Multiple sequence alignment - TraesCS5A01G482000

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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 TraesCS5A01G482000 chr5A 100.000 3778 0 0 1 3778 654063392 654067169 0.000000e+00 6977.0
1 TraesCS5A01G482000 chr5A 85.552 353 39 10 225 573 580422103 580422447 3.590000e-95 359.0
2 TraesCS5A01G482000 chr5A 84.943 352 48 5 225 573 599258883 599259232 6.000000e-93 351.0
3 TraesCS5A01G482000 chr5A 90.196 204 13 6 572 773 585007469 585007667 3.740000e-65 259.0
4 TraesCS5A01G482000 chr5A 90.206 194 12 6 572 763 580422883 580423071 2.910000e-61 246.0
5 TraesCS5A01G482000 chr5A 83.908 87 14 0 3436 3522 545128451 545128537 2.420000e-12 84.2
6 TraesCS5A01G482000 chr5B 96.184 1258 46 2 1894 3150 662645318 662646574 0.000000e+00 2056.0
7 TraesCS5A01G482000 chr5B 96.218 1084 36 3 797 1875 662644248 662645331 0.000000e+00 1770.0
8 TraesCS5A01G482000 chr5B 84.842 442 51 10 3307 3745 662646612 662647040 7.500000e-117 431.0
9 TraesCS5A01G482000 chr5B 87.075 147 18 1 3146 3292 241666139 241665994 8.400000e-37 165.0
10 TraesCS5A01G482000 chr5D 94.909 1257 57 5 1894 3150 526865470 526866719 0.000000e+00 1960.0
11 TraesCS5A01G482000 chr5D 95.410 1111 37 6 771 1875 526864381 526865483 0.000000e+00 1757.0
12 TraesCS5A01G482000 chr5D 93.778 225 14 0 1 225 526864169 526864393 4.670000e-89 339.0
13 TraesCS5A01G482000 chr5D 89.960 249 23 2 3527 3774 526867293 526867540 1.690000e-83 320.0
14 TraesCS5A01G482000 chr5D 86.321 212 22 3 568 774 453012789 453012580 1.370000e-54 224.0
15 TraesCS5A01G482000 chr5D 84.112 214 29 3 3311 3522 526866788 526866998 6.400000e-48 202.0
16 TraesCS5A01G482000 chr2A 92.837 349 21 2 225 573 27910084 27909740 1.570000e-138 503.0
17 TraesCS5A01G482000 chr4A 85.593 354 41 10 225 573 78176666 78176318 2.770000e-96 363.0
18 TraesCS5A01G482000 chr4A 90.686 204 12 5 572 773 78016452 78016254 8.050000e-67 265.0
19 TraesCS5A01G482000 chr4A 86.179 246 32 2 225 470 78017553 78017310 8.050000e-67 265.0
20 TraesCS5A01G482000 chr4A 90.244 205 13 4 572 773 78175881 78175681 1.040000e-65 261.0
21 TraesCS5A01G482000 chr4A 90.278 144 13 1 225 368 78017738 78017596 1.790000e-43 187.0
22 TraesCS5A01G482000 chr4A 83.505 97 15 1 3426 3522 101973744 101973649 5.200000e-14 89.8
23 TraesCS5A01G482000 chr3D 87.097 217 27 1 7 222 551035823 551036039 1.050000e-60 244.0
24 TraesCS5A01G482000 chr3D 94.068 118 7 0 106 223 396397620 396397503 3.000000e-41 180.0
25 TraesCS5A01G482000 chr3D 93.220 118 8 0 106 223 396397455 396397338 1.390000e-39 174.0
26 TraesCS5A01G482000 chr4B 84.793 217 32 1 9 224 489009063 489009279 2.290000e-52 217.0
27 TraesCS5A01G482000 chr2D 84.466 206 27 2 9 209 606195818 606195613 8.280000e-47 198.0
28 TraesCS5A01G482000 chr2D 90.566 53 5 0 3465 3517 638043912 638043860 1.880000e-08 71.3
29 TraesCS5A01G482000 chr2D 100.000 28 0 0 3471 3498 130844494 130844467 7.000000e-03 52.8
30 TraesCS5A01G482000 chr6B 84.848 198 22 8 575 769 666777982 666778174 3.850000e-45 193.0
31 TraesCS5A01G482000 chr7B 84.694 196 24 6 576 769 403411203 403411394 1.390000e-44 191.0
32 TraesCS5A01G482000 chr7B 83.673 196 24 5 576 769 567571218 567571407 1.080000e-40 178.0
33 TraesCS5A01G482000 chr2B 84.694 196 21 6 576 769 204918885 204918697 1.790000e-43 187.0
34 TraesCS5A01G482000 chr3B 78.438 320 34 18 230 546 780082867 780082580 3.880000e-40 176.0
35 TraesCS5A01G482000 chr6D 81.884 138 22 3 3387 3522 363594002 363594138 3.080000e-21 113.0
36 TraesCS5A01G482000 chr7A 87.500 96 12 0 3427 3522 274393107 274393202 1.110000e-20 111.0
37 TraesCS5A01G482000 chr1B 85.227 88 9 2 3435 3522 350800488 350800405 1.870000e-13 87.9


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 TraesCS5A01G482000 chr5A 654063392 654067169 3777 False 6977.0 6977 100.000000 1 3778 1 chr5A.!!$F4 3777
1 TraesCS5A01G482000 chr5A 580422103 580423071 968 False 302.5 359 87.879000 225 763 2 chr5A.!!$F5 538
2 TraesCS5A01G482000 chr5B 662644248 662647040 2792 False 1419.0 2056 92.414667 797 3745 3 chr5B.!!$F1 2948
3 TraesCS5A01G482000 chr5D 526864169 526867540 3371 False 915.6 1960 91.633800 1 3774 5 chr5D.!!$F1 3773
4 TraesCS5A01G482000 chr4A 78175681 78176666 985 True 312.0 363 87.918500 225 773 2 chr4A.!!$R3 548
5 TraesCS5A01G482000 chr4A 78016254 78017738 1484 True 239.0 265 89.047667 225 773 3 chr4A.!!$R2 548

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
346 347 0.303191 AAAAACAAAACATGCCGCGC 59.697 45.000 0.00 0.0 0.00 6.86 F
374 560 0.471211 ACTCCCGACCTCTGGTTTCA 60.471 55.000 0.00 0.0 35.25 2.69 F
