Multiple sequence alignment - TraesCS5D01G391800

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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 TraesCS5D01G391800 chr5D 100.000 2873 0 0 1 2873 460240343 460237471 0.000000e+00 5306.0
1 TraesCS5D01G391800 chr5D 78.965 908 128 33 1189 2058 460447030 460447912 6.950000e-156 560.0
2 TraesCS5D01G391800 chr5D 84.342 479 58 10 726 1191 460444377 460444851 1.210000e-123 453.0
3 TraesCS5D01G391800 chr5D 86.686 353 36 2 119 463 460444019 460444368 5.810000e-102 381.0
4 TraesCS5D01G391800 chr5D 90.000 50 5 0 2464 2513 460238010 460237961 6.640000e-07 65.8
5 TraesCS5D01G391800 chr5B 92.912 2342 127 23 100 2422 565900615 565898294 0.000000e+00 3369.0
6 TraesCS5D01G391800 chr5B 82.048 1387 197 30 726 2087 566122780 566124139 0.000000e+00 1134.0
7 TraesCS5D01G391800 chr5B 90.145 345 30 2 119 463 566122431 566122771 2.030000e-121 446.0
8 TraesCS5D01G391800 chr5B 88.986 345 34 2 119 463 566054735 566055075 9.520000e-115 424.0
9 TraesCS5D01G391800 chr5B 83.796 216 26 7 2667 2873 565898179 565897964 2.260000e-46 196.0
10 TraesCS5D01G391800 chr5B 88.542 96 6 2 763 853 566062927 566063022 8.410000e-21 111.0
11 TraesCS5D01G391800 chr5B 85.897 78 9 2 2529 2604 580370191 580370268 6.600000e-12 82.4
12 TraesCS5D01G391800 chr5B 94.340 53 3 0 2552 2604 640309868 640309816 6.600000e-12 82.4
13 TraesCS5D01G391800 chr5A 96.134 983 29 4 100 1077 580456584 580455606 0.000000e+00 1596.0
14 TraesCS5D01G391800 chr5A 81.303 1305 182 38 784 2044 580559589 580560875 0.000000e+00 1002.0
15 TraesCS5D01G391800 chr5A 87.776 859 81 16 1575 2422 580452974 580452129 0.000000e+00 983.0
16 TraesCS5D01G391800 chr5A 91.762 522 37 1 1065 1580 580454300 580453779 0.000000e+00 721.0
17 TraesCS5D01G391800 chr5A 89.423 208 19 1 119 326 580558831 580559035 2.840000e-65 259.0
18 TraesCS5D01G391800 chr5A 83.456 272 30 6 2528 2794 580452113 580451852 3.700000e-59 239.0
19 TraesCS5D01G391800 chr5A 94.805 77 4 0 2797 2873 580451817 580451741 1.400000e-23 121.0
20 TraesCS5D01G391800 chr4B 87.667 300 36 1 164 463 448804447 448804745 5.890000e-92 348.0
21 TraesCS5D01G391800 chr4B 86.878 221 20 4 724 937 448804751 448804969 3.700000e-59 239.0
22 TraesCS5D01G391800 chr4B 90.769 65 6 0 2540 2604 436251202 436251266 1.420000e-13 87.9
23 TraesCS5D01G391800 chr1A 91.589 107 9 0 2 108 567596740 567596846 6.410000e-32 148.0
24 TraesCS5D01G391800 chr6D 89.041 73 4 2 2552 2624 287386552 287386620 1.420000e-13 87.9
25 TraesCS5D01G391800 chr7D 89.552 67 7 0 2539 2605 508419568 508419634 5.100000e-13 86.1
26 TraesCS5D01G391800 chr7D 85.714 63 9 0 2540 2602 550547155 550547217 1.850000e-07 67.6
27 TraesCS5D01G391800 chr7D 82.143 84 8 6 2552 2633 214363132 214363054 6.640000e-07 65.8
28 TraesCS5D01G391800 chr3D 89.231 65 7 0 2539 2603 418006356 418006420 6.600000e-12 82.4
29 TraesCS5D01G391800 chr3B 88.235 68 4 3 2543 2608 413029507 413029442 8.530000e-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 TraesCS5D01G391800 chr5D 460237471 460240343 2872 True 2685.900000 5306 95.0000 1 2873 2 chr5D.!!$R1 2872
1 TraesCS5D01G391800 chr5D 460444019 460447912 3893 False 464.666667 560 83.3310 119 2058 3 chr5D.!!$F1 1939
2 TraesCS5D01G391800 chr5B 565897964 565900615 2651 True 1782.500000 3369 88.3540 100 2873 2 chr5B.!!$R2 2773
3 TraesCS5D01G391800 chr5B 566122431 566124139 1708 False 790.000000 1134 86.0965 119 2087 2 chr5B.!!$F4 1968
4 TraesCS5D01G391800 chr5A 580451741 580456584 4843 True 732.000000 1596 90.7866 100 2873 5 chr5A.!!$R1 2773
5 TraesCS5D01G391800 chr5A 580558831 580560875 2044 False 630.500000 1002 85.3630 119 2044 2 chr5A.!!$F1 1925
6 TraesCS5D01G391800 chr4B 448804447 448804969 522 False 293.500000 348 87.2725 164 937 2 chr4B.!!$F2 773

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
84 85 0.099791 AAAAACACAGTGCGTTCGGG 59.900 50.0 0.0 0.0 0.00 5.14 F
92 93 0.179145 AGTGCGTTCGGGAGTTATCG 60.179 55.0 0.0 0.0 0.00 2.92 F
93 94 0.179156 GTGCGTTCGGGAGTTATCGA 60.179 55.0 0.0 0.0 0.00 3.59 F
1840 6561 0.467844 AAGCCACTGCACAATGACCA 60.468 50.0 0.0 0.0 41.13 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 6357 0.109412 GACAAGGTGAAGCATGCAGC 60.109 55.0 21.98 11.7 44.41 5.25 R
1840 6561 0.324830 GAGGTAGCTCTCCAGGGTGT 60.325 60.0 14.73 0.0 0.00 4.16 R
1857 6578 0.673644 ACGTTCAAATCCCCGCTGAG 60.674 55.0 0.00 0.0 0.00 3.35 R
2648 7431 0.469494 ATCCTATGTGCATGACGCCA 59.531 50.0 0.00 0.0 41.33 5.69 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
21 22 2.556534 GCACATGCTTCAAGATCCAC 57.443 50.000 0.00 0.00 38.21 4.02
22 23 1.202110 GCACATGCTTCAAGATCCACG 60.202 52.381 0.00 0.00 38.21 4.94
23 24 1.089920 ACATGCTTCAAGATCCACGC 58.910 50.000 0.00 0.00 0.00 5.34
