Multiple sequence alignment - TraesCS1D01G390700

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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 TraesCS1D01G390700 chr1D 100.000 3020 0 0 1 3020 462094077 462091058 0.000000e+00 5578.0
1 TraesCS1D01G390700 chr1D 87.461 1292 100 27 318 1564 462108562 462107288 0.000000e+00 1432.0
2 TraesCS1D01G390700 chr1D 92.504 587 27 7 2224 2803 462106232 462105656 0.000000e+00 824.0
3 TraesCS1D01G390700 chr1D 85.802 655 79 8 774 1418 462115661 462115011 0.000000e+00 682.0
4 TraesCS1D01G390700 chr1D 97.959 392 8 0 1595 1986 462082222 462081831 0.000000e+00 680.0
5 TraesCS1D01G390700 chr1D 97.674 387 9 0 1597 1983 462080999 462081385 0.000000e+00 665.0
6 TraesCS1D01G390700 chr1D 90.462 346 21 3 1884 2218 462106628 462106284 2.140000e-121 446.0
7 TraesCS1D01G390700 chr1D 91.615 322 26 1 1563 1883 462106986 462106665 7.680000e-121 444.0
8 TraesCS1D01G390700 chr1D 84.857 350 35 5 1886 2218 462114376 462114028 1.340000e-88 337.0
9 TraesCS1D01G390700 chr1D 87.946 224 17 8 560 775 462115911 462115690 3.860000e-64 255.0
10 TraesCS1D01G390700 chr1D 88.136 118 10 3 400 517 462112213 462112100 1.460000e-28 137.0
11 TraesCS1D01G390700 chr1D 84.672 137 19 2 1436 1572 416664279 416664145 5.250000e-28 135.0
12 TraesCS1D01G390700 chr1B 91.606 2049 105 27 252 2255 636727742 636725716 0.000000e+00 2769.0
13 TraesCS1D01G390700 chr1B 84.188 917 86 27 560 1423 636739569 636738659 0.000000e+00 835.0
14 TraesCS1D01G390700 chr1B 91.935 558 22 7 2464 3020 636723099 636722564 0.000000e+00 760.0
15 TraesCS1D01G390700 chr1B 83.714 350 39 5 1886 2218 636738407 636738059 6.280000e-82 315.0
16 TraesCS1D01G390700 chr1B 94.915 177 9 0 2302 2478 636725720 636725544 8.250000e-71 278.0
17 TraesCS1D01G390700 chr1A 90.885 1119 90 8 774 1883 553958278 553957163 0.000000e+00 1491.0
18 TraesCS1D01G390700 chr1A 88.615 650 31 16 2214 2844 553956740 553956115 0.000000e+00 750.0
19 TraesCS1D01G390700 chr1A 81.364 660 85 14 774 1423 553971731 553971100 1.250000e-138 503.0
20 TraesCS1D01G390700 chr1A 90.909 341 19 5 1889 2218 553957121 553956782 5.940000e-122 448.0
21 TraesCS1D01G390700 chr1A 85.143 350 34 5 1886 2218 553964133 553963785 2.880000e-90 342.0
22 TraesCS1D01G390700 chr1A 85.227 176 17 3 318 493 553958725 553958559 4.000000e-39 172.0
23 TraesCS1D01G390700 chr2B 82.524 412 56 9 1007 1410 763473998 763474401 6.200000e-92 348.0
24 TraesCS1D01G390700 chr2B 78.447 515 77 22 913 1410 39156246 39156743 3.780000e-79 305.0
25 TraesCS1D01G390700 chr2B 81.944 144 26 0 1738 1881 39093573 39093716 4.090000e-24 122.0
26 TraesCS1D01G390700 chr2B 80.282 142 28 0 1742 1883 39156845 39156986 1.140000e-19 108.0
27 TraesCS1D01G390700 chr6A 91.870 246 20 0 6 251 36495880 36496125 8.020000e-91 344.0
28 TraesCS1D01G390700 chr6A 82.540 126 19 3 1441 1565 605869026 605869149 1.140000e-19 108.0
29 TraesCS1D01G390700 chr7D 90.909 253 21 1 1 251 82851184 82851436 3.730000e-89 339.0
30 TraesCS1D01G390700 chr7D 90.800 250 23 0 1 250 165122636 165122885 4.820000e-88 335.0
31 TraesCS1D01G390700 chr2A 91.129 248 20 1 6 251 434580017 434580264 4.820000e-88 335.0
32 TraesCS1D01G390700 chr2A 80.676 414 66 8 1007 1410 753419296 753419705 2.920000e-80 309.0
33 TraesCS1D01G390700 chr6D 90.514 253 20 3 1 251 139562231 139562481 6.240000e-87 331.0
34 TraesCS1D01G390700 chr6D 83.200 125 20 1 1441 1565 459927929 459928052 2.460000e-21 113.0
35 TraesCS1D01G390700 chr5D 89.883 257 24 1 1 255 536022285 536022029 2.240000e-86 329.0
36 TraesCS1D01G390700 chr5D 90.119 253 23 1 1 251 521864038 521864290 8.070000e-86 327.0
37 TraesCS1D01G390700 chr3B 90.157 254 23 1 1 252 816705802 816706055 2.240000e-86 329.0
38 TraesCS1D01G390700 chr7B 90.119 253 23 1 1 251 704665615 704665363 8.070000e-86 327.0
39 TraesCS1D01G390700 chr6B 83.077 130 21 1 1436 1565 142100595 142100467 1.900000e-22 117.0
40 TraesCS1D01G390700 chr3A 82.222 135 21 2 1437 1571 674401577 674401446 2.460000e-21 113.0
41 TraesCS1D01G390700 chr3D 81.600 125 21 1 1441 1565 554793827 554793705 5.330000e-18 102.0
42 TraesCS1D01G390700 chr5B 88.136 59 5 2 2157 2214 573407797 573407740 5.400000e-08 69.4
43 TraesCS1D01G390700 chr5A 77.419 124 19 8 2097 2214 586668685 586668565 6.990000e-07 65.8


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 TraesCS1D01G390700 chr1D 462091058 462094077 3019 True 5578.000 5578 100.000000 1 3020 1 chr1D.!!$R3 3019
1 TraesCS1D01G390700 chr1D 462105656 462115911 10255 True 569.625 1432 88.597875 318 2803 8 chr1D.!!$R4 2485
2 TraesCS1D01G390700 chr1B 636722564 636727742 5178 True 1269.000 2769 92.818667 252 3020 3 chr1B.!!$R1 2768
3 TraesCS1D01G390700 chr1B 636738059 636739569 1510 True 575.000 835 83.951000 560 2218 2 chr1B.!!$R2 1658
