Multiple sequence alignment - TraesCS5A01G552800

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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 TraesCS5A01G552800 chr5A 100.000 4157 0 0 1 4157 705573058 705568902 0.000000e+00 7677.0
1 TraesCS5A01G552800 chr5A 95.122 82 3 1 3391 3471 505896745 505896664 1.210000e-25 128.0
2 TraesCS5A01G552800 chr5A 86.316 95 13 0 1238 1332 688929079 688929173 2.040000e-18 104.0
3 TraesCS5A01G552800 chr5A 92.857 70 2 3 849 917 705572159 705572092 9.510000e-17 99.0
4 TraesCS5A01G552800 chr5A 92.857 70 2 3 900 967 705572210 705572142 9.510000e-17 99.0
5 TraesCS5A01G552800 chr5A 88.608 79 8 1 1719 1797 706546370 706546293 1.230000e-15 95.3
6 TraesCS5A01G552800 chr4B 95.009 1062 41 1 2131 3192 665567839 665566790 0.000000e+00 1657.0
7 TraesCS5A01G552800 chr4B 98.257 918 13 3 1 917 665570019 665569104 0.000000e+00 1604.0
8 TraesCS5A01G552800 chr4B 96.548 927 11 8 900 1813 665569173 665568255 0.000000e+00 1515.0
9 TraesCS5A01G552800 chr4B 88.392 715 38 9 3483 4157 665566525 665565816 0.000000e+00 819.0
10 TraesCS5A01G552800 chr4B 94.915 236 9 1 1902 2134 665568264 665568029 2.360000e-97 366.0
11 TraesCS5A01G552800 chr4B 94.872 195 6 4 3178 3368 665566726 665566532 6.750000e-78 302.0
12 TraesCS5A01G552800 chr4B 92.105 76 3 2 3851 3926 665918432 665918504 2.040000e-18 104.0
13 TraesCS5A01G552800 chr4B 89.706 68 6 1 1719 1786 667608824 667608890 7.400000e-13 86.1
14 TraesCS5A01G552800 chr5B 78.061 2156 392 52 988 3111 690329480 690331586 0.000000e+00 1286.0
15 TraesCS5A01G552800 chr5B 79.138 1740 297 45 930 2637 690600601 690602306 0.000000e+00 1142.0
16 TraesCS5A01G552800 chr5B 78.956 1283 239 23 1026 2294 690362977 690361712 0.000000e+00 845.0
17 TraesCS5A01G552800 chr5B 81.100 1000 149 25 938 1918 690334408 690335386 0.000000e+00 763.0
18 TraesCS5A01G552800 chr5B 76.408 746 146 23 1915 2640 690335467 690336202 3.920000e-100 375.0
19 TraesCS5A01G552800 chr5B 89.200 250 22 4 3 252 690896467 690896223 1.450000e-79 307.0
20 TraesCS5A01G552800 chr4A 81.618 1001 144 27 934 1907 621685149 621684162 0.000000e+00 793.0
21 TraesCS5A01G552800 chr4A 98.925 93 0 1 3393 3485 485006147 485006238 9.250000e-37 165.0
22 TraesCS5A01G552800 chr5D 83.264 723 99 14 926 1632 547255902 547256618 0.000000e+00 645.0
23 TraesCS5A01G552800 chr7A 92.937 269 13 5 1 265 75073259 75072993 1.810000e-103 387.0
24 TraesCS5A01G552800 chr7A 86.047 258 28 7 3 256 214310926 214311179 1.900000e-68 270.0
25 TraesCS5A01G552800 chr2A 90.514 253 18 3 1 252 777805097 777804850 3.100000e-86 329.0
26 TraesCS5A01G552800 chr2A 85.115 262 30 8 3 259 565322808 565323065 4.120000e-65 259.0
27 TraesCS5A01G552800 chr2A 73.733 217 46 6 1735 1947 40341516 40341307 1.600000e-09 75.0
28 TraesCS5A01G552800 chr2A 82.716 81 12 2 1735 1814 9201801 9201722 2.070000e-08 71.3
29 TraesCS5A01G552800 chr7D 91.949 236 15 2 22 257 553381292 553381061 1.110000e-85 327.0
30 TraesCS5A01G552800 chr7D 94.737 57 3 0 3391 3447 307127339 307127395 5.720000e-14 89.8
31 TraesCS5A01G552800 chrUn 90.079 252 20 4 1 252 365280221 365279975 5.180000e-84 322.0
32 TraesCS5A01G552800 chrUn 85.271 258 28 7 4 255 331923309 331923056 1.480000e-64 257.0
33 TraesCS5A01G552800 chrUn 100.000 59 0 0 3427 3485 182440379 182440321 4.390000e-20 110.0
34 TraesCS5A01G552800 chrUn 88.608 79 8 1 1719 1797 30031685 30031608 1.230000e-15 95.3
35 TraesCS5A01G552800 chr1A 100.000 95 0 0 3391 3485 94686217 94686311 4.270000e-40 176.0
36 TraesCS5A01G552800 chr1A 98.947 95 1 0 3391 3485 94558041 94557947 1.990000e-38 171.0
37 TraesCS5A01G552800 chr3A 100.000 87 0 0 3391 3477 653830915 653831001 1.200000e-35 161.0
38 TraesCS5A01G552800 chr7B 87.500 96 12 0 1237 1332 13244724 13244629 1.220000e-20 111.0
39 TraesCS5A01G552800 chr6D 100.000 59 0 0 3427 3485 108514762 108514704 4.390000e-20 110.0
40 TraesCS5A01G552800 chr6A 100.000 59 0 0 3427 3485 84405409 84405467 4.390000e-20 110.0
41 TraesCS5A01G552800 chr4D 100.000 59 0 0 3427 3485 398052320 398052378 4.390000e-20 110.0
42 TraesCS5A01G552800 chr4D 94.737 57 3 0 3391 3447 123272760 123272816 5.720000e-14 89.8
43 TraesCS5A01G552800 chr6B 94.737 57 3 0 3391 3447 297453804 297453860 5.720000e-14 89.8
44 TraesCS5A01G552800 chr3D 94.737 57 3 0 3391 3447 109601860 109601916 5.720000e-14 89.8
45 TraesCS5A01G552800 chr2D 81.250 80 15 0 1735 1814 36434645 36434566 9.650000e-07 65.8


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 TraesCS5A01G552800 chr5A 705568902 705573058 4156 True 2625.000000 7677 95.2380 1 4157 3 chr5A.!!$R3 4156
1 TraesCS5A01G552800 chr4B 665565816 665570019 4203 True 1043.833333 1657 94.6655 1 4157 6 chr4B.!!$R1 4156
2 TraesCS5A01G552800 chr5B 690600601 690602306 1705 False 1142.000000 1142 79.1380 930 2637 1 chr5B.!!$F1 1707
3 TraesCS5A01G552800 chr5B 690361712 690362977 1265 True 845.000000 845 78.9560 1026 2294 1 chr5B.!!$R1 1268
