Multiple sequence alignment - TraesCS7B01G410500

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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 TraesCS7B01G410500 chr7B 100.000 3887 0 0 1 3887 679674347 679670461 0.000000e+00 7179.0
1 TraesCS7B01G410500 chr7B 88.386 1214 135 6 1591 2801 679634876 679633666 0.000000e+00 1456.0
2 TraesCS7B01G410500 chr7B 88.054 745 86 2 1590 2331 679789283 679790027 0.000000e+00 880.0
3 TraesCS7B01G410500 chr7B 88.693 566 62 2 2327 2891 679793153 679793717 0.000000e+00 689.0
4 TraesCS7B01G410500 chr7B 90.595 521 43 4 1009 1523 679635569 679635049 0.000000e+00 686.0
5 TraesCS7B01G410500 chr7B 85.820 677 58 20 868 1523 679788488 679789147 0.000000e+00 684.0
6 TraesCS7B01G410500 chr7D 93.027 2524 94 24 838 3352 599810433 599807983 0.000000e+00 3611.0
7 TraesCS7B01G410500 chr7D 88.770 1309 141 5 1590 2894 600449058 600450364 0.000000e+00 1598.0
8 TraesCS7B01G410500 chr7D 87.735 1223 142 8 1583 2801 599798364 599797146 0.000000e+00 1421.0
9 TraesCS7B01G410500 chr7D 87.297 677 48 17 868 1523 600448263 600448922 0.000000e+00 739.0
10 TraesCS7B01G410500 chr7D 90.979 521 41 3 1009 1523 599799055 599798535 0.000000e+00 697.0
11 TraesCS7B01G410500 chr7D 88.248 468 44 5 3429 3887 599806876 599806411 2.040000e-152 549.0
12 TraesCS7B01G410500 chr7D 98.276 116 0 2 1 114 477407255 477407140 6.590000e-48 202.0
13 TraesCS7B01G410500 chr7A 93.771 1477 68 7 776 2250 692050042 692048588 0.000000e+00 2196.0
14 TraesCS7B01G410500 chr7A 91.454 1217 75 19 2246 3442 692045802 692044595 0.000000e+00 1644.0
15 TraesCS7B01G410500 chr7A 86.474 1316 142 15 1583 2894 692338340 692339623 0.000000e+00 1411.0
16 TraesCS7B01G410500 chr7A 87.173 1224 147 10 1583 2801 692027268 692026050 0.000000e+00 1382.0
17 TraesCS7B01G410500 chr7A 90.812 468 20 10 189 639 692050543 692050082 4.300000e-169 604.0
18 TraesCS7B01G410500 chr7A 86.694 496 46 10 950 1438 692038852 692038370 2.060000e-147 532.0
19 TraesCS7B01G410500 chr7A 83.784 481 57 11 3425 3887 692044007 692043530 1.660000e-118 436.0
20 TraesCS7B01G410500 chr7A 77.273 198 36 9 3200 3394 711368608 711368799 1.480000e-19 108.0
21 TraesCS7B01G410500 chr6B 77.403 1217 225 34 1706 2888 194860529 194861729 0.000000e+00 678.0
22 TraesCS7B01G410500 chr6B 80.310 452 75 14 1067 1512 194426093 194425650 2.900000e-86 329.0
23 TraesCS7B01G410500 chr6B 98.276 116 0 2 1 114 13380366 13380481 6.590000e-48 202.0
24 TraesCS7B01G410500 chr6D 80.998 421 71 9 1095 1512 106705149 106704735 3.750000e-85 326.0
25 TraesCS7B01G410500 chr6D 100.000 30 0 0 3200 3229 24577313 24577284 5.430000e-04 56.5
26 TraesCS7B01G410500 chr5D 98.276 116 0 2 1 114 367422038 367422153 6.590000e-48 202.0
27 TraesCS7B01G410500 chr5D 86.667 60 2 4 3198 3253 459732622 459732565 1.170000e-05 62.1
28 TraesCS7B01G410500 chr3D 98.276 116 0 2 1 114 18421770 18421885 6.590000e-48 202.0
29 TraesCS7B01G410500 chr3D 99.107 112 1 0 1 112 80602015 80601904 6.590000e-48 202.0
30 TraesCS7B01G410500 chr2D 98.276 116 0 2 1 114 18759139 18759024 6.590000e-48 202.0
31 TraesCS7B01G410500 chr1B 98.276 116 0 2 1 114 141756809 141756924 6.590000e-48 202.0
32 TraesCS7B01G410500 chr1B 98.276 116 0 2 1 114 685735960 685736075 6.590000e-48 202.0
33 TraesCS7B01G410500 chr1B 78.218 202 33 10 3201 3399 575228490 575228683 6.820000e-23 119.0
34 TraesCS7B01G410500 chr5B 98.261 115 0 2 2 114 521027881 521027767 2.370000e-47 200.0
35 TraesCS7B01G410500 chr2A 84.080 201 24 8 3200 3398 752550973 752551167 1.840000e-43 187.0
36 TraesCS7B01G410500 chr3B 81.095 201 30 8 3200 3398 777193185 777193379 1.870000e-33 154.0
37 TraesCS7B01G410500 chr1A 80.303 132 24 2 3264 3394 562725436 562725566 8.890000e-17 99.0
38 TraesCS7B01G410500 chr5A 80.992 121 16 6 3200 3318 678210063 678209948 5.350000e-14 89.8


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 TraesCS7B01G410500 chr7B 679670461 679674347 3886 True 7179.0 7179 100.000000 1 3887 1 chr7B.!!$R1 3886
1 TraesCS7B01G410500 chr7B 679633666 679635569 1903 True 1071.0 1456 89.490500 1009 2801 2 chr7B.!!$R2 1792
2 TraesCS7B01G410500 chr7B 679788488 679793717 5229 False 751.0 880 87.522333 868 2891 3 chr7B.!!$F1 2023
3 TraesCS7B01G410500 chr7D 599806411 599810433 4022 True 2080.0 3611 90.637500 838 3887 2 chr7D.!!$R3 3049
4 TraesCS7B01G410500 chr7D 600448263 600450364 2101 False 1168.5 1598 88.033500 868 2894 2 chr7D.!!$F1 2026
5 TraesCS7B01G410500 chr7D 599797146 599799055 1909 True 1059.0 1421 89.357000 1009 2801 2 chr7D.!!$R2 1792
6 TraesCS7B01G410500 chr7A 692338340 692339623 1283 False 1411.0 1411 86.474000 1583 2894 1 chr7A.!!$F1 1311
7 TraesCS7B01G410500 chr7A 692026050 692027268 1218 True 1382.0 1382 87.173000 1583 2801 1 chr7A.!!$R1 1218
8 TraesCS7B01G410500 chr7A 692043530 692050543 7013 True 1220.0 2196 89.955250 189 3887 4 chr7A.!!$R3 3698
9 TraesCS7B01G410500 chr6B 194860529 194861729 1200 False 678.0 678 77.403000 1706 2888 1 chr6B.!!$F2 1182

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
829 848 0.026803 GCTCCAGCGACAAATTAGCG 59.973 55.0 0.0 0.00 35.78 4.26 F
1005 1029 0.389037 ACCGATCGATCATCATGGCG 60.389 55.0 24.4 8.87 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1914 0.387202 CATGTCCTCAGCGAGTAGGG 59.613 60.0 0.0 0.0 33.40 3.53 R
