Multiple sequence alignment - TraesCS6A01G189000

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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 TraesCS6A01G189000 chr6A 100.000 3091 0 0 1 3091 233811942 233815032 0.000000e+00 5709
1 TraesCS6A01G189000 chr6A 86.747 166 15 5 1291 1449 77155960 77156125 8.810000e-41 178
2 TraesCS6A01G189000 chr4A 96.307 2681 58 18 448 3091 11705421 11708097 0.000000e+00 4364
3 TraesCS6A01G189000 chr4A 91.176 816 62 4 1450 2256 319831736 319830922 0.000000e+00 1099
4 TraesCS6A01G189000 chr4A 93.121 596 32 2 621 1207 28272559 28273154 0.000000e+00 865
5 TraesCS6A01G189000 chr2B 93.375 2566 106 22 544 3091 621182126 621184645 0.000000e+00 3738
6 TraesCS6A01G189000 chr2B 85.399 363 30 7 1 358 217286003 217286347 3.790000e-94 355
7 TraesCS6A01G189000 chr7D 97.840 1667 33 1 1425 3091 66988406 66986743 0.000000e+00 2876
8 TraesCS6A01G189000 chr7D 91.551 864 24 17 449 1301 66989677 66988852 0.000000e+00 1146
9 TraesCS6A01G189000 chr4B 89.933 1639 149 10 1450 3077 550673906 550675539 0.000000e+00 2098
10 TraesCS6A01G189000 chr4B 91.092 1538 123 9 1450 2978 16551846 16553378 0.000000e+00 2069
11 TraesCS6A01G189000 chr4B 92.308 221 13 2 449 666 104746182 104745963 8.320000e-81 311
12 TraesCS6A01G189000 chr7A 89.762 1641 145 15 1450 3075 228677161 228675529 0.000000e+00 2078
13 TraesCS6A01G189000 chr7A 90.441 816 68 4 1450 2256 439798394 439797580 0.000000e+00 1066
14 TraesCS6A01G189000 chr7A 85.000 180 20 3 186 358 70092611 70092790 3.170000e-40 176
15 TraesCS6A01G189000 chr7A 98.462 65 1 0 57 121 70089679 70089743 7.000000e-22 115
16 TraesCS6A01G189000 chr3B 91.027 1538 124 9 1450 2978 511031358 511029826 0.000000e+00 2063
17 TraesCS6A01G189000 chr3B 93.481 721 36 4 496 1207 395846864 395846146 0.000000e+00 1061
18 TraesCS6A01G189000 chr2A 96.543 1244 40 3 1849 3091 642960941 642959700 0.000000e+00 2056
19 TraesCS6A01G189000 chr2A 89.007 846 39 18 448 1293 642962444 642961653 0.000000e+00 998
20 TraesCS6A01G189000 chr2A 92.025 489 21 3 1335 1805 642961430 642960942 0.000000e+00 671
21 TraesCS6A01G189000 chr2A 91.791 134 11 0 448 581 572446806 572446939 1.460000e-43 187
22 TraesCS6A01G189000 chr1A 95.133 1274 34 7 1316 2564 121881032 121879762 0.000000e+00 1984
23 TraesCS6A01G189000 chr1A 86.978 814 46 24 485 1293 121882113 121881355 0.000000e+00 861
24 TraesCS6A01G189000 chr7B 93.571 871 53 2 2221 3091 725790700 725791567 0.000000e+00 1295
25 TraesCS6A01G189000 chr7B 95.074 406 20 0 802 1207 553229356 553229761 9.350000e-180 640
26 TraesCS6A01G189000 chr7B 78.788 363 51 18 1 356 718930195 718929852 1.440000e-53 220
27 TraesCS6A01G189000 chrUn 92.953 596 33 2 621 1207 391724490 391725085 0.000000e+00 859
28 TraesCS6A01G189000 chr4D 90.251 359 19 9 7 361 507451497 507451151 3.630000e-124 455
29 TraesCS6A01G189000 chr5D 90.000 360 20 8 3 358 15889920 15890267 4.700000e-123 451
30 TraesCS6A01G189000 chr1D 88.889 360 27 10 1 358 50444626 50444974 6.120000e-117 431
31 TraesCS6A01G189000 chr5A 94.697 132 7 0 450 581 554337233 554337364 4.040000e-49 206
32 TraesCS6A01G189000 chr5B 92.481 133 10 0 449 581 599529183 599529051 1.130000e-44 191
33 TraesCS6A01G189000 chr5B 92.481 133 10 0 449 581 599545469 599545337 1.130000e-44 191
34 TraesCS6A01G189000 chr3A 90.833 120 8 1 1 117 675682053 675682172 1.150000e-34 158


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 TraesCS6A01G189000 chr6A 233811942 233815032 3090 False 5709.000000 5709 100.0000 1 3091 1 chr6A.!!$F2 3090
1 TraesCS6A01G189000 chr4A 11705421 11708097 2676 False 4364.000000 4364 96.3070 448 3091 1 chr4A.!!$F1 2643
2 TraesCS6A01G189000 chr4A 319830922 319831736 814 True 1099.000000 1099 91.1760 1450 2256 1 chr4A.!!$R1 806
3 TraesCS6A01G189000 chr4A 28272559 28273154 595 False 865.000000 865 93.1210 621 1207 1 chr4A.!!$F2 586
4 TraesCS6A01G189000 chr2B 621182126 621184645 2519 False 3738.000000 3738 93.3750 544 3091 1 chr2B.!!$F2 2547
5 TraesCS6A01G189000 chr7D 66986743 66989677 2934 True 2011.000000 2876 94.6955 449 3091 2 chr7D.!!$R1 2642
6 TraesCS6A01G189000 chr4B 550673906 550675539 1633 False 2098.000000 2098 89.9330 1450 3077 1 chr4B.!!$F2 1627
7 TraesCS6A01G189000 chr4B 16551846 16553378 1532 False 2069.000000 2069 91.0920 1450 2978 1 chr4B.!!$F1 1528
8 TraesCS6A01G189000 chr7A 228675529 228677161 1632 True 2078.000000 2078 89.7620 1450 3075 1 chr7A.!!$R1 1625
9 TraesCS6A01G189000 chr7A 439797580 439798394 814 True 1066.000000 1066 90.4410 1450 2256 1 chr7A.!!$R2 806
10 TraesCS6A01G189000 chr3B 511029826 511031358 1532 True 2063.000000 2063 91.0270 1450 2978 1 chr3B.!!$R2 1528
11 TraesCS6A01G189000 chr3B 395846146 395846864 718 True 1061.000000 1061 93.4810 496 1207 1 chr3B.!!$R1 711
12 TraesCS6A01G189000 chr2A 642959700 642962444 2744 True 1241.666667 2056 92.5250 448 3091 3 chr2A.!!$R1 2643
13 TraesCS6A01G189000 chr1A 121879762 121882113 2351 True 1422.500000 1984 91.0555 485 2564 2 chr1A.!!$R1 2079
14 TraesCS6A01G189000 chr7B 725790700 725791567 867 False 1295.000000 1295 93.5710 2221 3091 1 chr7B.!!$F2 870
15 TraesCS6A01G189000 chrUn 391724490 391725085 595 False 859.000000 859 92.9530 621 1207 1 chrUn.!!$F1 586

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
404 405 0.036671 ACCATTCGGTTCGAGGGAAC 60.037 55.0 14.03 0.0 46.31 3.62 F
428 429 0.321671 CACCCAGTCCTATATGCGGG 59.678 60.0 0.00 0.0 39.72 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1372 1760 6.861144 TCTCTTTCATCAGTCACATACAGAG 58.139 40.000 0.0 0.0 0.0 3.35 R
