Multiple sequence alignment - TraesCS7B01G432100

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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 TraesCS7B01G432100 chr7B 100.000 2624 0 0 1 2624 700183178 700185801 0.000000e+00 4846.0
1 TraesCS7B01G432100 chr7B 79.439 214 32 11 1000 1207 43754611 43754404 9.790000e-30 141.0
2 TraesCS7B01G432100 chr7B 87.671 73 6 1 561 630 618521439 618521511 6.020000e-12 82.4
3 TraesCS7B01G432100 chr7D 84.718 2022 130 70 160 2068 611134827 611136782 0.000000e+00 1857.0
4 TraesCS7B01G432100 chr7D 77.871 479 87 12 2152 2622 611136862 611137329 1.990000e-71 279.0
5 TraesCS7B01G432100 chr7D 87.565 193 14 6 158 348 581657895 581658079 5.690000e-52 215.0
6 TraesCS7B01G432100 chr7D 87.568 185 12 7 158 339 581623432 581623608 1.230000e-48 204.0
7 TraesCS7B01G432100 chr7D 80.000 215 29 13 1000 1207 91143767 91143560 2.100000e-31 147.0
8 TraesCS7B01G432100 chr7A 86.728 1424 68 42 506 1850 701148934 701150315 0.000000e+00 1471.0
9 TraesCS7B01G432100 chr7A 86.062 739 49 29 1919 2622 701150539 701151258 0.000000e+00 745.0
10 TraesCS7B01G432100 chr7A 89.744 195 13 2 158 351 701126214 701126402 2.610000e-60 243.0
11 TraesCS7B01G432100 chr7A 91.509 106 7 2 49 153 1319513 1319617 7.570000e-31 145.0
12 TraesCS7B01G432100 chr7A 79.439 214 32 11 1000 1207 93081905 93082112 9.790000e-30 141.0
13 TraesCS7B01G432100 chr7A 87.395 119 7 4 517 635 701126541 701126651 2.120000e-26 130.0
14 TraesCS7B01G432100 chr7A 83.962 106 14 3 49 152 711848344 711848448 5.980000e-17 99.0
15 TraesCS7B01G432100 chr2B 89.119 193 11 7 158 348 779962969 779963153 5.650000e-57 231.0
16 TraesCS7B01G432100 chr2B 81.967 183 25 8 1001 1179 744058437 744058259 5.850000e-32 148.0
17 TraesCS7B01G432100 chr2B 87.671 73 6 1 561 630 770206150 770206078 6.020000e-12 82.4
18 TraesCS7B01G432100 chr6D 88.601 193 13 3 158 348 450542995 450542810 2.630000e-55 226.0
19 TraesCS7B01G432100 chr6D 87.374 198 14 7 153 348 58715850 58715662 1.580000e-52 217.0
20 TraesCS7B01G432100 chr6A 88.205 195 13 4 156 348 308850797 308850611 9.450000e-55 224.0
21 TraesCS7B01G432100 chr6A 85.849 106 12 3 49 154 583795399 583795501 2.760000e-20 110.0
22 TraesCS7B01G432100 chr5A 88.083 193 13 4 158 348 501461815 501461999 1.220000e-53 220.0
23 TraesCS7B01G432100 chr5A 89.041 73 5 2 561 630 101310824 101310752 1.290000e-13 87.9
24 TraesCS7B01G432100 chr5D 88.827 179 10 6 172 348 121680676 121680506 7.360000e-51 211.0
25 TraesCS7B01G432100 chr5D 84.762 105 14 2 49 152 475504591 475504488 1.280000e-18 104.0
26 TraesCS7B01G432100 chr4A 88.742 151 8 4 200 348 554405402 554405259 2.680000e-40 176.0
27 TraesCS7B01G432100 chr2D 82.320 181 28 4 1001 1179 609515761 609515583 1.260000e-33 154.0
28 TraesCS7B01G432100 chr2A 82.320 181 28 4 1001 1179 742293582 742293404 1.260000e-33 154.0
29 TraesCS7B01G432100 chr2A 91.000 100 7 2 49 148 170479257 170479354 1.640000e-27 134.0
30 TraesCS7B01G432100 chr2A 86.735 98 12 1 57 153 114498511 114498414 9.930000e-20 108.0
31 TraesCS7B01G432100 chr4D 86.792 106 12 2 49 153 401372965 401373069 1.650000e-22 117.0
32 TraesCS7B01G432100 chr1A 88.000 100 11 1 57 155 4384248 4384149 1.650000e-22 117.0
33 TraesCS7B01G432100 chr3A 87.629 97 11 1 57 152 697443767 697443671 7.680000e-21 111.0
34 TraesCS7B01G432100 chr3A 89.041 73 5 2 561 630 631789641 631789713 1.290000e-13 87.9
35 TraesCS7B01G432100 chr3B 89.041 73 5 1 561 630 130451116 130451188 1.290000e-13 87.9
36 TraesCS7B01G432100 chr3D 87.671 73 6 1 561 630 216611428 216611356 6.020000e-12 82.4


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 TraesCS7B01G432100 chr7B 700183178 700185801 2623 False 4846 4846 100.0000 1 2624 1 chr7B.!!$F2 2623
1 TraesCS7B01G432100 chr7D 611134827 611137329 2502 False 1068 1857 81.2945 160 2622 2 chr7D.!!$F3 2462
2 TraesCS7B01G432100 chr7A 701148934 701151258 2324 False 1108 1471 86.3950 506 2622 2 chr7A.!!$F5 2116

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
152 153 0.03601 ATGCTCATATACGGCCCTGC 60.036 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 1775 0.041684 AGGGGGCAAAGAGGAAATGG 59.958 55.0 0.0 0.0 0.0 3.16 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
39 40 2.398252 GGGGGTTACACTAGTTCAGC 57.602 55.000 0.00 0.00 0.00 4.26
40 41 1.626825 GGGGGTTACACTAGTTCAGCA 59.373 52.381 0.00 0.00 0.00 4.41
41 42 2.039348 GGGGGTTACACTAGTTCAGCAA 59.961 50.000 0.00 0.00 0.00 3.91
42 43 3.497227 GGGGGTTACACTAGTTCAGCAAA 60.497 47.826 0.00 0.00 0.00 3.68
43 44 3.751698 GGGGTTACACTAGTTCAGCAAAG 59.248 47.826 0.00 0.00 0.00 2.77
44 45 3.188667 GGGTTACACTAGTTCAGCAAAGC 59.811 47.826 0.00 0.00 0.00 3.51
