Multiple sequence alignment - TraesCS7B01G333400

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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 TraesCS7B01G333400 chr7B 100.000 4768 0 0 1 4768 588860892 588865659 0.000000e+00 8805.0
1 TraesCS7B01G333400 chr7A 95.117 3072 87 14 954 4009 627157534 627160558 0.000000e+00 4783.0
2 TraesCS7B01G333400 chr7A 94.821 753 34 4 1 751 627156711 627157460 0.000000e+00 1170.0
3 TraesCS7B01G333400 chr7A 94.858 739 33 3 4031 4768 627160543 627161277 0.000000e+00 1149.0
4 TraesCS7B01G333400 chr7A 89.451 237 19 2 4538 4768 627004430 627004666 1.300000e-75 294.0
5 TraesCS7B01G333400 chr7A 94.149 188 10 1 776 963 320981158 320981344 7.810000e-73 285.0
6 TraesCS7B01G333400 chr7A 79.679 187 27 7 4592 4768 627046040 627046225 1.800000e-24 124.0
7 TraesCS7B01G333400 chr7A 79.570 186 29 5 4592 4768 627234648 627234833 1.800000e-24 124.0
8 TraesCS7B01G333400 chr7A 100.000 41 0 0 752 792 627157495 627157535 5.120000e-10 76.8
9 TraesCS7B01G333400 chr7D 98.810 168 2 0 791 958 192936020 192936187 2.790000e-77 300.0
10 TraesCS7B01G333400 chr7D 88.263 213 25 0 4556 4768 545263008 545263220 6.120000e-64 255.0
11 TraesCS7B01G333400 chr7D 78.191 188 30 8 4592 4768 509602213 509602400 5.040000e-20 110.0
12 TraesCS7B01G333400 chr6A 93.939 198 7 5 775 969 24072077 24071882 1.300000e-75 294.0
13 TraesCS7B01G333400 chr2B 97.661 171 3 1 790 960 404425750 404425919 4.670000e-75 292.0
14 TraesCS7B01G333400 chr2B 96.045 177 5 2 791 967 190234927 190234753 2.170000e-73 287.0
15 TraesCS7B01G333400 chr5A 96.067 178 6 1 778 955 687682761 687682585 6.040000e-74 289.0
16 TraesCS7B01G333400 chr4D 95.580 181 7 1 789 969 154102404 154102225 6.040000e-74 289.0
17 TraesCS7B01G333400 chr1D 96.571 175 5 1 791 965 331539265 331539438 6.040000e-74 289.0
18 TraesCS7B01G333400 chr2A 97.024 168 3 1 789 956 310407934 310408099 1.010000e-71 281.0


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 TraesCS7B01G333400 chr7B 588860892 588865659 4767 False 8805.0 8805 100.000 1 4768 1 chr7B.!!$F1 4767
1 TraesCS7B01G333400 chr7A 627156711 627161277 4566 False 1794.7 4783 96.199 1 4768 4 chr7A.!!$F5 4767

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
307 308 1.001860 GGAGTTCTGCAGCAACTCTCT 59.998 52.381 33.42 16.91 46.2 3.10 F
805 842 1.076677 TGTTCTACTCCCTCCGTTCCT 59.923 52.381 0.00 0.00 0.0 3.36 F
2134 2176 0.260230 TGGCAGTGAAAAAGACCCCA 59.740 50.000 0.00 0.00 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 1457 0.033781 TGGAAAAGCAAGCATGTGGC 59.966 50.0 0.0 0.0 45.30 5.01 R
2757 2800 0.321298 GGAAGGCTTTGCTCACGGTA 60.321 55.0 0.0 0.0 0.00 4.02 R
3998 4051 0.375454 TTGCGAAAGGTGTCGTTGTG 59.625 50.0 0.0 0.0 43.06 3.33 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 8.990163 AAAGGGTAACATACTATATTGGGTTG 57.010 34.615 0.00 0.00 39.74 3.77
129 130 5.525378 AGCAACGAATTATCTGATCAACTCC 59.475 40.000 0.00 0.00 0.00 3.85
146 147 3.535561 ACTCCTTTGTCGATGCCTATTG 58.464 45.455 0.00 0.00 0.00 1.90
167 168 9.399797 CTATTGGCATAATATACATGGTGATGT 57.600 33.333 0.00 0.00 45.24 3.06
182 183 1.202639 TGATGTCGTGCTTCTTGGTGT 60.203 47.619 0.00 0.00 0.00 4.16
224 225 9.607333 TTTAACTCCTACATATCCTGATCATCT 57.393 33.333 0.00 0.00 0.00 2.90
226 227 7.716799 ACTCCTACATATCCTGATCATCTTC 57.283 40.000 0.00 0.00 0.00 2.87
228 229 5.654209 TCCTACATATCCTGATCATCTTCGG 59.346 44.000 0.00 0.00 0.00 4.30
242 243 2.193127 TCTTCGGGAAGGCTGGAAATA 58.807 47.619 8.46 0.00 38.88 1.40
258 259 4.977739 TGGAAATATCATTCTCCACCCTCT 59.022 41.667 0.00 0.00 32.97 3.69
288 289 2.806945 TTGAGCTATTTGGGAGGTGG 57.193 50.000 0.00 0.00 0.00 4.61
291 292 1.840635 GAGCTATTTGGGAGGTGGAGT 59.159 52.381 0.00 0.00 0.00 3.85
307 308 1.001860 GGAGTTCTGCAGCAACTCTCT 59.998 52.381 33.42 16.91 46.20 3.10
308 309 2.336667 GAGTTCTGCAGCAACTCTCTC 58.663 52.381 30.88 17.88 44.38 3.20
322 323 2.439507 ACTCTCTCTTGGGCTGTGAAAA 59.560 45.455 0.00 0.00 0.00 2.29
327 328 3.960102 TCTCTTGGGCTGTGAAAAACAAT 59.040 39.130 0.00 0.00 38.67 2.71
349 350 9.249457 ACAATGATACTATTCGTATGTCAACAG 57.751 33.333 0.00 0.00 38.90 3.16
379 380 4.475345 ACCTGATGATCCTACTAGTGTCC 58.525 47.826 5.39 0.00 0.00 4.02
400 401 3.699538 CCTTTAGGCCATTACAGAAACCC 59.300 47.826 5.01 0.00 0.00 4.11
417 418 1.677552 CCGTGGCTTAGGAGGTGTT 59.322 57.895 0.00 0.00 0.00 3.32
449 450 2.032681 ACAAGCGAGGGAACAGGC 59.967 61.111 0.00 0.00 0.00 4.85
471 472 3.565482 CCATATTTCCAAGGACGATGGTG 59.435 47.826 12.06 4.59 39.09 4.17
537 538 1.203187 AGTCCTGGCCTTCTAGTGTCA 60.203 52.381 3.32 0.00 0.00 3.58
566 567 3.570926 TTCCAAGTCGTAGTGCTGTAG 57.429 47.619 0.00 0.00 0.00 2.74
717 719 1.230324 GGTTTCACCTCTGTCTGCAC 58.770 55.000 0.00 0.00 34.73 4.57
799 836 9.482175 AGATATATGTTATGTTCTACTCCCTCC 57.518 37.037 0.00 0.00 0.00 4.30
800 837 4.939052 ATGTTATGTTCTACTCCCTCCG 57.061 45.455 0.00 0.00 0.00 4.63
801 838 3.705051 TGTTATGTTCTACTCCCTCCGT 58.295 45.455 0.00 0.00 0.00 4.69
802 839 4.091549 TGTTATGTTCTACTCCCTCCGTT 58.908 43.478 0.00 0.00 0.00 4.44
