Multiple sequence alignment - TraesCS2A01G269600

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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 TraesCS2A01G269600 chr2A 100.000 2413 0 0 1 2413 435640621 435643033 0.000000e+00 4457.0
1 TraesCS2A01G269600 chr2A 96.091 1100 31 3 184 1279 761803495 761804586 0.000000e+00 1783.0
2 TraesCS2A01G269600 chr2A 83.297 1383 142 40 213 1575 23627786 23629099 0.000000e+00 1192.0
3 TraesCS2A01G269600 chr2A 95.626 503 13 2 1761 2256 761805759 761806259 0.000000e+00 798.0
4 TraesCS2A01G269600 chr2A 95.652 391 15 1 1288 1678 761805372 761805760 5.660000e-176 627.0
5 TraesCS2A01G269600 chr2A 98.235 170 3 0 2244 2413 761806565 761806734 5.040000e-77 298.0
6 TraesCS2A01G269600 chr2A 96.226 106 4 0 40 145 761797233 761797338 8.870000e-40 174.0
7 TraesCS2A01G269600 chr2A 86.885 122 14 2 2294 2413 50415987 50415866 4.180000e-28 135.0
8 TraesCS2A01G269600 chr2A 86.992 123 13 2 2294 2413 780441621 780441499 4.180000e-28 135.0
9 TraesCS2A01G269600 chr2A 84.211 95 6 6 1581 1675 23629140 23629225 1.540000e-12 84.2
10 TraesCS2A01G269600 chr2A 76.923 130 23 5 2140 2266 761041526 761041651 1.550000e-07 67.6
11 TraesCS2A01G269600 chr3B 82.974 1392 134 48 213 1583 561705886 561704577 0.000000e+00 1162.0
12 TraesCS2A01G269600 chr3B 89.535 86 6 2 1987 2072 561704194 561704112 3.280000e-19 106.0
13 TraesCS2A01G269600 chr3B 90.741 54 4 1 1582 1634 561704543 561704490 1.200000e-08 71.3
14 TraesCS2A01G269600 chr1B 98.913 92 1 0 1677 1768 618002548 618002457 5.340000e-37 165.0
15 TraesCS2A01G269600 chr7A 96.939 98 2 1 1677 1773 608875111 608875208 1.920000e-36 163.0
16 TraesCS2A01G269600 chr7A 95.745 94 4 0 1669 1762 615341069 615341162 4.150000e-33 152.0
17 TraesCS2A01G269600 chr7A 86.992 123 13 2 2294 2413 133645663 133645541 4.180000e-28 135.0
18 TraesCS2A01G269600 chr5A 95.876 97 4 0 1677 1773 27637136 27637040 8.930000e-35 158.0
19 TraesCS2A01G269600 chr3D 97.826 92 1 1 1677 1768 535746857 535746947 8.930000e-35 158.0
20 TraesCS2A01G269600 chr3D 85.294 102 15 0 5 106 474611394 474611293 3.280000e-19 106.0
21 TraesCS2A01G269600 chr3D 84.536 97 14 1 5 100 560921114 560921210 7.100000e-16 95.3
22 TraesCS2A01G269600 chr2D 96.809 94 3 0 1673 1766 107899775 107899868 8.930000e-35 158.0
23 TraesCS2A01G269600 chr6A 91.304 115 6 4 1661 1773 20747109 20746997 1.160000e-33 154.0
24 TraesCS2A01G269600 chr7D 94.000 100 4 2 1670 1769 480517345 480517442 1.490000e-32 150.0
25 TraesCS2A01G269600 chr5B 94.059 101 1 4 1667 1762 322205050 322205150 5.370000e-32 148.0
26 TraesCS2A01G269600 chr5B 86.179 123 14 3 2294 2413 556631881 556632003 1.950000e-26 130.0
27 TraesCS2A01G269600 chr5B 82.836 134 15 8 2140 2266 688411934 688412066 1.960000e-21 113.0
28 TraesCS2A01G269600 chr5D 86.992 123 13 2 2294 2413 246023352 246023474 4.180000e-28 135.0
29 TraesCS2A01G269600 chr4A 86.179 123 14 2 2294 2413 659467469 659467347 1.950000e-26 130.0
30 TraesCS2A01G269600 chrUn 86.486 111 13 1 2294 2402 385096268 385096378 1.170000e-23 121.0
31 TraesCS2A01G269600 chr2B 83.333 96 16 0 5 100 575175962 575176057 3.300000e-14 89.8
32 TraesCS2A01G269600 chr6D 83.516 91 15 0 16 106 465845335 465845245 4.270000e-13 86.1
33 TraesCS2A01G269600 chr3A 86.207 58 6 2 2330 2387 211049008 211048953 7.200000e-06 62.1


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 TraesCS2A01G269600 chr2A 435640621 435643033 2412 False 4457.000000 4457 100.000 1 2413 1 chr2A.!!$F1 2412
1 TraesCS2A01G269600 chr2A 761803495 761806734 3239 False 876.500000 1783 96.401 184 2413 4 chr2A.!!$F5 2229
2 TraesCS2A01G269600 chr2A 23627786 23629225 1439 False 638.100000 1192 83.754 213 1675 2 chr2A.!!$F4 1462
3 TraesCS2A01G269600 chr3B 561704112 561705886 1774 True 446.433333 1162 87.750 213 2072 3 chr3B.!!$R1 1859

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
135 136 0.171455 GAGTGTCCTGGCAGTAGTCG 59.829 60.0 14.43 0.0 0.00 4.18 F
324 331 0.386858 CGACGAGAAGAGCACGGAAA 60.387 55.0 0.00 0.0 34.76 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1014 1026 0.251634 CTCCACCCTCTTCTTCCTGC 59.748 60.0 0.0 0.0 0.00 4.85 R
1833 2704 1.078709 CTCGAACATGCAACGACCAT 58.921 50.0 0.0 0.0 32.72 3.55 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
