Multiple sequence alignment - TraesCS6D01G196900

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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 TraesCS6D01G196900 chr6D 100.000 4177 0 0 1 4177 273826344 273830520 0.000000e+00 7714.0
1 TraesCS6D01G196900 chr6B 96.330 1962 42 7 1404 3365 435582090 435584021 0.000000e+00 3197.0
2 TraesCS6D01G196900 chr6B 93.548 434 6 7 808 1241 435581336 435581747 9.860000e-176 627.0
3 TraesCS6D01G196900 chr6B 94.545 330 16 2 3366 3695 435584181 435584508 3.730000e-140 508.0
4 TraesCS6D01G196900 chr6B 86.913 298 27 7 419 706 435579786 435580081 1.450000e-84 324.0
5 TraesCS6D01G196900 chr6B 91.453 234 15 2 3694 3926 435584564 435584793 2.420000e-82 316.0
6 TraesCS6D01G196900 chr6B 88.789 223 3 1 3977 4177 435584793 435585015 1.930000e-63 254.0
7 TraesCS6D01G196900 chr6B 94.595 111 6 0 705 815 435580151 435580261 5.550000e-39 172.0
8 TraesCS6D01G196900 chr6B 81.053 190 32 3 520 706 61211922 61212110 9.360000e-32 148.0
9 TraesCS6D01G196900 chr6A 95.566 1962 37 8 1259 3197 391251897 391253831 0.000000e+00 3096.0
10 TraesCS6D01G196900 chr6A 91.323 945 37 17 3122 4041 391253820 391254744 0.000000e+00 1249.0
11 TraesCS6D01G196900 chr6A 95.531 537 11 8 705 1241 391251390 391251913 0.000000e+00 846.0
12 TraesCS6D01G196900 chr6A 91.433 607 40 6 110 706 391250716 391251320 0.000000e+00 822.0
13 TraesCS6D01G196900 chr6A 97.842 139 3 0 4039 4177 391254809 391254947 1.500000e-59 241.0
14 TraesCS6D01G196900 chr6A 92.661 109 8 0 1 109 377183270 377183162 1.550000e-34 158.0
15 TraesCS6D01G196900 chr6A 91.071 112 8 2 1 111 251006459 251006569 2.600000e-32 150.0
16 TraesCS6D01G196900 chr6A 87.903 124 14 1 3731 3853 118284325 118284202 1.210000e-30 145.0
17 TraesCS6D01G196900 chr6A 97.561 41 1 0 3996 4036 391254745 391254785 2.080000e-08 71.3
18 TraesCS6D01G196900 chr7D 94.545 110 6 0 1 110 285695020 285694911 2.000000e-38 171.0
19 TraesCS6D01G196900 chr7D 92.857 112 8 0 1 112 374052545 374052434 3.340000e-36 163.0
20 TraesCS6D01G196900 chr7D 90.678 118 10 1 3737 3853 242791457 242791340 5.590000e-34 156.0
21 TraesCS6D01G196900 chr7D 89.344 122 12 1 3731 3851 447053625 447053504 7.230000e-33 152.0
22 TraesCS6D01G196900 chr7D 87.903 124 12 3 3731 3851 74596071 74596194 4.350000e-30 143.0
23 TraesCS6D01G196900 chr4D 95.192 104 4 1 1 103 401066067 401066170 3.340000e-36 163.0
24 TraesCS6D01G196900 chr4D 87.805 123 13 2 3731 3851 74079382 74079504 4.350000e-30 143.0
25 TraesCS6D01G196900 chr3D 93.636 110 6 1 1 109 26647842 26647951 3.340000e-36 163.0
26 TraesCS6D01G196900 chr2B 93.578 109 7 0 1 109 579581876 579581768 3.340000e-36 163.0
27 TraesCS6D01G196900 chr2B 92.661 109 8 0 1 109 579580582 579580474 1.550000e-34 158.0
28 TraesCS6D01G196900 chr2B 82.065 184 29 3 526 706 795074944 795075126 2.010000e-33 154.0
29 TraesCS6D01G196900 chr4A 83.429 175 25 3 535 706 685783831 685783658 4.320000e-35 159.0
30 TraesCS6D01G196900 chr4A 80.412 194 33 4 501 691 3192846 3192655 4.350000e-30 143.0
31 TraesCS6D01G196900 chr7A 91.818 110 9 0 1 110 317130450 317130559 2.010000e-33 154.0
32 TraesCS6D01G196900 chr2A 82.162 185 27 5 526 706 669747010 669746828 2.010000e-33 154.0
33 TraesCS6D01G196900 chr2A 88.281 128 14 1 3731 3857 141506439 141506312 7.230000e-33 152.0
34 TraesCS6D01G196900 chr2A 80.193 207 35 5 505 707 70042490 70042286 2.600000e-32 150.0
35 TraesCS6D01G196900 chr2A 80.874 183 31 3 530 709 729831211 729831030 1.570000e-29 141.0
36 TraesCS6D01G196900 chr4B 89.344 122 12 1 3731 3851 438375212 438375333 7.230000e-33 152.0
37 TraesCS6D01G196900 chr3A 81.818 187 28 4 526 709 688007363 688007180 7.230000e-33 152.0
38 TraesCS6D01G196900 chr3B 81.622 185 30 3 526 707 707027121 707026938 2.600000e-32 150.0
39 TraesCS6D01G196900 chr5B 78.771 179 36 1 530 706 485633742 485633564 7.340000e-23 119.0
40 TraesCS6D01G196900 chr1B 88.462 52 4 1 3673 3724 171125277 171125326 1.250000e-05 62.1


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 TraesCS6D01G196900 chr6D 273826344 273830520 4176 False 7714.000000 7714 100.000000 1 4177 1 chr6D.!!$F1 4176
