Multiple sequence alignment - TraesCS3B01G537700

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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 TraesCS3B01G537700 chr3B 100.000 2844 0 0 1 2844 777653092 777655935 0.000000e+00 5252.0
1 TraesCS3B01G537700 chr3B 86.248 1607 145 43 1246 2822 777756417 777757977 0.000000e+00 1674.0
2 TraesCS3B01G537700 chr3B 82.998 647 76 18 534 1153 777755153 777755792 3.200000e-154 555.0
3 TraesCS3B01G537700 chr3B 88.750 320 25 4 536 845 777690889 777691207 5.750000e-102 381.0
4 TraesCS3B01G537700 chr3B 81.714 350 34 18 1269 1614 777630053 777630376 6.040000e-67 265.0
5 TraesCS3B01G537700 chr3B 80.678 295 46 8 22 309 188227541 188227831 4.770000e-53 219.0
6 TraesCS3B01G537700 chr3B 81.356 118 18 3 34 148 432864275 432864391 3.020000e-15 93.5
7 TraesCS3B01G537700 chr3A 87.607 1291 77 31 723 1959 716806874 716808135 0.000000e+00 1421.0
8 TraesCS3B01G537700 chr3A 80.659 941 107 34 533 1434 716794506 716795410 0.000000e+00 660.0
9 TraesCS3B01G537700 chr3A 80.664 874 98 27 534 1351 716792117 716792975 1.870000e-171 612.0
10 TraesCS3B01G537700 chr3A 82.547 424 39 14 1462 1876 716795400 716795797 9.760000e-90 340.0
11 TraesCS3B01G537700 chr3A 90.171 234 16 2 526 753 716786801 716787033 5.960000e-77 298.0
12 TraesCS3B01G537700 chr3A 81.695 295 45 7 22 312 505014002 505013713 1.320000e-58 237.0
13 TraesCS3B01G537700 chr3A 80.851 329 21 21 1289 1614 716777757 716778046 1.330000e-53 220.0
14 TraesCS3B01G537700 chr3A 78.859 298 51 10 22 312 144495180 144495472 1.040000e-44 191.0
15 TraesCS3B01G537700 chr3A 87.349 166 10 4 884 1038 716787087 716787252 2.250000e-41 180.0
16 TraesCS3B01G537700 chr3A 88.406 69 7 1 20 87 599981793 599981725 6.530000e-12 82.4
17 TraesCS3B01G537700 chr3A 92.453 53 3 1 2064 2115 716808227 716808279 1.090000e-09 75.0
18 TraesCS3B01G537700 chr3D 80.838 1503 170 59 526 1951 581014067 581012606 0.000000e+00 1072.0
19 TraesCS3B01G537700 chr3D 87.753 939 64 20 534 1423 581060540 581059604 0.000000e+00 1050.0
20 TraesCS3B01G537700 chr3D 86.763 831 75 22 2005 2822 581012594 581011786 0.000000e+00 893.0
21 TraesCS3B01G537700 chr3D 85.634 710 64 27 2120 2817 580991820 580991137 0.000000e+00 712.0
22 TraesCS3B01G537700 chr3D 82.274 897 86 37 1245 2115 580912238 580911389 0.000000e+00 708.0
23 TraesCS3B01G537700 chr3D 87.954 606 48 11 1249 1847 580994081 580993494 0.000000e+00 691.0
24 TraesCS3B01G537700 chr3D 87.582 612 45 16 313 905 580919874 580919275 0.000000e+00 680.0
25 TraesCS3B01G537700 chr3D 82.805 599 75 22 2115 2692 581058410 581057819 7.030000e-141 510.0
26 TraesCS3B01G537700 chr3D 81.016 669 75 25 526 1183 580994948 580994321 4.260000e-133 484.0
27 TraesCS3B01G537700 chr3D 85.831 367 28 5 898 1240 580918854 580918488 4.480000e-98 368.0
28 TraesCS3B01G537700 chr3D 83.862 378 30 12 1464 1829 581059609 581059251 5.870000e-87 331.0
29 TraesCS3B01G537700 chr3D 82.849 344 38 13 1289 1624 581093451 581093121 3.580000e-74 289.0
30 TraesCS3B01G537700 chr3D 81.543 363 28 14 670 994 580974141 580973780 2.170000e-66 263.0
31 TraesCS3B01G537700 chr3D 85.385 260 22 7 1824 2070 580993192 580992936 3.640000e-64 255.0
32 TraesCS3B01G537700 chr3D 80.054 371 33 13 526 880 581084608 581084263 1.320000e-58 237.0
33 TraesCS3B01G537700 chr3D 93.750 128 7 1 2690 2817 581057583 581057457 1.040000e-44 191.0
34 TraesCS3B01G537700 chr3D 81.140 228 26 10 1442 1665 581068927 581068713 1.750000e-37 167.0
35 TraesCS3B01G537700 chr3D 78.095 210 17 10 884 1074 580987291 580987092 3.880000e-19 106.0
36 TraesCS3B01G537700 chr3D 100.000 28 0 0 20 47 293807562 293807589 5.000000e-03 52.8
37 TraesCS3B01G537700 chr4A 83.893 298 41 6 20 312 253619782 253619487 7.760000e-71 278.0
38 TraesCS3B01G537700 chr6D 85.500 200 23 4 22 217 21151179 21150982 1.340000e-48 204.0
39 TraesCS3B01G537700 chr6D 86.250 80 7 4 2688 2767 82961290 82961365 1.820000e-12 84.2


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 TraesCS3B01G537700 chr3B 777653092 777655935 2843 False 5252.000000 5252 100.0000 1 2844 1 chr3B.!!$F4 2843
1 TraesCS3B01G537700 chr3B 777755153 777757977 2824 False 1114.500000 1674 84.6230 534 2822 2 chr3B.!!$F6 2288
2 TraesCS3B01G537700 chr3A 716806874 716808279 1405 False 748.000000 1421 90.0300 723 2115 2 chr3A.!!$F5 1392
3 TraesCS3B01G537700 chr3A 716792117 716795797 3680 False 537.333333 660 81.2900 533 1876 3 chr3A.!!$F4 1343
4 TraesCS3B01G537700 chr3D 581011786 581014067 2281 True 982.500000 1072 83.8005 526 2822 2 chr3D.!!$R8 2296
5 TraesCS3B01G537700 chr3D 580911389 580912238 849 True 708.000000 708 82.2740 1245 2115 1 chr3D.!!$R1 870
6 TraesCS3B01G537700 chr3D 580918488 580919874 1386 True 524.000000 680 86.7065 313 1240 2 chr3D.!!$R6 927
7 TraesCS3B01G537700 chr3D 581057457 581060540 3083 True 520.500000 1050 87.0425 534 2817 4 chr3D.!!$R9 2283
8 TraesCS3B01G537700 chr3D 580987092 580994948 7856 True 449.600000 712 83.6168 526 2817 5 chr3D.!!$R7 2291

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
