Multiple sequence alignment - TraesCS5A01G183400

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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 TraesCS5A01G183400 chr5A 100.000 3387 0 0 1 3387 382783505 382780119 0.000000e+00 6255.0
1 TraesCS5A01G183400 chr5A 94.891 137 5 2 2800 2935 688512212 688512347 2.650000e-51 213.0
2 TraesCS5A01G183400 chr5B 91.767 1919 113 23 917 2810 331251978 331250080 0.000000e+00 2627.0
3 TraesCS5A01G183400 chr5B 86.192 478 38 11 2933 3385 331250082 331249608 3.040000e-135 492.0
4 TraesCS5A01G183400 chr3A 95.628 892 22 5 1 876 395750823 395751713 0.000000e+00 1415.0
5 TraesCS5A01G183400 chr3B 77.846 1300 212 43 1027 2290 686127722 686126463 0.000000e+00 736.0
6 TraesCS5A01G183400 chr3D 77.850 1237 198 45 1058 2262 520708868 520707676 0.000000e+00 697.0
7 TraesCS5A01G183400 chr3D 88.406 69 4 3 2431 2496 520706281 520706214 2.800000e-11 80.5
8 TraesCS5A01G183400 chr5D 89.668 271 24 2 3116 3385 290396620 290396353 3.240000e-90 342.0
9 TraesCS5A01G183400 chr5D 91.667 48 4 0 3066 3113 438974605 438974558 2.180000e-07 67.6
10 TraesCS5A01G183400 chr7A 96.947 131 4 0 2808 2938 680418987 680419117 1.580000e-53 220.0
11 TraesCS5A01G183400 chr1A 96.899 129 4 0 2808 2936 111151654 111151782 2.050000e-52 217.0
12 TraesCS5A01G183400 chr1A 94.853 136 7 0 2801 2936 311814078 311814213 2.650000e-51 213.0
13 TraesCS5A01G183400 chr7B 95.522 134 6 0 2807 2940 728671830 728671963 7.360000e-52 215.0
14 TraesCS5A01G183400 chr2B 95.455 132 6 0 2805 2936 93015856 93015987 9.520000e-51 211.0
15 TraesCS5A01G183400 chr2B 94.245 139 6 2 2797 2934 627325236 627325099 9.520000e-51 211.0
16 TraesCS5A01G183400 chr6A 92.517 147 9 2 2790 2934 599910795 599910941 3.420000e-50 209.0
17 TraesCS5A01G183400 chr2A 94.203 138 7 1 2803 2939 115451624 115451487 3.420000e-50 209.0
18 TraesCS5A01G183400 chr7D 77.049 122 24 4 123 242 442772844 442772725 2.180000e-07 67.6
19 TraesCS5A01G183400 chr2D 95.000 40 2 0 828 867 447150764 447150725 2.820000e-06 63.9


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 TraesCS5A01G183400 chr5A 382780119 382783505 3386 True 6255.00 6255 100.0000 1 3387 1 chr5A.!!$R1 3386
1 TraesCS5A01G183400 chr5B 331249608 331251978 2370 True 1559.50 2627 88.9795 917 3385 2 chr5B.!!$R1 2468
2 TraesCS5A01G183400 chr3A 395750823 395751713 890 False 1415.00 1415 95.6280 1 876 1 chr3A.!!$F1 875
3 TraesCS5A01G183400 chr3B 686126463 686127722 1259 True 736.00 736 77.8460 1027 2290 1 chr3B.!!$R1 1263
4 TraesCS5A01G183400 chr3D 520706214 520708868 2654 True 388.75 697 83.1280 1058 2496 2 chr3D.!!$R1 1438

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
890 906 0.035439 CCTACATTTCGTGGTGGGCT 60.035 55.0 0.0 0.0 0.0 5.19 F
895 911 0.036010 ATTTCGTGGTGGGCTGAGAG 60.036 55.0 0.0 0.0 0.0 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 2041 0.035881 TGAAGACCTTGAGCTGGCTG 59.964 55.0 0.0 0.0 0.00 4.85 R
2561 3879 0.179171 ATCGACTGGCTAACACGACG 60.179 55.0 0.0 0.0 35.91 5.12 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
38 39 1.003233 GGGCAGTGTTGGAGGAGAC 60.003 63.158 0.00 0.00 0.00 3.36
44 45 1.341531 AGTGTTGGAGGAGACGAACTG 59.658 52.381 0.00 0.00 31.59 3.16
119 120 2.254546 TTGCAAGACGAACTGGACAT 57.745 45.000 0.00 0.00 0.00 3.06
188 189 2.154389 GTCGCAGCATTCAAAAGCTTTG 59.846 45.455 13.54 7.34 39.50 2.77
296 297 2.115343 GGAGCGAATCCTTTGGACTT 57.885 50.000 0.09 0.00 45.64 3.01
312 313 2.125147 TTTGCCGCGGAGGATCTG 60.125 61.111 33.48 0.00 46.81 2.90
399 400 0.734889 ATTAATGGCGCTCACAGCAC 59.265 50.000 7.64 0.00 42.58 4.40
405 406 2.591429 CGCTCACAGCACCCACAA 60.591 61.111 0.00 0.00 42.58 3.33
521 522 2.805671 CGCATTCGGAGCCACAATAATA 59.194 45.455 0.00 0.00 0.00 0.98
601 602 3.068064 TGCTGTCTCCGGATGCGA 61.068 61.111 8.71 0.00 0.00 5.10
605 606 1.949847 CTGTCTCCGGATGCGAAGGT 61.950 60.000 8.71 0.00 0.00 3.50
611 615 1.364171 CGGATGCGAAGGTAGAGGG 59.636 63.158 0.00 0.00 0.00 4.30
686 690 2.563942 GCCGCATTTAACGCCACA 59.436 55.556 0.00 0.00 0.00 4.17
689 693 0.039978 CCGCATTTAACGCCACACAA 60.040 50.000 0.00 0.00 0.00 3.33
867 883 3.963676 CTCGAGAGGAGAGCCATTG 57.036 57.895 6.58 0.00 46.23 2.82
868 884 0.249405 CTCGAGAGGAGAGCCATTGC 60.249 60.000 6.58 0.00 46.23 3.56
870 886 1.684386 CGAGAGGAGAGCCATTGCCT 61.684 60.000 0.00 0.00 38.69 4.75
876 892 0.833287 GAGAGCCATTGCCTCCTACA 59.167 55.000 0.00 0.00 38.69 2.74
877 893 1.419387 GAGAGCCATTGCCTCCTACAT 59.581 52.381 0.00 0.00 38.69 2.29
878 894 1.849039 AGAGCCATTGCCTCCTACATT 59.151 47.619 0.00 0.00 38.69 2.71
879 895 2.243221 AGAGCCATTGCCTCCTACATTT 59.757 45.455 0.00 0.00 38.69 2.32
880 896 2.620585 GAGCCATTGCCTCCTACATTTC 59.379 50.000 0.00 0.00 38.69 2.17
881 897 1.334869 GCCATTGCCTCCTACATTTCG 59.665 52.381 0.00 0.00 0.00 3.46
882 898 2.643551 CCATTGCCTCCTACATTTCGT 58.356 47.619 0.00 0.00 0.00 3.85
883 899 2.355756 CCATTGCCTCCTACATTTCGTG 59.644 50.000 0.00 0.00 0.00 4.35
884 900 2.107950 TTGCCTCCTACATTTCGTGG 57.892 50.000 0.00 0.00 0.00 4.94
885 901 0.981183 TGCCTCCTACATTTCGTGGT 59.019 50.000 0.00 0.00 0.00 4.16