35 36 4.135153 CGCCTGGGAGGTCGTGAG 62.135 72.222 0.00 0.00 37.80 3.51
36 37 4.459089 GCCTGGGAGGTCGTGAGC 62.459 72.222 0.00 0.00 37.80 4.26
37 38 2.681778 CCTGGGAGGTCGTGAGCT 60.682 66.667 0.40 0.40 42.58 4.09
42 43 2.795297 GAGGTCGTGAGCTCGAGG 59.205 66.667 15.58 4.53 44.60 4.63
43 44 3.404141 GAGGTCGTGAGCTCGAGGC 62.404 68.421 15.58 6.77 44.60 4.70
44 45 3.749064 GGTCGTGAGCTCGAGGCA 61.749 66.667 15.58 0.00 44.79 4.75
45 46 2.258591 GTCGTGAGCTCGAGGCAA 59.741 61.111 15.58 0.00 44.79 4.52
46 47 2.089349 GTCGTGAGCTCGAGGCAAC 61.089 63.158 15.58 8.25 44.79 4.17
47 48 2.811317 CGTGAGCTCGAGGCAACC 60.811 66.667 15.58 0.00 44.79 3.77
48 49 2.435059 GTGAGCTCGAGGCAACCC 60.435 66.667 15.58 0.00 44.79 4.11
49 50 3.706373 TGAGCTCGAGGCAACCCC 61.706 66.667 15.58 0.00 44.79 4.95
50 51 4.821589 GAGCTCGAGGCAACCCCG 62.822 72.222 15.58 0.00 44.79 5.73
54 55 4.700448 TCGAGGCAACCCCGGGTA 62.700 66.667 21.85 0.00 39.21 3.69
55 56 4.157120 CGAGGCAACCCCGGGTAG 62.157 72.222 21.85 7.60 39.21 3.18
56 57 2.686106 GAGGCAACCCCGGGTAGA 60.686 66.667 21.85 0.00 39.21 2.59
57 58 3.007323 AGGCAACCCCGGGTAGAC 61.007 66.667 21.85 11.09 39.21 2.59
58 59 4.105553 GGCAACCCCGGGTAGACC 62.106 72.222 21.85 12.08 33.12 3.85
74 75 4.760047 CCGGGCAGGTTGTCGGAG 62.760 72.222 0.00 0.00 44.69 4.63
75 76 4.760047 CGGGCAGGTTGTCGGAGG 62.760 72.222 0.00 0.00 0.00 4.30
77 78 4.021925 GGCAGGTTGTCGGAGGCT 62.022 66.667 0.00 0.00 0.00 4.58
78 79 2.435059 GCAGGTTGTCGGAGGCTC 60.435 66.667 5.78 5.78 0.00 4.70
79 80 2.266055 CAGGTTGTCGGAGGCTCC 59.734 66.667 24.06 24.06 0.00 4.70
116 117 2.949106 CACGACTTGCAGCTTGGG 59.051 61.111 0.00 0.00 0.00 4.12
117 118 1.597854 CACGACTTGCAGCTTGGGA 60.598 57.895 0.00 0.00 0.00 4.37
118 119 1.302033 ACGACTTGCAGCTTGGGAG 60.302 57.895 0.00 0.00 0.00 4.30
119 120 1.302033 CGACTTGCAGCTTGGGAGT 60.302 57.895 0.00 0.00 0.00 3.85
120 121 1.572085 CGACTTGCAGCTTGGGAGTG 61.572 60.000 0.00 0.00 0.00 3.51
121 122 0.536006 GACTTGCAGCTTGGGAGTGT 60.536 55.000 0.00 0.00 0.00 3.55
122 123 0.536006 ACTTGCAGCTTGGGAGTGTC 60.536 55.000 0.00 0.00 0.00 3.67
123 124 1.228245 TTGCAGCTTGGGAGTGTCC 60.228 57.895 0.00 0.00 35.23 4.02
124 125 1.708993 TTGCAGCTTGGGAGTGTCCT 61.709 55.000 0.00 0.00 36.57 3.85
125 126 1.673665 GCAGCTTGGGAGTGTCCTG 60.674 63.158 0.00 0.00 36.57 3.86
126 127 1.002868 CAGCTTGGGAGTGTCCTGG 60.003 63.158 0.00 0.00 36.57 4.45
127 128 2.360475 GCTTGGGAGTGTCCTGGC 60.360 66.667 0.00 0.00 36.57 4.85
128 129 3.160585 CTTGGGAGTGTCCTGGCA 58.839 61.111 0.00 0.00 36.57 4.92
129 130 1.002868 CTTGGGAGTGTCCTGGCAG 60.003 63.158 7.75 7.75 36.57 4.85
130 131 1.770110 TTGGGAGTGTCCTGGCAGT 60.770 57.895 14.43 0.00 36.57 4.40
131 132 0.472925 TTGGGAGTGTCCTGGCAGTA 60.473 55.000 14.43 0.00 36.57 2.74
132 133 0.904865 TGGGAGTGTCCTGGCAGTAG 60.905 60.000 14.43 0.00 36.57 2.57
133 134 0.905337 GGGAGTGTCCTGGCAGTAGT 60.905 60.000 14.43 2.24 36.57 2.73
134 135 0.533032 GGAGTGTCCTGGCAGTAGTC 59.467 60.000 14.43 11.09 32.53 2.59
135 136 0.171455 GAGTGTCCTGGCAGTAGTCG 59.829 60.000 14.43 0.00 0.00 4.18
136 137 1.215647 GTGTCCTGGCAGTAGTCGG 59.784 63.158 14.43 0.00 0.00 4.79
137 138 2.184579 GTCCTGGCAGTAGTCGGC 59.815 66.667 14.43 0.00 0.00 5.54
138 139 3.449227 TCCTGGCAGTAGTCGGCG 61.449 66.667 14.43 0.00 35.70 6.46
139 140 3.449227 CCTGGCAGTAGTCGGCGA 61.449 66.667 14.43 4.99 35.70 5.54
140 141 2.202623 CTGGCAGTAGTCGGCGAC 60.203 66.667 31.33 31.33 35.70 5.19
141 142 3.701604 CTGGCAGTAGTCGGCGACC 62.702 68.421 34.04 20.90 35.70 4.79
142 143 3.450115 GGCAGTAGTCGGCGACCT 61.450 66.667 34.04 22.79 35.70 3.85
143 144 2.202623 GCAGTAGTCGGCGACCTG 60.203 66.667 34.04 31.55 32.18 4.00
144 145 2.490217 CAGTAGTCGGCGACCTGG 59.510 66.667 34.04 18.53 32.18 4.45
145 146 2.044555 CAGTAGTCGGCGACCTGGA 61.045 63.158 34.04 16.00 32.18 3.86
146 147 1.749638 AGTAGTCGGCGACCTGGAG 60.750 63.158 34.04 0.00 32.18 3.86
147 148 2.439701 TAGTCGGCGACCTGGAGG 60.440 66.667 34.04 0.00 42.17 4.30
148 149 2.975265 TAGTCGGCGACCTGGAGGA 61.975 63.158 34.04 10.02 38.94 3.71
149 150 2.888464 TAGTCGGCGACCTGGAGGAG 62.888 65.000 34.04 0.00 38.94 3.69
152 153 3.151022 GGCGACCTGGAGGAGGAG 61.151 72.222 0.00 0.00 46.33 3.69
153 154 3.151022 GCGACCTGGAGGAGGAGG 61.151 72.222 0.00 0.00 46.33 4.30
154 155 3.151022 CGACCTGGAGGAGGAGGC 61.151 72.222 0.00 0.00 46.33 4.70