4 TraesCS5A01G552800 chr5B 690329480 690336202 6722 False 808.000000 1286 78.5230 938 3111 3 chr5B.!!$F2 2173
5 TraesCS5A01G552800 chr4A 621684162 621685149 987 True 793.000000 793 81.6180 934 1907 1 chr4A.!!$R1 973
6 TraesCS5A01G552800 chr5D 547255902 547256618 716 False 645.000000 645 83.2640 926 1632 1 chr5D.!!$F1 706

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
660 661 0.394352 GTATGGGGCTGGTGAAGGTG 60.394 60.0 0.0 0.0 0.00 4.00 F
2331 7761 0.106708 GCGAGAATGGCATGGTAGGA 59.893 55.0 0.0 0.0 40.68 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2367 7797 0.107654 ATAGTGCAGGACGAAAGCCC 60.108 55.0 0.0 0.0 0.00 5.19 R
3408 8928 0.036858 AGAAAGGACTCAGCTTCCGC 60.037 55.0 0.0 0.0 38.29 5.54 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
54 55 7.065120 TCATTGTTTTGATCACTTTTGGGAT 57.935 32.000 0.00 0.00 46.98 3.85
135 136 1.898938 CCGACGTGATACTTTGCGTA 58.101 50.000 0.00 0.00 37.71 4.42
139 140 3.300944 CGACGTGATACTTTGCGTATGTG 60.301 47.826 0.00 0.00 38.90 3.21
166 167 1.202867 TGTTGGCTGTGTGCATCCTAA 60.203 47.619 0.00 0.00 45.15 2.69
180 181 4.298103 CATCCTAATTATGCAGAGGCCT 57.702 45.455 3.86 3.86 40.13 5.19
465 466 1.360852 AGGCCCCATCATTTGGTTGTA 59.639 47.619 0.00 0.00 44.83 2.41
660 661 0.394352 GTATGGGGCTGGTGAAGGTG 60.394 60.000 0.00 0.00 0.00 4.00
670 671 1.733526 GTGAAGGTGCCGTTTTGCT 59.266 52.632 0.00 0.00 0.00 3.91
685 686 5.426240 CGTTTTGCTTTCATTCTTCTTTGC 58.574 37.500 0.00 0.00 0.00 3.68
692 693 2.440409 TCATTCTTCTTTGCCCAGAGC 58.560 47.619 0.00 0.00 44.14 4.09
715 716 0.604780 CTTACTGTGCCAGCTGCTGT 60.605 55.000 26.41 10.77 42.00 4.40
881 882 9.496873 TCAAGTGTTCTTTATCGAATTAAAGGA 57.503 29.630 15.23 6.96 38.92 3.36
902 903 8.930846 AAGGAATATGCATAGATTTAGTTGCT 57.069 30.769 12.79 7.29 36.10 3.91
911 912 9.613428 TGCATAGATTTAGTTGCTAATAAGTGT 57.387 29.630 0.00 0.00 36.10 3.55
1278 1294 0.253044 TGCATCTTGGTAGCCAGGAC 59.747 55.000 2.05 0.00 42.29 3.85
1545 6560 6.652900 GTCTCCCTAATTATGATGAGCTTTCC 59.347 42.308 0.00 0.00 0.00 3.13
1669 6690 7.036829 GGTGGCTTTGTTTAGTTTCAAAGTTA 58.963 34.615 15.60 5.98 46.74 2.24
1834 6978 0.108019 GTTCCGTCTGGTTTCACCCT 59.892 55.000 0.00 0.00 37.50 4.34
1842 6986 2.207229 GGTTTCACCCTTGGCCACC 61.207 63.158 3.88 0.00 30.04 4.61
1843 6987 1.456705 GTTTCACCCTTGGCCACCA 60.457 57.895 3.88 0.00 0.00 4.17
1847 6991 4.740822 ACCCTTGGCCACCATCGC 62.741 66.667 3.88 0.00 31.53 4.58
1863 7007 2.095843 GCCGCGTTCGTCATGTTC 59.904 61.111 4.92 0.00 0.00 3.18
1875 7019 3.070446 TCGTCATGTTCCAGTTAAGTGGT 59.930 43.478 25.35 6.77 38.88 4.16
1956 7187 1.811266 CCTTCTGGACATGGCGTCG 60.811 63.158 0.00 0.00 46.42 5.12
1984 7215 1.797018 TACTCTGGGGTCGACCTGGT 61.797 60.000 32.52 23.18 40.03 4.00
2182 7612 1.609783 GGTCTGGAGGATTGGTGGG 59.390 63.158 0.00 0.00 0.00 4.61
2202 7632 1.266718 GACAAATGGCGTTGCTCTGAA 59.733 47.619 0.00 0.00 31.29 3.02
2299 7729 5.381174 TCCAAGTGCAGAAAATGAGATTG 57.619 39.130 0.00 0.00 0.00 2.67
2310 7740 5.250313 AGAAAATGAGATTGAGTCCTCACCT 59.750 40.000 0.00 0.00 41.59 4.00
2331 7761 0.106708 GCGAGAATGGCATGGTAGGA 59.893 55.000 0.00 0.00 40.68 2.94
2367 7797 2.287788 GCCACCTATGAATGATTTGCCG 60.288 50.000 0.00 0.00 0.00 5.69
2641 8080 1.326548 GCATGTACGAATCAACCGTCC 59.673 52.381 0.00 0.00 40.95 4.79
2679 8118 0.258774 GTTGTCCATGGGGTAGCCAT 59.741 55.000 13.02 1.66 34.93 4.40
2685 8124 1.073923 CCATGGGGTAGCCATACTTCC 59.926 57.143 14.06 0.00 35.13 3.46
2688 8127 1.294068 TGGGGTAGCCATACTTCCTCT 59.706 52.381 14.06 0.00 37.23 3.69
2690 8129 3.144125 TGGGGTAGCCATACTTCCTCTAT 59.856 47.826 14.06 0.00 37.23 1.98
2710 8149 2.593346 AGATAGCGTGAAGAGGCTTG 57.407 50.000 0.00 0.00 40.45 4.01
2754 8193 0.188587 ACGAGGATATGGGAGAGGCA 59.811 55.000 0.00 0.00 0.00 4.75
2760 8199 1.550524 GATATGGGAGAGGCATGCGTA 59.449 52.381 13.78 0.00 0.00 4.42
2778 8217 1.834263 GTAACTCTCTGGCATGGGACT 59.166 52.381 0.00 0.00 0.00 3.85
2819 8258 2.224744 TGGAACTTGTAGATGCAGGCAA 60.225 45.455 0.00 0.00 0.00 4.52
2822 8261 0.729116 CTTGTAGATGCAGGCAACGG 59.271 55.000 0.00 0.00 46.39 4.44
2877 8316 1.875157 CGTGATCATGTCGCCATGGAT 60.875 52.381 18.40 0.00 46.96 3.41
2889 8328 1.747206 GCCATGGATAAACTGGAGCGT 60.747 52.381 18.40 0.00 31.38 5.07
2949 8388 1.476488 GGTGGTGTGTTTGATATGCCC 59.524 52.381 0.00 0.00 0.00 5.36
2997 8436 2.089349 GGTGCGTCTGCTCGTCTTC 61.089 63.158 0.00 0.00 43.34 2.87
3006 8445 1.733399 GCTCGTCTTCGCTTCCGTT 60.733 57.895 0.00 0.00 36.96 4.44
3018 8457 0.601046 CTTCCGTTCAGTGCAGCAGA 60.601 55.000 0.00 0.00 0.00 4.26
3108 8547 1.996191 GCCAACGTGTTTTTCAAGCAA 59.004 42.857 0.00 0.00 0.00 3.91
3114 8553 2.276201 GTGTTTTTCAAGCAACCCACC 58.724 47.619 0.00 0.00 0.00 4.61
3120 8559 4.621087 AAGCAACCCACCCCTGGC 62.621 66.667 0.00 0.00 36.00 4.85
3141 8580 4.496507 GGCGGTATTGAATCTTTTCTGCTC 60.497 45.833 0.00 0.00 32.78 4.26
3310 8828 2.746904 CGACCTGCCATGACACAAATTA 59.253 45.455 0.00 0.00 0.00 1.40
3311 8829 3.378112 CGACCTGCCATGACACAAATTAT 59.622 43.478 0.00 0.00 0.00 1.28
