Multiple sequence alignment - TraesCS2D01G556600

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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 TraesCS2D01G556600 chr2D 100.000 3806 0 0 1 3806 630065295 630069100 0.000000e+00 7029.0
1 TraesCS2D01G556600 chr2D 90.649 2620 188 28 272 2863 629736386 629733796 0.000000e+00 3428.0
2 TraesCS2D01G556600 chr2D 90.080 1865 129 28 791 2622 630033514 630035355 0.000000e+00 2368.0
3 TraesCS2D01G556600 chr2D 92.433 1348 89 8 1526 2863 629975379 629976723 0.000000e+00 1912.0
4 TraesCS2D01G556600 chr2D 87.915 1506 171 10 1280 2781 630621351 630622849 0.000000e+00 1762.0
5 TraesCS2D01G556600 chr2D 87.881 1510 167 12 1280 2781 630098600 630097099 0.000000e+00 1760.0
6 TraesCS2D01G556600 chr2D 92.217 938 61 10 2864 3797 87969754 87968825 0.000000e+00 1317.0
7 TraesCS2D01G556600 chr2D 85.513 994 89 26 1891 2863 630638065 630637106 0.000000e+00 987.0
8 TraesCS2D01G556600 chr2D 87.428 692 43 21 758 1442 629974727 629975381 0.000000e+00 756.0
9 TraesCS2D01G556600 chr2D 95.911 269 11 0 1 269 467011279 467011547 1.620000e-118 436.0
10 TraesCS2D01G556600 chr2D 92.478 226 15 2 1013 1238 630098897 630098674 4.740000e-84 322.0
11 TraesCS2D01G556600 chr2D 92.377 223 16 1 1013 1235 630621053 630621274 2.210000e-82 316.0
12 TraesCS2D01G556600 chr2D 89.431 246 21 3 2618 2863 630044200 630044440 4.780000e-79 305.0
13 TraesCS2D01G556600 chr2B 93.285 1936 94 11 955 2858 773004296 773006227 0.000000e+00 2822.0
14 TraesCS2D01G556600 chr2B 87.541 1533 179 10 1280 2806 773723120 773724646 0.000000e+00 1762.0
15 TraesCS2D01G556600 chr2B 86.423 383 34 5 383 755 773003756 773004130 1.650000e-108 403.0
16 TraesCS2D01G556600 chr2B 82.276 457 38 15 3324 3744 790115799 790116248 4.680000e-94 355.0
17 TraesCS2D01G556600 chr2B 93.506 231 13 2 1013 1242 773722822 773723051 3.640000e-90 342.0
18 TraesCS2D01G556600 chr2B 82.143 364 33 14 3327 3665 670340225 670339869 2.240000e-72 283.0
19 TraesCS2D01G556600 chr2B 78.366 453 59 24 2855 3274 741230255 741229809 1.360000e-64 257.0
20 TraesCS2D01G556600 chr2B 95.918 49 2 0 874 922 773004247 773004295 3.150000e-11 80.5
21 TraesCS2D01G556600 chr2A 88.138 2411 183 58 426 2810 760776979 760774646 0.000000e+00 2772.0
22 TraesCS2D01G556600 chr2A 88.113 1489 163 12 1325 2806 760762036 760763517 0.000000e+00 1757.0
23 TraesCS2D01G556600 chr2A 95.694 209 9 0 1013 1221 760761696 760761904 1.690000e-88 337.0
24 TraesCS2D01G556600 chr2A 81.422 436 49 16 3324 3735 587740 588167 1.020000e-85 327.0
25 TraesCS2D01G556600 chr2A 80.653 429 56 14 2867 3274 30593802 30593380 1.330000e-79 307.0
26 TraesCS2D01G556600 chr6D 93.816 954 52 4 2855 3806 305365335 305366283 0.000000e+00 1428.0
27 TraesCS2D01G556600 chr6D 92.202 949 60 12 2855 3797 258035249 258034309 0.000000e+00 1330.0
28 TraesCS2D01G556600 chr6D 95.911 269 11 0 1 269 334484896 334485164 1.620000e-118 436.0
29 TraesCS2D01G556600 chr6D 95.911 269 8 1 1 269 433623698 433623963 2.100000e-117 433.0
30 TraesCS2D01G556600 chr6D 95.539 269 10 1 1 269 18574764 18574498 2.720000e-116 429.0
31 TraesCS2D01G556600 chr6A 81.446 1466 234 29 1336 2776 15628586 15627134 0.000000e+00 1166.0
32 TraesCS2D01G556600 chr6A 83.716 436 39 19 3324 3735 555091389 555091816 2.150000e-102 383.0
33 TraesCS2D01G556600 chr1D 92.038 741 51 7 3061 3797 383328459 383329195 0.000000e+00 1035.0
34 TraesCS2D01G556600 chr1D 95.911 269 11 0 1 269 448084677 448084945 1.620000e-118 436.0
35 TraesCS2D01G556600 chr1D 95.572 271 10 1 1 269 101660334 101660064 2.100000e-117 433.0
36 TraesCS2D01G556600 chr1D 95.880 267 11 0 1 267 168471958 168471692 2.100000e-117 433.0
37 TraesCS2D01G556600 chr1D 95.539 269 12 0 1 269 168478801 168478533 7.550000e-117 431.0
38 TraesCS2D01G556600 chr1D 89.140 221 18 5 2865 3083 383328234 383328450 1.740000e-68 270.0
39 TraesCS2D01G556600 chr5D 82.851 1003 69 23 2864 3797 36576756 36575788 0.000000e+00 804.0
40 TraesCS2D01G556600 chr5D 95.522 268 12 0 1 268 204364872 204365139 2.720000e-116 429.0
41 TraesCS2D01G556600 chr3B 92.387 486 33 4 3316 3797 43488080 43487595 0.000000e+00 689.0
42 TraesCS2D01G556600 chr5B 87.896 347 39 3 3454 3797 447451371 447451717 4.580000e-109 405.0
43 TraesCS2D01G556600 chr5B 90.604 149 11 3 3319 3464 447404593 447404741 1.080000e-45 195.0
44 TraesCS2D01G556600 chr4A 85.533 394 29 13 3324 3696 713746963 713747349 1.660000e-103 387.0
45 TraesCS2D01G556600 chr4A 87.037 54 4 3 3694 3744 713747359 713747412 1.480000e-04 58.4
46 TraesCS2D01G556600 chr3A 81.881 436 47 16 3324 3735 17900812 17901239 4.710000e-89 339.0
47 TraesCS2D01G556600 chr7D 81.282 390 40 20 2864 3237 560756397 560756769 6.220000e-73 285.0
48 TraesCS2D01G556600 chr6B 80.964 394 45 9 2867 3243 470913141 470912761 6.220000e-73 285.0
49 TraesCS2D01G556600 chrUn 80.506 395 43 14 2863 3237 235771617 235771997 4.840000e-69 272.0
50 TraesCS2D01G556600 chr7A 80.299 401 45 13 2855 3237 635104318 635104702 4.840000e-69 272.0