803 840 4.159135 TGTTATGTTCTACTCCCTCCGTTC 59.841 45.833 0.00 0.00 0.00 3.95
804 841 1.553706 TGTTCTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
805 842 1.076677 TGTTCTACTCCCTCCGTTCCT 59.923 52.381 0.00 0.00 0.00 3.36
806 843 2.309755 TGTTCTACTCCCTCCGTTCCTA 59.690 50.000 0.00 0.00 0.00 2.94
807 844 3.245371 TGTTCTACTCCCTCCGTTCCTAA 60.245 47.826 0.00 0.00 0.00 2.69
808 845 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
809 846 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
810 847 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
811 848 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
812 849 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
813 850 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
814 851 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
815 852 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
816 853 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
817 854 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
818 855 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
819 856 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
820 857 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
821 858 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
838 875 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
839 876 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
855 892 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
856 893 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
857 894 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
858 895 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
859 896 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
860 897 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
861 898 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
862 899 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
863 900 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
864 901 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
866 903 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
897 934 7.036220 AGTGTAGATTCACTCATTTTACTCCG 58.964 38.462 0.00 0.00 44.07 4.63
898 935 6.812160 GTGTAGATTCACTCATTTTACTCCGT 59.188 38.462 0.00 0.00 35.68 4.69
899 936 7.972277 GTGTAGATTCACTCATTTTACTCCGTA 59.028 37.037 0.00 0.00 35.68 4.02
900 937 8.692710 TGTAGATTCACTCATTTTACTCCGTAT 58.307 33.333 0.00 0.00 0.00 3.06
901 938 8.969267 GTAGATTCACTCATTTTACTCCGTATG 58.031 37.037 0.00 0.00 0.00 2.39
902 939 7.556844 AGATTCACTCATTTTACTCCGTATGT 58.443 34.615 0.00 0.00 0.00 2.29
903 940 8.692710 AGATTCACTCATTTTACTCCGTATGTA 58.307 33.333 0.00 0.00 0.00 2.29
904 941 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
905 942 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
906 943 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
907 944 7.121611 TCACTCATTTTACTCCGTATGTAGTCA 59.878 37.037 0.00 0.00 0.00 3.41
908 945 7.220300 CACTCATTTTACTCCGTATGTAGTCAC 59.780 40.741 0.00 0.00 0.00 3.67
909 946 7.122353 ACTCATTTTACTCCGTATGTAGTCACT 59.878 37.037 0.00 0.00 0.00 3.41
910 947 7.833786 TCATTTTACTCCGTATGTAGTCACTT 58.166 34.615 0.00 0.00 0.00 3.16
911 948 7.758076 TCATTTTACTCCGTATGTAGTCACTTG 59.242 37.037 0.00 0.00 0.00 3.16
912 949 6.579666 TTTACTCCGTATGTAGTCACTTGT 57.420 37.500 0.00 0.00 0.00 3.16
913 950 6.579666 TTACTCCGTATGTAGTCACTTGTT 57.420 37.500 0.00 0.00 0.00 2.83
914 951 4.806330 ACTCCGTATGTAGTCACTTGTTG 58.194 43.478 0.00 0.00 0.00 3.33
915 952 4.521639 ACTCCGTATGTAGTCACTTGTTGA 59.478 41.667 0.00 0.00 0.00 3.18
916 953 5.010314 ACTCCGTATGTAGTCACTTGTTGAA 59.990 40.000 0.00 0.00 35.39 2.69
917 954 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
918 955 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
919 956 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
920 957 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
921 958 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
922 959 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
923 960 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
924 961 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
925 962 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
926 963 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
927 964 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
928 965 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
929 966 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
930 967 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
931 968 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
932 969 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
933 970 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
949 986 9.413734 AGAAAGACAAATATTTAGGAATGGAGG 57.586 33.333 0.00 0.00 0.00 4.30
950 987 8.539117 AAAGACAAATATTTAGGAATGGAGGG 57.461 34.615 0.00 0.00 0.00 4.30
951 988 7.465900 AGACAAATATTTAGGAATGGAGGGA 57.534 36.000 0.00 0.00 0.00 4.20
952 989 7.521669 AGACAAATATTTAGGAATGGAGGGAG 58.478 38.462 0.00 0.00 0.00 4.30