155 156 3.151022 GACCTGGAGGAGGAGGCG 61.151 72.222 0.00 0.00 46.33 5.52
156 157 4.787280 ACCTGGAGGAGGAGGCGG 62.787 72.222 0.00 0.00 46.33 6.13
157 158 4.465446 CCTGGAGGAGGAGGCGGA 62.465 72.222 0.00 0.00 46.33 5.54
158 159 2.364317 CTGGAGGAGGAGGCGGAA 60.364 66.667 0.00 0.00 0.00 4.30
159 160 2.364317 TGGAGGAGGAGGCGGAAG 60.364 66.667 0.00 0.00 0.00 3.46
160 161 3.157949 GGAGGAGGAGGCGGAAGG 61.158 72.222 0.00 0.00 0.00 3.46
161 162 2.042843 GAGGAGGAGGCGGAAGGA 60.043 66.667 0.00 0.00 0.00 3.36
162 163 2.042435 AGGAGGAGGCGGAAGGAG 60.042 66.667 0.00 0.00 0.00 3.69
163 164 3.157949 GGAGGAGGCGGAAGGAGG 61.158 72.222 0.00 0.00 0.00 4.30
164 165 2.042843 GAGGAGGCGGAAGGAGGA 60.043 66.667 0.00 0.00 0.00 3.71
165 166 2.042435 AGGAGGCGGAAGGAGGAG 60.042 66.667 0.00 0.00 0.00 3.69
166 167 3.855853 GGAGGCGGAAGGAGGAGC 61.856 72.222 0.00 0.00 0.00 4.70
167 168 4.214327 GAGGCGGAAGGAGGAGCG 62.214 72.222 0.00 0.00 0.00 5.03
170 171 3.145551 GCGGAAGGAGGAGCGGTA 61.146 66.667 0.00 0.00 0.00 4.02
171 172 3.121019 CGGAAGGAGGAGCGGTAG 58.879 66.667 0.00 0.00 0.00 3.18
172 173 2.816012 GGAAGGAGGAGCGGTAGC 59.184 66.667 0.00 0.00 45.58 3.58
182 183 2.048503 GCGGTAGCAGGACGTGTT 60.049 61.111 0.00 0.00 44.35 3.32
201 202 1.852633 TAGCAGGTGCAGCTCTTCTA 58.147 50.000 17.16 14.15 45.16 2.10
248 251 2.163818 TCATCGTTGGTTCTGGTCAC 57.836 50.000 0.00 0.00 0.00 3.67
266 273 9.213777 TCTGGTCACTTGGAAGTTCTATAATAT 57.786 33.333 2.25 0.00 37.08 1.28
304 311 0.762461 TTTTCCTTGCCTTGGGGTGG 60.762 55.000 0.00 0.00 34.45 4.61
324 331 0.386858 CGACGAGAAGAGCACGGAAA 60.387 55.000 0.00 0.00 34.76 3.13
451 459 1.542328 CCTTCACACCCGACATGTTCA 60.542 52.381 0.00 0.00 0.00 3.18
666 674 1.374758 AGACAGCTACTGCGGCAAC 60.375 57.895 3.44 0.00 45.42 4.17
802 810 1.617018 CGGAATGCTCACCCTCCTCA 61.617 60.000 0.00 0.00 0.00 3.86
987 999 2.033194 GCGCGTTCTGCCCTTACTT 61.033 57.895 8.43 0.00 42.08 2.24
1014 1026 0.667487 CTCCTATGTATGCCGGCGTG 60.667 60.000 31.45 13.68 0.00 5.34
1015 1027 2.317609 CCTATGTATGCCGGCGTGC 61.318 63.158 31.45 29.49 0.00 5.34
1029 1041 1.674057 CGTGCAGGAAGAAGAGGGT 59.326 57.895 0.00 0.00 0.00 4.34
1030 1042 0.671781 CGTGCAGGAAGAAGAGGGTG 60.672 60.000 0.00 0.00 0.00 4.61
1031 1043 0.322008 GTGCAGGAAGAAGAGGGTGG 60.322 60.000 0.00 0.00 0.00 4.61
1032 1044 0.473694 TGCAGGAAGAAGAGGGTGGA 60.474 55.000 0.00 0.00 0.00 4.02
1033 1045 0.251634 GCAGGAAGAAGAGGGTGGAG 59.748 60.000 0.00 0.00 0.00 3.86
1034 1046 0.908198 CAGGAAGAAGAGGGTGGAGG 59.092 60.000 0.00 0.00 0.00 4.30
1035 1047 0.793617 AGGAAGAAGAGGGTGGAGGA 59.206 55.000 0.00 0.00 0.00 3.71
1036 1048 0.906066 GGAAGAAGAGGGTGGAGGAC 59.094 60.000 0.00 0.00 0.00 3.85
1211 1225 9.274206 GGTAGAATATTGGGAGTAAATCTGAAC 57.726 37.037 0.00 0.00 0.00 3.18
1256 1274 1.377366 GACAGAGCGTCGATCCTGGA 61.377 60.000 6.92 0.00 34.19 3.86
1367 2166 1.022735 GAGCTGAACCCGACGAGATA 58.977 55.000 0.00 0.00 0.00 1.98
1368 2167 1.609555 GAGCTGAACCCGACGAGATAT 59.390 52.381 0.00 0.00 0.00 1.63
1389 2188 1.705002 TATGGCCAGGAACATCCCCG 61.705 60.000 13.05 0.00 37.19 5.73
1411 2211 4.930405 CGAGATGAGTAATCTAGGCGACTA 59.070 45.833 0.00 0.00 46.12 2.59
1631 2475 9.770097 CTCTCTTTACAGATGCCTAATTCATTA 57.230 33.333 0.00 0.00 0.00 1.90
1660 2504 7.801547 TTCTTCGGTCTACTTATTAAACGTG 57.198 36.000 0.00 0.00 0.00 4.49
1661 2505 6.913170 TCTTCGGTCTACTTATTAAACGTGT 58.087 36.000 0.00 0.00 0.00 4.49
1678 2522 1.795286 GTGTGCAGTGCTCTCAGTTAC 59.205 52.381 17.60 3.77 0.00 2.50
1679 2523 1.688735 TGTGCAGTGCTCTCAGTTACT 59.311 47.619 17.60 0.00 0.00 2.24
1680 2524 2.288457 TGTGCAGTGCTCTCAGTTACTC 60.288 50.000 17.60 0.00 0.00 2.59
1681 2525 1.273606 TGCAGTGCTCTCAGTTACTCC 59.726 52.381 17.60 0.00 0.00 3.85
1682 2526 1.404851 GCAGTGCTCTCAGTTACTCCC 60.405 57.143 8.18 0.00 0.00 4.30
1683 2527 2.175202 CAGTGCTCTCAGTTACTCCCT 58.825 52.381 0.00 0.00 0.00 4.20
1684 2528 2.165437 CAGTGCTCTCAGTTACTCCCTC 59.835 54.545 0.00 0.00 0.00 4.30
1685 2529 1.478916 GTGCTCTCAGTTACTCCCTCC 59.521 57.143 0.00 0.00 0.00 4.30
1686 2530 0.741915 GCTCTCAGTTACTCCCTCCG 59.258 60.000 0.00 0.00 0.00 4.63
1687 2531 1.956159 GCTCTCAGTTACTCCCTCCGT 60.956 57.143 0.00 0.00 0.00 4.69
1688 2532 2.448453 CTCTCAGTTACTCCCTCCGTT 58.552 52.381 0.00 0.00 0.00 4.44
1689 2533 2.424246 CTCTCAGTTACTCCCTCCGTTC 59.576 54.545 0.00 0.00 0.00 3.95
