Multiple sequence alignment - TraesCS7D01G170300

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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 TraesCS7D01G170300 chr7D 100.000 3275 0 0 1 3275 122958549 122961823 0.000000e+00 6048.0
1 TraesCS7D01G170300 chr7D 84.923 1698 194 36 916 2584 157684934 157683270 0.000000e+00 1661.0
2 TraesCS7D01G170300 chr7D 93.750 48 3 0 2579 2626 448337050 448337003 4.530000e-09 73.1
3 TraesCS7D01G170300 chr7B 92.360 1335 80 7 959 2279 84115845 84117171 0.000000e+00 1881.0
4 TraesCS7D01G170300 chr7B 84.338 1692 206 32 935 2586 84110872 84112544 0.000000e+00 1602.0
5 TraesCS7D01G170300 chr7B 84.333 1334 190 10 982 2300 224727255 224725926 0.000000e+00 1288.0
6 TraesCS7D01G170300 chr7B 86.063 287 23 6 2884 3165 84117566 84117840 3.200000e-75 292.0
7 TraesCS7D01G170300 chr7B 82.282 333 44 7 2882 3209 224725492 224725170 1.160000e-69 274.0
8 TraesCS7D01G170300 chr7B 92.405 158 8 3 2431 2586 84117247 84117402 4.250000e-54 222.0
9 TraesCS7D01G170300 chr7B 89.412 85 9 0 2795 2879 26883096 26883012 1.240000e-19 108.0
10 TraesCS7D01G170300 chr7A 85.370 1661 180 38 130 1767 126096544 126094924 0.000000e+00 1663.0
11 TraesCS7D01G170300 chr7A 86.478 1346 139 16 968 2298 157965382 157966699 0.000000e+00 1437.0
12 TraesCS7D01G170300 chr7A 86.468 1345 141 14 968 2298 157973611 157974928 0.000000e+00 1437.0
13 TraesCS7D01G170300 chr7A 85.810 1346 148 16 968 2298 157957176 157958493 0.000000e+00 1387.0
14 TraesCS7D01G170300 chr7A 93.943 809 49 0 959 1767 125925311 125926119 0.000000e+00 1223.0
15 TraesCS7D01G170300 chr7A 82.184 1044 133 30 336 1354 125980552 125981567 0.000000e+00 848.0
16 TraesCS7D01G170300 chr7A 92.906 437 28 2 1862 2298 126094418 126093985 1.660000e-177 632.0
17 TraesCS7D01G170300 chr7A 92.067 416 30 2 1862 2277 125926624 125927036 1.690000e-162 582.0
18 TraesCS7D01G170300 chr7A 86.935 398 37 5 2883 3275 126058832 126058445 1.800000e-117 433.0
19 TraesCS7D01G170300 chr7A 93.365 211 9 3 2360 2567 126093954 126093746 1.140000e-79 307.0
20 TraesCS7D01G170300 chr7A 91.111 90 8 0 43 132 125980334 125980423 4.440000e-24 122.0
21 TraesCS7D01G170300 chr7A 91.781 73 3 3 34 104 126096612 126096541 7.480000e-17 99.0
22 TraesCS7D01G170300 chr7A 100.000 44 0 0 2583 2626 696849912 696849869 7.530000e-12 82.4
23 TraesCS7D01G170300 chr7A 97.826 46 1 0 2579 2624 4475114 4475069 2.710000e-11 80.5
24 TraesCS7D01G170300 chr7A 88.889 63 5 1 2576 2636 526138012 526137950 3.500000e-10 76.8
25 TraesCS7D01G170300 chr1A 89.888 89 9 0 2791 2879 578519954 578520042 7.430000e-22 115.0
26 TraesCS7D01G170300 chr1A 85.507 69 7 2 2583 2648 584314365 584314433 5.860000e-08 69.4
27 TraesCS7D01G170300 chr4D 89.655 87 9 0 2794 2880 498033946 498034032 9.610000e-21 111.0
28 TraesCS7D01G170300 chr4D 89.157 83 9 0 2794 2876 484189473 484189555 1.610000e-18 104.0
29 TraesCS7D01G170300 chr2A 88.636 88 10 0 2794 2881 70189449 70189536 1.240000e-19 108.0
30 TraesCS7D01G170300 chrUn 88.372 86 10 0 2794 2879 299168579 299168494 1.610000e-18 104.0
31 TraesCS7D01G170300 chrUn 100.000 42 0 0 2583 2624 18205121 18205080 9.740000e-11 78.7
32 TraesCS7D01G170300 chr6D 88.372 86 10 0 2794 2879 14174041 14173956 1.610000e-18 104.0
33 TraesCS7D01G170300 chr6D 88.372 86 10 0 2794 2879 54362577 54362492 1.610000e-18 104.0
34 TraesCS7D01G170300 chr6D 88.372 86 10 0 2794 2879 414567931 414567846 1.610000e-18 104.0
35 TraesCS7D01G170300 chr6D 100.000 42 0 0 2583 2624 59623259 59623218 9.740000e-11 78.7
36 TraesCS7D01G170300 chr5D 97.778 45 1 0 2580 2624 104396709 104396665 9.740000e-11 78.7
37 TraesCS7D01G170300 chr5B 97.778 45 1 0 2580 2624 113804081 113804037 9.740000e-11 78.7


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 TraesCS7D01G170300 chr7D 122958549 122961823 3274 False 6048.00 6048 100.0000 1 3275 1 chr7D.!!$F1 3274
1 TraesCS7D01G170300 chr7D 157683270 157684934 1664 True 1661.00 1661 84.9230 916 2584 1 chr7D.!!$R1 1668
2 TraesCS7D01G170300 chr7B 84110872 84117840 6968 False 999.25 1881 88.7915 935 3165 4 chr7B.!!$F1 2230
3 TraesCS7D01G170300 chr7B 224725170 224727255 2085 True 781.00 1288 83.3075 982 3209 2 chr7B.!!$R2 2227
4 TraesCS7D01G170300 chr7A 157965382 157966699 1317 False 1437.00 1437 86.4780 968 2298 1 chr7A.!!$F2 1330
5 TraesCS7D01G170300 chr7A 157973611 157974928 1317 False 1437.00 1437 86.4680 968 2298 1 chr7A.!!$F3 1330
6 TraesCS7D01G170300 chr7A 157957176 157958493 1317 False 1387.00 1387 85.8100 968 2298 1 chr7A.!!$F1 1330
7 TraesCS7D01G170300 chr7A 125925311 125927036 1725 False 902.50 1223 93.0050 959 2277 2 chr7A.!!$F4 1318
8 TraesCS7D01G170300 chr7A 126093746 126096612 2866 True 675.25 1663 90.8555 34 2567 4 chr7A.!!$R5 2533
9 TraesCS7D01G170300 chr7A 125980334 125981567 1233 False 485.00 848 86.6475 43 1354 2 chr7A.!!$F5 1311

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
46 47 0.107410 TGGGCAACATAAGTAGGCGG 60.107 55.0 0.00 0.00 39.74 6.13 F
148 149 0.179103 GATGCATTGCCGGGGAAAAG 60.179 55.0 4.68 2.32 0.00 2.27 F
1849 7374 0.460987 CATTGACCCGGAGACAGAGC 60.461 60.0 0.73 0.00 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 7533 0.842030 ACACCCTCCTCTGATGGCAA 60.842 55.000 0.00 0.0 29.89 4.52 R