24 25 1.339438 ACATGCTTCAAGATCCACGCT 60.339 47.619 0.00 0.00 0.00 5.07
25 26 2.093500 ACATGCTTCAAGATCCACGCTA 60.093 45.455 0.00 0.00 0.00 4.26
26 27 2.760634 TGCTTCAAGATCCACGCTAA 57.239 45.000 0.00 0.00 0.00 3.09
27 28 3.266510 TGCTTCAAGATCCACGCTAAT 57.733 42.857 0.00 0.00 0.00 1.73
28 29 3.609853 TGCTTCAAGATCCACGCTAATT 58.390 40.909 0.00 0.00 0.00 1.40
29 30 3.374988 TGCTTCAAGATCCACGCTAATTG 59.625 43.478 0.00 0.00 0.00 2.32
30 31 3.623060 GCTTCAAGATCCACGCTAATTGA 59.377 43.478 0.00 0.00 0.00 2.57
31 32 4.274459 GCTTCAAGATCCACGCTAATTGAT 59.726 41.667 0.00 0.00 0.00 2.57
32 33 5.559799 GCTTCAAGATCCACGCTAATTGATC 60.560 44.000 0.00 0.00 35.05 2.92
33 34 5.282055 TCAAGATCCACGCTAATTGATCT 57.718 39.130 0.00 0.00 44.32 2.75
34 35 6.405278 TCAAGATCCACGCTAATTGATCTA 57.595 37.500 4.63 0.00 42.25 1.98
35 36 6.816136 TCAAGATCCACGCTAATTGATCTAA 58.184 36.000 4.63 0.00 42.25 2.10
36 37 6.701841 TCAAGATCCACGCTAATTGATCTAAC 59.298 38.462 4.63 0.00 42.25 2.34
37 38 5.223382 AGATCCACGCTAATTGATCTAACG 58.777 41.667 2.71 0.00 41.51 3.18
38 39 4.642445 TCCACGCTAATTGATCTAACGA 57.358 40.909 0.00 0.00 0.00 3.85
39 40 5.196341 TCCACGCTAATTGATCTAACGAT 57.804 39.130 0.00 0.00 0.00 3.73
40 41 6.321848 TCCACGCTAATTGATCTAACGATA 57.678 37.500 0.00 0.00 0.00 2.92
41 42 6.147581 TCCACGCTAATTGATCTAACGATAC 58.852 40.000 0.00 0.00 0.00 2.24
42 43 5.918576 CCACGCTAATTGATCTAACGATACA 59.081 40.000 0.00 0.00 0.00 2.29
43 44 6.088217 CCACGCTAATTGATCTAACGATACAG 59.912 42.308 0.00 0.00 0.00 2.74
44 45 6.856426 CACGCTAATTGATCTAACGATACAGA 59.144 38.462 0.00 0.00 0.00 3.41
45 46 7.378728 CACGCTAATTGATCTAACGATACAGAA 59.621 37.037 0.00 0.00 0.00 3.02
46 47 7.378995 ACGCTAATTGATCTAACGATACAGAAC 59.621 37.037 0.00 0.00 0.00 3.01
47 48 7.408395 CGCTAATTGATCTAACGATACAGAACG 60.408 40.741 0.00 0.00 0.00 3.95
48 49 6.512177 AATTGATCTAACGATACAGAACGC 57.488 37.500 0.00 0.00 0.00 4.84
49 50 3.614588 TGATCTAACGATACAGAACGCG 58.385 45.455 3.53 3.53 0.00 6.01
50 51 3.064408 TGATCTAACGATACAGAACGCGT 59.936 43.478 5.58 5.58 38.81 6.01
51 52 3.476295 TCTAACGATACAGAACGCGTT 57.524 42.857 26.97 26.97 46.92 4.84
52 53 3.419915 TCTAACGATACAGAACGCGTTC 58.580 45.455 38.00 38.00 44.62 3.95
53 54 0.979811 AACGATACAGAACGCGTTCG 59.020 50.000 37.76 32.90 42.53 3.95
54 55 0.795735 ACGATACAGAACGCGTTCGG 60.796 55.000 38.37 38.37 43.97 4.30
55 56 0.521867 CGATACAGAACGCGTTCGGA 60.522 55.000 43.66 33.73 43.97 4.55
56 57 0.912528 GATACAGAACGCGTTCGGAC 59.087 55.000 43.66 31.58 43.97 4.79
57 58 0.524862 ATACAGAACGCGTTCGGACT 59.475 50.000 43.66 30.80 43.97 3.85
58 59 0.386352 TACAGAACGCGTTCGGACTG 60.386 55.000 43.66 35.37 43.97 3.51
59 60 1.371267 CAGAACGCGTTCGGACTGA 60.371 57.895 37.78 0.00 43.97 3.41
60 61 0.937699 CAGAACGCGTTCGGACTGAA 60.938 55.000 37.78 0.00 43.97 3.02
61 62 0.249155 AGAACGCGTTCGGACTGAAA 60.249 50.000 37.76 0.00 43.97 2.69
62 63 0.111398 GAACGCGTTCGGACTGAAAC 60.111 55.000 33.47 10.10 38.60 2.78
63 64 0.806884 AACGCGTTCGGACTGAAACA 60.807 50.000 20.79 0.00 38.60 2.83
64 65 1.200839 CGCGTTCGGACTGAAACAC 59.799 57.895 0.00 0.00 38.60 3.32
65 66 1.484227 CGCGTTCGGACTGAAACACA 61.484 55.000 0.00 0.00 38.60 3.72
66 67 0.653636 GCGTTCGGACTGAAACACAA 59.346 50.000 0.00 0.00 38.60 3.33
67 68 1.062880 GCGTTCGGACTGAAACACAAA 59.937 47.619 0.00 0.00 38.60 2.83
68 69 2.476519 GCGTTCGGACTGAAACACAAAA 60.477 45.455 0.00 0.00 38.60 2.44
69 70 3.749404 CGTTCGGACTGAAACACAAAAA 58.251 40.909 0.00 0.00 38.60 1.94
70 71 3.540738 CGTTCGGACTGAAACACAAAAAC 59.459 43.478 0.00 0.00 38.60 2.43
71 72 4.477780 GTTCGGACTGAAACACAAAAACA 58.522 39.130 0.00 0.00 38.60 2.83
72 73 4.086199 TCGGACTGAAACACAAAAACAC 57.914 40.909 0.00 0.00 0.00 3.32
73 74 3.502595 TCGGACTGAAACACAAAAACACA 59.497 39.130 0.00 0.00 0.00 3.72
74 75 3.851403 CGGACTGAAACACAAAAACACAG 59.149 43.478 0.00 0.00 0.00 3.66
75 76 4.614993 CGGACTGAAACACAAAAACACAGT 60.615 41.667 0.00 0.00 39.32 3.55
76 77 4.621034 GGACTGAAACACAAAAACACAGTG 59.379 41.667 0.00 0.00 37.27 3.66
77 78 3.987220 ACTGAAACACAAAAACACAGTGC 59.013 39.130 0.00 0.00 36.11 4.40
78 79 2.983136 TGAAACACAAAAACACAGTGCG 59.017 40.909 0.00 0.00 36.76 5.34
79 80 2.715737 AACACAAAAACACAGTGCGT 57.284 40.000 0.00 0.00 36.76 5.24
80 81 2.715737 ACACAAAAACACAGTGCGTT 57.284 40.000 0.00 0.00 36.76 4.84
81 82 2.591133 ACACAAAAACACAGTGCGTTC 58.409 42.857 0.00 0.00 36.76 3.95
82 83 1.577134 CACAAAAACACAGTGCGTTCG 59.423 47.619 0.00 0.00 0.00 3.95
83 84 1.187715 CAAAAACACAGTGCGTTCGG 58.812 50.000 0.00 0.00 0.00 4.30
84 85 0.099791 AAAAACACAGTGCGTTCGGG 59.900 50.000 0.00 0.00 0.00 5.14
85 86 0.745128 AAAACACAGTGCGTTCGGGA 60.745 50.000 0.00 0.00 0.00 5.14
86 87 1.157870 AAACACAGTGCGTTCGGGAG 61.158 55.000 0.00 0.00 0.00 4.30
