Multiple sequence alignment - TraesCS3A01G125200

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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 TraesCS3A01G125200 chr3A 100.000 3802 0 0 1 3802 100883827 100880026 0.000000e+00 7022
1 TraesCS3A01G125200 chr3A 83.368 1942 260 39 993 2882 100843145 100841215 0.000000e+00 1738
2 TraesCS3A01G125200 chr3A 83.324 1823 161 57 51 1816 100845631 100843895 0.000000e+00 1550
3 TraesCS3A01G125200 chr3A 94.973 557 25 2 3247 3801 100843897 100843342 0.000000e+00 870
4 TraesCS3A01G125200 chr3D 89.047 3022 217 49 115 3081 84502048 84499086 0.000000e+00 3642
5 TraesCS3A01G125200 chr3D 92.147 1719 97 11 746 2445 84505910 84504211 0.000000e+00 2392
6 TraesCS3A01G125200 chr3D 84.115 2260 267 51 685 2882 84565328 84563099 0.000000e+00 2100
7 TraesCS3A01G125200 chr3D 83.282 1944 264 39 990 2882 84498207 84496274 0.000000e+00 1733
8 TraesCS3A01G125200 chr3D 91.353 1064 53 13 2441 3495 84503867 84502834 0.000000e+00 1419
9 TraesCS3A01G125200 chr3D 95.044 686 31 2 3119 3801 84499085 84498400 0.000000e+00 1075
10 TraesCS3A01G125200 chr3D 97.826 92 2 0 3493 3584 84502604 84502513 3.930000e-35 159
11 TraesCS3A01G125200 chr3B 86.700 3406 301 76 115 3454 133199391 133202710 0.000000e+00 3640
12 TraesCS3A01G125200 chr3B 91.917 2363 153 12 746 3081 132005312 132007663 0.000000e+00 3271
13 TraesCS3A01G125200 chr3B 89.884 2422 172 28 713 3081 132906523 132904122 0.000000e+00 3048
14 TraesCS3A01G125200 chr3B 81.875 2229 270 75 689 2855 132089423 132091579 0.000000e+00 1755
15 TraesCS3A01G125200 chr3B 82.821 1950 273 40 976 2882 132903252 132901322 0.000000e+00 1688
16 TraesCS3A01G125200 chr3B 82.208 1377 201 26 1532 2879 133204206 133205567 0.000000e+00 1146
17 TraesCS3A01G125200 chr3B 93.651 693 31 5 3119 3800 132007664 132008354 0.000000e+00 1024
18 TraesCS3A01G125200 chr3B 93.228 694 32 5 3119 3801 132904121 132903432 0.000000e+00 1007
19 TraesCS3A01G125200 chr3B 90.229 655 46 8 630 1282 132977212 132976574 0.000000e+00 839


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 TraesCS3A01G125200 chr3A 100880026 100883827 3801 True 7022.000000 7022 100.000000 1 3802 1 chr3A.!!$R1 3801
1 TraesCS3A01G125200 chr3A 100841215 100845631 4416 True 1386.000000 1738 87.221667 51 3801 3 chr3A.!!$R2 3750
2 TraesCS3A01G125200 chr3D 84563099 84565328 2229 True 2100.000000 2100 84.115000 685 2882 1 chr3D.!!$R1 2197
3 TraesCS3A01G125200 chr3D 84496274 84505910 9636 True 1736.666667 3642 91.449833 115 3801 6 chr3D.!!$R2 3686
4 TraesCS3A01G125200 chr3B 133199391 133205567 6176 False 2393.000000 3640 84.454000 115 3454 2 chr3B.!!$F3 3339
5 TraesCS3A01G125200 chr3B 132005312 132008354 3042 False 2147.500000 3271 92.784000 746 3800 2 chr3B.!!$F2 3054
6 TraesCS3A01G125200 chr3B 132901322 132906523 5201 True 1914.333333 3048 88.644333 713 3801 3 chr3B.!!$R2 3088
7 TraesCS3A01G125200 chr3B 132089423 132091579 2156 False 1755.000000 1755 81.875000 689 2855 1 chr3B.!!$F1 2166
8 TraesCS3A01G125200 chr3B 132976574 132977212 638 True 839.000000 839 90.229000 630 1282 1 chr3B.!!$R1 652

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
842 4657 0.029834 CAAGTTGAAACGCTGCTGCT 59.970 50.0 14.03 0.0 36.97 4.24 F
1989 9372 0.103755 GCTGAGATGCGATGGTGAGA 59.896 55.0 0.00 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2391 9775 0.035152 TGGTGCCACAGGATCATCAC 60.035 55.0 0.0 0.0 0.00 3.06 R
3109 10510 0.391263 CCTAGTTGCTCCCACGGAAC 60.391 60.0 0.0 0.0 35.73 3.62 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
22 23 2.427232 TAAAACGACACACTCTCCGG 57.573 50.000 0.00 0.00 0.00 5.14
23 24 0.249741 AAAACGACACACTCTCCGGG 60.250 55.000 0.00 0.00 0.00 5.73
24 25 1.397390 AAACGACACACTCTCCGGGT 61.397 55.000 0.00 0.00 0.00 5.28
25 26 1.803366 AACGACACACTCTCCGGGTC 61.803 60.000 0.00 0.00 0.00 4.46
26 27 2.567049 GACACACTCTCCGGGTCG 59.433 66.667 0.00 0.00 0.00 4.79
29 30 3.681835 ACACTCTCCGGGTCGTGC 61.682 66.667 14.87 0.00 0.00 5.34
30 31 3.374402 CACTCTCCGGGTCGTGCT 61.374 66.667 0.00 0.00 0.00 4.40
31 32 3.063084 ACTCTCCGGGTCGTGCTC 61.063 66.667 0.00 0.00 0.00 4.26
32 33 3.827898 CTCTCCGGGTCGTGCTCC 61.828 72.222 0.00 0.00 0.00 4.70
33 34 4.671590 TCTCCGGGTCGTGCTCCA 62.672 66.667 0.00 0.00 0.00 3.86
34 35 4.436998 CTCCGGGTCGTGCTCCAC 62.437 72.222 0.00 0.00 0.00 4.02
37 38 4.742201 CGGGTCGTGCTCCACCAG 62.742 72.222 4.93 0.00 33.91 4.00
38 39 3.311110 GGGTCGTGCTCCACCAGA 61.311 66.667 4.93 0.00 33.91 3.86
39 40 2.262915 GGTCGTGCTCCACCAGAG 59.737 66.667 0.00 0.00 46.29 3.35
40 41 2.574955 GGTCGTGCTCCACCAGAGT 61.575 63.158 0.00 0.00 45.21 3.24
42 43 0.249911 GTCGTGCTCCACCAGAGTTT 60.250 55.000 0.00 0.00 45.21 2.66
44 45 1.272490 TCGTGCTCCACCAGAGTTTAG 59.728 52.381 0.00 0.00 45.21 1.85
45 46 1.272490 CGTGCTCCACCAGAGTTTAGA 59.728 52.381 0.00 0.00 45.21 2.10
47 48 2.300437 GTGCTCCACCAGAGTTTAGAGT 59.700 50.000 0.00 0.00 45.21 3.24