45 46 3.120649 GGTTACACTAGTTCAGCAAAGCG 60.121 47.826 0.00 0.00 0.00 4.68
46 47 2.526304 ACACTAGTTCAGCAAAGCGA 57.474 45.000 0.00 0.00 0.00 4.93
47 48 2.135933 ACACTAGTTCAGCAAAGCGAC 58.864 47.619 0.00 0.00 0.00 5.19
48 49 1.461127 CACTAGTTCAGCAAAGCGACC 59.539 52.381 0.00 0.00 0.00 4.79
49 50 1.079503 CTAGTTCAGCAAAGCGACCC 58.920 55.000 0.00 0.00 0.00 4.46
50 51 0.685097 TAGTTCAGCAAAGCGACCCT 59.315 50.000 0.00 0.00 0.00 4.34
51 52 0.685097 AGTTCAGCAAAGCGACCCTA 59.315 50.000 0.00 0.00 0.00 3.53
52 53 1.071699 AGTTCAGCAAAGCGACCCTAA 59.928 47.619 0.00 0.00 0.00 2.69
53 54 2.084546 GTTCAGCAAAGCGACCCTAAT 58.915 47.619 0.00 0.00 0.00 1.73
54 55 1.737838 TCAGCAAAGCGACCCTAATG 58.262 50.000 0.00 0.00 0.00 1.90
55 56 0.099436 CAGCAAAGCGACCCTAATGC 59.901 55.000 0.00 0.00 37.00 3.56
56 57 1.062525 GCAAAGCGACCCTAATGCG 59.937 57.895 0.00 0.00 30.14 4.73
57 58 1.644786 GCAAAGCGACCCTAATGCGT 61.645 55.000 0.00 0.00 30.14 5.24
58 59 0.802494 CAAAGCGACCCTAATGCGTT 59.198 50.000 0.00 0.00 0.00 4.84
59 60 1.084289 AAAGCGACCCTAATGCGTTC 58.916 50.000 0.00 0.00 0.00 3.95
60 61 0.036765 AAGCGACCCTAATGCGTTCA 60.037 50.000 0.00 0.00 0.00 3.18
61 62 0.036765 AGCGACCCTAATGCGTTCAA 60.037 50.000 0.00 0.00 0.00 2.69
62 63 1.014352 GCGACCCTAATGCGTTCAAT 58.986 50.000 0.00 0.00 0.00 2.57
63 64 1.400494 GCGACCCTAATGCGTTCAATT 59.600 47.619 0.00 0.00 0.00 2.32
64 65 2.610374 GCGACCCTAATGCGTTCAATTA 59.390 45.455 0.00 0.00 0.00 1.40
65 66 3.064271 GCGACCCTAATGCGTTCAATTAA 59.936 43.478 0.00 0.00 0.00 1.40
66 67 4.584394 CGACCCTAATGCGTTCAATTAAC 58.416 43.478 0.00 0.00 34.52 2.01
67 68 4.093703 CGACCCTAATGCGTTCAATTAACA 59.906 41.667 0.00 0.00 38.03 2.41
68 69 5.305139 ACCCTAATGCGTTCAATTAACAC 57.695 39.130 0.00 0.00 38.03 3.32
69 70 4.157105 ACCCTAATGCGTTCAATTAACACC 59.843 41.667 0.00 0.00 38.03 4.16
70 71 4.398044 CCCTAATGCGTTCAATTAACACCT 59.602 41.667 0.00 0.00 38.03 4.00
71 72 5.105917 CCCTAATGCGTTCAATTAACACCTT 60.106 40.000 0.00 0.00 38.03 3.50
72 73 5.799936 CCTAATGCGTTCAATTAACACCTTG 59.200 40.000 0.00 0.00 38.03 3.61
73 74 5.446143 AATGCGTTCAATTAACACCTTGA 57.554 34.783 0.00 0.00 38.03 3.02
74 75 5.643379 ATGCGTTCAATTAACACCTTGAT 57.357 34.783 0.00 0.00 38.03 2.57
75 76 5.446143 TGCGTTCAATTAACACCTTGATT 57.554 34.783 0.00 0.00 38.03 2.57
76 77 6.561737 TGCGTTCAATTAACACCTTGATTA 57.438 33.333 0.00 0.00 38.03 1.75
77 78 6.971602 TGCGTTCAATTAACACCTTGATTAA 58.028 32.000 0.00 0.00 38.03 1.40
78 79 6.858993 TGCGTTCAATTAACACCTTGATTAAC 59.141 34.615 0.00 0.00 38.03 2.01
79 80 6.858993 GCGTTCAATTAACACCTTGATTAACA 59.141 34.615 0.00 0.00 38.03 2.41
80 81 7.380065 GCGTTCAATTAACACCTTGATTAACAA 59.620 33.333 0.00 0.00 38.03 2.83
81 82 9.239002 CGTTCAATTAACACCTTGATTAACAAA 57.761 29.630 0.00 0.00 38.03 2.83
89 90 7.239763 ACACCTTGATTAACAAAAATAGGGG 57.760 36.000 0.00 0.00 38.08 4.79
90 91 6.212589 ACACCTTGATTAACAAAAATAGGGGG 59.787 38.462 0.00 0.00 38.08 5.40
104 105 2.996734 GGGGGCATGTGGTGTTGG 60.997 66.667 0.00 0.00 0.00 3.77
105 106 2.996734 GGGGCATGTGGTGTTGGG 60.997 66.667 0.00 0.00 0.00 4.12
106 107 2.996734 GGGCATGTGGTGTTGGGG 60.997 66.667 0.00 0.00 0.00 4.96
107 108 2.996734 GGCATGTGGTGTTGGGGG 60.997 66.667 0.00 0.00 0.00 5.40
108 109 2.203625 GCATGTGGTGTTGGGGGT 60.204 61.111 0.00 0.00 0.00 4.95
109 110 2.275380 GCATGTGGTGTTGGGGGTC 61.275 63.158 0.00 0.00 0.00 4.46
110 111 1.606313 CATGTGGTGTTGGGGGTCC 60.606 63.158 0.00 0.00 0.00 4.46
111 112 3.204467 ATGTGGTGTTGGGGGTCCG 62.204 63.158 0.00 0.00 35.24 4.79
112 113 4.653888 GTGGTGTTGGGGGTCCGG 62.654 72.222 0.00 0.00 35.24 5.14
114 115 3.893399 GGTGTTGGGGGTCCGGTT 61.893 66.667 0.00 0.00 35.24 4.44
115 116 2.281970 GTGTTGGGGGTCCGGTTC 60.282 66.667 0.00 0.00 35.24 3.62
116 117 3.943691 TGTTGGGGGTCCGGTTCG 61.944 66.667 0.00 0.00 35.24 3.95
126 127 4.796231 CCGGTTCGGTCGCTCCTG 62.796 72.222 0.00 0.00 42.73 3.86
127 128 4.052229 CGGTTCGGTCGCTCCTGT 62.052 66.667 0.00 0.00 0.00 4.00
128 129 2.342648 GGTTCGGTCGCTCCTGTT 59.657 61.111 0.00 0.00 0.00 3.16
129 130 2.027625 GGTTCGGTCGCTCCTGTTG 61.028 63.158 0.00 0.00 0.00 3.33
130 131 2.357034 TTCGGTCGCTCCTGTTGC 60.357 61.111 0.00 0.00 0.00 4.17
131 132 3.158537 TTCGGTCGCTCCTGTTGCA 62.159 57.895 0.00 0.00 0.00 4.08
132 133 3.414700 CGGTCGCTCCTGTTGCAC 61.415 66.667 0.00 0.00 0.00 4.57
133 134 2.280797 GGTCGCTCCTGTTGCACA 60.281 61.111 0.00 0.00 0.00 4.57
134 135 1.672356 GGTCGCTCCTGTTGCACAT 60.672 57.895 0.00 0.00 0.00 3.21
135 136 1.499056 GTCGCTCCTGTTGCACATG 59.501 57.895 0.00 0.00 0.00 3.21
136 137 2.177531 CGCTCCTGTTGCACATGC 59.822 61.111 0.00 0.00 42.50 4.06
137 138 2.330372 CGCTCCTGTTGCACATGCT 61.330 57.895 5.31 0.00 42.66 3.79