1690 2534 1.477295 CTCAGTTACTCCCTCCGTTCC 59.523 57.143 0.00 0.00 0.00 3.62
1691 2535 1.203087 TCAGTTACTCCCTCCGTTCCA 60.203 52.381 0.00 0.00 0.00 3.53
1692 2536 1.621814 CAGTTACTCCCTCCGTTCCAA 59.378 52.381 0.00 0.00 0.00 3.53
1693 2537 2.038033 CAGTTACTCCCTCCGTTCCAAA 59.962 50.000 0.00 0.00 0.00 3.28
1694 2538 2.910977 AGTTACTCCCTCCGTTCCAAAT 59.089 45.455 0.00 0.00 0.00 2.32
1695 2539 3.329814 AGTTACTCCCTCCGTTCCAAATT 59.670 43.478 0.00 0.00 0.00 1.82
1696 2540 4.533311 AGTTACTCCCTCCGTTCCAAATTA 59.467 41.667 0.00 0.00 0.00 1.40
1697 2541 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
1698 2542 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
1699 2543 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
1700 2544 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
1701 2545 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
1702 2546 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
1703 2547 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
1704 2548 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
1705 2549 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
1706 2550 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
1707 2551 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
1708 2552 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
1709 2553 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
1710 2554 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
1711 2555 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
1712 2556 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
1713 2557 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
1714 2558 6.365789 CCAAATTACTCGTCGTGGTTTTAGTA 59.634 38.462 0.00 0.00 0.00 1.82
1715 2559 6.934561 AATTACTCGTCGTGGTTTTAGTAC 57.065 37.500 0.00 0.00 0.00 2.73
1716 2560 3.988379 ACTCGTCGTGGTTTTAGTACA 57.012 42.857 0.00 0.00 0.00 2.90
1717 2561 4.305989 ACTCGTCGTGGTTTTAGTACAA 57.694 40.909 0.00 0.00 0.00 2.41
1718 2562 4.681744 ACTCGTCGTGGTTTTAGTACAAA 58.318 39.130 0.00 0.00 0.00 2.83
1719 2563 5.291971 ACTCGTCGTGGTTTTAGTACAAAT 58.708 37.500 0.00 0.00 0.00 2.32
1720 2564 5.754890 ACTCGTCGTGGTTTTAGTACAAATT 59.245 36.000 0.00 0.00 0.00 1.82
1721 2565 6.258507 ACTCGTCGTGGTTTTAGTACAAATTT 59.741 34.615 0.00 0.00 0.00 1.82
1722 2566 6.420588 TCGTCGTGGTTTTAGTACAAATTTG 58.579 36.000 16.67 16.67 0.00 2.32
1723 2567 6.257411 TCGTCGTGGTTTTAGTACAAATTTGA 59.743 34.615 24.64 5.76 0.00 2.69
1724 2568 6.906143 CGTCGTGGTTTTAGTACAAATTTGAA 59.094 34.615 24.64 5.59 0.00 2.69
1725 2569 7.097329 CGTCGTGGTTTTAGTACAAATTTGAAC 60.097 37.037 24.64 15.58 0.00 3.18
1726 2570 7.911727 GTCGTGGTTTTAGTACAAATTTGAACT 59.088 33.333 24.64 5.12 0.00 3.01
1727 2571 9.107177 TCGTGGTTTTAGTACAAATTTGAACTA 57.893 29.630 24.64 11.77 0.00 2.24
1728 2572 9.719279 CGTGGTTTTAGTACAAATTTGAACTAA 57.281 29.630 24.64 13.47 0.00 2.24
1735 2579 9.719279 TTAGTACAAATTTGAACTAAAACCACG 57.281 29.630 24.64 0.00 0.00 4.94
1736 2580 7.987649 AGTACAAATTTGAACTAAAACCACGA 58.012 30.769 24.64 0.00 0.00 4.35
1737 2581 7.911727 AGTACAAATTTGAACTAAAACCACGAC 59.088 33.333 24.64 0.00 0.00 4.34
1738 2582 5.740099 ACAAATTTGAACTAAAACCACGACG 59.260 36.000 24.64 0.00 0.00 5.12
1739 2583 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
1740 2584 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
1741 2585 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
1742 2586 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
1743 2587 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
1744 2588 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
1745 2589 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
1746 2590 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
1747 2591 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
1748 2592 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
1749 2593 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
1750 2594 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
1751 2595 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
1752 2596 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
1753 2597 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
1754 2598 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
1755 2599 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
