Multiple sequence alignment - TraesCS1A01G104400

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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 TraesCS1A01G104400 chr1A 100.000 2351 0 0 1 2351 100265490 100267840 0.000000e+00 4342.0
1 TraesCS1A01G104400 chr1A 84.993 693 72 16 892 1559 497831647 497830962 0.000000e+00 675.0
2 TraesCS1A01G104400 chr1A 94.403 268 13 2 532 797 541388486 541388753 6.050000e-111 411.0
3 TraesCS1A01G104400 chr1A 96.098 205 8 0 176 380 541388065 541388269 3.740000e-88 335.0
4 TraesCS1A01G104400 chr1A 94.531 128 5 1 384 511 541388386 541388511 1.840000e-46 196.0
5 TraesCS1A01G104400 chr1A 82.703 185 24 4 519 700 562888562 562888741 8.700000e-35 158.0
6 TraesCS1A01G104400 chr7A 92.688 1053 52 9 532 1559 671137141 671136089 0.000000e+00 1495.0
7 TraesCS1A01G104400 chr7A 92.414 290 16 3 174 463 671137655 671137372 2.170000e-110 409.0
8 TraesCS1A01G104400 chr7A 76.836 531 48 29 176 700 83221276 83221737 1.820000e-56 230.0
9 TraesCS1A01G104400 chr7A 96.491 57 2 0 455 511 671137172 671137116 6.920000e-16 95.3
10 TraesCS1A01G104400 chr2A 89.384 1168 54 27 421 1561 28469494 28468370 0.000000e+00 1406.0
11 TraesCS1A01G104400 chr2A 96.800 125 0 3 257 377 28469624 28469500 3.060000e-49 206.0
12 TraesCS1A01G104400 chr6B 90.347 1067 57 19 532 1559 48651150 48650091 0.000000e+00 1358.0
13 TraesCS1A01G104400 chr6B 93.155 336 17 4 176 511 48651454 48651125 2.720000e-134 488.0
14 TraesCS1A01G104400 chr5A 91.199 909 37 15 366 1257 25906639 25907521 0.000000e+00 1195.0
15 TraesCS1A01G104400 chr5A 85.653 697 64 15 892 1560 12578982 12579670 0.000000e+00 701.0
16 TraesCS1A01G104400 chr5A 85.591 694 67 15 892 1559 39310993 39311679 0.000000e+00 697.0
17 TraesCS1A01G104400 chr5A 85.260 692 68 15 892 1556 688535990 688536674 0.000000e+00 682.0
18 TraesCS1A01G104400 chr5A 93.720 207 8 3 176 382 25906346 25906547 2.940000e-79 305.0
19 TraesCS1A01G104400 chr5A 76.046 526 53 30 177 698 543958426 543958882 3.060000e-49 206.0
20 TraesCS1A01G104400 chr1D 90.496 726 39 10 1643 2351 81739189 81739901 0.000000e+00 931.0
21 TraesCS1A01G104400 chr1D 87.926 704 42 13 892 1559 476375697 476375001 0.000000e+00 789.0
22 TraesCS1A01G104400 chr1D 84.870 694 72 17 892 1559 416350969 416351655 0.000000e+00 669.0
23 TraesCS1A01G104400 chr1D 85.261 441 46 14 1132 1559 258498219 258497785 9.980000e-119 436.0
24 TraesCS1A01G104400 chr1D 84.568 162 19 4 176 336 258498978 258498822 3.130000e-34 156.0
25 TraesCS1A01G104400 chr1B 89.021 756 38 17 1611 2351 136625370 136626095 0.000000e+00 894.0
26 TraesCS1A01G104400 chr4A 84.857 700 71 18 892 1564 645865630 645866321 0.000000e+00 673.0
27 TraesCS1A01G104400 chr2D 84.848 693 72 14 892 1559 291873544 291872860 0.000000e+00 667.0
28 TraesCS1A01G104400 chr2D 81.155 329 46 14 577 899 299075066 299075384 1.390000e-62 250.0
29 TraesCS1A01G104400 chr3D 84.910 444 46 17 1129 1559 602218366 602218801 1.670000e-116 429.0
30 TraesCS1A01G104400 chr2B 84.529 446 50 15 1123 1560 249668320 249668754 7.770000e-115 424.0
31 TraesCS1A01G104400 chr2B 84.127 126 15 5 175 297 778838665 778838542 1.480000e-22 117.0
32 TraesCS1A01G104400 chr4B 88.652 282 21 7 631 901 272035335 272035054 1.350000e-87 333.0
33 TraesCS1A01G104400 chr4B 85.563 284 29 7 628 901 505279890 505280171 1.060000e-73 287.0
34 TraesCS1A01G104400 chr4B 80.270 370 44 21 168 534 272035723 272035380 3.880000e-63 252.0
35 TraesCS1A01G104400 chr4B 91.304 161 13 1 176 336 505279508 505279667 3.930000e-53 219.0
36 TraesCS1A01G104400 chr5B 82.647 340 38 8 576 901 624957129 624957461 4.950000e-72 281.0
37 TraesCS1A01G104400 chr5B 81.899 337 46 11 576 901 628530210 628530542 1.070000e-68 270.0
38 TraesCS1A01G104400 chr6D 81.662 349 36 13 563 901 407034504 407034174 4.980000e-67 265.0
39 TraesCS1A01G104400 chr3B 78.019 323 41 18 176 493 760384605 760384308 2.400000e-40 176.0
40 TraesCS1A01G104400 chr4D 87.719 114 12 2 176 288 479125329 479125217 5.270000e-27 132.0


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 TraesCS1A01G104400 chr1A 100265490 100267840 2350 False 4342.000000 4342 100.000000 1 2351 1 chr1A.!!$F1 2350
1 TraesCS1A01G104400 chr1A 497830962 497831647 685 True 675.000000 675 84.993000 892 1559 1 chr1A.!!$R1 667
2 TraesCS1A01G104400 chr1A 541388065 541388753 688 False 314.000000 411 95.010667 176 797 3 chr1A.!!$F3 621
3 TraesCS1A01G104400 chr7A 671136089 671137655 1566 True 666.433333 1495 93.864333 174 1559 3 chr7A.!!$R1 1385