138 139 1.505353 GCTCCTGTTGCACATGCTC 59.495 57.895 5.31 0.00 42.66 4.26
139 140 1.239296 GCTCCTGTTGCACATGCTCA 61.239 55.000 5.31 4.11 42.66 4.26
140 141 1.460504 CTCCTGTTGCACATGCTCAT 58.539 50.000 5.31 0.00 42.66 2.90
141 142 2.635714 CTCCTGTTGCACATGCTCATA 58.364 47.619 5.31 0.00 42.66 2.15
142 143 3.211865 CTCCTGTTGCACATGCTCATAT 58.788 45.455 5.31 0.00 42.66 1.78
143 144 4.383173 CTCCTGTTGCACATGCTCATATA 58.617 43.478 5.31 0.00 42.66 0.86
144 145 4.129380 TCCTGTTGCACATGCTCATATAC 58.871 43.478 5.31 0.00 42.66 1.47
145 146 3.059393 CCTGTTGCACATGCTCATATACG 60.059 47.826 5.31 0.00 42.66 3.06
146 147 2.871633 TGTTGCACATGCTCATATACGG 59.128 45.455 5.31 0.00 42.66 4.02
147 148 1.511850 TGCACATGCTCATATACGGC 58.488 50.000 5.31 0.00 42.66 5.68
148 149 0.798776 GCACATGCTCATATACGGCC 59.201 55.000 0.00 0.00 38.21 6.13
149 150 1.442769 CACATGCTCATATACGGCCC 58.557 55.000 0.00 0.00 0.00 5.80
150 151 1.002430 CACATGCTCATATACGGCCCT 59.998 52.381 0.00 0.00 0.00 5.19
151 152 1.002430 ACATGCTCATATACGGCCCTG 59.998 52.381 0.00 0.00 0.00 4.45
152 153 0.036010 ATGCTCATATACGGCCCTGC 60.036 55.000 0.00 0.00 0.00 4.85
153 154 1.121407 TGCTCATATACGGCCCTGCT 61.121 55.000 0.00 0.00 0.00 4.24
154 155 0.895530 GCTCATATACGGCCCTGCTA 59.104 55.000 0.00 0.00 0.00 3.49
155 156 1.134965 GCTCATATACGGCCCTGCTAG 60.135 57.143 0.00 0.00 0.00 3.42
156 157 1.478510 CTCATATACGGCCCTGCTAGG 59.521 57.143 0.00 0.00 34.30 3.02
168 169 0.472734 CTGCTAGGGGCTACCATCCT 60.473 60.000 0.00 0.00 43.89 3.24
169 170 0.764369 TGCTAGGGGCTACCATCCTG 60.764 60.000 0.00 0.00 43.89 3.86
171 172 1.482553 GCTAGGGGCTACCATCCTGTA 60.483 57.143 0.00 0.00 43.89 2.74
172 173 2.972348 CTAGGGGCTACCATCCTGTAA 58.028 52.381 0.97 0.00 43.89 2.41
175 176 2.509964 AGGGGCTACCATCCTGTAAAAG 59.490 50.000 0.97 0.00 43.89 2.27
183 184 6.127980 GCTACCATCCTGTAAAAGAAAGTTCC 60.128 42.308 0.00 0.00 0.00 3.62
202 203 8.661352 AAGTTCCTATAGTAAGACGAGACTAC 57.339 38.462 0.00 0.00 31.15 2.73
252 253 1.939838 GCTCACTCAACTACCAACCCG 60.940 57.143 0.00 0.00 0.00 5.28
254 255 2.233922 CTCACTCAACTACCAACCCGAT 59.766 50.000 0.00 0.00 0.00 4.18
300 301 0.107654 CCGACCCCTGAACCTGAATC 60.108 60.000 0.00 0.00 0.00 2.52
319 320 0.242825 CATGAAAGGCCAGCACACTG 59.757 55.000 5.01 0.00 44.05 3.66
344 345 3.877508 AGTGCTCACTTGACTTAACAACC 59.122 43.478 0.00 0.00 38.83 3.77
345 346 3.003378 GTGCTCACTTGACTTAACAACCC 59.997 47.826 0.00 0.00 0.00 4.11
346 347 3.211045 GCTCACTTGACTTAACAACCCA 58.789 45.455 0.00 0.00 0.00 4.51
347 348 3.821033 GCTCACTTGACTTAACAACCCAT 59.179 43.478 0.00 0.00 0.00 4.00
348 349 4.083271 GCTCACTTGACTTAACAACCCATC 60.083 45.833 0.00 0.00 0.00 3.51
349 350 5.042463 TCACTTGACTTAACAACCCATCA 57.958 39.130 0.00 0.00 0.00 3.07
360 361 0.899717 AACCCATCACCCATGCACAC 60.900 55.000 0.00 0.00 0.00 3.82
365 366 3.376078 CACCCATGCACACCTGCC 61.376 66.667 0.00 0.00 43.51 4.85
372 373 2.025898 CATGCACACCTGCCATGATAA 58.974 47.619 0.00 0.00 43.51 1.75
414 415 2.438975 CGGGCATGCATGTGAGGT 60.439 61.111 26.79 0.00 0.00 3.85
417 418 2.493030 GCATGCATGTGAGGTGCC 59.507 61.111 26.79 4.79 41.83 5.01
437 438 4.820744 GCCCGGCATCCACACCAT 62.821 66.667 3.91 0.00 0.00 3.55
438 439 2.829914 CCCGGCATCCACACCATG 60.830 66.667 0.00 0.00 0.00 3.66
439 440 2.271821 CCGGCATCCACACCATGA 59.728 61.111 0.00 0.00 0.00 3.07
440 441 2.114670 CCGGCATCCACACCATGAC 61.115 63.158 0.00 0.00 0.00 3.06
441 442 1.377072 CGGCATCCACACCATGACA 60.377 57.895 0.00 0.00 0.00 3.58
479 480 0.179124 GCCTCAGATCGTCCTGACAC 60.179 60.000 5.62 0.00 38.18 3.67
483 484 1.819288 TCAGATCGTCCTGACACCTTC 59.181 52.381 5.62 0.00 38.18 3.46
498 499 2.558359 CACCTTCGCATTTCTTTTCCCT 59.442 45.455 0.00 0.00 0.00 4.20
499 500 2.820197 ACCTTCGCATTTCTTTTCCCTC 59.180 45.455 0.00 0.00 0.00 4.30
500 501 3.084786 CCTTCGCATTTCTTTTCCCTCT 58.915 45.455 0.00 0.00 0.00 3.69
502 503 2.711542 TCGCATTTCTTTTCCCTCTCC 58.288 47.619 0.00 0.00 0.00 3.71
504 505 2.103373 GCATTTCTTTTCCCTCTCCCC 58.897 52.381 0.00 0.00 0.00 4.81
505 506 2.557452 GCATTTCTTTTCCCTCTCCCCA 60.557 50.000 0.00 0.00 0.00 4.96
540 541 1.508632 GCCTGCACTTTTGTCTCGTA 58.491 50.000 0.00 0.00 0.00 3.43
549 550 3.921021 ACTTTTGTCTCGTAGATTCGCTG 59.079 43.478 0.00 0.00 33.89 5.18
550 551 1.909376 TTGTCTCGTAGATTCGCTGC 58.091 50.000 0.00 0.00 33.89 5.25
551 552 1.095600 TGTCTCGTAGATTCGCTGCT 58.904 50.000 0.00 0.00 33.89 4.24
552 553 1.202188 TGTCTCGTAGATTCGCTGCTG 60.202 52.381 0.00 0.00 33.89 4.41
599 601 0.733150 TACGTCGTGCTGGATCTCAG 59.267 55.000 8.47 6.79 46.03 3.35
630 632 1.759445 AGATCCATCGCTTGTACTGCT 59.241 47.619 9.12 0.00 0.00 4.24
