Multiple sequence alignment - TraesCS3A01G169500

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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 TraesCS3A01G169500 chr3A 100.000 8120 0 0 1 8120 177686055 177694174 0.000000e+00 14995.0
1 TraesCS3A01G169500 chr3A 100.000 572 0 0 8221 8792 177694275 177694846 0.000000e+00 1057.0
2 TraesCS3A01G169500 chr3A 99.650 572 2 0 8221 8792 177699736 177700307 0.000000e+00 1046.0
3 TraesCS3A01G169500 chr1B 99.116 7805 61 4 321 8120 150784469 150792270 0.000000e+00 14024.0
4 TraesCS3A01G169500 chr1B 99.301 572 4 0 8221 8792 251846841 251847412 0.000000e+00 1035.0
5 TraesCS3A01G169500 chr1B 99.301 572 4 0 8221 8792 614569827 614570398 0.000000e+00 1035.0
6 TraesCS3A01G169500 chr4B 99.116 7805 60 6 321 8120 461635186 461642986 0.000000e+00 14022.0
7 TraesCS3A01G169500 chr4B 98.937 7805 68 6 321 8120 461673262 461681056 0.000000e+00 13939.0
8 TraesCS3A01G169500 chr4B 99.301 572 4 0 8221 8792 469029715 469030286 0.000000e+00 1035.0
9 TraesCS3A01G169500 chr4B 80.443 271 53 0 51 321 22487923 22488193 3.220000e-49 207.0
10 TraesCS3A01G169500 chr5A 99.026 7805 68 5 321 8120 74918112 74910311 0.000000e+00 13985.0
11 TraesCS3A01G169500 chr5A 98.988 7805 66 7 321 8120 74904100 74896304 0.000000e+00 13963.0
12 TraesCS3A01G169500 chr5A 98.975 7805 69 6 321 8120 74898635 74890837 0.000000e+00 13959.0
13 TraesCS3A01G169500 chrUn 98.949 7805 74 4 321 8120 207819439 207811638 0.000000e+00 13952.0
14 TraesCS3A01G169500 chrUn 99.650 572 2 0 8221 8792 245051133 245050562 0.000000e+00 1046.0
15 TraesCS3A01G169500 chrUn 99.301 572 4 0 8221 8792 183955228 183954657 0.000000e+00 1035.0
16 TraesCS3A01G169500 chrUn 99.301 572 4 0 8221 8792 207821451 207820880 0.000000e+00 1035.0
17 TraesCS3A01G169500 chrUn 94.872 39 2 0 251 289 31724228 31724266 2.650000e-05 62.1
18 TraesCS3A01G169500 chr4A 98.924 7810 71 5 321 8120 577484714 577476908 0.000000e+00 13945.0
19 TraesCS3A01G169500 chr2B 98.924 7805 76 4 321 8120 493323972 493316171 0.000000e+00 13941.0
20 TraesCS3A01G169500 chr2B 85.921 277 37 2 46 321 675535756 675535481 2.400000e-75 294.0
21 TraesCS3A01G169500 chr7B 99.301 572 4 0 8221 8792 731160845 731160274 0.000000e+00 1035.0
22 TraesCS3A01G169500 chr6A 99.301 572 4 0 8221 8792 297402351 297401780 0.000000e+00 1035.0
23 TraesCS3A01G169500 chr3D 96.573 321 11 0 1 321 152824828 152824508 4.670000e-147 532.0
24 TraesCS3A01G169500 chr3B 96.262 321 12 0 1 321 223964519 223964199 2.170000e-145 527.0
25 TraesCS3A01G169500 chr2D 92.857 42 3 0 251 292 643322145 643322104 2.650000e-05 62.1
26 TraesCS3A01G169500 chr2D 96.875 32 1 0 252 283 643267415 643267446 4.000000e-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 TraesCS3A01G169500 chr3A 177686055 177694846 8791 False 8026.0 14995 100.0000 1 8792 2 chr3A.!!$F2 8791
1 TraesCS3A01G169500 chr3A 177699736 177700307 571 False 1046.0 1046 99.6500 8221 8792 1 chr3A.!!$F1 571
2 TraesCS3A01G169500 chr1B 150784469 150792270 7801 False 14024.0 14024 99.1160 321 8120 1 chr1B.!!$F1 7799
3 TraesCS3A01G169500 chr1B 251846841 251847412 571 False 1035.0 1035 99.3010 8221 8792 1 chr1B.!!$F2 571
4 TraesCS3A01G169500 chr1B 614569827 614570398 571 False 1035.0 1035 99.3010 8221 8792 1 chr1B.!!$F3 571
5 TraesCS3A01G169500 chr4B 461635186 461642986 7800 False 14022.0 14022 99.1160 321 8120 1 chr4B.!!$F2 7799
6 TraesCS3A01G169500 chr4B 461673262 461681056 7794 False 13939.0 13939 98.9370 321 8120 1 chr4B.!!$F3 7799
7 TraesCS3A01G169500 chr4B 469029715 469030286 571 False 1035.0 1035 99.3010 8221 8792 1 chr4B.!!$F4 571
8 TraesCS3A01G169500 chr5A 74910311 74918112 7801 True 13985.0 13985 99.0260 321 8120 1 chr5A.!!$R1 7799
9 TraesCS3A01G169500 chr5A 74890837 74904100 13263 True 13961.0 13963 98.9815 321 8120 2 chr5A.!!$R2 7799
10 TraesCS3A01G169500 chrUn 207811638 207821451 9813 True 7493.5 13952 99.1250 321 8792 2 chrUn.!!$R3 8471
11 TraesCS3A01G169500 chrUn 245050562 245051133 571 True 1046.0 1046 99.6500 8221 8792 1 chrUn.!!$R2 571
12 TraesCS3A01G169500 chrUn 183954657 183955228 571 True 1035.0 1035 99.3010 8221 8792 1 chrUn.!!$R1 571
13 TraesCS3A01G169500 chr4A 577476908 577484714 7806 True 13945.0 13945 98.9240 321 8120 1 chr4A.!!$R1 7799
14 TraesCS3A01G169500 chr2B 493316171 493323972 7801 True 13941.0 13941 98.9240 321 8120 1 chr2B.!!$R1 7799
