Multiple sequence alignment - TraesCS1D01G364600

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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 TraesCS1D01G364600 chr1D 100.000 2649 0 0 1 2649 445388079 445385431 0.000000e+00 4892.0
1 TraesCS1D01G364600 chr1D 89.503 886 49 16 808 1689 445317316 445318161 0.000000e+00 1081.0
2 TraesCS1D01G364600 chr1D 85.081 992 105 29 807 1772 446558191 446559165 0.000000e+00 972.0
3 TraesCS1D01G364600 chr1D 91.845 699 40 13 822 1505 446436822 446437518 0.000000e+00 959.0
4 TraesCS1D01G364600 chr1A 89.157 1079 81 20 632 1684 541380903 541381971 0.000000e+00 1312.0
5 TraesCS1D01G364600 chr1A 90.628 971 70 12 822 1772 542170093 542171062 0.000000e+00 1269.0
6 TraesCS1D01G364600 chr1A 90.879 910 59 12 680 1573 541463769 541462868 0.000000e+00 1199.0
7 TraesCS1D01G364600 chr1A 90.200 898 57 15 1768 2649 542171090 542171972 0.000000e+00 1142.0
8 TraesCS1D01G364600 chr1A 86.154 975 91 21 807 1772 542358199 542359138 0.000000e+00 1013.0
9 TraesCS1D01G364600 chr1A 86.009 436 37 14 198 618 541464316 541463890 1.870000e-121 446.0
10 TraesCS1D01G364600 chr1A 82.158 241 19 9 315 543 541380299 541380527 4.500000e-43 185.0
11 TraesCS1D01G364600 chr1B 85.252 1329 116 39 490 1772 608463529 608462235 0.000000e+00 1295.0
12 TraesCS1D01G364600 chr1B 86.783 976 98 19 807 1772 611131192 611132146 0.000000e+00 1059.0
13 TraesCS1D01G364600 chr1B 88.380 895 60 15 807 1689 606839639 606840501 0.000000e+00 1037.0
14 TraesCS1D01G364600 chr1B 89.504 705 45 6 807 1508 607429793 607429115 0.000000e+00 865.0
15 TraesCS1D01G364600 chr1B 88.158 304 33 2 173 475 608465292 608464991 2.510000e-95 359.0
16 TraesCS1D01G364600 chr1B 88.950 181 11 7 1820 1995 556350075 556349899 5.740000e-52 215.0
17 TraesCS1D01G364600 chr1B 84.091 176 26 2 1599 1772 610966032 610966207 4.530000e-38 169.0
18 TraesCS1D01G364600 chr6D 87.535 714 52 20 803 1505 47812106 47812793 0.000000e+00 791.0
19 TraesCS1D01G364600 chr2B 83.445 447 62 8 181 623 161025515 161025953 3.180000e-109 405.0
20 TraesCS1D01G364600 chr7A 90.323 186 9 6 1819 1999 500547359 500547178 4.410000e-58 235.0
21 TraesCS1D01G364600 chr3B 90.361 166 9 5 1830 1992 647527110 647526949 7.430000e-51 211.0
22 TraesCS1D01G364600 chr3B 90.152 132 8 5 1822 1952 515161248 515161375 1.630000e-37 167.0
23 TraesCS1D01G364600 chr3B 89.552 134 9 5 1820 1952 518932983 518932854 5.870000e-37 165.0
24 TraesCS1D01G364600 chr3B 96.774 31 1 0 146 176 640696165 640696135 5.000000e-03 52.8
25 TraesCS1D01G364600 chr7D 84.018 219 26 8 1471 1689 16676085 16676294 4.470000e-48 202.0
26 TraesCS1D01G364600 chrUn 90.152 132 8 5 1822 1952 123973617 123973490 1.630000e-37 167.0
27 TraesCS1D01G364600 chrUn 90.152 132 8 5 1822 1952 131819963 131820090 1.630000e-37 167.0
28 TraesCS1D01G364600 chr5A 89.552 134 9 3 1862 1992 582919268 582919399 5.870000e-37 165.0


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 TraesCS1D01G364600 chr1D 445385431 445388079 2648 True 4892.0 4892 100.0000 1 2649 1 chr1D.!!$R1 2648
1 TraesCS1D01G364600 chr1D 445317316 445318161 845 False 1081.0 1081 89.5030 808 1689 1 chr1D.!!$F1 881
2 TraesCS1D01G364600 chr1D 446558191 446559165 974 False 972.0 972 85.0810 807 1772 1 chr1D.!!$F3 965
3 TraesCS1D01G364600 chr1D 446436822 446437518 696 False 959.0 959 91.8450 822 1505 1 chr1D.!!$F2 683
4 TraesCS1D01G364600 chr1A 542170093 542171972 1879 False 1205.5 1269 90.4140 822 2649 2 chr1A.!!$F3 1827
5 TraesCS1D01G364600 chr1A 542358199 542359138 939 False 1013.0 1013 86.1540 807 1772 1 chr1A.!!$F1 965
6 TraesCS1D01G364600 chr1A 541462868 541464316 1448 True 822.5 1199 88.4440 198 1573 2 chr1A.!!$R1 1375
7 TraesCS1D01G364600 chr1A 541380299 541381971 1672 False 748.5 1312 85.6575 315 1684 2 chr1A.!!$F2 1369
8 TraesCS1D01G364600 chr1B 611131192 611132146 954 False 1059.0 1059 86.7830 807 1772 1 chr1B.!!$F3 965
9 TraesCS1D01G364600 chr1B 606839639 606840501 862 False 1037.0 1037 88.3800 807 1689 1 chr1B.!!$F1 882
10 TraesCS1D01G364600 chr1B 607429115 607429793 678 True 865.0 865 89.5040 807 1508 1 chr1B.!!$R2 701
11 TraesCS1D01G364600 chr1B 608462235 608465292 3057 True 827.0 1295 86.7050 173 1772 2 chr1B.!!$R3 1599
12 TraesCS1D01G364600 chr6D 47812106 47812793 687 False 791.0 791 87.5350 803 1505 1 chr6D.!!$F1 702

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
