Multiple sequence alignment - TraesCS3D01G261000

Loading Multiple Alignment...

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 TraesCS3D01G261000 chr3D 100.000 4536 0 0 1 4536 363125856 363121321 0.000000e+00 8377.0
1 TraesCS3D01G261000 chr3D 81.034 174 32 1 3476 3649 574723279 574723107 2.200000e-28 137.0
2 TraesCS3D01G261000 chr3D 79.470 151 28 3 3734 3881 523338259 523338409 2.230000e-18 104.0
3 TraesCS3D01G261000 chr3D 87.692 65 8 0 3951 4015 528794930 528794994 4.870000e-10 76.8
4 TraesCS3D01G261000 chr3D 88.710 62 7 0 3954 4015 609002179 609002118 4.870000e-10 76.8
5 TraesCS3D01G261000 chr3A 95.750 4259 115 20 303 4536 483485044 483480827 0.000000e+00 6802.0
6 TraesCS3D01G261000 chr3A 78.155 206 37 7 3740 3939 635393854 635394057 1.710000e-24 124.0
7 TraesCS3D01G261000 chr3B 93.872 2774 103 25 685 3420 472913559 472910815 0.000000e+00 4119.0
8 TraesCS3D01G261000 chr3B 80.513 195 34 3 3743 3933 487873771 487873577 3.660000e-31 147.0
9 TraesCS3D01G261000 chr3B 88.710 62 7 0 3954 4015 525648259 525648198 4.870000e-10 76.8
10 TraesCS3D01G261000 chr7D 96.805 313 7 3 1 311 31123057 31123368 1.870000e-143 520.0
11 TraesCS3D01G261000 chr4D 97.368 304 8 0 1 304 435224011 435224314 6.730000e-143 518.0
12 TraesCS3D01G261000 chr4D 87.382 317 30 7 1463 1769 90989849 90989533 5.580000e-94 355.0
13 TraesCS3D01G261000 chr4D 78.621 145 25 6 3740 3881 509171489 509171348 1.740000e-14 91.6
14 TraesCS3D01G261000 chr4D 88.710 62 7 0 3954 4015 381886477 381886416 4.870000e-10 76.8
15 TraesCS3D01G261000 chr6D 96.452 310 7 2 1 309 402564399 402564093 4.050000e-140 508.0
16 TraesCS3D01G261000 chr6D 96.711 304 10 0 1 304 65650645 65650948 1.460000e-139 507.0
17 TraesCS3D01G261000 chr6A 96.154 312 11 1 1 311 7204314 7204003 4.050000e-140 508.0
18 TraesCS3D01G261000 chr2D 96.711 304 10 0 1 304 27776848 27777151 1.460000e-139 507.0
19 TraesCS3D01G261000 chr2D 83.243 185 24 5 3960 4140 628261291 628261110 3.630000e-36 163.0
20 TraesCS3D01G261000 chr2D 90.323 62 5 1 3962 4022 126974268 126974329 3.760000e-11 80.5
21 TraesCS3D01G261000 chr2D 88.710 62 7 0 3954 4015 532049048 532048987 4.870000e-10 76.8
22 TraesCS3D01G261000 chr5B 96.104 308 12 0 1 308 113870239 113869932 1.880000e-138 503.0
23 TraesCS3D01G261000 chrUn 96.104 308 11 1 1 307 103386502 103386809 6.770000e-138 501.0
24 TraesCS3D01G261000 chr1D 96.393 305 10 1 1 305 447461869 447461566 6.770000e-138 501.0
25 TraesCS3D01G261000 chr1D 77.358 212 37 10 3740 3945 211641348 211641554 1.030000e-21 115.0
26 TraesCS3D01G261000 chr1D 88.710 62 7 0 3954 4015 487311158 487311219 4.870000e-10 76.8
27 TraesCS3D01G261000 chr1D 95.000 40 2 0 3368 3407 285439567 285439606 3.790000e-06 63.9
28 TraesCS3D01G261000 chr4A 86.828 372 38 8 1408 1769 502902592 502902222 5.460000e-109 405.0
29 TraesCS3D01G261000 chr4B 83.568 213 26 6 1308 1512 127094364 127094153 1.670000e-44 191.0
30 TraesCS3D01G261000 chr7A 76.946 334 72 4 4203 4532 690511555 690511223 7.750000e-43 185.0
31 TraesCS3D01G261000 chr5A 81.313 198 27 9 3756 3945 347209996 347209801 7.860000e-33 152.0
32 TraesCS3D01G261000 chr5A 90.741 54 5 0 3353 3406 24777155 24777102 6.290000e-09 73.1
33 TraesCS3D01G261000 chr2A 80.193 207 36 4 3740 3941 753951141 753950935 2.830000e-32 150.0
34 TraesCS3D01G261000 chr6B 82.812 128 22 0 4335 4462 188656111 188655984 1.030000e-21 115.0
35 TraesCS3D01G261000 chr6B 100.000 32 0 0 3365 3396 212194611 212194580 4.900000e-05 60.2
36 TraesCS3D01G261000 chr2B 82.482 137 19 4 3740 3874 600491197 600491330 1.030000e-21 115.0
37 TraesCS3D01G261000 chr1A 79.412 102 20 1 3306 3407 560378880 560378780 2.260000e-08 71.3


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 TraesCS3D01G261000 chr3D 363121321 363125856 4535 True 8377 8377 100.000 1 4536 1 chr3D.!!$R1 4535
1 TraesCS3D01G261000 chr3A 483480827 483485044 4217 True 6802 6802 95.750 303 4536 1 chr3A.!!$R1 4233
2 TraesCS3D01G261000 chr3B 472910815 472913559 2744 True 4119 4119 93.872 685 3420 1 chr3B.!!$R1 2735

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
296 297 0.036388 TTTTGCGGGGTCTGCTAGAG 60.036 55.000 0.0 0.0 0.00 2.43 F
