Multiple sequence alignment - TraesCS1A01G210700

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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 TraesCS1A01G210700 chr1A 100.000 2882 0 0 1 2882 373265110 373262229 0.000000e+00 5323
1 TraesCS1A01G210700 chr1A 95.726 117 5 0 2360 2476 1161219 1161335 3.790000e-44 189
2 TraesCS1A01G210700 chr1B 91.645 2286 109 33 108 2359 403189456 403187219 0.000000e+00 3088
3 TraesCS1A01G210700 chr1B 91.436 397 16 12 2490 2881 403187195 403186812 1.970000e-146 529
4 TraesCS1A01G210700 chr1D 93.431 1568 45 23 836 2361 299052884 299051333 0.000000e+00 2272
5 TraesCS1A01G210700 chr1D 89.088 669 45 17 149 817 299053837 299053197 0.000000e+00 806
6 TraesCS1A01G210700 chr1D 89.104 413 18 14 2474 2880 299051335 299050944 3.340000e-134 488
7 TraesCS1A01G210700 chr5A 94.915 118 6 0 2359 2476 577433477 577433594 4.900000e-43 185
8 TraesCS1A01G210700 chr7D 94.017 117 7 0 2360 2476 277741949 277741833 8.210000e-41 178
9 TraesCS1A01G210700 chr2D 96.262 107 4 0 2370 2476 400383743 400383637 2.950000e-40 176
10 TraesCS1A01G210700 chr3B 89.683 126 13 0 2359 2484 526689436 526689561 8.260000e-36 161
11 TraesCS1A01G210700 chr3B 88.525 122 14 0 2362 2483 547060581 547060460 6.430000e-32 148
12 TraesCS1A01G210700 chr6D 87.218 133 15 2 2348 2478 94622310 94622178 1.790000e-32 150
13 TraesCS1A01G210700 chr6D 87.218 133 15 2 2348 2478 94622806 94622674 1.790000e-32 150
14 TraesCS1A01G210700 chr6D 85.714 133 17 2 2348 2478 94662532 94662400 3.870000e-29 139


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 TraesCS1A01G210700 chr1A 373262229 373265110 2881 True 5323.000000 5323 100.0000 1 2882 1 chr1A.!!$R1 2881
1 TraesCS1A01G210700 chr1B 403186812 403189456 2644 True 1808.500000 3088 91.5405 108 2881 2 chr1B.!!$R1 2773
2 TraesCS1A01G210700 chr1D 299050944 299053837 2893 True 1188.666667 2272 90.5410 149 2880 3 chr1D.!!$R1 2731

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
257 258 0.035458 ACCAGAAGAAGAAGCACGGG 59.965 55.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 2609 1.166531 AGGGCTGTGCGACAAGAAAC 61.167 55.0 0.0 0.0 0.0 2.78 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
23 24 5.059404 ACTTCCAAATCGTTTTATGCTGG 57.941 39.130 0.00 0.00 0.00 4.85
24 25 3.502191 TCCAAATCGTTTTATGCTGGC 57.498 42.857 0.00 0.00 0.00 4.85
25 26 3.088532 TCCAAATCGTTTTATGCTGGCT 58.911 40.909 0.00 0.00 0.00 4.75
26 27 3.119531 TCCAAATCGTTTTATGCTGGCTG 60.120 43.478 0.00 0.00 0.00 4.85
27 28 2.566952 AATCGTTTTATGCTGGCTGC 57.433 45.000 9.67 9.67 43.25 5.25
36 37 2.352805 GCTGGCTGCAGTAACCCT 59.647 61.111 16.64 0.00 42.31 4.34
37 38 1.746991 GCTGGCTGCAGTAACCCTC 60.747 63.158 16.64 0.00 42.31 4.30
38 39 1.986413 CTGGCTGCAGTAACCCTCT 59.014 57.895 16.64 0.00 0.00 3.69
39 40 1.195115 CTGGCTGCAGTAACCCTCTA 58.805 55.000 16.64 0.00 0.00 2.43
40 41 1.555075 CTGGCTGCAGTAACCCTCTAA 59.445 52.381 16.64 0.00 0.00 2.10
41 42 1.278127 TGGCTGCAGTAACCCTCTAAC 59.722 52.381 16.64 0.00 0.00 2.34
42 43 1.407025 GGCTGCAGTAACCCTCTAACC 60.407 57.143 16.64 0.00 0.00 2.85
43 44 1.739371 GCTGCAGTAACCCTCTAACCG 60.739 57.143 16.64 0.00 0.00 4.44
44 45 0.248289 TGCAGTAACCCTCTAACCGC 59.752 55.000 0.00 0.00 0.00 5.68
45 46 0.461516 GCAGTAACCCTCTAACCGCC 60.462 60.000 0.00 0.00 0.00 6.13
46 47 0.179119 CAGTAACCCTCTAACCGCCG 60.179 60.000 0.00 0.00 0.00 6.46
47 48 0.323725 AGTAACCCTCTAACCGCCGA 60.324 55.000 0.00 0.00 0.00 5.54
48 49 0.179127 GTAACCCTCTAACCGCCGAC 60.179 60.000 0.00 0.00 0.00 4.79
49 50 0.611618 TAACCCTCTAACCGCCGACA 60.612 55.000 0.00 0.00 0.00 4.35
50 51 1.262640 AACCCTCTAACCGCCGACAT 61.263 55.000 0.00 0.00 0.00 3.06
51 52 1.262640 ACCCTCTAACCGCCGACATT 61.263 55.000 0.00 0.00 0.00 2.71
52 53 0.107848 CCCTCTAACCGCCGACATTT 60.108 55.000 0.00 0.00 0.00 2.32
53 54 1.287425 CCTCTAACCGCCGACATTTC 58.713 55.000 0.00 0.00 0.00 2.17
54 55 0.921347 CTCTAACCGCCGACATTTCG 59.079 55.000 0.00 0.00 45.44 3.46
55 56 1.079875 TCTAACCGCCGACATTTCGC 61.080 55.000 0.00 0.00 44.43 4.70
56 57 2.342871 CTAACCGCCGACATTTCGCG 62.343 60.000 0.00 0.00 44.43 5.87
57 58 2.815825 TAACCGCCGACATTTCGCGA 62.816 55.000 3.71 3.71 44.43 5.87
58 59 3.483665 CCGCCGACATTTCGCGAA 61.484 61.111 19.38 19.38 44.43 4.70
59 60 2.275812 CGCCGACATTTCGCGAAC 60.276 61.111 23.33 9.20 44.43 3.95