4 TraesCS1A01G104400 chr2A 28468370 28469624 1254 True 806.000000 1406 93.092000 257 1561 2 chr2A.!!$R1 1304
5 TraesCS1A01G104400 chr6B 48650091 48651454 1363 True 923.000000 1358 91.751000 176 1559 2 chr6B.!!$R1 1383
6 TraesCS1A01G104400 chr5A 25906346 25907521 1175 False 750.000000 1195 92.459500 176 1257 2 chr5A.!!$F5 1081
7 TraesCS1A01G104400 chr5A 12578982 12579670 688 False 701.000000 701 85.653000 892 1560 1 chr5A.!!$F1 668
8 TraesCS1A01G104400 chr5A 39310993 39311679 686 False 697.000000 697 85.591000 892 1559 1 chr5A.!!$F2 667
9 TraesCS1A01G104400 chr5A 688535990 688536674 684 False 682.000000 682 85.260000 892 1556 1 chr5A.!!$F4 664
10 TraesCS1A01G104400 chr1D 81739189 81739901 712 False 931.000000 931 90.496000 1643 2351 1 chr1D.!!$F1 708
11 TraesCS1A01G104400 chr1D 476375001 476375697 696 True 789.000000 789 87.926000 892 1559 1 chr1D.!!$R1 667
12 TraesCS1A01G104400 chr1D 416350969 416351655 686 False 669.000000 669 84.870000 892 1559 1 chr1D.!!$F2 667
13 TraesCS1A01G104400 chr1D 258497785 258498978 1193 True 296.000000 436 84.914500 176 1559 2 chr1D.!!$R2 1383
14 TraesCS1A01G104400 chr1B 136625370 136626095 725 False 894.000000 894 89.021000 1611 2351 1 chr1B.!!$F1 740
15 TraesCS1A01G104400 chr4A 645865630 645866321 691 False 673.000000 673 84.857000 892 1564 1 chr4A.!!$F1 672
16 TraesCS1A01G104400 chr2D 291872860 291873544 684 True 667.000000 667 84.848000 892 1559 1 chr2D.!!$R1 667
17 TraesCS1A01G104400 chr4B 272035054 272035723 669 True 292.500000 333 84.461000 168 901 2 chr4B.!!$R1 733
18 TraesCS1A01G104400 chr4B 505279508 505280171 663 False 253.000000 287 88.433500 176 901 2 chr4B.!!$F1 725

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
94 95 0.027586 CCGAATTGTCCGGCGATTTC 59.972 55.0 9.3 2.92 40.54 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1598 2221 0.040958 CTTTGCGAGTGAACTGTGGC 60.041 55.0 0.0 0.0 0.0 5.01 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 4.425577 CTTTACAACATCCTGCCTTGTC 57.574 45.455 0.00 0.00 30.76 3.18
22 23 3.788227 TTACAACATCCTGCCTTGTCT 57.212 42.857 0.00 0.00 30.76 3.41
23 24 2.191128 ACAACATCCTGCCTTGTCTC 57.809 50.000 0.00 0.00 0.00 3.36
24 25 1.081892 CAACATCCTGCCTTGTCTCG 58.918 55.000 0.00 0.00 0.00 4.04
25 26 0.674895 AACATCCTGCCTTGTCTCGC 60.675 55.000 0.00 0.00 0.00 5.03
26 27 1.220206 CATCCTGCCTTGTCTCGCT 59.780 57.895 0.00 0.00 0.00 4.93
27 28 0.461548 CATCCTGCCTTGTCTCGCTA 59.538 55.000 0.00 0.00 0.00 4.26
28 29 1.134699 CATCCTGCCTTGTCTCGCTAA 60.135 52.381 0.00 0.00 0.00 3.09
29 30 0.532573 TCCTGCCTTGTCTCGCTAAG 59.467 55.000 0.00 0.00 0.00 2.18
30 31 0.460987 CCTGCCTTGTCTCGCTAAGG 60.461 60.000 0.00 0.00 44.97 2.69
31 32 0.532573 CTGCCTTGTCTCGCTAAGGA 59.467 55.000 7.17 0.00 44.98 3.36
32 33 0.973632 TGCCTTGTCTCGCTAAGGAA 59.026 50.000 7.17 0.00 44.98 3.36
33 34 1.346395 TGCCTTGTCTCGCTAAGGAAA 59.654 47.619 7.17 0.00 44.98 3.13
34 35 2.224426 TGCCTTGTCTCGCTAAGGAAAA 60.224 45.455 7.17 0.00 44.98 2.29
35 36 2.159824 GCCTTGTCTCGCTAAGGAAAAC 59.840 50.000 7.17 0.00 44.98 2.43
36 37 3.399330 CCTTGTCTCGCTAAGGAAAACA 58.601 45.455 0.00 0.00 44.98 2.83
37 38 3.813166 CCTTGTCTCGCTAAGGAAAACAA 59.187 43.478 0.00 0.00 44.98 2.83
38 39 4.274950 CCTTGTCTCGCTAAGGAAAACAAA 59.725 41.667 0.00 0.00 44.98 2.83
39 40 5.418310 TTGTCTCGCTAAGGAAAACAAAG 57.582 39.130 0.00 0.00 0.00 2.77
40 41 3.250040 TGTCTCGCTAAGGAAAACAAAGC 59.750 43.478 0.00 0.00 0.00 3.51
41 42 3.498777 GTCTCGCTAAGGAAAACAAAGCT 59.501 43.478 0.00 0.00 0.00 3.74
42 43 4.023963 GTCTCGCTAAGGAAAACAAAGCTT 60.024 41.667 0.00 0.00 0.00 3.74
43 44 4.024048 TCTCGCTAAGGAAAACAAAGCTTG 60.024 41.667 0.00 0.00 0.00 4.01
44 45 3.004315 TCGCTAAGGAAAACAAAGCTTGG 59.996 43.478 0.00 0.00 34.12 3.61
45 46 3.653344 GCTAAGGAAAACAAAGCTTGGG 58.347 45.455 5.66 1.04 34.12 4.12
46 47 3.554960 GCTAAGGAAAACAAAGCTTGGGG 60.555 47.826 5.66 0.00 34.12 4.96
47 48 2.470057 AGGAAAACAAAGCTTGGGGA 57.530 45.000 5.66 0.00 34.12 4.81
48 49 2.758130 AGGAAAACAAAGCTTGGGGAA 58.242 42.857 5.66 0.00 34.12 3.97
49 50 2.700371 AGGAAAACAAAGCTTGGGGAAG 59.300 45.455 5.66 0.00 34.12 3.46
50 51 2.434336 GGAAAACAAAGCTTGGGGAAGT 59.566 45.455 5.66 0.00 34.12 3.01
51 52 3.457234 GAAAACAAAGCTTGGGGAAGTG 58.543 45.455 5.66 0.00 34.12 3.16
52 53 1.413118 AACAAAGCTTGGGGAAGTGG 58.587 50.000 5.66 0.00 34.12 4.00
53 54 1.115326 ACAAAGCTTGGGGAAGTGGC 61.115 55.000 5.66 0.00 34.12 5.01
54 55 0.829182 CAAAGCTTGGGGAAGTGGCT 60.829 55.000 0.00 0.00 34.52 4.75
