Multiple sequence alignment - TraesCS2D01G473200

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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 TraesCS2D01G473200 chr2D 100.000 1582 0 0 938 2519 576925047 576923466 0.000000e+00 2922
1 TraesCS2D01G473200 chr2D 94.721 1629 34 16 938 2519 645195050 645196673 0.000000e+00 2484
2 TraesCS2D01G473200 chr2D 100.000 584 0 0 1 584 576925984 576925401 0.000000e+00 1079
3 TraesCS2D01G473200 chr2D 99.213 254 2 0 331 584 645194647 645194900 2.280000e-125 459
4 TraesCS2D01G473200 chr3D 95.625 1623 29 10 938 2519 571152202 571153823 0.000000e+00 2566
5 TraesCS2D01G473200 chr3D 94.653 1627 37 14 938 2519 537296745 537298366 0.000000e+00 2477
6 TraesCS2D01G473200 chr3D 90.703 1635 62 23 939 2519 536922479 536924077 0.000000e+00 2095
7 TraesCS2D01G473200 chr3D 98.846 260 2 1 325 584 512508434 512508692 1.770000e-126 462
8 TraesCS2D01G473200 chr6D 94.951 1624 36 11 938 2519 100359264 100360883 0.000000e+00 2503
9 TraesCS2D01G473200 chr6D 94.845 1610 32 15 956 2519 436433018 436434622 0.000000e+00 2466
10 TraesCS2D01G473200 chr6D 94.403 1626 41 14 938 2519 17067455 17069074 0.000000e+00 2453
11 TraesCS2D01G473200 chr6D 91.687 1612 58 29 938 2519 82906675 82908240 0.000000e+00 2165
12 TraesCS2D01G473200 chr6D 98.485 264 3 1 322 584 17067048 17067311 4.910000e-127 464
13 TraesCS2D01G473200 chr5D 94.935 1619 31 22 946 2519 537773843 537772231 0.000000e+00 2488
14 TraesCS2D01G473200 chr5D 94.023 1623 50 12 938 2519 233841568 233839952 0.000000e+00 2416
15 TraesCS2D01G473200 chr5D 99.216 255 2 0 330 584 79126813 79126559 6.350000e-126 460
16 TraesCS2D01G473200 chr5D 99.213 254 2 0 331 584 543865238 543865491 2.280000e-125 459
17 TraesCS2D01G473200 chr5D 98.824 255 3 0 330 584 537774291 537774037 2.950000e-124 455
18 TraesCS2D01G473200 chr7D 94.172 1630 36 17 938 2518 31039516 31037897 0.000000e+00 2429
19 TraesCS2D01G473200 chr7D 93.789 1610 54 12 938 2519 617526926 617528517 0.000000e+00 2377
20 TraesCS2D01G473200 chr7D 95.497 644 27 2 938 1581 629949964 629950605 0.000000e+00 1027
21 TraesCS2D01G473200 chr7D 98.833 257 3 0 328 584 3769842 3770098 2.280000e-125 459
22 TraesCS2D01G473200 chr3A 94.132 1619 48 18 943 2519 36049102 36050715 0.000000e+00 2420
23 TraesCS2D01G473200 chr3A 88.889 117 10 3 1532 1648 27493777 27493890 9.390000e-30 141
24 TraesCS2D01G473200 chr4D 93.746 1631 32 21 938 2519 36561220 36559611 0.000000e+00 2383
25 TraesCS2D01G473200 chr4D 88.607 1615 69 34 939 2519 455275197 455273664 0.000000e+00 1857