643 645 0.325296 TACTGCTTCCACGGGATCCT 60.325 55.000 12.58 0.00 0.00 3.24
672 682 8.026607 CCCCATAAAAACATACTGTAACACTTG 58.973 37.037 0.00 0.00 0.00 3.16
680 690 9.998106 AAACATACTGTAACACTTGAAGATACT 57.002 29.630 0.00 0.00 0.00 2.12
752 773 3.215244 CAACTAATGTGTCACGCGTTTC 58.785 45.455 10.22 6.21 0.00 2.78
753 774 1.454276 ACTAATGTGTCACGCGTTTCG 59.546 47.619 10.22 0.00 45.38 3.46
823 850 2.906897 AGCCGTGCAACCAACTGG 60.907 61.111 0.00 0.00 42.17 4.00
824 851 2.904866 GCCGTGCAACCAACTGGA 60.905 61.111 1.86 0.00 38.94 3.86
827 854 1.172180 CCGTGCAACCAACTGGATGT 61.172 55.000 1.86 0.00 39.81 3.06
870 919 1.009078 CCACACGCACGAATCATGAT 58.991 50.000 1.18 1.18 0.00 2.45
874 923 3.737774 CACACGCACGAATCATGATCTAT 59.262 43.478 9.06 0.00 0.00 1.98
902 955 3.249917 GCTTACAAGTGAGAGTGAGAGC 58.750 50.000 0.00 0.00 0.00 4.09
907 960 4.339748 ACAAGTGAGAGTGAGAGCAGATA 58.660 43.478 0.00 0.00 0.00 1.98
914 967 3.320541 AGAGTGAGAGCAGATAATTCGGG 59.679 47.826 0.00 0.00 0.00 5.14
958 1038 3.646637 GAGGAGAGAGGTCTAGCTAGAGT 59.353 52.174 23.87 14.06 30.97 3.24
964 1044 4.037927 AGAGGTCTAGCTAGAGTGAGAGT 58.962 47.826 23.87 3.68 32.01 3.24
970 1050 4.714802 TCTAGCTAGAGTGAGAGTGAGAGT 59.285 45.833 19.72 0.00 0.00 3.24
982 1062 3.198635 AGAGTGAGAGTGAGAGAGAGAGG 59.801 52.174 0.00 0.00 0.00 3.69
983 1063 2.239654 AGTGAGAGTGAGAGAGAGAGGG 59.760 54.545 0.00 0.00 0.00 4.30
984 1064 2.026262 GTGAGAGTGAGAGAGAGAGGGT 60.026 54.545 0.00 0.00 0.00 4.34
985 1065 2.026356 TGAGAGTGAGAGAGAGAGGGTG 60.026 54.545 0.00 0.00 0.00 4.61
986 1066 1.992557 AGAGTGAGAGAGAGAGGGTGT 59.007 52.381 0.00 0.00 0.00 4.16
987 1067 2.091541 GAGTGAGAGAGAGAGGGTGTG 58.908 57.143 0.00 0.00 0.00 3.82
988 1068 1.427368 AGTGAGAGAGAGAGGGTGTGT 59.573 52.381 0.00 0.00 0.00 3.72
989 1069 1.543802 GTGAGAGAGAGAGGGTGTGTG 59.456 57.143 0.00 0.00 0.00 3.82
990 1070 1.145945 TGAGAGAGAGAGGGTGTGTGT 59.854 52.381 0.00 0.00 0.00 3.72
991 1071 1.543802 GAGAGAGAGAGGGTGTGTGTG 59.456 57.143 0.00 0.00 0.00 3.82
992 1072 0.037790 GAGAGAGAGGGTGTGTGTGC 60.038 60.000 0.00 0.00 0.00 4.57
993 1073 0.470833 AGAGAGAGGGTGTGTGTGCT 60.471 55.000 0.00 0.00 0.00 4.40
994 1074 0.394565 GAGAGAGGGTGTGTGTGCTT 59.605 55.000 0.00 0.00 0.00 3.91
995 1075 0.107456 AGAGAGGGTGTGTGTGCTTG 59.893 55.000 0.00 0.00 0.00 4.01
996 1076 0.179045 GAGAGGGTGTGTGTGCTTGT 60.179 55.000 0.00 0.00 0.00 3.16
997 1077 0.255890 AGAGGGTGTGTGTGCTTGTT 59.744 50.000 0.00 0.00 0.00 2.83
998 1078 0.663153 GAGGGTGTGTGTGCTTGTTC 59.337 55.000 0.00 0.00 0.00 3.18
1021 1101 4.373116 ACTGGTACGCGTGGCTGG 62.373 66.667 24.59 10.54 0.00 4.85
1329 1415 2.821688 GCGGTACTCCTCGTCCTCG 61.822 68.421 0.00 0.00 38.55 4.63
1538 1654 2.829458 GGACGAGGAGGAGGACGG 60.829 72.222 0.00 0.00 0.00 4.79
1646 1762 3.106407 GCTGCGTGACGACTGACC 61.106 66.667 10.10 0.00 0.00 4.02
1657 1773 4.664677 ACTGACCACGCCGAGCAC 62.665 66.667 0.00 0.00 0.00 4.40
1671 1787 1.168714 GAGCACGCCATTTCCTCTTT 58.831 50.000 0.00 0.00 0.00 2.52
1674 1790 0.109132 CACGCCATTTCCTCTTTGCC 60.109 55.000 0.00 0.00 0.00 4.52
1684 1800 1.227380 CTCTTTGCCCCCTCGATCG 60.227 63.158 9.36 9.36 0.00 3.69
1693 1809 1.298713 CCCTCGATCGCTTCTCGTG 60.299 63.158 11.09 0.00 39.67 4.35
1694 1810 1.715862 CCCTCGATCGCTTCTCGTGA 61.716 60.000 11.09 0.00 39.67 4.35
1695 1811 0.309302 CCTCGATCGCTTCTCGTGAT 59.691 55.000 11.09 0.00 45.19 3.06
1765 1892 7.684428 GCCTCTGGTTTTGTCTTCTGTAAAATT 60.684 37.037 0.00 0.00 0.00 1.82
1766 1893 8.197439 CCTCTGGTTTTGTCTTCTGTAAAATTT 58.803 33.333 0.00 0.00 0.00 1.82
1767 1894 8.925161 TCTGGTTTTGTCTTCTGTAAAATTTG 57.075 30.769 0.00 0.00 0.00 2.32
1768 1895 7.978975 TCTGGTTTTGTCTTCTGTAAAATTTGG 59.021 33.333 0.00 0.00 0.00 3.28
1770 1897 7.045416 GGTTTTGTCTTCTGTAAAATTTGGGT 58.955 34.615 0.00 0.00 0.00 4.51
1773 1900 8.485976 TTTGTCTTCTGTAAAATTTGGGTTTG 57.514 30.769 0.00 0.00 0.00 2.93
1813 1953 1.738099 GAACGATCTGCGCACCACT 60.738 57.895 5.66 0.00 46.04 4.00
1842 1986 3.918544 GTGCACACCACACCAACT 58.081 55.556 13.17 0.00 44.06 3.16
1850 1994 0.746563 ACCACACCAACTGACCAACG 60.747 55.000 0.00 0.00 0.00 4.10
1851 1995 1.355210 CACACCAACTGACCAACGC 59.645 57.895 0.00 0.00 0.00 4.84
1852 1996 1.822186 ACACCAACTGACCAACGCC 60.822 57.895 0.00 0.00 0.00 5.68
1853 1997 2.590575 ACCAACTGACCAACGCCG 60.591 61.111 0.00 0.00 0.00 6.46
1872 2016 2.159338 CCGGCATGGTGAATTTCTCTTG 60.159 50.000 0.00 1.22 0.00 3.02
1877 2021 5.126707 GGCATGGTGAATTTCTCTTGAGAAT 59.873 40.000 13.04 0.63 0.00 2.40
1880 2024 7.699812 GCATGGTGAATTTCTCTTGAGAATTAC 59.300 37.037 13.04 7.01 0.00 1.89
1881 2025 8.954350 CATGGTGAATTTCTCTTGAGAATTACT 58.046 33.333 13.04 0.27 0.00 2.24
1883 2027 9.436957 TGGTGAATTTCTCTTGAGAATTACTAC 57.563 33.333 13.04 9.22 0.00 2.73
