Multiple sequence alignment - TraesCS3D01G531000

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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 TraesCS3D01G531000 chr3D 100.000 2540 0 0 853 3392 607226245 607223706 0.000000e+00 4691
1 TraesCS3D01G531000 chr3D 100.000 659 0 0 1 659 607227097 607226439 0.000000e+00 1218
2 TraesCS3D01G531000 chr3D 98.432 574 4 1 2824 3392 8714256 8713683 0.000000e+00 1005
3 TraesCS3D01G531000 chr3D 98.871 443 1 1 2954 3392 582780377 582780819 0.000000e+00 787
4 TraesCS3D01G531000 chr3D 80.662 393 54 10 2010 2385 607098454 607098067 5.540000e-73 285
5 TraesCS3D01G531000 chr3D 99.351 154 1 0 2815 2968 23519583 23519430 2.580000e-71 279
6 TraesCS3D01G531000 chr3D 85.772 246 20 8 1974 2209 607206968 607206728 2.610000e-61 246
7 TraesCS3D01G531000 chr3D 88.670 203 20 2 12 211 526937453 526937251 9.400000e-61 244
8 TraesCS3D01G531000 chr3D 88.832 197 19 2 17 210 317203594 317203398 4.370000e-59 239
9 TraesCS3D01G531000 chr3A 95.981 1045 25 3 1777 2820 739666570 739665542 0.000000e+00 1681
10 TraesCS3D01G531000 chr3A 85.275 910 41 30 855 1687 739667496 739666603 0.000000e+00 852
11 TraesCS3D01G531000 chr3A 83.753 437 39 8 244 659 739667958 739667533 5.310000e-103 385
12 TraesCS3D01G531000 chr3A 91.912 272 18 1 2121 2392 739613990 739613723 8.880000e-101 377
13 TraesCS3D01G531000 chr3A 84.091 352 32 11 1717 2054 739614429 739614088 5.460000e-83 318
14 TraesCS3D01G531000 chr3A 82.069 290 40 6 2104 2385 739567988 739567703 1.570000e-58 237
15 TraesCS3D01G531000 chr3A 86.500 200 23 3 14 210 396523287 396523485 2.050000e-52 217
16 TraesCS3D01G531000 chr3A 86.567 134 11 5 1447 1580 739614683 739614557 1.270000e-29 141
17 TraesCS3D01G531000 chr3A 92.000 75 6 0 1586 1660 739614517 739614443 4.630000e-19 106
18 TraesCS3D01G531000 chr3B 96.719 640 16 2 1795 2429 816613562 816612923 0.000000e+00 1061
19 TraesCS3D01G531000 chr3B 96.465 198 6 1 2624 2820 816612903 816612706 3.260000e-85 326
20 TraesCS3D01G531000 chr3B 87.368 285 18 6 855 1138 816614372 816614105 9.140000e-81 311
21 TraesCS3D01G531000 chr3B 80.000 445 43 15 244 658 816614844 816614416 1.540000e-73 287
22 TraesCS3D01G531000 chr3B 86.567 201 24 2 15 212 471248882 471249082 5.700000e-53 219
23 TraesCS3D01G531000 chr3B 93.056 144 6 1 1208 1347 816614014 816613871 1.230000e-49 207
24 TraesCS3D01G531000 chr3B 97.030 101 3 0 1378 1478 816613673 816613573 1.620000e-38 171
25 TraesCS3D01G531000 chr3B 87.234 141 15 1 2679 2816 816607755 816607615 1.260000e-34 158
26 TraesCS3D01G531000 chr7D 97.561 574 9 2 2819 3392 70413172 70413740 0.000000e+00 977
27 TraesCS3D01G531000 chr7D 97.565 575 5 3 2821 3392 55531989 55532557 0.000000e+00 976
28 TraesCS3D01G531000 chr7D 94.007 584 10 8 2821 3392 593251817 593252387 0.000000e+00 861
29 TraesCS3D01G531000 chr7D 99.545 440 1 1 2954 3392 45119483 45119044 0.000000e+00 800
30 TraesCS3D01G531000 chr7D 98.726 157 2 0 2812 2968 45119738 45119582 2.580000e-71 279
31 TraesCS3D01G531000 chr7D 99.346 153 1 0 2816 2968 579844174 579844022 9.270000e-71 278
32 TraesCS3D01G531000 chr7D 98.113 159 0 2 2812 2968 63000164 63000007 1.200000e-69 274
33 TraesCS3D01G531000 chr1D 94.983 598 4 1 2821 3392 444746656 444746059 0.000000e+00 915
34 TraesCS3D01G531000 chr1D 99.765 426 1 0 2967 3392 12894386 12894811 0.000000e+00 782
35 TraesCS3D01G531000 chr1D 96.237 186 7 0 2818 3003 11367534 11367719 4.250000e-79 305
36 TraesCS3D01G531000 chr1D 88.119 202 21 2 15 213 481697813 481698014 1.570000e-58 237
37 TraesCS3D01G531000 chr1D 83.684 190 24 6 17 202 385051517 385051331 4.500000e-39 172
38 TraesCS3D01G531000 chr1D 82.412 199 32 2 14 209 68455518 68455716 1.620000e-38 171
39 TraesCS3D01G531000 chr6D 99.765 426 1 0 2967 3392 24920898 24921323 0.000000e+00 782
40 TraesCS3D01G531000 chr6D 88.119 202 20 3 15 213 181729536 181729736 1.570000e-58 237
41 TraesCS3D01G531000 chr6D 87.310 197 22 2 17 210 42959673 42959869 4.410000e-54 222
42 TraesCS3D01G531000 chr6D 84.103 195 26 4 22 212 76195298 76195105 2.080000e-42 183
43 TraesCS3D01G531000 chr6D 86.792 159 18 2 47 202 437772505 437772347 1.250000e-39 174
44 TraesCS3D01G531000 chr6D 82.126 207 29 4 14 213 6167559 6167354 1.620000e-38 171
45 TraesCS3D01G531000 chr6D 83.636 165 24 3 49 210 392266430 392266266 5.860000e-33 152
46 TraesCS3D01G531000 chr5D 99.765 426 1 0 2967 3392 52605883 52606308 0.000000e+00 782
47 TraesCS3D01G531000 chr5D 86.207 203 24 3 14 212 362579490 362579288 2.050000e-52 217
48 TraesCS3D01G531000 chr5D 86.139 202 24 3 14 212 38979355 38979155 7.370000e-52 215
49 TraesCS3D01G531000 chr5D 83.500 200 30 2 14 210 468172031 468172230 2.080000e-42 183
50 TraesCS3D01G531000 chr4D 88.780 205 19 3 15 215 258893453 258893657 7.270000e-62 248
51 TraesCS3D01G531000 chr4D 86.070 201 25 2 15 212 391466798 391466598 2.650000e-51 213
52 TraesCS3D01G531000 chr4D 85.938 128 18 0 14 141 404680006 404680133 1.640000e-28 137
53 TraesCS3D01G531000 chr4D 82.576 132 19 2 48 175 369667852 369667721 2.770000e-21 113
54 TraesCS3D01G531000 chr2D 87.745 204 22 2 16 216 647674806 647674603 5.660000e-58 235
55 TraesCS3D01G531000 chr1A 87.805 205 20 4 16 215 504526020 504525816 5.660000e-58 235
56 TraesCS3D01G531000 chr1A 84.722 144 17 3 10 150 121564532 121564673 4.560000e-29 139
57 TraesCS3D01G531000 chr1A 82.036 167 25 4 48 210 525370802 525370967 1.640000e-28 137
