Multiple sequence alignment - TraesCS1A01G055500

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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 TraesCS1A01G055500 chr1A 100.000 2654 0 0 1 2654 36604149 36606802 0.000000e+00 4902.0
1 TraesCS1A01G055500 chr1A 89.652 1034 106 1 1621 2654 36614112 36615144 0.000000e+00 1315.0
2 TraesCS1A01G055500 chr1A 86.613 620 78 3 990 1605 37505339 37504721 0.000000e+00 680.0
3 TraesCS1A01G055500 chr1A 86.667 60 3 2 803 862 36612958 36613012 7.930000e-06 62.1
4 TraesCS1A01G055500 chr1D 91.216 1036 86 5 1621 2654 36623681 36622649 0.000000e+00 1404.0
5 TraesCS1A01G055500 chr1D 88.574 1024 117 0 1621 2644 37424762 37425785 0.000000e+00 1243.0
6 TraesCS1A01G055500 chr1D 87.100 1031 132 1 1624 2653 38258756 38257726 0.000000e+00 1166.0
7 TraesCS1A01G055500 chr1D 87.016 1032 130 4 1624 2653 38367099 38366070 0.000000e+00 1160.0
8 TraesCS1A01G055500 chr1D 83.668 747 96 16 865 1603 38560395 38559667 0.000000e+00 680.0
9 TraesCS1A01G055500 chr1D 87.716 578 68 1 1038 1612 37964748 37964171 0.000000e+00 671.0
10 TraesCS1A01G055500 chr1D 82.031 768 122 10 853 1612 37423689 37424448 8.010000e-180 640.0
11 TraesCS1A01G055500 chr1D 85.008 627 89 3 990 1612 38584024 38583399 1.340000e-177 632.0
12 TraesCS1A01G055500 chr1D 83.667 649 96 7 982 1623 38259708 38259063 1.050000e-168 603.0
13 TraesCS1A01G055500 chr1B 87.814 1034 120 4 1621 2653 56500874 56499846 0.000000e+00 1206.0
14 TraesCS1A01G055500 chr1B 86.893 1030 135 0 1624 2653 57790712 57789683 0.000000e+00 1155.0
15 TraesCS1A01G055500 chr1B 86.776 1036 130 5 1621 2654 56492691 56491661 0.000000e+00 1147.0
16 TraesCS1A01G055500 chr1B 87.089 821 81 12 812 1612 56620729 56619914 0.000000e+00 905.0
17 TraesCS1A01G055500 chr1B 87.737 791 57 12 834 1612 56493767 56493005 0.000000e+00 887.0
18 TraesCS1A01G055500 chr1B 88.812 581 62 1 1035 1612 56501766 56501186 0.000000e+00 710.0
19 TraesCS1A01G055500 chr1B 92.325 456 32 2 293 748 56621373 56620921 0.000000e+00 645.0
20 TraesCS1A01G055500 chr1B 90.393 458 42 2 291 748 277964998 277964543 3.780000e-168 601.0
21 TraesCS1A01G055500 chr1B 88.235 51 4 2 139 189 527384651 527384603 2.850000e-05 60.2
22 TraesCS1A01G055500 chr1B 92.683 41 2 1 151 191 268594388 268594349 1.030000e-04 58.4
23 TraesCS1A01G055500 chr2D 87.209 1032 125 7 1621 2649 579328419 579329446 0.000000e+00 1168.0
24 TraesCS1A01G055500 chr2D 83.684 190 22 6 1 186 585212096 585211912 1.260000e-38 171.0
25 TraesCS1A01G055500 chr6D 93.043 460 30 2 290 748 56208483 56208025 0.000000e+00 671.0
26 TraesCS1A01G055500 chr3B 91.285 459 38 2 290 748 704289049 704288593 2.240000e-175 625.0
27 TraesCS1A01G055500 chr3B 90.476 462 42 2 288 748 222147448 222146988 2.260000e-170 608.0
28 TraesCS1A01G055500 chr3D 91.068 459 35 4 292 749 345069330 345068877 1.350000e-172 616.0
29 TraesCS1A01G055500 chr3D 92.982 171 8 2 9 179 313814506 313814672 2.040000e-61 246.0
30 TraesCS1A01G055500 chr3D 88.406 69 7 1 1 68 481391091 481391023 6.090000e-12 82.4
31 TraesCS1A01G055500 chr3A 90.652 460 41 2 291 750 580560164 580560621 6.280000e-171 610.0
32 TraesCS1A01G055500 chr5B 90.789 456 41 1 293 748 72093166 72093620 2.260000e-170 608.0
33 TraesCS1A01G055500 chr5B 90.150 467 45 1 286 752 457448573 457449038 8.120000e-170 606.0
34 TraesCS1A01G055500 chr5B 89.130 46 3 2 134 179 520368790 520368833 3.690000e-04 56.5
35 TraesCS1A01G055500 chr4D 91.351 185 12 2 1 185 12195683 12195503 1.580000e-62 250.0
36 TraesCS1A01G055500 chr7D 92.308 169 9 2 9 177 607217641 607217477 1.230000e-58 237.0
37 TraesCS1A01G055500 chr7A 93.333 45 1 1 151 195 175352027 175352069 6.130000e-07 65.8
38 TraesCS1A01G055500 chr4A 97.222 36 0 1 148 182 543382984 543382949 2.850000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G055500 chr1A 36604149 36606802 2653 False 4902.00 4902 100.0000 1 2654 1 chr1A.!!$F1 2653
1 TraesCS1A01G055500 chr1A 36612958 36615144 2186 False 688.55 1315 88.1595 803 2654 2 chr1A.!!$F2 1851
2 TraesCS1A01G055500 chr1A 37504721 37505339 618 True 680.00 680 86.6130 990 1605 1 chr1A.!!$R1 615
3 TraesCS1A01G055500 chr1D 36622649 36623681 1032 True 1404.00 1404 91.2160 1621 2654 1 chr1D.!!$R1 1033
4 TraesCS1A01G055500 chr1D 38366070 38367099 1029 True 1160.00 1160 87.0160 1624 2653 1 chr1D.!!$R3 1029
5 TraesCS1A01G055500 chr1D 37423689 37425785 2096 False 941.50 1243 85.3025 853 2644 2 chr1D.!!$F1 1791
6 TraesCS1A01G055500 chr1D 38257726 38259708 1982 True 884.50 1166 85.3835 982 2653 2 chr1D.!!$R6 1671
7 TraesCS1A01G055500 chr1D 38559667 38560395 728 True 680.00 680 83.6680 865 1603 1 chr1D.!!$R4 738
8 TraesCS1A01G055500 chr1D 37964171 37964748 577 True 671.00 671 87.7160 1038 1612 1 chr1D.!!$R2 574
9 TraesCS1A01G055500 chr1D 38583399 38584024 625 True 632.00 632 85.0080 990 1612 1 chr1D.!!$R5 622
10 TraesCS1A01G055500 chr1B 57789683 57790712 1029 True 1155.00 1155 86.8930 1624 2653 1 chr1B.!!$R1 1029
11 TraesCS1A01G055500 chr1B 56491661 56493767 2106 True 1017.00 1147 87.2565 834 2654 2 chr1B.!!$R5 1820
12 TraesCS1A01G055500 chr1B 56499846 56501766 1920 True 958.00 1206 88.3130 1035 2653 2 chr1B.!!$R6 1618
13 TraesCS1A01G055500 chr1B 56619914 56621373 1459 True 775.00 905 89.7070 293 1612 2 chr1B.!!$R7 1319
14 TraesCS1A01G055500 chr2D 579328419 579329446 1027 False 1168.00 1168 87.2090 1621 2649 1 chr2D.!!$F1 1028