51 TraesCS2D01G556600 chr7A 78.311 438 65 13 2862 3274 204219608 204219176 4.880000e-64 255.0
52 TraesCS2D01G556600 chr7A 87.879 99 6 2 3228 3321 635159901 635159998 1.120000e-20 111.0
53 TraesCS2D01G556600 chr3D 78.182 385 43 25 2864 3229 305600029 305600391 1.390000e-49 207.0


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 TraesCS2D01G556600 chr2D 630065295 630069100 3805 False 7029.000000 7029 100.000000 1 3806 1 chr2D.!!$F4 3805
1 TraesCS2D01G556600 chr2D 629733796 629736386 2590 True 3428.000000 3428 90.649000 272 2863 1 chr2D.!!$R2 2591
2 TraesCS2D01G556600 chr2D 630033514 630035355 1841 False 2368.000000 2368 90.080000 791 2622 1 chr2D.!!$F2 1831
3 TraesCS2D01G556600 chr2D 629974727 629976723 1996 False 1334.000000 1912 89.930500 758 2863 2 chr2D.!!$F5 2105
4 TraesCS2D01G556600 chr2D 87968825 87969754 929 True 1317.000000 1317 92.217000 2864 3797 1 chr2D.!!$R1 933
5 TraesCS2D01G556600 chr2D 630097099 630098897 1798 True 1041.000000 1760 90.179500 1013 2781 2 chr2D.!!$R4 1768
6 TraesCS2D01G556600 chr2D 630621053 630622849 1796 False 1039.000000 1762 90.146000 1013 2781 2 chr2D.!!$F6 1768
7 TraesCS2D01G556600 chr2D 630637106 630638065 959 True 987.000000 987 85.513000 1891 2863 1 chr2D.!!$R3 972
8 TraesCS2D01G556600 chr2B 773003756 773006227 2471 False 1101.833333 2822 91.875333 383 2858 3 chr2B.!!$F2 2475
9 TraesCS2D01G556600 chr2B 773722822 773724646 1824 False 1052.000000 1762 90.523500 1013 2806 2 chr2B.!!$F3 1793
10 TraesCS2D01G556600 chr2A 760774646 760776979 2333 True 2772.000000 2772 88.138000 426 2810 1 chr2A.!!$R2 2384
11 TraesCS2D01G556600 chr2A 760761696 760763517 1821 False 1047.000000 1757 91.903500 1013 2806 2 chr2A.!!$F2 1793
12 TraesCS2D01G556600 chr6D 305365335 305366283 948 False 1428.000000 1428 93.816000 2855 3806 1 chr6D.!!$F1 951
13 TraesCS2D01G556600 chr6D 258034309 258035249 940 True 1330.000000 1330 92.202000 2855 3797 1 chr6D.!!$R2 942
14 TraesCS2D01G556600 chr6A 15627134 15628586 1452 True 1166.000000 1166 81.446000 1336 2776 1 chr6A.!!$R1 1440
15 TraesCS2D01G556600 chr1D 383328234 383329195 961 False 652.500000 1035 90.589000 2865 3797 2 chr1D.!!$F2 932
16 TraesCS2D01G556600 chr5D 36575788 36576756 968 True 804.000000 804 82.851000 2864 3797 1 chr5D.!!$R1 933

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
745 763 0.037590 TAAGAACATGCCCGCCTGTT 59.962 50.000 9.67 9.67 37.46 3.16 F
760 803 1.272212 CCTGTTAAAAACATGCCCGCT 59.728 47.619 0.00 0.00 41.26 5.52 F
2049 2293 1.367471 GATCATGACGGCCGGATCA 59.633 57.895 31.76 25.03 36.89 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 2144 0.394938 AATGGCGGCGTATACATCCA 59.605 50.000 9.37 5.59 0.00 3.41 R
2377 2635 1.368579 CCGTGTAGAACCACCCGTT 59.631 57.895 0.00 0.00 37.41 4.44 R
3068 3365 0.035820 CGAAATGGGAGGAACGGGAA 60.036 55.000 0.00 0.00 0.00 3.97 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
19 20 2.037385 ACTTCTCCTCTTCCCTTGCT 57.963 50.000 0.00 0.00 0.00 3.91
20 21 1.627834 ACTTCTCCTCTTCCCTTGCTG 59.372 52.381 0.00 0.00 0.00 4.41
21 22 0.987294 TTCTCCTCTTCCCTTGCTGG 59.013 55.000 0.00 0.00 0.00 4.85
22 23 0.117140 TCTCCTCTTCCCTTGCTGGA 59.883 55.000 0.00 0.00 38.35 3.86
23 24 1.211456 CTCCTCTTCCCTTGCTGGAT 58.789 55.000 0.00 0.00 38.35 3.41
24 25 1.140652 CTCCTCTTCCCTTGCTGGATC 59.859 57.143 0.00 0.00 38.35 3.36
25 26 0.914644 CCTCTTCCCTTGCTGGATCA 59.085 55.000 0.00 0.00 38.35 2.92
26 27 1.283029 CCTCTTCCCTTGCTGGATCAA 59.717 52.381 0.00 0.00 38.35 2.57
27 28 2.641305 CTCTTCCCTTGCTGGATCAAG 58.359 52.381 0.00 0.00 42.23 3.02
28 29 2.238144 CTCTTCCCTTGCTGGATCAAGA 59.762 50.000 0.00 0.00 44.61 3.02
29 30 2.644299 TCTTCCCTTGCTGGATCAAGAA 59.356 45.455 0.00 0.00 44.61 2.52
30 31 2.795231 TCCCTTGCTGGATCAAGAAG 57.205 50.000 0.00 2.15 44.61 2.85
31 32 1.283029 TCCCTTGCTGGATCAAGAAGG 59.717 52.381 16.02 16.02 44.61 3.46
32 33 1.283029 CCCTTGCTGGATCAAGAAGGA 59.717 52.381 21.16 3.00 44.61 3.36
33 34 2.641305 CCTTGCTGGATCAAGAAGGAG 58.359 52.381 17.24 0.00 44.61 3.69
34 35 2.641305 CTTGCTGGATCAAGAAGGAGG 58.359 52.381 0.00 0.00 44.61 4.30
35 36 1.956869 TGCTGGATCAAGAAGGAGGA 58.043 50.000 0.00 0.00 0.00 3.71
36 37 1.836166 TGCTGGATCAAGAAGGAGGAG 59.164 52.381 0.00 0.00 0.00 3.69
37 38 2.114616 GCTGGATCAAGAAGGAGGAGA 58.885 52.381 0.00 0.00 0.00 3.71
38 39 2.158971 GCTGGATCAAGAAGGAGGAGAC 60.159 54.545 0.00 0.00 0.00 3.36
39 40 2.100584 CTGGATCAAGAAGGAGGAGACG 59.899 54.545 0.00 0.00 0.00 4.18
40 41 2.104170 GGATCAAGAAGGAGGAGACGT 58.896 52.381 0.00 0.00 0.00 4.34
41 42 2.100087 GGATCAAGAAGGAGGAGACGTC 59.900 54.545 7.70 7.70 0.00 4.34
42 43 1.546961 TCAAGAAGGAGGAGACGTCC 58.453 55.000 13.01 3.55 44.33 4.79
43 44 0.533032 CAAGAAGGAGGAGACGTCCC 59.467 60.000 13.01 13.26 45.26 4.46
44 45 0.615261 AAGAAGGAGGAGACGTCCCC 60.615 60.000 13.01 10.64 45.26 4.81
45 46 2.362632 AAGGAGGAGACGTCCCCG 60.363 66.667 13.01 0.00 45.26 5.73
46 47 3.959329 AAGGAGGAGACGTCCCCGG 62.959 68.421 13.01 0.00 45.26 5.73
52 53 4.371417 AGACGTCCCCGGGCTGTA 62.371 66.667 17.73 0.00 38.78 2.74
