Multiple sequence alignment - TraesCS3D01G224900

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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 TraesCS3D01G224900 chr3D 100.000 2711 0 0 1 2711 306015911 306018621 0.000000e+00 5007.0
1 TraesCS3D01G224900 chr3B 88.165 2163 182 48 601 2707 415644911 415642767 0.000000e+00 2508.0
2 TraesCS3D01G224900 chr3B 91.765 340 27 1 180 518 415645587 415645248 3.160000e-129 472.0
3 TraesCS3D01G224900 chr3B 81.421 183 30 4 2482 2662 167252307 167252487 2.180000e-31 147.0
4 TraesCS3D01G224900 chr3A 94.118 1224 43 12 769 1973 424250187 424251400 0.000000e+00 1834.0
5 TraesCS3D01G224900 chr3A 91.813 342 23 3 180 518 424249575 424249914 3.160000e-129 472.0
6 TraesCS3D01G224900 chr3A 90.964 166 8 4 519 684 424249943 424250101 1.630000e-52 217.0
7 TraesCS3D01G224900 chr1B 91.160 181 13 3 6 183 577609844 577609664 2.700000e-60 243.0
8 TraesCS3D01G224900 chr1B 91.617 167 13 1 6 171 443589331 443589165 2.100000e-56 230.0
9 TraesCS3D01G224900 chr6D 91.061 179 14 2 6 182 464536717 464536539 9.700000e-60 241.0
10 TraesCS3D01G224900 chr5A 90.556 180 15 2 6 183 571424433 571424612 1.250000e-58 237.0
11 TraesCS3D01G224900 chr5A 77.922 154 24 6 2514 2662 473616553 473616405 1.340000e-13 87.9
12 TraesCS3D01G224900 chr2D 90.556 180 15 2 6 183 118372181 118372360 1.250000e-58 237.0
13 TraesCS3D01G224900 chr5D 90.055 181 16 2 6 184 460070737 460070557 1.620000e-57 233.0
14 TraesCS3D01G224900 chr5D 75.210 238 51 6 2455 2690 327995108 327994877 3.690000e-19 106.0
15 TraesCS3D01G224900 chr5D 76.829 164 32 3 2508 2668 370835448 370835288 1.340000e-13 87.9
16 TraesCS3D01G224900 chr5D 100.000 29 0 0 2573 2601 94063158 94063130 1.000000e-03 54.7
17 TraesCS3D01G224900 chr4D 89.444 180 17 2 6 183 409413 409234 2.720000e-55 226.0
18 TraesCS3D01G224900 chr4D 89.444 180 17 2 6 183 418387016 418386837 2.720000e-55 226.0
19 TraesCS3D01G224900 chr4A 88.649 185 17 4 8 190 647340983 647341165 3.510000e-54 222.0


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 TraesCS3D01G224900 chr3D 306015911 306018621 2710 False 5007 5007 100.000000 1 2711 1 chr3D.!!$F1 2710
1 TraesCS3D01G224900 chr3B 415642767 415645587 2820 True 1490 2508 89.965000 180 2707 2 chr3B.!!$R1 2527
2 TraesCS3D01G224900 chr3A 424249575 424251400 1825 False 841 1834 92.298333 180 1973 3 chr3A.!!$F1 1793

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
102 103 0.319469 AATTTTTGTTCCCGCGGCAG 60.319 50.0 22.85 7.49 0.0 4.85 F
152 153 0.521242 CTTGAATTTCGGGAAGCGCG 60.521 55.0 0.00 0.00 41.1 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 1506 0.028374 GCGAGAAGACGTAGAGGAGC 59.972 60.0 0.0 0.0 35.59 4.7 R
1933 2216 0.108992 GACACCATACAGCGACCGAA 60.109 55.0 0.0 0.0 0.00 4.3 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
22 23 5.265407 GTAGCTTTAACAACAAGACCGAG 57.735 43.478 0.00 0.00 0.00 4.63
23 24 3.805207 AGCTTTAACAACAAGACCGAGT 58.195 40.909 0.00 0.00 0.00 4.18
24 25 3.560068 AGCTTTAACAACAAGACCGAGTG 59.440 43.478 0.00 0.00 0.00 3.51
25 26 3.848554 GCTTTAACAACAAGACCGAGTGC 60.849 47.826 0.00 0.00 0.00 4.40
26 27 1.493772 TAACAACAAGACCGAGTGCG 58.506 50.000 0.00 0.00 37.24 5.34
41 42 4.386951 GCGGCGGGGGCAAAAATT 62.387 61.111 9.78 0.00 0.00 1.82
42 43 3.007973 GCGGCGGGGGCAAAAATTA 62.008 57.895 9.78 0.00 0.00 1.40
43 44 1.819905 CGGCGGGGGCAAAAATTAT 59.180 52.632 0.00 0.00 0.00 1.28
44 45 1.033574 CGGCGGGGGCAAAAATTATA 58.966 50.000 0.00 0.00 0.00 0.98
45 46 1.616374 CGGCGGGGGCAAAAATTATAT 59.384 47.619 0.00 0.00 0.00 0.86
46 47 2.352323 CGGCGGGGGCAAAAATTATATC 60.352 50.000 0.00 0.00 0.00 1.63
47 48 2.630580 GGCGGGGGCAAAAATTATATCA 59.369 45.455 0.00 0.00 0.00 2.15
48 49 3.554129 GGCGGGGGCAAAAATTATATCAC 60.554 47.826 0.00 0.00 0.00 3.06
49 50 3.320826 GCGGGGGCAAAAATTATATCACT 59.679 43.478 0.00 0.00 0.00 3.41
50 51 4.795962 GCGGGGGCAAAAATTATATCACTG 60.796 45.833 0.00 0.00 0.00 3.66
51 52 4.582656 CGGGGGCAAAAATTATATCACTGA 59.417 41.667 0.00 0.00 0.00 3.41
52 53 5.068460 CGGGGGCAAAAATTATATCACTGAA 59.932 40.000 0.00 0.00 0.00 3.02
53 54 6.239289 CGGGGGCAAAAATTATATCACTGAAT 60.239 38.462 0.00 0.00 0.00 2.57
54 55 7.508687 GGGGGCAAAAATTATATCACTGAATT 58.491 34.615 0.00 0.00 0.00 2.17
55 56 7.657354 GGGGGCAAAAATTATATCACTGAATTC 59.343 37.037 0.00 0.00 0.00 2.17
56 57 8.203485 GGGGCAAAAATTATATCACTGAATTCA 58.797 33.333 8.12 8.12 0.00 2.57
57 58 9.768662 GGGCAAAAATTATATCACTGAATTCAT 57.231 29.630 8.96 0.00 0.00 2.57
70 71 8.865590 TCACTGAATTCATATCGAAAATACGA 57.134 30.769 8.96 0.00 46.04 3.43
71 72 9.308318 TCACTGAATTCATATCGAAAATACGAA 57.692 29.630 8.96 0.00 45.16 3.85
79 80 9.877137 TTCATATCGAAAATACGAATTCATTGG 57.123 29.630 6.22 0.00 45.16 3.16
80 81 9.051679 TCATATCGAAAATACGAATTCATTGGT 57.948 29.630 6.22 0.00 45.16 3.67
96 97 8.940768 ATTCATTGGTATAATTTTTGTTCCCG 57.059 30.769 0.00 0.00 0.00 5.14
97 98 6.334202 TCATTGGTATAATTTTTGTTCCCGC 58.666 36.000 0.00 0.00 0.00 6.13
98 99 4.358494 TGGTATAATTTTTGTTCCCGCG 57.642 40.909 0.00 0.00 0.00 6.46
99 100 3.128938 TGGTATAATTTTTGTTCCCGCGG 59.871 43.478 21.04 21.04 0.00 6.46
100 101 2.287393 ATAATTTTTGTTCCCGCGGC 57.713 45.000 22.85 7.02 0.00 6.53
