Multiple sequence alignment - TraesCS3B01G207300

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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 TraesCS3B01G207300 chr3B 100.000 9431 0 0 1 9431 242878625 242869195 0.000000e+00 17416
1 TraesCS3B01G207300 chr3B 87.553 1422 121 16 2902 4289 771532257 771530858 0.000000e+00 1594
2 TraesCS3B01G207300 chr3D 96.592 5135 128 16 4312 9431 167769826 167764724 0.000000e+00 8469
3 TraesCS3B01G207300 chr3D 97.576 2269 52 1 1 2266 167772505 167770237 0.000000e+00 3882
4 TraesCS3B01G207300 chr3D 97.196 428 12 0 2350 2777 167770240 167769813 0.000000e+00 725
5 TraesCS3B01G207300 chr3A 96.105 5135 144 22 4312 9431 201501736 201506829 0.000000e+00 8323
6 TraesCS3B01G207300 chr3A 95.494 2286 68 12 1 2266 201499055 201501325 0.000000e+00 3618
7 TraesCS3B01G207300 chr3A 96.706 425 14 0 2350 2774 201501322 201501746 0.000000e+00 708
8 TraesCS3B01G207300 chr2B 90.334 1407 110 9 2902 4298 211866184 211867574 0.000000e+00 1821
9 TraesCS3B01G207300 chr2B 96.040 101 3 1 2803 2903 25123227 25123326 7.580000e-36 163
10 TraesCS3B01G207300 chr5B 88.850 1435 107 26 2902 4299 676011929 676013347 0.000000e+00 1714
11 TraesCS3B01G207300 chr5B 95.146 103 3 2 2802 2903 543932625 543932726 2.730000e-35 161
12 TraesCS3B01G207300 chr5B 89.691 97 6 2 2260 2356 249581806 249581898 4.630000e-23 121
13 TraesCS3B01G207300 chr5B 89.691 97 5 2 2259 2355 184285262 184285353 1.660000e-22 119
14 TraesCS3B01G207300 chr6B 88.128 1432 127 23 2902 4296 49352569 49351144 0.000000e+00 1663
15 TraesCS3B01G207300 chr6B 89.583 96 6 1 2263 2358 458503484 458503575 1.660000e-22 119
16 TraesCS3B01G207300 chr4B 88.009 1401 142 12 2902 4289 536815547 536814160 0.000000e+00 1633
17 TraesCS3B01G207300 chr4B 87.420 1415 120 30 2903 4282 291769632 291768241 0.000000e+00 1574
18 TraesCS3B01G207300 chr4B 93.458 107 5 2 2797 2903 440796928 440797032 3.530000e-34 158
19 TraesCS3B01G207300 chr4B 93.458 107 5 2 2797 2903 556233806 556233910 3.530000e-34 158
20 TraesCS3B01G207300 chr4B 93.458 107 5 2 2804 2908 658978360 658978254 3.530000e-34 158
21 TraesCS3B01G207300 chrUn 83.825 1391 141 38 2902 4289 102817800 102816491 0.000000e+00 1245
22 TraesCS3B01G207300 chrUn 89.362 94 6 1 2263 2356 101630800 101630889 2.150000e-21 115
23 TraesCS3B01G207300 chr7A 85.134 1157 95 30 3166 4286 270757183 270758298 0.000000e+00 1112
24 TraesCS3B01G207300 chr7A 88.903 793 77 6 2902 3686 39133579 39134368 0.000000e+00 966
25 TraesCS3B01G207300 chr6A 86.634 1010 111 7 3283 4289 34686769 34685781 0.000000e+00 1096
26 TraesCS3B01G207300 chr2D 90.734 777 62 6 2902 3670 559241751 559240977 0.000000e+00 1027
27 TraesCS3B01G207300 chr2D 88.264 622 65 4 3679 4296 559235347 559234730 0.000000e+00 737
28 TraesCS3B01G207300 chr2D 95.098 102 4 1 2802 2903 107204076 107204176 9.800000e-35 159
29 TraesCS3B01G207300 chr7D 90.400 125 7 4 2784 2903 407716506 407716630 9.800000e-35 159
30 TraesCS3B01G207300 chr7D 90.426 94 5 1 2263 2356 167548504 167548415 4.630000e-23 121
31 TraesCS3B01G207300 chr7D 87.879 99 8 2 2263 2361 4511732 4511638 7.740000e-21 113
32 TraesCS3B01G207300 chr1A 92.661 109 8 0 2797 2905 12578151 12578043 3.530000e-34 158
33 TraesCS3B01G207300 chr4A 92.593 108 8 0 2796 2903 650040871 650040978 1.270000e-33 156
34 TraesCS3B01G207300 chr4A 88.660 97 7 1 2263 2359 603447587 603447679 2.150000e-21 115
35 TraesCS3B01G207300 chr6D 89.109 101 6 4 2255 2354 462439590 462439494 4.630000e-23 121
36 TraesCS3B01G207300 chr2A 90.426 94 5 1 2263 2356 483604655 483604566 4.630000e-23 121
37 TraesCS3B01G207300 chr2A 86.667 105 9 2 2256 2359 203256259 203256159 2.780000e-20 111
38 TraesCS3B01G207300 chr4D 90.323 93 5 1 2263 2355 307492998 307493086 1.660000e-22 119
39 TraesCS3B01G207300 chr4D 87.850 107 5 5 2260 2365 320593823 320593724 1.660000e-22 119
40 TraesCS3B01G207300 chr1D 87.500 104 7 2 2259 2362 462985058 462985155 2.150000e-21 115
41 TraesCS3B01G207300 chr1D 87.879 99 8 2 2261 2359 340456246 340456152 7.740000e-21 113


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 TraesCS3B01G207300 chr3B 242869195 242878625 9430 True 17416.000000 17416 100.000000 1 9431 1 chr3B.!!$R1 9430
1 TraesCS3B01G207300 chr3B 771530858 771532257 1399 True 1594.000000 1594 87.553000 2902 4289 1 chr3B.!!$R2 1387
2 TraesCS3B01G207300 chr3D 167764724 167772505 7781 True 4358.666667 8469 97.121333 1 9431 3 chr3D.!!$R1 9430
3 TraesCS3B01G207300 chr3A 201499055 201506829 7774 False 4216.333333 8323 96.101667 1 9431 3 chr3A.!!$F1 9430
4 TraesCS3B01G207300 chr2B 211866184 211867574 1390 False 1821.000000 1821 90.334000 2902 4298 1 chr2B.!!$F2 1396
5 TraesCS3B01G207300 chr5B 676011929 676013347 1418 False 1714.000000 1714 88.850000 2902 4299 1 chr5B.!!$F4 1397