4 TraesCS1D01G390700 chr1A 553956115 553958725 2610 True 715.250 1491 88.909000 318 2844 4 chr1A.!!$R3 2526
5 TraesCS1D01G390700 chr1A 553971100 553971731 631 True 503.000 503 81.364000 774 1423 1 chr1A.!!$R2 649
6 TraesCS1D01G390700 chr2B 39156246 39156986 740 False 206.500 305 79.364500 913 1883 2 chr2B.!!$F3 970

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
151 152 0.103572 ATGCGCATTGCCAGAAATCC 59.896 50.000 19.28 0.0 45.60 3.01 F
207 208 0.251742 TTGAATCCTGGTGGGCTTGG 60.252 55.000 0.00 0.0 34.39 3.61 F
211 212 0.328450 ATCCTGGTGGGCTTGGGATA 60.328 55.000 0.00 0.0 35.34 2.59 F
1976 9514 1.135112 CCATCACGTCGTCCAGATCAA 60.135 52.381 0.00 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1108 8226 0.248012 TCCACATTGTCGCGGTACAT 59.752 50.000 6.13 0.0 0.00 2.29 R
1782 9284 2.289694 CCAGTTCAGGGTCTCAATCGTT 60.290 50.000 0.00 0.0 0.00 3.85 R
1996 9534 3.894547 TTTCGGGCTCGTTCCTGGC 62.895 63.158 5.57 0.0 37.69 4.85 R
2912 13010 0.377203 CCGTAGCTCGAAAAATGGGC 59.623 55.000 7.07 0.0 42.86 5.36 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
19 20 2.363788 TCACTCCTATGAACGCACAC 57.636 50.000 0.00 0.00 0.00 3.82
20 21 1.616374 TCACTCCTATGAACGCACACA 59.384 47.619 0.00 0.00 0.00 3.72
21 22 1.726791 CACTCCTATGAACGCACACAC 59.273 52.381 0.00 0.00 0.00 3.82
22 23 1.343142 ACTCCTATGAACGCACACACA 59.657 47.619 0.00 0.00 0.00 3.72
23 24 1.726791 CTCCTATGAACGCACACACAC 59.273 52.381 0.00 0.00 0.00 3.82
24 25 1.069358 TCCTATGAACGCACACACACA 59.931 47.619 0.00 0.00 0.00 3.72
25 26 1.194547 CCTATGAACGCACACACACAC 59.805 52.381 0.00 0.00 0.00 3.82
26 27 1.194547 CTATGAACGCACACACACACC 59.805 52.381 0.00 0.00 0.00 4.16
27 28 1.444119 ATGAACGCACACACACACCC 61.444 55.000 0.00 0.00 0.00 4.61
28 29 1.817941 GAACGCACACACACACCCT 60.818 57.895 0.00 0.00 0.00 4.34
29 30 0.531090 GAACGCACACACACACCCTA 60.531 55.000 0.00 0.00 0.00 3.53
31 32 0.320421 ACGCACACACACACCCTATC 60.320 55.000 0.00 0.00 0.00 2.08
32 33 1.019278 CGCACACACACACCCTATCC 61.019 60.000 0.00 0.00 0.00 2.59
33 34 0.676782 GCACACACACACCCTATCCC 60.677 60.000 0.00 0.00 0.00 3.85
34 35 0.984230 CACACACACACCCTATCCCT 59.016 55.000 0.00 0.00 0.00 4.20
36 37 2.771943 CACACACACACCCTATCCCTAT 59.228 50.000 0.00 0.00 0.00 2.57
38 39 3.038280 CACACACACCCTATCCCTATGA 58.962 50.000 0.00 0.00 0.00 2.15
40 41 2.037772 CACACACCCTATCCCTATGAGC 59.962 54.545 0.00 0.00 0.00 4.26
41 42 2.329267 CACACCCTATCCCTATGAGCA 58.671 52.381 0.00 0.00 0.00 4.26
42 43 2.037772 CACACCCTATCCCTATGAGCAC 59.962 54.545 0.00 0.00 0.00 4.40
43 44 2.090494 ACACCCTATCCCTATGAGCACT 60.090 50.000 0.00 0.00 0.00 4.40
44 45 2.975489 CACCCTATCCCTATGAGCACTT 59.025 50.000 0.00 0.00 0.00 3.16
45 46 3.392616 CACCCTATCCCTATGAGCACTTT 59.607 47.826 0.00 0.00 0.00 2.66
46 47 3.648545 ACCCTATCCCTATGAGCACTTTC 59.351 47.826 0.00 0.00 0.00 2.62
48 49 3.574396 CCTATCCCTATGAGCACTTTCGA 59.426 47.826 0.00 0.00 0.00 3.71
50 51 3.973206 TCCCTATGAGCACTTTCGAAA 57.027 42.857 10.71 10.71 0.00 3.46
51 52 4.280436 TCCCTATGAGCACTTTCGAAAA 57.720 40.909 12.41 0.00 0.00 2.29
53 54 4.454504 TCCCTATGAGCACTTTCGAAAAAC 59.545 41.667 12.41 4.33 0.00 2.43
54 55 4.455877 CCCTATGAGCACTTTCGAAAAACT 59.544 41.667 12.41 9.15 0.00 2.66
55 56 5.385617 CCTATGAGCACTTTCGAAAAACTG 58.614 41.667 12.41 8.51 0.00 3.16
56 57 5.179368 CCTATGAGCACTTTCGAAAAACTGA 59.821 40.000 12.41 4.26 0.00 3.41
58 59 3.242739 TGAGCACTTTCGAAAAACTGAGC 60.243 43.478 12.41 10.13 0.00 4.26
59 60 2.033424 AGCACTTTCGAAAAACTGAGCC 59.967 45.455 12.41 0.00 0.00 4.70
61 62 1.602377 ACTTTCGAAAAACTGAGCCGG 59.398 47.619 12.41 0.00 0.00 6.13
64 65 0.605319 TCGAAAAACTGAGCCGGCAT 60.605 50.000 31.54 14.28 0.00 4.40
66 67 1.670811 CGAAAAACTGAGCCGGCATAT 59.329 47.619 31.54 8.11 0.00 1.78
68 69 2.418368 AAAACTGAGCCGGCATATCA 57.582 45.000 31.54 22.44 0.00 2.15
69 70 2.645838 AAACTGAGCCGGCATATCAT 57.354 45.000 31.54 6.18 0.00 2.45
70 71 2.175878 AACTGAGCCGGCATATCATC 57.824 50.000 31.54 16.99 0.00 2.92
71 72 1.346062 ACTGAGCCGGCATATCATCT 58.654 50.000 31.54 4.27 0.00 2.90
72 73 1.696336 ACTGAGCCGGCATATCATCTT 59.304 47.619 31.54 3.33 0.00 2.40
74 75 3.324846 ACTGAGCCGGCATATCATCTTAA 59.675 43.478 31.54 0.00 0.00 1.85
75 76 3.930336 TGAGCCGGCATATCATCTTAAG 58.070 45.455 31.54 0.00 0.00 1.85
76 77 3.578282 TGAGCCGGCATATCATCTTAAGA 59.422 43.478 31.54 7.82 0.00 2.10
77 78 4.223700 TGAGCCGGCATATCATCTTAAGAT 59.776 41.667 31.54 12.37 34.56 2.40
78 79 5.171339 AGCCGGCATATCATCTTAAGATT 57.829 39.130 31.54 5.12 31.21 2.40
79 80 5.564550 AGCCGGCATATCATCTTAAGATTT 58.435 37.500 31.54 8.78 31.21 2.17
80 81 5.645497 AGCCGGCATATCATCTTAAGATTTC 59.355 40.000 31.54 0.00 31.21 2.17
81 82 5.163713 GCCGGCATATCATCTTAAGATTTCC 60.164 44.000 24.80 4.56 31.21 3.13
83 84 5.869344 CGGCATATCATCTTAAGATTTCCGA 59.131 40.000 15.49 10.07 34.93 4.55
