TGGTTTGTGTGGTGGTAGCAA 60.341 47.619 0.00 0.00 0.00 3.91
4313 5395 1.066454 GGTTTGTGTGGTGGTAGCAAC 59.934 52.381 2.13 2.13 0.00 4.17
4316 5398 0.817634 TGTGTGGTGGTAGCAACAGC 60.818 55.000 14.07 10.03 36.90 4.40
4319 5401 0.250295 GTGGTGGTAGCAACAGCAGA 60.250 55.000 14.07 0.00 45.69 4.26
4326 5408 3.323691 TGGTAGCAACAGCAGAAGTAGAA 59.676 43.478 0.00 0.00 0.00 2.10
4328 5410 4.322049 GGTAGCAACAGCAGAAGTAGAAGA 60.322 45.833 0.00 0.00 0.00 2.87
4329 5411 4.342862 AGCAACAGCAGAAGTAGAAGAA 57.657 40.909 0.00 0.00 0.00 2.52
4330 5412 4.314121 AGCAACAGCAGAAGTAGAAGAAG 58.686 43.478 0.00 0.00 0.00 2.85
4331 5413 4.039730 AGCAACAGCAGAAGTAGAAGAAGA 59.960 41.667 0.00 0.00 0.00 2.87
4333 5415 5.107143 GCAACAGCAGAAGTAGAAGAAGAAG 60.107 44.000 0.00 0.00 0.00 2.85
4334 5416 6.219473 CAACAGCAGAAGTAGAAGAAGAAGA 58.781 40.000 0.00 0.00 0.00 2.87
4335 5417 5.778862 ACAGCAGAAGTAGAAGAAGAAGAC 58.221 41.667 0.00 0.00 0.00 3.01
4336 5418 5.538433 ACAGCAGAAGTAGAAGAAGAAGACT 59.462 40.000 0.00 0.00 0.00 3.24
4337 5419 6.041523 ACAGCAGAAGTAGAAGAAGAAGACTT 59.958 38.462 0.00 0.00 39.24 3.01
4338 5420 6.365789 CAGCAGAAGTAGAAGAAGAAGACTTG 59.634 42.308 0.00 0.00 36.39 3.16
4339 5421 6.041523 AGCAGAAGTAGAAGAAGAAGACTTGT 59.958 38.462 0.00 0.00 36.39 3.16
4340 5422 6.145371 GCAGAAGTAGAAGAAGAAGACTTGTG 59.855 42.308 0.00 6.00 41.71 3.33
4341 5423 6.644592 CAGAAGTAGAAGAAGAAGACTTGTGG 59.355 42.308 0.00 0.00 37.61 4.17
4342 5424 6.325286 AGAAGTAGAAGAAGAAGACTTGTGGT 59.675 38.462 0.00 0.00 36.39 4.16
4343 5425 7.506261 AGAAGTAGAAGAAGAAGACTTGTGGTA 59.494 37.037 0.00 0.00 36.39 3.25
4353 5435 1.071699 GACTTGTGGTAAGCCCAGTGA 59.928 52.381 0.00 0.00 46.45 3.41
4354 5436 1.202770 ACTTGTGGTAAGCCCAGTGAC 60.203 52.381 0.00 0.00 46.45 3.67
4356 5438 1.375523 GTGGTAAGCCCAGTGACGG 60.376 63.158 0.00 0.00 46.45 4.79
4359 5441 2.033194 GTAAGCCCAGTGACGGTGC 61.033 63.158 0.00 0.00 0.00 5.01
4367 5449 0.861837 CAGTGACGGTGCTGTTCTTC 59.138 55.000 0.00 0.00 0.00 2.87
4372 5454 2.030185 TGACGGTGCTGTTCTTCTAGTC 60.030 50.000 0.00 0.00 0.00 2.59
4375 5457 1.623811 GGTGCTGTTCTTCTAGTCCCA 59.376 52.381 0.00 0.00 0.00 4.37
4383 5465 4.899457 TGTTCTTCTAGTCCCAGTTTCAGA 59.101 41.667 0.00 0.00 0.00 3.27
4384 5466 5.221461 TGTTCTTCTAGTCCCAGTTTCAGAC 60.221 44.000 0.00 0.00 0.00 3.51
4385 5467 4.742012 TCTTCTAGTCCCAGTTTCAGACT 58.258 43.478 0.00 0.00 43.17 3.24
4386 5468 5.148502 TCTTCTAGTCCCAGTTTCAGACTT 58.851 41.667 0.00 0.00 41.09 3.01
4387 5469 5.602978 TCTTCTAGTCCCAGTTTCAGACTTT 59.397 40.000 0.00 0.00 41.09 2.66
4388 5470 5.470047 TCTAGTCCCAGTTTCAGACTTTC 57.530 43.478 0.00 0.00 41.09 2.62
4389 5471 4.899457 TCTAGTCCCAGTTTCAGACTTTCA 59.101 41.667 0.00 0.00 41.09 2.69
4390 5472 4.078639 AGTCCCAGTTTCAGACTTTCAG 57.921 45.455 0.00 0.00 37.60 3.02
4391 5473 2.550180 GTCCCAGTTTCAGACTTTCAGC 59.450 50.000 0.00 0.00 36.10 4.26
4395 5477 3.003068 CCAGTTTCAGACTTTCAGCTGTG 59.997 47.826 14.67 3.29 36.10 3.66
4402 5484 1.265365 GACTTTCAGCTGTGCAAGGAC 59.735 52.381 14.67 9.35 0.00 3.85
4405 5487 2.928801 TTCAGCTGTGCAAGGACTAA 57.071 45.000 14.67 0.00 0.00 2.24
4415 5497 4.344102 TGTGCAAGGACTAAGTTCAGTAGT 59.656 41.667 0.00 0.00 34.46 2.73
4423 5505 5.291905 ACTAAGTTCAGTAGTTGGCAGTT 57.708 39.130 0.00 0.00 0.00 3.16
4424 5506 5.681639 ACTAAGTTCAGTAGTTGGCAGTTT 58.318 37.500 0.00 0.00 0.00 2.66
4452 5534 9.736414 ATCTATTATGTGATGATGAAAGAAGGG 57.264 33.333 0.00 0.00 0.00 3.95
4453 5535 8.717717 TCTATTATGTGATGATGAAAGAAGGGT 58.282 33.333 0.00 0.00 0.00 4.34
