Multiple sequence alignment - TraesCS2D01G130600

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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 TraesCS2D01G130600 chr2D 100.000 4001 0 0 1 4001 75753010 75757010 0.000000e+00 7389.0
1 TraesCS2D01G130600 chr2D 90.938 629 28 8 3373 4001 75690538 75689939 0.000000e+00 819.0
2 TraesCS2D01G130600 chr2D 74.040 755 190 6 1979 2730 153002118 153001367 1.810000e-78 303.0
3 TraesCS2D01G130600 chr2D 73.926 698 167 14 1976 2667 74992341 74993029 2.370000e-67 267.0
4 TraesCS2D01G130600 chr2D 73.445 659 168 7 1970 2626 472468064 472467411 1.440000e-59 241.0
5 TraesCS2D01G130600 chr2B 90.049 2844 198 34 561 3360 116395936 116393134 0.000000e+00 3605.0
6 TraesCS2D01G130600 chr2B 93.968 630 21 5 3373 4001 116472526 116473139 0.000000e+00 937.0
7 TraesCS2D01G130600 chr2B 90.030 331 13 10 239 557 116396305 116395983 1.030000e-110 411.0
8 TraesCS2D01G130600 chr2B 73.460 682 168 12 1976 2652 114496213 114496886 1.110000e-60 244.0
9 TraesCS2D01G130600 chr2B 73.525 627 161 5 1970 2595 551634373 551633751 2.400000e-57 233.0
10 TraesCS2D01G130600 chr2B 73.077 702 169 17 1976 2671 114549936 114550623 8.650000e-57 231.0
11 TraesCS2D01G130600 chr2B 92.437 119 5 2 109 224 116396409 116396292 2.470000e-37 167.0
12 TraesCS2D01G130600 chr2A 91.033 2632 173 25 610 3213 75636341 75633745 0.000000e+00 3494.0
13 TraesCS2D01G130600 chr2A 95.426 634 24 1 3373 4001 75653471 75654104 0.000000e+00 1005.0
14 TraesCS2D01G130600 chr2A 90.541 296 14 6 271 557 75637127 75636837 2.920000e-101 379.0
15 TraesCS2D01G130600 chr2A 81.679 393 30 19 570 932 75640141 75639761 5.060000e-74 289.0
16 TraesCS2D01G130600 chr2A 92.857 196 13 1 1079 1274 75639526 75639332 2.350000e-72 283.0
17 TraesCS2D01G130600 chr2A 73.615 758 180 18 1982 2730 147541949 147541203 1.420000e-69 274.0
18 TraesCS2D01G130600 chr2A 73.862 681 167 11 1976 2652 74776755 74777428 1.100000e-65 261.0
19 TraesCS2D01G130600 chr2A 93.197 147 5 3 390 536 75641219 75641078 1.130000e-50 211.0
20 TraesCS2D01G130600 chr2A 92.437 119 5 3 109 224 75637378 75637261 2.470000e-37 167.0
21 TraesCS2D01G130600 chr2A 89.916 119 8 2 239 357 75641336 75641222 2.490000e-32 150.0
22 TraesCS2D01G130600 chr2A 100.000 36 0 0 239 274 75637274 75637239 2.580000e-07 67.6
23 TraesCS2D01G130600 chr7A 72.844 777 188 18 1970 2730 49990282 49989513 1.110000e-60 244.0
24 TraesCS2D01G130600 chr7A 87.129 101 13 0 11 111 58336203 58336103 9.090000e-22 115.0
25 TraesCS2D01G130600 chr7D 88.660 97 9 2 10 105 54659705 54659800 2.530000e-22 117.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G130600 chr2D 75753010 75757010 4000 False 7389.000000 7389 100.000000 1 4001 1 chr2D.!!$F2 4000
1 TraesCS2D01G130600 chr2D 75689939 75690538 599 True 819.000000 819 90.938000 3373 4001 1 chr2D.!!$R1 628
2 TraesCS2D01G130600 chr2D 153001367 153002118 751 True 303.000000 303 74.040000 1979 2730 1 chr2D.!!$R2 751
3 TraesCS2D01G130600 chr2D 74992341 74993029 688 False 267.000000 267 73.926000 1976 2667 1 chr2D.!!$F1 691
4 TraesCS2D01G130600 chr2D 472467411 472468064 653 True 241.000000 241 73.445000 1970 2626 1 chr2D.!!$R3 656
5 TraesCS2D01G130600 chr2B 116393134 116396409 3275 True 1394.333333 3605 90.838667 109 3360 3 chr2B.!!$R2 3251
6 TraesCS2D01G130600 chr2B 116472526 116473139 613 False 937.000000 937 93.968000 3373 4001 1 chr2B.!!$F3 628
7 TraesCS2D01G130600 chr2B 114496213 114496886 673 False 244.000000 244 73.460000 1976 2652 1 chr2B.!!$F1 676
8 TraesCS2D01G130600 chr2B 551633751 551634373 622 True 233.000000 233 73.525000 1970 2595 1 chr2B.!!$R1 625
9 TraesCS2D01G130600 chr2B 114549936 114550623 687 False 231.000000 231 73.077000 1976 2671 1 chr2B.!!$F2 695
10 TraesCS2D01G130600 chr2A 75653471 75654104 633 False 1005.000000 1005 95.426000 3373 4001 1 chr2A.!!$F2 628
11 TraesCS2D01G130600 chr2A 75633745 75641336 7591 True 630.075000 3494 91.457500 109 3213 8 chr2A.!!$R2 3104
12 TraesCS2D01G130600 chr2A 147541203 147541949 746 True 274.000000 274 73.615000 1982 2730 1 chr2A.!!$R1 748
13 TraesCS2D01G130600 chr2A 74776755 74777428 673 False 261.000000 261 73.862000 1976 2652 1 chr2A.!!$F1 676
14 TraesCS2D01G130600 chr7A 49989513 49990282 769 True 244.000000 244 72.844000 1970 2730 1 chr7A.!!$R1 760

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
451 4429 0.036765 TGGATTGGACGTACTGGTGC 60.037 55.0 0.00 0.0 0.00 5.01 F
1500 5933 0.035534 ACAGCAACCATGTCGGCATA 60.036 50.0 0.16 0.0 39.03 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 6638 0.103572 GTCGAAGGCGGCCAATACTA 59.896 55.0 23.09 0.0 35.76 1.82 R
3361 7836 0.175760 GTTGCAGATGCCGACCTAGA 59.824 55.0 1.72 0.0 41.18 2.43 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
21 22 4.361451 CTTGCTGCCGAAAGTGATAATT 57.639 40.909 0.00 0.00 0.00 1.40
23 24 3.609853 TGCTGCCGAAAGTGATAATTCT 58.390 40.909 0.00 0.00 0.00 2.40
25 26 4.570772 TGCTGCCGAAAGTGATAATTCTAC 59.429 41.667 0.00 0.00 0.00 2.59
26 27 4.024809 GCTGCCGAAAGTGATAATTCTACC 60.025 45.833 0.00 0.00 0.00 3.18