417 419 0.320421 TCGAGTTCCGAGGCTTTTGG 60.32 55.0 0.0 0.0 43.23 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 8073 0.175531 CATGGCAAAATTCCGGGGAC 59.824 55.0 0.0 0.0 0.0 4.46 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 5.540400 TGAAGAGGTTTCCGACTTTTAGA 57.460 39.130 0.00 0.00 0.00 2.10
24 25 5.539048 TGAAGAGGTTTCCGACTTTTAGAG 58.461 41.667 0.00 0.00 0.00 2.43
25 26 5.070047 TGAAGAGGTTTCCGACTTTTAGAGT 59.930 40.000 0.00 0.00 42.70 3.24
26 27 6.266103 TGAAGAGGTTTCCGACTTTTAGAGTA 59.734 38.462 0.00 0.00 39.19 2.59
27 28 6.661304 AGAGGTTTCCGACTTTTAGAGTAA 57.339 37.500 0.00 0.00 39.19 2.24
28 29 6.689554 AGAGGTTTCCGACTTTTAGAGTAAG 58.310 40.000 0.00 0.00 39.19 2.34
29 30 6.267242 AGAGGTTTCCGACTTTTAGAGTAAGT 59.733 38.462 0.00 0.00 39.19 2.24
30 31 7.449704 AGAGGTTTCCGACTTTTAGAGTAAGTA 59.550 37.037 0.00 0.00 39.19 2.24
31 32 7.374272 AGGTTTCCGACTTTTAGAGTAAGTAC 58.626 38.462 0.00 0.00 39.19 2.73
32 33 7.014615 AGGTTTCCGACTTTTAGAGTAAGTACA 59.985 37.037 0.00 0.00 39.19 2.90
33 34 7.653311 GGTTTCCGACTTTTAGAGTAAGTACAA 59.347 37.037 0.00 0.00 39.19 2.41
34 35 9.201127 GTTTCCGACTTTTAGAGTAAGTACAAT 57.799 33.333 0.00 0.00 39.19 2.71
37 38 9.236006 TCCGACTTTTAGAGTAAGTACAATAGT 57.764 33.333 0.00 0.00 39.19 2.12
38 39 9.286946 CCGACTTTTAGAGTAAGTACAATAGTG 57.713 37.037 0.00 0.00 39.19 2.74
39 40 9.286946 CGACTTTTAGAGTAAGTACAATAGTGG 57.713 37.037 0.00 0.00 39.19 4.00
40 41 8.999220 ACTTTTAGAGTAAGTACAATAGTGGC 57.001 34.615 0.00 0.00 36.65 5.01
41 42 8.813951 ACTTTTAGAGTAAGTACAATAGTGGCT 58.186 33.333 0.00 0.00 36.65 4.75
42 43 9.654663 CTTTTAGAGTAAGTACAATAGTGGCTT 57.345 33.333 0.00 1.53 0.00 4.35
47 48 9.080097 AGAGTAAGTACAATAGTGGCTTATAGG 57.920 37.037 10.90 0.00 32.91 2.57
48 49 7.668492 AGTAAGTACAATAGTGGCTTATAGGC 58.332 38.462 10.90 0.00 41.77 3.93
57 58 2.474410 GGCTTATAGGCCGCTTACAT 57.526 50.000 10.49 0.00 42.82 2.29
58 59 2.076863 GGCTTATAGGCCGCTTACATG 58.923 52.381 10.49 0.00 42.82 3.21
59 60 2.550208 GGCTTATAGGCCGCTTACATGT 60.550 50.000 10.49 2.69 42.82 3.21
60 61 2.737252 GCTTATAGGCCGCTTACATGTC 59.263 50.000 0.00 0.00 0.00 3.06
61 62 3.802329 GCTTATAGGCCGCTTACATGTCA 60.802 47.826 0.00 0.00 0.00 3.58
62 63 4.569943 CTTATAGGCCGCTTACATGTCAT 58.430 43.478 0.00 0.00 0.00 3.06
63 64 3.492102 ATAGGCCGCTTACATGTCATT 57.508 42.857 0.00 0.00 0.00 2.57
64 65 2.128771 AGGCCGCTTACATGTCATTT 57.871 45.000 0.00 0.00 0.00 2.32
65 66 2.446435 AGGCCGCTTACATGTCATTTT 58.554 42.857 0.00 0.00 0.00 1.82
66 67 2.825532 AGGCCGCTTACATGTCATTTTT 59.174 40.909 0.00 0.00 0.00 1.94
67 68 2.923020 GGCCGCTTACATGTCATTTTTG 59.077 45.455 0.00 0.00 0.00 2.44
68 69 2.345341 GCCGCTTACATGTCATTTTTGC 59.655 45.455 0.00 0.00 0.00 3.68
69 70 2.923020 CCGCTTACATGTCATTTTTGCC 59.077 45.455 0.00 0.00 0.00 4.52
70 71 3.367292 CCGCTTACATGTCATTTTTGCCT 60.367 43.478 0.00 0.00 0.00 4.75
71 72 4.142491 CCGCTTACATGTCATTTTTGCCTA 60.142 41.667 0.00 0.00 0.00 3.93
72 73 5.450412 CCGCTTACATGTCATTTTTGCCTAT 60.450 40.000 0.00 0.00 0.00 2.57
73 74 5.456497 CGCTTACATGTCATTTTTGCCTATG 59.544 40.000 0.00 0.00 0.00 2.23
74 75 6.332630 GCTTACATGTCATTTTTGCCTATGT 58.667 36.000 0.00 0.00 0.00 2.29
75 76 6.254157 GCTTACATGTCATTTTTGCCTATGTG 59.746 38.462 0.00 0.00 0.00 3.21
76 77 5.726980 ACATGTCATTTTTGCCTATGTGT 57.273 34.783 0.00 0.00 0.00 3.72
77 78 6.832520 ACATGTCATTTTTGCCTATGTGTA 57.167 33.333 0.00 0.00 0.00 2.90
78 79 6.855836 ACATGTCATTTTTGCCTATGTGTAG 58.144 36.000 0.00 0.00 0.00 2.74
79 80 6.434028 ACATGTCATTTTTGCCTATGTGTAGT 59.566 34.615 0.00 0.00 0.00 2.73
80 81 6.892658 TGTCATTTTTGCCTATGTGTAGTT 57.107 33.333 0.00 0.00 0.00 2.24
81 82 6.676950 TGTCATTTTTGCCTATGTGTAGTTG 58.323 36.000 0.00 0.00 0.00 3.16
82 83 6.488344 TGTCATTTTTGCCTATGTGTAGTTGA 59.512 34.615 0.00 0.00 0.00 3.18
83 84 7.023575 GTCATTTTTGCCTATGTGTAGTTGAG 58.976 38.462 0.00 0.00 0.00 3.02
84 85 6.939730 TCATTTTTGCCTATGTGTAGTTGAGA 59.060 34.615 0.00 0.00 0.00 3.27
85 86 6.801539 TTTTTGCCTATGTGTAGTTGAGAG 57.198 37.500 0.00 0.00 0.00 3.20
86 87 5.738619 TTTGCCTATGTGTAGTTGAGAGA 57.261 39.130 0.00 0.00 0.00 3.10
87 88 5.939764 TTGCCTATGTGTAGTTGAGAGAT 57.060 39.130 0.00 0.00 0.00 2.75
88 89 5.939764 TGCCTATGTGTAGTTGAGAGATT 57.060 39.130 0.00 0.00 0.00 2.40
89 90 5.664457 TGCCTATGTGTAGTTGAGAGATTG 58.336 41.667 0.00 0.00 0.00 2.67
90 91 5.422012 TGCCTATGTGTAGTTGAGAGATTGA 59.578 40.000 0.00 0.00 0.00 2.57
91 92 6.070824 TGCCTATGTGTAGTTGAGAGATTGAA 60.071 38.462 0.00 0.00 0.00 2.69
92 93 6.818644 GCCTATGTGTAGTTGAGAGATTGAAA 59.181 38.462 0.00 0.00 0.00 2.69
93 94 7.334421 GCCTATGTGTAGTTGAGAGATTGAAAA 59.666 37.037 0.00 0.00 0.00 2.29
94 95 9.219603 CCTATGTGTAGTTGAGAGATTGAAAAA 57.780 33.333 0.00 0.00 0.00 1.94
96 97 8.682936 ATGTGTAGTTGAGAGATTGAAAAAGT 57.317 30.769 0.00 0.00 0.00 2.66
97 98 9.778741 ATGTGTAGTTGAGAGATTGAAAAAGTA 57.221 29.630 0.00 0.00 0.00 2.24
98 99 9.607988 TGTGTAGTTGAGAGATTGAAAAAGTAA 57.392 29.630 0.00 0.00 0.00 2.24
100 101 9.273016 TGTAGTTGAGAGATTGAAAAAGTAAGG 57.727 33.333 0.00 0.00 0.00 2.69
101 102 7.751768 AGTTGAGAGATTGAAAAAGTAAGGG 57.248 36.000 0.00 0.00 0.00 3.95
102 103 6.717084 AGTTGAGAGATTGAAAAAGTAAGGGG 59.283 38.462 0.00 0.00 0.00 4.79
103 104 6.448369 TGAGAGATTGAAAAAGTAAGGGGA 57.552 37.500 0.00 0.00 0.00 4.81
104 105 7.032598 TGAGAGATTGAAAAAGTAAGGGGAT 57.967 36.000 0.00 0.00 0.00 3.85
