Multiple sequence alignment - TraesCS3A01G029300

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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 TraesCS3A01G029300 chr3A 100.000 3143 0 0 1 3143 15479646 15476504 0.000000e+00 5805
1 TraesCS3A01G029300 chr3A 83.482 1459 123 62 1194 2614 15570833 15569455 0.000000e+00 1251
2 TraesCS3A01G029300 chr3A 80.108 186 21 9 2690 2870 15785005 15785179 1.180000e-24 124
3 TraesCS3A01G029300 chr2A 98.228 903 16 0 1 903 380712864 380713766 0.000000e+00 1580
4 TraesCS3A01G029300 chr3B 95.434 898 41 0 1 898 770049972 770050869 0.000000e+00 1432
5 TraesCS3A01G029300 chr3B 87.809 1132 93 18 1394 2498 12109089 12107976 0.000000e+00 1284
6 TraesCS3A01G029300 chr3B 87.042 1119 88 28 1421 2526 27866333 27865259 0.000000e+00 1210
7 TraesCS3A01G029300 chr3B 83.063 431 42 15 2087 2512 27861498 27861094 2.300000e-96 363
8 TraesCS3A01G029300 chr3B 84.058 345 16 5 1098 1409 27867040 27866702 2.370000e-76 296
9 TraesCS3A01G029300 chr3B 86.667 150 20 0 2993 3142 21258878 21259027 1.940000e-37 167
10 TraesCS3A01G029300 chr3B 85.246 122 13 2 2690 2807 12405016 12405136 1.530000e-23 121
11 TraesCS3A01G029300 chrUn 87.662 1078 58 25 1089 2119 35208060 35209109 0.000000e+00 1184
12 TraesCS3A01G029300 chrUn 86.707 993 75 22 1180 2145 34623950 34624912 0.000000e+00 1050
13 TraesCS3A01G029300 chrUn 75.057 441 59 22 2372 2805 261815073 261814677 1.170000e-34 158
14 TraesCS3A01G029300 chrUn 75.057 441 59 22 2372 2805 277277569 277277173 1.170000e-34 158
15 TraesCS3A01G029300 chr3D 87.324 994 76 30 1180 2145 5725509 5726480 0.000000e+00 1092
16 TraesCS3A01G029300 chr3D 93.443 244 13 1 1 244 472694505 472694745 2.980000e-95 359
17 TraesCS3A01G029300 chr3D 83.117 308 44 4 1454 1754 5628021 5627715 1.110000e-69 274
18 TraesCS3A01G029300 chr3D 86.364 154 10 4 1774 1927 330253153 330253011 1.170000e-34 158
19 TraesCS3A01G029300 chr3D 92.929 99 7 0 2267 2365 5726603 5726701 9.090000e-31 145
20 TraesCS3A01G029300 chr5D 89.836 669 61 5 237 902 332047550 332048214 0.000000e+00 852
21 TraesCS3A01G029300 chr5D 83.680 337 20 5 1812 2142 524484695 524485002 5.130000e-73 285
22 TraesCS3A01G029300 chr5D 83.012 259 35 8 659 909 76027994 76027737 3.150000e-55 226
23 TraesCS3A01G029300 chr5D 85.714 154 11 4 1774 1927 217741874 217742016 5.430000e-33 152
24 TraesCS3A01G029300 chr7D 89.820 668 61 5 237 901 500209491 500208828 0.000000e+00 850
25 TraesCS3A01G029300 chr7D 90.909 484 42 1 420 901 131712044 131711561 0.000000e+00 649
26 TraesCS3A01G029300 chr7B 88.393 672 50 8 237 900 698490925 698491576 0.000000e+00 784
27 TraesCS3A01G029300 chr7B 83.333 288 35 8 2857 3142 68305062 68305338 1.450000e-63 254
28 TraesCS3A01G029300 chr7B 86.667 150 20 0 2993 3142 216392857 216393006 1.940000e-37 167
29 TraesCS3A01G029300 chr7B 86.093 151 21 0 2992 3142 548985365 548985215 2.510000e-36 163
30 TraesCS3A01G029300 chr7B 93.396 106 7 0 2407 2512 376694742 376694637 1.170000e-34 158
31 TraesCS3A01G029300 chr2B 85.487 503 53 5 401 903 710095045 710095527 1.010000e-139 507
32 TraesCS3A01G029300 chr2B 82.986 288 37 7 2857 3142 144288 144565 1.870000e-62 250
33 TraesCS3A01G029300 chr2B 84.774 243 37 0 1535 1777 71349889 71349647 8.710000e-61 244
34 TraesCS3A01G029300 chr2B 76.688 459 55 20 2354 2805 277920673 277920260 1.140000e-49 207
35 TraesCS3A01G029300 chr2B 87.417 151 19 0 2992 3142 698156924 698157074 1.160000e-39 174
36 TraesCS3A01G029300 chr2B 86.755 151 20 0 2992 3142 98989094 98989244 5.390000e-38 169
37 TraesCS3A01G029300 chr2B 96.610 59 2 0 2285 2343 277920767 277920709 7.170000e-17 99
38 TraesCS3A01G029300 chr1B 93.852 244 14 1 1 244 685184252 685184494 1.780000e-97 366
39 TraesCS3A01G029300 chr1B 86.577 149 20 0 2992 3140 10180628 10180776 6.970000e-37 165
40 TraesCS3A01G029300 chr1B 86.184 152 20 1 2992 3142 534141529 534141680 2.510000e-36 163
41 TraesCS3A01G029300 chr1B 75.112 446 56 27 2369 2805 364949968 364950367 1.170000e-34 158
42 TraesCS3A01G029300 chr2D 79.695 394 50 16 1413 1777 44535599 44535207 1.120000e-64 257
43 TraesCS3A01G029300 chr5B 83.333 288 34 7 2857 3142 308734017 308734292 1.450000e-63 254
44 TraesCS3A01G029300 chr5B 86.093 151 21 0 2992 3142 77519952 77520102 2.510000e-36 163
45 TraesCS3A01G029300 chr5B 93.578 109 7 0 2404 2512 308733634 308733742 2.510000e-36 163
46 TraesCS3A01G029300 chr6B 82.414 290 39 6 2855 3142 10020421 10020142 3.130000e-60 243
47 TraesCS3A01G029300 chr6B 85.000 240 16 13 2289 2526 694874803 694874582 3.150000e-55 226
48 TraesCS3A01G029300 chr6B 86.093 151 21 0 2992 3142 15429619 15429469 2.510000e-36 163
49 TraesCS3A01G029300 chr6B 92.453 106 8 0 2407 2512 10020799 10020694 5.430000e-33 152
50 TraesCS3A01G029300 chr4A 86.111 144 14 2 2005 2142 5968914 5969057 1.950000e-32 150


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 TraesCS3A01G029300 chr3A 15476504 15479646 3142 True 5805.0 5805 100.0000 1 3143 1 chr3A.!!$R1 3142
1 TraesCS3A01G029300 chr3A 15569455 15570833 1378 True 1251.0 1251 83.4820 1194 2614 1 chr3A.!!$R2 1420
2 TraesCS3A01G029300 chr2A 380712864 380713766 902 False 1580.0 1580 98.2280 1 903 1 chr2A.!!$F1 902
3 TraesCS3A01G029300 chr3B 770049972 770050869 897 False 1432.0 1432 95.4340 1 898 1 chr3B.!!$F3 897
