Multiple sequence alignment - TraesCS6D01G021800

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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 TraesCS6D01G021800 chr6D 100.000 2246 0 0 1 2246 8560425 8562670 0.000000e+00 4148.0
1 TraesCS6D01G021800 chr6D 97.242 979 26 1 1 979 8808926 8807949 0.000000e+00 1657.0
2 TraesCS6D01G021800 chr6D 96.936 979 27 1 1 979 8543717 8544692 0.000000e+00 1639.0
3 TraesCS6D01G021800 chr6D 93.869 946 36 2 1323 2246 8544693 8545638 0.000000e+00 1406.0
4 TraesCS6D01G021800 chr6D 88.419 993 63 12 1 979 34082660 34081706 0.000000e+00 1149.0
5 TraesCS6D01G021800 chr6D 89.420 690 19 7 1323 1959 8807948 8807260 0.000000e+00 821.0
6 TraesCS6D01G021800 chr6D 81.277 689 67 29 1323 1959 34081705 34081027 3.330000e-138 501.0
7 TraesCS6D01G021800 chr6D 87.857 140 17 0 1952 2091 469786813 469786952 4.960000e-37 165.0
8 TraesCS6D01G021800 chr6D 86.429 140 19 0 1952 2091 469779159 469779298 1.070000e-33 154.0
9 TraesCS6D01G021800 chr6B 97.245 980 21 4 1 979 15209048 15210022 0.000000e+00 1655.0
10 TraesCS6D01G021800 chr6B 96.834 979 31 0 1 979 16441678 16440700 0.000000e+00 1637.0
11 TraesCS6D01G021800 chr6B 91.692 662 28 5 1323 1959 16440699 16440040 0.000000e+00 893.0
12 TraesCS6D01G021800 chr6B 91.265 664 29 5 1323 1959 15210023 15210684 0.000000e+00 878.0
13 TraesCS6D01G021800 chr6B 89.873 158 15 1 2090 2246 16440042 16439885 3.780000e-48 202.0
14 TraesCS6D01G021800 chr6A 94.882 977 48 2 4 979 9483605 9482630 0.000000e+00 1526.0
15 TraesCS6D01G021800 chr6A 87.356 696 28 26 1323 1959 9482629 9481935 0.000000e+00 743.0
16 TraesCS6D01G021800 chr5B 88.271 989 67 12 1 979 556784922 556785871 0.000000e+00 1138.0
17 TraesCS6D01G021800 chr5B 97.118 347 8 1 979 1323 57515490 57515144 3.210000e-163 584.0
18 TraesCS6D01G021800 chr5B 81.579 684 70 20 1323 1959 556785872 556786546 4.280000e-142 514.0
19 TraesCS6D01G021800 chrUn 97.688 346 7 1 979 1323 445187743 445188088 5.340000e-166 593.0
20 TraesCS6D01G021800 chrUn 96.821 346 10 1 979 1323 261569057 261568712 5.380000e-161 577.0
21 TraesCS6D01G021800 chr7B 97.688 346 7 1 979 1323 662755399 662755054 5.340000e-166 593.0
22 TraesCS6D01G021800 chr5D 97.688 346 7 1 979 1323 299972872 299972527 5.340000e-166 593.0
23 TraesCS6D01G021800 chr5D 97.391 345 9 0 979 1323 6253639 6253295 2.480000e-164 588.0
24 TraesCS6D01G021800 chr5D 86.400 125 16 1 1959 2082 170399748 170399624 3.890000e-28 135.0
25 TraesCS6D01G021800 chr3B 97.406 347 7 1 979 1323 101924511 101924857 6.910000e-165 590.0
26 TraesCS6D01G021800 chr3A 97.406 347 7 1 979 1323 105557322 105556976 6.910000e-165 590.0
27 TraesCS6D01G021800 chr1B 97.399 346 8 1 979 1323 633716607 633716952 2.480000e-164 588.0
28 TraesCS6D01G021800 chr4A 73.096 1011 189 53 1 980 737062551 737063509 1.310000e-72 283.0
29 TraesCS6D01G021800 chr4A 76.524 328 44 21 1324 1634 737063510 737063821 5.000000e-32 148.0
30 TraesCS6D01G021800 chr5A 85.185 81 12 0 1959 2039 648945562 648945642 1.430000e-12 84.2


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 TraesCS6D01G021800 chr6D 8560425 8562670 2245 False 4148.000000 4148 100.000000 1 2246 1 chr6D.!!$F1 2245
1 TraesCS6D01G021800 chr6D 8543717 8545638 1921 False 1522.500000 1639 95.402500 1 2246 2 chr6D.!!$F4 2245
2 TraesCS6D01G021800 chr6D 8807260 8808926 1666 True 1239.000000 1657 93.331000 1 1959 2 chr6D.!!$R1 1958
3 TraesCS6D01G021800 chr6D 34081027 34082660 1633 True 825.000000 1149 84.848000 1 1959 2 chr6D.!!$R2 1958
4 TraesCS6D01G021800 chr6B 15209048 15210684 1636 False 1266.500000 1655 94.255000 1 1959 2 chr6B.!!$F1 1958
5 TraesCS6D01G021800 chr6B 16439885 16441678 1793 True 910.666667 1637 92.799667 1 2246 3 chr6B.!!$R1 2245
6 TraesCS6D01G021800 chr6A 9481935 9483605 1670 True 1134.500000 1526 91.119000 4 1959 2 chr6A.!!$R1 1955
7 TraesCS6D01G021800 chr5B 556784922 556786546 1624 False 826.000000 1138 84.925000 1 1959 2 chr5B.!!$F1 1958
8 TraesCS6D01G021800 chr4A 737062551 737063821 1270 False 215.500000 283 74.810000 1 1634 2 chr4A.!!$F1 1633

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
987 1074 0.24746 TCCTGGAGCATTGACACGAG 59.753 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 2335 1.051008 TGCTCTCTGGTCTTTGCTCA 58.949 50.0 0.0 0.0 0.0 4.26 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
87 129 1.115467 AATGGCCAAACGGTTTGTCA 58.885 45.000 26.67 23.47 38.98 3.58
113 155 7.986889 AGATGCATATCACACAACAGTACAATA 59.013 33.333 0.00 0.00 35.70 1.90
133 175 3.838244 AGCCTAACTGTTTGTCTGACA 57.162 42.857 6.36 6.36 0.00 3.58
251 294 6.184580 ACAGTACAACGACAAAATTGTTCA 57.815 33.333 0.00 0.00 42.43 3.18
756 843 2.171448 GGCTCACCTTGTGATAGTCCAT 59.829 50.000 0.00 0.00 41.94 3.41
