Multiple sequence alignment - TraesCS5D01G204300

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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 TraesCS5D01G204300 chr5D 100.000 4540 0 0 1 4540 309674761 309679300 0.000000e+00 8384.0
1 TraesCS5D01G204300 chr5B 93.866 2315 95 18 306 2611 354782291 354784567 0.000000e+00 3445.0
2 TraesCS5D01G204300 chr5B 96.127 1007 32 4 2709 3710 354784586 354785590 0.000000e+00 1637.0
3 TraesCS5D01G204300 chr5B 78.676 408 68 11 4045 4435 430191471 430191066 2.100000e-63 254.0
4 TraesCS5D01G204300 chr5B 95.041 121 6 0 3715 3835 354785622 354785742 1.670000e-44 191.0
5 TraesCS5D01G204300 chr5A 93.248 2355 90 20 299 2633 402904652 402906957 0.000000e+00 3404.0
6 TraesCS5D01G204300 chr5A 93.610 1252 39 14 2694 3911 402907063 402908307 0.000000e+00 1831.0
7 TraesCS5D01G204300 chr5A 94.400 625 31 2 3914 4537 402908482 402909103 0.000000e+00 957.0
8 TraesCS5D01G204300 chrUn 85.112 1209 132 27 597 1763 31777638 31778840 0.000000e+00 1192.0
9 TraesCS5D01G204300 chrUn 89.876 563 55 1 1203 1763 31805400 31805962 0.000000e+00 723.0
10 TraesCS5D01G204300 chrUn 90.291 309 28 1 1203 1509 276916181 276916489 1.970000e-108 403.0
11 TraesCS5D01G204300 chrUn 90.291 309 28 1 1203 1509 276923611 276923919 1.970000e-108 403.0
12 TraesCS5D01G204300 chrUn 78.922 408 67 11 4045 4435 224616650 224617055 4.510000e-65 259.0
13 TraesCS5D01G204300 chrUn 78.676 408 68 11 4045 4435 249625480 249625885 2.100000e-63 254.0
14 TraesCS5D01G204300 chrUn 78.676 408 68 11 4045 4435 388402951 388403356 2.100000e-63 254.0
15 TraesCS5D01G204300 chrUn 85.776 232 20 5 765 983 31805105 31805336 2.730000e-57 233.0
16 TraesCS5D01G204300 chrUn 85.776 232 20 5 765 983 276915886 276916117 2.730000e-57 233.0
17 TraesCS5D01G204300 chrUn 85.776 232 20 5 765 983 276923316 276923547 2.730000e-57 233.0
18 TraesCS5D01G204300 chr2B 88.164 997 94 13 779 1764 775126571 775127554 0.000000e+00 1166.0
19 TraesCS5D01G204300 chr2B 80.000 270 44 8 5 266 615895212 615894945 1.670000e-44 191.0
20 TraesCS5D01G204300 chr2B 75.299 251 41 8 4040 4270 793812278 793812527 2.890000e-17 100.0
21 TraesCS5D01G204300 chr2A 84.965 572 61 8 765 1331 759853885 759853334 1.430000e-154 556.0
22 TraesCS5D01G204300 chr2A 81.893 243 40 4 34 273 460226832 460226591 7.700000e-48 202.0
23 TraesCS5D01G204300 chr2D 85.593 472 40 9 1349 1800 631896245 631896708 1.910000e-128 470.0
24 TraesCS5D01G204300 chr7D 89.416 274 22 4 1 272 236090783 236090515 5.630000e-89 339.0
25 TraesCS5D01G204300 chr7D 88.603 272 28 3 1 271 164633391 164633660 1.220000e-85 327.0
26 TraesCS5D01G204300 chr3A 89.011 273 25 3 1 273 729396514 729396247 2.620000e-87 333.0
27 TraesCS5D01G204300 chr3A 86.397 272 31 4 1 272 488628282 488628017 4.440000e-75 292.0
28 TraesCS5D01G204300 chr1D 86.813 273 24 5 1 272 110502091 110502352 1.240000e-75 294.0
29 TraesCS5D01G204300 chr1D 79.263 434 69 11 4020 4435 470797916 470797486 2.670000e-72 283.0
30 TraesCS5D01G204300 chr1D 84.982 273 22 6 1 271 488552248 488551993 4.510000e-65 259.0
31 TraesCS5D01G204300 chr7B 79.335 421 71 7 4045 4449 24414442 24414022 9.620000e-72 281.0
32 TraesCS5D01G204300 chr7B 75.510 245 40 8 4040 4265 605979502 605979745 8.040000e-18 102.0
33 TraesCS5D01G204300 chr6A 78.998 419 69 9 4033 4435 590096864 590097279 7.490000e-68 268.0
34 TraesCS5D01G204300 chr6B 78.802 434 64 19 4020 4432 57459347 57459773 2.690000e-67 267.0
35 TraesCS5D01G204300 chr6B 79.771 262 43 8 14 267 365738760 365739019 1.000000e-41 182.0
36 TraesCS5D01G204300 chr3B 76.400 250 40 7 4040 4270 828539628 828539379 2.870000e-22 117.0
37 TraesCS5D01G204300 chr3B 76.000 250 41 7 4040 4270 814212159 814211910 1.340000e-20 111.0
38 TraesCS5D01G204300 chr1B 76.400 250 40 7 4040 4270 491711209 491711458 2.870000e-22 117.0
39 TraesCS5D01G204300 chr4B 76.190 252 37 13 4040 4270 469009346 469009595 1.340000e-20 111.0
40 TraesCS5D01G204300 chr4B 76.000 250 41 7 4040 4270 574451254 574451503 1.340000e-20 111.0
41 TraesCS5D01G204300 chr4B 75.918 245 40 9 4040 4265 562613492 562613736 1.730000e-19 108.0
42 TraesCS5D01G204300 chr6D 91.111 45 3 1 1513 1557 14076816 14076859 4.900000e-05 60.2


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 TraesCS5D01G204300 chr5D 309674761 309679300 4539 False 8384.000000 8384 100.000000 1 4540 1 chr5D.!!$F1 4539
1 TraesCS5D01G204300 chr5B 354782291 354785742 3451 False 1757.666667 3445 95.011333 306 3835 3 chr5B.!!$F1 3529
2 TraesCS5D01G204300 chr5A 402904652 402909103 4451 False 2064.000000 3404 93.752667 299 4537 3 chr5A.!!$F1 4238
3 TraesCS5D01G204300 chrUn 31777638 31778840 1202 False 1192.000000 1192 85.112000 597 1763 1 chrUn.!!$F1 1166
4 TraesCS5D01G204300 chrUn 31805105 31805962 857 False 478.000000 723 87.826000 765 1763 2 chrUn.!!$F5 998
5 TraesCS5D01G204300 chrUn 276915886 276916489 603 False 318.000000 403 88.033500 765 1509 2 chrUn.!!$F6 744
6 TraesCS5D01G204300 chrUn 276923316 276923919 603 False 318.000000 403 88.033500 765 1509 2 chrUn.!!$F7 744
