Multiple sequence alignment - TraesCS2D01G108100

Loading Multiple Alignment...

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 TraesCS2D01G108100 chr2D 100.000 3316 0 0 1 3316 60066449 60063134 0.000000e+00 6124
1 TraesCS2D01G108100 chr2D 83.192 1178 138 42 1363 2512 60079063 60077918 0.000000e+00 1024
2 TraesCS2D01G108100 chr2D 82.821 553 65 18 2560 3110 25326231 25325707 5.010000e-128 468
3 TraesCS2D01G108100 chr2D 80.051 391 78 0 1927 2317 60015427 60015037 1.160000e-74 291
4 TraesCS2D01G108100 chr2D 82.569 327 57 0 1988 2314 59658679 59659005 4.190000e-74 289
5 TraesCS2D01G108100 chr2D 78.240 409 52 23 918 1302 60079574 60079179 9.250000e-56 228
6 TraesCS2D01G108100 chr2D 86.473 207 26 2 1368 1573 60166994 60166789 3.330000e-55 226
7 TraesCS2D01G108100 chr2D 80.628 191 33 4 1106 1294 60016164 60015976 9.590000e-31 145
8 TraesCS2D01G108100 chr2D 83.019 159 27 0 1145 1303 60138895 60138737 9.590000e-31 145
9 TraesCS2D01G108100 chr2A 89.177 1737 105 33 832 2511 60069636 60067926 0.000000e+00 2089
10 TraesCS2D01G108100 chr2A 87.302 756 40 26 82 817 60070338 60069619 0.000000e+00 813
11 TraesCS2D01G108100 chr2A 84.709 824 84 21 1673 2468 60078834 60078025 0.000000e+00 785
12 TraesCS2D01G108100 chr2A 80.144 695 78 34 919 1570 60079610 60078933 6.480000e-127 464
13 TraesCS2D01G108100 chr2A 83.385 325 54 0 1988 2312 59588148 59588472 5.380000e-78 302
14 TraesCS2D01G108100 chr2A 88.021 192 21 2 1368 1558 59718195 59718385 3.330000e-55 226
15 TraesCS2D01G108100 chr2A 85.990 207 27 2 1368 1573 60283504 60283299 1.550000e-53 220
16 TraesCS2D01G108100 chr2A 79.710 207 40 2 1097 1302 59587320 59587525 7.410000e-32 148
17 TraesCS2D01G108100 chr2A 80.723 166 32 0 1137 1302 60195771 60195606 2.680000e-26 130
18 TraesCS2D01G108100 chr2A 80.723 166 32 0 1137 1302 60609790 60609625 2.680000e-26 130
19 TraesCS2D01G108100 chr2B 93.415 820 46 3 1640 2451 93712032 93711213 0.000000e+00 1208
20 TraesCS2D01G108100 chr2B 78.437 1062 132 50 917 1917 93805208 93804183 1.320000e-168 603
21 TraesCS2D01G108100 chr2B 78.437 1062 132 50 917 1917 93883245 93882220 1.320000e-168 603
22 TraesCS2D01G108100 chr2B 85.522 594 61 13 1923 2512 93804133 93803561 6.120000e-167 597
23 TraesCS2D01G108100 chr2B 85.522 594 61 13 1923 2512 93882170 93881598 6.120000e-167 597
24 TraesCS2D01G108100 chr2B 90.667 450 23 12 370 817 93714668 93714236 6.170000e-162 580
25 TraesCS2D01G108100 chr2B 83.423 555 80 8 2562 3106 777066660 777067212 3.820000e-139 505
26 TraesCS2D01G108100 chr2B 84.440 527 50 13 832 1345 93714253 93713746 1.070000e-134 490
27 TraesCS2D01G108100 chr2B 87.080 387 35 6 4 375 93721323 93720937 1.100000e-114 424
28 TraesCS2D01G108100 chr2B 84.783 414 61 2 2695 3107 777068176 777068588 6.620000e-112 414
29 TraesCS2D01G108100 chr2B 95.582 249 11 0 1357 1605 93712670 93712422 1.850000e-107 399
30 TraesCS2D01G108100 chr2B 89.434 265 22 3 117 375 93731516 93731252 2.470000e-86 329
31 TraesCS2D01G108100 chr2B 88.554 166 18 1 3152 3316 541905714 541905879 2.020000e-47 200
32 TraesCS2D01G108100 chr2B 88.608 158 17 1 3152 3308 106226020 106225863 1.210000e-44 191
33 TraesCS2D01G108100 chr6D 85.714 553 71 7 2559 3105 456115208 456115758 7.980000e-161 577
34 TraesCS2D01G108100 chr6D 92.353 170 11 2 3148 3315 456115940 456116109 1.190000e-59 241
35 TraesCS2D01G108100 chr5D 85.882 510 57 9 2560 3068 515570360 515569865 2.270000e-146 529
36 TraesCS2D01G108100 chr5D 85.686 510 58 10 2560 3068 551245745 551245250 1.050000e-144 523
37 TraesCS2D01G108100 chr5D 85.300 517 54 13 2562 3067 370308548 370308043 6.340000e-142 514
38 TraesCS2D01G108100 chr5D 87.805 164 15 3 3152 3313 370307828 370307668 1.570000e-43 187
39 TraesCS2D01G108100 chr5D 86.905 168 16 4 3152 3316 515569695 515569531 2.030000e-42 183
40 TraesCS2D01G108100 chr3B 80.450 578 80 16 2562 3110 20381181 20380608 8.560000e-111 411
41 TraesCS2D01G108100 chr3A 83.683 429 65 5 2684 3110 673610841 673610416 1.850000e-107 399
42 TraesCS2D01G108100 chr5B 87.952 166 13 2 3152 3316 666365540 666365699 4.370000e-44 189
43 TraesCS2D01G108100 chr7D 89.726 146 14 1 3152 3296 119098970 119099115 5.650000e-43 185


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 TraesCS2D01G108100 chr2D 60063134 60066449 3315 True 6124.00 6124 100.0000 1 3316 1 chr2D.!!$R2 3315
1 TraesCS2D01G108100 chr2D 60077918 60079574 1656 True 626.00 1024 80.7160 918 2512 2 chr2D.!!$R6 1594
2 TraesCS2D01G108100 chr2D 25325707 25326231 524 True 468.00 468 82.8210 2560 3110 1 chr2D.!!$R1 550