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
110 111 0.034089 GGGGGTACTTGAGCAATGCT 60.034 55.0 7.79 7.79 43.88 3.79 F
283 284 0.102481 AACGCTCGTCTCAGTTGTGT 59.898 50.0 0.00 0.00 0.00 3.72 F
712 713 0.104120 CGATTAGGATGGACCGTGCA 59.896 55.0 8.06 0.00 44.74 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1680 0.791422 CATCCGTCCGTTTTGCGTAA 59.209 50.0 0.0 0.0 39.32 3.18 R
1479 1701 1.502163 GAAGCAGCACGTTCACAGCT 61.502 55.0 0.0 0.0 39.63 4.24 R
2519 3051 0.673437 CCAGCACGAAACAACCCATT 59.327 50.0 0.0 0.0 0.00 3.16 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
17 18 3.400188 GAACACCGGGGTCATCCT 58.600 61.111 11.43 0.00 35.33 3.24
18 19 1.683441 GAACACCGGGGTCATCCTT 59.317 57.895 11.43 0.00 35.33 3.36
19 20 0.037734 GAACACCGGGGTCATCCTTT 59.962 55.000 11.43 0.00 35.33 3.11
20 21 0.251165 AACACCGGGGTCATCCTTTG 60.251 55.000 11.43 0.00 35.33 2.77
21 22 2.046285 CACCGGGGTCATCCTTTGC 61.046 63.158 6.32 0.00 35.33 3.68
22 23 2.824041 CCGGGGTCATCCTTTGCG 60.824 66.667 0.00 0.00 35.33 4.85
23 24 2.267642 CGGGGTCATCCTTTGCGA 59.732 61.111 0.00 0.00 35.33 5.10
24 25 1.376683 CGGGGTCATCCTTTGCGAA 60.377 57.895 0.00 0.00 35.33 4.70
25 26 1.369091 CGGGGTCATCCTTTGCGAAG 61.369 60.000 6.73 6.73 35.33 3.79
35 36 2.358247 TTGCGAAGGCGGAAGGAC 60.358 61.111 0.00 0.00 43.00 3.85
36 37 4.735132 TGCGAAGGCGGAAGGACG 62.735 66.667 0.00 0.00 44.10 4.79
37 38 4.430765 GCGAAGGCGGAAGGACGA 62.431 66.667 0.00 0.00 38.16 4.20
38 39 2.506438 CGAAGGCGGAAGGACGAC 60.506 66.667 0.00 0.00 43.75 4.34
39 40 2.654877 GAAGGCGGAAGGACGACA 59.345 61.111 0.00 0.00 46.48 4.35
40 41 1.005394 GAAGGCGGAAGGACGACAA 60.005 57.895 0.00 0.00 46.48 3.18
41 42 1.004918 AAGGCGGAAGGACGACAAG 60.005 57.895 0.00 0.00 46.48 3.16
42 43 1.755393 AAGGCGGAAGGACGACAAGT 61.755 55.000 0.00 0.00 46.48 3.16
43 44 2.027625 GGCGGAAGGACGACAAGTG 61.028 63.158 0.00 0.00 42.70 3.16
44 45 1.006571 GCGGAAGGACGACAAGTGA 60.007 57.895 0.00 0.00 35.47 3.41
45 46 0.389948 GCGGAAGGACGACAAGTGAT 60.390 55.000 0.00 0.00 35.47 3.06
46 47 1.350193 CGGAAGGACGACAAGTGATG 58.650 55.000 0.00 0.00 35.47 3.07
47 48 1.067846 CGGAAGGACGACAAGTGATGA 60.068 52.381 0.00 0.00 35.47 2.92
48 49 2.338500 GGAAGGACGACAAGTGATGAC 58.662 52.381 0.00 0.00 0.00 3.06
49 50 2.288825 GGAAGGACGACAAGTGATGACA 60.289 50.000 0.00 0.00 0.00 3.58
50 51 3.589988 GAAGGACGACAAGTGATGACAT 58.410 45.455 0.00 0.00 0.00 3.06
51 52 2.964740 AGGACGACAAGTGATGACATG 58.035 47.619 0.00 0.00 0.00 3.21
52 53 2.002586 GGACGACAAGTGATGACATGG 58.997 52.381 0.00 0.00 0.00 3.66
53 54 2.002586 GACGACAAGTGATGACATGGG 58.997 52.381 0.00 0.00 0.00 4.00
54 55 1.347707 ACGACAAGTGATGACATGGGT 59.652 47.619 0.00 0.00 0.00 4.51
55 56 1.733912 CGACAAGTGATGACATGGGTG 59.266 52.381 0.00 0.00 0.00 4.61
56 57 2.612721 CGACAAGTGATGACATGGGTGA 60.613 50.000 0.00 0.00 0.00 4.02
57 58 3.005554 GACAAGTGATGACATGGGTGAG 58.994 50.000 0.00 0.00 0.00 3.51
58 59 2.639347 ACAAGTGATGACATGGGTGAGA 59.361 45.455 0.00 0.00 0.00 3.27
59 60 3.265221 ACAAGTGATGACATGGGTGAGAT 59.735 43.478 0.00 0.00 0.00 2.75
60 61 3.555527 AGTGATGACATGGGTGAGATG 57.444 47.619 0.00 0.00 0.00 2.90
61 62 2.842496 AGTGATGACATGGGTGAGATGT 59.158 45.455 0.00 0.00 36.73 3.06
62 63 3.118482 AGTGATGACATGGGTGAGATGTC 60.118 47.826 0.00 0.00 46.72 3.06
67 68 3.614092 GACATGGGTGAGATGTCATGTT 58.386 45.455 8.83 0.00 46.73 2.71
68 69 4.769688 GACATGGGTGAGATGTCATGTTA 58.230 43.478 8.83 0.00 46.73 2.41
69 70 5.178096 ACATGGGTGAGATGTCATGTTAA 57.822 39.130 0.00 0.00 45.19 2.01
70 71 5.569355 ACATGGGTGAGATGTCATGTTAAA 58.431 37.500 0.00 0.00 45.19 1.52
71 72 6.009589 ACATGGGTGAGATGTCATGTTAAAA 58.990 36.000 0.00 0.00 45.19 1.52
72 73 6.664816 ACATGGGTGAGATGTCATGTTAAAAT 59.335 34.615 0.00 0.00 45.19 1.82
73 74 7.833682 ACATGGGTGAGATGTCATGTTAAAATA 59.166 33.333 0.00 0.00 45.19 1.40
74 75 7.864108 TGGGTGAGATGTCATGTTAAAATAG 57.136 36.000 0.00 0.00 34.36 1.73
75 76 7.629157 TGGGTGAGATGTCATGTTAAAATAGA 58.371 34.615 0.00 0.00 34.36 1.98
76 77 7.770433 TGGGTGAGATGTCATGTTAAAATAGAG 59.230 37.037 0.00 0.00 34.36 2.43
77 78 7.987458 GGGTGAGATGTCATGTTAAAATAGAGA 59.013 37.037 0.00 0.00 34.36 3.10
78 79 9.383519 GGTGAGATGTCATGTTAAAATAGAGAA 57.616 33.333 0.00 0.00 34.36 2.87
80 81 9.942850 TGAGATGTCATGTTAAAATAGAGAACA 57.057 29.630 0.00 0.00 37.47 3.18
88 89 7.921786 TGTTAAAATAGAGAACATGGACAGG 57.078 36.000 0.00 0.00 0.00 4.00
89 90 7.685481 TGTTAAAATAGAGAACATGGACAGGA 58.315 34.615 0.00 0.00 0.00 3.86
90 91 7.824289 TGTTAAAATAGAGAACATGGACAGGAG 59.176 37.037 0.00 0.00 0.00 3.69
91 92 5.365021 AAATAGAGAACATGGACAGGAGG 57.635 43.478 0.00 0.00 0.00 4.30
92 93 1.577736 AGAGAACATGGACAGGAGGG 58.422 55.000 0.00 0.00 0.00 4.30
93 94 0.543749 GAGAACATGGACAGGAGGGG 59.456 60.000 0.00 0.00 0.00 4.79
94 95 0.916358 AGAACATGGACAGGAGGGGG 60.916 60.000 0.00 0.00 0.00 5.40
109 110 2.493547 GGGGGTACTTGAGCAATGC 58.506 57.895 0.00 0.00 0.00 3.56
110 111 0.034089 GGGGGTACTTGAGCAATGCT 60.034 55.000 7.79 7.79 43.88 3.79
111 112 1.616994 GGGGGTACTTGAGCAATGCTT 60.617 52.381 9.91 0.00 39.88 3.91
112 113 2.356741 GGGGGTACTTGAGCAATGCTTA 60.357 50.000 9.91 1.19 39.88 3.09
113 114 3.555966 GGGGTACTTGAGCAATGCTTAT 58.444 45.455 9.91 0.00 39.88 1.73
114 115 4.445735 GGGGGTACTTGAGCAATGCTTATA 60.446 45.833 9.91 0.00 39.88 0.98
115 116 5.316987 GGGGTACTTGAGCAATGCTTATAT 58.683 41.667 9.91 0.00 39.88 0.86