1 TraesCS6D01G196900 chr6B 435579786 435585015 5229 False 771.142857 3197 92.310429 419 4177 7 chr6B.!!$F2 3758
2 TraesCS6D01G196900 chr6A 391250716 391254947 4231 False 1054.216667 3096 94.876000 110 4177 6 chr6A.!!$F2 4067

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
217 218 0.039035 ACCTTTGCGAAATGGGCCTA 59.961 50.0 12.51 0.00 0.00 3.93 F
596 607 0.105964 TTAGCACGATGATTCCCCGG 59.894 55.0 0.00 0.00 0.00 5.73 F
1295 2459 0.813821 GCCCTGCAATTTGAGAGGAC 59.186 55.0 13.76 2.15 0.00 3.85 F
2411 3820 0.033781 GCAAGTTCCCAGCATTTGCA 59.966 50.0 5.20 0.00 45.16 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1386 2781 0.618458 TCGGACTTTGATCCCCAAGG 59.382 55.000 0.00 0.00 37.80 3.61 R
1486 2884 0.915364 ATTGAGCTCCTTCCCAGTCC 59.085 55.000 12.15 0.00 0.00 3.85 R
2591 4000 1.544093 CGGCATATCACCTTGCTCCAT 60.544 52.381 0.00 0.00 38.88 3.41 R
3534 5197 0.744281 AACGGGCCAACAAGAACTTG 59.256 50.000 4.39 12.22 45.58 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
25 26 8.964476 TTGGAATTCTATATCAAGGAAGTGTC 57.036 34.615 5.23 0.00 0.00 3.67
26 27 7.509546 TGGAATTCTATATCAAGGAAGTGTCC 58.490 38.462 5.23 0.00 45.35 4.02
34 35 4.898607 GGAAGTGTCCACCAGCAA 57.101 55.556 0.00 0.00 44.26 3.91
35 36 3.346426 GGAAGTGTCCACCAGCAAT 57.654 52.632 0.00 0.00 44.26 3.56
36 37 2.489938 GGAAGTGTCCACCAGCAATA 57.510 50.000 0.00 0.00 44.26 1.90
37 38 2.359900 GGAAGTGTCCACCAGCAATAG 58.640 52.381 0.00 0.00 44.26 1.73
38 39 2.290323 GGAAGTGTCCACCAGCAATAGT 60.290 50.000 0.00 0.00 44.26 2.12
39 40 3.055385 GGAAGTGTCCACCAGCAATAGTA 60.055 47.826 0.00 0.00 44.26 1.82
40 41 4.564821 GGAAGTGTCCACCAGCAATAGTAA 60.565 45.833 0.00 0.00 44.26 2.24
41 42 4.844349 AGTGTCCACCAGCAATAGTAAT 57.156 40.909 0.00 0.00 0.00 1.89
42 43 4.770795 AGTGTCCACCAGCAATAGTAATC 58.229 43.478 0.00 0.00 0.00 1.75
43 44 3.877508 GTGTCCACCAGCAATAGTAATCC 59.122 47.826 0.00 0.00 0.00 3.01
44 45 3.780294 TGTCCACCAGCAATAGTAATCCT 59.220 43.478 0.00 0.00 0.00 3.24
45 46 4.130118 GTCCACCAGCAATAGTAATCCTG 58.870 47.826 0.00 0.00 0.00 3.86
46 47 3.136443 TCCACCAGCAATAGTAATCCTGG 59.864 47.826 10.24 10.24 46.53 4.45
47 48 3.480470 CACCAGCAATAGTAATCCTGGG 58.520 50.000 14.28 0.00 45.65 4.45
48 49 2.443255 ACCAGCAATAGTAATCCTGGGG 59.557 50.000 14.28 0.00 45.65 4.96
49 50 2.508526 CAGCAATAGTAATCCTGGGGC 58.491 52.381 0.00 0.00 0.00 5.80
50 51 2.107204 CAGCAATAGTAATCCTGGGGCT 59.893 50.000 0.00 0.00 0.00 5.19
51 52 2.107204 AGCAATAGTAATCCTGGGGCTG 59.893 50.000 0.00 0.00 0.00 4.85
52 53 2.106511 GCAATAGTAATCCTGGGGCTGA 59.893 50.000 0.00 0.00 0.00 4.26
53 54 3.245052 GCAATAGTAATCCTGGGGCTGAT 60.245 47.826 0.00 0.00 0.00 2.90
54 55 4.330250 CAATAGTAATCCTGGGGCTGATG 58.670 47.826 0.00 0.00 0.00 3.07
55 56 2.196742 AGTAATCCTGGGGCTGATGA 57.803 50.000 0.00 0.00 0.00 2.92
56 57 2.711174 AGTAATCCTGGGGCTGATGAT 58.289 47.619 0.00 0.00 0.00 2.45
57 58 2.374504 AGTAATCCTGGGGCTGATGATG 59.625 50.000 0.00 0.00 0.00 3.07
58 59 1.526315 AATCCTGGGGCTGATGATGA 58.474 50.000 0.00 0.00 0.00 2.92
59 60 0.769873 ATCCTGGGGCTGATGATGAC 59.230 55.000 0.00 0.00 0.00 3.06
60 61 0.621280 TCCTGGGGCTGATGATGACA 60.621 55.000 0.00 0.00 0.00 3.58
61 62 0.465097 CCTGGGGCTGATGATGACAC 60.465 60.000 0.00 0.00 0.00 3.67
62 63 0.253894 CTGGGGCTGATGATGACACA 59.746 55.000 0.00 0.00 0.00 3.72
63 64 0.697658 TGGGGCTGATGATGACACAA 59.302 50.000 0.00 0.00 0.00 3.33
64 65 1.340308 TGGGGCTGATGATGACACAAG 60.340 52.381 0.00 0.00 0.00 3.16
65 66 1.386533 GGGCTGATGATGACACAAGG 58.613 55.000 0.00 0.00 0.00 3.61
66 67 1.386533 GGCTGATGATGACACAAGGG 58.613 55.000 0.00 0.00 0.00 3.95
67 68 1.340405 GGCTGATGATGACACAAGGGT 60.340 52.381 0.00 0.00 0.00 4.34
68 69 2.012673 GCTGATGATGACACAAGGGTC 58.987 52.381 0.00 0.00 38.29 4.46
75 76 2.363306 TGACACAAGGGTCATTTGCT 57.637 45.000 0.05 0.00 42.56 3.91
76 77 1.955778 TGACACAAGGGTCATTTGCTG 59.044 47.619 0.05 0.00 42.56 4.41
77 78 1.270550 GACACAAGGGTCATTTGCTGG 59.729 52.381 0.00 0.00 37.73 4.85
78 79 0.604578 CACAAGGGTCATTTGCTGGG 59.395 55.000 0.00 0.00 0.00 4.45
79 80 0.482446 ACAAGGGTCATTTGCTGGGA 59.518 50.000 0.00 0.00 0.00 4.37
80 81 1.077663 ACAAGGGTCATTTGCTGGGAT 59.922 47.619 0.00 0.00 0.00 3.85
