Multiple sequence alignment - TraesCS7A01G066600

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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 TraesCS7A01G066600 chr7A 100.000 3835 0 0 1 3835 33375130 33371296 0.000000e+00 7083.0
1 TraesCS7A01G066600 chr7A 83.814 1353 179 28 1049 2386 33449559 33448232 0.000000e+00 1249.0
2 TraesCS7A01G066600 chr7A 80.974 1335 203 25 1049 2348 33426179 33424861 0.000000e+00 1011.0
3 TraesCS7A01G066600 chr7A 82.495 1034 147 19 1049 2064 33419749 33418732 0.000000e+00 876.0
4 TraesCS7A01G066600 chr7A 91.093 247 22 0 1049 1295 33455348 33455102 6.140000e-88 335.0
5 TraesCS7A01G066600 chr7D 91.829 1542 91 17 1654 3182 33056527 33055008 0.000000e+00 2117.0
6 TraesCS7A01G066600 chr7D 80.963 1744 259 44 1296 3018 33098610 33096919 0.000000e+00 1314.0
7 TraesCS7A01G066600 chr7D 77.804 2086 325 81 1049 3074 33105759 33103752 0.000000e+00 1160.0
8 TraesCS7A01G066600 chr7D 93.234 606 28 8 3231 3835 33055010 33054417 0.000000e+00 880.0
9 TraesCS7A01G066600 chr7D 79.023 1249 177 49 1049 2253 33089024 33087817 0.000000e+00 776.0
10 TraesCS7A01G066600 chr7D 83.357 715 97 8 1845 2557 33095708 33095014 3.230000e-180 641.0
11 TraesCS7A01G066600 chr7D 93.396 212 14 0 1049 1260 33098824 33098613 8.000000e-82 315.0
12 TraesCS7A01G066600 chr4A 89.324 1508 94 25 1863 3350 693284076 693282616 0.000000e+00 1831.0
13 TraesCS7A01G066600 chr4A 80.737 2253 320 64 1049 3234 693452099 693449894 0.000000e+00 1652.0
14 TraesCS7A01G066600 chr4A 81.129 1452 204 42 1049 2455 693491493 693490067 0.000000e+00 1099.0
15 TraesCS7A01G066600 chr4A 80.974 1335 203 29 1049 2349 693445232 693443915 0.000000e+00 1011.0
16 TraesCS7A01G066600 chr4A 79.535 1119 154 39 1047 2102 693433297 693432191 0.000000e+00 728.0
17 TraesCS7A01G066600 chr4A 94.928 276 14 0 3390 3665 693282529 693282254 2.120000e-117 433.0
18 TraesCS7A01G066600 chr4A 79.323 266 45 7 3357 3619 693489313 693489055 1.090000e-40 178.0
19 TraesCS7A01G066600 chr4A 90.722 97 6 3 3741 3834 693282252 693282156 4.020000e-25 126.0
20 TraesCS7A01G066600 chr3A 92.291 895 47 10 1 878 422334885 422335774 0.000000e+00 1251.0
21 TraesCS7A01G066600 chr5B 91.723 894 52 10 1 877 483215081 483215969 0.000000e+00 1221.0
22 TraesCS7A01G066600 chr5B 89.362 893 68 12 4 877 564795071 564794187 0.000000e+00 1098.0
23 TraesCS7A01G066600 chr5B 88.172 93 9 2 788 879 548141634 548141725 4.050000e-20 110.0
24 TraesCS7A01G066600 chr6A 91.970 660 32 8 2940 3591 443059653 443060299 0.000000e+00 905.0
25 TraesCS7A01G066600 chr6A 82.109 313 40 15 571 879 162889903 162890203 1.770000e-63 254.0
26 TraesCS7A01G066600 chr6A 89.796 147 13 2 2755 2899 443059503 443059649 1.820000e-43 187.0
27 TraesCS7A01G066600 chr5D 80.192 520 75 21 384 881 444902702 444902189 7.830000e-97 364.0
28 TraesCS7A01G066600 chr4B 80.124 161 20 10 205 356 261073631 261073788 4.050000e-20 110.0
29 TraesCS7A01G066600 chr2A 79.882 169 19 9 492 647 660258134 660257968 4.050000e-20 110.0
30 TraesCS7A01G066600 chr1A 89.706 68 6 1 204 270 577067851 577067918 6.830000e-13 86.1
31 TraesCS7A01G066600 chr5A 81.720 93 16 1 793 885 106182868 106182777 4.110000e-10 76.8


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 TraesCS7A01G066600 chr7A 33371296 33375130 3834 True 7083.000000 7083 100.000000 1 3835 1 chr7A.!!$R1 3834
1 TraesCS7A01G066600 chr7A 33448232 33449559 1327 True 1249.000000 1249 83.814000 1049 2386 1 chr7A.!!$R4 1337
2 TraesCS7A01G066600 chr7A 33424861 33426179 1318 True 1011.000000 1011 80.974000 1049 2348 1 chr7A.!!$R3 1299
3 TraesCS7A01G066600 chr7A 33418732 33419749 1017 True 876.000000 876 82.495000 1049 2064 1 chr7A.!!$R2 1015
4 TraesCS7A01G066600 chr7D 33054417 33056527 2110 True 1498.500000 2117 92.531500 1654 3835 2 chr7D.!!$R3 2181
5 TraesCS7A01G066600 chr7D 33103752 33105759 2007 True 1160.000000 1160 77.804000 1049 3074 1 chr7D.!!$R2 2025
6 TraesCS7A01G066600 chr7D 33087817 33089024 1207 True 776.000000 776 79.023000 1049 2253 1 chr7D.!!$R1 1204
7 TraesCS7A01G066600 chr7D 33095014 33098824 3810 True 756.666667 1314 85.905333 1049 3018 3 chr7D.!!$R4 1969
8 TraesCS7A01G066600 chr4A 693449894 693452099 2205 True 1652.000000 1652 80.737000 1049 3234 1 chr4A.!!$R3 2185
9 TraesCS7A01G066600 chr4A 693443915 693445232 1317 True 1011.000000 1011 80.974000 1049 2349 1 chr4A.!!$R2 1300
10 TraesCS7A01G066600 chr4A 693282156 693284076 1920 True 796.666667 1831 91.658000 1863 3834 3 chr4A.!!$R4 1971
11 TraesCS7A01G066600 chr4A 693432191 693433297 1106 True 728.000000 728 79.535000 1047 2102 1 chr4A.!!$R1 1055
12 TraesCS7A01G066600 chr4A 693489055 693491493 2438 True 638.500000 1099 80.226000 1049 3619 2 chr4A.!!$R5 2570
13 TraesCS7A01G066600 chr3A 422334885 422335774 889 False 1251.000000 1251 92.291000 1 878 1 chr3A.!!$F1 877
14 TraesCS7A01G066600 chr5B 483215081 483215969 888 False 1221.000000 1221 91.723000 1 877 1 chr5B.!!$F1 876
15 TraesCS7A01G066600 chr5B 564794187 564795071 884 True 1098.000000 1098 89.362000 4 877 1 chr5B.!!$R1 873