773 1720 0.861837 GCGTCAAATAGGATCTGCCG 59.138 55.000 0.00 0.0 43.43 5.69 F
774 1721 1.538204 GCGTCAAATAGGATCTGCCGA 60.538 52.381 0.00 0.0 43.43 5.54 F
953 1901 1.669760 CCTAGCAAACCCGCGTTCA 60.670 57.895 4.92 0.0 36.85 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1331 2281 1.093496 CAGCATCAGCAGATTGGCGA 61.093 55.000 0.0 0.0 45.49 5.54 R
1730 2686 1.847737 AGCCAATAAACCCCGATACCA 59.152 47.619 0.0 0.0 0.00 3.25 R
2127 3083 2.416972 GGGTGGACACGACAGATAGTTC 60.417 54.545 0.0 0.0 0.00 3.01 R
2762 3718 3.695830 ATCTTCTACCGCAAACCTTCA 57.304 42.857 0.0 0.0 0.00 3.02 R
3095 4052 8.952278 AGAAACAATATTAAAACACGATGCCTA 58.048 29.630 0.0 0.0 0.00 3.93 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
23 24 4.431661 TGTGAAATATGTTTGCGATGCA 57.568 36.364 0.00 0.00 36.47 3.96
43 44 3.803021 GCATTTTTCTTCACATGTGGCCA 60.803 43.478 25.16 0.00 0.00 5.36
68 69 2.232941 ACTTTAGTGGTAAGCAGCGCTA 59.767 45.455 10.99 0.00 42.71 4.26
82 83 2.102553 GCTACGGAGCGGAGTGAC 59.897 66.667 2.50 0.00 40.38 3.67
102 103 3.869272 CCCGTGCTCGAATGCTGC 61.869 66.667 10.21 0.00 39.71 5.25
209 210 1.063649 GCGTCGCTCTCCGTATTCA 59.936 57.895 10.68 0.00 38.35 2.57
218 219 1.754803 TCTCCGTATTCACCGCAGAAT 59.245 47.619 5.96 5.96 40.99 2.40
219 220 1.860950 CTCCGTATTCACCGCAGAATG 59.139 52.381 9.88 0.00 38.60 2.67
266 267 2.330372 TGCGTCGAACGGTAGAGCT 61.330 57.895 0.00 0.00 42.82 4.09
325 326 2.854777 CAGCGTCGAACCTAGAATTCAG 59.145 50.000 8.44 3.29 0.00 3.02
326 327 1.588861 GCGTCGAACCTAGAATTCAGC 59.411 52.381 8.44 0.00 0.00 4.26
344 345 1.330213 AGCAAAAACAAAACATGCCGC 59.670 42.857 0.00 0.00 37.73 6.53
346 347 0.303191 AAAAACAAAACATGCCGCGC 59.697 45.000 0.00 0.00 0.00 6.86
352 353 1.570347 AAAACATGCCGCGCGAAGTA 61.570 50.000 34.63 16.08 0.00 2.24
368 554 2.131776 AGTAGAACTCCCGACCTCTG 57.868 55.000 0.00 0.00 0.00 3.35
372 558 0.685660 GAACTCCCGACCTCTGGTTT 59.314 55.000 0.00 0.00 35.25 3.27
374 560 0.471211 ACTCCCGACCTCTGGTTTCA 60.471 55.000 0.00 0.00 35.25 2.69
397 583 2.313317 AGACACTTGGTAACCACTCGA 58.687 47.619 0.00 0.00 30.78 4.04
401 587 3.118519 ACACTTGGTAACCACTCGAACTT 60.119 43.478 0.00 0.00 30.78 2.66
405 591 4.877378 TGGTAACCACTCGAACTTGTAT 57.123 40.909 0.00 0.00 0.00 2.29
407 593 4.281435 TGGTAACCACTCGAACTTGTATGA 59.719 41.667 0.00 0.00 0.00 2.15
411 597 6.525578 AACCACTCGAACTTGTATGATAGA 57.474 37.500 0.00 0.00 0.00 1.98
415 601 6.074088 CCACTCGAACTTGTATGATAGAATGC 60.074 42.308 0.00 0.00 0.00 3.56
445 631 6.059484 TGCAGCACTAAACTTTTAAGTACCT 58.941 36.000 0.00 0.00 38.57 3.08
447 633 7.881232 TGCAGCACTAAACTTTTAAGTACCTAT 59.119 33.333 0.00 0.00 38.57 2.57
448 634 8.388853 GCAGCACTAAACTTTTAAGTACCTATC 58.611 37.037 0.00 0.00 38.57 2.08
510 698 6.219417 ACATTCATGGAAAAACTGTGAACA 57.781 33.333 0.00 0.00 32.30 3.18
513 701 7.605691 ACATTCATGGAAAAACTGTGAACAAAA 59.394 29.630 0.00 0.00 32.30 2.44
517 705 9.658799 TCATGGAAAAACTGTGAACAAAATTTA 57.341 25.926 0.00 0.00 0.00 1.40
603 1548 6.413783 ACCGGGACAAAATAATTGAAAACT 57.586 33.333 6.32 0.00 0.00 2.66
612 1557 8.404765 ACAAAATAATTGAAAACTGGCCAAAAG 58.595 29.630 7.01 0.00 0.00 2.27
613 1558 8.619546 CAAAATAATTGAAAACTGGCCAAAAGA 58.380 29.630 7.01 0.00 0.00 2.52
614 1559 7.967890 AATAATTGAAAACTGGCCAAAAGAG 57.032 32.000 7.01 0.00 0.00 2.85
615 1560 5.357742 AATTGAAAACTGGCCAAAAGAGT 57.642 34.783 7.01 0.00 0.00 3.24
616 1561 3.799281 TGAAAACTGGCCAAAAGAGTG 57.201 42.857 7.01 0.00 0.00 3.51
617 1562 3.360867 TGAAAACTGGCCAAAAGAGTGA 58.639 40.909 7.01 0.00 0.00 3.41
618 1563 3.766591 TGAAAACTGGCCAAAAGAGTGAA 59.233 39.130 7.01 0.00 0.00 3.18
676 1623 2.099098 CCGCAAGAAACAAGGAAACAGT 59.901 45.455 0.00 0.00 43.02 3.55
686 1633 2.457366 AGGAAACAGTAGCGAACCAG 57.543 50.000 0.00 0.00 0.00 4.00
701 1648 2.423898 CCAGATCCGTACGTGGGCT 61.424 63.158 15.21 3.02 0.00 5.19
773 1720 0.861837 GCGTCAAATAGGATCTGCCG 59.138 55.000 0.00 0.00 43.43 5.69
774 1721 1.538204 GCGTCAAATAGGATCTGCCGA 60.538 52.381 0.00 0.00 43.43 5.54
775 1722 2.821546 CGTCAAATAGGATCTGCCGAA 58.178 47.619 0.00 0.00 43.43 4.30
953 1901 1.669760 CCTAGCAAACCCGCGTTCA 60.670 57.895 4.92 0.00 36.85 3.18
1171 2121 2.109181 GCGCTTCTATTCCCCGCT 59.891 61.111 0.00 0.00 41.28 5.52
1331 2281 1.736645 CGGCGTCGATGTCAAGGTT 60.737 57.895 1.44 0.00 39.00 3.50
1574 2526 3.066291 TCGGCTGGATGTGTATTTTGT 57.934 42.857 0.00 0.00 0.00 2.83
1698 2654 8.944138 TCCATATATTGGGACTATTTTCACAGA 58.056 33.333 4.69 0.00 46.45 3.41
1730 2686 2.642807 TCCCGAAGAGTTCTCCCAAAAT 59.357 45.455 0.00 0.00 0.00 1.82
1864 2820 8.554870 AGTTTATCCATCAGCCATCATATATGT 58.445 33.333 12.42 0.00 0.00 2.29