60 61 2.097728 GCCGACATTTCGCGAACC 59.902 61.111 23.33 10.10 44.43 3.62
61 62 2.388232 GCCGACATTTCGCGAACCT 61.388 57.895 23.33 9.33 44.43 3.50
62 63 1.908066 GCCGACATTTCGCGAACCTT 61.908 55.000 23.33 8.10 44.43 3.50
63 64 0.179225 CCGACATTTCGCGAACCTTG 60.179 55.000 23.33 20.46 44.43 3.61
64 65 0.511221 CGACATTTCGCGAACCTTGT 59.489 50.000 23.33 23.41 38.71 3.16
65 66 1.461888 CGACATTTCGCGAACCTTGTC 60.462 52.381 30.19 30.19 38.71 3.18
66 67 1.798813 GACATTTCGCGAACCTTGTCT 59.201 47.619 31.40 15.27 0.00 3.41
67 68 1.531149 ACATTTCGCGAACCTTGTCTG 59.469 47.619 23.33 12.18 0.00 3.51
68 69 1.135972 CATTTCGCGAACCTTGTCTGG 60.136 52.381 23.33 0.00 0.00 3.86
69 70 1.503818 TTTCGCGAACCTTGTCTGGC 61.504 55.000 23.33 0.00 0.00 4.85
70 71 3.777925 CGCGAACCTTGTCTGGCG 61.778 66.667 0.00 0.00 37.56 5.69
71 72 2.665185 GCGAACCTTGTCTGGCGT 60.665 61.111 0.00 0.00 0.00 5.68
72 73 2.251642 GCGAACCTTGTCTGGCGTT 61.252 57.895 0.00 0.00 0.00 4.84
73 74 0.947180 GCGAACCTTGTCTGGCGTTA 60.947 55.000 0.00 0.00 0.00 3.18
74 75 0.788391 CGAACCTTGTCTGGCGTTAC 59.212 55.000 0.00 0.00 0.00 2.50
75 76 1.604693 CGAACCTTGTCTGGCGTTACT 60.605 52.381 0.00 0.00 0.00 2.24
76 77 2.352030 CGAACCTTGTCTGGCGTTACTA 60.352 50.000 0.00 0.00 0.00 1.82
77 78 3.656559 GAACCTTGTCTGGCGTTACTAA 58.343 45.455 0.00 0.00 0.00 2.24
78 79 3.036075 ACCTTGTCTGGCGTTACTAAC 57.964 47.619 0.00 0.00 0.00 2.34
79 80 2.289257 ACCTTGTCTGGCGTTACTAACC 60.289 50.000 0.00 0.00 0.00 2.85
80 81 2.289195 CCTTGTCTGGCGTTACTAACCA 60.289 50.000 0.00 0.00 0.00 3.67
81 82 3.395639 CTTGTCTGGCGTTACTAACCAA 58.604 45.455 0.00 0.00 31.81 3.67
82 83 2.758009 TGTCTGGCGTTACTAACCAAC 58.242 47.619 0.00 0.00 31.81 3.77
83 84 2.366266 TGTCTGGCGTTACTAACCAACT 59.634 45.455 0.00 0.00 31.81 3.16
84 85 2.735134 GTCTGGCGTTACTAACCAACTG 59.265 50.000 0.00 0.00 31.81 3.16
85 86 1.463444 CTGGCGTTACTAACCAACTGC 59.537 52.381 0.00 0.00 31.81 4.40
86 87 1.202663 TGGCGTTACTAACCAACTGCA 60.203 47.619 0.00 0.00 31.55 4.41
87 88 2.081462 GGCGTTACTAACCAACTGCAT 58.919 47.619 0.00 0.00 31.55 3.96
88 89 2.159572 GGCGTTACTAACCAACTGCATG 60.160 50.000 0.00 0.00 31.55 4.06
89 90 2.727916 GCGTTACTAACCAACTGCATGC 60.728 50.000 11.82 11.82 0.00 4.06
90 91 2.482336 CGTTACTAACCAACTGCATGCA 59.518 45.455 21.29 21.29 0.00 3.96
99 100 4.477413 CTGCATGCAGGATCTCCC 57.523 61.111 35.39 0.00 40.17 4.30
100 101 1.530283 CTGCATGCAGGATCTCCCA 59.470 57.895 35.39 3.24 40.17 4.37
101 102 0.106868 CTGCATGCAGGATCTCCCAA 60.107 55.000 35.39 2.69 40.17 4.12
102 103 0.332293 TGCATGCAGGATCTCCCAAA 59.668 50.000 18.46 0.00 37.41 3.28
103 104 1.063492 TGCATGCAGGATCTCCCAAAT 60.063 47.619 18.46 0.00 37.41 2.32
104 105 2.037144 GCATGCAGGATCTCCCAAATT 58.963 47.619 14.21 0.00 37.41 1.82
105 106 3.225104 GCATGCAGGATCTCCCAAATTA 58.775 45.455 14.21 0.00 37.41 1.40
106 107 3.638160 GCATGCAGGATCTCCCAAATTAA 59.362 43.478 14.21 0.00 37.41 1.40
112 113 5.179555 GCAGGATCTCCCAAATTAATACGAC 59.820 44.000 0.00 0.00 37.41 4.34
123 124 6.183359 CCAAATTAATACGACTTGCAAGCAAC 60.183 38.462 26.27 16.01 0.00 4.17
134 135 1.926490 CAAGCAACACAAAAGCGCC 59.074 52.632 2.29 0.00 0.00 6.53
136 137 1.954362 AAGCAACACAAAAGCGCCCA 61.954 50.000 2.29 0.00 0.00 5.36
137 138 1.950630 GCAACACAAAAGCGCCCAG 60.951 57.895 2.29 0.00 0.00 4.45
166 167 1.535462 GCCAACAGATGTTAGCAACGT 59.465 47.619 10.60 0.00 41.25 3.99
167 168 2.739913 GCCAACAGATGTTAGCAACGTA 59.260 45.455 10.60 0.00 41.25 3.57
168 169 3.187637 GCCAACAGATGTTAGCAACGTAA 59.812 43.478 10.60 0.00 41.25 3.18
256 257 2.743636 TACCAGAAGAAGAAGCACGG 57.256 50.000 0.00 0.00 0.00 4.94
257 258 0.035458 ACCAGAAGAAGAAGCACGGG 59.965 55.000 0.00 0.00 0.00 5.28
258 259 0.321671 CCAGAAGAAGAAGCACGGGA 59.678 55.000 0.00 0.00 0.00 5.14
360 361 2.030451 GGCTCCAGCAAAAGAAGTGAAG 60.030 50.000 0.03 0.00 44.36 3.02
374 375 1.064825 GTGAAGGAGAAAGGGTGGGA 58.935 55.000 0.00 0.00 0.00 4.37
410 411 0.178906 TGATCACTCCCACCCTCACA 60.179 55.000 0.00 0.00 0.00 3.58
411 412 0.250513 GATCACTCCCACCCTCACAC 59.749 60.000 0.00 0.00 0.00 3.82
476 477 3.525221 CCCCCATCGCCACAAATC 58.475 61.111 0.00 0.00 0.00 2.17
519 521 1.642728 AAACGCAAACGGAAAAACCC 58.357 45.000 0.00 0.00 46.04 4.11
537 539 0.732538 CCAAAGCAAATCGAACGCCC 60.733 55.000 0.00 0.00 0.00 6.13
576 578 3.057018 CACAAAGTGCAGCGTTACG 57.943 52.632 0.00 0.00 0.00 3.18
577 579 0.303493 CACAAAGTGCAGCGTTACGT 59.697 50.000 6.63 0.00 0.00 3.57