28 29 3.493503 GCCGAAAGTGATAATTCTACCGG 59.506 47.826 0.00 0.00 34.43 5.28
29 30 4.690122 CCGAAAGTGATAATTCTACCGGT 58.310 43.478 13.98 13.98 0.00 5.28
30 31 4.506654 CCGAAAGTGATAATTCTACCGGTG 59.493 45.833 19.93 7.59 0.00 4.94
31 32 4.025979 CGAAAGTGATAATTCTACCGGTGC 60.026 45.833 19.93 0.00 0.00 5.01
32 33 3.470645 AGTGATAATTCTACCGGTGCC 57.529 47.619 19.93 0.00 0.00 5.01
33 34 2.132762 GTGATAATTCTACCGGTGCCG 58.867 52.381 19.93 5.62 39.44 5.69
44 45 1.139308 CGGTGCCGGTATGTAACGA 59.861 57.895 1.90 0.00 32.42 3.85
45 46 1.141591 CGGTGCCGGTATGTAACGAC 61.142 60.000 1.90 0.00 32.42 4.34
46 47 0.108709 GGTGCCGGTATGTAACGACA 60.109 55.000 1.90 0.00 40.72 4.35
49 50 2.029970 GTGCCGGTATGTAACGACAATG 59.970 50.000 1.90 0.00 39.59 2.82
50 51 2.273557 GCCGGTATGTAACGACAATGT 58.726 47.619 1.90 0.00 39.59 2.71
51 52 3.119209 TGCCGGTATGTAACGACAATGTA 60.119 43.478 1.90 0.00 39.59 2.29
52 53 4.053295 GCCGGTATGTAACGACAATGTAT 58.947 43.478 1.90 0.00 39.59 2.29
53 54 4.149396 GCCGGTATGTAACGACAATGTATC 59.851 45.833 1.90 0.00 39.59 2.24
54 55 4.682860 CCGGTATGTAACGACAATGTATCC 59.317 45.833 0.00 0.00 39.59 2.59
55 56 5.283294 CGGTATGTAACGACAATGTATCCA 58.717 41.667 0.00 0.00 39.59 3.41
56 57 5.174398 CGGTATGTAACGACAATGTATCCAC 59.826 44.000 0.00 0.00 39.59 4.02
57 58 5.464389 GGTATGTAACGACAATGTATCCACC 59.536 44.000 0.00 0.00 39.59 4.61
59 60 5.092554 TGTAACGACAATGTATCCACCAT 57.907 39.130 0.00 0.00 30.68 3.55
60 61 5.113383 TGTAACGACAATGTATCCACCATC 58.887 41.667 0.00 0.00 30.68 3.51
61 62 3.194005 ACGACAATGTATCCACCATCC 57.806 47.619 0.00 0.00 0.00 3.51
63 64 1.873591 GACAATGTATCCACCATCCGC 59.126 52.381 0.00 0.00 0.00 5.54
64 65 1.238439 CAATGTATCCACCATCCGCC 58.762 55.000 0.00 0.00 0.00 6.13
65 66 1.140312 AATGTATCCACCATCCGCCT 58.860 50.000 0.00 0.00 0.00 5.52
66 67 1.140312 ATGTATCCACCATCCGCCTT 58.860 50.000 0.00 0.00 0.00 4.35
67 68 0.180171 TGTATCCACCATCCGCCTTG 59.820 55.000 0.00 0.00 0.00 3.61
71 72 2.440796 CACCATCCGCCTTGGCAT 60.441 61.111 12.45 0.00 37.81 4.40
73 74 2.124193 CCATCCGCCTTGGCATCA 60.124 61.111 12.45 0.00 37.80 3.07
74 75 1.753848 CCATCCGCCTTGGCATCAA 60.754 57.895 12.45 0.00 37.80 2.57
89 90 3.759527 CATCAAGATTGGTGCAGTGAG 57.240 47.619 0.00 0.00 31.79 3.51
90 91 2.936919 TCAAGATTGGTGCAGTGAGT 57.063 45.000 0.00 0.00 0.00 3.41
91 92 3.213206 TCAAGATTGGTGCAGTGAGTT 57.787 42.857 0.00 0.00 0.00 3.01
92 93 2.880268 TCAAGATTGGTGCAGTGAGTTG 59.120 45.455 0.00 0.00 0.00 3.16
93 94 1.242076 AGATTGGTGCAGTGAGTTGC 58.758 50.000 0.00 0.00 44.33 4.17
106 107 5.728898 GCAGTGAGTTGCAGTATAAAGATGC 60.729 44.000 0.00 0.00 43.53 3.91
107 108 4.568359 AGTGAGTTGCAGTATAAAGATGCG 59.432 41.667 0.00 0.00 42.92 4.73
108 109 4.566759 GTGAGTTGCAGTATAAAGATGCGA 59.433 41.667 0.00 0.00 42.92 5.10
109 110 5.063438 GTGAGTTGCAGTATAAAGATGCGAA 59.937 40.000 0.00 0.00 42.92 4.70
111 112 6.316140 TGAGTTGCAGTATAAAGATGCGAAAT 59.684 34.615 0.00 0.00 42.92 2.17
112 113 7.494298 TGAGTTGCAGTATAAAGATGCGAAATA 59.506 33.333 0.00 0.00 42.92 1.40
113 114 7.855545 AGTTGCAGTATAAAGATGCGAAATAG 58.144 34.615 0.00 0.00 42.92 1.73
115 116 7.177498 TGCAGTATAAAGATGCGAAATAGTG 57.823 36.000 0.00 0.00 42.92 2.74
186 4039 4.036734 TCACTCATTTCAAAGAACTGTGGC 59.963 41.667 0.00 0.00 0.00 5.01
213 4066 3.701800 GGACTCTCCCTCTCCAACT 57.298 57.895 0.00 0.00 0.00 3.16
214 4067 1.480789 GGACTCTCCCTCTCCAACTC 58.519 60.000 0.00 0.00 0.00 3.01
215 4068 1.006639 GGACTCTCCCTCTCCAACTCT 59.993 57.143 0.00 0.00 0.00 3.24
216 4069 2.242708 GGACTCTCCCTCTCCAACTCTA 59.757 54.545 0.00 0.00 0.00 2.43
217 4070 3.309265 GGACTCTCCCTCTCCAACTCTAA 60.309 52.174 0.00 0.00 0.00 2.10
218 4071 4.345854 GACTCTCCCTCTCCAACTCTAAA 58.654 47.826 0.00 0.00 0.00 1.85
219 4072 4.753186 ACTCTCCCTCTCCAACTCTAAAA 58.247 43.478 0.00 0.00 0.00 1.52
220 4073 5.346270 ACTCTCCCTCTCCAACTCTAAAAT 58.654 41.667 0.00 0.00 0.00 1.82
221 4074 6.503944 ACTCTCCCTCTCCAACTCTAAAATA 58.496 40.000 0.00 0.00 0.00 1.40
222 4075 6.609616 ACTCTCCCTCTCCAACTCTAAAATAG 59.390 42.308 0.00 0.00 0.00 1.73
223 4076 5.364157 TCTCCCTCTCCAACTCTAAAATAGC 59.636 44.000 0.00 0.00 0.00 2.97
224 4077 5.281314 TCCCTCTCCAACTCTAAAATAGCT 58.719 41.667 0.00 0.00 0.00 3.32
225 4078 5.726793 TCCCTCTCCAACTCTAAAATAGCTT 59.273 40.000 0.00 0.00 0.00 3.74
226 4079 6.901300 TCCCTCTCCAACTCTAAAATAGCTTA 59.099 38.462 0.00 0.00 0.00 3.09
227 4080 6.987404 CCCTCTCCAACTCTAAAATAGCTTAC 59.013 42.308 0.00 0.00 0.00 2.34
228 4081 6.987404 CCTCTCCAACTCTAAAATAGCTTACC 59.013 42.308 0.00 0.00 0.00 2.85
229 4082 6.885922 TCTCCAACTCTAAAATAGCTTACCC 58.114 40.000 0.00 0.00 0.00 3.69
230 4083 5.667466 TCCAACTCTAAAATAGCTTACCCG 58.333 41.667 0.00 0.00 0.00 5.28
231 4084 4.272748 CCAACTCTAAAATAGCTTACCCGC 59.727 45.833 0.00 0.00 0.00 6.13
232 4085 4.748277 ACTCTAAAATAGCTTACCCGCA 57.252 40.909 0.00 0.00 0.00 5.69
233 4086 5.093849 ACTCTAAAATAGCTTACCCGCAA 57.906 39.130 0.00 0.00 0.00 4.85
234 4087 5.493809 ACTCTAAAATAGCTTACCCGCAAA 58.506 37.500 0.00 0.00 0.00 3.68
235 4088 5.941647 ACTCTAAAATAGCTTACCCGCAAAA 59.058 36.000 0.00 0.00 0.00 2.44