953 990 7.129504 AGACAAATATTTAGGAATGGAGGGAGT 59.870 37.037 0.00 0.00 0.00 3.85
1042 1079 9.860898 AAAATAGTAAAGCAAATCTGATGTTCC 57.139 29.630 0.00 0.00 0.00 3.62
1043 1080 8.579850 AATAGTAAAGCAAATCTGATGTTCCA 57.420 30.769 0.00 0.00 0.00 3.53
1044 1081 8.757982 ATAGTAAAGCAAATCTGATGTTCCAT 57.242 30.769 0.00 0.00 0.00 3.41
1045 1082 7.472334 AGTAAAGCAAATCTGATGTTCCATT 57.528 32.000 0.00 0.00 0.00 3.16
1046 1083 7.899973 AGTAAAGCAAATCTGATGTTCCATTT 58.100 30.769 0.00 0.00 0.00 2.32
1047 1084 8.031277 AGTAAAGCAAATCTGATGTTCCATTTC 58.969 33.333 0.00 0.00 0.00 2.17
1048 1085 5.988310 AGCAAATCTGATGTTCCATTTCA 57.012 34.783 0.00 0.00 0.00 2.69
1049 1086 6.540438 AGCAAATCTGATGTTCCATTTCAT 57.460 33.333 0.00 0.00 0.00 2.57
1050 1087 6.338146 AGCAAATCTGATGTTCCATTTCATG 58.662 36.000 0.00 0.00 0.00 3.07
1073 1110 5.163163 TGGGTGATATTTTATCTGCAGCTCT 60.163 40.000 9.47 0.00 0.00 4.09
1291 1333 2.550180 GAGGGCAAACAGTCAACTTCTC 59.450 50.000 0.00 0.00 0.00 2.87
1405 1447 6.071952 GCAAAAGGTTCATACAGGATTCTTCA 60.072 38.462 0.00 0.00 0.00 3.02
1406 1448 7.363268 GCAAAAGGTTCATACAGGATTCTTCAT 60.363 37.037 0.00 0.00 0.00 2.57
1415 1457 7.654923 TCATACAGGATTCTTCATTCGAATGAG 59.345 37.037 32.82 26.61 45.35 2.90
1421 1463 3.877559 TCTTCATTCGAATGAGCCACAT 58.122 40.909 32.82 0.00 45.35 3.21
1422 1464 3.624410 TCTTCATTCGAATGAGCCACATG 59.376 43.478 32.82 19.99 45.35 3.21
1423 1465 1.672363 TCATTCGAATGAGCCACATGC 59.328 47.619 31.83 0.00 40.32 4.06
1457 1499 7.042950 CCATTCAAATTGAGCCACATGATAAA 58.957 34.615 0.00 0.00 0.00 1.40
1482 1524 4.811555 TGTCCGTGAAAAACTTGATGAG 57.188 40.909 0.00 0.00 0.00 2.90
1516 1558 9.439500 CCAACAGATCAAAATTTGGATTAACAT 57.561 29.630 9.48 0.00 39.33 2.71
1529 1571 6.653526 TGGATTAACATGCCATCTAATTGG 57.346 37.500 0.00 0.00 39.94 3.16
1532 1574 7.782168 TGGATTAACATGCCATCTAATTGGTAA 59.218 33.333 0.00 0.00 39.11 2.85
1689 1731 3.120108 TCCTATAGTTGGTTTGGGAGGG 58.880 50.000 0.00 0.00 0.00 4.30
1843 1885 2.542205 GGTACCGGTGAAAGCAACAAAC 60.542 50.000 19.93 1.70 0.00 2.93
1866 1908 7.272037 ACAACTAAACCTGGAAATGTTACAG 57.728 36.000 0.00 0.00 0.00 2.74
1901 1943 6.183360 CGTGGGATTTTACAGGAGAAGAGATA 60.183 42.308 0.00 0.00 0.00 1.98
1905 1947 9.634021 GGGATTTTACAGGAGAAGAGATATTTT 57.366 33.333 0.00 0.00 0.00 1.82
1933 1975 6.539826 TGTACTTGATGACATGTGGAATGATC 59.460 38.462 1.15 0.00 36.20 2.92
2004 2046 3.746492 GTGGAAGTGTGATTGTAGTCACC 59.254 47.826 5.27 0.00 46.17 4.02
2059 2101 4.468510 AGACCCTGGAACAATATGACGTTA 59.531 41.667 0.00 0.00 38.70 3.18
2070 2112 8.883789 AACAATATGACGTTACAAAATTACCG 57.116 30.769 0.00 0.00 0.00 4.02
2099 2141 6.961359 TGAGTGTATGGAAGTATTTGTTCG 57.039 37.500 0.00 0.00 0.00 3.95
2134 2176 0.260230 TGGCAGTGAAAAAGACCCCA 59.740 50.000 0.00 0.00 0.00 4.96
2136 2178 1.341209 GGCAGTGAAAAAGACCCCAAG 59.659 52.381 0.00 0.00 0.00 3.61
2242 2284 4.425577 AGTCGAAATGTTGAAGAATGGC 57.574 40.909 0.00 0.00 0.00 4.40
2251 2293 3.512287 GAAGAATGGCGGCGCATCG 62.512 63.158 34.36 5.55 0.00 3.84
2295 2337 6.491403 ACATTGAGGGAAGCATAAATGGTATC 59.509 38.462 0.00 0.00 37.57 2.24
2331 2373 5.490139 AATTGAGTTATGATGCACTTCCG 57.510 39.130 0.00 0.00 0.00 4.30
2348 2390 3.260483 GCCTCATCTGCGAGCGTG 61.260 66.667 0.00 0.00 0.00 5.34
2353 2395 1.057822 CATCTGCGAGCGTGTTTCG 59.942 57.895 0.00 0.00 40.85 3.46
2370 2412 4.159120 GTTTCGCTTGCCTATCAACTTTC 58.841 43.478 0.00 0.00 0.00 2.62
2437 2479 1.301637 GCATTGGGGTTGTTGCACC 60.302 57.895 0.00 0.00 35.22 5.01
2499 2541 8.031277 GCAAAATACTTCCATGAACTTCTTGAT 58.969 33.333 0.00 0.00 0.00 2.57
2502 2544 8.970859 AATACTTCCATGAACTTCTTGATAGG 57.029 34.615 0.00 0.00 0.00 2.57
2556 2598 5.653507 GATGGCAGCATTCAGAAATGTAAA 58.346 37.500 0.00 0.00 43.54 2.01
2611 2653 2.481952 GTGTCCAGAAATGAGTGTGCTC 59.518 50.000 0.00 0.00 41.97 4.26
2638 2680 2.825532 AGTTGTGAAAAGGTTGCAGTGT 59.174 40.909 0.00 0.00 0.00 3.55
2645 2687 4.142403 TGAAAAGGTTGCAGTGTCTGAAAG 60.142 41.667 0.66 0.00 28.41 2.62
2671 2713 1.226974 CATCTAGTGTGGGACCGCG 60.227 63.158 0.00 0.00 0.00 6.46
2726 2769 0.521735 CTGAAAAGGGCACGTAAGGC 59.478 55.000 0.00 0.00 46.39 4.35
2733 2776 1.373748 GGCACGTAAGGCGAGAACA 60.374 57.895 0.00 0.00 44.77 3.18
2735 2778 1.076332 GCACGTAAGGCGAGAACATT 58.924 50.000 0.00 0.00 44.77 2.71
2757 2800 6.528537 TTTGCAAGCAGATACAATTATGGT 57.471 33.333 0.00 0.00 0.00 3.55
2796 2839 3.715315 TCCTCGAGGACCTATTCTCTACA 59.285 47.826 30.49 2.53 39.78 2.74
2866 2909 3.424962 GCTACCGAGTTCAGTTGCAAATC 60.425 47.826 0.00 0.00 35.27 2.17
2882 2925 3.432749 GCAAATCTGAGGCATCTGAGGTA 60.433 47.826 13.38 0.00 36.90 3.08
2934 2977 6.326583 TCAGAATCCTACCGAATTCCTTATGT 59.673 38.462 0.00 0.00 0.00 2.29
2936 2979 7.815068 CAGAATCCTACCGAATTCCTTATGTAG 59.185 40.741 0.00 3.88 0.00 2.74
2985 3032 1.892338 CCGGTGCAGCCAATTTGAT 59.108 52.632 10.90 0.00 36.97 2.57
3091 3138 3.304911 TTTGTGGTTGGTCTTCCATGA 57.695 42.857 0.00 0.00 43.91 3.07
3096 3143 3.573967 GTGGTTGGTCTTCCATGACATTT 59.426 43.478 0.00 0.00 43.91 2.32
3103 3150 9.125026 GTTGGTCTTCCATGACATTTCTATATT 57.875 33.333 0.00 0.00 43.91 1.28