105 106 7.470192 TGAGAGATTGAAAAAGTAAGGGGATT 58.530 34.615 0.00 0.00 0.00 3.01
106 107 7.394359 TGAGAGATTGAAAAAGTAAGGGGATTG 59.606 37.037 0.00 0.00 0.00 2.67
107 108 6.665248 AGAGATTGAAAAAGTAAGGGGATTGG 59.335 38.462 0.00 0.00 0.00 3.16
108 109 6.561294 AGATTGAAAAAGTAAGGGGATTGGA 58.439 36.000 0.00 0.00 0.00 3.53
109 110 6.437477 AGATTGAAAAAGTAAGGGGATTGGAC 59.563 38.462 0.00 0.00 0.00 4.02
110 111 5.333566 TGAAAAAGTAAGGGGATTGGACT 57.666 39.130 0.00 0.00 0.00 3.85
111 112 5.321927 TGAAAAAGTAAGGGGATTGGACTC 58.678 41.667 0.00 0.00 0.00 3.36
112 113 5.074515 TGAAAAAGTAAGGGGATTGGACTCT 59.925 40.000 0.00 0.00 0.00 3.24
113 114 4.846168 AAAGTAAGGGGATTGGACTCTC 57.154 45.455 0.00 0.00 0.00 3.20
114 115 3.491766 AGTAAGGGGATTGGACTCTCA 57.508 47.619 0.00 0.00 0.00 3.27
115 116 4.014273 AGTAAGGGGATTGGACTCTCAT 57.986 45.455 0.00 0.00 0.00 2.90
116 117 3.713764 AGTAAGGGGATTGGACTCTCATG 59.286 47.826 0.00 0.00 0.00 3.07
117 118 0.842635 AGGGGATTGGACTCTCATGC 59.157 55.000 0.00 0.00 0.00 4.06
118 119 0.548031 GGGGATTGGACTCTCATGCA 59.452 55.000 0.00 0.00 0.00 3.96
119 120 1.064463 GGGGATTGGACTCTCATGCAA 60.064 52.381 0.00 0.00 34.15 4.08
120 121 2.295885 GGGATTGGACTCTCATGCAAG 58.704 52.381 0.00 0.00 33.05 4.01
121 122 2.092753 GGGATTGGACTCTCATGCAAGA 60.093 50.000 0.00 0.00 33.05 3.02
122 123 3.204526 GGATTGGACTCTCATGCAAGAG 58.795 50.000 12.75 12.75 46.78 2.85
131 132 5.710513 CTCTCATGCAAGAGTCTAGCTAT 57.289 43.478 17.84 0.00 38.38 2.97
132 133 6.816134 CTCTCATGCAAGAGTCTAGCTATA 57.184 41.667 17.84 0.00 38.38 1.31
133 134 7.395190 CTCTCATGCAAGAGTCTAGCTATAT 57.605 40.000 17.84 0.00 38.38 0.86
134 135 8.504812 CTCTCATGCAAGAGTCTAGCTATATA 57.495 38.462 17.84 0.00 38.38 0.86
135 136 8.275015 TCTCATGCAAGAGTCTAGCTATATAC 57.725 38.462 17.84 0.00 36.97 1.47
136 137 7.885399 TCTCATGCAAGAGTCTAGCTATATACA 59.115 37.037 17.84 0.00 36.97 2.29
137 138 8.586879 TCATGCAAGAGTCTAGCTATATACAT 57.413 34.615 0.00 0.00 0.00 2.29
138 139 8.465201 TCATGCAAGAGTCTAGCTATATACATG 58.535 37.037 0.00 0.00 30.76 3.21
139 140 6.625362 TGCAAGAGTCTAGCTATATACATGC 58.375 40.000 0.00 2.98 0.00 4.06
140 141 6.435591 TGCAAGAGTCTAGCTATATACATGCT 59.564 38.462 15.25 1.15 40.43 3.79
141 142 7.039434 TGCAAGAGTCTAGCTATATACATGCTT 60.039 37.037 15.25 8.13 38.15 3.91
142 143 7.816995 GCAAGAGTCTAGCTATATACATGCTTT 59.183 37.037 0.00 0.00 38.15 3.51
143 144 9.703892 CAAGAGTCTAGCTATATACATGCTTTT 57.296 33.333 0.00 0.00 38.15 2.27
146 147 9.796120 GAGTCTAGCTATATACATGCTTTTAGG 57.204 37.037 0.00 0.00 38.15 2.69
147 148 8.254508 AGTCTAGCTATATACATGCTTTTAGGC 58.745 37.037 0.00 0.00 38.15 3.93
148 149 8.254508 GTCTAGCTATATACATGCTTTTAGGCT 58.745 37.037 0.00 0.00 38.15 4.58
149 150 9.475620 TCTAGCTATATACATGCTTTTAGGCTA 57.524 33.333 0.00 0.00 38.15 3.93
150 151 9.743057 CTAGCTATATACATGCTTTTAGGCTAG 57.257 37.037 13.51 13.51 38.51 3.42
151 152 8.140112 AGCTATATACATGCTTTTAGGCTAGT 57.860 34.615 0.00 0.00 32.61 2.57
152 153 9.256228 AGCTATATACATGCTTTTAGGCTAGTA 57.744 33.333 0.00 0.00 32.61 1.82
153 154 9.303537 GCTATATACATGCTTTTAGGCTAGTAC 57.696 37.037 0.00 0.00 0.00 2.73
159 160 8.801882 ACATGCTTTTAGGCTAGTACAATAAA 57.198 30.769 0.00 0.00 0.00 1.40
160 161 9.408648 ACATGCTTTTAGGCTAGTACAATAAAT 57.591 29.630 0.00 0.00 0.00 1.40
188 189 9.527157 TGAAGAAAGAGAAAGAGAGAAGATAGA 57.473 33.333 0.00 0.00 0.00 1.98
213 214 7.433708 AAAAATGCTTTTGTAATAGCCAACC 57.566 32.000 0.00 0.00 36.56 3.77
214 215 6.358974 AAATGCTTTTGTAATAGCCAACCT 57.641 33.333 0.00 0.00 36.56 3.50
215 216 6.358974 AATGCTTTTGTAATAGCCAACCTT 57.641 33.333 4.93 0.00 36.56 3.50
216 217 7.475137 AATGCTTTTGTAATAGCCAACCTTA 57.525 32.000 4.93 0.00 36.56 2.69
217 218 6.262193 TGCTTTTGTAATAGCCAACCTTAC 57.738 37.500 4.93 0.00 36.56 2.34
218 219 5.770663 TGCTTTTGTAATAGCCAACCTTACA 59.229 36.000 4.93 0.00 36.56 2.41
219 220 6.265649 TGCTTTTGTAATAGCCAACCTTACAA 59.734 34.615 4.93 3.66 41.25 2.41
220 221 6.584942 GCTTTTGTAATAGCCAACCTTACAAC 59.415 38.462 6.60 0.00 42.12 3.32
221 222 6.578163 TTTGTAATAGCCAACCTTACAACC 57.422 37.500 6.60 0.00 42.12 3.77
222 223 4.255301 TGTAATAGCCAACCTTACAACCG 58.745 43.478 0.00 0.00 33.64 4.44
223 224 3.706600 AATAGCCAACCTTACAACCGA 57.293 42.857 0.00 0.00 0.00 4.69
224 225 2.460757 TAGCCAACCTTACAACCGAC 57.539 50.000 0.00 0.00 0.00 4.79
225 226 0.470766 AGCCAACCTTACAACCGACA 59.529 50.000 0.00 0.00 0.00 4.35
226 227 1.073284 AGCCAACCTTACAACCGACAT 59.927 47.619 0.00 0.00 0.00 3.06
227 228 1.883926 GCCAACCTTACAACCGACATT 59.116 47.619 0.00 0.00 0.00 2.71
228 229 3.075884 GCCAACCTTACAACCGACATTA 58.924 45.455 0.00 0.00 0.00 1.90
229 230 3.692593 GCCAACCTTACAACCGACATTAT 59.307 43.478 0.00 0.00 0.00 1.28
230 231 4.157105 GCCAACCTTACAACCGACATTATT 59.843 41.667 0.00 0.00 0.00 1.40
231 232 5.636837 CCAACCTTACAACCGACATTATTG 58.363 41.667 0.00 0.00 0.00 1.90
232 233 5.182380 CCAACCTTACAACCGACATTATTGT 59.818 40.000 0.00 0.00 39.75 2.71
233 234 6.372103 CCAACCTTACAACCGACATTATTGTA 59.628 38.462 0.00 0.00 37.68 2.41
234 235 7.066525 CCAACCTTACAACCGACATTATTGTAT 59.933 37.037 0.00 0.00 38.31 2.29
235 236 7.548196 ACCTTACAACCGACATTATTGTATG 57.452 36.000 0.00 0.00 38.31 2.39
236 237 7.332557 ACCTTACAACCGACATTATTGTATGA 58.667 34.615 9.54 0.00 38.31 2.15
