Multiple sequence alignment - TraesCS1D01G296800

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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 TraesCS1D01G296800 chr1D 100.000 3145 0 0 1 3145 394893677 394896821 0.000000e+00 5808.0
1 TraesCS1D01G296800 chr1D 85.240 1206 77 28 809 1970 395973667 395972519 0.000000e+00 1147.0
2 TraesCS1D01G296800 chr1D 89.933 298 29 1 2148 2445 395969423 395969127 1.770000e-102 383.0
3 TraesCS1D01G296800 chr1D 83.641 379 49 12 2446 2819 41892833 41893203 8.350000e-91 344.0
4 TraesCS1D01G296800 chr1D 92.715 151 10 1 1962 2112 395969654 395969505 1.900000e-52 217.0
5 TraesCS1D01G296800 chr5D 88.624 712 50 11 2446 3143 17147047 17147741 0.000000e+00 837.0
6 TraesCS1D01G296800 chr5D 89.385 650 47 8 2514 3143 243173862 243173215 0.000000e+00 798.0
7 TraesCS1D01G296800 chr2D 86.508 756 96 6 1 752 278580672 278579919 0.000000e+00 826.0
8 TraesCS1D01G296800 chr4D 86.184 760 93 9 1 750 180216113 180216870 0.000000e+00 811.0
9 TraesCS1D01G296800 chr4D 86.005 736 96 7 1 733 245351991 245351260 0.000000e+00 782.0
10 TraesCS1D01G296800 chr3D 87.342 711 80 8 1 708 173238856 173238153 0.000000e+00 806.0
11 TraesCS1D01G296800 chr3D 85.620 758 101 8 1 753 209200200 209200954 0.000000e+00 789.0
12 TraesCS1D01G296800 chr7D 85.960 755 98 5 1 753 349521502 349522250 0.000000e+00 800.0
13 TraesCS1D01G296800 chr7D 85.927 739 94 6 6 736 305078679 305077943 0.000000e+00 780.0
14 TraesCS1D01G296800 chr6A 87.360 712 68 14 2446 3140 2686987 2687693 0.000000e+00 797.0
15 TraesCS1D01G296800 chr6A 83.493 521 60 14 2515 3031 596343711 596344209 2.210000e-126 462.0
16 TraesCS1D01G296800 chr3B 85.849 742 97 5 1 736 269137864 269138603 0.000000e+00 782.0
17 TraesCS1D01G296800 chr3B 86.350 337 32 12 2446 2771 804854768 804854435 3.860000e-94 355.0
18 TraesCS1D01G296800 chr7B 85.714 742 99 7 3 737 467418572 467419313 0.000000e+00 776.0
19 TraesCS1D01G296800 chr7B 92.857 252 18 0 2892 3143 695317891 695317640 1.780000e-97 366.0
20 TraesCS1D01G296800 chr5B 85.742 512 50 17 2446 2940 636662649 636662144 1.290000e-143 520.0
21 TraesCS1D01G296800 chr5B 81.818 407 49 16 2443 2834 378907173 378907569 5.060000e-83 318.0
22 TraesCS1D01G296800 chr2B 92.126 254 16 1 2890 3143 723343585 723343336 3.860000e-94 355.0
23 TraesCS1D01G296800 chr2B 82.908 392 51 15 2445 2823 799714478 799714866 3.890000e-89 339.0
24 TraesCS1D01G296800 chr4B 91.753 194 16 0 2891 3084 52580280 52580473 1.440000e-68 270.0
25 TraesCS1D01G296800 chr1A 83.389 301 38 12 1546 1839 482221016 482220721 5.170000e-68 268.0
26 TraesCS1D01G296800 chr1A 85.542 249 25 4 2152 2397 489286535 489286775 1.870000e-62 250.0
27 TraesCS1D01G296800 chr1A 91.447 152 13 0 2900 3051 14079443 14079292 3.180000e-50 209.0
28 TraesCS1D01G296800 chr1A 93.333 60 4 0 3084 3143 14079294 14079235 4.320000e-14 89.8
29 TraesCS1D01G296800 chr1B 84.231 260 34 5 2165 2419 526260000 526260257 2.420000e-61 246.0
30 TraesCS1D01G296800 chr7A 97.222 36 1 0 2317 2352 516153872 516153837 9.420000e-06 62.1


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 TraesCS1D01G296800 chr1D 394893677 394896821 3144 False 5808.000000 5808 100.000 1 3145 1 chr1D.!!$F2 3144
1 TraesCS1D01G296800 chr1D 395969127 395973667 4540 True 582.333333 1147 89.296 809 2445 3 chr1D.!!$R1 1636
2 TraesCS1D01G296800 chr5D 17147047 17147741 694 False 837.000000 837 88.624 2446 3143 1 chr5D.!!$F1 697
3 TraesCS1D01G296800 chr5D 243173215 243173862 647 True 798.000000 798 89.385 2514 3143 1 chr5D.!!$R1 629
4 TraesCS1D01G296800 chr2D 278579919 278580672 753 True 826.000000 826 86.508 1 752 1 chr2D.!!$R1 751
5 TraesCS1D01G296800 chr4D 180216113 180216870 757 False 811.000000 811 86.184 1 750 1 chr4D.!!$F1 749
6 TraesCS1D01G296800 chr4D 245351260 245351991 731 True 782.000000 782 86.005 1 733 1 chr4D.!!$R1 732
7 TraesCS1D01G296800 chr3D 173238153 173238856 703 True 806.000000 806 87.342 1 708 1 chr3D.!!$R1 707
8 TraesCS1D01G296800 chr3D 209200200 209200954 754 False 789.000000 789 85.620 1 753 1 chr3D.!!$F1 752
9 TraesCS1D01G296800 chr7D 349521502 349522250 748 False 800.000000 800 85.960 1 753 1 chr7D.!!$F1 752
10 TraesCS1D01G296800 chr7D 305077943 305078679 736 True 780.000000 780 85.927 6 736 1 chr7D.!!$R1 730
11 TraesCS1D01G296800 chr6A 2686987 2687693 706 False 797.000000 797 87.360 2446 3140 1 chr6A.!!$F1 694