2143 7668 3.119352 GCAAGGATCCATGACTTTTGGTC 60.119 47.826 21.00 0.0 44.70 4.02 R
2740 8303 0.321653 GACCGAAGACACAGGCCAAT 60.322 55.000 5.01 0.0 0.00 3.16 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
19 20 1.788258 CATGTAGCCGAGGTAGCATG 58.212 55.000 0.00 0.00 0.00 4.06
20 21 1.069204 CATGTAGCCGAGGTAGCATGT 59.931 52.381 0.00 0.00 31.84 3.21
21 22 2.061509 TGTAGCCGAGGTAGCATGTA 57.938 50.000 0.00 0.00 0.00 2.29
22 23 2.594131 TGTAGCCGAGGTAGCATGTAT 58.406 47.619 0.00 0.00 0.00 2.29
23 24 2.963101 TGTAGCCGAGGTAGCATGTATT 59.037 45.455 0.00 0.00 0.00 1.89
24 25 4.146564 TGTAGCCGAGGTAGCATGTATTA 58.853 43.478 0.00 0.00 0.00 0.98
25 26 4.585581 TGTAGCCGAGGTAGCATGTATTAA 59.414 41.667 0.00 0.00 0.00 1.40
26 27 3.991367 AGCCGAGGTAGCATGTATTAAC 58.009 45.455 0.00 0.00 0.00 2.01
27 28 3.641906 AGCCGAGGTAGCATGTATTAACT 59.358 43.478 0.00 0.00 0.00 2.24
28 29 3.741344 GCCGAGGTAGCATGTATTAACTG 59.259 47.826 0.00 0.00 0.00 3.16
29 30 4.307432 CCGAGGTAGCATGTATTAACTGG 58.693 47.826 0.00 0.00 0.00 4.00
30 31 4.307432 CGAGGTAGCATGTATTAACTGGG 58.693 47.826 0.00 0.00 0.00 4.45
31 32 4.065789 GAGGTAGCATGTATTAACTGGGC 58.934 47.826 0.00 0.00 0.00 5.36
32 33 3.458118 AGGTAGCATGTATTAACTGGGCA 59.542 43.478 0.00 0.00 0.00 5.36
33 34 4.080015 AGGTAGCATGTATTAACTGGGCAA 60.080 41.667 0.00 0.00 0.00 4.52
34 35 4.036380 GGTAGCATGTATTAACTGGGCAAC 59.964 45.833 0.00 0.00 0.00 4.17
35 36 3.696045 AGCATGTATTAACTGGGCAACA 58.304 40.909 0.00 0.00 39.74 3.33
36 37 4.280819 AGCATGTATTAACTGGGCAACAT 58.719 39.130 0.00 0.00 39.74 2.71
37 38 5.445069 AGCATGTATTAACTGGGCAACATA 58.555 37.500 0.00 0.00 39.74 2.29
38 39 5.890985 AGCATGTATTAACTGGGCAACATAA 59.109 36.000 0.00 0.00 39.74 1.90
39 40 6.039717 AGCATGTATTAACTGGGCAACATAAG 59.960 38.462 0.00 0.00 39.74 1.73
40 41 6.183360 GCATGTATTAACTGGGCAACATAAGT 60.183 38.462 0.00 0.00 39.74 2.24
41 42 7.012894 GCATGTATTAACTGGGCAACATAAGTA 59.987 37.037 0.00 0.00 39.74 2.24
42 43 8.559536 CATGTATTAACTGGGCAACATAAGTAG 58.440 37.037 0.00 0.00 39.74 2.57
43 44 7.051623 TGTATTAACTGGGCAACATAAGTAGG 58.948 38.462 0.00 0.00 39.74 3.18
44 45 2.420058 ACTGGGCAACATAAGTAGGC 57.580 50.000 0.00 0.00 39.74 3.93
45 46 1.299541 CTGGGCAACATAAGTAGGCG 58.700 55.000 0.00 0.00 39.74 5.52
46 47 0.107410 TGGGCAACATAAGTAGGCGG 60.107 55.000 0.00 0.00 39.74 6.13
47 48 0.179468 GGGCAACATAAGTAGGCGGA 59.821 55.000 0.00 0.00 39.74 5.54
48 49 1.296727 GGCAACATAAGTAGGCGGAC 58.703 55.000 0.00 0.00 0.00 4.79
102 103 0.896923 ATGCAACCCAATTGTGCGAT 59.103 45.000 13.06 6.77 40.77 4.58
105 106 1.981254 CAACCCAATTGTGCGATGAC 58.019 50.000 4.43 0.00 33.20 3.06
110 111 1.731709 CCAATTGTGCGATGACGAAGA 59.268 47.619 4.43 0.00 42.66 2.87
128 129 4.379813 CGAAGAAGGATCAACAAACCATGG 60.380 45.833 11.19 11.19 0.00 3.66
147 148 1.612395 GGATGCATTGCCGGGGAAAA 61.612 55.000 4.68 0.00 0.00 2.29
148 149 0.179103 GATGCATTGCCGGGGAAAAG 60.179 55.000 4.68 2.32 0.00 2.27
161 162 1.679032 GGGAAAAGTCTATGTGCCGCT 60.679 52.381 0.00 0.00 0.00 5.52
164 165 2.015736 AAAGTCTATGTGCCGCTCAG 57.984 50.000 1.16 0.00 0.00 3.35
187 188 2.621998 GCGGTACATAGTAGGAGCTTCA 59.378 50.000 0.00 0.00 0.00 3.02
216 217 1.216178 CTTGGCCAGCCCATTTTCG 59.784 57.895 5.11 0.00 44.89 3.46
293 300 5.445540 GCGTATTCAGTCCGGAAAGTTAAAG 60.446 44.000 5.23 0.00 0.00 1.85
613 643 7.696755 AGCTTCATGTTTTCAAATTTTGTTCC 58.303 30.769 8.89 0.00 0.00 3.62
785 832 3.366273 CGTCGGTTGCTACAGTACCTTTA 60.366 47.826 0.00 0.00 0.00 1.85
786 833 3.922850 GTCGGTTGCTACAGTACCTTTAC 59.077 47.826 0.00 0.00 0.00 2.01
796 843 6.210984 GCTACAGTACCTTTACTATATGGGCT 59.789 42.308 0.00 0.00 36.31 5.19
838 885 2.317609 CGTCACGCACCCAAAGGAG 61.318 63.158 0.00 0.00 36.73 3.69
842 889 3.058160 CGCACCCAAAGGAGGCAG 61.058 66.667 0.00 0.00 36.98 4.85
941 989 1.853250 AAGCCTCCCTTTCCCCTTCG 61.853 60.000 0.00 0.00 0.00 3.79
945 993 1.534717 TCCCTTTCCCCTTCGTCGT 60.535 57.895 0.00 0.00 0.00 4.34
999 1072 2.751436 CCACCCTGCACAATCCCG 60.751 66.667 0.00 0.00 0.00 5.14
1488 6527 0.895530 TGTTCCACTCCGAGACATCC 59.104 55.000 1.33 0.00 0.00 3.51
1566 6605 1.078426 CCCCACCAACACGGATCTC 60.078 63.158 0.00 0.00 38.63 2.75
1825 7350 3.300852 TCAACGCCAGTTACGACATAA 57.699 42.857 0.00 0.00 38.79 1.90
1833 7358 5.220586 CGCCAGTTACGACATAAACATCATT 60.221 40.000 0.00 0.00 0.00 2.57
1842 7367 4.199310 ACATAAACATCATTGACCCGGAG 58.801 43.478 0.73 0.00 0.00 4.63
1849 7374 0.460987 CATTGACCCGGAGACAGAGC 60.461 60.000 0.73 0.00 0.00 4.09
1851 7376 1.816863 TTGACCCGGAGACAGAGCAC 61.817 60.000 0.73 0.00 0.00 4.40
1858 7383 1.267121 GGAGACAGAGCACCCAACTA 58.733 55.000 0.00 0.00 0.00 2.24
1955 7480 0.955428 GAATGCACGGTCCAAGCTGA 60.955 55.000 0.00 0.00 0.00 4.26
2008 7533 1.376424 CCGACTGGAATGCTGCTGT 60.376 57.895 0.00 0.00 37.49 4.40
2073 7598 0.957395 ACTTCCAGCGCCTTGTGATG 60.957 55.000 2.29 0.00 0.00 3.07
2124 7649 5.772672 TGATGGTGTTGTTTACCTAATTGCT 59.227 36.000 0.00 0.00 39.01 3.91
2125 7650 5.446143 TGGTGTTGTTTACCTAATTGCTG 57.554 39.130 0.00 0.00 39.01 4.41
2126 7651 4.234574 GGTGTTGTTTACCTAATTGCTGC 58.765 43.478 0.00 0.00 35.30 5.25
2127 7652 3.911964 GTGTTGTTTACCTAATTGCTGCG 59.088 43.478 0.00 0.00 0.00 5.18