1756 2600 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1757 2601 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1758 2602 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
1759 2603 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
1760 2604 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
1761 2605 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
1855 2726 0.091344 GTCGTTGCATGTTCGAGACG 59.909 55.000 8.66 0.00 34.33 4.18
1882 2757 1.971505 CTGGTCATTGGCCGCTCCTA 61.972 60.000 2.25 0.00 35.26 2.94
1884 2759 1.095807 GGTCATTGGCCGCTCCTAAC 61.096 60.000 0.00 0.00 35.26 2.34
1888 2767 0.255890 ATTGGCCGCTCCTAACACAT 59.744 50.000 0.00 0.00 35.26 3.21
1928 2828 2.026169 CCAGCCATGAGATCCATATGCT 60.026 50.000 0.00 11.35 40.83 3.79
2125 3074 7.262772 TGACAGACTATACGGGTTTTTCTATG 58.737 38.462 0.00 0.00 0.00 2.23
2155 3104 3.827302 TCTCGCTAACTAATCTCCATCCC 59.173 47.826 0.00 0.00 0.00 3.85
2156 3105 3.829601 CTCGCTAACTAATCTCCATCCCT 59.170 47.826 0.00 0.00 0.00 4.20
2185 3134 2.368329 GGGTATGGGCCCCTCACT 60.368 66.667 22.27 0.75 42.89 3.41
2228 3177 1.486726 ACCCAGCTAAGCATCCTGTAC 59.513 52.381 0.00 0.00 0.00 2.90
2275 3542 5.007039 CGTGTAGCATTGCTCAGATTACAAT 59.993 40.000 15.81 0.00 40.44 2.71
2378 3645 4.339748 TGGCTGTCAAATTAAGGCATGTA 58.660 39.130 0.00 0.00 41.08 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.135153 CTCACGACCTCCCAGGCG 62.135 72.222 0.00 5.26 39.63 5.52
19 20 4.459089 GCTCACGACCTCCCAGGC 62.459 72.222 0.00 0.00 39.63 4.85
20 21 2.681778 AGCTCACGACCTCCCAGG 60.682 66.667 0.00 0.00 42.49 4.45
21 22 2.888863 GAGCTCACGACCTCCCAG 59.111 66.667 9.40 0.00 0.00 4.45
22 23 3.062466 CGAGCTCACGACCTCCCA 61.062 66.667 15.40 0.00 35.09 4.37
23 24 2.750637 TCGAGCTCACGACCTCCC 60.751 66.667 15.40 0.00 37.37 4.30
24 25 2.766400 CCTCGAGCTCACGACCTCC 61.766 68.421 15.40 0.00 37.37 4.30
25 26 2.795297 CCTCGAGCTCACGACCTC 59.205 66.667 15.40 0.00 37.37 3.85
26 27 3.444805 GCCTCGAGCTCACGACCT 61.445 66.667 15.40 0.00 38.99 3.85
27 28 3.282745 TTGCCTCGAGCTCACGACC 62.283 63.158 15.40 0.00 44.23 4.79
28 29 2.089349 GTTGCCTCGAGCTCACGAC 61.089 63.158 15.40 6.13 44.23 4.34
29 30 2.258591 GTTGCCTCGAGCTCACGA 59.741 61.111 15.40 5.89 44.23 4.35
30 31 2.811317 GGTTGCCTCGAGCTCACG 60.811 66.667 15.40 0.69 44.23 4.35
31 32 2.435059 GGGTTGCCTCGAGCTCAC 60.435 66.667 15.40 2.59 44.23 3.51
32 33 3.706373 GGGGTTGCCTCGAGCTCA 61.706 66.667 15.40 4.08 44.23 4.26
39 40 2.686106 TCTACCCGGGGTTGCCTC 60.686 66.667 26.48 0.00 37.09 4.70
40 41 3.007323 GTCTACCCGGGGTTGCCT 61.007 66.667 26.48 4.52 37.09 4.75
41 42 4.105553 GGTCTACCCGGGGTTGCC 62.106 72.222 26.48 21.82 37.09 4.52
57 58 4.760047 CTCCGACAACCTGCCCGG 62.760 72.222 0.00 0.00 37.95 5.73
58 59 4.760047 CCTCCGACAACCTGCCCG 62.760 72.222 0.00 0.00 0.00 6.13
60 61 3.959991 GAGCCTCCGACAACCTGCC 62.960 68.421 0.00 0.00 0.00 4.85
61 62 2.435059 GAGCCTCCGACAACCTGC 60.435 66.667 0.00 0.00 0.00 4.85
62 63 2.266055 GGAGCCTCCGACAACCTG 59.734 66.667 0.00 0.00 0.00 4.00
99 100 1.572085 CTCCCAAGCTGCAAGTCGTG 61.572 60.000 1.02 0.00 35.30 4.35
100 101 1.302033 CTCCCAAGCTGCAAGTCGT 60.302 57.895 1.02 0.00 35.30 4.34
101 102 1.302033 ACTCCCAAGCTGCAAGTCG 60.302 57.895 1.02 0.00 35.30 4.18
102 103 0.536006 ACACTCCCAAGCTGCAAGTC 60.536 55.000 1.02 0.00 35.30 3.01
103 104 0.536006 GACACTCCCAAGCTGCAAGT 60.536 55.000 1.02 0.00 35.30 3.16
104 105 1.239968 GGACACTCCCAAGCTGCAAG 61.240 60.000 1.02 0.00 0.00 4.01
105 106 1.228245 GGACACTCCCAAGCTGCAA 60.228 57.895 1.02 0.00 0.00 4.08
106 107 2.149383 AGGACACTCCCAAGCTGCA 61.149 57.895 1.02 0.00 37.19 4.41
107 108 1.673665 CAGGACACTCCCAAGCTGC 60.674 63.158 0.00 0.00 37.19 5.25
108 109 1.002868 CCAGGACACTCCCAAGCTG 60.003 63.158 0.00 0.00 37.19 4.24
109 110 2.900106 GCCAGGACACTCCCAAGCT 61.900 63.158 0.00 0.00 37.19 3.74
110 111 2.360475 GCCAGGACACTCCCAAGC 60.360 66.667 0.00 0.00 37.19 4.01
111 112 1.002868 CTGCCAGGACACTCCCAAG 60.003 63.158 0.00 0.00 37.19 3.61
112 113 0.472925 TACTGCCAGGACACTCCCAA 60.473 55.000 0.00 0.00 37.19 4.12
113 114 0.904865 CTACTGCCAGGACACTCCCA 60.905 60.000 0.00 0.00 37.19 4.37
114 115 0.905337 ACTACTGCCAGGACACTCCC 60.905 60.000 0.00 0.00 37.19 4.30
115 116 0.533032 GACTACTGCCAGGACACTCC 59.467 60.000 0.00 0.00 36.58 3.85
116 117 0.171455 CGACTACTGCCAGGACACTC 59.829 60.000 0.00 0.00 0.00 3.51