48 49 3.510360 GTGCTCCACCAGAGTTTAGAGTA 59.490 47.826 0.00 0.00 45.21 2.59
49 50 4.160626 GTGCTCCACCAGAGTTTAGAGTAT 59.839 45.833 0.00 0.00 45.21 2.12
99 100 3.119531 CCTTGTTTCATTGCTAATCGCCA 60.120 43.478 0.00 0.00 38.05 5.69
108 109 3.275617 TGCTAATCGCCACAGGTTATT 57.724 42.857 0.00 0.00 38.05 1.40
114 115 5.560966 AATCGCCACAGGTTATTTGTTAG 57.439 39.130 0.00 0.00 0.00 2.34
116 117 3.008157 TCGCCACAGGTTATTTGTTAGGA 59.992 43.478 0.00 0.00 0.00 2.94
117 118 3.374058 CGCCACAGGTTATTTGTTAGGAG 59.626 47.826 0.00 0.00 0.00 3.69
118 119 4.332828 GCCACAGGTTATTTGTTAGGAGT 58.667 43.478 0.00 0.00 0.00 3.85
119 120 5.493809 GCCACAGGTTATTTGTTAGGAGTA 58.506 41.667 0.00 0.00 0.00 2.59
120 121 5.353400 GCCACAGGTTATTTGTTAGGAGTAC 59.647 44.000 0.00 0.00 0.00 2.73
121 122 6.708285 CCACAGGTTATTTGTTAGGAGTACT 58.292 40.000 0.00 0.00 0.00 2.73
123 124 8.316214 CCACAGGTTATTTGTTAGGAGTACTAA 58.684 37.037 0.00 0.00 39.31 2.24
124 125 9.715121 CACAGGTTATTTGTTAGGAGTACTAAA 57.285 33.333 0.00 0.00 42.99 1.85
125 126 9.716531 ACAGGTTATTTGTTAGGAGTACTAAAC 57.283 33.333 0.00 1.82 42.99 2.01
126 127 9.939802 CAGGTTATTTGTTAGGAGTACTAAACT 57.060 33.333 13.41 7.73 42.99 2.66
134 1904 7.124052 TGTTAGGAGTACTAAACTAGGAGCAT 58.876 38.462 13.41 0.00 42.99 3.79
188 3944 1.574925 GCATGATGATGCGCTGAGG 59.425 57.895 9.73 0.00 45.50 3.86
204 3960 2.183046 GGAGCGAGGACAGACAGC 59.817 66.667 0.00 0.00 0.00 4.40
222 3978 2.533942 CAGCGAAACAAAACGGAAAAGG 59.466 45.455 0.00 0.00 0.00 3.11
224 3980 3.119424 AGCGAAACAAAACGGAAAAGGAA 60.119 39.130 0.00 0.00 0.00 3.36
241 4015 1.666189 GGAATACCTCTTTGCGACAGC 59.334 52.381 0.00 0.00 45.41 4.40
264 4039 7.010552 CAGCAAGTCTATACCAGTGTTGAATAC 59.989 40.741 0.00 0.00 0.00 1.89
271 4046 3.609853 ACCAGTGTTGAATACGATGCAT 58.390 40.909 0.00 0.00 0.00 3.96
280 4055 2.574006 ATACGATGCATTGCCTCCAT 57.426 45.000 14.18 0.00 0.00 3.41
292 4073 1.296392 CCTCCATTGGCGTCACTCA 59.704 57.895 0.00 0.00 0.00 3.41
324 4105 4.574828 ACTCGTATTTTCCAAATCGATGGG 59.425 41.667 0.00 4.14 41.05 4.00
326 4107 3.004315 CGTATTTTCCAAATCGATGGGGG 59.996 47.826 14.48 9.56 41.05 5.40
327 4108 2.614134 TTTTCCAAATCGATGGGGGT 57.386 45.000 14.48 0.00 41.05 4.95
328 4109 2.614134 TTTCCAAATCGATGGGGGTT 57.386 45.000 14.48 0.00 41.05 4.11
355 4136 3.829026 TCTCTGCAGAAGCTTCTCACTTA 59.171 43.478 26.18 9.95 42.74 2.24
367 4148 4.389374 CTTCTCACTTACAAAGGCCTGAA 58.611 43.478 5.69 0.00 0.00 3.02
390 4171 9.778741 TGAAAGGATACCAGACATTAATCATAC 57.221 33.333 0.00 0.00 37.17 2.39
391 4172 8.833231 AAAGGATACCAGACATTAATCATACG 57.167 34.615 0.00 0.00 37.17 3.06
392 4173 6.398918 AGGATACCAGACATTAATCATACGC 58.601 40.000 0.00 0.00 37.17 4.42
393 4174 6.211584 AGGATACCAGACATTAATCATACGCT 59.788 38.462 0.00 0.00 37.17 5.07
394 4175 6.311445 GGATACCAGACATTAATCATACGCTG 59.689 42.308 0.00 0.00 0.00 5.18
395 4176 5.023533 ACCAGACATTAATCATACGCTGT 57.976 39.130 0.00 0.00 0.00 4.40
396 4177 6.156748 ACCAGACATTAATCATACGCTGTA 57.843 37.500 0.00 0.00 0.00 2.74
410 4191 6.978659 TCATACGCTGTAAATCTTTGACTAGG 59.021 38.462 0.00 0.00 0.00 3.02
411 4192 5.148651 ACGCTGTAAATCTTTGACTAGGT 57.851 39.130 0.00 0.00 0.00 3.08
412 4193 6.276832 ACGCTGTAAATCTTTGACTAGGTA 57.723 37.500 0.00 0.00 0.00 3.08
414 4195 7.328737 ACGCTGTAAATCTTTGACTAGGTAAT 58.671 34.615 0.00 0.00 0.00 1.89
415 4196 8.472413 ACGCTGTAAATCTTTGACTAGGTAATA 58.528 33.333 0.00 0.00 0.00 0.98
416 4197 9.477484 CGCTGTAAATCTTTGACTAGGTAATAT 57.523 33.333 0.00 0.00 0.00 1.28
427 4208 9.547753 TTTGACTAGGTAATATGATCAAGAAGC 57.452 33.333 0.00 0.00 0.00 3.86
428 4209 7.371159 TGACTAGGTAATATGATCAAGAAGCG 58.629 38.462 0.00 0.00 0.00 4.68
429 4210 6.692486 ACTAGGTAATATGATCAAGAAGCGG 58.308 40.000 0.00 0.00 0.00 5.52
430 4211 5.808366 AGGTAATATGATCAAGAAGCGGA 57.192 39.130 0.00 0.00 0.00 5.54
431 4212 5.542779 AGGTAATATGATCAAGAAGCGGAC 58.457 41.667 0.00 0.00 0.00 4.79
432 4213 5.070446 AGGTAATATGATCAAGAAGCGGACA 59.930 40.000 0.00 0.00 0.00 4.02
433 4214 5.758296 GGTAATATGATCAAGAAGCGGACAA 59.242 40.000 0.00 0.00 0.00 3.18
436 4217 6.757897 ATATGATCAAGAAGCGGACAAAAA 57.242 33.333 0.00 0.00 0.00 1.94
455 4236 0.916086 AAATATCCCGCCCACTGTCA 59.084 50.000 0.00 0.00 0.00 3.58
464 4245 0.105964 GCCCACTGTCACAGTACACA 59.894 55.000 10.98 0.00 43.43 3.72
465 4246 1.474320 GCCCACTGTCACAGTACACAA 60.474 52.381 10.98 0.00 43.43 3.33
467 4248 2.872245 CCCACTGTCACAGTACACAAAG 59.128 50.000 10.98 0.00 43.43 2.77
468 4249 3.431626 CCCACTGTCACAGTACACAAAGA 60.432 47.826 10.98 0.00 43.43 2.52
469 4250 4.188462 CCACTGTCACAGTACACAAAGAA 58.812 43.478 10.98 0.00 43.43 2.52
470 4251 4.634004 CCACTGTCACAGTACACAAAGAAA 59.366 41.667 10.98 0.00 43.43 2.52
471 4252 5.123186 CCACTGTCACAGTACACAAAGAAAA 59.877 40.000 10.98 0.00 43.43 2.29
472 4253 6.183360 CCACTGTCACAGTACACAAAGAAAAT 60.183 38.462 10.98 0.00 43.43 1.82
473 4254 7.011950 CCACTGTCACAGTACACAAAGAAAATA 59.988 37.037 10.98 0.00 43.43 1.40
474 4255 8.394877 CACTGTCACAGTACACAAAGAAAATAA 58.605 33.333 10.98 0.00 43.43 1.40