7 TraesCS5D01G204300 chr2B 775126571 775127554 983 False 1166.000000 1166 88.164000 779 1764 1 chr2B.!!$F1 985
8 TraesCS5D01G204300 chr2A 759853334 759853885 551 True 556.000000 556 84.965000 765 1331 1 chr2A.!!$R2 566

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
304 305 0.033228 CTGGAGATGCTCTAAGCCCG 59.967 60.000 0.00 0.00 41.51 6.13 F
1581 1679 0.373716 GCCTCATAAGGTTCAACGCG 59.626 55.000 3.53 3.53 45.34 6.01 F
1866 1964 1.459592 GCATTCGTCGTGTACAAGCTT 59.540 47.619 3.67 0.00 0.00 3.74 F
2637 2737 0.240945 CACCAATTCGAAGTGTGGGC 59.759 55.000 22.57 0.00 35.32 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1587 1685 0.032615 TGGTGCCTTGGAAGTGGTTT 60.033 50.000 0.00 0.0 0.00 3.27 R
2392 2490 0.035725 TGTAAGGAGAGGAGCGACGA 60.036 55.000 0.00 0.0 0.00 4.20 R
2707 2852 2.288948 ACAAAATGTGCATGACGGCAAT 60.289 40.909 0.00 0.0 46.93 3.56 R
4142 4505 0.107017 GCATGTCATGGGTGCTACCT 60.107 55.000 14.64 0.0 38.64 3.08 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 2.814280 GAGAAGGACAACGAGGACAA 57.186 50.000 0.00 0.00 0.00 3.18
20 21 2.405172 GAGAAGGACAACGAGGACAAC 58.595 52.381 0.00 0.00 0.00 3.32
21 22 1.760613 AGAAGGACAACGAGGACAACA 59.239 47.619 0.00 0.00 0.00 3.33
22 23 2.135933 GAAGGACAACGAGGACAACAG 58.864 52.381 0.00 0.00 0.00 3.16
23 24 0.249911 AGGACAACGAGGACAACAGC 60.250 55.000 0.00 0.00 0.00 4.40
24 25 1.557443 GGACAACGAGGACAACAGCG 61.557 60.000 0.00 0.00 0.00 5.18
25 26 0.596600 GACAACGAGGACAACAGCGA 60.597 55.000 0.00 0.00 0.00 4.93
26 27 0.033504 ACAACGAGGACAACAGCGAT 59.966 50.000 0.00 0.00 0.00 4.58
27 28 0.439985 CAACGAGGACAACAGCGATG 59.560 55.000 0.00 0.00 0.00 3.84
28 29 0.670546 AACGAGGACAACAGCGATGG 60.671 55.000 5.32 0.00 0.00 3.51
29 30 2.456119 CGAGGACAACAGCGATGGC 61.456 63.158 5.32 0.00 40.37 4.40
30 31 2.434884 AGGACAACAGCGATGGCG 60.435 61.111 5.32 0.00 46.35 5.69
31 32 3.499737 GGACAACAGCGATGGCGG 61.500 66.667 5.32 0.00 46.35 6.13
32 33 4.166011 GACAACAGCGATGGCGGC 62.166 66.667 5.32 0.00 46.35 6.53
58 59 3.175240 CGACTTCGCCGTGCTGAG 61.175 66.667 0.00 0.00 0.00 3.35
59 60 3.482783 GACTTCGCCGTGCTGAGC 61.483 66.667 0.00 0.00 0.00 4.26
68 69 2.472049 GTGCTGAGCGCGTTCTTC 59.528 61.111 23.51 14.84 43.27 2.87
69 70 2.738521 TGCTGAGCGCGTTCTTCC 60.739 61.111 23.51 11.90 43.27 3.46
70 71 2.433318 GCTGAGCGCGTTCTTCCT 60.433 61.111 23.51 2.58 0.00 3.36
71 72 2.734673 GCTGAGCGCGTTCTTCCTG 61.735 63.158 23.51 9.65 0.00 3.86
72 73 1.373497 CTGAGCGCGTTCTTCCTGT 60.373 57.895 23.51 0.00 0.00 4.00
73 74 0.109272 CTGAGCGCGTTCTTCCTGTA 60.109 55.000 23.51 0.54 0.00 2.74
74 75 0.109272 TGAGCGCGTTCTTCCTGTAG 60.109 55.000 23.51 0.00 0.00 2.74
75 76 0.109226 GAGCGCGTTCTTCCTGTAGT 60.109 55.000 16.26 0.00 0.00 2.73
76 77 0.109226 AGCGCGTTCTTCCTGTAGTC 60.109 55.000 8.43 0.00 0.00 2.59
77 78 0.109226 GCGCGTTCTTCCTGTAGTCT 60.109 55.000 8.43 0.00 0.00 3.24
78 79 1.131883 GCGCGTTCTTCCTGTAGTCTA 59.868 52.381 8.43 0.00 0.00 2.59
79 80 2.791849 GCGCGTTCTTCCTGTAGTCTAG 60.792 54.545 8.43 0.00 0.00 2.43
80 81 2.223294 CGCGTTCTTCCTGTAGTCTAGG 60.223 54.545 0.00 0.00 36.63 3.02
81 82 2.479901 GCGTTCTTCCTGTAGTCTAGGC 60.480 54.545 0.00 0.00 35.23 3.93
82 83 2.099427 CGTTCTTCCTGTAGTCTAGGCC 59.901 54.545 0.00 0.00 35.23 5.19
83 84 3.367321 GTTCTTCCTGTAGTCTAGGCCT 58.633 50.000 11.78 11.78 35.23 5.19
84 85 3.759815 TCTTCCTGTAGTCTAGGCCTT 57.240 47.619 12.58 0.00 35.23 4.35
85 86 4.062490 TCTTCCTGTAGTCTAGGCCTTT 57.938 45.455 12.58 0.00 35.23 3.11
86 87 5.202746 TCTTCCTGTAGTCTAGGCCTTTA 57.797 43.478 12.58 0.00 35.23 1.85
87 88 5.778542 TCTTCCTGTAGTCTAGGCCTTTAT 58.221 41.667 12.58 0.00 35.23 1.40
88 89 6.203072 TCTTCCTGTAGTCTAGGCCTTTATT 58.797 40.000 12.58 0.00 35.23 1.40
89 90 6.672657 TCTTCCTGTAGTCTAGGCCTTTATTT 59.327 38.462 12.58 0.00 35.23 1.40
90 91 6.886178 TCCTGTAGTCTAGGCCTTTATTTT 57.114 37.500 12.58 0.00 35.23 1.82
91 92 7.266905 TCCTGTAGTCTAGGCCTTTATTTTT 57.733 36.000 12.58 0.00 35.23 1.94
142 143 4.976224 ACTGTTTAAGTTGCCGAAGTTT 57.024 36.364 0.00 0.00 34.57 2.66
144 145 6.628919 ACTGTTTAAGTTGCCGAAGTTTAT 57.371 33.333 0.00 0.00 34.57 1.40
145 146 6.435428 ACTGTTTAAGTTGCCGAAGTTTATG 58.565 36.000 0.00 0.00 34.57 1.90
146 147 5.216648 TGTTTAAGTTGCCGAAGTTTATGC 58.783 37.500 0.00 0.00 0.00 3.14
147 148 4.428615 TTAAGTTGCCGAAGTTTATGCC 57.571 40.909 0.00 0.00 0.00 4.40
148 149 1.173913 AGTTGCCGAAGTTTATGCCC 58.826 50.000 0.00 0.00 0.00 5.36
149 150 0.885196 GTTGCCGAAGTTTATGCCCA 59.115 50.000 0.00 0.00 0.00 5.36
150 151 1.476488 GTTGCCGAAGTTTATGCCCAT 59.524 47.619 0.00 0.00 0.00 4.00
151 152 1.846007 TGCCGAAGTTTATGCCCATT 58.154 45.000 0.00 0.00 0.00 3.16
152 153 2.175202 TGCCGAAGTTTATGCCCATTT 58.825 42.857 0.00 0.00 0.00 2.32
153 154 2.094286 TGCCGAAGTTTATGCCCATTTG 60.094 45.455 0.00 0.00 0.00 2.32
154 155 2.539476 CCGAAGTTTATGCCCATTTGC 58.461 47.619 0.00 0.00 0.00 3.68
155 156 2.539476 CGAAGTTTATGCCCATTTGCC 58.461 47.619 0.00 0.00 0.00 4.52
156 157 2.094286 CGAAGTTTATGCCCATTTGCCA 60.094 45.455 0.00 0.00 0.00 4.92
157 158 3.616076 CGAAGTTTATGCCCATTTGCCAA 60.616 43.478 0.00 0.00 0.00 4.52
