Multiple sequence alignment - TraesCS2D01G357800

Loading Multiple Alignment...

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 TraesCS2D01G357800 chr2D 100.000 5320 0 0 1 5320 459823315 459828634 0.000000e+00 9825.0
1 TraesCS2D01G357800 chr2D 86.288 846 110 4 3 844 459813728 459814571 0.000000e+00 915.0
2 TraesCS2D01G357800 chr2D 88.176 296 31 3 2504 2797 354745961 354745668 3.050000e-92 350.0
3 TraesCS2D01G357800 chr2D 81.333 150 28 0 2868 3017 354745185 354745036 7.240000e-24 122.0
4 TraesCS2D01G357800 chr2B 93.715 4869 202 35 26 4824 541092408 541097242 0.000000e+00 7201.0
5 TraesCS2D01G357800 chr2B 87.838 296 32 3 2504 2797 421710615 421710322 1.420000e-90 344.0
6 TraesCS2D01G357800 chr2B 82.443 393 64 5 3 391 541018583 541018974 6.600000e-89 339.0
7 TraesCS2D01G357800 chr2B 85.149 303 43 2 1679 1980 728190403 728190102 5.170000e-80 309.0
8 TraesCS2D01G357800 chr2B 92.350 183 13 1 658 840 541085884 541086065 5.290000e-65 259.0
9 TraesCS2D01G357800 chr2B 82.000 150 27 0 2868 3017 421709677 421709528 1.560000e-25 128.0
10 TraesCS2D01G357800 chr2A 95.409 2723 83 11 2064 4751 602799678 602802393 0.000000e+00 4298.0
11 TraesCS2D01G357800 chr2A 92.933 1217 58 10 878 2079 602797213 602798416 0.000000e+00 1746.0
12 TraesCS2D01G357800 chr2A 98.401 563 9 0 1 563 602777328 602777890 0.000000e+00 990.0
13 TraesCS2D01G357800 chr2A 92.833 293 21 0 559 851 602796610 602796902 4.920000e-115 425.0
14 TraesCS2D01G357800 chr2A 87.838 296 32 3 2504 2797 474312995 474312702 1.420000e-90 344.0
15 TraesCS2D01G357800 chr2A 81.333 150 28 0 2868 3017 474311878 474311729 7.240000e-24 122.0
16 TraesCS2D01G357800 chr1B 86.084 309 43 0 1679 1987 486310346 486310654 3.070000e-87 333.0
17 TraesCS2D01G357800 chr5A 87.356 261 28 3 5048 5303 690433185 690433445 1.450000e-75 294.0
18 TraesCS2D01G357800 chr5A 85.965 57 5 3 4774 4827 505030604 505030660 2.070000e-04 58.4
19 TraesCS2D01G357800 chr5D 86.590 261 30 2 5048 5303 141427784 141428044 3.140000e-72 283.0
20 TraesCS2D01G357800 chr5D 77.465 213 41 5 605 812 552422603 552422813 2.600000e-23 121.0
21 TraesCS2D01G357800 chr5D 82.540 126 16 5 694 813 543503611 543503736 7.290000e-19 106.0
22 TraesCS2D01G357800 chr4A 87.200 250 26 4 5048 5292 49971330 49971578 4.060000e-71 279.0
23 TraesCS2D01G357800 chr4A 81.977 172 27 4 605 774 616897327 616897496 5.550000e-30 143.0
24 TraesCS2D01G357800 chr4A 78.488 172 29 5 602 769 625479846 625479679 7.290000e-19 106.0
25 TraesCS2D01G357800 chr6B 85.000 280 31 9 5048 5320 196149738 196149463 1.890000e-69 274.0
26 TraesCS2D01G357800 chr3D 84.838 277 36 4 5048 5320 404457694 404457968 1.890000e-69 274.0
27 TraesCS2D01G357800 chr4B 85.878 262 30 5 5048 5303 517851065 517850805 6.790000e-69 272.0
28 TraesCS2D01G357800 chr1A 85.824 261 32 3 5048 5303 263071622 263071882 6.790000e-69 272.0
29 TraesCS2D01G357800 chr6A 85.130 269 34 4 5043 5306 558903072 558902805 2.440000e-68 270.0
30 TraesCS2D01G357800 chr6A 93.878 49 3 0 4782 4830 597861308 597861260 2.050000e-09 75.0
31 TraesCS2D01G357800 chr3B 85.075 268 35 3 5048 5311 800213203 800213469 8.780000e-68 268.0
32 TraesCS2D01G357800 chr5B 80.184 217 39 4 600 813 635346451 635346236 5.510000e-35 159.0


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 TraesCS2D01G357800 chr2D 459823315 459828634 5319 False 9825.000000 9825 100.0000 1 5320 1 chr2D.!!$F2 5319
1 TraesCS2D01G357800 chr2D 459813728 459814571 843 False 915.000000 915 86.2880 3 844 1 chr2D.!!$F1 841
2 TraesCS2D01G357800 chr2D 354745036 354745961 925 True 236.000000 350 84.7545 2504 3017 2 chr2D.!!$R1 513
3 TraesCS2D01G357800 chr2B 541092408 541097242 4834 False 7201.000000 7201 93.7150 26 4824 1 chr2B.!!$F3 4798
4 TraesCS2D01G357800 chr2B 421709528 421710615 1087 True 236.000000 344 84.9190 2504 3017 2 chr2B.!!$R2 513
5 TraesCS2D01G357800 chr2A 602796610 602802393 5783 False 2156.333333 4298 93.7250 559 4751 3 chr2A.!!$F2 4192
6 TraesCS2D01G357800 chr2A 602777328 602777890 562 False 990.000000 990 98.4010 1 563 1 chr2A.!!$F1 562
7 TraesCS2D01G357800 chr2A 474311729 474312995 1266 True 233.000000 344 84.5855 2504 3017 2 chr2A.!!$R1 513

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
217 221 0.249489 GGTGCTCACAAGACGTCACT 60.249 55.000 19.5 0.63 0.00 3.41 F
1579 1898 0.111061 ATGCTTCTGTTGAGGGCACA 59.889 50.000 0.0 0.00 36.31 4.57 F
2199 3795 0.607489 AACATCCTGGCTGTGCAGTC 60.607 55.000 3.6 0.00 0.00 3.51 F
3530 5923 2.661566 CGTTGCGTCACCAGCTCAG 61.662 63.158 0.0 0.00 35.28 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 2166 1.067283 ACTGCTTCAGTGATCAGACGG 60.067 52.381 22.33 10.11 43.63 4.79 R
3530 5923 1.351017 TCACCACTCCCAAAGGATGAC 59.649 52.381 0.00 0.00 42.93 3.06 R
4174 6573 2.820973 GGCCTGCAAAGTGCCAAA 59.179 55.556 10.40 0.00 44.23 3.28 R
4832 7268 0.107165 GAGAAAAGGGGTGGGATCGG 60.107 60.000 0.00 0.00 0.00 4.18 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
217 221 0.249489 GGTGCTCACAAGACGTCACT 60.249 55.000 19.50 0.63 0.00 3.41
490 494 4.515944 CCGATAGTATTTGAGAGGACGAGT 59.484 45.833 0.00 0.00 0.00 4.18