302 303 0.176910 GGGGTCTGCTAGAGTTGCTC 59.823 60.000 0.0 0.0 0.00 4.26 F
312 313 0.814457 AGAGTTGCTCTAGGCGTCTG 59.186 55.000 0.0 0.0 45.43 3.51 F
1217 1241 1.404583 GGTTGCATCATTTGGAGCACC 60.405 52.381 0.0 0.0 36.62 5.01 F
1291 1315 2.538437 CGAGAGCATCAGTGGAAGAAG 58.462 52.381 0.0 0.0 37.82 2.85 F
1453 1490 3.250762 CCTCTGAAATGAAACAACGAGCA 59.749 43.478 0.0 0.0 0.00 4.26 F
3178 3215 1.265365 GACAAGAGCACCAACTGAAGC 59.735 52.381 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1291 1315 0.036022 AGCTCTGTTCTTGTCTGCCC 59.964 55.000 0.00 0.00 0.00 5.36 R
1531 1568 3.200593 GCCATGGCTCGTGCTCTG 61.201 66.667 29.98 7.07 39.59 3.35 R
1606 1643 4.347453 CACGTTGCTTGCAGCCCC 62.347 66.667 4.00 0.00 41.51 5.80 R
2609 2646 0.320771 AGCTTCTTCATTGCCGACGT 60.321 50.000 0.00 0.00 0.00 4.34 R
2650 2687 2.512515 GTCGACCTGGCCTGCATC 60.513 66.667 3.51 3.09 0.00 3.91 R
3437 3481 3.489785 AGTCTTTACTTTTCACGCAGACG 59.510 43.478 0.00 0.00 37.86 4.18 R
4151 4206 0.913934 TTACAGGCTGCTGGGGATGA 60.914 55.000 15.89 0.00 0.00 2.92 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
27 28 3.747552 CGCTTTTATTTGCGCGCA 58.252 50.000 33.09 33.09 45.50 6.09
28 29 2.057980 CGCTTTTATTTGCGCGCAA 58.942 47.368 40.23 40.23 45.50 4.85
35 36 4.485554 TTTGCGCGCAAACTGTTT 57.514 44.444 45.17 0.00 40.51 2.83
36 37 3.624305 TTTGCGCGCAAACTGTTTA 57.376 42.105 45.17 28.20 40.51 2.01
37 38 2.126914 TTTGCGCGCAAACTGTTTAT 57.873 40.000 45.17 0.00 40.51 1.40
38 39 1.403493 TTGCGCGCAAACTGTTTATG 58.597 45.000 41.45 2.77 32.44 1.90
39 40 0.309302 TGCGCGCAAACTGTTTATGT 59.691 45.000 34.66 0.00 0.00 2.29
40 41 0.974836 GCGCGCAAACTGTTTATGTC 59.025 50.000 29.10 0.00 0.00 3.06
41 42 1.661743 GCGCGCAAACTGTTTATGTCA 60.662 47.619 29.10 0.00 0.00 3.58
42 43 2.850321 CGCGCAAACTGTTTATGTCAT 58.150 42.857 8.75 0.00 0.00 3.06
43 44 3.233578 CGCGCAAACTGTTTATGTCATT 58.766 40.909 8.75 0.00 0.00 2.57
44 45 3.668191 CGCGCAAACTGTTTATGTCATTT 59.332 39.130 8.75 0.00 0.00 2.32
45 46 4.431471 CGCGCAAACTGTTTATGTCATTTG 60.431 41.667 8.75 0.00 0.00 2.32
46 47 4.679197 GCGCAAACTGTTTATGTCATTTGA 59.321 37.500 0.30 0.00 30.35 2.69
47 48 5.174761 GCGCAAACTGTTTATGTCATTTGAA 59.825 36.000 0.30 0.00 30.35 2.69
48 49 6.128849 GCGCAAACTGTTTATGTCATTTGAAT 60.129 34.615 0.30 0.00 30.35 2.57
49 50 7.569226 GCGCAAACTGTTTATGTCATTTGAATT 60.569 33.333 0.30 0.00 30.35 2.17
50 51 8.274939 CGCAAACTGTTTATGTCATTTGAATTT 58.725 29.630 5.31 0.00 30.35 1.82
51 52 9.372541 GCAAACTGTTTATGTCATTTGAATTTG 57.627 29.630 5.31 0.00 30.35 2.32
63 64 9.299963 TGTCATTTGAATTTGAACTAGTTTGTG 57.700 29.630 10.02 0.00 0.00 3.33
64 65 9.515020 GTCATTTGAATTTGAACTAGTTTGTGA 57.485 29.630 10.02 0.00 0.00 3.58
68 69 8.696410 TTGAATTTGAACTAGTTTGTGAAACC 57.304 30.769 10.02 0.00 42.34 3.27
69 70 7.262048 TGAATTTGAACTAGTTTGTGAAACCC 58.738 34.615 10.02 0.00 42.34 4.11
70 71 7.123547 TGAATTTGAACTAGTTTGTGAAACCCT 59.876 33.333 10.02 0.00 42.34 4.34
71 72 8.528044 AATTTGAACTAGTTTGTGAAACCCTA 57.472 30.769 10.02 0.00 42.34 3.53
72 73 8.706322 ATTTGAACTAGTTTGTGAAACCCTAT 57.294 30.769 10.02 0.00 42.34 2.57
73 74 7.504924 TTGAACTAGTTTGTGAAACCCTATG 57.495 36.000 10.02 0.00 42.34 2.23
74 75 6.833041 TGAACTAGTTTGTGAAACCCTATGA 58.167 36.000 10.02 0.00 42.34 2.15
75 76 6.708949 TGAACTAGTTTGTGAAACCCTATGAC 59.291 38.462 10.02 0.00 42.34 3.06
76 77 6.182507 ACTAGTTTGTGAAACCCTATGACA 57.817 37.500 0.00 0.00 42.34 3.58
77 78 6.597562 ACTAGTTTGTGAAACCCTATGACAA 58.402 36.000 0.00 0.00 42.34 3.18
78 79 7.057894 ACTAGTTTGTGAAACCCTATGACAAA 58.942 34.615 0.00 0.00 42.34 2.83
79 80 6.976934 AGTTTGTGAAACCCTATGACAAAT 57.023 33.333 0.00 0.00 42.34 2.32
80 81 7.360113 AGTTTGTGAAACCCTATGACAAATT 57.640 32.000 0.00 0.00 42.34 1.82
81 82 7.791029 AGTTTGTGAAACCCTATGACAAATTT 58.209 30.769 0.00 0.00 42.34 1.82
82 83 7.926018 AGTTTGTGAAACCCTATGACAAATTTC 59.074 33.333 0.00 0.00 42.34 2.17
83 84 6.968263 TGTGAAACCCTATGACAAATTTCA 57.032 33.333 0.00 0.00 34.57 2.69
84 85 6.980593 TGTGAAACCCTATGACAAATTTCAG 58.019 36.000 0.00 0.00 36.89 3.02
85 86 6.775142 TGTGAAACCCTATGACAAATTTCAGA 59.225 34.615 0.00 0.00 36.89 3.27
86 87 7.451255 TGTGAAACCCTATGACAAATTTCAGAT 59.549 33.333 0.00 0.00 36.89 2.90