2198 2643 7.811236 ACTGTGATAGAGAAACAAAATTGCATG 59.189 33.333 0.0 0.0 0.0 4.06 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
21 22 3.975168 ACCGCAGTCTGTTATTAACCT 57.025 42.857 0.93 0.00 0.00 3.50
22 23 4.281898 ACCGCAGTCTGTTATTAACCTT 57.718 40.909 0.93 0.00 0.00 3.50
23 24 4.648651 ACCGCAGTCTGTTATTAACCTTT 58.351 39.130 0.93 0.00 0.00 3.11
24 25 5.067954 ACCGCAGTCTGTTATTAACCTTTT 58.932 37.500 0.93 0.00 0.00 2.27
25 26 5.180680 ACCGCAGTCTGTTATTAACCTTTTC 59.819 40.000 0.93 0.00 0.00 2.29
26 27 5.180492 CCGCAGTCTGTTATTAACCTTTTCA 59.820 40.000 0.93 0.00 0.00 2.69
27 28 6.077838 CGCAGTCTGTTATTAACCTTTTCAC 58.922 40.000 0.93 0.00 0.00 3.18
28 29 6.073222 CGCAGTCTGTTATTAACCTTTTCACT 60.073 38.462 0.93 0.00 0.00 3.41
29 30 7.519970 CGCAGTCTGTTATTAACCTTTTCACTT 60.520 37.037 0.93 0.00 0.00 3.16
30 31 8.135529 GCAGTCTGTTATTAACCTTTTCACTTT 58.864 33.333 0.93 0.00 0.00 2.66
31 32 9.450807 CAGTCTGTTATTAACCTTTTCACTTTG 57.549 33.333 4.17 0.00 0.00 2.77
32 33 9.185680 AGTCTGTTATTAACCTTTTCACTTTGT 57.814 29.630 4.17 0.00 0.00 2.83
33 34 9.797556 GTCTGTTATTAACCTTTTCACTTTGTT 57.202 29.630 4.17 0.00 0.00 2.83
43 44 8.762481 ACCTTTTCACTTTGTTATTACTTCCT 57.238 30.769 0.00 0.00 0.00 3.36
44 45 9.856162 ACCTTTTCACTTTGTTATTACTTCCTA 57.144 29.630 0.00 0.00 0.00 2.94
61 62 7.741554 ACTTCCTATGAGAGAATTGGTAAGT 57.258 36.000 0.00 0.00 0.00 2.24
62 63 8.840200 ACTTCCTATGAGAGAATTGGTAAGTA 57.160 34.615 0.00 0.00 29.92 2.24
63 64 8.697292 ACTTCCTATGAGAGAATTGGTAAGTAC 58.303 37.037 0.00 0.00 29.92 2.73
64 65 8.840200 TTCCTATGAGAGAATTGGTAAGTACT 57.160 34.615 0.00 0.00 0.00 2.73
65 66 8.466617 TCCTATGAGAGAATTGGTAAGTACTC 57.533 38.462 0.00 0.00 0.00 2.59
66 67 8.282982 TCCTATGAGAGAATTGGTAAGTACTCT 58.717 37.037 0.00 0.00 37.42 3.24
67 68 8.356657 CCTATGAGAGAATTGGTAAGTACTCTG 58.643 40.741 0.00 0.00 35.34 3.35
68 69 7.962995 ATGAGAGAATTGGTAAGTACTCTGA 57.037 36.000 0.00 0.00 35.34 3.27
69 70 7.397892 TGAGAGAATTGGTAAGTACTCTGAG 57.602 40.000 2.45 2.45 35.34 3.35
70 71 7.175797 TGAGAGAATTGGTAAGTACTCTGAGA 58.824 38.462 12.44 0.00 35.34 3.27
71 72 7.121463 TGAGAGAATTGGTAAGTACTCTGAGAC 59.879 40.741 12.44 5.49 35.34 3.36
72 73 6.948886 AGAGAATTGGTAAGTACTCTGAGACA 59.051 38.462 12.44 0.00 34.19 3.41
73 74 7.617723 AGAGAATTGGTAAGTACTCTGAGACAT 59.382 37.037 12.44 1.46 34.19 3.06
74 75 7.551585 AGAATTGGTAAGTACTCTGAGACATG 58.448 38.462 12.44 0.00 0.00 3.21
75 76 4.720649 TGGTAAGTACTCTGAGACATGC 57.279 45.455 12.44 2.48 0.00 4.06
76 77 3.447586 TGGTAAGTACTCTGAGACATGCC 59.552 47.826 12.44 11.06 0.00 4.40
77 78 3.447586 GGTAAGTACTCTGAGACATGCCA 59.552 47.826 12.44 0.00 0.00 4.92
78 79 4.081642 GGTAAGTACTCTGAGACATGCCAA 60.082 45.833 12.44 0.00 0.00 4.52
79 80 4.623932 AAGTACTCTGAGACATGCCAAA 57.376 40.909 12.44 0.00 0.00 3.28
80 81 4.623932 AGTACTCTGAGACATGCCAAAA 57.376 40.909 12.44 0.00 0.00 2.44
81 82 4.573900 AGTACTCTGAGACATGCCAAAAG 58.426 43.478 12.44 0.00 0.00 2.27
82 83 2.787994 ACTCTGAGACATGCCAAAAGG 58.212 47.619 12.44 0.00 0.00 3.11
83 84 2.089980 CTCTGAGACATGCCAAAAGGG 58.910 52.381 0.00 0.00 40.85 3.95
84 85 1.704628 TCTGAGACATGCCAAAAGGGA 59.295 47.619 0.00 0.00 40.01 4.20
85 86 2.309755 TCTGAGACATGCCAAAAGGGAT 59.690 45.455 0.00 0.00 40.01 3.85
86 87 2.686915 CTGAGACATGCCAAAAGGGATC 59.313 50.000 0.00 0.00 40.01 3.36
87 88 2.309755 TGAGACATGCCAAAAGGGATCT 59.690 45.455 0.00 0.00 40.01 2.75
88 89 2.948315 GAGACATGCCAAAAGGGATCTC 59.052 50.000 0.00 0.00 40.01 2.75
89 90 2.579860 AGACATGCCAAAAGGGATCTCT 59.420 45.455 0.00 0.00 40.01 3.10
90 91 2.948315 GACATGCCAAAAGGGATCTCTC 59.052 50.000 0.00 0.00 40.01 3.20
91 92 2.579860 ACATGCCAAAAGGGATCTCTCT 59.420 45.455 0.00 0.00 40.01 3.10
92 93 3.212685 CATGCCAAAAGGGATCTCTCTC 58.787 50.000 0.00 0.00 40.01 3.20
93 94 1.561542 TGCCAAAAGGGATCTCTCTCC 59.438 52.381 0.00 0.00 40.01 3.71
108 109 9.881773 GGATCTCTCTCCCTAATCATATTCTAT 57.118 37.037 0.00 0.00 0.00 1.98
127 128 7.624360 TTCTATCATTTTCTAATGTTGGCGT 57.376 32.000 0.00 0.00 41.54 5.68
128 129 7.015226 TCTATCATTTTCTAATGTTGGCGTG 57.985 36.000 0.00 0.00 41.54 5.34
129 130 4.433186 TCATTTTCTAATGTTGGCGTGG 57.567 40.909 0.00 0.00 41.54 4.94
130 131 4.075682 TCATTTTCTAATGTTGGCGTGGA 58.924 39.130 0.00 0.00 41.54 4.02
131 132 4.155826 TCATTTTCTAATGTTGGCGTGGAG 59.844 41.667 0.00 0.00 41.54 3.86
132 133 2.107950 TTCTAATGTTGGCGTGGAGG 57.892 50.000 0.00 0.00 0.00 4.30
133 134 0.392461 TCTAATGTTGGCGTGGAGGC 60.392 55.000 0.00 0.00 46.95 4.70
134 135 0.392998 CTAATGTTGGCGTGGAGGCT 60.393 55.000 0.00 0.00 46.88 4.58
135 136 0.906066 TAATGTTGGCGTGGAGGCTA 59.094 50.000 0.00 0.00 46.88 3.93
136 137 0.392998 AATGTTGGCGTGGAGGCTAG 60.393 55.000 0.00 0.00 46.88 3.42
137 138 2.820037 GTTGGCGTGGAGGCTAGC 60.820 66.667 6.04 6.04 46.88 3.42
138 139 3.003173 TTGGCGTGGAGGCTAGCT 61.003 61.111 15.72 0.00 46.88 3.32
139 140 2.592993 TTGGCGTGGAGGCTAGCTT 61.593 57.895 15.72 6.94 46.88 3.74
140 141 2.124507 TTGGCGTGGAGGCTAGCTTT 62.125 55.000 15.72 3.05 46.88 3.51
141 142 1.377333 GGCGTGGAGGCTAGCTTTT 60.377 57.895 15.72 0.21 42.90 2.27
142 143 0.107848 GGCGTGGAGGCTAGCTTTTA 60.108 55.000 15.72 0.00 42.90 1.52
143 144 1.677820 GGCGTGGAGGCTAGCTTTTAA 60.678 52.381 15.72 0.00 42.90 1.52
144 145 1.397343 GCGTGGAGGCTAGCTTTTAAC 59.603 52.381 15.72 6.10 0.00 2.01
145 146 2.695359 CGTGGAGGCTAGCTTTTAACA 58.305 47.619 15.72 2.68 0.00 2.41
146 147 3.270877 CGTGGAGGCTAGCTTTTAACAT 58.729 45.455 15.72 0.00 0.00 2.71
