Multiple sequence alignment - TraesCS3A01G175100

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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 TraesCS3A01G175100 chr3A 100.000 2375 0 0 1 2375 195157181 195154807 0.000000e+00 4386.0
1 TraesCS3A01G175100 chr3A 92.340 1436 87 9 942 2375 195148028 195146614 0.000000e+00 2021.0
2 TraesCS3A01G175100 chr3A 97.505 481 12 0 422 902 195148506 195148026 0.000000e+00 822.0
3 TraesCS3A01G175100 chr3A 85.890 163 21 2 422 583 669484304 669484465 3.140000e-39 172.0
4 TraesCS3A01G175100 chr5A 93.197 1367 87 6 422 1785 94795504 94794141 0.000000e+00 2004.0
5 TraesCS3A01G175100 chr5A 93.010 1359 90 5 422 1778 94783045 94781690 0.000000e+00 1978.0
6 TraesCS3A01G175100 chr5A 92.746 1158 76 7 422 1574 433069200 433068046 0.000000e+00 1666.0
7 TraesCS3A01G175100 chr5A 89.247 372 39 1 1037 1407 295687381 295687752 4.620000e-127 464.0
8 TraesCS3A01G175100 chr1D 95.254 611 28 1 1766 2375 282333852 282333242 0.000000e+00 966.0
9 TraesCS3A01G175100 chr6D 94.951 614 30 1 1763 2375 23233927 23234540 0.000000e+00 961.0
10 TraesCS3A01G175100 chr6D 94.614 427 21 2 1 426 389207906 389208331 0.000000e+00 660.0
11 TraesCS3A01G175100 chr6D 94.131 426 23 2 1 426 319468480 319468903 0.000000e+00 647.0
12 TraesCS3A01G175100 chr3D 95.082 610 30 0 1766 2375 294792571 294791962 0.000000e+00 961.0
13 TraesCS3A01G175100 chr3D 94.159 428 22 3 1 426 275388918 275388492 0.000000e+00 649.0
14 TraesCS3A01G175100 chrUn 94.780 613 31 1 1763 2374 367432906 367433518 0.000000e+00 953.0
15 TraesCS3A01G175100 chr2D 94.918 610 30 1 1766 2374 190380215 190379606 0.000000e+00 953.0
16 TraesCS3A01G175100 chr2D 94.918 610 30 1 1766 2374 190388386 190387777 0.000000e+00 953.0
17 TraesCS3A01G175100 chr2D 94.918 610 30 1 1766 2375 310859142 310858534 0.000000e+00 953.0
18 TraesCS3A01G175100 chr2D 93.750 64 4 0 1073 1136 414415777 414415840 1.940000e-16 97.1
19 TraesCS3A01G175100 chr4D 94.763 611 31 1 1766 2375 20334353 20333743 0.000000e+00 950.0
20 TraesCS3A01G175100 chr4D 94.763 611 31 1 1766 2375 20342442 20341832 0.000000e+00 950.0
21 TraesCS3A01G175100 chr5D 94.626 428 19 4 1 426 220745150 220745575 0.000000e+00 660.0
22 TraesCS3A01G175100 chr5D 94.601 426 21 2 1 426 241565766 241566189 0.000000e+00 658.0
23 TraesCS3A01G175100 chr5D 93.897 426 24 2 1 426 302419143 302419566 1.990000e-180 641.0
24 TraesCS3A01G175100 chr5D 83.798 574 66 24 422 986 82880130 82879575 9.730000e-144 520.0
25 TraesCS3A01G175100 chr7D 93.925 428 22 4 1 426 246413224 246413649 0.000000e+00 643.0
26 TraesCS3A01G175100 chr7D 93.897 426 25 1 1 426 174861694 174861270 1.990000e-180 641.0
27 TraesCS3A01G175100 chr7A 93.897 426 25 1 1 426 509131851 509132275 1.990000e-180 641.0
28 TraesCS3A01G175100 chr7A 86.538 520 55 12 422 934 324049557 324050068 2.060000e-155 558.0
29 TraesCS3A01G175100 chr1A 87.669 519 45 15 422 934 340353441 340353946 9.460000e-164 586.0
30 TraesCS3A01G175100 chr1A 85.470 117 15 2 1050 1165 374835336 374835451 1.150000e-23 121.0
31 TraesCS3A01G175100 chr4A 91.335 427 29 8 511 934 309517403 309517824 5.690000e-161 577.0
32 TraesCS3A01G175100 chr5B 81.458 631 88 26 422 1039 215571645 215571031 7.630000e-135 490.0
33 TraesCS3A01G175100 chr4B 88.636 176 18 2 410 584 417389655 417389829 1.850000e-51 213.0
34 TraesCS3A01G175100 chr2A 86.145 166 20 2 422 584 150626427 150626592 2.430000e-40 176.0
35 TraesCS3A01G175100 chr2A 85.976 164 22 1 421 584 232252943 232252781 8.730000e-40 174.0
36 TraesCS3A01G175100 chr2A 85.890 163 22 1 422 584 232245375 232245214 3.140000e-39 172.0
37 TraesCS3A01G175100 chr2B 93.651 63 4 0 1073 1135 488022157 488022219 6.990000e-16 95.3


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 TraesCS3A01G175100 chr3A 195154807 195157181 2374 True 4386.0 4386 100.0000 1 2375 1 chr3A.!!$R1 2374
1 TraesCS3A01G175100 chr3A 195146614 195148506 1892 True 1421.5 2021 94.9225 422 2375 2 chr3A.!!$R2 1953
2 TraesCS3A01G175100 chr5A 94794141 94795504 1363 True 2004.0 2004 93.1970 422 1785 1 chr5A.!!$R2 1363
3 TraesCS3A01G175100 chr5A 94781690 94783045 1355 True 1978.0 1978 93.0100 422 1778 1 chr5A.!!$R1 1356
4 TraesCS3A01G175100 chr5A 433068046 433069200 1154 True 1666.0 1666 92.7460 422 1574 1 chr5A.!!$R3 1152
5 TraesCS3A01G175100 chr1D 282333242 282333852 610 True 966.0 966 95.2540 1766 2375 1 chr1D.!!$R1 609
6 TraesCS3A01G175100 chr6D 23233927 23234540 613 False 961.0 961 94.9510 1763 2375 1 chr6D.!!$F1 612
7 TraesCS3A01G175100 chr3D 294791962 294792571 609 True 961.0 961 95.0820 1766 2375 1 chr3D.!!$R2 609
8 TraesCS3A01G175100 chrUn 367432906 367433518 612 False 953.0 953 94.7800 1763 2374 1 chrUn.!!$F1 611
9 TraesCS3A01G175100 chr2D 190379606 190380215 609 True 953.0 953 94.9180 1766 2374 1 chr2D.!!$R1 608
