Multiple sequence alignment - TraesCS2A01G010600

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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 TraesCS2A01G010600 chr2A 100.000 7289 0 0 1 7289 4082913 4090201 0.000000e+00 13461
1 TraesCS2A01G010600 chr2A 80.711 1576 210 42 4620 6164 718937542 718936030 0.000000e+00 1140
2 TraesCS2A01G010600 chr2D 94.944 4292 154 14 1901 6168 5436250 5440502 0.000000e+00 6665
3 TraesCS2A01G010600 chr2D 88.824 1897 145 26 1 1877 5434329 5436178 0.000000e+00 2266
4 TraesCS2A01G010600 chr2D 95.833 576 22 2 6167 6742 5440552 5441125 0.000000e+00 929
5 TraesCS2A01G010600 chr2D 89.583 192 16 3 7102 7289 5441364 5441555 2.630000e-59 241
6 TraesCS2A01G010600 chr2D 81.884 138 20 4 2349 2486 574823686 574823554 2.150000e-20 111
7 TraesCS2A01G010600 chr2D 85.714 98 13 1 2389 2486 528591384 528591288 1.290000e-17 102
8 TraesCS2A01G010600 chr2B 92.332 2204 135 10 1949 4133 5797898 5800086 0.000000e+00 3103
9 TraesCS2A01G010600 chr2B 91.778 1727 108 12 4462 6168 5804971 5806683 0.000000e+00 2372
10 TraesCS2A01G010600 chr2B 80.711 1576 211 39 4620 6164 705044940 705043427 0.000000e+00 1140
11 TraesCS2A01G010600 chr2B 84.853 614 63 14 618 1205 5796411 5797020 6.300000e-165 592
12 TraesCS2A01G010600 chr2B 87.786 524 39 10 1351 1873 5797301 5797800 2.260000e-164 590
13 TraesCS2A01G010600 chr2B 88.817 465 25 10 6739 7196 5807365 5807809 4.970000e-151 545
14 TraesCS2A01G010600 chr2B 82.471 599 57 18 618 1184 6007579 6006997 1.420000e-131 481
15 TraesCS2A01G010600 chr2B 86.881 404 30 11 6167 6548 5806733 5807135 1.450000e-116 431
16 TraesCS2A01G010600 chr2B 89.399 283 26 2 7011 7289 117787147 117787429 3.230000e-93 353
17 TraesCS2A01G010600 chr2B 88.339 283 29 2 7011 7289 859007 858725 3.260000e-88 337
18 TraesCS2A01G010600 chr2B 77.480 635 96 23 1 601 5793482 5794103 3.260000e-88 337
19 TraesCS2A01G010600 chr2B 83.333 282 33 5 1 270 5795799 5796078 1.570000e-61 248
20 TraesCS2A01G010600 chr2B 95.513 156 6 1 6587 6742 5807134 5807288 1.570000e-61 248
21 TraesCS2A01G010600 chr2B 77.377 305 50 10 1 290 6061842 6061542 5.850000e-36 163
22 TraesCS2A01G010600 chr2B 80.114 176 35 0 2125 2300 705047251 705047076 1.650000e-26 132
23 TraesCS2A01G010600 chrUn 86.255 1004 115 13 3726 4719 314771199 314772189 0.000000e+00 1068
24 TraesCS2A01G010600 chrUn 86.255 1004 115 13 3726 4719 356851667 356850677 0.000000e+00 1068
25 TraesCS2A01G010600 chrUn 86.155 1004 116 13 3726 4719 356853817 356852827 0.000000e+00 1062
26 TraesCS2A01G010600 chrUn 85.784 1020 113 19 3726 4719 11834619 11835632 0.000000e+00 1051
27 TraesCS2A01G010600 chrUn 87.150 856 77 16 3726 4557 327873471 327872625 0.000000e+00 941
28 TraesCS2A01G010600 chrUn 87.150 856 77 16 3726 4557 327882420 327881574 0.000000e+00 941
29 TraesCS2A01G010600 chrUn 87.150 856 77 16 3726 4557 446036462 446037308 0.000000e+00 941
30 TraesCS2A01G010600 chrUn 86.341 820 78 14 4718 5516 314772269 314773075 0.000000e+00 863
31 TraesCS2A01G010600 chrUn 85.976 820 81 14 4718 5516 356850597 356849791 0.000000e+00 846
32 TraesCS2A01G010600 chrUn 85.836 819 84 18 4718 5516 356852747 356851941 0.000000e+00 841
33 TraesCS2A01G010600 chrUn 85.645 822 83 15 4718 5516 320415090 320415899 0.000000e+00 832
34 TraesCS2A01G010600 chrUn 85.280 822 86 15 4718 5516 332696220 332697029 0.000000e+00 815
35 TraesCS2A01G010600 chrUn 85.280 822 86 15 4718 5516 457331509 457330700 0.000000e+00 815
36 TraesCS2A01G010600 chrUn 87.026 686 58 17 4850 5516 347954735 347954062 0.000000e+00 745
37 TraesCS2A01G010600 chrUn 85.756 688 67 11 4718 5387 384937984 384937310 0.000000e+00 699
38 TraesCS2A01G010600 chrUn 86.827 539 60 4 3185 3712 327883062 327882524 6.300000e-165 592
39 TraesCS2A01G010600 chrUn 86.456 539 62 4 3185 3712 327874113 327873575 1.360000e-161 580
40 TraesCS2A01G010600 chrUn 86.408 515 66 4 4587 5098 470748670 470749183 1.780000e-155 560
41 TraesCS2A01G010600 chrUn 87.248 447 51 2 3190 3631 320413466 320413911 8.440000e-139 505
42 TraesCS2A01G010600 chrUn 87.248 447 51 2 3190 3631 346259540 346259985 8.440000e-139 505
43 TraesCS2A01G010600 chrUn 86.830 448 51 2 3190 3631 11834017 11834462 1.830000e-135 494
44 TraesCS2A01G010600 chrUn 86.801 447 53 2 3190 3631 364656248 364655803 1.830000e-135 494
45 TraesCS2A01G010600 chrUn 87.126 435 49 3 4718 5146 11835712 11836145 3.060000e-133 486
46 TraesCS2A01G010600 chrUn 87.597 387 42 3 3190 3571 443893188 443893573 1.870000e-120 444
47 TraesCS2A01G010600 chrUn 85.714 98 11 1 3615 3709 446036258 446036355 4.650000e-17 100
48 TraesCS2A01G010600 chr5B 90.106 283 24 2 7011 7289 559152406 559152124 1.490000e-96 364
49 TraesCS2A01G010600 chr5B 89.046 283 27 2 7011 7289 571179429 571179147 1.510000e-91 348
50 TraesCS2A01G010600 chr5B 90.164 122 11 1 6884 7005 571179651 571179531 2.720000e-34 158
51 TraesCS2A01G010600 chr5B 92.000 100 8 0 2387 2486 70268979 70268880 2.740000e-29 141
52 TraesCS2A01G010600 chr7B 89.046 283 27 2 7011 7289 729077288 729077570 1.510000e-91 348
53 TraesCS2A01G010600 chr7B 89.046 283 27 2 7011 7289 729144810 729145092 1.510000e-91 348
54 TraesCS2A01G010600 chr7B 86.879 282 31 3 7014 7289 682925539 682925258 1.970000e-80 311
55 TraesCS2A01G010600 chr3D 88.933 253 24 2 7011 7259 349670195 349669943 7.100000e-80 309
56 TraesCS2A01G010600 chr3B 87.143 140 14 2 7124 7259 448590887 448590748 9.790000e-34 156