84 85 6.368791 CGGCATATCATCTTAAGATTTCCGAA 59.631 38.462 15.49 0.00 34.93 4.30
85 86 7.412346 CGGCATATCATCTTAAGATTTCCGAAG 60.412 40.741 15.49 3.04 34.93 3.79
87 88 8.439286 GCATATCATCTTAAGATTTCCGAAGTC 58.561 37.037 15.49 0.00 31.21 3.01
88 89 9.481340 CATATCATCTTAAGATTTCCGAAGTCA 57.519 33.333 15.49 0.00 31.21 3.41
89 90 7.778470 ATCATCTTAAGATTTCCGAAGTCAC 57.222 36.000 15.49 0.00 31.21 3.67
91 92 4.491676 TCTTAAGATTTCCGAAGTCACCG 58.508 43.478 0.00 0.00 0.00 4.94
92 93 2.833631 AAGATTTCCGAAGTCACCGT 57.166 45.000 6.43 0.00 0.00 4.83
93 94 3.947910 AAGATTTCCGAAGTCACCGTA 57.052 42.857 6.43 0.00 0.00 4.02
94 95 3.505464 AGATTTCCGAAGTCACCGTAG 57.495 47.619 6.43 0.00 0.00 3.51
106 107 3.207669 CCGTAGGCGCCTCGTAGT 61.208 66.667 36.73 11.27 46.14 2.73
107 108 2.768492 CCGTAGGCGCCTCGTAGTT 61.768 63.158 36.73 10.36 46.14 2.24
108 109 1.439353 CCGTAGGCGCCTCGTAGTTA 61.439 60.000 36.73 11.30 46.14 2.24
109 110 0.378257 CGTAGGCGCCTCGTAGTTAA 59.622 55.000 36.73 10.36 0.00 2.01
110 111 1.832600 GTAGGCGCCTCGTAGTTAAC 58.167 55.000 36.73 19.71 0.00 2.01
111 112 1.403323 GTAGGCGCCTCGTAGTTAACT 59.597 52.381 36.73 13.68 0.00 2.24
112 113 0.172803 AGGCGCCTCGTAGTTAACTG 59.827 55.000 27.08 2.38 0.00 3.16
117 118 2.340577 CGCCTCGTAGTTAACTGAAACG 59.659 50.000 18.56 18.75 34.46 3.60
118 119 3.311966 GCCTCGTAGTTAACTGAAACGT 58.688 45.455 22.24 0.00 35.21 3.99
120 121 4.791974 CCTCGTAGTTAACTGAAACGTCT 58.208 43.478 22.24 0.00 35.21 4.18
121 122 4.850470 CCTCGTAGTTAACTGAAACGTCTC 59.150 45.833 22.24 0.00 35.21 3.36
122 123 4.787598 TCGTAGTTAACTGAAACGTCTCC 58.212 43.478 22.24 0.00 35.21 3.71
123 124 4.516698 TCGTAGTTAACTGAAACGTCTCCT 59.483 41.667 22.24 0.00 35.21 3.69
125 126 4.254402 AGTTAACTGAAACGTCTCCTCC 57.746 45.455 7.48 0.00 34.46 4.30
126 127 3.006644 AGTTAACTGAAACGTCTCCTCCC 59.993 47.826 7.48 0.00 34.46 4.30
129 130 0.969894 CTGAAACGTCTCCTCCCACT 59.030 55.000 0.00 0.00 0.00 4.00
130 131 0.679505 TGAAACGTCTCCTCCCACTG 59.320 55.000 0.00 0.00 0.00 3.66
132 133 1.343465 GAAACGTCTCCTCCCACTGAA 59.657 52.381 0.00 0.00 0.00 3.02
133 134 1.645710 AACGTCTCCTCCCACTGAAT 58.354 50.000 0.00 0.00 0.00 2.57
134 135 0.898320 ACGTCTCCTCCCACTGAATG 59.102 55.000 0.00 0.00 0.00 2.67
135 136 0.460987 CGTCTCCTCCCACTGAATGC 60.461 60.000 0.00 0.00 0.00 3.56
136 137 0.460987 GTCTCCTCCCACTGAATGCG 60.461 60.000 0.00 0.00 0.00 4.73
137 138 1.817099 CTCCTCCCACTGAATGCGC 60.817 63.158 0.00 0.00 0.00 6.09
138 139 2.046023 CCTCCCACTGAATGCGCA 60.046 61.111 14.96 14.96 0.00 6.09
140 141 1.033746 CCTCCCACTGAATGCGCATT 61.034 55.000 34.41 34.41 0.00 3.56
142 143 1.517694 CCCACTGAATGCGCATTGC 60.518 57.895 38.34 27.21 46.70 3.56
143 144 1.517694 CCACTGAATGCGCATTGCC 60.518 57.895 38.34 24.99 45.60 4.52
144 145 1.213275 CACTGAATGCGCATTGCCA 59.787 52.632 38.34 27.90 45.60 4.92
146 147 0.961857 ACTGAATGCGCATTGCCAGA 60.962 50.000 37.99 20.22 45.60 3.86
147 148 0.171679 CTGAATGCGCATTGCCAGAA 59.828 50.000 38.34 15.71 45.60 3.02
149 150 1.205179 TGAATGCGCATTGCCAGAAAT 59.795 42.857 38.34 13.06 45.60 2.17
150 151 1.856597 GAATGCGCATTGCCAGAAATC 59.143 47.619 38.34 17.96 45.60 2.17
151 152 0.103572 ATGCGCATTGCCAGAAATCC 59.896 50.000 19.28 0.00 45.60 3.01
152 153 0.966875 TGCGCATTGCCAGAAATCCT 60.967 50.000 5.66 0.00 45.60 3.24
153 154 0.526954 GCGCATTGCCAGAAATCCTG 60.527 55.000 0.30 0.00 42.55 3.86
154 155 1.097232 CGCATTGCCAGAAATCCTGA 58.903 50.000 2.41 0.00 45.78 3.86
155 156 1.473677 CGCATTGCCAGAAATCCTGAA 59.526 47.619 2.41 0.00 45.78 3.02
156 157 2.094597 CGCATTGCCAGAAATCCTGAAA 60.095 45.455 2.41 0.00 45.78 2.69
157 158 3.429822 CGCATTGCCAGAAATCCTGAAAT 60.430 43.478 2.41 0.00 45.78 2.17
158 159 4.202040 CGCATTGCCAGAAATCCTGAAATA 60.202 41.667 2.41 0.00 45.78 1.40
160 161 6.108015 GCATTGCCAGAAATCCTGAAATAAA 58.892 36.000 0.00 0.00 45.78 1.40
161 162 6.764560 GCATTGCCAGAAATCCTGAAATAAAT 59.235 34.615 0.00 0.00 45.78 1.40
162 163 7.042254 GCATTGCCAGAAATCCTGAAATAAATC 60.042 37.037 0.00 0.00 45.78 2.17
163 164 6.469782 TGCCAGAAATCCTGAAATAAATCC 57.530 37.500 0.00 0.00 45.78 3.01
164 165 5.957168 TGCCAGAAATCCTGAAATAAATCCA 59.043 36.000 0.00 0.00 45.78 3.41
165 166 6.097270 TGCCAGAAATCCTGAAATAAATCCAG 59.903 38.462 0.00 0.00 45.78 3.86
166 167 6.322201 GCCAGAAATCCTGAAATAAATCCAGA 59.678 38.462 0.00 0.00 45.78 3.86
167 168 7.147846 GCCAGAAATCCTGAAATAAATCCAGAA 60.148 37.037 0.00 0.00 45.78 3.02
168 169 8.752187 CCAGAAATCCTGAAATAAATCCAGAAA 58.248 33.333 0.00 0.00 45.78 2.52
176 177 8.971321 CCTGAAATAAATCCAGAAATAAATGCG 58.029 33.333 0.00 0.00 0.00 4.73
178 179 9.734620 TGAAATAAATCCAGAAATAAATGCGAG 57.265 29.630 0.00 0.00 0.00 5.03
179 180 8.579682 AAATAAATCCAGAAATAAATGCGAGC 57.420 30.769 0.00 0.00 0.00 5.03
180 181 5.581126 AAATCCAGAAATAAATGCGAGCA 57.419 34.783 0.00 0.00 0.00 4.26