4 TraesCS3A01G029300 chr3B 12107976 12109089 1113 True 1284.0 1284 87.8090 1394 2498 1 chr3B.!!$R1 1104
5 TraesCS3A01G029300 chr3B 27861094 27867040 5946 True 623.0 1210 84.7210 1098 2526 3 chr3B.!!$R2 1428
6 TraesCS3A01G029300 chrUn 35208060 35209109 1049 False 1184.0 1184 87.6620 1089 2119 1 chrUn.!!$F2 1030
7 TraesCS3A01G029300 chrUn 34623950 34624912 962 False 1050.0 1050 86.7070 1180 2145 1 chrUn.!!$F1 965
8 TraesCS3A01G029300 chr3D 5725509 5726701 1192 False 618.5 1092 90.1265 1180 2365 2 chr3D.!!$F2 1185
9 TraesCS3A01G029300 chr5D 332047550 332048214 664 False 852.0 852 89.8360 237 902 1 chr5D.!!$F2 665
10 TraesCS3A01G029300 chr7D 500208828 500209491 663 True 850.0 850 89.8200 237 901 1 chr7D.!!$R2 664
11 TraesCS3A01G029300 chr7B 698490925 698491576 651 False 784.0 784 88.3930 237 900 1 chr7B.!!$F3 663
12 TraesCS3A01G029300 chr5B 308733634 308734292 658 False 208.5 254 88.4555 2404 3142 2 chr5B.!!$F2 738

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
940 950 0.032615 AGGAGGAGCGGAAGATGTCT 60.033 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2660 3182 0.179062 CAGCCGAGCAAGCCTAATCT 60.179 55.0 0.0 0.0 0.0 2.4 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
279 282 4.000988 TCCCTGTTGATTTTTCGCTACTC 58.999 43.478 0.00 0.00 0.00 2.59
352 358 1.005097 TCTCTGGCTACCCTACAACGA 59.995 52.381 0.00 0.00 0.00 3.85
399 405 2.436646 CATGCACCACGGGAGGTC 60.437 66.667 0.00 0.00 40.77 3.85
903 913 1.923227 GCGGCTAACACTGGCCTTTC 61.923 60.000 3.32 0.00 46.84 2.62
904 914 0.605319 CGGCTAACACTGGCCTTTCA 60.605 55.000 3.32 0.00 46.84 2.69
905 915 1.616159 GGCTAACACTGGCCTTTCAA 58.384 50.000 3.32 0.00 45.59 2.69
906 916 1.960689 GGCTAACACTGGCCTTTCAAA 59.039 47.619 3.32 0.00 45.59 2.69
907 917 2.364002 GGCTAACACTGGCCTTTCAAAA 59.636 45.455 3.32 0.00 45.59 2.44
908 918 3.181470 GGCTAACACTGGCCTTTCAAAAA 60.181 43.478 3.32 0.00 45.59 1.94
909 919 4.503123 GGCTAACACTGGCCTTTCAAAAAT 60.503 41.667 3.32 0.00 45.59 1.82
910 920 4.686091 GCTAACACTGGCCTTTCAAAAATC 59.314 41.667 3.32 0.00 0.00 2.17
911 921 4.751767 AACACTGGCCTTTCAAAAATCA 57.248 36.364 3.32 0.00 0.00 2.57
912 922 4.751767 ACACTGGCCTTTCAAAAATCAA 57.248 36.364 3.32 0.00 0.00 2.57
913 923 5.096443 ACACTGGCCTTTCAAAAATCAAA 57.904 34.783 3.32 0.00 0.00 2.69
914 924 5.495640 ACACTGGCCTTTCAAAAATCAAAA 58.504 33.333 3.32 0.00 0.00 2.44
915 925 5.942826 ACACTGGCCTTTCAAAAATCAAAAA 59.057 32.000 3.32 0.00 0.00 1.94
916 926 6.602803 ACACTGGCCTTTCAAAAATCAAAAAT 59.397 30.769 3.32 0.00 0.00 1.82
917 927 7.122501 ACACTGGCCTTTCAAAAATCAAAAATT 59.877 29.630 3.32 0.00 0.00 1.82
918 928 7.432838 CACTGGCCTTTCAAAAATCAAAAATTG 59.567 33.333 3.32 0.00 0.00 2.32
919 929 7.338957 ACTGGCCTTTCAAAAATCAAAAATTGA 59.661 29.630 3.32 0.00 45.01 2.57
920 930 8.059798 TGGCCTTTCAAAAATCAAAAATTGAA 57.940 26.923 3.32 0.00 43.95 2.69
921 931 8.526147 TGGCCTTTCAAAAATCAAAAATTGAAA 58.474 25.926 3.32 10.86 44.80 2.69
927 937 9.678260 TTCAAAAATCAAAAATTGAAAGGAGGA 57.322 25.926 0.00 0.00 43.95 3.71
928 938 9.328845 TCAAAAATCAAAAATTGAAAGGAGGAG 57.671 29.630 0.00 0.00 43.95 3.69
929 939 7.734924 AAAATCAAAAATTGAAAGGAGGAGC 57.265 32.000 0.00 0.00 43.95 4.70
930 940 4.503741 TCAAAAATTGAAAGGAGGAGCG 57.496 40.909 0.00 0.00 36.59 5.03
931 941 3.255642 TCAAAAATTGAAAGGAGGAGCGG 59.744 43.478 0.00 0.00 36.59 5.52
932 942 2.879103 AAATTGAAAGGAGGAGCGGA 57.121 45.000 0.00 0.00 0.00 5.54
933 943 2.879103 AATTGAAAGGAGGAGCGGAA 57.121 45.000 0.00 0.00 0.00 4.30
934 944 2.409948 ATTGAAAGGAGGAGCGGAAG 57.590 50.000 0.00 0.00 0.00 3.46
935 945 1.348064 TTGAAAGGAGGAGCGGAAGA 58.652 50.000 0.00 0.00 0.00 2.87
936 946 1.573108 TGAAAGGAGGAGCGGAAGAT 58.427 50.000 0.00 0.00 0.00 2.40
937 947 1.208052 TGAAAGGAGGAGCGGAAGATG 59.792 52.381 0.00 0.00 0.00 2.90
938 948 1.208293 GAAAGGAGGAGCGGAAGATGT 59.792 52.381 0.00 0.00 0.00 3.06
939 949 0.827368 AAGGAGGAGCGGAAGATGTC 59.173 55.000 0.00 0.00 0.00 3.06
940 950 0.032615 AGGAGGAGCGGAAGATGTCT 60.033 55.000 0.00 0.00 0.00 3.41
941 951 0.387565 GGAGGAGCGGAAGATGTCTC 59.612 60.000 0.00 0.00 0.00 3.36
942 952 1.398692 GAGGAGCGGAAGATGTCTCT 58.601 55.000 0.00 0.00 0.00 3.10
943 953 1.066908 GAGGAGCGGAAGATGTCTCTG 59.933 57.143 0.00 0.00 0.00 3.35
944 954 0.820871 GGAGCGGAAGATGTCTCTGT 59.179 55.000 0.00 0.00 0.00 3.41
945 955 1.202359 GGAGCGGAAGATGTCTCTGTC 60.202 57.143 0.00 0.00 0.00 3.51
946 956 1.748493 GAGCGGAAGATGTCTCTGTCT 59.252 52.381 0.00 0.00 0.00 3.41
947 957 1.748493 AGCGGAAGATGTCTCTGTCTC 59.252 52.381 0.00 0.00 0.00 3.36
948 958 1.748493 GCGGAAGATGTCTCTGTCTCT 59.252 52.381 0.00 0.00 0.00 3.10
949 959 2.223479 GCGGAAGATGTCTCTGTCTCTC 60.223 54.545 0.00 0.00 0.00 3.20
950 960 2.357637 CGGAAGATGTCTCTGTCTCTCC 59.642 54.545 0.00 0.00 0.00 3.71
951 961 3.631250 GGAAGATGTCTCTGTCTCTCCT 58.369 50.000 0.00 0.00 0.00 3.69
952 962 4.023291 GGAAGATGTCTCTGTCTCTCCTT 58.977 47.826 0.00 0.00 0.00 3.36
953 963 4.097892 GGAAGATGTCTCTGTCTCTCCTTC 59.902 50.000 0.00 0.00 0.00 3.46
954 964 4.314522 AGATGTCTCTGTCTCTCCTTCA 57.685 45.455 0.00 0.00 0.00 3.02
955 965 4.016444 AGATGTCTCTGTCTCTCCTTCAC 58.984 47.826 0.00 0.00 0.00 3.18
956 966 2.155279 TGTCTCTGTCTCTCCTTCACG 58.845 52.381 0.00 0.00 0.00 4.35
957 967 2.156098 GTCTCTGTCTCTCCTTCACGT 58.844 52.381 0.00 0.00 0.00 4.49