57 TraesCS2A01G010600 chr4D 84.828 145 14 3 2350 2486 346293411 346293267 9.860000e-29 139
58 TraesCS2A01G010600 chr7D 90.217 92 9 0 2387 2478 30934567 30934658 3.570000e-23 121
59 TraesCS2A01G010600 chr4A 89.362 94 9 1 2387 2479 723743288 723743195 4.620000e-22 117
60 TraesCS2A01G010600 chr5D 87.755 98 12 0 2389 2486 257806548 257806645 1.660000e-21 115


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 TraesCS2A01G010600 chr2A 4082913 4090201 7288 False 13461.00 13461 100.00000 1 7289 1 chr2A.!!$F1 7288
1 TraesCS2A01G010600 chr2A 718936030 718937542 1512 True 1140.00 1140 80.71100 4620 6164 1 chr2A.!!$R1 1544
2 TraesCS2A01G010600 chr2D 5434329 5441555 7226 False 2525.25 6665 92.29600 1 7289 4 chr2D.!!$F1 7288
3 TraesCS2A01G010600 chr2B 5793482 5800086 6604 False 974.00 3103 85.15680 1 4133 5 chr2B.!!$F2 4132
4 TraesCS2A01G010600 chr2B 5804971 5807809 2838 False 899.00 2372 90.74725 4462 7196 4 chr2B.!!$F3 2734
5 TraesCS2A01G010600 chr2B 705043427 705047251 3824 True 636.00 1140 80.41250 2125 6164 2 chr2B.!!$R4 4039
6 TraesCS2A01G010600 chr2B 6006997 6007579 582 True 481.00 481 82.47100 618 1184 1 chr2B.!!$R2 566
7 TraesCS2A01G010600 chrUn 314771199 314773075 1876 False 965.50 1068 86.29800 3726 5516 2 chrUn.!!$F6 1790
8 TraesCS2A01G010600 chrUn 356849791 356853817 4026 True 954.25 1068 86.05550 3726 5516 4 chrUn.!!$R7 1790
9 TraesCS2A01G010600 chrUn 332696220 332697029 809 False 815.00 815 85.28000 4718 5516 1 chrUn.!!$F1 798
10 TraesCS2A01G010600 chrUn 457330700 457331509 809 True 815.00 815 85.28000 4718 5516 1 chrUn.!!$R4 798
11 TraesCS2A01G010600 chrUn 327881574 327883062 1488 True 766.50 941 86.98850 3185 4557 2 chrUn.!!$R6 1372
12 TraesCS2A01G010600 chrUn 327872625 327874113 1488 True 760.50 941 86.80300 3185 4557 2 chrUn.!!$R5 1372
13 TraesCS2A01G010600 chrUn 347954062 347954735 673 True 745.00 745 87.02600 4850 5516 1 chrUn.!!$R1 666
14 TraesCS2A01G010600 chrUn 384937310 384937984 674 True 699.00 699 85.75600 4718 5387 1 chrUn.!!$R3 669
15 TraesCS2A01G010600 chrUn 11834017 11836145 2128 False 677.00 1051 86.58000 3190 5146 3 chrUn.!!$F5 1956
16 TraesCS2A01G010600 chrUn 320413466 320415899 2433 False 668.50 832 86.44650 3190 5516 2 chrUn.!!$F7 2326
17 TraesCS2A01G010600 chrUn 470748670 470749183 513 False 560.00 560 86.40800 4587 5098 1 chrUn.!!$F4 511
18 TraesCS2A01G010600 chrUn 446036258 446037308 1050 False 520.50 941 86.43200 3615 4557 2 chrUn.!!$F8 942
19 TraesCS2A01G010600 chr5B 571179147 571179651 504 True 253.00 348 89.60500 6884 7289 2 chr5B.!!$R3 405

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
190 198 0.034198 TCACATCGAACGGGAGCAAA 59.966 50.000 0.00 0.00 0.00 3.68 F
1245 3618 0.034337 GGTCGTGTGCCTGGTCTTTA 59.966 55.000 0.00 0.00 0.00 1.85 F
1599 4118 0.032952 CTCGAATTCCCGCGGGATTA 59.967 55.000 45.44 33.12 44.74 1.75 F
3358 5981 0.109412 GGAGCACAACAAGCTGATGC 60.109 55.000 0.00 0.00 43.58 3.91 F
3365 5988 1.068055 CAACAAGCTGATGCCTCCAAC 60.068 52.381 0.00 0.00 40.80 3.77 F
4375 9266 0.731417 AGAATTGTGATGAGCAGCGC 59.269 50.000 0.00 0.00 0.00 5.92 F
5065 10167 0.615331 GTCATGGAGAGGTTCAGGCA 59.385 55.000 0.00 0.00 0.00 4.75 F
5420 10540 2.131183 GATCTGAATCACTACCGCTGC 58.869 52.381 0.00 0.00 31.76 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1322 3695 0.108992 AAACGGCTGCGAGTAATCGA 60.109 50.0 17.94 0.65 34.64 3.59 R
2966 5574 0.179234 TTGACGTGCAAGGGTGAAGA 59.821 50.0 4.26 0.00 31.55 2.87 R
3365 5988 0.393402 TAAGCTGACCAGGCTGCATG 60.393 55.0 9.56 7.42 40.19 4.06 R
4230 9118 0.250901 ACCCTTGTGCACATCACTCC 60.251 55.0 22.39 0.00 45.81 3.85 R
4660 9641 0.319297 CTGCAGGTTGCTTTTGCTCC 60.319 55.0 5.57 0.00 45.31 4.70 R
5420 10540 0.099968 CAACTGCCATCCATGCTTCG 59.900 55.0 0.00 0.00 0.00 3.79 R
5972 11117 0.110104 AGCTGCTGGGATAATCTGCC 59.890 55.0 0.00 0.00 35.48 4.85 R
6970 12326 0.168128 GTTGCACGGTTGTATGGCTC 59.832 55.0 0.00 0.00 0.00 4.70 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
72 73 8.679344 AGTTTTCCATAGGTTATCCCAAATTT 57.321 30.769 0.00 0.00 34.66 1.82
185 193 2.279810 TGGCTCACATCGAACGGGA 61.280 57.895 0.00 0.00 0.00 5.14
186 194 1.519455 GGCTCACATCGAACGGGAG 60.519 63.158 12.02 12.02 0.00 4.30
189 197 0.389817 CTCACATCGAACGGGAGCAA 60.390 55.000 4.69 0.00 0.00 3.91
190 198 0.034198 TCACATCGAACGGGAGCAAA 59.966 50.000 0.00 0.00 0.00 3.68
191 199 0.443869 CACATCGAACGGGAGCAAAG 59.556 55.000 0.00 0.00 0.00 2.77
192 200 0.320374 ACATCGAACGGGAGCAAAGA 59.680 50.000 0.00 0.00 0.00 2.52
240 265 3.358932 ATCGCCCCGCCCAATTTCT 62.359 57.895 0.00 0.00 0.00 2.52
283 308 7.531716 GTTGTGGATTTATGGTCGATTTACAA 58.468 34.615 0.00 0.00 0.00 2.41
289 331 9.849166 GGATTTATGGTCGATTTACAAAAGAAA 57.151 29.630 0.00 0.00 0.00 2.52
297 339 5.066968 GATTTACAAAAGAAATCGCCCCA 57.933 39.130 0.00 0.00 34.53 4.96
302 344 2.286365 AAAGAAATCGCCCCAACTCA 57.714 45.000 0.00 0.00 0.00 3.41
312 354 2.519013 GCCCCAACTCAGAATTCAAGT 58.481 47.619 8.44 7.89 0.00 3.16
339 382 7.962964 TCAAGTAAAGTGTCAAGAATCGAAT 57.037 32.000 0.00 0.00 0.00 3.34
341 384 6.633668 AGTAAAGTGTCAAGAATCGAATCG 57.366 37.500 0.00 0.00 0.00 3.34
354 397 2.294074 TCGAATCGGGCCCAAAAATAG 58.706 47.619 24.92 2.86 0.00 1.73
370 413 6.808212 CCAAAAATAGAGAAAATGTGTGCGAT 59.192 34.615 0.00 0.00 0.00 4.58
374 417 2.095059 AGAGAAAATGTGTGCGATTGGC 60.095 45.455 0.00 0.00 43.96 4.52
375 418 1.888512 AGAAAATGTGTGCGATTGGCT 59.111 42.857 0.00 0.00 44.05 4.75
450 2695 3.509184 GGACCGACTAAAAGTCAGGTACT 59.491 47.826 18.18 4.02 45.26 2.73
