Multiple sequence alignment - TraesCS3D01G074900

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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 TraesCS3D01G074900 chr3D 100.000 3948 0 0 1 3948 36011832 36015779 0.000000e+00 7291.0
1 TraesCS3D01G074900 chr3D 89.217 779 75 7 2302 3078 36167339 36168110 0.000000e+00 965.0
2 TraesCS3D01G074900 chr3A 88.384 3452 247 73 1 3380 46833124 46836493 0.000000e+00 4012.0
3 TraesCS3D01G074900 chr3A 85.981 214 23 5 3344 3555 46836499 46836707 5.130000e-54 222.0
4 TraesCS3D01G074900 chr3B 93.247 1081 67 6 1699 2776 59034122 59035199 0.000000e+00 1587.0
5 TraesCS3D01G074900 chr3B 90.203 541 21 9 888 1428 59030712 59031220 0.000000e+00 676.0
6 TraesCS3D01G074900 chr3B 86.467 569 47 16 2769 3335 59036115 59036655 7.300000e-167 597.0
7 TraesCS3D01G074900 chr3B 87.335 529 41 12 1 524 59027775 59028282 2.040000e-162 582.0
8 TraesCS3D01G074900 chr3B 80.277 578 64 23 1107 1680 570489889 570489358 1.330000e-104 390.0
9 TraesCS3D01G074900 chr3B 92.857 252 15 1 1414 1665 59033872 59034120 2.900000e-96 363.0
10 TraesCS3D01G074900 chr3B 89.450 218 5 2 533 733 59028327 59028543 3.910000e-65 259.0
11 TraesCS3D01G074900 chr3B 96.364 55 1 1 3327 3380 59036674 59036728 5.430000e-14 89.8
12 TraesCS3D01G074900 chrUn 80.979 715 65 31 980 1680 359350305 359349648 5.890000e-138 501.0
13 TraesCS3D01G074900 chrUn 83.884 242 23 8 1934 2159 359349543 359349302 2.390000e-52 217.0
14 TraesCS3D01G074900 chrUn 85.000 100 2 6 1725 1811 359349639 359349540 5.430000e-14 89.8
15 TraesCS3D01G074900 chrUn 100.000 29 0 0 2147 2175 43094031 43094059 2.000000e-03 54.7
16 TraesCS3D01G074900 chrUn 100.000 29 0 0 2147 2175 43260527 43260499 2.000000e-03 54.7
17 TraesCS3D01G074900 chrUn 100.000 29 0 0 2147 2175 262840887 262840915 2.000000e-03 54.7
18 TraesCS3D01G074900 chrUn 100.000 29 0 0 2147 2175 293232854 293232882 2.000000e-03 54.7
19 TraesCS3D01G074900 chr5D 80.979 715 65 31 980 1680 553222266 553221609 5.890000e-138 501.0
20 TraesCS3D01G074900 chr5D 80.979 715 65 31 980 1680 553256591 553255934 5.890000e-138 501.0
21 TraesCS3D01G074900 chr5D 83.884 242 23 8 1934 2159 553221504 553221263 2.390000e-52 217.0
22 TraesCS3D01G074900 chr5D 85.000 100 2 6 1725 1811 553221600 553221501 5.430000e-14 89.8
23 TraesCS3D01G074900 chr6B 79.659 703 68 29 991 1680 699901448 699900808 1.680000e-118 436.0
24 TraesCS3D01G074900 chr6B 78.910 697 74 33 993 1680 699822188 699821556 4.750000e-109 405.0
25 TraesCS3D01G074900 chr6B 84.426 244 20 10 1934 2159 699821450 699821207 1.430000e-54 224.0
26 TraesCS3D01G074900 chr6B 84.016 244 21 10 1934 2159 699861182 699860939 6.640000e-53 219.0
27 TraesCS3D01G074900 chr2B 80.137 584 65 23 1101 1680 263184726 263185262 4.780000e-104 388.0
28 TraesCS3D01G074900 chr2B 84.490 245 22 9 1931 2159 263185365 263185609 1.100000e-55 228.0
29 TraesCS3D01G074900 chr2B 97.297 37 1 0 3783 3819 297463880 297463844 3.290000e-06 63.9
30 TraesCS3D01G074900 chr5B 79.931 578 65 24 1107 1680 534953244 534952714 1.040000e-100 377.0
31 TraesCS3D01G074900 chr5B 83.884 242 23 9 1934 2159 534952608 534952367 2.390000e-52 217.0
32 TraesCS3D01G074900 chr5B 97.222 36 1 0 3777 3812 506510377 506510412 1.180000e-05 62.1
33 TraesCS3D01G074900 chr5B 92.857 42 2 1 3783 3823 13176032 13176073 4.260000e-05 60.2
34 TraesCS3D01G074900 chr1B 78.931 636 74 32 3153 3757 332094048 332093442 1.040000e-100 377.0
35 TraesCS3D01G074900 chr1B 80.597 335 40 14 3149 3478 337938782 337939096 6.600000e-58 235.0
36 TraesCS3D01G074900 chr1B 79.412 272 36 13 3490 3755 337939422 337939679 1.460000e-39 174.0
37 TraesCS3D01G074900 chr1B 93.651 63 3 1 3882 3944 332093175 332093114 4.200000e-15 93.5
38 TraesCS3D01G074900 chr1B 97.222 36 1 0 3783 3818 259511867 259511832 1.180000e-05 62.1
39 TraesCS3D01G074900 chr1A 79.062 640 66 39 3152 3757 306682208 306682813 1.040000e-100 377.0
40 TraesCS3D01G074900 chr4A 84.774 243 20 10 1934 2159 743589280 743589038 1.100000e-55 228.0
41 TraesCS3D01G074900 chr1D 77.506 449 48 27 3340 3757 246002145 246002571 1.850000e-53 220.0
42 TraesCS3D01G074900 chr1D 95.000 60 2 1 3882 3941 246002838 246002896 4.200000e-15 93.5
43 TraesCS3D01G074900 chr1D 92.683 41 1 2 3780 3820 49932232 49932194 1.530000e-04 58.4
44 TraesCS3D01G074900 chr4D 91.667 48 1 1 3766 3810 494787661 494787708 3.290000e-06 63.9
45 TraesCS3D01G074900 chr4B 94.872 39 1 1 3783 3821 664775688 664775725 4.260000e-05 60.2
46 TraesCS3D01G074900 chr2D 85.714 63 2 4 3756 3811 392691218 392691156 4.260000e-05 60.2
47 TraesCS3D01G074900 chr7D 89.362 47 3 1 3765 3811 630328399 630328355 1.530000e-04 58.4


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 TraesCS3D01G074900 chr3D 36011832 36015779 3947 False 7291.000000 7291 100.000000 1 3948 1 chr3D.!!$F1 3947
1 TraesCS3D01G074900 chr3D 36167339 36168110 771 False 965.000000 965 89.217000 2302 3078 1 chr3D.!!$F2 776
2 TraesCS3D01G074900 chr3A 46833124 46836707 3583 False 2117.000000 4012 87.182500 1 3555 2 chr3A.!!$F1 3554
