Multiple sequence alignment - TraesCS5D01G455900

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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 TraesCS5D01G455900 chr5D 100.000 3533 0 0 1 3533 503047515 503051047 0.000000e+00 6525.0
1 TraesCS5D01G455900 chr5D 92.348 771 51 7 2768 3533 324410479 324409712 0.000000e+00 1090.0
2 TraesCS5D01G455900 chr5D 76.944 746 145 22 1657 2384 93862367 93861631 1.980000e-107 399.0
3 TraesCS5D01G455900 chr5A 94.061 2273 77 16 517 2750 631503317 631505570 0.000000e+00 3397.0
4 TraesCS5D01G455900 chr5A 76.882 744 149 20 1657 2384 87417185 87416449 1.980000e-107 399.0
5 TraesCS5D01G455900 chr5A 97.368 76 2 0 1 76 631502173 631502248 2.860000e-26 130.0
6 TraesCS5D01G455900 chr5A 93.220 59 4 0 73 131 631502623 631502565 1.750000e-13 87.9
7 TraesCS5D01G455900 chr5B 92.989 2282 100 23 506 2750 631825475 631827733 0.000000e+00 3273.0
8 TraesCS5D01G455900 chr2D 94.394 767 37 5 2773 3533 276936752 276935986 0.000000e+00 1173.0
9 TraesCS5D01G455900 chr2D 92.932 764 44 9 2776 3533 285349013 285349772 0.000000e+00 1103.0
10 TraesCS5D01G455900 chr7D 93.135 772 45 6 2769 3533 145920056 145919286 0.000000e+00 1125.0
11 TraesCS5D01G455900 chr7D 93.099 768 48 5 2769 3533 576645039 576644274 0.000000e+00 1120.0
12 TraesCS5D01G455900 chr7D 93.404 758 44 6 2779 3533 375298575 375299329 0.000000e+00 1118.0
13 TraesCS5D01G455900 chr7D 93.081 766 45 7 2773 3533 616465909 616465147 0.000000e+00 1114.0
14 TraesCS5D01G455900 chr7D 77.254 743 142 23 1660 2384 610420906 610420173 9.130000e-111 411.0
15 TraesCS5D01G455900 chr7D 81.013 316 54 4 1691 2003 401548300 401547988 2.720000e-61 246.0
16 TraesCS5D01G455900 chr6A 93.325 764 44 6 2775 3533 577715459 577716220 0.000000e+00 1122.0
17 TraesCS5D01G455900 chr1D 92.258 775 50 6 2767 3533 6180002 6180774 0.000000e+00 1090.0
18 TraesCS5D01G455900 chr1D 75.979 945 171 35 1476 2386 349082359 349081437 1.510000e-118 436.0
19 TraesCS5D01G455900 chr3A 78.884 753 142 16 1675 2417 604569215 604569960 8.810000e-136 494.0
20 TraesCS5D01G455900 chr3D 79.301 715 134 13 1675 2382 462073021 462073728 4.100000e-134 488.0
21 TraesCS5D01G455900 chr1A 76.196 941 176 31 1476 2386 449519755 449518833 1.500000e-123 453.0
22 TraesCS5D01G455900 chr1B 75.745 940 182 32 1476 2386 470717620 470716698 7.010000e-117 431.0
23 TraesCS5D01G455900 chr7A 76.439 747 147 25 1657 2384 700300901 700301637 9.260000e-101 377.0
24 TraesCS5D01G455900 chr7B 76.415 742 148 23 1661 2384 698683407 698684139 3.330000e-100 375.0
25 TraesCS5D01G455900 chr7B 82.986 288 45 3 1720 2003 411057518 411057231 1.260000e-64 257.0
26 TraesCS5D01G455900 chr2B 80.635 315 61 0 1691 2005 784773668 784773982 9.800000e-61 244.0
27 TraesCS5D01G455900 chr2A 75.828 302 63 10 1691 1987 211460572 211460868 1.020000e-30 145.0


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 TraesCS5D01G455900 chr5D 503047515 503051047 3532 False 6525.0 6525 100.0000 1 3533 1 chr5D.!!$F1 3532
1 TraesCS5D01G455900 chr5D 324409712 324410479 767 True 1090.0 1090 92.3480 2768 3533 1 chr5D.!!$R2 765
2 TraesCS5D01G455900 chr5D 93861631 93862367 736 True 399.0 399 76.9440 1657 2384 1 chr5D.!!$R1 727
3 TraesCS5D01G455900 chr5A 631502173 631505570 3397 False 1763.5 3397 95.7145 1 2750 2 chr5A.!!$F1 2749
4 TraesCS5D01G455900 chr5A 87416449 87417185 736 True 399.0 399 76.8820 1657 2384 1 chr5A.!!$R1 727
5 TraesCS5D01G455900 chr5B 631825475 631827733 2258 False 3273.0 3273 92.9890 506 2750 1 chr5B.!!$F1 2244
6 TraesCS5D01G455900 chr2D 276935986 276936752 766 True 1173.0 1173 94.3940 2773 3533 1 chr2D.!!$R1 760
7 TraesCS5D01G455900 chr2D 285349013 285349772 759 False 1103.0 1103 92.9320 2776 3533 1 chr2D.!!$F1 757
8 TraesCS5D01G455900 chr7D 145919286 145920056 770 True 1125.0 1125 93.1350 2769 3533 1 chr7D.!!$R1 764
9 TraesCS5D01G455900 chr7D 576644274 576645039 765 True 1120.0 1120 93.0990 2769 3533 1 chr7D.!!$R3 764
10 TraesCS5D01G455900 chr7D 375298575 375299329 754 False 1118.0 1118 93.4040 2779 3533 1 chr7D.!!$F1 754
11 TraesCS5D01G455900 chr7D 616465147 616465909 762 True 1114.0 1114 93.0810 2773 3533 1 chr7D.!!$R5 760
12 TraesCS5D01G455900 chr7D 610420173 610420906 733 True 411.0 411 77.2540 1660 2384 1 chr7D.!!$R4 724
13 TraesCS5D01G455900 chr6A 577715459 577716220 761 False 1122.0 1122 93.3250 2775 3533 1 chr6A.!!$F1 758
14 TraesCS5D01G455900 chr1D 6180002 6180774 772 False 1090.0 1090 92.2580 2767 3533 1 chr1D.!!$F1 766
15 TraesCS5D01G455900 chr1D 349081437 349082359 922 True 436.0 436 75.9790 1476 2386 1 chr1D.!!$R1 910
16 TraesCS5D01G455900 chr3A 604569215 604569960 745 False 494.0 494 78.8840 1675 2417 1 chr3A.!!$F1 742
17 TraesCS5D01G455900 chr3D 462073021 462073728 707 False 488.0 488 79.3010 1675 2382 1 chr3D.!!$F1 707
18 TraesCS5D01G455900 chr1A 449518833 449519755 922 True 453.0 453 76.1960 1476 2386 1 chr1A.!!$R1 910
19 TraesCS5D01G455900 chr1B 470716698 470717620 922 True 431.0 431 75.7450 1476 2386 1 chr1B.!!$R1 910
20 TraesCS5D01G455900 chr7A 700300901 700301637 736 False 377.0 377 76.4390 1657 2384 1 chr7A.!!$F1 727
21 TraesCS5D01G455900 chr7B 698683407 698684139 732 False 375.0 375 76.4150 1661 2384 1 chr7B.!!$F1 723

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