87 88 2.029073 CACAGTGCGTTCGGGAGT 59.971 61.111 0.00 0.00 0.00 3.85
88 89 1.594293 CACAGTGCGTTCGGGAGTT 60.594 57.895 0.00 0.00 0.00 3.01
89 90 0.319211 CACAGTGCGTTCGGGAGTTA 60.319 55.000 0.00 0.00 0.00 2.24
90 91 0.606604 ACAGTGCGTTCGGGAGTTAT 59.393 50.000 0.00 0.00 0.00 1.89
91 92 1.278238 CAGTGCGTTCGGGAGTTATC 58.722 55.000 0.00 0.00 0.00 1.75
92 93 0.179145 AGTGCGTTCGGGAGTTATCG 60.179 55.000 0.00 0.00 0.00 2.92
93 94 0.179156 GTGCGTTCGGGAGTTATCGA 60.179 55.000 0.00 0.00 0.00 3.59
94 95 0.742505 TGCGTTCGGGAGTTATCGAT 59.257 50.000 2.16 2.16 35.25 3.59
95 96 1.135527 TGCGTTCGGGAGTTATCGATT 59.864 47.619 1.71 0.00 35.25 3.34
96 97 1.785430 GCGTTCGGGAGTTATCGATTC 59.215 52.381 1.71 0.00 35.25 2.52
97 98 2.391879 CGTTCGGGAGTTATCGATTCC 58.608 52.381 1.71 4.42 35.25 3.01
98 99 2.391879 GTTCGGGAGTTATCGATTCCG 58.608 52.381 1.71 9.97 35.06 4.30
108 109 8.654215 GGGAGTTATCGATTCCGTTTTATTATC 58.346 37.037 1.71 0.00 35.06 1.75
195 196 5.464057 CACTATGTCTGGTTTTGTGACGTAA 59.536 40.000 0.00 0.00 33.52 3.18
245 246 7.759886 CACAGAAAATCCTGACGAGTTATCTTA 59.240 37.037 0.00 0.00 37.59 2.10
387 732 1.704641 GATGAGTAAAATGGGCCCCC 58.295 55.000 22.27 0.00 0.00 5.40
471 823 6.149973 TGAACTTCTTCCTGATGTATTTGCTG 59.850 38.462 0.00 0.00 33.43 4.41
642 995 7.776618 TTCTCTTGAGTAGTTTGTCCTCATA 57.223 36.000 0.00 0.00 35.32 2.15
643 996 7.962995 TCTCTTGAGTAGTTTGTCCTCATAT 57.037 36.000 0.00 0.00 35.32 1.78
686 1046 5.066893 TGAGATACTGGATTGCTTGCAATTC 59.933 40.000 19.90 18.51 0.00 2.17
687 1047 2.642139 ACTGGATTGCTTGCAATTCG 57.358 45.000 19.90 15.93 0.00 3.34
889 1277 7.147983 TGCAACTGATATTGTTAACCCCATAAC 60.148 37.037 2.48 0.00 36.52 1.89
974 1362 2.039818 TGTGTTCGGTGGCTTTAACA 57.960 45.000 0.00 0.00 0.00 2.41
1010 1400 8.653338 TGTCTAAAAATAGCTCATGTTTCGTAC 58.347 33.333 0.00 0.00 0.00 3.67
1291 5184 4.637276 TGATCTTGCGGTTAAGAGTTCAA 58.363 39.130 0.00 0.00 39.81 2.69
1350 5243 5.433051 TCAGGAGAACATTCCTTGGGATAAT 59.567 40.000 0.00 0.00 45.35 1.28
1468 5367 2.418976 CTGCATGTGACAGTCAAGATGG 59.581 50.000 19.05 5.63 0.00 3.51
1589 6298 1.138247 GCTTCATCTTTGCCGGCAG 59.862 57.895 30.75 19.71 0.00 4.85
1605 6314 1.440893 CAGGGTGCTCGAGGATGAG 59.559 63.158 15.58 0.00 39.05 2.90
1632 6341 1.732259 CTGGCGGACTACAACATTCAC 59.268 52.381 0.00 0.00 0.00 3.18
1637 6351 3.120649 GCGGACTACAACATTCACAAGTC 60.121 47.826 0.00 0.00 34.08 3.01
1638 6352 3.432252 CGGACTACAACATTCACAAGTCC 59.568 47.826 8.87 8.87 46.18 3.85
1642 6356 1.956477 ACAACATTCACAAGTCCTGGC 59.044 47.619 0.00 0.00 0.00 4.85
1643 6357 1.069022 CAACATTCACAAGTCCTGGCG 60.069 52.381 0.00 0.00 0.00 5.69
1644 6358 1.237285 ACATTCACAAGTCCTGGCGC 61.237 55.000 0.00 0.00 0.00 6.53
1649 6363 2.749044 CAAGTCCTGGCGCTGCAT 60.749 61.111 7.64 0.00 0.00 3.96
1666 6380 1.171308 CATGCTTCACCTTGTCCTGG 58.829 55.000 0.00 0.00 0.00 4.45
1669 6383 1.763770 CTTCACCTTGTCCTGGGCT 59.236 57.895 0.00 0.00 0.00 5.19
1672 6386 1.303643 CACCTTGTCCTGGGCTTCC 60.304 63.158 0.00 0.00 0.00 3.46
1674 6388 2.750350 CTTGTCCTGGGCTTCCGT 59.250 61.111 0.00 0.00 0.00 4.69
1747 6464 1.507141 GGTTGGCACTCAAGACACGG 61.507 60.000 0.00 0.00 35.80 4.94
1840 6561 0.467844 AAGCCACTGCACAATGACCA 60.468 50.000 0.00 0.00 41.13 4.02
1857 6578 1.617947 CCACACCCTGGAGAGCTACC 61.618 65.000 0.00 2.82 43.95 3.18
2033 6806 4.246458 GTCAATGGAGTCTAAGCGAAGTT 58.754 43.478 0.00 0.00 0.00 2.66
2052 6829 7.754027 GCGAAGTTGAACTGTTAGAAGTCTATA 59.246 37.037 0.00 0.00 0.00 1.31
2053 6830 9.790389 CGAAGTTGAACTGTTAGAAGTCTATAT 57.210 33.333 0.00 0.00 0.00 0.86
2096 6873 2.396601 CGCATGCAGTTTGTGTCAATT 58.603 42.857 19.57 0.00 0.00 2.32
2160 6937 3.181461 TGGTTTGTGTTGGCTTTAATGGG 60.181 43.478 0.00 0.00 0.00 4.00
2433 7216 1.673168 AAGGAAATCAGCGATGGAGC 58.327 50.000 0.00 0.00 37.41 4.70
2434 7217 0.179034 AGGAAATCAGCGATGGAGCC 60.179 55.000 0.00 0.00 38.01 4.70
2442 7225 4.847516 CGATGGAGCCGCGTCGAA 62.848 66.667 4.92 0.00 36.25 3.71
2443 7226 3.255379 GATGGAGCCGCGTCGAAC 61.255 66.667 4.92 0.00 0.00 3.95
2444 7227 3.701604 GATGGAGCCGCGTCGAACT 62.702 63.158 4.92 0.00 0.00 3.01
2445 7228 3.989698 ATGGAGCCGCGTCGAACTG 62.990 63.158 4.92 0.00 0.00 3.16
2449 7232 2.883730 GCCGCGTCGAACTGCATA 60.884 61.111 4.92 0.00 0.00 3.14
2450 7233 2.237751 GCCGCGTCGAACTGCATAT 61.238 57.895 4.92 0.00 0.00 1.78
2451 7234 1.846648 CCGCGTCGAACTGCATATC 59.153 57.895 4.92 0.00 0.00 1.63
2452 7235 0.869880 CCGCGTCGAACTGCATATCA 60.870 55.000 4.92 0.00 0.00 2.15
2454 7237 0.230769 GCGTCGAACTGCATATCAGC 59.769 55.000 0.00 0.00 46.76 4.26
2455 7238 0.500178 CGTCGAACTGCATATCAGCG 59.500 55.000 0.00 0.00 46.76 5.18
2456 7239 1.840181 GTCGAACTGCATATCAGCGA 58.160 50.000 0.00 0.00 46.76 4.93
2457 7240 2.193447 GTCGAACTGCATATCAGCGAA 58.807 47.619 0.00 0.00 46.76 4.70
