Multiple sequence alignment - TraesCS4D01G223000

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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 TraesCS4D01G223000 chr4D 100.000 3701 0 0 1 3701 380140947 380144647 0.000000e+00 6835.0
1 TraesCS4D01G223000 chr4D 87.225 227 26 3 1 225 211735027 211734802 4.740000e-64 255.0
2 TraesCS4D01G223000 chr4B 93.153 3067 158 24 6 3042 467099755 467102799 0.000000e+00 4453.0
3 TraesCS4D01G223000 chr4B 85.861 389 23 12 3314 3701 467102976 467103333 5.800000e-103 385.0
4 TraesCS4D01G223000 chr4B 89.222 167 11 6 3155 3314 139539473 139539307 6.270000e-48 202.0
5 TraesCS4D01G223000 chr4B 89.286 112 4 3 3047 3158 467102883 467102986 2.320000e-27 134.0
6 TraesCS4D01G223000 chr4A 95.564 1916 78 3 964 2878 84382370 84380461 0.000000e+00 3061.0
7 TraesCS4D01G223000 chr4A 89.985 649 52 9 10 653 84383549 84382909 0.000000e+00 826.0
8 TraesCS4D01G223000 chr4A 90.837 251 14 5 2876 3124 84380377 84380134 9.910000e-86 327.0
9 TraesCS4D01G223000 chr4A 96.000 50 2 0 758 807 84382777 84382728 8.520000e-12 82.4
10 TraesCS4D01G223000 chr6D 85.660 265 35 3 1 264 269682152 269681890 3.640000e-70 276.0
11 TraesCS4D01G223000 chr6D 79.808 208 33 7 2830 3034 3063151 3063352 3.850000e-30 143.0
12 TraesCS4D01G223000 chr5D 81.388 317 34 13 265 581 439007091 439007382 6.180000e-58 235.0
13 TraesCS4D01G223000 chr5D 84.141 227 32 4 1 225 92844 92620 2.240000e-52 217.0
14 TraesCS4D01G223000 chr3B 84.649 228 29 6 1 225 27162668 27162444 4.810000e-54 222.0
15 TraesCS4D01G223000 chr3B 87.912 182 22 0 263 444 108244554 108244373 8.050000e-52 215.0
16 TraesCS4D01G223000 chr3B 90.244 164 12 3 3155 3314 802100132 802099969 1.040000e-50 211.0
17 TraesCS4D01G223000 chr3B 85.350 157 20 3 2832 2987 243808760 243808914 3.830000e-35 159.0
18 TraesCS4D01G223000 chr2D 84.141 227 32 4 1 225 324612013 324612237 2.240000e-52 217.0
19 TraesCS4D01G223000 chr2D 82.969 229 33 4 1 224 628896820 628896593 6.270000e-48 202.0
20 TraesCS4D01G223000 chr2A 90.625 160 13 2 3155 3312 703579484 703579325 1.040000e-50 211.0
21 TraesCS4D01G223000 chr2A 92.517 147 10 1 3168 3313 96251931 96251785 3.750000e-50 209.0
22 TraesCS4D01G223000 chr2B 89.441 161 15 2 3155 3313 615587725 615587885 6.270000e-48 202.0
23 TraesCS4D01G223000 chr2B 89.024 164 14 3 3155 3314 741211712 741211875 2.250000e-47 200.0
24 TraesCS4D01G223000 chr1B 89.091 165 13 4 3155 3314 20558587 20558423 2.250000e-47 200.0
25 TraesCS4D01G223000 chr1B 88.554 166 15 3 3155 3316 321011741 321011906 8.110000e-47 198.0
26 TraesCS4D01G223000 chr1B 84.324 185 26 3 2835 3018 572646693 572646875 1.060000e-40 178.0
27 TraesCS4D01G223000 chr6B 88.957 163 14 3 3156 3314 712550506 712550668 8.110000e-47 198.0
28 TraesCS4D01G223000 chr3D 81.857 237 38 5 9 242 259208628 259208862 1.050000e-45 195.0
29 TraesCS4D01G223000 chr1A 83.511 188 29 2 2832 3018 519270134 519270320 1.370000e-39 174.0
30 TraesCS4D01G223000 chr1D 83.511 188 28 3 2832 3018 423268377 423268562 4.910000e-39 172.0
31 TraesCS4D01G223000 chr3A 85.443 158 18 5 2832 2987 198839437 198839283 3.830000e-35 159.0
32 TraesCS4D01G223000 chr7D 80.769 208 25 8 2832 3036 602100739 602100934 8.280000e-32 148.0
33 TraesCS4D01G223000 chr7B 84.932 73 7 4 590 661 701199821 701199752 1.840000e-08 71.3


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 TraesCS4D01G223000 chr4D 380140947 380144647 3700 False 6835.000000 6835 100.000000 1 3701 1 chr4D.!!$F1 3700
1 TraesCS4D01G223000 chr4B 467099755 467103333 3578 False 1657.333333 4453 89.433333 6 3701 3 chr4B.!!$F1 3695
2 TraesCS4D01G223000 chr4A 84380134 84383549 3415 True 1074.100000 3061 93.096500 10 3124 4 chr4A.!!$R1 3114

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
137 139 0.611896 TCCGAGATCCACAGCTCACA 60.612 55.000 0.0 0.0 34.42 3.58 F
148 150 0.620556 CAGCTCACAACCCCATACCT 59.379 55.000 0.0 0.0 0.00 3.08 F
741 801 1.003866 GGCGTGTTGGAAATATCGAGC 60.004 52.381 0.0 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1104 1414 0.320247 CACAACGCAGGAAGCTCTCT 60.320 55.000 0.00 0.00 42.61 3.10 R
1606 1916 1.298339 GGCCGTATTTGCGCATCAC 60.298 57.895 12.75 8.77 0.00 3.06 R
2701 3011 0.107831 ACAAACCTGCGCCTGAACTA 59.892 50.000 4.18 0.00 0.00 2.24 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
45 47 7.504574 TCATCATCAATACAATCAAAGCAGGAT 59.495 33.333 0.00 0.00 0.00 3.24
49 51 7.558161 TCAATACAATCAAAGCAGGATGTAG 57.442 36.000 0.00 0.00 39.31 2.74