3 TraesCS3D01G074900 chr3B 59027775 59036728 8953 False 593.400000 1587 90.846143 1 3380 7 chr3B.!!$F1 3379
4 TraesCS3D01G074900 chr3B 570489358 570489889 531 True 390.000000 390 80.277000 1107 1680 1 chr3B.!!$R1 573
5 TraesCS3D01G074900 chrUn 359349302 359350305 1003 True 269.266667 501 83.287667 980 2159 3 chrUn.!!$R2 1179
6 TraesCS3D01G074900 chr5D 553255934 553256591 657 True 501.000000 501 80.979000 980 1680 1 chr5D.!!$R1 700
7 TraesCS3D01G074900 chr5D 553221263 553222266 1003 True 269.266667 501 83.287667 980 2159 3 chr5D.!!$R2 1179
8 TraesCS3D01G074900 chr6B 699900808 699901448 640 True 436.000000 436 79.659000 991 1680 1 chr6B.!!$R2 689
9 TraesCS3D01G074900 chr6B 699821207 699822188 981 True 314.500000 405 81.668000 993 2159 2 chr6B.!!$R3 1166
10 TraesCS3D01G074900 chr2B 263184726 263185609 883 False 308.000000 388 82.313500 1101 2159 2 chr2B.!!$F1 1058
11 TraesCS3D01G074900 chr5B 534952367 534953244 877 True 297.000000 377 81.907500 1107 2159 2 chr5B.!!$R1 1052
12 TraesCS3D01G074900 chr1B 332093114 332094048 934 True 235.250000 377 86.291000 3153 3944 2 chr1B.!!$R2 791
13 TraesCS3D01G074900 chr1B 337938782 337939679 897 False 204.500000 235 80.004500 3149 3755 2 chr1B.!!$F1 606
14 TraesCS3D01G074900 chr1A 306682208 306682813 605 False 377.000000 377 79.062000 3152 3757 1 chr1A.!!$F1 605

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
462 470 0.253044 ATCCACCATTACAGCGTGCT 59.747 50.000 0.00 0.0 0.0 4.40 F
799 1587 0.317938 CCTGTCCGAACGATCCGATC 60.318 60.000 0.00 0.0 0.0 3.69 F
882 1683 0.468648 CCTAATCCAACTCCCCGACC 59.531 60.000 0.00 0.0 0.0 4.79 F
1199 3323 1.063811 GGTGCTCTACTACGCGGTC 59.936 63.158 12.47 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2363 7202 0.183014 AGATGATGCCCTGCTTGGAG 59.817 55.000 0.00 0.0 38.35 3.86 R
2757 7597 0.744771 GAAGGGCAAAGGCGAGGTAG 60.745 60.000 0.00 0.0 42.47 3.18 R
2896 8664 1.216064 TCCTCTGGGCAAGCATGTAT 58.784 50.000 0.00 0.0 0.00 2.29 R
3187 8957 1.860950 CATAATGGACGAGCACTTCCG 59.139 52.381 2.34 0.0 37.27 4.30 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
92 93 2.119495 TCCCAAACTAGAGCCTCCATC 58.881 52.381 0.00 0.00 0.00 3.51
162 164 4.469657 AGTTTTCAAACTGGCCTACATCA 58.530 39.130 3.32 0.00 46.80 3.07
163 165 4.278419 AGTTTTCAAACTGGCCTACATCAC 59.722 41.667 3.32 0.00 46.80 3.06
164 166 2.489938 TCAAACTGGCCTACATCACC 57.510 50.000 3.32 0.00 0.00 4.02
211 214 3.184379 TCTCGATTGTTTGCTTCAACGAG 59.816 43.478 19.81 19.81 41.55 4.18
238 241 1.065418 GGAGGCTTCTCGAAATTCCCA 60.065 52.381 0.00 0.00 38.38 4.37
283 286 2.543238 CCATTCTTACTACGGTCTCGCC 60.543 54.545 0.00 0.00 40.63 5.54
383 387 2.680370 AAGGCACCGATCTTCCCCC 61.680 63.158 0.00 0.00 0.00 5.40
384 388 4.547367 GGCACCGATCTTCCCCCG 62.547 72.222 0.00 0.00 0.00 5.73
386 390 2.987125 CACCGATCTTCCCCCGTT 59.013 61.111 0.00 0.00 0.00 4.44
387 391 1.449601 CACCGATCTTCCCCCGTTG 60.450 63.158 0.00 0.00 0.00 4.10
388 392 1.916777 ACCGATCTTCCCCCGTTGT 60.917 57.895 0.00 0.00 0.00 3.32
389 393 0.615544 ACCGATCTTCCCCCGTTGTA 60.616 55.000 0.00 0.00 0.00 2.41
420 424 4.370364 AACTCACAGTTTTGTTGCGATT 57.630 36.364 0.00 0.00 34.11 3.34
421 425 3.694734 ACTCACAGTTTTGTTGCGATTG 58.305 40.909 0.00 0.00 34.62 2.67
422 426 3.376859 ACTCACAGTTTTGTTGCGATTGA 59.623 39.130 0.00 0.00 34.62 2.57
423 427 3.951306 TCACAGTTTTGTTGCGATTGAG 58.049 40.909 0.00 0.00 34.62 3.02
424 428 3.376859 TCACAGTTTTGTTGCGATTGAGT 59.623 39.130 0.00 0.00 34.62 3.41
425 429 4.572795 TCACAGTTTTGTTGCGATTGAGTA 59.427 37.500 0.00 0.00 34.62 2.59
426 430 5.238432 TCACAGTTTTGTTGCGATTGAGTAT 59.762 36.000 0.00 0.00 34.62 2.12
427 431 5.914635 CACAGTTTTGTTGCGATTGAGTATT 59.085 36.000 0.00 0.00 34.62 1.89
435 439 6.337356 TGTTGCGATTGAGTATTGACAGATA 58.663 36.000 0.00 0.00 0.00 1.98
462 470 0.253044 ATCCACCATTACAGCGTGCT 59.747 50.000 0.00 0.00 0.00 4.40
581 625 3.077617 GAGCTGTTGGATCTGCTCC 57.922 57.895 12.28 0.00 46.34 4.70
711 773 1.654023 GCGGTTGGTTGGGTAGATGC 61.654 60.000 0.00 0.00 0.00 3.91
766 1554 4.341783 GCTGCTGCCCACCACTCT 62.342 66.667 3.85 0.00 0.00 3.24
797 1585 1.377594 TCCTGTCCGAACGATCCGA 60.378 57.895 0.00 0.00 0.00 4.55
798 1586 0.750546 TCCTGTCCGAACGATCCGAT 60.751 55.000 0.00 0.00 0.00 4.18
799 1587 0.317938 CCTGTCCGAACGATCCGATC 60.318 60.000 0.00 0.00 0.00 3.69
800 1588 0.317938 CTGTCCGAACGATCCGATCC 60.318 60.000 2.69 0.00 0.00 3.36
801 1589 1.370172 GTCCGAACGATCCGATCCG 60.370 63.158 2.69 1.24 0.00 4.18
808 1598 0.603172 ACGATCCGATCCGATCTCGT 60.603 55.000 18.10 14.95 37.16 4.18
878 1679 0.474614 GCCTCCTAATCCAACTCCCC 59.525 60.000 0.00 0.00 0.00 4.81
879 1680 0.759346 CCTCCTAATCCAACTCCCCG 59.241 60.000 0.00 0.00 0.00 5.73
880 1681 1.691482 CCTCCTAATCCAACTCCCCGA 60.691 57.143 0.00 0.00 0.00 5.14
881 1682 1.413077 CTCCTAATCCAACTCCCCGAC 59.587 57.143 0.00 0.00 0.00 4.79
882 1683 0.468648 CCTAATCCAACTCCCCGACC 59.531 60.000 0.00 0.00 0.00 4.79
883 1684 0.468648 CTAATCCAACTCCCCGACCC 59.531 60.000 0.00 0.00 0.00 4.46