101 102 0.959553 TAATTTTTGTTCCCGCGGCA 59.040 45.000 22.85 10.23 0.00 5.69
102 103 0.319469 AATTTTTGTTCCCGCGGCAG 60.319 50.000 22.85 7.49 0.00 4.85
103 104 1.460273 ATTTTTGTTCCCGCGGCAGT 61.460 50.000 22.85 0.00 0.00 4.40
104 105 2.065906 TTTTTGTTCCCGCGGCAGTC 62.066 55.000 22.85 10.22 0.00 3.51
114 115 3.403057 CGGCAGTCGGTCACGTTG 61.403 66.667 0.00 0.00 41.85 4.10
115 116 3.041940 GGCAGTCGGTCACGTTGG 61.042 66.667 0.00 0.00 41.85 3.77
116 117 2.279918 GCAGTCGGTCACGTTGGT 60.280 61.111 0.00 0.00 41.85 3.67
117 118 1.885850 GCAGTCGGTCACGTTGGTT 60.886 57.895 0.00 0.00 41.85 3.67
118 119 0.598158 GCAGTCGGTCACGTTGGTTA 60.598 55.000 0.00 0.00 41.85 2.85
119 120 1.855513 CAGTCGGTCACGTTGGTTAA 58.144 50.000 0.00 0.00 41.85 2.01
120 121 2.203401 CAGTCGGTCACGTTGGTTAAA 58.797 47.619 0.00 0.00 41.85 1.52
121 122 2.803956 CAGTCGGTCACGTTGGTTAAAT 59.196 45.455 0.00 0.00 41.85 1.40
122 123 3.249080 CAGTCGGTCACGTTGGTTAAATT 59.751 43.478 0.00 0.00 41.85 1.82
123 124 3.878699 AGTCGGTCACGTTGGTTAAATTT 59.121 39.130 0.00 0.00 41.85 1.82
124 125 5.050227 CAGTCGGTCACGTTGGTTAAATTTA 60.050 40.000 0.00 0.00 41.85 1.40
125 126 5.050159 AGTCGGTCACGTTGGTTAAATTTAC 60.050 40.000 0.00 0.00 41.85 2.01
126 127 4.084641 TCGGTCACGTTGGTTAAATTTACG 60.085 41.667 8.50 8.50 41.85 3.18
127 128 4.465921 GGTCACGTTGGTTAAATTTACGG 58.534 43.478 13.34 4.70 36.60 4.02
128 129 4.024133 GGTCACGTTGGTTAAATTTACGGT 60.024 41.667 13.34 0.00 36.60 4.83
129 130 5.139482 GTCACGTTGGTTAAATTTACGGTC 58.861 41.667 13.34 2.34 36.60 4.79
130 131 4.813161 TCACGTTGGTTAAATTTACGGTCA 59.187 37.500 13.34 1.58 36.60 4.02
131 132 5.295292 TCACGTTGGTTAAATTTACGGTCAA 59.705 36.000 13.34 6.53 36.60 3.18
132 133 5.970023 CACGTTGGTTAAATTTACGGTCAAA 59.030 36.000 13.34 0.00 36.60 2.69
133 134 5.970612 ACGTTGGTTAAATTTACGGTCAAAC 59.029 36.000 13.34 3.05 36.60 2.93
134 135 6.183360 ACGTTGGTTAAATTTACGGTCAAACT 60.183 34.615 13.34 0.00 36.60 2.66
135 136 6.692249 CGTTGGTTAAATTTACGGTCAAACTT 59.308 34.615 0.00 0.00 0.00 2.66
136 137 7.305533 CGTTGGTTAAATTTACGGTCAAACTTG 60.306 37.037 0.00 0.00 0.00 3.16
137 138 7.330900 TGGTTAAATTTACGGTCAAACTTGA 57.669 32.000 0.00 0.00 34.20 3.02
138 139 7.769220 TGGTTAAATTTACGGTCAAACTTGAA 58.231 30.769 0.00 0.00 39.21 2.69
139 140 8.414778 TGGTTAAATTTACGGTCAAACTTGAAT 58.585 29.630 0.00 0.00 39.21 2.57
140 141 9.251792 GGTTAAATTTACGGTCAAACTTGAATT 57.748 29.630 0.00 0.00 39.21 2.17
143 144 7.617533 AATTTACGGTCAAACTTGAATTTCG 57.382 32.000 0.00 0.15 39.21 3.46
144 145 3.619233 ACGGTCAAACTTGAATTTCGG 57.381 42.857 0.00 0.00 39.21 4.30
145 146 2.292292 ACGGTCAAACTTGAATTTCGGG 59.708 45.455 0.00 0.00 39.21 5.14
146 147 2.550606 CGGTCAAACTTGAATTTCGGGA 59.449 45.455 0.00 0.00 39.21 5.14
147 148 3.003897 CGGTCAAACTTGAATTTCGGGAA 59.996 43.478 0.00 0.00 39.21 3.97
148 149 4.546570 GGTCAAACTTGAATTTCGGGAAG 58.453 43.478 0.00 0.00 39.21 3.46
149 150 3.981416 GTCAAACTTGAATTTCGGGAAGC 59.019 43.478 0.00 0.00 39.21 3.86
150 151 2.979813 CAAACTTGAATTTCGGGAAGCG 59.020 45.455 0.00 0.00 0.00 4.68
151 152 0.521735 ACTTGAATTTCGGGAAGCGC 59.478 50.000 0.00 0.00 0.00 5.92
152 153 0.521242 CTTGAATTTCGGGAAGCGCG 60.521 55.000 0.00 0.00 41.10 6.86
153 154 1.917782 TTGAATTTCGGGAAGCGCGG 61.918 55.000 8.83 0.00 40.17 6.46
154 155 3.108357 GAATTTCGGGAAGCGCGGG 62.108 63.158 8.83 0.00 40.17 6.13
166 167 4.222589 CGCGGGCGCACTACATTG 62.223 66.667 8.62 0.00 42.06 2.82
167 168 3.124921 GCGGGCGCACTACATTGT 61.125 61.111 8.62 0.00 41.49 2.71
168 169 2.784596 CGGGCGCACTACATTGTG 59.215 61.111 8.62 0.00 40.62 3.33
169 170 1.739929 CGGGCGCACTACATTGTGA 60.740 57.895 8.62 0.00 40.12 3.58
170 171 1.295357 CGGGCGCACTACATTGTGAA 61.295 55.000 8.62 0.00 40.12 3.18
171 172 1.094785 GGGCGCACTACATTGTGAAT 58.905 50.000 10.83 0.00 40.12 2.57
172 173 1.202177 GGGCGCACTACATTGTGAATG 60.202 52.381 10.83 0.00 44.48 2.67
173 174 1.202177 GGCGCACTACATTGTGAATGG 60.202 52.381 10.83 0.00 43.21 3.16
174 175 1.737236 GCGCACTACATTGTGAATGGA 59.263 47.619 0.30 0.00 43.21 3.41
195 196 6.914665 TGGAGGGAATATGTCATTTCTTCAT 58.085 36.000 0.00 0.00 0.00 2.57
210 211 8.229811 TCATTTCTTCATGAGATTTTGTACACG 58.770 33.333 0.00 0.00 33.49 4.49
215 216 7.602265 TCTTCATGAGATTTTGTACACGATGAA 59.398 33.333 0.00 3.83 0.00 2.57
289 292 3.214023 TCTCCATCCGAGAGCATGT 57.786 52.632 0.00 0.00 42.97 3.21
303 306 1.086634 GCATGTGAAGTCGAGCTCCC 61.087 60.000 8.47 0.00 0.00 4.30
327 330 8.909923 CCCTTTTTAATATCCGACAAAATAGGT 58.090 33.333 0.00 0.00 0.00 3.08
442 446 5.637006 TGCCAATATAAACTCTTGCGTTT 57.363 34.783 0.00 0.00 40.06 3.60
445 449 5.511729 GCCAATATAAACTCTTGCGTTTGTC 59.488 40.000 0.00 0.00 37.63 3.18
466 470 6.058833 TGTCTTTCTTAAGCACACACCATAA 58.941 36.000 0.00 0.00 0.00 1.90
586 618 6.033341 GCGACTATAGGATCATCATGAAGTC 58.967 44.000 0.00 3.92 0.00 3.01
588 620 7.597386 CGACTATAGGATCATCATGAAGTCAA 58.403 38.462 13.07 2.41 32.34 3.18
595 627 6.825721 AGGATCATCATGAAGTCAAAAGGTAC 59.174 38.462 0.00 0.00 0.00 3.34
597 629 7.011857 GGATCATCATGAAGTCAAAAGGTACTC 59.988 40.741 0.00 0.00 38.49 2.59
684 945 6.484977 AGCTTAAGTTCCTTTTTGAGAGTGAG 59.515 38.462 4.02 0.00 0.00 3.51
685 946 6.293680 GCTTAAGTTCCTTTTTGAGAGTGAGG 60.294 42.308 4.02 0.00 0.00 3.86