15 TraesCS3A01G169500 chr7B 731160274 731160845 571 True 1035.0 1035 99.3010 8221 8792 1 chr7B.!!$R1 571
16 TraesCS3A01G169500 chr6A 297401780 297402351 571 True 1035.0 1035 99.3010 8221 8792 1 chr6A.!!$R1 571

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
262 263 0.030773 TGTATGCCTCGTCGAGCATC 59.969 55.000 25.24 19.18 46.58 3.91 F
263 264 0.030773 GTATGCCTCGTCGAGCATCA 59.969 55.000 25.24 18.43 46.58 3.07 F
264 265 0.030773 TATGCCTCGTCGAGCATCAC 59.969 55.000 25.24 11.09 46.58 3.06 F
308 309 0.106521 GAGGATCCTCTTGCTGCTCC 59.893 60.000 31.11 4.29 39.80 4.70 F
671 677 0.658368 ATCTGAGACGTCGGATCGTG 59.342 55.000 10.46 0.40 44.34 4.35 F
672 678 0.672711 TCTGAGACGTCGGATCGTGT 60.673 55.000 10.46 6.45 44.21 4.49 F
740 746 1.608025 GGCTGCGCCTATAAGTATGCA 60.608 52.381 4.18 0.00 46.69 3.96 F
973 979 1.964552 TCCGATCGTCTACTTCCTCC 58.035 55.000 15.09 0.00 0.00 4.30 F
2847 2853 2.094894 GCGAGATGAATGGTGTGTTGAG 59.905 50.000 0.00 0.00 0.00 3.02 F
5419 5427 3.057946 GGTCTCAATGTGTTCCAAAGCTC 60.058 47.826 0.00 0.00 0.00 4.09 F
5483 5491 2.365617 CACACCTATATGAGCCCGACTT 59.634 50.000 0.00 0.00 0.00 3.01 F
6553 6566 3.289834 CGCTGCTGCCACCAAAGT 61.290 61.111 10.24 0.00 35.36 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1184 1190 3.562141 ACATGCACGTACTAAGCAAACAA 59.438 39.130 1.35 0.0 42.15 2.83 R
2317 2323 1.549203 GCGCCATTCCCCATCAATAT 58.451 50.000 0.00 0.0 0.00 1.28 R
2536 2542 0.261991 TCCCTCCGCTCTCATAACCT 59.738 55.000 0.00 0.0 0.00 3.50 R
2847 2853 8.041323 TCATGAAGTATCTCTTTCCACCTTTAC 58.959 37.037 0.00 0.0 36.40 2.01 R
3369 3375 2.752354 CCCAAATTAATGCAGTCCACGA 59.248 45.455 0.00 0.0 0.00 4.35 R
4257 4263 4.047125 CTTCGCCCCCACCATGGT 62.047 66.667 13.00 13.0 35.17 3.55 R
4678 4684 1.672363 ACAGCATGCCAATGTACATCG 59.328 47.619 15.66 0.0 42.53 3.84 R
5099 5107 7.805542 GGAGTTTCTTAATTTTCTGACAGCTTC 59.194 37.037 0.00 0.0 0.00 3.86 R
5483 5491 4.403752 CCAATCTCATAGACTGTGACCAGA 59.596 45.833 0.00 0.0 41.50 3.86 R
7047 7060 2.069165 GCCTCCCACAAGTCCTTGGT 62.069 60.000 11.45 0.0 44.45 3.67 R
7462 7475 3.695830 AGTCGGTATTGTGTTGGACAT 57.304 42.857 0.00 0.0 33.40 3.06 R
8660 9693 5.583495 CCTCATTAACAACGAAACCAACAA 58.417 37.500 0.00 0.0 0.00 2.83 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
22 23 5.920193 CCCAATCCACAATGTACATTTCT 57.080 39.130 18.50 4.13 0.00 2.52
23 24 6.284891 CCCAATCCACAATGTACATTTCTT 57.715 37.500 18.50 3.50 0.00 2.52
24 25 6.101332 CCCAATCCACAATGTACATTTCTTG 58.899 40.000 18.50 14.60 0.00 3.02
25 26 6.295236 CCCAATCCACAATGTACATTTCTTGT 60.295 38.462 18.50 12.12 42.62 3.16
26 27 6.587226 CCAATCCACAATGTACATTTCTTGTG 59.413 38.462 23.89 23.89 45.00 3.33
27 28 6.899393 ATCCACAATGTACATTTCTTGTGT 57.101 33.333 26.51 16.91 44.30 3.72
28 29 6.070897 TCCACAATGTACATTTCTTGTGTG 57.929 37.500 26.51 24.04 44.30 3.82
29 30 5.592282 TCCACAATGTACATTTCTTGTGTGT 59.408 36.000 26.51 15.78 44.30 3.72
30 31 5.914635 CCACAATGTACATTTCTTGTGTGTC 59.085 40.000 26.51 0.00 44.30 3.67
31 32 6.459435 CCACAATGTACATTTCTTGTGTGTCA 60.459 38.462 26.51 0.00 44.30 3.58
32 33 7.140705 CACAATGTACATTTCTTGTGTGTCAT 58.859 34.615 23.07 0.00 42.08 3.06
33 34 8.288913 CACAATGTACATTTCTTGTGTGTCATA 58.711 33.333 23.07 0.00 42.08 2.15
34 35 9.013229 ACAATGTACATTTCTTGTGTGTCATAT 57.987 29.630 18.50 0.00 39.48 1.78
37 38 8.196802 TGTACATTTCTTGTGTGTCATATAGC 57.803 34.615 0.00 0.00 39.48 2.97
38 39 7.821846 TGTACATTTCTTGTGTGTCATATAGCA 59.178 33.333 0.00 0.00 39.48 3.49
39 40 7.870509 ACATTTCTTGTGTGTCATATAGCAT 57.129 32.000 0.00 0.00 37.11 3.79
40 41 7.923888 ACATTTCTTGTGTGTCATATAGCATC 58.076 34.615 0.00 0.00 37.11 3.91
41 42 6.588348 TTTCTTGTGTGTCATATAGCATCG 57.412 37.500 0.00 0.00 0.00 3.84
42 43 5.514274 TCTTGTGTGTCATATAGCATCGA 57.486 39.130 0.00 0.00 0.00 3.59
43 44 5.281727 TCTTGTGTGTCATATAGCATCGAC 58.718 41.667 0.00 0.00 0.00 4.20
44 45 3.977427 TGTGTGTCATATAGCATCGACC 58.023 45.455 0.00 0.00 0.00 4.79
45 46 3.636764 TGTGTGTCATATAGCATCGACCT 59.363 43.478 0.00 0.00 0.00 3.85
46 47 3.983988 GTGTGTCATATAGCATCGACCTG 59.016 47.826 0.00 0.00 0.00 4.00
47 48 2.989840 GTGTCATATAGCATCGACCTGC 59.010 50.000 2.71 2.71 42.62 4.85
53 54 3.512516 GCATCGACCTGCTTGGGC 61.513 66.667 3.74 0.00 41.70 5.36
54 55 2.270205 CATCGACCTGCTTGGGCT 59.730 61.111 0.00 0.00 43.44 5.19
55 56 1.817099 CATCGACCTGCTTGGGCTC 60.817 63.158 0.00 0.00 43.44 4.70
56 57 1.992277 ATCGACCTGCTTGGGCTCT 60.992 57.895 0.00 0.00 43.44 4.09