3312 8830 4.675510 GACCTGCCATGACACAAATTATG 58.324 43.478 0.00 0.00 0.00 1.90
3313 8831 4.088634 ACCTGCCATGACACAAATTATGT 58.911 39.130 0.00 0.00 45.34 2.29
3314 8832 5.260424 ACCTGCCATGACACAAATTATGTA 58.740 37.500 0.00 0.00 41.46 2.29
3315 8833 5.357878 ACCTGCCATGACACAAATTATGTAG 59.642 40.000 0.00 0.00 41.46 2.74
3316 8834 5.357878 CCTGCCATGACACAAATTATGTAGT 59.642 40.000 0.00 0.00 41.46 2.73
3317 8835 6.435430 TGCCATGACACAAATTATGTAGTC 57.565 37.500 0.00 0.00 41.46 2.59
3331 8851 3.502123 TGTAGTCTTTTGTTCCCCCTG 57.498 47.619 0.00 0.00 0.00 4.45
3360 8880 5.822519 TGTTTGTGAATTGTGACTAGCTCTT 59.177 36.000 0.00 0.00 0.00 2.85
3363 8883 5.473931 TGTGAATTGTGACTAGCTCTTCTC 58.526 41.667 0.00 0.00 0.00 2.87
3364 8884 5.244851 TGTGAATTGTGACTAGCTCTTCTCT 59.755 40.000 0.00 0.00 0.00 3.10
3365 8885 5.576384 GTGAATTGTGACTAGCTCTTCTCTG 59.424 44.000 0.00 0.00 0.00 3.35
3366 8886 3.584406 TTGTGACTAGCTCTTCTCTGC 57.416 47.619 0.00 0.00 0.00 4.26
3367 8887 2.801483 TGTGACTAGCTCTTCTCTGCT 58.199 47.619 0.00 0.00 42.67 4.24
3368 8888 2.491298 TGTGACTAGCTCTTCTCTGCTG 59.509 50.000 0.00 0.00 40.08 4.41
3369 8889 1.476085 TGACTAGCTCTTCTCTGCTGC 59.524 52.381 0.00 0.00 40.08 5.25
3370 8890 1.750778 GACTAGCTCTTCTCTGCTGCT 59.249 52.381 0.00 0.00 40.08 4.24
3371 8891 2.166254 GACTAGCTCTTCTCTGCTGCTT 59.834 50.000 0.00 0.00 40.08 3.91
3373 8893 0.108709 AGCTCTTCTCTGCTGCTTCG 60.109 55.000 0.00 0.00 38.21 3.79
3374 8894 0.108898 GCTCTTCTCTGCTGCTTCGA 60.109 55.000 0.00 0.00 0.00 3.71
3376 8896 2.891112 CTCTTCTCTGCTGCTTCGATT 58.109 47.619 0.00 0.00 0.00 3.34
3378 8898 3.668447 TCTTCTCTGCTGCTTCGATTTT 58.332 40.909 0.00 0.00 0.00 1.82
3379 8899 3.434641 TCTTCTCTGCTGCTTCGATTTTG 59.565 43.478 0.00 0.00 0.00 2.44
3380 8900 2.771089 TCTCTGCTGCTTCGATTTTGT 58.229 42.857 0.00 0.00 0.00 2.83
3381 8901 3.925379 TCTCTGCTGCTTCGATTTTGTA 58.075 40.909 0.00 0.00 0.00 2.41
3382 8902 4.507710 TCTCTGCTGCTTCGATTTTGTAT 58.492 39.130 0.00 0.00 0.00 2.29
3383 8903 4.568359 TCTCTGCTGCTTCGATTTTGTATC 59.432 41.667 0.00 0.00 0.00 2.24
3384 8904 3.623060 TCTGCTGCTTCGATTTTGTATCC 59.377 43.478 0.00 0.00 0.00 2.59
3385 8905 2.682856 TGCTGCTTCGATTTTGTATCCC 59.317 45.455 0.00 0.00 0.00 3.85
3386 8906 2.945668 GCTGCTTCGATTTTGTATCCCT 59.054 45.455 0.00 0.00 0.00 4.20
3387 8907 3.002759 GCTGCTTCGATTTTGTATCCCTC 59.997 47.826 0.00 0.00 0.00 4.30
3388 8908 4.191544 CTGCTTCGATTTTGTATCCCTCA 58.808 43.478 0.00 0.00 0.00 3.86
3389 8909 3.938963 TGCTTCGATTTTGTATCCCTCAC 59.061 43.478 0.00 0.00 0.00 3.51
3390 8910 4.192317 GCTTCGATTTTGTATCCCTCACT 58.808 43.478 0.00 0.00 0.00 3.41
3391 8911 4.271291 GCTTCGATTTTGTATCCCTCACTC 59.729 45.833 0.00 0.00 0.00 3.51
3392 8912 5.665459 CTTCGATTTTGTATCCCTCACTCT 58.335 41.667 0.00 0.00 0.00 3.24
3393 8913 5.263968 TCGATTTTGTATCCCTCACTCTC 57.736 43.478 0.00 0.00 0.00 3.20
3394 8914 4.099573 TCGATTTTGTATCCCTCACTCTCC 59.900 45.833 0.00 0.00 0.00 3.71
3395 8915 4.141937 CGATTTTGTATCCCTCACTCTCCA 60.142 45.833 0.00 0.00 0.00 3.86
3396 8916 5.453903 CGATTTTGTATCCCTCACTCTCCAT 60.454 44.000 0.00 0.00 0.00 3.41
3397 8917 5.359194 TTTTGTATCCCTCACTCTCCATC 57.641 43.478 0.00 0.00 0.00 3.51
3398 8918 2.587522 TGTATCCCTCACTCTCCATCG 58.412 52.381 0.00 0.00 0.00 3.84
3399 8919 2.174854 TGTATCCCTCACTCTCCATCGA 59.825 50.000 0.00 0.00 0.00 3.59
3400 8920 2.692709 ATCCCTCACTCTCCATCGAT 57.307 50.000 0.00 0.00 0.00 3.59
3401 8921 1.988293 TCCCTCACTCTCCATCGATC 58.012 55.000 0.00 0.00 0.00 3.69
3402 8922 1.215423 TCCCTCACTCTCCATCGATCA 59.785 52.381 0.00 0.00 0.00 2.92
3403 8923 1.339610 CCCTCACTCTCCATCGATCAC 59.660 57.143 0.00 0.00 0.00 3.06
3404 8924 2.305928 CCTCACTCTCCATCGATCACT 58.694 52.381 0.00 0.00 0.00 3.41
3405 8925 2.692557 CCTCACTCTCCATCGATCACTT 59.307 50.000 0.00 0.00 0.00 3.16
3406 8926 3.131933 CCTCACTCTCCATCGATCACTTT 59.868 47.826 0.00 0.00 0.00 2.66
3407 8927 4.382470 CCTCACTCTCCATCGATCACTTTT 60.382 45.833 0.00 0.00 0.00 2.27
3408 8928 4.498241 TCACTCTCCATCGATCACTTTTG 58.502 43.478 0.00 0.00 0.00 2.44
3409 8929 3.063180 CACTCTCCATCGATCACTTTTGC 59.937 47.826 0.00 0.00 0.00 3.68
3410 8930 2.270923 TCTCCATCGATCACTTTTGCG 58.729 47.619 0.00 0.00 0.00 4.85
3411 8931 1.328680 CTCCATCGATCACTTTTGCGG 59.671 52.381 0.00 0.00 0.00 5.69
3412 8932 1.066502 TCCATCGATCACTTTTGCGGA 60.067 47.619 0.00 0.00 0.00 5.54
3413 8933 1.737236 CCATCGATCACTTTTGCGGAA 59.263 47.619 0.00 0.00 0.00 4.30
3414 8934 2.223112 CCATCGATCACTTTTGCGGAAG 60.223 50.000 0.00 0.00 0.00 3.46
3428 8948 2.464157 CGGAAGCTGAGTCCTTTCTT 57.536 50.000 1.55 0.00 32.53 2.52
3429 8949 2.772287 CGGAAGCTGAGTCCTTTCTTT 58.228 47.619 1.55 0.00 32.53 2.52
3430 8950 3.142174 CGGAAGCTGAGTCCTTTCTTTT 58.858 45.455 1.55 0.00 32.53 2.27
3431 8951 3.187432 CGGAAGCTGAGTCCTTTCTTTTC 59.813 47.826 1.55 0.00 32.53 2.29
3432 8952 3.504134 GGAAGCTGAGTCCTTTCTTTTCC 59.496 47.826 0.00 0.00 31.94 3.13
3433 8953 3.864789 AGCTGAGTCCTTTCTTTTCCA 57.135 42.857 0.00 0.00 0.00 3.53