87 88 8.306761 GTGAAACCCTATGACAAATTTCAGATT 58.693 33.333 0.00 0.00 36.89 2.40
88 89 8.869109 TGAAACCCTATGACAAATTTCAGATTT 58.131 29.630 0.00 0.00 32.61 2.17
89 90 9.143631 GAAACCCTATGACAAATTTCAGATTTG 57.856 33.333 9.30 9.30 42.81 2.32
90 91 6.633856 ACCCTATGACAAATTTCAGATTTGC 58.366 36.000 10.47 5.58 41.36 3.68
91 92 6.211184 ACCCTATGACAAATTTCAGATTTGCA 59.789 34.615 10.47 9.84 41.36 4.08
92 93 6.755141 CCCTATGACAAATTTCAGATTTGCAG 59.245 38.462 10.47 4.59 41.36 4.41
93 94 7.318141 CCTATGACAAATTTCAGATTTGCAGT 58.682 34.615 10.47 1.63 41.36 4.40
94 95 7.816031 CCTATGACAAATTTCAGATTTGCAGTT 59.184 33.333 10.47 1.64 41.36 3.16
95 96 9.199982 CTATGACAAATTTCAGATTTGCAGTTT 57.800 29.630 10.47 0.00 41.36 2.66
96 97 7.846644 TGACAAATTTCAGATTTGCAGTTTT 57.153 28.000 10.47 0.00 41.36 2.43
97 98 8.266392 TGACAAATTTCAGATTTGCAGTTTTT 57.734 26.923 10.47 0.00 41.36 1.94
98 99 8.389603 TGACAAATTTCAGATTTGCAGTTTTTC 58.610 29.630 10.47 1.87 41.36 2.29
99 100 8.496707 ACAAATTTCAGATTTGCAGTTTTTCT 57.503 26.923 10.47 0.00 41.36 2.52
100 101 8.392612 ACAAATTTCAGATTTGCAGTTTTTCTG 58.607 29.630 10.47 6.95 46.12 3.02
101 102 8.392612 CAAATTTCAGATTTGCAGTTTTTCTGT 58.607 29.630 10.96 0.00 45.23 3.41
102 103 8.496707 AATTTCAGATTTGCAGTTTTTCTGTT 57.503 26.923 10.96 0.74 45.23 3.16
103 104 7.903995 TTTCAGATTTGCAGTTTTTCTGTTT 57.096 28.000 10.96 0.00 45.23 2.83
104 105 6.890663 TCAGATTTGCAGTTTTTCTGTTTG 57.109 33.333 10.96 0.00 45.23 2.93
105 106 5.291614 TCAGATTTGCAGTTTTTCTGTTTGC 59.708 36.000 10.96 0.00 45.23 3.68
106 107 3.987807 TTTGCAGTTTTTCTGTTTGCG 57.012 38.095 0.00 0.00 45.23 4.85
107 108 1.919918 TGCAGTTTTTCTGTTTGCGG 58.080 45.000 0.00 0.00 45.23 5.69
108 109 1.208259 GCAGTTTTTCTGTTTGCGGG 58.792 50.000 0.00 0.00 45.23 6.13
109 110 1.470805 GCAGTTTTTCTGTTTGCGGGT 60.471 47.619 0.00 0.00 45.23 5.28
110 111 2.459934 CAGTTTTTCTGTTTGCGGGTC 58.540 47.619 0.00 0.00 39.17 4.46
111 112 1.064952 AGTTTTTCTGTTTGCGGGTCG 59.935 47.619 0.00 0.00 0.00 4.79
112 113 1.096416 TTTTTCTGTTTGCGGGTCGT 58.904 45.000 0.00 0.00 0.00 4.34
113 114 1.096416 TTTTCTGTTTGCGGGTCGTT 58.904 45.000 0.00 0.00 0.00 3.85
114 115 0.378962 TTTCTGTTTGCGGGTCGTTG 59.621 50.000 0.00 0.00 0.00 4.10
115 116 2.051345 CTGTTTGCGGGTCGTTGC 60.051 61.111 0.00 0.00 0.00 4.17
116 117 3.855209 CTGTTTGCGGGTCGTTGCG 62.855 63.158 0.00 0.00 0.00 4.85
119 120 4.666397 TTGCGGGTCGTTGCGCTA 62.666 61.111 9.73 0.00 0.00 4.26
120 121 3.943479 TTGCGGGTCGTTGCGCTAT 62.943 57.895 9.73 0.00 0.00 2.97
121 122 3.192922 GCGGGTCGTTGCGCTATT 61.193 61.111 9.73 0.00 0.00 1.73
122 123 2.701006 CGGGTCGTTGCGCTATTG 59.299 61.111 9.73 0.00 0.00 1.90
123 124 2.403586 GGGTCGTTGCGCTATTGC 59.596 61.111 9.73 0.00 0.00 3.56
124 125 2.403586 GGTCGTTGCGCTATTGCC 59.596 61.111 9.73 1.68 35.36 4.52
125 126 2.403586 GTCGTTGCGCTATTGCCC 59.596 61.111 9.73 0.00 35.36 5.36
126 127 3.192230 TCGTTGCGCTATTGCCCG 61.192 61.111 9.73 0.00 35.36 6.13
127 128 3.192230 CGTTGCGCTATTGCCCGA 61.192 61.111 9.73 0.00 35.36 5.14
128 129 2.709475 GTTGCGCTATTGCCCGAG 59.291 61.111 9.73 0.00 35.36 4.63
129 130 3.202001 TTGCGCTATTGCCCGAGC 61.202 61.111 9.73 0.00 40.48 5.03
140 141 3.061848 CCCGAGCAAAACCCGCAT 61.062 61.111 0.00 0.00 0.00 4.73
141 142 1.747367 CCCGAGCAAAACCCGCATA 60.747 57.895 0.00 0.00 0.00 3.14
142 143 1.714899 CCCGAGCAAAACCCGCATAG 61.715 60.000 0.00 0.00 0.00 2.23
143 144 1.062525 CGAGCAAAACCCGCATAGC 59.937 57.895 0.00 0.00 0.00 2.97
144 145 1.433471 GAGCAAAACCCGCATAGCC 59.567 57.895 0.00 0.00 0.00 3.93
145 146 2.102161 GCAAAACCCGCATAGCCG 59.898 61.111 0.00 0.00 0.00 5.52
146 147 2.403378 GCAAAACCCGCATAGCCGA 61.403 57.895 0.00 0.00 0.00 5.54
147 148 1.427819 CAAAACCCGCATAGCCGAC 59.572 57.895 0.00 0.00 0.00 4.79
148 149 1.747745 AAAACCCGCATAGCCGACC 60.748 57.895 0.00 0.00 0.00 4.79
149 150 3.692370 AAACCCGCATAGCCGACCC 62.692 63.158 0.00 0.00 0.00 4.46
152 153 3.598715 CCGCATAGCCGACCCGTA 61.599 66.667 0.00 0.00 0.00 4.02
153 154 2.414179 CGCATAGCCGACCCGTAA 59.586 61.111 0.00 0.00 0.00 3.18
154 155 1.227031 CGCATAGCCGACCCGTAAA 60.227 57.895 0.00 0.00 0.00 2.01
155 156 0.806884 CGCATAGCCGACCCGTAAAA 60.807 55.000 0.00 0.00 0.00 1.52
156 157 1.371595 GCATAGCCGACCCGTAAAAA 58.628 50.000 0.00 0.00 0.00 1.94