884 1685 1.332144 TAATCCAACTCCCCGACCCG 61.332 60.000 0.00 0.00 0.00 5.28
886 1687 3.771160 CCAACTCCCCGACCCGAG 61.771 72.222 0.00 0.00 0.00 4.63
926 3015 2.030562 CTTCCGCCTCCGTGTTGT 59.969 61.111 0.00 0.00 0.00 3.32
1092 3214 2.188207 GCCTCCGGCTCTCCTTTC 59.812 66.667 0.00 0.00 46.69 2.62
1093 3215 2.904131 CCTCCGGCTCTCCTTTCC 59.096 66.667 0.00 0.00 0.00 3.13
1094 3216 1.687493 CCTCCGGCTCTCCTTTCCT 60.687 63.158 0.00 0.00 0.00 3.36
1105 3228 4.102367 GCTCTCCTTTCCTTGGATAGATGT 59.898 45.833 8.38 0.00 31.77 3.06
1162 3285 3.193691 TCTGACCAGTTCGGATCTCTTTC 59.806 47.826 0.00 0.00 34.38 2.62
1199 3323 1.063811 GGTGCTCTACTACGCGGTC 59.936 63.158 12.47 0.00 0.00 4.79
1305 3431 4.020543 GGAGGTCTGCTTCTCTTCTCTTA 58.979 47.826 0.00 0.00 0.00 2.10
1349 3478 4.282195 CACCTCTTTGAGTTGACTCCTAGT 59.718 45.833 8.56 0.00 42.20 2.57
1356 3485 6.920569 TTGAGTTGACTCCTAGTTTCAAAC 57.079 37.500 8.56 0.00 42.20 2.93
1420 6218 5.123502 GCAGTAACTTTTACCCTCTTAAGGC 59.876 44.000 1.85 0.00 41.85 4.35
1511 6312 5.032220 GGAGTTGACCAAACAGTAAAAACG 58.968 41.667 0.00 0.00 41.61 3.60
1572 6373 2.259439 CCGAGCCGAGTACCGCTAT 61.259 63.158 0.06 0.00 36.84 2.97
1666 6468 7.721842 TGTTCTGAATTTAATGTGGTGTCCTAA 59.278 33.333 0.00 0.00 0.00 2.69
1678 6480 4.938226 GTGGTGTCCTAATTCTTTCTGGAG 59.062 45.833 0.00 0.00 0.00 3.86
1903 6719 7.987458 TGGTCACTCTTTTGGTATCTATTCATC 59.013 37.037 0.00 0.00 0.00 2.92
2021 6839 1.372087 GCATCCTGTGGAGCTTTCCG 61.372 60.000 0.00 0.00 34.05 4.30
2043 6863 2.431057 GAGGTACCATCCGATCACTTGT 59.569 50.000 15.94 0.00 0.00 3.16
2093 6926 4.637483 ACTGGTTTGACAATGTTGACTG 57.363 40.909 0.00 0.00 0.00 3.51
2111 6945 7.066887 TGTTGACTGATCACTTGTACATTTGTT 59.933 33.333 0.00 0.00 33.38 2.83
2153 6987 9.994432 CATATTCTTGTAACTTCTTTGGTCATC 57.006 33.333 0.00 0.00 0.00 2.92
2265 7104 3.153919 ACATAATGCGGAGTTTGTTGGT 58.846 40.909 0.00 0.00 0.00 3.67
2273 7112 2.794350 CGGAGTTTGTTGGTTTTCATGC 59.206 45.455 0.00 0.00 0.00 4.06
2361 7200 8.548880 TTATGGCTCAGGTTAGTACTATTTCT 57.451 34.615 2.79 0.00 0.00 2.52
2363 7202 5.051153 GGCTCAGGTTAGTACTATTTCTGC 58.949 45.833 2.79 4.87 0.00 4.26
2421 7260 8.046708 AGGAAATTTACTGCCTTTTCAAAAACT 58.953 29.630 0.88 0.00 31.29 2.66
2423 7262 9.489393 GAAATTTACTGCCTTTTCAAAAACTTG 57.511 29.630 0.00 0.00 0.00 3.16
2429 7268 7.781056 ACTGCCTTTTCAAAAACTTGATCTTA 58.219 30.769 0.00 0.00 0.00 2.10
2486 7325 8.100164 TGCTTATATGCAGGTATAGCACATTTA 58.900 33.333 9.11 8.91 45.95 1.40
2506 7345 7.769044 ACATTTATGATATTGTATCCTACCGGC 59.231 37.037 0.00 0.00 0.00 6.13
2551 7390 5.818136 TTTACATTGCTCTGCCTTACATC 57.182 39.130 0.00 0.00 0.00 3.06
2592 7431 8.084985 ACCAAAAAGGAAAAGAAAACTCCATA 57.915 30.769 0.00 0.00 41.22 2.74
2868 8636 7.463515 CGGAACATTTTGTTGTTTAACTTGGAC 60.464 37.037 0.00 0.00 41.28 4.02
2896 8664 2.983030 GGGCCGCACATGTTCACA 60.983 61.111 0.00 0.00 0.00 3.58
2968 8736 1.694150 AGTTGCTGTGAGCCTTGTAGA 59.306 47.619 0.00 0.00 41.51 2.59
2972 8740 1.745141 GCTGTGAGCCTTGTAGATGGG 60.745 57.143 0.00 0.00 34.48 4.00
2999 8767 3.119849 GCAATGCAAACCCTACTACAGTG 60.120 47.826 0.00 0.00 0.00 3.66
3026 8795 4.891168 TGTTGTAGAGTAGTTGGTGTGAGA 59.109 41.667 0.00 0.00 0.00 3.27
3028 8797 5.899120 TGTAGAGTAGTTGGTGTGAGATC 57.101 43.478 0.00 0.00 0.00 2.75
3029 8798 4.395231 TGTAGAGTAGTTGGTGTGAGATCG 59.605 45.833 0.00 0.00 0.00 3.69
3030 8799 2.755655 AGAGTAGTTGGTGTGAGATCGG 59.244 50.000 0.00 0.00 0.00 4.18
3031 8800 2.492484 GAGTAGTTGGTGTGAGATCGGT 59.508 50.000 0.00 0.00 0.00 4.69
3032 8801 3.693085 GAGTAGTTGGTGTGAGATCGGTA 59.307 47.826 0.00 0.00 0.00 4.02
3033 8802 4.084287 AGTAGTTGGTGTGAGATCGGTAA 58.916 43.478 0.00 0.00 0.00 2.85
3034 8803 4.710375 AGTAGTTGGTGTGAGATCGGTAAT 59.290 41.667 0.00 0.00 0.00 1.89
3036 8805 4.504858 AGTTGGTGTGAGATCGGTAATTC 58.495 43.478 0.00 0.00 0.00 2.17
3037 8806 4.223032 AGTTGGTGTGAGATCGGTAATTCT 59.777 41.667 0.00 0.00 0.00 2.40
3038 8807 5.421056 AGTTGGTGTGAGATCGGTAATTCTA 59.579 40.000 0.00 0.00 0.00 2.10
3039 8808 6.098409 AGTTGGTGTGAGATCGGTAATTCTAT 59.902 38.462 0.00 0.00 0.00 1.98
3040 8809 6.479972 TGGTGTGAGATCGGTAATTCTATT 57.520 37.500 0.00 0.00 0.00 1.73
3041 8810 6.513180 TGGTGTGAGATCGGTAATTCTATTC 58.487 40.000 0.00 0.00 0.00 1.75
3042 8811 5.629849 GGTGTGAGATCGGTAATTCTATTCG 59.370 44.000 0.00 0.00 0.00 3.34
3043 8812 5.629849 GTGTGAGATCGGTAATTCTATTCGG 59.370 44.000 0.00 0.00 0.00 4.30
3096 8866 3.514706 TGATTGTTGGATTTCCCATGGTG 59.485 43.478 11.73 2.15 46.10 4.17
3101 8871 3.030873 TGGATTTCCCATGGTGGAATC 57.969 47.619 18.98 18.98 43.72 2.52
3102 8872 2.319844 GGATTTCCCATGGTGGAATCC 58.680 52.381 25.63 25.63 43.72 3.01
3115 8885 5.270794 TGGTGGAATCCATCATTGATCAAA 58.729 37.500 11.88 0.00 40.05 2.69
3145 8915 6.795144 ATTGAGCCAATGATTATGACCAAA 57.205 33.333 0.31 0.00 32.39 3.28
3146 8916 5.840243 TGAGCCAATGATTATGACCAAAG 57.160 39.130 0.00 0.00 0.00 2.77
3147 8917 5.508567 TGAGCCAATGATTATGACCAAAGA 58.491 37.500 0.00 0.00 0.00 2.52
3148 8918 5.951148 TGAGCCAATGATTATGACCAAAGAA 59.049 36.000 0.00 0.00 0.00 2.52