2458 7241 2.797156 GTCGAACTGCATATCAGCGAAT 59.203 45.455 0.00 0.00 46.76 3.34
2459 7242 2.796593 TCGAACTGCATATCAGCGAATG 59.203 45.455 0.00 0.00 46.76 2.67
2460 7243 2.661169 CGAACTGCATATCAGCGAATGC 60.661 50.000 8.17 8.17 46.76 3.56
2480 7263 5.499139 TGCTAAGGTGCATACATTTTAGC 57.501 39.130 13.44 13.44 43.58 3.09
2481 7264 4.338118 TGCTAAGGTGCATACATTTTAGCC 59.662 41.667 15.91 1.03 43.15 3.93
2482 7265 4.338118 GCTAAGGTGCATACATTTTAGCCA 59.662 41.667 10.87 0.00 40.75 4.75
2483 7266 5.010012 GCTAAGGTGCATACATTTTAGCCAT 59.990 40.000 10.87 0.00 40.75 4.40
2484 7267 6.206634 GCTAAGGTGCATACATTTTAGCCATA 59.793 38.462 10.87 0.00 40.75 2.74
2485 7268 7.255451 GCTAAGGTGCATACATTTTAGCCATAA 60.255 37.037 10.87 0.00 40.75 1.90
2486 7269 7.416964 AAGGTGCATACATTTTAGCCATAAA 57.583 32.000 0.00 0.00 0.00 1.40
2487 7270 7.416964 AGGTGCATACATTTTAGCCATAAAA 57.583 32.000 0.00 0.00 43.24 1.52
2488 7271 7.264947 AGGTGCATACATTTTAGCCATAAAAC 58.735 34.615 0.00 0.00 42.21 2.43
2489 7272 7.124147 AGGTGCATACATTTTAGCCATAAAACT 59.876 33.333 0.00 0.00 42.21 2.66
2490 7273 7.763985 GGTGCATACATTTTAGCCATAAAACTT 59.236 33.333 0.00 0.00 42.21 2.66
2491 7274 9.150348 GTGCATACATTTTAGCCATAAAACTTT 57.850 29.630 0.00 0.00 42.21 2.66
2492 7275 9.364989 TGCATACATTTTAGCCATAAAACTTTC 57.635 29.630 0.00 0.00 42.21 2.62
2493 7276 8.817100 GCATACATTTTAGCCATAAAACTTTCC 58.183 33.333 0.00 0.00 42.21 3.13
2494 7277 9.313118 CATACATTTTAGCCATAAAACTTTCCC 57.687 33.333 0.00 0.00 42.21 3.97
2495 7278 6.707290 ACATTTTAGCCATAAAACTTTCCCC 58.293 36.000 0.00 0.00 42.21 4.81
2496 7279 6.500400 ACATTTTAGCCATAAAACTTTCCCCT 59.500 34.615 0.00 0.00 42.21 4.79
2497 7280 7.017155 ACATTTTAGCCATAAAACTTTCCCCTT 59.983 33.333 0.00 0.00 42.21 3.95
2498 7281 7.381789 TTTTAGCCATAAAACTTTCCCCTTT 57.618 32.000 0.00 0.00 36.24 3.11
2499 7282 7.381789 TTTAGCCATAAAACTTTCCCCTTTT 57.618 32.000 0.00 0.00 0.00 2.27
2500 7283 5.904984 AGCCATAAAACTTTCCCCTTTTT 57.095 34.783 0.00 0.00 0.00 1.94
2501 7284 5.865085 AGCCATAAAACTTTCCCCTTTTTC 58.135 37.500 0.00 0.00 0.00 2.29
2502 7285 5.001232 GCCATAAAACTTTCCCCTTTTTCC 58.999 41.667 0.00 0.00 0.00 3.13
2503 7286 5.221843 GCCATAAAACTTTCCCCTTTTTCCT 60.222 40.000 0.00 0.00 0.00 3.36
2504 7287 6.690460 GCCATAAAACTTTCCCCTTTTTCCTT 60.690 38.462 0.00 0.00 0.00 3.36
2505 7288 7.287061 CCATAAAACTTTCCCCTTTTTCCTTT 58.713 34.615 0.00 0.00 0.00 3.11
2506 7289 7.444183 CCATAAAACTTTCCCCTTTTTCCTTTC 59.556 37.037 0.00 0.00 0.00 2.62
2507 7290 5.367945 AAACTTTCCCCTTTTTCCTTTCC 57.632 39.130 0.00 0.00 0.00 3.13
2508 7291 4.280789 ACTTTCCCCTTTTTCCTTTCCT 57.719 40.909 0.00 0.00 0.00 3.36
2509 7292 4.223953 ACTTTCCCCTTTTTCCTTTCCTC 58.776 43.478 0.00 0.00 0.00 3.71
2510 7293 4.078571 ACTTTCCCCTTTTTCCTTTCCTCT 60.079 41.667 0.00 0.00 0.00 3.69
2511 7294 4.552883 TTCCCCTTTTTCCTTTCCTCTT 57.447 40.909 0.00 0.00 0.00 2.85
2512 7295 4.552883 TCCCCTTTTTCCTTTCCTCTTT 57.447 40.909 0.00 0.00 0.00 2.52
2513 7296 4.223144 TCCCCTTTTTCCTTTCCTCTTTG 58.777 43.478 0.00 0.00 0.00 2.77
2514 7297 3.324846 CCCCTTTTTCCTTTCCTCTTTGG 59.675 47.826 0.00 0.00 37.10 3.28
2515 7298 3.967326 CCCTTTTTCCTTTCCTCTTTGGT 59.033 43.478 0.00 0.00 37.07 3.67
2516 7299 4.202253 CCCTTTTTCCTTTCCTCTTTGGTG 60.202 45.833 0.00 0.00 37.07 4.17
2517 7300 4.649218 CCTTTTTCCTTTCCTCTTTGGTGA 59.351 41.667 0.00 0.00 37.07 4.02
2518 7301 5.305386 CCTTTTTCCTTTCCTCTTTGGTGAT 59.695 40.000 0.00 0.00 37.07 3.06
2519 7302 6.493458 CCTTTTTCCTTTCCTCTTTGGTGATA 59.507 38.462 0.00 0.00 37.07 2.15
2520 7303 7.015195 CCTTTTTCCTTTCCTCTTTGGTGATAA 59.985 37.037 0.00 0.00 37.07 1.75
2521 7304 6.894339 TTTCCTTTCCTCTTTGGTGATAAC 57.106 37.500 0.00 0.00 37.07 1.89
2522 7305 5.576563 TCCTTTCCTCTTTGGTGATAACA 57.423 39.130 0.00 0.00 37.07 2.41
2523 7306 5.947663 TCCTTTCCTCTTTGGTGATAACAA 58.052 37.500 0.00 0.00 37.07 2.83
2524 7307 6.552008 TCCTTTCCTCTTTGGTGATAACAAT 58.448 36.000 0.00 0.00 37.07 2.71
2525 7308 7.010160 TCCTTTCCTCTTTGGTGATAACAATT 58.990 34.615 0.00 0.00 37.07 2.32
2526 7309 7.508977 TCCTTTCCTCTTTGGTGATAACAATTT 59.491 33.333 0.00 0.00 37.07 1.82
2527 7310 8.802267 CCTTTCCTCTTTGGTGATAACAATTTA 58.198 33.333 0.00 0.00 37.07 1.40
2531 7314 9.527157 TCCTCTTTGGTGATAACAATTTATTGA 57.473 29.630 9.32 0.00 37.88 2.57
2535 7318 8.715191 TTTGGTGATAACAATTTATTGATGGC 57.285 30.769 9.32 0.00 40.14 4.40
2536 7319 7.658525 TGGTGATAACAATTTATTGATGGCT 57.341 32.000 9.32 0.00 40.14 4.75
2537 7320 8.759481 TGGTGATAACAATTTATTGATGGCTA 57.241 30.769 9.32 0.00 40.14 3.93
2575 7358 0.321034 TGCATATCAGCGATGGAGCC 60.321 55.000 0.00 0.00 38.01 4.70
2583 7366 3.812203 CGATGGAGCCGCATCAAA 58.188 55.556 0.00 0.00 0.00 2.69
2603 7386 0.461961 CTCGGGTGAAGAGGTGATCC 59.538 60.000 0.00 0.00 32.38 3.36
2613 7396 0.462047 GAGGTGATCCGCCACGATTT 60.462 55.000 6.25 0.00 37.91 2.17