1957 2913 9.613428 TCGAACAATATTTACCAGAGAATGAAT 57.387 29.630 0.00 0.00 0.00 2.57
2116 3072 7.502226 AGACTGGTCTGTTTTATTTGTCATCAA 59.498 33.333 2.15 0.00 38.75 2.57
2189 3145 8.239314 GCTTCACTAATCTCAACATTGAAATCA 58.761 33.333 0.00 0.00 36.64 2.57
2215 3171 1.684983 GCCTGATTTCATGGTGGATGG 59.315 52.381 0.00 0.00 32.26 3.51
2385 3341 2.837947 TCAGGGATCACAACCAGAGAT 58.162 47.619 0.00 0.00 0.00 2.75
2446 3402 4.454504 CGTTGGCAGTTGGTAAGATAAAGT 59.545 41.667 0.00 0.00 0.00 2.66
2617 3573 9.014297 ACAAGTAGATTTTGCTTTACTATTGCT 57.986 29.630 0.00 0.00 28.30 3.91
2653 3609 8.913487 ATCATAGCAACATGAATGATTGTCTA 57.087 30.769 0.00 0.39 38.39 2.59
2871 3827 2.422276 ACAAATTTGCCGTTGAGCTC 57.578 45.000 18.12 6.82 0.00 4.09
2922 3878 6.889301 ACTTCATCGGCAATTCATGATTAT 57.111 33.333 0.00 0.00 0.00 1.28
3095 4052 5.174395 GTGTGCTGTATCATCTGTCTTTCT 58.826 41.667 0.00 0.00 0.00 2.52
3150 4107 8.009974 GCGAATTTGCTACAGTACATATTTAGG 58.990 37.037 10.62 0.00 0.00 2.69
3151 4108 8.495949 CGAATTTGCTACAGTACATATTTAGGG 58.504 37.037 0.00 0.00 0.00 3.53
3152 4109 9.555727 GAATTTGCTACAGTACATATTTAGGGA 57.444 33.333 0.00 0.00 0.00 4.20
3153 4110 8.904099 ATTTGCTACAGTACATATTTAGGGAC 57.096 34.615 0.00 0.00 0.00 4.46
3154 4111 7.670605 TTGCTACAGTACATATTTAGGGACT 57.329 36.000 0.00 0.00 46.37 3.85
3155 4112 7.286215 TGCTACAGTACATATTTAGGGACTC 57.714 40.000 0.00 0.00 41.75 3.36
3156 4113 7.067421 TGCTACAGTACATATTTAGGGACTCT 58.933 38.462 0.00 0.00 41.75 3.24
3157 4114 7.563924 TGCTACAGTACATATTTAGGGACTCTT 59.436 37.037 0.00 0.00 41.75 2.85
3158 4115 8.083462 GCTACAGTACATATTTAGGGACTCTTC 58.917 40.741 0.00 0.00 41.75 2.87
3159 4116 7.040473 ACAGTACATATTTAGGGACTCTTCG 57.960 40.000 0.00 0.00 41.75 3.79
3160 4117 6.040616 ACAGTACATATTTAGGGACTCTTCGG 59.959 42.308 0.00 0.00 41.75 4.30
3161 4118 6.264744 CAGTACATATTTAGGGACTCTTCGGA 59.735 42.308 0.00 0.00 41.75 4.55
3162 4119 7.011382 AGTACATATTTAGGGACTCTTCGGAT 58.989 38.462 0.00 0.00 41.75 4.18
3163 4120 6.749036 ACATATTTAGGGACTCTTCGGATT 57.251 37.500 0.00 0.00 41.75 3.01
3164 4121 7.850935 ACATATTTAGGGACTCTTCGGATTA 57.149 36.000 0.00 0.00 41.75 1.75
3165 4122 7.668492 ACATATTTAGGGACTCTTCGGATTAC 58.332 38.462 0.00 0.00 41.75 1.89
3166 4123 5.548181 ATTTAGGGACTCTTCGGATTACC 57.452 43.478 0.00 0.00 41.75 2.85
3167 4124 2.850695 AGGGACTCTTCGGATTACCT 57.149 50.000 0.00 0.00 33.64 3.08
3168 4125 2.668625 AGGGACTCTTCGGATTACCTC 58.331 52.381 0.00 0.00 33.21 3.85
3169 4126 1.687660 GGGACTCTTCGGATTACCTCC 59.312 57.143 0.00 0.00 41.07 4.30
3177 4134 2.208527 GGATTACCTCCGCTCCACA 58.791 57.895 0.00 0.00 33.29 4.17
3178 4135 0.105039 GGATTACCTCCGCTCCACAG 59.895 60.000 0.00 0.00 33.29 3.66
3179 4136 0.530870 GATTACCTCCGCTCCACAGC 60.531 60.000 0.00 0.00 42.96 4.40
3180 4137 0.978146 ATTACCTCCGCTCCACAGCT 60.978 55.000 0.00 0.00 44.40 4.24
3181 4138 1.605058 TTACCTCCGCTCCACAGCTC 61.605 60.000 0.00 0.00 44.40 4.09
3182 4139 4.154347 CCTCCGCTCCACAGCTCC 62.154 72.222 0.00 0.00 44.40 4.70
3183 4140 4.154347 CTCCGCTCCACAGCTCCC 62.154 72.222 0.00 0.00 44.40 4.30
3185 4142 4.767255 CCGCTCCACAGCTCCCAC 62.767 72.222 0.00 0.00 44.40 4.61
3186 4143 3.699894 CGCTCCACAGCTCCCACT 61.700 66.667 0.00 0.00 44.40 4.00
3187 4144 2.267324 GCTCCACAGCTCCCACTC 59.733 66.667 0.00 0.00 43.09 3.51
3188 4145 2.985456 CTCCACAGCTCCCACTCC 59.015 66.667 0.00 0.00 0.00 3.85
3189 4146 2.607750 TCCACAGCTCCCACTCCC 60.608 66.667 0.00 0.00 0.00 4.30
3190 4147 4.087892 CCACAGCTCCCACTCCCG 62.088 72.222 0.00 0.00 0.00 5.14
3191 4148 4.087892 CACAGCTCCCACTCCCGG 62.088 72.222 0.00 0.00 0.00 5.73
3192 4149 4.316823 ACAGCTCCCACTCCCGGA 62.317 66.667 0.73 0.00 0.00 5.14
3205 4162 3.072468 CCGGAGCGGGTGGAGTTA 61.072 66.667 0.00 0.00 44.15 2.24
3206 4163 2.183555 CGGAGCGGGTGGAGTTAC 59.816 66.667 0.00 0.00 0.00 2.50
3207 4164 2.642254 CGGAGCGGGTGGAGTTACA 61.642 63.158 0.00 0.00 0.00 2.41
3208 4165 1.218316 GGAGCGGGTGGAGTTACAG 59.782 63.158 0.00 0.00 0.00 2.74
3209 4166 1.542187 GGAGCGGGTGGAGTTACAGT 61.542 60.000 0.00 0.00 0.00 3.55
3210 4167 0.389948 GAGCGGGTGGAGTTACAGTG 60.390 60.000 0.00 0.00 0.00 3.66
3211 4168 1.375523 GCGGGTGGAGTTACAGTGG 60.376 63.158 0.00 0.00 0.00 4.00
3212 4169 1.823169 GCGGGTGGAGTTACAGTGGA 61.823 60.000 0.00 0.00 0.00 4.02
3213 4170 0.682852 CGGGTGGAGTTACAGTGGAA 59.317 55.000 0.00 0.00 0.00 3.53
3214 4171 1.071071 CGGGTGGAGTTACAGTGGAAA 59.929 52.381 0.00 0.00 0.00 3.13
3215 4172 2.485835 CGGGTGGAGTTACAGTGGAAAA 60.486 50.000 0.00 0.00 0.00 2.29
3216 4173 3.558033 GGGTGGAGTTACAGTGGAAAAA 58.442 45.455 0.00 0.00 0.00 1.94