53 54 4.139234 GACGTCCCCGGGCTGTAC 62.139 72.222 17.73 9.24 38.78 2.90
56 57 4.446413 GTCCCCGGGCTGTACGTG 62.446 72.222 17.73 0.00 0.00 4.49
58 59 4.752879 CCCCGGGCTGTACGTGTG 62.753 72.222 17.73 0.00 0.00 3.82
59 60 3.998672 CCCGGGCTGTACGTGTGT 61.999 66.667 8.08 0.00 0.00 3.72
60 61 2.029964 CCGGGCTGTACGTGTGTT 59.970 61.111 0.00 0.00 0.00 3.32
61 62 2.314647 CCGGGCTGTACGTGTGTTG 61.315 63.158 0.00 0.00 0.00 3.33
62 63 1.300311 CGGGCTGTACGTGTGTTGA 60.300 57.895 0.00 0.00 0.00 3.18
63 64 0.876777 CGGGCTGTACGTGTGTTGAA 60.877 55.000 0.00 0.00 0.00 2.69
64 65 0.584876 GGGCTGTACGTGTGTTGAAC 59.415 55.000 0.00 0.00 0.00 3.18
65 66 0.231279 GGCTGTACGTGTGTTGAACG 59.769 55.000 0.00 0.00 46.32 3.95
66 67 0.382636 GCTGTACGTGTGTTGAACGC 60.383 55.000 1.20 1.20 44.80 4.84
71 72 2.935955 GTGTGTTGAACGCGGAGG 59.064 61.111 12.47 0.00 0.00 4.30
72 73 2.970324 TGTGTTGAACGCGGAGGC 60.970 61.111 12.47 0.00 0.00 4.70
91 92 4.570663 CCCTCCGTTCGGCGCTAG 62.571 72.222 7.64 1.50 39.71 3.42
92 93 3.515286 CCTCCGTTCGGCGCTAGA 61.515 66.667 7.64 4.43 39.71 2.43
93 94 2.722487 CTCCGTTCGGCGCTAGAT 59.278 61.111 7.64 0.00 39.71 1.98
94 95 1.370657 CTCCGTTCGGCGCTAGATC 60.371 63.158 7.64 5.92 39.71 2.75
95 96 2.726180 CCGTTCGGCGCTAGATCG 60.726 66.667 21.14 21.14 39.71 3.69
96 97 2.726180 CGTTCGGCGCTAGATCGG 60.726 66.667 20.67 9.02 0.00 4.18
97 98 2.719979 GTTCGGCGCTAGATCGGA 59.280 61.111 7.64 0.00 0.00 4.55
98 99 1.286260 GTTCGGCGCTAGATCGGAT 59.714 57.895 7.64 0.00 0.00 4.18
99 100 0.729816 GTTCGGCGCTAGATCGGATC 60.730 60.000 7.64 10.02 0.00 3.36
100 101 0.889638 TTCGGCGCTAGATCGGATCT 60.890 55.000 22.96 22.96 43.33 2.75
101 102 0.889638 TCGGCGCTAGATCGGATCTT 60.890 55.000 24.36 9.91 40.76 2.40
102 103 0.455295 CGGCGCTAGATCGGATCTTC 60.455 60.000 24.36 15.48 40.76 2.87
103 104 0.109039 GGCGCTAGATCGGATCTTCC 60.109 60.000 24.36 16.11 40.76 3.46
126 127 3.151216 GATTTAAATCGCCGCGAGTAC 57.849 47.619 21.61 5.29 39.91 2.73
127 128 0.915904 TTTAAATCGCCGCGAGTACG 59.084 50.000 21.61 6.02 39.91 3.67
128 129 0.098552 TTAAATCGCCGCGAGTACGA 59.901 50.000 21.61 12.00 39.91 3.43
129 130 0.589729 TAAATCGCCGCGAGTACGAC 60.590 55.000 21.61 0.00 39.91 4.34
130 131 2.262471 AAATCGCCGCGAGTACGACT 62.262 55.000 21.61 0.00 39.91 4.18
131 132 2.262471 AATCGCCGCGAGTACGACTT 62.262 55.000 21.61 5.67 39.91 3.01
132 133 2.643764 ATCGCCGCGAGTACGACTTC 62.644 60.000 21.61 0.00 39.91 3.01
133 134 2.177531 GCCGCGAGTACGACTTCA 59.822 61.111 8.23 0.00 42.66 3.02
134 135 1.226603 GCCGCGAGTACGACTTCAT 60.227 57.895 8.23 0.00 42.66 2.57
135 136 1.201098 GCCGCGAGTACGACTTCATC 61.201 60.000 8.23 0.00 42.66 2.92
136 137 0.098200 CCGCGAGTACGACTTCATCA 59.902 55.000 8.23 0.00 42.66 3.07
137 138 1.466866 CCGCGAGTACGACTTCATCAA 60.467 52.381 8.23 0.00 42.66 2.57
138 139 1.578023 CGCGAGTACGACTTCATCAAC 59.422 52.381 0.00 0.00 42.66 3.18
139 140 1.918609 GCGAGTACGACTTCATCAACC 59.081 52.381 0.00 0.00 42.66 3.77
140 141 2.174764 CGAGTACGACTTCATCAACCG 58.825 52.381 0.00 0.00 42.66 4.44
141 142 1.918609 GAGTACGACTTCATCAACCGC 59.081 52.381 0.00 0.00 0.00 5.68
142 143 0.638746 GTACGACTTCATCAACCGCG 59.361 55.000 0.00 0.00 0.00 6.46
143 144 0.241749 TACGACTTCATCAACCGCGT 59.758 50.000 4.92 0.00 0.00 6.01
144 145 0.599204 ACGACTTCATCAACCGCGTT 60.599 50.000 4.92 0.00 0.00 4.84
145 146 0.093026 CGACTTCATCAACCGCGTTC 59.907 55.000 4.92 0.00 0.00 3.95
146 147 1.429463 GACTTCATCAACCGCGTTCT 58.571 50.000 4.92 0.00 0.00 3.01
147 148 2.602878 GACTTCATCAACCGCGTTCTA 58.397 47.619 4.92 0.00 0.00 2.10
148 149 2.599082 GACTTCATCAACCGCGTTCTAG 59.401 50.000 4.92 0.00 0.00 2.43
149 150 2.029290 ACTTCATCAACCGCGTTCTAGT 60.029 45.455 4.92 0.00 0.00 2.57
150 151 3.192001 ACTTCATCAACCGCGTTCTAGTA 59.808 43.478 4.92 0.00 0.00 1.82
151 152 3.853831 TCATCAACCGCGTTCTAGTAA 57.146 42.857 4.92 0.00 0.00 2.24
152 153 3.504863 TCATCAACCGCGTTCTAGTAAC 58.495 45.455 4.92 0.00 0.00 2.50
153 154 1.967762 TCAACCGCGTTCTAGTAACG 58.032 50.000 17.59 17.59 45.56 3.18
160 161 0.912528 CGTTCTAGTAACGCTTCCGC 59.087 55.000 12.33 0.00 36.82 5.54
161 162 1.467035 CGTTCTAGTAACGCTTCCGCT 60.467 52.381 12.33 0.00 36.82 5.52
162 163 2.603953 GTTCTAGTAACGCTTCCGCTT 58.396 47.619 0.00 0.00 38.22 4.68
163 164 3.728864 CGTTCTAGTAACGCTTCCGCTTA 60.729 47.826 12.33 0.00 36.82 3.09
164 165 3.687572 TCTAGTAACGCTTCCGCTTAG 57.312 47.619 0.00 0.00 38.22 2.18
165 166 2.117910 CTAGTAACGCTTCCGCTTAGC 58.882 52.381 0.00 0.00 38.22 3.09
178 179 2.317530 GCTTAGCGATCTTCAAGGGT 57.682 50.000 0.00 0.00 0.00 4.34
179 180 3.454371 GCTTAGCGATCTTCAAGGGTA 57.546 47.619 0.00 0.00 0.00 3.69
180 181 3.996480 GCTTAGCGATCTTCAAGGGTAT 58.004 45.455 0.00 0.00 0.00 2.73
181 182 3.743396 GCTTAGCGATCTTCAAGGGTATG 59.257 47.826 0.00 0.00 0.00 2.39
182 183 4.501571 GCTTAGCGATCTTCAAGGGTATGA 60.502 45.833 0.00 0.00 0.00 2.15
183 184 5.601662 CTTAGCGATCTTCAAGGGTATGAA 58.398 41.667 0.00 0.00 37.70 2.57
191 192 4.574674 TTCAAGGGTATGAAGATGCACT 57.425 40.909 0.00 0.00 34.50 4.40