57 58 1.557269 ATCGACCTGCTTGGGCTCTT 61.557 55.000 0.00 0.00 43.44 2.85
58 59 1.743252 CGACCTGCTTGGGCTCTTC 60.743 63.158 0.95 0.00 43.44 2.87
59 60 1.377856 GACCTGCTTGGGCTCTTCC 60.378 63.158 1.69 0.00 41.93 3.46
69 70 3.542046 GGCTCTTCCCTCTGACAAC 57.458 57.895 0.00 0.00 0.00 3.32
70 71 0.980423 GGCTCTTCCCTCTGACAACT 59.020 55.000 0.00 0.00 0.00 3.16
71 72 1.349357 GGCTCTTCCCTCTGACAACTT 59.651 52.381 0.00 0.00 0.00 2.66
72 73 2.614229 GGCTCTTCCCTCTGACAACTTC 60.614 54.545 0.00 0.00 0.00 3.01
73 74 2.614229 GCTCTTCCCTCTGACAACTTCC 60.614 54.545 0.00 0.00 0.00 3.46
74 75 2.634940 CTCTTCCCTCTGACAACTTCCA 59.365 50.000 0.00 0.00 0.00 3.53
75 76 3.251484 TCTTCCCTCTGACAACTTCCAT 58.749 45.455 0.00 0.00 0.00 3.41
76 77 3.008375 TCTTCCCTCTGACAACTTCCATG 59.992 47.826 0.00 0.00 0.00 3.66
77 78 1.630369 TCCCTCTGACAACTTCCATGG 59.370 52.381 4.97 4.97 0.00 3.66
78 79 1.457346 CCTCTGACAACTTCCATGGC 58.543 55.000 6.96 0.00 0.00 4.40
79 80 1.271543 CCTCTGACAACTTCCATGGCA 60.272 52.381 6.96 0.00 33.92 4.92
80 81 2.507484 CTCTGACAACTTCCATGGCAA 58.493 47.619 6.96 1.51 34.85 4.52
81 82 2.886523 CTCTGACAACTTCCATGGCAAA 59.113 45.455 6.96 0.00 34.85 3.68
82 83 2.886523 TCTGACAACTTCCATGGCAAAG 59.113 45.455 6.96 9.34 34.85 2.77
83 84 2.886523 CTGACAACTTCCATGGCAAAGA 59.113 45.455 17.74 0.00 34.85 2.52
84 85 2.622942 TGACAACTTCCATGGCAAAGAC 59.377 45.455 17.74 8.15 31.44 3.01
85 86 1.608590 ACAACTTCCATGGCAAAGACG 59.391 47.619 17.74 10.98 0.00 4.18
86 87 0.598065 AACTTCCATGGCAAAGACGC 59.402 50.000 17.74 0.00 0.00 5.19
103 104 2.505557 CCGAAGGCGTACACGTCC 60.506 66.667 2.22 5.06 46.54 4.79
104 105 2.872925 CGAAGGCGTACACGTCCG 60.873 66.667 2.22 0.00 46.54 4.79
105 106 2.256461 GAAGGCGTACACGTCCGT 59.744 61.111 2.22 3.35 46.54 4.69
106 107 2.049802 AAGGCGTACACGTCCGTG 60.050 61.111 17.52 17.52 46.54 4.94
114 115 4.039357 CACGTCCGTGTCGAGGCT 62.039 66.667 11.49 0.00 40.91 4.58
115 116 4.039357 ACGTCCGTGTCGAGGCTG 62.039 66.667 0.00 0.00 0.00 4.85
116 117 4.778415 CGTCCGTGTCGAGGCTGG 62.778 72.222 0.00 0.00 0.00 4.85
121 122 4.357947 GTGTCGAGGCTGGCACGA 62.358 66.667 18.65 18.65 0.00 4.35
135 136 3.456317 ACGACCGGTGAAGAAGCT 58.544 55.556 14.63 0.00 0.00 3.74
136 137 1.289380 ACGACCGGTGAAGAAGCTC 59.711 57.895 14.63 0.00 0.00 4.09
137 138 1.179814 ACGACCGGTGAAGAAGCTCT 61.180 55.000 14.63 0.00 0.00 4.09
138 139 0.456995 CGACCGGTGAAGAAGCTCTC 60.457 60.000 14.63 0.00 0.00 3.20
139 140 0.456995 GACCGGTGAAGAAGCTCTCG 60.457 60.000 14.63 0.00 0.00 4.04
140 141 1.179814 ACCGGTGAAGAAGCTCTCGT 61.180 55.000 6.12 0.00 0.00 4.18
141 142 0.734253 CCGGTGAAGAAGCTCTCGTG 60.734 60.000 0.00 0.00 0.00 4.35
142 143 1.347817 CGGTGAAGAAGCTCTCGTGC 61.348 60.000 0.00 0.00 0.00 5.34
143 144 1.347817 GGTGAAGAAGCTCTCGTGCG 61.348 60.000 0.00 0.00 38.13 5.34
144 145 1.734477 TGAAGAAGCTCTCGTGCGC 60.734 57.895 0.00 0.00 38.13 6.09
145 146 2.433318 AAGAAGCTCTCGTGCGCC 60.433 61.111 4.18 0.00 38.13 6.53
146 147 3.226429 AAGAAGCTCTCGTGCGCCA 62.226 57.895 4.18 0.00 38.13 5.69
147 148 2.510238 GAAGCTCTCGTGCGCCAT 60.510 61.111 4.18 0.00 38.13 4.40
148 149 2.806856 GAAGCTCTCGTGCGCCATG 61.807 63.158 4.18 0.00 38.13 3.66
149 150 3.596066 AAGCTCTCGTGCGCCATGT 62.596 57.895 4.18 0.00 38.13 3.21
150 151 2.202743 GCTCTCGTGCGCCATGTA 60.203 61.111 4.18 0.00 0.00 2.29
151 152 2.233654 GCTCTCGTGCGCCATGTAG 61.234 63.158 4.18 0.00 0.00 2.74
152 153 2.202743 TCTCGTGCGCCATGTAGC 60.203 61.111 4.18 3.04 0.00 3.58
153 154 3.264897 CTCGTGCGCCATGTAGCC 61.265 66.667 4.18 0.00 0.00 3.93
154 155 4.830765 TCGTGCGCCATGTAGCCC 62.831 66.667 4.18 0.00 0.00 5.19
159 160 3.849951 CGCCATGTAGCCCCGAGT 61.850 66.667 0.00 0.00 0.00 4.18
160 161 2.203070 GCCATGTAGCCCCGAGTG 60.203 66.667 0.00 0.00 0.00 3.51
161 162 2.203070 CCATGTAGCCCCGAGTGC 60.203 66.667 0.00 0.00 0.00 4.40
162 163 2.203070 CATGTAGCCCCGAGTGCC 60.203 66.667 0.00 0.00 0.00 5.01
163 164 3.480133 ATGTAGCCCCGAGTGCCC 61.480 66.667 0.00 0.00 0.00 5.36
181 182 4.389576 GCAACCGCCTGCGTTGAG 62.390 66.667 21.93 7.30 37.81 3.02
182 183 2.972505 CAACCGCCTGCGTTGAGT 60.973 61.111 10.94 0.00 37.81 3.41
183 184 2.972505 AACCGCCTGCGTTGAGTG 60.973 61.111 10.94 0.00 37.81 3.51
184 185 4.988598 ACCGCCTGCGTTGAGTGG 62.989 66.667 10.94 0.00 37.81 4.00
185 186 4.988598 CCGCCTGCGTTGAGTGGT 62.989 66.667 10.94 0.00 37.81 4.16
186 187 3.716006 CGCCTGCGTTGAGTGGTG 61.716 66.667 2.83 0.00 34.35 4.17
187 188 2.591715 GCCTGCGTTGAGTGGTGT 60.592 61.111 0.00 0.00 0.00 4.16