237 238 7.494625 ACCTTACAACCGACATTATTGTATGAG 59.505 37.037 9.54 1.42 38.31 2.90
238 239 7.494625 CCTTACAACCGACATTATTGTATGAGT 59.505 37.037 9.54 0.00 38.31 3.41
239 240 9.524106 CTTACAACCGACATTATTGTATGAGTA 57.476 33.333 0.00 0.00 38.31 2.59
240 241 9.872721 TTACAACCGACATTATTGTATGAGTAA 57.127 29.630 0.00 0.00 38.31 2.24
241 242 8.780846 ACAACCGACATTATTGTATGAGTAAA 57.219 30.769 0.00 0.00 35.79 2.01
242 243 9.391006 ACAACCGACATTATTGTATGAGTAAAT 57.609 29.630 0.00 0.00 35.79 1.40
271 272 7.895975 ATGATGACTATAAATGACATGACGG 57.104 36.000 0.00 0.00 0.00 4.79
272 273 6.816136 TGATGACTATAAATGACATGACGGT 58.184 36.000 0.00 0.00 0.00 4.83
273 274 7.272244 TGATGACTATAAATGACATGACGGTT 58.728 34.615 0.00 0.00 0.00 4.44
274 275 7.768582 TGATGACTATAAATGACATGACGGTTT 59.231 33.333 0.00 1.74 0.00 3.27
275 276 7.534085 TGACTATAAATGACATGACGGTTTC 57.466 36.000 0.00 0.00 0.00 2.78
276 277 7.100409 TGACTATAAATGACATGACGGTTTCA 58.900 34.615 0.00 0.00 39.11 2.69
277 278 7.768582 TGACTATAAATGACATGACGGTTTCAT 59.231 33.333 0.00 0.00 46.75 2.57
278 279 9.256477 GACTATAAATGACATGACGGTTTCATA 57.744 33.333 0.00 0.00 43.68 2.15
279 280 9.778741 ACTATAAATGACATGACGGTTTCATAT 57.221 29.630 0.00 0.00 43.68 1.78
284 285 8.675705 AATGACATGACGGTTTCATATAATCA 57.324 30.769 0.00 0.00 43.68 2.57
285 286 8.853077 ATGACATGACGGTTTCATATAATCAT 57.147 30.769 0.00 0.00 43.68 2.45
286 287 8.310406 TGACATGACGGTTTCATATAATCATC 57.690 34.615 0.00 0.00 43.68 2.92
287 288 7.930865 TGACATGACGGTTTCATATAATCATCA 59.069 33.333 0.00 0.00 43.68 3.07
288 289 8.853077 ACATGACGGTTTCATATAATCATCAT 57.147 30.769 0.00 0.00 43.68 2.45
289 290 8.939929 ACATGACGGTTTCATATAATCATCATC 58.060 33.333 0.00 0.00 43.68 2.92
290 291 9.159364 CATGACGGTTTCATATAATCATCATCT 57.841 33.333 0.00 0.00 43.68 2.90
291 292 8.538409 TGACGGTTTCATATAATCATCATCTG 57.462 34.615 0.00 0.00 0.00 2.90
292 293 7.603784 TGACGGTTTCATATAATCATCATCTGG 59.396 37.037 0.00 0.00 0.00 3.86
293 294 6.372659 ACGGTTTCATATAATCATCATCTGGC 59.627 38.462 0.00 0.00 0.00 4.85
294 295 6.596888 CGGTTTCATATAATCATCATCTGGCT 59.403 38.462 0.00 0.00 0.00 4.75
295 296 7.765819 CGGTTTCATATAATCATCATCTGGCTA 59.234 37.037 0.00 0.00 0.00 3.93
296 297 9.624373 GGTTTCATATAATCATCATCTGGCTAT 57.376 33.333 0.00 0.00 0.00 2.97
310 311 8.737168 TCATCTGGCTATATTATTAACCATGC 57.263 34.615 0.00 0.00 0.00 4.06
311 312 8.551440 TCATCTGGCTATATTATTAACCATGCT 58.449 33.333 0.00 0.00 0.00 3.79
345 346 2.089980 GTAAGAGCCGTCAGGTGACTA 58.910 52.381 8.44 0.00 42.66 2.59
353 354 3.262420 CCGTCAGGTGACTATTCCAAAG 58.738 50.000 8.44 0.00 42.66 2.77
355 356 2.673368 GTCAGGTGACTATTCCAAAGCG 59.327 50.000 2.72 0.00 41.65 4.68
374 375 2.656897 GCGGAAGAAAAATTGCTTCGTC 59.343 45.455 7.60 7.51 41.02 4.20
377 378 4.083802 CGGAAGAAAAATTGCTTCGTCTCT 60.084 41.667 7.60 0.00 41.02 3.10
379 380 4.152607 AGAAAAATTGCTTCGTCTCTGC 57.847 40.909 0.00 0.00 0.00 4.26
380 381 3.817647 AGAAAAATTGCTTCGTCTCTGCT 59.182 39.130 0.00 0.00 0.00 4.24
389 390 1.714794 TCGTCTCTGCTTTAAGCTGC 58.285 50.000 18.20 4.48 42.97 5.25
404 406 1.202698 AGCTGCTCCAAAAGTCGAGTT 60.203 47.619 0.00 0.00 0.00 3.01
406 408 1.801178 CTGCTCCAAAAGTCGAGTTCC 59.199 52.381 5.84 0.00 0.00 3.62
408 410 1.604693 GCTCCAAAAGTCGAGTTCCGA 60.605 52.381 5.84 1.62 46.35 4.55
417 419 0.320421 TCGAGTTCCGAGGCTTTTGG 60.320 55.000 0.00 0.00 43.23 3.28
423 425 0.472471 TCCGAGGCTTTTGGACTTGT 59.528 50.000 0.00 0.00 34.18 3.16
433 435 3.627395 TTTGGACTTGTGAGTGTGTCT 57.373 42.857 0.00 0.00 35.88 3.41
466 469 9.855021 CCAAGTTTAAATAACCATTTACTGAGG 57.145 33.333 0.00 0.00 36.55 3.86
485 488 5.684704 TGAGGGGAGCACTATCTTAAATTG 58.315 41.667 0.00 0.00 0.00 2.32
486 489 5.428457 TGAGGGGAGCACTATCTTAAATTGA 59.572 40.000 0.00 0.00 0.00 2.57
604 624 4.619973 CATCTGATCTCGAGCTAGCTTTT 58.380 43.478 20.42 0.00 0.00 2.27
668 694 1.170290 CCTTCCACCAACCCGTTCAC 61.170 60.000 0.00 0.00 0.00 3.18
738 796 4.595986 TGGCTAGTGTGTGTGTCTATCTA 58.404 43.478 0.00 0.00 0.00 1.98
752 810 6.266786 TGTGTCTATCTACTCAACAAACCTCA 59.733 38.462 0.00 0.00 0.00 3.86
905 1411 8.999431 GGAGTATCTACTATGCTCTATCTATGC 58.001 40.741 3.64 0.00 36.50 3.14
915 1421 3.081061 CTCTATCTATGCACTCTCCGCT 58.919 50.000 0.00 0.00 0.00 5.52
1059 1608 0.529337 ACGCAGCATCGATTCTCCTG 60.529 55.000 0.00 1.54 0.00 3.86
1066 1615 2.650813 ATCGATTCTCCTGGCACGCC 62.651 60.000 0.00 0.00 0.00 5.68
1178 4791 2.162809 TCGATCGTCATTTTCGACCTCA 59.837 45.455 15.94 0.00 40.07 3.86
1191 4804 6.422776 TTTCGACCTCAATGCTTATTTCTC 57.577 37.500 0.00 0.00 0.00 2.87
1198 4811 5.803967 CCTCAATGCTTATTTCTCAAACTGC 59.196 40.000 0.00 0.00 0.00 4.40
1220 4833 0.788995 CTGGATTCGCTGCATCGATC 59.211 55.000 14.07 12.44 38.37 3.69
1237 4850 2.704572 GATCCAGTTAGCTGCAGTGTT 58.295 47.619 16.64 4.17 41.26 3.32
1325 4992 3.222354 CTACTACCCATCCGCGGCC 62.222 68.421 23.51 0.00 0.00 6.13
1420 5096 1.951602 CATCGAGGGATGGTACGTACA 59.048 52.381 26.02 13.22 45.15 2.90
1434 5110 3.304721 TACACCCCACGACCACCG 61.305 66.667 0.00 0.00 45.44 4.94
1477 5154 2.361438 CGATACCACTACCACCTCCTTC 59.639 54.545 0.00 0.00 0.00 3.46
1493 5177 6.434340 CACCTCCTTCCTAACTTGCTTAATTT 59.566 38.462 0.00 0.00 0.00 1.82
1511 5195 2.754946 TTTCGCTAGTGATTTCCGGT 57.245 45.000 6.86 0.00 0.00 5.28