158 159 4.322567 GAAGTTTATGCCCATTTGCCAAA 58.677 39.130 0.00 0.00 0.00 3.28
159 160 4.573021 AGTTTATGCCCATTTGCCAAAT 57.427 36.364 0.00 0.00 0.00 2.32
160 161 5.690464 AGTTTATGCCCATTTGCCAAATA 57.310 34.783 1.66 0.00 0.00 1.40
161 162 6.059787 AGTTTATGCCCATTTGCCAAATAA 57.940 33.333 1.66 0.00 0.00 1.40
162 163 6.661777 AGTTTATGCCCATTTGCCAAATAAT 58.338 32.000 1.66 0.00 0.00 1.28
163 164 7.800092 AGTTTATGCCCATTTGCCAAATAATA 58.200 30.769 1.66 0.00 0.00 0.98
164 165 7.933033 AGTTTATGCCCATTTGCCAAATAATAG 59.067 33.333 1.66 0.00 0.00 1.73
165 166 4.070630 TGCCCATTTGCCAAATAATAGC 57.929 40.909 1.66 4.47 0.00 2.97
166 167 3.181456 TGCCCATTTGCCAAATAATAGCC 60.181 43.478 1.66 0.00 0.00 3.93
167 168 3.181456 GCCCATTTGCCAAATAATAGCCA 60.181 43.478 1.66 0.00 0.00 4.75
168 169 4.685575 GCCCATTTGCCAAATAATAGCCAA 60.686 41.667 1.66 0.00 0.00 4.52
169 170 5.435291 CCCATTTGCCAAATAATAGCCAAA 58.565 37.500 1.66 0.00 0.00 3.28
170 171 6.063404 CCCATTTGCCAAATAATAGCCAAAT 58.937 36.000 1.66 0.00 0.00 2.32
171 172 6.016943 CCCATTTGCCAAATAATAGCCAAATG 60.017 38.462 1.66 13.85 36.23 2.32
172 173 6.543100 CCATTTGCCAAATAATAGCCAAATGT 59.457 34.615 17.39 0.00 35.55 2.71
173 174 7.254863 CCATTTGCCAAATAATAGCCAAATGTC 60.255 37.037 17.39 0.00 35.55 3.06
174 175 6.543430 TTGCCAAATAATAGCCAAATGTCT 57.457 33.333 0.00 0.00 0.00 3.41
175 176 6.543430 TGCCAAATAATAGCCAAATGTCTT 57.457 33.333 0.00 0.00 0.00 3.01
176 177 7.652524 TGCCAAATAATAGCCAAATGTCTTA 57.347 32.000 0.00 0.00 0.00 2.10
177 178 8.248904 TGCCAAATAATAGCCAAATGTCTTAT 57.751 30.769 0.00 0.00 0.00 1.73
178 179 8.143193 TGCCAAATAATAGCCAAATGTCTTATG 58.857 33.333 0.00 0.00 0.00 1.90
179 180 8.359642 GCCAAATAATAGCCAAATGTCTTATGA 58.640 33.333 0.00 0.00 0.00 2.15
208 209 7.669089 AAAATTAAAAAGACTTCTGGGGTGA 57.331 32.000 0.00 0.00 0.00 4.02
209 210 6.650427 AATTAAAAAGACTTCTGGGGTGAC 57.350 37.500 0.00 0.00 0.00 3.67
245 246 4.646877 GAACCCGTTCGGCCCCAA 62.647 66.667 5.66 0.00 33.26 4.12
246 247 4.653888 AACCCGTTCGGCCCCAAG 62.654 66.667 5.66 0.00 33.26 3.61
266 267 1.850640 CGATTTTATCGCCGGGTCG 59.149 57.895 2.18 0.00 46.55 4.79
267 268 0.595567 CGATTTTATCGCCGGGTCGA 60.596 55.000 14.19 14.19 46.55 4.20
268 269 0.857287 GATTTTATCGCCGGGTCGAC 59.143 55.000 7.13 7.13 41.62 4.20
269 270 0.531311 ATTTTATCGCCGGGTCGACC 60.531 55.000 27.04 27.04 41.62 4.79
281 282 4.602159 TCGACCCCCGATTTTTCG 57.398 55.556 0.00 0.00 43.23 3.46
282 283 1.973760 TCGACCCCCGATTTTTCGA 59.026 52.632 0.00 0.00 43.23 3.71
283 284 0.108520 TCGACCCCCGATTTTTCGAG 60.109 55.000 0.00 0.00 43.23 4.04
284 285 1.087771 CGACCCCCGATTTTTCGAGG 61.088 60.000 0.00 0.49 41.76 4.63
285 286 1.374343 GACCCCCGATTTTTCGAGGC 61.374 60.000 0.00 0.00 34.64 4.70
286 287 1.077716 CCCCCGATTTTTCGAGGCT 60.078 57.895 0.00 0.00 34.64 4.58
287 288 1.376609 CCCCCGATTTTTCGAGGCTG 61.377 60.000 0.00 0.00 34.64 4.85
288 289 1.376609 CCCCGATTTTTCGAGGCTGG 61.377 60.000 0.00 0.00 34.64 4.85
289 290 0.392461 CCCGATTTTTCGAGGCTGGA 60.392 55.000 0.00 0.00 34.64 3.86
290 291 1.009829 CCGATTTTTCGAGGCTGGAG 58.990 55.000 0.00 0.00 34.64 3.86
291 292 1.405526 CCGATTTTTCGAGGCTGGAGA 60.406 52.381 0.00 0.00 34.64 3.71
292 293 2.555199 CGATTTTTCGAGGCTGGAGAT 58.445 47.619 0.00 0.00 34.64 2.75
293 294 2.286294 CGATTTTTCGAGGCTGGAGATG 59.714 50.000 0.00 0.00 34.64 2.90
294 295 1.453155 TTTTTCGAGGCTGGAGATGC 58.547 50.000 0.00 0.00 0.00 3.91
295 296 0.615331 TTTTCGAGGCTGGAGATGCT 59.385 50.000 0.00 0.00 0.00 3.79
296 297 0.176680 TTTCGAGGCTGGAGATGCTC 59.823 55.000 0.00 0.00 0.00 4.26
297 298 0.685785 TTCGAGGCTGGAGATGCTCT 60.686 55.000 0.00 0.00 0.00 4.09
304 305 0.033228 CTGGAGATGCTCTAAGCCCG 59.967 60.000 0.00 0.00 41.51 6.13
314 315 4.086457 TGCTCTAAGCCCGTGATATGATA 58.914 43.478 0.00 0.00 41.51 2.15
325 326 5.236478 CCCGTGATATGATAAACTTCCACAC 59.764 44.000 0.00 0.00 0.00 3.82
328 329 7.655732 CCGTGATATGATAAACTTCCACACATA 59.344 37.037 0.00 0.00 0.00 2.29
356 360 1.949465 CGTCCCCCTGCTATTGTAAC 58.051 55.000 0.00 0.00 0.00 2.50
404 420 9.811995 TTGTTAAGATGTACTGTAATTAGCGAT 57.188 29.630 0.00 0.00 0.00 4.58
428 444 2.106683 AACAGCCGCCAGTAATCGC 61.107 57.895 0.00 0.00 0.00 4.58
433 449 1.449601 CCGCCAGTAATCGCTTGGT 60.450 57.895 0.00 0.00 0.00 3.67
465 481 2.024369 TGTCACTCTGGGTCTAGCCATA 60.024 50.000 0.57 0.00 39.65 2.74
469 485 2.255406 CTCTGGGTCTAGCCATAGCAT 58.745 52.381 0.57 0.00 43.56 3.79
525 545 0.589223 GGTCATTTTCCACGACGCAA 59.411 50.000 0.00 0.00 0.00 4.85
546 568 4.508551 AGCAATACCAAGTCATCATCCA 57.491 40.909 0.00 0.00 0.00 3.41
548 570 4.641989 AGCAATACCAAGTCATCATCCAAC 59.358 41.667 0.00 0.00 0.00 3.77
549 571 4.398988 GCAATACCAAGTCATCATCCAACA 59.601 41.667 0.00 0.00 0.00 3.33
550 572 5.105797 GCAATACCAAGTCATCATCCAACAA 60.106 40.000 0.00 0.00 0.00 2.83
551 573 6.324819 CAATACCAAGTCATCATCCAACAAC 58.675 40.000 0.00 0.00 0.00 3.32
552 574 3.831323 ACCAAGTCATCATCCAACAACA 58.169 40.909 0.00 0.00 0.00 3.33
553 575 3.822735 ACCAAGTCATCATCCAACAACAG 59.177 43.478 0.00 0.00 0.00 3.16
554 576 3.366679 CCAAGTCATCATCCAACAACAGC 60.367 47.826 0.00 0.00 0.00 4.40