116 117 5.182001 GGGGTACTTGAGCAATGCTTATATG 59.818 44.000 9.91 4.53 39.88 1.78
117 118 5.182001 GGGTACTTGAGCAATGCTTATATGG 59.818 44.000 9.91 0.00 39.88 2.74
118 119 5.765182 GGTACTTGAGCAATGCTTATATGGT 59.235 40.000 9.91 5.92 39.88 3.55
119 120 6.263168 GGTACTTGAGCAATGCTTATATGGTT 59.737 38.462 9.91 0.00 39.88 3.67
120 121 7.444183 GGTACTTGAGCAATGCTTATATGGTTA 59.556 37.037 9.91 0.00 39.88 2.85
121 122 9.003658 GTACTTGAGCAATGCTTATATGGTTAT 57.996 33.333 9.91 0.00 39.88 1.89
122 123 8.469309 ACTTGAGCAATGCTTATATGGTTATT 57.531 30.769 9.91 0.00 39.88 1.40
123 124 9.573166 ACTTGAGCAATGCTTATATGGTTATTA 57.427 29.630 9.91 0.00 39.88 0.98
128 129 9.125026 AGCAATGCTTATATGGTTATTATAGGC 57.875 33.333 0.00 0.00 33.89 3.93
129 130 8.352942 GCAATGCTTATATGGTTATTATAGGCC 58.647 37.037 0.00 0.00 30.68 5.19
130 131 8.850156 CAATGCTTATATGGTTATTATAGGCCC 58.150 37.037 0.00 0.00 30.68 5.80
131 132 6.588204 TGCTTATATGGTTATTATAGGCCCG 58.412 40.000 0.00 0.00 30.68 6.13
132 133 5.469084 GCTTATATGGTTATTATAGGCCCGC 59.531 44.000 0.00 0.00 0.00 6.13
133 134 2.396590 ATGGTTATTATAGGCCCGCG 57.603 50.000 0.00 0.00 0.00 6.46
134 135 1.050204 TGGTTATTATAGGCCCGCGT 58.950 50.000 4.92 0.00 0.00 6.01
135 136 1.270412 TGGTTATTATAGGCCCGCGTG 60.270 52.381 4.92 0.00 0.00 5.34
136 137 1.001181 GGTTATTATAGGCCCGCGTGA 59.999 52.381 4.92 0.00 0.00 4.35
137 138 2.548493 GGTTATTATAGGCCCGCGTGAA 60.548 50.000 4.92 0.00 0.00 3.18
138 139 2.735134 GTTATTATAGGCCCGCGTGAAG 59.265 50.000 4.92 0.00 0.00 3.02
139 140 0.756903 ATTATAGGCCCGCGTGAAGT 59.243 50.000 4.92 0.00 0.00 3.01
140 141 0.538118 TTATAGGCCCGCGTGAAGTT 59.462 50.000 4.92 0.00 0.00 2.66
141 142 0.103572 TATAGGCCCGCGTGAAGTTC 59.896 55.000 4.92 0.00 0.00 3.01
142 143 1.614241 ATAGGCCCGCGTGAAGTTCT 61.614 55.000 4.92 0.00 0.00 3.01
143 144 1.823169 TAGGCCCGCGTGAAGTTCTT 61.823 55.000 4.92 0.00 0.00 2.52
144 145 2.258726 GGCCCGCGTGAAGTTCTTT 61.259 57.895 4.92 0.00 0.00 2.52
145 146 1.206831 GCCCGCGTGAAGTTCTTTC 59.793 57.895 4.92 0.00 36.29 2.62
146 147 1.866925 CCCGCGTGAAGTTCTTTCC 59.133 57.895 4.92 0.00 34.77 3.13
147 148 0.602905 CCCGCGTGAAGTTCTTTCCT 60.603 55.000 4.92 0.00 34.77 3.36
148 149 1.226746 CCGCGTGAAGTTCTTTCCTT 58.773 50.000 4.92 0.00 34.77 3.36
149 150 1.602377 CCGCGTGAAGTTCTTTCCTTT 59.398 47.619 4.92 0.00 34.77 3.11
150 151 2.349532 CCGCGTGAAGTTCTTTCCTTTC 60.350 50.000 4.92 0.00 34.77 2.62
151 152 2.659291 CGCGTGAAGTTCTTTCCTTTCG 60.659 50.000 4.17 0.00 34.77 3.46
152 153 2.287103 GCGTGAAGTTCTTTCCTTTCGT 59.713 45.455 4.17 0.00 34.77 3.85
153 154 3.242641 GCGTGAAGTTCTTTCCTTTCGTT 60.243 43.478 4.17 0.00 34.77 3.85
154 155 4.271687 CGTGAAGTTCTTTCCTTTCGTTG 58.728 43.478 4.17 0.00 34.77 4.10
155 156 4.035684 GTGAAGTTCTTTCCTTTCGTTGC 58.964 43.478 4.17 0.00 34.77 4.17
156 157 3.692101 TGAAGTTCTTTCCTTTCGTTGCA 59.308 39.130 4.17 0.00 34.77 4.08
157 158 4.156922 TGAAGTTCTTTCCTTTCGTTGCAA 59.843 37.500 4.17 0.00 34.77 4.08
158 159 4.028852 AGTTCTTTCCTTTCGTTGCAAC 57.971 40.909 19.89 19.89 0.00 4.17
167 168 4.659874 CGTTGCAACGCACGGACC 62.660 66.667 35.89 3.35 46.06 4.46
168 169 3.276846 GTTGCAACGCACGGACCT 61.277 61.111 14.90 0.00 38.71 3.85
169 170 2.515057 TTGCAACGCACGGACCTT 60.515 55.556 0.00 0.00 38.71 3.50
170 171 2.115911 TTGCAACGCACGGACCTTT 61.116 52.632 0.00 0.00 38.71 3.11
171 172 1.658686 TTGCAACGCACGGACCTTTT 61.659 50.000 0.00 0.00 38.71 2.27
172 173 1.065109 GCAACGCACGGACCTTTTT 59.935 52.632 0.00 0.00 0.00 1.94
173 174 0.308376 GCAACGCACGGACCTTTTTA 59.692 50.000 0.00 0.00 0.00 1.52
174 175 1.922880 GCAACGCACGGACCTTTTTAC 60.923 52.381 0.00 0.00 0.00 2.01
175 176 1.600485 CAACGCACGGACCTTTTTACT 59.400 47.619 0.00 0.00 0.00 2.24
176 177 2.801679 CAACGCACGGACCTTTTTACTA 59.198 45.455 0.00 0.00 0.00 1.82
177 178 2.680577 ACGCACGGACCTTTTTACTAG 58.319 47.619 0.00 0.00 0.00 2.57
178 179 2.036346 ACGCACGGACCTTTTTACTAGT 59.964 45.455 0.00 0.00 0.00 2.57
179 180 3.255642 ACGCACGGACCTTTTTACTAGTA 59.744 43.478 0.00 0.00 0.00 1.82
180 181 4.082026 ACGCACGGACCTTTTTACTAGTAT 60.082 41.667 2.79 0.00 0.00 2.12
181 182 4.501921 CGCACGGACCTTTTTACTAGTATC 59.498 45.833 2.79 0.00 0.00 2.24
182 183 5.413499 GCACGGACCTTTTTACTAGTATCA 58.587 41.667 2.79 0.00 0.00 2.15
183 184 6.047231 GCACGGACCTTTTTACTAGTATCAT 58.953 40.000 2.79 0.00 0.00 2.45
184 185 7.205297 GCACGGACCTTTTTACTAGTATCATA 58.795 38.462 2.79 0.00 0.00 2.15
185 186 7.707893 GCACGGACCTTTTTACTAGTATCATAA 59.292 37.037 2.79 0.00 0.00 1.90
186 187 9.760077 CACGGACCTTTTTACTAGTATCATAAT 57.240 33.333 2.79 0.00 0.00 1.28
198 199 8.522178 ACTAGTATCATAATTAAGCACGAAGC 57.478 34.615 0.00 0.00 46.19 3.86
209 210 0.110464 GCACGAAGCAGAAGTTGAGC 60.110 55.000 0.00 0.00 44.79 4.26
210 211 1.220529 CACGAAGCAGAAGTTGAGCA 58.779 50.000 0.00 0.00 0.00 4.26
211 212 1.802960 CACGAAGCAGAAGTTGAGCAT 59.197 47.619 0.00 0.00 0.00 3.79
212 213 1.802960 ACGAAGCAGAAGTTGAGCATG 59.197 47.619 0.00 0.00 0.00 4.06
213 214 2.071540 CGAAGCAGAAGTTGAGCATGA 58.928 47.619 0.00 0.00 0.00 3.07
214 215 2.481568 CGAAGCAGAAGTTGAGCATGAA 59.518 45.455 0.00 0.00 0.00 2.57
215 216 3.058708 CGAAGCAGAAGTTGAGCATGAAA 60.059 43.478 0.00 0.00 0.00 2.69
216 217 4.555313 CGAAGCAGAAGTTGAGCATGAAAA 60.555 41.667 0.00 0.00 0.00 2.29
217 218 4.234530 AGCAGAAGTTGAGCATGAAAAC 57.765 40.909 0.00 0.00 0.00 2.43
218 219 3.887716 AGCAGAAGTTGAGCATGAAAACT 59.112 39.130 0.00 0.00 0.00 2.66