3434 8954 3.749226 AGCTGAGTCCTTTCTTTTCCAG 58.251 45.455 0.00 0.00 0.00 3.86
3435 8955 2.227626 GCTGAGTCCTTTCTTTTCCAGC 59.772 50.000 0.00 0.00 38.88 4.85
3436 8956 3.480470 CTGAGTCCTTTCTTTTCCAGCA 58.520 45.455 0.00 0.00 0.00 4.41
3437 8957 3.885297 CTGAGTCCTTTCTTTTCCAGCAA 59.115 43.478 0.00 0.00 0.00 3.91
3438 8958 3.632145 TGAGTCCTTTCTTTTCCAGCAAC 59.368 43.478 0.00 0.00 0.00 4.17
3439 8959 3.885901 GAGTCCTTTCTTTTCCAGCAACT 59.114 43.478 0.00 0.00 0.00 3.16
3440 8960 4.281657 AGTCCTTTCTTTTCCAGCAACTT 58.718 39.130 0.00 0.00 0.00 2.66
3441 8961 4.339530 AGTCCTTTCTTTTCCAGCAACTTC 59.660 41.667 0.00 0.00 0.00 3.01
3442 8962 4.097892 GTCCTTTCTTTTCCAGCAACTTCA 59.902 41.667 0.00 0.00 0.00 3.02
3443 8963 4.709397 TCCTTTCTTTTCCAGCAACTTCAA 59.291 37.500 0.00 0.00 0.00 2.69
3444 8964 5.186797 TCCTTTCTTTTCCAGCAACTTCAAA 59.813 36.000 0.00 0.00 0.00 2.69
3445 8965 6.051074 CCTTTCTTTTCCAGCAACTTCAAAT 58.949 36.000 0.00 0.00 0.00 2.32
3446 8966 6.201615 CCTTTCTTTTCCAGCAACTTCAAATC 59.798 38.462 0.00 0.00 0.00 2.17
3447 8967 5.850557 TCTTTTCCAGCAACTTCAAATCA 57.149 34.783 0.00 0.00 0.00 2.57
3448 8968 5.835257 TCTTTTCCAGCAACTTCAAATCAG 58.165 37.500 0.00 0.00 0.00 2.90
3449 8969 5.593909 TCTTTTCCAGCAACTTCAAATCAGA 59.406 36.000 0.00 0.00 0.00 3.27
3450 8970 5.850557 TTTCCAGCAACTTCAAATCAGAA 57.149 34.783 0.00 0.00 0.00 3.02
3451 8971 5.850557 TTCCAGCAACTTCAAATCAGAAA 57.149 34.783 0.00 0.00 0.00 2.52
3452 8972 5.443185 TCCAGCAACTTCAAATCAGAAAG 57.557 39.130 0.00 0.00 0.00 2.62
3453 8973 3.985925 CCAGCAACTTCAAATCAGAAAGC 59.014 43.478 0.00 0.00 0.00 3.51
3454 8974 3.985925 CAGCAACTTCAAATCAGAAAGCC 59.014 43.478 0.00 0.00 0.00 4.35
3455 8975 3.006217 AGCAACTTCAAATCAGAAAGCCC 59.994 43.478 0.00 0.00 0.00 5.19
3456 8976 3.862264 GCAACTTCAAATCAGAAAGCCCC 60.862 47.826 0.00 0.00 0.00 5.80
3457 8977 2.162681 ACTTCAAATCAGAAAGCCCCG 58.837 47.619 0.00 0.00 0.00 5.73
3458 8978 2.224769 ACTTCAAATCAGAAAGCCCCGA 60.225 45.455 0.00 0.00 0.00 5.14
3459 8979 1.821216 TCAAATCAGAAAGCCCCGAC 58.179 50.000 0.00 0.00 0.00 4.79
3460 8980 1.351017 TCAAATCAGAAAGCCCCGACT 59.649 47.619 0.00 0.00 0.00 4.18
3461 8981 1.740025 CAAATCAGAAAGCCCCGACTC 59.260 52.381 0.00 0.00 0.00 3.36
3462 8982 0.253327 AATCAGAAAGCCCCGACTCC 59.747 55.000 0.00 0.00 0.00 3.85
3463 8983 1.627297 ATCAGAAAGCCCCGACTCCC 61.627 60.000 0.00 0.00 0.00 4.30
3464 8984 2.203938 AGAAAGCCCCGACTCCCA 60.204 61.111 0.00 0.00 0.00 4.37
3465 8985 1.616628 AGAAAGCCCCGACTCCCAT 60.617 57.895 0.00 0.00 0.00 4.00
3466 8986 0.326238 AGAAAGCCCCGACTCCCATA 60.326 55.000 0.00 0.00 0.00 2.74
3467 8987 0.544697 GAAAGCCCCGACTCCCATAA 59.455 55.000 0.00 0.00 0.00 1.90
3468 8988 0.996583 AAAGCCCCGACTCCCATAAA 59.003 50.000 0.00 0.00 0.00 1.40
3469 8989 0.546598 AAGCCCCGACTCCCATAAAG 59.453 55.000 0.00 0.00 0.00 1.85
3470 8990 0.326238 AGCCCCGACTCCCATAAAGA 60.326 55.000 0.00 0.00 0.00 2.52
3471 8991 0.544697 GCCCCGACTCCCATAAAGAA 59.455 55.000 0.00 0.00 0.00 2.52
3472 8992 1.143073 GCCCCGACTCCCATAAAGAAT 59.857 52.381 0.00 0.00 0.00 2.40
3473 8993 2.851195 CCCCGACTCCCATAAAGAATG 58.149 52.381 0.00 0.00 35.15 2.67
3474 8994 2.222027 CCCGACTCCCATAAAGAATGC 58.778 52.381 0.00 0.00 33.92 3.56
3475 8995 2.158755 CCCGACTCCCATAAAGAATGCT 60.159 50.000 0.00 0.00 33.92 3.79
3476 8996 3.545703 CCGACTCCCATAAAGAATGCTT 58.454 45.455 0.00 0.00 33.92 3.91
3477 8997 3.313526 CCGACTCCCATAAAGAATGCTTG 59.686 47.826 0.00 0.00 33.79 4.01
3478 8998 3.242870 CGACTCCCATAAAGAATGCTTGC 60.243 47.826 0.00 0.00 33.79 4.01
3479 8999 3.696051 GACTCCCATAAAGAATGCTTGCA 59.304 43.478 0.00 0.00 33.79 4.08
3480 9000 3.698040 ACTCCCATAAAGAATGCTTGCAG 59.302 43.478 0.87 0.00 33.79 4.41
3481 9001 3.949754 CTCCCATAAAGAATGCTTGCAGA 59.050 43.478 0.87 0.00 33.79 4.26
3482 9002 4.539726 TCCCATAAAGAATGCTTGCAGAT 58.460 39.130 0.87 0.00 33.79 2.90
3483 9003 4.581824 TCCCATAAAGAATGCTTGCAGATC 59.418 41.667 0.87 2.62 33.79 2.75
3484 9004 4.583489 CCCATAAAGAATGCTTGCAGATCT 59.417 41.667 0.87 4.86 33.79 2.75
3485 9005 5.766670 CCCATAAAGAATGCTTGCAGATCTA 59.233 40.000 12.09 1.85 33.79 1.98
3515 9035 6.902948 CACATCAACTTGAAAAACTGCAATTG 59.097 34.615 0.00 0.00 0.00 2.32
3524 9044 6.571605 TGAAAAACTGCAATTGATGTGAAGA 58.428 32.000 10.34 0.00 0.00 2.87
3557 9077 2.289882 TGTTGATGTGAGGAGCTTCAGG 60.290 50.000 0.00 0.00 0.00 3.86
3564 9084 0.037447 GAGGAGCTTCAGGTTTGGCT 59.963 55.000 0.00 0.00 37.77 4.75
3618 9138 4.370917 TGCCAGTTTCAATGAAGAAAAGC 58.629 39.130 0.00 0.00 39.05 3.51
3626 9146 1.514678 ATGAAGAAAAGCGCCGCACA 61.515 50.000 13.36 0.00 0.00 4.57
3637 9157 1.413767 CGCCGCACACACTAGCTTAG 61.414 60.000 0.00 0.00 0.00 2.18
3641 9161 2.921754 CCGCACACACTAGCTTAGTTAC 59.078 50.000 0.00 0.00 36.76 2.50
3651 9171 5.288712 CACTAGCTTAGTTACATCAACGTGG 59.711 44.000 0.00 0.00 42.35 4.94
3692 9212 3.960102 ACAAGGAAAAACAGCATCCAGAA 59.040 39.130 0.00 0.00 35.62 3.02
3732 9272 2.747460 GCTCGCTGCCCACATCAA 60.747 61.111 0.00 0.00 35.15 2.57