958 968 2.095466 GTCTCTGTCTCTCCTTCACGTG 60.095 54.545 9.94 9.94 0.00 4.49
959 969 1.201181 CTCTGTCTCTCCTTCACGTGG 59.799 57.143 17.00 0.00 0.00 4.94
960 970 0.389166 CTGTCTCTCCTTCACGTGGC 60.389 60.000 17.00 0.00 0.00 5.01
961 971 1.079750 GTCTCTCCTTCACGTGGCC 60.080 63.158 17.00 0.00 0.00 5.36
962 972 1.533033 TCTCTCCTTCACGTGGCCA 60.533 57.895 17.00 0.00 0.00 5.36
963 973 1.374758 CTCTCCTTCACGTGGCCAC 60.375 63.158 26.78 26.78 0.00 5.01
964 974 1.821061 CTCTCCTTCACGTGGCCACT 61.821 60.000 32.28 17.29 0.00 4.00
965 975 1.374758 CTCCTTCACGTGGCCACTC 60.375 63.158 32.28 8.96 0.00 3.51
966 976 2.358737 CCTTCACGTGGCCACTCC 60.359 66.667 32.28 8.14 0.00 3.85
967 977 2.358737 CTTCACGTGGCCACTCCC 60.359 66.667 32.28 7.73 0.00 4.30
968 978 3.901797 CTTCACGTGGCCACTCCCC 62.902 68.421 32.28 7.31 0.00 4.81
995 1005 3.589542 CACCACCCCACCACCCAT 61.590 66.667 0.00 0.00 0.00 4.00
996 1006 2.211575 ACCACCCCACCACCCATA 59.788 61.111 0.00 0.00 0.00 2.74
997 1007 2.235761 ACCACCCCACCACCCATAC 61.236 63.158 0.00 0.00 0.00 2.39
998 1008 2.680965 CACCCCACCACCCATACC 59.319 66.667 0.00 0.00 0.00 2.73
999 1009 2.615929 ACCCCACCACCCATACCC 60.616 66.667 0.00 0.00 0.00 3.69
1000 1010 2.615608 CCCCACCACCCATACCCA 60.616 66.667 0.00 0.00 0.00 4.51
1001 1011 2.012210 CCCCACCACCCATACCCAT 61.012 63.158 0.00 0.00 0.00 4.00
1002 1012 1.229927 CCCACCACCCATACCCATG 59.770 63.158 0.00 0.00 0.00 3.66
1009 1019 3.840437 CCATACCCATGGTTGCCG 58.160 61.111 11.73 0.00 45.92 5.69
1010 1020 1.225983 CCATACCCATGGTTGCCGA 59.774 57.895 11.73 0.00 45.92 5.54
1011 1021 0.178992 CCATACCCATGGTTGCCGAT 60.179 55.000 11.73 0.00 45.92 4.18
1012 1022 1.691196 CATACCCATGGTTGCCGATT 58.309 50.000 11.73 0.00 37.09 3.34
1013 1023 2.031120 CATACCCATGGTTGCCGATTT 58.969 47.619 11.73 0.00 37.09 2.17
1014 1024 1.468985 TACCCATGGTTGCCGATTTG 58.531 50.000 11.73 0.00 37.09 2.32
1015 1025 0.251564 ACCCATGGTTGCCGATTTGA 60.252 50.000 11.73 0.00 27.29 2.69
1016 1026 0.457035 CCCATGGTTGCCGATTTGAG 59.543 55.000 11.73 0.00 0.00 3.02
1017 1027 0.457035 CCATGGTTGCCGATTTGAGG 59.543 55.000 2.57 0.00 0.00 3.86
1026 1036 2.268730 CCGATTTGAGGCAAAAGAGC 57.731 50.000 0.00 0.00 36.90 4.09
1027 1037 1.815003 CCGATTTGAGGCAAAAGAGCT 59.185 47.619 0.00 0.00 36.90 4.09
1028 1038 2.159462 CCGATTTGAGGCAAAAGAGCTC 60.159 50.000 5.27 5.27 36.90 4.09
1029 1039 2.746362 CGATTTGAGGCAAAAGAGCTCT 59.254 45.455 11.45 11.45 36.90 4.09
1030 1040 3.425892 CGATTTGAGGCAAAAGAGCTCTG 60.426 47.826 19.06 7.08 36.90 3.35
1031 1041 1.242076 TTGAGGCAAAAGAGCTCTGC 58.758 50.000 19.06 17.28 35.28 4.26
1032 1042 0.109153 TGAGGCAAAAGAGCTCTGCA 59.891 50.000 23.20 9.37 37.83 4.41
1033 1043 0.803740 GAGGCAAAAGAGCTCTGCAG 59.196 55.000 23.20 7.63 37.83 4.41
1034 1044 0.110104 AGGCAAAAGAGCTCTGCAGT 59.890 50.000 23.20 10.59 37.83 4.40
1035 1045 0.520847 GGCAAAAGAGCTCTGCAGTC 59.479 55.000 23.20 12.27 37.83 3.51
1036 1046 1.521580 GCAAAAGAGCTCTGCAGTCT 58.478 50.000 19.06 12.10 36.09 3.24
1037 1047 1.197264 GCAAAAGAGCTCTGCAGTCTG 59.803 52.381 19.06 9.45 36.09 3.51
1038 1048 1.197264 CAAAAGAGCTCTGCAGTCTGC 59.803 52.381 19.06 18.32 45.29 4.26
1047 1057 4.085876 GCAGTCTGCACACCCATT 57.914 55.556 20.16 0.00 44.26 3.16
1048 1058 2.344535 GCAGTCTGCACACCCATTT 58.655 52.632 20.16 0.00 44.26 2.32
1049 1059 0.038892 GCAGTCTGCACACCCATTTG 60.039 55.000 20.16 0.00 44.26 2.32
1050 1060 0.038892 CAGTCTGCACACCCATTTGC 60.039 55.000 0.00 0.00 39.33 3.68
1051 1061 0.178981 AGTCTGCACACCCATTTGCT 60.179 50.000 0.00 0.00 39.62 3.91
1052 1062 0.038892 GTCTGCACACCCATTTGCTG 60.039 55.000 0.00 0.00 39.62 4.41
1053 1063 1.373748 CTGCACACCCATTTGCTGC 60.374 57.895 0.00 0.00 39.62 5.25
1054 1064 2.047939 GCACACCCATTTGCTGCC 60.048 61.111 0.00 0.00 35.74 4.85
1055 1065 2.658422 CACACCCATTTGCTGCCC 59.342 61.111 0.00 0.00 0.00 5.36
1056 1066 1.909781 CACACCCATTTGCTGCCCT 60.910 57.895 0.00 0.00 0.00 5.19
1057 1067 1.909781 ACACCCATTTGCTGCCCTG 60.910 57.895 0.00 0.00 0.00 4.45
1058 1068 1.607178 CACCCATTTGCTGCCCTGA 60.607 57.895 0.00 0.00 0.00 3.86
1059 1069 1.155859 ACCCATTTGCTGCCCTGAA 59.844 52.632 0.00 0.00 0.00 3.02
1060 1070 1.187567 ACCCATTTGCTGCCCTGAAC 61.188 55.000 0.00 0.00 0.00 3.18
1061 1071 1.593265 CCATTTGCTGCCCTGAACC 59.407 57.895 0.00 0.00 0.00 3.62
1062 1072 1.186917 CCATTTGCTGCCCTGAACCA 61.187 55.000 0.00 0.00 0.00 3.67
1063 1073 0.037975 CATTTGCTGCCCTGAACCAC 60.038 55.000 0.00 0.00 0.00 4.16
1064 1074 1.187567 ATTTGCTGCCCTGAACCACC 61.188 55.000 0.00 0.00 0.00 4.61
1065 1075 3.808218 TTGCTGCCCTGAACCACCC 62.808 63.158 0.00 0.00 0.00 4.61
1067 1077 3.579302 CTGCCCTGAACCACCCCA 61.579 66.667 0.00 0.00 0.00 4.96
1068 1078 2.863484 TGCCCTGAACCACCCCAT 60.863 61.111 0.00 0.00 0.00 4.00
1069 1079 2.043953 GCCCTGAACCACCCCATC 60.044 66.667 0.00 0.00 0.00 3.51
1070 1080 2.683475 CCCTGAACCACCCCATCC 59.317 66.667 0.00 0.00 0.00 3.51
1071 1081 2.272146 CCTGAACCACCCCATCCG 59.728 66.667 0.00 0.00 0.00 4.18
1072 1082 2.438434 CTGAACCACCCCATCCGC 60.438 66.667 0.00 0.00 0.00 5.54
1073 1083 3.995506 CTGAACCACCCCATCCGCC 62.996 68.421 0.00 0.00 0.00 6.13
1074 1084 3.728373 GAACCACCCCATCCGCCT 61.728 66.667 0.00 0.00 0.00 5.52
1075 1085 3.699134 GAACCACCCCATCCGCCTC 62.699 68.421 0.00 0.00 0.00 4.70