555 577 3.430042 AGTCATCATCCAACAACAGCT 57.570 42.857 0.00 0.00 0.00 4.24
556 578 3.341823 AGTCATCATCCAACAACAGCTC 58.658 45.455 0.00 0.00 0.00 4.09
557 579 3.076621 GTCATCATCCAACAACAGCTCA 58.923 45.455 0.00 0.00 0.00 4.26
558 580 3.503363 GTCATCATCCAACAACAGCTCAA 59.497 43.478 0.00 0.00 0.00 3.02
559 581 3.754850 TCATCATCCAACAACAGCTCAAG 59.245 43.478 0.00 0.00 0.00 3.02
560 582 3.490439 TCATCCAACAACAGCTCAAGA 57.510 42.857 0.00 0.00 0.00 3.02
561 583 3.819368 TCATCCAACAACAGCTCAAGAA 58.181 40.909 0.00 0.00 0.00 2.52
562 584 3.565482 TCATCCAACAACAGCTCAAGAAC 59.435 43.478 0.00 0.00 0.00 3.01
563 585 2.297701 TCCAACAACAGCTCAAGAACC 58.702 47.619 0.00 0.00 0.00 3.62
564 586 1.338020 CCAACAACAGCTCAAGAACCC 59.662 52.381 0.00 0.00 0.00 4.11
565 587 1.338020 CAACAACAGCTCAAGAACCCC 59.662 52.381 0.00 0.00 0.00 4.95
566 588 0.846693 ACAACAGCTCAAGAACCCCT 59.153 50.000 0.00 0.00 0.00 4.79
567 589 2.054799 ACAACAGCTCAAGAACCCCTA 58.945 47.619 0.00 0.00 0.00 3.53
568 590 2.441750 ACAACAGCTCAAGAACCCCTAA 59.558 45.455 0.00 0.00 0.00 2.69
569 591 3.117663 ACAACAGCTCAAGAACCCCTAAA 60.118 43.478 0.00 0.00 0.00 1.85
570 592 3.876309 ACAGCTCAAGAACCCCTAAAA 57.124 42.857 0.00 0.00 0.00 1.52
615 637 2.979813 CCAAATTAGCACTGCGTCAAAC 59.020 45.455 0.00 0.00 0.00 2.93
867 905 0.388659 TTTGTCCGCTTGCAATTGCT 59.611 45.000 29.37 0.00 42.66 3.91
1006 1075 3.495629 CGATCTTCATCACATCATGGGGT 60.496 47.826 0.00 0.00 0.00 4.95
1010 1079 1.212688 TCATCACATCATGGGGTGGAC 59.787 52.381 0.00 0.00 35.74 4.02
1059 1128 0.674895 CCTTACTGGTGTGCTGCTCC 60.675 60.000 0.00 1.75 0.00 4.70
1068 1137 1.375268 GTGCTGCTCCTGTGAGGTC 60.375 63.158 0.00 0.00 39.14 3.85
1332 1428 2.507102 ATCGACGCGGAGTTGCTG 60.507 61.111 12.47 0.00 34.17 4.41
1376 1472 1.024271 GTGAGCCTGCAGAACAACAA 58.976 50.000 17.39 0.00 0.00 2.83
1581 1679 0.373716 GCCTCATAAGGTTCAACGCG 59.626 55.000 3.53 3.53 45.34 6.01
1647 1745 2.418983 AGTTCGAGACCTTCAACGTC 57.581 50.000 0.00 0.00 0.00 4.34
1764 1862 2.284405 TTCTCCCCGTGTCCCTCC 60.284 66.667 0.00 0.00 0.00 4.30
1765 1863 4.753662 TCTCCCCGTGTCCCTCCG 62.754 72.222 0.00 0.00 0.00 4.63
1866 1964 1.459592 GCATTCGTCGTGTACAAGCTT 59.540 47.619 3.67 0.00 0.00 3.74
1919 2017 2.040544 CCATGGTCGGCAAGGACAC 61.041 63.158 2.57 0.00 38.70 3.67
2082 2180 3.479370 GTCACATCGACAGCTGCC 58.521 61.111 15.27 0.16 44.69 4.85
2118 2216 2.182030 CTGCGGTTCGAGGACCTC 59.818 66.667 11.87 11.87 37.56 3.85
2406 2504 1.517475 GCTTTCGTCGCTCCTCTCC 60.517 63.158 0.00 0.00 0.00 3.71
2415 2513 3.304123 CGTCGCTCCTCTCCTTACAATAG 60.304 52.174 0.00 0.00 0.00 1.73
2418 2516 4.580995 TCGCTCCTCTCCTTACAATAGAAG 59.419 45.833 0.00 0.00 0.00 2.85
2419 2517 4.580995 CGCTCCTCTCCTTACAATAGAAGA 59.419 45.833 0.00 0.00 0.00 2.87
2425 2523 6.435904 CCTCTCCTTACAATAGAAGATCGGAT 59.564 42.308 0.00 0.00 0.00 4.18
2449 2548 9.102757 GATGAAGAGAAATACAATCTGCTACAA 57.897 33.333 0.00 0.00 0.00 2.41
2453 2552 9.678260 AAGAGAAATACAATCTGCTACAAATCT 57.322 29.630 0.00 0.00 0.00 2.40
2454 2553 9.323985 AGAGAAATACAATCTGCTACAAATCTC 57.676 33.333 0.00 0.00 0.00 2.75
2455 2554 8.443953 AGAAATACAATCTGCTACAAATCTCC 57.556 34.615 0.00 0.00 0.00 3.71
2487 2586 7.867445 TTCAAACAAGAAAGTTTCAACACTC 57.133 32.000 17.65 0.00 39.55 3.51
2503 2602 5.294306 TCAACACTCGGAGCATCAAATTATC 59.706 40.000 4.58 0.00 36.25 1.75
2574 2674 5.431765 GTTCACTGGATGTATGGTCTGAAT 58.568 41.667 0.00 0.00 0.00 2.57
2635 2735 4.475944 GAATTCACCAATTCGAAGTGTGG 58.524 43.478 22.57 20.49 38.85 4.17
2636 2736 1.890876 TCACCAATTCGAAGTGTGGG 58.109 50.000 22.57 15.46 35.32 4.61
2637 2737 0.240945 CACCAATTCGAAGTGTGGGC 59.759 55.000 22.57 0.00 35.32 5.36
2639 2739 0.523072 CCAATTCGAAGTGTGGGCTG 59.477 55.000 22.57 4.09 0.00 4.85
2640 2740 0.523072 CAATTCGAAGTGTGGGCTGG 59.477 55.000 17.06 0.00 0.00 4.85
2641 2741 0.400213 AATTCGAAGTGTGGGCTGGA 59.600 50.000 3.35 0.00 0.00 3.86
2643 2743 1.271856 TTCGAAGTGTGGGCTGGATA 58.728 50.000 0.00 0.00 0.00 2.59
2644 2744 1.496060 TCGAAGTGTGGGCTGGATAT 58.504 50.000 0.00 0.00 0.00 1.63
2645 2745 1.138859 TCGAAGTGTGGGCTGGATATG 59.861 52.381 0.00 0.00 0.00 1.78
2646 2746 1.312815 GAAGTGTGGGCTGGATATGC 58.687 55.000 0.00 0.00 0.00 3.14
2672 2772 5.447624 AACCGTGGAAAGAAATTAGGTTG 57.552 39.130 0.00 0.00 39.03 3.77
2673 2773 4.466827 ACCGTGGAAAGAAATTAGGTTGT 58.533 39.130 0.00 0.00 0.00 3.32
2676 2776 5.918576 CCGTGGAAAGAAATTAGGTTGTTTC 59.081 40.000 0.00 0.00 39.07 2.78
2677 2777 6.460399 CCGTGGAAAGAAATTAGGTTGTTTCA 60.460 38.462 9.03 0.00 40.66 2.69
2679 2779 7.114811 CGTGGAAAGAAATTAGGTTGTTTCATG 59.885 37.037 9.03 0.00 40.66 3.07
2680 2780 6.928492 TGGAAAGAAATTAGGTTGTTTCATGC 59.072 34.615 9.03 0.00 40.66 4.06
2681 2781 6.928492 GGAAAGAAATTAGGTTGTTTCATGCA 59.072 34.615 9.03 0.00 40.66 3.96
2682 2782 7.095649 GGAAAGAAATTAGGTTGTTTCATGCAC 60.096 37.037 9.03 0.00 40.66 4.57
2683 2783 6.655078 AGAAATTAGGTTGTTTCATGCACT 57.345 33.333 0.00 0.00 36.92 4.40
2684 2784 7.054491 AGAAATTAGGTTGTTTCATGCACTT 57.946 32.000 0.00 0.00 36.92 3.16
2685 2785 7.500141 AGAAATTAGGTTGTTTCATGCACTTT 58.500 30.769 0.00 0.00 36.92 2.66