6 TraesCS3B01G207300 chr6B 49351144 49352569 1425 True 1663.000000 1663 88.128000 2902 4296 1 chr6B.!!$R1 1394
7 TraesCS3B01G207300 chr4B 536814160 536815547 1387 True 1633.000000 1633 88.009000 2902 4289 1 chr4B.!!$R2 1387
8 TraesCS3B01G207300 chr4B 291768241 291769632 1391 True 1574.000000 1574 87.420000 2903 4282 1 chr4B.!!$R1 1379
9 TraesCS3B01G207300 chrUn 102816491 102817800 1309 True 1245.000000 1245 83.825000 2902 4289 1 chrUn.!!$R1 1387
10 TraesCS3B01G207300 chr7A 270757183 270758298 1115 False 1112.000000 1112 85.134000 3166 4286 1 chr7A.!!$F2 1120
11 TraesCS3B01G207300 chr7A 39133579 39134368 789 False 966.000000 966 88.903000 2902 3686 1 chr7A.!!$F1 784
12 TraesCS3B01G207300 chr6A 34685781 34686769 988 True 1096.000000 1096 86.634000 3283 4289 1 chr6A.!!$R1 1006
13 TraesCS3B01G207300 chr2D 559240977 559241751 774 True 1027.000000 1027 90.734000 2902 3670 1 chr2D.!!$R2 768
14 TraesCS3B01G207300 chr2D 559234730 559235347 617 True 737.000000 737 88.264000 3679 4296 1 chr2D.!!$R1 617

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
917 931 0.033601 ATTCCAAATGGCAGGCGGTA 60.034 50.000 0.00 0.00 34.44 4.02 F
2491 2512 0.751643 GTCAGTTGGGTGCCTGTTGT 60.752 55.000 0.00 0.00 0.00 3.32 F
3116 3139 0.681733 AAAGACAAGGCTGAGCTCGA 59.318 50.000 9.64 0.00 0.00 4.04 F
4312 4447 1.227674 GGGACCGCTTAGCCATCTG 60.228 63.158 0.00 0.00 0.00 2.90 F
4616 4751 4.080975 GCCATTGGGGATCAAAATGAAAGA 60.081 41.667 4.53 0.00 39.05 2.52 F
5616 5757 0.683973 AGAGCCTCACTGTGTTCTGG 59.316 55.000 7.79 7.45 0.00 3.86 F
6631 6773 2.490115 CCGAGCATACTAGATGGGACTC 59.510 54.545 0.00 0.00 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2892 2913 1.269621 CGTGGCTTTATACTCCCTCCG 60.270 57.143 0.00 0.00 0.00 4.63 R
4026 4158 2.511600 GCTGGAACCGACCGATGG 60.512 66.667 0.00 0.00 0.00 3.51 R
4407 4542 4.273005 ACAAAACAAGTAAGCACTCACG 57.727 40.909 0.00 0.00 32.29 4.35 R
5177 5316 0.947244 CAGGTTAGCAATCCATCCGC 59.053 55.000 0.00 0.00 0.00 5.54 R
6372 6514 2.005370 ACCCACACGGAACTTCTCTA 57.995 50.000 0.00 0.00 34.64 2.43 R
6922 7064 2.222027 GTCCTGTGCTTGCTTACAACT 58.778 47.619 0.00 0.00 0.00 3.16 R
8511 8664 1.073025 AATTCACCTGCCGCAGTGA 59.927 52.632 18.98 17.68 0.00 3.41 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
33 34 3.250762 TCAGTTTTGACTGGATTTGAGCG 59.749 43.478 6.70 0.00 38.23 5.03
77 78 5.890985 AGGTATGGTGCATATGCTTTGTTTA 59.109 36.000 27.13 9.71 42.66 2.01
92 93 3.207265 TGTTTAGCCAGTTGAAGCAGA 57.793 42.857 0.00 0.00 0.00 4.26
731 735 1.332065 TCGCATGCTTCTCGAGTCTAG 59.668 52.381 17.13 9.62 0.00 2.43
815 829 2.139323 TACATGTGGTAGACTCGGCT 57.861 50.000 9.11 0.00 0.00 5.52
838 852 3.558418 TGCTGAAACCGTCTAGTTTGAAC 59.442 43.478 0.00 0.00 40.01 3.18
858 872 3.544684 ACTGCATCTGACTTTGACACAA 58.455 40.909 0.00 0.00 0.00 3.33
882 896 7.787725 ACGTCACTCTGTTTTCTTTTCTATT 57.212 32.000 0.00 0.00 0.00 1.73
917 931 0.033601 ATTCCAAATGGCAGGCGGTA 60.034 50.000 0.00 0.00 34.44 4.02
969 983 3.015327 GGATAGCCATCATCAATCCTGC 58.985 50.000 0.00 0.00 34.51 4.85
1225 1239 3.375299 AGTTGCGAAGATTCAAGGTATGC 59.625 43.478 0.00 0.00 0.00 3.14
1240 1254 4.508662 AGGTATGCACTTCTAGTTCTTGC 58.491 43.478 0.00 0.00 0.00 4.01
1259 1273 0.895559 CCCTCAAAACCTCCAGGCAC 60.896 60.000 0.00 0.00 39.32 5.01
1261 1275 1.479389 CCTCAAAACCTCCAGGCACTT 60.479 52.381 0.00 0.00 34.60 3.16
1277 1291 6.375455 CCAGGCACTTCTGAAACTATTATTGT 59.625 38.462 0.00 0.00 34.60 2.71
1279 1293 8.299570 CAGGCACTTCTGAAACTATTATTGTTT 58.700 33.333 4.60 4.60 37.09 2.83
1397 1411 6.317893 GGACTTGAAAGGTAGAACTTTTGTCA 59.682 38.462 16.31 1.89 40.55 3.58
1399 1413 7.762382 ACTTGAAAGGTAGAACTTTTGTCAAG 58.238 34.615 14.49 14.49 42.69 3.02
1431 1445 6.553100 ACTCCCAGGAATTTAATTGTGTTTGA 59.447 34.615 0.00 0.00 0.00 2.69
1433 1447 7.610865 TCCCAGGAATTTAATTGTGTTTGATC 58.389 34.615 0.00 0.00 0.00 2.92
2268 2289 9.780186 AAACAGCTAAAGATACATATTACTCCC 57.220 33.333 0.00 0.00 0.00 4.30
2269 2290 8.728596 ACAGCTAAAGATACATATTACTCCCT 57.271 34.615 0.00 0.00 0.00 4.20
2270 2291 8.808092 ACAGCTAAAGATACATATTACTCCCTC 58.192 37.037 0.00 0.00 0.00 4.30
2271 2292 8.254508 CAGCTAAAGATACATATTACTCCCTCC 58.745 40.741 0.00 0.00 0.00 4.30
2272 2293 7.122948 AGCTAAAGATACATATTACTCCCTCCG 59.877 40.741 0.00 0.00 0.00 4.63
2273 2294 7.093858 GCTAAAGATACATATTACTCCCTCCGT 60.094 40.741 0.00 0.00 0.00 4.69
2274 2295 9.458727 CTAAAGATACATATTACTCCCTCCGTA 57.541 37.037 0.00 0.00 0.00 4.02
2275 2296 8.716674 AAAGATACATATTACTCCCTCCGTAA 57.283 34.615 0.00 0.00 0.00 3.18
2276 2297 8.716674 AAGATACATATTACTCCCTCCGTAAA 57.283 34.615 0.00 0.00 31.36 2.01
2277 2298 8.350852 AGATACATATTACTCCCTCCGTAAAG 57.649 38.462 0.00 0.00 31.36 1.85
2278 2299 8.168725 AGATACATATTACTCCCTCCGTAAAGA 58.831 37.037 0.00 0.00 31.36 2.52
2279 2300 8.716674 ATACATATTACTCCCTCCGTAAAGAA 57.283 34.615 0.00 0.00 31.36 2.52