886 902 1.338674 TGCCTCCTACATTTCGTGGTG 60.339 52.381 0.00 0.00 0.00 4.17
887 903 2.012051 GCCTCCTACATTTCGTGGTGG 61.012 57.143 0.00 0.00 34.85 4.61
888 904 1.406887 CCTCCTACATTTCGTGGTGGG 60.407 57.143 0.00 0.00 37.03 4.61
889 905 0.035820 TCCTACATTTCGTGGTGGGC 60.036 55.000 0.00 0.00 35.79 5.36
890 906 0.035439 CCTACATTTCGTGGTGGGCT 60.035 55.000 0.00 0.00 0.00 5.19
891 907 1.086696 CTACATTTCGTGGTGGGCTG 58.913 55.000 0.00 0.00 0.00 4.85
892 908 0.687920 TACATTTCGTGGTGGGCTGA 59.312 50.000 0.00 0.00 0.00 4.26
893 909 0.606401 ACATTTCGTGGTGGGCTGAG 60.606 55.000 0.00 0.00 0.00 3.35
894 910 0.321564 CATTTCGTGGTGGGCTGAGA 60.322 55.000 0.00 0.00 0.00 3.27
895 911 0.036010 ATTTCGTGGTGGGCTGAGAG 60.036 55.000 0.00 0.00 0.00 3.20
896 912 1.118965 TTTCGTGGTGGGCTGAGAGA 61.119 55.000 0.00 0.00 0.00 3.10
897 913 1.118965 TTCGTGGTGGGCTGAGAGAA 61.119 55.000 0.00 0.00 0.00 2.87
898 914 0.904865 TCGTGGTGGGCTGAGAGAAT 60.905 55.000 0.00 0.00 0.00 2.40
899 915 0.824109 CGTGGTGGGCTGAGAGAATA 59.176 55.000 0.00 0.00 0.00 1.75
900 916 1.207089 CGTGGTGGGCTGAGAGAATAA 59.793 52.381 0.00 0.00 0.00 1.40
901 917 2.739932 CGTGGTGGGCTGAGAGAATAAG 60.740 54.545 0.00 0.00 0.00 1.73
902 918 2.501723 GTGGTGGGCTGAGAGAATAAGA 59.498 50.000 0.00 0.00 0.00 2.10
903 919 2.768527 TGGTGGGCTGAGAGAATAAGAG 59.231 50.000 0.00 0.00 0.00 2.85
904 920 2.484594 GGTGGGCTGAGAGAATAAGAGC 60.485 54.545 0.00 0.00 0.00 4.09
905 921 2.169352 GTGGGCTGAGAGAATAAGAGCA 59.831 50.000 0.00 0.00 0.00 4.26
906 922 3.044156 TGGGCTGAGAGAATAAGAGCAT 58.956 45.455 0.00 0.00 0.00 3.79
907 923 3.457380 TGGGCTGAGAGAATAAGAGCATT 59.543 43.478 0.00 0.00 0.00 3.56
908 924 4.064388 GGGCTGAGAGAATAAGAGCATTC 58.936 47.826 0.00 0.00 35.53 2.67
909 925 4.064388 GGCTGAGAGAATAAGAGCATTCC 58.936 47.826 0.00 0.00 35.85 3.01
910 926 4.444022 GGCTGAGAGAATAAGAGCATTCCA 60.444 45.833 0.00 0.00 35.85 3.53
911 927 4.751098 GCTGAGAGAATAAGAGCATTCCAG 59.249 45.833 0.00 0.00 35.85 3.86
912 928 5.684552 GCTGAGAGAATAAGAGCATTCCAGT 60.685 44.000 0.00 0.00 35.85 4.00
913 929 5.668471 TGAGAGAATAAGAGCATTCCAGTG 58.332 41.667 0.00 0.00 35.85 3.66
914 930 4.450053 AGAGAATAAGAGCATTCCAGTGC 58.550 43.478 0.00 0.00 45.38 4.40
926 942 2.644992 CAGTGCTGGCCGGAAAAC 59.355 61.111 18.31 10.14 0.00 2.43
927 943 2.192861 CAGTGCTGGCCGGAAAACA 61.193 57.895 18.31 0.00 0.00 2.83
928 944 1.898574 AGTGCTGGCCGGAAAACAG 60.899 57.895 18.31 8.66 35.40 3.16
935 951 0.594602 GGCCGGAAAACAGTGGTAAC 59.405 55.000 5.05 0.00 0.00 2.50
982 998 3.879892 GTGGGTCAGATCTTAAAGGCATC 59.120 47.826 0.00 0.00 0.00 3.91
984 1000 4.133078 GGGTCAGATCTTAAAGGCATCTG 58.867 47.826 0.00 4.37 43.38 2.90
989 1005 3.525199 AGATCTTAAAGGCATCTGGTGGT 59.475 43.478 0.00 0.00 0.00 4.16
991 1007 4.216411 TCTTAAAGGCATCTGGTGGTAC 57.784 45.455 0.00 0.00 0.00 3.34
993 1009 2.789409 AAAGGCATCTGGTGGTACTC 57.211 50.000 0.00 0.00 0.00 2.59
994 1010 0.537188 AAGGCATCTGGTGGTACTCG 59.463 55.000 0.00 0.00 0.00 4.18
995 1011 0.614979 AGGCATCTGGTGGTACTCGT 60.615 55.000 0.00 0.00 0.00 4.18
996 1012 1.108776 GGCATCTGGTGGTACTCGTA 58.891 55.000 0.00 0.00 0.00 3.43
997 1013 1.202382 GGCATCTGGTGGTACTCGTAC 60.202 57.143 0.00 0.00 35.40 3.67
998 1014 1.749634 GCATCTGGTGGTACTCGTACT 59.250 52.381 7.12 0.00 36.36 2.73
999 1015 2.947652 GCATCTGGTGGTACTCGTACTA 59.052 50.000 7.12 0.00 36.36 1.82
1000 1016 3.243002 GCATCTGGTGGTACTCGTACTAC 60.243 52.174 13.34 13.34 43.88 2.73
1011 1027 7.008810 GTGGTACTCGTACTACTATATAGTCGC 59.991 44.444 18.68 7.14 42.14 5.19
1012 1028 6.474102 GGTACTCGTACTACTATATAGTCGCC 59.526 46.154 18.68 8.88 36.36 5.54
1020 1049 2.824341 ACTATATAGTCGCCCCCGAAAG 59.176 50.000 9.71 0.00 46.34 2.62
1081 1119 1.911269 GGGGTTTCCGGTGGCAAAT 60.911 57.895 0.00 0.00 0.00 2.32
1094 1132 2.092429 GTGGCAAATATGGAGGGAGACA 60.092 50.000 0.00 0.00 0.00 3.41
1169 1207 5.682659 AGCTACTCGAACTAGTATTCCTGA 58.317 41.667 0.00 0.00 31.70 3.86
1240 1278 3.699484 CGCCGCATCATCGCTGAG 61.699 66.667 0.00 0.00 34.12 3.35
1328 1366 1.654440 CGTCGATGAGCGTACGCAT 60.654 57.895 38.58 25.85 44.88 4.73
1343 1381 4.082523 CATGGGTCGTGTCCGCCT 62.083 66.667 0.00 0.00 32.89 5.52
1402 1443 2.278206 CGTCGACATGCTCCCTCG 60.278 66.667 17.16 0.00 0.00 4.63
1484 1525 2.524394 GGCGGCCTCATCCTCCTA 60.524 66.667 12.87 0.00 0.00 2.94
1486 1527 1.369321 GCGGCCTCATCCTCCTAAG 59.631 63.158 0.00 0.00 0.00 2.18
1497 1538 0.737715 CCTCCTAAGTCAGTGCACGC 60.738 60.000 12.01 6.10 0.00 5.34
1522 1563 2.124403 GGACGAGGAGGAGCCGTA 60.124 66.667 0.00 0.00 43.43 4.02
1539 1580 1.334243 CGTATCTCTTCCACGACCTCC 59.666 57.143 0.00 0.00 37.89 4.30
1688 1735 6.532657 GCCTGTCAAATTTCAGAATAATGGTG 59.467 38.462 8.15 0.00 34.02 4.17
1691 1738 6.014755 TGTCAAATTTCAGAATAATGGTGGCA 60.015 34.615 0.00 0.00 0.00 4.92
1814 1870 1.676529 AGCAGCTTATACTTCGCTCGA 59.323 47.619 0.00 0.00 0.00 4.04
1850 1906 2.306805 TGTCTACTGGAGGACCGTAGAA 59.693 50.000 16.02 8.91 44.70 2.10
2007 2066 3.937706 CCAGCTCAAGGTCTTCATACAAG 59.062 47.826 0.00 0.00 0.00 3.16
2039 2098 2.621407 GGATGAATGGGTGCTGGAGAAA 60.621 50.000 0.00 0.00 0.00 2.52
2042 2101 1.821136 GAATGGGTGCTGGAGAAAAGG 59.179 52.381 0.00 0.00 0.00 3.11