4454 5536 9.347240 CTATTATGTGATGATGAAAGAAGGGTT 57.653 33.333 0.00 0.00 0.00 4.11
4456 5538 9.699410 ATTATGTGATGATGAAAGAAGGGTTAA 57.301 29.630 0.00 0.00 0.00 2.01
4457 5539 9.699410 TTATGTGATGATGAAAGAAGGGTTAAT 57.301 29.630 0.00 0.00 0.00 1.40
4467 5549 8.990163 TGAAAGAAGGGTTAATTAAGTTCAGT 57.010 30.769 13.48 4.87 0.00 3.41
4470 5552 9.856162 AAAGAAGGGTTAATTAAGTTCAGTACA 57.144 29.630 13.48 0.00 0.00 2.90
4486 5568 6.726258 TCAGTACATTGCTGTTAATCTGTG 57.274 37.500 0.00 0.00 36.79 3.66
4488 5570 6.368791 TCAGTACATTGCTGTTAATCTGTGTC 59.631 38.462 0.00 0.00 36.79 3.67
4489 5571 6.147656 CAGTACATTGCTGTTAATCTGTGTCA 59.852 38.462 0.00 0.00 36.79 3.58
4493 5575 6.376299 ACATTGCTGTTAATCTGTGTCATGAT 59.624 34.615 0.00 0.00 28.70 2.45
4497 5579 6.037830 TGCTGTTAATCTGTGTCATGATGATG 59.962 38.462 0.00 0.00 0.00 3.07
4498 5580 6.259387 GCTGTTAATCTGTGTCATGATGATGA 59.741 38.462 0.00 0.00 36.16 2.92
4499 5581 7.041303 GCTGTTAATCTGTGTCATGATGATGAT 60.041 37.037 0.00 0.00 40.78 2.45
4500 5582 8.149973 TGTTAATCTGTGTCATGATGATGATG 57.850 34.615 0.00 0.00 40.78 3.07
4501 5583 7.771826 TGTTAATCTGTGTCATGATGATGATGT 59.228 33.333 0.00 0.00 40.78 3.06
4502 5584 6.619801 AATCTGTGTCATGATGATGATGTG 57.380 37.500 0.00 0.00 40.78 3.21
4513 5595 5.871539 TGATGATGATGTGTTGATGAAACG 58.128 37.500 0.00 0.00 42.10 3.60
4515 5597 2.987413 TGATGTGTTGATGAAACGGC 57.013 45.000 0.00 0.00 42.10 5.68
4526 5608 3.442273 TGATGAAACGGCCAGGTTTAATC 59.558 43.478 19.52 19.52 43.57 1.75
4534 5616 4.398044 ACGGCCAGGTTTAATCTACAATTG 59.602 41.667 2.24 3.24 0.00 2.32
4535 5617 4.638421 CGGCCAGGTTTAATCTACAATTGA 59.362 41.667 13.59 0.00 0.00 2.57
4539 5621 7.875554 GGCCAGGTTTAATCTACAATTGAAAAA 59.124 33.333 13.59 0.69 0.00 1.94
4540 5622 8.708742 GCCAGGTTTAATCTACAATTGAAAAAC 58.291 33.333 13.59 11.54 0.00 2.43
4541 5623 9.981114 CCAGGTTTAATCTACAATTGAAAAACT 57.019 29.630 13.59 7.48 0.00 2.66
4551 5663 9.126151 TCTACAATTGAAAAACTGGTGTTATGA 57.874 29.630 13.59 0.00 34.96 2.15
4563 5675 6.245408 ACTGGTGTTATGAAATGTATGGTGT 58.755 36.000 0.00 0.00 0.00 4.16
4565 5677 7.094377 ACTGGTGTTATGAAATGTATGGTGTTC 60.094 37.037 0.00 0.00 0.00 3.18
4566 5678 6.717084 TGGTGTTATGAAATGTATGGTGTTCA 59.283 34.615 0.00 0.00 34.68 3.18
4575 5687 9.868277 TGAAATGTATGGTGTTCATTTTATTCC 57.132 29.630 0.00 0.00 40.38 3.01
4576 5688 9.868277 GAAATGTATGGTGTTCATTTTATTCCA 57.132 29.630 0.00 0.00 40.38 3.53
4597 5709 5.184096 TCCATTATAGCAGTAGCAGAGTAGC 59.816 44.000 0.00 0.00 45.49 3.58
4599 5711 5.697473 TTATAGCAGTAGCAGAGTAGCAG 57.303 43.478 0.00 0.00 45.49 4.24
4600 5712 2.136298 AGCAGTAGCAGAGTAGCAGA 57.864 50.000 0.00 0.00 45.49 4.26
4601 5713 1.748493 AGCAGTAGCAGAGTAGCAGAC 59.252 52.381 0.00 0.00 45.49 3.51
4602 5714 1.748493 GCAGTAGCAGAGTAGCAGACT 59.252 52.381 0.00 0.00 40.41 3.24
4603 5715 2.165437 GCAGTAGCAGAGTAGCAGACTT 59.835 50.000 0.00 0.00 38.66 3.01
4604 5716 3.768406 CAGTAGCAGAGTAGCAGACTTG 58.232 50.000 0.00 0.00 39.06 3.16
4605 5717 3.192422 CAGTAGCAGAGTAGCAGACTTGT 59.808 47.826 0.00 0.00 39.06 3.16
4606 5718 3.829601 AGTAGCAGAGTAGCAGACTTGTT 59.170 43.478 0.00 0.00 39.06 2.83
4607 5719 3.037431 AGCAGAGTAGCAGACTTGTTG 57.963 47.619 0.00 0.00 39.06 3.33
4608 5720 1.462670 GCAGAGTAGCAGACTTGTTGC 59.537 52.381 0.00 0.00 39.06 4.17
4609 5721 2.759191 CAGAGTAGCAGACTTGTTGCA 58.241 47.619 0.00 0.00 43.92 4.08
4610 5722 2.735663 CAGAGTAGCAGACTTGTTGCAG 59.264 50.000 0.00 0.00 43.92 4.41
4611 5723 2.366916 AGAGTAGCAGACTTGTTGCAGT 59.633 45.455 0.00 0.00 43.92 4.40
4613 5725 2.103094 AGTAGCAGACTTGTTGCAGTCA 59.897 45.455 6.59 0.00 45.08 3.41