12 TraesCS1D01G296800 chr3B 269137864 269138603 739 False 782.000000 782 85.849 1 736 1 chr3B.!!$F1 735
13 TraesCS1D01G296800 chr7B 467418572 467419313 741 False 776.000000 776 85.714 3 737 1 chr7B.!!$F1 734
14 TraesCS1D01G296800 chr5B 636662144 636662649 505 True 520.000000 520 85.742 2446 2940 1 chr5B.!!$R1 494

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
418 438 0.037419 GGAAACCACGTACGCCCTTA 60.037 55.0 16.72 0.00 0.0 2.69 F
2122 5134 0.108992 AACTCACCGCGCGAATTAGA 60.109 50.0 34.63 18.95 0.0 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2126 5138 0.035820 TTCGGGGGAAAGATTCACGG 60.036 55.0 0.00 0.0 32.51 4.94 R
2969 6017 0.323302 TGGGCGCTTGATGTAGTTCA 59.677 50.0 7.64 0.0 0.00 3.18 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
82 86 4.149346 CTCGCGAGGAGGATGAGA 57.851 61.111 28.40 0.00 39.22 3.27
144 160 2.630098 GGGAGTGAGAATGGATCGATCA 59.370 50.000 25.93 13.02 0.00 2.92
145 161 3.260380 GGGAGTGAGAATGGATCGATCAT 59.740 47.826 25.93 14.60 0.00 2.45
188 204 4.833390 CCTATACTTATAGTGGCCTTGGC 58.167 47.826 3.32 2.49 35.09 4.52
230 250 0.768622 TGGAAGGGATTCCACAACGT 59.231 50.000 5.62 0.00 45.55 3.99
304 324 0.040067 CCTGCAAAACTTCTGGTCGC 60.040 55.000 0.00 0.00 0.00 5.19
312 332 1.734477 CTTCTGGTCGCGACACAGG 60.734 63.158 35.73 25.40 33.41 4.00
377 397 3.680490 TGGTCTTATTGCACCGAAATGA 58.320 40.909 0.00 0.00 35.15 2.57
418 438 0.037419 GGAAACCACGTACGCCCTTA 60.037 55.000 16.72 0.00 0.00 2.69
422 442 1.187567 ACCACGTACGCCCTTACCTT 61.188 55.000 16.72 0.00 0.00 3.50
461 481 1.064314 ACTGTCCTCCTCTACGCTCAT 60.064 52.381 0.00 0.00 0.00 2.90
464 484 2.025155 GTCCTCCTCTACGCTCATTGA 58.975 52.381 0.00 0.00 0.00 2.57
470 490 1.153647 CTACGCTCATTGACGCCCA 60.154 57.895 8.05 0.00 0.00 5.36
473 493 2.359850 GCTCATTGACGCCCACCA 60.360 61.111 0.00 0.00 0.00 4.17
481 501 2.847234 ACGCCCACCAGACCTTGA 60.847 61.111 0.00 0.00 0.00 3.02
507 527 1.460504 TGGCTTACGTCATCGAGAGT 58.539 50.000 0.00 0.00 40.62 3.24
605 626 2.564975 CGTCGTTCGCCTACCAGT 59.435 61.111 0.00 0.00 0.00 4.00
640 661 0.701310 AGGGTCTTGTCCTTGGGGTT 60.701 55.000 0.00 0.00 0.00 4.11
714 735 0.619543 GGCAAGTCTAGGTACCCCCA 60.620 60.000 8.74 0.00 34.66 4.96
718 739 3.112263 CAAGTCTAGGTACCCCCAATCA 58.888 50.000 8.74 0.00 34.66 2.57
760 781 3.890674 GCCCAAGGCGTGTTCTAG 58.109 61.111 0.00 0.00 39.62 2.43
761 782 2.399356 GCCCAAGGCGTGTTCTAGC 61.399 63.158 0.00 0.00 39.62 3.42
762 783 1.296715 CCCAAGGCGTGTTCTAGCT 59.703 57.895 0.00 0.00 0.00 3.32
763 784 0.535335 CCCAAGGCGTGTTCTAGCTA 59.465 55.000 0.00 0.00 0.00 3.32
764 785 1.471676 CCCAAGGCGTGTTCTAGCTAG 60.472 57.143 15.01 15.01 0.00 3.42
765 786 1.281899 CAAGGCGTGTTCTAGCTAGC 58.718 55.000 16.35 6.62 0.00 3.42
766 787 0.179134 AAGGCGTGTTCTAGCTAGCG 60.179 55.000 16.35 14.12 0.00 4.26
767 788 1.139095 GGCGTGTTCTAGCTAGCGT 59.861 57.895 16.35 0.21 0.00 5.07
768 789 0.866483 GGCGTGTTCTAGCTAGCGTC 60.866 60.000 16.35 11.29 0.00 5.19
769 790 1.194896 GCGTGTTCTAGCTAGCGTCG 61.195 60.000 16.35 16.60 0.00 5.12
770 791 1.194896 CGTGTTCTAGCTAGCGTCGC 61.195 60.000 16.35 9.80 0.00 5.19
771 792 0.866483 GTGTTCTAGCTAGCGTCGCC 60.866 60.000 16.35 0.00 0.00 5.54
772 793 1.299240 GTTCTAGCTAGCGTCGCCC 60.299 63.158 16.35 2.60 0.00 6.13
773 794 2.487532 TTCTAGCTAGCGTCGCCCC 61.488 63.158 16.35 2.20 0.00 5.80
774 795 2.905935 TTCTAGCTAGCGTCGCCCCT 62.906 60.000 16.35 10.17 0.00 4.79
775 796 3.200887 CTAGCTAGCGTCGCCCCTG 62.201 68.421 14.86 2.80 0.00 4.45
800 821 6.579491 GTACTACACGGTGGAATATTGTTC 57.421 41.667 13.48 0.00 0.00 3.18
801 822 4.178540 ACTACACGGTGGAATATTGTTCG 58.821 43.478 13.48 0.00 0.00 3.95
802 823 2.352388 ACACGGTGGAATATTGTTCGG 58.648 47.619 13.48 0.00 0.00 4.30
803 824 1.063469 CACGGTGGAATATTGTTCGGC 59.937 52.381 0.00 0.00 0.00 5.54
804 825 0.303493 CGGTGGAATATTGTTCGGCG 59.697 55.000 0.00 0.00 0.00 6.46
805 826 0.661020 GGTGGAATATTGTTCGGCGG 59.339 55.000 7.21 0.00 0.00 6.13
806 827 1.658994 GTGGAATATTGTTCGGCGGA 58.341 50.000 7.21 0.00 0.00 5.54
807 828 2.218603 GTGGAATATTGTTCGGCGGAT 58.781 47.619 7.21 0.00 0.00 4.18
813 834 5.354234 GGAATATTGTTCGGCGGATATTCAT 59.646 40.000 26.87 9.39 40.61 2.57
816 837 7.915293 ATATTGTTCGGCGGATATTCATTTA 57.085 32.000 7.21 0.00 0.00 1.40
859 880 0.463620 GCTGAGAGGAGGATGACACC 59.536 60.000 0.00 0.00 0.00 4.16
868 889 1.118965 AGGATGACACCGACACACCA 61.119 55.000 0.00 0.00 34.73 4.17
873 894 2.023414 GACACCGACACACCACTCCA 62.023 60.000 0.00 0.00 0.00 3.86