553 557 2.208932 ACCGGGAAGAAGGGGGAA 59.791 61.111 6.32 0.00 0.00 3.97
574 578 1.133294 GTGGGGGACAAGGGAGAAAAA 60.133 52.381 0.00 0.00 0.00 1.94
575 579 1.792651 TGGGGGACAAGGGAGAAAAAT 59.207 47.619 0.00 0.00 0.00 1.82
592 596 4.530710 AAAATAGCACAGTACCGTCTCA 57.469 40.909 0.00 0.00 0.00 3.27
818 823 4.643387 GAGGCGTGGGTTGTGGCT 62.643 66.667 0.00 0.00 41.69 4.75
851 856 1.972872 CAACTGCTGGGTCTGAGTTT 58.027 50.000 0.00 0.00 0.00 2.66
852 857 2.810400 GCAACTGCTGGGTCTGAGTTTA 60.810 50.000 0.00 0.00 38.21 2.01
853 858 3.070018 CAACTGCTGGGTCTGAGTTTAG 58.930 50.000 0.00 0.00 0.00 1.85
855 860 0.324943 TGCTGGGTCTGAGTTTAGGC 59.675 55.000 0.00 0.00 0.00 3.93
856 861 0.393132 GCTGGGTCTGAGTTTAGGCC 60.393 60.000 0.00 0.00 41.82 5.19
858 863 0.984230 TGGGTCTGAGTTTAGGCCTG 59.016 55.000 17.99 0.00 42.20 4.85
859 864 0.393132 GGGTCTGAGTTTAGGCCTGC 60.393 60.000 17.99 5.53 42.20 4.85
860 865 0.393132 GGTCTGAGTTTAGGCCTGCC 60.393 60.000 17.99 0.00 39.40 4.85
876 882 2.740055 CCTGACAGGCTCACACGC 60.740 66.667 8.99 0.00 0.00 5.34
891 1187 2.032528 CGCTTGGGCTCAACCAGA 59.967 61.111 0.00 0.00 42.47 3.86
902 1198 2.047274 AACCAGATCGGCGTGTGG 60.047 61.111 18.87 18.87 39.03 4.17
1275 1580 3.263503 TTGCTACGACGCGCTCAGT 62.264 57.895 5.73 3.54 0.00 3.41
1414 1719 5.010282 ACCATACTTCCAATTCCTGAACAC 58.990 41.667 0.00 0.00 0.00 3.32
1415 1720 4.399303 CCATACTTCCAATTCCTGAACACC 59.601 45.833 0.00 0.00 0.00 4.16
1416 1721 2.876581 ACTTCCAATTCCTGAACACCC 58.123 47.619 0.00 0.00 0.00 4.61
1417 1722 1.812571 CTTCCAATTCCTGAACACCCG 59.187 52.381 0.00 0.00 0.00 5.28
1418 1723 0.608035 TCCAATTCCTGAACACCCGC 60.608 55.000 0.00 0.00 0.00 6.13
1472 1783 9.639601 TTCTGTAGATTGTGAGTGTTATACTTG 57.360 33.333 0.00 0.00 40.53 3.16
1482 1793 7.666804 TGTGAGTGTTATACTTGTACTACCTCA 59.333 37.037 0.00 0.00 40.53 3.86
1493 1811 8.410673 ACTTGTACTACCTCATATACTCCATG 57.589 38.462 0.00 0.00 0.00 3.66
1497 1815 7.783119 TGTACTACCTCATATACTCCATGTGTT 59.217 37.037 0.00 0.00 0.00 3.32
1579 1898 0.111061 ATGCTTCTGTTGAGGGCACA 59.889 50.000 0.00 0.00 36.31 4.57
1608 1927 4.114058 AGTGGCATTGCACATATCAAAC 57.886 40.909 11.39 0.00 0.00 2.93
1611 1930 3.451540 TGGCATTGCACATATCAAACCAT 59.548 39.130 11.39 0.00 32.36 3.55
1737 2056 9.658799 TGTAAAAGGAGATCTACAAGATTTCAG 57.341 33.333 7.93 0.00 37.52 3.02
1847 2166 3.141398 TGGCGAAATGATAGATCAAGGC 58.859 45.455 0.00 2.62 40.69 4.35
1851 2170 3.430218 CGAAATGATAGATCAAGGCCGTC 59.570 47.826 0.00 0.00 40.69 4.79
1853 2172 3.674528 ATGATAGATCAAGGCCGTCTG 57.325 47.619 11.62 5.01 40.69 3.51
1949 2268 7.108847 AGAGGACAGTGAAAGGATTTATCAAG 58.891 38.462 0.00 0.00 39.27 3.02
1987 2306 9.784531 TGGAATTATTCTTGAAGATCAGGTATC 57.215 33.333 4.87 0.00 34.52 2.24
2001 2320 7.881142 AGATCAGGTATCTTGATACTCTTTCG 58.119 38.462 17.10 5.39 42.62 3.46
2051 2370 6.183360 CCAGCTGTTTTGCTTCTATAACCTAC 60.183 42.308 13.81 0.00 41.98 3.18
2197 3793 1.825090 TAAACATCCTGGCTGTGCAG 58.175 50.000 3.60 0.00 0.00 4.41
2199 3795 0.607489 AACATCCTGGCTGTGCAGTC 60.607 55.000 3.60 0.00 0.00 3.51
2289 3885 3.327172 CCCTGGCTGACATCTCATATTCT 59.673 47.826 0.00 0.00 0.00 2.40
3224 5617 6.372103 ACTCACATATAGGCGTATAGAGTCAC 59.628 42.308 15.63 0.00 29.73 3.67
3243 5636 7.502895 AGAGTCACGTATGTACCATCTTCTATT 59.497 37.037 0.00 0.00 0.00 1.73
3244 5637 7.649973 AGTCACGTATGTACCATCTTCTATTC 58.350 38.462 0.00 0.00 0.00 1.75
3276 5669 7.620880 ACTGGTAGTTATTGTATGCTTCTTCA 58.379 34.615 0.00 0.00 0.00 3.02
3530 5923 2.661566 CGTTGCGTCACCAGCTCAG 61.662 63.158 0.00 0.00 35.28 3.35
4174 6573 9.941325 GTATGTTTCATTCATAGATCATCTCCT 57.059 33.333 0.00 0.00 0.00 3.69
4202 6601 4.666253 GCAGGCCTGGCTGGAACA 62.666 66.667 33.46 0.00 38.35 3.18
4226 6625 2.806945 TCATGGAAAGGCTTCGGAAT 57.193 45.000 0.00 0.00 31.77 3.01
4229 6628 0.251121 TGGAAAGGCTTCGGAATGCA 60.251 50.000 0.00 0.00 31.77 3.96
4362 6761 1.898472 CCCAGCATCCGATACTCAGAT 59.102 52.381 0.00 0.00 0.00 2.90
4366 6765 2.824936 AGCATCCGATACTCAGATGAGG 59.175 50.000 14.09 0.00 46.13 3.86
4370 6769 1.889829 CCGATACTCAGATGAGGGTCC 59.110 57.143 14.09 0.49 46.13 4.46
4384 6784 1.421646 AGGGTCCTGTTCCTTTGAGTG 59.578 52.381 0.00 0.00 0.00 3.51
4443 6851 1.741706 CTTGCTGCCTACATCCAGTTG 59.258 52.381 0.00 0.00 0.00 3.16
4450 6858 4.917385 TGCCTACATCCAGTTGTGTAAAT 58.083 39.130 0.00 0.00 31.05 1.40
4596 7006 2.780714 AGTACGACACTGAGCACTAGT 58.219 47.619 0.00 0.00 35.62 2.57
4597 7007 3.935315 AGTACGACACTGAGCACTAGTA 58.065 45.455 0.00 0.00 35.62 1.82
4598 7008 3.933955 AGTACGACACTGAGCACTAGTAG 59.066 47.826 0.00 0.00 35.62 2.57
4696 7132 2.583520 GCAGTGGCTGAGAGGAGG 59.416 66.667 0.00 0.00 36.96 4.30
4697 7133 1.986757 GCAGTGGCTGAGAGGAGGA 60.987 63.158 0.00 0.00 36.96 3.71
4698 7134 1.958902 GCAGTGGCTGAGAGGAGGAG 61.959 65.000 0.00 0.00 36.96 3.69
4699 7135 1.001503 AGTGGCTGAGAGGAGGAGG 59.998 63.158 0.00 0.00 0.00 4.30
4700 7136 1.000993 GTGGCTGAGAGGAGGAGGA 59.999 63.158 0.00 0.00 0.00 3.71
4701 7137 1.042559 GTGGCTGAGAGGAGGAGGAG 61.043 65.000 0.00 0.00 0.00 3.69
4742 7178 3.625649 AGAAGAGAAATGGAGGACAGC 57.374 47.619 0.00 0.00 0.00 4.40
4779 7215 1.151810 TGGGCCACCTCTTCCTTCT 60.152 57.895 0.00 0.00 37.76 2.85