2129 7654 4.276183 TGTTGTTTACCTAATTGCTGCGAA 59.724 37.500 0.00 0.00 0.00 4.70
2233 7764 2.496470 ACCGTAGAAGACCCAAGTGATC 59.504 50.000 0.00 0.00 0.00 2.92
2298 7835 3.609103 AATTCACACTGCAACGTCTTC 57.391 42.857 0.00 0.00 0.00 2.87
2299 7836 2.309528 TTCACACTGCAACGTCTTCT 57.690 45.000 0.00 0.00 0.00 2.85
2301 7838 1.933181 TCACACTGCAACGTCTTCTTG 59.067 47.619 0.00 0.00 0.00 3.02
2302 7839 0.657840 ACACTGCAACGTCTTCTTGC 59.342 50.000 2.20 2.20 43.69 4.01
2308 7845 1.129437 GCAACGTCTTCTTGCATCTCC 59.871 52.381 4.34 0.00 43.04 3.71
2309 7846 1.391485 CAACGTCTTCTTGCATCTCCG 59.609 52.381 0.00 0.00 0.00 4.63
2310 7847 0.737715 ACGTCTTCTTGCATCTCCGC 60.738 55.000 0.00 0.00 0.00 5.54
2311 7848 1.746727 CGTCTTCTTGCATCTCCGCG 61.747 60.000 0.00 0.00 33.35 6.46
2313 7850 2.047370 TTCTTGCATCTCCGCGCA 60.047 55.556 8.75 0.00 36.05 6.09
2314 7851 1.638388 CTTCTTGCATCTCCGCGCAA 61.638 55.000 8.75 0.00 45.45 4.85
2321 7859 0.371645 CATCTCCGCGCAAAGACTTC 59.628 55.000 8.75 0.00 0.00 3.01
2330 7868 2.095059 GCGCAAAGACTTCATTCCACAT 60.095 45.455 0.30 0.00 0.00 3.21
2332 7870 4.379394 GCGCAAAGACTTCATTCCACATTA 60.379 41.667 0.30 0.00 0.00 1.90
2372 7926 9.318041 CTATTTCTAAAAGAATCGTTGTGTGTG 57.682 33.333 0.00 0.00 33.67 3.82
2384 7938 3.485216 CGTTGTGTGTGTTTTCTCCTGTC 60.485 47.826 0.00 0.00 0.00 3.51
2385 7939 3.627395 TGTGTGTGTTTTCTCCTGTCT 57.373 42.857 0.00 0.00 0.00 3.41
2438 7996 4.032960 TGTTGGATGCAGTTATCTGGTT 57.967 40.909 3.05 0.00 41.57 3.67
2549 8110 4.188247 TGCTGTACGCAGTTTATCTCTT 57.812 40.909 8.05 0.00 45.47 2.85
2577 8138 5.756195 TGCTTGACATATCCATTTAGTGC 57.244 39.130 0.00 0.00 0.00 4.40
2578 8139 5.192176 TGCTTGACATATCCATTTAGTGCA 58.808 37.500 0.00 0.00 0.00 4.57
2579 8140 5.829391 TGCTTGACATATCCATTTAGTGCAT 59.171 36.000 0.00 0.00 0.00 3.96
2585 8146 9.407380 TGACATATCCATTTAGTGCATTTTACT 57.593 29.630 0.00 0.00 0.00 2.24
2586 8147 9.884465 GACATATCCATTTAGTGCATTTTACTC 57.116 33.333 0.00 0.00 0.00 2.59
2587 8148 8.850156 ACATATCCATTTAGTGCATTTTACTCC 58.150 33.333 0.00 0.00 0.00 3.85
2588 8149 6.715347 ATCCATTTAGTGCATTTTACTCCC 57.285 37.500 0.00 0.00 0.00 4.30
2589 8150 5.826643 TCCATTTAGTGCATTTTACTCCCT 58.173 37.500 0.00 0.00 0.00 4.20
2590 8151 5.885912 TCCATTTAGTGCATTTTACTCCCTC 59.114 40.000 0.00 0.00 0.00 4.30
2591 8152 5.067805 CCATTTAGTGCATTTTACTCCCTCC 59.932 44.000 0.00 0.00 0.00 4.30
2592 8153 2.403252 AGTGCATTTTACTCCCTCCG 57.597 50.000 0.00 0.00 0.00 4.63
2593 8154 1.628846 AGTGCATTTTACTCCCTCCGT 59.371 47.619 0.00 0.00 0.00 4.69
2594 8155 2.007608 GTGCATTTTACTCCCTCCGTC 58.992 52.381 0.00 0.00 0.00 4.79
2595 8156 1.065709 TGCATTTTACTCCCTCCGTCC 60.066 52.381 0.00 0.00 0.00 4.79
2596 8157 1.746171 GCATTTTACTCCCTCCGTCCC 60.746 57.143 0.00 0.00 0.00 4.46
2597 8158 1.557832 CATTTTACTCCCTCCGTCCCA 59.442 52.381 0.00 0.00 0.00 4.37
2598 8159 1.961133 TTTTACTCCCTCCGTCCCAT 58.039 50.000 0.00 0.00 0.00 4.00
2599 8160 2.852714 TTTACTCCCTCCGTCCCATA 57.147 50.000 0.00 0.00 0.00 2.74
2600 8161 2.852714 TTACTCCCTCCGTCCCATAA 57.147 50.000 0.00 0.00 0.00 1.90
2601 8162 3.339713 TTACTCCCTCCGTCCCATAAT 57.660 47.619 0.00 0.00 0.00 1.28
2602 8163 4.474303 TTACTCCCTCCGTCCCATAATA 57.526 45.455 0.00 0.00 0.00 0.98
2603 8164 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2604 8165 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2605 8166 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2606 8167 5.408824 ACTCCCTCCGTCCCATAATATAAA 58.591 41.667 0.00 0.00 0.00 1.40
2607 8168 5.847817 ACTCCCTCCGTCCCATAATATAAAA 59.152 40.000 0.00 0.00 0.00 1.52
2608 8169 6.013639 ACTCCCTCCGTCCCATAATATAAAAG 60.014 42.308 0.00 0.00 0.00 2.27
2609 8170 4.941873 CCCTCCGTCCCATAATATAAAAGC 59.058 45.833 0.00 0.00 0.00 3.51
2610 8171 4.630069 CCTCCGTCCCATAATATAAAAGCG 59.370 45.833 0.00 0.00 0.00 4.68
2611 8172 5.217978 TCCGTCCCATAATATAAAAGCGT 57.782 39.130 0.00 0.00 0.00 5.07
2612 8173 5.613329 TCCGTCCCATAATATAAAAGCGTT 58.387 37.500 0.00 0.00 0.00 4.84
2613 8174 6.056884 TCCGTCCCATAATATAAAAGCGTTT 58.943 36.000 2.53 2.53 0.00 3.60
2614 8175 6.543100 TCCGTCCCATAATATAAAAGCGTTTT 59.457 34.615 2.19 1.29 36.67 2.43
2615 8176 7.067251 TCCGTCCCATAATATAAAAGCGTTTTT 59.933 33.333 14.50 14.50 39.69 1.94
2616 8177 7.166804 CCGTCCCATAATATAAAAGCGTTTTTG 59.833 37.037 18.77 2.23 37.12 2.44
2617 8178 7.911205 CGTCCCATAATATAAAAGCGTTTTTGA 59.089 33.333 18.77 8.06 37.12 2.69
2618 8179 9.016623 GTCCCATAATATAAAAGCGTTTTTGAC 57.983 33.333 18.77 10.56 37.12 3.18
2619 8180 8.740906 TCCCATAATATAAAAGCGTTTTTGACA 58.259 29.630 18.77 5.33 37.12 3.58
2620 8181 8.803799 CCCATAATATAAAAGCGTTTTTGACAC 58.196 33.333 18.77 0.00 37.12 3.67
2621 8182 9.567848 CCATAATATAAAAGCGTTTTTGACACT 57.432 29.630 18.77 3.85 37.12 3.55
2625 8186 9.607285 AATATAAAAGCGTTTTTGACACTACTG 57.393 29.630 18.77 0.00 37.12 2.74
2626 8187 5.554822 AAAAGCGTTTTTGACACTACTGA 57.445 34.783 9.31 0.00 35.26 3.41
2627 8188 4.795970 AAGCGTTTTTGACACTACTGAG 57.204 40.909 0.00 0.00 0.00 3.35
2628 8189 3.131396 AGCGTTTTTGACACTACTGAGG 58.869 45.455 0.00 0.00 0.00 3.86
2629 8190 2.223377 GCGTTTTTGACACTACTGAGGG 59.777 50.000 0.00 0.00 0.00 4.30