3117 3164 1.532868 CTATATTTGAGCGGCTGCACC 59.467 52.381 21.93 11.67 46.23 5.01
3287 3334 4.701765 CTTGATCTGATGGAACCAGTAGG 58.298 47.826 0.00 0.00 42.21 3.18
3308 3355 1.460255 CCTTGAGTGGGCTGGGAAA 59.540 57.895 0.00 0.00 0.00 3.13
3326 3373 4.833390 GGAAACCTACATGTGCTTACTCT 58.167 43.478 9.11 0.00 0.00 3.24
3327 3374 4.870991 GGAAACCTACATGTGCTTACTCTC 59.129 45.833 9.11 0.00 0.00 3.20
3328 3375 3.784701 ACCTACATGTGCTTACTCTCG 57.215 47.619 9.11 0.00 0.00 4.04
3329 3376 3.090037 ACCTACATGTGCTTACTCTCGT 58.910 45.455 9.11 0.00 0.00 4.18
3330 3377 3.510360 ACCTACATGTGCTTACTCTCGTT 59.490 43.478 9.11 0.00 0.00 3.85
3331 3378 3.859961 CCTACATGTGCTTACTCTCGTTG 59.140 47.826 9.11 0.00 0.00 4.10
3332 3379 3.660501 ACATGTGCTTACTCTCGTTGA 57.339 42.857 0.00 0.00 0.00 3.18
3334 3381 2.065993 TGTGCTTACTCTCGTTGAGC 57.934 50.000 7.81 0.00 46.41 4.26
3335 3382 1.613925 TGTGCTTACTCTCGTTGAGCT 59.386 47.619 7.81 0.00 46.41 4.09
3336 3383 2.035961 TGTGCTTACTCTCGTTGAGCTT 59.964 45.455 7.81 0.00 46.41 3.74
3337 3384 2.664085 GTGCTTACTCTCGTTGAGCTTC 59.336 50.000 7.81 0.00 46.41 3.86
3338 3385 2.263945 GCTTACTCTCGTTGAGCTTCC 58.736 52.381 7.81 0.00 46.41 3.46
3339 3386 2.352814 GCTTACTCTCGTTGAGCTTCCA 60.353 50.000 7.81 0.00 46.41 3.53
3340 3387 3.861131 GCTTACTCTCGTTGAGCTTCCAA 60.861 47.826 7.81 0.00 46.41 3.53
3341 3388 2.910688 ACTCTCGTTGAGCTTCCAAA 57.089 45.000 7.81 0.00 46.41 3.28
3380 3427 5.008415 CAGAGAGCTTCAAATCTTGTGTGTT 59.992 40.000 0.00 0.00 0.00 3.32
3391 3438 7.933577 TCAAATCTTGTGTGTTATCTCTTCAGT 59.066 33.333 0.00 0.00 0.00 3.41
3392 3439 8.562892 CAAATCTTGTGTGTTATCTCTTCAGTT 58.437 33.333 0.00 0.00 0.00 3.16
3418 3465 0.867329 GATTCGCGATTGCAAAGGGC 60.867 55.000 10.88 6.44 42.97 5.19
3542 3589 2.167281 AGGATTATCATCTCATCCGCGG 59.833 50.000 22.12 22.12 41.38 6.46
3597 3644 8.599792 ACTTGTGAAGGGTAAGCTTATTAACTA 58.400 33.333 9.88 0.30 0.00 2.24
3627 3674 6.260870 TGAGTTTCTCAGCTAGTTACTCTG 57.739 41.667 13.11 0.00 35.39 3.35
3696 3744 9.710900 CATGTTCATATGCTTTACCTCACTATA 57.289 33.333 0.00 0.00 0.00 1.31
3763 3814 7.281040 TCATAAATCCTGATGGAAGAAATGC 57.719 36.000 0.00 0.00 46.80 3.56
3852 3903 7.612677 ACAGTGTCGATTAGGTTATTTCTTCT 58.387 34.615 0.00 0.00 0.00 2.85
3917 3968 2.711542 AGAATAAGCTGGACAAACGGG 58.288 47.619 0.00 0.00 0.00 5.28
3938 3989 5.354513 CGGGGTTTTTATTTGTTTTGTGGTT 59.645 36.000 0.00 0.00 0.00 3.67
3993 4046 4.453819 CGCCTTCTTTGACATTCTTCTTCT 59.546 41.667 0.00 0.00 0.00 2.85
3994 4047 5.639506 CGCCTTCTTTGACATTCTTCTTCTA 59.360 40.000 0.00 0.00 0.00 2.10
3995 4048 6.147821 CGCCTTCTTTGACATTCTTCTTCTAA 59.852 38.462 0.00 0.00 0.00 2.10
3996 4049 7.148340 CGCCTTCTTTGACATTCTTCTTCTAAT 60.148 37.037 0.00 0.00 0.00 1.73
3997 4050 9.167311 GCCTTCTTTGACATTCTTCTTCTAATA 57.833 33.333 0.00 0.00 0.00 0.98
4001 4054 9.996554 TCTTTGACATTCTTCTTCTAATACACA 57.003 29.630 0.00 0.00 0.00 3.72
4004 4057 8.239681 TGACATTCTTCTTCTAATACACAACG 57.760 34.615 0.00 0.00 0.00 4.10
4005 4058 8.085909 TGACATTCTTCTTCTAATACACAACGA 58.914 33.333 0.00 0.00 0.00 3.85
4006 4059 8.240883 ACATTCTTCTTCTAATACACAACGAC 57.759 34.615 0.00 0.00 0.00 4.34
4007 4060 7.870954 ACATTCTTCTTCTAATACACAACGACA 59.129 33.333 0.00 0.00 0.00 4.35
4008 4061 7.633361 TTCTTCTTCTAATACACAACGACAC 57.367 36.000 0.00 0.00 0.00 3.67
4009 4062 6.154445 TCTTCTTCTAATACACAACGACACC 58.846 40.000 0.00 0.00 0.00 4.16
4010 4063 5.717078 TCTTCTAATACACAACGACACCT 57.283 39.130 0.00 0.00 0.00 4.00
4011 4064 6.092955 TCTTCTAATACACAACGACACCTT 57.907 37.500 0.00 0.00 0.00 3.50
4012 4065 6.518493 TCTTCTAATACACAACGACACCTTT 58.482 36.000 0.00 0.00 0.00 3.11
4013 4066 6.643770 TCTTCTAATACACAACGACACCTTTC 59.356 38.462 0.00 0.00 0.00 2.62
4014 4067 4.919168 TCTAATACACAACGACACCTTTCG 59.081 41.667 0.00 0.00 44.87 3.46
4015 4068 1.210870 TACACAACGACACCTTTCGC 58.789 50.000 0.00 0.00 43.06 4.70
4016 4069 0.741574 ACACAACGACACCTTTCGCA 60.742 50.000 0.00 0.00 43.06 5.10
4017 4070 0.375454 CACAACGACACCTTTCGCAA 59.625 50.000 0.00 0.00 43.06 4.85
4018 4071 1.002900 CACAACGACACCTTTCGCAAT 60.003 47.619 0.00 0.00 43.06 3.56
4019 4072 2.222213 CACAACGACACCTTTCGCAATA 59.778 45.455 0.00 0.00 43.06 1.90
4020 4073 2.873472 ACAACGACACCTTTCGCAATAA 59.127 40.909 0.00 0.00 43.06 1.40
4021 4074 3.312973 ACAACGACACCTTTCGCAATAAA 59.687 39.130 0.00 0.00 43.06 1.40
4022 4075 4.023536 ACAACGACACCTTTCGCAATAAAT 60.024 37.500 0.00 0.00 43.06 1.40
4023 4076 5.179742 ACAACGACACCTTTCGCAATAAATA 59.820 36.000 0.00 0.00 43.06 1.40
4024 4077 5.866335 ACGACACCTTTCGCAATAAATAA 57.134 34.783 0.00 0.00 43.06 1.40
4025 4078 6.243811 ACGACACCTTTCGCAATAAATAAA 57.756 33.333 0.00 0.00 43.06 1.40
4026 4079 6.848451 ACGACACCTTTCGCAATAAATAAAT 58.152 32.000 0.00 0.00 43.06 1.40
4027 4080 7.976826 ACGACACCTTTCGCAATAAATAAATA 58.023 30.769 0.00 0.00 43.06 1.40
4028 4081 8.452534 ACGACACCTTTCGCAATAAATAAATAA 58.547 29.630 0.00 0.00 43.06 1.40
4029 4082 9.279904 CGACACCTTTCGCAATAAATAAATAAA 57.720 29.630 0.00 0.00 31.03 1.40
4056 4109 3.741344 ACACAACGACACAGCTTTAGATC 59.259 43.478 0.00 0.00 0.00 2.75