97 99 8.258708 GTCTGAAGTTATGTAAATACTGTCCCT 58.741 37.037 0.00 0.00 0.00 4.20
135 137 1.035923 GATCCGAGATCCACAGCTCA 58.964 55.000 3.31 0.00 34.42 4.26
136 138 0.749649 ATCCGAGATCCACAGCTCAC 59.250 55.000 0.00 0.00 34.42 3.51
137 139 0.611896 TCCGAGATCCACAGCTCACA 60.612 55.000 0.00 0.00 34.42 3.58
148 150 0.620556 CAGCTCACAACCCCATACCT 59.379 55.000 0.00 0.00 0.00 3.08
197 200 3.777106 TGGTGCTTCATTGAGAGTTCT 57.223 42.857 0.00 0.00 0.00 3.01
215 218 5.068636 AGTTCTGCTGTGAGATCAACAAAT 58.931 37.500 0.00 0.00 0.00 2.32
381 384 2.076100 TGATGAACGCGCTTTGAGAAT 58.924 42.857 5.73 0.00 0.00 2.40
484 487 2.154462 GATGGGGCGGAAATGTGATAG 58.846 52.381 0.00 0.00 0.00 2.08
492 495 3.495100 GCGGAAATGTGATAGGTCCTCAT 60.495 47.826 0.00 0.00 0.00 2.90
550 553 1.069049 GTTCAGCCAATGCAGGTTTGT 59.931 47.619 0.00 0.00 41.13 2.83
551 554 2.284754 TCAGCCAATGCAGGTTTGTA 57.715 45.000 0.00 0.00 41.13 2.41
552 555 2.161855 TCAGCCAATGCAGGTTTGTAG 58.838 47.619 0.00 0.00 41.13 2.74
593 596 7.162082 AGAAGGAGTTCACTTATCACGAAATT 58.838 34.615 0.00 0.00 34.82 1.82
649 652 8.771920 ATGTCTACGTACATTCATTTTCTTGA 57.228 30.769 0.00 0.00 36.71 3.02
650 653 8.014322 TGTCTACGTACATTCATTTTCTTGAC 57.986 34.615 0.00 0.00 0.00 3.18
651 654 7.654116 TGTCTACGTACATTCATTTTCTTGACA 59.346 33.333 0.00 0.00 0.00 3.58
653 656 8.708742 TCTACGTACATTCATTTTCTTGACAAG 58.291 33.333 9.03 9.03 0.00 3.16
657 717 7.744715 CGTACATTCATTTTCTTGACAAGGTAC 59.255 37.037 15.13 13.25 0.00 3.34
686 746 7.496591 TGGAACGAAGAAAGTACATTTTAGTGT 59.503 33.333 0.00 0.00 36.13 3.55
718 778 2.030007 CACGGTGTGATGGAGCAATTTT 60.030 45.455 0.00 0.00 35.23 1.82
734 794 4.450757 GCAATTTTTAGGCGTGTTGGAAAT 59.549 37.500 0.00 0.00 0.00 2.17
735 795 5.635700 GCAATTTTTAGGCGTGTTGGAAATA 59.364 36.000 0.00 0.00 0.00 1.40
736 796 6.312672 GCAATTTTTAGGCGTGTTGGAAATAT 59.687 34.615 0.00 0.00 0.00 1.28
737 797 7.464045 GCAATTTTTAGGCGTGTTGGAAATATC 60.464 37.037 0.00 0.00 0.00 1.63
738 798 4.868450 TTTAGGCGTGTTGGAAATATCG 57.132 40.909 0.00 0.00 0.00 2.92
739 799 2.684001 AGGCGTGTTGGAAATATCGA 57.316 45.000 0.00 0.00 0.00 3.59
740 800 2.550978 AGGCGTGTTGGAAATATCGAG 58.449 47.619 0.00 0.00 0.00 4.04
741 801 1.003866 GGCGTGTTGGAAATATCGAGC 60.004 52.381 0.00 0.00 0.00 5.03
742 802 1.663643 GCGTGTTGGAAATATCGAGCA 59.336 47.619 0.00 0.00 0.00 4.26
743 803 2.285834 GCGTGTTGGAAATATCGAGCAG 60.286 50.000 0.00 0.00 0.00 4.24
745 805 3.370978 CGTGTTGGAAATATCGAGCAGTT 59.629 43.478 0.00 0.00 0.00 3.16
829 993 3.944055 TTTTCTCCTCTCCAGACTTCG 57.056 47.619 0.00 0.00 0.00 3.79
851 1015 5.642063 TCGGTCACCTGTCATATTTTCTTTC 59.358 40.000 0.00 0.00 0.00 2.62
852 1016 5.445939 CGGTCACCTGTCATATTTTCTTTCG 60.446 44.000 0.00 0.00 0.00 3.46
853 1017 5.642063 GGTCACCTGTCATATTTTCTTTCGA 59.358 40.000 0.00 0.00 0.00 3.71
856 1020 7.278868 GTCACCTGTCATATTTTCTTTCGAGAT 59.721 37.037 0.00 0.00 0.00 2.75
857 1021 7.492669 TCACCTGTCATATTTTCTTTCGAGATC 59.507 37.037 0.00 0.00 0.00 2.75
858 1022 7.278646 CACCTGTCATATTTTCTTTCGAGATCA 59.721 37.037 0.00 0.00 0.00 2.92
859 1023 7.278868 ACCTGTCATATTTTCTTTCGAGATCAC 59.721 37.037 0.00 0.00 0.00 3.06
860 1024 7.493971 CCTGTCATATTTTCTTTCGAGATCACT 59.506 37.037 0.00 0.00 0.00 3.41
888 1072 1.852067 GCCAACACCATCACCGTGAC 61.852 60.000 2.57 0.00 35.17 3.67
927 1115 3.857157 TTCAAAGCCCACTAGAACACT 57.143 42.857 0.00 0.00 0.00 3.55
954 1142 2.354503 CCTATCATCATTCTCCCGCTGG 60.355 54.545 0.00 0.00 0.00 4.85
1021 1331 2.892425 GGCCATTCAGCCGTCTCG 60.892 66.667 0.00 0.00 44.57 4.04
1042 1352 1.827789 CCTCTCCTCCTCCTGCTCG 60.828 68.421 0.00 0.00 0.00 5.03
1134 1444 2.340809 CGTTGTGTGTCCCGCCTA 59.659 61.111 0.00 0.00 0.00 3.93
1233 1543 2.262915 CAGAACCTCCGCTTCGCT 59.737 61.111 0.00 0.00 0.00 4.93
1314 1624 4.577677 TCCGTGGCCTGCTGCAAA 62.578 61.111 3.32 0.00 43.89 3.68
1380 1690 3.303928 GGCCTATCCTACCGCGCT 61.304 66.667 5.56 0.00 0.00 5.92
1382 1692 1.212229 GCCTATCCTACCGCGCTAC 59.788 63.158 5.56 0.00 0.00 3.58
1856 2166 1.677217 GGACGAAGAAGCAATGCTCCT 60.677 52.381 8.71 0.00 38.25 3.69
1992 2302 3.128589 TCAAGTCACTGTTTCTTGGCAAC 59.871 43.478 16.36 0.00 38.99 4.17
1994 2304 4.150897 AGTCACTGTTTCTTGGCAACTA 57.849 40.909 0.00 0.00 37.61 2.24
1998 2308 3.627577 CACTGTTTCTTGGCAACTACAGT 59.372 43.478 21.92 21.92 44.94 3.55
2220 2530 2.352388 GCAACCGGTCTAAGCATGTTA 58.648 47.619 8.04 0.00 0.00 2.41
2365 2675 3.133003 CCAGTACTATGTCAAGTGGGGAG 59.867 52.174 0.00 0.00 31.25 4.30
2520 2830 2.289565 GTGGAGGGCAATACAAGCTAC 58.710 52.381 0.00 0.00 0.00 3.58
