Multiple sequence alignment - TraesCS4A01G340200

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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 TraesCS4A01G340200 chr4A 100.000 2564 0 0 1 2564 621480108 621482671 0.000000e+00 4735.0
1 TraesCS4A01G340200 chr5D 91.034 1305 97 7 487 1784 547426739 547425448 0.000000e+00 1744.0
2 TraesCS4A01G340200 chr5D 93.858 749 40 6 1820 2564 547425444 547424698 0.000000e+00 1123.0
3 TraesCS4A01G340200 chr5D 82.317 492 67 11 1890 2377 547417786 547417311 2.370000e-110 409.0
4 TraesCS4A01G340200 chr5D 85.764 288 26 4 142 421 547418160 547417880 8.970000e-75 291.0
5 TraesCS4A01G340200 chr5D 80.870 345 58 6 1286 1623 42135349 42135006 5.440000e-67 265.0
6 TraesCS4A01G340200 chr5D 82.581 155 14 7 571 725 547425429 547425288 9.630000e-25 124.0
7 TraesCS4A01G340200 chr5D 82.292 96 17 0 40 135 276551518 276551423 1.630000e-12 84.2
8 TraesCS4A01G340200 chr3D 80.556 504 79 11 764 1257 116088160 116088654 1.120000e-98 370.0
9 TraesCS4A01G340200 chr3D 85.185 324 30 10 1270 1580 58374076 58374394 1.480000e-82 316.0
10 TraesCS4A01G340200 chr3D 86.260 131 16 1 1 131 598635692 598635820 9.560000e-30 141.0
11 TraesCS4A01G340200 chr3D 84.956 113 17 0 3 115 604563646 604563534 5.800000e-22 115.0
12 TraesCS4A01G340200 chr1A 79.175 509 87 12 758 1257 148747060 148746562 4.090000e-88 335.0
13 TraesCS4A01G340200 chr1B 79.258 458 86 4 800 1255 196059315 196059765 6.890000e-81 311.0
14 TraesCS4A01G340200 chr1B 86.667 150 18 2 1473 1620 31253020 31253169 5.680000e-37 165.0
15 TraesCS4A01G340200 chr1B 89.216 102 11 0 1 102 653709292 653709191 7.450000e-26 128.0
16 TraesCS4A01G340200 chr1D 79.176 461 83 11 800 1255 141897349 141897801 8.910000e-80 307.0
17 TraesCS4A01G340200 chr1D 77.666 497 98 8 770 1257 373423575 373424067 8.970000e-75 291.0
18 TraesCS4A01G340200 chr5B 82.031 384 41 12 403 765 690949707 690949331 4.150000e-78 302.0
19 TraesCS4A01G340200 chr5B 98.246 57 1 0 1835 1891 690949545 690949489 1.620000e-17 100.0
20 TraesCS4A01G340200 chr4D 78.448 464 83 10 797 1257 128921781 128922230 1.160000e-73 287.0
21 TraesCS4A01G340200 chr4D 82.353 306 47 7 953 1255 22045156 22045457 2.530000e-65 259.0
22 TraesCS4A01G340200 chrUn 77.710 489 91 11 773 1257 323288270 323287796 1.500000e-72 283.0
23 TraesCS4A01G340200 chr7A 86.577 149 18 2 1473 1619 188888085 188888233 2.040000e-36 163.0
24 TraesCS4A01G340200 chr7A 86.577 149 18 2 1473 1619 619193722 619193870 2.040000e-36 163.0
25 TraesCS4A01G340200 chr2A 86.486 148 19 1 1473 1619 689768598 689768745 7.340000e-36 161.0
26 TraesCS4A01G340200 chr7D 84.848 132 18 2 1 131 382662110 382661980 5.760000e-27 132.0
27 TraesCS4A01G340200 chr2D 82.707 133 23 0 3 135 607984672 607984540 4.480000e-23 119.0
28 TraesCS4A01G340200 chr6A 85.981 107 15 0 1 107 33916205 33916311 5.800000e-22 115.0
29 TraesCS4A01G340200 chr4B 77.941 136 20 9 2006 2132 440584095 440583961 2.740000e-10 76.8


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 TraesCS4A01G340200 chr4A 621480108 621482671 2563 False 4735 4735 100.000000 1 2564 1 chr4A.!!$F1 2563
1 TraesCS4A01G340200 chr5D 547424698 547426739 2041 True 997 1744 89.157667 487 2564 3 chr5D.!!$R4 2077
2 TraesCS4A01G340200 chr5D 547417311 547418160 849 True 350 409 84.040500 142 2377 2 chr5D.!!$R3 2235

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
20 21 0.031111 TCCCCCTCAGTCATAGTGGG 60.031 60.0 0.0 0.0 39.07 4.61 F
21 22 0.031111 CCCCCTCAGTCATAGTGGGA 60.031 60.0 0.0 0.0 41.29 4.37 F
842 866 0.040058 ATGGAGCATGACAAGGGCAA 59.960 50.0 0.0 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1063 1087 0.032952 TTGACCTTGAACTCCGTCGG 59.967 55.0 4.39 4.39 0.0 4.79 R
1271 1295 0.034059 CCTTCTATTGCGCGGATCCT 59.966 55.0 8.83 0.00 0.0 3.24 R
2310 2353 0.107848 GGTTAGCTACACGGGCACAT 60.108 55.0 0.00 0.00 0.0 3.21 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 1.879575 TTCCCCCTCAGTCATAGTGG 58.120 55.000 0.00 0.00 0.00 4.00
20 21 0.031111 TCCCCCTCAGTCATAGTGGG 60.031 60.000 0.00 0.00 39.07 4.61
21 22 0.031111 CCCCCTCAGTCATAGTGGGA 60.031 60.000 0.00 0.00 41.29 4.37
22 23 1.418334 CCCCTCAGTCATAGTGGGAG 58.582 60.000 0.00 0.00 41.29 4.30
23 24 1.343478 CCCCTCAGTCATAGTGGGAGT 60.343 57.143 0.00 0.00 41.29 3.85
24 25 1.759445 CCCTCAGTCATAGTGGGAGTG 59.241 57.143 0.00 0.00 41.29 3.51
25 26 2.624293 CCCTCAGTCATAGTGGGAGTGA 60.624 54.545 0.00 0.00 41.29 3.41
26 27 3.099905 CCTCAGTCATAGTGGGAGTGAA 58.900 50.000 0.00 0.00 42.44 3.18
27 28 3.131933 CCTCAGTCATAGTGGGAGTGAAG 59.868 52.174 0.00 0.00 42.44 3.02
28 29 2.497675 TCAGTCATAGTGGGAGTGAAGC 59.502 50.000 0.00 0.00 40.70 3.86
29 30 1.478510 AGTCATAGTGGGAGTGAAGCG 59.521 52.381 0.00 0.00 0.00 4.68
30 31 0.824109 TCATAGTGGGAGTGAAGCGG 59.176 55.000 0.00 0.00 0.00 5.52
31 32 0.824109 CATAGTGGGAGTGAAGCGGA 59.176 55.000 0.00 0.00 0.00 5.54
32 33 1.414181 CATAGTGGGAGTGAAGCGGAT 59.586 52.381 0.00 0.00 0.00 4.18
33 34 0.824109 TAGTGGGAGTGAAGCGGATG 59.176 55.000 0.00 0.00 0.00 3.51
34 35 0.904865 AGTGGGAGTGAAGCGGATGA 60.905 55.000 0.00 0.00 0.00 2.92