686 947 4.779993 AGTTCCTTTTTGAGAGTGAGGT 57.220 40.909 0.00 0.00 0.00 3.85
687 948 4.455606 AGTTCCTTTTTGAGAGTGAGGTG 58.544 43.478 0.00 0.00 0.00 4.00
689 950 2.439507 TCCTTTTTGAGAGTGAGGTGCT 59.560 45.455 0.00 0.00 0.00 4.40
690 951 2.551459 CCTTTTTGAGAGTGAGGTGCTG 59.449 50.000 0.00 0.00 0.00 4.41
691 952 3.209410 CTTTTTGAGAGTGAGGTGCTGT 58.791 45.455 0.00 0.00 0.00 4.40
692 953 3.281727 TTTTGAGAGTGAGGTGCTGTT 57.718 42.857 0.00 0.00 0.00 3.16
693 954 3.281727 TTTGAGAGTGAGGTGCTGTTT 57.718 42.857 0.00 0.00 0.00 2.83
695 956 1.202687 TGAGAGTGAGGTGCTGTTTGG 60.203 52.381 0.00 0.00 0.00 3.28
698 959 1.604278 GAGTGAGGTGCTGTTTGGTTC 59.396 52.381 0.00 0.00 0.00 3.62
699 960 1.212935 AGTGAGGTGCTGTTTGGTTCT 59.787 47.619 0.00 0.00 0.00 3.01
700 961 2.438021 AGTGAGGTGCTGTTTGGTTCTA 59.562 45.455 0.00 0.00 0.00 2.10
702 963 2.224523 TGAGGTGCTGTTTGGTTCTAGG 60.225 50.000 0.00 0.00 0.00 3.02
703 964 1.774856 AGGTGCTGTTTGGTTCTAGGT 59.225 47.619 0.00 0.00 0.00 3.08
706 967 3.211045 GTGCTGTTTGGTTCTAGGTCAA 58.789 45.455 0.00 0.00 0.00 3.18
707 968 3.630312 GTGCTGTTTGGTTCTAGGTCAAA 59.370 43.478 0.00 0.00 0.00 2.69
708 969 4.278419 GTGCTGTTTGGTTCTAGGTCAAAT 59.722 41.667 8.48 0.00 33.72 2.32
710 971 4.518970 GCTGTTTGGTTCTAGGTCAAATCA 59.481 41.667 8.48 7.94 33.72 2.57
711 972 5.183904 GCTGTTTGGTTCTAGGTCAAATCAT 59.816 40.000 8.48 0.00 33.72 2.45
712 973 6.573664 TGTTTGGTTCTAGGTCAAATCATG 57.426 37.500 8.48 0.00 33.72 3.07
713 974 5.048083 TGTTTGGTTCTAGGTCAAATCATGC 60.048 40.000 8.48 0.00 33.72 4.06
714 975 3.620488 TGGTTCTAGGTCAAATCATGCC 58.380 45.455 0.00 0.00 0.00 4.40
715 976 3.010027 TGGTTCTAGGTCAAATCATGCCA 59.990 43.478 0.00 0.00 0.00 4.92
716 977 4.210331 GGTTCTAGGTCAAATCATGCCAT 58.790 43.478 0.00 0.00 0.00 4.40
717 978 5.104151 TGGTTCTAGGTCAAATCATGCCATA 60.104 40.000 0.00 0.00 0.00 2.74
718 979 5.239525 GGTTCTAGGTCAAATCATGCCATAC 59.760 44.000 0.00 0.00 0.00 2.39
720 981 6.252599 TCTAGGTCAAATCATGCCATACTT 57.747 37.500 0.00 0.00 0.00 2.24
721 982 6.662755 TCTAGGTCAAATCATGCCATACTTT 58.337 36.000 0.00 0.00 0.00 2.66
722 983 5.587388 AGGTCAAATCATGCCATACTTTG 57.413 39.130 5.29 5.29 0.00 2.77
724 985 4.114794 GTCAAATCATGCCATACTTTGCC 58.885 43.478 6.36 0.00 0.00 4.52
725 986 3.768215 TCAAATCATGCCATACTTTGCCA 59.232 39.130 6.36 0.00 0.00 4.92
726 987 4.406326 TCAAATCATGCCATACTTTGCCAT 59.594 37.500 6.36 0.00 0.00 4.40
727 988 4.330944 AATCATGCCATACTTTGCCATG 57.669 40.909 0.00 0.00 0.00 3.66
754 1015 7.961326 ATATTGCCACACTTTCCTTAGATTT 57.039 32.000 0.00 0.00 0.00 2.17
755 1016 5.452078 TTGCCACACTTTCCTTAGATTTG 57.548 39.130 0.00 0.00 0.00 2.32
757 1018 3.826729 GCCACACTTTCCTTAGATTTGGT 59.173 43.478 0.00 0.00 0.00 3.67
758 1019 4.280929 GCCACACTTTCCTTAGATTTGGTT 59.719 41.667 0.00 0.00 0.00 3.67
759 1020 5.564848 GCCACACTTTCCTTAGATTTGGTTC 60.565 44.000 0.00 0.00 0.00 3.62
760 1021 5.770162 CCACACTTTCCTTAGATTTGGTTCT 59.230 40.000 0.00 0.00 0.00 3.01
762 1023 7.119846 CCACACTTTCCTTAGATTTGGTTCTAG 59.880 40.741 0.00 0.00 30.20 2.43
763 1024 7.119846 CACACTTTCCTTAGATTTGGTTCTAGG 59.880 40.741 0.00 0.00 30.20 3.02
782 1044 3.844640 AGGCCTACCAAACACTTGAATT 58.155 40.909 1.29 0.00 39.06 2.17
783 1045 4.223144 AGGCCTACCAAACACTTGAATTT 58.777 39.130 1.29 0.00 39.06 1.82
784 1046 4.653801 AGGCCTACCAAACACTTGAATTTT 59.346 37.500 1.29 0.00 39.06 1.82
823 1090 3.767309 AGGCTCCCTATATACTCCTGG 57.233 52.381 0.00 0.00 28.47 4.45
1460 1739 4.778143 AATCGGCGCCGGAAAGCT 62.778 61.111 44.95 21.89 40.25 3.74
1735 2018 1.502163 GAGTTGCAACAGTGAGCGCT 61.502 55.000 30.11 11.27 0.00 5.92
1810 2093 5.741982 GTGCCTTGTTTAGTGTACAAGTTTG 59.258 40.000 12.97 1.99 46.98 2.93
2011 2294 1.254570 GACGCACGTACGAATTGGATC 59.745 52.381 24.41 6.10 36.70 3.36
2012 2295 1.273688 CGCACGTACGAATTGGATCA 58.726 50.000 24.41 0.00 34.06 2.92
2054 2344 3.257624 ACAAGAGTCGAATTACTTCCCGT 59.742 43.478 0.00 0.00 0.00 5.28
2057 2347 2.921754 GAGTCGAATTACTTCCCGTGTG 59.078 50.000 0.00 0.00 0.00 3.82
2079 2370 4.578105 TGAATGCATATTATCGTTGCCACA 59.422 37.500 0.00 0.00 35.51 4.17
2092 2383 2.980378 GCCACACGCATGATGCACA 61.980 57.895 18.47 0.00 45.36 4.57
2093 2384 1.580437 CCACACGCATGATGCACAA 59.420 52.632 18.47 0.00 45.36 3.33
2098 2389 2.030096 ACACGCATGATGCACAAAATGA 60.030 40.909 18.47 0.00 45.36 2.57
2100 2391 2.190161 CGCATGATGCACAAAATGAGG 58.810 47.619 18.47 0.00 45.36 3.86
2102 2393 2.546778 CATGATGCACAAAATGAGGCC 58.453 47.619 0.00 0.00 0.00 5.19
2109 2400 1.068333 CACAAAATGAGGCCAACTCCG 60.068 52.381 5.01 0.00 46.01 4.63
2110 2401 1.247567 CAAAATGAGGCCAACTCCGT 58.752 50.000 5.01 0.00 46.01 4.69
2111 2402 1.613437 CAAAATGAGGCCAACTCCGTT 59.387 47.619 5.01 0.00 46.01 4.44
2130 2421 4.704007 CGCTACCGCATTAGTCGT 57.296 55.556 0.00 0.00 35.30 4.34
2131 2422 2.953669 CGCTACCGCATTAGTCGTT 58.046 52.632 0.00 0.00 35.30 3.85
2133 2424 1.254570 CGCTACCGCATTAGTCGTTTC 59.745 52.381 0.00 0.00 35.30 2.78
2137 2428 2.762745 ACCGCATTAGTCGTTTCTGTT 58.237 42.857 0.00 0.00 0.00 3.16
2138 2429 2.478894 ACCGCATTAGTCGTTTCTGTTG 59.521 45.455 0.00 0.00 0.00 3.33
2139 2430 2.159707 CCGCATTAGTCGTTTCTGTTGG 60.160 50.000 0.00 0.00 0.00 3.77