3217 4174 4.149598 GGGTGGAGTTACAGTGGAAAAAT 58.850 43.478 0.00 0.00 0.00 1.82
3218 4175 4.022329 GGGTGGAGTTACAGTGGAAAAATG 60.022 45.833 0.00 0.00 0.00 2.32
3219 4176 4.583073 GGTGGAGTTACAGTGGAAAAATGT 59.417 41.667 0.00 0.00 0.00 2.71
3220 4177 5.507315 GGTGGAGTTACAGTGGAAAAATGTG 60.507 44.000 0.00 0.00 0.00 3.21
3221 4178 4.582656 TGGAGTTACAGTGGAAAAATGTGG 59.417 41.667 0.00 0.00 0.00 4.17
3222 4179 4.825085 GGAGTTACAGTGGAAAAATGTGGA 59.175 41.667 0.00 0.00 0.00 4.02
3223 4180 5.048713 GGAGTTACAGTGGAAAAATGTGGAG 60.049 44.000 0.00 0.00 0.00 3.86
3224 4181 4.278419 AGTTACAGTGGAAAAATGTGGAGC 59.722 41.667 0.00 0.00 0.00 4.70
3225 4182 1.608590 ACAGTGGAAAAATGTGGAGCG 59.391 47.619 0.00 0.00 0.00 5.03
3226 4183 0.598065 AGTGGAAAAATGTGGAGCGC 59.402 50.000 0.00 0.00 0.00 5.92
3227 4184 0.388520 GTGGAAAAATGTGGAGCGCC 60.389 55.000 2.29 0.00 0.00 6.53
3228 4185 0.539438 TGGAAAAATGTGGAGCGCCT 60.539 50.000 8.34 0.00 34.31 5.52
3229 4186 0.109132 GGAAAAATGTGGAGCGCCTG 60.109 55.000 8.34 0.00 34.31 4.85
3230 4187 0.598065 GAAAAATGTGGAGCGCCTGT 59.402 50.000 8.34 0.00 34.31 4.00
3231 4188 1.000274 GAAAAATGTGGAGCGCCTGTT 60.000 47.619 8.34 0.00 34.31 3.16
3232 4189 1.039856 AAAATGTGGAGCGCCTGTTT 58.960 45.000 8.34 3.40 34.31 2.83
3233 4190 0.598065 AAATGTGGAGCGCCTGTTTC 59.402 50.000 8.34 0.00 34.31 2.78
3234 4191 1.244019 AATGTGGAGCGCCTGTTTCC 61.244 55.000 8.34 4.38 34.31 3.13
3235 4192 2.032681 GTGGAGCGCCTGTTTCCT 59.967 61.111 8.34 0.00 34.31 3.36
3236 4193 1.295423 GTGGAGCGCCTGTTTCCTA 59.705 57.895 8.34 0.00 34.31 2.94
3237 4194 0.741221 GTGGAGCGCCTGTTTCCTAG 60.741 60.000 8.34 0.00 34.31 3.02
3238 4195 1.815840 GGAGCGCCTGTTTCCTAGC 60.816 63.158 2.29 0.00 0.00 3.42
3239 4196 1.219393 GAGCGCCTGTTTCCTAGCT 59.781 57.895 2.29 0.00 37.69 3.32
3240 4197 0.808060 GAGCGCCTGTTTCCTAGCTC 60.808 60.000 2.29 0.00 43.11 4.09
3241 4198 1.815840 GCGCCTGTTTCCTAGCTCC 60.816 63.158 0.00 0.00 0.00 4.70
3242 4199 1.596934 CGCCTGTTTCCTAGCTCCA 59.403 57.895 0.00 0.00 0.00 3.86
3243 4200 0.741221 CGCCTGTTTCCTAGCTCCAC 60.741 60.000 0.00 0.00 0.00 4.02
3244 4201 0.324943 GCCTGTTTCCTAGCTCCACA 59.675 55.000 0.00 0.00 0.00 4.17
3245 4202 1.677217 GCCTGTTTCCTAGCTCCACAG 60.677 57.143 0.00 0.00 35.59 3.66
3254 4211 3.713650 GCTCCACAGCTCCTGGTA 58.286 61.111 6.81 0.00 43.09 3.25
3255 4212 2.216148 GCTCCACAGCTCCTGGTAT 58.784 57.895 6.81 0.00 43.09 2.73
3256 4213 0.543749 GCTCCACAGCTCCTGGTATT 59.456 55.000 6.81 0.00 43.09 1.89
3257 4214 1.065126 GCTCCACAGCTCCTGGTATTT 60.065 52.381 6.81 0.00 43.09 1.40
3258 4215 2.911484 CTCCACAGCTCCTGGTATTTC 58.089 52.381 6.81 0.00 35.51 2.17
3259 4216 1.207089 TCCACAGCTCCTGGTATTTCG 59.793 52.381 6.81 0.00 35.51 3.46
3260 4217 1.009829 CACAGCTCCTGGTATTTCGC 58.990 55.000 0.00 0.00 35.51 4.70
3261 4218 0.460284 ACAGCTCCTGGTATTTCGCG 60.460 55.000 0.00 0.00 35.51 5.87
3262 4219 1.144057 AGCTCCTGGTATTTCGCGG 59.856 57.895 6.13 0.00 0.00 6.46
3263 4220 1.143183 GCTCCTGGTATTTCGCGGA 59.857 57.895 6.13 0.00 0.00 5.54
3264 4221 0.876342 GCTCCTGGTATTTCGCGGAG 60.876 60.000 6.13 2.22 43.18 4.63
3278 4235 2.772739 CGGAGCAAGTGGGATTCTG 58.227 57.895 0.00 0.00 0.00 3.02
3279 4236 0.250234 CGGAGCAAGTGGGATTCTGA 59.750 55.000 0.00 0.00 0.00 3.27
3280 4237 1.339055 CGGAGCAAGTGGGATTCTGAA 60.339 52.381 0.00 0.00 0.00 3.02
3281 4238 2.087646 GGAGCAAGTGGGATTCTGAAC 58.912 52.381 0.00 0.00 0.00 3.18
3282 4239 2.553028 GGAGCAAGTGGGATTCTGAACA 60.553 50.000 0.00 0.00 0.00 3.18
3283 4240 2.746362 GAGCAAGTGGGATTCTGAACAG 59.254 50.000 0.00 0.00 0.00 3.16
3284 4241 1.815003 GCAAGTGGGATTCTGAACAGG 59.185 52.381 1.93 0.00 0.00 4.00
3285 4242 2.440409 CAAGTGGGATTCTGAACAGGG 58.560 52.381 1.93 0.00 0.00 4.45
3286 4243 0.329596 AGTGGGATTCTGAACAGGGC 59.670 55.000 1.93 0.00 0.00 5.19
3287 4244 0.681243 GTGGGATTCTGAACAGGGCC 60.681 60.000 0.00 0.00 0.00 5.80
3288 4245 0.846427 TGGGATTCTGAACAGGGCCT 60.846 55.000 0.00 0.00 0.00 5.19
3289 4246 0.332972 GGGATTCTGAACAGGGCCTT 59.667 55.000 1.32 0.00 0.00 4.35
3290 4247 1.564348 GGGATTCTGAACAGGGCCTTA 59.436 52.381 1.32 0.00 0.00 2.69
3291 4248 2.422093 GGGATTCTGAACAGGGCCTTAG 60.422 54.545 1.32 0.00 0.00 2.18
3307 4265 5.656859 GGGCCTTAGATAAAACATTCTGGTT 59.343 40.000 0.84 0.00 0.00 3.67
3308 4266 6.405842 GGGCCTTAGATAAAACATTCTGGTTG 60.406 42.308 0.84 0.00 0.00 3.77
3309 4267 6.152831 GGCCTTAGATAAAACATTCTGGTTGT 59.847 38.462 0.00 0.00 0.00 3.32
3333 4340 2.548057 TGAAATTTCTCTTGAGCGCGTT 59.452 40.909 18.64 0.00 0.00 4.84
3342 4349 1.197721 CTTGAGCGCGTTTGGAAATCT 59.802 47.619 8.43 0.00 0.00 2.40
3384 4391 2.434331 CCCCTTCCGGTTGCTTGA 59.566 61.111 0.00 0.00 0.00 3.02
