Multiple sequence alignment - TraesCS1A01G281500

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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 TraesCS1A01G281500 chr1A 100.000 2692 0 0 1 2692 479836158 479833467 0.000000e+00 4972
1 TraesCS1A01G281500 chr1A 100.000 299 0 0 2934 3232 479833225 479832927 1.310000e-153 553
2 TraesCS1A01G281500 chr1A 97.222 72 2 0 1 72 240310201 240310130 4.380000e-24 122
3 TraesCS1A01G281500 chr5A 98.457 2268 29 3 428 2692 561525148 561527412 0.000000e+00 3989
4 TraesCS1A01G281500 chr5A 97.177 2267 42 3 429 2692 501834608 501836855 0.000000e+00 3812
5 TraesCS1A01G281500 chr5A 98.986 296 3 0 2934 3229 561528279 561528574 6.140000e-147 531
6 TraesCS1A01G281500 chr4A 98.368 2267 30 2 429 2692 495079462 495081724 0.000000e+00 3975
7 TraesCS1A01G281500 chr4A 96.124 2296 44 8 424 2692 647219073 647216796 0.000000e+00 3705
8 TraesCS1A01G281500 chr4A 100.000 299 0 0 2934 3232 495082403 495082701 1.310000e-153 553
9 TraesCS1A01G281500 chr7A 98.324 2267 35 1 429 2692 670242552 670240286 0.000000e+00 3973
10 TraesCS1A01G281500 chr7A 100.000 299 0 0 2934 3232 670239609 670239311 1.310000e-153 553
11 TraesCS1A01G281500 chr7A 89.412 85 8 1 1 85 422830896 422830979 4.410000e-19 106
12 TraesCS1A01G281500 chr7D 97.266 2268 26 7 429 2692 401545958 401543723 0.000000e+00 3812
13 TraesCS1A01G281500 chr7D 96.949 1573 40 6 429 1993 510009128 510010700 0.000000e+00 2632
14 TraesCS1A01G281500 chr7D 99.331 299 2 0 2934 3232 430129211 430129509 2.840000e-150 542
15 TraesCS1A01G281500 chr7D 98.662 299 4 0 2934 3232 510015893 510016191 6.140000e-147 531
16 TraesCS1A01G281500 chr2D 97.221 2267 32 6 429 2692 178274832 178272594 0.000000e+00 3808
17 TraesCS1A01G281500 chr2D 96.874 2271 33 6 429 2692 511935177 511932938 0.000000e+00 3766
18 TraesCS1A01G281500 chr2D 98.997 299 3 0 2934 3232 178271918 178271620 1.320000e-148 536
19 TraesCS1A01G281500 chr2D 85.577 104 12 2 1 104 93080100 93080200 4.410000e-19 106
20 TraesCS1A01G281500 chr3B 95.921 2280 45 9 440 2692 312175381 312173123 0.000000e+00 3651
21 TraesCS1A01G281500 chr1B 96.063 2235 43 13 485 2692 313093410 313091194 0.000000e+00 3598
22 TraesCS1A01G281500 chr1B 94.213 432 6 6 1 417 507851819 507851392 2.720000e-180 641
23 TraesCS1A01G281500 chr1D 97.649 1744 20 5 428 2167 197732545 197730819 0.000000e+00 2974
24 TraesCS1A01G281500 chr1D 98.325 418 5 2 1 417 379141345 379140929 0.000000e+00 732
25 TraesCS1A01G281500 chr1D 98.662 299 4 0 2934 3232 197729893 197729595 6.140000e-147 531
26 TraesCS1A01G281500 chr1D 97.222 72 2 0 1 72 246650052 246649981 4.380000e-24 122
27 TraesCS1A01G281500 chr6D 98.997 299 3 0 2934 3232 119145682 119145980 1.320000e-148 536
28 TraesCS1A01G281500 chr4B 98.328 299 5 0 2934 3232 311365100 311364802 2.860000e-145 525
29 TraesCS1A01G281500 chr4B 94.805 77 4 0 1 77 146469287 146469211 1.570000e-23 121
30 TraesCS1A01G281500 chr4B 95.890 73 3 0 1 73 506907651 506907579 5.660000e-23 119
31 TraesCS1A01G281500 chr7B 92.593 81 6 0 1 81 44939625 44939545 2.040000e-22 117


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 TraesCS1A01G281500 chr1A 479832927 479836158 3231 True 2762.5 4972 100.0000 1 3232 2 chr1A.!!$R2 3231
1 TraesCS1A01G281500 chr5A 501834608 501836855 2247 False 3812.0 3812 97.1770 429 2692 1 chr5A.!!$F1 2263
2 TraesCS1A01G281500 chr5A 561525148 561528574 3426 False 2260.0 3989 98.7215 428 3229 2 chr5A.!!$F2 2801
3 TraesCS1A01G281500 chr4A 647216796 647219073 2277 True 3705.0 3705 96.1240 424 2692 1 chr4A.!!$R1 2268
4 TraesCS1A01G281500 chr4A 495079462 495082701 3239 False 2264.0 3975 99.1840 429 3232 2 chr4A.!!$F1 2803
5 TraesCS1A01G281500 chr7A 670239311 670242552 3241 True 2263.0 3973 99.1620 429 3232 2 chr7A.!!$R1 2803
6 TraesCS1A01G281500 chr7D 401543723 401545958 2235 True 3812.0 3812 97.2660 429 2692 1 chr7D.!!$R1 2263
7 TraesCS1A01G281500 chr7D 510009128 510010700 1572 False 2632.0 2632 96.9490 429 1993 1 chr7D.!!$F2 1564
8 TraesCS1A01G281500 chr2D 511932938 511935177 2239 True 3766.0 3766 96.8740 429 2692 1 chr2D.!!$R1 2263
9 TraesCS1A01G281500 chr2D 178271620 178274832 3212 True 2172.0 3808 98.1090 429 3232 2 chr2D.!!$R2 2803
10 TraesCS1A01G281500 chr3B 312173123 312175381 2258 True 3651.0 3651 95.9210 440 2692 1 chr3B.!!$R1 2252
11 TraesCS1A01G281500 chr1B 313091194 313093410 2216 True 3598.0 3598 96.0630 485 2692 1 chr1B.!!$R1 2207
12 TraesCS1A01G281500 chr1D 197729595 197732545 2950 True 1752.5 2974 98.1555 428 3232 2 chr1D.!!$R3 2804

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
276 277 0.105964 TCTGGGGCTAGCCTCTAGTG 60.106 60.0 33.32 19.92 37.51 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2478 2573 3.177228 AGTGCTGGAAGAGTATGGAAGT 58.823 45.455 0.0 0.0 34.07 3.01 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
29 30 9.607988 AAAACGTGTCTATATACATCCAATTCA 57.392 29.630 0.00 0.00 0.00 2.57
30 31 8.818141 AACGTGTCTATATACATCCAATTCAG 57.182 34.615 0.00 0.00 0.00 3.02
31 32 7.378966 ACGTGTCTATATACATCCAATTCAGG 58.621 38.462 0.00 0.00 0.00 3.86
32 33 7.232737 ACGTGTCTATATACATCCAATTCAGGA 59.767 37.037 0.00 0.00 43.01 3.86
33 34 8.088365 CGTGTCTATATACATCCAATTCAGGAA 58.912 37.037 0.00 0.00 41.92 3.36
34 35 9.778741 GTGTCTATATACATCCAATTCAGGAAA 57.221 33.333 0.00 0.00 41.92 3.13
41 42 5.857268 ACATCCAATTCAGGAAAAAGTTGG 58.143 37.500 5.99 5.99 41.92 3.77