2280 2301 7.427989 ACATATTACTCCCTCCGTAAAGAAA 57.572 36.000 0.00 0.00 31.36 2.52
2281 2302 8.030913 ACATATTACTCCCTCCGTAAAGAAAT 57.969 34.615 0.00 0.00 31.36 2.17
2282 2303 9.151177 ACATATTACTCCCTCCGTAAAGAAATA 57.849 33.333 0.00 0.00 31.36 1.40
2283 2304 9.991906 CATATTACTCCCTCCGTAAAGAAATAA 57.008 33.333 0.00 0.00 31.36 1.40
2295 2316 9.754382 TCCGTAAAGAAATAAATATAAGAGCGT 57.246 29.630 0.00 0.00 0.00 5.07
2346 2367 9.566432 AATGCTCTTATATTTCTTTACAGAGGG 57.434 33.333 0.00 0.00 0.00 4.30
2347 2368 8.319057 TGCTCTTATATTTCTTTACAGAGGGA 57.681 34.615 0.00 0.00 0.00 4.20
2348 2369 8.768397 TGCTCTTATATTTCTTTACAGAGGGAA 58.232 33.333 0.00 0.00 0.00 3.97
2491 2512 0.751643 GTCAGTTGGGTGCCTGTTGT 60.752 55.000 0.00 0.00 0.00 3.32
2610 2631 7.343357 CCATTTCTGGATAAGTTGTACCCTTA 58.657 38.462 5.00 5.00 46.37 2.69
2659 2680 6.882610 TGCTCTGTTGAGTTGTCAATATTT 57.117 33.333 0.00 0.00 44.58 1.40
2742 2763 4.156556 GCACTATGCTTTCCAGATCAAACA 59.843 41.667 0.00 0.00 40.96 2.83
2743 2764 5.675575 GCACTATGCTTTCCAGATCAAACAG 60.676 44.000 0.00 0.00 40.96 3.16
2775 2796 6.245408 TGTGTAGGTTCTTGGCTCAAATATT 58.755 36.000 0.00 0.00 0.00 1.28
2776 2797 7.398829 TGTGTAGGTTCTTGGCTCAAATATTA 58.601 34.615 0.00 0.00 0.00 0.98
2777 2798 7.335924 TGTGTAGGTTCTTGGCTCAAATATTAC 59.664 37.037 0.00 0.00 0.00 1.89
2778 2799 6.826741 TGTAGGTTCTTGGCTCAAATATTACC 59.173 38.462 0.00 0.00 0.00 2.85
2779 2800 4.881850 AGGTTCTTGGCTCAAATATTACCG 59.118 41.667 0.00 0.00 0.00 4.02
2780 2801 4.879545 GGTTCTTGGCTCAAATATTACCGA 59.120 41.667 0.00 0.00 0.00 4.69
2781 2802 5.355910 GGTTCTTGGCTCAAATATTACCGAA 59.644 40.000 0.00 0.00 0.00 4.30
2782 2803 6.127842 GGTTCTTGGCTCAAATATTACCGAAA 60.128 38.462 0.00 0.00 0.00 3.46
2783 2804 6.677781 TCTTGGCTCAAATATTACCGAAAG 57.322 37.500 0.00 0.00 0.00 2.62
2784 2805 6.411376 TCTTGGCTCAAATATTACCGAAAGA 58.589 36.000 0.00 0.00 0.00 2.52
2785 2806 6.538742 TCTTGGCTCAAATATTACCGAAAGAG 59.461 38.462 0.00 0.00 0.00 2.85
2786 2807 5.123227 TGGCTCAAATATTACCGAAAGAGG 58.877 41.667 0.00 0.00 37.30 3.69
2787 2808 4.515567 GGCTCAAATATTACCGAAAGAGGG 59.484 45.833 0.00 0.00 35.02 4.30
2788 2809 5.123936 GCTCAAATATTACCGAAAGAGGGT 58.876 41.667 0.00 0.00 41.62 4.34
2789 2810 5.589050 GCTCAAATATTACCGAAAGAGGGTT 59.411 40.000 0.00 0.00 38.99 4.11
2790 2811 6.095021 GCTCAAATATTACCGAAAGAGGGTTT 59.905 38.462 0.00 0.00 38.99 3.27
2791 2812 7.619964 TCAAATATTACCGAAAGAGGGTTTC 57.380 36.000 0.00 0.00 38.99 2.78
2792 2813 6.600427 TCAAATATTACCGAAAGAGGGTTTCC 59.400 38.462 0.00 0.00 38.99 3.13
2793 2814 2.865119 TTACCGAAAGAGGGTTTCCC 57.135 50.000 0.00 0.00 45.90 3.97
2811 2832 7.456725 GGTTTCCCCCTACTTTATATTACTCC 58.543 42.308 0.00 0.00 0.00 3.85
2812 2833 7.456725 GTTTCCCCCTACTTTATATTACTCCC 58.543 42.308 0.00 0.00 0.00 4.30
2813 2834 6.572198 TCCCCCTACTTTATATTACTCCCT 57.428 41.667 0.00 0.00 0.00 4.20
2814 2835 6.568795 TCCCCCTACTTTATATTACTCCCTC 58.431 44.000 0.00 0.00 0.00 4.30
2815 2836 6.106645 TCCCCCTACTTTATATTACTCCCTCA 59.893 42.308 0.00 0.00 0.00 3.86
2816 2837 6.440965 CCCCCTACTTTATATTACTCCCTCAG 59.559 46.154 0.00 0.00 0.00 3.35
2817 2838 7.017531 CCCCTACTTTATATTACTCCCTCAGT 58.982 42.308 0.00 0.00 39.41 3.41
2818 2839 7.513091 CCCCTACTTTATATTACTCCCTCAGTT 59.487 40.741 0.00 0.00 36.43 3.16
2819 2840 8.586744 CCCTACTTTATATTACTCCCTCAGTTC 58.413 40.741 0.00 0.00 36.43 3.01
2820 2841 8.586744 CCTACTTTATATTACTCCCTCAGTTCC 58.413 40.741 0.00 0.00 36.43 3.62
2821 2842 7.989947 ACTTTATATTACTCCCTCAGTTCCA 57.010 36.000 0.00 0.00 36.43 3.53
2822 2843 8.388656 ACTTTATATTACTCCCTCAGTTCCAA 57.611 34.615 0.00 0.00 36.43 3.53
2823 2844 8.832735 ACTTTATATTACTCCCTCAGTTCCAAA 58.167 33.333 0.00 0.00 36.43 3.28
2824 2845 9.681062 CTTTATATTACTCCCTCAGTTCCAAAA 57.319 33.333 0.00 0.00 36.43 2.44
2828 2849 6.945636 TTACTCCCTCAGTTCCAAAATAGA 57.054 37.500 0.00 0.00 36.43 1.98
2829 2850 7.510675 TTACTCCCTCAGTTCCAAAATAGAT 57.489 36.000 0.00 0.00 36.43 1.98
2830 2851 5.749462 ACTCCCTCAGTTCCAAAATAGATG 58.251 41.667 0.00 0.00 26.56 2.90
2831 2852 5.488919 ACTCCCTCAGTTCCAAAATAGATGA 59.511 40.000 0.00 0.00 26.56 2.92
2832 2853 5.745227 TCCCTCAGTTCCAAAATAGATGAC 58.255 41.667 0.00 0.00 0.00 3.06
2833 2854 5.488919 TCCCTCAGTTCCAAAATAGATGACT 59.511 40.000 0.00 0.00 0.00 3.41
2834 2855 5.819901 CCCTCAGTTCCAAAATAGATGACTC 59.180 44.000 0.00 0.00 0.00 3.36
2835 2856 6.409704 CCTCAGTTCCAAAATAGATGACTCA 58.590 40.000 0.00 0.00 0.00 3.41
2836 2857 6.881065 CCTCAGTTCCAAAATAGATGACTCAA 59.119 38.462 0.00 0.00 0.00 3.02
2837 2858 7.148340 CCTCAGTTCCAAAATAGATGACTCAAC 60.148 40.741 0.00 0.00 0.00 3.18
2838 2859 7.453393 TCAGTTCCAAAATAGATGACTCAACT 58.547 34.615 0.00 0.00 0.00 3.16
2839 2860 7.939039 TCAGTTCCAAAATAGATGACTCAACTT 59.061 33.333 0.00 0.00 0.00 2.66
2840 2861 8.571336 CAGTTCCAAAATAGATGACTCAACTTT 58.429 33.333 0.00 0.00 0.00 2.66
2841 2862 8.571336 AGTTCCAAAATAGATGACTCAACTTTG 58.429 33.333 0.00 0.00 0.00 2.77