1520 5204 6.094061 GCTAGTGATTTCCGGTCTGATATAC 58.906 44.000 0.00 0.00 0.00 1.47
1544 5229 4.576463 AGTGTCTGAATTTGGTGTGTTCTC 59.424 41.667 0.00 0.00 0.00 2.87
1554 5239 2.703536 TGGTGTGTTCTCTTTCAGCCTA 59.296 45.455 0.00 0.00 0.00 3.93
1648 5336 2.028020 AGAAGTTGGTGCTAGTGCCTAC 60.028 50.000 9.80 9.80 38.71 3.18
1660 5355 3.521947 AGTGCCTACGAAGAACATACC 57.478 47.619 0.00 0.00 0.00 2.73
1677 5385 4.710375 ACATACCCATACAGAGAGTCGTTT 59.290 41.667 0.00 0.00 0.00 3.60
1690 5402 7.595502 ACAGAGAGTCGTTTCTTAATTACAGTG 59.404 37.037 0.00 0.00 0.00 3.66
1698 5414 9.107177 TCGTTTCTTAATTACAGTGGTTTGTTA 57.893 29.630 0.00 0.00 32.56 2.41
1699 5415 9.161684 CGTTTCTTAATTACAGTGGTTTGTTAC 57.838 33.333 0.00 0.00 32.56 2.50
1742 5470 1.680105 AATAACCGAGAACGCGTGCG 61.680 55.000 14.98 17.33 46.03 5.34
1800 5532 8.342634 GTGCGTCACACCTATAATCAATTTTAT 58.657 33.333 5.30 0.00 44.02 1.40
1862 5918 4.691860 AAAGATAACATCTGCTGTGCAC 57.308 40.909 10.75 10.75 40.13 4.57
1931 6000 2.806745 GCAGTCACTTGTGCAGAGGTAA 60.807 50.000 0.00 0.00 39.62 2.85
1945 6029 4.082679 GCAGAGGTAATAGTAGTGGGATCG 60.083 50.000 0.00 0.00 0.00 3.69
1948 6032 4.664392 AGGTAATAGTAGTGGGATCGAGG 58.336 47.826 0.00 0.00 0.00 4.63
2052 6136 0.107508 ATGCAGATCGAGTGGGGTTG 60.108 55.000 0.00 0.00 0.00 3.77
2109 8017 1.197812 TGGCAGCAAGAGAGAGCATA 58.802 50.000 0.00 0.00 0.00 3.14
2136 8070 2.825532 ACAGCCCGAACTAAATTTGCAT 59.174 40.909 0.00 0.00 0.00 3.96
2139 8073 4.091800 CAGCCCGAACTAAATTTGCATTTG 59.908 41.667 0.00 0.00 34.29 2.32
2141 8075 4.091365 GCCCGAACTAAATTTGCATTTGTC 59.909 41.667 0.00 0.00 34.29 3.18
2190 8125 1.160137 GGCTTTGTCTCGCTTCATGT 58.840 50.000 0.00 0.00 0.00 3.21
2234 8172 2.187946 GGCACCCTCCTGTCGATG 59.812 66.667 0.00 0.00 0.00 3.84
2239 8177 1.000283 CACCCTCCTGTCGATGCTATC 60.000 57.143 0.00 0.00 0.00 2.08
2240 8178 0.605589 CCCTCCTGTCGATGCTATCC 59.394 60.000 0.00 0.00 0.00 2.59
2273 8217 7.591426 CCAAGTAGCTTCTGTTTGTACATTTTC 59.409 37.037 0.00 0.00 32.86 2.29
2382 8326 5.691305 TGTTCACTGCACATTAGAAAAATGC 59.309 36.000 0.00 0.00 36.81 3.56
2386 8330 7.307694 TCACTGCACATTAGAAAAATGCTAAG 58.692 34.615 0.00 0.00 37.20 2.18
2388 8332 6.209391 ACTGCACATTAGAAAAATGCTAAGGT 59.791 34.615 0.00 0.00 41.76 3.50
2413 8357 5.972382 GGTGTACAAAATTAGTTCGCACAAA 59.028 36.000 0.00 0.00 0.00 2.83
2620 8575 8.998989 CACATAGTTAGAAAAATGTTATGCACG 58.001 33.333 0.00 0.00 30.32 5.34
2818 9016 0.316278 CTCGCAGTAGACGATCACCG 60.316 60.000 0.00 0.00 45.44 4.94
2826 9052 0.106669 AGACGATCACCGGATCCAGA 60.107 55.000 9.46 6.78 45.89 3.86
2843 9069 5.462530 TCCAGATTTACTTCGTCTCACAA 57.537 39.130 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.110411 TCTAAAAGTCGGAAACCTCTTCAT 57.890 37.500 0.00 0.00 0.00 2.57
1 2 5.070047 ACTCTAAAAGTCGGAAACCTCTTCA 59.930 40.000 0.00 0.00 30.02 3.02
2 3 5.539979 ACTCTAAAAGTCGGAAACCTCTTC 58.460 41.667 0.00 0.00 30.02 2.87
3 4 5.548181 ACTCTAAAAGTCGGAAACCTCTT 57.452 39.130 0.00 0.00 30.02 2.85
4 5 6.267242 ACTTACTCTAAAAGTCGGAAACCTCT 59.733 38.462 0.00 0.00 39.55 3.69
5 6 6.453943 ACTTACTCTAAAAGTCGGAAACCTC 58.546 40.000 0.00 0.00 39.55 3.85
6 7 6.416631 ACTTACTCTAAAAGTCGGAAACCT 57.583 37.500 0.00 0.00 39.55 3.50
7 8 7.147976 TGTACTTACTCTAAAAGTCGGAAACC 58.852 38.462 0.00 0.00 39.55 3.27
8 9 8.579682 TTGTACTTACTCTAAAAGTCGGAAAC 57.420 34.615 0.00 0.00 39.55 2.78
11 12 9.236006 ACTATTGTACTTACTCTAAAAGTCGGA 57.764 33.333 0.00 0.00 39.55 4.55
12 13 9.286946 CACTATTGTACTTACTCTAAAAGTCGG 57.713 37.037 0.00 0.00 39.55 4.79
13 14 9.286946 CCACTATTGTACTTACTCTAAAAGTCG 57.713 37.037 0.00 0.00 39.55 4.18
14 15 9.085250 GCCACTATTGTACTTACTCTAAAAGTC 57.915 37.037 0.00 0.00 39.55 3.01
15 16 8.813951 AGCCACTATTGTACTTACTCTAAAAGT 58.186 33.333 0.00 0.00 42.33 2.66
16 17 9.654663 AAGCCACTATTGTACTTACTCTAAAAG 57.345 33.333 0.00 0.00 0.00 2.27
21 22 9.080097 CCTATAAGCCACTATTGTACTTACTCT 57.920 37.037 0.00 0.00 31.32 3.24
22 23 7.813627 GCCTATAAGCCACTATTGTACTTACTC 59.186 40.741 0.00 0.00 31.32 2.59
23 24 7.668492 GCCTATAAGCCACTATTGTACTTACT 58.332 38.462 0.00 0.37 31.32 2.24
24 25 7.886405 GCCTATAAGCCACTATTGTACTTAC 57.114 40.000 0.00 0.00 31.32 2.34
39 40 2.737252 GACATGTAAGCGGCCTATAAGC 59.263 50.000 0.00 0.00 0.00 3.09
40 41 3.990092 TGACATGTAAGCGGCCTATAAG 58.010 45.455 0.00 0.00 0.00 1.73
41 42 4.617253 ATGACATGTAAGCGGCCTATAA 57.383 40.909 0.00 0.00 0.00 0.98
42 43 4.617253 AATGACATGTAAGCGGCCTATA 57.383 40.909 0.00 0.00 0.00 1.31
43 44 3.492102 AATGACATGTAAGCGGCCTAT 57.508 42.857 0.00 0.00 0.00 2.57
44 45 3.275617 AAATGACATGTAAGCGGCCTA 57.724 42.857 0.00 0.00 0.00 3.93
45 46 2.128771 AAATGACATGTAAGCGGCCT 57.871 45.000 0.00 0.00 0.00 5.19
46 47 2.923020 CAAAAATGACATGTAAGCGGCC 59.077 45.455 0.00 0.00 0.00 6.13
47 48 2.345341 GCAAAAATGACATGTAAGCGGC 59.655 45.455 0.00 0.00 0.00 6.53
48 49 2.923020 GGCAAAAATGACATGTAAGCGG 59.077 45.455 0.00 0.00 0.00 5.52
49 50 3.836949 AGGCAAAAATGACATGTAAGCG 58.163 40.909 0.00 0.00 0.00 4.68
50 51 6.254157 CACATAGGCAAAAATGACATGTAAGC 59.746 38.462 0.00 0.00 0.00 3.09
51 52 7.315142 ACACATAGGCAAAAATGACATGTAAG 58.685 34.615 0.00 0.00 0.00 2.34
52 53 7.225784 ACACATAGGCAAAAATGACATGTAA 57.774 32.000 0.00 0.00 0.00 2.41