26 TraesCS2D01G473200 chr4D 98.819 254 3 0 331 584 36561616 36561363 1.060000e-123 453
27 TraesCS2D01G473200 chrUn 90.566 1643 72 32 939 2519 111371745 111370124 0.000000e+00 2098
28 TraesCS2D01G473200 chr7B 89.797 1627 68 25 939 2518 585992730 585994305 0.000000e+00 1995
29 TraesCS2D01G473200 chr6A 94.485 1088 30 7 938 1996 575493875 575494961 0.000000e+00 1650
30 TraesCS2D01G473200 chr1D 99.216 255 2 0 330 584 10554225 10554479 6.350000e-126 460
31 TraesCS2D01G473200 chr2B 85.256 156 14 3 147 297 84990982 84991133 4.340000e-33 152


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 TraesCS2D01G473200 chr2D 576923466 576925984 2518 True 2000.5 2922 100.0000 1 2519 2 chr2D.!!$R1 2518
1 TraesCS2D01G473200 chr2D 645194647 645196673 2026 False 1471.5 2484 96.9670 331 2519 2 chr2D.!!$F1 2188
2 TraesCS2D01G473200 chr3D 571152202 571153823 1621 False 2566.0 2566 95.6250 938 2519 1 chr3D.!!$F4 1581
3 TraesCS2D01G473200 chr3D 537296745 537298366 1621 False 2477.0 2477 94.6530 938 2519 1 chr3D.!!$F3 1581
4 TraesCS2D01G473200 chr3D 536922479 536924077 1598 False 2095.0 2095 90.7030 939 2519 1 chr3D.!!$F2 1580
5 TraesCS2D01G473200 chr6D 100359264 100360883 1619 False 2503.0 2503 94.9510 938 2519 1 chr6D.!!$F2 1581
6 TraesCS2D01G473200 chr6D 436433018 436434622 1604 False 2466.0 2466 94.8450 956 2519 1 chr6D.!!$F3 1563
7 TraesCS2D01G473200 chr6D 82906675 82908240 1565 False 2165.0 2165 91.6870 938 2519 1 chr6D.!!$F1 1581
8 TraesCS2D01G473200 chr6D 17067048 17069074 2026 False 1458.5 2453 96.4440 322 2519 2 chr6D.!!$F4 2197
9 TraesCS2D01G473200 chr5D 233839952 233841568 1616 True 2416.0 2416 94.0230 938 2519 1 chr5D.!!$R2 1581
10 TraesCS2D01G473200 chr5D 537772231 537774291 2060 True 1471.5 2488 96.8795 330 2519 2 chr5D.!!$R3 2189
11 TraesCS2D01G473200 chr7D 31037897 31039516 1619 True 2429.0 2429 94.1720 938 2518 1 chr7D.!!$R1 1580
12 TraesCS2D01G473200 chr7D 617526926 617528517 1591 False 2377.0 2377 93.7890 938 2519 1 chr7D.!!$F2 1581
13 TraesCS2D01G473200 chr7D 629949964 629950605 641 False 1027.0 1027 95.4970 938 1581 1 chr7D.!!$F3 643
14 TraesCS2D01G473200 chr3A 36049102 36050715 1613 False 2420.0 2420 94.1320 943 2519 1 chr3A.!!$F2 1576
15 TraesCS2D01G473200 chr4D 455273664 455275197 1533 True 1857.0 1857 88.6070 939 2519 1 chr4D.!!$R1 1580
16 TraesCS2D01G473200 chr4D 36559611 36561616 2005 True 1418.0 2383 96.2825 331 2519 2 chr4D.!!$R2 2188
17 TraesCS2D01G473200 chrUn 111370124 111371745 1621 True 2098.0 2098 90.5660 939 2519 1 chrUn.!!$R1 1580
18 TraesCS2D01G473200 chr7B 585992730 585994305 1575 False 1995.0 1995 89.7970 939 2518 1 chr7B.!!$F1 1579
