Multiple sequence alignment - TraesCS7A01G325400

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 TraesCS7A01G325400 chr7A 100.000 2432 0 0 1 2432 473673420 473675851 0.000000e+00 4492.0
1 TraesCS7A01G325400 chr7A 92.459 305 23 0 1124 1428 473807678 473807982 1.030000e-118 436.0
2 TraesCS7A01G325400 chr7B 92.158 1900 90 28 562 2432 426788237 426790106 0.000000e+00 2628.0
3 TraesCS7A01G325400 chr7B 92.131 305 24 0 1124 1428 426833518 426833822 4.800000e-117 431.0
4 TraesCS7A01G325400 chr7D 91.925 1127 39 17 750 1850 412234622 412235722 0.000000e+00 1530.0
5 TraesCS7A01G325400 chr7D 92.459 305 23 0 1124 1428 412394869 412395173 1.030000e-118 436.0
6 TraesCS7A01G325400 chr7D 85.519 366 40 9 175 529 412229663 412230026 1.060000e-98 370.0
7 TraesCS7A01G325400 chr7D 91.228 171 6 3 592 753 412232642 412232812 8.750000e-55 224.0
8 TraesCS7A01G325400 chr7D 90.385 52 5 0 551 602 412230019 412230070 4.340000e-08 69.4
9 TraesCS7A01G325400 chr5D 83.636 330 40 11 206 530 328245344 328245664 5.080000e-77 298.0
10 TraesCS7A01G325400 chr5D 88.506 174 19 1 1 174 81391877 81392049 2.450000e-50 209.0
11 TraesCS7A01G325400 chr5D 88.506 174 19 1 1 174 257860962 257861134 2.450000e-50 209.0
12 TraesCS7A01G325400 chr5D 87.356 174 22 0 1 174 520456635 520456808 1.470000e-47 200.0
13 TraesCS7A01G325400 chr5D 75.200 250 48 13 203 446 556884021 556884262 3.310000e-19 106.0
14 TraesCS7A01G325400 chr5D 86.301 73 7 3 457 529 489250026 489249957 2.590000e-10 76.8
15 TraesCS7A01G325400 chr3B 80.886 361 51 13 176 529 756831621 756831272 3.990000e-68 268.0
16 TraesCS7A01G325400 chr5B 80.214 374 58 15 176 540 618133973 618133607 1.430000e-67 267.0
17 TraesCS7A01G325400 chr5B 82.955 264 35 8 220 476 6464126 6463866 1.880000e-56 230.0
18 TraesCS7A01G325400 chr5B 78.947 95 11 8 501 587 6463827 6463734 3.380000e-04 56.5
19 TraesCS7A01G325400 chr3A 90.230 174 16 1 1 174 336169403 336169231 2.430000e-55 226.0
20 TraesCS7A01G325400 chr3A 77.670 206 32 14 252 449 60608244 60608045 1.980000e-21 113.0
21 TraesCS7A01G325400 chr4A 89.143 175 15 3 1 174 50207190 50207019 5.270000e-52 215.0
22 TraesCS7A01G325400 chr6B 88.571 175 20 0 1 175 152942489 152942315 1.890000e-51 213.0
23 TraesCS7A01G325400 chr1D 88.571 175 20 0 1 175 402578539 402578713 1.890000e-51 213.0
24 TraesCS7A01G325400 chr2D 80.351 285 45 10 248 529 441531868 441532144 3.170000e-49 206.0
25 TraesCS7A01G325400 chr2D 76.923 221 36 13 308 520 548672427 548672640 7.110000e-21 111.0
26 TraesCS7A01G325400 chr2A 87.791 172 20 1 3 174 595412802 595412632 1.470000e-47 200.0
27 TraesCS7A01G325400 chr2A 76.062 259 47 13 197 449 644219837 644219588 1.180000e-23 121.0
28 TraesCS7A01G325400 chr2B 87.356 174 21 1 1 174 91940254 91940082 5.300000e-47 198.0
29 TraesCS7A01G325400 chr2B 77.606 259 44 13 178 432 680065053 680064805 7.010000e-31 145.0
30 TraesCS7A01G325400 chr4B 80.347 173 18 7 358 530 89357538 89357694 1.530000e-22 117.0


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 TraesCS7A01G325400 chr7A 473673420 473675851 2431 False 4492.00 4492 100.00000 1 2432 1 chr7A.!!$F1 2431
1 TraesCS7A01G325400 chr7B 426788237 426790106 1869 False 2628.00 2628 92.15800 562 2432 1 chr7B.!!$F1 1870
2 TraesCS7A01G325400 chr7D 412229663 412235722 6059 False 548.35 1530 89.76425 175 1850 4 chr7D.!!$F2 1675

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
39 40 0.033504 GACGCTGTCCTGTCTTCCAA 59.966 55.0 0.0 0.0 32.37 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 5944 0.241213 ATCGGTGTATCGATCTGGCG 59.759 55.0 0.0 0.0 45.43 5.69 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
23 24 4.935205 TGTTGATCCCATAAACTTCTGACG 59.065 41.667 0.00 0.00 0.00 4.35
24 25 3.531538 TGATCCCATAAACTTCTGACGC 58.468 45.455 0.00 0.00 0.00 5.19
25 26 3.197766 TGATCCCATAAACTTCTGACGCT 59.802 43.478 0.00 0.00 0.00 5.07
26 27 2.972625 TCCCATAAACTTCTGACGCTG 58.027 47.619 0.00 0.00 0.00 5.18
27 28 2.301870 TCCCATAAACTTCTGACGCTGT 59.698 45.455 0.00 0.00 0.00 4.40
28 29 2.673368 CCCATAAACTTCTGACGCTGTC 59.327 50.000 2.32 2.32 0.00 3.51
29 30 2.673368 CCATAAACTTCTGACGCTGTCC 59.327 50.000 6.30 0.00 0.00 4.02
30 31 3.589988 CATAAACTTCTGACGCTGTCCT 58.410 45.455 6.30 0.00 0.00 3.85
31 32 1.871080 AAACTTCTGACGCTGTCCTG 58.129 50.000 6.30 1.07 0.00 3.86
32 33 0.753262 AACTTCTGACGCTGTCCTGT 59.247 50.000 6.30 0.00 0.00 4.00
33 34 0.315568 ACTTCTGACGCTGTCCTGTC 59.684 55.000 6.30 0.00 35.67 3.51
34 35 0.600557 CTTCTGACGCTGTCCTGTCT 59.399 55.000 6.30 0.00 36.10 3.41
35 36 1.000283 CTTCTGACGCTGTCCTGTCTT 60.000 52.381 6.30 0.00 36.10 3.01
36 37 0.598562 TCTGACGCTGTCCTGTCTTC 59.401 55.000 6.30 0.00 36.10 2.87
37 38 0.389166 CTGACGCTGTCCTGTCTTCC 60.389 60.000 6.30 0.00 36.10 3.46
38 39 1.112916 TGACGCTGTCCTGTCTTCCA 61.113 55.000 6.30 0.00 36.10 3.53