4077 4130 6.934645 AGATCTGTGGTTGAGAAAACGAATAA 59.065 34.615 0.00 0.00 0.00 1.40
4078 4131 6.539649 TCTGTGGTTGAGAAAACGAATAAG 57.460 37.500 0.00 0.00 0.00 1.73
4127 4180 5.754782 ACACAATATATTCTTGAGGGTGCA 58.245 37.500 9.61 0.00 0.00 4.57
4142 4195 2.368548 GGGTGCACTTCCATTTCCTTTT 59.631 45.455 17.98 0.00 0.00 2.27
4191 4244 0.668401 GTTGCATGAGCTTTGGCACC 60.668 55.000 0.00 0.00 42.74 5.01
4205 4258 5.782047 CTTTGGCACCAGTTTGATTCATTA 58.218 37.500 0.00 0.00 0.00 1.90
4220 4273 6.943981 TGATTCATTAGCGCAGTTACATTAC 58.056 36.000 11.47 0.00 0.00 1.89
4371 4425 1.263484 CATCGATGGATTGTGCTGCTC 59.737 52.381 17.96 0.00 0.00 4.26
4393 4447 0.032952 TGTAACACAGTCGACCAGGC 59.967 55.000 13.01 0.00 0.00 4.85
4487 4541 5.608449 ACTCCCACTTAGTACAAAACTGAC 58.392 41.667 0.00 0.00 39.39 3.51
4524 4578 5.301805 TGTCTGTACACACTCTGAATTCTGA 59.698 40.000 13.64 13.64 0.00 3.27
4549 4603 2.174424 AGGAAAGCTCCATGATCCTTCC 59.826 50.000 0.00 0.61 45.24 3.46
4553 4607 1.211457 AGCTCCATGATCCTTCCACAC 59.789 52.381 0.00 0.00 0.00 3.82
4570 4624 5.155161 TCCACACCTTCCAGCTATATATGT 58.845 41.667 0.00 0.00 0.00 2.29
4575 4629 7.332926 CACACCTTCCAGCTATATATGTCATTC 59.667 40.741 0.00 0.00 0.00 2.67
4576 4630 7.016563 ACACCTTCCAGCTATATATGTCATTCA 59.983 37.037 0.00 0.00 0.00 2.57
4684 4738 2.156098 TGTCCGGCTTGATTGGTTTAC 58.844 47.619 0.00 0.00 0.00 2.01
4709 4763 0.548926 TATCTTCACCAGCACCCCCA 60.549 55.000 0.00 0.00 0.00 4.96
4719 4773 2.124983 CACCCCCATCACTCAGCG 60.125 66.667 0.00 0.00 0.00 5.18
4745 4799 2.189499 CCGCTTAGGCTCCATTGGC 61.189 63.158 0.00 0.00 36.09 4.52
4752 4806 3.207669 GCTCCATTGGCAGCCTCG 61.208 66.667 14.15 0.26 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.409712 AGTAAAGAGTAGGTTACCCTTGGT 58.590 41.667 0.00 0.00 42.66 3.67
51 52 8.808240 TCCTAGTTTCCAACCCAATATAGTAT 57.192 34.615 0.00 0.00 0.00 2.12
66 67 5.420739 ACTTGATGTCTCTCTCCTAGTTTCC 59.579 44.000 0.00 0.00 0.00 3.13
72 73 4.081972 GCAACACTTGATGTCTCTCTCCTA 60.082 45.833 0.00 0.00 42.31 2.94
146 147 5.874810 ACGACATCACCATGTATATTATGCC 59.125 40.000 0.00 0.00 43.79 4.40
151 152 4.960938 AGCACGACATCACCATGTATATT 58.039 39.130 0.00 0.00 43.79 1.28
157 158 1.730501 AGAAGCACGACATCACCATG 58.269 50.000 0.00 0.00 35.92 3.66
160 161 0.798776 CCAAGAAGCACGACATCACC 59.201 55.000 0.00 0.00 0.00 4.02
167 168 1.891919 GGCACACCAAGAAGCACGA 60.892 57.895 0.00 0.00 35.26 4.35
182 183 3.118445 AGTTAAAGCAAAGCCAAAAGGCA 60.118 39.130 9.42 0.00 37.35 4.75
224 225 2.507886 TGATATTTCCAGCCTTCCCGAA 59.492 45.455 0.00 0.00 0.00 4.30
226 227 2.638480 TGATATTTCCAGCCTTCCCG 57.362 50.000 0.00 0.00 0.00 5.14
228 229 4.764308 GGAGAATGATATTTCCAGCCTTCC 59.236 45.833 0.00 0.00 0.00 3.46
242 243 5.779241 TTGTTTAGAGGGTGGAGAATGAT 57.221 39.130 0.00 0.00 0.00 2.45
288 289 2.029110 AGAGAGAGTTGCTGCAGAACTC 60.029 50.000 30.98 30.98 46.58 3.01
291 292 2.549563 CCAAGAGAGAGTTGCTGCAGAA 60.550 50.000 20.43 2.96 0.00 3.02
307 308 3.703556 TCATTGTTTTTCACAGCCCAAGA 59.296 39.130 0.00 0.00 36.48 3.02
308 309 4.057406 TCATTGTTTTTCACAGCCCAAG 57.943 40.909 0.00 0.00 36.48 3.61
322 323 9.594478 TGTTGACATACGAATAGTATCATTGTT 57.406 29.630 0.00 0.00 43.78 2.83
327 328 9.297586 GTTTCTGTTGACATACGAATAGTATCA 57.702 33.333 0.00 0.00 43.78 2.15
349 350 6.426646 AGTAGGATCATCAGGTATGGTTTC 57.573 41.667 0.00 0.00 36.15 2.78
379 380 3.377172 CGGGTTTCTGTAATGGCCTAAAG 59.623 47.826 3.32 0.00 0.00 1.85
400 401 0.608640 AGAACACCTCCTAAGCCACG 59.391 55.000 0.00 0.00 0.00 4.94
417 418 2.688446 CGCTTGTCTGTATCCCTGTAGA 59.312 50.000 0.00 0.00 0.00 2.59
449 450 3.565482 CACCATCGTCCTTGGAAATATGG 59.435 47.826 17.53 17.53 37.69 2.74
471 472 2.358737 CCACTGGCGACCTTGGAC 60.359 66.667 0.00 0.00 31.70 4.02
476 477 3.168528 AACCACCACTGGCGACCT 61.169 61.111 0.00 0.00 42.08 3.85
537 538 6.430000 AGCACTACGACTTGGAATAAAACAAT 59.570 34.615 0.00 0.00 0.00 2.71
566 567 4.080299 ACTGAAGAACATAACCATCCTCCC 60.080 45.833 0.00 0.00 0.00 4.30
728 730 4.190772 CCACAAAAGGAAAAGTGCACAAT 58.809 39.130 21.04 4.21 0.00 2.71
791 828 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
792 829 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
793 830 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
794 831 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
795 832 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
812 849 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
813 850 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
817 854 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
818 855 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
819 856 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
820 857 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
821 858 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
822 859 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
823 860 7.254455 CGTATGTGGTAGTCCATTTGAAATCTC 60.254 40.741 0.00 0.00 46.20 2.75
824 861 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