42 43 5.602145 ACATCCAATTCAGGAAAAAGTTGGA 59.398 36.000 14.02 14.02 46.25 3.53
43 44 6.099557 ACATCCAATTCAGGAAAAAGTTGGAA 59.900 34.615 15.10 4.08 45.59 3.53
44 45 5.912892 TCCAATTCAGGAAAAAGTTGGAAC 58.087 37.500 10.76 0.00 41.34 3.62
45 46 5.423610 TCCAATTCAGGAAAAAGTTGGAACA 59.576 36.000 10.76 0.00 41.34 3.18
46 47 6.099557 TCCAATTCAGGAAAAAGTTGGAACAT 59.900 34.615 10.76 0.00 41.34 2.71
47 48 6.424812 CCAATTCAGGAAAAAGTTGGAACATC 59.575 38.462 6.35 0.00 39.30 3.06
48 49 6.983906 ATTCAGGAAAAAGTTGGAACATCT 57.016 33.333 0.00 0.00 40.52 2.90
50 51 7.889873 TTCAGGAAAAAGTTGGAACATCTTA 57.110 32.000 0.00 0.00 46.30 2.10
51 52 8.477419 TTCAGGAAAAAGTTGGAACATCTTAT 57.523 30.769 0.00 0.00 46.30 1.73
52 53 9.581289 TTCAGGAAAAAGTTGGAACATCTTATA 57.419 29.630 0.00 0.00 46.30 0.98
53 54 9.753674 TCAGGAAAAAGTTGGAACATCTTATAT 57.246 29.630 0.00 0.00 46.30 0.86
62 63 8.450964 AGTTGGAACATCTTATATTTGTGAACG 58.549 33.333 0.00 0.00 39.30 3.95
63 64 7.315247 TGGAACATCTTATATTTGTGAACGG 57.685 36.000 0.00 0.00 0.00 4.44
64 65 7.106890 TGGAACATCTTATATTTGTGAACGGA 58.893 34.615 0.00 0.00 0.00 4.69
65 66 7.279981 TGGAACATCTTATATTTGTGAACGGAG 59.720 37.037 0.00 0.00 0.00 4.63
66 67 7.254795 GGAACATCTTATATTTGTGAACGGAGG 60.255 40.741 0.00 0.00 0.00 4.30
67 68 6.055588 ACATCTTATATTTGTGAACGGAGGG 58.944 40.000 0.00 0.00 0.00 4.30
68 69 5.943349 TCTTATATTTGTGAACGGAGGGA 57.057 39.130 0.00 0.00 0.00 4.20
69 70 5.914033 TCTTATATTTGTGAACGGAGGGAG 58.086 41.667 0.00 0.00 0.00 4.30
70 71 5.424252 TCTTATATTTGTGAACGGAGGGAGT 59.576 40.000 0.00 0.00 0.00 3.85
71 72 6.608405 TCTTATATTTGTGAACGGAGGGAGTA 59.392 38.462 0.00 0.00 0.00 2.59
72 73 3.611766 ATTTGTGAACGGAGGGAGTAG 57.388 47.619 0.00 0.00 0.00 2.57
73 74 0.606604 TTGTGAACGGAGGGAGTAGC 59.393 55.000 0.00 0.00 0.00 3.58
74 75 0.541063 TGTGAACGGAGGGAGTAGCA 60.541 55.000 0.00 0.00 0.00 3.49
75 76 0.824759 GTGAACGGAGGGAGTAGCAT 59.175 55.000 0.00 0.00 0.00 3.79
76 77 2.029623 GTGAACGGAGGGAGTAGCATA 58.970 52.381 0.00 0.00 0.00 3.14
77 78 2.628657 GTGAACGGAGGGAGTAGCATAT 59.371 50.000 0.00 0.00 0.00 1.78
78 79 3.825014 GTGAACGGAGGGAGTAGCATATA 59.175 47.826 0.00 0.00 0.00 0.86
79 80 4.280174 GTGAACGGAGGGAGTAGCATATAA 59.720 45.833 0.00 0.00 0.00 0.98
80 81 5.047235 GTGAACGGAGGGAGTAGCATATAAT 60.047 44.000 0.00 0.00 0.00 1.28
81 82 6.152323 GTGAACGGAGGGAGTAGCATATAATA 59.848 42.308 0.00 0.00 0.00 0.98
82 83 6.377429 TGAACGGAGGGAGTAGCATATAATAG 59.623 42.308 0.00 0.00 0.00 1.73
83 84 4.645588 ACGGAGGGAGTAGCATATAATAGC 59.354 45.833 0.00 0.00 0.00 2.97
84 85 4.645136 CGGAGGGAGTAGCATATAATAGCA 59.355 45.833 0.00 0.00 0.00 3.49
85 86 5.303078 CGGAGGGAGTAGCATATAATAGCAT 59.697 44.000 0.00 0.00 0.00 3.79
86 87 6.183360 CGGAGGGAGTAGCATATAATAGCATT 60.183 42.308 0.00 0.00 0.00 3.56
87 88 6.989169 GGAGGGAGTAGCATATAATAGCATTG 59.011 42.308 0.00 0.00 0.00 2.82
88 89 6.893583 AGGGAGTAGCATATAATAGCATTGG 58.106 40.000 0.00 0.00 0.00 3.16
89 90 6.673978 AGGGAGTAGCATATAATAGCATTGGA 59.326 38.462 0.00 0.00 0.00 3.53
90 91 7.349330 AGGGAGTAGCATATAATAGCATTGGAT 59.651 37.037 0.00 0.00 0.00 3.41
91 92 8.651389 GGGAGTAGCATATAATAGCATTGGATA 58.349 37.037 0.00 0.00 0.00 2.59
92 93 9.703892 GGAGTAGCATATAATAGCATTGGATAG 57.296 37.037 0.00 0.00 0.00 2.08
93 94 9.202273 GAGTAGCATATAATAGCATTGGATAGC 57.798 37.037 0.00 0.00 0.00 2.97
94 95 8.932610 AGTAGCATATAATAGCATTGGATAGCT 58.067 33.333 0.00 0.00 44.55 3.32
95 96 9.553064 GTAGCATATAATAGCATTGGATAGCTT 57.447 33.333 0.00 0.00 42.05 3.74
96 97 8.447924 AGCATATAATAGCATTGGATAGCTTG 57.552 34.615 0.00 0.00 42.05 4.01
97 98 8.051535 AGCATATAATAGCATTGGATAGCTTGT 58.948 33.333 0.00 0.00 42.05 3.16
98 99 8.680903 GCATATAATAGCATTGGATAGCTTGTT 58.319 33.333 0.00 0.00 42.05 2.83
102 103 6.780457 ATAGCATTGGATAGCTTGTTTTGT 57.220 33.333 0.00 0.00 42.05 2.83
103 104 5.473066 AGCATTGGATAGCTTGTTTTGTT 57.527 34.783 0.00 0.00 38.01 2.83
104 105 5.232463 AGCATTGGATAGCTTGTTTTGTTG 58.768 37.500 0.00 0.00 38.01 3.33
105 106 4.389687 GCATTGGATAGCTTGTTTTGTTGG 59.610 41.667 0.00 0.00 0.00 3.77
106 107 5.540911 CATTGGATAGCTTGTTTTGTTGGT 58.459 37.500 0.00 0.00 0.00 3.67
107 108 5.606348 TTGGATAGCTTGTTTTGTTGGTT 57.394 34.783 0.00 0.00 0.00 3.67
108 109 5.606348 TGGATAGCTTGTTTTGTTGGTTT 57.394 34.783 0.00 0.00 0.00 3.27
109 110 5.355596 TGGATAGCTTGTTTTGTTGGTTTG 58.644 37.500 0.00 0.00 0.00 2.93
110 111 5.127845 TGGATAGCTTGTTTTGTTGGTTTGA 59.872 36.000 0.00 0.00 0.00 2.69
111 112 5.691754 GGATAGCTTGTTTTGTTGGTTTGAG 59.308 40.000 0.00 0.00 0.00 3.02
112 113 3.860641 AGCTTGTTTTGTTGGTTTGAGG 58.139 40.909 0.00 0.00 0.00 3.86
113 114 3.260632 AGCTTGTTTTGTTGGTTTGAGGT 59.739 39.130 0.00 0.00 0.00 3.85
114 115 4.000325 GCTTGTTTTGTTGGTTTGAGGTT 59.000 39.130 0.00 0.00 0.00 3.50
115 116 4.454161 GCTTGTTTTGTTGGTTTGAGGTTT 59.546 37.500 0.00 0.00 0.00 3.27
116 117 5.049060 GCTTGTTTTGTTGGTTTGAGGTTTT 60.049 36.000 0.00 0.00 0.00 2.43
117 118 6.147985 GCTTGTTTTGTTGGTTTGAGGTTTTA 59.852 34.615 0.00 0.00 0.00 1.52
118 119 7.308049 GCTTGTTTTGTTGGTTTGAGGTTTTAA 60.308 33.333 0.00 0.00 0.00 1.52
119 120 7.659652 TGTTTTGTTGGTTTGAGGTTTTAAG 57.340 32.000 0.00 0.00 0.00 1.85
120 121 7.217906 TGTTTTGTTGGTTTGAGGTTTTAAGT 58.782 30.769 0.00 0.00 0.00 2.24
121 122 8.365647 TGTTTTGTTGGTTTGAGGTTTTAAGTA 58.634 29.630 0.00 0.00 0.00 2.24
122 123 8.649841 GTTTTGTTGGTTTGAGGTTTTAAGTAC 58.350 33.333 0.00 0.00 0.00 2.73
123 124 7.706100 TTGTTGGTTTGAGGTTTTAAGTACT 57.294 32.000 0.00 0.00 0.00 2.73
