Multiple sequence alignment - TraesCS4B01G045100

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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 TraesCS4B01G045100 chr4B 100.000 3062 0 0 1 3062 32425934 32422873 0.000000e+00 5655.0
1 TraesCS4B01G045100 chr4B 89.707 1059 53 9 978 2033 32278146 32279151 0.000000e+00 1301.0
2 TraesCS4B01G045100 chr4B 86.709 158 6 7 841 983 32277961 32278118 8.790000e-36 161.0
3 TraesCS4B01G045100 chr4A 90.654 2140 127 29 976 3062 581201313 581199194 0.000000e+00 2776.0
4 TraesCS4B01G045100 chr4A 95.238 84 4 0 2388 2471 581229301 581229218 1.920000e-27 134.0
5 TraesCS4B01G045100 chr4A 96.053 76 3 0 2312 2387 581229403 581229328 1.150000e-24 124.0
6 TraesCS4B01G045100 chr4A 86.408 103 7 5 264 366 581202134 581202039 4.180000e-19 106.0
7 TraesCS4B01G045100 chr4D 90.015 1983 95 36 845 2755 20435960 20434009 0.000000e+00 2470.0
8 TraesCS4B01G045100 chr4D 91.448 1029 57 11 976 2002 20081789 20082788 0.000000e+00 1384.0
9 TraesCS4B01G045100 chr4D 96.429 308 9 1 2755 3062 20433979 20433674 9.800000e-140 507.0
10 TraesCS4B01G045100 chr4D 83.395 271 16 19 255 511 20076136 20076391 1.100000e-54 224.0
11 TraesCS4B01G045100 chr4D 84.925 199 14 10 262 450 20137487 20137679 1.450000e-43 187.0
12 TraesCS4B01G045100 chr4D 78.351 291 25 18 328 597 20081090 20081363 1.470000e-33 154.0
13 TraesCS4B01G045100 chr4D 78.212 179 20 12 656 834 20436161 20436002 2.510000e-16 97.1
14 TraesCS4B01G045100 chr4D 81.132 106 10 6 229 334 20080941 20081036 3.270000e-10 76.8
15 TraesCS4B01G045100 chr5A 82.386 528 49 17 2167 2657 491372049 491372569 1.310000e-113 420.0
16 TraesCS4B01G045100 chr5D 79.777 539 55 20 2167 2657 388334933 388335465 2.920000e-90 342.0
17 TraesCS4B01G045100 chr5D 87.018 285 21 5 2391 2663 388590939 388591219 1.070000e-79 307.0
18 TraesCS4B01G045100 chr6D 87.143 280 22 4 2391 2659 106895703 106895979 3.840000e-79 305.0
19 TraesCS4B01G045100 chr6D 89.320 103 7 4 1 101 129156514 129156614 3.210000e-25 126.0
20 TraesCS4B01G045100 chr6D 88.776 98 8 3 1 96 129156602 129156506 1.930000e-22 117.0
21 TraesCS4B01G045100 chr7B 96.970 132 4 0 102 233 635489340 635489471 3.970000e-54 222.0
22 TraesCS4B01G045100 chr7B 87.429 175 19 3 68 242 633011275 633011104 6.700000e-47 198.0
23 TraesCS4B01G045100 chr3B 86.935 199 17 5 43 232 525928944 525929142 6.650000e-52 215.0
24 TraesCS4B01G045100 chr3B 85.027 187 27 1 43 229 178387623 178387438 4.030000e-44 189.0
25 TraesCS4B01G045100 chr7A 92.208 154 6 6 97 247 43463164 43463014 2.390000e-51 213.0
26 TraesCS4B01G045100 chr7A 91.558 154 7 6 97 247 43444710 43444560 1.110000e-49 207.0
27 TraesCS4B01G045100 chr1A 90.506 158 14 1 77 234 118503668 118503824 1.110000e-49 207.0
28 TraesCS4B01G045100 chr5B 88.889 171 14 4 71 237 437181346 437181177 4.000000e-49 206.0
29 TraesCS4B01G045100 chr2D 88.304 171 14 3 71 241 484901102 484901266 1.860000e-47 200.0
30 TraesCS4B01G045100 chr1B 90.196 102 7 2 1 99 674374663 674374764 2.480000e-26 130.0
31 TraesCS4B01G045100 chr3D 88.571 105 10 2 1 103 105124501 105124605 3.210000e-25 126.0
32 TraesCS4B01G045100 chr3A 89.583 96 7 3 7 99 327803608 327803513 5.360000e-23 119.0
33 TraesCS4B01G045100 chr6A 89.474 95 7 3 3 96 61597806 61597898 1.930000e-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 TraesCS4B01G045100 chr4B 32422873 32425934 3061 True 5655.000000 5655 100.000000 1 3062 1 chr4B.!!$R1 3061
1 TraesCS4B01G045100 chr4B 32277961 32279151 1190 False 731.000000 1301 88.208000 841 2033 2 chr4B.!!$F1 1192
2 TraesCS4B01G045100 chr4A 581199194 581202134 2940 True 1441.000000 2776 88.531000 264 3062 2 chr4A.!!$R1 2798
3 TraesCS4B01G045100 chr4D 20433674 20436161 2487 True 1024.700000 2470 88.218667 656 3062 3 chr4D.!!$R1 2406
4 TraesCS4B01G045100 chr4D 20080941 20082788 1847 False 538.266667 1384 83.643667 229 2002 3 chr4D.!!$F3 1773
5 TraesCS4B01G045100 chr5A 491372049 491372569 520 False 420.000000 420 82.386000 2167 2657 1 chr5A.!!$F1 490
6 TraesCS4B01G045100 chr5D 388334933 388335465 532 False 342.000000 342 79.777000 2167 2657 1 chr5D.!!$F1 490