1083 1093 3.801997 CATCCGCCTCCCCTGCTT 61.802 66.667 0.00 0.00 0.00 3.91
1084 1094 3.483869 ATCCGCCTCCCCTGCTTC 61.484 66.667 0.00 0.00 0.00 3.86
1087 1097 4.168291 CGCCTCCCCTGCTTCCTC 62.168 72.222 0.00 0.00 0.00 3.71
1093 1103 1.617839 CCCCTGCTTCCTCCTCCTT 60.618 63.158 0.00 0.00 0.00 3.36
1094 1104 1.631071 CCCCTGCTTCCTCCTCCTTC 61.631 65.000 0.00 0.00 0.00 3.46
1096 1106 0.620121 CCTGCTTCCTCCTCCTTCCT 60.620 60.000 0.00 0.00 0.00 3.36
1237 1277 4.386951 CGACGGTGATGGTGGCCA 62.387 66.667 0.00 0.00 38.19 5.36
1329 1369 1.968017 CTGCTCCTTGCCGCTCAAA 60.968 57.895 0.00 0.00 42.00 2.69
1409 1457 2.423892 TGATTCTCCTTCTTCCGTCTCG 59.576 50.000 0.00 0.00 0.00 4.04
1411 1459 1.226435 CTCCTTCTTCCGTCTCGCG 60.226 63.158 0.00 0.00 40.95 5.87
1419 1471 3.112075 CCGTCTCGCGCACACAAT 61.112 61.111 8.75 0.00 39.71 2.71
1989 2414 2.753029 GCCAAGGTGGAGAGCTGT 59.247 61.111 0.00 0.00 40.96 4.40
2085 2510 0.470833 ATGGAGGAGGGATCGTCCTG 60.471 60.000 17.78 0.00 46.92 3.86
2111 2542 1.790387 GCATCGACAAGCAGGTCAC 59.210 57.895 8.27 0.00 37.66 3.67
2164 2595 4.942761 TTACTTACTTGGTCACCTTCGT 57.057 40.909 0.00 0.00 0.00 3.85
2211 2646 7.408543 TCGCCTTAACCTGGAGTACTATATAT 58.591 38.462 0.00 0.00 0.00 0.86
2212 2647 8.551440 TCGCCTTAACCTGGAGTACTATATATA 58.449 37.037 0.00 0.00 0.00 0.86
2213 2648 8.619546 CGCCTTAACCTGGAGTACTATATATAC 58.380 40.741 0.00 0.00 0.00 1.47
2214 2649 9.697990 GCCTTAACCTGGAGTACTATATATACT 57.302 37.037 0.00 5.19 35.54 2.12
2250 2685 3.627395 AGACATTGGCGATTTGGTAGA 57.373 42.857 0.00 0.00 0.00 2.59
2251 2686 3.950397 AGACATTGGCGATTTGGTAGAA 58.050 40.909 0.00 0.00 0.00 2.10
2252 2687 4.526970 AGACATTGGCGATTTGGTAGAAT 58.473 39.130 0.00 0.00 0.00 2.40
2255 2716 1.388547 TGGCGATTTGGTAGAATGGC 58.611 50.000 0.00 0.00 39.22 4.40
2279 2765 2.301870 TGAACTGGTGTGGTAGTGATCC 59.698 50.000 0.00 0.00 0.00 3.36
2302 2788 1.152830 TTGGACCTTGGTTGGGCTC 59.847 57.895 0.00 0.00 34.90 4.70
2349 2835 1.566018 GCCAATGTATCGCGTAGGCC 61.566 60.000 5.77 0.00 34.71 5.19
2368 2856 2.936553 GCCATATATGCGGCTGATGACA 60.937 50.000 7.24 0.00 45.29 3.58
2370 2858 3.368739 CCATATATGCGGCTGATGACAGA 60.369 47.826 7.24 0.00 46.03 3.41
2399 2895 4.104831 AGTAATCCTACTTGGCCTGTTCT 58.895 43.478 3.32 0.00 34.53 3.01
2400 2896 3.636153 AATCCTACTTGGCCTGTTCTC 57.364 47.619 3.32 0.00 35.26 2.87
2415 2911 2.202610 CTCGTCGATCGCTTGCCA 60.203 61.111 11.09 0.00 39.67 4.92
2454 2950 2.355756 TGTTTGACTGCTGCAGTTCTTC 59.644 45.455 33.33 21.63 45.44 2.87
2498 2995 7.805071 CACTTTGTAGGATCTTGATTGTTTGTC 59.195 37.037 0.00 0.00 0.00 3.18
2506 3003 7.068593 AGGATCTTGATTGTTTGTCTGTGAAAA 59.931 33.333 0.00 0.00 0.00 2.29
2512 3009 6.806249 TGATTGTTTGTCTGTGAAAACTGAAC 59.194 34.615 0.00 0.00 37.22 3.18
2513 3010 5.697473 TGTTTGTCTGTGAAAACTGAACA 57.303 34.783 0.00 0.00 37.22 3.18
2515 3012 7.384439 TGTTTGTCTGTGAAAACTGAACATA 57.616 32.000 0.00 0.00 37.22 2.29
2516 3013 7.821652 TGTTTGTCTGTGAAAACTGAACATAA 58.178 30.769 0.00 0.00 37.22 1.90
2526 3023 6.710295 TGAAAACTGAACATAAAGCAGCTAGA 59.290 34.615 0.00 0.00 33.03 2.43
2527 3024 7.228507 TGAAAACTGAACATAAAGCAGCTAGAA 59.771 33.333 0.00 0.00 33.03 2.10
2528 3025 6.487689 AACTGAACATAAAGCAGCTAGAAC 57.512 37.500 0.00 0.00 33.03 3.01
2529 3026 4.938226 ACTGAACATAAAGCAGCTAGAACC 59.062 41.667 0.00 0.00 33.03 3.62
2530 3027 4.261801 TGAACATAAAGCAGCTAGAACCC 58.738 43.478 0.00 0.00 0.00 4.11
2532 3029 4.301072 ACATAAAGCAGCTAGAACCCAA 57.699 40.909 0.00 0.00 0.00 4.12
2533 3030 4.860022 ACATAAAGCAGCTAGAACCCAAT 58.140 39.130 0.00 0.00 0.00 3.16
2534 3031 6.001449 ACATAAAGCAGCTAGAACCCAATA 57.999 37.500 0.00 0.00 0.00 1.90
2535 3032 6.058183 ACATAAAGCAGCTAGAACCCAATAG 58.942 40.000 0.00 0.00 0.00 1.73
2536 3033 4.576330 AAAGCAGCTAGAACCCAATAGT 57.424 40.909 0.00 0.00 0.00 2.12
2537 3034 3.828875 AGCAGCTAGAACCCAATAGTC 57.171 47.619 0.00 0.00 0.00 2.59
2538 3035 2.436173 AGCAGCTAGAACCCAATAGTCC 59.564 50.000 0.00 0.00 0.00 3.85
2539 3036 2.170607 GCAGCTAGAACCCAATAGTCCA 59.829 50.000 0.00 0.00 0.00 4.02
2553 3055 6.127054 CCCAATAGTCCACAGTAGAGAAATGA 60.127 42.308 0.00 0.00 0.00 2.57
2605 3121 3.097342 AGCCTGCCATTTTCTCTGAAT 57.903 42.857 0.00 0.00 0.00 2.57
2606 3122 4.240881 AGCCTGCCATTTTCTCTGAATA 57.759 40.909 0.00 0.00 0.00 1.75
2609 3125 5.659971 AGCCTGCCATTTTCTCTGAATATTT 59.340 36.000 0.00 0.00 0.00 1.40
2611 3127 7.508296 AGCCTGCCATTTTCTCTGAATATTTAT 59.492 33.333 0.00 0.00 0.00 1.40
2612 3128 7.597743 GCCTGCCATTTTCTCTGAATATTTATG 59.402 37.037 0.00 0.00 0.00 1.90
2613 3129 8.853126 CCTGCCATTTTCTCTGAATATTTATGA 58.147 33.333 0.00 0.00 0.00 2.15
2614 3130 9.674824 CTGCCATTTTCTCTGAATATTTATGAC 57.325 33.333 0.00 0.00 0.00 3.06
2615 3131 9.412460 TGCCATTTTCTCTGAATATTTATGACT 57.588 29.630 0.00 0.00 0.00 3.41
2616 3132 9.674824 GCCATTTTCTCTGAATATTTATGACTG 57.325 33.333 0.00 0.00 0.00 3.51
2636 3154 8.593492 TGACTGATATTTACGGATCAAGATTG 57.407 34.615 0.00 0.00 31.83 2.67
2638 3156 6.992123 ACTGATATTTACGGATCAAGATTGCA 59.008 34.615 0.00 0.00 31.83 4.08
2674 3196 4.319118 GCAACGATTAGATTAGGCTTGCTC 60.319 45.833 0.00 0.00 31.97 4.26
2677 3199 2.240493 TTAGATTAGGCTTGCTCGGC 57.760 50.000 0.00 0.00 0.00 5.54
2682 3204 1.613317 TTAGGCTTGCTCGGCTGCTA 61.613 55.000 11.15 0.00 40.35 3.49
2684 3206 2.125350 GCTTGCTCGGCTGCTAGT 60.125 61.111 0.00 0.00 37.92 2.57