16 TraesCS7A01G066600 chr6A 443059503 443060299 796 False 546.000000 905 90.883000 2755 3591 2 chr6A.!!$F2 836
17 TraesCS7A01G066600 chr5D 444902189 444902702 513 True 364.000000 364 80.192000 384 881 1 chr5D.!!$R1 497

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
226 228 0.314935 AAATCACCCGCTGCAACAAG 59.685 50.0 0.0 0.0 0.0 3.16 F
1034 1066 0.103937 CGCTCCCAGATGAACTCCTC 59.896 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 1725 0.105142 ATCCATGGGCGTAGTAGGGT 60.105 55.0 13.02 0.0 0.00 4.34 R
2895 3100 0.318120 CTTGGTGACATGGCCAAACC 59.682 55.0 10.96 16.1 43.29 3.27 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 68 4.966965 AGCATCAAATTCAGAGAGCTTG 57.033 40.909 0.00 0.00 29.48 4.01
170 172 0.682852 CCCCAACTGTCACCTAACGA 59.317 55.000 0.00 0.00 0.00 3.85
171 173 1.278127 CCCCAACTGTCACCTAACGAT 59.722 52.381 0.00 0.00 0.00 3.73
181 183 4.468510 TGTCACCTAACGATAAGGGAACAT 59.531 41.667 0.00 0.00 38.54 2.71
226 228 0.314935 AAATCACCCGCTGCAACAAG 59.685 50.000 0.00 0.00 0.00 3.16
306 308 2.805671 CCACATCTACACAGCAAAACGA 59.194 45.455 0.00 0.00 0.00 3.85
364 367 1.600636 CAGGCGAGCACAAAAGGGA 60.601 57.895 0.00 0.00 0.00 4.20
367 370 2.335712 GCGAGCACAAAAGGGAGGG 61.336 63.158 0.00 0.00 0.00 4.30
404 408 4.380867 GCGGATCCATGAAGAACAACAAAT 60.381 41.667 13.41 0.00 0.00 2.32
414 419 8.464404 CATGAAGAACAACAAATAGACATCCAT 58.536 33.333 0.00 0.00 0.00 3.41
430 442 5.063204 ACATCCATGAAGACGAAAACTCAA 58.937 37.500 0.00 0.00 0.00 3.02
477 489 0.684805 ACAAGCAAAAACACCCGGGA 60.685 50.000 32.02 0.00 0.00 5.14
480 492 3.035727 CAAAAACACCCGGGACCG 58.964 61.111 32.02 17.79 39.44 4.79
553 569 5.278758 GGGAGGACAAAATCAAAATCGAACA 60.279 40.000 0.00 0.00 0.00 3.18
557 573 6.039270 AGGACAAAATCAAAATCGAACAGTGA 59.961 34.615 0.00 0.00 0.00 3.41
604 633 3.591835 CGCTCGAGCTCTCTCCCC 61.592 72.222 32.88 3.35 39.32 4.81
646 675 3.496331 GACCCAAATGAAAAGGGAGACA 58.504 45.455 3.32 0.00 45.80 3.41
670 699 1.200020 CCCACTCCGAAATTCAAGCAC 59.800 52.381 0.00 0.00 0.00 4.40
762 794 0.600255 CCAAACCGAGCGAACAGAGT 60.600 55.000 0.00 0.00 0.00 3.24
775 807 3.684990 AGAGTGCCAGCGCGAAGA 61.685 61.111 12.10 0.00 38.08 2.87
881 913 8.231837 TGACTGTAAAATAGCAAATCCGTAAAC 58.768 33.333 0.00 0.00 0.00 2.01
882 914 7.532571 ACTGTAAAATAGCAAATCCGTAAACC 58.467 34.615 0.00 0.00 0.00 3.27
883 915 7.175293 ACTGTAAAATAGCAAATCCGTAAACCA 59.825 33.333 0.00 0.00 0.00 3.67
884 916 7.883217 TGTAAAATAGCAAATCCGTAAACCAA 58.117 30.769 0.00 0.00 0.00 3.67
885 917 8.524487 TGTAAAATAGCAAATCCGTAAACCAAT 58.476 29.630 0.00 0.00 0.00 3.16
886 918 9.016623 GTAAAATAGCAAATCCGTAAACCAATC 57.983 33.333 0.00 0.00 0.00 2.67
887 919 3.757745 AGCAAATCCGTAAACCAATCG 57.242 42.857 0.00 0.00 0.00 3.34
888 920 3.078837 AGCAAATCCGTAAACCAATCGT 58.921 40.909 0.00 0.00 0.00 3.73
889 921 4.255301 AGCAAATCCGTAAACCAATCGTA 58.745 39.130 0.00 0.00 0.00 3.43
890 922 4.879545 AGCAAATCCGTAAACCAATCGTAT 59.120 37.500 0.00 0.00 0.00 3.06
891 923 6.050432 AGCAAATCCGTAAACCAATCGTATA 58.950 36.000 0.00 0.00 0.00 1.47
892 924 6.708949 AGCAAATCCGTAAACCAATCGTATAT 59.291 34.615 0.00 0.00 0.00 0.86
893 925 7.227910 AGCAAATCCGTAAACCAATCGTATATT 59.772 33.333 0.00 0.00 0.00 1.28
894 926 7.322699 GCAAATCCGTAAACCAATCGTATATTG 59.677 37.037 0.00 0.00 0.00 1.90
895 927 8.339714 CAAATCCGTAAACCAATCGTATATTGT 58.660 33.333 0.00 0.00 0.00 2.71
896 928 7.647907 ATCCGTAAACCAATCGTATATTGTC 57.352 36.000 0.00 0.00 0.00 3.18
897 929 6.808829 TCCGTAAACCAATCGTATATTGTCT 58.191 36.000 0.00 0.00 0.00 3.41
898 930 6.698329 TCCGTAAACCAATCGTATATTGTCTG 59.302 38.462 0.00 0.00 0.00 3.51
899 931 6.698329 CCGTAAACCAATCGTATATTGTCTGA 59.302 38.462 0.00 0.00 0.00 3.27
900 932 7.384115 CCGTAAACCAATCGTATATTGTCTGAT 59.616 37.037 0.00 0.00 0.00 2.90
901 933 9.401873 CGTAAACCAATCGTATATTGTCTGATA 57.598 33.333 0.00 0.00 0.00 2.15
904 936 6.978338 ACCAATCGTATATTGTCTGATACGT 58.022 36.000 12.56 0.00 46.92 3.57
905 937 8.102800 ACCAATCGTATATTGTCTGATACGTA 57.897 34.615 12.56 0.00 46.92 3.57
906 938 8.019669 ACCAATCGTATATTGTCTGATACGTAC 58.980 37.037 12.56 0.00 46.92 3.67
907 939 8.235226 CCAATCGTATATTGTCTGATACGTACT 58.765 37.037 12.56 0.00 46.92 2.73
908 940 9.052080 CAATCGTATATTGTCTGATACGTACTG 57.948 37.037 12.56 0.00 46.92 2.74
909 941 6.596703 TCGTATATTGTCTGATACGTACTGC 58.403 40.000 12.56 0.00 46.92 4.40
910 942 6.203338 TCGTATATTGTCTGATACGTACTGCA 59.797 38.462 12.56 0.00 46.92 4.41
911 943 7.021790 CGTATATTGTCTGATACGTACTGCAT 58.978 38.462 0.00 0.00 43.67 3.96
912 944 8.173130 CGTATATTGTCTGATACGTACTGCATA 58.827 37.037 0.00 0.00 43.67 3.14
916 948 6.870971 TGTCTGATACGTACTGCATATACA 57.129 37.500 0.00 0.18 0.00 2.29
917 949 6.665465 TGTCTGATACGTACTGCATATACAC 58.335 40.000 0.00 0.00 0.00 2.90
918 950 6.261381 TGTCTGATACGTACTGCATATACACA 59.739 38.462 0.00 1.88 0.00 3.72
919 951 7.136772 GTCTGATACGTACTGCATATACACAA 58.863 38.462 0.00 0.00 0.00 3.33
920 952 7.646526 GTCTGATACGTACTGCATATACACAAA 59.353 37.037 0.00 0.00 0.00 2.83