136 137 0.035534 ATGCATGCCCTCGTGTTGTA 60.036 50.0 16.68 0.0 0.0 2.41 F
429 1123 0.103208 AGATACGAGCGAGGCCAAAG 59.897 55.0 5.01 0.0 0.0 2.77 F
909 1631 0.742281 CTCGCCTTGATCACCACCAG 60.742 60.0 0.00 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 2129 1.920835 GGAGGCCCACCAGAAGACT 60.921 63.158 11.18 0.0 39.06 3.24 R
2028 2774 3.992641 TCCTCGTCCTCTGGGGCA 61.993 66.667 0.00 0.0 36.96 5.36 R
2690 3497 0.604578 TATAATAGACGTGGCCGGCC 59.395 55.000 39.40 39.4 45.85 6.13 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
58 59 0.601046 ATAGCATCGCCATCACACGG 60.601 55.000 0.00 0.00 0.00 4.94
76 77 1.156736 GGCGCTTCTTGCTGACTAAA 58.843 50.000 7.64 0.00 40.11 1.85
78 79 1.801178 GCGCTTCTTGCTGACTAAAGT 59.199 47.619 0.00 0.00 40.11 2.66
79 80 2.224314 GCGCTTCTTGCTGACTAAAGTT 59.776 45.455 0.00 0.00 40.11 2.66
80 81 3.665585 GCGCTTCTTGCTGACTAAAGTTC 60.666 47.826 0.00 0.00 40.11 3.01
82 83 4.212214 CGCTTCTTGCTGACTAAAGTTCTT 59.788 41.667 0.00 0.00 40.11 2.52
83 84 5.613577 CGCTTCTTGCTGACTAAAGTTCTTC 60.614 44.000 0.00 0.00 40.11 2.87
84 85 5.334491 GCTTCTTGCTGACTAAAGTTCTTCC 60.334 44.000 0.00 0.00 38.95 3.46
85 86 4.307432 TCTTGCTGACTAAAGTTCTTCCG 58.693 43.478 0.00 0.00 0.00 4.30
86 87 2.413837 TGCTGACTAAAGTTCTTCCGC 58.586 47.619 0.00 0.00 0.00 5.54
87 88 1.732809 GCTGACTAAAGTTCTTCCGCC 59.267 52.381 0.00 0.00 0.00 6.13
88 89 1.993370 CTGACTAAAGTTCTTCCGCCG 59.007 52.381 0.00 0.00 0.00 6.46
89 90 1.337447 TGACTAAAGTTCTTCCGCCGG 60.337 52.381 0.00 0.00 0.00 6.13
90 91 0.683412 ACTAAAGTTCTTCCGCCGGT 59.317 50.000 1.63 0.00 0.00 5.28
92 93 0.971386 TAAAGTTCTTCCGCCGGTCT 59.029 50.000 1.63 0.00 0.00 3.85
93 94 0.320508 AAAGTTCTTCCGCCGGTCTC 60.321 55.000 1.63 0.00 0.00 3.36
95 96 2.987547 TTCTTCCGCCGGTCTCGT 60.988 61.111 1.63 0.00 33.95 4.18
96 97 2.567497 TTCTTCCGCCGGTCTCGTT 61.567 57.895 1.63 0.00 33.95 3.85
97 98 2.048503 CTTCCGCCGGTCTCGTTT 60.049 61.111 1.63 0.00 33.95 3.60
98 99 2.048877 TTCCGCCGGTCTCGTTTC 60.049 61.111 1.63 0.00 33.95 2.78
99 100 2.758770 CTTCCGCCGGTCTCGTTTCA 62.759 60.000 1.63 0.00 33.95 2.69
100 101 2.356553 CCGCCGGTCTCGTTTCAA 60.357 61.111 1.90 0.00 33.95 2.69
102 103 1.693083 CCGCCGGTCTCGTTTCAATC 61.693 60.000 1.90 0.00 33.95 2.67
105 106 2.613691 GCCGGTCTCGTTTCAATCTAA 58.386 47.619 1.90 0.00 33.95 2.10
106 107 3.195661 GCCGGTCTCGTTTCAATCTAAT 58.804 45.455 1.90 0.00 33.95 1.73
107 108 3.245519 GCCGGTCTCGTTTCAATCTAATC 59.754 47.826 1.90 0.00 33.95 1.75
108 109 4.683832 CCGGTCTCGTTTCAATCTAATCT 58.316 43.478 0.00 0.00 33.95 2.40
109 110 4.740695 CCGGTCTCGTTTCAATCTAATCTC 59.259 45.833 0.00 0.00 33.95 2.75
110 111 4.740695 CGGTCTCGTTTCAATCTAATCTCC 59.259 45.833 0.00 0.00 0.00 3.71
112 113 5.341617 GTCTCGTTTCAATCTAATCTCCGT 58.658 41.667 0.00 0.00 0.00 4.69
113 114 6.459298 GGTCTCGTTTCAATCTAATCTCCGTA 60.459 42.308 0.00 0.00 0.00 4.02
114 115 6.633634 GTCTCGTTTCAATCTAATCTCCGTAG 59.366 42.308 0.00 0.00 0.00 3.51
133 134 3.594568 CATGCATGCCCTCGTGTT 58.405 55.556 14.93 0.00 0.00 3.32
135 136 1.303561 ATGCATGCCCTCGTGTTGT 60.304 52.632 16.68 0.00 0.00 3.32
136 137 0.035534 ATGCATGCCCTCGTGTTGTA 60.036 50.000 16.68 0.00 0.00 2.41
137 138 0.250510 TGCATGCCCTCGTGTTGTAA 60.251 50.000 16.68 0.00 0.00 2.41
138 139 0.447801 GCATGCCCTCGTGTTGTAAG 59.552 55.000 6.36 0.00 0.00 2.34
139 140 1.943968 GCATGCCCTCGTGTTGTAAGA 60.944 52.381 6.36 0.00 0.00 2.10
140 141 2.422597 CATGCCCTCGTGTTGTAAGAA 58.577 47.619 0.00 0.00 0.00 2.52
141 142 2.163818 TGCCCTCGTGTTGTAAGAAG 57.836 50.000 0.00 0.00 0.00 2.85
142 143 1.689813 TGCCCTCGTGTTGTAAGAAGA 59.310 47.619 0.00 0.00 0.00 2.87
143 144 2.301870 TGCCCTCGTGTTGTAAGAAGAT 59.698 45.455 0.00 0.00 0.00 2.40
144 145 2.673368 GCCCTCGTGTTGTAAGAAGATG 59.327 50.000 0.00 0.00 0.00 2.90
145 146 3.616560 GCCCTCGTGTTGTAAGAAGATGA 60.617 47.826 0.00 0.00 0.00 2.92
146 147 4.759782 CCCTCGTGTTGTAAGAAGATGAT 58.240 43.478 0.00 0.00 0.00 2.45
147 148 4.568359 CCCTCGTGTTGTAAGAAGATGATG 59.432 45.833 0.00 0.00 0.00 3.07
148 149 4.568359 CCTCGTGTTGTAAGAAGATGATGG 59.432 45.833 0.00 0.00 0.00 3.51
149 150 5.400066 TCGTGTTGTAAGAAGATGATGGA 57.600 39.130 0.00 0.00 0.00 3.41
150 151 5.789521 TCGTGTTGTAAGAAGATGATGGAA 58.210 37.500 0.00 0.00 0.00 3.53
153 154 6.173339 GTGTTGTAAGAAGATGATGGAAGGA 58.827 40.000 0.00 0.00 0.00 3.36
154 155 6.092807 GTGTTGTAAGAAGATGATGGAAGGAC 59.907 42.308 0.00 0.00 0.00 3.85
155 156 5.359194 TGTAAGAAGATGATGGAAGGACC 57.641 43.478 0.00 0.00 39.54 4.46
157 158 1.765314 AGAAGATGATGGAAGGACCGG 59.235 52.381 0.00 0.00 42.61 5.28
158 159 0.839946 AAGATGATGGAAGGACCGGG 59.160 55.000 6.32 0.00 42.61 5.73
159 160 1.227973 GATGATGGAAGGACCGGGC 60.228 63.158 6.32 0.21 42.61 6.13
160 161 2.682582 GATGATGGAAGGACCGGGCC 62.683 65.000 22.85 22.85 42.61 5.80
162 163 3.090532 ATGGAAGGACCGGGCCTC 61.091 66.667 34.46 23.07 42.61 4.70
163 164 3.943137 ATGGAAGGACCGGGCCTCA 62.943 63.158 34.46 26.12 42.61 3.86
164 165 3.090532 GGAAGGACCGGGCCTCAT 61.091 66.667 34.46 17.13 37.26 2.90
165 166 2.506472 GAAGGACCGGGCCTCATC 59.494 66.667 34.46 22.45 37.26 2.92
166 167 2.041265 AAGGACCGGGCCTCATCT 59.959 61.111 34.46 12.13 37.26 2.90
167 168 1.616628 AAGGACCGGGCCTCATCTT 60.617 57.895 34.46 11.61 37.26 2.40
168 169 1.915078 AAGGACCGGGCCTCATCTTG 61.915 60.000 34.46 0.00 37.26 3.02