55 56 0.105504 AAAGCTTGGGGAAGTGGCTT 60.106 50.000 0.00 0.00 43.75 4.35
56 57 0.105504 AAGCTTGGGGAAGTGGCTTT 60.106 50.000 0.00 0.00 39.76 3.51
57 58 0.105504 AGCTTGGGGAAGTGGCTTTT 60.106 50.000 0.00 0.00 0.00 2.27
58 59 0.033920 GCTTGGGGAAGTGGCTTTTG 59.966 55.000 0.00 0.00 0.00 2.44
59 60 1.703411 CTTGGGGAAGTGGCTTTTGA 58.297 50.000 0.00 0.00 0.00 2.69
60 61 1.615392 CTTGGGGAAGTGGCTTTTGAG 59.385 52.381 0.00 0.00 0.00 3.02
61 62 0.850100 TGGGGAAGTGGCTTTTGAGA 59.150 50.000 0.00 0.00 0.00 3.27
62 63 1.202927 TGGGGAAGTGGCTTTTGAGAG 60.203 52.381 0.00 0.00 0.00 3.20
63 64 1.539157 GGGAAGTGGCTTTTGAGAGG 58.461 55.000 0.00 0.00 0.00 3.69
64 65 1.539157 GGAAGTGGCTTTTGAGAGGG 58.461 55.000 0.00 0.00 0.00 4.30
65 66 0.884514 GAAGTGGCTTTTGAGAGGGC 59.115 55.000 0.00 0.00 0.00 5.19
66 67 0.540597 AAGTGGCTTTTGAGAGGGCC 60.541 55.000 0.00 0.00 44.31 5.80
68 69 3.686760 GGCTTTTGAGAGGGCCAC 58.313 61.111 6.18 0.00 43.59 5.01
69 70 1.228552 GGCTTTTGAGAGGGCCACA 60.229 57.895 6.18 0.00 43.59 4.17
70 71 0.827507 GGCTTTTGAGAGGGCCACAA 60.828 55.000 6.18 6.51 43.59 3.33
71 72 0.315251 GCTTTTGAGAGGGCCACAAC 59.685 55.000 6.18 0.00 0.00 3.32
72 73 0.961753 CTTTTGAGAGGGCCACAACC 59.038 55.000 6.18 0.00 0.00 3.77
73 74 0.555769 TTTTGAGAGGGCCACAACCT 59.444 50.000 6.18 0.00 42.18 3.50
78 79 4.974438 AGGGCCACAACCTCCCGA 62.974 66.667 6.18 0.00 44.70 5.14
79 80 3.961414 GGGCCACAACCTCCCGAA 61.961 66.667 4.39 0.00 0.00 4.30
80 81 2.355115 GGCCACAACCTCCCGAAT 59.645 61.111 0.00 0.00 0.00 3.34
81 82 1.304134 GGCCACAACCTCCCGAATT 60.304 57.895 0.00 0.00 0.00 2.17
82 83 1.595093 GGCCACAACCTCCCGAATTG 61.595 60.000 0.00 0.00 0.00 2.32
83 84 0.893727 GCCACAACCTCCCGAATTGT 60.894 55.000 0.00 0.00 37.02 2.71
84 85 1.165270 CCACAACCTCCCGAATTGTC 58.835 55.000 0.00 0.00 34.36 3.18
85 86 1.165270 CACAACCTCCCGAATTGTCC 58.835 55.000 0.00 0.00 34.36 4.02
86 87 0.321298 ACAACCTCCCGAATTGTCCG 60.321 55.000 0.00 0.00 30.82 4.79
87 88 1.024579 CAACCTCCCGAATTGTCCGG 61.025 60.000 0.00 0.00 46.10 5.14
88 89 2.513897 CCTCCCGAATTGTCCGGC 60.514 66.667 0.00 0.00 45.24 6.13
89 90 2.890474 CTCCCGAATTGTCCGGCG 60.890 66.667 0.00 0.00 45.24 6.46
90 91 3.365291 CTCCCGAATTGTCCGGCGA 62.365 63.158 9.30 0.00 45.24 5.54
91 92 2.203015 CCCGAATTGTCCGGCGAT 60.203 61.111 9.30 0.00 45.24 4.58
92 93 1.817941 CCCGAATTGTCCGGCGATT 60.818 57.895 9.30 10.12 45.24 3.34
93 94 1.373590 CCCGAATTGTCCGGCGATTT 61.374 55.000 9.30 0.00 45.24 2.17
94 95 0.027586 CCGAATTGTCCGGCGATTTC 59.972 55.000 9.30 2.92 40.54 2.17
95 96 0.027586 CGAATTGTCCGGCGATTTCC 59.972 55.000 9.30 0.00 31.53 3.13
96 97 0.380733 GAATTGTCCGGCGATTTCCC 59.619 55.000 9.30 0.00 31.53 3.97
97 98 1.035385 AATTGTCCGGCGATTTCCCC 61.035 55.000 9.30 0.00 0.00 4.81
98 99 2.904178 ATTGTCCGGCGATTTCCCCC 62.904 60.000 9.30 0.00 0.00 5.40
99 100 4.104183 GTCCGGCGATTTCCCCCA 62.104 66.667 9.30 0.00 0.00 4.96
100 101 4.104183 TCCGGCGATTTCCCCCAC 62.104 66.667 9.30 0.00 0.00 4.61
103 104 4.833989 GGCGATTTCCCCCACCCC 62.834 72.222 0.00 0.00 0.00 4.95
105 106 4.499633 CGATTTCCCCCACCCCGG 62.500 72.222 0.00 0.00 0.00 5.73
106 107 4.833989 GATTTCCCCCACCCCGGC 62.834 72.222 0.00 0.00 0.00 6.13
114 115 4.047125 CCACCCCGGCAGTTCCAT 62.047 66.667 0.00 0.00 34.01 3.41
115 116 2.751436 CACCCCGGCAGTTCCATG 60.751 66.667 0.00 0.00 34.01 3.66
116 117 4.740822 ACCCCGGCAGTTCCATGC 62.741 66.667 0.00 0.00 45.74 4.06
117 118 4.431131 CCCCGGCAGTTCCATGCT 62.431 66.667 0.00 0.00 45.75 3.79
118 119 2.589540 CCCGGCAGTTCCATGCTA 59.410 61.111 0.00 0.00 45.75 3.49
119 120 1.524621 CCCGGCAGTTCCATGCTAG 60.525 63.158 0.00 0.00 45.75 3.42
120 121 2.182842 CCGGCAGTTCCATGCTAGC 61.183 63.158 8.10 8.10 45.75 3.42
121 122 1.450134 CGGCAGTTCCATGCTAGCA 60.450 57.895 21.85 21.85 45.75 3.49
122 123 1.026182 CGGCAGTTCCATGCTAGCAA 61.026 55.000 23.54 1.65 45.75 3.91
123 124 1.176527 GGCAGTTCCATGCTAGCAAA 58.823 50.000 23.54 9.05 45.75 3.68
124 125 1.135286 GGCAGTTCCATGCTAGCAAAC 60.135 52.381 23.54 20.73 45.75 2.93
125 126 1.815003 GCAGTTCCATGCTAGCAAACT 59.185 47.619 23.54 22.63 43.07 2.66
126 127 2.159462 GCAGTTCCATGCTAGCAAACTC 60.159 50.000 24.00 16.87 43.07 3.01
127 128 3.076621 CAGTTCCATGCTAGCAAACTCA 58.923 45.455 24.00 6.60 0.00 3.41
128 129 3.693085 CAGTTCCATGCTAGCAAACTCAT 59.307 43.478 24.00 5.46 0.00 2.90
129 130 4.157289 CAGTTCCATGCTAGCAAACTCATT 59.843 41.667 24.00 4.76 0.00 2.57
130 131 4.157289 AGTTCCATGCTAGCAAACTCATTG 59.843 41.667 23.54 13.25 42.21 2.82