3789 9329 2.024414 GAAACTTCAACACCTGCACCT 58.976 47.619 0.00 0.00 0.00 4.00
3790 9330 3.211045 GAAACTTCAACACCTGCACCTA 58.789 45.455 0.00 0.00 0.00 3.08
3791 9331 2.256117 ACTTCAACACCTGCACCTAC 57.744 50.000 0.00 0.00 0.00 3.18
3820 9360 6.042143 CACAAGGCAAACACAAAGAAGTTAT 58.958 36.000 0.00 0.00 0.00 1.89
3875 9415 3.428999 GCTGTCCGCTAGAGAAATGTGTA 60.429 47.826 0.00 0.00 35.14 2.90
3876 9416 4.355437 CTGTCCGCTAGAGAAATGTGTAG 58.645 47.826 0.00 0.00 0.00 2.74
3967 9507 1.068264 TCGCCTAGCTTGAGCATATCG 60.068 52.381 5.70 3.98 45.16 2.92
4002 9548 2.355108 GCAGGTAGCCAAGAGATCACAA 60.355 50.000 0.00 0.00 37.23 3.33
4017 9563 4.641989 AGATCACAACTTTCACAGCAACTT 59.358 37.500 0.00 0.00 0.00 2.66
4026 9572 7.992180 ACTTTCACAGCAACTTTTTATTGAG 57.008 32.000 0.00 0.00 0.00 3.02
4033 9579 5.215160 AGCAACTTTTTATTGAGCTGAACG 58.785 37.500 0.00 0.00 0.00 3.95
4034 9580 4.382754 GCAACTTTTTATTGAGCTGAACGG 59.617 41.667 0.00 0.00 0.00 4.44
4048 9601 3.619038 GCTGAACGGTCTATTTTCAGAGG 59.381 47.826 13.42 0.00 46.16 3.69
4051 9604 1.209747 ACGGTCTATTTTCAGAGGCCC 59.790 52.381 0.00 0.00 33.61 5.80
4054 9607 3.282885 GGTCTATTTTCAGAGGCCCAAG 58.717 50.000 0.00 0.00 30.71 3.61
4063 9616 2.708861 TCAGAGGCCCAAGAAAGTAACA 59.291 45.455 0.00 0.00 0.00 2.41
4067 9620 3.222603 AGGCCCAAGAAAGTAACAACAG 58.777 45.455 0.00 0.00 0.00 3.16
4068 9621 2.956333 GGCCCAAGAAAGTAACAACAGT 59.044 45.455 0.00 0.00 0.00 3.55
4081 9637 6.058183 AGTAACAACAGTTTCTGAGCTGAAT 58.942 36.000 15.10 4.41 37.52 2.57
4082 9638 5.429957 AACAACAGTTTCTGAGCTGAATC 57.570 39.130 15.10 0.00 37.52 2.52
4087 9643 8.097038 ACAACAGTTTCTGAGCTGAATCTATAA 58.903 33.333 15.10 0.00 37.52 0.98
4091 9647 9.322773 CAGTTTCTGAGCTGAATCTATAAATGA 57.677 33.333 0.00 0.00 36.32 2.57
4120 9676 6.985653 TTTCTTTGGGTGTTAATGATCCAA 57.014 33.333 0.00 0.00 35.91 3.53
4122 9678 5.640147 TCTTTGGGTGTTAATGATCCAACT 58.360 37.500 2.42 0.00 37.24 3.16
4123 9679 6.074648 TCTTTGGGTGTTAATGATCCAACTT 58.925 36.000 2.42 0.00 37.24 2.66
4132 9689 9.431887 GTGTTAATGATCCAACTTACTACTGAA 57.568 33.333 0.00 0.00 0.00 3.02
4146 9703 9.962783 ACTTACTACTGAACTTTAGTTACACAG 57.037 33.333 7.76 7.76 38.56 3.66
4150 9707 8.450385 CTACTGAACTTTAGTTACACAGTAGC 57.550 38.462 23.00 2.85 44.49 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.761504 AAAACAATGATTGATGACATACAACAA 57.238 25.926 12.80 0.00 43.34 2.83
135 136 2.618241 CACAGCCAACACTAACACACAT 59.382 45.455 0.00 0.00 0.00 3.21
139 140 1.268539 GCACACAGCCAACACTAACAC 60.269 52.381 0.00 0.00 37.23 3.32
166 167 0.921896 ACACCAGGCCTCTGCATAAT 59.078 50.000 0.00 0.00 39.61 1.28
180 181 7.276878 CGATACAATTGTAATGAGTACACACCA 59.723 37.037 21.57 0.00 42.56 4.17
660 661 3.642705 AGAAGAATGAAAGCAAAACGGC 58.357 40.909 0.00 0.00 0.00 5.68
670 671 3.256631 GCTCTGGGCAAAGAAGAATGAAA 59.743 43.478 0.00 0.00 41.35 2.69
685 686 2.555199 GCACAGTAAGTATGCTCTGGG 58.445 52.381 4.85 1.72 36.40 4.45
876 877 9.359653 AGCAACTAAATCTATGCATATTCCTTT 57.640 29.630 6.92 7.36 41.18 3.11
877 878 8.930846 AGCAACTAAATCTATGCATATTCCTT 57.069 30.769 6.92 1.82 41.18 3.36
885 886 9.613428 ACACTTATTAGCAACTAAATCTATGCA 57.387 29.630 0.00 0.00 41.18 3.96
1632 6653 0.539051 AAGCCACCGGAGAATCAGAG 59.461 55.000 9.46 0.00 36.25 3.35
1669 6690 0.977395 GCAAGTGACCCTGTACCTCT 59.023 55.000 0.00 0.00 0.00 3.69
1710 6750 3.259876 TGTACGTAGCTTTCCAGTTCCAT 59.740 43.478 0.00 0.00 0.00 3.41
1809 6953 3.872771 GTGAAACCAGACGGAACAAGTAA 59.127 43.478 0.00 0.00 35.59 2.24
1847 6991 1.955529 CTGGAACATGACGAACGCGG 61.956 60.000 12.47 0.00 39.23 6.46
1848 6992 1.282248 ACTGGAACATGACGAACGCG 61.282 55.000 3.53 3.53 40.49 6.01
1875 7019 9.491675 TCGACTCTGTTGTAACCATTTTTATTA 57.508 29.630 0.00 0.00 0.00 0.98
1956 7187 1.275573 GACCCCAGAGTACTGAACACC 59.724 57.143 0.00 0.00 46.03 4.16
1984 7215 2.976185 TGGTCCACAGGAAACTACATGA 59.024 45.455 0.00 0.00 40.21 3.07
2182 7612 0.874390 TCAGAGCAACGCCATTTGTC 59.126 50.000 0.00 0.00 0.00 3.18
2202 7632 4.289672 ACATCCTGTGAAATCACTAGGGTT 59.710 41.667 21.36 11.88 46.55 4.11
2299 7729 0.603569 TTCTCGCAAGGTGAGGACTC 59.396 55.000 6.93 0.00 40.20 3.36
2310 7740 1.667236 CTACCATGCCATTCTCGCAA 58.333 50.000 0.00 0.00 40.22 4.85
2328 7758 0.769873 GCATCATCCCCATGAGTCCT 59.230 55.000 0.00 0.00 42.53 3.85
2331 7761 0.184451 GTGGCATCATCCCCATGAGT 59.816 55.000 0.00 0.00 42.53 3.41
2367 7797 0.107654 ATAGTGCAGGACGAAAGCCC 60.108 55.000 0.00 0.00 0.00 5.19
2641 8080 5.957798 ACAACATATGCACCTCAAATCTTG 58.042 37.500 1.58 0.00 0.00 3.02
2679 8118 7.677892 TCTTCACGCTATCTATAGAGGAAGTA 58.322 38.462 8.70 0.00 37.91 2.24
2685 8124 4.941263 AGCCTCTTCACGCTATCTATAGAG 59.059 45.833 8.70 0.44 36.43 2.43
2688 8127 4.827835 ACAAGCCTCTTCACGCTATCTATA 59.172 41.667 0.00 0.00 34.11 1.31
2690 8129 3.024547 ACAAGCCTCTTCACGCTATCTA 58.975 45.455 0.00 0.00 34.11 1.98
2754 8193 1.473965 CCATGCCAGAGAGTTACGCAT 60.474 52.381 0.00 0.00 40.69 4.73