117 118 1.251527 CCGACTACTGCCAGGACACT 61.252 60.000 0.00 0.00 0.00 3.55
118 119 1.215647 CCGACTACTGCCAGGACAC 59.784 63.158 0.00 0.00 0.00 3.67
119 120 2.646175 GCCGACTACTGCCAGGACA 61.646 63.158 0.00 0.00 0.00 4.02
120 121 2.184579 GCCGACTACTGCCAGGAC 59.815 66.667 0.00 0.00 0.00 3.85
121 122 3.449227 CGCCGACTACTGCCAGGA 61.449 66.667 0.00 0.00 0.00 3.86
122 123 3.449227 TCGCCGACTACTGCCAGG 61.449 66.667 0.00 0.00 0.00 4.45
123 124 2.202623 GTCGCCGACTACTGCCAG 60.203 66.667 10.56 0.00 0.00 4.85
124 125 3.755628 GGTCGCCGACTACTGCCA 61.756 66.667 17.76 0.00 32.47 4.92
125 126 3.450115 AGGTCGCCGACTACTGCC 61.450 66.667 17.76 0.00 32.47 4.85
126 127 2.202623 CAGGTCGCCGACTACTGC 60.203 66.667 17.76 0.00 32.47 4.40
127 128 1.994507 CTCCAGGTCGCCGACTACTG 61.995 65.000 17.76 15.71 32.47 2.74
128 129 1.749638 CTCCAGGTCGCCGACTACT 60.750 63.158 17.76 3.53 32.47 2.57
129 130 2.772691 CCTCCAGGTCGCCGACTAC 61.773 68.421 17.76 0.86 32.47 2.73
130 131 2.439701 CCTCCAGGTCGCCGACTA 60.440 66.667 17.76 0.00 32.47 2.59
131 132 4.361971 TCCTCCAGGTCGCCGACT 62.362 66.667 17.76 0.01 36.34 4.18
132 133 3.827898 CTCCTCCAGGTCGCCGAC 61.828 72.222 9.15 9.15 36.34 4.79
135 136 3.151022 CTCCTCCTCCAGGTCGCC 61.151 72.222 0.00 0.00 43.95 5.54
136 137 3.151022 CCTCCTCCTCCAGGTCGC 61.151 72.222 0.00 0.00 43.95 5.19
137 138 3.151022 GCCTCCTCCTCCAGGTCG 61.151 72.222 0.00 0.00 43.95 4.79
138 139 3.151022 CGCCTCCTCCTCCAGGTC 61.151 72.222 0.00 0.00 43.95 3.85
139 140 4.787280 CCGCCTCCTCCTCCAGGT 62.787 72.222 0.00 0.00 43.95 4.00
140 141 3.984186 TTCCGCCTCCTCCTCCAGG 62.984 68.421 0.00 0.00 45.15 4.45
141 142 2.364317 TTCCGCCTCCTCCTCCAG 60.364 66.667 0.00 0.00 0.00 3.86
142 143 2.364317 CTTCCGCCTCCTCCTCCA 60.364 66.667 0.00 0.00 0.00 3.86
143 144 3.157949 CCTTCCGCCTCCTCCTCC 61.158 72.222 0.00 0.00 0.00 4.30
144 145 2.042843 TCCTTCCGCCTCCTCCTC 60.043 66.667 0.00 0.00 0.00 3.71
145 146 2.042435 CTCCTTCCGCCTCCTCCT 60.042 66.667 0.00 0.00 0.00 3.69
146 147 3.157949 CCTCCTTCCGCCTCCTCC 61.158 72.222 0.00 0.00 0.00 4.30
147 148 2.042843 TCCTCCTTCCGCCTCCTC 60.043 66.667 0.00 0.00 0.00 3.71
148 149 2.042435 CTCCTCCTTCCGCCTCCT 60.042 66.667 0.00 0.00 0.00 3.69
149 150 3.855853 GCTCCTCCTTCCGCCTCC 61.856 72.222 0.00 0.00 0.00 4.30
150 151 4.214327 CGCTCCTCCTTCCGCCTC 62.214 72.222 0.00 0.00 0.00 4.70
153 154 3.140225 CTACCGCTCCTCCTTCCGC 62.140 68.421 0.00 0.00 0.00 5.54
154 155 3.121019 CTACCGCTCCTCCTTCCG 58.879 66.667 0.00 0.00 0.00 4.30
155 156 2.022240 CTGCTACCGCTCCTCCTTCC 62.022 65.000 0.00 0.00 36.97 3.46
156 157 1.439644 CTGCTACCGCTCCTCCTTC 59.560 63.158 0.00 0.00 36.97 3.46
157 158 2.060980 CCTGCTACCGCTCCTCCTT 61.061 63.158 0.00 0.00 36.97 3.36
158 159 2.443016 CCTGCTACCGCTCCTCCT 60.443 66.667 0.00 0.00 36.97 3.69
159 160 2.442272 TCCTGCTACCGCTCCTCC 60.442 66.667 0.00 0.00 36.97 4.30
160 161 2.809010 GTCCTGCTACCGCTCCTC 59.191 66.667 0.00 0.00 36.97 3.71
161 162 3.141488 CGTCCTGCTACCGCTCCT 61.141 66.667 0.00 0.00 36.97 3.69
162 163 3.450115 ACGTCCTGCTACCGCTCC 61.450 66.667 0.00 0.00 36.97 4.70
163 164 2.202623 CACGTCCTGCTACCGCTC 60.203 66.667 0.00 0.00 36.97 5.03
164 165 1.246056 TAACACGTCCTGCTACCGCT 61.246 55.000 0.00 0.00 36.97 5.52
165 166 0.801067 CTAACACGTCCTGCTACCGC 60.801 60.000 0.00 0.00 0.00 5.68
166 167 0.801067 GCTAACACGTCCTGCTACCG 60.801 60.000 0.00 0.00 0.00 4.02
167 168 0.245539 TGCTAACACGTCCTGCTACC 59.754 55.000 0.00 0.00 0.00 3.18
168 169 1.630148 CTGCTAACACGTCCTGCTAC 58.370 55.000 0.00 0.00 0.00 3.58
169 170 0.530744 CCTGCTAACACGTCCTGCTA 59.469 55.000 0.00 0.00 0.00 3.49
170 171 1.293498 CCTGCTAACACGTCCTGCT 59.707 57.895 0.00 0.00 0.00 4.24
171 172 1.004918 ACCTGCTAACACGTCCTGC 60.005 57.895 0.00 0.00 0.00 4.85
172 173 1.291877 GCACCTGCTAACACGTCCTG 61.292 60.000 0.00 0.00 38.21 3.86
173 174 1.004918 GCACCTGCTAACACGTCCT 60.005 57.895 0.00 0.00 38.21 3.85
174 175 1.291877 CTGCACCTGCTAACACGTCC 61.292 60.000 0.00 0.00 42.66 4.79
175 176 1.901650 GCTGCACCTGCTAACACGTC 61.902 60.000 0.00 0.00 42.66 4.34
176 177 1.961277 GCTGCACCTGCTAACACGT 60.961 57.895 0.00 0.00 42.66 4.49
177 178 1.630244 GAGCTGCACCTGCTAACACG 61.630 60.000 1.02 0.00 38.70 4.49
178 179 0.321122 AGAGCTGCACCTGCTAACAC 60.321 55.000 1.02 0.00 38.70 3.32
179 180 0.397941 AAGAGCTGCACCTGCTAACA 59.602 50.000 1.02 0.00 38.70 2.41