131 132 3.954200 TCCATGCTAGCAAACTCATTGA 58.046 40.909 23.54 2.25 41.85 2.57
132 133 3.943381 TCCATGCTAGCAAACTCATTGAG 59.057 43.478 23.54 12.17 41.85 3.02
133 134 3.943381 CCATGCTAGCAAACTCATTGAGA 59.057 43.478 23.54 0.00 41.85 3.27
134 135 4.397103 CCATGCTAGCAAACTCATTGAGAA 59.603 41.667 23.54 0.00 41.85 2.87
135 136 5.448768 CCATGCTAGCAAACTCATTGAGAAG 60.449 44.000 23.54 9.89 41.85 2.85
136 137 4.898320 TGCTAGCAAACTCATTGAGAAGA 58.102 39.130 16.84 0.00 41.85 2.87
137 138 5.308014 TGCTAGCAAACTCATTGAGAAGAA 58.692 37.500 16.84 0.24 41.85 2.52
138 139 5.180117 TGCTAGCAAACTCATTGAGAAGAAC 59.820 40.000 16.84 5.68 41.85 3.01
139 140 5.391416 GCTAGCAAACTCATTGAGAAGAACC 60.391 44.000 20.33 3.75 41.85 3.62
140 141 4.464008 AGCAAACTCATTGAGAAGAACCA 58.536 39.130 20.33 0.00 41.85 3.67
141 142 5.075493 AGCAAACTCATTGAGAAGAACCAT 58.925 37.500 20.33 0.00 41.85 3.55
142 143 5.537674 AGCAAACTCATTGAGAAGAACCATT 59.462 36.000 20.33 0.00 41.85 3.16
143 144 5.632347 GCAAACTCATTGAGAAGAACCATTG 59.368 40.000 20.33 11.30 41.85 2.82
144 145 5.382618 AACTCATTGAGAAGAACCATTGC 57.617 39.130 20.33 0.00 33.32 3.56
145 146 4.401022 ACTCATTGAGAAGAACCATTGCA 58.599 39.130 20.33 0.00 33.32 4.08
146 147 5.014858 ACTCATTGAGAAGAACCATTGCAT 58.985 37.500 20.33 0.00 33.32 3.96
147 148 5.479375 ACTCATTGAGAAGAACCATTGCATT 59.521 36.000 20.33 0.00 33.32 3.56
148 149 5.716094 TCATTGAGAAGAACCATTGCATTG 58.284 37.500 1.49 1.49 0.00 2.82
149 150 5.244402 TCATTGAGAAGAACCATTGCATTGT 59.756 36.000 7.75 0.00 0.00 2.71
150 151 4.508461 TGAGAAGAACCATTGCATTGTG 57.492 40.909 7.75 2.48 0.00 3.33
151 152 3.890756 TGAGAAGAACCATTGCATTGTGT 59.109 39.130 7.75 3.04 0.00 3.72
152 153 4.341806 TGAGAAGAACCATTGCATTGTGTT 59.658 37.500 12.33 12.33 0.00 3.32
153 154 4.874970 AGAAGAACCATTGCATTGTGTTC 58.125 39.130 22.13 22.13 36.45 3.18
154 155 3.287312 AGAACCATTGCATTGTGTTCG 57.713 42.857 22.70 8.05 40.08 3.95
155 156 2.030007 AGAACCATTGCATTGTGTTCGG 60.030 45.455 22.70 7.61 40.08 4.30
156 157 1.327303 ACCATTGCATTGTGTTCGGT 58.673 45.000 7.75 0.00 0.00 4.69
157 158 1.000385 ACCATTGCATTGTGTTCGGTG 60.000 47.619 7.75 0.00 0.00 4.94
158 159 1.269174 CCATTGCATTGTGTTCGGTGA 59.731 47.619 7.75 0.00 0.00 4.02
159 160 2.094597 CCATTGCATTGTGTTCGGTGAT 60.095 45.455 7.75 0.00 0.00 3.06
160 161 2.702898 TTGCATTGTGTTCGGTGATG 57.297 45.000 0.00 0.00 0.00 3.07
161 162 0.240678 TGCATTGTGTTCGGTGATGC 59.759 50.000 0.00 0.00 42.48 3.91
162 163 0.794229 GCATTGTGTTCGGTGATGCG 60.794 55.000 0.00 0.00 34.50 4.73
163 164 0.179192 CATTGTGTTCGGTGATGCGG 60.179 55.000 0.00 0.00 0.00 5.69
164 165 1.305219 ATTGTGTTCGGTGATGCGGG 61.305 55.000 0.00 0.00 0.00 6.13
165 166 2.047655 GTGTTCGGTGATGCGGGA 60.048 61.111 0.00 0.00 0.00 5.14
166 167 2.047655 TGTTCGGTGATGCGGGAC 60.048 61.111 0.00 0.00 0.00 4.46
167 168 2.818274 GTTCGGTGATGCGGGACC 60.818 66.667 0.00 0.00 0.00 4.46
168 169 3.000819 TTCGGTGATGCGGGACCT 61.001 61.111 0.00 0.00 0.00 3.85
169 170 2.589157 TTCGGTGATGCGGGACCTT 61.589 57.895 0.00 0.00 0.00 3.50
170 171 2.796483 TTCGGTGATGCGGGACCTTG 62.796 60.000 0.00 0.00 0.00 3.61
171 172 2.351276 GGTGATGCGGGACCTTGT 59.649 61.111 0.00 0.00 0.00 3.16
172 173 2.040544 GGTGATGCGGGACCTTGTG 61.041 63.158 0.00 0.00 0.00 3.33
231 233 1.555967 GCACAGGGCCCAAAATTCTA 58.444 50.000 27.56 0.00 36.11 2.10
572 1090 1.186200 CCCTTGACATCGACTCCTCA 58.814 55.000 0.00 0.00 0.00 3.86
808 1364 6.432581 ACTTTGGTTCCTATTCCTAATTCCC 58.567 40.000 0.00 0.00 0.00 3.97
1094 1652 7.338196 TCATGCCAAAAGAAAATATCGAACCTA 59.662 33.333 0.00 0.00 0.00 3.08
1095 1653 6.848451 TGCCAAAAGAAAATATCGAACCTAC 58.152 36.000 0.00 0.00 0.00 3.18
1224 1798 4.872691 GCTATTGAAGTCCTATATGCGCAT 59.127 41.667 28.23 28.23 0.00 4.73
1247 1821 7.515841 GCATTACTATGACACATCAAAGACTCG 60.516 40.741 0.00 0.00 38.69 4.18
1261 1835 3.085443 AGACTCGATGATTTGGCTACG 57.915 47.619 0.00 0.00 0.00 3.51
1331 1910 8.408601 CGAGGGTATGATTGAAGATTTCATTTT 58.591 33.333 0.00 0.00 39.84 1.82
1391 1971 7.504926 AACAAACTGGAGTTGGATAGGTATA 57.495 36.000 0.71 0.00 38.44 1.47
1418 2000 9.816354 ACCTTTTTATATGTCCAATTGTTATGC 57.184 29.630 4.43 0.00 0.00 3.14
1537 2158 0.039035 TTTAGTTTCGCATGGGGCCT 59.961 50.000 10.21 6.04 40.31 5.19
1577 2200 2.238353 CTTGTGAGCAACCAGACGG 58.762 57.895 0.00 0.00 38.77 4.79
1578 2201 1.845809 CTTGTGAGCAACCAGACGGC 61.846 60.000 0.00 0.00 34.57 5.68
1579 2202 2.280797 GTGAGCAACCAGACGGCA 60.281 61.111 0.00 0.00 34.57 5.69
1580 2203 1.672356 GTGAGCAACCAGACGGCAT 60.672 57.895 0.00 0.00 34.57 4.40