58 TraesCS3D01G531000 chr5B 85.787 197 25 2 17 210 473808040 473808236 4.440000e-49 206


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 TraesCS3D01G531000 chr3D 607223706 607227097 3391 True 2954.500000 4691 100.000000 1 3392 2 chr3D.!!$R7 3391
1 TraesCS3D01G531000 chr3D 8713683 8714256 573 True 1005.000000 1005 98.432000 2824 3392 1 chr3D.!!$R1 568
2 TraesCS3D01G531000 chr3A 739665542 739667958 2416 True 972.666667 1681 88.336333 244 2820 3 chr3A.!!$R3 2576
3 TraesCS3D01G531000 chr3A 739613723 739614683 960 True 235.500000 377 88.642500 1447 2392 4 chr3A.!!$R2 945
4 TraesCS3D01G531000 chr3B 816612706 816614844 2138 True 393.833333 1061 91.773000 244 2820 6 chr3B.!!$R2 2576
5 TraesCS3D01G531000 chr7D 70413172 70413740 568 False 977.000000 977 97.561000 2819 3392 1 chr7D.!!$F2 573
6 TraesCS3D01G531000 chr7D 55531989 55532557 568 False 976.000000 976 97.565000 2821 3392 1 chr7D.!!$F1 571
7 TraesCS3D01G531000 chr7D 593251817 593252387 570 False 861.000000 861 94.007000 2821 3392 1 chr7D.!!$F3 571
8 TraesCS3D01G531000 chr7D 45119044 45119738 694 True 539.500000 800 99.135500 2812 3392 2 chr7D.!!$R3 580
9 TraesCS3D01G531000 chr1D 444746059 444746656 597 True 915.000000 915 94.983000 2821 3392 1 chr1D.!!$R2 571

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
917 958 0.028110 GTTGATTGATTCGGAGGCGC 59.972 55.0 0.00 0.0 0.0 6.53 F
1490 1773 0.032403 ACGTACGGCTTGTGTGCTTA 59.968 50.0 21.06 0.0 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 2090 0.670239 CCACACACTAGCATGTCGCA 60.670 55.000 0.0 0.0 46.13 5.10 R
2724 3141 1.730772 CGAGCTCAAGTTCCACTCTCG 60.731 57.143 15.4 0.0 34.25 4.04 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 4.147701 CCTCCGCCATTGCCTAAG 57.852 61.111 0.00 0.00 0.00 2.18
18 19 1.526917 CCTCCGCCATTGCCTAAGG 60.527 63.158 0.00 0.00 0.00 2.69
30 31 2.825086 GCCTAAGGCGTTGTACAATG 57.175 50.000 21.23 21.23 39.62 2.82
38 39 2.974165 GCGTTGTACAATGCTAGATGC 58.026 47.619 34.98 15.82 46.74 3.91
39 40 2.609459 GCGTTGTACAATGCTAGATGCT 59.391 45.455 34.98 0.00 46.74 3.79
40 41 3.063997 GCGTTGTACAATGCTAGATGCTT 59.936 43.478 34.98 0.00 46.74 3.91
41 42 4.270084 GCGTTGTACAATGCTAGATGCTTA 59.730 41.667 34.98 0.00 46.74 3.09
42 43 5.557136 GCGTTGTACAATGCTAGATGCTTAG 60.557 44.000 34.98 6.59 46.74 2.18
43 44 5.050769 CGTTGTACAATGCTAGATGCTTAGG 60.051 44.000 14.61 0.00 43.37 2.69
44 45 5.869649 TGTACAATGCTAGATGCTTAGGA 57.130 39.130 0.00 0.00 43.37 2.94
45 46 6.233905 TGTACAATGCTAGATGCTTAGGAA 57.766 37.500 0.00 0.00 43.37 3.36
46 47 6.283694 TGTACAATGCTAGATGCTTAGGAAG 58.716 40.000 0.00 0.00 43.37 3.46
47 48 4.712476 ACAATGCTAGATGCTTAGGAAGG 58.288 43.478 0.00 0.00 43.37 3.46
48 49 4.164988 ACAATGCTAGATGCTTAGGAAGGT 59.835 41.667 0.00 0.00 43.37 3.50
49 50 3.827008 TGCTAGATGCTTAGGAAGGTG 57.173 47.619 0.00 0.00 43.37 4.00
50 51 2.158900 TGCTAGATGCTTAGGAAGGTGC 60.159 50.000 0.00 0.00 43.37 5.01
51 52 2.158900 GCTAGATGCTTAGGAAGGTGCA 60.159 50.000 0.00 0.00 39.83 4.57
53 54 4.262635 GCTAGATGCTTAGGAAGGTGCATA 60.263 45.833 0.00 0.00 44.80 3.14
54 55 4.778213 AGATGCTTAGGAAGGTGCATAA 57.222 40.909 0.00 0.00 44.80 1.90
55 56 5.116084 AGATGCTTAGGAAGGTGCATAAA 57.884 39.130 0.00 0.00 44.80 1.40
56 57 5.509498 AGATGCTTAGGAAGGTGCATAAAA 58.491 37.500 0.00 0.00 44.80 1.52
57 58 5.951747 AGATGCTTAGGAAGGTGCATAAAAA 59.048 36.000 0.00 0.00 44.80 1.94
79 80 7.780008 AAAATTAAACCGGGTTTTTCTGAAG 57.220 32.000 28.50 0.00 37.01 3.02
80 81 2.882927 AAACCGGGTTTTTCTGAAGC 57.117 45.000 19.22 0.00 31.10 3.86
81 82 1.770294 AACCGGGTTTTTCTGAAGCA 58.230 45.000 6.59 0.00 0.00 3.91
82 83 1.029681 ACCGGGTTTTTCTGAAGCAC 58.970 50.000 6.32 0.00 0.00 4.40
83 84 0.313987 CCGGGTTTTTCTGAAGCACC 59.686 55.000 10.25 10.25 0.00 5.01
84 85 1.028905 CGGGTTTTTCTGAAGCACCA 58.971 50.000 17.20 0.00 0.00 4.17
85 86 1.001378 CGGGTTTTTCTGAAGCACCAG 60.001 52.381 17.20 11.81 35.55 4.00
86 87 2.031870 GGGTTTTTCTGAAGCACCAGT 58.968 47.619 17.20 0.00 35.71 4.00
87 88 2.223805 GGGTTTTTCTGAAGCACCAGTG 60.224 50.000 17.20 0.00 35.71 3.66
102 103 4.832248 CACCAGTGCTTATTTCTACAGGA 58.168 43.478 0.00 0.00 0.00 3.86
103 104 4.872691 CACCAGTGCTTATTTCTACAGGAG 59.127 45.833 0.00 0.00 0.00 3.69
104 105 4.777896 ACCAGTGCTTATTTCTACAGGAGA 59.222 41.667 0.00 0.00 0.00 3.71
105 106 5.105146 ACCAGTGCTTATTTCTACAGGAGAG 60.105 44.000 0.00 0.00 34.93 3.20
106 107 5.127845 CCAGTGCTTATTTCTACAGGAGAGA 59.872 44.000 0.00 0.00 34.93 3.10
107 108 6.039616 CAGTGCTTATTTCTACAGGAGAGAC 58.960 44.000 0.00 0.00 34.93 3.36
108 109 5.038033 GTGCTTATTTCTACAGGAGAGACG 58.962 45.833 0.00 0.00 34.93 4.18
109 110 4.045783 GCTTATTTCTACAGGAGAGACGC 58.954 47.826 0.00 0.00 34.93 5.19
110 111 4.612943 CTTATTTCTACAGGAGAGACGCC 58.387 47.826 0.00 0.00 34.93 5.68
111 112 2.217510 TTTCTACAGGAGAGACGCCT 57.782 50.000 0.00 0.00 34.93 5.52
112 113 3.361281 TTTCTACAGGAGAGACGCCTA 57.639 47.619 0.00 0.00 34.93 3.93
113 114 3.361281 TTCTACAGGAGAGACGCCTAA 57.639 47.619 0.00 0.00 34.93 2.69
114 115 3.579534 TCTACAGGAGAGACGCCTAAT 57.420 47.619 0.00 0.00 31.11 1.73
115 116 3.899726 TCTACAGGAGAGACGCCTAATT 58.100 45.455 0.00 0.00 31.11 1.40
116 117 5.045012 TCTACAGGAGAGACGCCTAATTA 57.955 43.478 0.00 0.00 31.11 1.40
117 118 5.443283 TCTACAGGAGAGACGCCTAATTAA 58.557 41.667 0.00 0.00 31.11 1.40
118 119 4.657436 ACAGGAGAGACGCCTAATTAAG 57.343 45.455 0.00 0.00 31.11 1.85