2760 8199 1.366319 AAGTCCCATGCCAGAGAGTT 58.634 50.000 0.00 0.00 0.00 3.01
2778 8217 3.151554 CAGCATCAGCCTGGCATATAAA 58.848 45.455 22.65 0.00 43.56 1.40
2789 8228 2.012673 CTACAAGTTCCAGCATCAGCC 58.987 52.381 0.00 0.00 43.56 4.85
2819 8258 0.179045 GATGCCAGGCTTATCACCGT 60.179 55.000 14.15 0.00 0.00 4.83
2822 8261 4.841422 AGATATGATGCCAGGCTTATCAC 58.159 43.478 15.13 5.05 34.04 3.06
2877 8316 1.405526 GGCATCAGACGCTCCAGTTTA 60.406 52.381 0.00 0.00 0.00 2.01
2988 8427 1.675524 GAACGGAAGCGAAGACGAGC 61.676 60.000 0.00 0.00 42.66 5.03
2997 8436 2.856032 CTGCACTGAACGGAAGCG 59.144 61.111 0.00 0.00 0.00 4.68
3006 8445 4.611961 GCATCTCTGCTGCACTGA 57.388 55.556 0.00 0.00 45.32 3.41
3018 8457 3.733507 CTGGCTGGCATGGGCATCT 62.734 63.158 3.74 0.00 43.71 2.90
3051 8490 0.667487 ACACAACGGTCATGAGCTCG 60.667 55.000 21.73 15.55 0.00 5.03
3057 8496 0.884259 TGAGCCACACAACGGTCATG 60.884 55.000 0.00 0.00 0.00 3.07
3114 8553 2.348411 AAGATTCAATACCGCCAGGG 57.652 50.000 0.00 0.00 43.47 4.45
3120 8559 4.635765 TGGAGCAGAAAAGATTCAATACCG 59.364 41.667 0.00 0.00 38.06 4.02
3141 8580 1.484240 CTCTCTTAACAGAGGGCCTGG 59.516 57.143 12.95 5.31 46.17 4.45
3176 8615 4.837860 TCAAGCCCCAACATAAAGAACAAT 59.162 37.500 0.00 0.00 0.00 2.71
3191 8708 2.028112 GGTTTCAAAAGGATCAAGCCCC 60.028 50.000 0.00 0.00 0.00 5.80
3310 8828 3.397955 ACAGGGGGAACAAAAGACTACAT 59.602 43.478 0.00 0.00 0.00 2.29
3311 8829 2.781174 ACAGGGGGAACAAAAGACTACA 59.219 45.455 0.00 0.00 0.00 2.74
3312 8830 3.503800 ACAGGGGGAACAAAAGACTAC 57.496 47.619 0.00 0.00 0.00 2.73
3313 8831 5.853572 ATAACAGGGGGAACAAAAGACTA 57.146 39.130 0.00 0.00 0.00 2.59
3314 8832 4.741928 ATAACAGGGGGAACAAAAGACT 57.258 40.909 0.00 0.00 0.00 3.24
3315 8833 4.587262 ACAATAACAGGGGGAACAAAAGAC 59.413 41.667 0.00 0.00 0.00 3.01
3316 8834 4.810345 ACAATAACAGGGGGAACAAAAGA 58.190 39.130 0.00 0.00 0.00 2.52
3317 8835 5.545063 AACAATAACAGGGGGAACAAAAG 57.455 39.130 0.00 0.00 0.00 2.27
3331 8851 8.076178 AGCTAGTCACAATTCACAAACAATAAC 58.924 33.333 0.00 0.00 0.00 1.89
3360 8880 2.771089 ACAAAATCGAAGCAGCAGAGA 58.229 42.857 0.00 0.00 0.00 3.10
3363 8883 3.242870 GGGATACAAAATCGAAGCAGCAG 60.243 47.826 0.00 0.00 39.74 4.24
3364 8884 2.682856 GGGATACAAAATCGAAGCAGCA 59.317 45.455 0.00 0.00 39.74 4.41
3365 8885 2.945668 AGGGATACAAAATCGAAGCAGC 59.054 45.455 0.00 0.00 39.74 5.25
3366 8886 4.034510 GTGAGGGATACAAAATCGAAGCAG 59.965 45.833 0.00 0.00 39.74 4.24
3367 8887 3.938963 GTGAGGGATACAAAATCGAAGCA 59.061 43.478 0.00 0.00 39.74 3.91
3368 8888 4.192317 AGTGAGGGATACAAAATCGAAGC 58.808 43.478 0.00 0.00 39.74 3.86
3369 8889 5.665459 AGAGTGAGGGATACAAAATCGAAG 58.335 41.667 0.00 0.00 39.74 3.79
3370 8890 5.395324 GGAGAGTGAGGGATACAAAATCGAA 60.395 44.000 0.00 0.00 39.74 3.71
3371 8891 4.099573 GGAGAGTGAGGGATACAAAATCGA 59.900 45.833 0.00 0.00 39.74 3.59
3373 8893 5.359194 TGGAGAGTGAGGGATACAAAATC 57.641 43.478 0.00 0.00 39.74 2.17
3374 8894 5.453903 CGATGGAGAGTGAGGGATACAAAAT 60.454 44.000 0.00 0.00 39.74 1.82
3376 8896 3.384789 CGATGGAGAGTGAGGGATACAAA 59.615 47.826 0.00 0.00 39.74 2.83
3378 8898 2.174854 TCGATGGAGAGTGAGGGATACA 59.825 50.000 0.00 0.00 39.74 2.29
3379 8899 2.865079 TCGATGGAGAGTGAGGGATAC 58.135 52.381 0.00 0.00 0.00 2.24
3380 8900 3.074538 TGATCGATGGAGAGTGAGGGATA 59.925 47.826 0.54 0.00 0.00 2.59
3381 8901 2.158400 TGATCGATGGAGAGTGAGGGAT 60.158 50.000 0.54 0.00 0.00 3.85
3382 8902 1.215423 TGATCGATGGAGAGTGAGGGA 59.785 52.381 0.54 0.00 0.00 4.20
3383 8903 1.339610 GTGATCGATGGAGAGTGAGGG 59.660 57.143 0.54 0.00 0.00 4.30
3384 8904 2.305928 AGTGATCGATGGAGAGTGAGG 58.694 52.381 0.54 0.00 0.00 3.86
3385 8905 4.383850 AAAGTGATCGATGGAGAGTGAG 57.616 45.455 0.54 0.00 0.00 3.51
3386 8906 4.498241 CAAAAGTGATCGATGGAGAGTGA 58.502 43.478 0.54 0.00 0.00 3.41
3387 8907 3.063180 GCAAAAGTGATCGATGGAGAGTG 59.937 47.826 0.54 0.00 0.00 3.51
3388 8908 3.265791 GCAAAAGTGATCGATGGAGAGT 58.734 45.455 0.54 0.00 0.00 3.24
3389 8909 2.283617 CGCAAAAGTGATCGATGGAGAG 59.716 50.000 0.54 0.00 0.00 3.20
3390 8910 2.270923 CGCAAAAGTGATCGATGGAGA 58.729 47.619 0.54 0.00 0.00 3.71
3391 8911 1.328680 CCGCAAAAGTGATCGATGGAG 59.671 52.381 0.54 0.00 0.00 3.86
3392 8912 1.066502 TCCGCAAAAGTGATCGATGGA 60.067 47.619 0.54 0.00 0.00 3.41
3393 8913 1.368641 TCCGCAAAAGTGATCGATGG 58.631 50.000 0.54 0.00 0.00 3.51
3394 8914 2.789092 GCTTCCGCAAAAGTGATCGATG 60.789 50.000 0.54 0.00 35.78 3.84
3395 8915 1.398390 GCTTCCGCAAAAGTGATCGAT 59.602 47.619 0.00 0.00 35.78 3.59
3396 8916 0.796312 GCTTCCGCAAAAGTGATCGA 59.204 50.000 0.00 0.00 35.78 3.59
3397 8917 0.798776 AGCTTCCGCAAAAGTGATCG 59.201 50.000 0.00 0.00 39.10 3.69
3398 8918 1.806542 TCAGCTTCCGCAAAAGTGATC 59.193 47.619 0.00 0.00 39.10 2.92
3399 8919 1.808945 CTCAGCTTCCGCAAAAGTGAT 59.191 47.619 0.00 0.00 39.10 3.06
3400 8920 1.229428 CTCAGCTTCCGCAAAAGTGA 58.771 50.000 0.00 0.70 39.10 3.41
3401 8921 0.947244 ACTCAGCTTCCGCAAAAGTG 59.053 50.000 0.00 0.00 39.10 3.16
3402 8922 1.230324 GACTCAGCTTCCGCAAAAGT 58.770 50.000 0.00 0.00 39.10 2.66