4836 7272 3.717294 GGCACCACCTCCACCGAT 61.717 66.667 0.00 0.00 34.51 4.18
4837 7273 2.125106 GCACCACCTCCACCGATC 60.125 66.667 0.00 0.00 0.00 3.69
4838 7274 2.584608 CACCACCTCCACCGATCC 59.415 66.667 0.00 0.00 0.00 3.36
4839 7275 2.687566 ACCACCTCCACCGATCCC 60.688 66.667 0.00 0.00 0.00 3.85
4840 7276 2.687200 CCACCTCCACCGATCCCA 60.687 66.667 0.00 0.00 0.00 4.37
4841 7277 2.584608 CACCTCCACCGATCCCAC 59.415 66.667 0.00 0.00 0.00 4.61
4842 7278 2.687566 ACCTCCACCGATCCCACC 60.688 66.667 0.00 0.00 0.00 4.61
4843 7279 3.480133 CCTCCACCGATCCCACCC 61.480 72.222 0.00 0.00 0.00 4.61
4844 7280 3.480133 CTCCACCGATCCCACCCC 61.480 72.222 0.00 0.00 0.00 4.95
4845 7281 4.019513 TCCACCGATCCCACCCCT 62.020 66.667 0.00 0.00 0.00 4.79
4846 7282 3.015145 CCACCGATCCCACCCCTT 61.015 66.667 0.00 0.00 0.00 3.95
4847 7283 2.612493 CCACCGATCCCACCCCTTT 61.612 63.158 0.00 0.00 0.00 3.11
4848 7284 1.382629 CACCGATCCCACCCCTTTT 59.617 57.895 0.00 0.00 0.00 2.27
4849 7285 0.679960 CACCGATCCCACCCCTTTTC 60.680 60.000 0.00 0.00 0.00 2.29
4850 7286 0.845102 ACCGATCCCACCCCTTTTCT 60.845 55.000 0.00 0.00 0.00 2.52
4851 7287 0.107165 CCGATCCCACCCCTTTTCTC 60.107 60.000 0.00 0.00 0.00 2.87
4852 7288 0.462047 CGATCCCACCCCTTTTCTCG 60.462 60.000 0.00 0.00 0.00 4.04
4853 7289 0.748367 GATCCCACCCCTTTTCTCGC 60.748 60.000 0.00 0.00 0.00 5.03
4854 7290 1.208165 ATCCCACCCCTTTTCTCGCT 61.208 55.000 0.00 0.00 0.00 4.93
4855 7291 1.074951 CCCACCCCTTTTCTCGCTT 59.925 57.895 0.00 0.00 0.00 4.68
4856 7292 1.244019 CCCACCCCTTTTCTCGCTTG 61.244 60.000 0.00 0.00 0.00 4.01
4857 7293 0.537371 CCACCCCTTTTCTCGCTTGT 60.537 55.000 0.00 0.00 0.00 3.16
4858 7294 1.318576 CACCCCTTTTCTCGCTTGTT 58.681 50.000 0.00 0.00 0.00 2.83
4859 7295 1.681264 CACCCCTTTTCTCGCTTGTTT 59.319 47.619 0.00 0.00 0.00 2.83
4860 7296 2.100749 CACCCCTTTTCTCGCTTGTTTT 59.899 45.455 0.00 0.00 0.00 2.43
4861 7297 2.361119 ACCCCTTTTCTCGCTTGTTTTC 59.639 45.455 0.00 0.00 0.00 2.29
4862 7298 2.288213 CCCCTTTTCTCGCTTGTTTTCC 60.288 50.000 0.00 0.00 0.00 3.13
4863 7299 2.288213 CCCTTTTCTCGCTTGTTTTCCC 60.288 50.000 0.00 0.00 0.00 3.97
4864 7300 2.604614 CCTTTTCTCGCTTGTTTTCCCG 60.605 50.000 0.00 0.00 0.00 5.14
4865 7301 1.956297 TTTCTCGCTTGTTTTCCCGA 58.044 45.000 0.00 0.00 0.00 5.14
4866 7302 2.178912 TTCTCGCTTGTTTTCCCGAT 57.821 45.000 0.00 0.00 0.00 4.18
4867 7303 1.722011 TCTCGCTTGTTTTCCCGATC 58.278 50.000 0.00 0.00 0.00 3.69
4868 7304 0.370273 CTCGCTTGTTTTCCCGATCG 59.630 55.000 8.51 8.51 0.00 3.69
4869 7305 0.320073 TCGCTTGTTTTCCCGATCGT 60.320 50.000 15.09 0.00 0.00 3.73
4870 7306 1.067706 TCGCTTGTTTTCCCGATCGTA 60.068 47.619 15.09 0.00 0.00 3.43
4871 7307 1.727880 CGCTTGTTTTCCCGATCGTAA 59.272 47.619 15.09 5.18 0.00 3.18
4872 7308 2.473376 CGCTTGTTTTCCCGATCGTAAC 60.473 50.000 15.09 12.38 0.00 2.50
4873 7309 2.481185 GCTTGTTTTCCCGATCGTAACA 59.519 45.455 15.09 14.62 0.00 2.41
4874 7310 3.058777 GCTTGTTTTCCCGATCGTAACAA 60.059 43.478 22.24 22.24 36.63 2.83
4875 7311 4.555116 GCTTGTTTTCCCGATCGTAACAAA 60.555 41.667 23.06 12.56 37.99 2.83
4876 7312 5.496133 TTGTTTTCCCGATCGTAACAAAA 57.504 34.783 21.82 14.88 36.20 2.44
4877 7313 5.496133 TGTTTTCCCGATCGTAACAAAAA 57.504 34.783 15.09 9.67 0.00 1.94
4896 7332 1.510844 AAAAATCCGCCATCCACGC 59.489 52.632 0.00 0.00 0.00 5.34
4897 7333 1.247419 AAAAATCCGCCATCCACGCA 61.247 50.000 0.00 0.00 0.00 5.24
4898 7334 1.933115 AAAATCCGCCATCCACGCAC 61.933 55.000 0.00 0.00 0.00 5.34
4903 7339 4.541482 GCCATCCACGCACGCATG 62.541 66.667 0.00 0.00 0.00 4.06
4904 7340 3.126879 CCATCCACGCACGCATGT 61.127 61.111 0.00 0.00 0.00 3.21
4905 7341 2.400798 CATCCACGCACGCATGTC 59.599 61.111 0.00 0.00 0.00 3.06
4906 7342 2.102438 CATCCACGCACGCATGTCT 61.102 57.895 0.00 0.00 0.00 3.41
4907 7343 1.811266 ATCCACGCACGCATGTCTC 60.811 57.895 0.00 0.00 0.00 3.36
4908 7344 2.230994 ATCCACGCACGCATGTCTCT 62.231 55.000 0.00 0.00 0.00 3.10
4909 7345 2.029288 CCACGCACGCATGTCTCTT 61.029 57.895 0.00 0.00 0.00 2.85
4910 7346 1.417592 CACGCACGCATGTCTCTTC 59.582 57.895 0.00 0.00 0.00 2.87
4911 7347 1.738099 ACGCACGCATGTCTCTTCC 60.738 57.895 0.00 0.00 0.00 3.46
4912 7348 1.446792 CGCACGCATGTCTCTTCCT 60.447 57.895 0.00 0.00 0.00 3.36
4913 7349 1.690283 CGCACGCATGTCTCTTCCTG 61.690 60.000 0.00 0.00 0.00 3.86
4914 7350 1.975363 GCACGCATGTCTCTTCCTGC 61.975 60.000 0.00 0.00 0.00 4.85
4916 7352 3.805267 GCATGTCTCTTCCTGCGG 58.195 61.111 0.00 0.00 0.00 5.69
4917 7353 2.467826 GCATGTCTCTTCCTGCGGC 61.468 63.158 0.00 0.00 0.00 6.53
4918 7354 1.817099 CATGTCTCTTCCTGCGGCC 60.817 63.158 0.00 0.00 0.00 6.13
4919 7355 3.036429 ATGTCTCTTCCTGCGGCCC 62.036 63.158 0.00 0.00 0.00 5.80
4920 7356 4.475135 GTCTCTTCCTGCGGCCCC 62.475 72.222 0.00 0.00 0.00 5.80
4944 7380 2.436646 CCGCTCCACCGAAAGCAT 60.437 61.111 0.00 0.00 38.45 3.79
4945 7381 1.153449 CCGCTCCACCGAAAGCATA 60.153 57.895 0.00 0.00 38.45 3.14
4946 7382 1.154205 CCGCTCCACCGAAAGCATAG 61.154 60.000 0.00 0.00 38.45 2.23
4947 7383 1.154205 CGCTCCACCGAAAGCATAGG 61.154 60.000 0.00 0.00 38.45 2.57
4948 7384 1.440145 GCTCCACCGAAAGCATAGGC 61.440 60.000 0.00 0.00 38.42 3.93
