Multiple sequence alignment - TraesCS7B01G161300

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 TraesCS7B01G161300 chr7B 100.000 4769 0 0 1 4769 220298842 220294074 0 8807
1 TraesCS7B01G161300 chr1A 98.915 2672 28 1 2098 4769 147691725 147689055 0 4772
2 TraesCS7B01G161300 chr6D 84.324 3802 504 54 1000 4769 72039604 72035863 0 3635
3 TraesCS7B01G161300 chr7A 83.856 3797 544 35 1004 4769 652174811 652171053 0 3552
4 TraesCS7B01G161300 chr7D 83.130 3118 430 53 1687 4769 95071038 95074094 0 2756
5 TraesCS7B01G161300 chr7D 87.732 970 101 10 4 965 225200566 225201525 0 1116
6 TraesCS7B01G161300 chr4B 82.663 3132 470 44 1000 4097 246307962 246311054 0 2708
7 TraesCS7B01G161300 chr1D 82.883 3108 435 61 1000 4072 107598810 107601855 0 2702
8 TraesCS7B01G161300 chr2A 94.457 1317 70 3 2888 4203 709062716 709061402 0 2025
9 TraesCS7B01G161300 chr2A 83.564 1588 235 16 3190 4769 642732543 642734112 0 1463
10 TraesCS7B01G161300 chr5D 82.395 2255 320 29 2534 4769 363187363 363185167 0 1893
11 TraesCS7B01G161300 chr4A 83.184 1897 282 24 2887 4769 680343770 680341897 0 1701
12 TraesCS7B01G161300 chr4A 83.026 1897 284 24 2887 4769 680333562 680331690 0 1685
13 TraesCS7B01G161300 chr6B 83.448 1311 182 17 3465 4769 413739999 413738718 0 1186
14 TraesCS7B01G161300 chrUn 100.000 392 0 0 2514 2905 479805443 479805834 0 725


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 TraesCS7B01G161300 chr7B 220294074 220298842 4768 True 8807 8807 100.000 1 4769 1 chr7B.!!$R1 4768
1 TraesCS7B01G161300 chr1A 147689055 147691725 2670 True 4772 4772 98.915 2098 4769 1 chr1A.!!$R1 2671
2 TraesCS7B01G161300 chr6D 72035863 72039604 3741 True 3635 3635 84.324 1000 4769 1 chr6D.!!$R1 3769
3 TraesCS7B01G161300 chr7A 652171053 652174811 3758 True 3552 3552 83.856 1004 4769 1 chr7A.!!$R1 3765
4 TraesCS7B01G161300 chr7D 95071038 95074094 3056 False 2756 2756 83.130 1687 4769 1 chr7D.!!$F1 3082
5 TraesCS7B01G161300 chr7D 225200566 225201525 959 False 1116 1116 87.732 4 965 1 chr7D.!!$F2 961
6 TraesCS7B01G161300 chr4B 246307962 246311054 3092 False 2708 2708 82.663 1000 4097 1 chr4B.!!$F1 3097
7 TraesCS7B01G161300 chr1D 107598810 107601855 3045 False 2702 2702 82.883 1000 4072 1 chr1D.!!$F1 3072
8 TraesCS7B01G161300 chr2A 709061402 709062716 1314 True 2025 2025 94.457 2888 4203 1 chr2A.!!$R1 1315
9 TraesCS7B01G161300 chr2A 642732543 642734112 1569 False 1463 1463 83.564 3190 4769 1 chr2A.!!$F1 1579
10 TraesCS7B01G161300 chr5D 363185167 363187363 2196 True 1893 1893 82.395 2534 4769 1 chr5D.!!$R1 2235
11 TraesCS7B01G161300 chr4A 680341897 680343770 1873 True 1701 1701 83.184 2887 4769 1 chr4A.!!$R2 1882
12 TraesCS7B01G161300 chr4A 680331690 680333562 1872 True 1685 1685 83.026 2887 4769 1 chr4A.!!$R1 1882
13 TraesCS7B01G161300 chr6B 413738718 413739999 1281 True 1186 1186 83.448 3465 4769 1 chr6B.!!$R1 1304

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
904 912 0.109132 GCAAAATCCTTCGCCACTGG 60.109 55.0 0.0 0.0 0.0 4.00 F
945 953 0.179119 ACTCGCCGTTCCTTATTCCG 60.179 55.0 0.0 0.0 0.0 4.30 F
946 954 0.179119 CTCGCCGTTCCTTATTCCGT 60.179 55.0 0.0 0.0 0.0 4.69 F
1557 1566 0.250640 CTGTTGCTGCCTTCACTCCT 60.251 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2016 2038 0.168348 AGTGGAAGACGACGATCACG 59.832 55.000 0.00 7.58 45.75 4.35 R
2058 2080 0.518636 CGTGGTGCTTGTGGATGAAG 59.481 55.000 0.00 0.00 0.00 3.02 R
2905 2937 1.228769 ACTGCCTGACCGGACTACA 60.229 57.895 9.46 0.80 33.16 2.74 R
4334 4396 2.703798 CCGCACCATGGCAAAGAGG 61.704 63.158 13.04 7.06 0.00 3.69 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
24 25 0.658536 GTGCTTTCACTTGTCGCTGC 60.659 55.000 0.00 0.00 40.03 5.25
25 26 1.094650 TGCTTTCACTTGTCGCTGCA 61.095 50.000 0.00 0.00 0.00 4.41
73 74 3.214328 TGCCAAAGAGGACAAGTCTTTC 58.786 45.455 0.00 0.00 41.37 2.62
89 90 6.560253 AGTCTTTCAATTATCAACGTTGCT 57.440 33.333 23.47 16.63 0.00 3.91
106 107 7.938563 ACGTTGCTTATCTCATAGAGATTTC 57.061 36.000 14.06 5.66 45.86 2.17
129 130 3.646162 TCTTGACAGTTTAAGCCAGGAGA 59.354 43.478 0.00 0.00 0.00 3.71
130 131 4.287067 TCTTGACAGTTTAAGCCAGGAGAT 59.713 41.667 0.00 0.00 0.00 2.75
131 132 3.942829 TGACAGTTTAAGCCAGGAGATG 58.057 45.455 0.00 0.00 0.00 2.90
146 147 3.461085 AGGAGATGGGTGAATATGCTGTT 59.539 43.478 0.00 0.00 0.00 3.16
166 167 8.935844 TGCTGTTCAGTTTAATTAGATGTACAG 58.064 33.333 18.57 18.57 40.28 2.74
179 180 9.988815 AATTAGATGTACAGATAATGTCCTGAC 57.011 33.333 13.32 0.00 42.70 3.51
193 194 5.246981 TGTCCTGACAAAGAAGGATGAAT 57.753 39.130 0.00 0.00 44.30 2.57
264 265 8.157476 AGTTAGTTGATGTTACCTGAAATGTCT 58.843 33.333 0.00 0.00 0.00 3.41
334 335 5.784177 TGTGCTTAAACTAGGACTCTCAAG 58.216 41.667 0.00 0.00 37.38 3.02
348 349 7.158021 AGGACTCTCAAGATTTTACTGACAAG 58.842 38.462 0.00 0.00 0.00 3.16
351 352 5.560724 TCTCAAGATTTTACTGACAAGGGG 58.439 41.667 0.00 0.00 0.00 4.79
352 353 4.079253 TCAAGATTTTACTGACAAGGGGC 58.921 43.478 0.00 0.00 0.00 5.80
353 354 4.082125 CAAGATTTTACTGACAAGGGGCT 58.918 43.478 0.00 0.00 0.00 5.19
355 356 5.104259 AGATTTTACTGACAAGGGGCTAG 57.896 43.478 0.00 0.00 0.00 3.42
356 357 4.536489 AGATTTTACTGACAAGGGGCTAGT 59.464 41.667 0.00 0.00 0.00 2.57