578 580 1.523515 CACAAAGTGCAGCGTTACGTA 59.476 47.619 6.63 0.00 0.00 3.57
661 663 5.138125 TGGAAAAGGTACGGTACTTACTG 57.862 43.478 17.14 0.00 33.31 2.74
707 709 3.799755 GTCGGGATGCCAACGTGC 61.800 66.667 3.39 0.00 0.00 5.34
769 771 2.372264 CCATGTTTCAGTGAGGATGGG 58.628 52.381 14.93 4.28 0.00 4.00
770 772 2.372264 CATGTTTCAGTGAGGATGGGG 58.628 52.381 0.00 0.00 0.00 4.96
792 794 4.162690 GGGAGTGGCGTGGGCTAG 62.163 72.222 0.00 0.00 39.81 3.42
806 808 1.044611 GGCTAGTGGAGATGGGACTC 58.955 60.000 0.00 0.00 36.31 3.36
817 819 1.892819 ATGGGACTCGGCAGTGTGAG 61.893 60.000 11.53 11.53 38.21 3.51
831 833 1.664965 GTGAGGTCAGTGACACGGC 60.665 63.158 24.20 10.56 33.68 5.68
924 1220 1.228429 CACCACCACCCGTTCCATT 60.228 57.895 0.00 0.00 0.00 3.16
943 1239 4.373116 GCCCAGCGAACCACGAGA 62.373 66.667 0.00 0.00 45.77 4.04
944 1240 2.125912 CCCAGCGAACCACGAGAG 60.126 66.667 0.00 0.00 45.77 3.20
946 1242 2.259818 CAGCGAACCACGAGAGCT 59.740 61.111 0.00 0.00 45.77 4.09
1220 1550 1.685421 AGGAGAGGCAGCAGGAGTC 60.685 63.158 0.00 0.00 0.00 3.36
1227 1557 4.504916 CAGCAGGAGTCGGCGAGG 62.505 72.222 11.20 0.00 39.08 4.63
1813 2143 4.082523 ACTCCGTGGACATGGGCG 62.083 66.667 10.48 5.25 38.05 6.13
1926 2279 2.036217 CGCCCATCGTACCTAATTACCA 59.964 50.000 0.00 0.00 0.00 3.25
1928 2281 4.648651 GCCCATCGTACCTAATTACCATT 58.351 43.478 0.00 0.00 0.00 3.16
1956 2309 6.707440 TTTTGTCTCTTGCTTAACATTCCA 57.293 33.333 0.00 0.00 0.00 3.53
2014 2367 6.183360 ACGTAGAATTGACAGAGATCATCGAA 60.183 38.462 0.00 0.00 0.00 3.71
2019 2372 3.849911 TGACAGAGATCATCGAACCAAC 58.150 45.455 0.00 0.00 0.00 3.77
2056 2410 9.521503 AAACAGTAAAAGATTGCTTCTTCTTTC 57.478 29.630 3.44 0.95 44.09 2.62
2057 2411 8.457238 ACAGTAAAAGATTGCTTCTTCTTTCT 57.543 30.769 3.44 2.62 44.09 2.52
2058 2412 8.563732 ACAGTAAAAGATTGCTTCTTCTTTCTC 58.436 33.333 3.44 0.00 44.09 2.87
2059 2413 8.782144 CAGTAAAAGATTGCTTCTTCTTTCTCT 58.218 33.333 3.44 0.00 44.09 3.10
2068 2422 4.908730 GCTTCTTCTTTCTCTTTTTGCTCG 59.091 41.667 0.00 0.00 0.00 5.03
2070 2424 2.949714 TCTTTCTCTTTTTGCTCGCG 57.050 45.000 0.00 0.00 0.00 5.87
2170 2524 1.215244 CCTCTCTGCATGCATGTACG 58.785 55.000 26.79 16.07 0.00 3.67
2178 2535 0.301687 CATGCATGTACGAACTCCGC 59.698 55.000 18.91 0.00 43.32 5.54
2218 2575 2.230266 GTGGCATCTTTTCCCGCTTTTA 59.770 45.455 0.00 0.00 0.00 1.52
2252 2609 5.391629 GGATTTGTCTGCGTAGGTTTAAAGG 60.392 44.000 0.00 0.00 0.00 3.11
2269 2626 1.166531 AGGTTTCTTGTCGCACAGCC 61.167 55.000 0.00 0.00 0.00 4.85
2359 2720 2.510613 CGTATGGGGTTTTTGTCAGGT 58.489 47.619 0.00 0.00 0.00 4.00
2360 2721 3.559597 CCGTATGGGGTTTTTGTCAGGTA 60.560 47.826 0.00 0.00 0.00 3.08
2361 2722 3.437741 CGTATGGGGTTTTTGTCAGGTAC 59.562 47.826 0.00 0.00 0.00 3.34
2362 2723 3.895704 ATGGGGTTTTTGTCAGGTACT 57.104 42.857 0.00 0.00 43.88 2.73
2363 2724 3.217681 TGGGGTTTTTGTCAGGTACTC 57.782 47.619 0.00 0.00 34.60 2.59
2364 2725 2.158579 TGGGGTTTTTGTCAGGTACTCC 60.159 50.000 0.00 0.00 34.60 3.85
2365 2726 2.511659 GGGTTTTTGTCAGGTACTCCC 58.488 52.381 0.00 0.00 34.60 4.30
2367 2728 3.436035 GGGTTTTTGTCAGGTACTCCCTT 60.436 47.826 0.00 0.00 42.73 3.95
2368 2729 3.819337 GGTTTTTGTCAGGTACTCCCTTC 59.181 47.826 0.00 0.00 42.73 3.46
2369 2730 3.396260 TTTTGTCAGGTACTCCCTTCG 57.604 47.619 0.00 0.00 42.73 3.79
2370 2731 2.005370 TTGTCAGGTACTCCCTTCGT 57.995 50.000 0.00 0.00 42.73 3.85
2371 2732 1.542492 TGTCAGGTACTCCCTTCGTC 58.458 55.000 0.00 0.00 42.73 4.20
2372 2733 0.816373 GTCAGGTACTCCCTTCGTCC 59.184 60.000 0.00 0.00 42.73 4.79
2373 2734 0.679002 TCAGGTACTCCCTTCGTCCG 60.679 60.000 0.00 0.00 42.73 4.79
2374 2735 1.379576 AGGTACTCCCTTCGTCCGG 60.380 63.158 0.00 0.00 42.73 5.14
2375 2736 1.379044 GGTACTCCCTTCGTCCGGA 60.379 63.158 0.00 0.00 0.00 5.14
2376 2737 0.967380 GGTACTCCCTTCGTCCGGAA 60.967 60.000 5.23 0.00 0.00 4.30
2377 2738 0.890683 GTACTCCCTTCGTCCGGAAA 59.109 55.000 5.23 0.00 33.34 3.13
2378 2739 1.479730 GTACTCCCTTCGTCCGGAAAT 59.520 52.381 5.23 0.00 33.34 2.17
2379 2740 1.856629 ACTCCCTTCGTCCGGAAATA 58.143 50.000 5.23 0.00 33.34 1.40
2380 2741 1.479730 ACTCCCTTCGTCCGGAAATAC 59.520 52.381 5.23 0.00 33.34 1.89
2381 2742 1.755380 CTCCCTTCGTCCGGAAATACT 59.245 52.381 5.23 0.00 33.34 2.12
2382 2743 2.167900 CTCCCTTCGTCCGGAAATACTT 59.832 50.000 5.23 0.00 33.34 2.24
2383 2744 2.093869 TCCCTTCGTCCGGAAATACTTG 60.094 50.000 5.23 0.00 33.34 3.16