2083 2142 0.031585 CGTGAGGTTGAAGGTGACGA 59.968 55.000 0.00 0.00 0.00 4.20
2092 2151 3.303881 TGAAGGTGACGATGAGTTGAG 57.696 47.619 0.00 0.00 0.00 3.02
2114 2173 2.280971 CGTCGACATGCTGAAGAAGATG 59.719 50.000 17.16 0.00 0.00 2.90
2116 2175 1.329906 CGACATGCTGAAGAAGATGGC 59.670 52.381 0.00 0.00 0.00 4.40
2138 2197 3.637273 GTGGCGGAGGGGTCTGTT 61.637 66.667 0.00 0.00 0.00 3.16
2205 2264 0.391661 CACCATGGAGTGTAAGCGCT 60.392 55.000 21.47 2.64 38.31 5.92
2272 3584 2.366837 ATGGCCTCCCACGATCCA 60.367 61.111 3.32 0.00 45.77 3.41
2296 3608 1.825090 TGCTTACCATGAACCAGCAG 58.175 50.000 0.00 0.00 35.56 4.24
2300 3612 3.679389 CTTACCATGAACCAGCAGTCTT 58.321 45.455 0.00 0.00 0.00 3.01
2350 3662 9.302345 AGTATGAACTGTATTAAGTGATCAACG 57.698 33.333 0.00 0.00 33.57 4.10
2366 3678 3.930336 TCAACGATCAATCTTGAGCTGT 58.070 40.909 6.61 3.92 41.19 4.40
2479 3797 7.262772 ACATTATCATTGTTGCATTCTCCTTG 58.737 34.615 0.00 0.00 0.00 3.61
2514 3832 0.447406 TTGATTGATGGAAGCGTGCG 59.553 50.000 0.00 0.00 0.00 5.34
2515 3833 1.353103 GATTGATGGAAGCGTGCGG 59.647 57.895 0.00 0.00 0.00 5.69
2538 3856 3.777106 TTTCAGAAGCTGTCCACTGAT 57.223 42.857 0.00 0.00 38.79 2.90
2558 3876 6.072618 ACTGATTGCTGTTGAGATTTCTTCTG 60.073 38.462 0.00 0.00 33.74 3.02
2560 3878 5.428496 TTGCTGTTGAGATTTCTTCTGTG 57.572 39.130 0.00 0.00 33.74 3.66
2561 3879 3.251729 TGCTGTTGAGATTTCTTCTGTGC 59.748 43.478 0.00 0.00 33.74 4.57
2572 3890 0.435008 CTTCTGTGCGTCGTGTTAGC 59.565 55.000 0.00 0.00 0.00 3.09
2578 3896 2.434134 GCGTCGTGTTAGCCAGTCG 61.434 63.158 0.00 0.00 0.00 4.18
2585 3903 4.031426 GTCGTGTTAGCCAGTCGATTTTAG 59.969 45.833 0.00 0.00 33.35 1.85
2645 3973 1.449778 GGTTAGAGCCCGCCACTTC 60.450 63.158 0.00 0.00 0.00 3.01
2697 4025 7.607250 TGATGAAAATTTAGTTGCCGGTAATT 58.393 30.769 8.64 6.92 0.00 1.40
2705 4033 4.563140 AGTTGCCGGTAATTCCTAGAAA 57.437 40.909 8.64 0.00 0.00 2.52
2706 4034 4.514401 AGTTGCCGGTAATTCCTAGAAAG 58.486 43.478 8.64 0.00 0.00 2.62
2707 4035 4.019591 AGTTGCCGGTAATTCCTAGAAAGT 60.020 41.667 8.64 0.00 0.00 2.66
2708 4036 4.133013 TGCCGGTAATTCCTAGAAAGTC 57.867 45.455 1.90 0.00 0.00 3.01
2709 4037 3.118519 TGCCGGTAATTCCTAGAAAGTCC 60.119 47.826 1.90 0.00 0.00 3.85
2710 4038 3.118519 GCCGGTAATTCCTAGAAAGTCCA 60.119 47.826 1.90 0.00 0.00 4.02
2711 4039 4.694339 CCGGTAATTCCTAGAAAGTCCAG 58.306 47.826 0.00 0.00 0.00 3.86
2713 4041 4.404715 CGGTAATTCCTAGAAAGTCCAGGA 59.595 45.833 0.00 0.00 36.68 3.86
2716 4044 6.070136 GGTAATTCCTAGAAAGTCCAGGAGTT 60.070 42.308 3.33 3.33 40.36 3.01
2719 4047 5.228945 TCCTAGAAAGTCCAGGAGTTTTG 57.771 43.478 21.33 14.56 35.63 2.44
2720 4048 4.041691 TCCTAGAAAGTCCAGGAGTTTTGG 59.958 45.833 21.33 20.87 35.63 3.28
2753 4081 4.365514 TCAAATGGTGGCAAGAGTTCTA 57.634 40.909 0.00 0.00 0.00 2.10
2760 4088 3.010420 GTGGCAAGAGTTCTACCCATTC 58.990 50.000 0.00 0.00 31.72 2.67
2761 4089 2.912956 TGGCAAGAGTTCTACCCATTCT 59.087 45.455 0.00 0.00 0.00 2.40
2762 4090 4.081087 GTGGCAAGAGTTCTACCCATTCTA 60.081 45.833 0.00 0.00 31.72 2.10
2801 4129 7.100409 ACTAGAAAGAATACCAGAGTTTGCTC 58.900 38.462 0.00 0.00 41.94 4.26
2813 4141 3.787785 GAGTTTGCTCTTAGCTACTCCC 58.212 50.000 16.87 2.67 42.38 4.30
2814 4142 3.445987 AGTTTGCTCTTAGCTACTCCCT 58.554 45.455 0.00 0.00 42.97 4.20
2815 4143 3.449377 AGTTTGCTCTTAGCTACTCCCTC 59.551 47.826 0.00 0.00 42.97 4.30
2816 4144 2.074729 TGCTCTTAGCTACTCCCTCC 57.925 55.000 0.00 0.00 42.97 4.30
2817 4145 0.955905 GCTCTTAGCTACTCCCTCCG 59.044 60.000 0.00 0.00 38.45 4.63
2818 4146 1.751382 GCTCTTAGCTACTCCCTCCGT 60.751 57.143 0.00 0.00 38.45 4.69
2819 4147 2.657143 CTCTTAGCTACTCCCTCCGTT 58.343 52.381 0.00 0.00 0.00 4.44
2820 4148 2.619646 CTCTTAGCTACTCCCTCCGTTC 59.380 54.545 0.00 0.00 0.00 3.95
2821 4149 2.241685 TCTTAGCTACTCCCTCCGTTCT 59.758 50.000 0.00 0.00 0.00 3.01
2822 4150 2.054232 TAGCTACTCCCTCCGTTCTG 57.946 55.000 0.00 0.00 0.00 3.02
2823 4151 0.331954 AGCTACTCCCTCCGTTCTGA 59.668 55.000 0.00 0.00 0.00 3.27
2824 4152 1.183549 GCTACTCCCTCCGTTCTGAA 58.816 55.000 0.00 0.00 0.00 3.02
2825 4153 1.757699 GCTACTCCCTCCGTTCTGAAT 59.242 52.381 0.00 0.00 0.00 2.57
2826 4154 2.168728 GCTACTCCCTCCGTTCTGAATT 59.831 50.000 0.00 0.00 0.00 2.17
2827 4155 3.383825 GCTACTCCCTCCGTTCTGAATTA 59.616 47.826 0.00 0.00 0.00 1.40
2828 4156 3.889520 ACTCCCTCCGTTCTGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
2829 4157 3.442076 ACTCCCTCCGTTCTGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
2830 4158 3.838903 ACTCCCTCCGTTCTGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
2831 4159 4.184629 CTCCCTCCGTTCTGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
2832 4160 3.581332 TCCCTCCGTTCTGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
2833 4161 3.933332 CCCTCCGTTCTGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2834 4162 4.322801 CCCTCCGTTCTGAATTACTTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
2835 4163 5.238583 CCTCCGTTCTGAATTACTTGTCTT 58.761 41.667 0.00 0.00 0.00 3.01
2836 4164 6.395629 CCTCCGTTCTGAATTACTTGTCTTA 58.604 40.000 0.00 0.00 0.00 2.10
2837 4165 6.531948 CCTCCGTTCTGAATTACTTGTCTTAG 59.468 42.308 0.00 0.00 0.00 2.18