359 360 2.625282 ACTGACAAGGGGCTAGTAGT 57.375 50.000 0.00 0.00 0.00 2.73
371 372 3.462021 GGCTAGTAGTGAAGCATCAAGG 58.538 50.000 0.00 0.00 40.61 3.61
391 393 7.066781 TCAAGGGGAAACTTTCTTACAAATCT 58.933 34.615 1.57 0.00 0.00 2.40
393 395 7.914427 AGGGGAAACTTTCTTACAAATCTTT 57.086 32.000 1.57 0.00 0.00 2.52
397 399 9.894783 GGGAAACTTTCTTACAAATCTTTAGAC 57.105 33.333 1.57 0.00 0.00 2.59
407 409 5.815581 ACAAATCTTTAGACACTATGCCCA 58.184 37.500 0.00 0.00 0.00 5.36
446 450 1.713937 CGCACAACACCAACAGCAGA 61.714 55.000 0.00 0.00 0.00 4.26
463 467 2.810852 GCAGATTAGCTAGGCATCCAAC 59.189 50.000 0.00 0.00 0.00 3.77
468 472 6.939163 CAGATTAGCTAGGCATCCAACTAAAT 59.061 38.462 0.00 0.00 0.00 1.40
470 474 8.830741 AGATTAGCTAGGCATCCAACTAAATAT 58.169 33.333 0.00 0.00 0.00 1.28
474 478 5.416952 GCTAGGCATCCAACTAAATATGCAT 59.583 40.000 3.79 3.79 45.13 3.96
476 480 7.121168 GCTAGGCATCCAACTAAATATGCATTA 59.879 37.037 3.54 0.00 45.13 1.90
491 495 5.700722 ATGCATTATCACCACATCATGAC 57.299 39.130 0.00 0.00 0.00 3.06
498 502 8.501580 CATTATCACCACATCATGACAAGATAC 58.498 37.037 0.00 0.00 0.00 2.24
521 525 4.810491 CCAAGAACCCAAAATCAAAGTGTG 59.190 41.667 0.00 0.00 0.00 3.82
525 529 3.731089 ACCCAAAATCAAAGTGTGCATG 58.269 40.909 0.00 0.00 0.00 4.06
555 559 3.361794 TCAAGCTAGCTAGAGCAATCG 57.638 47.619 25.15 4.87 45.43 3.34
558 562 1.410517 AGCTAGCTAGAGCAATCGCAA 59.589 47.619 25.15 0.00 45.43 4.85
561 565 1.933247 AGCTAGAGCAATCGCAAGTC 58.067 50.000 4.01 0.00 45.16 3.01
578 582 4.082895 GCAAGTCATCATGCCAAGATATCC 60.083 45.833 0.00 0.00 36.56 2.59
588 592 5.894298 TGCCAAGATATCCTGATTACAGT 57.106 39.130 2.71 0.00 42.05 3.55
595 599 7.559590 AGATATCCTGATTACAGTTTTGCAC 57.440 36.000 0.00 0.00 42.05 4.57
602 606 5.587289 TGATTACAGTTTTGCACTTTGACC 58.413 37.500 0.00 0.00 30.92 4.02
635 639 4.990543 TTGCTGTTAGTTTGATCGTCTG 57.009 40.909 0.00 0.00 0.00 3.51
638 642 4.686091 TGCTGTTAGTTTGATCGTCTGAAG 59.314 41.667 0.00 0.00 0.00 3.02
639 643 4.923871 GCTGTTAGTTTGATCGTCTGAAGA 59.076 41.667 0.00 0.00 0.00 2.87
648 652 5.661056 TGATCGTCTGAAGAATAAGGTGT 57.339 39.130 0.00 0.00 0.00 4.16
653 657 4.988540 CGTCTGAAGAATAAGGTGTGACAA 59.011 41.667 0.00 0.00 0.00 3.18
669 673 8.281212 GGTGTGACAACCTCTTAAATATCATT 57.719 34.615 0.00 0.00 37.24 2.57
703 707 3.433274 CGCAAGCAGAAATCTAACACAGA 59.567 43.478 0.00 0.00 37.79 3.41
708 712 3.125316 GCAGAAATCTAACACAGAACGGG 59.875 47.826 0.00 0.00 36.67 5.28
717 721 1.086696 CACAGAACGGGCATGGTTAG 58.913 55.000 0.00 0.00 0.00 2.34
729 733 4.051922 GGCATGGTTAGAAGTACTCATCG 58.948 47.826 0.00 0.00 0.00 3.84
732 740 5.915758 GCATGGTTAGAAGTACTCATCGTAG 59.084 44.000 0.00 0.00 0.00 3.51
774 782 2.300437 GGCTGTAGACTTGTGTTCCTCT 59.700 50.000 0.00 0.00 0.00 3.69
778 786 5.788450 CTGTAGACTTGTGTTCCTCTTCAT 58.212 41.667 0.00 0.00 0.00 2.57
784 792 6.214412 AGACTTGTGTTCCTCTTCATATCCTT 59.786 38.462 0.00 0.00 0.00 3.36
790 798 5.966935 TGTTCCTCTTCATATCCTTCTCCTT 59.033 40.000 0.00 0.00 0.00 3.36
807 815 2.569853 TCCTTTCTTCATACCGGCTTGA 59.430 45.455 0.00 1.10 0.00 3.02
810 818 4.446371 CTTTCTTCATACCGGCTTGAGAT 58.554 43.478 0.00 0.00 0.00 2.75
817 825 1.953138 CCGGCTTGAGATAGCTGCG 60.953 63.158 0.00 0.00 44.48 5.18
819 827 1.485838 CGGCTTGAGATAGCTGCGTG 61.486 60.000 0.00 0.00 40.38 5.34
833 841 2.464189 CGTGCACTACGCGTGAAC 59.536 61.111 24.59 9.33 46.89 3.18
844 852 4.027755 CGTGAACGCTGAAGGTGT 57.972 55.556 0.00 0.00 40.81 4.16
850 858 2.664851 CGCTGAAGGTGTTGCGGA 60.665 61.111 0.00 0.00 43.97 5.54
851 859 2.946762 GCTGAAGGTGTTGCGGAC 59.053 61.111 0.00 0.00 0.00 4.79
852 860 2.954753 GCTGAAGGTGTTGCGGACG 61.955 63.158 0.00 0.00 0.00 4.79
853 861 1.594293 CTGAAGGTGTTGCGGACGT 60.594 57.895 0.00 0.00 0.00 4.34
854 862 1.557443 CTGAAGGTGTTGCGGACGTC 61.557 60.000 7.13 7.13 0.00 4.34
855 863 1.593209 GAAGGTGTTGCGGACGTCA 60.593 57.895 18.91 0.00 0.00 4.35
856 864 1.828331 GAAGGTGTTGCGGACGTCAC 61.828 60.000 18.91 9.44 0.00 3.67
857 865 3.343421 GGTGTTGCGGACGTCACC 61.343 66.667 18.91 11.94 42.40 4.02
858 866 2.586635 GTGTTGCGGACGTCACCA 60.587 61.111 18.91 10.56 0.00 4.17
859 867 2.174969 GTGTTGCGGACGTCACCAA 61.175 57.895 18.91 15.97 0.00 3.67
860 868 1.449778 TGTTGCGGACGTCACCAAA 60.450 52.632 18.91 3.01 0.00 3.28
861 869 1.278637 GTTGCGGACGTCACCAAAG 59.721 57.895 18.91 2.19 0.00 2.77
862 870 1.890041 TTGCGGACGTCACCAAAGG 60.890 57.895 18.91 0.00 0.00 3.11
863 871 2.280592 GCGGACGTCACCAAAGGT 60.281 61.111 18.91 0.00 35.62 3.50
872 880 4.870190 ACCAAAGGTGACACGTCC 57.130 55.556 0.47 0.00 32.98 4.79
873 881 1.227438 ACCAAAGGTGACACGTCCG 60.227 57.895 0.47 0.00 32.98 4.79
874 882 1.068417 CCAAAGGTGACACGTCCGA 59.932 57.895 0.47 0.00 0.00 4.55
875 883 0.531090 CCAAAGGTGACACGTCCGAA 60.531 55.000 0.47 0.00 0.00 4.30
876 884 0.859232 CAAAGGTGACACGTCCGAAG 59.141 55.000 0.47 0.00 0.00 3.79
877 885 0.878961 AAAGGTGACACGTCCGAAGC 60.879 55.000 0.47 0.00 0.00 3.86
878 886 2.710724 AAGGTGACACGTCCGAAGCC 62.711 60.000 0.47 0.00 0.00 4.35
879 887 2.028484 GTGACACGTCCGAAGCCA 59.972 61.111 0.00 0.00 0.00 4.75
880 888 1.374252 GTGACACGTCCGAAGCCAT 60.374 57.895 0.00 0.00 0.00 4.40
881 889 1.080093 TGACACGTCCGAAGCCATC 60.080 57.895 0.00 0.00 0.00 3.51