2630 8191 3.724374 CGTTTTTGACACTACTGAGGGA 58.276 45.455 0.00 0.00 0.00 4.20
2631 8192 4.124238 CGTTTTTGACACTACTGAGGGAA 58.876 43.478 0.00 0.00 0.00 3.97
2686 8248 5.637387 GTGTTTGTGATTTGTGGTCAACTTT 59.363 36.000 0.00 0.00 32.93 2.66
2722 8284 7.930513 TTAGCAACATATATCTCTCGTTGTG 57.069 36.000 12.08 0.00 39.27 3.33
2723 8285 6.149129 AGCAACATATATCTCTCGTTGTGA 57.851 37.500 12.08 0.00 39.27 3.58
2724 8286 6.212235 AGCAACATATATCTCTCGTTGTGAG 58.788 40.000 12.08 0.00 46.72 3.51
2740 8303 9.093970 CTCGTTGTGAGTATTTTATTGGACATA 57.906 33.333 0.00 0.00 40.03 2.29
2741 8304 9.607988 TCGTTGTGAGTATTTTATTGGACATAT 57.392 29.630 0.00 0.00 0.00 1.78
2796 8390 4.751098 TGTTTCAACCGACTTGTATGGTAC 59.249 41.667 0.00 0.00 34.11 3.34
2798 8392 4.445452 TCAACCGACTTGTATGGTACTC 57.555 45.455 0.00 0.00 34.11 2.59
2799 8393 3.827876 TCAACCGACTTGTATGGTACTCA 59.172 43.478 0.00 0.00 34.11 3.41
2800 8394 3.863142 ACCGACTTGTATGGTACTCAC 57.137 47.619 0.00 0.00 33.25 3.51
2801 8395 3.428532 ACCGACTTGTATGGTACTCACT 58.571 45.455 0.00 0.00 33.25 3.41
2802 8396 4.592942 ACCGACTTGTATGGTACTCACTA 58.407 43.478 0.00 0.00 33.25 2.74
2803 8397 5.198965 ACCGACTTGTATGGTACTCACTAT 58.801 41.667 0.00 0.00 33.25 2.12
2804 8398 5.067413 ACCGACTTGTATGGTACTCACTATG 59.933 44.000 0.00 0.00 33.25 2.23
2805 8399 5.067413 CCGACTTGTATGGTACTCACTATGT 59.933 44.000 0.00 0.00 0.00 2.29
2806 8400 6.261603 CCGACTTGTATGGTACTCACTATGTA 59.738 42.308 0.00 0.00 0.00 2.29
2807 8401 7.201758 CCGACTTGTATGGTACTCACTATGTAA 60.202 40.741 0.00 0.00 0.00 2.41
2808 8402 8.186163 CGACTTGTATGGTACTCACTATGTAAA 58.814 37.037 0.00 0.00 0.00 2.01
2809 8403 9.517609 GACTTGTATGGTACTCACTATGTAAAG 57.482 37.037 0.00 0.00 0.00 1.85
2810 8404 9.251440 ACTTGTATGGTACTCACTATGTAAAGA 57.749 33.333 0.00 0.00 0.00 2.52
2829 8423 9.880157 TGTAAAGAAATATAAGAGCGTTTAGGT 57.120 29.630 0.00 0.00 0.00 3.08
2843 8437 4.726416 CGTTTAGGTCGCTACTTTAGTGA 58.274 43.478 0.00 0.00 42.56 3.41
2844 8438 5.338365 CGTTTAGGTCGCTACTTTAGTGAT 58.662 41.667 0.06 0.00 45.90 3.06
2845 8439 5.454877 CGTTTAGGTCGCTACTTTAGTGATC 59.545 44.000 0.06 0.00 45.90 2.92
2850 8444 6.809297 GGTCGCTACTTTAGTGATCTAAAC 57.191 41.667 0.06 0.00 45.90 2.01
2851 8445 6.562518 GGTCGCTACTTTAGTGATCTAAACT 58.437 40.000 0.06 0.00 45.90 2.66
2852 8446 7.701445 GGTCGCTACTTTAGTGATCTAAACTA 58.299 38.462 0.06 0.00 45.90 2.24
2853 8447 8.351461 GGTCGCTACTTTAGTGATCTAAACTAT 58.649 37.037 0.06 0.00 45.90 2.12
2854 8448 9.384682 GTCGCTACTTTAGTGATCTAAACTATC 57.615 37.037 0.06 0.00 45.90 2.08
2855 8449 9.339850 TCGCTACTTTAGTGATCTAAACTATCT 57.660 33.333 0.00 0.00 40.15 1.98
2856 8450 9.953697 CGCTACTTTAGTGATCTAAACTATCTT 57.046 33.333 0.00 0.00 40.05 2.40
2874 8468 9.853177 AACTATCTTGTATTTCTTTATGGAGGG 57.147 33.333 0.00 0.00 0.00 4.30
2875 8469 9.225682 ACTATCTTGTATTTCTTTATGGAGGGA 57.774 33.333 0.00 0.00 0.00 4.20
2876 8470 9.717942 CTATCTTGTATTTCTTTATGGAGGGAG 57.282 37.037 0.00 0.00 0.00 4.30
2877 8471 7.510675 TCTTGTATTTCTTTATGGAGGGAGT 57.489 36.000 0.00 0.00 0.00 3.85
2878 8472 8.618240 TCTTGTATTTCTTTATGGAGGGAGTA 57.382 34.615 0.00 0.00 0.00 2.59
2879 8473 8.483758 TCTTGTATTTCTTTATGGAGGGAGTAC 58.516 37.037 0.00 0.00 0.00 2.73
2880 8474 7.989947 TGTATTTCTTTATGGAGGGAGTACT 57.010 36.000 0.00 0.00 0.00 2.73
2908 8502 4.523943 TGAAGAATCCATGTGGTTCTTTGG 59.476 41.667 17.94 0.00 41.30 3.28
2917 8511 5.104527 CCATGTGGTTCTTTGGTCTCCTATA 60.105 44.000 0.00 0.00 0.00 1.31
2918 8512 6.409695 CCATGTGGTTCTTTGGTCTCCTATAT 60.410 42.308 0.00 0.00 0.00 0.86
2919 8513 7.202093 CCATGTGGTTCTTTGGTCTCCTATATA 60.202 40.741 0.00 0.00 0.00 0.86
2924 8518 7.567250 TGGTTCTTTGGTCTCCTATATATGACA 59.433 37.037 0.00 0.00 0.00 3.58
2941 8535 3.819368 TGACATGTGTCTGTTCAATGGT 58.181 40.909 1.15 0.00 44.99 3.55
2942 8536 3.565063 TGACATGTGTCTGTTCAATGGTG 59.435 43.478 1.15 0.00 44.99 4.17
2943 8537 3.814842 GACATGTGTCTGTTCAATGGTGA 59.185 43.478 1.15 0.00 41.65 4.02
2944 8538 4.401022 ACATGTGTCTGTTCAATGGTGAT 58.599 39.130 0.00 0.00 32.48 3.06
2945 8539 5.559770 ACATGTGTCTGTTCAATGGTGATA 58.440 37.500 0.00 0.00 32.48 2.15
2946 8540 6.003326 ACATGTGTCTGTTCAATGGTGATAA 58.997 36.000 0.00 0.00 32.48 1.75
2947 8541 6.489700 ACATGTGTCTGTTCAATGGTGATAAA 59.510 34.615 0.00 0.00 32.48 1.40
2948 8542 6.312399 TGTGTCTGTTCAATGGTGATAAAC 57.688 37.500 0.00 0.00 32.48 2.01
2964 8559 7.888021 TGGTGATAAACTGATAATGTTGAAGGT 59.112 33.333 0.00 0.00 0.00 3.50
2984 8579 4.697352 AGGTCATAAGATTTGTGTGTGCTC 59.303 41.667 0.00 0.00 0.00 4.26
2990 8585 3.462982 AGATTTGTGTGTGCTCGTTGTA 58.537 40.909 0.00 0.00 0.00 2.41
3078 8682 6.601613 TCTTTGTCCTTTCACATTGTACACTT 59.398 34.615 0.00 0.00 0.00 3.16
3084 8688 6.770303 TCCTTTCACATTGTACACTTGATCAA 59.230 34.615 8.12 8.12 0.00 2.57
3173 8777 6.211515 ACAGAAACATGAGAGTTGAATTTGC 58.788 36.000 0.00 0.00 0.00 3.68
3181 8785 8.143193 ACATGAGAGTTGAATTTGCATAAAACA 58.857 29.630 0.00 0.00 0.00 2.83
3182 8786 8.980610 CATGAGAGTTGAATTTGCATAAAACAA 58.019 29.630 0.00 0.00 0.00 2.83
3212 8816 4.689612 TGTTAGCAACAGAAGAGGAAGT 57.310 40.909 0.00 0.00 36.25 3.01
3213 8817 4.380531 TGTTAGCAACAGAAGAGGAAGTG 58.619 43.478 0.00 0.00 36.25 3.16
3214 8818 4.100963 TGTTAGCAACAGAAGAGGAAGTGA 59.899 41.667 0.00 0.00 36.25 3.41