980 1067 3.491208 CTCCCTTCCTGGAGCATTG 57.509 57.895 0.00 0.00 45.13 2.82
981 1068 0.914644 CTCCCTTCCTGGAGCATTGA 59.085 55.000 0.00 0.00 45.13 2.57
982 1069 0.620556 TCCCTTCCTGGAGCATTGAC 59.379 55.000 0.00 0.00 38.35 3.18
983 1070 0.329261 CCCTTCCTGGAGCATTGACA 59.671 55.000 0.00 0.00 38.35 3.58
984 1071 1.457346 CCTTCCTGGAGCATTGACAC 58.543 55.000 0.00 0.00 38.35 3.67
985 1072 1.081892 CTTCCTGGAGCATTGACACG 58.918 55.000 0.00 0.00 0.00 4.49
986 1073 0.684535 TTCCTGGAGCATTGACACGA 59.315 50.000 0.00 0.00 0.00 4.35
987 1074 0.247460 TCCTGGAGCATTGACACGAG 59.753 55.000 0.00 0.00 0.00 4.18
988 1075 0.742281 CCTGGAGCATTGACACGAGG 60.742 60.000 0.00 0.00 0.00 4.63
989 1076 0.247460 CTGGAGCATTGACACGAGGA 59.753 55.000 0.00 0.00 0.00 3.71
990 1077 0.684535 TGGAGCATTGACACGAGGAA 59.315 50.000 0.00 0.00 0.00 3.36
991 1078 1.079503 GGAGCATTGACACGAGGAAC 58.920 55.000 0.00 0.00 0.00 3.62
993 1080 2.094182 GGAGCATTGACACGAGGAACTA 60.094 50.000 0.00 0.00 41.55 2.24
994 1081 2.924290 GAGCATTGACACGAGGAACTAC 59.076 50.000 0.00 0.00 41.55 2.73
995 1082 2.563179 AGCATTGACACGAGGAACTACT 59.437 45.455 0.00 0.00 41.55 2.57
996 1083 2.924290 GCATTGACACGAGGAACTACTC 59.076 50.000 0.00 0.00 41.55 2.59
997 1084 3.614150 GCATTGACACGAGGAACTACTCA 60.614 47.826 0.00 0.00 41.55 3.41
998 1085 3.637998 TTGACACGAGGAACTACTCAC 57.362 47.619 0.00 0.00 41.55 3.51
999 1086 1.884579 TGACACGAGGAACTACTCACC 59.115 52.381 0.00 0.00 41.55 4.02
1000 1087 1.884579 GACACGAGGAACTACTCACCA 59.115 52.381 0.00 0.00 41.55 4.17
1001 1088 2.492484 GACACGAGGAACTACTCACCAT 59.508 50.000 0.00 0.00 41.55 3.55
1002 1089 2.231478 ACACGAGGAACTACTCACCATG 59.769 50.000 0.00 0.00 41.55 3.66
1003 1090 2.492088 CACGAGGAACTACTCACCATGA 59.508 50.000 0.00 0.00 41.55 3.07
1004 1091 3.056821 CACGAGGAACTACTCACCATGAA 60.057 47.826 0.00 0.00 41.55 2.57
1005 1092 3.769844 ACGAGGAACTACTCACCATGAAT 59.230 43.478 0.00 0.00 41.55 2.57
1006 1093 4.142138 ACGAGGAACTACTCACCATGAATC 60.142 45.833 0.00 0.00 41.55 2.52
1007 1094 4.698575 GAGGAACTACTCACCATGAATCC 58.301 47.826 0.00 0.00 41.55 3.01
1008 1095 4.104086 AGGAACTACTCACCATGAATCCA 58.896 43.478 0.00 0.00 36.02 3.41
1009 1096 4.080863 AGGAACTACTCACCATGAATCCAC 60.081 45.833 0.00 0.00 36.02 4.02
1010 1097 4.080863 GGAACTACTCACCATGAATCCACT 60.081 45.833 0.00 0.00 0.00 4.00
1011 1098 5.128827 GGAACTACTCACCATGAATCCACTA 59.871 44.000 0.00 0.00 0.00 2.74
1012 1099 6.351881 GGAACTACTCACCATGAATCCACTAA 60.352 42.308 0.00 0.00 0.00 2.24
1013 1100 6.814954 ACTACTCACCATGAATCCACTAAT 57.185 37.500 0.00 0.00 0.00 1.73
1014 1101 7.200434 ACTACTCACCATGAATCCACTAATT 57.800 36.000 0.00 0.00 0.00 1.40
1015 1102 7.050377 ACTACTCACCATGAATCCACTAATTG 58.950 38.462 0.00 0.00 0.00 2.32
1016 1103 5.819991 ACTCACCATGAATCCACTAATTGT 58.180 37.500 0.00 0.00 0.00 2.71
1017 1104 6.248433 ACTCACCATGAATCCACTAATTGTT 58.752 36.000 0.00 0.00 0.00 2.83
1018 1105 6.721208 ACTCACCATGAATCCACTAATTGTTT 59.279 34.615 0.00 0.00 0.00 2.83
1019 1106 7.094205 ACTCACCATGAATCCACTAATTGTTTC 60.094 37.037 0.00 0.00 0.00 2.78
1020 1107 6.947733 TCACCATGAATCCACTAATTGTTTCT 59.052 34.615 0.00 0.00 0.00 2.52
1021 1108 7.031372 CACCATGAATCCACTAATTGTTTCTG 58.969 38.462 0.00 0.00 0.00 3.02
1022 1109 6.038356 CCATGAATCCACTAATTGTTTCTGC 58.962 40.000 0.00 0.00 0.00 4.26
1023 1110 6.127535 CCATGAATCCACTAATTGTTTCTGCT 60.128 38.462 0.00 0.00 0.00 4.24
1024 1111 6.899393 TGAATCCACTAATTGTTTCTGCTT 57.101 33.333 0.00 0.00 0.00 3.91
1025 1112 6.913170 TGAATCCACTAATTGTTTCTGCTTC 58.087 36.000 0.00 0.00 0.00 3.86
1026 1113 6.716628 TGAATCCACTAATTGTTTCTGCTTCT 59.283 34.615 0.00 0.00 0.00 2.85
1027 1114 5.947228 TCCACTAATTGTTTCTGCTTCTG 57.053 39.130 0.00 0.00 0.00 3.02
1028 1115 5.376625 TCCACTAATTGTTTCTGCTTCTGT 58.623 37.500 0.00 0.00 0.00 3.41
1029 1116 5.827797 TCCACTAATTGTTTCTGCTTCTGTT 59.172 36.000 0.00 0.00 0.00 3.16
1030 1117 6.995686 TCCACTAATTGTTTCTGCTTCTGTTA 59.004 34.615 0.00 0.00 0.00 2.41
1031 1118 7.665559 TCCACTAATTGTTTCTGCTTCTGTTAT 59.334 33.333 0.00 0.00 0.00 1.89
1032 1119 8.299570 CCACTAATTGTTTCTGCTTCTGTTATT 58.700 33.333 0.00 0.00 0.00 1.40
1033 1120 9.121517 CACTAATTGTTTCTGCTTCTGTTATTG 57.878 33.333 0.00 0.00 0.00 1.90
1034 1121 7.809806 ACTAATTGTTTCTGCTTCTGTTATTGC 59.190 33.333 0.00 0.00 0.00 3.56
1035 1122 5.772825 TTGTTTCTGCTTCTGTTATTGCT 57.227 34.783 0.00 0.00 0.00 3.91
1036 1123 5.112220 TGTTTCTGCTTCTGTTATTGCTG 57.888 39.130 0.00 0.00 0.00 4.41
1037 1124 3.837213 TTCTGCTTCTGTTATTGCTGC 57.163 42.857 0.00 0.00 0.00 5.25
1038 1125 3.063510 TCTGCTTCTGTTATTGCTGCT 57.936 42.857 0.00 0.00 0.00 4.24
1039 1126 2.745821 TCTGCTTCTGTTATTGCTGCTG 59.254 45.455 0.00 0.00 0.00 4.41