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
604 728 0.034337 TCACGGTAGCCCAGTCAAAC 59.966 55.0 0.0 0.0 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2510 2955 1.10992 TCTCGCTGAGGATGTAGGGC 61.11 60.0 5.87 0.0 0.0 5.19 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
24 25 7.602517 CCGTCTCAAAATTCTTGTCTTAGAT 57.397 36.000 0.00 0.00 0.00 1.98
25 26 8.034058 CCGTCTCAAAATTCTTGTCTTAGATT 57.966 34.615 0.00 0.00 0.00 2.40
26 27 8.507249 CCGTCTCAAAATTCTTGTCTTAGATTT 58.493 33.333 0.00 0.00 0.00 2.17
27 28 9.322776 CGTCTCAAAATTCTTGTCTTAGATTTG 57.677 33.333 0.00 0.00 30.65 2.32
30 31 9.617975 CTCAAAATTCTTGTCTTAGATTTGACC 57.382 33.333 2.09 0.00 32.41 4.02
31 32 9.130661 TCAAAATTCTTGTCTTAGATTTGACCA 57.869 29.630 2.09 0.00 32.41 4.02
32 33 9.403110 CAAAATTCTTGTCTTAGATTTGACCAG 57.597 33.333 0.00 0.00 30.83 4.00
33 34 8.924511 AAATTCTTGTCTTAGATTTGACCAGA 57.075 30.769 0.00 0.00 34.55 3.86
34 35 9.525826 AAATTCTTGTCTTAGATTTGACCAGAT 57.474 29.630 0.00 0.00 35.74 2.90
36 37 9.829507 ATTCTTGTCTTAGATTTGACCAGATAG 57.170 33.333 0.00 0.00 35.74 2.08
37 38 8.367660 TCTTGTCTTAGATTTGACCAGATAGT 57.632 34.615 0.00 0.00 32.44 2.12
38 39 9.475620 TCTTGTCTTAGATTTGACCAGATAGTA 57.524 33.333 0.00 0.00 32.44 1.82
51 52 9.822727 TTGACCAGATAGTATTAGATACATCCA 57.177 33.333 1.42 0.00 38.21 3.41
52 53 9.997172 TGACCAGATAGTATTAGATACATCCAT 57.003 33.333 1.42 0.00 38.21 3.41
86 87 8.587952 AAATTTAAGACAAGAATTTTGGGACG 57.412 30.769 0.00 0.00 31.00 4.79
87 88 5.699097 TTAAGACAAGAATTTTGGGACGG 57.301 39.130 0.00 0.00 0.00 4.79
88 89 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
89 90 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
90 91 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
91 92 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
92 93 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
93 94 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
94 95 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
95 96 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
96 97 1.272807 TTTTGGGACGGAGGGAGTAG 58.727 55.000 0.00 0.00 0.00 2.57
97 98 0.115745 TTTGGGACGGAGGGAGTAGT 59.884 55.000 0.00 0.00 0.00 2.73
98 99 1.002069 TTGGGACGGAGGGAGTAGTA 58.998 55.000 0.00 0.00 0.00 1.82
99 100 1.229131 TGGGACGGAGGGAGTAGTAT 58.771 55.000 0.00 0.00 0.00 2.12
100 101 2.421725 TGGGACGGAGGGAGTAGTATA 58.578 52.381 0.00 0.00 0.00 1.47
101 102 2.785269 TGGGACGGAGGGAGTAGTATAA 59.215 50.000 0.00 0.00 0.00 0.98
102 103 3.400322 TGGGACGGAGGGAGTAGTATAAT 59.600 47.826 0.00 0.00 0.00 1.28
103 104 4.603171 TGGGACGGAGGGAGTAGTATAATA 59.397 45.833 0.00 0.00 0.00 0.98
104 105 5.074929 TGGGACGGAGGGAGTAGTATAATAA 59.925 44.000 0.00 0.00 0.00 1.40
105 106 6.193504 GGGACGGAGGGAGTAGTATAATAAT 58.806 44.000 0.00 0.00 0.00 1.28
106 107 7.036644 TGGGACGGAGGGAGTAGTATAATAATA 60.037 40.741 0.00 0.00 0.00 0.98
107 108 7.284261 GGGACGGAGGGAGTAGTATAATAATAC 59.716 44.444 0.00 0.00 38.64 1.89
118 119 9.939424 AGTAGTATAATAATACTCCCTCCATCC 57.061 37.037 1.46 0.00 44.05 3.51
119 120 7.899648 AGTATAATAATACTCCCTCCATCCG 57.100 40.000 0.00 0.00 44.05 4.18
120 121 7.649715 AGTATAATAATACTCCCTCCATCCGA 58.350 38.462 0.00 0.00 44.05 4.55
121 122 8.120538 AGTATAATAATACTCCCTCCATCCGAA 58.879 37.037 0.00 0.00 44.05 4.30
122 123 7.808279 ATAATAATACTCCCTCCATCCGAAA 57.192 36.000 0.00 0.00 0.00 3.46
123 124 6.509523 AATAATACTCCCTCCATCCGAAAA 57.490 37.500 0.00 0.00 0.00 2.29
124 125 6.704056 ATAATACTCCCTCCATCCGAAAAT 57.296 37.500 0.00 0.00 0.00 1.82
125 126 7.808279 ATAATACTCCCTCCATCCGAAAATA 57.192 36.000 0.00 0.00 0.00 1.40
126 127 3.840124 ACTCCCTCCATCCGAAAATAC 57.160 47.619 0.00 0.00 0.00 1.89
127 128 3.385115 ACTCCCTCCATCCGAAAATACT 58.615 45.455 0.00 0.00 0.00 2.12
128 129 3.780850 ACTCCCTCCATCCGAAAATACTT 59.219 43.478 0.00 0.00 0.00 2.24
129 130 4.130118 CTCCCTCCATCCGAAAATACTTG 58.870 47.826 0.00 0.00 0.00 3.16
130 131 3.521937 TCCCTCCATCCGAAAATACTTGT 59.478 43.478 0.00 0.00 0.00 3.16
131 132 3.877508 CCCTCCATCCGAAAATACTTGTC 59.122 47.826 0.00 0.00 0.00 3.18
132 133 4.513442 CCTCCATCCGAAAATACTTGTCA 58.487 43.478 0.00 0.00 0.00 3.58