471 2716 4.216687 ACTTGAAATTATTTCCCGCGTCAA 59.783 37.500 14.22 3.26 38.90 3.18
534 2779 1.592223 GTCGTCTTCCACCTCCCAG 59.408 63.158 0.00 0.00 0.00 4.45
557 2802 4.525024 CTGCTTTCTTCTTCCCATGATCT 58.475 43.478 0.00 0.00 0.00 2.75
567 2854 1.223858 TCCCATGATCTGATCCTCCCA 59.776 52.381 14.71 0.00 0.00 4.37
581 2869 4.031129 CCCACCTCTGCAGCTGCT 62.031 66.667 36.61 16.02 42.66 4.24
590 2878 4.106925 GCAGCTGCTGGCCTACCT 62.107 66.667 31.33 0.00 43.05 3.08
635 2961 4.899239 CGCCTCTCCGCCATGTCC 62.899 72.222 0.00 0.00 0.00 4.02
659 2985 0.250513 CTCAACCTCCACCTAGCACC 59.749 60.000 0.00 0.00 0.00 5.01
727 3057 2.629336 GAAGAATTCTGGCGATCCCT 57.371 50.000 9.17 0.00 43.23 4.20
728 3058 2.216898 GAAGAATTCTGGCGATCCCTG 58.783 52.381 9.17 2.25 43.23 4.45
729 3059 0.179034 AGAATTCTGGCGATCCCTGC 60.179 55.000 7.30 0.00 32.89 4.85
730 3060 0.464373 GAATTCTGGCGATCCCTGCA 60.464 55.000 0.00 0.00 32.89 4.41
731 3061 0.184451 AATTCTGGCGATCCCTGCAT 59.816 50.000 0.00 0.00 32.89 3.96
732 3062 0.250640 ATTCTGGCGATCCCTGCATC 60.251 55.000 0.00 0.00 32.89 3.91
733 3063 2.281345 CTGGCGATCCCTGCATCC 60.281 66.667 0.00 0.00 0.00 3.51
734 3064 3.839353 CTGGCGATCCCTGCATCCC 62.839 68.421 0.00 0.00 0.00 3.85
737 3067 3.170672 CGATCCCTGCATCCCCCA 61.171 66.667 0.00 0.00 0.00 4.96
742 3072 3.341629 CCTGCATCCCCCACACCT 61.342 66.667 0.00 0.00 0.00 4.00
743 3077 2.000701 CCTGCATCCCCCACACCTA 61.001 63.158 0.00 0.00 0.00 3.08
753 3087 4.898268 TCCCCCACACCTATATAAGACAA 58.102 43.478 0.00 0.00 0.00 3.18
758 3092 8.390921 CCCCCACACCTATATAAGACAAATAAT 58.609 37.037 0.00 0.00 0.00 1.28
852 3205 1.473434 CCTAAAGCGGTGACCTGATCC 60.473 57.143 0.00 0.00 0.00 3.36
877 3241 1.606994 GCGAAACCCCAAAACCAATCC 60.607 52.381 0.00 0.00 0.00 3.01
904 3268 6.879276 ATAAATACTCTCTCGGTTCGATGA 57.121 37.500 0.00 0.00 34.61 2.92
960 3332 2.832129 ACACGCTTCCCATCTTCTCTTA 59.168 45.455 0.00 0.00 0.00 2.10
970 3342 0.246635 TCTTCTCTTACCTGGCACGC 59.753 55.000 0.00 0.00 0.00 5.34
974 3346 2.031919 CTTACCTGGCACGCCACA 59.968 61.111 6.67 0.00 41.89 4.17
1113 3485 3.300934 CTACCTGTGAGCAGCGCCA 62.301 63.158 2.29 0.00 41.26 5.69
1144 3517 3.093172 CTCCCCCTTCTCCCCAGC 61.093 72.222 0.00 0.00 0.00 4.85
1166 3539 4.521062 GCTGCGTCTGCCCTCGAT 62.521 66.667 0.00 0.00 41.78 3.59
1178 3551 2.256764 CTCGATCTGATCCCGCCG 59.743 66.667 11.84 0.98 0.00 6.46
1179 3552 2.518587 TCGATCTGATCCCGCCGT 60.519 61.111 11.84 0.00 0.00 5.68
1185 3558 4.585526 TGATCCCGCCGTGATCGC 62.586 66.667 5.14 0.00 41.22 4.58
1206 3579 3.106672 CGCGACTAGTAGCTCGAATTTT 58.893 45.455 23.09 0.00 31.24 1.82
1207 3580 3.178033 CGCGACTAGTAGCTCGAATTTTC 59.822 47.826 23.09 6.04 31.24 2.29
1208 3581 4.352887 GCGACTAGTAGCTCGAATTTTCT 58.647 43.478 19.44 0.00 31.24 2.52
1220 3593 2.158871 CGAATTTTCTGGGGGTCGGATA 60.159 50.000 0.00 0.00 0.00 2.59
1222 3595 4.262721 CGAATTTTCTGGGGGTCGGATATA 60.263 45.833 0.00 0.00 0.00 0.86
1233 3606 1.952296 GTCGGATATAGGTGGTCGTGT 59.048 52.381 0.00 0.00 0.00 4.49
1243 3616 2.426023 GGTCGTGTGCCTGGTCTT 59.574 61.111 0.00 0.00 0.00 3.01
1244 3617 1.227853 GGTCGTGTGCCTGGTCTTT 60.228 57.895 0.00 0.00 0.00 2.52
1245 3618 0.034337 GGTCGTGTGCCTGGTCTTTA 59.966 55.000 0.00 0.00 0.00 1.85
1247 3620 2.423577 GTCGTGTGCCTGGTCTTTATT 58.576 47.619 0.00 0.00 0.00 1.40
1259 3632 3.118408 TGGTCTTTATTCGGATCTGGGTG 60.118 47.826 0.62 0.00 0.00 4.61
1290 3663 0.616371 TGGGATCGAACGGATTGGTT 59.384 50.000 0.00 0.00 34.82 3.67
1312 3685 0.464452 ATCGAGGGCTTAGGGTTTCG 59.536 55.000 0.00 0.00 0.00 3.46
1314 3687 1.451567 GAGGGCTTAGGGTTTCGCC 60.452 63.158 0.00 0.00 41.75 5.54
1323 3696 3.351450 GGTTTCGCCCACTTGGTC 58.649 61.111 0.00 0.00 36.04 4.02
1324 3697 2.613506 GGTTTCGCCCACTTGGTCG 61.614 63.158 0.00 0.00 36.04 4.79
1325 3698 1.595929 GTTTCGCCCACTTGGTCGA 60.596 57.895 0.00 0.00 39.69 4.20
1326 3699 0.953960 GTTTCGCCCACTTGGTCGAT 60.954 55.000 1.68 0.00 40.59 3.59
1327 3700 0.250553 TTTCGCCCACTTGGTCGATT 60.251 50.000 1.68 0.00 40.59 3.34
1328 3701 0.609151 TTCGCCCACTTGGTCGATTA 59.391 50.000 1.68 0.00 40.59 1.75
1329 3702 0.108520 TCGCCCACTTGGTCGATTAC 60.109 55.000 0.00 0.00 37.61 1.89
1330 3703 0.108329 CGCCCACTTGGTCGATTACT 60.108 55.000 0.00 0.00 36.23 2.24
1331 3704 1.653151 GCCCACTTGGTCGATTACTC 58.347 55.000 0.00 0.00 36.04 2.59
1351 3870 0.517316 GCAGCCGTTTCTCGACAATT 59.483 50.000 0.00 0.00 42.86 2.32
1358 3877 2.092838 CGTTTCTCGACAATTCCTGCTC 59.907 50.000 0.00 0.00 42.86 4.26
1428 3947 2.202566 GCTAGGTAGATTGGTTCGTGC 58.797 52.381 0.00 0.00 0.00 5.34
1433 3952 2.159338 GGTAGATTGGTTCGTGCGTAGA 60.159 50.000 0.00 0.00 0.00 2.59
1434 3953 2.279582 AGATTGGTTCGTGCGTAGAG 57.720 50.000 0.00 0.00 0.00 2.43
1443 3962 1.881973 TCGTGCGTAGAGTACTGGTTT 59.118 47.619 0.00 0.00 33.01 3.27
1446 3965 3.387397 GTGCGTAGAGTACTGGTTTTGT 58.613 45.455 0.00 0.00 32.41 2.83
1451 3970 5.287226 CGTAGAGTACTGGTTTTGTTCTGT 58.713 41.667 0.00 0.00 0.00 3.41
1531 4050 3.435327 TGTTACATTTCACGATGTGCCTC 59.565 43.478 0.00 0.00 40.33 4.70
1550 4069 7.013750 TGTGCCTCAACTGTTTGACAAATATTA 59.986 33.333 3.49 0.00 36.79 0.98
1551 4070 8.028938 GTGCCTCAACTGTTTGACAAATATTAT 58.971 33.333 3.49 0.00 36.79 1.28
1552 4071 8.028354 TGCCTCAACTGTTTGACAAATATTATG 58.972 33.333 3.49 1.84 36.79 1.90
1553 4072 7.009540 GCCTCAACTGTTTGACAAATATTATGC 59.990 37.037 3.49 0.00 36.79 3.14
1554 4073 8.028354 CCTCAACTGTTTGACAAATATTATGCA 58.972 33.333 3.49 0.00 36.79 3.96
1588 4107 4.433615 TGATGACTTGGTAGCTCGAATTC 58.566 43.478 0.00 0.00 0.00 2.17