825 862 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
826 863 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
827 864 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
828 865 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
829 866 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
830 867 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
831 868 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
832 869 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
833 870 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
834 871 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
835 872 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
836 873 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
837 874 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
838 875 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
840 877 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
859 896 9.860650 AGTGAATCTACACTCTAAGATATGTCT 57.139 33.333 0.00 0.00 46.36 3.41
873 910 6.812160 ACGGAGTAAAATGAGTGAATCTACAC 59.188 38.462 0.00 0.00 41.94 2.90
874 911 6.931838 ACGGAGTAAAATGAGTGAATCTACA 58.068 36.000 0.00 0.00 41.94 2.74
890 927 7.255555 TTCAACAAGTGACTACATACGGAGTAA 60.256 37.037 0.00 0.00 41.03 2.24
891 928 6.207221 TTCAACAAGTGACTACATACGGAGTA 59.793 38.462 0.00 0.00 41.66 2.59
892 929 5.010314 TTCAACAAGTGACTACATACGGAGT 59.990 40.000 0.00 0.00 39.84 3.85
893 930 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
894 931 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
895 932 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
896 933 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
897 934 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
899 936 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
900 937 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
901 938 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
902 939 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
903 940 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
904 941 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
905 942 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
906 943 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
907 944 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
923 960 9.413734 CCTCCATTCCTAAATATTTGTCTTTCT 57.586 33.333 11.05 0.00 0.00 2.52
924 961 8.633561 CCCTCCATTCCTAAATATTTGTCTTTC 58.366 37.037 11.05 0.00 0.00 2.62
925 962 8.343787 TCCCTCCATTCCTAAATATTTGTCTTT 58.656 33.333 11.05 0.00 0.00 2.52
926 963 7.882755 TCCCTCCATTCCTAAATATTTGTCTT 58.117 34.615 11.05 0.00 0.00 3.01
927 964 7.129504 ACTCCCTCCATTCCTAAATATTTGTCT 59.870 37.037 11.05 0.00 0.00 3.41
928 965 7.290813 ACTCCCTCCATTCCTAAATATTTGTC 58.709 38.462 11.05 0.00 0.00 3.18
929 966 7.226059 ACTCCCTCCATTCCTAAATATTTGT 57.774 36.000 11.05 0.00 0.00 2.83
930 967 7.391833 GCTACTCCCTCCATTCCTAAATATTTG 59.608 40.741 11.05 1.40 0.00 2.32
931 968 7.295911 AGCTACTCCCTCCATTCCTAAATATTT 59.704 37.037 5.89 5.89 0.00 1.40
932 969 6.795000 AGCTACTCCCTCCATTCCTAAATATT 59.205 38.462 0.00 0.00 0.00 1.28
933 970 6.335115 AGCTACTCCCTCCATTCCTAAATAT 58.665 40.000 0.00 0.00 0.00 1.28
934 971 5.727630 AGCTACTCCCTCCATTCCTAAATA 58.272 41.667 0.00 0.00 0.00 1.40
935 972 4.571951 AGCTACTCCCTCCATTCCTAAAT 58.428 43.478 0.00 0.00 0.00 1.40
936 973 4.008916 AGCTACTCCCTCCATTCCTAAA 57.991 45.455 0.00 0.00 0.00 1.85
937 974 3.708236 AGCTACTCCCTCCATTCCTAA 57.292 47.619 0.00 0.00 0.00 2.69
938 975 4.170251 AGTTAGCTACTCCCTCCATTCCTA 59.830 45.833 0.00 0.00 28.23 2.94
939 976 3.051727 AGTTAGCTACTCCCTCCATTCCT 60.052 47.826 0.00 0.00 28.23 3.36
940 977 3.310193 AGTTAGCTACTCCCTCCATTCC 58.690 50.000 0.00 0.00 28.23 3.01
941 978 5.540719 ACATAGTTAGCTACTCCCTCCATTC 59.459 44.000 0.00 0.00 38.33 2.67
942 979 5.468658 ACATAGTTAGCTACTCCCTCCATT 58.531 41.667 0.00 0.00 38.33 3.16
943 980 5.081315 ACATAGTTAGCTACTCCCTCCAT 57.919 43.478 0.00 0.00 38.33 3.41
944 981 4.537945 ACATAGTTAGCTACTCCCTCCA 57.462 45.455 0.00 0.00 38.33 3.86
945 982 6.246919 TCATACATAGTTAGCTACTCCCTCC 58.753 44.000 0.00 0.00 38.33 4.30
946 983 7.762588 TTCATACATAGTTAGCTACTCCCTC 57.237 40.000 0.00 0.00 38.33 4.30
947 984 8.589338 CATTTCATACATAGTTAGCTACTCCCT 58.411 37.037 0.00 0.00 38.33 4.20
948 985 8.585881 TCATTTCATACATAGTTAGCTACTCCC 58.414 37.037 0.00 0.00 38.33 4.30
949 986 9.413048 GTCATTTCATACATAGTTAGCTACTCC 57.587 37.037 0.00 0.00 38.33 3.85
950 987 9.967346 TGTCATTTCATACATAGTTAGCTACTC 57.033 33.333 0.00 0.00 38.33 2.59
951 988 9.973450 CTGTCATTTCATACATAGTTAGCTACT 57.027 33.333 0.00 0.00 41.04 2.57
952 989 9.751542 ACTGTCATTTCATACATAGTTAGCTAC 57.248 33.333 0.00 0.00 0.00 3.58
1042 1079 8.361889 TGCAGATAAAATATCACCCATGAAATG 58.638 33.333 0.00 0.00 46.21 2.32
1043 1080 8.481492 TGCAGATAAAATATCACCCATGAAAT 57.519 30.769 0.00 0.00 38.69 2.17
1044 1081 7.470424 GCTGCAGATAAAATATCACCCATGAAA 60.470 37.037 20.43 0.00 38.69 2.69
1045 1082 6.016024 GCTGCAGATAAAATATCACCCATGAA 60.016 38.462 20.43 0.00 38.69 2.57