2919 9024 0.099613 CGCTCACTCACTCGTGCTAT 59.900 55.0 0.0 0.0 34.92 2.97 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
17 18 2.358737 AAAAGCCTCGCCTGACCG 60.359 61.111 0.00 0.00 0.00 4.79
39 40 2.663196 CGGAGCCCGGAGAAACTT 59.337 61.111 0.73 0.00 44.15 2.66
40 41 1.895238 CGGAGCCCGGAGAAACTTA 59.105 57.895 0.73 0.00 44.15 2.24
41 42 0.464452 CGGAGCCCGGAGAAACTTAT 59.536 55.000 0.73 0.00 44.15 1.73
42 43 1.134491 CGGAGCCCGGAGAAACTTATT 60.134 52.381 0.73 0.00 44.15 1.40
43 44 2.562635 GGAGCCCGGAGAAACTTATTC 58.437 52.381 0.73 0.00 0.00 1.75
44 45 2.562635 GAGCCCGGAGAAACTTATTCC 58.437 52.381 0.73 0.00 0.00 3.01
50 51 1.587034 GGAGAAACTTATTCCGACGCG 59.413 52.381 3.53 3.53 0.00 6.01
51 52 2.523015 GAGAAACTTATTCCGACGCGA 58.477 47.619 15.93 0.00 0.00 5.87
52 53 2.257034 AGAAACTTATTCCGACGCGAC 58.743 47.619 15.93 5.54 0.00 5.19
53 54 1.987770 GAAACTTATTCCGACGCGACA 59.012 47.619 15.93 0.00 0.00 4.35
54 55 1.343506 AACTTATTCCGACGCGACAC 58.656 50.000 15.93 2.51 0.00 3.67
55 56 0.457337 ACTTATTCCGACGCGACACC 60.457 55.000 15.93 0.00 0.00 4.16
56 57 0.457166 CTTATTCCGACGCGACACCA 60.457 55.000 15.93 0.00 0.00 4.17
57 58 0.733566 TTATTCCGACGCGACACCAC 60.734 55.000 15.93 0.00 0.00 4.16
58 59 2.546645 TATTCCGACGCGACACCACC 62.547 60.000 15.93 0.00 0.00 4.61
84 85 4.200283 CTCGGCAGCGTCTCCCTC 62.200 72.222 0.00 0.00 0.00 4.30
86 87 4.069232 CGGCAGCGTCTCCCTCAA 62.069 66.667 0.00 0.00 0.00 3.02
87 88 2.435059 GGCAGCGTCTCCCTCAAC 60.435 66.667 0.00 0.00 0.00 3.18
88 89 2.435059 GCAGCGTCTCCCTCAACC 60.435 66.667 0.00 0.00 0.00 3.77
89 90 2.266055 CAGCGTCTCCCTCAACCC 59.734 66.667 0.00 0.00 0.00 4.11
90 91 2.120718 AGCGTCTCCCTCAACCCT 59.879 61.111 0.00 0.00 0.00 4.34
91 92 0.970937 CAGCGTCTCCCTCAACCCTA 60.971 60.000 0.00 0.00 0.00 3.53
92 93 0.252103 AGCGTCTCCCTCAACCCTAA 60.252 55.000 0.00 0.00 0.00 2.69
93 94 0.108281 GCGTCTCCCTCAACCCTAAC 60.108 60.000 0.00 0.00 0.00 2.34
94 95 0.535797 CGTCTCCCTCAACCCTAACC 59.464 60.000 0.00 0.00 0.00 2.85
95 96 0.910338 GTCTCCCTCAACCCTAACCC 59.090 60.000 0.00 0.00 0.00 4.11
96 97 0.797579 TCTCCCTCAACCCTAACCCT 59.202 55.000 0.00 0.00 0.00 4.34
97 98 2.013006 TCTCCCTCAACCCTAACCCTA 58.987 52.381 0.00 0.00 0.00 3.53
98 99 2.117051 CTCCCTCAACCCTAACCCTAC 58.883 57.143 0.00 0.00 0.00 3.18
99 100 1.210538 CCCTCAACCCTAACCCTACC 58.789 60.000 0.00 0.00 0.00 3.18
100 101 1.556238 CCCTCAACCCTAACCCTACCA 60.556 57.143 0.00 0.00 0.00 3.25
101 102 1.558294 CCTCAACCCTAACCCTACCAC 59.442 57.143 0.00 0.00 0.00 4.16
102 103 2.262637 CTCAACCCTAACCCTACCACA 58.737 52.381 0.00 0.00 0.00 4.17
103 104 1.980036 TCAACCCTAACCCTACCACAC 59.020 52.381 0.00 0.00 0.00 3.82
104 105 1.003928 CAACCCTAACCCTACCACACC 59.996 57.143 0.00 0.00 0.00 4.16
105 106 0.548439 ACCCTAACCCTACCACACCC 60.548 60.000 0.00 0.00 0.00 4.61
106 107 0.548197 CCCTAACCCTACCACACCCA 60.548 60.000 0.00 0.00 0.00 4.51
107 108 0.616891 CCTAACCCTACCACACCCAC 59.383 60.000 0.00 0.00 0.00 4.61
108 109 0.616891 CTAACCCTACCACACCCACC 59.383 60.000 0.00 0.00 0.00 4.61
109 110 0.194080 TAACCCTACCACACCCACCT 59.806 55.000 0.00 0.00 0.00 4.00
110 111 0.194080 AACCCTACCACACCCACCTA 59.806 55.000 0.00 0.00 0.00 3.08
111 112 0.252558 ACCCTACCACACCCACCTAG 60.253 60.000 0.00 0.00 0.00 3.02
112 113 1.623542 CCCTACCACACCCACCTAGC 61.624 65.000 0.00 0.00 0.00 3.42
113 114 1.515954 CTACCACACCCACCTAGCG 59.484 63.158 0.00 0.00 0.00 4.26
114 115 1.228956 TACCACACCCACCTAGCGT 60.229 57.895 0.00 0.00 0.00 5.07
115 116 1.252904 TACCACACCCACCTAGCGTC 61.253 60.000 0.00 0.00 0.00 5.19
116 117 2.579657 CCACACCCACCTAGCGTCA 61.580 63.158 0.00 0.00 0.00 4.35
117 118 1.374252 CACACCCACCTAGCGTCAC 60.374 63.158 0.00 0.00 0.00 3.67
118 119 1.533273 ACACCCACCTAGCGTCACT 60.533 57.895 0.00 0.00 0.00 3.41
119 120 1.079819 CACCCACCTAGCGTCACTG 60.080 63.158 0.00 0.00 0.00 3.66
120 121 1.533273 ACCCACCTAGCGTCACTGT 60.533 57.895 0.00 0.00 0.00 3.55
121 122 0.251474 ACCCACCTAGCGTCACTGTA 60.251 55.000 0.00 0.00 0.00 2.74
122 123 1.112113 CCCACCTAGCGTCACTGTAT 58.888 55.000 0.00 0.00 0.00 2.29
123 124 1.067212 CCCACCTAGCGTCACTGTATC 59.933 57.143 0.00 0.00 0.00 2.24
124 125 2.025155 CCACCTAGCGTCACTGTATCT 58.975 52.381 0.00 0.00 0.00 1.98
125 126 2.223595 CCACCTAGCGTCACTGTATCTG 60.224 54.545 0.00 0.00 0.00 2.90
126 127 2.683362 CACCTAGCGTCACTGTATCTGA 59.317 50.000 0.00 0.00 0.00 3.27
127 128 3.316588 CACCTAGCGTCACTGTATCTGAT 59.683 47.826 0.00 0.00 0.00 2.90
128 129 3.954904 ACCTAGCGTCACTGTATCTGATT 59.045 43.478 0.00 0.00 0.00 2.57
129 130 4.202060 ACCTAGCGTCACTGTATCTGATTG 60.202 45.833 0.00 0.00 0.00 2.67
130 131 3.876274 AGCGTCACTGTATCTGATTGT 57.124 42.857 0.00 0.00 0.00 2.71
131 132 3.515630 AGCGTCACTGTATCTGATTGTG 58.484 45.455 0.00 3.93 0.00 3.33
132 133 2.029728 GCGTCACTGTATCTGATTGTGC 59.970 50.000 0.00 0.00 0.00 4.57
133 134 3.253230 CGTCACTGTATCTGATTGTGCA 58.747 45.455 0.00 0.00 0.00 4.57
134 135 3.679502 CGTCACTGTATCTGATTGTGCAA 59.320 43.478 0.00 0.00 0.00 4.08
135 136 4.201656 CGTCACTGTATCTGATTGTGCAAG 60.202 45.833 0.00 0.00 0.00 4.01
136 137 4.692625 GTCACTGTATCTGATTGTGCAAGT 59.307 41.667 0.00 0.00 0.00 3.16
137 138 4.692155 TCACTGTATCTGATTGTGCAAGTG 59.308 41.667 0.00 0.00 0.00 3.16
138 139 3.438087 ACTGTATCTGATTGTGCAAGTGC 59.562 43.478 0.00 0.00 42.50 4.40