475 4256 9.120538 ACTGTCACAGTACACAAAGAAAATAAT 57.879 29.630 9.30 0.00 43.46 1.28
476 4257 9.950680 CTGTCACAGTACACAAAGAAAATAATT 57.049 29.630 0.00 0.00 0.00 1.40
483 4264 9.458374 AGTACACAAAGAAAATAATTTTGACGG 57.542 29.630 0.00 0.00 36.09 4.79
484 4265 9.240159 GTACACAAAGAAAATAATTTTGACGGT 57.760 29.630 3.49 0.00 36.09 4.83
485 4266 8.125728 ACACAAAGAAAATAATTTTGACGGTG 57.874 30.769 3.49 0.00 36.09 4.94
486 4267 7.976734 ACACAAAGAAAATAATTTTGACGGTGA 59.023 29.630 0.00 0.00 36.09 4.02
491 4272 7.484975 AGAAAATAATTTTGACGGTGACACAA 58.515 30.769 8.08 0.00 31.94 3.33
492 4273 7.976734 AGAAAATAATTTTGACGGTGACACAAA 59.023 29.630 8.08 0.00 35.52 2.83
505 4286 5.343058 CGGTGACACAAAGAAAATAATGCAG 59.657 40.000 8.08 0.00 0.00 4.41
509 4293 6.696583 TGACACAAAGAAAATAATGCAGTGTG 59.303 34.615 0.00 0.00 37.76 3.82
514 4298 9.793252 ACAAAGAAAATAATGCAGTGTGATATC 57.207 29.630 0.00 0.00 0.00 1.63
525 4310 4.277672 GCAGTGTGATATCATTGGCAGAAT 59.722 41.667 9.02 0.00 0.00 2.40
527 4312 4.753610 AGTGTGATATCATTGGCAGAATCG 59.246 41.667 9.02 0.00 0.00 3.34
537 4322 1.443407 GCAGAATCGGCTGGCTCTA 59.557 57.895 0.00 0.00 36.41 2.43
548 4333 0.107945 CTGGCTCTACCTTCCACAGC 60.108 60.000 0.00 0.00 40.22 4.40
562 4354 1.534595 CCACAGCTTTGAGAGTTGAGC 59.465 52.381 0.17 0.00 38.75 4.26
596 4388 0.671781 ACGGCAAGTCAGCATCAGAC 60.672 55.000 0.00 0.00 35.83 3.51
597 4389 1.364626 CGGCAAGTCAGCATCAGACC 61.365 60.000 0.00 0.00 36.68 3.85
602 4394 3.001414 CAAGTCAGCATCAGACCTGAAG 58.999 50.000 3.62 0.86 43.58 3.02
604 4396 2.233431 AGTCAGCATCAGACCTGAAGAC 59.767 50.000 3.62 9.56 43.58 3.01
620 4413 2.361610 ACCATCCGGGCAGCAAAG 60.362 61.111 0.00 0.00 42.05 2.77
649 4442 4.499526 GCATTGAATGGCGTCCAAATCATA 60.500 41.667 7.35 8.79 36.95 2.15
650 4443 5.775686 CATTGAATGGCGTCCAAATCATAT 58.224 37.500 14.03 9.96 36.95 1.78
702 4495 1.404181 GCTAATCTGCGCCATCCGATA 60.404 52.381 4.18 0.00 40.02 2.92
705 4498 1.189752 ATCTGCGCCATCCGATATCT 58.810 50.000 4.18 0.00 40.02 1.98
711 4509 1.401905 CGCCATCCGATATCTGATCGA 59.598 52.381 6.66 0.00 43.59 3.59
761 4570 6.652481 TGGTTCAGAAGTGAAGAAGATTCATC 59.348 38.462 0.00 0.00 43.55 2.92
804 4619 0.389037 GACTGACGTGAGAGCATGCA 60.389 55.000 21.98 0.00 34.29 3.96
834 4649 2.561569 AGAGGTGACCAAGTTGAAACG 58.438 47.619 3.63 0.00 0.00 3.60
835 4650 1.002792 GAGGTGACCAAGTTGAAACGC 60.003 52.381 3.63 2.08 0.00 4.84
836 4651 1.021968 GGTGACCAAGTTGAAACGCT 58.978 50.000 3.87 0.00 0.00 5.07
837 4652 1.268539 GGTGACCAAGTTGAAACGCTG 60.269 52.381 3.87 0.00 0.00 5.18
838 4653 0.380378 TGACCAAGTTGAAACGCTGC 59.620 50.000 3.87 0.00 0.00 5.25
839 4654 0.663153 GACCAAGTTGAAACGCTGCT 59.337 50.000 3.87 0.00 0.00 4.24
840 4655 0.381801 ACCAAGTTGAAACGCTGCTG 59.618 50.000 3.87 0.00 0.00 4.41
841 4656 0.936297 CCAAGTTGAAACGCTGCTGC 60.936 55.000 3.87 5.34 0.00 5.25
842 4657 0.029834 CAAGTTGAAACGCTGCTGCT 59.970 50.000 14.03 0.00 36.97 4.24
843 4658 0.029834 AAGTTGAAACGCTGCTGCTG 59.970 50.000 14.03 9.56 36.97 4.41
861 4687 2.764314 GCGCTGCACCCATTCGATT 61.764 57.895 0.00 0.00 0.00 3.34
918 4755 3.648067 ACCAGGTGCTGCTGTATATACAT 59.352 43.478 15.81 0.00 35.36 2.29
954 4791 1.767692 GGCTTCCAAGTCCTCCCAA 59.232 57.895 0.00 0.00 0.00 4.12
968 4805 0.679505 TCCCAACTTGACAGACTCCG 59.320 55.000 0.00 0.00 0.00 4.63
971 4808 1.423395 CAACTTGACAGACTCCGCTC 58.577 55.000 0.00 0.00 0.00 5.03
1155 4992 2.045926 AGCTTCATCACCACGCCC 60.046 61.111 0.00 0.00 0.00 6.13
1183 5020 1.899437 CGCTAGGTTGGAGGGCTTCA 61.899 60.000 0.00 0.00 0.00 3.02
1440 5277 1.589716 GCGACATTGCAAGGGAGCTT 61.590 55.000 20.41 0.00 34.99 3.74
1665 5527 3.482786 GACGTGTGTACTACCTTACGTG 58.517 50.000 13.81 0.00 43.69 4.49
1736 5603 3.064207 TCAGATGTTTGTTACGCCAGTC 58.936 45.455 0.00 0.00 0.00 3.51
1744 5611 1.667830 TTACGCCAGTCACAGCTGC 60.668 57.895 15.27 0.00 35.28 5.25
1813 9196 3.457380 AGACCATCTTGCAGGTACATCAT 59.543 43.478 0.00 0.00 38.50 2.45
1815 9198 5.130975 AGACCATCTTGCAGGTACATCATTA 59.869 40.000 0.00 0.00 38.50 1.90
1823 9206 6.682423 TGCAGGTACATCATTATTCACAAG 57.318 37.500 0.00 0.00 0.00 3.16
1835 9218 8.722480 TCATTATTCACAAGAATGTACTGGAG 57.278 34.615 4.09 0.00 44.03 3.86
1836 9219 6.985188 TTATTCACAAGAATGTACTGGAGC 57.015 37.500 0.00 0.00 44.03 4.70
1843 9226 3.866651 AGAATGTACTGGAGCATGTCAC 58.133 45.455 0.00 0.00 0.00 3.67
1850 9233 2.504585 ACTGGAGCATGTCACAGATGAT 59.495 45.455 16.05 0.00 37.14 2.45
1869 9252 4.814147 TGATAATGAGCTCATCACGATCC 58.186 43.478 28.83 13.97 41.91 3.36
1871 9254 0.316522 ATGAGCTCATCACGATCCCG 59.683 55.000 23.75 0.00 41.91 5.14
1877 9260 1.223487 CATCACGATCCCGGGGTTT 59.777 57.895 23.50 5.83 40.21 3.27
1893 9276 1.823610 GGTTTCCTACACCGCTAGAGT 59.176 52.381 0.00 0.00 0.00 3.24
1897 9280 3.014304 TCCTACACCGCTAGAGTTGAT 57.986 47.619 0.00 0.00 0.00 2.57
1898 9281 2.688446 TCCTACACCGCTAGAGTTGATG 59.312 50.000 0.00 0.00 0.00 3.07
1907 9290 4.047822 CGCTAGAGTTGATGAAGGCTAAG 58.952 47.826 0.00 0.00 0.00 2.18
1909 9292 5.423886 GCTAGAGTTGATGAAGGCTAAGTT 58.576 41.667 0.00 0.00 0.00 2.66