3149 8919 6.095860 TGAGCCAATGATTATGACCAAAGAAG 59.904 38.462 0.00 0.00 0.00 2.85
3150 8920 5.954150 AGCCAATGATTATGACCAAAGAAGT 59.046 36.000 0.00 0.00 0.00 3.01
3198 8968 1.996292 TTCATCTTCGGAAGTGCTCG 58.004 50.000 16.78 3.63 0.00 5.03
3223 8993 6.370994 GTCCATTATGAGCCAATGACTAGATG 59.629 42.308 0.00 0.00 35.77 2.90
3255 9025 4.114794 CAAGGAAAACTTTTGTGGAGCAG 58.885 43.478 0.00 0.00 37.29 4.24
3399 9217 2.435805 TGTATTTGGGGTTGCAAGCAAA 59.564 40.909 28.22 20.67 37.70 3.68
3403 9221 1.036707 TGGGGTTGCAAGCAAACTAC 58.963 50.000 28.22 14.76 42.77 2.73
3404 9222 0.039527 GGGGTTGCAAGCAAACTACG 60.040 55.000 28.22 0.00 42.77 3.51
3405 9223 0.663269 GGGTTGCAAGCAAACTACGC 60.663 55.000 28.22 8.97 42.77 4.42
3407 9225 1.335872 GGTTGCAAGCAAACTACGCAT 60.336 47.619 23.18 0.00 40.25 4.73
3410 9228 4.201871 GGTTGCAAGCAAACTACGCATATA 60.202 41.667 23.18 0.00 40.25 0.86
3414 9232 5.755861 TGCAAGCAAACTACGCATATATGTA 59.244 36.000 14.14 0.00 31.43 2.29
3417 9235 7.148573 GCAAGCAAACTACGCATATATGTAGAT 60.149 37.037 14.14 1.69 40.36 1.98
3478 9298 5.352569 GGATGTACAACAGTCTGAATTGGAG 59.647 44.000 6.91 0.00 0.00 3.86
3479 9299 4.065088 TGTACAACAGTCTGAATTGGAGC 58.935 43.478 6.91 0.00 0.00 4.70
3486 9306 2.158986 AGTCTGAATTGGAGCGAGATGG 60.159 50.000 0.00 0.00 0.00 3.51
3498 9632 1.534203 GAGATGGGGGCTTCCTTCC 59.466 63.158 8.73 0.00 33.05 3.46
3504 9638 1.767692 GGGGCTTCCTTCCAAGTCA 59.232 57.895 0.00 0.00 28.74 3.41
3506 9640 0.402121 GGGCTTCCTTCCAAGTCACT 59.598 55.000 0.00 0.00 28.74 3.41
3555 9690 6.934645 TCTGATTTACTGTTCCTGTTAACCAG 59.065 38.462 2.48 5.29 41.15 4.00
3556 9691 6.597562 TGATTTACTGTTCCTGTTAACCAGT 58.402 36.000 15.67 15.67 39.74 4.00
3557 9692 7.737869 TGATTTACTGTTCCTGTTAACCAGTA 58.262 34.615 14.12 14.12 39.74 2.74
3558 9693 7.876068 TGATTTACTGTTCCTGTTAACCAGTAG 59.124 37.037 16.23 3.58 39.74 2.57
3559 9694 4.618920 ACTGTTCCTGTTAACCAGTAGG 57.381 45.455 11.34 7.77 39.74 3.18
3560 9695 4.228824 ACTGTTCCTGTTAACCAGTAGGA 58.771 43.478 11.34 9.75 39.74 2.94
3561 9696 4.283722 ACTGTTCCTGTTAACCAGTAGGAG 59.716 45.833 11.34 4.89 40.21 3.69
3571 9706 9.715121 CTGTTAACCAGTAGGAGTATTAAACAA 57.285 33.333 2.48 0.00 38.69 2.83
3578 9713 7.280205 CCAGTAGGAGTATTAAACAACCATGTC 59.720 40.741 0.00 0.00 36.26 3.06
3587 9722 2.922740 ACAACCATGTCCACGTTAGT 57.077 45.000 0.00 0.00 33.41 2.24
3588 9723 3.202829 ACAACCATGTCCACGTTAGTT 57.797 42.857 0.00 0.00 33.41 2.24
3589 9724 3.135994 ACAACCATGTCCACGTTAGTTC 58.864 45.455 0.00 0.00 33.41 3.01
3590 9725 2.074547 ACCATGTCCACGTTAGTTCG 57.925 50.000 0.00 0.00 0.00 3.95
3622 9757 8.471361 AAGCAAAAGAAAAGAAAAACAGAGAG 57.529 30.769 0.00 0.00 0.00 3.20
3624 9759 6.533012 GCAAAAGAAAAGAAAAACAGAGAGCT 59.467 34.615 0.00 0.00 0.00 4.09
3631 9766 5.747951 AGAAAAACAGAGAGCTCAAACTG 57.252 39.130 23.87 23.87 36.58 3.16
3637 9772 1.830477 AGAGAGCTCAAACTGGCCTAG 59.170 52.381 17.77 2.01 0.00 3.02
3647 9782 0.687354 ACTGGCCTAGGTGTGTTCTG 59.313 55.000 11.31 1.13 0.00 3.02
3648 9783 0.976641 CTGGCCTAGGTGTGTTCTGA 59.023 55.000 11.31 0.00 0.00 3.27
3668 9805 5.015178 TCTGAAATCTCATGGTTTAGGGGTT 59.985 40.000 0.00 0.00 0.00 4.11
3669 9806 5.650283 TGAAATCTCATGGTTTAGGGGTTT 58.350 37.500 0.00 0.00 0.00 3.27
3673 9812 3.089284 CTCATGGTTTAGGGGTTTCCAC 58.911 50.000 0.00 0.00 38.24 4.02
3677 9819 2.244695 GGTTTAGGGGTTTCCACCTTG 58.755 52.381 0.00 0.00 43.65 3.61
3679 9821 1.536644 TTAGGGGTTTCCACCTTGGT 58.463 50.000 0.00 0.00 43.65 3.67
3683 9825 2.042569 AGGGGTTTCCACCTTGGTATTC 59.957 50.000 0.00 0.00 43.65 1.75
3693 9835 4.142381 CCACCTTGGTATTCTAGCAAAAGC 60.142 45.833 0.00 0.00 44.47 3.51
3694 9836 3.689649 ACCTTGGTATTCTAGCAAAAGCG 59.310 43.478 0.00 0.00 44.47 4.68
3699 9841 4.155280 TGGTATTCTAGCAAAAGCGAAACC 59.845 41.667 0.00 0.00 32.53 3.27
3710 9852 3.838244 AAGCGAAACCAGGCTATATCA 57.162 42.857 0.00 0.00 38.88 2.15
3712 9854 5.483685 AAGCGAAACCAGGCTATATCATA 57.516 39.130 0.00 0.00 38.88 2.15
3716 9858 8.478775 AGCGAAACCAGGCTATATCATATATA 57.521 34.615 0.00 0.00 37.83 0.86
3718 9860 7.326305 GCGAAACCAGGCTATATCATATATACG 59.674 40.741 0.00 0.00 0.00 3.06
3725 9867 8.580720 CAGGCTATATCATATATACGGAAAGCT 58.419 37.037 0.00 0.00 0.00 3.74
3726 9868 8.798402 AGGCTATATCATATATACGGAAAGCTC 58.202 37.037 0.00 0.00 0.00 4.09
3727 9869 7.751348 GGCTATATCATATATACGGAAAGCTCG 59.249 40.741 0.00 0.00 0.00 5.03
3728 9870 7.751348 GCTATATCATATATACGGAAAGCTCGG 59.249 40.741 0.00 0.00 0.00 4.63
3729 9871 4.106029 TCATATATACGGAAAGCTCGGC 57.894 45.455 0.00 0.00 0.00 5.54
3731 9873 4.945543 TCATATATACGGAAAGCTCGGCTA 59.054 41.667 0.00 0.00 38.25 3.93
3733 9875 2.726832 ATACGGAAAGCTCGGCTATC 57.273 50.000 0.00 0.00 38.25 2.08
3734 9876 1.688772 TACGGAAAGCTCGGCTATCT 58.311 50.000 0.00 0.00 38.25 1.98
3735 9877 0.824759 ACGGAAAGCTCGGCTATCTT 59.175 50.000 0.00 0.00 38.25 2.40
3743 9885 2.159170 AGCTCGGCTATCTTGTCAGAAC 60.159 50.000 0.00 0.00 36.99 3.01
3757 9899 9.900710 ATCTTGTCAGAACGTCATATAAGATAC 57.099 33.333 10.31 0.00 32.42 2.24