170 171 3.329542 GACCGGGCCTCATCTTGCA 62.330 63.158 6.32 0.00 0.00 4.08
171 172 2.194056 CCGGGCCTCATCTTGCAT 59.806 61.111 0.84 0.00 0.00 3.96
172 173 2.191513 CCGGGCCTCATCTTGCATG 61.192 63.158 0.84 0.00 0.00 4.06
174 175 0.536687 CGGGCCTCATCTTGCATGAT 60.537 55.000 9.20 9.20 0.00 2.45
175 176 0.959553 GGGCCTCATCTTGCATGATG 59.040 55.000 28.16 28.16 43.66 3.07
176 177 0.959553 GGCCTCATCTTGCATGATGG 59.040 55.000 31.19 23.66 42.82 3.51
177 178 0.314302 GCCTCATCTTGCATGATGGC 59.686 55.000 31.19 26.05 42.82 4.40
178 179 1.687563 CCTCATCTTGCATGATGGCA 58.312 50.000 31.19 18.38 42.82 4.92
195 196 1.547372 GGCAACAGCAGAAATGGATGT 59.453 47.619 0.00 0.00 36.25 3.06
196 197 2.028748 GGCAACAGCAGAAATGGATGTT 60.029 45.455 0.00 0.00 44.84 2.71
197 198 3.248266 GCAACAGCAGAAATGGATGTTC 58.752 45.455 0.00 0.00 42.39 3.18
199 200 4.232221 CAACAGCAGAAATGGATGTTCAC 58.768 43.478 0.00 0.00 42.39 3.18
200 201 3.759581 ACAGCAGAAATGGATGTTCACT 58.240 40.909 0.00 0.00 29.14 3.41
201 202 3.504906 ACAGCAGAAATGGATGTTCACTG 59.495 43.478 0.00 0.00 37.41 3.66
202 203 3.087031 AGCAGAAATGGATGTTCACTGG 58.913 45.455 0.00 0.00 0.00 4.00
203 204 3.084039 GCAGAAATGGATGTTCACTGGA 58.916 45.455 0.00 0.00 0.00 3.86
204 205 3.507233 GCAGAAATGGATGTTCACTGGAA 59.493 43.478 0.00 0.00 0.00 3.53
205 206 4.022068 GCAGAAATGGATGTTCACTGGAAA 60.022 41.667 0.00 0.00 34.13 3.13
207 208 5.242393 CAGAAATGGATGTTCACTGGAAACT 59.758 40.000 0.00 0.00 34.13 2.66
208 209 5.242393 AGAAATGGATGTTCACTGGAAACTG 59.758 40.000 0.00 0.00 34.13 3.16
209 210 2.229792 TGGATGTTCACTGGAAACTGC 58.770 47.619 0.00 0.00 34.13 4.40
210 211 2.229792 GGATGTTCACTGGAAACTGCA 58.770 47.619 0.00 0.00 34.13 4.41
212 213 3.550842 GGATGTTCACTGGAAACTGCAAC 60.551 47.826 0.00 0.00 34.13 4.17
213 214 1.748493 TGTTCACTGGAAACTGCAACC 59.252 47.619 0.00 0.00 34.13 3.77
214 215 1.748493 GTTCACTGGAAACTGCAACCA 59.252 47.619 0.00 0.00 34.13 3.67
216 217 1.955778 TCACTGGAAACTGCAACCATG 59.044 47.619 0.00 0.00 33.08 3.66
228 229 1.511850 CAACCATGCACGAAGTCTGA 58.488 50.000 0.00 0.00 41.61 3.27
229 230 1.872952 CAACCATGCACGAAGTCTGAA 59.127 47.619 0.00 0.00 41.61 3.02
230 231 1.512926 ACCATGCACGAAGTCTGAAC 58.487 50.000 0.00 0.00 41.61 3.18
231 232 0.798776 CCATGCACGAAGTCTGAACC 59.201 55.000 0.00 0.00 41.61 3.62
233 234 0.687354 ATGCACGAAGTCTGAACCCT 59.313 50.000 0.00 0.00 41.61 4.34
236 237 1.978542 CACGAAGTCTGAACCCTACG 58.021 55.000 0.00 0.00 41.61 3.51
237 238 0.886563 ACGAAGTCTGAACCCTACGG 59.113 55.000 0.00 0.00 29.74 4.02
238 239 2.495739 ACGAAGTCTGAACCCTACGGG 61.496 57.143 0.00 0.00 44.92 5.28
248 249 3.012722 CCTACGGGGAAGGGGCAA 61.013 66.667 0.00 0.00 37.23 4.52
249 250 2.383601 CCTACGGGGAAGGGGCAAT 61.384 63.158 0.00 0.00 37.23 3.56
250 251 1.152963 CTACGGGGAAGGGGCAATG 60.153 63.158 0.00 0.00 0.00 2.82
251 252 2.624674 CTACGGGGAAGGGGCAATGG 62.625 65.000 0.00 0.00 0.00 3.16
252 253 3.738481 CGGGGAAGGGGCAATGGA 61.738 66.667 0.00 0.00 0.00 3.41
253 254 3.027787 GGGGAAGGGGCAATGGAT 58.972 61.111 0.00 0.00 0.00 3.41
254 255 1.458209 GGGGAAGGGGCAATGGATG 60.458 63.158 0.00 0.00 0.00 3.51
255 256 1.311059 GGGAAGGGGCAATGGATGT 59.689 57.895 0.00 0.00 0.00 3.06
257 258 1.114627 GGAAGGGGCAATGGATGTTC 58.885 55.000 0.00 0.00 0.00 3.18
258 259 1.619432 GGAAGGGGCAATGGATGTTCA 60.619 52.381 0.00 0.00 0.00 3.18
259 260 1.478105 GAAGGGGCAATGGATGTTCAC 59.522 52.381 0.00 0.00 0.00 3.18
260 261 0.706433 AGGGGCAATGGATGTTCACT 59.294 50.000 0.00 0.00 0.00 3.41
261 262 0.819582 GGGGCAATGGATGTTCACTG 59.180 55.000 0.00 0.00 0.00 3.66
262 263 1.616725 GGGGCAATGGATGTTCACTGA 60.617 52.381 0.00 0.00 0.00 3.41
263 264 2.170166 GGGCAATGGATGTTCACTGAA 58.830 47.619 0.00 0.00 0.00 3.02
264 265 2.562298 GGGCAATGGATGTTCACTGAAA 59.438 45.455 0.00 0.00 0.00 2.69
265 266 3.006752 GGGCAATGGATGTTCACTGAAAA 59.993 43.478 0.00 0.00 0.00 2.29
266 267 3.989817 GGCAATGGATGTTCACTGAAAAC 59.010 43.478 0.00 0.00 0.00 2.43
267 268 4.262164 GGCAATGGATGTTCACTGAAAACT 60.262 41.667 0.00 0.00 0.00 2.66
269 270 5.278660 GCAATGGATGTTCACTGAAAACTCT 60.279 40.000 0.00 0.00 0.00 3.24
270 271 6.736794 GCAATGGATGTTCACTGAAAACTCTT 60.737 38.462 0.00 0.00 0.00 2.85
271 272 5.756195 TGGATGTTCACTGAAAACTCTTG 57.244 39.130 0.00 0.00 0.00 3.02
272 273 4.036734 TGGATGTTCACTGAAAACTCTTGC 59.963 41.667 0.00 0.00 0.00 4.01
273 274 4.036734 GGATGTTCACTGAAAACTCTTGCA 59.963 41.667 0.00 0.00 0.00 4.08
275 276 3.181497 TGTTCACTGAAAACTCTTGCAGC 60.181 43.478 0.00 0.00 41.48 5.25
276 277 2.923121 TCACTGAAAACTCTTGCAGCT 58.077 42.857 0.00 0.00 41.48 4.24
277 278 2.615447 TCACTGAAAACTCTTGCAGCTG 59.385 45.455 10.11 10.11 41.48 4.24
278 279 1.336125 ACTGAAAACTCTTGCAGCTGC 59.664 47.619 31.89 31.89 41.48 5.25
306 307 6.839124 TGGTAACAGCAGAAATGATCAAAT 57.161 33.333 0.00 0.00 46.17 2.32
308 309 6.433716 TGGTAACAGCAGAAATGATCAAATGA 59.566 34.615 0.00 0.00 46.17 2.57
309 310 7.039853 TGGTAACAGCAGAAATGATCAAATGAA 60.040 33.333 0.00 0.00 46.17 2.57
312 313 6.931838 ACAGCAGAAATGATCAAATGAACAT 58.068 32.000 0.00 0.81 38.89 2.71
313 314 8.058667 ACAGCAGAAATGATCAAATGAACATA 57.941 30.769 0.00 0.00 36.69 2.29
314 315 7.972277 ACAGCAGAAATGATCAAATGAACATAC 59.028 33.333 0.00 5.14 36.69 2.39
315 316 7.971722 CAGCAGAAATGATCAAATGAACATACA 59.028 33.333 0.00 0.00 36.69 2.29