2842 2863 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2843 2864 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2844 2865 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2845 2866 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2876 2897 8.617290 AAGTACAAAGTTAGTACAGAATTGGG 57.383 34.615 6.30 0.00 43.24 4.12
2877 2898 7.742767 AGTACAAAGTTAGTACAGAATTGGGT 58.257 34.615 6.30 0.00 43.24 4.51
2878 2899 7.876582 AGTACAAAGTTAGTACAGAATTGGGTC 59.123 37.037 6.30 0.00 43.24 4.46
2879 2900 6.597562 ACAAAGTTAGTACAGAATTGGGTCA 58.402 36.000 0.00 0.00 0.00 4.02
2880 2901 7.231467 ACAAAGTTAGTACAGAATTGGGTCAT 58.769 34.615 0.00 0.00 0.00 3.06
2881 2902 7.390718 ACAAAGTTAGTACAGAATTGGGTCATC 59.609 37.037 0.00 0.00 0.00 2.92
2882 2903 6.875972 AGTTAGTACAGAATTGGGTCATCT 57.124 37.500 0.00 0.00 0.00 2.90
2883 2904 7.973048 AGTTAGTACAGAATTGGGTCATCTA 57.027 36.000 0.00 0.00 0.00 1.98
2884 2905 8.554490 AGTTAGTACAGAATTGGGTCATCTAT 57.446 34.615 0.00 0.00 0.00 1.98
2885 2906 8.993424 AGTTAGTACAGAATTGGGTCATCTATT 58.007 33.333 0.00 0.00 0.00 1.73
2886 2907 9.614792 GTTAGTACAGAATTGGGTCATCTATTT 57.385 33.333 0.00 0.00 0.00 1.40
2888 2909 8.511604 AGTACAGAATTGGGTCATCTATTTTG 57.488 34.615 0.00 0.00 0.00 2.44
2889 2910 6.780457 ACAGAATTGGGTCATCTATTTTGG 57.220 37.500 0.00 0.00 0.00 3.28
2890 2911 6.493166 ACAGAATTGGGTCATCTATTTTGGA 58.507 36.000 0.00 0.00 0.00 3.53
2891 2912 6.953520 ACAGAATTGGGTCATCTATTTTGGAA 59.046 34.615 0.00 0.00 0.00 3.53
2892 2913 7.093771 ACAGAATTGGGTCATCTATTTTGGAAC 60.094 37.037 0.00 0.00 0.00 3.62
2893 2914 5.835113 ATTGGGTCATCTATTTTGGAACG 57.165 39.130 0.00 0.00 0.00 3.95
2894 2915 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
2895 2916 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
2896 2917 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
2897 2918 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
2898 2919 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2899 2920 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2900 2921 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2909 2930 2.224233 GGAACGGAGGGAGTATAAAGCC 60.224 54.545 0.00 0.00 0.00 4.35
2988 3009 1.306654 ACCCAAGGCCGGATACAGA 60.307 57.895 5.05 0.00 0.00 3.41
3116 3139 0.681733 AAAGACAAGGCTGAGCTCGA 59.318 50.000 9.64 0.00 0.00 4.04
3117 3140 0.681733 AAGACAAGGCTGAGCTCGAA 59.318 50.000 9.64 0.00 0.00 3.71
3210 3233 1.396653 GATCATGGCTTTCACCTGGG 58.603 55.000 0.00 0.00 0.00 4.45
3521 3553 1.843368 ACCGACCGATGAGAGGTAAA 58.157 50.000 0.00 0.00 43.01 2.01
3602 3635 1.615424 GGTAGGGGAGAGGGTTGCA 60.615 63.158 0.00 0.00 0.00 4.08
3693 3774 3.936203 GGAGCCACCACACCACGA 61.936 66.667 0.00 0.00 38.79 4.35
4038 4170 4.752879 CGCCACCATCGGTCGGTT 62.753 66.667 0.00 0.00 33.25 4.44
4252 4385 2.368011 GCGGCTAGGGTTTCCTCCT 61.368 63.158 0.00 0.00 43.66 3.69
4310 4445 2.111251 GGGGACCGCTTAGCCATC 59.889 66.667 0.24 0.00 40.86 3.51
4311 4446 2.444256 GGGGACCGCTTAGCCATCT 61.444 63.158 0.24 0.00 40.86 2.90
4312 4447 1.227674 GGGACCGCTTAGCCATCTG 60.228 63.158 0.00 0.00 0.00 2.90
4313 4448 1.227674 GGACCGCTTAGCCATCTGG 60.228 63.158 0.00 0.00 38.53 3.86
4474 4609 5.590259 GGTGTAACAGAGCCAACATATGAAT 59.410 40.000 10.38 0.00 39.98 2.57
4616 4751 4.080975 GCCATTGGGGATCAAAATGAAAGA 60.081 41.667 4.53 0.00 39.05 2.52
4617 4752 5.397109 GCCATTGGGGATCAAAATGAAAGAT 60.397 40.000 4.53 0.00 39.05 2.40
4635 4770 9.620259 ATGAAAGATAGTCATTTCCTAGGAAAC 57.380 33.333 34.06 23.98 45.34 2.78
4721 4856 5.671493 AGTTCCTATGTTTTCCGATAGTGG 58.329 41.667 0.00 0.00 0.00 4.00
4983 5118 9.395707 GTAGATCTCACTGGTAACGTATTTATG 57.604 37.037 0.00 0.00 42.51 1.90
4986 5121 9.178427 GATCTCACTGGTAACGTATTTATGTAC 57.822 37.037 0.00 0.00 42.51 2.90
5116 5255 6.208204 CCTGAATCAGAAGTGGAGAACAAATT 59.792 38.462 12.53 0.00 32.44 1.82
5157 5296 6.545504 TGCTTGTGTAAAGAGAAATGACTC 57.454 37.500 0.00 0.00 37.19 3.36
5177 5316 6.936900 TGACTCATTTTAGAAAGAGAACAGGG 59.063 38.462 5.36 0.00 34.92 4.45
5208 5347 7.445402 TGGATTGCTAACCTGAAGCTTATATTC 59.555 37.037 0.00 0.00 40.73 1.75
5274 5413 2.235650 CTCCTTTGATGCACCTGAGAGA 59.764 50.000 0.00 0.00 0.00 3.10
5616 5757 0.683973 AGAGCCTCACTGTGTTCTGG 59.316 55.000 7.79 7.45 0.00 3.86
5971 6113 6.595326 TCGATTGATAAAATGACAACTCAGCT 59.405 34.615 0.00 0.00 0.00 4.24
5980 6122 5.866159 ATGACAACTCAGCTGATATGAGA 57.134 39.130 26.69 16.32 45.80 3.27
6119 6261 5.934625 ACTTGATAACACTCTTGCTACAAGG 59.065 40.000 7.44 1.77 37.22 3.61
6315 6457 4.507388 ACAAATTTTGCAACTTCACATCCG 59.493 37.500 9.04 0.00 0.00 4.18
6372 6514 9.956640 AAGAATGTAAGAAGTCTGAAGAATCAT 57.043 29.630 0.00 0.00 34.37 2.45
6385 6527 6.378564 TCTGAAGAATCATAGAGAAGTTCCGT 59.621 38.462 0.00 0.00 34.37 4.69
6631 6773 2.490115 CCGAGCATACTAGATGGGACTC 59.510 54.545 0.00 0.00 0.00 3.36