19 TraesCS2D01G473200 chr6A 575493875 575494961 1086 False 1650.0 1650 94.4850 938 1996 1 chr6A.!!$F1 1058

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
86 87 0.040336 CGATGGCATGCTCAATCTGC 60.04 55.0 18.92 0.0 35.16 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 1803 0.03254 GGCAGCCCAGTCTTGTTTTG 59.967 55.0 0.0 0.0 0.0 2.44 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.741476 GCAGGCAGCCTTTCCGTG 61.741 66.667 12.86 0.57 37.23 4.94
24 25 3.058160 CAGGCAGCCTTTCCGTGG 61.058 66.667 12.86 0.00 0.00 4.94
31 32 2.644992 CCTTTCCGTGGCACAAGC 59.355 61.111 19.09 0.00 44.16 4.01
32 33 2.252260 CTTTCCGTGGCACAAGCG 59.748 61.111 19.09 3.06 44.16 4.68
33 34 2.203084 TTTCCGTGGCACAAGCGA 60.203 55.556 19.09 4.05 44.16 4.93
34 35 2.175184 CTTTCCGTGGCACAAGCGAG 62.175 60.000 19.09 4.65 44.16 5.03
35 36 4.680237 TCCGTGGCACAAGCGAGG 62.680 66.667 19.09 9.51 44.16 4.63
36 37 4.680237 CCGTGGCACAAGCGAGGA 62.680 66.667 19.09 0.00 44.16 3.71
37 38 3.414700 CGTGGCACAAGCGAGGAC 61.415 66.667 19.09 0.00 44.16 3.85
38 39 3.050275 GTGGCACAAGCGAGGACC 61.050 66.667 13.86 0.00 44.16 4.46
39 40 3.241530 TGGCACAAGCGAGGACCT 61.242 61.111 0.00 0.00 43.41 3.85
40 41 2.032681 GGCACAAGCGAGGACCTT 59.967 61.111 0.00 0.00 43.41 3.50
41 42 2.035442 GGCACAAGCGAGGACCTTC 61.035 63.158 0.00 0.00 43.41 3.46
42 43 1.301716 GCACAAGCGAGGACCTTCA 60.302 57.895 0.00 0.00 0.00 3.02
43 44 1.294659 GCACAAGCGAGGACCTTCAG 61.295 60.000 0.00 0.00 0.00 3.02
44 45 0.671781 CACAAGCGAGGACCTTCAGG 60.672 60.000 0.00 0.00 42.17 3.86
56 57 1.539157 CCTTCAGGTCAAAGAAGCCC 58.461 55.000 0.00 0.00 39.85 5.19
57 58 1.074566 CCTTCAGGTCAAAGAAGCCCT 59.925 52.381 0.00 0.00 39.85 5.19
58 59 2.489802 CCTTCAGGTCAAAGAAGCCCTT 60.490 50.000 0.00 0.00 39.85 3.95
59 60 2.276732 TCAGGTCAAAGAAGCCCTTG 57.723 50.000 0.00 0.00 34.79 3.61
60 61 1.774254 TCAGGTCAAAGAAGCCCTTGA 59.226 47.619 0.00 0.00 34.79 3.02
61 62 2.376518 TCAGGTCAAAGAAGCCCTTGAT 59.623 45.455 0.00 0.00 34.79 2.57
62 63 2.490903 CAGGTCAAAGAAGCCCTTGATG 59.509 50.000 0.00 0.00 34.79 3.07
63 64 1.821136 GGTCAAAGAAGCCCTTGATGG 59.179 52.381 0.00 0.00 34.79 3.51
64 65 2.555227 GGTCAAAGAAGCCCTTGATGGA 60.555 50.000 0.00 0.00 38.35 3.41
65 66 3.359950 GTCAAAGAAGCCCTTGATGGAT 58.640 45.455 0.00 0.00 38.35 3.41
66 67 3.766051 GTCAAAGAAGCCCTTGATGGATT 59.234 43.478 0.00 0.00 36.54 3.01
69 70 2.332063 GAAGCCCTTGATGGATTCGA 57.668 50.000 0.00 0.00 40.61 3.71
70 71 2.856222 GAAGCCCTTGATGGATTCGAT 58.144 47.619 0.00 0.00 40.61 3.59
71 72 2.267174 AGCCCTTGATGGATTCGATG 57.733 50.000 0.00 0.00 38.35 3.84