316 317 8.692710 AGCAGAAATGATCAAATGAACATACAT 58.307 29.630 0.00 0.00 36.69 2.29
318 319 9.244799 CAGAAATGATCAAATGAACATACATGG 57.755 33.333 0.00 0.00 36.69 3.66
329 978 2.094675 ACATACATGGCAGCCAAGTTC 58.905 47.619 26.71 0.00 36.76 3.01
332 981 1.636148 ACATGGCAGCCAAGTTCAAT 58.364 45.000 20.84 0.00 36.95 2.57
333 982 1.547372 ACATGGCAGCCAAGTTCAATC 59.453 47.619 20.84 0.00 36.95 2.67
334 983 1.546923 CATGGCAGCCAAGTTCAATCA 59.453 47.619 20.84 0.00 36.95 2.57
335 984 1.702182 TGGCAGCCAAGTTCAATCAA 58.298 45.000 13.33 0.00 0.00 2.57
339 988 3.056322 GGCAGCCAAGTTCAATCAAGATT 60.056 43.478 6.55 0.00 0.00 2.40
340 989 8.736788 ATGGCAGCCAAGTTCAATCAAGATTG 62.737 42.308 20.84 14.98 42.27 2.67
371 1022 2.203126 GCATTCTCAGAGGCCGGG 60.203 66.667 2.18 0.00 0.00 5.73
374 1025 3.642741 ATTCTCAGAGGCCGGGGGT 62.643 63.158 2.18 0.00 0.00 4.95
375 1026 2.252012 ATTCTCAGAGGCCGGGGGTA 62.252 60.000 2.18 0.00 0.00 3.69
376 1027 2.840102 CTCAGAGGCCGGGGGTAG 60.840 72.222 2.18 0.00 0.00 3.18
389 1083 3.371595 CCGGGGGTAGAAGAATGTCAAAT 60.372 47.826 0.00 0.00 0.00 2.32
391 1085 3.877508 GGGGGTAGAAGAATGTCAAATCG 59.122 47.826 0.00 0.00 0.00 3.34
392 1086 4.514401 GGGGTAGAAGAATGTCAAATCGT 58.486 43.478 0.00 0.00 0.00 3.73
393 1087 4.941873 GGGGTAGAAGAATGTCAAATCGTT 59.058 41.667 0.00 0.00 0.00 3.85
394 1088 5.414765 GGGGTAGAAGAATGTCAAATCGTTT 59.585 40.000 0.00 0.00 0.00 3.60
395 1089 6.314784 GGGTAGAAGAATGTCAAATCGTTTG 58.685 40.000 4.67 4.67 41.96 2.93
396 1090 6.148811 GGGTAGAAGAATGTCAAATCGTTTGA 59.851 38.462 8.47 8.47 46.68 2.69
429 1123 0.103208 AGATACGAGCGAGGCCAAAG 59.897 55.000 5.01 0.00 0.00 2.77
430 1124 1.491505 GATACGAGCGAGGCCAAAGC 61.492 60.000 5.01 7.34 38.76 3.51
432 1126 3.793144 CGAGCGAGGCCAAAGCAC 61.793 66.667 17.31 11.10 42.56 4.40
435 1129 2.669569 GCGAGGCCAAAGCACAGA 60.670 61.111 5.01 0.00 42.56 3.41
437 1131 1.004560 CGAGGCCAAAGCACAGAGA 60.005 57.895 5.01 0.00 42.56 3.10
439 1133 1.609208 GAGGCCAAAGCACAGAGAAA 58.391 50.000 5.01 0.00 42.56 2.52
441 1135 2.560105 GAGGCCAAAGCACAGAGAAAAT 59.440 45.455 5.01 0.00 42.56 1.82
442 1136 3.758554 GAGGCCAAAGCACAGAGAAAATA 59.241 43.478 5.01 0.00 42.56 1.40
444 1138 3.507622 GGCCAAAGCACAGAGAAAATAGT 59.492 43.478 0.00 0.00 42.56 2.12
445 1139 4.700213 GGCCAAAGCACAGAGAAAATAGTA 59.300 41.667 0.00 0.00 42.56 1.82
446 1140 5.183140 GGCCAAAGCACAGAGAAAATAGTAA 59.817 40.000 0.00 0.00 42.56 2.24
447 1141 6.086871 GCCAAAGCACAGAGAAAATAGTAAC 58.913 40.000 0.00 0.00 39.53 2.50
448 1142 6.293955 GCCAAAGCACAGAGAAAATAGTAACA 60.294 38.462 0.00 0.00 39.53 2.41
449 1143 7.648142 CCAAAGCACAGAGAAAATAGTAACAA 58.352 34.615 0.00 0.00 0.00 2.83
450 1144 8.134895 CCAAAGCACAGAGAAAATAGTAACAAA 58.865 33.333 0.00 0.00 0.00 2.83
451 1145 8.958043 CAAAGCACAGAGAAAATAGTAACAAAC 58.042 33.333 0.00 0.00 0.00 2.93
452 1146 7.801716 AGCACAGAGAAAATAGTAACAAACA 57.198 32.000 0.00 0.00 0.00 2.83
453 1147 7.639945 AGCACAGAGAAAATAGTAACAAACAC 58.360 34.615 0.00 0.00 0.00 3.32
454 1148 6.573725 GCACAGAGAAAATAGTAACAAACACG 59.426 38.462 0.00 0.00 0.00 4.49
455 1149 7.627340 CACAGAGAAAATAGTAACAAACACGT 58.373 34.615 0.00 0.00 0.00 4.49
457 1151 7.001922 CAGAGAAAATAGTAACAAACACGTCG 58.998 38.462 0.00 0.00 0.00 5.12
459 1153 7.862372 AGAGAAAATAGTAACAAACACGTCGTA 59.138 33.333 0.00 0.00 0.00 3.43
461 1155 6.452244 AAATAGTAACAAACACGTCGTACC 57.548 37.500 0.00 0.00 0.00 3.34
462 1156 2.384382 AGTAACAAACACGTCGTACCG 58.616 47.619 0.00 0.00 0.00 4.02
463 1157 2.116366 GTAACAAACACGTCGTACCGT 58.884 47.619 0.00 0.00 42.87 4.83
465 1159 0.929824 ACAAACACGTCGTACCGTCG 60.930 55.000 0.00 2.06 42.97 5.12
466 1160 2.010817 AAACACGTCGTACCGTCGC 61.011 57.895 0.00 0.00 41.34 5.19
468 1162 4.724697 CACGTCGTACCGTCGCGT 62.725 66.667 5.77 0.00 41.34 6.01
469 1163 4.430423 ACGTCGTACCGTCGCGTC 62.430 66.667 5.77 0.00 41.34 5.19
471 1165 4.134187 GTCGTACCGTCGCGTCGA 62.134 66.667 26.46 14.43 0.00 4.20
473 1167 2.716484 CGTACCGTCGCGTCGATC 60.716 66.667 26.46 14.24 38.42 3.69
474 1168 2.716484 GTACCGTCGCGTCGATCG 60.716 66.667 26.46 9.36 38.42 3.69
475 1169 2.885164 TACCGTCGCGTCGATCGA 60.885 61.111 26.46 15.15 42.86 3.59
476 1170 2.451990 TACCGTCGCGTCGATCGAA 61.452 57.895 26.46 0.22 42.86 3.71
477 1171 2.616776 TACCGTCGCGTCGATCGAAC 62.617 60.000 26.46 13.38 42.86 3.95
478 1172 2.572388 CGTCGCGTCGATCGAACA 60.572 61.111 21.31 0.59 42.86 3.18
479 1173 2.141631 CGTCGCGTCGATCGAACAA 61.142 57.895 21.31 2.90 42.86 2.83
480 1174 1.336164 GTCGCGTCGATCGAACAAC 59.664 57.895 21.31 11.90 42.86 3.32
481 1175 2.141631 TCGCGTCGATCGAACAACG 61.142 57.895 21.31 20.04 42.86 4.10
482 1176 2.687436 GCGTCGATCGAACAACGG 59.313 61.111 21.31 6.31 42.86 4.44
483 1177 2.084681 GCGTCGATCGAACAACGGT 61.085 57.895 21.31 0.00 42.86 4.83
488 1182 2.650163 GATCGAACAACGGTCCTCG 58.350 57.895 0.00 0.00 45.20 4.63
497 1191 4.477975 CGGTCCTCGTCGCCACTC 62.478 72.222 0.00 0.00 0.00 3.51
498 1192 4.477975 GGTCCTCGTCGCCACTCG 62.478 72.222 0.00 0.00 40.15 4.18
502 1196 4.498520 CTCGTCGCCACTCGCCAT 62.499 66.667 0.00 0.00 38.27 4.40
503 1197 4.492160 TCGTCGCCACTCGCCATC 62.492 66.667 0.00 0.00 38.27 3.51
504 1198 4.498520 CGTCGCCACTCGCCATCT 62.499 66.667 0.00 0.00 38.27 2.90
548 1242 1.197949 CTTGAGCAAGACGAGACGAGA 59.802 52.381 4.22 0.00 40.79 4.04