2523 2833 2.419574 GGAGGGCAATACAAGCTACGAA 60.420 50.000 0.00 0.00 0.00 3.85
2678 2988 1.452833 GGAAGGGACAGAGGCATGC 60.453 63.158 9.90 9.90 0.00 4.06
2694 3004 3.385755 GGCATGCTGGATTGGTTTTAGAT 59.614 43.478 18.92 0.00 0.00 1.98
2701 3011 8.537728 TGCTGGATTGGTTTTAGATATTTGAT 57.462 30.769 0.00 0.00 0.00 2.57
2728 3041 0.102300 GCGCAGGTTTGTGTTCCTTT 59.898 50.000 0.30 0.00 37.15 3.11
2734 3047 3.314080 CAGGTTTGTGTTCCTTTTAGCGA 59.686 43.478 0.00 0.00 30.91 4.93
2746 3059 5.997385 TCCTTTTAGCGAATGTTTCTCAAC 58.003 37.500 0.00 0.00 0.00 3.18
2793 3107 1.337703 GTCTCTTGCAATGTTGTGCCA 59.662 47.619 0.00 0.00 44.26 4.92
2812 3126 4.447054 TGCCAAATTATGCTGTCGTTTTTG 59.553 37.500 1.41 0.00 0.00 2.44
2947 3347 4.861102 AGGAGAACCAAAGCTGAAAATG 57.139 40.909 0.00 0.00 38.94 2.32
3091 3571 9.473007 TTTTTCCATACATGTTCCATATTGAGA 57.527 29.630 2.30 0.00 0.00 3.27
3103 3583 9.631257 TGTTCCATATTGAGATGACATGTTTAT 57.369 29.630 0.00 0.00 0.00 1.40
3104 3584 9.888878 GTTCCATATTGAGATGACATGTTTATG 57.111 33.333 0.00 0.00 40.24 1.90
3143 3623 3.112263 ACAAGTTATGGGTGGCTAGCTA 58.888 45.455 15.72 5.44 0.00 3.32
3149 3629 5.844516 AGTTATGGGTGGCTAGCTATTTAGA 59.155 40.000 15.72 0.00 0.00 2.10
3150 3630 6.502158 AGTTATGGGTGGCTAGCTATTTAGAT 59.498 38.462 15.72 1.00 0.00 1.98
3151 3631 7.678598 AGTTATGGGTGGCTAGCTATTTAGATA 59.321 37.037 15.72 0.08 0.00 1.98
3152 3632 8.487028 GTTATGGGTGGCTAGCTATTTAGATAT 58.513 37.037 15.72 1.16 0.00 1.63
3153 3633 6.546428 TGGGTGGCTAGCTATTTAGATATC 57.454 41.667 15.72 0.00 0.00 1.63
3154 3634 5.127194 TGGGTGGCTAGCTATTTAGATATCG 59.873 44.000 15.72 0.00 0.00 2.92
3155 3635 5.360144 GGGTGGCTAGCTATTTAGATATCGA 59.640 44.000 15.72 0.00 0.00 3.59
3156 3636 6.127423 GGGTGGCTAGCTATTTAGATATCGAA 60.127 42.308 15.72 0.00 0.00 3.71
3157 3637 6.975772 GGTGGCTAGCTATTTAGATATCGAAG 59.024 42.308 15.72 0.00 0.00 3.79
3158 3638 6.975772 GTGGCTAGCTATTTAGATATCGAAGG 59.024 42.308 15.72 0.00 0.00 3.46
3159 3639 6.096987 TGGCTAGCTATTTAGATATCGAAGGG 59.903 42.308 15.72 0.00 0.00 3.95
3160 3640 5.980715 GCTAGCTATTTAGATATCGAAGGGC 59.019 44.000 7.70 4.64 0.00 5.19
3161 3641 6.183360 GCTAGCTATTTAGATATCGAAGGGCT 60.183 42.308 7.70 18.01 0.00 5.19
3162 3642 7.013464 GCTAGCTATTTAGATATCGAAGGGCTA 59.987 40.741 7.70 18.19 0.00 3.93
3163 3643 7.719871 AGCTATTTAGATATCGAAGGGCTAA 57.280 36.000 14.87 0.00 0.00 3.09
3164 3644 8.312669 AGCTATTTAGATATCGAAGGGCTAAT 57.687 34.615 14.87 3.27 0.00 1.73
3165 3645 9.422681 AGCTATTTAGATATCGAAGGGCTAATA 57.577 33.333 14.87 4.01 0.00 0.98
3171 3651 7.060383 AGATATCGAAGGGCTAATATGATGG 57.940 40.000 0.00 0.00 0.00 3.51
3172 3652 3.334583 TCGAAGGGCTAATATGATGGC 57.665 47.619 0.00 0.00 0.00 4.40
3173 3653 2.002586 CGAAGGGCTAATATGATGGCG 58.997 52.381 0.00 0.00 0.00 5.69
3174 3654 2.612972 CGAAGGGCTAATATGATGGCGT 60.613 50.000 0.00 0.00 0.00 5.68
3175 3655 3.368013 CGAAGGGCTAATATGATGGCGTA 60.368 47.826 0.00 0.00 0.00 4.42
3176 3656 3.611766 AGGGCTAATATGATGGCGTAC 57.388 47.619 0.00 0.00 0.00 3.67
3177 3657 2.094182 AGGGCTAATATGATGGCGTACG 60.094 50.000 11.84 11.84 0.00 3.67
3178 3658 2.094390 GGGCTAATATGATGGCGTACGA 60.094 50.000 21.65 0.00 0.00 3.43
3179 3659 3.179830 GGCTAATATGATGGCGTACGAG 58.820 50.000 21.65 4.09 0.00 4.18
3180 3660 3.119602 GGCTAATATGATGGCGTACGAGA 60.120 47.826 21.65 4.00 0.00 4.04
3181 3661 4.440250 GGCTAATATGATGGCGTACGAGAT 60.440 45.833 21.65 9.43 0.00 2.75
3182 3662 5.103000 GCTAATATGATGGCGTACGAGATT 58.897 41.667 21.65 9.11 0.00 2.40
3183 3663 5.004821 GCTAATATGATGGCGTACGAGATTG 59.995 44.000 21.65 3.53 0.00 2.67
3184 3664 1.502231 ATGATGGCGTACGAGATTGC 58.498 50.000 21.65 0.00 0.00 3.56
3185 3665 0.869880 TGATGGCGTACGAGATTGCG 60.870 55.000 21.65 0.00 37.29 4.85
3186 3666 0.594028 GATGGCGTACGAGATTGCGA 60.594 55.000 21.65 0.00 34.83 5.10
3187 3667 0.179121 ATGGCGTACGAGATTGCGAA 60.179 50.000 21.65 0.00 34.83 4.70
3188 3668 0.800683 TGGCGTACGAGATTGCGAAG 60.801 55.000 21.65 0.00 34.83 3.79
3189 3669 0.801067 GGCGTACGAGATTGCGAAGT 60.801 55.000 21.65 0.00 34.83 3.01
3190 3670 0.989890 GCGTACGAGATTGCGAAGTT 59.010 50.000 21.65 0.00 34.83 2.66
3191 3671 1.007319 GCGTACGAGATTGCGAAGTTC 60.007 52.381 21.65 0.00 34.83 3.01
3192 3672 2.247637 CGTACGAGATTGCGAAGTTCA 58.752 47.619 10.44 0.00 34.83 3.18
3193 3673 2.276540 CGTACGAGATTGCGAAGTTCAG 59.723 50.000 10.44 0.00 34.83 3.02
3194 3674 1.071605 ACGAGATTGCGAAGTTCAGC 58.928 50.000 3.32 8.06 34.83 4.26
3195 3675 1.337260 ACGAGATTGCGAAGTTCAGCT 60.337 47.619 16.71 1.05 34.83 4.24