921 953 8.357402 TCTGATACGTACTGCATATACACAAAT 58.643 33.333 0.00 0.00 0.00 2.32
922 954 9.620660 CTGATACGTACTGCATATACACAAATA 57.379 33.333 0.00 0.00 0.00 1.40
923 955 9.401873 TGATACGTACTGCATATACACAAATAC 57.598 33.333 0.00 0.00 0.00 1.89
924 956 8.752766 ATACGTACTGCATATACACAAATACC 57.247 34.615 0.00 0.00 0.00 2.73
925 957 6.575267 ACGTACTGCATATACACAAATACCA 58.425 36.000 8.52 0.00 0.00 3.25
926 958 6.700081 ACGTACTGCATATACACAAATACCAG 59.300 38.462 8.52 0.00 0.00 4.00
927 959 6.700081 CGTACTGCATATACACAAATACCAGT 59.300 38.462 8.52 0.00 34.37 4.00
928 960 6.925610 ACTGCATATACACAAATACCAGTG 57.074 37.500 0.00 0.00 41.40 3.66
929 961 6.649155 ACTGCATATACACAAATACCAGTGA 58.351 36.000 0.00 0.00 39.03 3.41
930 962 6.763135 ACTGCATATACACAAATACCAGTGAG 59.237 38.462 0.00 0.00 39.03 3.51
931 963 6.054941 TGCATATACACAAATACCAGTGAGG 58.945 40.000 0.00 0.00 45.67 3.86
932 964 6.126911 TGCATATACACAAATACCAGTGAGGA 60.127 38.462 0.00 0.00 41.22 3.71
933 965 6.936900 GCATATACACAAATACCAGTGAGGAT 59.063 38.462 0.00 0.00 41.22 3.24
934 966 7.445402 GCATATACACAAATACCAGTGAGGATT 59.555 37.037 0.00 0.00 41.22 3.01
935 967 8.777413 CATATACACAAATACCAGTGAGGATTG 58.223 37.037 0.00 0.00 41.22 2.67
936 968 4.335416 ACACAAATACCAGTGAGGATTGG 58.665 43.478 0.00 0.00 41.22 3.16
937 969 3.696051 CACAAATACCAGTGAGGATTGGG 59.304 47.826 0.00 0.00 41.22 4.12
938 970 3.591527 ACAAATACCAGTGAGGATTGGGA 59.408 43.478 0.00 0.00 41.22 4.37
939 971 4.044065 ACAAATACCAGTGAGGATTGGGAA 59.956 41.667 0.00 0.00 41.22 3.97
940 972 3.933861 ATACCAGTGAGGATTGGGAAC 57.066 47.619 0.00 0.00 41.22 3.62
956 988 2.783135 GGAACCTTGCTCTCATTGTCA 58.217 47.619 0.00 0.00 0.00 3.58
957 989 3.350833 GGAACCTTGCTCTCATTGTCAT 58.649 45.455 0.00 0.00 0.00 3.06
958 990 3.376546 GGAACCTTGCTCTCATTGTCATC 59.623 47.826 0.00 0.00 0.00 2.92
959 991 2.996631 ACCTTGCTCTCATTGTCATCC 58.003 47.619 0.00 0.00 0.00 3.51
960 992 2.295885 CCTTGCTCTCATTGTCATCCC 58.704 52.381 0.00 0.00 0.00 3.85
961 993 2.295885 CTTGCTCTCATTGTCATCCCC 58.704 52.381 0.00 0.00 0.00 4.81
962 994 0.548031 TGCTCTCATTGTCATCCCCC 59.452 55.000 0.00 0.00 0.00 5.40
963 995 0.548031 GCTCTCATTGTCATCCCCCA 59.452 55.000 0.00 0.00 0.00 4.96
964 996 1.144503 GCTCTCATTGTCATCCCCCAT 59.855 52.381 0.00 0.00 0.00 4.00
965 997 2.813354 GCTCTCATTGTCATCCCCCATC 60.813 54.545 0.00 0.00 0.00 3.51
966 998 1.417517 TCTCATTGTCATCCCCCATCG 59.582 52.381 0.00 0.00 0.00 3.84
967 999 1.141657 CTCATTGTCATCCCCCATCGT 59.858 52.381 0.00 0.00 0.00 3.73
968 1000 1.140852 TCATTGTCATCCCCCATCGTC 59.859 52.381 0.00 0.00 0.00 4.20
969 1001 1.141657 CATTGTCATCCCCCATCGTCT 59.858 52.381 0.00 0.00 0.00 4.18
970 1002 0.541392 TTGTCATCCCCCATCGTCTG 59.459 55.000 0.00 0.00 0.00 3.51
971 1003 1.227674 GTCATCCCCCATCGTCTGC 60.228 63.158 0.00 0.00 0.00 4.26
972 1004 1.383109 TCATCCCCCATCGTCTGCT 60.383 57.895 0.00 0.00 0.00 4.24
973 1005 1.070445 CATCCCCCATCGTCTGCTC 59.930 63.158 0.00 0.00 0.00 4.26
974 1006 2.502492 ATCCCCCATCGTCTGCTCG 61.502 63.158 0.00 0.00 0.00 5.03
975 1007 3.461773 CCCCCATCGTCTGCTCGT 61.462 66.667 0.00 0.00 0.00 4.18
976 1008 2.579201 CCCCATCGTCTGCTCGTT 59.421 61.111 0.00 0.00 0.00 3.85
977 1009 1.811266 CCCCATCGTCTGCTCGTTG 60.811 63.158 0.00 0.00 0.00 4.10
978 1010 2.456119 CCCATCGTCTGCTCGTTGC 61.456 63.158 0.00 0.00 43.25 4.17
979 1011 1.446792 CCATCGTCTGCTCGTTGCT 60.447 57.895 5.00 0.00 43.37 3.91
980 1012 1.690283 CCATCGTCTGCTCGTTGCTG 61.690 60.000 5.00 4.67 43.37 4.41
981 1013 1.446792 ATCGTCTGCTCGTTGCTGG 60.447 57.895 9.19 2.13 43.37 4.85
982 1014 2.159819 ATCGTCTGCTCGTTGCTGGT 62.160 55.000 9.19 0.00 43.37 4.00
983 1015 1.956170 CGTCTGCTCGTTGCTGGTT 60.956 57.895 9.19 0.00 43.37 3.67
984 1016 1.862806 GTCTGCTCGTTGCTGGTTC 59.137 57.895 9.19 0.69 43.37 3.62
985 1017 1.301716 TCTGCTCGTTGCTGGTTCC 60.302 57.895 9.19 0.00 43.37 3.62
986 1018 2.281484 TGCTCGTTGCTGGTTCCC 60.281 61.111 5.00 0.00 43.37 3.97
987 1019 2.281484 GCTCGTTGCTGGTTCCCA 60.281 61.111 0.00 0.00 38.95 4.37
988 1020 1.675641 GCTCGTTGCTGGTTCCCAT 60.676 57.895 0.00 0.00 38.95 4.00
989 1021 1.648467 GCTCGTTGCTGGTTCCCATC 61.648 60.000 0.00 0.00 38.95 3.51
990 1022 1.002624 TCGTTGCTGGTTCCCATCC 60.003 57.895 0.00 0.00 30.82 3.51
991 1023 1.002134 CGTTGCTGGTTCCCATCCT 60.002 57.895 0.00 0.00 30.82 3.24
992 1024 1.026718 CGTTGCTGGTTCCCATCCTC 61.027 60.000 0.00 0.00 30.82 3.71
993 1025 1.026718 GTTGCTGGTTCCCATCCTCG 61.027 60.000 0.00 0.00 30.82 4.63
994 1026 1.488705 TTGCTGGTTCCCATCCTCGT 61.489 55.000 0.00 0.00 30.82 4.18
995 1027 1.153349 GCTGGTTCCCATCCTCGTC 60.153 63.158 0.00 0.00 30.82 4.20
996 1028 1.522569 CTGGTTCCCATCCTCGTCC 59.477 63.158 0.00 0.00 30.82 4.79
997 1029 0.978146 CTGGTTCCCATCCTCGTCCT 60.978 60.000 0.00 0.00 30.82 3.85
998 1030 0.976073 TGGTTCCCATCCTCGTCCTC 60.976 60.000 0.00 0.00 0.00 3.71
999 1031 0.688087 GGTTCCCATCCTCGTCCTCT 60.688 60.000 0.00 0.00 0.00 3.69
1000 1032 0.461961 GTTCCCATCCTCGTCCTCTG 59.538 60.000 0.00 0.00 0.00 3.35
1001 1033 1.330655 TTCCCATCCTCGTCCTCTGC 61.331 60.000 0.00 0.00 0.00 4.26