35 36 0.179000 GTGGGAGTGAAGCGGATGAT 59.821 55.000 0.00 0.00 0.00 2.45
36 37 0.178767 TGGGAGTGAAGCGGATGATG 59.821 55.000 0.00 0.00 0.00 3.07
37 38 0.465705 GGGAGTGAAGCGGATGATGA 59.534 55.000 0.00 0.00 0.00 2.92
38 39 1.576356 GGAGTGAAGCGGATGATGAC 58.424 55.000 0.00 0.00 0.00 3.06
39 40 1.203928 GAGTGAAGCGGATGATGACG 58.796 55.000 0.00 0.00 0.00 4.35
40 41 0.817654 AGTGAAGCGGATGATGACGA 59.182 50.000 0.00 0.00 0.00 4.20
41 42 0.924090 GTGAAGCGGATGATGACGAC 59.076 55.000 0.00 0.00 0.00 4.34
42 43 0.817654 TGAAGCGGATGATGACGACT 59.182 50.000 0.00 0.00 0.00 4.18
43 44 1.203928 GAAGCGGATGATGACGACTG 58.796 55.000 0.00 0.00 0.00 3.51
44 45 0.817654 AAGCGGATGATGACGACTGA 59.182 50.000 0.00 0.00 0.00 3.41
45 46 0.817654 AGCGGATGATGACGACTGAA 59.182 50.000 0.00 0.00 0.00 3.02
46 47 1.410517 AGCGGATGATGACGACTGAAT 59.589 47.619 0.00 0.00 0.00 2.57
47 48 2.159043 AGCGGATGATGACGACTGAATT 60.159 45.455 0.00 0.00 0.00 2.17
48 49 2.609459 GCGGATGATGACGACTGAATTT 59.391 45.455 0.00 0.00 0.00 1.82
49 50 3.544834 GCGGATGATGACGACTGAATTTG 60.545 47.826 0.00 0.00 0.00 2.32
50 51 3.865164 CGGATGATGACGACTGAATTTGA 59.135 43.478 0.00 0.00 0.00 2.69
51 52 4.329801 CGGATGATGACGACTGAATTTGAA 59.670 41.667 0.00 0.00 0.00 2.69
52 53 5.501413 CGGATGATGACGACTGAATTTGAAG 60.501 44.000 0.00 0.00 0.00 3.02
53 54 5.352569 GGATGATGACGACTGAATTTGAAGT 59.647 40.000 0.00 0.00 0.00 3.01
54 55 5.845985 TGATGACGACTGAATTTGAAGTC 57.154 39.130 0.00 6.76 39.57 3.01
55 56 5.541845 TGATGACGACTGAATTTGAAGTCT 58.458 37.500 12.36 3.54 40.57 3.24
56 57 5.991606 TGATGACGACTGAATTTGAAGTCTT 59.008 36.000 12.36 5.78 40.57 3.01
57 58 5.657470 TGACGACTGAATTTGAAGTCTTG 57.343 39.130 12.36 4.08 40.57 3.02
58 59 4.024893 TGACGACTGAATTTGAAGTCTTGC 60.025 41.667 12.36 5.26 40.57 4.01
59 60 3.876914 ACGACTGAATTTGAAGTCTTGCA 59.123 39.130 12.36 0.00 40.57 4.08
60 61 4.214437 CGACTGAATTTGAAGTCTTGCAC 58.786 43.478 12.36 0.00 40.57 4.57
61 62 4.024556 CGACTGAATTTGAAGTCTTGCACT 60.025 41.667 12.36 0.00 40.57 4.40
72 73 5.904362 AAGTCTTGCACTTCTGTCTTTTT 57.096 34.783 0.00 0.00 42.07 1.94
73 74 5.491635 AGTCTTGCACTTCTGTCTTTTTC 57.508 39.130 0.00 0.00 26.56 2.29
74 75 5.189180 AGTCTTGCACTTCTGTCTTTTTCT 58.811 37.500 0.00 0.00 26.56 2.52
75 76 5.295540 AGTCTTGCACTTCTGTCTTTTTCTC 59.704 40.000 0.00 0.00 26.56 2.87
76 77 4.576463 TCTTGCACTTCTGTCTTTTTCTCC 59.424 41.667 0.00 0.00 0.00 3.71
77 78 2.872245 TGCACTTCTGTCTTTTTCTCCG 59.128 45.455 0.00 0.00 0.00 4.63
78 79 2.349912 GCACTTCTGTCTTTTTCTCCGC 60.350 50.000 0.00 0.00 0.00 5.54
79 80 3.134458 CACTTCTGTCTTTTTCTCCGCT 58.866 45.455 0.00 0.00 0.00 5.52
80 81 4.307432 CACTTCTGTCTTTTTCTCCGCTA 58.693 43.478 0.00 0.00 0.00 4.26
81 82 4.150804 CACTTCTGTCTTTTTCTCCGCTAC 59.849 45.833 0.00 0.00 0.00 3.58
82 83 4.202223 ACTTCTGTCTTTTTCTCCGCTACA 60.202 41.667 0.00 0.00 0.00 2.74
83 84 4.537135 TCTGTCTTTTTCTCCGCTACAT 57.463 40.909 0.00 0.00 0.00 2.29
84 85 4.495422 TCTGTCTTTTTCTCCGCTACATC 58.505 43.478 0.00 0.00 0.00 3.06
85 86 4.021456 TCTGTCTTTTTCTCCGCTACATCA 60.021 41.667 0.00 0.00 0.00 3.07
86 87 4.832248 TGTCTTTTTCTCCGCTACATCAT 58.168 39.130 0.00 0.00 0.00 2.45
87 88 4.870426 TGTCTTTTTCTCCGCTACATCATC 59.130 41.667 0.00 0.00 0.00 2.92
88 89 4.870426 GTCTTTTTCTCCGCTACATCATCA 59.130 41.667 0.00 0.00 0.00 3.07
89 90 5.525378 GTCTTTTTCTCCGCTACATCATCAT 59.475 40.000 0.00 0.00 0.00 2.45
90 91 5.755375 TCTTTTTCTCCGCTACATCATCATC 59.245 40.000 0.00 0.00 0.00 2.92
91 92 4.670896 TTTCTCCGCTACATCATCATCA 57.329 40.909 0.00 0.00 0.00 3.07
92 93 4.670896 TTCTCCGCTACATCATCATCAA 57.329 40.909 0.00 0.00 0.00 2.57
93 94 3.982475 TCTCCGCTACATCATCATCAAC 58.018 45.455 0.00 0.00 0.00 3.18
94 95 3.638627 TCTCCGCTACATCATCATCAACT 59.361 43.478 0.00 0.00 0.00 3.16
95 96 3.721035 TCCGCTACATCATCATCAACTG 58.279 45.455 0.00 0.00 0.00 3.16
96 97 2.222678 CCGCTACATCATCATCAACTGC 59.777 50.000 0.00 0.00 0.00 4.40
97 98 2.097056 CGCTACATCATCATCAACTGCG 60.097 50.000 0.00 0.00 0.00 5.18
98 99 2.868583 GCTACATCATCATCAACTGCGT 59.131 45.455 0.00 0.00 0.00 5.24
99 100 3.060003 GCTACATCATCATCAACTGCGTC 60.060 47.826 0.00 0.00 0.00 5.19
100 101 3.257469 ACATCATCATCAACTGCGTCT 57.743 42.857 0.00 0.00 0.00 4.18
101 102 3.193263 ACATCATCATCAACTGCGTCTC 58.807 45.455 0.00 0.00 0.00 3.36
102 103 3.118847 ACATCATCATCAACTGCGTCTCT 60.119 43.478 0.00 0.00 0.00 3.10
103 104 2.884827 TCATCATCAACTGCGTCTCTG 58.115 47.619 0.00 0.00 0.00 3.35
104 105 2.493278 TCATCATCAACTGCGTCTCTGA 59.507 45.455 0.00 0.00 0.00 3.27
105 106 3.131755 TCATCATCAACTGCGTCTCTGAT 59.868 43.478 0.00 0.00 0.00 2.90
106 107 2.884827 TCATCAACTGCGTCTCTGATG 58.115 47.619 11.22 11.22 44.24 3.07
107 108 2.232208 TCATCAACTGCGTCTCTGATGT 59.768 45.455 14.85 0.00 43.62 3.06
108 109 2.070262 TCAACTGCGTCTCTGATGTG 57.930 50.000 0.00 0.00 0.00 3.21
109 110 1.341209 TCAACTGCGTCTCTGATGTGT 59.659 47.619 0.00 0.00 0.00 3.72
110 111 1.723542 CAACTGCGTCTCTGATGTGTC 59.276 52.381 0.00 0.00 0.00 3.67
111 112 0.109551 ACTGCGTCTCTGATGTGTCG 60.110 55.000 0.00 0.00 0.00 4.35
112 113 0.169009 CTGCGTCTCTGATGTGTCGA 59.831 55.000 0.00 0.00 0.00 4.20