119 120 3.181474 ACAGGAGAGACGCCTAATTAAGC 60.181 47.826 0.00 0.00 31.11 3.09
128 129 3.180891 GCCTAATTAAGCGTCTGTCCT 57.819 47.619 0.00 0.00 0.00 3.85
129 130 2.866762 GCCTAATTAAGCGTCTGTCCTG 59.133 50.000 0.00 0.00 0.00 3.86
130 131 3.679083 GCCTAATTAAGCGTCTGTCCTGT 60.679 47.826 0.00 0.00 0.00 4.00
131 132 4.441079 GCCTAATTAAGCGTCTGTCCTGTA 60.441 45.833 0.00 0.00 0.00 2.74
132 133 5.739358 GCCTAATTAAGCGTCTGTCCTGTAT 60.739 44.000 0.00 0.00 0.00 2.29
133 134 6.516194 GCCTAATTAAGCGTCTGTCCTGTATA 60.516 42.308 0.00 0.00 0.00 1.47
134 135 7.431249 CCTAATTAAGCGTCTGTCCTGTATAA 58.569 38.462 0.00 0.00 0.00 0.98
135 136 7.924412 CCTAATTAAGCGTCTGTCCTGTATAAA 59.076 37.037 0.00 0.00 0.00 1.40
136 137 9.477484 CTAATTAAGCGTCTGTCCTGTATAAAT 57.523 33.333 0.00 0.00 0.00 1.40
138 139 9.826574 AATTAAGCGTCTGTCCTGTATAAATAA 57.173 29.630 0.00 0.00 0.00 1.40
139 140 8.867112 TTAAGCGTCTGTCCTGTATAAATAAG 57.133 34.615 0.00 0.00 0.00 1.73
140 141 5.290386 AGCGTCTGTCCTGTATAAATAAGC 58.710 41.667 0.00 0.00 0.00 3.09
141 142 5.047847 GCGTCTGTCCTGTATAAATAAGCA 58.952 41.667 0.00 0.00 0.00 3.91
142 143 5.696724 GCGTCTGTCCTGTATAAATAAGCAT 59.303 40.000 0.00 0.00 0.00 3.79
143 144 6.128795 GCGTCTGTCCTGTATAAATAAGCATC 60.129 42.308 0.00 0.00 0.00 3.91
144 145 6.088217 CGTCTGTCCTGTATAAATAAGCATCG 59.912 42.308 0.00 0.00 0.00 3.84
145 146 6.366332 GTCTGTCCTGTATAAATAAGCATCGG 59.634 42.308 0.00 0.00 0.00 4.18
146 147 6.041637 TCTGTCCTGTATAAATAAGCATCGGT 59.958 38.462 0.00 0.00 0.00 4.69
147 148 5.989168 TGTCCTGTATAAATAAGCATCGGTG 59.011 40.000 0.00 0.00 0.00 4.94
159 160 1.813513 CATCGGTGCTGAAGGAAAGT 58.186 50.000 0.00 0.00 0.00 2.66
160 161 2.972625 CATCGGTGCTGAAGGAAAGTA 58.027 47.619 0.00 0.00 0.00 2.24
161 162 3.535561 CATCGGTGCTGAAGGAAAGTAT 58.464 45.455 0.00 0.00 0.00 2.12
162 163 3.695830 TCGGTGCTGAAGGAAAGTATT 57.304 42.857 0.00 0.00 0.00 1.89
163 164 4.015872 TCGGTGCTGAAGGAAAGTATTT 57.984 40.909 0.00 0.00 43.98 1.40
164 165 4.394729 TCGGTGCTGAAGGAAAGTATTTT 58.605 39.130 0.00 0.00 39.27 1.82
165 166 5.553123 TCGGTGCTGAAGGAAAGTATTTTA 58.447 37.500 0.00 0.00 39.27 1.52
166 167 6.177610 TCGGTGCTGAAGGAAAGTATTTTAT 58.822 36.000 0.00 0.00 39.27 1.40
167 168 6.657541 TCGGTGCTGAAGGAAAGTATTTTATT 59.342 34.615 0.00 0.00 39.27 1.40
168 169 7.175990 TCGGTGCTGAAGGAAAGTATTTTATTT 59.824 33.333 0.00 0.00 39.27 1.40
169 170 7.484959 CGGTGCTGAAGGAAAGTATTTTATTTC 59.515 37.037 0.00 0.00 39.27 2.17
170 171 8.523658 GGTGCTGAAGGAAAGTATTTTATTTCT 58.476 33.333 7.63 0.00 39.27 2.52
171 172 9.914131 GTGCTGAAGGAAAGTATTTTATTTCTT 57.086 29.630 7.63 0.00 39.27 2.52
188 189 9.614792 TTTATTTCTTCAATACCTCTCCTAAGC 57.385 33.333 0.00 0.00 0.00 3.09
189 190 6.620877 TTTCTTCAATACCTCTCCTAAGCA 57.379 37.500 0.00 0.00 0.00 3.91
190 191 5.599999 TCTTCAATACCTCTCCTAAGCAC 57.400 43.478 0.00 0.00 0.00 4.40
191 192 4.406003 TCTTCAATACCTCTCCTAAGCACC 59.594 45.833 0.00 0.00 0.00 5.01
192 193 3.995636 TCAATACCTCTCCTAAGCACCT 58.004 45.455 0.00 0.00 0.00 4.00
193 194 4.362677 TCAATACCTCTCCTAAGCACCTT 58.637 43.478 0.00 0.00 0.00 3.50
194 195 4.162320 TCAATACCTCTCCTAAGCACCTTG 59.838 45.833 0.00 0.00 0.00 3.61
195 196 2.031495 ACCTCTCCTAAGCACCTTGT 57.969 50.000 0.00 0.00 0.00 3.16
196 197 3.185880 ACCTCTCCTAAGCACCTTGTA 57.814 47.619 0.00 0.00 0.00 2.41
197 198 3.725634 ACCTCTCCTAAGCACCTTGTAT 58.274 45.455 0.00 0.00 0.00 2.29
198 199 4.104831 ACCTCTCCTAAGCACCTTGTATT 58.895 43.478 0.00 0.00 0.00 1.89
199 200 4.080863 ACCTCTCCTAAGCACCTTGTATTG 60.081 45.833 0.00 0.00 0.00 1.90
200 201 4.080863 CCTCTCCTAAGCACCTTGTATTGT 60.081 45.833 0.00 0.00 0.00 2.71
201 202 5.128827 CCTCTCCTAAGCACCTTGTATTGTA 59.871 44.000 0.00 0.00 0.00 2.41
202 203 6.183361 CCTCTCCTAAGCACCTTGTATTGTAT 60.183 42.308 0.00 0.00 0.00 2.29
203 204 7.015292 CCTCTCCTAAGCACCTTGTATTGTATA 59.985 40.741 0.00 0.00 0.00 1.47
204 205 8.313944 TCTCCTAAGCACCTTGTATTGTATAA 57.686 34.615 0.00 0.00 0.00 0.98
205 206 8.421784 TCTCCTAAGCACCTTGTATTGTATAAG 58.578 37.037 0.00 0.00 0.00 1.73
215 216 8.166422 CCTTGTATTGTATAAGGCCTAAAAGG 57.834 38.462 5.16 3.77 39.65 3.11
216 217 7.778382 CCTTGTATTGTATAAGGCCTAAAAGGT 59.222 37.037 5.16 0.00 39.65 3.50
217 218 8.514330 TTGTATTGTATAAGGCCTAAAAGGTG 57.486 34.615 5.16 0.00 37.80 4.00
218 219 6.544564 TGTATTGTATAAGGCCTAAAAGGTGC 59.455 38.462 5.16 0.00 37.80 5.01
219 220 3.893521 TGTATAAGGCCTAAAAGGTGCC 58.106 45.455 5.16 0.00 45.70 5.01
222 223 3.274067 GGCCTAAAAGGTGCCGTG 58.726 61.111 0.00 0.00 37.80 4.94
223 224 2.566529 GCCTAAAAGGTGCCGTGC 59.433 61.111 0.00 0.00 37.80 5.34
224 225 2.989881 GCCTAAAAGGTGCCGTGCC 61.990 63.158 0.00 0.00 37.80 5.01
225 226 1.303317 CCTAAAAGGTGCCGTGCCT 60.303 57.895 0.00 0.00 38.11 4.75
226 227 1.586154 CCTAAAAGGTGCCGTGCCTG 61.586 60.000 0.00 0.00 36.30 4.85
227 228 0.889186 CTAAAAGGTGCCGTGCCTGT 60.889 55.000 0.00 0.00 36.30 4.00
228 229 0.397187 TAAAAGGTGCCGTGCCTGTA 59.603 50.000 0.00 0.00 36.30 2.74
229 230 0.889186 AAAAGGTGCCGTGCCTGTAG 60.889 55.000 0.00 0.00 36.30 2.74
230 231 2.748058 AAAGGTGCCGTGCCTGTAGG 62.748 60.000 0.00 0.00 36.30 3.18
231 232 4.778143 GGTGCCGTGCCTGTAGGG 62.778 72.222 0.00 0.00 35.18 3.53
232 233 4.778143 GTGCCGTGCCTGTAGGGG 62.778 72.222 0.00 0.00 35.18 4.79
234 235 4.778143 GCCGTGCCTGTAGGGGTG 62.778 72.222 0.00 0.00 35.18 4.61
235 236 4.096003 CCGTGCCTGTAGGGGTGG 62.096 72.222 0.00 0.00 35.18 4.61
236 237 4.096003 CGTGCCTGTAGGGGTGGG 62.096 72.222 0.00 0.00 35.18 4.61