4949 7385 0.107703 CTCCACCGAAAGCATAGGCA 60.108 55.000 0.67 0.00 44.61 4.75
4950 7386 0.392461 TCCACCGAAAGCATAGGCAC 60.392 55.000 0.67 0.00 44.61 5.01
4951 7387 1.705337 CCACCGAAAGCATAGGCACG 61.705 60.000 0.67 4.42 44.61 5.34
4952 7388 1.019278 CACCGAAAGCATAGGCACGT 61.019 55.000 0.67 0.00 44.61 4.49
4953 7389 0.533491 ACCGAAAGCATAGGCACGTA 59.467 50.000 0.67 0.00 44.61 3.57
4954 7390 0.928229 CCGAAAGCATAGGCACGTAC 59.072 55.000 0.67 0.00 44.61 3.67
4955 7391 0.570734 CGAAAGCATAGGCACGTACG 59.429 55.000 15.01 15.01 44.61 3.67
4956 7392 0.300789 GAAAGCATAGGCACGTACGC 59.699 55.000 16.72 0.00 44.61 4.42
4963 7399 4.514569 GGCACGTACGCCGCATTG 62.515 66.667 25.75 13.35 43.52 2.82
4976 7412 1.493311 GCATTGCGATACTAGCGGC 59.507 57.895 0.00 0.00 37.44 6.53
4977 7413 1.901650 GCATTGCGATACTAGCGGCC 61.902 60.000 0.00 0.00 37.44 6.13
4978 7414 1.372997 ATTGCGATACTAGCGGCCG 60.373 57.895 24.05 24.05 37.44 6.13
4979 7415 2.083835 ATTGCGATACTAGCGGCCGT 62.084 55.000 28.70 16.08 37.44 5.68
4980 7416 1.446516 TTGCGATACTAGCGGCCGTA 61.447 55.000 28.70 16.36 37.44 4.02
4981 7417 1.441682 GCGATACTAGCGGCCGTAC 60.442 63.158 28.70 11.34 0.00 3.67
4982 7418 1.849976 GCGATACTAGCGGCCGTACT 61.850 60.000 28.70 18.78 0.00 2.73
4983 7419 0.110328 CGATACTAGCGGCCGTACTG 60.110 60.000 28.70 16.61 0.00 2.74
4984 7420 0.240411 GATACTAGCGGCCGTACTGG 59.760 60.000 28.70 20.01 42.50 4.00
4985 7421 0.179009 ATACTAGCGGCCGTACTGGA 60.179 55.000 28.70 11.94 42.00 3.86
4986 7422 0.816825 TACTAGCGGCCGTACTGGAG 60.817 60.000 28.70 16.36 42.00 3.86
4987 7423 1.822613 CTAGCGGCCGTACTGGAGA 60.823 63.158 28.70 0.00 42.00 3.71
4988 7424 2.061182 CTAGCGGCCGTACTGGAGAC 62.061 65.000 28.70 6.22 42.00 3.36
4989 7425 4.509737 GCGGCCGTACTGGAGACC 62.510 72.222 28.70 0.93 42.00 3.85
4990 7426 4.189188 CGGCCGTACTGGAGACCG 62.189 72.222 19.50 7.22 42.00 4.79
4991 7427 4.509737 GGCCGTACTGGAGACCGC 62.510 72.222 7.77 0.00 42.00 5.68
4992 7428 3.755628 GCCGTACTGGAGACCGCA 61.756 66.667 7.77 0.00 42.00 5.69
4993 7429 2.490217 CCGTACTGGAGACCGCAG 59.510 66.667 0.00 0.00 42.00 5.18
4994 7430 2.202623 CGTACTGGAGACCGCAGC 60.203 66.667 0.00 0.00 0.00 5.25
4995 7431 2.202623 GTACTGGAGACCGCAGCG 60.203 66.667 8.18 8.18 0.00 5.18
4996 7432 2.360726 TACTGGAGACCGCAGCGA 60.361 61.111 18.75 0.00 0.00 4.93
4997 7433 2.407428 TACTGGAGACCGCAGCGAG 61.407 63.158 18.75 9.19 0.00 5.03
4998 7434 2.814913 TACTGGAGACCGCAGCGAGA 62.815 60.000 18.75 0.00 0.00 4.04
4999 7435 3.691744 CTGGAGACCGCAGCGAGAC 62.692 68.421 18.75 7.00 0.00 3.36
5000 7436 4.500116 GGAGACCGCAGCGAGACC 62.500 72.222 18.75 10.28 0.00 3.85
5001 7437 3.749064 GAGACCGCAGCGAGACCA 61.749 66.667 18.75 0.00 0.00 4.02
5002 7438 3.973267 GAGACCGCAGCGAGACCAC 62.973 68.421 18.75 0.65 0.00 4.16
5010 7446 4.760047 GCGAGACCACCACGCCAT 62.760 66.667 0.00 0.00 45.35 4.40
5011 7447 2.509336 CGAGACCACCACGCCATC 60.509 66.667 0.00 0.00 0.00 3.51
5012 7448 2.509336 GAGACCACCACGCCATCG 60.509 66.667 0.00 0.00 42.43 3.84
5013 7449 4.760047 AGACCACCACGCCATCGC 62.760 66.667 0.00 0.00 39.84 4.58
5014 7450 4.760047 GACCACCACGCCATCGCT 62.760 66.667 0.00 0.00 39.84 4.93
5015 7451 4.760047 ACCACCACGCCATCGCTC 62.760 66.667 0.00 0.00 39.84 5.03
5017 7453 4.758251 CACCACGCCATCGCTCCA 62.758 66.667 0.00 0.00 39.84 3.86
5018 7454 4.457496 ACCACGCCATCGCTCCAG 62.457 66.667 0.00 0.00 39.84 3.86
5019 7455 4.147449 CCACGCCATCGCTCCAGA 62.147 66.667 0.00 0.00 39.84 3.86
5020 7456 2.887568 CACGCCATCGCTCCAGAC 60.888 66.667 0.00 0.00 39.84 3.51
5021 7457 4.498520 ACGCCATCGCTCCAGACG 62.499 66.667 0.00 0.00 39.84 4.18
5022 7458 4.193334 CGCCATCGCTCCAGACGA 62.193 66.667 0.00 0.00 44.75 4.20
5023 7459 2.583593 GCCATCGCTCCAGACGAC 60.584 66.667 0.00 0.00 43.23 4.34
5024 7460 2.278206 CCATCGCTCCAGACGACG 60.278 66.667 0.00 0.00 43.23 5.12
5025 7461 2.278206 CATCGCTCCAGACGACGG 60.278 66.667 0.00 0.00 43.23 4.79
5026 7462 2.750637 ATCGCTCCAGACGACGGT 60.751 61.111 0.00 0.00 43.23 4.83
5027 7463 3.052620 ATCGCTCCAGACGACGGTG 62.053 63.158 0.00 0.00 43.23 4.94
5029 7465 4.357947 GCTCCAGACGACGGTGCA 62.358 66.667 13.92 0.00 41.59 4.57
5030 7466 2.430921 CTCCAGACGACGGTGCAC 60.431 66.667 8.80 8.80 0.00 4.57
5045 7481 4.778415 CACGACGTCCCGCTGGAG 62.778 72.222 10.58 0.00 42.85 3.86
5048 7484 3.138798 GACGTCCCGCTGGAGCTA 61.139 66.667 3.51 0.00 42.85 3.32
5049 7485 3.412879 GACGTCCCGCTGGAGCTAC 62.413 68.421 3.51 0.00 42.85 3.58
5050 7486 3.141488 CGTCCCGCTGGAGCTACT 61.141 66.667 0.00 0.00 42.85 2.57
5051 7487 2.809010 GTCCCGCTGGAGCTACTC 59.191 66.667 0.00 0.00 42.85 2.59
5059 7495 2.279408 GGAGCTACTCCCTCCGGT 59.721 66.667 0.00 0.00 44.36 5.28
5060 7496 1.829096 GGAGCTACTCCCTCCGGTC 60.829 68.421 0.00 0.00 44.36 4.79
5061 7497 1.076923 GAGCTACTCCCTCCGGTCA 60.077 63.158 0.00 0.00 0.00 4.02
5062 7498 0.468400 GAGCTACTCCCTCCGGTCAT 60.468 60.000 0.00 0.00 0.00 3.06
5063 7499 0.032017 AGCTACTCCCTCCGGTCATT 60.032 55.000 0.00 0.00 0.00 2.57
5064 7500 0.831307 GCTACTCCCTCCGGTCATTT 59.169 55.000 0.00 0.00 0.00 2.32
5065 7501 1.209747 GCTACTCCCTCCGGTCATTTT 59.790 52.381 0.00 0.00 0.00 1.82