6827 6969 5.359576 ACCAACAAATACTTCAAAGTGCTGA 59.640 36.000 5.66 0.00 40.07 4.26
6922 7064 8.802267 CACCAATTAAGATTGAAGGGACTAAAA 58.198 33.333 0.92 0.00 44.37 1.52
7037 7179 5.122519 TCATTTCGCCACAGCAGAATTATA 58.877 37.500 0.00 0.00 39.83 0.98
7065 7207 4.259356 CTCCATCAAGAGAACATTGCAGA 58.741 43.478 0.00 0.00 35.82 4.26
7297 7439 4.556699 GCGACAAAAGGGCATTATACATCC 60.557 45.833 0.00 0.00 0.00 3.51
7437 7582 6.128035 ACAAAAGTGGGCAAAAAGATCAAAAC 60.128 34.615 0.00 0.00 0.00 2.43
7451 7596 8.697507 AAAGATCAAAACTCCAGTCACTTAAT 57.302 30.769 0.00 0.00 0.00 1.40
7487 7632 6.791775 GCATTAACATAAACAAACTTTGCTGC 59.208 34.615 1.14 0.00 0.00 5.25
7488 7633 6.503616 TTAACATAAACAAACTTTGCTGCG 57.496 33.333 1.14 0.00 0.00 5.18
7915 8060 7.933577 TGGAGCTTGAGTTATGGACAATAATAG 59.066 37.037 0.00 0.00 33.32 1.73
8495 8648 9.930693 CTTTTGAGAGTACACTACTTTAGGAAT 57.069 33.333 0.00 0.00 39.59 3.01
8511 8664 1.883926 GGAATTGTACTGCCGGTTTGT 59.116 47.619 1.90 2.06 0.00 2.83
8514 8667 1.301423 TTGTACTGCCGGTTTGTCAC 58.699 50.000 1.90 0.00 0.00 3.67
8515 8668 0.466543 TGTACTGCCGGTTTGTCACT 59.533 50.000 1.90 0.00 0.00 3.41
8735 8888 7.115095 GTGGTCGTATTTAGCTAGCTGATTTAG 59.885 40.741 27.68 13.99 0.00 1.85
8758 8911 6.324819 AGTTACATGTCAAAGTAATGCATGC 58.675 36.000 11.82 11.82 37.86 4.06
8784 8937 4.287766 AGGCCAGAACAGTAACTTAAGG 57.712 45.455 5.01 0.00 0.00 2.69
8844 8997 6.438763 CAAGGGAAACAACTGATCACTTAAC 58.561 40.000 0.00 0.00 34.69 2.01
8861 9014 0.842467 AACAGCAGGTAAGGGGCTCT 60.842 55.000 0.00 0.00 35.27 4.09
8878 9031 6.615726 AGGGGCTCTTGTTAGTTAATAGATGA 59.384 38.462 0.00 0.00 0.00 2.92
8990 9143 5.150715 ACACCATCAAGGATCAGCTATCTA 58.849 41.667 0.00 0.00 41.22 1.98
8996 9149 8.512956 CCATCAAGGATCAGCTATCTAAATTTG 58.487 37.037 0.00 0.00 41.22 2.32
9014 9167 1.121378 TGGACCTTCCGTACACACAA 58.879 50.000 0.00 0.00 40.17 3.33
9037 9190 7.435488 ACAAACCGATATACTCTTCGAAGAATG 59.565 37.037 26.87 18.92 45.90 2.67
9038 9191 5.462405 ACCGATATACTCTTCGAAGAATGC 58.538 41.667 26.87 14.19 45.90 3.56
9039 9192 5.241949 ACCGATATACTCTTCGAAGAATGCT 59.758 40.000 26.87 12.86 45.90 3.79
9040 9193 5.797934 CCGATATACTCTTCGAAGAATGCTC 59.202 44.000 26.87 17.84 45.90 4.26
9041 9194 6.348950 CCGATATACTCTTCGAAGAATGCTCT 60.349 42.308 26.87 11.50 45.90 4.09
9042 9195 7.081349 CGATATACTCTTCGAAGAATGCTCTT 58.919 38.462 26.87 10.17 45.90 2.85
9043 9196 8.231161 CGATATACTCTTCGAAGAATGCTCTTA 58.769 37.037 26.87 12.75 45.90 2.10
9044 9197 9.337091 GATATACTCTTCGAAGAATGCTCTTAC 57.663 37.037 26.87 10.54 45.90 2.34
9045 9198 5.652994 ACTCTTCGAAGAATGCTCTTACT 57.347 39.130 26.87 0.00 45.90 2.24
9046 9199 6.031751 ACTCTTCGAAGAATGCTCTTACTT 57.968 37.500 26.87 0.00 45.90 2.24
9047 9200 7.159322 ACTCTTCGAAGAATGCTCTTACTTA 57.841 36.000 26.87 1.57 45.90 2.24
9048 9201 7.603651 ACTCTTCGAAGAATGCTCTTACTTAA 58.396 34.615 26.87 0.93 45.90 1.85
9049 9202 8.254508 ACTCTTCGAAGAATGCTCTTACTTAAT 58.745 33.333 26.87 0.00 45.90 1.40
9058 9224 8.260818 AGAATGCTCTTACTTAATGCTCTTACA 58.739 33.333 0.00 0.00 0.00 2.41
9176 9342 6.817184 ACGTATCTTATGTAAGCAAGGATGT 58.183 36.000 0.00 0.00 33.40 3.06
9281 9447 3.074412 TCTCATTGCCTTCCGAAGTTTC 58.926 45.455 7.37 0.00 0.00 2.78
9305 9471 1.203364 ACTTCATCCCACCTCTCCTGT 60.203 52.381 0.00 0.00 0.00 4.00
9344 9510 6.679542 TGACAGGAGAATATAGTTCCCACTA 58.320 40.000 0.00 0.00 39.94 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.186200 GGGATCTTTTGGTCAAGGGC 58.814 55.000 0.00 0.00 0.00 5.19
77 78 0.892814 GGCTTCTGCTTCAACTGGCT 60.893 55.000 0.00 0.00 39.59 4.75
92 93 4.447762 GGAGATAACATAACCATGGGGCTT 60.448 45.833 18.09 3.80 37.90 4.35
142 143 4.410228 TCCATAGAAGTTCCTGCAGCTAAT 59.590 41.667 8.66 0.00 0.00 1.73
731 735 3.976169 TGACCAAGTATTTTGTTGCAGC 58.024 40.909 0.00 0.00 0.00 5.25
815 829 3.799366 TCAAACTAGACGGTTTCAGCAA 58.201 40.909 0.00 0.00 37.32 3.91
838 852 3.605461 CGTTGTGTCAAAGTCAGATGCAG 60.605 47.826 0.00 0.00 0.00 4.41
858 872 7.787725 AATAGAAAAGAAAACAGAGTGACGT 57.212 32.000 0.00 0.00 0.00 4.34
917 931 4.021719 CCTGTTTCATTCTTTGCTGGTGAT 60.022 41.667 0.00 0.00 0.00 3.06
969 983 4.333926 GCCTAGCAAGTTATCACCAAGAAG 59.666 45.833 0.00 0.00 0.00 2.85
1225 1239 3.685139 TGAGGGCAAGAACTAGAAGTG 57.315 47.619 0.00 0.00 0.00 3.16
1240 1254 0.895559 GTGCCTGGAGGTTTTGAGGG 60.896 60.000 0.00 0.00 37.57 4.30
1399 1413 9.239551 ACAATTAAATTCCTGGGAGTAGTAAAC 57.760 33.333 0.00 0.00 0.00 2.01
1440 1454 6.883756 AGCAAACCCATTTTTCTTTCTTGAAA 59.116 30.769 0.00 0.00 34.55 2.69
1684 1705 8.469309 TCAAACAATCAAGAAAGGAAGATTCT 57.531 30.769 0.00 0.00 38.75 2.40
1687 1708 9.702494 GAATTCAAACAATCAAGAAAGGAAGAT 57.298 29.630 0.00 0.00 0.00 2.40
1688 1709 8.694540 TGAATTCAAACAATCAAGAAAGGAAGA 58.305 29.630 5.45 0.00 0.00 2.87
1735 1756 6.962182 TCAGAAAATACATCACCTGGAGAAT 58.038 36.000 0.00 0.00 0.00 2.40