237 238 3.728373 GTGCCTGTAGGGGTGGGG 61.728 72.222 0.00 0.00 35.18 4.96
240 241 3.015145 CCTGTAGGGGTGGGGGTG 61.015 72.222 0.00 0.00 0.00 4.61
241 242 3.015145 CTGTAGGGGTGGGGGTGG 61.015 72.222 0.00 0.00 0.00 4.61
242 243 3.543626 TGTAGGGGTGGGGGTGGA 61.544 66.667 0.00 0.00 0.00 4.02
268 269 3.241868 CGTATGTACGCTGGTAAAGTTGC 60.242 47.826 0.00 0.00 43.14 4.17
272 273 2.566529 GCTGGTAAAGTTGCGCCC 59.433 61.111 4.18 0.00 0.00 6.13
292 293 0.458669 TGATCTAGGCCGTCCGTTTC 59.541 55.000 0.00 0.00 37.47 2.78
297 298 0.751277 TAGGCCGTCCGTTTCCGATA 60.751 55.000 0.00 0.00 37.47 2.92
301 302 1.930567 CCGTCCGTTTCCGATACAAT 58.069 50.000 0.00 0.00 35.63 2.71
303 304 1.591158 CGTCCGTTTCCGATACAATGG 59.409 52.381 0.00 0.00 35.63 3.16
306 310 4.183101 GTCCGTTTCCGATACAATGGTAA 58.817 43.478 0.00 0.00 35.63 2.85
309 313 4.495184 CCGTTTCCGATACAATGGTAAAGC 60.495 45.833 0.00 0.00 35.63 3.51
320 324 6.095432 ACAATGGTAAAGCTATGTTTTGCA 57.905 33.333 0.00 0.00 0.00 4.08
321 325 6.520272 ACAATGGTAAAGCTATGTTTTGCAA 58.480 32.000 0.00 0.00 0.00 4.08
322 326 6.423604 ACAATGGTAAAGCTATGTTTTGCAAC 59.576 34.615 0.00 0.00 0.00 4.17
325 329 5.751028 TGGTAAAGCTATGTTTTGCAACAAC 59.249 36.000 0.00 8.01 46.17 3.32
327 331 3.011949 AGCTATGTTTTGCAACAACGG 57.988 42.857 0.00 3.77 46.17 4.44
333 337 4.391140 TGTTTTGCAACAACGGAAAAAC 57.609 36.364 0.00 0.00 40.10 2.43
340 344 2.926838 CAACAACGGAAAAACAACTGGG 59.073 45.455 0.00 0.00 0.00 4.45
343 347 3.449377 ACAACGGAAAAACAACTGGGAAT 59.551 39.130 0.00 0.00 0.00 3.01
344 348 4.645588 ACAACGGAAAAACAACTGGGAATA 59.354 37.500 0.00 0.00 0.00 1.75
346 350 6.183360 ACAACGGAAAAACAACTGGGAATATT 60.183 34.615 0.00 0.00 0.00 1.28
357 361 5.640158 ACTGGGAATATTATGGGTCGAAA 57.360 39.130 0.00 0.00 0.00 3.46
358 362 5.374071 ACTGGGAATATTATGGGTCGAAAC 58.626 41.667 0.00 0.00 0.00 2.78
365 369 2.112297 TGGGTCGAAACTGCCCAC 59.888 61.111 6.64 0.00 46.59 4.61
367 371 2.029964 GGTCGAAACTGCCCACGA 59.970 61.111 0.00 0.00 0.00 4.35
402 406 1.753368 GACTAGGCTAGCAGGGGCAG 61.753 65.000 21.26 6.04 44.61 4.85
435 451 2.888111 GGAGAACCGACGTACCCC 59.112 66.667 0.00 0.00 0.00 4.95
624 663 2.797278 CCAGACCGGAAGCGGCTAT 61.797 63.158 9.46 0.00 36.56 2.97
882 923 1.547760 GGGGTGGGGGTTTTGGTTA 59.452 57.895 0.00 0.00 0.00 2.85
883 924 0.117541 GGGGTGGGGGTTTTGGTTAT 59.882 55.000 0.00 0.00 0.00 1.89
912 953 0.995803 TGGGGGTTGATTGATTCGGA 59.004 50.000 0.00 0.00 0.00 4.55
917 958 0.028110 GTTGATTGATTCGGAGGCGC 59.972 55.000 0.00 0.00 0.00 6.53
953 1000 4.158764 CGTCTAGGGTTTCTGAACTCTGAT 59.841 45.833 2.06 0.00 46.04 2.90
972 1019 6.647229 TCTGATGCTTACTGTTGATTGATCT 58.353 36.000 0.00 0.00 0.00 2.75
1138 1195 0.034059 CCTGCAGTTCGACAAGGTCT 59.966 55.000 13.81 0.00 0.00 3.85
1139 1196 1.423395 CTGCAGTTCGACAAGGTCTC 58.577 55.000 5.25 0.00 0.00 3.36
1140 1197 0.750249 TGCAGTTCGACAAGGTCTCA 59.250 50.000 0.00 0.00 0.00 3.27
1141 1198 1.138069 TGCAGTTCGACAAGGTCTCAA 59.862 47.619 0.00 0.00 0.00 3.02
1155 1212 3.809905 GGTCTCAACCAAGTTTCTCTGT 58.190 45.455 0.00 0.00 45.68 3.41
1156 1213 3.561725 GGTCTCAACCAAGTTTCTCTGTG 59.438 47.826 0.00 0.00 45.68 3.66
1158 1215 4.876107 GTCTCAACCAAGTTTCTCTGTGAA 59.124 41.667 0.00 0.00 0.00 3.18
1159 1216 5.529060 GTCTCAACCAAGTTTCTCTGTGAAT 59.471 40.000 0.00 0.00 34.24 2.57
1160 1217 5.528690 TCTCAACCAAGTTTCTCTGTGAATG 59.471 40.000 0.00 0.00 34.24 2.67
1175 1244 7.662669 TCTCTGTGAATGAAACTCATCAATCAA 59.337 33.333 0.00 0.00 35.76 2.57
1176 1245 8.344446 TCTGTGAATGAAACTCATCAATCAAT 57.656 30.769 0.00 0.00 35.76 2.57
1177 1246 8.456471 TCTGTGAATGAAACTCATCAATCAATC 58.544 33.333 0.00 0.00 35.76 2.67
1178 1247 8.113173 TGTGAATGAAACTCATCAATCAATCA 57.887 30.769 0.00 0.00 35.76 2.57
1179 1248 8.578151 TGTGAATGAAACTCATCAATCAATCAA 58.422 29.630 0.00 0.00 35.76 2.57
1190 1259 9.788960 CTCATCAATCAATCAATATATTGCTGG 57.211 33.333 18.89 8.72 36.89 4.85
1191 1260 8.745590 TCATCAATCAATCAATATATTGCTGGG 58.254 33.333 18.89 9.42 36.89 4.45
1192 1261 8.528643 CATCAATCAATCAATATATTGCTGGGT 58.471 33.333 18.89 2.24 36.89 4.51
1193 1262 7.888424 TCAATCAATCAATATATTGCTGGGTG 58.112 34.615 18.89 16.76 36.89 4.61
1194 1263 5.710513 TCAATCAATATATTGCTGGGTGC 57.289 39.130 18.89 0.00 43.25 5.01
1324 1432 4.815308 ACTCTCTTGTGCTATGCATTCATC 59.185 41.667 3.54 0.20 41.91 2.92
1325 1433 4.132336 TCTCTTGTGCTATGCATTCATCC 58.868 43.478 3.54 0.00 41.91 3.51
1326 1434 3.881089 CTCTTGTGCTATGCATTCATCCA 59.119 43.478 3.54 0.00 41.91 3.41
1327 1435 4.466827 TCTTGTGCTATGCATTCATCCAT 58.533 39.130 3.54 0.00 41.91 3.41
1344 1452 2.092267 TCCATCCATCCCTGTGATTGTG 60.092 50.000 0.00 0.00 0.00 3.33
1349 1622 2.686405 CCATCCCTGTGATTGTGATGTG 59.314 50.000 0.00 0.00 32.78 3.21
1478 1761 4.155310 TGATGCTATGTATGACGTACGG 57.845 45.455 21.06 1.43 36.01 4.02
1489 1772 1.219522 GACGTACGGCTTGTGTGCTT 61.220 55.000 21.06 0.00 0.00 3.91
1490 1773 0.032403 ACGTACGGCTTGTGTGCTTA 59.968 50.000 21.06 0.00 0.00 3.09
1491 1774 1.141645 CGTACGGCTTGTGTGCTTAA 58.858 50.000 7.57 0.00 0.00 1.85
1641 1962 2.286872 CACATGTTCCAGGAGATCTGC 58.713 52.381 6.03 6.03 42.05 4.26
1647 1968 0.829333 TCCAGGAGATCTGCTTGCTC 59.171 55.000 14.94 0.00 42.05 4.26
1687 2029 6.478512 TGGAACTGTATATGTGCTCATGTA 57.521 37.500 11.46 6.34 35.70 2.29
1688 2030 7.066307 TGGAACTGTATATGTGCTCATGTAT 57.934 36.000 11.46 0.80 35.70 2.29
1689 2031 7.154656 TGGAACTGTATATGTGCTCATGTATC 58.845 38.462 11.46 3.97 35.70 2.24
