Multiple sequence alignment - TraesCS2A01G199700

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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 TraesCS2A01G199700 chr2A 100.000 4971 0 0 1 4971 172218843 172213873 0.000000e+00 9180.0
1 TraesCS2A01G199700 chr2A 90.583 223 21 0 33 255 61973564 61973342 3.760000e-76 296.0
2 TraesCS2A01G199700 chr2D 95.133 3041 80 14 285 3281 161377641 161374625 0.000000e+00 4734.0
3 TraesCS2A01G199700 chr2D 98.213 1063 17 2 3314 4376 161374467 161373407 0.000000e+00 1857.0
4 TraesCS2A01G199700 chr2D 90.728 453 32 7 4524 4971 161367821 161367374 3.310000e-166 595.0
5 TraesCS2A01G199700 chr2D 85.714 56 6 2 4352 4405 563940392 563940447 1.930000e-04 58.4
6 TraesCS2A01G199700 chr2D 96.970 33 0 1 4344 4376 351841510 351841541 3.000000e-03 54.7
7 TraesCS2A01G199700 chr2B 93.639 1682 63 23 3294 4962 217790909 217789259 0.000000e+00 2473.0
8 TraesCS2A01G199700 chr2B 92.390 1774 61 35 285 2005 217794103 217792351 0.000000e+00 2460.0
9 TraesCS2A01G199700 chr2B 96.462 1272 35 2 2010 3281 217792316 217791055 0.000000e+00 2091.0
10 TraesCS2A01G199700 chr2B 87.076 619 57 5 2234 2848 37606301 37606900 0.000000e+00 678.0
11 TraesCS2A01G199700 chr2B 85.276 326 29 8 1684 1995 37605655 37605975 8.030000e-83 318.0
12 TraesCS2A01G199700 chr2B 85.276 326 29 8 1684 1995 130060544 130060864 8.030000e-83 318.0
13 TraesCS2A01G199700 chr2B 84.444 270 23 3 2006 2269 37606038 37606294 1.070000e-61 248.0
14 TraesCS2A01G199700 chr2B 96.970 33 0 1 4344 4376 662194912 662194881 3.000000e-03 54.7
15 TraesCS2A01G199700 chr2B 94.444 36 1 1 4343 4378 783822934 783822900 3.000000e-03 54.7
16 TraesCS2A01G199700 chr2B 100.000 28 0 0 5 32 217794126 217794099 9.000000e-03 52.8
17 TraesCS2A01G199700 chr4B 85.493 1034 85 32 878 1907 314324190 314325162 0.000000e+00 1018.0
18 TraesCS2A01G199700 chr4B 90.300 433 35 5 1479 1907 605510407 605510836 1.210000e-155 560.0
19 TraesCS2A01G199700 chr4B 86.036 444 45 6 2523 2962 97356152 97355722 1.260000e-125 460.0
20 TraesCS2A01G199700 chr4B 88.148 270 24 4 2006 2269 97356817 97356550 1.040000e-81 315.0
21 TraesCS2A01G199700 chr4B 81.851 281 33 8 1728 1995 97357150 97356875 2.330000e-53 220.0
22 TraesCS2A01G199700 chr4B 97.143 35 0 1 4344 4378 433369968 433369935 1.930000e-04 58.4
23 TraesCS2A01G199700 chr5D 88.690 725 57 6 2234 2954 353960862 353960159 0.000000e+00 861.0
24 TraesCS2A01G199700 chr5D 83.114 456 57 12 1100 1545 515118592 515118147 1.000000e-106 398.0
25 TraesCS2A01G199700 chr5D 87.500 96 7 1 4415 4505 549650171 549650076 6.810000e-19 106.0
26 TraesCS2A01G199700 chr5B 86.333 739 75 8 2234 2967 111271923 111272640 0.000000e+00 782.0
27 TraesCS2A01G199700 chr5B 85.250 400 47 6 1149 1545 647944227 647943837 7.750000e-108 401.0
28 TraesCS2A01G199700 chr5B 89.209 278 24 2 1998 2269 111271639 111271916 4.770000e-90 342.0
29 TraesCS2A01G199700 chr5B 84.661 339 31 12 1670 1995 111271255 111271585 8.030000e-83 318.0
30 TraesCS2A01G199700 chr5B 89.030 237 23 3 20 256 463201245 463201012 1.750000e-74 291.0
31 TraesCS2A01G199700 chr5B 90.455 220 21 0 30 249 477555897 477556116 1.750000e-74 291.0
32 TraesCS2A01G199700 chr5B 97.059 34 0 1 4343 4376 273244390 273244422 6.950000e-04 56.5
33 TraesCS2A01G199700 chr1B 87.261 628 57 6 2234 2857 233942051 233941443 0.000000e+00 695.0
34 TraesCS2A01G199700 chr1B 91.150 226 20 0 30 255 403528860 403528635 1.740000e-79 307.0
35 TraesCS2A01G199700 chr1B 84.356 326 32 8 1684 1995 233942696 233942376 8.090000e-78 302.0
36 TraesCS2A01G199700 chr1B 89.655 87 4 1 4415 4496 546953952 546954038 6.810000e-19 106.0
37 TraesCS2A01G199700 chr6B 87.122 629 56 7 2234 2857 627911535 627910927 0.000000e+00 689.0
38 TraesCS2A01G199700 chr6B 86.804 629 58 8 2234 2857 627681086 627680478 0.000000e+00 678.0
39 TraesCS2A01G199700 chr6B 83.764 271 24 3 2006 2269 627911799 627911542 6.430000e-59 239.0
40 TraesCS2A01G199700 chr6B 83.395 271 25 3 2006 2269 627681350 627681093 2.990000e-57 233.0
41 TraesCS2A01G199700 chr6B 89.205 176 14 1 2764 2934 475722608 475722433 1.080000e-51 215.0
42 TraesCS2A01G199700 chr6B 94.444 72 3 1 1683 1753 475722942 475722871 5.260000e-20 110.0
43 TraesCS2A01G199700 chr5A 83.261 460 61 7 1094 1545 643332952 643332501 4.630000e-110 409.0
44 TraesCS2A01G199700 chr5A 89.137 313 16 11 2048 2343 544166911 544167222 1.690000e-99 374.0
45 TraesCS2A01G199700 chr5A 86.667 90 7 1 4421 4505 11283822 11283733 1.470000e-15 95.3
46 TraesCS2A01G199700 chr3B 91.000 300 20 5 2048 2343 748431653 748431949 1.000000e-106 398.0
47 TraesCS2A01G199700 chr3B 85.583 326 28 8 1684 1995 162678256 162678576 1.730000e-84 324.0
48 TraesCS2A01G199700 chr3B 84.663 326 31 8 1684 1995 124056235 124055915 1.740000e-79 307.0
49 TraesCS2A01G199700 chr3B 91.031 223 19 1 33 255 795224533 795224312 2.910000e-77 300.0
50 TraesCS2A01G199700 chr7A 88.818 313 17 11 2048 2343 59611071 59610760 7.860000e-98 368.0
51 TraesCS2A01G199700 chr7A 89.474 228 24 0 28 255 676396880 676396653 6.300000e-74 289.0
52 TraesCS2A01G199700 chr7A 86.641 262 29 5 30 285 638749630 638749891 8.140000e-73 285.0
53 TraesCS2A01G199700 chr3D 83.587 329 54 0 1215 1543 457018927 457019255 4.830000e-80 309.0
54 TraesCS2A01G199700 chr3D 85.714 98 7 3 4415 4505 8970024 8969927 4.100000e-16 97.1