182 183 4.355543 TCCAGAAATAAATGCGAGCAAC 57.644 40.909 0.57 0.00 0.00 4.17
183 184 3.755905 TCCAGAAATAAATGCGAGCAACA 59.244 39.130 0.57 0.00 0.00 3.33
184 185 4.100529 CCAGAAATAAATGCGAGCAACAG 58.899 43.478 0.57 0.00 0.00 3.16
187 188 4.641989 AGAAATAAATGCGAGCAACAGGAT 59.358 37.500 0.57 0.00 0.00 3.24
188 189 4.989279 AATAAATGCGAGCAACAGGATT 57.011 36.364 0.57 0.00 0.00 3.01
189 190 4.989279 ATAAATGCGAGCAACAGGATTT 57.011 36.364 0.57 0.00 40.54 2.17
190 191 2.642139 AATGCGAGCAACAGGATTTG 57.358 45.000 0.57 0.00 0.00 2.32
191 192 1.825090 ATGCGAGCAACAGGATTTGA 58.175 45.000 0.57 0.00 0.00 2.69
193 194 2.161855 TGCGAGCAACAGGATTTGAAT 58.838 42.857 0.00 0.00 0.00 2.57
194 195 2.162208 TGCGAGCAACAGGATTTGAATC 59.838 45.455 0.00 0.00 34.66 2.52
205 206 2.460669 GATTTGAATCCTGGTGGGCTT 58.539 47.619 0.00 0.00 34.39 4.35
207 208 0.251742 TTGAATCCTGGTGGGCTTGG 60.252 55.000 0.00 0.00 34.39 3.61
208 209 1.380380 GAATCCTGGTGGGCTTGGG 60.380 63.158 0.00 0.00 34.39 4.12
210 211 1.224003 AATCCTGGTGGGCTTGGGAT 61.224 55.000 0.00 0.00 38.29 3.85
211 212 0.328450 ATCCTGGTGGGCTTGGGATA 60.328 55.000 0.00 0.00 35.34 2.59
212 213 1.227383 CCTGGTGGGCTTGGGATAC 59.773 63.158 0.00 0.00 0.00 2.24
229 230 3.371965 GATACCACAGTCCCTCTAACCA 58.628 50.000 0.00 0.00 0.00 3.67
231 232 2.188817 ACCACAGTCCCTCTAACCATC 58.811 52.381 0.00 0.00 0.00 3.51
234 235 2.571653 CACAGTCCCTCTAACCATCCAA 59.428 50.000 0.00 0.00 0.00 3.53
236 237 2.092914 CAGTCCCTCTAACCATCCAACC 60.093 54.545 0.00 0.00 0.00 3.77
237 238 1.913419 GTCCCTCTAACCATCCAACCA 59.087 52.381 0.00 0.00 0.00 3.67
241 242 2.356125 CCTCTAACCATCCAACCACAGG 60.356 54.545 0.00 0.00 0.00 4.00
242 243 2.305927 CTCTAACCATCCAACCACAGGT 59.694 50.000 0.00 0.00 37.65 4.00
244 245 3.911260 TCTAACCATCCAACCACAGGTTA 59.089 43.478 0.40 0.00 45.01 2.85
245 246 3.603965 AACCATCCAACCACAGGTTAA 57.396 42.857 0.40 0.00 45.01 2.01
246 247 3.825908 ACCATCCAACCACAGGTTAAT 57.174 42.857 0.40 0.00 45.01 1.40
247 248 4.126520 ACCATCCAACCACAGGTTAATT 57.873 40.909 0.40 0.00 45.01 1.40
248 249 4.086457 ACCATCCAACCACAGGTTAATTC 58.914 43.478 0.40 0.00 45.01 2.17
249 250 3.128589 CCATCCAACCACAGGTTAATTCG 59.871 47.826 0.40 0.00 45.01 3.34
250 251 2.156098 TCCAACCACAGGTTAATTCGC 58.844 47.619 0.40 0.00 45.01 4.70
268 269 7.730364 AATTCGCTAATCCAACGATTTCTAT 57.270 32.000 0.00 0.00 39.49 1.98
270 271 7.633361 TTCGCTAATCCAACGATTTCTATAC 57.367 36.000 0.00 0.00 39.49 1.47
283 284 5.621555 CGATTTCTATACGGTAGATGTGGGG 60.622 48.000 1.34 0.00 0.00 4.96
315 317 2.661718 TGTCGATCCTATGTGGTGCTA 58.338 47.619 0.00 0.00 37.07 3.49
350 7383 1.415289 CATCTCCACTGCCAGCTATCA 59.585 52.381 0.00 0.00 0.00 2.15
360 7393 1.858091 CCAGCTATCACTACCGCAAG 58.142 55.000 0.00 0.00 0.00 4.01
451 7485 2.621338 CATCGAGCAGAAACAAGGCTA 58.379 47.619 0.00 0.00 38.15 3.93
462 7496 3.611766 AACAAGGCTACGCTCAATACT 57.388 42.857 0.00 0.00 0.00 2.12
463 7497 2.893637 ACAAGGCTACGCTCAATACTG 58.106 47.619 0.00 0.00 0.00 2.74
516 7550 6.860080 TGTACATTAGGTGTTCTAGTGCTAC 58.140 40.000 0.00 0.00 42.29 3.58
538 7572 5.730550 ACGCTTAAGATCCTGTGACATTTA 58.269 37.500 6.67 0.00 0.00 1.40
539 7573 6.349300 ACGCTTAAGATCCTGTGACATTTAT 58.651 36.000 6.67 0.00 0.00 1.40
585 7620 2.202311 ACGACGTGCTCATCGACG 60.202 61.111 11.48 11.64 46.89 5.12
626 7663 3.671716 CACTAAGGTGGTAGACAAACCC 58.328 50.000 1.28 0.00 38.90 4.11
740 7791 1.153025 ACCGCTGCATGCATGAGAT 60.153 52.632 30.64 1.01 43.06 2.75
875 7986 3.122278 GCGAGTGCTATAAAAACACGTCA 59.878 43.478 0.00 0.00 39.31 4.35
918 8029 1.468565 GCCAGTGTGCGTAGATCGTTA 60.469 52.381 0.00 0.00 42.13 3.18
1017 8135 1.585006 GATGTCTGTCGACGTGGGT 59.415 57.895 11.62 0.00 43.21 4.51
1306 8460 1.683790 CGCCGATTTGTGGTCGTCTC 61.684 60.000 0.00 0.00 37.39 3.36
1410 8570 3.361794 AGCTCATCATGCTGTACGTAG 57.638 47.619 0.00 0.00 39.56 3.51
1430 8590 5.048364 CGTAGAGATAGATCCCCAACTTGAG 60.048 48.000 0.00 0.00 0.00 3.02
1434 8594 5.032846 AGATAGATCCCCAACTTGAGTCAA 58.967 41.667 5.25 5.25 0.00 3.18
1644 9109 6.862608 CACTGAATTTCAATGATTTCGGTTGA 59.137 34.615 14.45 0.00 0.00 3.18
1758 9260 1.688772 GATGAATGGATGCAGCCAGT 58.311 50.000 29.74 27.90 42.15 4.00
1782 9284 2.530497 GGCGTTCGTGACAGTTGCA 61.530 57.895 0.00 0.00 0.00 4.08
1976 9514 1.135112 CCATCACGTCGTCCAGATCAA 60.135 52.381 0.00 0.00 0.00 2.57
1977 9515 2.481969 CCATCACGTCGTCCAGATCAAT 60.482 50.000 0.00 0.00 0.00 2.57
2017 9555 0.673644 CAGGAACGAGCCCGAAATGT 60.674 55.000 0.00 0.00 39.50 2.71
2169 9723 2.187958 CAGGGGTCAAGTACTGGATCA 58.812 52.381 12.70 0.00 0.00 2.92
2218 9772 2.897350 GGGCGGCTACATCTGCAC 60.897 66.667 9.56 0.00 40.04 4.57
2306 9906 6.726490 TCGGAATTAAGTAAGCTCACCTAT 57.274 37.500 0.00 0.00 0.00 2.57
2424 10032 3.517602 TCATCGTCAATTCCACCGTAAG 58.482 45.455 0.00 0.00 0.00 2.34