2614 7397 0.035439 AGGTGATCCGCCACGATTTT 60.035 50.000 6.25 0.00 37.91 1.82
2615 7398 0.098728 GGTGATCCGCCACGATTTTG 59.901 55.000 0.00 0.00 37.91 2.44
2616 7399 1.083489 GTGATCCGCCACGATTTTGA 58.917 50.000 0.00 0.00 0.00 2.69
2617 7400 1.670811 GTGATCCGCCACGATTTTGAT 59.329 47.619 0.00 0.00 0.00 2.57
2618 7401 2.097466 GTGATCCGCCACGATTTTGATT 59.903 45.455 0.00 0.00 0.00 2.57
2619 7402 2.752354 TGATCCGCCACGATTTTGATTT 59.248 40.909 0.00 0.00 0.00 2.17
2650 7433 2.755469 CCGGTGATGGGCCTTTGG 60.755 66.667 4.53 0.00 0.00 3.28
2671 7454 3.653344 GCGTCATGCACATAGGATTCTA 58.347 45.455 0.00 0.00 45.45 2.10
2677 7460 2.034179 TGCACATAGGATTCTACGGTCG 59.966 50.000 0.00 0.00 0.00 4.79
2704 7487 8.686334 TGATTTTTATCTAGGCTGATGGTTTTC 58.314 33.333 0.00 0.00 0.00 2.29
2709 7492 1.021390 AGGCTGATGGTTTTCGAGCG 61.021 55.000 0.00 0.00 0.00 5.03
2729 7512 4.679662 GCGAATGCTAAGGTTCTACTGTA 58.320 43.478 0.00 0.00 38.39 2.74
2756 7543 6.256321 TCTCAGTTTTGTTTACGTGACTTACC 59.744 38.462 0.00 0.00 0.00 2.85
2765 7552 5.950758 TTACGTGACTTACCATGCAAAAT 57.049 34.783 0.00 0.00 0.00 1.82
2770 7557 6.205853 ACGTGACTTACCATGCAAAATAAGAA 59.794 34.615 16.71 6.03 0.00 2.52
2771 7558 6.523201 CGTGACTTACCATGCAAAATAAGAAC 59.477 38.462 16.71 13.39 0.00 3.01
2783 7570 6.483974 TGCAAAATAAGAACGGTGAAAGTAGA 59.516 34.615 0.00 0.00 0.00 2.59
2848 7667 9.612620 CTAAAGTTTACTGATTGTTTTAGCCAG 57.387 33.333 0.00 0.00 0.00 4.85
2856 7675 7.224297 ACTGATTGTTTTAGCCAGAACTAAGA 58.776 34.615 0.00 0.00 33.80 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.202110 CGTGGATCTTGAAGCATGTGC 60.202 52.381 0.00 0.00 42.49 4.57
3 4 1.202110 GCGTGGATCTTGAAGCATGTG 60.202 52.381 0.00 0.00 0.00 3.21
4 5 1.089920 GCGTGGATCTTGAAGCATGT 58.910 50.000 0.00 0.00 0.00 3.21
5 6 1.376543 AGCGTGGATCTTGAAGCATG 58.623 50.000 0.00 0.00 0.00 4.06
6 7 2.988010 TAGCGTGGATCTTGAAGCAT 57.012 45.000 0.00 0.00 0.00 3.79
8 9 3.623060 TCAATTAGCGTGGATCTTGAAGC 59.377 43.478 0.00 0.00 0.00 3.86
9 10 5.757320 AGATCAATTAGCGTGGATCTTGAAG 59.243 40.000 0.00 0.00 42.77 3.02
10 11 5.674525 AGATCAATTAGCGTGGATCTTGAA 58.325 37.500 0.00 0.00 42.77 2.69
12 13 6.346120 CGTTAGATCAATTAGCGTGGATCTTG 60.346 42.308 10.60 1.57 42.77 3.02
13 14 5.692204 CGTTAGATCAATTAGCGTGGATCTT 59.308 40.000 10.60 0.00 42.77 2.40
14 15 5.009710 TCGTTAGATCAATTAGCGTGGATCT 59.990 40.000 10.30 10.30 46.02 2.75
15 16 5.220381 TCGTTAGATCAATTAGCGTGGATC 58.780 41.667 0.00 0.00 37.11 3.36
16 17 5.196341 TCGTTAGATCAATTAGCGTGGAT 57.804 39.130 0.00 0.00 0.00 3.41
17 18 4.642445 TCGTTAGATCAATTAGCGTGGA 57.358 40.909 0.00 0.00 0.00 4.02
18 19 5.918576 TGTATCGTTAGATCAATTAGCGTGG 59.081 40.000 0.00 0.00 38.26 4.94
19 20 6.856426 TCTGTATCGTTAGATCAATTAGCGTG 59.144 38.462 0.00 0.00 38.26 5.34
20 21 6.967135 TCTGTATCGTTAGATCAATTAGCGT 58.033 36.000 0.00 0.00 38.26 5.07
21 22 7.408395 CGTTCTGTATCGTTAGATCAATTAGCG 60.408 40.741 0.00 0.00 38.26 4.26
22 23 7.617528 GCGTTCTGTATCGTTAGATCAATTAGC 60.618 40.741 0.00 0.00 38.26 3.09
23 24 7.408395 CGCGTTCTGTATCGTTAGATCAATTAG 60.408 40.741 0.00 0.00 38.26 1.73
24 25 6.358822 CGCGTTCTGTATCGTTAGATCAATTA 59.641 38.462 0.00 0.00 38.26 1.40
25 26 5.173312 CGCGTTCTGTATCGTTAGATCAATT 59.827 40.000 0.00 0.00 38.26 2.32
26 27 4.675565 CGCGTTCTGTATCGTTAGATCAAT 59.324 41.667 0.00 0.00 38.26 2.57
27 28 4.033019 CGCGTTCTGTATCGTTAGATCAA 58.967 43.478 0.00 0.00 38.26 2.57
28 29 3.064408 ACGCGTTCTGTATCGTTAGATCA 59.936 43.478 5.58 0.00 38.26 2.92
29 30 3.615614 ACGCGTTCTGTATCGTTAGATC 58.384 45.455 5.58 0.00 38.26 2.75
30 31 3.687572 ACGCGTTCTGTATCGTTAGAT 57.312 42.857 5.58 0.00 40.76 1.98
31 32 3.419915 GAACGCGTTCTGTATCGTTAGA 58.580 45.455 37.61 0.00 43.91 2.10
32 33 2.210485 CGAACGCGTTCTGTATCGTTAG 59.790 50.000 39.54 21.87 43.91 2.34
33 34 2.168384 CGAACGCGTTCTGTATCGTTA 58.832 47.619 39.54 0.00 43.91 3.18
34 35 0.979811 CGAACGCGTTCTGTATCGTT 59.020 50.000 39.54 11.42 46.11 3.85
35 36 0.795735 CCGAACGCGTTCTGTATCGT 60.796 55.000 39.54 12.20 37.44 3.73
36 37 0.521867 TCCGAACGCGTTCTGTATCG 60.522 55.000 39.54 29.59 37.44 2.92
37 38 0.912528 GTCCGAACGCGTTCTGTATC 59.087 55.000 39.54 25.71 37.44 2.24
38 39 0.524862 AGTCCGAACGCGTTCTGTAT 59.475 50.000 39.54 26.05 37.44 2.29
39 40 0.386352 CAGTCCGAACGCGTTCTGTA 60.386 55.000 39.54 25.88 37.44 2.74
40 41 1.660575 CAGTCCGAACGCGTTCTGT 60.661 57.895 39.54 23.23 37.44 3.41
41 42 0.937699 TTCAGTCCGAACGCGTTCTG 60.938 55.000 39.54 34.95 37.44 3.02
42 43 0.249155 TTTCAGTCCGAACGCGTTCT 60.249 50.000 39.54 24.39 37.44 3.01
43 44 0.111398 GTTTCAGTCCGAACGCGTTC 60.111 55.000 35.95 35.95 31.73 3.95
44 45 0.806884 TGTTTCAGTCCGAACGCGTT 60.807 50.000 26.97 26.97 31.73 4.84
45 46 1.227031 TGTTTCAGTCCGAACGCGT 60.227 52.632 5.58 5.58 31.73 6.01