147 148 3.063997 CGTGGAGGCTAGCTTTTAACATG 59.936 47.826 15.72 7.07 0.00 3.21
148 149 3.016736 TGGAGGCTAGCTTTTAACATGC 58.983 45.455 15.72 0.00 0.00 4.06
149 150 3.016736 GGAGGCTAGCTTTTAACATGCA 58.983 45.455 15.72 0.00 0.00 3.96
150 151 3.443681 GGAGGCTAGCTTTTAACATGCAA 59.556 43.478 15.72 0.00 0.00 4.08
151 152 4.439289 GGAGGCTAGCTTTTAACATGCAAG 60.439 45.833 15.72 0.00 0.00 4.01
152 153 3.119352 AGGCTAGCTTTTAACATGCAAGC 60.119 43.478 15.72 10.17 42.81 4.01
153 154 3.367292 GGCTAGCTTTTAACATGCAAGCA 60.367 43.478 15.72 0.00 44.57 3.91
154 155 4.427312 GCTAGCTTTTAACATGCAAGCAT 58.573 39.130 7.70 0.86 44.57 3.79
179 180 1.293924 CAGGCATGCAGTACTACAGC 58.706 55.000 21.36 5.64 0.00 4.40
180 181 1.134580 CAGGCATGCAGTACTACAGCT 60.135 52.381 21.36 0.00 31.40 4.24
181 182 2.101415 CAGGCATGCAGTACTACAGCTA 59.899 50.000 21.36 0.26 31.40 3.32
182 183 2.101582 AGGCATGCAGTACTACAGCTAC 59.898 50.000 21.36 0.00 31.40 3.58
183 184 2.159099 GGCATGCAGTACTACAGCTACA 60.159 50.000 21.36 0.00 31.40 2.74
184 185 3.119291 GCATGCAGTACTACAGCTACAG 58.881 50.000 14.21 0.00 31.40 2.74
185 186 3.711086 CATGCAGTACTACAGCTACAGG 58.289 50.000 1.61 0.00 31.40 4.00
186 187 1.476891 TGCAGTACTACAGCTACAGGC 59.523 52.381 0.00 0.00 42.19 4.85
187 188 1.476891 GCAGTACTACAGCTACAGGCA 59.523 52.381 0.00 0.00 44.79 4.75
188 189 2.735762 GCAGTACTACAGCTACAGGCAC 60.736 54.545 0.00 0.00 44.79 5.01
189 190 2.755655 CAGTACTACAGCTACAGGCACT 59.244 50.000 0.00 0.00 44.79 4.40
203 204 2.877866 AGGCACTGAGTACTGTACTGT 58.122 47.619 24.15 14.06 39.59 3.55
204 205 2.820787 AGGCACTGAGTACTGTACTGTC 59.179 50.000 24.15 12.46 39.59 3.51
205 206 2.557056 GGCACTGAGTACTGTACTGTCA 59.443 50.000 24.15 15.58 39.59 3.58
206 207 3.366476 GGCACTGAGTACTGTACTGTCAG 60.366 52.174 24.15 24.27 39.59 3.51
207 208 3.827625 CACTGAGTACTGTACTGTCAGC 58.172 50.000 24.15 10.39 39.59 4.26
208 209 3.253432 CACTGAGTACTGTACTGTCAGCA 59.747 47.826 24.15 14.09 39.59 4.41
209 210 4.082517 CACTGAGTACTGTACTGTCAGCAT 60.083 45.833 24.15 9.19 39.59 3.79
210 211 4.082517 ACTGAGTACTGTACTGTCAGCATG 60.083 45.833 24.15 11.42 39.59 4.06
211 212 3.826729 TGAGTACTGTACTGTCAGCATGT 59.173 43.478 24.15 0.00 39.59 3.21
212 213 4.280929 TGAGTACTGTACTGTCAGCATGTT 59.719 41.667 24.15 0.00 39.59 2.71
213 214 4.810790 AGTACTGTACTGTCAGCATGTTC 58.189 43.478 19.09 0.00 37.69 3.18
214 215 3.751479 ACTGTACTGTCAGCATGTTCA 57.249 42.857 0.00 0.00 38.84 3.18
215 216 3.657634 ACTGTACTGTCAGCATGTTCAG 58.342 45.455 0.00 0.00 41.71 3.02
216 217 3.070159 ACTGTACTGTCAGCATGTTCAGT 59.930 43.478 8.58 8.58 46.61 3.41
217 218 3.653344 TGTACTGTCAGCATGTTCAGTC 58.347 45.455 7.10 2.18 45.06 3.51
218 219 2.916702 ACTGTCAGCATGTTCAGTCA 57.083 45.000 0.00 0.00 43.86 3.41
219 220 2.487934 ACTGTCAGCATGTTCAGTCAC 58.512 47.619 0.00 0.00 43.86 3.67
220 221 2.158914 ACTGTCAGCATGTTCAGTCACA 60.159 45.455 0.00 0.00 43.86 3.58
221 222 2.479275 CTGTCAGCATGTTCAGTCACAG 59.521 50.000 0.00 0.00 37.40 3.66
222 223 2.158914 TGTCAGCATGTTCAGTCACAGT 60.159 45.455 0.00 0.00 37.40 3.55
223 224 2.478134 GTCAGCATGTTCAGTCACAGTC 59.522 50.000 0.00 0.00 37.40 3.51
224 225 2.366590 TCAGCATGTTCAGTCACAGTCT 59.633 45.455 0.00 0.00 37.40 3.24
225 226 2.479275 CAGCATGTTCAGTCACAGTCTG 59.521 50.000 0.00 0.00 0.00 3.51
226 227 2.366590 AGCATGTTCAGTCACAGTCTGA 59.633 45.455 6.91 0.00 39.71 3.27
227 228 7.961827 TCAGCATGTTCAGTCACAGTCTGAC 62.962 48.000 6.91 0.00 43.25 3.51
237 238 3.772387 TCACAGTCTGACAGAGATTCCT 58.228 45.455 5.10 0.00 31.63 3.36
238 239 3.509184 TCACAGTCTGACAGAGATTCCTG 59.491 47.826 5.10 11.45 39.93 3.86
240 241 3.900601 ACAGTCTGACAGAGATTCCTGTT 59.099 43.478 16.10 5.20 46.45 3.16
241 242 4.244066 CAGTCTGACAGAGATTCCTGTTG 58.756 47.826 5.10 6.26 46.45 3.33
242 243 2.999355 GTCTGACAGAGATTCCTGTTGC 59.001 50.000 5.10 0.00 46.45 4.17
243 244 2.902486 TCTGACAGAGATTCCTGTTGCT 59.098 45.455 0.00 0.00 46.45 3.91
244 245 3.001414 CTGACAGAGATTCCTGTTGCTG 58.999 50.000 0.00 0.00 46.45 4.41
245 246 1.736681 GACAGAGATTCCTGTTGCTGC 59.263 52.381 8.56 0.00 46.45 5.25
246 247 1.350351 ACAGAGATTCCTGTTGCTGCT 59.650 47.619 0.00 0.00 44.32 4.24
247 248 2.568956 ACAGAGATTCCTGTTGCTGCTA 59.431 45.455 0.00 0.00 44.32 3.49
248 249 2.935201 CAGAGATTCCTGTTGCTGCTAC 59.065 50.000 7.29 7.29 0.00 3.58
249 250 2.836981 AGAGATTCCTGTTGCTGCTACT 59.163 45.455 14.81 0.00 0.00 2.57
250 251 3.118811 AGAGATTCCTGTTGCTGCTACTC 60.119 47.826 14.81 4.39 0.00 2.59
251 252 2.836981 AGATTCCTGTTGCTGCTACTCT 59.163 45.455 14.81 6.47 0.00 3.24
252 253 3.262915 AGATTCCTGTTGCTGCTACTCTT 59.737 43.478 14.81 0.00 0.00 2.85
253 254 3.492102 TTCCTGTTGCTGCTACTCTTT 57.508 42.857 14.81 0.00 0.00 2.52
254 255 3.492102 TCCTGTTGCTGCTACTCTTTT 57.508 42.857 14.81 0.00 0.00 2.27
255 256 3.820557 TCCTGTTGCTGCTACTCTTTTT 58.179 40.909 14.81 0.00 0.00 1.94
256 257 4.968259 TCCTGTTGCTGCTACTCTTTTTA 58.032 39.130 14.81 0.00 0.00 1.52
257 258 5.560724 TCCTGTTGCTGCTACTCTTTTTAT 58.439 37.500 14.81 0.00 0.00 1.40
258 259 6.003950 TCCTGTTGCTGCTACTCTTTTTATT 58.996 36.000 14.81 0.00 0.00 1.40
259 260 7.165485 TCCTGTTGCTGCTACTCTTTTTATTA 58.835 34.615 14.81 0.00 0.00 0.98
260 261 7.829211 TCCTGTTGCTGCTACTCTTTTTATTAT 59.171 33.333 14.81 0.00 0.00 1.28
261 262 7.912250 CCTGTTGCTGCTACTCTTTTTATTATG 59.088 37.037 14.81 0.00 0.00 1.90
262 263 8.335532 TGTTGCTGCTACTCTTTTTATTATGT 57.664 30.769 14.81 0.00 0.00 2.29
263 264 9.443323 TGTTGCTGCTACTCTTTTTATTATGTA 57.557 29.630 14.81 0.00 0.00 2.29