2477 12551 7.229306 ACGTGAAACCATATATCATGCTCATTT 59.771 33.333 0.00 0.00 34.23 2.32
2478 12552 7.536281 CGTGAAACCATATATCATGCTCATTTG 59.464 37.037 0.00 0.00 0.00 2.32
2479 12553 8.355169 GTGAAACCATATATCATGCTCATTTGT 58.645 33.333 0.00 0.00 0.00 2.83
2480 12554 8.916062 TGAAACCATATATCATGCTCATTTGTT 58.084 29.630 0.00 0.00 0.00 2.83
2481 12555 9.754382 GAAACCATATATCATGCTCATTTGTTT 57.246 29.630 0.00 0.00 0.00 2.83
2632 12712 0.592148 CGAGCCCGAGTATGGACTAC 59.408 60.000 0.00 0.00 35.45 2.73
2655 12742 2.119655 CGAGGGTAGGTGGAGACGG 61.120 68.421 0.00 0.00 0.00 4.79
2708 12795 9.081997 CAGTGTTGTTTGCTTAAGTTTATTTGA 57.918 29.630 4.02 0.00 0.00 2.69
2709 12796 9.816354 AGTGTTGTTTGCTTAAGTTTATTTGAT 57.184 25.926 4.02 0.00 0.00 2.57
2887 12985 3.567576 TCTTTCTTCTCTGTCTGCTCG 57.432 47.619 0.00 0.00 0.00 5.03
2912 13010 4.468510 TCATACTGTACCACTTACTTGGGG 59.531 45.833 0.00 0.00 41.49 4.96
2915 13013 0.034767 GTACCACTTACTTGGGGCCC 60.035 60.000 18.17 18.17 41.49 5.80
2919 13017 1.552254 CCACTTACTTGGGGCCCATTT 60.552 52.381 29.34 18.87 31.53 2.32
2929 13027 0.738975 GGGCCCATTTTTCGAGCTAC 59.261 55.000 19.95 0.00 0.00 3.58
2937 13035 2.902705 TTTTCGAGCTACGGCCATAT 57.097 45.000 2.24 0.00 42.82 1.78
2948 13046 3.838244 ACGGCCATATTGATACTGTGT 57.162 42.857 2.24 0.00 0.00 3.72
2959 13057 1.255667 ATACTGTGTTCGGCTCCGGT 61.256 55.000 8.59 0.01 40.25 5.28
2960 13058 0.608856 TACTGTGTTCGGCTCCGGTA 60.609 55.000 8.59 0.00 40.25 4.02
2996 13094 6.545666 TGATCTAGTGATTGTGTTTTGTGGTT 59.454 34.615 0.00 0.00 32.19 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.726791 GTGTGTGCGTTCATAGGAGTG 59.273 52.381 0.00 0.00 0.00 3.51
2 3 1.343142 TGTGTGTGCGTTCATAGGAGT 59.657 47.619 0.00 0.00 0.00 3.85
3 4 1.726791 GTGTGTGTGCGTTCATAGGAG 59.273 52.381 0.00 0.00 0.00 3.69
4 5 1.069358 TGTGTGTGTGCGTTCATAGGA 59.931 47.619 0.00 0.00 0.00 2.94
5 6 1.194547 GTGTGTGTGTGCGTTCATAGG 59.805 52.381 0.00 0.00 0.00 2.57
6 7 1.194547 GGTGTGTGTGTGCGTTCATAG 59.805 52.381 0.00 0.00 0.00 2.23
7 8 1.222300 GGTGTGTGTGTGCGTTCATA 58.778 50.000 0.00 0.00 0.00 2.15
9 10 2.109739 GGGTGTGTGTGTGCGTTCA 61.110 57.895 0.00 0.00 0.00 3.18
12 13 0.320421 GATAGGGTGTGTGTGTGCGT 60.320 55.000 0.00 0.00 0.00 5.24
13 14 1.019278 GGATAGGGTGTGTGTGTGCG 61.019 60.000 0.00 0.00 0.00 5.34
14 15 0.676782 GGGATAGGGTGTGTGTGTGC 60.677 60.000 0.00 0.00 0.00 4.57
15 16 0.984230 AGGGATAGGGTGTGTGTGTG 59.016 55.000 0.00 0.00 0.00 3.82
16 17 2.634639 TAGGGATAGGGTGTGTGTGT 57.365 50.000 0.00 0.00 0.00 3.72
17 18 3.038280 TCATAGGGATAGGGTGTGTGTG 58.962 50.000 0.00 0.00 0.00 3.82
18 19 3.309296 CTCATAGGGATAGGGTGTGTGT 58.691 50.000 0.00 0.00 0.00 3.72
19 20 2.037772 GCTCATAGGGATAGGGTGTGTG 59.962 54.545 0.00 0.00 0.00 3.82
20 21 2.330216 GCTCATAGGGATAGGGTGTGT 58.670 52.381 0.00 0.00 0.00 3.72
21 22 2.037772 GTGCTCATAGGGATAGGGTGTG 59.962 54.545 0.00 0.00 0.00 3.82
22 23 2.090494 AGTGCTCATAGGGATAGGGTGT 60.090 50.000 0.00 0.00 0.00 4.16
23 24 2.614259 AGTGCTCATAGGGATAGGGTG 58.386 52.381 0.00 0.00 0.00 4.61
24 25 3.352611 AAGTGCTCATAGGGATAGGGT 57.647 47.619 0.00 0.00 0.00 4.34
25 26 3.306364 CGAAAGTGCTCATAGGGATAGGG 60.306 52.174 0.00 0.00 0.00 3.53
26 27 3.574396 TCGAAAGTGCTCATAGGGATAGG 59.426 47.826 0.00 0.00 0.00 2.57
27 28 4.855715 TCGAAAGTGCTCATAGGGATAG 57.144 45.455 0.00 0.00 0.00 2.08
28 29 5.607939 TTTCGAAAGTGCTCATAGGGATA 57.392 39.130 6.47 0.00 0.00 2.59
29 30 4.487714 TTTCGAAAGTGCTCATAGGGAT 57.512 40.909 6.47 0.00 0.00 3.85
31 32 4.455877 AGTTTTTCGAAAGTGCTCATAGGG 59.544 41.667 10.98 0.00 0.00 3.53
32 33 5.179368 TCAGTTTTTCGAAAGTGCTCATAGG 59.821 40.000 10.98 0.03 34.07 2.57
33 34 6.228273 TCAGTTTTTCGAAAGTGCTCATAG 57.772 37.500 10.98 0.34 34.07 2.23
34 35 5.334105 GCTCAGTTTTTCGAAAGTGCTCATA 60.334 40.000 10.98 0.00 34.07 2.15
36 37 3.242739 GCTCAGTTTTTCGAAAGTGCTCA 60.243 43.478 10.98 0.00 34.07 4.26
38 39 2.033424 GGCTCAGTTTTTCGAAAGTGCT 59.967 45.455 10.98 7.75 34.07 4.40
40 41 2.602217 CCGGCTCAGTTTTTCGAAAGTG 60.602 50.000 10.98 10.12 35.08 3.16
41 42 1.602377 CCGGCTCAGTTTTTCGAAAGT 59.398 47.619 10.98 0.00 0.00 2.66
42 43 1.663161 GCCGGCTCAGTTTTTCGAAAG 60.663 52.381 22.15 0.00 0.00 2.62
43 44 0.309612 GCCGGCTCAGTTTTTCGAAA 59.690 50.000 22.15 6.47 0.00 3.46
44 45 0.816018 TGCCGGCTCAGTTTTTCGAA 60.816 50.000 29.70 0.00 0.00 3.71
45 46 0.605319 ATGCCGGCTCAGTTTTTCGA 60.605 50.000 29.70 1.81 0.00 3.71
46 47 1.083489 TATGCCGGCTCAGTTTTTCG 58.917 50.000 29.70 0.00 0.00 3.46
48 49 2.722094 TGATATGCCGGCTCAGTTTTT 58.278 42.857 29.70 3.35 0.00 1.94
50 51 2.105477 AGATGATATGCCGGCTCAGTTT 59.895 45.455 29.70 8.26 0.00 2.66
51 52 1.696336 AGATGATATGCCGGCTCAGTT 59.304 47.619 29.70 9.04 0.00 3.16
53 54 2.469274 AAGATGATATGCCGGCTCAG 57.531 50.000 29.70 0.00 0.00 3.35
54 55 3.578282 TCTTAAGATGATATGCCGGCTCA 59.422 43.478 29.70 23.34 0.00 4.26