2685 3207 2.459442 GCTTGCTCGGCTGCTAGTG 61.459 63.158 0.00 0.00 37.92 2.74
2686 3208 1.079543 CTTGCTCGGCTGCTAGTGT 60.080 57.895 0.00 0.00 32.65 3.55
2689 3211 1.079819 GCTCGGCTGCTAGTGTTGA 60.080 57.895 0.00 0.00 0.00 3.18
2725 3250 5.043762 TCCTAAATGGGACCTTGTAGGATT 58.956 41.667 15.70 0.00 36.04 3.01
2731 3256 5.853572 TGGGACCTTGTAGGATTTTAACT 57.146 39.130 0.00 0.00 37.67 2.24
2735 3260 6.235664 GGACCTTGTAGGATTTTAACTGTCA 58.764 40.000 0.00 0.00 37.67 3.58
2736 3261 6.148976 GGACCTTGTAGGATTTTAACTGTCAC 59.851 42.308 0.00 0.00 37.67 3.67
2743 3268 4.750098 AGGATTTTAACTGTCACTGTGTCG 59.250 41.667 7.79 2.09 0.00 4.35
2783 3312 6.726230 CAGCTATGACTGAATTTCCAATCTG 58.274 40.000 0.00 0.00 40.25 2.90
2799 3328 2.226962 TCTGGTGGGTAGTAGTGGAC 57.773 55.000 0.00 0.00 0.00 4.02
2821 3353 5.010933 ACTGCTAGTCTAGTTGCTCTTACA 58.989 41.667 8.68 0.00 0.00 2.41
2827 3359 7.432838 GCTAGTCTAGTTGCTCTTACAATGTAC 59.567 40.741 8.68 0.00 0.00 2.90
2829 3361 7.841956 AGTCTAGTTGCTCTTACAATGTACAT 58.158 34.615 1.41 1.41 0.00 2.29
2830 3362 7.976734 AGTCTAGTTGCTCTTACAATGTACATC 59.023 37.037 9.23 0.00 0.00 3.06
2831 3363 6.972901 TCTAGTTGCTCTTACAATGTACATCG 59.027 38.462 9.23 0.00 0.00 3.84
2833 3365 5.807520 AGTTGCTCTTACAATGTACATCGAG 59.192 40.000 9.23 10.75 0.00 4.04
2834 3366 5.324784 TGCTCTTACAATGTACATCGAGT 57.675 39.130 9.23 10.76 0.00 4.18
2835 3367 6.445357 TGCTCTTACAATGTACATCGAGTA 57.555 37.500 9.23 9.80 0.00 2.59
2836 3368 6.495706 TGCTCTTACAATGTACATCGAGTAG 58.504 40.000 9.23 4.52 32.19 2.57
2837 3369 5.399892 GCTCTTACAATGTACATCGAGTAGC 59.600 44.000 9.23 10.40 32.19 3.58
2838 3370 5.828747 TCTTACAATGTACATCGAGTAGCC 58.171 41.667 9.23 0.00 32.19 3.93
2850 3382 4.238761 TCGAGTAGCCGGATCTTAATTG 57.761 45.455 5.05 0.00 0.00 2.32
2852 3384 3.982058 CGAGTAGCCGGATCTTAATTGTC 59.018 47.826 5.05 0.00 0.00 3.18
2873 3405 6.693466 TGTCGGTGTCTCAAAACTGAATATA 58.307 36.000 0.00 0.00 33.59 0.86
2917 3449 1.000843 GAAGCCGGCCTGTTTTCAATT 59.999 47.619 26.15 6.34 0.00 2.32
2918 3450 1.047801 AGCCGGCCTGTTTTCAATTT 58.952 45.000 26.15 0.00 0.00 1.82
2919 3451 2.243810 AGCCGGCCTGTTTTCAATTTA 58.756 42.857 26.15 0.00 0.00 1.40
2920 3452 2.231235 AGCCGGCCTGTTTTCAATTTAG 59.769 45.455 26.15 0.00 0.00 1.85
2984 3520 5.632764 CCTCTTACAATGCAGTAGATGATCG 59.367 44.000 0.00 0.00 0.00 3.69
2985 3521 5.532557 TCTTACAATGCAGTAGATGATCGG 58.467 41.667 0.00 0.00 0.00 4.18
2986 3522 3.117491 ACAATGCAGTAGATGATCGGG 57.883 47.619 0.00 0.00 0.00 5.14
2987 3523 2.435805 ACAATGCAGTAGATGATCGGGT 59.564 45.455 0.00 0.00 0.00 5.28
2988 3524 3.118261 ACAATGCAGTAGATGATCGGGTT 60.118 43.478 0.00 0.00 0.00 4.11
2989 3525 3.845781 ATGCAGTAGATGATCGGGTTT 57.154 42.857 0.00 0.00 0.00 3.27
2990 3526 3.627395 TGCAGTAGATGATCGGGTTTT 57.373 42.857 0.00 0.00 0.00 2.43
2991 3527 3.950397 TGCAGTAGATGATCGGGTTTTT 58.050 40.909 0.00 0.00 0.00 1.94
3032 3568 2.159324 GCCCTGCTGCTATGAACTTTTC 60.159 50.000 0.00 0.00 0.00 2.29
3088 3624 1.132453 GCGTGTTTCCCTAAATCCTGC 59.868 52.381 0.00 0.00 0.00 4.85
3090 3626 1.743394 GTGTTTCCCTAAATCCTGCGG 59.257 52.381 0.00 0.00 0.00 5.69
3108 3644 4.637276 TGCGGTTCTTCAGTTCTTTATCA 58.363 39.130 0.00 0.00 0.00 2.15
3142 3678 5.066893 TCCTGCTGAATGTCATGCTAATTTC 59.933 40.000 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
279 282 0.179000 AAGTAGCAAGCATCTCCGGG 59.821 55.000 0.00 0.00 0.00 5.73
352 358 0.981183 TTCTATGGGCGTCAGGTGTT 59.019 50.000 0.00 0.00 0.00 3.32
640 646 2.488355 CCGTCGTCGTAGGCATGT 59.512 61.111 0.71 0.00 35.01 3.21
649 655 4.175489 ATCAGGTCGCCGTCGTCG 62.175 66.667 0.00 0.00 36.96 5.12
903 913 8.071967 GCTCCTCCTTTCAATTTTTGATTTTTG 58.928 33.333 0.00 0.00 39.84 2.44
904 914 7.041848 CGCTCCTCCTTTCAATTTTTGATTTTT 60.042 33.333 0.00 0.00 39.84 1.94
905 915 6.424812 CGCTCCTCCTTTCAATTTTTGATTTT 59.575 34.615 0.00 0.00 39.84 1.82
906 916 5.928264 CGCTCCTCCTTTCAATTTTTGATTT 59.072 36.000 0.00 0.00 39.84 2.17
907 917 5.473039 CGCTCCTCCTTTCAATTTTTGATT 58.527 37.500 0.00 0.00 39.84 2.57
908 918 4.082026 CCGCTCCTCCTTTCAATTTTTGAT 60.082 41.667 0.00 0.00 39.84 2.57
909 919 3.255642 CCGCTCCTCCTTTCAATTTTTGA 59.744 43.478 0.00 0.00 38.04 2.69
910 920 3.255642 TCCGCTCCTCCTTTCAATTTTTG 59.744 43.478 0.00 0.00 0.00 2.44
911 921 3.496331 TCCGCTCCTCCTTTCAATTTTT 58.504 40.909 0.00 0.00 0.00 1.94
912 922 3.154827 TCCGCTCCTCCTTTCAATTTT 57.845 42.857 0.00 0.00 0.00 1.82
913 923 2.879103 TCCGCTCCTCCTTTCAATTT 57.121 45.000 0.00 0.00 0.00 1.82
914 924 2.305927 TCTTCCGCTCCTCCTTTCAATT 59.694 45.455 0.00 0.00 0.00 2.32
915 925 1.909302 TCTTCCGCTCCTCCTTTCAAT 59.091 47.619 0.00 0.00 0.00 2.57
916 926 1.348064 TCTTCCGCTCCTCCTTTCAA 58.652 50.000 0.00 0.00 0.00 2.69
917 927 1.208052 CATCTTCCGCTCCTCCTTTCA 59.792 52.381 0.00 0.00 0.00 2.69
918 928 1.208293 ACATCTTCCGCTCCTCCTTTC 59.792 52.381 0.00 0.00 0.00 2.62
919 929 1.208293 GACATCTTCCGCTCCTCCTTT 59.792 52.381 0.00 0.00 0.00 3.11
920 930 0.827368 GACATCTTCCGCTCCTCCTT 59.173 55.000 0.00 0.00 0.00 3.36
921 931 0.032615 AGACATCTTCCGCTCCTCCT 60.033 55.000 0.00 0.00 0.00 3.69
922 932 0.387565 GAGACATCTTCCGCTCCTCC 59.612 60.000 0.00 0.00 0.00 4.30
923 933 1.066908 CAGAGACATCTTCCGCTCCTC 59.933 57.143 0.00 0.00 31.64 3.71
924 934 1.110442 CAGAGACATCTTCCGCTCCT 58.890 55.000 0.00 0.00 31.64 3.69