2686 2786 7.986889 AGAAATTAGGTTGTTTCATGCACTTTT 59.013 29.630 0.00 0.00 36.92 2.27
2687 2787 9.255304 GAAATTAGGTTGTTTCATGCACTTTTA 57.745 29.630 0.00 0.00 35.09 1.52
2688 2788 8.816640 AATTAGGTTGTTTCATGCACTTTTAG 57.183 30.769 0.00 0.00 0.00 1.85
2689 2789 7.575414 TTAGGTTGTTTCATGCACTTTTAGA 57.425 32.000 0.00 0.00 0.00 2.10
2690 2790 6.076981 AGGTTGTTTCATGCACTTTTAGAG 57.923 37.500 0.00 0.00 0.00 2.43
2691 2791 5.827797 AGGTTGTTTCATGCACTTTTAGAGA 59.172 36.000 0.00 0.00 0.00 3.10
2707 2852 7.719633 ACTTTTAGAGAACAATCTTGTGGCTAA 59.280 33.333 0.00 3.23 41.31 3.09
2774 2920 5.801947 GCTAACACATGCCAACTTTTATGAG 59.198 40.000 0.00 0.00 0.00 2.90
2820 2966 5.653330 TCCTGATTCTTTCTGCATGCATTAA 59.347 36.000 22.97 15.78 0.00 1.40
2832 2978 8.158169 TCTGCATGCATTAATTCTTAGTAAGG 57.842 34.615 22.97 2.91 0.00 2.69
2881 3030 5.968387 AGTAAAATGTTATTCCGAGCGAG 57.032 39.130 0.00 0.00 0.00 5.03
2891 3040 2.304751 TCCGAGCGAGGAAAATAACC 57.695 50.000 0.55 0.00 37.36 2.85
2892 3041 1.551430 TCCGAGCGAGGAAAATAACCA 59.449 47.619 0.55 0.00 37.36 3.67
3658 3807 8.098912 TGAGATTATATTCATCACACTCCCATG 58.901 37.037 0.00 0.00 0.00 3.66
3662 3811 3.786368 TTCATCACACTCCCATGTTGA 57.214 42.857 0.00 0.00 0.00 3.18
3691 3852 5.010112 TCCTTCACTCAGTGACTACAAAGAG 59.990 44.000 7.12 0.00 42.60 2.85
3806 3995 8.581057 TCGCTCTTATCTGATTGTAAGATTTC 57.419 34.615 0.00 0.00 36.61 2.17
3811 4000 9.464714 TCTTATCTGATTGTAAGATTTCGCTAC 57.535 33.333 0.00 0.00 35.92 3.58
3857 4048 1.076332 ATTAACGGTGAGCGTGCTTC 58.924 50.000 11.46 0.00 0.00 3.86
3870 4061 1.471501 CGTGCTTCGATCCAGGATTGA 60.472 52.381 14.89 14.89 42.86 2.57
3871 4062 2.804572 CGTGCTTCGATCCAGGATTGAT 60.805 50.000 18.95 0.00 42.86 2.57
3872 4063 3.209410 GTGCTTCGATCCAGGATTGATT 58.791 45.455 18.95 0.00 33.11 2.57
3873 4064 3.629398 GTGCTTCGATCCAGGATTGATTT 59.371 43.478 18.95 0.00 33.11 2.17
3901 4092 1.604604 TTTGAGAAACCGGCTGAAGG 58.395 50.000 0.00 0.00 0.00 3.46
3911 4102 1.151668 CGGCTGAAGGACTGTCTTTG 58.848 55.000 10.07 0.00 0.00 2.77
3948 4311 1.169661 TGCACAAAGAATCGCCGGTT 61.170 50.000 1.90 0.00 0.00 4.44
3993 4356 1.001020 ATGAACCCCTTGCGCATGA 60.001 52.632 23.56 2.86 0.00 3.07
4002 4365 2.839324 CTTGCGCATGACTCCAACGC 62.839 60.000 17.78 0.00 45.91 4.84
4110 4473 2.405892 CTTTGCGGACCTTCAAAGTG 57.594 50.000 19.75 5.15 42.34 3.16
4142 4505 2.018644 GCCATTGAAAGATCTGGCCGA 61.019 52.381 9.68 0.00 46.76 5.54
4159 4522 0.465705 CGAGGTAGCACCCATGACAT 59.534 55.000 0.00 0.00 39.75 3.06
4200 4563 2.183555 CCCCCGCACGACTAAGAC 59.816 66.667 0.00 0.00 0.00 3.01
4276 4639 4.489679 CATCTTCCAGATGTCGTCGATA 57.510 45.455 0.00 0.00 45.33 2.92
4277 4640 3.965292 TCTTCCAGATGTCGTCGATAC 57.035 47.619 0.00 0.00 0.00 2.24
4302 4665 2.297315 CCACTATCTGCATCCGCTTCTA 59.703 50.000 0.00 0.00 39.64 2.10
4303 4666 3.056250 CCACTATCTGCATCCGCTTCTAT 60.056 47.826 0.00 0.00 39.64 1.98
4396 4760 1.920574 CACAAGGATGTCATCGTCGTC 59.079 52.381 8.42 0.00 37.82 4.20
4397 4761 1.544246 ACAAGGATGTCATCGTCGTCA 59.456 47.619 8.42 0.00 33.41 4.35
4398 4762 2.166459 ACAAGGATGTCATCGTCGTCAT 59.834 45.455 8.42 0.00 33.41 3.06
4413 4777 4.433615 GTCGTCATGGCATCTCTTCTTAA 58.566 43.478 0.00 0.00 0.00 1.85
4414 4778 4.505922 GTCGTCATGGCATCTCTTCTTAAG 59.494 45.833 0.00 0.00 0.00 1.85
4435 4799 9.712305 CTTAAGAAGACTAGTTCTCAAATCCAA 57.288 33.333 0.00 0.00 35.65 3.53
4439 4803 6.426646 AGACTAGTTCTCAAATCCAACACT 57.573 37.500 0.00 0.00 0.00 3.55
4441 4805 5.308825 ACTAGTTCTCAAATCCAACACTGG 58.691 41.667 0.00 0.00 45.08 4.00
4512 4876 2.679837 CAGTTCTCAAATCCATCACCGG 59.320 50.000 0.00 0.00 0.00 5.28
4516 4880 0.038890 TCAAATCCATCACCGGCCAA 59.961 50.000 0.00 0.00 0.00 4.52
4537 4901 4.759516 AAAAAGCCAATTACATCGTCGT 57.240 36.364 0.00 0.00 0.00 4.34
4538 4902 4.759516 AAAAGCCAATTACATCGTCGTT 57.240 36.364 0.00 0.00 0.00 3.85
4539 4903 3.740044 AAGCCAATTACATCGTCGTTG 57.260 42.857 1.75 1.75 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.223971 TGTTGTCCTCGTTGTCCTTCTC 60.224 50.000 0.00 0.00 0.00 2.87
1 2 1.760613 TGTTGTCCTCGTTGTCCTTCT 59.239 47.619 0.00 0.00 0.00 2.85
2 3 2.135933 CTGTTGTCCTCGTTGTCCTTC 58.864 52.381 0.00 0.00 0.00 3.46
3 4 1.810412 GCTGTTGTCCTCGTTGTCCTT 60.810 52.381 0.00 0.00 0.00 3.36
4 5 0.249911 GCTGTTGTCCTCGTTGTCCT 60.250 55.000 0.00 0.00 0.00 3.85
5 6 1.557443 CGCTGTTGTCCTCGTTGTCC 61.557 60.000 0.00 0.00 0.00 4.02
6 7 0.596600 TCGCTGTTGTCCTCGTTGTC 60.597 55.000 0.00 0.00 0.00 3.18
7 8 0.033504 ATCGCTGTTGTCCTCGTTGT 59.966 50.000 0.00 0.00 0.00 3.32
8 9 0.439985 CATCGCTGTTGTCCTCGTTG 59.560 55.000 0.00 0.00 0.00 4.10
9 10 0.670546 CCATCGCTGTTGTCCTCGTT 60.671 55.000 0.00 0.00 0.00 3.85
10 11 1.079819 CCATCGCTGTTGTCCTCGT 60.080 57.895 0.00 0.00 0.00 4.18
11 12 2.456119 GCCATCGCTGTTGTCCTCG 61.456 63.158 0.00 0.00 0.00 4.63
12 13 2.456119 CGCCATCGCTGTTGTCCTC 61.456 63.158 0.00 0.00 0.00 3.71
13 14 2.434884 CGCCATCGCTGTTGTCCT 60.435 61.111 0.00 0.00 0.00 3.85
14 15 3.499737 CCGCCATCGCTGTTGTCC 61.500 66.667 0.00 0.00 0.00 4.02
15 16 4.166011 GCCGCCATCGCTGTTGTC 62.166 66.667 0.00 0.00 0.00 3.18