133 134 5.126067 CCTCCATCCGAAAATACTTGTCAT 58.874 41.667 0.00 0.00 0.00 3.06
134 135 5.237344 CCTCCATCCGAAAATACTTGTCATC 59.763 44.000 0.00 0.00 0.00 2.92
135 136 5.739959 TCCATCCGAAAATACTTGTCATCA 58.260 37.500 0.00 0.00 0.00 3.07
136 137 6.176896 TCCATCCGAAAATACTTGTCATCAA 58.823 36.000 0.00 0.00 0.00 2.57
137 138 6.657117 TCCATCCGAAAATACTTGTCATCAAA 59.343 34.615 0.00 0.00 32.87 2.69
138 139 7.175816 TCCATCCGAAAATACTTGTCATCAAAA 59.824 33.333 0.00 0.00 32.87 2.44
139 140 7.975616 CCATCCGAAAATACTTGTCATCAAAAT 59.024 33.333 0.00 0.00 32.87 1.82
140 141 8.800972 CATCCGAAAATACTTGTCATCAAAATG 58.199 33.333 0.00 0.00 32.87 2.32
141 142 7.312154 TCCGAAAATACTTGTCATCAAAATGG 58.688 34.615 0.00 0.00 33.42 3.16
142 143 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
143 144 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
144 145 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
145 146 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
146 147 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
147 148 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
148 149 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
150 151 8.145316 ACTTGTCATCAAAATGGACAAAAATG 57.855 30.769 7.70 0.11 34.98 2.32
151 152 7.986320 ACTTGTCATCAAAATGGACAAAAATGA 59.014 29.630 7.70 0.00 34.98 2.57
152 153 8.728337 TTGTCATCAAAATGGACAAAAATGAA 57.272 26.923 4.15 0.00 33.71 2.57
153 154 8.905660 TGTCATCAAAATGGACAAAAATGAAT 57.094 26.923 0.00 0.00 33.42 2.57
154 155 8.775527 TGTCATCAAAATGGACAAAAATGAATG 58.224 29.630 0.00 0.00 33.42 2.67
155 156 8.776470 GTCATCAAAATGGACAAAAATGAATGT 58.224 29.630 0.00 0.00 33.42 2.71
156 157 9.993454 TCATCAAAATGGACAAAAATGAATGTA 57.007 25.926 0.00 0.00 33.42 2.29
159 160 9.775854 TCAAAATGGACAAAAATGAATGTATGT 57.224 25.926 0.00 0.00 0.00 2.29
165 166 9.295825 TGGACAAAAATGAATGTATGTAGAACT 57.704 29.630 0.00 0.00 0.00 3.01
211 212 9.918630 CTCCTTTTATTCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
218 219 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
219 220 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
220 221 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
221 222 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
222 223 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
223 224 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
224 225 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
225 226 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
226 227 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
227 228 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
235 236 0.539901 CCGGACGGAGGGAGTATGAT 60.540 60.000 4.40 0.00 37.50 2.45
250 251 7.673926 AGGGAGTATGATATTTTGGTTGTTGTT 59.326 33.333 0.00 0.00 0.00 2.83
252 253 9.783256 GGAGTATGATATTTTGGTTGTTGTTAC 57.217 33.333 0.00 0.00 0.00 2.50
262 263 9.791820 ATTTTGGTTGTTGTTACTTGTTAGTAC 57.208 29.630 0.00 0.00 36.61 2.73
273 274 3.749609 ACTTGTTAGTACAAACGGCCATC 59.250 43.478 2.24 0.00 43.33 3.51
276 277 2.282701 TAGTACAAACGGCCATCGAC 57.717 50.000 2.24 0.00 42.43 4.20
278 279 2.095847 TACAAACGGCCATCGACGC 61.096 57.895 2.24 0.00 42.43 5.19
279 280 2.766875 TACAAACGGCCATCGACGCA 62.767 55.000 2.24 0.00 42.43 5.24
313 314 2.751259 ACAAGACAAAGATGCATGCGAT 59.249 40.909 14.09 7.77 0.00 4.58
351 407 2.740826 GCCTTCGCCGTAGCAACA 60.741 61.111 0.00 0.00 39.83 3.33
374 439 3.078836 TCCCGTCGGTCCCAATCC 61.079 66.667 11.06 0.00 0.00 3.01
390 455 0.673644 ATCCAGGCGAACCGTTCTTG 60.674 55.000 9.55 5.31 42.76 3.02
394 459 4.084888 GCGAACCGTTCTTGGCCG 62.085 66.667 9.55 0.00 0.00 6.13
395 460 2.663852 CGAACCGTTCTTGGCCGT 60.664 61.111 9.55 0.00 0.00 5.68
400 465 2.388232 CCGTTCTTGGCCGTAGCAC 61.388 63.158 0.00 0.00 42.56 4.40
401 466 2.388232 CGTTCTTGGCCGTAGCACC 61.388 63.158 0.00 0.00 42.56 5.01
402 467 2.047655 TTCTTGGCCGTAGCACCG 60.048 61.111 0.00 0.00 42.56 4.94
403 468 2.575893 TTCTTGGCCGTAGCACCGA 61.576 57.895 0.00 0.00 42.56 4.69
416 497 1.352156 GCACCGACGATCAAGACACC 61.352 60.000 0.00 0.00 0.00 4.16
418 499 0.243907 ACCGACGATCAAGACACCAG 59.756 55.000 0.00 0.00 0.00 4.00
450 532 4.083862 GTCGACAGCCCCCTGGAC 62.084 72.222 11.55 0.00 43.53 4.02