10 TraesCS3A01G175100 chr2D 190387777 190388386 609 True 953.0 953 94.9180 1766 2374 1 chr2D.!!$R2 608
11 TraesCS3A01G175100 chr2D 310858534 310859142 608 True 953.0 953 94.9180 1766 2375 1 chr2D.!!$R3 609
12 TraesCS3A01G175100 chr4D 20333743 20334353 610 True 950.0 950 94.7630 1766 2375 1 chr4D.!!$R1 609
13 TraesCS3A01G175100 chr4D 20341832 20342442 610 True 950.0 950 94.7630 1766 2375 1 chr4D.!!$R2 609
14 TraesCS3A01G175100 chr5D 82879575 82880130 555 True 520.0 520 83.7980 422 986 1 chr5D.!!$R1 564
15 TraesCS3A01G175100 chr7A 324049557 324050068 511 False 558.0 558 86.5380 422 934 1 chr7A.!!$F1 512
16 TraesCS3A01G175100 chr1A 340353441 340353946 505 False 586.0 586 87.6690 422 934 1 chr1A.!!$F1 512
17 TraesCS3A01G175100 chr5B 215571031 215571645 614 True 490.0 490 81.4580 422 1039 1 chr5B.!!$R1 617

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
319 320 0.035152 TGGTCTCATGGCATGGACAC 60.035 55.0 31.6 24.94 34.33 3.67 F
1104 1119 1.045350 CCATTCCCCTCGCTCTCTCA 61.045 60.0 0.0 0.00 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1320 1335 0.394762 GAGGTTGCCAGGATGATGCA 60.395 55.000 0.0 0.0 39.69 3.96 R
2171 2188 4.314121 CCATTAGATAGCCTGAACAGCTC 58.686 47.826 0.0 0.0 41.83 4.09 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 4.663636 GAGAGGGAACAATACACGTTTG 57.336 45.455 0.00 0.00 0.00 2.93
22 23 4.312443 GAGAGGGAACAATACACGTTTGA 58.688 43.478 5.50 0.00 0.00 2.69
23 24 4.906618 AGAGGGAACAATACACGTTTGAT 58.093 39.130 5.50 0.00 0.00 2.57
24 25 4.695455 AGAGGGAACAATACACGTTTGATG 59.305 41.667 5.50 0.00 0.00 3.07
25 26 4.647611 AGGGAACAATACACGTTTGATGA 58.352 39.130 5.50 0.00 0.00 2.92
26 27 4.454504 AGGGAACAATACACGTTTGATGAC 59.545 41.667 5.50 0.00 0.00 3.06
28 29 4.150980 GGAACAATACACGTTTGATGACGA 59.849 41.667 5.50 0.00 45.47 4.20
29 30 5.333492 GGAACAATACACGTTTGATGACGAA 60.333 40.000 5.50 0.00 45.47 3.85
30 31 5.013861 ACAATACACGTTTGATGACGAAC 57.986 39.130 5.50 0.00 45.47 3.95
36 37 2.074547 GTTTGATGACGAACGGGAGA 57.925 50.000 0.00 0.00 31.85 3.71
37 38 2.618053 GTTTGATGACGAACGGGAGAT 58.382 47.619 0.00 0.00 31.85 2.75
38 39 3.777478 GTTTGATGACGAACGGGAGATA 58.223 45.455 0.00 0.00 31.85 1.98
39 40 4.178540 GTTTGATGACGAACGGGAGATAA 58.821 43.478 0.00 0.00 31.85 1.75
40 41 3.431922 TGATGACGAACGGGAGATAAC 57.568 47.619 0.00 0.00 0.00 1.89
41 42 3.021695 TGATGACGAACGGGAGATAACT 58.978 45.455 0.00 0.00 0.00 2.24
42 43 3.446161 TGATGACGAACGGGAGATAACTT 59.554 43.478 0.00 0.00 0.00 2.66
43 44 3.498927 TGACGAACGGGAGATAACTTC 57.501 47.619 0.00 0.00 0.00 3.01
44 45 2.165030 TGACGAACGGGAGATAACTTCC 59.835 50.000 0.00 0.00 38.40 3.46
45 46 2.426381 GACGAACGGGAGATAACTTCCT 59.574 50.000 0.00 0.00 39.59 3.36
46 47 2.426381 ACGAACGGGAGATAACTTCCTC 59.574 50.000 0.00 0.00 39.59 3.71
47 48 2.688958 CGAACGGGAGATAACTTCCTCT 59.311 50.000 0.00 0.00 39.59 3.69
48 49 3.130693 CGAACGGGAGATAACTTCCTCTT 59.869 47.826 0.00 0.00 39.59 2.85
49 50 4.337555 CGAACGGGAGATAACTTCCTCTTA 59.662 45.833 0.00 0.00 39.59 2.10
50 51 5.590145 GAACGGGAGATAACTTCCTCTTAC 58.410 45.833 0.00 0.00 39.59 2.34
51 52 3.631227 ACGGGAGATAACTTCCTCTTACG 59.369 47.826 0.00 0.00 39.59 3.18
52 53 3.004524 CGGGAGATAACTTCCTCTTACGG 59.995 52.174 0.00 0.00 39.59 4.02
53 54 3.243805 GGGAGATAACTTCCTCTTACGGC 60.244 52.174 0.00 0.00 38.71 5.68
54 55 3.243805 GGAGATAACTTCCTCTTACGGCC 60.244 52.174 0.00 0.00 0.00 6.13
55 56 3.637694 GAGATAACTTCCTCTTACGGCCT 59.362 47.826 0.00 0.00 0.00 5.19
56 57 4.031611 AGATAACTTCCTCTTACGGCCTT 58.968 43.478 0.00 0.00 0.00 4.35
57 58 2.764439 AACTTCCTCTTACGGCCTTC 57.236 50.000 0.00 0.00 0.00 3.46
58 59 1.640917 ACTTCCTCTTACGGCCTTCA 58.359 50.000 0.00 0.00 0.00 3.02
59 60 1.975680 ACTTCCTCTTACGGCCTTCAA 59.024 47.619 0.00 0.00 0.00 2.69
60 61 2.572104 ACTTCCTCTTACGGCCTTCAAT 59.428 45.455 0.00 0.00 0.00 2.57
61 62 3.009143 ACTTCCTCTTACGGCCTTCAATT 59.991 43.478 0.00 0.00 0.00 2.32
62 63 3.713826 TCCTCTTACGGCCTTCAATTT 57.286 42.857 0.00 0.00 0.00 1.82
63 64 4.028993 TCCTCTTACGGCCTTCAATTTT 57.971 40.909 0.00 0.00 0.00 1.82
64 65 4.403734 TCCTCTTACGGCCTTCAATTTTT 58.596 39.130 0.00 0.00 0.00 1.94
94 95 7.175995 CGTTTAACGTGCACTAATACAATTG 57.824 36.000 16.19 3.24 36.74 2.32
95 96 6.793203 CGTTTAACGTGCACTAATACAATTGT 59.207 34.615 16.68 16.68 36.74 2.71
96 97 7.005857 CGTTTAACGTGCACTAATACAATTGTC 59.994 37.037 15.85 0.00 36.74 3.18
97 98 5.933187 AACGTGCACTAATACAATTGTCA 57.067 34.783 15.85 1.78 0.00 3.58
98 99 6.494893 AACGTGCACTAATACAATTGTCAT 57.505 33.333 15.85 7.80 0.00 3.06
99 100 5.868257 ACGTGCACTAATACAATTGTCATG 58.132 37.500 15.85 12.36 0.00 3.07
100 101 5.411361 ACGTGCACTAATACAATTGTCATGT 59.589 36.000 15.85 12.99 34.81 3.21