3 TraesCS2D01G108100 chr2D 60015037 60016164 1127 True 218.00 291 80.3395 1106 2317 2 chr2D.!!$R5 1211
4 TraesCS2D01G108100 chr2A 60067926 60070338 2412 True 1451.00 2089 88.2395 82 2511 2 chr2A.!!$R4 2429
5 TraesCS2D01G108100 chr2A 60078025 60079610 1585 True 624.50 785 82.4265 919 2468 2 chr2A.!!$R5 1549
6 TraesCS2D01G108100 chr2A 59587320 59588472 1152 False 225.00 302 81.5475 1097 2312 2 chr2A.!!$F2 1215
7 TraesCS2D01G108100 chr2B 93711213 93714668 3455 True 669.25 1208 91.0260 370 2451 4 chr2B.!!$R4 2081
8 TraesCS2D01G108100 chr2B 93803561 93805208 1647 True 600.00 603 81.9795 917 2512 2 chr2B.!!$R5 1595
9 TraesCS2D01G108100 chr2B 93881598 93883245 1647 True 600.00 603 81.9795 917 2512 2 chr2B.!!$R6 1595
10 TraesCS2D01G108100 chr2B 777066660 777068588 1928 False 459.50 505 84.1030 2562 3107 2 chr2B.!!$F2 545
11 TraesCS2D01G108100 chr6D 456115208 456116109 901 False 409.00 577 89.0335 2559 3315 2 chr6D.!!$F1 756
12 TraesCS2D01G108100 chr5D 515569531 515570360 829 True 356.00 529 86.3935 2560 3316 2 chr5D.!!$R3 756
13 TraesCS2D01G108100 chr5D 370307668 370308548 880 True 350.50 514 86.5525 2562 3313 2 chr5D.!!$R2 751
14 TraesCS2D01G108100 chr3B 20380608 20381181 573 True 411.00 411 80.4500 2562 3110 1 chr3B.!!$R1 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
194 195 0.179000 GCACTCTGGATTGGGTCGAT 59.821 55.0 0.00 0.00 0.00 3.59 F
656 679 0.179018 AAGGCCATATCGAACTGCCC 60.179 55.0 5.01 2.85 43.18 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 1403 0.179156 ACTAACGTCCGTGCGTATGG 60.179 55.0 5.23 5.23 45.0 2.74 R
2373 4115 0.178932 AGGTGCTGGTACTGGTCTCA 60.179 55.0 0.00 0.00 0.0 3.27 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
30 31 9.562583 TCATACAATTTCCAACTTTTAATACGC 57.437 29.630 0.00 0.00 0.00 4.42
31 32 6.921332 ACAATTTCCAACTTTTAATACGCG 57.079 33.333 3.53 3.53 0.00 6.01
32 33 6.670233 ACAATTTCCAACTTTTAATACGCGA 58.330 32.000 15.93 0.00 0.00 5.87
33 34 7.140048 ACAATTTCCAACTTTTAATACGCGAA 58.860 30.769 15.93 0.00 0.00 4.70
34 35 7.325097 ACAATTTCCAACTTTTAATACGCGAAG 59.675 33.333 15.93 7.35 0.00 3.79
35 36 5.927954 TTCCAACTTTTAATACGCGAAGT 57.072 34.783 15.93 8.13 34.03 3.01
36 37 5.927954 TCCAACTTTTAATACGCGAAGTT 57.072 34.783 15.93 14.45 41.55 2.66
39 40 6.963017 CAACTTTTAATACGCGAAGTTGTT 57.037 33.333 27.41 14.32 46.86 2.83
40 41 7.007738 CAACTTTTAATACGCGAAGTTGTTC 57.992 36.000 27.41 0.00 46.86 3.18
41 42 6.535274 ACTTTTAATACGCGAAGTTGTTCT 57.465 33.333 15.93 0.00 0.00 3.01
42 43 7.642071 ACTTTTAATACGCGAAGTTGTTCTA 57.358 32.000 15.93 0.00 0.00 2.10
43 44 7.504818 ACTTTTAATACGCGAAGTTGTTCTAC 58.495 34.615 15.93 0.00 0.00 2.59
44 45 7.383300 ACTTTTAATACGCGAAGTTGTTCTACT 59.617 33.333 15.93 0.00 0.00 2.57
45 46 7.642071 TTTAATACGCGAAGTTGTTCTACTT 57.358 32.000 15.93 0.00 40.92 2.24
46 47 7.642071 TTAATACGCGAAGTTGTTCTACTTT 57.358 32.000 15.93 0.00 38.43 2.66
47 48 3.854286 ACGCGAAGTTGTTCTACTTTG 57.146 42.857 15.93 9.04 40.84 2.77
48 49 3.450578 ACGCGAAGTTGTTCTACTTTGA 58.549 40.909 15.93 0.00 40.50 2.69
49 50 3.866910 ACGCGAAGTTGTTCTACTTTGAA 59.133 39.130 15.93 0.00 40.50 2.69
50 51 4.025979 ACGCGAAGTTGTTCTACTTTGAAG 60.026 41.667 15.93 11.03 40.50 3.02
51 52 4.212150 GCGAAGTTGTTCTACTTTGAAGC 58.788 43.478 14.94 8.98 40.50 3.86
52 53 4.260620 GCGAAGTTGTTCTACTTTGAAGCA 60.261 41.667 14.94 0.00 40.50 3.91
53 54 5.198274 CGAAGTTGTTCTACTTTGAAGCAC 58.802 41.667 8.07 0.00 40.50 4.40
54 55 5.006746 CGAAGTTGTTCTACTTTGAAGCACT 59.993 40.000 8.07 0.00 40.50 4.40
55 56 6.456988 CGAAGTTGTTCTACTTTGAAGCACTT 60.457 38.462 8.07 0.00 40.50 3.16
56 57 7.254319 CGAAGTTGTTCTACTTTGAAGCACTTA 60.254 37.037 8.07 0.00 40.50 2.24
57 58 8.451908 AAGTTGTTCTACTTTGAAGCACTTAT 57.548 30.769 0.00 0.00 34.81 1.73
58 59 8.451908 AGTTGTTCTACTTTGAAGCACTTATT 57.548 30.769 0.00 0.00 0.00 1.40
59 60 8.903820 AGTTGTTCTACTTTGAAGCACTTATTT 58.096 29.630 0.00 0.00 0.00 1.40
60 61 9.516314 GTTGTTCTACTTTGAAGCACTTATTTT 57.484 29.630 0.00 0.00 0.00 1.82
66 67 9.827411 CTACTTTGAAGCACTTATTTTACTTCC 57.173 33.333 0.00 0.00 36.71 3.46
67 68 8.232913 ACTTTGAAGCACTTATTTTACTTCCA 57.767 30.769 0.00 0.00 36.71 3.53
68 69 8.691797 ACTTTGAAGCACTTATTTTACTTCCAA 58.308 29.630 0.00 0.00 36.71 3.53
69 70 9.696917 CTTTGAAGCACTTATTTTACTTCCAAT 57.303 29.630 0.00 0.00 36.71 3.16
75 76 9.586435 AGCACTTATTTTACTTCCAATTAATGC 57.414 29.630 0.00 0.00 0.00 3.56
76 77 9.364989 GCACTTATTTTACTTCCAATTAATGCA 57.635 29.630 0.00 0.00 0.00 3.96