60 61 0.033366 GGCTCCCGCAAATGTTTTGT 59.967 50.0 2.32 0.0 38.1 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 3630 0.110238 CACATTCAACAACGGGCTCG 60.11 55.0 3.27 3.27 43.02 5.03 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
21 22 4.230314 CCTGGAGCCGACATATATATCG 57.770 50.000 6.42 6.42 38.08 2.92
31 32 4.912187 CGACATATATATCGGAATCGCAGG 59.088 45.833 5.47 0.00 34.67 4.85
32 33 4.621991 ACATATATATCGGAATCGCAGGC 58.378 43.478 0.00 0.00 36.13 4.85
33 34 2.209838 ATATATCGGAATCGCAGGCG 57.790 50.000 7.46 7.46 41.35 5.52
34 35 0.172578 TATATCGGAATCGCAGGCGG 59.827 55.000 14.24 0.00 40.25 6.13
35 36 1.816863 ATATCGGAATCGCAGGCGGT 61.817 55.000 14.24 3.08 40.25 5.68
36 37 2.023414 TATCGGAATCGCAGGCGGTT 62.023 55.000 12.49 12.49 46.15 4.44
37 38 2.869503 ATCGGAATCGCAGGCGGTTT 62.870 55.000 13.88 7.94 43.30 3.27
38 39 1.812093 CGGAATCGCAGGCGGTTTA 60.812 57.895 13.88 0.00 43.30 2.01
39 40 1.157870 CGGAATCGCAGGCGGTTTAT 61.158 55.000 13.88 0.00 43.30 1.40
40 41 0.307760 GGAATCGCAGGCGGTTTATG 59.692 55.000 13.88 0.00 43.30 1.90
41 42 0.307760 GAATCGCAGGCGGTTTATGG 59.692 55.000 13.88 0.00 43.30 2.74
42 43 1.101049 AATCGCAGGCGGTTTATGGG 61.101 55.000 14.24 0.00 40.06 4.00
43 44 3.887868 CGCAGGCGGTTTATGGGC 61.888 66.667 5.63 0.00 35.56 5.36
44 45 2.440247 GCAGGCGGTTTATGGGCT 60.440 61.111 0.00 0.00 39.98 5.19
45 46 2.481471 GCAGGCGGTTTATGGGCTC 61.481 63.158 0.00 0.00 36.88 4.70
46 47 1.823899 CAGGCGGTTTATGGGCTCC 60.824 63.158 0.00 0.00 36.88 4.70
47 48 2.518587 GGCGGTTTATGGGCTCCC 60.519 66.667 0.00 0.00 0.00 4.30
48 49 2.900337 GCGGTTTATGGGCTCCCG 60.900 66.667 0.00 0.00 41.50 5.14
49 50 2.900337 CGGTTTATGGGCTCCCGC 60.900 66.667 0.00 0.00 39.42 6.13
50 51 2.274104 GGTTTATGGGCTCCCGCA 59.726 61.111 0.00 0.00 39.42 5.69
51 52 1.379309 GGTTTATGGGCTCCCGCAA 60.379 57.895 0.00 0.00 39.42 4.85
52 53 0.968393 GGTTTATGGGCTCCCGCAAA 60.968 55.000 0.00 0.52 39.42 3.68
53 54 1.111277 GTTTATGGGCTCCCGCAAAT 58.889 50.000 0.00 0.00 39.42 2.32
54 55 1.110442 TTTATGGGCTCCCGCAAATG 58.890 50.000 0.00 0.00 39.42 2.32
55 56 0.033601 TTATGGGCTCCCGCAAATGT 60.034 50.000 0.00 0.00 39.42 2.71
56 57 0.033601 TATGGGCTCCCGCAAATGTT 60.034 50.000 0.00 0.00 39.42 2.71
57 58 0.904394 ATGGGCTCCCGCAAATGTTT 60.904 50.000 0.00 0.00 39.42 2.83
58 59 1.118356 TGGGCTCCCGCAAATGTTTT 61.118 50.000 0.00 0.00 39.42 2.43
59 60 0.670239 GGGCTCCCGCAAATGTTTTG 60.670 55.000 0.00 0.00 38.10 2.44
60 61 0.033366 GGCTCCCGCAAATGTTTTGT 59.967 50.000 2.32 0.00 38.10 2.83
61 62 1.139163 GCTCCCGCAAATGTTTTGTG 58.861 50.000 6.56 6.56 35.78 3.33
62 63 1.782044 CTCCCGCAAATGTTTTGTGG 58.218 50.000 20.45 20.45 46.64 4.17
64 65 2.233681 CCGCAAATGTTTTGTGGGC 58.766 52.632 19.90 0.00 44.16 5.36
65 66 0.531532 CCGCAAATGTTTTGTGGGCA 60.532 50.000 19.90 0.00 44.16 5.36
66 67 0.860533 CGCAAATGTTTTGTGGGCAG 59.139 50.000 5.79 0.00 0.00 4.85
67 68 1.228533 GCAAATGTTTTGTGGGCAGG 58.771 50.000 2.32 0.00 0.00 4.85
68 69 1.881591 CAAATGTTTTGTGGGCAGGG 58.118 50.000 0.00 0.00 0.00 4.45
69 70 0.108396 AAATGTTTTGTGGGCAGGGC 59.892 50.000 0.00 0.00 0.00 5.19
85 86 3.691342 GCCCTTTTTGGCGGACCC 61.691 66.667 0.00 0.00 42.54 4.46
86 87 3.370231 CCCTTTTTGGCGGACCCG 61.370 66.667 3.73 3.73 43.09 5.28
101 102 3.884900 CCGCTCGGGTCGAAATTT 58.115 55.556 0.00 0.00 34.74 1.82
102 103 2.168054 CCGCTCGGGTCGAAATTTT 58.832 52.632 0.00 0.00 34.74 1.82
103 104 1.361793 CCGCTCGGGTCGAAATTTTA 58.638 50.000 0.00 0.00 34.74 1.52
104 105 1.326548 CCGCTCGGGTCGAAATTTTAG 59.673 52.381 0.00 0.00 34.74 1.85
105 106 1.326548 CGCTCGGGTCGAAATTTTAGG 59.673 52.381 0.00 0.00 34.74 2.69
106 107 2.353323 GCTCGGGTCGAAATTTTAGGT 58.647 47.619 0.00 0.00 34.74 3.08
107 108 2.350804 GCTCGGGTCGAAATTTTAGGTC 59.649 50.000 0.00 0.00 34.74 3.85
108 109 2.601763 CTCGGGTCGAAATTTTAGGTCG 59.398 50.000 0.00 0.00 34.74 4.79
109 110 2.029110 TCGGGTCGAAATTTTAGGTCGT 60.029 45.455 0.00 0.00 36.21 4.34
110 111 2.346545 CGGGTCGAAATTTTAGGTCGTC 59.653 50.000 0.00 0.00 36.21 4.20
111 112 2.674852 GGGTCGAAATTTTAGGTCGTCC 59.325 50.000 4.74 4.74 40.68 4.79
112 113 2.674852 GGTCGAAATTTTAGGTCGTCCC 59.325 50.000 0.00 0.00 37.12 4.46
113 114 3.328505 GTCGAAATTTTAGGTCGTCCCA 58.671 45.455 0.00 0.00 36.21 4.37
114 115 3.937079 GTCGAAATTTTAGGTCGTCCCAT 59.063 43.478 0.00 0.00 36.21 4.00
115 116 5.111293 GTCGAAATTTTAGGTCGTCCCATA 58.889 41.667 0.00 0.00 36.21 2.74
116 117 5.581874 GTCGAAATTTTAGGTCGTCCCATAA 59.418 40.000 0.00 0.00 36.21 1.90
117 118 6.092533 GTCGAAATTTTAGGTCGTCCCATAAA 59.907 38.462 0.00 0.00 36.21 1.40