192 193 4.142609 TCAAGGGTATGAAGATGCACTC 57.857 45.455 0.00 0.00 25.83 3.51
193 194 3.118261 TCAAGGGTATGAAGATGCACTCC 60.118 47.826 0.00 0.00 25.83 3.85
194 195 1.771255 AGGGTATGAAGATGCACTCCC 59.229 52.381 0.00 0.00 35.54 4.30
195 196 1.771255 GGGTATGAAGATGCACTCCCT 59.229 52.381 0.00 0.00 33.77 4.20
196 197 2.224402 GGGTATGAAGATGCACTCCCTC 60.224 54.545 0.00 0.00 33.77 4.30
197 198 2.703007 GGTATGAAGATGCACTCCCTCT 59.297 50.000 0.00 0.00 0.00 3.69
198 199 3.898123 GGTATGAAGATGCACTCCCTCTA 59.102 47.826 0.00 0.00 0.00 2.43
199 200 4.530161 GGTATGAAGATGCACTCCCTCTAT 59.470 45.833 0.00 0.00 0.00 1.98
200 201 4.620589 ATGAAGATGCACTCCCTCTATG 57.379 45.455 0.00 0.00 0.00 2.23
201 202 3.378512 TGAAGATGCACTCCCTCTATGT 58.621 45.455 0.00 0.00 0.00 2.29
202 203 3.386078 TGAAGATGCACTCCCTCTATGTC 59.614 47.826 0.00 0.00 0.00 3.06
203 204 3.326946 AGATGCACTCCCTCTATGTCT 57.673 47.619 0.00 0.00 0.00 3.41
204 205 3.230134 AGATGCACTCCCTCTATGTCTC 58.770 50.000 0.00 0.00 0.00 3.36
205 206 2.836636 TGCACTCCCTCTATGTCTCT 57.163 50.000 0.00 0.00 0.00 3.10
206 207 2.660572 TGCACTCCCTCTATGTCTCTC 58.339 52.381 0.00 0.00 0.00 3.20
207 208 1.606668 GCACTCCCTCTATGTCTCTCG 59.393 57.143 0.00 0.00 0.00 4.04
208 209 2.925724 CACTCCCTCTATGTCTCTCGT 58.074 52.381 0.00 0.00 0.00 4.18
209 210 3.283751 CACTCCCTCTATGTCTCTCGTT 58.716 50.000 0.00 0.00 0.00 3.85
210 211 3.066064 CACTCCCTCTATGTCTCTCGTTG 59.934 52.174 0.00 0.00 0.00 4.10
211 212 2.025155 TCCCTCTATGTCTCTCGTTGC 58.975 52.381 0.00 0.00 0.00 4.17
212 213 2.028130 CCCTCTATGTCTCTCGTTGCT 58.972 52.381 0.00 0.00 0.00 3.91
213 214 3.118000 TCCCTCTATGTCTCTCGTTGCTA 60.118 47.826 0.00 0.00 0.00 3.49
214 215 3.252215 CCCTCTATGTCTCTCGTTGCTAG 59.748 52.174 0.00 0.00 0.00 3.42
215 216 3.880490 CCTCTATGTCTCTCGTTGCTAGT 59.120 47.826 0.00 0.00 0.00 2.57
216 217 5.057819 CCTCTATGTCTCTCGTTGCTAGTA 58.942 45.833 0.00 0.00 0.00 1.82
217 218 5.703592 CCTCTATGTCTCTCGTTGCTAGTAT 59.296 44.000 0.00 0.00 0.00 2.12
218 219 6.874664 CCTCTATGTCTCTCGTTGCTAGTATA 59.125 42.308 0.00 0.00 0.00 1.47
219 220 7.551262 CCTCTATGTCTCTCGTTGCTAGTATAT 59.449 40.741 0.00 0.00 0.00 0.86
220 221 8.481974 TCTATGTCTCTCGTTGCTAGTATATC 57.518 38.462 0.00 0.00 0.00 1.63
221 222 5.943706 TGTCTCTCGTTGCTAGTATATCC 57.056 43.478 0.00 0.00 0.00 2.59
222 223 5.622180 TGTCTCTCGTTGCTAGTATATCCT 58.378 41.667 0.00 0.00 0.00 3.24
223 224 6.766429 TGTCTCTCGTTGCTAGTATATCCTA 58.234 40.000 0.00 0.00 0.00 2.94
224 225 6.874664 TGTCTCTCGTTGCTAGTATATCCTAG 59.125 42.308 0.00 0.00 37.96 3.02
225 226 7.098477 GTCTCTCGTTGCTAGTATATCCTAGA 58.902 42.308 6.53 0.00 37.24 2.43
226 227 7.767198 GTCTCTCGTTGCTAGTATATCCTAGAT 59.233 40.741 6.53 0.00 37.24 1.98
227 228 8.322828 TCTCTCGTTGCTAGTATATCCTAGATT 58.677 37.037 6.53 0.00 37.24 2.40
228 229 8.270080 TCTCGTTGCTAGTATATCCTAGATTG 57.730 38.462 6.53 0.00 37.24 2.67
229 230 8.101419 TCTCGTTGCTAGTATATCCTAGATTGA 58.899 37.037 6.53 0.00 37.24 2.57
230 231 8.809468 TCGTTGCTAGTATATCCTAGATTGAT 57.191 34.615 6.53 0.00 37.24 2.57
231 232 8.894731 TCGTTGCTAGTATATCCTAGATTGATC 58.105 37.037 6.53 0.00 37.24 2.92
232 233 8.898761 CGTTGCTAGTATATCCTAGATTGATCT 58.101 37.037 6.53 0.00 37.24 2.75
235 236 9.194972 TGCTAGTATATCCTAGATTGATCTTGG 57.805 37.037 13.24 13.24 46.71 3.61
236 237 9.196139 GCTAGTATATCCTAGATTGATCTTGGT 57.804 37.037 17.17 9.92 45.88 3.67
239 240 9.030452 AGTATATCCTAGATTGATCTTGGTGAC 57.970 37.037 17.17 12.13 45.88 3.67
240 241 7.862274 ATATCCTAGATTGATCTTGGTGACA 57.138 36.000 17.17 3.27 45.88 3.58
241 242 5.344743 TCCTAGATTGATCTTGGTGACAC 57.655 43.478 17.17 0.00 45.88 3.67
242 243 4.115516 CCTAGATTGATCTTGGTGACACG 58.884 47.826 11.74 0.00 42.44 4.49
243 244 3.685139 AGATTGATCTTGGTGACACGT 57.315 42.857 0.00 0.00 42.67 4.49
244 245 4.801330 AGATTGATCTTGGTGACACGTA 57.199 40.909 0.00 0.00 42.67 3.57
245 246 4.748892 AGATTGATCTTGGTGACACGTAG 58.251 43.478 0.00 0.00 42.67 3.51
246 247 4.462834 AGATTGATCTTGGTGACACGTAGA 59.537 41.667 9.78 9.78 42.67 2.59
247 248 4.594123 TTGATCTTGGTGACACGTAGAA 57.406 40.909 11.01 0.00 42.67 2.10
248 249 4.594123 TGATCTTGGTGACACGTAGAAA 57.406 40.909 11.01 2.76 42.67 2.52
249 250 4.951254 TGATCTTGGTGACACGTAGAAAA 58.049 39.130 11.01 2.49 42.67 2.29
250 251 5.361427 TGATCTTGGTGACACGTAGAAAAA 58.639 37.500 11.01 0.60 42.67 1.94
251 252 5.995282 TGATCTTGGTGACACGTAGAAAAAT 59.005 36.000 11.01 0.00 42.67 1.82
252 253 6.485313 TGATCTTGGTGACACGTAGAAAAATT 59.515 34.615 11.01 0.00 42.67 1.82
253 254 6.687081 TCTTGGTGACACGTAGAAAAATTT 57.313 33.333 0.00 0.00 42.67 1.82
254 255 7.090953 TCTTGGTGACACGTAGAAAAATTTT 57.909 32.000 0.00 0.00 42.67 1.82
255 256 6.970043 TCTTGGTGACACGTAGAAAAATTTTG 59.030 34.615 3.73 0.00 42.67 2.44
256 257 6.438259 TGGTGACACGTAGAAAAATTTTGA 57.562 33.333 3.73 0.00 33.40 2.69
257 258 6.853720 TGGTGACACGTAGAAAAATTTTGAA 58.146 32.000 3.73 0.00 33.40 2.69
258 259 7.484975 TGGTGACACGTAGAAAAATTTTGAAT 58.515 30.769 3.73 0.00 33.40 2.57
259 260 7.976734 TGGTGACACGTAGAAAAATTTTGAATT 59.023 29.630 3.73 0.00 33.40 2.17