925 935 0.820871 ACAGAGACATCTTCCGCTCC 59.179 55.000 0.00 0.00 31.64 4.70
926 936 1.748493 AGACAGAGACATCTTCCGCTC 59.252 52.381 0.00 0.00 31.64 5.03
927 937 1.748493 GAGACAGAGACATCTTCCGCT 59.252 52.381 0.00 0.00 31.64 5.52
928 938 1.748493 AGAGACAGAGACATCTTCCGC 59.252 52.381 0.00 0.00 31.64 5.54
929 939 2.357637 GGAGAGACAGAGACATCTTCCG 59.642 54.545 0.00 0.00 31.64 4.30
930 940 3.631250 AGGAGAGACAGAGACATCTTCC 58.369 50.000 0.00 0.00 31.64 3.46
931 941 4.704540 TGAAGGAGAGACAGAGACATCTTC 59.295 45.833 0.00 0.00 31.64 2.87
932 942 4.462483 GTGAAGGAGAGACAGAGACATCTT 59.538 45.833 0.00 0.00 31.64 2.40
933 943 4.016444 GTGAAGGAGAGACAGAGACATCT 58.984 47.826 0.00 0.00 35.63 2.90
934 944 3.181501 CGTGAAGGAGAGACAGAGACATC 60.182 52.174 0.00 0.00 0.00 3.06
935 945 2.752354 CGTGAAGGAGAGACAGAGACAT 59.248 50.000 0.00 0.00 0.00 3.06
936 946 2.155279 CGTGAAGGAGAGACAGAGACA 58.845 52.381 0.00 0.00 0.00 3.41
937 947 2.095466 CACGTGAAGGAGAGACAGAGAC 60.095 54.545 10.90 0.00 0.00 3.36
938 948 2.155279 CACGTGAAGGAGAGACAGAGA 58.845 52.381 10.90 0.00 0.00 3.10
939 949 1.201181 CCACGTGAAGGAGAGACAGAG 59.799 57.143 19.30 0.00 0.00 3.35
940 950 1.248486 CCACGTGAAGGAGAGACAGA 58.752 55.000 19.30 0.00 0.00 3.41
941 951 0.389166 GCCACGTGAAGGAGAGACAG 60.389 60.000 19.30 0.00 0.00 3.51
942 952 1.666011 GCCACGTGAAGGAGAGACA 59.334 57.895 19.30 0.00 0.00 3.41
943 953 1.079750 GGCCACGTGAAGGAGAGAC 60.080 63.158 19.30 0.00 0.00 3.36
944 954 1.533033 TGGCCACGTGAAGGAGAGA 60.533 57.895 19.30 0.00 0.00 3.10
945 955 1.374758 GTGGCCACGTGAAGGAGAG 60.375 63.158 22.49 0.00 0.00 3.20
946 956 1.816863 GAGTGGCCACGTGAAGGAGA 61.817 60.000 29.68 0.00 36.20 3.71
947 957 1.374758 GAGTGGCCACGTGAAGGAG 60.375 63.158 29.68 0.00 36.20 3.69
948 958 2.741092 GAGTGGCCACGTGAAGGA 59.259 61.111 29.68 0.00 36.20 3.36
949 959 2.358737 GGAGTGGCCACGTGAAGG 60.359 66.667 29.68 0.50 36.34 3.46
950 960 2.358737 GGGAGTGGCCACGTGAAG 60.359 66.667 29.68 1.58 38.95 3.02
951 961 3.948719 GGGGAGTGGCCACGTGAA 61.949 66.667 29.68 0.00 38.95 3.18
978 988 2.235028 TATGGGTGGTGGGGTGGTG 61.235 63.158 0.00 0.00 0.00 4.17
979 989 2.211575 TATGGGTGGTGGGGTGGT 59.788 61.111 0.00 0.00 0.00 4.16
980 990 2.680965 GTATGGGTGGTGGGGTGG 59.319 66.667 0.00 0.00 0.00 4.61
981 991 2.680965 GGTATGGGTGGTGGGGTG 59.319 66.667 0.00 0.00 0.00 4.61
982 992 2.615929 GGGTATGGGTGGTGGGGT 60.616 66.667 0.00 0.00 0.00 4.95
983 993 2.012210 ATGGGTATGGGTGGTGGGG 61.012 63.158 0.00 0.00 0.00 4.96
984 994 1.229927 CATGGGTATGGGTGGTGGG 59.770 63.158 0.00 0.00 0.00 4.61
993 1003 1.691196 AATCGGCAACCATGGGTATG 58.309 50.000 18.09 13.01 33.12 2.39
994 1004 2.031120 CAAATCGGCAACCATGGGTAT 58.969 47.619 18.09 0.00 33.12 2.73
995 1005 1.004862 TCAAATCGGCAACCATGGGTA 59.995 47.619 18.09 0.00 33.12 3.69
996 1006 0.251564 TCAAATCGGCAACCATGGGT 60.252 50.000 18.09 6.57 37.65 4.51
997 1007 0.457035 CTCAAATCGGCAACCATGGG 59.543 55.000 18.09 0.00 0.00 4.00
998 1008 0.457035 CCTCAAATCGGCAACCATGG 59.543 55.000 11.19 11.19 0.00 3.66
999 1009 0.179129 GCCTCAAATCGGCAACCATG 60.179 55.000 0.00 0.00 46.77 3.66
1000 1010 2.192605 GCCTCAAATCGGCAACCAT 58.807 52.632 0.00 0.00 46.77 3.55
1001 1011 3.680156 GCCTCAAATCGGCAACCA 58.320 55.556 0.00 0.00 46.77 3.67
1007 1017 1.815003 AGCTCTTTTGCCTCAAATCGG 59.185 47.619 0.00 0.00 33.19 4.18
1008 1018 2.746362 AGAGCTCTTTTGCCTCAAATCG 59.254 45.455 11.45 0.00 33.19 3.34
1009 1019 3.672781 GCAGAGCTCTTTTGCCTCAAATC 60.673 47.826 15.27 0.00 33.19 2.17
1010 1020 2.230750 GCAGAGCTCTTTTGCCTCAAAT 59.769 45.455 15.27 0.00 33.19 2.32
1011 1021 1.610522 GCAGAGCTCTTTTGCCTCAAA 59.389 47.619 15.27 0.00 31.79 2.69
1012 1022 1.242076 GCAGAGCTCTTTTGCCTCAA 58.758 50.000 15.27 0.00 31.79 3.02
1013 1023 0.109153 TGCAGAGCTCTTTTGCCTCA 59.891 50.000 15.27 0.00 37.03 3.86
1014 1024 0.803740 CTGCAGAGCTCTTTTGCCTC 59.196 55.000 15.27 0.00 37.03 4.70
1015 1025 0.110104 ACTGCAGAGCTCTTTTGCCT 59.890 50.000 23.35 0.74 37.03 4.75
1016 1026 0.520847 GACTGCAGAGCTCTTTTGCC 59.479 55.000 23.35 0.00 37.03 4.52
1017 1027 1.197264 CAGACTGCAGAGCTCTTTTGC 59.803 52.381 23.35 16.42 38.30 3.68
1018 1028 1.197264 GCAGACTGCAGAGCTCTTTTG 59.803 52.381 23.35 6.40 44.26 2.44
1019 1029 1.521580 GCAGACTGCAGAGCTCTTTT 58.478 50.000 23.35 0.00 44.26 2.27
1020 1030 3.230115 GCAGACTGCAGAGCTCTTT 57.770 52.632 23.35 0.00 44.26 2.52
1030 1040 0.038892 CAAATGGGTGTGCAGACTGC 60.039 55.000 20.86 20.86 45.29 4.40
1031 1041 0.038892 GCAAATGGGTGTGCAGACTG 60.039 55.000 14.32 4.91 40.58 3.51
1032 1042 0.178981 AGCAAATGGGTGTGCAGACT 60.179 50.000 14.32 0.00 43.42 3.24
1033 1043 0.038892 CAGCAAATGGGTGTGCAGAC 60.039 55.000 5.20 5.20 43.42 3.51
1034 1044 1.808531 GCAGCAAATGGGTGTGCAGA 61.809 55.000 0.00 0.00 46.68 4.26
1035 1045 1.373748 GCAGCAAATGGGTGTGCAG 60.374 57.895 0.00 0.00 46.68 4.41
1036 1046 2.735883 GCAGCAAATGGGTGTGCA 59.264 55.556 0.00 0.00 46.68 4.57
1037 1047 2.047939 GGCAGCAAATGGGTGTGC 60.048 61.111 0.00 0.00 46.68 4.57
1038 1048 1.909781 AGGGCAGCAAATGGGTGTG 60.910 57.895 0.00 0.00 46.68 3.82
1039 1049 1.909781 CAGGGCAGCAAATGGGTGT 60.910 57.895 0.00 0.00 46.68 4.16
1041 1051 1.155859 TTCAGGGCAGCAAATGGGT 59.844 52.632 0.00 0.00 0.00 4.51
1042 1052 1.593265 GTTCAGGGCAGCAAATGGG 59.407 57.895 0.00 0.00 0.00 4.00
1043 1053 1.186917 TGGTTCAGGGCAGCAAATGG 61.187 55.000 0.00 0.00 0.00 3.16