2384 2745 2.354403 CCCTTCGTCCGGAAATACTTGT 60.354 50.000 5.23 0.00 33.34 3.16
2385 2746 2.928116 CCTTCGTCCGGAAATACTTGTC 59.072 50.000 5.23 0.00 33.34 3.18
2386 2747 2.660189 TCGTCCGGAAATACTTGTCC 57.340 50.000 5.23 0.00 0.00 4.02
2387 2748 1.205417 TCGTCCGGAAATACTTGTCCC 59.795 52.381 5.23 0.00 0.00 4.46
2388 2749 1.066716 CGTCCGGAAATACTTGTCCCA 60.067 52.381 5.23 0.00 0.00 4.37
2389 2750 2.613474 CGTCCGGAAATACTTGTCCCAA 60.613 50.000 5.23 0.00 0.00 4.12
2390 2751 3.414269 GTCCGGAAATACTTGTCCCAAA 58.586 45.455 5.23 0.00 0.00 3.28
2391 2752 3.822167 GTCCGGAAATACTTGTCCCAAAA 59.178 43.478 5.23 0.00 0.00 2.44
2392 2753 4.278919 GTCCGGAAATACTTGTCCCAAAAA 59.721 41.667 5.23 0.00 0.00 1.94
2393 2754 5.047590 GTCCGGAAATACTTGTCCCAAAAAT 60.048 40.000 5.23 0.00 0.00 1.82
2394 2755 6.151480 GTCCGGAAATACTTGTCCCAAAAATA 59.849 38.462 5.23 0.00 0.00 1.40
2395 2756 6.376018 TCCGGAAATACTTGTCCCAAAAATAG 59.624 38.462 0.00 0.00 0.00 1.73
2396 2757 6.376018 CCGGAAATACTTGTCCCAAAAATAGA 59.624 38.462 0.00 0.00 0.00 1.98
2397 2758 7.068226 CCGGAAATACTTGTCCCAAAAATAGAT 59.932 37.037 0.00 0.00 0.00 1.98
2398 2759 7.915397 CGGAAATACTTGTCCCAAAAATAGATG 59.085 37.037 0.00 0.00 0.00 2.90
2399 2760 8.749354 GGAAATACTTGTCCCAAAAATAGATGT 58.251 33.333 0.00 0.00 0.00 3.06
2405 2766 9.838339 ACTTGTCCCAAAAATAGATGTATCTAG 57.162 33.333 7.57 0.00 42.20 2.43
2407 2768 9.832445 TTGTCCCAAAAATAGATGTATCTAGAC 57.168 33.333 0.00 7.60 42.20 2.59
2408 2769 8.141909 TGTCCCAAAAATAGATGTATCTAGACG 58.858 37.037 0.00 0.00 42.20 4.18
2409 2770 8.142551 GTCCCAAAAATAGATGTATCTAGACGT 58.857 37.037 0.00 0.00 42.20 4.34
2410 2771 9.358406 TCCCAAAAATAGATGTATCTAGACGTA 57.642 33.333 0.00 0.00 42.20 3.57
2431 2792 9.327529 GACGTATTTTAGTTCTAGATACATCCG 57.672 37.037 0.00 0.00 0.00 4.18
2432 2793 8.844244 ACGTATTTTAGTTCTAGATACATCCGT 58.156 33.333 0.00 0.00 0.00 4.69
2433 2794 9.674824 CGTATTTTAGTTCTAGATACATCCGTT 57.325 33.333 0.00 0.00 0.00 4.44
2447 2808 9.716507 AGATACATCCGTTTTTATTCATTTTCG 57.283 29.630 0.00 0.00 0.00 3.46
2448 2809 9.498307 GATACATCCGTTTTTATTCATTTTCGT 57.502 29.630 0.00 0.00 0.00 3.85
2451 2812 9.120422 ACATCCGTTTTTATTCATTTTCGTAAC 57.880 29.630 0.00 0.00 0.00 2.50
2452 2813 9.119329 CATCCGTTTTTATTCATTTTCGTAACA 57.881 29.630 0.00 0.00 0.00 2.41
2453 2814 9.680315 ATCCGTTTTTATTCATTTTCGTAACAA 57.320 25.926 0.00 0.00 0.00 2.83
2454 2815 9.171701 TCCGTTTTTATTCATTTTCGTAACAAG 57.828 29.630 0.00 0.00 0.00 3.16
2455 2816 8.960075 CCGTTTTTATTCATTTTCGTAACAAGT 58.040 29.630 0.00 0.00 0.00 3.16
2469 2830 5.938883 GTAACAAGTAATTACGGACGGAG 57.061 43.478 9.91 0.01 0.00 4.63
2470 2831 2.884827 ACAAGTAATTACGGACGGAGC 58.115 47.619 9.91 0.00 0.00 4.70
2471 2832 1.850441 CAAGTAATTACGGACGGAGCG 59.150 52.381 9.91 0.00 0.00 5.03
2472 2833 1.382522 AGTAATTACGGACGGAGCGA 58.617 50.000 9.91 0.00 0.00 4.93
2473 2834 1.332997 AGTAATTACGGACGGAGCGAG 59.667 52.381 9.91 0.00 0.00 5.03
2605 2974 2.431683 GTCCCTTGCTGCCTGTCA 59.568 61.111 0.00 0.00 0.00 3.58
2619 2998 2.288948 GCCTGTCACATTGCCAAATTGA 60.289 45.455 0.00 0.00 0.00 2.57
2623 3002 4.958509 TGTCACATTGCCAAATTGACATT 58.041 34.783 16.39 0.00 38.03 2.71
2624 3003 4.750598 TGTCACATTGCCAAATTGACATTG 59.249 37.500 16.39 0.00 38.03 2.82
2625 3004 3.747010 TCACATTGCCAAATTGACATTGC 59.253 39.130 4.51 0.00 0.00 3.56
2626 3005 3.749088 CACATTGCCAAATTGACATTGCT 59.251 39.130 4.51 0.00 0.00 3.91
2627 3006 4.214545 CACATTGCCAAATTGACATTGCTT 59.785 37.500 4.51 0.00 0.00 3.91
2628 3007 4.214545 ACATTGCCAAATTGACATTGCTTG 59.785 37.500 4.51 0.71 0.00 4.01
2629 3008 2.144730 TGCCAAATTGACATTGCTTGC 58.855 42.857 0.00 0.00 0.00 4.01
2630 3009 2.224329 TGCCAAATTGACATTGCTTGCT 60.224 40.909 0.00 0.00 0.00 3.91
2631 3010 2.414138 GCCAAATTGACATTGCTTGCTC 59.586 45.455 0.00 0.00 0.00 4.26
2632 3011 3.863400 GCCAAATTGACATTGCTTGCTCT 60.863 43.478 0.00 0.00 0.00 4.09
2633 3012 3.678072 CCAAATTGACATTGCTTGCTCTG 59.322 43.478 0.00 0.00 0.00 3.35
2634 3013 4.304110 CAAATTGACATTGCTTGCTCTGT 58.696 39.130 0.00 0.00 0.00 3.41
2635 3014 3.844577 ATTGACATTGCTTGCTCTGTC 57.155 42.857 15.77 15.77 38.74 3.51
2713 3092 2.479566 TGTCTTCAGGTGATCTTGCC 57.520 50.000 0.00 0.00 0.00 4.52
2761 3140 4.377021 TCAGTGTCATTTTCGTTGCTACT 58.623 39.130 0.00 0.00 0.00 2.57
2775 3154 3.936372 TGCTACTACTTCAGTGTCACC 57.064 47.619 0.00 0.00 38.24 4.02