39 40 0.033504 GACGCTGTCCTGTCTTCCAA 59.966 55.000 0.00 0.00 32.37 3.53
40 41 0.687354 ACGCTGTCCTGTCTTCCAAT 59.313 50.000 0.00 0.00 0.00 3.16
41 42 1.081892 CGCTGTCCTGTCTTCCAATG 58.918 55.000 0.00 0.00 0.00 2.82
42 43 0.807496 GCTGTCCTGTCTTCCAATGC 59.193 55.000 0.00 0.00 0.00 3.56
43 44 1.457346 CTGTCCTGTCTTCCAATGCC 58.543 55.000 0.00 0.00 0.00 4.40
44 45 0.770499 TGTCCTGTCTTCCAATGCCA 59.230 50.000 0.00 0.00 0.00 4.92
45 46 1.168714 GTCCTGTCTTCCAATGCCAC 58.831 55.000 0.00 0.00 0.00 5.01
46 47 0.770499 TCCTGTCTTCCAATGCCACA 59.230 50.000 0.00 0.00 0.00 4.17
47 48 1.144708 TCCTGTCTTCCAATGCCACAA 59.855 47.619 0.00 0.00 0.00 3.33
48 49 1.270550 CCTGTCTTCCAATGCCACAAC 59.729 52.381 0.00 0.00 0.00 3.32
49 50 2.233271 CTGTCTTCCAATGCCACAACT 58.767 47.619 0.00 0.00 0.00 3.16
50 51 3.411446 CTGTCTTCCAATGCCACAACTA 58.589 45.455 0.00 0.00 0.00 2.24
51 52 4.012374 CTGTCTTCCAATGCCACAACTAT 58.988 43.478 0.00 0.00 0.00 2.12
52 53 3.758023 TGTCTTCCAATGCCACAACTATG 59.242 43.478 0.00 0.00 0.00 2.23
53 54 2.754552 TCTTCCAATGCCACAACTATGC 59.245 45.455 0.00 0.00 0.00 3.14
54 55 1.473258 TCCAATGCCACAACTATGCC 58.527 50.000 0.00 0.00 0.00 4.40
55 56 0.461135 CCAATGCCACAACTATGCCC 59.539 55.000 0.00 0.00 0.00 5.36
56 57 0.461135 CAATGCCACAACTATGCCCC 59.539 55.000 0.00 0.00 0.00 5.80
57 58 0.336048 AATGCCACAACTATGCCCCT 59.664 50.000 0.00 0.00 0.00 4.79
58 59 1.221635 ATGCCACAACTATGCCCCTA 58.778 50.000 0.00 0.00 0.00 3.53
59 60 0.254747 TGCCACAACTATGCCCCTAC 59.745 55.000 0.00 0.00 0.00 3.18
60 61 0.546598 GCCACAACTATGCCCCTACT 59.453 55.000 0.00 0.00 0.00 2.57
61 62 1.766496 GCCACAACTATGCCCCTACTA 59.234 52.381 0.00 0.00 0.00 1.82
62 63 2.171870 GCCACAACTATGCCCCTACTAA 59.828 50.000 0.00 0.00 0.00 2.24
63 64 3.181443 GCCACAACTATGCCCCTACTAAT 60.181 47.826 0.00 0.00 0.00 1.73
64 65 4.389374 CCACAACTATGCCCCTACTAATG 58.611 47.826 0.00 0.00 0.00 1.90
65 66 4.141482 CCACAACTATGCCCCTACTAATGT 60.141 45.833 0.00 0.00 0.00 2.71
66 67 5.057149 CACAACTATGCCCCTACTAATGTC 58.943 45.833 0.00 0.00 0.00 3.06
67 68 4.719773 ACAACTATGCCCCTACTAATGTCA 59.280 41.667 0.00 0.00 0.00 3.58
68 69 5.369699 ACAACTATGCCCCTACTAATGTCAT 59.630 40.000 0.00 0.00 0.00 3.06
69 70 6.557253 ACAACTATGCCCCTACTAATGTCATA 59.443 38.462 0.00 0.00 0.00 2.15
70 71 6.607004 ACTATGCCCCTACTAATGTCATAC 57.393 41.667 0.00 0.00 0.00 2.39
71 72 4.910458 ATGCCCCTACTAATGTCATACC 57.090 45.455 0.00 0.00 0.00 2.73
72 73 3.659841 TGCCCCTACTAATGTCATACCA 58.340 45.455 0.00 0.00 0.00 3.25
73 74 4.041464 TGCCCCTACTAATGTCATACCAA 58.959 43.478 0.00 0.00 0.00 3.67
74 75 4.475381 TGCCCCTACTAATGTCATACCAAA 59.525 41.667 0.00 0.00 0.00 3.28
75 76 5.133660 TGCCCCTACTAATGTCATACCAAAT 59.866 40.000 0.00 0.00 0.00 2.32
76 77 6.330514 TGCCCCTACTAATGTCATACCAAATA 59.669 38.462 0.00 0.00 0.00 1.40
77 78 7.147284 TGCCCCTACTAATGTCATACCAAATAA 60.147 37.037 0.00 0.00 0.00 1.40
78 79 7.390718 GCCCCTACTAATGTCATACCAAATAAG 59.609 40.741 0.00 0.00 0.00 1.73
79 80 7.390718 CCCCTACTAATGTCATACCAAATAAGC 59.609 40.741 0.00 0.00 0.00 3.09
80 81 7.390718 CCCTACTAATGTCATACCAAATAAGCC 59.609 40.741 0.00 0.00 0.00 4.35
81 82 7.936847 CCTACTAATGTCATACCAAATAAGCCA 59.063 37.037 0.00 0.00 0.00 4.75
82 83 9.337396 CTACTAATGTCATACCAAATAAGCCAA 57.663 33.333 0.00 0.00 0.00 4.52
83 84 7.996385 ACTAATGTCATACCAAATAAGCCAAC 58.004 34.615 0.00 0.00 0.00 3.77
84 85 4.955925 TGTCATACCAAATAAGCCAACG 57.044 40.909 0.00 0.00 0.00 4.10
85 86 4.328536 TGTCATACCAAATAAGCCAACGT 58.671 39.130 0.00 0.00 0.00 3.99
86 87 4.393680 TGTCATACCAAATAAGCCAACGTC 59.606 41.667 0.00 0.00 0.00 4.34
87 88 4.393680 GTCATACCAAATAAGCCAACGTCA 59.606 41.667 0.00 0.00 0.00 4.35
88 89 4.393680 TCATACCAAATAAGCCAACGTCAC 59.606 41.667 0.00 0.00 0.00 3.67
89 90 2.577700 ACCAAATAAGCCAACGTCACA 58.422 42.857 0.00 0.00 0.00 3.58
90 91 2.952978 ACCAAATAAGCCAACGTCACAA 59.047 40.909 0.00 0.00 0.00 3.33
91 92 3.243267 ACCAAATAAGCCAACGTCACAAC 60.243 43.478 0.00 0.00 0.00 3.32
92 93 3.004315 CCAAATAAGCCAACGTCACAACT 59.996 43.478 0.00 0.00 0.00 3.16
93 94 4.214545 CCAAATAAGCCAACGTCACAACTA 59.785 41.667 0.00 0.00 0.00 2.24
94 95 5.106317 CCAAATAAGCCAACGTCACAACTAT 60.106 40.000 0.00 0.00 0.00 2.12
95 96 6.378582 CAAATAAGCCAACGTCACAACTATT 58.621 36.000 0.00 0.00 0.00 1.73
96 97 6.569179 AATAAGCCAACGTCACAACTATTT 57.431 33.333 0.00 0.00 0.00 1.40
97 98 7.675962 AATAAGCCAACGTCACAACTATTTA 57.324 32.000 0.00 0.00 0.00 1.40
98 99 7.675962 ATAAGCCAACGTCACAACTATTTAA 57.324 32.000 0.00 0.00 0.00 1.52
99 100 6.380095 AAGCCAACGTCACAACTATTTAAA 57.620 33.333 0.00 0.00 0.00 1.52
100 101 6.380095 AGCCAACGTCACAACTATTTAAAA 57.620 33.333 0.00 0.00 0.00 1.52
101 102 6.977213 AGCCAACGTCACAACTATTTAAAAT 58.023 32.000 0.00 0.00 0.00 1.82
102 103 8.101654 AGCCAACGTCACAACTATTTAAAATA 57.898 30.769 0.00 0.00 0.00 1.40
103 104 8.569641 AGCCAACGTCACAACTATTTAAAATAA 58.430 29.630 0.00 0.00 0.00 1.40