160 161 2.972713 AGTTCCAACTCCACAGAAGCTA 59.027 45.455 0.00 0.00 32.86 3.32
166 167 4.137543 CAACTCCACAGAAGCTAAAACCT 58.862 43.478 0.00 0.00 0.00 3.50
172 173 4.394300 CCACAGAAGCTAAAACCTGATCTG 59.606 45.833 5.02 5.02 38.91 2.90
194 195 0.179000 GCACTCTGGATTGGGTCGAT 59.821 55.000 0.00 0.00 0.00 3.59
197 198 1.759445 ACTCTGGATTGGGTCGATCAG 59.241 52.381 0.00 0.00 0.00 2.90
201 202 0.815615 GGATTGGGTCGATCAGGTGC 60.816 60.000 0.00 0.00 0.00 5.01
217 218 8.612619 CGATCAGGTGCTTACTACAAAATAAAT 58.387 33.333 0.00 0.00 0.00 1.40
287 288 2.010145 ACATAGATGTGTGTGCGTCC 57.990 50.000 0.00 0.00 40.03 4.79
303 304 2.587194 CCGAGAATGCAGAGGCCG 60.587 66.667 0.00 0.00 40.13 6.13
308 309 3.100862 GAATGCAGAGGCCGCGAAC 62.101 63.158 8.23 0.00 40.13 3.95
322 323 3.181500 GCCGCGAACTTTATCCTTCATTT 60.181 43.478 8.23 0.00 0.00 2.32
398 408 5.579753 TCGGATCTACTCTATGGTAACCT 57.420 43.478 0.00 0.00 0.00 3.50
400 410 5.071370 CGGATCTACTCTATGGTAACCTGT 58.929 45.833 0.00 0.00 0.00 4.00
470 482 7.644062 TCCCATGTGTTTAACCCATATAGAAA 58.356 34.615 0.00 0.00 0.00 2.52
472 484 8.923270 CCCATGTGTTTAACCCATATAGAAAAT 58.077 33.333 0.00 0.00 0.00 1.82
520 543 3.746045 TCTGCGGATTAGTTGATACCC 57.254 47.619 0.00 0.00 0.00 3.69
600 623 5.535753 TGTATCCTGCCGATATGATATGG 57.464 43.478 0.00 0.00 35.87 2.74
634 657 4.442073 GCATGTTTTCGCCTAAGCAATATG 59.558 41.667 0.00 0.00 39.83 1.78
656 679 0.179018 AAGGCCATATCGAACTGCCC 60.179 55.000 5.01 2.85 43.18 5.36
704 727 6.591062 GTGAATAATGCAGCCAAATTCTTTGA 59.409 34.615 0.00 0.00 43.26 2.69
717 740 2.004583 TCTTTGACCGAATAGTGCCG 57.995 50.000 0.00 0.00 0.00 5.69
755 778 8.013378 GCCGTATAATTTTATGTTGAATACGCT 58.987 33.333 0.00 0.00 39.34 5.07
756 779 9.313323 CCGTATAATTTTATGTTGAATACGCTG 57.687 33.333 0.00 0.00 39.34 5.18
757 780 9.858247 CGTATAATTTTATGTTGAATACGCTGT 57.142 29.630 0.00 0.00 35.76 4.40
761 784 7.618502 ATTTTATGTTGAATACGCTGTACCA 57.381 32.000 0.00 0.00 0.00 3.25
762 785 7.436430 TTTTATGTTGAATACGCTGTACCAA 57.564 32.000 0.00 0.00 0.00 3.67
763 786 7.436430 TTTATGTTGAATACGCTGTACCAAA 57.564 32.000 0.00 0.00 0.00 3.28
764 787 4.735662 TGTTGAATACGCTGTACCAAAC 57.264 40.909 0.00 0.00 0.00 2.93
765 788 4.382291 TGTTGAATACGCTGTACCAAACT 58.618 39.130 0.00 0.00 0.00 2.66
766 789 4.212425 TGTTGAATACGCTGTACCAAACTG 59.788 41.667 0.00 0.00 0.00 3.16
767 790 3.331150 TGAATACGCTGTACCAAACTGG 58.669 45.455 0.00 0.00 45.02 4.00
785 808 6.992063 AACTGGTAATCAGATCAATGTGAC 57.008 37.500 0.00 0.00 46.18 3.67
809 832 2.537529 CGTTCCATGTTAAGCTCATGCG 60.538 50.000 8.09 3.95 45.42 4.73
810 833 1.667236 TCCATGTTAAGCTCATGCGG 58.333 50.000 8.09 0.00 45.42 5.69
811 834 1.209261 TCCATGTTAAGCTCATGCGGA 59.791 47.619 8.09 0.00 45.42 5.54
812 835 2.016318 CCATGTTAAGCTCATGCGGAA 58.984 47.619 8.09 0.00 45.42 4.30
813 836 2.620115 CCATGTTAAGCTCATGCGGAAT 59.380 45.455 8.09 0.00 45.42 3.01
814 837 3.814842 CCATGTTAAGCTCATGCGGAATA 59.185 43.478 8.09 0.00 45.42 1.75
815 838 4.083643 CCATGTTAAGCTCATGCGGAATAG 60.084 45.833 8.09 0.00 45.42 1.73
816 839 4.400529 TGTTAAGCTCATGCGGAATAGA 57.599 40.909 0.00 0.00 45.42 1.98
817 840 4.119862 TGTTAAGCTCATGCGGAATAGAC 58.880 43.478 0.00 0.00 45.42 2.59
818 841 2.246719 AAGCTCATGCGGAATAGACC 57.753 50.000 0.00 0.00 45.42 3.85
819 842 0.394565 AGCTCATGCGGAATAGACCC 59.605 55.000 0.00 0.00 45.42 4.46
820 843 0.603975 GCTCATGCGGAATAGACCCC 60.604 60.000 0.00 0.00 0.00 4.95
821 844 1.051812 CTCATGCGGAATAGACCCCT 58.948 55.000 0.00 0.00 0.00 4.79
822 845 1.001406 CTCATGCGGAATAGACCCCTC 59.999 57.143 0.00 0.00 0.00 4.30
823 846 0.758734 CATGCGGAATAGACCCCTCA 59.241 55.000 0.00 0.00 0.00 3.86
824 847 1.140852 CATGCGGAATAGACCCCTCAA 59.859 52.381 0.00 0.00 0.00 3.02
825 848 1.281419 TGCGGAATAGACCCCTCAAA 58.719 50.000 0.00 0.00 0.00 2.69
826 849 1.631388 TGCGGAATAGACCCCTCAAAA 59.369 47.619 0.00 0.00 0.00 2.44
827 850 2.040545 TGCGGAATAGACCCCTCAAAAA 59.959 45.455 0.00 0.00 0.00 1.94
856 879 7.574021 AGCTCATGGGGAATAGATGTTTATA 57.426 36.000 0.00 0.00 0.00 0.98
904 927 5.230942 ACCATTCTCGACGATAATGATTCC 58.769 41.667 27.86 0.00 30.86 3.01
909 932 3.390135 TCGACGATAATGATTCCCAAGC 58.610 45.455 0.00 0.00 0.00 4.01
952 975 4.210328 GGCACAAAATTTGGACGTTTTAGG 59.790 41.667 10.71 0.00 34.12 2.69
953 976 4.318475 GCACAAAATTTGGACGTTTTAGGC 60.318 41.667 10.71 0.00 34.12 3.93
954 977 5.047188 CACAAAATTTGGACGTTTTAGGCT 58.953 37.500 10.71 0.00 34.12 4.58
955 978 5.522097 CACAAAATTTGGACGTTTTAGGCTT 59.478 36.000 10.71 0.00 34.12 4.35
956 979 6.036626 CACAAAATTTGGACGTTTTAGGCTTT 59.963 34.615 10.71 0.00 34.12 3.51