124 125 7.706100 TGTTGGTTTGAGGTTTTAAGTACTT 57.294 32.000 13.68 13.68 0.00 2.24
125 126 7.764331 TGTTGGTTTGAGGTTTTAAGTACTTC 58.236 34.615 12.39 0.00 0.00 3.01
126 127 7.393796 TGTTGGTTTGAGGTTTTAAGTACTTCA 59.606 33.333 12.39 0.00 30.84 3.02
127 128 8.410912 GTTGGTTTGAGGTTTTAAGTACTTCAT 58.589 33.333 12.39 0.00 32.59 2.57
128 129 9.629878 TTGGTTTGAGGTTTTAAGTACTTCATA 57.370 29.630 12.39 0.00 32.59 2.15
129 130 9.280174 TGGTTTGAGGTTTTAAGTACTTCATAG 57.720 33.333 12.39 0.00 32.59 2.23
130 131 9.498176 GGTTTGAGGTTTTAAGTACTTCATAGA 57.502 33.333 12.39 0.00 32.59 1.98
132 133 8.773404 TTGAGGTTTTAAGTACTTCATAGAGC 57.227 34.615 12.39 4.45 32.59 4.09
133 134 7.903145 TGAGGTTTTAAGTACTTCATAGAGCA 58.097 34.615 12.39 2.17 28.14 4.26
134 135 8.540388 TGAGGTTTTAAGTACTTCATAGAGCAT 58.460 33.333 12.39 0.00 28.14 3.79
135 136 8.950208 AGGTTTTAAGTACTTCATAGAGCATC 57.050 34.615 12.39 0.00 0.00 3.91
149 150 3.391227 GAGCATCTTTTACCGTGAAGC 57.609 47.619 0.00 0.00 0.00 3.86
150 151 2.742053 GAGCATCTTTTACCGTGAAGCA 59.258 45.455 0.00 0.00 0.00 3.91
151 152 3.146066 AGCATCTTTTACCGTGAAGCAA 58.854 40.909 0.00 0.00 0.00 3.91
152 153 3.758554 AGCATCTTTTACCGTGAAGCAAT 59.241 39.130 0.00 0.00 0.00 3.56
153 154 3.853671 GCATCTTTTACCGTGAAGCAATG 59.146 43.478 0.00 0.00 0.00 2.82
154 155 4.379394 GCATCTTTTACCGTGAAGCAATGA 60.379 41.667 0.00 0.00 0.00 2.57
155 156 5.698832 CATCTTTTACCGTGAAGCAATGAA 58.301 37.500 0.00 0.00 0.00 2.57
156 157 5.103290 TCTTTTACCGTGAAGCAATGAAC 57.897 39.130 0.00 0.00 0.00 3.18
157 158 4.819630 TCTTTTACCGTGAAGCAATGAACT 59.180 37.500 0.00 0.00 0.00 3.01
158 159 5.992829 TCTTTTACCGTGAAGCAATGAACTA 59.007 36.000 0.00 0.00 0.00 2.24
159 160 6.653320 TCTTTTACCGTGAAGCAATGAACTAT 59.347 34.615 0.00 0.00 0.00 2.12
160 161 7.820386 TCTTTTACCGTGAAGCAATGAACTATA 59.180 33.333 0.00 0.00 0.00 1.31
161 162 8.500753 TTTTACCGTGAAGCAATGAACTATAT 57.499 30.769 0.00 0.00 0.00 0.86
162 163 9.602568 TTTTACCGTGAAGCAATGAACTATATA 57.397 29.630 0.00 0.00 0.00 0.86
163 164 9.772973 TTTACCGTGAAGCAATGAACTATATAT 57.227 29.630 0.00 0.00 0.00 0.86
194 195 9.859427 TCTTTAAATTCTGCTTGTTGATAATGG 57.141 29.630 0.00 0.00 0.00 3.16
195 196 8.477984 TTTAAATTCTGCTTGTTGATAATGGC 57.522 30.769 0.00 0.00 0.00 4.40
196 197 5.927281 AATTCTGCTTGTTGATAATGGCT 57.073 34.783 0.00 0.00 0.00 4.75
197 198 4.707030 TTCTGCTTGTTGATAATGGCTG 57.293 40.909 0.00 0.00 0.00 4.85
198 199 2.424601 TCTGCTTGTTGATAATGGCTGC 59.575 45.455 0.00 0.00 0.00 5.25
199 200 2.164827 CTGCTTGTTGATAATGGCTGCA 59.835 45.455 0.50 0.00 0.00 4.41
200 201 2.164827 TGCTTGTTGATAATGGCTGCAG 59.835 45.455 10.11 10.11 0.00 4.41
201 202 2.165030 GCTTGTTGATAATGGCTGCAGT 59.835 45.455 16.64 0.00 0.00 4.40
202 203 3.367703 GCTTGTTGATAATGGCTGCAGTT 60.368 43.478 16.64 4.32 0.00 3.16
203 204 4.813027 CTTGTTGATAATGGCTGCAGTTT 58.187 39.130 16.64 9.50 0.00 2.66
204 205 4.870123 TGTTGATAATGGCTGCAGTTTT 57.130 36.364 16.64 9.14 0.00 2.43
205 206 4.808558 TGTTGATAATGGCTGCAGTTTTC 58.191 39.130 16.64 7.25 0.00 2.29
206 207 4.523943 TGTTGATAATGGCTGCAGTTTTCT 59.476 37.500 16.64 0.00 0.00 2.52
254 255 2.743636 TTGATCCTGTCAACTCGACC 57.256 50.000 0.00 0.00 44.71 4.79
255 256 1.627864 TGATCCTGTCAACTCGACCA 58.372 50.000 0.00 0.00 44.71 4.02
256 257 1.967779 TGATCCTGTCAACTCGACCAA 59.032 47.619 0.00 0.00 44.71 3.67
257 258 2.567169 TGATCCTGTCAACTCGACCAAT 59.433 45.455 0.00 0.00 44.71 3.16
258 259 2.743636 TCCTGTCAACTCGACCAATC 57.256 50.000 0.00 0.00 44.71 2.67
259 260 2.248248 TCCTGTCAACTCGACCAATCT 58.752 47.619 0.00 0.00 44.71 2.40
260 261 2.029020 TCCTGTCAACTCGACCAATCTG 60.029 50.000 0.00 0.00 44.71 2.90
261 262 2.341257 CTGTCAACTCGACCAATCTGG 58.659 52.381 0.00 0.00 44.71 3.86
262 263 1.001974 TGTCAACTCGACCAATCTGGG 59.998 52.381 0.00 0.00 44.71 4.45
263 264 0.613260 TCAACTCGACCAATCTGGGG 59.387 55.000 0.00 0.00 43.37 4.96
264 265 1.026718 CAACTCGACCAATCTGGGGC 61.027 60.000 0.00 0.00 43.37 5.80
265 266 1.201429 AACTCGACCAATCTGGGGCT 61.201 55.000 0.00 0.00 43.37 5.19
266 267 0.325296 ACTCGACCAATCTGGGGCTA 60.325 55.000 0.00 0.00 43.37 3.93
267 268 0.390860 CTCGACCAATCTGGGGCTAG 59.609 60.000 0.00 0.00 43.37 3.42
268 269 1.227674 CGACCAATCTGGGGCTAGC 60.228 63.158 6.04 6.04 43.37 3.42
269 270 1.149401 GACCAATCTGGGGCTAGCC 59.851 63.158 26.55 26.55 43.37 3.93
270 271 1.308216 ACCAATCTGGGGCTAGCCT 60.308 57.895 32.18 10.40 43.37 4.58
271 272 1.348775 ACCAATCTGGGGCTAGCCTC 61.349 60.000 32.18 30.17 43.37 4.70
272 273 1.059006 CCAATCTGGGGCTAGCCTCT 61.059 60.000 33.32 11.97 37.51 3.69
273 274 1.722034 CAATCTGGGGCTAGCCTCTA 58.278 55.000 33.32 21.92 37.51 2.43
274 275 1.622811 CAATCTGGGGCTAGCCTCTAG 59.377 57.143 33.32 26.64 37.51 2.43
275 276 0.863956 ATCTGGGGCTAGCCTCTAGT 59.136 55.000 33.32 16.39 37.51 2.57
276 277 0.105964 TCTGGGGCTAGCCTCTAGTG 60.106 60.000 33.32 19.92 37.51 2.74
277 278 1.075226 TGGGGCTAGCCTCTAGTGG 60.075 63.158 33.32 6.47 37.51 4.00
286 287 3.386543 CCTCTAGTGGCATTTCCCG 57.613 57.895 0.00 0.00 0.00 5.14
287 288 0.830648 CCTCTAGTGGCATTTCCCGA 59.169 55.000 0.00 0.00 0.00 5.14
288 289 1.209504 CCTCTAGTGGCATTTCCCGAA 59.790 52.381 0.00 0.00 0.00 4.30
289 290 2.158755 CCTCTAGTGGCATTTCCCGAAT 60.159 50.000 0.00 0.00 0.00 3.34
290 291 3.071023 CCTCTAGTGGCATTTCCCGAATA 59.929 47.826 0.00 0.00 0.00 1.75
291 292 4.444306 CCTCTAGTGGCATTTCCCGAATAA 60.444 45.833 0.00 0.00 0.00 1.40