460 545 1.672898 CCCCTGGACCGTACGAAAA 59.327 57.895 18.76 0.00 0.00 2.29
479 564 1.081376 GAAAGCACAGCAGCAGCAG 60.081 57.895 3.17 0.00 45.49 4.24
480 565 3.208884 AAAGCACAGCAGCAGCAGC 62.209 57.895 3.17 0.46 45.49 5.25
481 566 4.949098 AGCACAGCAGCAGCAGCA 62.949 61.111 12.92 0.00 45.49 4.41
495 580 2.156891 CAGCAGCAAATGATGTGCAAAC 59.843 45.455 10.66 0.00 44.74 2.93
496 581 2.136728 GCAGCAAATGATGTGCAAACA 58.863 42.857 10.66 0.00 44.74 2.83
497 582 2.739913 GCAGCAAATGATGTGCAAACAT 59.260 40.909 10.66 0.00 44.74 2.71
498 583 3.187637 GCAGCAAATGATGTGCAAACATT 59.812 39.130 10.66 7.97 44.74 2.71
499 584 4.319911 GCAGCAAATGATGTGCAAACATTT 60.320 37.500 10.66 16.08 44.74 2.32
500 585 5.753744 CAGCAAATGATGTGCAAACATTTT 58.246 33.333 10.66 7.89 44.74 1.82
501 586 5.623264 CAGCAAATGATGTGCAAACATTTTG 59.377 36.000 10.66 13.42 44.74 2.44
502 587 4.912766 GCAAATGATGTGCAAACATTTTGG 59.087 37.500 18.01 12.24 40.63 3.28
503 588 4.752661 AATGATGTGCAAACATTTTGGC 57.247 36.364 7.97 0.00 31.46 4.52
504 589 3.472283 TGATGTGCAAACATTTTGGCT 57.528 38.095 0.00 0.00 0.00 4.75
505 590 4.597404 TGATGTGCAAACATTTTGGCTA 57.403 36.364 0.00 0.00 0.00 3.93
506 591 5.149973 TGATGTGCAAACATTTTGGCTAT 57.850 34.783 0.00 0.00 0.00 2.97
507 592 5.170021 TGATGTGCAAACATTTTGGCTATC 58.830 37.500 0.00 0.00 0.00 2.08
512 597 3.430790 GCAAACATTTTGGCTATCCCCTC 60.431 47.826 1.07 0.00 0.00 4.30
566 690 1.962306 CGTCGCTTTCCCCGGAAAA 60.962 57.895 0.73 1.94 42.61 2.29
567 691 1.577922 GTCGCTTTCCCCGGAAAAC 59.422 57.895 0.73 5.12 42.61 2.43
592 716 2.290464 CAAAACCACCAAGTCACGGTA 58.710 47.619 0.00 0.00 34.02 4.02
597 721 1.839747 ACCAAGTCACGGTAGCCCA 60.840 57.895 0.00 0.00 34.02 5.36
599 723 1.671742 CAAGTCACGGTAGCCCAGT 59.328 57.895 0.00 0.00 0.00 4.00
602 726 0.830444 AGTCACGGTAGCCCAGTCAA 60.830 55.000 0.00 0.00 0.00 3.18
604 728 0.034337 TCACGGTAGCCCAGTCAAAC 59.966 55.000 0.00 0.00 0.00 2.93
606 730 1.290955 CGGTAGCCCAGTCAAACGA 59.709 57.895 0.00 0.00 0.00 3.85
607 731 0.736325 CGGTAGCCCAGTCAAACGAG 60.736 60.000 0.00 0.00 0.00 4.18
608 732 0.606604 GGTAGCCCAGTCAAACGAGA 59.393 55.000 0.00 0.00 0.00 4.04
616 776 2.353208 CCAGTCAAACGAGAAGGAGGAG 60.353 54.545 0.00 0.00 0.00 3.69
627 787 2.437281 AGAAGGAGGAGGATCGTACGTA 59.563 50.000 16.05 2.34 39.27 3.57
629 789 1.202746 AGGAGGAGGATCGTACGTACC 60.203 57.143 19.67 18.28 39.27 3.34
632 792 0.583917 GGAGGATCGTACGTACCGAC 59.416 60.000 19.67 16.40 37.12 4.79
682 864 2.758770 ATCGGTCCGTGTCGTTGGTG 62.759 60.000 11.88 0.00 0.00 4.17
726 917 1.347817 GAAACGGTCTCAGCTCGCTG 61.348 60.000 12.54 12.54 44.86 5.18
752 949 1.863880 CGCACGCGTCTACTCACTC 60.864 63.158 9.86 0.00 34.35 3.51
753 950 1.863880 GCACGCGTCTACTCACTCG 60.864 63.158 9.86 0.00 0.00 4.18
754 951 1.785951 CACGCGTCTACTCACTCGA 59.214 57.895 9.86 0.00 0.00 4.04
755 952 0.518764 CACGCGTCTACTCACTCGAC 60.519 60.000 9.86 0.00 0.00 4.20
1665 2021 4.380628 AGGCACGACGACGACGAC 62.381 66.667 25.15 15.83 42.66 4.34
1743 2099 1.396301 GCCTCGAAGCTGACATTCAAG 59.604 52.381 0.00 0.00 0.00 3.02
1907 2266 4.193334 CGAGATGCTCCACGGCGA 62.193 66.667 16.62 0.00 34.52 5.54
1995 2360 1.960689 GAGGATCTCCCGGAGAAGAAG 59.039 57.143 21.20 0.00 42.27 2.85
2006 2371 1.404851 GGAGAAGAAGCACGGAGAAGG 60.405 57.143 0.00 0.00 0.00 3.46
2065 2430 2.094957 ACGAACAGAAGACTCTAGCAGC 60.095 50.000 0.00 0.00 0.00 5.25
2066 2431 2.095008 CGAACAGAAGACTCTAGCAGCA 60.095 50.000 0.00 0.00 0.00 4.41
2072 2445 3.569701 AGAAGACTCTAGCAGCATAGCTC 59.430 47.826 0.00 0.00 45.26 4.09
2116 2489 8.288208 CACATAGCAGATATGGTTTCTTGATTC 58.712 37.037 10.43 0.00 44.86 2.52
2140 2517 7.161404 TCAGTTGTATTGATAGCAGTTGAACT 58.839 34.615 0.00 0.00 0.00 3.01
2264 2645 2.866156 CGAAGAACAGAGAGCAAACACA 59.134 45.455 0.00 0.00 0.00 3.72
2265 2646 3.060003 CGAAGAACAGAGAGCAAACACAG 60.060 47.826 0.00 0.00 0.00 3.66
2266 2647 2.843701 AGAACAGAGAGCAAACACAGG 58.156 47.619 0.00 0.00 0.00 4.00
2277 2658 3.503748 AGCAAACACAGGAAGCTTATGTC 59.496 43.478 12.63 3.65 29.98 3.06
2367 2750 4.275810 ACATGCTGCAAACCTCAGATAAT 58.724 39.130 6.36 0.00 33.54 1.28
2397 2804 3.963374 TGAAGCTACCAGTATCATCAGCT 59.037 43.478 0.00 0.00 40.94 4.24