113 114 0.109735 TGCGTCTCTGATGTGTCGAC 60.110 55.000 9.11 9.11 0.00 4.20
114 115 0.109735 GCGTCTCTGATGTGTCGACA 60.110 55.000 15.76 15.76 36.22 4.35
115 116 1.607713 CGTCTCTGATGTGTCGACAC 58.392 55.000 36.01 36.01 46.59 3.67
116 117 1.729472 CGTCTCTGATGTGTCGACACC 60.729 57.143 38.12 26.71 45.88 4.16
117 118 1.542030 GTCTCTGATGTGTCGACACCT 59.458 52.381 38.12 31.41 45.88 4.00
118 119 2.747989 GTCTCTGATGTGTCGACACCTA 59.252 50.000 38.12 25.27 45.88 3.08
119 120 3.010420 TCTCTGATGTGTCGACACCTAG 58.990 50.000 38.12 31.03 45.88 3.02
120 121 2.750166 CTCTGATGTGTCGACACCTAGT 59.250 50.000 38.12 24.34 45.88 2.57
121 122 2.488153 TCTGATGTGTCGACACCTAGTG 59.512 50.000 38.12 25.44 45.88 2.74
122 123 2.488153 CTGATGTGTCGACACCTAGTGA 59.512 50.000 38.12 23.23 45.88 3.41
123 124 2.488153 TGATGTGTCGACACCTAGTGAG 59.512 50.000 38.12 0.00 45.88 3.51
134 135 2.593346 CCTAGTGAGGTGACTGCATC 57.407 55.000 0.00 0.00 44.43 3.91
135 136 1.827344 CCTAGTGAGGTGACTGCATCA 59.173 52.381 0.00 0.00 44.43 3.07
191 192 3.480133 GGGGGTGAGATCGGTGGG 61.480 72.222 0.00 0.00 0.00 4.61
192 193 4.176752 GGGGTGAGATCGGTGGGC 62.177 72.222 0.00 0.00 0.00 5.36
193 194 4.530857 GGGTGAGATCGGTGGGCG 62.531 72.222 0.00 0.00 0.00 6.13
194 195 3.458163 GGTGAGATCGGTGGGCGA 61.458 66.667 0.00 0.00 0.00 5.54
313 320 1.369209 CCGCGCGCCTGATATTTTG 60.369 57.895 27.36 6.94 0.00 2.44
315 322 1.727467 GCGCGCCTGATATTTTGGT 59.273 52.632 23.24 0.00 0.00 3.67
333 340 0.875059 GTTTTGTCCTCTTGCTCCGG 59.125 55.000 0.00 0.00 0.00 5.14
344 351 2.517166 GCTCCGGGCTGGGAAATC 60.517 66.667 13.58 0.00 38.76 2.17
352 359 2.275418 CTGGGAAATCGGGGTGGG 59.725 66.667 0.00 0.00 0.00 4.61
353 360 2.533232 TGGGAAATCGGGGTGGGT 60.533 61.111 0.00 0.00 0.00 4.51
354 361 1.229886 TGGGAAATCGGGGTGGGTA 60.230 57.895 0.00 0.00 0.00 3.69
355 362 1.276140 TGGGAAATCGGGGTGGGTAG 61.276 60.000 0.00 0.00 0.00 3.18
356 363 1.530283 GGAAATCGGGGTGGGTAGG 59.470 63.158 0.00 0.00 0.00 3.18
357 364 1.530283 GAAATCGGGGTGGGTAGGG 59.470 63.158 0.00 0.00 0.00 3.53
364 371 2.036731 GGTGGGTAGGGTTTGGCC 59.963 66.667 0.00 0.00 0.00 5.36
366 373 1.001269 GTGGGTAGGGTTTGGCCTC 60.001 63.158 3.32 0.00 37.43 4.70
377 384 2.038814 TTTGGCCTCGAGTGAGCACA 62.039 55.000 12.31 5.60 41.13 4.57
389 396 1.098712 TGAGCACACGGTTTGGGTTC 61.099 55.000 0.00 0.00 39.29 3.62
394 401 1.824760 CACGGTTTGGGTTCGGGTT 60.825 57.895 0.00 0.00 0.00 4.11
395 402 1.076850 ACGGTTTGGGTTCGGGTTT 60.077 52.632 0.00 0.00 0.00 3.27
396 403 1.360911 CGGTTTGGGTTCGGGTTTG 59.639 57.895 0.00 0.00 0.00 2.93
397 404 1.743391 GGTTTGGGTTCGGGTTTGG 59.257 57.895 0.00 0.00 0.00 3.28
411 420 1.412079 GTTTGGATGGGCATGGCATA 58.588 50.000 22.06 9.78 0.00 3.14
434 443 2.504032 CACCATATGGACGGCCGT 59.496 61.111 34.89 34.89 38.94 5.68
435 444 1.887242 CACCATATGGACGGCCGTG 60.887 63.158 39.65 22.08 38.94 4.94
436 445 2.280797 CCATATGGACGGCCGTGG 60.281 66.667 39.65 25.83 37.39 4.94
437 446 2.802724 CCATATGGACGGCCGTGGA 61.803 63.158 39.65 22.54 36.47 4.02
438 447 1.145156 CATATGGACGGCCGTGGAA 59.855 57.895 39.65 21.32 36.79 3.53
439 448 1.145377 ATATGGACGGCCGTGGAAC 59.855 57.895 39.65 21.66 36.79 3.62
440 449 2.319890 ATATGGACGGCCGTGGAACC 62.320 60.000 39.65 30.10 36.79 3.62
442 451 4.629523 GGACGGCCGTGGAACCAA 62.630 66.667 39.65 0.00 0.00 3.67
443 452 3.047877 GACGGCCGTGGAACCAAG 61.048 66.667 39.65 0.00 0.00 3.61
444 453 3.819877 GACGGCCGTGGAACCAAGT 62.820 63.158 39.65 6.34 0.00 3.16
445 454 2.344500 CGGCCGTGGAACCAAGTA 59.656 61.111 19.50 0.00 0.00 2.24
446 455 2.030958 CGGCCGTGGAACCAAGTAC 61.031 63.158 19.50 0.00 0.00 2.73
447 456 2.030958 GGCCGTGGAACCAAGTACG 61.031 63.158 6.10 0.00 36.39 3.67
448 457 1.301165 GCCGTGGAACCAAGTACGT 60.301 57.895 0.00 0.00 34.96 3.57
449 458 1.287041 GCCGTGGAACCAAGTACGTC 61.287 60.000 0.00 0.00 34.96 4.34
450 459 1.005294 CCGTGGAACCAAGTACGTCG 61.005 60.000 0.00 0.00 34.96 5.12
451 460 1.611592 CGTGGAACCAAGTACGTCGC 61.612 60.000 0.00 0.00 0.00 5.19
452 461 1.372004 TGGAACCAAGTACGTCGCG 60.372 57.895 0.00 0.00 0.00 5.87
453 462 1.081242 GGAACCAAGTACGTCGCGA 60.081 57.895 3.71 3.71 0.00 5.87
454 463 1.339946 GGAACCAAGTACGTCGCGAC 61.340 60.000 28.96 28.96 0.00 5.19
467 476 4.083862 GCGACGAGGGGAGCCTTT 62.084 66.667 0.00 0.00 0.00 3.11
468 477 2.125512 CGACGAGGGGAGCCTTTG 60.126 66.667 0.00 0.00 0.00 2.77
469 478 2.436824 GACGAGGGGAGCCTTTGC 60.437 66.667 0.00 0.00 37.95 3.68
479 488 3.769201 GCCTTTGCTCTGGTTGCT 58.231 55.556 0.00 0.00 33.53 3.91
480 489 2.044452 GCCTTTGCTCTGGTTGCTT 58.956 52.632 0.00 0.00 33.53 3.91
481 490 0.319297 GCCTTTGCTCTGGTTGCTTG 60.319 55.000 0.00 0.00 33.53 4.01
482 491 0.316204 CCTTTGCTCTGGTTGCTTGG 59.684 55.000 0.00 0.00 0.00 3.61
483 492 0.319297 CTTTGCTCTGGTTGCTTGGC 60.319 55.000 0.00 0.00 0.00 4.52
484 493 1.042003 TTTGCTCTGGTTGCTTGGCA 61.042 50.000 0.00 0.00 36.47 4.92
485 494 1.457823 TTGCTCTGGTTGCTTGGCAG 61.458 55.000 0.00 0.00 40.61 4.85
525 534 1.639635 ATGGGGGCATCAGTCCAGTC 61.640 60.000 0.00 0.00 43.06 3.51
534 543 2.913777 TCAGTCCAGTCATTACGTCG 57.086 50.000 0.00 0.00 0.00 5.12
535 544 1.135489 TCAGTCCAGTCATTACGTCGC 60.135 52.381 0.00 0.00 0.00 5.19