1040 1127 2.745821 CTGCTTCTGTTATTGCTGCTGA 59.254 45.455 0.00 0.00 0.00 4.26
1041 1128 3.148412 TGCTTCTGTTATTGCTGCTGAA 58.852 40.909 0.00 0.00 0.00 3.02
1042 1129 3.760151 TGCTTCTGTTATTGCTGCTGAAT 59.240 39.130 0.00 0.00 0.00 2.57
1043 1130 4.219070 TGCTTCTGTTATTGCTGCTGAATT 59.781 37.500 0.00 0.00 0.00 2.17
1044 1131 4.561606 GCTTCTGTTATTGCTGCTGAATTG 59.438 41.667 0.00 0.00 0.00 2.32
1045 1132 4.707030 TCTGTTATTGCTGCTGAATTGG 57.293 40.909 0.00 0.00 0.00 3.16
1046 1133 3.119388 TCTGTTATTGCTGCTGAATTGGC 60.119 43.478 0.00 0.00 0.00 4.52
1047 1134 2.094078 TGTTATTGCTGCTGAATTGGCC 60.094 45.455 0.00 0.00 0.00 5.36
1048 1135 0.740149 TATTGCTGCTGAATTGGCCG 59.260 50.000 0.00 0.00 0.00 6.13
1049 1136 1.252904 ATTGCTGCTGAATTGGCCGT 61.253 50.000 0.00 0.00 0.00 5.68
1050 1137 0.607762 TTGCTGCTGAATTGGCCGTA 60.608 50.000 0.00 0.00 0.00 4.02
1051 1138 1.026182 TGCTGCTGAATTGGCCGTAG 61.026 55.000 0.00 0.00 0.00 3.51
1067 1154 2.213499 CGTAGGGCTTGCTTCTATTGG 58.787 52.381 0.00 0.00 0.00 3.16
1068 1155 2.158957 CGTAGGGCTTGCTTCTATTGGA 60.159 50.000 0.00 0.00 0.00 3.53
1069 1156 2.426842 AGGGCTTGCTTCTATTGGAC 57.573 50.000 0.00 0.00 0.00 4.02
1070 1157 1.064389 AGGGCTTGCTTCTATTGGACC 60.064 52.381 0.00 0.00 0.00 4.46
1071 1158 1.064389 GGGCTTGCTTCTATTGGACCT 60.064 52.381 0.00 0.00 0.00 3.85
1072 1159 2.019984 GGCTTGCTTCTATTGGACCTG 58.980 52.381 0.00 0.00 0.00 4.00
1073 1160 2.019984 GCTTGCTTCTATTGGACCTGG 58.980 52.381 0.00 0.00 0.00 4.45
1074 1161 2.356125 GCTTGCTTCTATTGGACCTGGA 60.356 50.000 0.00 0.00 0.00 3.86
1075 1162 3.539604 CTTGCTTCTATTGGACCTGGAG 58.460 50.000 0.00 0.00 0.00 3.86
1076 1163 2.551270 TGCTTCTATTGGACCTGGAGT 58.449 47.619 0.00 0.00 0.00 3.85
1077 1164 2.912956 TGCTTCTATTGGACCTGGAGTT 59.087 45.455 0.00 0.00 0.00 3.01
1078 1165 3.274288 GCTTCTATTGGACCTGGAGTTG 58.726 50.000 0.00 0.00 0.00 3.16
1079 1166 3.878778 CTTCTATTGGACCTGGAGTTGG 58.121 50.000 0.00 0.00 0.00 3.77
1080 1167 2.915869 TCTATTGGACCTGGAGTTGGT 58.084 47.619 0.00 0.00 41.07 3.67
1087 1174 3.329300 CCTGGAGTTGGTCAAGGTG 57.671 57.895 0.00 0.00 41.29 4.00
1088 1175 0.890996 CCTGGAGTTGGTCAAGGTGC 60.891 60.000 0.00 0.00 41.29 5.01
1089 1176 0.109342 CTGGAGTTGGTCAAGGTGCT 59.891 55.000 0.00 0.00 0.00 4.40
1090 1177 0.179020 TGGAGTTGGTCAAGGTGCTG 60.179 55.000 0.00 0.00 0.00 4.41
1091 1178 1.518903 GGAGTTGGTCAAGGTGCTGC 61.519 60.000 0.00 0.00 0.00 5.25
1092 1179 0.536006 GAGTTGGTCAAGGTGCTGCT 60.536 55.000 0.00 0.00 0.00 4.24
1093 1180 0.820891 AGTTGGTCAAGGTGCTGCTG 60.821 55.000 0.00 0.00 0.00 4.41
1094 1181 2.195567 TTGGTCAAGGTGCTGCTGC 61.196 57.895 8.89 8.89 40.20 5.25
1103 1190 2.981909 TGCTGCTGCAGGACAAGC 60.982 61.111 29.05 16.04 45.31 4.01
1104 1191 2.672307 GCTGCTGCAGGACAAGCT 60.672 61.111 29.05 0.00 39.41 3.74
1105 1192 2.979197 GCTGCTGCAGGACAAGCTG 61.979 63.158 29.05 5.87 39.41 4.24
1106 1193 1.600076 CTGCTGCAGGACAAGCTGT 60.600 57.895 21.71 0.00 34.00 4.40
1107 1194 0.321034 CTGCTGCAGGACAAGCTGTA 60.321 55.000 21.71 0.00 34.00 2.74
1108 1195 0.321034 TGCTGCAGGACAAGCTGTAG 60.321 55.000 17.12 0.00 36.58 2.74
1109 1196 0.036952 GCTGCAGGACAAGCTGTAGA 60.037 55.000 17.12 0.00 35.75 2.59
1110 1197 1.609061 GCTGCAGGACAAGCTGTAGAA 60.609 52.381 17.12 0.00 35.75 2.10
1111 1198 2.344950 CTGCAGGACAAGCTGTAGAAG 58.655 52.381 5.57 0.00 35.75 2.85
1112 1199 1.002430 TGCAGGACAAGCTGTAGAAGG 59.998 52.381 0.00 0.00 0.00 3.46
1113 1200 1.002544 GCAGGACAAGCTGTAGAAGGT 59.997 52.381 0.00 0.00 38.63 3.50
1114 1201 2.233922 GCAGGACAAGCTGTAGAAGGTA 59.766 50.000 0.00 0.00 34.84 3.08
1115 1202 3.118592 GCAGGACAAGCTGTAGAAGGTAT 60.119 47.826 0.00 0.00 34.84 2.73
1116 1203 4.624125 GCAGGACAAGCTGTAGAAGGTATT 60.624 45.833 0.00 0.00 34.84 1.89
1117 1204 4.872691 CAGGACAAGCTGTAGAAGGTATTG 59.127 45.833 0.00 0.00 34.84 1.90
1118 1205 3.623510 GGACAAGCTGTAGAAGGTATTGC 59.376 47.826 0.00 0.00 34.84 3.56
1119 1206 3.262420 ACAAGCTGTAGAAGGTATTGCG 58.738 45.455 0.00 0.00 34.84 4.85
1120 1207 3.056107 ACAAGCTGTAGAAGGTATTGCGA 60.056 43.478 0.00 0.00 34.84 5.10
1121 1208 3.444703 AGCTGTAGAAGGTATTGCGAG 57.555 47.619 0.00 0.00 33.90 5.03
1122 1209 3.024547 AGCTGTAGAAGGTATTGCGAGA 58.975 45.455 0.00 0.00 33.90 4.04
1123 1210 3.117046 GCTGTAGAAGGTATTGCGAGAC 58.883 50.000 0.00 0.00 0.00 3.36
1124 1211 3.428999 GCTGTAGAAGGTATTGCGAGACA 60.429 47.826 0.29 0.00 0.00 3.41
1125 1212 4.355437 CTGTAGAAGGTATTGCGAGACAG 58.645 47.826 0.29 0.00 0.00 3.51
1126 1213 2.301577 AGAAGGTATTGCGAGACAGC 57.698 50.000 0.29 0.00 37.71 4.40
1127 1214 1.134670 AGAAGGTATTGCGAGACAGCC 60.135 52.381 0.29 0.00 36.02 4.85
1128 1215 0.613260 AAGGTATTGCGAGACAGCCA 59.387 50.000 0.29 0.00 36.02 4.75
1129 1216 0.176680 AGGTATTGCGAGACAGCCAG 59.823 55.000 0.29 0.00 36.02 4.85