2427 2843 5.012046 ACATCATCTGTCTGGACAAACTACA 59.988 40.000 4.94 0.00 41.33 2.74
2428 2844 5.545063 TCATCTGTCTGGACAAACTACAA 57.455 39.130 4.94 0.00 41.33 2.41
2429 2845 5.297547 TCATCTGTCTGGACAAACTACAAC 58.702 41.667 4.94 0.00 41.33 3.32
2430 2846 4.746535 TCTGTCTGGACAAACTACAACA 57.253 40.909 4.94 0.00 41.33 3.33
2479 2899 1.134367 CATGGAGCTGTTTGGCTGATG 59.866 52.381 0.00 0.00 43.20 3.07
2510 2955 2.560105 TGATCTGAGATACTCCCATGCG 59.440 50.000 0.00 0.00 0.00 4.73
2679 3126 3.941483 CTGGTAGGGTGAAAGCAATACTG 59.059 47.826 0.00 0.00 34.77 2.74
2752 3205 2.676121 CCGGCCATTCAAGTGCCA 60.676 61.111 2.24 0.00 45.63 4.92
3008 3492 2.010145 TAAACATGAGCTCTGCCGTC 57.990 50.000 16.19 0.00 0.00 4.79
3032 3516 4.592485 AACTTGGTTGAACAAACACACA 57.408 36.364 4.71 0.00 37.81 3.72
3037 3521 2.602660 GGTTGAACAAACACACACATGC 59.397 45.455 0.00 0.00 40.86 4.06
3055 3539 2.868583 ATGCGCACTAAGAAGCATAGTG 59.131 45.455 14.90 8.87 46.93 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.322776 CAAATCTAAGACAAGAATTTTGAGACG 57.677 33.333 7.18 0.00 31.51 4.18
4 5 9.617975 GGTCAAATCTAAGACAAGAATTTTGAG 57.382 33.333 7.18 0.00 36.16 3.02
5 6 9.130661 TGGTCAAATCTAAGACAAGAATTTTGA 57.869 29.630 7.18 0.00 34.47 2.69
6 7 9.403110 CTGGTCAAATCTAAGACAAGAATTTTG 57.597 33.333 0.00 0.00 37.91 2.44
7 8 9.354673 TCTGGTCAAATCTAAGACAAGAATTTT 57.645 29.630 0.00 0.00 40.82 1.82
8 9 8.924511 TCTGGTCAAATCTAAGACAAGAATTT 57.075 30.769 0.00 0.00 40.82 1.82
10 11 9.829507 CTATCTGGTCAAATCTAAGACAAGAAT 57.170 33.333 3.99 0.00 45.27 2.40
11 12 8.816894 ACTATCTGGTCAAATCTAAGACAAGAA 58.183 33.333 3.99 0.00 45.27 2.52
12 13 8.367660 ACTATCTGGTCAAATCTAAGACAAGA 57.632 34.615 2.46 2.46 45.95 3.02
25 26 9.822727 TGGATGTATCTAATACTATCTGGTCAA 57.177 33.333 0.00 0.00 36.70 3.18
26 27 9.997172 ATGGATGTATCTAATACTATCTGGTCA 57.003 33.333 0.00 0.00 36.70 4.02
60 61 9.685828 CGTCCCAAAATTCTTGTCTTAAATTTA 57.314 29.630 0.00 0.00 32.84 1.40
61 62 7.655732 CCGTCCCAAAATTCTTGTCTTAAATTT 59.344 33.333 0.00 0.00 34.86 1.82
62 63 7.014808 TCCGTCCCAAAATTCTTGTCTTAAATT 59.985 33.333 0.00 0.00 0.00 1.82
63 64 6.492087 TCCGTCCCAAAATTCTTGTCTTAAAT 59.508 34.615 0.00 0.00 0.00 1.40
64 65 5.828859 TCCGTCCCAAAATTCTTGTCTTAAA 59.171 36.000 0.00 0.00 0.00 1.52
65 66 5.378332 TCCGTCCCAAAATTCTTGTCTTAA 58.622 37.500 0.00 0.00 0.00 1.85
66 67 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
67 68 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
68 69 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
69 70 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
70 71 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
71 72 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
72 73 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
73 74 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
74 75 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
75 76 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
76 77 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
77 78 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
78 79 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
79 80 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
80 81 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
81 82 3.515602 TTATACTACTCCCTCCGTCCC 57.484 52.381 0.00 0.00 0.00 4.46
82 83 8.052141 AGTATTATTATACTACTCCCTCCGTCC 58.948 40.741 2.55 0.00 44.01 4.79
83 84 9.108284 GAGTATTATTATACTACTCCCTCCGTC 57.892 40.741 14.89 0.00 45.43 4.79
92 93 9.939424 GGATGGAGGGAGTATTATTATACTACT 57.061 37.037 12.65 10.05 45.43 2.57
93 94 8.848182 CGGATGGAGGGAGTATTATTATACTAC 58.152 40.741 5.65 5.65 45.43 2.73
94 95 8.784880 TCGGATGGAGGGAGTATTATTATACTA 58.215 37.037 4.42 0.00 45.43 1.82
96 97 7.893124 TCGGATGGAGGGAGTATTATTATAC 57.107 40.000 0.00 0.00 37.48 1.47
97 98 8.904648 TTTCGGATGGAGGGAGTATTATTATA 57.095 34.615 0.00 0.00 0.00 0.98
98 99 7.808279 TTTCGGATGGAGGGAGTATTATTAT 57.192 36.000 0.00 0.00 0.00 1.28
99 100 7.621006 TTTTCGGATGGAGGGAGTATTATTA 57.379 36.000 0.00 0.00 0.00 0.98
100 101 6.509523 TTTTCGGATGGAGGGAGTATTATT 57.490 37.500 0.00 0.00 0.00 1.40