1886 2030 9.574458 TGAATTTCTCTTGAGAATTACTACTCG 57.426 33.333 13.04 0.00 36.11 4.18
1895 2190 6.688578 TGAGAATTACTACTCGCTGAAACTT 58.311 36.000 0.00 0.00 36.11 2.66
1902 2197 0.520404 CTCGCTGAAACTTGCTGCAT 59.480 50.000 1.84 0.00 0.00 3.96
1903 2198 0.239082 TCGCTGAAACTTGCTGCATG 59.761 50.000 13.31 13.31 0.00 4.06
1904 2199 0.239082 CGCTGAAACTTGCTGCATGA 59.761 50.000 20.66 0.00 0.00 3.07
1906 2201 2.670229 CGCTGAAACTTGCTGCATGAAT 60.670 45.455 20.66 9.46 0.00 2.57
1913 2208 3.012518 ACTTGCTGCATGAATAGTGGAC 58.987 45.455 20.66 0.00 0.00 4.02
1915 2210 1.281577 TGCTGCATGAATAGTGGACCA 59.718 47.619 0.00 0.00 0.00 4.02
1927 2229 0.681733 GTGGACCAGCTTCAGACAGA 59.318 55.000 0.00 0.00 0.00 3.41
1942 2244 2.693069 GACAGACAGTCAACCTCCATG 58.307 52.381 2.66 0.00 46.77 3.66
2019 2321 2.492019 AAAAGGCGCACAACTTCTTC 57.508 45.000 10.83 0.00 0.00 2.87
2063 2366 3.062763 ACAACTTGATGAGAAGCGACAG 58.937 45.455 0.00 0.00 0.00 3.51
2068 2371 1.078848 ATGAGAAGCGACAGCCACC 60.079 57.895 0.00 0.00 46.67 4.61
2069 2372 2.811317 GAGAAGCGACAGCCACCG 60.811 66.667 0.00 0.00 46.67 4.94
2070 2373 3.282745 GAGAAGCGACAGCCACCGA 62.283 63.158 0.00 0.00 46.67 4.69
2072 2375 2.357517 AAGCGACAGCCACCGAAG 60.358 61.111 0.00 0.00 46.67 3.79
2080 2383 1.073025 AGCCACCGAAGCACATCAA 59.927 52.632 0.00 0.00 0.00 2.57
2093 2396 2.209273 CACATCAACAGACGACAACCA 58.791 47.619 0.00 0.00 0.00 3.67
2098 2401 1.192312 CAACAGACGACAACCACATCG 59.808 52.381 0.00 0.00 43.97 3.84
2223 2553 1.145803 GTACACAAGGACAAGGACGC 58.854 55.000 0.00 0.00 0.00 5.19
2272 2602 8.123639 TCTTCCATTAACGGGATATCTAAGAG 57.876 38.462 2.05 0.00 33.63 2.85
2276 2606 5.723672 TTAACGGGATATCTAAGAGCAGG 57.276 43.478 2.05 0.00 0.00 4.85
2295 2637 3.650942 CAGGGGTAATTGTAGGCTATCCA 59.349 47.826 0.00 0.00 33.74 3.41
2348 2692 0.617249 AGGGGAGAGCTCTGAAGGTG 60.617 60.000 23.91 0.00 32.07 4.00
2366 2710 2.033151 GGTGTTTTCTTCGAACTGGACG 60.033 50.000 0.00 0.00 0.00 4.79
2386 2730 1.183030 CCGTCTGTGTGGGTCTGGTA 61.183 60.000 0.00 0.00 0.00 3.25
2387 2731 0.038526 CGTCTGTGTGGGTCTGGTAC 60.039 60.000 0.00 0.00 0.00 3.34
2392 2736 0.179145 GTGTGGGTCTGGTACGATCG 60.179 60.000 14.88 14.88 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.626825 TGCTGAACTAGTGTAACCCCC 59.373 52.381 0.00 0.00 37.80 5.40
21 22 3.412237 TTGCTGAACTAGTGTAACCCC 57.588 47.619 0.00 0.00 37.80 4.95
22 23 3.188667 GCTTTGCTGAACTAGTGTAACCC 59.811 47.826 0.00 0.00 37.80 4.11
23 24 3.120649 CGCTTTGCTGAACTAGTGTAACC 60.121 47.826 0.00 0.00 37.80 2.85
24 25 3.739300 TCGCTTTGCTGAACTAGTGTAAC 59.261 43.478 0.00 0.00 0.00 2.50
25 26 3.739300 GTCGCTTTGCTGAACTAGTGTAA 59.261 43.478 0.00 0.00 0.00 2.41
26 27 3.314553 GTCGCTTTGCTGAACTAGTGTA 58.685 45.455 0.00 0.00 0.00 2.90
27 28 2.135933 GTCGCTTTGCTGAACTAGTGT 58.864 47.619 0.00 0.00 0.00 3.55
28 29 1.461127 GGTCGCTTTGCTGAACTAGTG 59.539 52.381 0.00 0.00 0.00 2.74
29 30 1.608283 GGGTCGCTTTGCTGAACTAGT 60.608 52.381 0.00 0.00 0.00 2.57
30 31 1.079503 GGGTCGCTTTGCTGAACTAG 58.920 55.000 0.00 0.00 0.00 2.57
31 32 0.685097 AGGGTCGCTTTGCTGAACTA 59.315 50.000 0.00 0.00 0.00 2.24
32 33 0.685097 TAGGGTCGCTTTGCTGAACT 59.315 50.000 0.00 0.00 0.00 3.01
33 34 1.519408 TTAGGGTCGCTTTGCTGAAC 58.481 50.000 0.00 0.00 0.00 3.18
34 35 2.083774 CATTAGGGTCGCTTTGCTGAA 58.916 47.619 0.00 0.00 0.00 3.02
35 36 1.737838 CATTAGGGTCGCTTTGCTGA 58.262 50.000 0.00 0.00 0.00 4.26
36 37 0.099436 GCATTAGGGTCGCTTTGCTG 59.901 55.000 13.85 2.05 0.00 4.41
37 38 1.369091 CGCATTAGGGTCGCTTTGCT 61.369 55.000 16.99 0.00 0.00 3.91
38 39 1.062525 CGCATTAGGGTCGCTTTGC 59.937 57.895 12.03 12.03 0.00 3.68
39 40 0.802494 AACGCATTAGGGTCGCTTTG 59.198 50.000 0.00 0.00 40.41 2.77
40 41 1.084289 GAACGCATTAGGGTCGCTTT 58.916 50.000 0.00 0.00 40.41 3.51
41 42 0.036765 TGAACGCATTAGGGTCGCTT 60.037 50.000 0.00 0.00 40.41 4.68
42 43 0.036765 TTGAACGCATTAGGGTCGCT 60.037 50.000 0.00 0.00 40.41 4.93
43 44 1.014352 ATTGAACGCATTAGGGTCGC 58.986 50.000 0.00 0.00 40.41 5.19
44 45 4.093703 TGTTAATTGAACGCATTAGGGTCG 59.906 41.667 0.00 0.00 41.35 4.79
45 46 5.329493 GTGTTAATTGAACGCATTAGGGTC 58.671 41.667 0.00 0.00 46.07 4.46
46 47 5.305139 GTGTTAATTGAACGCATTAGGGT 57.695 39.130 0.00 0.00 46.07 4.34
54 55 6.858993 TGTTAATCAAGGTGTTAATTGAACGC 59.141 34.615 0.00 0.00 46.07 4.84
55 56 8.789881 TTGTTAATCAAGGTGTTAATTGAACG 57.210 30.769 0.00 0.00 41.35 3.95
63 64 8.808092 CCCCTATTTTTGTTAATCAAGGTGTTA 58.192 33.333 0.00 0.00 37.35 2.41
64 65 7.256511 CCCCCTATTTTTGTTAATCAAGGTGTT 60.257 37.037 0.00 0.00 37.35 3.32
65 66 6.212589 CCCCCTATTTTTGTTAATCAAGGTGT 59.787 38.462 0.00 0.00 37.35 4.16