882 890 1.810030 GACACGTCCGAAGCCATCC 60.810 63.158 0.00 0.00 0.00 3.51
883 891 2.227089 GACACGTCCGAAGCCATCCT 62.227 60.000 0.00 0.00 0.00 3.24
884 892 1.519455 CACGTCCGAAGCCATCCTC 60.519 63.158 0.00 0.00 0.00 3.71
885 893 2.278857 CGTCCGAAGCCATCCTCG 60.279 66.667 0.00 0.00 0.00 4.63
886 894 2.586357 GTCCGAAGCCATCCTCGC 60.586 66.667 0.00 0.00 0.00 5.03
887 895 3.074369 TCCGAAGCCATCCTCGCA 61.074 61.111 0.00 0.00 0.00 5.10
888 896 2.125147 CCGAAGCCATCCTCGCAA 60.125 61.111 0.00 0.00 0.00 4.85
889 897 1.745115 CCGAAGCCATCCTCGCAAA 60.745 57.895 0.00 0.00 0.00 3.68
890 898 1.305219 CCGAAGCCATCCTCGCAAAA 61.305 55.000 0.00 0.00 0.00 2.44
891 899 0.734889 CGAAGCCATCCTCGCAAAAT 59.265 50.000 0.00 0.00 0.00 1.82
892 900 1.268234 CGAAGCCATCCTCGCAAAATC 60.268 52.381 0.00 0.00 0.00 2.17
893 901 1.066152 GAAGCCATCCTCGCAAAATCC 59.934 52.381 0.00 0.00 0.00 3.01
894 902 0.257039 AGCCATCCTCGCAAAATCCT 59.743 50.000 0.00 0.00 0.00 3.24
895 903 1.106285 GCCATCCTCGCAAAATCCTT 58.894 50.000 0.00 0.00 0.00 3.36
896 904 1.066152 GCCATCCTCGCAAAATCCTTC 59.934 52.381 0.00 0.00 0.00 3.46
897 905 1.331756 CCATCCTCGCAAAATCCTTCG 59.668 52.381 0.00 0.00 0.00 3.79
898 906 1.017387 ATCCTCGCAAAATCCTTCGC 58.983 50.000 0.00 0.00 0.00 4.70
899 907 1.024579 TCCTCGCAAAATCCTTCGCC 61.025 55.000 0.00 0.00 0.00 5.54
900 908 1.305219 CCTCGCAAAATCCTTCGCCA 61.305 55.000 0.00 0.00 0.00 5.69
901 909 0.179189 CTCGCAAAATCCTTCGCCAC 60.179 55.000 0.00 0.00 0.00 5.01
902 910 0.605319 TCGCAAAATCCTTCGCCACT 60.605 50.000 0.00 0.00 0.00 4.00
903 911 0.454957 CGCAAAATCCTTCGCCACTG 60.455 55.000 0.00 0.00 0.00 3.66
904 912 0.109132 GCAAAATCCTTCGCCACTGG 60.109 55.000 0.00 0.00 0.00 4.00
905 913 1.533625 CAAAATCCTTCGCCACTGGA 58.466 50.000 0.00 0.00 0.00 3.86
906 914 1.885887 CAAAATCCTTCGCCACTGGAA 59.114 47.619 0.00 0.00 33.20 3.53
907 915 2.493278 CAAAATCCTTCGCCACTGGAAT 59.507 45.455 0.00 0.00 33.20 3.01
908 916 2.044123 AATCCTTCGCCACTGGAATC 57.956 50.000 0.00 0.00 33.20 2.52
909 917 0.911769 ATCCTTCGCCACTGGAATCA 59.088 50.000 0.00 0.00 33.20 2.57
910 918 0.690192 TCCTTCGCCACTGGAATCAA 59.310 50.000 0.00 0.00 0.00 2.57
911 919 1.089920 CCTTCGCCACTGGAATCAAG 58.910 55.000 0.00 0.00 0.00 3.02
912 920 1.089920 CTTCGCCACTGGAATCAAGG 58.910 55.000 0.00 0.00 0.00 3.61
913 921 0.690192 TTCGCCACTGGAATCAAGGA 59.310 50.000 0.00 0.00 0.00 3.36
914 922 0.690192 TCGCCACTGGAATCAAGGAA 59.310 50.000 0.00 0.00 0.00 3.36
915 923 0.804989 CGCCACTGGAATCAAGGAAC 59.195 55.000 0.00 0.00 0.00 3.62
916 924 1.881925 CGCCACTGGAATCAAGGAACA 60.882 52.381 0.00 0.00 0.00 3.18
917 925 1.541588 GCCACTGGAATCAAGGAACAC 59.458 52.381 0.00 0.00 0.00 3.32
918 926 1.806542 CCACTGGAATCAAGGAACACG 59.193 52.381 0.00 0.00 0.00 4.49
919 927 2.549992 CCACTGGAATCAAGGAACACGA 60.550 50.000 0.00 0.00 0.00 4.35
920 928 2.738846 CACTGGAATCAAGGAACACGAG 59.261 50.000 0.00 0.00 0.00 4.18
921 929 2.632996 ACTGGAATCAAGGAACACGAGA 59.367 45.455 0.00 0.00 0.00 4.04
922 930 3.261897 ACTGGAATCAAGGAACACGAGAT 59.738 43.478 0.00 0.00 0.00 2.75
923 931 4.466370 ACTGGAATCAAGGAACACGAGATA 59.534 41.667 0.00 0.00 0.00 1.98
924 932 5.011090 TGGAATCAAGGAACACGAGATAG 57.989 43.478 0.00 0.00 0.00 2.08
925 933 4.709886 TGGAATCAAGGAACACGAGATAGA 59.290 41.667 0.00 0.00 0.00 1.98
926 934 5.186992 TGGAATCAAGGAACACGAGATAGAA 59.813 40.000 0.00 0.00 0.00 2.10
927 935 5.520649 GGAATCAAGGAACACGAGATAGAAC 59.479 44.000 0.00 0.00 0.00 3.01
928 936 5.923733 ATCAAGGAACACGAGATAGAACT 57.076 39.130 0.00 0.00 0.00 3.01
929 937 5.312120 TCAAGGAACACGAGATAGAACTC 57.688 43.478 0.00 0.00 0.00 3.01
944 952 1.931841 GAACTCGCCGTTCCTTATTCC 59.068 52.381 6.24 0.00 45.00 3.01
945 953 0.179119 ACTCGCCGTTCCTTATTCCG 60.179 55.000 0.00 0.00 0.00 4.30
946 954 0.179119 CTCGCCGTTCCTTATTCCGT 60.179 55.000 0.00 0.00 0.00 4.69
947 955 1.066002 CTCGCCGTTCCTTATTCCGTA 59.934 52.381 0.00 0.00 0.00 4.02
948 956 1.202290 TCGCCGTTCCTTATTCCGTAC 60.202 52.381 0.00 0.00 0.00 3.67
949 957 1.575244 GCCGTTCCTTATTCCGTACC 58.425 55.000 0.00 0.00 0.00 3.34
950 958 1.807755 GCCGTTCCTTATTCCGTACCC 60.808 57.143 0.00 0.00 0.00 3.69
951 959 1.202568 CCGTTCCTTATTCCGTACCCC 60.203 57.143 0.00 0.00 0.00 4.95
952 960 1.481772 CGTTCCTTATTCCGTACCCCA 59.518 52.381 0.00 0.00 0.00 4.96
953 961 2.739609 CGTTCCTTATTCCGTACCCCAC 60.740 54.545 0.00 0.00 0.00 4.61
954 962 2.236893 GTTCCTTATTCCGTACCCCACA 59.763 50.000 0.00 0.00 0.00 4.17
955 963 2.549082 TCCTTATTCCGTACCCCACAA 58.451 47.619 0.00 0.00 0.00 3.33
956 964 2.911636 TCCTTATTCCGTACCCCACAAA 59.088 45.455 0.00 0.00 0.00 2.83
957 965 3.011818 CCTTATTCCGTACCCCACAAAC 58.988 50.000 0.00 0.00 0.00 2.93
958 966 3.559597 CCTTATTCCGTACCCCACAAACA 60.560 47.826 0.00 0.00 0.00 2.83
959 967 2.660670 ATTCCGTACCCCACAAACAA 57.339 45.000 0.00 0.00 0.00 2.83
960 968 1.970092 TTCCGTACCCCACAAACAAG 58.030 50.000 0.00 0.00 0.00 3.16
961 969 1.129917 TCCGTACCCCACAAACAAGA 58.870 50.000 0.00 0.00 0.00 3.02
962 970 1.202675 TCCGTACCCCACAAACAAGAC 60.203 52.381 0.00 0.00 0.00 3.01
963 971 1.232119 CGTACCCCACAAACAAGACC 58.768 55.000 0.00 0.00 0.00 3.85
964 972 1.475392 CGTACCCCACAAACAAGACCA 60.475 52.381 0.00 0.00 0.00 4.02
965 973 2.657143 GTACCCCACAAACAAGACCAA 58.343 47.619 0.00 0.00 0.00 3.67