1130 1217 0.175760 GGTATTGCGAGACAGCCAGA 59.824 55.000 0.29 0.00 36.02 3.86
1131 1218 1.405526 GGTATTGCGAGACAGCCAGAA 60.406 52.381 0.29 0.00 36.02 3.02
1132 1219 1.929836 GTATTGCGAGACAGCCAGAAG 59.070 52.381 0.00 0.00 36.02 2.85
1133 1220 1.023513 ATTGCGAGACAGCCAGAAGC 61.024 55.000 0.00 0.00 44.25 3.86
1147 1234 5.236655 GCCAGAAGCAGAAGGTAAAATAC 57.763 43.478 0.00 0.00 42.97 1.89
1148 1235 4.201822 GCCAGAAGCAGAAGGTAAAATACG 60.202 45.833 0.00 0.00 42.97 3.06
1149 1236 5.175859 CCAGAAGCAGAAGGTAAAATACGA 58.824 41.667 0.00 0.00 0.00 3.43
1150 1237 5.292101 CCAGAAGCAGAAGGTAAAATACGAG 59.708 44.000 0.00 0.00 0.00 4.18
1151 1238 5.292101 CAGAAGCAGAAGGTAAAATACGAGG 59.708 44.000 0.00 0.00 0.00 4.63
1152 1239 4.820894 AGCAGAAGGTAAAATACGAGGT 57.179 40.909 0.00 0.00 0.00 3.85
1153 1240 5.927281 AGCAGAAGGTAAAATACGAGGTA 57.073 39.130 0.00 0.00 0.00 3.08
1154 1241 5.658468 AGCAGAAGGTAAAATACGAGGTAC 58.342 41.667 0.00 0.00 0.00 3.34
1156 1243 6.070938 AGCAGAAGGTAAAATACGAGGTACTT 60.071 38.462 0.00 0.00 41.55 2.24
1157 1244 6.592994 GCAGAAGGTAAAATACGAGGTACTTT 59.407 38.462 0.00 0.00 41.55 2.66
1158 1245 7.761249 GCAGAAGGTAAAATACGAGGTACTTTA 59.239 37.037 0.00 0.00 41.55 1.85
1159 1246 9.813446 CAGAAGGTAAAATACGAGGTACTTTAT 57.187 33.333 0.00 0.00 41.55 1.40
1162 1249 8.429493 AGGTAAAATACGAGGTACTTTATTGC 57.571 34.615 0.00 0.00 41.55 3.56
1163 1250 8.262933 AGGTAAAATACGAGGTACTTTATTGCT 58.737 33.333 0.00 0.00 41.55 3.91
1164 1251 8.886719 GGTAAAATACGAGGTACTTTATTGCTT 58.113 33.333 0.00 0.00 41.55 3.91
1167 1254 9.662947 AAAATACGAGGTACTTTATTGCTTAGT 57.337 29.630 0.00 0.00 41.55 2.24
1168 1255 8.868635 AATACGAGGTACTTTATTGCTTAGTC 57.131 34.615 0.00 0.00 41.55 2.59
1169 1256 6.527057 ACGAGGTACTTTATTGCTTAGTCT 57.473 37.500 0.00 0.00 41.55 3.24
1170 1257 7.636150 ACGAGGTACTTTATTGCTTAGTCTA 57.364 36.000 0.00 0.00 41.55 2.59
1171 1258 7.705214 ACGAGGTACTTTATTGCTTAGTCTAG 58.295 38.462 0.00 0.00 41.55 2.43
1172 1259 6.637658 CGAGGTACTTTATTGCTTAGTCTAGC 59.362 42.308 0.00 0.00 41.55 3.42
1173 1260 7.468906 CGAGGTACTTTATTGCTTAGTCTAGCT 60.469 40.741 0.00 0.00 41.55 3.32
1174 1261 8.080363 AGGTACTTTATTGCTTAGTCTAGCTT 57.920 34.615 0.00 0.00 37.47 3.74
1175 1262 8.541234 AGGTACTTTATTGCTTAGTCTAGCTTT 58.459 33.333 0.00 0.00 37.47 3.51
1176 1263 9.163899 GGTACTTTATTGCTTAGTCTAGCTTTT 57.836 33.333 0.00 0.00 41.76 2.27
1181 1268 9.899661 TTTATTGCTTAGTCTAGCTTTTATGGA 57.100 29.630 0.00 0.00 41.76 3.41
1182 1269 9.899661 TTATTGCTTAGTCTAGCTTTTATGGAA 57.100 29.630 0.00 0.00 41.76 3.53
1183 1270 7.849804 TTGCTTAGTCTAGCTTTTATGGAAG 57.150 36.000 0.00 0.00 41.76 3.46
1202 1289 7.775053 TGGAAGCTTTAACAATTTATGGACT 57.225 32.000 0.00 0.00 0.00 3.85
1203 1290 8.871629 TGGAAGCTTTAACAATTTATGGACTA 57.128 30.769 0.00 0.00 0.00 2.59
1204 1291 8.956426 TGGAAGCTTTAACAATTTATGGACTAG 58.044 33.333 0.00 0.00 0.00 2.57
1205 1292 8.957466 GGAAGCTTTAACAATTTATGGACTAGT 58.043 33.333 0.00 0.00 0.00 2.57
1208 1295 9.297037 AGCTTTAACAATTTATGGACTAGTTGT 57.703 29.630 0.00 0.00 0.00 3.32
1209 1296 9.341899 GCTTTAACAATTTATGGACTAGTTGTG 57.658 33.333 0.00 0.00 30.96 3.33
1210 1297 9.840427 CTTTAACAATTTATGGACTAGTTGTGG 57.160 33.333 0.00 0.00 30.96 4.17
1211 1298 5.897377 ACAATTTATGGACTAGTTGTGGC 57.103 39.130 0.00 0.00 0.00 5.01
1212 1299 5.321102 ACAATTTATGGACTAGTTGTGGCA 58.679 37.500 0.00 0.00 0.00 4.92
1213 1300 5.183140 ACAATTTATGGACTAGTTGTGGCAC 59.817 40.000 11.55 11.55 0.00 5.01
1214 1301 4.634012 TTTATGGACTAGTTGTGGCACT 57.366 40.909 19.83 0.54 0.00 4.40
1215 1302 5.748670 TTTATGGACTAGTTGTGGCACTA 57.251 39.130 19.83 8.69 0.00 2.74
1219 1306 2.373938 CTAGTTGTGGCACTAGCGC 58.626 57.895 19.83 0.00 39.86 5.92
1220 1307 0.108615 CTAGTTGTGGCACTAGCGCT 60.109 55.000 17.26 17.26 39.86 5.92
1221 1308 0.320374 TAGTTGTGGCACTAGCGCTT 59.680 50.000 18.68 0.00 43.41 4.68
1222 1309 0.535102 AGTTGTGGCACTAGCGCTTT 60.535 50.000 18.68 0.00 43.41 3.51
1223 1310 0.310854 GTTGTGGCACTAGCGCTTTT 59.689 50.000 18.68 0.00 43.41 2.27
1224 1311 1.533731 GTTGTGGCACTAGCGCTTTTA 59.466 47.619 18.68 0.00 43.41 1.52
1225 1312 2.107950 TGTGGCACTAGCGCTTTTAT 57.892 45.000 18.68 0.00 43.41 1.40
1226 1313 2.432444 TGTGGCACTAGCGCTTTTATT 58.568 42.857 18.68 0.00 43.41 1.40
1227 1314 2.817258 TGTGGCACTAGCGCTTTTATTT 59.183 40.909 18.68 0.00 43.41 1.40
1228 1315 3.171277 GTGGCACTAGCGCTTTTATTTG 58.829 45.455 18.68 5.22 43.41 2.32
1229 1316 3.078097 TGGCACTAGCGCTTTTATTTGA 58.922 40.909 18.68 0.00 43.41 2.69
1230 1317 3.126858 TGGCACTAGCGCTTTTATTTGAG 59.873 43.478 18.68 6.63 43.41 3.02
1231 1318 3.374058 GGCACTAGCGCTTTTATTTGAGA 59.626 43.478 18.68 0.00 43.41 3.27
1232 1319 4.142687 GGCACTAGCGCTTTTATTTGAGAA 60.143 41.667 18.68 0.00 43.41 2.87