55 TraesCS2A01G199700 chr3D 86.022 93 6 2 4415 4500 29699632 29699540 5.300000e-15 93.5
56 TraesCS2A01G199700 chr1A 82.849 344 57 2 1201 1543 487741422 487741080 1.740000e-79 307.0
57 TraesCS2A01G199700 chr1A 90.135 223 22 0 33 255 557124580 557124358 1.750000e-74 291.0
58 TraesCS2A01G199700 chr1A 85.556 90 8 3 4410 4494 95850366 95850277 6.850000e-14 89.8
59 TraesCS2A01G199700 chr1D 82.558 344 58 2 1201 1543 388651047 388650705 8.090000e-78 302.0
60 TraesCS2A01G199700 chr3A 90.909 220 20 0 30 249 343800975 343801194 3.760000e-76 296.0
61 TraesCS2A01G199700 chr7B 92.000 75 5 1 4422 4496 137526331 137526404 2.450000e-18 104.0
62 TraesCS2A01G199700 chr7B 100.000 32 0 0 4351 4382 672525137 672525168 5.370000e-05 60.2
63 TraesCS2A01G199700 chr7D 88.750 80 5 3 4415 4494 613714743 613714668 1.470000e-15 95.3
64 TraesCS2A01G199700 chr7D 97.059 34 1 0 4352 4385 180681951 180681918 1.930000e-04 58.4
65 TraesCS2A01G199700 chr6D 92.857 42 0 3 4340 4381 63730182 63730144 1.930000e-04 58.4
66 TraesCS2A01G199700 chr6D 96.970 33 0 1 4344 4376 68386312 68386281 3.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G199700 chr2A 172213873 172218843 4970 True 9180.000000 9180 100.000000 1 4971 1 chr2A.!!$R2 4970
1 TraesCS2A01G199700 chr2D 161373407 161377641 4234 True 3295.500000 4734 96.673000 285 4376 2 chr2D.!!$R2 4091
2 TraesCS2A01G199700 chr2B 217789259 217794126 4867 True 1769.200000 2473 95.622750 5 4962 4 chr2B.!!$R3 4957
3 TraesCS2A01G199700 chr2B 37605655 37606900 1245 False 414.666667 678 85.598667 1684 2848 3 chr2B.!!$F2 1164
4 TraesCS2A01G199700 chr4B 314324190 314325162 972 False 1018.000000 1018 85.493000 878 1907 1 chr4B.!!$F1 1029
5 TraesCS2A01G199700 chr4B 97355722 97357150 1428 True 331.666667 460 85.345000 1728 2962 3 chr4B.!!$R2 1234
6 TraesCS2A01G199700 chr5D 353960159 353960862 703 True 861.000000 861 88.690000 2234 2954 1 chr5D.!!$R1 720
7 TraesCS2A01G199700 chr5B 111271255 111272640 1385 False 480.666667 782 86.734333 1670 2967 3 chr5B.!!$F3 1297
8 TraesCS2A01G199700 chr1B 233941443 233942696 1253 True 498.500000 695 85.808500 1684 2857 2 chr1B.!!$R2 1173
9 TraesCS2A01G199700 chr6B 627910927 627911799 872 True 464.000000 689 85.443000 2006 2857 2 chr6B.!!$R3 851
10 TraesCS2A01G199700 chr6B 627680478 627681350 872 True 455.500000 678 85.099500 2006 2857 2 chr6B.!!$R2 851

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
638 643 0.243095 GAAGAAGGCAAGCAAGGCTG 59.757 55.000 5.27 0.0 44.47 4.85 F
1110 1177 1.000771 GAAGCCCAACCCCTTCTCC 60.001 63.158 0.00 0.0 35.67 3.71 F
2168 2314 0.037303 ACATGGCTCCAGAGGTGTTG 59.963 55.000 0.00 0.0 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1556 1623 0.922626 AGAGGAAGGAATCAAGGGGC 59.077 55.000 0.0 0.0 0.0 5.80 R
2192 2338 1.271597 ACTCCTGCACTCCAAACATCC 60.272 52.381 0.0 0.0 0.0 3.51 R
3980 4441 1.164411 TCACAACTTGCCTATTGCGG 58.836 50.000 0.0 0.0 45.6 5.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 5.008712 CAGAGCAGCACATGATGTTGATTAT 59.991 40.000 0.00 0.00 38.38 1.28
28 29 5.008712 AGAGCAGCACATGATGTTGATTATG 59.991 40.000 0.00 0.00 38.38 1.90
29 30 4.885325 AGCAGCACATGATGTTGATTATGA 59.115 37.500 0.00 0.00 41.87 2.15
30 31 5.008712 AGCAGCACATGATGTTGATTATGAG 59.991 40.000 0.00 0.00 41.87 2.90
31 32 5.008316 GCAGCACATGATGTTGATTATGAGA 59.992 40.000 0.00 0.00 41.87 3.27
32 33 6.427974 CAGCACATGATGTTGATTATGAGAC 58.572 40.000 0.00 0.00 41.87 3.36
33 34 6.260271 CAGCACATGATGTTGATTATGAGACT 59.740 38.462 0.00 0.00 41.87 3.24
34 35 6.260271 AGCACATGATGTTGATTATGAGACTG 59.740 38.462 0.00 0.00 31.48 3.51
35 36 6.427974 CACATGATGTTGATTATGAGACTGC 58.572 40.000 0.00 0.00 31.48 4.40
36 37 5.530171 ACATGATGTTGATTATGAGACTGCC 59.470 40.000 0.00 0.00 31.48 4.85
37 38 4.454678 TGATGTTGATTATGAGACTGCCC 58.545 43.478 0.00 0.00 0.00 5.36
38 39 2.905075 TGTTGATTATGAGACTGCCCG 58.095 47.619 0.00 0.00 0.00 6.13
39 40 2.236146 TGTTGATTATGAGACTGCCCGT 59.764 45.455 0.00 0.00 0.00 5.28
40 41 3.449377 TGTTGATTATGAGACTGCCCGTA 59.551 43.478 0.00 0.00 0.00 4.02
41 42 4.081365 TGTTGATTATGAGACTGCCCGTAA 60.081 41.667 0.00 0.00 0.00 3.18
42 43 4.955811 TGATTATGAGACTGCCCGTAAT 57.044 40.909 0.00 0.00 0.00 1.89
43 44 6.183360 TGTTGATTATGAGACTGCCCGTAATA 60.183 38.462 0.00 0.00 0.00 0.98
44 45 6.025749 TGATTATGAGACTGCCCGTAATAG 57.974 41.667 0.00 0.00 0.00 1.73
45 46 4.866508 TTATGAGACTGCCCGTAATAGG 57.133 45.455 0.00 0.00 0.00 2.57
46 47 2.447408 TGAGACTGCCCGTAATAGGA 57.553 50.000 0.00 0.00 0.00 2.94
47 48 2.307768 TGAGACTGCCCGTAATAGGAG 58.692 52.381 0.00 0.00 0.00 3.69
48 49 2.308690 GAGACTGCCCGTAATAGGAGT 58.691 52.381 0.00 0.00 0.00 3.85
49 50 3.117776 TGAGACTGCCCGTAATAGGAGTA 60.118 47.826 0.00 0.00 0.00 2.59
50 51 4.080687 GAGACTGCCCGTAATAGGAGTAT 58.919 47.826 0.00 0.00 0.00 2.12
51 52 4.481072 AGACTGCCCGTAATAGGAGTATT 58.519 43.478 0.00 0.00 33.25 1.89
52 53 5.638133 AGACTGCCCGTAATAGGAGTATTA 58.362 41.667 0.00 0.00 31.04 0.98
53 54 6.254522 AGACTGCCCGTAATAGGAGTATTAT 58.745 40.000 0.00 0.00 34.34 1.28
54 55 7.408543 AGACTGCCCGTAATAGGAGTATTATA 58.591 38.462 0.00 0.00 34.34 0.98
55 56 7.892241 AGACTGCCCGTAATAGGAGTATTATAA 59.108 37.037 0.00 0.00 34.34 0.98
56 57 8.064336 ACTGCCCGTAATAGGAGTATTATAAG 57.936 38.462 0.00 0.00 34.34 1.73