966 974 1.775385 ACCCCACAAACAAGACCAAG 58.225 50.000 0.00 0.00 0.00 3.61
967 975 1.286553 ACCCCACAAACAAGACCAAGA 59.713 47.619 0.00 0.00 0.00 3.02
968 976 2.291930 ACCCCACAAACAAGACCAAGAA 60.292 45.455 0.00 0.00 0.00 2.52
969 977 2.763448 CCCCACAAACAAGACCAAGAAA 59.237 45.455 0.00 0.00 0.00 2.52
970 978 3.387699 CCCCACAAACAAGACCAAGAAAT 59.612 43.478 0.00 0.00 0.00 2.17
971 979 4.586841 CCCCACAAACAAGACCAAGAAATA 59.413 41.667 0.00 0.00 0.00 1.40
972 980 5.508994 CCCCACAAACAAGACCAAGAAATAC 60.509 44.000 0.00 0.00 0.00 1.89
973 981 5.301805 CCCACAAACAAGACCAAGAAATACT 59.698 40.000 0.00 0.00 0.00 2.12
974 982 6.208644 CCACAAACAAGACCAAGAAATACTG 58.791 40.000 0.00 0.00 0.00 2.74
975 983 6.208644 CACAAACAAGACCAAGAAATACTGG 58.791 40.000 0.00 0.00 0.00 4.00
976 984 6.039270 CACAAACAAGACCAAGAAATACTGGA 59.961 38.462 0.00 0.00 0.00 3.86
977 985 6.777580 ACAAACAAGACCAAGAAATACTGGAT 59.222 34.615 0.00 0.00 0.00 3.41
978 986 7.040409 ACAAACAAGACCAAGAAATACTGGATC 60.040 37.037 0.00 0.00 0.00 3.36
979 987 6.126863 ACAAGACCAAGAAATACTGGATCA 57.873 37.500 0.00 0.00 0.00 2.92
980 988 6.176183 ACAAGACCAAGAAATACTGGATCAG 58.824 40.000 0.00 0.00 37.52 2.90
981 989 6.013379 ACAAGACCAAGAAATACTGGATCAGA 60.013 38.462 1.59 0.00 35.18 3.27
982 990 6.821616 AGACCAAGAAATACTGGATCAGAT 57.178 37.500 1.59 0.00 35.18 2.90
983 991 6.590068 AGACCAAGAAATACTGGATCAGATG 58.410 40.000 1.59 0.00 35.18 2.90
984 992 6.157645 AGACCAAGAAATACTGGATCAGATGT 59.842 38.462 1.59 0.00 35.18 3.06
985 993 6.118170 ACCAAGAAATACTGGATCAGATGTG 58.882 40.000 1.59 0.00 35.18 3.21
986 994 6.118170 CCAAGAAATACTGGATCAGATGTGT 58.882 40.000 1.59 0.00 35.18 3.72
987 995 6.037940 CCAAGAAATACTGGATCAGATGTGTG 59.962 42.308 1.59 0.00 35.18 3.82
988 996 6.550938 AGAAATACTGGATCAGATGTGTGA 57.449 37.500 1.59 0.00 35.18 3.58
989 997 6.344500 AGAAATACTGGATCAGATGTGTGAC 58.656 40.000 1.59 0.00 35.18 3.67
990 998 4.679373 ATACTGGATCAGATGTGTGACC 57.321 45.455 1.59 0.00 35.18 4.02
991 999 1.556911 ACTGGATCAGATGTGTGACCC 59.443 52.381 1.59 0.00 35.18 4.46
992 1000 1.836166 CTGGATCAGATGTGTGACCCT 59.164 52.381 0.00 0.00 32.44 4.34
993 1001 1.833630 TGGATCAGATGTGTGACCCTC 59.166 52.381 0.00 0.00 0.00 4.30
994 1002 1.833630 GGATCAGATGTGTGACCCTCA 59.166 52.381 0.00 0.00 0.00 3.86
995 1003 2.237143 GGATCAGATGTGTGACCCTCAA 59.763 50.000 0.00 0.00 0.00 3.02
996 1004 3.118112 GGATCAGATGTGTGACCCTCAAT 60.118 47.826 0.00 0.00 0.00 2.57
997 1005 4.101585 GGATCAGATGTGTGACCCTCAATA 59.898 45.833 0.00 0.00 0.00 1.90
998 1006 5.396772 GGATCAGATGTGTGACCCTCAATAA 60.397 44.000 0.00 0.00 0.00 1.40
1095 1104 3.075005 GCCCAGTCCCAGACGCTA 61.075 66.667 0.00 0.00 37.67 4.26
1146 1155 2.917227 CCGCTGCCTTGGGGTTTT 60.917 61.111 0.00 0.00 35.60 2.43
1147 1156 2.506957 CCGCTGCCTTGGGGTTTTT 61.507 57.895 0.00 0.00 35.60 1.94
1202 1211 1.622811 AGATTCCGATCCAGATCCAGC 59.377 52.381 2.11 0.00 34.40 4.85
1240 1249 3.775654 CACCTCCTGGTCGCCCTC 61.776 72.222 0.00 0.00 46.60 4.30
1254 1263 4.891727 CCTCCCGGCGTGGATTCG 62.892 72.222 15.77 6.42 42.00 3.34
1284 1293 4.070552 GTCTTGGAGACGCCGCCT 62.071 66.667 0.00 0.00 40.66 5.52
1324 1333 1.219213 TCCCAACCACCACCTTCAATT 59.781 47.619 0.00 0.00 0.00 2.32
1333 1342 2.290577 ACCACCTTCAATTCTCCTGCTC 60.291 50.000 0.00 0.00 0.00 4.26
1357 1366 4.373116 GCTCCGCCAACCTGACGA 62.373 66.667 0.00 0.00 0.00 4.20
1365 1374 1.522668 CCAACCTGACGAGCATTGAA 58.477 50.000 0.00 0.00 0.00 2.69
1368 1377 0.674895 ACCTGACGAGCATTGAAGGC 60.675 55.000 0.00 0.00 32.35 4.35
1377 1386 2.682856 GAGCATTGAAGGCGTTAATGGA 59.317 45.455 16.96 0.00 33.54 3.41
1380 1389 2.122783 TTGAAGGCGTTAATGGAGGG 57.877 50.000 0.00 0.00 0.00 4.30
1384 1393 0.912487 AGGCGTTAATGGAGGGGACA 60.912 55.000 0.00 0.00 0.00 4.02
1484 1493 3.855853 GGGGCTCGAGGAGGAAGC 61.856 72.222 15.58 0.00 0.00 3.86
1489 1498 3.114647 CTCGAGGAGGAAGCGACGG 62.115 68.421 3.91 0.00 0.00 4.79
1511 1520 3.649277 CTTGGACCGAGGTCAGGCG 62.649 68.421 22.17 5.39 46.20 5.52
1557 1566 0.250640 CTGTTGCTGCCTTCACTCCT 60.251 55.000 0.00 0.00 0.00 3.69
1587 1597 1.133792 CCTCCCGCATGGATAAAAGGT 60.134 52.381 0.00 0.00 44.07 3.50
1797 1816 3.706373 CCACCCACGTCCTCCCAG 61.706 72.222 0.00 0.00 0.00 4.45
1798 1817 2.923035 CACCCACGTCCTCCCAGT 60.923 66.667 0.00 0.00 0.00 4.00
1799 1818 2.122547 ACCCACGTCCTCCCAGTT 60.123 61.111 0.00 0.00 0.00 3.16
1810 1829 1.304381 TCCCAGTTTGCCATGGCTC 60.304 57.895 35.53 24.43 42.51 4.70
1815 1837 1.000396 GTTTGCCATGGCTCCCTCT 60.000 57.895 35.53 0.00 42.51 3.69
1821 1843 4.172512 ATGGCTCCCTCTGCTGCG 62.173 66.667 0.00 0.00 0.00 5.18
1830 1852 3.921767 CTCTGCTGCGTCTTCGGCA 62.922 63.158 0.00 0.00 37.56 5.69
1884 1906 1.667830 CGCCGTCATCCACAACACT 60.668 57.895 0.00 0.00 0.00 3.55
1898 1920 3.818787 CACTCCGGCCATGCAAGC 61.819 66.667 2.24 3.55 0.00 4.01
1899 1921 4.039092 ACTCCGGCCATGCAAGCT 62.039 61.111 2.24 0.00 0.00 3.74
1923 1945 1.386533 CTGCGCTTCTGGAATCCAAT 58.613 50.000 9.73 0.00 30.80 3.16
1947 1969 4.309950 GTGGCCTGGTTCGACCGT 62.310 66.667 3.32 0.00 42.58 4.83
1950 1972 2.264794 GCCTGGTTCGACCGTGAT 59.735 61.111 0.00 0.00 42.58 3.06
1951 1973 1.375523 GCCTGGTTCGACCGTGATT 60.376 57.895 0.00 0.00 42.58 2.57