292 293 4.703897 TCTAGTGGCATTTCCCGAATAAG 58.296 43.478 0.00 0.00 0.00 1.73
293 294 2.654863 AGTGGCATTTCCCGAATAAGG 58.345 47.619 0.00 0.00 0.00 2.69
294 295 2.241176 AGTGGCATTTCCCGAATAAGGA 59.759 45.455 0.00 0.00 0.00 3.36
295 296 3.020984 GTGGCATTTCCCGAATAAGGAA 58.979 45.455 0.00 0.00 41.69 3.36
304 305 6.509418 TTCCCGAATAAGGAAAAACATGAG 57.491 37.500 0.00 0.00 40.46 2.90
305 306 5.566469 TCCCGAATAAGGAAAAACATGAGT 58.434 37.500 0.00 0.00 0.00 3.41
306 307 6.713276 TCCCGAATAAGGAAAAACATGAGTA 58.287 36.000 0.00 0.00 0.00 2.59
307 308 6.596497 TCCCGAATAAGGAAAAACATGAGTAC 59.404 38.462 0.00 0.00 0.00 2.73
308 309 6.183360 CCCGAATAAGGAAAAACATGAGTACC 60.183 42.308 0.00 0.00 0.00 3.34
309 310 6.183360 CCGAATAAGGAAAAACATGAGTACCC 60.183 42.308 0.00 0.00 0.00 3.69
310 311 6.373216 CGAATAAGGAAAAACATGAGTACCCA 59.627 38.462 0.00 0.00 0.00 4.51
311 312 7.462571 AATAAGGAAAAACATGAGTACCCAC 57.537 36.000 0.00 0.00 0.00 4.61
312 313 3.763057 AGGAAAAACATGAGTACCCACC 58.237 45.455 0.00 0.00 0.00 4.61
313 314 3.397955 AGGAAAAACATGAGTACCCACCT 59.602 43.478 0.00 0.00 0.00 4.00
314 315 3.506067 GGAAAAACATGAGTACCCACCTG 59.494 47.826 0.00 0.00 0.00 4.00
315 316 4.394729 GAAAAACATGAGTACCCACCTGA 58.605 43.478 0.00 0.00 0.00 3.86
316 317 4.657814 AAAACATGAGTACCCACCTGAT 57.342 40.909 0.00 0.00 0.00 2.90
317 318 3.634397 AACATGAGTACCCACCTGATG 57.366 47.619 0.00 0.00 0.00 3.07
328 329 1.457346 CACCTGATGGAGTTTGAGCC 58.543 55.000 0.00 0.00 37.04 4.70
329 330 1.004044 CACCTGATGGAGTTTGAGCCT 59.996 52.381 0.00 0.00 37.04 4.58
330 331 1.280421 ACCTGATGGAGTTTGAGCCTC 59.720 52.381 0.00 0.00 37.04 4.70
331 332 1.280133 CCTGATGGAGTTTGAGCCTCA 59.720 52.381 0.00 0.00 34.57 3.86
332 333 2.290514 CCTGATGGAGTTTGAGCCTCAA 60.291 50.000 2.24 2.24 32.56 3.02
333 334 3.415212 CTGATGGAGTTTGAGCCTCAAA 58.585 45.455 15.70 15.70 43.37 2.69
334 335 3.822735 CTGATGGAGTTTGAGCCTCAAAA 59.177 43.478 20.80 6.60 46.53 2.44
335 336 3.822735 TGATGGAGTTTGAGCCTCAAAAG 59.177 43.478 20.80 0.00 46.53 2.27
336 337 1.956477 TGGAGTTTGAGCCTCAAAAGC 59.044 47.619 20.80 14.89 46.53 3.51
337 338 2.234143 GGAGTTTGAGCCTCAAAAGCT 58.766 47.619 20.80 14.62 46.53 3.74
338 339 2.030451 GGAGTTTGAGCCTCAAAAGCTG 60.030 50.000 20.80 0.00 46.53 4.24
339 340 1.959282 AGTTTGAGCCTCAAAAGCTGG 59.041 47.619 20.80 0.00 46.53 4.85
340 341 1.683385 GTTTGAGCCTCAAAAGCTGGT 59.317 47.619 20.80 0.00 46.53 4.00
341 342 1.321474 TTGAGCCTCAAAAGCTGGTG 58.679 50.000 4.27 0.00 41.75 4.17
342 343 0.538057 TGAGCCTCAAAAGCTGGTGG 60.538 55.000 0.00 0.00 41.75 4.61
343 344 1.228675 AGCCTCAAAAGCTGGTGGG 60.229 57.895 0.00 0.00 39.69 4.61
344 345 2.935740 GCCTCAAAAGCTGGTGGGC 61.936 63.158 11.22 11.22 0.00 5.36
345 346 1.531365 CCTCAAAAGCTGGTGGGCA 60.531 57.895 0.00 0.00 34.17 5.36
346 347 1.530013 CCTCAAAAGCTGGTGGGCAG 61.530 60.000 0.00 0.00 34.17 4.85
347 348 1.530013 CTCAAAAGCTGGTGGGCAGG 61.530 60.000 0.00 0.00 34.17 4.85
348 349 2.919328 AAAAGCTGGTGGGCAGGC 60.919 61.111 0.00 0.00 34.17 4.85
361 362 3.373226 CAGGCCTGCAAAGCACAT 58.627 55.556 22.33 0.00 33.79 3.21
362 363 1.214589 CAGGCCTGCAAAGCACATC 59.785 57.895 22.33 0.00 33.79 3.06
363 364 1.228644 AGGCCTGCAAAGCACATCA 60.229 52.632 3.11 0.00 33.79 3.07
364 365 1.214589 GGCCTGCAAAGCACATCAG 59.785 57.895 10.30 0.00 33.79 2.90
365 366 1.445582 GCCTGCAAAGCACATCAGC 60.446 57.895 3.57 0.00 33.79 4.26
372 373 4.315588 AGCACATCAGCTTGCTCC 57.684 55.556 4.77 0.00 46.31 4.70
373 374 1.377612 AGCACATCAGCTTGCTCCA 59.622 52.632 4.77 0.00 46.31 3.86
374 375 0.677098 AGCACATCAGCTTGCTCCAG 60.677 55.000 4.77 0.00 46.31 3.86
375 376 1.801332 CACATCAGCTTGCTCCAGC 59.199 57.895 0.00 0.00 40.44 4.85
385 386 4.215349 GCTCCAGCTAGCAACCTG 57.785 61.111 18.83 6.08 42.30 4.00
386 387 1.599047 GCTCCAGCTAGCAACCTGA 59.401 57.895 18.83 4.61 42.30 3.86
387 388 0.179936 GCTCCAGCTAGCAACCTGAT 59.820 55.000 18.83 0.00 42.30 2.90
388 389 1.809651 GCTCCAGCTAGCAACCTGATC 60.810 57.143 18.83 0.00 42.30 2.92
389 390 1.483827 CTCCAGCTAGCAACCTGATCA 59.516 52.381 18.83 0.00 0.00 2.92
390 391 1.483827 TCCAGCTAGCAACCTGATCAG 59.516 52.381 18.83 16.24 0.00 2.90
391 392 1.483827 CCAGCTAGCAACCTGATCAGA 59.516 52.381 24.62 1.62 0.00 3.27
392 393 2.548875 CAGCTAGCAACCTGATCAGAC 58.451 52.381 24.62 10.19 0.00 3.51
393 394 1.135915 AGCTAGCAACCTGATCAGACG 59.864 52.381 24.62 10.75 0.00 4.18
394 395 1.565305 CTAGCAACCTGATCAGACGC 58.435 55.000 24.62 20.69 0.00 5.19
395 396 1.135915 CTAGCAACCTGATCAGACGCT 59.864 52.381 24.62 25.61 33.66 5.07
396 397 0.108424 AGCAACCTGATCAGACGCTC 60.108 55.000 24.62 8.76 0.00 5.03
397 398 0.390340 GCAACCTGATCAGACGCTCA 60.390 55.000 24.62 0.00 0.00 4.26
398 399 1.354040 CAACCTGATCAGACGCTCAC 58.646 55.000 24.62 0.00 0.00 3.51
399 400 1.067283 CAACCTGATCAGACGCTCACT 60.067 52.381 24.62 0.00 0.00 3.41
400 401 0.814457 ACCTGATCAGACGCTCACTC 59.186 55.000 24.62 0.00 0.00 3.51
401 402 0.813821 CCTGATCAGACGCTCACTCA 59.186 55.000 24.62 0.00 0.00 3.41
402 403 1.468908 CCTGATCAGACGCTCACTCAC 60.469 57.143 24.62 0.00 0.00 3.51
403 404 0.169009 TGATCAGACGCTCACTCACG 59.831 55.000 0.00 0.00 0.00 4.35
404 405 0.169230 GATCAGACGCTCACTCACGT 59.831 55.000 0.00 0.00 46.91 4.49
405 406 0.109551 ATCAGACGCTCACTCACGTG 60.110 55.000 9.94 9.94 43.71 4.49
406 407 1.008424 CAGACGCTCACTCACGTGT 60.008 57.895 16.51 0.00 43.71 4.49
407 408 0.595053 CAGACGCTCACTCACGTGTT 60.595 55.000 16.51 0.47 43.71 3.32
408 409 0.317938 AGACGCTCACTCACGTGTTC 60.318 55.000 16.51 0.96 43.71 3.18