3196 3676 1.728971 CGAGATTGCGAAGTTCAGCTT 59.271 47.619 16.71 7.80 40.76 3.74
3197 3677 2.158449 CGAGATTGCGAAGTTCAGCTTT 59.842 45.455 16.71 7.54 37.59 3.51
3198 3678 3.486584 GAGATTGCGAAGTTCAGCTTTG 58.513 45.455 16.71 0.00 40.72 2.77
3199 3679 3.141398 AGATTGCGAAGTTCAGCTTTGA 58.859 40.909 16.71 5.33 40.30 2.69
3200 3680 3.755378 AGATTGCGAAGTTCAGCTTTGAT 59.245 39.130 16.71 8.57 40.30 2.57
3201 3681 4.937620 AGATTGCGAAGTTCAGCTTTGATA 59.062 37.500 16.71 0.00 40.30 2.15
3202 3682 5.412594 AGATTGCGAAGTTCAGCTTTGATAA 59.587 36.000 16.71 6.05 40.30 1.75
3203 3683 5.627499 TTGCGAAGTTCAGCTTTGATAAT 57.373 34.783 16.71 0.00 40.30 1.28
3204 3684 6.735678 TTGCGAAGTTCAGCTTTGATAATA 57.264 33.333 16.71 0.00 40.30 0.98
3205 3685 6.349973 TGCGAAGTTCAGCTTTGATAATAG 57.650 37.500 16.71 0.00 40.30 1.73
3206 3686 6.106003 TGCGAAGTTCAGCTTTGATAATAGA 58.894 36.000 16.71 0.00 40.30 1.98
3207 3687 6.763135 TGCGAAGTTCAGCTTTGATAATAGAT 59.237 34.615 16.71 0.00 40.30 1.98
3208 3688 7.280876 TGCGAAGTTCAGCTTTGATAATAGATT 59.719 33.333 16.71 0.00 40.30 2.40
3209 3689 8.125448 GCGAAGTTCAGCTTTGATAATAGATTT 58.875 33.333 3.32 0.00 40.30 2.17
3210 3690 9.430838 CGAAGTTCAGCTTTGATAATAGATTTG 57.569 33.333 3.32 0.00 40.30 2.32
3214 3694 9.674824 GTTCAGCTTTGATAATAGATTTGATGG 57.325 33.333 0.00 0.00 0.00 3.51
3215 3695 8.985315 TCAGCTTTGATAATAGATTTGATGGT 57.015 30.769 0.00 0.00 0.00 3.55
3216 3696 8.843262 TCAGCTTTGATAATAGATTTGATGGTG 58.157 33.333 0.00 0.00 0.00 4.17
3217 3697 8.627403 CAGCTTTGATAATAGATTTGATGGTGT 58.373 33.333 0.00 0.00 0.00 4.16
3218 3698 8.627403 AGCTTTGATAATAGATTTGATGGTGTG 58.373 33.333 0.00 0.00 0.00 3.82
3219 3699 7.380602 GCTTTGATAATAGATTTGATGGTGTGC 59.619 37.037 0.00 0.00 0.00 4.57
3220 3700 8.523915 TTTGATAATAGATTTGATGGTGTGCT 57.476 30.769 0.00 0.00 0.00 4.40
3221 3701 8.523915 TTGATAATAGATTTGATGGTGTGCTT 57.476 30.769 0.00 0.00 0.00 3.91
3222 3702 8.158169 TGATAATAGATTTGATGGTGTGCTTC 57.842 34.615 0.00 0.00 0.00 3.86
3223 3703 7.994911 TGATAATAGATTTGATGGTGTGCTTCT 59.005 33.333 0.00 0.00 0.00 2.85
3224 3704 8.757982 ATAATAGATTTGATGGTGTGCTTCTT 57.242 30.769 0.00 0.00 0.00 2.52
3225 3705 9.851686 ATAATAGATTTGATGGTGTGCTTCTTA 57.148 29.630 0.00 0.00 0.00 2.10
3226 3706 8.579850 AATAGATTTGATGGTGTGCTTCTTAA 57.420 30.769 0.00 0.00 0.00 1.85
3227 3707 8.757982 ATAGATTTGATGGTGTGCTTCTTAAT 57.242 30.769 0.00 0.00 0.00 1.40
3228 3708 9.851686 ATAGATTTGATGGTGTGCTTCTTAATA 57.148 29.630 0.00 0.00 0.00 0.98
3229 3709 8.218338 AGATTTGATGGTGTGCTTCTTAATAG 57.782 34.615 0.00 0.00 0.00 1.73
3230 3710 7.831193 AGATTTGATGGTGTGCTTCTTAATAGT 59.169 33.333 0.00 0.00 0.00 2.12
3231 3711 6.741992 TTGATGGTGTGCTTCTTAATAGTG 57.258 37.500 0.00 0.00 0.00 2.74
3232 3712 5.804639 TGATGGTGTGCTTCTTAATAGTGT 58.195 37.500 0.00 0.00 0.00 3.55
3233 3713 6.237901 TGATGGTGTGCTTCTTAATAGTGTT 58.762 36.000 0.00 0.00 0.00 3.32
3234 3714 6.371548 TGATGGTGTGCTTCTTAATAGTGTTC 59.628 38.462 0.00 0.00 0.00 3.18
3235 3715 5.001232 TGGTGTGCTTCTTAATAGTGTTCC 58.999 41.667 0.00 0.00 0.00 3.62
3236 3716 4.092968 GGTGTGCTTCTTAATAGTGTTCCG 59.907 45.833 0.00 0.00 0.00 4.30
3237 3717 3.682858 TGTGCTTCTTAATAGTGTTCCGC 59.317 43.478 0.00 0.00 0.00 5.54
3238 3718 3.063588 GTGCTTCTTAATAGTGTTCCGCC 59.936 47.826 0.00 0.00 0.00 6.13
3239 3719 2.612672 GCTTCTTAATAGTGTTCCGCCC 59.387 50.000 0.00 0.00 0.00 6.13
3240 3720 3.681874 GCTTCTTAATAGTGTTCCGCCCT 60.682 47.826 0.00 0.00 0.00 5.19
3241 3721 3.536956 TCTTAATAGTGTTCCGCCCTG 57.463 47.619 0.00 0.00 0.00 4.45
3242 3722 1.940613 CTTAATAGTGTTCCGCCCTGC 59.059 52.381 0.00 0.00 0.00 4.85
3255 3735 3.719699 CCCTGCGTGGCTAAAATTG 57.280 52.632 0.00 0.00 0.00 2.32
3256 3736 0.887933 CCCTGCGTGGCTAAAATTGT 59.112 50.000 0.00 0.00 0.00 2.71
3257 3737 2.088423 CCCTGCGTGGCTAAAATTGTA 58.912 47.619 0.00 0.00 0.00 2.41
3258 3738 2.490115 CCCTGCGTGGCTAAAATTGTAA 59.510 45.455 0.00 0.00 0.00 2.41
3259 3739 3.498082 CCTGCGTGGCTAAAATTGTAAC 58.502 45.455 0.00 0.00 0.00 2.50
3260 3740 3.160545 CTGCGTGGCTAAAATTGTAACG 58.839 45.455 0.00 0.00 0.00 3.18
3261 3741 2.095668 TGCGTGGCTAAAATTGTAACGG 60.096 45.455 1.62 0.00 0.00 4.44
3262 3742 2.160022 GCGTGGCTAAAATTGTAACGGA 59.840 45.455 1.62 0.00 0.00 4.69
3263 3743 3.181504 GCGTGGCTAAAATTGTAACGGAT 60.182 43.478 1.62 0.00 0.00 4.18
3264 3744 4.339429 CGTGGCTAAAATTGTAACGGATG 58.661 43.478 0.00 0.00 0.00 3.51
3265 3745 4.093703 CGTGGCTAAAATTGTAACGGATGA 59.906 41.667 0.00 0.00 0.00 2.92