139 140 2.416202 TGTATCTGATTGTGCAAGTGCG 59.584 45.455 0.00 0.00 45.83 5.34
140 141 0.806868 ATCTGATTGTGCAAGTGCGG 59.193 50.000 0.00 0.00 45.83 5.69
141 142 0.534877 TCTGATTGTGCAAGTGCGGT 60.535 50.000 0.00 0.00 45.83 5.68
142 143 0.311790 CTGATTGTGCAAGTGCGGTT 59.688 50.000 0.00 0.00 45.83 4.44
143 144 0.030504 TGATTGTGCAAGTGCGGTTG 59.969 50.000 0.00 0.00 45.83 3.77
144 145 0.664166 GATTGTGCAAGTGCGGTTGG 60.664 55.000 0.00 0.00 45.83 3.77
145 146 2.697992 ATTGTGCAAGTGCGGTTGGC 62.698 55.000 0.00 0.00 45.83 4.52
154 155 2.650196 GCGGTTGGCAGCATCAAA 59.350 55.556 3.14 0.00 42.87 2.69
155 156 1.006337 GCGGTTGGCAGCATCAAAA 60.006 52.632 3.14 0.00 42.87 2.44
156 157 0.599728 GCGGTTGGCAGCATCAAAAA 60.600 50.000 3.14 0.00 42.87 1.94
174 175 4.729227 AAAAAGGAAGTCGAGGCAAAAA 57.271 36.364 0.00 0.00 0.00 1.94
175 176 4.937201 AAAAGGAAGTCGAGGCAAAAAT 57.063 36.364 0.00 0.00 0.00 1.82
176 177 4.937201 AAAGGAAGTCGAGGCAAAAATT 57.063 36.364 0.00 0.00 0.00 1.82
177 178 4.937201 AAGGAAGTCGAGGCAAAAATTT 57.063 36.364 0.00 0.00 0.00 1.82
178 179 6.399639 AAAGGAAGTCGAGGCAAAAATTTA 57.600 33.333 0.00 0.00 0.00 1.40
179 180 5.629079 AGGAAGTCGAGGCAAAAATTTAG 57.371 39.130 0.00 0.00 0.00 1.85
180 181 5.070685 AGGAAGTCGAGGCAAAAATTTAGT 58.929 37.500 0.00 0.00 0.00 2.24
181 182 5.048713 AGGAAGTCGAGGCAAAAATTTAGTG 60.049 40.000 0.00 0.00 0.00 2.74
182 183 4.766404 AGTCGAGGCAAAAATTTAGTGG 57.234 40.909 0.00 0.00 0.00 4.00
183 184 4.142038 AGTCGAGGCAAAAATTTAGTGGT 58.858 39.130 0.00 0.00 0.00 4.16
184 185 4.023193 AGTCGAGGCAAAAATTTAGTGGTG 60.023 41.667 0.00 0.00 0.00 4.17
185 186 4.023536 GTCGAGGCAAAAATTTAGTGGTGA 60.024 41.667 0.00 0.00 0.00 4.02
186 187 4.764823 TCGAGGCAAAAATTTAGTGGTGAT 59.235 37.500 0.00 0.00 0.00 3.06
187 188 5.941058 TCGAGGCAAAAATTTAGTGGTGATA 59.059 36.000 0.00 0.00 0.00 2.15
198 199 0.108329 GTGGTGATAGTGGTGACCCG 60.108 60.000 0.00 0.00 0.00 5.28
255 256 3.472652 TGTTTTAATGCGAGGCCGATAT 58.527 40.909 0.00 0.00 38.22 1.63
256 257 3.249799 TGTTTTAATGCGAGGCCGATATG 59.750 43.478 0.00 0.00 38.22 1.78
314 326 1.673920 GAAAGGTCCAGTGTTTTCGCA 59.326 47.619 0.00 0.00 0.00 5.10
315 327 1.757682 AAGGTCCAGTGTTTTCGCAA 58.242 45.000 0.00 0.00 0.00 4.85
355 372 4.159506 CAGGTGGTCCTCTCTCTCTAAAAG 59.840 50.000 0.00 0.00 43.07 2.27
356 373 3.449377 GGTGGTCCTCTCTCTCTAAAAGG 59.551 52.174 0.00 0.00 0.00 3.11
357 374 4.345854 GTGGTCCTCTCTCTCTAAAAGGA 58.654 47.826 0.00 0.00 33.79 3.36
358 375 4.773149 GTGGTCCTCTCTCTCTAAAAGGAA 59.227 45.833 0.00 0.00 37.85 3.36
359 376 5.246429 GTGGTCCTCTCTCTCTAAAAGGAAA 59.754 44.000 0.00 0.00 37.85 3.13
360 377 5.482175 TGGTCCTCTCTCTCTAAAAGGAAAG 59.518 44.000 0.00 0.00 37.85 2.62
361 378 5.105106 GGTCCTCTCTCTCTAAAAGGAAAGG 60.105 48.000 0.00 0.00 37.85 3.11
362 379 5.482526 GTCCTCTCTCTCTAAAAGGAAAGGT 59.517 44.000 0.00 0.00 37.85 3.50
363 380 6.664384 GTCCTCTCTCTCTAAAAGGAAAGGTA 59.336 42.308 0.00 0.00 37.85 3.08
364 381 6.664384 TCCTCTCTCTCTAAAAGGAAAGGTAC 59.336 42.308 0.00 0.00 33.27 3.34
365 382 7.477975 TCCTCTCTCTCTAAAAGGAAAGGTACT 60.478 40.741 0.00 0.00 33.27 2.73
408 425 2.940467 TGGCTTGGGGCTGATCCA 60.940 61.111 0.00 0.00 41.46 3.41
415 432 0.773014 TGGGGCTGATCCATGGTATG 59.227 55.000 12.58 2.17 36.21 2.39
493 510 6.484288 TGGAATCTTGATTCTTGTACATGGT 58.516 36.000 18.96 0.00 0.00 3.55
511 528 7.338800 ACATGGTTTAATAAGATTGAGCAGG 57.661 36.000 0.00 0.00 0.00 4.85
563 580 6.235231 ACGATAGAAATGTACATGTCCCTT 57.765 37.500 20.40 5.96 41.38 3.95
633 652 4.830826 AAAACGGTTTCCAGAAGATCAC 57.169 40.909 6.57 0.00 0.00 3.06
634 653 2.080286 ACGGTTTCCAGAAGATCACG 57.920 50.000 0.00 0.00 0.00 4.35
635 654 1.337823 ACGGTTTCCAGAAGATCACGG 60.338 52.381 0.00 0.00 0.00 4.94
636 655 1.067142 CGGTTTCCAGAAGATCACGGA 60.067 52.381 0.00 0.00 0.00 4.69
637 656 2.418746 CGGTTTCCAGAAGATCACGGAT 60.419 50.000 0.00 0.00 0.00 4.18
638 657 3.610911 GGTTTCCAGAAGATCACGGATT 58.389 45.455 0.00 0.00 0.00 3.01
639 658 4.010349 GGTTTCCAGAAGATCACGGATTT 58.990 43.478 0.00 0.00 0.00 2.17
640 659 4.459337 GGTTTCCAGAAGATCACGGATTTT 59.541 41.667 0.00 0.00 0.00 1.82
641 660 5.048013 GGTTTCCAGAAGATCACGGATTTTT 60.048 40.000 0.00 0.00 0.00 1.94
642 661 5.880054 TTCCAGAAGATCACGGATTTTTC 57.120 39.130 0.00 0.00 0.00 2.29
643 662 4.905429 TCCAGAAGATCACGGATTTTTCA 58.095 39.130 0.00 0.00 0.00 2.69
644 663 4.937620 TCCAGAAGATCACGGATTTTTCAG 59.062 41.667 0.00 0.00 0.00 3.02
645 664 4.937620 CCAGAAGATCACGGATTTTTCAGA 59.062 41.667 0.00 0.00 0.00 3.27
646 665 5.587844 CCAGAAGATCACGGATTTTTCAGAT 59.412 40.000 0.00 0.00 0.00 2.90
647 666 6.094603 CCAGAAGATCACGGATTTTTCAGATT 59.905 38.462 0.00 0.00 0.00 2.40
648 667 7.362401 CCAGAAGATCACGGATTTTTCAGATTT 60.362 37.037 0.00 0.00 0.00 2.17
649 668 8.025445 CAGAAGATCACGGATTTTTCAGATTTT 58.975 33.333 0.00 0.00 0.00 1.82
650 669 8.579863 AGAAGATCACGGATTTTTCAGATTTTT 58.420 29.630 0.00 0.00 0.00 1.94
673 692 9.853177 TTTTTGGGCCTGAAATATTTAAAAGAA 57.147 25.926 4.53 0.00 0.00 2.52
703 722 4.123276 TCGATAACACTTGCGTCAAAAC 57.877 40.909 0.00 0.00 0.00 2.43
710 729 9.716507 GATAACACTTGCGTCAAAACATATTAT 57.283 29.630 0.00 0.00 0.00 1.28
716 735 7.277098 ACTTGCGTCAAAACATATTATCGTACT 59.723 33.333 0.00 0.00 0.00 2.73
718 737 8.806177 TGCGTCAAAACATATTATCGTACTAT 57.194 30.769 0.00 0.00 0.00 2.12
719 738 9.896263 TGCGTCAAAACATATTATCGTACTATA 57.104 29.630 0.00 0.00 0.00 1.31