2838 4166 7.223260 TCCGTTCTGAATTACTTGTCTTAGA 57.777 36.000 0.00 0.00 0.00 2.10
2839 4167 7.837863 TCCGTTCTGAATTACTTGTCTTAGAT 58.162 34.615 0.00 0.00 0.00 1.98
2840 4168 8.311836 TCCGTTCTGAATTACTTGTCTTAGATT 58.688 33.333 0.00 0.00 0.00 2.40
2841 4169 8.936864 CCGTTCTGAATTACTTGTCTTAGATTT 58.063 33.333 0.00 0.00 0.00 2.17
2842 4170 9.746711 CGTTCTGAATTACTTGTCTTAGATTTG 57.253 33.333 0.00 0.00 0.00 2.32
2853 4181 8.407064 ACTTGTCTTAGATTTGTCTAGATACGG 58.593 37.037 0.00 0.00 0.00 4.02
2854 4182 7.273320 TGTCTTAGATTTGTCTAGATACGGG 57.727 40.000 0.00 0.00 0.00 5.28
2855 4183 6.264744 TGTCTTAGATTTGTCTAGATACGGGG 59.735 42.308 0.00 0.00 0.00 5.73
2856 4184 6.264970 GTCTTAGATTTGTCTAGATACGGGGT 59.735 42.308 0.00 0.00 0.00 4.95
2857 4185 6.837568 TCTTAGATTTGTCTAGATACGGGGTT 59.162 38.462 0.00 0.00 0.00 4.11
2858 4186 8.000709 TCTTAGATTTGTCTAGATACGGGGTTA 58.999 37.037 0.00 0.00 0.00 2.85
2859 4187 8.716674 TTAGATTTGTCTAGATACGGGGTTAT 57.283 34.615 0.00 0.00 0.00 1.89
2860 4188 7.229581 AGATTTGTCTAGATACGGGGTTATC 57.770 40.000 0.00 0.00 0.00 1.75
2861 4189 7.011382 AGATTTGTCTAGATACGGGGTTATCT 58.989 38.462 0.00 0.00 36.96 1.98
2862 4190 8.168725 AGATTTGTCTAGATACGGGGTTATCTA 58.831 37.037 0.00 0.00 35.03 1.98
2863 4191 7.756395 TTTGTCTAGATACGGGGTTATCTAG 57.244 40.000 16.30 16.30 46.80 2.43
2864 4192 5.251764 TGTCTAGATACGGGGTTATCTAGC 58.748 45.833 17.10 13.89 45.84 3.42
2865 4193 5.221986 TGTCTAGATACGGGGTTATCTAGCA 60.222 44.000 17.10 15.44 45.84 3.49
2866 4194 5.123661 GTCTAGATACGGGGTTATCTAGCAC 59.876 48.000 17.10 13.58 45.84 4.40
2867 4195 4.115398 AGATACGGGGTTATCTAGCACT 57.885 45.455 0.00 0.00 31.79 4.40
2868 4196 5.252586 AGATACGGGGTTATCTAGCACTA 57.747 43.478 0.00 0.00 31.79 2.74
2869 4197 5.638133 AGATACGGGGTTATCTAGCACTAA 58.362 41.667 0.00 0.00 31.79 2.24
2870 4198 6.073314 AGATACGGGGTTATCTAGCACTAAA 58.927 40.000 0.00 0.00 31.79 1.85
2871 4199 6.552350 AGATACGGGGTTATCTAGCACTAAAA 59.448 38.462 0.00 0.00 31.79 1.52
2872 4200 5.625568 ACGGGGTTATCTAGCACTAAAAT 57.374 39.130 0.00 0.00 0.00 1.82
2873 4201 5.365619 ACGGGGTTATCTAGCACTAAAATG 58.634 41.667 0.00 0.00 0.00 2.32
2874 4202 5.129815 ACGGGGTTATCTAGCACTAAAATGA 59.870 40.000 0.00 0.00 0.00 2.57
2875 4203 5.696724 CGGGGTTATCTAGCACTAAAATGAG 59.303 44.000 0.00 0.00 0.00 2.90
2876 4204 6.592870 GGGGTTATCTAGCACTAAAATGAGT 58.407 40.000 0.00 0.00 0.00 3.41
2877 4205 6.706716 GGGGTTATCTAGCACTAAAATGAGTC 59.293 42.308 0.00 0.00 0.00 3.36
2878 4206 7.419172 GGGGTTATCTAGCACTAAAATGAGTCT 60.419 40.741 0.00 0.00 0.00 3.24
2879 4207 8.639761 GGGTTATCTAGCACTAAAATGAGTCTA 58.360 37.037 0.00 0.00 0.00 2.59
2880 4208 9.685828 GGTTATCTAGCACTAAAATGAGTCTAG 57.314 37.037 0.00 0.00 33.29 2.43
2885 4213 9.628500 TCTAGCACTAAAATGAGTCTAGATACA 57.372 33.333 0.00 0.00 34.65 2.29
2888 4216 9.142014 AGCACTAAAATGAGTCTAGATACATCT 57.858 33.333 12.66 0.00 40.86 2.90
2889 4217 9.190858 GCACTAAAATGAGTCTAGATACATCTG 57.809 37.037 12.66 7.80 37.76 2.90
2908 4236 8.311395 ACATCTGTATCTAGACAAATCCAAGA 57.689 34.615 0.00 0.00 0.00 3.02
2909 4237 8.200792 ACATCTGTATCTAGACAAATCCAAGAC 58.799 37.037 0.00 0.00 0.00 3.01
2910 4238 7.718334 TCTGTATCTAGACAAATCCAAGACA 57.282 36.000 0.00 0.00 0.00 3.41
2911 4239 8.134202 TCTGTATCTAGACAAATCCAAGACAA 57.866 34.615 0.00 0.00 0.00 3.18
2912 4240 8.253810 TCTGTATCTAGACAAATCCAAGACAAG 58.746 37.037 0.00 0.00 0.00 3.16
2913 4241 7.907389 TGTATCTAGACAAATCCAAGACAAGT 58.093 34.615 0.00 0.00 0.00 3.16
2914 4242 9.031537 TGTATCTAGACAAATCCAAGACAAGTA 57.968 33.333 0.00 0.00 0.00 2.24
2915 4243 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
2917 4245 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
2918 4246 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
2919 4247 7.133891 AGACAAATCCAAGACAAGTAATTCG 57.866 36.000 0.00 0.00 0.00 3.34
2920 4248 6.149474 AGACAAATCCAAGACAAGTAATTCGG 59.851 38.462 0.00 0.00 0.00 4.30
2921 4249 6.001460 ACAAATCCAAGACAAGTAATTCGGA 58.999 36.000 0.00 0.00 0.00 4.55
2922 4250 6.488683 ACAAATCCAAGACAAGTAATTCGGAA 59.511 34.615 0.00 0.00 0.00 4.30
2923 4251 6.496338 AATCCAAGACAAGTAATTCGGAAC 57.504 37.500 0.00 0.00 0.00 3.62
2924 4252 4.963373 TCCAAGACAAGTAATTCGGAACA 58.037 39.130 0.00 0.00 0.00 3.18
2925 4253 4.994852 TCCAAGACAAGTAATTCGGAACAG 59.005 41.667 0.00 0.00 0.00 3.16
2926 4254 4.994852 CCAAGACAAGTAATTCGGAACAGA 59.005 41.667 0.00 0.00 0.00 3.41
2927 4255 5.120830 CCAAGACAAGTAATTCGGAACAGAG 59.879 44.000 0.00 0.00 0.00 3.35
2928 4256 4.822026 AGACAAGTAATTCGGAACAGAGG 58.178 43.478 0.00 0.00 0.00 3.69
2929 4257 3.933332 GACAAGTAATTCGGAACAGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2930 4258 3.581332 ACAAGTAATTCGGAACAGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
2931 4259 4.184629 CAAGTAATTCGGAACAGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
2932 4260 3.442076 AGTAATTCGGAACAGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
2933 4261 4.607239 AGTAATTCGGAACAGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
2934 4262 3.889520 AATTCGGAACAGAGGGAGTAC 57.110 47.619 0.00 0.00 0.00 2.73