957 980 6.596106 ACAAAATTTGGACGTTTTAGGCTTTT 59.404 30.769 10.71 0.00 34.12 2.27
958 981 7.764901 ACAAAATTTGGACGTTTTAGGCTTTTA 59.235 29.630 10.71 0.00 34.12 1.52
959 982 7.940178 AAATTTGGACGTTTTAGGCTTTTAG 57.060 32.000 0.00 0.00 0.00 1.85
1018 1043 3.928727 ATATGTGCAATGCTGGTATGC 57.071 42.857 6.82 0.00 40.45 3.14
1077 1106 3.651803 CGGGAAGCACCAAATAACAAA 57.348 42.857 2.58 0.00 41.20 2.83
1082 1111 4.306600 GAAGCACCAAATAACAAAGTGGG 58.693 43.478 0.00 0.00 35.32 4.61
1083 1112 2.037121 AGCACCAAATAACAAAGTGGGC 59.963 45.455 0.00 0.00 35.32 5.36
1092 1149 2.584835 ACAAAGTGGGCAGATTAGCA 57.415 45.000 0.00 0.00 35.83 3.49
1179 1236 1.513586 GTCGCCGACGTTCTACCAG 60.514 63.158 0.00 0.00 41.18 4.00
1239 1296 1.973281 CCAGGCCGCAGTCAACAAT 60.973 57.895 0.00 0.00 0.00 2.71
1302 1359 0.239347 ACTGCTTTGTCGATGCAAGC 59.761 50.000 15.57 15.57 37.89 4.01
1310 1367 1.446099 TCGATGCAAGCCTCACGTC 60.446 57.895 0.00 0.00 0.00 4.34
1327 1403 3.979495 CACGTCACCTTAGTCAGTTGTAC 59.021 47.826 0.00 0.00 0.00 2.90
1332 1408 6.098017 GTCACCTTAGTCAGTTGTACCATAC 58.902 44.000 0.00 0.00 0.00 2.39
1347 1509 1.186030 CATACGCACGGACGTTAGTC 58.814 55.000 10.26 0.00 45.75 2.59
1348 1510 1.089920 ATACGCACGGACGTTAGTCT 58.910 50.000 10.26 0.00 45.75 3.24
1349 1511 0.443869 TACGCACGGACGTTAGTCTC 59.556 55.000 10.26 0.00 45.75 3.36
1350 1512 1.208358 CGCACGGACGTTAGTCTCA 59.792 57.895 0.00 0.00 46.29 3.27
1351 1513 1.063951 CGCACGGACGTTAGTCTCAC 61.064 60.000 0.00 0.00 46.29 3.51
1354 1516 2.925306 GCACGGACGTTAGTCTCACATT 60.925 50.000 0.00 0.00 46.29 2.71
1612 2906 2.283298 GATTCTGCACATGGTCGATGT 58.717 47.619 0.00 0.00 46.98 3.06
1622 2916 5.868043 ACATGGTCGATGTGCATTATATG 57.132 39.130 0.00 0.00 44.12 1.78
1624 2918 5.179929 ACATGGTCGATGTGCATTATATGTG 59.820 40.000 0.00 0.00 44.12 3.21
1626 2920 4.511082 TGGTCGATGTGCATTATATGTGTG 59.489 41.667 0.00 0.00 0.00 3.82
1628 2922 5.434706 GTCGATGTGCATTATATGTGTGTG 58.565 41.667 0.00 0.00 0.00 3.82
1630 2924 5.006552 TCGATGTGCATTATATGTGTGTGTG 59.993 40.000 0.00 0.00 0.00 3.82
1631 2925 5.220643 CGATGTGCATTATATGTGTGTGTGT 60.221 40.000 0.00 0.00 0.00 3.72
1638 3287 7.984617 TGCATTATATGTGTGTGTGTGTACTAT 59.015 33.333 0.00 0.00 0.00 2.12
1676 3337 7.768120 TGGTTTGAAATTAAAATTCTGTGCAGT 59.232 29.630 0.00 0.00 0.00 4.40
1747 3408 1.402456 GCAAGCAAGACCAATGCAGAG 60.402 52.381 0.00 0.00 46.22 3.35
1952 3681 2.048597 ACGCTCGGACAATCGCAA 60.049 55.556 0.00 0.00 0.00 4.85
1977 3706 3.146066 CGGTTTTTCAGGAACAGGATCA 58.854 45.455 0.00 0.00 0.00 2.92
2192 3924 2.565841 GACAACACAGTCCTGAGCTTT 58.434 47.619 0.40 0.00 32.36 3.51
2195 3927 0.181114 ACACAGTCCTGAGCTTTGCA 59.819 50.000 0.40 0.00 0.00 4.08
2341 4073 4.116328 CCGCCGACGCTCTTCTGA 62.116 66.667 0.00 0.00 38.22 3.27
2342 4074 2.126463 CGCCGACGCTCTTCTGAA 60.126 61.111 0.00 0.00 0.00 3.02
2373 4115 8.562892 CGCATGAATGAATTAAATAAGGTCTCT 58.437 33.333 0.00 0.00 0.00 3.10
2465 4217 3.249917 CATGTGTGCGTCTACATGTGTA 58.750 45.455 9.11 0.00 45.58 2.90
2466 4218 3.372660 TGTGTGCGTCTACATGTGTAA 57.627 42.857 9.11 0.00 32.43 2.41
2467 4219 3.054166 TGTGTGCGTCTACATGTGTAAC 58.946 45.455 9.11 2.87 32.43 2.50
2468 4220 2.090041 GTGTGCGTCTACATGTGTAACG 59.910 50.000 19.10 19.10 42.39 3.18
2512 4266 5.762218 CGGATGATTGCTTCCTTTTATCTCT 59.238 40.000 0.00 0.00 36.47 3.10
2513 4267 6.073331 CGGATGATTGCTTCCTTTTATCTCTC 60.073 42.308 0.00 0.00 36.47 3.20
2514 4268 6.997476 GGATGATTGCTTCCTTTTATCTCTCT 59.003 38.462 0.00 0.00 35.89 3.10
2515 4269 7.173047 GGATGATTGCTTCCTTTTATCTCTCTC 59.827 40.741 0.00 0.00 35.89 3.20
2516 4270 7.192852 TGATTGCTTCCTTTTATCTCTCTCT 57.807 36.000 0.00 0.00 0.00 3.10
2517 4271 8.311395 TGATTGCTTCCTTTTATCTCTCTCTA 57.689 34.615 0.00 0.00 0.00 2.43
2518 4272 8.932610 TGATTGCTTCCTTTTATCTCTCTCTAT 58.067 33.333 0.00 0.00 0.00 1.98
2549 4303 8.129496 TCATACTGTACTTTGAGATGTTACCA 57.871 34.615 0.00 0.00 0.00 3.25
2550 4304 8.758829 TCATACTGTACTTTGAGATGTTACCAT 58.241 33.333 0.00 0.00 0.00 3.55
2551 4305 9.035607 CATACTGTACTTTGAGATGTTACCATC 57.964 37.037 0.00 0.00 46.56 3.51
2666 4420 3.883744 CTGCGGCGGGAAACTCAGT 62.884 63.158 9.78 0.00 0.00 3.41
2667 4421 2.668550 GCGGCGGGAAACTCAGTT 60.669 61.111 9.78 0.00 0.00 3.16
2671 4425 1.959226 GCGGGAAACTCAGTTGCGA 60.959 57.895 0.00 0.00 0.00 5.10
2679 4452 1.884235 ACTCAGTTGCGAGGGAAAAG 58.116 50.000 0.00 0.00 37.34 2.27
2681 4454 2.039084 ACTCAGTTGCGAGGGAAAAGAT 59.961 45.455 0.00 0.00 37.34 2.40
2682 4455 2.675348 CTCAGTTGCGAGGGAAAAGATC 59.325 50.000 0.00 0.00 0.00 2.75