3403 8923 0.519077 GGACTCAGCTTCCGCAAAAG 59.481 55.000 0.00 0.00 39.10 2.27
3404 8924 0.108585 AGGACTCAGCTTCCGCAAAA 59.891 50.000 0.00 0.00 38.29 2.44
3405 8925 0.108585 AAGGACTCAGCTTCCGCAAA 59.891 50.000 0.00 0.00 38.29 3.68
3406 8926 0.108585 AAAGGACTCAGCTTCCGCAA 59.891 50.000 0.00 0.00 38.29 4.85
3407 8927 0.320771 GAAAGGACTCAGCTTCCGCA 60.321 55.000 0.00 0.00 38.29 5.69
3408 8928 0.036858 AGAAAGGACTCAGCTTCCGC 60.037 55.000 0.00 0.00 38.29 5.54
3409 8929 2.464157 AAGAAAGGACTCAGCTTCCG 57.536 50.000 0.00 0.00 38.29 4.30
3410 8930 3.504134 GGAAAAGAAAGGACTCAGCTTCC 59.496 47.826 0.00 0.00 0.00 3.46
3411 8931 4.137543 TGGAAAAGAAAGGACTCAGCTTC 58.862 43.478 0.00 0.00 0.00 3.86
3412 8932 4.140536 CTGGAAAAGAAAGGACTCAGCTT 58.859 43.478 0.00 0.00 0.00 3.74
3413 8933 3.749226 CTGGAAAAGAAAGGACTCAGCT 58.251 45.455 0.00 0.00 0.00 4.24
3414 8934 2.227626 GCTGGAAAAGAAAGGACTCAGC 59.772 50.000 0.00 0.00 39.32 4.26
3415 8935 3.480470 TGCTGGAAAAGAAAGGACTCAG 58.520 45.455 0.00 0.00 0.00 3.35
3416 8936 3.576078 TGCTGGAAAAGAAAGGACTCA 57.424 42.857 0.00 0.00 0.00 3.41
3417 8937 3.885901 AGTTGCTGGAAAAGAAAGGACTC 59.114 43.478 0.00 0.00 0.00 3.36
3418 8938 3.903467 AGTTGCTGGAAAAGAAAGGACT 58.097 40.909 0.00 0.00 0.00 3.85
3419 8939 4.097892 TGAAGTTGCTGGAAAAGAAAGGAC 59.902 41.667 0.00 0.00 0.00 3.85
3420 8940 4.277476 TGAAGTTGCTGGAAAAGAAAGGA 58.723 39.130 0.00 0.00 0.00 3.36
3421 8941 4.654091 TGAAGTTGCTGGAAAAGAAAGG 57.346 40.909 0.00 0.00 0.00 3.11
3422 8942 6.757947 TGATTTGAAGTTGCTGGAAAAGAAAG 59.242 34.615 0.00 0.00 0.00 2.62
3423 8943 6.638610 TGATTTGAAGTTGCTGGAAAAGAAA 58.361 32.000 0.00 0.00 0.00 2.52
3424 8944 6.096705 TCTGATTTGAAGTTGCTGGAAAAGAA 59.903 34.615 0.00 0.00 0.00 2.52
3425 8945 5.593909 TCTGATTTGAAGTTGCTGGAAAAGA 59.406 36.000 0.00 0.00 0.00 2.52
3426 8946 5.835257 TCTGATTTGAAGTTGCTGGAAAAG 58.165 37.500 0.00 0.00 0.00 2.27
3427 8947 5.850557 TCTGATTTGAAGTTGCTGGAAAA 57.149 34.783 0.00 0.00 0.00 2.29
3428 8948 5.850557 TTCTGATTTGAAGTTGCTGGAAA 57.149 34.783 0.00 0.00 0.00 3.13
3429 8949 5.737063 GCTTTCTGATTTGAAGTTGCTGGAA 60.737 40.000 0.00 0.00 0.00 3.53
3430 8950 4.261741 GCTTTCTGATTTGAAGTTGCTGGA 60.262 41.667 0.00 0.00 0.00 3.86
3431 8951 3.985925 GCTTTCTGATTTGAAGTTGCTGG 59.014 43.478 0.00 0.00 0.00 4.85
3432 8952 3.985925 GGCTTTCTGATTTGAAGTTGCTG 59.014 43.478 0.00 0.00 0.00 4.41
3433 8953 3.006217 GGGCTTTCTGATTTGAAGTTGCT 59.994 43.478 0.00 0.00 0.00 3.91
3434 8954 3.320626 GGGCTTTCTGATTTGAAGTTGC 58.679 45.455 0.00 0.00 0.00 4.17
3435 8955 3.612479 CGGGGCTTTCTGATTTGAAGTTG 60.612 47.826 0.00 0.00 0.00 3.16
3436 8956 2.558359 CGGGGCTTTCTGATTTGAAGTT 59.442 45.455 0.00 0.00 0.00 2.66
3437 8957 2.162681 CGGGGCTTTCTGATTTGAAGT 58.837 47.619 0.00 0.00 0.00 3.01
3438 8958 2.162408 GTCGGGGCTTTCTGATTTGAAG 59.838 50.000 0.00 0.00 0.00 3.02
3439 8959 2.159382 GTCGGGGCTTTCTGATTTGAA 58.841 47.619 0.00 0.00 0.00 2.69
3440 8960 1.351017 AGTCGGGGCTTTCTGATTTGA 59.649 47.619 0.00 0.00 0.00 2.69
3441 8961 1.740025 GAGTCGGGGCTTTCTGATTTG 59.260 52.381 0.00 0.00 0.00 2.32
3442 8962 1.340114 GGAGTCGGGGCTTTCTGATTT 60.340 52.381 0.00 0.00 0.00 2.17
3443 8963 0.253327 GGAGTCGGGGCTTTCTGATT 59.747 55.000 0.00 0.00 0.00 2.57
3444 8964 1.627297 GGGAGTCGGGGCTTTCTGAT 61.627 60.000 0.00 0.00 0.00 2.90
3445 8965 2.291043 GGGAGTCGGGGCTTTCTGA 61.291 63.158 0.00 0.00 0.00 3.27
3446 8966 1.915078 ATGGGAGTCGGGGCTTTCTG 61.915 60.000 0.00 0.00 0.00 3.02
3447 8967 0.326238 TATGGGAGTCGGGGCTTTCT 60.326 55.000 0.00 0.00 0.00 2.52
3448 8968 0.544697 TTATGGGAGTCGGGGCTTTC 59.455 55.000 0.00 0.00 0.00 2.62
3449 8969 0.996583 TTTATGGGAGTCGGGGCTTT 59.003 50.000 0.00 0.00 0.00 3.51
3450 8970 0.546598 CTTTATGGGAGTCGGGGCTT 59.453 55.000 0.00 0.00 0.00 4.35
3451 8971 0.326238 TCTTTATGGGAGTCGGGGCT 60.326 55.000 0.00 0.00 0.00 5.19
3452 8972 0.544697 TTCTTTATGGGAGTCGGGGC 59.455 55.000 0.00 0.00 0.00 5.80
3453 8973 2.851195 CATTCTTTATGGGAGTCGGGG 58.149 52.381 0.00 0.00 0.00 5.73
3454 8974 2.158755 AGCATTCTTTATGGGAGTCGGG 60.159 50.000 0.00 0.00 34.66 5.14
3455 8975 3.199880 AGCATTCTTTATGGGAGTCGG 57.800 47.619 0.00 0.00 34.66 4.79
3456 8976 3.242870 GCAAGCATTCTTTATGGGAGTCG 60.243 47.826 0.00 0.00 34.66 4.18
3457 8977 3.696051 TGCAAGCATTCTTTATGGGAGTC 59.304 43.478 0.00 0.00 34.66 3.36
3458 8978 3.698040 CTGCAAGCATTCTTTATGGGAGT 59.302 43.478 0.00 0.00 34.66 3.85
3459 8979 3.949754 TCTGCAAGCATTCTTTATGGGAG 59.050 43.478 0.00 0.00 34.66 4.30
3460 8980 3.966979 TCTGCAAGCATTCTTTATGGGA 58.033 40.909 0.00 0.00 34.66 4.37
3461 8981 4.583489 AGATCTGCAAGCATTCTTTATGGG 59.417 41.667 0.00 0.00 34.66 4.00
3462 8982 5.769484 AGATCTGCAAGCATTCTTTATGG 57.231 39.130 0.00 0.00 34.66 2.74
3463 8983 7.803659 CACATAGATCTGCAAGCATTCTTTATG 59.196 37.037 5.18 11.73 37.31 1.90
3464 8984 7.521748 GCACATAGATCTGCAAGCATTCTTTAT 60.522 37.037 5.18 0.91 33.31 1.40
3465 8985 6.238566 GCACATAGATCTGCAAGCATTCTTTA 60.239 38.462 5.18 0.00 33.31 1.85