4614 5726 2.267174 AGCAGACTTGTTGCAGTCAT 57.733 45.000 6.59 0.00 45.08 3.06
4633 5801 4.268405 GTCATTGTTTCACTTGTGCAAAGG 59.732 41.667 11.59 0.00 0.00 3.11
4635 5803 1.824230 TGTTTCACTTGTGCAAAGGCT 59.176 42.857 11.59 0.00 41.91 4.58
4654 5822 2.873245 GCTGAGTTCAGTCAATGGCAGA 60.873 50.000 10.57 0.00 45.45 4.26
4665 6934 7.157347 TCAGTCAATGGCAGATAATCTATGTC 58.843 38.462 0.00 0.00 0.00 3.06
4667 6936 7.606839 CAGTCAATGGCAGATAATCTATGTCAT 59.393 37.037 0.00 0.00 40.83 3.06
4668 6937 7.606839 AGTCAATGGCAGATAATCTATGTCATG 59.393 37.037 0.00 0.00 38.27 3.07
4689 6958 7.912250 GTCATGATGATTAGTTGATGAACCAAC 59.088 37.037 0.00 0.00 44.92 3.77
4711 6980 3.571401 CCAGGTTTAATCCATGATGAGCC 59.429 47.826 5.38 0.00 0.00 4.70
4716 6985 0.471191 AATCCATGATGAGCCGCAGA 59.529 50.000 0.00 0.00 0.00 4.26
4721 6990 0.757512 ATGATGAGCCGCAGATGTCT 59.242 50.000 0.00 0.00 0.00 3.41
4722 6991 0.179092 TGATGAGCCGCAGATGTCTG 60.179 55.000 5.66 5.66 46.40 3.51
4723 6992 0.879400 GATGAGCCGCAGATGTCTGG 60.879 60.000 11.66 2.59 43.94 3.86
4724 6993 1.332889 ATGAGCCGCAGATGTCTGGA 61.333 55.000 11.66 0.00 43.94 3.86
4725 6994 1.332889 TGAGCCGCAGATGTCTGGAT 61.333 55.000 11.66 0.00 43.94 3.41
4726 6995 0.879400 GAGCCGCAGATGTCTGGATG 60.879 60.000 11.66 0.00 43.94 3.51
4727 6996 1.144716 GCCGCAGATGTCTGGATGA 59.855 57.895 11.66 0.00 43.94 2.92
4728 6997 0.462581 GCCGCAGATGTCTGGATGAA 60.463 55.000 11.66 0.00 43.94 2.57
4729 6998 1.579698 CCGCAGATGTCTGGATGAAG 58.420 55.000 11.66 0.00 43.94 3.02
4730 6999 1.134580 CCGCAGATGTCTGGATGAAGT 60.135 52.381 11.66 0.00 43.94 3.01
4731 7000 2.101415 CCGCAGATGTCTGGATGAAGTA 59.899 50.000 11.66 0.00 43.94 2.24
4796 7065 0.657312 CTCACGTGCATGTGTGTTGT 59.343 50.000 32.41 0.00 40.74 3.32
4797 7066 1.063912 CTCACGTGCATGTGTGTTGTT 59.936 47.619 32.41 0.00 40.74 2.83
4798 7067 1.190249 CACGTGCATGTGTGTTGTTG 58.810 50.000 27.52 2.83 35.12 3.33
4808 7077 3.982475 TGTGTGTTGTTGCTTTTGTTCA 58.018 36.364 0.00 0.00 0.00 3.18
4831 7108 8.099364 TCACTGGTGAGAATAAAAATCTTGTC 57.901 34.615 0.00 0.00 34.14 3.18
4847 7124 1.967319 TGTCTTTGGAGTTGAGGCAC 58.033 50.000 0.00 0.00 0.00 5.01
4865 7142 2.383527 CGTGGCGCCTCTCTTTGTC 61.384 63.158 29.70 5.65 0.00 3.18
4867 7144 1.016653 GTGGCGCCTCTCTTTGTCTC 61.017 60.000 29.70 0.00 0.00 3.36
4881 7159 3.904800 TTGTCTCAGTTTGTCTCCACA 57.095 42.857 0.00 0.00 0.00 4.17
4882 7160 3.459232 TGTCTCAGTTTGTCTCCACAG 57.541 47.619 0.00 0.00 32.71 3.66
4883 7161 2.766263 TGTCTCAGTTTGTCTCCACAGT 59.234 45.455 0.00 0.00 32.71 3.55
4884 7162 3.958147 TGTCTCAGTTTGTCTCCACAGTA 59.042 43.478 0.00 0.00 32.71 2.74
4901 7179 2.677836 CAGTATGTTCCCACGTGATTGG 59.322 50.000 19.30 10.29 36.26 3.16
4919 7197 6.826741 GTGATTGGAGGCTTAAACTAATGGTA 59.173 38.462 0.00 0.00 0.00 3.25
4937 7215 4.585879 TGGTACAGGGAATTCTTGCTTAC 58.414 43.478 5.23 4.62 0.00 2.34
4965 7251 6.094742 TCTGAAGTTTGAACATGCAAGTGTTA 59.905 34.615 5.69 0.00 42.08 2.41
4967 7253 6.696583 TGAAGTTTGAACATGCAAGTGTTATG 59.303 34.615 5.69 0.00 42.08 1.90
4996 7286 8.134202 TCTTTCTGTTAACTGTCCATGATCTA 57.866 34.615 7.22 0.00 0.00 1.98
5021 7314 6.989169 ACAGAGAAATGATATCCACTACTTGC 59.011 38.462 0.00 0.00 0.00 4.01
5029 7322 3.629142 ATCCACTACTTGCCTGGTTAC 57.371 47.619 0.00 0.00 0.00 2.50
5034 7327 4.385825 CACTACTTGCCTGGTTACTGAAA 58.614 43.478 0.00 0.00 0.00 2.69
5035 7328 4.452455 CACTACTTGCCTGGTTACTGAAAG 59.548 45.833 0.00 0.00 42.29 2.62
5036 7329 2.230660 ACTTGCCTGGTTACTGAAAGC 58.769 47.619 0.00 0.00 37.60 3.51