3424 4431 5.100259 ACACGGTACAATAGAAGTTGATCG 58.900 41.667 0.00 0.00 33.37 3.69
3448 4455 2.384828 ACACGAGCATATACTCACCCA 58.615 47.619 3.86 0.00 36.42 4.51
3456 4463 6.478016 CGAGCATATACTCACCCATATGAATG 59.522 42.308 3.65 2.01 37.32 2.67
3457 4464 6.118170 AGCATATACTCACCCATATGAATGC 58.882 40.000 3.65 5.37 38.52 3.56
3498 4505 0.453793 ATGAGCACTTCCGAGAGACG 59.546 55.000 0.00 0.00 42.18 4.18
3527 4825 8.954350 GTTGGCATAGCATCTTGAGATAATAAT 58.046 33.333 0.00 0.00 32.63 1.28
3602 4902 9.770097 TTATTCACTTGCAATGAAAATTTACCA 57.230 25.926 20.54 0.00 39.43 3.25
3614 4914 2.109425 ATTTACCAGGAGACAACGCC 57.891 50.000 0.00 0.00 36.22 5.68
3622 4922 2.699954 AGGAGACAACGCCTGTAATTG 58.300 47.619 0.00 0.00 44.29 2.32
3646 4946 4.415846 GGGATCCTATTGGGTAAACTTCCT 59.584 45.833 12.58 0.00 36.25 3.36
3647 4947 5.103643 GGGATCCTATTGGGTAAACTTCCTT 60.104 44.000 12.58 0.00 36.25 3.36
3651 4951 4.157840 CCTATTGGGTAAACTTCCTTGTGC 59.842 45.833 0.00 0.00 0.00 4.57
3700 5001 0.250553 TTTCACGAAACTGGGCCGAT 60.251 50.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.964741 AAAATGCATCGCAAACATATTTCA 57.035 29.167 0.00 0.00 43.62 2.69
23 24 4.895668 ATGGCCACATGTGAAGAAAAAT 57.104 36.364 27.46 7.69 35.57 1.82
43 44 4.094442 GCGCTGCTTACCACTAAAGTAAAT 59.906 41.667 0.00 0.00 29.68 1.40
68 69 3.735029 GACGTCACTCCGCTCCGT 61.735 66.667 11.55 0.00 0.00 4.69
102 103 4.722194 TCGAAAAATCAAAAGAGATGCCG 58.278 39.130 0.00 0.00 0.00 5.69
133 134 3.512724 ACACACCGCCAGTAGTTAATAGT 59.487 43.478 0.00 0.00 0.00 2.12
135 136 3.765511 AGACACACCGCCAGTAGTTAATA 59.234 43.478 0.00 0.00 0.00 0.98
136 137 2.565834 AGACACACCGCCAGTAGTTAAT 59.434 45.455 0.00 0.00 0.00 1.40
144 145 0.670546 CCACTAAGACACACCGCCAG 60.671 60.000 0.00 0.00 0.00 4.85
179 180 4.662961 CGACGCACACAGGAGCCA 62.663 66.667 0.00 0.00 0.00 4.75
218 219 1.756950 AATAGGAGGTCTCGCCGCA 60.757 57.895 0.00 0.00 43.70 5.69
219 220 1.300233 CAATAGGAGGTCTCGCCGC 60.300 63.158 0.00 0.00 43.70 6.53
220 221 0.744874 TTCAATAGGAGGTCTCGCCG 59.255 55.000 0.00 0.00 43.70 6.46
221 222 1.536284 CGTTCAATAGGAGGTCTCGCC 60.536 57.143 0.00 0.00 37.58 5.54
222 223 1.841450 CGTTCAATAGGAGGTCTCGC 58.159 55.000 0.00 0.00 0.00 5.03
223 224 1.536284 GGCGTTCAATAGGAGGTCTCG 60.536 57.143 0.00 0.00 0.00 4.04
325 326 1.740805 GCGGCATGTTTTGTTTTTGC 58.259 45.000 0.00 0.00 0.00 3.68
326 327 1.915110 GCGCGGCATGTTTTGTTTTTG 60.915 47.619 8.83 0.00 0.00 2.44
344 345 0.522915 GTCGGGAGTTCTACTTCGCG 60.523 60.000 0.00 0.00 35.12 5.87
346 347 1.401199 GAGGTCGGGAGTTCTACTTCG 59.599 57.143 0.00 0.00 0.00 3.79
352 353 0.178929 AACCAGAGGTCGGGAGTTCT 60.179 55.000 2.90 0.00 33.12 3.01
368 554 4.275196 GGTTACCAAGTGTCTTCTGAAACC 59.725 45.833 0.00 0.00 30.77 3.27
372 558 3.709653 AGTGGTTACCAAGTGTCTTCTGA 59.290 43.478 5.33 0.00 34.18 3.27
374 560 3.243771 CGAGTGGTTACCAAGTGTCTTCT 60.244 47.826 5.33 0.00 34.18 2.85
377 563 2.313317 TCGAGTGGTTACCAAGTGTCT 58.687 47.619 5.33 0.00 34.18 3.41
378 564 2.798847 GTTCGAGTGGTTACCAAGTGTC 59.201 50.000 5.33 0.00 34.18 3.67
381 567 3.118519 ACAAGTTCGAGTGGTTACCAAGT 60.119 43.478 5.33 0.00 34.18 3.16
382 568 3.463944 ACAAGTTCGAGTGGTTACCAAG 58.536 45.455 5.33 0.70 34.18 3.61
383 569 3.547054 ACAAGTTCGAGTGGTTACCAA 57.453 42.857 5.33 0.00 34.18 3.67
397 583 9.956720 GCATTTTAGCATTCTATCATACAAGTT 57.043 29.630 0.00 0.00 0.00 2.66
401 587 7.229106 TGCTGCATTTTAGCATTCTATCATACA 59.771 33.333 0.00 0.00 45.52 2.29
415 601 9.463443 ACTTAAAAGTTTAGTGCTGCATTTTAG 57.537 29.630 5.27 6.38 35.21 1.85
445 631 7.997773 AAAGACGGATATGCTACTGTAGATA 57.002 36.000 18.64 12.51 0.00 1.98
447 633 6.710597 AAAAGACGGATATGCTACTGTAGA 57.289 37.500 18.64 4.46 0.00 2.59
484 672 7.920151 TGTTCACAGTTTTTCCATGAATGTTAG 59.080 33.333 0.00 0.00 32.30 2.34
581 1526 5.637387 CCAGTTTTCAATTATTTTGTCCCGG 59.363 40.000 0.00 0.00 0.00 5.73
587 1532 8.619546 TCTTTTGGCCAGTTTTCAATTATTTTG 58.380 29.630 5.11 0.00 0.00 2.44
592 1537 6.097554 TCACTCTTTTGGCCAGTTTTCAATTA 59.902 34.615 5.11 0.00 0.00 1.40
595 1540 3.766591 TCACTCTTTTGGCCAGTTTTCAA 59.233 39.130 5.11 0.00 0.00 2.69
657 1604 4.290969 GCTACTGTTTCCTTGTTTCTTGC 58.709 43.478 0.00 0.00 0.00 4.01
676 1623 0.659427 CGTACGGATCTGGTTCGCTA 59.341 55.000 7.57 0.00 0.00 4.26
686 1633 2.106332 CCAGCCCACGTACGGATC 59.894 66.667 21.06 5.63 0.00 3.36
1171 2121 1.125633 TATCTGGATCAGCTGCAGCA 58.874 50.000 38.24 21.24 42.69 4.41
1226 2176 3.680786 CACCCGAGGTCGAGCACA 61.681 66.667 18.15 0.00 43.02 4.57
1331 2281 1.093496 CAGCATCAGCAGATTGGCGA 61.093 55.000 0.00 0.00 45.49 5.54
1495 2445 3.853330 CGAACCTGCGGCGACATG 61.853 66.667 12.98 8.06 0.00 3.21