236 4089 6.431852 ACTCTAAAATAGCTTACCCGCAAAAA 59.568 34.615 0.00 0.00 0.00 1.94
331 4299 2.143876 CCCCCTTGTATGGGTCAAAG 57.856 55.000 0.00 0.00 45.70 2.77
345 4313 1.181098 TCAAAGCAAAGGAGCAGCCC 61.181 55.000 0.00 0.00 37.37 5.19
359 4327 1.478288 GCAGCCCAGCCTCAAGATTAT 60.478 52.381 0.00 0.00 0.00 1.28
388 4357 7.992180 AGCAAACAGAAAACAATAAAGACTG 57.008 32.000 0.00 0.00 0.00 3.51
392 4361 6.942532 ACAGAAAACAATAAAGACTGCAGA 57.057 33.333 23.35 0.00 0.00 4.26
451 4429 0.036765 TGGATTGGACGTACTGGTGC 60.037 55.000 0.00 0.00 0.00 5.01
487 4465 6.969993 ACAACAGTGTATATTTTGGTTGGT 57.030 33.333 0.00 0.00 38.66 3.67
489 4467 7.206687 ACAACAGTGTATATTTTGGTTGGTTG 58.793 34.615 0.00 0.00 38.66 3.77
493 4471 7.070074 ACAGTGTATATTTTGGTTGGTTGGAAA 59.930 33.333 0.00 0.00 0.00 3.13
554 4532 3.449737 ACGGATAAAGACGGGATGAAAGA 59.550 43.478 0.00 0.00 0.00 2.52
557 4535 4.383770 GGATAAAGACGGGATGAAAGACCA 60.384 45.833 0.00 0.00 0.00 4.02
559 4537 0.250513 AGACGGGATGAAAGACCAGC 59.749 55.000 0.00 0.00 0.00 4.85
560 4538 0.744771 GACGGGATGAAAGACCAGCC 60.745 60.000 0.00 0.00 41.63 4.85
561 4539 1.815421 CGGGATGAAAGACCAGCCG 60.815 63.158 0.00 0.00 43.19 5.52
562 4540 1.299976 GGGATGAAAGACCAGCCGT 59.700 57.895 0.00 0.00 43.19 5.68
594 4619 4.990426 GTGATTGCTTGCAACACCTTAAAT 59.010 37.500 19.95 2.33 0.00 1.40
595 4620 6.015519 AGTGATTGCTTGCAACACCTTAAATA 60.016 34.615 23.53 0.00 32.76 1.40
596 4621 6.813152 GTGATTGCTTGCAACACCTTAAATAT 59.187 34.615 19.95 1.36 0.00 1.28
632 5054 2.634453 TGTGGCTGATCTGTTCTCTTGA 59.366 45.455 1.27 0.00 0.00 3.02
732 5154 4.350346 GCATCGCATGTTAACTTATTGCA 58.650 39.130 7.22 0.00 32.94 4.08
738 5160 5.163864 CGCATGTTAACTTATTGCAGTCTCA 60.164 40.000 7.22 0.00 32.94 3.27
816 5238 0.533755 GGCCACGCATTCAGATAGCT 60.534 55.000 0.00 0.00 0.00 3.32
844 5267 1.298602 GCATGGTCGCATCATACACA 58.701 50.000 0.00 0.00 0.00 3.72
856 5279 4.202080 GCATCATACACATGACTTTGGCAT 60.202 41.667 0.00 0.00 43.89 4.40
857 5280 5.680408 GCATCATACACATGACTTTGGCATT 60.680 40.000 0.00 0.00 43.89 3.56
859 5282 5.008980 TCATACACATGACTTTGGCATTCA 58.991 37.500 0.00 0.00 36.22 2.57
860 5283 3.928727 ACACATGACTTTGGCATTCAG 57.071 42.857 0.00 0.00 0.00 3.02
862 5285 4.084287 ACACATGACTTTGGCATTCAGAT 58.916 39.130 0.00 0.00 0.00 2.90
863 5286 5.255687 ACACATGACTTTGGCATTCAGATA 58.744 37.500 0.00 0.00 0.00 1.98
864 5287 5.356190 ACACATGACTTTGGCATTCAGATAG 59.644 40.000 0.00 0.00 0.00 2.08
865 5288 4.337555 ACATGACTTTGGCATTCAGATAGC 59.662 41.667 0.00 0.00 0.00 2.97
866 5289 4.226427 TGACTTTGGCATTCAGATAGCT 57.774 40.909 0.00 0.00 0.00 3.32
902 5332 4.756642 TGTACTTGTACGTGTGTAGTAGCT 59.243 41.667 0.00 0.00 0.00 3.32
908 5338 6.688637 TGTACGTGTGTAGTAGCTGAATAT 57.311 37.500 0.00 0.00 0.00 1.28
924 5354 6.424812 AGCTGAATATTGCAAACAACTTTTCC 59.575 34.615 1.71 0.00 38.99 3.13
930 5360 3.855858 TGCAAACAACTTTTCCCACTTC 58.144 40.909 0.00 0.00 0.00 3.01
931 5361 3.194861 GCAAACAACTTTTCCCACTTCC 58.805 45.455 0.00 0.00 0.00 3.46
932 5362 3.368948 GCAAACAACTTTTCCCACTTCCA 60.369 43.478 0.00 0.00 0.00 3.53
933 5363 4.683129 GCAAACAACTTTTCCCACTTCCAT 60.683 41.667 0.00 0.00 0.00 3.41
934 5364 4.670896 AACAACTTTTCCCACTTCCATG 57.329 40.909 0.00 0.00 0.00 3.66
935 5365 3.909732 ACAACTTTTCCCACTTCCATGA 58.090 40.909 0.00 0.00 0.00 3.07
936 5366 4.285863 ACAACTTTTCCCACTTCCATGAA 58.714 39.130 0.00 0.00 0.00 2.57
937 5367 4.342092 ACAACTTTTCCCACTTCCATGAAG 59.658 41.667 0.00 2.40 44.37 3.02
938 5368 2.893489 ACTTTTCCCACTTCCATGAAGC 59.107 45.455 3.82 0.00 42.79 3.86
939 5369 2.978156 TTTCCCACTTCCATGAAGCT 57.022 45.000 3.82 0.00 42.79 3.74
940 5370 4.202567 ACTTTTCCCACTTCCATGAAGCTA 60.203 41.667 3.82 0.00 42.79 3.32
941 5371 3.634397 TTCCCACTTCCATGAAGCTAG 57.366 47.619 3.82 0.00 42.79 3.42
942 5372 2.832838 TCCCACTTCCATGAAGCTAGA 58.167 47.619 3.82 0.00 42.79 2.43
943 5373 3.387962 TCCCACTTCCATGAAGCTAGAT 58.612 45.455 3.82 0.00 42.79 1.98
944 5374 3.389329 TCCCACTTCCATGAAGCTAGATC 59.611 47.826 3.82 0.00 42.79 2.75
945 5375 3.388308 CCACTTCCATGAAGCTAGATCG 58.612 50.000 3.82 0.00 42.79 3.69
946 5376 3.181471 CCACTTCCATGAAGCTAGATCGT 60.181 47.826 3.82 0.00 42.79 3.73
947 5377 4.437239 CACTTCCATGAAGCTAGATCGTT 58.563 43.478 3.82 0.00 42.79 3.85
948 5378 5.451937 CCACTTCCATGAAGCTAGATCGTTA 60.452 44.000 3.82 0.00 42.79 3.18
954 5384 3.305720 TGAAGCTAGATCGTTACCCCAT 58.694 45.455 0.00 0.00 0.00 4.00
958 5388 2.364324 GCTAGATCGTTACCCCATCACA 59.636 50.000 0.00 0.00 0.00 3.58
963 5393 2.468915 TCGTTACCCCATCACATACCA 58.531 47.619 0.00 0.00 0.00 3.25
965 5395 3.118555 TCGTTACCCCATCACATACCAAG 60.119 47.826 0.00 0.00 0.00 3.61
970 5400 1.401552 CCCATCACATACCAAGTTGCG 59.598 52.381 0.00 0.00 0.00 4.85
979 5409 1.220749 CCAAGTTGCGGCCTAGCTA 59.779 57.895 0.00 0.00 38.13 3.32
980 5410 0.811616 CCAAGTTGCGGCCTAGCTAG 60.812 60.000 14.20 14.20 38.13 3.42
981 5411 1.153349 AAGTTGCGGCCTAGCTAGC 60.153 57.895 15.74 6.62 38.13 3.42
982 5412 1.617947 AAGTTGCGGCCTAGCTAGCT 61.618 55.000 23.12 23.12 38.13 3.32