53 54 6.832520 ACACATAGGCAAAAATGACATGTA 57.167 33.333 0.00 0.00 0.00 2.29
54 55 5.726980 ACACATAGGCAAAAATGACATGT 57.273 34.783 0.00 0.00 0.00 3.21
55 56 6.855836 ACTACACATAGGCAAAAATGACATG 58.144 36.000 0.00 0.00 32.08 3.21
56 57 7.176515 TCAACTACACATAGGCAAAAATGACAT 59.823 33.333 0.00 0.00 32.08 3.06
57 58 6.488344 TCAACTACACATAGGCAAAAATGACA 59.512 34.615 0.00 0.00 32.08 3.58
58 59 6.908825 TCAACTACACATAGGCAAAAATGAC 58.091 36.000 0.00 0.00 32.08 3.06
59 60 6.939730 TCTCAACTACACATAGGCAAAAATGA 59.060 34.615 0.00 0.00 32.08 2.57
60 61 7.119699 TCTCTCAACTACACATAGGCAAAAATG 59.880 37.037 0.00 0.00 32.08 2.32
61 62 7.168219 TCTCTCAACTACACATAGGCAAAAAT 58.832 34.615 0.00 0.00 32.08 1.82
62 63 6.530120 TCTCTCAACTACACATAGGCAAAAA 58.470 36.000 0.00 0.00 32.08 1.94
63 64 6.109156 TCTCTCAACTACACATAGGCAAAA 57.891 37.500 0.00 0.00 32.08 2.44
64 65 5.738619 TCTCTCAACTACACATAGGCAAA 57.261 39.130 0.00 0.00 32.08 3.68
65 66 5.939764 ATCTCTCAACTACACATAGGCAA 57.060 39.130 0.00 0.00 32.08 4.52
66 67 5.422012 TCAATCTCTCAACTACACATAGGCA 59.578 40.000 0.00 0.00 32.08 4.75
67 68 5.907207 TCAATCTCTCAACTACACATAGGC 58.093 41.667 0.00 0.00 32.08 3.93
68 69 8.777865 TTTTCAATCTCTCAACTACACATAGG 57.222 34.615 0.00 0.00 32.08 2.57
70 71 9.778741 ACTTTTTCAATCTCTCAACTACACATA 57.221 29.630 0.00 0.00 0.00 2.29
71 72 8.682936 ACTTTTTCAATCTCTCAACTACACAT 57.317 30.769 0.00 0.00 0.00 3.21
72 73 9.607988 TTACTTTTTCAATCTCTCAACTACACA 57.392 29.630 0.00 0.00 0.00 3.72
74 75 9.273016 CCTTACTTTTTCAATCTCTCAACTACA 57.727 33.333 0.00 0.00 0.00 2.74
75 76 8.722394 CCCTTACTTTTTCAATCTCTCAACTAC 58.278 37.037 0.00 0.00 0.00 2.73
76 77 7.883311 CCCCTTACTTTTTCAATCTCTCAACTA 59.117 37.037 0.00 0.00 0.00 2.24
77 78 6.717084 CCCCTTACTTTTTCAATCTCTCAACT 59.283 38.462 0.00 0.00 0.00 3.16
78 79 6.715264 TCCCCTTACTTTTTCAATCTCTCAAC 59.285 38.462 0.00 0.00 0.00 3.18
79 80 6.848069 TCCCCTTACTTTTTCAATCTCTCAA 58.152 36.000 0.00 0.00 0.00 3.02
80 81 6.448369 TCCCCTTACTTTTTCAATCTCTCA 57.552 37.500 0.00 0.00 0.00 3.27
81 82 7.148000 CCAATCCCCTTACTTTTTCAATCTCTC 60.148 40.741 0.00 0.00 0.00 3.20
82 83 6.665248 CCAATCCCCTTACTTTTTCAATCTCT 59.335 38.462 0.00 0.00 0.00 3.10
83 84 6.663523 TCCAATCCCCTTACTTTTTCAATCTC 59.336 38.462 0.00 0.00 0.00 2.75
84 85 6.437477 GTCCAATCCCCTTACTTTTTCAATCT 59.563 38.462 0.00 0.00 0.00 2.40
85 86 6.437477 AGTCCAATCCCCTTACTTTTTCAATC 59.563 38.462 0.00 0.00 0.00 2.67
86 87 6.322931 AGTCCAATCCCCTTACTTTTTCAAT 58.677 36.000 0.00 0.00 0.00 2.57
87 88 5.711698 AGTCCAATCCCCTTACTTTTTCAA 58.288 37.500 0.00 0.00 0.00 2.69
88 89 5.074515 AGAGTCCAATCCCCTTACTTTTTCA 59.925 40.000 0.00 0.00 0.00 2.69
89 90 5.571285 AGAGTCCAATCCCCTTACTTTTTC 58.429 41.667 0.00 0.00 0.00 2.29
90 91 5.074515 TGAGAGTCCAATCCCCTTACTTTTT 59.925 40.000 0.00 0.00 0.00 1.94
91 92 4.601857 TGAGAGTCCAATCCCCTTACTTTT 59.398 41.667 0.00 0.00 0.00 2.27
92 93 4.175962 TGAGAGTCCAATCCCCTTACTTT 58.824 43.478 0.00 0.00 0.00 2.66
93 94 3.803340 TGAGAGTCCAATCCCCTTACTT 58.197 45.455 0.00 0.00 0.00 2.24
94 95 3.491766 TGAGAGTCCAATCCCCTTACT 57.508 47.619 0.00 0.00 0.00 2.24
95 96 3.745797 GCATGAGAGTCCAATCCCCTTAC 60.746 52.174 0.00 0.00 0.00 2.34
96 97 2.439507 GCATGAGAGTCCAATCCCCTTA 59.560 50.000 0.00 0.00 0.00 2.69
97 98 1.213926 GCATGAGAGTCCAATCCCCTT 59.786 52.381 0.00 0.00 0.00 3.95
98 99 0.842635 GCATGAGAGTCCAATCCCCT 59.157 55.000 0.00 0.00 0.00 4.79
99 100 0.548031 TGCATGAGAGTCCAATCCCC 59.452 55.000 0.00 0.00 0.00 4.81
100 101 2.092753 TCTTGCATGAGAGTCCAATCCC 60.093 50.000 0.00 0.00 0.00 3.85
101 102 3.204526 CTCTTGCATGAGAGTCCAATCC 58.795 50.000 21.89 0.00 38.65 3.01
109 110 5.710513 ATAGCTAGACTCTTGCATGAGAG 57.289 43.478 30.27 21.99 46.82 3.20
110 111 7.885399 TGTATATAGCTAGACTCTTGCATGAGA 59.115 37.037 30.27 11.88 34.89 3.27
111 112 8.049655 TGTATATAGCTAGACTCTTGCATGAG 57.950 38.462 23.98 23.98 34.89 2.90
112 113 8.465201 CATGTATATAGCTAGACTCTTGCATGA 58.535 37.037 13.91 1.92 34.89 3.07
113 114 7.222417 GCATGTATATAGCTAGACTCTTGCATG 59.778 40.741 13.91 15.20 34.89 4.06
114 115 7.123997 AGCATGTATATAGCTAGACTCTTGCAT 59.876 37.037 22.07 8.82 36.73 3.96
115 116 6.435591 AGCATGTATATAGCTAGACTCTTGCA 59.564 38.462 22.07 7.31 36.73 4.08
116 117 6.862209 AGCATGTATATAGCTAGACTCTTGC 58.138 40.000 16.98 16.98 36.73 4.01
117 118 9.703892 AAAAGCATGTATATAGCTAGACTCTTG 57.296 33.333 0.00 2.06 37.70 3.02
120 121 9.796120 CCTAAAAGCATGTATATAGCTAGACTC 57.204 37.037 0.00 0.00 37.70 3.36
121 122 8.254508 GCCTAAAAGCATGTATATAGCTAGACT 58.745 37.037 0.00 0.00 37.70 3.24
122 123 8.254508 AGCCTAAAAGCATGTATATAGCTAGAC 58.745 37.037 0.00 0.00 37.70 2.59
123 124 8.367660 AGCCTAAAAGCATGTATATAGCTAGA 57.632 34.615 0.00 0.00 37.70 2.43
124 125 9.743057 CTAGCCTAAAAGCATGTATATAGCTAG 57.257 37.037 0.00 12.76 37.70 3.42
125 126 9.256228 ACTAGCCTAAAAGCATGTATATAGCTA 57.744 33.333 0.00 0.00 37.70 3.32
126 127 8.140112 ACTAGCCTAAAAGCATGTATATAGCT 57.860 34.615 0.00 0.00 41.03 3.32
127 128 9.303537 GTACTAGCCTAAAAGCATGTATATAGC 57.696 37.037 0.00 0.00 34.23 2.97
133 134 9.893634 TTTATTGTACTAGCCTAAAAGCATGTA 57.106 29.630 0.00 0.00 34.23 2.29
134 135 8.801882 TTTATTGTACTAGCCTAAAAGCATGT 57.198 30.769 0.00 0.00 34.23 3.21