282 283 6.785488 ATGTAATTGTACATATCGGTGCTG 57.215 37.500 0.00 0.00 46.91 4.41
283 284 5.666462 TGTAATTGTACATATCGGTGCTGT 58.334 37.500 0.00 0.00 35.23 4.40
284 285 6.110033 TGTAATTGTACATATCGGTGCTGTT 58.890 36.000 0.00 0.00 35.23 3.16
285 286 5.734855 AATTGTACATATCGGTGCTGTTC 57.265 39.130 0.00 0.00 0.00 3.18
286 287 2.804647 TGTACATATCGGTGCTGTTCG 58.195 47.619 0.00 0.00 0.00 3.95
287 288 2.124903 GTACATATCGGTGCTGTTCGG 58.875 52.381 0.00 0.00 0.00 4.30
288 289 0.535335 ACATATCGGTGCTGTTCGGT 59.465 50.000 0.00 0.00 0.00 4.69
289 290 1.209128 CATATCGGTGCTGTTCGGTC 58.791 55.000 0.00 0.00 0.00 4.79
290 291 0.821517 ATATCGGTGCTGTTCGGTCA 59.178 50.000 0.00 0.00 0.00 4.02
291 292 0.108992 TATCGGTGCTGTTCGGTCAC 60.109 55.000 0.00 0.00 0.00 3.67
292 293 2.094757 ATCGGTGCTGTTCGGTCACA 62.095 55.000 0.00 0.00 32.69 3.58
293 294 2.594962 CGGTGCTGTTCGGTCACAC 61.595 63.158 0.00 0.00 32.69 3.82
294 295 2.251642 GGTGCTGTTCGGTCACACC 61.252 63.158 0.00 0.00 43.57 4.16
295 296 2.110213 TGCTGTTCGGTCACACCC 59.890 61.111 0.00 0.00 33.75 4.61
304 305 2.967397 GTCACACCCGATGACCGA 59.033 61.111 0.00 0.00 40.56 4.69
305 306 1.290955 GTCACACCCGATGACCGAA 59.709 57.895 0.00 0.00 40.56 4.30
306 307 1.012486 GTCACACCCGATGACCGAAC 61.012 60.000 0.00 0.00 40.56 3.95
307 308 1.740296 CACACCCGATGACCGAACC 60.740 63.158 0.00 0.00 41.76 3.62
308 309 2.508439 CACCCGATGACCGAACCG 60.508 66.667 0.00 0.00 41.76 4.44
309 310 2.677524 ACCCGATGACCGAACCGA 60.678 61.111 0.00 0.00 41.76 4.69
310 311 2.056223 ACCCGATGACCGAACCGAT 61.056 57.895 0.00 0.00 41.76 4.18
311 312 1.299926 CCCGATGACCGAACCGATC 60.300 63.158 0.00 0.00 41.76 3.69
312 313 1.734137 CCGATGACCGAACCGATCT 59.266 57.895 0.00 0.00 41.76 2.75
313 314 0.317938 CCGATGACCGAACCGATCTC 60.318 60.000 0.00 0.00 41.76 2.75
314 315 0.663688 CGATGACCGAACCGATCTCT 59.336 55.000 0.00 0.00 41.76 3.10
315 316 1.334239 CGATGACCGAACCGATCTCTC 60.334 57.143 0.00 0.00 41.76 3.20
316 317 0.663688 ATGACCGAACCGATCTCTCG 59.336 55.000 0.00 0.00 44.62 4.04
374 375 6.658188 AACTGATTGGCTAGTATAGAGACC 57.342 41.667 0.00 0.00 42.77 3.85
375 376 4.762765 ACTGATTGGCTAGTATAGAGACCG 59.237 45.833 0.00 0.00 42.77 4.79
376 377 4.981812 TGATTGGCTAGTATAGAGACCGA 58.018 43.478 0.00 0.00 42.77 4.69
377 378 5.382616 TGATTGGCTAGTATAGAGACCGAA 58.617 41.667 0.00 0.00 42.77 4.30
378 379 5.473846 TGATTGGCTAGTATAGAGACCGAAG 59.526 44.000 0.00 0.00 42.77 3.79
379 380 4.701651 TGGCTAGTATAGAGACCGAAGA 57.298 45.455 0.00 0.00 42.77 2.87
380 381 5.045012 TGGCTAGTATAGAGACCGAAGAA 57.955 43.478 0.00 0.00 42.77 2.52
381 382 4.820716 TGGCTAGTATAGAGACCGAAGAAC 59.179 45.833 0.00 0.00 42.77 3.01
382 383 4.216042 GGCTAGTATAGAGACCGAAGAACC 59.784 50.000 0.00 0.00 42.77 3.62
383 384 4.083908 GCTAGTATAGAGACCGAAGAACCG 60.084 50.000 0.00 0.00 42.77 4.44
384 385 2.617774 AGTATAGAGACCGAAGAACCGC 59.382 50.000 0.00 0.00 0.00 5.68
385 386 1.471119 ATAGAGACCGAAGAACCGCA 58.529 50.000 0.00 0.00 0.00 5.69
386 387 0.524862 TAGAGACCGAAGAACCGCAC 59.475 55.000 0.00 0.00 0.00 5.34
387 388 1.737008 GAGACCGAAGAACCGCACC 60.737 63.158 0.00 0.00 0.00 5.01
388 389 2.029964 GACCGAAGAACCGCACCA 59.970 61.111 0.00 0.00 0.00 4.17
389 390 1.375523 GACCGAAGAACCGCACCAT 60.376 57.895 0.00 0.00 0.00 3.55
390 391 0.953960 GACCGAAGAACCGCACCATT 60.954 55.000 0.00 0.00 0.00 3.16
391 392 0.953960 ACCGAAGAACCGCACCATTC 60.954 55.000 0.00 0.00 0.00 2.67
392 393 1.419922 CGAAGAACCGCACCATTCG 59.580 57.895 0.00 0.00 37.09 3.34
400 401 3.486263 GCACCATTCGGTTCGAGG 58.514 61.111 0.00 0.00 46.31 4.63
401 402 2.106683 GCACCATTCGGTTCGAGGG 61.107 63.158 8.01 8.01 46.31 4.30
402 403 1.594833 CACCATTCGGTTCGAGGGA 59.405 57.895 14.03 0.00 46.31 4.20
403 404 0.036765 CACCATTCGGTTCGAGGGAA 60.037 55.000 14.03 0.00 46.31 3.97
404 405 0.036671 ACCATTCGGTTCGAGGGAAC 60.037 55.000 14.03 0.00 46.31 3.62
416 417 2.833957 GGGAACCGAACACCCAGT 59.166 61.111 0.00 0.00 40.86 4.00
417 418 1.302271 GGGAACCGAACACCCAGTC 60.302 63.158 0.00 0.00 40.86 3.51
418 419 1.302271 GGAACCGAACACCCAGTCC 60.302 63.158 0.00 0.00 0.00 3.85
419 420 1.752833 GAACCGAACACCCAGTCCT 59.247 57.895 0.00 0.00 0.00 3.85
420 421 0.971386 GAACCGAACACCCAGTCCTA 59.029 55.000 0.00 0.00 0.00 2.94
421 422 1.553704 GAACCGAACACCCAGTCCTAT 59.446 52.381 0.00 0.00 0.00 2.57
422 423 2.537633 ACCGAACACCCAGTCCTATA 57.462 50.000 0.00 0.00 0.00 1.31
423 424 3.042059 ACCGAACACCCAGTCCTATAT 57.958 47.619 0.00 0.00 0.00 0.86
424 425 2.698797 ACCGAACACCCAGTCCTATATG 59.301 50.000 0.00 0.00 0.00 1.78
425 426 2.548067 CCGAACACCCAGTCCTATATGC 60.548 54.545 0.00 0.00 0.00 3.14
426 427 2.755650 GAACACCCAGTCCTATATGCG 58.244 52.381 0.00 0.00 0.00 4.73
427 428 1.048601 ACACCCAGTCCTATATGCGG 58.951 55.000 0.00 0.00 0.00 5.69
428 429 0.321671 CACCCAGTCCTATATGCGGG 59.678 60.000 0.00 0.00 39.72 6.13
429 430 1.296715 CCCAGTCCTATATGCGGGC 59.703 63.158 0.00 0.00 0.00 6.13
430 431 1.296715 CCAGTCCTATATGCGGGCC 59.703 63.158 0.00 0.00 0.00 5.80
431 432 1.480212 CCAGTCCTATATGCGGGCCA 61.480 60.000 4.39 0.00 0.00 5.36
432 433 0.396435 CAGTCCTATATGCGGGCCAA 59.604 55.000 4.39 0.00 0.00 4.52
433 434 1.003580 CAGTCCTATATGCGGGCCAAT 59.996 52.381 4.39 0.00 0.00 3.16
434 435 1.279271 AGTCCTATATGCGGGCCAATC 59.721 52.381 4.39 0.00 0.00 2.67
435 436 1.279271 GTCCTATATGCGGGCCAATCT 59.721 52.381 4.39 0.00 0.00 2.40
436 437 1.985159 TCCTATATGCGGGCCAATCTT 59.015 47.619 4.39 0.00 0.00 2.40
437 438 2.027192 TCCTATATGCGGGCCAATCTTC 60.027 50.000 4.39 0.00 0.00 2.87