983 5413 1.884926 GTTGCGGCCTAGCTAGCTG 60.885 63.158 27.68 16.13 39.73 4.24
984 5414 2.359169 TTGCGGCCTAGCTAGCTGT 61.359 57.895 27.68 4.38 38.92 4.40
986 5416 1.287503 GCGGCCTAGCTAGCTGTAG 59.712 63.158 27.68 17.00 38.92 2.74
987 5417 1.457009 GCGGCCTAGCTAGCTGTAGT 61.457 60.000 27.68 2.70 38.92 2.73
989 5419 1.693627 GGCCTAGCTAGCTGTAGTGA 58.306 55.000 27.68 4.87 0.00 3.41
992 5422 1.604755 CCTAGCTAGCTGTAGTGACGG 59.395 57.143 27.68 9.97 34.77 4.79
998 5428 2.202623 CTGTAGTGACGGCTCCGC 60.203 66.667 8.41 2.21 44.19 5.54
999 5429 3.701604 CTGTAGTGACGGCTCCGCC 62.702 68.421 8.41 0.00 46.75 6.13
1011 5441 1.731720 GCTCCGCCATGATAATCCTC 58.268 55.000 0.00 0.00 0.00 3.71
1028 5458 4.219392 TCCTCCATAGATCCATCCTTGT 57.781 45.455 0.00 0.00 0.00 3.16
1034 5464 6.620429 TCCATAGATCCATCCTTGTGTACTA 58.380 40.000 0.00 0.00 0.00 1.82
1036 5466 6.267699 CCATAGATCCATCCTTGTGTACTACA 59.732 42.308 0.00 0.00 37.56 2.74
1047 5477 4.123497 TGTGTACTACATGTGCCTCATC 57.877 45.455 9.11 0.00 34.09 2.92
1076 5506 1.140852 CCTTGGCCCGAATCATGTAGA 59.859 52.381 0.00 0.00 0.00 2.59
1077 5507 2.487934 CTTGGCCCGAATCATGTAGAG 58.512 52.381 0.00 0.00 0.00 2.43
1132 5565 2.203126 GCTTCCAGGGAGCCGATG 60.203 66.667 8.90 0.00 0.00 3.84
1323 5756 2.973899 GACAAGGAGAGCAGCGGA 59.026 61.111 0.00 0.00 0.00 5.54
1347 5780 1.140134 TGGCCTTCTTTGTAGCCCCT 61.140 55.000 3.32 0.00 45.14 4.79
1455 5888 2.507324 GCCGAGCTCGACACCTTC 60.507 66.667 36.59 12.30 43.02 3.46
1500 5933 0.035534 ACAGCAACCATGTCGGCATA 60.036 50.000 0.16 0.00 39.03 3.14
1509 5942 2.473816 CATGTCGGCATAGACGTCAAT 58.526 47.619 19.50 0.00 43.70 2.57
1605 6038 0.979665 ATAGTGGGGATCCGATGCAG 59.020 55.000 5.45 0.00 35.24 4.41
1617 6050 1.812922 GATGCAGCTGTGGGTCGAG 60.813 63.158 16.64 0.00 0.00 4.04
1631 6064 2.464865 GGTCGAGTATGATGCACAGAC 58.535 52.381 0.00 0.00 40.55 3.51
1650 6083 0.891373 CCACACAGGTCATCTCGACT 59.109 55.000 0.00 0.00 44.70 4.18
1651 6084 1.135257 CCACACAGGTCATCTCGACTC 60.135 57.143 0.00 0.00 44.70 3.36
1695 6128 0.096976 CTCGCAGGCCATTGTTTACG 59.903 55.000 5.01 0.00 0.00 3.18
1713 6146 2.529744 GGCCACCACCAACCTCTCT 61.530 63.158 0.00 0.00 0.00 3.10
1723 6156 1.277273 CCAACCTCTCTGATGTGCTCA 59.723 52.381 0.00 0.00 0.00 4.26
1838 6271 1.135315 CCCGGCAATCAACATCACAAG 60.135 52.381 0.00 0.00 0.00 3.16
1869 6302 0.460722 TGTTTCGTGGTCGTCAGGAA 59.539 50.000 10.70 10.70 45.17 3.36
1890 6323 2.012673 GCTCGATCCAAAGTCTTGCAT 58.987 47.619 0.00 0.00 0.00 3.96
1924 6357 1.965930 GCCACCGCAGTGTTCATCA 60.966 57.895 0.00 0.00 42.88 3.07
1967 6400 2.561733 CTTCTCGTACGAAGGCATCA 57.438 50.000 20.00 0.00 37.37 3.07
2049 6482 3.937814 CAAGGACTTGTACCATGCTACA 58.062 45.455 3.93 0.00 35.92 2.74
2073 6506 6.641169 GAAGGATTCAAGAACAAGAACCTT 57.359 37.500 0.00 0.00 46.62 3.50
2125 6558 2.508751 GGAGTGCTCCCCGTATCCC 61.509 68.421 6.98 0.00 43.94 3.85
2199 6638 1.445582 GTTCATCGCCGAGGTCGTT 60.446 57.895 0.00 0.00 37.74 3.85
2499 6941 1.657751 GGCTCGGTGATTTTGGCCTC 61.658 60.000 3.32 0.00 36.96 4.70
2643 7086 2.554032 CGGCACATTTCTTCTTGAGGTT 59.446 45.455 0.00 0.00 0.00 3.50
2743 7186 0.310854 CAACGGAACCCTCTTGCAAC 59.689 55.000 0.00 0.00 0.00 4.17
2757 7200 3.072330 TCTTGCAACCTATGGACACAAGA 59.928 43.478 0.00 12.23 36.59 3.02
2781 7224 5.667626 ACTCCATGGTAACTATGACAAGGAT 59.332 40.000 12.58 0.00 31.27 3.24
2782 7225 5.928976 TCCATGGTAACTATGACAAGGATG 58.071 41.667 12.58 0.00 37.61 3.51
2790 7233 1.293062 ATGACAAGGATGAGGCCAGT 58.707 50.000 5.01 0.00 0.00 4.00
2853 7296 1.378911 TGCGAGGCCAAGCATGAAT 60.379 52.632 19.33 0.00 38.59 2.57
2872 7315 4.777366 TGAATCAAGTCATGGAGTACCTCA 59.223 41.667 0.00 0.00 37.04 3.86
2873 7316 5.105187 TGAATCAAGTCATGGAGTACCTCAG 60.105 44.000 0.00 0.00 37.04 3.35
2874 7317 3.779444 TCAAGTCATGGAGTACCTCAGT 58.221 45.455 0.00 0.00 37.04 3.41
2883 7326 2.291024 GGAGTACCTCAGTGGAGAGACA 60.291 54.545 0.00 0.00 44.26 3.41
2884 7327 3.422796 GAGTACCTCAGTGGAGAGACAA 58.577 50.000 0.00 0.00 44.26 3.18
2896 7339 1.813786 GAGAGACAACGCTACCAGAGT 59.186 52.381 0.00 0.00 0.00 3.24
2910 7353 0.751277 CAGAGTTGGCACCCACACAA 60.751 55.000 0.00 0.00 30.78 3.33
2934 7377 2.686558 ACAACGTCAACATGATGCAC 57.313 45.000 0.00 0.00 36.89 4.57
2949 7392 0.770499 TGCACATCAGAGGGTTTCCA 59.230 50.000 0.00 0.00 34.83 3.53
2958 7401 2.637872 CAGAGGGTTTCCAGACCTAACA 59.362 50.000 0.00 0.00 39.71 2.41
3016 7462 3.002656 GCGATGATGACCTATGTTTGTGG 59.997 47.826 0.00 0.00 0.00 4.17
3027 7473 8.735315 TGACCTATGTTTGTGGTGTTTAATATG 58.265 33.333 0.00 0.00 33.74 1.78
3053 7512 4.350368 TGTACTTGCATCTGAAGGAACA 57.650 40.909 0.00 0.00 0.00 3.18
3056 7515 4.623932 ACTTGCATCTGAAGGAACAGTA 57.376 40.909 0.00 0.00 38.79 2.74
3062 7521 4.865365 GCATCTGAAGGAACAGTAGTGTAC 59.135 45.833 3.00 0.39 35.08 2.90
3063 7522 5.566826 GCATCTGAAGGAACAGTAGTGTACA 60.567 44.000 3.00 0.00 35.08 2.90
3118 7577 5.081315 AGTAGACTTAGTATGATGCCCCT 57.919 43.478 0.00 0.00 0.00 4.79
3135 7598 8.733080 GATGCCCCTAGGGAATAGCAATCAAT 62.733 46.154 30.78 13.80 42.34 2.57
3139 7602 6.070656 CCCTAGGGAATAGCAATCAATTGAA 58.929 40.000 24.99 0.00 37.43 2.69