188 189 2.896801 GCCTGCGTTGAGTGGTGTG 61.897 63.158 0.00 0.00 0.00 3.82
189 190 1.523711 CCTGCGTTGAGTGGTGTGT 60.524 57.895 0.00 0.00 0.00 3.72
190 191 1.498865 CCTGCGTTGAGTGGTGTGTC 61.499 60.000 0.00 0.00 0.00 3.67
191 192 1.821241 CTGCGTTGAGTGGTGTGTCG 61.821 60.000 0.00 0.00 0.00 4.35
192 193 2.928361 CGTTGAGTGGTGTGTCGC 59.072 61.111 0.00 0.00 0.00 5.19
193 194 1.591594 CGTTGAGTGGTGTGTCGCT 60.592 57.895 0.00 0.00 0.00 4.93
194 195 1.548973 CGTTGAGTGGTGTGTCGCTC 61.549 60.000 0.00 0.00 42.72 5.03
195 196 1.069090 TTGAGTGGTGTGTCGCTCC 59.931 57.895 0.00 0.00 41.98 4.70
196 197 1.681486 TTGAGTGGTGTGTCGCTCCA 61.681 55.000 3.03 3.03 41.98 3.86
197 198 1.293498 GAGTGGTGTGTCGCTCCAT 59.707 57.895 10.23 0.81 42.04 3.41
198 199 0.737715 GAGTGGTGTGTCGCTCCATC 60.738 60.000 10.23 6.00 42.04 3.51
199 200 2.094659 GTGGTGTGTCGCTCCATCG 61.095 63.158 10.23 0.00 42.04 3.84
200 201 2.272447 TGGTGTGTCGCTCCATCGA 61.272 57.895 3.03 0.00 35.98 3.59
201 202 1.517257 GGTGTGTCGCTCCATCGAG 60.517 63.158 0.00 0.00 39.34 4.04
212 213 3.728474 CATCGAGCTGGATGGCAC 58.272 61.111 26.18 0.00 40.07 5.01
213 214 2.107750 ATCGAGCTGGATGGCACG 59.892 61.111 10.78 0.00 44.89 5.34
214 215 3.451556 ATCGAGCTGGATGGCACGG 62.452 63.158 10.78 0.00 44.00 4.94
234 235 4.821589 GAGGCCGAAGTCGCCCAG 62.822 72.222 3.32 0.00 39.63 4.45
246 247 4.715523 GCCCAGCCGCACCTTGTA 62.716 66.667 0.00 0.00 0.00 2.41
247 248 2.272146 CCCAGCCGCACCTTGTAT 59.728 61.111 0.00 0.00 0.00 2.29
248 249 2.114670 CCCAGCCGCACCTTGTATG 61.115 63.158 0.00 0.00 0.00 2.39
249 250 2.764314 CCAGCCGCACCTTGTATGC 61.764 63.158 0.00 0.00 39.81 3.14
250 251 2.438434 AGCCGCACCTTGTATGCC 60.438 61.111 0.00 0.00 40.09 4.40
251 252 2.438434 GCCGCACCTTGTATGCCT 60.438 61.111 0.00 0.00 40.09 4.75
252 253 2.472909 GCCGCACCTTGTATGCCTC 61.473 63.158 0.00 0.00 40.09 4.70
253 254 2.173669 CCGCACCTTGTATGCCTCG 61.174 63.158 0.00 0.00 40.09 4.63
254 255 1.447838 CGCACCTTGTATGCCTCGT 60.448 57.895 0.00 0.00 40.09 4.18
255 256 1.421410 CGCACCTTGTATGCCTCGTC 61.421 60.000 0.00 0.00 40.09 4.20
256 257 1.421410 GCACCTTGTATGCCTCGTCG 61.421 60.000 0.00 0.00 37.08 5.12
257 258 0.172578 CACCTTGTATGCCTCGTCGA 59.827 55.000 0.00 0.00 0.00 4.20
258 259 0.456221 ACCTTGTATGCCTCGTCGAG 59.544 55.000 15.53 15.53 0.00 4.04
259 260 0.872021 CCTTGTATGCCTCGTCGAGC 60.872 60.000 17.02 12.43 0.00 5.03
260 261 0.179137 CTTGTATGCCTCGTCGAGCA 60.179 55.000 17.02 17.34 44.45 4.26
262 263 0.030773 TGTATGCCTCGTCGAGCATC 59.969 55.000 25.24 19.18 46.58 3.91
263 264 0.030773 GTATGCCTCGTCGAGCATCA 59.969 55.000 25.24 18.43 46.58 3.07
264 265 0.030773 TATGCCTCGTCGAGCATCAC 59.969 55.000 25.24 11.09 46.58 3.06
265 266 2.943680 ATGCCTCGTCGAGCATCACG 62.944 60.000 17.02 3.25 46.58 4.35
266 267 2.485582 CCTCGTCGAGCATCACGT 59.514 61.111 17.02 0.00 39.46 4.49
267 268 1.154016 CCTCGTCGAGCATCACGTT 60.154 57.895 17.02 0.00 39.46 3.99
268 269 1.406219 CCTCGTCGAGCATCACGTTG 61.406 60.000 17.02 0.00 39.46 4.10
269 270 2.002963 CTCGTCGAGCATCACGTTGC 62.003 60.000 9.74 3.99 43.09 4.17
275 276 3.058160 GCATCACGTTGCTGGGCT 61.058 61.111 4.97 0.00 39.57 5.19
276 277 2.629656 GCATCACGTTGCTGGGCTT 61.630 57.895 4.97 0.00 39.57 4.35
277 278 1.210931 CATCACGTTGCTGGGCTTG 59.789 57.895 0.00 0.00 0.00 4.01
278 279 1.073025 ATCACGTTGCTGGGCTTGA 59.927 52.632 0.00 0.00 0.00 3.02
279 280 1.237285 ATCACGTTGCTGGGCTTGAC 61.237 55.000 0.00 0.00 0.00 3.18
280 281 2.972505 ACGTTGCTGGGCTTGACG 60.973 61.111 10.20 10.20 36.65 4.35
281 282 2.972505 CGTTGCTGGGCTTGACGT 60.973 61.111 0.00 0.00 0.00 4.34
282 283 2.946762 GTTGCTGGGCTTGACGTC 59.053 61.111 9.11 9.11 0.00 4.34
283 284 2.281484 TTGCTGGGCTTGACGTCC 60.281 61.111 14.12 0.00 38.12 4.79
284 285 3.842925 TTGCTGGGCTTGACGTCCC 62.843 63.158 14.12 8.22 42.93 4.46
285 286 4.021925 GCTGGGCTTGACGTCCCT 62.022 66.667 14.12 0.00 43.04 4.20
286 287 2.046892 CTGGGCTTGACGTCCCTG 60.047 66.667 14.12 7.81 43.04 4.45
287 288 2.847234 TGGGCTTGACGTCCCTGT 60.847 61.111 14.12 0.00 43.04 4.00
288 289 2.358737 GGGCTTGACGTCCCTGTG 60.359 66.667 14.12 0.00 39.46 3.66
289 290 2.358737 GGCTTGACGTCCCTGTGG 60.359 66.667 14.12 0.00 0.00 4.17
290 291 2.741092 GCTTGACGTCCCTGTGGA 59.259 61.111 14.12 0.00 38.75 4.02
291 292 1.374758 GCTTGACGTCCCTGTGGAG 60.375 63.158 14.12 1.06 42.85 3.86
307 308 3.684693 GAGGATCCTCTTGCTGCTC 57.315 57.895 31.11 5.32 39.80 4.26