46 47 1.200839 GTGTTTCAGTCCGAACGCG 59.799 57.895 3.53 3.53 31.73 6.01
47 48 0.653636 TTGTGTTTCAGTCCGAACGC 59.346 50.000 0.00 0.00 31.73 4.84
48 49 3.392769 TTTTGTGTTTCAGTCCGAACG 57.607 42.857 0.00 0.00 31.73 3.95
49 50 4.322539 GTGTTTTTGTGTTTCAGTCCGAAC 59.677 41.667 0.00 0.00 31.73 3.95
50 51 4.023107 TGTGTTTTTGTGTTTCAGTCCGAA 60.023 37.500 0.00 0.00 0.00 4.30
51 52 3.502595 TGTGTTTTTGTGTTTCAGTCCGA 59.497 39.130 0.00 0.00 0.00 4.55
52 53 3.827625 TGTGTTTTTGTGTTTCAGTCCG 58.172 40.909 0.00 0.00 0.00 4.79
53 54 4.621034 CACTGTGTTTTTGTGTTTCAGTCC 59.379 41.667 0.00 0.00 33.35 3.85
54 55 4.089923 GCACTGTGTTTTTGTGTTTCAGTC 59.910 41.667 9.86 0.00 33.35 3.51
55 56 3.987220 GCACTGTGTTTTTGTGTTTCAGT 59.013 39.130 9.86 0.00 35.49 3.41
56 57 3.059306 CGCACTGTGTTTTTGTGTTTCAG 59.941 43.478 9.86 0.00 34.52 3.02
57 58 2.983136 CGCACTGTGTTTTTGTGTTTCA 59.017 40.909 9.86 0.00 34.52 2.69
58 59 2.983803 ACGCACTGTGTTTTTGTGTTTC 59.016 40.909 9.86 0.00 34.52 2.78
59 60 3.019933 ACGCACTGTGTTTTTGTGTTT 57.980 38.095 9.86 0.00 34.52 2.83
60 61 2.715737 ACGCACTGTGTTTTTGTGTT 57.284 40.000 9.86 0.00 34.52 3.32
61 62 2.591133 GAACGCACTGTGTTTTTGTGT 58.409 42.857 9.32 0.00 36.34 3.72
62 63 1.577134 CGAACGCACTGTGTTTTTGTG 59.423 47.619 9.32 0.00 36.34 3.33
63 64 1.466697 CCGAACGCACTGTGTTTTTGT 60.467 47.619 9.32 0.00 36.34 2.83
64 65 1.187715 CCGAACGCACTGTGTTTTTG 58.812 50.000 9.32 6.70 36.34 2.44
65 66 0.099791 CCCGAACGCACTGTGTTTTT 59.900 50.000 9.32 0.23 36.34 1.94
66 67 0.745128 TCCCGAACGCACTGTGTTTT 60.745 50.000 9.32 2.79 36.34 2.43
67 68 1.153329 TCCCGAACGCACTGTGTTT 60.153 52.632 9.32 3.16 36.34 2.83
68 69 1.594293 CTCCCGAACGCACTGTGTT 60.594 57.895 7.71 7.71 39.06 3.32
69 70 2.029073 CTCCCGAACGCACTGTGT 59.971 61.111 9.86 0.00 0.00 3.72
70 71 0.319211 TAACTCCCGAACGCACTGTG 60.319 55.000 2.76 2.76 0.00 3.66
71 72 0.606604 ATAACTCCCGAACGCACTGT 59.393 50.000 0.00 0.00 0.00 3.55
72 73 1.278238 GATAACTCCCGAACGCACTG 58.722 55.000 0.00 0.00 0.00 3.66
73 74 0.179145 CGATAACTCCCGAACGCACT 60.179 55.000 0.00 0.00 0.00 4.40
74 75 0.179156 TCGATAACTCCCGAACGCAC 60.179 55.000 0.00 0.00 0.00 5.34
75 76 0.742505 ATCGATAACTCCCGAACGCA 59.257 50.000 0.00 0.00 38.36 5.24
76 77 1.785430 GAATCGATAACTCCCGAACGC 59.215 52.381 0.00 0.00 38.36 4.84
77 78 2.391879 GGAATCGATAACTCCCGAACG 58.608 52.381 0.00 0.00 38.36 3.95
78 79 2.223665 ACGGAATCGATAACTCCCGAAC 60.224 50.000 21.44 0.00 40.10 3.95
79 80 2.026641 ACGGAATCGATAACTCCCGAA 58.973 47.619 21.44 0.00 40.10 4.30
80 81 1.683943 ACGGAATCGATAACTCCCGA 58.316 50.000 21.44 0.00 40.10 5.14
81 82 2.503920 AACGGAATCGATAACTCCCG 57.496 50.000 16.24 16.24 42.30 5.14
82 83 6.856135 AATAAAACGGAATCGATAACTCCC 57.144 37.500 8.68 1.07 40.11 4.30
83 84 9.420551 AGATAATAAAACGGAATCGATAACTCC 57.579 33.333 0.00 0.78 40.11 3.85
87 88 9.767228 TGGAAGATAATAAAACGGAATCGATAA 57.233 29.630 0.00 0.00 40.11 1.75
88 89 9.767228 TTGGAAGATAATAAAACGGAATCGATA 57.233 29.630 0.00 0.00 40.11 2.92
89 90 8.671384 TTGGAAGATAATAAAACGGAATCGAT 57.329 30.769 0.00 0.00 40.11 3.59
90 91 7.767198 ACTTGGAAGATAATAAAACGGAATCGA 59.233 33.333 0.00 0.00 40.11 3.59
91 92 7.850982 CACTTGGAAGATAATAAAACGGAATCG 59.149 37.037 0.00 0.00 43.02 3.34
92 93 7.644157 GCACTTGGAAGATAATAAAACGGAATC 59.356 37.037 0.00 0.00 0.00 2.52
93 94 7.122055 TGCACTTGGAAGATAATAAAACGGAAT 59.878 33.333 0.00 0.00 0.00 3.01
94 95 6.431543 TGCACTTGGAAGATAATAAAACGGAA 59.568 34.615 0.00 0.00 0.00 4.30
95 96 5.941058 TGCACTTGGAAGATAATAAAACGGA 59.059 36.000 0.00 0.00 0.00 4.69
96 97 6.027749 GTGCACTTGGAAGATAATAAAACGG 58.972 40.000 10.32 0.00 0.00 4.44
97 98 6.027749 GGTGCACTTGGAAGATAATAAAACG 58.972 40.000 17.98 0.00 0.00 3.60
98 99 6.919721 TGGTGCACTTGGAAGATAATAAAAC 58.080 36.000 17.98 0.00 0.00 2.43
108 109 4.853924 AATACTTTGGTGCACTTGGAAG 57.146 40.909 17.98 16.32 0.00 3.46
245 246 4.260170 GTGCAAGAGAATGACAGAGGAAT 58.740 43.478 0.00 0.00 0.00 3.01
403 755 6.691255 AGTGTAGGGTTTGTCCACTTAATA 57.309 37.500 0.00 0.00 38.11 0.98
471 823 3.954258 CCCCTCCAAATTAATCCACAGAC 59.046 47.826 0.00 0.00 0.00 3.51
686 1046 1.266718 AGCTAAAACACACACATGCCG 59.733 47.619 0.00 0.00 0.00 5.69
687 1047 3.243367 TGAAGCTAAAACACACACATGCC 60.243 43.478 0.00 0.00 0.00 4.40
889 1277 2.485426 AGCCACAACAAATCGACAGATG 59.515 45.455 0.00 0.00 37.14 2.90
1010 1400 2.404265 TTGCATCTGTTGAACAAGCG 57.596 45.000 0.00 0.00 0.00 4.68
1291 5184 3.009723 CCTTGACGTGCTTGATGGTATT 58.990 45.455 0.00 0.00 0.00 1.89
1350 5243 0.250234 CGGCAAAGATGAGACCCTGA 59.750 55.000 0.00 0.00 0.00 3.86
1468 5367 1.014044 TCAATGCTCTCGCCGTTCAC 61.014 55.000 0.00 0.00 34.43 3.18
1562 5461 0.179145 AAAGATGAAGCGCTGCATGC 60.179 50.000 35.47 24.07 38.57 4.06
1605 6314 3.142838 TAGTCCGCCAGGGTACGC 61.143 66.667 0.77 0.77 38.33 4.42