726 1429 1.867812 CGTCATGTGATCGCGACGT 60.868 57.895 21.32 0.00 44.61 4.34
865 1577 1.649171 CAAGAAACCGATCGTGAGTCG 59.351 52.381 15.09 0.00 41.41 4.18
886 1598 2.105766 GTCCACCATAAGTAGGGTCGT 58.894 52.381 0.00 0.00 38.49 4.34
897 1615 2.776370 TAGGGTCGTGGTCTCGCCTT 62.776 60.000 0.00 0.00 38.35 4.35
909 1631 0.742281 CTCGCCTTGATCACCACCAG 60.742 60.000 0.00 0.00 0.00 4.00
924 1649 4.021192 CACCACCAGTTATTTGCTTCCATT 60.021 41.667 0.00 0.00 0.00 3.16
929 1654 5.095490 CCAGTTATTTGCTTCCATTTCGTC 58.905 41.667 0.00 0.00 0.00 4.20
1014 1742 2.143419 GGAGATGCGAGGGGTGGAT 61.143 63.158 0.00 0.00 0.00 3.41
1021 1749 3.105928 GAGGGGTGGATGGGGCAT 61.106 66.667 0.00 0.00 0.00 4.40
1380 2108 3.384348 GTCCCCGACCAGCTGTTA 58.616 61.111 13.81 0.00 0.00 2.41
1902 2630 1.130749 GTGTACGACATCGAGCTCACT 59.869 52.381 15.40 0.00 43.02 3.41
2028 2774 1.679898 CCCCAAGAAGAAGGACGCT 59.320 57.895 0.00 0.00 0.00 5.07
2689 3496 1.657751 GCGGGAATGGAAAGGCTGAC 61.658 60.000 0.00 0.00 0.00 3.51
2690 3497 1.369091 CGGGAATGGAAAGGCTGACG 61.369 60.000 0.00 0.00 0.00 4.35
2691 3498 1.032114 GGGAATGGAAAGGCTGACGG 61.032 60.000 0.00 0.00 0.00 4.79
2692 3499 1.657751 GGAATGGAAAGGCTGACGGC 61.658 60.000 0.00 0.00 40.90 5.68
2727 3536 6.754702 ATTATAGCTGCTCATTTGGCTATG 57.245 37.500 4.91 0.00 44.44 2.23
2746 3555 3.940209 TGAAGCTTCGAAAATGCCAAT 57.060 38.095 21.11 0.00 0.00 3.16
2747 3556 5.581126 ATGAAGCTTCGAAAATGCCAATA 57.419 34.783 21.11 0.00 0.00 1.90
2748 3557 5.581126 TGAAGCTTCGAAAATGCCAATAT 57.419 34.783 21.11 0.00 0.00 1.28
2749 3558 5.342433 TGAAGCTTCGAAAATGCCAATATG 58.658 37.500 21.11 0.00 0.00 1.78
2750 3559 4.989279 AGCTTCGAAAATGCCAATATGT 57.011 36.364 0.00 0.00 0.00 2.29
2751 3560 4.675510 AGCTTCGAAAATGCCAATATGTG 58.324 39.130 0.00 0.00 0.00 3.21
2765 3574 6.817765 CCAATATGTGGTTTGTAACTGACT 57.182 37.500 0.00 0.00 43.20 3.41
2766 3575 6.842163 CCAATATGTGGTTTGTAACTGACTC 58.158 40.000 0.00 0.00 43.20 3.36
2771 3580 7.730364 ATGTGGTTTGTAACTGACTCTTTAG 57.270 36.000 0.00 0.00 0.00 1.85
2783 3592 5.769162 ACTGACTCTTTAGTTTAGGACGACT 59.231 40.000 0.00 0.00 35.56 4.18
2825 3634 1.071699 GTTAAGGAGTCTGCCCACACA 59.928 52.381 0.00 0.00 0.00 3.72
2858 3667 1.207791 CTAAGAGGACCAGCCCACAT 58.792 55.000 0.00 0.00 37.37 3.21
2892 3701 2.031157 GCAAAACAACTAGCGTCCACAT 60.031 45.455 0.00 0.00 0.00 3.21
3087 3905 3.623060 CAGTTGCCATGTCGCTAAACTAT 59.377 43.478 0.00 0.00 0.00 2.12
3185 4005 2.340210 TTGGACAACTGCAGCTGTTA 57.660 45.000 22.87 13.00 0.00 2.41
3190 4010 3.334691 GACAACTGCAGCTGTTACCATA 58.665 45.455 22.87 0.00 0.00 2.74
3258 4078 4.262765 GGTTGCCACCTACTAACACTAAGT 60.263 45.833 0.00 0.00 40.44 2.24
3273 4093 4.876107 ACACTAAGTAGTTGCCATGTATGC 59.124 41.667 0.00 0.00 33.46 3.14
3288 4108 6.483307 GCCATGTATGCTCTGATTTACTACAA 59.517 38.462 0.00 0.00 0.00 2.41
3456 4279 3.687212 CGTGTACCCTGCAAAACATATGA 59.313 43.478 10.38 0.00 0.00 2.15
3480 4303 5.212194 CAACTGACATGTTCGGGTAAAAAG 58.788 41.667 0.00 0.00 34.44 2.27
3481 4304 3.818773 ACTGACATGTTCGGGTAAAAAGG 59.181 43.478 0.00 0.00 34.44 3.11
3490 4318 5.305128 TGTTCGGGTAAAAAGGAGAGAGTTA 59.695 40.000 0.00 0.00 0.00 2.24
3501 4329 3.450457 AGGAGAGAGTTACCATCTGCTTG 59.550 47.826 3.30 0.00 38.43 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.879103 ATACACACCCAGTCCTTTGG 57.121 50.000 0.00 0.00 38.00 3.28
76 77 2.971452 GAGACCGGCGGAAGAACT 59.029 61.111 35.78 21.26 0.00 3.01
78 79 2.091102 AAACGAGACCGGCGGAAGAA 62.091 55.000 35.78 0.00 40.78 2.52
79 80 2.482296 GAAACGAGACCGGCGGAAGA 62.482 60.000 35.78 0.00 40.78 2.87
80 81 2.048503 AAACGAGACCGGCGGAAG 60.049 61.111 35.78 21.31 40.78 3.46
82 83 2.162338 ATTGAAACGAGACCGGCGGA 62.162 55.000 35.78 5.91 40.78 5.54
83 84 1.693083 GATTGAAACGAGACCGGCGG 61.693 60.000 27.06 27.06 40.78 6.13
84 85 0.736325 AGATTGAAACGAGACCGGCG 60.736 55.000 0.00 0.00 40.78 6.46
85 86 2.288961 TAGATTGAAACGAGACCGGC 57.711 50.000 0.00 0.00 40.78 6.13
86 87 4.683832 AGATTAGATTGAAACGAGACCGG 58.316 43.478 0.00 0.00 40.78 5.28
87 88 4.740695 GGAGATTAGATTGAAACGAGACCG 59.259 45.833 0.00 0.00 42.50 4.79
88 89 4.740695 CGGAGATTAGATTGAAACGAGACC 59.259 45.833 0.00 0.00 0.00 3.85
89 90 5.341617 ACGGAGATTAGATTGAAACGAGAC 58.658 41.667 0.00 0.00 0.00 3.36
90 91 5.578005 ACGGAGATTAGATTGAAACGAGA 57.422 39.130 0.00 0.00 0.00 4.04
92 93 5.735354 GCCTACGGAGATTAGATTGAAACGA 60.735 44.000 0.00 0.00 0.00 3.85
93 94 4.444720 GCCTACGGAGATTAGATTGAAACG 59.555 45.833 0.00 0.00 0.00 3.60
95 96 5.607939 TGCCTACGGAGATTAGATTGAAA 57.392 39.130 0.00 0.00 0.00 2.69
96 97 5.541845 CATGCCTACGGAGATTAGATTGAA 58.458 41.667 0.00 0.00 0.00 2.69
97 98 4.561530 GCATGCCTACGGAGATTAGATTGA 60.562 45.833 6.36 0.00 0.00 2.57
98 99 3.681897 GCATGCCTACGGAGATTAGATTG 59.318 47.826 6.36 0.00 0.00 2.67
99 100 3.324846 TGCATGCCTACGGAGATTAGATT 59.675 43.478 16.68 0.00 0.00 2.40
100 101 2.899900 TGCATGCCTACGGAGATTAGAT 59.100 45.455 16.68 0.00 0.00 1.98
102 103 2.820059 TGCATGCCTACGGAGATTAG 57.180 50.000 16.68 0.00 0.00 1.73
105 106 3.620061 CATGCATGCCTACGGAGAT 57.380 52.632 14.93 0.00 0.00 2.75
116 117 1.138036 CAACACGAGGGCATGCATG 59.862 57.895 22.70 22.70 0.00 4.06
118 119 0.250510 TTACAACACGAGGGCATGCA 60.251 50.000 21.36 0.00 0.00 3.96
119 120 0.447801 CTTACAACACGAGGGCATGC 59.552 55.000 9.90 9.90 0.00 4.06