2794 3173 1.228552 GGAAGCCCTGTTCAGCCAA 60.229 57.895 0.00 0.00 0.00 4.52
2795 3174 0.613012 GGAAGCCCTGTTCAGCCAAT 60.613 55.000 0.00 0.00 0.00 3.16
2841 3220 9.610104 AGGTAGTACCATAACCATACAATATCA 57.390 33.333 21.49 0.00 41.95 2.15
2842 3221 9.649167 GGTAGTACCATAACCATACAATATCAC 57.351 37.037 14.82 0.00 38.42 3.06
2881 3260 2.887783 ACGGTATTGCATTGTTTGGTCA 59.112 40.909 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.469479 CCAGCATAAAACGATTTGGAAGTT 58.531 37.500 0.28 0.00 0.00 2.66
1 2 4.618227 GCCAGCATAAAACGATTTGGAAGT 60.618 41.667 0.28 0.00 0.00 3.01
2 3 3.859386 GCCAGCATAAAACGATTTGGAAG 59.141 43.478 0.28 0.00 0.00 3.46
3 4 3.509575 AGCCAGCATAAAACGATTTGGAA 59.490 39.130 0.28 0.00 0.00 3.53
4 5 3.088532 AGCCAGCATAAAACGATTTGGA 58.911 40.909 0.28 0.00 0.00 3.53
5 6 3.181397 CAGCCAGCATAAAACGATTTGG 58.819 45.455 0.28 0.00 0.00 3.28
6 7 2.599973 GCAGCCAGCATAAAACGATTTG 59.400 45.455 0.28 0.00 44.79 2.32
7 8 2.879826 GCAGCCAGCATAAAACGATTT 58.120 42.857 0.00 0.00 44.79 2.17
8 9 2.566952 GCAGCCAGCATAAAACGATT 57.433 45.000 0.00 0.00 44.79 3.34
19 20 1.746991 GAGGGTTACTGCAGCCAGC 60.747 63.158 15.27 10.07 43.02 4.85
20 21 1.195115 TAGAGGGTTACTGCAGCCAG 58.805 55.000 15.27 0.00 44.80 4.85
21 22 1.278127 GTTAGAGGGTTACTGCAGCCA 59.722 52.381 15.27 0.00 36.72 4.75
22 23 1.407025 GGTTAGAGGGTTACTGCAGCC 60.407 57.143 15.27 7.00 34.19 4.85
23 24 1.739371 CGGTTAGAGGGTTACTGCAGC 60.739 57.143 15.27 0.00 0.00 5.25
24 25 1.739371 GCGGTTAGAGGGTTACTGCAG 60.739 57.143 13.48 13.48 42.36 4.41
25 26 0.248289 GCGGTTAGAGGGTTACTGCA 59.752 55.000 0.00 0.00 42.36 4.41
26 27 0.461516 GGCGGTTAGAGGGTTACTGC 60.462 60.000 0.00 0.00 42.13 4.40
27 28 0.179119 CGGCGGTTAGAGGGTTACTG 60.179 60.000 0.00 0.00 0.00 2.74
28 29 0.323725 TCGGCGGTTAGAGGGTTACT 60.324 55.000 7.21 0.00 0.00 2.24
29 30 0.179127 GTCGGCGGTTAGAGGGTTAC 60.179 60.000 7.21 0.00 0.00 2.50
30 31 0.611618 TGTCGGCGGTTAGAGGGTTA 60.612 55.000 7.21 0.00 0.00 2.85
31 32 1.262640 ATGTCGGCGGTTAGAGGGTT 61.263 55.000 7.21 0.00 0.00 4.11
32 33 1.262640 AATGTCGGCGGTTAGAGGGT 61.263 55.000 7.21 0.00 0.00 4.34
33 34 0.107848 AAATGTCGGCGGTTAGAGGG 60.108 55.000 7.21 0.00 0.00 4.30
34 35 1.287425 GAAATGTCGGCGGTTAGAGG 58.713 55.000 7.21 0.00 0.00 3.69
35 36 0.921347 CGAAATGTCGGCGGTTAGAG 59.079 55.000 7.21 0.00 43.81 2.43
36 37 3.038946 CGAAATGTCGGCGGTTAGA 57.961 52.632 7.21 0.00 43.81 2.10
46 47 1.798813 AGACAAGGTTCGCGAAATGTC 59.201 47.619 33.77 33.77 0.00 3.06
47 48 1.531149 CAGACAAGGTTCGCGAAATGT 59.469 47.619 25.24 25.97 0.00 2.71
48 49 1.135972 CCAGACAAGGTTCGCGAAATG 60.136 52.381 25.24 23.09 0.00 2.32
49 50 1.156736 CCAGACAAGGTTCGCGAAAT 58.843 50.000 25.24 12.80 0.00 2.17
50 51 1.503818 GCCAGACAAGGTTCGCGAAA 61.504 55.000 25.24 4.87 0.00 3.46
51 52 1.959226 GCCAGACAAGGTTCGCGAA 60.959 57.895 19.38 19.38 0.00 4.70
52 53 2.357034 GCCAGACAAGGTTCGCGA 60.357 61.111 3.71 3.71 0.00 5.87
53 54 3.777925 CGCCAGACAAGGTTCGCG 61.778 66.667 0.00 0.00 0.00 5.87
54 55 0.947180 TAACGCCAGACAAGGTTCGC 60.947 55.000 0.00 0.00 0.00 4.70
55 56 0.788391 GTAACGCCAGACAAGGTTCG 59.212 55.000 0.00 0.00 0.00 3.95
56 57 2.165319 AGTAACGCCAGACAAGGTTC 57.835 50.000 0.00 0.00 0.00 3.62
57 58 3.396560 GTTAGTAACGCCAGACAAGGTT 58.603 45.455 0.00 0.00 0.00 3.50
58 59 2.289257 GGTTAGTAACGCCAGACAAGGT 60.289 50.000 6.94 0.00 0.00 3.50
59 60 2.289195 TGGTTAGTAACGCCAGACAAGG 60.289 50.000 6.94 0.00 0.00 3.61
60 61 3.034721 TGGTTAGTAACGCCAGACAAG 57.965 47.619 6.94 0.00 0.00 3.16
61 62 3.132925 GTTGGTTAGTAACGCCAGACAA 58.867 45.455 6.94 2.14 33.41 3.18
62 63 2.366266 AGTTGGTTAGTAACGCCAGACA 59.634 45.455 6.94 0.00 33.41 3.41
63 64 2.735134 CAGTTGGTTAGTAACGCCAGAC 59.265 50.000 6.94 1.92 33.41 3.51
64 65 2.868839 GCAGTTGGTTAGTAACGCCAGA 60.869 50.000 6.94 0.00 33.41 3.86
65 66 1.463444 GCAGTTGGTTAGTAACGCCAG 59.537 52.381 6.94 0.00 33.41 4.85
66 67 1.202663 TGCAGTTGGTTAGTAACGCCA 60.203 47.619 6.94 0.00 33.39 5.69
67 68 1.515081 TGCAGTTGGTTAGTAACGCC 58.485 50.000 6.94 0.00 33.39 5.68
68 69 2.727916 GCATGCAGTTGGTTAGTAACGC 60.728 50.000 14.21 5.13 33.39 4.84
69 70 2.482336 TGCATGCAGTTGGTTAGTAACG 59.518 45.455 18.46 0.00 33.39 3.18
70 71 3.119849 CCTGCATGCAGTTGGTTAGTAAC 60.120 47.826 38.22 4.32 42.15 2.50
71 72 3.081061 CCTGCATGCAGTTGGTTAGTAA 58.919 45.455 38.22 6.16 42.15 2.24