2683 4456 2.038426 TCAGTTGCGAGGGAAAAGATCA 59.962 45.455 0.00 0.00 0.00 2.92
2684 4457 2.160417 CAGTTGCGAGGGAAAAGATCAC 59.840 50.000 0.00 0.00 0.00 3.06
2688 4461 1.716172 GAGGGAAAAGATCACGCGC 59.284 57.895 5.73 0.00 36.19 6.86
2689 4462 0.741221 GAGGGAAAAGATCACGCGCT 60.741 55.000 5.73 0.00 36.19 5.92
2698 4508 2.960819 AGATCACGCGCTCTAGTTTTT 58.039 42.857 5.73 0.00 0.00 1.94
2704 4514 1.491563 CGCTCTAGTTTTTGCGCGT 59.508 52.632 8.43 0.00 41.85 6.01
2763 4574 2.370445 CCCTCCCACCGCTCTTCAT 61.370 63.158 0.00 0.00 0.00 2.57
2767 4578 1.144936 CCCACCGCTCTTCATCTCC 59.855 63.158 0.00 0.00 0.00 3.71
2923 4735 2.185608 GGCTCCTTCTCTGCCGAC 59.814 66.667 0.00 0.00 37.11 4.79
2972 4784 4.373116 GCACCTTCGAGACCGCCA 62.373 66.667 0.00 0.00 35.37 5.69
3110 4935 1.025041 CTCATCACCGACGAGGATCA 58.975 55.000 8.56 0.00 45.00 2.92
3111 4936 1.001924 CTCATCACCGACGAGGATCAG 60.002 57.143 8.56 0.00 45.00 2.90
3114 4939 2.750637 ACCGACGAGGATCAGCGT 60.751 61.111 11.22 11.22 45.00 5.07
3119 4944 2.024871 CGAGGATCAGCGTCGTCC 59.975 66.667 0.00 0.00 46.56 4.79
3120 4945 2.473760 CGAGGATCAGCGTCGTCCT 61.474 63.158 1.97 1.97 46.56 3.85
3121 4946 1.064946 GAGGATCAGCGTCGTCCTG 59.935 63.158 6.85 0.52 42.27 3.86
3123 4948 2.415608 GGATCAGCGTCGTCCTGGA 61.416 63.158 0.00 0.00 0.00 3.86
3124 4949 1.064946 GATCAGCGTCGTCCTGGAG 59.935 63.158 0.00 0.00 0.00 3.86
3125 4950 2.945398 GATCAGCGTCGTCCTGGAGC 62.945 65.000 0.00 0.00 0.00 4.70
3126 4951 4.056125 CAGCGTCGTCCTGGAGCA 62.056 66.667 0.00 0.00 0.00 4.26
3127 4952 3.753434 AGCGTCGTCCTGGAGCAG 61.753 66.667 0.00 0.00 0.00 4.24
3129 4954 3.753434 CGTCGTCCTGGAGCAGCT 61.753 66.667 0.00 0.00 0.00 4.24
3130 4955 2.407428 CGTCGTCCTGGAGCAGCTA 61.407 63.158 0.00 0.00 0.00 3.32
3131 4956 1.435515 GTCGTCCTGGAGCAGCTAG 59.564 63.158 0.00 0.00 0.00 3.42
3133 4958 2.055042 CGTCCTGGAGCAGCTAGGT 61.055 63.158 10.56 0.00 45.05 3.08
3135 4960 0.972983 GTCCTGGAGCAGCTAGGTGA 60.973 60.000 25.66 3.47 45.05 4.02
3136 4961 0.252239 TCCTGGAGCAGCTAGGTGAA 60.252 55.000 25.66 6.51 45.05 3.18
3138 4963 0.461693 CTGGAGCAGCTAGGTGAAGC 60.462 60.000 25.66 10.32 43.11 3.86
3139 4964 1.194121 TGGAGCAGCTAGGTGAAGCA 61.194 55.000 25.66 2.56 45.30 3.91
3141 4966 1.297664 GAGCAGCTAGGTGAAGCATG 58.702 55.000 25.66 0.00 45.30 4.06
3142 4967 0.107312 AGCAGCTAGGTGAAGCATGG 60.107 55.000 25.66 0.00 45.30 3.66
3143 4968 0.393537 GCAGCTAGGTGAAGCATGGT 60.394 55.000 25.66 0.00 45.30 3.55
3149 5265 1.379044 GGTGAAGCATGGTCCTGGG 60.379 63.158 0.00 0.00 0.00 4.45
3193 5310 5.552870 ATTTAACATCGACCTAGGAGCAT 57.447 39.130 17.98 0.15 0.00 3.79
3198 5315 0.107361 TCGACCTAGGAGCATCGTCA 60.107 55.000 17.98 0.00 36.03 4.35
3270 5388 2.501610 GAGGACATCACCGAGGCC 59.498 66.667 0.00 0.00 34.73 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.562583 GCGTATTAAAAGTTGGAAATTGTATGA 57.437 29.630 0.00 0.00 0.00 2.15
5 6 8.520258 CGCGTATTAAAAGTTGGAAATTGTATG 58.480 33.333 0.00 0.00 0.00 2.39
6 7 8.452534 TCGCGTATTAAAAGTTGGAAATTGTAT 58.547 29.630 5.77 0.00 0.00 2.29
7 8 7.804712 TCGCGTATTAAAAGTTGGAAATTGTA 58.195 30.769 5.77 0.00 0.00 2.41
8 9 6.670233 TCGCGTATTAAAAGTTGGAAATTGT 58.330 32.000 5.77 0.00 0.00 2.71
9 10 7.325097 ACTTCGCGTATTAAAAGTTGGAAATTG 59.675 33.333 5.77 0.00 0.00 2.32
10 11 7.364970 ACTTCGCGTATTAAAAGTTGGAAATT 58.635 30.769 5.77 0.00 0.00 1.82
11 12 6.905578 ACTTCGCGTATTAAAAGTTGGAAAT 58.094 32.000 5.77 0.00 0.00 2.17
12 13 6.303021 ACTTCGCGTATTAAAAGTTGGAAA 57.697 33.333 5.77 0.00 0.00 3.13
13 14 5.927954 ACTTCGCGTATTAAAAGTTGGAA 57.072 34.783 5.77 0.00 0.00 3.53
14 15 5.927954 AACTTCGCGTATTAAAAGTTGGA 57.072 34.783 17.33 0.00 39.72 3.53
17 18 6.951643 AGAACAACTTCGCGTATTAAAAGTT 58.048 32.000 13.64 13.64 41.36 2.66
18 19 6.535274 AGAACAACTTCGCGTATTAAAAGT 57.465 33.333 5.77 4.15 33.53 2.66
19 20 7.727017 AGTAGAACAACTTCGCGTATTAAAAG 58.273 34.615 5.77 3.41 0.00 2.27
20 21 7.642071 AGTAGAACAACTTCGCGTATTAAAA 57.358 32.000 5.77 0.00 0.00 1.52
21 22 7.642071 AAGTAGAACAACTTCGCGTATTAAA 57.358 32.000 5.77 0.00 34.60 1.52
22 23 7.381948 TCAAAGTAGAACAACTTCGCGTATTAA 59.618 33.333 5.77 0.00 38.76 1.40
23 24 6.862608 TCAAAGTAGAACAACTTCGCGTATTA 59.137 34.615 5.77 0.00 38.76 0.98
24 25 5.693104 TCAAAGTAGAACAACTTCGCGTATT 59.307 36.000 5.77 0.00 38.76 1.89
25 26 5.224888 TCAAAGTAGAACAACTTCGCGTAT 58.775 37.500 5.77 0.00 38.76 3.06
26 27 4.609947 TCAAAGTAGAACAACTTCGCGTA 58.390 39.130 5.77 0.00 38.76 4.42
27 28 3.450578 TCAAAGTAGAACAACTTCGCGT 58.549 40.909 5.77 0.00 38.76 6.01
28 29 4.446234 CTTCAAAGTAGAACAACTTCGCG 58.554 43.478 0.00 0.00 38.76 5.87