81 82 2.181975 CAAGGGTCATTTGCTGGGATT 58.818 47.619 0.00 0.00 0.00 3.01
82 83 2.568509 CAAGGGTCATTTGCTGGGATTT 59.431 45.455 0.00 0.00 0.00 2.17
83 84 2.906568 AGGGTCATTTGCTGGGATTTT 58.093 42.857 0.00 0.00 0.00 1.82
84 85 4.059773 AGGGTCATTTGCTGGGATTTTA 57.940 40.909 0.00 0.00 0.00 1.52
85 86 4.623863 AGGGTCATTTGCTGGGATTTTAT 58.376 39.130 0.00 0.00 0.00 1.40
86 87 4.406649 AGGGTCATTTGCTGGGATTTTATG 59.593 41.667 0.00 0.00 0.00 1.90
87 88 4.162131 GGGTCATTTGCTGGGATTTTATGT 59.838 41.667 0.00 0.00 0.00 2.29
88 89 5.351458 GGTCATTTGCTGGGATTTTATGTC 58.649 41.667 0.00 0.00 0.00 3.06
89 90 5.351458 GTCATTTGCTGGGATTTTATGTCC 58.649 41.667 0.00 0.00 34.92 4.02
97 98 4.380841 GGGATTTTATGTCCCGGAAAAC 57.619 45.455 0.73 0.00 45.47 2.43
98 99 3.131577 GGGATTTTATGTCCCGGAAAACC 59.868 47.826 0.73 2.07 45.47 3.27
99 100 3.181494 GGATTTTATGTCCCGGAAAACCG 60.181 47.826 0.73 0.00 0.00 4.44
106 107 2.360600 CCGGAAAACCGGCCATGA 60.361 61.111 14.59 0.00 46.47 3.07
107 108 2.696759 CCGGAAAACCGGCCATGAC 61.697 63.158 14.59 0.00 46.47 3.06
108 109 1.969064 CGGAAAACCGGCCATGACA 60.969 57.895 0.00 0.00 0.00 3.58
139 140 3.476552 GGGTTTGATCGATCTTATGCCA 58.523 45.455 25.02 1.69 0.00 4.92
202 203 1.005924 CTGCCCCTTACATTGGACCTT 59.994 52.381 0.00 0.00 0.00 3.50
208 209 2.817258 CCTTACATTGGACCTTTGCGAA 59.183 45.455 0.00 0.00 0.00 4.70
210 211 4.082245 CCTTACATTGGACCTTTGCGAAAT 60.082 41.667 0.00 0.00 0.00 2.17
217 218 0.039035 ACCTTTGCGAAATGGGCCTA 59.961 50.000 12.51 0.00 0.00 3.93
275 276 4.873129 CACCGTCATCGCCCCTCG 62.873 72.222 0.00 0.00 40.15 4.63
310 311 2.490903 CCCTGCTCTCATTCTTGTTTGG 59.509 50.000 0.00 0.00 0.00 3.28
378 379 3.425162 AGGAACAATGTCTCCCACTTC 57.575 47.619 9.78 0.00 31.50 3.01
387 388 2.762459 TCCCACTTCCGATCCCCG 60.762 66.667 0.00 0.00 38.18 5.73
389 390 2.499685 CCACTTCCGATCCCCGTC 59.500 66.667 0.00 0.00 36.31 4.79
451 452 0.247576 GTCTTCGTCGAATCTCGCGA 60.248 55.000 9.26 9.26 42.80 5.87
470 471 3.879932 GAAATTCGGTTCGATGGATCC 57.120 47.619 4.20 4.20 35.23 3.36
507 518 2.400399 TGTTCGTCTTCGGTCATGTTC 58.600 47.619 0.00 0.00 37.69 3.18
564 575 1.723608 TTGTTGTTCTGGTGCGCTGG 61.724 55.000 9.73 0.00 0.00 4.85
596 607 0.105964 TTAGCACGATGATTCCCCGG 59.894 55.000 0.00 0.00 0.00 5.73
686 697 4.891168 TCACTCCAGTACTTGTAGTTGTCA 59.109 41.667 0.00 0.00 0.00 3.58
693 704 6.087522 CAGTACTTGTAGTTGTCACTAGCTC 58.912 44.000 0.00 0.00 36.09 4.09
706 717 2.230508 CACTAGCTCGTCCACAAACCTA 59.769 50.000 0.00 0.00 0.00 3.08
896 2060 3.056821 GTGGAACAAGATAAAACCCAGCC 60.057 47.826 0.00 0.00 44.16 4.85
967 2131 3.700350 CCCTCCACCCCCTCTCCT 61.700 72.222 0.00 0.00 0.00 3.69
968 2132 2.456840 CCTCCACCCCCTCTCCTT 59.543 66.667 0.00 0.00 0.00 3.36
1106 2270 2.015726 TCCTCTCCCCCTCCTCCTC 61.016 68.421 0.00 0.00 0.00 3.71
1107 2271 2.612251 CTCTCCCCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1108 2272 2.018086 CTCTCCCCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1154 2318 2.760092 GCTCTTAATGGCATTGGTTCCA 59.240 45.455 22.57 0.00 36.70 3.53
1155 2319 3.385755 GCTCTTAATGGCATTGGTTCCAT 59.614 43.478 22.57 0.00 44.46 3.41
1184 2348 6.222389 ACTGCCTGTACTAGTATCGTAGTAG 58.778 44.000 5.75 5.61 36.40 2.57
1185 2349 6.166984 TGCCTGTACTAGTATCGTAGTAGT 57.833 41.667 5.75 13.46 44.72 2.73
1186 2350 7.014711 ACTGCCTGTACTAGTATCGTAGTAGTA 59.985 40.741 5.75 12.10 41.78 1.82
1241 2405 6.808829 TGTTTCCTCGTGATTATACGGTATT 58.191 36.000 5.89 0.00 43.85 1.89
1242 2406 7.267128 TGTTTCCTCGTGATTATACGGTATTT 58.733 34.615 5.89 0.00 43.85 1.40
1244 2408 8.606602 GTTTCCTCGTGATTATACGGTATTTTT 58.393 33.333 5.89 0.00 43.85 1.94
1270 2434 7.412760 TTTTTGCGAAATTCGTGATTATACG 57.587 32.000 17.05 0.00 42.81 3.06
1271 2435 4.702247 TGCGAAATTCGTGATTATACGG 57.298 40.909 17.05 0.00 42.81 4.02
1272 2436 4.114073 TGCGAAATTCGTGATTATACGGT 58.886 39.130 17.05 0.00 42.81 4.83
1273 2437 5.280164 TGCGAAATTCGTGATTATACGGTA 58.720 37.500 17.05 0.00 42.81 4.02
1274 2438 5.921976 TGCGAAATTCGTGATTATACGGTAT 59.078 36.000 17.05 5.87 42.81 2.73
1295 2459 0.813821 GCCCTGCAATTTGAGAGGAC 59.186 55.000 13.76 2.15 0.00 3.85
1299 2463 0.960364 TGCAATTTGAGAGGACCGGC 60.960 55.000 0.00 0.00 0.00 6.13