1910 9293 5.293079 GCTAGAGTTGATGAAGGCTAAGTTG 59.707 44.000 0.00 0.00 0.00 3.16
1920 9303 2.568003 GCTAAGTTGCCAGGAACCC 58.432 57.895 0.00 0.00 0.00 4.11
1926 9309 0.961753 GTTGCCAGGAACCCTTTCTG 59.038 55.000 0.00 0.00 31.71 3.02
1964 9347 6.034591 GCAAATCCATGAGAAGATGTTTGAG 58.965 40.000 0.00 0.00 28.02 3.02
1975 9358 2.500910 AGATGTTTGAGGAGGAGCTGAG 59.499 50.000 0.00 0.00 0.00 3.35
1977 9360 2.544721 TGTTTGAGGAGGAGCTGAGAT 58.455 47.619 0.00 0.00 0.00 2.75
1979 9362 0.829333 TTGAGGAGGAGCTGAGATGC 59.171 55.000 0.00 0.00 0.00 3.91
1989 9372 0.103755 GCTGAGATGCGATGGTGAGA 59.896 55.000 0.00 0.00 0.00 3.27
1993 9376 2.223900 TGAGATGCGATGGTGAGATCAC 60.224 50.000 4.33 4.33 45.72 3.06
1997 9380 4.282957 AGATGCGATGGTGAGATCACTAAT 59.717 41.667 12.43 7.07 45.73 1.73
2004 9387 6.515696 CGATGGTGAGATCACTAATAGCTTCA 60.516 42.308 12.43 0.00 45.73 3.02
2006 9389 6.946340 TGGTGAGATCACTAATAGCTTCAAA 58.054 36.000 12.43 0.00 45.73 2.69
2044 9427 6.182627 TGTACATTGAATCCTTTGAGCAGAT 58.817 36.000 0.00 0.00 0.00 2.90
2045 9428 7.337938 TGTACATTGAATCCTTTGAGCAGATA 58.662 34.615 0.00 0.00 0.00 1.98
2050 9433 6.748333 TGAATCCTTTGAGCAGATAACAAG 57.252 37.500 0.00 0.00 0.00 3.16
2064 9447 5.046304 CAGATAACAAGGAAGAAGGTCTGGA 60.046 44.000 0.00 0.00 0.00 3.86
2066 9449 2.408565 ACAAGGAAGAAGGTCTGGACA 58.591 47.619 3.10 0.00 0.00 4.02
2095 9478 2.743928 GTGCCTCTGCCACCGAAG 60.744 66.667 0.00 0.00 36.33 3.79
2114 9498 2.598394 AGCAACACAATGGCCGCT 60.598 55.556 0.00 0.00 0.00 5.52
2117 9501 1.802636 CAACACAATGGCCGCTAGG 59.197 57.895 0.00 0.00 41.62 3.02
2120 9504 3.015145 ACAATGGCCGCTAGGGGT 61.015 61.111 25.32 4.65 38.20 4.95
2138 9522 1.467342 GGTAACAAGGCGTCAATGGAC 59.533 52.381 0.00 0.00 40.77 4.02
2195 9579 2.355108 GCCAGGCTCAGTGATCTTTGTA 60.355 50.000 3.29 0.00 0.00 2.41
2247 9631 2.435372 ACAACTTGTTGAGCTGGGAA 57.565 45.000 18.82 0.00 0.00 3.97
2255 9639 0.620556 TTGAGCTGGGAATGGGACTC 59.379 55.000 0.00 0.00 0.00 3.36
2264 9648 0.827368 GAATGGGACTCGAAGCCTCT 59.173 55.000 3.53 0.00 0.00 3.69
2298 9682 1.909700 TTGGGTGATCAAAGCAGGAC 58.090 50.000 0.00 0.00 0.00 3.85
2304 9688 3.307762 GGTGATCAAAGCAGGACCTAAGT 60.308 47.826 0.00 0.00 0.00 2.24
2375 9759 5.883685 AAGACAGAGGCATGATCATAAGA 57.116 39.130 8.15 0.00 0.00 2.10
2378 9762 3.244491 ACAGAGGCATGATCATAAGAGGC 60.244 47.826 8.15 8.49 0.00 4.70
2429 9813 3.967332 CAAGCCATTGGAGGATTTGTT 57.033 42.857 6.95 0.00 34.48 2.83
2503 9887 0.604578 ATCACATGGCCACACTTTGC 59.395 50.000 8.16 0.00 0.00 3.68
2504 9888 0.754587 TCACATGGCCACACTTTGCA 60.755 50.000 8.16 0.00 0.00 4.08
2547 9931 0.598065 GGTGGTGGATGTGCTGAAAC 59.402 55.000 0.00 0.00 0.00 2.78
2555 9939 2.554344 GGATGTGCTGAAACTTGGGGTA 60.554 50.000 0.00 0.00 0.00 3.69
2568 9952 1.198759 TGGGGTAGAGGTTGGAGTGC 61.199 60.000 0.00 0.00 0.00 4.40
2577 9961 1.202818 AGGTTGGAGTGCAAGGAGTTC 60.203 52.381 0.00 0.00 0.00 3.01
2595 9979 0.472471 TCCACAGTGGGGAAGTGAAC 59.528 55.000 20.14 0.00 38.32 3.18
2696 10080 5.075858 AGTTGAGAATGAGAGCAGAAGAG 57.924 43.478 0.00 0.00 0.00 2.85
2707 10091 1.303309 GCAGAAGAGTGCGCCATTAT 58.697 50.000 4.18 0.00 32.74 1.28
2775 10159 7.174253 ACGTAAGGCTGTTAATTCAAGAAATGA 59.826 33.333 0.00 0.00 46.39 2.57
2811 10195 7.413475 AATGCATGTCGTTGATAGAGATTAC 57.587 36.000 0.00 0.00 0.00 1.89
2844 10237 6.750039 CACTTTTTCGGTGTAAACATGAAGTT 59.250 34.615 0.00 0.00 43.89 2.66
2892 10285 7.665559 TCATCATATAGAATTTTGTACCAGGCC 59.334 37.037 0.00 0.00 0.00 5.19
2916 10309 7.389053 GCCCACAGGTGATTATTTAGAGATTAG 59.611 40.741 0.00 0.00 34.57 1.73
2935 10328 8.338072 AGATTAGAGATGATCCAAATGAATGC 57.662 34.615 0.00 0.00 0.00 3.56
2938 10331 6.145338 AGAGATGATCCAAATGAATGCAAC 57.855 37.500 0.00 0.00 0.00 4.17
2941 10334 6.884832 AGATGATCCAAATGAATGCAACATT 58.115 32.000 14.05 14.05 39.25 2.71
2942 10335 6.761242 AGATGATCCAAATGAATGCAACATTG 59.239 34.615 18.49 13.58 37.89 2.82
2943 10336 5.179533 TGATCCAAATGAATGCAACATTGG 58.820 37.500 18.49 19.07 37.89 3.16
2947 10348 4.390603 CCAAATGAATGCAACATTGGTCTG 59.609 41.667 18.49 13.87 37.89 3.51
2997 10398 5.119279 CACATAACAACTACACAGTCTGCTC 59.881 44.000 0.00 0.00 32.29 4.26
3022 10423 1.482593 AGATGGTTACGCTCTCCCTTG 59.517 52.381 0.00 0.00 0.00 3.61
3052 10453 2.048222 GCTGCACGACTAGCCACA 60.048 61.111 0.00 0.00 33.89 4.17
3056 10457 0.599991 TGCACGACTAGCCACAGTTG 60.600 55.000 0.00 0.00 36.21 3.16
3081 10482 2.168728 GAGGTGTAGGACAATGACTCCC 59.831 54.545 0.00 0.00 0.00 4.30
3082 10483 1.906574 GGTGTAGGACAATGACTCCCA 59.093 52.381 0.00 0.00 0.00 4.37
3083 10484 2.505819 GGTGTAGGACAATGACTCCCAT 59.494 50.000 0.00 0.00 36.99 4.00
3084 10485 3.535561 GTGTAGGACAATGACTCCCATG 58.464 50.000 0.00 0.00 35.24 3.66
3085 10486 3.197766 GTGTAGGACAATGACTCCCATGA 59.802 47.826 0.00 0.00 35.24 3.07
3086 10487 4.040047 TGTAGGACAATGACTCCCATGAT 58.960 43.478 0.00 0.00 35.24 2.45
3087 10488 3.572632 AGGACAATGACTCCCATGATG 57.427 47.619 0.00 0.00 35.24 3.07