877 898 0.677288 CCGACACACCACTCCAAGTA 59.323 55.000 0.00 0.00 0.00 2.24
878 899 1.336887 CCGACACACCACTCCAAGTAG 60.337 57.143 0.00 0.00 0.00 2.57
880 901 2.231478 CGACACACCACTCCAAGTAGAT 59.769 50.000 0.00 0.00 0.00 1.98
881 902 3.442625 CGACACACCACTCCAAGTAGATA 59.557 47.826 0.00 0.00 0.00 1.98
882 903 4.438880 CGACACACCACTCCAAGTAGATAG 60.439 50.000 0.00 0.00 0.00 2.08
883 904 4.673968 ACACACCACTCCAAGTAGATAGA 58.326 43.478 0.00 0.00 0.00 1.98
906 927 1.576577 TCTGATGGATCACTGGCACT 58.423 50.000 0.00 0.00 32.50 4.40
942 965 3.937447 CGCCCGGTTCCTATCCCC 61.937 72.222 0.00 0.00 0.00 4.81
944 967 2.517798 GCCCGGTTCCTATCCCCTC 61.518 68.421 0.00 0.00 0.00 4.30
949 972 1.213296 GGTTCCTATCCCCTCTGCAA 58.787 55.000 0.00 0.00 0.00 4.08
974 997 5.630680 ACATCAAACATGTCGATTTTCTTGC 59.369 36.000 0.00 0.00 0.00 4.01
1012 1055 7.819415 CGGACAATCCTAAAGCATATATCAAGA 59.181 37.037 0.00 0.00 33.30 3.02
1025 1068 9.627395 AGCATATATCAAGATAGACGTACAAAC 57.373 33.333 0.00 0.00 0.00 2.93
1043 1086 3.382048 AACGACTTAGACCAACCAGAC 57.618 47.619 0.00 0.00 0.00 3.51
1044 1087 1.268899 ACGACTTAGACCAACCAGACG 59.731 52.381 0.00 0.00 0.00 4.18
1046 1089 2.485426 CGACTTAGACCAACCAGACGTA 59.515 50.000 0.00 0.00 0.00 3.57
1047 1090 3.669023 CGACTTAGACCAACCAGACGTAC 60.669 52.174 0.00 0.00 0.00 3.67
1048 1091 3.225104 ACTTAGACCAACCAGACGTACA 58.775 45.455 0.00 0.00 0.00 2.90
1049 1092 3.638160 ACTTAGACCAACCAGACGTACAA 59.362 43.478 0.00 0.00 0.00 2.41
1050 1093 4.099881 ACTTAGACCAACCAGACGTACAAA 59.900 41.667 0.00 0.00 0.00 2.83
1052 1095 2.168936 AGACCAACCAGACGTACAAACA 59.831 45.455 0.00 0.00 0.00 2.83
1053 1096 3.135994 GACCAACCAGACGTACAAACAT 58.864 45.455 0.00 0.00 0.00 2.71
1054 1097 2.875933 ACCAACCAGACGTACAAACATG 59.124 45.455 0.00 0.00 0.00 3.21
1055 1098 2.875933 CCAACCAGACGTACAAACATGT 59.124 45.455 0.00 0.00 0.00 3.21
1073 1116 2.039974 TTGATCTGCGCAATGCCGT 61.040 52.632 13.05 0.00 45.60 5.68
1076 1119 1.135699 GATCTGCGCAATGCCGTTTG 61.136 55.000 13.05 0.00 45.60 2.93
1090 1133 7.094975 GCAATGCCGTTTGTTACTCCATATATA 60.095 37.037 0.00 0.00 0.00 0.86
1095 1138 7.623506 GCCGTTTGTTACTCCATATATACATGC 60.624 40.741 0.00 0.00 0.00 4.06
1097 1140 8.935844 CGTTTGTTACTCCATATATACATGCAT 58.064 33.333 0.00 0.00 0.00 3.96
1120 1163 8.413229 GCATGTAGTAAAATCAAATGTATGGGT 58.587 33.333 0.00 0.00 0.00 4.51
1121 1164 9.734620 CATGTAGTAAAATCAAATGTATGGGTG 57.265 33.333 0.00 0.00 0.00 4.61
1128 1171 3.554934 TCAAATGTATGGGTGGCAGATC 58.445 45.455 0.00 0.00 0.00 2.75
1157 1200 2.842208 TTCACAGCCAAAAAGACACG 57.158 45.000 0.00 0.00 0.00 4.49
1159 1202 1.021202 CACAGCCAAAAAGACACGGA 58.979 50.000 0.00 0.00 0.00 4.69
1179 1222 0.172803 GGATCACGCGAGTTACCACT 59.827 55.000 15.93 0.00 46.40 4.00
1180 1223 1.403780 GGATCACGCGAGTTACCACTT 60.404 52.381 15.93 0.00 46.40 3.16
1181 1224 2.159338 GGATCACGCGAGTTACCACTTA 60.159 50.000 15.93 0.00 46.40 2.24
1182 1225 2.336554 TCACGCGAGTTACCACTTAC 57.663 50.000 15.93 0.00 46.40 2.34
1183 1226 1.068333 TCACGCGAGTTACCACTTACC 60.068 52.381 15.93 0.00 46.40 2.85
1184 1227 0.961019 ACGCGAGTTACCACTTACCA 59.039 50.000 15.93 0.00 46.40 3.25
1185 1228 1.336240 ACGCGAGTTACCACTTACCAC 60.336 52.381 15.93 0.00 46.40 4.16
1186 1229 1.718396 GCGAGTTACCACTTACCACC 58.282 55.000 0.00 0.00 31.22 4.61
1187 1230 1.673923 GCGAGTTACCACTTACCACCC 60.674 57.143 0.00 0.00 31.22 4.61
1188 1231 1.403249 CGAGTTACCACTTACCACCCG 60.403 57.143 0.00 0.00 31.22 5.28
1189 1232 1.620323 GAGTTACCACTTACCACCCGT 59.380 52.381 0.00 0.00 31.22 5.28
1190 1233 1.345415 AGTTACCACTTACCACCCGTG 59.655 52.381 0.00 0.00 0.00 4.94
1240 1283 1.930908 GCAACCATGGACTGCTGCTC 61.931 60.000 26.39 6.79 32.35 4.26
1242 1285 2.124403 CCATGGACTGCTGCTCCC 60.124 66.667 5.56 0.00 0.00 4.30
1243 1286 2.672908 CATGGACTGCTGCTCCCA 59.327 61.111 0.00 5.96 0.00 4.37
1246 1292 3.640407 GGACTGCTGCTCCCACCA 61.640 66.667 0.00 0.00 0.00 4.17
1250 1296 4.624364 TGCTGCTCCCACCACGTG 62.624 66.667 9.08 9.08 0.00 4.49
1255 1301 3.030652 CTCCCACCACGTGTTTGC 58.969 61.111 15.65 0.00 0.00 3.68
1269 1315 3.986572 CGTGTTTGCATTTGCCTTCATTA 59.013 39.130 0.00 0.00 41.18 1.90
1274 1320 6.202570 TGTTTGCATTTGCCTTCATTACTTTC 59.797 34.615 0.00 0.00 41.18 2.62
1279 1325 6.628844 GCATTTGCCTTCATTACTTTCTGGAT 60.629 38.462 0.00 0.00 34.31 3.41
1290 1336 1.971505 TTTCTGGATCATCGGCGGCT 61.972 55.000 7.21 0.00 0.00 5.52
1306 1352 0.315568 GGCTCGGCTATCATCGTCTT 59.684 55.000 0.00 0.00 0.00 3.01