1592 4111 0.461339 TTGGTAGCTCGAATTCCCGC 60.461 55.000 0.00 2.70 0.00 6.13
1599 4118 0.032952 CTCGAATTCCCGCGGGATTA 59.967 55.000 45.44 33.12 44.74 1.75
1631 4150 3.091633 CCAGATCTGGGTGGTTTGATT 57.908 47.619 31.14 0.00 46.81 2.57
1636 4155 4.708421 AGATCTGGGTGGTTTGATTGAATG 59.292 41.667 0.00 0.00 0.00 2.67
1646 4167 0.988063 TGATTGAATGGGGTCGGACA 59.012 50.000 10.76 0.00 0.00 4.02
1647 4168 1.339631 TGATTGAATGGGGTCGGACAC 60.340 52.381 10.76 6.08 0.00 3.67
1671 4192 0.611714 GTCGAGGGCTTAGGGTTTCA 59.388 55.000 0.00 0.00 0.00 2.69
1861 4385 6.278172 TGCATGATGTTTTTGGTAATGCTA 57.722 33.333 0.00 0.00 39.65 3.49
1877 4401 8.110908 TGGTAATGCTATTTAGTTGGTTTAGGT 58.889 33.333 0.00 0.00 0.00 3.08
1881 4405 7.457024 TGCTATTTAGTTGGTTTAGGTTTCC 57.543 36.000 0.00 0.00 0.00 3.13
1884 4408 6.964807 ATTTAGTTGGTTTAGGTTTCCGTT 57.035 33.333 0.00 0.00 0.00 4.44
1886 4410 8.640063 ATTTAGTTGGTTTAGGTTTCCGTTAT 57.360 30.769 0.00 0.00 0.00 1.89
1887 4411 5.952526 AGTTGGTTTAGGTTTCCGTTATG 57.047 39.130 0.00 0.00 0.00 1.90
1888 4412 5.623169 AGTTGGTTTAGGTTTCCGTTATGA 58.377 37.500 0.00 0.00 0.00 2.15
1891 4462 5.240121 TGGTTTAGGTTTCCGTTATGAGAC 58.760 41.667 0.00 0.00 0.00 3.36
1893 4464 6.211184 TGGTTTAGGTTTCCGTTATGAGACTA 59.789 38.462 0.00 0.00 0.00 2.59
1894 4465 6.755607 GGTTTAGGTTTCCGTTATGAGACTAG 59.244 42.308 0.00 0.00 0.00 2.57
1898 4479 6.766429 AGGTTTCCGTTATGAGACTAGTTTT 58.234 36.000 0.00 0.00 0.00 2.43
2030 4611 8.955061 ATTGTGAGAACAATTTGAGTAATTCG 57.045 30.769 2.79 0.00 37.03 3.34
2177 4758 5.128663 ACCTACCAAATTGGCCACATATTTC 59.871 40.000 12.67 0.00 42.67 2.17
2182 4763 2.228545 TTGGCCACATATTTCCAGCA 57.771 45.000 3.88 0.00 0.00 4.41
2202 4783 3.707316 CACAAGTATTCCCCCAATTCCA 58.293 45.455 0.00 0.00 0.00 3.53
2323 4904 4.293415 GACAGCCTTTTCATGTGTTTCTG 58.707 43.478 0.00 0.00 0.00 3.02
2341 4922 4.027674 TCTGCTAGTTAATTGGGCAACA 57.972 40.909 0.00 0.00 39.74 3.33
2346 4927 4.095036 GCTAGTTAATTGGGCAACAGAGAC 59.905 45.833 0.00 0.00 39.74 3.36
2541 5130 7.885297 AGCATTAGATGTTTTCTTTACTTGCA 58.115 30.769 0.00 0.00 35.79 4.08
2558 5147 6.325849 ACTTGCACACGTTTTAAATTTGAC 57.674 33.333 0.00 0.00 0.00 3.18
2694 5287 8.806177 TCAGATTTTGAATTTGATTCTGTGTG 57.194 30.769 2.74 0.00 39.96 3.82
2966 5574 3.157087 CCTAGTGCCAAACCAGAACATT 58.843 45.455 0.00 0.00 0.00 2.71
3056 5676 2.629017 ACTTTCAGCCCATGGGAATT 57.371 45.000 36.00 15.97 37.50 2.17
3062 5682 2.106511 TCAGCCCATGGGAATTACTAGC 59.893 50.000 36.00 15.27 37.50 3.42
3067 5687 2.224281 CCATGGGAATTACTAGCGCAGA 60.224 50.000 11.47 0.00 0.00 4.26
3093 5713 1.987855 GTCCAGTCCGGTCCATGGA 60.988 63.158 11.44 11.44 39.50 3.41
3202 5822 3.517296 TGGGTCAAAGCCAGTTATTCA 57.483 42.857 0.00 0.00 41.50 2.57
3225 5845 3.305539 GCCAAATTCTCAGCACAATCACA 60.306 43.478 0.00 0.00 0.00 3.58
3266 5886 0.176680 CTATTGGAGTGCGACAGCCT 59.823 55.000 0.00 0.00 44.33 4.58
3334 5957 1.067974 GGGCACACAAAGGTACCAAAC 59.932 52.381 15.94 0.00 0.00 2.93
3335 5958 2.028876 GGCACACAAAGGTACCAAACT 58.971 47.619 15.94 0.00 0.00 2.66
3358 5981 0.109412 GGAGCACAACAAGCTGATGC 60.109 55.000 0.00 0.00 43.58 3.91
3365 5988 1.068055 CAACAAGCTGATGCCTCCAAC 60.068 52.381 0.00 0.00 40.80 3.77
3521 6150 6.611381 CACTTTGTTTTGTCAGAACTCTCAA 58.389 36.000 7.67 0.00 0.00 3.02
3539 6169 5.175859 TCTCAAATTCCAGGTACTTAAGCG 58.824 41.667 1.29 0.00 34.60 4.68
3657 6290 6.885952 TTCAGCTATGATGAGGAGTACTAC 57.114 41.667 0.00 0.00 34.73 2.73
3660 6293 5.767665 CAGCTATGATGAGGAGTACTACAGT 59.232 44.000 8.10 0.00 0.00 3.55
3767 8644 7.381789 TCCTAATATGGGTAGTTATGCACAA 57.618 36.000 0.00 0.00 0.00 3.33
4005 8891 3.551846 TCCTCAGTTTTTGGAACTGGAC 58.448 45.455 16.28 0.00 45.66 4.02
4015 8901 1.202964 TGGAACTGGACCGTAGAGTCA 60.203 52.381 0.00 0.00 38.59 3.41
4040 8926 4.593206 TCTTCCAACACTAACAGAGGTCAT 59.407 41.667 0.00 0.00 0.00 3.06
4043 8929 5.305585 TCCAACACTAACAGAGGTCATTTC 58.694 41.667 0.00 0.00 0.00 2.17
4152 9040 6.611613 ACAATTCTCATCACTACCTGAAGA 57.388 37.500 0.00 0.00 30.60 2.87
4153 9041 6.638610 ACAATTCTCATCACTACCTGAAGAG 58.361 40.000 0.00 0.00 43.41 2.85
4230 9118 4.083643 ACTGAATTTGATGTCGTTGCAGAG 60.084 41.667 0.00 0.00 0.00 3.35
4234 9122 0.969149 TGATGTCGTTGCAGAGGAGT 59.031 50.000 0.00 0.00 0.00 3.85
4235 9123 1.337167 TGATGTCGTTGCAGAGGAGTG 60.337 52.381 0.00 0.00 0.00 3.51
4236 9124 0.969149 ATGTCGTTGCAGAGGAGTGA 59.031 50.000 0.00 0.00 0.00 3.41
4306 9197 6.765036 TCATACATCATTTTCTGGCTCTTCTC 59.235 38.462 0.00 0.00 0.00 2.87
4330 9221 4.347607 AGAGGAATAAAACTTGCCATGCT 58.652 39.130 0.00 0.00 0.00 3.79
4375 9266 0.731417 AGAATTGTGATGAGCAGCGC 59.269 50.000 0.00 0.00 0.00 5.92
4660 9641 8.087750 TGTTTATCCTTTTTCATTTGCAGTAGG 58.912 33.333 0.00 0.00 0.00 3.18
4767 9830 6.949449 GCAATGATAACTACTTGCTAGGAAC 58.051 40.000 0.00 0.00 40.55 3.62
4824 9902 2.237392 AGTCTTGGTCTTCCAGTATGCC 59.763 50.000 0.00 0.00 45.22 4.40
4832 9910 1.281867 CTTCCAGTATGCCCAAGTCCA 59.718 52.381 0.00 0.00 31.97 4.02
4848 9926 2.605607 CCATGAGGCCCTCACCACA 61.606 63.158 17.46 0.00 43.63 4.17
5065 10167 0.615331 GTCATGGAGAGGTTCAGGCA 59.385 55.000 0.00 0.00 0.00 4.75
5165 10279 5.105513 TGAGCTCATGAATTGTTGCAATCAT 60.106 36.000 13.74 4.80 32.94 2.45
5184 10298 8.119226 GCAATCATTTATACTGACAGTTCTGTC 58.881 37.037 21.57 21.57 35.64 3.51
5221 10335 9.698309 ATGTAATTGTAACCTCAGATAAGATCG 57.302 33.333 0.00 0.00 0.00 3.69
5272 10386 9.807921 TCTGTTAATTCAATTAGGTCTTTCCTT 57.192 29.630 0.00 0.00 45.67 3.36
