Multiple sequence alignment - TraesCS2A01G586700

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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 TraesCS2A01G586700 chr2A 100.000 3243 0 0 1 3243 777100698 777097456 0.000000e+00 5989.0
1 TraesCS2A01G586700 chr2A 85.816 141 17 3 2484 2622 193449775 193449636 2.610000e-31 147.0
2 TraesCS2A01G586700 chr2D 89.668 2168 130 33 230 2367 650926877 650928980 0.000000e+00 2676.0
3 TraesCS2A01G586700 chr2D 93.359 768 43 6 2480 3243 650929438 650930201 0.000000e+00 1129.0
4 TraesCS2A01G586700 chr2D 85.333 150 21 1 2483 2632 533780295 533780147 1.560000e-33 154.0
5 TraesCS2A01G586700 chr2D 86.170 94 13 0 105 198 154294618 154294711 5.720000e-18 102.0
6 TraesCS2A01G586700 chrUn 89.897 1841 127 29 520 2334 23424438 23426245 0.000000e+00 2314.0
7 TraesCS2A01G586700 chrUn 80.101 397 56 17 520 904 23417699 23418084 1.150000e-69 274.0
8 TraesCS2A01G586700 chrUn 85.020 247 34 3 230 474 23423915 23424160 6.950000e-62 248.0
9 TraesCS2A01G586700 chrUn 84.615 247 35 3 230 474 23417175 23417420 3.230000e-60 243.0
10 TraesCS2A01G586700 chr2B 80.851 376 53 14 520 887 779888512 779888876 8.860000e-71 278.0
11 TraesCS2A01G586700 chr2B 85.532 235 28 6 230 461 779892244 779892475 1.160000e-59 241.0
12 TraesCS2A01G586700 chr2B 88.421 190 10 6 720 904 779883733 779883915 5.450000e-53 219.0
13 TraesCS2A01G586700 chr2B 80.328 122 22 2 525 645 9843130 9843010 1.240000e-14 91.6
14 TraesCS2A01G586700 chr3B 85.549 173 22 3 2482 2652 173123258 173123429 9.250000e-41 178.0
15 TraesCS2A01G586700 chr3B 97.500 80 2 0 1 80 560870256 560870177 1.570000e-28 137.0
16 TraesCS2A01G586700 chr3B 94.444 36 2 0 229 264 418312549 418312514 4.520000e-04 56.5
17 TraesCS2A01G586700 chr6D 84.706 170 21 2 2483 2652 1486633 1486469 7.200000e-37 165.0
18 TraesCS2A01G586700 chr6D 79.295 227 42 5 476 700 447099137 447099360 1.560000e-33 154.0
19 TraesCS2A01G586700 chr6D 85.714 91 12 1 479 568 320204282 320204192 9.580000e-16 95.3
20 TraesCS2A01G586700 chr6D 100.000 29 0 0 230 258 151901788 151901816 2.000000e-03 54.7
21 TraesCS2A01G586700 chr5A 100.000 79 0 0 1 79 13094780 13094858 2.610000e-31 147.0
22 TraesCS2A01G586700 chr5A 100.000 76 0 0 1 76 565702357 565702432 1.210000e-29 141.0
23 TraesCS2A01G586700 chr6B 100.000 76 0 0 1 76 214033784 214033859 1.210000e-29 141.0
24 TraesCS2A01G586700 chr6B 81.176 170 26 3 2483 2652 5789117 5788954 7.300000e-27 132.0
25 TraesCS2A01G586700 chr6B 100.000 29 0 0 230 258 151723477 151723449 2.000000e-03 54.7
26 TraesCS2A01G586700 chr4A 98.734 79 1 0 1 79 685852426 685852504 1.210000e-29 141.0
27 TraesCS2A01G586700 chr4A 100.000 28 0 0 685 712 651836606 651836633 6.000000e-03 52.8
28 TraesCS2A01G586700 chr5D 83.125 160 19 6 2474 2632 385904507 385904355 4.360000e-29 139.0
29 TraesCS2A01G586700 chr7D 83.117 154 22 4 2481 2632 513211741 513211590 1.570000e-28 137.0
30 TraesCS2A01G586700 chr4D 83.333 150 24 1 2483 2632 466669248 466669396 1.570000e-28 137.0
31 TraesCS2A01G586700 chr7A 97.500 80 1 1 1 79 452753086 452753007 5.640000e-28 135.0
32 TraesCS2A01G586700 chr3A 98.684 76 1 0 1 76 456384177 456384252 5.640000e-28 135.0
33 TraesCS2A01G586700 chr3A 97.468 79 2 0 1 79 549331098 549331020 5.640000e-28 135.0
34 TraesCS2A01G586700 chr1A 97.468 79 2 0 1 79 588945951 588945873 5.640000e-28 135.0
35 TraesCS2A01G586700 chr1B 79.651 172 18 9 81 236 637542434 637542604 1.230000e-19 108.0
36 TraesCS2A01G586700 chr6A 100.000 32 0 0 230 261 11156774 11156743 3.490000e-05 60.2
37 TraesCS2A01G586700 chr5B 100.000 29 0 0 230 258 489654615 489654643 2.000000e-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 TraesCS2A01G586700 chr2A 777097456 777100698 3242 True 5989.0 5989 100.0000 1 3243 1 chr2A.!!$R2 3242
1 TraesCS2A01G586700 chr2D 650926877 650930201 3324 False 1902.5 2676 91.5135 230 3243 2 chr2D.!!$F2 3013
2 TraesCS2A01G586700 chrUn 23423915 23426245 2330 False 1281.0 2314 87.4585 230 2334 2 chrUn.!!$F2 2104
3 TraesCS2A01G586700 chrUn 23417175 23418084 909 False 258.5 274 82.3580 230 904 2 chrUn.!!$F1 674
4 TraesCS2A01G586700 chr2B 779888512 779892475 3963 False 259.5 278 83.1915 230 887 2 chr2B.!!$F2 657

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
190 191 0.039618 AATGTGTGGGATGTGGGACC 59.960 55.0 0.00 0.0 0.00 4.46 F
218 219 0.104120 GCTTGAACCAAACACCCACC 59.896 55.0 0.00 0.0 0.00 4.61 F
657 896 0.243636 AGCACCAGCATTTAAACGCC 59.756 50.0 2.03 0.0 45.49 5.68 F
680 919 0.252197 GGGCCGAGAATACCACTGTT 59.748 55.0 0.00 0.0 0.00 3.16 F
1992 4911 0.793853 GACGAGGACGAGAAGAACGC 60.794 60.0 0.00 0.0 42.66 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1492 4402 0.108424 AGCACATCGACTCTGCTTCC 60.108 55.000 7.35 0.0 38.07 3.46 R
1514 4424 1.290324 CCACGTCCTCCACAGTGAG 59.710 63.158 0.62 0.0 33.77 3.51 R
1992 4911 1.294659 GCTCGTGAAAGCTGAGGTGG 61.295 60.000 0.00 0.0 39.27 4.61 R