222 223 4.746361 CATCTGTGCTAGCCCTCG 57.254 61.111 13.29 0.00 0.00 4.63
223 224 1.593750 CATCTGTGCTAGCCCTCGC 60.594 63.158 13.29 0.00 0.00 5.03
224 225 2.801631 ATCTGTGCTAGCCCTCGCC 61.802 63.158 13.29 0.00 34.57 5.54
225 226 4.880537 CTGTGCTAGCCCTCGCCG 62.881 72.222 13.29 0.00 34.57 6.46
241 242 3.601685 CGGCCCGCAAAAGTGGTT 61.602 61.111 0.00 0.00 0.00 3.67
242 243 2.818841 GGCCCGCAAAAGTGGTTT 59.181 55.556 0.00 0.00 0.00 3.27
243 244 1.145156 GGCCCGCAAAAGTGGTTTT 59.855 52.632 0.00 0.00 36.22 2.43
249 250 2.950877 CAAAAGTGGTTTTGCGCGA 58.049 47.368 12.10 0.00 44.56 5.87
250 251 1.272781 CAAAAGTGGTTTTGCGCGAA 58.727 45.000 12.10 5.81 44.56 4.70
251 252 1.006494 CAAAAGTGGTTTTGCGCGAAC 60.006 47.619 12.10 13.55 44.56 3.95
252 253 0.454196 AAAGTGGTTTTGCGCGAACT 59.546 45.000 12.10 9.65 0.00 3.01
253 254 0.248458 AAGTGGTTTTGCGCGAACTG 60.248 50.000 12.10 0.00 0.00 3.16
254 255 2.025441 TGGTTTTGCGCGAACTGC 59.975 55.556 12.10 10.64 41.47 4.40
255 256 2.025441 GGTTTTGCGCGAACTGCA 59.975 55.556 12.10 0.00 46.97 4.41
263 264 2.351888 GCGAACTGCAAACGCGTT 60.352 55.556 20.79 20.79 45.45 4.84
264 265 1.937362 GCGAACTGCAAACGCGTTT 60.937 52.632 30.36 30.36 45.45 3.60
265 266 1.468340 GCGAACTGCAAACGCGTTTT 61.468 50.000 33.05 19.44 45.45 2.43
266 267 0.223513 CGAACTGCAAACGCGTTTTG 59.776 50.000 33.05 26.38 46.57 2.44
291 292 4.700365 GCGTTTTGCGGGGTCTGC 62.700 66.667 0.00 0.00 41.69 4.26
292 293 2.978010 CGTTTTGCGGGGTCTGCT 60.978 61.111 0.30 0.00 36.85 4.24
293 294 1.669760 CGTTTTGCGGGGTCTGCTA 60.670 57.895 0.30 0.00 36.85 3.49
294 295 1.635663 CGTTTTGCGGGGTCTGCTAG 61.636 60.000 0.30 0.00 36.85 3.42
295 296 0.321298 GTTTTGCGGGGTCTGCTAGA 60.321 55.000 0.00 0.00 0.00 2.43
296 297 0.036388 TTTTGCGGGGTCTGCTAGAG 60.036 55.000 0.00 0.00 0.00 2.43
297 298 1.192146 TTTGCGGGGTCTGCTAGAGT 61.192 55.000 0.00 0.00 0.00 3.24
298 299 1.192146 TTGCGGGGTCTGCTAGAGTT 61.192 55.000 0.00 0.00 0.00 3.01
299 300 1.153549 GCGGGGTCTGCTAGAGTTG 60.154 63.158 0.00 0.00 0.00 3.16
300 301 1.153549 CGGGGTCTGCTAGAGTTGC 60.154 63.158 0.00 0.00 0.00 4.17
301 302 1.608717 CGGGGTCTGCTAGAGTTGCT 61.609 60.000 0.00 0.00 0.00 3.91
302 303 0.176910 GGGGTCTGCTAGAGTTGCTC 59.823 60.000 0.00 0.00 0.00 4.26
303 304 1.190643 GGGTCTGCTAGAGTTGCTCT 58.809 55.000 4.02 4.02 43.83 4.09
304 305 2.379972 GGGTCTGCTAGAGTTGCTCTA 58.620 52.381 0.00 5.84 41.50 2.43
312 313 0.814457 AGAGTTGCTCTAGGCGTCTG 59.186 55.000 0.00 0.00 45.43 3.51
385 386 8.924511 AGTTGGAAAATGAACAGAAATAGAGA 57.075 30.769 0.00 0.00 0.00 3.10
386 387 9.007901 AGTTGGAAAATGAACAGAAATAGAGAG 57.992 33.333 0.00 0.00 0.00 3.20
449 450 4.264380 CGCTAACAAATTAACGGGATTTGC 59.736 41.667 15.70 5.77 44.42 3.68
468 469 1.868519 GCGTGGGAATAAGACCTAGCG 60.869 57.143 0.00 0.00 0.00 4.26
493 494 4.986708 TTTTCACCCTGGCGGCCC 62.987 66.667 17.97 0.00 33.26 5.80
505 506 2.202756 CGGCCCGTCTTAGTGCTC 60.203 66.667 0.00 0.00 0.00 4.26
518 519 4.217767 TCTTAGTGCTCGTGTTGTAGATGT 59.782 41.667 0.00 0.00 0.00 3.06
545 546 9.551734 TCTAAGGTTTACTTCAAAGTTTACTCC 57.448 33.333 0.00 0.00 40.64 3.85
673 679 2.611518 AGAAGAAGAAGCCGAATGACG 58.388 47.619 0.00 0.00 42.18 4.35
816 838 3.439540 GGCCAAAAGGCATCGCGA 61.440 61.111 13.09 13.09 41.81 5.87
828 851 2.539476 GCATCGCGAAAAATCCCATTT 58.461 42.857 15.24 0.00 0.00 2.32
901 924 3.691498 CGAAATAAATTGAACGGGAGCC 58.309 45.455 0.00 0.00 0.00 4.70
1036 1060 2.169352 TGCCAAGAAGGATAGAGCTGAC 59.831 50.000 0.00 0.00 41.22 3.51
1074 1098 4.868171 CCTCGTTTAGCAGCACATAAACTA 59.132 41.667 11.82 3.31 38.93 2.24
1159 1183 5.181690 TGTGAACCTACAAATTTGTCTGC 57.818 39.130 26.46 13.22 42.35 4.26
1203 1227 6.526526 TGTATACACTTCTTGTTAGGTTGCA 58.473 36.000 0.08 0.00 39.91 4.08
1217 1241 1.404583 GGTTGCATCATTTGGAGCACC 60.405 52.381 0.00 0.00 36.62 5.01
1291 1315 2.538437 CGAGAGCATCAGTGGAAGAAG 58.462 52.381 0.00 0.00 37.82 2.85
1363 1387 3.767131 TGGACGACTTGACATATCTTCCA 59.233 43.478 9.43 9.43 38.17 3.53
1391 1428 8.546244 GTTTCTTGGAGTACTGTTTAACTGTAC 58.454 37.037 26.75 26.75 46.95 2.90
1453 1490 3.250762 CCTCTGAAATGAAACAACGAGCA 59.749 43.478 0.00 0.00 0.00 4.26
2666 2703 4.147449 CGATGCAGGCCAGGTCGA 62.147 66.667 5.01 0.00 34.46 4.20