3758 9900 9.121658 TCTTGTCAGAACGTCATATAAGATACT 57.878 33.333 0.00 0.00 0.00 2.12
3761 9903 9.557061 TGTCAGAACGTCATATAAGATACTACT 57.443 33.333 0.00 0.00 0.00 2.57
3763 9905 9.217278 TCAGAACGTCATATAAGATACTACTCC 57.783 37.037 0.00 0.00 0.00 3.85
3764 9906 9.000486 CAGAACGTCATATAAGATACTACTCCA 58.000 37.037 0.00 0.00 0.00 3.86
3765 9907 9.742144 AGAACGTCATATAAGATACTACTCCAT 57.258 33.333 0.00 0.00 0.00 3.41
3781 9923 7.953752 ACTACTCCATATAAAGTTGTAGGAGC 58.046 38.462 0.00 0.00 43.76 4.70
3782 9924 5.844004 ACTCCATATAAAGTTGTAGGAGCG 58.156 41.667 0.00 0.00 43.76 5.03
3783 9925 5.597182 ACTCCATATAAAGTTGTAGGAGCGA 59.403 40.000 0.00 0.00 43.76 4.93
3784 9926 5.839621 TCCATATAAAGTTGTAGGAGCGAC 58.160 41.667 0.00 0.00 0.00 5.19
3785 9927 5.361571 TCCATATAAAGTTGTAGGAGCGACA 59.638 40.000 0.00 0.00 0.00 4.35
3786 9928 5.462398 CCATATAAAGTTGTAGGAGCGACAC 59.538 44.000 0.00 0.00 0.00 3.67
3787 9929 4.803098 ATAAAGTTGTAGGAGCGACACT 57.197 40.909 0.00 0.00 0.00 3.55
3788 9930 3.470645 AAAGTTGTAGGAGCGACACTT 57.529 42.857 0.00 0.00 0.00 3.16
3789 9931 4.595762 AAAGTTGTAGGAGCGACACTTA 57.404 40.909 0.00 0.00 0.00 2.24
3790 9932 4.803098 AAGTTGTAGGAGCGACACTTAT 57.197 40.909 0.00 0.00 0.00 1.73
3791 9933 4.803098 AGTTGTAGGAGCGACACTTATT 57.197 40.909 0.00 0.00 0.00 1.40
3792 9934 5.148651 AGTTGTAGGAGCGACACTTATTT 57.851 39.130 0.00 0.00 0.00 1.40
3793 9935 5.548406 AGTTGTAGGAGCGACACTTATTTT 58.452 37.500 0.00 0.00 0.00 1.82
3794 9936 5.408604 AGTTGTAGGAGCGACACTTATTTTG 59.591 40.000 0.00 0.00 0.00 2.44
3795 9937 4.250464 TGTAGGAGCGACACTTATTTTGG 58.750 43.478 0.00 0.00 0.00 3.28
3796 9938 2.711542 AGGAGCGACACTTATTTTGGG 58.288 47.619 0.00 0.00 0.00 4.12
3797 9939 2.304761 AGGAGCGACACTTATTTTGGGA 59.695 45.455 0.00 0.00 0.00 4.37
3798 9940 2.418976 GGAGCGACACTTATTTTGGGAC 59.581 50.000 0.00 0.00 0.00 4.46
3799 9941 2.073816 AGCGACACTTATTTTGGGACG 58.926 47.619 0.00 0.00 0.00 4.79
3800 9942 1.129811 GCGACACTTATTTTGGGACGG 59.870 52.381 0.00 0.00 0.00 4.79
3801 9943 2.690786 CGACACTTATTTTGGGACGGA 58.309 47.619 0.00 0.00 0.00 4.69
3802 9944 2.671396 CGACACTTATTTTGGGACGGAG 59.329 50.000 0.00 0.00 0.00 4.63
3810 9952 2.852714 TTTGGGACGGAGGGAGTATA 57.147 50.000 0.00 0.00 0.00 1.47
3826 9968 5.123979 GGGAGTATAACTTTTGCAAGTGAGG 59.876 44.000 0.00 0.00 42.89 3.86
3830 9972 6.770785 AGTATAACTTTTGCAAGTGAGGACAA 59.229 34.615 0.00 0.00 42.89 3.18
3831 9973 3.782889 ACTTTTGCAAGTGAGGACAAC 57.217 42.857 0.00 0.00 42.05 3.32
3846 9988 7.177921 AGTGAGGACAACATGATTTGAAATGAT 59.822 33.333 0.00 0.00 0.00 2.45
3855 9997 8.780616 ACATGATTTGAAATGATTGGGGTATA 57.219 30.769 0.00 0.00 0.00 1.47
3856 9998 9.211410 ACATGATTTGAAATGATTGGGGTATAA 57.789 29.630 0.00 0.00 0.00 0.98
3860 10002 8.837099 ATTTGAAATGATTGGGGTATAACTGA 57.163 30.769 0.00 0.00 0.00 3.41
3862 10004 7.880160 TGAAATGATTGGGGTATAACTGAAG 57.120 36.000 0.00 0.00 0.00 3.02
3865 10007 7.451731 AATGATTGGGGTATAACTGAAGAGA 57.548 36.000 0.00 0.00 0.00 3.10
3871 10013 4.434520 GGGTATAACTGAAGAGAGTGCAC 58.565 47.826 9.40 9.40 0.00 4.57
3921 10251 3.476552 CAAGCCACACTCTTCCTGTTAA 58.523 45.455 0.00 0.00 0.00 2.01
3926 10256 4.065789 CCACACTCTTCCTGTTAACTTCC 58.934 47.826 7.22 0.00 0.00 3.46
3941 10271 7.930217 TGTTAACTTCCTGTCTGAATTTTCTG 58.070 34.615 7.22 0.00 0.00 3.02
3944 10274 6.874288 ACTTCCTGTCTGAATTTTCTGAAG 57.126 37.500 2.00 0.00 36.99 3.02
3945 10275 6.595682 ACTTCCTGTCTGAATTTTCTGAAGA 58.404 36.000 0.00 0.00 36.99 2.87
3946 10276 6.484977 ACTTCCTGTCTGAATTTTCTGAAGAC 59.515 38.462 0.00 2.85 36.99 3.01
3947 10277 5.308825 TCCTGTCTGAATTTTCTGAAGACC 58.691 41.667 2.00 0.00 37.13 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
151 153 2.731571 GGAGCGGTGATGTAGGCCA 61.732 63.158 5.01 0.00 0.00 5.36
154 156 2.032620 AGTAAGGAGCGGTGATGTAGG 58.967 52.381 0.00 0.00 0.00 3.18
158 160 1.478510 AGTCAGTAAGGAGCGGTGATG 59.521 52.381 0.00 0.00 0.00 3.07
162 164 1.339097 ACAAGTCAGTAAGGAGCGGT 58.661 50.000 0.00 0.00 0.00 5.68
163 165 2.457366 AACAAGTCAGTAAGGAGCGG 57.543 50.000 0.00 0.00 0.00 5.52
164 166 4.813296 AAAAACAAGTCAGTAAGGAGCG 57.187 40.909 0.00 0.00 0.00 5.03
189 192 3.127589 TCGTTGAAGCAAACAATCGAGA 58.872 40.909 0.00 0.00 32.29 4.04
205 208 1.805945 GCCTCCGTACTGCTCGTTG 60.806 63.158 0.00 0.00 0.00 4.10
206 209 1.533469 AAGCCTCCGTACTGCTCGTT 61.533 55.000 0.00 0.00 33.36 3.85
211 214 1.226717 CGAGAAGCCTCCGTACTGC 60.227 63.158 0.00 0.00 36.04 4.40
238 241 1.286260 GTCTGGCAACTCGTCGTCT 59.714 57.895 0.00 0.00 37.61 4.18
383 387 2.037511 TGAGTTACAAGGGGGTACAACG 59.962 50.000 0.00 0.00 0.00 4.10
384 388 3.181452 TGTGAGTTACAAGGGGGTACAAC 60.181 47.826 0.00 0.00 36.06 3.32
386 390 2.635915 CTGTGAGTTACAAGGGGGTACA 59.364 50.000 0.00 0.00 39.20 2.90
387 391 2.636403 ACTGTGAGTTACAAGGGGGTAC 59.364 50.000 0.00 0.00 39.20 3.34
388 392 2.980548 ACTGTGAGTTACAAGGGGGTA 58.019 47.619 0.00 0.00 39.20 3.69
389 393 1.815757 ACTGTGAGTTACAAGGGGGT 58.184 50.000 0.00 0.00 39.20 4.95
420 424 8.414003 GGATGTTACAGTATCTGTCAATACTCA 58.586 37.037 5.66 0.00 41.21 3.41