1581 2204 1.375908 TGAGCAACCAGACGGCATC 60.376 57.895 0.00 0.00 34.57 3.91
1582 2205 2.045926 AGCAACCAGACGGCATCC 60.046 61.111 0.00 0.00 34.57 3.51
1583 2206 3.134127 GCAACCAGACGGCATCCC 61.134 66.667 0.00 0.00 34.57 3.85
1584 2207 2.350895 CAACCAGACGGCATCCCA 59.649 61.111 0.00 0.00 34.57 4.37
1585 2208 1.077501 CAACCAGACGGCATCCCAT 60.078 57.895 0.00 0.00 34.57 4.00
1586 2209 1.077501 AACCAGACGGCATCCCATG 60.078 57.895 0.00 0.00 34.57 3.66
1587 2210 2.203252 CCAGACGGCATCCCATGG 60.203 66.667 4.14 4.14 0.00 3.66
1588 2211 2.203252 CAGACGGCATCCCATGGG 60.203 66.667 26.30 26.30 0.00 4.00
1598 2221 2.211375 TCCCATGGGATCAGACACG 58.789 57.895 30.62 0.00 39.76 4.49
1599 2222 1.524621 CCCATGGGATCAGACACGC 60.525 63.158 28.27 0.00 37.50 5.34
1600 2223 1.524621 CCATGGGATCAGACACGCC 60.525 63.158 2.85 0.00 0.00 5.68
1601 2224 1.221566 CATGGGATCAGACACGCCA 59.778 57.895 0.00 0.00 0.00 5.69
1602 2225 1.091771 CATGGGATCAGACACGCCAC 61.092 60.000 0.00 0.00 0.00 5.01
1603 2226 1.552799 ATGGGATCAGACACGCCACA 61.553 55.000 0.00 0.00 0.00 4.17
1604 2227 1.448540 GGGATCAGACACGCCACAG 60.449 63.158 0.00 0.00 0.00 3.66
1605 2228 1.293498 GGATCAGACACGCCACAGT 59.707 57.895 0.00 0.00 0.00 3.55
1606 2229 0.320771 GGATCAGACACGCCACAGTT 60.321 55.000 0.00 0.00 0.00 3.16
1607 2230 1.071605 GATCAGACACGCCACAGTTC 58.928 55.000 0.00 0.00 0.00 3.01
1608 2231 0.392706 ATCAGACACGCCACAGTTCA 59.607 50.000 0.00 0.00 0.00 3.18
1609 2232 0.529773 TCAGACACGCCACAGTTCAC 60.530 55.000 0.00 0.00 0.00 3.18
1612 2235 1.548973 GACACGCCACAGTTCACTCG 61.549 60.000 0.00 0.00 0.00 4.18
1694 2319 4.867599 CCGCGGCTTCCCTCGTAC 62.868 72.222 14.67 0.00 37.63 3.67
1781 2407 4.154347 CCTCCACAGCCTCGCTCC 62.154 72.222 0.00 0.00 36.40 4.70
1803 2430 2.314647 ACATTCGCACCCGTGAACG 61.315 57.895 0.00 0.00 44.10 3.95
1817 2458 0.967887 TGAACGCTCTCCTCTCCCTG 60.968 60.000 0.00 0.00 0.00 4.45
1842 2483 2.858476 TTCCAGAAGCCAGGGCCA 60.858 61.111 6.18 0.00 43.17 5.36
2066 2719 1.075151 GATCCTCGTCCCCTCCCTT 60.075 63.158 0.00 0.00 0.00 3.95
2145 2798 2.049156 TCTGCAACTCCGTCTGCG 60.049 61.111 0.00 0.00 41.63 5.18
2180 2833 4.162690 GTCGCTCTCCCGCCCAAT 62.163 66.667 0.00 0.00 0.00 3.16
2200 2853 3.282157 CCCCGCGATCTGCATTGG 61.282 66.667 8.23 0.00 46.97 3.16
2240 2893 7.836685 TGGATTAGGGTTTTGATGTGCTTTATA 59.163 33.333 0.00 0.00 0.00 0.98
2245 2898 6.437162 AGGGTTTTGATGTGCTTTATATGTGT 59.563 34.615 0.00 0.00 0.00 3.72
2246 2899 6.531240 GGGTTTTGATGTGCTTTATATGTGTG 59.469 38.462 0.00 0.00 0.00 3.82
2247 2900 6.034898 GGTTTTGATGTGCTTTATATGTGTGC 59.965 38.462 0.00 0.00 0.00 4.57
2248 2901 6.513806 TTTGATGTGCTTTATATGTGTGCT 57.486 33.333 0.00 0.00 0.00 4.40
2249 2902 7.622893 TTTGATGTGCTTTATATGTGTGCTA 57.377 32.000 0.00 0.00 0.00 3.49
2250 2903 7.622893 TTGATGTGCTTTATATGTGTGCTAA 57.377 32.000 0.00 0.00 0.00 3.09
2251 2904 7.015226 TGATGTGCTTTATATGTGTGCTAAC 57.985 36.000 0.00 0.00 0.00 2.34
2252 2905 6.823182 TGATGTGCTTTATATGTGTGCTAACT 59.177 34.615 0.00 0.00 0.00 2.24
2253 2906 6.421377 TGTGCTTTATATGTGTGCTAACTG 57.579 37.500 0.00 0.00 0.00 3.16
2296 2949 2.215196 GTTCTGCACGGTTTTCCTGTA 58.785 47.619 0.00 0.00 37.95 2.74
2307 2960 5.221986 ACGGTTTTCCTGTACTAATTTCCCT 60.222 40.000 0.00 0.00 37.95 4.20
2309 2962 5.353400 GGTTTTCCTGTACTAATTTCCCTCG 59.647 44.000 0.00 0.00 36.94 4.63
2310 2963 5.750352 TTTCCTGTACTAATTTCCCTCGT 57.250 39.130 0.00 0.00 0.00 4.18
2318 2971 0.035439 AATTTCCCTCGTGCGGTGAT 60.035 50.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.353704 CGAGACAAGGCAGGATGTTGTA 60.354 50.000 0.00 0.00 35.73 2.41
4 5 1.609061 CGAGACAAGGCAGGATGTTGT 60.609 52.381 0.00 0.00 37.91 3.32
7 8 1.078848 GCGAGACAAGGCAGGATGT 60.079 57.895 0.00 0.00 39.31 3.06
8 9 0.461548 TAGCGAGACAAGGCAGGATG 59.538 55.000 0.00 0.00 40.87 3.51
9 10 1.137872 CTTAGCGAGACAAGGCAGGAT 59.862 52.381 0.00 0.00 0.00 3.24
10 11 0.532573 CTTAGCGAGACAAGGCAGGA 59.467 55.000 0.00 0.00 0.00 3.86
11 12 0.460987 CCTTAGCGAGACAAGGCAGG 60.461 60.000 0.00 0.00 35.24 4.85
12 13 0.532573 TCCTTAGCGAGACAAGGCAG 59.467 55.000 0.00 0.00 41.01 4.85
13 14 0.973632 TTCCTTAGCGAGACAAGGCA 59.026 50.000 0.00 0.00 41.01 4.75
14 15 2.094762 TTTCCTTAGCGAGACAAGGC 57.905 50.000 0.00 0.00 41.01 4.35
15 16 3.399330 TGTTTTCCTTAGCGAGACAAGG 58.601 45.455 0.00 0.00 42.34 3.61
16 17 5.418310 TTTGTTTTCCTTAGCGAGACAAG 57.582 39.130 0.00 0.00 0.00 3.16
17 18 4.261031 GCTTTGTTTTCCTTAGCGAGACAA 60.261 41.667 0.00 0.00 0.00 3.18