745 764 4.474394 CTTCCAAGGAAAAGGAAAGAGGT 58.526 43.478 2.78 0.00 42.91 3.85
746 765 4.536295 TCCAAGGAAAAGGAAAGAGGTT 57.464 40.909 0.00 0.00 0.00 3.50
747 766 5.656549 TCCAAGGAAAAGGAAAGAGGTTA 57.343 39.130 0.00 0.00 0.00 2.85
748 767 5.382616 TCCAAGGAAAAGGAAAGAGGTTAC 58.617 41.667 0.00 0.00 0.00 2.50
749 768 4.523173 CCAAGGAAAAGGAAAGAGGTTACC 59.477 45.833 0.00 0.00 0.00 2.85
750 769 4.383931 AGGAAAAGGAAAGAGGTTACCC 57.616 45.455 0.00 0.00 0.00 3.69
751 770 3.988186 AGGAAAAGGAAAGAGGTTACCCT 59.012 43.478 0.00 0.00 46.66 4.34
789 808 9.950496 GGAAAAGGAAAGAGAGATGCATATATA 57.050 33.333 0.00 0.00 0.00 0.86
794 813 6.695278 GGAAAGAGAGATGCATATATACGAGC 59.305 42.308 0.00 0.00 0.00 5.03
814 833 3.945921 AGCTAGGAAAATAAAACGGCTCC 59.054 43.478 0.00 0.00 0.00 4.70
816 835 4.201920 GCTAGGAAAATAAAACGGCTCCAG 60.202 45.833 0.00 0.00 0.00 3.86
817 836 2.492088 AGGAAAATAAAACGGCTCCAGC 59.508 45.455 0.00 0.00 41.14 4.85
818 837 2.515912 GAAAATAAAACGGCTCCAGCG 58.484 47.619 0.00 0.00 43.26 5.18
819 838 1.816074 AAATAAAACGGCTCCAGCGA 58.184 45.000 0.00 0.00 43.26 4.93
820 839 1.084289 AATAAAACGGCTCCAGCGAC 58.916 50.000 0.00 0.00 43.26 5.19
823 842 1.098712 AAAACGGCTCCAGCGACAAA 61.099 50.000 0.00 0.00 43.26 2.83
824 843 0.889186 AAACGGCTCCAGCGACAAAT 60.889 50.000 0.00 0.00 43.26 2.32
825 844 0.889186 AACGGCTCCAGCGACAAATT 60.889 50.000 0.00 0.00 43.26 1.82
826 845 0.036765 ACGGCTCCAGCGACAAATTA 60.037 50.000 0.00 0.00 43.26 1.40
827 846 0.652592 CGGCTCCAGCGACAAATTAG 59.347 55.000 0.00 0.00 43.26 1.73
828 847 0.378610 GGCTCCAGCGACAAATTAGC 59.621 55.000 0.00 0.00 43.26 3.09
829 848 0.026803 GCTCCAGCGACAAATTAGCG 59.973 55.000 0.00 0.00 35.78 4.26
830 849 1.359848 CTCCAGCGACAAATTAGCGT 58.640 50.000 0.00 0.00 35.78 5.07
831 850 1.061131 CTCCAGCGACAAATTAGCGTG 59.939 52.381 0.00 0.00 35.78 5.34
832 851 0.521242 CCAGCGACAAATTAGCGTGC 60.521 55.000 0.00 0.00 35.78 5.34
833 852 0.521242 CAGCGACAAATTAGCGTGCC 60.521 55.000 0.00 0.00 35.78 5.01
834 853 1.226295 GCGACAAATTAGCGTGCCC 60.226 57.895 0.00 0.00 0.00 5.36
835 854 1.917782 GCGACAAATTAGCGTGCCCA 61.918 55.000 0.00 0.00 0.00 5.36
836 855 0.519519 CGACAAATTAGCGTGCCCAA 59.480 50.000 0.00 0.00 0.00 4.12
883 907 2.837498 AGCAAAACCTTCCACAAATGC 58.163 42.857 0.00 0.00 0.00 3.56
884 908 2.435437 AGCAAAACCTTCCACAAATGCT 59.565 40.909 0.00 0.00 38.01 3.79
887 911 1.412079 AACCTTCCACAAATGCTGCA 58.588 45.000 4.13 4.13 0.00 4.41
928 952 5.738225 CCGTCTCTTCTAAACTAATCACGAC 59.262 44.000 0.00 0.00 0.00 4.34
931 955 7.164498 CGTCTCTTCTAAACTAATCACGACATC 59.836 40.741 0.00 0.00 0.00 3.06
1002 1026 3.133691 ACCAAACCGATCGATCATCATG 58.866 45.455 24.40 16.24 0.00 3.07
1003 1027 2.481568 CCAAACCGATCGATCATCATGG 59.518 50.000 24.40 20.48 0.00 3.66
1004 1028 1.800805 AACCGATCGATCATCATGGC 58.199 50.000 24.40 0.00 0.00 4.40
1005 1029 0.389037 ACCGATCGATCATCATGGCG 60.389 55.000 24.40 8.87 0.00 5.69
1006 1030 1.080435 CCGATCGATCATCATGGCGG 61.080 60.000 24.40 14.00 0.00 6.13
1007 1031 1.690283 CGATCGATCATCATGGCGGC 61.690 60.000 24.40 0.00 0.00 6.53
1165 1207 3.126703 TTCAACAAGCCTGCCCCGA 62.127 57.895 0.00 0.00 0.00 5.14
1347 1389 4.379243 CTCGCCTGCAACCTCCGT 62.379 66.667 0.00 0.00 0.00 4.69
1758 1918 4.424566 GACGTGTTCGCCGCCCTA 62.425 66.667 0.00 0.00 41.18 3.53
1809 1972 0.737715 GCAACATCGACCTCTCGCTT 60.738 55.000 0.00 0.00 39.96 4.68
2222 2407 1.009900 CCTACGACGACGATGGAGC 60.010 63.158 15.32 0.00 42.66 4.70
2244 2429 2.743928 GACCTGCAGTGGAAGCGG 60.744 66.667 13.81 0.00 38.10 5.52
2250 5225 1.675641 GCAGTGGAAGCGGATGGTT 60.676 57.895 0.00 0.00 38.83 3.67
2411 8516 2.456119 GCGTCATCACCTTCAGCGG 61.456 63.158 0.00 0.00 0.00 5.52
2661 8766 2.034812 GGCGATCACGAGGAAGTATTCT 59.965 50.000 0.00 0.00 43.09 2.40
2781 8886 0.615331 TGAGCGGCTTCTCCAAGAAT 59.385 50.000 2.97 0.00 33.13 2.40
2820 8925 1.412710 GAGGGCGAATACATCCTGTCA 59.587 52.381 0.00 0.00 0.00 3.58
2894 8999 5.179929 TCGTTGTGTTCGACTGAATAGTAGA 59.820 40.000 0.00 0.00 37.25 2.59
2896 9001 6.380190 GTTGTGTTCGACTGAATAGTAGACT 58.620 40.000 0.00 0.00 38.12 3.24
2897 9002 5.939457 TGTGTTCGACTGAATAGTAGACTG 58.061 41.667 0.00 0.00 38.12 3.51
2900 9005 4.617808 TCGACTGAATAGTAGACTGTGC 57.382 45.455 0.00 0.00 37.25 4.57
2904 9009 6.037281 TCGACTGAATAGTAGACTGTGCTAAG 59.963 42.308 0.00 0.00 37.25 2.18
3041 9154 2.010145 TAGAGCTGTCCATGAAACGC 57.990 50.000 0.00 1.11 0.00 4.84
3107 9224 4.877378 AATGCAAAAAGGAAGATGAGCA 57.123 36.364 0.00 0.00 35.03 4.26
3188 9310 6.700520 ACAGAGACTTTTTACTTGTAGGAACG 59.299 38.462 0.00 0.00 0.00 3.95
3211 9333 5.107913 CGCAAAACGTGACAATTTTGATGAT 60.108 36.000 21.80 0.00 44.85 2.45
3292 9417 6.633234 CCGTATCATAATAGTGCTATGCTACG 59.367 42.308 14.46 14.46 44.06 3.51
3301 9429 4.799678 AGTGCTATGCTACGATATGTCAC 58.200 43.478 0.00 0.00 0.00 3.67
3326 9454 6.261118 GCATGACAACAAATAAGGTCATCTC 58.739 40.000 0.00 0.00 45.15 2.75
3343 9825 8.584157 AGGTCATCTCAGATACTGATATTTGAC 58.416 37.037 16.09 16.09 39.92 3.18
3420 9902 3.118992 TGCTATCCACTACAGACAGCTTG 60.119 47.826 0.00 0.00 0.00 4.01
3423 10586 3.876274 TCCACTACAGACAGCTTGATC 57.124 47.619 0.00 0.00 0.00 2.92
3427 10590 4.569966 CCACTACAGACAGCTTGATCAATC 59.430 45.833 8.96 4.70 0.00 2.67
3440 10603 5.741673 GCTTGATCAATCTCCTCCTTAGACC 60.742 48.000 8.96 0.00 0.00 3.85
3443 10606 4.338795 TCAATCTCCTCCTTAGACCTGT 57.661 45.455 0.00 0.00 0.00 4.00