536 545 0.172803 AGTCCAGTCATTACGTCGCC 59.827 55.000 0.00 0.00 0.00 5.54
582 595 0.106708 TGCTGACGAAACTGCTCCTT 59.893 50.000 0.00 0.00 36.10 3.36
590 603 0.179018 AAACTGCTCCTTTGCTCCGT 60.179 50.000 0.00 0.00 0.00 4.69
658 680 4.112634 TCTCGAACAAATGGATCATCGAC 58.887 43.478 0.00 0.00 35.68 4.20
707 729 0.673644 ACATACGCAGAAGTGGTGGC 60.674 55.000 0.00 0.00 0.00 5.01
782 806 6.392353 TGATTTTGTGCTTTTCATAATGCG 57.608 33.333 0.00 0.00 37.26 4.73
791 815 4.319766 GCTTTTCATAATGCGGATCGACAT 60.320 41.667 0.00 0.00 0.00 3.06
793 817 2.687370 TCATAATGCGGATCGACATGG 58.313 47.619 0.00 0.00 0.00 3.66
802 826 3.000041 CGGATCGACATGGAAAACAAGA 59.000 45.455 0.00 0.00 0.00 3.02
842 866 0.040058 ATGGAGCATGACAAGGGCAA 59.960 50.000 0.00 0.00 0.00 4.52
844 868 0.610232 GGAGCATGACAAGGGCAAGT 60.610 55.000 0.00 0.00 0.00 3.16
913 937 2.048222 CCACAGACGGCGACATGT 60.048 61.111 16.62 12.30 0.00 3.21
949 973 2.970324 GCGGCAAGTGTCGGAACA 60.970 61.111 7.49 0.00 44.35 3.18
951 975 1.852067 GCGGCAAGTGTCGGAACAAT 61.852 55.000 7.49 0.00 44.35 2.71
960 984 1.084289 GTCGGAACAATGGCCACTAC 58.916 55.000 8.16 0.00 0.00 2.73
975 999 0.912486 ACTACCATGAGAAGGGTGGC 59.088 55.000 0.00 0.00 39.07 5.01
993 1017 1.194218 GCCCAACCCACTAATGCAAT 58.806 50.000 0.00 0.00 0.00 3.56
1030 1054 1.565759 AGCTTGAGGCCATACCAATGA 59.434 47.619 5.01 0.00 43.14 2.57
1031 1055 2.176364 AGCTTGAGGCCATACCAATGAT 59.824 45.455 5.01 0.00 43.14 2.45
1055 1079 6.479884 TCCTAGACTTTACGAAGTACTTCCT 58.520 40.000 26.12 18.50 45.76 3.36
1059 1083 3.577415 ACTTTACGAAGTACTTCCTGGCT 59.423 43.478 26.12 9.14 45.76 4.75
1063 1087 1.443802 GAAGTACTTCCTGGCTGTGC 58.556 55.000 22.74 0.00 33.64 4.57
1118 1142 1.615883 CTCATGGAGGGTCACTATCCG 59.384 57.143 0.00 0.00 35.78 4.18
1127 1151 2.367567 GGGTCACTATCCGGCTGATTAA 59.632 50.000 0.00 0.00 34.76 1.40
1165 1189 2.780924 AGGGTTGGGCCACCTTCA 60.781 61.111 19.97 0.00 39.65 3.02
1166 1190 2.169810 AGGGTTGGGCCACCTTCAT 61.170 57.895 19.97 1.42 39.65 2.57
1175 1199 1.589630 CCACCTTCATCGTCGTCCA 59.410 57.895 0.00 0.00 0.00 4.02
1176 1200 0.736325 CCACCTTCATCGTCGTCCAC 60.736 60.000 0.00 0.00 0.00 4.02
1189 1213 2.166459 GTCGTCCACCAGATCAAGATCA 59.834 50.000 12.21 0.00 40.22 2.92
1209 1233 5.401531 TCAGGTACATAGTGACCTTCAAC 57.598 43.478 0.00 0.00 43.87 3.18
1214 1238 3.412386 ACATAGTGACCTTCAACTTGCC 58.588 45.455 0.00 0.00 0.00 4.52
1228 1252 2.989055 CTTGCCGACTCCCAACACGT 62.989 60.000 0.00 0.00 0.00 4.49
1283 1307 4.776322 CACCCAGGATCCGCGCAA 62.776 66.667 8.75 0.00 0.00 4.85
1292 1316 0.601311 GATCCGCGCAATAGAAGGCT 60.601 55.000 8.75 0.00 0.00 4.58
1294 1318 1.815421 CCGCGCAATAGAAGGCTGT 60.815 57.895 8.75 0.00 0.00 4.40
1318 1342 1.463214 TCACCCCGGCCATATCCAT 60.463 57.895 2.24 0.00 0.00 3.41
1323 1347 1.561769 CCCGGCCATATCCATGCCTA 61.562 60.000 2.24 0.00 0.00 3.93
1333 1357 2.108514 CCATGCCTACACGCACCAG 61.109 63.158 0.00 0.00 42.70 4.00
1365 1389 4.457496 CCTCGTCGCCACAGCCAT 62.457 66.667 0.00 0.00 34.57 4.40
1385 1409 3.415087 GGCCCTCTGCACCTCCAT 61.415 66.667 0.00 0.00 43.89 3.41
1387 1411 2.673200 GCCCTCTGCACCTCCATGA 61.673 63.158 0.00 0.00 40.77 3.07
1393 1417 2.821366 GCACCTCCATGAGCCACG 60.821 66.667 0.00 0.00 0.00 4.94
1632 1656 1.535833 CGAGAGGTGACAGTACCACT 58.464 55.000 0.00 0.00 43.11 4.00
1642 1666 7.069986 AGGTGACAGTACCACTCAATATCTAT 58.930 38.462 0.00 0.00 43.37 1.98
1653 1677 6.238511 CCACTCAATATCTATAGATCCGTCCG 60.239 46.154 18.59 7.26 36.05 4.79
1655 1679 4.579340 TCAATATCTATAGATCCGTCCGCC 59.421 45.833 18.59 0.00 36.05 6.13
1657 1681 2.581216 TCTATAGATCCGTCCGCCTT 57.419 50.000 0.00 0.00 0.00 4.35
1700 1724 0.184692 TGAGCACATGGTTTGGGTGA 59.815 50.000 0.00 0.00 34.52 4.02
1746 1770 0.763035 GCCCGTGGAACCACCTATAT 59.237 55.000 16.85 0.00 43.49 0.86
1747 1771 1.542547 GCCCGTGGAACCACCTATATG 60.543 57.143 16.85 3.42 43.49 1.78
1749 1773 2.967201 CCCGTGGAACCACCTATATGTA 59.033 50.000 16.85 0.00 43.49 2.29
1752 1776 3.650139 GTGGAACCACCTATATGTAGCG 58.350 50.000 12.42 0.00 40.79 4.26
1755 1779 3.562505 GAACCACCTATATGTAGCGACG 58.437 50.000 0.00 0.00 0.00 5.12
1784 1808 4.648626 TGCTTGCGAGGCTTGCCT 62.649 61.111 23.60 14.69 0.00 4.75
1791 1815 4.774503 GAGGCTTGCCTCGCAGCT 62.775 66.667 23.58 0.00 40.61 4.24
1798 1822 4.112341 GCCTCGCAGCTGGCAAAG 62.112 66.667 17.12 7.96 43.90 2.77
1799 1823 2.670934 CCTCGCAGCTGGCAAAGT 60.671 61.111 17.12 0.00 45.17 2.66
1800 1824 2.263741 CCTCGCAGCTGGCAAAGTT 61.264 57.895 17.12 0.00 45.17 2.66
1801 1825 1.081641 CTCGCAGCTGGCAAAGTTG 60.082 57.895 17.12 0.00 45.17 3.16
1802 1826 1.509644 CTCGCAGCTGGCAAAGTTGA 61.510 55.000 17.12 0.00 45.17 3.18
1803 1827 0.890542 TCGCAGCTGGCAAAGTTGAT 60.891 50.000 17.12 0.00 45.17 2.57
1804 1828 0.731514 CGCAGCTGGCAAAGTTGATG 60.732 55.000 17.12 0.00 45.17 3.07
1805 1829 0.599558 GCAGCTGGCAAAGTTGATGA 59.400 50.000 17.12 0.00 39.36 2.92
1806 1830 1.402456 GCAGCTGGCAAAGTTGATGAG 60.402 52.381 17.12 0.00 39.36 2.90
1807 1831 1.201647 CAGCTGGCAAAGTTGATGAGG 59.798 52.381 5.57 0.00 39.36 3.86
1808 1832 0.529378 GCTGGCAAAGTTGATGAGGG 59.471 55.000 0.00 0.00 0.00 4.30