3266 3746 5.220777 CGTGGCTAAAATTGTAACGGATGAT 60.221 40.000 0.00 0.00 0.00 2.45
3267 3747 6.560711 GTGGCTAAAATTGTAACGGATGATT 58.439 36.000 0.00 0.00 0.00 2.57
3268 3748 6.472163 GTGGCTAAAATTGTAACGGATGATTG 59.528 38.462 0.00 0.00 0.00 2.67
3269 3749 6.151985 TGGCTAAAATTGTAACGGATGATTGT 59.848 34.615 0.00 0.00 0.00 2.71
3270 3750 7.337184 TGGCTAAAATTGTAACGGATGATTGTA 59.663 33.333 0.00 0.00 0.00 2.41
3271 3751 8.349983 GGCTAAAATTGTAACGGATGATTGTAT 58.650 33.333 0.00 0.00 0.00 2.29
3272 3752 9.169468 GCTAAAATTGTAACGGATGATTGTATG 57.831 33.333 0.00 0.00 0.00 2.39
3424 3904 4.726035 AGCATGATGAATCCTCAGGAAT 57.274 40.909 0.00 0.00 34.34 3.01
3436 3916 5.429681 TCCTCAGGAATCGGAAACATAAA 57.570 39.130 0.00 0.00 0.00 1.40
3437 3917 5.811190 TCCTCAGGAATCGGAAACATAAAA 58.189 37.500 0.00 0.00 0.00 1.52
3442 3922 6.071672 TCAGGAATCGGAAACATAAAAATGCA 60.072 34.615 0.00 0.00 0.00 3.96
3445 3925 6.018832 GGAATCGGAAACATAAAAATGCATGG 60.019 38.462 0.00 0.00 0.00 3.66
3458 3938 7.671495 AAAAATGCATGGTAAAACTTGATCC 57.329 32.000 0.00 0.00 0.00 3.36
3504 3985 8.145122 TGACGAATTATGTGTATGCCATAGTTA 58.855 33.333 0.00 0.00 28.52 2.24
3543 4024 1.950216 CTATCTACGAGGCTGCACTCA 59.050 52.381 15.25 0.61 37.34 3.41
3544 4025 0.743688 ATCTACGAGGCTGCACTCAG 59.256 55.000 15.25 11.17 43.16 3.35
3555 4036 3.526825 GCACTCAGCGAAACGTTTT 57.473 47.368 15.89 0.00 0.00 2.43
3556 4037 1.385999 GCACTCAGCGAAACGTTTTC 58.614 50.000 15.89 10.26 0.00 2.29
3557 4038 1.003866 GCACTCAGCGAAACGTTTTCT 60.004 47.619 15.89 12.37 0.00 2.52
3558 4039 2.538939 GCACTCAGCGAAACGTTTTCTT 60.539 45.455 15.89 0.65 0.00 2.52
3559 4040 3.680789 CACTCAGCGAAACGTTTTCTTT 58.319 40.909 15.89 0.00 0.00 2.52
3560 4041 4.784079 GCACTCAGCGAAACGTTTTCTTTA 60.784 41.667 15.89 5.66 0.00 1.85
3565 4046 6.721321 TCAGCGAAACGTTTTCTTTAGATTT 58.279 32.000 15.89 0.00 0.00 2.17
3584 4065 4.890158 TTTCAATGCAGAGTAGACCAGA 57.110 40.909 0.00 0.00 0.00 3.86
3585 4066 4.890158 TTCAATGCAGAGTAGACCAGAA 57.110 40.909 0.00 0.00 0.00 3.02
3586 4067 4.462508 TCAATGCAGAGTAGACCAGAAG 57.537 45.455 0.00 0.00 0.00 2.85
3587 4068 4.089361 TCAATGCAGAGTAGACCAGAAGA 58.911 43.478 0.00 0.00 0.00 2.87
3588 4069 4.528206 TCAATGCAGAGTAGACCAGAAGAA 59.472 41.667 0.00 0.00 0.00 2.52
3589 4070 5.012046 TCAATGCAGAGTAGACCAGAAGAAA 59.988 40.000 0.00 0.00 0.00 2.52
3590 4071 4.955811 TGCAGAGTAGACCAGAAGAAAA 57.044 40.909 0.00 0.00 0.00 2.29
3591 4072 5.290493 TGCAGAGTAGACCAGAAGAAAAA 57.710 39.130 0.00 0.00 0.00 1.94
3598 4079 8.700973 AGAGTAGACCAGAAGAAAAATCCTATC 58.299 37.037 0.00 0.00 0.00 2.08
3601 4082 6.342111 AGACCAGAAGAAAAATCCTATCGTC 58.658 40.000 0.00 0.00 0.00 4.20
3608 4089 9.137459 AGAAGAAAAATCCTATCGTCTCTATGA 57.863 33.333 0.00 0.00 27.82 2.15
3694 4175 8.992835 AAGCAGAAATAAAGAATCCATTTCAC 57.007 30.769 12.19 6.50 39.86 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.809159 ATGATGATGTATCGAGTAGAAACTTG 57.191 34.615 0.00 0.00 38.71 3.16
1 2 8.633561 TGATGATGATGTATCGAGTAGAAACTT 58.366 33.333 0.00 0.00 38.71 2.66
2 3 8.171164 TGATGATGATGTATCGAGTAGAAACT 57.829 34.615 0.00 0.00 38.71 2.66
3 4 8.803201 TTGATGATGATGTATCGAGTAGAAAC 57.197 34.615 0.00 0.00 38.71 2.78
7 8 9.846248 TTGTATTGATGATGATGTATCGAGTAG 57.154 33.333 0.00 0.00 38.71 2.57
45 47 5.845734 TCTCAAAGAGGTAATACCCCTACA 58.154 41.667 5.71 0.00 39.75 2.74
72 74 8.375493 AGGGACAGTATTTACATAACTTCAGA 57.625 34.615 0.00 0.00 0.00 3.27
78 80 7.010830 GGACGAAAGGGACAGTATTTACATAAC 59.989 40.741 0.00 0.00 0.00 1.89
79 81 7.043565 GGACGAAAGGGACAGTATTTACATAA 58.956 38.462 0.00 0.00 0.00 1.90
148 150 1.310904 GTAAAACCGGCACACCTCAA 58.689 50.000 0.00 0.00 0.00 3.02
258 261 3.881688 CTGCTAAAGCTGGACATAAGCAT 59.118 43.478 3.26 0.00 43.37 3.79
363 366 1.131126 CCATTCTCAAAGCGCGTTCAT 59.869 47.619 8.43 0.00 0.00 2.57
381 384 1.508667 ATGAATGGCCTGGTGTCCCA 61.509 55.000 3.32 0.00 38.87 4.37
392 395 1.869767 CTAGCTCCGTTCATGAATGGC 59.130 52.381 33.37 24.74 45.02 4.40
458 461 0.625849 ATTTCCGCCCCATCAGTCTT 59.374 50.000 0.00 0.00 0.00 3.01
484 487 0.833949 GAAGGAGGGTGATGAGGACC 59.166 60.000 0.00 0.00 0.00 4.46
492 495 2.986050 ACTACCAAAGAAGGAGGGTGA 58.014 47.619 0.00 0.00 34.88 4.02
528 531 1.708341 AACCTGCATTGGCTGAACTT 58.292 45.000 0.00 0.00 41.06 2.66
550 553 7.092354 ACTCCTTCTCAACTCTCCATACTACTA 60.092 40.741 0.00 0.00 0.00 1.82
551 554 6.080969 TCCTTCTCAACTCTCCATACTACT 57.919 41.667 0.00 0.00 0.00 2.57
552 555 5.889289 ACTCCTTCTCAACTCTCCATACTAC 59.111 44.000 0.00 0.00 0.00 2.73
631 634 6.668323 ACCTTGTCAAGAAAATGAATGTACG 58.332 36.000 14.42 0.00 0.00 3.67