3448 10611 6.800072 ATCTCCTCCTTAGACCTGTAAAAG 57.200 41.667 0.00 0.00 0.00 2.27
3451 10614 6.210984 TCTCCTCCTTAGACCTGTAAAAGAAC 59.789 42.308 0.00 0.00 0.00 3.01
3500 10664 1.656652 AATGTGCAGATCCTACACGC 58.343 50.000 0.00 0.00 37.11 5.34
3573 10738 0.035317 ATCGCACACTCCTCAAAGCA 59.965 50.000 0.00 0.00 0.00 3.91
3592 10757 2.289320 GCAGCTCAGAGAAAGAGGAACA 60.289 50.000 0.00 0.00 33.72 3.18
3593 10758 3.805108 GCAGCTCAGAGAAAGAGGAACAA 60.805 47.826 0.00 0.00 33.72 2.83
3621 10786 2.159240 CGACCATTTCCGATGAGTCAGA 60.159 50.000 0.00 0.00 0.00 3.27
3629 10794 1.680207 CCGATGAGTCAGATCAGAGCA 59.320 52.381 0.00 0.00 31.44 4.26
3631 10796 3.243805 CCGATGAGTCAGATCAGAGCAAT 60.244 47.826 0.00 0.00 31.44 3.56
3673 10846 1.282875 CGAGTGTGAGACTGTGCGA 59.717 57.895 0.00 0.00 33.83 5.10
3675 10848 1.130561 CGAGTGTGAGACTGTGCGATA 59.869 52.381 0.00 0.00 33.83 2.92
3687 10860 4.579869 ACTGTGCGATATTTCTCAAAGGT 58.420 39.130 0.00 0.00 27.89 3.50
3718 10891 1.674057 CCCTCACCGCTCACTCTTT 59.326 57.895 0.00 0.00 0.00 2.52
3729 10902 2.408050 CTCACTCTTTGTTGTCTCCCG 58.592 52.381 0.00 0.00 0.00 5.14
3740 10913 1.323271 TGTCTCCCGCATCACTCTCC 61.323 60.000 0.00 0.00 0.00 3.71
3745 10918 1.760086 CCGCATCACTCTCCCCTCT 60.760 63.158 0.00 0.00 0.00 3.69
3747 10920 0.754957 CGCATCACTCTCCCCTCTCT 60.755 60.000 0.00 0.00 0.00 3.10
3748 10921 1.477740 CGCATCACTCTCCCCTCTCTA 60.478 57.143 0.00 0.00 0.00 2.43
3751 10924 3.500289 GCATCACTCTCCCCTCTCTATCT 60.500 52.174 0.00 0.00 0.00 1.98
3770 10943 1.081242 GCGGTTCCACTAACGTCGA 60.081 57.895 0.00 0.00 39.13 4.20
3809 10982 0.976073 GGTGGGAAGATCTGGACGGA 60.976 60.000 0.00 0.00 0.00 4.69
3816 10989 3.637229 GGAAGATCTGGACGGAGAACATA 59.363 47.826 0.00 0.00 0.00 2.29
3817 10990 4.282195 GGAAGATCTGGACGGAGAACATAT 59.718 45.833 0.00 0.00 0.00 1.78
3819 10992 3.576118 AGATCTGGACGGAGAACATATGG 59.424 47.826 7.80 0.00 0.00 2.74
3822 11001 0.600255 GGACGGAGAACATATGGGCG 60.600 60.000 7.80 0.00 0.00 6.13
3826 11005 1.472552 CGGAGAACATATGGGCGACAA 60.473 52.381 7.80 0.00 0.00 3.18
3834 11013 5.248870 ACATATGGGCGACAAAAAGATTC 57.751 39.130 7.80 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.358737 CGGTCAGGCGAGGCTTTT 60.359 61.111 0.00 0.00 0.00 2.27
18 19 3.291101 TTTCTCCGGGCTCCGTTCG 62.291 63.158 0.00 0.00 46.80 3.95
19 20 1.740664 GTTTCTCCGGGCTCCGTTC 60.741 63.158 0.00 0.00 46.80 3.95
20 21 1.765597 AAGTTTCTCCGGGCTCCGTT 61.766 55.000 0.00 0.00 46.80 4.44
21 22 0.901580 TAAGTTTCTCCGGGCTCCGT 60.902 55.000 0.00 0.00 46.80 4.69
23 24 2.562635 GAATAAGTTTCTCCGGGCTCC 58.437 52.381 0.00 0.00 0.00 4.70
24 25 2.562635 GGAATAAGTTTCTCCGGGCTC 58.437 52.381 0.00 0.00 0.00 4.70
25 26 1.134491 CGGAATAAGTTTCTCCGGGCT 60.134 52.381 14.53 0.00 46.66 5.19
26 27 1.296727 CGGAATAAGTTTCTCCGGGC 58.703 55.000 14.53 0.00 46.66 6.13
30 31 1.587034 CGCGTCGGAATAAGTTTCTCC 59.413 52.381 0.00 0.00 0.00 3.71
31 32 2.278354 GTCGCGTCGGAATAAGTTTCTC 59.722 50.000 5.77 0.00 0.00 2.87
32 33 2.257034 GTCGCGTCGGAATAAGTTTCT 58.743 47.619 5.77 0.00 0.00 2.52
33 34 1.987770 TGTCGCGTCGGAATAAGTTTC 59.012 47.619 5.77 0.00 0.00 2.78
34 35 1.723003 GTGTCGCGTCGGAATAAGTTT 59.277 47.619 5.77 0.00 0.00 2.66
35 36 1.343506 GTGTCGCGTCGGAATAAGTT 58.656 50.000 5.77 0.00 0.00 2.66
36 37 0.457337 GGTGTCGCGTCGGAATAAGT 60.457 55.000 5.77 0.00 0.00 2.24
37 38 0.457166 TGGTGTCGCGTCGGAATAAG 60.457 55.000 5.77 0.00 0.00 1.73
38 39 0.733566 GTGGTGTCGCGTCGGAATAA 60.734 55.000 5.77 0.00 0.00 1.40
39 40 1.153978 GTGGTGTCGCGTCGGAATA 60.154 57.895 5.77 0.00 0.00 1.75
40 41 2.431942 GTGGTGTCGCGTCGGAAT 60.432 61.111 5.77 0.00 0.00 3.01
41 42 4.651008 GGTGGTGTCGCGTCGGAA 62.651 66.667 5.77 0.00 0.00 4.30
67 68 4.200283 GAGGGAGACGCTGCCGAG 62.200 72.222 10.70 0.00 46.84 4.63
69 70 4.069232 TTGAGGGAGACGCTGCCG 62.069 66.667 10.70 0.00 46.84 5.69
70 71 2.435059 GTTGAGGGAGACGCTGCC 60.435 66.667 8.90 8.90 42.52 4.85
71 72 2.435059 GGTTGAGGGAGACGCTGC 60.435 66.667 0.00 0.00 0.00 5.25
72 73 0.970937 TAGGGTTGAGGGAGACGCTG 60.971 60.000 3.70 0.00 39.12 5.18
73 74 0.252103 TTAGGGTTGAGGGAGACGCT 60.252 55.000 0.00 0.00 41.26 5.07
74 75 0.108281 GTTAGGGTTGAGGGAGACGC 60.108 60.000 0.00 0.00 0.00 5.19
75 76 0.535797 GGTTAGGGTTGAGGGAGACG 59.464 60.000 0.00 0.00 0.00 4.18
76 77 0.910338 GGGTTAGGGTTGAGGGAGAC 59.090 60.000 0.00 0.00 0.00 3.36
77 78 0.797579 AGGGTTAGGGTTGAGGGAGA 59.202 55.000 0.00 0.00 0.00 3.71
78 79 2.117051 GTAGGGTTAGGGTTGAGGGAG 58.883 57.143 0.00 0.00 0.00 4.30
79 80 1.274011 GGTAGGGTTAGGGTTGAGGGA 60.274 57.143 0.00 0.00 0.00 4.20
80 81 1.210538 GGTAGGGTTAGGGTTGAGGG 58.789 60.000 0.00 0.00 0.00 4.30
81 82 1.558294 GTGGTAGGGTTAGGGTTGAGG 59.442 57.143 0.00 0.00 0.00 3.86
82 83 2.027469 GTGTGGTAGGGTTAGGGTTGAG 60.027 54.545 0.00 0.00 0.00 3.02
83 84 1.980036 GTGTGGTAGGGTTAGGGTTGA 59.020 52.381 0.00 0.00 0.00 3.18
84 85 1.003928 GGTGTGGTAGGGTTAGGGTTG 59.996 57.143 0.00 0.00 0.00 3.77
85 86 1.365293 GGTGTGGTAGGGTTAGGGTT 58.635 55.000 0.00 0.00 0.00 4.11
86 87 0.548439 GGGTGTGGTAGGGTTAGGGT 60.548 60.000 0.00 0.00 0.00 4.34
87 88 0.548197 TGGGTGTGGTAGGGTTAGGG 60.548 60.000 0.00 0.00 0.00 3.53
88 89 0.616891 GTGGGTGTGGTAGGGTTAGG 59.383 60.000 0.00 0.00 0.00 2.69
89 90 0.616891 GGTGGGTGTGGTAGGGTTAG 59.383 60.000 0.00 0.00 0.00 2.34