2668 2705 4.101448 ATGCAGGCCAGGTCGACC 62.101 66.667 27.67 27.67 0.00 4.79
2734 2771 4.208686 GAGTACCTGAGCGGGCGG 62.209 72.222 0.00 0.00 36.97 6.13
2907 2944 3.069318 GGAGGCGGAGAAGACGGT 61.069 66.667 0.00 0.00 0.00 4.83
3178 3215 1.265365 GACAAGAGCACCAACTGAAGC 59.735 52.381 0.00 0.00 0.00 3.86
3290 3328 1.797025 CGGTCTGGTCCTCTTTTGAC 58.203 55.000 0.00 0.00 0.00 3.18
3433 3477 6.757010 GTCTACCAAGTATAGGTGTTGTCATG 59.243 42.308 0.00 0.00 40.26 3.07
3437 3481 7.272978 ACCAAGTATAGGTGTTGTCATGTATC 58.727 38.462 0.00 0.00 38.13 2.24
3452 3496 3.021269 TGTATCGTCTGCGTGAAAAGT 57.979 42.857 0.00 0.00 39.49 2.66
3482 3526 7.161404 ACTTTATCTGTTTCATGCACTAGTGA 58.839 34.615 27.08 11.86 0.00 3.41
3499 3543 2.231235 AGTGATCGTGTATGTGCACTCA 59.769 45.455 19.41 11.67 37.24 3.41
3744 3788 8.920509 ATGTTTTTACAAGTAACAACACTTCC 57.079 30.769 20.52 0.00 43.84 3.46
3745 3789 8.113173 TGTTTTTACAAGTAACAACACTTCCT 57.887 30.769 16.44 0.00 39.41 3.36
3746 3790 8.238631 TGTTTTTACAAGTAACAACACTTCCTC 58.761 33.333 16.44 0.00 39.41 3.71
3747 3791 8.456471 GTTTTTACAAGTAACAACACTTCCTCT 58.544 33.333 14.00 0.00 36.61 3.69
3748 3792 9.669887 TTTTTACAAGTAACAACACTTCCTCTA 57.330 29.630 0.00 0.00 36.61 2.43
3749 3793 9.841295 TTTTACAAGTAACAACACTTCCTCTAT 57.159 29.630 0.00 0.00 36.61 1.98
3750 3794 9.841295 TTTACAAGTAACAACACTTCCTCTATT 57.159 29.630 0.00 0.00 36.61 1.73
3751 3795 9.841295 TTACAAGTAACAACACTTCCTCTATTT 57.159 29.630 0.00 0.00 36.61 1.40
3752 3796 8.379457 ACAAGTAACAACACTTCCTCTATTTC 57.621 34.615 0.00 0.00 36.61 2.17
3798 3842 9.936759 TTTTTCAAAAGGTCAAATCTACAAACT 57.063 25.926 0.00 0.00 0.00 2.66
3821 3865 8.265165 ACTTTGATCGGGTTTATAGAGAAAAC 57.735 34.615 0.00 0.00 36.34 2.43
3876 3920 8.432013 ACATATGAGGCTACAACTTATGATGAA 58.568 33.333 10.38 0.00 0.00 2.57
3928 3972 7.925483 TGTCAATATTTTTCTCCACAAACTTGG 59.075 33.333 0.00 0.00 38.10 3.61
3933 3977 4.981806 TTTCTCCACAAACTTGGTCAAG 57.018 40.909 8.97 8.97 43.79 3.02
4044 4098 9.277783 AGTCTTTAAATATTCGAATGGATCCTG 57.722 33.333 20.87 6.52 0.00 3.86
4092 4146 5.423015 TCAGGCATCAACTAACTTCTCATC 58.577 41.667 0.00 0.00 0.00 2.92
4107 4161 3.176411 TCTCATCTGCAAAGAGAGGGAA 58.824 45.455 7.98 0.00 33.75 3.97
4108 4162 3.584406 TCTCATCTGCAAAGAGAGGGAAA 59.416 43.478 7.98 0.00 33.75 3.13
4130 4184 2.946346 CGCAAGGGCCCTGCAATTT 61.946 57.895 32.26 14.98 36.38 1.82
4162 4217 6.872585 AAATAAGAAAAATCATCCCCAGCA 57.127 33.333 0.00 0.00 0.00 4.41
4163 4218 6.475596 AATAAGAAAAATCATCCCCAGCAG 57.524 37.500 0.00 0.00 0.00 4.24
4165 4220 1.137675 GAAAAATCATCCCCAGCAGCC 59.862 52.381 0.00 0.00 0.00 4.85
4166 4221 0.337428 AAAATCATCCCCAGCAGCCT 59.663 50.000 0.00 0.00 0.00 4.58
4167 4222 0.396695 AAATCATCCCCAGCAGCCTG 60.397 55.000 0.00 0.00 38.85 4.85
4174 4235 1.303561 CCCAGCAGCCTGTAAAGCA 60.304 57.895 0.00 0.00 37.38 3.91
4258 4319 4.389374 CCAGCCTCTACTCTTGTTGAAAA 58.611 43.478 0.00 0.00 0.00 2.29
4284 4345 2.113860 TCACCACCTCAATTAGCAGC 57.886 50.000 0.00 0.00 0.00 5.25
4325 4386 5.293079 GGATCGATTGTTTTCCTCTTCTCTG 59.707 44.000 0.00 0.00 0.00 3.35
4389 4450 2.332063 AAACACTAGGATCATGCGGG 57.668 50.000 0.00 0.00 0.00 6.13
4409 4470 7.051623 TGCGGGTAAATATGATGAAAAGTAGT 58.948 34.615 0.00 0.00 0.00 2.73
4454 4515 1.666888 CCAGAAAACTGACGCAATGCC 60.667 52.381 0.00 0.00 0.00 4.40
4462 4523 2.598394 ACGCAATGCCCACAGCTT 60.598 55.556 0.00 0.00 44.23 3.74
4483 4544 5.738783 GCTTTCACCTGCCTTTGATGTTTAA 60.739 40.000 0.00 0.00 0.00 1.52
4484 4545 6.418057 TTTCACCTGCCTTTGATGTTTAAT 57.582 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.783711 CATAAACAGTTTGCGCGCAAA 59.216 42.857 45.17 45.17 42.77 3.68
19 20 1.268794 ACATAAACAGTTTGCGCGCAA 60.269 42.857 40.23 40.23 0.00 4.85
20 21 0.309302 ACATAAACAGTTTGCGCGCA 59.691 45.000 33.09 33.09 0.00 6.09
21 22 0.974836 GACATAAACAGTTTGCGCGC 59.025 50.000 27.26 27.26 0.00 6.86
22 23 2.308347 TGACATAAACAGTTTGCGCG 57.692 45.000 8.93 0.00 0.00 6.86
23 24 4.679197 TCAAATGACATAAACAGTTTGCGC 59.321 37.500 8.93 0.00 0.00 6.09
24 25 6.746104 TTCAAATGACATAAACAGTTTGCG 57.254 33.333 8.93 2.16 0.00 4.85
25 26 9.372541 CAAATTCAAATGACATAAACAGTTTGC 57.627 29.630 8.93 0.00 0.00 3.68