219 220 4.023365 AGCAGAAGTTGAGCATGAAAACTC 60.023 41.667 0.00 0.00 0.00 3.01
220 221 4.023365 GCAGAAGTTGAGCATGAAAACTCT 60.023 41.667 0.00 0.40 33.92 3.24
221 222 5.450171 CAGAAGTTGAGCATGAAAACTCTG 58.550 41.667 0.00 8.27 33.92 3.35
222 223 5.008415 CAGAAGTTGAGCATGAAAACTCTGT 59.992 40.000 0.00 0.00 33.92 3.41
223 224 4.825546 AGTTGAGCATGAAAACTCTGTG 57.174 40.909 0.00 0.00 33.92 3.66
224 225 4.454678 AGTTGAGCATGAAAACTCTGTGA 58.545 39.130 0.00 0.00 33.92 3.58
225 226 5.068636 AGTTGAGCATGAAAACTCTGTGAT 58.931 37.500 0.00 0.00 33.92 3.06
226 227 6.233434 AGTTGAGCATGAAAACTCTGTGATA 58.767 36.000 0.00 0.00 33.92 2.15
227 228 6.370994 AGTTGAGCATGAAAACTCTGTGATAG 59.629 38.462 0.00 0.00 33.92 2.08
228 229 5.181009 TGAGCATGAAAACTCTGTGATAGG 58.819 41.667 0.00 0.00 33.92 2.57
229 230 4.521146 AGCATGAAAACTCTGTGATAGGG 58.479 43.478 0.00 0.00 0.00 3.53
230 231 4.225942 AGCATGAAAACTCTGTGATAGGGA 59.774 41.667 0.00 0.00 0.00 4.20
231 232 4.574013 GCATGAAAACTCTGTGATAGGGAG 59.426 45.833 0.00 0.00 0.00 4.30
232 233 5.627735 GCATGAAAACTCTGTGATAGGGAGA 60.628 44.000 0.00 0.00 0.00 3.71
233 234 6.590068 CATGAAAACTCTGTGATAGGGAGAT 58.410 40.000 0.00 0.00 0.00 2.75
234 235 5.982356 TGAAAACTCTGTGATAGGGAGATG 58.018 41.667 0.00 0.00 0.00 2.90
235 236 5.104776 TGAAAACTCTGTGATAGGGAGATGG 60.105 44.000 0.00 0.00 0.00 3.51
236 237 2.969628 ACTCTGTGATAGGGAGATGGG 58.030 52.381 0.00 0.00 0.00 4.00
237 238 2.520120 ACTCTGTGATAGGGAGATGGGA 59.480 50.000 0.00 0.00 0.00 4.37
238 239 2.896685 CTCTGTGATAGGGAGATGGGAC 59.103 54.545 0.00 0.00 0.00 4.46
239 240 1.974236 CTGTGATAGGGAGATGGGACC 59.026 57.143 0.00 0.00 0.00 4.46
240 241 1.353091 GTGATAGGGAGATGGGACCC 58.647 60.000 2.45 2.45 45.88 4.46
243 244 1.912043 GATAGGGAGATGGGACCCATG 59.088 57.143 31.39 0.00 45.26 3.66
244 245 0.768221 TAGGGAGATGGGACCCATGC 60.768 60.000 31.39 20.66 45.26 4.06
245 246 2.517919 GGAGATGGGACCCATGCC 59.482 66.667 31.39 25.20 45.26 4.40
250 251 2.275089 TGGGACCCATGCCAATCG 59.725 61.111 9.95 0.00 44.66 3.34
251 252 2.304831 TGGGACCCATGCCAATCGA 61.305 57.895 9.95 0.00 44.66 3.59
252 253 1.823899 GGGACCCATGCCAATCGAC 60.824 63.158 5.33 0.00 36.03 4.20
253 254 1.823899 GGACCCATGCCAATCGACC 60.824 63.158 0.00 0.00 0.00 4.79
254 255 2.124736 ACCCATGCCAATCGACCG 60.125 61.111 0.00 0.00 0.00 4.79
255 256 2.189257 CCCATGCCAATCGACCGA 59.811 61.111 0.00 0.00 0.00 4.69
256 257 1.451207 CCCATGCCAATCGACCGAA 60.451 57.895 0.00 0.00 0.00 4.30
257 258 1.029408 CCCATGCCAATCGACCGAAA 61.029 55.000 0.00 0.00 0.00 3.46
258 259 1.024271 CCATGCCAATCGACCGAAAT 58.976 50.000 0.00 0.00 0.00 2.17
259 260 1.405105 CCATGCCAATCGACCGAAATT 59.595 47.619 0.00 0.00 0.00 1.82
260 261 2.616376 CCATGCCAATCGACCGAAATTA 59.384 45.455 0.00 0.00 0.00 1.40
261 262 3.303990 CCATGCCAATCGACCGAAATTAG 60.304 47.826 0.00 0.00 0.00 1.73
262 263 1.668751 TGCCAATCGACCGAAATTAGC 59.331 47.619 0.00 0.00 0.00 3.09
263 264 1.332904 GCCAATCGACCGAAATTAGCG 60.333 52.381 0.00 0.00 0.00 4.26
264 265 2.198406 CCAATCGACCGAAATTAGCGA 58.802 47.619 0.00 0.00 35.32 4.93
265 266 2.605818 CCAATCGACCGAAATTAGCGAA 59.394 45.455 0.00 0.00 34.46 4.70
266 267 3.543460 CCAATCGACCGAAATTAGCGAAC 60.543 47.826 0.00 0.00 34.46 3.95
267 268 1.261989 TCGACCGAAATTAGCGAACG 58.738 50.000 2.55 7.36 0.00 3.95
268 269 0.314021 CGACCGAAATTAGCGAACGC 60.314 55.000 11.31 11.31 42.33 4.84
279 280 4.535425 CGAACGCTCGTCTCAGTT 57.465 55.556 0.00 0.00 40.33 3.16
280 281 2.054801 CGAACGCTCGTCTCAGTTG 58.945 57.895 0.00 0.00 40.33 3.16
281 282 0.660595 CGAACGCTCGTCTCAGTTGT 60.661 55.000 0.00 0.00 40.33 3.32
282 283 0.778815 GAACGCTCGTCTCAGTTGTG 59.221 55.000 0.00 0.00 0.00 3.33
283 284 0.102481 AACGCTCGTCTCAGTTGTGT 59.898 50.000 0.00 0.00 0.00 3.72
284 285 0.595053 ACGCTCGTCTCAGTTGTGTG 60.595 55.000 0.00 0.00 0.00 3.82
285 286 0.317854 CGCTCGTCTCAGTTGTGTGA 60.318 55.000 0.00 0.00 0.00 3.58
286 287 1.132588 GCTCGTCTCAGTTGTGTGAC 58.867 55.000 0.00 0.00 41.73 3.67
287 288 1.269309 GCTCGTCTCAGTTGTGTGACT 60.269 52.381 6.16 0.00 42.57 3.41
288 289 2.031069 GCTCGTCTCAGTTGTGTGACTA 60.031 50.000 6.16 0.00 42.57 2.59
289 290 3.556513 CTCGTCTCAGTTGTGTGACTAC 58.443 50.000 6.16 0.00 42.57 2.73
290 291 2.946990 TCGTCTCAGTTGTGTGACTACA 59.053 45.455 6.16 0.00 42.57 2.74
319 320 1.823899 CCAAACGGGCCAGGATAGC 60.824 63.158 8.08 0.00 0.00 2.97
504 505 5.957842 TTTTTGTGTATCCTGATGTGACC 57.042 39.130 0.00 0.00 0.00 4.02
542 543 3.136750 AAAAATGCCCAGTGCGCA 58.863 50.000 5.66 5.66 45.60 6.09
555 556 0.740737 GTGCGCAAAATAGGAGGCAT 59.259 50.000 14.00 0.00 32.53 4.40
565 566 0.902531 TAGGAGGCATATTAGCGGGC 59.097 55.000 0.00 0.00 34.64 6.13
607 608 2.553028 CCTGATTAGCATATGGGCCGTT 60.553 50.000 2.17 0.00 0.00 4.44
667 668 2.673043 CGGCCCGTATAATAATCGTGCT 60.673 50.000 0.00 0.00 0.00 4.40
705 706 0.758734 CCAGGCACGATTAGGATGGA 59.241 55.000 0.00 0.00 0.00 3.41
712 713 0.104120 CGATTAGGATGGACCGTGCA 59.896 55.000 8.06 0.00 44.74 4.57
749 750 2.702592 CCCGTTTGGCCAGTTATAGA 57.297 50.000 5.11 0.00 0.00 1.98
750 751 2.285977 CCCGTTTGGCCAGTTATAGAC 58.714 52.381 5.11 0.00 0.00 2.59
751 752 2.093128 CCCGTTTGGCCAGTTATAGACT 60.093 50.000 5.11 0.00 39.89 3.24
771 889 1.341089 TGCACGACTATCTCCACTCCT 60.341 52.381 0.00 0.00 0.00 3.69
773 891 1.066303 CACGACTATCTCCACTCCTGC 59.934 57.143 0.00 0.00 0.00 4.85
774 892 0.671251 CGACTATCTCCACTCCTGCC 59.329 60.000 0.00 0.00 0.00 4.85
775 893 1.781786 GACTATCTCCACTCCTGCCA 58.218 55.000 0.00 0.00 0.00 4.92