308 309 0.106521 GAGGATCCTCTTGCTGCTCC 59.893 60.000 31.11 4.29 39.80 4.70
309 310 1.148048 GGATCCTCTTGCTGCTCCC 59.852 63.158 3.84 0.00 0.00 4.30
310 311 1.227497 GATCCTCTTGCTGCTCCCG 60.227 63.158 0.00 0.00 0.00 5.14
311 312 1.965754 GATCCTCTTGCTGCTCCCGT 61.966 60.000 0.00 0.00 0.00 5.28
312 313 2.249413 ATCCTCTTGCTGCTCCCGTG 62.249 60.000 0.00 0.00 0.00 4.94
313 314 2.435586 CTCTTGCTGCTCCCGTGG 60.436 66.667 0.00 0.00 0.00 4.94
314 315 3.241530 TCTTGCTGCTCCCGTGGT 61.242 61.111 0.00 0.00 0.00 4.16
315 316 3.052082 CTTGCTGCTCCCGTGGTG 61.052 66.667 0.00 0.00 0.00 4.17
316 317 3.535629 CTTGCTGCTCCCGTGGTGA 62.536 63.158 0.00 0.00 0.00 4.02
317 318 3.113514 TTGCTGCTCCCGTGGTGAA 62.114 57.895 0.00 0.00 0.00 3.18
318 319 2.743928 GCTGCTCCCGTGGTGAAG 60.744 66.667 0.00 0.00 0.00 3.02
319 320 2.046892 CTGCTCCCGTGGTGAAGG 60.047 66.667 0.00 0.00 0.00 3.46
463 464 6.023603 AGGAGAGTTGGAGTGGTTTATAAGA 58.976 40.000 0.00 0.00 0.00 2.10
671 677 0.658368 ATCTGAGACGTCGGATCGTG 59.342 55.000 10.46 0.40 44.34 4.35
672 678 0.672711 TCTGAGACGTCGGATCGTGT 60.673 55.000 10.46 6.45 44.21 4.49
740 746 1.608025 GGCTGCGCCTATAAGTATGCA 60.608 52.381 4.18 0.00 46.69 3.96
973 979 1.964552 TCCGATCGTCTACTTCCTCC 58.035 55.000 15.09 0.00 0.00 4.30
1184 1190 9.137459 ACTAGCAGTATGTGTAGATTTGTCTAT 57.863 33.333 0.00 0.00 39.31 1.98
2317 2323 2.123208 TCACAGGTCACGGGTCCA 60.123 61.111 3.17 0.00 0.00 4.02
2536 2542 9.323985 CAAAATATGGACTCTTTGTTGGAAAAA 57.676 29.630 0.00 0.00 0.00 1.94
2699 2705 4.889995 GGCTAGCCAAGTTGGATTTAATCT 59.110 41.667 29.33 12.98 40.96 2.40
2847 2853 2.094894 GCGAGATGAATGGTGTGTTGAG 59.905 50.000 0.00 0.00 0.00 3.02
4183 4189 3.636300 TGAAACAAGCACCTAAGCAATGT 59.364 39.130 0.00 0.00 38.10 2.71
4257 4263 7.124573 AGGCTGACAAATGTGTATACTATCA 57.875 36.000 4.17 1.88 38.41 2.15
5099 5107 8.400947 CCACCAAACACATAAGAATGAGATTAG 58.599 37.037 0.00 0.00 36.54 1.73
5419 5427 3.057946 GGTCTCAATGTGTTCCAAAGCTC 60.058 47.826 0.00 0.00 0.00 4.09
5483 5491 2.365617 CACACCTATATGAGCCCGACTT 59.634 50.000 0.00 0.00 0.00 3.01
6553 6566 3.289834 CGCTGCTGCCACCAAAGT 61.290 61.111 10.24 0.00 35.36 2.66
6592 6605 3.819902 CCTACTGGAGGGTATAACTCGTC 59.180 52.174 0.00 0.00 42.39 4.20
7025 7038 3.889538 TGATCGGAGATAAACTGGTCGAT 59.110 43.478 0.00 0.00 45.12 3.59
7462 7475 0.476771 AAGCCCAAGGGAAAGAACGA 59.523 50.000 9.92 0.00 37.50 3.85
7655 7668 3.021695 CAATGAGAATGGTGCATCTGGT 58.978 45.455 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.920193 AGAAATGTACATTGTGGATTGGG 57.080 39.130 21.46 0.00 0.00 4.12
1 2 6.587226 CACAAGAAATGTACATTGTGGATTGG 59.413 38.462 23.42 11.84 45.49 3.16
8 9 6.691754 TGACACACAAGAAATGTACATTGT 57.308 33.333 21.46 13.62 41.46 2.71
11 12 8.830580 GCTATATGACACACAAGAAATGTACAT 58.169 33.333 1.41 1.41 41.46 2.29
12 13 7.821846 TGCTATATGACACACAAGAAATGTACA 59.178 33.333 0.00 0.00 41.46 2.90
13 14 8.196802 TGCTATATGACACACAAGAAATGTAC 57.803 34.615 0.00 0.00 41.46 2.90
14 15 8.962884 ATGCTATATGACACACAAGAAATGTA 57.037 30.769 0.00 0.00 41.46 2.29
15 16 7.254556 CGATGCTATATGACACACAAGAAATGT 60.255 37.037 0.00 0.00 45.34 2.71
16 17 7.042523 TCGATGCTATATGACACACAAGAAATG 60.043 37.037 0.00 0.00 0.00 2.32
17 18 6.986231 TCGATGCTATATGACACACAAGAAAT 59.014 34.615 0.00 0.00 0.00 2.17
18 19 6.255670 GTCGATGCTATATGACACACAAGAAA 59.744 38.462 0.00 0.00 0.00 2.52
19 20 5.748630 GTCGATGCTATATGACACACAAGAA 59.251 40.000 0.00 0.00 0.00 2.52
20 21 5.281727 GTCGATGCTATATGACACACAAGA 58.718 41.667 0.00 0.00 0.00 3.02
21 22 4.445718 GGTCGATGCTATATGACACACAAG 59.554 45.833 0.00 0.00 33.04 3.16
22 23 4.099419 AGGTCGATGCTATATGACACACAA 59.901 41.667 0.00 0.00 33.04 3.33
23 24 3.636764 AGGTCGATGCTATATGACACACA 59.363 43.478 0.00 0.00 33.04 3.72
24 25 3.983988 CAGGTCGATGCTATATGACACAC 59.016 47.826 0.00 0.00 33.04 3.82
25 26 3.552890 GCAGGTCGATGCTATATGACACA 60.553 47.826 3.74 0.00 43.07 3.72
26 27 2.989840 GCAGGTCGATGCTATATGACAC 59.010 50.000 3.74 0.00 43.07 3.67
27 28 3.303881 GCAGGTCGATGCTATATGACA 57.696 47.619 3.74 0.00 43.07 3.58
36 37 3.512516 GCCCAAGCAGGTCGATGC 61.513 66.667 2.71 2.71 46.88 3.91
37 38 1.817099 GAGCCCAAGCAGGTCGATG 60.817 63.158 0.00 0.00 43.56 3.84
38 39 1.557269 AAGAGCCCAAGCAGGTCGAT 61.557 55.000 0.00 0.00 43.56 3.59
39 40 2.172483 GAAGAGCCCAAGCAGGTCGA 62.172 60.000 0.00 0.00 43.56 4.20
40 41 1.743252 GAAGAGCCCAAGCAGGTCG 60.743 63.158 0.00 0.00 43.56 4.79
41 42 1.377856 GGAAGAGCCCAAGCAGGTC 60.378 63.158 0.00 0.00 43.56 3.85