37 38 9.299963 CACAAACTAGTTCAAATTCAAATGACA 57.700 29.630 8.95 0.00 0.00 3.58
38 39 9.515020 TCACAAACTAGTTCAAATTCAAATGAC 57.485 29.630 8.95 0.00 0.00 3.06
42 43 9.145865 GGTTTCACAAACTAGTTCAAATTCAAA 57.854 29.630 8.95 0.08 41.14 2.69
43 44 7.762159 GGGTTTCACAAACTAGTTCAAATTCAA 59.238 33.333 8.95 0.00 41.14 2.69
44 45 7.123547 AGGGTTTCACAAACTAGTTCAAATTCA 59.876 33.333 8.95 0.00 41.14 2.57
45 46 7.489160 AGGGTTTCACAAACTAGTTCAAATTC 58.511 34.615 8.95 3.79 41.14 2.17
46 47 7.418337 AGGGTTTCACAAACTAGTTCAAATT 57.582 32.000 8.95 0.00 41.14 1.82
47 48 8.576442 CATAGGGTTTCACAAACTAGTTCAAAT 58.424 33.333 8.95 0.00 41.14 2.32
48 49 7.776030 TCATAGGGTTTCACAAACTAGTTCAAA 59.224 33.333 8.95 3.58 41.14 2.69
49 50 7.227910 GTCATAGGGTTTCACAAACTAGTTCAA 59.772 37.037 8.95 0.00 41.14 2.69
50 51 6.708949 GTCATAGGGTTTCACAAACTAGTTCA 59.291 38.462 8.95 0.00 41.14 3.18
51 52 6.708949 TGTCATAGGGTTTCACAAACTAGTTC 59.291 38.462 8.95 0.00 41.14 3.01
52 53 6.597562 TGTCATAGGGTTTCACAAACTAGTT 58.402 36.000 1.12 1.12 41.14 2.24
53 54 6.182507 TGTCATAGGGTTTCACAAACTAGT 57.817 37.500 0.00 0.00 41.14 2.57
54 55 7.504924 TTTGTCATAGGGTTTCACAAACTAG 57.495 36.000 0.00 0.00 41.14 2.57
55 56 8.472007 AATTTGTCATAGGGTTTCACAAACTA 57.528 30.769 0.00 0.00 39.19 2.24
56 57 6.976934 ATTTGTCATAGGGTTTCACAAACT 57.023 33.333 0.00 0.00 39.19 2.66
57 58 7.708752 TGAAATTTGTCATAGGGTTTCACAAAC 59.291 33.333 0.00 0.00 39.19 2.93
58 59 7.786030 TGAAATTTGTCATAGGGTTTCACAAA 58.214 30.769 0.00 0.00 40.31 2.83
59 60 7.286546 TCTGAAATTTGTCATAGGGTTTCACAA 59.713 33.333 0.00 0.00 33.53 3.33
60 61 6.775142 TCTGAAATTTGTCATAGGGTTTCACA 59.225 34.615 0.00 0.00 33.53 3.58
61 62 7.214467 TCTGAAATTTGTCATAGGGTTTCAC 57.786 36.000 0.00 0.00 33.53 3.18
62 63 8.421249 AATCTGAAATTTGTCATAGGGTTTCA 57.579 30.769 0.00 0.00 35.19 2.69
63 64 9.143631 CAAATCTGAAATTTGTCATAGGGTTTC 57.856 33.333 0.00 0.00 35.07 2.78
64 65 7.603784 GCAAATCTGAAATTTGTCATAGGGTTT 59.396 33.333 11.03 0.00 40.19 3.27
65 66 7.099120 GCAAATCTGAAATTTGTCATAGGGTT 58.901 34.615 11.03 0.00 40.19 4.11
66 67 6.211184 TGCAAATCTGAAATTTGTCATAGGGT 59.789 34.615 11.03 0.00 40.19 4.34
67 68 6.632909 TGCAAATCTGAAATTTGTCATAGGG 58.367 36.000 11.03 0.00 40.19 3.53
68 69 7.318141 ACTGCAAATCTGAAATTTGTCATAGG 58.682 34.615 11.03 3.43 40.19 2.57
69 70 8.752766 AACTGCAAATCTGAAATTTGTCATAG 57.247 30.769 11.03 7.85 40.19 2.23
70 71 9.545105 AAAACTGCAAATCTGAAATTTGTCATA 57.455 25.926 11.03 0.00 40.19 2.15
71 72 8.441312 AAAACTGCAAATCTGAAATTTGTCAT 57.559 26.923 11.03 0.00 40.19 3.06
72 73 7.846644 AAAACTGCAAATCTGAAATTTGTCA 57.153 28.000 11.03 8.85 40.19 3.58
73 74 8.606602 AGAAAAACTGCAAATCTGAAATTTGTC 58.393 29.630 11.03 5.58 40.19 3.18
74 75 8.392612 CAGAAAAACTGCAAATCTGAAATTTGT 58.607 29.630 11.03 0.00 39.85 2.83
75 76 8.762149 CAGAAAAACTGCAAATCTGAAATTTG 57.238 30.769 0.00 6.21 39.85 2.32
91 92 1.064952 CGACCCGCAAACAGAAAAACT 59.935 47.619 0.00 0.00 0.00 2.66
92 93 1.202211 ACGACCCGCAAACAGAAAAAC 60.202 47.619 0.00 0.00 0.00 2.43
93 94 1.096416 ACGACCCGCAAACAGAAAAA 58.904 45.000 0.00 0.00 0.00 1.94
94 95 1.096416 AACGACCCGCAAACAGAAAA 58.904 45.000 0.00 0.00 0.00 2.29
95 96 0.378962 CAACGACCCGCAAACAGAAA 59.621 50.000 0.00 0.00 0.00 2.52
96 97 2.018544 CAACGACCCGCAAACAGAA 58.981 52.632 0.00 0.00 0.00 3.02
97 98 2.539338 GCAACGACCCGCAAACAGA 61.539 57.895 0.00 0.00 0.00 3.41
98 99 2.051345 GCAACGACCCGCAAACAG 60.051 61.111 0.00 0.00 0.00 3.16
99 100 3.943034 CGCAACGACCCGCAAACA 61.943 61.111 0.00 0.00 0.00 2.83
105 106 2.701006 CAATAGCGCAACGACCCG 59.299 61.111 11.47 0.00 0.00 5.28
106 107 2.403586 GCAATAGCGCAACGACCC 59.596 61.111 11.47 0.00 0.00 4.46
107 108 2.403586 GGCAATAGCGCAACGACC 59.596 61.111 11.47 0.73 43.41 4.79
123 124 1.714899 CTATGCGGGTTTTGCTCGGG 61.715 60.000 0.00 0.00 42.38 5.14
124 125 1.721487 CTATGCGGGTTTTGCTCGG 59.279 57.895 0.00 0.00 42.38 4.63
125 126 1.062525 GCTATGCGGGTTTTGCTCG 59.937 57.895 0.00 0.00 45.55 5.03
126 127 1.433471 GGCTATGCGGGTTTTGCTC 59.567 57.895 0.00 0.00 0.00 4.26
127 128 2.406616 CGGCTATGCGGGTTTTGCT 61.407 57.895 0.00 0.00 0.00 3.91
128 129 2.102161 CGGCTATGCGGGTTTTGC 59.898 61.111 0.00 0.00 0.00 3.68
129 130 1.427819 GTCGGCTATGCGGGTTTTG 59.572 57.895 0.00 0.00 0.00 2.44