1358 2753 3.195825 AGATTCAGTTTACTGGTCTCCGG 59.804 47.826 9.82 0.00 43.91 5.14
1361 2756 3.499338 TCAGTTTACTGGTCTCCGGTTA 58.501 45.455 9.82 0.00 40.77 2.85
1364 2759 3.762823 AGTTTACTGGTCTCCGGTTAGAG 59.237 47.826 0.00 0.00 40.77 2.43
1380 2775 5.354234 CGGTTAGAGTTGCCTCAATAAATGT 59.646 40.000 0.00 0.00 40.40 2.71
1381 2776 6.555315 GGTTAGAGTTGCCTCAATAAATGTG 58.445 40.000 0.00 0.00 40.40 3.21
1382 2777 6.374333 GGTTAGAGTTGCCTCAATAAATGTGA 59.626 38.462 0.00 0.00 40.40 3.58
1383 2778 7.067494 GGTTAGAGTTGCCTCAATAAATGTGAT 59.933 37.037 0.00 0.00 40.40 3.06
1384 2779 8.462016 GTTAGAGTTGCCTCAATAAATGTGATT 58.538 33.333 0.00 0.00 40.40 2.57
1385 2780 7.472334 AGAGTTGCCTCAATAAATGTGATTT 57.528 32.000 0.00 0.00 40.40 2.17
1386 2781 7.542025 AGAGTTGCCTCAATAAATGTGATTTC 58.458 34.615 0.00 0.00 40.40 2.17
1387 2782 6.633856 AGTTGCCTCAATAAATGTGATTTCC 58.366 36.000 0.00 0.00 33.82 3.13
1388 2783 6.438425 AGTTGCCTCAATAAATGTGATTTCCT 59.562 34.615 0.00 0.00 33.82 3.36
1389 2784 6.855763 TGCCTCAATAAATGTGATTTCCTT 57.144 33.333 0.00 0.00 33.82 3.36
1390 2785 6.632909 TGCCTCAATAAATGTGATTTCCTTG 58.367 36.000 0.00 0.00 33.82 3.61
1391 2786 6.044682 GCCTCAATAAATGTGATTTCCTTGG 58.955 40.000 0.00 0.00 33.82 3.61
1392 2787 6.576185 CCTCAATAAATGTGATTTCCTTGGG 58.424 40.000 0.00 0.00 33.82 4.12
1393 2788 6.407299 CCTCAATAAATGTGATTTCCTTGGGG 60.407 42.308 0.00 0.00 38.34 4.96
1394 2789 6.259893 TCAATAAATGTGATTTCCTTGGGGA 58.740 36.000 0.00 0.00 40.36 4.81
1395 2790 6.902416 TCAATAAATGTGATTTCCTTGGGGAT 59.098 34.615 0.00 0.00 41.87 3.85
1396 2791 6.983906 ATAAATGTGATTTCCTTGGGGATC 57.016 37.500 0.00 0.00 41.87 3.36
1397 2792 4.335735 AATGTGATTTCCTTGGGGATCA 57.664 40.909 0.00 3.11 41.87 2.92
1398 2793 3.824001 TGTGATTTCCTTGGGGATCAA 57.176 42.857 0.00 0.00 41.87 2.57
1399 2794 4.125124 TGTGATTTCCTTGGGGATCAAA 57.875 40.909 0.00 1.60 41.87 2.69
1400 2795 4.088634 TGTGATTTCCTTGGGGATCAAAG 58.911 43.478 0.00 0.00 41.87 2.77
1401 2796 4.089361 GTGATTTCCTTGGGGATCAAAGT 58.911 43.478 0.00 0.00 41.87 2.66
1402 2797 4.158579 GTGATTTCCTTGGGGATCAAAGTC 59.841 45.833 0.00 0.00 41.87 3.01
1483 2881 6.591062 TGGATTTGTATGTAAACTCGTGTACC 59.409 38.462 0.00 0.00 0.00 3.34
1484 2882 6.815142 GGATTTGTATGTAAACTCGTGTACCT 59.185 38.462 0.00 0.00 0.00 3.08
1485 2883 7.201496 GGATTTGTATGTAAACTCGTGTACCTG 60.201 40.741 0.00 0.00 0.00 4.00
1486 2884 5.063180 TGTATGTAAACTCGTGTACCTGG 57.937 43.478 0.00 0.00 0.00 4.45
1487 2885 3.604875 ATGTAAACTCGTGTACCTGGG 57.395 47.619 0.00 0.00 0.00 4.45
1488 2886 2.596346 TGTAAACTCGTGTACCTGGGA 58.404 47.619 0.00 0.00 0.00 4.37
1520 2918 2.689983 GCTCAATCATTGGTAACTGGGG 59.310 50.000 0.00 0.00 37.61 4.96
1541 2939 3.550842 GGCACTGTACTGCTTCTTTTTGG 60.551 47.826 7.01 0.00 37.33 3.28
1639 3048 4.714632 TGGCTCCAACATTACTAATAGCC 58.285 43.478 10.75 10.75 46.71 3.93
1790 3199 7.077605 CGCAAGTTATATTTATGGTCCACATG 58.922 38.462 0.00 0.00 40.82 3.21
1871 3280 0.179009 TCTCAAGGTTGCTTGCTGCT 60.179 50.000 0.00 0.00 43.37 4.24
2411 3820 0.033781 GCAAGTTCCCAGCATTTGCA 59.966 50.000 5.20 0.00 45.16 4.08
2591 4000 6.265196 AGAATATTGGTGTCAACAAAGCTCAA 59.735 34.615 7.53 0.00 35.48 3.02
2654 4063 0.747283 GCAGGCAGAAGGTGGAGATG 60.747 60.000 0.00 0.00 0.00 2.90
2708 4117 4.876107 TCTAAGGAAAACATCGGCAAGATC 59.124 41.667 0.00 0.00 37.52 2.75
2825 4234 6.387192 TCTCTTATTCAGAAATGTCCCCAA 57.613 37.500 0.00 0.00 0.00 4.12
2846 4255 6.279882 CCAAGCTTTTGGTTTGAACATAGAA 58.720 36.000 0.00 0.00 38.20 2.10
2888 4297 4.656112 ACAGAGTTTTTCCTGGAGAGAGAA 59.344 41.667 0.00 0.00 34.85 2.87
3098 4507 0.692756 TGACTGGTTGTGGGGTGAGA 60.693 55.000 0.00 0.00 0.00 3.27
3251 4724 4.522722 AGCGTTAATAGCCTGGTAGATC 57.477 45.455 0.00 0.00 34.64 2.75
3351 4824 1.091771 CGTGCGGCATTTGAGAGGAT 61.092 55.000 5.72 0.00 0.00 3.24
3401 5033 3.937706 GTCATGCTCTTCTGTACTTGCAT 59.062 43.478 0.00 0.00 41.08 3.96
3476 5108 3.868619 TTACTGTTGGTGGCTTAGGTT 57.131 42.857 0.00 0.00 0.00 3.50
3518 5181 2.364647 TCAGTTGGCAATGTCAAATGCA 59.635 40.909 21.19 9.11 41.89 3.96
3526 5189 3.803231 GCAATGTCAAATGCAGTTGTTCA 59.197 39.130 24.60 22.72 42.12 3.18