42 43 3.482783 GCTCAGCACGGCGAAGTC 61.483 66.667 16.62 2.31 0.00 3.01
53 54 2.433318 AGGAAGAACGCGCTCAGC 60.433 61.111 12.67 2.74 43.95 4.26
54 55 0.109272 TACAGGAAGAACGCGCTCAG 60.109 55.000 12.67 0.00 0.00 3.35
55 56 0.109272 CTACAGGAAGAACGCGCTCA 60.109 55.000 12.67 0.00 0.00 4.26
56 57 0.109226 ACTACAGGAAGAACGCGCTC 60.109 55.000 5.73 2.65 0.00 5.03
57 58 0.109226 GACTACAGGAAGAACGCGCT 60.109 55.000 5.73 0.00 0.00 5.92
58 59 0.109226 AGACTACAGGAAGAACGCGC 60.109 55.000 5.73 0.00 0.00 6.86
59 60 2.223294 CCTAGACTACAGGAAGAACGCG 60.223 54.545 3.53 3.53 34.91 6.01
60 61 2.479901 GCCTAGACTACAGGAAGAACGC 60.480 54.545 0.00 0.00 34.91 4.84
61 62 2.099427 GGCCTAGACTACAGGAAGAACG 59.901 54.545 0.00 0.00 34.91 3.95
62 63 3.367321 AGGCCTAGACTACAGGAAGAAC 58.633 50.000 1.29 0.00 34.91 3.01
63 64 3.759815 AGGCCTAGACTACAGGAAGAA 57.240 47.619 1.29 0.00 34.91 2.52
64 65 3.759815 AAGGCCTAGACTACAGGAAGA 57.240 47.619 5.16 0.00 34.91 2.87
65 66 6.487299 AATAAAGGCCTAGACTACAGGAAG 57.513 41.667 5.16 0.00 34.91 3.46
66 67 6.886178 AAATAAAGGCCTAGACTACAGGAA 57.114 37.500 5.16 0.00 34.91 3.36
67 68 6.886178 AAAATAAAGGCCTAGACTACAGGA 57.114 37.500 5.16 0.00 34.91 3.86
108 109 9.026074 GCAACTTAAACAGTTTTTACATAGCAA 57.974 29.630 3.25 0.00 43.89 3.91
109 110 7.650104 GGCAACTTAAACAGTTTTTACATAGCA 59.350 33.333 3.25 0.00 43.89 3.49
110 111 7.149031 CGGCAACTTAAACAGTTTTTACATAGC 60.149 37.037 3.25 1.13 43.89 2.97
111 112 8.071368 TCGGCAACTTAAACAGTTTTTACATAG 58.929 33.333 3.25 0.00 43.89 2.23
112 113 7.928103 TCGGCAACTTAAACAGTTTTTACATA 58.072 30.769 3.25 0.00 43.89 2.29
113 114 6.797454 TCGGCAACTTAAACAGTTTTTACAT 58.203 32.000 3.25 0.00 43.89 2.29
114 115 6.192234 TCGGCAACTTAAACAGTTTTTACA 57.808 33.333 3.25 0.00 43.89 2.41
115 116 6.748658 ACTTCGGCAACTTAAACAGTTTTTAC 59.251 34.615 3.25 0.00 43.89 2.01
116 117 6.854778 ACTTCGGCAACTTAAACAGTTTTTA 58.145 32.000 3.25 0.00 43.89 1.52
117 118 5.716094 ACTTCGGCAACTTAAACAGTTTTT 58.284 33.333 3.25 0.00 43.89 1.94
118 119 5.319140 ACTTCGGCAACTTAAACAGTTTT 57.681 34.783 3.25 0.00 43.89 2.43
119 120 4.976224 ACTTCGGCAACTTAAACAGTTT 57.024 36.364 3.49 3.49 43.89 2.66
121 122 4.976224 AAACTTCGGCAACTTAAACAGT 57.024 36.364 0.00 0.00 37.30 3.55
122 123 5.342259 GCATAAACTTCGGCAACTTAAACAG 59.658 40.000 0.00 0.00 0.00 3.16
123 124 5.216648 GCATAAACTTCGGCAACTTAAACA 58.783 37.500 0.00 0.00 0.00 2.83
124 125 4.619760 GGCATAAACTTCGGCAACTTAAAC 59.380 41.667 0.00 0.00 0.00 2.01
125 126 4.321378 GGGCATAAACTTCGGCAACTTAAA 60.321 41.667 0.00 0.00 0.00 1.52
126 127 3.191791 GGGCATAAACTTCGGCAACTTAA 59.808 43.478 0.00 0.00 0.00 1.85
127 128 2.750712 GGGCATAAACTTCGGCAACTTA 59.249 45.455 0.00 0.00 0.00 2.24
128 129 1.544246 GGGCATAAACTTCGGCAACTT 59.456 47.619 0.00 0.00 0.00 2.66
129 130 1.173913 GGGCATAAACTTCGGCAACT 58.826 50.000 0.00 0.00 0.00 3.16
130 131 0.885196 TGGGCATAAACTTCGGCAAC 59.115 50.000 0.00 0.00 0.00 4.17
131 132 1.846007 ATGGGCATAAACTTCGGCAA 58.154 45.000 0.00 0.00 0.00 4.52
132 133 1.846007 AATGGGCATAAACTTCGGCA 58.154 45.000 0.00 0.00 0.00 5.69
133 134 2.539476 CAAATGGGCATAAACTTCGGC 58.461 47.619 0.00 0.00 0.00 5.54
134 135 2.539476 GCAAATGGGCATAAACTTCGG 58.461 47.619 0.00 0.00 0.00 4.30
135 136 2.539476 GGCAAATGGGCATAAACTTCG 58.461 47.619 0.00 0.00 42.77 3.79
145 146 3.181456 TGGCTATTATTTGGCAAATGGGC 60.181 43.478 30.48 25.85 38.89 5.36
146 147 4.686191 TGGCTATTATTTGGCAAATGGG 57.314 40.909 30.48 18.88 35.82 4.00
151 152 6.543430 AGACATTTGGCTATTATTTGGCAA 57.457 33.333 0.00 0.00 44.88 4.52
152 153 6.543430 AAGACATTTGGCTATTATTTGGCA 57.457 33.333 0.00 0.00 36.96 4.92
153 154 8.359642 TCATAAGACATTTGGCTATTATTTGGC 58.640 33.333 0.00 0.00 29.55 4.52
183 184 7.985184 GTCACCCCAGAAGTCTTTTTAATTTTT 59.015 33.333 0.00 0.00 0.00 1.94
184 185 7.418597 GGTCACCCCAGAAGTCTTTTTAATTTT 60.419 37.037 0.00 0.00 0.00 1.82
185 186 6.041637 GGTCACCCCAGAAGTCTTTTTAATTT 59.958 38.462 0.00 0.00 0.00 1.82
186 187 5.538813 GGTCACCCCAGAAGTCTTTTTAATT 59.461 40.000 0.00 0.00 0.00 1.40
187 188 5.077564 GGTCACCCCAGAAGTCTTTTTAAT 58.922 41.667 0.00 0.00 0.00 1.40
188 189 4.466827 GGTCACCCCAGAAGTCTTTTTAA 58.533 43.478 0.00 0.00 0.00 1.52
189 190 4.094830 GGTCACCCCAGAAGTCTTTTTA 57.905 45.455 0.00 0.00 0.00 1.52
190 191 2.945456 GGTCACCCCAGAAGTCTTTTT 58.055 47.619 0.00 0.00 0.00 1.94
191 192 2.658807 GGTCACCCCAGAAGTCTTTT 57.341 50.000 0.00 0.00 0.00 2.27
228 229 4.646877 TTGGGGCCGAACGGGTTC 62.647 66.667 15.01 1.45 38.44 3.62
229 230 4.653888 CTTGGGGCCGAACGGGTT 62.654 66.667 15.01 0.00 38.44 4.11
249 250 0.857287 GTCGACCCGGCGATAAAATC 59.143 55.000 9.30 0.00 42.82 2.17
250 251 0.531311 GGTCGACCCGGCGATAAAAT 60.531 55.000 24.75 0.00 42.82 1.82
251 252 1.153588 GGTCGACCCGGCGATAAAA 60.154 57.895 24.75 0.00 42.82 1.52
252 253 2.495866 GGTCGACCCGGCGATAAA 59.504 61.111 24.75 0.00 42.82 1.40
265 266 2.380081 CTCGAAAAATCGGGGGTCG 58.620 57.895 0.00 0.00 40.90 4.79
270 271 0.392461 TCCAGCCTCGAAAAATCGGG 60.392 55.000 0.00 0.00 0.00 5.14
271 272 1.009829 CTCCAGCCTCGAAAAATCGG 58.990 55.000 0.00 0.00 0.00 4.18