1311 1357 1.609840 GGCTATCATCGTCTTCGCGC 61.610 60.000 0.00 0.00 36.96 6.86
1316 1362 1.297378 CATCGTCTTCGCGCTCGTA 60.297 57.895 5.56 0.00 36.96 3.43
1317 1363 0.657659 CATCGTCTTCGCGCTCGTAT 60.658 55.000 5.56 0.00 36.96 3.06
1322 1374 1.004185 GTCTTCGCGCTCGTATCAGTA 60.004 52.381 5.56 0.00 36.96 2.74
1333 1385 2.158914 TCGTATCAGTAGCCTACACGGA 60.159 50.000 11.16 3.70 33.16 4.69
1362 1414 1.402456 GCACCACGTTCGAGTACATCT 60.402 52.381 0.00 0.00 0.00 2.90
1374 1426 4.141287 CGAGTACATCTTCCTCTCCATCT 58.859 47.826 0.00 0.00 0.00 2.90
1383 1435 0.665835 CCTCTCCATCTTCCTCGTCG 59.334 60.000 0.00 0.00 0.00 5.12
1392 1444 0.744874 CTTCCTCGTCGCCTGGATAA 59.255 55.000 0.00 0.00 0.00 1.75
1393 1445 0.744874 TTCCTCGTCGCCTGGATAAG 59.255 55.000 0.00 0.00 0.00 1.73
1411 1463 2.094904 GCTTCGGCGCCAATTTCTA 58.905 52.632 28.98 1.48 0.00 2.10
1416 1468 2.022762 GCGCCAATTTCTACCGCG 59.977 61.111 0.00 0.00 45.35 6.46
1420 1472 1.079875 GCCAATTTCTACCGCGTCGA 61.080 55.000 4.92 0.00 0.00 4.20
1421 1473 0.643820 CCAATTTCTACCGCGTCGAC 59.356 55.000 5.18 5.18 0.00 4.20
1453 1505 4.436998 GTCGTGGTCGGAGCTGGG 62.437 72.222 8.82 0.00 37.69 4.45
1524 1576 4.441695 TCAGCCGGCTTCTCTGCG 62.442 66.667 30.60 14.48 0.00 5.18
1527 1579 2.886124 GCCGGCTTCTCTGCGTAC 60.886 66.667 22.15 0.00 0.00 3.67
1596 1657 1.428448 CGTTGATCTTCCGCAGTTCA 58.572 50.000 0.00 0.00 30.51 3.18
1607 1668 1.005294 CGCAGTTCATGGTGCAAAGC 61.005 55.000 13.68 0.00 39.83 3.51
1618 1679 0.663153 GTGCAAAGCGGAAGTGTTCT 59.337 50.000 0.00 0.00 0.00 3.01
1627 1688 2.048127 AAGTGTTCTCGAGCCGCC 60.048 61.111 7.81 0.00 0.00 6.13
1628 1689 3.916392 AAGTGTTCTCGAGCCGCCG 62.916 63.158 7.81 0.00 0.00 6.46
1658 1719 2.579787 CTCACCGCGGACGACATC 60.580 66.667 35.90 0.00 43.93 3.06
1905 1969 2.472115 TGTTCGTGTAAATGTCGTTCCG 59.528 45.455 0.00 0.00 0.00 4.30
1912 1976 1.529226 AAATGTCGTTCCGATTGCCA 58.471 45.000 0.00 0.00 38.42 4.92
1914 1978 1.024579 ATGTCGTTCCGATTGCCACC 61.025 55.000 0.00 0.00 38.42 4.61
1916 1980 1.024579 GTCGTTCCGATTGCCACCAT 61.025 55.000 0.00 0.00 38.42 3.55
1940 2005 3.284793 TTTTTCCGGGTGAACAAGAGA 57.715 42.857 0.00 0.00 31.05 3.10
1950 2015 3.279434 GTGAACAAGAGACCACCACTTT 58.721 45.455 0.00 0.00 0.00 2.66
2031 4969 7.119407 TGTCGCTCATATATAGTACTTCCTCAC 59.881 40.741 0.00 0.00 0.00 3.51
2036 4974 8.637196 TCATATATAGTACTTCCTCACCACAG 57.363 38.462 0.00 0.00 0.00 3.66
2048 4986 3.057315 CCTCACCACAGCACTTATTTTGG 60.057 47.826 0.00 0.00 0.00 3.28
2073 5011 7.808381 GGAACATAGAAAGTACTTTTGGCTTTC 59.192 37.037 21.40 18.51 44.83 2.62
2079 5017 1.893137 GTACTTTTGGCTTTCTGGGGG 59.107 52.381 0.00 0.00 0.00 5.40
2083 5095 1.406860 TTTGGCTTTCTGGGGGCAAC 61.407 55.000 0.00 0.00 45.20 4.17
2111 5123 1.354337 CTGCATGGTCGAACTCACCG 61.354 60.000 0.33 0.00 36.61 4.94
2112 5124 2.740714 GCATGGTCGAACTCACCGC 61.741 63.158 0.33 0.00 36.61 5.68
2117 5129 4.331166 TCGAACTCACCGCGCGAA 62.331 61.111 34.63 15.46 0.00 4.70
2118 5130 3.179265 CGAACTCACCGCGCGAAT 61.179 61.111 34.63 16.98 0.00 3.34
2119 5131 2.726691 CGAACTCACCGCGCGAATT 61.727 57.895 34.63 17.10 0.00 2.17
2120 5132 1.407721 CGAACTCACCGCGCGAATTA 61.408 55.000 34.63 12.68 0.00 1.40
2121 5133 0.297820 GAACTCACCGCGCGAATTAG 59.702 55.000 34.63 23.39 0.00 1.73
2122 5134 0.108992 AACTCACCGCGCGAATTAGA 60.109 50.000 34.63 18.95 0.00 2.10
2123 5135 0.801067 ACTCACCGCGCGAATTAGAC 60.801 55.000 34.63 0.00 0.00 2.59
2124 5136 0.800683 CTCACCGCGCGAATTAGACA 60.801 55.000 34.63 4.66 0.00 3.41
2125 5137 0.388778 TCACCGCGCGAATTAGACAA 60.389 50.000 34.63 2.57 0.00 3.18
2126 5138 0.247145 CACCGCGCGAATTAGACAAC 60.247 55.000 34.63 0.00 0.00 3.32
2127 5139 1.347221 CCGCGCGAATTAGACAACC 59.653 57.895 34.63 0.00 0.00 3.77
2128 5140 1.013755 CGCGCGAATTAGACAACCG 60.014 57.895 28.94 0.00 0.00 4.44
2129 5141 1.680105 CGCGCGAATTAGACAACCGT 61.680 55.000 28.94 0.00 0.00 4.83
2130 5142 0.247145 GCGCGAATTAGACAACCGTG 60.247 55.000 12.10 0.00 0.00 4.94
2131 5143 1.342555 CGCGAATTAGACAACCGTGA 58.657 50.000 0.00 0.00 33.21 4.35
2132 5144 1.722464 CGCGAATTAGACAACCGTGAA 59.278 47.619 0.00 0.00 33.21 3.18
2133 5145 2.347452 CGCGAATTAGACAACCGTGAAT 59.653 45.455 0.00 0.00 33.21 2.57
2134 5146 3.541516 CGCGAATTAGACAACCGTGAATC 60.542 47.826 0.00 0.00 33.21 2.52
2135 5147 3.617263 GCGAATTAGACAACCGTGAATCT 59.383 43.478 0.00 0.00 0.00 2.40
2136 5148 4.092968 GCGAATTAGACAACCGTGAATCTT 59.907 41.667 0.00 0.00 0.00 2.40
2137 5149 5.390567 GCGAATTAGACAACCGTGAATCTTT 60.391 40.000 0.00 0.00 0.00 2.52