72 73 2.304470 TCCTGCATGCAGTTGGTTAGTA 59.696 45.455 38.22 11.93 42.15 1.82
73 74 1.073763 TCCTGCATGCAGTTGGTTAGT 59.926 47.619 38.22 0.00 42.15 2.24
74 75 1.825090 TCCTGCATGCAGTTGGTTAG 58.175 50.000 38.22 24.47 42.15 2.34
75 76 2.025981 AGATCCTGCATGCAGTTGGTTA 60.026 45.455 38.22 20.39 42.15 2.85
76 77 1.180029 GATCCTGCATGCAGTTGGTT 58.820 50.000 38.22 23.32 42.15 3.67
77 78 0.330604 AGATCCTGCATGCAGTTGGT 59.669 50.000 38.22 24.88 42.15 3.67
78 79 1.022735 GAGATCCTGCATGCAGTTGG 58.977 55.000 38.22 27.77 42.15 3.77
79 80 1.022735 GGAGATCCTGCATGCAGTTG 58.977 55.000 38.22 27.05 42.15 3.16
80 81 0.106819 GGGAGATCCTGCATGCAGTT 60.107 55.000 38.22 28.03 42.15 3.16
81 82 1.276859 TGGGAGATCCTGCATGCAGT 61.277 55.000 38.22 25.71 42.15 4.40
82 83 0.106868 TTGGGAGATCCTGCATGCAG 60.107 55.000 35.88 35.88 43.26 4.41
83 84 0.332293 TTTGGGAGATCCTGCATGCA 59.668 50.000 21.29 21.29 36.20 3.96
84 85 1.700955 ATTTGGGAGATCCTGCATGC 58.299 50.000 11.82 11.82 36.20 4.06
85 86 6.348786 CGTATTAATTTGGGAGATCCTGCATG 60.349 42.308 0.00 0.00 36.20 4.06
86 87 5.707298 CGTATTAATTTGGGAGATCCTGCAT 59.293 40.000 0.00 0.00 36.20 3.96
87 88 5.063204 CGTATTAATTTGGGAGATCCTGCA 58.937 41.667 0.00 0.00 36.20 4.41
88 89 5.179555 GTCGTATTAATTTGGGAGATCCTGC 59.820 44.000 0.00 0.00 36.20 4.85
89 90 6.525629 AGTCGTATTAATTTGGGAGATCCTG 58.474 40.000 0.00 0.00 36.20 3.86
90 91 6.749036 AGTCGTATTAATTTGGGAGATCCT 57.251 37.500 0.00 0.00 36.20 3.24
91 92 6.293462 GCAAGTCGTATTAATTTGGGAGATCC 60.293 42.308 0.00 0.00 0.00 3.36
92 93 6.260050 TGCAAGTCGTATTAATTTGGGAGATC 59.740 38.462 0.00 0.00 0.00 2.75
93 94 6.119536 TGCAAGTCGTATTAATTTGGGAGAT 58.880 36.000 0.00 0.00 0.00 2.75
94 95 5.492895 TGCAAGTCGTATTAATTTGGGAGA 58.507 37.500 0.00 0.00 0.00 3.71
95 96 5.811399 TGCAAGTCGTATTAATTTGGGAG 57.189 39.130 0.00 0.00 0.00 4.30
96 97 5.392595 GCTTGCAAGTCGTATTAATTTGGGA 60.393 40.000 26.55 0.00 0.00 4.37
97 98 4.798387 GCTTGCAAGTCGTATTAATTTGGG 59.202 41.667 26.55 0.00 0.00 4.12
98 99 5.398169 TGCTTGCAAGTCGTATTAATTTGG 58.602 37.500 26.55 0.00 0.00 3.28
99 100 6.362016 TGTTGCTTGCAAGTCGTATTAATTTG 59.638 34.615 26.55 0.00 0.00 2.32
100 101 6.362283 GTGTTGCTTGCAAGTCGTATTAATTT 59.638 34.615 26.55 0.00 0.00 1.82
101 102 5.856455 GTGTTGCTTGCAAGTCGTATTAATT 59.144 36.000 26.55 0.00 0.00 1.40
102 103 5.049060 TGTGTTGCTTGCAAGTCGTATTAAT 60.049 36.000 26.55 0.00 0.00 1.40
103 104 4.273724 TGTGTTGCTTGCAAGTCGTATTAA 59.726 37.500 26.55 8.85 0.00 1.40
104 105 3.810386 TGTGTTGCTTGCAAGTCGTATTA 59.190 39.130 26.55 6.76 0.00 0.98
105 106 2.616376 TGTGTTGCTTGCAAGTCGTATT 59.384 40.909 26.55 0.00 0.00 1.89
106 107 2.217750 TGTGTTGCTTGCAAGTCGTAT 58.782 42.857 26.55 0.00 0.00 3.06
112 113 1.005766 CGCTTTTGTGTTGCTTGCAAG 60.006 47.619 22.44 22.44 0.00 4.01
123 124 1.579429 GGTACTGGGCGCTTTTGTG 59.421 57.895 7.64 0.00 0.00 3.33
134 135 2.359478 GTTGGCGGTGGGTACTGG 60.359 66.667 0.00 0.00 33.62 4.00
136 137 1.198759 ATCTGTTGGCGGTGGGTACT 61.199 55.000 0.00 0.00 0.00 2.73
137 138 1.024579 CATCTGTTGGCGGTGGGTAC 61.025 60.000 0.00 0.00 0.00 3.34
166 167 4.851843 TGACTGTCTCCTCTCCGTTATTA 58.148 43.478 9.51 0.00 0.00 0.98
167 168 3.698289 TGACTGTCTCCTCTCCGTTATT 58.302 45.455 9.51 0.00 0.00 1.40
168 169 3.367646 TGACTGTCTCCTCTCCGTTAT 57.632 47.619 9.51 0.00 0.00 1.89
228 229 6.836007 TGCTTCTTCTTCTGGTATCTATCTGA 59.164 38.462 0.00 0.00 0.00 3.27
281 282 1.082690 CTTCTTTCTTGGAGCTCCGC 58.917 55.000 27.43 5.60 39.43 5.54
282 283 2.072298 CACTTCTTTCTTGGAGCTCCG 58.928 52.381 27.43 14.58 39.43 4.63
360 361 2.832129 GGATTTTTCCCACCCTTTCTCC 59.168 50.000 0.00 0.00 0.00 3.71
374 375 7.120138 GGAGTGATCATTTGCATTTGGATTTTT 59.880 33.333 0.00 0.00 0.00 1.94
410 411 3.241530 TGCTCGGGCCAAGTGAGT 61.242 61.111 3.94 0.00 37.74 3.41
411 412 2.249413 ATCTGCTCGGGCCAAGTGAG 62.249 60.000 3.94 7.14 37.74 3.51
460 461 1.067516 GATTGATTTGTGGCGATGGGG 59.932 52.381 0.00 0.00 0.00 4.96
466 467 2.159430 TCGACTTGATTGATTTGTGGCG 59.841 45.455 0.00 0.00 0.00 5.69
468 469 8.741101 TTTATTTCGACTTGATTGATTTGTGG 57.259 30.769 0.00 0.00 0.00 4.17
519 521 0.039617 TGGGCGTTCGATTTGCTTTG 60.040 50.000 0.00 0.00 0.00 2.77
537 539 1.266175 CTGGTCTTTTGAGCTGTGCTG 59.734 52.381 0.00 0.00 46.30 4.41
572 574 5.121768 GGAGACAAGGTACTACGTTACGTAA 59.878 44.000 18.29 3.29 41.82 3.18
574 576 3.437049 GGAGACAAGGTACTACGTTACGT 59.563 47.826 16.31 16.31 38.49 3.57