3088 10489 2.174210 AGGACAATGACTCCCATGATGG 59.826 50.000 3.98 3.98 35.24 3.51
3089 10490 2.092212 GGACAATGACTCCCATGATGGT 60.092 50.000 11.09 0.00 35.17 3.55
3090 10491 2.947652 GACAATGACTCCCATGATGGTG 59.052 50.000 11.09 5.48 35.17 4.17
3091 10492 1.679680 CAATGACTCCCATGATGGTGC 59.320 52.381 11.09 0.00 35.17 5.01
3092 10493 0.184451 ATGACTCCCATGATGGTGCC 59.816 55.000 11.09 0.00 35.17 5.01
3093 10494 1.524621 GACTCCCATGATGGTGCCG 60.525 63.158 11.09 0.00 35.17 5.69
3094 10495 2.903855 CTCCCATGATGGTGCCGC 60.904 66.667 11.09 0.00 35.17 6.53
3095 10496 4.504596 TCCCATGATGGTGCCGCC 62.505 66.667 11.09 0.00 35.17 6.13
3116 10517 4.025401 GCCAAGCACCGTTCCGTG 62.025 66.667 0.00 0.00 36.80 4.94
3117 10518 3.353836 CCAAGCACCGTTCCGTGG 61.354 66.667 0.00 0.00 34.16 4.94
3169 10570 3.837093 CACTGCGCTGTTGCATTG 58.163 55.556 18.01 1.43 45.26 2.82
3239 10641 3.936453 TCGCTGCGGTCTTGTATTAAATT 59.064 39.130 23.03 0.00 0.00 1.82
3242 10644 5.502606 GCTGCGGTCTTGTATTAAATTCTC 58.497 41.667 0.00 0.00 0.00 2.87
3418 10820 3.814504 ATTTTCCATGTCACTGGGAGT 57.185 42.857 0.00 0.00 36.89 3.85
3436 10838 4.263112 GGGAGTTCCTTTTAGCTTCTCACT 60.263 45.833 0.00 0.00 35.95 3.41
3445 10847 7.773690 TCCTTTTAGCTTCTCACTAACAAAACT 59.226 33.333 0.00 0.00 29.52 2.66
3459 10861 8.836413 CACTAACAAAACTCTGAAAGGATACAA 58.164 33.333 0.00 0.00 41.41 2.41
3481 10883 6.326323 ACAAACAAGAAAATTCCACCCACTAT 59.674 34.615 0.00 0.00 0.00 2.12
3486 10896 5.256474 AGAAAATTCCACCCACTATCACAG 58.744 41.667 0.00 0.00 0.00 3.66
3500 10910 6.350528 CCACTATCACAGTACACTGAATGACT 60.351 42.308 16.05 4.14 46.59 3.41
3577 10987 4.157246 TCCACAGCCTTGAGAGTTAAGTA 58.843 43.478 0.00 0.00 0.00 2.24
3612 11022 2.676839 GACAAGTCAGCATCAGACATGG 59.323 50.000 0.00 0.00 38.59 3.66
3643 11053 6.552008 TCCAAATCCTGTAAAAATGACTCCT 58.448 36.000 0.00 0.00 0.00 3.69
3687 11097 1.559682 GGTGGTTAATCTGAGCCCTCA 59.440 52.381 0.00 0.00 38.06 3.86
3698 11108 2.169978 CTGAGCCCTCAATGTCTGATCA 59.830 50.000 0.00 0.00 39.39 2.92
3716 11126 1.487976 TCAGATGGCCTGGATTCTGAC 59.512 52.381 15.42 0.00 43.12 3.51
3753 11165 2.408271 TTCATCCACATGGCTGACTC 57.592 50.000 3.94 0.00 39.76 3.36
3757 11169 1.742880 CCACATGGCTGACTCCACG 60.743 63.158 0.00 0.00 39.25 4.94
3759 11171 0.738762 CACATGGCTGACTCCACGAG 60.739 60.000 0.00 0.00 39.25 4.18
3771 11183 2.768527 ACTCCACGAGTCCATGATTGAT 59.231 45.455 0.00 0.00 38.71 2.57
3790 11202 0.668401 TGTGAGAGCATGCGTCACTG 60.668 55.000 35.71 0.08 41.06 3.66
3800 11212 2.320587 GCGTCACTGGCAAGAGGTG 61.321 63.158 0.00 5.04 0.00 4.00
3801 11213 1.669115 CGTCACTGGCAAGAGGTGG 60.669 63.158 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.119388 CCCGGAGAGTGTGTCGTTTTATA 60.119 47.826 0.73 0.00 0.00 0.98
2 3 2.353406 CCCGGAGAGTGTGTCGTTTTAT 60.353 50.000 0.73 0.00 0.00 1.40
3 4 1.000060 CCCGGAGAGTGTGTCGTTTTA 60.000 52.381 0.73 0.00 0.00 1.52
6 7 1.803366 GACCCGGAGAGTGTGTCGTT 61.803 60.000 0.73 0.00 0.00 3.85
8 9 2.567049 GACCCGGAGAGTGTGTCG 59.433 66.667 0.73 0.00 0.00 4.35
11 12 2.258591 CACGACCCGGAGAGTGTG 59.741 66.667 0.73 0.00 0.00 3.82
12 13 3.681835 GCACGACCCGGAGAGTGT 61.682 66.667 19.16 2.85 36.99 3.55
14 15 3.063084 GAGCACGACCCGGAGAGT 61.063 66.667 0.73 0.00 0.00 3.24
16 17 4.671590 TGGAGCACGACCCGGAGA 62.672 66.667 0.73 0.00 0.00 3.71
17 18 4.436998 GTGGAGCACGACCCGGAG 62.437 72.222 0.73 0.00 0.00 4.63
20 21 4.742201 CTGGTGGAGCACGACCCG 62.742 72.222 12.50 2.69 42.88 5.28
21 22 3.302347 CTCTGGTGGAGCACGACCC 62.302 68.421 12.50 0.00 42.88 4.46
22 23 2.100879 AACTCTGGTGGAGCACGACC 62.101 60.000 8.38 8.38 45.48 4.79
23 24 0.249911 AAACTCTGGTGGAGCACGAC 60.250 55.000 0.00 0.00 45.48 4.34
24 25 1.272490 CTAAACTCTGGTGGAGCACGA 59.728 52.381 0.00 0.00 45.48 4.35
25 26 1.272490 TCTAAACTCTGGTGGAGCACG 59.728 52.381 0.00 0.00 45.48 5.34
26 27 2.300437 ACTCTAAACTCTGGTGGAGCAC 59.700 50.000 0.00 0.00 45.48 4.40
29 30 6.239176 GGATGATACTCTAAACTCTGGTGGAG 60.239 46.154 0.00 0.00 46.87 3.86
30 31 5.598830 GGATGATACTCTAAACTCTGGTGGA 59.401 44.000 0.00 0.00 0.00 4.02
31 32 5.363868 TGGATGATACTCTAAACTCTGGTGG 59.636 44.000 0.00 0.00 0.00 4.61
32 33 6.471233 TGGATGATACTCTAAACTCTGGTG 57.529 41.667 0.00 0.00 0.00 4.17
33 34 7.682787 ATTGGATGATACTCTAAACTCTGGT 57.317 36.000 0.00 0.00 0.00 4.00
99 100 9.716531 GTTTAGTACTCCTAACAAATAACCTGT 57.283 33.333 0.00 0.00 35.36 4.00
108 109 6.950041 TGCTCCTAGTTTAGTACTCCTAACAA 59.050 38.462 0.00 0.00 38.33 2.83
146 1916 6.454981 GCACACAAAACCAAATAAACACACTC 60.455 38.462 0.00 0.00 0.00 3.51
147 1917 5.350091 GCACACAAAACCAAATAAACACACT 59.650 36.000 0.00 0.00 0.00 3.55
148 1918 5.120830 TGCACACAAAACCAAATAAACACAC 59.879 36.000 0.00 0.00 0.00 3.82
149 1919 5.237815 TGCACACAAAACCAAATAAACACA 58.762 33.333 0.00 0.00 0.00 3.72
156 3902 4.958509 TCATCATGCACACAAAACCAAAT 58.041 34.783 0.00 0.00 0.00 2.32
188 3944 2.201436 TTCGCTGTCTGTCCTCGCTC 62.201 60.000 0.00 0.00 0.00 5.03
204 3960 5.400188 GGTATTCCTTTTCCGTTTTGTTTCG 59.600 40.000 0.00 0.00 0.00 3.46