101 102 6.704056 ATTTTCGGATGGAGGGAGTATTAT 57.296 37.500 0.00 0.00 0.00 1.28
102 103 6.785963 AGTATTTTCGGATGGAGGGAGTATTA 59.214 38.462 0.00 0.00 0.00 0.98
103 104 5.607171 AGTATTTTCGGATGGAGGGAGTATT 59.393 40.000 0.00 0.00 0.00 1.89
104 105 5.155905 AGTATTTTCGGATGGAGGGAGTAT 58.844 41.667 0.00 0.00 0.00 2.12
105 106 4.553678 AGTATTTTCGGATGGAGGGAGTA 58.446 43.478 0.00 0.00 0.00 2.59
106 107 3.385115 AGTATTTTCGGATGGAGGGAGT 58.615 45.455 0.00 0.00 0.00 3.85
107 108 4.130118 CAAGTATTTTCGGATGGAGGGAG 58.870 47.826 0.00 0.00 0.00 4.30
108 109 3.521937 ACAAGTATTTTCGGATGGAGGGA 59.478 43.478 0.00 0.00 0.00 4.20
109 110 3.877508 GACAAGTATTTTCGGATGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
110 111 4.513442 TGACAAGTATTTTCGGATGGAGG 58.487 43.478 0.00 0.00 0.00 4.30
111 112 5.817296 TGATGACAAGTATTTTCGGATGGAG 59.183 40.000 0.00 0.00 0.00 3.86
112 113 5.739959 TGATGACAAGTATTTTCGGATGGA 58.260 37.500 0.00 0.00 0.00 3.41
113 114 6.435430 TTGATGACAAGTATTTTCGGATGG 57.565 37.500 0.00 0.00 0.00 3.51
114 115 8.800972 CATTTTGATGACAAGTATTTTCGGATG 58.199 33.333 0.00 0.00 37.32 3.51
115 116 7.975616 CCATTTTGATGACAAGTATTTTCGGAT 59.024 33.333 0.00 0.00 37.32 4.18
116 117 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
117 118 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
118 119 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
119 120 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
120 121 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
121 122 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
122 123 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
124 125 9.258826 CATTTTTGTCCATTTTGATGACAAGTA 57.741 29.630 0.00 0.00 37.13 2.24
125 126 7.986320 TCATTTTTGTCCATTTTGATGACAAGT 59.014 29.630 0.00 0.00 37.13 3.16
126 127 8.367943 TCATTTTTGTCCATTTTGATGACAAG 57.632 30.769 0.00 0.00 37.13 3.16
127 128 8.728337 TTCATTTTTGTCCATTTTGATGACAA 57.272 26.923 0.00 0.00 34.47 3.18
128 129 8.775527 CATTCATTTTTGTCCATTTTGATGACA 58.224 29.630 0.00 0.00 0.00 3.58
129 130 8.776470 ACATTCATTTTTGTCCATTTTGATGAC 58.224 29.630 0.00 0.00 0.00 3.06
130 131 8.905660 ACATTCATTTTTGTCCATTTTGATGA 57.094 26.923 0.00 0.00 0.00 2.92
133 134 9.775854 ACATACATTCATTTTTGTCCATTTTGA 57.224 25.926 0.00 0.00 0.00 2.69
139 140 9.295825 AGTTCTACATACATTCATTTTTGTCCA 57.704 29.630 0.00 0.00 0.00 4.02
185 186 9.918630 ACTTGTCATCAAAATGAATAAAAGGAG 57.081 29.630 0.00 0.00 43.42 3.69
193 194 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
194 195 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
195 196 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
196 197 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
197 198 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
198 199 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
199 200 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
200 201 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
201 202 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
202 203 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
203 204 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
204 205 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
205 206 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
206 207 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
207 208 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
208 209 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
209 210 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
210 211 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
211 212 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
212 213 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
213 214 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
214 215 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
215 216 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
216 217 0.539901 ATCATACTCCCTCCGTCCGG 60.540 60.000 0.00 0.00 0.00 5.14
217 218 2.195741 TATCATACTCCCTCCGTCCG 57.804 55.000 0.00 0.00 0.00 4.79
218 219 5.238583 CAAAATATCATACTCCCTCCGTCC 58.761 45.833 0.00 0.00 0.00 4.79