18 19 3.250040 GCTTTGTTTTCCTTAGCGAGACA 59.750 43.478 0.00 0.00 0.00 3.41
19 20 3.498777 AGCTTTGTTTTCCTTAGCGAGAC 59.501 43.478 0.00 0.00 36.96 3.36
20 21 3.740115 AGCTTTGTTTTCCTTAGCGAGA 58.260 40.909 0.00 0.00 36.96 4.04
21 22 4.222114 CAAGCTTTGTTTTCCTTAGCGAG 58.778 43.478 0.00 0.00 36.96 5.03
22 23 3.004315 CCAAGCTTTGTTTTCCTTAGCGA 59.996 43.478 0.00 0.00 36.96 4.93
23 24 3.308530 CCAAGCTTTGTTTTCCTTAGCG 58.691 45.455 0.00 0.00 36.96 4.26
24 25 3.554960 CCCCAAGCTTTGTTTTCCTTAGC 60.555 47.826 0.00 0.00 0.00 3.09
25 26 3.895041 TCCCCAAGCTTTGTTTTCCTTAG 59.105 43.478 0.00 0.00 0.00 2.18
26 27 3.917300 TCCCCAAGCTTTGTTTTCCTTA 58.083 40.909 0.00 0.00 0.00 2.69
27 28 2.758130 TCCCCAAGCTTTGTTTTCCTT 58.242 42.857 0.00 0.00 0.00 3.36
28 29 2.470057 TCCCCAAGCTTTGTTTTCCT 57.530 45.000 0.00 0.00 0.00 3.36
29 30 2.434336 ACTTCCCCAAGCTTTGTTTTCC 59.566 45.455 0.00 0.00 32.09 3.13
30 31 3.457234 CACTTCCCCAAGCTTTGTTTTC 58.543 45.455 0.00 0.00 32.09 2.29
31 32 2.170397 CCACTTCCCCAAGCTTTGTTTT 59.830 45.455 0.00 0.00 32.09 2.43
32 33 1.762370 CCACTTCCCCAAGCTTTGTTT 59.238 47.619 0.00 0.00 32.09 2.83
33 34 1.413118 CCACTTCCCCAAGCTTTGTT 58.587 50.000 0.00 0.00 32.09 2.83
34 35 1.115326 GCCACTTCCCCAAGCTTTGT 61.115 55.000 0.00 0.00 32.09 2.83
35 36 0.829182 AGCCACTTCCCCAAGCTTTG 60.829 55.000 0.00 0.00 32.09 2.77
36 37 0.105504 AAGCCACTTCCCCAAGCTTT 60.106 50.000 0.00 0.00 40.76 3.51
37 38 0.105504 AAAGCCACTTCCCCAAGCTT 60.106 50.000 0.00 0.00 45.28 3.74
38 39 0.105504 AAAAGCCACTTCCCCAAGCT 60.106 50.000 0.00 0.00 32.09 3.74
39 40 0.033920 CAAAAGCCACTTCCCCAAGC 59.966 55.000 0.00 0.00 32.09 4.01
40 41 1.615392 CTCAAAAGCCACTTCCCCAAG 59.385 52.381 0.00 0.00 35.50 3.61
41 42 1.216678 TCTCAAAAGCCACTTCCCCAA 59.783 47.619 0.00 0.00 0.00 4.12
42 43 0.850100 TCTCAAAAGCCACTTCCCCA 59.150 50.000 0.00 0.00 0.00 4.96
43 44 1.539157 CTCTCAAAAGCCACTTCCCC 58.461 55.000 0.00 0.00 0.00 4.81
44 45 1.539157 CCTCTCAAAAGCCACTTCCC 58.461 55.000 0.00 0.00 0.00 3.97
45 46 1.539157 CCCTCTCAAAAGCCACTTCC 58.461 55.000 0.00 0.00 0.00 3.46
46 47 0.884514 GCCCTCTCAAAAGCCACTTC 59.115 55.000 0.00 0.00 0.00 3.01
47 48 0.540597 GGCCCTCTCAAAAGCCACTT 60.541 55.000 0.00 0.00 45.07 3.16
48 49 1.075659 GGCCCTCTCAAAAGCCACT 59.924 57.895 0.00 0.00 45.07 4.00
49 50 3.686760 GGCCCTCTCAAAAGCCAC 58.313 61.111 0.00 0.00 45.07 5.01
51 52 0.827507 TTGTGGCCCTCTCAAAAGCC 60.828 55.000 0.00 0.00 45.96 4.35
52 53 0.315251 GTTGTGGCCCTCTCAAAAGC 59.685 55.000 0.00 0.00 31.67 3.51
53 54 0.961753 GGTTGTGGCCCTCTCAAAAG 59.038 55.000 0.00 0.00 31.67 2.27
54 55 0.555769 AGGTTGTGGCCCTCTCAAAA 59.444 50.000 0.00 0.00 31.67 2.44
55 56 0.110486 GAGGTTGTGGCCCTCTCAAA 59.890 55.000 0.00 0.00 44.29 2.69
56 57 1.761174 GAGGTTGTGGCCCTCTCAA 59.239 57.895 0.00 0.00 44.29 3.02
57 58 2.224159 GGAGGTTGTGGCCCTCTCA 61.224 63.158 0.00 0.00 46.43 3.27
58 59 2.671682 GGAGGTTGTGGCCCTCTC 59.328 66.667 0.00 0.00 46.43 3.20
59 60 2.936032 GGGAGGTTGTGGCCCTCT 60.936 66.667 0.00 0.00 46.43 3.69
60 61 4.410400 CGGGAGGTTGTGGCCCTC 62.410 72.222 0.00 0.00 46.49 4.30
61 62 4.974438 TCGGGAGGTTGTGGCCCT 62.974 66.667 0.00 0.00 39.79 5.19
62 63 2.781431 AATTCGGGAGGTTGTGGCCC 62.781 60.000 0.00 0.00 38.53 5.80
63 64 1.304134 AATTCGGGAGGTTGTGGCC 60.304 57.895 0.00 0.00 0.00 5.36
64 65 0.893727 ACAATTCGGGAGGTTGTGGC 60.894 55.000 0.00 0.00 37.57 5.01
65 66 1.165270 GACAATTCGGGAGGTTGTGG 58.835 55.000 6.34 0.00 38.52 4.17
66 67 1.165270 GGACAATTCGGGAGGTTGTG 58.835 55.000 6.34 0.00 38.52 3.33
67 68 0.321298 CGGACAATTCGGGAGGTTGT 60.321 55.000 0.00 0.00 40.15 3.32
68 69 1.024579 CCGGACAATTCGGGAGGTTG 61.025 60.000 0.00 0.00 43.52 3.77
69 70 1.298667 CCGGACAATTCGGGAGGTT 59.701 57.895 0.00 0.00 43.52 3.50
70 71 2.987125 CCGGACAATTCGGGAGGT 59.013 61.111 0.00 0.00 43.52 3.85
71 72 2.513897 GCCGGACAATTCGGGAGG 60.514 66.667 5.05 0.00 46.86 4.30
72 73 2.644555 ATCGCCGGACAATTCGGGAG 62.645 60.000 5.05 0.00 46.86 4.30
73 74 2.246761 AATCGCCGGACAATTCGGGA 62.247 55.000 5.05 2.88 46.86 5.14
74 75 1.373590 AAATCGCCGGACAATTCGGG 61.374 55.000 5.05 0.00 46.86 5.14
76 77 0.027586 GGAAATCGCCGGACAATTCG 59.972 55.000 5.05 0.00 0.00 3.34
77 78 0.380733 GGGAAATCGCCGGACAATTC 59.619 55.000 5.05 3.59 0.00 2.17
78 79 1.035385 GGGGAAATCGCCGGACAATT 61.035 55.000 5.05 0.00 39.23 2.32
79 80 1.453197 GGGGAAATCGCCGGACAAT 60.453 57.895 5.05 0.00 39.23 2.71
80 81 2.045731 GGGGAAATCGCCGGACAA 60.046 61.111 5.05 0.00 39.23 3.18
88 89 4.499633 CCGGGGTGGGGGAAATCG 62.500 72.222 0.00 0.00 0.00 3.34