438 439 2.290260 CCTATATGCGGGCCAATCTTCA 60.290 50.000 4.39 0.00 0.00 3.02
439 440 2.592102 ATATGCGGGCCAATCTTCAT 57.408 45.000 4.39 0.47 0.00 2.57
440 441 1.608055 TATGCGGGCCAATCTTCATG 58.392 50.000 4.39 0.00 0.00 3.07
441 442 1.111116 ATGCGGGCCAATCTTCATGG 61.111 55.000 4.39 0.00 41.08 3.66
446 447 3.846180 CCAATCTTCATGGCCCCG 58.154 61.111 0.00 0.00 0.00 5.73
479 480 6.575244 TCCCTATAAAATGAAGAGAAGGCA 57.425 37.500 0.00 0.00 0.00 4.75
500 501 5.455899 GGCAGAGAACCAAATCATCCTATCT 60.456 44.000 0.00 0.00 0.00 1.98
570 571 9.443323 AAACATGTTTTATGCTTTAATTACCCC 57.557 29.630 18.13 0.00 0.00 4.95
902 977 2.143419 GTCGCCATCCCTCCTCCAT 61.143 63.158 0.00 0.00 0.00 3.41
1304 1392 5.297776 ACAGGAAATTGATAAGGCAAGATCG 59.702 40.000 0.00 0.00 0.00 3.69
1340 1728 7.205992 TGTTAATTTGTATTTCTGTTGCTGCA 58.794 30.769 0.00 0.00 0.00 4.41
1670 2100 3.186205 GGCAATGGTTAACAAATGTGTGC 59.814 43.478 8.10 7.36 38.27 4.57
1743 2181 8.659925 ATGAAATGCAAAACTGTTCATTTGTA 57.340 26.923 17.92 9.17 38.71 2.41
1885 2325 7.600375 CACGATGTCCTATATTTCTATGCTTGT 59.400 37.037 0.00 0.00 0.00 3.16
2198 2643 1.807142 GGTTCCTTGCTACAACTCTGC 59.193 52.381 0.00 0.00 0.00 4.26
2217 2662 6.016024 ACTCTGCATGCAATTTTGTTTCTCTA 60.016 34.615 22.88 0.00 0.00 2.43
2256 2701 7.747799 CGATCCATTATTAGCTACAAATGCTTG 59.252 37.037 16.66 9.46 41.46 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.281898 AGGTTAATAACAGACTGCGGTT 57.718 40.909 0.00 0.00 36.41 4.44
1 2 3.975168 AGGTTAATAACAGACTGCGGT 57.025 42.857 0.00 0.00 0.00 5.68
3 4 6.073222 AGTGAAAAGGTTAATAACAGACTGCG 60.073 38.462 1.25 0.00 0.00 5.18
4 5 7.203255 AGTGAAAAGGTTAATAACAGACTGC 57.797 36.000 1.25 0.00 0.00 4.40
5 6 9.450807 CAAAGTGAAAAGGTTAATAACAGACTG 57.549 33.333 5.45 0.00 0.00 3.51
6 7 9.185680 ACAAAGTGAAAAGGTTAATAACAGACT 57.814 29.630 5.45 0.00 0.00 3.24
7 8 9.797556 AACAAAGTGAAAAGGTTAATAACAGAC 57.202 29.630 5.45 0.00 0.00 3.51
17 18 9.197306 AGGAAGTAATAACAAAGTGAAAAGGTT 57.803 29.630 0.00 0.00 0.00 3.50
18 19 8.762481 AGGAAGTAATAACAAAGTGAAAAGGT 57.238 30.769 0.00 0.00 0.00 3.50
35 36 9.268282 ACTTACCAATTCTCTCATAGGAAGTAA 57.732 33.333 0.00 0.00 0.00 2.24
36 37 8.840200 ACTTACCAATTCTCTCATAGGAAGTA 57.160 34.615 0.00 0.00 0.00 2.24
37 38 7.741554 ACTTACCAATTCTCTCATAGGAAGT 57.258 36.000 0.00 0.00 0.00 3.01
38 39 8.919145 AGTACTTACCAATTCTCTCATAGGAAG 58.081 37.037 0.00 0.00 0.00 3.46
39 40 8.840200 AGTACTTACCAATTCTCTCATAGGAA 57.160 34.615 0.00 0.00 0.00 3.36
40 41 8.282982 AGAGTACTTACCAATTCTCTCATAGGA 58.717 37.037 0.00 0.00 0.00 2.94
41 42 8.356657 CAGAGTACTTACCAATTCTCTCATAGG 58.643 40.741 0.00 0.00 31.19 2.57
42 43 9.126151 TCAGAGTACTTACCAATTCTCTCATAG 57.874 37.037 0.00 0.00 31.19 2.23
43 44 9.126151 CTCAGAGTACTTACCAATTCTCTCATA 57.874 37.037 0.00 0.00 31.19 2.15
44 45 7.836685 TCTCAGAGTACTTACCAATTCTCTCAT 59.163 37.037 0.00 0.00 31.19 2.90
45 46 7.121463 GTCTCAGAGTACTTACCAATTCTCTCA 59.879 40.741 0.00 0.00 31.19 3.27
46 47 7.121463 TGTCTCAGAGTACTTACCAATTCTCTC 59.879 40.741 0.00 0.00 31.19 3.20
47 48 6.948886 TGTCTCAGAGTACTTACCAATTCTCT 59.051 38.462 0.00 0.00 33.38 3.10
48 49 7.159322 TGTCTCAGAGTACTTACCAATTCTC 57.841 40.000 0.00 0.00 0.00 2.87
49 50 7.551585 CATGTCTCAGAGTACTTACCAATTCT 58.448 38.462 0.00 0.00 0.00 2.40
50 51 6.256757 GCATGTCTCAGAGTACTTACCAATTC 59.743 42.308 0.00 0.00 0.00 2.17
51 52 6.109359 GCATGTCTCAGAGTACTTACCAATT 58.891 40.000 0.00 0.00 0.00 2.32
52 53 5.395768 GGCATGTCTCAGAGTACTTACCAAT 60.396 44.000 0.00 0.00 0.00 3.16
53 54 4.081642 GGCATGTCTCAGAGTACTTACCAA 60.082 45.833 0.00 0.00 0.00 3.67
54 55 3.447586 GGCATGTCTCAGAGTACTTACCA 59.552 47.826 0.00 0.00 0.00 3.25
55 56 3.447586 TGGCATGTCTCAGAGTACTTACC 59.552 47.826 0.00 0.00 0.00 2.85
56 57 4.720649 TGGCATGTCTCAGAGTACTTAC 57.279 45.455 0.00 0.00 0.00 2.34
57 58 5.738619 TTTGGCATGTCTCAGAGTACTTA 57.261 39.130 0.00 0.00 0.00 2.24
58 59 4.623932 TTTGGCATGTCTCAGAGTACTT 57.376 40.909 0.00 0.00 0.00 2.24
59 60 4.564406 CCTTTTGGCATGTCTCAGAGTACT 60.564 45.833 0.00 0.00 0.00 2.73
60 61 3.686726 CCTTTTGGCATGTCTCAGAGTAC 59.313 47.826 0.00 0.00 0.00 2.73
61 62 3.307691 CCCTTTTGGCATGTCTCAGAGTA 60.308 47.826 0.00 0.00 38.58 2.59
62 63 2.553904 CCCTTTTGGCATGTCTCAGAGT 60.554 50.000 0.00 0.00 38.58 3.24
63 64 2.089980 CCCTTTTGGCATGTCTCAGAG 58.910 52.381 0.00 0.00 38.58 3.35
64 65 1.704628 TCCCTTTTGGCATGTCTCAGA 59.295 47.619 0.00 0.00 38.58 3.27
65 66 2.205022 TCCCTTTTGGCATGTCTCAG 57.795 50.000 0.00 0.00 38.58 3.35
66 67 2.309755 AGATCCCTTTTGGCATGTCTCA 59.690 45.455 0.00 0.00 38.58 3.27
67 68 2.948315 GAGATCCCTTTTGGCATGTCTC 59.052 50.000 0.00 0.00 38.58 3.36
68 69 2.579860 AGAGATCCCTTTTGGCATGTCT 59.420 45.455 0.00 0.00 38.58 3.41
69 70 2.948315 GAGAGATCCCTTTTGGCATGTC 59.052 50.000 0.00 0.00 38.58 3.06
70 71 2.579860 AGAGAGATCCCTTTTGGCATGT 59.420 45.455 0.00 0.00 38.58 3.21
71 72 3.212685 GAGAGAGATCCCTTTTGGCATG 58.787 50.000 0.00 0.00 38.58 4.06
72 73 2.174424 GGAGAGAGATCCCTTTTGGCAT 59.826 50.000 0.00 0.00 38.58 4.40
73 74 1.561542 GGAGAGAGATCCCTTTTGGCA 59.438 52.381 0.00 0.00 38.58 4.92
74 75 2.340210 GGAGAGAGATCCCTTTTGGC 57.660 55.000 0.00 0.00 38.58 4.52
82 83 9.881773 ATAGAATATGATTAGGGAGAGAGATCC 57.118 37.037 0.00 0.00 38.76 3.36
101 102 9.337396 ACGCCAACATTAGAAAATGATAGAATA 57.663 29.630 5.18 0.00 44.50 1.75
102 103 8.131100 CACGCCAACATTAGAAAATGATAGAAT 58.869 33.333 5.18 0.00 44.50 2.40
103 104 7.415095 CCACGCCAACATTAGAAAATGATAGAA 60.415 37.037 5.18 0.00 44.50 2.10
104 105 6.038161 CCACGCCAACATTAGAAAATGATAGA 59.962 38.462 5.18 0.00 44.50 1.98