55 56 4.193826 TCTTAAGATGATATGCCGGCTC 57.806 45.455 29.70 17.89 0.00 4.70
56 57 4.833478 ATCTTAAGATGATATGCCGGCT 57.167 40.909 29.70 15.76 32.68 5.52
58 59 5.063944 CGGAAATCTTAAGATGATATGCCGG 59.936 44.000 20.23 0.00 34.49 6.13
59 60 5.869344 TCGGAAATCTTAAGATGATATGCCG 59.131 40.000 21.33 21.33 35.41 5.69
61 62 8.316640 ACTTCGGAAATCTTAAGATGATATGC 57.683 34.615 18.61 9.73 34.49 3.14
64 65 7.926555 GGTGACTTCGGAAATCTTAAGATGATA 59.073 37.037 18.61 1.07 34.49 2.15
66 67 6.106673 GGTGACTTCGGAAATCTTAAGATGA 58.893 40.000 18.61 8.72 34.49 2.92
68 69 5.109903 CGGTGACTTCGGAAATCTTAAGAT 58.890 41.667 12.37 12.37 36.07 2.40
69 70 4.021719 ACGGTGACTTCGGAAATCTTAAGA 60.022 41.667 7.82 7.82 0.00 2.10
70 71 4.243270 ACGGTGACTTCGGAAATCTTAAG 58.757 43.478 0.62 0.00 0.00 1.85
71 72 4.261578 ACGGTGACTTCGGAAATCTTAA 57.738 40.909 0.62 0.00 0.00 1.85
72 73 3.947910 ACGGTGACTTCGGAAATCTTA 57.052 42.857 0.62 0.00 0.00 2.10
74 75 2.165845 CCTACGGTGACTTCGGAAATCT 59.834 50.000 0.62 0.00 0.00 2.40
75 76 2.537401 CCTACGGTGACTTCGGAAATC 58.463 52.381 0.00 0.00 0.00 2.17
76 77 1.405121 GCCTACGGTGACTTCGGAAAT 60.405 52.381 0.00 0.00 0.00 2.17
77 78 0.037975 GCCTACGGTGACTTCGGAAA 60.038 55.000 0.00 0.00 0.00 3.13
78 79 1.588082 GCCTACGGTGACTTCGGAA 59.412 57.895 0.00 0.00 0.00 4.30
79 80 2.693762 CGCCTACGGTGACTTCGGA 61.694 63.158 0.00 0.00 34.74 4.55
80 81 2.202570 CGCCTACGGTGACTTCGG 60.203 66.667 0.00 0.00 34.74 4.30
81 82 2.879462 GCGCCTACGGTGACTTCG 60.879 66.667 0.00 0.00 40.57 3.79
85 86 4.849329 CGAGGCGCCTACGGTGAC 62.849 72.222 32.97 14.51 42.50 3.67
87 88 3.465296 CTACGAGGCGCCTACGGTG 62.465 68.421 34.97 26.78 40.57 4.94
88 89 3.207669 CTACGAGGCGCCTACGGT 61.208 66.667 34.97 30.33 40.57 4.83
89 90 1.439353 TAACTACGAGGCGCCTACGG 61.439 60.000 34.97 27.37 40.57 4.02
91 92 1.403323 AGTTAACTACGAGGCGCCTAC 59.597 52.381 32.97 21.36 0.00 3.18
92 93 1.402968 CAGTTAACTACGAGGCGCCTA 59.597 52.381 32.97 14.06 0.00 3.93
93 94 0.172803 CAGTTAACTACGAGGCGCCT 59.827 55.000 33.48 33.48 0.00 5.52
94 95 0.171903 TCAGTTAACTACGAGGCGCC 59.828 55.000 21.89 21.89 0.00 6.53
95 96 1.986698 TTCAGTTAACTACGAGGCGC 58.013 50.000 8.04 0.00 0.00 6.53
96 97 2.340577 CGTTTCAGTTAACTACGAGGCG 59.659 50.000 19.84 12.55 34.36 5.52
98 99 4.791974 AGACGTTTCAGTTAACTACGAGG 58.208 43.478 27.51 15.48 36.21 4.63
99 100 4.850470 GGAGACGTTTCAGTTAACTACGAG 59.150 45.833 27.51 13.51 36.21 4.18
100 101 4.516698 AGGAGACGTTTCAGTTAACTACGA 59.483 41.667 27.51 12.67 36.21 3.43
101 102 4.791974 AGGAGACGTTTCAGTTAACTACG 58.208 43.478 21.87 21.87 38.14 3.51
102 103 5.159925 GGAGGAGACGTTTCAGTTAACTAC 58.840 45.833 8.04 2.26 0.00 2.73
103 104 4.219288 GGGAGGAGACGTTTCAGTTAACTA 59.781 45.833 8.04 0.00 0.00 2.24
104 105 3.006644 GGGAGGAGACGTTTCAGTTAACT 59.993 47.826 8.50 1.12 0.00 2.24
106 107 2.967201 TGGGAGGAGACGTTTCAGTTAA 59.033 45.455 8.50 0.00 0.00 2.01
107 108 2.298163 GTGGGAGGAGACGTTTCAGTTA 59.702 50.000 8.50 0.00 0.00 2.24
108 109 1.070289 GTGGGAGGAGACGTTTCAGTT 59.930 52.381 8.50 0.00 0.00 3.16
109 110 0.680061 GTGGGAGGAGACGTTTCAGT 59.320 55.000 8.50 0.00 0.00 3.41
110 111 0.969894 AGTGGGAGGAGACGTTTCAG 59.030 55.000 8.50 0.00 0.00 3.02
111 112 0.679505 CAGTGGGAGGAGACGTTTCA 59.320 55.000 8.50 0.00 0.00 2.69
112 113 0.966920 TCAGTGGGAGGAGACGTTTC 59.033 55.000 0.00 0.00 0.00 2.78
117 118 0.460987 CGCATTCAGTGGGAGGAGAC 60.461 60.000 0.00 0.00 43.02 3.36
118 119 1.900351 CGCATTCAGTGGGAGGAGA 59.100 57.895 0.00 0.00 43.02 3.71
120 121 1.913951 ATGCGCATTCAGTGGGAGGA 61.914 55.000 19.28 0.00 43.02 3.71
121 122 1.033746 AATGCGCATTCAGTGGGAGG 61.034 55.000 29.36 0.00 43.02 4.30
122 123 0.099968 CAATGCGCATTCAGTGGGAG 59.900 55.000 31.88 14.87 43.02 4.30
123 124 1.936436 GCAATGCGCATTCAGTGGGA 61.936 55.000 31.88 0.00 43.02 4.37
125 126 1.517694 GGCAATGCGCATTCAGTGG 60.518 57.895 31.88 20.95 45.17 4.00
126 127 0.800683 CTGGCAATGCGCATTCAGTG 60.801 55.000 31.88 22.40 45.17 3.66
129 130 0.602060 TTTCTGGCAATGCGCATTCA 59.398 45.000 31.88 24.97 45.17 2.57
130 131 1.856597 GATTTCTGGCAATGCGCATTC 59.143 47.619 31.88 23.96 45.17 2.67
132 133 0.103572 GGATTTCTGGCAATGCGCAT 59.896 50.000 19.28 19.28 45.17 4.73
133 134 0.966875 AGGATTTCTGGCAATGCGCA 60.967 50.000 14.96 14.96 45.17 6.09
134 135 0.526954 CAGGATTTCTGGCAATGCGC 60.527 55.000 0.00 0.00 39.76 6.09
135 136 1.097232 TCAGGATTTCTGGCAATGCG 58.903 50.000 0.00 0.00 43.53 4.73
136 137 3.598019 TTTCAGGATTTCTGGCAATGC 57.402 42.857 0.00 0.00 43.53 3.56
137 138 7.440255 GGATTTATTTCAGGATTTCTGGCAATG 59.560 37.037 0.00 0.00 43.53 2.82
138 139 7.126115 TGGATTTATTTCAGGATTTCTGGCAAT 59.874 33.333 0.00 0.00 43.53 3.56
140 141 5.957168 TGGATTTATTTCAGGATTTCTGGCA 59.043 36.000 0.00 0.00 43.53 4.92
142 143 7.886629 TCTGGATTTATTTCAGGATTTCTGG 57.113 36.000 0.00 0.00 43.53 3.86