1002 1034 2.801631 CCCATCCTCGTCCTCTGCC 61.802 68.421 0.00 0.00 0.00 4.85
1003 1035 2.801631 CCATCCTCGTCCTCTGCCC 61.802 68.421 0.00 0.00 0.00 5.36
1004 1036 1.760086 CATCCTCGTCCTCTGCCCT 60.760 63.158 0.00 0.00 0.00 5.19
1005 1037 0.468214 CATCCTCGTCCTCTGCCCTA 60.468 60.000 0.00 0.00 0.00 3.53
1006 1038 0.468400 ATCCTCGTCCTCTGCCCTAC 60.468 60.000 0.00 0.00 0.00 3.18
1007 1039 1.076632 CCTCGTCCTCTGCCCTACT 60.077 63.158 0.00 0.00 0.00 2.57
1008 1040 1.104577 CCTCGTCCTCTGCCCTACTC 61.105 65.000 0.00 0.00 0.00 2.59
1009 1041 0.106918 CTCGTCCTCTGCCCTACTCT 60.107 60.000 0.00 0.00 0.00 3.24
1010 1042 1.141254 CTCGTCCTCTGCCCTACTCTA 59.859 57.143 0.00 0.00 0.00 2.43
1011 1043 1.562942 TCGTCCTCTGCCCTACTCTAA 59.437 52.381 0.00 0.00 0.00 2.10
1012 1044 2.175069 TCGTCCTCTGCCCTACTCTAAT 59.825 50.000 0.00 0.00 0.00 1.73
1013 1045 2.294791 CGTCCTCTGCCCTACTCTAATG 59.705 54.545 0.00 0.00 0.00 1.90
1014 1046 2.630580 GTCCTCTGCCCTACTCTAATGG 59.369 54.545 0.00 0.00 0.00 3.16
1015 1047 1.346068 CCTCTGCCCTACTCTAATGGC 59.654 57.143 0.00 0.00 44.27 4.40
1017 1049 4.363034 GCCCTACTCTAATGGCGC 57.637 61.111 0.00 0.00 33.59 6.53
1018 1050 1.749033 GCCCTACTCTAATGGCGCT 59.251 57.895 7.64 0.00 33.59 5.92
1019 1051 0.319986 GCCCTACTCTAATGGCGCTC 60.320 60.000 7.64 0.00 33.59 5.03
1020 1052 0.318762 CCCTACTCTAATGGCGCTCC 59.681 60.000 7.64 0.00 0.00 4.70
1021 1053 0.318762 CCTACTCTAATGGCGCTCCC 59.681 60.000 7.64 0.00 0.00 4.30
1029 1061 2.268920 TGGCGCTCCCAGATGAAC 59.731 61.111 7.64 0.00 39.18 3.18
1030 1062 2.293318 TGGCGCTCCCAGATGAACT 61.293 57.895 7.64 0.00 39.18 3.01
1031 1063 1.522580 GGCGCTCCCAGATGAACTC 60.523 63.158 7.64 0.00 0.00 3.01
1032 1064 1.522580 GCGCTCCCAGATGAACTCC 60.523 63.158 0.00 0.00 0.00 3.85
1033 1065 1.965754 GCGCTCCCAGATGAACTCCT 61.966 60.000 0.00 0.00 0.00 3.69
1034 1066 0.103937 CGCTCCCAGATGAACTCCTC 59.896 60.000 0.00 0.00 0.00 3.71
1035 1067 0.103937 GCTCCCAGATGAACTCCTCG 59.896 60.000 0.00 0.00 0.00 4.63
1036 1068 1.769026 CTCCCAGATGAACTCCTCGA 58.231 55.000 0.00 0.00 0.00 4.04
1037 1069 2.103373 CTCCCAGATGAACTCCTCGAA 58.897 52.381 0.00 0.00 0.00 3.71
1038 1070 2.100584 CTCCCAGATGAACTCCTCGAAG 59.899 54.545 0.00 0.00 0.00 3.79
1039 1071 2.103373 CCCAGATGAACTCCTCGAAGA 58.897 52.381 0.00 0.00 0.00 2.87
1257 1306 2.364317 TCCTGCTCCTTCCTCCCG 60.364 66.667 0.00 0.00 0.00 5.14
1313 1386 4.442454 CCTTTTCTCCCCCGCCCC 62.442 72.222 0.00 0.00 0.00 5.80
1440 1531 0.681887 TAGCCGACCAAGTCCATCGA 60.682 55.000 0.00 0.00 38.10 3.59
1450 1541 4.347865 TCCATCGACCGGACATCA 57.652 55.556 9.46 0.00 0.00 3.07
1452 1543 1.989706 TCCATCGACCGGACATCATA 58.010 50.000 9.46 0.00 0.00 2.15
1453 1544 1.611977 TCCATCGACCGGACATCATAC 59.388 52.381 9.46 0.00 0.00 2.39
1455 1546 2.029020 CCATCGACCGGACATCATACAT 60.029 50.000 9.46 0.00 0.00 2.29
1548 1642 3.289834 CGGTGCACAGCCAAGCTT 61.290 61.111 20.43 0.00 36.40 3.74
1614 1708 7.324354 TGATCCTATCACATTTGACATGTTG 57.676 36.000 0.00 0.00 33.38 3.33
1620 1714 4.151121 TCACATTTGACATGTTGGGATGT 58.849 39.130 0.00 6.07 39.34 3.06
1624 1718 5.070180 ACATTTGACATGTTGGGATGTTTGA 59.930 36.000 0.00 0.00 36.67 2.69
1627 1721 4.151121 TGACATGTTGGGATGTTTGATGT 58.849 39.130 0.00 0.00 36.67 3.06
1630 1724 4.219070 ACATGTTGGGATGTTTGATGTCAG 59.781 41.667 0.00 0.00 32.38 3.51
1631 1725 4.097551 TGTTGGGATGTTTGATGTCAGA 57.902 40.909 0.00 0.00 0.00 3.27
1632 1726 3.820467 TGTTGGGATGTTTGATGTCAGAC 59.180 43.478 0.00 0.00 0.00 3.51
1660 1758 1.041447 GCCCATGGATGCTTCTGCTT 61.041 55.000 15.22 0.00 40.48 3.91
1672 1780 1.882623 CTTCTGCTTGGAGGTTTGTCC 59.117 52.381 0.00 0.00 37.10 4.02
1719 1827 0.402121 ACAAAGGCTGGAGTTCTCCC 59.598 55.000 15.20 2.11 0.00 4.30
1750 1859 3.993535 GCCTCCACTTGGCTCTTG 58.006 61.111 0.00 0.00 46.38 3.02
1753 1862 1.271379 GCCTCCACTTGGCTCTTGTAA 60.271 52.381 0.00 0.00 46.38 2.41
1834 1978 2.567169 AGCATACTGAAGCTGGTGTGTA 59.433 45.455 11.08 2.14 40.13 2.90
1836 1980 3.864540 GCATACTGAAGCTGGTGTGTACA 60.865 47.826 0.00 0.00 0.00 2.90
1848 1992 4.500127 TGGTGTGTACAAATACCATCTCG 58.500 43.478 18.72 0.00 38.23 4.04
1860 2004 8.367911 ACAAATACCATCTCGTGTATGATGTAT 58.632 33.333 0.00 0.00 38.59 2.29
1861 2005 9.208022 CAAATACCATCTCGTGTATGATGTATT 57.792 33.333 0.00 0.00 38.59 1.89
1938 2082 2.412870 TGCCGGTGAATTATCGCTATG 58.587 47.619 1.90 0.00 36.30 2.23
2079 2230 0.899019 TGGTCGCTGTGCCATAACTA 59.101 50.000 1.14 0.00 0.00 2.24
2104 2255 1.043816 CTGTATGCCGATCTCCCACT 58.956 55.000 0.00 0.00 0.00 4.00
2112 2263 0.176680 CGATCTCCCACTGTCCTTGG 59.823 60.000 0.00 0.00 0.00 3.61
2276 2442 2.544267 GGTCCTGTATTAACGCTGATGC 59.456 50.000 0.00 0.00 0.00 3.91
2304 2478 8.528643 GCCAAGTTACTTTTCACCCTTATAATT 58.471 33.333 0.00 0.00 0.00 1.40
2400 2590 3.869623 TCAGGATGAGCAAGAAGCC 57.130 52.632 0.00 0.00 42.56 4.35
2514 2708 1.667236 TAGGCTGGATTTGACATGCG 58.333 50.000 0.00 0.00 0.00 4.73
2536 2730 1.628846 TGGCTACTTTCCCTTGAGTCC 59.371 52.381 0.00 0.00 0.00 3.85
2656 2853 4.093998 CGTTCTTCTCCTTGACCATTGATG 59.906 45.833 0.00 0.00 0.00 3.07