219 220 5.221661 ACCAAAATATCATACTCCCTCCGTC 60.222 44.000 0.00 0.00 0.00 4.79
220 221 4.658901 ACCAAAATATCATACTCCCTCCGT 59.341 41.667 0.00 0.00 0.00 4.69
221 222 5.228945 ACCAAAATATCATACTCCCTCCG 57.771 43.478 0.00 0.00 0.00 4.63
222 223 6.365520 ACAACCAAAATATCATACTCCCTCC 58.634 40.000 0.00 0.00 0.00 4.30
223 224 7.339466 ACAACAACCAAAATATCATACTCCCTC 59.661 37.037 0.00 0.00 0.00 4.30
224 225 7.182060 ACAACAACCAAAATATCATACTCCCT 58.818 34.615 0.00 0.00 0.00 4.20
225 226 7.404671 ACAACAACCAAAATATCATACTCCC 57.595 36.000 0.00 0.00 0.00 4.30
226 227 9.783256 GTAACAACAACCAAAATATCATACTCC 57.217 33.333 0.00 0.00 0.00 3.85
250 251 4.333913 TGGCCGTTTGTACTAACAAGTA 57.666 40.909 18.14 1.71 45.99 2.24
252 253 3.181524 CGATGGCCGTTTGTACTAACAAG 60.182 47.826 18.14 10.74 45.99 3.16
253 254 2.737783 CGATGGCCGTTTGTACTAACAA 59.262 45.455 18.14 3.45 43.85 2.83
254 255 2.029200 TCGATGGCCGTTTGTACTAACA 60.029 45.455 18.14 1.53 39.75 2.41
255 256 2.346545 GTCGATGGCCGTTTGTACTAAC 59.653 50.000 9.78 9.78 39.75 2.34
256 257 2.609350 GTCGATGGCCGTTTGTACTAA 58.391 47.619 0.00 0.00 39.75 2.24
257 258 1.467883 CGTCGATGGCCGTTTGTACTA 60.468 52.381 0.00 0.00 39.75 1.82
260 261 2.095847 GCGTCGATGGCCGTTTGTA 61.096 57.895 6.79 0.00 39.75 2.41
262 263 2.450960 TTTGCGTCGATGGCCGTTTG 62.451 55.000 6.79 0.00 39.75 2.93
278 279 4.044336 TGTCTTGTGTTCATGGCTTTTG 57.956 40.909 0.00 0.00 0.00 2.44
279 280 4.734398 TTGTCTTGTGTTCATGGCTTTT 57.266 36.364 0.00 0.00 0.00 2.27
313 314 2.416836 CGTATGGTTTTCCTCTCTCGCA 60.417 50.000 0.00 0.00 41.38 5.10
315 316 2.194271 GCGTATGGTTTTCCTCTCTCG 58.806 52.381 0.00 0.00 41.38 4.04
316 317 2.168728 AGGCGTATGGTTTTCCTCTCTC 59.831 50.000 0.00 0.00 41.38 3.20
317 318 2.188817 AGGCGTATGGTTTTCCTCTCT 58.811 47.619 0.00 0.00 41.38 3.10
374 439 2.966309 GCCAAGAACGGTTCGCCTG 61.966 63.158 14.70 12.77 34.30 4.85
390 455 4.203076 ATCGTCGGTGCTACGGCC 62.203 66.667 0.00 0.00 40.68 6.13
394 459 1.135489 TGTCTTGATCGTCGGTGCTAC 60.135 52.381 0.00 0.00 0.00 3.58
395 460 1.135489 GTGTCTTGATCGTCGGTGCTA 60.135 52.381 0.00 0.00 0.00 3.49
400 465 0.458543 CCTGGTGTCTTGATCGTCGG 60.459 60.000 0.00 0.00 0.00 4.79
401 466 0.526211 TCCTGGTGTCTTGATCGTCG 59.474 55.000 0.00 0.00 0.00 5.12
402 467 1.737363 GCTCCTGGTGTCTTGATCGTC 60.737 57.143 0.00 0.00 0.00 4.20
403 468 0.247736 GCTCCTGGTGTCTTGATCGT 59.752 55.000 0.00 0.00 0.00 3.73
441 522 1.829523 TTTTCGTACGGTCCAGGGGG 61.830 60.000 16.52 0.00 0.00 5.40
450 532 2.661979 GCTGTGCTTTCTTTTCGTACGG 60.662 50.000 16.52 0.00 0.00 4.02
456 541 2.391879 CTGCTGCTGTGCTTTCTTTTC 58.608 47.619 0.00 0.00 0.00 2.29
460 545 1.516365 CTGCTGCTGCTGTGCTTTCT 61.516 55.000 17.00 0.00 40.48 2.52
479 564 4.912766 CCAAAATGTTTGCACATCATTTGC 59.087 37.500 17.61 0.00 43.34 3.68
480 565 4.912766 GCCAAAATGTTTGCACATCATTTG 59.087 37.500 17.61 12.40 43.34 2.32
481 566 4.822896 AGCCAAAATGTTTGCACATCATTT 59.177 33.333 13.59 13.59 43.34 2.32
495 580 2.618709 GTTCGAGGGGATAGCCAAAATG 59.381 50.000 0.00 0.00 35.15 2.32
496 581 2.422945 GGTTCGAGGGGATAGCCAAAAT 60.423 50.000 0.00 0.00 35.15 1.82
497 582 1.064979 GGTTCGAGGGGATAGCCAAAA 60.065 52.381 0.00 0.00 35.15 2.44
498 583 0.544697 GGTTCGAGGGGATAGCCAAA 59.455 55.000 0.00 0.00 35.15 3.28
499 584 1.682451 CGGTTCGAGGGGATAGCCAA 61.682 60.000 0.00 0.00 35.15 4.52
500 585 2.131709 CGGTTCGAGGGGATAGCCA 61.132 63.158 0.00 0.00 35.15 4.75
501 586 2.735237 CGGTTCGAGGGGATAGCC 59.265 66.667 0.00 0.00 0.00 3.93
502 587 1.683418 AACCGGTTCGAGGGGATAGC 61.683 60.000 15.86 0.00 0.00 2.97
503 588 0.388294 GAACCGGTTCGAGGGGATAG 59.612 60.000 30.33 0.00 0.00 2.08
504 589 0.324552 TGAACCGGTTCGAGGGGATA 60.325 55.000 35.42 17.56 42.28 2.59
505 590 1.196104 TTGAACCGGTTCGAGGGGAT 61.196 55.000 35.42 6.06 42.28 3.85
506 591 1.823169 CTTGAACCGGTTCGAGGGGA 61.823 60.000 40.43 23.35 43.89 4.81
507 592 1.375523 CTTGAACCGGTTCGAGGGG 60.376 63.158 40.43 25.53 43.89 4.79
512 597 0.032952 TGGAGACTTGAACCGGTTCG 59.967 55.000 35.42 26.41 42.28 3.95
548 672 1.962306 TTTTCCGGGGAAAGCGACG 60.962 57.895 12.29 0.00 43.75 5.12
592 716 0.035458 CCTTCTCGTTTGACTGGGCT 59.965 55.000 0.00 0.00 0.00 5.19