89 90 4.833989 GCCGGGGTGGGGGAAATC 62.834 72.222 2.18 0.00 38.63 2.17
97 98 4.047125 ATGGAACTGCCGGGGTGG 62.047 66.667 2.18 0.00 40.66 4.61
98 99 2.751436 CATGGAACTGCCGGGGTG 60.751 66.667 2.18 0.00 40.66 4.61
99 100 4.740822 GCATGGAACTGCCGGGGT 62.741 66.667 2.18 0.00 40.66 4.95
100 101 2.947938 CTAGCATGGAACTGCCGGGG 62.948 65.000 2.18 0.00 43.33 5.73
101 102 1.524621 CTAGCATGGAACTGCCGGG 60.525 63.158 2.18 0.00 43.33 5.73
102 103 2.182842 GCTAGCATGGAACTGCCGG 61.183 63.158 10.63 0.00 43.33 6.13
103 104 1.026182 TTGCTAGCATGGAACTGCCG 61.026 55.000 20.13 0.00 43.33 5.69
104 105 1.135286 GTTTGCTAGCATGGAACTGCC 60.135 52.381 20.13 0.00 43.33 4.85
105 106 1.815003 AGTTTGCTAGCATGGAACTGC 59.185 47.619 25.32 5.77 42.62 4.40
106 107 3.076621 TGAGTTTGCTAGCATGGAACTG 58.923 45.455 29.10 0.00 31.24 3.16
107 108 3.423539 TGAGTTTGCTAGCATGGAACT 57.576 42.857 25.93 25.93 33.58 3.01
108 109 4.156556 TCAATGAGTTTGCTAGCATGGAAC 59.843 41.667 20.13 19.35 35.16 3.62
109 110 4.334552 TCAATGAGTTTGCTAGCATGGAA 58.665 39.130 20.13 7.29 35.16 3.53
110 111 3.943381 CTCAATGAGTTTGCTAGCATGGA 59.057 43.478 20.13 4.36 35.16 3.41
111 112 3.943381 TCTCAATGAGTTTGCTAGCATGG 59.057 43.478 20.13 0.00 35.16 3.66
112 113 5.353400 TCTTCTCAATGAGTTTGCTAGCATG 59.647 40.000 20.13 12.05 35.16 4.06
113 114 5.494724 TCTTCTCAATGAGTTTGCTAGCAT 58.505 37.500 20.13 3.01 35.16 3.79
114 115 4.898320 TCTTCTCAATGAGTTTGCTAGCA 58.102 39.130 14.93 14.93 35.16 3.49
115 116 5.391416 GGTTCTTCTCAATGAGTTTGCTAGC 60.391 44.000 8.10 8.10 35.16 3.42
116 117 5.702670 TGGTTCTTCTCAATGAGTTTGCTAG 59.297 40.000 10.36 0.69 35.16 3.42
117 118 5.620206 TGGTTCTTCTCAATGAGTTTGCTA 58.380 37.500 10.36 0.00 35.16 3.49
118 119 4.464008 TGGTTCTTCTCAATGAGTTTGCT 58.536 39.130 10.36 0.00 35.16 3.91
119 120 4.836125 TGGTTCTTCTCAATGAGTTTGC 57.164 40.909 10.36 0.00 35.16 3.68
120 121 5.632347 GCAATGGTTCTTCTCAATGAGTTTG 59.368 40.000 10.36 2.34 36.61 2.93
121 122 5.302568 TGCAATGGTTCTTCTCAATGAGTTT 59.697 36.000 10.36 0.00 0.00 2.66
122 123 4.828939 TGCAATGGTTCTTCTCAATGAGTT 59.171 37.500 10.36 0.00 0.00 3.01
123 124 4.401022 TGCAATGGTTCTTCTCAATGAGT 58.599 39.130 10.36 0.00 0.00 3.41
124 125 5.578005 ATGCAATGGTTCTTCTCAATGAG 57.422 39.130 3.38 3.38 0.00 2.90
125 126 5.244402 ACAATGCAATGGTTCTTCTCAATGA 59.756 36.000 6.73 0.00 0.00 2.57
126 127 5.347635 CACAATGCAATGGTTCTTCTCAATG 59.652 40.000 6.73 0.00 0.00 2.82
127 128 5.011329 ACACAATGCAATGGTTCTTCTCAAT 59.989 36.000 6.73 0.00 0.00 2.57
128 129 4.341806 ACACAATGCAATGGTTCTTCTCAA 59.658 37.500 6.73 0.00 0.00 3.02
129 130 3.890756 ACACAATGCAATGGTTCTTCTCA 59.109 39.130 6.73 0.00 0.00 3.27
130 131 4.510038 ACACAATGCAATGGTTCTTCTC 57.490 40.909 6.73 0.00 0.00 2.87
131 132 4.557296 CGAACACAATGCAATGGTTCTTCT 60.557 41.667 22.57 1.49 36.57 2.85
132 133 3.670055 CGAACACAATGCAATGGTTCTTC 59.330 43.478 22.57 11.15 36.57 2.87
133 134 3.552684 CCGAACACAATGCAATGGTTCTT 60.553 43.478 22.57 5.37 36.57 2.52
134 135 2.030007 CCGAACACAATGCAATGGTTCT 60.030 45.455 22.57 2.41 36.57 3.01
135 136 2.288152 ACCGAACACAATGCAATGGTTC 60.288 45.455 18.58 18.58 35.65 3.62
136 137 1.686052 ACCGAACACAATGCAATGGTT 59.314 42.857 6.73 7.45 0.00 3.67
137 138 1.000385 CACCGAACACAATGCAATGGT 60.000 47.619 6.73 0.00 0.00 3.55
138 139 1.269174 TCACCGAACACAATGCAATGG 59.731 47.619 6.73 0.00 0.00 3.16
139 140 2.702898 TCACCGAACACAATGCAATG 57.297 45.000 0.00 0.00 0.00 2.82
140 141 2.671914 GCATCACCGAACACAATGCAAT 60.672 45.455 0.00 0.00 41.75 3.56
141 142 1.335780 GCATCACCGAACACAATGCAA 60.336 47.619 0.00 0.00 41.75 4.08
142 143 0.240678 GCATCACCGAACACAATGCA 59.759 50.000 0.00 0.00 41.75 3.96
143 144 0.794229 CGCATCACCGAACACAATGC 60.794 55.000 0.00 0.00 39.41 3.56
144 145 0.179192 CCGCATCACCGAACACAATG 60.179 55.000 0.00 0.00 0.00 2.82
145 146 1.305219 CCCGCATCACCGAACACAAT 61.305 55.000 0.00 0.00 0.00 2.71
146 147 1.963855 CCCGCATCACCGAACACAA 60.964 57.895 0.00 0.00 0.00 3.33
147 148 2.358125 CCCGCATCACCGAACACA 60.358 61.111 0.00 0.00 0.00 3.72
148 149 2.047655 TCCCGCATCACCGAACAC 60.048 61.111 0.00 0.00 0.00 3.32
149 150 2.047655 GTCCCGCATCACCGAACA 60.048 61.111 0.00 0.00 0.00 3.18
150 151 2.798148 AAGGTCCCGCATCACCGAAC 62.798 60.000 0.00 0.00 37.79 3.95
151 152 2.589157 AAGGTCCCGCATCACCGAA 61.589 57.895 0.00 0.00 37.79 4.30
152 153 3.000819 AAGGTCCCGCATCACCGA 61.001 61.111 0.00 0.00 37.79 4.69
153 154 2.819595 CAAGGTCCCGCATCACCG 60.820 66.667 0.00 0.00 37.79 4.94
154 155 2.040544 CACAAGGTCCCGCATCACC 61.041 63.158 0.00 0.00 0.00 4.02