150 151 8.971321 CGCATTTATTTCTGGATTTATTTCAGG 58.029 33.333 0.00 0.00 0.00 3.86
151 152 9.734620 TCGCATTTATTTCTGGATTTATTTCAG 57.265 29.630 0.00 0.00 0.00 3.02
152 153 9.734620 CTCGCATTTATTTCTGGATTTATTTCA 57.265 29.630 0.00 0.00 0.00 2.69
153 154 8.694394 GCTCGCATTTATTTCTGGATTTATTTC 58.306 33.333 0.00 0.00 0.00 2.17
154 155 8.196771 TGCTCGCATTTATTTCTGGATTTATTT 58.803 29.630 0.00 0.00 0.00 1.40
155 156 7.715657 TGCTCGCATTTATTTCTGGATTTATT 58.284 30.769 0.00 0.00 0.00 1.40
156 157 7.275888 TGCTCGCATTTATTTCTGGATTTAT 57.724 32.000 0.00 0.00 0.00 1.40
157 158 6.691754 TGCTCGCATTTATTTCTGGATTTA 57.308 33.333 0.00 0.00 0.00 1.40
158 159 5.581126 TGCTCGCATTTATTTCTGGATTT 57.419 34.783 0.00 0.00 0.00 2.17
160 161 4.398988 TGTTGCTCGCATTTATTTCTGGAT 59.601 37.500 0.00 0.00 0.00 3.41
161 162 3.755905 TGTTGCTCGCATTTATTTCTGGA 59.244 39.130 0.00 0.00 0.00 3.86
162 163 4.095410 TGTTGCTCGCATTTATTTCTGG 57.905 40.909 0.00 0.00 0.00 3.86
163 164 4.100529 CCTGTTGCTCGCATTTATTTCTG 58.899 43.478 0.00 0.00 0.00 3.02
164 165 4.009675 TCCTGTTGCTCGCATTTATTTCT 58.990 39.130 0.00 0.00 0.00 2.52
165 166 4.355543 TCCTGTTGCTCGCATTTATTTC 57.644 40.909 0.00 0.00 0.00 2.17
166 167 4.989279 ATCCTGTTGCTCGCATTTATTT 57.011 36.364 0.00 0.00 0.00 1.40
167 168 4.989279 AATCCTGTTGCTCGCATTTATT 57.011 36.364 0.00 0.00 0.00 1.40
168 169 4.398988 TCAAATCCTGTTGCTCGCATTTAT 59.601 37.500 0.00 0.00 0.00 1.40
169 170 3.755905 TCAAATCCTGTTGCTCGCATTTA 59.244 39.130 0.00 0.00 0.00 1.40
170 171 2.557924 TCAAATCCTGTTGCTCGCATTT 59.442 40.909 0.00 0.00 0.00 2.32
171 172 2.161855 TCAAATCCTGTTGCTCGCATT 58.838 42.857 0.00 0.00 0.00 3.56
172 173 1.825090 TCAAATCCTGTTGCTCGCAT 58.175 45.000 0.00 0.00 0.00 4.73
173 174 1.603456 TTCAAATCCTGTTGCTCGCA 58.397 45.000 0.00 0.00 0.00 5.10
174 175 2.790387 GATTCAAATCCTGTTGCTCGC 58.210 47.619 0.00 0.00 0.00 5.03
184 185 2.889756 AAGCCCACCAGGATTCAAATCC 60.890 50.000 12.94 12.94 41.74 3.01
187 188 1.631405 CAAGCCCACCAGGATTCAAA 58.369 50.000 0.00 0.00 41.74 2.69
188 189 0.251742 CCAAGCCCACCAGGATTCAA 60.252 55.000 0.00 0.00 41.74 2.69
189 190 1.383799 CCAAGCCCACCAGGATTCA 59.616 57.895 0.00 0.00 41.74 2.57
190 191 1.380380 CCCAAGCCCACCAGGATTC 60.380 63.158 0.00 0.00 41.74 2.52
193 194 1.083895 TATCCCAAGCCCACCAGGA 59.916 57.895 0.00 0.00 38.24 3.86
194 195 1.227383 GTATCCCAAGCCCACCAGG 59.773 63.158 0.00 0.00 39.47 4.45
195 196 1.227383 GGTATCCCAAGCCCACCAG 59.773 63.158 0.00 0.00 0.00 4.00
196 197 1.542628 TGGTATCCCAAGCCCACCA 60.543 57.895 0.00 0.00 37.98 4.17
197 198 1.076995 GTGGTATCCCAAGCCCACC 60.077 63.158 0.00 0.00 44.15 4.61
198 199 0.394352 CTGTGGTATCCCAAGCCCAC 60.394 60.000 0.00 0.00 44.15 4.61
199 200 0.844661 ACTGTGGTATCCCAAGCCCA 60.845 55.000 0.00 0.00 44.15 5.36
200 201 0.107165 GACTGTGGTATCCCAAGCCC 60.107 60.000 0.00 0.00 44.15 5.19
201 202 0.107165 GGACTGTGGTATCCCAAGCC 60.107 60.000 0.00 0.00 44.15 4.35
207 208 2.699321 GGTTAGAGGGACTGTGGTATCC 59.301 54.545 0.00 0.00 41.55 2.59
208 209 3.371965 TGGTTAGAGGGACTGTGGTATC 58.628 50.000 0.00 0.00 41.55 2.24
210 211 3.371965 GATGGTTAGAGGGACTGTGGTA 58.628 50.000 0.00 0.00 41.55 3.25
211 212 2.188817 GATGGTTAGAGGGACTGTGGT 58.811 52.381 0.00 0.00 41.55 4.16
212 213 1.486726 GGATGGTTAGAGGGACTGTGG 59.513 57.143 0.00 0.00 41.55 4.17
213 214 2.187958 TGGATGGTTAGAGGGACTGTG 58.812 52.381 0.00 0.00 41.55 3.66
214 215 2.572104 GTTGGATGGTTAGAGGGACTGT 59.428 50.000 0.00 0.00 41.55 3.55
217 218 1.913419 TGGTTGGATGGTTAGAGGGAC 59.087 52.381 0.00 0.00 0.00 4.46
218 219 1.913419 GTGGTTGGATGGTTAGAGGGA 59.087 52.381 0.00 0.00 0.00 4.20
219 220 1.633432 TGTGGTTGGATGGTTAGAGGG 59.367 52.381 0.00 0.00 0.00 4.30
220 221 2.356125 CCTGTGGTTGGATGGTTAGAGG 60.356 54.545 0.00 0.00 0.00 3.69
222 223 2.344592 ACCTGTGGTTGGATGGTTAGA 58.655 47.619 0.00 0.00 27.29 2.10
223 224 2.879103 ACCTGTGGTTGGATGGTTAG 57.121 50.000 0.00 0.00 27.29 2.34
224 225 4.726035 TTAACCTGTGGTTGGATGGTTA 57.274 40.909 11.78 0.00 46.35 2.85
225 226 3.603965 TTAACCTGTGGTTGGATGGTT 57.396 42.857 11.78 0.00 46.35 3.67
226 227 3.825908 ATTAACCTGTGGTTGGATGGT 57.174 42.857 11.78 0.00 46.35 3.55
227 228 3.128589 CGAATTAACCTGTGGTTGGATGG 59.871 47.826 11.78 0.00 46.35 3.51
229 230 2.752903 GCGAATTAACCTGTGGTTGGAT 59.247 45.455 11.78 3.88 46.35 3.41
231 232 2.159382 AGCGAATTAACCTGTGGTTGG 58.841 47.619 11.78 0.00 46.35 3.77
234 235 4.196971 GGATTAGCGAATTAACCTGTGGT 58.803 43.478 0.00 0.00 37.65 4.16
236 237 5.569413 GTTGGATTAGCGAATTAACCTGTG 58.431 41.667 0.00 0.00 0.00 3.66
237 238 4.331717 CGTTGGATTAGCGAATTAACCTGT 59.668 41.667 11.90 0.00 34.68 4.00
241 242 7.407337 AGAAATCGTTGGATTAGCGAATTAAC 58.593 34.615 0.00 2.67 45.11 2.01
242 243 7.548196 AGAAATCGTTGGATTAGCGAATTAA 57.452 32.000 0.00 0.00 45.11 1.40