2221 5149 2.125147 TCTGCCATACTGTGCGCC 60.125 61.111 4.18 0.0 0.00 6.53 R
2935 6209 0.937304 CAATCACCCGCTGAATACCG 59.063 55.000 0.00 0.0 30.60 4.02 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
19 20 1.476074 GTGACACAAAACATGCACGG 58.524 50.000 0.00 0.00 0.00 4.94
20 21 1.098869 TGACACAAAACATGCACGGT 58.901 45.000 0.00 0.00 0.00 4.83
21 22 1.202234 TGACACAAAACATGCACGGTG 60.202 47.619 3.15 3.15 0.00 4.94
22 23 0.102120 ACACAAAACATGCACGGTGG 59.898 50.000 10.60 0.00 0.00 4.61
23 24 0.102120 CACAAAACATGCACGGTGGT 59.898 50.000 10.60 0.00 0.00 4.16
32 33 2.358737 CACGGTGGTGCCTTCCTC 60.359 66.667 0.00 0.00 37.35 3.71
33 34 3.637273 ACGGTGGTGCCTTCCTCC 61.637 66.667 0.00 0.00 37.66 4.30
34 35 4.410400 CGGTGGTGCCTTCCTCCC 62.410 72.222 0.00 0.00 37.72 4.30
35 36 3.256960 GGTGGTGCCTTCCTCCCA 61.257 66.667 0.00 0.00 35.72 4.37
36 37 2.616458 GGTGGTGCCTTCCTCCCAT 61.616 63.158 0.00 0.00 35.72 4.00
37 38 1.279025 GGTGGTGCCTTCCTCCCATA 61.279 60.000 0.00 0.00 35.72 2.74
38 39 0.181350 GTGGTGCCTTCCTCCCATAG 59.819 60.000 0.00 0.00 0.00 2.23
39 40 1.149401 GGTGCCTTCCTCCCATAGC 59.851 63.158 0.00 0.00 0.00 2.97
40 41 1.149401 GTGCCTTCCTCCCATAGCC 59.851 63.158 0.00 0.00 0.00 3.93
41 42 1.004758 TGCCTTCCTCCCATAGCCT 59.995 57.895 0.00 0.00 0.00 4.58
42 43 0.624500 TGCCTTCCTCCCATAGCCTT 60.625 55.000 0.00 0.00 0.00 4.35
43 44 1.345009 TGCCTTCCTCCCATAGCCTTA 60.345 52.381 0.00 0.00 0.00 2.69
44 45 1.349357 GCCTTCCTCCCATAGCCTTAG 59.651 57.143 0.00 0.00 0.00 2.18
45 46 2.695585 CCTTCCTCCCATAGCCTTAGT 58.304 52.381 0.00 0.00 0.00 2.24
46 47 3.858135 CCTTCCTCCCATAGCCTTAGTA 58.142 50.000 0.00 0.00 0.00 1.82
47 48 3.835395 CCTTCCTCCCATAGCCTTAGTAG 59.165 52.174 0.00 0.00 0.00 2.57
48 49 3.544698 TCCTCCCATAGCCTTAGTAGG 57.455 52.381 0.00 0.00 45.02 3.18
49 50 2.795960 TCCTCCCATAGCCTTAGTAGGT 59.204 50.000 0.00 0.00 44.00 3.08
50 51 3.209152 TCCTCCCATAGCCTTAGTAGGTT 59.791 47.826 0.00 0.00 44.00 3.50
51 52 4.421231 TCCTCCCATAGCCTTAGTAGGTTA 59.579 45.833 0.00 0.00 44.00 2.85
52 53 4.773149 CCTCCCATAGCCTTAGTAGGTTAG 59.227 50.000 0.00 0.00 44.00 2.34
53 54 4.158015 TCCCATAGCCTTAGTAGGTTAGC 58.842 47.826 0.00 0.00 44.00 3.09
54 55 4.140758 TCCCATAGCCTTAGTAGGTTAGCT 60.141 45.833 0.00 0.00 44.00 3.32
55 56 4.021016 CCCATAGCCTTAGTAGGTTAGCTG 60.021 50.000 0.00 0.00 44.00 4.24
56 57 4.021016 CCATAGCCTTAGTAGGTTAGCTGG 60.021 50.000 0.00 0.00 44.00 4.85
57 58 3.117552 AGCCTTAGTAGGTTAGCTGGT 57.882 47.619 0.00 0.00 44.00 4.00
58 59 3.451890 AGCCTTAGTAGGTTAGCTGGTT 58.548 45.455 0.00 0.00 44.00 3.67
59 60 3.844804 AGCCTTAGTAGGTTAGCTGGTTT 59.155 43.478 0.00 0.00 44.00 3.27
60 61 4.081031 AGCCTTAGTAGGTTAGCTGGTTTC 60.081 45.833 0.00 0.00 44.00 2.78
61 62 4.430908 CCTTAGTAGGTTAGCTGGTTTCG 58.569 47.826 0.00 0.00 36.74 3.46
62 63 4.430908 CTTAGTAGGTTAGCTGGTTTCGG 58.569 47.826 0.00 0.00 0.00 4.30
63 64 1.066358 AGTAGGTTAGCTGGTTTCGGC 60.066 52.381 0.00 0.00 45.35 5.54
69 70 2.785258 GCTGGTTTCGGCTTAGCG 59.215 61.111 0.00 0.00 41.88 4.26
70 71 2.750888 GCTGGTTTCGGCTTAGCGG 61.751 63.158 5.37 5.37 41.88 5.52
71 72 2.744709 TGGTTTCGGCTTAGCGGC 60.745 61.111 6.91 0.00 0.00 6.53
78 79 3.497879 GGCTTAGCGGCGTTCAAT 58.502 55.556 9.37 0.00 0.00 2.57
79 80 1.800681 GGCTTAGCGGCGTTCAATT 59.199 52.632 9.37 0.00 0.00 2.32
80 81 0.248094 GGCTTAGCGGCGTTCAATTC 60.248 55.000 9.37 0.00 0.00 2.17
81 82 0.248094 GCTTAGCGGCGTTCAATTCC 60.248 55.000 9.37 0.00 0.00 3.01
82 83 1.083489 CTTAGCGGCGTTCAATTCCA 58.917 50.000 9.37 0.00 0.00 3.53
83 84 1.670811 CTTAGCGGCGTTCAATTCCAT 59.329 47.619 9.37 0.00 0.00 3.41
84 85 2.605837 TAGCGGCGTTCAATTCCATA 57.394 45.000 9.37 0.00 0.00 2.74
85 86 1.014352 AGCGGCGTTCAATTCCATAC 58.986 50.000 9.37 0.00 0.00 2.39
86 87 0.730265 GCGGCGTTCAATTCCATACA 59.270 50.000 9.37 0.00 0.00 2.29
87 88 1.131504 GCGGCGTTCAATTCCATACAA 59.868 47.619 9.37 0.00 0.00 2.41
88 89 2.223479 GCGGCGTTCAATTCCATACAAT 60.223 45.455 9.37 0.00 0.00 2.71
89 90 3.362295 CGGCGTTCAATTCCATACAATG 58.638 45.455 0.00 0.00 0.00 2.82
90 91 3.181501 CGGCGTTCAATTCCATACAATGT 60.182 43.478 0.00 0.00 0.00 2.71
91 92 4.674101 CGGCGTTCAATTCCATACAATGTT 60.674 41.667 0.00 0.00 0.00 2.71
92 93 4.562394 GGCGTTCAATTCCATACAATGTTG 59.438 41.667 0.00 0.00 0.00 3.33
93 94 4.562394 GCGTTCAATTCCATACAATGTTGG 59.438 41.667 0.00 0.00 0.00 3.77
94 95 4.562394 CGTTCAATTCCATACAATGTTGGC 59.438 41.667 8.92 0.00 32.80 4.52
95 96 5.477510 GTTCAATTCCATACAATGTTGGCA 58.522 37.500 8.92 0.00 32.80 4.92
96 97 5.735285 TCAATTCCATACAATGTTGGCAA 57.265 34.783 0.00 0.00 32.80 4.52
97 98 6.106648 TCAATTCCATACAATGTTGGCAAA 57.893 33.333 0.00 0.00 32.80 3.68
98 99 5.931146 TCAATTCCATACAATGTTGGCAAAC 59.069 36.000 0.00 0.00 36.78 2.93
99 100 5.743636 ATTCCATACAATGTTGGCAAACT 57.256 34.783 0.00 0.00 37.19 2.66
100 101 5.543507 TTCCATACAATGTTGGCAAACTT 57.456 34.783 0.00 0.00 37.19 2.66
101 102 6.656632 TTCCATACAATGTTGGCAAACTTA 57.343 33.333 0.00 0.00 37.19 2.24