260 261 9.453325 GGTGACACGTAGAAAAATTTTGAATTA 57.547 29.630 3.73 0.00 0.00 1.40
270 271 8.372521 AGAAAAATTTTGAATTATTGCTACGCG 58.627 29.630 3.53 3.53 0.00 6.01
275 276 6.650239 TTTGAATTATTGCTACGCGTTCTA 57.350 33.333 20.78 7.47 0.00 2.10
314 315 6.041979 CCAAGATGAAAGGAAGAAGGGAAAAA 59.958 38.462 0.00 0.00 0.00 1.94
334 335 3.512033 AGTAACTGGCGCAAAACAAAA 57.488 38.095 10.83 0.00 0.00 2.44
344 345 4.450757 GGCGCAAAACAAAATTTCAGGTAT 59.549 37.500 10.83 0.00 0.00 2.73
364 365 6.211584 AGGTATCTGAGAAGTAGCAAAACTGA 59.788 38.462 0.00 0.00 0.00 3.41
408 409 8.379457 ACAAACTAAGTTGTGTTTAGAGGATC 57.621 34.615 8.00 0.00 40.22 3.36
428 429 6.327887 AGGATCTAGGATAAGAAAACAGGACC 59.672 42.308 0.00 0.00 0.00 4.46
431 432 1.664151 GGATAAGAAAACAGGACCGCG 59.336 52.381 0.00 0.00 0.00 6.46
465 466 2.485479 CCGATCCCGATCCAACTGAAAT 60.485 50.000 0.00 0.00 38.22 2.17
509 512 1.890876 TGCAAGTTGCCTGAACGTAT 58.109 45.000 24.59 0.00 44.23 3.06
541 544 6.058833 TCTTCTAGGAGTAGTAGACATGCAG 58.941 44.000 0.00 0.00 30.06 4.41
545 548 2.690497 GGAGTAGTAGACATGCAGAGCA 59.310 50.000 0.00 0.00 44.86 4.26
554 564 0.108804 CATGCAGAGCAAAGGCAAGG 60.109 55.000 0.00 0.00 43.62 3.61
570 580 2.513753 CAAGGCCAACCAACTGACATA 58.486 47.619 5.01 0.00 39.06 2.29
586 596 4.523083 TGACATATGACCTTTAGCAACCC 58.477 43.478 10.38 0.00 0.00 4.11
610 628 2.618241 TGTCACACTCCATTGCAGAAAC 59.382 45.455 0.00 0.00 0.00 2.78
628 646 1.299850 CGTGTCGTGCTGTTGGAGA 60.300 57.895 0.00 0.00 0.00 3.71
629 647 0.874175 CGTGTCGTGCTGTTGGAGAA 60.874 55.000 0.00 0.00 0.00 2.87
630 648 0.861837 GTGTCGTGCTGTTGGAGAAG 59.138 55.000 0.00 0.00 0.00 2.85
644 662 2.965147 TGGAGAAGGCCTTTGAAAAAGG 59.035 45.455 21.54 13.37 40.39 3.11
645 663 2.300152 GGAGAAGGCCTTTGAAAAAGGG 59.700 50.000 21.54 0.73 37.88 3.95
659 677 6.115448 TGAAAAAGGGAAGGAAAAACAACA 57.885 33.333 0.00 0.00 0.00 3.33
709 727 1.715862 TAGCAGCACGGACGCTAGAG 61.716 60.000 0.00 0.00 41.38 2.43
726 744 7.324178 ACGCTAGAGAACAAGAATAAGACAAT 58.676 34.615 0.00 0.00 0.00 2.71
745 763 0.037590 TAAGAACATGCCCGCCTGTT 59.962 50.000 9.67 9.67 37.46 3.16
755 778 1.708822 CCCGCCTGTTAAAAACATGC 58.291 50.000 9.22 9.22 45.70 4.06
756 779 1.671556 CCCGCCTGTTAAAAACATGCC 60.672 52.381 12.42 0.00 46.20 4.40
757 780 1.671556 CCGCCTGTTAAAAACATGCCC 60.672 52.381 12.42 0.00 46.20 5.36
760 803 1.272212 CCTGTTAAAAACATGCCCGCT 59.728 47.619 0.00 0.00 41.26 5.52
912 970 4.358841 CCGTCCCATGCCACCCAA 62.359 66.667 0.00 0.00 0.00 4.12
1124 1193 2.687902 CCCCTCCCTCGTCTACCA 59.312 66.667 0.00 0.00 0.00 3.25
1255 1354 3.056107 CCCTCGTCCTTGTGATTCTGTAA 60.056 47.826 0.00 0.00 0.00 2.41
1256 1355 4.562757 CCCTCGTCCTTGTGATTCTGTAAA 60.563 45.833 0.00 0.00 0.00 2.01
1487 1700 3.730761 CGTCTTCGTCGACCCGGT 61.731 66.667 10.58 0.00 0.00 5.28
1597 1825 2.041265 ATCAGTTCCCTCCGGCCT 59.959 61.111 0.00 0.00 0.00 5.19
1611 1845 4.162690 GCCTCGGCCACGGATCTT 62.163 66.667 11.36 0.00 41.39 2.40
1871 2105 4.856801 CTGGGGAATGGCCGTCGG 62.857 72.222 6.99 6.99 37.63 4.79
1990 2231 1.375013 CTTGCAATGCTGGCCAACC 60.375 57.895 7.01 0.66 0.00 3.77
2049 2293 1.367471 GATCATGACGGCCGGATCA 59.633 57.895 31.76 25.03 36.89 2.92
2787 3045 2.283966 ACTCGCAGGGGTAGCAGT 60.284 61.111 0.00 0.00 0.00 4.40
2788 3046 1.000019 ACTCGCAGGGGTAGCAGTA 60.000 57.895 0.00 0.00 0.00 2.74
2789 3047 1.038130 ACTCGCAGGGGTAGCAGTAG 61.038 60.000 0.00 0.00 0.00 2.57
2844 3109 3.639561 GGGCAAAGGGTTTGTCTCTAAAA 59.360 43.478 4.16 0.00 44.41 1.52
2885 3150 3.243602 CCCAAAACCTAAAAAGTGGTCGG 60.244 47.826 0.00 0.00 35.17 4.79
3029 3294 3.060000 TGGCGTCGTGGTCGAGAT 61.060 61.111 0.00 0.00 46.96 2.75
3032 3297 3.047718 GCGTCGTGGTCGAGATCCA 62.048 63.158 0.00 0.00 46.96 3.41
3039 3304 1.760613 GTGGTCGAGATCCATTGGGTA 59.239 52.381 2.09 0.00 37.30 3.69
3068 3365 2.835431 CTCGTCTCGCCTCCCCAT 60.835 66.667 0.00 0.00 0.00 4.00
3089 3386 0.462047 CCCGTTCCTCCCATTTCGAG 60.462 60.000 0.00 0.00 0.00 4.04
3092 3389 1.067142 CGTTCCTCCCATTTCGAGACA 60.067 52.381 0.00 0.00 0.00 3.41
3097 3394 0.976641 TCCCATTTCGAGACAGCTGT 59.023 50.000 21.88 21.88 0.00 4.40
3377 3687 3.708220 GACGCGGCAGAGGAGGAAG 62.708 68.421 7.34 0.00 0.00 3.46
3424 3734 3.134127 AGAGGGGCAAAATCGCGC 61.134 61.111 0.00 0.00 43.66 6.86
3486 3796 2.030628 CCGCGTTTAGGTTGTCCAAATT 60.031 45.455 4.92 0.00 35.89 1.82
3489 3799 4.614993 CGCGTTTAGGTTGTCCAAATTGAT 60.615 41.667 0.00 0.00 35.89 2.57
3519 3838 4.097361 GGCAGAGGGGGAACGACC 62.097 72.222 0.00 0.00 38.08 4.79
3643 3962 3.242518 GAAGCACTCGTTAATTTTGGGC 58.757 45.455 0.00 0.00 0.00 5.36
3724 4073 2.716217 AGCCTTGGTGCTGTAGATTTC 58.284 47.619 0.00 0.00 40.90 2.17
3728 4077 4.074970 CCTTGGTGCTGTAGATTTCTGTT 58.925 43.478 0.00 0.00 0.00 3.16
3802 4153 1.144057 GTGCTGTAGATGTCGGGGG 59.856 63.158 0.00 0.00 0.00 5.40
3804 4155 0.907704 TGCTGTAGATGTCGGGGGTT 60.908 55.000 0.00 0.00 0.00 4.11
3805 4156 0.462047 GCTGTAGATGTCGGGGGTTG 60.462 60.000 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.627834 CAGCAAGGGAAGAGGAGAAGT 59.372 52.381 0.00 0.00 0.00 3.01