118 119 6.092533 TCGAAATTTTAGGTCGTCCCATAAAC 59.907 38.462 0.00 0.00 36.21 2.01
119 120 6.519679 AAATTTTAGGTCGTCCCATAAACC 57.480 37.500 0.00 0.00 34.66 3.27
120 121 3.632643 TTTAGGTCGTCCCATAAACCC 57.367 47.619 0.00 0.00 34.66 4.11
121 122 1.113788 TAGGTCGTCCCATAAACCCG 58.886 55.000 0.00 0.00 34.66 5.28
122 123 1.816679 GGTCGTCCCATAAACCCGC 60.817 63.158 0.00 0.00 0.00 6.13
123 124 1.816679 GTCGTCCCATAAACCCGCC 60.817 63.158 0.00 0.00 0.00 6.13
124 125 2.893404 CGTCCCATAAACCCGCCG 60.893 66.667 0.00 0.00 0.00 6.46
125 126 2.585698 GTCCCATAAACCCGCCGA 59.414 61.111 0.00 0.00 0.00 5.54
126 127 1.078285 GTCCCATAAACCCGCCGAA 60.078 57.895 0.00 0.00 0.00 4.30
127 128 0.677414 GTCCCATAAACCCGCCGAAA 60.677 55.000 0.00 0.00 0.00 3.46
128 129 0.037877 TCCCATAAACCCGCCGAAAA 59.962 50.000 0.00 0.00 0.00 2.29
129 130 0.889306 CCCATAAACCCGCCGAAAAA 59.111 50.000 0.00 0.00 0.00 1.94
149 150 4.171103 GCACCCCGGCGAGGTTAT 62.171 66.667 11.53 0.00 38.74 1.89
150 151 2.799452 GCACCCCGGCGAGGTTATA 61.799 63.158 11.53 0.00 38.74 0.98
151 152 2.055299 CACCCCGGCGAGGTTATAT 58.945 57.895 11.53 0.00 38.74 0.86
152 153 0.320421 CACCCCGGCGAGGTTATATG 60.320 60.000 11.53 0.00 38.74 1.78
153 154 1.295423 CCCCGGCGAGGTTATATGG 59.705 63.158 9.30 0.00 38.74 2.74
154 155 1.295423 CCCGGCGAGGTTATATGGG 59.705 63.158 9.30 0.00 38.74 4.00
155 156 1.189524 CCCGGCGAGGTTATATGGGA 61.190 60.000 9.30 0.00 37.35 4.37
156 157 0.902531 CCGGCGAGGTTATATGGGAT 59.097 55.000 9.30 0.00 34.51 3.85
157 158 1.134788 CCGGCGAGGTTATATGGGATC 60.135 57.143 9.30 0.00 34.51 3.36
158 159 1.825474 CGGCGAGGTTATATGGGATCT 59.175 52.381 0.00 0.00 0.00 2.75
159 160 2.417379 CGGCGAGGTTATATGGGATCTG 60.417 54.545 0.00 0.00 0.00 2.90
160 161 2.622436 GCGAGGTTATATGGGATCTGC 58.378 52.381 0.00 0.00 0.00 4.26
161 162 2.234908 GCGAGGTTATATGGGATCTGCT 59.765 50.000 0.00 0.00 0.00 4.24
162 163 3.447586 GCGAGGTTATATGGGATCTGCTA 59.552 47.826 0.00 0.00 0.00 3.49
163 164 4.440802 GCGAGGTTATATGGGATCTGCTAG 60.441 50.000 0.00 0.00 0.00 3.42
164 165 4.950475 CGAGGTTATATGGGATCTGCTAGA 59.050 45.833 0.00 0.00 0.00 2.43
165 166 5.067153 CGAGGTTATATGGGATCTGCTAGAG 59.933 48.000 0.00 0.00 0.00 2.43
166 167 6.159172 AGGTTATATGGGATCTGCTAGAGA 57.841 41.667 0.00 0.00 34.25 3.10
167 168 6.751050 AGGTTATATGGGATCTGCTAGAGAT 58.249 40.000 0.00 0.00 44.78 2.75
168 169 6.610830 AGGTTATATGGGATCTGCTAGAGATG 59.389 42.308 8.78 0.00 41.91 2.90
169 170 6.279882 GTTATATGGGATCTGCTAGAGATGC 58.720 44.000 12.25 12.25 46.34 3.91
170 171 2.395336 TGGGATCTGCTAGAGATGCT 57.605 50.000 16.99 0.00 46.30 3.79
171 172 2.246469 TGGGATCTGCTAGAGATGCTC 58.754 52.381 16.99 11.13 46.30 4.26
191 192 5.508872 GCTCTGAGCACATTGTTAATGATC 58.491 41.667 24.02 4.55 41.89 2.92
196 197 7.065443 TCTGAGCACATTGTTAATGATCTGAAG 59.935 37.037 8.41 5.31 41.46 3.02
239 240 5.747565 TGATTACAAGCTTCAAACGAACAG 58.252 37.500 0.00 0.00 0.00 3.16
244 245 4.576463 ACAAGCTTCAAACGAACAGAATCT 59.424 37.500 0.00 0.00 0.00 2.40
333 336 5.856156 TCGTTAATTCACCTGGTGAGTAAA 58.144 37.500 26.94 18.99 43.69 2.01
336 339 6.854381 CGTTAATTCACCTGGTGAGTAAAAAC 59.146 38.462 26.94 23.81 43.69 2.43
390 400 7.910584 ACATCAAGAATTTTAGAATTTGGCCT 58.089 30.769 3.32 0.00 35.65 5.19
394 404 7.872483 TCAAGAATTTTAGAATTTGGCCTTGTC 59.128 33.333 3.32 0.00 36.16 3.18
404 414 1.384191 GGCCTTGTCTGGTTGGGAT 59.616 57.895 0.00 0.00 0.00 3.85
457 467 1.340991 ACCAAATGGACAGATTCCCGG 60.341 52.381 6.42 0.00 45.17 5.73
486 508 4.634184 TGTCACGAATCCTAGAAGTAGC 57.366 45.455 0.00 0.00 0.00 3.58
510 1967 6.400091 GCGACTTACAGAAACATCAGTAGTTG 60.400 42.308 0.00 0.00 0.00 3.16
675 2471 5.401531 AGTAGCAATCACCGAAACTCTTA 57.598 39.130 0.00 0.00 0.00 2.10
688 2484 8.812329 CACCGAAACTCTTATATTCTTCTCAAG 58.188 37.037 0.00 0.00 0.00 3.02
720 2517 6.292703 CCACTAGTTTCGTCAATTCTCGTTTT 60.293 38.462 0.00 0.00 0.00 2.43
737 2565 3.113322 GTTTTGGCTGAGGTTTTCGTTC 58.887 45.455 0.00 0.00 0.00 3.95
842 2670 1.276421 ACTCGTCTCCAACCAATCAGG 59.724 52.381 0.00 0.00 45.67 3.86
1028 2875 1.754234 CCGCCCATTCCCCTTCTTG 60.754 63.158 0.00 0.00 0.00 3.02
1051 2909 1.619363 TCACCCCCATTCCTCCCAG 60.619 63.158 0.00 0.00 0.00 4.45
1078 2956 0.182299 CCAAATCTCCTCAGCCTCCC 59.818 60.000 0.00 0.00 0.00 4.30
1090 2971 4.292178 CCTCCCGCGCATCTCCTC 62.292 72.222 8.75 0.00 0.00 3.71
1515 3403 4.522971 GGGCCTAAGCTCTGTTCG 57.477 61.111 0.84 0.00 36.14 3.95
1516 3404 1.597461 GGGCCTAAGCTCTGTTCGT 59.403 57.895 0.84 0.00 36.14 3.85