102 103 6.849085 TCCATACAATGTTGGCAAACTTAT 57.151 33.333 0.00 0.00 37.19 1.73
103 104 7.946381 TCCATACAATGTTGGCAAACTTATA 57.054 32.000 0.00 0.00 37.19 0.98
104 105 8.532186 TCCATACAATGTTGGCAAACTTATAT 57.468 30.769 0.00 0.00 37.19 0.86
105 106 9.634021 TCCATACAATGTTGGCAAACTTATATA 57.366 29.630 0.00 0.00 37.19 0.86
109 110 8.361169 ACAATGTTGGCAAACTTATATAAGGT 57.639 30.769 23.24 16.33 37.62 3.50
110 111 8.811994 ACAATGTTGGCAAACTTATATAAGGTT 58.188 29.630 23.24 20.86 43.57 3.50
113 114 9.695155 ATGTTGGCAAACTTATATAAGGTTAGT 57.305 29.630 22.37 1.71 41.01 2.24
114 115 9.523168 TGTTGGCAAACTTATATAAGGTTAGTT 57.477 29.630 22.37 7.97 41.01 2.24
152 153 6.024552 CCATAAGTTGGCAAGCTTAAAAGA 57.975 37.500 19.04 5.79 39.09 2.52
153 154 6.454795 CCATAAGTTGGCAAGCTTAAAAGAA 58.545 36.000 19.04 5.28 39.09 2.52
154 155 7.099120 CCATAAGTTGGCAAGCTTAAAAGAAT 58.901 34.615 19.04 6.80 39.09 2.40
155 156 7.276438 CCATAAGTTGGCAAGCTTAAAAGAATC 59.724 37.037 19.04 0.00 39.09 2.52
156 157 6.410942 AAGTTGGCAAGCTTAAAAGAATCT 57.589 33.333 0.00 0.00 0.00 2.40
157 158 6.410942 AGTTGGCAAGCTTAAAAGAATCTT 57.589 33.333 0.00 0.00 0.00 2.40
158 159 7.524717 AGTTGGCAAGCTTAAAAGAATCTTA 57.475 32.000 0.00 0.00 0.00 2.10
159 160 7.371159 AGTTGGCAAGCTTAAAAGAATCTTAC 58.629 34.615 0.00 0.00 0.00 2.34
160 161 6.267496 TGGCAAGCTTAAAAGAATCTTACC 57.733 37.500 0.00 0.00 0.00 2.85
161 162 5.772672 TGGCAAGCTTAAAAGAATCTTACCA 59.227 36.000 0.00 0.00 30.19 3.25
162 163 6.093404 GGCAAGCTTAAAAGAATCTTACCAC 58.907 40.000 0.00 0.00 0.00 4.16
163 164 6.294508 GGCAAGCTTAAAAGAATCTTACCACA 60.295 38.462 0.00 0.00 0.00 4.17
164 165 6.582672 GCAAGCTTAAAAGAATCTTACCACAC 59.417 38.462 0.00 0.00 0.00 3.82
165 166 7.522236 GCAAGCTTAAAAGAATCTTACCACACT 60.522 37.037 0.00 0.00 0.00 3.55
166 167 8.352942 CAAGCTTAAAAGAATCTTACCACACTT 58.647 33.333 0.00 0.00 0.00 3.16
167 168 8.465273 AGCTTAAAAGAATCTTACCACACTTT 57.535 30.769 0.00 0.00 0.00 2.66
168 169 8.914011 AGCTTAAAAGAATCTTACCACACTTTT 58.086 29.630 0.00 0.00 39.62 2.27
169 170 9.529325 GCTTAAAAGAATCTTACCACACTTTTT 57.471 29.630 0.00 0.00 38.16 1.94
174 175 9.533253 AAAGAATCTTACCACACTTTTTGAATG 57.467 29.630 0.00 0.00 0.00 2.67
175 176 8.237811 AGAATCTTACCACACTTTTTGAATGT 57.762 30.769 0.00 0.00 0.00 2.71
176 177 8.137437 AGAATCTTACCACACTTTTTGAATGTG 58.863 33.333 5.48 5.48 42.75 3.21
177 178 6.767524 TCTTACCACACTTTTTGAATGTGT 57.232 33.333 6.54 6.54 46.74 3.72
183 184 4.947645 ACACTTTTTGAATGTGTGGGATG 58.052 39.130 10.38 0.00 44.87 3.51
184 185 4.405358 ACACTTTTTGAATGTGTGGGATGT 59.595 37.500 10.38 0.00 44.87 3.06
185 186 4.746115 CACTTTTTGAATGTGTGGGATGTG 59.254 41.667 0.00 0.00 33.33 3.21
186 187 4.202243 ACTTTTTGAATGTGTGGGATGTGG 60.202 41.667 0.00 0.00 0.00 4.17
187 188 1.921982 TTGAATGTGTGGGATGTGGG 58.078 50.000 0.00 0.00 0.00 4.61
188 189 1.071434 TGAATGTGTGGGATGTGGGA 58.929 50.000 0.00 0.00 0.00 4.37
189 190 1.271871 TGAATGTGTGGGATGTGGGAC 60.272 52.381 0.00 0.00 0.00 4.46
190 191 0.039618 AATGTGTGGGATGTGGGACC 59.960 55.000 0.00 0.00 0.00 4.46
191 192 0.846427 ATGTGTGGGATGTGGGACCT 60.846 55.000 0.00 0.00 0.00 3.85
192 193 1.065410 TGTGTGGGATGTGGGACCTT 61.065 55.000 0.00 0.00 0.00 3.50
193 194 0.988832 GTGTGGGATGTGGGACCTTA 59.011 55.000 0.00 0.00 0.00 2.69
194 195 1.065418 GTGTGGGATGTGGGACCTTAG 60.065 57.143 0.00 0.00 0.00 2.18
195 196 1.286248 GTGGGATGTGGGACCTTAGT 58.714 55.000 0.00 0.00 0.00 2.24
196 197 1.065418 GTGGGATGTGGGACCTTAGTG 60.065 57.143 0.00 0.00 0.00 2.74
197 198 1.286248 GGGATGTGGGACCTTAGTGT 58.714 55.000 0.00 0.00 0.00 3.55
198 199 2.225675 TGGGATGTGGGACCTTAGTGTA 60.226 50.000 0.00 0.00 0.00 2.90
199 200 2.434702 GGGATGTGGGACCTTAGTGTAG 59.565 54.545 0.00 0.00 0.00 2.74
200 201 2.158943 GGATGTGGGACCTTAGTGTAGC 60.159 54.545 0.00 0.00 0.00 3.58
201 202 2.320681 TGTGGGACCTTAGTGTAGCT 57.679 50.000 0.00 0.00 0.00 3.32
202 203 2.616524 TGTGGGACCTTAGTGTAGCTT 58.383 47.619 0.00 0.00 0.00 3.74
203 204 2.301870 TGTGGGACCTTAGTGTAGCTTG 59.698 50.000 0.00 0.00 0.00 4.01
204 205 2.565834 GTGGGACCTTAGTGTAGCTTGA 59.434 50.000 0.00 0.00 0.00 3.02
205 206 3.007614 GTGGGACCTTAGTGTAGCTTGAA 59.992 47.826 0.00 0.00 0.00 2.69
206 207 3.007614 TGGGACCTTAGTGTAGCTTGAAC 59.992 47.826 0.00 0.00 0.00 3.18
207 208 3.597255 GGACCTTAGTGTAGCTTGAACC 58.403 50.000 0.00 0.00 0.00 3.62
208 209 3.007614 GGACCTTAGTGTAGCTTGAACCA 59.992 47.826 0.00 0.00 0.00 3.67
209 210 4.504340 GGACCTTAGTGTAGCTTGAACCAA 60.504 45.833 0.00 0.00 0.00 3.67
210 211 5.043737 ACCTTAGTGTAGCTTGAACCAAA 57.956 39.130 0.00 0.00 0.00 3.28
211 212 4.820173 ACCTTAGTGTAGCTTGAACCAAAC 59.180 41.667 0.00 0.00 0.00 2.93
212 213 4.819630 CCTTAGTGTAGCTTGAACCAAACA 59.180 41.667 0.00 0.00 0.00 2.83
213 214 5.277828 CCTTAGTGTAGCTTGAACCAAACAC 60.278 44.000 0.00 0.00 34.66 3.32
214 215 2.949644 AGTGTAGCTTGAACCAAACACC 59.050 45.455 8.20 0.00 34.86 4.16
215 216 2.034179 GTGTAGCTTGAACCAAACACCC 59.966 50.000 0.00 0.00 30.82 4.61