632 635 8.784043 AGTACCTTGTCAAGAAAATGAATGTAC 58.216 33.333 14.42 12.76 0.00 2.90
639 642 7.038154 TCCAAAGTACCTTGTCAAGAAAATG 57.962 36.000 14.42 5.38 0.00 2.32
644 647 4.124238 CGTTCCAAAGTACCTTGTCAAGA 58.876 43.478 14.42 0.00 0.00 3.02
645 648 4.124238 TCGTTCCAAAGTACCTTGTCAAG 58.876 43.478 5.53 5.53 0.00 3.02
648 651 4.374399 TCTTCGTTCCAAAGTACCTTGTC 58.626 43.478 3.60 0.00 0.00 3.18
649 652 4.411256 TCTTCGTTCCAAAGTACCTTGT 57.589 40.909 3.60 0.00 0.00 3.16
650 653 5.296035 ACTTTCTTCGTTCCAAAGTACCTTG 59.704 40.000 0.00 0.00 38.34 3.61
651 654 5.434408 ACTTTCTTCGTTCCAAAGTACCTT 58.566 37.500 0.00 0.00 38.34 3.50
657 717 9.382244 CTAAAATGTACTTTCTTCGTTCCAAAG 57.618 33.333 0.00 0.00 33.98 2.77
686 746 1.079317 CACACCGTGTCACGTCACAA 61.079 55.000 23.01 0.00 40.58 3.33
701 761 4.176271 GCCTAAAAATTGCTCCATCACAC 58.824 43.478 0.00 0.00 0.00 3.82
718 778 4.116961 CTCGATATTTCCAACACGCCTAA 58.883 43.478 0.00 0.00 0.00 2.69
755 816 1.379527 CAACTGCTCGGTATTTCCCC 58.620 55.000 0.00 0.00 0.00 4.81
829 993 5.642063 TCGAAAGAAAATATGACAGGTGACC 59.358 40.000 0.00 0.00 37.03 4.02
851 1015 1.298413 CGCGTGGGTAGTGATCTCG 60.298 63.158 0.00 0.00 0.00 4.04
852 1016 1.589196 GCGCGTGGGTAGTGATCTC 60.589 63.158 8.43 0.00 0.00 2.75
853 1017 2.494918 GCGCGTGGGTAGTGATCT 59.505 61.111 8.43 0.00 0.00 2.75
856 1020 3.617735 TTGGCGCGTGGGTAGTGA 61.618 61.111 8.43 0.00 0.00 3.41
857 1021 3.419759 GTTGGCGCGTGGGTAGTG 61.420 66.667 8.43 0.00 0.00 2.74
858 1022 3.931247 TGTTGGCGCGTGGGTAGT 61.931 61.111 8.43 0.00 0.00 2.73
859 1023 3.419759 GTGTTGGCGCGTGGGTAG 61.420 66.667 8.43 0.00 0.00 3.18
860 1024 4.992511 GGTGTTGGCGCGTGGGTA 62.993 66.667 8.43 0.00 0.00 3.69
888 1072 2.011122 ATATGGTAGGTGGACTCCCG 57.989 55.000 0.00 0.00 34.29 5.14
927 1115 5.798132 CGGGAGAATGATGATAGGATCAAA 58.202 41.667 0.00 0.00 43.50 2.69
1021 1331 2.133641 GCAGGAGGAGGAGAGGAGC 61.134 68.421 0.00 0.00 0.00 4.70
1042 1352 2.100603 CGAAGGCGAGACGAGGAC 59.899 66.667 0.00 0.00 40.82 3.85
1104 1414 0.320247 CACAACGCAGGAAGCTCTCT 60.320 55.000 0.00 0.00 42.61 3.10
1606 1916 1.298339 GGCCGTATTTGCGCATCAC 60.298 57.895 12.75 8.77 0.00 3.06
1856 2166 1.887956 GCTGCCATTTGGTCAGGAGAA 60.888 52.381 17.13 0.00 38.72 2.87
2031 2341 3.932710 CGCTTGGCTTAATGTCTAGTTCA 59.067 43.478 0.00 0.00 0.00 3.18
2220 2530 3.775202 CTCTTCGACGATCTTGGTGAAT 58.225 45.455 0.00 0.00 0.00 2.57
2520 2830 1.672356 CCACACCTTGGCCTCTTCG 60.672 63.158 3.32 0.00 39.07 3.79
2523 2833 3.260100 CCCCACACCTTGGCCTCT 61.260 66.667 3.32 0.00 45.37 3.69
2694 3004 3.118408 ACCTGCGCCTGAACTATCAAATA 60.118 43.478 4.18 0.00 34.49 1.40
2701 3011 0.107831 ACAAACCTGCGCCTGAACTA 59.892 50.000 4.18 0.00 0.00 2.24
2728 3041 9.737427 TTTTATTTGTTGAGAAACATTCGCTAA 57.263 25.926 0.00 0.00 32.01 3.09
2793 3107 6.510960 GCAAACCAAAAACGACAGCATAATTT 60.511 34.615 0.00 0.00 0.00 1.82
2812 3126 7.882179 TCTAGTTTCTTTTATTCCTGCAAACC 58.118 34.615 0.00 0.00 0.00 3.27
2916 3316 6.481644 CAGCTTTGGTTCTCCTATTATCACTC 59.518 42.308 0.00 0.00 34.23 3.51
2920 3320 7.865706 TTTCAGCTTTGGTTCTCCTATTATC 57.134 36.000 0.00 0.00 34.23 1.75
2947 3347 9.350357 GAATAATCAAACACCATGATCATATGC 57.650 33.333 8.15 0.00 36.53 3.14
3108 3588 8.700973 ACCCATAACTTGTTTTTCTTAACATGT 58.299 29.630 0.00 0.00 43.83 3.21
3131 3611 5.360144 TCGATATCTAAATAGCTAGCCACCC 59.640 44.000 12.13 0.00 0.00 4.61
3149 3629 5.615289 GCCATCATATTAGCCCTTCGATAT 58.385 41.667 0.00 0.00 0.00 1.63
3150 3630 4.441495 CGCCATCATATTAGCCCTTCGATA 60.441 45.833 0.00 0.00 0.00 2.92
3151 3631 3.679917 CGCCATCATATTAGCCCTTCGAT 60.680 47.826 0.00 0.00 0.00 3.59
3152 3632 2.353704 CGCCATCATATTAGCCCTTCGA 60.354 50.000 0.00 0.00 0.00 3.71
3153 3633 2.002586 CGCCATCATATTAGCCCTTCG 58.997 52.381 0.00 0.00 0.00 3.79
3154 3634 3.059352 ACGCCATCATATTAGCCCTTC 57.941 47.619 0.00 0.00 0.00 3.46
3155 3635 3.616560 CGTACGCCATCATATTAGCCCTT 60.617 47.826 0.52 0.00 0.00 3.95
3156 3636 2.094182 CGTACGCCATCATATTAGCCCT 60.094 50.000 0.52 0.00 0.00 5.19
3157 3637 2.094390 TCGTACGCCATCATATTAGCCC 60.094 50.000 11.24 0.00 0.00 5.19
3158 3638 3.119602 TCTCGTACGCCATCATATTAGCC 60.120 47.826 11.24 0.00 0.00 3.93
3159 3639 4.092771 TCTCGTACGCCATCATATTAGC 57.907 45.455 11.24 0.00 0.00 3.09
3160 3640 5.004821 GCAATCTCGTACGCCATCATATTAG 59.995 44.000 11.24 0.00 0.00 1.73
3161 3641 4.862574 GCAATCTCGTACGCCATCATATTA 59.137 41.667 11.24 0.00 0.00 0.98
3162 3642 3.679980 GCAATCTCGTACGCCATCATATT 59.320 43.478 11.24 0.00 0.00 1.28