5066 7502 2.355818 GCTACTCCCTCCGGTCATTTTT 60.356 50.000 0.00 0.00 0.00 1.94
5067 7503 3.118519 GCTACTCCCTCCGGTCATTTTTA 60.119 47.826 0.00 0.00 0.00 1.52
5068 7504 4.624604 GCTACTCCCTCCGGTCATTTTTAA 60.625 45.833 0.00 0.00 0.00 1.52
5069 7505 4.586306 ACTCCCTCCGGTCATTTTTAAT 57.414 40.909 0.00 0.00 0.00 1.40
5070 7506 4.930696 ACTCCCTCCGGTCATTTTTAATT 58.069 39.130 0.00 0.00 0.00 1.40
5071 7507 4.948004 ACTCCCTCCGGTCATTTTTAATTC 59.052 41.667 0.00 0.00 0.00 2.17
5072 7508 3.942748 TCCCTCCGGTCATTTTTAATTCG 59.057 43.478 0.00 0.00 0.00 3.34
5073 7509 3.942748 CCCTCCGGTCATTTTTAATTCGA 59.057 43.478 0.00 0.00 0.00 3.71
5074 7510 4.396790 CCCTCCGGTCATTTTTAATTCGAA 59.603 41.667 0.00 0.00 0.00 3.71
5075 7511 5.067283 CCCTCCGGTCATTTTTAATTCGAAT 59.933 40.000 4.39 4.39 0.00 3.34
5076 7512 6.261381 CCCTCCGGTCATTTTTAATTCGAATA 59.739 38.462 11.83 0.00 0.00 1.75
5077 7513 7.040686 CCCTCCGGTCATTTTTAATTCGAATAT 60.041 37.037 11.83 4.70 0.00 1.28
5078 7514 8.995220 CCTCCGGTCATTTTTAATTCGAATATA 58.005 33.333 11.83 3.73 0.00 0.86
5174 7610 7.719778 TCAATATCAGTAGATGTGTCATTGC 57.280 36.000 0.00 0.00 35.67 3.56
5175 7611 7.503549 TCAATATCAGTAGATGTGTCATTGCT 58.496 34.615 0.00 0.00 35.67 3.91
5176 7612 7.989170 TCAATATCAGTAGATGTGTCATTGCTT 59.011 33.333 0.00 0.00 35.67 3.91
5177 7613 9.264719 CAATATCAGTAGATGTGTCATTGCTTA 57.735 33.333 0.00 0.00 35.67 3.09
5178 7614 9.836864 AATATCAGTAGATGTGTCATTGCTTAA 57.163 29.630 0.00 0.00 35.67 1.85
5179 7615 9.836864 ATATCAGTAGATGTGTCATTGCTTAAA 57.163 29.630 0.00 0.00 35.67 1.52
5180 7616 8.743085 ATCAGTAGATGTGTCATTGCTTAAAT 57.257 30.769 0.00 0.00 31.91 1.40
5181 7617 8.565896 TCAGTAGATGTGTCATTGCTTAAATT 57.434 30.769 0.00 0.00 0.00 1.82
5182 7618 9.013229 TCAGTAGATGTGTCATTGCTTAAATTT 57.987 29.630 0.00 0.00 0.00 1.82
5183 7619 9.630098 CAGTAGATGTGTCATTGCTTAAATTTT 57.370 29.630 0.00 0.00 0.00 1.82
5184 7620 9.846248 AGTAGATGTGTCATTGCTTAAATTTTC 57.154 29.630 0.00 0.00 0.00 2.29
5185 7621 9.624697 GTAGATGTGTCATTGCTTAAATTTTCA 57.375 29.630 0.00 0.00 0.00 2.69
5206 7642 9.853555 TTTTCATATTGTACAACTTTAGCATGG 57.146 29.630 11.22 0.00 0.00 3.66
5207 7643 8.574251 TTCATATTGTACAACTTTAGCATGGT 57.426 30.769 11.22 1.62 0.00 3.55
5208 7644 9.674068 TTCATATTGTACAACTTTAGCATGGTA 57.326 29.630 11.22 0.00 0.00 3.25
5209 7645 9.325198 TCATATTGTACAACTTTAGCATGGTAG 57.675 33.333 11.22 0.00 0.00 3.18
5210 7646 9.325198 CATATTGTACAACTTTAGCATGGTAGA 57.675 33.333 11.22 0.00 0.00 2.59
5212 7648 7.609760 TTGTACAACTTTAGCATGGTAGATG 57.390 36.000 3.59 4.27 0.00 2.90
5213 7649 6.707290 TGTACAACTTTAGCATGGTAGATGT 58.293 36.000 13.12 13.12 0.00 3.06
5214 7650 7.165485 TGTACAACTTTAGCATGGTAGATGTT 58.835 34.615 13.62 12.24 0.00 2.71
5215 7651 8.315482 TGTACAACTTTAGCATGGTAGATGTTA 58.685 33.333 13.62 4.25 0.00 2.41
5216 7652 9.158233 GTACAACTTTAGCATGGTAGATGTTAA 57.842 33.333 13.62 1.25 0.00 2.01
5217 7653 8.807948 ACAACTTTAGCATGGTAGATGTTAAT 57.192 30.769 4.57 2.23 0.00 1.40
5218 7654 9.899661 ACAACTTTAGCATGGTAGATGTTAATA 57.100 29.630 4.57 0.00 0.00 0.98
5308 7744 7.860918 AAAAAGACGGAAGGGAGTAATATTC 57.139 36.000 0.00 0.00 0.00 1.75
5309 7745 6.555463 AAAGACGGAAGGGAGTAATATTCA 57.445 37.500 0.00 0.00 0.00 2.57
5310 7746 6.749036 AAGACGGAAGGGAGTAATATTCAT 57.251 37.500 0.00 0.00 0.00 2.57
5311 7747 6.102897 AGACGGAAGGGAGTAATATTCATG 57.897 41.667 0.00 0.00 0.00 3.07
5312 7748 4.642429 ACGGAAGGGAGTAATATTCATGC 58.358 43.478 0.00 0.00 0.00 4.06
5313 7749 3.679980 CGGAAGGGAGTAATATTCATGCG 59.320 47.826 0.00 0.00 0.00 4.73
5314 7750 3.437049 GGAAGGGAGTAATATTCATGCGC 59.563 47.826 0.00 0.00 0.00 6.09
5315 7751 3.059352 AGGGAGTAATATTCATGCGCC 57.941 47.619 4.18 0.00 0.00 6.53
5316 7752 2.639839 AGGGAGTAATATTCATGCGCCT 59.360 45.455 4.18 0.00 0.00 5.52
5317 7753 3.073062 AGGGAGTAATATTCATGCGCCTT 59.927 43.478 4.18 0.00 0.00 4.35
5318 7754 3.821033 GGGAGTAATATTCATGCGCCTTT 59.179 43.478 4.18 0.00 0.00 3.11
5319 7755 4.083271 GGGAGTAATATTCATGCGCCTTTC 60.083 45.833 4.18 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
217 221 4.980592 TCCTGTGCCTGGAGCCCA 62.981 66.667 0.00 0.00 42.71 5.36
490 494 4.193334 CTCGACTCGCGCCATGGA 62.193 66.667 18.40 0.00 40.61 3.41
535 539 2.198304 CTTCCCCCTTCTTCCCGGTG 62.198 65.000 0.00 0.00 0.00 4.94
553 557 0.402861 TTTCTCCCTTGTCCCCCACT 60.403 55.000 0.00 0.00 0.00 4.00
574 578 2.290916 CGATGAGACGGTACTGTGCTAT 59.709 50.000 13.27 3.08 0.00 2.97
575 579 1.669265 CGATGAGACGGTACTGTGCTA 59.331 52.381 13.27 0.00 0.00 3.49
622 626 4.351938 CGCGAGTTCCACCGGACA 62.352 66.667 9.46 0.00 0.00 4.02
818 823 1.819305 GCAGTTGCTCCTTCCTTTCCA 60.819 52.381 0.00 0.00 38.21 3.53
847 852 0.326264 CTGTCAGGCAGGCCTAAACT 59.674 55.000 13.37 0.00 46.28 2.66
859 864 2.721971 AAGCGTGTGAGCCTGTCAGG 62.722 60.000 15.15 15.15 35.13 3.86
860 865 1.301244 AAGCGTGTGAGCCTGTCAG 60.301 57.895 0.00 0.00 35.13 3.51
862 867 2.320587 CCAAGCGTGTGAGCCTGTC 61.321 63.158 0.00 0.00 38.01 3.51
876 882 0.745845 CCGATCTGGTTGAGCCCAAG 60.746 60.000 0.00 0.00 33.07 3.61
908 1204 0.821711 CCGGTCCCACTTTGCAGAAA 60.822 55.000 0.00 0.00 0.00 2.52
909 1205 1.228124 CCGGTCCCACTTTGCAGAA 60.228 57.895 0.00 0.00 0.00 3.02