3215 8819 3.399440 AGCAACAGAAGAGGAAGTGAG 57.601 47.619 0.00 0.00 0.00 3.51
3216 8820 2.038295 AGCAACAGAAGAGGAAGTGAGG 59.962 50.000 0.00 0.00 0.00 3.86
3217 8821 2.421619 CAACAGAAGAGGAAGTGAGGC 58.578 52.381 0.00 0.00 0.00 4.70
3218 8822 0.980423 ACAGAAGAGGAAGTGAGGCC 59.020 55.000 0.00 0.00 0.00 5.19
3219 8823 1.274712 CAGAAGAGGAAGTGAGGCCT 58.725 55.000 3.86 3.86 37.18 5.19
3220 8824 1.627834 CAGAAGAGGAAGTGAGGCCTT 59.372 52.381 6.77 0.00 33.84 4.35
3221 8825 2.039613 CAGAAGAGGAAGTGAGGCCTTT 59.960 50.000 6.77 0.00 33.84 3.11
3222 8826 2.713708 AGAAGAGGAAGTGAGGCCTTTT 59.286 45.455 6.77 1.59 33.84 2.27
3223 8827 2.575805 AGAGGAAGTGAGGCCTTTTG 57.424 50.000 6.77 0.00 33.84 2.44
3224 8828 1.777272 AGAGGAAGTGAGGCCTTTTGT 59.223 47.619 6.77 0.00 33.84 2.83
3225 8829 2.155279 GAGGAAGTGAGGCCTTTTGTC 58.845 52.381 6.77 2.50 33.84 3.18
3226 8830 1.777272 AGGAAGTGAGGCCTTTTGTCT 59.223 47.619 6.77 0.00 0.00 3.41
3227 8831 2.155279 GGAAGTGAGGCCTTTTGTCTC 58.845 52.381 6.77 0.00 0.00 3.36
3228 8832 2.224646 GGAAGTGAGGCCTTTTGTCTCT 60.225 50.000 6.77 0.00 0.00 3.10
3229 8833 2.849294 AGTGAGGCCTTTTGTCTCTC 57.151 50.000 6.77 0.00 0.00 3.20
3230 8834 2.050144 AGTGAGGCCTTTTGTCTCTCA 58.950 47.619 6.77 0.00 32.79 3.27
3231 8835 2.038295 AGTGAGGCCTTTTGTCTCTCAG 59.962 50.000 6.77 0.00 35.48 3.35
3232 8836 2.037772 GTGAGGCCTTTTGTCTCTCAGA 59.962 50.000 6.77 0.00 35.48 3.27
3233 8837 2.037772 TGAGGCCTTTTGTCTCTCAGAC 59.962 50.000 6.77 0.00 45.26 3.51
3234 8838 2.301583 GAGGCCTTTTGTCTCTCAGACT 59.698 50.000 6.77 0.00 45.27 3.24
3235 8839 2.301583 AGGCCTTTTGTCTCTCAGACTC 59.698 50.000 0.00 0.00 45.27 3.36
3236 8840 2.614229 GGCCTTTTGTCTCTCAGACTCC 60.614 54.545 0.00 0.00 45.27 3.85
3237 8841 2.301583 GCCTTTTGTCTCTCAGACTCCT 59.698 50.000 5.31 0.00 45.27 3.69
3238 8842 3.244387 GCCTTTTGTCTCTCAGACTCCTT 60.244 47.826 5.31 0.00 45.27 3.36
3239 8843 4.565022 CCTTTTGTCTCTCAGACTCCTTC 58.435 47.826 5.31 0.00 45.27 3.46
3240 8844 4.039730 CCTTTTGTCTCTCAGACTCCTTCA 59.960 45.833 5.31 0.00 45.27 3.02
3241 8845 5.453903 CCTTTTGTCTCTCAGACTCCTTCAA 60.454 44.000 5.31 0.00 45.27 2.69
3242 8846 5.614324 TTTGTCTCTCAGACTCCTTCAAA 57.386 39.130 5.31 0.00 45.27 2.69
3243 8847 5.614324 TTGTCTCTCAGACTCCTTCAAAA 57.386 39.130 5.31 0.00 45.27 2.44
3244 8848 5.815233 TGTCTCTCAGACTCCTTCAAAAT 57.185 39.130 5.31 0.00 45.27 1.82
3245 8849 6.179906 TGTCTCTCAGACTCCTTCAAAATT 57.820 37.500 5.31 0.00 45.27 1.82
3246 8850 6.595682 TGTCTCTCAGACTCCTTCAAAATTT 58.404 36.000 5.31 0.00 45.27 1.82
3247 8851 6.708054 TGTCTCTCAGACTCCTTCAAAATTTC 59.292 38.462 5.31 0.00 45.27 2.17
3248 8852 6.708054 GTCTCTCAGACTCCTTCAAAATTTCA 59.292 38.462 0.00 0.00 41.88 2.69
3249 8853 7.227512 GTCTCTCAGACTCCTTCAAAATTTCAA 59.772 37.037 0.00 0.00 41.88 2.69
3250 8854 7.775093 TCTCTCAGACTCCTTCAAAATTTCAAA 59.225 33.333 0.00 0.00 0.00 2.69
3251 8855 8.292444 TCTCAGACTCCTTCAAAATTTCAAAA 57.708 30.769 0.00 0.00 0.00 2.44
3252 8856 8.917088 TCTCAGACTCCTTCAAAATTTCAAAAT 58.083 29.630 0.00 0.00 0.00 1.82
3253 8857 9.538508 CTCAGACTCCTTCAAAATTTCAAAATT 57.461 29.630 0.00 0.00 40.15 1.82
3254 8858 9.533253 TCAGACTCCTTCAAAATTTCAAAATTC 57.467 29.630 1.43 0.00 37.62 2.17
3255 8859 9.316730 CAGACTCCTTCAAAATTTCAAAATTCA 57.683 29.630 1.43 0.00 37.62 2.57
3256 8860 9.889128 AGACTCCTTCAAAATTTCAAAATTCAA 57.111 25.926 1.43 0.00 37.62 2.69
3257 8861 9.920826 GACTCCTTCAAAATTTCAAAATTCAAC 57.079 29.630 1.43 0.00 37.62 3.18
3258 8862 9.671279 ACTCCTTCAAAATTTCAAAATTCAACT 57.329 25.926 1.43 0.00 37.62 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.414158 ACATGCTACCTCGGCTACAT 58.586 50.000 0.00 0.00 0.00 2.29
2 3 2.061509 TACATGCTACCTCGGCTACA 57.938 50.000 0.00 0.00 0.00 2.74
3 4 3.662247 AATACATGCTACCTCGGCTAC 57.338 47.619 0.00 0.00 0.00 3.58
4 5 4.831155 AGTTAATACATGCTACCTCGGCTA 59.169 41.667 0.00 0.00 0.00 3.93
7 8 4.307432 CCAGTTAATACATGCTACCTCGG 58.693 47.826 0.00 0.00 0.00 4.63
8 9 4.307432 CCCAGTTAATACATGCTACCTCG 58.693 47.826 0.00 0.00 0.00 4.63
9 10 4.065789 GCCCAGTTAATACATGCTACCTC 58.934 47.826 0.00 0.00 0.00 3.85
10 11 3.458118 TGCCCAGTTAATACATGCTACCT 59.542 43.478 0.00 0.00 0.00 3.08
12 13 4.638421 TGTTGCCCAGTTAATACATGCTAC 59.362 41.667 0.00 0.00 0.00 3.58
13 14 4.849518 TGTTGCCCAGTTAATACATGCTA 58.150 39.130 0.00 0.00 0.00 3.49
14 15 3.696045 TGTTGCCCAGTTAATACATGCT 58.304 40.909 0.00 0.00 0.00 3.79
16 17 7.333528 ACTTATGTTGCCCAGTTAATACATG 57.666 36.000 0.00 0.00 0.00 3.21
17 18 7.719633 CCTACTTATGTTGCCCAGTTAATACAT 59.280 37.037 0.00 0.00 0.00 2.29
18 19 7.051623 CCTACTTATGTTGCCCAGTTAATACA 58.948 38.462 0.00 0.00 0.00 2.29
19 20 6.017357 GCCTACTTATGTTGCCCAGTTAATAC 60.017 42.308 0.00 0.00 0.00 1.89
20 21 6.059484 GCCTACTTATGTTGCCCAGTTAATA 58.941 40.000 0.00 0.00 0.00 0.98
21 22 4.887655 GCCTACTTATGTTGCCCAGTTAAT 59.112 41.667 0.00 0.00 0.00 1.40
22 23 4.266714 GCCTACTTATGTTGCCCAGTTAA 58.733 43.478 0.00 0.00 0.00 2.01
23 24 3.680475 CGCCTACTTATGTTGCCCAGTTA 60.680 47.826 0.00 0.00 0.00 2.24
24 25 2.723273 GCCTACTTATGTTGCCCAGTT 58.277 47.619 0.00 0.00 0.00 3.16
25 26 1.406887 CGCCTACTTATGTTGCCCAGT 60.407 52.381 0.00 0.00 0.00 4.00
26 27 1.299541 CGCCTACTTATGTTGCCCAG 58.700 55.000 0.00 0.00 0.00 4.45