29 30 4.212150 GCTTCAAAGTAGAACAACTTCGC 58.788 43.478 0.00 0.00 38.76 4.70
30 31 5.006746 AGTGCTTCAAAGTAGAACAACTTCG 59.993 40.000 0.00 0.00 38.76 3.79
31 32 6.364945 AGTGCTTCAAAGTAGAACAACTTC 57.635 37.500 0.00 0.00 38.76 3.01
32 33 6.759497 AAGTGCTTCAAAGTAGAACAACTT 57.241 33.333 0.00 0.00 41.46 2.66
33 34 8.451908 AATAAGTGCTTCAAAGTAGAACAACT 57.548 30.769 0.00 0.00 0.00 3.16
34 35 9.516314 AAAATAAGTGCTTCAAAGTAGAACAAC 57.484 29.630 0.00 0.00 0.00 3.32
40 41 9.827411 GGAAGTAAAATAAGTGCTTCAAAGTAG 57.173 33.333 0.00 0.00 37.77 2.57
41 42 9.344772 TGGAAGTAAAATAAGTGCTTCAAAGTA 57.655 29.630 0.00 0.00 37.77 2.24
42 43 8.232913 TGGAAGTAAAATAAGTGCTTCAAAGT 57.767 30.769 0.00 0.00 37.77 2.66
43 44 9.696917 ATTGGAAGTAAAATAAGTGCTTCAAAG 57.303 29.630 0.00 0.00 37.77 2.77
49 50 9.586435 GCATTAATTGGAAGTAAAATAAGTGCT 57.414 29.630 0.00 0.00 0.00 4.40
50 51 9.364989 TGCATTAATTGGAAGTAAAATAAGTGC 57.635 29.630 0.00 0.00 0.00 4.40
55 56 9.814899 CACCATGCATTAATTGGAAGTAAAATA 57.185 29.630 10.25 0.00 34.52 1.40
56 57 7.769970 CCACCATGCATTAATTGGAAGTAAAAT 59.230 33.333 10.25 0.00 34.52 1.82
57 58 7.102346 CCACCATGCATTAATTGGAAGTAAAA 58.898 34.615 10.25 0.00 34.52 1.52
58 59 6.351711 CCCACCATGCATTAATTGGAAGTAAA 60.352 38.462 10.25 0.00 34.52 2.01
59 60 5.128499 CCCACCATGCATTAATTGGAAGTAA 59.872 40.000 10.25 0.00 34.52 2.24
60 61 4.648762 CCCACCATGCATTAATTGGAAGTA 59.351 41.667 10.25 0.00 34.52 2.24
61 62 3.451902 CCCACCATGCATTAATTGGAAGT 59.548 43.478 10.25 0.00 34.52 3.01
62 63 3.181463 CCCCACCATGCATTAATTGGAAG 60.181 47.826 10.25 2.57 34.52 3.46
63 64 2.770802 CCCCACCATGCATTAATTGGAA 59.229 45.455 10.25 0.00 34.52 3.53
64 65 2.396608 CCCCACCATGCATTAATTGGA 58.603 47.619 10.25 0.00 34.52 3.53
65 66 1.417145 CCCCCACCATGCATTAATTGG 59.583 52.381 0.00 0.00 36.56 3.16
66 67 2.914695 CCCCCACCATGCATTAATTG 57.085 50.000 0.00 0.00 0.00 2.32
97 98 0.545071 AAGGCCCAACCCAAATCTGG 60.545 55.000 0.00 0.00 43.10 3.86
107 108 4.137543 CCTATGTGATCTTAAGGCCCAAC 58.862 47.826 0.00 0.00 0.00 3.77
160 161 2.107204 AGAGTGCACCAGATCAGGTTTT 59.893 45.455 14.63 0.00 40.77 2.43
166 167 1.576577 ATCCAGAGTGCACCAGATCA 58.423 50.000 14.63 0.00 0.00 2.92
172 173 0.678048 GACCCAATCCAGAGTGCACC 60.678 60.000 14.63 5.12 0.00 5.01
194 195 9.906660 CAAATTTATTTTGTAGTAAGCACCTGA 57.093 29.630 0.00 0.00 39.93 3.86
273 274 0.666274 TTCTCGGACGCACACACATC 60.666 55.000 0.00 0.00 0.00 3.06
283 284 1.880340 GCCTCTGCATTCTCGGACG 60.880 63.158 0.00 0.00 37.47 4.79
284 285 1.522580 GGCCTCTGCATTCTCGGAC 60.523 63.158 0.00 0.00 40.13 4.79
287 288 3.267860 GCGGCCTCTGCATTCTCG 61.268 66.667 0.00 0.00 40.13 4.04
303 304 7.867445 TTTTGAAATGAAGGATAAAGTTCGC 57.133 32.000 0.00 0.00 0.00 4.70
384 394 4.639310 CGAGTACACAGGTTACCATAGAGT 59.361 45.833 3.51 0.74 0.00 3.24
398 408 6.201425 GGTTCAAATACAAACTCGAGTACACA 59.799 38.462 20.39 5.39 0.00 3.72
400 410 5.697633 GGGTTCAAATACAAACTCGAGTACA 59.302 40.000 20.39 4.63 0.00 2.90
472 484 9.325198 GTTGTGTATAATGTGTCATTATCTCCA 57.675 33.333 15.31 9.98 0.00 3.86
520 543 3.813443 CAGTTTGATCTATGGGTCAGGG 58.187 50.000 0.00 0.00 0.00 4.45
569 592 1.865865 GGCAGGATACATACACCACG 58.134 55.000 0.00 0.00 41.41 4.94
600 623 3.429085 CGAAAACATGCACTCTATTGGC 58.571 45.455 0.00 0.00 0.00 4.52
602 625 3.127548 AGGCGAAAACATGCACTCTATTG 59.872 43.478 0.00 0.00 0.00 1.90
603 626 3.347216 AGGCGAAAACATGCACTCTATT 58.653 40.909 0.00 0.00 0.00 1.73
604 627 2.991250 AGGCGAAAACATGCACTCTAT 58.009 42.857 0.00 0.00 0.00 1.98
605 628 2.472695 AGGCGAAAACATGCACTCTA 57.527 45.000 0.00 0.00 0.00 2.43
606 629 2.472695 TAGGCGAAAACATGCACTCT 57.527 45.000 0.00 0.00 0.00 3.24
634 657 3.003480 GGCAGTTCGATATGGCCTTATC 58.997 50.000 22.90 22.90 41.39 1.75
676 699 5.655532 AGAATTTGGCTGCATTATTCACTCT 59.344 36.000 16.62 0.55 0.00 3.24
704 727 0.108329 CCAAGTCGGCACTATTCGGT 60.108 55.000 0.00 0.00 30.14 4.69
717 740 2.389962 TATACGGCCAACACCAAGTC 57.610 50.000 2.24 0.00 0.00 3.01
759 782 6.375174 TCACATTGATCTGATTACCAGTTTGG 59.625 38.462 0.00 0.00 45.02 3.28
760 783 7.094677 TGTCACATTGATCTGATTACCAGTTTG 60.095 37.037 0.00 0.00 43.38 2.93
761 784 6.942005 TGTCACATTGATCTGATTACCAGTTT 59.058 34.615 0.00 0.00 43.38 2.66
762 785 6.475504 TGTCACATTGATCTGATTACCAGTT 58.524 36.000 0.00 0.00 43.38 3.16
763 786 6.053632 TGTCACATTGATCTGATTACCAGT 57.946 37.500 0.00 0.00 43.38 4.00
764 787 6.456047 CGTTGTCACATTGATCTGATTACCAG 60.456 42.308 0.00 0.00 44.27 4.00
765 788 5.351189 CGTTGTCACATTGATCTGATTACCA 59.649 40.000 0.00 0.00 0.00 3.25