1517 3405 0.460459 GGGCCTAAGCTCTGTTCGTC 60.460 60.000 0.84 0.00 36.14 4.20
1519 3407 0.109226 GCCTAAGCTCTGTTCGTCGT 60.109 55.000 0.00 0.00 35.50 4.34
1520 3408 1.897641 CCTAAGCTCTGTTCGTCGTC 58.102 55.000 0.00 0.00 0.00 4.20
1521 3409 1.525596 CTAAGCTCTGTTCGTCGTCG 58.474 55.000 0.00 0.00 38.55 5.12
1522 3410 0.870393 TAAGCTCTGTTCGTCGTCGT 59.130 50.000 1.33 0.00 38.33 4.34
1523 3411 0.385723 AAGCTCTGTTCGTCGTCGTC 60.386 55.000 1.33 0.00 38.33 4.20
1524 3412 1.207085 GCTCTGTTCGTCGTCGTCT 59.793 57.895 1.33 0.00 38.33 4.18
1525 3413 1.060726 GCTCTGTTCGTCGTCGTCTG 61.061 60.000 1.33 2.13 38.33 3.51
1526 3414 0.235144 CTCTGTTCGTCGTCGTCTGT 59.765 55.000 1.33 0.00 38.33 3.41
1527 3415 0.659427 TCTGTTCGTCGTCGTCTGTT 59.341 50.000 1.33 0.00 38.33 3.16
1535 3437 0.792640 TCGTCGTCTGTTAGTCGTCC 59.207 55.000 0.00 0.00 0.00 4.79
1544 3446 3.018149 CTGTTAGTCGTCCTCTTAGCCT 58.982 50.000 0.00 0.00 0.00 4.58
1589 3507 1.591158 CGTGCTAGTGTTTGTTCGTGT 59.409 47.619 0.00 0.00 0.00 4.49
1591 3509 1.855978 TGCTAGTGTTTGTTCGTGTCG 59.144 47.619 0.00 0.00 0.00 4.35
1596 3514 1.000884 TGTTTGTTCGTGTCGTGGTC 58.999 50.000 0.00 0.00 0.00 4.02
1684 3604 5.452496 GCTATCTGTTCTAAGATCTGTGCCA 60.452 44.000 0.00 0.00 37.98 4.92
1707 3627 7.073265 CCATTTGATGCTTGTTTTTCATTGTC 58.927 34.615 0.00 0.00 0.00 3.18
1710 3630 4.746115 TGATGCTTGTTTTTCATTGTCTGC 59.254 37.500 0.00 0.00 0.00 4.26
1716 3636 0.881118 TTTTCATTGTCTGCGAGCCC 59.119 50.000 0.00 0.00 0.00 5.19
1743 3663 3.689347 TGAATGTGATTCCTCAACTGGG 58.311 45.455 0.00 0.00 38.50 4.45
1744 3664 3.330405 TGAATGTGATTCCTCAACTGGGA 59.670 43.478 0.00 0.00 38.50 4.37
1852 3814 7.343057 TCAGTTCTGTGTATCCATCTGTTCTAT 59.657 37.037 0.00 0.00 0.00 1.98
1854 3816 8.200792 AGTTCTGTGTATCCATCTGTTCTATTC 58.799 37.037 0.00 0.00 0.00 1.75
1858 3820 7.492524 TGTGTATCCATCTGTTCTATTCTGTC 58.507 38.462 0.00 0.00 0.00 3.51
1860 3822 8.200792 GTGTATCCATCTGTTCTATTCTGTCTT 58.799 37.037 0.00 0.00 0.00 3.01
1865 3827 7.179160 TCCATCTGTTCTATTCTGTCTTTCTGA 59.821 37.037 0.00 0.00 0.00 3.27
1883 3845 8.143835 TCTTTCTGATTTTTCCTGTTTCCAATC 58.856 33.333 0.00 0.00 0.00 2.67
1886 3848 7.661040 TCTGATTTTTCCTGTTTCCAATCTTC 58.339 34.615 0.00 0.00 0.00 2.87
1888 3850 7.209475 TGATTTTTCCTGTTTCCAATCTTCAC 58.791 34.615 0.00 0.00 0.00 3.18
1898 3860 3.926616 TCCAATCTTCACTTTCGACTCC 58.073 45.455 0.00 0.00 0.00 3.85
1907 3869 1.139058 ACTTTCGACTCCTGCAACTGT 59.861 47.619 0.00 0.00 0.00 3.55
1911 3873 0.532862 CGACTCCTGCAACTGTTGGT 60.533 55.000 21.01 10.38 0.00 3.67
1915 3877 2.949644 ACTCCTGCAACTGTTGGTAAAC 59.050 45.455 21.01 5.53 36.78 2.01
1916 3878 2.948979 CTCCTGCAACTGTTGGTAAACA 59.051 45.455 21.01 9.60 44.06 2.83
1943 3905 8.221251 ACTCTTACTCTCAGATGTACCATGATA 58.779 37.037 0.00 0.00 0.00 2.15
1954 3916 7.981789 CAGATGTACCATGATAACAACTACACT 59.018 37.037 0.00 0.00 0.00 3.55
1991 3953 8.256611 TGCAGATAGACAAAAGATGTTTCTAC 57.743 34.615 0.00 0.00 44.12 2.59
1993 3955 9.587772 GCAGATAGACAAAAGATGTTTCTACTA 57.412 33.333 0.00 0.00 44.12 1.82
1999 3961 8.940952 AGACAAAAGATGTTTCTACTATCTTGC 58.059 33.333 0.00 0.00 44.12 4.01
2000 3962 8.621532 ACAAAAGATGTTTCTACTATCTTGCA 57.378 30.769 0.00 0.00 40.06 4.08
2002 3964 9.499585 CAAAAGATGTTTCTACTATCTTGCATG 57.500 33.333 0.00 0.00 40.12 4.06
2003 3965 7.798596 AAGATGTTTCTACTATCTTGCATGG 57.201 36.000 0.00 0.00 39.12 3.66
2005 3967 7.341805 AGATGTTTCTACTATCTTGCATGGTT 58.658 34.615 0.00 0.00 0.00 3.67
2006 3968 6.985188 TGTTTCTACTATCTTGCATGGTTC 57.015 37.500 0.00 0.00 0.00 3.62
2023 3986 6.678900 GCATGGTTCTGTTTGTTCTATGATCC 60.679 42.308 0.00 0.00 0.00 3.36
2024 3987 5.875224 TGGTTCTGTTTGTTCTATGATCCA 58.125 37.500 0.00 0.00 0.00 3.41
2025 3988 6.484288 TGGTTCTGTTTGTTCTATGATCCAT 58.516 36.000 0.00 0.00 0.00 3.41
2026 3989 6.947733 TGGTTCTGTTTGTTCTATGATCCATT 59.052 34.615 0.00 0.00 0.00 3.16
2027 3990 7.451255 TGGTTCTGTTTGTTCTATGATCCATTT 59.549 33.333 0.00 0.00 0.00 2.32
2083 4046 6.147328 GTGTGATTGAGGTAGAAAGTGTAACC 59.853 42.308 0.00 0.00 37.80 2.85
2119 4082 6.258287 CAGATGAAACTGCTAGATCAGAAAGG 59.742 42.308 4.57 0.00 37.51 3.11
2123 4086 6.596888 TGAAACTGCTAGATCAGAAAGGAATG 59.403 38.462 4.57 0.00 37.51 2.67
2129 4092 8.027524 TGCTAGATCAGAAAGGAATGTAGATT 57.972 34.615 0.00 0.00 0.00 2.40
2157 4120 9.052759 GTTGAGTAACTTTATGTTGGAAAGAGA 57.947 33.333 2.31 0.00 39.55 3.10
2162 4125 9.994432 GTAACTTTATGTTGGAAAGAGATCATG 57.006 33.333 0.00 0.00 39.55 3.07
2164 4127 9.739276 AACTTTATGTTGGAAAGAGATCATGTA 57.261 29.630 0.00 0.00 37.52 2.29