57 58 7.673082 ACTGCCCGTAATAGGAGTATTATAAGT 59.327 37.037 0.00 0.00 34.34 2.24
58 59 9.182214 CTGCCCGTAATAGGAGTATTATAAGTA 57.818 37.037 0.00 0.00 34.34 2.24
59 60 9.182214 TGCCCGTAATAGGAGTATTATAAGTAG 57.818 37.037 0.00 0.00 34.34 2.57
60 61 9.183368 GCCCGTAATAGGAGTATTATAAGTAGT 57.817 37.037 0.00 0.00 34.34 2.73
80 81 7.820648 AGTAGTATTATGCATGCCAATTAAGC 58.179 34.615 16.68 6.74 0.00 3.09
81 82 6.653526 AGTATTATGCATGCCAATTAAGCA 57.346 33.333 16.68 4.92 45.94 3.91
82 83 7.053316 AGTATTATGCATGCCAATTAAGCAA 57.947 32.000 16.68 0.00 44.83 3.91
83 84 7.673180 AGTATTATGCATGCCAATTAAGCAAT 58.327 30.769 16.68 0.00 44.83 3.56
84 85 8.152246 AGTATTATGCATGCCAATTAAGCAATT 58.848 29.630 16.68 0.00 44.83 2.32
85 86 7.811117 ATTATGCATGCCAATTAAGCAATTT 57.189 28.000 16.68 0.00 44.83 1.82
86 87 7.627298 TTATGCATGCCAATTAAGCAATTTT 57.373 28.000 16.68 0.00 44.83 1.82
87 88 5.298197 TGCATGCCAATTAAGCAATTTTG 57.702 34.783 16.68 2.45 44.83 2.44
88 89 5.001874 TGCATGCCAATTAAGCAATTTTGA 58.998 33.333 16.68 0.00 44.83 2.69
89 90 5.648526 TGCATGCCAATTAAGCAATTTTGAT 59.351 32.000 16.68 0.00 44.83 2.57
90 91 5.968848 GCATGCCAATTAAGCAATTTTGATG 59.031 36.000 6.36 0.93 44.83 3.07
91 92 6.183360 GCATGCCAATTAAGCAATTTTGATGA 60.183 34.615 6.36 0.00 44.83 2.92
92 93 6.971527 TGCCAATTAAGCAATTTTGATGAG 57.028 33.333 0.02 0.00 37.28 2.90
93 94 6.699366 TGCCAATTAAGCAATTTTGATGAGA 58.301 32.000 0.02 0.00 37.28 3.27
94 95 7.332557 TGCCAATTAAGCAATTTTGATGAGAT 58.667 30.769 0.02 0.00 37.28 2.75
95 96 7.279090 TGCCAATTAAGCAATTTTGATGAGATG 59.721 33.333 0.02 0.00 37.28 2.90
96 97 7.493320 GCCAATTAAGCAATTTTGATGAGATGA 59.507 33.333 0.00 0.00 31.82 2.92
97 98 8.814235 CCAATTAAGCAATTTTGATGAGATGAC 58.186 33.333 0.00 0.00 31.82 3.06
98 99 9.361315 CAATTAAGCAATTTTGATGAGATGACA 57.639 29.630 0.00 0.00 31.82 3.58
100 101 8.920509 TTAAGCAATTTTGATGAGATGACATG 57.079 30.769 0.00 0.00 0.00 3.21
101 102 6.769134 AGCAATTTTGATGAGATGACATGA 57.231 33.333 0.00 0.00 0.00 3.07
102 103 7.165460 AGCAATTTTGATGAGATGACATGAA 57.835 32.000 0.00 0.00 0.00 2.57
103 104 7.608153 AGCAATTTTGATGAGATGACATGAAA 58.392 30.769 0.00 0.00 33.23 2.69
104 105 8.258007 AGCAATTTTGATGAGATGACATGAAAT 58.742 29.630 0.00 0.00 34.56 2.17
105 106 8.879759 GCAATTTTGATGAGATGACATGAAATT 58.120 29.630 0.00 0.00 34.56 1.82
129 130 8.627208 TTAAATGAAGAAAGAGATGCTTGAGT 57.373 30.769 0.00 0.00 36.80 3.41
130 131 9.725019 TTAAATGAAGAAAGAGATGCTTGAGTA 57.275 29.630 0.00 0.00 36.80 2.59
131 132 8.804912 AAATGAAGAAAGAGATGCTTGAGTAT 57.195 30.769 0.00 0.00 36.80 2.12
132 133 8.436046 AATGAAGAAAGAGATGCTTGAGTATC 57.564 34.615 1.38 1.38 36.80 2.24
178 179 7.503521 TTAAATGATGTGCTACTTTGTGTCA 57.496 32.000 0.00 0.00 0.00 3.58
179 180 6.579666 AAATGATGTGCTACTTTGTGTCAT 57.420 33.333 0.00 0.00 0.00 3.06
180 181 5.556355 ATGATGTGCTACTTTGTGTCATG 57.444 39.130 0.00 0.00 0.00 3.07
181 182 3.189080 TGATGTGCTACTTTGTGTCATGC 59.811 43.478 0.00 0.00 0.00 4.06
182 183 2.570135 TGTGCTACTTTGTGTCATGCA 58.430 42.857 0.00 0.00 0.00 3.96
183 184 3.148412 TGTGCTACTTTGTGTCATGCAT 58.852 40.909 0.00 0.00 34.18 3.96
184 185 3.058085 TGTGCTACTTTGTGTCATGCATG 60.058 43.478 21.07 21.07 34.18 4.06
185 186 2.488937 TGCTACTTTGTGTCATGCATGG 59.511 45.455 25.97 10.76 0.00 3.66
186 187 2.489329 GCTACTTTGTGTCATGCATGGT 59.511 45.455 25.97 15.83 0.00 3.55
187 188 3.689161 GCTACTTTGTGTCATGCATGGTA 59.311 43.478 25.97 16.09 0.00 3.25
188 189 4.155826 GCTACTTTGTGTCATGCATGGTAA 59.844 41.667 25.97 13.00 0.00 2.85
189 190 5.163622 GCTACTTTGTGTCATGCATGGTAAT 60.164 40.000 25.97 7.06 0.00 1.89
190 191 6.038161 GCTACTTTGTGTCATGCATGGTAATA 59.962 38.462 25.97 3.72 0.00 0.98
191 192 6.832520 ACTTTGTGTCATGCATGGTAATAA 57.167 33.333 25.97 13.13 0.00 1.40
192 193 7.225784 ACTTTGTGTCATGCATGGTAATAAA 57.774 32.000 25.97 18.49 0.00 1.40
193 194 7.839907 ACTTTGTGTCATGCATGGTAATAAAT 58.160 30.769 25.97 4.83 0.00 1.40
194 195 8.965819 ACTTTGTGTCATGCATGGTAATAAATA 58.034 29.630 25.97 0.55 0.00 1.40
195 196 9.970395 CTTTGTGTCATGCATGGTAATAAATAT 57.030 29.630 25.97 0.00 0.00 1.28
251 252 8.707938 TGCATTACAGATGTAGTATCATATGC 57.292 34.615 13.04 13.04 39.65 3.14
252 253 8.534496 TGCATTACAGATGTAGTATCATATGCT 58.466 33.333 17.61 0.00 39.65 3.79
259 260 9.283420 CAGATGTAGTATCATATGCTAGAAACG 57.717 37.037 0.00 0.00 31.88 3.60
260 261 9.232473 AGATGTAGTATCATATGCTAGAAACGA 57.768 33.333 0.00 0.00 0.00 3.85
261 262 9.497030 GATGTAGTATCATATGCTAGAAACGAG 57.503 37.037 0.00 0.00 0.00 4.18
262 263 8.617290 TGTAGTATCATATGCTAGAAACGAGA 57.383 34.615 0.00 0.00 0.00 4.04
263 264 9.232473 TGTAGTATCATATGCTAGAAACGAGAT 57.768 33.333 0.00 0.00 0.00 2.75
266 267 9.456147 AGTATCATATGCTAGAAACGAGATACT 57.544 33.333 13.65 13.65 40.18 2.12
267 268 9.710979 GTATCATATGCTAGAAACGAGATACTC 57.289 37.037 0.00 0.00 34.99 2.59
268 269 7.987750 TCATATGCTAGAAACGAGATACTCT 57.012 36.000 0.00 0.00 0.00 3.24
269 270 8.397575 TCATATGCTAGAAACGAGATACTCTT 57.602 34.615 0.00 0.00 0.00 2.85
270 271 8.508062 TCATATGCTAGAAACGAGATACTCTTC 58.492 37.037 0.00 0.00 0.00 2.87
271 272 5.158101 TGCTAGAAACGAGATACTCTTCG 57.842 43.478 0.00 0.00 0.00 3.79
272 273 4.634883 TGCTAGAAACGAGATACTCTTCGT 59.365 41.667 0.00 0.00 40.76 3.85
274 275 6.314648 TGCTAGAAACGAGATACTCTTCGTTA 59.685 38.462 11.93 0.00 46.13 3.18
275 276 6.628461 GCTAGAAACGAGATACTCTTCGTTAC 59.372 42.308 11.93 0.00 46.13 2.50