5301 10415 2.279741 CGACATTGTACCACATGGGAG 58.720 52.381 0.00 0.00 41.15 4.30
5394 10514 5.700832 TGAAGCGAGTTTTCAATCATACAGT 59.299 36.000 0.00 0.00 31.98 3.55
5420 10540 2.131183 GATCTGAATCACTACCGCTGC 58.869 52.381 0.00 0.00 31.76 5.25
5458 10578 2.861274 TGCATGTCATTTGAGTGTGGA 58.139 42.857 0.00 0.00 0.00 4.02
5659 10786 9.168451 TGTACTTTCAACAATTCTTGTCACTTA 57.832 29.630 0.00 0.00 44.59 2.24
5824 10951 4.961511 TGCCGTGTCGCTTTCGCT 62.962 61.111 0.00 0.00 35.26 4.93
5972 11117 1.484356 CGGTTAAGCTATTCGTCCCG 58.516 55.000 2.76 0.00 0.00 5.14
6015 11160 1.798223 CGGTGCTCAGAAATGACGAAA 59.202 47.619 0.00 0.00 0.00 3.46
6044 11189 1.973812 GCCAAGGTGAGTTGAGCCC 60.974 63.158 0.00 0.00 0.00 5.19
6128 11273 2.092968 TGACAATAGCTTCTTCGCCCAT 60.093 45.455 0.00 0.00 0.00 4.00
6279 11526 0.036732 GTGGGTGGAAGAGATGTGCA 59.963 55.000 0.00 0.00 0.00 4.57
6432 11685 8.445275 TGTAGATGATGTAAACTGTTGTGTTT 57.555 30.769 0.00 0.00 42.10 2.83
6441 11694 3.757745 ACTGTTGTGTTTGTACTGTGC 57.242 42.857 0.00 0.00 0.00 4.57
6477 11747 9.233649 GTAGAATAGCAGCTTAGGATAAGTAGA 57.766 37.037 0.00 0.00 0.00 2.59
6480 11750 5.068215 AGCAGCTTAGGATAAGTAGAGGA 57.932 43.478 0.00 0.00 0.00 3.71
6603 11873 6.985117 TGTGGTAGTAAGAAACAGTTCGTAT 58.015 36.000 0.00 0.00 38.90 3.06
6658 11928 3.947196 TGTGTTGTGCTCAATGAGAAAGT 59.053 39.130 15.38 0.00 35.92 2.66
6664 11934 5.798132 TGTGCTCAATGAGAAAGTATCAGT 58.202 37.500 15.38 0.00 0.00 3.41
6695 11965 9.515020 TCGGCATCTTAATTTGTTGAATTTATC 57.485 29.630 0.00 0.00 38.80 1.75
6696 11966 9.520204 CGGCATCTTAATTTGTTGAATTTATCT 57.480 29.630 0.00 0.00 38.80 1.98
6726 11996 5.125417 CGGACAAATTACATCTCCCATGTTT 59.875 40.000 0.00 0.00 33.76 2.83
6763 12114 2.683211 AGGGTGAACCAGATTTGCTT 57.317 45.000 1.16 0.00 43.89 3.91
6786 12137 3.509575 TGATGAAATTCCGGTGAAAAGGG 59.490 43.478 0.00 0.00 33.32 3.95
6787 12138 2.952116 TGAAATTCCGGTGAAAAGGGT 58.048 42.857 0.00 0.00 33.32 4.34
6788 12139 2.625790 TGAAATTCCGGTGAAAAGGGTG 59.374 45.455 0.00 0.00 33.32 4.61
6789 12140 2.668144 AATTCCGGTGAAAAGGGTGA 57.332 45.000 0.00 0.00 33.32 4.02
6790 12141 2.668144 ATTCCGGTGAAAAGGGTGAA 57.332 45.000 0.00 0.00 33.32 3.18
6791 12142 1.682740 TTCCGGTGAAAAGGGTGAAC 58.317 50.000 0.00 0.00 0.00 3.18
6792 12143 0.179012 TCCGGTGAAAAGGGTGAACC 60.179 55.000 0.00 0.00 40.67 3.62
6793 12144 0.466555 CCGGTGAAAAGGGTGAACCA 60.467 55.000 1.16 0.00 43.89 3.67
6794 12145 0.951558 CGGTGAAAAGGGTGAACCAG 59.048 55.000 1.16 0.00 43.89 4.00
6795 12146 1.476110 CGGTGAAAAGGGTGAACCAGA 60.476 52.381 1.16 0.00 43.89 3.86
6796 12147 2.814097 CGGTGAAAAGGGTGAACCAGAT 60.814 50.000 1.16 0.00 43.89 2.90
6797 12148 3.230976 GGTGAAAAGGGTGAACCAGATT 58.769 45.455 1.16 0.00 43.89 2.40
6798 12149 3.641436 GGTGAAAAGGGTGAACCAGATTT 59.359 43.478 1.16 0.00 43.89 2.17
6799 12150 4.501400 GGTGAAAAGGGTGAACCAGATTTG 60.501 45.833 1.16 0.00 43.89 2.32
6800 12151 3.069443 TGAAAAGGGTGAACCAGATTTGC 59.931 43.478 1.16 0.00 43.89 3.68
6801 12152 2.683211 AAGGGTGAACCAGATTTGCT 57.317 45.000 1.16 0.00 43.89 3.91
6802 12153 2.206576 AGGGTGAACCAGATTTGCTC 57.793 50.000 1.16 0.00 43.89 4.26
6803 12154 1.177401 GGGTGAACCAGATTTGCTCC 58.823 55.000 1.16 0.00 39.85 4.70
6804 12155 0.804989 GGTGAACCAGATTTGCTCCG 59.195 55.000 0.00 0.00 35.64 4.63
6805 12156 1.610624 GGTGAACCAGATTTGCTCCGA 60.611 52.381 0.00 0.00 35.64 4.55
6806 12157 2.359900 GTGAACCAGATTTGCTCCGAT 58.640 47.619 0.00 0.00 0.00 4.18
6811 12162 2.755103 ACCAGATTTGCTCCGATTTTCC 59.245 45.455 0.00 0.00 0.00 3.13
6813 12164 3.382546 CCAGATTTGCTCCGATTTTCCAT 59.617 43.478 0.00 0.00 0.00 3.41
6846 12197 4.338964 TGATGCTGTATTGGCACCTTATTG 59.661 41.667 0.00 0.00 42.69 1.90
6848 12199 2.426738 GCTGTATTGGCACCTTATTGCA 59.573 45.455 0.00 0.00 44.94 4.08
6888 12244 7.818930 GCATTCTGATGAAATTCCACCTTTTTA 59.181 33.333 0.00 0.00 35.63 1.52
6993 12351 2.609244 GCCATACAACCGTGCAACATTT 60.609 45.455 0.00 0.00 35.74 2.32
7001 12359 4.846779 ACCGTGCAACATTTCAGTTATT 57.153 36.364 0.00 0.00 35.74 1.40
7009 12463 6.208402 TGCAACATTTCAGTTATTCCAGCTAA 59.792 34.615 0.00 0.00 0.00 3.09
7034 12488 3.072038 TGGAGTAACGGGATCGATCTCTA 59.928 47.826 22.53 6.93 40.11 2.43
7065 12519 5.220624 GCTGTGATCATCTTAAGAGCAACAG 60.221 44.000 20.91 20.91 35.58 3.16
7078 12532 0.536006 GCAACAGGGCAGTCTGTCTT 60.536 55.000 4.09 0.00 46.17 3.01
7094 12548 8.031864 CAGTCTGTCTTCACTTCAATATGTAGT 58.968 37.037 0.00 0.00 0.00 2.73
7116 12570 2.598394 TCCACTGCAAGGCAAGGC 60.598 61.111 0.00 0.00 38.41 4.35
7120 12574 1.076192 ACTGCAAGGCAAGGCTCAT 59.924 52.632 0.00 0.00 38.41 2.90
7188 12642 2.683152 GCCCTCAGTTCTCTGCATGATT 60.683 50.000 0.00 0.00 41.10 2.57
7201 12658 8.476064 TCTCTGCATGATTAGAAGATCTTACT 57.524 34.615 8.25 9.89 0.00 2.24
7202 12659 8.922237 TCTCTGCATGATTAGAAGATCTTACTT 58.078 33.333 8.25 0.00 0.00 2.24
7264 12722 1.005037 AAGCGCAGAACATCCGTCA 60.005 52.632 11.47 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 7.092623 GGGGAAAACAAATTTGGGATAACCTAT 60.093 37.037 21.74 0.00 41.11 2.57
185 193 1.228245 TCTTTGCGCCCTCTTTGCT 60.228 52.632 4.18 0.00 0.00 3.91
186 194 1.211190 CTCTTTGCGCCCTCTTTGC 59.789 57.895 4.18 0.00 0.00 3.68
189 197 2.360475 GCCTCTTTGCGCCCTCTT 60.360 61.111 4.18 0.00 0.00 2.85
190 198 4.416738 GGCCTCTTTGCGCCCTCT 62.417 66.667 4.18 0.00 39.39 3.69
283 308 2.162681 CTGAGTTGGGGCGATTTCTTT 58.837 47.619 0.00 0.00 0.00 2.52
289 331 1.281867 TGAATTCTGAGTTGGGGCGAT 59.718 47.619 7.05 0.00 0.00 4.58
302 344 9.788960 GACACTTTACTTGAAAACTTGAATTCT 57.211 29.630 7.05 0.00 0.00 2.40