27 28 0.107410 CCGCCTACTTATGTTGCCCA 60.107 55.000 0.00 0.00 0.00 5.36
28 29 0.179468 TCCGCCTACTTATGTTGCCC 59.821 55.000 0.00 0.00 0.00 5.36
29 30 1.296727 GTCCGCCTACTTATGTTGCC 58.703 55.000 0.00 0.00 0.00 4.52
30 31 2.018542 TGTCCGCCTACTTATGTTGC 57.981 50.000 0.00 0.00 0.00 4.17
31 32 2.794910 CGATGTCCGCCTACTTATGTTG 59.205 50.000 0.00 0.00 0.00 3.33
32 33 2.429610 ACGATGTCCGCCTACTTATGTT 59.570 45.455 0.00 0.00 43.32 2.71
33 34 2.029623 ACGATGTCCGCCTACTTATGT 58.970 47.619 0.00 0.00 43.32 2.29
34 35 2.795175 ACGATGTCCGCCTACTTATG 57.205 50.000 0.00 0.00 43.32 1.90
35 36 3.216800 TGTACGATGTCCGCCTACTTAT 58.783 45.455 0.00 0.00 43.32 1.73
36 37 2.642427 TGTACGATGTCCGCCTACTTA 58.358 47.619 0.00 0.00 43.32 2.24
37 38 1.466856 TGTACGATGTCCGCCTACTT 58.533 50.000 0.00 0.00 43.32 2.24
38 39 1.404391 CTTGTACGATGTCCGCCTACT 59.596 52.381 0.00 0.00 43.32 2.57
39 40 1.402968 TCTTGTACGATGTCCGCCTAC 59.597 52.381 0.00 0.00 43.32 3.18
40 41 1.402968 GTCTTGTACGATGTCCGCCTA 59.597 52.381 0.00 0.00 43.32 3.93
41 42 0.172803 GTCTTGTACGATGTCCGCCT 59.827 55.000 0.00 0.00 43.32 5.52
42 43 2.662150 GTCTTGTACGATGTCCGCC 58.338 57.895 0.00 0.00 43.32 6.13
102 103 3.813166 GGTTTGTTGATCCTTCTTCGTCA 59.187 43.478 0.00 0.00 0.00 4.35
105 106 4.379813 CCATGGTTTGTTGATCCTTCTTCG 60.380 45.833 2.57 0.00 0.00 3.79
110 111 3.541242 TCCCATGGTTTGTTGATCCTT 57.459 42.857 11.73 0.00 0.00 3.36
128 129 1.612395 TTTTCCCCGGCAATGCATCC 61.612 55.000 7.79 0.00 0.00 3.51
147 148 0.174389 CACTGAGCGGCACATAGACT 59.826 55.000 1.45 0.00 0.00 3.24
148 149 1.424493 GCACTGAGCGGCACATAGAC 61.424 60.000 1.45 0.00 0.00 2.59
161 162 3.211865 CTCCTACTATGTACCGCACTGA 58.788 50.000 0.00 0.00 0.00 3.41
164 165 1.955080 AGCTCCTACTATGTACCGCAC 59.045 52.381 0.00 0.00 0.00 5.34
173 174 4.362677 TCTTTGGGTGAAGCTCCTACTAT 58.637 43.478 0.00 0.00 0.00 2.12
279 280 6.768861 TGAGAACATTTCTTTAACTTTCCGGA 59.231 34.615 0.00 0.00 40.87 5.14
280 281 6.966021 TGAGAACATTTCTTTAACTTTCCGG 58.034 36.000 0.00 0.00 40.87 5.14
485 514 8.647256 AGAGGATGAAGATTTCTTGAATTTGT 57.353 30.769 0.00 0.00 36.11 2.83
507 536 7.712264 TTAATGTGCCAACAAATTTTGAGAG 57.288 32.000 15.81 4.76 40.46 3.20
715 753 3.582148 CCGCCCGGTTTTTAGTCC 58.418 61.111 0.00 0.00 0.00 3.85
828 875 2.234296 CCTCCTGCCTCCTTTGGGT 61.234 63.158 0.00 0.00 0.00 4.51
829 876 2.679716 CCTCCTGCCTCCTTTGGG 59.320 66.667 0.00 0.00 0.00 4.12
832 879 0.992695 GTAACCCTCCTGCCTCCTTT 59.007 55.000 0.00 0.00 0.00 3.11
838 885 2.686106 TCCGGTAACCCTCCTGCC 60.686 66.667 0.00 0.00 0.00 4.85
842 889 1.683418 AATCGCTCCGGTAACCCTCC 61.683 60.000 0.00 0.00 0.00 4.30
906 953 3.883744 CTTGAAGGGCGGACGCTGT 62.884 63.158 16.72 1.06 39.39 4.40
988 1061 1.303970 TTGCCATCGGGATTGTGCA 60.304 52.632 0.00 0.00 35.59 4.57
1118 6146 2.747686 GGTTGGCGAGAAGGGACA 59.252 61.111 0.00 0.00 0.00 4.02
1566 6605 9.706691 ATGACGTTGGAAGTATAATGGTAATAG 57.293 33.333 0.00 0.00 0.00 1.73
1780 7305 1.998315 CAGATGGACAAGCTTGAGACG 59.002 52.381 32.50 6.30 0.00 4.18
1808 7333 3.029320 TGTTTATGTCGTAACTGGCGT 57.971 42.857 0.00 0.00 0.00 5.68
1825 7350 1.628340 TGTCTCCGGGTCAATGATGTT 59.372 47.619 0.00 0.00 0.00 2.71
1833 7358 2.117423 TGCTCTGTCTCCGGGTCA 59.883 61.111 0.00 0.00 0.00 4.02
1842 7367 1.373570 GCATAGTTGGGTGCTCTGTC 58.626 55.000 0.00 0.00 38.30 3.51
1851 7376 1.212688 TCATCCACCAGCATAGTTGGG 59.787 52.381 4.92 0.00 40.11 4.12
1858 7383 1.611419 CCCAGTCATCCACCAGCAT 59.389 57.895 0.00 0.00 0.00 3.79
1955 7480 5.733620 ATCAGTTTTGATTGCAACCTCAT 57.266 34.783 0.00 0.00 41.24 2.90
2008 7533 0.842030 ACACCCTCCTCTGATGGCAA 60.842 55.000 0.00 0.00 29.89 4.52
2124 7649 4.141733 TGGTCATATGATTTCTCCTTCGCA 60.142 41.667 9.02 0.00 0.00 5.10
2125 7650 4.380531 TGGTCATATGATTTCTCCTTCGC 58.619 43.478 9.02 0.00 0.00 4.70
2126 7651 6.925610 TTTGGTCATATGATTTCTCCTTCG 57.074 37.500 9.02 0.00 0.00 3.79
2127 7652 8.286191 ACTTTTGGTCATATGATTTCTCCTTC 57.714 34.615 9.02 0.00 0.00 3.46
2129 7654 7.872113 GACTTTTGGTCATATGATTTCTCCT 57.128 36.000 9.02 0.00 43.94 3.69
2143 7668 3.119352 GCAAGGATCCATGACTTTTGGTC 60.119 47.826 21.00 0.00 44.70 4.02
2299 7836 1.670730 TCTTTGCGCGGAGATGCAA 60.671 52.632 8.83 0.00 45.76 4.08
2301 7838 1.639298 AAGTCTTTGCGCGGAGATGC 61.639 55.000 8.83 4.52 0.00 3.91
2302 7839 0.371645 GAAGTCTTTGCGCGGAGATG 59.628 55.000 8.83 0.00 0.00 2.90
2303 7840 0.037326 TGAAGTCTTTGCGCGGAGAT 60.037 50.000 8.83 1.36 0.00 2.75
2308 7845 0.516877 TGGAATGAAGTCTTTGCGCG 59.483 50.000 0.00 0.00 0.00 6.86
2309 7846 1.266718 TGTGGAATGAAGTCTTTGCGC 59.733 47.619 0.00 0.00 34.24 6.09
2310 7847 3.837213 ATGTGGAATGAAGTCTTTGCG 57.163 42.857 0.00 0.00 0.00 4.85
2311 7848 6.914757 GCTATAATGTGGAATGAAGTCTTTGC 59.085 38.462 0.00 0.00 0.00 3.68
2313 7850 7.118723 TGGCTATAATGTGGAATGAAGTCTTT 58.881 34.615 0.00 0.00 0.00 2.52
2314 7851 6.662755 TGGCTATAATGTGGAATGAAGTCTT 58.337 36.000 0.00 0.00 0.00 3.01
2321 7859 8.582437 AGATGAATTTGGCTATAATGTGGAATG 58.418 33.333 0.00 0.00 0.00 2.67
2358 7896 4.035208 AGGAGAAAACACACACAACGATTC 59.965 41.667 0.00 0.00 0.00 2.52
2363 7901 3.689649 AGACAGGAGAAAACACACACAAC 59.310 43.478 0.00 0.00 0.00 3.32
2368 7922 3.798202 AGACAGACAGGAGAAAACACAC 58.202 45.455 0.00 0.00 0.00 3.82