243 244 8.827177 ATAGAAATCGTTGGATTAGCGAATTA 57.173 30.769 0.00 0.00 45.11 1.40
244 245 7.730364 ATAGAAATCGTTGGATTAGCGAATT 57.270 32.000 0.00 0.00 45.11 2.17
245 246 7.061905 CGTATAGAAATCGTTGGATTAGCGAAT 59.938 37.037 0.00 0.00 45.11 3.34
246 247 6.361481 CGTATAGAAATCGTTGGATTAGCGAA 59.639 38.462 0.00 0.00 45.11 4.70
247 248 5.854866 CGTATAGAAATCGTTGGATTAGCGA 59.145 40.000 0.00 0.00 46.01 4.93
248 249 5.060569 CCGTATAGAAATCGTTGGATTAGCG 59.939 44.000 0.00 0.00 41.99 4.26
249 250 5.924825 ACCGTATAGAAATCGTTGGATTAGC 59.075 40.000 0.00 0.00 41.99 3.09
250 251 8.509690 TCTACCGTATAGAAATCGTTGGATTAG 58.490 37.037 0.00 0.00 41.99 1.73
268 269 2.071778 GGTACCCCACATCTACCGTA 57.928 55.000 0.00 0.00 0.00 4.02
283 284 6.208994 ACATAGGATCGACAATTAGAGGGTAC 59.791 42.308 0.00 0.00 0.00 3.34
292 293 3.118261 AGCACCACATAGGATCGACAATT 60.118 43.478 0.00 0.00 41.22 2.32
294 295 1.831106 AGCACCACATAGGATCGACAA 59.169 47.619 0.00 0.00 41.22 3.18
315 317 1.754226 GAGATGGTCTTCGCCTCTCTT 59.246 52.381 0.00 0.00 33.74 2.85
350 7383 1.004918 GCACTCACCTTGCGGTAGT 60.005 57.895 0.00 0.00 43.24 2.73
381 7414 1.129809 CGTTACGTCTTTGGCAGCG 59.870 57.895 0.00 0.00 0.00 5.18
390 7423 2.397549 GTTACACCTTGCGTTACGTCT 58.602 47.619 6.63 0.00 0.00 4.18
451 7485 5.978814 AGATTTCTTACCAGTATTGAGCGT 58.021 37.500 0.00 0.00 0.00 5.07
462 7496 8.868522 ACAATGAGATTTGAGATTTCTTACCA 57.131 30.769 0.00 0.00 0.00 3.25
463 7497 8.950210 TGACAATGAGATTTGAGATTTCTTACC 58.050 33.333 0.00 0.00 0.00 2.85
516 7550 6.851222 ATAAATGTCACAGGATCTTAAGCG 57.149 37.500 0.00 0.00 0.00 4.68
585 7620 0.955919 CACCTTCGCCTTCCAGTTCC 60.956 60.000 0.00 0.00 0.00 3.62
626 7663 5.973651 AACATATGAGACTGCAATGTACG 57.026 39.130 10.38 0.00 30.85 3.67
740 7791 5.867716 GGTAACGAGCTACATTTTCTCTTGA 59.132 40.000 0.00 0.00 0.00 3.02
875 7986 0.109458 CGCTCAAGCATGCATGTGTT 60.109 50.000 26.79 17.71 42.21 3.32
918 8029 1.558756 CTGGGAGAGAAAGCCATGTCT 59.441 52.381 0.00 0.00 0.00 3.41
1005 8123 1.006688 CATGTCACCCACGTCGACA 60.007 57.895 17.16 8.54 43.35 4.35
1017 8135 3.649502 ACCTATCCATCATCAGCATGTCA 59.350 43.478 0.00 0.00 37.40 3.58
1079 8197 2.429767 CGCAGCCTCTCCTCCATGA 61.430 63.158 0.00 0.00 0.00 3.07
1108 8226 0.248012 TCCACATTGTCGCGGTACAT 59.752 50.000 6.13 0.00 0.00 2.29
1306 8460 2.354773 GGAGTTATCCTCGCCGCG 60.355 66.667 6.39 6.39 42.94 6.46
1410 8570 4.651503 TGACTCAAGTTGGGGATCTATCTC 59.348 45.833 7.84 0.00 0.00 2.75
1466 8626 9.962759 GTGAAATTAATGAAATTCAGTGAATGC 57.037 29.630 18.94 14.08 36.76 3.56
1531 8691 6.494893 TTCATGTGTACTACTGAAATTGCC 57.505 37.500 0.00 0.00 0.00 4.52
1644 9109 8.721019 TTTCAGTTTCAGAAAATTTTCAGCAT 57.279 26.923 28.00 8.82 39.61 3.79
1758 9260 2.970324 GTCACGAACGCCCAGCAA 60.970 61.111 0.00 0.00 0.00 3.91
1782 9284 2.289694 CCAGTTCAGGGTCTCAATCGTT 60.290 50.000 0.00 0.00 0.00 3.85
1996 9534 3.894547 TTTCGGGCTCGTTCCTGGC 62.895 63.158 5.57 0.00 37.69 4.85
2218 9772 2.297701 CCCATTTTCGGGTAGGTGATG 58.702 52.381 0.00 0.00 41.83 3.07
2238 9838 2.884894 CCGTAGGTACATTCACCTCC 57.115 55.000 0.00 0.00 46.34 4.30
2276 9876 5.105063 AGCTTACTTAATTCCGAACGTACC 58.895 41.667 0.00 0.00 0.00 3.34
2306 9906 2.044650 GATGCTGCTGCCTCCCAA 60.045 61.111 13.47 0.00 38.71 4.12
2446 10057 7.042051 AGCATGATATATGGTTTCACGTACAAC 60.042 37.037 0.00 0.00 0.00 3.32
2632 12712 3.528370 CCACCTACCCTCGCTCCG 61.528 72.222 0.00 0.00 0.00 4.63
2708 12795 7.876068 AGTTTTGTGATGCTCAATTCAATCAAT 59.124 29.630 0.00 0.00 0.00 2.57
2709 12796 7.211573 AGTTTTGTGATGCTCAATTCAATCAA 58.788 30.769 0.00 0.00 0.00 2.57
2710 12797 6.751157 AGTTTTGTGATGCTCAATTCAATCA 58.249 32.000 0.00 0.00 0.00 2.57
2711 12798 8.025445 AGTAGTTTTGTGATGCTCAATTCAATC 58.975 33.333 0.00 0.00 0.00 2.67
2712 12799 7.889469 AGTAGTTTTGTGATGCTCAATTCAAT 58.111 30.769 0.00 0.00 0.00 2.57
2781 12878 4.096003 CGGGGCGTCATCAACCCT 62.096 66.667 0.00 0.00 43.68 4.34
2808 12906 2.811317 CAGTCGTGGAAGCCGAGC 60.811 66.667 0.00 0.00 34.56 5.03
2887 12985 5.416947 CCAAGTAAGTGGTACAGTATGACC 58.583 45.833 0.00 0.00 43.84 4.02
2912 13010 0.377203 CCGTAGCTCGAAAAATGGGC 59.623 55.000 7.07 0.00 42.86 5.36
2915 13013 1.083489 TGGCCGTAGCTCGAAAAATG 58.917 50.000 0.00 0.00 42.86 2.32
2919 13017 2.101750 TCAATATGGCCGTAGCTCGAAA 59.898 45.455 11.11 0.00 42.86 3.46
2929 13027 3.184379 CGAACACAGTATCAATATGGCCG 59.816 47.826 0.00 0.00 0.00 6.13
2937 13035 1.403647 CGGAGCCGAACACAGTATCAA 60.404 52.381 2.00 0.00 42.83 2.57
2948 13046 2.046023 TCGACTACCGGAGCCGAA 60.046 61.111 9.46 0.00 42.83 4.30
2959 13057 3.067833 CACTAGATCATCGGCTCGACTA 58.932 50.000 0.00 0.00 39.18 2.59
2960 13058 1.876799 CACTAGATCATCGGCTCGACT 59.123 52.381 0.00 0.00 39.18 4.18
2996 13094 2.900273 GCCATAGGCCAGACGACA 59.100 61.111 5.01 0.00 44.06 4.35


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

AutoCloner maintained by Alex Coulton.