90 91 0.194080 AGGTGGGTGTGGTAGGGTTA 59.806 55.000 0.00 0.00 0.00 2.85
91 92 0.194080 TAGGTGGGTGTGGTAGGGTT 59.806 55.000 0.00 0.00 0.00 4.11
92 93 0.252558 CTAGGTGGGTGTGGTAGGGT 60.253 60.000 0.00 0.00 0.00 4.34
93 94 1.623542 GCTAGGTGGGTGTGGTAGGG 61.624 65.000 0.00 0.00 0.00 3.53
94 95 1.905512 GCTAGGTGGGTGTGGTAGG 59.094 63.158 0.00 0.00 0.00 3.18
95 96 1.255667 ACGCTAGGTGGGTGTGGTAG 61.256 60.000 0.00 0.00 40.49 3.18
96 97 1.228956 ACGCTAGGTGGGTGTGGTA 60.229 57.895 0.00 0.00 40.49 3.25
97 98 2.525877 ACGCTAGGTGGGTGTGGT 60.526 61.111 0.00 0.00 40.49 4.16
98 99 2.264794 GACGCTAGGTGGGTGTGG 59.735 66.667 0.00 0.00 42.14 4.17
99 100 1.374252 GTGACGCTAGGTGGGTGTG 60.374 63.158 0.00 0.00 42.14 3.82
100 101 1.533273 AGTGACGCTAGGTGGGTGT 60.533 57.895 0.00 0.00 42.14 4.16
101 102 1.079819 CAGTGACGCTAGGTGGGTG 60.080 63.158 0.00 0.00 42.14 4.61
102 103 0.251474 TACAGTGACGCTAGGTGGGT 60.251 55.000 0.00 0.00 44.89 4.51
103 104 1.067212 GATACAGTGACGCTAGGTGGG 59.933 57.143 0.00 0.00 0.00 4.61
104 105 2.025155 AGATACAGTGACGCTAGGTGG 58.975 52.381 0.00 0.00 0.00 4.61
105 106 2.683362 TCAGATACAGTGACGCTAGGTG 59.317 50.000 0.00 0.00 0.00 4.00
106 107 3.000684 TCAGATACAGTGACGCTAGGT 57.999 47.619 0.00 0.00 0.00 3.08
107 108 4.202060 ACAATCAGATACAGTGACGCTAGG 60.202 45.833 0.00 0.00 0.00 3.02
108 109 4.737279 CACAATCAGATACAGTGACGCTAG 59.263 45.833 0.00 0.00 32.14 3.42
109 110 4.672409 CACAATCAGATACAGTGACGCTA 58.328 43.478 0.00 0.00 32.14 4.26
110 111 3.515630 CACAATCAGATACAGTGACGCT 58.484 45.455 0.00 0.00 32.14 5.07
111 112 2.029728 GCACAATCAGATACAGTGACGC 59.970 50.000 12.43 0.99 32.14 5.19
112 113 3.253230 TGCACAATCAGATACAGTGACG 58.747 45.455 12.43 0.00 32.14 4.35
113 114 4.692625 ACTTGCACAATCAGATACAGTGAC 59.307 41.667 12.43 6.47 32.14 3.67
114 115 4.692155 CACTTGCACAATCAGATACAGTGA 59.308 41.667 12.43 0.00 32.14 3.41
115 116 4.670992 GCACTTGCACAATCAGATACAGTG 60.671 45.833 0.00 3.06 41.59 3.66
116 117 3.438087 GCACTTGCACAATCAGATACAGT 59.562 43.478 0.00 0.00 41.59 3.55
117 118 3.484721 CGCACTTGCACAATCAGATACAG 60.485 47.826 1.48 0.00 42.21 2.74
118 119 2.416202 CGCACTTGCACAATCAGATACA 59.584 45.455 1.48 0.00 42.21 2.29
119 120 2.223112 CCGCACTTGCACAATCAGATAC 60.223 50.000 1.48 0.00 42.21 2.24
120 121 2.009051 CCGCACTTGCACAATCAGATA 58.991 47.619 1.48 0.00 42.21 1.98
121 122 0.806868 CCGCACTTGCACAATCAGAT 59.193 50.000 1.48 0.00 42.21 2.90
122 123 0.534877 ACCGCACTTGCACAATCAGA 60.535 50.000 1.48 0.00 42.21 3.27
123 124 0.311790 AACCGCACTTGCACAATCAG 59.688 50.000 1.48 0.00 42.21 2.90
124 125 0.030504 CAACCGCACTTGCACAATCA 59.969 50.000 1.48 0.00 42.21 2.57
125 126 0.664166 CCAACCGCACTTGCACAATC 60.664 55.000 1.48 0.00 42.21 2.67
126 127 1.363443 CCAACCGCACTTGCACAAT 59.637 52.632 1.48 0.00 42.21 2.71
127 128 2.804167 CCAACCGCACTTGCACAA 59.196 55.556 1.48 0.00 42.21 3.33
128 129 3.898509 GCCAACCGCACTTGCACA 61.899 61.111 1.48 0.00 42.21 4.57
129 130 3.829272 CTGCCAACCGCACTTGCAC 62.829 63.158 1.48 0.00 44.64 4.57
130 131 3.594775 CTGCCAACCGCACTTGCA 61.595 61.111 1.48 0.00 44.64 4.08
132 133 2.807631 GATGCTGCCAACCGCACTTG 62.808 60.000 0.00 0.00 44.64 3.16
133 134 2.598394 ATGCTGCCAACCGCACTT 60.598 55.556 0.00 0.00 44.64 3.16
134 135 3.058160 GATGCTGCCAACCGCACT 61.058 61.111 0.00 0.00 44.64 4.40
135 136 2.419057 TTTGATGCTGCCAACCGCAC 62.419 55.000 0.00 0.00 44.64 5.34
137 138 0.599728 TTTTTGATGCTGCCAACCGC 60.600 50.000 0.00 0.00 38.31 5.68
138 139 3.584586 TTTTTGATGCTGCCAACCG 57.415 47.368 0.00 0.00 0.00 4.44
153 154 4.729227 TTTTTGCCTCGACTTCCTTTTT 57.271 36.364 0.00 0.00 0.00 1.94
154 155 4.937201 ATTTTTGCCTCGACTTCCTTTT 57.063 36.364 0.00 0.00 0.00 2.27
155 156 4.937201 AATTTTTGCCTCGACTTCCTTT 57.063 36.364 0.00 0.00 0.00 3.11
156 157 4.937201 AAATTTTTGCCTCGACTTCCTT 57.063 36.364 0.00 0.00 0.00 3.36
157 158 5.048713 CACTAAATTTTTGCCTCGACTTCCT 60.049 40.000 0.00 0.00 0.00 3.36
158 159 5.154222 CACTAAATTTTTGCCTCGACTTCC 58.846 41.667 0.00 0.00 0.00 3.46
159 160 5.154222 CCACTAAATTTTTGCCTCGACTTC 58.846 41.667 0.00 0.00 0.00 3.01
160 161 4.583073 ACCACTAAATTTTTGCCTCGACTT 59.417 37.500 0.00 0.00 0.00 3.01
161 162 4.023193 CACCACTAAATTTTTGCCTCGACT 60.023 41.667 0.00 0.00 0.00 4.18
162 163 4.023536 TCACCACTAAATTTTTGCCTCGAC 60.024 41.667 0.00 0.00 0.00 4.20
163 164 4.138290 TCACCACTAAATTTTTGCCTCGA 58.862 39.130 0.00 0.00 0.00 4.04
164 165 4.497473 TCACCACTAAATTTTTGCCTCG 57.503 40.909 0.00 0.00 0.00 4.63
165 166 7.029563 CACTATCACCACTAAATTTTTGCCTC 58.970 38.462 0.00 0.00 0.00 4.70
166 167 6.071391 CCACTATCACCACTAAATTTTTGCCT 60.071 38.462 0.00 0.00 0.00 4.75
167 168 6.099341 CCACTATCACCACTAAATTTTTGCC 58.901 40.000 0.00 0.00 0.00 4.52
168 169 6.586082 CACCACTATCACCACTAAATTTTTGC 59.414 38.462 0.00 0.00 0.00 3.68
169 170 7.807907 GTCACCACTATCACCACTAAATTTTTG 59.192 37.037 0.00 0.00 0.00 2.44
170 171 7.039993 GGTCACCACTATCACCACTAAATTTTT 60.040 37.037 0.00 0.00 0.00 1.94
171 172 6.433093 GGTCACCACTATCACCACTAAATTTT 59.567 38.462 0.00 0.00 0.00 1.82
172 173 5.944007 GGTCACCACTATCACCACTAAATTT 59.056 40.000 0.00 0.00 0.00 1.82
173 174 5.497474 GGTCACCACTATCACCACTAAATT 58.503 41.667 0.00 0.00 0.00 1.82
174 175 4.080526 GGGTCACCACTATCACCACTAAAT 60.081 45.833 0.00 0.00 36.50 1.40
175 176 3.262405 GGGTCACCACTATCACCACTAAA 59.738 47.826 0.00 0.00 36.50 1.85