2372 7926 7.548097 TGTATATGAGACAGACAGGAGAAAAC 58.452 38.462 0.00 0.00 0.00 2.43
2438 7996 1.490490 GCCCATATGGTCTCCAGTTCA 59.510 52.381 20.46 0.00 36.75 3.18
2466 8024 2.231964 TCATGCTGAATTTGTTCCTGCC 59.768 45.455 0.00 0.00 0.00 4.85
2549 8110 3.998913 TGGATATGTCAAGCAAGACCA 57.001 42.857 6.16 0.00 37.73 4.02
2577 8138 1.557832 TGGGACGGAGGGAGTAAAATG 59.442 52.381 0.00 0.00 0.00 2.32
2578 8139 1.961133 TGGGACGGAGGGAGTAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2579 8140 1.961133 ATGGGACGGAGGGAGTAAAA 58.039 50.000 0.00 0.00 0.00 1.52
2583 8144 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2584 8145 6.368779 TTTTATATTATGGGACGGAGGGAG 57.631 41.667 0.00 0.00 0.00 4.30
2585 8146 5.280317 GCTTTTATATTATGGGACGGAGGGA 60.280 44.000 0.00 0.00 0.00 4.20
2586 8147 4.941873 GCTTTTATATTATGGGACGGAGGG 59.058 45.833 0.00 0.00 0.00 4.30
2587 8148 4.630069 CGCTTTTATATTATGGGACGGAGG 59.370 45.833 0.00 0.00 0.00 4.30
2588 8149 5.235516 ACGCTTTTATATTATGGGACGGAG 58.764 41.667 0.00 0.00 0.00 4.63
2589 8150 5.217978 ACGCTTTTATATTATGGGACGGA 57.782 39.130 0.00 0.00 0.00 4.69
2590 8151 5.934935 AACGCTTTTATATTATGGGACGG 57.065 39.130 0.00 0.00 0.00 4.79
2591 8152 7.911205 TCAAAAACGCTTTTATATTATGGGACG 59.089 33.333 0.00 0.00 32.85 4.79
2592 8153 9.016623 GTCAAAAACGCTTTTATATTATGGGAC 57.983 33.333 0.00 0.00 32.85 4.46
2593 8154 8.740906 TGTCAAAAACGCTTTTATATTATGGGA 58.259 29.630 0.00 0.00 32.85 4.37
2594 8155 8.803799 GTGTCAAAAACGCTTTTATATTATGGG 58.196 33.333 0.00 0.00 32.85 4.00
2595 8156 9.567848 AGTGTCAAAAACGCTTTTATATTATGG 57.432 29.630 0.00 0.00 46.62 2.74
2599 8160 9.607285 CAGTAGTGTCAAAAACGCTTTTATATT 57.393 29.630 0.00 0.00 46.62 1.28
2600 8161 8.995220 TCAGTAGTGTCAAAAACGCTTTTATAT 58.005 29.630 0.00 0.00 46.62 0.86
2601 8162 8.367943 TCAGTAGTGTCAAAAACGCTTTTATA 57.632 30.769 0.00 0.00 46.62 0.98
2602 8163 7.254227 TCAGTAGTGTCAAAAACGCTTTTAT 57.746 32.000 0.00 0.00 46.62 1.40
2603 8164 6.238266 CCTCAGTAGTGTCAAAAACGCTTTTA 60.238 38.462 0.00 0.00 46.62 1.52
2604 8165 5.448632 CCTCAGTAGTGTCAAAAACGCTTTT 60.449 40.000 0.00 0.00 46.62 2.27
2605 8166 4.035208 CCTCAGTAGTGTCAAAAACGCTTT 59.965 41.667 0.00 0.00 46.62 3.51
2606 8167 3.560068 CCTCAGTAGTGTCAAAAACGCTT 59.440 43.478 0.00 0.00 46.62 4.68
2608 8169 2.223377 CCCTCAGTAGTGTCAAAAACGC 59.777 50.000 0.00 0.00 38.74 4.84
2609 8170 3.724374 TCCCTCAGTAGTGTCAAAAACG 58.276 45.455 0.00 0.00 0.00 3.60
2610 8171 6.935208 AGTATTCCCTCAGTAGTGTCAAAAAC 59.065 38.462 0.00 0.00 0.00 2.43
2611 8172 7.074653 AGTATTCCCTCAGTAGTGTCAAAAA 57.925 36.000 0.00 0.00 0.00 1.94
2612 8173 6.681729 AGTATTCCCTCAGTAGTGTCAAAA 57.318 37.500 0.00 0.00 0.00 2.44
2613 8174 7.399191 ACATAGTATTCCCTCAGTAGTGTCAAA 59.601 37.037 0.00 0.00 0.00 2.69
2614 8175 6.895756 ACATAGTATTCCCTCAGTAGTGTCAA 59.104 38.462 0.00 0.00 0.00 3.18
2615 8176 6.432581 ACATAGTATTCCCTCAGTAGTGTCA 58.567 40.000 0.00 0.00 0.00 3.58
2616 8177 6.963083 ACATAGTATTCCCTCAGTAGTGTC 57.037 41.667 0.00 0.00 0.00 3.67
2617 8178 8.280084 TCTAACATAGTATTCCCTCAGTAGTGT 58.720 37.037 0.00 0.00 0.00 3.55
2618 8179 8.693120 TCTAACATAGTATTCCCTCAGTAGTG 57.307 38.462 0.00 0.00 0.00 2.74
2622 8183 9.656323 TTGTATCTAACATAGTATTCCCTCAGT 57.344 33.333 0.00 0.00 38.10 3.41
2624 8185 9.877222 TCTTGTATCTAACATAGTATTCCCTCA 57.123 33.333 0.00 0.00 38.10 3.86
2626 8187 9.656323 TGTCTTGTATCTAACATAGTATTCCCT 57.344 33.333 0.00 0.00 38.10 4.20
2660 8222 4.790765 TGACCACAAATCACAAACACAA 57.209 36.364 0.00 0.00 0.00 3.33
2699 8261 7.013369 ACTCACAACGAGAGATATATGTTGCTA 59.987 37.037 11.01 2.21 45.45 3.49
2722 8284 8.299570 CAGGCCAATATGTCCAATAAAATACTC 58.700 37.037 5.01 0.00 0.00 2.59
2723 8285 7.784550 ACAGGCCAATATGTCCAATAAAATACT 59.215 33.333 5.01 0.00 0.00 2.12
2724 8286 7.867403 CACAGGCCAATATGTCCAATAAAATAC 59.133 37.037 5.01 0.00 0.00 1.89
2729 8292 4.865905 ACACAGGCCAATATGTCCAATAA 58.134 39.130 5.01 0.00 0.00 1.40
2731 8294 3.053395 AGACACAGGCCAATATGTCCAAT 60.053 43.478 19.28 4.77 41.99 3.16
2740 8303 0.321653 GACCGAAGACACAGGCCAAT 60.322 55.000 5.01 0.00 0.00 3.16
2741 8304 1.070786 GACCGAAGACACAGGCCAA 59.929 57.895 5.01 0.00 0.00 4.52
2803 8397 9.880157 ACCTAAACGCTCTTATATTTCTTTACA 57.120 29.630 0.00 0.00 0.00 2.41
2805 8399 9.241317 CGACCTAAACGCTCTTATATTTCTTTA 57.759 33.333 0.00 0.00 0.00 1.85
2806 8400 8.128016 CGACCTAAACGCTCTTATATTTCTTT 57.872 34.615 0.00 0.00 0.00 2.52
2807 8401 7.695869 CGACCTAAACGCTCTTATATTTCTT 57.304 36.000 0.00 0.00 0.00 2.52
2821 8415 4.726416 TCACTAAAGTAGCGACCTAAACG 58.274 43.478 0.00 0.00 0.00 3.60
2822 8416 6.562518 AGATCACTAAAGTAGCGACCTAAAC 58.437 40.000 0.00 0.00 0.00 2.01
2823 8417 6.770746 AGATCACTAAAGTAGCGACCTAAA 57.229 37.500 0.00 0.00 0.00 1.85
2824 8418 7.870509 TTAGATCACTAAAGTAGCGACCTAA 57.129 36.000 0.00 0.00 35.92 2.69
2825 8419 7.555554 AGTTTAGATCACTAAAGTAGCGACCTA 59.444 37.037 0.00 0.00 45.05 3.08
2826 8420 6.377712 AGTTTAGATCACTAAAGTAGCGACCT 59.622 38.462 0.00 0.00 45.05 3.85
2827 8421 6.562518 AGTTTAGATCACTAAAGTAGCGACC 58.437 40.000 0.00 0.00 45.05 4.79
2848 8442 9.853177 CCCTCCATAAAGAAATACAAGATAGTT 57.147 33.333 0.00 0.00 0.00 2.24