1545 2497 2.033801 CACATCCAGCCGAATTCCATTC 59.966 50.000 0.00 0.00 35.94 2.67
1555 2507 2.487762 ACACAAAATACACATCCAGCCG 59.512 45.455 0.00 0.00 0.00 5.52
1623 2579 3.640498 TGAACCAATCAAGCCACATTTCA 59.360 39.130 0.00 0.00 34.30 2.69
1698 2654 7.201929 GGAGAACTCTTCGGGACTATATTTCTT 60.202 40.741 1.86 0.00 34.02 2.52
1730 2686 1.847737 AGCCAATAAACCCCGATACCA 59.152 47.619 0.00 0.00 0.00 3.25
1802 2758 8.247562 TGGTTATATTTTAACAACTCATGGCAC 58.752 33.333 0.00 0.00 0.00 5.01
1880 2836 9.985318 CTGTTATGCAACATTTTCTTTCAAAAA 57.015 25.926 0.00 0.00 43.58 1.94
1881 2837 9.376075 TCTGTTATGCAACATTTTCTTTCAAAA 57.624 25.926 0.00 0.00 43.58 2.44
1882 2838 8.939201 TCTGTTATGCAACATTTTCTTTCAAA 57.061 26.923 0.00 0.00 43.58 2.69
1883 2839 8.980610 CATCTGTTATGCAACATTTTCTTTCAA 58.019 29.630 0.00 0.00 43.58 2.69
1884 2840 7.599621 CCATCTGTTATGCAACATTTTCTTTCA 59.400 33.333 0.00 0.00 43.58 2.69
1885 2841 7.412237 GCCATCTGTTATGCAACATTTTCTTTC 60.412 37.037 0.00 0.00 43.58 2.62
1886 2842 6.369615 GCCATCTGTTATGCAACATTTTCTTT 59.630 34.615 0.00 0.00 43.58 2.52
1887 2843 5.870978 GCCATCTGTTATGCAACATTTTCTT 59.129 36.000 0.00 0.00 43.58 2.52
1888 2844 5.047164 TGCCATCTGTTATGCAACATTTTCT 60.047 36.000 0.00 0.00 43.58 2.52
1889 2845 5.170021 TGCCATCTGTTATGCAACATTTTC 58.830 37.500 0.00 0.00 43.58 2.29
1890 2846 5.149973 TGCCATCTGTTATGCAACATTTT 57.850 34.783 0.00 0.00 43.58 1.82
1891 2847 4.804868 TGCCATCTGTTATGCAACATTT 57.195 36.364 0.00 0.00 43.58 2.32
1892 2848 4.804868 TTGCCATCTGTTATGCAACATT 57.195 36.364 0.00 0.00 43.58 2.71
1893 2849 4.804868 TTTGCCATCTGTTATGCAACAT 57.195 36.364 0.00 0.00 43.58 2.71
1894 2850 4.202192 TGTTTTGCCATCTGTTATGCAACA 60.202 37.500 0.00 0.00 42.84 3.33
1895 2851 4.150451 GTGTTTTGCCATCTGTTATGCAAC 59.850 41.667 0.00 0.00 42.84 4.17
1896 2852 4.202192 TGTGTTTTGCCATCTGTTATGCAA 60.202 37.500 0.00 0.00 41.57 4.08
1897 2853 3.320256 TGTGTTTTGCCATCTGTTATGCA 59.680 39.130 0.00 0.00 0.00 3.96
1898 2854 3.911868 TGTGTTTTGCCATCTGTTATGC 58.088 40.909 0.00 0.00 0.00 3.14
1899 2855 6.035843 GGTATGTGTTTTGCCATCTGTTATG 58.964 40.000 0.00 0.00 0.00 1.90
1900 2856 5.951747 AGGTATGTGTTTTGCCATCTGTTAT 59.048 36.000 0.00 0.00 0.00 1.89
1901 2857 5.321102 AGGTATGTGTTTTGCCATCTGTTA 58.679 37.500 0.00 0.00 0.00 2.41
1902 2858 4.151883 AGGTATGTGTTTTGCCATCTGTT 58.848 39.130 0.00 0.00 0.00 3.16
1903 2859 3.766545 AGGTATGTGTTTTGCCATCTGT 58.233 40.909 0.00 0.00 0.00 3.41
1904 2860 4.699735 TGTAGGTATGTGTTTTGCCATCTG 59.300 41.667 0.00 0.00 0.00 2.90
1957 2913 7.370905 ACATTCTCATATCTCCAACTGATGA 57.629 36.000 0.00 0.00 0.00 2.92
2077 3033 5.297029 ACAGACCAGTCTCAAAAGTTTTAGC 59.703 40.000 0.00 0.00 37.98 3.09
2081 3037 6.590234 AAAACAGACCAGTCTCAAAAGTTT 57.410 33.333 0.00 2.78 37.98 2.66
2116 3072 4.750098 CGACAGATAGTTCGGCCAAATATT 59.250 41.667 2.24 0.00 0.00 1.28
2127 3083 2.416972 GGGTGGACACGACAGATAGTTC 60.417 54.545 0.00 0.00 0.00 3.01
2215 3171 7.331791 ACAGTCCTTGATCTGGTATTTCTAAC 58.668 38.462 0.00 0.00 36.17 2.34
2385 3341 4.202295 CCCAGCTCACAAGATATAGCTTCA 60.202 45.833 0.00 0.00 42.52 3.02
2446 3402 4.112634 CGATAGTCAGCCGATTCTTTGAA 58.887 43.478 0.00 0.00 0.00 2.69
2610 3566 7.094933 TGCTATGATATCAACTGCAAGCAATAG 60.095 37.037 20.67 10.84 37.60 1.73
2617 3573 6.543100 TCATGTTGCTATGATATCAACTGCAA 59.457 34.615 25.62 25.62 40.34 4.08
2699 3655 3.730269 AGGCCTCAGGAGAGATACTTTT 58.270 45.455 0.00 0.00 44.98 2.27
2762 3718 3.695830 ATCTTCTACCGCAAACCTTCA 57.304 42.857 0.00 0.00 0.00 3.02
3095 4052 8.952278 AGAAACAATATTAAAACACGATGCCTA 58.048 29.630 0.00 0.00 0.00 3.93
3159 4116 0.105039 CTGTGGAGCGGAGGTAATCC 59.895 60.000 0.00 0.00 45.64 3.01
3160 4117 0.530870 GCTGTGGAGCGGAGGTAATC 60.531 60.000 0.00 0.00 39.88 1.75
3161 4118 1.522569 GCTGTGGAGCGGAGGTAAT 59.477 57.895 0.00 0.00 39.88 1.89
3162 4119 2.978824 GCTGTGGAGCGGAGGTAA 59.021 61.111 0.00 0.00 39.88 2.85
3170 4127 2.267324 GAGTGGGAGCTGTGGAGC 59.733 66.667 0.00 0.00 46.64 4.70
3171 4128 2.664081 GGGAGTGGGAGCTGTGGAG 61.664 68.421 0.00 0.00 0.00 3.86
3172 4129 2.607750 GGGAGTGGGAGCTGTGGA 60.608 66.667 0.00 0.00 0.00 4.02
3173 4130 4.087892 CGGGAGTGGGAGCTGTGG 62.088 72.222 0.00 0.00 0.00 4.17
3174 4131 4.087892 CCGGGAGTGGGAGCTGTG 62.088 72.222 0.00 0.00 0.00 3.66
3175 4132 4.316823 TCCGGGAGTGGGAGCTGT 62.317 66.667 0.00 0.00 0.00 4.40
3176 4133 3.465403 CTCCGGGAGTGGGAGCTG 61.465 72.222 16.15 0.00 44.18 4.24
3189 4146 2.183555 GTAACTCCACCCGCTCCG 59.816 66.667 0.00 0.00 0.00 4.63
3190 4147 1.218316 CTGTAACTCCACCCGCTCC 59.782 63.158 0.00 0.00 0.00 4.70
3191 4148 0.389948 CACTGTAACTCCACCCGCTC 60.390 60.000 0.00 0.00 0.00 5.03