2678 2875 6.308371 TGGCTTTAGTTAGTTAGTTTGTGC 57.692 37.500 0.00 0.00 0.00 4.57
2703 2900 4.082190 GGGATCCATTCATCAGATTGCATG 60.082 45.833 15.23 0.00 0.00 4.06
2828 3033 6.038050 TGCATCATGTGTAATAAATTCTCGCA 59.962 34.615 0.00 0.00 0.00 5.10
2843 3048 2.011947 CTCGCATTTGGCTGATGAGAA 58.988 47.619 8.00 0.00 41.67 2.87
2869 3074 1.198637 GTTCAGCTGAGGTTGCATGAC 59.801 52.381 17.43 5.05 0.00 3.06
2893 3098 6.920758 ACGCAGCATGTTAAATTTTTGTTCTA 59.079 30.769 0.00 0.00 39.31 2.10
2895 3100 7.894247 CGCAGCATGTTAAATTTTTGTTCTATG 59.106 33.333 0.00 0.00 39.31 2.23
2897 3102 9.206870 CAGCATGTTAAATTTTTGTTCTATGGT 57.793 29.630 0.00 0.00 0.00 3.55
2915 3121 0.319813 GTTTGGCCATGTCACCAAGC 60.320 55.000 6.09 10.09 46.20 4.01
2928 3134 0.466922 ACCAAGCTATCATGCCTGGC 60.467 55.000 12.87 12.87 45.71 4.85
2937 3143 4.151582 ATGCCTGGCGCCATTTGC 62.152 61.111 32.87 30.32 36.24 3.68
2950 3156 0.458889 CATTTGCGGTGGAATGGCTG 60.459 55.000 0.00 0.00 31.28 4.85
2961 3170 1.621107 GAATGGCTGTGATTTGTGCG 58.379 50.000 0.00 0.00 0.00 5.34
2986 3195 5.813080 AAATTGACCGTAGTGGCTTATTC 57.187 39.130 0.00 0.00 43.94 1.75
3123 4028 2.799126 TGACCCGATAACCATGCTTT 57.201 45.000 0.00 0.00 0.00 3.51
3124 4029 3.080300 TGACCCGATAACCATGCTTTT 57.920 42.857 0.00 0.00 0.00 2.27
3140 4062 6.128580 CCATGCTTTTATTTGCAACTGTAACC 60.129 38.462 0.00 0.00 42.74 2.85
3175 4098 1.574428 GTGGCAAGCACAGTAACCG 59.426 57.895 0.00 0.00 0.00 4.44
3181 4104 1.531149 CAAGCACAGTAACCGAACCAG 59.469 52.381 0.00 0.00 0.00 4.00
3186 4109 0.320374 CAGTAACCGAACCAGCCTCA 59.680 55.000 0.00 0.00 0.00 3.86
3193 4116 1.138859 CCGAACCAGCCTCATACATCA 59.861 52.381 0.00 0.00 0.00 3.07
3196 4119 3.679917 CGAACCAGCCTCATACATCAACT 60.680 47.826 0.00 0.00 0.00 3.16
3197 4120 4.265073 GAACCAGCCTCATACATCAACTT 58.735 43.478 0.00 0.00 0.00 2.66
3210 4133 3.440173 ACATCAACTTTTAGGCATGGACG 59.560 43.478 0.00 0.00 0.00 4.79
3227 4150 2.223525 GGACGGCTGAGACATACACTAC 60.224 54.545 0.00 0.00 0.00 2.73
3295 4269 1.740025 GCATCTTGTAACAGCTGGGTC 59.260 52.381 19.93 7.94 0.00 4.46
3525 5213 4.155826 TGCAAATAAGAGTTGAATCCGTGG 59.844 41.667 0.00 0.00 0.00 4.94
3605 5294 6.204688 CACTCCAAAAGTAGCTGTTTGTATCA 59.795 38.462 14.52 1.02 36.07 2.15
3655 5344 7.207383 TGTATTATGGTGAGTTAACATCCTCG 58.793 38.462 8.61 0.00 0.00 4.63
3673 5362 2.766828 CTCGTTCCCATTTACTCCCTCT 59.233 50.000 0.00 0.00 0.00 3.69
3721 5410 7.921787 AGAGATTTCAGTACAGACTACATACG 58.078 38.462 0.00 0.00 33.32 3.06
3722 5411 7.553402 AGAGATTTCAGTACAGACTACATACGT 59.447 37.037 0.00 0.00 33.32 3.57
3723 5412 8.053026 AGATTTCAGTACAGACTACATACGTT 57.947 34.615 0.00 0.00 33.32 3.99
3724 5413 8.521176 AGATTTCAGTACAGACTACATACGTTT 58.479 33.333 0.00 0.00 33.32 3.60
3725 5414 7.862741 TTTCAGTACAGACTACATACGTTTG 57.137 36.000 4.33 4.33 33.32 2.93
3730 5419 5.204409 ACAGACTACATACGTTTGGAACA 57.796 39.130 10.79 0.00 0.00 3.18
3735 5424 3.764237 ACATACGTTTGGAACAGAGGT 57.236 42.857 10.79 0.00 43.70 3.85
3754 5446 9.476928 ACAGAGGTAGTAGTATATTTCAGTTGT 57.523 33.333 0.00 0.00 0.00 3.32
3831 5523 9.273016 TCTATTCCTCAGTTTGTTTCAGTTTAG 57.727 33.333 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 39 9.001542 GCTCTCTGAATTTGATGCTTCTATTAT 57.998 33.333 0.88 0.00 0.00 1.28
66 68 2.415090 GCATGTCTGAATGTGTTCCAGC 60.415 50.000 0.00 0.00 33.26 4.85
170 172 3.372675 GCTTGGGGTGTATGTTCCCTTAT 60.373 47.826 0.00 0.00 43.00 1.73
171 173 2.025699 GCTTGGGGTGTATGTTCCCTTA 60.026 50.000 0.00 0.00 43.00 2.69
181 183 1.651737 TTCTGCTAGCTTGGGGTGTA 58.348 50.000 17.23 0.00 0.00 2.90
226 228 1.141234 GTGGAGGTAGGCGTACTGC 59.859 63.158 15.62 8.24 45.38 4.40
271 273 6.992715 GTGTAGATGTGGATGTAGGCTTTTAT 59.007 38.462 0.00 0.00 0.00 1.40
306 308 1.144298 AGTTGCGGGTTCTAGGGTTTT 59.856 47.619 0.00 0.00 0.00 2.43
404 408 6.037786 AGTTTTCGTCTTCATGGATGTCTA 57.962 37.500 0.00 0.00 0.00 2.59
414 419 7.042051 CCAAATCTAGTTGAGTTTTCGTCTTCA 60.042 37.037 0.00 0.00 29.76 3.02
430 442 4.525487 TGGTCGTGTAGTTCCAAATCTAGT 59.475 41.667 0.00 0.00 0.00 2.57
477 489 2.772622 CCCTAATCCCCTGCCGGT 60.773 66.667 1.90 0.00 0.00 5.28
480 492 1.537172 GTTCCCCTAATCCCCTGCC 59.463 63.158 0.00 0.00 0.00 4.85
483 495 2.144450 GATTGGTTCCCCTAATCCCCT 58.856 52.381 0.00 0.00 0.00 4.79
510 523 1.382146 TATTCTCTTCGCCCCCGGT 60.382 57.895 0.00 0.00 34.56 5.28
553 569 2.474816 GCGATTCCGAGCTATTTCACT 58.525 47.619 0.00 0.00 38.22 3.41
557 573 1.689273 AGAGGCGATTCCGAGCTATTT 59.311 47.619 0.00 0.00 40.77 1.40
604 633 1.571919 CTCTGTTTCGATAAGGCCGG 58.428 55.000 0.00 0.00 0.00 6.13
646 675 2.649531 TGAATTTCGGAGTGGGTGTT 57.350 45.000 0.00 0.00 0.00 3.32
670 699 3.722665 CGCGGTACTATTGGTTTTTGTCG 60.723 47.826 0.00 0.00 0.00 4.35
698 728 5.130292 TCTTTATCTCAACTCGAAACCGT 57.870 39.130 0.00 0.00 0.00 4.83
707 737 5.472478 GGGTTCGGTTTTCTTTATCTCAACT 59.528 40.000 0.00 0.00 0.00 3.16
762 794 3.426545 TTTTTCTTCGCGCTGGCA 58.573 50.000 5.56 0.00 39.92 4.92
812 844 2.823924 TTCGAATTTCTGTCCGTCCA 57.176 45.000 0.00 0.00 0.00 4.02
845 877 6.152379 GCTATTTTACAGTCAGCTGCTTTTT 58.848 36.000 9.47 0.00 46.30 1.94