272 273 2.010145 TCTCCAGCCTCGAAAAATCG 57.990 50.000 0.00 0.00 0.00 3.34
273 274 2.032675 GCATCTCCAGCCTCGAAAAATC 59.967 50.000 0.00 0.00 0.00 2.17
274 275 2.019984 GCATCTCCAGCCTCGAAAAAT 58.980 47.619 0.00 0.00 0.00 1.82
275 276 1.003580 AGCATCTCCAGCCTCGAAAAA 59.996 47.619 0.00 0.00 0.00 1.94
276 277 0.615331 AGCATCTCCAGCCTCGAAAA 59.385 50.000 0.00 0.00 0.00 2.29
277 278 0.176680 GAGCATCTCCAGCCTCGAAA 59.823 55.000 0.00 0.00 0.00 3.46
278 279 1.819229 GAGCATCTCCAGCCTCGAA 59.181 57.895 0.00 0.00 0.00 3.71
279 280 3.531283 GAGCATCTCCAGCCTCGA 58.469 61.111 0.00 0.00 0.00 4.04
290 291 3.056536 TCATATCACGGGCTTAGAGCATC 60.057 47.826 2.04 0.00 44.75 3.91
291 292 2.899900 TCATATCACGGGCTTAGAGCAT 59.100 45.455 2.04 0.00 44.75 3.79
292 293 2.316108 TCATATCACGGGCTTAGAGCA 58.684 47.619 2.04 0.00 44.75 4.26
293 294 3.601443 ATCATATCACGGGCTTAGAGC 57.399 47.619 0.00 0.00 41.46 4.09
294 295 6.692486 AGTTTATCATATCACGGGCTTAGAG 58.308 40.000 0.00 0.00 0.00 2.43
295 296 6.665992 AGTTTATCATATCACGGGCTTAGA 57.334 37.500 0.00 0.00 0.00 2.10
296 297 6.369065 GGAAGTTTATCATATCACGGGCTTAG 59.631 42.308 0.00 0.00 0.00 2.18
297 298 6.183361 TGGAAGTTTATCATATCACGGGCTTA 60.183 38.462 0.00 0.00 0.00 3.09
304 305 9.547753 AGTATGTGTGGAAGTTTATCATATCAC 57.452 33.333 0.00 0.00 0.00 3.06
314 315 5.049680 CGCAAGTAAGTATGTGTGGAAGTTT 60.050 40.000 0.00 0.00 0.00 2.66
356 360 8.752766 ACAAATTTGTTTGCTCTATCAGAATG 57.247 30.769 18.13 0.00 38.47 2.67
404 420 2.390306 TACTGGCGGCTGTTGCTTCA 62.390 55.000 25.67 4.83 39.59 3.02
428 444 3.822735 AGTGACATGTGGAATCAACCAAG 59.177 43.478 1.15 0.00 41.87 3.61
433 449 3.559811 CCCAGAGTGACATGTGGAATCAA 60.560 47.826 1.15 0.00 35.65 2.57
465 481 2.283298 CGATCTGTTGGTGCTTATGCT 58.717 47.619 1.96 0.00 40.48 3.79
469 485 0.392461 GGCCGATCTGTTGGTGCTTA 60.392 55.000 0.00 0.00 0.00 3.09
495 515 0.673437 AAAATGACCGTGTTGGCTGG 59.327 50.000 0.00 0.00 43.94 4.85
525 545 4.508551 TGGATGATGACTTGGTATTGCT 57.491 40.909 0.00 0.00 0.00 3.91
546 568 1.215423 AGGGGTTCTTGAGCTGTTGTT 59.785 47.619 0.00 0.00 0.00 2.83
548 570 2.859165 TAGGGGTTCTTGAGCTGTTG 57.141 50.000 0.00 0.00 0.00 3.33
549 571 3.876309 TTTAGGGGTTCTTGAGCTGTT 57.124 42.857 0.00 0.00 0.00 3.16
550 572 3.876309 TTTTAGGGGTTCTTGAGCTGT 57.124 42.857 0.00 0.00 0.00 4.40
569 591 2.804212 GCATGTGCCTCAAGCTGTTTTT 60.804 45.455 0.00 0.00 44.23 1.94
570 592 1.269936 GCATGTGCCTCAAGCTGTTTT 60.270 47.619 0.00 0.00 44.23 2.43
583 605 2.094078 TGCTAATTTGGAAGGCATGTGC 60.094 45.455 0.00 0.00 41.14 4.57
615 637 3.057245 TGGTGAACTGAACAGAGATCTCG 60.057 47.826 16.97 13.83 34.09 4.04
1006 1075 3.241530 AGCCACGGCAAGAGTCCA 61.242 61.111 11.35 0.00 44.88 4.02
1010 1079 3.429141 CAGCAGCCACGGCAAGAG 61.429 66.667 11.35 0.00 44.88 2.85
1059 1128 0.818296 CCTTACCTCGGACCTCACAG 59.182 60.000 0.00 0.00 0.00 3.66
1068 1137 1.712977 CGTCGTCCTCCTTACCTCGG 61.713 65.000 0.00 0.00 0.00 4.63
1290 1386 1.228094 GCTGAGGCCTAGGGATTGC 60.228 63.158 4.42 0.00 0.00 3.56
1293 1389 2.525381 CCGCTGAGGCCTAGGGAT 60.525 66.667 20.51 0.00 34.44 3.85
1581 1679 2.543031 GCCTTGGAAGTGGTTTTCGTTC 60.543 50.000 0.00 0.00 0.00 3.95
1587 1685 0.032615 TGGTGCCTTGGAAGTGGTTT 60.033 50.000 0.00 0.00 0.00 3.27
1647 1745 0.944386 CGGTGAGGTTGTTGTTGGAG 59.056 55.000 0.00 0.00 0.00 3.86
1765 1863 2.610532 GATTTGCTCTCCCCGGACCC 62.611 65.000 0.73 0.00 0.00 4.46
1766 1864 1.153147 GATTTGCTCTCCCCGGACC 60.153 63.158 0.73 0.00 0.00 4.46
1767 1865 0.035439 TTGATTTGCTCTCCCCGGAC 60.035 55.000 0.73 0.00 0.00 4.79
1768 1866 0.695924 TTTGATTTGCTCTCCCCGGA 59.304 50.000 0.73 0.00 0.00 5.14
1769 1867 1.098050 CTTTGATTTGCTCTCCCCGG 58.902 55.000 0.00 0.00 0.00 5.73
1866 1964 1.434188 TGTTCCTCTTCCTGGAGCAA 58.566 50.000 0.00 0.00 40.85 3.91
1919 2017 2.551270 GGTTGCTGCTGTCGAACG 59.449 61.111 0.00 0.00 0.00 3.95
2118 2216 3.068691 TCCGCGGGAGACTTGAGG 61.069 66.667 27.83 0.00 0.00 3.86
2301 2399 4.476410 GCGGCGCAGTAAAAGGCC 62.476 66.667 29.21 0.00 42.14 5.19
2388 2486 1.517475 GGAGAGGAGCGACGAAAGC 60.517 63.158 0.00 0.00 0.00 3.51
2391 2489 1.093159 GTAAGGAGAGGAGCGACGAA 58.907 55.000 0.00 0.00 0.00 3.85
2392 2490 0.035725 TGTAAGGAGAGGAGCGACGA 60.036 55.000 0.00 0.00 0.00 4.20
2393 2491 0.809385 TTGTAAGGAGAGGAGCGACG 59.191 55.000 0.00 0.00 0.00 5.12
2394 2492 3.884091 TCTATTGTAAGGAGAGGAGCGAC 59.116 47.826 0.00 0.00 0.00 5.19
2406 2504 8.572185 TCTCTTCATCCGATCTTCTATTGTAAG 58.428 37.037 0.00 0.00 0.00 2.34
2415 2513 8.600449 ATTGTATTTCTCTTCATCCGATCTTC 57.400 34.615 0.00 0.00 0.00 2.87
2418 2516 7.359933 GCAGATTGTATTTCTCTTCATCCGATC 60.360 40.741 0.00 0.00 0.00 3.69
2419 2517 6.426328 GCAGATTGTATTTCTCTTCATCCGAT 59.574 38.462 0.00 0.00 0.00 4.18
2425 2523 8.846943 TTTGTAGCAGATTGTATTTCTCTTCA 57.153 30.769 0.00 0.00 0.00 3.02
2449 2548 8.868522 TTCTTGTTTGAATCTATGTGGAGATT 57.131 30.769 0.00 0.00 46.57 2.40
2453 2552 8.463930 AACTTTCTTGTTTGAATCTATGTGGA 57.536 30.769 0.00 0.00 0.00 4.02
2454 2553 9.185192 GAAACTTTCTTGTTTGAATCTATGTGG 57.815 33.333 0.00 0.00 39.86 4.17
2455 2554 9.734620 TGAAACTTTCTTGTTTGAATCTATGTG 57.265 29.630 3.22 0.00 39.86 3.21