1953 1975 0.320421 CCTGGTTCGACCGTGATTGT 60.320 55.000 0.00 0.00 42.58 2.71
1969 1991 4.980805 GTCGCGCCTCCACCAACA 62.981 66.667 0.00 0.00 0.00 3.33
1982 2004 4.999939 CAACAAGGTTGCGGCGGC 63.000 66.667 9.78 9.68 40.52 6.53
2005 2027 2.892425 CAGACGGGATTGGCGCTC 60.892 66.667 7.64 0.00 0.00 5.03
2073 2095 1.154150 GCGCTTCATCCACAAGCAC 60.154 57.895 0.00 0.00 45.66 4.40
2159 2182 2.573340 GCGTTTGGAAGGCCATGG 59.427 61.111 7.63 7.63 45.46 3.66
2184 2207 3.771160 GTCGACCTCGGCCACCAT 61.771 66.667 3.51 0.00 38.15 3.55
2188 2211 3.249189 ACCTCGGCCACCATGTGT 61.249 61.111 2.24 0.00 0.00 3.72
4334 4396 1.007387 CGCCACCTCAACCTTTTGC 60.007 57.895 0.00 0.00 32.17 3.68
4339 4401 2.310538 CACCTCAACCTTTTGCCTCTT 58.689 47.619 0.00 0.00 32.17 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.543653 GCGACAAGTGAAAGCACCAATT 60.544 45.455 0.00 0.00 46.32 2.32
1 2 1.001378 GCGACAAGTGAAAGCACCAAT 60.001 47.619 0.00 0.00 46.32 3.16
54 55 6.396829 AATTGAAAGACTTGTCCTCTTTGG 57.603 37.500 0.00 0.00 37.95 3.28
73 74 9.803130 CTATGAGATAAGCAACGTTGATAATTG 57.197 33.333 31.62 4.45 0.00 2.32
106 107 3.999663 CTCCTGGCTTAAACTGTCAAGAG 59.000 47.826 6.35 0.00 0.00 2.85
114 115 2.025887 CACCCATCTCCTGGCTTAAACT 60.026 50.000 0.00 0.00 44.46 2.66
121 122 2.787994 CATATTCACCCATCTCCTGGC 58.212 52.381 0.00 0.00 44.46 4.85
129 130 4.240881 ACTGAACAGCATATTCACCCAT 57.759 40.909 1.46 0.00 32.67 4.00
130 131 3.719268 ACTGAACAGCATATTCACCCA 57.281 42.857 1.46 0.00 32.67 4.51
131 132 6.509418 TTAAACTGAACAGCATATTCACCC 57.491 37.500 1.46 0.00 32.67 4.61
166 167 7.050377 TCATCCTTCTTTGTCAGGACATTATC 58.950 38.462 2.52 0.00 42.20 1.75
179 180 8.399425 CAGAATGAAGAGATTCATCCTTCTTTG 58.601 37.037 15.82 7.11 40.51 2.77
284 285 9.034800 TCTTCAGGATGCAATTTATTTTTAGGT 57.965 29.630 0.00 0.00 34.76 3.08
334 335 4.844884 ACTAGCCCCTTGTCAGTAAAATC 58.155 43.478 0.00 0.00 0.00 2.17
342 343 2.615986 TCACTACTAGCCCCTTGTCA 57.384 50.000 0.00 0.00 0.00 3.58
343 344 2.418884 GCTTCACTACTAGCCCCTTGTC 60.419 54.545 0.00 0.00 0.00 3.18
348 349 1.762957 TGATGCTTCACTACTAGCCCC 59.237 52.381 0.00 0.00 36.56 5.80
351 352 3.462021 CCCTTGATGCTTCACTACTAGC 58.538 50.000 1.02 0.00 37.89 3.42
352 353 3.706594 TCCCCTTGATGCTTCACTACTAG 59.293 47.826 1.02 0.00 0.00 2.57
353 354 3.719871 TCCCCTTGATGCTTCACTACTA 58.280 45.455 1.02 0.00 0.00 1.82
355 356 3.350219 TTCCCCTTGATGCTTCACTAC 57.650 47.619 1.02 0.00 0.00 2.73
356 357 3.330701 AGTTTCCCCTTGATGCTTCACTA 59.669 43.478 1.02 0.00 0.00 2.74
359 360 2.978156 AGTTTCCCCTTGATGCTTCA 57.022 45.000 0.00 0.00 0.00 3.02
371 372 9.894783 GTCTAAAGATTTGTAAGAAAGTTTCCC 57.105 33.333 12.05 1.74 0.00 3.97
428 432 0.670162 ATCTGCTGTTGGTGTTGTGC 59.330 50.000 0.00 0.00 0.00 4.57
446 450 7.337942 GCATATTTAGTTGGATGCCTAGCTAAT 59.662 37.037 0.00 0.00 39.00 1.73
463 467 9.783256 CATGATGTGGTGATAATGCATATTTAG 57.217 33.333 0.00 0.00 0.00 1.85
468 472 6.297582 TGTCATGATGTGGTGATAATGCATA 58.702 36.000 0.00 0.00 0.00 3.14
470 474 4.525024 TGTCATGATGTGGTGATAATGCA 58.475 39.130 0.00 0.00 0.00 3.96
474 478 6.992123 GGTATCTTGTCATGATGTGGTGATAA 59.008 38.462 10.69 0.00 0.00 1.75
476 480 5.104402 TGGTATCTTGTCATGATGTGGTGAT 60.104 40.000 10.69 0.85 0.00 3.06
491 495 6.588719 TGATTTTGGGTTCTTGGTATCTTG 57.411 37.500 0.00 0.00 0.00 3.02
498 502 4.810491 CACACTTTGATTTTGGGTTCTTGG 59.190 41.667 0.00 0.00 0.00 3.61
525 529 2.492012 AGCTAGCTTGATGCATGTAGC 58.508 47.619 12.68 17.72 45.94 3.58
555 559 4.082895 GGATATCTTGGCATGATGACTTGC 60.083 45.833 22.14 8.82 43.44 4.01
558 562 4.596212 TCAGGATATCTTGGCATGATGACT 59.404 41.667 22.14 14.94 0.00 3.41
561 565 6.882678 TGTAATCAGGATATCTTGGCATGATG 59.117 38.462 22.14 9.66 0.00 3.07
578 582 5.687285 GGTCAAAGTGCAAAACTGTAATCAG 59.313 40.000 0.00 0.00 46.18 2.90
588 592 1.202245 GCAGTCGGTCAAAGTGCAAAA 60.202 47.619 0.00 0.00 41.68 2.44
595 599 4.697300 CAAATTTTGCAGTCGGTCAAAG 57.303 40.909 0.00 0.00 34.21 2.77
618 622 9.140286 CTTATTCTTCAGACGATCAAACTAACA 57.860 33.333 0.00 0.00 0.00 2.41
624 628 6.368791 CACACCTTATTCTTCAGACGATCAAA 59.631 38.462 0.00 0.00 0.00 2.69
669 673 0.735471 TGCTTGCGCAAGTGTGTTTA 59.265 45.000 41.19 21.25 44.62 2.01
689 693 3.071479 TGCCCGTTCTGTGTTAGATTTC 58.929 45.455 0.00 0.00 34.80 2.17
695 699 0.398696 ACCATGCCCGTTCTGTGTTA 59.601 50.000 0.00 0.00 0.00 2.41
696 700 0.467290 AACCATGCCCGTTCTGTGTT 60.467 50.000 0.00 0.00 0.00 3.32
703 707 2.570302 AGTACTTCTAACCATGCCCGTT 59.430 45.455 0.00 0.00 0.00 4.44
708 712 4.683832 ACGATGAGTACTTCTAACCATGC 58.316 43.478 0.00 0.00 0.00 4.06
717 721 7.633361 TTTGTTTGTCTACGATGAGTACTTC 57.367 36.000 0.00 0.00 0.00 3.01
749 757 3.437049 GGAACACAAGTCTACAGCCAATC 59.563 47.826 0.00 0.00 0.00 2.67
750 758 3.073062 AGGAACACAAGTCTACAGCCAAT 59.927 43.478 0.00 0.00 0.00 3.16
755 763 5.201713 TGAAGAGGAACACAAGTCTACAG 57.798 43.478 0.00 0.00 0.00 2.74
757 765 6.981559 GGATATGAAGAGGAACACAAGTCTAC 59.018 42.308 0.00 0.00 0.00 2.59
760 768 5.983540 AGGATATGAAGAGGAACACAAGTC 58.016 41.667 0.00 0.00 0.00 3.01
762 770 6.648192 AGAAGGATATGAAGAGGAACACAAG 58.352 40.000 0.00 0.00 0.00 3.16
774 782 8.432805 GGTATGAAGAAAGGAGAAGGATATGAA 58.567 37.037 0.00 0.00 0.00 2.57
778 786 5.304614 CCGGTATGAAGAAAGGAGAAGGATA 59.695 44.000 0.00 0.00 0.00 2.59