910 1206 2.429930 CCGGTCCCACTTTGCAGA 59.570 61.111 0.00 0.00 0.00 4.26
911 1207 2.672996 CCCGGTCCCACTTTGCAG 60.673 66.667 0.00 0.00 0.00 4.41
977 1282 4.043200 GTTTGCCACTGCCCGCTC 62.043 66.667 0.00 0.00 36.33 5.03
1472 1783 7.762588 ACACATGGAGTATATGAGGTAGTAC 57.237 40.000 0.00 0.00 0.00 2.73
1522 1841 3.501445 GCACAAGAGCAAATTCTCACTCT 59.499 43.478 0.00 0.00 41.18 3.24
1579 1898 2.563620 TGTGCAATGCCACTTGATCAAT 59.436 40.909 8.96 0.00 36.68 2.57
1608 1927 5.505173 AGTGAAGAACAAACTTGTGATGG 57.495 39.130 0.00 0.00 41.31 3.51
1772 2091 3.379372 GCCTTGCAGCAGATATTGAGAAA 59.621 43.478 0.00 0.00 0.00 2.52
1820 2139 5.724328 TGATCTATCATTTCGCCATAGGAC 58.276 41.667 0.00 0.00 0.00 3.85
1847 2166 1.067283 ACTGCTTCAGTGATCAGACGG 60.067 52.381 22.33 10.11 43.63 4.79
1851 2170 4.298744 TCGATACTGCTTCAGTGATCAG 57.701 45.455 16.79 16.79 45.01 2.90
1853 2172 5.048364 AGGTATCGATACTGCTTCAGTGATC 60.048 44.000 29.40 12.07 45.01 2.92
1949 2268 3.893326 ATAATTCCAGCAAAACCAGCC 57.107 42.857 0.00 0.00 0.00 4.85
1999 2318 6.795098 ATTTAGTAAACAGCACAACATCGA 57.205 33.333 0.00 0.00 0.00 3.59
2001 2320 9.503427 GGATAATTTAGTAAACAGCACAACATC 57.497 33.333 0.00 0.00 0.00 3.06
2062 3658 7.332926 ACTCTAGTTCAGTGATGCAATAGTTTG 59.667 37.037 0.00 0.00 35.85 2.93
2363 3959 9.995003 AAGTGCAATGGAAATAGAATGTTTAAA 57.005 25.926 0.00 0.00 0.00 1.52
2364 3960 9.995003 AAAGTGCAATGGAAATAGAATGTTTAA 57.005 25.926 0.00 0.00 0.00 1.52
2502 4098 2.023673 TGCTTTTGGTGACACCTTCAG 58.976 47.619 24.81 17.11 42.67 3.02
3109 5502 8.092687 GGACACAACTACTCCTTTTAGTGATAA 58.907 37.037 0.00 0.00 29.93 1.75
3119 5512 3.838903 CCCTTAGGACACAACTACTCCTT 59.161 47.826 0.00 0.00 35.87 3.36
3243 5636 5.818678 ACAATAACTACCAGTTCACAGGA 57.181 39.130 0.00 0.00 39.51 3.86
3244 5637 6.037172 GCATACAATAACTACCAGTTCACAGG 59.963 42.308 0.00 0.00 39.51 4.00
3276 5669 4.903049 ACCCACATGATATGCCATCAAATT 59.097 37.500 0.00 0.00 0.00 1.82
3530 5923 1.351017 TCACCACTCCCAAAGGATGAC 59.649 52.381 0.00 0.00 42.93 3.06
3630 6023 3.312421 TGAACTGCTTGCTTCACTTGTAC 59.688 43.478 0.00 0.00 0.00 2.90
3986 6385 3.515602 AGCAGGAACAGAAGGAAACAT 57.484 42.857 0.00 0.00 0.00 2.71
4174 6573 2.820973 GGCCTGCAAAGTGCCAAA 59.179 55.556 10.40 0.00 44.23 3.28
4202 6601 4.792068 TCCGAAGCCTTTCCATGATATTT 58.208 39.130 0.00 0.00 0.00 1.40
4226 6625 1.199615 TGTCCGAATCCATAGGTGCA 58.800 50.000 0.00 0.00 0.00 4.57
4229 6628 1.489230 GGGTTGTCCGAATCCATAGGT 59.511 52.381 0.00 0.00 33.83 3.08
4362 6761 1.699634 CTCAAAGGAACAGGACCCTCA 59.300 52.381 0.00 0.00 31.17 3.86
4366 6765 1.143073 ACCACTCAAAGGAACAGGACC 59.857 52.381 0.00 0.00 0.00 4.46
4370 6769 3.748568 GCTTCTACCACTCAAAGGAACAG 59.251 47.826 0.00 0.00 0.00 3.16
4443 6851 4.527564 GCAGTATGATGCGGAATTTACAC 58.472 43.478 0.00 0.00 39.69 2.90
4466 6874 3.196685 AGGAAGACTAGTTCTGGATGCAC 59.803 47.826 0.00 0.00 33.46 4.57
4549 6957 4.353777 TCCTTGTGTAGCAGAGGAATACT 58.646 43.478 0.00 0.00 34.10 2.12
4596 7006 9.032624 AGTTAAGCCTAGAGTGTGTATTTTCTA 57.967 33.333 0.00 0.00 0.00 2.10
4597 7007 7.908453 AGTTAAGCCTAGAGTGTGTATTTTCT 58.092 34.615 0.00 0.00 0.00 2.52
4598 7008 8.549338 AAGTTAAGCCTAGAGTGTGTATTTTC 57.451 34.615 0.00 0.00 0.00 2.29
4696 7132 2.092699 CCCCAAGTTCATCCTTCTCCTC 60.093 54.545 0.00 0.00 0.00 3.71
4697 7133 1.918957 CCCCAAGTTCATCCTTCTCCT 59.081 52.381 0.00 0.00 0.00 3.69
4698 7134 1.916181 TCCCCAAGTTCATCCTTCTCC 59.084 52.381 0.00 0.00 0.00 3.71
4699 7135 3.264450 TCTTCCCCAAGTTCATCCTTCTC 59.736 47.826 0.00 0.00 0.00 2.87
4700 7136 3.260205 TCTTCCCCAAGTTCATCCTTCT 58.740 45.455 0.00 0.00 0.00 2.85
4701 7137 3.721087 TCTTCCCCAAGTTCATCCTTC 57.279 47.619 0.00 0.00 0.00 3.46
4742 7178 6.491062 TGGCCCAGATATGAAATGAAACTATG 59.509 38.462 0.00 0.00 0.00 2.23
4824 7260 2.584608 GTGGGATCGGTGGAGGTG 59.415 66.667 0.00 0.00 0.00 4.00
4825 7261 2.687566 GGTGGGATCGGTGGAGGT 60.688 66.667 0.00 0.00 0.00 3.85
4826 7262 3.480133 GGGTGGGATCGGTGGAGG 61.480 72.222 0.00 0.00 0.00 4.30
4827 7263 3.480133 GGGGTGGGATCGGTGGAG 61.480 72.222 0.00 0.00 0.00 3.86
4828 7264 3.572715 AAGGGGTGGGATCGGTGGA 62.573 63.158 0.00 0.00 0.00 4.02
4829 7265 2.150014 AAAAGGGGTGGGATCGGTGG 62.150 60.000 0.00 0.00 0.00 4.61
4830 7266 0.679960 GAAAAGGGGTGGGATCGGTG 60.680 60.000 0.00 0.00 0.00 4.94
4831 7267 0.845102 AGAAAAGGGGTGGGATCGGT 60.845 55.000 0.00 0.00 0.00 4.69
4832 7268 0.107165 GAGAAAAGGGGTGGGATCGG 60.107 60.000 0.00 0.00 0.00 4.18
4833 7269 0.462047 CGAGAAAAGGGGTGGGATCG 60.462 60.000 0.00 0.00 0.00 3.69
4834 7270 0.748367 GCGAGAAAAGGGGTGGGATC 60.748 60.000 0.00 0.00 0.00 3.36
4835 7271 1.208165 AGCGAGAAAAGGGGTGGGAT 61.208 55.000 0.00 0.00 0.00 3.85
4836 7272 1.423794 AAGCGAGAAAAGGGGTGGGA 61.424 55.000 0.00 0.00 0.00 4.37
4837 7273 1.074951 AAGCGAGAAAAGGGGTGGG 59.925 57.895 0.00 0.00 0.00 4.61
4838 7274 0.537371 ACAAGCGAGAAAAGGGGTGG 60.537 55.000 0.00 0.00 0.00 4.61
4839 7275 1.318576 AACAAGCGAGAAAAGGGGTG 58.681 50.000 0.00 0.00 0.00 4.61
4840 7276 2.067365 AAACAAGCGAGAAAAGGGGT 57.933 45.000 0.00 0.00 0.00 4.95
4841 7277 2.288213 GGAAAACAAGCGAGAAAAGGGG 60.288 50.000 0.00 0.00 0.00 4.79