5137 7694 4.170468 AGAGGTCCAATTGTCTTGTGTT 57.830 40.909 4.43 0.00 0.00 3.32
5153 7715 4.409718 TGTGTTAGTGGTTACTGCAAGA 57.590 40.909 0.00 0.00 37.78 3.02
5164 7726 7.603024 AGTGGTTACTGCAAGAACTAACTAATC 59.397 37.037 9.55 0.00 37.43 1.75
5166 7728 6.035758 GGTTACTGCAAGAACTAACTAATCCG 59.964 42.308 9.55 0.00 37.43 4.18
5221 7784 5.378230 AGTGGCATCTTTATGATCCTGAA 57.622 39.130 0.00 0.00 34.84 3.02
5246 7809 3.007635 TCAGAATGTTGCAGCTCATGAG 58.992 45.455 18.84 18.84 37.40 2.90
5262 7825 5.064071 GCTCATGAGAACTTGGCTAAACTAC 59.936 44.000 27.04 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 36 2.425312 CGAGATGACTAGAGTGGTGCTT 59.575 50.000 0.00 0.00 0.00 3.91
686 736 8.673711 TCATTCGGATGAAAATTATTCGTCTTT 58.326 29.630 3.16 0.00 39.29 2.52
708 758 9.434420 TGATTTTCGGAATTGCTAATTTTCATT 57.566 25.926 0.00 0.00 0.00 2.57
770 820 2.680841 GTTTTGGCTTTTGGGTTTGGTC 59.319 45.455 0.00 0.00 0.00 4.02
783 843 2.937959 TTTGAGGCGGGGTTTTGGCT 62.938 55.000 0.00 0.00 44.53 4.75
906 969 1.388531 GGGGAGGAGTGAGAGGTGA 59.611 63.158 0.00 0.00 0.00 4.02
908 971 1.864559 AGGGGGAGGAGTGAGAGGT 60.865 63.158 0.00 0.00 0.00 3.85
910 973 1.075600 GGAGGGGGAGGAGTGAGAG 60.076 68.421 0.00 0.00 0.00 3.20
911 974 2.637640 GGGAGGGGGAGGAGTGAGA 61.638 68.421 0.00 0.00 0.00 3.27
912 975 2.041405 GGGAGGGGGAGGAGTGAG 60.041 72.222 0.00 0.00 0.00 3.51
917 980 3.791076 GATGGGGGAGGGGGAGGA 61.791 72.222 0.00 0.00 0.00 3.71
925 988 3.147595 TCGCAGTCGATGGGGGAG 61.148 66.667 10.42 0.00 42.02 4.30
971 1034 3.015145 AGTGGGCGGCTGGGTTAT 61.015 61.111 9.56 0.00 0.00 1.89
978 1041 0.678048 GATGAAAAGAGTGGGCGGCT 60.678 55.000 9.56 0.00 0.00 5.52
979 1042 1.657751 GGATGAAAAGAGTGGGCGGC 61.658 60.000 0.00 0.00 0.00 6.53
981 1044 1.032114 GGGGATGAAAAGAGTGGGCG 61.032 60.000 0.00 0.00 0.00 6.13
1013 1094 1.999071 CTCGCTCGGAGAACAGAGGG 61.999 65.000 9.69 0.00 46.23 4.30
1033 1114 3.092301 GTTTCCCTCCCCAAGATTCAAG 58.908 50.000 0.00 0.00 0.00 3.02
1046 1127 1.032114 CCTTGGCCATCGTTTCCCTC 61.032 60.000 6.09 0.00 0.00 4.30
1047 1128 1.000896 CCTTGGCCATCGTTTCCCT 60.001 57.895 6.09 0.00 0.00 4.20
1048 1129 2.710902 GCCTTGGCCATCGTTTCCC 61.711 63.158 6.09 0.00 0.00 3.97
1049 1130 2.885113 GCCTTGGCCATCGTTTCC 59.115 61.111 6.09 0.00 0.00 3.13
1050 1131 2.485122 CGCCTTGGCCATCGTTTC 59.515 61.111 6.09 0.00 0.00 2.78
1051 1132 3.061848 CCGCCTTGGCCATCGTTT 61.062 61.111 6.09 0.00 0.00 3.60
1052 1133 3.976701 CTCCGCCTTGGCCATCGTT 62.977 63.158 6.09 0.00 37.80 3.85
1053 1134 4.473520 CTCCGCCTTGGCCATCGT 62.474 66.667 6.09 0.00 37.80 3.73
1054 1135 3.680620 TTCTCCGCCTTGGCCATCG 62.681 63.158 6.09 11.06 37.80 3.84
1206 1287 2.202676 GAGGCGCTCGTTCCAGAG 60.203 66.667 7.64 0.00 41.03 3.35
1385 1466 2.970974 GAAGAGCTGCGGCACAACC 61.971 63.158 21.93 2.92 41.70 3.77
1388 1469 2.666190 GTGAAGAGCTGCGGCACA 60.666 61.111 21.93 11.18 41.70 4.57
1562 1643 1.865788 GCTTCTTGCCGCCATTCACA 61.866 55.000 0.00 0.00 35.15 3.58
1571 1652 2.974489 CTGCTGGTGCTTCTTGCCG 61.974 63.158 0.00 0.00 42.00 5.69
1828 1918 3.379445 CCAGGTCGTAGGTGGCGT 61.379 66.667 0.00 0.00 0.00 5.68
2312 2402 2.181021 GACACGCGGAGGTACCAG 59.819 66.667 15.94 6.17 38.90 4.00
2447 2537 2.202878 CGGTTCGCCATGATCGGT 60.203 61.111 0.00 0.00 37.00 4.69
2498 2588 0.664166 GCTCGGCAACCACAAACATG 60.664 55.000 0.00 0.00 0.00 3.21
2771 2861 3.788766 CTGCTGTACGCCGTTGCC 61.789 66.667 0.00 0.00 38.05 4.52
2915 3005 2.202260 TTCGCGACGCAGTACGAG 60.202 61.111 21.35 1.10 46.86 4.18
3081 3171 1.757682 GTGGTGTTGTTGTTCCCTGA 58.242 50.000 0.00 0.00 0.00 3.86