597 721 1.896465 CCTCCTCCTTCTCGTTTGACT 59.104 52.381 0.00 0.00 0.00 3.41
599 723 2.304221 TCCTCCTCCTTCTCGTTTGA 57.696 50.000 0.00 0.00 0.00 2.69
602 726 1.341187 ACGATCCTCCTCCTTCTCGTT 60.341 52.381 0.00 0.00 36.04 3.85
604 728 1.874872 GTACGATCCTCCTCCTTCTCG 59.125 57.143 0.00 0.00 0.00 4.04
606 730 1.212441 ACGTACGATCCTCCTCCTTCT 59.788 52.381 24.41 0.00 0.00 2.85
607 731 1.677942 ACGTACGATCCTCCTCCTTC 58.322 55.000 24.41 0.00 0.00 3.46
608 732 2.570135 GTACGTACGATCCTCCTCCTT 58.430 52.381 24.41 0.00 0.00 3.36
702 893 0.600255 AGCTGAGACCGTTTCCGTTG 60.600 55.000 0.00 0.00 0.00 4.10
753 950 1.080025 CTTTCCCGGTCGACTGGTC 60.080 63.158 35.48 10.80 40.86 4.02
754 951 2.580601 CCTTTCCCGGTCGACTGGT 61.581 63.158 35.48 0.00 40.86 4.00
755 952 2.227089 CTCCTTTCCCGGTCGACTGG 62.227 65.000 32.82 32.82 42.13 4.00
804 1005 3.365265 GCCAAGGCGTTGTCCAGG 61.365 66.667 17.23 3.45 30.95 4.45
805 1006 3.365265 GGCCAAGGCGTTGTCCAG 61.365 66.667 13.96 1.91 43.06 3.86
823 1024 1.081509 TGATCGGCGTTTGCTTTGC 60.082 52.632 6.85 0.00 42.25 3.68
903 1174 3.617284 CCTGGTGTTTTATACCCCACTC 58.383 50.000 0.00 0.00 37.40 3.51
904 1175 2.291346 GCCTGGTGTTTTATACCCCACT 60.291 50.000 0.00 0.00 37.40 4.00
905 1176 2.097036 GCCTGGTGTTTTATACCCCAC 58.903 52.381 0.00 0.00 37.40 4.61
906 1177 1.006162 GGCCTGGTGTTTTATACCCCA 59.994 52.381 0.00 0.00 37.40 4.96
924 1198 0.603065 GGTGATCAGGTGGTTTTGGC 59.397 55.000 0.00 0.00 0.00 4.52
1588 1932 4.530857 GGCCGGATCCTCGTGGTG 62.531 72.222 5.05 0.00 34.23 4.17
1703 2059 3.787001 CCTTGTCTCCCTCCGGCC 61.787 72.222 0.00 0.00 0.00 6.13
1837 2193 4.363990 CCTGTCGTCGGTGCTGCT 62.364 66.667 0.00 0.00 0.00 4.24
1883 2239 1.743995 TGGAGCATCTCGTCGTCGA 60.744 57.895 4.42 4.42 44.12 4.20
1907 2266 3.133014 CATCGGCCAGATCCTCGT 58.867 61.111 2.24 0.00 37.52 4.18
1995 2360 1.686325 TATCCTGCCCTTCTCCGTGC 61.686 60.000 0.00 0.00 0.00 5.34
2087 2460 6.425210 AGAAACCATATCTGCTATGTGCTA 57.575 37.500 0.00 0.00 43.37 3.49
2088 2461 5.301835 AGAAACCATATCTGCTATGTGCT 57.698 39.130 0.00 0.00 43.37 4.40
2089 2462 5.528690 TCAAGAAACCATATCTGCTATGTGC 59.471 40.000 0.00 0.00 43.25 4.57
2090 2463 7.741027 ATCAAGAAACCATATCTGCTATGTG 57.259 36.000 0.00 0.00 36.27 3.21
2091 2464 7.994911 TGAATCAAGAAACCATATCTGCTATGT 59.005 33.333 0.00 0.00 36.27 2.29
2092 2465 8.387190 TGAATCAAGAAACCATATCTGCTATG 57.613 34.615 0.00 0.00 37.54 2.23
2101 2474 9.513906 TCAATACAACTGAATCAAGAAACCATA 57.486 29.630 0.00 0.00 0.00 2.74
2116 2489 7.369803 AGTTCAACTGCTATCAATACAACTG 57.630 36.000 0.00 0.00 0.00 3.16
2140 2517 8.168790 TGATCTGCAATATATAGCTGCAAAAA 57.831 30.769 18.11 10.43 44.94 1.94
2264 2645 2.826128 TCACTGACGACATAAGCTTCCT 59.174 45.455 0.00 0.00 0.00 3.36
2265 2646 3.232213 TCACTGACGACATAAGCTTCC 57.768 47.619 0.00 0.00 0.00 3.46
2266 2647 6.266323 TCTTATCACTGACGACATAAGCTTC 58.734 40.000 0.00 0.00 0.00 3.86
2277 2658 2.033424 TCGAGGCATCTTATCACTGACG 59.967 50.000 0.00 0.00 0.00 4.35
2367 2750 6.896883 TGATACTGGTAGCTTCAGTAGTAGA 58.103 40.000 24.19 11.39 46.67 2.59
2397 2804 2.825532 TCCAGACAGATGATGTTCGTCA 59.174 45.455 0.00 0.00 44.17 4.35
2427 2843 5.506708 AGTTTCTTAGTCAGGGTGTTTGTT 58.493 37.500 0.00 0.00 0.00 2.83
2428 2844 5.112129 AGTTTCTTAGTCAGGGTGTTTGT 57.888 39.130 0.00 0.00 0.00 2.83
2429 2845 5.179555 GCTAGTTTCTTAGTCAGGGTGTTTG 59.820 44.000 0.00 0.00 0.00 2.93
2430 2846 5.163237 TGCTAGTTTCTTAGTCAGGGTGTTT 60.163 40.000 0.00 0.00 0.00 2.83
2479 2899 7.148086 GGGAGTATCTCAGATCAGATGTATGTC 60.148 44.444 5.94 0.00 33.91 3.06
2510 2955 1.109920 TCTCGCTGAGGATGTAGGGC 61.110 60.000 5.87 0.00 0.00 5.19
2679 3126 1.534595 CTGCTTGTCAGTCAGCTTTCC 59.465 52.381 0.00 0.00 38.02 3.13
2708 3158 8.597662 TGTAACTGGTAGTTGTTTAGTTCATC 57.402 34.615 4.56 0.00 39.11 2.92
2752 3205 9.150348 CTTGTTTTACCTTTGACACTTGATTTT 57.850 29.630 0.00 0.00 0.00 1.82
3008 3492 5.235186 TGTGTGTTTGTTCAACCAAGTTTTG 59.765 36.000 0.00 0.00 33.97 2.44
3032 3516 1.742761 ATGCTTCTTAGTGCGCATGT 58.257 45.000 15.91 6.96 41.17 3.21
3037 3521 3.511699 TGTCACTATGCTTCTTAGTGCG 58.488 45.455 12.35 0.00 44.00 5.34


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

AutoCloner maintained by Alex Coulton.