216 217 2.303175 GTAGCTTGAACCAAACACCCA 58.697 47.619 0.00 0.00 0.00 4.51
217 218 1.111277 AGCTTGAACCAAACACCCAC 58.889 50.000 0.00 0.00 0.00 4.61
218 219 0.104120 GCTTGAACCAAACACCCACC 59.896 55.000 0.00 0.00 0.00 4.61
219 220 1.775385 CTTGAACCAAACACCCACCT 58.225 50.000 0.00 0.00 0.00 4.00
220 221 2.938838 CTTGAACCAAACACCCACCTA 58.061 47.619 0.00 0.00 0.00 3.08
221 222 3.292460 CTTGAACCAAACACCCACCTAA 58.708 45.455 0.00 0.00 0.00 2.69
222 223 2.938838 TGAACCAAACACCCACCTAAG 58.061 47.619 0.00 0.00 0.00 2.18
223 224 2.242708 TGAACCAAACACCCACCTAAGT 59.757 45.455 0.00 0.00 0.00 2.24
224 225 3.293337 GAACCAAACACCCACCTAAGTT 58.707 45.455 0.00 0.00 0.00 2.66
225 226 2.661718 ACCAAACACCCACCTAAGTTG 58.338 47.619 0.00 0.00 0.00 3.16
226 227 2.242708 ACCAAACACCCACCTAAGTTGA 59.757 45.455 0.00 0.00 0.00 3.18
227 228 3.117284 ACCAAACACCCACCTAAGTTGAT 60.117 43.478 0.00 0.00 0.00 2.57
228 229 3.895041 CCAAACACCCACCTAAGTTGATT 59.105 43.478 0.00 0.00 0.00 2.57
250 251 8.912988 TGATTCAAACTTAGTCTCAAACCAAAT 58.087 29.630 0.00 0.00 0.00 2.32
261 262 5.656859 GTCTCAAACCAAATAGCCCCTAAAT 59.343 40.000 0.00 0.00 0.00 1.40
267 268 8.704668 CAAACCAAATAGCCCCTAAATTAAGAT 58.295 33.333 0.00 0.00 0.00 2.40
414 415 5.823861 AATTTTAATTTGGCACAGGGTCT 57.176 34.783 0.00 0.00 42.39 3.85
431 432 2.304761 GGTCTCATGTTTGGGAGGTACA 59.695 50.000 0.00 0.00 31.32 2.90
456 458 4.261614 CCTGGGAGCAACTTTTTAACTGTC 60.262 45.833 0.00 0.00 0.00 3.51
461 463 6.475727 GGGAGCAACTTTTTAACTGTCTTTTC 59.524 38.462 0.00 0.00 0.00 2.29
462 464 6.196538 GGAGCAACTTTTTAACTGTCTTTTCG 59.803 38.462 0.00 0.00 0.00 3.46
463 465 6.617879 AGCAACTTTTTAACTGTCTTTTCGT 58.382 32.000 0.00 0.00 0.00 3.85
464 466 6.745907 AGCAACTTTTTAACTGTCTTTTCGTC 59.254 34.615 0.00 0.00 0.00 4.20
465 467 6.745907 GCAACTTTTTAACTGTCTTTTCGTCT 59.254 34.615 0.00 0.00 0.00 4.18
466 468 7.253321 GCAACTTTTTAACTGTCTTTTCGTCTG 60.253 37.037 0.00 0.00 0.00 3.51
493 729 1.530323 AACACACCCGCAAATCCTAC 58.470 50.000 0.00 0.00 0.00 3.18
500 736 3.071892 CACCCGCAAATCCTACCCTTATA 59.928 47.826 0.00 0.00 0.00 0.98
513 749 5.244178 CCTACCCTTATAAGCATCTTCGAGT 59.756 44.000 6.99 0.00 0.00 4.18
516 752 5.305644 ACCCTTATAAGCATCTTCGAGTGAT 59.694 40.000 6.99 0.00 0.00 3.06
521 757 9.469807 CTTATAAGCATCTTCGAGTGATTTAGT 57.530 33.333 0.00 0.00 0.00 2.24
568 805 2.341101 ACCACAGACGCCTCGTAGG 61.341 63.158 0.00 0.00 41.37 3.18
604 843 2.156891 TCTTTCACTAAACACGCATCGC 59.843 45.455 0.00 0.00 0.00 4.58
646 885 3.568538 CAAGAATAACACAAGCACCAGC 58.431 45.455 0.00 0.00 42.56 4.85
657 896 0.243636 AGCACCAGCATTTAAACGCC 59.756 50.000 2.03 0.00 45.49 5.68
659 898 1.604185 GCACCAGCATTTAAACGCCAA 60.604 47.619 2.03 0.00 41.58 4.52
680 919 0.252197 GGGCCGAGAATACCACTGTT 59.748 55.000 0.00 0.00 0.00 3.16
681 920 1.339727 GGGCCGAGAATACCACTGTTT 60.340 52.381 0.00 0.00 0.00 2.83
700 939 6.015434 ACTGTTTTTCTAACCATCCAATCACC 60.015 38.462 0.00 0.00 0.00 4.02
718 965 1.416049 CGATTGGTTCGCGTGTCTG 59.584 57.895 5.77 0.00 41.69 3.51
731 978 2.733858 GCGTGTCTGTTTTGCCTTTTGA 60.734 45.455 0.00 0.00 0.00 2.69
825 1074 3.435169 GGTTTCAGGGGAGAAAGTGAAGT 60.435 47.826 0.00 0.00 38.11 3.01
826 1075 3.492102 TTCAGGGGAGAAAGTGAAGTG 57.508 47.619 0.00 0.00 0.00 3.16
827 1076 2.689658 TCAGGGGAGAAAGTGAAGTGA 58.310 47.619 0.00 0.00 0.00 3.41
828 1077 3.045634 TCAGGGGAGAAAGTGAAGTGAA 58.954 45.455 0.00 0.00 0.00 3.18
829 1078 3.071602 TCAGGGGAGAAAGTGAAGTGAAG 59.928 47.826 0.00 0.00 0.00 3.02
833 1082 3.071747 GGGAGAAAGTGAAGTGAAGGAGT 59.928 47.826 0.00 0.00 0.00 3.85
835 1084 5.474825 GGAGAAAGTGAAGTGAAGGAGTAG 58.525 45.833 0.00 0.00 0.00 2.57
920 2262 1.079503 TGTTTGCGTGCGTGCATATA 58.920 45.000 3.33 0.00 45.78 0.86
1026 2368 1.377856 GGGGTTTCTGCTGGAGAGC 60.378 63.158 0.00 0.00 46.44 4.09
1514 4424 2.459442 GCAGAGTCGATGTGCTGGC 61.459 63.158 8.81 0.00 44.63 4.85
1519 4429 1.079543 GTCGATGTGCTGGCTCACT 60.080 57.895 10.74 0.00 37.81 3.41
1766 4685 4.500116 GCTCCTCCCTCGACGCAC 62.500 72.222 0.00 0.00 0.00 5.34
1767 4686 3.827898 CTCCTCCCTCGACGCACC 61.828 72.222 0.00 0.00 0.00 5.01
1770 4689 3.461773 CTCCCTCGACGCACCCAT 61.462 66.667 0.00 0.00 0.00 4.00
1771 4690 3.432051 CTCCCTCGACGCACCCATC 62.432 68.421 0.00 0.00 0.00 3.51
1772 4691 4.873129 CCCTCGACGCACCCATCG 62.873 72.222 0.00 0.00 39.72 3.84
1992 4911 0.793853 GACGAGGACGAGAAGAACGC 60.794 60.000 0.00 0.00 42.66 4.84
2143 5062 2.357517 GTGTGGGTGCTGGACGAG 60.358 66.667 0.00 0.00 0.00 4.18
2146 5065 3.311110 TGGGTGCTGGACGAGGAC 61.311 66.667 0.24 0.24 42.23 3.85
2255 5183 2.582052 CAGAGTAATCTCGGCTCCTCT 58.418 52.381 0.00 0.00 44.65 3.69
2269 5197 2.744494 GCTCCTCTCGGAATGCAAGAAT 60.744 50.000 0.00 0.00 39.29 2.40
2375 5342 4.496360 GAACCAAAGCTAGTCCTGAGTAC 58.504 47.826 0.00 0.00 0.00 2.73
2377 5344 3.511934 ACCAAAGCTAGTCCTGAGTACTG 59.488 47.826 0.00 0.00 0.00 2.74
2403 5370 3.550437 TCCTTTTGAGCCTGCTAGATC 57.450 47.619 0.00 0.00 0.00 2.75