2935 4263 2.297698 TTCGGAACAGAGGGAGTACA 57.702 50.000 0.00 0.00 0.00 2.90
2936 4264 2.297698 TCGGAACAGAGGGAGTACAA 57.702 50.000 0.00 0.00 0.00 2.41
2968 4296 5.128205 CCTGATGATTTAGACAATGCCTCA 58.872 41.667 0.00 0.00 0.00 3.86
2978 4306 2.362077 GACAATGCCTCAACACCAAACT 59.638 45.455 0.00 0.00 0.00 2.66
2983 4311 1.318576 CCTCAACACCAAACTCACCC 58.681 55.000 0.00 0.00 0.00 4.61
2984 4312 1.318576 CTCAACACCAAACTCACCCC 58.681 55.000 0.00 0.00 0.00 4.95
2999 4327 2.890311 TCACCCCAGTAAAATGCACAAG 59.110 45.455 0.00 0.00 0.00 3.16
3001 4329 3.511146 CACCCCAGTAAAATGCACAAGAT 59.489 43.478 0.00 0.00 0.00 2.40
3008 4336 5.048504 CAGTAAAATGCACAAGATCACCACT 60.049 40.000 0.00 0.00 0.00 4.00
3013 4341 2.813754 TGCACAAGATCACCACTTTAGC 59.186 45.455 0.00 0.00 0.00 3.09
3014 4342 3.077359 GCACAAGATCACCACTTTAGCT 58.923 45.455 0.00 0.00 0.00 3.32
3035 4363 6.112994 GCTTCATAGCTCTTGGAAAACTAC 57.887 41.667 0.00 0.00 44.27 2.73
3039 4367 5.248477 TCATAGCTCTTGGAAAACTACCACT 59.752 40.000 0.00 0.00 37.13 4.00
3074 4427 2.017138 TTTCGCACAGAACACTGACA 57.983 45.000 0.00 0.00 38.83 3.58
3109 4462 4.143200 GCGTTTTGATGACGTCACTAATCA 60.143 41.667 22.71 17.67 42.22 2.57
3130 4483 0.179045 CCGGGCTCAAGGTGGATTAG 60.179 60.000 0.00 0.00 0.00 1.73
3137 4490 1.559682 TCAAGGTGGATTAGGAGTGCC 59.440 52.381 0.00 0.00 0.00 5.01
3159 4512 5.056480 CCAGATATCACCGCTCATAACAAA 58.944 41.667 5.32 0.00 0.00 2.83
3213 4566 9.958180 TTTCTCAACAAGTATAATTCTCCATGA 57.042 29.630 0.00 0.00 0.00 3.07
3216 4569 8.948631 TCAACAAGTATAATTCTCCATGAGTC 57.051 34.615 0.00 0.00 0.00 3.36
3218 4571 9.166173 CAACAAGTATAATTCTCCATGAGTCAA 57.834 33.333 0.00 0.00 0.00 3.18
3226 4579 5.688814 TTCTCCATGAGTCAACATCATCT 57.311 39.130 0.00 0.00 35.20 2.90
3229 4582 3.776417 TCCATGAGTCAACATCATCTGGA 59.224 43.478 0.00 0.00 34.81 3.86
3256 4609 4.956700 CCCACTATTCACACTCTCTTCCTA 59.043 45.833 0.00 0.00 0.00 2.94
3262 4615 5.651387 TTCACACTCTCTTCCTAGTGATG 57.349 43.478 9.30 4.63 44.79 3.07
3272 4625 3.129262 TCCTAGTGATGGGATGGTTGA 57.871 47.619 0.00 0.00 0.00 3.18
3290 4643 4.058124 GTTGAATCCTTTTGGTGGAAAGC 58.942 43.478 0.00 0.00 41.38 3.51
3292 4645 3.321682 TGAATCCTTTTGGTGGAAAGCTG 59.678 43.478 0.00 0.00 41.38 4.24
3296 4649 2.224042 CCTTTTGGTGGAAAGCTGTTCC 60.224 50.000 16.35 16.35 35.73 3.62
3298 4651 0.181587 TTGGTGGAAAGCTGTTCCGA 59.818 50.000 17.40 8.43 41.43 4.55
3299 4652 0.250295 TGGTGGAAAGCTGTTCCGAG 60.250 55.000 17.40 0.00 41.43 4.63
3300 4653 0.034896 GGTGGAAAGCTGTTCCGAGA 59.965 55.000 17.40 3.82 41.43 4.04
3318 4671 5.894393 TCCGAGAAGACTTCTATCCATCTTT 59.106 40.000 17.71 0.00 40.87 2.52
3345 4698 7.833285 ACAATTTTCAGTATGTAAACCTGGT 57.167 32.000 0.00 0.00 38.18 4.00
3385 4738 0.539438 TTGGACTGATGGTTGGTGGC 60.539 55.000 0.00 0.00 0.00 5.01
3386 4739 1.380302 GGACTGATGGTTGGTGGCT 59.620 57.895 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 2.124983 GGGCATCTTGAGCGCTCA 60.125 61.111 35.30 35.30 41.20 4.26
172 173 2.486918 GCCACAAAGCTTTTGAATGCT 58.513 42.857 9.53 0.00 40.65 3.79
188 189 3.691744 CTGTCTCGCCTCTCGCCAC 62.692 68.421 0.00 0.00 38.27 5.01
296 297 4.838152 GCAGATCCTCCGCGGCAA 62.838 66.667 23.51 8.52 0.00 4.52
468 469 2.473760 CGTCGGCGATCTCCTCTGT 61.474 63.158 14.79 0.00 41.33 3.41
587 588 0.681887 TACCTTCGCATCCGGAGACA 60.682 55.000 11.34 0.00 42.89 3.41
601 602 2.356780 CGTTCCGGCCCTCTACCTT 61.357 63.158 0.00 0.00 0.00 3.50
605 606 4.064768 TCCCGTTCCGGCCCTCTA 62.065 66.667 0.00 0.00 46.86 2.43
611 615 4.547367 CCATCCTCCCGTTCCGGC 62.547 72.222 0.00 0.00 46.86 6.13
686 690 2.044946 GGCCGCATCTTCCCTTGT 60.045 61.111 0.00 0.00 0.00 3.16
866 882 0.981183 ACCACGAAATGTAGGAGGCA 59.019 50.000 0.00 0.00 0.00 4.75
867 883 1.369625 CACCACGAAATGTAGGAGGC 58.630 55.000 0.00 0.00 0.00 4.70
868 884 1.406887 CCCACCACGAAATGTAGGAGG 60.407 57.143 0.00 0.00 32.93 4.30
870 886 0.035820 GCCCACCACGAAATGTAGGA 60.036 55.000 0.00 0.00 0.00 2.94
876 892 0.036010 CTCTCAGCCCACCACGAAAT 60.036 55.000 0.00 0.00 0.00 2.17
877 893 1.118965 TCTCTCAGCCCACCACGAAA 61.119 55.000 0.00 0.00 0.00 3.46
878 894 1.118965 TTCTCTCAGCCCACCACGAA 61.119 55.000 0.00 0.00 0.00 3.85
879 895 0.904865 ATTCTCTCAGCCCACCACGA 60.905 55.000 0.00 0.00 0.00 4.35
880 896 0.824109 TATTCTCTCAGCCCACCACG 59.176 55.000 0.00 0.00 0.00 4.94
881 897 2.501723 TCTTATTCTCTCAGCCCACCAC 59.498 50.000 0.00 0.00 0.00 4.16
882 898 2.768527 CTCTTATTCTCTCAGCCCACCA 59.231 50.000 0.00 0.00 0.00 4.17
883 899 2.484594 GCTCTTATTCTCTCAGCCCACC 60.485 54.545 0.00 0.00 0.00 4.61
884 900 2.169352 TGCTCTTATTCTCTCAGCCCAC 59.831 50.000 0.00 0.00 0.00 4.61
885 901 2.470990 TGCTCTTATTCTCTCAGCCCA 58.529 47.619 0.00 0.00 0.00 5.36
886 902 3.767902 ATGCTCTTATTCTCTCAGCCC 57.232 47.619 0.00 0.00 0.00 5.19
887 903 4.064388 GGAATGCTCTTATTCTCTCAGCC 58.936 47.826 0.00 0.00 37.26 4.85
888 904 4.701765 TGGAATGCTCTTATTCTCTCAGC 58.298 43.478 0.00 0.00 37.26 4.26
889 905 5.754406 CACTGGAATGCTCTTATTCTCTCAG 59.246 44.000 0.00 0.00 37.26 3.35
890 906 5.668471 CACTGGAATGCTCTTATTCTCTCA 58.332 41.667 0.00 0.00 37.26 3.27
891 907 4.511082 GCACTGGAATGCTCTTATTCTCTC 59.489 45.833 0.00 0.00 42.62 3.20