105 106 6.038161 TCCACGCCAACATTAGAAAATGATAG 59.962 38.462 5.18 0.00 44.50 2.08
106 107 5.883115 TCCACGCCAACATTAGAAAATGATA 59.117 36.000 5.18 0.00 44.50 2.15
107 108 4.704540 TCCACGCCAACATTAGAAAATGAT 59.295 37.500 5.18 0.00 44.50 2.45
108 109 4.075682 TCCACGCCAACATTAGAAAATGA 58.924 39.130 5.18 0.00 44.50 2.57
109 110 4.414852 CTCCACGCCAACATTAGAAAATG 58.585 43.478 0.00 0.00 46.66 2.32
110 111 3.443681 CCTCCACGCCAACATTAGAAAAT 59.556 43.478 0.00 0.00 0.00 1.82
111 112 2.817258 CCTCCACGCCAACATTAGAAAA 59.183 45.455 0.00 0.00 0.00 2.29
112 113 2.432444 CCTCCACGCCAACATTAGAAA 58.568 47.619 0.00 0.00 0.00 2.52
113 114 1.948611 GCCTCCACGCCAACATTAGAA 60.949 52.381 0.00 0.00 0.00 2.10
114 115 0.392461 GCCTCCACGCCAACATTAGA 60.392 55.000 0.00 0.00 0.00 2.10
115 116 0.392998 AGCCTCCACGCCAACATTAG 60.393 55.000 0.00 0.00 0.00 1.73
116 117 0.906066 TAGCCTCCACGCCAACATTA 59.094 50.000 0.00 0.00 0.00 1.90
117 118 0.392998 CTAGCCTCCACGCCAACATT 60.393 55.000 0.00 0.00 0.00 2.71
118 119 1.221840 CTAGCCTCCACGCCAACAT 59.778 57.895 0.00 0.00 0.00 2.71
119 120 2.662596 CTAGCCTCCACGCCAACA 59.337 61.111 0.00 0.00 0.00 3.33
120 121 2.804828 AAGCTAGCCTCCACGCCAAC 62.805 60.000 12.13 0.00 0.00 3.77
121 122 2.124507 AAAGCTAGCCTCCACGCCAA 62.125 55.000 12.13 0.00 0.00 4.52
122 123 2.124507 AAAAGCTAGCCTCCACGCCA 62.125 55.000 12.13 0.00 0.00 5.69
123 124 0.107848 TAAAAGCTAGCCTCCACGCC 60.108 55.000 12.13 0.00 0.00 5.68
124 125 1.397343 GTTAAAAGCTAGCCTCCACGC 59.603 52.381 12.13 0.00 0.00 5.34
125 126 2.695359 TGTTAAAAGCTAGCCTCCACG 58.305 47.619 12.13 0.00 0.00 4.94
126 127 3.181496 GCATGTTAAAAGCTAGCCTCCAC 60.181 47.826 12.13 2.91 0.00 4.02
127 128 3.016736 GCATGTTAAAAGCTAGCCTCCA 58.983 45.455 12.13 0.23 0.00 3.86
128 129 3.016736 TGCATGTTAAAAGCTAGCCTCC 58.983 45.455 12.13 0.00 0.00 4.30
129 130 4.666237 CTTGCATGTTAAAAGCTAGCCTC 58.334 43.478 12.13 0.00 0.00 4.70
130 131 3.119352 GCTTGCATGTTAAAAGCTAGCCT 60.119 43.478 12.13 0.00 46.39 4.58
131 132 3.182182 GCTTGCATGTTAAAAGCTAGCC 58.818 45.455 12.13 0.00 46.39 3.93
133 134 5.944049 CATGCTTGCATGTTAAAAGCTAG 57.056 39.130 23.00 6.34 45.21 3.42
160 161 1.134580 AGCTGTAGTACTGCATGCCTG 60.135 52.381 27.55 10.76 44.20 4.85
161 162 1.198713 AGCTGTAGTACTGCATGCCT 58.801 50.000 27.55 7.36 44.20 4.75
162 163 2.159099 TGTAGCTGTAGTACTGCATGCC 60.159 50.000 27.55 15.29 44.20 4.40
163 164 3.119291 CTGTAGCTGTAGTACTGCATGC 58.881 50.000 27.55 17.76 44.20 4.06
164 165 3.711086 CCTGTAGCTGTAGTACTGCATG 58.289 50.000 27.55 16.21 44.20 4.06
165 166 2.101582 GCCTGTAGCTGTAGTACTGCAT 59.898 50.000 27.55 17.38 44.20 3.96
166 167 1.476891 GCCTGTAGCTGTAGTACTGCA 59.523 52.381 27.55 13.33 44.20 4.41
167 168 1.476891 TGCCTGTAGCTGTAGTACTGC 59.523 52.381 21.00 21.00 44.23 4.40
168 169 2.755655 AGTGCCTGTAGCTGTAGTACTG 59.244 50.000 5.39 2.16 44.23 2.74
169 170 2.755655 CAGTGCCTGTAGCTGTAGTACT 59.244 50.000 0.00 0.00 44.23 2.73
170 171 2.753452 TCAGTGCCTGTAGCTGTAGTAC 59.247 50.000 0.00 0.00 44.23 2.73
171 172 3.017442 CTCAGTGCCTGTAGCTGTAGTA 58.983 50.000 0.00 0.00 44.23 1.82
172 173 1.821753 CTCAGTGCCTGTAGCTGTAGT 59.178 52.381 0.00 0.00 44.23 2.73
173 174 1.821753 ACTCAGTGCCTGTAGCTGTAG 59.178 52.381 0.00 0.00 44.23 2.74
174 175 1.924731 ACTCAGTGCCTGTAGCTGTA 58.075 50.000 0.00 0.00 44.23 2.74
175 176 1.546476 GTACTCAGTGCCTGTAGCTGT 59.454 52.381 0.00 0.00 44.23 4.40
176 177 1.821753 AGTACTCAGTGCCTGTAGCTG 59.178 52.381 0.00 0.00 44.23 4.24
177 178 1.821753 CAGTACTCAGTGCCTGTAGCT 59.178 52.381 0.00 0.00 44.23 3.32
178 179 1.546476 ACAGTACTCAGTGCCTGTAGC 59.454 52.381 9.57 0.00 44.14 3.58
179 180 4.011023 AGTACAGTACTCAGTGCCTGTAG 58.989 47.826 15.76 2.57 32.47 2.74
180 181 3.756963 CAGTACAGTACTCAGTGCCTGTA 59.243 47.826 10.54 12.74 36.76 2.74
181 182 2.558795 CAGTACAGTACTCAGTGCCTGT 59.441 50.000 10.54 14.36 36.76 4.00
182 183 2.558795 ACAGTACAGTACTCAGTGCCTG 59.441 50.000 10.54 5.08 36.76 4.85
183 184 2.820787 GACAGTACAGTACTCAGTGCCT 59.179 50.000 10.54 0.00 36.76 4.75
184 185 2.557056 TGACAGTACAGTACTCAGTGCC 59.443 50.000 10.54 0.00 36.76 5.01
185 186 3.827625 CTGACAGTACAGTACTCAGTGC 58.172 50.000 10.54 0.00 36.76 4.40
186 187 3.253432 TGCTGACAGTACAGTACTCAGTG 59.747 47.826 22.14 11.89 39.73 3.66
187 188 3.487372 TGCTGACAGTACAGTACTCAGT 58.513 45.455 22.14 14.54 39.73 3.41
188 189 4.082517 ACATGCTGACAGTACAGTACTCAG 60.083 45.833 19.17 19.17 39.73 3.35
189 190 3.826729 ACATGCTGACAGTACAGTACTCA 59.173 43.478 10.54 5.94 39.73 3.41
190 191 4.442375 ACATGCTGACAGTACAGTACTC 57.558 45.455 10.54 1.78 39.73 2.59
191 192 4.280929 TGAACATGCTGACAGTACAGTACT 59.719 41.667 7.48 7.48 39.73 2.73
192 193 4.556233 TGAACATGCTGACAGTACAGTAC 58.444 43.478 3.99 2.05 39.73 2.73
193 194 4.280929 ACTGAACATGCTGACAGTACAGTA 59.719 41.667 11.23 0.00 37.04 2.74
194 195 3.070159 ACTGAACATGCTGACAGTACAGT 59.930 43.478 3.99 6.53 37.04 3.55
195 196 3.657634 ACTGAACATGCTGACAGTACAG 58.342 45.455 3.99 5.91 37.04 2.74
196 197 3.069443 TGACTGAACATGCTGACAGTACA 59.931 43.478 3.99 10.15 38.07 2.90
197 198 3.430218 GTGACTGAACATGCTGACAGTAC 59.570 47.826 3.99 8.84 38.07 2.73
198 199 3.069443 TGTGACTGAACATGCTGACAGTA 59.931 43.478 3.99 0.00 38.07 2.74
199 200 2.158914 TGTGACTGAACATGCTGACAGT 60.159 45.455 3.99 12.20 39.48 3.55
200 201 2.479275 CTGTGACTGAACATGCTGACAG 59.521 50.000 0.00 0.00 34.06 3.51
201 202 2.158914 ACTGTGACTGAACATGCTGACA 60.159 45.455 0.00 0.00 0.00 3.58
202 203 2.478134 GACTGTGACTGAACATGCTGAC 59.522 50.000 0.00 0.00 0.00 3.51