66 67 6.639563 CCCCCTATTTTTGTTAATCAAGGTG 58.360 40.000 0.00 0.00 37.35 4.00
67 68 6.867519 CCCCCTATTTTTGTTAATCAAGGT 57.132 37.500 0.00 0.00 37.35 3.50
87 88 2.996734 CCAACACCACATGCCCCC 60.997 66.667 0.00 0.00 0.00 5.40
88 89 2.996734 CCCAACACCACATGCCCC 60.997 66.667 0.00 0.00 0.00 5.80
89 90 2.996734 CCCCAACACCACATGCCC 60.997 66.667 0.00 0.00 0.00 5.36
90 91 2.996734 CCCCCAACACCACATGCC 60.997 66.667 0.00 0.00 0.00 4.40
91 92 2.203625 ACCCCCAACACCACATGC 60.204 61.111 0.00 0.00 0.00 4.06
92 93 1.606313 GGACCCCCAACACCACATG 60.606 63.158 0.00 0.00 0.00 3.21
93 94 2.851045 GGACCCCCAACACCACAT 59.149 61.111 0.00 0.00 0.00 3.21
94 95 3.879885 CGGACCCCCAACACCACA 61.880 66.667 0.00 0.00 0.00 4.17
95 96 4.653888 CCGGACCCCCAACACCAC 62.654 72.222 0.00 0.00 0.00 4.16
97 98 3.855503 GAACCGGACCCCCAACACC 62.856 68.421 9.46 0.00 0.00 4.16
98 99 2.281970 GAACCGGACCCCCAACAC 60.282 66.667 9.46 0.00 0.00 3.32
99 100 3.943691 CGAACCGGACCCCCAACA 61.944 66.667 9.46 0.00 0.00 3.33
110 111 3.569049 AACAGGAGCGACCGAACCG 62.569 63.158 0.00 0.00 44.74 4.44
111 112 2.027625 CAACAGGAGCGACCGAACC 61.028 63.158 0.00 0.00 44.74 3.62
112 113 2.668280 GCAACAGGAGCGACCGAAC 61.668 63.158 0.00 0.00 44.74 3.95
113 114 2.357034 GCAACAGGAGCGACCGAA 60.357 61.111 0.00 0.00 44.74 4.30
114 115 3.611674 TGCAACAGGAGCGACCGA 61.612 61.111 0.00 0.00 44.74 4.69
115 116 3.414700 GTGCAACAGGAGCGACCG 61.415 66.667 0.00 0.00 44.74 4.79
116 117 2.280797 TGTGCAACAGGAGCGACC 60.281 61.111 0.00 0.00 45.67 4.79
126 127 2.349817 GCCGTATATGAGCATGTGCAAC 60.350 50.000 7.83 1.89 45.16 4.17
127 128 1.872952 GCCGTATATGAGCATGTGCAA 59.127 47.619 7.83 0.00 45.16 4.08
128 129 1.511850 GCCGTATATGAGCATGTGCA 58.488 50.000 7.83 0.00 45.16 4.57
129 130 0.798776 GGCCGTATATGAGCATGTGC 59.201 55.000 0.00 0.00 42.49 4.57
130 131 1.002430 AGGGCCGTATATGAGCATGTG 59.998 52.381 0.00 0.00 0.00 3.21
131 132 1.002430 CAGGGCCGTATATGAGCATGT 59.998 52.381 0.00 0.00 0.00 3.21
132 133 1.730501 CAGGGCCGTATATGAGCATG 58.269 55.000 0.00 0.00 0.00 4.06
133 134 0.036010 GCAGGGCCGTATATGAGCAT 60.036 55.000 0.00 0.00 0.00 3.79
134 135 1.121407 AGCAGGGCCGTATATGAGCA 61.121 55.000 0.00 0.00 0.00 4.26
135 136 0.895530 TAGCAGGGCCGTATATGAGC 59.104 55.000 0.00 0.00 0.00 4.26
136 137 1.478510 CCTAGCAGGGCCGTATATGAG 59.521 57.143 0.00 0.00 0.00 2.90
137 138 1.557099 CCTAGCAGGGCCGTATATGA 58.443 55.000 0.00 0.00 0.00 2.15
148 149 1.484444 GGATGGTAGCCCCTAGCAGG 61.484 65.000 9.59 0.00 45.52 4.85
149 150 0.472734 AGGATGGTAGCCCCTAGCAG 60.473 60.000 9.59 0.00 45.52 4.24
150 151 0.764369 CAGGATGGTAGCCCCTAGCA 60.764 60.000 6.60 6.60 46.19 3.49
151 152 0.764752 ACAGGATGGTAGCCCCTAGC 60.765 60.000 3.09 0.00 43.62 3.42
152 153 2.696526 TACAGGATGGTAGCCCCTAG 57.303 55.000 3.09 0.00 43.62 3.02
153 154 3.424724 TTTACAGGATGGTAGCCCCTA 57.575 47.619 3.09 0.00 43.62 3.53
154 155 2.280308 TTTACAGGATGGTAGCCCCT 57.720 50.000 0.00 0.00 43.62 4.79
155 156 2.508300 TCTTTTACAGGATGGTAGCCCC 59.492 50.000 0.00 0.00 43.62 5.80
156 157 3.926058 TCTTTTACAGGATGGTAGCCC 57.074 47.619 0.00 0.00 43.62 5.19
157 158 5.254115 ACTTTCTTTTACAGGATGGTAGCC 58.746 41.667 0.00 0.00 43.62 3.93
158 159 6.127980 GGAACTTTCTTTTACAGGATGGTAGC 60.128 42.308 0.00 0.00 43.62 3.58
171 172 9.857957 CTCGTCTTACTATAGGAACTTTCTTTT 57.142 33.333 4.43 0.00 41.75 2.27
172 173 9.240734 TCTCGTCTTACTATAGGAACTTTCTTT 57.759 33.333 4.43 0.00 41.75 2.52
175 176 8.212317 AGTCTCGTCTTACTATAGGAACTTTC 57.788 38.462 4.43 0.00 41.75 2.62
191 192 6.063404 CCTCCTTTTATAGGTAGTCTCGTCT 58.937 44.000 0.00 0.00 45.03 4.18
194 195 4.583489 TGCCTCCTTTTATAGGTAGTCTCG 59.417 45.833 0.00 0.00 45.03 4.04
196 197 6.689177 GCATTGCCTCCTTTTATAGGTAGTCT 60.689 42.308 0.00 0.00 45.03 3.24
202 203 4.646492 ACTTGCATTGCCTCCTTTTATAGG 59.354 41.667 6.12 0.00 46.27 2.57
300 301 0.242825 CAGTGTGCTGGCCTTTCATG 59.757 55.000 3.32 0.00 39.01 3.07
342 343 1.304381 GTGTGCATGGGTGATGGGT 60.304 57.895 0.00 0.00 31.99 4.51
343 344 2.053865 GGTGTGCATGGGTGATGGG 61.054 63.158 0.00 0.00 31.99 4.00
344 345 1.000521 AGGTGTGCATGGGTGATGG 60.001 57.895 0.00 0.00 31.99 3.51
345 346 2.186155 CAGGTGTGCATGGGTGATG 58.814 57.895 0.00 0.00 34.84 3.07
346 347 4.749323 CAGGTGTGCATGGGTGAT 57.251 55.556 0.00 0.00 0.00 3.06
360 361 2.624838 GGTTGATGGTTATCATGGCAGG 59.375 50.000 0.00 0.00 42.60 4.85
365 366 1.264020 CGCCGGTTGATGGTTATCATG 59.736 52.381 1.90 0.00 42.60 3.07
397 398 2.438975 ACCTCACATGCATGCCCG 60.439 61.111 26.53 15.03 0.00 6.13
403 404 2.669229 CGTGGCACCTCACATGCA 60.669 61.111 12.86 0.00 45.27 3.96
429 430 2.083774 GTATGTGGTGTCATGGTGTGG 58.916 52.381 0.00 0.00 0.00 4.17
430 431 2.483877 GTGTATGTGGTGTCATGGTGTG 59.516 50.000 0.00 0.00 0.00 3.82