42 43 2.759795 GGAAGAGCCCAAGCAGGT 59.240 61.111 0.00 0.00 43.56 4.00
51 52 0.980423 AGTTGTCAGAGGGAAGAGCC 59.020 55.000 0.00 0.00 0.00 4.70
52 53 2.614229 GGAAGTTGTCAGAGGGAAGAGC 60.614 54.545 0.00 0.00 0.00 4.09
53 54 2.634940 TGGAAGTTGTCAGAGGGAAGAG 59.365 50.000 0.00 0.00 0.00 2.85
54 55 2.689658 TGGAAGTTGTCAGAGGGAAGA 58.310 47.619 0.00 0.00 0.00 2.87
55 56 3.341823 CATGGAAGTTGTCAGAGGGAAG 58.658 50.000 0.00 0.00 0.00 3.46
56 57 2.040278 CCATGGAAGTTGTCAGAGGGAA 59.960 50.000 5.56 0.00 0.00 3.97
57 58 1.630369 CCATGGAAGTTGTCAGAGGGA 59.370 52.381 5.56 0.00 0.00 4.20
58 59 1.952367 GCCATGGAAGTTGTCAGAGGG 60.952 57.143 18.40 0.00 0.00 4.30
59 60 1.271543 TGCCATGGAAGTTGTCAGAGG 60.272 52.381 18.40 0.00 0.00 3.69
60 61 2.189594 TGCCATGGAAGTTGTCAGAG 57.810 50.000 18.40 0.00 0.00 3.35
61 62 2.655090 TTGCCATGGAAGTTGTCAGA 57.345 45.000 18.40 0.00 0.00 3.27
62 63 2.886523 TCTTTGCCATGGAAGTTGTCAG 59.113 45.455 18.40 0.86 0.00 3.51
63 64 2.622942 GTCTTTGCCATGGAAGTTGTCA 59.377 45.455 18.40 0.00 0.00 3.58
64 65 2.350772 CGTCTTTGCCATGGAAGTTGTC 60.351 50.000 18.40 0.00 0.00 3.18
65 66 1.608590 CGTCTTTGCCATGGAAGTTGT 59.391 47.619 18.40 0.00 0.00 3.32
66 67 1.666888 GCGTCTTTGCCATGGAAGTTG 60.667 52.381 18.40 9.10 0.00 3.16
67 68 0.598065 GCGTCTTTGCCATGGAAGTT 59.402 50.000 18.40 0.00 0.00 2.66
68 69 2.257353 GCGTCTTTGCCATGGAAGT 58.743 52.632 18.40 0.00 0.00 3.01
85 86 3.177249 GACGTGTACGCCTTCGGC 61.177 66.667 4.06 0.00 46.75 5.54
86 87 2.505557 GGACGTGTACGCCTTCGG 60.506 66.667 4.06 0.00 44.43 4.30
87 88 2.872925 CGGACGTGTACGCCTTCG 60.873 66.667 4.06 0.00 44.43 3.79
88 89 2.084681 CACGGACGTGTACGCCTTC 61.085 63.158 16.06 0.00 41.51 3.46
89 90 2.049802 CACGGACGTGTACGCCTT 60.050 61.111 16.06 0.00 41.51 4.35
98 99 4.039357 CAGCCTCGACACGGACGT 62.039 66.667 0.00 0.00 0.00 4.34
99 100 4.778415 CCAGCCTCGACACGGACG 62.778 72.222 0.00 0.00 0.00 4.79
104 105 4.357947 TCGTGCCAGCCTCGACAC 62.358 66.667 3.57 0.00 0.00 3.67
112 113 4.980805 TTCACCGGTCGTGCCAGC 62.981 66.667 2.59 0.00 42.69 4.85
113 114 2.709125 TTCTTCACCGGTCGTGCCAG 62.709 60.000 2.59 0.00 42.69 4.85
114 115 2.709125 CTTCTTCACCGGTCGTGCCA 62.709 60.000 2.59 0.00 42.69 4.92
115 116 2.027625 CTTCTTCACCGGTCGTGCC 61.028 63.158 2.59 0.00 42.69 5.01
116 117 2.668280 GCTTCTTCACCGGTCGTGC 61.668 63.158 2.59 0.00 42.69 5.34
117 118 1.006102 AGCTTCTTCACCGGTCGTG 60.006 57.895 2.59 0.00 44.50 4.35
118 119 1.179814 AGAGCTTCTTCACCGGTCGT 61.180 55.000 2.59 0.00 0.00 4.34
119 120 0.456995 GAGAGCTTCTTCACCGGTCG 60.457 60.000 2.59 0.00 0.00 4.79
120 121 0.456995 CGAGAGCTTCTTCACCGGTC 60.457 60.000 2.59 0.00 0.00 4.79
121 122 1.179814 ACGAGAGCTTCTTCACCGGT 61.180 55.000 0.00 0.00 0.00 5.28
122 123 0.734253 CACGAGAGCTTCTTCACCGG 60.734 60.000 0.00 0.00 0.00 5.28
123 124 1.347817 GCACGAGAGCTTCTTCACCG 61.348 60.000 0.00 0.00 0.00 4.94
124 125 1.347817 CGCACGAGAGCTTCTTCACC 61.348 60.000 0.00 0.00 0.00 4.02
125 126 1.950098 GCGCACGAGAGCTTCTTCAC 61.950 60.000 0.30 0.00 37.60 3.18
126 127 1.734477 GCGCACGAGAGCTTCTTCA 60.734 57.895 0.30 0.00 37.60 3.02
127 128 2.448705 GGCGCACGAGAGCTTCTTC 61.449 63.158 10.83 0.00 40.70 2.87
128 129 2.433318 GGCGCACGAGAGCTTCTT 60.433 61.111 10.83 0.00 40.70 2.52
129 130 3.011635 ATGGCGCACGAGAGCTTCT 62.012 57.895 10.83 0.00 40.70 2.85
130 131 2.510238 ATGGCGCACGAGAGCTTC 60.510 61.111 10.83 0.00 40.70 3.86
131 132 2.225791 TACATGGCGCACGAGAGCTT 62.226 55.000 10.83 0.00 40.70 3.74
132 133 2.619840 CTACATGGCGCACGAGAGCT 62.620 60.000 10.83 0.00 40.70 4.09
133 134 2.202743 TACATGGCGCACGAGAGC 60.203 61.111 10.83 0.00 40.11 4.09
134 135 2.233654 GCTACATGGCGCACGAGAG 61.234 63.158 10.83 1.09 0.00 3.20
135 136 2.202743 GCTACATGGCGCACGAGA 60.203 61.111 10.83 0.00 0.00 4.04
136 137 3.264897 GGCTACATGGCGCACGAG 61.265 66.667 10.83 0.00 0.00 4.18
137 138 4.830765 GGGCTACATGGCGCACGA 62.831 66.667 10.83 0.00 43.28 4.35
142 143 3.849951 ACTCGGGGCTACATGGCG 61.850 66.667 0.00 0.00 42.84 5.69
143 144 2.203070 CACTCGGGGCTACATGGC 60.203 66.667 0.00 0.00 40.96 4.40
144 145 2.203070 GCACTCGGGGCTACATGG 60.203 66.667 0.00 0.00 0.00 3.66
145 146 2.203070 GGCACTCGGGGCTACATG 60.203 66.667 0.00 0.00 0.00 3.21
146 147 3.480133 GGGCACTCGGGGCTACAT 61.480 66.667 0.00 0.00 0.00 2.29
164 165 4.389576 CTCAACGCAGGCGGTTGC 62.390 66.667 18.63 1.24 44.69 4.17
165 166 2.972505 ACTCAACGCAGGCGGTTG 60.973 61.111 18.63 17.62 44.69 3.77