120 121 2.093306 TCTTACAACACGAGGGCATG 57.907 50.000 0.00 0.00 0.00 4.06
122 123 1.689813 TCTTCTTACAACACGAGGGCA 59.310 47.619 0.00 0.00 0.00 5.36
123 124 2.450609 TCTTCTTACAACACGAGGGC 57.549 50.000 0.00 0.00 0.00 5.19
129 130 6.092807 GTCCTTCCATCATCTTCTTACAACAC 59.907 42.308 0.00 0.00 0.00 3.32
131 132 5.586643 GGTCCTTCCATCATCTTCTTACAAC 59.413 44.000 0.00 0.00 35.97 3.32
132 133 5.626809 CGGTCCTTCCATCATCTTCTTACAA 60.627 44.000 0.00 0.00 35.57 2.41
133 134 4.141937 CGGTCCTTCCATCATCTTCTTACA 60.142 45.833 0.00 0.00 35.57 2.41
135 136 3.388024 CCGGTCCTTCCATCATCTTCTTA 59.612 47.826 0.00 0.00 35.57 2.10
136 137 2.171448 CCGGTCCTTCCATCATCTTCTT 59.829 50.000 0.00 0.00 35.57 2.52
137 138 1.765314 CCGGTCCTTCCATCATCTTCT 59.235 52.381 0.00 0.00 35.57 2.85
138 139 1.202698 CCCGGTCCTTCCATCATCTTC 60.203 57.143 0.00 0.00 35.57 2.87
139 140 0.839946 CCCGGTCCTTCCATCATCTT 59.160 55.000 0.00 0.00 35.57 2.40
140 141 1.700042 GCCCGGTCCTTCCATCATCT 61.700 60.000 0.00 0.00 35.57 2.90
141 142 1.227973 GCCCGGTCCTTCCATCATC 60.228 63.158 0.00 0.00 35.57 2.92
142 143 2.757124 GGCCCGGTCCTTCCATCAT 61.757 63.158 0.00 0.00 35.57 2.45
143 144 3.407967 GGCCCGGTCCTTCCATCA 61.408 66.667 0.00 0.00 35.57 3.07
144 145 3.090532 AGGCCCGGTCCTTCCATC 61.091 66.667 0.00 0.00 35.57 3.51
145 146 3.090532 GAGGCCCGGTCCTTCCAT 61.091 66.667 5.01 0.00 36.38 3.41
146 147 3.943137 ATGAGGCCCGGTCCTTCCA 62.943 63.158 5.01 0.00 36.38 3.53
147 148 3.090532 ATGAGGCCCGGTCCTTCC 61.091 66.667 5.01 0.00 36.38 3.46
148 149 1.627297 AAGATGAGGCCCGGTCCTTC 61.627 60.000 5.01 0.00 36.38 3.46
149 150 1.616628 AAGATGAGGCCCGGTCCTT 60.617 57.895 5.01 0.00 36.38 3.36
150 151 2.041265 AAGATGAGGCCCGGTCCT 59.959 61.111 2.06 2.06 39.67 3.85
153 154 2.683465 ATGCAAGATGAGGCCCGGT 61.683 57.895 0.00 0.00 0.00 5.28
154 155 2.191513 CATGCAAGATGAGGCCCGG 61.192 63.158 0.00 0.00 0.00 5.73
155 156 0.536687 ATCATGCAAGATGAGGCCCG 60.537 55.000 3.12 0.00 0.00 6.13
157 158 0.959553 CCATCATGCAAGATGAGGCC 59.040 55.000 28.67 0.00 46.51 5.19
158 159 0.314302 GCCATCATGCAAGATGAGGC 59.686 55.000 28.67 21.66 46.51 4.70
159 160 1.687563 TGCCATCATGCAAGATGAGG 58.312 50.000 28.67 16.62 46.51 3.86
167 168 0.609681 TCTGCTGTTGCCATCATGCA 60.610 50.000 0.00 0.00 40.07 3.96
168 169 0.528924 TTCTGCTGTTGCCATCATGC 59.471 50.000 0.00 0.00 38.71 4.06
170 171 2.167693 CCATTTCTGCTGTTGCCATCAT 59.832 45.455 0.00 0.00 38.71 2.45
171 172 1.546923 CCATTTCTGCTGTTGCCATCA 59.453 47.619 0.00 0.00 38.71 3.07
172 173 1.820519 TCCATTTCTGCTGTTGCCATC 59.179 47.619 0.00 0.00 38.71 3.51
174 175 1.546923 CATCCATTTCTGCTGTTGCCA 59.453 47.619 0.00 0.00 38.71 4.92
175 176 1.547372 ACATCCATTTCTGCTGTTGCC 59.453 47.619 0.00 0.00 38.71 4.52
176 177 3.248266 GAACATCCATTTCTGCTGTTGC 58.752 45.455 0.00 0.00 40.20 4.17
177 178 4.022589 AGTGAACATCCATTTCTGCTGTTG 60.023 41.667 0.00 0.00 31.07 3.33
178 179 4.022589 CAGTGAACATCCATTTCTGCTGTT 60.023 41.667 0.00 0.00 32.59 3.16
179 180 3.504906 CAGTGAACATCCATTTCTGCTGT 59.495 43.478 0.00 0.00 0.00 4.40
180 181 3.119602 CCAGTGAACATCCATTTCTGCTG 60.120 47.826 0.00 0.00 31.98 4.41
181 182 3.087031 CCAGTGAACATCCATTTCTGCT 58.913 45.455 0.00 0.00 0.00 4.24
182 183 3.084039 TCCAGTGAACATCCATTTCTGC 58.916 45.455 0.00 0.00 0.00 4.26
183 184 5.242393 AGTTTCCAGTGAACATCCATTTCTG 59.758 40.000 0.00 0.00 0.00 3.02
184 185 5.242393 CAGTTTCCAGTGAACATCCATTTCT 59.758 40.000 0.00 0.00 0.00 2.52
186 187 4.262164 GCAGTTTCCAGTGAACATCCATTT 60.262 41.667 0.00 0.00 0.00 2.32
188 189 2.821969 GCAGTTTCCAGTGAACATCCAT 59.178 45.455 0.00 0.00 0.00 3.41
190 191 2.229792 TGCAGTTTCCAGTGAACATCC 58.770 47.619 0.00 0.00 0.00 3.51
191 192 3.550842 GGTTGCAGTTTCCAGTGAACATC 60.551 47.826 0.00 0.00 0.00 3.06
195 196 2.136298 TGGTTGCAGTTTCCAGTGAA 57.864 45.000 0.00 0.00 0.00 3.18
196 197 1.955778 CATGGTTGCAGTTTCCAGTGA 59.044 47.619 0.00 0.00 34.62 3.41
197 198 2.427232 CATGGTTGCAGTTTCCAGTG 57.573 50.000 7.74 0.00 34.62 3.66
209 210 1.511850 TCAGACTTCGTGCATGGTTG 58.488 50.000 5.98 0.00 0.00 3.77
210 211 1.873591 GTTCAGACTTCGTGCATGGTT 59.126 47.619 5.98 0.00 0.00 3.67
212 213 0.798776 GGTTCAGACTTCGTGCATGG 59.201 55.000 5.98 0.00 0.00 3.66
213 214 0.798776 GGGTTCAGACTTCGTGCATG 59.201 55.000 0.00 0.00 0.00 4.06
214 215 0.687354 AGGGTTCAGACTTCGTGCAT 59.313 50.000 0.00 0.00 0.00 3.96
216 217 1.711206 GTAGGGTTCAGACTTCGTGC 58.289 55.000 0.00 0.00 0.00 5.34
217 218 1.978542 CGTAGGGTTCAGACTTCGTG 58.021 55.000 0.00 0.00 0.00 4.35
233 234 2.685534 CCATTGCCCCTTCCCCGTA 61.686 63.158 0.00 0.00 0.00 4.02
236 237 1.458209 CATCCATTGCCCCTTCCCC 60.458 63.158 0.00 0.00 0.00 4.81
237 238 0.325577 AACATCCATTGCCCCTTCCC 60.326 55.000 0.00 0.00 0.00 3.97
238 239 1.114627 GAACATCCATTGCCCCTTCC 58.885 55.000 0.00 0.00 0.00 3.46
240 241 1.077663 AGTGAACATCCATTGCCCCTT 59.922 47.619 0.00 0.00 0.00 3.95
241 242 0.706433 AGTGAACATCCATTGCCCCT 59.294 50.000 0.00 0.00 0.00 4.79
242 243 0.819582 CAGTGAACATCCATTGCCCC 59.180 55.000 0.00 0.00 0.00 5.80
243 244 1.838112 TCAGTGAACATCCATTGCCC 58.162 50.000 0.00 0.00 0.00 5.36
244 245 3.940209 TTTCAGTGAACATCCATTGCC 57.060 42.857 4.68 0.00 0.00 4.52
245 246 4.874970 AGTTTTCAGTGAACATCCATTGC 58.125 39.130 4.68 0.00 0.00 3.56
248 249 5.278660 GCAAGAGTTTTCAGTGAACATCCAT 60.279 40.000 4.68 0.00 0.00 3.41