104 105 9.182933 GCCAACGTCACAACTATTTAAAATAAA 57.817 29.630 0.00 0.00 0.00 1.40
119 120 9.651913 ATTTAAAATAAATAGTGCTGGTGTTGG 57.348 29.630 0.00 0.00 0.00 3.77
120 121 6.664428 AAAATAAATAGTGCTGGTGTTGGT 57.336 33.333 0.00 0.00 0.00 3.67
121 122 6.664428 AAATAAATAGTGCTGGTGTTGGTT 57.336 33.333 0.00 0.00 0.00 3.67
122 123 5.643379 ATAAATAGTGCTGGTGTTGGTTG 57.357 39.130 0.00 0.00 0.00 3.77
123 124 2.656947 ATAGTGCTGGTGTTGGTTGT 57.343 45.000 0.00 0.00 0.00 3.32
124 125 3.780804 ATAGTGCTGGTGTTGGTTGTA 57.219 42.857 0.00 0.00 0.00 2.41
125 126 2.428544 AGTGCTGGTGTTGGTTGTAA 57.571 45.000 0.00 0.00 0.00 2.41
126 127 2.729194 AGTGCTGGTGTTGGTTGTAAA 58.271 42.857 0.00 0.00 0.00 2.01
127 128 3.295973 AGTGCTGGTGTTGGTTGTAAAT 58.704 40.909 0.00 0.00 0.00 1.40
128 129 3.068024 AGTGCTGGTGTTGGTTGTAAATG 59.932 43.478 0.00 0.00 0.00 2.32
129 130 2.363680 TGCTGGTGTTGGTTGTAAATGG 59.636 45.455 0.00 0.00 0.00 3.16
130 131 2.866065 GCTGGTGTTGGTTGTAAATGGC 60.866 50.000 0.00 0.00 0.00 4.40
131 132 1.338337 TGGTGTTGGTTGTAAATGGCG 59.662 47.619 0.00 0.00 0.00 5.69
132 133 1.338655 GGTGTTGGTTGTAAATGGCGT 59.661 47.619 0.00 0.00 0.00 5.68
133 134 2.389998 GTGTTGGTTGTAAATGGCGTG 58.610 47.619 0.00 0.00 0.00 5.34
134 135 1.269309 TGTTGGTTGTAAATGGCGTGC 60.269 47.619 0.00 0.00 0.00 5.34
135 136 0.315568 TTGGTTGTAAATGGCGTGCC 59.684 50.000 3.30 3.30 0.00 5.01
144 145 4.858680 TGGCGTGCCACCAACGAA 62.859 61.111 10.06 0.00 41.89 3.85
145 146 3.587933 GGCGTGCCACCAACGAAA 61.588 61.111 5.89 0.00 35.81 3.46
146 147 2.051345 GCGTGCCACCAACGAAAG 60.051 61.111 0.00 0.00 0.00 2.62
160 161 2.914059 ACGAAAGTTGTGGCTAACACT 58.086 42.857 0.00 0.00 46.40 3.55
161 162 3.275999 ACGAAAGTTGTGGCTAACACTT 58.724 40.909 0.00 0.00 46.40 3.16
162 163 3.692593 ACGAAAGTTGTGGCTAACACTTT 59.307 39.130 7.39 7.39 46.40 2.66
163 164 4.157105 ACGAAAGTTGTGGCTAACACTTTT 59.843 37.500 8.68 5.48 46.40 2.27
164 165 5.336134 ACGAAAGTTGTGGCTAACACTTTTT 60.336 36.000 8.68 3.61 46.40 1.94
165 166 7.113236 ACGAAAGTTGTGGCTAACACTTTTTC 61.113 38.462 8.68 9.48 46.40 2.29
166 167 9.900090 ACGAAAGTTGTGGCTAACACTTTTTCC 62.900 40.741 8.68 0.00 46.40 3.13
171 172 5.358298 GTGGCTAACACTTTTTCCACTAG 57.642 43.478 0.00 0.00 46.72 2.57
172 173 4.820173 GTGGCTAACACTTTTTCCACTAGT 59.180 41.667 0.00 0.00 46.72 2.57
173 174 4.819630 TGGCTAACACTTTTTCCACTAGTG 59.180 41.667 16.34 16.34 43.72 2.74
191 192 2.478894 AGTGCGGTGAACAGTAAAATCG 59.521 45.455 0.00 0.00 0.00 3.34
192 193 2.477375 GTGCGGTGAACAGTAAAATCGA 59.523 45.455 0.00 0.00 0.00 3.59
193 194 2.734606 TGCGGTGAACAGTAAAATCGAG 59.265 45.455 0.00 0.00 0.00 4.04
194 195 2.093783 GCGGTGAACAGTAAAATCGAGG 59.906 50.000 0.00 0.00 0.00 4.63
213 220 9.981114 AATCGAGGATAAAACAAATTCAAAAGT 57.019 25.926 0.00 0.00 0.00 2.66
215 222 9.458374 TCGAGGATAAAACAAATTCAAAAGTTC 57.542 29.630 0.00 0.00 0.00 3.01
219 226 9.325198 GGATAAAACAAATTCAAAAGTTCCTGT 57.675 29.630 0.00 0.00 0.00 4.00
259 266 6.279123 TGACAAATTTTCTATGTGCTTGCAA 58.721 32.000 0.00 0.00 0.00 4.08
278 285 8.074972 GCTTGCAAAAATTTACCATGAATGAAA 58.925 29.630 0.00 0.00 0.00 2.69
292 299 8.859090 ACCATGAATGAAAATTTCTGTAAGTCA 58.141 29.630 7.29 2.30 33.76 3.41
299 306 7.147312 TGAAAATTTCTGTAAGTCATGGCAAG 58.853 34.615 7.29 0.00 33.76 4.01
304 311 6.707440 TTCTGTAAGTCATGGCAAGAAAAA 57.293 33.333 0.00 0.00 33.76 1.94
305 312 6.072112 TCTGTAAGTCATGGCAAGAAAAAC 57.928 37.500 0.00 0.00 33.76 2.43
306 313 5.827797 TCTGTAAGTCATGGCAAGAAAAACT 59.172 36.000 0.00 0.00 33.76 2.66
308 315 7.500892 TCTGTAAGTCATGGCAAGAAAAACTAA 59.499 33.333 0.00 0.00 33.76 2.24
310 317 8.637986 TGTAAGTCATGGCAAGAAAAACTAAAT 58.362 29.630 0.00 0.00 0.00 1.40
311 318 9.129209 GTAAGTCATGGCAAGAAAAACTAAATC 57.871 33.333 0.00 0.00 0.00 2.17
312 319 6.381801 AGTCATGGCAAGAAAAACTAAATCG 58.618 36.000 0.00 0.00 0.00 3.34
314 321 7.029563 GTCATGGCAAGAAAAACTAAATCGAT 58.970 34.615 0.00 0.00 0.00 3.59
315 322 8.181573 GTCATGGCAAGAAAAACTAAATCGATA 58.818 33.333 0.00 0.00 0.00 2.92
317 324 7.681939 TGGCAAGAAAAACTAAATCGATACT 57.318 32.000 0.00 0.00 0.00 2.12
318 325 8.106247 TGGCAAGAAAAACTAAATCGATACTT 57.894 30.769 0.00 0.00 0.00 2.24
319 326 9.221933 TGGCAAGAAAAACTAAATCGATACTTA 57.778 29.630 0.00 0.00 0.00 2.24
361 368 5.580911 GCATTTTAGAGTGCTGGTTTTTG 57.419 39.130 0.00 0.00 38.30 2.44
366 377 6.959671 TTTAGAGTGCTGGTTTTTGTTTTG 57.040 33.333 0.00 0.00 0.00 2.44
370 381 1.003580 TGCTGGTTTTTGTTTTGGCCA 59.996 42.857 0.00 0.00 0.00 5.36
392 403 5.327091 CATGACTTCCACGAATGTCATTTC 58.673 41.667 0.00 0.00 44.62 2.17
421 432 9.415544 GATGAACATTTTCAAGCATAGAAAACT 57.584 29.630 11.48 2.72 45.01 2.66
497 509 6.973229 TTTAAGTTTACTATTCACCCGAGC 57.027 37.500 0.00 0.00 0.00 5.03
529 541 2.158813 TCGGGAGCAGAAGAACACTTTT 60.159 45.455 0.00 0.00 0.00 2.27
530 542 3.070446 TCGGGAGCAGAAGAACACTTTTA 59.930 43.478 0.00 0.00 0.00 1.52
531 543 3.433615 CGGGAGCAGAAGAACACTTTTAG 59.566 47.826 0.00 0.00 0.00 1.85