3192 4149 1.671742 CACTGTAACTCCACCCGCT 59.328 57.895 0.00 0.00 0.00 5.52
3193 4150 1.375523 CCACTGTAACTCCACCCGC 60.376 63.158 0.00 0.00 0.00 6.13
3194 4151 0.682852 TTCCACTGTAACTCCACCCG 59.317 55.000 0.00 0.00 0.00 5.28
3195 4152 2.943036 TTTCCACTGTAACTCCACCC 57.057 50.000 0.00 0.00 0.00 4.61
3196 4153 4.583073 ACATTTTTCCACTGTAACTCCACC 59.417 41.667 0.00 0.00 0.00 4.61
3197 4154 5.507315 CCACATTTTTCCACTGTAACTCCAC 60.507 44.000 0.00 0.00 0.00 4.02
3198 4155 4.582656 CCACATTTTTCCACTGTAACTCCA 59.417 41.667 0.00 0.00 0.00 3.86
3199 4156 4.825085 TCCACATTTTTCCACTGTAACTCC 59.175 41.667 0.00 0.00 0.00 3.85
3200 4157 5.562890 GCTCCACATTTTTCCACTGTAACTC 60.563 44.000 0.00 0.00 0.00 3.01
3201 4158 4.278419 GCTCCACATTTTTCCACTGTAACT 59.722 41.667 0.00 0.00 0.00 2.24
3202 4159 4.546570 GCTCCACATTTTTCCACTGTAAC 58.453 43.478 0.00 0.00 0.00 2.50
3203 4160 3.252215 CGCTCCACATTTTTCCACTGTAA 59.748 43.478 0.00 0.00 0.00 2.41
3204 4161 2.811431 CGCTCCACATTTTTCCACTGTA 59.189 45.455 0.00 0.00 0.00 2.74
3205 4162 1.608590 CGCTCCACATTTTTCCACTGT 59.391 47.619 0.00 0.00 0.00 3.55
3206 4163 1.666888 GCGCTCCACATTTTTCCACTG 60.667 52.381 0.00 0.00 0.00 3.66
3207 4164 0.598065 GCGCTCCACATTTTTCCACT 59.402 50.000 0.00 0.00 0.00 4.00
3208 4165 0.388520 GGCGCTCCACATTTTTCCAC 60.389 55.000 7.64 0.00 0.00 4.02
3209 4166 0.539438 AGGCGCTCCACATTTTTCCA 60.539 50.000 7.64 0.00 33.74 3.53
3210 4167 0.109132 CAGGCGCTCCACATTTTTCC 60.109 55.000 7.64 0.00 33.74 3.13
3211 4168 0.598065 ACAGGCGCTCCACATTTTTC 59.402 50.000 7.64 0.00 33.74 2.29
3212 4169 1.039856 AACAGGCGCTCCACATTTTT 58.960 45.000 7.64 0.00 33.74 1.94
3213 4170 1.000274 GAAACAGGCGCTCCACATTTT 60.000 47.619 7.64 0.00 33.74 1.82
3214 4171 0.598065 GAAACAGGCGCTCCACATTT 59.402 50.000 7.64 0.00 33.74 2.32
3215 4172 1.244019 GGAAACAGGCGCTCCACATT 61.244 55.000 7.64 0.00 33.74 2.71
3216 4173 1.675641 GGAAACAGGCGCTCCACAT 60.676 57.895 7.64 0.00 33.74 3.21
3217 4174 1.476845 TAGGAAACAGGCGCTCCACA 61.477 55.000 14.34 0.00 33.74 4.17
3218 4175 0.741221 CTAGGAAACAGGCGCTCCAC 60.741 60.000 14.34 0.00 33.74 4.02
3219 4176 1.596934 CTAGGAAACAGGCGCTCCA 59.403 57.895 14.34 1.12 33.74 3.86
3220 4177 1.815840 GCTAGGAAACAGGCGCTCC 60.816 63.158 7.64 5.83 0.00 4.70
3221 4178 0.808060 GAGCTAGGAAACAGGCGCTC 60.808 60.000 7.64 0.00 37.35 5.03
3222 4179 1.219393 GAGCTAGGAAACAGGCGCT 59.781 57.895 7.64 0.00 35.68 5.92
3223 4180 1.815840 GGAGCTAGGAAACAGGCGC 60.816 63.158 0.00 0.00 35.68 6.53
3224 4181 0.741221 GTGGAGCTAGGAAACAGGCG 60.741 60.000 0.00 0.00 35.68 5.52
3225 4182 0.324943 TGTGGAGCTAGGAAACAGGC 59.675 55.000 0.00 0.00 0.00 4.85
3226 4183 1.677217 GCTGTGGAGCTAGGAAACAGG 60.677 57.143 12.77 0.47 42.52 4.00
3227 4184 1.731720 GCTGTGGAGCTAGGAAACAG 58.268 55.000 8.57 8.57 42.52 3.16
3228 4185 3.935993 GCTGTGGAGCTAGGAAACA 57.064 52.632 0.00 0.00 42.52 2.83
3237 4194 0.543749 AATACCAGGAGCTGTGGAGC 59.456 55.000 17.05 0.00 46.64 4.70
3238 4195 2.739932 CGAAATACCAGGAGCTGTGGAG 60.740 54.545 17.05 0.00 38.57 3.86
3239 4196 1.207089 CGAAATACCAGGAGCTGTGGA 59.793 52.381 17.05 3.26 38.57 4.02
3240 4197 1.656652 CGAAATACCAGGAGCTGTGG 58.343 55.000 9.76 9.76 41.30 4.17
3241 4198 1.009829 GCGAAATACCAGGAGCTGTG 58.990 55.000 0.00 0.00 0.00 3.66
3242 4199 0.460284 CGCGAAATACCAGGAGCTGT 60.460 55.000 0.00 0.00 0.00 4.40
3243 4200 1.154205 CCGCGAAATACCAGGAGCTG 61.154 60.000 8.23 0.00 0.00 4.24
3244 4201 1.144057 CCGCGAAATACCAGGAGCT 59.856 57.895 8.23 0.00 0.00 4.09
3245 4202 0.876342 CTCCGCGAAATACCAGGAGC 60.876 60.000 8.23 0.00 41.48 4.70
3246 4203 3.274393 CTCCGCGAAATACCAGGAG 57.726 57.895 8.23 0.00 41.91 3.69
3247 4204 1.143183 GCTCCGCGAAATACCAGGA 59.857 57.895 8.23 0.00 0.00 3.86
3248 4205 0.742990 TTGCTCCGCGAAATACCAGG 60.743 55.000 8.23 0.00 0.00 4.45
3249 4206 0.652592 CTTGCTCCGCGAAATACCAG 59.347 55.000 8.23 0.00 0.00 4.00
3250 4207 0.036765 ACTTGCTCCGCGAAATACCA 60.037 50.000 8.23 0.00 0.00 3.25
3251 4208 0.373716 CACTTGCTCCGCGAAATACC 59.626 55.000 8.23 0.00 0.00 2.73
3252 4209 0.373716 CCACTTGCTCCGCGAAATAC 59.626 55.000 8.23 0.00 0.00 1.89
3253 4210 0.742990 CCCACTTGCTCCGCGAAATA 60.743 55.000 8.23 0.00 0.00 1.40
3254 4211 2.040544 CCCACTTGCTCCGCGAAAT 61.041 57.895 8.23 0.00 0.00 2.17
3255 4212 2.463589 ATCCCACTTGCTCCGCGAAA 62.464 55.000 8.23 0.00 0.00 3.46
3256 4213 2.463589 AATCCCACTTGCTCCGCGAA 62.464 55.000 8.23 0.00 0.00 4.70
3257 4214 2.852495 GAATCCCACTTGCTCCGCGA 62.852 60.000 8.23 0.00 0.00 5.87
3258 4215 2.436646 AATCCCACTTGCTCCGCG 60.437 61.111 0.00 0.00 0.00 6.46