2242 2263 9.780186 GGGAGTAATATGTATCTTTAGCTGTTT 57.220 33.333 0.00 0.00 0.00 2.83
2245 2266 8.254508 GGAGGGAGTAATATGTATCTTTAGCTG 58.745 40.741 0.00 0.00 0.00 4.24
2269 2290 9.754382 ACGCTCTTATATTTATTTCTTTACGGA 57.246 29.630 0.00 0.00 0.00 4.69
2320 2341 9.566432 CCCTCTGTAAAGAAATATAAGAGCATT 57.434 33.333 0.00 0.00 0.00 3.56
2321 2342 8.938883 TCCCTCTGTAAAGAAATATAAGAGCAT 58.061 33.333 0.00 0.00 0.00 3.79
2322 2343 8.319057 TCCCTCTGTAAAGAAATATAAGAGCA 57.681 34.615 0.00 0.00 0.00 4.26
2323 2344 9.785982 ATTCCCTCTGTAAAGAAATATAAGAGC 57.214 33.333 0.00 0.00 0.00 4.09
2426 2447 4.377839 ACTACATCACAGTCAGGATTCG 57.622 45.455 0.00 0.00 0.00 3.34
2536 2557 7.556275 GTCCAACACCTCCTTAAAATATCATGA 59.444 37.037 0.00 0.00 0.00 3.07
2537 2558 7.339212 TGTCCAACACCTCCTTAAAATATCATG 59.661 37.037 0.00 0.00 0.00 3.07
2538 2559 7.339466 GTGTCCAACACCTCCTTAAAATATCAT 59.661 37.037 0.00 0.00 43.05 2.45
2610 2631 7.220030 AGCTCTCGTGTCATTATATTGGAAAT 58.780 34.615 0.00 0.00 0.00 2.17
2659 2680 4.712476 ACATGCTACCCAAAATTTTGCAA 58.288 34.783 22.90 10.62 36.86 4.08
2787 2808 7.294245 AGGGAGTAATATAAAGTAGGGGGAAAC 59.706 40.741 0.00 0.00 0.00 2.78
2788 2809 7.384037 AGGGAGTAATATAAAGTAGGGGGAAA 58.616 38.462 0.00 0.00 0.00 3.13
2789 2810 6.953479 AGGGAGTAATATAAAGTAGGGGGAA 58.047 40.000 0.00 0.00 0.00 3.97
2790 2811 6.106645 TGAGGGAGTAATATAAAGTAGGGGGA 59.893 42.308 0.00 0.00 0.00 4.81
2791 2812 6.328592 TGAGGGAGTAATATAAAGTAGGGGG 58.671 44.000 0.00 0.00 0.00 5.40
2792 2813 7.017531 ACTGAGGGAGTAATATAAAGTAGGGG 58.982 42.308 0.00 0.00 30.86 4.79
2793 2814 8.493787 AACTGAGGGAGTAATATAAAGTAGGG 57.506 38.462 0.00 0.00 33.09 3.53
2794 2815 8.586744 GGAACTGAGGGAGTAATATAAAGTAGG 58.413 40.741 0.00 0.00 33.09 3.18
2795 2816 9.144298 TGGAACTGAGGGAGTAATATAAAGTAG 57.856 37.037 0.00 0.00 33.09 2.57
2796 2817 9.496710 TTGGAACTGAGGGAGTAATATAAAGTA 57.503 33.333 0.00 0.00 33.09 2.24
2797 2818 7.989947 TGGAACTGAGGGAGTAATATAAAGT 57.010 36.000 0.00 0.00 33.09 2.66
2798 2819 9.681062 TTTTGGAACTGAGGGAGTAATATAAAG 57.319 33.333 0.00 0.00 33.09 1.85
2802 2823 9.225682 TCTATTTTGGAACTGAGGGAGTAATAT 57.774 33.333 0.00 0.00 33.09 1.28
2803 2824 8.618240 TCTATTTTGGAACTGAGGGAGTAATA 57.382 34.615 0.00 0.00 33.09 0.98
2804 2825 7.510675 TCTATTTTGGAACTGAGGGAGTAAT 57.489 36.000 0.00 0.00 33.09 1.89
2805 2826 6.945636 TCTATTTTGGAACTGAGGGAGTAA 57.054 37.500 0.00 0.00 33.09 2.24
2806 2827 6.672218 TCATCTATTTTGGAACTGAGGGAGTA 59.328 38.462 0.00 0.00 33.09 2.59
2807 2828 5.488919 TCATCTATTTTGGAACTGAGGGAGT 59.511 40.000 0.00 0.00 35.94 3.85
2808 2829 5.819901 GTCATCTATTTTGGAACTGAGGGAG 59.180 44.000 0.00 0.00 0.00 4.30
2809 2830 5.488919 AGTCATCTATTTTGGAACTGAGGGA 59.511 40.000 0.00 0.00 0.00 4.20
2810 2831 5.749462 AGTCATCTATTTTGGAACTGAGGG 58.251 41.667 0.00 0.00 0.00 4.30
2811 2832 6.409704 TGAGTCATCTATTTTGGAACTGAGG 58.590 40.000 0.00 0.00 0.00 3.86
2812 2833 7.605691 AGTTGAGTCATCTATTTTGGAACTGAG 59.394 37.037 1.70 0.00 0.00 3.35
2813 2834 7.453393 AGTTGAGTCATCTATTTTGGAACTGA 58.547 34.615 1.70 0.00 0.00 3.41
2814 2835 7.678947 AGTTGAGTCATCTATTTTGGAACTG 57.321 36.000 1.70 0.00 0.00 3.16
2815 2836 8.571336 CAAAGTTGAGTCATCTATTTTGGAACT 58.429 33.333 4.14 0.00 35.65 3.01
2816 2837 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2817 2838 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2818 2839 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2819 2840 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2850 2871 9.715121 CCCAATTCTGTACTAACTTTGTACTTA 57.285 33.333 12.73 1.60 40.44 2.24
2851 2872 8.215736 ACCCAATTCTGTACTAACTTTGTACTT 58.784 33.333 12.73 0.00 40.44 2.24
2852 2873 7.742767 ACCCAATTCTGTACTAACTTTGTACT 58.257 34.615 12.73 0.00 40.44 2.73
2853 2874 7.658575 TGACCCAATTCTGTACTAACTTTGTAC 59.341 37.037 6.58 6.58 40.27 2.90
2854 2875 7.737869 TGACCCAATTCTGTACTAACTTTGTA 58.262 34.615 0.00 0.00 0.00 2.41
2855 2876 6.597562 TGACCCAATTCTGTACTAACTTTGT 58.402 36.000 0.00 0.00 0.00 2.83
2856 2877 7.607991 AGATGACCCAATTCTGTACTAACTTTG 59.392 37.037 0.00 0.00 0.00 2.77
2857 2878 7.690256 AGATGACCCAATTCTGTACTAACTTT 58.310 34.615 0.00 0.00 0.00 2.66
2858 2879 7.259088 AGATGACCCAATTCTGTACTAACTT 57.741 36.000 0.00 0.00 0.00 2.66
2859 2880 6.875972 AGATGACCCAATTCTGTACTAACT 57.124 37.500 0.00 0.00 0.00 2.24
2860 2881 9.614792 AAATAGATGACCCAATTCTGTACTAAC 57.385 33.333 0.00 0.00 0.00 2.34
2862 2883 9.613428 CAAAATAGATGACCCAATTCTGTACTA 57.387 33.333 0.00 0.00 0.00 1.82
2863 2884 7.557719 CCAAAATAGATGACCCAATTCTGTACT 59.442 37.037 0.00 0.00 0.00 2.73
2864 2885 7.556275 TCCAAAATAGATGACCCAATTCTGTAC 59.444 37.037 0.00 0.00 0.00 2.90
2865 2886 7.638444 TCCAAAATAGATGACCCAATTCTGTA 58.362 34.615 0.00 0.00 0.00 2.74
2866 2887 6.493166 TCCAAAATAGATGACCCAATTCTGT 58.507 36.000 0.00 0.00 0.00 3.41
2867 2888 7.260603 GTTCCAAAATAGATGACCCAATTCTG 58.739 38.462 0.00 0.00 0.00 3.02