3534 5197 6.801862 GTCAAATGCAGTTGTTCAATACTACC 59.198 38.462 24.60 0.00 33.64 3.18
3607 5270 9.549509 TTTTTATGAACGTTATTTCTTCCATCG 57.450 29.630 0.00 0.00 0.00 3.84
3682 5345 5.350365 TCCATATTAACTGACGCACACTTTC 59.650 40.000 0.00 0.00 0.00 2.62
3722 5442 6.880484 AGTGTACGTCAATTAATATGGGTCA 58.120 36.000 0.00 0.00 0.00 4.02
3788 5509 7.906010 CGTTTTAGTGTGTTTGTTCACTCATTA 59.094 33.333 1.08 0.00 42.77 1.90
3854 5576 2.526888 ATGAACGGAGGGAGTACTCA 57.473 50.000 23.91 1.66 39.27 3.41
3871 5593 8.515473 GAGTACTCACTCTCTTTCTTTCTTTC 57.485 38.462 18.20 0.00 46.56 2.62
3914 5636 4.693566 TCGAAGTTAAATGTTGTAGCCAGG 59.306 41.667 0.00 0.00 0.00 4.45
3949 5671 1.947456 GGAAAGTCCCGGCAATATGAC 59.053 52.381 0.00 0.00 0.00 3.06
3950 5672 2.639065 GAAAGTCCCGGCAATATGACA 58.361 47.619 0.00 0.00 0.00 3.58
3951 5673 2.332063 AAGTCCCGGCAATATGACAG 57.668 50.000 0.00 0.00 0.00 3.51
3952 5674 0.469917 AGTCCCGGCAATATGACAGG 59.530 55.000 0.00 0.00 0.00 4.00
3953 5675 0.180406 GTCCCGGCAATATGACAGGT 59.820 55.000 0.00 0.00 0.00 4.00
3954 5676 0.916086 TCCCGGCAATATGACAGGTT 59.084 50.000 0.00 0.00 0.00 3.50
3955 5677 1.134220 TCCCGGCAATATGACAGGTTC 60.134 52.381 0.00 0.00 0.00 3.62
3956 5678 1.408127 CCCGGCAATATGACAGGTTCA 60.408 52.381 0.00 0.00 39.11 3.18
3957 5679 1.942657 CCGGCAATATGACAGGTTCAG 59.057 52.381 0.00 0.00 37.77 3.02
3969 5691 2.880890 ACAGGTTCAGTGCAGATTTGTC 59.119 45.455 0.00 0.00 0.00 3.18
3985 5707 7.596494 CAGATTTGTCACTTCCATGTATTGTT 58.404 34.615 0.00 0.00 0.00 2.83
4061 5850 5.527582 AGCCTATTCGTTTAGGTAGCAATTG 59.472 40.000 0.00 0.00 40.83 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.993183 GGACACTTCCTTGATATAGAATTCCAA 59.007 37.037 0.65 0.00 39.13 3.53
1 2 7.127186 TGGACACTTCCTTGATATAGAATTCCA 59.873 37.037 0.65 0.00 43.31 3.53
2 3 7.442666 GTGGACACTTCCTTGATATAGAATTCC 59.557 40.741 0.65 0.00 43.31 3.01
3 4 7.442666 GGTGGACACTTCCTTGATATAGAATTC 59.557 40.741 0.00 0.00 43.31 2.17
4 5 7.092444 TGGTGGACACTTCCTTGATATAGAATT 60.092 37.037 2.13 0.00 43.31 2.17
5 6 6.386927 TGGTGGACACTTCCTTGATATAGAAT 59.613 38.462 2.13 0.00 43.31 2.40
6 7 5.724370 TGGTGGACACTTCCTTGATATAGAA 59.276 40.000 2.13 0.00 43.31 2.10
7 8 5.277250 TGGTGGACACTTCCTTGATATAGA 58.723 41.667 2.13 0.00 43.31 1.98
8 9 5.605534 CTGGTGGACACTTCCTTGATATAG 58.394 45.833 2.13 0.00 43.31 1.31
9 10 4.141711 GCTGGTGGACACTTCCTTGATATA 60.142 45.833 2.13 0.00 43.31 0.86
10 11 3.370953 GCTGGTGGACACTTCCTTGATAT 60.371 47.826 2.13 0.00 43.31 1.63
11 12 2.027192 GCTGGTGGACACTTCCTTGATA 60.027 50.000 2.13 0.00 43.31 2.15
12 13 1.271597 GCTGGTGGACACTTCCTTGAT 60.272 52.381 2.13 0.00 43.31 2.57
13 14 0.108585 GCTGGTGGACACTTCCTTGA 59.891 55.000 2.13 0.00 43.31 3.02
14 15 0.179020 TGCTGGTGGACACTTCCTTG 60.179 55.000 2.13 0.00 43.31 3.61
15 16 0.550914 TTGCTGGTGGACACTTCCTT 59.449 50.000 2.13 0.00 43.31 3.36
16 17 0.773644 ATTGCTGGTGGACACTTCCT 59.226 50.000 2.13 0.00 43.31 3.36
17 18 2.290323 ACTATTGCTGGTGGACACTTCC 60.290 50.000 2.13 0.00 43.19 3.46
18 19 3.059352 ACTATTGCTGGTGGACACTTC 57.941 47.619 2.13 0.00 0.00 3.01
19 20 4.634012 TTACTATTGCTGGTGGACACTT 57.366 40.909 2.13 0.00 0.00 3.16
20 21 4.384208 GGATTACTATTGCTGGTGGACACT 60.384 45.833 2.13 0.00 0.00 3.55
21 22 3.877508 GGATTACTATTGCTGGTGGACAC 59.122 47.826 0.00 0.00 0.00 3.67
22 23 3.780294 AGGATTACTATTGCTGGTGGACA 59.220 43.478 0.00 0.00 0.00 4.02
23 24 4.130118 CAGGATTACTATTGCTGGTGGAC 58.870 47.826 0.00 0.00 0.00 4.02
24 25 3.136443 CCAGGATTACTATTGCTGGTGGA 59.864 47.826 9.34 0.00 44.94 4.02
25 26 3.480470 CCAGGATTACTATTGCTGGTGG 58.520 50.000 9.34 0.00 44.94 4.61
29 30 2.107204 AGCCCCAGGATTACTATTGCTG 59.893 50.000 0.00 0.00 32.84 4.41
30 31 2.107204 CAGCCCCAGGATTACTATTGCT 59.893 50.000 0.00 0.00 0.00 3.91
31 32 2.106511 TCAGCCCCAGGATTACTATTGC 59.893 50.000 0.00 0.00 0.00 3.56
32 33 4.042062 TCATCAGCCCCAGGATTACTATTG 59.958 45.833 0.00 0.00 0.00 1.90
33 34 4.242811 TCATCAGCCCCAGGATTACTATT 58.757 43.478 0.00 0.00 0.00 1.73
34 35 3.874316 TCATCAGCCCCAGGATTACTAT 58.126 45.455 0.00 0.00 0.00 2.12
35 36 3.344535 TCATCAGCCCCAGGATTACTA 57.655 47.619 0.00 0.00 0.00 1.82
36 37 2.196742 TCATCAGCCCCAGGATTACT 57.803 50.000 0.00 0.00 0.00 2.24