101 102 5.734035 CGTGCACTAATACAATTGTCATGTG 59.266 40.000 15.85 18.70 32.27 3.21
102 103 6.402011 CGTGCACTAATACAATTGTCATGTGA 60.402 38.462 24.77 8.09 32.27 3.58
103 104 7.304735 GTGCACTAATACAATTGTCATGTGAA 58.695 34.615 24.77 17.63 32.27 3.18
104 105 7.807433 GTGCACTAATACAATTGTCATGTGAAA 59.193 33.333 24.77 15.33 32.27 2.69
105 106 8.355913 TGCACTAATACAATTGTCATGTGAAAA 58.644 29.630 24.77 13.76 32.27 2.29
106 107 9.357652 GCACTAATACAATTGTCATGTGAAAAT 57.642 29.630 24.77 8.00 33.57 1.82
111 112 9.775854 AATACAATTGTCATGTGAAAATTTGGA 57.224 25.926 15.85 3.15 39.32 3.53
112 113 9.775854 ATACAATTGTCATGTGAAAATTTGGAA 57.224 25.926 15.85 0.00 39.32 3.53
113 114 8.503458 ACAATTGTCATGTGAAAATTTGGAAA 57.497 26.923 4.92 0.00 39.32 3.13
114 115 8.954350 ACAATTGTCATGTGAAAATTTGGAAAA 58.046 25.926 4.92 0.00 39.32 2.29
115 116 9.953697 CAATTGTCATGTGAAAATTTGGAAAAT 57.046 25.926 8.14 0.00 39.32 1.82
119 120 9.170734 TGTCATGTGAAAATTTGGAAAATTTCA 57.829 25.926 8.09 10.08 42.38 2.69
120 121 9.654417 GTCATGTGAAAATTTGGAAAATTTCAG 57.346 29.630 13.24 5.36 44.10 3.02
121 122 8.344098 TCATGTGAAAATTTGGAAAATTTCAGC 58.656 29.630 13.24 9.97 44.10 4.26
122 123 6.713520 TGTGAAAATTTGGAAAATTTCAGCG 58.286 32.000 13.24 0.00 44.10 5.18
123 124 6.135400 GTGAAAATTTGGAAAATTTCAGCGG 58.865 36.000 13.24 0.00 44.10 5.52
124 125 5.819901 TGAAAATTTGGAAAATTTCAGCGGT 59.180 32.000 8.09 0.00 40.76 5.68
125 126 5.922739 AAATTTGGAAAATTTCAGCGGTC 57.077 34.783 8.09 0.00 0.00 4.79
126 127 4.599047 ATTTGGAAAATTTCAGCGGTCA 57.401 36.364 8.09 0.00 0.00 4.02
127 128 4.599047 TTTGGAAAATTTCAGCGGTCAT 57.401 36.364 8.09 0.00 0.00 3.06
128 129 4.599047 TTGGAAAATTTCAGCGGTCATT 57.401 36.364 8.09 0.00 0.00 2.57
129 130 4.599047 TGGAAAATTTCAGCGGTCATTT 57.401 36.364 8.09 0.00 0.00 2.32
130 131 4.305769 TGGAAAATTTCAGCGGTCATTTG 58.694 39.130 8.09 0.00 0.00 2.32
131 132 4.038522 TGGAAAATTTCAGCGGTCATTTGA 59.961 37.500 8.09 0.00 0.00 2.69
132 133 4.385748 GGAAAATTTCAGCGGTCATTTGAC 59.614 41.667 8.09 1.99 44.04 3.18
205 206 8.334263 TCAAATTTGAACTACATCTACATGCA 57.666 30.769 18.45 0.00 33.55 3.96
206 207 8.791675 TCAAATTTGAACTACATCTACATGCAA 58.208 29.630 18.45 0.00 33.55 4.08
207 208 8.853345 CAAATTTGAACTACATCTACATGCAAC 58.147 33.333 13.08 0.00 32.57 4.17
208 209 5.778161 TTGAACTACATCTACATGCAACG 57.222 39.130 0.00 0.00 32.57 4.10
209 210 4.180817 TGAACTACATCTACATGCAACGG 58.819 43.478 0.00 0.00 32.57 4.44
210 211 2.550978 ACTACATCTACATGCAACGGC 58.449 47.619 0.00 0.00 41.68 5.68
211 212 2.168521 ACTACATCTACATGCAACGGCT 59.831 45.455 0.00 0.00 41.91 5.52
212 213 2.979814 ACATCTACATGCAACGGCTA 57.020 45.000 0.00 0.00 41.91 3.93
213 214 3.260475 ACATCTACATGCAACGGCTAA 57.740 42.857 0.00 0.00 41.91 3.09
214 215 2.936498 ACATCTACATGCAACGGCTAAC 59.064 45.455 0.00 0.00 41.91 2.34
215 216 2.018542 TCTACATGCAACGGCTAACC 57.981 50.000 0.00 0.00 41.91 2.85
239 240 8.491331 CCGGAATGGTTTGAAAAATCATATTT 57.509 30.769 0.00 0.00 0.00 1.40
240 241 8.389603 CCGGAATGGTTTGAAAAATCATATTTG 58.610 33.333 0.00 0.00 0.00 2.32
241 242 8.934825 CGGAATGGTTTGAAAAATCATATTTGT 58.065 29.630 0.00 0.00 0.00 2.83
254 255 9.502145 AAAATCATATTTGTATACTTGTGTGCG 57.498 29.630 4.17 0.00 0.00 5.34
255 256 8.432110 AATCATATTTGTATACTTGTGTGCGA 57.568 30.769 4.17 0.00 0.00 5.10
256 257 8.607441 ATCATATTTGTATACTTGTGTGCGAT 57.393 30.769 4.17 0.00 0.00 4.58
257 258 8.432110 TCATATTTGTATACTTGTGTGCGATT 57.568 30.769 4.17 0.00 0.00 3.34
258 259 8.888716 TCATATTTGTATACTTGTGTGCGATTT 58.111 29.630 4.17 0.00 0.00 2.17
263 264 9.549509 TTTGTATACTTGTGTGCGATTTAATTC 57.450 29.630 4.17 0.00 0.00 2.17
264 265 7.690228 TGTATACTTGTGTGCGATTTAATTCC 58.310 34.615 4.17 0.00 0.00 3.01
265 266 6.751514 ATACTTGTGTGCGATTTAATTCCA 57.248 33.333 0.00 0.00 0.00 3.53
266 267 5.643379 ACTTGTGTGCGATTTAATTCCAT 57.357 34.783 0.00 0.00 0.00 3.41
267 268 5.401550 ACTTGTGTGCGATTTAATTCCATG 58.598 37.500 0.00 0.00 0.00 3.66
268 269 5.048083 ACTTGTGTGCGATTTAATTCCATGT 60.048 36.000 0.00 0.00 0.00 3.21
269 270 4.731720 TGTGTGCGATTTAATTCCATGTG 58.268 39.130 0.00 0.00 0.00 3.21
270 271 3.547468 GTGTGCGATTTAATTCCATGTGC 59.453 43.478 0.00 0.00 0.00 4.57
271 272 3.192212 TGTGCGATTTAATTCCATGTGCA 59.808 39.130 0.00 0.00 0.00 4.57
272 273 3.792956 GTGCGATTTAATTCCATGTGCAG 59.207 43.478 0.00 0.00 0.00 4.41
273 274 3.443329 TGCGATTTAATTCCATGTGCAGT 59.557 39.130 0.00 0.00 0.00 4.40
274 275 4.637977 TGCGATTTAATTCCATGTGCAGTA 59.362 37.500 0.00 0.00 0.00 2.74
275 276 5.124617 TGCGATTTAATTCCATGTGCAGTAA 59.875 36.000 0.00 0.00 0.00 2.24
276 277 6.033341 GCGATTTAATTCCATGTGCAGTAAA 58.967 36.000 0.00 0.00 0.00 2.01
277 278 6.697019 GCGATTTAATTCCATGTGCAGTAAAT 59.303 34.615 0.00 0.00 0.00 1.40
278 279 7.222611 GCGATTTAATTCCATGTGCAGTAAATT 59.777 33.333 0.00 0.00 0.00 1.82
279 280 9.729023 CGATTTAATTCCATGTGCAGTAAATTA 57.271 29.630 0.00 0.00 0.00 1.40