766 789 5.351465 ACGTTGTCACATTGATCTGATTACC 59.649 40.000 0.00 0.00 0.00 2.85
767 790 6.408858 ACGTTGTCACATTGATCTGATTAC 57.591 37.500 0.00 0.00 0.00 1.89
768 791 6.092122 GGAACGTTGTCACATTGATCTGATTA 59.908 38.462 5.00 0.00 0.00 1.75
774 797 4.083324 ACATGGAACGTTGTCACATTGATC 60.083 41.667 5.00 0.00 0.00 2.92
785 808 4.406069 CATGAGCTTAACATGGAACGTTG 58.594 43.478 5.00 0.00 40.66 4.10
828 851 5.522641 ACATCTATTCCCCATGAGCTTTTT 58.477 37.500 0.00 0.00 0.00 1.94
829 852 5.134725 ACATCTATTCCCCATGAGCTTTT 57.865 39.130 0.00 0.00 0.00 2.27
830 853 4.803329 ACATCTATTCCCCATGAGCTTT 57.197 40.909 0.00 0.00 0.00 3.51
831 854 4.803329 AACATCTATTCCCCATGAGCTT 57.197 40.909 0.00 0.00 0.00 3.74
832 855 4.803329 AAACATCTATTCCCCATGAGCT 57.197 40.909 0.00 0.00 0.00 4.09
833 856 7.500559 GGATATAAACATCTATTCCCCATGAGC 59.499 40.741 0.00 0.00 0.00 4.26
834 857 8.551440 TGGATATAAACATCTATTCCCCATGAG 58.449 37.037 0.00 0.00 0.00 2.90
835 858 8.461685 TGGATATAAACATCTATTCCCCATGA 57.538 34.615 0.00 0.00 0.00 3.07
836 859 9.128404 CATGGATATAAACATCTATTCCCCATG 57.872 37.037 0.00 0.00 39.78 3.66
837 860 7.781693 GCATGGATATAAACATCTATTCCCCAT 59.218 37.037 0.00 0.00 0.00 4.00
838 861 7.036644 AGCATGGATATAAACATCTATTCCCCA 60.037 37.037 0.00 0.00 0.00 4.96
839 862 7.349598 AGCATGGATATAAACATCTATTCCCC 58.650 38.462 0.00 0.00 0.00 4.81
840 863 9.905713 TTAGCATGGATATAAACATCTATTCCC 57.094 33.333 0.00 0.00 0.00 3.97
856 879 2.951642 CCCACAAACGATTAGCATGGAT 59.048 45.455 0.00 0.00 0.00 3.41
884 907 5.468540 TGGGAATCATTATCGTCGAGAAT 57.531 39.130 9.24 9.24 0.00 2.40
886 909 4.796290 GCTTGGGAATCATTATCGTCGAGA 60.796 45.833 0.00 0.00 0.00 4.04
904 927 3.440173 ACTTGTCCATAAACATCGCTTGG 59.560 43.478 0.00 0.00 0.00 3.61
909 932 4.634004 TGCCTAACTTGTCCATAAACATCG 59.366 41.667 0.00 0.00 0.00 3.84
952 975 0.746923 CGGTACCCTGGGCTAAAAGC 60.747 60.000 14.08 2.33 41.46 3.51
953 976 0.616891 ACGGTACCCTGGGCTAAAAG 59.383 55.000 14.08 2.23 0.00 2.27
954 977 0.325602 CACGGTACCCTGGGCTAAAA 59.674 55.000 14.08 0.00 0.00 1.52
955 978 1.555477 CCACGGTACCCTGGGCTAAA 61.555 60.000 19.35 0.00 0.00 1.85
956 979 1.991167 CCACGGTACCCTGGGCTAA 60.991 63.158 19.35 0.00 0.00 3.09
957 980 2.364579 CCACGGTACCCTGGGCTA 60.365 66.667 19.35 1.55 0.00 3.93
1018 1043 1.871772 CCGTGGCTTGCAAGAGAAG 59.128 57.895 30.39 15.83 0.00 2.85
1058 1087 4.306600 CACTTTGTTATTTGGTGCTTCCC 58.693 43.478 0.00 0.00 34.77 3.97
1059 1088 4.306600 CCACTTTGTTATTTGGTGCTTCC 58.693 43.478 0.00 0.00 0.00 3.46
1076 1105 2.381911 CCATTGCTAATCTGCCCACTT 58.618 47.619 0.00 0.00 0.00 3.16
1077 1106 2.025863 GCCATTGCTAATCTGCCCACT 61.026 52.381 0.00 0.00 33.53 4.00
1191 1248 1.709147 GGATGATGAACAGCGCGCTT 61.709 55.000 34.58 19.89 35.55 4.68
1233 1290 1.140161 CATGCGGGGCTCATTGTTG 59.860 57.895 0.00 0.00 0.00 3.33
1302 1359 1.887198 ACTGACTAAGGTGACGTGAGG 59.113 52.381 0.00 0.00 0.00 3.86
1327 1403 0.179156 ACTAACGTCCGTGCGTATGG 60.179 55.000 5.23 5.23 45.00 2.74
1332 1408 1.063951 GTGAGACTAACGTCCGTGCG 61.064 60.000 0.00 0.00 41.16 5.34
1365 2621 3.009115 ACCCGTCACATCCCTGGG 61.009 66.667 6.33 6.33 45.70 4.45
1612 2906 6.169800 AGTACACACACACACATATAATGCA 58.830 36.000 0.00 0.00 0.00 3.96
1618 2912 9.502091 AAGAAAATAGTACACACACACACATAT 57.498 29.630 0.00 0.00 0.00 1.78
1620 2914 7.255104 CCAAGAAAATAGTACACACACACACAT 60.255 37.037 0.00 0.00 0.00 3.21
1622 2916 6.037830 ACCAAGAAAATAGTACACACACACAC 59.962 38.462 0.00 0.00 0.00 3.82
1624 2918 6.613755 ACCAAGAAAATAGTACACACACAC 57.386 37.500 0.00 0.00 0.00 3.82
1626 2920 7.434013 CCAAAACCAAGAAAATAGTACACACAC 59.566 37.037 0.00 0.00 0.00 3.82
1628 2922 7.485810 ACCAAAACCAAGAAAATAGTACACAC 58.514 34.615 0.00 0.00 0.00 3.82
1630 2924 8.813282 CAAACCAAAACCAAGAAAATAGTACAC 58.187 33.333 0.00 0.00 0.00 2.90
1631 2925 8.750298 TCAAACCAAAACCAAGAAAATAGTACA 58.250 29.630 0.00 0.00 0.00 2.90
1676 3337 3.727258 CCATGTCGGCCCTCCCAA 61.727 66.667 0.00 0.00 0.00 4.12
1747 3408 2.170817 GGTAGGAGGTGGAAGGTCATTC 59.829 54.545 0.00 0.00 37.17 2.67
1952 3681 1.613437 CTGTTCCTGAAAAACCGGCAT 59.387 47.619 0.00 0.00 0.00 4.40
1977 3706 1.336755 GTTGATGTTGGCCTCGTTGTT 59.663 47.619 3.32 0.00 0.00 2.83
2373 4115 0.178932 AGGTGCTGGTACTGGTCTCA 60.179 55.000 0.00 0.00 0.00 3.27
2492 4246 7.192852 AGAGAGAGATAAAAGGAAGCAATCA 57.807 36.000 0.00 0.00 0.00 2.57
2523 4277 8.758829 TGGTAACATCTCAAAGTACAGTATGAT 58.241 33.333 0.00 0.00 46.17 2.45
2524 4278 8.129496 TGGTAACATCTCAAAGTACAGTATGA 57.871 34.615 0.00 0.00 46.17 2.15
2543 4297 3.798202 CTCTAAGGTGGCAGATGGTAAC 58.202 50.000 0.00 0.00 0.00 2.50