276 277 6.492007 AGAAACGAGATACTCTTCGTTACA 57.508 37.500 11.93 0.00 46.13 2.41
277 278 6.906659 AGAAACGAGATACTCTTCGTTACAA 58.093 36.000 11.93 0.00 46.13 2.41
278 279 6.800892 AGAAACGAGATACTCTTCGTTACAAC 59.199 38.462 11.93 5.72 46.13 3.32
279 280 4.979388 ACGAGATACTCTTCGTTACAACC 58.021 43.478 0.00 0.00 35.08 3.77
280 281 4.456911 ACGAGATACTCTTCGTTACAACCA 59.543 41.667 0.00 0.00 35.08 3.67
281 282 5.029014 CGAGATACTCTTCGTTACAACCAG 58.971 45.833 0.00 0.00 0.00 4.00
282 283 4.745649 AGATACTCTTCGTTACAACCAGC 58.254 43.478 0.00 0.00 0.00 4.85
283 284 2.165319 ACTCTTCGTTACAACCAGCC 57.835 50.000 0.00 0.00 0.00 4.85
346 347 7.540745 CGGTGGGATTAAATGTTTCTTTTGTAG 59.459 37.037 0.00 0.00 0.00 2.74
347 348 8.364894 GGTGGGATTAAATGTTTCTTTTGTAGT 58.635 33.333 0.00 0.00 0.00 2.73
406 407 4.271533 ACAGCACAAAAATTTGCACAGATG 59.728 37.500 5.82 5.64 41.79 2.90
418 419 3.275999 TGCACAGATGATGGTTGATGAG 58.724 45.455 0.00 0.00 0.00 2.90
419 420 3.054948 TGCACAGATGATGGTTGATGAGA 60.055 43.478 0.00 0.00 0.00 3.27
422 423 5.123936 CACAGATGATGGTTGATGAGACAT 58.876 41.667 0.00 0.00 0.00 3.06
428 429 8.900781 AGATGATGGTTGATGAGACATTTTAAG 58.099 33.333 0.00 0.00 0.00 1.85
499 501 0.534412 CGCAGTCCCTTGATCACTCT 59.466 55.000 0.00 0.00 0.00 3.24
516 518 2.108425 ACTCTCCCAAAAAGTTCTCCCC 59.892 50.000 0.00 0.00 0.00 4.81
517 519 2.108250 CTCTCCCAAAAAGTTCTCCCCA 59.892 50.000 0.00 0.00 0.00 4.96
518 520 2.516277 TCTCCCAAAAAGTTCTCCCCAA 59.484 45.455 0.00 0.00 0.00 4.12
559 564 1.355971 ACAAAGCCGCGTAGTACATG 58.644 50.000 4.92 0.00 0.00 3.21
564 569 2.690786 AGCCGCGTAGTACATGAAAAA 58.309 42.857 4.92 0.00 0.00 1.94
565 570 2.414138 AGCCGCGTAGTACATGAAAAAC 59.586 45.455 4.92 0.00 0.00 2.43
630 635 4.061596 AGAAAACGAGAGAAGAAGGCAAG 58.938 43.478 0.00 0.00 0.00 4.01
631 636 1.802069 AACGAGAGAAGAAGGCAAGC 58.198 50.000 0.00 0.00 0.00 4.01
632 637 0.681733 ACGAGAGAAGAAGGCAAGCA 59.318 50.000 0.00 0.00 0.00 3.91
634 639 1.731160 CGAGAGAAGAAGGCAAGCAAG 59.269 52.381 0.00 0.00 0.00 4.01
635 640 2.083002 GAGAGAAGAAGGCAAGCAAGG 58.917 52.381 0.00 0.00 0.00 3.61
636 641 0.525311 GAGAAGAAGGCAAGCAAGGC 59.475 55.000 0.00 0.00 0.00 4.35
638 643 0.243095 GAAGAAGGCAAGCAAGGCTG 59.757 55.000 5.27 0.00 44.47 4.85
792 844 1.087771 GTCTACACCAAATCCCCGCG 61.088 60.000 0.00 0.00 0.00 6.46
816 868 2.021318 TTTAACCACCCCACCCCACC 62.021 60.000 0.00 0.00 0.00 4.61
905 967 1.075970 GATTTGGCCCCTTCCCCTC 60.076 63.158 0.00 0.00 0.00 4.30
906 968 2.589610 GATTTGGCCCCTTCCCCTCC 62.590 65.000 0.00 0.00 0.00 4.30
923 990 2.187424 CCTGCTCTGCTCTGCTCC 59.813 66.667 0.00 0.00 0.00 4.70
1110 1177 1.000771 GAAGCCCAACCCCTTCTCC 60.001 63.158 0.00 0.00 35.67 3.71
1548 1615 2.262915 GAGGTCGTGCAGGTGAGG 59.737 66.667 6.26 0.00 0.00 3.86
1556 1623 4.051922 GTCGTGCAGGTGAGGATAAATAG 58.948 47.826 6.26 0.00 0.00 1.73
1574 1641 0.922626 AGCCCCTTGATTCCTTCCTC 59.077 55.000 0.00 0.00 0.00 3.71
1615 1683 3.490759 CACACTCACGGGATGCGC 61.491 66.667 0.00 0.00 0.00 6.09
1635 1703 2.543012 GCTCATTCTGTGATGTGATCCG 59.457 50.000 0.00 0.00 35.97 4.18
1642 1710 2.588877 GATGTGATCCGCCGTGGG 60.589 66.667 0.00 0.00 38.76 4.61
1659 1727 3.692101 CGTGGGAATATTTGTTGGCTACA 59.308 43.478 0.00 0.00 34.12 2.74
1675 1743 3.003068 GGCTACATGTCACATGATTCTGC 59.997 47.826 24.98 17.49 0.00 4.26
1681 1749 4.806640 TGTCACATGATTCTGCTGTCTA 57.193 40.909 0.00 0.00 0.00 2.59
1809 1881 3.564644 TGGTAGCAGTAGTTAGATCGCTC 59.435 47.826 0.00 0.00 0.00 5.03
1830 1903 3.699038 TCCAACTTCCCTTTTTGTCTGTG 59.301 43.478 0.00 0.00 0.00 3.66
1945 2027 1.858458 GCAAACAAGAAAGAAACCGCC 59.142 47.619 0.00 0.00 0.00 6.13
1947 2029 1.385528 AACAAGAAAGAAACCGCCGT 58.614 45.000 0.00 0.00 0.00 5.68
2114 2260 4.494199 GCTAATTGTTCGTGATGTGTAGGC 60.494 45.833 0.00 0.00 0.00 3.93
2124 2270 0.606604 ATGTGTAGGCGAACGGTTCT 59.393 50.000 17.94 3.10 0.00 3.01
2168 2314 0.037303 ACATGGCTCCAGAGGTGTTG 59.963 55.000 0.00 0.00 0.00 3.33
2192 2338 3.054802 AGAGAAACTATGGCCAAGAGGTG 60.055 47.826 10.96 0.00 37.19 4.00
2237 2426 5.705609 TTCTTTACATCCTTCTTTGTGGC 57.294 39.130 0.00 0.00 0.00 5.01
2376 2566 1.880819 CTGCACAAAGGGGCCATGTC 61.881 60.000 4.39 2.89 0.00 3.06
2377 2567 2.649129 GCACAAAGGGGCCATGTCC 61.649 63.158 4.39 0.00 0.00 4.02
2378 2568 1.077265 CACAAAGGGGCCATGTCCT 59.923 57.895 4.39 0.00 34.29 3.85
2379 2569 0.542702 CACAAAGGGGCCATGTCCTT 60.543 55.000 4.39 4.91 44.53 3.36
2380 2570 1.080638 ACAAAGGGGCCATGTCCTTA 58.919 50.000 11.02 0.00 42.06 2.69
2381 2571 1.272480 ACAAAGGGGCCATGTCCTTAC 60.272 52.381 11.02 0.00 42.06 2.34
2382 2572 1.005924 CAAAGGGGCCATGTCCTTACT 59.994 52.381 11.02 0.00 42.06 2.24
2383 2573 1.382914 AAGGGGCCATGTCCTTACTT 58.617 50.000 9.10 2.28 41.19 2.24
2384 2574 2.280308 AGGGGCCATGTCCTTACTTA 57.720 50.000 4.39 0.00 0.00 2.24
2397 2587 5.413833 TGTCCTTACTTAGTCACCTTCTACG 59.586 44.000 0.00 0.00 0.00 3.51
2421 2611 7.222031 ACGCTGAAGTTTTGTTTTCCTTATTTC 59.778 33.333 0.00 0.00 0.00 2.17
2629 2944 7.334421 GTCTCAGATAATGCAAAAGACCTTGTA 59.666 37.037 0.00 0.00 0.00 2.41
2828 3146 2.624364 TGCATTGCTTGTGTCTCATGTT 59.376 40.909 10.49 0.00 0.00 2.71
2895 3215 6.515272 TTAAGAAGGCTCCAAATGTCAATC 57.485 37.500 0.00 0.00 0.00 2.67
3022 3342 5.700722 TCACGTTAGACTTGCTTTCTAGA 57.299 39.130 0.00 0.00 0.00 2.43