2140 2431 2.478894 CGCATTAGTCGTTTCTGTTGGT 59.521 45.455 0.00 0.00 0.00 3.67
2141 2432 3.059188 CGCATTAGTCGTTTCTGTTGGTT 60.059 43.478 0.00 0.00 0.00 3.67
2147 2438 3.128068 AGTCGTTTCTGTTGGTTTGGTTC 59.872 43.478 0.00 0.00 0.00 3.62
2154 2445 1.811359 TGTTGGTTTGGTTCGAAACGT 59.189 42.857 8.98 0.00 36.80 3.99
2158 2449 2.608546 TGGTTTGGTTCGAAACGTACAG 59.391 45.455 16.31 0.00 36.80 2.74
2162 2453 5.323105 GTTTGGTTCGAAACGTACAGAAAA 58.677 37.500 8.98 0.00 0.00 2.29
2163 2454 5.738118 TTGGTTCGAAACGTACAGAAAAT 57.262 34.783 8.98 0.00 0.00 1.82
2165 2456 6.214205 TGGTTCGAAACGTACAGAAAATAC 57.786 37.500 8.98 0.00 0.00 1.89
2173 2464 4.240883 CGTACAGAAAATACGGCTCAAC 57.759 45.455 0.00 0.00 41.33 3.18
2183 2474 2.742372 GGCTCAACGTGCCGATGT 60.742 61.111 0.00 0.00 41.03 3.06
2187 2478 1.396996 GCTCAACGTGCCGATGTAAAT 59.603 47.619 0.00 0.00 31.79 1.40
2193 2484 2.209273 CGTGCCGATGTAAATGGATGA 58.791 47.619 0.00 0.00 0.00 2.92
2194 2485 2.221749 CGTGCCGATGTAAATGGATGAG 59.778 50.000 0.00 0.00 0.00 2.90
2198 2489 3.248602 GCCGATGTAAATGGATGAGTGTC 59.751 47.826 0.00 0.00 0.00 3.67
2202 2493 5.586243 CGATGTAAATGGATGAGTGTCCTTT 59.414 40.000 0.00 0.00 39.12 3.11
2203 2494 6.238211 CGATGTAAATGGATGAGTGTCCTTTC 60.238 42.308 0.00 0.00 39.12 2.62
2205 2496 4.664688 AAATGGATGAGTGTCCTTTCCT 57.335 40.909 0.00 0.00 39.12 3.36
2207 2498 2.338809 TGGATGAGTGTCCTTTCCTGT 58.661 47.619 0.00 0.00 39.12 4.00
2208 2499 2.711009 TGGATGAGTGTCCTTTCCTGTT 59.289 45.455 0.00 0.00 39.12 3.16
2209 2500 3.138283 TGGATGAGTGTCCTTTCCTGTTT 59.862 43.478 0.00 0.00 39.12 2.83
2211 2502 3.924114 TGAGTGTCCTTTCCTGTTTCA 57.076 42.857 0.00 0.00 0.00 2.69
2212 2503 4.437682 TGAGTGTCCTTTCCTGTTTCAT 57.562 40.909 0.00 0.00 0.00 2.57
2216 2507 6.149129 AGTGTCCTTTCCTGTTTCATTTTC 57.851 37.500 0.00 0.00 0.00 2.29
2217 2508 4.976116 GTGTCCTTTCCTGTTTCATTTTCG 59.024 41.667 0.00 0.00 0.00 3.46
2219 2510 4.037565 GTCCTTTCCTGTTTCATTTTCGGT 59.962 41.667 0.00 0.00 0.00 4.69
2222 2513 2.510613 TCCTGTTTCATTTTCGGTCCC 58.489 47.619 0.00 0.00 0.00 4.46
2225 2516 3.258123 CCTGTTTCATTTTCGGTCCCAAT 59.742 43.478 0.00 0.00 0.00 3.16
2228 2519 6.406692 TGTTTCATTTTCGGTCCCAATTTA 57.593 33.333 0.00 0.00 0.00 1.40
2240 2531 0.242555 CCAATTTAGGCCGCGTTTGT 59.757 50.000 4.92 0.00 0.00 2.83
2244 2535 1.833434 TTTAGGCCGCGTTTGTGTCG 61.833 55.000 4.92 0.00 0.00 4.35
2245 2536 2.696409 TTAGGCCGCGTTTGTGTCGA 62.696 55.000 4.92 0.00 0.00 4.20
2284 2575 2.899838 TGGGACGCACACACTTGC 60.900 61.111 0.00 0.00 39.28 4.01
2305 2596 3.650950 CCCACCCCCACTCACCTG 61.651 72.222 0.00 0.00 0.00 4.00
2306 2597 2.854032 CCACCCCCACTCACCTGT 60.854 66.667 0.00 0.00 0.00 4.00
2307 2598 2.750350 CACCCCCACTCACCTGTC 59.250 66.667 0.00 0.00 0.00 3.51
2308 2599 2.923035 ACCCCCACTCACCTGTCG 60.923 66.667 0.00 0.00 0.00 4.35
2311 2602 3.706373 CCCACTCACCTGTCGGGG 61.706 72.222 1.89 0.00 40.03 5.73
2312 2603 4.394712 CCACTCACCTGTCGGGGC 62.395 72.222 1.89 0.00 40.03 5.80
2313 2604 3.625897 CACTCACCTGTCGGGGCA 61.626 66.667 1.89 0.00 40.03 5.36
2314 2605 3.626924 ACTCACCTGTCGGGGCAC 61.627 66.667 1.89 0.00 40.03 5.01
2316 2607 3.883744 CTCACCTGTCGGGGCACAC 62.884 68.421 1.89 0.00 40.03 3.82
2324 2615 2.220586 TCGGGGCACACCATTCTCA 61.221 57.895 0.00 0.00 42.91 3.27
2332 2623 3.259123 GGCACACCATTCTCATTTTCCTT 59.741 43.478 0.00 0.00 35.26 3.36
2336 2627 6.753744 GCACACCATTCTCATTTTCCTTATTC 59.246 38.462 0.00 0.00 0.00 1.75
2341 2632 6.835488 CCATTCTCATTTTCCTTATTCCCTCA 59.165 38.462 0.00 0.00 0.00 3.86
2360 2651 1.381076 CAAAAACCCTCCCGCCCTA 59.619 57.895 0.00 0.00 0.00 3.53
2361 2652 0.963856 CAAAAACCCTCCCGCCCTAC 60.964 60.000 0.00 0.00 0.00 3.18
2363 2654 3.574395 AAACCCTCCCGCCCTACCT 62.574 63.158 0.00 0.00 0.00 3.08
2364 2655 3.997756 AACCCTCCCGCCCTACCTC 62.998 68.421 0.00 0.00 0.00 3.85
2365 2656 4.159108 CCCTCCCGCCCTACCTCT 62.159 72.222 0.00 0.00 0.00 3.69
2366 2657 2.522193 CCTCCCGCCCTACCTCTC 60.522 72.222 0.00 0.00 0.00 3.20
2367 2658 2.522193 CTCCCGCCCTACCTCTCC 60.522 72.222 0.00 0.00 0.00 3.71
2388 2679 1.193462 CCATGGCCACCACACCAAAT 61.193 55.000 8.16 0.00 39.96 2.32
2392 2704 2.650196 CCACCACACCAAATGCCG 59.350 61.111 0.00 0.00 0.00 5.69
2394 2706 2.203480 ACCACACCAAATGCCGCT 60.203 55.556 0.00 0.00 0.00 5.52
2399 2711 3.131478 ACCAAATGCCGCTACCGC 61.131 61.111 0.00 0.00 0.00 5.68
2431 2746 2.038837 GCCCCGAAGAAGAAACCCG 61.039 63.158 0.00 0.00 0.00 5.28
2437 2752 2.338500 CGAAGAAGAAACCCGAGAAGG 58.662 52.381 0.00 0.00 40.63 3.46
2446 2761 2.811317 CCGAGAAGGTGCTCACGC 60.811 66.667 0.00 0.00 34.56 5.34
2503 2818 4.373116 GGAGGGACGTTGCTGCGA 62.373 66.667 7.42 0.00 35.59 5.10
2506 2821 3.423154 GGGACGTTGCTGCGAAGG 61.423 66.667 7.71 5.59 35.59 3.46
2513 2828 4.722700 TGCTGCGAAGGGGAAGGC 62.723 66.667 0.00 0.00 0.00 4.35
2563 2878 4.326766 CGCAACACAAGGCCACCG 62.327 66.667 5.01 0.00 0.00 4.94
2574 2889 2.951642 CAAGGCCACCGTTGATGATAAT 59.048 45.455 5.01 0.00 38.72 1.28
2626 2941 0.106819 GATGCAACATGCCCTCCTCT 60.107 55.000 0.00 0.00 44.23 3.69
2642 2957 1.676014 CCTCTTGCTAGGGTTCAACCG 60.676 57.143 0.00 0.00 39.83 4.44
2659 2974 3.219198 GACCCATGCCGGCCATTC 61.219 66.667 26.77 9.46 29.71 2.67