2405 5372 1.596727 CTTTTGAGCCTGCTAGATCGC 59.403 52.381 0.00 0.00 0.00 4.58
2411 5378 1.757118 AGCCTGCTAGATCGCTGTTAA 59.243 47.619 0.00 0.00 0.00 2.01
2412 5379 2.131183 GCCTGCTAGATCGCTGTTAAG 58.869 52.381 0.00 0.00 0.00 1.85
2413 5380 2.482142 GCCTGCTAGATCGCTGTTAAGT 60.482 50.000 0.00 0.00 0.00 2.24
2414 5381 3.119291 CCTGCTAGATCGCTGTTAAGTG 58.881 50.000 0.00 0.00 35.08 3.16
2443 5690 4.628963 TTAGTTTCCTTACTTTCCGGCT 57.371 40.909 0.00 0.00 0.00 5.52
2462 5709 5.060446 CCGGCTAGCGTTATTTTTCAAAAAG 59.940 40.000 9.00 0.00 0.00 2.27
2507 5781 4.149046 CAGTTTTGCTAAGTCTCAGTCGAC 59.851 45.833 7.70 7.70 0.00 4.20
2651 5925 2.017782 GTCGACTGAGATCTAGCCACA 58.982 52.381 8.70 0.00 0.00 4.17
2692 5966 8.496751 GTTTGCAAAAAGTACAAAACACCTTAA 58.503 29.630 14.67 0.00 35.25 1.85
2693 5967 7.583860 TGCAAAAAGTACAAAACACCTTAAC 57.416 32.000 0.00 0.00 0.00 2.01
2731 6005 3.420893 ACCATCAAATGACCAATGTCGT 58.579 40.909 0.00 0.00 44.86 4.34
2736 6010 4.888917 TCAAATGACCAATGTCGTCAGTA 58.111 39.130 0.00 0.00 44.86 2.74
2742 6016 3.596214 ACCAATGTCGTCAGTAATGGAC 58.404 45.455 11.42 0.00 0.00 4.02
2766 6040 2.287915 GTCATTGTCGCCGCTTTCATAT 59.712 45.455 0.00 0.00 0.00 1.78
2785 6059 2.691409 TTGGAGCCGGTCTAATCTTG 57.309 50.000 1.90 0.00 0.00 3.02
2787 6061 1.906574 TGGAGCCGGTCTAATCTTGTT 59.093 47.619 1.90 0.00 0.00 2.83
2792 6066 4.950050 AGCCGGTCTAATCTTGTTGATAG 58.050 43.478 1.90 0.00 34.45 2.08
2809 6083 8.380743 TGTTGATAGTAGCCGAAAAGTTTTTA 57.619 30.769 1.64 0.00 0.00 1.52
2833 6107 3.688414 GCACATGCCCCTAATTAAGTCCT 60.688 47.826 0.00 0.00 34.31 3.85
2835 6109 5.308825 CACATGCCCCTAATTAAGTCCTAG 58.691 45.833 0.00 0.00 0.00 3.02
2845 6119 6.260936 CCTAATTAAGTCCTAGAACCGTCGTA 59.739 42.308 0.00 0.00 0.00 3.43
2850 6124 1.470098 TCCTAGAACCGTCGTAGTTGC 59.530 52.381 0.00 0.00 0.00 4.17
2852 6126 2.516923 CTAGAACCGTCGTAGTTGCTG 58.483 52.381 0.00 0.00 0.00 4.41
2882 6156 9.178758 CCTTATTTGGTCTAAACTCTTAGCATT 57.821 33.333 0.00 0.00 35.42 3.56
2974 6248 6.321181 TGATTGTTAGCTAATGGGAAATGGAC 59.679 38.462 9.88 0.00 0.00 4.02
2975 6249 4.196193 TGTTAGCTAATGGGAAATGGACG 58.804 43.478 9.88 0.00 0.00 4.79
2981 6255 2.046700 GGGAAATGGACGTGCCGA 60.047 61.111 4.04 0.00 40.66 5.54
2992 6266 0.250124 ACGTGCCGATTTGGTTCTCA 60.250 50.000 1.50 0.00 41.21 3.27
3075 6546 9.898152 TTCAAGTGGGAAAAACAAGAATTATTT 57.102 25.926 0.00 0.00 0.00 1.40
3155 6628 4.082081 TCCCAAATGCACATCTTCATGTTC 60.082 41.667 0.00 0.00 40.66 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.202245 ACCGTGCATGTTTTGTGTCAC 60.202 47.619 4.96 0.00 0.00 3.67
1 2 1.098869 ACCGTGCATGTTTTGTGTCA 58.901 45.000 4.96 0.00 0.00 3.58
2 3 1.476074 CACCGTGCATGTTTTGTGTC 58.524 50.000 4.96 0.00 0.00 3.67
3 4 0.102120 CCACCGTGCATGTTTTGTGT 59.898 50.000 4.96 0.00 0.00 3.72
4 5 0.102120 ACCACCGTGCATGTTTTGTG 59.898 50.000 4.96 5.67 0.00 3.33
5 6 0.102120 CACCACCGTGCATGTTTTGT 59.898 50.000 4.96 0.00 32.04 2.83
6 7 2.884146 CACCACCGTGCATGTTTTG 58.116 52.632 4.96 0.00 32.04 2.44
15 16 2.358737 GAGGAAGGCACCACCGTG 60.359 66.667 3.78 0.00 46.52 4.94
16 17 3.637273 GGAGGAAGGCACCACCGT 61.637 66.667 3.78 0.00 46.52 4.83
17 18 4.410400 GGGAGGAAGGCACCACCG 62.410 72.222 9.96 0.00 46.52 4.94
18 19 1.279025 TATGGGAGGAAGGCACCACC 61.279 60.000 8.24 8.24 39.41 4.61
19 20 0.181350 CTATGGGAGGAAGGCACCAC 59.819 60.000 3.78 0.00 35.52 4.16
20 21 1.635817 GCTATGGGAGGAAGGCACCA 61.636 60.000 3.78 0.00 37.41 4.17
21 22 1.149401 GCTATGGGAGGAAGGCACC 59.851 63.158 0.00 0.00 0.00 5.01
22 23 1.149401 GGCTATGGGAGGAAGGCAC 59.851 63.158 0.00 0.00 35.95 5.01
23 24 0.624500 AAGGCTATGGGAGGAAGGCA 60.625 55.000 0.00 0.00 38.21 4.75
24 25 1.349357 CTAAGGCTATGGGAGGAAGGC 59.651 57.143 0.00 0.00 36.13 4.35
25 26 2.695585 ACTAAGGCTATGGGAGGAAGG 58.304 52.381 0.00 0.00 0.00 3.46
26 27 3.835395 CCTACTAAGGCTATGGGAGGAAG 59.165 52.174 6.70 0.00 35.64 3.46
27 28 3.858135 CCTACTAAGGCTATGGGAGGAA 58.142 50.000 6.70 0.00 35.64 3.36
28 29 3.544698 CCTACTAAGGCTATGGGAGGA 57.455 52.381 6.70 0.00 35.64 3.71
40 41 4.430908 CCGAAACCAGCTAACCTACTAAG 58.569 47.826 0.00 0.00 0.00 2.18
41 42 3.368739 GCCGAAACCAGCTAACCTACTAA 60.369 47.826 0.00 0.00 0.00 2.24
42 43 2.167075 GCCGAAACCAGCTAACCTACTA 59.833 50.000 0.00 0.00 0.00 1.82
43 44 1.066358 GCCGAAACCAGCTAACCTACT 60.066 52.381 0.00 0.00 0.00 2.57
44 45 1.066358 AGCCGAAACCAGCTAACCTAC 60.066 52.381 0.00 0.00 37.64 3.18
45 46 1.272807 AGCCGAAACCAGCTAACCTA 58.727 50.000 0.00 0.00 37.64 3.08
46 47 0.400594 AAGCCGAAACCAGCTAACCT 59.599 50.000 0.00 0.00 38.74 3.50
47 48 2.007608 CTAAGCCGAAACCAGCTAACC 58.992 52.381 0.00 0.00 38.74 2.85
48 49 1.397343 GCTAAGCCGAAACCAGCTAAC 59.603 52.381 0.00 0.00 38.74 2.34
49 50 1.734163 GCTAAGCCGAAACCAGCTAA 58.266 50.000 0.00 0.00 38.74 3.09
50 51 0.459585 CGCTAAGCCGAAACCAGCTA 60.460 55.000 0.00 0.00 38.74 3.32
51 52 1.741770 CGCTAAGCCGAAACCAGCT 60.742 57.895 0.00 0.00 42.40 4.24
52 53 2.750888 CCGCTAAGCCGAAACCAGC 61.751 63.158 0.00 0.00 0.00 4.85