1809 1833 0.529378 CTGGCAAAGTTGATGAGGGC 59.471 55.000 0.00 0.00 0.00 5.19
1810 1834 0.178967 TGGCAAAGTTGATGAGGGCA 60.179 50.000 0.00 0.00 0.00 5.36
1811 1835 1.188863 GGCAAAGTTGATGAGGGCAT 58.811 50.000 0.00 0.00 37.47 4.40
1841 1865 3.064207 TCATTACGTCACCAGAAAGTGC 58.936 45.455 0.00 0.00 37.68 4.40
1867 1891 3.861341 CTCCCCGAGCTCATTTCAA 57.139 52.632 15.40 0.00 0.00 2.69
1894 1918 3.568007 GGATGAACAGTACAAGCCAAACA 59.432 43.478 0.00 0.00 0.00 2.83
1897 1921 3.568007 TGAACAGTACAAGCCAAACATCC 59.432 43.478 0.00 0.00 0.00 3.51
1919 1943 5.121454 TCCAACAAATGTTTTGAGTGTTTGC 59.879 36.000 6.96 0.00 35.83 3.68
1943 1967 6.951530 GCGAATTTTCATCATGAAACAACATG 59.048 34.615 12.58 0.00 45.03 3.21
2137 2179 6.957920 TCTTGATTTCACTGTTCATCCAAA 57.042 33.333 0.00 0.00 0.00 3.28
2228 2270 1.066143 ACTGATGGGTGATCGAACCAC 60.066 52.381 8.50 10.13 42.47 4.16
2262 2304 6.152379 AGCATTTTCCTCGTGAAGAAAATTC 58.848 36.000 13.75 10.64 45.74 2.17
2263 2305 5.920273 GCATTTTCCTCGTGAAGAAAATTCA 59.080 36.000 13.75 0.00 45.74 2.57
2269 2312 4.455533 CCTCGTGAAGAAAATTCACCATCA 59.544 41.667 13.50 0.00 44.29 3.07
2302 2345 3.403558 GCTCCACTCCACCCCCTC 61.404 72.222 0.00 0.00 0.00 4.30
2310 2353 3.000819 CCACCCCCTCGCTGTACA 61.001 66.667 0.00 0.00 0.00 2.90
2315 2358 1.815421 CCCCTCGCTGTACATGTGC 60.815 63.158 9.11 8.01 0.00 4.57
2328 2371 1.006832 CATGTGCCCGTGTAGCTAAC 58.993 55.000 0.00 0.00 0.00 2.34
2332 2375 2.905681 CCCGTGTAGCTAACCCCC 59.094 66.667 0.00 0.00 0.00 5.40
2344 2387 2.488347 GCTAACCCCCAGAGTTTTCACA 60.488 50.000 0.00 0.00 0.00 3.58
2486 2529 5.048782 TGCAGCTAGTTTAGGTTCAACAATG 60.049 40.000 0.00 0.00 33.57 2.82
2560 2603 4.936685 AAGATAACAGGCTTTCCTCCTT 57.063 40.909 0.00 0.00 41.93 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.879575 CCACTATGACTGAGGGGGAA 58.120 55.000 0.00 0.00 33.41 3.97
1 2 3.635099 CCACTATGACTGAGGGGGA 57.365 57.895 0.00 0.00 33.41 4.81
3 4 1.343478 ACTCCCACTATGACTGAGGGG 60.343 57.143 0.00 0.00 40.02 4.79
4 5 1.759445 CACTCCCACTATGACTGAGGG 59.241 57.143 0.00 0.00 40.98 4.30
5 6 2.739943 TCACTCCCACTATGACTGAGG 58.260 52.381 0.00 0.00 0.00 3.86
6 7 3.430098 GCTTCACTCCCACTATGACTGAG 60.430 52.174 0.00 0.00 0.00 3.35
7 8 2.497675 GCTTCACTCCCACTATGACTGA 59.502 50.000 0.00 0.00 0.00 3.41
8 9 2.736719 CGCTTCACTCCCACTATGACTG 60.737 54.545 0.00 0.00 0.00 3.51
9 10 1.478510 CGCTTCACTCCCACTATGACT 59.521 52.381 0.00 0.00 0.00 3.41
10 11 1.471676 CCGCTTCACTCCCACTATGAC 60.472 57.143 0.00 0.00 0.00 3.06
11 12 0.824109 CCGCTTCACTCCCACTATGA 59.176 55.000 0.00 0.00 0.00 2.15
12 13 0.824109 TCCGCTTCACTCCCACTATG 59.176 55.000 0.00 0.00 0.00 2.23
13 14 1.414181 CATCCGCTTCACTCCCACTAT 59.586 52.381 0.00 0.00 0.00 2.12
14 15 0.824109 CATCCGCTTCACTCCCACTA 59.176 55.000 0.00 0.00 0.00 2.74
15 16 0.904865 TCATCCGCTTCACTCCCACT 60.905 55.000 0.00 0.00 0.00 4.00
16 17 0.179000 ATCATCCGCTTCACTCCCAC 59.821 55.000 0.00 0.00 0.00 4.61
17 18 0.178767 CATCATCCGCTTCACTCCCA 59.821 55.000 0.00 0.00 0.00 4.37
18 19 0.465705 TCATCATCCGCTTCACTCCC 59.534 55.000 0.00 0.00 0.00 4.30
19 20 1.576356 GTCATCATCCGCTTCACTCC 58.424 55.000 0.00 0.00 0.00 3.85
20 21 1.202302 TCGTCATCATCCGCTTCACTC 60.202 52.381 0.00 0.00 0.00 3.51
21 22 0.817654 TCGTCATCATCCGCTTCACT 59.182 50.000 0.00 0.00 0.00 3.41
22 23 0.924090 GTCGTCATCATCCGCTTCAC 59.076 55.000 0.00 0.00 0.00 3.18
23 24 0.817654 AGTCGTCATCATCCGCTTCA 59.182 50.000 0.00 0.00 0.00 3.02
24 25 1.202302 TCAGTCGTCATCATCCGCTTC 60.202 52.381 0.00 0.00 0.00 3.86
25 26 0.817654 TCAGTCGTCATCATCCGCTT 59.182 50.000 0.00 0.00 0.00 4.68
26 27 0.817654 TTCAGTCGTCATCATCCGCT 59.182 50.000 0.00 0.00 0.00 5.52
27 28 1.858091 ATTCAGTCGTCATCATCCGC 58.142 50.000 0.00 0.00 0.00 5.54
28 29 3.865164 TCAAATTCAGTCGTCATCATCCG 59.135 43.478 0.00 0.00 0.00 4.18
29 30 5.352569 ACTTCAAATTCAGTCGTCATCATCC 59.647 40.000 0.00 0.00 0.00 3.51
30 31 6.312426 AGACTTCAAATTCAGTCGTCATCATC 59.688 38.462 6.71 0.00 43.69 2.92
31 32 6.169094 AGACTTCAAATTCAGTCGTCATCAT 58.831 36.000 6.71 0.00 43.69 2.45
32 33 5.541845 AGACTTCAAATTCAGTCGTCATCA 58.458 37.500 6.71 0.00 43.69 3.07
33 34 6.302615 CAAGACTTCAAATTCAGTCGTCATC 58.697 40.000 6.71 0.00 43.69 2.92
34 35 5.334414 GCAAGACTTCAAATTCAGTCGTCAT 60.334 40.000 6.71 0.00 43.69 3.06
35 36 4.024893 GCAAGACTTCAAATTCAGTCGTCA 60.025 41.667 6.71 0.00 43.69 4.35
36 37 4.024893 TGCAAGACTTCAAATTCAGTCGTC 60.025 41.667 6.71 0.00 43.69 4.20
37 38 3.876914 TGCAAGACTTCAAATTCAGTCGT 59.123 39.130 6.71 2.36 43.69 4.34
38 39 4.024556 AGTGCAAGACTTCAAATTCAGTCG 60.025 41.667 0.00 0.00 43.69 4.18
39 40 5.429957 AGTGCAAGACTTCAAATTCAGTC 57.570 39.130 0.00 4.83 39.92 3.51
40 41 5.841957 AAGTGCAAGACTTCAAATTCAGT 57.158 34.783 0.00 0.00 41.37 3.41
51 52 5.189180 AGAAAAAGACAGAAGTGCAAGACT 58.811 37.500 0.00 0.00 35.94 3.24
52 53 5.491635 AGAAAAAGACAGAAGTGCAAGAC 57.508 39.130 0.00 0.00 0.00 3.01
53 54 4.576463 GGAGAAAAAGACAGAAGTGCAAGA 59.424 41.667 0.00 0.00 0.00 3.02
54 55 4.553547 CGGAGAAAAAGACAGAAGTGCAAG 60.554 45.833 0.00 0.00 0.00 4.01
55 56 3.312421 CGGAGAAAAAGACAGAAGTGCAA 59.688 43.478 0.00 0.00 0.00 4.08