3163 3643 3.254060 GCAATCTCGTACGCCATCATAT 58.746 45.455 11.24 0.00 0.00 1.78
3164 3644 2.672714 GCAATCTCGTACGCCATCATA 58.327 47.619 11.24 0.00 0.00 2.15
3165 3645 1.502231 GCAATCTCGTACGCCATCAT 58.498 50.000 11.24 0.00 0.00 2.45
3166 3646 0.869880 CGCAATCTCGTACGCCATCA 60.870 55.000 11.24 0.00 0.00 3.07
3167 3647 0.594028 TCGCAATCTCGTACGCCATC 60.594 55.000 11.24 0.00 0.00 3.51
3168 3648 0.179121 TTCGCAATCTCGTACGCCAT 60.179 50.000 11.24 1.32 0.00 4.40
3169 3649 0.800683 CTTCGCAATCTCGTACGCCA 60.801 55.000 11.24 0.00 0.00 5.69
3170 3650 0.801067 ACTTCGCAATCTCGTACGCC 60.801 55.000 11.24 0.00 0.00 5.68
3171 3651 0.989890 AACTTCGCAATCTCGTACGC 59.010 50.000 11.24 0.00 0.00 4.42
3172 3652 2.247637 TGAACTTCGCAATCTCGTACG 58.752 47.619 9.53 9.53 0.00 3.67
3173 3653 2.028165 GCTGAACTTCGCAATCTCGTAC 59.972 50.000 0.00 0.00 0.00 3.67
3174 3654 2.094700 AGCTGAACTTCGCAATCTCGTA 60.095 45.455 0.00 0.00 0.00 3.43
3175 3655 1.071605 GCTGAACTTCGCAATCTCGT 58.928 50.000 0.00 0.00 0.00 4.18
3176 3656 1.354040 AGCTGAACTTCGCAATCTCG 58.646 50.000 0.00 0.00 0.00 4.04
3177 3657 3.187227 TCAAAGCTGAACTTCGCAATCTC 59.813 43.478 0.00 0.00 37.75 2.75
3178 3658 3.141398 TCAAAGCTGAACTTCGCAATCT 58.859 40.909 0.00 0.00 37.75 2.40
3179 3659 3.542712 TCAAAGCTGAACTTCGCAATC 57.457 42.857 0.00 0.00 37.75 2.67
3180 3660 5.627499 TTATCAAAGCTGAACTTCGCAAT 57.373 34.783 0.00 1.24 37.75 3.56
3181 3661 5.627499 ATTATCAAAGCTGAACTTCGCAA 57.373 34.783 0.00 0.00 37.75 4.85
3182 3662 6.106003 TCTATTATCAAAGCTGAACTTCGCA 58.894 36.000 0.00 0.00 37.75 5.10
3183 3663 6.589830 TCTATTATCAAAGCTGAACTTCGC 57.410 37.500 0.00 0.00 37.75 4.70
3184 3664 9.430838 CAAATCTATTATCAAAGCTGAACTTCG 57.569 33.333 0.00 0.00 37.75 3.79
3188 3668 9.674824 CCATCAAATCTATTATCAAAGCTGAAC 57.325 33.333 0.00 0.00 34.49 3.18
3189 3669 9.412460 ACCATCAAATCTATTATCAAAGCTGAA 57.588 29.630 0.00 0.00 34.49 3.02
3190 3670 8.843262 CACCATCAAATCTATTATCAAAGCTGA 58.157 33.333 0.00 0.00 35.56 4.26
3191 3671 8.627403 ACACCATCAAATCTATTATCAAAGCTG 58.373 33.333 0.00 0.00 0.00 4.24
3192 3672 8.627403 CACACCATCAAATCTATTATCAAAGCT 58.373 33.333 0.00 0.00 0.00 3.74
3193 3673 7.380602 GCACACCATCAAATCTATTATCAAAGC 59.619 37.037 0.00 0.00 0.00 3.51
3194 3674 8.627403 AGCACACCATCAAATCTATTATCAAAG 58.373 33.333 0.00 0.00 0.00 2.77
3195 3675 8.523915 AGCACACCATCAAATCTATTATCAAA 57.476 30.769 0.00 0.00 0.00 2.69
3196 3676 8.523915 AAGCACACCATCAAATCTATTATCAA 57.476 30.769 0.00 0.00 0.00 2.57
3197 3677 7.994911 AGAAGCACACCATCAAATCTATTATCA 59.005 33.333 0.00 0.00 0.00 2.15
3198 3678 8.388484 AGAAGCACACCATCAAATCTATTATC 57.612 34.615 0.00 0.00 0.00 1.75
3199 3679 8.757982 AAGAAGCACACCATCAAATCTATTAT 57.242 30.769 0.00 0.00 0.00 1.28
3200 3680 9.679661 TTAAGAAGCACACCATCAAATCTATTA 57.320 29.630 0.00 0.00 0.00 0.98
3201 3681 8.579850 TTAAGAAGCACACCATCAAATCTATT 57.420 30.769 0.00 0.00 0.00 1.73
3202 3682 8.757982 ATTAAGAAGCACACCATCAAATCTAT 57.242 30.769 0.00 0.00 0.00 1.98
3203 3683 9.330063 CTATTAAGAAGCACACCATCAAATCTA 57.670 33.333 0.00 0.00 0.00 1.98
3204 3684 7.831193 ACTATTAAGAAGCACACCATCAAATCT 59.169 33.333 0.00 0.00 0.00 2.40
3205 3685 7.912250 CACTATTAAGAAGCACACCATCAAATC 59.088 37.037 0.00 0.00 0.00 2.17
3206 3686 7.394359 ACACTATTAAGAAGCACACCATCAAAT 59.606 33.333 0.00 0.00 0.00 2.32
3207 3687 6.714810 ACACTATTAAGAAGCACACCATCAAA 59.285 34.615 0.00 0.00 0.00 2.69
3208 3688 6.237901 ACACTATTAAGAAGCACACCATCAA 58.762 36.000 0.00 0.00 0.00 2.57
3209 3689 5.804639 ACACTATTAAGAAGCACACCATCA 58.195 37.500 0.00 0.00 0.00 3.07
3210 3690 6.183360 GGAACACTATTAAGAAGCACACCATC 60.183 42.308 0.00 0.00 0.00 3.51
3211 3691 5.648092 GGAACACTATTAAGAAGCACACCAT 59.352 40.000 0.00 0.00 0.00 3.55
3212 3692 5.001232 GGAACACTATTAAGAAGCACACCA 58.999 41.667 0.00 0.00 0.00 4.17
3213 3693 4.092968 CGGAACACTATTAAGAAGCACACC 59.907 45.833 0.00 0.00 0.00 4.16
3214 3694 4.435651 GCGGAACACTATTAAGAAGCACAC 60.436 45.833 0.00 0.00 0.00 3.82
3215 3695 3.682858 GCGGAACACTATTAAGAAGCACA 59.317 43.478 0.00 0.00 0.00 4.57
3216 3696 3.063588 GGCGGAACACTATTAAGAAGCAC 59.936 47.826 0.00 0.00 0.00 4.40
3217 3697 3.267483 GGCGGAACACTATTAAGAAGCA 58.733 45.455 0.00 0.00 0.00 3.91
3218 3698 2.612672 GGGCGGAACACTATTAAGAAGC 59.387 50.000 0.00 0.00 0.00 3.86
3219 3699 3.871594 CAGGGCGGAACACTATTAAGAAG 59.128 47.826 0.00 0.00 0.00 2.85
3220 3700 3.869065 CAGGGCGGAACACTATTAAGAA 58.131 45.455 0.00 0.00 0.00 2.52
3221 3701 2.419574 GCAGGGCGGAACACTATTAAGA 60.420 50.000 0.00 0.00 0.00 2.10