4 5 1.140652 GATCCAGCAAGGGAAGAGGAG 59.859 57.143 0.00 0.00 41.12 3.69
5 6 1.207791 GATCCAGCAAGGGAAGAGGA 58.792 55.000 0.00 0.00 41.12 3.71
6 7 0.914644 TGATCCAGCAAGGGAAGAGG 59.085 55.000 0.00 0.00 41.12 3.69
7 8 2.238144 TCTTGATCCAGCAAGGGAAGAG 59.762 50.000 4.79 0.00 44.14 2.85
8 9 2.269023 TCTTGATCCAGCAAGGGAAGA 58.731 47.619 4.79 0.00 44.14 2.87
9 10 2.795231 TCTTGATCCAGCAAGGGAAG 57.205 50.000 4.79 0.00 44.14 3.46
10 11 2.291153 CCTTCTTGATCCAGCAAGGGAA 60.291 50.000 4.79 0.00 44.14 3.97
11 12 1.283029 CCTTCTTGATCCAGCAAGGGA 59.717 52.381 4.79 0.00 44.14 4.20
12 13 1.283029 TCCTTCTTGATCCAGCAAGGG 59.717 52.381 17.39 0.00 44.14 3.95
13 14 2.641305 CTCCTTCTTGATCCAGCAAGG 58.359 52.381 14.03 14.03 44.14 3.61
14 15 2.238144 TCCTCCTTCTTGATCCAGCAAG 59.762 50.000 0.00 0.00 45.10 4.01
15 16 2.238144 CTCCTCCTTCTTGATCCAGCAA 59.762 50.000 0.00 0.00 0.00 3.91
16 17 1.836166 CTCCTCCTTCTTGATCCAGCA 59.164 52.381 0.00 0.00 0.00 4.41
17 18 2.114616 TCTCCTCCTTCTTGATCCAGC 58.885 52.381 0.00 0.00 0.00 4.85
18 19 2.100584 CGTCTCCTCCTTCTTGATCCAG 59.899 54.545 0.00 0.00 0.00 3.86
19 20 2.103373 CGTCTCCTCCTTCTTGATCCA 58.897 52.381 0.00 0.00 0.00 3.41
20 21 2.100087 GACGTCTCCTCCTTCTTGATCC 59.900 54.545 8.70 0.00 0.00 3.36
21 22 2.100087 GGACGTCTCCTCCTTCTTGATC 59.900 54.545 16.46 0.00 33.07 2.92
22 23 2.104170 GGACGTCTCCTCCTTCTTGAT 58.896 52.381 16.46 0.00 33.07 2.57
23 24 1.546961 GGACGTCTCCTCCTTCTTGA 58.453 55.000 16.46 0.00 33.07 3.02
24 25 0.533032 GGGACGTCTCCTCCTTCTTG 59.467 60.000 16.46 0.00 36.68 3.02
25 26 0.615261 GGGGACGTCTCCTCCTTCTT 60.615 60.000 27.83 0.00 36.68 2.52
26 27 1.000612 GGGGACGTCTCCTCCTTCT 59.999 63.158 27.83 0.00 36.68 2.85
27 28 3.618652 GGGGACGTCTCCTCCTTC 58.381 66.667 27.83 0.00 36.68 3.46
39 40 4.446413 CACGTACAGCCCGGGGAC 62.446 72.222 25.28 6.25 0.00 4.46
41 42 4.752879 CACACGTACAGCCCGGGG 62.753 72.222 25.28 9.31 31.63 5.73
42 43 3.524648 AACACACGTACAGCCCGGG 62.525 63.158 19.09 19.09 34.16 5.73
43 44 2.029964 AACACACGTACAGCCCGG 59.970 61.111 0.00 0.00 0.00 5.73
44 45 0.876777 TTCAACACACGTACAGCCCG 60.877 55.000 0.00 0.00 0.00 6.13
45 46 0.584876 GTTCAACACACGTACAGCCC 59.415 55.000 0.00 0.00 0.00 5.19
46 47 0.231279 CGTTCAACACACGTACAGCC 59.769 55.000 0.00 0.00 32.80 4.85
47 48 0.382636 GCGTTCAACACACGTACAGC 60.383 55.000 0.00 0.00 39.92 4.40
48 49 0.111878 CGCGTTCAACACACGTACAG 60.112 55.000 0.00 0.00 39.92 2.74
49 50 1.481019 CCGCGTTCAACACACGTACA 61.481 55.000 4.92 0.00 39.92 2.90
50 51 1.199859 CCGCGTTCAACACACGTAC 59.800 57.895 4.92 0.00 39.92 3.67
51 52 0.935831 CTCCGCGTTCAACACACGTA 60.936 55.000 4.92 0.00 39.92 3.57
52 53 2.202770 TCCGCGTTCAACACACGT 60.203 55.556 4.92 0.00 39.92 4.49
53 54 2.544359 CTCCGCGTTCAACACACG 59.456 61.111 4.92 0.00 40.75 4.49
54 55 2.935955 CCTCCGCGTTCAACACAC 59.064 61.111 4.92 0.00 0.00 3.82
55 56 2.970324 GCCTCCGCGTTCAACACA 60.970 61.111 4.92 0.00 0.00 3.72
74 75 4.570663 CTAGCGCCGAACGGAGGG 62.571 72.222 17.63 6.27 43.93 4.30
75 76 2.734756 GATCTAGCGCCGAACGGAGG 62.735 65.000 17.63 8.69 43.93 4.30
76 77 1.370657 GATCTAGCGCCGAACGGAG 60.371 63.158 17.63 14.79 43.93 4.63
77 78 2.719979 GATCTAGCGCCGAACGGA 59.280 61.111 17.63 0.00 43.93 4.69
78 79 2.726180 CGATCTAGCGCCGAACGG 60.726 66.667 15.85 9.00 43.93 4.44
80 81 0.729816 GATCCGATCTAGCGCCGAAC 60.730 60.000 2.29 0.00 0.00 3.95
81 82 0.889638 AGATCCGATCTAGCGCCGAA 60.890 55.000 9.27 0.00 38.00 4.30
82 83 0.889638 AAGATCCGATCTAGCGCCGA 60.890 55.000 11.39 0.39 39.08 5.54
83 84 0.455295 GAAGATCCGATCTAGCGCCG 60.455 60.000 11.39 0.00 39.08 6.46
84 85 0.109039 GGAAGATCCGATCTAGCGCC 60.109 60.000 11.39 7.37 39.08 6.53
85 86 3.410098 GGAAGATCCGATCTAGCGC 57.590 57.895 11.39 0.00 39.08 5.92
106 107 2.408110 CGTACTCGCGGCGATTTAAATC 60.408 50.000 26.60 16.79 34.61 2.17
107 108 1.519758 CGTACTCGCGGCGATTTAAAT 59.480 47.619 26.60 9.68 34.61 1.40
108 109 0.915904 CGTACTCGCGGCGATTTAAA 59.084 50.000 26.60 2.28 34.61 1.52
109 110 0.098552 TCGTACTCGCGGCGATTTAA 59.901 50.000 26.60 8.68 34.61 1.52
110 111 0.589729 GTCGTACTCGCGGCGATTTA 60.590 55.000 26.60 16.67 37.00 1.40
111 112 1.870901 GTCGTACTCGCGGCGATTT 60.871 57.895 26.60 17.71 37.00 2.17
112 113 2.262471 AAGTCGTACTCGCGGCGATT 62.262 55.000 26.60 22.48 41.85 3.34
113 114 2.643764 GAAGTCGTACTCGCGGCGAT 62.644 60.000 26.60 17.43 41.85 4.58
114 115 3.372676 GAAGTCGTACTCGCGGCGA 62.373 63.158 24.84 24.84 41.85 5.54
115 116 2.914797 ATGAAGTCGTACTCGCGGCG 62.915 60.000 17.70 17.70 41.85 6.46
116 117 1.201098 GATGAAGTCGTACTCGCGGC 61.201 60.000 6.13 0.00 36.96 6.53
117 118 0.098200 TGATGAAGTCGTACTCGCGG 59.902 55.000 6.13 0.00 36.96 6.46
118 119 1.578023 GTTGATGAAGTCGTACTCGCG 59.422 52.381 0.00 0.00 36.96 5.87
119 120 1.918609 GGTTGATGAAGTCGTACTCGC 59.081 52.381 0.00 0.00 36.96 5.03
120 121 2.174764 CGGTTGATGAAGTCGTACTCG 58.825 52.381 0.00 0.00 38.55 4.18
121 122 1.918609 GCGGTTGATGAAGTCGTACTC 59.081 52.381 0.00 0.00 0.00 2.59
122 123 1.731424 CGCGGTTGATGAAGTCGTACT 60.731 52.381 0.00 0.00 0.00 2.73