249 250 4.036734 GCAAGAGTTTTCAGTGAACATCCA 59.963 41.667 4.68 0.00 0.00 3.41
250 251 4.036734 TGCAAGAGTTTTCAGTGAACATCC 59.963 41.667 4.68 0.00 0.00 3.51
251 252 5.173774 TGCAAGAGTTTTCAGTGAACATC 57.826 39.130 4.68 4.19 0.00 3.06
252 253 4.498682 GCTGCAAGAGTTTTCAGTGAACAT 60.499 41.667 4.68 0.00 34.07 2.71
253 254 3.181497 GCTGCAAGAGTTTTCAGTGAACA 60.181 43.478 4.68 0.00 34.07 3.18
254 255 3.065925 AGCTGCAAGAGTTTTCAGTGAAC 59.934 43.478 4.68 0.00 34.07 3.18
255 256 3.065786 CAGCTGCAAGAGTTTTCAGTGAA 59.934 43.478 0.00 0.08 34.07 3.18
257 258 2.857489 GCAGCTGCAAGAGTTTTCAGTG 60.857 50.000 33.36 0.00 41.59 3.66
258 259 1.336125 GCAGCTGCAAGAGTTTTCAGT 59.664 47.619 33.36 0.00 41.59 3.41
259 260 2.047679 GCAGCTGCAAGAGTTTTCAG 57.952 50.000 33.36 0.00 41.59 3.02
282 283 5.885230 TTGATCATTTCTGCTGTTACCAG 57.115 39.130 0.00 0.00 41.91 4.00
283 284 6.433716 TCATTTGATCATTTCTGCTGTTACCA 59.566 34.615 0.00 0.00 0.00 3.25
284 285 6.855836 TCATTTGATCATTTCTGCTGTTACC 58.144 36.000 0.00 0.00 0.00 2.85
285 286 7.809331 TGTTCATTTGATCATTTCTGCTGTTAC 59.191 33.333 0.00 0.00 0.00 2.50
287 288 6.751157 TGTTCATTTGATCATTTCTGCTGTT 58.249 32.000 0.00 0.00 0.00 3.16
288 289 6.335471 TGTTCATTTGATCATTTCTGCTGT 57.665 33.333 0.00 0.00 0.00 4.40
289 290 7.971722 TGTATGTTCATTTGATCATTTCTGCTG 59.028 33.333 8.88 0.00 36.31 4.41
291 292 8.752254 CATGTATGTTCATTTGATCATTTCTGC 58.248 33.333 8.88 0.00 36.31 4.26
292 293 9.244799 CCATGTATGTTCATTTGATCATTTCTG 57.755 33.333 8.88 5.36 36.31 3.02
293 294 7.924412 GCCATGTATGTTCATTTGATCATTTCT 59.076 33.333 8.88 0.00 36.31 2.52
294 295 7.707464 TGCCATGTATGTTCATTTGATCATTTC 59.293 33.333 8.88 5.17 36.31 2.17
295 296 7.557724 TGCCATGTATGTTCATTTGATCATTT 58.442 30.769 8.88 0.00 36.31 2.32
296 297 7.114866 TGCCATGTATGTTCATTTGATCATT 57.885 32.000 8.88 0.00 36.31 2.57
297 298 6.718522 TGCCATGTATGTTCATTTGATCAT 57.281 33.333 0.00 8.67 37.93 2.45
298 299 5.450826 GCTGCCATGTATGTTCATTTGATCA 60.451 40.000 0.00 0.00 0.00 2.92
299 300 4.980434 GCTGCCATGTATGTTCATTTGATC 59.020 41.667 0.00 0.00 0.00 2.92
302 303 3.119065 TGGCTGCCATGTATGTTCATTTG 60.119 43.478 19.30 0.00 0.00 2.32
303 304 3.098377 TGGCTGCCATGTATGTTCATTT 58.902 40.909 19.30 0.00 0.00 2.32
304 305 2.737544 TGGCTGCCATGTATGTTCATT 58.262 42.857 19.30 0.00 0.00 2.57
306 307 2.093890 CTTGGCTGCCATGTATGTTCA 58.906 47.619 24.03 2.67 31.53 3.18
308 309 2.220653 ACTTGGCTGCCATGTATGTT 57.779 45.000 31.59 12.49 39.59 2.71
309 310 2.094675 GAACTTGGCTGCCATGTATGT 58.905 47.619 32.39 21.18 40.31 2.29
312 313 2.284754 TTGAACTTGGCTGCCATGTA 57.715 45.000 32.39 19.72 40.31 2.29
313 314 1.547372 GATTGAACTTGGCTGCCATGT 59.453 47.619 28.54 28.54 42.50 3.21
314 315 1.546923 TGATTGAACTTGGCTGCCATG 59.453 47.619 27.33 27.33 35.21 3.66
315 316 1.927487 TGATTGAACTTGGCTGCCAT 58.073 45.000 24.03 7.75 31.53 4.40
316 317 1.614903 CTTGATTGAACTTGGCTGCCA 59.385 47.619 19.30 19.30 0.00 4.92
318 319 3.863142 ATCTTGATTGAACTTGGCTGC 57.137 42.857 0.00 0.00 0.00 5.25
332 981 3.402110 ACTGCGTGTGAATCAATCTTGA 58.598 40.909 0.00 0.00 42.14 3.02
333 982 3.818961 ACTGCGTGTGAATCAATCTTG 57.181 42.857 0.00 0.00 0.00 3.02
334 983 7.283058 AATGCACTGCGTGTGAATCAATCTT 62.283 40.000 12.91 0.00 43.94 2.40
335 984 5.871477 AATGCACTGCGTGTGAATCAATCT 61.871 41.667 12.91 0.00 43.94 2.40
339 988 1.197492 GAATGCACTGCGTGTGAATCA 59.803 47.619 12.91 3.15 43.94 2.57
340 989 1.466167 AGAATGCACTGCGTGTGAATC 59.534 47.619 12.91 7.46 43.94 2.52
341 990 1.466167 GAGAATGCACTGCGTGTGAAT 59.534 47.619 12.91 5.68 46.60 2.57
346 997 0.720027 CTCTGAGAATGCACTGCGTG 59.280 55.000 0.00 4.61 36.51 5.34
348 999 1.703438 GCCTCTGAGAATGCACTGCG 61.703 60.000 6.17 0.00 0.00 5.18
362 1013 2.041819 CTTCTACCCCCGGCCTCT 60.042 66.667 0.00 0.00 0.00 3.69
371 1022 6.148811 TCAAACGATTTGACATTCTTCTACCC 59.851 38.462 8.47 0.00 44.21 3.69
403 1097 2.930682 GCCTCGCTCGTATCTTCTTTTT 59.069 45.455 0.00 0.00 0.00 1.94
404 1098 2.541556 GCCTCGCTCGTATCTTCTTTT 58.458 47.619 0.00 0.00 0.00 2.27
405 1099 1.202428 GGCCTCGCTCGTATCTTCTTT 60.202 52.381 0.00 0.00 0.00 2.52
406 1100 0.386113 GGCCTCGCTCGTATCTTCTT 59.614 55.000 0.00 0.00 0.00 2.52
407 1101 0.752009 TGGCCTCGCTCGTATCTTCT 60.752 55.000 3.32 0.00 0.00 2.85
408 1102 0.102481 TTGGCCTCGCTCGTATCTTC 59.898 55.000 3.32 0.00 0.00 2.87
409 1103 0.535335 TTTGGCCTCGCTCGTATCTT 59.465 50.000 3.32 0.00 0.00 2.40
410 1104 0.103208 CTTTGGCCTCGCTCGTATCT 59.897 55.000 3.32 0.00 0.00 1.98
411 1105 1.491505 GCTTTGGCCTCGCTCGTATC 61.492 60.000 3.32 0.00 0.00 2.24
412 1106 1.521681 GCTTTGGCCTCGCTCGTAT 60.522 57.895 3.32 0.00 0.00 3.06
413 1107 2.125673 GCTTTGGCCTCGCTCGTA 60.126 61.111 3.32 0.00 0.00 3.43
429 1123 6.573725 CGTGTTTGTTACTATTTTCTCTGTGC 59.426 38.462 0.00 0.00 0.00 4.57
430 1124 7.627340 ACGTGTTTGTTACTATTTTCTCTGTG 58.373 34.615 0.00 0.00 0.00 3.66
432 1126 7.001922 CGACGTGTTTGTTACTATTTTCTCTG 58.998 38.462 0.00 0.00 0.00 3.35
435 1129 6.833342 ACGACGTGTTTGTTACTATTTTCT 57.167 33.333 0.00 0.00 0.00 2.52
437 1131 6.876804 GGTACGACGTGTTTGTTACTATTTT 58.123 36.000 11.56 0.00 0.00 1.82
457 1151 2.616776 TTCGATCGACGCGACGGTAC 62.617 60.000 28.61 18.50 39.18 3.34
459 1153 3.792047 TTCGATCGACGCGACGGT 61.792 61.111 28.61 23.92 39.18 4.83
461 1155 2.141631 TTGTTCGATCGACGCGACG 61.142 57.895 24.29 24.29 39.18 5.12