409 410 0.317938 GACGCTCACTCACGTGTTCT 60.318 55.000 16.51 0.00 43.71 3.01
410 411 0.595053 ACGCTCACTCACGTGTTCTG 60.595 55.000 16.51 9.25 41.76 3.02
411 412 0.317854 CGCTCACTCACGTGTTCTGA 60.318 55.000 16.51 12.88 41.89 3.27
412 413 1.667177 CGCTCACTCACGTGTTCTGAT 60.667 52.381 16.51 0.00 41.89 2.90
413 414 2.414161 CGCTCACTCACGTGTTCTGATA 60.414 50.000 16.51 0.00 41.89 2.15
414 415 3.732169 CGCTCACTCACGTGTTCTGATAT 60.732 47.826 16.51 0.00 41.89 1.63
415 416 4.495844 CGCTCACTCACGTGTTCTGATATA 60.496 45.833 16.51 0.00 41.89 0.86
416 417 4.735822 GCTCACTCACGTGTTCTGATATAC 59.264 45.833 16.51 2.19 41.89 1.47
417 418 5.449314 GCTCACTCACGTGTTCTGATATACT 60.449 44.000 16.51 0.00 41.89 2.12
418 419 6.120378 TCACTCACGTGTTCTGATATACTC 57.880 41.667 16.51 0.00 41.89 2.59
419 420 5.066117 TCACTCACGTGTTCTGATATACTCC 59.934 44.000 16.51 0.00 41.89 3.85
420 421 4.338682 ACTCACGTGTTCTGATATACTCCC 59.661 45.833 16.51 0.00 0.00 4.30
421 422 4.533815 TCACGTGTTCTGATATACTCCCT 58.466 43.478 16.51 0.00 0.00 4.20
422 423 4.954202 TCACGTGTTCTGATATACTCCCTT 59.046 41.667 16.51 0.00 0.00 3.95
426 427 5.450137 CGTGTTCTGATATACTCCCTTCGTT 60.450 44.000 0.00 0.00 0.00 3.85
877 880 1.202915 TCCAGCAAGATCCAACAAGCA 60.203 47.619 0.00 0.00 0.00 3.91
932 993 0.394216 TGTTTGTGGCTGTCTGCTGT 60.394 50.000 1.44 0.00 42.39 4.40
1706 1780 3.042560 GGCCACACCTTCAACTGC 58.957 61.111 0.00 0.00 34.51 4.40
1714 1788 2.671177 CCTTCAACTGCCGTCTGCG 61.671 63.158 0.00 0.00 45.60 5.18
1816 1890 2.042831 GCCCTCAATCAGCAGCGTT 61.043 57.895 0.00 0.00 0.00 4.84
2478 2573 7.040271 GGTTGTAAGCTAGGGAAACAAATACAA 60.040 37.037 0.00 0.00 32.32 2.41
2564 2659 2.097110 GGTCCTTCCCCCTTTGTTTT 57.903 50.000 0.00 0.00 0.00 2.43
2659 2754 4.024556 AGCATCGTTCTGAGTTGTTTTCTG 60.025 41.667 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.607988 TGAATTGGATGTATATAGACACGTTTT 57.392 29.630 1.52 0.00 30.52 2.43
4 5 9.261180 CTGAATTGGATGTATATAGACACGTTT 57.739 33.333 1.52 0.00 30.52 3.60
5 6 7.872993 CCTGAATTGGATGTATATAGACACGTT 59.127 37.037 1.52 0.00 30.52 3.99
6 7 7.232737 TCCTGAATTGGATGTATATAGACACGT 59.767 37.037 1.52 0.00 30.52 4.49
7 8 7.602753 TCCTGAATTGGATGTATATAGACACG 58.397 38.462 1.52 0.00 30.52 4.49
8 9 9.778741 TTTCCTGAATTGGATGTATATAGACAC 57.221 33.333 1.52 0.00 35.83 3.67
15 16 8.748412 CCAACTTTTTCCTGAATTGGATGTATA 58.252 33.333 4.65 0.00 39.15 1.47
16 17 7.454380 TCCAACTTTTTCCTGAATTGGATGTAT 59.546 33.333 8.06 0.00 40.44 2.29
17 18 6.780031 TCCAACTTTTTCCTGAATTGGATGTA 59.220 34.615 8.06 0.00 40.44 2.29
18 19 5.602145 TCCAACTTTTTCCTGAATTGGATGT 59.398 36.000 8.06 0.00 40.44 3.06
19 20 6.100404 TCCAACTTTTTCCTGAATTGGATG 57.900 37.500 8.06 0.00 40.44 3.51
20 21 6.099557 TGTTCCAACTTTTTCCTGAATTGGAT 59.900 34.615 11.48 0.00 43.75 3.41
21 22 5.423610 TGTTCCAACTTTTTCCTGAATTGGA 59.576 36.000 8.06 8.06 42.90 3.53
22 23 5.669477 TGTTCCAACTTTTTCCTGAATTGG 58.331 37.500 4.36 4.36 38.35 3.16
23 24 7.212274 AGATGTTCCAACTTTTTCCTGAATTG 58.788 34.615 0.00 0.00 0.00 2.32
24 25 7.365497 AGATGTTCCAACTTTTTCCTGAATT 57.635 32.000 0.00 0.00 0.00 2.17
25 26 6.983906 AGATGTTCCAACTTTTTCCTGAAT 57.016 33.333 0.00 0.00 0.00 2.57
26 27 6.790232 AAGATGTTCCAACTTTTTCCTGAA 57.210 33.333 0.00 0.00 0.00 3.02
27 28 9.753674 ATATAAGATGTTCCAACTTTTTCCTGA 57.246 29.630 0.00 0.00 29.69 3.86
36 37 8.450964 CGTTCACAAATATAAGATGTTCCAACT 58.549 33.333 0.00 0.00 0.00 3.16
37 38 7.696453 CCGTTCACAAATATAAGATGTTCCAAC 59.304 37.037 0.00 0.00 0.00 3.77
38 39 7.608376 TCCGTTCACAAATATAAGATGTTCCAA 59.392 33.333 0.00 0.00 0.00 3.53
39 40 7.106890 TCCGTTCACAAATATAAGATGTTCCA 58.893 34.615 0.00 0.00 0.00 3.53
40 41 7.254795 CCTCCGTTCACAAATATAAGATGTTCC 60.255 40.741 0.00 0.00 0.00 3.62
41 42 7.254795 CCCTCCGTTCACAAATATAAGATGTTC 60.255 40.741 0.00 0.00 0.00 3.18
42 43 6.542370 CCCTCCGTTCACAAATATAAGATGTT 59.458 38.462 0.00 0.00 0.00 2.71
43 44 6.055588 CCCTCCGTTCACAAATATAAGATGT 58.944 40.000 0.00 0.00 0.00 3.06
44 45 6.288294 TCCCTCCGTTCACAAATATAAGATG 58.712 40.000 0.00 0.00 0.00 2.90
45 46 6.099845 ACTCCCTCCGTTCACAAATATAAGAT 59.900 38.462 0.00 0.00 0.00 2.40
46 47 5.424252 ACTCCCTCCGTTCACAAATATAAGA 59.576 40.000 0.00 0.00 0.00 2.10
47 48 5.671493 ACTCCCTCCGTTCACAAATATAAG 58.329 41.667 0.00 0.00 0.00 1.73
48 49 5.687166 ACTCCCTCCGTTCACAAATATAA 57.313 39.130 0.00 0.00 0.00 0.98
49 50 5.221382 GCTACTCCCTCCGTTCACAAATATA 60.221 44.000 0.00 0.00 0.00 0.86
50 51 4.443034 GCTACTCCCTCCGTTCACAAATAT 60.443 45.833 0.00 0.00 0.00 1.28
51 52 3.118884 GCTACTCCCTCCGTTCACAAATA 60.119 47.826 0.00 0.00 0.00 1.40
52 53 2.354805 GCTACTCCCTCCGTTCACAAAT 60.355 50.000 0.00 0.00 0.00 2.32
53 54 1.001633 GCTACTCCCTCCGTTCACAAA 59.998 52.381 0.00 0.00 0.00 2.83
54 55 0.606604 GCTACTCCCTCCGTTCACAA 59.393 55.000 0.00 0.00 0.00 3.33
55 56 0.541063 TGCTACTCCCTCCGTTCACA 60.541 55.000 0.00 0.00 0.00 3.58
56 57 0.824759 ATGCTACTCCCTCCGTTCAC 59.175 55.000 0.00 0.00 0.00 3.18
57 58 2.447408 TATGCTACTCCCTCCGTTCA 57.553 50.000 0.00 0.00 0.00 3.18
58 59 5.662674 ATTATATGCTACTCCCTCCGTTC 57.337 43.478 0.00 0.00 0.00 3.95
59 60 5.127356 GCTATTATATGCTACTCCCTCCGTT 59.873 44.000 0.00 0.00 0.00 4.44
60 61 4.645588 GCTATTATATGCTACTCCCTCCGT 59.354 45.833 0.00 0.00 0.00 4.69
61 62 4.645136 TGCTATTATATGCTACTCCCTCCG 59.355 45.833 0.00 0.00 0.00 4.63
62 63 6.739331 ATGCTATTATATGCTACTCCCTCC 57.261 41.667 0.00 0.00 0.00 4.30
63 64 6.989169 CCAATGCTATTATATGCTACTCCCTC 59.011 42.308 0.00 0.00 0.00 4.30