203 204 2.366590 AGACTGTGACTGAACATGCTGA 59.633 45.455 0.00 0.00 0.00 4.26
204 205 2.479275 CAGACTGTGACTGAACATGCTG 59.521 50.000 0.00 0.00 37.54 4.41
205 206 2.366590 TCAGACTGTGACTGAACATGCT 59.633 45.455 1.59 0.00 40.70 3.79
206 207 2.759191 TCAGACTGTGACTGAACATGC 58.241 47.619 1.59 0.00 40.70 4.06
216 217 3.509184 CAGGAATCTCTGTCAGACTGTGA 59.491 47.826 12.86 12.86 32.26 3.58
217 218 3.257873 ACAGGAATCTCTGTCAGACTGTG 59.742 47.826 17.68 2.70 43.82 3.66
218 219 3.505386 ACAGGAATCTCTGTCAGACTGT 58.495 45.455 14.29 14.29 43.82 3.55
219 220 4.244066 CAACAGGAATCTCTGTCAGACTG 58.756 47.826 13.26 13.26 46.17 3.51
220 221 3.306641 GCAACAGGAATCTCTGTCAGACT 60.307 47.826 0.00 0.00 46.17 3.24
221 222 2.999355 GCAACAGGAATCTCTGTCAGAC 59.001 50.000 0.00 0.00 46.17 3.51
222 223 2.902486 AGCAACAGGAATCTCTGTCAGA 59.098 45.455 1.78 1.78 46.17 3.27
223 224 3.001414 CAGCAACAGGAATCTCTGTCAG 58.999 50.000 5.16 0.00 46.17 3.51
224 225 2.873245 GCAGCAACAGGAATCTCTGTCA 60.873 50.000 5.16 0.00 46.17 3.58
225 226 1.736681 GCAGCAACAGGAATCTCTGTC 59.263 52.381 5.16 0.00 46.17 3.51
227 228 2.110901 AGCAGCAACAGGAATCTCTG 57.889 50.000 0.00 0.00 40.40 3.35
228 229 2.836981 AGTAGCAGCAACAGGAATCTCT 59.163 45.455 0.00 0.00 0.00 3.10
229 230 3.118811 AGAGTAGCAGCAACAGGAATCTC 60.119 47.826 0.00 0.00 0.00 2.75
230 231 2.836981 AGAGTAGCAGCAACAGGAATCT 59.163 45.455 0.00 0.00 0.00 2.40
231 232 3.258971 AGAGTAGCAGCAACAGGAATC 57.741 47.619 0.00 0.00 0.00 2.52
232 233 3.710209 AAGAGTAGCAGCAACAGGAAT 57.290 42.857 0.00 0.00 0.00 3.01
233 234 3.492102 AAAGAGTAGCAGCAACAGGAA 57.508 42.857 0.00 0.00 0.00 3.36
234 235 3.492102 AAAAGAGTAGCAGCAACAGGA 57.508 42.857 0.00 0.00 0.00 3.86
235 236 5.886960 ATAAAAAGAGTAGCAGCAACAGG 57.113 39.130 0.00 0.00 0.00 4.00
236 237 8.454106 ACATAATAAAAAGAGTAGCAGCAACAG 58.546 33.333 0.00 0.00 0.00 3.16
237 238 8.335532 ACATAATAAAAAGAGTAGCAGCAACA 57.664 30.769 0.00 0.00 0.00 3.33
260 261 5.666462 ACAGCACCGATATGTACAATTACA 58.334 37.500 0.00 0.00 42.53 2.41
261 262 6.561533 CGAACAGCACCGATATGTACAATTAC 60.562 42.308 0.00 0.00 0.00 1.89
262 263 5.460748 CGAACAGCACCGATATGTACAATTA 59.539 40.000 0.00 0.00 0.00 1.40
263 264 4.270084 CGAACAGCACCGATATGTACAATT 59.730 41.667 0.00 0.00 0.00 2.32
264 265 3.802139 CGAACAGCACCGATATGTACAAT 59.198 43.478 0.00 0.00 0.00 2.71
265 266 3.183754 CGAACAGCACCGATATGTACAA 58.816 45.455 0.00 0.00 0.00 2.41
266 267 2.480587 CCGAACAGCACCGATATGTACA 60.481 50.000 0.00 0.00 0.00 2.90
267 268 2.124903 CCGAACAGCACCGATATGTAC 58.875 52.381 0.00 0.00 0.00 2.90
268 269 1.752498 ACCGAACAGCACCGATATGTA 59.248 47.619 0.00 0.00 0.00 2.29
269 270 0.535335 ACCGAACAGCACCGATATGT 59.465 50.000 0.00 0.00 0.00 2.29
270 271 1.209128 GACCGAACAGCACCGATATG 58.791 55.000 0.00 0.00 0.00 1.78
271 272 0.821517 TGACCGAACAGCACCGATAT 59.178 50.000 0.00 0.00 0.00 1.63
272 273 0.108992 GTGACCGAACAGCACCGATA 60.109 55.000 0.00 0.00 0.00 2.92
273 274 1.374252 GTGACCGAACAGCACCGAT 60.374 57.895 0.00 0.00 0.00 4.18
274 275 2.028484 GTGACCGAACAGCACCGA 59.972 61.111 0.00 0.00 0.00 4.69
275 276 2.279851 TGTGACCGAACAGCACCG 60.280 61.111 0.00 0.00 0.00 4.94
276 277 2.251642 GGTGTGACCGAACAGCACC 61.252 63.158 9.28 11.35 45.66 5.01
277 278 3.330275 GGTGTGACCGAACAGCAC 58.670 61.111 9.28 0.00 45.66 4.40
287 288 1.012486 GTTCGGTCATCGGGTGTGAC 61.012 60.000 0.00 0.00 44.01 3.67
288 289 1.290955 GTTCGGTCATCGGGTGTGA 59.709 57.895 0.00 0.00 39.77 3.58
289 290 1.740296 GGTTCGGTCATCGGGTGTG 60.740 63.158 0.00 0.00 39.77 3.82
290 291 2.660802 GGTTCGGTCATCGGGTGT 59.339 61.111 0.00 0.00 39.77 4.16
291 292 2.292794 ATCGGTTCGGTCATCGGGTG 62.293 60.000 0.00 0.00 39.77 4.61
292 293 2.012902 GATCGGTTCGGTCATCGGGT 62.013 60.000 0.00 0.00 36.93 5.28
293 294 1.299926 GATCGGTTCGGTCATCGGG 60.300 63.158 0.00 0.00 36.93 5.14
294 295 0.317938 GAGATCGGTTCGGTCATCGG 60.318 60.000 3.40 0.00 39.71 4.18
295 296 0.663688 AGAGATCGGTTCGGTCATCG 59.336 55.000 3.40 0.00 39.71 3.84
296 297 1.334239 CGAGAGATCGGTTCGGTCATC 60.334 57.143 3.40 0.58 39.71 2.92
297 298 0.663688 CGAGAGATCGGTTCGGTCAT 59.336 55.000 3.40 0.00 39.71 3.06
298 299 1.374343 CCGAGAGATCGGTTCGGTCA 61.374 60.000 20.45 0.00 46.56 4.02
299 300 1.355916 CCGAGAGATCGGTTCGGTC 59.644 63.158 20.45 0.00 46.56 4.79
300 301 3.510846 CCGAGAGATCGGTTCGGT 58.489 61.111 20.45 0.00 46.56 4.69
348 349 8.808092 GGTCTCTATACTAGCCAATCAGTTAAT 58.192 37.037 0.00 0.00 0.00 1.40
349 350 7.040617 CGGTCTCTATACTAGCCAATCAGTTAA 60.041 40.741 0.00 0.00 0.00 2.01
350 351 6.430308 CGGTCTCTATACTAGCCAATCAGTTA 59.570 42.308 0.00 0.00 0.00 2.24
351 352 5.241949 CGGTCTCTATACTAGCCAATCAGTT 59.758 44.000 0.00 0.00 0.00 3.16
352 353 4.762765 CGGTCTCTATACTAGCCAATCAGT 59.237 45.833 0.00 0.00 0.00 3.41
353 354 5.004448 TCGGTCTCTATACTAGCCAATCAG 58.996 45.833 0.00 0.00 0.00 2.90
354 355 4.981812 TCGGTCTCTATACTAGCCAATCA 58.018 43.478 0.00 0.00 0.00 2.57
355 356 5.706369 TCTTCGGTCTCTATACTAGCCAATC 59.294 44.000 0.00 0.00 0.00 2.67
356 357 5.632118 TCTTCGGTCTCTATACTAGCCAAT 58.368 41.667 0.00 0.00 0.00 3.16
357 358 5.045012 TCTTCGGTCTCTATACTAGCCAA 57.955 43.478 0.00 0.00 0.00 4.52
358 359 4.701651 TCTTCGGTCTCTATACTAGCCA 57.298 45.455 0.00 0.00 0.00 4.75
359 360 4.216042 GGTTCTTCGGTCTCTATACTAGCC 59.784 50.000 0.00 0.00 0.00 3.93
360 361 4.083908 CGGTTCTTCGGTCTCTATACTAGC 60.084 50.000 0.00 0.00 0.00 3.42
361 362 4.083908 GCGGTTCTTCGGTCTCTATACTAG 60.084 50.000 0.00 0.00 0.00 2.57
362 363 3.812053 GCGGTTCTTCGGTCTCTATACTA 59.188 47.826 0.00 0.00 0.00 1.82