892 908 4.450053 GCACTGGAATGCTCTTATTCTCT 58.550 43.478 0.00 0.00 42.62 3.10
893 909 4.809815 GCACTGGAATGCTCTTATTCTC 57.190 45.455 0.00 0.00 42.62 2.87
909 925 2.133742 CTGTTTTCCGGCCAGCACTG 62.134 60.000 2.24 0.00 0.00 3.66
910 926 1.898574 CTGTTTTCCGGCCAGCACT 60.899 57.895 2.24 0.00 0.00 4.40
911 927 2.193536 ACTGTTTTCCGGCCAGCAC 61.194 57.895 2.24 0.00 0.00 4.40
912 928 2.192861 CACTGTTTTCCGGCCAGCA 61.193 57.895 2.24 0.00 0.00 4.41
913 929 2.644992 CACTGTTTTCCGGCCAGC 59.355 61.111 2.24 0.00 0.00 4.85
914 930 0.250553 TACCACTGTTTTCCGGCCAG 60.251 55.000 2.24 2.44 0.00 4.85
915 931 0.183014 TTACCACTGTTTTCCGGCCA 59.817 50.000 2.24 0.00 0.00 5.36
916 932 0.594602 GTTACCACTGTTTTCCGGCC 59.405 55.000 0.00 0.00 0.00 6.13
917 933 0.594602 GGTTACCACTGTTTTCCGGC 59.405 55.000 0.00 0.00 0.00 6.13
918 934 1.970092 TGGTTACCACTGTTTTCCGG 58.030 50.000 0.00 0.00 0.00 5.14
935 951 1.478105 GCCTTTTTAGCCCATCAGTGG 59.522 52.381 0.00 0.00 45.61 4.00
948 964 0.105246 TGACCCACCATGGCCTTTTT 60.105 50.000 13.04 0.00 35.79 1.94
950 966 1.077265 CTGACCCACCATGGCCTTT 59.923 57.895 13.04 0.00 35.79 3.11
982 998 8.310382 ACTATATAGTAGTACGAGTACCACCAG 58.690 40.741 13.88 3.02 36.75 4.00
984 1000 7.486551 CGACTATATAGTAGTACGAGTACCACC 59.513 44.444 15.42 0.00 36.50 4.61
989 1005 6.405953 GGGGCGACTATATAGTAGTACGAGTA 60.406 46.154 20.03 0.00 36.50 2.59
991 1007 4.808364 GGGGCGACTATATAGTAGTACGAG 59.192 50.000 20.03 7.45 36.50 4.18
993 1009 3.873952 GGGGGCGACTATATAGTAGTACG 59.126 52.174 20.08 17.12 36.50 3.67
994 1010 3.873952 CGGGGGCGACTATATAGTAGTAC 59.126 52.174 20.08 14.50 36.50 2.73
995 1011 3.774766 TCGGGGGCGACTATATAGTAGTA 59.225 47.826 20.08 2.25 36.50 1.82
996 1012 2.573462 TCGGGGGCGACTATATAGTAGT 59.427 50.000 20.08 0.92 36.50 2.73
997 1013 3.272574 TCGGGGGCGACTATATAGTAG 57.727 52.381 15.42 15.89 36.50 2.57
998 1014 3.719268 TTCGGGGGCGACTATATAGTA 57.281 47.619 15.42 0.00 36.50 1.82
999 1015 2.592102 TTCGGGGGCGACTATATAGT 57.408 50.000 15.37 15.37 39.71 2.12
1000 1016 2.416972 GCTTTCGGGGGCGACTATATAG 60.417 54.545 8.27 8.27 0.00 1.31
1011 1027 1.678970 CCTTGGAAGCTTTCGGGGG 60.679 63.158 0.00 0.00 0.00 5.40
1012 1028 1.678970 CCCTTGGAAGCTTTCGGGG 60.679 63.158 17.78 17.78 0.00 5.73
1020 1049 0.034960 GAGGAGGAACCCTTGGAAGC 60.035 60.000 0.00 0.00 40.05 3.86
1081 1119 1.395045 CGCTGCTGTCTCCCTCCATA 61.395 60.000 0.00 0.00 0.00 2.74
1150 1188 3.633065 GGCTCAGGAATACTAGTTCGAGT 59.367 47.826 0.00 0.00 0.00 4.18
1169 1207 2.366570 GAGTGAGGAGGGGAGGCT 59.633 66.667 0.00 0.00 0.00 4.58
1252 1290 4.840005 GGAAGCGGCCGAGGAAGG 62.840 72.222 33.48 0.00 0.00 3.46
1343 1381 1.002624 GAAGACGGGGTTGCATCCA 60.003 57.895 15.63 0.00 0.00 3.41
1345 1383 0.744771 GGAGAAGACGGGGTTGCATC 60.745 60.000 0.00 0.00 0.00 3.91
1379 1420 1.213013 GAGCATGTCGACGGTGTCT 59.787 57.895 18.30 15.64 0.00 3.41
1402 1443 0.667792 AAAGTCGAGCGAGAAGTGCC 60.668 55.000 0.00 0.00 0.00 5.01
1476 1517 1.478510 CGTGCACTGACTTAGGAGGAT 59.521 52.381 16.19 0.00 0.00 3.24
1484 1525 3.640000 GCGTGCGTGCACTGACTT 61.640 61.111 21.36 0.00 44.16 3.01
1497 1538 4.180946 CTCCTCGTCCTCGGCGTG 62.181 72.222 6.85 3.87 37.69 5.34
1522 1563 1.770294 GAGGAGGTCGTGGAAGAGAT 58.230 55.000 0.00 0.00 0.00 2.75
1814 1870 2.038387 AGACATAGCGGGCGAAATTT 57.962 45.000 0.00 0.00 0.00 1.82
1850 1906 2.749621 GTCAAGGACAATGATTTCGGCT 59.250 45.455 0.00 0.00 32.09 5.52
1981 2040 0.322975 GAAGACCTTGAGCTGGCTGA 59.677 55.000 0.00 0.00 0.00 4.26
1982 2041 0.035881 TGAAGACCTTGAGCTGGCTG 59.964 55.000 0.00 0.00 0.00 4.85
1988 2047 3.338249 TGCTTGTATGAAGACCTTGAGC 58.662 45.455 0.00 0.00 0.00 4.26
2007 2066 0.822532 CATTCATCCCTGCCCTCTGC 60.823 60.000 0.00 0.00 41.77 4.26
2039 2098 1.228367 CTGCTGCAGTTGGACCCTT 60.228 57.895 21.21 0.00 0.00 3.95
2073 2132 1.996191 GCTCAACTCATCGTCACCTTC 59.004 52.381 0.00 0.00 0.00 3.46
2083 2142 1.633561 CATGTCGACGCTCAACTCAT 58.366 50.000 11.62 0.00 0.00 2.90
2092 2151 0.368227 CTTCTTCAGCATGTCGACGC 59.632 55.000 11.62 9.26 37.40 5.19
2138 2197 2.680841 GCCTTTGTCTGTACACAACACA 59.319 45.455 5.95 0.45 35.97 3.72
2205 2264 4.297299 AGTACTTGTTCTCGTCGTGAAA 57.703 40.909 11.03 0.00 0.00 2.69
2272 3584 2.821969 CTGGTTCATGGTAAGCAAGCTT 59.178 45.455 12.42 12.42 36.50 3.74
2300 3612 6.552859 TGAGAACAAAATAAACAGATCGCA 57.447 33.333 0.00 0.00 0.00 5.10
2345 3657 3.930336 ACAGCTCAAGATTGATCGTTGA 58.070 40.909 0.00 0.00 36.46 3.18
2346 3658 4.675190 AACAGCTCAAGATTGATCGTTG 57.325 40.909 0.00 0.00 36.46 4.10
2347 3659 5.455392 CAAAACAGCTCAAGATTGATCGTT 58.545 37.500 0.00 0.00 36.46 3.85
2348 3660 4.614535 GCAAAACAGCTCAAGATTGATCGT 60.615 41.667 0.00 0.00 36.46 3.73
2349 3661 3.850273 GCAAAACAGCTCAAGATTGATCG 59.150 43.478 0.00 0.00 36.46 3.69
2350 3662 4.801891 TGCAAAACAGCTCAAGATTGATC 58.198 39.130 0.00 0.00 36.46 2.92
2366 3678 6.857777 AAATTCATGGAACGAAATGCAAAA 57.142 29.167 0.00 0.00 0.00 2.44
2421 3739 6.877611 TCCAAGGAACTGAAATACTTGAAC 57.122 37.500 0.00 0.00 40.86 3.18
2479 3797 7.175641 CCATCAATCAAGATATTTCCCCTACAC 59.824 40.741 0.00 0.00 0.00 2.90