532 544 4.390264 GGGAGCAGAAGAACACTTTTAGT 58.610 43.478 0.00 0.00 0.00 2.24
548 560 8.642908 CACTTTTAGTGTTTTCTTTTTAGGGG 57.357 34.615 0.00 0.00 41.19 4.79
549 561 8.255206 CACTTTTAGTGTTTTCTTTTTAGGGGT 58.745 33.333 0.00 0.00 41.19 4.95
550 562 9.478238 ACTTTTAGTGTTTTCTTTTTAGGGGTA 57.522 29.630 0.00 0.00 0.00 3.69
553 565 8.820153 TTAGTGTTTTCTTTTTAGGGGTAACA 57.180 30.769 0.00 0.00 39.74 2.41
554 566 7.104043 AGTGTTTTCTTTTTAGGGGTAACAC 57.896 36.000 0.00 0.00 42.51 3.32
624 3218 3.706086 ACATTGCCACCTCAAAAGAAGTT 59.294 39.130 0.00 0.00 0.00 2.66
626 3220 5.362430 ACATTGCCACCTCAAAAGAAGTTAA 59.638 36.000 0.00 0.00 0.00 2.01
637 3240 9.945904 CCTCAAAAGAAGTTAATAGTTCCTAGT 57.054 33.333 0.00 0.00 34.79 2.57
850 5266 3.397482 CCCATCCAAGCGAAGATAAGAG 58.603 50.000 0.00 0.00 0.00 2.85
880 5296 3.660571 CCCTCCACATGGCACCCA 61.661 66.667 0.00 0.00 38.19 4.51
951 5368 1.861542 CGCTCGCCTATCCTCTCCAG 61.862 65.000 0.00 0.00 0.00 3.86
956 5373 1.191489 GCCTATCCTCTCCAGCTCCC 61.191 65.000 0.00 0.00 0.00 4.30
1251 5672 0.468400 GGATCGACCTGCCCTACTCT 60.468 60.000 0.00 0.00 35.41 3.24
1489 5910 9.278978 TCGAGCTGATATCATATTATCTCCTAC 57.721 37.037 5.72 0.00 31.19 3.18
1490 5911 9.061435 CGAGCTGATATCATATTATCTCCTACA 57.939 37.037 5.72 0.00 31.19 2.74
1520 5952 0.533531 TGCATGGACATCGCCAGATC 60.534 55.000 0.00 0.00 42.15 2.75
1521 5953 1.563435 GCATGGACATCGCCAGATCG 61.563 60.000 0.00 0.00 42.15 3.69
1522 5954 0.032540 CATGGACATCGCCAGATCGA 59.967 55.000 0.00 0.00 42.15 3.59
1621 6053 7.992180 ACCTTTTTGTACCGTAAGATATACG 57.008 36.000 1.23 1.23 43.02 3.06
1622 6054 7.547227 ACCTTTTTGTACCGTAAGATATACGT 58.453 34.615 7.18 0.00 39.09 3.57
1623 6055 8.682710 ACCTTTTTGTACCGTAAGATATACGTA 58.317 33.333 0.00 0.00 39.09 3.57
1624 6056 8.958043 CCTTTTTGTACCGTAAGATATACGTAC 58.042 37.037 0.00 9.33 39.09 3.67
1711 6143 5.697473 TGAGGCGTCTCTCTGATTAATAG 57.303 43.478 19.37 0.00 40.58 1.73
1712 6144 5.133941 TGAGGCGTCTCTCTGATTAATAGT 58.866 41.667 19.37 0.00 40.58 2.12
1713 6145 6.296803 TGAGGCGTCTCTCTGATTAATAGTA 58.703 40.000 19.37 0.00 40.58 1.82
1782 6227 6.793505 TCTTACCTGGGACTTTCTTCTATC 57.206 41.667 0.00 0.00 0.00 2.08
1785 6232 3.519913 ACCTGGGACTTTCTTCTATCCAC 59.480 47.826 0.00 0.00 32.45 4.02
1839 6293 8.407832 CAATATGAGTTGCACAATTTCCTCATA 58.592 33.333 17.01 17.01 42.68 2.15
1852 6306 9.418045 ACAATTTCCTCATAATTTTGTTTACCG 57.582 29.630 0.00 0.00 0.00 4.02
1864 6318 1.345415 TGTTTACCGACAAGGAGACCC 59.655 52.381 0.00 0.00 45.00 4.46
1893 6347 3.254166 CCCACTCATTTTTGTCCTCACTG 59.746 47.826 0.00 0.00 0.00 3.66
1916 6370 4.939439 GCTGATTTGCTCCAATCCATTTTT 59.061 37.500 0.00 0.00 0.00 1.94
1940 6394 9.823647 TTTAATGAAGCTTTGGACAACAATTTA 57.176 25.926 0.00 0.00 39.21 1.40
1945 6399 7.598493 TGAAGCTTTGGACAACAATTTAATAGC 59.402 33.333 0.00 0.00 39.21 2.97
1962 6416 5.779529 AATAGCTTTGCCCATTATCACTG 57.220 39.130 0.00 0.00 0.00 3.66
1966 6421 4.082026 AGCTTTGCCCATTATCACTGAAAC 60.082 41.667 0.00 0.00 0.00 2.78
1980 6435 4.821805 TCACTGAAACAACAGAGATTTCCC 59.178 41.667 0.00 0.00 40.63 3.97
1981 6436 4.022849 CACTGAAACAACAGAGATTTCCCC 60.023 45.833 0.00 0.00 40.63 4.81
1991 6446 7.091993 ACAACAGAGATTTCCCCTATAATCCAA 60.092 37.037 0.00 0.00 32.43 3.53
1998 6453 8.572221 AGATTTCCCCTATAATCCAATATGCAT 58.428 33.333 3.79 3.79 32.43 3.96
1999 6454 7.959658 TTTCCCCTATAATCCAATATGCATG 57.040 36.000 10.16 0.00 0.00 4.06
2003 6458 7.064866 CCCCTATAATCCAATATGCATGTGAT 58.935 38.462 10.16 0.00 0.00 3.06
2006 6461 9.842775 CCTATAATCCAATATGCATGTGATACT 57.157 33.333 10.16 0.00 0.00 2.12
2020 6475 9.166173 TGCATGTGATACTATTATTATCTTGCC 57.834 33.333 14.25 0.00 32.27 4.52
2055 6510 5.108517 TGCAAATTCAACAAGTTCAGAACC 58.891 37.500 9.85 0.00 0.00 3.62
2069 6524 6.860080 AGTTCAGAACCTATTGATGCATTTG 58.140 36.000 9.85 0.00 0.00 2.32
2122 6578 4.364470 ACAAATCCATGATGGTTCCCATT 58.636 39.130 11.87 0.30 45.26 3.16
2127 6583 3.896888 TCCATGATGGTTCCCATTAATGC 59.103 43.478 11.87 0.00 45.26 3.56
2140 6596 4.341806 CCCATTAATGCACCTGCTCATAAA 59.658 41.667 10.11 0.00 42.66 1.40
2144 6600 4.660789 AATGCACCTGCTCATAAAATCC 57.339 40.909 0.00 0.00 42.66 3.01
2167 6623 4.034975 CAGCAACTCTCAGCTATTTTAGGC 59.965 45.833 0.00 0.00 39.50 3.93
2169 6625 4.272261 GCAACTCTCAGCTATTTTAGGCTC 59.728 45.833 0.00 0.00 36.59 4.70
2170 6626 4.681074 ACTCTCAGCTATTTTAGGCTCC 57.319 45.455 0.00 0.00 36.59 4.70
2185 6641 1.158484 GCTCCGCCGAGGGTAATTTC 61.158 60.000 4.20 0.00 41.52 2.17
2231 6687 4.735369 TCTTGGCATTTCTAAACCCAAGA 58.265 39.130 22.75 22.75 46.40 3.02
2237 6693 6.042552 TGGCATTTCTAAACCCAAGATTGAAA 59.957 34.615 0.00 0.00 0.00 2.69
2244 6700 8.376889 TCTAAACCCAAGATTGAAAATTTTGC 57.623 30.769 8.47 1.07 0.00 3.68
2245 6701 8.210265 TCTAAACCCAAGATTGAAAATTTTGCT 58.790 29.630 8.47 0.00 0.00 3.91
2246 6702 6.866010 AACCCAAGATTGAAAATTTTGCTC 57.134 33.333 8.47 2.35 0.00 4.26