2138 5150 6.241385 CGAATTAGACAACCGTGAATCTTTC 58.759 40.000 0.00 0.00 0.00 2.62
2139 5151 6.496338 AATTAGACAACCGTGAATCTTTCC 57.504 37.500 0.00 0.00 0.00 3.13
2140 5152 2.779506 AGACAACCGTGAATCTTTCCC 58.220 47.619 0.00 0.00 0.00 3.97
2141 5153 1.810755 GACAACCGTGAATCTTTCCCC 59.189 52.381 0.00 0.00 0.00 4.81
2142 5154 1.173913 CAACCGTGAATCTTTCCCCC 58.826 55.000 0.00 0.00 0.00 5.40
2143 5155 0.322187 AACCGTGAATCTTTCCCCCG 60.322 55.000 0.00 0.00 0.00 5.73
2144 5156 1.196104 ACCGTGAATCTTTCCCCCGA 61.196 55.000 0.00 0.00 0.00 5.14
2145 5157 0.035820 CCGTGAATCTTTCCCCCGAA 60.036 55.000 0.00 0.00 0.00 4.30
2146 5158 1.612199 CCGTGAATCTTTCCCCCGAAA 60.612 52.381 0.00 0.00 36.55 3.46
2177 5189 8.455903 ACTGTGAATCTTTGAATTCTTGAAGA 57.544 30.769 16.34 16.34 36.73 2.87
2200 5212 4.944962 TGCATAATAGCACACTGTTCAC 57.055 40.909 0.00 0.00 40.11 3.18
2207 5219 0.663153 GCACACTGTTCACCTGTTCC 59.337 55.000 0.00 0.00 0.00 3.62
2208 5220 1.747206 GCACACTGTTCACCTGTTCCT 60.747 52.381 0.00 0.00 0.00 3.36
2209 5221 2.484770 GCACACTGTTCACCTGTTCCTA 60.485 50.000 0.00 0.00 0.00 2.94
2232 5244 3.691049 TTTTTCAAGCGAGACCTGTTG 57.309 42.857 0.00 0.00 0.00 3.33
2246 5258 7.042335 CGAGACCTGTTGATTCTTTATAACCT 58.958 38.462 0.00 0.00 0.00 3.50
2278 5290 8.109634 ACCAATAGAACAATAGAATTCACACCT 58.890 33.333 8.44 0.00 0.00 4.00
2281 5293 9.911788 AATAGAACAATAGAATTCACACCTGAT 57.088 29.630 8.44 0.00 0.00 2.90
2302 5314 8.504815 CCTGATCTATAAATCAAAGATGCACAG 58.495 37.037 0.00 0.00 35.32 3.66
2311 5323 3.565482 TCAAAGATGCACAGAACCAACTC 59.435 43.478 0.00 0.00 0.00 3.01
2349 5361 3.149196 CACCATGACAAACCTGTAGCTT 58.851 45.455 0.00 0.00 35.30 3.74
2355 5367 6.238897 CCATGACAAACCTGTAGCTTAACAAA 60.239 38.462 0.00 0.00 35.30 2.83
2437 5449 3.455910 ACCCTTGAGCATAGTAGCATTCA 59.544 43.478 0.00 0.00 36.85 2.57
2646 5684 0.520404 GAGCGGTTAGTCTCACGACA 59.480 55.000 0.00 0.00 42.73 4.35
2659 5697 1.100510 CACGACACCGATCCTAGGAA 58.899 55.000 17.30 0.00 39.50 3.36
2668 5706 1.067212 CGATCCTAGGAACTTCCACCG 59.933 57.143 17.30 5.79 39.61 4.94
2717 5755 1.330155 TAATCTCCTCTCCCTGGGGT 58.670 55.000 14.00 0.00 36.47 4.95
2718 5756 0.327000 AATCTCCTCTCCCTGGGGTG 60.327 60.000 14.00 6.61 36.47 4.61
2719 5757 1.531981 ATCTCCTCTCCCTGGGGTGT 61.532 60.000 14.00 0.00 36.47 4.16
2724 5763 4.039092 CTCCCTGGGGTGTGGCAG 62.039 72.222 14.00 0.00 36.47 4.85
2764 5803 6.085555 TCACATCGGTTCCATAGATTAGAC 57.914 41.667 0.00 0.00 0.00 2.59
2947 5995 1.409427 GCCGAGCCATACAAGTCTACT 59.591 52.381 0.00 0.00 0.00 2.57
2988 6036 0.323302 TGAACTACATCAAGCGCCCA 59.677 50.000 2.29 0.00 0.00 5.36
3047 6095 2.464459 CCAGAATCGCGTGGCTTCC 61.464 63.158 5.77 0.00 0.00 3.46
3069 6117 2.333938 GGCGGCATGTGCATGATC 59.666 61.111 15.53 6.21 44.36 2.92
3070 6118 2.333938 GCGGCATGTGCATGATCC 59.666 61.111 15.53 7.40 44.36 3.36
3071 6119 2.483197 GCGGCATGTGCATGATCCA 61.483 57.895 15.53 0.00 44.36 3.41
3072 6120 1.652563 CGGCATGTGCATGATCCAG 59.347 57.895 15.53 2.59 44.36 3.86
3073 6121 1.362717 GGCATGTGCATGATCCAGC 59.637 57.895 15.53 0.00 44.36 4.85
3074 6122 1.388837 GGCATGTGCATGATCCAGCA 61.389 55.000 15.53 5.18 44.36 4.41
3075 6123 0.030773 GCATGTGCATGATCCAGCAG 59.969 55.000 15.53 0.74 42.14 4.24
3076 6124 0.668535 CATGTGCATGATCCAGCAGG 59.331 55.000 9.18 0.00 42.14 4.85
3077 6125 1.107538 ATGTGCATGATCCAGCAGGC 61.108 55.000 9.18 0.00 45.06 4.85
3079 6127 3.962421 GCATGATCCAGCAGGCGC 61.962 66.667 0.00 0.00 35.78 6.53
3080 6128 3.646976 CATGATCCAGCAGGCGCG 61.647 66.667 0.00 0.00 45.49 6.86
3114 6174 1.003355 CTGGAGAGCCGGCTTCAAA 60.003 57.895 33.34 16.17 36.79 2.69
3119 6179 2.203337 AGCCGGCTTCAAACAGCA 60.203 55.556 27.08 0.00 42.10 4.41
3128 6188 1.034838 TTCAAACAGCAACGCCCTGT 61.035 50.000 0.00 0.00 44.92 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 86 4.697352 GCTCATCCACTGTACTTGTTCATT 59.303 41.667 0.00 0.00 0.00 2.57
144 160 0.927767 AGTCTCCACCGTAGAGGGAT 59.072 55.000 0.00 0.00 46.96 3.85
145 161 1.489649 CTAGTCTCCACCGTAGAGGGA 59.510 57.143 0.00 0.00 46.96 4.20
188 204 3.307339 GCCTAAGCTATGAGGGAAGATGG 60.307 52.174 10.42 0.00 35.50 3.51
230 250 4.125124 TCATGTCCCCTTTCAAATTGGA 57.875 40.909 0.00 0.00 0.00 3.53
304 324 4.394712 GAGCCCACCCCTGTGTCG 62.395 72.222 0.00 0.00 41.09 4.35
312 332 2.764128 TCATCTCCGAGCCCACCC 60.764 66.667 0.00 0.00 0.00 4.61
377 397 1.241485 AGGAGTCCCCCAAAGGTTTT 58.759 50.000 5.25 0.00 34.66 2.43