1690 2032 7.154656 GGAACTGTATATGTGCTCATGTATCA 58.845 38.462 11.46 8.80 35.70 2.15
1691 2033 7.657354 GGAACTGTATATGTGCTCATGTATCAA 59.343 37.037 11.46 0.00 35.70 2.57
1692 2034 7.953158 ACTGTATATGTGCTCATGTATCAAC 57.047 36.000 11.46 1.08 35.70 3.18
1693 2035 7.500141 ACTGTATATGTGCTCATGTATCAACA 58.500 34.615 11.46 5.34 40.69 3.33
1708 2050 7.951530 TGTATCAACATGAGCACATATACAG 57.048 36.000 11.24 0.00 33.28 2.74
1709 2051 7.500141 TGTATCAACATGAGCACATATACAGT 58.500 34.615 11.24 0.00 33.28 3.55
1710 2052 7.653311 TGTATCAACATGAGCACATATACAGTC 59.347 37.037 11.24 0.00 33.28 3.51
1711 2053 5.976458 TCAACATGAGCACATATACAGTCA 58.024 37.500 0.00 0.00 35.09 3.41
1712 2054 6.044682 TCAACATGAGCACATATACAGTCAG 58.955 40.000 0.00 0.00 35.09 3.51
1713 2055 5.604758 ACATGAGCACATATACAGTCAGT 57.395 39.130 0.00 0.00 35.09 3.41
1714 2056 5.982356 ACATGAGCACATATACAGTCAGTT 58.018 37.500 0.00 0.00 35.09 3.16
1715 2057 7.112452 ACATGAGCACATATACAGTCAGTTA 57.888 36.000 0.00 0.00 35.09 2.24
1748 2090 5.654650 CAGACTATCAGAGGGTAAACTGTCT 59.345 44.000 0.00 0.00 35.84 3.41
1758 2100 2.069273 GTAAACTGTCTGCGACATGCT 58.931 47.619 10.93 3.12 46.63 3.79
1761 2103 0.891373 ACTGTCTGCGACATGCTAGT 59.109 50.000 10.93 4.04 46.63 2.57
1766 2108 0.717784 CTGCGACATGCTAGTGTGTG 59.282 55.000 6.84 2.37 46.63 3.82
1773 2115 4.032900 CGACATGCTAGTGTGTGGATTAAC 59.967 45.833 6.84 0.00 31.16 2.01
2158 2575 7.854422 CACAATATTGCAATCTGTAGTCATGTC 59.146 37.037 16.86 0.00 0.00 3.06
2429 2846 1.152756 GGCGCCATCCCCAAACTAT 60.153 57.895 24.80 0.00 0.00 2.12
2469 2886 2.159462 GCAACTTCCATTGTGCTAGAGC 60.159 50.000 0.00 0.00 42.50 4.09
2530 2947 3.181496 GGAATGATGGTTTCGCTCTTTCC 60.181 47.826 0.00 0.00 36.60 3.13
2563 2980 7.200434 ACATAACTTATGGATGAGTGGAACT 57.800 36.000 12.48 0.00 45.77 3.01
2578 2995 5.968387 GTGGAACTACGAATAGAATGTGG 57.032 43.478 0.00 0.00 32.23 4.17
2676 3093 7.883391 AAGCACTACATAGTACATACAGACT 57.117 36.000 0.00 0.00 34.13 3.24
2724 3141 0.324943 TTACTCCAAGGACAGCTGCC 59.675 55.000 15.27 16.08 0.00 4.85
3123 3669 1.630878 TGGTGGGTTTGCTTTTGGTTT 59.369 42.857 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.526917 CCTTAGGCAATGGCGGAGG 60.527 63.158 14.61 14.61 42.47 4.30
1 2 4.147701 CCTTAGGCAATGGCGGAG 57.852 61.111 0.00 3.41 42.47 4.63
11 12 1.202143 GCATTGTACAACGCCTTAGGC 60.202 52.381 15.54 14.22 46.75 3.93
12 13 2.356135 AGCATTGTACAACGCCTTAGG 58.644 47.619 21.99 0.00 28.37 2.69
13 14 4.430007 TCTAGCATTGTACAACGCCTTAG 58.570 43.478 21.99 17.27 28.37 2.18
14 15 4.459390 TCTAGCATTGTACAACGCCTTA 57.541 40.909 21.99 8.95 28.37 2.69
15 16 3.328382 TCTAGCATTGTACAACGCCTT 57.672 42.857 21.99 8.24 28.37 4.35
16 17 3.198068 CATCTAGCATTGTACAACGCCT 58.802 45.455 21.99 14.54 28.37 5.52
17 18 2.286418 GCATCTAGCATTGTACAACGCC 60.286 50.000 21.99 8.24 44.79 5.68
18 19 2.974165 GCATCTAGCATTGTACAACGC 58.026 47.619 18.48 18.48 44.79 4.84
30 31 2.158900 TGCACCTTCCTAAGCATCTAGC 60.159 50.000 0.00 0.00 46.19 3.42
31 32 3.827008 TGCACCTTCCTAAGCATCTAG 57.173 47.619 0.00 0.00 31.05 2.43
32 33 5.887214 TTATGCACCTTCCTAAGCATCTA 57.113 39.130 1.65 0.00 43.67 1.98
33 34 4.778213 TTATGCACCTTCCTAAGCATCT 57.222 40.909 1.65 0.00 43.67 2.90
34 35 5.835113 TTTTATGCACCTTCCTAAGCATC 57.165 39.130 1.65 0.00 43.67 3.91
54 55 7.201661 GCTTCAGAAAAACCCGGTTTAATTTTT 60.202 33.333 16.03 6.31 34.43 1.94
55 56 6.259167 GCTTCAGAAAAACCCGGTTTAATTTT 59.741 34.615 16.03 6.68 34.43 1.82
56 57 5.756347 GCTTCAGAAAAACCCGGTTTAATTT 59.244 36.000 16.03 7.04 34.43 1.82
57 58 5.163395 TGCTTCAGAAAAACCCGGTTTAATT 60.163 36.000 16.03 7.76 34.43 1.40
58 59 4.342665 TGCTTCAGAAAAACCCGGTTTAAT 59.657 37.500 16.03 8.32 34.43 1.40
59 60 3.700038 TGCTTCAGAAAAACCCGGTTTAA 59.300 39.130 16.03 5.60 34.43 1.52
60 61 3.067040 GTGCTTCAGAAAAACCCGGTTTA 59.933 43.478 16.03 0.00 34.43 2.01
61 62 2.104170 TGCTTCAGAAAAACCCGGTTT 58.896 42.857 9.92 9.92 37.34 3.27
62 63 1.407618 GTGCTTCAGAAAAACCCGGTT 59.592 47.619 0.00 0.00 0.00 4.44
63 64 1.029681 GTGCTTCAGAAAAACCCGGT 58.970 50.000 0.00 0.00 0.00 5.28
64 65 0.313987 GGTGCTTCAGAAAAACCCGG 59.686 55.000 0.00 0.00 0.00 5.73
65 66 1.001378 CTGGTGCTTCAGAAAAACCCG 60.001 52.381 10.23 2.44 36.93 5.28
66 67 2.031870 ACTGGTGCTTCAGAAAAACCC 58.968 47.619 12.54 0.00 38.11 4.11
67 68 3.084070 CACTGGTGCTTCAGAAAAACC 57.916 47.619 12.54 6.89 38.11 3.27
80 81 4.832248 TCCTGTAGAAATAAGCACTGGTG 58.168 43.478 0.00 0.00 33.23 4.17
81 82 4.777896 TCTCCTGTAGAAATAAGCACTGGT 59.222 41.667 0.00 0.00 33.23 4.00
82 83 5.127845 TCTCTCCTGTAGAAATAAGCACTGG 59.872 44.000 0.00 0.00 32.46 4.00
83 84 6.039616 GTCTCTCCTGTAGAAATAAGCACTG 58.960 44.000 0.00 0.00 32.46 3.66
84 85 5.163602 CGTCTCTCCTGTAGAAATAAGCACT 60.164 44.000 0.00 0.00 32.46 4.40
85 86 5.038033 CGTCTCTCCTGTAGAAATAAGCAC 58.962 45.833 0.00 0.00 32.46 4.40
86 87 4.440250 GCGTCTCTCCTGTAGAAATAAGCA 60.440 45.833 0.00 0.00 32.46 3.91
87 88 4.045783 GCGTCTCTCCTGTAGAAATAAGC 58.954 47.826 0.00 0.00 32.46 3.09
88 89 4.339814 AGGCGTCTCTCCTGTAGAAATAAG 59.660 45.833 0.00 0.00 32.46 1.73
89 90 4.279145 AGGCGTCTCTCCTGTAGAAATAA 58.721 43.478 0.00 0.00 32.46 1.40
90 91 3.899726 AGGCGTCTCTCCTGTAGAAATA 58.100 45.455 0.00 0.00 32.46 1.40
91 92 2.741145 AGGCGTCTCTCCTGTAGAAAT 58.259 47.619 0.00 0.00 32.46 2.17
92 93 2.217510 AGGCGTCTCTCCTGTAGAAA 57.782 50.000 0.00 0.00 32.46 2.52
93 94 3.361281 TTAGGCGTCTCTCCTGTAGAA 57.639 47.619 0.00 0.00 35.21 2.10
94 95 3.579534 ATTAGGCGTCTCTCCTGTAGA 57.420 47.619 0.00 0.00 35.21 2.59