363 364 2.617774 GCGGTTCTTCGGTCTCTATACT 59.382 50.000 0.00 0.00 0.00 2.12
364 365 2.357009 TGCGGTTCTTCGGTCTCTATAC 59.643 50.000 0.00 0.00 0.00 1.47
365 366 2.357009 GTGCGGTTCTTCGGTCTCTATA 59.643 50.000 0.00 0.00 0.00 1.31
366 367 1.134560 GTGCGGTTCTTCGGTCTCTAT 59.865 52.381 0.00 0.00 0.00 1.98
367 368 0.524862 GTGCGGTTCTTCGGTCTCTA 59.475 55.000 0.00 0.00 0.00 2.43
368 369 1.289380 GTGCGGTTCTTCGGTCTCT 59.711 57.895 0.00 0.00 0.00 3.10
369 370 1.737008 GGTGCGGTTCTTCGGTCTC 60.737 63.158 0.00 0.00 0.00 3.36
370 371 1.827399 ATGGTGCGGTTCTTCGGTCT 61.827 55.000 0.00 0.00 0.00 3.85
371 372 0.953960 AATGGTGCGGTTCTTCGGTC 60.954 55.000 0.00 0.00 0.00 4.79
372 373 0.953960 GAATGGTGCGGTTCTTCGGT 60.954 55.000 0.00 0.00 0.00 4.69
373 374 1.794222 GAATGGTGCGGTTCTTCGG 59.206 57.895 0.00 0.00 0.00 4.30
374 375 1.419922 CGAATGGTGCGGTTCTTCG 59.580 57.895 0.00 0.00 33.66 3.79
375 376 1.794222 CCGAATGGTGCGGTTCTTC 59.206 57.895 0.00 0.00 43.66 2.87
376 377 3.981308 CCGAATGGTGCGGTTCTT 58.019 55.556 0.00 0.00 43.66 2.52
386 387 2.763651 GTTCCCTCGAACCGAATGG 58.236 57.895 0.00 0.00 42.26 3.16
394 395 1.368579 GGTGTTCGGTTCCCTCGAA 59.631 57.895 0.00 0.00 43.18 3.71
395 396 2.576832 GGGTGTTCGGTTCCCTCGA 61.577 63.158 0.00 0.00 38.29 4.04
396 397 2.047560 GGGTGTTCGGTTCCCTCG 60.048 66.667 0.00 0.00 38.29 4.63
397 398 1.003718 CTGGGTGTTCGGTTCCCTC 60.004 63.158 0.00 0.00 41.58 4.30
398 399 1.765597 GACTGGGTGTTCGGTTCCCT 61.766 60.000 0.00 0.00 41.58 4.20
399 400 1.302271 GACTGGGTGTTCGGTTCCC 60.302 63.158 0.00 0.00 41.41 3.97
400 401 1.302271 GGACTGGGTGTTCGGTTCC 60.302 63.158 0.00 0.00 0.00 3.62
401 402 0.971386 TAGGACTGGGTGTTCGGTTC 59.029 55.000 0.00 0.00 0.00 3.62
402 403 1.652947 ATAGGACTGGGTGTTCGGTT 58.347 50.000 0.00 0.00 0.00 4.44
403 404 2.537633 TATAGGACTGGGTGTTCGGT 57.462 50.000 0.00 0.00 0.00 4.69
404 405 2.548067 GCATATAGGACTGGGTGTTCGG 60.548 54.545 0.00 0.00 0.00 4.30
405 406 2.755650 GCATATAGGACTGGGTGTTCG 58.244 52.381 0.00 0.00 0.00 3.95
406 407 2.548067 CCGCATATAGGACTGGGTGTTC 60.548 54.545 0.00 0.00 0.00 3.18
407 408 1.416401 CCGCATATAGGACTGGGTGTT 59.584 52.381 0.00 0.00 0.00 3.32
408 409 1.048601 CCGCATATAGGACTGGGTGT 58.951 55.000 0.00 0.00 0.00 4.16
409 410 0.321671 CCCGCATATAGGACTGGGTG 59.678 60.000 2.62 0.00 31.82 4.61
410 411 1.481056 GCCCGCATATAGGACTGGGT 61.481 60.000 10.30 0.00 38.93 4.51
411 412 1.296715 GCCCGCATATAGGACTGGG 59.703 63.158 5.67 5.67 39.72 4.45
412 413 1.296715 GGCCCGCATATAGGACTGG 59.703 63.158 0.00 0.00 0.00 4.00
413 414 0.396435 TTGGCCCGCATATAGGACTG 59.604 55.000 0.00 0.00 29.76 3.51
414 415 1.279271 GATTGGCCCGCATATAGGACT 59.721 52.381 0.00 0.00 29.76 3.85
415 416 1.279271 AGATTGGCCCGCATATAGGAC 59.721 52.381 0.00 0.00 0.00 3.85
416 417 1.656587 AGATTGGCCCGCATATAGGA 58.343 50.000 0.00 0.00 0.00 2.94
417 418 2.290260 TGAAGATTGGCCCGCATATAGG 60.290 50.000 0.00 0.00 0.00 2.57
418 419 3.057969 TGAAGATTGGCCCGCATATAG 57.942 47.619 0.00 0.00 0.00 1.31
419 420 3.346315 CATGAAGATTGGCCCGCATATA 58.654 45.455 0.00 0.00 0.00 0.86
420 421 2.165167 CATGAAGATTGGCCCGCATAT 58.835 47.619 0.00 0.00 0.00 1.78
421 422 1.608055 CATGAAGATTGGCCCGCATA 58.392 50.000 0.00 0.00 0.00 3.14
422 423 1.111116 CCATGAAGATTGGCCCGCAT 61.111 55.000 0.00 0.00 0.00 4.73
423 424 1.753848 CCATGAAGATTGGCCCGCA 60.754 57.895 0.00 0.00 0.00 5.69
424 425 3.122850 CCATGAAGATTGGCCCGC 58.877 61.111 0.00 0.00 0.00 6.13
429 430 0.182537 TACGGGGCCATGAAGATTGG 59.817 55.000 4.39 0.00 37.31 3.16
430 431 2.154462 GATACGGGGCCATGAAGATTG 58.846 52.381 4.39 0.00 0.00 2.67
431 432 2.057922 AGATACGGGGCCATGAAGATT 58.942 47.619 4.39 0.00 0.00 2.40
432 433 1.734655 AGATACGGGGCCATGAAGAT 58.265 50.000 4.39 0.00 0.00 2.40
433 434 1.968493 GTAGATACGGGGCCATGAAGA 59.032 52.381 4.39 0.00 0.00 2.87
434 435 1.971357 AGTAGATACGGGGCCATGAAG 59.029 52.381 4.39 0.00 0.00 3.02
435 436 2.097110 AGTAGATACGGGGCCATGAA 57.903 50.000 4.39 0.00 0.00 2.57
436 437 2.984435 TAGTAGATACGGGGCCATGA 57.016 50.000 4.39 0.00 0.00 3.07
437 438 2.431057 GGATAGTAGATACGGGGCCATG 59.569 54.545 4.39 0.00 0.00 3.66
438 439 2.626149 GGGATAGTAGATACGGGGCCAT 60.626 54.545 4.39 0.00 0.00 4.40
439 440 1.272872 GGGATAGTAGATACGGGGCCA 60.273 57.143 4.39 0.00 0.00 5.36
440 441 1.006878 AGGGATAGTAGATACGGGGCC 59.993 57.143 0.00 0.00 0.00 5.80
441 442 2.528673 AGGGATAGTAGATACGGGGC 57.471 55.000 0.00 0.00 0.00 5.80
442 443 8.639761 CATTTTATAGGGATAGTAGATACGGGG 58.360 40.741 0.00 0.00 0.00 5.73
443 444 9.417561 TCATTTTATAGGGATAGTAGATACGGG 57.582 37.037 0.00 0.00 0.00 5.28
475 476 2.579860 AGGATGATTTGGTTCTCTGCCT 59.420 45.455 0.00 0.00 0.00 4.75
479 480 9.163894 TGAATAGATAGGATGATTTGGTTCTCT 57.836 33.333 0.00 0.00 0.00 3.10
500 501 7.861629 AGACCATCAGATTGTAGGTTTGAATA 58.138 34.615 0.00 0.00 31.57 1.75
882 957 3.917760 GAGGAGGGATGGCGACGG 61.918 72.222 0.00 0.00 0.00 4.79
885 960 2.142761 CATGGAGGAGGGATGGCGA 61.143 63.158 0.00 0.00 0.00 5.54
1314 1702 7.381948 TGCAGCAACAGAAATACAAATTAACAG 59.618 33.333 0.00 0.00 0.00 3.16
1372 1760 6.861144 TCTCTTTCATCAGTCACATACAGAG 58.139 40.000 0.00 0.00 0.00 3.35
2198 2643 7.811236 ACTGTGATAGAGAAACAAAATTGCATG 59.189 33.333 0.00 0.00 0.00 4.06
2256 2701 7.933215 ACCTTGTACCCATCTGTTTATAAAC 57.067 36.000 19.44 19.44 39.33 2.01
2797 3247 8.506168 AACGGTTGATTACTTCATATGTTGAT 57.494 30.769 1.90 0.00 33.34 2.57
3039 3491 1.001378 CGGTTGGAGCAGAAAACAAGG 60.001 52.381 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.