2544 4298 2.170607 GCTCTAAGGTGGCAGATGGTAA 59.829 50.000 0.00 0.00 0.00 2.85
2545 4299 1.762957 GCTCTAAGGTGGCAGATGGTA 59.237 52.381 0.00 0.00 0.00 3.25
2546 4300 0.543749 GCTCTAAGGTGGCAGATGGT 59.456 55.000 0.00 0.00 0.00 3.55
2547 4301 0.543277 TGCTCTAAGGTGGCAGATGG 59.457 55.000 0.00 0.00 0.00 3.51
2548 4302 2.104451 AGATGCTCTAAGGTGGCAGATG 59.896 50.000 0.00 0.00 39.38 2.90
2549 4303 2.368221 GAGATGCTCTAAGGTGGCAGAT 59.632 50.000 0.00 0.00 39.38 2.90
2550 4304 1.759445 GAGATGCTCTAAGGTGGCAGA 59.241 52.381 0.00 0.00 39.38 4.26
2551 4305 1.761784 AGAGATGCTCTAAGGTGGCAG 59.238 52.381 0.00 0.00 39.28 4.85
2552 4306 1.871418 AGAGATGCTCTAAGGTGGCA 58.129 50.000 0.00 0.00 39.28 4.92
2649 4403 3.469863 AACTGAGTTTCCCGCCGCA 62.470 57.895 0.00 0.00 0.00 5.69
2666 4420 1.438651 CGTGATCTTTTCCCTCGCAA 58.561 50.000 0.00 0.00 0.00 4.85
2667 4421 1.019278 GCGTGATCTTTTCCCTCGCA 61.019 55.000 0.00 0.00 37.64 5.10
2671 4425 0.741221 GAGCGCGTGATCTTTTCCCT 60.741 55.000 8.43 0.00 0.00 4.20
2679 4452 2.784665 GCAAAAACTAGAGCGCGTGATC 60.785 50.000 8.43 6.01 0.00 2.92
2681 4454 0.511221 GCAAAAACTAGAGCGCGTGA 59.489 50.000 8.43 0.00 0.00 4.35
2682 4455 0.785708 CGCAAAAACTAGAGCGCGTG 60.786 55.000 8.43 0.00 43.80 5.34
2683 4456 1.491563 CGCAAAAACTAGAGCGCGT 59.508 52.632 8.43 0.00 43.80 6.01
2684 4457 4.326058 CGCAAAAACTAGAGCGCG 57.674 55.556 0.00 0.00 43.80 6.86
2687 4460 0.452784 CCACGCGCAAAAACTAGAGC 60.453 55.000 5.73 0.00 0.00 4.09
2688 4461 0.452784 GCCACGCGCAAAAACTAGAG 60.453 55.000 5.73 0.00 37.47 2.43
2689 4462 1.572447 GCCACGCGCAAAAACTAGA 59.428 52.632 5.73 0.00 37.47 2.43
2709 4519 1.268539 GCATTTATAAAGCGCGCTGGT 60.269 47.619 37.24 27.33 0.00 4.00
2712 4522 1.670811 ACTGCATTTATAAAGCGCGCT 59.329 42.857 31.32 31.32 0.00 5.92
2778 4589 3.077556 GGGGAGAGAGCGGCAGAA 61.078 66.667 1.45 0.00 0.00 3.02
2834 4646 4.805231 CATGGTGGCGCGACGGTA 62.805 66.667 16.58 5.89 0.00 4.02
3090 4915 1.025812 GATCCTCGTCGGTGATGAGT 58.974 55.000 13.38 0.00 42.32 3.41
3093 4918 0.596083 GCTGATCCTCGTCGGTGATG 60.596 60.000 2.73 0.00 0.00 3.07
3110 4935 3.753434 CTGCTCCAGGACGACGCT 61.753 66.667 0.00 0.00 0.00 5.07
3114 4939 1.754621 CCTAGCTGCTCCAGGACGA 60.755 63.158 12.24 0.00 31.21 4.20
3115 4940 2.055042 ACCTAGCTGCTCCAGGACG 61.055 63.158 22.15 0.07 33.44 4.79
3116 4941 0.972983 TCACCTAGCTGCTCCAGGAC 60.973 60.000 22.15 0.00 33.44 3.85
3117 4942 0.252239 TTCACCTAGCTGCTCCAGGA 60.252 55.000 22.15 7.54 33.44 3.86
3118 4943 0.177604 CTTCACCTAGCTGCTCCAGG 59.822 60.000 15.35 15.35 35.45 4.45
3119 4944 0.461693 GCTTCACCTAGCTGCTCCAG 60.462 60.000 4.91 0.00 38.15 3.86
3120 4945 1.194121 TGCTTCACCTAGCTGCTCCA 61.194 55.000 4.91 0.00 41.76 3.86
3121 4946 0.179936 ATGCTTCACCTAGCTGCTCC 59.820 55.000 4.91 0.00 41.76 4.70
3123 4948 0.107312 CCATGCTTCACCTAGCTGCT 60.107 55.000 7.57 7.57 41.76 4.24
3124 4949 0.393537 ACCATGCTTCACCTAGCTGC 60.394 55.000 0.00 0.00 41.76 5.25
3125 4950 1.661341 GACCATGCTTCACCTAGCTG 58.339 55.000 0.00 0.00 41.76 4.24
3126 4951 0.543749 GGACCATGCTTCACCTAGCT 59.456 55.000 0.00 0.00 41.76 3.32
3127 4952 0.543749 AGGACCATGCTTCACCTAGC 59.456 55.000 0.00 0.00 41.59 3.42
3128 4953 1.134280 CCAGGACCATGCTTCACCTAG 60.134 57.143 0.00 0.00 0.00 3.02
3129 4954 0.911769 CCAGGACCATGCTTCACCTA 59.088 55.000 0.00 0.00 0.00 3.08
3130 4955 1.687612 CCAGGACCATGCTTCACCT 59.312 57.895 0.00 0.00 0.00 4.00
3131 4956 1.379044 CCCAGGACCATGCTTCACC 60.379 63.158 0.00 0.00 0.00 4.02
3133 4958 1.490490 GTATCCCAGGACCATGCTTCA 59.510 52.381 0.00 0.00 0.00 3.02
3135 4960 0.469917 CGTATCCCAGGACCATGCTT 59.530 55.000 0.00 0.00 0.00 3.91
3136 4961 2.044806 GCGTATCCCAGGACCATGCT 62.045 60.000 0.00 0.00 0.00 3.79
3138 4963 1.300931 CGCGTATCCCAGGACCATG 60.301 63.158 0.00 0.00 0.00 3.66
3139 4964 2.507854 CCGCGTATCCCAGGACCAT 61.508 63.158 4.92 0.00 0.00 3.55
3141 4966 2.365095 CTTCCGCGTATCCCAGGACC 62.365 65.000 4.92 0.00 31.69 4.46
3142 4967 1.067582 CTTCCGCGTATCCCAGGAC 59.932 63.158 4.92 0.00 31.69 3.85
3143 4968 2.792947 GCTTCCGCGTATCCCAGGA 61.793 63.158 4.92 0.00 0.00 3.86
3163 5280 2.676342 GGTCGATGTTAAATTGAGCGGT 59.324 45.455 0.00 0.00 0.00 5.68
3174 5291 2.552743 CGATGCTCCTAGGTCGATGTTA 59.447 50.000 12.88 0.00 36.25 2.41
3193 5310 1.753078 CGGAGTCCCAGGATGACGA 60.753 63.158 2.80 0.00 39.69 4.20
3198 5315 1.038130 CGTCTTCGGAGTCCCAGGAT 61.038 60.000 2.80 0.00 0.00 3.24
3270 5388 2.125229 TCCTCCGACTCCGACTCG 60.125 66.667 0.00 0.00 38.22 4.18


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

AutoCloner maintained by Alex Coulton.