1632 6341 2.749044 ATGCAGCGCCAGGACTTG 60.749 61.111 2.29 0.00 0.00 3.16
1643 6357 0.109412 GACAAGGTGAAGCATGCAGC 60.109 55.000 21.98 11.70 44.41 5.25
1644 6358 0.524862 GGACAAGGTGAAGCATGCAG 59.475 55.000 21.98 1.43 0.00 4.41
1649 6363 1.455849 CCCAGGACAAGGTGAAGCA 59.544 57.895 0.00 0.00 0.00 3.91
1666 6380 1.068741 CACTCCATACCTACGGAAGCC 59.931 57.143 0.00 0.00 0.00 4.35
1669 6383 3.317149 CGAATCACTCCATACCTACGGAA 59.683 47.826 0.00 0.00 0.00 4.30
1672 6386 2.034179 TGCGAATCACTCCATACCTACG 59.966 50.000 0.00 0.00 0.00 3.51
1674 6388 3.895041 TGATGCGAATCACTCCATACCTA 59.105 43.478 0.51 0.00 0.00 3.08
1678 6392 4.371786 GTCTTGATGCGAATCACTCCATA 58.628 43.478 5.28 0.00 0.00 2.74
1681 6395 1.590238 CGTCTTGATGCGAATCACTCC 59.410 52.381 5.28 0.00 0.00 3.85
1738 6455 2.069273 GACATCCTCAACCGTGTCTTG 58.931 52.381 0.00 0.00 38.29 3.02
1747 6464 1.667724 CATCGCCTTGACATCCTCAAC 59.332 52.381 0.00 0.00 33.65 3.18
1840 6561 0.324830 GAGGTAGCTCTCCAGGGTGT 60.325 60.000 14.73 0.00 0.00 4.16
1857 6578 0.673644 ACGTTCAAATCCCCGCTGAG 60.674 55.000 0.00 0.00 0.00 3.35
2052 6829 5.335661 GGGCGACTTCTGACAAAATTACAAT 60.336 40.000 0.00 0.00 0.00 2.71
2053 6830 4.023536 GGGCGACTTCTGACAAAATTACAA 60.024 41.667 0.00 0.00 0.00 2.41
2061 6838 2.357034 GCGGGCGACTTCTGACAA 60.357 61.111 0.00 0.00 0.00 3.18
2096 6873 0.181114 AGCCACAAACAGTCAGCTGA 59.819 50.000 13.74 13.74 45.28 4.26
2160 6937 1.202405 CCAACCAGCAAAGACAACCAC 60.202 52.381 0.00 0.00 0.00 4.16
2425 7208 4.847516 TTCGACGCGGCTCCATCG 62.848 66.667 11.76 9.57 35.91 3.84
2426 7209 3.255379 GTTCGACGCGGCTCCATC 61.255 66.667 11.76 0.00 0.00 3.51
2427 7210 3.760035 AGTTCGACGCGGCTCCAT 61.760 61.111 11.76 0.00 0.00 3.41
2428 7211 4.717629 CAGTTCGACGCGGCTCCA 62.718 66.667 11.76 0.00 0.00 3.86
2433 7216 0.869880 TGATATGCAGTTCGACGCGG 60.870 55.000 12.47 0.00 0.00 6.46
2434 7217 0.500178 CTGATATGCAGTTCGACGCG 59.500 55.000 3.53 3.53 39.85 6.01
2436 7219 0.500178 CGCTGATATGCAGTTCGACG 59.500 55.000 0.00 0.00 46.62 5.12
2437 7220 1.840181 TCGCTGATATGCAGTTCGAC 58.160 50.000 0.00 0.00 46.62 4.20
2439 7222 2.661169 GCATTCGCTGATATGCAGTTCG 60.661 50.000 0.00 0.00 46.62 3.95
2440 7223 2.913613 GCATTCGCTGATATGCAGTTC 58.086 47.619 0.00 0.00 46.62 3.01
2459 7242 4.338118 TGGCTAAAATGTATGCACCTTAGC 59.662 41.667 21.08 21.08 42.01 3.09
2460 7243 6.639632 ATGGCTAAAATGTATGCACCTTAG 57.360 37.500 0.00 8.52 0.00 2.18
2461 7244 8.526667 TTTATGGCTAAAATGTATGCACCTTA 57.473 30.769 0.00 0.00 0.00 2.69
2462 7245 7.416964 TTTATGGCTAAAATGTATGCACCTT 57.583 32.000 0.00 0.00 0.00 3.50
2463 7246 7.124147 AGTTTTATGGCTAAAATGTATGCACCT 59.876 33.333 0.00 0.00 38.66 4.00
2464 7247 7.264947 AGTTTTATGGCTAAAATGTATGCACC 58.735 34.615 0.00 0.00 38.66 5.01
2465 7248 8.702163 AAGTTTTATGGCTAAAATGTATGCAC 57.298 30.769 0.00 0.00 38.66 4.57
2466 7249 9.364989 GAAAGTTTTATGGCTAAAATGTATGCA 57.635 29.630 0.00 0.00 38.66 3.96
2467 7250 8.817100 GGAAAGTTTTATGGCTAAAATGTATGC 58.183 33.333 0.00 0.00 38.66 3.14
2468 7251 9.313118 GGGAAAGTTTTATGGCTAAAATGTATG 57.687 33.333 0.00 0.00 38.66 2.39
2469 7252 8.482943 GGGGAAAGTTTTATGGCTAAAATGTAT 58.517 33.333 0.00 0.00 38.66 2.29
2470 7253 7.676468 AGGGGAAAGTTTTATGGCTAAAATGTA 59.324 33.333 0.00 0.00 38.66 2.29
2471 7254 6.500400 AGGGGAAAGTTTTATGGCTAAAATGT 59.500 34.615 0.00 0.00 38.66 2.71
2472 7255 6.946340 AGGGGAAAGTTTTATGGCTAAAATG 58.054 36.000 0.00 0.00 38.66 2.32
2473 7256 7.568128 AAGGGGAAAGTTTTATGGCTAAAAT 57.432 32.000 0.00 0.00 38.66 1.82
2474 7257 7.381789 AAAGGGGAAAGTTTTATGGCTAAAA 57.618 32.000 0.00 0.00 35.07 1.52
2475 7258 7.381789 AAAAGGGGAAAGTTTTATGGCTAAA 57.618 32.000 0.00 0.00 0.00 1.85
2476 7259 7.381789 AAAAAGGGGAAAGTTTTATGGCTAA 57.618 32.000 0.00 0.00 0.00 3.09
2477 7260 6.014070 GGAAAAAGGGGAAAGTTTTATGGCTA 60.014 38.462 0.00 0.00 0.00 3.93
2478 7261 5.221843 GGAAAAAGGGGAAAGTTTTATGGCT 60.222 40.000 0.00 0.00 0.00 4.75
2479 7262 5.001232 GGAAAAAGGGGAAAGTTTTATGGC 58.999 41.667 0.00 0.00 0.00 4.40
2480 7263 6.433847 AGGAAAAAGGGGAAAGTTTTATGG 57.566 37.500 0.00 0.00 0.00 2.74
2481 7264 7.444183 GGAAAGGAAAAAGGGGAAAGTTTTATG 59.556 37.037 0.00 0.00 0.00 1.90
2482 7265 7.349859 AGGAAAGGAAAAAGGGGAAAGTTTTAT 59.650 33.333 0.00 0.00 0.00 1.40
2483 7266 6.674861 AGGAAAGGAAAAAGGGGAAAGTTTTA 59.325 34.615 0.00 0.00 0.00 1.52
2484 7267 5.491078 AGGAAAGGAAAAAGGGGAAAGTTTT 59.509 36.000 0.00 0.00 0.00 2.43
2485 7268 5.036916 AGGAAAGGAAAAAGGGGAAAGTTT 58.963 37.500 0.00 0.00 0.00 2.66
2486 7269 4.631234 AGGAAAGGAAAAAGGGGAAAGTT 58.369 39.130 0.00 0.00 0.00 2.66
2487 7270 4.078571 AGAGGAAAGGAAAAAGGGGAAAGT 60.079 41.667 0.00 0.00 0.00 2.66
2488 7271 4.483950 AGAGGAAAGGAAAAAGGGGAAAG 58.516 43.478 0.00 0.00 0.00 2.62
2489 7272 4.552883 AGAGGAAAGGAAAAAGGGGAAA 57.447 40.909 0.00 0.00 0.00 3.13