284 285 6.757897 TTCCATGTGCAGTAAATTAGAAGG 57.242 37.500 0.00 0.00 0.00 3.46
285 286 6.061022 TCCATGTGCAGTAAATTAGAAGGA 57.939 37.500 0.00 0.00 0.00 3.36
286 287 6.480763 TCCATGTGCAGTAAATTAGAAGGAA 58.519 36.000 0.00 0.00 0.00 3.36
287 288 7.118723 TCCATGTGCAGTAAATTAGAAGGAAT 58.881 34.615 0.00 0.00 0.00 3.01
288 289 7.615365 TCCATGTGCAGTAAATTAGAAGGAATT 59.385 33.333 0.00 0.00 0.00 2.17
289 290 8.253113 CCATGTGCAGTAAATTAGAAGGAATTT 58.747 33.333 0.00 0.00 41.00 1.82
290 291 9.643693 CATGTGCAGTAAATTAGAAGGAATTTT 57.356 29.630 0.00 0.00 39.27 1.82
291 292 9.860898 ATGTGCAGTAAATTAGAAGGAATTTTC 57.139 29.630 0.00 0.00 39.27 2.29
292 293 8.855110 TGTGCAGTAAATTAGAAGGAATTTTCA 58.145 29.630 0.00 0.00 39.27 2.69
293 294 9.691362 GTGCAGTAAATTAGAAGGAATTTTCAA 57.309 29.630 0.00 0.00 39.27 2.69
311 312 9.768662 AATTTTCAAATATATTGGTCTCATGGC 57.231 29.630 0.00 0.00 0.00 4.40
312 313 7.894753 TTTCAAATATATTGGTCTCATGGCA 57.105 32.000 0.00 0.00 0.00 4.92
313 314 8.481492 TTTCAAATATATTGGTCTCATGGCAT 57.519 30.769 0.00 0.00 0.00 4.40
314 315 7.457024 TCAAATATATTGGTCTCATGGCATG 57.543 36.000 21.42 21.42 0.00 4.06
315 316 6.434965 TCAAATATATTGGTCTCATGGCATGG 59.565 38.462 26.15 16.88 0.00 3.66
316 317 5.784398 ATATATTGGTCTCATGGCATGGA 57.216 39.130 26.15 18.77 0.00 3.41
317 318 2.062971 ATTGGTCTCATGGCATGGAC 57.937 50.000 27.14 27.14 32.91 4.02
318 319 0.697658 TTGGTCTCATGGCATGGACA 59.302 50.000 31.60 21.77 34.33 4.02
319 320 0.035152 TGGTCTCATGGCATGGACAC 60.035 55.000 31.60 24.94 34.33 3.67
320 321 0.035152 GGTCTCATGGCATGGACACA 60.035 55.000 31.60 15.22 34.33 3.72
321 322 1.409241 GGTCTCATGGCATGGACACAT 60.409 52.381 31.60 0.08 37.99 3.21
353 354 5.893897 GCCATGGCATTTTAATTCCAAAA 57.106 34.783 32.08 0.00 35.38 2.44
354 355 6.264841 GCCATGGCATTTTAATTCCAAAAA 57.735 33.333 32.08 0.00 35.38 1.94
384 385 7.951530 AAAATGATCAGAAACACATGAAACC 57.048 32.000 0.00 0.00 0.00 3.27
385 386 6.906157 AATGATCAGAAACACATGAAACCT 57.094 33.333 0.00 0.00 0.00 3.50
386 387 6.906157 ATGATCAGAAACACATGAAACCTT 57.094 33.333 0.00 0.00 0.00 3.50
387 388 6.075762 TGATCAGAAACACATGAAACCTTG 57.924 37.500 0.00 0.00 0.00 3.61
388 389 4.305989 TCAGAAACACATGAAACCTTGC 57.694 40.909 0.00 0.00 0.00 4.01
389 390 3.953612 TCAGAAACACATGAAACCTTGCT 59.046 39.130 0.00 0.00 0.00 3.91
390 391 4.402155 TCAGAAACACATGAAACCTTGCTT 59.598 37.500 0.00 0.00 0.00 3.91
391 392 4.505191 CAGAAACACATGAAACCTTGCTTG 59.495 41.667 0.00 0.00 0.00 4.01
392 393 4.402155 AGAAACACATGAAACCTTGCTTGA 59.598 37.500 0.00 0.00 0.00 3.02
393 394 4.942761 AACACATGAAACCTTGCTTGAT 57.057 36.364 0.00 0.00 0.00 2.57
394 395 6.265196 AGAAACACATGAAACCTTGCTTGATA 59.735 34.615 0.00 0.00 0.00 2.15
395 396 5.376854 ACACATGAAACCTTGCTTGATAC 57.623 39.130 0.00 0.00 0.00 2.24
396 397 4.826733 ACACATGAAACCTTGCTTGATACA 59.173 37.500 0.00 0.00 0.00 2.29
397 398 5.301551 ACACATGAAACCTTGCTTGATACAA 59.698 36.000 0.00 0.00 0.00 2.41
398 399 6.015180 ACACATGAAACCTTGCTTGATACAAT 60.015 34.615 0.00 0.00 0.00 2.71
399 400 6.309494 CACATGAAACCTTGCTTGATACAATG 59.691 38.462 0.00 0.00 0.00 2.82
400 401 6.015180 ACATGAAACCTTGCTTGATACAATGT 60.015 34.615 0.00 0.00 0.00 2.71
401 402 6.012658 TGAAACCTTGCTTGATACAATGTC 57.987 37.500 0.00 0.00 0.00 3.06
402 403 5.534278 TGAAACCTTGCTTGATACAATGTCA 59.466 36.000 0.00 0.00 0.00 3.58
403 404 6.209192 TGAAACCTTGCTTGATACAATGTCAT 59.791 34.615 0.00 0.00 0.00 3.06
404 405 5.571784 ACCTTGCTTGATACAATGTCATG 57.428 39.130 0.00 0.00 0.00 3.07
405 406 4.142315 ACCTTGCTTGATACAATGTCATGC 60.142 41.667 0.00 0.00 43.26 4.06
406 407 4.357142 CTTGCTTGATACAATGTCATGCC 58.643 43.478 9.37 0.00 42.67 4.40
407 408 3.354467 TGCTTGATACAATGTCATGCCA 58.646 40.909 9.37 0.00 42.67 4.92
408 409 3.129113 TGCTTGATACAATGTCATGCCAC 59.871 43.478 9.37 0.00 42.67 5.01
409 410 3.489738 GCTTGATACAATGTCATGCCACC 60.490 47.826 0.00 0.00 39.49 4.61
410 411 3.362870 TGATACAATGTCATGCCACCA 57.637 42.857 0.00 0.00 0.00 4.17
411 412 3.694926 TGATACAATGTCATGCCACCAA 58.305 40.909 0.00 0.00 0.00 3.67
412 413 3.695556 TGATACAATGTCATGCCACCAAG 59.304 43.478 0.00 0.00 0.00 3.61
413 414 2.291209 ACAATGTCATGCCACCAAGA 57.709 45.000 0.00 0.00 0.00 3.02
414 415 2.811410 ACAATGTCATGCCACCAAGAT 58.189 42.857 0.00 0.00 0.00 2.40
415 416 2.494471 ACAATGTCATGCCACCAAGATG 59.506 45.455 0.00 0.00 0.00 2.90
416 417 2.756207 CAATGTCATGCCACCAAGATGA 59.244 45.455 0.00 0.00 0.00 2.92
417 418 2.812836 TGTCATGCCACCAAGATGAT 57.187 45.000 0.00 0.00 0.00 2.45
418 419 2.371306 TGTCATGCCACCAAGATGATG 58.629 47.619 0.00 0.00 0.00 3.07
419 420 2.291089 TGTCATGCCACCAAGATGATGT 60.291 45.455 0.00 0.00 0.00 3.06
420 421 2.098607 GTCATGCCACCAAGATGATGTG 59.901 50.000 0.00 0.00 0.00 3.21