3163 3483 6.409524 AATTTTGATGAACTGAAGCTTGGA 57.590 33.333 2.10 0.00 0.00 3.53
3281 3601 9.736023 CTTTTGCAACTCTTTGTTATTAGACTT 57.264 29.630 0.00 0.00 37.07 3.01
3283 3603 7.801716 TGCAACTCTTTGTTATTAGACTTGT 57.198 32.000 0.00 0.00 37.07 3.16
3285 3605 9.332502 TGCAACTCTTTGTTATTAGACTTGTAA 57.667 29.630 0.00 0.00 37.07 2.41
3312 3765 7.231925 GGTAACTCACCCCTCTTAAATTTCAAA 59.768 37.037 0.00 0.00 42.07 2.69
3397 3850 6.770746 ATGATCATTTAGCATTAGATGGGC 57.229 37.500 1.18 0.00 26.62 5.36
3569 4022 1.466360 GGCAATGACGAACATCTGCAC 60.466 52.381 21.01 13.87 40.81 4.57
3779 4240 7.613022 TCCTTTTGATTGCTATCATTTGACTCT 59.387 33.333 11.66 0.00 40.37 3.24
4286 4747 6.030548 TGTTTTGTTCATCTGTTTGGTTGA 57.969 33.333 0.00 0.00 0.00 3.18
4350 4811 9.651718 GACAGCTTAATTCCTAATAAAATCACG 57.348 33.333 0.00 0.00 0.00 4.35
4376 4837 2.163613 CCCTCCGTTCCAAAATAAGTGC 59.836 50.000 0.00 0.00 0.00 4.40
4409 4870 8.474025 ACAGACAATTTTGAACTAAAACCATGA 58.526 29.630 0.00 0.00 40.80 3.07
4418 4879 8.514330 TTGAACTAAAACCATGACACTTACTT 57.486 30.769 0.00 0.00 0.00 2.24
4424 4885 2.233922 ACCATGACACTTACTTCCTCCG 59.766 50.000 0.00 0.00 0.00 4.63
4428 4889 5.475719 CATGACACTTACTTCCTCCGTAAA 58.524 41.667 0.00 0.00 0.00 2.01
4429 4890 5.534207 TGACACTTACTTCCTCCGTAAAA 57.466 39.130 0.00 0.00 0.00 1.52
4568 5048 8.783903 TGTAAGTATTGGGAGGGTGTATTATTT 58.216 33.333 0.00 0.00 0.00 1.40
4571 5051 5.869649 ATTGGGAGGGTGTATTATTTTGC 57.130 39.130 0.00 0.00 0.00 3.68
4572 5052 4.323569 TGGGAGGGTGTATTATTTTGCA 57.676 40.909 0.00 0.00 0.00 4.08
4573 5053 4.678256 TGGGAGGGTGTATTATTTTGCAA 58.322 39.130 0.00 0.00 0.00 4.08
4574 5054 4.709397 TGGGAGGGTGTATTATTTTGCAAG 59.291 41.667 0.00 0.00 0.00 4.01
4575 5055 4.709886 GGGAGGGTGTATTATTTTGCAAGT 59.290 41.667 0.00 0.00 0.00 3.16
4576 5056 5.889289 GGGAGGGTGTATTATTTTGCAAGTA 59.111 40.000 0.00 0.00 0.00 2.24
4577 5057 6.549736 GGGAGGGTGTATTATTTTGCAAGTAT 59.450 38.462 0.00 0.13 0.00 2.12
4578 5058 7.255486 GGGAGGGTGTATTATTTTGCAAGTATC 60.255 40.741 0.00 0.00 0.00 2.24
4579 5059 7.284489 GGAGGGTGTATTATTTTGCAAGTATCA 59.716 37.037 0.00 0.00 0.00 2.15
4580 5060 8.766994 AGGGTGTATTATTTTGCAAGTATCAT 57.233 30.769 0.00 0.00 0.00 2.45
4581 5061 9.200817 AGGGTGTATTATTTTGCAAGTATCATT 57.799 29.630 0.00 0.00 0.00 2.57
4582 5062 9.248291 GGGTGTATTATTTTGCAAGTATCATTG 57.752 33.333 0.00 0.00 0.00 2.82
4583 5063 9.801873 GGTGTATTATTTTGCAAGTATCATTGT 57.198 29.630 0.00 0.00 32.56 2.71
4589 5069 9.679661 TTATTTTGCAAGTATCATTGTAGAGGA 57.320 29.630 0.00 0.00 32.56 3.71
4590 5070 8.757982 ATTTTGCAAGTATCATTGTAGAGGAT 57.242 30.769 0.00 0.00 32.68 3.24
4591 5071 7.792374 TTTGCAAGTATCATTGTAGAGGATC 57.208 36.000 0.00 0.00 30.22 3.36
4665 5145 0.249784 ATGATAGCTGAGCACGCTGG 60.250 55.000 7.39 0.00 38.38 4.85
4676 5156 1.607148 AGCACGCTGGGTTTACTTTTC 59.393 47.619 0.00 0.00 0.00 2.29
4683 5164 2.223745 TGGGTTTACTTTTCGAGTGCC 58.776 47.619 0.00 0.00 39.48 5.01
4697 5178 2.853542 TGCCCAGAGCCTGTTCCA 60.854 61.111 2.18 0.00 42.71 3.53
4726 5207 0.452987 CCAGAAATGGTCCGTGCATG 59.547 55.000 0.00 0.00 0.00 4.06
4798 5279 4.261322 CCGGTCAAGAATCTATGGCATTTG 60.261 45.833 4.78 2.91 0.00 2.32
4799 5280 4.614946 GGTCAAGAATCTATGGCATTTGC 58.385 43.478 4.78 0.00 41.14 3.68
4800 5281 4.098349 GGTCAAGAATCTATGGCATTTGCA 59.902 41.667 4.78 0.00 44.36 4.08
4830 5311 4.272018 CGGAGCAAAGGATGACTCATTAAG 59.728 45.833 0.00 0.00 35.31 1.85
4903 5386 1.602377 GGCACGGGTATTTCATACTGC 59.398 52.381 0.00 0.00 35.14 4.40
4904 5387 2.285083 GCACGGGTATTTCATACTGCA 58.715 47.619 0.00 0.00 35.64 4.41
4905 5388 2.878406 GCACGGGTATTTCATACTGCAT 59.122 45.455 0.00 0.00 35.64 3.96
4906 5389 3.315191 GCACGGGTATTTCATACTGCATT 59.685 43.478 0.00 0.00 35.64 3.56
4911 5394 4.036262 GGGTATTTCATACTGCATTTGCGA 59.964 41.667 0.00 0.00 36.80 5.10
4915 5398 1.006086 CATACTGCATTTGCGACCGA 58.994 50.000 0.00 0.00 45.83 4.69
4935 5418 4.154347 GGGAGCTGCCGTCCTCTG 62.154 72.222 9.14 0.00 37.63 3.35
4936 5419 4.154347 GGAGCTGCCGTCCTCTGG 62.154 72.222 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.450025 ACATCATGTGCTGCTCTGTG 58.550 50.000 0.00 1.57 0.00 3.66
2 3 1.810755 CAACATCATGTGCTGCTCTGT 59.189 47.619 0.00 0.00 0.00 3.41
3 4 2.081462 TCAACATCATGTGCTGCTCTG 58.919 47.619 0.00 0.00 0.00 3.35
27 28 2.307768 CTCCTATTACGGGCAGTCTCA 58.692 52.381 0.00 0.00 0.00 3.27
28 29 2.308690 ACTCCTATTACGGGCAGTCTC 58.691 52.381 0.00 0.00 0.00 3.36
29 30 2.456073 ACTCCTATTACGGGCAGTCT 57.544 50.000 0.00 0.00 0.00 3.24
30 31 4.868314 AATACTCCTATTACGGGCAGTC 57.132 45.455 0.00 0.00 0.00 3.51
31 32 7.673082 ACTTATAATACTCCTATTACGGGCAGT 59.327 37.037 0.00 0.00 29.31 4.40
32 33 8.064336 ACTTATAATACTCCTATTACGGGCAG 57.936 38.462 0.00 0.00 29.31 4.85
33 34 9.182214 CTACTTATAATACTCCTATTACGGGCA 57.818 37.037 0.00 0.00 29.31 5.36
34 35 9.183368 ACTACTTATAATACTCCTATTACGGGC 57.817 37.037 0.00 0.00 29.31 6.13
54 55 8.299570 GCTTAATTGGCATGCATAATACTACTT 58.700 33.333 21.36 6.71 0.00 2.24
55 56 7.448161 TGCTTAATTGGCATGCATAATACTACT 59.552 33.333 21.36 6.65 34.56 2.57
56 57 7.592938 TGCTTAATTGGCATGCATAATACTAC 58.407 34.615 21.36 10.37 34.56 2.73
57 58 7.757941 TGCTTAATTGGCATGCATAATACTA 57.242 32.000 21.36 7.05 34.56 1.82
58 59 6.653526 TGCTTAATTGGCATGCATAATACT 57.346 33.333 21.36 7.97 34.56 2.12
59 60 7.894376 ATTGCTTAATTGGCATGCATAATAC 57.106 32.000 21.36 10.08 39.54 1.89