2227 4190 1.876156 CTTCGCTGCAGAGGAAAAAGT 59.124 47.619 20.43 0.00 0.00 2.66
2264 4227 8.160765 TCTGGTTTAATGAACTGAAGAACCATA 58.839 33.333 5.61 0.00 42.70 2.74
2289 4252 2.136298 CTAGCTGAGGAGGTGAGACA 57.864 55.000 0.00 0.00 0.00 3.41
2326 4289 5.240403 GCAACAGAAATTCCTTCTCTGAACT 59.760 40.000 10.37 0.00 42.84 3.01
2346 4309 2.549754 CTGTCGGACATGTTTTTGCTCT 59.450 45.455 11.86 0.00 0.00 4.09
2388 4351 5.126222 TCTGCATATAATTTCCGTTTTGGCA 59.874 36.000 0.00 0.00 37.80 4.92
2400 4363 7.397892 TTCCGTTTTGGCATCTATTTTATCA 57.602 32.000 0.00 0.00 37.80 2.15
2433 4396 1.296715 CCCAGGTCCAGGAAAGACG 59.703 63.158 0.82 0.00 34.97 4.18
2434 4397 1.192146 CCCAGGTCCAGGAAAGACGA 61.192 60.000 0.82 0.00 34.97 4.20
2437 4400 0.317479 AGGTCCAGGAAAGACGAACG 59.683 55.000 0.00 0.00 34.97 3.95
2442 4405 1.402984 CCAGGAAAGACGAACGAGGAG 60.403 57.143 0.14 0.00 0.00 3.69
2443 4406 0.244178 AGGAAAGACGAACGAGGAGC 59.756 55.000 0.14 0.00 0.00 4.70
2444 4407 0.244178 GGAAAGACGAACGAGGAGCT 59.756 55.000 0.14 0.00 0.00 4.09
2445 4408 1.619983 GAAAGACGAACGAGGAGCTC 58.380 55.000 4.71 4.71 0.00 4.09
2446 4409 1.200484 GAAAGACGAACGAGGAGCTCT 59.800 52.381 14.64 0.00 0.00 4.09
2448 4411 2.110901 AGACGAACGAGGAGCTCTTA 57.889 50.000 14.64 0.00 0.00 2.10
2451 4414 2.161030 ACGAACGAGGAGCTCTTAAGT 58.839 47.619 14.64 7.14 0.00 2.24
2459 4422 6.100668 ACGAGGAGCTCTTAAGTAATTCAAC 58.899 40.000 14.64 0.00 0.00 3.18
2486 4449 6.759497 AGGTACAGAATTAGCATTGAAACC 57.241 37.500 0.00 0.00 0.00 3.27
2514 4477 6.964677 CGTGAGCATGATTTTATTCATCAC 57.035 37.500 0.00 0.00 34.09 3.06
2530 4493 4.507710 TCATCACCTCATTTCAGTACTGC 58.492 43.478 18.45 0.00 0.00 4.40
2534 4497 3.681897 CACCTCATTTCAGTACTGCAGTC 59.318 47.826 25.56 15.02 0.00 3.51
2564 4527 5.038683 CGAAATGGCGTTGTATGTAGTAGA 58.961 41.667 0.00 0.00 0.00 2.59
2573 4536 6.457934 GCGTTGTATGTAGTAGAGCAGTTCTA 60.458 42.308 0.00 0.00 37.36 2.10
2621 4584 1.769026 TGTACCTTGTTGCTTGCCAA 58.231 45.000 0.00 0.00 0.00 4.52
2623 4586 2.100584 TGTACCTTGTTGCTTGCCAAAG 59.899 45.455 0.00 0.00 34.68 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.230314 CGATATATATGTCGGCTCCAGG 57.770 50.000 20.54 0.00 37.69 4.45
8 9 4.912187 CCTGCGATTCCGATATATATGTCG 59.088 45.833 21.14 21.14 40.46 4.35
9 10 4.681942 GCCTGCGATTCCGATATATATGTC 59.318 45.833 0.00 0.00 38.22 3.06
10 11 4.621991 GCCTGCGATTCCGATATATATGT 58.378 43.478 0.00 0.00 38.22 2.29
11 12 3.670523 CGCCTGCGATTCCGATATATATG 59.329 47.826 5.43 0.00 42.83 1.78
12 13 3.305403 CCGCCTGCGATTCCGATATATAT 60.305 47.826 13.94 0.00 42.83 0.86
13 14 2.034179 CCGCCTGCGATTCCGATATATA 59.966 50.000 13.94 0.00 42.83 0.86
14 15 1.202417 CCGCCTGCGATTCCGATATAT 60.202 52.381 13.94 0.00 42.83 0.86
15 16 0.172578 CCGCCTGCGATTCCGATATA 59.827 55.000 13.94 0.00 42.83 0.86
16 17 1.079819 CCGCCTGCGATTCCGATAT 60.080 57.895 13.94 0.00 42.83 1.63
17 18 2.023414 AACCGCCTGCGATTCCGATA 62.023 55.000 13.94 0.00 42.83 2.92
18 19 2.869503 AAACCGCCTGCGATTCCGAT 62.870 55.000 13.94 0.00 42.83 4.18
19 20 2.228389 TAAACCGCCTGCGATTCCGA 62.228 55.000 13.94 0.00 42.83 4.55
20 21 1.157870 ATAAACCGCCTGCGATTCCG 61.158 55.000 13.94 0.00 42.83 4.30
21 22 0.307760 CATAAACCGCCTGCGATTCC 59.692 55.000 13.94 0.00 42.83 3.01
22 23 0.307760 CCATAAACCGCCTGCGATTC 59.692 55.000 13.94 0.00 42.83 2.52
23 24 1.101049 CCCATAAACCGCCTGCGATT 61.101 55.000 13.94 10.06 42.83 3.34
24 25 1.525995 CCCATAAACCGCCTGCGAT 60.526 57.895 13.94 0.00 42.83 4.58
25 26 2.124901 CCCATAAACCGCCTGCGA 60.125 61.111 13.94 0.00 42.83 5.10
26 27 3.887868 GCCCATAAACCGCCTGCG 61.888 66.667 4.20 4.20 39.44 5.18
27 28 2.440247 AGCCCATAAACCGCCTGC 60.440 61.111 0.00 0.00 0.00 4.85
28 29 1.823899 GGAGCCCATAAACCGCCTG 60.824 63.158 0.00 0.00 0.00 4.85
29 30 2.595655 GGAGCCCATAAACCGCCT 59.404 61.111 0.00 0.00 0.00 5.52
30 31 2.518587 GGGAGCCCATAAACCGCC 60.519 66.667 0.00 0.00 35.81 6.13
31 32 2.900337 CGGGAGCCCATAAACCGC 60.900 66.667 6.34 0.00 37.93 5.68
43 44 1.605202 CCCACAAAACATTTGCGGGAG 60.605 52.381 19.47 5.94 42.85 4.30
44 45 0.390860 CCCACAAAACATTTGCGGGA 59.609 50.000 19.47 0.00 42.85 5.14
45 46 1.227342 GCCCACAAAACATTTGCGGG 61.227 55.000 19.75 19.75 43.03 6.13
46 47 0.531532 TGCCCACAAAACATTTGCGG 60.532 50.000 2.88 3.19 0.00 5.69
47 48 0.860533 CTGCCCACAAAACATTTGCG 59.139 50.000 2.88 0.00 0.00 4.85
48 49 1.228533 CCTGCCCACAAAACATTTGC 58.771 50.000 2.88 0.00 0.00 3.68
49 50 1.881591 CCCTGCCCACAAAACATTTG 58.118 50.000 1.47 1.47 0.00 2.32