64 65 6.673978 TCCAATGCTATTATATGCTACTCCCT 59.326 38.462 0.00 0.00 0.00 4.20
65 66 6.889198 TCCAATGCTATTATATGCTACTCCC 58.111 40.000 0.00 0.00 0.00 4.30
66 67 9.703892 CTATCCAATGCTATTATATGCTACTCC 57.296 37.037 0.00 0.00 0.00 3.85
67 68 9.202273 GCTATCCAATGCTATTATATGCTACTC 57.798 37.037 0.00 0.00 0.00 2.59
68 69 8.932610 AGCTATCCAATGCTATTATATGCTACT 58.067 33.333 0.00 0.00 37.81 2.57
69 70 9.553064 AAGCTATCCAATGCTATTATATGCTAC 57.447 33.333 0.00 0.00 38.75 3.58
70 71 9.551734 CAAGCTATCCAATGCTATTATATGCTA 57.448 33.333 0.00 0.00 38.75 3.49
71 72 8.051535 ACAAGCTATCCAATGCTATTATATGCT 58.948 33.333 0.00 0.00 38.75 3.79
72 73 8.218338 ACAAGCTATCCAATGCTATTATATGC 57.782 34.615 0.00 0.00 38.75 3.14
76 77 8.917088 ACAAAACAAGCTATCCAATGCTATTAT 58.083 29.630 0.00 0.00 38.75 1.28
77 78 8.292444 ACAAAACAAGCTATCCAATGCTATTA 57.708 30.769 0.00 0.00 38.75 0.98
78 79 7.174107 ACAAAACAAGCTATCCAATGCTATT 57.826 32.000 0.00 0.00 38.75 1.73
79 80 6.780457 ACAAAACAAGCTATCCAATGCTAT 57.220 33.333 0.00 0.00 38.75 2.97
80 81 6.389091 CAACAAAACAAGCTATCCAATGCTA 58.611 36.000 0.00 0.00 38.75 3.49
81 82 5.232463 CAACAAAACAAGCTATCCAATGCT 58.768 37.500 0.00 0.00 41.82 3.79
82 83 4.389687 CCAACAAAACAAGCTATCCAATGC 59.610 41.667 0.00 0.00 0.00 3.56
83 84 5.540911 ACCAACAAAACAAGCTATCCAATG 58.459 37.500 0.00 0.00 0.00 2.82
84 85 5.806654 ACCAACAAAACAAGCTATCCAAT 57.193 34.783 0.00 0.00 0.00 3.16
85 86 5.606348 AACCAACAAAACAAGCTATCCAA 57.394 34.783 0.00 0.00 0.00 3.53
86 87 5.127845 TCAAACCAACAAAACAAGCTATCCA 59.872 36.000 0.00 0.00 0.00 3.41
87 88 5.596845 TCAAACCAACAAAACAAGCTATCC 58.403 37.500 0.00 0.00 0.00 2.59
88 89 5.691754 CCTCAAACCAACAAAACAAGCTATC 59.308 40.000 0.00 0.00 0.00 2.08
89 90 5.128663 ACCTCAAACCAACAAAACAAGCTAT 59.871 36.000 0.00 0.00 0.00 2.97
90 91 4.464597 ACCTCAAACCAACAAAACAAGCTA 59.535 37.500 0.00 0.00 0.00 3.32
91 92 3.260632 ACCTCAAACCAACAAAACAAGCT 59.739 39.130 0.00 0.00 0.00 3.74
92 93 3.595173 ACCTCAAACCAACAAAACAAGC 58.405 40.909 0.00 0.00 0.00 4.01
93 94 6.552859 AAAACCTCAAACCAACAAAACAAG 57.447 33.333 0.00 0.00 0.00 3.16
94 95 7.715686 ACTTAAAACCTCAAACCAACAAAACAA 59.284 29.630 0.00 0.00 0.00 2.83
95 96 7.217906 ACTTAAAACCTCAAACCAACAAAACA 58.782 30.769 0.00 0.00 0.00 2.83
96 97 7.661127 ACTTAAAACCTCAAACCAACAAAAC 57.339 32.000 0.00 0.00 0.00 2.43
97 98 8.586744 AGTACTTAAAACCTCAAACCAACAAAA 58.413 29.630 0.00 0.00 0.00 2.44
98 99 8.124808 AGTACTTAAAACCTCAAACCAACAAA 57.875 30.769 0.00 0.00 0.00 2.83
99 100 7.706100 AGTACTTAAAACCTCAAACCAACAA 57.294 32.000 0.00 0.00 0.00 2.83
100 101 7.393796 TGAAGTACTTAAAACCTCAAACCAACA 59.606 33.333 8.42 0.00 0.00 3.33
101 102 7.764331 TGAAGTACTTAAAACCTCAAACCAAC 58.236 34.615 8.42 0.00 0.00 3.77
102 103 7.941431 TGAAGTACTTAAAACCTCAAACCAA 57.059 32.000 8.42 0.00 0.00 3.67
103 104 9.280174 CTATGAAGTACTTAAAACCTCAAACCA 57.720 33.333 8.42 0.00 0.00 3.67
104 105 9.498176 TCTATGAAGTACTTAAAACCTCAAACC 57.502 33.333 8.42 0.00 0.00 3.27
106 107 9.216117 GCTCTATGAAGTACTTAAAACCTCAAA 57.784 33.333 8.42 0.00 0.00 2.69
107 108 8.372459 TGCTCTATGAAGTACTTAAAACCTCAA 58.628 33.333 8.42 0.00 0.00 3.02
108 109 7.903145 TGCTCTATGAAGTACTTAAAACCTCA 58.097 34.615 8.42 0.44 0.00 3.86
109 110 8.950208 ATGCTCTATGAAGTACTTAAAACCTC 57.050 34.615 8.42 0.00 0.00 3.85
110 111 8.763601 AGATGCTCTATGAAGTACTTAAAACCT 58.236 33.333 8.42 0.00 0.00 3.50
111 112 8.950208 AGATGCTCTATGAAGTACTTAAAACC 57.050 34.615 8.42 0.00 0.00 3.27
117 118 7.707035 CGGTAAAAGATGCTCTATGAAGTACTT 59.293 37.037 8.13 8.13 0.00 2.24
118 119 7.147880 ACGGTAAAAGATGCTCTATGAAGTACT 60.148 37.037 0.00 0.00 0.00 2.73
119 120 6.979238 ACGGTAAAAGATGCTCTATGAAGTAC 59.021 38.462 0.00 0.00 0.00 2.73
120 121 6.978659 CACGGTAAAAGATGCTCTATGAAGTA 59.021 38.462 0.00 0.00 0.00 2.24
121 122 5.812642 CACGGTAAAAGATGCTCTATGAAGT 59.187 40.000 0.00 0.00 0.00 3.01
122 123 6.042777 TCACGGTAAAAGATGCTCTATGAAG 58.957 40.000 0.00 0.00 0.00 3.02
123 124 5.972935 TCACGGTAAAAGATGCTCTATGAA 58.027 37.500 0.00 0.00 0.00 2.57
124 125 5.592104 TCACGGTAAAAGATGCTCTATGA 57.408 39.130 0.00 0.00 0.00 2.15
125 126 5.277058 GCTTCACGGTAAAAGATGCTCTATG 60.277 44.000 6.62 0.00 31.88 2.23
126 127 4.811557 GCTTCACGGTAAAAGATGCTCTAT 59.188 41.667 6.62 0.00 31.88 1.98
127 128 4.181578 GCTTCACGGTAAAAGATGCTCTA 58.818 43.478 6.62 0.00 31.88 2.43
128 129 3.003480 GCTTCACGGTAAAAGATGCTCT 58.997 45.455 6.62 0.00 31.88 4.09
129 130 2.742053 TGCTTCACGGTAAAAGATGCTC 59.258 45.455 6.62 0.00 34.62 4.26
130 131 2.778299 TGCTTCACGGTAAAAGATGCT 58.222 42.857 6.62 0.00 34.62 3.79
131 132 3.552604 TTGCTTCACGGTAAAAGATGC 57.447 42.857 6.62 2.88 34.25 3.91
132 133 5.295431 TCATTGCTTCACGGTAAAAGATG 57.705 39.130 6.62 3.50 0.00 2.90
133 134 5.473504 AGTTCATTGCTTCACGGTAAAAGAT 59.526 36.000 6.62 0.00 0.00 2.40
134 135 4.819630 AGTTCATTGCTTCACGGTAAAAGA 59.180 37.500 6.62 0.00 0.00 2.52
135 136 5.108385 AGTTCATTGCTTCACGGTAAAAG 57.892 39.130 0.00 0.00 0.00 2.27
136 137 6.811253 ATAGTTCATTGCTTCACGGTAAAA 57.189 33.333 0.00 0.00 0.00 1.52
137 138 9.772973 ATATATAGTTCATTGCTTCACGGTAAA 57.227 29.630 0.00 0.00 0.00 2.01
168 169 9.859427 CCATTATCAACAAGCAGAATTTAAAGA 57.141 29.630 0.00 0.00 0.00 2.52
169 170 8.598075 GCCATTATCAACAAGCAGAATTTAAAG 58.402 33.333 0.00 0.00 0.00 1.85
170 171 8.313292 AGCCATTATCAACAAGCAGAATTTAAA 58.687 29.630 0.00 0.00 0.00 1.52
171 172 7.760794 CAGCCATTATCAACAAGCAGAATTTAA 59.239 33.333 0.00 0.00 0.00 1.52