155 156 1.003839 TCACAAGGTCCCGCATCAC 60.004 57.895 0.00 0.00 0.00 3.06
156 157 1.296392 CTCACAAGGTCCCGCATCA 59.704 57.895 0.00 0.00 0.00 3.07
157 158 2.109126 GCTCACAAGGTCCCGCATC 61.109 63.158 0.00 0.00 0.00 3.91
158 159 2.045926 GCTCACAAGGTCCCGCAT 60.046 61.111 0.00 0.00 0.00 4.73
159 160 3.535629 CTGCTCACAAGGTCCCGCA 62.536 63.158 0.00 0.00 0.00 5.69
160 161 2.743928 CTGCTCACAAGGTCCCGC 60.744 66.667 0.00 0.00 0.00 6.13
161 162 2.046892 CCTGCTCACAAGGTCCCG 60.047 66.667 0.00 0.00 0.00 5.14
162 163 2.352805 CCCTGCTCACAAGGTCCC 59.647 66.667 0.00 0.00 0.00 4.46
163 164 2.360475 GCCCTGCTCACAAGGTCC 60.360 66.667 0.00 0.00 29.21 4.46
164 165 2.360475 GGCCCTGCTCACAAGGTC 60.360 66.667 0.00 0.00 29.21 3.85
165 166 4.335647 CGGCCCTGCTCACAAGGT 62.336 66.667 0.00 0.00 29.21 3.50
439 695 1.639628 ACGATCCCGATCCCTATAGGT 59.360 52.381 17.72 0.00 39.50 3.08
444 700 1.906824 GCCACGATCCCGATCCCTA 60.907 63.158 0.00 0.00 39.50 3.53
622 1141 4.872664 AGTCCGAATTCCGATTGATCTAC 58.127 43.478 0.00 0.00 41.76 2.59
668 1205 1.005394 GACAGGAAGGAAACGGCGA 60.005 57.895 16.62 0.00 0.00 5.54
1224 1798 7.153217 TCGAGTCTTTGATGTGTCATAGTAA 57.847 36.000 0.00 0.00 35.63 2.24
1276 1855 5.559148 ATCTTCTCCAACACTTCACTCTT 57.441 39.130 0.00 0.00 0.00 2.85
1368 1948 7.336396 GTTATACCTATCCAACTCCAGTTTGT 58.664 38.462 0.00 0.00 35.83 2.83
1531 2152 3.518068 CGCAAAATCCGAGGCCCC 61.518 66.667 0.00 0.00 0.00 5.80
1564 2187 2.109126 GGATGCCGTCTGGTTGCTC 61.109 63.158 0.00 0.00 37.67 4.26
1565 2188 2.045926 GGATGCCGTCTGGTTGCT 60.046 61.111 0.00 0.00 37.67 3.91
1566 2189 3.134127 GGGATGCCGTCTGGTTGC 61.134 66.667 0.00 0.00 37.67 4.17
1567 2190 1.077501 ATGGGATGCCGTCTGGTTG 60.078 57.895 0.00 0.00 37.67 3.77
1568 2191 1.077501 CATGGGATGCCGTCTGGTT 60.078 57.895 0.00 0.00 37.67 3.67
1569 2192 2.591753 CATGGGATGCCGTCTGGT 59.408 61.111 0.00 0.00 37.67 4.00
1570 2193 2.203252 CCATGGGATGCCGTCTGG 60.203 66.667 2.85 0.00 38.77 3.86
1571 2194 2.203252 CCCATGGGATGCCGTCTG 60.203 66.667 28.27 0.00 37.50 3.51
1572 2195 2.366837 TCCCATGGGATGCCGTCT 60.367 61.111 30.62 0.00 39.76 4.18
1581 2204 1.524621 GCGTGTCTGATCCCATGGG 60.525 63.158 26.30 26.30 0.00 4.00
1582 2205 1.524621 GGCGTGTCTGATCCCATGG 60.525 63.158 4.14 4.14 0.00 3.66
1583 2206 1.091771 GTGGCGTGTCTGATCCCATG 61.092 60.000 0.00 0.00 0.00 3.66
1584 2207 1.221840 GTGGCGTGTCTGATCCCAT 59.778 57.895 0.00 0.00 0.00 4.00
1585 2208 2.171209 CTGTGGCGTGTCTGATCCCA 62.171 60.000 0.00 0.00 0.00 4.37
1586 2209 1.448540 CTGTGGCGTGTCTGATCCC 60.449 63.158 0.00 0.00 0.00 3.85
1587 2210 0.320771 AACTGTGGCGTGTCTGATCC 60.321 55.000 0.00 0.00 0.00 3.36
1588 2211 1.071605 GAACTGTGGCGTGTCTGATC 58.928 55.000 0.00 0.00 0.00 2.92
1589 2212 0.392706 TGAACTGTGGCGTGTCTGAT 59.607 50.000 0.00 0.00 0.00 2.90
1590 2213 0.529773 GTGAACTGTGGCGTGTCTGA 60.530 55.000 0.00 0.00 0.00 3.27
1591 2214 0.530650 AGTGAACTGTGGCGTGTCTG 60.531 55.000 0.00 0.00 0.00 3.51
1592 2215 0.249489 GAGTGAACTGTGGCGTGTCT 60.249 55.000 0.00 0.00 0.00 3.41
1593 2216 1.548973 CGAGTGAACTGTGGCGTGTC 61.549 60.000 0.00 0.00 0.00 3.67
1594 2217 1.591594 CGAGTGAACTGTGGCGTGT 60.592 57.895 0.00 0.00 0.00 4.49
1595 2218 2.943345 GCGAGTGAACTGTGGCGTG 61.943 63.158 0.00 0.00 0.00 5.34
1596 2219 2.661866 GCGAGTGAACTGTGGCGT 60.662 61.111 0.00 0.00 0.00 5.68
1597 2220 1.771073 TTTGCGAGTGAACTGTGGCG 61.771 55.000 0.00 0.00 0.00 5.69
1598 2221 0.040958 CTTTGCGAGTGAACTGTGGC 60.041 55.000 0.00 0.00 0.00 5.01
1599 2222 0.040958 GCTTTGCGAGTGAACTGTGG 60.041 55.000 0.00 0.00 0.00 4.17
1600 2223 3.444657 GCTTTGCGAGTGAACTGTG 57.555 52.632 0.00 0.00 0.00 3.66
1619 2242 2.430921 AGCAGACGCGTGTGTAGC 60.431 61.111 33.02 21.46 45.49 3.58
1620 2243 1.801913 GGAGCAGACGCGTGTGTAG 60.802 63.158 33.02 12.69 45.49 2.74
1669 2293 2.970324 GAAGCCGCGGTTGTGTCA 60.970 61.111 28.70 0.00 0.00 3.58
1781 2407 2.047274 ACGGGTGCGAATGTGAGG 60.047 61.111 0.00 0.00 0.00 3.86
1803 2430 0.325203 AGGTTCAGGGAGAGGAGAGC 60.325 60.000 0.00 0.00 0.00 4.09
2066 2719 2.276116 GGTCCTGACGAGGCTGTCA 61.276 63.158 15.61 15.61 46.15 3.58
2185 2838 1.063006 CAACCAATGCAGATCGCGG 59.937 57.895 6.13 0.00 46.97 6.46
2186 2839 0.247814 GACAACCAATGCAGATCGCG 60.248 55.000 0.00 0.00 46.97 5.87
2296 2949 0.611714 ACCGCACGAGGGAAATTAGT 59.388 50.000 0.00 0.00 35.02 2.24
2333 2986 2.653702 AGCCATAGATCTCGCGGC 59.346 61.111 17.98 17.98 43.31 6.53


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

AutoCloner maintained by Alex Coulton.