3154 7617 6.849588 TCAATTGAACCGATCAGATGTATG 57.150 37.500 5.45 0.00 39.77 2.39
3171 7634 3.838317 TGTATGAGCCCTCTGTTGTAACT 59.162 43.478 0.00 0.00 0.00 2.24
3176 7639 3.679389 AGCCCTCTGTTGTAACTTGATG 58.321 45.455 0.00 0.00 0.00 3.07
3195 7658 4.947388 TGATGTGGTTATTTTCACTAGGGC 59.053 41.667 0.00 0.00 35.15 5.19
3228 7693 1.953559 TGTGACACTCAACAGCCTTC 58.046 50.000 7.20 0.00 0.00 3.46
3243 7708 2.208431 GCCTTCTGCTAGCATAGTGTG 58.792 52.381 19.72 5.38 41.93 3.82
3247 7712 3.510388 TCTGCTAGCATAGTGTGACAC 57.490 47.619 19.72 7.83 41.93 3.67
3256 7721 4.767409 AGCATAGTGTGACACTCAAGAGTA 59.233 41.667 23.04 2.69 41.21 2.59
3268 7733 6.983984 ACACTCAAGAGTAAAGACCTACTTC 58.016 40.000 1.86 0.00 40.20 3.01
3271 7736 6.015265 ACTCAAGAGTAAAGACCTACTTCCAC 60.015 42.308 0.00 0.00 40.43 4.02
3272 7737 5.245526 TCAAGAGTAAAGACCTACTTCCACC 59.754 44.000 0.00 0.00 37.93 4.61
3279 7744 2.100989 GACCTACTTCCACCGTCTCAT 58.899 52.381 0.00 0.00 0.00 2.90
3280 7745 1.825474 ACCTACTTCCACCGTCTCATG 59.175 52.381 0.00 0.00 0.00 3.07
3285 7750 2.124983 CCACCGTCTCATGCCAGG 60.125 66.667 0.00 0.00 0.00 4.45
3289 7754 0.620556 ACCGTCTCATGCCAGGAATT 59.379 50.000 0.00 0.00 0.00 2.17
3293 7758 2.611292 CGTCTCATGCCAGGAATTTCTC 59.389 50.000 0.00 0.00 0.00 2.87
3294 7759 2.948315 GTCTCATGCCAGGAATTTCTCC 59.052 50.000 0.00 0.00 45.81 3.71
3317 7782 3.679389 CCTCATTACACTTTCAGCCTGT 58.321 45.455 0.00 0.00 0.00 4.00
3337 7812 2.634940 GTCCTAGCCCATATTGCTCTCA 59.365 50.000 0.00 0.00 40.23 3.27
3341 7816 3.760580 AGCCCATATTGCTCTCACTAC 57.239 47.619 0.00 0.00 32.41 2.73
3345 7820 3.305676 CCCATATTGCTCTCACTACGAGG 60.306 52.174 0.00 0.00 42.55 4.63
3355 7830 8.809468 TGCTCTCACTACGAGGATTATATTAT 57.191 34.615 0.00 0.00 42.55 1.28
3409 7884 1.049251 CGCGCACAATGTTACCAAAC 58.951 50.000 8.75 0.00 36.07 2.93
3424 7899 1.227556 AAACCACTCGTGCTCGCTT 60.228 52.632 2.69 0.00 36.96 4.68
3461 7936 4.866486 GCATTTCACCTTCCAATAAGCTTG 59.134 41.667 9.86 0.00 0.00 4.01
3662 8142 0.249398 AGTAGATGCCAACACCGTCC 59.751 55.000 0.00 0.00 0.00 4.79
3674 8154 2.126071 CCGTCCGTGTACTGCCTG 60.126 66.667 0.00 0.00 0.00 4.85
3675 8155 2.809601 CGTCCGTGTACTGCCTGC 60.810 66.667 0.00 0.00 0.00 4.85
3676 8156 2.809601 GTCCGTGTACTGCCTGCG 60.810 66.667 0.00 0.00 0.00 5.18
3677 8157 4.063967 TCCGTGTACTGCCTGCGG 62.064 66.667 0.00 0.00 43.32 5.69
3678 8158 4.063967 CCGTGTACTGCCTGCGGA 62.064 66.667 4.70 0.00 44.57 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.095483 AGAATTATCACTTTCGGCAGCAAG 59.905 41.667 0.00 0.00 0.00 4.01
1 2 4.009675 AGAATTATCACTTTCGGCAGCAA 58.990 39.130 0.00 0.00 0.00 3.91
2 3 3.609853 AGAATTATCACTTTCGGCAGCA 58.390 40.909 0.00 0.00 0.00 4.41
3 4 4.024809 GGTAGAATTATCACTTTCGGCAGC 60.025 45.833 0.00 0.00 0.00 5.25
6 7 3.493503 CCGGTAGAATTATCACTTTCGGC 59.506 47.826 0.00 0.00 0.00 5.54
7 8 4.506654 CACCGGTAGAATTATCACTTTCGG 59.493 45.833 6.87 0.00 36.93 4.30
8 9 4.025979 GCACCGGTAGAATTATCACTTTCG 60.026 45.833 6.87 0.00 0.00 3.46
9 10 4.272748 GGCACCGGTAGAATTATCACTTTC 59.727 45.833 6.87 0.00 0.00 2.62
10 11 4.196971 GGCACCGGTAGAATTATCACTTT 58.803 43.478 6.87 0.00 0.00 2.66
12 13 2.223971 CGGCACCGGTAGAATTATCACT 60.224 50.000 6.87 0.00 35.56 3.41
13 14 2.132762 CGGCACCGGTAGAATTATCAC 58.867 52.381 6.87 0.00 35.56 3.06
14 15 2.519377 CGGCACCGGTAGAATTATCA 57.481 50.000 6.87 0.00 35.56 2.15
26 27 1.139308 TCGTTACATACCGGCACCG 59.861 57.895 0.00 1.02 39.44 4.94
28 29 1.712401 TTGTCGTTACATACCGGCAC 58.288 50.000 0.00 0.00 38.56 5.01
29 30 2.272678 CATTGTCGTTACATACCGGCA 58.727 47.619 0.00 0.00 36.83 5.69
30 31 2.273557 ACATTGTCGTTACATACCGGC 58.726 47.619 0.00 0.00 34.97 6.13
31 32 4.682860 GGATACATTGTCGTTACATACCGG 59.317 45.833 0.00 0.00 34.97 5.28
32 33 5.283294 TGGATACATTGTCGTTACATACCG 58.717 41.667 0.00 0.00 46.17 4.02
46 47 5.893518 CCAAGGCGGATGGTGGATACATT 62.894 52.174 0.00 0.00 44.97 2.71
49 50 0.535102 CCAAGGCGGATGGTGGATAC 60.535 60.000 0.00 0.00 36.56 2.24
50 51 1.836391 CCAAGGCGGATGGTGGATA 59.164 57.895 0.00 0.00 36.56 2.59
51 52 2.597340 CCAAGGCGGATGGTGGAT 59.403 61.111 0.00 0.00 36.56 3.41
52 53 4.424711 GCCAAGGCGGATGGTGGA 62.425 66.667 0.00 0.00 40.23 4.02
53 54 4.738998 TGCCAAGGCGGATGGTGG 62.739 66.667 6.60 0.00 45.51 4.61
54 55 2.440796 ATGCCAAGGCGGATGGTG 60.441 61.111 6.60 0.00 45.51 4.17
55 56 2.124151 GATGCCAAGGCGGATGGT 60.124 61.111 6.60 0.00 45.51 3.55
56 57 1.731433 CTTGATGCCAAGGCGGATGG 61.731 60.000 6.60 3.09 44.58 3.51
57 58 1.731700 CTTGATGCCAAGGCGGATG 59.268 57.895 6.60 0.00 44.58 3.51
65 66 1.546923 CTGCACCAATCTTGATGCCAA 59.453 47.619 6.80 0.00 37.26 4.52
66 67 1.179152 CTGCACCAATCTTGATGCCA 58.821 50.000 6.80 0.00 37.26 4.92
67 68 1.135199 CACTGCACCAATCTTGATGCC 60.135 52.381 6.80 0.00 37.26 4.40
71 72 2.880268 CAACTCACTGCACCAATCTTGA 59.120 45.455 0.00 0.00 0.00 3.02
73 74 1.610522 GCAACTCACTGCACCAATCTT 59.389 47.619 0.00 0.00 42.17 2.40
74 75 1.242076 GCAACTCACTGCACCAATCT 58.758 50.000 0.00 0.00 42.17 2.40
75 76 3.780925 GCAACTCACTGCACCAATC 57.219 52.632 0.00 0.00 42.17 2.67