421 425 8.414003 TGGATGTTACAGTATCTGTCAATACTC 58.586 37.037 5.66 0.00 41.21 2.59
422 426 8.198109 GTGGATGTTACAGTATCTGTCAATACT 58.802 37.037 5.66 0.00 41.21 2.12
423 427 7.438459 GGTGGATGTTACAGTATCTGTCAATAC 59.562 40.741 5.66 1.39 41.21 1.89
424 428 7.125053 TGGTGGATGTTACAGTATCTGTCAATA 59.875 37.037 5.66 0.16 41.21 1.90
425 429 6.070251 TGGTGGATGTTACAGTATCTGTCAAT 60.070 38.462 5.66 0.00 41.21 2.57
426 430 5.247337 TGGTGGATGTTACAGTATCTGTCAA 59.753 40.000 5.66 0.00 41.21 3.18
427 431 4.775253 TGGTGGATGTTACAGTATCTGTCA 59.225 41.667 5.66 0.36 41.21 3.58
462 470 4.339872 AATTGCTTCCATGTTTTCAGCA 57.660 36.364 0.00 0.00 0.00 4.41
524 532 0.240411 AGAACAGAGCACGACCGTAC 59.760 55.000 0.00 0.00 0.00 3.67
527 535 0.318699 TTCAGAACAGAGCACGACCG 60.319 55.000 0.00 0.00 0.00 4.79
528 536 1.269831 ACTTCAGAACAGAGCACGACC 60.270 52.381 0.00 0.00 0.00 4.79
529 537 2.141535 ACTTCAGAACAGAGCACGAC 57.858 50.000 0.00 0.00 0.00 4.34
531 539 2.609459 ACAAACTTCAGAACAGAGCACG 59.391 45.455 0.00 0.00 0.00 5.34
581 625 1.986378 CACCGTTTTCAGTAGCTCTCG 59.014 52.381 0.00 0.00 0.00 4.04
582 626 1.727335 GCACCGTTTTCAGTAGCTCTC 59.273 52.381 0.00 0.00 0.00 3.20
584 628 0.438830 CGCACCGTTTTCAGTAGCTC 59.561 55.000 0.00 0.00 0.00 4.09
696 758 0.392461 GCTCGCATCTACCCAACCAA 60.392 55.000 0.00 0.00 0.00 3.67
754 1542 1.152247 AGTGAGAGAGTGGTGGGCA 60.152 57.895 0.00 0.00 0.00 5.36
755 1543 1.594310 GAGTGAGAGAGTGGTGGGC 59.406 63.158 0.00 0.00 0.00 5.36
756 1544 1.886585 CGAGTGAGAGAGTGGTGGG 59.113 63.158 0.00 0.00 0.00 4.61
766 1554 1.299562 GACAGGACGAGCGAGTGAGA 61.300 60.000 0.00 0.00 0.00 3.27
799 1587 2.287909 GGAAGGAATCTGACGAGATCGG 60.288 54.545 7.22 0.00 44.95 4.18
800 1588 2.359214 TGGAAGGAATCTGACGAGATCG 59.641 50.000 0.00 0.00 38.03 3.69
801 1589 3.634448 TCTGGAAGGAATCTGACGAGATC 59.366 47.826 0.00 0.00 38.03 2.75
808 1598 5.256474 GGTTTGAATCTGGAAGGAATCTGA 58.744 41.667 0.00 0.00 0.00 3.27
1081 3203 3.041946 TCTATCCAAGGAAAGGAGAGCC 58.958 50.000 0.00 0.00 42.73 4.70
1082 3204 4.102367 ACATCTATCCAAGGAAAGGAGAGC 59.898 45.833 0.00 0.00 42.73 4.09
1083 3205 5.885449 ACATCTATCCAAGGAAAGGAGAG 57.115 43.478 0.00 0.00 44.02 3.20
1084 3206 6.270927 CCATACATCTATCCAAGGAAAGGAGA 59.729 42.308 0.00 0.00 38.83 3.71
1087 3209 6.439636 TCCATACATCTATCCAAGGAAAGG 57.560 41.667 0.00 0.00 0.00 3.11
1088 3210 6.883217 CCATCCATACATCTATCCAAGGAAAG 59.117 42.308 0.00 0.00 0.00 2.62
1089 3211 6.562223 TCCATCCATACATCTATCCAAGGAAA 59.438 38.462 0.00 0.00 0.00 3.13
1090 3212 6.090870 TCCATCCATACATCTATCCAAGGAA 58.909 40.000 0.00 0.00 0.00 3.36
1092 3214 6.354938 CATCCATCCATACATCTATCCAAGG 58.645 44.000 0.00 0.00 0.00 3.61
1093 3215 6.157471 TCCATCCATCCATACATCTATCCAAG 59.843 42.308 0.00 0.00 0.00 3.61
1094 3216 6.031386 TCCATCCATCCATACATCTATCCAA 58.969 40.000 0.00 0.00 0.00 3.53
1105 3228 4.151943 ACCAGAGATCCATCCATCCATA 57.848 45.455 0.00 0.00 0.00 2.74
1162 3285 4.362476 GCGCCCTGCCAACCAAAG 62.362 66.667 0.00 0.00 37.76 2.77
1290 3414 6.127196 GGGAAGAAGATAAGAGAAGAGAAGCA 60.127 42.308 0.00 0.00 0.00 3.91
1349 3478 7.544217 GCTCTTTTACCAAGTCAAAGTTTGAAA 59.456 33.333 19.63 6.94 42.15 2.69
1356 3485 6.317789 TCATGCTCTTTTACCAAGTCAAAG 57.682 37.500 0.00 0.00 30.69 2.77
1420 6218 7.810282 CCTACTTGATCTATATGAGAAACCACG 59.190 40.741 0.00 0.00 37.85 4.94
1511 6312 3.134127 GGGCACCGCATTCAGACC 61.134 66.667 0.00 0.00 40.86 3.85
1550 6351 1.804326 CGGTACTCGGCTCGGTTTG 60.804 63.158 0.00 0.00 34.75 2.93
1551 6352 2.570181 CGGTACTCGGCTCGGTTT 59.430 61.111 0.00 0.00 34.75 3.27
1572 6373 2.543031 CGGTGTTTCGACAAGTCTCTCA 60.543 50.000 0.00 0.00 0.00 3.27
1878 6694 8.207545 AGATGAATAGATACCAAAAGAGTGACC 58.792 37.037 0.00 0.00 0.00 4.02
2021 6839 1.705873 AGTGATCGGATGGTACCTCC 58.294 55.000 14.36 15.61 0.00 4.30
2043 6863 6.533730 AGTTTCATCAATCCAGTACAACTCA 58.466 36.000 0.00 0.00 0.00 3.41
2093 6926 6.917477 TCTGCAAAACAAATGTACAAGTGATC 59.083 34.615 14.26 0.00 0.00 2.92
2111 6945 7.175467 ACAAGAATATGAGATTGTGTCTGCAAA 59.825 33.333 0.00 0.00 37.29 3.68
2153 6987 1.153489 CTCGGTGATGGACCAGCTG 60.153 63.158 11.74 6.78 46.55 4.24
2273 7112 8.655092 GCCGAAGAAAGAATATCTAATGATCTG 58.345 37.037 0.00 0.00 34.32 2.90
2311 7150 2.242043 CAGGAAGGTGCAAATCCAAGT 58.758 47.619 14.18 0.00 35.62 3.16
2363 7202 0.183014 AGATGATGCCCTGCTTGGAG 59.817 55.000 0.00 0.00 38.35 3.86
2407 7246 9.920826 CTTTTAAGATCAAGTTTTTGAAAAGGC 57.079 29.630 0.00 0.00 45.82 4.35
2486 7325 5.163301 GGATGCCGGTAGGATACAATATCAT 60.163 44.000 1.90 0.00 45.43 2.45
2525 7364 5.709631 TGTAAGGCAGAGCAATGTAAATCAA 59.290 36.000 0.00 0.00 0.00 2.57
2530 7369 4.842574 TGATGTAAGGCAGAGCAATGTAA 58.157 39.130 0.00 0.00 0.00 2.41
2551 7390 9.292195 TCCTTTTTGGTTATTCTAGTTACCTTG 57.708 33.333 0.00 0.00 37.07 3.61
2757 7597 0.744771 GAAGGGCAAAGGCGAGGTAG 60.745 60.000 0.00 0.00 42.47 3.18
2896 8664 1.216064 TCCTCTGGGCAAGCATGTAT 58.784 50.000 0.00 0.00 0.00 2.29
2989 8757 7.147143 ACTCTACAACATGACACTGTAGTAG 57.853 40.000 19.04 17.22 42.04 2.57
2990 8758 7.881751 ACTACTCTACAACATGACACTGTAGTA 59.118 37.037 19.04 12.21 42.04 1.82