4842 7278 2.288213 GGGAAAACAAGCGAGAAAAGGG 60.288 50.000 0.00 0.00 0.00 3.95
4843 7279 2.604614 CGGGAAAACAAGCGAGAAAAGG 60.605 50.000 0.00 0.00 0.00 3.11
4844 7280 2.289547 TCGGGAAAACAAGCGAGAAAAG 59.710 45.455 0.00 0.00 0.00 2.27
4845 7281 2.290464 TCGGGAAAACAAGCGAGAAAA 58.710 42.857 0.00 0.00 0.00 2.29
4846 7282 1.956297 TCGGGAAAACAAGCGAGAAA 58.044 45.000 0.00 0.00 0.00 2.52
4847 7283 2.073816 GATCGGGAAAACAAGCGAGAA 58.926 47.619 0.00 0.00 0.00 2.87
4848 7284 1.722011 GATCGGGAAAACAAGCGAGA 58.278 50.000 0.00 0.00 0.00 4.04
4849 7285 0.370273 CGATCGGGAAAACAAGCGAG 59.630 55.000 7.38 0.00 0.00 5.03
4850 7286 0.320073 ACGATCGGGAAAACAAGCGA 60.320 50.000 20.98 0.00 0.00 4.93
4851 7287 1.352114 TACGATCGGGAAAACAAGCG 58.648 50.000 20.98 0.00 0.00 4.68
4852 7288 2.481185 TGTTACGATCGGGAAAACAAGC 59.519 45.455 20.98 1.19 0.00 4.01
4853 7289 4.735662 TTGTTACGATCGGGAAAACAAG 57.264 40.909 23.95 0.00 35.69 3.16
4854 7290 5.496133 TTTTGTTACGATCGGGAAAACAA 57.504 34.783 23.95 23.95 38.04 2.83
4855 7291 5.496133 TTTTTGTTACGATCGGGAAAACA 57.504 34.783 20.98 18.99 0.00 2.83
4878 7314 1.247419 TGCGTGGATGGCGGATTTTT 61.247 50.000 0.00 0.00 0.00 1.94
4879 7315 1.677300 TGCGTGGATGGCGGATTTT 60.677 52.632 0.00 0.00 0.00 1.82
4880 7316 2.045438 TGCGTGGATGGCGGATTT 60.045 55.556 0.00 0.00 0.00 2.17
4881 7317 2.824041 GTGCGTGGATGGCGGATT 60.824 61.111 0.00 0.00 31.50 3.01
4886 7322 4.541482 CATGCGTGCGTGGATGGC 62.541 66.667 6.15 0.00 34.42 4.40
4887 7323 3.099619 GACATGCGTGCGTGGATGG 62.100 63.158 17.57 0.00 41.46 3.51
4888 7324 2.028766 GAGACATGCGTGCGTGGATG 62.029 60.000 17.57 7.75 42.68 3.51
4889 7325 1.811266 GAGACATGCGTGCGTGGAT 60.811 57.895 17.57 6.06 37.27 3.41
4890 7326 2.432456 GAGACATGCGTGCGTGGA 60.432 61.111 17.57 0.00 37.27 4.02
4891 7327 1.959899 GAAGAGACATGCGTGCGTGG 61.960 60.000 17.57 1.22 37.27 4.94
4892 7328 1.417592 GAAGAGACATGCGTGCGTG 59.582 57.895 12.31 12.31 38.78 5.34
4893 7329 1.738099 GGAAGAGACATGCGTGCGT 60.738 57.895 5.64 0.00 0.00 5.24
4894 7330 1.446792 AGGAAGAGACATGCGTGCG 60.447 57.895 5.64 0.00 0.00 5.34
4895 7331 1.975363 GCAGGAAGAGACATGCGTGC 61.975 60.000 5.64 0.00 37.78 5.34
4896 7332 2.084844 GCAGGAAGAGACATGCGTG 58.915 57.895 3.82 3.82 37.78 5.34
4897 7333 4.606071 GCAGGAAGAGACATGCGT 57.394 55.556 0.00 0.00 37.78 5.24
4927 7363 1.153449 TATGCTTTCGGTGGAGCGG 60.153 57.895 0.00 0.00 41.75 5.52
4928 7364 1.154205 CCTATGCTTTCGGTGGAGCG 61.154 60.000 0.00 0.00 41.75 5.03
4929 7365 1.440145 GCCTATGCTTTCGGTGGAGC 61.440 60.000 0.00 0.00 39.33 4.70
4930 7366 0.107703 TGCCTATGCTTTCGGTGGAG 60.108 55.000 0.00 0.00 38.71 3.86
4931 7367 0.392461 GTGCCTATGCTTTCGGTGGA 60.392 55.000 0.00 0.00 38.71 4.02
4932 7368 1.705337 CGTGCCTATGCTTTCGGTGG 61.705 60.000 0.00 0.00 38.71 4.61
4933 7369 1.019278 ACGTGCCTATGCTTTCGGTG 61.019 55.000 0.00 0.00 38.71 4.94
4934 7370 0.533491 TACGTGCCTATGCTTTCGGT 59.467 50.000 0.00 0.00 38.71 4.69
4935 7371 0.928229 GTACGTGCCTATGCTTTCGG 59.072 55.000 0.00 0.00 38.71 4.30
4936 7372 0.570734 CGTACGTGCCTATGCTTTCG 59.429 55.000 7.22 0.00 38.71 3.46
4937 7373 0.300789 GCGTACGTGCCTATGCTTTC 59.699 55.000 17.90 0.00 38.71 2.62
4938 7374 2.380081 GCGTACGTGCCTATGCTTT 58.620 52.632 17.90 0.00 38.71 3.51
4939 7375 4.104143 GCGTACGTGCCTATGCTT 57.896 55.556 17.90 0.00 38.71 3.91
4958 7394 1.493311 GCCGCTAGTATCGCAATGC 59.507 57.895 0.00 0.00 0.00 3.56
4959 7395 1.617755 CGGCCGCTAGTATCGCAATG 61.618 60.000 14.67 0.00 0.00 2.82
4960 7396 1.372997 CGGCCGCTAGTATCGCAAT 60.373 57.895 14.67 0.00 0.00 3.56
4961 7397 1.446516 TACGGCCGCTAGTATCGCAA 61.447 55.000 28.58 0.00 0.00 4.85
4962 7398 1.893335 TACGGCCGCTAGTATCGCA 60.893 57.895 28.58 0.00 0.00 5.10
4963 7399 1.441682 GTACGGCCGCTAGTATCGC 60.442 63.158 28.58 0.67 0.00 4.58
4964 7400 0.110328 CAGTACGGCCGCTAGTATCG 60.110 60.000 28.58 1.37 0.00 2.92
4965 7401 0.240411 CCAGTACGGCCGCTAGTATC 59.760 60.000 28.58 7.83 0.00 2.24
4966 7402 0.179009 TCCAGTACGGCCGCTAGTAT 60.179 55.000 28.58 7.06 33.14 2.12
4967 7403 0.816825 CTCCAGTACGGCCGCTAGTA 60.817 60.000 28.58 7.17 33.14 1.82
4968 7404 2.044650 TCCAGTACGGCCGCTAGT 60.045 61.111 28.58 16.51 33.14 2.57
4969 7405 1.822613 TCTCCAGTACGGCCGCTAG 60.823 63.158 28.58 13.00 33.14 3.42
4970 7406 2.117156 GTCTCCAGTACGGCCGCTA 61.117 63.158 28.58 14.34 33.14 4.26
4971 7407 3.450115 GTCTCCAGTACGGCCGCT 61.450 66.667 28.58 13.09 33.14 5.52
4972 7408 4.509737 GGTCTCCAGTACGGCCGC 62.510 72.222 28.58 10.42 33.14 6.53
4973 7409 4.189188 CGGTCTCCAGTACGGCCG 62.189 72.222 26.86 26.86 33.14 6.13
4974 7410 4.509737 GCGGTCTCCAGTACGGCC 62.510 72.222 0.00 0.00 37.25 6.13
4975 7411 3.701604 CTGCGGTCTCCAGTACGGC 62.702 68.421 0.00 0.00 41.88 5.68
4976 7412 2.490217 CTGCGGTCTCCAGTACGG 59.510 66.667 0.00 0.00 0.00 4.02
4977 7413 2.202623 GCTGCGGTCTCCAGTACG 60.203 66.667 0.00 0.00 32.93 3.67
4978 7414 2.202623 CGCTGCGGTCTCCAGTAC 60.203 66.667 15.40 0.00 32.93 2.73
4979 7415 2.360726 TCGCTGCGGTCTCCAGTA 60.361 61.111 23.03 0.00 32.93 2.74
4980 7416 3.753434 CTCGCTGCGGTCTCCAGT 61.753 66.667 23.03 0.00 32.93 4.00
4981 7417 3.443925 TCTCGCTGCGGTCTCCAG 61.444 66.667 23.03 10.95 0.00 3.86