776 894 2.324541 GACTATCTCCACTCCTGCCAT 58.675 52.381 0.00 0.00 0.00 4.40
777 895 2.298729 GACTATCTCCACTCCTGCCATC 59.701 54.545 0.00 0.00 0.00 3.51
778 896 1.271934 CTATCTCCACTCCTGCCATCG 59.728 57.143 0.00 0.00 0.00 3.84
779 897 0.397675 ATCTCCACTCCTGCCATCGA 60.398 55.000 0.00 0.00 0.00 3.59
780 898 0.614697 TCTCCACTCCTGCCATCGAA 60.615 55.000 0.00 0.00 0.00 3.71
783 901 0.877649 CCACTCCTGCCATCGAATCG 60.878 60.000 0.00 0.00 0.00 3.34
823 960 1.135746 CACTCCGTACGAACTCCAGTC 60.136 57.143 18.76 0.00 0.00 3.51
947 1123 0.179000 CGCCACTCCTCCAGCTTTAT 59.821 55.000 0.00 0.00 0.00 1.40
962 1138 0.691078 TTTATCTCTGCGGCTCCCCT 60.691 55.000 0.00 0.00 0.00 4.79
1023 1222 4.082523 CGCATCCACCTCCACCGT 62.083 66.667 0.00 0.00 0.00 4.83
1042 1259 1.984570 CGCCTCTTCTCCTCCACCA 60.985 63.158 0.00 0.00 0.00 4.17
1070 1287 4.452733 GCGTTCCTGGTCTCCCCG 62.453 72.222 0.00 0.00 35.15 5.73
1211 1430 4.394712 CTTCCTTGCCGCCCTCGT 62.395 66.667 0.00 0.00 0.00 4.18
1245 1467 2.509916 GGAGCCTGCAGAGATGGG 59.490 66.667 17.39 0.00 0.00 4.00
1403 1625 2.202676 CTTCGCTCGCCTCCTCAC 60.203 66.667 0.00 0.00 0.00 3.51
1458 1680 2.039084 CACCTTCCTTAAGTGCCTCTGT 59.961 50.000 0.97 0.00 0.00 3.41
1479 1701 1.863491 CGCAAAACGGACGGATGAA 59.137 52.632 0.00 0.00 38.44 2.57
1612 1834 0.749049 CGACCTGCTCCAGATGATGA 59.251 55.000 0.00 0.00 32.44 2.92
1614 1836 0.835941 ACCTGCTCCAGATGATGACC 59.164 55.000 0.00 0.00 32.44 4.02
1616 1838 1.202663 CCTGCTCCAGATGATGACCAG 60.203 57.143 0.00 0.00 32.44 4.00
1618 1840 2.369203 CTGCTCCAGATGATGACCAGAT 59.631 50.000 0.00 0.00 32.44 2.90
1932 2463 5.157940 ACGGATGAAGCTATGCTCATATT 57.842 39.130 0.00 0.00 38.25 1.28
2063 2594 3.028850 CAGATGATTGCCATGGGAGTTT 58.971 45.455 15.13 0.00 35.17 2.66
2145 2676 1.043022 AAAGCCAAGGAGCTGGTTTG 58.957 50.000 0.00 0.00 44.11 2.93
2242 2774 3.825328 AGGAAGGATTATGGATGCACAC 58.175 45.455 0.00 0.00 0.00 3.82
2347 2879 6.237901 AGTCGGCAATATGGATAAAGCATTA 58.762 36.000 0.00 0.00 0.00 1.90
2447 2979 7.539034 TGTAGAAATGGAAGGATCGATGATA 57.461 36.000 0.54 0.00 0.00 2.15
2467 2999 6.918626 TGATAGTTTGACTCTGTTCAGAGAG 58.081 40.000 29.07 14.42 44.50 3.20
2501 3033 7.881775 AAGAGAATTAAACCTGACACTGTTT 57.118 32.000 4.33 4.33 38.22 2.83
2512 3044 6.179756 ACCTGACACTGTTTCATATTGCATA 58.820 36.000 0.00 0.00 0.00 3.14
2557 3089 0.884704 GGAGAACTGTTGCCGCAAGA 60.885 55.000 5.91 4.11 43.02 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.037734 AAAGGATGACCCCGGTGTTC 59.962 55.000 0.00 0.00 36.73 3.18
1 2 0.251165 CAAAGGATGACCCCGGTGTT 60.251 55.000 0.00 0.00 36.73 3.32
2 3 1.378762 CAAAGGATGACCCCGGTGT 59.621 57.895 0.00 0.00 36.73 4.16
3 4 2.046285 GCAAAGGATGACCCCGGTG 61.046 63.158 0.00 0.00 36.73 4.94
4 5 2.355115 GCAAAGGATGACCCCGGT 59.645 61.111 0.00 0.00 36.73 5.28
5 6 2.813226 TTCGCAAAGGATGACCCCGG 62.813 60.000 0.00 0.00 36.73 5.73
6 7 1.369091 CTTCGCAAAGGATGACCCCG 61.369 60.000 0.00 0.00 36.73 5.73
7 8 2.482326 CTTCGCAAAGGATGACCCC 58.518 57.895 0.00 0.00 36.73 4.95
16 17 1.671054 TCCTTCCGCCTTCGCAAAG 60.671 57.895 0.00 0.00 34.03 2.77
17 18 1.964373 GTCCTTCCGCCTTCGCAAA 60.964 57.895 0.00 0.00 34.03 3.68
18 19 2.358247 GTCCTTCCGCCTTCGCAA 60.358 61.111 0.00 0.00 34.03 4.85
19 20 4.735132 CGTCCTTCCGCCTTCGCA 62.735 66.667 0.00 0.00 34.03 5.10
20 21 4.430765 TCGTCCTTCCGCCTTCGC 62.431 66.667 0.00 0.00 0.00 4.70
21 22 2.506438 GTCGTCCTTCCGCCTTCG 60.506 66.667 0.00 0.00 0.00 3.79
22 23 1.005394 TTGTCGTCCTTCCGCCTTC 60.005 57.895 0.00 0.00 0.00 3.46
23 24 1.004918 CTTGTCGTCCTTCCGCCTT 60.005 57.895 0.00 0.00 0.00 4.35
24 25 2.207924 ACTTGTCGTCCTTCCGCCT 61.208 57.895 0.00 0.00 0.00 5.52
25 26 2.027625 CACTTGTCGTCCTTCCGCC 61.028 63.158 0.00 0.00 0.00 6.13
26 27 0.389948 ATCACTTGTCGTCCTTCCGC 60.390 55.000 0.00 0.00 0.00 5.54
27 28 1.067846 TCATCACTTGTCGTCCTTCCG 60.068 52.381 0.00 0.00 0.00 4.30
28 29 2.288825 TGTCATCACTTGTCGTCCTTCC 60.289 50.000 0.00 0.00 0.00 3.46
29 30 3.026630 TGTCATCACTTGTCGTCCTTC 57.973 47.619 0.00 0.00 0.00 3.46
30 31 3.329386 CATGTCATCACTTGTCGTCCTT 58.671 45.455 0.00 0.00 0.00 3.36
31 32 2.354103 CCATGTCATCACTTGTCGTCCT 60.354 50.000 0.00 0.00 0.00 3.85
32 33 2.002586 CCATGTCATCACTTGTCGTCC 58.997 52.381 0.00 0.00 0.00 4.79
33 34 2.002586 CCCATGTCATCACTTGTCGTC 58.997 52.381 0.00 0.00 0.00 4.20
34 35 1.347707 ACCCATGTCATCACTTGTCGT 59.652 47.619 0.00 0.00 0.00 4.34
35 36 1.733912 CACCCATGTCATCACTTGTCG 59.266 52.381 0.00 0.00 0.00 4.35
36 37 3.005554 CTCACCCATGTCATCACTTGTC 58.994 50.000 0.00 0.00 0.00 3.18
37 38 2.639347 TCTCACCCATGTCATCACTTGT 59.361 45.455 0.00 0.00 0.00 3.16
38 39 3.339253 TCTCACCCATGTCATCACTTG 57.661 47.619 0.00 0.00 0.00 3.16
39 40 3.265221 ACATCTCACCCATGTCATCACTT 59.735 43.478 0.00 0.00 27.49 3.16
40 41 2.842496 ACATCTCACCCATGTCATCACT 59.158 45.455 0.00 0.00 27.49 3.41
41 42 3.201290 GACATCTCACCCATGTCATCAC 58.799 50.000 7.74 0.00 46.48 3.06
42 43 3.548745 GACATCTCACCCATGTCATCA 57.451 47.619 7.74 0.00 46.48 3.07
46 47 3.272574 ACATGACATCTCACCCATGTC 57.727 47.619 0.00 5.96 44.17 3.06
48 49 6.513806 TTTTAACATGACATCTCACCCATG 57.486 37.500 0.00 0.00 41.40 3.66
49 50 8.274322 TCTATTTTAACATGACATCTCACCCAT 58.726 33.333 0.00 0.00 0.00 4.00
50 51 7.629157 TCTATTTTAACATGACATCTCACCCA 58.371 34.615 0.00 0.00 0.00 4.51
51 52 7.987458 TCTCTATTTTAACATGACATCTCACCC 59.013 37.037 0.00 0.00 0.00 4.61
52 53 8.948631 TCTCTATTTTAACATGACATCTCACC 57.051 34.615 0.00 0.00 0.00 4.02