2868 2889 6.095440 CGTTCCAAAATAGATGACCCAATTCT 59.905 38.462 0.00 0.00 0.00 2.40
2869 2890 6.265577 CGTTCCAAAATAGATGACCCAATTC 58.734 40.000 0.00 0.00 0.00 2.17
2870 2891 5.127031 CCGTTCCAAAATAGATGACCCAATT 59.873 40.000 0.00 0.00 0.00 2.32
2871 2892 4.644685 CCGTTCCAAAATAGATGACCCAAT 59.355 41.667 0.00 0.00 0.00 3.16
2872 2893 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
2873 2894 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
2874 2895 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
2875 2896 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
2876 2897 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2877 2898 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2878 2899 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2879 2900 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2880 2901 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2881 2902 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2882 2903 6.811634 TTATACTCCCTCCGTTCCAAAATA 57.188 37.500 0.00 0.00 0.00 1.40
2883 2904 5.703730 TTATACTCCCTCCGTTCCAAAAT 57.296 39.130 0.00 0.00 0.00 1.82
2884 2905 5.493809 CTTTATACTCCCTCCGTTCCAAAA 58.506 41.667 0.00 0.00 0.00 2.44
2885 2906 4.624604 GCTTTATACTCCCTCCGTTCCAAA 60.625 45.833 0.00 0.00 0.00 3.28
2886 2907 3.118519 GCTTTATACTCCCTCCGTTCCAA 60.119 47.826 0.00 0.00 0.00 3.53
2887 2908 2.433239 GCTTTATACTCCCTCCGTTCCA 59.567 50.000 0.00 0.00 0.00 3.53
2888 2909 2.224233 GGCTTTATACTCCCTCCGTTCC 60.224 54.545 0.00 0.00 0.00 3.62
2889 2910 2.433239 TGGCTTTATACTCCCTCCGTTC 59.567 50.000 0.00 0.00 0.00 3.95
2890 2911 2.169978 GTGGCTTTATACTCCCTCCGTT 59.830 50.000 0.00 0.00 0.00 4.44
2891 2912 1.761198 GTGGCTTTATACTCCCTCCGT 59.239 52.381 0.00 0.00 0.00 4.69
2892 2913 1.269621 CGTGGCTTTATACTCCCTCCG 60.270 57.143 0.00 0.00 0.00 4.63
2893 2914 2.037144 TCGTGGCTTTATACTCCCTCC 58.963 52.381 0.00 0.00 0.00 4.30
2894 2915 3.321111 TGATCGTGGCTTTATACTCCCTC 59.679 47.826 0.00 0.00 0.00 4.30
2895 2916 3.069729 GTGATCGTGGCTTTATACTCCCT 59.930 47.826 0.00 0.00 0.00 4.20
2896 2917 3.391049 GTGATCGTGGCTTTATACTCCC 58.609 50.000 0.00 0.00 0.00 4.30
2897 2918 3.391049 GGTGATCGTGGCTTTATACTCC 58.609 50.000 0.00 0.00 0.00 3.85
2898 2919 3.050619 CGGTGATCGTGGCTTTATACTC 58.949 50.000 0.00 0.00 0.00 2.59
2899 2920 2.691526 TCGGTGATCGTGGCTTTATACT 59.308 45.455 0.00 0.00 40.32 2.12
2900 2921 3.088194 TCGGTGATCGTGGCTTTATAC 57.912 47.619 0.00 0.00 40.32 1.47
2909 2930 2.844122 TGTCTGTATCGGTGATCGTG 57.156 50.000 0.00 0.00 40.32 4.35
2988 3009 1.136828 TGTGGCTGTTCCTGTACCTT 58.863 50.000 0.00 0.00 35.26 3.50
3098 3121 0.681733 TTCGAGCTCAGCCTTGTCTT 59.318 50.000 15.40 0.00 0.00 3.01
3116 3139 2.093447 CGTCTTGGAGGCCTACATTCTT 60.093 50.000 21.32 0.00 0.00 2.52
3117 3140 1.482593 CGTCTTGGAGGCCTACATTCT 59.517 52.381 21.32 0.00 0.00 2.40
3210 3233 3.738590 GCTACTCTTCCCCTTCGAATGAC 60.739 52.174 0.00 0.00 0.00 3.06
3677 3734 2.665185 GTCGTGGTGTGGTGGCTC 60.665 66.667 0.00 0.00 0.00 4.70
3933 4025 3.866582 GATCTGGCCCTCCGGGTG 61.867 72.222 0.00 0.00 46.51 4.61
3934 4026 4.095400 AGATCTGGCCCTCCGGGT 62.095 66.667 0.00 0.00 46.51 5.28
4025 4157 2.978824 CTGGAACCGACCGATGGT 59.021 61.111 0.00 0.00 42.98 3.55
4026 4158 2.511600 GCTGGAACCGACCGATGG 60.512 66.667 0.00 0.00 0.00 3.51
4028 4160 4.814294 GCGCTGGAACCGACCGAT 62.814 66.667 0.00 0.00 0.00 4.18
4306 4441 6.739565 GCCCTTTTAATATTTGAGCCAGATGG 60.740 42.308 0.00 0.00 38.53 3.51
4307 4442 6.218746 GCCCTTTTAATATTTGAGCCAGATG 58.781 40.000 0.00 0.00 0.00 2.90
4308 4443 5.305386 GGCCCTTTTAATATTTGAGCCAGAT 59.695 40.000 0.00 0.00 37.80 2.90
4309 4444 4.649218 GGCCCTTTTAATATTTGAGCCAGA 59.351 41.667 0.00 0.00 37.80 3.86
4310 4445 4.651045 AGGCCCTTTTAATATTTGAGCCAG 59.349 41.667 0.00 0.00 40.37 4.85
4311 4446 4.619679 AGGCCCTTTTAATATTTGAGCCA 58.380 39.130 0.00 0.00 40.37 4.75
4312 4447 4.649218 TGAGGCCCTTTTAATATTTGAGCC 59.351 41.667 0.00 0.00 38.16 4.70
4313 4448 5.852282 TGAGGCCCTTTTAATATTTGAGC 57.148 39.130 0.00 0.00 0.00 4.26
4314 4449 7.352079 ACATGAGGCCCTTTTAATATTTGAG 57.648 36.000 0.00 0.00 0.00 3.02
4315 4450 8.830915 TTACATGAGGCCCTTTTAATATTTGA 57.169 30.769 0.00 0.00 0.00 2.69
4407 4542 4.273005 ACAAAACAAGTAAGCACTCACG 57.727 40.909 0.00 0.00 32.29 4.35
4474 4609 8.394971 ACAGTGTTCAAGAAATCATGATAACA 57.605 30.769 9.04 11.55 0.00 2.41
4575 4710 6.715718 CCAATGGCTCTCTATCATTTTGATCT 59.284 38.462 0.00 0.00 38.26 2.75
4616 4751 8.772250 TGATTCTGTTTCCTAGGAAATGACTAT 58.228 33.333 33.92 24.30 44.52 2.12
4617 4752 8.146053 TGATTCTGTTTCCTAGGAAATGACTA 57.854 34.615 33.92 21.64 44.52 2.59
5116 5255 3.995636 AGCATAGGAGGGTTTAGTGAGA 58.004 45.455 0.00 0.00 0.00 3.27
5130 5269 7.335422 AGTCATTTCTCTTTACACAAGCATAGG 59.665 37.037 0.00 0.00 0.00 2.57
5157 5296 4.142600 CCGCCCTGTTCTCTTTCTAAAATG 60.143 45.833 0.00 0.00 0.00 2.32