1046 1083 5.474532 GCTGCAGATAAAATATCACCCATGA 59.525 40.000 20.43 0.00 39.83 3.07
1047 1084 5.475909 AGCTGCAGATAAAATATCACCCATG 59.524 40.000 20.43 0.00 0.00 3.66
1048 1085 5.638133 AGCTGCAGATAAAATATCACCCAT 58.362 37.500 20.43 0.00 0.00 4.00
1049 1086 5.052693 AGCTGCAGATAAAATATCACCCA 57.947 39.130 20.43 0.00 0.00 4.51
1050 1087 5.312079 AGAGCTGCAGATAAAATATCACCC 58.688 41.667 20.43 0.00 0.00 4.61
1051 1088 6.874288 AAGAGCTGCAGATAAAATATCACC 57.126 37.500 20.43 0.00 0.00 4.02
1052 1089 8.186821 ACAAAAGAGCTGCAGATAAAATATCAC 58.813 33.333 20.43 0.00 0.00 3.06
1053 1090 8.186163 CACAAAAGAGCTGCAGATAAAATATCA 58.814 33.333 20.43 0.00 0.00 2.15
1054 1091 7.167136 GCACAAAAGAGCTGCAGATAAAATATC 59.833 37.037 20.43 0.00 0.00 1.63
1064 1101 2.503920 AAAGCACAAAAGAGCTGCAG 57.496 45.000 10.11 10.11 41.70 4.41
1220 1257 4.600062 ACTCAGTGACCTTTCCAACTTTT 58.400 39.130 0.00 0.00 0.00 2.27
1291 1333 6.166279 TGTCTAACCACTCTTTAAGAGCATG 58.834 40.000 20.59 12.63 46.12 4.06
1415 1457 0.033781 TGGAAAAGCAAGCATGTGGC 59.966 50.000 0.00 0.00 45.30 5.01
1421 1463 5.366460 TCAATTTGAATGGAAAAGCAAGCA 58.634 33.333 0.00 0.00 0.00 3.91
1422 1464 5.616204 GCTCAATTTGAATGGAAAAGCAAGC 60.616 40.000 0.01 0.00 0.00 4.01
1423 1465 5.106830 GGCTCAATTTGAATGGAAAAGCAAG 60.107 40.000 0.01 0.00 0.00 4.01
1424 1466 4.756135 GGCTCAATTTGAATGGAAAAGCAA 59.244 37.500 0.01 0.00 0.00 3.91
1425 1467 4.202336 TGGCTCAATTTGAATGGAAAAGCA 60.202 37.500 0.01 0.00 0.00 3.91
1426 1468 4.152938 GTGGCTCAATTTGAATGGAAAAGC 59.847 41.667 0.01 0.00 0.00 3.51
1457 1499 5.530915 TCATCAAGTTTTTCACGGACATCTT 59.469 36.000 0.00 0.00 0.00 2.40
1482 1524 7.437267 CCAAATTTTGATCTGTTGGATGCTATC 59.563 37.037 10.72 0.00 41.05 2.08
1516 1558 4.865905 ACATGGTTACCAATTAGATGGCA 58.134 39.130 8.63 0.00 44.75 4.92
1689 1731 3.195396 TGGCCAATGCAGTTTTTCCTATC 59.805 43.478 0.61 0.00 40.13 2.08
1826 1868 1.923864 GTTGTTTGTTGCTTTCACCGG 59.076 47.619 0.00 0.00 0.00 5.28
1843 1885 6.149633 GCTGTAACATTTCCAGGTTTAGTTG 58.850 40.000 0.00 0.00 0.00 3.16
1901 1943 7.448161 TCCACATGTCATCAAGTACAAGAAAAT 59.552 33.333 0.00 0.00 0.00 1.82
1905 1947 5.482163 TCCACATGTCATCAAGTACAAGA 57.518 39.130 0.00 0.00 0.00 3.02
1933 1975 4.078639 ACTCTTCCCAGTCAGAAACTTG 57.921 45.455 0.00 0.00 35.45 3.16
2004 2046 0.771756 CAACATTTGAACTGCGCGTG 59.228 50.000 8.43 3.52 0.00 5.34
2059 2101 4.458989 ACACTCATCATGCGGTAATTTTGT 59.541 37.500 0.00 0.00 0.00 2.83
2070 2112 7.012704 ACAAATACTTCCATACACTCATCATGC 59.987 37.037 0.00 0.00 0.00 4.06
2099 2141 2.020131 CCATCTCTGAATGCGCACC 58.980 57.895 14.90 8.72 0.00 5.01
2134 2176 3.889538 GAGTTCCCCAGTTTTAGCAACTT 59.110 43.478 0.00 0.00 0.00 2.66
2136 2178 2.557056 GGAGTTCCCCAGTTTTAGCAAC 59.443 50.000 0.00 0.00 0.00 4.17
2242 2284 2.275812 GTTTTCGTCGATGCGCCG 60.276 61.111 4.18 1.29 0.00 6.46
2251 2293 4.086199 TGTTCCACAGTTTGTTTTCGTC 57.914 40.909 0.00 0.00 0.00 4.20
2257 2299 3.384467 CCCTCAATGTTCCACAGTTTGTT 59.616 43.478 0.00 0.00 0.00 2.83
2295 2337 9.844790 TCATAACTCAATTTTAATGCTGTCAAG 57.155 29.630 0.00 0.00 0.00 3.02
2331 2373 3.260483 CACGCTCGCAGATGAGGC 61.260 66.667 0.00 0.00 36.47 4.70
2348 2390 3.831715 AAGTTGATAGGCAAGCGAAAC 57.168 42.857 0.00 0.00 37.12 2.78
2353 2395 1.401905 CGGGAAAGTTGATAGGCAAGC 59.598 52.381 0.00 0.00 37.12 4.01
2370 2412 4.417426 AAACATATGGTAGTCCTTCGGG 57.583 45.455 7.80 0.00 34.23 5.14
2394 2436 6.183360 CCATCCAGAACATAACAAGGTGATTC 60.183 42.308 0.00 0.00 0.00 2.52
2454 2496 4.794278 TGCTCCATTAGTTAACGTCTCA 57.206 40.909 0.00 0.00 0.00 3.27
2458 2500 7.916914 AGTATTTTGCTCCATTAGTTAACGT 57.083 32.000 0.00 0.00 0.00 3.99
2499 2541 5.853572 ATTGGTCTTGTAAAAGGGACCTA 57.146 39.130 11.44 5.30 45.85 3.08
2502 2544 9.628500 AGAATATATTGGTCTTGTAAAAGGGAC 57.372 33.333 1.78 0.00 0.00 4.46
2568 2610 5.928264 CACCGATATTGCTAGATCATGAACA 59.072 40.000 0.00 0.00 0.00 3.18
2611 2653 5.406649 TGCAACCTTTTCACAACTAACAAG 58.593 37.500 0.00 0.00 0.00 3.16
2638 2680 5.717178 ACACTAGATGCCTAACTCTTTCAGA 59.283 40.000 0.00 0.00 0.00 3.27
2645 2687 3.031736 TCCCACACTAGATGCCTAACTC 58.968 50.000 0.00 0.00 0.00 3.01
2650 2692 1.330655 CGGTCCCACACTAGATGCCT 61.331 60.000 0.00 0.00 0.00 4.75
2684 2726 4.641989 GCTGCTTAGGAAATTTCAGATCCA 59.358 41.667 19.49 9.51 35.62 3.41
2726 2769 2.975410 TCTGCTTGCAAATGTTCTCG 57.025 45.000 0.00 0.00 0.00 4.04
2733 2776 7.116075 ACCATAATTGTATCTGCTTGCAAAT 57.884 32.000 0.00 0.00 0.00 2.32
2735 2778 6.039270 GGTACCATAATTGTATCTGCTTGCAA 59.961 38.462 7.15 0.00 0.00 4.08
2757 2800 0.321298 GGAAGGCTTTGCTCACGGTA 60.321 55.000 0.00 0.00 0.00 4.02
2866 2909 1.786937 AGGTACCTCAGATGCCTCAG 58.213 55.000 9.21 0.00 0.00 3.35
2882 2925 7.496346 TTCTTGTTCCATTGTAGATCTAGGT 57.504 36.000 1.64 0.00 0.00 3.08
2934 2977 8.154203 TGAACTGTTTGTAGATTCACCAATCTA 58.846 33.333 0.00 1.08 45.99 1.98
2936 2979 7.202016 TGAACTGTTTGTAGATTCACCAATC 57.798 36.000 0.00 0.00 39.10 2.67
2985 3032 1.064240 TCCATACGTCCTGGTAGCTCA 60.064 52.381 14.74 0.00 35.19 4.26
3091 3138 4.023707 GCAGCCGCTCAAATATAGAAATGT 60.024 41.667 0.00 0.00 34.30 2.71