53 54 2.750888 GCCGCTAAGCCGAAACCAG 61.751 63.158 0.00 0.00 0.00 4.00
54 55 2.744709 GCCGCTAAGCCGAAACCA 60.745 61.111 0.00 0.00 0.00 3.67
55 56 3.861263 CGCCGCTAAGCCGAAACC 61.861 66.667 0.00 0.00 0.00 3.27
56 57 2.558717 GAACGCCGCTAAGCCGAAAC 62.559 60.000 0.00 0.00 0.00 2.78
57 58 2.357760 AACGCCGCTAAGCCGAAA 60.358 55.556 0.00 0.00 0.00 3.46
58 59 2.812178 GAACGCCGCTAAGCCGAA 60.812 61.111 0.00 0.00 0.00 4.30
59 60 2.845752 ATTGAACGCCGCTAAGCCGA 62.846 55.000 0.00 0.00 0.00 5.54
60 61 1.977594 AATTGAACGCCGCTAAGCCG 61.978 55.000 0.00 0.00 0.00 5.52
61 62 0.248094 GAATTGAACGCCGCTAAGCC 60.248 55.000 0.00 0.00 0.00 4.35
62 63 0.248094 GGAATTGAACGCCGCTAAGC 60.248 55.000 0.00 0.00 0.00 3.09
63 64 1.083489 TGGAATTGAACGCCGCTAAG 58.917 50.000 0.00 0.00 0.00 2.18
64 65 1.745232 ATGGAATTGAACGCCGCTAA 58.255 45.000 0.00 0.00 0.00 3.09
65 66 2.206750 GTATGGAATTGAACGCCGCTA 58.793 47.619 0.00 0.00 0.00 4.26
66 67 1.014352 GTATGGAATTGAACGCCGCT 58.986 50.000 0.00 0.00 0.00 5.52
67 68 0.730265 TGTATGGAATTGAACGCCGC 59.270 50.000 0.00 0.00 0.00 6.53
68 69 3.181501 ACATTGTATGGAATTGAACGCCG 60.182 43.478 0.00 0.00 33.60 6.46
69 70 4.370364 ACATTGTATGGAATTGAACGCC 57.630 40.909 0.00 0.00 33.60 5.68
70 71 4.562394 CCAACATTGTATGGAATTGAACGC 59.438 41.667 10.66 0.00 39.12 4.84
71 72 4.562394 GCCAACATTGTATGGAATTGAACG 59.438 41.667 17.06 0.00 39.12 3.95
72 73 5.477510 TGCCAACATTGTATGGAATTGAAC 58.522 37.500 17.06 3.85 39.12 3.18
73 74 5.735285 TGCCAACATTGTATGGAATTGAA 57.265 34.783 17.06 0.00 39.12 2.69
74 75 5.735285 TTGCCAACATTGTATGGAATTGA 57.265 34.783 17.06 0.00 39.12 2.57
75 76 5.933463 AGTTTGCCAACATTGTATGGAATTG 59.067 36.000 17.06 0.24 39.12 2.32
76 77 6.112927 AGTTTGCCAACATTGTATGGAATT 57.887 33.333 17.06 0.00 39.12 2.17
77 78 5.743636 AGTTTGCCAACATTGTATGGAAT 57.256 34.783 17.06 0.05 39.12 3.01
78 79 5.543507 AAGTTTGCCAACATTGTATGGAA 57.456 34.783 17.06 7.92 39.12 3.53
79 80 6.849085 ATAAGTTTGCCAACATTGTATGGA 57.151 33.333 17.06 0.27 39.12 3.41
83 84 9.469097 ACCTTATATAAGTTTGCCAACATTGTA 57.531 29.630 18.91 0.00 35.05 2.41
84 85 8.361169 ACCTTATATAAGTTTGCCAACATTGT 57.639 30.769 18.91 4.57 35.05 2.71
87 88 9.695155 ACTAACCTTATATAAGTTTGCCAACAT 57.305 29.630 18.91 0.00 35.05 2.71
88 89 9.523168 AACTAACCTTATATAAGTTTGCCAACA 57.477 29.630 18.91 0.00 35.05 3.33
130 131 8.031277 AGATTCTTTTAAGCTTGCCAACTTATG 58.969 33.333 9.86 0.00 0.00 1.90
131 132 8.127150 AGATTCTTTTAAGCTTGCCAACTTAT 57.873 30.769 9.86 0.00 0.00 1.73
132 133 7.524717 AGATTCTTTTAAGCTTGCCAACTTA 57.475 32.000 9.86 0.00 0.00 2.24
133 134 6.410942 AGATTCTTTTAAGCTTGCCAACTT 57.589 33.333 9.86 0.00 0.00 2.66
134 135 6.410942 AAGATTCTTTTAAGCTTGCCAACT 57.589 33.333 9.86 0.00 0.00 3.16
135 136 6.586463 GGTAAGATTCTTTTAAGCTTGCCAAC 59.414 38.462 9.86 0.00 39.93 3.77
136 137 6.266558 TGGTAAGATTCTTTTAAGCTTGCCAA 59.733 34.615 18.80 6.89 44.51 4.52
137 138 5.772672 TGGTAAGATTCTTTTAAGCTTGCCA 59.227 36.000 17.67 17.67 45.01 4.92
138 139 6.093404 GTGGTAAGATTCTTTTAAGCTTGCC 58.907 40.000 9.86 13.66 40.38 4.52
139 140 6.582672 GTGTGGTAAGATTCTTTTAAGCTTGC 59.417 38.462 9.86 0.00 0.00 4.01
140 141 7.875971 AGTGTGGTAAGATTCTTTTAAGCTTG 58.124 34.615 9.86 0.00 0.00 4.01
141 142 8.465273 AAGTGTGGTAAGATTCTTTTAAGCTT 57.535 30.769 3.48 3.48 0.00 3.74
142 143 8.465273 AAAGTGTGGTAAGATTCTTTTAAGCT 57.535 30.769 3.86 0.00 0.00 3.74
143 144 9.529325 AAAAAGTGTGGTAAGATTCTTTTAAGC 57.471 29.630 3.86 0.00 35.17 3.09
148 149 9.533253 CATTCAAAAAGTGTGGTAAGATTCTTT 57.467 29.630 3.86 0.00 0.00 2.52
149 150 8.695456 ACATTCAAAAAGTGTGGTAAGATTCTT 58.305 29.630 4.03 4.03 0.00 2.52
150 151 8.137437 CACATTCAAAAAGTGTGGTAAGATTCT 58.863 33.333 0.00 0.00 39.54 2.40
151 152 7.920682 ACACATTCAAAAAGTGTGGTAAGATTC 59.079 33.333 9.23 0.00 45.60 2.52
152 153 7.781056 ACACATTCAAAAAGTGTGGTAAGATT 58.219 30.769 9.23 0.00 45.60 2.40
153 154 7.346751 ACACATTCAAAAAGTGTGGTAAGAT 57.653 32.000 9.23 0.00 45.60 2.40
154 155 6.767524 ACACATTCAAAAAGTGTGGTAAGA 57.232 33.333 9.23 0.00 45.60 2.10
161 162 4.405358 ACATCCCACACATTCAAAAAGTGT 59.595 37.500 0.00 0.00 46.54 3.55
162 163 4.746115 CACATCCCACACATTCAAAAAGTG 59.254 41.667 0.00 0.00 39.12 3.16
163 164 4.202243 CCACATCCCACACATTCAAAAAGT 60.202 41.667 0.00 0.00 0.00 2.66
164 165 4.309099 CCACATCCCACACATTCAAAAAG 58.691 43.478 0.00 0.00 0.00 2.27
165 166 3.070734 CCCACATCCCACACATTCAAAAA 59.929 43.478 0.00 0.00 0.00 1.94
166 167 2.632028 CCCACATCCCACACATTCAAAA 59.368 45.455 0.00 0.00 0.00 2.44
167 168 2.158400 TCCCACATCCCACACATTCAAA 60.158 45.455 0.00 0.00 0.00 2.69
168 169 1.426983 TCCCACATCCCACACATTCAA 59.573 47.619 0.00 0.00 0.00 2.69
169 170 1.071434 TCCCACATCCCACACATTCA 58.929 50.000 0.00 0.00 0.00 2.57
170 171 1.463674 GTCCCACATCCCACACATTC 58.536 55.000 0.00 0.00 0.00 2.67
171 172 0.039618 GGTCCCACATCCCACACATT 59.960 55.000 0.00 0.00 0.00 2.71
172 173 0.846427 AGGTCCCACATCCCACACAT 60.846 55.000 0.00 0.00 0.00 3.21