50 51 0.108396 GCCCTGCCCACAAAACATTT 59.892 50.000 0.00 0.00 0.00 2.32
51 52 1.754107 GCCCTGCCCACAAAACATT 59.246 52.632 0.00 0.00 0.00 2.71
52 53 2.216331 GGCCCTGCCCACAAAACAT 61.216 57.895 0.00 0.00 44.06 2.71
53 54 2.841988 GGCCCTGCCCACAAAACA 60.842 61.111 0.00 0.00 44.06 2.83
69 70 3.370231 CGGGTCCGCCAAAAAGGG 61.370 66.667 0.00 0.00 38.09 3.95
84 85 1.326548 CTAAAATTTCGACCCGAGCGG 59.673 52.381 1.06 1.06 37.14 5.52
85 86 1.326548 CCTAAAATTTCGACCCGAGCG 59.673 52.381 0.00 0.00 37.14 5.03
86 87 2.350804 GACCTAAAATTTCGACCCGAGC 59.649 50.000 0.00 0.00 37.14 5.03
87 88 2.601763 CGACCTAAAATTTCGACCCGAG 59.398 50.000 0.00 0.00 37.14 4.63
88 89 2.029110 ACGACCTAAAATTTCGACCCGA 60.029 45.455 3.62 0.00 36.58 5.14
89 90 2.340337 ACGACCTAAAATTTCGACCCG 58.660 47.619 3.62 2.84 36.58 5.28
90 91 2.674852 GGACGACCTAAAATTTCGACCC 59.325 50.000 3.62 1.48 40.32 4.46
91 92 2.674852 GGGACGACCTAAAATTTCGACC 59.325 50.000 3.44 8.77 43.81 4.79
92 93 3.328505 TGGGACGACCTAAAATTTCGAC 58.671 45.455 3.44 0.00 41.11 4.20
93 94 3.681593 TGGGACGACCTAAAATTTCGA 57.318 42.857 3.44 0.00 41.11 3.71
94 95 6.253013 GTTTATGGGACGACCTAAAATTTCG 58.747 40.000 3.44 0.00 41.11 3.46
95 96 6.405065 GGGTTTATGGGACGACCTAAAATTTC 60.405 42.308 3.44 0.00 41.11 2.17
96 97 5.419788 GGGTTTATGGGACGACCTAAAATTT 59.580 40.000 3.44 0.00 41.11 1.82
97 98 4.951715 GGGTTTATGGGACGACCTAAAATT 59.048 41.667 3.44 0.00 41.11 1.82
98 99 4.529897 GGGTTTATGGGACGACCTAAAAT 58.470 43.478 3.44 0.00 41.11 1.82
99 100 3.619487 CGGGTTTATGGGACGACCTAAAA 60.619 47.826 3.44 0.00 41.11 1.52
100 101 2.093553 CGGGTTTATGGGACGACCTAAA 60.094 50.000 3.44 0.00 41.11 1.85
101 102 1.481772 CGGGTTTATGGGACGACCTAA 59.518 52.381 3.44 0.00 41.11 2.69
102 103 1.113788 CGGGTTTATGGGACGACCTA 58.886 55.000 3.44 0.00 41.11 3.08
103 104 1.902556 CGGGTTTATGGGACGACCT 59.097 57.895 3.44 0.00 41.11 3.85
104 105 1.816679 GCGGGTTTATGGGACGACC 60.817 63.158 0.00 0.00 40.81 4.79
105 106 1.816679 GGCGGGTTTATGGGACGAC 60.817 63.158 0.00 0.00 0.00 4.34
106 107 2.585698 GGCGGGTTTATGGGACGA 59.414 61.111 0.00 0.00 0.00 4.20
107 108 2.855880 TTCGGCGGGTTTATGGGACG 62.856 60.000 7.21 0.00 0.00 4.79
108 109 0.677414 TTTCGGCGGGTTTATGGGAC 60.677 55.000 7.21 0.00 0.00 4.46
109 110 0.037877 TTTTCGGCGGGTTTATGGGA 59.962 50.000 7.21 0.00 0.00 4.37
110 111 0.889306 TTTTTCGGCGGGTTTATGGG 59.111 50.000 7.21 0.00 0.00 4.00
132 133 2.108278 ATATAACCTCGCCGGGGTGC 62.108 60.000 10.71 0.00 37.13 5.01
133 134 0.320421 CATATAACCTCGCCGGGGTG 60.320 60.000 10.71 16.01 37.13 4.61
134 135 1.477685 CCATATAACCTCGCCGGGGT 61.478 60.000 19.13 0.69 38.94 4.95
135 136 1.295423 CCATATAACCTCGCCGGGG 59.705 63.158 13.31 13.31 36.97 5.73
136 137 1.189524 TCCCATATAACCTCGCCGGG 61.190 60.000 2.18 0.00 36.97 5.73
137 138 0.902531 ATCCCATATAACCTCGCCGG 59.097 55.000 0.00 0.00 39.35 6.13
138 139 1.825474 AGATCCCATATAACCTCGCCG 59.175 52.381 0.00 0.00 0.00 6.46
139 140 2.678190 GCAGATCCCATATAACCTCGCC 60.678 54.545 0.00 0.00 0.00 5.54
140 141 2.234908 AGCAGATCCCATATAACCTCGC 59.765 50.000 0.00 0.00 0.00 5.03
141 142 4.950475 TCTAGCAGATCCCATATAACCTCG 59.050 45.833 0.00 0.00 0.00 4.63
142 143 6.191315 TCTCTAGCAGATCCCATATAACCTC 58.809 44.000 0.00 0.00 0.00 3.85
143 144 6.159172 TCTCTAGCAGATCCCATATAACCT 57.841 41.667 0.00 0.00 0.00 3.50
144 145 6.685116 GCATCTCTAGCAGATCCCATATAACC 60.685 46.154 0.00 0.00 40.20 2.85
145 146 6.098124 AGCATCTCTAGCAGATCCCATATAAC 59.902 42.308 0.00 0.00 40.20 1.89
146 147 6.200852 AGCATCTCTAGCAGATCCCATATAA 58.799 40.000 0.00 0.00 40.20 0.98
147 148 5.775268 AGCATCTCTAGCAGATCCCATATA 58.225 41.667 0.00 0.00 40.20 0.86
148 149 4.622815 AGCATCTCTAGCAGATCCCATAT 58.377 43.478 0.00 0.00 40.20 1.78
149 150 4.022603 GAGCATCTCTAGCAGATCCCATA 58.977 47.826 0.00 0.00 40.20 2.74
150 151 2.833338 GAGCATCTCTAGCAGATCCCAT 59.167 50.000 0.00 0.00 40.20 4.00
151 152 2.246469 GAGCATCTCTAGCAGATCCCA 58.754 52.381 0.00 0.00 40.20 4.37
167 168 4.325972 TCATTAACAATGTGCTCAGAGCA 58.674 39.130 21.85 21.85 42.39 4.26
168 169 4.952262 TCATTAACAATGTGCTCAGAGC 57.048 40.909 16.21 16.21 39.87 4.09
169 170 6.537660 TCAGATCATTAACAATGTGCTCAGAG 59.462 38.462 0.00 0.00 39.87 3.35
170 171 6.408869 TCAGATCATTAACAATGTGCTCAGA 58.591 36.000 0.00 0.00 39.87 3.27
171 172 6.673154 TCAGATCATTAACAATGTGCTCAG 57.327 37.500 0.00 0.00 39.87 3.35
185 186 3.549827 CGCTCGCTAGACTTCAGATCATT 60.550 47.826 0.00 0.00 0.00 2.57
191 192 3.990141 GCGCTCGCTAGACTTCAG 58.010 61.111 0.00 0.00 38.26 3.02