2247 6703 5.308014 ACCCAAGATTGAAAATTTTGCTCC 58.692 37.500 8.47 0.00 0.00 4.70
2248 6704 5.072193 ACCCAAGATTGAAAATTTTGCTCCT 59.928 36.000 8.47 0.00 0.00 3.69
2249 6705 5.640783 CCCAAGATTGAAAATTTTGCTCCTC 59.359 40.000 8.47 0.00 0.00 3.71
2250 6706 6.461640 CCAAGATTGAAAATTTTGCTCCTCT 58.538 36.000 8.47 0.87 0.00 3.69
2251 6707 7.309990 CCCAAGATTGAAAATTTTGCTCCTCTA 60.310 37.037 8.47 0.00 0.00 2.43
2252 6708 8.090214 CCAAGATTGAAAATTTTGCTCCTCTAA 58.910 33.333 8.47 0.00 0.00 2.10
2283 6739 3.895232 TGGATCTAGACTTGCTGGTTC 57.105 47.619 0.00 0.00 0.00 3.62
2302 6758 4.273318 GTTCCTCCACAATGCTTTCCTAT 58.727 43.478 0.00 0.00 0.00 2.57
2352 6808 8.476447 GTCTATTTTCACTAGCCTACCTACTTT 58.524 37.037 0.00 0.00 0.00 2.66
2360 6816 4.762289 AGCCTACCTACTTTCTTCATGG 57.238 45.455 0.00 0.00 0.00 3.66
2374 6830 3.330701 TCTTCATGGGCAGTTTAGACCTT 59.669 43.478 0.00 0.00 37.66 3.50
2379 6835 1.613520 GGGCAGTTTAGACCTTCCCAC 60.614 57.143 0.00 0.00 32.29 4.61
2391 6847 1.142870 CCTTCCCACAGGAGTTGTTGA 59.857 52.381 0.00 0.00 45.19 3.18
2395 6851 1.409521 CCCACAGGAGTTGTTGACCAA 60.410 52.381 0.00 0.00 38.16 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.935205 CGTCAGAAGTTTATGGGATCAACA 59.065 41.667 0.00 0.00 0.00 3.33
1 2 4.201822 GCGTCAGAAGTTTATGGGATCAAC 60.202 45.833 0.00 0.00 0.00 3.18
2 3 3.938963 GCGTCAGAAGTTTATGGGATCAA 59.061 43.478 0.00 0.00 0.00 2.57
3 4 3.197766 AGCGTCAGAAGTTTATGGGATCA 59.802 43.478 0.00 0.00 0.00 2.92
4 5 3.557595 CAGCGTCAGAAGTTTATGGGATC 59.442 47.826 0.00 0.00 0.00 3.36
5 6 3.055094 ACAGCGTCAGAAGTTTATGGGAT 60.055 43.478 0.00 0.00 0.00 3.85
6 7 2.301870 ACAGCGTCAGAAGTTTATGGGA 59.698 45.455 0.00 0.00 0.00 4.37
7 8 2.673368 GACAGCGTCAGAAGTTTATGGG 59.327 50.000 4.20 0.00 32.09 4.00
8 9 2.673368 GGACAGCGTCAGAAGTTTATGG 59.327 50.000 10.14 0.00 33.68 2.74
9 10 3.369147 CAGGACAGCGTCAGAAGTTTATG 59.631 47.826 10.14 0.00 33.68 1.90
10 11 3.006967 ACAGGACAGCGTCAGAAGTTTAT 59.993 43.478 10.14 0.00 33.68 1.40
11 12 2.364324 ACAGGACAGCGTCAGAAGTTTA 59.636 45.455 10.14 0.00 33.68 2.01
12 13 1.139058 ACAGGACAGCGTCAGAAGTTT 59.861 47.619 10.14 0.00 33.68 2.66
13 14 0.753262 ACAGGACAGCGTCAGAAGTT 59.247 50.000 10.14 0.00 33.68 2.66
14 15 0.315568 GACAGGACAGCGTCAGAAGT 59.684 55.000 10.14 3.71 33.68 3.01
15 16 0.600557 AGACAGGACAGCGTCAGAAG 59.399 55.000 10.14 1.17 34.48 2.85
16 17 1.000163 GAAGACAGGACAGCGTCAGAA 60.000 52.381 10.14 0.00 34.48 3.02
17 18 0.598562 GAAGACAGGACAGCGTCAGA 59.401 55.000 10.14 0.00 34.48 3.27
18 19 0.389166 GGAAGACAGGACAGCGTCAG 60.389 60.000 10.14 5.36 34.48 3.51
19 20 1.112916 TGGAAGACAGGACAGCGTCA 61.113 55.000 10.14 0.00 34.48 4.35
20 21 0.033504 TTGGAAGACAGGACAGCGTC 59.966 55.000 0.79 0.79 0.00 5.19
21 22 0.687354 ATTGGAAGACAGGACAGCGT 59.313 50.000 0.00 0.00 0.00 5.07
22 23 1.081892 CATTGGAAGACAGGACAGCG 58.918 55.000 0.00 0.00 0.00 5.18
23 24 0.807496 GCATTGGAAGACAGGACAGC 59.193 55.000 0.00 0.00 0.00 4.40
24 25 1.271543 TGGCATTGGAAGACAGGACAG 60.272 52.381 0.00 0.00 0.00 3.51
25 26 0.770499 TGGCATTGGAAGACAGGACA 59.230 50.000 0.00 0.00 0.00 4.02
26 27 1.168714 GTGGCATTGGAAGACAGGAC 58.831 55.000 0.00 0.00 0.00 3.85
27 28 0.770499 TGTGGCATTGGAAGACAGGA 59.230 50.000 0.00 0.00 0.00 3.86
28 29 1.270550 GTTGTGGCATTGGAAGACAGG 59.729 52.381 0.00 0.00 0.00 4.00
29 30 2.233271 AGTTGTGGCATTGGAAGACAG 58.767 47.619 0.00 0.00 0.00 3.51
30 31 2.363306 AGTTGTGGCATTGGAAGACA 57.637 45.000 0.00 0.00 0.00 3.41
31 32 3.428045 GCATAGTTGTGGCATTGGAAGAC 60.428 47.826 0.00 0.00 0.00 3.01
32 33 2.754552 GCATAGTTGTGGCATTGGAAGA 59.245 45.455 0.00 0.00 0.00 2.87
33 34 2.159198 GGCATAGTTGTGGCATTGGAAG 60.159 50.000 0.00 0.00 43.52 3.46
34 35 1.824230 GGCATAGTTGTGGCATTGGAA 59.176 47.619 0.00 0.00 43.52 3.53
35 36 1.473258 GGCATAGTTGTGGCATTGGA 58.527 50.000 0.00 0.00 43.52 3.53
36 37 0.461135 GGGCATAGTTGTGGCATTGG 59.539 55.000 4.93 0.00 45.63 3.16
37 38 0.461135 GGGGCATAGTTGTGGCATTG 59.539 55.000 4.93 0.00 45.63 2.82
38 39 0.336048 AGGGGCATAGTTGTGGCATT 59.664 50.000 4.93 0.00 45.63 3.56
39 40 1.133792 GTAGGGGCATAGTTGTGGCAT 60.134 52.381 4.93 0.00 45.63 4.40
40 41 0.254747 GTAGGGGCATAGTTGTGGCA 59.745 55.000 4.93 0.00 45.63 4.92
41 42 0.546598 AGTAGGGGCATAGTTGTGGC 59.453 55.000 0.00 0.00 43.34 5.01
42 43 4.141482 ACATTAGTAGGGGCATAGTTGTGG 60.141 45.833 0.00 0.00 0.00 4.17
43 44 5.036117 ACATTAGTAGGGGCATAGTTGTG 57.964 43.478 0.00 0.00 0.00 3.33
44 45 4.719773 TGACATTAGTAGGGGCATAGTTGT 59.280 41.667 0.00 0.00 0.00 3.32
45 46 5.290493 TGACATTAGTAGGGGCATAGTTG 57.710 43.478 0.00 0.00 0.00 3.16
46 47 6.013639 GGTATGACATTAGTAGGGGCATAGTT 60.014 42.308 0.00 0.00 0.00 2.24
47 48 5.484290 GGTATGACATTAGTAGGGGCATAGT 59.516 44.000 0.00 0.00 0.00 2.12
48 49 5.483937 TGGTATGACATTAGTAGGGGCATAG 59.516 44.000 0.00 0.00 0.00 2.23
49 50 5.407936 TGGTATGACATTAGTAGGGGCATA 58.592 41.667 0.00 0.00 0.00 3.14