890 922 9.005777 TGTATATGCAGTACGTATCAGACAATA 57.994 33.333 0.00 0.00 32.55 1.90
891 923 7.808381 GTGTATATGCAGTACGTATCAGACAAT 59.192 37.037 0.00 0.00 32.55 2.71
892 924 7.136772 GTGTATATGCAGTACGTATCAGACAA 58.863 38.462 0.00 0.00 32.55 3.18
893 925 6.261381 TGTGTATATGCAGTACGTATCAGACA 59.739 38.462 0.00 2.03 32.55 3.41
894 926 6.665465 TGTGTATATGCAGTACGTATCAGAC 58.335 40.000 0.00 0.00 32.55 3.51
895 927 6.870971 TGTGTATATGCAGTACGTATCAGA 57.129 37.500 0.00 0.00 32.55 3.27
896 928 7.924103 TTTGTGTATATGCAGTACGTATCAG 57.076 36.000 0.00 0.00 32.55 2.90
897 929 9.401873 GTATTTGTGTATATGCAGTACGTATCA 57.598 33.333 0.00 0.00 32.55 2.15
898 930 8.857216 GGTATTTGTGTATATGCAGTACGTATC 58.143 37.037 0.00 0.00 32.55 2.24
899 931 8.361889 TGGTATTTGTGTATATGCAGTACGTAT 58.638 33.333 0.00 0.00 34.72 3.06
900 932 7.714703 TGGTATTTGTGTATATGCAGTACGTA 58.285 34.615 0.00 0.00 0.00 3.57
901 933 6.575267 TGGTATTTGTGTATATGCAGTACGT 58.425 36.000 0.00 0.00 0.00 3.57
902 934 6.700081 ACTGGTATTTGTGTATATGCAGTACG 59.300 38.462 0.00 0.00 0.00 3.67
903 935 7.709182 TCACTGGTATTTGTGTATATGCAGTAC 59.291 37.037 0.00 0.00 35.82 2.73
904 936 7.787028 TCACTGGTATTTGTGTATATGCAGTA 58.213 34.615 0.00 0.00 35.82 2.74
905 937 6.649155 TCACTGGTATTTGTGTATATGCAGT 58.351 36.000 0.00 0.00 35.82 4.40
906 938 6.203530 CCTCACTGGTATTTGTGTATATGCAG 59.796 42.308 0.00 0.00 35.82 4.41
907 939 6.054941 CCTCACTGGTATTTGTGTATATGCA 58.945 40.000 0.00 0.00 35.82 3.96
908 940 6.288294 TCCTCACTGGTATTTGTGTATATGC 58.712 40.000 0.00 0.00 37.07 3.14
909 941 8.777413 CAATCCTCACTGGTATTTGTGTATATG 58.223 37.037 0.00 0.00 37.07 1.78
910 942 7.939039 CCAATCCTCACTGGTATTTGTGTATAT 59.061 37.037 0.00 0.00 37.07 0.86
911 943 7.279615 CCAATCCTCACTGGTATTTGTGTATA 58.720 38.462 0.00 0.00 37.07 1.47
912 944 6.122277 CCAATCCTCACTGGTATTTGTGTAT 58.878 40.000 0.00 0.00 37.07 2.29
913 945 5.496556 CCAATCCTCACTGGTATTTGTGTA 58.503 41.667 0.00 0.00 37.07 2.90
914 946 4.335416 CCAATCCTCACTGGTATTTGTGT 58.665 43.478 0.00 0.00 37.07 3.72
915 947 3.696051 CCCAATCCTCACTGGTATTTGTG 59.304 47.826 0.00 0.00 37.07 3.33
916 948 3.591527 TCCCAATCCTCACTGGTATTTGT 59.408 43.478 0.00 0.00 37.07 2.83
917 949 4.235079 TCCCAATCCTCACTGGTATTTG 57.765 45.455 0.00 0.00 37.07 2.32
918 950 4.569865 GGTTCCCAATCCTCACTGGTATTT 60.570 45.833 0.00 0.00 37.07 1.40
919 951 3.053619 GGTTCCCAATCCTCACTGGTATT 60.054 47.826 0.00 0.00 37.07 1.89
920 952 2.509964 GGTTCCCAATCCTCACTGGTAT 59.490 50.000 0.00 0.00 37.07 2.73
921 953 1.913419 GGTTCCCAATCCTCACTGGTA 59.087 52.381 0.00 0.00 37.07 3.25
922 954 0.698818 GGTTCCCAATCCTCACTGGT 59.301 55.000 0.00 0.00 37.07 4.00
923 955 0.995024 AGGTTCCCAATCCTCACTGG 59.005 55.000 0.00 0.00 37.10 4.00
924 956 2.440409 CAAGGTTCCCAATCCTCACTG 58.560 52.381 0.00 0.00 33.09 3.66
925 957 1.272147 GCAAGGTTCCCAATCCTCACT 60.272 52.381 0.00 0.00 33.09 3.41
926 958 1.177401 GCAAGGTTCCCAATCCTCAC 58.823 55.000 0.00 0.00 33.09 3.51
927 959 1.004745 GAGCAAGGTTCCCAATCCTCA 59.995 52.381 0.00 0.00 33.09 3.86
928 960 1.283321 AGAGCAAGGTTCCCAATCCTC 59.717 52.381 0.00 0.00 33.09 3.71
929 961 1.283321 GAGAGCAAGGTTCCCAATCCT 59.717 52.381 0.00 0.00 35.34 3.24
930 962 1.004745 TGAGAGCAAGGTTCCCAATCC 59.995 52.381 0.00 0.00 0.00 3.01
931 963 2.496899 TGAGAGCAAGGTTCCCAATC 57.503 50.000 0.00 0.00 0.00 2.67
932 964 3.094572 CAATGAGAGCAAGGTTCCCAAT 58.905 45.455 0.00 0.00 0.00 3.16
933 965 2.158475 ACAATGAGAGCAAGGTTCCCAA 60.158 45.455 0.00 0.00 0.00 4.12
934 966 1.425066 ACAATGAGAGCAAGGTTCCCA 59.575 47.619 0.00 0.00 0.00 4.37
935 967 2.087646 GACAATGAGAGCAAGGTTCCC 58.912 52.381 0.00 0.00 0.00 3.97
936 968 2.783135 TGACAATGAGAGCAAGGTTCC 58.217 47.619 0.00 0.00 0.00 3.62
937 969 3.376546 GGATGACAATGAGAGCAAGGTTC 59.623 47.826 0.00 0.00 0.00 3.62
938 970 3.350833 GGATGACAATGAGAGCAAGGTT 58.649 45.455 0.00 0.00 0.00 3.50
939 971 2.356535 GGGATGACAATGAGAGCAAGGT 60.357 50.000 0.00 0.00 0.00 3.50
940 972 2.295885 GGGATGACAATGAGAGCAAGG 58.704 52.381 0.00 0.00 0.00 3.61
941 973 2.295885 GGGGATGACAATGAGAGCAAG 58.704 52.381 0.00 0.00 0.00 4.01
942 974 1.064463 GGGGGATGACAATGAGAGCAA 60.064 52.381 0.00 0.00 0.00 3.91
943 975 0.548031 GGGGGATGACAATGAGAGCA 59.452 55.000 0.00 0.00 0.00 4.26
944 976 0.548031 TGGGGGATGACAATGAGAGC 59.452 55.000 0.00 0.00 0.00 4.09
945 977 2.549563 CGATGGGGGATGACAATGAGAG 60.550 54.545 0.00 0.00 0.00 3.20
946 978 1.417517 CGATGGGGGATGACAATGAGA 59.582 52.381 0.00 0.00 0.00 3.27
947 979 1.141657 ACGATGGGGGATGACAATGAG 59.858 52.381 0.00 0.00 0.00 2.90
948 980 1.140852 GACGATGGGGGATGACAATGA 59.859 52.381 0.00 0.00 0.00 2.57
949 981 1.141657 AGACGATGGGGGATGACAATG 59.858 52.381 0.00 0.00 0.00 2.82
950 982 1.141657 CAGACGATGGGGGATGACAAT 59.858 52.381 0.00 0.00 0.00 2.71
951 983 0.541392 CAGACGATGGGGGATGACAA 59.459 55.000 0.00 0.00 0.00 3.18
952 984 1.971505 GCAGACGATGGGGGATGACA 61.972 60.000 0.00 0.00 0.00 3.58
953 985 1.227674 GCAGACGATGGGGGATGAC 60.228 63.158 0.00 0.00 0.00 3.06
954 986 1.383109 AGCAGACGATGGGGGATGA 60.383 57.895 0.00 0.00 0.00 2.92