95 96 5.764131 CTTAATTAGGCGTCTCTCCTGTAG 58.236 45.833 0.00 0.00 35.21 2.74
96 97 4.037684 GCTTAATTAGGCGTCTCTCCTGTA 59.962 45.833 3.59 0.00 35.21 2.74
97 98 3.181474 GCTTAATTAGGCGTCTCTCCTGT 60.181 47.826 3.59 0.00 35.21 4.00
98 99 3.385577 GCTTAATTAGGCGTCTCTCCTG 58.614 50.000 3.59 0.00 35.21 3.86
99 100 2.034812 CGCTTAATTAGGCGTCTCTCCT 59.965 50.000 28.00 0.00 45.15 3.69
100 101 2.395654 CGCTTAATTAGGCGTCTCTCC 58.604 52.381 28.00 0.00 45.15 3.71
108 109 2.866762 CAGGACAGACGCTTAATTAGGC 59.133 50.000 9.43 9.43 0.00 3.93
109 110 4.124851 ACAGGACAGACGCTTAATTAGG 57.875 45.455 0.00 0.00 0.00 2.69
110 111 8.867112 TTTATACAGGACAGACGCTTAATTAG 57.133 34.615 0.00 0.00 0.00 1.73
112 113 9.826574 TTATTTATACAGGACAGACGCTTAATT 57.173 29.630 0.00 0.00 0.00 1.40
113 114 9.477484 CTTATTTATACAGGACAGACGCTTAAT 57.523 33.333 0.00 0.00 0.00 1.40
114 115 7.437267 GCTTATTTATACAGGACAGACGCTTAA 59.563 37.037 0.00 0.00 0.00 1.85
115 116 6.921857 GCTTATTTATACAGGACAGACGCTTA 59.078 38.462 0.00 0.00 0.00 3.09
116 117 5.753921 GCTTATTTATACAGGACAGACGCTT 59.246 40.000 0.00 0.00 0.00 4.68
117 118 5.163447 TGCTTATTTATACAGGACAGACGCT 60.163 40.000 0.00 0.00 0.00 5.07
118 119 5.047847 TGCTTATTTATACAGGACAGACGC 58.952 41.667 0.00 0.00 0.00 5.19
119 120 6.088217 CGATGCTTATTTATACAGGACAGACG 59.912 42.308 0.00 0.00 0.00 4.18
120 121 6.366332 CCGATGCTTATTTATACAGGACAGAC 59.634 42.308 0.00 0.00 0.00 3.51
121 122 6.041637 ACCGATGCTTATTTATACAGGACAGA 59.958 38.462 0.00 0.00 0.00 3.41
122 123 6.146184 CACCGATGCTTATTTATACAGGACAG 59.854 42.308 0.00 0.00 0.00 3.51
123 124 5.989168 CACCGATGCTTATTTATACAGGACA 59.011 40.000 0.00 0.00 0.00 4.02
124 125 6.467723 CACCGATGCTTATTTATACAGGAC 57.532 41.667 0.00 0.00 0.00 3.85
140 141 1.813513 ACTTTCCTTCAGCACCGATG 58.186 50.000 0.00 0.00 0.00 3.84
141 142 3.914426 ATACTTTCCTTCAGCACCGAT 57.086 42.857 0.00 0.00 0.00 4.18
142 143 3.695830 AATACTTTCCTTCAGCACCGA 57.304 42.857 0.00 0.00 0.00 4.69
143 144 4.766404 AAAATACTTTCCTTCAGCACCG 57.234 40.909 0.00 0.00 0.00 4.94
144 145 8.523658 AGAAATAAAATACTTTCCTTCAGCACC 58.476 33.333 0.00 0.00 32.90 5.01
145 146 9.914131 AAGAAATAAAATACTTTCCTTCAGCAC 57.086 29.630 0.00 0.00 32.90 4.40
162 163 9.614792 GCTTAGGAGAGGTATTGAAGAAATAAA 57.385 33.333 0.00 0.00 32.47 1.40
163 164 8.768397 TGCTTAGGAGAGGTATTGAAGAAATAA 58.232 33.333 0.00 0.00 32.47 1.40
164 165 8.204836 GTGCTTAGGAGAGGTATTGAAGAAATA 58.795 37.037 0.00 0.00 0.00 1.40
165 166 7.051000 GTGCTTAGGAGAGGTATTGAAGAAAT 58.949 38.462 0.00 0.00 0.00 2.17
166 167 6.407202 GTGCTTAGGAGAGGTATTGAAGAAA 58.593 40.000 0.00 0.00 0.00 2.52
167 168 5.104900 GGTGCTTAGGAGAGGTATTGAAGAA 60.105 44.000 0.00 0.00 0.00 2.52
168 169 4.406003 GGTGCTTAGGAGAGGTATTGAAGA 59.594 45.833 0.00 0.00 0.00 2.87
169 170 4.407296 AGGTGCTTAGGAGAGGTATTGAAG 59.593 45.833 0.00 0.00 0.00 3.02
170 171 4.362677 AGGTGCTTAGGAGAGGTATTGAA 58.637 43.478 0.00 0.00 0.00 2.69
171 172 3.995636 AGGTGCTTAGGAGAGGTATTGA 58.004 45.455 0.00 0.00 0.00 2.57
172 173 4.080863 ACAAGGTGCTTAGGAGAGGTATTG 60.081 45.833 0.00 0.00 0.00 1.90
173 174 4.104831 ACAAGGTGCTTAGGAGAGGTATT 58.895 43.478 0.00 0.00 0.00 1.89
174 175 3.725634 ACAAGGTGCTTAGGAGAGGTAT 58.274 45.455 0.00 0.00 0.00 2.73
175 176 3.185880 ACAAGGTGCTTAGGAGAGGTA 57.814 47.619 0.00 0.00 0.00 3.08
176 177 2.031495 ACAAGGTGCTTAGGAGAGGT 57.969 50.000 0.00 0.00 0.00 3.85
177 178 4.080863 ACAATACAAGGTGCTTAGGAGAGG 60.081 45.833 0.00 0.00 0.00 3.69
178 179 5.091261 ACAATACAAGGTGCTTAGGAGAG 57.909 43.478 0.00 0.00 0.00 3.20
179 180 6.808321 ATACAATACAAGGTGCTTAGGAGA 57.192 37.500 0.00 0.00 0.00 3.71
180 181 7.657761 CCTTATACAATACAAGGTGCTTAGGAG 59.342 40.741 0.00 0.00 35.18 3.69
181 182 7.506114 CCTTATACAATACAAGGTGCTTAGGA 58.494 38.462 0.00 0.00 35.18 2.94
182 183 6.204882 GCCTTATACAATACAAGGTGCTTAGG 59.795 42.308 0.00 0.00 40.84 2.69
183 184 6.204882 GGCCTTATACAATACAAGGTGCTTAG 59.795 42.308 0.00 0.00 40.84 2.18
184 185 6.059484 GGCCTTATACAATACAAGGTGCTTA 58.941 40.000 0.00 0.00 40.84 3.09
185 186 4.887655 GGCCTTATACAATACAAGGTGCTT 59.112 41.667 0.00 0.00 40.84 3.91
186 187 4.166144 AGGCCTTATACAATACAAGGTGCT 59.834 41.667 0.00 0.00 40.84 4.40
187 188 4.461198 AGGCCTTATACAATACAAGGTGC 58.539 43.478 0.00 0.00 40.84 5.01
188 189 8.514330 TTTTAGGCCTTATACAATACAAGGTG 57.486 34.615 12.58 0.00 40.84 4.00
189 190 7.778382 CCTTTTAGGCCTTATACAATACAAGGT 59.222 37.037 12.58 0.00 40.84 3.50
190 191 7.778382 ACCTTTTAGGCCTTATACAATACAAGG 59.222 37.037 12.58 11.74 39.63 3.61
191 192 8.621286 CACCTTTTAGGCCTTATACAATACAAG 58.379 37.037 12.58 0.00 39.63 3.16
192 193 7.067737 GCACCTTTTAGGCCTTATACAATACAA 59.932 37.037 12.58 0.00 39.63 2.41
193 194 6.544564 GCACCTTTTAGGCCTTATACAATACA 59.455 38.462 12.58 0.00 39.63 2.29
194 195 6.016527 GGCACCTTTTAGGCCTTATACAATAC 60.017 42.308 12.58 0.00 44.32 1.89
195 196 6.066032 GGCACCTTTTAGGCCTTATACAATA 58.934 40.000 12.58 0.00 44.32 1.90
196 197 4.893524 GGCACCTTTTAGGCCTTATACAAT 59.106 41.667 12.58 0.00 44.32 2.71
197 198 4.274978 GGCACCTTTTAGGCCTTATACAA 58.725 43.478 12.58 0.00 44.32 2.41
198 199 3.683281 CGGCACCTTTTAGGCCTTATACA 60.683 47.826 12.58 0.00 45.53 2.29
199 200 2.876550 CGGCACCTTTTAGGCCTTATAC 59.123 50.000 12.58 0.00 45.53 1.47
200 201 2.506644 ACGGCACCTTTTAGGCCTTATA 59.493 45.455 12.58 0.00 45.53 0.98
201 202 1.283905 ACGGCACCTTTTAGGCCTTAT 59.716 47.619 12.58 0.00 45.53 1.73