222 3978 2.346803 TGCTGTCGCAAAGAGGTATTC 58.653 47.619 0.00 0.00 44.62 1.75
241 4015 7.255569 TCGTATTCAACACTGGTATAGACTTG 58.744 38.462 0.00 0.00 0.00 3.16
251 4026 4.345288 CAATGCATCGTATTCAACACTGG 58.655 43.478 0.00 0.00 0.00 4.00
264 4039 0.031585 CCAATGGAGGCAATGCATCG 59.968 55.000 13.84 0.00 39.36 3.84
324 4105 2.227626 GCTTCTGCAGAGAAAAGAACCC 59.772 50.000 17.43 0.00 37.77 4.11
326 4107 4.514816 AGAAGCTTCTGCAGAGAAAAGAAC 59.485 41.667 27.96 6.54 42.74 3.01
327 4108 4.712476 AGAAGCTTCTGCAGAGAAAAGAA 58.288 39.130 27.96 0.00 42.74 2.52
328 4109 4.202295 TGAGAAGCTTCTGCAGAGAAAAGA 60.202 41.667 33.07 0.00 42.74 2.52
355 4136 2.378547 TGGTATCCTTTCAGGCCTTTGT 59.621 45.455 0.00 0.00 34.61 2.83
367 4148 6.874134 GCGTATGATTAATGTCTGGTATCCTT 59.126 38.462 0.00 0.00 0.00 3.36
375 4156 8.982685 AGATTTACAGCGTATGATTAATGTCTG 58.017 33.333 0.00 0.00 0.00 3.51
378 4159 9.935682 CAAAGATTTACAGCGTATGATTAATGT 57.064 29.630 0.00 0.00 0.00 2.71
382 4163 8.942338 AGTCAAAGATTTACAGCGTATGATTA 57.058 30.769 0.00 0.00 0.00 1.75
383 4164 7.849804 AGTCAAAGATTTACAGCGTATGATT 57.150 32.000 0.00 0.00 0.00 2.57
385 4166 6.978659 CCTAGTCAAAGATTTACAGCGTATGA 59.021 38.462 0.00 0.00 0.00 2.15
386 4167 6.757010 ACCTAGTCAAAGATTTACAGCGTATG 59.243 38.462 0.00 0.00 0.00 2.39
387 4168 6.875076 ACCTAGTCAAAGATTTACAGCGTAT 58.125 36.000 0.00 0.00 0.00 3.06
389 4170 5.148651 ACCTAGTCAAAGATTTACAGCGT 57.851 39.130 0.00 0.00 0.00 5.07
390 4171 7.772332 ATTACCTAGTCAAAGATTTACAGCG 57.228 36.000 0.00 0.00 0.00 5.18
410 4191 6.844696 TTGTCCGCTTCTTGATCATATTAC 57.155 37.500 0.00 0.00 0.00 1.89
411 4192 7.857734 TTTTGTCCGCTTCTTGATCATATTA 57.142 32.000 0.00 0.00 0.00 0.98
412 4193 6.757897 TTTTGTCCGCTTCTTGATCATATT 57.242 33.333 0.00 0.00 0.00 1.28
436 4217 0.916086 TGACAGTGGGCGGGATATTT 59.084 50.000 0.00 0.00 0.00 1.40
439 4220 1.610967 TGTGACAGTGGGCGGGATA 60.611 57.895 0.00 0.00 0.00 2.59
442 4223 2.579657 TACTGTGACAGTGGGCGGG 61.580 63.158 27.18 0.00 45.01 6.13
445 4226 0.105964 TGTGTACTGTGACAGTGGGC 59.894 55.000 27.18 16.86 45.01 5.36
464 4245 7.976734 TGTGTCACCGTCAAAATTATTTTCTTT 59.023 29.630 0.00 0.00 0.00 2.52
465 4246 7.484975 TGTGTCACCGTCAAAATTATTTTCTT 58.515 30.769 0.00 0.00 0.00 2.52
467 4248 7.687005 TTGTGTCACCGTCAAAATTATTTTC 57.313 32.000 0.00 0.00 0.00 2.29
468 4249 7.976734 TCTTTGTGTCACCGTCAAAATTATTTT 59.023 29.630 0.00 0.00 32.06 1.82
469 4250 7.484975 TCTTTGTGTCACCGTCAAAATTATTT 58.515 30.769 0.00 0.00 32.06 1.40
470 4251 7.033530 TCTTTGTGTCACCGTCAAAATTATT 57.966 32.000 0.00 0.00 32.06 1.40
471 4252 6.627395 TCTTTGTGTCACCGTCAAAATTAT 57.373 33.333 0.00 0.00 32.06 1.28
472 4253 6.438259 TTCTTTGTGTCACCGTCAAAATTA 57.562 33.333 0.00 0.00 32.06 1.40
473 4254 4.974368 TCTTTGTGTCACCGTCAAAATT 57.026 36.364 0.00 0.00 32.06 1.82
474 4255 4.974368 TTCTTTGTGTCACCGTCAAAAT 57.026 36.364 0.00 0.00 32.06 1.82
475 4256 4.768130 TTTCTTTGTGTCACCGTCAAAA 57.232 36.364 0.00 0.00 32.06 2.44
476 4257 4.768130 TTTTCTTTGTGTCACCGTCAAA 57.232 36.364 0.00 0.00 0.00 2.69
477 4258 4.974368 ATTTTCTTTGTGTCACCGTCAA 57.026 36.364 0.00 0.00 0.00 3.18
478 4259 6.434596 CATTATTTTCTTTGTGTCACCGTCA 58.565 36.000 0.00 0.00 0.00 4.35
479 4260 5.342259 GCATTATTTTCTTTGTGTCACCGTC 59.658 40.000 0.00 0.00 0.00 4.79
480 4261 5.219633 GCATTATTTTCTTTGTGTCACCGT 58.780 37.500 0.00 0.00 0.00 4.83
481 4262 5.218885 TGCATTATTTTCTTTGTGTCACCG 58.781 37.500 0.00 0.00 0.00 4.94
482 4263 6.144402 CACTGCATTATTTTCTTTGTGTCACC 59.856 38.462 0.00 0.00 0.00 4.02
483 4264 6.697019 ACACTGCATTATTTTCTTTGTGTCAC 59.303 34.615 0.00 0.00 31.64 3.67
484 4265 6.696583 CACACTGCATTATTTTCTTTGTGTCA 59.303 34.615 0.00 0.00 34.49 3.58
485 4266 6.917477 TCACACTGCATTATTTTCTTTGTGTC 59.083 34.615 0.00 0.00 34.49 3.67
486 4267 6.804677 TCACACTGCATTATTTTCTTTGTGT 58.195 32.000 0.00 0.00 36.70 3.72
492 4273 9.961265 CAATGATATCACACTGCATTATTTTCT 57.039 29.630 7.78 0.00 0.00 2.52
505 4286 4.083643 CCGATTCTGCCAATGATATCACAC 60.084 45.833 7.78 0.00 0.00 3.82
509 4293 3.126514 CAGCCGATTCTGCCAATGATATC 59.873 47.826 0.00 0.00 0.00 1.63
514 4298 1.731700 CCAGCCGATTCTGCCAATG 59.268 57.895 0.00 0.00 32.87 2.82
525 4310 2.058595 GGAAGGTAGAGCCAGCCGA 61.059 63.158 0.00 0.00 40.61 5.54
527 4312 1.222113 GTGGAAGGTAGAGCCAGCC 59.778 63.158 0.00 0.00 40.61 4.85
537 4322 1.771255 ACTCTCAAAGCTGTGGAAGGT 59.229 47.619 3.47 0.00 38.63 3.50
548 4333 1.534595 GGTGCTGCTCAACTCTCAAAG 59.465 52.381 0.00 0.00 0.00 2.77
562 4354 0.518636 GCCGTATATGCATGGTGCTG 59.481 55.000 10.16 0.00 45.31 4.41
596 4388 2.190578 GCCCGGATGGTCTTCAGG 59.809 66.667 0.73 0.00 36.04 3.86
597 4389 1.153289 CTGCCCGGATGGTCTTCAG 60.153 63.158 0.73 0.00 36.04 3.02
602 4394 2.361104 TTTGCTGCCCGGATGGTC 60.361 61.111 0.73 0.00 36.04 4.02
604 4396 2.361610 ACTTTGCTGCCCGGATGG 60.362 61.111 0.73 0.00 37.09 3.51
620 4413 0.523072 ACGCCATTCAATGCACTGAC 59.477 50.000 0.00 0.00 0.00 3.51
649 4442 5.253330 TGCCGAAAGAGGAGTCATTTTTAT 58.747 37.500 0.00 0.00 0.00 1.40