54 55 9.942850 TGTTCTCTATTTTAACATGACATCTCA 57.057 29.630 0.00 0.00 0.00 3.27
63 64 8.328758 TCCTGTCCATGTTCTCTATTTTAACAT 58.671 33.333 0.00 0.00 42.91 2.71
64 65 7.685481 TCCTGTCCATGTTCTCTATTTTAACA 58.315 34.615 0.00 0.00 37.51 2.41
65 66 7.281100 CCTCCTGTCCATGTTCTCTATTTTAAC 59.719 40.741 0.00 0.00 0.00 2.01
66 67 7.338710 CCTCCTGTCCATGTTCTCTATTTTAA 58.661 38.462 0.00 0.00 0.00 1.52
67 68 6.126768 CCCTCCTGTCCATGTTCTCTATTTTA 60.127 42.308 0.00 0.00 0.00 1.52
68 69 5.339530 CCCTCCTGTCCATGTTCTCTATTTT 60.340 44.000 0.00 0.00 0.00 1.82
69 70 4.164988 CCCTCCTGTCCATGTTCTCTATTT 59.835 45.833 0.00 0.00 0.00 1.40
70 71 3.713764 CCCTCCTGTCCATGTTCTCTATT 59.286 47.826 0.00 0.00 0.00 1.73
71 72 3.312890 CCCTCCTGTCCATGTTCTCTAT 58.687 50.000 0.00 0.00 0.00 1.98
72 73 2.626950 CCCCTCCTGTCCATGTTCTCTA 60.627 54.545 0.00 0.00 0.00 2.43
73 74 1.577736 CCCTCCTGTCCATGTTCTCT 58.422 55.000 0.00 0.00 0.00 3.10
74 75 0.543749 CCCCTCCTGTCCATGTTCTC 59.456 60.000 0.00 0.00 0.00 2.87
75 76 0.916358 CCCCCTCCTGTCCATGTTCT 60.916 60.000 0.00 0.00 0.00 3.01
76 77 1.609783 CCCCCTCCTGTCCATGTTC 59.390 63.158 0.00 0.00 0.00 3.18
77 78 3.841078 CCCCCTCCTGTCCATGTT 58.159 61.111 0.00 0.00 0.00 2.71
91 92 0.034089 AGCATTGCTCAAGTACCCCC 60.034 55.000 5.03 0.00 30.62 5.40
92 93 1.839424 AAGCATTGCTCAAGTACCCC 58.161 50.000 12.39 0.00 38.25 4.95
93 94 5.182001 CCATATAAGCATTGCTCAAGTACCC 59.818 44.000 12.39 0.00 38.25 3.69
94 95 5.765182 ACCATATAAGCATTGCTCAAGTACC 59.235 40.000 12.39 0.00 38.25 3.34
95 96 6.867662 ACCATATAAGCATTGCTCAAGTAC 57.132 37.500 12.39 0.00 38.25 2.73
96 97 9.573166 AATAACCATATAAGCATTGCTCAAGTA 57.427 29.630 12.39 0.64 38.25 2.24
97 98 8.469309 AATAACCATATAAGCATTGCTCAAGT 57.531 30.769 12.39 0.00 38.25 3.16
102 103 9.125026 GCCTATAATAACCATATAAGCATTGCT 57.875 33.333 5.03 5.03 42.56 3.91
103 104 8.352942 GGCCTATAATAACCATATAAGCATTGC 58.647 37.037 0.00 0.00 28.55 3.56
104 105 8.850156 GGGCCTATAATAACCATATAAGCATTG 58.150 37.037 0.84 0.00 28.55 2.82
105 106 7.719633 CGGGCCTATAATAACCATATAAGCATT 59.280 37.037 0.84 0.00 28.55 3.56
106 107 7.224297 CGGGCCTATAATAACCATATAAGCAT 58.776 38.462 0.84 0.00 28.55 3.79
107 108 6.588204 CGGGCCTATAATAACCATATAAGCA 58.412 40.000 0.84 0.00 28.55 3.91
108 109 5.469084 GCGGGCCTATAATAACCATATAAGC 59.531 44.000 0.84 0.00 0.00 3.09
109 110 5.694910 CGCGGGCCTATAATAACCATATAAG 59.305 44.000 0.84 0.00 0.00 1.73
110 111 5.129155 ACGCGGGCCTATAATAACCATATAA 59.871 40.000 12.47 0.00 0.00 0.98
111 112 4.650588 ACGCGGGCCTATAATAACCATATA 59.349 41.667 12.47 0.00 0.00 0.86
112 113 3.453353 ACGCGGGCCTATAATAACCATAT 59.547 43.478 12.47 0.00 0.00 1.78
113 114 2.833338 ACGCGGGCCTATAATAACCATA 59.167 45.455 12.47 0.00 0.00 2.74
114 115 1.626825 ACGCGGGCCTATAATAACCAT 59.373 47.619 12.47 0.00 0.00 3.55
115 116 1.050204 ACGCGGGCCTATAATAACCA 58.950 50.000 12.47 0.00 0.00 3.67
116 117 1.001181 TCACGCGGGCCTATAATAACC 59.999 52.381 12.47 0.00 0.00 2.85
117 118 2.443887 TCACGCGGGCCTATAATAAC 57.556 50.000 12.47 0.00 0.00 1.89
118 119 2.366266 ACTTCACGCGGGCCTATAATAA 59.634 45.455 12.47 0.00 0.00 1.40
119 120 1.965643 ACTTCACGCGGGCCTATAATA 59.034 47.619 12.47 0.00 0.00 0.98
120 121 0.756903 ACTTCACGCGGGCCTATAAT 59.243 50.000 12.47 0.00 0.00 1.28
121 122 0.538118 AACTTCACGCGGGCCTATAA 59.462 50.000 12.47 0.00 0.00 0.98
122 123 0.103572 GAACTTCACGCGGGCCTATA 59.896 55.000 12.47 0.00 0.00 1.31
123 124 1.153429 GAACTTCACGCGGGCCTAT 60.153 57.895 12.47 0.00 0.00 2.57
124 125 1.823169 AAGAACTTCACGCGGGCCTA 61.823 55.000 12.47 0.00 0.00 3.93
125 126 2.676163 AAAGAACTTCACGCGGGCCT 62.676 55.000 12.47 0.00 0.00 5.19
126 127 2.183858 GAAAGAACTTCACGCGGGCC 62.184 60.000 12.47 0.00 33.86 5.80
127 128 1.206831 GAAAGAACTTCACGCGGGC 59.793 57.895 12.47 0.00 33.86 6.13
128 129 0.602905 AGGAAAGAACTTCACGCGGG 60.603 55.000 12.47 6.51 35.55 6.13
129 130 1.226746 AAGGAAAGAACTTCACGCGG 58.773 50.000 12.47 0.00 35.55 6.46
130 131 2.659291 CGAAAGGAAAGAACTTCACGCG 60.659 50.000 3.53 3.53 35.55 6.01
131 132 2.287103 ACGAAAGGAAAGAACTTCACGC 59.713 45.455 0.00 0.00 35.55 5.34
132 133 4.271687 CAACGAAAGGAAAGAACTTCACG 58.728 43.478 0.00 0.00 35.55 4.35
133 134 4.035684 GCAACGAAAGGAAAGAACTTCAC 58.964 43.478 0.00 0.00 35.55 3.18
134 135 3.692101 TGCAACGAAAGGAAAGAACTTCA 59.308 39.130 0.00 0.00 35.55 3.02
135 136 4.287238 TGCAACGAAAGGAAAGAACTTC 57.713 40.909 0.00 0.00 0.00 3.01
136 137 4.421058 GTTGCAACGAAAGGAAAGAACTT 58.579 39.130 14.90 0.00 0.00 2.66
137 138 4.028852 GTTGCAACGAAAGGAAAGAACT 57.971 40.909 14.90 0.00 0.00 3.01
151 152 2.331019 AAAGGTCCGTGCGTTGCAAC 62.331 55.000 19.89 19.89 41.47 4.17
152 153 1.658686 AAAAGGTCCGTGCGTTGCAA 61.659 50.000 0.00 0.00 41.47 4.08
153 154 1.658686 AAAAAGGTCCGTGCGTTGCA 61.659 50.000 0.00 0.00 35.60 4.08
154 155 0.308376 TAAAAAGGTCCGTGCGTTGC 59.692 50.000 0.00 0.00 0.00 4.17
155 156 1.600485 AGTAAAAAGGTCCGTGCGTTG 59.400 47.619 0.00 0.00 0.00 4.10
156 157 1.957668 AGTAAAAAGGTCCGTGCGTT 58.042 45.000 0.00 0.00 0.00 4.84
157 158 2.036346 ACTAGTAAAAAGGTCCGTGCGT 59.964 45.455 0.00 0.00 0.00 5.24
158 159 2.680577 ACTAGTAAAAAGGTCCGTGCG 58.319 47.619 0.00 0.00 0.00 5.34
159 160 5.413499 TGATACTAGTAAAAAGGTCCGTGC 58.587 41.667 6.70 0.00 0.00 5.34
160 161 9.760077 ATTATGATACTAGTAAAAAGGTCCGTG 57.240 33.333 6.70 0.00 0.00 4.94
172 173 9.622004 GCTTCGTGCTTAATTATGATACTAGTA 57.378 33.333 4.77 4.77 38.95 1.82