215 216 6.204688 TCTGTTCGTTTGAAGCTTGTAATCAT 59.795 34.615 2.10 0.00 33.98 2.45
239 240 3.092301 AGGCAAAAACCCTGCTAGATTC 58.908 45.455 0.00 0.00 39.82 2.52
244 245 0.109723 ACGAGGCAAAAACCCTGCTA 59.890 50.000 0.00 0.00 39.82 3.49
303 306 2.084546 AGGTGAATTAACGAGCCAAGC 58.915 47.619 0.00 0.00 0.00 4.01
304 307 2.420022 CCAGGTGAATTAACGAGCCAAG 59.580 50.000 0.00 0.00 0.00 3.61
305 308 2.224670 ACCAGGTGAATTAACGAGCCAA 60.225 45.455 0.00 0.00 0.00 4.52
306 309 1.349688 ACCAGGTGAATTAACGAGCCA 59.650 47.619 0.00 0.00 0.00 4.75
333 336 3.399330 TCTTCCATTTCGAGAAGCGTTT 58.601 40.909 7.15 0.00 39.48 3.60
336 339 4.151798 GTTTTCTTCCATTTCGAGAAGCG 58.848 43.478 7.15 0.00 39.48 4.68
378 388 3.806949 ACCAGACAAGGCCAAATTCTA 57.193 42.857 5.01 0.00 0.00 2.10
381 391 1.693606 CCAACCAGACAAGGCCAAATT 59.306 47.619 5.01 0.00 0.00 1.82
384 394 1.152567 CCCAACCAGACAAGGCCAA 60.153 57.895 5.01 0.00 0.00 4.52
477 487 6.564709 TGTTTCTGTAAGTCGCTACTTCTA 57.435 37.500 6.93 0.00 42.42 2.10
478 488 5.449107 TGTTTCTGTAAGTCGCTACTTCT 57.551 39.130 6.93 0.00 42.42 2.85
486 508 6.089551 CCAACTACTGATGTTTCTGTAAGTCG 59.910 42.308 0.00 0.00 36.30 4.18
510 1967 3.423154 GCTGTAGCACACACGCCC 61.423 66.667 0.00 0.00 41.59 6.13
588 2311 6.968904 GTGCTAATTCATCATAAACACTGGTG 59.031 38.462 0.00 0.00 0.00 4.17
590 2313 7.087409 TGTGCTAATTCATCATAAACACTGG 57.913 36.000 0.00 0.00 0.00 4.00
648 2444 5.978814 AGTTTCGGTGATTGCTACTAGAAT 58.021 37.500 0.00 0.00 0.00 2.40
654 2450 7.948278 ATATAAGAGTTTCGGTGATTGCTAC 57.052 36.000 0.00 0.00 0.00 3.58
655 2451 8.421784 AGAATATAAGAGTTTCGGTGATTGCTA 58.578 33.333 0.00 0.00 0.00 3.49
675 2471 9.883142 CTAGTGGTTCTTTCTTGAGAAGAATAT 57.117 33.333 0.00 0.00 46.15 1.28
688 2484 5.978934 TTGACGAAACTAGTGGTTCTTTC 57.021 39.130 0.00 0.00 37.12 2.62
720 2517 0.882927 CCGAACGAAAACCTCAGCCA 60.883 55.000 0.00 0.00 0.00 4.75
784 2612 2.493278 AGGCAGATGAAACGAAAATGGG 59.507 45.455 0.00 0.00 0.00 4.00
995 2837 0.105408 GGCGGCGTTAAATAGGAGGA 59.895 55.000 9.37 0.00 0.00 3.71
1028 2875 1.988982 GAGGAATGGGGGTGAGGAGC 61.989 65.000 0.00 0.00 0.00 4.70
1051 2909 1.063717 TGAGGAGATTTGGGGGATTGC 60.064 52.381 0.00 0.00 0.00 3.56
1078 2956 3.490793 ATGTCGGAGGAGATGCGCG 62.491 63.158 0.00 0.00 43.36 6.86
1515 3403 1.463198 GGACGACTAACAGACGACGAC 60.463 57.143 0.00 0.00 36.90 4.34
1516 3404 0.792640 GGACGACTAACAGACGACGA 59.207 55.000 0.00 0.00 36.90 4.20
1517 3405 0.795085 AGGACGACTAACAGACGACG 59.205 55.000 5.14 0.00 36.90 5.12
1519 3407 2.469274 AGAGGACGACTAACAGACGA 57.531 50.000 5.14 0.00 36.90 4.20
1520 3408 3.485546 GCTAAGAGGACGACTAACAGACG 60.486 52.174 0.00 0.00 39.17 4.18
1521 3409 3.181498 GGCTAAGAGGACGACTAACAGAC 60.181 52.174 0.00 0.00 0.00 3.51
1522 3410 3.015327 GGCTAAGAGGACGACTAACAGA 58.985 50.000 0.00 0.00 0.00 3.41
1523 3411 3.018149 AGGCTAAGAGGACGACTAACAG 58.982 50.000 0.00 0.00 0.00 3.16
1524 3412 2.753452 CAGGCTAAGAGGACGACTAACA 59.247 50.000 0.00 0.00 0.00 2.41
1525 3413 3.015327 TCAGGCTAAGAGGACGACTAAC 58.985 50.000 0.00 0.00 0.00 2.34
1526 3414 3.361281 TCAGGCTAAGAGGACGACTAA 57.639 47.619 0.00 0.00 0.00 2.24
1527 3415 3.215151 CATCAGGCTAAGAGGACGACTA 58.785 50.000 0.00 0.00 0.00 2.59
1535 3437 3.801050 CGATGAACACATCAGGCTAAGAG 59.199 47.826 10.15 0.00 42.53 2.85
1544 3446 2.849294 TTCCACCGATGAACACATCA 57.151 45.000 10.15 0.00 43.67 3.07
1591 3509 2.030185 ACAGACACACTACATCGACCAC 60.030 50.000 0.00 0.00 0.00 4.16
1596 3514 4.160736 TCAGAACAGACACACTACATCG 57.839 45.455 0.00 0.00 0.00 3.84
1684 3604 7.519328 GCAGACAATGAAAAACAAGCATCAAAT 60.519 33.333 0.00 0.00 0.00 2.32
1707 3627 1.577328 ATTCAACAACGGGCTCGCAG 61.577 55.000 5.51 0.00 40.63 5.18
1710 3630 0.110238 CACATTCAACAACGGGCTCG 60.110 55.000 3.27 3.27 43.02 5.03
1716 3636 4.747540 TGAGGAATCACATTCAACAACG 57.252 40.909 0.00 0.00 41.03 4.10
1743 3663 5.584649 TCACGAGTTGGGATAATCAAATGTC 59.415 40.000 0.00 0.00 0.00 3.06
1744 3664 5.496556 TCACGAGTTGGGATAATCAAATGT 58.503 37.500 0.00 0.00 0.00 2.71
1811 3764 2.568623 ACTGAAGGACGAGCCAAAAT 57.431 45.000 0.00 0.00 40.02 1.82
1812 3765 2.158813 AGAACTGAAGGACGAGCCAAAA 60.159 45.455 0.00 0.00 40.02 2.44
1813 3766 1.416401 AGAACTGAAGGACGAGCCAAA 59.584 47.619 0.00 0.00 40.02 3.28
1852 3814 7.645058 AACAGGAAAAATCAGAAAGACAGAA 57.355 32.000 0.00 0.00 0.00 3.02
1854 3816 6.920210 GGAAACAGGAAAAATCAGAAAGACAG 59.080 38.462 0.00 0.00 0.00 3.51
1858 3820 8.146412 AGATTGGAAACAGGAAAAATCAGAAAG 58.854 33.333 0.00 0.00 44.54 2.62