2514 3832 2.952310 AGTGGACAGCTTCTGAAAAACC 59.048 45.455 0.29 0.00 35.18 3.27
2515 3833 3.627577 TCAGTGGACAGCTTCTGAAAAAC 59.372 43.478 0.29 0.00 34.61 2.43
2538 3856 4.261322 GCACAGAAGAAATCTCAACAGCAA 60.261 41.667 0.00 0.00 35.73 3.91
2558 3876 1.615107 GACTGGCTAACACGACGCAC 61.615 60.000 0.00 0.00 0.00 5.34
2560 3878 2.434134 CGACTGGCTAACACGACGC 61.434 63.158 0.00 0.00 0.00 5.19
2561 3879 0.179171 ATCGACTGGCTAACACGACG 60.179 55.000 0.00 0.00 35.91 5.12
2572 3890 3.614616 GCTCTCACACTAAAATCGACTGG 59.385 47.826 0.00 0.00 0.00 4.00
2578 3896 8.364142 AGGTATCATAGCTCTCACACTAAAATC 58.636 37.037 0.00 0.00 0.00 2.17
2585 3903 5.163509 TGTGAAGGTATCATAGCTCTCACAC 60.164 44.000 23.56 18.19 42.33 3.82
2645 3973 7.156876 TGGATTATAAAGTTGGTCTTGCAAG 57.843 36.000 20.81 20.81 36.40 4.01
2733 4061 3.191371 GGTAGAACTCTTGCCACCATTTG 59.809 47.826 0.00 0.00 0.00 2.32
2734 4062 3.421844 GGTAGAACTCTTGCCACCATTT 58.578 45.455 0.00 0.00 0.00 2.32
2740 4068 2.912956 AGAATGGGTAGAACTCTTGCCA 59.087 45.455 0.00 0.00 0.00 4.92
2801 4129 2.359531 CAGAACGGAGGGAGTAGCTAAG 59.640 54.545 0.00 0.00 0.00 2.18
2802 4130 2.025605 TCAGAACGGAGGGAGTAGCTAA 60.026 50.000 0.00 0.00 0.00 3.09
2810 4138 3.581332 ACAAGTAATTCAGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
2811 4139 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2812 4140 4.822026 AGACAAGTAATTCAGAACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
2813 4141 7.313646 TCTAAGACAAGTAATTCAGAACGGAG 58.686 38.462 0.00 0.00 0.00 4.63
2814 4142 7.223260 TCTAAGACAAGTAATTCAGAACGGA 57.777 36.000 0.00 0.00 0.00 4.69
2815 4143 8.480643 AATCTAAGACAAGTAATTCAGAACGG 57.519 34.615 0.00 0.00 0.00 4.44
2816 4144 9.746711 CAAATCTAAGACAAGTAATTCAGAACG 57.253 33.333 0.00 0.00 0.00 3.95
2827 4155 8.407064 CCGTATCTAGACAAATCTAAGACAAGT 58.593 37.037 0.00 0.00 36.98 3.16
2828 4156 7.863375 CCCGTATCTAGACAAATCTAAGACAAG 59.137 40.741 0.00 0.00 36.98 3.16
2829 4157 7.201884 CCCCGTATCTAGACAAATCTAAGACAA 60.202 40.741 0.00 0.00 36.98 3.18
2830 4158 6.264744 CCCCGTATCTAGACAAATCTAAGACA 59.735 42.308 0.00 0.00 36.98 3.41
2831 4159 6.264970 ACCCCGTATCTAGACAAATCTAAGAC 59.735 42.308 0.00 0.00 36.98 3.01
2832 4160 6.371278 ACCCCGTATCTAGACAAATCTAAGA 58.629 40.000 0.00 0.00 36.98 2.10
2833 4161 6.651975 ACCCCGTATCTAGACAAATCTAAG 57.348 41.667 0.00 0.00 36.98 2.18
2834 4162 8.716674 ATAACCCCGTATCTAGACAAATCTAA 57.283 34.615 0.00 0.00 36.98 2.10
2835 4163 8.168725 AGATAACCCCGTATCTAGACAAATCTA 58.831 37.037 0.00 0.00 38.74 1.98
2836 4164 7.011382 AGATAACCCCGTATCTAGACAAATCT 58.989 38.462 0.00 0.00 38.74 2.40
2837 4165 7.229581 AGATAACCCCGTATCTAGACAAATC 57.770 40.000 0.00 0.00 38.74 2.17
2845 4173 5.252586 AGTGCTAGATAACCCCGTATCTA 57.747 43.478 0.00 2.79 40.54 1.98
2846 4174 4.115398 AGTGCTAGATAACCCCGTATCT 57.885 45.455 0.00 0.78 42.32 1.98
2847 4175 5.972107 TTAGTGCTAGATAACCCCGTATC 57.028 43.478 0.00 0.00 0.00 2.24
2848 4176 6.736110 TTTTAGTGCTAGATAACCCCGTAT 57.264 37.500 0.00 0.00 0.00 3.06
2849 4177 6.324512 TCATTTTAGTGCTAGATAACCCCGTA 59.675 38.462 0.00 0.00 0.00 4.02
2850 4178 5.129815 TCATTTTAGTGCTAGATAACCCCGT 59.870 40.000 0.00 0.00 0.00 5.28
2851 4179 5.607477 TCATTTTAGTGCTAGATAACCCCG 58.393 41.667 0.00 0.00 0.00 5.73
2852 4180 6.592870 ACTCATTTTAGTGCTAGATAACCCC 58.407 40.000 0.00 0.00 0.00 4.95
2853 4181 7.501844 AGACTCATTTTAGTGCTAGATAACCC 58.498 38.462 0.00 0.00 0.00 4.11
2854 4182 9.685828 CTAGACTCATTTTAGTGCTAGATAACC 57.314 37.037 0.00 0.00 33.59 2.85
2859 4187 9.628500 TGTATCTAGACTCATTTTAGTGCTAGA 57.372 33.333 0.00 0.00 38.76 2.43
2862 4190 9.142014 AGATGTATCTAGACTCATTTTAGTGCT 57.858 33.333 11.25 2.44 34.85 4.40
2863 4191 9.190858 CAGATGTATCTAGACTCATTTTAGTGC 57.809 37.037 11.25 0.69 34.85 4.40
2882 4210 9.421399 TCTTGGATTTGTCTAGATACAGATGTA 57.579 33.333 0.00 0.00 34.67 2.29
2883 4211 8.200792 GTCTTGGATTTGTCTAGATACAGATGT 58.799 37.037 0.00 0.00 0.00 3.06
2884 4212 8.200120 TGTCTTGGATTTGTCTAGATACAGATG 58.800 37.037 0.00 0.00 0.00 2.90
2885 4213 8.311395 TGTCTTGGATTTGTCTAGATACAGAT 57.689 34.615 0.00 0.00 0.00 2.90
2886 4214 7.718334 TGTCTTGGATTTGTCTAGATACAGA 57.282 36.000 0.00 0.00 0.00 3.41
2887 4215 8.037758 ACTTGTCTTGGATTTGTCTAGATACAG 58.962 37.037 0.00 0.00 0.00 2.74
2888 4216 7.907389 ACTTGTCTTGGATTTGTCTAGATACA 58.093 34.615 0.00 0.00 0.00 2.29
2889 4217 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
2891 4219 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
2892 4220 9.436957 GAATTACTTGTCTTGGATTTGTCTAGA 57.563 33.333 0.00 0.00 0.00 2.43
2893 4221 8.383619 CGAATTACTTGTCTTGGATTTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
2894 4222 7.333423 CCGAATTACTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
2895 4223 6.149474 CCGAATTACTTGTCTTGGATTTGTCT 59.851 38.462 0.00 0.00 0.00 3.41
2896 4224 6.148811 TCCGAATTACTTGTCTTGGATTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
2897 4225 6.001460 TCCGAATTACTTGTCTTGGATTTGT 58.999 36.000 0.00 0.00 0.00 2.83
2898 4226 6.494893 TCCGAATTACTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
2899 4227 6.488683 TGTTCCGAATTACTTGTCTTGGATTT 59.511 34.615 0.00 0.00 0.00 2.17