3222 3702 1.940613 GCAGGGCGGAACACTATTAAG 59.059 52.381 0.00 0.00 0.00 1.85
3223 3703 2.032680 GCAGGGCGGAACACTATTAA 57.967 50.000 0.00 0.00 0.00 1.40
3224 3704 3.772619 GCAGGGCGGAACACTATTA 57.227 52.632 0.00 0.00 0.00 0.98
3225 3705 4.637771 GCAGGGCGGAACACTATT 57.362 55.556 0.00 0.00 0.00 1.73
3237 3717 0.887933 ACAATTTTAGCCACGCAGGG 59.112 50.000 0.00 0.00 38.09 4.45
3238 3718 3.498082 GTTACAATTTTAGCCACGCAGG 58.502 45.455 0.00 0.00 41.84 4.85
3239 3719 3.160545 CGTTACAATTTTAGCCACGCAG 58.839 45.455 0.00 0.00 0.00 5.18
3240 3720 2.095668 CCGTTACAATTTTAGCCACGCA 60.096 45.455 0.00 0.00 0.00 5.24
3241 3721 2.160022 TCCGTTACAATTTTAGCCACGC 59.840 45.455 0.00 0.00 0.00 5.34
3242 3722 4.093703 TCATCCGTTACAATTTTAGCCACG 59.906 41.667 0.00 0.00 0.00 4.94
3243 3723 5.554822 TCATCCGTTACAATTTTAGCCAC 57.445 39.130 0.00 0.00 0.00 5.01
3244 3724 6.151985 ACAATCATCCGTTACAATTTTAGCCA 59.848 34.615 0.00 0.00 0.00 4.75
3245 3725 6.560711 ACAATCATCCGTTACAATTTTAGCC 58.439 36.000 0.00 0.00 0.00 3.93
3246 3726 9.169468 CATACAATCATCCGTTACAATTTTAGC 57.831 33.333 0.00 0.00 0.00 3.09
3309 3789 9.813446 ACGTTTAAGTATCTCCGATATCTTTTT 57.187 29.630 0.34 0.00 0.00 1.94
3310 3790 9.245962 CACGTTTAAGTATCTCCGATATCTTTT 57.754 33.333 0.34 0.00 0.00 2.27
3311 3791 8.627403 TCACGTTTAAGTATCTCCGATATCTTT 58.373 33.333 0.34 0.00 0.00 2.52
3312 3792 8.162878 TCACGTTTAAGTATCTCCGATATCTT 57.837 34.615 0.34 0.00 0.00 2.40
3313 3793 7.660617 TCTCACGTTTAAGTATCTCCGATATCT 59.339 37.037 0.34 0.00 0.00 1.98
3314 3794 7.804712 TCTCACGTTTAAGTATCTCCGATATC 58.195 38.462 0.00 0.00 0.00 1.63
3320 3800 7.829378 ACATTTCTCACGTTTAAGTATCTCC 57.171 36.000 0.00 0.00 0.00 3.71
3333 3813 5.065218 AGCTAGCCATTTTACATTTCTCACG 59.935 40.000 12.13 0.00 0.00 4.35
3395 3875 5.467735 TGAGGATTCATCATGCTACAATTCG 59.532 40.000 0.00 0.00 32.63 3.34
3424 3904 5.398603 ACCATGCATTTTTATGTTTCCGA 57.601 34.783 0.00 0.00 0.00 4.55
3436 3916 5.047377 ACGGATCAAGTTTTACCATGCATTT 60.047 36.000 0.00 0.00 0.00 2.32
3437 3917 4.462483 ACGGATCAAGTTTTACCATGCATT 59.538 37.500 0.00 0.00 0.00 3.56
3442 3922 3.417101 TGCACGGATCAAGTTTTACCAT 58.583 40.909 0.00 0.00 0.00 3.55
3445 3925 4.083537 TGTGATGCACGGATCAAGTTTTAC 60.084 41.667 2.55 0.00 37.14 2.01
3475 3956 4.127171 GGCATACACATAATTCGTCAGGT 58.873 43.478 0.00 0.00 0.00 4.00
3477 3958 5.929697 ATGGCATACACATAATTCGTCAG 57.070 39.130 0.00 0.00 0.00 3.51
3478 3959 6.521162 ACTATGGCATACACATAATTCGTCA 58.479 36.000 2.32 0.00 31.02 4.35
3479 3960 7.421530 AACTATGGCATACACATAATTCGTC 57.578 36.000 2.32 0.00 31.02 4.20
3481 3962 9.759259 CAATAACTATGGCATACACATAATTCG 57.241 33.333 2.32 0.00 31.02 3.34
3485 3966 9.719355 CCTACAATAACTATGGCATACACATAA 57.281 33.333 2.32 0.00 31.02 1.90
3508 3989 8.195436 CCTCGTAGATAGTTTCATTTGTTCCTA 58.805 37.037 0.00 0.00 33.89 2.94
3543 4024 6.721321 TGAAATCTAAAGAAAACGTTTCGCT 58.279 32.000 15.01 11.91 0.00 4.93
3544 4025 6.963017 TGAAATCTAAAGAAAACGTTTCGC 57.037 33.333 15.01 9.72 0.00 4.70
3545 4026 7.939386 GCATTGAAATCTAAAGAAAACGTTTCG 59.061 33.333 15.01 0.00 0.00 3.46
3546 4027 8.751335 TGCATTGAAATCTAAAGAAAACGTTTC 58.249 29.630 15.01 8.08 0.00 2.78
3547 4028 8.641499 TGCATTGAAATCTAAAGAAAACGTTT 57.359 26.923 7.96 7.96 0.00 3.60
3548 4029 8.134895 TCTGCATTGAAATCTAAAGAAAACGTT 58.865 29.630 0.00 0.00 0.00 3.99
3549 4030 7.648142 TCTGCATTGAAATCTAAAGAAAACGT 58.352 30.769 0.00 0.00 0.00 3.99
3550 4031 7.805071 ACTCTGCATTGAAATCTAAAGAAAACG 59.195 33.333 0.00 0.00 0.00 3.60
3553 4034 9.725019 TCTACTCTGCATTGAAATCTAAAGAAA 57.275 29.630 0.00 0.00 0.00 2.52
3554 4035 9.155975 GTCTACTCTGCATTGAAATCTAAAGAA 57.844 33.333 0.00 0.00 0.00 2.52
3555 4036 7.766278 GGTCTACTCTGCATTGAAATCTAAAGA 59.234 37.037 0.00 0.00 0.00 2.52
3556 4037 7.550551 TGGTCTACTCTGCATTGAAATCTAAAG 59.449 37.037 0.00 0.00 0.00 1.85
3557 4038 7.394016 TGGTCTACTCTGCATTGAAATCTAAA 58.606 34.615 0.00 0.00 0.00 1.85
3558 4039 6.946340 TGGTCTACTCTGCATTGAAATCTAA 58.054 36.000 0.00 0.00 0.00 2.10
3559 4040 6.381133 TCTGGTCTACTCTGCATTGAAATCTA 59.619 38.462 0.00 0.00 0.00 1.98
3560 4041 5.188555 TCTGGTCTACTCTGCATTGAAATCT 59.811 40.000 0.00 0.00 0.00 2.40
3565 4046 4.089361 TCTTCTGGTCTACTCTGCATTGA 58.911 43.478 0.00 0.00 0.00 2.57
3590 4071 9.787435 GGTCTATATCATAGAGACGATAGGATT 57.213 37.037 12.34 0.00 45.46 3.01
3591 4072 8.939932 TGGTCTATATCATAGAGACGATAGGAT 58.060 37.037 12.34 0.00 45.46 3.24


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

AutoCloner maintained by Alex Coulton.