173 174 1.065410 AAGGTCCCACATCCCACACA 61.065 55.000 0.00 0.00 0.00 3.72
174 175 0.988832 TAAGGTCCCACATCCCACAC 59.011 55.000 0.00 0.00 0.00 3.82
175 176 1.285280 CTAAGGTCCCACATCCCACA 58.715 55.000 0.00 0.00 0.00 4.17
176 177 1.065418 CACTAAGGTCCCACATCCCAC 60.065 57.143 0.00 0.00 0.00 4.61
177 178 1.285280 CACTAAGGTCCCACATCCCA 58.715 55.000 0.00 0.00 0.00 4.37
178 179 1.286248 ACACTAAGGTCCCACATCCC 58.714 55.000 0.00 0.00 0.00 3.85
179 180 2.158943 GCTACACTAAGGTCCCACATCC 60.159 54.545 0.00 0.00 0.00 3.51
180 181 2.766828 AGCTACACTAAGGTCCCACATC 59.233 50.000 0.00 0.00 0.00 3.06
181 182 2.834113 AGCTACACTAAGGTCCCACAT 58.166 47.619 0.00 0.00 0.00 3.21
182 183 2.301870 CAAGCTACACTAAGGTCCCACA 59.698 50.000 0.00 0.00 0.00 4.17
183 184 2.565834 TCAAGCTACACTAAGGTCCCAC 59.434 50.000 0.00 0.00 0.00 4.61
184 185 2.897350 TCAAGCTACACTAAGGTCCCA 58.103 47.619 0.00 0.00 0.00 4.37
185 186 3.597255 GTTCAAGCTACACTAAGGTCCC 58.403 50.000 0.00 0.00 0.00 4.46
186 187 3.007614 TGGTTCAAGCTACACTAAGGTCC 59.992 47.826 0.00 0.00 0.00 4.46
187 188 4.267349 TGGTTCAAGCTACACTAAGGTC 57.733 45.455 0.00 0.00 0.00 3.85
188 189 4.699925 TTGGTTCAAGCTACACTAAGGT 57.300 40.909 0.00 0.00 0.00 3.50
189 190 4.819630 TGTTTGGTTCAAGCTACACTAAGG 59.180 41.667 0.00 0.00 0.00 2.69
190 191 5.277828 GGTGTTTGGTTCAAGCTACACTAAG 60.278 44.000 18.55 0.00 34.62 2.18
191 192 4.577283 GGTGTTTGGTTCAAGCTACACTAA 59.423 41.667 18.55 0.00 34.62 2.24
192 193 4.131596 GGTGTTTGGTTCAAGCTACACTA 58.868 43.478 18.55 0.00 34.62 2.74
193 194 2.949644 GGTGTTTGGTTCAAGCTACACT 59.050 45.455 18.55 0.00 34.62 3.55
194 195 2.034179 GGGTGTTTGGTTCAAGCTACAC 59.966 50.000 13.75 13.75 33.98 2.90
195 196 2.303175 GGGTGTTTGGTTCAAGCTACA 58.697 47.619 0.00 0.00 0.00 2.74
196 197 2.034179 GTGGGTGTTTGGTTCAAGCTAC 59.966 50.000 0.00 0.00 0.00 3.58
197 198 2.303175 GTGGGTGTTTGGTTCAAGCTA 58.697 47.619 0.00 0.00 0.00 3.32
198 199 1.111277 GTGGGTGTTTGGTTCAAGCT 58.889 50.000 0.00 0.00 0.00 3.74
199 200 0.104120 GGTGGGTGTTTGGTTCAAGC 59.896 55.000 0.00 0.00 0.00 4.01
200 201 1.775385 AGGTGGGTGTTTGGTTCAAG 58.225 50.000 0.00 0.00 0.00 3.02
201 202 3.292460 CTTAGGTGGGTGTTTGGTTCAA 58.708 45.455 0.00 0.00 0.00 2.69
202 203 2.242708 ACTTAGGTGGGTGTTTGGTTCA 59.757 45.455 0.00 0.00 0.00 3.18
203 204 2.940158 ACTTAGGTGGGTGTTTGGTTC 58.060 47.619 0.00 0.00 0.00 3.62
204 205 3.028130 CAACTTAGGTGGGTGTTTGGTT 58.972 45.455 0.00 0.00 0.00 3.67
205 206 2.242708 TCAACTTAGGTGGGTGTTTGGT 59.757 45.455 0.00 0.00 0.00 3.67
206 207 2.938838 TCAACTTAGGTGGGTGTTTGG 58.061 47.619 0.00 0.00 0.00 3.28
207 208 4.582656 TGAATCAACTTAGGTGGGTGTTTG 59.417 41.667 0.00 0.00 0.00 2.93
208 209 4.798882 TGAATCAACTTAGGTGGGTGTTT 58.201 39.130 0.00 0.00 0.00 2.83
209 210 4.447138 TGAATCAACTTAGGTGGGTGTT 57.553 40.909 0.00 0.00 0.00 3.32
210 211 4.447138 TTGAATCAACTTAGGTGGGTGT 57.553 40.909 0.00 0.00 0.00 4.16
211 212 4.827284 AGTTTGAATCAACTTAGGTGGGTG 59.173 41.667 0.00 0.00 0.00 4.61
212 213 5.061721 AGTTTGAATCAACTTAGGTGGGT 57.938 39.130 0.00 0.00 0.00 4.51
213 214 6.715264 ACTAAGTTTGAATCAACTTAGGTGGG 59.285 38.462 28.00 16.25 38.20 4.61
214 215 7.661847 AGACTAAGTTTGAATCAACTTAGGTGG 59.338 37.037 28.00 16.46 38.20 4.61
215 216 8.608844 AGACTAAGTTTGAATCAACTTAGGTG 57.391 34.615 28.00 16.66 38.20 4.00
216 217 8.429641 TGAGACTAAGTTTGAATCAACTTAGGT 58.570 33.333 28.00 21.36 38.20 3.08
217 218 8.833231 TGAGACTAAGTTTGAATCAACTTAGG 57.167 34.615 28.00 18.88 38.20 2.69
220 221 8.406297 GGTTTGAGACTAAGTTTGAATCAACTT 58.594 33.333 12.72 12.72 0.00 2.66
221 222 7.556275 TGGTTTGAGACTAAGTTTGAATCAACT 59.444 33.333 0.00 0.00 0.00 3.16
222 223 7.703328 TGGTTTGAGACTAAGTTTGAATCAAC 58.297 34.615 0.00 0.00 0.00 3.18
223 224 7.873719 TGGTTTGAGACTAAGTTTGAATCAA 57.126 32.000 0.00 0.00 0.00 2.57
224 225 7.873719 TTGGTTTGAGACTAAGTTTGAATCA 57.126 32.000 0.00 0.00 0.00 2.57
227 228 8.349983 GCTATTTGGTTTGAGACTAAGTTTGAA 58.650 33.333 0.00 0.00 29.89 2.69
228 229 7.040686 GGCTATTTGGTTTGAGACTAAGTTTGA 60.041 37.037 0.00 0.00 29.89 2.69
250 251 9.131791 GACAAATTCATCTTAATTTAGGGGCTA 57.868 33.333 0.00 0.00 37.03 3.93
252 253 7.781056 TGACAAATTCATCTTAATTTAGGGGC 58.219 34.615 0.00 0.00 37.03 5.80
261 262 7.230849 AGCCAACATGACAAATTCATCTTAA 57.769 32.000 0.00 0.00 43.68 1.85
267 268 7.517614 TTAGTTAGCCAACATGACAAATTCA 57.482 32.000 0.00 0.00 37.10 2.57
302 303 0.880718 TGCCAATTGTGTACGTCGCA 60.881 50.000 4.43 1.17 34.52 5.10
414 415 1.004277 GGCTGTACCTCCCAAACATGA 59.996 52.381 0.00 0.00 34.51 3.07
431 432 2.628178 GTTAAAAAGTTGCTCCCAGGCT 59.372 45.455 0.00 0.00 0.00 4.58
493 729 5.201713 TCACTCGAAGATGCTTATAAGGG 57.798 43.478 14.28 0.00 33.89 3.95
500 736 4.800993 CGACTAAATCACTCGAAGATGCTT 59.199 41.667 1.21 0.00 33.89 3.91
521 757 9.516314 CTTCGTCAATATAAGATTATATGCCGA 57.484 33.333 5.98 9.96 36.67 5.54
537 773 3.610821 CGTCTGTGGTGACTTCGTCAATA 60.611 47.826 0.00 0.00 44.49 1.90