60 61 8.905660 AAATTGCTTAATTGGCATGCATAATA 57.094 26.923 21.36 4.21 39.54 0.98
61 62 7.811117 AAATTGCTTAATTGGCATGCATAAT 57.189 28.000 21.36 16.00 39.54 1.28
62 63 7.336176 TCAAAATTGCTTAATTGGCATGCATAA 59.664 29.630 21.36 14.33 39.54 1.90
63 64 6.822170 TCAAAATTGCTTAATTGGCATGCATA 59.178 30.769 21.36 6.74 39.54 3.14
64 65 5.648526 TCAAAATTGCTTAATTGGCATGCAT 59.351 32.000 21.36 1.70 39.54 3.96
65 66 5.001874 TCAAAATTGCTTAATTGGCATGCA 58.998 33.333 21.36 0.00 39.54 3.96
66 67 5.548706 TCAAAATTGCTTAATTGGCATGC 57.451 34.783 9.90 9.90 39.54 4.06
67 68 7.279090 TCTCATCAAAATTGCTTAATTGGCATG 59.721 33.333 8.38 0.00 39.54 4.06
68 69 7.332557 TCTCATCAAAATTGCTTAATTGGCAT 58.667 30.769 8.38 0.00 39.54 4.40
69 70 6.699366 TCTCATCAAAATTGCTTAATTGGCA 58.301 32.000 4.21 4.21 37.97 4.92
70 71 7.493320 TCATCTCATCAAAATTGCTTAATTGGC 59.507 33.333 0.00 0.00 0.00 4.52
71 72 8.814235 GTCATCTCATCAAAATTGCTTAATTGG 58.186 33.333 0.00 0.00 0.00 3.16
72 73 9.361315 TGTCATCTCATCAAAATTGCTTAATTG 57.639 29.630 0.00 0.00 0.00 2.32
74 75 9.529325 CATGTCATCTCATCAAAATTGCTTAAT 57.471 29.630 0.00 0.00 0.00 1.40
75 76 8.741841 TCATGTCATCTCATCAAAATTGCTTAA 58.258 29.630 0.00 0.00 0.00 1.85
76 77 8.283699 TCATGTCATCTCATCAAAATTGCTTA 57.716 30.769 0.00 0.00 0.00 3.09
77 78 7.165460 TCATGTCATCTCATCAAAATTGCTT 57.835 32.000 0.00 0.00 0.00 3.91
78 79 6.769134 TCATGTCATCTCATCAAAATTGCT 57.231 33.333 0.00 0.00 0.00 3.91
79 80 7.821595 TTTCATGTCATCTCATCAAAATTGC 57.178 32.000 0.00 0.00 0.00 3.56
103 104 9.240734 ACTCAAGCATCTCTTTCTTCATTTAAT 57.759 29.630 0.00 0.00 31.27 1.40
104 105 8.627208 ACTCAAGCATCTCTTTCTTCATTTAA 57.373 30.769 0.00 0.00 31.27 1.52
105 106 9.896645 ATACTCAAGCATCTCTTTCTTCATTTA 57.103 29.630 0.00 0.00 31.27 1.40
106 107 8.804912 ATACTCAAGCATCTCTTTCTTCATTT 57.195 30.769 0.00 0.00 31.27 2.32
107 108 8.045507 TGATACTCAAGCATCTCTTTCTTCATT 58.954 33.333 0.00 0.00 31.27 2.57
108 109 7.563020 TGATACTCAAGCATCTCTTTCTTCAT 58.437 34.615 0.00 0.00 31.27 2.57
109 110 6.939622 TGATACTCAAGCATCTCTTTCTTCA 58.060 36.000 0.00 0.00 31.27 3.02
110 111 9.709495 ATATGATACTCAAGCATCTCTTTCTTC 57.291 33.333 0.00 0.00 31.27 2.87
152 153 9.225436 TGACACAAAGTAGCACATCATTTAATA 57.775 29.630 0.00 0.00 0.00 0.98
153 154 8.109705 TGACACAAAGTAGCACATCATTTAAT 57.890 30.769 0.00 0.00 0.00 1.40
154 155 7.503521 TGACACAAAGTAGCACATCATTTAA 57.496 32.000 0.00 0.00 0.00 1.52
155 156 7.529158 CATGACACAAAGTAGCACATCATTTA 58.471 34.615 0.00 0.00 0.00 1.40
156 157 6.384224 CATGACACAAAGTAGCACATCATTT 58.616 36.000 0.00 0.00 0.00 2.32
157 158 5.620654 GCATGACACAAAGTAGCACATCATT 60.621 40.000 0.00 0.00 0.00 2.57
158 159 4.142534 GCATGACACAAAGTAGCACATCAT 60.143 41.667 0.00 0.00 0.00 2.45
159 160 3.189080 GCATGACACAAAGTAGCACATCA 59.811 43.478 0.00 0.00 0.00 3.07
160 161 3.189080 TGCATGACACAAAGTAGCACATC 59.811 43.478 0.00 0.00 30.65 3.06
161 162 3.148412 TGCATGACACAAAGTAGCACAT 58.852 40.909 0.00 0.00 30.65 3.21
162 163 2.570135 TGCATGACACAAAGTAGCACA 58.430 42.857 0.00 0.00 30.65 4.57
163 164 3.495193 CATGCATGACACAAAGTAGCAC 58.505 45.455 22.59 0.00 36.06 4.40
164 165 2.488937 CCATGCATGACACAAAGTAGCA 59.511 45.455 28.31 0.00 37.13 3.49
165 166 2.489329 ACCATGCATGACACAAAGTAGC 59.511 45.455 28.31 0.00 0.00 3.58
166 167 5.878332 TTACCATGCATGACACAAAGTAG 57.122 39.130 28.31 9.32 0.00 2.57
167 168 7.929941 TTATTACCATGCATGACACAAAGTA 57.070 32.000 28.31 15.65 0.00 2.24
168 169 6.832520 TTATTACCATGCATGACACAAAGT 57.167 33.333 28.31 16.65 0.00 2.66
169 170 9.970395 ATATTTATTACCATGCATGACACAAAG 57.030 29.630 28.31 11.52 0.00 2.77
225 226 9.322773 GCATATGATACTACATCTGTAATGCAT 57.677 33.333 6.97 0.00 37.28 3.96
226 227 8.534496 AGCATATGATACTACATCTGTAATGCA 58.466 33.333 6.97 0.00 38.55 3.96
227 228 8.939201 AGCATATGATACTACATCTGTAATGC 57.061 34.615 6.97 10.67 37.43 3.56
233 234 9.283420 CGTTTCTAGCATATGATACTACATCTG 57.717 37.037 6.97 0.00 0.00 2.90
234 235 9.232473 TCGTTTCTAGCATATGATACTACATCT 57.768 33.333 6.97 0.00 0.00 2.90
235 236 9.497030 CTCGTTTCTAGCATATGATACTACATC 57.503 37.037 6.97 0.00 0.00 3.06
236 237 9.232473 TCTCGTTTCTAGCATATGATACTACAT 57.768 33.333 6.97 0.00 0.00 2.29
237 238 8.617290 TCTCGTTTCTAGCATATGATACTACA 57.383 34.615 6.97 0.00 0.00 2.74
240 241 9.456147 AGTATCTCGTTTCTAGCATATGATACT 57.544 33.333 6.97 0.00 39.14 2.12
241 242 9.710979 GAGTATCTCGTTTCTAGCATATGATAC 57.289 37.037 6.97 0.00 36.02 2.24
261 262 3.864003 GGCTGGTTGTAACGAAGAGTATC 59.136 47.826 0.00 0.00 0.00 2.24
262 263 3.514309 AGGCTGGTTGTAACGAAGAGTAT 59.486 43.478 0.00 0.00 0.00 2.12
263 264 2.895404 AGGCTGGTTGTAACGAAGAGTA 59.105 45.455 0.00 0.00 0.00 2.59
264 265 1.692519 AGGCTGGTTGTAACGAAGAGT 59.307 47.619 0.00 0.00 0.00 3.24
265 266 2.069273 CAGGCTGGTTGTAACGAAGAG 58.931 52.381 6.61 0.00 0.00 2.85
266 267 1.689813 TCAGGCTGGTTGTAACGAAGA 59.310 47.619 15.73 0.00 0.00 2.87
267 268 2.069273 CTCAGGCTGGTTGTAACGAAG 58.931 52.381 15.73 0.00 0.00 3.79
268 269 1.689813 TCTCAGGCTGGTTGTAACGAA 59.310 47.619 15.73 0.00 0.00 3.85
269 270 1.272490 CTCTCAGGCTGGTTGTAACGA 59.728 52.381 15.73 0.00 0.00 3.85
270 271 1.673033 CCTCTCAGGCTGGTTGTAACG 60.673 57.143 15.73 0.00 0.00 3.18
271 272 2.100605 CCTCTCAGGCTGGTTGTAAC 57.899 55.000 15.73 0.00 0.00 2.50
282 283 2.125753 GCTGTCACGCCTCTCAGG 60.126 66.667 0.00 0.00 38.80 3.86