1233 1320 4.788609 GCACTAGCGCTTTTATTTGAGAAC 59.211 41.667 18.68 0.00 0.00 3.01
1234 1321 5.324697 CACTAGCGCTTTTATTTGAGAACC 58.675 41.667 18.68 0.00 0.00 3.62
1235 1322 3.850122 AGCGCTTTTATTTGAGAACCC 57.150 42.857 2.64 0.00 0.00 4.11
1236 1323 3.421844 AGCGCTTTTATTTGAGAACCCT 58.578 40.909 2.64 0.00 0.00 4.34
1237 1324 3.826729 AGCGCTTTTATTTGAGAACCCTT 59.173 39.130 2.64 0.00 0.00 3.95
1238 1325 4.280929 AGCGCTTTTATTTGAGAACCCTTT 59.719 37.500 2.64 0.00 0.00 3.11
1239 1326 4.988540 GCGCTTTTATTTGAGAACCCTTTT 59.011 37.500 0.00 0.00 0.00 2.27
1240 1327 5.107491 GCGCTTTTATTTGAGAACCCTTTTG 60.107 40.000 0.00 0.00 0.00 2.44
1241 1328 5.983118 CGCTTTTATTTGAGAACCCTTTTGT 59.017 36.000 0.00 0.00 0.00 2.83
1242 1329 6.478673 CGCTTTTATTTGAGAACCCTTTTGTT 59.521 34.615 0.00 0.00 0.00 2.83
1243 1330 7.011016 CGCTTTTATTTGAGAACCCTTTTGTTT 59.989 33.333 0.00 0.00 0.00 2.83
1244 1331 9.320352 GCTTTTATTTGAGAACCCTTTTGTTTA 57.680 29.630 0.00 0.00 0.00 2.01
1315 1402 8.973835 TTTTAGTAAATTGGTATTTGCTTCCG 57.026 30.769 6.55 0.00 41.92 4.30
1316 1403 4.993905 AGTAAATTGGTATTTGCTTCCGC 58.006 39.130 0.00 0.00 41.92 5.54
1317 1404 3.951775 AAATTGGTATTTGCTTCCGCA 57.048 38.095 0.00 0.00 46.24 5.69
1440 1547 6.206634 TCCACCTCAATAAATTCCGCATAATC 59.793 38.462 0.00 0.00 0.00 1.75
1545 1653 0.976641 TACCCACAGCAAGGAGACTG 59.023 55.000 0.00 0.00 42.68 3.51
1575 1683 1.208293 AGGAGGAAGAAAGCTAAGCGG 59.792 52.381 0.00 0.00 0.00 5.52
1713 1894 5.317733 TCTCTTTCGTCCTTTCTCATCTC 57.682 43.478 0.00 0.00 0.00 2.75
1783 1991 6.295688 GGTTAGACATAGTTTCCTTGGAGACA 60.296 42.308 12.01 0.53 39.83 3.41
1827 2040 6.689561 TCCCTAGATACCTCTTATGTTCCAA 58.310 40.000 0.00 0.00 32.66 3.53
1856 2069 2.030946 CCATCTGTTTACAGCTAAGCGC 59.969 50.000 0.00 0.00 43.46 5.92
2018 2232 2.747855 GCGCCAGGTTAGCAGCTT 60.748 61.111 0.00 0.00 0.00 3.74
2020 2234 1.078848 CGCCAGGTTAGCAGCTTCT 60.079 57.895 0.00 0.00 0.00 2.85
2039 2253 7.440556 CAGCTTCTCATATTACAACTACATGCT 59.559 37.037 0.00 0.00 0.00 3.79
2050 2264 3.430565 TACATGCTGCTCCGCTCCG 62.431 63.158 0.00 0.00 0.00 4.63
2139 2354 1.051008 TGAGCAAAGACCAGAGAGCA 58.949 50.000 0.00 0.00 0.00 4.26
2197 2412 1.922135 GCTTTGGCTTTCGCATCGGA 61.922 55.000 0.00 0.00 38.10 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 129 5.733676 TGTACTGTTGTGTGATATGCATCT 58.266 37.500 0.19 0.00 31.93 2.90
113 155 3.838244 TGTCAGACAAACAGTTAGGCT 57.162 42.857 0.00 0.00 0.00 4.58
979 1066 1.884579 GGTGAGTAGTTCCTCGTGTCA 59.115 52.381 0.00 0.00 34.04 3.58
980 1067 1.884579 TGGTGAGTAGTTCCTCGTGTC 59.115 52.381 0.00 0.00 34.04 3.67
981 1068 1.991121 TGGTGAGTAGTTCCTCGTGT 58.009 50.000 0.00 0.00 34.04 4.49
982 1069 2.492088 TCATGGTGAGTAGTTCCTCGTG 59.508 50.000 0.00 0.00 34.04 4.35
983 1070 2.803956 TCATGGTGAGTAGTTCCTCGT 58.196 47.619 0.00 0.00 34.04 4.18
984 1071 3.868757 TTCATGGTGAGTAGTTCCTCG 57.131 47.619 0.00 0.00 34.04 4.63
985 1072 4.162320 TGGATTCATGGTGAGTAGTTCCTC 59.838 45.833 0.00 0.00 0.00 3.71
986 1073 4.080863 GTGGATTCATGGTGAGTAGTTCCT 60.081 45.833 0.00 0.00 0.00 3.36
987 1074 4.080863 AGTGGATTCATGGTGAGTAGTTCC 60.081 45.833 0.00 0.00 0.00 3.62
988 1075 5.091261 AGTGGATTCATGGTGAGTAGTTC 57.909 43.478 0.00 0.00 0.00 3.01
989 1076 6.620877 TTAGTGGATTCATGGTGAGTAGTT 57.379 37.500 0.00 0.00 0.00 2.24
990 1077 6.814954 ATTAGTGGATTCATGGTGAGTAGT 57.185 37.500 0.00 0.00 0.00 2.73
991 1078 7.050377 ACAATTAGTGGATTCATGGTGAGTAG 58.950 38.462 0.00 0.00 0.00 2.57
992 1079 6.957631 ACAATTAGTGGATTCATGGTGAGTA 58.042 36.000 0.00 0.00 0.00 2.59
993 1080 5.819991 ACAATTAGTGGATTCATGGTGAGT 58.180 37.500 0.00 0.00 0.00 3.41
994 1081 6.764308 AACAATTAGTGGATTCATGGTGAG 57.236 37.500 0.00 0.00 0.00 3.51
995 1082 6.947733 AGAAACAATTAGTGGATTCATGGTGA 59.052 34.615 0.00 0.00 32.45 4.02
996 1083 7.031372 CAGAAACAATTAGTGGATTCATGGTG 58.969 38.462 0.00 0.00 32.45 4.17
997 1084 6.350445 GCAGAAACAATTAGTGGATTCATGGT 60.350 38.462 0.00 0.00 32.45 3.55
998 1085 6.038356 GCAGAAACAATTAGTGGATTCATGG 58.962 40.000 0.00 0.00 32.45 3.66
999 1086 6.860080 AGCAGAAACAATTAGTGGATTCATG 58.140 36.000 4.04 0.00 32.45 3.07
1000 1087 7.395489 AGAAGCAGAAACAATTAGTGGATTCAT 59.605 33.333 0.00 0.00 32.45 2.57
1001 1088 6.716628 AGAAGCAGAAACAATTAGTGGATTCA 59.283 34.615 0.00 0.00 32.45 2.57
1002 1089 7.025963 CAGAAGCAGAAACAATTAGTGGATTC 58.974 38.462 0.00 0.00 0.00 2.52
1003 1090 6.491403 ACAGAAGCAGAAACAATTAGTGGATT 59.509 34.615 0.00 0.00 0.00 3.01
1004 1091 6.006449 ACAGAAGCAGAAACAATTAGTGGAT 58.994 36.000 0.00 0.00 0.00 3.41
1005 1092 5.376625 ACAGAAGCAGAAACAATTAGTGGA 58.623 37.500 0.00 0.00 0.00 4.02
1006 1093 5.695851 ACAGAAGCAGAAACAATTAGTGG 57.304 39.130 0.00 0.00 0.00 4.00
1007 1094 9.121517 CAATAACAGAAGCAGAAACAATTAGTG 57.878 33.333 0.00 0.00 0.00 2.74