650 4443 4.647611 TGCCGAAAGAGGAGTCATTTTTA 58.352 39.130 0.00 0.00 0.00 1.52
683 4476 2.654749 TATCGGATGGCGCAGATTAG 57.345 50.000 10.83 0.00 0.00 1.73
702 4495 1.043116 TCCAGGCGGTTCGATCAGAT 61.043 55.000 0.00 0.00 0.00 2.90
705 4498 1.143838 CATCCAGGCGGTTCGATCA 59.856 57.895 0.00 0.00 0.00 2.92
761 4570 1.137872 GACTCCTAGTCAGCCATGTGG 59.862 57.143 2.22 0.00 44.45 4.17
804 4619 5.334421 ACTTGGTCACCTCTTACTAGTGAT 58.666 41.667 5.39 0.00 42.14 3.06
841 4656 4.170062 CGAATGGGTGCAGCGCAG 62.170 66.667 11.47 1.31 43.40 5.18
842 4657 3.974835 ATCGAATGGGTGCAGCGCA 62.975 57.895 11.47 9.57 44.29 6.09
843 4658 2.764314 AATCGAATGGGTGCAGCGC 61.764 57.895 10.24 0.00 0.00 5.92
936 4773 0.609406 GTTGGGAGGACTTGGAAGCC 60.609 60.000 0.00 0.00 0.00 4.35
954 4791 1.581954 CGAGCGGAGTCTGTCAAGT 59.418 57.895 0.00 0.00 0.00 3.16
1129 4966 1.681166 GGTGATGAAGCTGACCTGCAT 60.681 52.381 0.00 0.00 42.83 3.96
1130 4967 0.321919 GGTGATGAAGCTGACCTGCA 60.322 55.000 0.00 0.00 32.28 4.41
1155 4992 2.431942 AACCTAGCGGCGTTGACG 60.432 61.111 9.37 0.00 43.27 4.35
1440 5277 3.785859 GTGAGCCTCGGGATGCCA 61.786 66.667 3.39 0.00 0.00 4.92
1665 5527 7.872163 TGCAGTTTGAATTACATGTTTCATC 57.128 32.000 12.55 9.58 32.27 2.92
1721 5588 1.333791 GCTGTGACTGGCGTAACAAAC 60.334 52.381 2.21 0.00 34.10 2.93
1736 5603 1.232119 TGACACATCAAGCAGCTGTG 58.768 50.000 16.64 6.80 46.92 3.66
1744 5611 4.214758 TGCAGACATCTTTGACACATCAAG 59.785 41.667 0.00 0.00 45.54 3.02
1813 9196 6.472016 TGCTCCAGTACATTCTTGTGAATAA 58.528 36.000 0.00 0.00 40.61 1.40
1815 9198 4.910195 TGCTCCAGTACATTCTTGTGAAT 58.090 39.130 0.00 0.00 43.10 2.57
1823 9206 3.599343 TGTGACATGCTCCAGTACATTC 58.401 45.455 0.00 0.00 0.00 2.67
1830 9213 2.685850 TCATCTGTGACATGCTCCAG 57.314 50.000 0.00 0.00 0.00 3.86
1832 9215 5.303165 TCATTATCATCTGTGACATGCTCC 58.697 41.667 0.00 0.00 37.14 4.70
1835 9218 4.755629 AGCTCATTATCATCTGTGACATGC 59.244 41.667 0.00 0.00 37.14 4.06
1836 9219 5.989777 TGAGCTCATTATCATCTGTGACATG 59.010 40.000 13.74 0.00 37.14 3.21
1850 9233 2.029918 CGGGATCGTGATGAGCTCATTA 60.030 50.000 29.26 23.00 30.98 1.90
1869 9252 2.266689 CGGTGTAGGAAACCCCGG 59.733 66.667 0.00 0.00 40.87 5.73
1871 9254 0.177373 CTAGCGGTGTAGGAAACCCC 59.823 60.000 0.00 0.00 33.88 4.95
1877 9260 2.502142 TCAACTCTAGCGGTGTAGGA 57.498 50.000 0.00 0.00 0.00 2.94
1886 9269 5.017294 ACTTAGCCTTCATCAACTCTAGC 57.983 43.478 0.00 0.00 0.00 3.42
1907 9290 0.961753 CAGAAAGGGTTCCTGGCAAC 59.038 55.000 0.00 0.00 33.92 4.17
1909 9292 0.555769 AACAGAAAGGGTTCCTGGCA 59.444 50.000 0.00 0.00 33.92 4.92
1910 9293 1.248486 GAACAGAAAGGGTTCCTGGC 58.752 55.000 0.00 0.00 38.92 4.85
1919 9302 1.557832 TCCATACCCGGAACAGAAAGG 59.442 52.381 0.73 0.00 29.93 3.11
1920 9303 2.906354 CTCCATACCCGGAACAGAAAG 58.094 52.381 0.73 0.00 33.65 2.62
1926 9309 1.947456 GATTTGCTCCATACCCGGAAC 59.053 52.381 0.73 0.00 33.65 3.62
1948 9331 4.383989 GCTCCTCCTCAAACATCTTCTCAT 60.384 45.833 0.00 0.00 0.00 2.90
1950 9333 3.197549 AGCTCCTCCTCAAACATCTTCTC 59.802 47.826 0.00 0.00 0.00 2.87
1956 9339 2.544721 TCTCAGCTCCTCCTCAAACAT 58.455 47.619 0.00 0.00 0.00 2.71
1958 9341 2.903798 CATCTCAGCTCCTCCTCAAAC 58.096 52.381 0.00 0.00 0.00 2.93
1959 9342 1.209019 GCATCTCAGCTCCTCCTCAAA 59.791 52.381 0.00 0.00 0.00 2.69
1964 9347 0.319727 CATCGCATCTCAGCTCCTCC 60.320 60.000 0.00 0.00 0.00 4.30
2004 9387 2.028112 TGTACAATGCCTCGAGCTCTTT 60.028 45.455 12.85 2.81 44.23 2.52
2006 9389 1.186200 TGTACAATGCCTCGAGCTCT 58.814 50.000 12.85 0.00 44.23 4.09
2012 9395 3.879295 AGGATTCAATGTACAATGCCTCG 59.121 43.478 6.02 0.00 0.00 4.63
2016 9399 5.517770 GCTCAAAGGATTCAATGTACAATGC 59.482 40.000 6.02 0.00 0.00 3.56
2044 9427 3.971305 TGTCCAGACCTTCTTCCTTGTTA 59.029 43.478 0.00 0.00 0.00 2.41
2045 9428 2.777692 TGTCCAGACCTTCTTCCTTGTT 59.222 45.455 0.00 0.00 0.00 2.83
2050 9433 1.067495 CGACTGTCCAGACCTTCTTCC 60.067 57.143 1.55 0.00 0.00 3.46
2064 9447 2.672996 GCACATTGGCCCGACTGT 60.673 61.111 0.00 0.00 0.00 3.55
2095 9478 2.431260 CGGCCATTGTGTTGCTGC 60.431 61.111 2.24 0.00 0.00 5.25
2114 9498 1.350071 TTGACGCCTTGTTACCCCTA 58.650 50.000 0.00 0.00 0.00 3.53
2117 9501 0.808755 CCATTGACGCCTTGTTACCC 59.191 55.000 0.00 0.00 0.00 3.69
2138 9522 1.859427 ATTGCAAGCACTGTGCCTCG 61.859 55.000 27.74 17.45 46.52 4.63
2247 9631 2.035632 CTTAGAGGCTTCGAGTCCCAT 58.964 52.381 0.00 0.00 0.00 4.00
2255 9639 2.365408 ACGGTTTCTTAGAGGCTTCG 57.635 50.000 0.00 0.00 0.00 3.79
2264 9648 6.715718 TGATCACCCAAATAAACGGTTTCTTA 59.284 34.615 9.78 0.00 0.00 2.10
2298 9682 3.510360 TCCTCGACTTCTGGAAACTTAGG 59.490 47.826 0.00 0.00 0.00 2.69
2304 9688 2.615493 GCCATTCCTCGACTTCTGGAAA 60.615 50.000 7.12 0.00 42.28 3.13
2378 9762 4.415150 ATCACCTGTGGCGCCCAG 62.415 66.667 28.16 28.16 32.34 4.45
2391 9775 0.035152 TGGTGCCACAGGATCATCAC 60.035 55.000 0.00 0.00 0.00 3.06
2393 9777 1.386533 CTTGGTGCCACAGGATCATC 58.613 55.000 0.00 0.00 0.00 2.92
2426 9810 1.227704 CCACCCACAGTGCGTAACA 60.228 57.895 0.00 0.00 45.83 2.41