3466 8986 5.450137 GCACATAGATCTGCAAGCATTCTTT 60.450 40.000 5.18 3.67 33.31 2.52
3467 8987 4.036498 GCACATAGATCTGCAAGCATTCTT 59.964 41.667 5.18 1.01 33.31 2.52
3468 8988 3.564644 GCACATAGATCTGCAAGCATTCT 59.435 43.478 5.18 11.01 33.31 2.40
3469 8989 3.314357 TGCACATAGATCTGCAAGCATTC 59.686 43.478 5.18 0.00 40.45 2.67
3470 8990 3.066342 GTGCACATAGATCTGCAAGCATT 59.934 43.478 13.17 0.00 44.82 3.56
3471 8991 2.617308 GTGCACATAGATCTGCAAGCAT 59.383 45.455 13.17 0.00 44.82 3.79
3472 8992 2.011947 GTGCACATAGATCTGCAAGCA 58.988 47.619 13.17 8.00 44.82 3.91
3473 8993 2.011947 TGTGCACATAGATCTGCAAGC 58.988 47.619 17.42 5.34 44.82 4.01
3474 8994 3.875134 TGATGTGCACATAGATCTGCAAG 59.125 43.478 31.45 0.00 44.82 4.01
3475 8995 3.876341 TGATGTGCACATAGATCTGCAA 58.124 40.909 31.45 2.20 44.82 4.08
3476 8996 3.547054 TGATGTGCACATAGATCTGCA 57.453 42.857 31.45 19.85 41.13 4.41
3477 8997 3.875727 AGTTGATGTGCACATAGATCTGC 59.124 43.478 31.45 17.52 36.57 4.26
3478 8998 5.583457 TCAAGTTGATGTGCACATAGATCTG 59.417 40.000 31.45 23.38 36.57 2.90
3479 8999 5.737860 TCAAGTTGATGTGCACATAGATCT 58.262 37.500 31.45 21.99 36.57 2.75
3480 9000 6.426980 TTCAAGTTGATGTGCACATAGATC 57.573 37.500 31.45 20.41 36.57 2.75
3481 9001 6.822667 TTTCAAGTTGATGTGCACATAGAT 57.177 33.333 31.45 11.76 36.57 1.98
3482 9002 6.631971 TTTTCAAGTTGATGTGCACATAGA 57.368 33.333 31.45 19.73 36.57 1.98
3483 9003 6.919662 AGTTTTTCAAGTTGATGTGCACATAG 59.080 34.615 31.45 16.53 36.57 2.23
3484 9004 6.696583 CAGTTTTTCAAGTTGATGTGCACATA 59.303 34.615 31.45 15.27 36.57 2.29
3485 9005 5.521010 CAGTTTTTCAAGTTGATGTGCACAT 59.479 36.000 31.82 31.82 39.70 3.21
3515 9035 2.749621 ACGCCTTTCCAATCTTCACATC 59.250 45.455 0.00 0.00 0.00 3.06
3524 9044 2.030007 CACATCAACACGCCTTTCCAAT 60.030 45.455 0.00 0.00 0.00 3.16
3557 9077 2.409870 CCAGATGCCCGAGCCAAAC 61.410 63.158 0.00 0.00 38.69 2.93
3564 9084 4.802051 GCTTGCCCAGATGCCCGA 62.802 66.667 0.00 0.00 0.00 5.14
3618 9138 1.413767 CTAAGCTAGTGTGTGCGGCG 61.414 60.000 0.51 0.51 0.00 6.46
3626 9146 5.862323 CACGTTGATGTAACTAAGCTAGTGT 59.138 40.000 0.00 0.00 39.39 3.55
3637 9157 5.693104 TGACTCTTTACCACGTTGATGTAAC 59.307 40.000 0.00 0.00 35.90 2.50
3641 9161 4.055360 TGTGACTCTTTACCACGTTGATG 58.945 43.478 0.00 0.00 33.78 3.07
3651 9171 5.923684 CCTTGTCTCTCTTGTGACTCTTTAC 59.076 44.000 0.00 0.00 37.52 2.01
3692 9212 4.274602 TGCAAATCATGGTGATTGCTTT 57.725 36.364 14.74 1.68 45.57 3.51
3732 9272 1.445582 GCATTTCGTCGTCGACCCT 60.446 57.895 19.29 0.00 46.03 4.34
3738 9278 1.855360 GGAGAGATGCATTTCGTCGTC 59.145 52.381 11.26 4.00 35.85 4.20
3752 9292 3.209812 CATCCGGTCGCGGAGAGA 61.210 66.667 6.13 0.00 41.77 3.10
3789 9329 3.814625 TGTGTTTGCCTTGTGAGATGTA 58.185 40.909 0.00 0.00 0.00 2.29
3790 9330 2.653726 TGTGTTTGCCTTGTGAGATGT 58.346 42.857 0.00 0.00 0.00 3.06
3791 9331 3.713858 TTGTGTTTGCCTTGTGAGATG 57.286 42.857 0.00 0.00 0.00 2.90
3820 9360 1.142314 GTTGTGTCGCGGCCCTATA 59.858 57.895 8.89 0.00 0.00 1.31
3875 9415 6.256757 CGAAAACTCTGAAACTGAAACTCTCT 59.743 38.462 0.00 0.00 0.00 3.10
3876 9416 6.255887 TCGAAAACTCTGAAACTGAAACTCTC 59.744 38.462 0.00 0.00 0.00 3.20
3967 9507 2.573340 CTGCCGCATTGGAAACCC 59.427 61.111 0.00 0.00 42.00 4.11
4002 9548 6.476706 GCTCAATAAAAAGTTGCTGTGAAAGT 59.523 34.615 0.00 0.00 0.00 2.66
4017 9563 7.681939 AAATAGACCGTTCAGCTCAATAAAA 57.318 32.000 0.00 0.00 0.00 1.52
4026 9572 3.619038 CCTCTGAAAATAGACCGTTCAGC 59.381 47.826 7.59 0.00 45.13 4.26
4032 9578 1.209504 TGGGCCTCTGAAAATAGACCG 59.790 52.381 4.53 0.00 0.00 4.79
4033 9579 3.054361 TCTTGGGCCTCTGAAAATAGACC 60.054 47.826 4.53 0.00 0.00 3.85
4034 9580 4.222124 TCTTGGGCCTCTGAAAATAGAC 57.778 45.455 4.53 0.00 0.00 2.59
4048 9601 4.649088 AACTGTTGTTACTTTCTTGGGC 57.351 40.909 0.00 0.00 34.15 5.36
4051 9604 6.688813 GCTCAGAAACTGTTGTTACTTTCTTG 59.311 38.462 0.00 0.00 34.96 3.02
4054 9607 6.037172 TCAGCTCAGAAACTGTTGTTACTTTC 59.963 38.462 0.00 0.00 34.96 2.62
4063 9616 9.678260 ATTTATAGATTCAGCTCAGAAACTGTT 57.322 29.630 6.78 0.00 33.44 3.16
4107 9663 9.431887 GTTCAGTAGTAAGTTGGATCATTAACA 57.568 33.333 0.00 0.00 0.00 2.41
4108 9664 9.654663 AGTTCAGTAGTAAGTTGGATCATTAAC 57.345 33.333 0.00 0.00 0.00 2.01
4112 9668 9.877178 CTAAAGTTCAGTAGTAAGTTGGATCAT 57.123 33.333 0.00 0.00 0.00 2.45
4114 9670 9.708092 AACTAAAGTTCAGTAGTAAGTTGGATC 57.292 33.333 0.00 0.00 31.64 3.36
4116 9672 9.971922 GTAACTAAAGTTCAGTAGTAAGTTGGA 57.028 33.333 0.00 0.00 39.31 3.53
4117 9673 9.754382 TGTAACTAAAGTTCAGTAGTAAGTTGG 57.246 33.333 0.00 0.00 39.31 3.77
4120 9676 9.962783 CTGTGTAACTAAAGTTCAGTAGTAAGT 57.037 33.333 0.00 0.00 39.31 2.24
4132 9689 4.922103 GCTTCGCTACTGTGTAACTAAAGT 59.078 41.667 0.00 0.00 38.04 2.66
4135 9692 3.841643 GGCTTCGCTACTGTGTAACTAA 58.158 45.455 0.00 0.00 38.04 2.24
4136 9693 3.498927 GGCTTCGCTACTGTGTAACTA 57.501 47.619 0.00 0.00 38.04 2.24


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

AutoCloner maintained by Alex Coulton.