1008 1095 7.809806 GCAATAACAGAAGCAGAAACAATTAGT 59.190 33.333 0.00 0.00 0.00 2.24
1009 1096 8.025445 AGCAATAACAGAAGCAGAAACAATTAG 58.975 33.333 0.00 0.00 0.00 1.73
1010 1097 7.809331 CAGCAATAACAGAAGCAGAAACAATTA 59.191 33.333 0.00 0.00 0.00 1.40
1011 1098 6.643770 CAGCAATAACAGAAGCAGAAACAATT 59.356 34.615 0.00 0.00 0.00 2.32
1012 1099 6.154445 CAGCAATAACAGAAGCAGAAACAAT 58.846 36.000 0.00 0.00 0.00 2.71
1013 1100 5.522456 CAGCAATAACAGAAGCAGAAACAA 58.478 37.500 0.00 0.00 0.00 2.83
1014 1101 4.557296 GCAGCAATAACAGAAGCAGAAACA 60.557 41.667 0.00 0.00 0.00 2.83
1015 1102 3.916776 GCAGCAATAACAGAAGCAGAAAC 59.083 43.478 0.00 0.00 0.00 2.78
1016 1103 3.822735 AGCAGCAATAACAGAAGCAGAAA 59.177 39.130 0.00 0.00 0.00 2.52
1017 1104 3.189910 CAGCAGCAATAACAGAAGCAGAA 59.810 43.478 0.00 0.00 0.00 3.02
1018 1105 2.745821 CAGCAGCAATAACAGAAGCAGA 59.254 45.455 0.00 0.00 0.00 4.26
1019 1106 2.745821 TCAGCAGCAATAACAGAAGCAG 59.254 45.455 0.00 0.00 0.00 4.24
1020 1107 2.781923 TCAGCAGCAATAACAGAAGCA 58.218 42.857 0.00 0.00 0.00 3.91
1021 1108 3.837213 TTCAGCAGCAATAACAGAAGC 57.163 42.857 0.00 0.00 0.00 3.86
1022 1109 5.100259 CCAATTCAGCAGCAATAACAGAAG 58.900 41.667 0.00 0.00 0.00 2.85
1023 1110 4.618927 GCCAATTCAGCAGCAATAACAGAA 60.619 41.667 0.00 0.00 0.00 3.02
1024 1111 3.119388 GCCAATTCAGCAGCAATAACAGA 60.119 43.478 0.00 0.00 0.00 3.41
1025 1112 3.184541 GCCAATTCAGCAGCAATAACAG 58.815 45.455 0.00 0.00 0.00 3.16
1026 1113 2.094078 GGCCAATTCAGCAGCAATAACA 60.094 45.455 0.00 0.00 0.00 2.41
1027 1114 2.543641 GGCCAATTCAGCAGCAATAAC 58.456 47.619 0.00 0.00 0.00 1.89
1028 1115 1.134753 CGGCCAATTCAGCAGCAATAA 59.865 47.619 2.24 0.00 0.00 1.40
1029 1116 0.740149 CGGCCAATTCAGCAGCAATA 59.260 50.000 2.24 0.00 0.00 1.90
1030 1117 1.252904 ACGGCCAATTCAGCAGCAAT 61.253 50.000 2.24 0.00 0.00 3.56
1031 1118 0.607762 TACGGCCAATTCAGCAGCAA 60.608 50.000 2.24 0.00 0.00 3.91
1032 1119 1.002746 TACGGCCAATTCAGCAGCA 60.003 52.632 2.24 0.00 0.00 4.41
1033 1120 1.718757 CCTACGGCCAATTCAGCAGC 61.719 60.000 2.24 0.00 0.00 5.25
1034 1121 1.097547 CCCTACGGCCAATTCAGCAG 61.098 60.000 2.24 0.00 0.00 4.24
1035 1122 1.077787 CCCTACGGCCAATTCAGCA 60.078 57.895 2.24 0.00 0.00 4.41
1036 1123 3.827634 CCCTACGGCCAATTCAGC 58.172 61.111 2.24 0.00 0.00 4.26
1046 1133 2.213499 CAATAGAAGCAAGCCCTACGG 58.787 52.381 0.00 0.00 0.00 4.02
1047 1134 2.158957 TCCAATAGAAGCAAGCCCTACG 60.159 50.000 0.00 0.00 0.00 3.51
1048 1135 3.206964 GTCCAATAGAAGCAAGCCCTAC 58.793 50.000 0.00 0.00 0.00 3.18
1049 1136 2.172717 GGTCCAATAGAAGCAAGCCCTA 59.827 50.000 0.00 0.00 0.00 3.53
1050 1137 1.064389 GGTCCAATAGAAGCAAGCCCT 60.064 52.381 0.00 0.00 0.00 5.19
1051 1138 1.064389 AGGTCCAATAGAAGCAAGCCC 60.064 52.381 0.00 0.00 0.00 5.19
1052 1139 2.019984 CAGGTCCAATAGAAGCAAGCC 58.980 52.381 0.00 0.00 0.00 4.35
1053 1140 2.019984 CCAGGTCCAATAGAAGCAAGC 58.980 52.381 0.00 0.00 0.00 4.01
1054 1141 3.054802 ACTCCAGGTCCAATAGAAGCAAG 60.055 47.826 0.00 0.00 0.00 4.01
1055 1142 2.912956 ACTCCAGGTCCAATAGAAGCAA 59.087 45.455 0.00 0.00 0.00 3.91
1056 1143 2.551270 ACTCCAGGTCCAATAGAAGCA 58.449 47.619 0.00 0.00 0.00 3.91
1057 1144 3.274288 CAACTCCAGGTCCAATAGAAGC 58.726 50.000 0.00 0.00 0.00 3.86
1058 1145 3.264450 ACCAACTCCAGGTCCAATAGAAG 59.736 47.826 0.00 0.00 32.90 2.85
1059 1146 3.256704 ACCAACTCCAGGTCCAATAGAA 58.743 45.455 0.00 0.00 32.90 2.10
1060 1147 2.915869 ACCAACTCCAGGTCCAATAGA 58.084 47.619 0.00 0.00 32.90 1.98
1068 1155 0.474184 CACCTTGACCAACTCCAGGT 59.526 55.000 0.00 0.00 43.46 4.00
1069 1156 0.890996 GCACCTTGACCAACTCCAGG 60.891 60.000 0.00 0.00 0.00 4.45
1070 1157 0.109342 AGCACCTTGACCAACTCCAG 59.891 55.000 0.00 0.00 0.00 3.86
1071 1158 0.179020 CAGCACCTTGACCAACTCCA 60.179 55.000 0.00 0.00 0.00 3.86
1072 1159 1.518903 GCAGCACCTTGACCAACTCC 61.519 60.000 0.00 0.00 0.00 3.85
1073 1160 0.536006 AGCAGCACCTTGACCAACTC 60.536 55.000 0.00 0.00 0.00 3.01
1074 1161 0.820891 CAGCAGCACCTTGACCAACT 60.821 55.000 0.00 0.00 0.00 3.16
1075 1162 1.656441 CAGCAGCACCTTGACCAAC 59.344 57.895 0.00 0.00 0.00 3.77
1076 1163 2.195567 GCAGCAGCACCTTGACCAA 61.196 57.895 0.00 0.00 41.58 3.67
1077 1164 2.595463 GCAGCAGCACCTTGACCA 60.595 61.111 0.00 0.00 41.58 4.02
1087 1174 2.672307 AGCTTGTCCTGCAGCAGC 60.672 61.111 17.81 12.31 42.57 5.25
1088 1175 0.321034 TACAGCTTGTCCTGCAGCAG 60.321 55.000 16.23 16.23 36.29 4.24
1089 1176 0.321034 CTACAGCTTGTCCTGCAGCA 60.321 55.000 8.66 0.00 36.29 4.41
1090 1177 0.036952 TCTACAGCTTGTCCTGCAGC 60.037 55.000 8.66 0.00 36.29 5.25
1091 1178 2.344950 CTTCTACAGCTTGTCCTGCAG 58.655 52.381 6.78 6.78 36.29 4.41
1092 1179 1.002430 CCTTCTACAGCTTGTCCTGCA 59.998 52.381 0.00 0.00 36.29 4.41