2849 8443 9.225682 TCCCTCCATAAAGAAATACAAGATAGT 57.774 33.333 0.00 0.00 0.00 2.12
2850 8444 9.717942 CTCCCTCCATAAAGAAATACAAGATAG 57.282 37.037 0.00 0.00 0.00 2.08
2851 8445 9.225682 ACTCCCTCCATAAAGAAATACAAGATA 57.774 33.333 0.00 0.00 0.00 1.98
2852 8446 8.107196 ACTCCCTCCATAAAGAAATACAAGAT 57.893 34.615 0.00 0.00 0.00 2.40
2853 8447 7.510675 ACTCCCTCCATAAAGAAATACAAGA 57.489 36.000 0.00 0.00 0.00 3.02
2854 8448 8.487028 AGTACTCCCTCCATAAAGAAATACAAG 58.513 37.037 0.00 0.00 0.00 3.16
2855 8449 8.388656 AGTACTCCCTCCATAAAGAAATACAA 57.611 34.615 0.00 0.00 0.00 2.41
2856 8450 7.989947 AGTACTCCCTCCATAAAGAAATACA 57.010 36.000 0.00 0.00 0.00 2.29
2857 8451 8.265764 ACAAGTACTCCCTCCATAAAGAAATAC 58.734 37.037 0.00 0.00 0.00 1.89
2858 8452 8.388656 ACAAGTACTCCCTCCATAAAGAAATA 57.611 34.615 0.00 0.00 0.00 1.40
2859 8453 7.272144 ACAAGTACTCCCTCCATAAAGAAAT 57.728 36.000 0.00 0.00 0.00 2.17
2860 8454 6.697641 ACAAGTACTCCCTCCATAAAGAAA 57.302 37.500 0.00 0.00 0.00 2.52
2861 8455 6.697641 AACAAGTACTCCCTCCATAAAGAA 57.302 37.500 0.00 0.00 0.00 2.52
2862 8456 6.271391 TCAAACAAGTACTCCCTCCATAAAGA 59.729 38.462 0.00 0.00 0.00 2.52
2863 8457 6.472887 TCAAACAAGTACTCCCTCCATAAAG 58.527 40.000 0.00 0.00 0.00 1.85
2864 8458 6.442541 TCAAACAAGTACTCCCTCCATAAA 57.557 37.500 0.00 0.00 0.00 1.40
2865 8459 6.271391 TCTTCAAACAAGTACTCCCTCCATAA 59.729 38.462 0.00 0.00 0.00 1.90
2866 8460 5.783360 TCTTCAAACAAGTACTCCCTCCATA 59.217 40.000 0.00 0.00 0.00 2.74
2867 8461 4.597507 TCTTCAAACAAGTACTCCCTCCAT 59.402 41.667 0.00 0.00 0.00 3.41
2868 8462 3.971305 TCTTCAAACAAGTACTCCCTCCA 59.029 43.478 0.00 0.00 0.00 3.86
2869 8463 4.618920 TCTTCAAACAAGTACTCCCTCC 57.381 45.455 0.00 0.00 0.00 4.30
2870 8464 5.644206 GGATTCTTCAAACAAGTACTCCCTC 59.356 44.000 0.00 0.00 0.00 4.30
2871 8465 5.073144 TGGATTCTTCAAACAAGTACTCCCT 59.927 40.000 0.00 0.00 0.00 4.20
2872 8466 5.313712 TGGATTCTTCAAACAAGTACTCCC 58.686 41.667 0.00 0.00 0.00 4.30
2873 8467 6.431234 ACATGGATTCTTCAAACAAGTACTCC 59.569 38.462 0.00 0.00 0.00 3.85
2874 8468 7.301054 CACATGGATTCTTCAAACAAGTACTC 58.699 38.462 0.00 0.00 0.00 2.59
2875 8469 6.207417 CCACATGGATTCTTCAAACAAGTACT 59.793 38.462 0.00 0.00 37.39 2.73
2876 8470 6.016276 ACCACATGGATTCTTCAAACAAGTAC 60.016 38.462 4.53 0.00 38.94 2.73
2877 8471 6.068010 ACCACATGGATTCTTCAAACAAGTA 58.932 36.000 4.53 0.00 38.94 2.24
2878 8472 4.895297 ACCACATGGATTCTTCAAACAAGT 59.105 37.500 4.53 0.00 38.94 3.16
2879 8473 5.458041 ACCACATGGATTCTTCAAACAAG 57.542 39.130 4.53 0.00 38.94 3.16
2880 8474 5.598005 AGAACCACATGGATTCTTCAAACAA 59.402 36.000 4.53 0.00 38.94 2.83
2918 8512 8.013812 ATCACCATTGAACAGACACATGTCATA 61.014 37.037 14.23 0.00 40.41 2.15
2919 8513 7.249758 ATCACCATTGAACAGACACATGTCAT 61.250 38.462 14.23 0.00 40.41 3.06
2924 8518 6.716628 AGTTTATCACCATTGAACAGACACAT 59.283 34.615 0.00 0.00 34.61 3.21
2941 8535 9.685276 ATGACCTTCAACATTATCAGTTTATCA 57.315 29.630 0.00 0.00 0.00 2.15
2945 8539 9.739276 TCTTATGACCTTCAACATTATCAGTTT 57.261 29.630 0.00 0.00 0.00 2.66
2946 8540 9.911788 ATCTTATGACCTTCAACATTATCAGTT 57.088 29.630 0.00 0.00 0.00 3.16
2947 8541 9.911788 AATCTTATGACCTTCAACATTATCAGT 57.088 29.630 0.00 0.00 0.00 3.41
2964 8559 4.314961 ACGAGCACACACAAATCTTATGA 58.685 39.130 0.00 0.00 0.00 2.15
2984 8579 4.442706 AGTAGGCAATCTGGAATACAACG 58.557 43.478 0.00 0.00 0.00 4.10
2990 8585 4.263905 TGGTTCAAGTAGGCAATCTGGAAT 60.264 41.667 0.00 0.00 0.00 3.01
3028 8631 9.315525 GAGACATTTTCAGTAAATACTACTCCC 57.684 37.037 0.00 0.00 34.69 4.30
3044 8647 6.795399 TGTGAAAGGACAAAGAGACATTTTC 58.205 36.000 0.00 0.00 0.00 2.29
3150 8754 6.210796 TGCAAATTCAACTCTCATGTTTCTG 58.789 36.000 0.00 0.00 0.00 3.02
3199 8803 0.980423 GGCCTCACTTCCTCTTCTGT 59.020 55.000 0.00 0.00 0.00 3.41
3200 8804 1.274712 AGGCCTCACTTCCTCTTCTG 58.725 55.000 0.00 0.00 0.00 3.02
3209 8813 2.439507 TGAGAGACAAAAGGCCTCACTT 59.560 45.455 5.23 0.00 0.00 3.16
3210 8814 2.038295 CTGAGAGACAAAAGGCCTCACT 59.962 50.000 5.23 0.00 31.45 3.41
3211 8815 2.037772 TCTGAGAGACAAAAGGCCTCAC 59.962 50.000 5.23 0.00 31.45 3.51
3212 8816 2.037772 GTCTGAGAGACAAAAGGCCTCA 59.962 50.000 5.23 0.00 44.45 3.86
3213 8817 2.694213 GTCTGAGAGACAAAAGGCCTC 58.306 52.381 5.23 0.00 44.45 4.70
3214 8818 2.849294 GTCTGAGAGACAAAAGGCCT 57.151 50.000 0.00 0.00 44.45 5.19
3223 8827 6.708054 TGAAATTTTGAAGGAGTCTGAGAGAC 59.292 38.462 0.00 0.00 45.38 3.36
3224 8828 6.830912 TGAAATTTTGAAGGAGTCTGAGAGA 58.169 36.000 0.00 0.00 0.00 3.10
3225 8829 7.502120 TTGAAATTTTGAAGGAGTCTGAGAG 57.498 36.000 0.00 0.00 0.00 3.20
3226 8830 7.880160 TTTGAAATTTTGAAGGAGTCTGAGA 57.120 32.000 0.00 0.00 0.00 3.27
3227 8831 9.538508 AATTTTGAAATTTTGAAGGAGTCTGAG 57.461 29.630 0.00 0.00 35.16 3.35
3228 8832 9.533253 GAATTTTGAAATTTTGAAGGAGTCTGA 57.467 29.630 3.45 0.00 38.64 3.27
3229 8833 9.316730 TGAATTTTGAAATTTTGAAGGAGTCTG 57.683 29.630 3.45 0.00 38.64 3.51
3230 8834 9.889128 TTGAATTTTGAAATTTTGAAGGAGTCT 57.111 25.926 3.45 0.00 38.64 3.24
3231 8835 9.920826 GTTGAATTTTGAAATTTTGAAGGAGTC 57.079 29.630 3.45 0.00 38.64 3.36
3232 8836 9.671279 AGTTGAATTTTGAAATTTTGAAGGAGT 57.329 25.926 3.45 0.00 38.64 3.85


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

AutoCloner maintained by Alex Coulton.