3082 3172 0.380378 CGTGGTGTTGTTGTTCCCTG 59.620 55.000 0.00 0.00 0.00 4.45
3083 3173 0.750182 CCGTGGTGTTGTTGTTCCCT 60.750 55.000 0.00 0.00 0.00 4.20
3084 3174 1.033202 ACCGTGGTGTTGTTGTTCCC 61.033 55.000 0.00 0.00 0.00 3.97
3085 3175 0.099791 CACCGTGGTGTTGTTGTTCC 59.900 55.000 10.94 0.00 40.91 3.62
3086 3176 0.099791 CCACCGTGGTGTTGTTGTTC 59.900 55.000 17.31 0.00 44.02 3.18
3087 3177 1.939769 GCCACCGTGGTGTTGTTGTT 61.940 55.000 18.95 0.00 44.02 2.83
3088 3178 2.411504 GCCACCGTGGTGTTGTTGT 61.412 57.895 18.95 0.00 44.02 3.32
3089 3179 2.118404 AGCCACCGTGGTGTTGTTG 61.118 57.895 18.95 3.37 44.02 3.33
3257 3347 0.964860 ACATGTTGCCGGCATTGCTA 60.965 50.000 33.25 12.81 0.00 3.49
3435 3525 4.980805 GTGCGAGCGGTGGTCCAA 62.981 66.667 0.00 0.00 0.00 3.53
3527 3617 4.681978 ACCAGCTCGAACCACCGC 62.682 66.667 0.00 0.00 0.00 5.68
3584 3674 0.580104 CGAACACCAGGAACGTGAAC 59.420 55.000 0.00 0.00 35.17 3.18
3736 3844 4.838486 CCTCGTCCAGCTCGTCGC 62.838 72.222 0.00 0.00 39.57 5.19
4067 4178 0.603975 GCAGGATATCGGCCTTGGAC 60.604 60.000 0.00 0.00 32.12 4.02
4079 4190 6.127394 GCAGAGATTGAGATCATAGCAGGATA 60.127 42.308 0.00 0.00 34.60 2.59
4088 4199 3.734463 CAGCTGCAGAGATTGAGATCAT 58.266 45.455 20.43 0.00 34.60 2.45
4103 4214 1.142474 GTCACCAATTTTGCAGCTGC 58.858 50.000 31.89 31.89 42.50 5.25
4116 4255 1.000506 GTCGCAAGGTTAGAGTCACCA 59.999 52.381 2.71 0.00 36.67 4.17
4120 4259 0.524862 TCGGTCGCAAGGTTAGAGTC 59.475 55.000 0.00 0.00 38.47 3.36
4124 4263 1.927174 CTGAATCGGTCGCAAGGTTAG 59.073 52.381 0.00 0.00 38.47 2.34
4131 4272 1.403647 CCACTAACTGAATCGGTCGCA 60.404 52.381 0.00 0.00 0.00 5.10
4133 4274 2.649331 ACCACTAACTGAATCGGTCG 57.351 50.000 0.00 0.00 0.00 4.79
4170 4311 2.092753 TCCTTCCAAGCATCATCCACTC 60.093 50.000 0.00 0.00 0.00 3.51
4185 4330 3.350219 TCTTGCCACTACATTCCTTCC 57.650 47.619 0.00 0.00 0.00 3.46
4186 4331 4.518970 TGTTTCTTGCCACTACATTCCTTC 59.481 41.667 0.00 0.00 0.00 3.46
4191 4336 5.852282 AGTTTGTTTCTTGCCACTACATT 57.148 34.783 0.00 0.00 0.00 2.71
4192 4337 5.127031 ACAAGTTTGTTTCTTGCCACTACAT 59.873 36.000 5.72 0.00 43.97 2.29
4194 4339 4.993905 ACAAGTTTGTTTCTTGCCACTAC 58.006 39.130 5.72 0.00 43.97 2.73
4199 5277 3.740832 GGCATACAAGTTTGTTTCTTGCC 59.259 43.478 17.26 17.26 43.97 4.52
4264 5342 7.488471 CAGGATACACTAACTAACACTAACAGC 59.512 40.741 0.00 0.00 41.41 4.40
4281 5363 2.226437 CACACAAACCAGCAGGATACAC 59.774 50.000 0.35 0.00 38.69 2.90
4294 5376 1.746220 TGTTGCTACCACCACACAAAC 59.254 47.619 0.00 0.00 0.00 2.93
4301 5383 0.472044 TTCTGCTGTTGCTACCACCA 59.528 50.000 0.00 0.00 40.48 4.17
4302 5384 1.160137 CTTCTGCTGTTGCTACCACC 58.840 55.000 0.00 0.00 40.48 4.61
4305 5387 3.594603 TCTACTTCTGCTGTTGCTACC 57.405 47.619 0.00 0.00 40.48 3.18
4306 5388 4.810790 TCTTCTACTTCTGCTGTTGCTAC 58.189 43.478 0.00 0.00 40.48 3.58
4307 5389 5.243954 TCTTCTTCTACTTCTGCTGTTGCTA 59.756 40.000 0.00 0.00 40.48 3.49
4308 5390 4.039730 TCTTCTTCTACTTCTGCTGTTGCT 59.960 41.667 0.00 0.00 40.48 3.91
4309 5391 4.310769 TCTTCTTCTACTTCTGCTGTTGC 58.689 43.478 0.00 0.00 40.20 4.17
4310 5392 6.145371 GTCTTCTTCTTCTACTTCTGCTGTTG 59.855 42.308 0.00 0.00 0.00 3.33
4311 5393 6.041523 AGTCTTCTTCTTCTACTTCTGCTGTT 59.958 38.462 0.00 0.00 0.00 3.16
4312 5394 5.538433 AGTCTTCTTCTTCTACTTCTGCTGT 59.462 40.000 0.00 0.00 0.00 4.40
4313 5395 6.024552 AGTCTTCTTCTTCTACTTCTGCTG 57.975 41.667 0.00 0.00 0.00 4.41
4316 5398 6.644592 CCACAAGTCTTCTTCTTCTACTTCTG 59.355 42.308 0.00 0.00 0.00 3.02
4319 5401 6.487299 ACCACAAGTCTTCTTCTTCTACTT 57.513 37.500 0.00 0.00 0.00 2.24