130 131 1.747745 GGTCGGCTATGCGGGTTTT 60.748 57.895 0.00 0.00 0.00 2.43
131 132 2.124860 GGTCGGCTATGCGGGTTT 60.125 61.111 0.00 0.00 0.00 3.27
132 133 4.171103 GGGTCGGCTATGCGGGTT 62.171 66.667 0.00 0.00 0.00 4.11
135 136 2.632136 TTTACGGGTCGGCTATGCGG 62.632 60.000 0.00 0.00 0.00 5.69
136 137 0.806884 TTTTACGGGTCGGCTATGCG 60.807 55.000 0.00 0.00 0.00 4.73
137 138 1.371595 TTTTTACGGGTCGGCTATGC 58.628 50.000 0.00 0.00 0.00 3.14
205 206 1.593750 GCGAGGGCTAGCACAGATG 60.594 63.158 21.39 6.57 35.83 2.90
206 207 2.801631 GGCGAGGGCTAGCACAGAT 61.802 63.158 21.39 0.00 39.81 2.90
207 208 3.461773 GGCGAGGGCTAGCACAGA 61.462 66.667 21.39 0.00 39.81 3.41
208 209 4.880537 CGGCGAGGGCTAGCACAG 62.881 72.222 21.39 13.94 39.81 3.66
224 225 2.636778 AAAACCACTTTTGCGGGCCG 62.637 55.000 24.35 24.35 0.00 6.13
225 226 1.145156 AAAACCACTTTTGCGGGCC 59.855 52.632 0.00 0.00 0.00 5.80
226 227 2.306383 CAAAACCACTTTTGCGGGC 58.694 52.632 0.00 0.00 39.82 6.13
231 232 1.006494 GTTCGCGCAAAACCACTTTTG 60.006 47.619 8.75 2.20 46.30 2.44
232 233 1.135228 AGTTCGCGCAAAACCACTTTT 60.135 42.857 16.51 0.00 0.00 2.27
233 234 0.454196 AGTTCGCGCAAAACCACTTT 59.546 45.000 16.51 0.00 0.00 2.66
234 235 0.248458 CAGTTCGCGCAAAACCACTT 60.248 50.000 16.51 0.00 0.00 3.16
235 236 1.355210 CAGTTCGCGCAAAACCACT 59.645 52.632 16.51 2.34 0.00 4.00
236 237 2.292916 GCAGTTCGCGCAAAACCAC 61.293 57.895 16.51 7.61 0.00 4.16
237 238 2.025441 GCAGTTCGCGCAAAACCA 59.975 55.556 16.51 0.00 0.00 3.67
238 239 1.587613 TTGCAGTTCGCGCAAAACC 60.588 52.632 16.51 5.74 45.91 3.27
239 240 3.990141 TTGCAGTTCGCGCAAAAC 58.010 50.000 8.75 11.52 45.91 2.43
243 244 4.954680 GCGTTTGCAGTTCGCGCA 62.955 61.111 8.75 0.00 46.97 6.09
246 247 1.468340 AAAACGCGTTTGCAGTTCGC 61.468 50.000 35.31 17.67 45.28 4.70
247 248 0.223513 CAAAACGCGTTTGCAGTTCG 59.776 50.000 35.31 15.11 40.25 3.95
273 274 4.038080 CAGACCCCGCAAAACGCC 62.038 66.667 0.00 0.00 41.76 5.68
274 275 4.700365 GCAGACCCCGCAAAACGC 62.700 66.667 0.00 0.00 41.76 4.84
275 276 1.635663 CTAGCAGACCCCGCAAAACG 61.636 60.000 0.00 0.00 43.15 3.60
276 277 0.321298 TCTAGCAGACCCCGCAAAAC 60.321 55.000 0.00 0.00 0.00 2.43
277 278 0.036388 CTCTAGCAGACCCCGCAAAA 60.036 55.000 0.00 0.00 0.00 2.44
278 279 1.192146 ACTCTAGCAGACCCCGCAAA 61.192 55.000 0.00 0.00 0.00 3.68
279 280 1.192146 AACTCTAGCAGACCCCGCAA 61.192 55.000 0.00 0.00 0.00 4.85
280 281 1.609501 AACTCTAGCAGACCCCGCA 60.610 57.895 0.00 0.00 0.00 5.69
281 282 1.153549 CAACTCTAGCAGACCCCGC 60.154 63.158 0.00 0.00 0.00 6.13
282 283 1.153549 GCAACTCTAGCAGACCCCG 60.154 63.158 0.00 0.00 0.00 5.73
283 284 0.176910 GAGCAACTCTAGCAGACCCC 59.823 60.000 0.00 0.00 0.00 4.95
284 285 1.190643 AGAGCAACTCTAGCAGACCC 58.809 55.000 0.00 0.00 39.28 4.46
292 293 2.017782 CAGACGCCTAGAGCAACTCTA 58.982 52.381 4.38 4.38 41.50 2.43
293 294 0.814457 CAGACGCCTAGAGCAACTCT 59.186 55.000 2.23 2.23 43.83 3.24
294 295 0.528470 ACAGACGCCTAGAGCAACTC 59.472 55.000 0.00 0.00 44.04 3.01
295 296 0.244994 CACAGACGCCTAGAGCAACT 59.755 55.000 0.00 0.00 44.04 3.16
296 297 1.355066 GCACAGACGCCTAGAGCAAC 61.355 60.000 0.00 0.00 44.04 4.17
297 298 1.079819 GCACAGACGCCTAGAGCAA 60.080 57.895 0.00 0.00 44.04 3.91
298 299 2.218037 CTGCACAGACGCCTAGAGCA 62.218 60.000 0.00 0.00 44.04 4.26
299 300 1.518133 CTGCACAGACGCCTAGAGC 60.518 63.158 0.00 0.00 38.52 4.09
300 301 0.179150 GACTGCACAGACGCCTAGAG 60.179 60.000 4.31 0.00 0.00 2.43
301 302 0.609406 AGACTGCACAGACGCCTAGA 60.609 55.000 4.31 0.00 0.00 2.43
302 303 0.457509 CAGACTGCACAGACGCCTAG 60.458 60.000 4.31 0.00 0.00 3.02
303 304 1.586541 CAGACTGCACAGACGCCTA 59.413 57.895 4.31 0.00 0.00 3.93
304 305 2.341543 CAGACTGCACAGACGCCT 59.658 61.111 4.31 0.00 0.00 5.52
305 306 3.418068 GCAGACTGCACAGACGCC 61.418 66.667 22.62 0.00 44.26 5.68
439 440 0.253610 TATTCCCACGCAAATCCCGT 59.746 50.000 0.00 0.00 39.91 5.28
449 450 1.269621 CCGCTAGGTCTTATTCCCACG 60.270 57.143 0.00 0.00 0.00 4.94
468 469 1.839424 CCAGGGTGAAAATCCTGTCC 58.161 55.000 4.40 0.00 46.75 4.02
493 494 1.767289 ACAACACGAGCACTAAGACG 58.233 50.000 0.00 0.00 0.00 4.18
505 506 6.780706 AAACCTTAGAACATCTACAACACG 57.219 37.500 0.00 0.00 0.00 4.49