37 38 2.373169 TCATCATCAGCCCCAGGATTAC 59.627 50.000 0.00 0.00 0.00 1.89
38 39 2.373169 GTCATCATCAGCCCCAGGATTA 59.627 50.000 0.00 0.00 0.00 1.75
39 40 1.144503 GTCATCATCAGCCCCAGGATT 59.855 52.381 0.00 0.00 0.00 3.01
40 41 0.769873 GTCATCATCAGCCCCAGGAT 59.230 55.000 0.00 0.00 0.00 3.24
41 42 0.621280 TGTCATCATCAGCCCCAGGA 60.621 55.000 0.00 0.00 0.00 3.86
42 43 0.465097 GTGTCATCATCAGCCCCAGG 60.465 60.000 0.00 0.00 0.00 4.45
43 44 0.253894 TGTGTCATCATCAGCCCCAG 59.746 55.000 0.00 0.00 0.00 4.45
44 45 0.697658 TTGTGTCATCATCAGCCCCA 59.302 50.000 0.00 0.00 0.00 4.96
45 46 1.386533 CTTGTGTCATCATCAGCCCC 58.613 55.000 0.00 0.00 0.00 5.80
46 47 1.386533 CCTTGTGTCATCATCAGCCC 58.613 55.000 0.00 0.00 0.00 5.19
47 48 1.340405 ACCCTTGTGTCATCATCAGCC 60.340 52.381 0.00 0.00 0.00 4.85
48 49 2.012673 GACCCTTGTGTCATCATCAGC 58.987 52.381 0.00 0.00 35.29 4.26
49 50 3.339253 TGACCCTTGTGTCATCATCAG 57.661 47.619 0.00 0.00 40.22 2.90
57 58 1.270550 CCAGCAAATGACCCTTGTGTC 59.729 52.381 0.00 0.00 35.77 3.67
58 59 1.331214 CCAGCAAATGACCCTTGTGT 58.669 50.000 0.00 0.00 0.00 3.72
59 60 0.604578 CCCAGCAAATGACCCTTGTG 59.395 55.000 0.00 0.00 0.00 3.33
60 61 0.482446 TCCCAGCAAATGACCCTTGT 59.518 50.000 0.00 0.00 0.00 3.16
61 62 1.856629 ATCCCAGCAAATGACCCTTG 58.143 50.000 0.00 0.00 0.00 3.61
62 63 2.629017 AATCCCAGCAAATGACCCTT 57.371 45.000 0.00 0.00 0.00 3.95
63 64 2.629017 AAATCCCAGCAAATGACCCT 57.371 45.000 0.00 0.00 0.00 4.34
64 65 4.162131 ACATAAAATCCCAGCAAATGACCC 59.838 41.667 0.00 0.00 0.00 4.46
65 66 5.343307 ACATAAAATCCCAGCAAATGACC 57.657 39.130 0.00 0.00 0.00 4.02
66 67 5.351458 GGACATAAAATCCCAGCAAATGAC 58.649 41.667 0.00 0.00 0.00 3.06
67 68 5.596836 GGACATAAAATCCCAGCAAATGA 57.403 39.130 0.00 0.00 0.00 2.57
77 78 4.380841 GGTTTTCCGGGACATAAAATCC 57.619 45.455 0.00 0.00 35.28 3.01
91 92 0.893727 ACTGTCATGGCCGGTTTTCC 60.894 55.000 1.90 0.00 0.00 3.13
92 93 0.958822 AACTGTCATGGCCGGTTTTC 59.041 50.000 1.90 0.00 0.00 2.29
93 94 1.408969 AAACTGTCATGGCCGGTTTT 58.591 45.000 1.90 0.00 38.00 2.43
94 95 1.883926 GTAAACTGTCATGGCCGGTTT 59.116 47.619 20.00 20.00 42.46 3.27
95 96 1.202830 TGTAAACTGTCATGGCCGGTT 60.203 47.619 1.90 0.00 32.88 4.44
96 97 0.398696 TGTAAACTGTCATGGCCGGT 59.601 50.000 1.90 0.00 0.00 5.28
97 98 1.401552 CATGTAAACTGTCATGGCCGG 59.598 52.381 0.00 0.00 38.10 6.13
98 99 2.830772 CATGTAAACTGTCATGGCCG 57.169 50.000 0.00 0.00 38.10 6.13
102 103 4.522405 TCAAACCCCATGTAAACTGTCATG 59.478 41.667 0.00 2.01 40.46 3.07
103 104 4.735369 TCAAACCCCATGTAAACTGTCAT 58.265 39.130 0.00 0.00 0.00 3.06
104 105 4.171878 TCAAACCCCATGTAAACTGTCA 57.828 40.909 0.00 0.00 0.00 3.58
105 106 4.142687 CGATCAAACCCCATGTAAACTGTC 60.143 45.833 0.00 0.00 0.00 3.51
106 107 3.756434 CGATCAAACCCCATGTAAACTGT 59.244 43.478 0.00 0.00 0.00 3.55
107 108 4.006989 TCGATCAAACCCCATGTAAACTG 58.993 43.478 0.00 0.00 0.00 3.16
108 109 4.295141 TCGATCAAACCCCATGTAAACT 57.705 40.909 0.00 0.00 0.00 2.66
123 124 3.834231 TGGAGATGGCATAAGATCGATCA 59.166 43.478 26.47 8.05 0.00 2.92
139 140 2.703947 AGGAGATGCCAAGATGGAGAT 58.296 47.619 0.00 0.00 40.96 2.75
181 182 0.331616 GGTCCAATGTAAGGGGCAGT 59.668 55.000 0.00 0.00 0.00 4.40
188 189 4.497473 TTTCGCAAAGGTCCAATGTAAG 57.503 40.909 0.00 0.00 0.00 2.34
202 203 1.312371 GCAGTAGGCCCATTTCGCAA 61.312 55.000 0.00 0.00 36.11 4.85
217 218 2.036256 GGTGGGAAGCATGGCAGT 59.964 61.111 0.00 0.00 0.00 4.40
284 285 0.252881 AGAATGAGAGCAGGGTCCCA 60.253 55.000 11.55 0.00 0.00 4.37
296 297 2.665519 CGCCGAACCAAACAAGAATGAG 60.666 50.000 0.00 0.00 0.00 2.90
324 325 2.203538 AAAGCCACACAGCCCCAG 60.204 61.111 0.00 0.00 0.00 4.45
326 327 3.305516 CCAAAGCCACACAGCCCC 61.306 66.667 0.00 0.00 0.00 5.80
330 331 0.461135 ACTTTGCCAAAGCCACACAG 59.539 50.000 16.89 0.00 42.27 3.66
378 379 2.737180 CATCAGGACGGGGATCGG 59.263 66.667 0.00 0.00 44.45 4.18
387 388 1.871408 CGCTAGATGCACCATCAGGAC 60.871 57.143 7.83 0.00 42.72 3.85
389 390 0.105593 ACGCTAGATGCACCATCAGG 59.894 55.000 7.83 1.74 42.72 3.86
410 411 1.737029 CGCCATCACACGTTCTCTGAT 60.737 52.381 0.00 0.00 0.00 2.90
470 471 3.612860 CGAACAAAGACTGGATCCTAACG 59.387 47.826 14.23 1.42 0.00 3.18