82 83 5.728898 GCATCTTTATACTGCAACTCACTGC 60.729 44.000 0.00 0.00 42.95 4.40
83 84 5.501413 CGCATCTTTATACTGCAACTCACTG 60.501 44.000 0.00 0.00 35.64 3.66
84 85 4.568359 CGCATCTTTATACTGCAACTCACT 59.432 41.667 0.00 0.00 35.64 3.41
86 87 4.754322 TCGCATCTTTATACTGCAACTCA 58.246 39.130 0.00 0.00 35.64 3.41
87 88 5.718649 TTCGCATCTTTATACTGCAACTC 57.281 39.130 0.00 0.00 35.64 3.01
89 90 7.584123 CACTATTTCGCATCTTTATACTGCAAC 59.416 37.037 0.00 0.00 35.64 4.17
90 91 7.494298 TCACTATTTCGCATCTTTATACTGCAA 59.506 33.333 0.00 0.00 35.64 4.08
91 92 6.983890 TCACTATTTCGCATCTTTATACTGCA 59.016 34.615 0.00 0.00 35.64 4.41
92 93 7.042725 TGTCACTATTTCGCATCTTTATACTGC 60.043 37.037 0.00 0.00 0.00 4.40
93 94 8.269424 GTGTCACTATTTCGCATCTTTATACTG 58.731 37.037 0.00 0.00 0.00 2.74
94 95 8.198109 AGTGTCACTATTTCGCATCTTTATACT 58.802 33.333 2.87 0.00 0.00 2.12
96 97 8.194769 TGAGTGTCACTATTTCGCATCTTTATA 58.805 33.333 5.21 0.00 0.00 0.98
97 98 7.041721 TGAGTGTCACTATTTCGCATCTTTAT 58.958 34.615 5.21 0.00 0.00 1.40
98 99 6.394809 TGAGTGTCACTATTTCGCATCTTTA 58.605 36.000 5.21 0.00 0.00 1.85
100 101 4.820897 TGAGTGTCACTATTTCGCATCTT 58.179 39.130 5.21 0.00 0.00 2.40
101 102 4.456280 TGAGTGTCACTATTTCGCATCT 57.544 40.909 5.21 0.00 0.00 2.90
102 103 5.725110 AATGAGTGTCACTATTTCGCATC 57.275 39.130 5.21 0.00 0.00 3.91
103 104 7.609760 TTAAATGAGTGTCACTATTTCGCAT 57.390 32.000 5.21 1.12 0.00 4.73
104 105 7.428282 TTTAAATGAGTGTCACTATTTCGCA 57.572 32.000 5.21 0.00 0.00 5.10
155 4008 6.064846 TCTTTGAAATGAGTGAAAGCAGTC 57.935 37.500 0.00 0.00 43.38 3.51
186 4039 4.950479 GGAGAGTCCCATGCAGTG 57.050 61.111 0.00 0.00 0.00 3.66
210 4063 5.093849 TGCGGGTAAGCTATTTTAGAGTT 57.906 39.130 0.00 0.00 38.13 3.01
211 4064 4.748277 TGCGGGTAAGCTATTTTAGAGT 57.252 40.909 0.00 0.00 38.13 3.24
212 4065 6.431198 TTTTGCGGGTAAGCTATTTTAGAG 57.569 37.500 0.00 0.00 38.13 2.43
213 4066 6.821031 TTTTTGCGGGTAAGCTATTTTAGA 57.179 33.333 0.00 0.00 38.13 2.10
331 4299 3.756727 GCTGGGCTGCTCCTTTGC 61.757 66.667 0.00 1.58 34.39 3.68
345 4313 6.441093 TTGCTAACAATAATCTTGAGGCTG 57.559 37.500 0.00 0.00 0.00 4.85
359 4327 9.862371 TCTTTATTGTTTTCTGTTTGCTAACAA 57.138 25.926 14.52 0.00 43.33 2.83
377 4346 8.633075 TTTTGAAAAGTCTGCAGTCTTTATTG 57.367 30.769 30.37 0.00 33.52 1.90
388 4357 6.729187 AGTGTCATACTTTTGAAAAGTCTGC 58.271 36.000 24.86 19.41 35.67 4.26
414 4383 6.400568 CAATCCAAGTGGCATGAAAAATACT 58.599 36.000 0.00 0.00 34.44 2.12
415 4384 5.581874 CCAATCCAAGTGGCATGAAAAATAC 59.418 40.000 0.00 0.00 34.44 1.89
417 4386 4.286549 TCCAATCCAAGTGGCATGAAAAAT 59.713 37.500 0.00 0.00 35.99 1.82
418 4387 3.645212 TCCAATCCAAGTGGCATGAAAAA 59.355 39.130 0.00 0.00 35.99 1.94
419 4388 3.006752 GTCCAATCCAAGTGGCATGAAAA 59.993 43.478 0.00 0.00 35.99 2.29
420 4389 2.562298 GTCCAATCCAAGTGGCATGAAA 59.438 45.455 0.00 0.00 35.99 2.69
487 4465 0.385751 TCGCACCGCAAAATTTCCAA 59.614 45.000 0.00 0.00 0.00 3.53
489 4467 0.239879 TCTCGCACCGCAAAATTTCC 59.760 50.000 0.00 0.00 0.00 3.13
493 4471 3.263941 GGTCTCGCACCGCAAAAT 58.736 55.556 0.00 0.00 34.56 1.82
523 4501 5.047092 TCCCGTCTTTATCCGTAGAACTTTT 60.047 40.000 0.00 0.00 0.00 2.27
554 4532 0.681564 CACTCTCTCCTACGGCTGGT 60.682 60.000 0.00 0.00 0.00 4.00
557 4535 2.028130 CAATCACTCTCTCCTACGGCT 58.972 52.381 0.00 0.00 0.00 5.52
559 4537 2.028130 AGCAATCACTCTCTCCTACGG 58.972 52.381 0.00 0.00 0.00 4.02
560 4538 3.443037 CAAGCAATCACTCTCTCCTACG 58.557 50.000 0.00 0.00 0.00 3.51
561 4539 3.194062 GCAAGCAATCACTCTCTCCTAC 58.806 50.000 0.00 0.00 0.00 3.18
562 4540 2.833943 TGCAAGCAATCACTCTCTCCTA 59.166 45.455 0.00 0.00 0.00 2.94
568 4593 1.610522 GGTGTTGCAAGCAATCACTCT 59.389 47.619 24.99 0.00 37.70 3.24
632 5054 0.033366 GCCTTTTCAATGGCACGGTT 59.967 50.000 10.78 0.00 45.65 4.44
732 5154 9.936759 TTTTTACCTTTTTGTTGAATTGAGACT 57.063 25.926 0.00 0.00 0.00 3.24
816 5238 2.517650 TGCGACCATGCGACATATAA 57.482 45.000 0.00 0.00 37.81 0.98
844 5267 4.789807 AGCTATCTGAATGCCAAAGTCAT 58.210 39.130 0.00 0.00 0.00 3.06
857 5280 9.582431 GTACAACACAGTTTATAAGCTATCTGA 57.418 33.333 1.10 0.00 0.00 3.27
863 5286 8.985805 GTACAAGTACAACACAGTTTATAAGCT 58.014 33.333 5.53 0.00 36.15 3.74
864 5287 7.948363 CGTACAAGTACAACACAGTTTATAAGC 59.052 37.037 10.63 0.00 35.87 3.09
865 5288 8.971321 ACGTACAAGTACAACACAGTTTATAAG 58.029 33.333 10.63 0.00 35.87 1.73
866 5289 8.754096 CACGTACAAGTACAACACAGTTTATAA 58.246 33.333 10.63 0.00 35.87 0.98
902 5332 6.481644 GTGGGAAAAGTTGTTTGCAATATTCA 59.518 34.615 0.00 0.00 36.92 2.57
908 5338 3.971245 AGTGGGAAAAGTTGTTTGCAA 57.029 38.095 0.00 0.00 0.00 4.08
924 5354 3.181471 ACGATCTAGCTTCATGGAAGTGG 60.181 47.826 7.71 0.00 41.27 4.00
930 5360 3.555168 GGGGTAACGATCTAGCTTCATGG 60.555 52.174 0.00 0.00 37.60 3.66
931 5361 3.069586 TGGGGTAACGATCTAGCTTCATG 59.930 47.826 0.00 0.00 37.60 3.07
932 5362 3.305720 TGGGGTAACGATCTAGCTTCAT 58.694 45.455 0.00 0.00 37.60 2.57
933 5363 2.742348 TGGGGTAACGATCTAGCTTCA 58.258 47.619 0.00 0.00 37.60 3.02
934 5364 3.321111 TGATGGGGTAACGATCTAGCTTC 59.679 47.826 0.00 0.00 37.60 3.86
935 5365 3.069729 GTGATGGGGTAACGATCTAGCTT 59.930 47.826 0.00 0.00 37.60 3.74