2660 2975 3.721370 GACCCATGCCGGCCATTCT 62.721 63.158 26.77 2.80 29.71 2.40
2661 2976 2.442643 CCCATGCCGGCCATTCTT 60.443 61.111 26.77 0.00 29.71 2.52
2662 2977 1.152777 CCCATGCCGGCCATTCTTA 60.153 57.895 26.77 2.60 29.71 2.10
2675 2993 4.849310 TCTTACCGCCATGGCCGC 62.849 66.667 30.79 6.76 43.94 6.53
2707 3025 1.515521 CTTGTTGGCCGTTCACCCTC 61.516 60.000 0.00 0.00 0.00 4.30
2708 3026 2.671963 GTTGGCCGTTCACCCTCC 60.672 66.667 0.00 0.00 0.00 4.30
2709 3027 3.172106 TTGGCCGTTCACCCTCCA 61.172 61.111 0.00 0.00 0.00 3.86
2710 3028 3.485346 TTGGCCGTTCACCCTCCAC 62.485 63.158 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.748600 ACTCGGTCTTGTTGTTAAAGCTAC 59.251 41.667 0.00 0.00 0.00 3.58
1 2 4.748102 CACTCGGTCTTGTTGTTAAAGCTA 59.252 41.667 0.00 0.00 0.00 3.32
2 3 3.560068 CACTCGGTCTTGTTGTTAAAGCT 59.440 43.478 0.00 0.00 0.00 3.74
3 4 3.848554 GCACTCGGTCTTGTTGTTAAAGC 60.849 47.826 0.00 0.00 0.00 3.51
4 5 3.603857 CGCACTCGGTCTTGTTGTTAAAG 60.604 47.826 0.00 0.00 0.00 1.85
5 6 2.285756 CGCACTCGGTCTTGTTGTTAAA 59.714 45.455 0.00 0.00 0.00 1.52
6 7 1.862201 CGCACTCGGTCTTGTTGTTAA 59.138 47.619 0.00 0.00 0.00 2.01
7 8 1.493772 CGCACTCGGTCTTGTTGTTA 58.506 50.000 0.00 0.00 0.00 2.41
8 9 2.307363 CGCACTCGGTCTTGTTGTT 58.693 52.632 0.00 0.00 0.00 2.83
9 10 4.027755 CGCACTCGGTCTTGTTGT 57.972 55.556 0.00 0.00 0.00 3.32
24 25 2.304901 ATAATTTTTGCCCCCGCCGC 62.305 55.000 0.00 0.00 0.00 6.53
25 26 1.033574 TATAATTTTTGCCCCCGCCG 58.966 50.000 0.00 0.00 0.00 6.46
26 27 2.630580 TGATATAATTTTTGCCCCCGCC 59.369 45.455 0.00 0.00 0.00 6.13
27 28 3.320826 AGTGATATAATTTTTGCCCCCGC 59.679 43.478 0.00 0.00 0.00 6.13
28 29 4.582656 TCAGTGATATAATTTTTGCCCCCG 59.417 41.667 0.00 0.00 0.00 5.73
29 30 6.478512 TTCAGTGATATAATTTTTGCCCCC 57.521 37.500 0.00 0.00 0.00 5.40
30 31 8.203485 TGAATTCAGTGATATAATTTTTGCCCC 58.797 33.333 3.38 0.00 0.00 5.80
31 32 9.768662 ATGAATTCAGTGATATAATTTTTGCCC 57.231 29.630 14.54 0.00 0.00 5.36
44 45 9.476202 TCGTATTTTCGATATGAATTCAGTGAT 57.524 29.630 14.54 7.10 36.22 3.06
45 46 8.865590 TCGTATTTTCGATATGAATTCAGTGA 57.134 30.769 14.54 6.02 36.22 3.41
53 54 9.877137 CCAATGAATTCGTATTTTCGATATGAA 57.123 29.630 0.00 2.52 39.57 2.57
54 55 9.051679 ACCAATGAATTCGTATTTTCGATATGA 57.948 29.630 0.00 0.00 39.57 2.15
70 71 9.377312 CGGGAACAAAAATTATACCAATGAATT 57.623 29.630 0.00 0.00 0.00 2.17
71 72 7.494298 GCGGGAACAAAAATTATACCAATGAAT 59.506 33.333 0.00 0.00 0.00 2.57
72 73 6.814146 GCGGGAACAAAAATTATACCAATGAA 59.186 34.615 0.00 0.00 0.00 2.57
73 74 6.334202 GCGGGAACAAAAATTATACCAATGA 58.666 36.000 0.00 0.00 0.00 2.57
74 75 5.231147 CGCGGGAACAAAAATTATACCAATG 59.769 40.000 0.00 0.00 0.00 2.82
75 76 5.344884 CGCGGGAACAAAAATTATACCAAT 58.655 37.500 0.00 0.00 0.00 3.16
76 77 4.380655 CCGCGGGAACAAAAATTATACCAA 60.381 41.667 20.10 0.00 0.00 3.67
77 78 3.128938 CCGCGGGAACAAAAATTATACCA 59.871 43.478 20.10 0.00 0.00 3.25
78 79 3.697982 CCGCGGGAACAAAAATTATACC 58.302 45.455 20.10 0.00 0.00 2.73
79 80 3.110358 GCCGCGGGAACAAAAATTATAC 58.890 45.455 29.38 0.00 0.00 1.47
80 81 2.753452 TGCCGCGGGAACAAAAATTATA 59.247 40.909 29.38 0.00 0.00 0.98
81 82 1.546476 TGCCGCGGGAACAAAAATTAT 59.454 42.857 29.38 0.00 0.00 1.28
82 83 0.959553 TGCCGCGGGAACAAAAATTA 59.040 45.000 29.38 0.00 0.00 1.40
83 84 0.319469 CTGCCGCGGGAACAAAAATT 60.319 50.000 29.38 0.00 0.00 1.82
84 85 1.288752 CTGCCGCGGGAACAAAAAT 59.711 52.632 29.38 0.00 0.00 1.82
85 86 2.065906 GACTGCCGCGGGAACAAAAA 62.066 55.000 29.38 0.00 0.00 1.94
86 87 2.517402 ACTGCCGCGGGAACAAAA 60.517 55.556 29.38 0.00 0.00 2.44
87 88 2.975799 GACTGCCGCGGGAACAAA 60.976 61.111 29.38 0.00 0.00 2.83
97 98 3.403057 CAACGTGACCGACTGCCG 61.403 66.667 0.00 0.00 37.88 5.69
98 99 3.041940 CCAACGTGACCGACTGCC 61.042 66.667 0.00 0.00 37.88 4.85
99 100 0.598158 TAACCAACGTGACCGACTGC 60.598 55.000 0.00 0.00 37.88 4.40
100 101 1.855513 TTAACCAACGTGACCGACTG 58.144 50.000 0.00 0.00 37.88 3.51
101 102 2.600470 TTTAACCAACGTGACCGACT 57.400 45.000 0.00 0.00 37.88 4.18
102 103 3.883631 AATTTAACCAACGTGACCGAC 57.116 42.857 0.00 0.00 37.88 4.79
103 104 4.084641 CGTAAATTTAACCAACGTGACCGA 60.085 41.667 0.00 0.00 37.88 4.69
104 105 4.143116 CGTAAATTTAACCAACGTGACCG 58.857 43.478 0.00 0.00 40.83 4.79
105 106 4.024133 ACCGTAAATTTAACCAACGTGACC 60.024 41.667 0.00 0.00 31.87 4.02
106 107 5.094429 ACCGTAAATTTAACCAACGTGAC 57.906 39.130 0.00 0.00 31.87 3.67
107 108 4.813161 TGACCGTAAATTTAACCAACGTGA 59.187 37.500 0.00 0.00 31.87 4.35
108 109 5.093169 TGACCGTAAATTTAACCAACGTG 57.907 39.130 0.00 0.00 31.87 4.49
109 110 5.747951 TTGACCGTAAATTTAACCAACGT 57.252 34.783 0.00 0.00 31.87 3.99
110 111 6.200808 AGTTTGACCGTAAATTTAACCAACG 58.799 36.000 0.00 1.44 0.00 4.10
111 112 7.701501 TCAAGTTTGACCGTAAATTTAACCAAC 59.298 33.333 0.00 1.91 31.01 3.77
112 113 7.769220 TCAAGTTTGACCGTAAATTTAACCAA 58.231 30.769 0.00 0.05 31.01 3.67
113 114 7.330900 TCAAGTTTGACCGTAAATTTAACCA 57.669 32.000 0.00 0.00 31.01 3.67
114 115 8.806177 ATTCAAGTTTGACCGTAAATTTAACC 57.194 30.769 0.00 0.00 36.83 2.85
117 118 9.171701 CGAAATTCAAGTTTGACCGTAAATTTA 57.828 29.630 0.00 0.00 36.83 1.40
118 119 7.168469 CCGAAATTCAAGTTTGACCGTAAATTT 59.832 33.333 0.00 0.00 36.83 1.82