431 432 2.105649 TGTGTATGTGGTGTCATGGTGT 59.894 45.455 0.00 0.00 0.00 4.16
432 433 2.743664 CTGTGTATGTGGTGTCATGGTG 59.256 50.000 0.00 0.00 0.00 4.17
433 434 2.875672 GCTGTGTATGTGGTGTCATGGT 60.876 50.000 0.00 0.00 0.00 3.55
434 435 1.739466 GCTGTGTATGTGGTGTCATGG 59.261 52.381 0.00 0.00 0.00 3.66
435 436 1.394572 CGCTGTGTATGTGGTGTCATG 59.605 52.381 0.00 0.00 0.00 3.07
436 437 1.275010 TCGCTGTGTATGTGGTGTCAT 59.725 47.619 0.00 0.00 0.00 3.06
437 438 0.676736 TCGCTGTGTATGTGGTGTCA 59.323 50.000 0.00 0.00 0.00 3.58
438 439 1.927174 GATCGCTGTGTATGTGGTGTC 59.073 52.381 0.00 0.00 0.00 3.67
439 440 1.550524 AGATCGCTGTGTATGTGGTGT 59.449 47.619 0.00 0.00 0.00 4.16
440 441 1.929169 CAGATCGCTGTGTATGTGGTG 59.071 52.381 0.00 0.00 37.37 4.17
441 442 1.740380 GCAGATCGCTGTGTATGTGGT 60.740 52.381 0.00 0.00 44.17 4.16
470 471 1.464997 GAAATGCGAAGGTGTCAGGAC 59.535 52.381 0.00 0.00 0.00 3.85
471 472 1.347707 AGAAATGCGAAGGTGTCAGGA 59.652 47.619 0.00 0.00 0.00 3.86
479 480 3.084786 AGAGGGAAAAGAAATGCGAAGG 58.915 45.455 0.00 0.00 0.00 3.46
483 484 1.745653 GGGAGAGGGAAAAGAAATGCG 59.254 52.381 0.00 0.00 0.00 4.73
498 499 4.880426 GGCGGGGAGATGGGGAGA 62.880 72.222 0.00 0.00 0.00 3.71
499 500 4.888325 AGGCGGGGAGATGGGGAG 62.888 72.222 0.00 0.00 0.00 4.30
500 501 3.962530 AAAGGCGGGGAGATGGGGA 62.963 63.158 0.00 0.00 0.00 4.81
502 503 2.193248 GAAAGGCGGGGAGATGGG 59.807 66.667 0.00 0.00 0.00 4.00
504 505 2.203070 CGGAAAGGCGGGGAGATG 60.203 66.667 0.00 0.00 0.00 2.90
505 506 4.176752 GCGGAAAGGCGGGGAGAT 62.177 66.667 0.00 0.00 0.00 2.75
523 524 4.201532 CGAATCTACGAGACAAAAGTGCAG 60.202 45.833 0.00 0.00 35.09 4.41
577 578 1.065701 GAGATCCAGCACGACGTACAT 59.934 52.381 0.00 0.00 0.00 2.29
599 601 2.869636 GCGATGGATCTGGATTCTGGAC 60.870 54.545 0.00 0.00 0.00 4.02
605 607 3.389329 AGTACAAGCGATGGATCTGGATT 59.611 43.478 0.00 0.00 0.00 3.01
630 632 1.764854 GGGCTAGGATCCCGTGGAA 60.765 63.158 8.55 0.00 34.34 3.53
672 682 5.730010 GCGTGTGTACACTCCTAGTATCTTC 60.730 48.000 25.60 0.00 44.34 2.87
679 689 2.085320 AGAGCGTGTGTACACTCCTAG 58.915 52.381 25.60 11.40 44.34 3.02
680 690 2.195741 AGAGCGTGTGTACACTCCTA 57.804 50.000 25.60 3.51 44.34 2.94
681 691 1.000163 CAAGAGCGTGTGTACACTCCT 60.000 52.381 25.60 19.37 44.34 3.69
848 897 1.019278 ATGATTCGTGCGTGTGGGAC 61.019 55.000 0.00 0.00 0.00 4.46
870 919 1.679680 ACTTGTAAGCGCGGCTATAGA 59.320 47.619 8.83 0.00 38.25 1.98
874 923 0.457853 CTCACTTGTAAGCGCGGCTA 60.458 55.000 8.83 0.00 38.25 3.93
902 955 5.918608 TCTTCTTCTTCCCCGAATTATCTG 58.081 41.667 0.00 0.00 0.00 2.90
907 960 3.009584 AGCTTCTTCTTCTTCCCCGAATT 59.990 43.478 0.00 0.00 0.00 2.17
914 967 1.364721 GGCGAGCTTCTTCTTCTTCC 58.635 55.000 0.00 0.00 0.00 3.46
958 1038 3.837731 TCTCTCTCTCACTCTCACTCTCA 59.162 47.826 0.00 0.00 0.00 3.27
964 1044 2.026356 CACCCTCTCTCTCTCACTCTCA 60.026 54.545 0.00 0.00 0.00 3.27
970 1050 1.145945 ACACACACCCTCTCTCTCTCA 59.854 52.381 0.00 0.00 0.00 3.27
982 1062 0.944386 ATCGAACAAGCACACACACC 59.056 50.000 0.00 0.00 0.00 4.16
983 1063 1.334059 CCATCGAACAAGCACACACAC 60.334 52.381 0.00 0.00 0.00 3.82
984 1064 0.943673 CCATCGAACAAGCACACACA 59.056 50.000 0.00 0.00 0.00 3.72
985 1065 1.069906 GTCCATCGAACAAGCACACAC 60.070 52.381 0.00 0.00 0.00 3.82
986 1066 1.202639 AGTCCATCGAACAAGCACACA 60.203 47.619 0.00 0.00 0.00 3.72
987 1067 1.195448 CAGTCCATCGAACAAGCACAC 59.805 52.381 0.00 0.00 0.00 3.82
988 1068 1.511850 CAGTCCATCGAACAAGCACA 58.488 50.000 0.00 0.00 0.00 4.57
989 1069 0.798776 CCAGTCCATCGAACAAGCAC 59.201 55.000 0.00 0.00 0.00 4.40
990 1070 0.396435 ACCAGTCCATCGAACAAGCA 59.604 50.000 0.00 0.00 0.00 3.91
991 1071 2.000447 GTACCAGTCCATCGAACAAGC 59.000 52.381 0.00 0.00 0.00 4.01
992 1072 2.259618 CGTACCAGTCCATCGAACAAG 58.740 52.381 0.00 0.00 0.00 3.16
993 1073 1.670674 GCGTACCAGTCCATCGAACAA 60.671 52.381 0.00 0.00 0.00 2.83
994 1074 0.108992 GCGTACCAGTCCATCGAACA 60.109 55.000 0.00 0.00 0.00 3.18
995 1075 1.138047 CGCGTACCAGTCCATCGAAC 61.138 60.000 0.00 0.00 0.00 3.95
996 1076 1.138036 CGCGTACCAGTCCATCGAA 59.862 57.895 0.00 0.00 0.00 3.71
997 1077 2.042259 ACGCGTACCAGTCCATCGA 61.042 57.895 11.67 0.00 0.00 3.59
998 1078 1.872234 CACGCGTACCAGTCCATCG 60.872 63.158 13.44 0.00 0.00 3.84
1569 1685 1.656875 CTTGATCTCGCTCTCGCCG 60.657 63.158 0.00 0.00 35.26 6.46
1630 1746 2.016704 GTGGTCAGTCGTCACGCAG 61.017 63.158 0.00 0.00 0.00 5.18
1635 1751 4.337060 CGGCGTGGTCAGTCGTCA 62.337 66.667 0.00 0.00 0.00 4.35
1657 1773 1.512694 GGGCAAAGAGGAAATGGCG 59.487 57.895 0.00 0.00 40.24 5.69
1659 1775 0.041684 AGGGGGCAAAGAGGAAATGG 59.958 55.000 0.00 0.00 0.00 3.16