784 792 2.467880 AGCCGGTATGAAGAAAGGAGA 58.532 47.619 1.90 0.00 0.00 3.71
790 798 4.501571 GCTATCTCAAGCCGGTATGAAGAA 60.502 45.833 1.90 0.00 36.45 2.52
807 815 0.248661 CGTAGTGCACGCAGCTATCT 60.249 55.000 12.01 0.00 45.03 1.98
827 835 0.042188 CAACACCTTCAGCGTTCACG 60.042 55.000 0.00 0.00 43.27 4.35
835 843 1.557443 GACGTCCGCAACACCTTCAG 61.557 60.000 3.51 0.00 0.00 3.02
836 844 1.593209 GACGTCCGCAACACCTTCA 60.593 57.895 3.51 0.00 0.00 3.02
837 845 1.593209 TGACGTCCGCAACACCTTC 60.593 57.895 14.12 0.00 0.00 3.46
838 846 1.885850 GTGACGTCCGCAACACCTT 60.886 57.895 14.12 0.00 0.00 3.50
839 847 2.279918 GTGACGTCCGCAACACCT 60.280 61.111 14.12 0.00 0.00 4.00
840 848 3.343421 GGTGACGTCCGCAACACC 61.343 66.667 14.12 9.65 44.23 4.16
841 849 1.707239 TTTGGTGACGTCCGCAACAC 61.707 55.000 14.12 3.50 31.69 3.32
842 850 1.433053 CTTTGGTGACGTCCGCAACA 61.433 55.000 14.12 0.37 0.00 3.33
843 851 1.278637 CTTTGGTGACGTCCGCAAC 59.721 57.895 14.12 3.98 0.00 4.17
844 852 1.890041 CCTTTGGTGACGTCCGCAA 60.890 57.895 14.12 8.13 0.00 4.85
845 853 2.280524 CCTTTGGTGACGTCCGCA 60.281 61.111 14.12 2.62 0.00 5.69
846 854 2.280592 ACCTTTGGTGACGTCCGC 60.281 61.111 14.12 5.87 32.98 5.54
855 863 1.227438 CGGACGTGTCACCTTTGGT 60.227 57.895 0.00 0.00 35.62 3.67
856 864 0.531090 TTCGGACGTGTCACCTTTGG 60.531 55.000 0.00 0.00 0.00 3.28
857 865 0.859232 CTTCGGACGTGTCACCTTTG 59.141 55.000 0.00 0.00 0.00 2.77
858 866 0.878961 GCTTCGGACGTGTCACCTTT 60.879 55.000 0.00 0.00 0.00 3.11
859 867 1.300697 GCTTCGGACGTGTCACCTT 60.301 57.895 0.00 0.00 0.00 3.50
860 868 2.338984 GCTTCGGACGTGTCACCT 59.661 61.111 0.00 0.00 0.00 4.00
861 869 2.737376 GGCTTCGGACGTGTCACC 60.737 66.667 0.00 0.00 0.00 4.02
862 870 1.352156 GATGGCTTCGGACGTGTCAC 61.352 60.000 0.00 0.00 0.00 3.67
863 871 1.080093 GATGGCTTCGGACGTGTCA 60.080 57.895 0.00 0.00 0.00 3.58
864 872 1.810030 GGATGGCTTCGGACGTGTC 60.810 63.158 0.00 0.00 0.00 3.67
865 873 2.227089 GAGGATGGCTTCGGACGTGT 62.227 60.000 0.00 0.00 0.00 4.49
866 874 1.519455 GAGGATGGCTTCGGACGTG 60.519 63.158 0.00 0.00 0.00 4.49
867 875 2.893398 GAGGATGGCTTCGGACGT 59.107 61.111 0.00 0.00 0.00 4.34
868 876 2.278857 CGAGGATGGCTTCGGACG 60.279 66.667 0.00 0.00 39.63 4.79
869 877 2.586357 GCGAGGATGGCTTCGGAC 60.586 66.667 0.00 0.00 43.05 4.79
870 878 2.178876 TTTGCGAGGATGGCTTCGGA 62.179 55.000 0.00 0.00 43.05 4.55
871 879 1.305219 TTTTGCGAGGATGGCTTCGG 61.305 55.000 0.00 0.00 43.05 4.30
872 880 0.734889 ATTTTGCGAGGATGGCTTCG 59.265 50.000 0.00 0.00 45.28 3.79
873 881 1.066152 GGATTTTGCGAGGATGGCTTC 59.934 52.381 0.00 0.00 41.95 3.86
874 882 1.106285 GGATTTTGCGAGGATGGCTT 58.894 50.000 0.00 0.00 41.95 4.35
875 883 0.257039 AGGATTTTGCGAGGATGGCT 59.743 50.000 0.00 0.00 41.95 4.75
876 884 1.066152 GAAGGATTTTGCGAGGATGGC 59.934 52.381 0.00 0.00 41.71 4.40
877 885 1.331756 CGAAGGATTTTGCGAGGATGG 59.668 52.381 0.00 0.00 0.00 3.51
878 886 1.268234 GCGAAGGATTTTGCGAGGATG 60.268 52.381 0.00 0.00 34.18 3.51
879 887 1.017387 GCGAAGGATTTTGCGAGGAT 58.983 50.000 0.00 0.00 34.18 3.24
880 888 1.024579 GGCGAAGGATTTTGCGAGGA 61.025 55.000 0.00 0.00 43.44 3.71
881 889 1.305219 TGGCGAAGGATTTTGCGAGG 61.305 55.000 0.00 0.00 43.44 4.63
882 890 0.179189 GTGGCGAAGGATTTTGCGAG 60.179 55.000 0.00 0.00 43.44 5.03
883 891 0.605319 AGTGGCGAAGGATTTTGCGA 60.605 50.000 0.00 0.00 43.44 5.10
884 892 0.454957 CAGTGGCGAAGGATTTTGCG 60.455 55.000 0.00 0.00 43.44 4.85
885 893 0.109132 CCAGTGGCGAAGGATTTTGC 60.109 55.000 0.00 0.00 42.05 3.68
886 894 1.533625 TCCAGTGGCGAAGGATTTTG 58.466 50.000 3.51 0.00 0.00 2.44
887 895 2.286365 TTCCAGTGGCGAAGGATTTT 57.714 45.000 3.51 0.00 0.00 1.82
888 896 2.290896 TGATTCCAGTGGCGAAGGATTT 60.291 45.455 3.51 0.00 0.00 2.17
889 897 1.281867 TGATTCCAGTGGCGAAGGATT 59.718 47.619 3.51 0.00 0.00 3.01
890 898 0.911769 TGATTCCAGTGGCGAAGGAT 59.088 50.000 3.51 0.00 0.00 3.24
891 899 0.690192 TTGATTCCAGTGGCGAAGGA 59.310 50.000 3.51 0.00 0.00 3.36
892 900 1.089920 CTTGATTCCAGTGGCGAAGG 58.910 55.000 3.51 0.00 0.00 3.46
893 901 1.089920 CCTTGATTCCAGTGGCGAAG 58.910 55.000 3.51 3.53 0.00 3.79
894 902 0.690192 TCCTTGATTCCAGTGGCGAA 59.310 50.000 3.51 0.00 0.00 4.70
895 903 0.690192 TTCCTTGATTCCAGTGGCGA 59.310 50.000 3.51 0.00 0.00 5.54
896 904 0.804989 GTTCCTTGATTCCAGTGGCG 59.195 55.000 3.51 0.00 0.00 5.69
897 905 1.541588 GTGTTCCTTGATTCCAGTGGC 59.458 52.381 3.51 0.00 0.00 5.01
898 906 1.806542 CGTGTTCCTTGATTCCAGTGG 59.193 52.381 1.40 1.40 0.00 4.00
899 907 2.738846 CTCGTGTTCCTTGATTCCAGTG 59.261 50.000 0.00 0.00 0.00 3.66
900 908 2.632996 TCTCGTGTTCCTTGATTCCAGT 59.367 45.455 0.00 0.00 0.00 4.00
901 909 3.319137 TCTCGTGTTCCTTGATTCCAG 57.681 47.619 0.00 0.00 0.00 3.86
902 910 3.981071 ATCTCGTGTTCCTTGATTCCA 57.019 42.857 0.00 0.00 0.00 3.53
903 911 5.263968 TCTATCTCGTGTTCCTTGATTCC 57.736 43.478 0.00 0.00 0.00 3.01
904 912 6.334202 AGTTCTATCTCGTGTTCCTTGATTC 58.666 40.000 0.00 0.00 0.00 2.52
905 913 6.287589 AGTTCTATCTCGTGTTCCTTGATT 57.712 37.500 0.00 0.00 0.00 2.57
906 914 5.897050 GAGTTCTATCTCGTGTTCCTTGAT 58.103 41.667 0.00 0.00 0.00 2.57
907 915 5.312120 GAGTTCTATCTCGTGTTCCTTGA 57.688 43.478 0.00 0.00 0.00 3.02