283 284 1.445754 CTGCTGTCACGCCTCTCAG 60.446 63.158 0.00 0.00 0.00 3.35
305 306 1.335872 CCACCGTGGAAATCAAGCAAC 60.336 52.381 12.68 0.00 40.96 4.17
346 347 1.958417 CGCAACGTTTTCATGGGTAC 58.042 50.000 0.00 0.00 0.00 3.34
347 348 0.238817 GCGCAACGTTTTCATGGGTA 59.761 50.000 0.30 0.00 0.00 3.69
348 349 1.007849 GCGCAACGTTTTCATGGGT 60.008 52.632 0.30 0.00 0.00 4.51
406 407 7.121168 TGGACTTAAAATGTCTCATCAACCATC 59.879 37.037 0.00 0.00 35.04 3.51
418 419 3.492337 TGGTGGGTGGACTTAAAATGTC 58.508 45.455 0.00 0.00 0.00 3.06
419 420 3.603965 TGGTGGGTGGACTTAAAATGT 57.396 42.857 0.00 0.00 0.00 2.71
422 423 3.032459 GGTTTGGTGGGTGGACTTAAAA 58.968 45.455 0.00 0.00 0.00 1.52
428 429 1.228459 GGAGGTTTGGTGGGTGGAC 60.228 63.158 0.00 0.00 0.00 4.02
499 501 2.023888 TGTTGGGGAGAACTTTTTGGGA 60.024 45.455 0.00 0.00 0.00 4.37
516 518 1.522668 TGGCGAGGATGACTTTGTTG 58.477 50.000 0.00 0.00 0.00 3.33
517 519 2.496899 ATGGCGAGGATGACTTTGTT 57.503 45.000 0.00 0.00 0.00 2.83
518 520 2.496899 AATGGCGAGGATGACTTTGT 57.503 45.000 0.00 0.00 0.00 2.83
559 564 7.402640 TGTTGTTTATTTCCATTGCGTTTTTC 58.597 30.769 0.00 0.00 0.00 2.29
564 569 6.910536 TTTTGTTGTTTATTTCCATTGCGT 57.089 29.167 0.00 0.00 0.00 5.24
589 594 1.226945 GCCTGCTTGTTTGTTGCGT 60.227 52.632 0.00 0.00 0.00 5.24
630 635 3.130160 CCGAGCCTTCAGCCTTGC 61.130 66.667 0.00 0.00 45.47 4.01
631 636 3.130160 GCCGAGCCTTCAGCCTTG 61.130 66.667 0.00 0.00 45.47 3.61
632 637 4.767255 CGCCGAGCCTTCAGCCTT 62.767 66.667 0.00 0.00 45.47 4.35
792 844 1.317431 GGTGGGGTGGTTAAATCGGC 61.317 60.000 0.00 0.00 0.00 5.54
905 967 2.187424 GAGCAGAGCAGAGCAGGG 59.813 66.667 0.00 0.00 0.00 4.45
906 968 2.187424 GGAGCAGAGCAGAGCAGG 59.813 66.667 0.00 0.00 0.00 4.85
907 969 2.202770 CGGAGCAGAGCAGAGCAG 60.203 66.667 0.00 0.00 0.00 4.24
1110 1177 0.524816 CCGACCGGTTGTACTCGATG 60.525 60.000 20.63 0.00 0.00 3.84
1548 1615 5.712446 GGAAGGAATCAAGGGGCTATTTATC 59.288 44.000 0.00 0.00 0.00 1.75
1556 1623 0.922626 AGAGGAAGGAATCAAGGGGC 59.077 55.000 0.00 0.00 0.00 5.80
1615 1683 2.543012 GCGGATCACATCACAGAATGAG 59.457 50.000 0.00 0.00 41.91 2.90
1635 1703 1.470805 GCCAACAAATATTCCCACGGC 60.471 52.381 0.00 0.00 0.00 5.68
1642 1710 6.851609 TGTGACATGTAGCCAACAAATATTC 58.148 36.000 0.00 0.00 42.70 1.75
1659 1727 4.217836 AGACAGCAGAATCATGTGACAT 57.782 40.909 0.00 0.00 0.00 3.06
1793 1862 4.640789 AGTTGGAGCGATCTAACTACTG 57.359 45.455 27.84 0.00 39.19 2.74
1805 1877 1.681264 ACAAAAAGGGAAGTTGGAGCG 59.319 47.619 0.00 0.00 0.00 5.03
1809 1881 3.447229 ACACAGACAAAAAGGGAAGTTGG 59.553 43.478 0.00 0.00 0.00 3.77
1830 1903 4.921470 ATGCACACACGTTATTCACTAC 57.079 40.909 0.00 0.00 0.00 2.73
2114 2260 2.947852 ACAATCTCAGAGAACCGTTCG 58.052 47.619 3.63 0.00 34.02 3.95
2124 2270 4.982241 AAGGACTTCCAACAATCTCAGA 57.018 40.909 0.00 0.00 38.89 3.27
2168 2314 4.195416 CCTCTTGGCCATAGTTTCTCTTC 58.805 47.826 6.09 0.00 0.00 2.87
2192 2338 1.271597 ACTCCTGCACTCCAAACATCC 60.272 52.381 0.00 0.00 0.00 3.51
2376 2566 4.398673 AGCGTAGAAGGTGACTAAGTAAGG 59.601 45.833 0.00 0.00 42.68 2.69
2377 2567 5.123502 TCAGCGTAGAAGGTGACTAAGTAAG 59.876 44.000 0.00 0.00 42.80 2.34
2378 2568 5.005740 TCAGCGTAGAAGGTGACTAAGTAA 58.994 41.667 0.00 0.00 42.80 2.24
2379 2569 4.582869 TCAGCGTAGAAGGTGACTAAGTA 58.417 43.478 0.00 0.00 42.80 2.24
2380 2570 3.418995 TCAGCGTAGAAGGTGACTAAGT 58.581 45.455 0.00 0.00 42.80 2.24
2381 2571 4.416620 CTTCAGCGTAGAAGGTGACTAAG 58.583 47.826 10.08 0.00 46.60 2.18
2382 2572 4.436242 CTTCAGCGTAGAAGGTGACTAA 57.564 45.455 10.08 0.00 46.60 2.24
2383 2573 4.280174 AAACTTCAGCGTAGAAGGTGACTA 59.720 41.667 18.67 0.00 44.44 2.59
2384 2574 3.069729 AAACTTCAGCGTAGAAGGTGACT 59.930 43.478 18.67 0.57 44.44 3.41
2397 2587 7.555582 CGAAATAAGGAAAACAAAACTTCAGC 58.444 34.615 0.00 0.00 0.00 4.26
2421 2611 2.124570 CCAATCACCCCAGAGGCG 60.125 66.667 0.00 0.00 40.58 5.52
2474 2664 3.304559 CAGAAAGAGCGTTCAATAGGACG 59.695 47.826 1.01 0.00 0.00 4.79
2629 2944 2.000048 TCTGGGTTAAGCATTCCCCTT 59.000 47.619 7.03 0.00 39.46 3.95
2764 3082 7.542130 GCGGAAATCTTCTGAAATTTACACAAT 59.458 33.333 14.72 0.00 38.34 2.71
2895 3215 1.339151 GGCCTTAACTGTCTCACCCAG 60.339 57.143 0.00 0.00 36.01 4.45
3163 3483 3.237268 TGGTGGCCAAGTTTATTCAGT 57.763 42.857 7.24 0.00 0.00 3.41
3287 3607 7.754851 TTGAAATTTAAGAGGGGTGAGTTAC 57.245 36.000 0.00 0.00 0.00 2.50
3289 3609 7.508977 TCATTTGAAATTTAAGAGGGGTGAGTT 59.491 33.333 0.00 0.00 0.00 3.01
3290 3610 7.010160 TCATTTGAAATTTAAGAGGGGTGAGT 58.990 34.615 0.00 0.00 0.00 3.41
3291 3611 7.363268 CCTCATTTGAAATTTAAGAGGGGTGAG 60.363 40.741 11.99 3.06 37.97 3.51
3293 3613 6.437162 TCCTCATTTGAAATTTAAGAGGGGTG 59.563 38.462 17.06 0.00 41.09 4.61
3294 3614 6.561294 TCCTCATTTGAAATTTAAGAGGGGT 58.439 36.000 17.06 0.00 41.09 4.95
3296 3616 8.127150 AGTTCCTCATTTGAAATTTAAGAGGG 57.873 34.615 17.06 4.63 41.09 4.30
3297 3617 9.415544 CAAGTTCCTCATTTGAAATTTAAGAGG 57.584 33.333 13.11 13.11 41.88 3.69
3298 3618 9.971922 ACAAGTTCCTCATTTGAAATTTAAGAG 57.028 29.630 0.00 0.00 28.48 2.85
3305 3625 6.267471 TGCCTTACAAGTTCCTCATTTGAAAT 59.733 34.615 0.00 0.00 0.00 2.17
3306 3626 5.596361 TGCCTTACAAGTTCCTCATTTGAAA 59.404 36.000 0.00 0.00 0.00 2.69
3307 3627 5.136828 TGCCTTACAAGTTCCTCATTTGAA 58.863 37.500 0.00 0.00 0.00 2.69
3308 3628 4.724399 TGCCTTACAAGTTCCTCATTTGA 58.276 39.130 0.00 0.00 0.00 2.69