312 354 8.203937 TCGATTCTTGACACTTTACTTGAAAA 57.796 30.769 0.00 0.00 0.00 2.29
339 382 3.443145 TTTCTCTATTTTTGGGCCCGA 57.557 42.857 19.37 14.11 0.00 5.14
341 384 5.178061 CACATTTTCTCTATTTTTGGGCCC 58.822 41.667 17.59 17.59 0.00 5.80
354 397 2.095059 AGCCAATCGCACACATTTTCTC 60.095 45.455 0.00 0.00 41.38 2.87
370 413 3.726557 AGTTCCAATCATCAGAGCCAA 57.273 42.857 0.00 0.00 0.00 4.52
374 417 5.709164 ACTTCCAAAGTTCCAATCATCAGAG 59.291 40.000 0.00 0.00 39.04 3.35
375 418 5.634118 ACTTCCAAAGTTCCAATCATCAGA 58.366 37.500 0.00 0.00 39.04 3.27
450 2695 4.477780 GTTGACGCGGGAAATAATTTCAA 58.522 39.130 12.47 4.05 41.43 2.69
487 2732 0.248907 GTTCGATGAAGATCCGGCGA 60.249 55.000 9.30 0.00 0.00 5.54
534 2779 2.440409 TCATGGGAAGAAGAAAGCAGC 58.560 47.619 0.00 0.00 0.00 5.25
557 2802 0.979709 CTGCAGAGGTGGGAGGATCA 60.980 60.000 8.42 0.00 36.25 2.92
567 2854 4.719106 GCCAGCAGCTGCAGAGGT 62.719 66.667 38.24 16.73 45.16 3.85
624 2950 4.414956 AGGGGAGGACATGGCGGA 62.415 66.667 0.00 0.00 0.00 5.54
630 2956 0.621862 GGAGGTTGAGGGGAGGACAT 60.622 60.000 0.00 0.00 0.00 3.06
635 2961 0.042731 TAGGTGGAGGTTGAGGGGAG 59.957 60.000 0.00 0.00 0.00 4.30
674 3004 3.168528 TTAGAGGGATGGCCGGGC 61.169 66.667 23.42 23.42 33.83 6.13
703 3033 0.460284 TCGCCAGAATTCTTCTCCGC 60.460 55.000 4.86 2.04 38.11 5.54
727 3057 2.132303 ATATAGGTGTGGGGGATGCA 57.868 50.000 0.00 0.00 0.00 3.96
728 3058 3.844211 TCTTATATAGGTGTGGGGGATGC 59.156 47.826 0.00 0.00 0.00 3.91
729 3059 4.844085 TGTCTTATATAGGTGTGGGGGATG 59.156 45.833 0.00 0.00 0.00 3.51
730 3060 5.101254 TGTCTTATATAGGTGTGGGGGAT 57.899 43.478 0.00 0.00 0.00 3.85
731 3061 4.562934 TGTCTTATATAGGTGTGGGGGA 57.437 45.455 0.00 0.00 0.00 4.81
732 3062 5.640158 TTTGTCTTATATAGGTGTGGGGG 57.360 43.478 0.00 0.00 0.00 5.40
758 3092 7.068593 CCACCATCTATTGAAAGAATTGCCTTA 59.931 37.037 0.00 0.00 0.00 2.69
836 3189 0.620556 ATTGGATCAGGTCACCGCTT 59.379 50.000 0.00 0.00 0.00 4.68
837 3190 1.414181 CTATTGGATCAGGTCACCGCT 59.586 52.381 0.00 0.00 0.00 5.52
852 3205 2.297597 TGGTTTTGGGGTTTCGCTATTG 59.702 45.455 0.00 0.00 0.00 1.90
877 3241 7.187244 TCGAACCGAGAGAGTATTTATACTG 57.813 40.000 7.12 0.00 43.27 2.74
904 3268 1.373497 CGCAGTCGCTTTCTCACCT 60.373 57.895 0.00 0.00 35.30 4.00
933 3297 1.137872 AGATGGGAAGCGTGTGAGATC 59.862 52.381 0.00 0.00 0.00 2.75
1047 3419 2.556459 CGTCTCCGCCTCGATCCAT 61.556 63.158 0.00 0.00 0.00 3.41
1113 3485 1.700985 GGGAGGAGAGAGGAGTGGT 59.299 63.158 0.00 0.00 0.00 4.16
1151 3524 2.755876 AGATCGAGGGCAGACGCA 60.756 61.111 0.00 0.00 41.24 5.24
1166 3539 2.845550 CGATCACGGCGGGATCAGA 61.846 63.158 40.81 17.41 40.93 3.27
1178 3551 0.992757 GCTACTAGTCGCGCGATCAC 60.993 60.000 37.03 23.77 0.00 3.06
1179 3552 1.158484 AGCTACTAGTCGCGCGATCA 61.158 55.000 37.03 24.34 0.00 2.92
1185 3558 2.386501 AATTCGAGCTACTAGTCGCG 57.613 50.000 13.17 0.00 36.11 5.87
1189 3562 4.141914 CCCCAGAAAATTCGAGCTACTAGT 60.142 45.833 0.00 0.00 0.00 2.57
1192 3565 2.092914 CCCCCAGAAAATTCGAGCTACT 60.093 50.000 0.00 0.00 0.00 2.57
1206 3579 1.164313 ACCTATATCCGACCCCCAGA 58.836 55.000 0.00 0.00 0.00 3.86
1207 3580 1.267121 CACCTATATCCGACCCCCAG 58.733 60.000 0.00 0.00 0.00 4.45
1208 3581 0.178915 CCACCTATATCCGACCCCCA 60.179 60.000 0.00 0.00 0.00 4.96
1220 3593 1.596934 CAGGCACACGACCACCTAT 59.403 57.895 0.00 0.00 0.00 2.57
1222 3595 3.941188 CCAGGCACACGACCACCT 61.941 66.667 0.00 0.00 0.00 4.00
1233 3606 2.771943 AGATCCGAATAAAGACCAGGCA 59.228 45.455 0.00 0.00 0.00 4.75
1243 3616 1.411246 CGACCACCCAGATCCGAATAA 59.589 52.381 0.00 0.00 0.00 1.40
1244 3617 1.037493 CGACCACCCAGATCCGAATA 58.963 55.000 0.00 0.00 0.00 1.75
1245 3618 1.686325 CCGACCACCCAGATCCGAAT 61.686 60.000 0.00 0.00 0.00 3.34
1247 3620 2.583298 ATCCGACCACCCAGATCCGA 62.583 60.000 0.00 0.00 0.00 4.55
1270 3643 0.178068 ACCAATCCGTTCGATCCCAG 59.822 55.000 0.00 0.00 0.00 4.45
1290 3663 1.271840 AACCCTAAGCCCTCGATGCA 61.272 55.000 9.43 0.00 0.00 3.96
1312 3685 1.653151 GAGTAATCGACCAAGTGGGC 58.347 55.000 1.69 0.00 42.05 5.36
1314 3687 1.278238 GCGAGTAATCGACCAAGTGG 58.722 55.000 17.94 0.00 42.17 4.00
1316 3689 1.736032 GCTGCGAGTAATCGACCAAGT 60.736 52.381 17.94 0.00 34.64 3.16
1319 3692 1.141019 GGCTGCGAGTAATCGACCA 59.859 57.895 17.94 4.72 34.64 4.02
1322 3695 0.108992 AAACGGCTGCGAGTAATCGA 60.109 50.000 17.94 0.65 34.64 3.59
1323 3696 0.297820 GAAACGGCTGCGAGTAATCG 59.702 55.000 8.47 8.47 0.00 3.34
1324 3697 1.588861 GAGAAACGGCTGCGAGTAATC 59.411 52.381 0.00 0.00 0.00 1.75
1325 3698 1.641577 GAGAAACGGCTGCGAGTAAT 58.358 50.000 0.00 0.00 0.00 1.89
1326 3699 0.731514 CGAGAAACGGCTGCGAGTAA 60.732 55.000 0.00 0.00 38.46 2.24
1327 3700 1.154093 CGAGAAACGGCTGCGAGTA 60.154 57.895 0.00 0.00 38.46 2.59
1328 3701 2.430921 CGAGAAACGGCTGCGAGT 60.431 61.111 0.00 0.00 38.46 4.18
1329 3702 2.126463 TCGAGAAACGGCTGCGAG 60.126 61.111 0.00 0.00 42.82 5.03
1330 3703 2.430244 GTCGAGAAACGGCTGCGA 60.430 61.111 0.00 0.00 43.76 5.10
1351 3870 3.226429 AAAGCAGACGCGAGCAGGA 62.226 57.895 15.93 0.00 45.49 3.86
1358 3877 2.497628 GCAACGAAAGCAGACGCG 60.498 61.111 3.53 3.53 45.49 6.01
1428 3947 5.287226 ACAGAACAAAACCAGTACTCTACG 58.713 41.667 0.00 0.00 0.00 3.51
1433 3952 4.411212 ACCCTACAGAACAAAACCAGTACT 59.589 41.667 0.00 0.00 0.00 2.73
1434 3953 4.711399 ACCCTACAGAACAAAACCAGTAC 58.289 43.478 0.00 0.00 0.00 2.73
1443 3962 3.564053 AACGGAAACCCTACAGAACAA 57.436 42.857 0.00 0.00 0.00 2.83
1446 3965 4.344679 TCAAGTAACGGAAACCCTACAGAA 59.655 41.667 0.00 0.00 0.00 3.02