162 163 9.527157 TCTATCTTCTCTCTTTCTCTTTCTTCA 57.473 33.333 0.00 0.00 0.00 3.02
191 192 6.358974 AGGTTGGCTATTACAAAAGCATTT 57.641 33.333 0.00 0.00 42.41 2.32
192 193 6.358974 AAGGTTGGCTATTACAAAAGCATT 57.641 33.333 0.00 0.00 40.61 3.56
193 194 6.435904 TGTAAGGTTGGCTATTACAAAAGCAT 59.564 34.615 0.00 0.00 40.61 3.79
194 195 5.770663 TGTAAGGTTGGCTATTACAAAAGCA 59.229 36.000 0.00 0.00 40.61 3.91
195 196 6.262193 TGTAAGGTTGGCTATTACAAAAGC 57.738 37.500 0.00 0.00 36.69 3.51
196 197 7.088272 GGTTGTAAGGTTGGCTATTACAAAAG 58.912 38.462 8.51 0.00 45.72 2.27
197 198 6.294065 CGGTTGTAAGGTTGGCTATTACAAAA 60.294 38.462 8.51 0.00 45.72 2.44
198 199 5.181622 CGGTTGTAAGGTTGGCTATTACAAA 59.818 40.000 8.51 0.00 45.72 2.83
199 200 4.696402 CGGTTGTAAGGTTGGCTATTACAA 59.304 41.667 4.04 4.04 43.48 2.41
200 201 4.020396 TCGGTTGTAAGGTTGGCTATTACA 60.020 41.667 0.00 0.00 37.57 2.41
201 202 4.330894 GTCGGTTGTAAGGTTGGCTATTAC 59.669 45.833 0.00 0.00 0.00 1.89
202 203 4.020396 TGTCGGTTGTAAGGTTGGCTATTA 60.020 41.667 0.00 0.00 0.00 0.98
203 204 3.244630 TGTCGGTTGTAAGGTTGGCTATT 60.245 43.478 0.00 0.00 0.00 1.73
204 205 2.303600 TGTCGGTTGTAAGGTTGGCTAT 59.696 45.455 0.00 0.00 0.00 2.97
205 206 1.693062 TGTCGGTTGTAAGGTTGGCTA 59.307 47.619 0.00 0.00 0.00 3.93
206 207 0.470766 TGTCGGTTGTAAGGTTGGCT 59.529 50.000 0.00 0.00 0.00 4.75
207 208 1.530323 ATGTCGGTTGTAAGGTTGGC 58.470 50.000 0.00 0.00 0.00 4.52
208 209 5.182380 ACAATAATGTCGGTTGTAAGGTTGG 59.818 40.000 0.00 0.00 33.41 3.77
209 210 6.249035 ACAATAATGTCGGTTGTAAGGTTG 57.751 37.500 0.00 0.00 33.41 3.77
210 211 7.825270 TCATACAATAATGTCGGTTGTAAGGTT 59.175 33.333 1.88 0.00 40.47 3.50
211 212 7.332557 TCATACAATAATGTCGGTTGTAAGGT 58.667 34.615 1.88 0.00 40.47 3.50
212 213 7.494625 ACTCATACAATAATGTCGGTTGTAAGG 59.505 37.037 1.88 0.00 40.47 2.69
213 214 8.420374 ACTCATACAATAATGTCGGTTGTAAG 57.580 34.615 1.88 0.00 40.47 2.34
214 215 9.872721 TTACTCATACAATAATGTCGGTTGTAA 57.127 29.630 1.88 0.00 40.47 2.41
215 216 9.872721 TTTACTCATACAATAATGTCGGTTGTA 57.127 29.630 0.00 0.00 41.09 2.41
216 217 8.780846 TTTACTCATACAATAATGTCGGTTGT 57.219 30.769 0.00 0.00 41.05 3.32
245 246 8.777413 CCGTCATGTCATTTATAGTCATCATTT 58.223 33.333 0.00 0.00 0.00 2.32
246 247 7.933577 ACCGTCATGTCATTTATAGTCATCATT 59.066 33.333 0.00 0.00 0.00 2.57
247 248 7.445121 ACCGTCATGTCATTTATAGTCATCAT 58.555 34.615 0.00 0.00 0.00 2.45
248 249 6.816136 ACCGTCATGTCATTTATAGTCATCA 58.184 36.000 0.00 0.00 0.00 3.07
249 250 7.715265 AACCGTCATGTCATTTATAGTCATC 57.285 36.000 0.00 0.00 0.00 2.92
250 251 7.768582 TGAAACCGTCATGTCATTTATAGTCAT 59.231 33.333 0.00 0.00 0.00 3.06
251 252 7.100409 TGAAACCGTCATGTCATTTATAGTCA 58.900 34.615 0.00 0.00 0.00 3.41
252 253 7.534085 TGAAACCGTCATGTCATTTATAGTC 57.466 36.000 0.00 0.00 0.00 2.59
253 254 9.778741 ATATGAAACCGTCATGTCATTTATAGT 57.221 29.630 0.20 0.00 46.85 2.12
258 259 9.119418 TGATTATATGAAACCGTCATGTCATTT 57.881 29.630 0.20 0.00 46.85 2.32
259 260 8.675705 TGATTATATGAAACCGTCATGTCATT 57.324 30.769 0.20 0.00 46.85 2.57
260 261 8.853077 ATGATTATATGAAACCGTCATGTCAT 57.147 30.769 0.00 0.00 46.85 3.06
261 262 7.930865 TGATGATTATATGAAACCGTCATGTCA 59.069 33.333 0.00 0.00 46.85 3.58
262 263 8.310406 TGATGATTATATGAAACCGTCATGTC 57.690 34.615 0.00 0.00 46.85 3.06
263 264 8.853077 ATGATGATTATATGAAACCGTCATGT 57.147 30.769 0.00 0.00 46.85 3.21
264 265 9.159364 AGATGATGATTATATGAAACCGTCATG 57.841 33.333 0.00 0.00 46.85 3.07
266 267 7.603784 CCAGATGATGATTATATGAAACCGTCA 59.396 37.037 0.00 0.00 41.67 4.35
267 268 7.413438 GCCAGATGATGATTATATGAAACCGTC 60.413 40.741 0.00 0.00 0.00 4.79
268 269 6.372659 GCCAGATGATGATTATATGAAACCGT 59.627 38.462 0.00 0.00 0.00 4.83
269 270 6.596888 AGCCAGATGATGATTATATGAAACCG 59.403 38.462 0.00 0.00 0.00 4.44
270 271 7.934855 AGCCAGATGATGATTATATGAAACC 57.065 36.000 0.00 0.00 0.00 3.27
284 285 9.347240 GCATGGTTAATAATATAGCCAGATGAT 57.653 33.333 0.00 0.00 39.18 2.45
285 286 8.551440 AGCATGGTTAATAATATAGCCAGATGA 58.449 33.333 0.00 0.00 39.18 2.92
286 287 8.743085 AGCATGGTTAATAATATAGCCAGATG 57.257 34.615 0.00 0.00 39.18 2.90
288 289 9.267071 TCTAGCATGGTTAATAATATAGCCAGA 57.733 33.333 1.12 0.00 39.18 3.86
297 298 8.890472 TCAAGGGTATCTAGCATGGTTAATAAT 58.110 33.333 1.12 0.00 0.00 1.28
298 299 8.270137 TCAAGGGTATCTAGCATGGTTAATAA 57.730 34.615 1.12 0.00 0.00 1.40
299 300 7.865530 TCAAGGGTATCTAGCATGGTTAATA 57.134 36.000 1.12 0.00 0.00 0.98
300 301 6.763715 TCAAGGGTATCTAGCATGGTTAAT 57.236 37.500 1.12 0.00 0.00 1.40
301 302 6.101150 ACATCAAGGGTATCTAGCATGGTTAA 59.899 38.462 1.12 0.00 0.00 2.01
302 303 5.606749 ACATCAAGGGTATCTAGCATGGTTA 59.393 40.000 1.12 0.00 0.00 2.85
303 304 4.413520 ACATCAAGGGTATCTAGCATGGTT 59.586 41.667 1.12 0.00 0.00 3.67
304 305 3.976654 ACATCAAGGGTATCTAGCATGGT 59.023 43.478 1.62 1.62 0.00 3.55
305 306 4.630644 ACATCAAGGGTATCTAGCATGG 57.369 45.455 0.00 0.00 0.00 3.66
306 307 6.997655 TCTTACATCAAGGGTATCTAGCATG 58.002 40.000 0.00 0.00 34.76 4.06
307 308 6.295575 GCTCTTACATCAAGGGTATCTAGCAT 60.296 42.308 0.00 0.00 37.04 3.79
308 309 5.011125 GCTCTTACATCAAGGGTATCTAGCA 59.989 44.000 0.00 0.00 37.04 3.49
309 310 5.474825 GCTCTTACATCAAGGGTATCTAGC 58.525 45.833 0.00 0.00 37.04 3.42