2900 4228 6.001460 TGTTCCGAATTACTTGTCTTGGATT 58.999 36.000 0.00 0.00 0.00 3.01
2901 4229 5.556915 TGTTCCGAATTACTTGTCTTGGAT 58.443 37.500 0.00 0.00 0.00 3.41
2902 4230 4.963373 TGTTCCGAATTACTTGTCTTGGA 58.037 39.130 0.00 0.00 0.00 3.53
2903 4231 4.994852 TCTGTTCCGAATTACTTGTCTTGG 59.005 41.667 0.00 0.00 0.00 3.61
2904 4232 5.120830 CCTCTGTTCCGAATTACTTGTCTTG 59.879 44.000 0.00 0.00 0.00 3.02
2905 4233 5.238583 CCTCTGTTCCGAATTACTTGTCTT 58.761 41.667 0.00 0.00 0.00 3.01
2906 4234 4.322801 CCCTCTGTTCCGAATTACTTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
2907 4235 3.933332 CCCTCTGTTCCGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2908 4236 3.581332 TCCCTCTGTTCCGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
2909 4237 4.184629 CTCCCTCTGTTCCGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
2910 4238 3.838903 ACTCCCTCTGTTCCGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
2911 4239 3.442076 ACTCCCTCTGTTCCGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
2912 4240 3.889520 ACTCCCTCTGTTCCGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
2913 4241 4.346730 TGTACTCCCTCTGTTCCGAATTA 58.653 43.478 0.00 0.00 0.00 1.40
2914 4242 3.170717 TGTACTCCCTCTGTTCCGAATT 58.829 45.455 0.00 0.00 0.00 2.17
2915 4243 2.816411 TGTACTCCCTCTGTTCCGAAT 58.184 47.619 0.00 0.00 0.00 3.34
2916 4244 2.297698 TGTACTCCCTCTGTTCCGAA 57.702 50.000 0.00 0.00 0.00 4.30
2917 4245 2.168496 CTTGTACTCCCTCTGTTCCGA 58.832 52.381 0.00 0.00 0.00 4.55
2918 4246 1.404315 GCTTGTACTCCCTCTGTTCCG 60.404 57.143 0.00 0.00 0.00 4.30
2919 4247 1.066071 GGCTTGTACTCCCTCTGTTCC 60.066 57.143 0.00 0.00 0.00 3.62
2920 4248 1.903183 AGGCTTGTACTCCCTCTGTTC 59.097 52.381 0.00 0.00 0.00 3.18
2921 4249 2.031495 AGGCTTGTACTCCCTCTGTT 57.969 50.000 0.00 0.00 0.00 3.16
2922 4250 2.225293 TGTAGGCTTGTACTCCCTCTGT 60.225 50.000 0.00 0.00 0.00 3.41
2923 4251 2.457598 TGTAGGCTTGTACTCCCTCTG 58.542 52.381 0.00 0.00 0.00 3.35
2924 4252 2.832733 GTTGTAGGCTTGTACTCCCTCT 59.167 50.000 0.00 0.00 0.00 3.69
2925 4253 2.093606 GGTTGTAGGCTTGTACTCCCTC 60.094 54.545 0.00 0.00 0.00 4.30
2926 4254 1.907255 GGTTGTAGGCTTGTACTCCCT 59.093 52.381 0.00 0.00 0.00 4.20
2927 4255 1.907255 AGGTTGTAGGCTTGTACTCCC 59.093 52.381 0.00 0.00 0.00 4.30
2928 4256 2.565834 TCAGGTTGTAGGCTTGTACTCC 59.434 50.000 0.00 0.00 0.00 3.85
2929 4257 3.955650 TCAGGTTGTAGGCTTGTACTC 57.044 47.619 0.00 0.00 0.00 2.59
2930 4258 3.838317 TCATCAGGTTGTAGGCTTGTACT 59.162 43.478 0.00 0.00 0.00 2.73
2931 4259 4.202245 TCATCAGGTTGTAGGCTTGTAC 57.798 45.455 0.00 0.00 0.00 2.90
2932 4260 5.435686 AATCATCAGGTTGTAGGCTTGTA 57.564 39.130 0.00 0.00 0.00 2.41
2933 4261 4.307032 AATCATCAGGTTGTAGGCTTGT 57.693 40.909 0.00 0.00 0.00 3.16
2934 4262 6.037610 GTCTAAATCATCAGGTTGTAGGCTTG 59.962 42.308 0.00 0.00 0.00 4.01
2935 4263 6.116126 GTCTAAATCATCAGGTTGTAGGCTT 58.884 40.000 0.00 0.00 0.00 4.35
2936 4264 5.189736 TGTCTAAATCATCAGGTTGTAGGCT 59.810 40.000 0.00 0.00 0.00 4.58
2968 4296 0.629058 ACTGGGGTGAGTTTGGTGTT 59.371 50.000 0.00 0.00 0.00 3.32
2978 4306 2.666272 TGTGCATTTTACTGGGGTGA 57.334 45.000 0.00 0.00 0.00 4.02
2983 4311 4.218200 TGGTGATCTTGTGCATTTTACTGG 59.782 41.667 0.00 0.00 0.00 4.00
2984 4312 5.048504 AGTGGTGATCTTGTGCATTTTACTG 60.049 40.000 0.00 0.00 0.00 2.74
2999 4327 5.665381 GCTATGAAGCTAAAGTGGTGATC 57.335 43.478 0.00 0.00 45.85 2.92
3013 4341 6.092807 GTGGTAGTTTTCCAAGAGCTATGAAG 59.907 42.308 0.63 0.00 36.68 3.02
3014 4342 5.938125 GTGGTAGTTTTCCAAGAGCTATGAA 59.062 40.000 0.63 0.00 36.68 2.57
3035 4363 7.540400 TGCGAAATGTCATATTTTGTAAAGTGG 59.460 33.333 0.00 0.00 0.00 4.00
3039 4367 8.293157 TCTGTGCGAAATGTCATATTTTGTAAA 58.707 29.630 0.00 0.00 0.00 2.01
3049 4377 3.058708 CAGTGTTCTGTGCGAAATGTCAT 60.059 43.478 0.00 0.00 36.97 3.06
3074 4427 2.778299 TCAAAACGCTTAGCATCCACT 58.222 42.857 4.70 0.00 0.00 4.00
3130 4483 0.601311 GCGGTGATATCTGGCACTCC 60.601 60.000 3.98 0.00 35.43 3.85
3137 4490 5.333645 GCTTTGTTATGAGCGGTGATATCTG 60.334 44.000 3.98 0.00 0.00 2.90
3213 4566 4.082125 GGGTTTTCCAGATGATGTTGACT 58.918 43.478 0.00 0.00 42.91 3.41
3226 4579 4.104102 AGAGTGTGAATAGTGGGTTTTCCA 59.896 41.667 0.00 0.00 44.79 3.53
3229 4582 5.568620 AGAGAGTGTGAATAGTGGGTTTT 57.431 39.130 0.00 0.00 0.00 2.43
3256 4609 2.854967 AGGATTCAACCATCCCATCACT 59.145 45.455 0.00 0.00 43.68 3.41
3262 4615 3.055891 CACCAAAAGGATTCAACCATCCC 60.056 47.826 0.00 0.00 43.68 3.85
3272 4625 3.308401 ACAGCTTTCCACCAAAAGGATT 58.692 40.909 0.00 0.00 36.86 3.01
3290 4643 4.399618 TGGATAGAAGTCTTCTCGGAACAG 59.600 45.833 18.49 0.00 41.14 3.16
3292 4645 4.985538 TGGATAGAAGTCTTCTCGGAAC 57.014 45.455 18.49 6.98 41.14 3.62
3296 4649 9.026074 GTTTAAAGATGGATAGAAGTCTTCTCG 57.974 37.037 18.49 0.00 41.14 4.04
3325 4678 5.240623 CAGCACCAGGTTTACATACTGAAAA 59.759 40.000 0.00 0.00 34.21 2.29
3329 4682 3.009723 CCAGCACCAGGTTTACATACTG 58.990 50.000 0.00 0.00 0.00 2.74
3333 4686 0.112218 TGCCAGCACCAGGTTTACAT 59.888 50.000 0.00 0.00 0.00 2.29
3336 4689 0.106469 TGTTGCCAGCACCAGGTTTA 60.106 50.000 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.