2991 8759 6.715718 ACTACTCTACAACATGACACTGTAGT 59.284 38.462 19.04 14.87 42.04 2.73
2999 8767 5.405571 CACACCAACTACTCTACAACATGAC 59.594 44.000 0.00 0.00 0.00 3.06
3043 8812 2.467566 ACACAGGTCGGGTAATTCAC 57.532 50.000 0.00 0.00 0.00 3.18
3096 8866 6.735145 GCAGAGTTTGATCAATGATGGATTCC 60.735 42.308 9.40 0.00 0.00 3.01
3101 8871 4.976224 TGCAGAGTTTGATCAATGATGG 57.024 40.909 9.40 1.04 0.00 3.51
3102 8872 6.560711 TCAATGCAGAGTTTGATCAATGATG 58.439 36.000 9.40 7.43 0.00 3.07
3141 8911 6.064060 TGATAGGATTATGCCACTTCTTTGG 58.936 40.000 0.00 0.00 39.98 3.28
3142 8912 6.994496 TCTGATAGGATTATGCCACTTCTTTG 59.006 38.462 0.00 0.00 0.00 2.77
3143 8913 7.141758 TCTGATAGGATTATGCCACTTCTTT 57.858 36.000 0.00 0.00 0.00 2.52
3144 8914 6.753913 TCTGATAGGATTATGCCACTTCTT 57.246 37.500 0.00 0.00 0.00 2.52
3145 8915 6.949117 ATCTGATAGGATTATGCCACTTCT 57.051 37.500 0.00 0.00 0.00 2.85
3146 8916 9.507329 TTTTATCTGATAGGATTATGCCACTTC 57.493 33.333 0.00 0.00 0.00 3.01
3147 8917 9.512588 CTTTTATCTGATAGGATTATGCCACTT 57.487 33.333 0.00 0.00 0.00 3.16
3148 8918 7.609532 GCTTTTATCTGATAGGATTATGCCACT 59.390 37.037 0.00 0.00 0.00 4.00
3149 8919 7.391554 TGCTTTTATCTGATAGGATTATGCCAC 59.608 37.037 0.00 0.00 0.00 5.01
3150 8920 7.460910 TGCTTTTATCTGATAGGATTATGCCA 58.539 34.615 0.00 0.00 0.00 4.92
3187 8957 1.860950 CATAATGGACGAGCACTTCCG 59.139 52.381 2.34 0.00 37.27 4.30
3198 8968 5.858381 TCTAGTCATTGGCTCATAATGGAC 58.142 41.667 0.00 0.00 36.44 4.02
3231 9001 4.112634 GCTCCACAAAAGTTTTCCTTGTC 58.887 43.478 0.00 0.00 32.32 3.18
3243 9013 3.146066 GTGTACCATCTGCTCCACAAAA 58.854 45.455 0.00 0.00 0.00 2.44
3255 9025 5.354234 CCTGTGAAATAACCAGTGTACCATC 59.646 44.000 0.00 0.00 0.00 3.51
3304 9074 9.606631 TGTAACAAGATTGTACATATGCACATA 57.393 29.630 9.58 2.22 41.31 2.29
3325 9095 8.665685 CCTGTGTAATGTTAAGGATCTTGTAAC 58.334 37.037 0.00 0.21 0.00 2.50
3466 9286 2.208431 CCATCTCGCTCCAATTCAGAC 58.792 52.381 0.00 0.00 0.00 3.51
3478 9298 2.949705 GAAGGAAGCCCCCATCTCGC 62.950 65.000 0.00 0.00 34.66 5.03
3479 9299 1.147153 GAAGGAAGCCCCCATCTCG 59.853 63.158 0.00 0.00 34.66 4.04
3486 9306 0.609406 GTGACTTGGAAGGAAGCCCC 60.609 60.000 0.00 0.00 0.00 5.80
3504 9638 9.508721 AAGGACCTCTTAAGGAATAATCTTAGT 57.491 33.333 1.85 0.00 46.67 2.24
3506 9640 9.731001 AGAAGGACCTCTTAAGGAATAATCTTA 57.269 33.333 1.85 0.00 46.67 2.10
3555 9690 7.065443 GTGGACATGGTTGTTTAATACTCCTAC 59.935 40.741 0.00 0.00 35.79 3.18
3556 9691 7.107542 GTGGACATGGTTGTTTAATACTCCTA 58.892 38.462 0.00 0.00 35.79 2.94
3557 9692 5.944007 GTGGACATGGTTGTTTAATACTCCT 59.056 40.000 0.00 0.00 35.79 3.69
3558 9693 5.163794 CGTGGACATGGTTGTTTAATACTCC 60.164 44.000 0.00 0.00 35.79 3.85
3559 9694 5.410439 ACGTGGACATGGTTGTTTAATACTC 59.590 40.000 0.00 0.00 35.79 2.59
3560 9695 5.310451 ACGTGGACATGGTTGTTTAATACT 58.690 37.500 0.00 0.00 35.79 2.12
3561 9696 5.616488 ACGTGGACATGGTTGTTTAATAC 57.384 39.130 0.00 0.00 35.79 1.89
3571 9706 1.342174 ACGAACTAACGTGGACATGGT 59.658 47.619 0.00 0.00 44.84 3.55
3587 9722 9.790389 TTTCTTTTCTTTTGCTTTATACACGAA 57.210 25.926 0.00 0.00 0.00 3.85
3588 9723 9.790389 TTTTCTTTTCTTTTGCTTTATACACGA 57.210 25.926 0.00 0.00 0.00 4.35
3595 9730 9.921637 TCTCTGTTTTTCTTTTCTTTTGCTTTA 57.078 25.926 0.00 0.00 0.00 1.85
3597 9732 7.063898 GCTCTCTGTTTTTCTTTTCTTTTGCTT 59.936 33.333 0.00 0.00 0.00 3.91
3599 9734 6.533012 AGCTCTCTGTTTTTCTTTTCTTTTGC 59.467 34.615 0.00 0.00 0.00 3.68
3600 9735 7.756722 TGAGCTCTCTGTTTTTCTTTTCTTTTG 59.243 33.333 16.19 0.00 0.00 2.44
3616 9751 0.324285 AGGCCAGTTTGAGCTCTCTG 59.676 55.000 16.19 18.31 0.00 3.35
3618 9753 1.134551 CCTAGGCCAGTTTGAGCTCTC 60.135 57.143 16.19 5.70 0.00 3.20
3622 9757 0.036875 ACACCTAGGCCAGTTTGAGC 59.963 55.000 9.30 0.00 0.00 4.26
3624 9759 1.136828 ACACACCTAGGCCAGTTTGA 58.863 50.000 9.30 0.00 0.00 2.69
3631 9766 2.561478 TTTCAGAACACACCTAGGCC 57.439 50.000 9.30 0.00 0.00 5.19
3637 9772 4.074970 ACCATGAGATTTCAGAACACACC 58.925 43.478 0.00 0.00 36.61 4.16
3647 9782 5.127194 GGAAACCCCTAAACCATGAGATTTC 59.873 44.000 0.00 0.00 0.00 2.17
3648 9783 5.023452 GGAAACCCCTAAACCATGAGATTT 58.977 41.667 0.00 0.00 0.00 2.17
3668 9805 4.919774 TTGCTAGAATACCAAGGTGGAA 57.080 40.909 1.07 0.00 40.96 3.53
3669 9806 4.919774 TTTGCTAGAATACCAAGGTGGA 57.080 40.909 1.07 0.00 40.96 4.02
3673 9812 3.938963 TCGCTTTTGCTAGAATACCAAGG 59.061 43.478 0.00 0.00 44.80 3.61
3677 9819 4.155280 TGGTTTCGCTTTTGCTAGAATACC 59.845 41.667 0.00 0.00 44.80 2.73
3679 9821 4.394920 CCTGGTTTCGCTTTTGCTAGAATA 59.605 41.667 0.00 0.00 44.80 1.75
3683 9825 1.401539 GCCTGGTTTCGCTTTTGCTAG 60.402 52.381 0.00 0.00 44.80 3.42
3693 9835 7.808381 CCGTATATATGATATAGCCTGGTTTCG 59.192 40.741 3.36 0.00 0.00 3.46
3694 9836 8.857098 TCCGTATATATGATATAGCCTGGTTTC 58.143 37.037 3.36 0.00 0.00 2.78
3699 9841 8.580720 AGCTTTCCGTATATATGATATAGCCTG 58.419 37.037 3.36 0.00 0.00 4.85
3710 9852 5.828859 AGATAGCCGAGCTTTCCGTATATAT 59.171 40.000 3.71 0.00 40.44 0.86
3712 9854 4.017808 AGATAGCCGAGCTTTCCGTATAT 58.982 43.478 3.71 0.00 40.44 0.86