583 594 0.179045 AGAAAGCCGGGGAATCATCG 60.179 55.000 2.18 0.00 0.00 3.84
596 607 5.220381 GGGCAAAACTTGTTAGTAGAAAGC 58.780 41.667 0.00 0.00 33.17 3.51
653 664 1.367471 CTGGAGTGAGCCAACGACA 59.633 57.895 0.00 0.00 37.52 4.35
655 666 0.601558 GTACTGGAGTGAGCCAACGA 59.398 55.000 0.00 0.00 37.52 3.85
686 697 1.339097 AGGTTTGTGGACGAGCTAGT 58.661 50.000 0.00 0.00 0.00 2.57
842 2006 5.590259 CACCCGAAACTGAAATATCTCCAAT 59.410 40.000 0.00 0.00 0.00 3.16
896 2060 1.341209 GAAGCTGTTTGGGACTTTGGG 59.659 52.381 0.00 0.00 0.00 4.12
952 2116 1.997874 CCAAGGAGAGGGGGTGGAG 60.998 68.421 0.00 0.00 0.00 3.86
953 2117 2.124996 CCAAGGAGAGGGGGTGGA 59.875 66.667 0.00 0.00 0.00 4.02
955 2119 3.732849 GCCCAAGGAGAGGGGGTG 61.733 72.222 0.00 0.00 46.86 4.61
1154 2318 8.632906 ACGATACTAGTACAGGCAGTAATAAT 57.367 34.615 4.31 0.00 33.35 1.28
1155 2319 9.212641 CTACGATACTAGTACAGGCAGTAATAA 57.787 37.037 4.31 0.00 33.35 1.40
1156 2320 8.370940 ACTACGATACTAGTACAGGCAGTAATA 58.629 37.037 4.31 0.00 33.72 0.98
1184 2348 6.042208 AGCTCCAATCCCTACTCAACTAATAC 59.958 42.308 0.00 0.00 0.00 1.89
1185 2349 6.143915 AGCTCCAATCCCTACTCAACTAATA 58.856 40.000 0.00 0.00 0.00 0.98
1186 2350 4.971924 AGCTCCAATCCCTACTCAACTAAT 59.028 41.667 0.00 0.00 0.00 1.73
1190 2354 3.274288 CAAGCTCCAATCCCTACTCAAC 58.726 50.000 0.00 0.00 0.00 3.18
1246 2410 6.466413 CCGTATAATCACGAATTTCGCAAAAA 59.534 34.615 18.24 2.83 45.12 1.94
1247 2411 5.960683 CCGTATAATCACGAATTTCGCAAAA 59.039 36.000 18.24 2.51 45.12 2.44
1248 2412 5.063691 ACCGTATAATCACGAATTTCGCAAA 59.936 36.000 18.24 4.92 45.12 3.68
1249 2413 4.567558 ACCGTATAATCACGAATTTCGCAA 59.432 37.500 18.24 7.38 45.12 4.85
1250 2414 4.114073 ACCGTATAATCACGAATTTCGCA 58.886 39.130 18.24 6.14 45.12 5.10
1251 2415 4.703899 ACCGTATAATCACGAATTTCGC 57.296 40.909 18.24 0.00 45.12 4.70
1252 2416 6.730619 GCAATACCGTATAATCACGAATTTCG 59.269 38.462 16.84 16.84 44.69 3.46
1253 2417 7.013529 GGCAATACCGTATAATCACGAATTTC 58.986 38.462 0.00 0.00 44.69 2.17
1254 2418 6.072893 GGGCAATACCGTATAATCACGAATTT 60.073 38.462 0.00 0.00 44.69 1.82
1255 2419 5.410439 GGGCAATACCGTATAATCACGAATT 59.590 40.000 0.00 0.00 44.69 2.17
1256 2420 4.933400 GGGCAATACCGTATAATCACGAAT 59.067 41.667 0.00 0.00 44.69 3.34
1257 2421 4.039488 AGGGCAATACCGTATAATCACGAA 59.961 41.667 0.00 0.00 44.69 3.85
1258 2422 3.575256 AGGGCAATACCGTATAATCACGA 59.425 43.478 0.00 0.00 44.69 4.35
1259 2423 3.678072 CAGGGCAATACCGTATAATCACG 59.322 47.826 0.00 0.00 40.62 4.35
1260 2424 3.435671 GCAGGGCAATACCGTATAATCAC 59.564 47.826 0.00 0.00 40.62 3.06
1261 2425 3.071747 TGCAGGGCAATACCGTATAATCA 59.928 43.478 0.00 0.00 40.62 2.57
1262 2426 3.670625 TGCAGGGCAATACCGTATAATC 58.329 45.455 0.00 0.00 40.62 1.75
1263 2427 3.780804 TGCAGGGCAATACCGTATAAT 57.219 42.857 0.00 0.00 40.62 1.28
1264 2428 3.562343 TTGCAGGGCAATACCGTATAA 57.438 42.857 0.00 0.00 43.99 0.98
1295 2459 0.804544 TCGACTAAGATTTGCGCCGG 60.805 55.000 4.18 0.00 0.00 6.13
1364 2759 6.633856 AGGAAATCACATTTATTGAGGCAAC 58.366 36.000 0.00 0.00 31.47 4.17
1386 2781 0.618458 TCGGACTTTGATCCCCAAGG 59.382 55.000 0.00 0.00 37.80 3.61
1387 2782 2.489938 TTCGGACTTTGATCCCCAAG 57.510 50.000 0.00 0.00 35.94 3.61
1388 2783 2.961531 TTTCGGACTTTGATCCCCAA 57.038 45.000 0.00 0.00 35.03 4.12
1389 2784 2.961531 TTTTCGGACTTTGATCCCCA 57.038 45.000 0.00 0.00 35.03 4.96
1390 2785 3.418047 TCTTTTTCGGACTTTGATCCCC 58.582 45.455 0.00 0.00 35.03 4.81
1391 2786 6.753107 TTATCTTTTTCGGACTTTGATCCC 57.247 37.500 0.00 0.00 35.03 3.85
1392 2787 8.244113 ACAATTATCTTTTTCGGACTTTGATCC 58.756 33.333 0.00 0.00 35.16 3.36
1393 2788 9.065871 CACAATTATCTTTTTCGGACTTTGATC 57.934 33.333 0.00 0.00 0.00 2.92
1394 2789 7.542130 GCACAATTATCTTTTTCGGACTTTGAT 59.458 33.333 0.00 0.00 0.00 2.57
1395 2790 6.861055 GCACAATTATCTTTTTCGGACTTTGA 59.139 34.615 0.00 0.00 0.00 2.69
1396 2791 6.183359 CGCACAATTATCTTTTTCGGACTTTG 60.183 38.462 0.00 0.00 0.00 2.77
1397 2792 5.856455 CGCACAATTATCTTTTTCGGACTTT 59.144 36.000 0.00 0.00 0.00 2.66
1398 2793 5.390613 CGCACAATTATCTTTTTCGGACTT 58.609 37.500 0.00 0.00 0.00 3.01
1399 2794 4.142687 CCGCACAATTATCTTTTTCGGACT 60.143 41.667 0.00 0.00 36.77 3.85