926 934 0.179119 CGGAATAAGGAACGGCGAGT 60.179 55.000 16.62 0.00 0.00 4.18
927 935 0.179119 ACGGAATAAGGAACGGCGAG 60.179 55.000 16.62 0.00 0.00 5.03
928 936 1.102154 TACGGAATAAGGAACGGCGA 58.898 50.000 16.62 0.00 0.00 5.54
929 937 1.203065 GTACGGAATAAGGAACGGCG 58.797 55.000 4.80 4.80 0.00 6.46
930 938 1.575244 GGTACGGAATAAGGAACGGC 58.425 55.000 0.00 0.00 0.00 5.68
931 939 1.202568 GGGGTACGGAATAAGGAACGG 60.203 57.143 0.00 0.00 0.00 4.44
932 940 1.481772 TGGGGTACGGAATAAGGAACG 59.518 52.381 0.00 0.00 0.00 3.95
933 941 2.236893 TGTGGGGTACGGAATAAGGAAC 59.763 50.000 0.00 0.00 0.00 3.62
934 942 2.549082 TGTGGGGTACGGAATAAGGAA 58.451 47.619 0.00 0.00 0.00 3.36
935 943 2.250921 TGTGGGGTACGGAATAAGGA 57.749 50.000 0.00 0.00 0.00 3.36
936 944 3.011818 GTTTGTGGGGTACGGAATAAGG 58.988 50.000 0.00 0.00 0.00 2.69
937 945 3.677190 TGTTTGTGGGGTACGGAATAAG 58.323 45.455 0.00 0.00 0.00 1.73
938 946 3.784511 TGTTTGTGGGGTACGGAATAA 57.215 42.857 0.00 0.00 0.00 1.40
939 947 3.327172 TCTTGTTTGTGGGGTACGGAATA 59.673 43.478 0.00 0.00 0.00 1.75
940 948 2.106857 TCTTGTTTGTGGGGTACGGAAT 59.893 45.455 0.00 0.00 0.00 3.01
941 949 1.489649 TCTTGTTTGTGGGGTACGGAA 59.510 47.619 0.00 0.00 0.00 4.30
942 950 1.129917 TCTTGTTTGTGGGGTACGGA 58.870 50.000 0.00 0.00 0.00 4.69
943 951 1.232119 GTCTTGTTTGTGGGGTACGG 58.768 55.000 0.00 0.00 0.00 4.02
944 952 1.232119 GGTCTTGTTTGTGGGGTACG 58.768 55.000 0.00 0.00 0.00 3.67
945 953 2.351706 TGGTCTTGTTTGTGGGGTAC 57.648 50.000 0.00 0.00 0.00 3.34
946 954 2.510382 TCTTGGTCTTGTTTGTGGGGTA 59.490 45.455 0.00 0.00 0.00 3.69
947 955 1.286553 TCTTGGTCTTGTTTGTGGGGT 59.713 47.619 0.00 0.00 0.00 4.95
948 956 2.065899 TCTTGGTCTTGTTTGTGGGG 57.934 50.000 0.00 0.00 0.00 4.96
949 957 4.670896 ATTTCTTGGTCTTGTTTGTGGG 57.329 40.909 0.00 0.00 0.00 4.61
950 958 6.208644 CAGTATTTCTTGGTCTTGTTTGTGG 58.791 40.000 0.00 0.00 0.00 4.17
951 959 6.039270 TCCAGTATTTCTTGGTCTTGTTTGTG 59.961 38.462 0.00 0.00 0.00 3.33
952 960 6.126409 TCCAGTATTTCTTGGTCTTGTTTGT 58.874 36.000 0.00 0.00 0.00 2.83
953 961 6.633500 TCCAGTATTTCTTGGTCTTGTTTG 57.367 37.500 0.00 0.00 0.00 2.93
954 962 7.004086 TGATCCAGTATTTCTTGGTCTTGTTT 58.996 34.615 0.00 0.00 0.00 2.83
955 963 6.542821 TGATCCAGTATTTCTTGGTCTTGTT 58.457 36.000 0.00 0.00 0.00 2.83
956 964 6.013379 TCTGATCCAGTATTTCTTGGTCTTGT 60.013 38.462 0.00 0.00 32.61 3.16
957 965 6.409704 TCTGATCCAGTATTTCTTGGTCTTG 58.590 40.000 0.00 0.00 32.61 3.02
958 966 6.627087 TCTGATCCAGTATTTCTTGGTCTT 57.373 37.500 0.00 0.00 32.61 3.01
959 967 6.157645 ACATCTGATCCAGTATTTCTTGGTCT 59.842 38.462 0.00 0.00 32.61 3.85
960 968 6.259608 CACATCTGATCCAGTATTTCTTGGTC 59.740 42.308 0.00 0.00 32.61 4.02
961 969 6.118170 CACATCTGATCCAGTATTTCTTGGT 58.882 40.000 0.00 0.00 32.61 3.67
962 970 6.037940 CACACATCTGATCCAGTATTTCTTGG 59.962 42.308 0.00 0.00 32.61 3.61
963 971 6.820152 TCACACATCTGATCCAGTATTTCTTG 59.180 38.462 0.00 0.00 32.61 3.02
964 972 6.820656 GTCACACATCTGATCCAGTATTTCTT 59.179 38.462 0.00 0.00 32.61 2.52
965 973 6.344500 GTCACACATCTGATCCAGTATTTCT 58.656 40.000 0.00 0.00 32.61 2.52
966 974 5.525378 GGTCACACATCTGATCCAGTATTTC 59.475 44.000 0.00 0.00 32.61 2.17
967 975 5.431765 GGTCACACATCTGATCCAGTATTT 58.568 41.667 0.00 0.00 32.61 1.40
968 976 4.141620 GGGTCACACATCTGATCCAGTATT 60.142 45.833 0.00 0.00 40.75 1.89
969 977 3.389329 GGGTCACACATCTGATCCAGTAT 59.611 47.826 0.00 0.00 40.75 2.12
970 978 2.766263 GGGTCACACATCTGATCCAGTA 59.234 50.000 0.00 0.00 40.75 2.74
971 979 1.556911 GGGTCACACATCTGATCCAGT 59.443 52.381 0.00 0.00 40.75 4.00
972 980 1.836166 AGGGTCACACATCTGATCCAG 59.164 52.381 1.43 0.00 43.22 3.86
973 981 1.833630 GAGGGTCACACATCTGATCCA 59.166 52.381 1.43 0.00 43.22 3.41
974 982 1.833630 TGAGGGTCACACATCTGATCC 59.166 52.381 0.00 0.00 41.31 3.36
975 983 3.616956 TTGAGGGTCACACATCTGATC 57.383 47.619 0.00 0.00 0.00 2.92
976 984 5.045651 TGTTATTGAGGGTCACACATCTGAT 60.046 40.000 0.00 0.00 0.00 2.90
977 985 4.285775 TGTTATTGAGGGTCACACATCTGA 59.714 41.667 0.00 0.00 0.00 3.27
978 986 4.578871 TGTTATTGAGGGTCACACATCTG 58.421 43.478 0.00 0.00 0.00 2.90
979 987 4.908601 TGTTATTGAGGGTCACACATCT 57.091 40.909 0.00 0.00 0.00 2.90
980 988 4.943705 ACATGTTATTGAGGGTCACACATC 59.056 41.667 0.00 0.00 0.00 3.06
981 989 4.922206 ACATGTTATTGAGGGTCACACAT 58.078 39.130 0.00 0.00 0.00 3.21
982 990 4.323417 GACATGTTATTGAGGGTCACACA 58.677 43.478 0.00 0.00 0.00 3.72
983 991 3.689649 GGACATGTTATTGAGGGTCACAC 59.310 47.826 0.00 0.00 0.00 3.82
984 992 3.618752 CGGACATGTTATTGAGGGTCACA 60.619 47.826 0.00 0.00 0.00 3.58
985 993 2.936498 CGGACATGTTATTGAGGGTCAC 59.064 50.000 0.00 0.00 0.00 3.67
986 994 2.679639 GCGGACATGTTATTGAGGGTCA 60.680 50.000 0.00 0.00 0.00 4.02
987 995 1.940613 GCGGACATGTTATTGAGGGTC 59.059 52.381 0.00 0.00 0.00 4.46
988 996 1.559682 AGCGGACATGTTATTGAGGGT 59.440 47.619 0.00 0.00 0.00 4.34
989 997 2.213499 GAGCGGACATGTTATTGAGGG 58.787 52.381 0.00 0.00 0.00 4.30
990 998 2.213499 GGAGCGGACATGTTATTGAGG 58.787 52.381 0.00 0.00 0.00 3.86
991 999 2.213499 GGGAGCGGACATGTTATTGAG 58.787 52.381 0.00 0.00 0.00 3.02
992 1000 1.472552 CGGGAGCGGACATGTTATTGA 60.473 52.381 0.00 0.00 0.00 2.57
993 1001 0.937304 CGGGAGCGGACATGTTATTG 59.063 55.000 0.00 0.00 0.00 1.90