166 167 2.972505 CACTCAACGCAGGCGGTT 60.973 61.111 18.63 7.10 44.69 4.44
167 168 4.988598 CCACTCAACGCAGGCGGT 62.989 66.667 18.63 8.85 44.69 5.68
168 169 4.988598 ACCACTCAACGCAGGCGG 62.989 66.667 18.63 2.36 44.69 6.13
169 170 3.716006 CACCACTCAACGCAGGCG 61.716 66.667 12.71 12.71 46.03 5.52
170 171 2.591715 ACACCACTCAACGCAGGC 60.592 61.111 0.00 0.00 0.00 4.85
171 172 1.498865 GACACACCACTCAACGCAGG 61.499 60.000 0.00 0.00 0.00 4.85
172 173 1.821241 CGACACACCACTCAACGCAG 61.821 60.000 0.00 0.00 0.00 5.18
173 174 1.880796 CGACACACCACTCAACGCA 60.881 57.895 0.00 0.00 0.00 5.24
174 175 2.928361 CGACACACCACTCAACGC 59.072 61.111 0.00 0.00 0.00 4.84
175 176 1.548973 GAGCGACACACCACTCAACG 61.549 60.000 0.00 0.00 0.00 4.10
176 177 1.222115 GGAGCGACACACCACTCAAC 61.222 60.000 0.00 0.00 0.00 3.18
177 178 1.069090 GGAGCGACACACCACTCAA 59.931 57.895 0.00 0.00 0.00 3.02
178 179 1.471829 ATGGAGCGACACACCACTCA 61.472 55.000 0.00 0.00 42.26 3.41
179 180 0.737715 GATGGAGCGACACACCACTC 60.738 60.000 0.00 0.00 42.26 3.51
180 181 1.293498 GATGGAGCGACACACCACT 59.707 57.895 0.00 0.00 42.26 4.00
181 182 2.094659 CGATGGAGCGACACACCAC 61.095 63.158 0.00 0.00 42.26 4.16
182 183 2.212900 CTCGATGGAGCGACACACCA 62.213 60.000 0.00 0.00 43.72 4.17
183 184 1.517257 CTCGATGGAGCGACACACC 60.517 63.158 0.00 0.00 36.17 4.16
184 185 4.079090 CTCGATGGAGCGACACAC 57.921 61.111 0.00 0.00 36.17 3.82
195 196 3.728474 GTGCCATCCAGCTCGATG 58.272 61.111 13.82 13.82 39.54 3.84
229 230 3.995506 ATACAAGGTGCGGCTGGGC 62.996 63.158 0.00 0.00 0.00 5.36
230 231 2.114670 CATACAAGGTGCGGCTGGG 61.115 63.158 0.00 0.00 0.00 4.45
231 232 2.764314 GCATACAAGGTGCGGCTGG 61.764 63.158 0.00 0.00 32.29 4.85
232 233 2.764314 GGCATACAAGGTGCGGCTG 61.764 63.158 0.00 0.00 43.40 4.85
233 234 2.438434 GGCATACAAGGTGCGGCT 60.438 61.111 0.00 0.00 43.40 5.52
234 235 2.438434 AGGCATACAAGGTGCGGC 60.438 61.111 0.00 0.00 43.40 6.53
235 236 2.173669 CGAGGCATACAAGGTGCGG 61.174 63.158 0.00 0.00 43.40 5.69
236 237 1.421410 GACGAGGCATACAAGGTGCG 61.421 60.000 0.00 0.00 43.40 5.34
237 238 1.421410 CGACGAGGCATACAAGGTGC 61.421 60.000 0.00 0.00 41.78 5.01
238 239 0.172578 TCGACGAGGCATACAAGGTG 59.827 55.000 0.00 0.00 0.00 4.00
239 240 0.456221 CTCGACGAGGCATACAAGGT 59.544 55.000 17.27 0.00 0.00 3.50
240 241 0.872021 GCTCGACGAGGCATACAAGG 60.872 60.000 25.31 0.00 0.00 3.61
241 242 0.179137 TGCTCGACGAGGCATACAAG 60.179 55.000 25.31 0.00 33.23 3.16
242 243 0.459899 ATGCTCGACGAGGCATACAA 59.540 50.000 25.31 3.39 45.74 2.41
243 244 2.115510 ATGCTCGACGAGGCATACA 58.884 52.632 25.31 14.71 45.74 2.29
247 248 2.181777 GTGATGCTCGACGAGGCA 59.818 61.111 25.31 21.94 42.80 4.75
248 249 2.951745 CGTGATGCTCGACGAGGC 60.952 66.667 25.31 17.47 37.81 4.70
249 250 1.154016 AACGTGATGCTCGACGAGG 60.154 57.895 25.31 10.58 38.94 4.63
250 251 1.983907 CAACGTGATGCTCGACGAG 59.016 57.895 20.56 20.56 38.94 4.18
251 252 2.086426 GCAACGTGATGCTCGACGA 61.086 57.895 4.97 0.00 43.06 4.20
252 253 2.391821 GCAACGTGATGCTCGACG 59.608 61.111 4.97 0.00 43.06 5.12
258 259 2.629656 AAGCCCAGCAACGTGATGC 61.630 57.895 3.99 3.99 46.78 3.91
259 260 1.210931 CAAGCCCAGCAACGTGATG 59.789 57.895 0.00 0.00 32.77 3.07
260 261 1.073025 TCAAGCCCAGCAACGTGAT 59.927 52.632 0.00 0.00 0.00 3.06
261 262 1.891919 GTCAAGCCCAGCAACGTGA 60.892 57.895 0.00 0.00 0.00 4.35
262 263 2.639286 GTCAAGCCCAGCAACGTG 59.361 61.111 0.00 0.00 0.00 4.49
263 264 2.972505 CGTCAAGCCCAGCAACGT 60.973 61.111 0.00 0.00 30.76 3.99
264 265 2.954753 GACGTCAAGCCCAGCAACG 61.955 63.158 11.55 7.36 37.30 4.10
265 266 2.617274 GGACGTCAAGCCCAGCAAC 61.617 63.158 18.91 0.00 0.00 4.17
266 267 2.281484 GGACGTCAAGCCCAGCAA 60.281 61.111 18.91 0.00 0.00 3.91
267 268 4.329545 GGGACGTCAAGCCCAGCA 62.330 66.667 18.91 0.00 44.07 4.41
271 272 2.358737 CACAGGGACGTCAAGCCC 60.359 66.667 18.91 10.14 45.04 5.19
272 273 2.358737 CCACAGGGACGTCAAGCC 60.359 66.667 18.91 9.63 35.59 4.35
273 274 1.374758 CTCCACAGGGACGTCAAGC 60.375 63.158 18.91 0.00 38.64 4.01
274 275 1.185618 TCCTCCACAGGGACGTCAAG 61.186 60.000 18.91 8.69 40.80 3.02
275 276 0.544357 ATCCTCCACAGGGACGTCAA 60.544 55.000 18.91 0.00 40.80 3.18
276 277 0.970937 GATCCTCCACAGGGACGTCA 60.971 60.000 18.91 0.00 40.80 4.35
277 278 1.677637 GGATCCTCCACAGGGACGTC 61.678 65.000 7.13 7.13 40.80 4.34
278 279 1.686110 GGATCCTCCACAGGGACGT 60.686 63.158 3.84 0.00 40.80 4.34
279 280 1.381872 AGGATCCTCCACAGGGACG 60.382 63.158 9.02 0.00 39.61 4.79