173 174 8.141909 TGCTTCGTGCTTAATTATGATACTAGT 58.858 33.333 0.00 0.00 43.37 2.57
174 175 8.520835 TGCTTCGTGCTTAATTATGATACTAG 57.479 34.615 2.66 0.00 43.37 2.57
175 176 8.357402 TCTGCTTCGTGCTTAATTATGATACTA 58.643 33.333 2.66 0.00 43.37 1.82
176 177 7.210174 TCTGCTTCGTGCTTAATTATGATACT 58.790 34.615 2.66 0.00 43.37 2.12
177 178 7.408132 TCTGCTTCGTGCTTAATTATGATAC 57.592 36.000 2.66 0.76 43.37 2.24
178 179 7.710907 ACTTCTGCTTCGTGCTTAATTATGATA 59.289 33.333 2.66 0.00 43.37 2.15
179 180 6.540189 ACTTCTGCTTCGTGCTTAATTATGAT 59.460 34.615 2.66 0.00 43.37 2.45
180 181 5.874810 ACTTCTGCTTCGTGCTTAATTATGA 59.125 36.000 2.66 0.00 43.37 2.15
181 182 6.111768 ACTTCTGCTTCGTGCTTAATTATG 57.888 37.500 5.00 0.00 43.37 1.90
182 183 6.371548 TCAACTTCTGCTTCGTGCTTAATTAT 59.628 34.615 5.00 0.00 43.37 1.28
183 184 5.699001 TCAACTTCTGCTTCGTGCTTAATTA 59.301 36.000 5.00 0.00 43.37 1.40
184 185 4.515191 TCAACTTCTGCTTCGTGCTTAATT 59.485 37.500 5.00 0.00 43.37 1.40
185 186 4.065088 TCAACTTCTGCTTCGTGCTTAAT 58.935 39.130 5.00 0.00 43.37 1.40
186 187 3.462982 TCAACTTCTGCTTCGTGCTTAA 58.537 40.909 5.00 0.00 43.37 1.85
187 188 3.059884 CTCAACTTCTGCTTCGTGCTTA 58.940 45.455 5.00 0.00 43.37 3.09
188 189 1.869767 CTCAACTTCTGCTTCGTGCTT 59.130 47.619 5.00 0.00 43.37 3.91
189 190 1.506493 CTCAACTTCTGCTTCGTGCT 58.494 50.000 5.00 0.00 43.37 4.40
190 191 0.110464 GCTCAACTTCTGCTTCGTGC 60.110 55.000 0.00 0.00 43.25 5.34
191 192 1.220529 TGCTCAACTTCTGCTTCGTG 58.779 50.000 0.00 0.00 0.00 4.35
192 193 1.802960 CATGCTCAACTTCTGCTTCGT 59.197 47.619 0.00 0.00 0.00 3.85
193 194 2.071540 TCATGCTCAACTTCTGCTTCG 58.928 47.619 0.00 0.00 0.00 3.79
194 195 4.494350 TTTCATGCTCAACTTCTGCTTC 57.506 40.909 0.00 0.00 0.00 3.86
195 196 4.340381 AGTTTTCATGCTCAACTTCTGCTT 59.660 37.500 0.00 0.00 0.00 3.91
196 197 3.887716 AGTTTTCATGCTCAACTTCTGCT 59.112 39.130 0.00 0.00 0.00 4.24
197 198 4.023365 AGAGTTTTCATGCTCAACTTCTGC 60.023 41.667 5.73 0.00 34.39 4.26
198 199 5.008415 ACAGAGTTTTCATGCTCAACTTCTG 59.992 40.000 17.39 17.39 34.85 3.02
199 200 5.008415 CACAGAGTTTTCATGCTCAACTTCT 59.992 40.000 5.73 3.26 34.39 2.85
200 201 5.008019 TCACAGAGTTTTCATGCTCAACTTC 59.992 40.000 5.73 1.60 34.39 3.01
201 202 4.883585 TCACAGAGTTTTCATGCTCAACTT 59.116 37.500 5.73 0.00 34.39 2.66
202 203 4.454678 TCACAGAGTTTTCATGCTCAACT 58.545 39.130 4.27 4.27 34.39 3.16
203 204 4.818534 TCACAGAGTTTTCATGCTCAAC 57.181 40.909 1.63 0.00 34.39 3.18
204 205 5.645067 CCTATCACAGAGTTTTCATGCTCAA 59.355 40.000 1.63 0.00 34.39 3.02
205 206 5.181009 CCTATCACAGAGTTTTCATGCTCA 58.819 41.667 1.63 0.00 34.39 4.26
206 207 4.574013 CCCTATCACAGAGTTTTCATGCTC 59.426 45.833 0.00 0.00 0.00 4.26
207 208 4.225942 TCCCTATCACAGAGTTTTCATGCT 59.774 41.667 0.00 0.00 0.00 3.79
208 209 4.517285 TCCCTATCACAGAGTTTTCATGC 58.483 43.478 0.00 0.00 0.00 4.06
209 210 5.982356 TCTCCCTATCACAGAGTTTTCATG 58.018 41.667 0.00 0.00 0.00 3.07
210 211 6.409005 CCATCTCCCTATCACAGAGTTTTCAT 60.409 42.308 0.00 0.00 0.00 2.57
211 212 5.104776 CCATCTCCCTATCACAGAGTTTTCA 60.105 44.000 0.00 0.00 0.00 2.69
212 213 5.363939 CCATCTCCCTATCACAGAGTTTTC 58.636 45.833 0.00 0.00 0.00 2.29
213 214 4.164988 CCCATCTCCCTATCACAGAGTTTT 59.835 45.833 0.00 0.00 0.00 2.43
214 215 3.713764 CCCATCTCCCTATCACAGAGTTT 59.286 47.826 0.00 0.00 0.00 2.66
215 216 3.051803 TCCCATCTCCCTATCACAGAGTT 60.052 47.826 0.00 0.00 0.00 3.01
216 217 2.520120 TCCCATCTCCCTATCACAGAGT 59.480 50.000 0.00 0.00 0.00 3.24
217 218 2.896685 GTCCCATCTCCCTATCACAGAG 59.103 54.545 0.00 0.00 0.00 3.35
218 219 2.426414 GGTCCCATCTCCCTATCACAGA 60.426 54.545 0.00 0.00 0.00 3.41
219 220 1.974236 GGTCCCATCTCCCTATCACAG 59.026 57.143 0.00 0.00 0.00 3.66
220 221 1.414538 GGGTCCCATCTCCCTATCACA 60.415 57.143 1.78 0.00 40.48 3.58
221 222 1.353091 GGGTCCCATCTCCCTATCAC 58.647 60.000 1.78 0.00 40.48 3.06
222 223 0.948816 TGGGTCCCATCTCCCTATCA 59.051 55.000 6.47 0.00 43.74 2.15
223 224 1.912043 CATGGGTCCCATCTCCCTATC 59.088 57.143 21.49 0.00 43.15 2.08
224 225 2.050754 CATGGGTCCCATCTCCCTAT 57.949 55.000 21.49 0.00 43.15 2.57
225 226 0.768221 GCATGGGTCCCATCTCCCTA 60.768 60.000 21.49 0.00 43.15 3.53
226 227 2.081161 GCATGGGTCCCATCTCCCT 61.081 63.158 21.49 0.00 43.15 4.20
227 228 2.517919 GCATGGGTCCCATCTCCC 59.482 66.667 21.49 6.06 43.15 4.30
228 229 1.936767 TTGGCATGGGTCCCATCTCC 61.937 60.000 21.49 22.69 43.15 3.71
229 230 0.186873 ATTGGCATGGGTCCCATCTC 59.813 55.000 21.49 15.53 43.15 2.75
230 231 0.186873 GATTGGCATGGGTCCCATCT 59.813 55.000 21.49 0.00 43.15 2.90
231 232 1.174712 CGATTGGCATGGGTCCCATC 61.175 60.000 21.49 14.87 43.15 3.51
232 233 1.152694 CGATTGGCATGGGTCCCAT 60.153 57.895 18.56 18.56 46.37 4.00
233 234 2.275089 CGATTGGCATGGGTCCCA 59.725 61.111 14.64 14.64 38.19 4.37
234 235 1.823899 GTCGATTGGCATGGGTCCC 60.824 63.158 0.00 0.00 0.00 4.46
235 236 1.823899 GGTCGATTGGCATGGGTCC 60.824 63.158 0.00 0.00 0.00 4.46
236 237 2.180204 CGGTCGATTGGCATGGGTC 61.180 63.158 0.00 0.00 0.00 4.46
237 238 2.124736 CGGTCGATTGGCATGGGT 60.125 61.111 0.00 0.00 0.00 4.51
238 239 1.029408 TTTCGGTCGATTGGCATGGG 61.029 55.000 0.00 0.00 0.00 4.00
239 240 1.024271 ATTTCGGTCGATTGGCATGG 58.976 50.000 0.00 0.00 0.00 3.66
240 241 2.849880 AATTTCGGTCGATTGGCATG 57.150 45.000 0.00 0.00 0.00 4.06
241 242 2.290641 GCTAATTTCGGTCGATTGGCAT 59.709 45.455 9.17 0.00 38.92 4.40
242 243 1.668751 GCTAATTTCGGTCGATTGGCA 59.331 47.619 9.17 0.00 38.92 4.92