3716 9858 0.824759 AAGATAGCCGAGCTTTCCGT 59.175 50.000 3.71 0.00 40.44 4.69
3718 9860 2.205911 GACAAGATAGCCGAGCTTTCC 58.794 52.381 3.71 0.00 40.44 3.13
3725 9867 1.816835 ACGTTCTGACAAGATAGCCGA 59.183 47.619 0.00 0.00 30.72 5.54
3726 9868 2.186076 GACGTTCTGACAAGATAGCCG 58.814 52.381 0.00 0.00 30.72 5.52
3727 9869 3.232213 TGACGTTCTGACAAGATAGCC 57.768 47.619 0.00 0.00 30.72 3.93
3728 9870 8.076781 TCTTATATGACGTTCTGACAAGATAGC 58.923 37.037 0.00 0.00 30.72 2.97
3731 9873 9.900710 GTATCTTATATGACGTTCTGACAAGAT 57.099 33.333 13.25 13.25 30.72 2.40
3735 9877 9.557061 AGTAGTATCTTATATGACGTTCTGACA 57.443 33.333 0.00 0.00 0.00 3.58
3757 9899 7.040617 TCGCTCCTACAACTTTATATGGAGTAG 60.041 40.741 0.00 0.00 40.99 2.57
3758 9900 6.774170 TCGCTCCTACAACTTTATATGGAGTA 59.226 38.462 0.00 0.00 40.99 2.59
3759 9901 5.597182 TCGCTCCTACAACTTTATATGGAGT 59.403 40.000 0.00 0.00 40.99 3.85
3760 9902 5.921408 GTCGCTCCTACAACTTTATATGGAG 59.079 44.000 0.00 0.00 41.61 3.86
3761 9903 5.361571 TGTCGCTCCTACAACTTTATATGGA 59.638 40.000 0.00 0.00 0.00 3.41
3762 9904 5.462398 GTGTCGCTCCTACAACTTTATATGG 59.538 44.000 0.00 0.00 0.00 2.74
3763 9905 6.273825 AGTGTCGCTCCTACAACTTTATATG 58.726 40.000 0.00 0.00 0.00 1.78
3764 9906 6.466885 AGTGTCGCTCCTACAACTTTATAT 57.533 37.500 0.00 0.00 0.00 0.86
3765 9907 5.909621 AGTGTCGCTCCTACAACTTTATA 57.090 39.130 0.00 0.00 0.00 0.98
3766 9908 4.803098 AGTGTCGCTCCTACAACTTTAT 57.197 40.909 0.00 0.00 0.00 1.40
3767 9909 4.595762 AAGTGTCGCTCCTACAACTTTA 57.404 40.909 0.00 0.00 0.00 1.85
3768 9910 3.470645 AAGTGTCGCTCCTACAACTTT 57.529 42.857 0.00 0.00 0.00 2.66
3769 9911 4.803098 ATAAGTGTCGCTCCTACAACTT 57.197 40.909 0.00 0.00 0.00 2.66
3770 9912 4.803098 AATAAGTGTCGCTCCTACAACT 57.197 40.909 0.00 0.00 0.00 3.16
3771 9913 5.390567 CCAAAATAAGTGTCGCTCCTACAAC 60.391 44.000 0.00 0.00 0.00 3.32
3772 9914 4.693566 CCAAAATAAGTGTCGCTCCTACAA 59.306 41.667 0.00 0.00 0.00 2.41
3773 9915 4.250464 CCAAAATAAGTGTCGCTCCTACA 58.750 43.478 0.00 0.00 0.00 2.74
3774 9916 3.621715 CCCAAAATAAGTGTCGCTCCTAC 59.378 47.826 0.00 0.00 0.00 3.18
3775 9917 3.516300 TCCCAAAATAAGTGTCGCTCCTA 59.484 43.478 0.00 0.00 0.00 2.94
3776 9918 2.304761 TCCCAAAATAAGTGTCGCTCCT 59.695 45.455 0.00 0.00 0.00 3.69
3777 9919 2.418976 GTCCCAAAATAAGTGTCGCTCC 59.581 50.000 0.00 0.00 0.00 4.70
3778 9920 2.093783 CGTCCCAAAATAAGTGTCGCTC 59.906 50.000 0.00 0.00 0.00 5.03
3779 9921 2.073816 CGTCCCAAAATAAGTGTCGCT 58.926 47.619 0.00 0.00 0.00 4.93
3780 9922 1.129811 CCGTCCCAAAATAAGTGTCGC 59.870 52.381 0.00 0.00 0.00 5.19
3781 9923 2.671396 CTCCGTCCCAAAATAAGTGTCG 59.329 50.000 0.00 0.00 0.00 4.35
3782 9924 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
3783 9925 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
3784 9926 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3785 9927 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3786 9928 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3787 9929 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3788 9930 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3789 9931 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3790 9932 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
3791 9933 2.767960 GTTATACTCCCTCCGTCCCAAA 59.232 50.000 0.00 0.00 0.00 3.28
3792 9934 2.023695 AGTTATACTCCCTCCGTCCCAA 60.024 50.000 0.00 0.00 0.00 4.12
3793 9935 1.572415 AGTTATACTCCCTCCGTCCCA 59.428 52.381 0.00 0.00 0.00 4.37
3794 9936 2.378378 AGTTATACTCCCTCCGTCCC 57.622 55.000 0.00 0.00 0.00 4.46
3795 9937 4.439968 CAAAAGTTATACTCCCTCCGTCC 58.560 47.826 0.00 0.00 0.00 4.79
3796 9938 3.869832 GCAAAAGTTATACTCCCTCCGTC 59.130 47.826 0.00 0.00 0.00 4.79
3797 9939 3.262405 TGCAAAAGTTATACTCCCTCCGT 59.738 43.478 0.00 0.00 0.00 4.69
3798 9940 3.869065 TGCAAAAGTTATACTCCCTCCG 58.131 45.455 0.00 0.00 0.00 4.63
3799 9941 5.123979 CACTTGCAAAAGTTATACTCCCTCC 59.876 44.000 0.00 0.00 0.00 4.30
3800 9942 5.938125 TCACTTGCAAAAGTTATACTCCCTC 59.062 40.000 0.00 0.00 0.00 4.30
3801 9943 5.876357 TCACTTGCAAAAGTTATACTCCCT 58.124 37.500 0.00 0.00 0.00 4.20
3802 9944 5.123979 CCTCACTTGCAAAAGTTATACTCCC 59.876 44.000 0.00 0.00 0.00 4.30
3810 9952 3.509575 TGTTGTCCTCACTTGCAAAAGTT 59.490 39.130 0.00 0.00 0.00 2.66
3826 9968 6.314400 CCCCAATCATTTCAAATCATGTTGTC 59.686 38.462 0.00 0.00 0.00 3.18
3830 9972 7.679732 ATACCCCAATCATTTCAAATCATGT 57.320 32.000 0.00 0.00 0.00 3.21
3831 9973 9.480053 GTTATACCCCAATCATTTCAAATCATG 57.520 33.333 0.00 0.00 0.00 3.07
3846 9988 4.081087 GCACTCTCTTCAGTTATACCCCAA 60.081 45.833 0.00 0.00 0.00 4.12
3855 9997 1.765314 AGTGGTGCACTCTCTTCAGTT 59.235 47.619 17.98 0.00 41.21 3.16
3856 9998 1.418334 AGTGGTGCACTCTCTTCAGT 58.582 50.000 17.98 4.90 41.21 3.41
3871 10013 4.021104 TCACAGAGTGGTTATTCAGAGTGG 60.021 45.833 0.00 0.00 33.87 4.00
3921 10251 6.484977 GTCTTCAGAAAATTCAGACAGGAAGT 59.515 38.462 0.00 0.00 35.04 3.01


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

AutoCloner maintained by Alex Coulton.