936 5366 2.628657 GTGATGGGGTAACGATCTAGCT 59.371 50.000 0.00 0.00 37.60 3.32
937 5367 2.364324 TGTGATGGGGTAACGATCTAGC 59.636 50.000 0.00 0.00 37.60 3.42
938 5368 4.873746 ATGTGATGGGGTAACGATCTAG 57.126 45.455 0.00 0.00 37.60 2.43
939 5369 4.525487 GGTATGTGATGGGGTAACGATCTA 59.475 45.833 0.00 0.00 37.60 1.98
940 5370 3.323979 GGTATGTGATGGGGTAACGATCT 59.676 47.826 0.00 0.00 37.60 2.75
941 5371 3.070446 TGGTATGTGATGGGGTAACGATC 59.930 47.826 0.00 0.00 37.60 3.69
942 5372 3.042682 TGGTATGTGATGGGGTAACGAT 58.957 45.455 0.00 0.00 37.60 3.73
943 5373 2.468915 TGGTATGTGATGGGGTAACGA 58.531 47.619 0.00 0.00 37.60 3.85
944 5374 2.992124 TGGTATGTGATGGGGTAACG 57.008 50.000 0.00 0.00 37.60 3.18
945 5375 4.230745 ACTTGGTATGTGATGGGGTAAC 57.769 45.455 0.00 0.00 0.00 2.50
946 5376 4.594970 CAACTTGGTATGTGATGGGGTAA 58.405 43.478 0.00 0.00 0.00 2.85
947 5377 3.623703 GCAACTTGGTATGTGATGGGGTA 60.624 47.826 0.00 0.00 0.00 3.69
948 5378 2.883888 GCAACTTGGTATGTGATGGGGT 60.884 50.000 0.00 0.00 0.00 4.95
954 5384 0.958382 GGCCGCAACTTGGTATGTGA 60.958 55.000 0.00 0.00 0.00 3.58
958 5388 0.463833 GCTAGGCCGCAACTTGGTAT 60.464 55.000 0.00 0.00 0.00 2.73
963 5393 1.153349 GCTAGCTAGGCCGCAACTT 60.153 57.895 22.10 0.00 0.00 2.66
965 5395 1.884926 CAGCTAGCTAGGCCGCAAC 60.885 63.158 18.86 3.65 0.00 4.17
970 5400 1.338655 GTCACTACAGCTAGCTAGGCC 59.661 57.143 18.86 6.58 0.00 5.19
979 5409 2.701780 CGGAGCCGTCACTACAGCT 61.702 63.158 0.00 0.00 42.13 4.24
980 5410 2.202623 CGGAGCCGTCACTACAGC 60.203 66.667 0.00 0.00 34.35 4.40
994 5424 1.728323 TGGAGGATTATCATGGCGGA 58.272 50.000 0.00 0.00 0.00 5.54
995 5425 2.795231 ATGGAGGATTATCATGGCGG 57.205 50.000 0.00 0.00 0.00 6.13
996 5426 4.743057 TCTATGGAGGATTATCATGGCG 57.257 45.455 0.00 0.00 0.00 5.69
997 5427 5.131642 TGGATCTATGGAGGATTATCATGGC 59.868 44.000 0.00 0.00 0.00 4.40
998 5428 6.819947 TGGATCTATGGAGGATTATCATGG 57.180 41.667 0.00 0.00 0.00 3.66
999 5429 7.292827 AGGATGGATCTATGGAGGATTATCATG 59.707 40.741 0.00 0.00 0.00 3.07
1000 5430 7.379953 AGGATGGATCTATGGAGGATTATCAT 58.620 38.462 0.00 0.00 0.00 2.45
1001 5431 6.760466 AGGATGGATCTATGGAGGATTATCA 58.240 40.000 0.00 0.00 0.00 2.15
1002 5432 7.127032 ACAAGGATGGATCTATGGAGGATTATC 59.873 40.741 0.00 0.00 0.00 1.75
1003 5433 6.970640 ACAAGGATGGATCTATGGAGGATTAT 59.029 38.462 0.00 0.00 0.00 1.28
1004 5434 6.214208 CACAAGGATGGATCTATGGAGGATTA 59.786 42.308 0.00 0.00 0.00 1.75
1005 5435 5.013913 CACAAGGATGGATCTATGGAGGATT 59.986 44.000 0.00 0.00 0.00 3.01
1006 5436 4.535294 CACAAGGATGGATCTATGGAGGAT 59.465 45.833 0.00 0.00 0.00 3.24
1007 5437 3.906218 CACAAGGATGGATCTATGGAGGA 59.094 47.826 0.00 0.00 0.00 3.71
1008 5438 3.649981 ACACAAGGATGGATCTATGGAGG 59.350 47.826 0.00 0.00 0.00 4.30
1011 5441 5.815233 AGTACACAAGGATGGATCTATGG 57.185 43.478 0.00 0.00 0.00 2.74
1028 5458 4.202253 GGATGATGAGGCACATGTAGTACA 60.202 45.833 5.24 5.24 39.56 2.90
1034 5464 2.104451 GAGAGGATGATGAGGCACATGT 59.896 50.000 1.04 0.00 39.56 3.21
1036 5466 1.698532 GGAGAGGATGATGAGGCACAT 59.301 52.381 0.00 0.00 42.47 3.21
1047 5477 2.922234 GGGCCAAGGGAGAGGATG 59.078 66.667 4.39 0.00 0.00 3.51
1347 5780 3.068881 CCGGAGAAGTTCCTGCCA 58.931 61.111 0.00 0.00 44.41 4.92
1383 5816 2.347490 GCGTTGAAGAGGCCCAGA 59.653 61.111 0.00 0.00 33.08 3.86
1455 5888 2.281208 TTGAACTCCCCGTTGCCG 60.281 61.111 0.00 0.00 35.56 5.69
1500 5933 2.103263 GGAGATTAGCCCATTGACGTCT 59.897 50.000 17.92 0.00 0.00 4.18
1509 5942 1.406887 GCTTCAACGGAGATTAGCCCA 60.407 52.381 0.00 0.00 0.00 5.36
1605 6038 1.858091 CATCATACTCGACCCACAGC 58.142 55.000 0.00 0.00 0.00 4.40
1617 6050 2.674852 CTGTGTGGTCTGTGCATCATAC 59.325 50.000 0.00 0.00 0.00 2.39
1631 6064 3.425578 GTCGAGATGACCTGTGTGG 57.574 57.895 0.00 0.00 42.04 4.17
1642 6075 1.456705 GGGGAGCCAGAGTCGAGAT 60.457 63.158 0.00 0.00 0.00 2.75
1644 6077 2.043450 AGGGGAGCCAGAGTCGAG 60.043 66.667 0.00 0.00 0.00 4.04
1695 6128 2.034221 GAGAGGTTGGTGGTGGCC 59.966 66.667 0.00 0.00 0.00 5.36
1713 6146 0.994247 ATGGGTCCTTGAGCACATCA 59.006 50.000 0.00 0.00 35.62 3.07
1723 6156 1.970640 GCCAACAAAAGATGGGTCCTT 59.029 47.619 0.00 0.00 37.19 3.36
1776 6209 0.981183 TCCAACCAAGCACGGAGTAT 59.019 50.000 0.00 0.00 41.61 2.12
1838 6271 1.923864 CACGAAACAACTTGGGCAAAC 59.076 47.619 0.00 0.00 0.00 2.93
1869 6302 1.002430 TGCAAGACTTTGGATCGAGCT 59.998 47.619 0.00 0.00 34.79 4.09
1924 6357 4.740822 GGCGGTTCCCATGGCTGT 62.741 66.667 6.09 0.00 0.00 4.40
1967 6400 2.888863 GCAGCTCAGCGTACCTCT 59.111 61.111 0.00 0.00 0.00 3.69
2049 6482 5.946486 AGGTTCTTGTTCTTGAATCCTTCT 58.054 37.500 0.00 0.00 0.00 2.85
2073 6506 0.537188 CAAAGCCTCCTTCGCCTAGA 59.463 55.000 0.00 0.00 0.00 2.43
2125 6558 2.669569 CACGGCCACCTCCAAGTG 60.670 66.667 2.24 0.00 37.51 3.16
2199 6638 0.103572 GTCGAAGGCGGCCAATACTA 59.896 55.000 23.09 0.00 35.76 1.82
2499 6941 5.351465 GGTACCATGATCATATAACCTTGCG 59.649 44.000 18.55 1.71 0.00 4.85
2643 7086 1.126948 TGGGTCTCTGTCCACATGCA 61.127 55.000 0.00 0.00 0.00 3.96
2688 7131 1.007479 ACCCAATCCACCAGCATGATT 59.993 47.619 0.00 0.00 39.69 2.57