2487 2586 4.916983 TTTGGGATAATTTGATGCTCCG 57.083 40.909 0.00 0.00 0.00 4.63
2537 2636 6.576662 TCCAGTGAACGGATATAATCTCTC 57.423 41.667 0.00 0.00 0.00 3.20
2597 2697 4.611366 GTGAATTCTTGGCGTTTCTTTACG 59.389 41.667 7.05 0.00 44.09 3.18
2599 2699 4.580995 TGGTGAATTCTTGGCGTTTCTTTA 59.419 37.500 7.05 0.00 0.00 1.85
2636 2736 0.751643 ACGGTTTGGGCATATCCAGC 60.752 55.000 0.00 0.00 38.17 4.85
2637 2737 1.024271 CACGGTTTGGGCATATCCAG 58.976 55.000 0.00 0.00 38.17 3.86
2639 2739 0.106918 TCCACGGTTTGGGCATATCC 60.107 55.000 0.00 0.00 46.92 2.59
2640 2740 1.757682 TTCCACGGTTTGGGCATATC 58.242 50.000 0.00 0.00 46.92 1.63
2641 2741 2.099405 CTTTCCACGGTTTGGGCATAT 58.901 47.619 0.00 0.00 46.92 1.78
2643 2743 0.178975 TCTTTCCACGGTTTGGGCAT 60.179 50.000 0.00 0.00 46.92 4.40
2644 2744 0.395862 TTCTTTCCACGGTTTGGGCA 60.396 50.000 0.00 0.00 46.92 5.36
2645 2745 0.747852 TTTCTTTCCACGGTTTGGGC 59.252 50.000 0.00 0.00 46.92 5.36
2646 2746 3.744238 AATTTCTTTCCACGGTTTGGG 57.256 42.857 0.00 0.00 46.92 4.12
2666 2766 6.995686 TCTCTAAAAGTGCATGAAACAACCTA 59.004 34.615 0.00 0.00 0.00 3.08
2669 2769 6.972328 TGTTCTCTAAAAGTGCATGAAACAAC 59.028 34.615 0.00 0.00 0.00 3.32
2672 2772 8.078596 AGATTGTTCTCTAAAAGTGCATGAAAC 58.921 33.333 0.00 0.00 0.00 2.78
2673 2773 8.169977 AGATTGTTCTCTAAAAGTGCATGAAA 57.830 30.769 0.00 0.00 0.00 2.69
2676 2776 7.325338 CACAAGATTGTTCTCTAAAAGTGCATG 59.675 37.037 0.00 0.00 39.91 4.06
2677 2777 7.365741 CACAAGATTGTTCTCTAAAAGTGCAT 58.634 34.615 0.00 0.00 39.91 3.96
2679 2779 6.145535 CCACAAGATTGTTCTCTAAAAGTGC 58.854 40.000 0.00 0.00 39.91 4.40
2680 2780 6.016777 AGCCACAAGATTGTTCTCTAAAAGTG 60.017 38.462 0.00 0.00 39.91 3.16
2681 2781 6.064717 AGCCACAAGATTGTTCTCTAAAAGT 58.935 36.000 0.00 0.00 39.91 2.66
2682 2782 6.566197 AGCCACAAGATTGTTCTCTAAAAG 57.434 37.500 0.00 0.00 39.91 2.27
2683 2783 8.635765 ATTAGCCACAAGATTGTTCTCTAAAA 57.364 30.769 11.66 0.91 39.91 1.52
2684 2784 8.514594 CAATTAGCCACAAGATTGTTCTCTAAA 58.485 33.333 11.66 1.14 39.91 1.85
2685 2785 7.362056 GCAATTAGCCACAAGATTGTTCTCTAA 60.362 37.037 0.00 4.93 39.91 2.10
2686 2786 6.094048 GCAATTAGCCACAAGATTGTTCTCTA 59.906 38.462 0.00 0.00 39.91 2.43
2687 2787 5.105997 GCAATTAGCCACAAGATTGTTCTCT 60.106 40.000 0.00 0.00 39.91 3.10
2688 2788 5.098211 GCAATTAGCCACAAGATTGTTCTC 58.902 41.667 0.00 0.00 39.91 2.87
2689 2789 5.064441 GCAATTAGCCACAAGATTGTTCT 57.936 39.130 0.00 0.00 39.91 3.01
2707 2852 2.288948 ACAAAATGTGCATGACGGCAAT 60.289 40.909 0.00 0.00 46.93 3.56
2713 2858 4.263677 CGATTGCTACAAAATGTGCATGAC 59.736 41.667 0.00 0.00 35.51 3.06
2820 2966 8.910944 TCGAAGTAGCATAACCTTACTAAGAAT 58.089 33.333 0.00 0.00 0.00 2.40
2881 3030 5.351740 CGAGAAGAACCTCTGGTTATTTTCC 59.648 44.000 16.35 4.67 45.47 3.13
2891 3040 2.420372 TCATCGTCGAGAAGAACCTCTG 59.580 50.000 0.00 0.00 0.00 3.35
2892 3041 2.712709 TCATCGTCGAGAAGAACCTCT 58.287 47.619 0.00 0.00 0.00 3.69
3500 3649 4.180946 CTGTCGTCCTCCTCGCGG 62.181 72.222 6.13 0.00 0.00 6.46
3658 3807 4.876107 TCACTGAGTGAAGGAAAGTTCAAC 59.124 41.667 13.74 0.00 39.78 3.18
3662 3811 4.762289 AGTCACTGAGTGAAGGAAAGTT 57.238 40.909 18.01 0.00 44.49 2.66
3691 3852 8.023128 TGTGCAATGAAAAATTAAGACTAGAGC 58.977 33.333 0.00 0.00 0.00 4.09
3806 3995 4.555348 TTGGTTACAAAGTTTGGTAGCG 57.445 40.909 19.45 0.00 32.66 4.26
3880 4071 2.360801 CCTTCAGCCGGTTTCTCAAAAA 59.639 45.455 1.90 0.00 0.00 1.94
3911 4102 3.062234 GCAAAGGCTGGCATTTTGTGC 62.062 52.381 14.44 10.00 44.70 4.57
3961 4324 7.558604 CAAGGGGTTCATCAATATTGATTGTT 58.441 34.615 25.16 5.88 45.13 2.83
3993 4356 2.140792 AGGTGACAGGCGTTGGAGT 61.141 57.895 0.00 0.00 0.00 3.85
4033 4396 3.436704 TGAAGAGGTGATTTGTCGCATTC 59.563 43.478 0.00 0.00 0.00 2.67
4038 4401 2.076863 GGGTGAAGAGGTGATTTGTCG 58.923 52.381 0.00 0.00 0.00 4.35
4042 4405 1.339151 GCTCGGGTGAAGAGGTGATTT 60.339 52.381 0.00 0.00 36.31 2.17
4098 4461 6.447162 CCTTTGGTAAATCACTTTGAAGGTC 58.553 40.000 0.00 0.00 0.00 3.85
4110 4473 6.036577 TCTTTCAATGGCCTTTGGTAAATC 57.963 37.500 26.26 0.00 0.00 2.17
4142 4505 0.107017 GCATGTCATGGGTGCTACCT 60.107 55.000 14.64 0.00 38.64 3.08
4159 4522 1.137675 CAGATCTGGAGTTCGATGGCA 59.862 52.381 15.38 0.00 0.00 4.92
4200 4563 1.472728 CGTATGGTTTCCTTCTCCGGG 60.473 57.143 0.00 0.00 0.00 5.73
4276 4639 1.410517 CGGATGCAGATAGTGGTCTGT 59.589 52.381 5.87 0.00 45.80 3.41
4277 4640 1.871408 GCGGATGCAGATAGTGGTCTG 60.871 57.143 0.00 0.00 46.59 3.51
4302 4665 2.292918 TGTGGAGCTTGGGAGGTAGTAT 60.293 50.000 0.00 0.00 32.79 2.12
4303 4666 1.078159 TGTGGAGCTTGGGAGGTAGTA 59.922 52.381 0.00 0.00 32.79 1.82
4388 4752 1.035923 AGAGATGCCATGACGACGAT 58.964 50.000 0.00 0.00 0.00 3.73
4413 4777 6.931840 GTGTTGGATTTGAGAACTAGTCTTCT 59.068 38.462 0.00 0.00 36.41 2.85
4414 4778 6.931840 AGTGTTGGATTTGAGAACTAGTCTTC 59.068 38.462 0.00 0.00 36.41 2.87
4441 4805 2.353579 ACGACGTAATTGGCTTTATGGC 59.646 45.455 0.00 1.91 42.18 4.40
4516 4880 4.759516 ACGACGATGTAATTGGCTTTTT 57.240 36.364 0.00 0.00 31.58 1.94


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

AutoCloner maintained by Alex Coulton.