488 489 7.980662 TGGTGCCATGTCATCATAATTAAAAAG 59.019 33.333 0.00 0.00 32.47 2.27
631 633 5.890424 ATTTAACATGTAGGAACCAACCG 57.110 39.130 0.00 0.00 34.73 4.44
645 648 5.407084 GGAACCAACCGTAAATGGATTTTTG 59.593 40.000 0.00 0.00 39.12 2.44
784 791 5.387113 TCAGCAGGTAATTATGTGGGAAT 57.613 39.130 0.00 0.00 0.00 3.01
992 1007 4.602259 CGTGGTGGACGCCTGTGT 62.602 66.667 3.31 0.00 42.21 3.72
1005 1020 1.301637 CTGTGTGTCGTCCATGGCA 60.302 57.895 6.96 0.00 0.00 4.92
1014 1029 3.006133 TCCATGGCACGGCTACCA 61.006 61.111 6.96 0.00 41.06 3.25
1053 1068 1.675483 CATGCCGCCAAGCTGTATAAA 59.325 47.619 0.00 0.00 0.00 1.40
1074 1089 2.605295 CTCCCCACCCCGTACACA 60.605 66.667 0.00 0.00 0.00 3.72
1104 1119 1.045350 CCATTCCCCTCGCTCTCTCA 61.045 60.000 0.00 0.00 0.00 3.27
1172 1187 2.575108 TCGTCTTAGCCACGACCAT 58.425 52.632 0.00 0.00 41.27 3.55
1242 1257 3.878103 GTCTGCATCTTCTACTCTACCGA 59.122 47.826 0.00 0.00 0.00 4.69
1255 1270 1.682451 CTACCGAATCAAGGCCGGGA 61.682 60.000 2.18 0.00 46.83 5.14
1302 1317 3.790437 CCTCCGCCATGGCTGTCT 61.790 66.667 33.07 0.00 39.32 3.41
1320 1335 2.079158 TCTAACACCGTCGTTCGATCT 58.921 47.619 0.00 0.00 42.86 2.75
1330 1345 1.683385 TCGTTCGATCTGCATCATCCT 59.317 47.619 0.00 0.00 0.00 3.24
1340 1355 1.442526 GCATCATCCTGGCAACCTCG 61.443 60.000 0.00 0.00 0.00 4.63
1385 1400 0.244994 TCGCAGTGAGCTCCTCTTTC 59.755 55.000 12.15 3.65 42.61 2.62
1425 1442 1.106944 CCTCCCGTTGTTGTTTGCCT 61.107 55.000 0.00 0.00 0.00 4.75
1591 1608 2.103538 GCATCTACCGCCGTTCGA 59.896 61.111 0.00 0.00 41.67 3.71
1676 1693 1.895707 GCTGCTGCCTGACTGTTGT 60.896 57.895 3.85 0.00 0.00 3.32
1683 1700 0.603707 GCCTGACTGTTGTGCTGCTA 60.604 55.000 0.00 0.00 0.00 3.49
1764 1781 1.451747 GAGACCCGTCCTACTCGCT 60.452 63.158 0.00 0.00 0.00 4.93
1768 1785 1.822613 CCCGTCCTACTCGCTGCTA 60.823 63.158 0.00 0.00 0.00 3.49
1785 1802 2.244117 CTATGCCTGACTGCCGTGGT 62.244 60.000 0.00 0.00 0.00 4.16
1795 1812 2.397413 CTGCCGTGGTCTCCCTTGTT 62.397 60.000 0.00 0.00 0.00 2.83
2115 2132 7.546316 GTCTATGTTCTGTTAGGAGAGAAAACC 59.454 40.741 0.00 0.00 36.98 3.27
2302 2319 4.926832 CGGAAAACAACCAAGTGAAGTTTT 59.073 37.500 0.00 0.00 42.91 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.312443 TCAAACGTGTATTGTTCCCTCTC 58.688 43.478 0.00 0.00 0.00 3.20
1 2 4.345859 TCAAACGTGTATTGTTCCCTCT 57.654 40.909 0.00 0.00 0.00 3.69
2 3 4.693566 TCATCAAACGTGTATTGTTCCCTC 59.306 41.667 0.00 0.00 0.00 4.30
3 4 4.454504 GTCATCAAACGTGTATTGTTCCCT 59.545 41.667 0.00 0.00 0.00 4.20
4 5 4.668177 CGTCATCAAACGTGTATTGTTCCC 60.668 45.833 0.00 0.00 37.86 3.97
5 6 4.150980 TCGTCATCAAACGTGTATTGTTCC 59.849 41.667 0.00 0.00 43.08 3.62
6 7 5.258685 TCGTCATCAAACGTGTATTGTTC 57.741 39.130 0.00 0.00 43.08 3.18
7 8 5.437263 GTTCGTCATCAAACGTGTATTGTT 58.563 37.500 0.00 0.00 43.08 2.83
8 9 4.375606 CGTTCGTCATCAAACGTGTATTGT 60.376 41.667 0.00 0.00 42.37 2.71
9 10 4.072244 CGTTCGTCATCAAACGTGTATTG 58.928 43.478 0.00 0.00 42.37 1.90
10 11 3.122278 CCGTTCGTCATCAAACGTGTATT 59.878 43.478 6.85 0.00 45.03 1.89
11 12 2.664568 CCGTTCGTCATCAAACGTGTAT 59.335 45.455 6.85 0.00 45.03 2.29
12 13 2.052891 CCGTTCGTCATCAAACGTGTA 58.947 47.619 6.85 0.00 45.03 2.90
13 14 0.856641 CCGTTCGTCATCAAACGTGT 59.143 50.000 6.85 0.00 45.03 4.49
14 15 0.162933 CCCGTTCGTCATCAAACGTG 59.837 55.000 6.85 0.00 45.03 4.49
15 16 0.032403 TCCCGTTCGTCATCAAACGT 59.968 50.000 6.85 0.00 45.03 3.99
16 17 0.713883 CTCCCGTTCGTCATCAAACG 59.286 55.000 0.93 0.93 45.83 3.60
17 18 2.074547 TCTCCCGTTCGTCATCAAAC 57.925 50.000 0.00 0.00 0.00 2.93
18 19 4.081862 AGTTATCTCCCGTTCGTCATCAAA 60.082 41.667 0.00 0.00 0.00 2.69
19 20 3.446161 AGTTATCTCCCGTTCGTCATCAA 59.554 43.478 0.00 0.00 0.00 2.57
20 21 3.021695 AGTTATCTCCCGTTCGTCATCA 58.978 45.455 0.00 0.00 0.00 3.07
21 22 3.712091 AGTTATCTCCCGTTCGTCATC 57.288 47.619 0.00 0.00 0.00 2.92
22 23 3.181478 GGAAGTTATCTCCCGTTCGTCAT 60.181 47.826 0.00 0.00 0.00 3.06
23 24 2.165030 GGAAGTTATCTCCCGTTCGTCA 59.835 50.000 0.00 0.00 0.00 4.35
24 25 2.426381 AGGAAGTTATCTCCCGTTCGTC 59.574 50.000 0.00 0.00 0.00 4.20
25 26 2.426381 GAGGAAGTTATCTCCCGTTCGT 59.574 50.000 0.00 0.00 0.00 3.85
26 27 2.688958 AGAGGAAGTTATCTCCCGTTCG 59.311 50.000 3.01 0.00 0.00 3.95
27 28 4.739587 AAGAGGAAGTTATCTCCCGTTC 57.260 45.455 3.01 0.00 0.00 3.95
28 29 4.097589 CGTAAGAGGAAGTTATCTCCCGTT 59.902 45.833 3.01 0.00 43.02 4.44
29 30 3.631227 CGTAAGAGGAAGTTATCTCCCGT 59.369 47.826 3.01 0.00 43.02 5.28
30 31 3.004524 CCGTAAGAGGAAGTTATCTCCCG 59.995 52.174 3.01 3.36 43.02 5.14
31 32 3.243805 GCCGTAAGAGGAAGTTATCTCCC 60.244 52.174 3.01 0.00 43.02 4.30
32 33 3.243805 GGCCGTAAGAGGAAGTTATCTCC 60.244 52.174 0.00 0.00 43.02 3.71
33 34 3.637694 AGGCCGTAAGAGGAAGTTATCTC 59.362 47.826 0.00 0.00 43.02 2.75
34 35 3.644335 AGGCCGTAAGAGGAAGTTATCT 58.356 45.455 0.00 0.00 43.02 1.98