648 650 4.932200 TCATTCGGCTTCTTCTTCTTCTTC 59.068 41.667 0.00 0.00 0.00 2.87
651 653 3.061429 CGTCATTCGGCTTCTTCTTCTTC 59.939 47.826 0.00 0.00 35.71 2.87
652 654 2.996621 CGTCATTCGGCTTCTTCTTCTT 59.003 45.455 0.00 0.00 35.71 2.52
816 838 9.467796 TTTGGAGTAAAACAAAATGGGATTTTT 57.532 25.926 0.00 0.00 40.27 1.94
828 851 2.962421 CTGGGGCTTTGGAGTAAAACAA 59.038 45.455 0.00 0.00 0.00 2.83
901 924 6.552629 TGTCTCTAGCAATTAGTAACTGACG 58.447 40.000 0.00 0.00 0.00 4.35
1036 1060 0.508641 CGAGGACAAGTGTTTCAGCG 59.491 55.000 0.00 0.00 0.00 5.18
1074 1098 0.118144 AGAGGCAAAGGAGAGAGGGT 59.882 55.000 0.00 0.00 0.00 4.34
1159 1183 3.005261 ACAAGCTGCTCGTATATCCTCAG 59.995 47.826 1.00 0.00 0.00 3.35
1291 1315 0.036022 AGCTCTGTTCTTGTCTGCCC 59.964 55.000 0.00 0.00 0.00 5.36
1363 1387 7.773690 ACAGTTAAACAGTACTCCAAGAAACAT 59.226 33.333 0.00 0.00 0.00 2.71
1453 1490 4.401022 TCAGCTTGTCCATGTCAGATTTT 58.599 39.130 0.00 0.00 0.00 1.82
1531 1568 3.200593 GCCATGGCTCGTGCTCTG 61.201 66.667 29.98 7.07 39.59 3.35
1606 1643 4.347453 CACGTTGCTTGCAGCCCC 62.347 66.667 4.00 0.00 41.51 5.80
2479 2516 1.906253 CAGCATGGTCAGCTCCTCT 59.094 57.895 0.00 0.00 41.14 3.69
2609 2646 0.320771 AGCTTCTTCATTGCCGACGT 60.321 50.000 0.00 0.00 0.00 4.34
2650 2687 2.512515 GTCGACCTGGCCTGCATC 60.513 66.667 3.51 3.09 0.00 3.91
3433 3477 5.344128 TCTTTACTTTTCACGCAGACGATAC 59.656 40.000 0.00 0.00 43.93 2.24
3437 3481 3.489785 AGTCTTTACTTTTCACGCAGACG 59.510 43.478 0.00 0.00 37.86 4.18
3452 3496 8.621532 AGTGCATGAAACAGATAAAGTCTTTA 57.378 30.769 7.49 7.49 34.00 1.85
3536 3580 6.122850 TCTCGGATTCAACATTAATTGCAG 57.877 37.500 0.00 0.00 0.00 4.41
3632 3676 5.300034 TCCAATTTGTAGCCATCACATCATC 59.700 40.000 0.00 0.00 0.00 2.92
3728 3772 8.378172 TGAAATAGAGGAAGTGTTGTTACTTG 57.622 34.615 0.00 0.00 40.78 3.16
3733 3777 9.520515 ACATTATGAAATAGAGGAAGTGTTGTT 57.479 29.630 0.00 0.00 0.00 2.83
3737 3781 9.823647 CACTACATTATGAAATAGAGGAAGTGT 57.176 33.333 0.00 0.00 0.00 3.55
3738 3782 8.768955 GCACTACATTATGAAATAGAGGAAGTG 58.231 37.037 0.00 0.00 32.40 3.16
3739 3783 8.486210 TGCACTACATTATGAAATAGAGGAAGT 58.514 33.333 0.00 0.00 0.00 3.01
3740 3784 8.893219 TGCACTACATTATGAAATAGAGGAAG 57.107 34.615 0.00 0.00 0.00 3.46
3772 3816 9.936759 AGTTTGTAGATTTGACCTTTTGAAAAA 57.063 25.926 0.00 0.00 0.00 1.94
3777 3821 8.925161 TCAAAGTTTGTAGATTTGACCTTTTG 57.075 30.769 15.08 0.00 37.86 2.44
3798 3842 7.098477 TCGTTTTCTCTATAAACCCGATCAAA 58.902 34.615 0.00 0.00 33.07 2.69
4036 4090 3.083349 CTCCGGCACCAGGATCCA 61.083 66.667 15.82 0.00 37.13 3.41
4070 4124 5.293814 CAGATGAGAAGTTAGTTGATGCCTG 59.706 44.000 0.00 0.00 0.00 4.85
4092 4146 1.882623 GTGGTTTCCCTCTCTTTGCAG 59.117 52.381 0.00 0.00 0.00 4.41
4107 4161 4.974721 CAGGGCCCTTGCGTGGTT 62.975 66.667 26.10 0.00 38.85 3.67
4142 4197 3.701040 GCTGCTGGGGATGATTTTTCTTA 59.299 43.478 0.00 0.00 0.00 2.10
4143 4198 2.498885 GCTGCTGGGGATGATTTTTCTT 59.501 45.455 0.00 0.00 0.00 2.52
4151 4206 0.913934 TTACAGGCTGCTGGGGATGA 60.914 55.000 15.89 0.00 0.00 2.92
4165 4220 6.035327 GCATTTATTTGGAGCTTGCTTTACAG 59.965 38.462 0.00 0.00 0.00 2.74
4166 4221 5.868801 GCATTTATTTGGAGCTTGCTTTACA 59.131 36.000 0.00 0.00 0.00 2.41
4167 4222 5.868801 TGCATTTATTTGGAGCTTGCTTTAC 59.131 36.000 0.00 0.00 0.00 2.01
4174 4235 8.900983 TTAGTTTTTGCATTTATTTGGAGCTT 57.099 26.923 0.00 0.00 0.00 3.74
4258 4319 4.220602 GCTAATTGAGGTGGTGAATGGTTT 59.779 41.667 0.00 0.00 0.00 3.27
4267 4328 1.026718 GCGCTGCTAATTGAGGTGGT 61.027 55.000 0.00 0.00 0.00 4.16
4297 4358 2.009774 AGGAAAACAATCGATCCTGCG 58.990 47.619 0.00 0.00 40.73 5.18
4301 4362 5.293079 CAGAGAAGAGGAAAACAATCGATCC 59.707 44.000 0.00 0.00 0.00 3.36
4311 4372 2.572104 GGGCCTACAGAGAAGAGGAAAA 59.428 50.000 0.84 0.00 31.45 2.29
4325 4386 2.113243 CTCCTATTGGGCGGGCCTAC 62.113 65.000 22.12 0.00 36.10 3.18
4409 4470 2.334977 TGTGAAAAGCCAGGACCTCTA 58.665 47.619 0.00 0.00 0.00 2.43
4462 4523 7.531857 TTATTAAACATCAAAGGCAGGTGAA 57.468 32.000 0.00 0.00 0.00 3.18
4483 4544 4.230455 AGTGGCTGGATAGAGAGCTTTAT 58.770 43.478 0.00 0.00 35.42 1.40
4484 4545 3.647636 AGTGGCTGGATAGAGAGCTTTA 58.352 45.455 0.00 0.00 35.42 1.85


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

AutoCloner maintained by Alex Coulton.