1044 1054 0.037975 GTGGTTCAGGGCAGCAAATG 60.038 55.000 0.00 0.00 0.00 2.32
1045 1055 1.187567 GGTGGTTCAGGGCAGCAAAT 61.188 55.000 0.00 0.00 0.00 2.32
1046 1056 1.832167 GGTGGTTCAGGGCAGCAAA 60.832 57.895 0.00 0.00 0.00 3.68
1047 1057 2.203480 GGTGGTTCAGGGCAGCAA 60.203 61.111 0.00 0.00 0.00 3.91
1048 1058 4.284550 GGGTGGTTCAGGGCAGCA 62.285 66.667 0.00 0.00 0.00 4.41
1050 1060 2.843912 GATGGGGTGGTTCAGGGCAG 62.844 65.000 0.00 0.00 0.00 4.85
1051 1061 2.863484 ATGGGGTGGTTCAGGGCA 60.863 61.111 0.00 0.00 0.00 5.36
1052 1062 2.043953 GATGGGGTGGTTCAGGGC 60.044 66.667 0.00 0.00 0.00 5.19
1053 1063 2.683475 GGATGGGGTGGTTCAGGG 59.317 66.667 0.00 0.00 0.00 4.45
1054 1064 2.272146 CGGATGGGGTGGTTCAGG 59.728 66.667 0.00 0.00 0.00 3.86
1055 1065 2.438434 GCGGATGGGGTGGTTCAG 60.438 66.667 0.00 0.00 0.00 3.02
1056 1066 4.041762 GGCGGATGGGGTGGTTCA 62.042 66.667 0.00 0.00 0.00 3.18
1057 1067 3.699134 GAGGCGGATGGGGTGGTTC 62.699 68.421 0.00 0.00 0.00 3.62
1058 1068 3.728373 GAGGCGGATGGGGTGGTT 61.728 66.667 0.00 0.00 0.00 3.67
1066 1076 3.764160 GAAGCAGGGGAGGCGGATG 62.764 68.421 0.00 0.00 36.08 3.51
1067 1077 3.483869 GAAGCAGGGGAGGCGGAT 61.484 66.667 0.00 0.00 36.08 4.18
1070 1080 4.168291 GAGGAAGCAGGGGAGGCG 62.168 72.222 0.00 0.00 36.08 5.52
1071 1081 3.803162 GGAGGAAGCAGGGGAGGC 61.803 72.222 0.00 0.00 0.00 4.70
1072 1082 2.041928 AGGAGGAAGCAGGGGAGG 59.958 66.667 0.00 0.00 0.00 4.30
1073 1083 2.069430 GGAGGAGGAAGCAGGGGAG 61.069 68.421 0.00 0.00 0.00 4.30
1074 1084 2.041265 GGAGGAGGAAGCAGGGGA 59.959 66.667 0.00 0.00 0.00 4.81
1075 1085 1.617839 AAGGAGGAGGAAGCAGGGG 60.618 63.158 0.00 0.00 0.00 4.79
1076 1086 1.631071 GGAAGGAGGAGGAAGCAGGG 61.631 65.000 0.00 0.00 0.00 4.45
1077 1087 0.620121 AGGAAGGAGGAGGAAGCAGG 60.620 60.000 0.00 0.00 0.00 4.85
1078 1088 0.829990 GAGGAAGGAGGAGGAAGCAG 59.170 60.000 0.00 0.00 0.00 4.24
1079 1089 0.618968 GGAGGAAGGAGGAGGAAGCA 60.619 60.000 0.00 0.00 0.00 3.91
1080 1090 1.341913 GGGAGGAAGGAGGAGGAAGC 61.342 65.000 0.00 0.00 0.00 3.86
1081 1091 1.045911 CGGGAGGAAGGAGGAGGAAG 61.046 65.000 0.00 0.00 0.00 3.46
1082 1092 1.001760 CGGGAGGAAGGAGGAGGAA 59.998 63.158 0.00 0.00 0.00 3.36
1083 1093 2.690452 CGGGAGGAAGGAGGAGGA 59.310 66.667 0.00 0.00 0.00 3.71
1084 1094 3.157949 GCGGGAGGAAGGAGGAGG 61.158 72.222 0.00 0.00 0.00 4.30
1085 1095 1.341156 AATGCGGGAGGAAGGAGGAG 61.341 60.000 0.00 0.00 0.00 3.69
1086 1096 1.306997 AATGCGGGAGGAAGGAGGA 60.307 57.895 0.00 0.00 0.00 3.71
1087 1097 1.147153 GAATGCGGGAGGAAGGAGG 59.853 63.158 0.00 0.00 0.00 4.30
1093 1103 2.286121 AAGGGGAATGCGGGAGGA 60.286 61.111 0.00 0.00 0.00 3.71
1094 1104 2.193248 GAAGGGGAATGCGGGAGG 59.807 66.667 0.00 0.00 0.00 4.30
1096 1106 3.416880 GGGAAGGGGAATGCGGGA 61.417 66.667 0.00 0.00 0.00 5.14
1161 1177 3.670377 GGCGGCAACACCCAGTTC 61.670 66.667 3.07 0.00 38.74 3.01
1409 1457 3.244976 AGAAGCAAATTATTGTGTGCGC 58.755 40.909 0.00 0.00 41.90 6.09
1411 1459 4.433283 CGCAAGAAGCAAATTATTGTGTGC 60.433 41.667 1.49 0.00 42.76 4.57
1807 2232 2.669569 GAGCAGGAACAGCCGCAA 60.670 61.111 0.00 0.00 43.90 4.85
2211 2646 9.607988 CAATGTCTAACCATGGTAAATACAGTA 57.392 33.333 20.12 2.96 0.00 2.74
2212 2647 7.556275 CCAATGTCTAACCATGGTAAATACAGT 59.444 37.037 20.12 15.91 0.00 3.55
2213 2648 7.468631 GCCAATGTCTAACCATGGTAAATACAG 60.469 40.741 20.12 8.77 0.00 2.74
2214 2649 6.320164 GCCAATGTCTAACCATGGTAAATACA 59.680 38.462 20.12 19.31 0.00 2.29
2215 2650 6.512741 CGCCAATGTCTAACCATGGTAAATAC 60.513 42.308 20.12 14.36 0.00 1.89
2250 2685 1.321474 CACACCAGTTCACTGCCATT 58.679 50.000 1.01 0.00 42.47 3.16
2251 2686 0.538057 CCACACCAGTTCACTGCCAT 60.538 55.000 1.01 0.00 42.47 4.40
2252 2687 1.152984 CCACACCAGTTCACTGCCA 60.153 57.895 1.01 0.00 42.47 4.92
2255 2716 2.102420 TCACTACCACACCAGTTCACTG 59.898 50.000 0.00 0.00 43.40 3.66
2302 2788 3.284617 TGCCATGGACAGAATCAATCAG 58.715 45.455 18.40 0.00 0.00 2.90
2349 2835 3.853475 TCTGTCATCAGCCGCATATATG 58.147 45.455 8.45 8.45 41.10 1.78
2358 2846 7.600752 GGATTACTAGTTTATCTGTCATCAGCC 59.399 40.741 0.00 0.00 41.10 4.85
2365 2853 9.968870 CCAAGTAGGATTACTAGTTTATCTGTC 57.031 37.037 0.00 0.96 41.47 3.51
2368 2856 7.790314 AGGCCAAGTAGGATTACTAGTTTATCT 59.210 37.037 5.01 0.00 41.47 1.98
2370 2858 7.347485 ACAGGCCAAGTAGGATTACTAGTTTAT 59.653 37.037 5.01 0.00 41.47 1.40
2399 2895 2.202610 CTGGCAAGCGATCGACGA 60.203 61.111 21.57 0.00 45.77 4.20
2400 2896 2.014093 GAACTGGCAAGCGATCGACG 62.014 60.000 21.57 6.90 45.66 5.12
2415 2911 9.614792 AGTCAAACAAGTAGAGTAAAATGAACT 57.385 29.630 0.00 0.00 0.00 3.01
2454 2950 3.338249 AGTGACATTTGTTCATCCTCGG 58.662 45.455 0.00 0.00 0.00 4.63
2498 2995 5.400485 GCTGCTTTATGTTCAGTTTTCACAG 59.600 40.000 0.00 0.00 0.00 3.66
2506 3003 4.938226 GGTTCTAGCTGCTTTATGTTCAGT 59.062 41.667 7.79 0.00 0.00 3.41
2512 3009 6.058183 ACTATTGGGTTCTAGCTGCTTTATG 58.942 40.000 7.79 0.00 0.00 1.90
2513 3010 6.253946 ACTATTGGGTTCTAGCTGCTTTAT 57.746 37.500 7.79 0.00 0.00 1.40
2515 3012 4.518249 GACTATTGGGTTCTAGCTGCTTT 58.482 43.478 7.79 0.00 0.00 3.51
2516 3013 3.118223 GGACTATTGGGTTCTAGCTGCTT 60.118 47.826 7.79 0.00 0.00 3.91
2526 3023 4.684724 TCTCTACTGTGGACTATTGGGTT 58.315 43.478 0.00 0.00 0.00 4.11
2527 3024 4.332683 TCTCTACTGTGGACTATTGGGT 57.667 45.455 0.00 0.00 0.00 4.51