1093 1180 1.002544 ACCTTCTACAGCTTGTCCTGC 59.997 52.381 0.00 0.00 36.29 4.85
1094 1181 4.744795 ATACCTTCTACAGCTTGTCCTG 57.255 45.455 0.00 0.00 38.78 3.86
1095 1182 4.624125 GCAATACCTTCTACAGCTTGTCCT 60.624 45.833 0.00 0.00 0.00 3.85
1096 1183 3.623510 GCAATACCTTCTACAGCTTGTCC 59.376 47.826 0.00 0.00 0.00 4.02
1097 1184 3.307242 CGCAATACCTTCTACAGCTTGTC 59.693 47.826 0.00 0.00 0.00 3.18
1098 1185 3.056107 TCGCAATACCTTCTACAGCTTGT 60.056 43.478 0.00 0.00 0.00 3.16
1099 1186 3.521560 TCGCAATACCTTCTACAGCTTG 58.478 45.455 0.00 0.00 0.00 4.01
1100 1187 3.447586 TCTCGCAATACCTTCTACAGCTT 59.552 43.478 0.00 0.00 0.00 3.74
1101 1188 3.024547 TCTCGCAATACCTTCTACAGCT 58.975 45.455 0.00 0.00 0.00 4.24
1102 1189 3.117046 GTCTCGCAATACCTTCTACAGC 58.883 50.000 0.00 0.00 0.00 4.40
1103 1190 4.355437 CTGTCTCGCAATACCTTCTACAG 58.645 47.826 0.00 0.00 0.00 2.74
1104 1191 3.428999 GCTGTCTCGCAATACCTTCTACA 60.429 47.826 0.00 0.00 0.00 2.74
1105 1192 3.117046 GCTGTCTCGCAATACCTTCTAC 58.883 50.000 0.00 0.00 0.00 2.59
1106 1193 2.100916 GGCTGTCTCGCAATACCTTCTA 59.899 50.000 0.00 0.00 0.00 2.10
1107 1194 1.134670 GGCTGTCTCGCAATACCTTCT 60.135 52.381 0.00 0.00 0.00 2.85
1108 1195 1.291132 GGCTGTCTCGCAATACCTTC 58.709 55.000 0.00 0.00 0.00 3.46
1109 1196 0.613260 TGGCTGTCTCGCAATACCTT 59.387 50.000 0.00 0.00 0.00 3.50
1110 1197 0.176680 CTGGCTGTCTCGCAATACCT 59.823 55.000 0.00 0.00 0.00 3.08
1111 1198 0.175760 TCTGGCTGTCTCGCAATACC 59.824 55.000 0.00 0.00 0.00 2.73
1112 1199 1.929836 CTTCTGGCTGTCTCGCAATAC 59.070 52.381 0.00 0.00 0.00 1.89
1113 1200 1.740380 GCTTCTGGCTGTCTCGCAATA 60.740 52.381 0.00 0.00 38.06 1.90
1114 1201 1.023513 GCTTCTGGCTGTCTCGCAAT 61.024 55.000 0.00 0.00 38.06 3.56
1115 1202 1.669115 GCTTCTGGCTGTCTCGCAA 60.669 57.895 0.00 0.00 38.06 4.85
1116 1203 2.047844 GCTTCTGGCTGTCTCGCA 60.048 61.111 0.00 0.00 38.06 5.10
1117 1204 2.047844 TGCTTCTGGCTGTCTCGC 60.048 61.111 0.00 0.00 42.39 5.03
1118 1205 0.037882 TTCTGCTTCTGGCTGTCTCG 60.038 55.000 0.00 0.00 42.39 4.04
1119 1206 1.675415 CCTTCTGCTTCTGGCTGTCTC 60.675 57.143 0.00 0.00 42.39 3.36
1120 1207 0.324285 CCTTCTGCTTCTGGCTGTCT 59.676 55.000 0.00 0.00 42.39 3.41
1121 1208 0.036022 ACCTTCTGCTTCTGGCTGTC 59.964 55.000 0.00 0.00 42.39 3.51
1122 1209 1.352083 TACCTTCTGCTTCTGGCTGT 58.648 50.000 0.00 0.00 42.39 4.40
1123 1210 2.479566 TTACCTTCTGCTTCTGGCTG 57.520 50.000 0.00 0.00 42.39 4.85
1124 1211 3.508845 TTTTACCTTCTGCTTCTGGCT 57.491 42.857 0.00 0.00 42.39 4.75
1125 1212 4.201822 CGTATTTTACCTTCTGCTTCTGGC 60.202 45.833 0.00 0.00 42.22 4.85
1126 1213 5.175859 TCGTATTTTACCTTCTGCTTCTGG 58.824 41.667 0.00 0.00 0.00 3.86
1127 1214 5.292101 CCTCGTATTTTACCTTCTGCTTCTG 59.708 44.000 0.00 0.00 0.00 3.02
1128 1215 5.046520 ACCTCGTATTTTACCTTCTGCTTCT 60.047 40.000 0.00 0.00 0.00 2.85
1129 1216 5.176592 ACCTCGTATTTTACCTTCTGCTTC 58.823 41.667 0.00 0.00 0.00 3.86
1130 1217 5.161943 ACCTCGTATTTTACCTTCTGCTT 57.838 39.130 0.00 0.00 0.00 3.91
1131 1218 4.820894 ACCTCGTATTTTACCTTCTGCT 57.179 40.909 0.00 0.00 0.00 4.24
1132 1219 5.658468 AGTACCTCGTATTTTACCTTCTGC 58.342 41.667 0.00 0.00 0.00 4.26
1133 1220 9.813446 ATAAAGTACCTCGTATTTTACCTTCTG 57.187 33.333 2.74 0.00 34.66 3.02
1136 1223 8.886719 GCAATAAAGTACCTCGTATTTTACCTT 58.113 33.333 2.74 0.00 34.66 3.50
1137 1224 8.262933 AGCAATAAAGTACCTCGTATTTTACCT 58.737 33.333 2.74 0.00 34.66 3.08
1138 1225 8.429493 AGCAATAAAGTACCTCGTATTTTACC 57.571 34.615 2.74 0.00 34.66 2.85
1141 1228 9.662947 ACTAAGCAATAAAGTACCTCGTATTTT 57.337 29.630 0.00 0.00 33.68 1.82
1142 1229 9.310716 GACTAAGCAATAAAGTACCTCGTATTT 57.689 33.333 0.00 0.00 0.00 1.40
1143 1230 8.693625 AGACTAAGCAATAAAGTACCTCGTATT 58.306 33.333 0.00 0.00 0.00 1.89
1144 1231 8.235359 AGACTAAGCAATAAAGTACCTCGTAT 57.765 34.615 0.00 0.00 0.00 3.06
1145 1232 7.636150 AGACTAAGCAATAAAGTACCTCGTA 57.364 36.000 0.00 0.00 0.00 3.43
1146 1233 6.527057 AGACTAAGCAATAAAGTACCTCGT 57.473 37.500 0.00 0.00 0.00 4.18
1147 1234 6.637658 GCTAGACTAAGCAATAAAGTACCTCG 59.362 42.308 0.00 0.00 42.30 4.63
1148 1235 7.718525 AGCTAGACTAAGCAATAAAGTACCTC 58.281 38.462 0.00 0.00 45.30 3.85
1149 1236 7.663043 AGCTAGACTAAGCAATAAAGTACCT 57.337 36.000 0.00 0.00 45.30 3.08
1150 1237 8.719560 AAAGCTAGACTAAGCAATAAAGTACC 57.280 34.615 0.00 0.00 45.30 3.34
1155 1242 9.899661 TCCATAAAAGCTAGACTAAGCAATAAA 57.100 29.630 0.00 0.00 45.30 1.40
1156 1243 9.899661 TTCCATAAAAGCTAGACTAAGCAATAA 57.100 29.630 0.00 0.00 45.30 1.40
1157 1244 9.547753 CTTCCATAAAAGCTAGACTAAGCAATA 57.452 33.333 0.00 0.00 45.30 1.90
1158 1245 7.012799 GCTTCCATAAAAGCTAGACTAAGCAAT 59.987 37.037 0.00 0.00 46.51 3.56
1159 1246 6.316390 GCTTCCATAAAAGCTAGACTAAGCAA 59.684 38.462 0.00 0.00 46.51 3.91
1160 1247 5.817816 GCTTCCATAAAAGCTAGACTAAGCA 59.182 40.000 0.00 0.00 46.51 3.91