575 812 5.725864 GCGTGTTTAGTGAAAGAAGACGTTT 60.726 40.000 6.81 0.00 40.69 3.60
637 876 1.336795 GGCGTTTAAATGCTGGTGCTT 60.337 47.619 26.96 0.00 40.71 3.91
657 896 1.134098 AGTGGTATTCTCGGCCCATTG 60.134 52.381 0.00 0.00 0.00 2.82
659 898 0.469917 CAGTGGTATTCTCGGCCCAT 59.530 55.000 0.00 0.00 0.00 4.00
667 906 7.393515 GGATGGTTAGAAAAACAGTGGTATTCT 59.606 37.037 10.24 10.24 35.27 2.40
680 919 4.912586 TCGGTGATTGGATGGTTAGAAAA 58.087 39.130 0.00 0.00 0.00 2.29
681 920 4.561500 TCGGTGATTGGATGGTTAGAAA 57.438 40.909 0.00 0.00 0.00 2.52
709 948 0.248458 AAAGGCAAAACAGACACGCG 60.248 50.000 3.53 3.53 0.00 6.01
718 965 5.580691 AGCACTACTTTTCAAAAGGCAAAAC 59.419 36.000 14.47 0.00 0.00 2.43
731 978 1.421646 ACTGGGAGCAGCACTACTTTT 59.578 47.619 0.00 0.00 0.00 2.27
825 1074 3.023832 TGTGATCGATGCTACTCCTTCA 58.976 45.455 0.54 0.00 0.00 3.02
826 1075 3.181486 TGTGTGATCGATGCTACTCCTTC 60.181 47.826 0.54 0.00 0.00 3.46
827 1076 2.760650 TGTGTGATCGATGCTACTCCTT 59.239 45.455 0.54 0.00 0.00 3.36
828 1077 2.099921 GTGTGTGATCGATGCTACTCCT 59.900 50.000 0.54 0.00 0.00 3.69
829 1078 2.464865 GTGTGTGATCGATGCTACTCC 58.535 52.381 0.54 0.00 0.00 3.85
833 1082 0.455815 AGCGTGTGTGATCGATGCTA 59.544 50.000 0.54 0.00 0.00 3.49
835 1084 1.346197 CAGCGTGTGTGATCGATGC 59.654 57.895 0.54 0.00 36.73 3.91
920 2262 2.331194 GCAAAATGTTGAGCGCAGATT 58.669 42.857 11.47 0.00 36.83 2.40
981 2323 4.632458 TACGCACGCACTCACGCA 62.632 61.111 0.00 0.00 36.19 5.24
996 2338 1.303806 AAACCCCGCCACCATGTAC 60.304 57.895 0.00 0.00 0.00 2.90
1339 2685 0.806102 ATCAGCGGACATGTACGTGC 60.806 55.000 30.03 15.58 39.57 5.34
1492 4402 0.108424 AGCACATCGACTCTGCTTCC 60.108 55.000 7.35 0.00 38.07 3.46
1514 4424 1.290324 CCACGTCCTCCACAGTGAG 59.710 63.158 0.62 0.00 33.77 3.51
1519 4429 4.293648 CGCACCACGTCCTCCACA 62.294 66.667 0.00 0.00 36.87 4.17
1902 4821 1.305046 GAGGAAGAGGACGGGGACA 60.305 63.158 0.00 0.00 0.00 4.02
1992 4911 1.294659 GCTCGTGAAAGCTGAGGTGG 61.295 60.000 0.00 0.00 39.27 4.61
2143 5062 3.775654 CCCACCAGCTCCTCGTCC 61.776 72.222 0.00 0.00 0.00 4.79
2221 5149 2.125147 TCTGCCATACTGTGCGCC 60.125 61.111 4.18 0.00 0.00 6.53
2255 5183 3.153130 TGGTGAAATTCTTGCATTCCGA 58.847 40.909 0.00 0.00 0.00 4.55
2375 5342 4.219288 AGCAGGCTCAAAAGGATTAAACAG 59.781 41.667 0.00 0.00 0.00 3.16
2377 5344 4.790765 AGCAGGCTCAAAAGGATTAAAC 57.209 40.909 0.00 0.00 0.00 2.01
2414 5381 9.603298 CGGAAAGTAAGGAAACTAAATGTTAAC 57.397 33.333 0.00 0.00 42.68 2.01
2426 5673 2.675889 CGCTAGCCGGAAAGTAAGGAAA 60.676 50.000 5.05 0.00 0.00 3.13
2439 5686 5.854338 TCTTTTTGAAAAATAACGCTAGCCG 59.146 36.000 9.66 7.08 44.21 5.52
2477 5724 9.726438 ACTGAGACTTAGCAAAACTGTTATAAT 57.274 29.630 0.00 0.00 0.00 1.28
2478 5725 9.204570 GACTGAGACTTAGCAAAACTGTTATAA 57.795 33.333 0.00 0.00 0.00 0.98
2663 5937 7.227711 AGGTGTTTTGTACTTTTTGCAAACTTT 59.772 29.630 12.39 0.99 39.27 2.66
2671 5945 8.522178 TGTGTTAAGGTGTTTTGTACTTTTTG 57.478 30.769 0.00 0.00 0.00 2.44
2680 5954 4.274950 ACCTCGATGTGTTAAGGTGTTTTG 59.725 41.667 0.00 0.00 40.59 2.44
2684 5958 2.897969 AGACCTCGATGTGTTAAGGTGT 59.102 45.455 0.00 0.00 42.15 4.16
2708 5982 3.181497 CGACATTGGTCATTTGATGGTCC 60.181 47.826 0.00 0.00 44.54 4.46
2709 5983 3.440173 ACGACATTGGTCATTTGATGGTC 59.560 43.478 0.00 0.00 44.54 4.02
2714 5988 3.738982 ACTGACGACATTGGTCATTTGA 58.261 40.909 0.00 0.00 44.54 2.69
2731 6005 4.242475 GACAATGACACGTCCATTACTGA 58.758 43.478 11.11 0.00 33.35 3.41
2736 6010 0.796312 GCGACAATGACACGTCCATT 59.204 50.000 6.83 6.83 34.83 3.16
2742 6016 2.170260 AAAGCGGCGACAATGACACG 62.170 55.000 12.98 0.00 0.00 4.49
2766 6040 1.906574 ACAAGATTAGACCGGCTCCAA 59.093 47.619 0.00 0.00 0.00 3.53
2785 6059 9.274065 CATAAAAACTTTTCGGCTACTATCAAC 57.726 33.333 0.00 0.00 0.00 3.18
2787 6061 7.119992 TGCATAAAAACTTTTCGGCTACTATCA 59.880 33.333 10.30 0.00 33.30 2.15
2792 6066 5.216648 TGTGCATAAAAACTTTTCGGCTAC 58.783 37.500 0.00 8.18 33.30 3.58
2809 6083 3.891366 GACTTAATTAGGGGCATGTGCAT 59.109 43.478 7.36 0.00 44.36 3.96
2833 6107 2.153645 TCAGCAACTACGACGGTTCTA 58.846 47.619 0.00 0.00 0.00 2.10
2835 6109 1.774639 TTCAGCAACTACGACGGTTC 58.225 50.000 0.00 0.00 0.00 3.62
2845 6119 5.574188 AGACCAAATAAGGATTCAGCAACT 58.426 37.500 0.00 0.00 0.00 3.16
2850 6124 9.454859 AAGAGTTTAGACCAAATAAGGATTCAG 57.545 33.333 0.00 0.00 0.00 3.02
2882 6156 9.026121 ACACTAGCAAGAGAGAAATAAACTAGA 57.974 33.333 0.00 0.00 0.00 2.43
2928 6202 3.492011 CACCCGCTGAATACCGTTATTAC 59.508 47.826 0.00 0.00 0.00 1.89
2935 6209 0.937304 CAATCACCCGCTGAATACCG 59.063 55.000 0.00 0.00 30.60 4.02
2944 6218 2.290641 CCATTAGCTAACAATCACCCGC 59.709 50.000 8.70 0.00 0.00 6.13
2974 6248 1.265635 TTTGAGAACCAAATCGGCACG 59.734 47.619 0.00 0.00 46.57 5.34
2975 6249 3.049912 GTTTTGAGAACCAAATCGGCAC 58.950 45.455 0.00 0.00 43.59 5.01
2981 6255 2.955660 TGCTCCGTTTTGAGAACCAAAT 59.044 40.909 0.00 0.00 43.59 2.32
2992 6266 2.436521 CCCCCTTTTGCTCCGTTTT 58.563 52.632 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.