2528 3025 5.677319 TTTCTCTACTGTGGACTATTGGG 57.323 43.478 0.00 0.00 0.00 4.12
2529 3026 6.878317 TCATTTCTCTACTGTGGACTATTGG 58.122 40.000 0.00 0.00 0.00 3.16
2530 3027 7.819415 TGTTCATTTCTCTACTGTGGACTATTG 59.181 37.037 0.00 0.00 0.00 1.90
2532 3029 7.039011 TGTGTTCATTTCTCTACTGTGGACTAT 60.039 37.037 0.00 0.00 0.00 2.12
2533 3030 6.266786 TGTGTTCATTTCTCTACTGTGGACTA 59.733 38.462 0.00 0.00 0.00 2.59
2534 3031 5.070446 TGTGTTCATTTCTCTACTGTGGACT 59.930 40.000 0.00 0.00 0.00 3.85
2535 3032 5.297547 TGTGTTCATTTCTCTACTGTGGAC 58.702 41.667 0.00 0.00 0.00 4.02
2536 3033 5.545063 TGTGTTCATTTCTCTACTGTGGA 57.455 39.130 0.00 0.00 0.00 4.02
2537 3034 7.063898 CAGTATGTGTTCATTTCTCTACTGTGG 59.936 40.741 0.00 0.00 32.76 4.17
2538 3035 7.412346 GCAGTATGTGTTCATTTCTCTACTGTG 60.412 40.741 0.00 0.00 36.42 3.66
2539 3036 6.591834 GCAGTATGTGTTCATTTCTCTACTGT 59.408 38.462 0.00 0.00 36.42 3.55
2553 3055 3.348647 TGCCTGTATGCAGTATGTGTT 57.651 42.857 10.09 0.00 41.02 3.32
2611 3127 7.171508 GCAATCTTGATCCGTAAATATCAGTCA 59.828 37.037 0.00 0.00 33.83 3.41
2612 3128 7.171508 TGCAATCTTGATCCGTAAATATCAGTC 59.828 37.037 0.00 0.00 33.83 3.51
2613 3129 6.992123 TGCAATCTTGATCCGTAAATATCAGT 59.008 34.615 0.00 0.00 33.83 3.41
2614 3130 7.172190 ACTGCAATCTTGATCCGTAAATATCAG 59.828 37.037 0.00 0.00 33.83 2.90
2615 3131 6.992123 ACTGCAATCTTGATCCGTAAATATCA 59.008 34.615 0.00 0.00 0.00 2.15
2616 3132 7.293745 CACTGCAATCTTGATCCGTAAATATC 58.706 38.462 0.00 0.00 0.00 1.63
2617 3133 6.205464 CCACTGCAATCTTGATCCGTAAATAT 59.795 38.462 0.00 0.00 0.00 1.28
2618 3134 5.527214 CCACTGCAATCTTGATCCGTAAATA 59.473 40.000 0.00 0.00 0.00 1.40
2621 3137 3.270027 CCACTGCAATCTTGATCCGTAA 58.730 45.455 0.00 0.00 0.00 3.18
2623 3139 1.742761 CCACTGCAATCTTGATCCGT 58.257 50.000 0.00 0.00 0.00 4.69
2624 3140 0.379669 GCCACTGCAATCTTGATCCG 59.620 55.000 0.00 0.00 37.47 4.18
2660 3182 0.179062 CAGCCGAGCAAGCCTAATCT 60.179 55.000 0.00 0.00 0.00 2.40
2661 3183 1.780025 GCAGCCGAGCAAGCCTAATC 61.780 60.000 0.00 0.00 0.00 1.75
2663 3185 1.613317 TAGCAGCCGAGCAAGCCTAA 61.613 55.000 8.78 0.00 36.85 2.69
2666 3188 2.894387 CTAGCAGCCGAGCAAGCC 60.894 66.667 8.78 0.00 36.85 4.35
2674 3196 1.662629 CAAGATCAACACTAGCAGCCG 59.337 52.381 0.00 0.00 0.00 5.52
2677 3199 4.118410 CCTAGCAAGATCAACACTAGCAG 58.882 47.826 0.00 0.00 31.06 4.24
2682 3204 4.472833 AGGAATCCTAGCAAGATCAACACT 59.527 41.667 0.00 0.00 28.47 3.55
2684 3206 6.560003 TTAGGAATCCTAGCAAGATCAACA 57.440 37.500 9.22 0.00 37.42 3.33
2685 3207 7.040823 CCATTTAGGAATCCTAGCAAGATCAAC 60.041 40.741 9.22 0.00 41.22 3.18
2686 3208 7.000472 CCATTTAGGAATCCTAGCAAGATCAA 59.000 38.462 9.22 0.00 41.22 2.57
2689 3211 5.612688 TCCCATTTAGGAATCCTAGCAAGAT 59.387 40.000 9.22 0.00 41.22 2.40
2725 3250 3.554324 GCTTCGACACAGTGACAGTTAAA 59.446 43.478 7.81 0.00 0.00 1.52
2731 3256 0.744281 TCAGCTTCGACACAGTGACA 59.256 50.000 7.81 0.00 0.00 3.58
2735 3260 2.031682 GCATTTTCAGCTTCGACACAGT 60.032 45.455 0.00 0.00 0.00 3.55
2736 3261 2.031769 TGCATTTTCAGCTTCGACACAG 60.032 45.455 0.00 0.00 0.00 3.66
2762 3291 6.039047 CCACCAGATTGGAAATTCAGTCATAG 59.961 42.308 1.40 0.00 40.96 2.23
2783 3312 0.535797 GCAGTCCACTACTACCCACC 59.464 60.000 0.00 0.00 35.76 4.61
2799 3328 5.568685 TGTAAGAGCAACTAGACTAGCAG 57.431 43.478 9.52 3.64 0.00 4.24
2821 3353 2.304092 TCCGGCTACTCGATGTACATT 58.696 47.619 10.30 0.00 0.00 2.71
2827 3359 3.917329 TTAAGATCCGGCTACTCGATG 57.083 47.619 0.00 0.00 0.00 3.84
2829 3361 3.635373 ACAATTAAGATCCGGCTACTCGA 59.365 43.478 0.00 0.00 0.00 4.04
2830 3362 3.978687 ACAATTAAGATCCGGCTACTCG 58.021 45.455 0.00 0.00 0.00 4.18
2831 3363 3.982058 CGACAATTAAGATCCGGCTACTC 59.018 47.826 0.00 0.00 0.00 2.59
2833 3365 3.057734 CCGACAATTAAGATCCGGCTAC 58.942 50.000 0.00 0.00 0.00 3.58
2834 3366 2.696707 ACCGACAATTAAGATCCGGCTA 59.303 45.455 0.00 0.00 40.48 3.93
2835 3367 1.485066 ACCGACAATTAAGATCCGGCT 59.515 47.619 0.00 0.00 40.48 5.52
2836 3368 1.597663 CACCGACAATTAAGATCCGGC 59.402 52.381 0.00 0.00 40.48 6.13
2837 3369 2.864343 GACACCGACAATTAAGATCCGG 59.136 50.000 0.00 0.00 42.30 5.14
2838 3370 3.782046 AGACACCGACAATTAAGATCCG 58.218 45.455 0.00 0.00 0.00 4.18
2850 3382 6.812160 ACTATATTCAGTTTTGAGACACCGAC 59.188 38.462 0.00 0.00 34.15 4.79
2852 3384 7.596749 AACTATATTCAGTTTTGAGACACCG 57.403 36.000 0.00 0.00 35.16 4.94
2893 3425 2.351924 AAAACAGGCCGGCTTCTCCA 62.352 55.000 28.56 0.00 34.01 3.86
2898 3430 1.047801 AATTGAAAACAGGCCGGCTT 58.952 45.000 28.56 18.19 0.00 4.35
2917 3449 2.384375 TCCCAGTTCTCCCCACTACTAA 59.616 50.000 0.00 0.00 0.00 2.24
2918 3450 2.005350 TCCCAGTTCTCCCCACTACTA 58.995 52.381 0.00 0.00 0.00 1.82
2919 3451 0.790993 TCCCAGTTCTCCCCACTACT 59.209 55.000 0.00 0.00 0.00 2.57
2920 3452 1.555533 CTTCCCAGTTCTCCCCACTAC 59.444 57.143 0.00 0.00 0.00 2.73
3006 3542 2.825836 ATAGCAGCAGGGCGCAAC 60.826 61.111 10.83 0.24 46.13 4.17
3013 3549 4.771590 TTGAAAAGTTCATAGCAGCAGG 57.228 40.909 0.00 0.00 39.84 4.85
3088 3624 8.034058 AGAATTGATAAAGAACTGAAGAACCG 57.966 34.615 0.00 0.00 0.00 4.44
3090 3626 9.535270 CGAAGAATTGATAAAGAACTGAAGAAC 57.465 33.333 0.00 0.00 0.00 3.01
3108 3644 4.074970 ACATTCAGCAGGAACGAAGAATT 58.925 39.130 0.00 0.00 38.60 2.17


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

AutoCloner maintained by Alex Coulton.