202 203 0.694196 ACGGCACCTTTTAGGCCTTA 59.306 50.000 12.58 0.00 45.53 2.69
203 204 0.893727 CACGGCACCTTTTAGGCCTT 60.894 55.000 12.58 0.00 45.53 4.35
204 205 1.303317 CACGGCACCTTTTAGGCCT 60.303 57.895 11.78 11.78 45.53 5.19
205 206 2.989881 GCACGGCACCTTTTAGGCC 61.990 63.158 0.00 0.00 39.63 5.19
206 207 2.566529 GCACGGCACCTTTTAGGC 59.433 61.111 0.00 0.00 39.63 3.93
207 208 1.303317 AGGCACGGCACCTTTTAGG 60.303 57.895 0.00 0.00 42.49 2.69
208 209 0.889186 ACAGGCACGGCACCTTTTAG 60.889 55.000 0.00 0.00 34.42 1.85
209 210 0.397187 TACAGGCACGGCACCTTTTA 59.603 50.000 0.00 0.00 34.42 1.52
210 211 0.889186 CTACAGGCACGGCACCTTTT 60.889 55.000 0.00 0.00 34.42 2.27
211 212 1.302511 CTACAGGCACGGCACCTTT 60.303 57.895 0.00 0.00 34.42 3.11
212 213 2.347490 CTACAGGCACGGCACCTT 59.653 61.111 0.00 0.00 34.42 3.50
213 214 3.706373 CCTACAGGCACGGCACCT 61.706 66.667 0.00 0.00 38.35 4.00
214 215 4.778143 CCCTACAGGCACGGCACC 62.778 72.222 0.00 0.00 0.00 5.01
215 216 4.778143 CCCCTACAGGCACGGCAC 62.778 72.222 0.00 0.00 0.00 5.01
217 218 4.778143 CACCCCTACAGGCACGGC 62.778 72.222 0.00 0.00 0.00 5.68
218 219 4.096003 CCACCCCTACAGGCACGG 62.096 72.222 0.00 0.00 0.00 4.94
219 220 4.096003 CCCACCCCTACAGGCACG 62.096 72.222 0.00 0.00 0.00 5.34
220 221 3.728373 CCCCACCCCTACAGGCAC 61.728 72.222 0.00 0.00 0.00 5.01
223 224 3.015145 CACCCCCACCCCTACAGG 61.015 72.222 0.00 0.00 0.00 4.00
224 225 3.015145 CCACCCCCACCCCTACAG 61.015 72.222 0.00 0.00 0.00 2.74
225 226 2.440196 ATTCCACCCCCACCCCTACA 62.440 60.000 0.00 0.00 0.00 2.74
226 227 1.621514 ATTCCACCCCCACCCCTAC 60.622 63.158 0.00 0.00 0.00 3.18
227 228 1.308392 GATTCCACCCCCACCCCTA 60.308 63.158 0.00 0.00 0.00 3.53
228 229 2.617215 GATTCCACCCCCACCCCT 60.617 66.667 0.00 0.00 0.00 4.79
229 230 3.751018 GGATTCCACCCCCACCCC 61.751 72.222 0.00 0.00 0.00 4.95
230 231 4.123545 CGGATTCCACCCCCACCC 62.124 72.222 3.09 0.00 0.00 4.61
231 232 1.350310 ATACGGATTCCACCCCCACC 61.350 60.000 3.09 0.00 0.00 4.61
232 233 0.179029 CATACGGATTCCACCCCCAC 60.179 60.000 3.09 0.00 0.00 4.61
233 234 0.622154 ACATACGGATTCCACCCCCA 60.622 55.000 3.09 0.00 0.00 4.96
234 235 1.071228 GTACATACGGATTCCACCCCC 59.929 57.143 3.09 0.00 0.00 5.40
235 236 1.269936 CGTACATACGGATTCCACCCC 60.270 57.143 3.09 0.00 45.30 4.95
236 237 2.144482 CGTACATACGGATTCCACCC 57.856 55.000 3.09 0.00 45.30 4.61
257 258 0.037590 ATCAGGGCGCAACTTTACCA 59.962 50.000 10.83 0.00 0.00 3.25
272 273 0.460311 AAACGGACGGCCTAGATCAG 59.540 55.000 5.33 0.00 0.00 2.90
292 293 6.861065 AACATAGCTTTACCATTGTATCGG 57.139 37.500 0.00 0.00 0.00 4.18
297 298 6.095432 TGCAAAACATAGCTTTACCATTGT 57.905 33.333 0.00 0.00 0.00 2.71
301 302 5.521906 TGTTGCAAAACATAGCTTTACCA 57.478 34.783 0.00 0.00 0.00 3.25
303 304 5.108027 CCGTTGTTGCAAAACATAGCTTTAC 60.108 40.000 18.24 2.69 32.01 2.01
306 310 3.067461 TCCGTTGTTGCAAAACATAGCTT 59.933 39.130 18.24 0.00 32.01 3.74
309 313 5.957910 TTTTCCGTTGTTGCAAAACATAG 57.042 34.783 18.24 10.23 32.01 2.23
320 324 2.826725 TCCCAGTTGTTTTTCCGTTGTT 59.173 40.909 0.00 0.00 0.00 2.83
321 325 2.448453 TCCCAGTTGTTTTTCCGTTGT 58.552 42.857 0.00 0.00 0.00 3.32
322 326 3.512033 TTCCCAGTTGTTTTTCCGTTG 57.488 42.857 0.00 0.00 0.00 4.10
323 327 6.413783 AATATTCCCAGTTGTTTTTCCGTT 57.586 33.333 0.00 0.00 0.00 4.44
325 329 6.978080 CCATAATATTCCCAGTTGTTTTTCCG 59.022 38.462 0.00 0.00 0.00 4.30
327 331 7.847096 ACCCATAATATTCCCAGTTGTTTTTC 58.153 34.615 0.00 0.00 0.00 2.29
333 337 4.968259 TCGACCCATAATATTCCCAGTTG 58.032 43.478 0.00 0.00 0.00 3.16
340 344 4.215613 GGGCAGTTTCGACCCATAATATTC 59.784 45.833 3.22 0.00 43.64 1.75
343 347 3.202829 GGGCAGTTTCGACCCATAATA 57.797 47.619 3.22 0.00 43.64 0.98
344 348 2.052782 GGGCAGTTTCGACCCATAAT 57.947 50.000 3.22 0.00 43.64 1.28
402 406 4.135306 GTTCTCCGGATTAATTCCCCTTC 58.865 47.826 3.57 0.00 42.06 3.46
447 463 3.640498 GGGAAGGTATATATAGCCCGGAC 59.360 52.174 16.49 0.00 0.00 4.79
542 576 2.196229 CGAGGTCCGGGAGAGGAT 59.804 66.667 0.00 0.00 43.04 3.24
613 652 0.750850 TGGTACTGATAGCCGCTTCC 59.249 55.000 0.00 0.00 0.00 3.46
853 892 3.361977 CCACCCCCGAAAGCAACG 61.362 66.667 0.00 0.00 0.00 4.10
866 905 1.179152 CGATAACCAAAACCCCCACC 58.821 55.000 0.00 0.00 0.00 4.61
882 923 4.843331 ACCCCCATGGCTCCCGAT 62.843 66.667 6.09 0.00 37.83 4.18
953 1000 6.108687 CCTGTAGATCAATCAACAGTAAGCA 58.891 40.000 0.00 0.00 0.00 3.91
972 1019 1.608336 CGTGACCCCTGTCCCTGTA 60.608 63.158 0.00 0.00 41.01 2.74
989 1046 2.520982 TCGCCATCCCTCCTACCG 60.521 66.667 0.00 0.00 0.00 4.02
992 1049 2.520982 CCGTCGCCATCCCTCCTA 60.521 66.667 0.00 0.00 0.00 2.94
1053 1110 3.384014 CTCGTCCAGCGTCTCCGTC 62.384 68.421 0.00 0.00 42.13 4.79
1056 1113 1.064946 CATCTCGTCCAGCGTCTCC 59.935 63.158 0.00 0.00 42.13 3.71
1138 1195 5.436175 TCATTCACAGAGAAACTTGGTTGA 58.564 37.500 0.00 0.00 40.22 3.18
1139 1196 5.756195 TCATTCACAGAGAAACTTGGTTG 57.244 39.130 0.00 0.00 40.22 3.77
1140 1197 6.564328 GTTTCATTCACAGAGAAACTTGGTT 58.436 36.000 9.33 0.00 44.60 3.67
1141 1198 6.136541 GTTTCATTCACAGAGAAACTTGGT 57.863 37.500 9.33 0.00 44.60 3.67
1146 1203 7.194607 TGATGAGTTTCATTCACAGAGAAAC 57.805 36.000 8.71 8.71 46.98 2.78
1148 1205 7.662669 TGATTGATGAGTTTCATTCACAGAGAA 59.337 33.333 0.00 0.00 37.20 2.87
1149 1206 7.163441 TGATTGATGAGTTTCATTCACAGAGA 58.837 34.615 0.00 0.00 37.20 3.10
1153 1210 8.113173 TGATTGATTGATGAGTTTCATTCACA 57.887 30.769 0.00 0.00 37.20 3.58
1154 1211 8.975410 TTGATTGATTGATGAGTTTCATTCAC 57.025 30.769 0.00 0.00 37.20 3.18