35 36 4.142004 TGAAGGCCGTAAGAGGAAGTTATC 60.142 45.833 0.00 0.00 43.02 1.75
36 37 3.773119 TGAAGGCCGTAAGAGGAAGTTAT 59.227 43.478 0.00 0.00 43.02 1.89
37 38 3.167485 TGAAGGCCGTAAGAGGAAGTTA 58.833 45.455 0.00 0.00 43.02 2.24
38 39 1.975680 TGAAGGCCGTAAGAGGAAGTT 59.024 47.619 0.00 0.00 43.02 2.66
39 40 1.640917 TGAAGGCCGTAAGAGGAAGT 58.359 50.000 0.00 0.00 43.02 3.01
40 41 2.762535 TTGAAGGCCGTAAGAGGAAG 57.237 50.000 0.00 0.00 43.02 3.46
41 42 3.713826 AATTGAAGGCCGTAAGAGGAA 57.286 42.857 0.00 0.00 43.02 3.36
42 43 3.713826 AAATTGAAGGCCGTAAGAGGA 57.286 42.857 0.00 0.00 43.02 3.71
43 44 4.783764 AAAAATTGAAGGCCGTAAGAGG 57.216 40.909 0.00 0.00 43.02 3.69
71 72 7.799447 TGACAATTGTATTAGTGCACGTTAAAC 59.201 33.333 11.95 8.18 0.00 2.01
72 73 7.862648 TGACAATTGTATTAGTGCACGTTAAA 58.137 30.769 11.95 5.35 0.00 1.52
73 74 7.422878 TGACAATTGTATTAGTGCACGTTAA 57.577 32.000 11.95 6.09 0.00 2.01
74 75 7.118535 ACATGACAATTGTATTAGTGCACGTTA 59.881 33.333 11.95 0.72 0.00 3.18
75 76 5.933187 TGACAATTGTATTAGTGCACGTT 57.067 34.783 11.95 2.73 0.00 3.99
76 77 5.411361 ACATGACAATTGTATTAGTGCACGT 59.589 36.000 11.95 4.40 0.00 4.49
77 78 5.734035 CACATGACAATTGTATTAGTGCACG 59.266 40.000 11.95 0.00 0.00 5.34
78 79 6.841119 TCACATGACAATTGTATTAGTGCAC 58.159 36.000 11.95 9.40 0.00 4.57
79 80 7.446001 TTCACATGACAATTGTATTAGTGCA 57.554 32.000 11.95 3.62 0.00 4.57
80 81 8.741101 TTTTCACATGACAATTGTATTAGTGC 57.259 30.769 11.95 0.00 0.00 4.40
85 86 9.775854 TCCAAATTTTCACATGACAATTGTATT 57.224 25.926 11.95 1.35 35.38 1.89
86 87 9.775854 TTCCAAATTTTCACATGACAATTGTAT 57.224 25.926 11.95 3.08 35.38 2.29
87 88 9.605275 TTTCCAAATTTTCACATGACAATTGTA 57.395 25.926 11.95 0.61 35.38 2.41
88 89 8.503458 TTTCCAAATTTTCACATGACAATTGT 57.497 26.923 11.78 11.78 35.38 2.71
89 90 9.953697 ATTTTCCAAATTTTCACATGACAATTG 57.046 25.926 3.24 3.24 35.38 2.32
93 94 9.170734 TGAAATTTTCCAAATTTTCACATGACA 57.829 25.926 14.02 2.14 40.45 3.58
94 95 9.654417 CTGAAATTTTCCAAATTTTCACATGAC 57.346 29.630 14.02 0.20 40.45 3.06
95 96 8.344098 GCTGAAATTTTCCAAATTTTCACATGA 58.656 29.630 14.02 0.00 40.45 3.07
96 97 7.321746 CGCTGAAATTTTCCAAATTTTCACATG 59.678 33.333 14.02 0.00 40.45 3.21
97 98 7.354257 CGCTGAAATTTTCCAAATTTTCACAT 58.646 30.769 14.02 0.00 40.45 3.21
98 99 6.238320 CCGCTGAAATTTTCCAAATTTTCACA 60.238 34.615 14.02 5.58 40.45 3.58
99 100 6.135400 CCGCTGAAATTTTCCAAATTTTCAC 58.865 36.000 14.02 11.33 40.45 3.18
100 101 5.819901 ACCGCTGAAATTTTCCAAATTTTCA 59.180 32.000 15.91 15.91 41.80 2.69
101 102 6.018343 TGACCGCTGAAATTTTCCAAATTTTC 60.018 34.615 6.68 8.64 38.11 2.29
102 103 5.819901 TGACCGCTGAAATTTTCCAAATTTT 59.180 32.000 6.68 0.24 30.68 1.82
103 104 5.363939 TGACCGCTGAAATTTTCCAAATTT 58.636 33.333 6.68 6.86 32.98 1.82
104 105 4.954875 TGACCGCTGAAATTTTCCAAATT 58.045 34.783 6.68 0.00 0.00 1.82
105 106 4.599047 TGACCGCTGAAATTTTCCAAAT 57.401 36.364 6.68 0.00 0.00 2.32
106 107 4.599047 ATGACCGCTGAAATTTTCCAAA 57.401 36.364 6.68 0.00 0.00 3.28
107 108 4.599047 AATGACCGCTGAAATTTTCCAA 57.401 36.364 6.68 0.00 0.00 3.53
108 109 4.038522 TCAAATGACCGCTGAAATTTTCCA 59.961 37.500 6.68 0.00 0.00 3.53
109 110 4.385748 GTCAAATGACCGCTGAAATTTTCC 59.614 41.667 6.68 0.00 39.07 3.13
110 111 5.500740 GTCAAATGACCGCTGAAATTTTC 57.499 39.130 2.04 2.05 39.07 2.29
178 179 9.793252 GCATGTAGATGTAGTTCAAATTTGAAT 57.207 29.630 30.63 22.05 39.29 2.57
179 180 8.791675 TGCATGTAGATGTAGTTCAAATTTGAA 58.208 29.630 26.01 26.01 37.09 2.69
180 181 8.334263 TGCATGTAGATGTAGTTCAAATTTGA 57.666 30.769 16.91 16.91 31.62 2.69
181 182 8.853345 GTTGCATGTAGATGTAGTTCAAATTTG 58.147 33.333 12.15 12.15 31.50 2.32
182 183 7.750458 CGTTGCATGTAGATGTAGTTCAAATTT 59.250 33.333 1.37 0.00 31.50 1.82
183 184 7.243487 CGTTGCATGTAGATGTAGTTCAAATT 58.757 34.615 1.37 0.00 31.50 1.82
184 185 6.183360 CCGTTGCATGTAGATGTAGTTCAAAT 60.183 38.462 1.37 0.00 31.50 2.32
185 186 5.121611 CCGTTGCATGTAGATGTAGTTCAAA 59.878 40.000 1.37 0.00 31.50 2.69
186 187 4.629634 CCGTTGCATGTAGATGTAGTTCAA 59.370 41.667 1.37 0.00 31.50 2.69
187 188 4.180817 CCGTTGCATGTAGATGTAGTTCA 58.819 43.478 1.37 0.00 31.50 3.18
188 189 3.001330 GCCGTTGCATGTAGATGTAGTTC 59.999 47.826 1.37 0.00 37.47 3.01
189 190 2.936498 GCCGTTGCATGTAGATGTAGTT 59.064 45.455 1.37 0.00 37.47 2.24
190 191 2.168521 AGCCGTTGCATGTAGATGTAGT 59.831 45.455 1.37 0.00 41.13 2.73
191 192 2.826428 AGCCGTTGCATGTAGATGTAG 58.174 47.619 1.37 0.00 41.13 2.74
192 193 2.979814 AGCCGTTGCATGTAGATGTA 57.020 45.000 1.37 0.00 41.13 2.29
193 194 2.936498 GTTAGCCGTTGCATGTAGATGT 59.064 45.455 1.37 0.00 41.13 3.06
194 195 2.287915 GGTTAGCCGTTGCATGTAGATG 59.712 50.000 0.00 0.00 41.13 2.90
195 196 2.561569 GGTTAGCCGTTGCATGTAGAT 58.438 47.619 0.00 0.00 41.13 1.98
196 197 2.018542 GGTTAGCCGTTGCATGTAGA 57.981 50.000 0.00 0.00 41.13 2.59