56 57 2.872245 CGGAGAAAAAGACAGAAGTGCA 59.128 45.455 0.00 0.00 0.00 4.57
57 58 2.349912 GCGGAGAAAAAGACAGAAGTGC 60.350 50.000 0.00 0.00 0.00 4.40
58 59 3.134458 AGCGGAGAAAAAGACAGAAGTG 58.866 45.455 0.00 0.00 0.00 3.16
59 60 3.477210 AGCGGAGAAAAAGACAGAAGT 57.523 42.857 0.00 0.00 0.00 3.01
60 61 4.307432 TGTAGCGGAGAAAAAGACAGAAG 58.693 43.478 0.00 0.00 0.00 2.85
61 62 4.330944 TGTAGCGGAGAAAAAGACAGAA 57.669 40.909 0.00 0.00 0.00 3.02
62 63 4.021456 TGATGTAGCGGAGAAAAAGACAGA 60.021 41.667 0.00 0.00 0.00 3.41
63 64 4.245660 TGATGTAGCGGAGAAAAAGACAG 58.754 43.478 0.00 0.00 0.00 3.51
64 65 4.265904 TGATGTAGCGGAGAAAAAGACA 57.734 40.909 0.00 0.00 0.00 3.41
65 66 4.870426 TGATGATGTAGCGGAGAAAAAGAC 59.130 41.667 0.00 0.00 0.00 3.01
66 67 5.084818 TGATGATGTAGCGGAGAAAAAGA 57.915 39.130 0.00 0.00 0.00 2.52
67 68 5.525012 TGATGATGATGTAGCGGAGAAAAAG 59.475 40.000 0.00 0.00 0.00 2.27
68 69 5.427378 TGATGATGATGTAGCGGAGAAAAA 58.573 37.500 0.00 0.00 0.00 1.94
69 70 5.022282 TGATGATGATGTAGCGGAGAAAA 57.978 39.130 0.00 0.00 0.00 2.29
70 71 4.670896 TGATGATGATGTAGCGGAGAAA 57.329 40.909 0.00 0.00 0.00 2.52
71 72 4.100035 AGTTGATGATGATGTAGCGGAGAA 59.900 41.667 0.00 0.00 0.00 2.87
72 73 3.638627 AGTTGATGATGATGTAGCGGAGA 59.361 43.478 0.00 0.00 0.00 3.71
73 74 3.739810 CAGTTGATGATGATGTAGCGGAG 59.260 47.826 0.00 0.00 0.00 4.63
74 75 3.721035 CAGTTGATGATGATGTAGCGGA 58.279 45.455 0.00 0.00 0.00 5.54
75 76 2.222678 GCAGTTGATGATGATGTAGCGG 59.777 50.000 0.00 0.00 0.00 5.52
76 77 2.097056 CGCAGTTGATGATGATGTAGCG 60.097 50.000 0.00 0.00 35.42 4.26
77 78 2.868583 ACGCAGTTGATGATGATGTAGC 59.131 45.455 0.00 0.00 37.78 3.58
93 94 0.169009 TCGACACATCAGAGACGCAG 59.831 55.000 0.00 0.00 0.00 5.18
94 95 0.109735 GTCGACACATCAGAGACGCA 60.110 55.000 11.55 0.00 0.00 5.24
95 96 0.109735 TGTCGACACATCAGAGACGC 60.110 55.000 15.76 0.00 34.82 5.19
96 97 1.607713 GTGTCGACACATCAGAGACG 58.392 55.000 37.16 0.00 45.75 4.18
130 131 3.112205 ATCCCCGGCAGAGTGATGC 62.112 63.158 0.00 0.00 45.74 3.91
131 132 1.227764 CATCCCCGGCAGAGTGATG 60.228 63.158 0.00 0.00 0.00 3.07
132 133 0.398522 TACATCCCCGGCAGAGTGAT 60.399 55.000 0.00 0.00 0.00 3.06
133 134 0.616395 TTACATCCCCGGCAGAGTGA 60.616 55.000 0.00 0.00 0.00 3.41
134 135 0.469917 ATTACATCCCCGGCAGAGTG 59.530 55.000 0.00 0.00 0.00 3.51
135 136 1.971357 CTATTACATCCCCGGCAGAGT 59.029 52.381 0.00 0.00 0.00 3.24
136 137 1.971357 ACTATTACATCCCCGGCAGAG 59.029 52.381 0.00 0.00 0.00 3.35
137 138 2.097110 ACTATTACATCCCCGGCAGA 57.903 50.000 0.00 0.00 0.00 4.26
138 139 4.315803 CTTTACTATTACATCCCCGGCAG 58.684 47.826 0.00 0.00 0.00 4.85
139 140 3.495453 GCTTTACTATTACATCCCCGGCA 60.495 47.826 0.00 0.00 0.00 5.69
140 141 3.072211 GCTTTACTATTACATCCCCGGC 58.928 50.000 0.00 0.00 0.00 6.13
193 194 0.252197 ACCAAATACCACGAGCCCTC 59.748 55.000 0.00 0.00 0.00 4.30
194 195 0.035439 CACCAAATACCACGAGCCCT 60.035 55.000 0.00 0.00 0.00 5.19
206 207 4.531351 CCCCCGTTTCCACCAAAT 57.469 55.556 0.00 0.00 0.00 2.32
242 243 2.251409 TATACTCAGTCCCGAGTCGG 57.749 55.000 25.12 25.12 42.70 4.79
258 259 4.193090 CCAACCAAACCGTGTGCTATATA 58.807 43.478 0.00 0.00 0.00 0.86
259 260 3.013921 CCAACCAAACCGTGTGCTATAT 58.986 45.455 0.00 0.00 0.00 0.86
260 261 2.224572 ACCAACCAAACCGTGTGCTATA 60.225 45.455 0.00 0.00 0.00 1.31
261 262 1.243902 CCAACCAAACCGTGTGCTAT 58.756 50.000 0.00 0.00 0.00 2.97
313 320 0.875059 CGGAGCAAGAGGACAAAACC 59.125 55.000 0.00 0.00 0.00 3.27
315 322 0.250727 CCCGGAGCAAGAGGACAAAA 60.251 55.000 0.73 0.00 0.00 2.44
333 340 2.440247 CACCCCGATTTCCCAGCC 60.440 66.667 0.00 0.00 0.00 4.85
344 351 2.353573 CAAACCCTACCCACCCCG 59.646 66.667 0.00 0.00 0.00 5.73
352 359 0.391263 CACTCGAGGCCAAACCCTAC 60.391 60.000 18.41 0.00 40.58 3.18
353 360 0.543410 TCACTCGAGGCCAAACCCTA 60.543 55.000 18.41 0.00 40.58 3.53
354 361 1.831652 CTCACTCGAGGCCAAACCCT 61.832 60.000 18.41 0.00 40.58 4.34
355 362 1.376037 CTCACTCGAGGCCAAACCC 60.376 63.158 18.41 0.00 40.58 4.11
356 363 2.035442 GCTCACTCGAGGCCAAACC 61.035 63.158 18.41 0.00 39.88 3.27
357 364 1.301716 TGCTCACTCGAGGCCAAAC 60.302 57.895 18.41 1.47 39.88 2.93
366 373 1.564622 CAAACCGTGTGCTCACTCG 59.435 57.895 16.23 15.05 44.80 4.18
377 384 1.076850 AAACCCGAACCCAAACCGT 60.077 52.632 0.00 0.00 0.00 4.83
383 390 1.075836 CCATCCAAACCCGAACCCA 59.924 57.895 0.00 0.00 0.00 4.51
389 396 2.425569 CCATGCCCATCCAAACCCG 61.426 63.158 0.00 0.00 0.00 5.28
394 401 0.822944 CGTATGCCATGCCCATCCAA 60.823 55.000 0.96 0.00 0.00 3.53
395 402 1.228215 CGTATGCCATGCCCATCCA 60.228 57.895 0.96 0.00 0.00 3.41
396 403 1.228245 ACGTATGCCATGCCCATCC 60.228 57.895 0.00 0.00 0.00 3.51
397 404 1.951510 CACGTATGCCATGCCCATC 59.048 57.895 0.00 0.00 0.00 3.51
421 430 1.145377 GTTCCACGGCCGTCCATAT 59.855 57.895 31.80 1.65 0.00 1.78
422 431 2.580276 GTTCCACGGCCGTCCATA 59.420 61.111 31.80 11.34 0.00 2.74
423 432 4.404098 GGTTCCACGGCCGTCCAT 62.404 66.667 31.80 3.15 0.00 3.41
426 435 2.438951 TACTTGGTTCCACGGCCGTC 62.439 60.000 31.80 17.78 0.00 4.79
427 436 2.509651 TACTTGGTTCCACGGCCGT 61.510 57.895 28.70 28.70 0.00 5.68
428 437 2.030958 GTACTTGGTTCCACGGCCG 61.031 63.158 26.86 26.86 0.00 6.13