1671 1787 3.849951 GAAGCGATCGAGGGGGCA 61.850 66.667 21.57 0.00 0.00 5.36
1674 1790 2.333225 CGAGAAGCGATCGAGGGG 59.667 66.667 21.57 0.00 44.57 4.79
1693 1809 7.687005 AGAAAAACAGTAATCTCGATCGATC 57.313 36.000 19.78 15.68 0.00 3.69
1694 1810 7.010552 CCAAGAAAAACAGTAATCTCGATCGAT 59.989 37.037 19.78 6.61 0.00 3.59
1695 1811 6.310467 CCAAGAAAAACAGTAATCTCGATCGA 59.690 38.462 18.32 18.32 0.00 3.59
1696 1812 6.090898 ACCAAGAAAAACAGTAATCTCGATCG 59.909 38.462 9.36 9.36 0.00 3.69
1765 1892 3.053991 TCAGTTCTTCACTCCAAACCCAA 60.054 43.478 0.00 0.00 30.92 4.12
1766 1893 2.507886 TCAGTTCTTCACTCCAAACCCA 59.492 45.455 0.00 0.00 30.92 4.51
1767 1894 3.208747 TCAGTTCTTCACTCCAAACCC 57.791 47.619 0.00 0.00 30.92 4.11
1768 1895 4.451900 TCTTCAGTTCTTCACTCCAAACC 58.548 43.478 0.00 0.00 30.92 3.27
1770 1897 5.928976 TGATCTTCAGTTCTTCACTCCAAA 58.071 37.500 0.00 0.00 30.92 3.28
1773 1900 5.788450 TCTTGATCTTCAGTTCTTCACTCC 58.212 41.667 0.00 0.00 30.92 3.85
1813 1953 3.563808 GTGGTGTGCACATAGTTTCAGAA 59.436 43.478 24.69 0.00 0.00 3.02
1850 1994 0.101219 GAGAAATTCACCATGCCGGC 59.899 55.000 22.73 22.73 39.03 6.13
1851 1995 1.755179 AGAGAAATTCACCATGCCGG 58.245 50.000 0.00 0.00 42.50 6.13
1852 1996 2.749076 TCAAGAGAAATTCACCATGCCG 59.251 45.455 0.00 0.00 0.00 5.69
1853 1997 4.012374 TCTCAAGAGAAATTCACCATGCC 58.988 43.478 0.00 0.00 33.91 4.40
1872 2016 6.454450 GCAAGTTTCAGCGAGTAGTAATTCTC 60.454 42.308 0.00 0.00 0.00 2.87
1877 2021 3.987868 CAGCAAGTTTCAGCGAGTAGTAA 59.012 43.478 0.00 0.00 35.48 2.24
1880 2024 1.127582 GCAGCAAGTTTCAGCGAGTAG 59.872 52.381 0.00 0.00 35.48 2.57
1881 2025 1.148310 GCAGCAAGTTTCAGCGAGTA 58.852 50.000 0.00 0.00 35.48 2.59
1882 2026 0.815213 TGCAGCAAGTTTCAGCGAGT 60.815 50.000 0.00 0.00 35.48 4.18
1883 2027 0.520404 ATGCAGCAAGTTTCAGCGAG 59.480 50.000 0.00 0.00 35.48 5.03
1886 2030 2.427232 TTCATGCAGCAAGTTTCAGC 57.573 45.000 0.00 0.00 0.00 4.26
1895 2190 1.281577 TGGTCCACTATTCATGCAGCA 59.718 47.619 0.00 0.00 0.00 4.41
1902 2197 3.055819 GTCTGAAGCTGGTCCACTATTCA 60.056 47.826 7.91 7.91 0.00 2.57
1903 2198 3.055819 TGTCTGAAGCTGGTCCACTATTC 60.056 47.826 0.00 0.00 0.00 1.75
1904 2199 2.906389 TGTCTGAAGCTGGTCCACTATT 59.094 45.455 0.00 0.00 0.00 1.73
1906 2201 1.895798 CTGTCTGAAGCTGGTCCACTA 59.104 52.381 0.00 0.00 0.00 2.74
1913 2208 1.342496 TGACTGTCTGTCTGAAGCTGG 59.658 52.381 9.51 0.00 45.54 4.85
1915 2210 2.224161 GGTTGACTGTCTGTCTGAAGCT 60.224 50.000 9.51 0.00 45.54 3.74
1964 2266 8.696043 TGAGTTCGGTATAGGCTAACTAATAA 57.304 34.615 0.00 0.00 34.79 1.40
1965 2267 8.696043 TTGAGTTCGGTATAGGCTAACTAATA 57.304 34.615 0.00 0.00 34.79 0.98
1966 2268 7.287235 ACTTGAGTTCGGTATAGGCTAACTAAT 59.713 37.037 0.00 0.00 34.79 1.73
2002 2304 1.680338 AAGAAGAAGTTGTGCGCCTT 58.320 45.000 4.18 0.00 0.00 4.35
2004 2306 2.492019 AAAAGAAGAAGTTGTGCGCC 57.508 45.000 4.18 0.00 0.00 6.53
2033 2336 3.066621 TCTCATCAAGTTGTGCGCTTTTT 59.933 39.130 9.73 0.00 0.00 1.94
2039 2342 1.463034 CGCTTCTCATCAAGTTGTGCG 60.463 52.381 2.11 5.58 35.22 5.34
2043 2346 2.159734 GCTGTCGCTTCTCATCAAGTTG 60.160 50.000 0.00 0.00 0.00 3.16
2063 2366 1.210155 GTTGATGTGCTTCGGTGGC 59.790 57.895 0.00 0.00 0.00 5.01
2068 2371 1.125021 GTCGTCTGTTGATGTGCTTCG 59.875 52.381 0.00 0.00 0.00 3.79
2069 2372 2.135139 TGTCGTCTGTTGATGTGCTTC 58.865 47.619 0.00 0.00 0.00 3.86
2070 2373 2.238942 TGTCGTCTGTTGATGTGCTT 57.761 45.000 0.00 0.00 0.00 3.91
2072 2375 1.069906 GGTTGTCGTCTGTTGATGTGC 60.070 52.381 0.00 0.00 0.00 4.57
2080 2383 0.671796 TCGATGTGGTTGTCGTCTGT 59.328 50.000 0.00 0.00 38.85 3.41
2093 2396 4.023107 CACACGGGATAGATAAGTCGATGT 60.023 45.833 0.00 0.00 0.00 3.06
2098 2401 5.258456 TGAACACACGGGATAGATAAGTC 57.742 43.478 0.00 0.00 0.00 3.01
2128 2431 0.249489 AGGAGCCATAACGATGTCGC 60.249 55.000 1.77 0.00 44.43 5.19
2223 2553 9.218440 AGAAATTGTTTGTATAAATGGCTTTGG 57.782 29.630 0.00 0.00 0.00 3.28
2256 2586 2.900546 CCCTGCTCTTAGATATCCCGTT 59.099 50.000 0.00 0.00 0.00 4.44
2272 2602 3.559384 GGATAGCCTACAATTACCCCTGC 60.559 52.174 0.00 0.00 0.00 4.85
2276 2606 4.288626 TGGATGGATAGCCTACAATTACCC 59.711 45.833 0.00 0.00 32.18 3.69
2295 2637 4.820775 TCTAGGGAGCTGAGTAATTGGAT 58.179 43.478 0.00 0.00 0.00 3.41
2348 2692 1.070108 GGCGTCCAGTTCGAAGAAAAC 60.070 52.381 0.00 0.00 45.90 2.43
2366 2710 2.357517 CAGACCCACACAGACGGC 60.358 66.667 0.00 0.00 0.00 5.68
2460 2806 9.710900 GGAAATTCACAGAAATGTAAAAATCCT 57.289 29.630 0.00 0.00 0.00 3.24
2464 2810 9.658799 TTGTGGAAATTCACAGAAATGTAAAAA 57.341 25.926 0.00 0.00 46.61 1.94
2475 2821 3.636300 TGACCCTTTGTGGAAATTCACAG 59.364 43.478 0.00 0.00 46.61 3.66


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

AutoCloner maintained by Alex Coulton.