406 426 1.260544 AAGAAGGTAAGGGCGTACGT 58.739 50.000 17.90 0.00 0.00 3.57
418 438 2.979678 TCCTCTTTGGTGCTAAGAAGGT 59.020 45.455 0.00 0.00 37.07 3.50
422 442 4.141482 ACAGTTTCCTCTTTGGTGCTAAGA 60.141 41.667 0.00 0.00 37.07 2.10
461 481 2.448582 AAGGTCTGGTGGGCGTCAA 61.449 57.895 0.00 0.00 0.00 3.18
464 484 2.185310 GATCAAGGTCTGGTGGGCGT 62.185 60.000 0.00 0.00 0.00 5.68
470 490 1.208052 CCATGACGATCAAGGTCTGGT 59.792 52.381 0.00 0.00 31.05 4.00
473 493 1.198713 AGCCATGACGATCAAGGTCT 58.801 50.000 0.00 6.05 37.54 3.85
481 501 2.743938 GATGACGTAAGCCATGACGAT 58.256 47.619 11.17 0.00 41.93 3.73
507 527 1.681327 GGTACCCAGCCTCACGAGA 60.681 63.158 0.00 0.00 0.00 4.04
640 661 1.297364 GGTACGGCCCAGCTACAAA 59.703 57.895 0.00 0.00 0.00 2.83
714 735 2.910688 ACTGTCGGTGTTCTGTGATT 57.089 45.000 0.00 0.00 0.00 2.57
753 774 1.432251 GGCGACGCTAGCTAGAACA 59.568 57.895 25.15 0.00 34.52 3.18
754 775 1.299240 GGGCGACGCTAGCTAGAAC 60.299 63.158 25.15 12.57 34.52 3.01
755 776 2.487532 GGGGCGACGCTAGCTAGAA 61.488 63.158 25.15 0.00 40.76 2.10
756 777 2.905880 GGGGCGACGCTAGCTAGA 60.906 66.667 25.15 0.00 40.76 2.43
769 790 2.202703 CGTGTAGTACGCAGGGGC 60.203 66.667 13.98 0.00 46.92 5.80
777 798 5.230726 CGAACAATATTCCACCGTGTAGTAC 59.769 44.000 0.00 0.00 0.00 2.73
778 799 5.342433 CGAACAATATTCCACCGTGTAGTA 58.658 41.667 0.00 0.00 0.00 1.82
779 800 4.178540 CGAACAATATTCCACCGTGTAGT 58.821 43.478 0.00 0.00 0.00 2.73
780 801 3.554324 CCGAACAATATTCCACCGTGTAG 59.446 47.826 0.00 0.00 0.00 2.74
781 802 3.523547 CCGAACAATATTCCACCGTGTA 58.476 45.455 0.00 0.00 0.00 2.90
782 803 2.352388 CCGAACAATATTCCACCGTGT 58.648 47.619 0.00 0.00 0.00 4.49
783 804 1.063469 GCCGAACAATATTCCACCGTG 59.937 52.381 0.00 0.00 0.00 4.94
784 805 1.375551 GCCGAACAATATTCCACCGT 58.624 50.000 0.00 0.00 0.00 4.83
785 806 0.303493 CGCCGAACAATATTCCACCG 59.697 55.000 0.00 0.00 0.00 4.94
786 807 0.661020 CCGCCGAACAATATTCCACC 59.339 55.000 0.00 0.00 0.00 4.61
787 808 1.658994 TCCGCCGAACAATATTCCAC 58.341 50.000 0.00 0.00 0.00 4.02
788 809 2.631160 ATCCGCCGAACAATATTCCA 57.369 45.000 0.00 0.00 0.00 3.53
789 810 4.693566 TGAATATCCGCCGAACAATATTCC 59.306 41.667 13.64 3.76 39.04 3.01
790 811 5.856126 TGAATATCCGCCGAACAATATTC 57.144 39.130 11.26 11.26 39.71 1.75
791 812 6.817765 AATGAATATCCGCCGAACAATATT 57.182 33.333 0.00 0.00 0.00 1.28
792 813 6.817765 AAATGAATATCCGCCGAACAATAT 57.182 33.333 0.00 0.00 0.00 1.28
793 814 6.128769 CGTAAATGAATATCCGCCGAACAATA 60.129 38.462 0.00 0.00 0.00 1.90
794 815 5.333798 CGTAAATGAATATCCGCCGAACAAT 60.334 40.000 0.00 0.00 0.00 2.71
795 816 4.025563 CGTAAATGAATATCCGCCGAACAA 60.026 41.667 0.00 0.00 0.00 2.83
796 817 3.491639 CGTAAATGAATATCCGCCGAACA 59.508 43.478 0.00 0.00 0.00 3.18
797 818 3.492011 ACGTAAATGAATATCCGCCGAAC 59.508 43.478 0.00 0.00 0.00 3.95
798 819 3.491639 CACGTAAATGAATATCCGCCGAA 59.508 43.478 0.00 0.00 0.00 4.30
799 820 3.054166 CACGTAAATGAATATCCGCCGA 58.946 45.455 0.00 0.00 0.00 5.54
800 821 2.798283 ACACGTAAATGAATATCCGCCG 59.202 45.455 0.00 0.00 0.00 6.46
801 822 3.558418 ACACACGTAAATGAATATCCGCC 59.442 43.478 0.00 0.00 0.00 6.13
802 823 4.514506 CACACACGTAAATGAATATCCGC 58.485 43.478 0.00 0.00 0.00 5.54
803 824 4.514506 GCACACACGTAAATGAATATCCG 58.485 43.478 0.00 0.00 0.00 4.18
804 825 4.033587 ACGCACACACGTAAATGAATATCC 59.966 41.667 0.00 0.00 46.19 2.59
805 826 5.138800 ACGCACACACGTAAATGAATATC 57.861 39.130 0.00 0.00 46.19 1.63
838 859 1.067250 GTCATCCTCCTCTCAGCGC 59.933 63.158 0.00 0.00 0.00 5.92
840 861 0.463620 GGTGTCATCCTCCTCTCAGC 59.536 60.000 0.00 0.00 0.00 4.26
841 862 0.743688 CGGTGTCATCCTCCTCTCAG 59.256 60.000 0.00 0.00 0.00 3.35
842 863 0.331616 TCGGTGTCATCCTCCTCTCA 59.668 55.000 0.00 0.00 0.00 3.27
843 864 0.741915 GTCGGTGTCATCCTCCTCTC 59.258 60.000 0.00 0.00 0.00 3.20
848 869 0.389948 GGTGTGTCGGTGTCATCCTC 60.390 60.000 0.00 0.00 0.00 3.71
859 880 1.611977 TCTACTTGGAGTGGTGTGTCG 59.388 52.381 0.00 0.00 0.00 4.35
868 889 9.253832 CCATCAGATATTCTATCTACTTGGAGT 57.746 37.037 10.65 0.00 0.00 3.85
877 898 7.147689 GCCAGTGATCCATCAGATATTCTATCT 60.148 40.741 0.00 0.00 37.51 1.98
878 899 6.985645 GCCAGTGATCCATCAGATATTCTATC 59.014 42.308 0.00 0.00 37.51 2.08
880 901 5.781818 TGCCAGTGATCCATCAGATATTCTA 59.218 40.000 0.00 0.00 37.51 2.10
881 902 4.596212 TGCCAGTGATCCATCAGATATTCT 59.404 41.667 0.00 0.00 37.51 2.40
882 903 4.694509 GTGCCAGTGATCCATCAGATATTC 59.305 45.833 0.00 0.00 37.51 1.75