119 120 6.639279 CCGAAATTCAAGTTTGACCGTAAATT 59.361 34.615 0.00 0.00 36.83 1.82
120 121 6.146898 CCGAAATTCAAGTTTGACCGTAAAT 58.853 36.000 0.00 0.00 36.83 1.40
121 122 5.505985 CCCGAAATTCAAGTTTGACCGTAAA 60.506 40.000 0.00 0.00 36.83 2.01
122 123 4.023878 CCCGAAATTCAAGTTTGACCGTAA 60.024 41.667 0.00 0.00 36.83 3.18
123 124 3.499157 CCCGAAATTCAAGTTTGACCGTA 59.501 43.478 0.00 0.00 36.83 4.02
124 125 2.292292 CCCGAAATTCAAGTTTGACCGT 59.708 45.455 0.00 0.00 36.83 4.83
125 126 2.550606 TCCCGAAATTCAAGTTTGACCG 59.449 45.455 0.00 0.00 36.83 4.79
126 127 4.546570 CTTCCCGAAATTCAAGTTTGACC 58.453 43.478 0.00 0.00 36.83 4.02
127 128 3.981416 GCTTCCCGAAATTCAAGTTTGAC 59.019 43.478 0.00 0.00 36.83 3.18
128 129 3.304391 CGCTTCCCGAAATTCAAGTTTGA 60.304 43.478 0.00 0.00 40.02 2.69
129 130 2.979813 CGCTTCCCGAAATTCAAGTTTG 59.020 45.455 0.00 0.00 40.02 2.93
130 131 2.607038 GCGCTTCCCGAAATTCAAGTTT 60.607 45.455 0.00 0.00 40.02 2.66
131 132 1.068541 GCGCTTCCCGAAATTCAAGTT 60.069 47.619 0.00 0.00 40.02 2.66
132 133 0.521735 GCGCTTCCCGAAATTCAAGT 59.478 50.000 0.00 0.00 40.02 3.16
133 134 0.521242 CGCGCTTCCCGAAATTCAAG 60.521 55.000 5.56 0.00 40.02 3.02
134 135 1.499949 CGCGCTTCCCGAAATTCAA 59.500 52.632 5.56 0.00 40.02 2.69
135 136 2.395360 CCGCGCTTCCCGAAATTCA 61.395 57.895 5.56 0.00 40.02 2.57
136 137 2.403586 CCGCGCTTCCCGAAATTC 59.596 61.111 5.56 0.00 40.02 2.17
137 138 3.131478 CCCGCGCTTCCCGAAATT 61.131 61.111 5.56 0.00 40.02 1.82
149 150 4.222589 CAATGTAGTGCGCCCGCG 62.223 66.667 4.18 4.36 45.51 6.46
150 151 3.124921 ACAATGTAGTGCGCCCGC 61.125 61.111 4.18 5.60 42.35 6.13
151 152 1.295357 TTCACAATGTAGTGCGCCCG 61.295 55.000 4.18 0.00 39.35 6.13
152 153 1.094785 ATTCACAATGTAGTGCGCCC 58.905 50.000 4.18 0.00 39.35 6.13
153 154 1.202177 CCATTCACAATGTAGTGCGCC 60.202 52.381 4.18 0.00 39.35 6.53
154 155 1.737236 TCCATTCACAATGTAGTGCGC 59.263 47.619 0.00 0.00 39.35 6.09
155 156 2.352651 CCTCCATTCACAATGTAGTGCG 59.647 50.000 0.00 0.00 39.35 5.34
156 157 2.684881 CCCTCCATTCACAATGTAGTGC 59.315 50.000 0.00 0.00 39.35 4.40
157 158 4.220693 TCCCTCCATTCACAATGTAGTG 57.779 45.455 0.00 0.00 40.85 2.74
158 159 4.927267 TTCCCTCCATTCACAATGTAGT 57.073 40.909 0.00 0.00 37.18 2.73
159 160 7.000472 ACATATTCCCTCCATTCACAATGTAG 59.000 38.462 0.00 0.00 37.18 2.74
160 161 6.910191 ACATATTCCCTCCATTCACAATGTA 58.090 36.000 0.00 0.00 37.18 2.29
161 162 5.769835 ACATATTCCCTCCATTCACAATGT 58.230 37.500 0.00 0.00 37.18 2.71
162 163 5.829391 TGACATATTCCCTCCATTCACAATG 59.171 40.000 0.00 0.00 38.63 2.82
163 164 6.017211 TGACATATTCCCTCCATTCACAAT 57.983 37.500 0.00 0.00 0.00 2.71
164 165 5.449297 TGACATATTCCCTCCATTCACAA 57.551 39.130 0.00 0.00 0.00 3.33
165 166 5.651612 ATGACATATTCCCTCCATTCACA 57.348 39.130 0.00 0.00 0.00 3.58
166 167 6.774656 AGAAATGACATATTCCCTCCATTCAC 59.225 38.462 0.00 0.00 0.00 3.18
167 168 6.914665 AGAAATGACATATTCCCTCCATTCA 58.085 36.000 0.00 0.00 0.00 2.57
168 169 7.503566 TGAAGAAATGACATATTCCCTCCATTC 59.496 37.037 0.00 0.00 0.00 2.67
169 170 7.356680 TGAAGAAATGACATATTCCCTCCATT 58.643 34.615 0.00 0.00 0.00 3.16
170 171 6.914665 TGAAGAAATGACATATTCCCTCCAT 58.085 36.000 0.00 0.00 0.00 3.41
171 172 6.325993 TGAAGAAATGACATATTCCCTCCA 57.674 37.500 0.00 0.00 0.00 3.86
172 173 7.000472 TCATGAAGAAATGACATATTCCCTCC 59.000 38.462 0.00 0.00 31.58 4.30
173 174 7.935755 TCTCATGAAGAAATGACATATTCCCTC 59.064 37.037 0.00 0.00 33.08 4.30
174 175 7.809238 TCTCATGAAGAAATGACATATTCCCT 58.191 34.615 0.00 0.00 33.08 4.20
175 176 8.632906 ATCTCATGAAGAAATGACATATTCCC 57.367 34.615 0.00 0.00 37.61 3.97
195 196 7.722795 TCTTTTCATCGTGTACAAAATCTCA 57.277 32.000 0.00 0.00 0.00 3.27
289 292 2.930826 AAAAAGGGAGCTCGACTTCA 57.069 45.000 18.87 0.00 0.00 3.02
351 354 4.035208 GCGAAGAAGGAGTCAAACAAAGAA 59.965 41.667 0.00 0.00 0.00 2.52
442 446 3.879998 TGGTGTGTGCTTAAGAAAGACA 58.120 40.909 6.67 5.61 34.37 3.41
445 449 7.199766 TGTTTTATGGTGTGTGCTTAAGAAAG 58.800 34.615 6.67 0.00 35.68 2.62
563 595 7.150783 TGACTTCATGATGATCCTATAGTCG 57.849 40.000 15.03 0.00 32.38 4.18
564 596 9.770097 TTTTGACTTCATGATGATCCTATAGTC 57.230 33.333 15.03 13.17 31.12 2.59
567 599 8.717717 ACCTTTTGACTTCATGATGATCCTATA 58.282 33.333 15.03 0.00 0.00 1.31
569 601 6.962182 ACCTTTTGACTTCATGATGATCCTA 58.038 36.000 15.03 0.00 0.00 2.94
570 602 5.824421 ACCTTTTGACTTCATGATGATCCT 58.176 37.500 15.03 0.00 0.00 3.24
571 603 6.825721 AGTACCTTTTGACTTCATGATGATCC 59.174 38.462 15.03 4.95 0.00 3.36
595 627 3.640967 AGTCTTGGCTAGCTCATAAGGAG 59.359 47.826 15.72 5.28 46.93 3.69
597 629 4.125703 CAAGTCTTGGCTAGCTCATAAGG 58.874 47.826 15.72 3.02 0.00 2.69
599 631 5.420725 TTCAAGTCTTGGCTAGCTCATAA 57.579 39.130 15.72 4.57 0.00 1.90
684 945 2.152016 GACCTAGAACCAAACAGCACC 58.848 52.381 0.00 0.00 0.00 5.01
685 946 2.846193 TGACCTAGAACCAAACAGCAC 58.154 47.619 0.00 0.00 0.00 4.40
686 947 3.569194 TTGACCTAGAACCAAACAGCA 57.431 42.857 0.00 0.00 0.00 4.41
687 948 4.518970 TGATTTGACCTAGAACCAAACAGC 59.481 41.667 0.00 0.00 33.33 4.40
689 950 5.048083 GCATGATTTGACCTAGAACCAAACA 60.048 40.000 0.00 1.52 33.33 2.83
690 951 5.402398 GCATGATTTGACCTAGAACCAAAC 58.598 41.667 0.00 0.00 33.33 2.93