4326 5408 3.244596 GGGCTTACCACAAGTCTTCTTCT 60.245 47.826 0.00 0.00 39.85 2.85
4328 5410 2.441750 TGGGCTTACCACAAGTCTTCTT 59.558 45.455 0.00 0.00 46.80 2.52
4329 5411 2.039084 CTGGGCTTACCACAAGTCTTCT 59.961 50.000 0.00 0.00 46.80 2.85
4330 5412 2.224548 ACTGGGCTTACCACAAGTCTTC 60.225 50.000 0.00 0.00 46.80 2.87
4331 5413 1.774856 ACTGGGCTTACCACAAGTCTT 59.225 47.619 0.00 0.00 46.80 3.01
4333 5415 1.071699 TCACTGGGCTTACCACAAGTC 59.928 52.381 0.00 0.00 46.80 3.01
4334 5416 1.136828 TCACTGGGCTTACCACAAGT 58.863 50.000 0.00 0.00 46.80 3.16
4335 5417 1.523758 GTCACTGGGCTTACCACAAG 58.476 55.000 0.00 0.00 46.80 3.16
4336 5418 0.250124 CGTCACTGGGCTTACCACAA 60.250 55.000 0.00 0.00 46.80 3.33
4337 5419 1.369692 CGTCACTGGGCTTACCACA 59.630 57.895 0.00 0.00 46.80 4.17
4338 5420 1.375523 CCGTCACTGGGCTTACCAC 60.376 63.158 0.00 0.00 46.80 4.16
4340 5422 1.375523 CACCGTCACTGGGCTTACC 60.376 63.158 0.00 0.00 40.81 2.85
4341 5423 2.033194 GCACCGTCACTGGGCTTAC 61.033 63.158 0.00 0.00 0.00 2.34
4342 5424 2.214216 AGCACCGTCACTGGGCTTA 61.214 57.895 0.00 0.00 33.47 3.09
4343 5425 3.560251 AGCACCGTCACTGGGCTT 61.560 61.111 0.00 0.00 33.47 4.35
4353 5435 1.272769 GGACTAGAAGAACAGCACCGT 59.727 52.381 0.00 0.00 0.00 4.83
4354 5436 1.404315 GGGACTAGAAGAACAGCACCG 60.404 57.143 0.00 0.00 0.00 4.94
4356 5438 2.300437 ACTGGGACTAGAAGAACAGCAC 59.700 50.000 0.00 0.00 0.00 4.40
4359 5441 5.011125 TCTGAAACTGGGACTAGAAGAACAG 59.989 44.000 0.00 0.11 0.00 3.16
4367 5449 5.215252 TGAAAGTCTGAAACTGGGACTAG 57.785 43.478 0.00 0.00 39.09 2.57
4372 5454 2.551459 CAGCTGAAAGTCTGAAACTGGG 59.449 50.000 8.42 0.00 39.43 4.45
4375 5457 2.615912 GCACAGCTGAAAGTCTGAAACT 59.384 45.455 23.35 0.00 39.43 2.66
4383 5465 1.133976 AGTCCTTGCACAGCTGAAAGT 60.134 47.619 23.35 0.00 35.30 2.66
4384 5466 1.602311 AGTCCTTGCACAGCTGAAAG 58.398 50.000 23.35 18.97 0.00 2.62
4385 5467 2.928801 TAGTCCTTGCACAGCTGAAA 57.071 45.000 23.35 10.67 0.00 2.69
4386 5468 2.104792 ACTTAGTCCTTGCACAGCTGAA 59.895 45.455 23.35 3.06 0.00 3.02
4387 5469 1.694150 ACTTAGTCCTTGCACAGCTGA 59.306 47.619 23.35 0.00 0.00 4.26
4388 5470 2.175878 ACTTAGTCCTTGCACAGCTG 57.824 50.000 13.48 13.48 0.00 4.24
4389 5471 2.104792 TGAACTTAGTCCTTGCACAGCT 59.895 45.455 0.00 0.00 0.00 4.24
4390 5472 2.481952 CTGAACTTAGTCCTTGCACAGC 59.518 50.000 0.00 0.00 0.00 4.40
4391 5473 3.733337 ACTGAACTTAGTCCTTGCACAG 58.267 45.455 0.00 0.00 0.00 3.66
4395 5477 4.691216 CCAACTACTGAACTTAGTCCTTGC 59.309 45.833 0.00 0.00 32.19 4.01
4402 5484 7.724305 TTAAACTGCCAACTACTGAACTTAG 57.276 36.000 0.00 0.00 0.00 2.18
4405 5487 6.534634 AGATTAAACTGCCAACTACTGAACT 58.465 36.000 0.00 0.00 0.00 3.01
4415 5497 9.625747 TCATCACATAATAGATTAAACTGCCAA 57.374 29.630 0.00 0.00 0.00 4.52
4448 5530 8.520351 GCAATGTACTGAACTTAATTAACCCTT 58.480 33.333 0.00 0.00 0.00 3.95
4450 5532 7.968405 CAGCAATGTACTGAACTTAATTAACCC 59.032 37.037 0.00 0.00 37.32 4.11
4451 5533 8.512138 ACAGCAATGTACTGAACTTAATTAACC 58.488 33.333 0.00 0.00 38.55 2.85
4452 5534 9.893305 AACAGCAATGTACTGAACTTAATTAAC 57.107 29.630 0.00 0.00 38.55 2.01
4457 5539 9.502091 AGATTAACAGCAATGTACTGAACTTAA 57.498 29.630 0.00 0.00 38.55 1.85
4464 5546 6.147656 TGACACAGATTAACAGCAATGTACTG 59.852 38.462 0.00 0.00 41.08 2.74
4467 5549 6.878389 TCATGACACAGATTAACAGCAATGTA 59.122 34.615 0.00 0.00 0.00 2.29
4469 5551 6.185852 TCATGACACAGATTAACAGCAATG 57.814 37.500 0.00 0.00 0.00 2.82
4470 5552 6.600427 TCATCATGACACAGATTAACAGCAAT 59.400 34.615 0.00 0.00 0.00 3.56
4486 5568 6.613755 TCATCAACACATCATCATCATGAC 57.386 37.500 0.00 0.00 42.05 3.06