575 577 3.436704 TGGAGACAAGGTACTACGTTACG 59.563 47.826 2.19 2.19 38.49 3.18
606 608 5.272283 ACGTACCACTATTCCGATTTGAT 57.728 39.130 0.00 0.00 0.00 2.57
614 616 6.730960 TTGAAATCAACGTACCACTATTCC 57.269 37.500 0.00 0.00 0.00 3.01
661 663 0.107508 TCATGCTTAGTCCTGGCAGC 60.108 55.000 9.56 0.00 39.38 5.25
696 698 4.704833 AGGCGAGCACGTTGGCAT 62.705 61.111 5.23 0.00 41.98 4.40
750 752 2.291153 ACCCCATCCTCACTGAAACATG 60.291 50.000 0.00 0.00 0.00 3.21
751 753 1.995542 ACCCCATCCTCACTGAAACAT 59.004 47.619 0.00 0.00 0.00 2.71
752 754 1.073763 CACCCCATCCTCACTGAAACA 59.926 52.381 0.00 0.00 0.00 2.83
769 771 2.436646 CACGCCACTCCCATCACC 60.437 66.667 0.00 0.00 0.00 4.02
770 772 2.436646 CCACGCCACTCCCATCAC 60.437 66.667 0.00 0.00 0.00 3.06
792 794 2.303549 CTGCCGAGTCCCATCTCCAC 62.304 65.000 0.00 0.00 0.00 4.02
806 808 1.665916 CACTGACCTCACACTGCCG 60.666 63.158 0.00 0.00 0.00 5.69
1128 1458 4.436998 GACGCCACCGAGTCCCTG 62.437 72.222 0.00 0.00 38.29 4.45
1227 1557 1.746991 CTTCTTCTTGGGCCGAGGC 60.747 63.158 20.82 5.37 41.06 4.70
1230 1560 2.351276 GGCTTCTTCTTGGGCCGA 59.649 61.111 0.00 0.00 35.08 5.54
1413 1743 4.458829 ATCGCCTCCACCTCCGGA 62.459 66.667 2.93 2.93 0.00 5.14
1458 1788 3.220999 CTCCTCGAACCGTGCCACA 62.221 63.158 0.00 0.00 0.00 4.17
1926 2279 8.225603 TGTTAAGCAAGAGACAAAAAGAGAAT 57.774 30.769 0.00 0.00 0.00 2.40
1928 2281 7.807977 ATGTTAAGCAAGAGACAAAAAGAGA 57.192 32.000 0.00 0.00 0.00 3.10
2014 2367 3.028130 CTGTTTTACACAAGGGGTTGGT 58.972 45.455 0.00 0.00 33.87 3.67
2019 2372 6.702716 TCTTTTACTGTTTTACACAAGGGG 57.297 37.500 0.00 0.00 33.87 4.79
2056 2410 2.383298 TTCAACGCGAGCAAAAAGAG 57.617 45.000 15.93 0.00 0.00 2.85
2057 2411 2.548057 AGATTCAACGCGAGCAAAAAGA 59.452 40.909 15.93 0.00 0.00 2.52
2058 2412 2.904932 GAGATTCAACGCGAGCAAAAAG 59.095 45.455 15.93 0.00 0.00 2.27
2059 2413 2.289274 TGAGATTCAACGCGAGCAAAAA 59.711 40.909 15.93 0.00 0.00 1.94
2068 2422 5.032863 CCATTTCAAGATGAGATTCAACGC 58.967 41.667 0.00 0.00 0.00 4.84
2070 2424 6.917533 ACACCATTTCAAGATGAGATTCAAC 58.082 36.000 0.00 0.00 0.00 3.18
2170 2524 5.586643 AGGATAAAATTTCAGAGCGGAGTTC 59.413 40.000 0.00 0.00 38.31 3.01
2178 2535 6.690530 TGCCACAAAGGATAAAATTTCAGAG 58.309 36.000 0.00 0.00 41.22 3.35
2218 2575 4.344865 ACAAATCCCTGCGCCGGT 62.345 61.111 17.16 0.00 0.00 5.28
2252 2609 1.166531 AGGGCTGTGCGACAAGAAAC 61.167 55.000 0.00 0.00 0.00 2.78
2269 2626 1.001406 AGGAGAAGCAAACACGAGAGG 59.999 52.381 0.00 0.00 0.00 3.69
2359 2720 1.856629 ATTTCCGGACGAAGGGAGTA 58.143 50.000 1.83 0.00 33.01 2.59
2360 2721 1.479730 GTATTTCCGGACGAAGGGAGT 59.520 52.381 1.83 0.00 33.01 3.85
2361 2722 1.755380 AGTATTTCCGGACGAAGGGAG 59.245 52.381 1.83 0.00 33.01 4.30
2362 2723 1.856629 AGTATTTCCGGACGAAGGGA 58.143 50.000 1.83 0.00 0.00 4.20
2363 2724 2.277084 CAAGTATTTCCGGACGAAGGG 58.723 52.381 1.83 0.00 0.00 3.95
2364 2725 2.928116 GACAAGTATTTCCGGACGAAGG 59.072 50.000 1.83 0.00 0.00 3.46
2365 2726 2.928116 GGACAAGTATTTCCGGACGAAG 59.072 50.000 1.83 0.00 0.00 3.79
2366 2727 2.354003 GGGACAAGTATTTCCGGACGAA 60.354 50.000 1.83 0.00 32.00 3.85
2367 2728 1.205417 GGGACAAGTATTTCCGGACGA 59.795 52.381 1.83 0.00 32.00 4.20
2368 2729 1.066716 TGGGACAAGTATTTCCGGACG 60.067 52.381 1.83 0.00 31.92 4.79
2369 2730 2.773993 TGGGACAAGTATTTCCGGAC 57.226 50.000 1.83 0.00 31.92 4.79
2379 2740 9.838339 CTAGATACATCTATTTTTGGGACAAGT 57.162 33.333 0.00 0.00 40.37 3.16
2381 2742 9.832445 GTCTAGATACATCTATTTTTGGGACAA 57.168 33.333 0.00 0.00 40.37 3.18
2382 2743 8.141909 CGTCTAGATACATCTATTTTTGGGACA 58.858 37.037 0.00 0.00 38.60 4.02
2383 2744 8.142551 ACGTCTAGATACATCTATTTTTGGGAC 58.857 37.037 0.00 2.21 38.60 4.46
2384 2745 8.246430 ACGTCTAGATACATCTATTTTTGGGA 57.754 34.615 0.00 0.00 38.60 4.37
2405 2766 9.327529 CGGATGTATCTAGAACTAAAATACGTC 57.672 37.037 17.13 17.13 37.78 4.34
2406 2767 8.844244 ACGGATGTATCTAGAACTAAAATACGT 58.156 33.333 0.00 0.00 0.00 3.57
2407 2768 9.674824 AACGGATGTATCTAGAACTAAAATACG 57.325 33.333 0.00 0.00 0.00 3.06
2421 2782 9.716507 CGAAAATGAATAAAAACGGATGTATCT 57.283 29.630 0.00 0.00 0.00 1.98
2422 2783 9.498307 ACGAAAATGAATAAAAACGGATGTATC 57.502 29.630 0.00 0.00 0.00 2.24
2425 2786 9.120422 GTTACGAAAATGAATAAAAACGGATGT 57.880 29.630 0.00 0.00 0.00 3.06
2426 2787 9.119329 TGTTACGAAAATGAATAAAAACGGATG 57.881 29.630 0.00 0.00 0.00 3.51
2427 2788 9.680315 TTGTTACGAAAATGAATAAAAACGGAT 57.320 25.926 0.00 0.00 0.00 4.18