1860 3822 7.601705 AGATTGGAAACAGGAAAAATCAGAA 57.398 32.000 0.00 0.00 44.54 3.02
1865 3827 7.365497 AGTGAAGATTGGAAACAGGAAAAAT 57.635 32.000 0.00 0.00 44.54 1.82
1883 3845 2.154854 TGCAGGAGTCGAAAGTGAAG 57.845 50.000 0.00 0.00 0.00 3.02
1886 3848 1.528586 CAGTTGCAGGAGTCGAAAGTG 59.471 52.381 0.00 0.00 0.00 3.16
1888 3850 1.871080 ACAGTTGCAGGAGTCGAAAG 58.129 50.000 0.00 0.00 0.00 2.62
1907 3869 7.356089 TCTGAGAGTAAGAGTTGTTTACCAA 57.644 36.000 0.00 0.00 32.66 3.67
1911 3873 8.521176 GGTACATCTGAGAGTAAGAGTTGTTTA 58.479 37.037 0.00 0.00 0.00 2.01
1915 3877 6.516739 TGGTACATCTGAGAGTAAGAGTTG 57.483 41.667 0.00 0.00 0.00 3.16
1943 3905 8.537016 TGCATCCTATTTAGTAGTGTAGTTGTT 58.463 33.333 0.00 0.00 0.00 2.83
1963 3925 6.690194 AACATCTTTTGTCTATCTGCATCC 57.310 37.500 0.00 0.00 37.68 3.51
1991 3953 5.633830 ACAAACAGAACCATGCAAGATAG 57.366 39.130 0.00 0.00 0.00 2.08
1993 3955 4.586001 AGAACAAACAGAACCATGCAAGAT 59.414 37.500 0.00 0.00 0.00 2.40
1995 3957 4.311816 AGAACAAACAGAACCATGCAAG 57.688 40.909 0.00 0.00 0.00 4.01
1996 3958 5.534278 TCATAGAACAAACAGAACCATGCAA 59.466 36.000 0.00 0.00 0.00 4.08
1997 3959 5.069318 TCATAGAACAAACAGAACCATGCA 58.931 37.500 0.00 0.00 0.00 3.96
1999 3961 6.375174 TGGATCATAGAACAAACAGAACCATG 59.625 38.462 0.00 0.00 0.00 3.66
2000 3962 6.484288 TGGATCATAGAACAAACAGAACCAT 58.516 36.000 0.00 0.00 0.00 3.55
2002 3964 7.396540 AATGGATCATAGAACAAACAGAACC 57.603 36.000 0.00 0.00 0.00 3.62
2003 3965 8.514594 TCAAATGGATCATAGAACAAACAGAAC 58.485 33.333 0.00 0.00 0.00 3.01
2005 3967 8.680001 CATCAAATGGATCATAGAACAAACAGA 58.320 33.333 0.00 0.00 32.57 3.41
2006 3968 8.851960 CATCAAATGGATCATAGAACAAACAG 57.148 34.615 0.00 0.00 32.57 3.16
2023 3986 3.449737 AGGTGCAGGAAATCCATCAAATG 59.550 43.478 1.67 0.00 38.89 2.32
2024 3987 3.449737 CAGGTGCAGGAAATCCATCAAAT 59.550 43.478 1.67 0.00 38.89 2.32
2025 3988 2.827322 CAGGTGCAGGAAATCCATCAAA 59.173 45.455 1.67 0.00 38.89 2.69
2026 3989 2.449464 CAGGTGCAGGAAATCCATCAA 58.551 47.619 1.67 0.00 38.89 2.57
2027 3990 1.956636 GCAGGTGCAGGAAATCCATCA 60.957 52.381 1.67 0.00 41.59 3.07
2040 4003 2.129607 CACTGTTGAATTTGCAGGTGC 58.870 47.619 0.00 0.00 42.50 5.01
2054 4017 5.760253 CACTTTCTACCTCAATCACACTGTT 59.240 40.000 0.00 0.00 0.00 3.16
2055 4018 5.163301 ACACTTTCTACCTCAATCACACTGT 60.163 40.000 0.00 0.00 0.00 3.55
2083 4046 2.163010 AGTTTCATCTGCGCCATCTTTG 59.837 45.455 4.18 0.00 0.00 2.77
2097 4060 6.305272 TCCTTTCTGATCTAGCAGTTTCAT 57.695 37.500 0.00 0.00 37.20 2.57
2129 4092 9.179909 TCTTTCCAACATAAAGTTACTCAACAA 57.820 29.630 0.00 0.00 38.74 2.83
2162 4125 9.827411 GACTGTTCTACATTCCTTTTTCATTAC 57.173 33.333 0.00 0.00 0.00 1.89
2164 4127 8.697507 AGACTGTTCTACATTCCTTTTTCATT 57.302 30.769 0.00 0.00 29.13 2.57
2306 4269 5.119898 CGACAGTTCAGAGAAGGAATTTCTG 59.880 44.000 0.00 0.00 46.12 3.02
2326 4289 2.571212 AGAGCAAAAACATGTCCGACA 58.429 42.857 3.10 3.10 0.00 4.35
2378 4341 8.647143 AAATGATAAAATAGATGCCAAAACGG 57.353 30.769 0.00 0.00 38.11 4.44
2400 4363 6.975949 TGGACCTGGGTACATGTAAATAAAT 58.024 36.000 7.25 0.00 33.38 1.40
2433 4396 6.331061 TGAATTACTTAAGAGCTCCTCGTTC 58.669 40.000 10.93 5.39 35.36 3.95
2434 4397 6.282199 TGAATTACTTAAGAGCTCCTCGTT 57.718 37.500 10.93 0.01 35.36 3.85
2437 4400 7.324178 TGAGTTGAATTACTTAAGAGCTCCTC 58.676 38.462 10.93 5.08 0.00 3.71
2442 4405 7.674471 ACCTTGAGTTGAATTACTTAAGAGC 57.326 36.000 10.09 0.00 41.65 4.09
2443 4406 9.706691 TGTACCTTGAGTTGAATTACTTAAGAG 57.293 33.333 10.09 6.96 41.65 2.85
2444 4407 9.706691 CTGTACCTTGAGTTGAATTACTTAAGA 57.293 33.333 10.09 0.00 41.65 2.10
2445 4408 9.706691 TCTGTACCTTGAGTTGAATTACTTAAG 57.293 33.333 0.00 0.00 39.89 1.85
2448 4411 9.574516 AATTCTGTACCTTGAGTTGAATTACTT 57.425 29.630 0.00 0.00 33.71 2.24
2451 4414 9.162764 GCTAATTCTGTACCTTGAGTTGAATTA 57.837 33.333 0.00 0.00 35.40 1.40
2459 4422 7.615582 TTCAATGCTAATTCTGTACCTTGAG 57.384 36.000 0.00 0.00 0.00 3.02
2502 4465 9.739276 AGTACTGAAATGAGGTGATGAATAAAA 57.261 29.630 0.00 0.00 0.00 1.52
2509 4472 4.256110 TGCAGTACTGAAATGAGGTGATG 58.744 43.478 27.08 0.00 0.00 3.07
2513 4476 3.615110 CGACTGCAGTACTGAAATGAGGT 60.615 47.826 27.08 9.75 0.00 3.85
2514 4477 2.926200 CGACTGCAGTACTGAAATGAGG 59.074 50.000 27.08 6.28 0.00 3.86
2551 4514 7.426410 GCATAGAACTGCTCTACTACATACAA 58.574 38.462 0.00 0.00 39.52 2.41
2623 4586 2.481471 GGCGGGCAAGATAGGCAAC 61.481 63.158 0.00 0.00 35.46 4.17


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

AutoCloner maintained by Alex Coulton.