1451 3970 4.040706 ACACATCAAGTAACGGAAACCCTA 59.959 41.667 0.00 0.00 0.00 3.53
1531 4050 8.597227 CCATGCATAATATTTGTCAAACAGTTG 58.403 33.333 0.00 0.00 35.95 3.16
1553 4072 4.546570 CAAGTCATCATAAGCATGCCATG 58.453 43.478 15.66 17.84 31.73 3.66
1554 4073 3.572682 CCAAGTCATCATAAGCATGCCAT 59.427 43.478 15.66 6.44 31.73 4.40
1613 4132 4.387026 TTCAATCAAACCACCCAGATCT 57.613 40.909 0.00 0.00 0.00 2.75
1615 4134 3.770933 CCATTCAATCAAACCACCCAGAT 59.229 43.478 0.00 0.00 0.00 2.90
1631 4150 0.695924 AATGTGTCCGACCCCATTCA 59.304 50.000 7.40 0.00 0.00 2.57
1636 4155 1.376812 GACCAATGTGTCCGACCCC 60.377 63.158 0.00 0.00 0.00 4.95
1646 4167 0.541863 CCTAAGCCCTCGACCAATGT 59.458 55.000 0.00 0.00 0.00 2.71
1647 4168 0.179045 CCCTAAGCCCTCGACCAATG 60.179 60.000 0.00 0.00 0.00 2.82
1671 4192 0.753262 AGATAATCGGCCAAGCGAGT 59.247 50.000 2.24 0.00 0.00 4.18
1839 4360 7.775397 AATAGCATTACCAAAAACATCATGC 57.225 32.000 0.00 0.00 36.59 4.06
1861 4385 6.964807 AACGGAAACCTAAACCAACTAAAT 57.035 33.333 0.00 0.00 0.00 1.40
1873 4397 7.472334 AAACTAGTCTCATAACGGAAACCTA 57.528 36.000 0.00 0.00 0.00 3.08
1874 4398 5.997384 AACTAGTCTCATAACGGAAACCT 57.003 39.130 0.00 0.00 0.00 3.50
1919 4500 9.043079 GCATAACCAAACTAGTCTTATTACTCC 57.957 37.037 0.00 0.00 0.00 3.85
1920 4501 9.595823 TGCATAACCAAACTAGTCTTATTACTC 57.404 33.333 0.00 0.00 0.00 2.59
1921 4502 9.601217 CTGCATAACCAAACTAGTCTTATTACT 57.399 33.333 0.00 0.00 0.00 2.24
1922 4503 9.595823 TCTGCATAACCAAACTAGTCTTATTAC 57.404 33.333 0.00 0.00 0.00 1.89
1927 4508 6.296026 TGTTCTGCATAACCAAACTAGTCTT 58.704 36.000 11.96 0.00 0.00 3.01
2030 4611 9.489084 AACTTAGCAGAACAATTTAAAATTCCC 57.511 29.630 0.00 0.00 0.00 3.97
2111 4692 7.511028 AGGAAATGGGGTTAGTAAACATCAAAA 59.489 33.333 0.00 0.00 37.34 2.44
2122 4703 8.736097 AAAATTTAGAAGGAAATGGGGTTAGT 57.264 30.769 0.00 0.00 0.00 2.24
2150 4731 2.645297 TGTGGCCAATTTGGTAGGTCTA 59.355 45.455 7.24 0.00 40.46 2.59
2177 4758 0.331278 TGGGGGAATACTTGTGCTGG 59.669 55.000 0.00 0.00 0.00 4.85
2182 4763 4.289245 CATGGAATTGGGGGAATACTTGT 58.711 43.478 0.00 0.00 0.00 3.16
2202 4783 3.099141 CAATAAGTGTTTGGGCCTCCAT 58.901 45.455 4.53 0.00 43.63 3.41
2323 4904 4.095036 GTCTCTGTTGCCCAATTAACTAGC 59.905 45.833 0.00 0.00 0.00 3.42
2404 4992 1.745115 CCAGAAATGCGCTCCCGAA 60.745 57.895 9.73 0.00 36.29 4.30
2414 5002 2.409870 GGGTGAGGCGCCAGAAATG 61.410 63.158 31.54 0.00 35.42 2.32
2478 5067 8.394040 TCCAATTAAAAAGAAAGGAGAGATCCT 58.606 33.333 0.00 0.00 43.04 3.24
2541 5130 8.145122 ACATAATGGGTCAAATTTAAAACGTGT 58.855 29.630 0.00 0.00 0.00 4.49
2920 5528 5.511373 CCTGAAGTTTGAGGTGTCATAGACA 60.511 44.000 0.00 0.00 40.50 3.41
2966 5574 0.179234 TTGACGTGCAAGGGTGAAGA 59.821 50.000 4.26 0.00 31.55 2.87
3056 5676 3.217017 CCCGGCTCTGCGCTAGTA 61.217 66.667 9.73 0.00 39.13 1.82
3093 5713 2.236223 CTGGCTCCTGACTGCATCGT 62.236 60.000 0.00 0.00 0.00 3.73
3181 5801 4.019174 CTGAATAACTGGCTTTGACCCAT 58.981 43.478 0.00 0.00 0.00 4.00
3202 5822 3.057033 GTGATTGTGCTGAGAATTTGGCT 60.057 43.478 0.00 0.00 0.00 4.75
3225 5845 5.203528 AGCACTATCATTTTGGCCAAGTAT 58.796 37.500 19.48 13.38 0.00 2.12
3334 5957 1.266175 CAGCTTGTTGTGCTCCAAGAG 59.734 52.381 8.41 3.53 40.36 2.85
3335 5958 1.134128 TCAGCTTGTTGTGCTCCAAGA 60.134 47.619 8.41 0.00 40.36 3.02
3358 5981 2.050350 CCAGGCTGCATGTTGGAGG 61.050 63.158 13.64 0.00 36.25 4.30
3365 5988 0.393402 TAAGCTGACCAGGCTGCATG 60.393 55.000 9.56 7.42 40.19 4.06
3521 6150 2.238898 AGCCGCTTAAGTACCTGGAATT 59.761 45.455 0.00 0.00 0.00 2.17
3558 6188 5.798125 TTGGAGTTTTATGGCATTCACAA 57.202 34.783 4.78 1.14 0.00 3.33
3647 6280 8.136563 TCGAGATCATATACTGTAGTACTCCT 57.863 38.462 0.00 0.00 32.72 3.69
4005 8891 3.927142 GTGTTGGAAGAATGACTCTACGG 59.073 47.826 0.00 0.00 32.46 4.02
4015 8901 5.071788 TGACCTCTGTTAGTGTTGGAAGAAT 59.928 40.000 0.00 0.00 0.00 2.40
4040 8926 8.386012 AGATTCATCTCTAGGAAAAGGAGAAA 57.614 34.615 0.00 0.00 39.17 2.52
4043 8929 7.790027 TGAAGATTCATCTCTAGGAAAAGGAG 58.210 38.462 0.00 0.00 35.76 3.69
4076 8962 2.813172 TGACAGAGATGCGCAAAATCAA 59.187 40.909 17.11 0.00 0.00 2.57
4152 9040 6.494893 TGCGTTTGTATTGATTAGCTTTCT 57.505 33.333 0.00 0.00 0.00 2.52
4153 9041 7.561237 TTTGCGTTTGTATTGATTAGCTTTC 57.439 32.000 0.00 0.00 0.00 2.62
4216 9104 1.067565 TCACTCCTCTGCAACGACATC 60.068 52.381 0.00 0.00 0.00 3.06
4230 9118 0.250901 ACCCTTGTGCACATCACTCC 60.251 55.000 22.39 0.00 45.81 3.85
4234 9122 2.064434 TCAAACCCTTGTGCACATCA 57.936 45.000 22.39 5.59 33.94 3.07
4235 9123 2.288395 CCTTCAAACCCTTGTGCACATC 60.288 50.000 22.39 0.00 33.94 3.06
4236 9124 1.688197 CCTTCAAACCCTTGTGCACAT 59.312 47.619 22.39 1.80 33.94 3.21
4244 9135 1.231963 AGGTCCACCTTCAAACCCTT 58.768 50.000 0.00 0.00 46.09 3.95
4306 9197 4.731773 GCATGGCAAGTTTTATTCCTCTCG 60.732 45.833 0.00 0.00 0.00 4.04
4330 9221 7.157347 GCAACTGATATCCTGTATTCATCTCA 58.843 38.462 0.00 0.00 0.00 3.27
4421 9312 4.921547 GCTATTGCTTTTACCTACCTTGC 58.078 43.478 0.00 0.00 36.03 4.01
4503 9434 5.237815 TGTTGACAGTTCCAACTAGCTATG 58.762 41.667 0.00 0.00 43.05 2.23
4660 9641 0.319297 CTGCAGGTTGCTTTTGCTCC 60.319 55.000 5.57 0.00 45.31 4.70
4824 9902 1.225704 GAGGGCCTCATGGACTTGG 59.774 63.158 28.55 0.00 42.43 3.61
4832 9910 1.611419 CATGTGGTGAGGGCCTCAT 59.389 57.895 36.94 19.69 42.73 2.90
4848 9926 2.094675 GTGCTACCACTGGATTTGCAT 58.905 47.619 0.71 0.00 38.93 3.96
4872 9956 3.150949 CTGGAGCACAGGGTGACA 58.849 61.111 0.00 0.00 43.70 3.58
5065 10167 0.608640 GTGTTCCATCTCCACCTCGT 59.391 55.000 0.00 0.00 0.00 4.18