429 438 2.030958 CGTACTTGGTTCCACGGCC 61.031 63.158 0.00 0.00 0.00 6.13
430 439 1.287041 GACGTACTTGGTTCCACGGC 61.287 60.000 0.00 0.00 38.67 5.68
431 440 1.005294 CGACGTACTTGGTTCCACGG 61.005 60.000 0.00 0.00 38.67 4.94
432 441 1.611592 GCGACGTACTTGGTTCCACG 61.612 60.000 0.00 0.00 40.15 4.94
433 442 1.611592 CGCGACGTACTTGGTTCCAC 61.612 60.000 0.00 0.00 0.00 4.02
434 443 1.372004 CGCGACGTACTTGGTTCCA 60.372 57.895 0.00 0.00 0.00 3.53
435 444 1.081242 TCGCGACGTACTTGGTTCC 60.081 57.895 3.71 0.00 0.00 3.62
436 445 2.057183 GTCGCGACGTACTTGGTTC 58.943 57.895 25.19 0.00 0.00 3.62
437 446 4.233408 GTCGCGACGTACTTGGTT 57.767 55.556 25.19 0.00 0.00 3.67
450 459 4.083862 AAAGGCTCCCCTCGTCGC 62.084 66.667 0.00 0.00 41.90 5.19
451 460 2.125512 CAAAGGCTCCCCTCGTCG 60.126 66.667 0.00 0.00 41.90 5.12
452 461 2.436824 GCAAAGGCTCCCCTCGTC 60.437 66.667 0.00 0.00 41.90 4.20
462 471 0.319297 CAAGCAACCAGAGCAAAGGC 60.319 55.000 0.00 0.00 41.61 4.35
463 472 0.316204 CCAAGCAACCAGAGCAAAGG 59.684 55.000 0.00 0.00 0.00 3.11
464 473 0.319297 GCCAAGCAACCAGAGCAAAG 60.319 55.000 0.00 0.00 0.00 2.77
465 474 1.042003 TGCCAAGCAACCAGAGCAAA 61.042 50.000 0.00 0.00 34.76 3.68
466 475 1.455402 TGCCAAGCAACCAGAGCAA 60.455 52.632 0.00 0.00 34.76 3.91
467 476 1.900016 CTGCCAAGCAACCAGAGCA 60.900 57.895 0.00 0.00 38.41 4.26
468 477 2.960170 CTGCCAAGCAACCAGAGC 59.040 61.111 0.00 0.00 38.41 4.09
478 487 1.682854 TCAACTTTTCCAGCTGCCAAG 59.317 47.619 8.66 11.74 0.00 3.61
479 488 1.774110 TCAACTTTTCCAGCTGCCAA 58.226 45.000 8.66 0.00 0.00 4.52
480 489 1.774110 TTCAACTTTTCCAGCTGCCA 58.226 45.000 8.66 0.00 0.00 4.92
481 490 3.507622 ACTATTCAACTTTTCCAGCTGCC 59.492 43.478 8.66 0.00 0.00 4.85
482 491 4.773323 ACTATTCAACTTTTCCAGCTGC 57.227 40.909 8.66 0.00 0.00 5.25
483 492 6.317789 TCAACTATTCAACTTTTCCAGCTG 57.682 37.500 6.78 6.78 0.00 4.24
484 493 6.071728 CCATCAACTATTCAACTTTTCCAGCT 60.072 38.462 0.00 0.00 0.00 4.24
485 494 6.095377 CCATCAACTATTCAACTTTTCCAGC 58.905 40.000 0.00 0.00 0.00 4.85
490 499 4.222810 GCCCCCATCAACTATTCAACTTTT 59.777 41.667 0.00 0.00 0.00 2.27
525 534 2.355132 ACTCTACTCTGGCGACGTAATG 59.645 50.000 0.00 0.00 0.00 1.90
534 543 5.070047 AGACTCTACTCTACTCTACTCTGGC 59.930 48.000 0.00 0.00 0.00 4.85
535 544 6.462487 CCAGACTCTACTCTACTCTACTCTGG 60.462 50.000 0.00 0.00 36.22 3.86
536 545 6.097839 ACCAGACTCTACTCTACTCTACTCTG 59.902 46.154 0.00 0.00 0.00 3.35
590 603 3.507162 TCCCAAACTGAAATGAGCTCA 57.493 42.857 20.79 20.79 0.00 4.26
658 680 8.700722 TCATTATGAAAATTCCCAAACAATCG 57.299 30.769 0.00 0.00 0.00 3.34
746 770 5.865552 AGCACAAAATCATGAAAAAGATCGG 59.134 36.000 0.00 0.00 0.00 4.18
782 806 3.181506 GCTCTTGTTTTCCATGTCGATCC 60.182 47.826 0.00 0.00 0.00 3.36
791 815 2.091885 ACCTCCTTGCTCTTGTTTTCCA 60.092 45.455 0.00 0.00 0.00 3.53
793 817 2.294512 CCACCTCCTTGCTCTTGTTTTC 59.705 50.000 0.00 0.00 0.00 2.29
802 826 4.335647 CGGCACCACCTCCTTGCT 62.336 66.667 0.00 0.00 36.46 3.91
820 844 1.108776 CCCTTGTCATGCTCCATTGG 58.891 55.000 0.00 0.00 0.00 3.16
896 920 1.667830 AACATGTCGCCGTCTGTGG 60.668 57.895 0.00 0.00 0.00 4.17
910 934 4.115199 GGGCTCCTCCGGCAACAT 62.115 66.667 0.00 0.00 34.94 2.71
934 958 0.240945 CCATTGTTCCGACACTTGCC 59.759 55.000 0.00 0.00 34.98 4.52
940 964 0.687920 TAGTGGCCATTGTTCCGACA 59.312 50.000 9.72 0.00 0.00 4.35
949 973 2.092212 CCTTCTCATGGTAGTGGCCATT 60.092 50.000 9.72 7.59 46.33 3.16
951 975 0.911769 CCTTCTCATGGTAGTGGCCA 59.088 55.000 0.00 0.00 43.48 5.36
960 984 2.153898 TTGGGCCACCCTTCTCATGG 62.154 60.000 5.23 0.00 45.70 3.66
975 999 2.094078 CACATTGCATTAGTGGGTTGGG 60.094 50.000 5.95 0.00 0.00 4.12
981 1005 6.441274 GGTCATAATCACATTGCATTAGTGG 58.559 40.000 12.05 0.00 34.17 4.00
986 1010 3.318839 CGGGGTCATAATCACATTGCATT 59.681 43.478 0.00 0.00 0.00 3.56
993 1017 1.837439 AGCTTCGGGGTCATAATCACA 59.163 47.619 0.00 0.00 0.00 3.58
1030 1054 7.067251 CAGGAAGTACTTCGTAAAGTCTAGGAT 59.933 40.741 25.81 0.00 44.64 3.24
1031 1055 6.373774 CAGGAAGTACTTCGTAAAGTCTAGGA 59.626 42.308 25.81 0.00 44.64 2.94
1059 1083 1.300620 CTTGAACTCCGTCGGCACA 60.301 57.895 6.34 0.98 0.00 4.57
1063 1087 0.032952 TTGACCTTGAACTCCGTCGG 59.967 55.000 4.39 4.39 0.00 4.79
1078 1102 1.533129 GCAACCGGTGTTTGTCTTGAC 60.533 52.381 8.52 0.00 30.42 3.18
1118 1142 1.077716 ACCCTGCCGTTAATCAGCC 60.078 57.895 0.00 0.00 0.00 4.85
1143 1167 2.438434 GTGGCCCAACCCTGATCG 60.438 66.667 0.00 0.00 37.83 3.69
1165 1189 1.135139 CTTGATCTGGTGGACGACGAT 59.865 52.381 0.00 0.00 0.00 3.73
1166 1190 0.526211 CTTGATCTGGTGGACGACGA 59.474 55.000 0.00 0.00 0.00 4.20
1176 1200 6.266330 TCACTATGTACCTGATCTTGATCTGG 59.734 42.308 25.15 25.15 42.98 3.86
1194 1218 2.416547 CGGCAAGTTGAAGGTCACTATG 59.583 50.000 7.16 0.00 0.00 2.23
1197 1221 0.468226 TCGGCAAGTTGAAGGTCACT 59.532 50.000 7.16 0.00 0.00 3.41
1209 1233 2.317609 CGTGTTGGGAGTCGGCAAG 61.318 63.158 0.00 0.00 0.00 4.01
1214 1238 0.859232 CTTGAACGTGTTGGGAGTCG 59.141 55.000 0.00 0.00 0.00 4.18
1228 1252 4.452114 CGTCATTGAAGACATGACCTTGAA 59.548 41.667 0.00 3.40 41.01 2.69
1271 1295 0.034059 CCTTCTATTGCGCGGATCCT 59.966 55.000 8.83 0.00 0.00 3.24