214 215 8.389603 CAAATATGATTTTTCAAACCATTCCGG 58.610 33.333 0.00 0.00 42.50 5.14
215 216 8.934825 ACAAATATGATTTTTCAAACCATTCCG 58.065 29.630 0.00 0.00 0.00 4.30
228 229 9.502145 CGCACACAAGTATACAAATATGATTTT 57.498 29.630 5.50 0.00 0.00 1.82
229 230 8.888716 TCGCACACAAGTATACAAATATGATTT 58.111 29.630 5.50 0.00 0.00 2.17
230 231 8.432110 TCGCACACAAGTATACAAATATGATT 57.568 30.769 5.50 0.00 0.00 2.57
231 232 8.607441 ATCGCACACAAGTATACAAATATGAT 57.393 30.769 5.50 0.00 0.00 2.45
232 233 8.432110 AATCGCACACAAGTATACAAATATGA 57.568 30.769 5.50 0.00 0.00 2.15
237 238 9.549509 GAATTAAATCGCACACAAGTATACAAA 57.450 29.630 5.50 0.00 0.00 2.83
238 239 8.178964 GGAATTAAATCGCACACAAGTATACAA 58.821 33.333 5.50 0.00 0.00 2.41
239 240 7.334671 TGGAATTAAATCGCACACAAGTATACA 59.665 33.333 5.50 0.00 0.00 2.29
240 241 7.690228 TGGAATTAAATCGCACACAAGTATAC 58.310 34.615 0.00 0.00 0.00 1.47
241 242 7.851387 TGGAATTAAATCGCACACAAGTATA 57.149 32.000 0.00 0.00 0.00 1.47
242 243 6.751514 TGGAATTAAATCGCACACAAGTAT 57.248 33.333 0.00 0.00 0.00 2.12
243 244 6.150307 ACATGGAATTAAATCGCACACAAGTA 59.850 34.615 0.00 0.00 0.00 2.24
244 245 5.048083 ACATGGAATTAAATCGCACACAAGT 60.048 36.000 0.00 0.00 0.00 3.16
245 246 5.286797 CACATGGAATTAAATCGCACACAAG 59.713 40.000 0.00 0.00 0.00 3.16
246 247 5.159925 CACATGGAATTAAATCGCACACAA 58.840 37.500 0.00 0.00 0.00 3.33
247 248 4.731720 CACATGGAATTAAATCGCACACA 58.268 39.130 0.00 0.00 0.00 3.72
248 249 3.547468 GCACATGGAATTAAATCGCACAC 59.453 43.478 0.00 0.00 0.00 3.82
249 250 3.192212 TGCACATGGAATTAAATCGCACA 59.808 39.130 0.00 0.00 0.00 4.57
250 251 3.768406 TGCACATGGAATTAAATCGCAC 58.232 40.909 0.00 0.00 0.00 5.34
251 252 3.443329 ACTGCACATGGAATTAAATCGCA 59.557 39.130 0.00 0.00 0.00 5.10
252 253 4.032703 ACTGCACATGGAATTAAATCGC 57.967 40.909 0.00 0.00 0.00 4.58
253 254 8.633075 AATTTACTGCACATGGAATTAAATCG 57.367 30.769 0.00 0.00 0.00 3.34
258 259 8.902806 CCTTCTAATTTACTGCACATGGAATTA 58.097 33.333 0.00 0.00 0.00 1.40
259 260 7.615365 TCCTTCTAATTTACTGCACATGGAATT 59.385 33.333 0.00 0.00 0.00 2.17
260 261 7.118723 TCCTTCTAATTTACTGCACATGGAAT 58.881 34.615 0.00 0.00 0.00 3.01
261 262 6.480763 TCCTTCTAATTTACTGCACATGGAA 58.519 36.000 0.00 0.00 0.00 3.53
262 263 6.061022 TCCTTCTAATTTACTGCACATGGA 57.939 37.500 0.00 0.00 0.00 3.41
263 264 6.757897 TTCCTTCTAATTTACTGCACATGG 57.242 37.500 0.00 0.00 0.00 3.66
264 265 9.643693 AAAATTCCTTCTAATTTACTGCACATG 57.356 29.630 0.00 0.00 37.93 3.21
265 266 9.860898 GAAAATTCCTTCTAATTTACTGCACAT 57.139 29.630 0.00 0.00 37.93 3.21
266 267 8.855110 TGAAAATTCCTTCTAATTTACTGCACA 58.145 29.630 0.00 0.00 37.93 4.57
267 268 9.691362 TTGAAAATTCCTTCTAATTTACTGCAC 57.309 29.630 0.00 0.00 37.93 4.57
285 286 9.768662 GCCATGAGACCAATATATTTGAAAATT 57.231 29.630 3.66 0.00 0.00 1.82
286 287 8.926374 TGCCATGAGACCAATATATTTGAAAAT 58.074 29.630 3.66 0.00 0.00 1.82
287 288 8.303780 TGCCATGAGACCAATATATTTGAAAA 57.696 30.769 3.66 0.00 0.00 2.29
288 289 7.894753 TGCCATGAGACCAATATATTTGAAA 57.105 32.000 3.66 0.00 0.00 2.69
289 290 7.039574 CCATGCCATGAGACCAATATATTTGAA 60.040 37.037 6.18 0.00 0.00 2.69
290 291 6.434965 CCATGCCATGAGACCAATATATTTGA 59.565 38.462 6.18 0.00 0.00 2.69
291 292 6.434965 TCCATGCCATGAGACCAATATATTTG 59.565 38.462 6.18 0.00 0.00 2.32
292 293 6.435277 GTCCATGCCATGAGACCAATATATTT 59.565 38.462 6.18 0.00 0.00 1.40
293 294 5.948162 GTCCATGCCATGAGACCAATATATT 59.052 40.000 6.18 0.00 0.00 1.28
294 295 5.014438 TGTCCATGCCATGAGACCAATATAT 59.986 40.000 17.86 0.00 32.79 0.86
295 296 4.350520 TGTCCATGCCATGAGACCAATATA 59.649 41.667 17.86 2.53 32.79 0.86
296 297 3.138839 TGTCCATGCCATGAGACCAATAT 59.861 43.478 17.86 0.00 32.79 1.28
297 298 2.509131 TGTCCATGCCATGAGACCAATA 59.491 45.455 17.86 3.32 32.79 1.90
298 299 1.285667 TGTCCATGCCATGAGACCAAT 59.714 47.619 17.86 0.00 32.79 3.16
299 300 0.697658 TGTCCATGCCATGAGACCAA 59.302 50.000 17.86 4.11 32.79 3.67
300 301 0.035152 GTGTCCATGCCATGAGACCA 60.035 55.000 17.86 8.20 32.79 4.02
301 302 0.035152 TGTGTCCATGCCATGAGACC 60.035 55.000 17.86 12.23 32.79 3.85
302 303 1.674441 CATGTGTCCATGCCATGAGAC 59.326 52.381 6.18 12.03 41.88 3.36
303 304 2.047002 CATGTGTCCATGCCATGAGA 57.953 50.000 6.18 0.00 41.88 3.27
331 332 5.893897 TTTTGGAATTAAAATGCCATGGC 57.106 34.783 30.54 30.54 43.67 4.40
359 360 8.206189 AGGTTTCATGTGTTTCTGATCATTTTT 58.794 29.630 0.00 0.00 0.00 1.94
360 361 7.729116 AGGTTTCATGTGTTTCTGATCATTTT 58.271 30.769 0.00 0.00 0.00 1.82
361 362 7.294017 AGGTTTCATGTGTTTCTGATCATTT 57.706 32.000 0.00 0.00 0.00 2.32
362 363 6.906157 AGGTTTCATGTGTTTCTGATCATT 57.094 33.333 0.00 0.00 0.00 2.57
363 364 6.684686 CAAGGTTTCATGTGTTTCTGATCAT 58.315 36.000 0.00 0.00 0.00 2.45
364 365 5.507817 GCAAGGTTTCATGTGTTTCTGATCA 60.508 40.000 0.00 0.00 0.00 2.92