5087 10189 1.689273 GTCGATGGGCCTCTTAGTCAT 59.311 52.381 4.53 0.00 0.00 3.06
5135 10237 4.160642 ACAATTCATGAGCTCAGCCATA 57.839 40.909 22.96 5.95 0.00 2.74
5201 10315 6.769134 TGACGATCTTATCTGAGGTTACAA 57.231 37.500 0.00 0.00 0.00 2.41
5202 10316 6.293462 CGATGACGATCTTATCTGAGGTTACA 60.293 42.308 0.00 0.00 42.66 2.41
5203 10317 6.081049 CGATGACGATCTTATCTGAGGTTAC 58.919 44.000 0.00 0.00 42.66 2.50
5204 10318 5.334957 GCGATGACGATCTTATCTGAGGTTA 60.335 44.000 0.00 0.00 42.66 2.85
5205 10319 4.557695 GCGATGACGATCTTATCTGAGGTT 60.558 45.833 0.00 0.00 42.66 3.50
5206 10320 3.057876 GCGATGACGATCTTATCTGAGGT 60.058 47.826 0.00 0.00 42.66 3.85
5272 10386 2.167487 TGGTACAATGTCGCTCATGCTA 59.833 45.455 0.00 0.00 36.81 3.49
5301 10415 3.181397 CAATCCAACATTGTGCCGATTC 58.819 45.455 0.00 0.00 0.00 2.52
5394 10514 2.223502 GGTAGTGATTCAGATCGCGACA 60.224 50.000 12.93 0.00 44.91 4.35
5420 10540 0.099968 CAACTGCCATCCATGCTTCG 59.900 55.000 0.00 0.00 0.00 3.79
5458 10578 0.324738 TTGATCCAGAGTCCGAGGCT 60.325 55.000 0.00 0.00 0.00 4.58
5659 10786 5.130145 AGAGCCTCATTACTAGCATTCTGTT 59.870 40.000 0.00 0.00 0.00 3.16
5717 10844 6.531923 AGATATGCTGAGCACTGTATCAATT 58.468 36.000 21.74 5.53 43.04 2.32
5824 10951 5.009610 GTGGCAAAGACAGATTTAAAGGTCA 59.990 40.000 15.54 0.00 32.79 4.02
5972 11117 0.110104 AGCTGCTGGGATAATCTGCC 59.890 55.000 0.00 0.00 35.48 4.85
6015 11160 0.617413 CACCTTGGCACCTCATCTCT 59.383 55.000 0.00 0.00 0.00 3.10
6044 11189 2.993899 ACGAAGTAGAAAAGCATGGTCG 59.006 45.455 0.00 0.00 41.94 4.79
6094 11239 4.666253 TGTCAAGCAGCTGGGGCC 62.666 66.667 17.12 0.00 39.73 5.80
6279 11526 1.134007 TGATCCATTTCTCATGCGGCT 60.134 47.619 0.00 0.00 0.00 5.52
6323 11570 6.655062 TCTTCAATACTACAACAAACAAGCG 58.345 36.000 0.00 0.00 0.00 4.68
6429 11682 5.103000 ACATCTATCTCGCACAGTACAAAC 58.897 41.667 0.00 0.00 0.00 2.93
6432 11685 5.365619 TCTACATCTATCTCGCACAGTACA 58.634 41.667 0.00 0.00 0.00 2.90
6441 11694 6.435430 AGCTGCTATTCTACATCTATCTCG 57.565 41.667 0.00 0.00 0.00 4.04
6477 11747 6.003950 TCGAATTCCAAACAGAATTTCTCCT 58.996 36.000 0.00 0.00 44.52 3.69
6480 11750 7.141363 CAGTTCGAATTCCAAACAGAATTTCT 58.859 34.615 16.48 0.00 44.52 2.52
6562 11832 5.391312 ACCACAAGTAAATTGCAGGATTC 57.609 39.130 7.20 0.00 43.15 2.52
6603 11873 3.053768 TCAAGTCCCATTCACCATGCATA 60.054 43.478 0.00 0.00 0.00 3.14
6658 11928 3.610040 AAGATGCCGACACAACTGATA 57.390 42.857 0.00 0.00 0.00 2.15
6664 11934 5.009110 TCAACAAATTAAGATGCCGACACAA 59.991 36.000 0.00 0.00 0.00 3.33
6695 11965 5.490139 AGATGTAATTTGTCCGAATGCAG 57.510 39.130 0.00 0.00 0.00 4.41
6696 11966 4.335315 GGAGATGTAATTTGTCCGAATGCA 59.665 41.667 0.00 0.00 0.00 3.96
6726 11996 1.344438 CCTTCCAGCACAGTGACAGTA 59.656 52.381 4.15 0.00 0.00 2.74
6763 12114 4.021544 CCCTTTTCACCGGAATTTCATCAA 60.022 41.667 9.46 0.00 31.93 2.57
6786 12137 1.808411 TCGGAGCAAATCTGGTTCAC 58.192 50.000 0.00 0.00 34.76 3.18
6787 12138 2.787473 ATCGGAGCAAATCTGGTTCA 57.213 45.000 0.00 0.00 34.76 3.18
6788 12139 4.415735 GAAAATCGGAGCAAATCTGGTTC 58.584 43.478 0.00 0.00 36.56 3.62
6789 12140 3.193479 GGAAAATCGGAGCAAATCTGGTT 59.807 43.478 0.00 0.00 39.45 3.67
6790 12141 2.755103 GGAAAATCGGAGCAAATCTGGT 59.245 45.455 0.00 0.00 34.76 4.00
6791 12142 2.754552 TGGAAAATCGGAGCAAATCTGG 59.245 45.455 0.00 0.00 34.76 3.86
6792 12143 4.337555 AGATGGAAAATCGGAGCAAATCTG 59.662 41.667 0.00 0.00 35.40 2.90
6793 12144 4.337555 CAGATGGAAAATCGGAGCAAATCT 59.662 41.667 0.00 0.00 0.00 2.40
6794 12145 4.096984 ACAGATGGAAAATCGGAGCAAATC 59.903 41.667 0.00 0.00 0.00 2.17
6795 12146 4.019174 ACAGATGGAAAATCGGAGCAAAT 58.981 39.130 0.00 0.00 0.00 2.32
6796 12147 3.420893 ACAGATGGAAAATCGGAGCAAA 58.579 40.909 0.00 0.00 0.00 3.68
6797 12148 3.071874 ACAGATGGAAAATCGGAGCAA 57.928 42.857 0.00 0.00 0.00 3.91
6798 12149 2.787473 ACAGATGGAAAATCGGAGCA 57.213 45.000 0.00 0.00 0.00 4.26
6799 12150 4.060038 TCTACAGATGGAAAATCGGAGC 57.940 45.455 0.00 0.00 0.00 4.70
6813 12164 5.604565 CCAATACAGCATCACATCTACAGA 58.395 41.667 0.00 0.00 0.00 3.41
6825 12176 3.068590 GCAATAAGGTGCCAATACAGCAT 59.931 43.478 0.00 0.00 43.29 3.79
6846 12197 4.802039 CAGAATGCCATAAATTGACAGTGC 59.198 41.667 0.00 0.00 0.00 4.40
6848 12199 6.604396 TCATCAGAATGCCATAAATTGACAGT 59.396 34.615 0.00 0.00 34.76 3.55
6888 12244 2.586648 AAAACTCCCTTTCATCCGCT 57.413 45.000 0.00 0.00 0.00 5.52
6964 12320 1.600107 GGTTGTATGGCTCGGGTCA 59.400 57.895 0.00 0.00 0.00 4.02
6970 12326 0.168128 GTTGCACGGTTGTATGGCTC 59.832 55.000 0.00 0.00 0.00 4.70
6993 12351 5.189736 ACTCCATGTTAGCTGGAATAACTGA 59.810 40.000 0.00 0.00 42.12 3.41
7001 12359 2.167693 CCGTTACTCCATGTTAGCTGGA 59.832 50.000 0.00 0.00 40.49 3.86
7009 12463 1.771565 TCGATCCCGTTACTCCATGT 58.228 50.000 0.00 0.00 37.05 3.21
7034 12488 3.562343 AAGATGATCACAGCAGCAGAT 57.438 42.857 0.00 0.00 34.60 2.90
7065 12519 1.070758 TGAAGTGAAGACAGACTGCCC 59.929 52.381 1.25 0.00 0.00 5.36
7078 12532 4.868171 GGACGCAACTACATATTGAAGTGA 59.132 41.667 0.00 0.00 0.00 3.41
7094 12548 3.286751 GCCTTGCAGTGGACGCAA 61.287 61.111 11.41 0.00 46.67 4.85
7116 12570 1.427809 TCCTGCATGGAGGGTATGAG 58.572 55.000 30.58 5.77 40.56 2.90
7188 12642 7.815068 GCAAGACAGTTCAAGTAAGATCTTCTA 59.185 37.037 12.24 0.00 0.00 2.10
7212 12669 2.472059 GCGCCGGAATGATTCTGCA 61.472 57.895 5.05 0.00 34.66 4.41
7264 12722 1.385528 GGTGGACCAAACTCAACGTT 58.614 50.000 0.00 0.00 37.47 3.99


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

AutoCloner maintained by Alex Coulton.