180 181 1.082690 GAAGAGCTGCACCTGCTAAC 58.917 55.000 1.02 0.00 38.70 2.34
181 182 0.979665 AGAAGAGCTGCACCTGCTAA 59.020 50.000 1.02 0.00 38.70 3.09
182 183 1.753649 CTAGAAGAGCTGCACCTGCTA 59.246 52.381 1.02 6.05 38.70 3.49
201 202 1.134371 GCCTAGAATCCAAGAACGCCT 60.134 52.381 0.00 0.00 0.00 5.52
248 251 8.697507 AAAGCCCATATTATAGAACTTCCAAG 57.302 34.615 0.00 0.00 0.00 3.61
266 273 0.467290 AACGAAAGCAGGAAAGCCCA 60.467 50.000 0.00 0.00 37.41 5.36
304 311 2.797866 TTCCGTGCTCTTCTCGTCGC 62.798 60.000 0.00 0.00 0.00 5.19
324 331 3.003763 GGTTCCCTCACCGGCTCT 61.004 66.667 0.00 0.00 0.00 4.09
526 534 0.740868 CGATGTACCCACTGTGGCAG 60.741 60.000 21.47 11.20 35.79 4.85
666 674 1.537202 CTTTTCCTTTGGACCTCTGCG 59.463 52.381 0.00 0.00 0.00 5.18
802 810 0.470833 ATAGCCTCATCCTCGCCACT 60.471 55.000 0.00 0.00 0.00 4.00
987 999 0.033920 CATACATAGGAGCTGCCGCA 59.966 55.000 0.00 0.00 43.43 5.69
1014 1026 0.251634 CTCCACCCTCTTCTTCCTGC 59.748 60.000 0.00 0.00 0.00 4.85
1015 1027 0.908198 CCTCCACCCTCTTCTTCCTG 59.092 60.000 0.00 0.00 0.00 3.86
1029 1041 1.997311 CATGCCCTCCAGTCCTCCA 60.997 63.158 0.00 0.00 0.00 3.86
1030 1042 2.914289 CATGCCCTCCAGTCCTCC 59.086 66.667 0.00 0.00 0.00 4.30
1031 1043 2.191641 GCATGCCCTCCAGTCCTC 59.808 66.667 6.36 0.00 0.00 3.71
1032 1044 3.415087 GGCATGCCCTCCAGTCCT 61.415 66.667 27.24 0.00 0.00 3.85
1211 1225 3.691049 AGATGTCCACAAAAACACACG 57.309 42.857 0.00 0.00 0.00 4.49
1256 1274 1.296727 TCATGTAGTCGATCGCGTCT 58.703 50.000 11.09 10.92 39.19 4.18
1367 2166 2.582636 GGGGATGTTCCTGGCCATATAT 59.417 50.000 5.51 0.00 36.57 0.86
1368 2167 1.992557 GGGGATGTTCCTGGCCATATA 59.007 52.381 5.51 0.00 36.57 0.86
1389 2188 5.353123 CCTAGTCGCCTAGATTACTCATCTC 59.647 48.000 1.17 0.00 42.90 2.75
1411 2211 1.593787 CTGACGACAGTGGATGCCT 59.406 57.895 6.73 0.00 39.11 4.75
1660 2504 2.333014 GAGTAACTGAGAGCACTGCAC 58.667 52.381 3.30 0.00 0.00 4.57
1661 2505 1.273606 GGAGTAACTGAGAGCACTGCA 59.726 52.381 3.30 0.00 30.56 4.41
1678 2522 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
1679 2523 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
1680 2524 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1681 2525 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1682 2526 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
1683 2527 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
1684 2528 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
1685 2529 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
1686 2530 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
1687 2531 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
1688 2532 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
1689 2533 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
1690 2534 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
1691 2535 6.922957 TGTACTAAAACCACGACGAGTAATTT 59.077 34.615 0.00 0.34 0.00 1.82
1692 2536 6.446318 TGTACTAAAACCACGACGAGTAATT 58.554 36.000 0.00 1.08 0.00 1.40
1693 2537 6.012658 TGTACTAAAACCACGACGAGTAAT 57.987 37.500 0.00 0.00 0.00 1.89
1694 2538 5.431420 TGTACTAAAACCACGACGAGTAA 57.569 39.130 0.00 0.00 0.00 2.24
1695 2539 5.431420 TTGTACTAAAACCACGACGAGTA 57.569 39.130 0.00 0.00 0.00 2.59
1696 2540 3.988379 TGTACTAAAACCACGACGAGT 57.012 42.857 0.00 0.00 0.00 4.18
1697 2541 5.834239 ATTTGTACTAAAACCACGACGAG 57.166 39.130 0.00 0.00 0.00 4.18
1698 2542 6.257411 TCAAATTTGTACTAAAACCACGACGA 59.743 34.615 17.47 0.00 0.00 4.20
1699 2543 6.420588 TCAAATTTGTACTAAAACCACGACG 58.579 36.000 17.47 0.00 0.00 5.12
1700 2544 7.911727 AGTTCAAATTTGTACTAAAACCACGAC 59.088 33.333 24.00 0.00 37.09 4.34
1701 2545 7.987649 AGTTCAAATTTGTACTAAAACCACGA 58.012 30.769 24.00 0.00 37.09 4.35
1702 2546 9.719279 TTAGTTCAAATTTGTACTAAAACCACG 57.281 29.630 31.64 2.88 43.40 4.94
1709 2553 9.719279 CGTGGTTTTAGTTCAAATTTGTACTAA 57.281 29.630 30.79 30.79 44.11 2.24
1710 2554 9.107177 TCGTGGTTTTAGTTCAAATTTGTACTA 57.893 29.630 25.23 25.23 39.18 1.82
1711 2555 7.911727 GTCGTGGTTTTAGTTCAAATTTGTACT 59.088 33.333 26.92 26.92 40.98 2.73
1712 2556 7.097329 CGTCGTGGTTTTAGTTCAAATTTGTAC 60.097 37.037 17.43 17.43 0.00 2.90
1713 2557 6.906143 CGTCGTGGTTTTAGTTCAAATTTGTA 59.094 34.615 17.47 5.71 0.00 2.41
1714 2558 5.740099 CGTCGTGGTTTTAGTTCAAATTTGT 59.260 36.000 17.47 1.67 0.00 2.83