1161 1248 6.293713 GCTTCCATAAAAGCTAGACTAAGC 57.706 41.667 0.00 0.00 46.51 3.09
1176 1263 9.474313 AGTCCATAAATTGTTAAAGCTTCCATA 57.526 29.630 0.00 0.00 0.00 2.74
1177 1264 8.366359 AGTCCATAAATTGTTAAAGCTTCCAT 57.634 30.769 0.00 0.00 0.00 3.41
1178 1265 7.775053 AGTCCATAAATTGTTAAAGCTTCCA 57.225 32.000 0.00 0.00 0.00 3.53
1179 1266 8.957466 ACTAGTCCATAAATTGTTAAAGCTTCC 58.043 33.333 0.00 0.00 0.00 3.46
1182 1269 9.297037 ACAACTAGTCCATAAATTGTTAAAGCT 57.703 29.630 0.00 0.00 0.00 3.74
1183 1270 9.341899 CACAACTAGTCCATAAATTGTTAAAGC 57.658 33.333 0.00 0.00 0.00 3.51
1184 1271 9.840427 CCACAACTAGTCCATAAATTGTTAAAG 57.160 33.333 0.00 0.00 0.00 1.85
1185 1272 8.301002 GCCACAACTAGTCCATAAATTGTTAAA 58.699 33.333 0.00 0.00 0.00 1.52
1186 1273 7.448777 TGCCACAACTAGTCCATAAATTGTTAA 59.551 33.333 0.00 0.00 0.00 2.01
1187 1274 6.943146 TGCCACAACTAGTCCATAAATTGTTA 59.057 34.615 0.00 0.00 0.00 2.41
1188 1275 5.772672 TGCCACAACTAGTCCATAAATTGTT 59.227 36.000 0.00 0.00 0.00 2.83
1189 1276 5.183140 GTGCCACAACTAGTCCATAAATTGT 59.817 40.000 0.00 0.00 0.00 2.71
1190 1277 5.415701 AGTGCCACAACTAGTCCATAAATTG 59.584 40.000 0.00 0.00 0.00 2.32
1191 1278 5.570320 AGTGCCACAACTAGTCCATAAATT 58.430 37.500 0.00 0.00 0.00 1.82
1192 1279 5.179452 AGTGCCACAACTAGTCCATAAAT 57.821 39.130 0.00 0.00 0.00 1.40
1193 1280 4.634012 AGTGCCACAACTAGTCCATAAA 57.366 40.909 0.00 0.00 0.00 1.40
1194 1281 5.339008 CTAGTGCCACAACTAGTCCATAA 57.661 43.478 0.00 0.00 43.11 1.90
1196 1283 3.895232 CTAGTGCCACAACTAGTCCAT 57.105 47.619 0.00 0.00 43.11 3.41
1202 1289 0.320374 AAGCGCTAGTGCCACAACTA 59.680 50.000 24.25 0.00 35.36 2.24
1203 1290 0.535102 AAAGCGCTAGTGCCACAACT 60.535 50.000 24.25 1.87 35.36 3.16
1204 1291 0.310854 AAAAGCGCTAGTGCCACAAC 59.689 50.000 24.25 0.00 35.36 3.32
1205 1292 1.885560 TAAAAGCGCTAGTGCCACAA 58.114 45.000 24.25 5.81 35.36 3.33
1206 1293 2.107950 ATAAAAGCGCTAGTGCCACA 57.892 45.000 24.25 8.18 35.36 4.17
1207 1294 3.119990 TCAAATAAAAGCGCTAGTGCCAC 60.120 43.478 24.25 0.00 35.36 5.01
1208 1295 3.078097 TCAAATAAAAGCGCTAGTGCCA 58.922 40.909 24.25 8.18 35.36 4.92
1209 1296 3.374058 TCTCAAATAAAAGCGCTAGTGCC 59.626 43.478 24.25 7.11 35.36 5.01
1210 1297 4.600012 TCTCAAATAAAAGCGCTAGTGC 57.400 40.909 20.73 20.73 0.00 4.40
1211 1298 5.324697 GGTTCTCAAATAAAAGCGCTAGTG 58.675 41.667 12.05 2.82 0.00 2.74
1212 1299 4.395231 GGGTTCTCAAATAAAAGCGCTAGT 59.605 41.667 12.05 3.71 0.00 2.57
1213 1300 4.636206 AGGGTTCTCAAATAAAAGCGCTAG 59.364 41.667 12.05 0.76 0.00 3.42
1214 1301 4.585879 AGGGTTCTCAAATAAAAGCGCTA 58.414 39.130 12.05 0.00 0.00 4.26
1215 1302 3.421844 AGGGTTCTCAAATAAAAGCGCT 58.578 40.909 2.64 2.64 0.00 5.92
1216 1303 3.850122 AGGGTTCTCAAATAAAAGCGC 57.150 42.857 0.00 0.00 0.00 5.92
1217 1304 5.983118 ACAAAAGGGTTCTCAAATAAAAGCG 59.017 36.000 0.00 0.00 0.00 4.68
1218 1305 7.786178 AACAAAAGGGTTCTCAAATAAAAGC 57.214 32.000 0.00 0.00 0.00 3.51
1289 1376 9.413048 CGGAAGCAAATACCAATTTACTAAAAA 57.587 29.630 0.00 0.00 33.45 1.94
1290 1377 8.973835 CGGAAGCAAATACCAATTTACTAAAA 57.026 30.769 0.00 0.00 33.45 1.52
1316 1403 0.034767 TCCAGGAGCTGCAGGAATTG 60.035 55.000 17.19 0.00 0.00 2.32
1317 1404 0.700564 TTCCAGGAGCTGCAGGAATT 59.299 50.000 25.11 0.00 35.35 2.17
1318 1405 0.034670 GTTCCAGGAGCTGCAGGAAT 60.035 55.000 29.88 0.00 41.71 3.01
1319 1406 1.130054 AGTTCCAGGAGCTGCAGGAA 61.130 55.000 25.11 25.11 37.79 3.36
1320 1407 1.537397 AGTTCCAGGAGCTGCAGGA 60.537 57.895 15.60 15.60 0.00 3.86
1321 1408 1.376942 CAGTTCCAGGAGCTGCAGG 60.377 63.158 19.49 10.65 34.48 4.85
1440 1547 5.751243 AGCTATTTACTATTTTGGTGCCG 57.249 39.130 0.00 0.00 0.00 5.69
1545 1653 1.867363 TCTTCCTCCTTGGTAGCTCC 58.133 55.000 0.00 0.00 33.77 4.70
1575 1683 0.252284 TTCACTCCCTGTCCTCTCCC 60.252 60.000 0.00 0.00 0.00 4.30
1713 1894 9.146270 CGAAAATAATCAAAAGTTGCAGTTTTG 57.854 29.630 21.75 21.75 45.28 2.44
1805 2018 7.604657 AGTTGGAACATAAGAGGTATCTAGG 57.395 40.000 0.00 0.00 39.30 3.02
1827 2040 5.631119 AGCTGTAAACAGATGGGTAAAAGT 58.369 37.500 14.21 0.00 46.59 2.66
1887 2101 4.787598 TGTCGTTTTCGGTCTCTAGTAAC 58.212 43.478 0.00 0.00 44.25 2.50
2018 2232 6.820335 AGCAGCATGTAGTTGTAATATGAGA 58.180 36.000 0.00 0.00 39.31 3.27
2020 2234 5.991606 GGAGCAGCATGTAGTTGTAATATGA 59.008 40.000 0.00 0.00 39.31 2.15
2050 2264 2.817396 GCTCTGCAACTCCGCTCC 60.817 66.667 0.00 0.00 0.00 4.70
2084 2298 3.743396 GGACCAGAGCATTATTAAGAGCG 59.257 47.826 0.00 0.00 0.00 5.03
2120 2335 1.051008 TGCTCTCTGGTCTTTGCTCA 58.949 50.000 0.00 0.00 0.00 4.26
2139 2354 3.387374 TGCATCCAGACAAAACCAACAAT 59.613 39.130 0.00 0.00 0.00 2.71
2197 2412 1.612726 GCAAAGACCAGGCAGATGACT 60.613 52.381 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.