3312 3765 5.700402 ATACTGCCTTACAAGTTCCTCAT 57.300 39.130 0.00 0.00 0.00 2.90
3427 3880 9.582648 AAATATATAATAAAAACACCCCTCGCT 57.417 29.630 0.00 0.00 0.00 4.93
3569 4022 5.276270 CGATCAAAGTATCCAAATGCCTTG 58.724 41.667 0.00 0.00 34.52 3.61
3695 4148 4.756502 GGTGAGTTACCTTATCAGTGTCC 58.243 47.826 0.00 0.00 46.51 4.02
3779 4240 7.274603 TCACAATGTTCATCATTTCAGTCAA 57.725 32.000 0.00 0.00 43.33 3.18
3980 4441 1.164411 TCACAACTTGCCTATTGCGG 58.836 50.000 0.00 0.00 45.60 5.69
4286 4747 8.153550 CACCCTTTCAGCTTCAGAATATACTAT 58.846 37.037 0.00 0.00 0.00 2.12
4350 4811 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
4376 4837 1.336440 TCAAAATTGTCTGTGCCACGG 59.664 47.619 0.00 0.00 0.00 4.94
4384 4845 8.755018 GTCATGGTTTTAGTTCAAAATTGTCTG 58.245 33.333 0.00 0.00 38.36 3.51
4385 4846 8.474025 TGTCATGGTTTTAGTTCAAAATTGTCT 58.526 29.630 0.00 0.00 38.36 3.41
4544 5024 9.635404 CAAAATAATACACCCTCCCAATACTTA 57.365 33.333 0.00 0.00 0.00 2.24
4568 5048 7.129457 AGATCCTCTACAATGATACTTGCAA 57.871 36.000 0.00 0.00 0.00 4.08
4571 5051 8.309656 TGCATAGATCCTCTACAATGATACTTG 58.690 37.037 0.00 0.00 30.79 3.16
4572 5052 8.427902 TGCATAGATCCTCTACAATGATACTT 57.572 34.615 0.00 0.00 30.79 2.24
4573 5053 7.892771 TCTGCATAGATCCTCTACAATGATACT 59.107 37.037 0.00 0.00 30.79 2.12
4574 5054 8.060931 TCTGCATAGATCCTCTACAATGATAC 57.939 38.462 0.00 0.00 30.79 2.24
4575 5055 8.112183 TCTCTGCATAGATCCTCTACAATGATA 58.888 37.037 0.00 0.00 30.79 2.15
4576 5056 6.952938 TCTCTGCATAGATCCTCTACAATGAT 59.047 38.462 0.00 0.00 30.79 2.45
4577 5057 6.310149 TCTCTGCATAGATCCTCTACAATGA 58.690 40.000 0.00 0.00 30.79 2.57
4578 5058 6.587206 TCTCTGCATAGATCCTCTACAATG 57.413 41.667 0.00 0.00 30.79 2.82
4579 5059 7.454066 TGAATCTCTGCATAGATCCTCTACAAT 59.546 37.037 14.36 0.00 35.10 2.71
4580 5060 6.779539 TGAATCTCTGCATAGATCCTCTACAA 59.220 38.462 14.36 0.00 35.10 2.41
4581 5061 6.310149 TGAATCTCTGCATAGATCCTCTACA 58.690 40.000 14.36 6.53 35.10 2.74
4582 5062 6.832520 TGAATCTCTGCATAGATCCTCTAC 57.167 41.667 14.36 4.49 35.10 2.59
4583 5063 7.180663 TGATGAATCTCTGCATAGATCCTCTA 58.819 38.462 14.36 2.92 35.10 2.43
4584 5064 6.017830 TGATGAATCTCTGCATAGATCCTCT 58.982 40.000 14.36 0.00 35.10 3.69
4585 5065 6.283544 TGATGAATCTCTGCATAGATCCTC 57.716 41.667 14.36 10.14 35.10 3.71
4586 5066 6.683312 TTGATGAATCTCTGCATAGATCCT 57.317 37.500 14.36 0.82 35.10 3.24
4587 5067 7.064847 GTGATTGATGAATCTCTGCATAGATCC 59.935 40.741 14.36 3.24 39.10 3.36
4588 5068 7.064847 GGTGATTGATGAATCTCTGCATAGATC 59.935 40.741 14.36 9.08 39.10 2.75
4589 5069 6.879993 GGTGATTGATGAATCTCTGCATAGAT 59.120 38.462 8.71 8.71 39.10 1.98
4590 5070 6.183361 TGGTGATTGATGAATCTCTGCATAGA 60.183 38.462 4.05 4.05 39.10 1.98
4591 5071 5.995897 TGGTGATTGATGAATCTCTGCATAG 59.004 40.000 6.46 0.00 39.10 2.23
4592 5072 5.932455 TGGTGATTGATGAATCTCTGCATA 58.068 37.500 6.46 0.00 39.10 3.14
4593 5073 4.788679 TGGTGATTGATGAATCTCTGCAT 58.211 39.130 6.46 0.00 39.10 3.96
4594 5074 4.224991 TGGTGATTGATGAATCTCTGCA 57.775 40.909 6.46 0.00 39.10 4.41
4595 5075 5.571784 TTTGGTGATTGATGAATCTCTGC 57.428 39.130 6.46 0.00 39.10 4.26
4596 5076 5.357314 AGCTTTGGTGATTGATGAATCTCTG 59.643 40.000 6.46 0.00 39.10 3.35
4597 5077 5.507637 AGCTTTGGTGATTGATGAATCTCT 58.492 37.500 6.46 0.00 39.10 3.10
4598 5078 5.831702 AGCTTTGGTGATTGATGAATCTC 57.168 39.130 6.46 2.64 39.10 2.75
4599 5079 5.713389 TCAAGCTTTGGTGATTGATGAATCT 59.287 36.000 6.46 0.00 39.10 2.40
4600 5080 5.803967 GTCAAGCTTTGGTGATTGATGAATC 59.196 40.000 0.00 0.00 38.85 2.52
4601 5081 5.244402 TGTCAAGCTTTGGTGATTGATGAAT 59.756 36.000 0.00 0.00 34.45 2.57
4602 5082 4.583907 TGTCAAGCTTTGGTGATTGATGAA 59.416 37.500 0.00 0.00 34.45 2.57
4603 5083 4.143543 TGTCAAGCTTTGGTGATTGATGA 58.856 39.130 0.00 0.00 34.45 2.92
4604 5084 4.508461 TGTCAAGCTTTGGTGATTGATG 57.492 40.909 0.00 0.00 34.45 3.07
4605 5085 4.341806 TGTTGTCAAGCTTTGGTGATTGAT 59.658 37.500 0.00 0.00 34.45 2.57
4606 5086 3.698539 TGTTGTCAAGCTTTGGTGATTGA 59.301 39.130 0.00 0.00 0.00 2.57
4665 5145 2.223745 TGGGCACTCGAAAAGTAAACC 58.776 47.619 0.00 0.00 36.07 3.27
4676 5156 3.245668 AACAGGCTCTGGGCACTCG 62.246 63.158 0.21 0.00 44.01 4.18
4714 5195 0.036022 TTCATCACATGCACGGACCA 59.964 50.000 0.00 0.00 0.00 4.02
4726 5207 3.587797 TCTACCAGTTCCGTTCATCAC 57.412 47.619 0.00 0.00 0.00 3.06
4798 5279 3.259425 CTTTGCTCCGTGCCTGTGC 62.259 63.158 0.00 0.00 42.00 4.57
4799 5280 2.620112 CCTTTGCTCCGTGCCTGTG 61.620 63.158 0.00 0.00 42.00 3.66
4800 5281 2.129555 ATCCTTTGCTCCGTGCCTGT 62.130 55.000 0.00 0.00 42.00 4.00
4830 5311 2.485038 CCAACCATTTTTCTGGCAATGC 59.515 45.455 0.00 0.00 40.15 3.56
4875 5358 1.238625 AATACCCGTGCCAACCAACG 61.239 55.000 0.00 0.00 0.00 4.10
4903 5386 0.447801 CTCCCTTTCGGTCGCAAATG 59.552 55.000 0.00 0.00 0.00 2.32
4904 5387 1.305930 GCTCCCTTTCGGTCGCAAAT 61.306 55.000 0.00 0.00 31.91 2.32
4905 5388 1.964373 GCTCCCTTTCGGTCGCAAA 60.964 57.895 0.00 0.00 31.91 3.68
4906 5389 2.358247 GCTCCCTTTCGGTCGCAA 60.358 61.111 0.00 0.00 31.91 4.85
4911 5394 4.394712 CGGCAGCTCCCTTTCGGT 62.395 66.667 0.00 0.00 0.00 4.69
4915 5398 2.930562 AGGACGGCAGCTCCCTTT 60.931 61.111 0.00 0.00 0.00 3.11
4935 5418 1.227943 TGCTGTTGAGGTGTCTGCC 60.228 57.895 0.00 0.00 0.00 4.85
4936 5419 1.849976 GCTGCTGTTGAGGTGTCTGC 61.850 60.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.