883 904 4.350225 AGTGCCAGTGATCCATCAGATATT 59.650 41.667 0.00 0.00 37.51 1.28
942 965 3.910170 CGACATGTTTGATGTTTGCAGAG 59.090 43.478 0.00 0.00 31.52 3.35
944 967 3.887741 TCGACATGTTTGATGTTTGCAG 58.112 40.909 0.00 0.00 31.52 4.41
949 972 6.144402 GCAAGAAAATCGACATGTTTGATGTT 59.856 34.615 14.11 14.11 31.52 2.71
974 997 2.250188 GATTGTCCGCATTGTTTTCCG 58.750 47.619 0.00 0.00 0.00 4.30
1025 1068 1.268899 ACGTCTGGTTGGTCTAAGTCG 59.731 52.381 0.00 0.00 0.00 4.18
1043 1086 3.407252 CGCAGATCAACATGTTTGTACG 58.593 45.455 8.77 4.83 34.06 3.67
1044 1087 3.163594 GCGCAGATCAACATGTTTGTAC 58.836 45.455 8.77 1.26 34.06 2.90
1046 1089 1.608109 TGCGCAGATCAACATGTTTGT 59.392 42.857 5.66 0.00 37.82 2.83
1047 1090 2.334971 TGCGCAGATCAACATGTTTG 57.665 45.000 5.66 5.97 0.00 2.93
1048 1091 3.247442 CATTGCGCAGATCAACATGTTT 58.753 40.909 11.31 0.00 0.00 2.83
1049 1092 2.871133 CATTGCGCAGATCAACATGTT 58.129 42.857 11.31 4.92 0.00 2.71
1050 1093 1.468565 GCATTGCGCAGATCAACATGT 60.469 47.619 11.31 0.00 41.79 3.21
1052 1095 0.101759 GGCATTGCGCAGATCAACAT 59.898 50.000 11.31 0.00 45.17 2.71
1053 1096 1.507630 GGCATTGCGCAGATCAACA 59.492 52.632 11.31 0.00 45.17 3.33
1054 1097 1.584483 CGGCATTGCGCAGATCAAC 60.584 57.895 11.31 0.00 45.17 3.18
1055 1098 1.585267 AACGGCATTGCGCAGATCAA 61.585 50.000 11.31 0.00 45.17 2.57
1073 1116 9.791801 ACATGCATGTATATATGGAGTAACAAA 57.208 29.630 30.50 0.00 39.68 2.83
1095 1138 9.734620 CACCCATACATTTGATTTTACTACATG 57.265 33.333 0.00 0.00 0.00 3.21
1097 1140 7.147983 GCCACCCATACATTTGATTTTACTACA 60.148 37.037 0.00 0.00 0.00 2.74
1098 1141 7.147983 TGCCACCCATACATTTGATTTTACTAC 60.148 37.037 0.00 0.00 0.00 2.73
1128 1171 1.456296 TGGCTGTGAAATGCTAGCAG 58.544 50.000 23.89 8.53 37.89 4.24
1157 1200 0.248949 GGTAACTCGCGTGATCCTCC 60.249 60.000 16.04 6.11 0.00 4.30
1159 1202 0.172803 GTGGTAACTCGCGTGATCCT 59.827 55.000 16.04 0.00 37.61 3.24
1213 1256 3.443045 CCATGGTTGCCGCCTGAC 61.443 66.667 2.57 0.00 0.00 3.51
1240 1283 0.103937 AAATGCAAACACGTGGTGGG 59.896 50.000 21.57 10.90 37.94 4.61
1242 1285 0.576328 GCAAATGCAAACACGTGGTG 59.424 50.000 21.57 17.87 41.59 4.17
1243 1286 0.529555 GGCAAATGCAAACACGTGGT 60.530 50.000 21.57 11.47 44.36 4.16
1246 1292 1.135915 TGAAGGCAAATGCAAACACGT 59.864 42.857 7.80 0.00 44.36 4.49
1250 1296 6.424812 AGAAAGTAATGAAGGCAAATGCAAAC 59.575 34.615 7.80 0.00 44.36 2.93
1255 1301 6.271488 TCCAGAAAGTAATGAAGGCAAATG 57.729 37.500 0.00 0.00 0.00 2.32
1269 1315 0.179073 CCGCCGATGATCCAGAAAGT 60.179 55.000 0.00 0.00 0.00 2.66
1274 1320 2.356793 GAGCCGCCGATGATCCAG 60.357 66.667 0.00 0.00 0.00 3.86
1290 1336 0.040336 GCGAAGACGATGATAGCCGA 60.040 55.000 0.00 0.00 42.66 5.54
1306 1352 1.278937 GCTACTGATACGAGCGCGA 59.721 57.895 19.05 0.00 41.64 5.87
1311 1357 2.223611 CCGTGTAGGCTACTGATACGAG 59.776 54.545 26.96 17.20 33.46 4.18
1316 1362 1.409427 GCTTCCGTGTAGGCTACTGAT 59.591 52.381 24.07 0.00 40.77 2.90
1317 1363 0.815734 GCTTCCGTGTAGGCTACTGA 59.184 55.000 24.07 15.13 40.77 3.41
1322 1374 3.771160 CCGGCTTCCGTGTAGGCT 61.771 66.667 4.47 0.00 46.80 4.58
1354 1406 4.898861 GGAAGATGGAGAGGAAGATGTACT 59.101 45.833 0.00 0.00 0.00 2.73
1362 1414 2.379972 GACGAGGAAGATGGAGAGGAA 58.620 52.381 0.00 0.00 0.00 3.36
1374 1426 0.744874 CTTATCCAGGCGACGAGGAA 59.255 55.000 9.62 0.00 41.63 3.36
1383 1435 2.247437 CGCCGAAGCTTATCCAGGC 61.247 63.158 15.20 15.20 41.03 4.85
1392 1444 0.392461 TAGAAATTGGCGCCGAAGCT 60.392 50.000 22.97 19.37 36.60 3.74
1393 1445 0.248094 GTAGAAATTGGCGCCGAAGC 60.248 55.000 22.97 12.93 0.00 3.86
1409 1461 1.868251 GCAGAAGTCGACGCGGTAG 60.868 63.158 12.47 0.36 0.00 3.18
1411 1463 4.719369 GGCAGAAGTCGACGCGGT 62.719 66.667 12.47 0.00 0.00 5.68
1416 1468 2.507324 GAGCGGGCAGAAGTCGAC 60.507 66.667 7.70 7.70 0.00 4.20
1420 1472 1.078848 GACATGAGCGGGCAGAAGT 60.079 57.895 0.00 0.00 0.00 3.01
1421 1473 2.169789 CGACATGAGCGGGCAGAAG 61.170 63.158 0.00 0.00 0.00 2.85
1459 1511 3.376918 GAAGCTTGGCCAGGCACC 61.377 66.667 37.69 25.39 35.69 5.01
1460 1512 2.282745 AGAAGCTTGGCCAGGCAC 60.283 61.111 37.69 29.40 35.69 5.01
1461 1513 2.034687 GAGAAGCTTGGCCAGGCA 59.965 61.111 37.69 9.24 35.69 4.75
1462 1514 3.130160 CGAGAAGCTTGGCCAGGC 61.130 66.667 31.28 31.28 0.00 4.85
1463 1515 2.437359 CCGAGAAGCTTGGCCAGG 60.437 66.667 11.24 11.24 0.00 4.45
1540 1592 2.333938 GCCATAGCTTGCCGCATG 59.666 61.111 0.00 0.00 42.61 4.06
1579 1640 2.290260 ACCATGAACTGCGGAAGATCAA 60.290 45.455 0.00 0.00 40.67 2.57