462 1156 1.336164 GTTGTTCGATCGACGCGAC 59.664 57.895 19.26 18.43 39.18 5.19
463 1157 2.141631 CGTTGTTCGATCGACGCGA 61.142 57.895 19.26 10.84 42.86 5.87
465 1159 1.995253 GACCGTTGTTCGATCGACGC 61.995 60.000 24.54 14.21 41.98 5.19
466 1160 1.400990 GGACCGTTGTTCGATCGACG 61.401 60.000 23.46 23.46 42.67 5.12
468 1162 0.169672 GAGGACCGTTGTTCGATCGA 59.830 55.000 15.15 15.15 42.86 3.59
469 1163 1.132199 CGAGGACCGTTGTTCGATCG 61.132 60.000 9.36 9.36 42.86 3.69
471 1165 4.883026 CGAGGACCGTTGTTCGAT 57.117 55.556 0.00 0.00 42.86 3.59
480 1174 4.477975 GAGTGGCGACGAGGACCG 62.478 72.222 0.00 0.00 45.44 4.79
481 1175 4.477975 CGAGTGGCGACGAGGACC 62.478 72.222 0.00 0.00 44.57 4.46
489 1183 4.819761 GCAGATGGCGAGTGGCGA 62.820 66.667 0.00 0.00 44.92 5.54
491 1185 4.783621 TGGCAGATGGCGAGTGGC 62.784 66.667 1.68 1.25 46.16 5.01
492 1186 2.184830 CATGGCAGATGGCGAGTGG 61.185 63.158 1.68 0.00 46.16 4.00
493 1187 2.184830 CCATGGCAGATGGCGAGTG 61.185 63.158 0.00 1.34 46.16 3.51
494 1188 2.191375 CCATGGCAGATGGCGAGT 59.809 61.111 0.00 0.00 46.16 4.18
548 1242 1.367659 GACTCGCTACAGTAGGTCGT 58.632 55.000 9.74 2.72 0.00 4.34
726 1429 2.582226 GTGCCGTCATGCGATCGA 60.582 61.111 21.57 4.34 44.77 3.59
763 1466 0.391263 CTGGCTTACCCGTGAAGGAC 60.391 60.000 0.00 0.00 45.00 3.85
865 1577 1.411612 CGACCCTACTTATGGTGGACC 59.588 57.143 0.00 0.00 34.20 4.46
886 1598 1.191489 TGGTGATCAAGGCGAGACCA 61.191 55.000 0.00 0.00 43.14 4.02
897 1615 4.032960 AGCAAATAACTGGTGGTGATCA 57.967 40.909 0.00 0.00 0.00 2.92
909 1631 5.938322 TGAGACGAAATGGAAGCAAATAAC 58.062 37.500 0.00 0.00 0.00 1.89
924 1649 2.035961 CAGAACCCAGAACTGAGACGAA 59.964 50.000 3.19 0.00 34.07 3.85
929 1654 0.322008 GGCCAGAACCCAGAACTGAG 60.322 60.000 0.00 0.00 34.07 3.35
966 1691 7.760340 GGACTAGCTCGAATTCTTCTCTTTTTA 59.240 37.037 3.52 0.00 0.00 1.52
969 1694 5.656480 GGACTAGCTCGAATTCTTCTCTTT 58.344 41.667 3.52 0.00 0.00 2.52
979 1707 2.722487 CGGCGGACTAGCTCGAAT 59.278 61.111 0.00 0.00 37.29 3.34
1401 2129 1.920835 GGAGGCCCACCAGAAGACT 60.921 63.158 11.18 0.00 39.06 3.24
1902 2630 4.134623 GTGTTGGAGTGCACGGAA 57.865 55.556 12.01 2.54 0.00 4.30
2028 2774 3.992641 TCCTCGTCCTCTGGGGCA 61.993 66.667 0.00 0.00 36.96 5.36
2364 3143 4.070552 GGCGTCAGGTTCTCGGCT 62.071 66.667 0.00 0.00 44.45 5.52
2689 3496 2.430382 ATAATAGACGTGGCCGGCCG 62.430 60.000 39.00 29.84 45.85 6.13
2690 3497 0.604578 TATAATAGACGTGGCCGGCC 59.395 55.000 39.40 39.40 45.85 6.13
2691 3498 1.992170 CTATAATAGACGTGGCCGGC 58.008 55.000 21.18 21.18 44.68 6.13
2692 3499 1.544691 AGCTATAATAGACGTGGCCGG 59.455 52.381 0.00 0.00 38.78 6.13
2727 3536 5.230726 CACATATTGGCATTTTCGAAGCTTC 59.769 40.000 16.84 16.84 0.00 3.86
2746 3555 8.426489 ACTAAAGAGTCAGTTACAAACCACATA 58.574 33.333 0.00 0.00 0.00 2.29
2747 3556 7.280356 ACTAAAGAGTCAGTTACAAACCACAT 58.720 34.615 0.00 0.00 0.00 3.21
2748 3557 6.646267 ACTAAAGAGTCAGTTACAAACCACA 58.354 36.000 0.00 0.00 0.00 4.17
2749 3558 7.549615 AACTAAAGAGTCAGTTACAAACCAC 57.450 36.000 0.00 0.00 33.58 4.16
2750 3559 9.321562 CTAAACTAAAGAGTCAGTTACAAACCA 57.678 33.333 0.00 0.00 33.92 3.67
2751 3560 8.771766 CCTAAACTAAAGAGTCAGTTACAAACC 58.228 37.037 0.00 0.00 33.92 3.27
2752 3561 9.538508 TCCTAAACTAAAGAGTCAGTTACAAAC 57.461 33.333 0.00 0.00 33.92 2.93
2753 3562 9.538508 GTCCTAAACTAAAGAGTCAGTTACAAA 57.461 33.333 0.00 0.00 33.92 2.83
2754 3563 7.864379 CGTCCTAAACTAAAGAGTCAGTTACAA 59.136 37.037 0.00 0.00 33.92 2.41
2755 3564 7.229306 TCGTCCTAAACTAAAGAGTCAGTTACA 59.771 37.037 0.00 0.00 33.92 2.41
2756 3565 7.536964 GTCGTCCTAAACTAAAGAGTCAGTTAC 59.463 40.741 0.00 0.00 33.92 2.50
2757 3566 7.446625 AGTCGTCCTAAACTAAAGAGTCAGTTA 59.553 37.037 0.00 0.00 33.92 2.24
2758 3567 6.264970 AGTCGTCCTAAACTAAAGAGTCAGTT 59.735 38.462 0.00 0.00 36.56 3.16
2759 3568 5.769162 AGTCGTCCTAAACTAAAGAGTCAGT 59.231 40.000 0.00 0.00 33.58 3.41
2760 3569 6.256912 AGTCGTCCTAAACTAAAGAGTCAG 57.743 41.667 0.00 0.00 33.58 3.51
2761 3570 7.934855 ATAGTCGTCCTAAACTAAAGAGTCA 57.065 36.000 0.00 0.00 33.58 3.41
2762 3571 9.715123 GTTATAGTCGTCCTAAACTAAAGAGTC 57.285 37.037 0.00 0.00 33.58 3.36
2763 3572 9.460019 AGTTATAGTCGTCCTAAACTAAAGAGT 57.540 33.333 0.00 0.00 37.59 3.24
2771 3580 7.585573 CGTGTGATAGTTATAGTCGTCCTAAAC 59.414 40.741 0.00 0.00 0.00 2.01
2825 3634 3.157087 CCTCTTAGGCACCACACAAAAT 58.843 45.455 0.00 0.00 0.00 1.82
3087 3905 2.831685 AGTTGTCCGACATGCAACTA 57.168 45.000 12.28 0.00 0.00 2.24
3138 3957 1.980765 TCTGGCACTTGACCTGAGATT 59.019 47.619 0.00 0.00 32.11 2.40
3190 4010 7.071950 TGGCAACTATAGTAAACCAGACCATAT 59.928 37.037 5.65 0.00 37.61 1.78
3224 4044 3.917329 GGTGGCAACCTCTAAAGTTTC 57.083 47.619 1.77 0.00 43.84 2.78
3258 4078 4.694760 ATCAGAGCATACATGGCAACTA 57.305 40.909 0.00 0.00 37.61 2.24
3288 4108 8.421249 TCCTAAGGTTTTCAAATCATGACAAT 57.579 30.769 0.00 0.00 37.92 2.71
3456 4279 3.478857 TTACCCGAACATGTCAGTTGT 57.521 42.857 0.00 0.00 0.00 3.32
3480 4303 3.791245 CAAGCAGATGGTAACTCTCTCC 58.209 50.000 0.00 0.00 37.61 3.71
3481 4304 3.194062 GCAAGCAGATGGTAACTCTCTC 58.806 50.000 0.00 0.00 37.61 3.20
3501 4329 1.001378 CAACTACCCTTGTGTGCTTGC 60.001 52.381 0.00 0.00 0.00 4.01
3511 4339 2.642807 AGTGTACATGGCAACTACCCTT 59.357 45.455 0.00 0.00 37.61 3.95


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

AutoCloner maintained by Alex Coulton.