176 177 2.835764 GGGTCACCACTATCACCACTAA 59.164 50.000 0.00 0.00 36.50 2.24
177 178 2.463752 GGGTCACCACTATCACCACTA 58.536 52.381 0.00 0.00 36.50 2.74
178 179 1.276622 GGGTCACCACTATCACCACT 58.723 55.000 0.00 0.00 36.50 4.00
179 180 0.108329 CGGGTCACCACTATCACCAC 60.108 60.000 0.00 0.00 36.13 4.16
180 181 0.251877 TCGGGTCACCACTATCACCA 60.252 55.000 0.00 0.00 36.13 4.17
181 182 0.899720 TTCGGGTCACCACTATCACC 59.100 55.000 0.00 0.00 36.13 4.02
182 183 1.549170 AGTTCGGGTCACCACTATCAC 59.451 52.381 0.00 0.00 36.13 3.06
183 184 1.933021 AGTTCGGGTCACCACTATCA 58.067 50.000 0.00 0.00 36.13 2.15
184 185 3.000727 CAAAGTTCGGGTCACCACTATC 58.999 50.000 0.00 0.00 36.13 2.08
185 186 2.635915 TCAAAGTTCGGGTCACCACTAT 59.364 45.455 0.00 0.00 36.13 2.12
186 187 2.040939 TCAAAGTTCGGGTCACCACTA 58.959 47.619 0.00 0.00 36.13 2.74
187 188 0.834612 TCAAAGTTCGGGTCACCACT 59.165 50.000 0.00 0.00 36.13 4.00
255 256 3.998913 TGACATTCCAGAAGCCATACA 57.001 42.857 0.00 0.00 0.00 2.29
256 257 4.009675 TGTTGACATTCCAGAAGCCATAC 58.990 43.478 0.00 0.00 0.00 2.39
262 263 5.835257 ACAACAATGTTGACATTCCAGAAG 58.165 37.500 30.09 1.65 44.10 2.85
292 304 2.287009 GCGAAAACACTGGACCTTTCAG 60.287 50.000 0.00 0.00 38.16 3.02
386 403 0.475906 ATCAGCCCCAAGCCAGATAC 59.524 55.000 0.00 0.00 45.47 2.24
408 425 4.264172 TGGTTTTCCTAAGCCACATACCAT 60.264 41.667 0.00 0.00 39.41 3.55
415 432 2.802719 TCCATGGTTTTCCTAAGCCAC 58.197 47.619 12.58 0.00 45.79 5.01
532 549 6.426980 TGTACATTTCTATCGTAGTGTCGT 57.573 37.500 0.00 0.00 0.00 4.34
534 551 7.378995 GGACATGTACATTTCTATCGTAGTGTC 59.621 40.741 18.86 13.35 34.44 3.67
535 552 7.201145 GGACATGTACATTTCTATCGTAGTGT 58.799 38.462 18.86 5.88 0.00 3.55
536 553 6.641314 GGGACATGTACATTTCTATCGTAGTG 59.359 42.308 18.86 2.85 0.00 2.74
543 560 6.575244 TGGAAGGGACATGTACATTTCTAT 57.425 37.500 14.68 7.56 0.00 1.98
577 596 3.119245 CCAGTAGAAAACCGGAATCGAGA 60.119 47.826 9.46 0.00 39.00 4.04
647 666 9.853177 TTCTTTTAAATATTTCAGGCCCAAAAA 57.147 25.926 3.39 0.00 0.00 1.94
669 688 8.915654 GCAAGTGTTATCGAATTCAAAATTCTT 58.084 29.630 6.22 0.00 0.00 2.52
670 689 7.271223 CGCAAGTGTTATCGAATTCAAAATTCT 59.729 33.333 6.22 0.00 0.00 2.40
671 690 7.375781 CGCAAGTGTTATCGAATTCAAAATTC 58.624 34.615 6.22 2.93 0.00 2.17
672 691 7.264448 CGCAAGTGTTATCGAATTCAAAATT 57.736 32.000 6.22 0.00 0.00 1.82
673 692 6.853279 CGCAAGTGTTATCGAATTCAAAAT 57.147 33.333 6.22 0.00 0.00 1.82
710 729 6.855763 TTCCTTGGAAGGTTTATAGTACGA 57.144 37.500 5.33 0.00 46.54 3.43
716 735 8.228905 TCTTTCCTTTTCCTTGGAAGGTTTATA 58.771 33.333 5.33 0.00 46.54 0.98
718 737 6.436890 TCTTTCCTTTTCCTTGGAAGGTTTA 58.563 36.000 5.33 0.00 46.54 2.01
719 738 5.277250 TCTTTCCTTTTCCTTGGAAGGTTT 58.723 37.500 5.33 0.00 46.54 3.27
723 742 4.474394 ACCTCTTTCCTTTTCCTTGGAAG 58.526 43.478 2.16 0.00 42.46 3.46
724 743 4.536295 ACCTCTTTCCTTTTCCTTGGAA 57.464 40.909 0.00 0.00 40.21 3.53
725 744 4.536295 AACCTCTTTCCTTTTCCTTGGA 57.464 40.909 0.00 0.00 0.00 3.53
726 745 4.523173 GGTAACCTCTTTCCTTTTCCTTGG 59.477 45.833 0.00 0.00 0.00 3.61
727 746 5.707242 GGTAACCTCTTTCCTTTTCCTTG 57.293 43.478 0.00 0.00 0.00 3.61
758 777 6.324770 TGCATCTCTCTTTCCTTTTCCTTTTT 59.675 34.615 0.00 0.00 0.00 1.94
759 778 5.835280 TGCATCTCTCTTTCCTTTTCCTTTT 59.165 36.000 0.00 0.00 0.00 2.27
760 779 5.388654 TGCATCTCTCTTTCCTTTTCCTTT 58.611 37.500 0.00 0.00 0.00 3.11
761 780 4.990526 TGCATCTCTCTTTCCTTTTCCTT 58.009 39.130 0.00 0.00 0.00 3.36
762 781 4.647564 TGCATCTCTCTTTCCTTTTCCT 57.352 40.909 0.00 0.00 0.00 3.36
763 782 8.860780 ATATATGCATCTCTCTTTCCTTTTCC 57.139 34.615 0.19 0.00 0.00 3.13
765 784 9.429359 CGTATATATGCATCTCTCTTTCCTTTT 57.571 33.333 0.19 0.00 0.00 2.27
766 785 8.807118 TCGTATATATGCATCTCTCTTTCCTTT 58.193 33.333 0.19 0.00 0.00 3.11
767 786 8.354711 TCGTATATATGCATCTCTCTTTCCTT 57.645 34.615 0.19 0.00 0.00 3.36
768 787 7.416213 GCTCGTATATATGCATCTCTCTTTCCT 60.416 40.741 0.19 0.00 0.00 3.36
769 788 6.695278 GCTCGTATATATGCATCTCTCTTTCC 59.305 42.308 0.19 0.00 0.00 3.13
770 789 7.479980 AGCTCGTATATATGCATCTCTCTTTC 58.520 38.462 0.19 0.00 0.00 2.62
771 790 7.403312 AGCTCGTATATATGCATCTCTCTTT 57.597 36.000 0.19 0.00 0.00 2.52
772 791 7.228507 CCTAGCTCGTATATATGCATCTCTCTT 59.771 40.741 0.19 0.00 0.00 2.85
773 792 6.710295 CCTAGCTCGTATATATGCATCTCTCT 59.290 42.308 0.19 0.00 0.00 3.10
774 793 6.708502 TCCTAGCTCGTATATATGCATCTCTC 59.291 42.308 0.19 0.00 0.00 3.20
789 808 3.373130 GCCGTTTTATTTTCCTAGCTCGT 59.627 43.478 0.00 0.00 0.00 4.18
790 809 3.621715 AGCCGTTTTATTTTCCTAGCTCG 59.378 43.478 0.00 0.00 0.00 5.03
794 813 4.201920 GCTGGAGCCGTTTTATTTTCCTAG 60.202 45.833 0.00 0.00 34.31 3.02
814 833 0.521242 GGCACGCTAATTTGTCGCTG 60.521 55.000 4.35 4.15 0.00 5.18
816 835 1.226295 GGGCACGCTAATTTGTCGC 60.226 57.895 4.35 0.00 0.00 5.19
817 836 0.519519 TTGGGCACGCTAATTTGTCG 59.480 50.000 0.00 0.00 0.00 4.35
818 837 2.939460 ATTGGGCACGCTAATTTGTC 57.061 45.000 0.00 0.00 0.00 3.18
819 838 2.094234 GGAATTGGGCACGCTAATTTGT 60.094 45.455 6.36 0.00 0.00 2.83
820 839 2.539476 GGAATTGGGCACGCTAATTTG 58.461 47.619 6.36 0.00 0.00 2.32
823 842 0.107410 TCGGAATTGGGCACGCTAAT 60.107 50.000 0.00 0.00 0.00 1.73
824 843 0.742990 CTCGGAATTGGGCACGCTAA 60.743 55.000 0.00 0.00 0.00 3.09
825 844 1.153449 CTCGGAATTGGGCACGCTA 60.153 57.895 0.00 0.00 0.00 4.26
826 845 2.436646 CTCGGAATTGGGCACGCT 60.437 61.111 0.00 0.00 0.00 5.07