123 124 0.638746 CGCGGTTGATGAAGTCGTAC 59.361 55.000 0.00 0.00 0.00 3.67
124 125 0.241749 ACGCGGTTGATGAAGTCGTA 59.758 50.000 12.47 0.00 0.00 3.43
125 126 0.599204 AACGCGGTTGATGAAGTCGT 60.599 50.000 12.47 0.00 0.00 4.34
126 127 0.093026 GAACGCGGTTGATGAAGTCG 59.907 55.000 12.47 0.00 0.00 4.18
127 128 1.429463 AGAACGCGGTTGATGAAGTC 58.571 50.000 12.47 0.00 0.00 3.01
128 129 2.029290 ACTAGAACGCGGTTGATGAAGT 60.029 45.455 12.47 0.00 0.00 3.01
129 130 2.607187 ACTAGAACGCGGTTGATGAAG 58.393 47.619 12.47 0.00 0.00 3.02
130 131 2.736144 ACTAGAACGCGGTTGATGAA 57.264 45.000 12.47 0.00 0.00 2.57
131 132 3.504863 GTTACTAGAACGCGGTTGATGA 58.495 45.455 12.47 0.00 0.00 2.92
132 133 2.278094 CGTTACTAGAACGCGGTTGATG 59.722 50.000 12.47 0.00 36.82 3.07
133 134 2.523015 CGTTACTAGAACGCGGTTGAT 58.477 47.619 12.47 0.00 36.82 2.57
134 135 1.967762 CGTTACTAGAACGCGGTTGA 58.032 50.000 12.47 0.00 36.82 3.18
159 160 2.317530 ACCCTTGAAGATCGCTAAGC 57.682 50.000 0.00 0.00 0.00 3.09
160 161 5.201713 TCATACCCTTGAAGATCGCTAAG 57.798 43.478 0.00 0.00 0.00 2.18
161 162 5.607939 TTCATACCCTTGAAGATCGCTAA 57.392 39.130 0.00 0.00 32.07 3.09
170 171 4.517285 GAGTGCATCTTCATACCCTTGAA 58.483 43.478 0.00 0.00 34.55 2.69
171 172 3.118261 GGAGTGCATCTTCATACCCTTGA 60.118 47.826 0.00 0.00 0.00 3.02
172 173 3.209410 GGAGTGCATCTTCATACCCTTG 58.791 50.000 0.00 0.00 0.00 3.61
173 174 2.173569 GGGAGTGCATCTTCATACCCTT 59.826 50.000 0.00 0.00 34.08 3.95
174 175 1.771255 GGGAGTGCATCTTCATACCCT 59.229 52.381 0.00 0.00 34.08 4.34
175 176 1.771255 AGGGAGTGCATCTTCATACCC 59.229 52.381 0.00 0.00 35.74 3.69
176 177 2.703007 AGAGGGAGTGCATCTTCATACC 59.297 50.000 0.00 0.00 0.00 2.73
177 178 5.011533 ACATAGAGGGAGTGCATCTTCATAC 59.988 44.000 3.57 0.00 0.00 2.39
178 179 5.150715 ACATAGAGGGAGTGCATCTTCATA 58.849 41.667 3.57 0.00 0.00 2.15
179 180 3.972638 ACATAGAGGGAGTGCATCTTCAT 59.027 43.478 3.57 0.00 0.00 2.57
180 181 3.378512 ACATAGAGGGAGTGCATCTTCA 58.621 45.455 3.57 0.00 0.00 3.02
181 182 3.640967 AGACATAGAGGGAGTGCATCTTC 59.359 47.826 3.57 0.00 0.00 2.87
182 183 3.640967 GAGACATAGAGGGAGTGCATCTT 59.359 47.826 3.57 0.00 0.00 2.40
183 184 3.117169 AGAGACATAGAGGGAGTGCATCT 60.117 47.826 3.78 3.78 0.00 2.90
184 185 3.230134 AGAGACATAGAGGGAGTGCATC 58.770 50.000 0.00 0.00 0.00 3.91
185 186 3.230134 GAGAGACATAGAGGGAGTGCAT 58.770 50.000 0.00 0.00 0.00 3.96
186 187 2.660572 GAGAGACATAGAGGGAGTGCA 58.339 52.381 0.00 0.00 0.00 4.57
187 188 1.606668 CGAGAGACATAGAGGGAGTGC 59.393 57.143 0.00 0.00 0.00 4.40
188 189 2.925724 ACGAGAGACATAGAGGGAGTG 58.074 52.381 0.00 0.00 0.00 3.51
189 190 3.283751 CAACGAGAGACATAGAGGGAGT 58.716 50.000 0.00 0.00 0.00 3.85
190 191 2.034053 GCAACGAGAGACATAGAGGGAG 59.966 54.545 0.00 0.00 0.00 4.30
191 192 2.025155 GCAACGAGAGACATAGAGGGA 58.975 52.381 0.00 0.00 0.00 4.20
192 193 2.028130 AGCAACGAGAGACATAGAGGG 58.972 52.381 0.00 0.00 0.00 4.30
193 194 3.880490 ACTAGCAACGAGAGACATAGAGG 59.120 47.826 0.00 0.00 0.00 3.69
194 195 6.795098 ATACTAGCAACGAGAGACATAGAG 57.205 41.667 0.00 0.00 0.00 2.43
195 196 7.549842 GGATATACTAGCAACGAGAGACATAGA 59.450 40.741 0.00 0.00 0.00 1.98
196 197 7.551262 AGGATATACTAGCAACGAGAGACATAG 59.449 40.741 0.00 0.00 0.00 2.23
197 198 7.395617 AGGATATACTAGCAACGAGAGACATA 58.604 38.462 0.00 0.00 0.00 2.29
198 199 6.242396 AGGATATACTAGCAACGAGAGACAT 58.758 40.000 0.00 0.00 0.00 3.06
199 200 5.622180 AGGATATACTAGCAACGAGAGACA 58.378 41.667 0.00 0.00 0.00 3.41
200 201 7.098477 TCTAGGATATACTAGCAACGAGAGAC 58.902 42.308 16.25 0.00 40.18 3.36
201 202 7.242322 TCTAGGATATACTAGCAACGAGAGA 57.758 40.000 16.25 0.00 40.18 3.10
202 203 8.394877 CAATCTAGGATATACTAGCAACGAGAG 58.605 40.741 16.25 0.00 40.18 3.20
203 204 8.101419 TCAATCTAGGATATACTAGCAACGAGA 58.899 37.037 16.25 0.65 40.18 4.04
204 205 8.270080 TCAATCTAGGATATACTAGCAACGAG 57.730 38.462 16.25 4.33 40.18 4.18
205 206 8.809468 ATCAATCTAGGATATACTAGCAACGA 57.191 34.615 16.25 10.34 40.18 3.85
206 207 8.898761 AGATCAATCTAGGATATACTAGCAACG 58.101 37.037 16.25 5.83 40.18 4.10
209 210 9.194972 CCAAGATCAATCTAGGATATACTAGCA 57.805 37.037 16.25 6.81 40.18 3.49
210 211 9.196139 ACCAAGATCAATCTAGGATATACTAGC 57.804 37.037 16.25 2.53 40.18 3.42
213 214 9.030452 GTCACCAAGATCAATCTAGGATATACT 57.970 37.037 0.00 0.00 35.76 2.12
214 215 8.807118 TGTCACCAAGATCAATCTAGGATATAC 58.193 37.037 0.00 0.00 35.76 1.47
215 216 8.807118 GTGTCACCAAGATCAATCTAGGATATA 58.193 37.037 0.00 0.00 35.76 0.86
216 217 7.524532 CGTGTCACCAAGATCAATCTAGGATAT 60.525 40.741 0.00 0.00 35.76 1.63
217 218 6.239036 CGTGTCACCAAGATCAATCTAGGATA 60.239 42.308 0.00 0.00 35.76 2.59
218 219 5.452496 CGTGTCACCAAGATCAATCTAGGAT 60.452 44.000 0.00 0.00 35.76 3.24
219 220 4.142160 CGTGTCACCAAGATCAATCTAGGA 60.142 45.833 0.00 0.00 35.76 2.94
220 221 4.115516 CGTGTCACCAAGATCAATCTAGG 58.884 47.826 0.00 0.00 35.76 3.02
221 222 4.748892 ACGTGTCACCAAGATCAATCTAG 58.251 43.478 0.00 0.00 35.76 2.43
222 223 4.801330 ACGTGTCACCAAGATCAATCTA 57.199 40.909 0.00 0.00 35.76 1.98
223 224 3.685139 ACGTGTCACCAAGATCAATCT 57.315 42.857 0.00 0.00 39.22 2.40