4488 5570 6.413818 CGTTTCATCAACACATCATCATCATG 59.586 38.462 0.00 0.00 34.68 3.07
4489 5571 6.459161 CCGTTTCATCAACACATCATCATCAT 60.459 38.462 0.00 0.00 34.68 2.45
4493 5575 3.119884 GCCGTTTCATCAACACATCATCA 60.120 43.478 0.00 0.00 34.68 3.07
4497 5579 1.539388 TGGCCGTTTCATCAACACATC 59.461 47.619 0.00 0.00 34.68 3.06
4498 5580 1.541147 CTGGCCGTTTCATCAACACAT 59.459 47.619 0.00 0.00 34.68 3.21
4499 5581 0.950836 CTGGCCGTTTCATCAACACA 59.049 50.000 0.00 0.00 34.68 3.72
4500 5582 0.240945 CCTGGCCGTTTCATCAACAC 59.759 55.000 0.00 0.00 34.68 3.32
4501 5583 0.179004 ACCTGGCCGTTTCATCAACA 60.179 50.000 0.00 0.00 34.68 3.33
4502 5584 0.958822 AACCTGGCCGTTTCATCAAC 59.041 50.000 0.00 0.00 0.00 3.18
4513 5595 6.524101 TTCAATTGTAGATTAAACCTGGCC 57.476 37.500 5.13 0.00 0.00 5.36
4515 5597 9.981114 AGTTTTTCAATTGTAGATTAAACCTGG 57.019 29.630 5.13 0.00 0.00 4.45
4526 5608 9.743057 TTCATAACACCAGTTTTTCAATTGTAG 57.257 29.630 5.13 0.00 39.15 2.74
4534 5616 9.139174 CCATACATTTCATAACACCAGTTTTTC 57.861 33.333 0.00 0.00 39.15 2.29
4535 5617 8.646900 ACCATACATTTCATAACACCAGTTTTT 58.353 29.630 0.00 0.00 39.15 1.94
4539 5621 6.245408 ACACCATACATTTCATAACACCAGT 58.755 36.000 0.00 0.00 0.00 4.00
4540 5622 6.757897 ACACCATACATTTCATAACACCAG 57.242 37.500 0.00 0.00 0.00 4.00
4541 5623 6.717084 TGAACACCATACATTTCATAACACCA 59.283 34.615 0.00 0.00 0.00 4.17
4542 5624 7.151999 TGAACACCATACATTTCATAACACC 57.848 36.000 0.00 0.00 0.00 4.16
4572 5684 6.294787 GCTACTCTGCTACTGCTATAATGGAA 60.295 42.308 0.00 0.00 40.48 3.53
4573 5685 5.184096 GCTACTCTGCTACTGCTATAATGGA 59.816 44.000 0.00 0.00 40.48 3.41
4574 5686 5.047731 TGCTACTCTGCTACTGCTATAATGG 60.048 44.000 0.00 0.00 40.48 3.16
4575 5687 6.018589 TGCTACTCTGCTACTGCTATAATG 57.981 41.667 0.00 0.00 40.48 1.90
4576 5688 6.007076 TCTGCTACTCTGCTACTGCTATAAT 58.993 40.000 0.00 0.00 40.48 1.28
4577 5689 5.239744 GTCTGCTACTCTGCTACTGCTATAA 59.760 44.000 0.00 0.00 40.48 0.98
4578 5690 4.757657 GTCTGCTACTCTGCTACTGCTATA 59.242 45.833 0.00 0.00 40.48 1.31
4579 5691 3.568007 GTCTGCTACTCTGCTACTGCTAT 59.432 47.826 0.00 0.00 40.48 2.97
4580 5692 2.946329 GTCTGCTACTCTGCTACTGCTA 59.054 50.000 0.00 0.00 40.48 3.49
4597 5709 3.976793 ACAATGACTGCAACAAGTCTG 57.023 42.857 5.54 0.00 45.69 3.51
4599 5711 4.500477 GTGAAACAATGACTGCAACAAGTC 59.500 41.667 0.00 0.00 41.36 3.01
4600 5712 4.158394 AGTGAAACAATGACTGCAACAAGT 59.842 37.500 0.00 0.00 41.43 3.16
4601 5713 4.675510 AGTGAAACAATGACTGCAACAAG 58.324 39.130 0.00 0.00 41.43 3.16
4602 5714 4.717233 AGTGAAACAATGACTGCAACAA 57.283 36.364 0.00 0.00 41.43 2.83
4603 5715 4.082300 ACAAGTGAAACAATGACTGCAACA 60.082 37.500 0.00 0.00 41.43 3.33
4604 5716 4.266029 CACAAGTGAAACAATGACTGCAAC 59.734 41.667 0.00 0.00 41.43 4.17
4605 5717 4.422840 CACAAGTGAAACAATGACTGCAA 58.577 39.130 0.00 0.00 41.43 4.08
4606 5718 3.734597 GCACAAGTGAAACAATGACTGCA 60.735 43.478 4.04 0.00 41.43 4.41
4607 5719 2.791004 GCACAAGTGAAACAATGACTGC 59.209 45.455 4.04 0.00 41.43 4.40
4608 5720 4.031418 TGCACAAGTGAAACAATGACTG 57.969 40.909 4.04 0.00 41.43 3.51
4609 5721 4.717233 TTGCACAAGTGAAACAATGACT 57.283 36.364 4.04 0.00 41.43 3.41
4610 5722 4.268405 CCTTTGCACAAGTGAAACAATGAC 59.732 41.667 4.04 0.00 41.43 3.06
4611 5723 4.431809 CCTTTGCACAAGTGAAACAATGA 58.568 39.130 4.04 0.00 41.43 2.57
4613 5725 3.118665 AGCCTTTGCACAAGTGAAACAAT 60.119 39.130 4.04 0.00 39.03 2.71
4614 5726 2.233431 AGCCTTTGCACAAGTGAAACAA 59.767 40.909 4.04 0.00 39.03 2.83
4635 5803 3.708403 ATCTGCCATTGACTGAACTCA 57.292 42.857 0.00 0.00 0.00 3.41