4982 7418 3.749064 GTCTCGCTGCGGTCTCCA 61.749 66.667 23.03 0.00 0.00 3.86
4983 7419 4.500116 GGTCTCGCTGCGGTCTCC 62.500 72.222 23.03 15.03 0.00 3.71
4984 7420 3.749064 TGGTCTCGCTGCGGTCTC 61.749 66.667 23.03 10.37 0.00 3.36
4985 7421 4.057428 GTGGTCTCGCTGCGGTCT 62.057 66.667 23.03 0.00 0.00 3.85
4994 7430 2.509336 GATGGCGTGGTGGTCTCG 60.509 66.667 0.00 0.00 0.00 4.04
4995 7431 2.509336 CGATGGCGTGGTGGTCTC 60.509 66.667 0.00 0.00 0.00 3.36
4996 7432 4.760047 GCGATGGCGTGGTGGTCT 62.760 66.667 0.00 0.00 40.36 3.85
4997 7433 4.760047 AGCGATGGCGTGGTGGTC 62.760 66.667 0.00 0.00 46.35 4.02
4998 7434 4.760047 GAGCGATGGCGTGGTGGT 62.760 66.667 0.00 0.00 46.35 4.16
5000 7436 4.758251 TGGAGCGATGGCGTGGTG 62.758 66.667 0.00 0.00 46.35 4.17
5001 7437 4.457496 CTGGAGCGATGGCGTGGT 62.457 66.667 0.00 0.00 46.35 4.16
5002 7438 4.147449 TCTGGAGCGATGGCGTGG 62.147 66.667 0.00 0.00 46.35 4.94
5003 7439 2.887568 GTCTGGAGCGATGGCGTG 60.888 66.667 0.00 0.00 46.35 5.34
5004 7440 4.498520 CGTCTGGAGCGATGGCGT 62.499 66.667 0.00 0.00 46.35 5.68
5005 7441 4.193334 TCGTCTGGAGCGATGGCG 62.193 66.667 0.00 0.00 46.35 5.69
5006 7442 2.583593 GTCGTCTGGAGCGATGGC 60.584 66.667 0.00 0.00 40.59 4.40
5007 7443 2.278206 CGTCGTCTGGAGCGATGG 60.278 66.667 0.00 0.00 40.47 3.51
5008 7444 2.278206 CCGTCGTCTGGAGCGATG 60.278 66.667 0.00 0.00 42.86 3.84
5009 7445 2.750637 ACCGTCGTCTGGAGCGAT 60.751 61.111 0.00 0.00 40.59 4.58
5010 7446 3.733960 CACCGTCGTCTGGAGCGA 61.734 66.667 0.00 0.00 35.89 4.93
5012 7448 4.357947 TGCACCGTCGTCTGGAGC 62.358 66.667 5.99 5.99 42.57 4.70
5013 7449 2.430921 GTGCACCGTCGTCTGGAG 60.431 66.667 5.22 0.00 0.00 3.86
5014 7450 4.337060 CGTGCACCGTCGTCTGGA 62.337 66.667 12.15 0.00 0.00 3.86
5015 7451 4.337060 TCGTGCACCGTCGTCTGG 62.337 66.667 12.15 0.00 37.94 3.86
5016 7452 3.097728 GTCGTGCACCGTCGTCTG 61.098 66.667 12.15 0.00 37.94 3.51
5017 7453 4.678269 CGTCGTGCACCGTCGTCT 62.678 66.667 12.15 0.00 41.92 4.18
5148 7584 8.781196 GCAATGACACATCTACTGATATTGATT 58.219 33.333 0.00 0.00 0.00 2.57
5149 7585 8.155510 AGCAATGACACATCTACTGATATTGAT 58.844 33.333 0.00 0.00 0.00 2.57
5150 7586 7.503549 AGCAATGACACATCTACTGATATTGA 58.496 34.615 0.00 0.00 0.00 2.57
5151 7587 7.725818 AGCAATGACACATCTACTGATATTG 57.274 36.000 0.00 0.00 0.00 1.90
5152 7588 9.836864 TTAAGCAATGACACATCTACTGATATT 57.163 29.630 0.00 0.00 0.00 1.28
5153 7589 9.836864 TTTAAGCAATGACACATCTACTGATAT 57.163 29.630 0.00 0.00 0.00 1.63
5154 7590 9.836864 ATTTAAGCAATGACACATCTACTGATA 57.163 29.630 0.00 0.00 0.00 2.15
5155 7591 8.743085 ATTTAAGCAATGACACATCTACTGAT 57.257 30.769 0.00 0.00 0.00 2.90
5156 7592 8.565896 AATTTAAGCAATGACACATCTACTGA 57.434 30.769 0.00 0.00 0.00 3.41
5157 7593 9.630098 AAAATTTAAGCAATGACACATCTACTG 57.370 29.630 0.00 0.00 0.00 2.74
5158 7594 9.846248 GAAAATTTAAGCAATGACACATCTACT 57.154 29.630 0.00 0.00 0.00 2.57
5159 7595 9.624697 TGAAAATTTAAGCAATGACACATCTAC 57.375 29.630 0.00 0.00 0.00 2.59
5180 7616 9.853555 CCATGCTAAAGTTGTACAATATGAAAA 57.146 29.630 12.26 0.00 0.00 2.29
5181 7617 9.019656 ACCATGCTAAAGTTGTACAATATGAAA 57.980 29.630 12.26 0.00 0.00 2.69
5182 7618 8.574251 ACCATGCTAAAGTTGTACAATATGAA 57.426 30.769 12.26 0.00 0.00 2.57
5183 7619 9.325198 CTACCATGCTAAAGTTGTACAATATGA 57.675 33.333 12.26 0.00 0.00 2.15
5184 7620 9.325198 TCTACCATGCTAAAGTTGTACAATATG 57.675 33.333 12.26 7.96 0.00 1.78
5186 7622 9.325198 CATCTACCATGCTAAAGTTGTACAATA 57.675 33.333 12.26 0.00 0.00 1.90
5187 7623 7.829211 ACATCTACCATGCTAAAGTTGTACAAT 59.171 33.333 12.26 0.00 0.00 2.71
5188 7624 7.165485 ACATCTACCATGCTAAAGTTGTACAA 58.835 34.615 3.59 3.59 0.00 2.41
5189 7625 6.707290 ACATCTACCATGCTAAAGTTGTACA 58.293 36.000 0.00 0.00 0.00 2.90
5190 7626 7.611213 AACATCTACCATGCTAAAGTTGTAC 57.389 36.000 0.00 0.00 0.00 2.90
5191 7627 9.899661 ATTAACATCTACCATGCTAAAGTTGTA 57.100 29.630 0.00 0.00 0.00 2.41
5192 7628 8.807948 ATTAACATCTACCATGCTAAAGTTGT 57.192 30.769 0.00 0.00 0.00 3.32
5284 7720 7.399634 TGAATATTACTCCCTTCCGTCTTTTT 58.600 34.615 0.00 0.00 0.00 1.94
5285 7721 6.954232 TGAATATTACTCCCTTCCGTCTTTT 58.046 36.000 0.00 0.00 0.00 2.27
5286 7722 6.555463 TGAATATTACTCCCTTCCGTCTTT 57.445 37.500 0.00 0.00 0.00 2.52
5287 7723 6.525629 CATGAATATTACTCCCTTCCGTCTT 58.474 40.000 0.00 0.00 0.00 3.01
5288 7724 5.511545 GCATGAATATTACTCCCTTCCGTCT 60.512 44.000 0.00 0.00 0.00 4.18
5289 7725 4.691216 GCATGAATATTACTCCCTTCCGTC 59.309 45.833 0.00 0.00 0.00 4.79
5290 7726 4.642429 GCATGAATATTACTCCCTTCCGT 58.358 43.478 0.00 0.00 0.00 4.69
5291 7727 3.679980 CGCATGAATATTACTCCCTTCCG 59.320 47.826 0.00 0.00 0.00 4.30
5292 7728 3.437049 GCGCATGAATATTACTCCCTTCC 59.563 47.826 0.30 0.00 0.00 3.46
5293 7729 3.437049 GGCGCATGAATATTACTCCCTTC 59.563 47.826 10.83 0.00 0.00 3.46
5294 7730 3.073062 AGGCGCATGAATATTACTCCCTT 59.927 43.478 10.83 0.00 0.00 3.95
5295 7731 2.639839 AGGCGCATGAATATTACTCCCT 59.360 45.455 10.83 0.00 0.00 4.20
5296 7732 3.059352 AGGCGCATGAATATTACTCCC 57.941 47.619 10.83 0.00 0.00 4.30
5297 7733 5.035784 GAAAGGCGCATGAATATTACTCC 57.964 43.478 10.83 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.