1283 1307 1.066587 GAGCGCGACAGCCTTCTAT 59.933 57.895 12.10 0.00 41.18 1.98
1349 1373 3.190849 CATGGCTGTGGCGACGAG 61.191 66.667 0.00 0.00 39.81 4.18
1431 1455 4.742201 CGAGGTCCCGGCTGTGTG 62.742 72.222 0.00 0.00 0.00 3.82
1432 1456 4.988716 TCGAGGTCCCGGCTGTGT 62.989 66.667 0.00 0.00 0.00 3.72
1436 1460 2.519780 GATCTCGAGGTCCCGGCT 60.520 66.667 15.13 0.00 0.00 5.52
1530 1554 2.443016 CCCTCTCTCCCCTCACCG 60.443 72.222 0.00 0.00 0.00 4.94
1544 1568 1.947254 TAGGGCCCTCCTTCTCCCT 60.947 63.158 32.80 1.90 45.47 4.20
1632 1656 4.579340 GGCGGACGGATCTATAGATATTGA 59.421 45.833 15.31 0.00 34.37 2.57
1642 1666 1.410004 ATCAAAGGCGGACGGATCTA 58.590 50.000 0.00 0.00 0.00 1.98
1653 1677 3.616821 GGCCAAACGAAAATATCAAAGGC 59.383 43.478 0.00 0.00 37.69 4.35
1655 1679 4.864247 CCAGGCCAAACGAAAATATCAAAG 59.136 41.667 5.01 0.00 0.00 2.77
1657 1681 4.082845 TCCAGGCCAAACGAAAATATCAA 58.917 39.130 5.01 0.00 0.00 2.57
1728 1752 1.766496 ACATATAGGTGGTTCCACGGG 59.234 52.381 14.63 4.42 37.79 5.28
1746 1770 2.707849 GGCTCCCTTCGTCGCTACA 61.708 63.158 0.00 0.00 0.00 2.74
1747 1771 2.104530 GGCTCCCTTCGTCGCTAC 59.895 66.667 0.00 0.00 0.00 3.58
1749 1773 3.453679 GAGGCTCCCTTCGTCGCT 61.454 66.667 2.15 0.00 31.76 4.93
1752 1776 2.185608 GCAGAGGCTCCCTTCGTC 59.814 66.667 11.71 0.00 31.76 4.20
1784 1808 0.890542 ATCAACTTTGCCAGCTGCGA 60.891 50.000 8.66 0.64 45.60 5.10
1786 1810 0.599558 TCATCAACTTTGCCAGCTGC 59.400 50.000 8.66 4.57 41.77 5.25
1787 1811 1.201647 CCTCATCAACTTTGCCAGCTG 59.798 52.381 6.78 6.78 0.00 4.24
1788 1812 1.542492 CCTCATCAACTTTGCCAGCT 58.458 50.000 0.00 0.00 0.00 4.24
1789 1813 0.529378 CCCTCATCAACTTTGCCAGC 59.471 55.000 0.00 0.00 0.00 4.85
1790 1814 0.529378 GCCCTCATCAACTTTGCCAG 59.471 55.000 0.00 0.00 0.00 4.85
1791 1815 0.178967 TGCCCTCATCAACTTTGCCA 60.179 50.000 0.00 0.00 0.00 4.92
1792 1816 1.135721 GATGCCCTCATCAACTTTGCC 59.864 52.381 0.81 0.00 46.44 4.52
1793 1817 2.573941 GATGCCCTCATCAACTTTGC 57.426 50.000 0.81 0.00 46.44 3.68
1802 1826 1.848388 TGATTGGACTGATGCCCTCAT 59.152 47.619 0.00 0.00 32.10 2.90
1803 1827 1.288188 TGATTGGACTGATGCCCTCA 58.712 50.000 0.00 0.00 0.00 3.86
1804 1828 2.653234 ATGATTGGACTGATGCCCTC 57.347 50.000 0.00 0.00 0.00 4.30
1805 1829 3.745480 CGTAATGATTGGACTGATGCCCT 60.745 47.826 0.00 0.00 0.00 5.19
1806 1830 2.549754 CGTAATGATTGGACTGATGCCC 59.450 50.000 0.00 0.00 0.00 5.36
1807 1831 3.206150 ACGTAATGATTGGACTGATGCC 58.794 45.455 0.00 0.00 0.00 4.40
1808 1832 3.871006 TGACGTAATGATTGGACTGATGC 59.129 43.478 0.00 0.00 0.00 3.91
1809 1833 4.271049 GGTGACGTAATGATTGGACTGATG 59.729 45.833 0.00 0.00 0.00 3.07
1810 1834 4.081142 TGGTGACGTAATGATTGGACTGAT 60.081 41.667 0.00 0.00 0.00 2.90
1811 1835 3.259625 TGGTGACGTAATGATTGGACTGA 59.740 43.478 0.00 0.00 0.00 3.41
1812 1836 3.595173 TGGTGACGTAATGATTGGACTG 58.405 45.455 0.00 0.00 0.00 3.51
1813 1837 3.513912 TCTGGTGACGTAATGATTGGACT 59.486 43.478 0.00 0.00 0.00 3.85
1814 1838 3.857052 TCTGGTGACGTAATGATTGGAC 58.143 45.455 0.00 0.00 0.00 4.02
1815 1839 4.545208 TTCTGGTGACGTAATGATTGGA 57.455 40.909 0.00 0.00 0.00 3.53
1816 1840 4.695455 ACTTTCTGGTGACGTAATGATTGG 59.305 41.667 0.00 0.00 0.00 3.16
1817 1841 5.621422 CACTTTCTGGTGACGTAATGATTG 58.379 41.667 0.00 0.00 39.34 2.67
1818 1842 4.154195 GCACTTTCTGGTGACGTAATGATT 59.846 41.667 0.00 0.00 39.34 2.57
1867 1891 3.763897 GGCTTGTACTGTTCATCCCAAAT 59.236 43.478 0.00 0.00 0.00 2.32
1894 1918 6.183360 GCAAACACTCAAAACATTTGTTGGAT 60.183 34.615 0.00 0.00 38.44 3.41
1897 1921 5.014483 CGCAAACACTCAAAACATTTGTTG 58.986 37.500 0.00 4.76 38.44 3.33
1919 1943 6.951530 GCATGTTGTTTCATGATGAAAATTCG 59.048 34.615 20.94 9.70 46.53 3.34
1943 1967 0.382515 TTTTGCCACCACTTGTACGC 59.617 50.000 0.00 0.00 0.00 4.42
2123 2165 5.291178 TCAAATGCTTTTGGATGAACAGTG 58.709 37.500 21.07 0.00 42.10 3.66
2175 2217 1.747924 GGGAAAGAGATGCCTTCAAGC 59.252 52.381 0.00 0.00 0.00 4.01
2228 2270 2.544267 GAGGAAAATGCTTATCGGTCCG 59.456 50.000 4.39 4.39 0.00 4.79
2262 2304 5.696822 CAAGTCAAGTGAGAAATGATGGTG 58.303 41.667 0.00 0.00 0.00 4.17
2263 2305 4.217118 GCAAGTCAAGTGAGAAATGATGGT 59.783 41.667 0.00 0.00 0.00 3.55
2269 2312 3.817647 GTGGAGCAAGTCAAGTGAGAAAT 59.182 43.478 0.00 0.00 0.00 2.17
2302 2345 2.434185 ACGGGCACATGTACAGCG 60.434 61.111 0.00 0.00 0.00 5.18
2305 2348 0.390603 GCTACACGGGCACATGTACA 60.391 55.000 0.00 0.00 31.57 2.90
2310 2353 0.107848 GGTTAGCTACACGGGCACAT 60.108 55.000 0.00 0.00 0.00 3.21
2315 2358 1.968050 CTGGGGGTTAGCTACACGGG 61.968 65.000 0.00 0.00 0.00 5.28
2328 2371 0.951558 CGTTGTGAAAACTCTGGGGG 59.048 55.000 0.00 0.00 0.00 5.40
2332 2375 5.657470 TCAGAATCGTTGTGAAAACTCTG 57.343 39.130 0.00 0.00 29.08 3.35
2344 2387 5.745227 AGGGTTTCACATATCAGAATCGTT 58.255 37.500 0.00 0.00 0.00 3.85
2438 2481 8.383619 GCACTAACTCAGTATTTGTCACATTAG 58.616 37.037 0.00 0.00 34.98 1.73
2449 2492 5.923733 ACTAGCTGCACTAACTCAGTATT 57.076 39.130 1.02 0.00 34.98 1.89
2486 2529 7.942990 AGGTTTACTATACAGCTCAGTATGTC 58.057 38.462 6.91 0.00 36.23 3.06


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

AutoCloner maintained by Alex Coulton.