4665 6934 7.148035 TGGTTGGTTCATCAACTAATCATCATG 60.148 37.037 3.02 0.00 38.72 3.07
4667 6936 6.244654 TGGTTGGTTCATCAACTAATCATCA 58.755 36.000 3.02 0.00 38.72 3.07
4668 6937 6.183360 CCTGGTTGGTTCATCAACTAATCATC 60.183 42.308 0.00 0.00 41.69 2.92
4689 6958 3.571401 GGCTCATCATGGATTAAACCTGG 59.429 47.826 3.17 0.00 0.00 4.45
4697 6966 0.471191 TCTGCGGCTCATCATGGATT 59.529 50.000 0.00 0.00 0.00 3.01
4698 6967 0.691332 ATCTGCGGCTCATCATGGAT 59.309 50.000 0.00 0.00 0.00 3.41
4711 6980 2.306341 ACTTCATCCAGACATCTGCG 57.694 50.000 3.18 0.00 42.47 5.18
4721 6990 9.747898 ACCAAACATTTACTATTACTTCATCCA 57.252 29.630 0.00 0.00 0.00 3.41
4725 6994 9.787435 ACAGACCAAACATTTACTATTACTTCA 57.213 29.630 0.00 0.00 0.00 3.02
4746 7015 3.350833 TCCCGGTCTTAGAAGTACAGAC 58.649 50.000 0.00 0.00 36.91 3.51
4757 7026 1.416401 GAGGCATCATTCCCGGTCTTA 59.584 52.381 0.00 0.00 0.00 2.10
4796 7065 3.351740 TCTCACCAGTGAACAAAAGCAA 58.648 40.909 1.58 0.00 39.39 3.91
4797 7066 2.997980 TCTCACCAGTGAACAAAAGCA 58.002 42.857 1.58 0.00 39.39 3.91
4798 7067 4.574599 ATTCTCACCAGTGAACAAAAGC 57.425 40.909 1.58 0.00 39.39 3.51
4808 7077 8.697507 AAGACAAGATTTTTATTCTCACCAGT 57.302 30.769 0.00 0.00 0.00 4.00
4831 7108 0.588252 CACGTGCCTCAACTCCAAAG 59.412 55.000 0.82 0.00 0.00 2.77
4847 7124 2.357517 ACAAAGAGAGGCGCCACG 60.358 61.111 31.54 11.81 0.00 4.94
4859 7136 4.191544 TGTGGAGACAAACTGAGACAAAG 58.808 43.478 0.00 0.00 46.06 2.77
4865 7142 4.887748 ACATACTGTGGAGACAAACTGAG 58.112 43.478 0.00 0.00 46.06 3.35
4867 7144 4.452455 GGAACATACTGTGGAGACAAACTG 59.548 45.833 0.00 0.00 46.06 3.16
4881 7159 2.569853 TCCAATCACGTGGGAACATACT 59.430 45.455 17.00 0.00 46.14 2.12
4882 7160 2.936498 CTCCAATCACGTGGGAACATAC 59.064 50.000 17.00 0.00 46.14 2.39
4883 7161 2.093181 CCTCCAATCACGTGGGAACATA 60.093 50.000 17.00 0.00 46.14 2.29
4884 7162 1.340017 CCTCCAATCACGTGGGAACAT 60.340 52.381 17.00 0.00 46.14 2.71
4893 7171 5.220854 CCATTAGTTTAAGCCTCCAATCACG 60.221 44.000 0.00 0.00 0.00 4.35
4901 7179 5.104652 TCCCTGTACCATTAGTTTAAGCCTC 60.105 44.000 0.00 0.00 0.00 4.70
4919 7197 2.039879 ACCGTAAGCAAGAATTCCCTGT 59.960 45.455 0.65 0.00 0.00 4.00
4937 7215 2.290367 TGCATGTTCAAACTTCAGACCG 59.710 45.455 0.00 0.00 0.00 4.79
4965 7251 6.591935 TGGACAGTTAACAGAAAGAAGACAT 58.408 36.000 8.61 0.00 0.00 3.06
4967 7253 6.706270 TCATGGACAGTTAACAGAAAGAAGAC 59.294 38.462 8.61 0.00 0.00 3.01
4996 7286 6.989169 GCAAGTAGTGGATATCATTTCTCTGT 59.011 38.462 4.83 0.00 0.00 3.41
5021 7314 3.744660 AGAACAGCTTTCAGTAACCAGG 58.255 45.455 10.08 0.00 0.00 4.45
5029 7322 4.084118 GCACTAGACAAGAACAGCTTTCAG 60.084 45.833 0.00 5.85 33.60 3.02
5034 7327 1.694150 TGGCACTAGACAAGAACAGCT 59.306 47.619 0.00 0.00 0.00 4.24
5035 7328 2.072298 CTGGCACTAGACAAGAACAGC 58.928 52.381 0.00 0.00 27.50 4.40
5036 7329 3.062763 CACTGGCACTAGACAAGAACAG 58.937 50.000 0.00 0.00 27.50 3.16
5137 7694 6.415206 AGTTAGTTCTTGCAGTAACCACTA 57.585 37.500 9.02 0.00 34.32 2.74
5153 7715 6.282199 ACAGATGACACGGATTAGTTAGTT 57.718 37.500 0.00 0.00 0.00 2.24
5164 7726 1.511850 TGCTTCAACAGATGACACGG 58.488 50.000 0.00 0.00 37.92 4.94
5166 7728 4.453478 TCTGATTGCTTCAACAGATGACAC 59.547 41.667 0.00 0.00 37.92 3.67
5221 7784 4.859304 TGAGCTGCAACATTCTGAATTT 57.141 36.364 1.02 0.00 0.00 1.82
5246 7809 2.415512 CGCCAGTAGTTTAGCCAAGTTC 59.584 50.000 0.00 0.00 0.00 3.01
5331 7894 4.978083 ATGGAGCAATCATCACTGAAAC 57.022 40.909 0.00 0.00 34.37 2.78


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

AutoCloner maintained by Alex Coulton.