50 51 4.239495 TGGTATGACATTAGTAGGGGCAT 58.761 43.478 0.00 0.00 0.00 4.40
51 52 3.659841 TGGTATGACATTAGTAGGGGCA 58.340 45.455 0.00 0.00 0.00 5.36
52 53 4.699925 TTGGTATGACATTAGTAGGGGC 57.300 45.455 0.00 0.00 0.00 5.80
53 54 7.390718 GCTTATTTGGTATGACATTAGTAGGGG 59.609 40.741 0.00 0.00 0.00 4.79
54 55 7.390718 GGCTTATTTGGTATGACATTAGTAGGG 59.609 40.741 0.00 0.00 0.00 3.53
55 56 7.936847 TGGCTTATTTGGTATGACATTAGTAGG 59.063 37.037 0.00 0.00 0.00 3.18
56 57 8.902540 TGGCTTATTTGGTATGACATTAGTAG 57.097 34.615 0.00 0.00 0.00 2.57
57 58 9.116067 GTTGGCTTATTTGGTATGACATTAGTA 57.884 33.333 0.00 0.00 0.00 1.82
58 59 7.201696 CGTTGGCTTATTTGGTATGACATTAGT 60.202 37.037 0.00 0.00 0.00 2.24
59 60 7.132213 CGTTGGCTTATTTGGTATGACATTAG 58.868 38.462 0.00 0.00 0.00 1.73
60 61 6.600032 ACGTTGGCTTATTTGGTATGACATTA 59.400 34.615 0.00 0.00 0.00 1.90
61 62 5.417580 ACGTTGGCTTATTTGGTATGACATT 59.582 36.000 0.00 0.00 0.00 2.71
62 63 4.947388 ACGTTGGCTTATTTGGTATGACAT 59.053 37.500 0.00 0.00 0.00 3.06
63 64 4.328536 ACGTTGGCTTATTTGGTATGACA 58.671 39.130 0.00 0.00 0.00 3.58
64 65 4.393680 TGACGTTGGCTTATTTGGTATGAC 59.606 41.667 0.00 0.00 0.00 3.06
65 66 4.393680 GTGACGTTGGCTTATTTGGTATGA 59.606 41.667 0.00 0.00 0.00 2.15
66 67 4.155099 TGTGACGTTGGCTTATTTGGTATG 59.845 41.667 0.00 0.00 0.00 2.39
67 68 4.328536 TGTGACGTTGGCTTATTTGGTAT 58.671 39.130 0.00 0.00 0.00 2.73
68 69 3.741249 TGTGACGTTGGCTTATTTGGTA 58.259 40.909 0.00 0.00 0.00 3.25
69 70 2.577700 TGTGACGTTGGCTTATTTGGT 58.422 42.857 0.00 0.00 0.00 3.67
70 71 3.004315 AGTTGTGACGTTGGCTTATTTGG 59.996 43.478 0.00 0.00 0.00 3.28
71 72 4.223320 AGTTGTGACGTTGGCTTATTTG 57.777 40.909 0.00 0.00 0.00 2.32
72 73 6.569179 AATAGTTGTGACGTTGGCTTATTT 57.431 33.333 0.00 0.00 0.00 1.40
73 74 6.569179 AAATAGTTGTGACGTTGGCTTATT 57.431 33.333 0.00 0.00 0.00 1.40
74 75 7.675962 TTAAATAGTTGTGACGTTGGCTTAT 57.324 32.000 0.00 0.00 0.00 1.73
75 76 7.493743 TTTAAATAGTTGTGACGTTGGCTTA 57.506 32.000 0.00 0.00 0.00 3.09
76 77 6.380095 TTTAAATAGTTGTGACGTTGGCTT 57.620 33.333 0.00 0.00 0.00 4.35
77 78 6.380095 TTTTAAATAGTTGTGACGTTGGCT 57.620 33.333 0.00 0.00 0.00 4.75
78 79 8.730970 TTATTTTAAATAGTTGTGACGTTGGC 57.269 30.769 0.00 0.00 0.00 4.52
93 94 9.651913 CCAACACCAGCACTATTTATTTTAAAT 57.348 29.630 0.00 0.00 0.00 1.40
94 95 8.643324 ACCAACACCAGCACTATTTATTTTAAA 58.357 29.630 0.00 0.00 0.00 1.52
95 96 8.184304 ACCAACACCAGCACTATTTATTTTAA 57.816 30.769 0.00 0.00 0.00 1.52
96 97 7.768807 ACCAACACCAGCACTATTTATTTTA 57.231 32.000 0.00 0.00 0.00 1.52
97 98 6.664428 ACCAACACCAGCACTATTTATTTT 57.336 33.333 0.00 0.00 0.00 1.82
98 99 6.041523 ACAACCAACACCAGCACTATTTATTT 59.958 34.615 0.00 0.00 0.00 1.40
99 100 5.538433 ACAACCAACACCAGCACTATTTATT 59.462 36.000 0.00 0.00 0.00 1.40
100 101 5.076873 ACAACCAACACCAGCACTATTTAT 58.923 37.500 0.00 0.00 0.00 1.40
101 102 4.465886 ACAACCAACACCAGCACTATTTA 58.534 39.130 0.00 0.00 0.00 1.40
102 103 3.295973 ACAACCAACACCAGCACTATTT 58.704 40.909 0.00 0.00 0.00 1.40
103 104 2.944129 ACAACCAACACCAGCACTATT 58.056 42.857 0.00 0.00 0.00 1.73
104 105 2.656947 ACAACCAACACCAGCACTAT 57.343 45.000 0.00 0.00 0.00 2.12
105 106 3.562343 TTACAACCAACACCAGCACTA 57.438 42.857 0.00 0.00 0.00 2.74
106 107 2.428544 TTACAACCAACACCAGCACT 57.571 45.000 0.00 0.00 0.00 4.40
107 108 3.380142 CATTTACAACCAACACCAGCAC 58.620 45.455 0.00 0.00 0.00 4.40
108 109 2.363680 CCATTTACAACCAACACCAGCA 59.636 45.455 0.00 0.00 0.00 4.41
109 110 2.866065 GCCATTTACAACCAACACCAGC 60.866 50.000 0.00 0.00 0.00 4.85
110 111 2.606795 CGCCATTTACAACCAACACCAG 60.607 50.000 0.00 0.00 0.00 4.00
111 112 1.338337 CGCCATTTACAACCAACACCA 59.662 47.619 0.00 0.00 0.00 4.17
112 113 1.338655 ACGCCATTTACAACCAACACC 59.661 47.619 0.00 0.00 0.00 4.16
113 114 2.389998 CACGCCATTTACAACCAACAC 58.610 47.619 0.00 0.00 0.00 3.32
114 115 1.269309 GCACGCCATTTACAACCAACA 60.269 47.619 0.00 0.00 0.00 3.33
115 116 1.414378 GCACGCCATTTACAACCAAC 58.586 50.000 0.00 0.00 0.00 3.77
116 117 0.315568 GGCACGCCATTTACAACCAA 59.684 50.000 2.36 0.00 35.81 3.67
117 118 0.823769 TGGCACGCCATTTACAACCA 60.824 50.000 6.67 0.00 41.89 3.67
118 119 1.960612 TGGCACGCCATTTACAACC 59.039 52.632 6.67 0.00 41.89 3.77
129 130 2.051345 CTTTCGTTGGTGGCACGC 60.051 61.111 12.17 5.35 37.57 5.34
130 131 0.591236 CAACTTTCGTTGGTGGCACG 60.591 55.000 12.17 0.00 45.28 5.34
131 132 3.250220 CAACTTTCGTTGGTGGCAC 57.750 52.632 9.70 9.70 45.28 5.01
139 140 3.685836 GTGTTAGCCACAACTTTCGTT 57.314 42.857 0.00 0.00 43.92 3.85
149 150 4.820173 ACTAGTGGAAAAAGTGTTAGCCAC 59.180 41.667 9.10 9.10 44.57 5.01
150 151 4.819630 CACTAGTGGAAAAAGTGTTAGCCA 59.180 41.667 15.49 0.00 36.66 4.75
151 152 4.320275 GCACTAGTGGAAAAAGTGTTAGCC 60.320 45.833 23.95 0.00 42.10 3.93
152 153 4.610680 CGCACTAGTGGAAAAAGTGTTAGC 60.611 45.833 23.95 3.64 42.10 3.09