172 173 7.259882 CAGCCATTATCAACAAGCAGAATTTA 58.740 34.615 0.00 0.00 0.00 1.40
173 174 6.103997 CAGCCATTATCAACAAGCAGAATTT 58.896 36.000 0.00 0.00 0.00 1.82
174 175 5.657474 CAGCCATTATCAACAAGCAGAATT 58.343 37.500 0.00 0.00 0.00 2.17
175 176 4.441079 GCAGCCATTATCAACAAGCAGAAT 60.441 41.667 0.00 0.00 0.00 2.40
176 177 3.119388 GCAGCCATTATCAACAAGCAGAA 60.119 43.478 0.00 0.00 0.00 3.02
177 178 2.424601 GCAGCCATTATCAACAAGCAGA 59.575 45.455 0.00 0.00 0.00 4.26
178 179 2.164827 TGCAGCCATTATCAACAAGCAG 59.835 45.455 0.00 0.00 0.00 4.24
179 180 2.164827 CTGCAGCCATTATCAACAAGCA 59.835 45.455 0.00 0.00 0.00 3.91
180 181 2.165030 ACTGCAGCCATTATCAACAAGC 59.835 45.455 15.27 0.00 0.00 4.01
181 182 4.445452 AACTGCAGCCATTATCAACAAG 57.555 40.909 15.27 0.00 0.00 3.16
182 183 4.870123 AAACTGCAGCCATTATCAACAA 57.130 36.364 15.27 0.00 0.00 2.83
183 184 4.523943 AGAAAACTGCAGCCATTATCAACA 59.476 37.500 15.27 0.00 0.00 3.33
184 185 4.860907 CAGAAAACTGCAGCCATTATCAAC 59.139 41.667 15.27 0.00 0.00 3.18
185 186 4.523943 ACAGAAAACTGCAGCCATTATCAA 59.476 37.500 15.27 0.00 0.00 2.57
186 187 4.081406 ACAGAAAACTGCAGCCATTATCA 58.919 39.130 15.27 0.00 0.00 2.15
187 188 4.708726 ACAGAAAACTGCAGCCATTATC 57.291 40.909 15.27 4.08 0.00 1.75
188 189 4.813027 CAACAGAAAACTGCAGCCATTAT 58.187 39.130 15.27 0.46 0.00 1.28
189 190 3.552684 GCAACAGAAAACTGCAGCCATTA 60.553 43.478 15.27 0.00 36.09 1.90
190 191 2.804212 GCAACAGAAAACTGCAGCCATT 60.804 45.455 15.27 6.26 36.09 3.16
191 192 1.269936 GCAACAGAAAACTGCAGCCAT 60.270 47.619 15.27 0.00 36.09 4.40
192 193 0.102844 GCAACAGAAAACTGCAGCCA 59.897 50.000 15.27 0.00 36.09 4.75
193 194 0.598419 GGCAACAGAAAACTGCAGCC 60.598 55.000 15.27 14.26 39.28 4.85
194 195 0.102844 TGGCAACAGAAAACTGCAGC 59.897 50.000 15.27 0.00 46.17 5.25
244 245 0.613260 CCCCAGATTGGTCGAGTTGA 59.387 55.000 0.00 0.00 35.17 3.18
245 246 1.026718 GCCCCAGATTGGTCGAGTTG 61.027 60.000 0.00 0.00 35.17 3.16
246 247 1.201429 AGCCCCAGATTGGTCGAGTT 61.201 55.000 0.00 0.00 35.17 3.01
247 248 0.325296 TAGCCCCAGATTGGTCGAGT 60.325 55.000 0.00 0.00 35.17 4.18
248 249 0.390860 CTAGCCCCAGATTGGTCGAG 59.609 60.000 0.00 0.00 35.17 4.04
249 250 1.686325 GCTAGCCCCAGATTGGTCGA 61.686 60.000 2.29 0.00 35.17 4.20
250 251 1.227674 GCTAGCCCCAGATTGGTCG 60.228 63.158 2.29 0.00 35.17 4.79
251 252 1.149401 GGCTAGCCCCAGATTGGTC 59.851 63.158 24.19 0.00 35.17 4.02
252 253 1.308216 AGGCTAGCCCCAGATTGGT 60.308 57.895 30.42 5.22 35.17 3.67
253 254 1.059006 AGAGGCTAGCCCCAGATTGG 61.059 60.000 30.42 0.00 37.25 3.16
254 255 1.622811 CTAGAGGCTAGCCCCAGATTG 59.377 57.143 30.42 10.36 36.58 2.67
255 256 1.221781 ACTAGAGGCTAGCCCCAGATT 59.778 52.381 30.42 10.75 36.58 2.40
256 257 0.863956 ACTAGAGGCTAGCCCCAGAT 59.136 55.000 30.42 11.60 36.58 2.90
257 258 0.105964 CACTAGAGGCTAGCCCCAGA 60.106 60.000 30.42 12.30 36.58 3.86
258 259 1.118356 CCACTAGAGGCTAGCCCCAG 61.118 65.000 30.42 24.35 36.58 4.45
259 260 1.075226 CCACTAGAGGCTAGCCCCA 60.075 63.158 30.42 14.35 36.58 4.96
260 261 3.878358 CCACTAGAGGCTAGCCCC 58.122 66.667 30.42 19.96 36.58 5.80
268 269 0.830648 TCGGGAAATGCCACTAGAGG 59.169 55.000 1.14 1.14 38.95 3.69
269 270 2.691409 TTCGGGAAATGCCACTAGAG 57.309 50.000 0.00 0.00 38.95 2.43
270 271 4.444306 CCTTATTCGGGAAATGCCACTAGA 60.444 45.833 0.00 0.00 38.95 2.43
271 272 3.815401 CCTTATTCGGGAAATGCCACTAG 59.185 47.826 0.00 0.00 38.95 2.57
272 273 3.456644 TCCTTATTCGGGAAATGCCACTA 59.543 43.478 0.00 0.00 38.95 2.74
273 274 2.241176 TCCTTATTCGGGAAATGCCACT 59.759 45.455 0.00 0.00 38.95 4.00
274 275 2.650322 TCCTTATTCGGGAAATGCCAC 58.350 47.619 0.00 0.00 38.95 5.01
275 276 3.374042 TTCCTTATTCGGGAAATGCCA 57.626 42.857 0.00 0.00 39.56 4.92
280 281 6.492087 ACTCATGTTTTTCCTTATTCGGGAAA 59.508 34.615 4.09 4.09 46.96 3.13
281 282 6.007703 ACTCATGTTTTTCCTTATTCGGGAA 58.992 36.000 0.00 0.00 40.61 3.97
282 283 5.566469 ACTCATGTTTTTCCTTATTCGGGA 58.434 37.500 0.00 0.00 0.00 5.14
283 284 5.897377 ACTCATGTTTTTCCTTATTCGGG 57.103 39.130 0.00 0.00 0.00 5.14
284 285 6.183360 GGGTACTCATGTTTTTCCTTATTCGG 60.183 42.308 0.00 0.00 0.00 4.30
285 286 6.373216 TGGGTACTCATGTTTTTCCTTATTCG 59.627 38.462 0.00 0.00 0.00 3.34
286 287 7.362660 GGTGGGTACTCATGTTTTTCCTTATTC 60.363 40.741 0.00 0.00 0.00 1.75
287 288 6.436218 GGTGGGTACTCATGTTTTTCCTTATT 59.564 38.462 0.00 0.00 0.00 1.40
288 289 5.949952 GGTGGGTACTCATGTTTTTCCTTAT 59.050 40.000 0.00 0.00 0.00 1.73
289 290 5.073965 AGGTGGGTACTCATGTTTTTCCTTA 59.926 40.000 0.00 0.00 0.00 2.69
290 291 4.141018 AGGTGGGTACTCATGTTTTTCCTT 60.141 41.667 0.00 0.00 0.00 3.36
291 292 3.397955 AGGTGGGTACTCATGTTTTTCCT 59.602 43.478 0.00 0.00 0.00 3.36
292 293 3.506067 CAGGTGGGTACTCATGTTTTTCC 59.494 47.826 0.00 0.00 0.00 3.13
293 294 4.394729 TCAGGTGGGTACTCATGTTTTTC 58.605 43.478 0.00 0.00 0.00 2.29
294 295 4.447138 TCAGGTGGGTACTCATGTTTTT 57.553 40.909 0.00 0.00 0.00 1.94
295 296 4.335416 CATCAGGTGGGTACTCATGTTTT 58.665 43.478 0.00 0.00 0.00 2.43
296 297 3.308402 CCATCAGGTGGGTACTCATGTTT 60.308 47.826 0.00 0.00 44.79 2.83
297 298 2.239654 CCATCAGGTGGGTACTCATGTT 59.760 50.000 0.00 0.00 44.79 2.71
298 299 1.839994 CCATCAGGTGGGTACTCATGT 59.160 52.381 0.00 0.00 44.79 3.21
299 300 2.627515 CCATCAGGTGGGTACTCATG 57.372 55.000 0.00 0.00 44.79 3.07
309 310 1.004044 AGGCTCAAACTCCATCAGGTG 59.996 52.381 0.00 0.00 35.89 4.00
310 311 1.280421 GAGGCTCAAACTCCATCAGGT 59.720 52.381 10.25 0.00 35.89 4.00