224 225 4.744570 TCTACGTGTCACCAAGATCAATC 58.255 43.478 0.00 0.00 0.00 2.67
225 226 4.801330 TCTACGTGTCACCAAGATCAAT 57.199 40.909 0.00 0.00 0.00 2.57
226 227 4.594123 TTCTACGTGTCACCAAGATCAA 57.406 40.909 0.00 0.00 0.00 2.57
227 228 4.594123 TTTCTACGTGTCACCAAGATCA 57.406 40.909 0.00 0.00 0.00 2.92
228 229 5.917541 TTTTTCTACGTGTCACCAAGATC 57.082 39.130 0.00 0.00 0.00 2.75
229 230 6.877611 AATTTTTCTACGTGTCACCAAGAT 57.122 33.333 0.00 0.00 0.00 2.40
230 231 6.687081 AAATTTTTCTACGTGTCACCAAGA 57.313 33.333 0.00 0.00 0.00 3.02
231 232 6.970043 TCAAAATTTTTCTACGTGTCACCAAG 59.030 34.615 0.00 0.00 0.00 3.61
232 233 6.853720 TCAAAATTTTTCTACGTGTCACCAA 58.146 32.000 0.00 0.00 0.00 3.67
233 234 6.438259 TCAAAATTTTTCTACGTGTCACCA 57.562 33.333 0.00 0.00 0.00 4.17
234 235 7.924103 ATTCAAAATTTTTCTACGTGTCACC 57.076 32.000 0.00 0.00 0.00 4.02
264 265 1.650536 CTCGCCGTAGAACGCGTAG 60.651 63.158 14.46 0.00 40.91 3.51
265 266 2.400798 CTCGCCGTAGAACGCGTA 59.599 61.111 14.46 0.00 40.91 4.42
266 267 4.471726 CCTCGCCGTAGAACGCGT 62.472 66.667 5.58 5.58 40.91 6.01
267 268 4.471726 ACCTCGCCGTAGAACGCG 62.472 66.667 3.53 3.53 40.91 6.01
268 269 2.578981 GACCTCGCCGTAGAACGC 60.579 66.667 0.00 0.00 40.91 4.84
269 270 2.101770 GGACCTCGCCGTAGAACG 59.898 66.667 0.00 0.00 42.11 3.95
270 271 2.101770 CGGACCTCGCCGTAGAAC 59.898 66.667 0.00 0.00 46.07 3.01
288 289 2.757314 CCCTTCTTCCTTTCATCTTGGC 59.243 50.000 0.00 0.00 0.00 4.52
314 315 3.512033 TTTTGTTTTGCGCCAGTTACT 57.488 38.095 4.18 0.00 0.00 2.24
344 345 7.120579 TGTTTTTCAGTTTTGCTACTTCTCAGA 59.879 33.333 0.00 0.00 0.00 3.27
384 385 8.608844 AGATCCTCTAAACACAACTTAGTTTG 57.391 34.615 0.00 0.69 38.33 2.93
388 389 8.294954 TCCTAGATCCTCTAAACACAACTTAG 57.705 38.462 0.00 0.00 0.00 2.18
408 409 4.120589 GCGGTCCTGTTTTCTTATCCTAG 58.879 47.826 0.00 0.00 0.00 3.02
422 423 3.883744 AAGGAAGCACGCGGTCCTG 62.884 63.158 19.39 6.85 0.00 3.86
428 429 1.131826 CGGTAAAAGGAAGCACGCG 59.868 57.895 3.53 3.53 0.00 6.01
431 432 2.014857 GGGATCGGTAAAAGGAAGCAC 58.985 52.381 0.00 0.00 0.00 4.40
509 512 9.835389 GTCTACTACTCCTAGAAGATTAAGTGA 57.165 37.037 0.00 0.00 0.00 3.41
554 564 2.423538 GGTCATATGTCAGTTGGTTGGC 59.576 50.000 1.90 0.00 0.00 4.52
570 580 0.696501 ACGGGGTTGCTAAAGGTCAT 59.303 50.000 0.00 0.00 0.00 3.06
586 596 0.884259 TGCAATGGAGTGTGACACGG 60.884 55.000 10.41 0.00 39.64 4.94
610 628 0.874175 TTCTCCAACAGCACGACACG 60.874 55.000 0.00 0.00 0.00 4.49
628 646 2.705658 CCTTCCCTTTTTCAAAGGCCTT 59.294 45.455 13.78 13.78 36.10 4.35
629 647 2.090775 TCCTTCCCTTTTTCAAAGGCCT 60.091 45.455 0.00 0.00 38.52 5.19
630 648 2.325484 TCCTTCCCTTTTTCAAAGGCC 58.675 47.619 9.46 0.00 38.52 5.19
644 662 3.130633 GGCACATGTTGTTTTTCCTTCC 58.869 45.455 0.00 0.00 0.00 3.46
645 663 3.791245 TGGCACATGTTGTTTTTCCTTC 58.209 40.909 0.00 0.00 0.00 3.46
659 677 3.009473 ACCAAGATGTAGAGTTGGCACAT 59.991 43.478 4.20 0.00 43.99 3.21
726 744 0.037590 AACAGGCGGGCATGTTCTTA 59.962 50.000 16.89 0.00 46.01 2.10
745 763 3.060736 TCACTAGCGGGCATGTTTTTA 57.939 42.857 0.00 0.00 0.00 1.52
802 846 2.664436 CCACGCCGTTTTCGTCCTC 61.664 63.158 0.00 0.00 42.35 3.71
1255 1354 1.014352 GTGGCGAAGAACACACACTT 58.986 50.000 0.00 0.00 37.01 3.16
1256 1355 0.814010 GGTGGCGAAGAACACACACT 60.814 55.000 0.00 0.00 38.38 3.55
1597 1825 0.747644 TACGTAAGATCCGTGGCCGA 60.748 55.000 0.00 0.00 39.22 5.54
1611 1845 3.376218 GAGGAGCCTCTCGTACGTA 57.624 57.895 16.05 4.02 39.80 3.57
1749 1983 3.181429 ACACCATGGTCACCAAGAAGATT 60.181 43.478 16.53 0.00 36.95 2.40
1899 2133 0.750249 ATACATCCATGGCGTCGACA 59.250 50.000 17.16 1.64 0.00 4.35
1910 2144 0.394938 AATGGCGGCGTATACATCCA 59.605 50.000 9.37 5.59 0.00 3.41
2377 2635 1.368579 CCGTGTAGAACCACCCGTT 59.631 57.895 0.00 0.00 37.41 4.44
2632 2890 4.592192 CCGGCTCCACGCGATCAT 62.592 66.667 15.93 0.00 40.44 2.45
2787 3045 2.234661 ACACTACATCTTGCTGCTGCTA 59.765 45.455 17.00 8.35 40.48 3.49
2788 3046 1.002888 ACACTACATCTTGCTGCTGCT 59.997 47.619 17.00 0.00 40.48 4.24
2789 3047 1.446907 ACACTACATCTTGCTGCTGC 58.553 50.000 8.89 8.89 40.20 5.25
2844 3109 4.762220 TGGGAAGGAAAAAGGGATCAAAT 58.238 39.130 0.00 0.00 0.00 2.32
2885 3150 1.623811 TCTGTAAGACAAGGGAGCACC 59.376 52.381 0.00 0.00 38.67 5.01
2976 3241 2.053638 CGCACGCATCGATGAAGC 60.054 61.111 29.20 23.96 0.00 3.86
3029 3294 0.824109 CGCTCTGAGTACCCAATGGA 59.176 55.000 0.00 0.00 34.81 3.41
3032 3297 0.824759 GACCGCTCTGAGTACCCAAT 59.175 55.000 6.53 0.00 0.00 3.16
3039 3304 1.003112 AGACGAGACCGCTCTGAGT 60.003 57.895 6.53 0.00 39.06 3.41
3068 3365 0.035820 CGAAATGGGAGGAACGGGAA 60.036 55.000 0.00 0.00 0.00 3.97
3089 3386 2.858868 CTGCGCTTGACAGCTGTC 59.141 61.111 35.04 35.04 44.85 3.51
3282 3592 2.819552 GCAGCACGAACAACACGGT 61.820 57.895 0.00 0.00 34.93 4.83
3424 3734 1.743394 GGCTTACAGGGATTTGTTCGG 59.257 52.381 0.00 0.00 32.56 4.30
3724 4073 1.181786 AACCCCAACACACACAACAG 58.818 50.000 0.00 0.00 0.00 3.16
3728 4077 1.214217 TCCTAACCCCAACACACACA 58.786 50.000 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.