2428 2789 9.171701 CTTGTTACGAAAATGAATAAAAACGGA 57.828 29.630 0.00 0.00 0.00 4.69
2429 2790 8.960075 ACTTGTTACGAAAATGAATAAAAACGG 58.040 29.630 0.00 0.00 0.00 4.44
2447 2808 4.266265 GCTCCGTCCGTAATTACTTGTTAC 59.734 45.833 13.56 3.98 0.00 2.50
2448 2809 4.423732 GCTCCGTCCGTAATTACTTGTTA 58.576 43.478 13.56 0.00 0.00 2.41
2449 2810 3.256558 GCTCCGTCCGTAATTACTTGTT 58.743 45.455 13.56 0.00 0.00 2.83
2450 2811 2.733227 CGCTCCGTCCGTAATTACTTGT 60.733 50.000 13.56 0.00 0.00 3.16
2451 2812 1.850441 CGCTCCGTCCGTAATTACTTG 59.150 52.381 13.56 5.06 0.00 3.16
2452 2813 1.745087 TCGCTCCGTCCGTAATTACTT 59.255 47.619 13.56 0.00 0.00 2.24
2453 2814 1.332997 CTCGCTCCGTCCGTAATTACT 59.667 52.381 13.56 0.00 0.00 2.24
2454 2815 1.064654 ACTCGCTCCGTCCGTAATTAC 59.935 52.381 5.47 5.47 0.00 1.89
2455 2816 1.382522 ACTCGCTCCGTCCGTAATTA 58.617 50.000 0.00 0.00 0.00 1.40
2456 2817 1.332997 CTACTCGCTCCGTCCGTAATT 59.667 52.381 0.00 0.00 0.00 1.40
2457 2818 0.942962 CTACTCGCTCCGTCCGTAAT 59.057 55.000 0.00 0.00 0.00 1.89
2458 2819 1.091771 CCTACTCGCTCCGTCCGTAA 61.092 60.000 0.00 0.00 0.00 3.18
2459 2820 1.522355 CCTACTCGCTCCGTCCGTA 60.522 63.158 0.00 0.00 0.00 4.02
2460 2821 2.605854 ATCCTACTCGCTCCGTCCGT 62.606 60.000 0.00 0.00 0.00 4.69
2461 2822 0.602106 TATCCTACTCGCTCCGTCCG 60.602 60.000 0.00 0.00 0.00 4.79
2462 2823 1.823797 ATATCCTACTCGCTCCGTCC 58.176 55.000 0.00 0.00 0.00 4.79
2463 2824 4.252073 TCTTATATCCTACTCGCTCCGTC 58.748 47.826 0.00 0.00 0.00 4.79
2464 2825 4.255301 CTCTTATATCCTACTCGCTCCGT 58.745 47.826 0.00 0.00 0.00 4.69
2465 2826 3.623960 CCTCTTATATCCTACTCGCTCCG 59.376 52.174 0.00 0.00 0.00 4.63
2466 2827 4.846040 TCCTCTTATATCCTACTCGCTCC 58.154 47.826 0.00 0.00 0.00 4.70
2467 2828 5.941647 ACTTCCTCTTATATCCTACTCGCTC 59.058 44.000 0.00 0.00 0.00 5.03
2468 2829 5.883180 ACTTCCTCTTATATCCTACTCGCT 58.117 41.667 0.00 0.00 0.00 4.93
2469 2830 6.383415 CAACTTCCTCTTATATCCTACTCGC 58.617 44.000 0.00 0.00 0.00 5.03
2470 2831 6.570764 GCCAACTTCCTCTTATATCCTACTCG 60.571 46.154 0.00 0.00 0.00 4.18
2471 2832 6.267928 TGCCAACTTCCTCTTATATCCTACTC 59.732 42.308 0.00 0.00 0.00 2.59
2472 2833 6.143915 TGCCAACTTCCTCTTATATCCTACT 58.856 40.000 0.00 0.00 0.00 2.57
2473 2834 6.420913 TGCCAACTTCCTCTTATATCCTAC 57.579 41.667 0.00 0.00 0.00 3.18
2577 2946 2.118294 AAGGGACCAAAGGCAGGC 59.882 61.111 0.00 0.00 0.00 4.85
2578 2947 2.278330 GCAAGGGACCAAAGGCAGG 61.278 63.158 0.00 0.00 0.00 4.85
2579 2948 1.228675 AGCAAGGGACCAAAGGCAG 60.229 57.895 0.00 0.00 0.00 4.85
2580 2949 1.531365 CAGCAAGGGACCAAAGGCA 60.531 57.895 0.00 0.00 0.00 4.75
2605 2974 4.010667 AGCAATGTCAATTTGGCAATGT 57.989 36.364 17.72 5.07 35.45 2.71
2619 2998 0.957395 CGGGACAGAGCAAGCAATGT 60.957 55.000 2.40 2.40 0.00 2.71
2623 3002 1.301716 GAACGGGACAGAGCAAGCA 60.302 57.895 0.00 0.00 0.00 3.91
2624 3003 0.246635 TAGAACGGGACAGAGCAAGC 59.753 55.000 0.00 0.00 0.00 4.01
2625 3004 1.134965 CCTAGAACGGGACAGAGCAAG 60.135 57.143 0.00 0.00 0.00 4.01
2626 3005 0.895530 CCTAGAACGGGACAGAGCAA 59.104 55.000 0.00 0.00 0.00 3.91
2627 3006 1.605058 GCCTAGAACGGGACAGAGCA 61.605 60.000 0.00 0.00 0.00 4.26
2628 3007 1.142097 GCCTAGAACGGGACAGAGC 59.858 63.158 0.00 0.00 0.00 4.09
2629 3008 0.741915 GAGCCTAGAACGGGACAGAG 59.258 60.000 0.00 0.00 0.00 3.35
2630 3009 1.030488 CGAGCCTAGAACGGGACAGA 61.030 60.000 0.00 0.00 0.00 3.41
2631 3010 1.313812 ACGAGCCTAGAACGGGACAG 61.314 60.000 0.00 0.00 0.00 3.51
2632 3011 1.303888 ACGAGCCTAGAACGGGACA 60.304 57.895 0.00 0.00 0.00 4.02
2633 3012 1.139095 CACGAGCCTAGAACGGGAC 59.861 63.158 0.00 0.00 31.82 4.46
2634 3013 0.395311 ATCACGAGCCTAGAACGGGA 60.395 55.000 9.63 9.63 43.31 5.14
2635 3014 0.030908 GATCACGAGCCTAGAACGGG 59.969 60.000 0.00 0.00 0.00 5.28
2761 3140 1.000506 GCTTCCGGTGACACTGAAGTA 59.999 52.381 25.47 7.20 0.00 2.24
2775 3154 2.747855 GGCTGAACAGGGCTTCCG 60.748 66.667 3.99 0.00 35.17 4.30
2794 3173 1.661341 GAATCAGCCAGTTCAGCGAT 58.339 50.000 0.00 0.00 34.64 4.58
2795 3174 0.391661 GGAATCAGCCAGTTCAGCGA 60.392 55.000 0.00 0.00 34.64 4.93
2819 3198 8.506196 AGGTGATATTGTATGGTTATGGTACT 57.494 34.615 0.00 0.00 0.00 2.73
2841 3220 4.957954 ACCGTAAAAGAAAAGGGAAAAGGT 59.042 37.500 0.00 0.00 0.00 3.50
2842 3221 5.524971 ACCGTAAAAGAAAAGGGAAAAGG 57.475 39.130 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.