310 311 5.336055 CGGCTCTTACATCAAGGGTATCTAG 60.336 48.000 0.00 0.00 37.04 2.43
311 312 4.523173 CGGCTCTTACATCAAGGGTATCTA 59.477 45.833 0.00 0.00 37.04 1.98
316 317 1.207329 GACGGCTCTTACATCAAGGGT 59.793 52.381 0.00 0.00 37.04 4.34
353 354 2.656897 GACGAAGCAATTTTTCTTCCGC 59.343 45.455 0.00 0.00 36.29 5.54
355 356 5.149977 CAGAGACGAAGCAATTTTTCTTCC 58.850 41.667 0.00 0.00 36.29 3.46
374 375 2.105006 TGGAGCAGCTTAAAGCAGAG 57.895 50.000 0.00 0.00 45.56 3.35
377 378 2.958355 ACTTTTGGAGCAGCTTAAAGCA 59.042 40.909 18.37 3.02 45.56 3.91
379 380 3.498397 TCGACTTTTGGAGCAGCTTAAAG 59.502 43.478 17.47 17.47 33.27 1.85
380 381 3.472652 TCGACTTTTGGAGCAGCTTAAA 58.527 40.909 0.00 0.00 0.00 1.52
389 390 2.329379 CTCGGAACTCGACTTTTGGAG 58.671 52.381 0.00 0.00 43.74 3.86
404 406 0.472471 ACAAGTCCAAAAGCCTCGGA 59.528 50.000 0.00 0.00 0.00 4.55
406 408 1.532868 CTCACAAGTCCAAAAGCCTCG 59.467 52.381 0.00 0.00 0.00 4.63
408 410 2.301346 CACTCACAAGTCCAAAAGCCT 58.699 47.619 0.00 0.00 31.71 4.58
411 413 3.941483 AGACACACTCACAAGTCCAAAAG 59.059 43.478 0.00 0.00 31.71 2.27
414 416 3.179443 GAGACACACTCACAAGTCCAA 57.821 47.619 0.00 0.00 44.36 3.53
462 465 5.428457 TCAATTTAAGATAGTGCTCCCCTCA 59.572 40.000 0.00 0.00 0.00 3.86
463 466 5.930135 TCAATTTAAGATAGTGCTCCCCTC 58.070 41.667 0.00 0.00 0.00 4.30
465 468 7.404671 TTTTCAATTTAAGATAGTGCTCCCC 57.595 36.000 0.00 0.00 0.00 4.81
511 515 2.101415 GCTGTTTGGAGCCTTCTTTGTT 59.899 45.455 0.00 0.00 32.35 2.83
643 669 1.077716 GGTTGGTGGAAGGGATCGG 60.078 63.158 0.00 0.00 0.00 4.18
668 694 0.674534 ATCTAGAAGTTAGCCGGCCG 59.325 55.000 26.15 21.04 0.00 6.13
738 796 2.624838 CAATGGCTGAGGTTTGTTGAGT 59.375 45.455 0.00 0.00 0.00 3.41
752 810 0.393402 TGCTGCTCGAATCAATGGCT 60.393 50.000 0.00 0.00 0.00 4.75
905 1411 1.302033 AACAGGCAAGCGGAGAGTG 60.302 57.895 0.00 0.00 0.00 3.51
915 1421 3.276091 CACCGTCGCAACAGGCAA 61.276 61.111 0.00 0.00 45.17 4.52
1042 1591 1.505477 GCCAGGAGAATCGATGCTGC 61.505 60.000 16.84 16.84 35.03 5.25
1085 4027 3.621715 TCCATCACGTATCTATCGATCGG 59.378 47.826 16.41 0.00 0.00 4.18
1178 4791 4.737054 CGGCAGTTTGAGAAATAAGCATT 58.263 39.130 0.00 0.00 0.00 3.56
1191 4804 1.135315 CGAATCCAGCGGCAGTTTG 59.865 57.895 1.45 0.00 0.00 2.93
1198 4811 2.890109 GATGCAGCGAATCCAGCGG 61.890 63.158 0.00 0.00 40.04 5.52
1220 4833 1.532868 GACAACACTGCAGCTAACTGG 59.467 52.381 15.27 0.00 44.63 4.00
1237 4850 0.599558 CTCGGGGTACGTTGAAGACA 59.400 55.000 0.00 0.00 44.69 3.41
1288 4948 2.024588 CTGCACACGCACACCAAC 59.975 61.111 0.00 0.00 45.36 3.77
1289 4949 3.208383 CCTGCACACGCACACCAA 61.208 61.111 0.00 0.00 45.36 3.67
1325 4992 4.430423 GCTTGACGTTGCTCCGCG 62.430 66.667 0.00 0.00 0.00 6.46
1477 5154 6.961554 CACTAGCGAAAATTAAGCAAGTTAGG 59.038 38.462 0.00 0.00 0.00 2.69
1493 5177 1.822990 AGACCGGAAATCACTAGCGAA 59.177 47.619 9.46 0.00 0.00 4.70
1511 5195 7.765819 CACCAAATTCAGACACTGTATATCAGA 59.234 37.037 8.56 0.00 46.27 3.27
1520 5204 4.336433 AGAACACACCAAATTCAGACACTG 59.664 41.667 0.00 0.00 0.00 3.66
1630 5315 0.246635 CGTAGGCACTAGCACCAACT 59.753 55.000 4.56 0.00 44.14 3.16
1648 5336 5.067936 ACTCTCTGTATGGGTATGTTCTTCG 59.932 44.000 0.00 0.00 0.00 3.79
1660 5355 9.021863 GTAATTAAGAAACGACTCTCTGTATGG 57.978 37.037 0.00 0.00 0.00 2.74
1690 5402 8.537049 AACCTAAAACAACAAAGTAACAAACC 57.463 30.769 0.00 0.00 0.00 3.27
1698 5414 4.439563 CCGCAGAACCTAAAACAACAAAGT 60.440 41.667 0.00 0.00 0.00 2.66
1699 5415 4.041723 CCGCAGAACCTAAAACAACAAAG 58.958 43.478 0.00 0.00 0.00 2.77
1742 5470 4.088762 CATCACACCCGCACGCAC 62.089 66.667 0.00 0.00 0.00 5.34
1745 5473 3.118454 GGACATCACACCCGCACG 61.118 66.667 0.00 0.00 0.00 5.34
1751 5479 3.431766 GGTAGGTACATGGACATCACACC 60.432 52.174 10.99 3.74 0.00 4.16
1800 5532 2.485795 GCCCGATAATTTGGCGCCA 61.486 57.895 29.03 29.03 35.08 5.69
1862 5918 5.579511 CCTCTGCAAATAAAAGCCTTCATTG 59.420 40.000 0.00 0.00 0.00 2.82
1931 6000 5.952347 AAAAACCTCGATCCCACTACTAT 57.048 39.130 0.00 0.00 0.00 2.12
1962 6046 9.838339 CCTGACTTGATACCACTATATTTCTTT 57.162 33.333 0.00 0.00 0.00 2.52
1963 6047 8.993424 ACCTGACTTGATACCACTATATTTCTT 58.007 33.333 0.00 0.00 0.00 2.52
2079 7987 2.040330 TGCTGCCAAACGAGCAATT 58.960 47.368 0.00 0.00 42.22 2.32
2109 8017 4.755266 ATTTAGTTCGGGCTGTCTACAT 57.245 40.909 0.00 0.00 0.00 2.29
2136 8070 0.682292 GGCAAAATTCCGGGGACAAA 59.318 50.000 0.00 0.00 0.00 2.83
2139 8073 0.175531 CATGGCAAAATTCCGGGGAC 59.824 55.000 0.00 0.00 0.00 4.46
2141 8075 1.122227 ATCATGGCAAAATTCCGGGG 58.878 50.000 0.00 0.00 0.00 5.73
2232 8170 2.687418 CTTGGCTGGCCGGATAGCAT 62.687 60.000 25.46 0.00 41.63 3.79
2234 8172 2.040009 TACTTGGCTGGCCGGATAGC 62.040 60.000 18.31 18.83 39.42 2.97
2239 8177 3.628646 AAGCTACTTGGCTGGCCGG 62.629 63.158 7.41 7.41 42.24 6.13
2240 8178 2.045926 AAGCTACTTGGCTGGCCG 60.046 61.111 7.14 0.00 42.24 6.13
2382 8326 7.515643 CGAACTAATTTTGTACACCACCTTAG 58.484 38.462 0.00 2.16 0.00 2.18
2386 8330 4.023878 TGCGAACTAATTTTGTACACCACC 60.024 41.667 0.00 0.00 0.00 4.61
2388 8332 4.575236 TGTGCGAACTAATTTTGTACACCA 59.425 37.500 0.00 0.00 38.80 4.17
2620 8575 9.829637 GAAACACGTTGAACATTTTCTTTAATC 57.170 29.630 0.00 0.00 32.36 1.75


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

AutoCloner maintained by Alex Coulton.