3259 4216 1.078143 AGAATCCCACTTGCTCCGC 60.078 57.895 0.00 0.00 0.00 5.54
3260 4217 0.250234 TCAGAATCCCACTTGCTCCG 59.750 55.000 0.00 0.00 0.00 4.63
3261 4218 2.087646 GTTCAGAATCCCACTTGCTCC 58.912 52.381 0.00 0.00 0.00 4.70
3262 4219 2.746362 CTGTTCAGAATCCCACTTGCTC 59.254 50.000 0.00 0.00 0.00 4.26
3263 4220 2.553904 CCTGTTCAGAATCCCACTTGCT 60.554 50.000 1.00 0.00 0.00 3.91
3264 4221 1.815003 CCTGTTCAGAATCCCACTTGC 59.185 52.381 1.00 0.00 0.00 4.01
3265 4222 2.440409 CCCTGTTCAGAATCCCACTTG 58.560 52.381 1.00 0.00 0.00 3.16
3266 4223 1.272147 GCCCTGTTCAGAATCCCACTT 60.272 52.381 1.00 0.00 0.00 3.16
3267 4224 0.329596 GCCCTGTTCAGAATCCCACT 59.670 55.000 1.00 0.00 0.00 4.00
3268 4225 0.681243 GGCCCTGTTCAGAATCCCAC 60.681 60.000 0.00 0.00 0.00 4.61
3269 4226 0.846427 AGGCCCTGTTCAGAATCCCA 60.846 55.000 0.00 0.00 0.00 4.37
3270 4227 0.332972 AAGGCCCTGTTCAGAATCCC 59.667 55.000 0.00 0.00 0.00 3.85
3271 4228 2.505819 TCTAAGGCCCTGTTCAGAATCC 59.494 50.000 0.00 0.19 0.00 3.01
3272 4229 3.914426 TCTAAGGCCCTGTTCAGAATC 57.086 47.619 0.00 0.00 0.00 2.52
3273 4230 5.975988 TTATCTAAGGCCCTGTTCAGAAT 57.024 39.130 0.00 0.00 0.00 2.40
3274 4231 5.772393 TTTATCTAAGGCCCTGTTCAGAA 57.228 39.130 0.00 0.00 0.00 3.02
3275 4232 5.013704 TGTTTTATCTAAGGCCCTGTTCAGA 59.986 40.000 0.00 0.00 0.00 3.27
3276 4233 5.253330 TGTTTTATCTAAGGCCCTGTTCAG 58.747 41.667 0.00 0.00 0.00 3.02
3277 4234 5.249780 TGTTTTATCTAAGGCCCTGTTCA 57.750 39.130 0.00 0.00 0.00 3.18
3278 4235 6.603599 AGAATGTTTTATCTAAGGCCCTGTTC 59.396 38.462 0.00 0.00 0.00 3.18
3279 4236 6.378280 CAGAATGTTTTATCTAAGGCCCTGTT 59.622 38.462 0.00 0.00 0.00 3.16
3280 4237 5.888161 CAGAATGTTTTATCTAAGGCCCTGT 59.112 40.000 0.00 0.00 0.00 4.00
3281 4238 5.300286 CCAGAATGTTTTATCTAAGGCCCTG 59.700 44.000 0.00 0.00 0.00 4.45
3282 4239 5.044105 ACCAGAATGTTTTATCTAAGGCCCT 60.044 40.000 0.00 0.00 0.00 5.19
3283 4240 5.201243 ACCAGAATGTTTTATCTAAGGCCC 58.799 41.667 0.00 0.00 0.00 5.80
3284 4241 6.152831 ACAACCAGAATGTTTTATCTAAGGCC 59.847 38.462 0.00 0.00 0.00 5.19
3285 4242 7.158099 ACAACCAGAATGTTTTATCTAAGGC 57.842 36.000 0.00 0.00 0.00 4.35
3286 4243 9.014297 AGAACAACCAGAATGTTTTATCTAAGG 57.986 33.333 0.00 0.00 40.90 2.69
3287 4244 9.831737 CAGAACAACCAGAATGTTTTATCTAAG 57.168 33.333 0.00 0.00 40.90 2.18
3288 4245 9.567776 TCAGAACAACCAGAATGTTTTATCTAA 57.432 29.630 0.00 0.00 40.90 2.10
3289 4246 9.567776 TTCAGAACAACCAGAATGTTTTATCTA 57.432 29.630 0.00 0.00 40.90 1.98
3290 4247 8.463930 TTCAGAACAACCAGAATGTTTTATCT 57.536 30.769 0.00 0.00 40.90 1.98
3291 4248 9.696917 ATTTCAGAACAACCAGAATGTTTTATC 57.303 29.630 0.00 0.00 40.90 1.75
3307 4265 4.319766 GCGCTCAAGAGAAATTTCAGAACA 60.320 41.667 19.99 0.61 0.00 3.18
3308 4266 4.154717 GCGCTCAAGAGAAATTTCAGAAC 58.845 43.478 19.99 8.39 0.00 3.01
3309 4267 3.120546 CGCGCTCAAGAGAAATTTCAGAA 60.121 43.478 19.99 0.60 0.00 3.02
3333 4340 7.765695 AGTCATTTCTAAGCAAGATTTCCAA 57.234 32.000 0.00 0.00 33.05 3.53
3342 4349 4.278170 CACCACCAAGTCATTTCTAAGCAA 59.722 41.667 0.00 0.00 0.00 3.91
3405 4412 6.700081 TGTATGCGATCAACTTCTATTGTACC 59.300 38.462 0.00 0.00 0.00 3.34
3419 4426 3.575965 ATATGCTCGTGTATGCGATCA 57.424 42.857 0.00 0.00 40.46 2.92
3424 4431 3.921021 GGTGAGTATATGCTCGTGTATGC 59.079 47.826 15.02 1.25 38.28 3.14
3439 4446 4.074259 GCATGCATTCATATGGGTGAGTA 58.926 43.478 14.21 0.00 32.15 2.59
3457 4464 0.394762 AGGTAGGGTGTGCATGCATG 60.395 55.000 25.64 22.70 0.00 4.06
3465 4472 2.101582 GTGCTCATAGAGGTAGGGTGTG 59.898 54.545 0.00 0.00 0.00 3.82
3469 4476 2.630580 GGAAGTGCTCATAGAGGTAGGG 59.369 54.545 0.00 0.00 0.00 3.53
3498 4505 2.877168 CTCAAGATGCTATGCCAACTCC 59.123 50.000 0.00 0.00 0.00 3.85
3527 4825 5.303078 TGCCTTAGCCAGTTTGATTTTGTTA 59.697 36.000 0.00 0.00 38.69 2.41
3578 4876 7.388500 CCTGGTAAATTTTCATTGCAAGTGAAT 59.612 33.333 18.60 8.82 35.68 2.57
3593 4893 2.817844 GGCGTTGTCTCCTGGTAAATTT 59.182 45.455 0.00 0.00 0.00 1.82
3602 4902 2.615493 CCAATTACAGGCGTTGTCTCCT 60.615 50.000 0.00 0.00 41.29 3.69
3614 4914 4.106341 ACCCAATAGGATCCCCAATTACAG 59.894 45.833 8.55 1.80 39.89 2.74
3622 4922 4.447325 GGAAGTTTACCCAATAGGATCCCC 60.447 50.000 8.55 0.00 39.89 4.81
3646 4946 1.439644 GCAGAAAAACGGGGCACAA 59.560 52.632 0.00 0.00 0.00 3.33
3647 4947 2.494530 GGCAGAAAAACGGGGCACA 61.495 57.895 0.00 0.00 0.00 4.57
3651 4951 2.153547 AATGCGGCAGAAAAACGGGG 62.154 55.000 9.25 0.00 0.00 5.73
3700 5001 4.361971 ACGGTGAGGAGAGGGCGA 62.362 66.667 0.00 0.00 0.00 5.54
3711 5012 0.736053 GAAAAGGCACAACACGGTGA 59.264 50.000 16.29 0.00 41.32 4.02


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

AutoCloner maintained by Alex Coulton.