2757 7200 5.030147 TCCTTGTCATAGTTACCATGGAGT 58.970 41.667 21.47 1.80 30.37 3.85
2781 7224 3.420893 CTTCAAAACCATACTGGCCTCA 58.579 45.455 3.32 0.00 42.67 3.86
2782 7225 2.164422 GCTTCAAAACCATACTGGCCTC 59.836 50.000 3.32 0.00 42.67 4.70
2834 7277 1.381928 ATTCATGCTTGGCCTCGCAG 61.382 55.000 21.03 14.30 39.82 5.18
2872 7315 0.889306 GGTAGCGTTGTCTCTCCACT 59.111 55.000 0.00 0.00 0.00 4.00
2873 7316 0.601558 TGGTAGCGTTGTCTCTCCAC 59.398 55.000 0.00 0.00 0.00 4.02
2874 7317 0.888619 CTGGTAGCGTTGTCTCTCCA 59.111 55.000 0.00 0.00 0.00 3.86
2883 7326 0.602905 GTGCCAACTCTGGTAGCGTT 60.603 55.000 0.00 0.00 45.53 4.84
2884 7327 1.004918 GTGCCAACTCTGGTAGCGT 60.005 57.895 0.00 0.00 45.53 5.07
2896 7339 1.137872 GTTGATTTGTGTGGGTGCCAA 59.862 47.619 0.00 0.00 34.18 4.52
2910 7353 4.229096 GCATCATGTTGACGTTGTTGATT 58.771 39.130 7.98 0.00 0.00 2.57
2934 7377 1.912043 AGGTCTGGAAACCCTCTGATG 59.088 52.381 0.00 0.00 40.42 3.07
2943 7386 2.479275 GCTCGTTGTTAGGTCTGGAAAC 59.521 50.000 0.00 0.00 0.00 2.78
2949 7392 1.135083 CCGATGCTCGTTGTTAGGTCT 60.135 52.381 5.15 0.00 38.40 3.85
2958 7401 0.391661 AGAATGTGCCGATGCTCGTT 60.392 50.000 5.15 0.00 41.52 3.85
3016 7462 9.787532 ATGCAAGTACATGTTCATATTAAACAC 57.212 29.630 2.30 0.00 39.29 3.32
3027 7473 4.937620 TCCTTCAGATGCAAGTACATGTTC 59.062 41.667 2.30 0.00 0.00 3.18
3031 7490 4.910195 TGTTCCTTCAGATGCAAGTACAT 58.090 39.130 0.00 0.00 0.00 2.29
3053 7512 8.618702 AGCACTCGTATATAATGTACACTACT 57.381 34.615 0.00 0.00 0.00 2.57
3056 7515 7.713750 ACAAGCACTCGTATATAATGTACACT 58.286 34.615 0.00 0.00 0.00 3.55
3062 7521 8.757164 TTCCATACAAGCACTCGTATATAATG 57.243 34.615 0.00 0.00 0.00 1.90
3063 7522 9.772973 TTTTCCATACAAGCACTCGTATATAAT 57.227 29.630 0.00 0.00 0.00 1.28
3071 7530 9.438291 CTAATTTATTTTCCATACAAGCACTCG 57.562 33.333 0.00 0.00 0.00 4.18
3118 7577 5.530915 CGGTTCAATTGATTGCTATTCCCTA 59.469 40.000 9.40 0.00 37.68 3.53
3135 7598 4.371786 GCTCATACATCTGATCGGTTCAA 58.628 43.478 0.42 0.00 32.78 2.69
3139 7602 1.620819 GGGCTCATACATCTGATCGGT 59.379 52.381 0.42 0.00 0.00 4.69
3154 7617 3.402628 TCAAGTTACAACAGAGGGCTC 57.597 47.619 0.00 0.00 0.00 4.70
3171 7634 5.417580 GCCCTAGTGAAAATAACCACATCAA 59.582 40.000 0.00 0.00 35.84 2.57
3176 7639 2.681344 CGGCCCTAGTGAAAATAACCAC 59.319 50.000 0.00 0.00 0.00 4.16
3195 7658 1.135257 TGTCACAAAAGTGCAAACCGG 60.135 47.619 0.00 0.00 0.00 5.28
3228 7693 3.119352 TGAGTGTCACACTATGCTAGCAG 60.119 47.826 23.89 12.94 45.44 4.24
3237 7702 6.238953 GGTCTTTACTCTTGAGTGTCACACTA 60.239 42.308 11.42 0.00 45.44 2.74
3243 7708 6.578163 AGTAGGTCTTTACTCTTGAGTGTC 57.422 41.667 12.99 0.00 0.00 3.67
3247 7712 6.391537 GTGGAAGTAGGTCTTTACTCTTGAG 58.608 44.000 0.00 0.00 36.40 3.02
3256 7721 2.561858 GAGACGGTGGAAGTAGGTCTTT 59.438 50.000 0.00 0.00 38.03 2.52
3268 7733 2.124983 CCTGGCATGAGACGGTGG 60.125 66.667 0.00 0.00 0.00 4.61
3271 7736 1.672881 GAAATTCCTGGCATGAGACGG 59.327 52.381 0.00 0.00 0.00 4.79
3272 7737 2.611292 GAGAAATTCCTGGCATGAGACG 59.389 50.000 0.00 0.00 0.00 4.18
3279 7744 1.378514 GGCGGAGAAATTCCTGGCA 60.379 57.895 10.38 0.00 44.41 4.92
3280 7745 1.077429 AGGCGGAGAAATTCCTGGC 60.077 57.895 8.17 8.17 44.41 4.85
3285 7750 4.192317 AGTGTAATGAGGCGGAGAAATTC 58.808 43.478 0.00 0.00 0.00 2.17
3289 7754 3.007506 TGAAAGTGTAATGAGGCGGAGAA 59.992 43.478 0.00 0.00 0.00 2.87
3293 7758 1.398390 GCTGAAAGTGTAATGAGGCGG 59.602 52.381 0.00 0.00 35.30 6.13
3294 7759 1.398390 GGCTGAAAGTGTAATGAGGCG 59.602 52.381 0.00 0.00 35.30 5.52
3299 7764 3.679389 AGGACAGGCTGAAAGTGTAATG 58.321 45.455 23.66 0.00 35.30 1.90
3304 7769 1.677217 GGCTAGGACAGGCTGAAAGTG 60.677 57.143 23.66 9.15 46.26 3.16
3317 7782 2.634940 GTGAGAGCAATATGGGCTAGGA 59.365 50.000 2.37 0.00 42.78 2.94
3355 7830 4.526650 TGCAGATGCCGACCTAGATATAAA 59.473 41.667 1.72 0.00 41.18 1.40
3360 7835 1.123077 TTGCAGATGCCGACCTAGAT 58.877 50.000 1.72 0.00 41.18 1.98
3361 7836 0.175760 GTTGCAGATGCCGACCTAGA 59.824 55.000 1.72 0.00 41.18 2.43
3362 7837 1.148157 CGTTGCAGATGCCGACCTAG 61.148 60.000 1.72 0.00 41.18 3.02
3363 7838 1.153647 CGTTGCAGATGCCGACCTA 60.154 57.895 1.72 0.00 41.18 3.08
3364 7839 1.884075 TACGTTGCAGATGCCGACCT 61.884 55.000 9.86 0.00 41.18 3.85
3365 7840 1.447140 TACGTTGCAGATGCCGACC 60.447 57.895 9.86 0.00 41.18 4.79
3366 7841 1.693083 GGTACGTTGCAGATGCCGAC 61.693 60.000 9.86 4.80 41.18 4.79
3367 7842 1.447140 GGTACGTTGCAGATGCCGA 60.447 57.895 9.86 0.00 41.18 5.54
3368 7843 1.019278 AAGGTACGTTGCAGATGCCG 61.019 55.000 0.00 2.20 41.18 5.69
3369 7844 0.727398 GAAGGTACGTTGCAGATGCC 59.273 55.000 5.36 0.00 41.18 4.40
3370 7845 1.128692 GTGAAGGTACGTTGCAGATGC 59.871 52.381 5.36 0.00 42.50 3.91
3371 7846 1.390123 CGTGAAGGTACGTTGCAGATG 59.610 52.381 5.36 0.00 39.13 2.90
3409 7884 3.175240 CGAAGCGAGCACGAGTGG 61.175 66.667 8.01 0.00 42.66 4.00
3461 7936 3.984508 TCTGTATCTGTTACGCTAGCC 57.015 47.619 9.66 0.00 33.15 3.93
3575 8050 1.038130 AAGACGACCCTCCGAGGATG 61.038 60.000 16.69 7.42 37.67 3.51


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

AutoCloner maintained by Alex Coulton.