994 1002 0.828022 TCGGGAGCGGACATGTTATT 59.172 50.000 0.00 0.00 0.00 1.40
995 1003 0.104304 GTCGGGAGCGGACATGTTAT 59.896 55.000 0.00 0.00 34.54 1.89
996 1004 1.514087 GTCGGGAGCGGACATGTTA 59.486 57.895 0.00 0.00 34.54 2.41
997 1005 2.264794 GTCGGGAGCGGACATGTT 59.735 61.111 0.00 0.00 34.54 2.71
998 1006 3.771160 GGTCGGGAGCGGACATGT 61.771 66.667 0.00 0.00 35.79 3.21
1080 1089 0.757188 AGGATAGCGTCTGGGACTGG 60.757 60.000 0.00 0.00 0.00 4.00
1084 1093 0.851469 AGGTAGGATAGCGTCTGGGA 59.149 55.000 0.00 0.00 45.38 4.37
1095 1104 1.308216 AAGGCAGGCCAGGTAGGAT 60.308 57.895 13.63 0.00 41.22 3.24
1177 1186 2.018866 CTGGATCGGAATCTCGCGC 61.019 63.158 0.00 0.00 32.12 6.86
1182 1191 1.622811 GCTGGATCTGGATCGGAATCT 59.377 52.381 4.75 0.00 38.69 2.40
1185 1194 1.139654 CAAGCTGGATCTGGATCGGAA 59.860 52.381 4.75 0.00 38.69 4.30
1188 1197 0.250209 CCCAAGCTGGATCTGGATCG 60.250 60.000 2.79 0.00 40.96 3.69
1202 1211 4.168291 GCGGAGGAGAGCCCCAAG 62.168 72.222 0.00 0.00 34.66 3.61
1210 1219 3.663815 GAGGTGGAGGCGGAGGAGA 62.664 68.421 0.00 0.00 0.00 3.71
1240 1249 4.891727 CTCCGAATCCACGCCGGG 62.892 72.222 2.18 0.00 43.16 5.73
1251 1260 2.915659 ACGCAGTCCACCTCCGAA 60.916 61.111 0.00 0.00 29.74 4.30
1270 1279 4.069232 CTCAGGCGGCGTCTCCAA 62.069 66.667 12.87 0.00 34.01 3.53
1316 1325 2.641305 CTGGAGCAGGAGAATTGAAGG 58.359 52.381 0.00 0.00 0.00 3.46
1341 1350 2.125912 CTCGTCAGGTTGGCGGAG 60.126 66.667 3.08 0.00 46.79 4.63
1352 1361 0.602638 AACGCCTTCAATGCTCGTCA 60.603 50.000 0.00 0.00 32.53 4.35
1354 1363 1.803334 TTAACGCCTTCAATGCTCGT 58.197 45.000 0.00 0.00 34.63 4.18
1357 1366 2.684881 CTCCATTAACGCCTTCAATGCT 59.315 45.455 0.00 0.00 0.00 3.79
1365 1374 0.912487 TGTCCCCTCCATTAACGCCT 60.912 55.000 0.00 0.00 0.00 5.52
1368 1377 2.629051 GAACTGTCCCCTCCATTAACG 58.371 52.381 0.00 0.00 0.00 3.18
1377 1386 1.995626 CCATCCCGAACTGTCCCCT 60.996 63.158 0.00 0.00 0.00 4.79
1380 1389 1.026718 CAAGCCATCCCGAACTGTCC 61.027 60.000 0.00 0.00 0.00 4.02
1384 1393 2.436646 CGCAAGCCATCCCGAACT 60.437 61.111 0.00 0.00 0.00 3.01
1431 1440 1.078918 CGGGAGTGATTGCTCAGCA 60.079 57.895 0.00 0.00 37.24 4.41
1494 1503 3.691342 CGCCTGACCTCGGTCCAA 61.691 66.667 13.22 0.00 43.97 3.53
1533 1542 2.670934 AAGGCAGCAACAGGAGCG 60.671 61.111 0.00 0.00 37.01 5.03
1536 1545 0.250467 GAGTGAAGGCAGCAACAGGA 60.250 55.000 0.00 0.00 0.00 3.86
1575 1585 4.228210 TGGAAGCAGAGACCTTTTATCCAT 59.772 41.667 0.00 0.00 0.00 3.41
1587 1597 2.001076 TGAGACAGTGGAAGCAGAGA 57.999 50.000 0.00 0.00 0.00 3.10
1663 1673 4.227134 CGCTATGTGGCCGGAGCT 62.227 66.667 5.05 0.00 39.73 4.09
1782 1792 1.768888 AAACTGGGAGGACGTGGGT 60.769 57.895 0.00 0.00 0.00 4.51
1786 1805 1.779061 ATGGCAAACTGGGAGGACGT 61.779 55.000 0.00 0.00 0.00 4.34
1787 1806 1.002134 ATGGCAAACTGGGAGGACG 60.002 57.895 0.00 0.00 0.00 4.79
1789 1808 1.383799 CCATGGCAAACTGGGAGGA 59.616 57.895 0.00 0.00 0.00 3.71
1791 1810 1.304713 AGCCATGGCAAACTGGGAG 60.305 57.895 37.18 0.00 44.88 4.30
1792 1811 1.304381 GAGCCATGGCAAACTGGGA 60.304 57.895 37.18 0.00 44.88 4.37
1797 1816 1.000396 AGAGGGAGCCATGGCAAAC 60.000 57.895 37.18 25.74 44.88 2.93
1798 1817 1.000521 CAGAGGGAGCCATGGCAAA 60.001 57.895 37.18 0.00 44.88 3.68
1799 1818 2.679092 CAGAGGGAGCCATGGCAA 59.321 61.111 37.18 0.00 44.88 4.52
1810 1829 2.507992 CGAAGACGCAGCAGAGGG 60.508 66.667 0.00 0.00 0.00 4.30
1815 1837 3.120385 CATGCCGAAGACGCAGCA 61.120 61.111 0.00 0.00 39.85 4.41
1821 1843 2.825836 CCAGCCCATGCCGAAGAC 60.826 66.667 0.00 0.00 38.69 3.01
1830 1852 2.759114 CTGTGGTCACCAGCCCAT 59.241 61.111 0.00 0.00 32.34 4.00
1870 1892 1.298859 GCCGGAGTGTTGTGGATGAC 61.299 60.000 5.05 0.00 0.00 3.06
1884 1906 3.982316 CTCAGCTTGCATGGCCGGA 62.982 63.158 5.05 6.35 0.00 5.14
1905 1927 1.097232 CATTGGATTCCAGAAGCGCA 58.903 50.000 11.47 0.00 33.81 6.09
1911 1933 0.630673 CCACCCCATTGGATTCCAGA 59.369 55.000 3.62 0.00 39.24 3.86
1947 1969 2.434185 GTGGAGGCGCGACAATCA 60.434 61.111 17.71 6.21 0.00 2.57
1950 1972 4.243008 TTGGTGGAGGCGCGACAA 62.243 61.111 17.71 0.00 0.00 3.18
1951 1973 4.980805 GTTGGTGGAGGCGCGACA 62.981 66.667 17.71 1.17 0.00 4.35
1953 1975 4.243008 TTGTTGGTGGAGGCGCGA 62.243 61.111 12.10 0.00 0.00 5.87
1982 2004 1.889105 CCAATCCCGTCTGCGATGG 60.889 63.158 9.13 9.13 41.33 3.51
1994 2016 3.512516 GCACCAGAGCGCCAATCC 61.513 66.667 2.29 0.00 0.00 3.01
2004 2026 2.994995 ATCACGTCCGGCACCAGA 60.995 61.111 0.00 0.00 0.00 3.86
2005 2027 2.509336 GATCACGTCCGGCACCAG 60.509 66.667 0.00 0.00 0.00 4.00
2016 2038 0.168348 AGTGGAAGACGACGATCACG 59.832 55.000 0.00 7.58 45.75 4.35
2019 2041 1.469423 GGGAAGTGGAAGACGACGATC 60.469 57.143 0.00 0.00 0.00 3.69
2058 2080 0.518636 CGTGGTGCTTGTGGATGAAG 59.481 55.000 0.00 0.00 0.00 3.02
2079 2101 2.320587 GCGGGATGATGCGATGTCC 61.321 63.158 0.00 0.00 0.00 4.02
2159 2182 2.502080 CGAGGTCGACGTGCTCAC 60.502 66.667 16.63 0.00 43.02 3.51
2184 2207 2.917227 TCGAGGCAGAGGCACACA 60.917 61.111 0.00 0.00 43.71 3.72
2905 2937 1.228769 ACTGCCTGACCGGACTACA 60.229 57.895 9.46 0.80 33.16 2.74
4334 4396 2.703798 CCGCACCATGGCAAAGAGG 61.704 63.158 13.04 7.06 0.00 3.69
4339 4401 2.405805 CGAATCCGCACCATGGCAA 61.406 57.895 13.04 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.