2429 9813 1.070105 GTTCCACCCACAGTGCGTA 59.930 57.895 0.00 0.00 45.83 4.42
2503 9887 4.916249 GCTTCTCATTCAAAAACTGCTCTG 59.084 41.667 0.00 0.00 0.00 3.35
2504 9888 4.826183 AGCTTCTCATTCAAAAACTGCTCT 59.174 37.500 0.00 0.00 0.00 4.09
2547 9931 1.279271 CACTCCAACCTCTACCCCAAG 59.721 57.143 0.00 0.00 0.00 3.61
2555 9939 0.689623 CTCCTTGCACTCCAACCTCT 59.310 55.000 0.00 0.00 0.00 3.69
2568 9952 0.250901 CCCCACTGTGGAACTCCTTG 60.251 60.000 27.94 8.33 40.96 3.61
2577 9961 0.182537 TGTTCACTTCCCCACTGTGG 59.817 55.000 20.01 20.01 37.25 4.17
2595 9979 5.556915 TCTGGTAACCATAACCTCTTGTTG 58.443 41.667 0.00 0.00 37.83 3.33
2707 10091 2.034066 CGAAAGCCCTCCTTGCCA 59.966 61.111 0.00 0.00 33.01 4.92
2775 10159 4.036734 ACGACATGCATTTGTCTTGTTTCT 59.963 37.500 16.31 0.00 43.10 2.52
2811 10195 3.139077 ACACCGAAAAAGTGAGCTTAGG 58.861 45.455 0.00 0.00 38.63 2.69
2820 10213 6.445357 ACTTCATGTTTACACCGAAAAAGT 57.555 33.333 0.00 0.00 0.00 2.66
2892 10285 9.703892 CTCTAATCTCTAAATAATCACCTGTGG 57.296 37.037 0.00 0.00 0.00 4.17
2916 10309 5.898174 TGTTGCATTCATTTGGATCATCTC 58.102 37.500 0.00 0.00 0.00 2.75
2933 10326 4.153296 CGTACATAACAGACCAATGTTGCA 59.847 41.667 2.48 0.00 43.14 4.08
2935 10328 4.391830 AGCGTACATAACAGACCAATGTTG 59.608 41.667 2.48 0.00 43.14 3.33
2938 10331 4.433615 AGAGCGTACATAACAGACCAATG 58.566 43.478 0.00 0.00 0.00 2.82
2941 10334 4.021807 TGAAAGAGCGTACATAACAGACCA 60.022 41.667 0.00 0.00 0.00 4.02
2942 10335 4.491676 TGAAAGAGCGTACATAACAGACC 58.508 43.478 0.00 0.00 0.00 3.85
2943 10336 5.005779 CCATGAAAGAGCGTACATAACAGAC 59.994 44.000 0.00 0.00 0.00 3.51
2947 10348 3.621268 TGCCATGAAAGAGCGTACATAAC 59.379 43.478 0.00 0.00 0.00 1.89
2997 10398 3.004944 GGGAGAGCGTAACCATCTAGAAG 59.995 52.174 0.00 0.00 0.00 2.85
3052 10453 1.349067 GTCCTACACCTCCACCAACT 58.651 55.000 0.00 0.00 0.00 3.16
3056 10457 1.906574 TCATTGTCCTACACCTCCACC 59.093 52.381 0.00 0.00 0.00 4.61
3064 10465 3.449918 TCATGGGAGTCATTGTCCTACA 58.550 45.455 0.00 0.00 32.92 2.74
3109 10510 0.391263 CCTAGTTGCTCCCACGGAAC 60.391 60.000 0.00 0.00 35.73 3.62
3110 10511 1.550130 CCCTAGTTGCTCCCACGGAA 61.550 60.000 0.00 0.00 0.00 4.30
3111 10512 1.987855 CCCTAGTTGCTCCCACGGA 60.988 63.158 0.00 0.00 0.00 4.69
3112 10513 1.961180 CTCCCTAGTTGCTCCCACGG 61.961 65.000 0.00 0.00 0.00 4.94
3113 10514 1.517832 CTCCCTAGTTGCTCCCACG 59.482 63.158 0.00 0.00 0.00 4.94
3114 10515 1.627297 CCCTCCCTAGTTGCTCCCAC 61.627 65.000 0.00 0.00 0.00 4.61
3115 10516 1.306997 CCCTCCCTAGTTGCTCCCA 60.307 63.158 0.00 0.00 0.00 4.37
3116 10517 2.073101 CCCCTCCCTAGTTGCTCCC 61.073 68.421 0.00 0.00 0.00 4.30
3117 10518 2.747443 GCCCCTCCCTAGTTGCTCC 61.747 68.421 0.00 0.00 0.00 4.70
3169 10570 1.064621 CATGTACAATGCCTGGCGC 59.935 57.895 14.98 0.00 38.31 6.53
3171 10572 1.438814 GCCATGTACAATGCCTGGC 59.561 57.895 18.88 18.88 44.91 4.85
3179 10580 8.519526 CAAGGTCTTTTATTAAGCCATGTACAA 58.480 33.333 0.00 0.00 0.00 2.41
3197 10598 5.551760 CGATTAGCATGAAACAAGGTCTT 57.448 39.130 0.00 0.00 0.00 3.01
3275 10677 2.880890 GCACACAGACCAAATGAACTCT 59.119 45.455 0.00 0.00 0.00 3.24
3281 10683 3.571571 CTTCATGCACACAGACCAAATG 58.428 45.455 0.00 0.00 0.00 2.32
3285 10687 2.632643 GCTTCATGCACACAGACCA 58.367 52.632 0.00 0.00 42.31 4.02
3407 10809 3.075148 GCTAAAAGGAACTCCCAGTGAC 58.925 50.000 0.00 0.00 38.49 3.67
3418 10820 8.403236 GTTTTGTTAGTGAGAAGCTAAAAGGAA 58.597 33.333 0.00 0.00 31.22 3.36
3436 10838 9.179909 TGTTTGTATCCTTTCAGAGTTTTGTTA 57.820 29.630 0.00 0.00 0.00 2.41
3445 10847 9.965824 GAATTTTCTTGTTTGTATCCTTTCAGA 57.034 29.630 0.00 0.00 0.00 3.27
3459 10861 6.015434 GTGATAGTGGGTGGAATTTTCTTGTT 60.015 38.462 0.00 0.00 0.00 2.83
3481 10883 5.529581 TTCAGTCATTCAGTGTACTGTGA 57.470 39.130 11.44 6.58 44.12 3.58
3486 10896 5.578727 GTGGAGATTCAGTCATTCAGTGTAC 59.421 44.000 0.00 0.00 0.00 2.90
3500 10910 6.433716 TGCATTATTTTCTGTGTGGAGATTCA 59.566 34.615 0.00 0.00 0.00 2.57
3577 10987 4.816392 TGACTTGTCGTATATGCACACTT 58.184 39.130 0.00 0.00 0.00 3.16
3612 11022 6.790232 TTTTTACAGGATTTGGATGATCCC 57.210 37.500 9.36 0.00 43.36 3.85
3643 11053 1.664649 CGCCTGTCACGCTCAAAGA 60.665 57.895 0.00 0.00 0.00 2.52
3667 11077 1.559682 TGAGGGCTCAGATTAACCACC 59.440 52.381 0.00 0.00 34.14 4.61
3687 11097 2.158652 CCAGGCCATCTGATCAGACATT 60.159 50.000 27.37 9.59 46.18 2.71
3698 11108 0.467384 CGTCAGAATCCAGGCCATCT 59.533 55.000 5.01 0.00 0.00 2.90
3727 11137 3.552875 AGCCATGTGGATGAATCTTCAG 58.447 45.455 2.55 0.00 36.75 3.02
3753 11165 2.610833 CACATCAATCATGGACTCGTGG 59.389 50.000 0.00 0.00 36.72 4.94
3757 11169 3.808726 GCTCTCACATCAATCATGGACTC 59.191 47.826 0.00 0.00 36.72 3.36
3759 11171 3.538591 TGCTCTCACATCAATCATGGAC 58.461 45.455 0.00 0.00 36.72 4.02
3767 11179 1.338011 TGACGCATGCTCTCACATCAA 60.338 47.619 17.13 0.00 0.00 2.57
3771 11183 0.668401 CAGTGACGCATGCTCTCACA 60.668 55.000 31.28 16.82 37.39 3.58


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

AutoCloner maintained by Alex Coulton.