1586 1647 0.821301 TTTGCACCATGAACTGCGGA 60.821 50.000 0.00 0.00 36.08 5.54
1596 1657 0.823356 ACACTTCCGCTTTGCACCAT 60.823 50.000 0.00 0.00 0.00 3.55
1607 1668 1.801913 CGGCTCGAGAACACTTCCG 60.802 63.158 18.75 13.76 0.00 4.30
1950 2015 8.704668 TGAGGCATCAATCTACTGTATAGAAAA 58.295 33.333 0.00 0.00 30.61 2.29
2031 4969 4.582701 TGTTCCAAAATAAGTGCTGTGG 57.417 40.909 0.00 0.00 0.00 4.17
2036 4974 9.556030 GTACTTTCTATGTTCCAAAATAAGTGC 57.444 33.333 0.00 0.00 0.00 4.40
2048 4986 8.729529 GAAAGCCAAAAGTACTTTCTATGTTC 57.270 34.615 20.78 16.39 43.73 3.18
2073 5011 0.895559 GTGAGAAAGGTTGCCCCCAG 60.896 60.000 0.00 0.00 0.00 4.45
2079 5017 1.068055 CCATGCAGTGAGAAAGGTTGC 60.068 52.381 0.00 0.00 35.42 4.17
2083 5095 1.081892 CGACCATGCAGTGAGAAAGG 58.918 55.000 0.00 0.00 0.00 3.11
2089 5101 0.678950 TGAGTTCGACCATGCAGTGA 59.321 50.000 0.00 0.00 0.00 3.41
2111 5123 0.247145 CACGGTTGTCTAATTCGCGC 60.247 55.000 0.00 0.00 0.00 6.86
2112 5124 1.342555 TCACGGTTGTCTAATTCGCG 58.657 50.000 0.00 0.00 0.00 5.87
2114 5126 5.779806 AAGATTCACGGTTGTCTAATTCG 57.220 39.130 0.00 0.00 0.00 3.34
2115 5127 6.403309 GGGAAAGATTCACGGTTGTCTAATTC 60.403 42.308 0.00 0.00 0.00 2.17
2116 5128 5.414765 GGGAAAGATTCACGGTTGTCTAATT 59.585 40.000 0.00 0.00 0.00 1.40
2117 5129 4.941873 GGGAAAGATTCACGGTTGTCTAAT 59.058 41.667 0.00 0.00 0.00 1.73
2118 5130 4.320870 GGGAAAGATTCACGGTTGTCTAA 58.679 43.478 0.00 0.00 0.00 2.10
2119 5131 3.307199 GGGGAAAGATTCACGGTTGTCTA 60.307 47.826 0.00 0.00 32.51 2.59
2120 5132 2.552373 GGGGAAAGATTCACGGTTGTCT 60.552 50.000 0.00 0.00 32.51 3.41
2121 5133 1.810755 GGGGAAAGATTCACGGTTGTC 59.189 52.381 0.00 0.00 32.51 3.18
2122 5134 1.546998 GGGGGAAAGATTCACGGTTGT 60.547 52.381 0.00 0.00 32.51 3.32
2123 5135 1.173913 GGGGGAAAGATTCACGGTTG 58.826 55.000 0.00 0.00 32.51 3.77
2124 5136 0.322187 CGGGGGAAAGATTCACGGTT 60.322 55.000 0.00 0.00 32.51 4.44
2125 5137 1.196104 TCGGGGGAAAGATTCACGGT 61.196 55.000 0.00 0.00 32.51 4.83
2126 5138 0.035820 TTCGGGGGAAAGATTCACGG 60.036 55.000 0.00 0.00 32.51 4.94
2127 5139 1.816074 TTTCGGGGGAAAGATTCACG 58.184 50.000 0.00 0.00 32.51 4.35
2150 5162 9.525409 CTTCAAGAATTCAAAGATTCACAGTTT 57.475 29.630 8.44 0.00 38.27 2.66
2154 5166 9.687210 CAATCTTCAAGAATTCAAAGATTCACA 57.313 29.630 25.23 7.18 41.75 3.58
2163 5175 9.740239 GCTATTATGCAATCTTCAAGAATTCAA 57.260 29.630 8.44 0.00 0.00 2.69
2177 5189 5.163622 GGTGAACAGTGTGCTATTATGCAAT 60.164 40.000 2.13 0.00 45.12 3.56
2221 5233 7.042335 AGGTTATAAAGAATCAACAGGTCTCG 58.958 38.462 0.00 0.00 0.00 4.04
2225 5237 8.934023 TGAAAGGTTATAAAGAATCAACAGGT 57.066 30.769 0.00 0.00 0.00 4.00
2259 5271 7.856145 AGATCAGGTGTGAATTCTATTGTTC 57.144 36.000 7.05 3.79 35.88 3.18
2273 5285 7.994911 TGCATCTTTGATTTATAGATCAGGTGT 59.005 33.333 6.11 0.00 37.35 4.16
2278 5290 9.617523 TTCTGTGCATCTTTGATTTATAGATCA 57.382 29.630 1.89 1.89 34.37 2.92
2281 5293 7.828717 TGGTTCTGTGCATCTTTGATTTATAGA 59.171 33.333 0.00 0.00 0.00 1.98
2302 5314 7.486232 GCTCTTTGCTTTATAATGAGTTGGTTC 59.514 37.037 2.66 0.00 38.95 3.62
2311 5323 6.694411 GTCATGGTGCTCTTTGCTTTATAATG 59.306 38.462 0.00 0.00 43.37 1.90
2332 5344 6.952773 TTTGTTAAGCTACAGGTTTGTCAT 57.047 33.333 0.00 0.00 38.76 3.06
2371 5383 9.685276 TGACCACTTGATAAATGTTTGAGATAT 57.315 29.630 0.00 0.00 0.00 1.63
2375 5387 6.578545 CGTTGACCACTTGATAAATGTTTGAG 59.421 38.462 0.00 0.00 0.00 3.02
2383 5395 6.627395 ATTTCACGTTGACCACTTGATAAA 57.373 33.333 0.00 0.00 33.83 1.40
2600 5638 5.772393 ACCATGTGGAAAACTGTAGGATA 57.228 39.130 5.96 0.00 38.94 2.59
2609 5647 4.035208 CCGCTCTAATACCATGTGGAAAAC 59.965 45.833 5.96 0.00 38.94 2.43
2646 5684 2.108970 GTGGAAGTTCCTAGGATCGGT 58.891 52.381 22.41 5.56 37.46 4.69
2717 5755 0.322366 TTGATCAATCGGCTGCCACA 60.322 50.000 20.29 4.43 0.00 4.17
2718 5756 0.810648 TTTGATCAATCGGCTGCCAC 59.189 50.000 20.29 1.34 0.00 5.01
2719 5757 1.473677 CTTTTGATCAATCGGCTGCCA 59.526 47.619 20.29 6.38 0.00 4.92
2764 5803 7.775093 TGGAATTGACCTAATCTATGAAAGTGG 59.225 37.037 0.00 0.00 0.00 4.00
2966 6014 1.394917 GGCGCTTGATGTAGTTCACTG 59.605 52.381 7.64 0.00 0.00 3.66
2969 6017 0.323302 TGGGCGCTTGATGTAGTTCA 59.677 50.000 7.64 0.00 0.00 3.18
2988 6036 3.391382 CCGGCTCGGGGAAGACTT 61.391 66.667 5.79 0.00 44.15 3.01
3008 6056 2.738521 GCTCGACCAAGCTTGCGA 60.739 61.111 21.43 21.96 39.27 5.10
3059 6107 1.751544 GCCTGCTGGATCATGCACA 60.752 57.895 14.77 0.00 35.20 4.57


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

AutoCloner maintained by Alex Coulton.