365 366 4.919754 GCAAGGTTTCATGTGTTTCTGATC 59.080 41.667 0.00 0.00 0.00 2.92
366 367 4.586001 AGCAAGGTTTCATGTGTTTCTGAT 59.414 37.500 0.00 0.00 0.00 2.90
367 368 3.953612 AGCAAGGTTTCATGTGTTTCTGA 59.046 39.130 0.00 0.00 0.00 3.27
368 369 4.311816 AGCAAGGTTTCATGTGTTTCTG 57.688 40.909 0.00 0.00 0.00 3.02
369 370 4.402155 TCAAGCAAGGTTTCATGTGTTTCT 59.598 37.500 0.00 0.00 0.00 2.52
370 371 4.681744 TCAAGCAAGGTTTCATGTGTTTC 58.318 39.130 0.00 0.00 0.00 2.78
371 372 4.734398 TCAAGCAAGGTTTCATGTGTTT 57.266 36.364 0.00 0.00 0.00 2.83
372 373 4.942761 ATCAAGCAAGGTTTCATGTGTT 57.057 36.364 0.00 0.00 0.00 3.32
373 374 4.826733 TGTATCAAGCAAGGTTTCATGTGT 59.173 37.500 0.00 0.00 0.00 3.72
374 375 5.375417 TGTATCAAGCAAGGTTTCATGTG 57.625 39.130 0.00 0.00 0.00 3.21
375 376 6.015180 ACATTGTATCAAGCAAGGTTTCATGT 60.015 34.615 0.00 0.00 37.54 3.21
376 377 6.392354 ACATTGTATCAAGCAAGGTTTCATG 58.608 36.000 0.00 0.00 37.54 3.07
377 378 6.209192 TGACATTGTATCAAGCAAGGTTTCAT 59.791 34.615 0.00 0.00 40.29 2.57
378 379 5.534278 TGACATTGTATCAAGCAAGGTTTCA 59.466 36.000 0.00 0.00 40.29 2.69
379 380 6.012658 TGACATTGTATCAAGCAAGGTTTC 57.987 37.500 0.00 0.00 40.29 2.78
380 381 6.392354 CATGACATTGTATCAAGCAAGGTTT 58.608 36.000 0.00 0.00 40.29 3.27
381 382 5.622914 GCATGACATTGTATCAAGCAAGGTT 60.623 40.000 0.00 0.00 40.29 3.50
382 383 4.142315 GCATGACATTGTATCAAGCAAGGT 60.142 41.667 0.00 0.00 42.41 3.50
383 384 4.357142 GCATGACATTGTATCAAGCAAGG 58.643 43.478 0.00 0.00 39.86 3.61
384 385 4.142337 TGGCATGACATTGTATCAAGCAAG 60.142 41.667 0.00 0.00 41.44 4.01
385 386 3.762823 TGGCATGACATTGTATCAAGCAA 59.237 39.130 0.00 0.00 41.44 3.91
386 387 3.129113 GTGGCATGACATTGTATCAAGCA 59.871 43.478 3.50 0.00 41.44 3.91
387 388 3.489738 GGTGGCATGACATTGTATCAAGC 60.490 47.826 3.50 0.00 39.48 4.01
388 389 3.695556 TGGTGGCATGACATTGTATCAAG 59.304 43.478 3.50 0.00 0.00 3.02
389 390 3.694926 TGGTGGCATGACATTGTATCAA 58.305 40.909 3.50 0.00 0.00 2.57
390 391 3.362870 TGGTGGCATGACATTGTATCA 57.637 42.857 3.50 0.00 0.00 2.15
391 392 3.947196 TCTTGGTGGCATGACATTGTATC 59.053 43.478 3.50 0.00 0.00 2.24
392 393 3.966979 TCTTGGTGGCATGACATTGTAT 58.033 40.909 3.50 0.00 0.00 2.29
393 394 3.431673 TCTTGGTGGCATGACATTGTA 57.568 42.857 3.50 0.00 0.00 2.41
394 395 2.291209 TCTTGGTGGCATGACATTGT 57.709 45.000 3.50 0.00 0.00 2.71
395 396 2.756207 TCATCTTGGTGGCATGACATTG 59.244 45.455 3.50 0.00 0.00 2.82
396 397 3.090210 TCATCTTGGTGGCATGACATT 57.910 42.857 3.50 0.00 0.00 2.71
397 398 2.812836 TCATCTTGGTGGCATGACAT 57.187 45.000 3.50 0.00 0.00 3.06
398 399 2.291089 ACATCATCTTGGTGGCATGACA 60.291 45.455 0.00 0.00 31.38 3.58
399 400 2.098607 CACATCATCTTGGTGGCATGAC 59.901 50.000 0.00 0.00 31.38 3.06
400 401 2.291089 ACACATCATCTTGGTGGCATGA 60.291 45.455 0.00 0.00 36.87 3.07
401 402 2.097036 ACACATCATCTTGGTGGCATG 58.903 47.619 0.00 0.00 36.87 4.06
402 403 2.097036 CACACATCATCTTGGTGGCAT 58.903 47.619 0.00 0.00 36.87 4.40
403 404 1.202915 ACACACATCATCTTGGTGGCA 60.203 47.619 0.00 0.00 36.87 4.92
404 405 1.538047 ACACACATCATCTTGGTGGC 58.462 50.000 0.00 0.00 36.87 5.01
405 406 4.071423 TGTTACACACATCATCTTGGTGG 58.929 43.478 0.00 0.00 36.87 4.61
488 489 4.312443 TGGAACAACGTGAGGATTAGAAC 58.688 43.478 0.00 0.00 31.92 3.01
631 633 7.495606 CCTAGGGCAATTCAAAAATCCATTTAC 59.504 37.037 0.00 0.00 0.00 2.01
1005 1020 4.712425 GACGCGTGTGGTAGCCGT 62.712 66.667 20.70 0.00 0.00 5.68
1053 1068 3.944411 TACGGGGTGGGGAGGGTT 61.944 66.667 0.00 0.00 0.00 4.11
1074 1089 0.927029 GGGGAATGGAGCTAGGGTTT 59.073 55.000 0.00 0.00 0.00 3.27
1104 1119 3.600388 GTCCAAATCGAAGATGGTGAGT 58.400 45.455 12.50 0.00 45.12 3.41
1242 1257 1.843851 TGATACTTCCCGGCCTTGATT 59.156 47.619 0.00 0.00 0.00 2.57
1255 1270 2.202703 GCGTCGCGGGTGATACTT 60.203 61.111 6.13 0.00 0.00 2.24
1302 1317 1.730121 GCAGATCGAACGACGGTGTTA 60.730 52.381 0.00 0.00 42.82 2.41
1320 1335 0.394762 GAGGTTGCCAGGATGATGCA 60.395 55.000 0.00 0.00 39.69 3.96
1399 1416 1.462627 AACAACGGGAGGAAGGGGA 60.463 57.895 0.00 0.00 0.00 4.81
1444 1461 2.733218 CGAACTCGCACAAGCCGA 60.733 61.111 0.00 0.00 37.52 5.54
1480 1497 4.961511 GCGCACACGTGGAGGTGA 62.962 66.667 21.57 0.00 42.83 4.02
1519 1536 2.407616 CGCATCACGCCTAGACGA 59.592 61.111 5.13 0.00 37.30 4.20
1621 1638 2.186384 GCAGAGGTCAGCGAGCAT 59.814 61.111 9.70 0.00 31.89 3.79
1764 1781 2.187685 CGGCAGTCAGGCATAGCA 59.812 61.111 0.00 0.00 44.47 3.49
1768 1785 3.612247 GACCACGGCAGTCAGGCAT 62.612 63.158 0.00 0.00 44.47 4.40
1785 1802 2.654877 GCGGACGAACAAGGGAGA 59.345 61.111 0.00 0.00 0.00 3.71
2115 2132 8.139521 AGTTAAGACAGTAAACCTCTTTTTCG 57.860 34.615 0.00 0.00 0.00 3.46
2171 2188 4.314121 CCATTAGATAGCCTGAACAGCTC 58.686 47.826 0.00 0.00 41.83 4.09


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

AutoCloner maintained by Alex Coulton.