1400 2795 4.095610 CCGCACAATTATCTTTTTCGGAC 58.904 43.478 0.00 0.00 36.77 4.79
1401 2796 3.426963 GCCGCACAATTATCTTTTTCGGA 60.427 43.478 0.00 0.00 36.77 4.55
1402 2797 2.851824 GCCGCACAATTATCTTTTTCGG 59.148 45.455 0.00 0.00 37.60 4.30
1457 2855 6.721571 ACACGAGTTTACATACAAATCCAG 57.278 37.500 0.00 0.00 0.00 3.86
1483 2881 1.614824 AGCTCCTTCCCAGTCCCAG 60.615 63.158 0.00 0.00 0.00 4.45
1484 2882 1.613630 GAGCTCCTTCCCAGTCCCA 60.614 63.158 0.87 0.00 0.00 4.37
1485 2883 1.201429 TTGAGCTCCTTCCCAGTCCC 61.201 60.000 12.15 0.00 0.00 4.46
1486 2884 0.915364 ATTGAGCTCCTTCCCAGTCC 59.085 55.000 12.15 0.00 0.00 3.85
1487 2885 1.556911 TGATTGAGCTCCTTCCCAGTC 59.443 52.381 12.15 0.00 0.00 3.51
1488 2886 1.661463 TGATTGAGCTCCTTCCCAGT 58.339 50.000 12.15 0.00 0.00 4.00
1520 2918 3.066760 ACCAAAAAGAAGCAGTACAGTGC 59.933 43.478 0.57 0.57 44.35 4.40
1541 2939 7.096147 CGTCTCTGGTTCTTACTTCTGTTAAAC 60.096 40.741 0.00 0.00 0.00 2.01
1604 3013 5.245531 TGTTGGAGCCAGTAACTAATGAAG 58.754 41.667 0.00 0.00 0.00 3.02
1790 3199 4.573607 TCATCAGCATCTGCAACATAGTTC 59.426 41.667 4.79 0.00 45.16 3.01
1871 3280 2.037772 AGCTTTCGCTTCCTCTCTTTCA 59.962 45.455 0.00 0.00 46.47 2.69
2306 3715 4.432741 GCTCCCCCTGAGGTTGGC 62.433 72.222 0.00 0.00 41.73 4.52
2411 3820 5.276461 TCTTGCGATCCACATTGTAGTAT 57.724 39.130 0.00 0.00 0.00 2.12
2591 4000 1.544093 CGGCATATCACCTTGCTCCAT 60.544 52.381 0.00 0.00 38.88 3.41
2654 4063 4.218852 AGTTCAGTAAGGTAGCTCACAGTC 59.781 45.833 0.00 0.00 0.00 3.51
2708 4117 2.215907 GATGAGGACATCGTGTGAGG 57.784 55.000 0.00 0.00 42.45 3.86
2825 4234 7.288810 TGATTCTATGTTCAAACCAAAAGCT 57.711 32.000 0.00 0.00 0.00 3.74
2846 4255 2.012673 GTGATCGGCTTCAGCTTTGAT 58.987 47.619 0.00 0.62 41.70 2.57
2888 4297 2.360165 GCCAATTTCCTCGATGCTGAAT 59.640 45.455 0.00 0.00 0.00 2.57
3098 4507 6.005823 TGACAACATCTGGTTCAGAATCAAT 58.994 36.000 0.00 0.00 44.04 2.57
3251 4724 4.990543 TCTTGTGTGCTGAAAACTATCG 57.009 40.909 0.00 0.00 0.00 2.92
3390 5022 2.153645 TCAACTGCCATGCAAGTACAG 58.846 47.619 7.44 7.44 38.41 2.74
3401 5033 1.375908 GCGAGTCCATCAACTGCCA 60.376 57.895 0.00 0.00 0.00 4.92
3476 5108 3.514309 GAGGGAAGTCACCTAAACTAGCA 59.486 47.826 0.00 0.00 38.79 3.49
3518 5181 7.773690 ACAAGAACTTGGTAGTATTGAACAACT 59.226 33.333 17.05 0.00 44.45 3.16
3526 5189 4.765339 GGCCAACAAGAACTTGGTAGTATT 59.235 41.667 17.05 0.92 44.45 1.89
3534 5197 0.744281 AACGGGCCAACAAGAACTTG 59.256 50.000 4.39 12.22 45.58 3.16
3766 5487 7.551262 ACTGTAATGAGTGAACAAACACACTAA 59.449 33.333 0.00 0.00 45.54 2.24
3824 5546 8.258850 ACTCCCTCCGTTCATAAATATAAGAA 57.741 34.615 0.00 0.00 0.00 2.52
3854 5576 6.881602 ACACACAAGAAAGAAAGAAAGAGAGT 59.118 34.615 0.00 0.00 0.00 3.24
3867 5589 6.436843 ACTTTAACCTCACACACAAGAAAG 57.563 37.500 0.00 0.00 0.00 2.62
3868 5590 6.402766 CGAACTTTAACCTCACACACAAGAAA 60.403 38.462 0.00 0.00 0.00 2.52
3869 5591 5.064198 CGAACTTTAACCTCACACACAAGAA 59.936 40.000 0.00 0.00 0.00 2.52
3870 5592 4.569162 CGAACTTTAACCTCACACACAAGA 59.431 41.667 0.00 0.00 0.00 3.02
3871 5593 4.569162 TCGAACTTTAACCTCACACACAAG 59.431 41.667 0.00 0.00 0.00 3.16
3949 5671 2.880268 TGACAAATCTGCACTGAACCTG 59.120 45.455 0.00 0.00 0.00 4.00
3950 5672 2.880890 GTGACAAATCTGCACTGAACCT 59.119 45.455 0.00 0.00 31.13 3.50
3951 5673 2.880890 AGTGACAAATCTGCACTGAACC 59.119 45.455 0.00 0.00 38.03 3.62
3952 5674 4.531332 GAAGTGACAAATCTGCACTGAAC 58.469 43.478 0.00 0.00 38.83 3.18
3953 5675 3.565482 GGAAGTGACAAATCTGCACTGAA 59.435 43.478 0.00 0.00 38.83 3.02
3954 5676 3.141398 GGAAGTGACAAATCTGCACTGA 58.859 45.455 0.00 0.00 38.83 3.41
3955 5677 2.880268 TGGAAGTGACAAATCTGCACTG 59.120 45.455 0.00 0.00 38.83 3.66
3956 5678 3.213206 TGGAAGTGACAAATCTGCACT 57.787 42.857 0.00 0.00 39.83 4.40
3957 5679 3.254166 ACATGGAAGTGACAAATCTGCAC 59.746 43.478 0.00 0.00 32.82 4.57
3969 5691 6.092670 ACGAAGATCAACAATACATGGAAGTG 59.907 38.462 0.00 0.00 0.00 3.16
3985 5707 4.654091 TGACTGCATCATACGAAGATCA 57.346 40.909 0.00 0.00 29.99 2.92
4061 5850 3.438781 TGATCGGTACAAATTTGGCTGAC 59.561 43.478 21.74 13.05 0.00 3.51


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

AutoCloner maintained by Alex Coulton.