311 312 1.280133 TGAGGCTCAAACTCCATCAGG 59.720 52.381 16.28 0.00 34.06 3.86
312 313 2.775911 TGAGGCTCAAACTCCATCAG 57.224 50.000 16.28 0.00 34.06 2.90
313 314 3.507162 TTTGAGGCTCAAACTCCATCA 57.493 42.857 32.85 13.42 41.02 3.07
314 315 3.366781 GCTTTTGAGGCTCAAACTCCATC 60.367 47.826 35.46 17.19 45.03 3.51
315 316 2.560105 GCTTTTGAGGCTCAAACTCCAT 59.440 45.455 35.46 0.00 45.03 3.41
316 317 1.956477 GCTTTTGAGGCTCAAACTCCA 59.044 47.619 35.46 22.72 45.03 3.86
317 318 2.030451 CAGCTTTTGAGGCTCAAACTCC 60.030 50.000 35.46 25.94 45.03 3.85
318 319 2.030451 CCAGCTTTTGAGGCTCAAACTC 60.030 50.000 35.46 28.36 45.03 3.01
319 320 1.959282 CCAGCTTTTGAGGCTCAAACT 59.041 47.619 35.46 27.74 45.03 2.66
320 321 1.683385 ACCAGCTTTTGAGGCTCAAAC 59.317 47.619 35.46 26.24 45.03 2.93
321 322 1.682854 CACCAGCTTTTGAGGCTCAAA 59.317 47.619 32.85 32.85 43.84 2.69
322 323 1.321474 CACCAGCTTTTGAGGCTCAA 58.679 50.000 25.38 25.38 38.03 3.02
323 324 0.538057 CCACCAGCTTTTGAGGCTCA 60.538 55.000 14.43 14.43 38.03 4.26
324 325 1.246737 CCCACCAGCTTTTGAGGCTC 61.247 60.000 7.79 7.79 38.03 4.70
325 326 1.228675 CCCACCAGCTTTTGAGGCT 60.229 57.895 0.00 0.00 41.07 4.58
326 327 2.935740 GCCCACCAGCTTTTGAGGC 61.936 63.158 7.61 7.61 32.59 4.70
327 328 1.530013 CTGCCCACCAGCTTTTGAGG 61.530 60.000 0.00 0.00 34.21 3.86
328 329 1.530013 CCTGCCCACCAGCTTTTGAG 61.530 60.000 0.00 0.00 40.36 3.02
329 330 1.531365 CCTGCCCACCAGCTTTTGA 60.531 57.895 0.00 0.00 40.36 2.69
330 331 3.053828 CCTGCCCACCAGCTTTTG 58.946 61.111 0.00 0.00 40.36 2.44
331 332 2.919328 GCCTGCCCACCAGCTTTT 60.919 61.111 0.00 0.00 40.36 2.27
344 345 1.214589 GATGTGCTTTGCAGGCCTG 59.785 57.895 29.34 29.34 40.08 4.85
345 346 1.228644 TGATGTGCTTTGCAGGCCT 60.229 52.632 0.00 0.00 40.08 5.19
346 347 1.214589 CTGATGTGCTTTGCAGGCC 59.785 57.895 0.00 0.00 40.08 5.19
347 348 1.445582 GCTGATGTGCTTTGCAGGC 60.446 57.895 6.77 6.77 40.08 4.85
348 349 2.264124 AGCTGATGTGCTTTGCAGG 58.736 52.632 0.00 0.00 40.93 4.85
356 357 1.801332 CTGGAGCAAGCTGATGTGC 59.199 57.895 0.00 0.00 41.22 4.57
357 358 1.801332 GCTGGAGCAAGCTGATGTG 59.199 57.895 0.00 0.00 40.20 3.21
358 359 4.315588 GCTGGAGCAAGCTGATGT 57.684 55.556 0.00 0.00 40.20 3.06
368 369 4.215349 CAGGTTGCTAGCTGGAGC 57.785 61.111 17.23 11.31 44.30 4.70
373 374 1.135915 CGTCTGATCAGGTTGCTAGCT 59.864 52.381 22.42 0.00 0.00 3.32
374 375 1.565305 CGTCTGATCAGGTTGCTAGC 58.435 55.000 22.42 8.10 0.00 3.42
375 376 1.135915 AGCGTCTGATCAGGTTGCTAG 59.864 52.381 25.60 11.68 32.04 3.42
376 377 1.135139 GAGCGTCTGATCAGGTTGCTA 59.865 52.381 26.33 6.39 33.24 3.49
377 378 0.108424 GAGCGTCTGATCAGGTTGCT 60.108 55.000 26.49 26.49 34.82 3.91
378 379 0.390340 TGAGCGTCTGATCAGGTTGC 60.390 55.000 22.42 21.12 35.14 4.17
379 380 1.067283 AGTGAGCGTCTGATCAGGTTG 60.067 52.381 22.42 13.09 42.03 3.77
380 381 1.203523 GAGTGAGCGTCTGATCAGGTT 59.796 52.381 22.42 5.47 42.03 3.50
381 382 0.814457 GAGTGAGCGTCTGATCAGGT 59.186 55.000 22.42 3.71 42.03 4.00
382 383 0.813821 TGAGTGAGCGTCTGATCAGG 59.186 55.000 22.42 8.67 42.03 3.86
383 384 1.793353 CGTGAGTGAGCGTCTGATCAG 60.793 57.143 17.07 17.07 42.03 2.90
384 385 0.169009 CGTGAGTGAGCGTCTGATCA 59.831 55.000 0.00 0.00 38.40 2.92
385 386 0.169230 ACGTGAGTGAGCGTCTGATC 59.831 55.000 0.00 0.00 46.97 2.92
386 387 2.258317 ACGTGAGTGAGCGTCTGAT 58.742 52.632 0.00 0.00 46.97 2.90
387 388 3.745912 ACGTGAGTGAGCGTCTGA 58.254 55.556 0.00 0.00 46.97 3.27
398 399 4.580995 AGGGAGTATATCAGAACACGTGAG 59.419 45.833 25.01 9.06 0.00 3.51
399 400 4.533815 AGGGAGTATATCAGAACACGTGA 58.466 43.478 25.01 0.00 0.00 4.35
400 401 4.920640 AGGGAGTATATCAGAACACGTG 57.079 45.455 15.48 15.48 0.00 4.49
401 402 4.036498 CGAAGGGAGTATATCAGAACACGT 59.964 45.833 0.00 0.00 0.00 4.49
402 403 4.036498 ACGAAGGGAGTATATCAGAACACG 59.964 45.833 0.00 0.00 0.00 4.49
403 404 5.517322 ACGAAGGGAGTATATCAGAACAC 57.483 43.478 0.00 0.00 0.00 3.32
404 405 5.892119 AGAACGAAGGGAGTATATCAGAACA 59.108 40.000 0.00 0.00 0.00 3.18
405 406 6.183360 ACAGAACGAAGGGAGTATATCAGAAC 60.183 42.308 0.00 0.00 0.00 3.01
406 407 5.892119 ACAGAACGAAGGGAGTATATCAGAA 59.108 40.000 0.00 0.00 0.00 3.02
407 408 5.446860 ACAGAACGAAGGGAGTATATCAGA 58.553 41.667 0.00 0.00 0.00 3.27
408 409 5.776173 ACAGAACGAAGGGAGTATATCAG 57.224 43.478 0.00 0.00 0.00 2.90
409 410 7.341256 ACTTAACAGAACGAAGGGAGTATATCA 59.659 37.037 0.00 0.00 0.00 2.15
410 411 7.714703 ACTTAACAGAACGAAGGGAGTATATC 58.285 38.462 0.00 0.00 0.00 1.63
411 412 7.657023 ACTTAACAGAACGAAGGGAGTATAT 57.343 36.000 0.00 0.00 0.00 0.86
412 413 8.757982 ATACTTAACAGAACGAAGGGAGTATA 57.242 34.615 0.00 0.00 0.00 1.47
413 414 5.997384 ACTTAACAGAACGAAGGGAGTAT 57.003 39.130 0.00 0.00 0.00 2.12
414 415 8.757982 ATATACTTAACAGAACGAAGGGAGTA 57.242 34.615 0.00 0.00 0.00 2.59
415 416 5.997384 ATACTTAACAGAACGAAGGGAGT 57.003 39.130 0.00 0.00 0.00 3.85
416 417 9.627395 CATATATACTTAACAGAACGAAGGGAG 57.373 37.037 0.00 0.00 0.00 4.30
417 418 9.139734 ACATATATACTTAACAGAACGAAGGGA 57.860 33.333 0.00 0.00 0.00 4.20
418 419 9.760077 AACATATATACTTAACAGAACGAAGGG 57.240 33.333 0.00 0.00 0.00 3.95
877 880 3.474798 TCTCACTGGATAGAAGGTGGT 57.525 47.619 0.00 0.00 0.00 4.16
932 993 2.224606 CAGGCAGCAACAAGAGAAGAA 58.775 47.619 0.00 0.00 0.00 2.52
2478 2573 3.177228 AGTGCTGGAAGAGTATGGAAGT 58.823 45.455 0.00 0.00 34.07 3.01
2564 2659 5.772672 ACATAATGTTTGTGGCTACCTTTCA 59.227 36.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.