153 154 5.018695 CGCACTAGTGGAAAAAGTGTTAG 57.981 43.478 23.95 0.00 42.10 2.34
155 156 3.963383 CGCACTAGTGGAAAAAGTGTT 57.037 42.857 23.95 0.00 42.10 3.32
166 167 2.717580 TACTGTTCACCGCACTAGTG 57.282 50.000 18.93 18.93 36.54 2.74
167 168 3.738830 TTTACTGTTCACCGCACTAGT 57.261 42.857 0.00 0.00 0.00 2.57
168 169 4.201589 CGATTTTACTGTTCACCGCACTAG 60.202 45.833 0.00 0.00 0.00 2.57
169 170 3.676172 CGATTTTACTGTTCACCGCACTA 59.324 43.478 0.00 0.00 0.00 2.74
170 171 2.478894 CGATTTTACTGTTCACCGCACT 59.521 45.455 0.00 0.00 0.00 4.40
171 172 2.477375 TCGATTTTACTGTTCACCGCAC 59.523 45.455 0.00 0.00 0.00 5.34
172 173 2.734606 CTCGATTTTACTGTTCACCGCA 59.265 45.455 0.00 0.00 0.00 5.69
173 174 2.093783 CCTCGATTTTACTGTTCACCGC 59.906 50.000 0.00 0.00 0.00 5.68
191 192 9.764363 AGGAACTTTTGAATTTGTTTTATCCTC 57.236 29.630 0.00 0.00 27.25 3.71
192 193 9.546428 CAGGAACTTTTGAATTTGTTTTATCCT 57.454 29.630 0.00 0.00 34.60 3.24
193 194 9.325198 ACAGGAACTTTTGAATTTGTTTTATCC 57.675 29.630 0.00 0.00 34.60 2.59
226 233 9.191995 CACATAGAAAATTTGTCAAAGGTTACC 57.808 33.333 4.03 0.00 0.00 2.85
267 274 9.865321 ATGACTTACAGAAATTTTCATTCATGG 57.135 29.630 11.53 0.00 0.00 3.66
278 285 6.899393 TTCTTGCCATGACTTACAGAAATT 57.101 33.333 0.00 0.00 0.00 1.82
286 293 8.020819 CGATTTAGTTTTTCTTGCCATGACTTA 58.979 33.333 0.00 0.00 0.00 2.24
291 298 8.184192 AGTATCGATTTAGTTTTTCTTGCCATG 58.816 33.333 1.71 0.00 0.00 3.66
292 299 8.281212 AGTATCGATTTAGTTTTTCTTGCCAT 57.719 30.769 1.71 0.00 0.00 4.40
339 346 5.049828 ACAAAAACCAGCACTCTAAAATGC 58.950 37.500 0.00 0.00 42.39 3.56
346 353 3.860641 CCAAAACAAAAACCAGCACTCT 58.139 40.909 0.00 0.00 0.00 3.24
351 358 1.743996 TGGCCAAAACAAAAACCAGC 58.256 45.000 0.61 0.00 0.00 4.85
355 362 4.035091 GGAAGTCATGGCCAAAACAAAAAC 59.965 41.667 10.96 0.00 0.00 2.43
360 367 1.686052 GTGGAAGTCATGGCCAAAACA 59.314 47.619 10.96 0.00 32.68 2.83
361 368 1.335872 CGTGGAAGTCATGGCCAAAAC 60.336 52.381 10.96 11.55 32.68 2.43
366 377 0.734889 CATTCGTGGAAGTCATGGCC 59.265 55.000 0.00 0.00 33.31 5.36
392 403 6.545508 TCTATGCTTGAAAATGTTCATCACG 58.454 36.000 0.00 0.00 43.29 4.35
401 412 9.853921 GACAAAAGTTTTCTATGCTTGAAAATG 57.146 29.630 0.00 10.06 42.76 2.32
476 488 5.927281 AGCTCGGGTGAATAGTAAACTTA 57.073 39.130 0.00 0.00 0.00 2.24
479 491 7.279313 TCAAATAAGCTCGGGTGAATAGTAAAC 59.721 37.037 0.00 0.00 0.00 2.01
486 498 2.945668 GCTCAAATAAGCTCGGGTGAAT 59.054 45.455 0.00 0.00 39.27 2.57
487 499 2.356135 GCTCAAATAAGCTCGGGTGAA 58.644 47.619 0.00 0.00 39.27 3.18
529 541 8.224389 GTGTTACCCCTAAAAAGAAAACACTA 57.776 34.615 7.54 0.00 41.22 2.74
530 542 6.893554 AGTGTTACCCCTAAAAAGAAAACACT 59.106 34.615 10.75 10.75 46.50 3.55
531 543 7.104043 AGTGTTACCCCTAAAAAGAAAACAC 57.896 36.000 6.85 6.85 43.48 3.32
532 544 7.721409 AAGTGTTACCCCTAAAAAGAAAACA 57.279 32.000 0.00 0.00 0.00 2.83
535 547 9.478238 ACTAAAAGTGTTACCCCTAAAAAGAAA 57.522 29.630 0.00 0.00 0.00 2.52
536 548 8.905850 CACTAAAAGTGTTACCCCTAAAAAGAA 58.094 33.333 0.00 0.00 41.19 2.52
537 549 8.454570 CACTAAAAGTGTTACCCCTAAAAAGA 57.545 34.615 0.00 0.00 41.19 2.52
554 566 9.417284 CGAAAACTGTAACAGTAACACTAAAAG 57.583 33.333 0.00 0.00 44.62 2.27
555 567 8.934825 ACGAAAACTGTAACAGTAACACTAAAA 58.065 29.630 0.00 0.00 44.62 1.52
556 568 8.477984 ACGAAAACTGTAACAGTAACACTAAA 57.522 30.769 0.00 0.00 44.62 1.85
557 569 8.477984 AACGAAAACTGTAACAGTAACACTAA 57.522 30.769 0.00 0.00 44.62 2.24
558 570 7.758980 TGAACGAAAACTGTAACAGTAACACTA 59.241 33.333 0.00 0.00 44.62 2.74
559 571 6.591062 TGAACGAAAACTGTAACAGTAACACT 59.409 34.615 0.00 0.00 44.62 3.55
560 572 6.764094 TGAACGAAAACTGTAACAGTAACAC 58.236 36.000 0.00 0.00 44.62 3.32
624 3218 7.835682 TGTGTGGCTACTAACTAGGAACTATTA 59.164 37.037 0.64 0.00 41.70 0.98
626 3220 6.096564 GTGTGTGGCTACTAACTAGGAACTAT 59.903 42.308 0.64 0.00 41.70 2.12
637 3240 2.354704 GCTCCATGTGTGTGGCTACTAA 60.355 50.000 0.64 0.00 39.19 2.24
741 3344 0.459585 CGGGGACATAAGTGGTCACG 60.460 60.000 0.00 0.00 39.60 4.35
850 5266 3.412408 GAGGGAAGGGAGTGGGCC 61.412 72.222 0.00 0.00 0.00 5.80
880 5296 3.393609 GGAATAAGTAAGGGATTCGGGGT 59.606 47.826 0.00 0.00 31.57 4.95
884 5300 3.064931 GCGGGAATAAGTAAGGGATTCG 58.935 50.000 0.00 0.00 31.57 3.34
885 5301 3.409570 GGCGGGAATAAGTAAGGGATTC 58.590 50.000 0.00 0.00 0.00 2.52
951 5368 3.618780 CTCTGTGTGGCTGGGGAGC 62.619 68.421 0.00 0.00 0.00 4.70
956 5373 1.805869 CTCTTTCTCTGTGTGGCTGG 58.194 55.000 0.00 0.00 0.00 4.85
1460 5881 8.243426 GGAGATAATATGATATCAGCTCGATCC 58.757 40.741 11.78 9.13 35.22 3.36
1512 5944 0.241213 ATCGGTGTATCGATCTGGCG 59.759 55.000 0.00 0.00 45.43 5.69
1520 5952 3.120338 AGCACAAAACAATCGGTGTATCG 60.120 43.478 0.00 0.00 40.60 2.92
1521 5953 4.403453 GAGCACAAAACAATCGGTGTATC 58.597 43.478 0.00 0.00 40.60 2.24
1522 5954 3.120338 CGAGCACAAAACAATCGGTGTAT 60.120 43.478 0.00 0.00 40.60 2.29
1523 5955 2.222213 CGAGCACAAAACAATCGGTGTA 59.778 45.455 0.00 0.00 40.60 2.90