243 244 1.332904 CGCTAATTTCGGTCGATTGGC 60.333 52.381 0.00 5.41 36.68 4.52
244 245 2.198406 TCGCTAATTTCGGTCGATTGG 58.802 47.619 0.00 0.00 0.00 3.16
245 246 3.594312 GTTCGCTAATTTCGGTCGATTG 58.406 45.455 0.00 0.00 0.00 2.67
246 247 2.280708 CGTTCGCTAATTTCGGTCGATT 59.719 45.455 0.00 0.00 0.00 3.34
247 248 1.850441 CGTTCGCTAATTTCGGTCGAT 59.150 47.619 0.00 0.00 0.00 3.59
248 249 1.261989 CGTTCGCTAATTTCGGTCGA 58.738 50.000 0.00 0.00 0.00 4.20
249 250 0.314021 GCGTTCGCTAATTTCGGTCG 60.314 55.000 9.99 0.00 0.00 4.79
250 251 0.997196 AGCGTTCGCTAATTTCGGTC 59.003 50.000 18.04 0.00 40.00 4.79
251 252 0.997196 GAGCGTTCGCTAATTTCGGT 59.003 50.000 19.41 0.00 42.08 4.69
252 253 0.044161 CGAGCGTTCGCTAATTTCGG 60.044 55.000 19.41 1.44 42.08 4.30
253 254 3.382964 CGAGCGTTCGCTAATTTCG 57.617 52.632 19.41 14.22 42.08 3.46
263 264 0.778815 CACAACTGAGACGAGCGTTC 59.221 55.000 0.00 0.00 0.00 3.95
264 265 0.102481 ACACAACTGAGACGAGCGTT 59.898 50.000 0.00 0.00 0.00 4.84
265 266 0.595053 CACACAACTGAGACGAGCGT 60.595 55.000 0.00 0.00 0.00 5.07
266 267 0.317854 TCACACAACTGAGACGAGCG 60.318 55.000 0.00 0.00 0.00 5.03
267 268 1.132588 GTCACACAACTGAGACGAGC 58.867 55.000 0.00 0.00 29.75 5.03
268 269 2.783828 AGTCACACAACTGAGACGAG 57.216 50.000 0.00 0.00 41.48 4.18
269 270 2.946990 TGTAGTCACACAACTGAGACGA 59.053 45.455 0.00 0.00 41.48 4.20
270 271 3.349488 TGTAGTCACACAACTGAGACG 57.651 47.619 0.00 0.00 41.48 4.18
281 282 3.028850 GGCCACCTATAGTGTAGTCACA 58.971 50.000 0.00 0.00 45.74 3.58
282 283 3.028850 TGGCCACCTATAGTGTAGTCAC 58.971 50.000 0.00 0.00 45.74 3.67
283 284 3.391799 TGGCCACCTATAGTGTAGTCA 57.608 47.619 0.00 0.00 45.74 3.41
284 285 4.439968 GTTTGGCCACCTATAGTGTAGTC 58.560 47.826 3.88 0.00 45.74 2.59
285 286 3.118884 CGTTTGGCCACCTATAGTGTAGT 60.119 47.826 3.88 0.00 45.74 2.73
286 287 3.454375 CGTTTGGCCACCTATAGTGTAG 58.546 50.000 3.88 0.00 45.74 2.74
287 288 2.168936 CCGTTTGGCCACCTATAGTGTA 59.831 50.000 3.88 0.00 45.74 2.90
288 289 1.065709 CCGTTTGGCCACCTATAGTGT 60.066 52.381 3.88 0.00 45.74 3.55
289 290 1.663695 CCGTTTGGCCACCTATAGTG 58.336 55.000 3.88 0.00 46.83 2.74
290 291 0.544697 CCCGTTTGGCCACCTATAGT 59.455 55.000 3.88 0.00 0.00 2.12
291 292 3.396951 CCCGTTTGGCCACCTATAG 57.603 57.895 3.88 0.00 0.00 1.31
374 375 2.440247 GCCTGGCCCGTTTAGCAT 60.440 61.111 7.66 0.00 0.00 3.79
487 488 3.270877 GTTGGGTCACATCAGGATACAC 58.729 50.000 0.00 0.00 41.41 2.90
542 543 4.589908 CCCGCTAATATGCCTCCTATTTT 58.410 43.478 0.00 0.00 0.00 1.82
555 556 1.663739 CACGCTAGGCCCGCTAATA 59.336 57.895 12.27 0.00 0.00 0.98
588 589 2.552155 GGAACGGCCCATATGCTAATCA 60.552 50.000 0.00 0.00 0.00 2.57
743 744 5.238868 GTGGAGATAGTCGTGCAGTCTATAA 59.761 44.000 0.00 0.00 32.67 0.98
748 749 1.746220 AGTGGAGATAGTCGTGCAGTC 59.254 52.381 0.00 0.00 0.00 3.51
749 750 1.746220 GAGTGGAGATAGTCGTGCAGT 59.254 52.381 0.00 0.00 0.00 4.40
750 751 1.066303 GGAGTGGAGATAGTCGTGCAG 59.934 57.143 0.00 0.00 0.00 4.41
751 752 1.103803 GGAGTGGAGATAGTCGTGCA 58.896 55.000 0.00 0.00 0.00 4.57
753 754 1.066303 GCAGGAGTGGAGATAGTCGTG 59.934 57.143 0.00 0.00 38.36 4.35
755 756 0.671251 GGCAGGAGTGGAGATAGTCG 59.329 60.000 0.00 0.00 0.00 4.18
757 758 2.324541 GATGGCAGGAGTGGAGATAGT 58.675 52.381 0.00 0.00 0.00 2.12
759 760 1.133482 TCGATGGCAGGAGTGGAGATA 60.133 52.381 0.00 0.00 0.00 1.98
760 761 0.397675 TCGATGGCAGGAGTGGAGAT 60.398 55.000 0.00 0.00 0.00 2.75
771 889 2.394930 TTTCCTTCGATTCGATGGCA 57.605 45.000 27.46 18.92 46.29 4.92
794 912 1.511768 GTACGGAGTGGAGACAGCC 59.488 63.158 0.00 0.00 45.73 4.85
798 916 1.130186 GAGTTCGTACGGAGTGGAGAC 59.870 57.143 16.52 0.00 45.73 3.36
923 1099 2.363018 TGGAGGAGTGGCGGAGAG 60.363 66.667 0.00 0.00 0.00 3.20
924 1100 2.363018 CTGGAGGAGTGGCGGAGA 60.363 66.667 0.00 0.00 0.00 3.71
978 1154 2.667199 GTGGTGGTGGTGCGGTAC 60.667 66.667 0.00 0.00 0.00 3.34
1023 1222 1.682684 GGTGGAGGAGAAGAGGCGA 60.683 63.158 0.00 0.00 0.00 5.54
1380 1602 4.803426 AGGCGAGCGAAGAAGGCG 62.803 66.667 0.00 0.00 35.00 5.52
1458 1680 0.791422 CATCCGTCCGTTTTGCGTAA 59.209 50.000 0.00 0.00 39.32 3.18
1479 1701 1.502163 GAAGCAGCACGTTCACAGCT 61.502 55.000 0.00 0.00 39.63 4.24
1612 1834 4.042062 TGACTTGTCATTTCTCCATCTGGT 59.958 41.667 0.00 0.00 36.34 4.00
1614 1836 4.634883 CCTGACTTGTCATTTCTCCATCTG 59.365 45.833 3.79 0.00 0.00 2.90
1616 1838 3.944015 CCCTGACTTGTCATTTCTCCATC 59.056 47.826 3.79 0.00 0.00 3.51
1618 1840 2.711009 ACCCTGACTTGTCATTTCTCCA 59.289 45.455 3.79 0.00 0.00 3.86
1654 2181 5.120830 AGTCATTAACGAGCTGCAAGTAAAG 59.879 40.000 1.02 0.00 35.30 1.85
1932 2463 2.229302 CCTTTTTCCCGCATTTCCGTAA 59.771 45.455 0.00 0.00 0.00 3.18
2063 2594 4.751098 GTGATAAACAGTTGTGTCCGGTTA 59.249 41.667 0.00 0.00 35.08 2.85
2145 2676 7.830739 AGGAATACCTTTGTTCATCATTTCAC 58.169 34.615 0.00 0.00 45.36 3.18
2242 2774 9.698309 ATGTCTATAACCAAGTCAAAGATATCG 57.302 33.333 0.00 0.00 0.00 2.92
2347 2879 7.667219 ACTGATTCCATGACATCAAGTACTTTT 59.333 33.333 5.07 0.00 0.00 2.27
2467 2999 4.515432 GTTTAATTCTCTTACGCGGCATC 58.485 43.478 12.47 0.00 0.00 3.91
2507 3039 6.977502 CGAAACAACCCATTCATTATTATGCA 59.022 34.615 0.00 0.00 0.00 3.96
2512 3044 5.047377 AGCACGAAACAACCCATTCATTATT 60.047 36.000 0.00 0.00 0.00 1.40
2516 3048 2.030007 CAGCACGAAACAACCCATTCAT 60.030 45.455 0.00 0.00 0.00 2.57
2519 3051 0.673437 CCAGCACGAAACAACCCATT 59.327 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.