955 987 1.070445 GAGCAGACGATGGGGGATG 59.930 63.158 0.00 0.00 0.00 3.51
956 988 2.502492 CGAGCAGACGATGGGGGAT 61.502 63.158 0.00 0.00 35.09 3.85
957 989 3.147595 CGAGCAGACGATGGGGGA 61.148 66.667 0.00 0.00 35.09 4.81
958 990 3.019003 AACGAGCAGACGATGGGGG 62.019 63.158 5.12 0.00 37.03 5.40
959 991 1.811266 CAACGAGCAGACGATGGGG 60.811 63.158 5.12 0.00 33.64 4.96
960 992 2.456119 GCAACGAGCAGACGATGGG 61.456 63.158 5.12 0.00 44.79 4.00
961 993 3.084579 GCAACGAGCAGACGATGG 58.915 61.111 5.12 0.00 44.79 3.51
981 1013 0.461961 CAGAGGACGAGGATGGGAAC 59.538 60.000 0.00 0.00 0.00 3.62
982 1014 1.330655 GCAGAGGACGAGGATGGGAA 61.331 60.000 0.00 0.00 0.00 3.97
983 1015 1.758514 GCAGAGGACGAGGATGGGA 60.759 63.158 0.00 0.00 0.00 4.37
984 1016 2.801631 GGCAGAGGACGAGGATGGG 61.802 68.421 0.00 0.00 0.00 4.00
985 1017 2.801631 GGGCAGAGGACGAGGATGG 61.802 68.421 0.00 0.00 0.00 3.51
986 1018 0.468214 TAGGGCAGAGGACGAGGATG 60.468 60.000 0.00 0.00 0.00 3.51
987 1019 0.468400 GTAGGGCAGAGGACGAGGAT 60.468 60.000 0.00 0.00 0.00 3.24
988 1020 1.076923 GTAGGGCAGAGGACGAGGA 60.077 63.158 0.00 0.00 0.00 3.71
989 1021 1.076632 AGTAGGGCAGAGGACGAGG 60.077 63.158 0.00 0.00 0.00 4.63
990 1022 0.106918 AGAGTAGGGCAGAGGACGAG 60.107 60.000 0.00 0.00 0.00 4.18
991 1023 1.210538 TAGAGTAGGGCAGAGGACGA 58.789 55.000 0.00 0.00 0.00 4.20
992 1024 2.054232 TTAGAGTAGGGCAGAGGACG 57.946 55.000 0.00 0.00 0.00 4.79
993 1025 2.630580 CCATTAGAGTAGGGCAGAGGAC 59.369 54.545 0.00 0.00 0.00 3.85
994 1026 2.964209 CCATTAGAGTAGGGCAGAGGA 58.036 52.381 0.00 0.00 0.00 3.71
995 1027 1.346068 GCCATTAGAGTAGGGCAGAGG 59.654 57.143 0.00 0.00 45.70 3.69
996 1028 1.000283 CGCCATTAGAGTAGGGCAGAG 60.000 57.143 0.00 0.00 46.75 3.35
997 1029 1.040646 CGCCATTAGAGTAGGGCAGA 58.959 55.000 0.00 0.00 46.75 4.26
998 1030 0.601311 GCGCCATTAGAGTAGGGCAG 60.601 60.000 0.00 0.00 46.75 4.85
999 1031 1.048724 AGCGCCATTAGAGTAGGGCA 61.049 55.000 2.29 0.00 46.75 5.36
1000 1032 0.319986 GAGCGCCATTAGAGTAGGGC 60.320 60.000 2.29 0.00 42.98 5.19
1001 1033 0.318762 GGAGCGCCATTAGAGTAGGG 59.681 60.000 2.29 0.00 0.00 3.53
1002 1034 0.318762 GGGAGCGCCATTAGAGTAGG 59.681 60.000 9.31 0.00 35.15 3.18
1003 1035 1.000283 CTGGGAGCGCCATTAGAGTAG 60.000 57.143 9.31 0.00 35.15 2.57
1004 1036 1.040646 CTGGGAGCGCCATTAGAGTA 58.959 55.000 9.31 0.00 35.15 2.59
1005 1037 0.687757 TCTGGGAGCGCCATTAGAGT 60.688 55.000 9.31 0.00 35.15 3.24
1006 1038 0.683973 ATCTGGGAGCGCCATTAGAG 59.316 55.000 9.31 0.00 35.15 2.43
1007 1039 0.394192 CATCTGGGAGCGCCATTAGA 59.606 55.000 9.31 9.21 35.15 2.10
1008 1040 0.394192 TCATCTGGGAGCGCCATTAG 59.606 55.000 9.31 3.51 35.15 1.73
1009 1041 0.836606 TTCATCTGGGAGCGCCATTA 59.163 50.000 9.31 0.00 35.15 1.90
1010 1042 0.749454 GTTCATCTGGGAGCGCCATT 60.749 55.000 9.31 0.00 35.15 3.16
1011 1043 1.153086 GTTCATCTGGGAGCGCCAT 60.153 57.895 9.31 0.00 35.15 4.40
1012 1044 2.244117 GAGTTCATCTGGGAGCGCCA 62.244 60.000 9.31 0.00 35.15 5.69
1013 1045 1.522580 GAGTTCATCTGGGAGCGCC 60.523 63.158 2.29 0.00 0.00 6.53
1014 1046 1.522580 GGAGTTCATCTGGGAGCGC 60.523 63.158 0.00 0.00 0.00 5.92
1015 1047 0.103937 GAGGAGTTCATCTGGGAGCG 59.896 60.000 0.00 0.00 0.00 5.03
1016 1048 0.103937 CGAGGAGTTCATCTGGGAGC 59.896 60.000 0.00 0.00 0.00 4.70
1017 1049 1.769026 TCGAGGAGTTCATCTGGGAG 58.231 55.000 0.00 0.00 0.00 4.30
1018 1050 2.103373 CTTCGAGGAGTTCATCTGGGA 58.897 52.381 0.00 0.00 0.00 4.37
1019 1051 2.100584 CTCTTCGAGGAGTTCATCTGGG 59.899 54.545 15.98 0.00 0.00 4.45
1020 1052 3.020274 TCTCTTCGAGGAGTTCATCTGG 58.980 50.000 22.31 0.00 35.11 3.86
1021 1053 4.580167 AGATCTCTTCGAGGAGTTCATCTG 59.420 45.833 27.53 4.54 35.60 2.90
1022 1054 4.792068 AGATCTCTTCGAGGAGTTCATCT 58.208 43.478 27.53 22.24 35.60 2.90
1023 1055 5.514274 AAGATCTCTTCGAGGAGTTCATC 57.486 43.478 27.53 20.82 35.60 2.92
1024 1056 5.514274 GAAGATCTCTTCGAGGAGTTCAT 57.486 43.478 27.53 20.29 42.33 2.57
1025 1057 4.974368 GAAGATCTCTTCGAGGAGTTCA 57.026 45.455 27.53 11.46 42.33 3.18
1036 1068 2.501610 GGCGGCGGAAGATCTCTT 59.498 61.111 9.78 0.00 39.23 2.85
1037 1069 3.905678 CGGCGGCGGAAGATCTCT 61.906 66.667 25.36 0.00 0.00 3.10
1038 1070 3.900892 TCGGCGGCGGAAGATCTC 61.901 66.667 31.73 0.00 0.00 2.75
1039 1071 4.208686 GTCGGCGGCGGAAGATCT 62.209 66.667 31.73 0.00 0.00 2.75
1105 1137 3.483869 GCGGAGGAAGGGATGGCT 61.484 66.667 0.00 0.00 0.00 4.75
1389 1480 2.124942 GCAGGCAGCAGGAGGTAC 60.125 66.667 0.00 0.00 44.79 3.34
1440 1531 1.138069 TCGCAATGTATGATGTCCGGT 59.862 47.619 0.00 0.00 0.00 5.28
1450 1541 0.839946 AGGAAGGGCTCGCAATGTAT 59.160 50.000 0.00 0.00 0.00 2.29
1452 1543 0.962356 CAAGGAAGGGCTCGCAATGT 60.962 55.000 0.00 0.00 0.00 2.71
1453 1544 1.805254 CAAGGAAGGGCTCGCAATG 59.195 57.895 0.00 0.00 0.00 2.82
1455 1546 2.672996 GCAAGGAAGGGCTCGCAA 60.673 61.111 0.00 0.00 0.00 4.85
1488 1579 2.490115 GTCTGTGAATGACGAGTCCTCT 59.510 50.000 0.34 0.00 0.00 3.69
1548 1642 2.820787 GGAAGAGAAGACGAAGAGGACA 59.179 50.000 0.00 0.00 0.00 4.02
1614 1708 2.025887 AGGGTCTGACATCAAACATCCC 60.026 50.000 10.38 0.00 33.60 3.85