1166 1235 8.528643 ACCCAGCAATATATTGATTGATTGATG 58.471 33.333 26.22 10.13 42.49 3.07
1186 1255 0.387239 GATCAAAACGTGCACCCAGC 60.387 55.000 12.15 0.00 45.96 4.85
1187 1256 0.240945 GGATCAAAACGTGCACCCAG 59.759 55.000 12.15 0.00 0.00 4.45
1190 1259 0.240945 CCAGGATCAAAACGTGCACC 59.759 55.000 12.15 0.00 0.00 5.01
1191 1260 0.951558 ACCAGGATCAAAACGTGCAC 59.048 50.000 6.82 6.82 0.00 4.57
1192 1261 1.202758 AGACCAGGATCAAAACGTGCA 60.203 47.619 0.00 0.00 0.00 4.57
1193 1262 1.523758 AGACCAGGATCAAAACGTGC 58.476 50.000 0.00 0.00 0.00 5.34
1194 1263 2.878406 ACAAGACCAGGATCAAAACGTG 59.122 45.455 0.00 0.00 0.00 4.49
1283 1387 3.573967 AGAGTAGGCAATTTGGTTGGTTG 59.426 43.478 0.00 0.00 38.29 3.77
1324 1432 2.092267 TCACAATCACAGGGATGGATGG 60.092 50.000 0.00 0.00 36.02 3.51
1325 1433 3.286329 TCACAATCACAGGGATGGATG 57.714 47.619 0.00 0.00 36.02 3.51
1326 1434 3.203710 ACATCACAATCACAGGGATGGAT 59.796 43.478 9.87 0.00 39.63 3.41
1327 1435 2.577563 ACATCACAATCACAGGGATGGA 59.422 45.455 9.87 0.00 39.63 3.41
1344 1452 3.383761 CCTTGAAACAAACCTGCACATC 58.616 45.455 0.00 0.00 0.00 3.06
1349 1622 3.751479 ATTCCCTTGAAACAAACCTGC 57.249 42.857 0.00 0.00 33.32 4.85
1490 1773 9.669353 CGCAGAGCAATTTACTTGATAATTATT 57.331 29.630 0.00 0.00 36.97 1.40
1491 1774 8.840321 ACGCAGAGCAATTTACTTGATAATTAT 58.160 29.630 0.00 0.00 36.97 1.28
1543 1826 5.607939 TTCCGGAGAAGTATAAATCTGCA 57.392 39.130 3.34 0.00 34.06 4.41
1660 1981 7.340232 ACATGAGCACATATACAGTTCCAATTT 59.660 33.333 0.00 0.00 35.09 1.82
1661 1982 6.830324 ACATGAGCACATATACAGTTCCAATT 59.170 34.615 0.00 0.00 35.09 2.32
1662 1983 6.359804 ACATGAGCACATATACAGTTCCAAT 58.640 36.000 0.00 0.00 35.09 3.16
1663 1984 5.744171 ACATGAGCACATATACAGTTCCAA 58.256 37.500 0.00 0.00 35.09 3.53
1664 1985 5.357742 ACATGAGCACATATACAGTTCCA 57.642 39.130 0.00 0.00 35.09 3.53
1665 1986 7.154656 TGATACATGAGCACATATACAGTTCC 58.845 38.462 0.00 0.00 35.09 3.62
1666 1987 8.491152 GTTGATACATGAGCACATATACAGTTC 58.509 37.037 0.00 0.00 35.09 3.01
1667 1988 7.986889 TGTTGATACATGAGCACATATACAGTT 59.013 33.333 0.00 0.00 35.09 3.16
1668 1989 7.500141 TGTTGATACATGAGCACATATACAGT 58.500 34.615 0.00 0.00 35.09 3.55
1669 1990 7.951530 TGTTGATACATGAGCACATATACAG 57.048 36.000 0.00 0.00 35.09 2.74
1687 2029 6.585416 TGACTGTATATGTGCTCATGTTGAT 58.415 36.000 11.46 0.00 35.70 2.57
1688 2030 5.976458 TGACTGTATATGTGCTCATGTTGA 58.024 37.500 11.46 0.00 35.70 3.18
1689 2031 5.814188 ACTGACTGTATATGTGCTCATGTTG 59.186 40.000 11.46 2.38 35.70 3.33
1690 2032 5.982356 ACTGACTGTATATGTGCTCATGTT 58.018 37.500 11.46 1.95 35.70 2.71
1691 2033 5.604758 ACTGACTGTATATGTGCTCATGT 57.395 39.130 11.46 7.35 35.70 3.21
1692 2034 9.696917 TTATAACTGACTGTATATGTGCTCATG 57.303 33.333 11.46 0.00 35.70 3.07
1696 2038 8.993121 GCAATTATAACTGACTGTATATGTGCT 58.007 33.333 0.00 0.00 0.00 4.40
1697 2039 8.993121 AGCAATTATAACTGACTGTATATGTGC 58.007 33.333 0.00 0.00 0.00 4.57
1702 2044 9.967346 GTCTGAGCAATTATAACTGACTGTATA 57.033 33.333 0.00 0.00 0.00 1.47
1703 2045 8.700051 AGTCTGAGCAATTATAACTGACTGTAT 58.300 33.333 0.00 0.00 37.97 2.29
1704 2046 8.067751 AGTCTGAGCAATTATAACTGACTGTA 57.932 34.615 0.00 0.00 37.97 2.74
1705 2047 6.940739 AGTCTGAGCAATTATAACTGACTGT 58.059 36.000 0.00 0.00 37.97 3.55
1706 2048 9.190858 GATAGTCTGAGCAATTATAACTGACTG 57.809 37.037 16.31 7.16 39.06 3.51
1707 2049 8.918116 TGATAGTCTGAGCAATTATAACTGACT 58.082 33.333 13.43 13.43 40.67 3.41
1708 2050 9.190858 CTGATAGTCTGAGCAATTATAACTGAC 57.809 37.037 0.00 0.81 0.00 3.51
1709 2051 9.136323 TCTGATAGTCTGAGCAATTATAACTGA 57.864 33.333 0.00 0.00 0.00 3.41
1710 2052 9.409312 CTCTGATAGTCTGAGCAATTATAACTG 57.591 37.037 1.73 0.00 36.04 3.16
1711 2053 8.584157 CCTCTGATAGTCTGAGCAATTATAACT 58.416 37.037 7.96 0.00 40.00 2.24
1712 2054 7.816995 CCCTCTGATAGTCTGAGCAATTATAAC 59.183 40.741 7.96 0.00 40.00 1.89
1713 2055 7.510685 ACCCTCTGATAGTCTGAGCAATTATAA 59.489 37.037 7.96 0.00 40.00 0.98
1714 2056 7.013220 ACCCTCTGATAGTCTGAGCAATTATA 58.987 38.462 7.96 0.00 40.00 0.98
1715 2057 5.843421 ACCCTCTGATAGTCTGAGCAATTAT 59.157 40.000 7.96 0.00 40.00 1.28
1724 2066 5.654650 AGACAGTTTACCCTCTGATAGTCTG 59.345 44.000 0.00 0.00 35.84 3.51
1748 2090 0.670239 CCACACACTAGCATGTCGCA 60.670 55.000 0.00 0.00 46.13 5.10
1758 2100 6.043938 AGGAAAGGAAGTTAATCCACACACTA 59.956 38.462 0.00 0.00 42.27 2.74
1761 2103 5.070001 CAGGAAAGGAAGTTAATCCACACA 58.930 41.667 0.00 0.00 42.27 3.72
1766 2108 5.416013 CAGGAACAGGAAAGGAAGTTAATCC 59.584 44.000 0.00 0.00 39.96 3.01
1773 2115 3.778954 AGTCAGGAACAGGAAAGGAAG 57.221 47.619 0.00 0.00 0.00 3.46
1894 2241 5.794894 ACACATAAGTCTGTTCTCGGAAAT 58.205 37.500 0.00 0.00 0.00 2.17
2158 2575 8.080417 GTGAATGAAATCAATGTATGGATGGAG 58.920 37.037 0.00 0.00 0.00 3.86
2469 2886 9.474920 AACAATAACAACTTCACAAATACCATG 57.525 29.630 0.00 0.00 0.00 3.66
2563 2980 6.037062 CACAAAGATGCCACATTCTATTCGTA 59.963 38.462 0.00 0.00 0.00 3.43
2578 2995 8.746922 TTGAATACAGAAAATCACAAAGATGC 57.253 30.769 0.00 0.00 36.96 3.91
2676 3093 9.997482 GTTCACTTTCAACTTGTAAATAGTTCA 57.003 29.630 0.00 0.00 33.73 3.18
2724 3141 1.730772 CGAGCTCAAGTTCCACTCTCG 60.731 57.143 15.40 0.00 34.25 4.04
2968 3385 3.545724 GACCTTTAGTCCCGGTTGG 57.454 57.895 0.00 0.00 39.84 3.77
3123 3669 2.371841 AACACCTTGTGTGCATAGGAGA 59.628 45.455 12.35 0.00 46.79 3.71


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

AutoCloner maintained by Alex Coulton.