5177 5316 0.947244 CAGGTTAGCAATCCATCCGC 59.053 55.000 0.00 0.00 0.00 5.54
5499 5638 9.965824 CACTGTCTTCAACTTTAATGGTAAAAT 57.034 29.630 0.00 0.00 0.00 1.82
5870 6011 6.169094 AGGCTCATAGAAATGATGAATACCG 58.831 40.000 0.00 0.00 41.29 4.02
5971 6113 7.234166 TGGCAGATCTAAATGAGTCTCATATCA 59.766 37.037 15.77 3.68 35.76 2.15
5980 6122 9.412460 TCATTAATTTGGCAGATCTAAATGAGT 57.588 29.630 14.20 0.00 36.22 3.41
6247 6389 6.126863 TCTCAAATGTTCCACTGTATCCTT 57.873 37.500 0.00 0.00 0.00 3.36
6315 6457 3.971245 ATCTTCAGTTCCTGAGTGGAC 57.029 47.619 0.00 0.00 46.14 4.02
6372 6514 2.005370 ACCCACACGGAACTTCTCTA 57.995 50.000 0.00 0.00 34.64 2.43
6385 6527 2.443632 TCATGAACCTTGGTAACCCACA 59.556 45.455 0.00 0.00 41.67 4.17
6507 6649 7.712639 GGAAATCTTACAGATTCTGCATAGACA 59.287 37.037 13.64 0.00 43.67 3.41
6631 6773 3.881089 TCTGATGCATCTTGGCTACATTG 59.119 43.478 26.32 3.89 34.04 2.82
6850 6992 6.708949 TCTTCAGTTACATTGGGAACAGTTAC 59.291 38.462 6.51 0.00 44.54 2.50
6922 7064 2.222027 GTCCTGTGCTTGCTTACAACT 58.778 47.619 0.00 0.00 0.00 3.16
7037 7179 3.242867 TGTTCTCTTGATGGAGGACTGT 58.757 45.455 4.81 0.00 41.22 3.55
7065 7207 6.485313 TCATATGTTTCTTTGTCTCGTTGGTT 59.515 34.615 1.90 0.00 0.00 3.67
7297 7439 4.590850 TCAACCGATCCAGATATCACTG 57.409 45.455 5.32 0.00 37.61 3.66
7437 7582 7.637229 CATATGAAAGCATTAAGTGACTGGAG 58.363 38.462 0.00 0.00 35.94 3.86
7451 7596 9.866798 TTGTTTATGTTAATGCATATGAAAGCA 57.133 25.926 6.97 0.00 45.92 3.91
7487 7632 8.185003 TGTAATCACTTGAATAGATGTGAACG 57.815 34.615 0.00 0.00 41.78 3.95
7762 7907 3.131933 AGTCCACTATCTAGCAGCAGTTG 59.868 47.826 0.00 0.00 0.00 3.16
7811 7956 3.198068 TGAACAGTGAACAGTGAAGCTC 58.802 45.455 15.25 7.41 35.75 4.09
7915 8060 9.665264 AGTCTCGTGTTAATTTGAATTTCTTTC 57.335 29.630 0.00 0.00 34.72 2.62
7929 8074 8.942338 ATAGCAATCATAAAGTCTCGTGTTAA 57.058 30.769 0.00 0.00 0.00 2.01
8075 8220 6.180472 CCTAACTGTATCCCATCACTGTTTT 58.820 40.000 2.98 0.00 37.76 2.43
8081 8226 8.191534 AGTATAACCTAACTGTATCCCATCAC 57.808 38.462 0.00 0.00 0.00 3.06
8082 8227 9.305555 GTAGTATAACCTAACTGTATCCCATCA 57.694 37.037 0.00 0.00 0.00 3.07
8489 8642 3.244630 ACAAACCGGCAGTACAATTCCTA 60.245 43.478 0.00 0.00 0.00 2.94
8495 8648 1.134340 AGTGACAAACCGGCAGTACAA 60.134 47.619 0.00 0.00 0.00 2.41
8511 8664 1.073025 AATTCACCTGCCGCAGTGA 59.927 52.632 18.98 17.68 0.00 3.41
8514 8667 2.180017 GCAATTCACCTGCCGCAG 59.820 61.111 13.82 13.82 33.51 5.18
8515 8668 2.282391 AGCAATTCACCTGCCGCA 60.282 55.556 0.00 0.00 40.86 5.69
8617 8770 8.675705 TTCTCATTCATAGTTTGTTCACTCAA 57.324 30.769 0.00 0.00 0.00 3.02
8710 8863 5.531122 AATCAGCTAGCTAAATACGACCA 57.469 39.130 18.86 0.00 0.00 4.02
8735 8888 5.516339 GGCATGCATTACTTTGACATGTAAC 59.484 40.000 21.36 0.00 40.15 2.50
8758 8911 4.222124 AGTTACTGTTCTGGCCTTATGG 57.778 45.455 3.32 0.00 0.00 2.74
8822 8975 5.690865 TGTTAAGTGATCAGTTGTTTCCCT 58.309 37.500 23.36 0.00 0.00 4.20
8844 8997 0.393537 CAAGAGCCCCTTACCTGCTG 60.394 60.000 0.00 0.00 34.99 4.41
8878 9031 4.229639 GCTACAGGTAAGGGTAAGGGTAT 58.770 47.826 0.00 0.00 0.00 2.73
8910 9063 1.398390 GATGCGAACTAACCAAGCCTG 59.602 52.381 0.00 0.00 0.00 4.85
8990 9143 3.566742 GTGTGTACGGAAGGTCCAAATTT 59.433 43.478 0.00 0.00 35.91 1.82
8996 9149 1.869132 GTTTGTGTGTACGGAAGGTCC 59.131 52.381 0.00 0.00 0.00 4.46
9014 9167 5.921408 GCATTCTTCGAAGAGTATATCGGTT 59.079 40.000 25.73 0.00 38.43 4.44
9037 9190 7.262048 AGACTGTAAGAGCATTAAGTAAGAGC 58.738 38.462 0.00 0.00 37.43 4.09
9040 9193 9.303537 GGTAAGACTGTAAGAGCATTAAGTAAG 57.696 37.037 0.00 0.00 37.43 2.34
9041 9194 8.255905 GGGTAAGACTGTAAGAGCATTAAGTAA 58.744 37.037 0.00 0.00 37.43 2.24
9042 9195 7.618512 AGGGTAAGACTGTAAGAGCATTAAGTA 59.381 37.037 0.00 0.00 37.43 2.24
9043 9196 6.440965 AGGGTAAGACTGTAAGAGCATTAAGT 59.559 38.462 0.00 0.00 37.43 2.24
9044 9197 6.879400 AGGGTAAGACTGTAAGAGCATTAAG 58.121 40.000 0.00 0.00 37.43 1.85
9045 9198 6.869206 AGGGTAAGACTGTAAGAGCATTAA 57.131 37.500 0.00 0.00 37.43 1.40
9046 9199 6.668283 AGAAGGGTAAGACTGTAAGAGCATTA 59.332 38.462 0.00 0.00 37.43 1.90
9047 9200 5.485708 AGAAGGGTAAGACTGTAAGAGCATT 59.514 40.000 0.00 0.00 37.43 3.56
9048 9201 5.026790 AGAAGGGTAAGACTGTAAGAGCAT 58.973 41.667 0.00 0.00 37.43 3.79
9049 9202 4.417437 AGAAGGGTAAGACTGTAAGAGCA 58.583 43.478 0.00 0.00 37.43 4.26
9058 9224 6.995091 GCATGATATTGAAGAAGGGTAAGACT 59.005 38.462 0.00 0.00 0.00 3.24
9176 9342 4.099633 AGTTCACTTCCAGAGATGGATCA 58.900 43.478 0.00 0.00 37.87 2.92
9281 9447 1.484240 GAGAGGTGGGATGAAGTGAGG 59.516 57.143 0.00 0.00 0.00 3.86
9305 9471 6.003326 TCTCCTGTCAAACATTTATGCAGAA 58.997 36.000 0.00 0.00 0.00 3.02
9344 9510 2.574006 TTGAGCTTGAGCCTCACAAT 57.426 45.000 0.00 0.00 43.38 2.71
9392 9558 0.749454 GGACCCATGGTGATGCTGAC 60.749 60.000 11.73 0.00 35.25 3.51


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

AutoCloner maintained by Alex Coulton.