3096 3143 2.483876 GTGCAGCCGCTCAAATATAGA 58.516 47.619 0.00 0.00 39.64 1.98
3117 3164 5.354513 TCCTTCTGTGAGTGATACTAACTCG 59.645 44.000 0.00 0.00 45.81 4.18
3124 3171 5.491982 ACCAAATCCTTCTGTGAGTGATAC 58.508 41.667 0.00 0.00 0.00 2.24
3308 3355 3.090037 ACGAGAGTAAGCACATGTAGGT 58.910 45.455 0.00 0.00 46.88 3.08
3334 3381 1.302832 AGCCCACGAGCTTTGGAAG 60.303 57.895 15.33 2.83 41.41 3.46
3335 3382 2.836154 AGCCCACGAGCTTTGGAA 59.164 55.556 15.33 0.00 41.41 3.53
3391 3438 1.130373 GCAATCGCGAATCAGGACAAA 59.870 47.619 15.24 0.00 0.00 2.83
3392 3439 0.726827 GCAATCGCGAATCAGGACAA 59.273 50.000 15.24 0.00 0.00 3.18
3418 3465 3.483959 GCTCGGCAGCTTCTCAAG 58.516 61.111 0.00 0.00 43.09 3.02
3542 3589 4.848562 TCGATGTGTATGACAGGGATAC 57.151 45.455 0.00 0.00 38.23 2.24
3576 3623 8.370266 TCTGTAGTTAATAAGCTTACCCTTCA 57.630 34.615 8.70 5.69 0.00 3.02
3597 3644 6.107901 ACTAGCTGAGAAACTCAAATCTGT 57.892 37.500 0.00 0.00 40.18 3.41
3696 3744 3.636764 TCGTGTCTCCTGTACATGCATAT 59.363 43.478 0.00 0.00 34.51 1.78
3697 3745 3.020984 TCGTGTCTCCTGTACATGCATA 58.979 45.455 0.00 0.00 34.51 3.14
3698 3746 1.824852 TCGTGTCTCCTGTACATGCAT 59.175 47.619 0.00 0.00 34.51 3.96
3761 3812 3.616821 CCGAATATGAACTTCTTCACGCA 59.383 43.478 0.00 0.00 39.28 5.24
3763 3814 6.255670 TCATTCCGAATATGAACTTCTTCACG 59.744 38.462 0.00 0.00 39.28 4.35
3805 3856 0.678048 GGAATCCACTGACAGGGTGC 60.678 60.000 7.51 0.00 33.78 5.01
3817 3868 4.819105 AATCGACACTGTAAGGAATCCA 57.181 40.909 0.61 0.00 39.30 3.41
3852 3903 8.233868 GTGTTACAGATGTTGCAAATACATGTA 58.766 33.333 8.27 8.27 36.41 2.29
3993 4046 3.429543 GCGAAAGGTGTCGTTGTGTATTA 59.570 43.478 0.00 0.00 43.06 0.98
3994 4047 2.222445 GCGAAAGGTGTCGTTGTGTATT 59.778 45.455 0.00 0.00 43.06 1.89
3995 4048 1.796459 GCGAAAGGTGTCGTTGTGTAT 59.204 47.619 0.00 0.00 43.06 2.29
3996 4049 1.210870 GCGAAAGGTGTCGTTGTGTA 58.789 50.000 0.00 0.00 43.06 2.90
3997 4050 0.741574 TGCGAAAGGTGTCGTTGTGT 60.742 50.000 0.00 0.00 43.06 3.72
3998 4051 0.375454 TTGCGAAAGGTGTCGTTGTG 59.625 50.000 0.00 0.00 43.06 3.33
3999 4052 1.305201 ATTGCGAAAGGTGTCGTTGT 58.695 45.000 0.00 0.00 43.06 3.32
4000 4053 3.529634 TTATTGCGAAAGGTGTCGTTG 57.470 42.857 0.00 0.00 43.06 4.10
4001 4054 4.759516 ATTTATTGCGAAAGGTGTCGTT 57.240 36.364 0.00 0.00 43.06 3.85
4002 4055 5.866335 TTATTTATTGCGAAAGGTGTCGT 57.134 34.783 0.00 0.00 43.06 4.34
4003 4056 8.829514 TTATTTATTTATTGCGAAAGGTGTCG 57.170 30.769 0.00 0.00 43.98 4.35
4022 4075 9.976255 GCTGTGTCGTTGTGTATTATTTATTTA 57.024 29.630 0.00 0.00 0.00 1.40
4023 4076 8.726988 AGCTGTGTCGTTGTGTATTATTTATTT 58.273 29.630 0.00 0.00 0.00 1.40
4024 4077 8.263940 AGCTGTGTCGTTGTGTATTATTTATT 57.736 30.769 0.00 0.00 0.00 1.40
4025 4078 7.843490 AGCTGTGTCGTTGTGTATTATTTAT 57.157 32.000 0.00 0.00 0.00 1.40
4026 4079 7.661127 AAGCTGTGTCGTTGTGTATTATTTA 57.339 32.000 0.00 0.00 0.00 1.40
4027 4080 6.554334 AAGCTGTGTCGTTGTGTATTATTT 57.446 33.333 0.00 0.00 0.00 1.40
4028 4081 6.554334 AAAGCTGTGTCGTTGTGTATTATT 57.446 33.333 0.00 0.00 0.00 1.40
4029 4082 7.094631 TCTAAAGCTGTGTCGTTGTGTATTAT 58.905 34.615 0.00 0.00 0.00 1.28
4056 4109 5.147162 GCTTATTCGTTTTCTCAACCACAG 58.853 41.667 0.00 0.00 0.00 3.66
4077 4130 1.228063 CAAGCACAGGTGTCTGGCT 60.228 57.895 0.91 0.00 44.99 4.75
4078 4131 0.819259 TTCAAGCACAGGTGTCTGGC 60.819 55.000 0.91 0.00 44.99 4.85
4113 4166 1.425066 TGGAAGTGCACCCTCAAGAAT 59.575 47.619 14.63 0.00 0.00 2.40
4127 4180 8.379428 AGGCATAATAAAAAGGAAATGGAAGT 57.621 30.769 0.00 0.00 0.00 3.01
4191 4244 4.346734 ACTGCGCTAATGAATCAAACTG 57.653 40.909 9.73 0.00 0.00 3.16
4205 4258 4.441792 TCATCATGTAATGTAACTGCGCT 58.558 39.130 9.73 0.00 46.80 5.92
4243 4296 3.321111 AGACAGCTTCGTCCAGACTTAAA 59.679 43.478 0.75 0.00 36.52 1.52
4371 4425 0.031043 TGGTCGACTGTGTTACACCG 59.969 55.000 16.46 9.22 32.73 4.94
4393 4447 4.112634 TCTCTAAATCTTGTCCAATCGCG 58.887 43.478 0.00 0.00 0.00 5.87
4467 4521 5.181245 CCATGTCAGTTTTGTACTAAGTGGG 59.819 44.000 12.93 5.92 34.56 4.61
4469 4523 5.763204 ACCCATGTCAGTTTTGTACTAAGTG 59.237 40.000 8.82 8.82 34.56 3.16
4475 4529 5.938125 ACAGATACCCATGTCAGTTTTGTAC 59.062 40.000 0.00 0.00 0.00 2.90
4476 4530 6.121776 ACAGATACCCATGTCAGTTTTGTA 57.878 37.500 0.00 0.00 0.00 2.41
4477 4531 4.985538 ACAGATACCCATGTCAGTTTTGT 58.014 39.130 0.00 0.00 0.00 2.83
4478 4532 5.241506 ACAACAGATACCCATGTCAGTTTTG 59.758 40.000 0.00 0.00 0.00 2.44
4479 4533 5.385198 ACAACAGATACCCATGTCAGTTTT 58.615 37.500 0.00 0.00 0.00 2.43
4480 4534 4.985538 ACAACAGATACCCATGTCAGTTT 58.014 39.130 0.00 0.00 0.00 2.66
4487 4541 4.870426 GTGTACAGACAACAGATACCCATG 59.130 45.833 0.00 0.00 37.31 3.66
4524 4578 2.420687 GGATCATGGAGCTTTCCTCGTT 60.421 50.000 0.00 0.00 41.71 3.85
4553 4607 7.879677 TGTTGAATGACATATATAGCTGGAAGG 59.120 37.037 0.00 0.00 0.00 3.46
4585 4639 4.277239 CGGAGGTTTGATGCGACA 57.723 55.556 0.00 0.00 32.76 4.35
4684 4738 3.123804 GGTGCTGGTGAAGATACATACG 58.876 50.000 0.00 0.00 0.00 3.06
4709 4763 2.185350 CCTTCCGCGCTGAGTGAT 59.815 61.111 5.56 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.