827 846 3.508840 CCTCGGAATTGGGCACGC 61.509 66.667 0.00 0.00 0.00 5.34
828 847 0.105964 TATCCTCGGAATTGGGCACG 59.894 55.000 0.00 0.00 0.00 5.34
829 848 2.222027 CTTATCCTCGGAATTGGGCAC 58.778 52.381 0.00 0.00 0.00 5.01
830 849 1.142870 CCTTATCCTCGGAATTGGGCA 59.857 52.381 0.00 0.00 0.00 5.36
831 850 1.420138 TCCTTATCCTCGGAATTGGGC 59.580 52.381 0.00 0.00 0.00 5.36
832 851 3.617531 CGATCCTTATCCTCGGAATTGGG 60.618 52.174 0.00 0.00 32.12 4.12
833 852 3.589988 CGATCCTTATCCTCGGAATTGG 58.410 50.000 0.00 0.00 32.12 3.16
883 907 1.851021 TTTTGCGGTGGATCGTGCAG 61.851 55.000 0.00 0.00 38.75 4.41
884 908 1.240641 ATTTTGCGGTGGATCGTGCA 61.241 50.000 0.00 0.00 35.15 4.57
887 911 1.366111 CGGATTTTGCGGTGGATCGT 61.366 55.000 0.00 0.00 0.00 3.73
928 952 6.803154 GGGGGATTTTTAAGATCGTAGATG 57.197 41.667 0.00 0.00 45.12 2.90
1530 1572 0.178992 TCCACTGCTTCTTTGGGGTG 60.179 55.000 0.00 0.00 0.00 4.61
1754 1914 0.387202 CATGTCCTCAGCGAGTAGGG 59.613 60.000 0.00 0.00 33.40 3.53
1758 1918 1.550327 TCTTCATGTCCTCAGCGAGT 58.450 50.000 0.00 0.00 0.00 4.18
1764 1924 2.165234 CGAGAGCTTCTTCATGTCCTCA 59.835 50.000 0.00 0.00 0.00 3.86
2781 8886 2.166459 CTCGAGGAACAGCTTCACCATA 59.834 50.000 3.91 0.00 0.00 2.74
2911 9016 3.508012 ACTCACTCGTGCTATTCTTCAGT 59.492 43.478 0.00 0.00 0.00 3.41
2912 9017 3.856521 CACTCACTCGTGCTATTCTTCAG 59.143 47.826 0.00 0.00 0.00 3.02
2919 9024 0.099613 CGCTCACTCACTCGTGCTAT 59.900 55.000 0.00 0.00 34.92 2.97
2923 9028 3.834350 CACGCTCACTCACTCGTG 58.166 61.111 0.00 0.00 44.62 4.35
2924 9029 1.167155 AGTCACGCTCACTCACTCGT 61.167 55.000 0.00 0.00 35.35 4.18
2925 9030 0.727457 CAGTCACGCTCACTCACTCG 60.727 60.000 0.00 0.00 0.00 4.18
2926 9031 1.006314 GCAGTCACGCTCACTCACTC 61.006 60.000 0.00 0.00 0.00 3.51
2927 9032 1.006805 GCAGTCACGCTCACTCACT 60.007 57.895 0.00 0.00 0.00 3.41
2950 9058 5.335191 GGAAACAGCTACAGAGAAAACCATG 60.335 44.000 0.00 0.00 0.00 3.66
3012 9125 7.517614 TCATGGACAGCTCTAAACTATAGAG 57.482 40.000 6.78 7.90 42.87 2.43
3170 9289 6.075780 CGTTTTGCGTTCCTACAAGTAAAAAG 60.076 38.462 0.00 0.00 35.54 2.27
3172 9291 5.264712 CGTTTTGCGTTCCTACAAGTAAAA 58.735 37.500 0.00 0.00 35.54 1.52
3188 9310 5.633996 TCATCAAAATTGTCACGTTTTGC 57.366 34.783 11.46 0.00 42.26 3.68
3283 9408 3.821841 TGCGTGACATATCGTAGCATAG 58.178 45.455 0.00 0.00 0.00 2.23
3301 9429 4.418013 TGACCTTATTTGTTGTCATGCG 57.582 40.909 0.00 0.00 33.09 4.73
3355 9837 7.953493 TGATACCAATGTATGATACTACCTCCA 59.047 37.037 4.03 0.00 37.80 3.86
3356 9838 8.362464 TGATACCAATGTATGATACTACCTCC 57.638 38.462 4.03 0.00 37.80 4.30
3403 9885 3.165071 TGATCAAGCTGTCTGTAGTGGA 58.835 45.455 0.00 0.00 0.00 4.02
3413 9895 3.113824 AGGAGGAGATTGATCAAGCTGT 58.886 45.455 29.68 16.79 37.15 4.40
3420 9902 4.898861 ACAGGTCTAAGGAGGAGATTGATC 59.101 45.833 0.00 0.00 0.00 2.92
3423 10586 6.546428 TTTACAGGTCTAAGGAGGAGATTG 57.454 41.667 0.00 0.00 0.00 2.67
3427 10590 6.399743 GTTCTTTTACAGGTCTAAGGAGGAG 58.600 44.000 0.00 0.00 0.00 3.69
3448 10611 9.342308 TCCATTCATGTCTATTTTAGATGGTTC 57.658 33.333 0.00 0.00 37.13 3.62
3451 10614 9.565090 TCTTCCATTCATGTCTATTTTAGATGG 57.435 33.333 0.00 0.00 37.13 3.51
3464 10627 5.711506 TGCACATTTACTCTTCCATTCATGT 59.288 36.000 0.00 0.00 0.00 3.21
3500 10664 8.357966 CAAATAAAACGATCAATCAAACACGAG 58.642 33.333 0.00 0.00 0.00 4.18
3531 10696 4.263209 CCAAGCCAAACGCGCACA 62.263 61.111 5.73 0.00 44.76 4.57
3573 10738 4.906747 ATTGTTCCTCTTTCTCTGAGCT 57.093 40.909 0.00 0.00 0.00 4.09
3592 10757 4.881273 TCATCGGAAATGGTCGATTCAATT 59.119 37.500 0.00 0.00 43.19 2.32
3593 10758 4.450976 TCATCGGAAATGGTCGATTCAAT 58.549 39.130 0.00 0.00 43.19 2.57
3621 10786 2.758979 CCCTCTTTGCAATTGCTCTGAT 59.241 45.455 29.37 0.00 42.66 2.90
3629 10794 1.290009 GCGTGCCCTCTTTGCAATT 59.710 52.632 0.00 0.00 41.06 2.32
3631 10796 3.659092 CGCGTGCCCTCTTTGCAA 61.659 61.111 0.00 0.00 41.06 4.08
3657 10822 3.876274 AATATCGCACAGTCTCACACT 57.124 42.857 0.00 0.00 34.67 3.55
3659 10824 4.082245 TGAGAAATATCGCACAGTCTCACA 60.082 41.667 0.00 0.00 37.25 3.58
3669 10842 3.126858 GCACACCTTTGAGAAATATCGCA 59.873 43.478 0.00 0.00 33.23 5.10
3718 10891 0.037326 GAGTGATGCGGGAGACAACA 60.037 55.000 0.00 0.00 0.00 3.33
3729 10902 2.373335 TAGAGAGGGGAGAGTGATGC 57.627 55.000 0.00 0.00 0.00 3.91
3740 10913 0.676736 GGAACCGCAGATAGAGAGGG 59.323 60.000 0.00 0.00 0.00 4.30
3745 10918 2.098607 CGTTAGTGGAACCGCAGATAGA 59.901 50.000 7.16 0.00 37.80 1.98
3747 10920 1.820519 ACGTTAGTGGAACCGCAGATA 59.179 47.619 7.16 0.00 37.80 1.98
3748 10921 0.606604 ACGTTAGTGGAACCGCAGAT 59.393 50.000 7.16 0.00 37.80 2.90
3751 10924 1.372004 CGACGTTAGTGGAACCGCA 60.372 57.895 7.16 0.00 37.80 5.69
3809 10982 4.331968 TCTTTTTGTCGCCCATATGTTCT 58.668 39.130 1.24 0.00 0.00 3.01
3816 10989 1.472480 CCGAATCTTTTTGTCGCCCAT 59.528 47.619 0.00 0.00 33.46 4.00
3817 10990 0.878416 CCGAATCTTTTTGTCGCCCA 59.122 50.000 0.00 0.00 33.46 5.36
3819 10992 1.533731 TGTCCGAATCTTTTTGTCGCC 59.466 47.619 0.00 0.00 33.46 5.54
3822 11001 4.319549 GGTCACTGTCCGAATCTTTTTGTC 60.320 45.833 0.00 0.00 0.00 3.18
3826 11005 3.485463 TGGTCACTGTCCGAATCTTTT 57.515 42.857 0.00 0.00 0.00 2.27
3834 11013 1.714794 GTTGAGATGGTCACTGTCCG 58.285 55.000 0.00 0.00 33.71 4.79


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

AutoCloner maintained by Alex Coulton.