691 952 4.462483 GGCATGATTTGACCTAGAACCAAA 59.538 41.667 0.00 0.00 34.76 3.28
692 953 4.016444 GGCATGATTTGACCTAGAACCAA 58.984 43.478 0.00 0.00 0.00 3.67
693 954 3.010027 TGGCATGATTTGACCTAGAACCA 59.990 43.478 0.00 0.00 29.16 3.67
695 956 6.058183 AGTATGGCATGATTTGACCTAGAAC 58.942 40.000 10.98 0.00 29.16 3.01
698 959 6.732154 CAAAGTATGGCATGATTTGACCTAG 58.268 40.000 23.86 5.84 33.69 3.02
699 960 5.067674 GCAAAGTATGGCATGATTTGACCTA 59.932 40.000 28.64 0.27 33.69 3.08
700 961 4.142093 GCAAAGTATGGCATGATTTGACCT 60.142 41.667 28.64 3.06 33.69 3.85
731 992 6.152661 CCAAATCTAAGGAAAGTGTGGCAATA 59.847 38.462 0.00 0.00 0.00 1.90
732 993 5.047092 CCAAATCTAAGGAAAGTGTGGCAAT 60.047 40.000 0.00 0.00 0.00 3.56
733 994 4.280677 CCAAATCTAAGGAAAGTGTGGCAA 59.719 41.667 0.00 0.00 0.00 4.52
734 995 3.826157 CCAAATCTAAGGAAAGTGTGGCA 59.174 43.478 0.00 0.00 0.00 4.92
735 996 3.826729 ACCAAATCTAAGGAAAGTGTGGC 59.173 43.478 0.00 0.00 0.00 5.01
736 997 5.770162 AGAACCAAATCTAAGGAAAGTGTGG 59.230 40.000 0.00 0.00 0.00 4.17
737 998 6.884280 AGAACCAAATCTAAGGAAAGTGTG 57.116 37.500 0.00 0.00 0.00 3.82
738 999 7.168905 CCTAGAACCAAATCTAAGGAAAGTGT 58.831 38.462 0.00 0.00 31.76 3.55
741 1002 5.590663 GGCCTAGAACCAAATCTAAGGAAAG 59.409 44.000 0.00 0.00 31.76 2.62
746 1007 5.130477 TGGTAGGCCTAGAACCAAATCTAAG 59.870 44.000 21.43 0.00 40.28 2.18
747 1008 5.034200 TGGTAGGCCTAGAACCAAATCTAA 58.966 41.667 21.43 0.00 40.28 2.10
748 1009 4.627015 TGGTAGGCCTAGAACCAAATCTA 58.373 43.478 21.43 0.00 40.28 1.98
750 1011 3.926058 TGGTAGGCCTAGAACCAAATC 57.074 47.619 21.43 3.24 40.28 2.17
754 1015 2.039348 GTGTTTGGTAGGCCTAGAACCA 59.961 50.000 20.11 20.11 41.47 3.67
755 1016 2.305052 AGTGTTTGGTAGGCCTAGAACC 59.695 50.000 14.38 14.95 35.27 3.62
757 1018 3.649023 TCAAGTGTTTGGTAGGCCTAGAA 59.351 43.478 14.38 6.38 34.97 2.10
758 1019 3.244582 TCAAGTGTTTGGTAGGCCTAGA 58.755 45.455 14.38 0.00 34.97 2.43
759 1020 3.695830 TCAAGTGTTTGGTAGGCCTAG 57.304 47.619 14.38 0.00 34.97 3.02
760 1021 4.650972 ATTCAAGTGTTTGGTAGGCCTA 57.349 40.909 8.91 8.91 34.97 3.93
762 1023 4.600692 AAATTCAAGTGTTTGGTAGGCC 57.399 40.909 0.00 0.00 34.97 5.19
823 1090 1.334243 AGATAGACGCTGCGGAAGTAC 59.666 52.381 26.95 12.32 0.00 2.73
879 1146 2.223803 AGTGAGAGGAGTGTGGGTAG 57.776 55.000 0.00 0.00 0.00 3.18
976 1247 2.725008 CGGCTAGGCGAAGAGAGG 59.275 66.667 32.94 0.51 0.00 3.69
1102 1381 2.131067 GGAAGGAGCGGGAGAGGAG 61.131 68.421 0.00 0.00 0.00 3.69
1227 1506 0.028374 GCGAGAAGACGTAGAGGAGC 59.972 60.000 0.00 0.00 35.59 4.70
1589 1871 2.564553 GATGAACGCCTCGACTGCCT 62.565 60.000 0.00 0.00 0.00 4.75
1735 2018 2.200370 ACACTCGTCACCCTCCCA 59.800 61.111 0.00 0.00 0.00 4.37
1810 2093 3.459232 AAGACAAGAAGCAAAAAGGCC 57.541 42.857 0.00 0.00 0.00 5.19
1933 2216 0.108992 GACACCATACAGCGACCGAA 60.109 55.000 0.00 0.00 0.00 4.30
1936 2219 1.518572 CCGACACCATACAGCGACC 60.519 63.158 0.00 0.00 0.00 4.79
1943 2226 2.510691 CGTGGGCCGACACCATAC 60.511 66.667 18.72 0.00 40.70 2.39
2028 2311 6.636044 CGGGAAGTAATTCGACTCTTGTATAC 59.364 42.308 0.00 0.00 0.00 1.47
2035 2325 2.824341 ACACGGGAAGTAATTCGACTCT 59.176 45.455 0.00 0.00 0.00 3.24
2054 2344 4.578105 TGGCAACGATAATATGCATTCACA 59.422 37.500 3.54 0.00 41.80 3.58
2057 2347 4.911610 GTGTGGCAACGATAATATGCATTC 59.088 41.667 3.54 0.00 41.80 2.67
2087 2378 1.340889 GAGTTGGCCTCATTTTGTGCA 59.659 47.619 3.32 0.00 40.17 4.57
2088 2379 1.337167 GGAGTTGGCCTCATTTTGTGC 60.337 52.381 3.32 0.00 42.40 4.57
2092 2383 3.745723 ACGGAGTTGGCCTCATTTT 57.254 47.368 3.32 0.00 37.78 1.82
2115 2406 3.508762 ACAGAAACGACTAATGCGGTAG 58.491 45.455 0.00 0.00 0.00 3.18
2116 2407 3.581024 ACAGAAACGACTAATGCGGTA 57.419 42.857 0.00 0.00 0.00 4.02
2125 2416 2.718563 ACCAAACCAACAGAAACGACT 58.281 42.857 0.00 0.00 0.00 4.18
2127 2418 2.096174 CGAACCAAACCAACAGAAACGA 59.904 45.455 0.00 0.00 0.00 3.85
2128 2419 2.096174 TCGAACCAAACCAACAGAAACG 59.904 45.455 0.00 0.00 0.00 3.60
2129 2420 3.768468 TCGAACCAAACCAACAGAAAC 57.232 42.857 0.00 0.00 0.00 2.78
2130 2421 4.487019 GTTTCGAACCAAACCAACAGAAA 58.513 39.130 0.00 0.00 31.10 2.52
2131 2422 3.426426 CGTTTCGAACCAAACCAACAGAA 60.426 43.478 0.00 0.00 33.37 3.02
2133 2424 2.159490 ACGTTTCGAACCAAACCAACAG 60.159 45.455 0.00 0.00 33.37 3.16
2137 2428 2.608546 CTGTACGTTTCGAACCAAACCA 59.391 45.455 0.00 0.00 33.37 3.67
2138 2429 2.865551 TCTGTACGTTTCGAACCAAACC 59.134 45.455 0.00 0.00 33.37 3.27
2139 2430 4.519191 TTCTGTACGTTTCGAACCAAAC 57.481 40.909 0.00 0.00 33.57 2.93
2140 2431 5.542616 TTTTCTGTACGTTTCGAACCAAA 57.457 34.783 0.00 0.00 0.00 3.28
2141 2432 5.738118 ATTTTCTGTACGTTTCGAACCAA 57.262 34.783 0.00 0.00 0.00 3.67
2147 2438 3.365820 AGCCGTATTTTCTGTACGTTTCG 59.634 43.478 0.00 0.00 42.37 3.46
2154 2445 3.676172 CACGTTGAGCCGTATTTTCTGTA 59.324 43.478 0.00 0.00 39.45 2.74
2158 2449 1.465187 GGCACGTTGAGCCGTATTTTC 60.465 52.381 0.00 0.00 43.15 2.29
2177 2468 3.809832 GGACACTCATCCATTTACATCGG 59.190 47.826 0.00 0.00 38.77 4.18
2181 2472 5.014123 AGGAAAGGACACTCATCCATTTACA 59.986 40.000 0.00 0.00 41.73 2.41
2182 2473 5.355350 CAGGAAAGGACACTCATCCATTTAC 59.645 44.000 0.00 0.00 41.73 2.01
2183 2474 5.014123 ACAGGAAAGGACACTCATCCATTTA 59.986 40.000 0.00 0.00 41.73 1.40