1533 5965 3.983344 AGCAATTCATTCGAGCACAAAAC 59.017 39.130 0.00 0.00 0.00 2.43
1534 5966 4.229096 GAGCAATTCATTCGAGCACAAAA 58.771 39.130 0.00 0.00 0.00 2.44
1581 6013 8.441312 ACAAAAAGGTAGTAATTCGAAGACAA 57.559 30.769 13.68 0.00 34.32 3.18
1621 6053 6.019479 ACACGCTAGTATTACGACAGTAGTAC 60.019 42.308 0.00 0.00 42.70 2.73
1622 6054 6.042777 ACACGCTAGTATTACGACAGTAGTA 58.957 40.000 0.00 0.00 33.87 1.82
1623 6055 4.872691 ACACGCTAGTATTACGACAGTAGT 59.127 41.667 0.00 0.00 33.87 2.73
1624 6056 5.401033 ACACGCTAGTATTACGACAGTAG 57.599 43.478 0.00 0.00 33.87 2.57
1731 6163 4.111375 TCAAGTAATTCAGCCGTCTCTC 57.889 45.455 0.00 0.00 0.00 3.20
1738 6170 6.690194 AGATGTTCATCAAGTAATTCAGCC 57.310 37.500 14.05 0.00 0.00 4.85
1782 6227 3.433274 CGTAGCATGCACCTATTATGTGG 59.567 47.826 21.98 0.00 34.27 4.17
1785 6232 4.560128 AGTCGTAGCATGCACCTATTATG 58.440 43.478 21.98 7.82 0.00 1.90
1839 6293 5.009310 GGTCTCCTTGTCGGTAAACAAAATT 59.991 40.000 0.00 0.00 38.60 1.82
1864 6318 3.500343 ACAAAAATGAGTGGGGAGAAGG 58.500 45.455 0.00 0.00 0.00 3.46
1868 6322 3.084786 GAGGACAAAAATGAGTGGGGAG 58.915 50.000 0.00 0.00 0.00 4.30
1872 6326 3.304928 GCAGTGAGGACAAAAATGAGTGG 60.305 47.826 0.00 0.00 0.00 4.00
1893 6347 3.814005 AATGGATTGGAGCAAATCAGC 57.186 42.857 8.48 0.00 38.14 4.26
1916 6370 9.995003 ATTAAATTGTTGTCCAAAGCTTCATTA 57.005 25.926 0.00 0.00 36.44 1.90
1940 6394 5.448654 TCAGTGATAATGGGCAAAGCTATT 58.551 37.500 0.00 0.00 0.00 1.73
1945 6399 5.389859 TGTTTCAGTGATAATGGGCAAAG 57.610 39.130 0.00 0.00 0.00 2.77
1962 6416 8.753497 ATTATAGGGGAAATCTCTGTTGTTTC 57.247 34.615 0.00 0.00 0.00 2.78
1966 6421 6.841601 TGGATTATAGGGGAAATCTCTGTTG 58.158 40.000 0.00 0.00 33.50 3.33
1980 6435 9.842775 AGTATCACATGCATATTGGATTATAGG 57.157 33.333 0.00 0.00 0.00 2.57
1998 6453 8.374743 TGCAGGCAAGATAATAATAGTATCACA 58.625 33.333 9.91 0.00 31.49 3.58
1999 6454 8.777865 TGCAGGCAAGATAATAATAGTATCAC 57.222 34.615 9.91 0.27 31.49 3.06
2003 6458 7.824289 GGACATGCAGGCAAGATAATAATAGTA 59.176 37.037 0.00 0.00 0.00 1.82
2006 6461 5.945784 GGGACATGCAGGCAAGATAATAATA 59.054 40.000 0.00 0.00 0.00 0.98
2055 6510 6.042143 GTGTAAACCCCAAATGCATCAATAG 58.958 40.000 0.00 0.00 0.00 1.73
2069 6524 1.003233 CCTGAGACCTGTGTAAACCCC 59.997 57.143 0.00 0.00 0.00 4.95
2122 6578 5.199723 TGGATTTTATGAGCAGGTGCATTA 58.800 37.500 4.48 0.00 45.16 1.90
2127 6583 3.018856 TGCTGGATTTTATGAGCAGGTG 58.981 45.455 0.00 0.00 36.54 4.00
2140 6596 4.500499 AATAGCTGAGAGTTGCTGGATT 57.500 40.909 0.00 0.00 40.08 3.01
2144 6600 4.034975 GCCTAAAATAGCTGAGAGTTGCTG 59.965 45.833 0.00 0.00 40.08 4.41
2167 6623 0.532196 GGAAATTACCCTCGGCGGAG 60.532 60.000 14.06 14.06 40.14 4.63
2169 6625 1.525306 GGGAAATTACCCTCGGCGG 60.525 63.158 7.21 0.00 45.90 6.13
2170 6626 4.136250 GGGAAATTACCCTCGGCG 57.864 61.111 0.00 0.00 45.90 6.46
2177 6633 6.379133 CCAAGGTAAGTAAAGGGGAAATTACC 59.621 42.308 4.08 4.08 41.50 2.85
2181 6637 5.315109 AGTCCAAGGTAAGTAAAGGGGAAAT 59.685 40.000 0.00 0.00 0.00 2.17
2185 6641 4.567116 GGAAGTCCAAGGTAAGTAAAGGGG 60.567 50.000 0.00 0.00 35.64 4.79
2237 6693 7.781324 TCCTTTTCATTAGAGGAGCAAAATT 57.219 32.000 0.00 0.00 34.74 1.82
2242 6698 5.044919 TCCAATCCTTTTCATTAGAGGAGCA 60.045 40.000 0.00 0.00 42.47 4.26
2243 6699 5.440610 TCCAATCCTTTTCATTAGAGGAGC 58.559 41.667 0.00 0.00 42.47 4.70
2244 6700 7.516452 AGATCCAATCCTTTTCATTAGAGGAG 58.484 38.462 0.00 0.00 42.47 3.69
2245 6701 7.457380 AGATCCAATCCTTTTCATTAGAGGA 57.543 36.000 0.00 0.00 43.29 3.71
2246 6702 8.654997 TCTAGATCCAATCCTTTTCATTAGAGG 58.345 37.037 0.00 0.00 0.00 3.69
2247 6703 9.487790 GTCTAGATCCAATCCTTTTCATTAGAG 57.512 37.037 0.00 0.00 0.00 2.43
2248 6704 9.218525 AGTCTAGATCCAATCCTTTTCATTAGA 57.781 33.333 0.00 0.00 0.00 2.10
2249 6705 9.844257 AAGTCTAGATCCAATCCTTTTCATTAG 57.156 33.333 0.00 0.00 0.00 1.73
2250 6706 9.618890 CAAGTCTAGATCCAATCCTTTTCATTA 57.381 33.333 0.00 0.00 0.00 1.90
2251 6707 7.067981 GCAAGTCTAGATCCAATCCTTTTCATT 59.932 37.037 0.00 0.00 0.00 2.57
2252 6708 6.545298 GCAAGTCTAGATCCAATCCTTTTCAT 59.455 38.462 0.00 0.00 0.00 2.57
2283 6739 2.954318 CCATAGGAAAGCATTGTGGAGG 59.046 50.000 0.00 0.00 0.00 4.30
2302 6758 5.551305 TCACAAGAATGAGTTTCTCTCCA 57.449 39.130 0.00 0.00 44.09 3.86
2326 6782 7.585579 AGTAGGTAGGCTAGTGAAAATAGAC 57.414 40.000 0.00 0.00 44.48 2.59
2330 6786 7.497773 AGAAAGTAGGTAGGCTAGTGAAAAT 57.502 36.000 0.00 0.00 0.00 1.82
2331 6787 6.930068 AGAAAGTAGGTAGGCTAGTGAAAA 57.070 37.500 0.00 0.00 0.00 2.29
2352 6808 2.912956 AGGTCTAAACTGCCCATGAAGA 59.087 45.455 0.00 0.00 0.00 2.87
2360 6816 1.073284 TGTGGGAAGGTCTAAACTGCC 59.927 52.381 0.00 0.00 0.00 4.85
2374 6830 0.472471 GGTCAACAACTCCTGTGGGA 59.528 55.000 0.00 0.00 38.67 4.37
2379 6835 9.927668 ATTTATTAATTTGGTCAACAACTCCTG 57.072 29.630 0.00 0.00 39.19 3.86


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

AutoCloner maintained by Alex Coulton.