2490 7273 4.552883 AAGAGGAAAGGAAAAAGGGGAA 57.447 40.909 0.00 0.00 0.00 3.97
2491 7274 4.223144 CAAAGAGGAAAGGAAAAAGGGGA 58.777 43.478 0.00 0.00 0.00 4.81
2492 7275 3.324846 CCAAAGAGGAAAGGAAAAAGGGG 59.675 47.826 0.00 0.00 41.22 4.79
2493 7276 3.967326 ACCAAAGAGGAAAGGAAAAAGGG 59.033 43.478 0.00 0.00 41.22 3.95
2494 7277 4.649218 TCACCAAAGAGGAAAGGAAAAAGG 59.351 41.667 0.00 0.00 41.22 3.11
2495 7278 5.852282 TCACCAAAGAGGAAAGGAAAAAG 57.148 39.130 0.00 0.00 41.22 2.27
2496 7279 7.343316 TGTTATCACCAAAGAGGAAAGGAAAAA 59.657 33.333 0.00 0.00 41.22 1.94
2497 7280 6.836527 TGTTATCACCAAAGAGGAAAGGAAAA 59.163 34.615 0.00 0.00 41.22 2.29
2498 7281 6.369629 TGTTATCACCAAAGAGGAAAGGAAA 58.630 36.000 0.00 0.00 41.22 3.13
2499 7282 5.947663 TGTTATCACCAAAGAGGAAAGGAA 58.052 37.500 0.00 0.00 41.22 3.36
2500 7283 5.576563 TGTTATCACCAAAGAGGAAAGGA 57.423 39.130 0.00 0.00 41.22 3.36
2501 7284 6.840780 ATTGTTATCACCAAAGAGGAAAGG 57.159 37.500 0.00 0.00 41.22 3.11
2505 7288 9.527157 TCAATAAATTGTTATCACCAAAGAGGA 57.473 29.630 2.80 0.00 38.73 3.71
2509 7292 8.819974 GCCATCAATAAATTGTTATCACCAAAG 58.180 33.333 2.80 0.00 38.84 2.77
2510 7293 8.538701 AGCCATCAATAAATTGTTATCACCAAA 58.461 29.630 2.80 0.00 38.84 3.28
2511 7294 8.076910 AGCCATCAATAAATTGTTATCACCAA 57.923 30.769 2.80 0.00 38.84 3.67
2512 7295 7.658525 AGCCATCAATAAATTGTTATCACCA 57.341 32.000 2.80 0.00 38.84 4.17
2519 7302 9.603921 CCTCAAAATAGCCATCAATAAATTGTT 57.396 29.630 2.80 0.00 38.84 2.83
2520 7303 8.761689 ACCTCAAAATAGCCATCAATAAATTGT 58.238 29.630 2.80 0.00 38.84 2.71
2521 7304 9.252962 GACCTCAAAATAGCCATCAATAAATTG 57.747 33.333 0.00 0.00 39.10 2.32
2522 7305 8.424133 GGACCTCAAAATAGCCATCAATAAATT 58.576 33.333 0.00 0.00 0.00 1.82
2523 7306 7.564660 TGGACCTCAAAATAGCCATCAATAAAT 59.435 33.333 0.00 0.00 0.00 1.40
2524 7307 6.894654 TGGACCTCAAAATAGCCATCAATAAA 59.105 34.615 0.00 0.00 0.00 1.40
2525 7308 6.430864 TGGACCTCAAAATAGCCATCAATAA 58.569 36.000 0.00 0.00 0.00 1.40
2526 7309 6.012337 TGGACCTCAAAATAGCCATCAATA 57.988 37.500 0.00 0.00 0.00 1.90
2527 7310 4.870636 TGGACCTCAAAATAGCCATCAAT 58.129 39.130 0.00 0.00 0.00 2.57
2528 7311 4.314522 TGGACCTCAAAATAGCCATCAA 57.685 40.909 0.00 0.00 0.00 2.57
2529 7312 4.314522 TTGGACCTCAAAATAGCCATCA 57.685 40.909 0.00 0.00 31.46 3.07
2530 7313 5.659440 TTTTGGACCTCAAAATAGCCATC 57.341 39.130 0.00 0.00 46.73 3.51
2556 7339 0.321034 GGCTCCATCGCTGATATGCA 60.321 55.000 0.00 0.00 0.00 3.96
2575 7358 0.443869 CTTCACCCGAGTTTGATGCG 59.556 55.000 0.00 0.00 0.00 4.73
2578 7361 1.978580 ACCTCTTCACCCGAGTTTGAT 59.021 47.619 0.00 0.00 0.00 2.57
2581 7364 1.420430 TCACCTCTTCACCCGAGTTT 58.580 50.000 0.00 0.00 0.00 2.66
2583 7366 1.187087 GATCACCTCTTCACCCGAGT 58.813 55.000 0.00 0.00 0.00 4.18
2603 7386 4.143347 CCAAAAGAAATCAAAATCGTGGCG 60.143 41.667 0.00 0.00 0.00 5.69
2613 7396 3.739519 CGGCAACCACCAAAAGAAATCAA 60.740 43.478 0.00 0.00 0.00 2.57
2614 7397 2.223923 CGGCAACCACCAAAAGAAATCA 60.224 45.455 0.00 0.00 0.00 2.57
2615 7398 2.403259 CGGCAACCACCAAAAGAAATC 58.597 47.619 0.00 0.00 0.00 2.17
2616 7399 1.069978 CCGGCAACCACCAAAAGAAAT 59.930 47.619 0.00 0.00 0.00 2.17
2617 7400 0.461961 CCGGCAACCACCAAAAGAAA 59.538 50.000 0.00 0.00 0.00 2.52
2618 7401 0.684805 ACCGGCAACCACCAAAAGAA 60.685 50.000 0.00 0.00 0.00 2.52
2619 7402 1.076632 ACCGGCAACCACCAAAAGA 60.077 52.632 0.00 0.00 0.00 2.52
2648 7431 0.469494 ATCCTATGTGCATGACGCCA 59.531 50.000 0.00 0.00 41.33 5.69
2650 7433 2.487934 AGAATCCTATGTGCATGACGC 58.512 47.619 0.00 0.00 42.89 5.19
2651 7434 3.670523 CGTAGAATCCTATGTGCATGACG 59.329 47.826 0.00 0.00 0.00 4.35
2652 7435 3.990469 CCGTAGAATCCTATGTGCATGAC 59.010 47.826 0.00 0.00 31.45 3.06
2662 7445 5.587388 AAAATCACGACCGTAGAATCCTA 57.413 39.130 0.00 0.00 0.00 2.94
2665 7448 7.695869 AGATAAAAATCACGACCGTAGAATC 57.304 36.000 0.00 0.00 0.00 2.52
2671 7454 4.117685 GCCTAGATAAAAATCACGACCGT 58.882 43.478 0.00 0.00 0.00 4.83
2677 7460 7.573968 AACCATCAGCCTAGATAAAAATCAC 57.426 36.000 0.00 0.00 0.00 3.06
2709 7492 8.198109 TGAGAATACAGTAGAACCTTAGCATTC 58.802 37.037 0.00 0.00 0.00 2.67
2729 7512 6.920569 AGTCACGTAAACAAAACTGAGAAT 57.079 33.333 0.00 0.00 0.00 2.40
2756 7543 5.920273 ACTTTCACCGTTCTTATTTTGCATG 59.080 36.000 0.00 0.00 0.00 4.06
2765 7552 7.893124 AGGATATCTACTTTCACCGTTCTTA 57.107 36.000 2.05 0.00 0.00 2.10
2770 7557 4.523558 GCCTAGGATATCTACTTTCACCGT 59.476 45.833 14.75 0.00 0.00 4.83
2771 7558 4.523173 TGCCTAGGATATCTACTTTCACCG 59.477 45.833 14.75 0.00 0.00 4.94
2783 7570 6.942163 ACATGTCAATAGTGCCTAGGATAT 57.058 37.500 14.75 4.34 0.00 1.63
2787 7574 4.336433 CCAAACATGTCAATAGTGCCTAGG 59.664 45.833 3.67 3.67 0.00 3.02
2848 7667 5.808030 GTCCAGTTGTAGATGCTCTTAGTTC 59.192 44.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.