2187 2478 2.338809 ACAGGAAAGGACACTCATCCA 58.661 47.619 0.00 0.00 41.73 3.41
2193 2484 5.221048 CGAAAATGAAACAGGAAAGGACACT 60.221 40.000 0.00 0.00 0.00 3.55
2194 2485 4.976116 CGAAAATGAAACAGGAAAGGACAC 59.024 41.667 0.00 0.00 0.00 3.67
2198 2489 4.546570 GACCGAAAATGAAACAGGAAAGG 58.453 43.478 0.00 0.00 0.00 3.11
2202 2493 2.158593 TGGGACCGAAAATGAAACAGGA 60.159 45.455 0.00 0.00 0.00 3.86
2203 2494 2.235016 TGGGACCGAAAATGAAACAGG 58.765 47.619 0.00 0.00 0.00 4.00
2205 2496 4.946478 AATTGGGACCGAAAATGAAACA 57.054 36.364 0.00 0.00 0.00 2.83
2207 2498 5.567823 GCCTAAATTGGGACCGAAAATGAAA 60.568 40.000 0.00 0.00 0.00 2.69
2208 2499 4.081917 GCCTAAATTGGGACCGAAAATGAA 60.082 41.667 0.00 0.00 0.00 2.57
2209 2500 3.445805 GCCTAAATTGGGACCGAAAATGA 59.554 43.478 0.00 0.00 0.00 2.57
2211 2502 2.764010 GGCCTAAATTGGGACCGAAAAT 59.236 45.455 0.00 0.00 0.00 1.82
2212 2503 2.172679 GGCCTAAATTGGGACCGAAAA 58.827 47.619 0.00 0.00 0.00 2.29
2216 2507 2.478033 GCGGCCTAAATTGGGACCG 61.478 63.158 20.38 20.38 42.20 4.79
2217 2508 2.478033 CGCGGCCTAAATTGGGACC 61.478 63.158 0.00 0.00 0.00 4.46
2219 2510 0.609681 AAACGCGGCCTAAATTGGGA 60.610 50.000 12.47 0.00 0.00 4.37
2222 2513 1.335506 ACACAAACGCGGCCTAAATTG 60.336 47.619 12.47 3.88 0.00 2.32
2225 2516 1.833434 CGACACAAACGCGGCCTAAA 61.833 55.000 12.47 0.00 0.00 1.85
2228 2519 4.595538 TCGACACAAACGCGGCCT 62.596 61.111 12.47 0.00 0.00 5.19
2240 2531 0.653636 GCACCTTGTTCGTTTCGACA 59.346 50.000 0.00 0.00 34.89 4.35
2244 2535 0.658897 TTCCGCACCTTGTTCGTTTC 59.341 50.000 0.00 0.00 0.00 2.78
2245 2536 0.661020 CTTCCGCACCTTGTTCGTTT 59.339 50.000 0.00 0.00 0.00 3.60
2249 2540 2.251642 ACGCTTCCGCACCTTGTTC 61.252 57.895 0.00 0.00 38.22 3.18
2250 2541 2.203153 ACGCTTCCGCACCTTGTT 60.203 55.556 0.00 0.00 38.22 2.83
2267 2558 2.899838 GCAAGTGTGTGCGTCCCA 60.900 61.111 0.00 0.00 34.21 4.37
2288 2579 3.650950 CAGGTGAGTGGGGGTGGG 61.651 72.222 0.00 0.00 0.00 4.61
2290 2581 2.750350 GACAGGTGAGTGGGGGTG 59.250 66.667 0.00 0.00 0.00 4.61
2291 2582 2.923035 CGACAGGTGAGTGGGGGT 60.923 66.667 0.00 0.00 0.00 4.95
2294 2585 3.706373 CCCCGACAGGTGAGTGGG 61.706 72.222 0.00 0.00 39.69 4.61
2295 2586 4.394712 GCCCCGACAGGTGAGTGG 62.395 72.222 0.00 0.00 35.12 4.00
2297 2588 3.626924 GTGCCCCGACAGGTGAGT 61.627 66.667 0.00 0.00 35.12 3.41
2299 2590 3.936203 GTGTGCCCCGACAGGTGA 61.936 66.667 0.00 0.00 35.12 4.02
2303 2594 2.034066 AATGGTGTGCCCCGACAG 59.966 61.111 0.00 0.00 0.00 3.51
2305 2596 1.745489 GAGAATGGTGTGCCCCGAC 60.745 63.158 0.00 0.00 0.00 4.79
2306 2597 1.561769 ATGAGAATGGTGTGCCCCGA 61.562 55.000 0.00 0.00 0.00 5.14
2307 2598 0.680921 AATGAGAATGGTGTGCCCCG 60.681 55.000 0.00 0.00 0.00 5.73
2308 2599 1.560505 AAATGAGAATGGTGTGCCCC 58.439 50.000 0.00 0.00 0.00 5.80
2311 2602 4.525912 AAGGAAAATGAGAATGGTGTGC 57.474 40.909 0.00 0.00 0.00 4.57
2312 2603 7.260603 GGAATAAGGAAAATGAGAATGGTGTG 58.739 38.462 0.00 0.00 0.00 3.82
2313 2604 6.381133 GGGAATAAGGAAAATGAGAATGGTGT 59.619 38.462 0.00 0.00 0.00 4.16
2314 2605 6.608808 AGGGAATAAGGAAAATGAGAATGGTG 59.391 38.462 0.00 0.00 0.00 4.17
2316 2607 6.835488 TGAGGGAATAAGGAAAATGAGAATGG 59.165 38.462 0.00 0.00 0.00 3.16
2324 2615 7.450074 GGTTTTTGTGAGGGAATAAGGAAAAT 58.550 34.615 0.00 0.00 0.00 1.82
2332 2623 3.245479 GGGAGGGTTTTTGTGAGGGAATA 60.245 47.826 0.00 0.00 0.00 1.75
2336 2627 0.893727 CGGGAGGGTTTTTGTGAGGG 60.894 60.000 0.00 0.00 0.00 4.30
2341 2632 1.428718 TAGGGCGGGAGGGTTTTTGT 61.429 55.000 0.00 0.00 0.00 2.83
2361 2652 4.864334 GTGGCCATGGCGGAGAGG 62.864 72.222 29.90 0.00 43.06 3.69
2382 2673 3.131478 GCGGTAGCGGCATTTGGT 61.131 61.111 17.08 0.00 0.00 3.67
2416 2728 2.338500 CTTCTCGGGTTTCTTCTTCGG 58.662 52.381 0.00 0.00 0.00 4.30
2451 2766 0.602905 CCTTTTCTCGGGCGAGTTGT 60.603 55.000 0.00 0.00 42.49 3.32
2454 2769 2.047179 GCCTTTTCTCGGGCGAGT 60.047 61.111 0.00 0.00 42.49 4.18
2458 2773 1.362406 CTCTTCGCCTTTTCTCGGGC 61.362 60.000 0.00 0.00 44.43 6.13
2492 2807 3.469863 TTCCCCTTCGCAGCAACGT 62.470 57.895 0.00 0.00 0.00 3.99
2494 2809 2.335712 CCTTCCCCTTCGCAGCAAC 61.336 63.158 0.00 0.00 0.00 4.17
2544 2859 4.645921 GTGGCCTTGTGTTGCGCC 62.646 66.667 4.18 0.00 41.99 6.53
2560 2875 2.487265 GGGCCTCATTATCATCAACGGT 60.487 50.000 0.84 0.00 0.00 4.83
2563 2878 3.070018 CGAGGGCCTCATTATCATCAAC 58.930 50.000 31.69 2.04 0.00 3.18
2610 2925 1.941999 GCAAGAGGAGGGCATGTTGC 61.942 60.000 0.00 0.00 45.42 4.17
2613 2928 0.835941 CTAGCAAGAGGAGGGCATGT 59.164 55.000 0.00 0.00 0.00 3.21
2614 2929 0.108207 CCTAGCAAGAGGAGGGCATG 59.892 60.000 0.00 0.00 39.15 4.06
2626 2941 0.035739 GGTCGGTTGAACCCTAGCAA 59.964 55.000 9.08 0.00 33.75 3.91
2634 2949 2.686816 CGGCATGGGTCGGTTGAAC 61.687 63.158 0.00 0.00 38.79 3.18
2642 2957 3.219198 GAATGGCCGGCATGGGTC 61.219 66.667 30.85 13.71 38.63 4.46
2648 2963 2.124901 CGGTAAGAATGGCCGGCA 60.125 61.111 30.85 15.30 41.60 5.69
2649 2964 3.583086 GCGGTAAGAATGGCCGGC 61.583 66.667 21.18 21.18 45.02 6.13
2653 2968 2.032981 CCATGGCGGTAAGAATGGC 58.967 57.895 0.00 0.00 33.64 4.40
2680 2998 4.645921 GGCCAACAAGCACGTGCC 62.646 66.667 35.51 18.64 43.38 5.01
2690 3008 2.112297 GAGGGTGAACGGCCAACA 59.888 61.111 2.24 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.