280 281 0.031616 AGAGGATCCTCCACAGGGAC 60.032 60.000 33.81 10.44 43.70 4.46
281 282 0.719015 AAGAGGATCCTCCACAGGGA 59.281 55.000 33.81 0.00 43.70 4.20
282 283 0.835941 CAAGAGGATCCTCCACAGGG 59.164 60.000 33.81 15.69 43.70 4.45
283 284 0.179936 GCAAGAGGATCCTCCACAGG 59.820 60.000 33.81 20.69 43.70 4.00
284 285 1.134461 CAGCAAGAGGATCCTCCACAG 60.134 57.143 33.81 22.50 43.70 3.66
285 286 0.907486 CAGCAAGAGGATCCTCCACA 59.093 55.000 33.81 0.00 43.70 4.17
286 287 0.463474 GCAGCAAGAGGATCCTCCAC 60.463 60.000 33.81 23.91 43.70 4.02
287 288 0.619832 AGCAGCAAGAGGATCCTCCA 60.620 55.000 33.81 0.00 43.70 3.86
288 289 0.106521 GAGCAGCAAGAGGATCCTCC 59.893 60.000 33.81 20.81 43.70 4.30
289 290 0.106521 GGAGCAGCAAGAGGATCCTC 59.893 60.000 31.27 31.27 43.03 3.71
290 291 1.344191 GGGAGCAGCAAGAGGATCCT 61.344 60.000 16.13 16.13 33.66 3.24
291 292 1.148048 GGGAGCAGCAAGAGGATCC 59.852 63.158 2.48 2.48 33.66 3.36
292 293 1.227497 CGGGAGCAGCAAGAGGATC 60.227 63.158 0.00 0.00 0.00 3.36
293 294 1.992277 ACGGGAGCAGCAAGAGGAT 60.992 57.895 0.00 0.00 0.00 3.24
294 295 2.604686 ACGGGAGCAGCAAGAGGA 60.605 61.111 0.00 0.00 0.00 3.71
295 296 2.435586 CACGGGAGCAGCAAGAGG 60.436 66.667 0.00 0.00 0.00 3.69
296 297 2.435586 CCACGGGAGCAGCAAGAG 60.436 66.667 0.00 0.00 0.00 2.85
297 298 3.241530 ACCACGGGAGCAGCAAGA 61.242 61.111 0.00 0.00 0.00 3.02
298 299 3.052082 CACCACGGGAGCAGCAAG 61.052 66.667 0.00 0.00 0.00 4.01
299 300 3.113514 TTCACCACGGGAGCAGCAA 62.114 57.895 0.00 0.00 0.00 3.91
300 301 3.535629 CTTCACCACGGGAGCAGCA 62.536 63.158 0.00 0.00 0.00 4.41
301 302 2.743928 CTTCACCACGGGAGCAGC 60.744 66.667 0.00 0.00 0.00 5.25
302 303 2.046892 CCTTCACCACGGGAGCAG 60.047 66.667 0.00 0.00 0.00 4.24
303 304 2.847234 ACCTTCACCACGGGAGCA 60.847 61.111 0.00 0.00 0.00 4.26
304 305 2.358737 CACCTTCACCACGGGAGC 60.359 66.667 0.00 0.00 0.00 4.70
305 306 2.358737 GCACCTTCACCACGGGAG 60.359 66.667 0.00 0.00 0.00 4.30
306 307 2.847234 AGCACCTTCACCACGGGA 60.847 61.111 0.00 0.00 0.00 5.14
307 308 2.669569 CAGCACCTTCACCACGGG 60.670 66.667 0.00 0.00 0.00 5.28
308 309 0.817634 TTTCAGCACCTTCACCACGG 60.818 55.000 0.00 0.00 0.00 4.94
309 310 1.197721 GATTTCAGCACCTTCACCACG 59.802 52.381 0.00 0.00 0.00 4.94
310 311 2.227388 CAGATTTCAGCACCTTCACCAC 59.773 50.000 0.00 0.00 0.00 4.16
311 312 2.106338 TCAGATTTCAGCACCTTCACCA 59.894 45.455 0.00 0.00 0.00 4.17
312 313 2.746362 CTCAGATTTCAGCACCTTCACC 59.254 50.000 0.00 0.00 0.00 4.02
313 314 3.668447 TCTCAGATTTCAGCACCTTCAC 58.332 45.455 0.00 0.00 0.00 3.18
314 315 4.259356 CATCTCAGATTTCAGCACCTTCA 58.741 43.478 0.00 0.00 0.00 3.02
315 316 3.626670 CCATCTCAGATTTCAGCACCTTC 59.373 47.826 0.00 0.00 0.00 3.46
316 317 3.618351 CCATCTCAGATTTCAGCACCTT 58.382 45.455 0.00 0.00 0.00 3.50
317 318 2.092538 CCCATCTCAGATTTCAGCACCT 60.093 50.000 0.00 0.00 0.00 4.00
318 319 2.295885 CCCATCTCAGATTTCAGCACC 58.704 52.381 0.00 0.00 0.00 5.01
319 320 1.674962 GCCCATCTCAGATTTCAGCAC 59.325 52.381 0.00 0.00 0.00 4.40
463 464 7.187824 TCCAATAGCATGTAGAAGAGAAACT 57.812 36.000 0.00 0.00 0.00 2.66
671 677 2.048127 GAGTCCGTGACAGCCCAC 60.048 66.667 6.78 0.00 34.60 4.61
672 678 3.680786 CGAGTCCGTGACAGCCCA 61.681 66.667 6.78 0.00 34.60 5.36
740 746 1.685491 CGGCTAGGGTTAGGAGACACT 60.685 57.143 0.00 0.00 37.07 3.55
986 992 1.009829 GGACATGGTGATGACGAAGC 58.990 55.000 0.00 0.00 33.36 3.86
1184 1190 3.562141 ACATGCACGTACTAAGCAAACAA 59.438 39.130 1.35 0.00 42.15 2.83
2317 2323 1.549203 GCGCCATTCCCCATCAATAT 58.451 50.000 0.00 0.00 0.00 1.28
2536 2542 0.261991 TCCCTCCGCTCTCATAACCT 59.738 55.000 0.00 0.00 0.00 3.50
2847 2853 8.041323 TCATGAAGTATCTCTTTCCACCTTTAC 58.959 37.037 0.00 0.00 36.40 2.01
3369 3375 2.752354 CCCAAATTAATGCAGTCCACGA 59.248 45.455 0.00 0.00 0.00 4.35
4257 4263 4.047125 CTTCGCCCCCACCATGGT 62.047 66.667 13.00 13.00 35.17 3.55
4678 4684 1.672363 ACAGCATGCCAATGTACATCG 59.328 47.619 15.66 0.00 42.53 3.84
5099 5107 7.805542 GGAGTTTCTTAATTTTCTGACAGCTTC 59.194 37.037 0.00 0.00 0.00 3.86
5483 5491 4.403752 CCAATCTCATAGACTGTGACCAGA 59.596 45.833 0.00 0.00 41.50 3.86
6592 6605 5.551233 TGAAAATAATCAGGAGCGGGATAG 58.449 41.667 0.00 0.00 0.00 2.08
7047 7060 2.069165 GCCTCCCACAAGTCCTTGGT 62.069 60.000 11.45 0.00 44.45 3.67
7462 7475 3.695830 AGTCGGTATTGTGTTGGACAT 57.304 42.857 0.00 0.00 33.40 3.06
8660 9693 5.583495 CCTCATTAACAACGAAACCAACAA 58.417 37.500 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.