1715 2559 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
1716 2560 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
1717 2561 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
1718 2562 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
1719 2563 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
1720 2564 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
1721 2565 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
1722 2566 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
1723 2567 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
1724 2568 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
1725 2569 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
1726 2570 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
1727 2571 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
1728 2572 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
1729 2573 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
1730 2574 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
1731 2575 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
1732 2576 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
1733 2577 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
1734 2578 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
1735 2579 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
1736 2580 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
1737 2581 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
1738 2582 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
1739 2583 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
1740 2584 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
1741 2585 4.098894 ACTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
1742 2586 2.910977 ACTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
1743 2587 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
1744 2588 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
1745 2589 2.905415 TACTACTCCCTCCGTTCCAA 57.095 50.000 0.00 0.00 0.00 3.53
1746 2590 2.905415 TTACTACTCCCTCCGTTCCA 57.095 50.000 0.00 0.00 0.00 3.53
1747 2591 4.750021 AAATTACTACTCCCTCCGTTCC 57.250 45.455 0.00 0.00 0.00 3.62
1748 2592 7.201470 CGTTTTAAATTACTACTCCCTCCGTTC 60.201 40.741 0.00 0.00 0.00 3.95
1749 2593 6.591448 CGTTTTAAATTACTACTCCCTCCGTT 59.409 38.462 0.00 0.00 0.00 4.44
1750 2594 6.101997 CGTTTTAAATTACTACTCCCTCCGT 58.898 40.000 0.00 0.00 0.00 4.69
1751 2595 6.101997 ACGTTTTAAATTACTACTCCCTCCG 58.898 40.000 0.00 0.00 0.00 4.63
1752 2596 8.034804 TGTACGTTTTAAATTACTACTCCCTCC 58.965 37.037 0.00 0.00 0.00 4.30
1753 2597 8.864024 GTGTACGTTTTAAATTACTACTCCCTC 58.136 37.037 0.00 0.00 0.00 4.30
1754 2598 8.367156 TGTGTACGTTTTAAATTACTACTCCCT 58.633 33.333 0.00 0.00 0.00 4.20
1755 2599 8.435430 GTGTGTACGTTTTAAATTACTACTCCC 58.565 37.037 0.00 0.00 0.00 4.30
1756 2600 9.196552 AGTGTGTACGTTTTAAATTACTACTCC 57.803 33.333 0.00 0.00 0.00 3.85
1758 2602 9.748708 TGAGTGTGTACGTTTTAAATTACTACT 57.251 29.630 0.00 1.85 0.00 2.57
1761 2605 9.872757 CATTGAGTGTGTACGTTTTAAATTACT 57.127 29.630 0.00 0.00 0.00 2.24
1833 2704 1.078709 CTCGAACATGCAACGACCAT 58.921 50.000 0.00 0.00 32.72 3.55
1855 2726 1.221414 GCCAATGACCAGAGATACGC 58.779 55.000 0.00 0.00 0.00 4.42
1882 2757 7.495934 GGCACTTCACTACTCATTATATGTGTT 59.504 37.037 0.00 0.00 37.98 3.32
1884 2759 6.986231 TGGCACTTCACTACTCATTATATGTG 59.014 38.462 0.00 0.00 0.00 3.21
1888 2767 5.453339 GGCTGGCACTTCACTACTCATTATA 60.453 44.000 0.00 0.00 0.00 0.98
1928 2828 4.061596 TGTGTGTAAGAATTGCATCGTCA 58.938 39.130 0.00 0.00 44.07 4.35
2100 3049 5.733620 AGAAAAACCCGTATAGTCTGTCA 57.266 39.130 0.00 0.00 0.00 3.58
2105 3054 6.165700 TCCCATAGAAAAACCCGTATAGTC 57.834 41.667 0.00 0.00 0.00 2.59
2125 3074 6.091718 AGATTAGTTAGCGAGAAGAATCCC 57.908 41.667 0.00 0.00 0.00 3.85
2155 3104 3.633986 GCCCATACCCTTGAAAATCAGAG 59.366 47.826 0.00 0.00 0.00 3.35
2156 3105 3.627237 GGCCCATACCCTTGAAAATCAGA 60.627 47.826 0.00 0.00 0.00 3.27
2228 3177 4.798387 GCACGGGCAGATTTTTACTAAATG 59.202 41.667 3.77 0.00 40.72 2.32
2275 3542 8.236643 AGACCCTTGGGTATGTGTATAACTATA 58.763 37.037 11.86 0.00 0.00 1.31
2387 3654 6.391227 TTTCCACTGATTTTGAAGAGAACC 57.609 37.500 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.