1620 1714 3.119245 GCGTAGTAGGGTCTGACATCAAA 60.119 47.826 10.38 0.00 0.00 2.69
1624 1718 1.400737 GGCGTAGTAGGGTCTGACAT 58.599 55.000 10.38 0.00 0.00 3.06
1627 1721 0.260816 ATGGGCGTAGTAGGGTCTGA 59.739 55.000 0.00 0.00 0.00 3.27
1630 1724 0.757935 TCCATGGGCGTAGTAGGGTC 60.758 60.000 13.02 0.00 0.00 4.46
1631 1725 0.105142 ATCCATGGGCGTAGTAGGGT 60.105 55.000 13.02 0.00 0.00 4.34
1632 1726 0.321671 CATCCATGGGCGTAGTAGGG 59.678 60.000 13.02 0.00 0.00 3.53
1660 1758 0.395312 GTCTTCCGGACAAACCTCCA 59.605 55.000 1.83 0.00 43.94 3.86
1672 1780 3.175240 CGAGCAGCGTGTCTTCCG 61.175 66.667 0.00 0.00 34.64 4.30
1719 1827 3.316573 GAGGCGGGAGGTCAACAGG 62.317 68.421 0.00 0.00 0.00 4.00
1746 1854 1.004277 GGCCATGTCCCACTTACAAGA 59.996 52.381 0.00 0.00 0.00 3.02
1750 1859 1.750778 CAATGGCCATGTCCCACTTAC 59.249 52.381 21.63 0.00 34.68 2.34
1753 1862 0.612732 CACAATGGCCATGTCCCACT 60.613 55.000 21.63 0.00 34.68 4.00
1834 1978 6.582636 ACATCATACACGAGATGGTATTTGT 58.417 36.000 7.26 0.00 44.50 2.83
1836 1980 9.208022 CAATACATCATACACGAGATGGTATTT 57.792 33.333 7.26 0.00 44.50 1.40
1938 2082 0.749454 CCAGCTACACCCAAGATGCC 60.749 60.000 0.00 0.00 0.00 4.40
2079 2230 1.109920 AGATCGGCATACAGGTCGCT 61.110 55.000 0.00 0.00 35.49 4.93
2112 2263 0.455815 CTTCAAATAGTTGGCGGGGC 59.544 55.000 2.65 0.00 35.29 5.80
2276 2442 1.268625 GGGTGAAAAGTAACTTGGCCG 59.731 52.381 0.00 0.00 0.00 6.13
2304 2478 8.621532 AACACTTACAAGCAATAAGAATGAGA 57.378 30.769 8.21 0.00 34.36 3.27
2323 2497 7.402862 ACCATTAGAATAGCACCTAAACACTT 58.597 34.615 0.00 0.00 0.00 3.16
2400 2590 9.552114 GTCATATTCACAAGATGAGAAACAAAG 57.448 33.333 0.00 0.00 39.55 2.77
2514 2708 3.075148 GACTCAAGGGAAAGTAGCCAAC 58.925 50.000 0.00 0.00 0.00 3.77
2656 2853 6.371389 CAGCACAAACTAACTAACTAAAGCC 58.629 40.000 0.00 0.00 0.00 4.35
2678 2875 3.506455 GCAATCTGATGAATGGATCCCAG 59.494 47.826 9.90 8.18 36.75 4.45
2703 2900 1.946768 TGCTGTAACACTTGGTGCTTC 59.053 47.619 0.00 0.00 36.98 3.86
2828 3033 4.597004 ACTGTGATTCTCATCAGCCAAAT 58.403 39.130 0.00 0.00 40.28 2.32
2869 3074 6.214205 AGAACAAAAATTTAACATGCTGCG 57.786 33.333 0.00 0.00 0.00 5.18
2895 3100 0.318120 CTTGGTGACATGGCCAAACC 59.682 55.000 10.96 16.10 43.29 3.27
2897 3102 0.469705 AGCTTGGTGACATGGCCAAA 60.470 50.000 10.96 0.00 43.29 3.28
2904 3110 2.174210 AGGCATGATAGCTTGGTGACAT 59.826 45.455 0.00 0.00 42.32 3.06
2937 3143 1.135315 CAAATCACAGCCATTCCACCG 60.135 52.381 0.00 0.00 0.00 4.94
2950 3156 3.917985 GGTCAATTTACCGCACAAATCAC 59.082 43.478 0.00 0.00 0.00 3.06
2961 3170 2.981898 AGCCACTACGGTCAATTTACC 58.018 47.619 0.00 0.00 36.97 2.85
3050 3260 6.833933 GGGGTCTAATTTACAAACATCAGGAT 59.166 38.462 0.00 0.00 0.00 3.24
3110 3752 7.331687 ACAGTTGCAAATAAAAGCATGGTTATC 59.668 33.333 11.15 0.00 40.94 1.75
3123 4028 5.178623 CAGAGTCGGTTACAGTTGCAAATAA 59.821 40.000 0.00 0.00 0.00 1.40
3124 4029 4.688879 CAGAGTCGGTTACAGTTGCAAATA 59.311 41.667 0.00 0.00 0.00 1.40
3175 4098 3.878778 AGTTGATGTATGAGGCTGGTTC 58.121 45.455 0.00 0.00 0.00 3.62
3181 4104 4.640201 TGCCTAAAAGTTGATGTATGAGGC 59.360 41.667 0.00 0.00 45.79 4.70
3186 4109 5.296780 CGTCCATGCCTAAAAGTTGATGTAT 59.703 40.000 0.00 0.00 0.00 2.29
3193 4116 1.173913 GCCGTCCATGCCTAAAAGTT 58.826 50.000 0.00 0.00 0.00 2.66
3196 4119 0.326595 TCAGCCGTCCATGCCTAAAA 59.673 50.000 0.00 0.00 0.00 1.52
3197 4120 0.107703 CTCAGCCGTCCATGCCTAAA 60.108 55.000 0.00 0.00 0.00 1.85
3210 4133 4.339530 TCTGATGTAGTGTATGTCTCAGCC 59.660 45.833 0.00 0.00 31.08 4.85
3254 4226 4.182339 GCCACTAGGTAGAAGCTTAACAC 58.818 47.826 0.00 0.00 37.19 3.32
3525 5213 3.062504 GCGTCCAATTTGATTGAAATGCC 59.937 43.478 0.00 0.00 42.83 4.40
3556 5245 8.119226 GTGTCACTAAAAATCACTATGCTGATC 58.881 37.037 0.00 0.00 30.12 2.92
3648 5337 3.467803 GGAGTAAATGGGAACGAGGATG 58.532 50.000 0.00 0.00 0.00 3.51
3655 5344 4.262617 GAACAGAGGGAGTAAATGGGAAC 58.737 47.826 0.00 0.00 0.00 3.62
3703 5392 5.706833 TCCAAACGTATGTAGTCTGTACTGA 59.293 40.000 0.00 0.00 36.36 3.41
3706 5395 6.151691 TGTTCCAAACGTATGTAGTCTGTAC 58.848 40.000 0.00 0.00 0.00 2.90
3710 5399 5.336531 CCTCTGTTCCAAACGTATGTAGTCT 60.337 44.000 0.00 0.00 0.00 3.24
3714 5403 4.877378 ACCTCTGTTCCAAACGTATGTA 57.123 40.909 0.00 0.00 0.00 2.29
3715 5404 3.764237 ACCTCTGTTCCAAACGTATGT 57.236 42.857 0.00 0.00 0.00 2.29
3716 5405 4.817517 ACTACCTCTGTTCCAAACGTATG 58.182 43.478 0.00 0.00 0.00 2.39
3717 5406 5.713861 ACTACTACCTCTGTTCCAAACGTAT 59.286 40.000 0.00 0.00 0.00 3.06
3718 5407 5.072741 ACTACTACCTCTGTTCCAAACGTA 58.927 41.667 0.00 0.00 0.00 3.57
3719 5408 3.893813 ACTACTACCTCTGTTCCAAACGT 59.106 43.478 0.00 0.00 0.00 3.99
3720 5409 4.516365 ACTACTACCTCTGTTCCAAACG 57.484 45.455 0.00 0.00 0.00 3.60
3723 5412 9.483489 TGAAATATACTACTACCTCTGTTCCAA 57.517 33.333 0.00 0.00 0.00 3.53
3724 5413 9.132923 CTGAAATATACTACTACCTCTGTTCCA 57.867 37.037 0.00 0.00 0.00 3.53
3725 5414 9.134055 ACTGAAATATACTACTACCTCTGTTCC 57.866 37.037 0.00 0.00 0.00 3.62
3754 5446 6.459670 TCTACACGAAGCCAGAAATGTATA 57.540 37.500 0.00 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.