72 73 1.202855 AGCCCTTGATGGATTCGATGG 60.203 52.381 0.00 0.00 38.35 3.51
73 74 1.242076 CCCTTGATGGATTCGATGGC 58.758 55.000 0.00 0.00 38.35 4.40
74 75 1.477377 CCCTTGATGGATTCGATGGCA 60.477 52.381 0.00 0.00 38.35 4.92
75 76 2.511659 CCTTGATGGATTCGATGGCAT 58.488 47.619 0.00 0.00 38.35 4.40
76 77 2.228103 CCTTGATGGATTCGATGGCATG 59.772 50.000 3.81 0.00 38.35 4.06
77 78 1.241165 TGATGGATTCGATGGCATGC 58.759 50.000 9.90 9.90 0.00 4.06
78 79 1.202842 TGATGGATTCGATGGCATGCT 60.203 47.619 18.92 0.00 0.00 3.79
79 80 1.467734 GATGGATTCGATGGCATGCTC 59.532 52.381 18.92 7.30 0.00 4.26
80 81 0.180878 TGGATTCGATGGCATGCTCA 59.819 50.000 18.92 14.25 0.00 4.26
81 82 1.311859 GGATTCGATGGCATGCTCAA 58.688 50.000 18.92 4.07 0.00 3.02
82 83 1.884579 GGATTCGATGGCATGCTCAAT 59.115 47.619 18.92 9.17 0.00 2.57
83 84 2.095364 GGATTCGATGGCATGCTCAATC 60.095 50.000 18.92 16.26 0.00 2.67
84 85 2.336945 TTCGATGGCATGCTCAATCT 57.663 45.000 18.92 0.00 0.00 2.40
85 86 1.589803 TCGATGGCATGCTCAATCTG 58.410 50.000 18.92 13.43 0.00 2.90
86 87 0.040336 CGATGGCATGCTCAATCTGC 60.040 55.000 18.92 0.00 35.16 4.26
87 88 1.029681 GATGGCATGCTCAATCTGCA 58.970 50.000 18.92 4.44 44.95 4.41
88 89 1.001268 GATGGCATGCTCAATCTGCAG 60.001 52.381 18.92 7.63 44.04 4.41
89 90 1.065928 GGCATGCTCAATCTGCAGC 59.934 57.895 18.92 0.00 44.04 5.25
94 95 2.704464 TGCTCAATCTGCAGCATAGT 57.296 45.000 9.47 0.00 40.80 2.12
95 96 2.285977 TGCTCAATCTGCAGCATAGTG 58.714 47.619 9.47 1.43 40.80 2.74
96 97 1.002684 GCTCAATCTGCAGCATAGTGC 60.003 52.381 9.47 7.60 45.46 4.40
119 120 8.278729 TGCACTACACATGATTTTCATATTCA 57.721 30.769 0.00 0.00 34.28 2.57
120 121 8.905850 TGCACTACACATGATTTTCATATTCAT 58.094 29.630 0.00 0.00 34.28 2.57
136 137 8.437360 TCATATTCATGTTGAGTTGTATCACC 57.563 34.615 0.00 0.00 33.57 4.02
137 138 7.498900 TCATATTCATGTTGAGTTGTATCACCC 59.501 37.037 0.00 0.00 33.57 4.61
138 139 4.632327 TCATGTTGAGTTGTATCACCCA 57.368 40.909 0.00 0.00 0.00 4.51
139 140 5.178096 TCATGTTGAGTTGTATCACCCAT 57.822 39.130 0.00 0.00 0.00 4.00
140 141 5.569355 TCATGTTGAGTTGTATCACCCATT 58.431 37.500 0.00 0.00 0.00 3.16
141 142 6.716284 TCATGTTGAGTTGTATCACCCATTA 58.284 36.000 0.00 0.00 0.00 1.90
142 143 6.823182 TCATGTTGAGTTGTATCACCCATTAG 59.177 38.462 0.00 0.00 0.00 1.73
143 144 6.121776 TGTTGAGTTGTATCACCCATTAGT 57.878 37.500 0.00 0.00 0.00 2.24
144 145 7.247456 TGTTGAGTTGTATCACCCATTAGTA 57.753 36.000 0.00 0.00 0.00 1.82
145 146 7.857456 TGTTGAGTTGTATCACCCATTAGTAT 58.143 34.615 0.00 0.00 0.00 2.12
146 147 8.983789 TGTTGAGTTGTATCACCCATTAGTATA 58.016 33.333 0.00 0.00 0.00 1.47
147 148 9.826574 GTTGAGTTGTATCACCCATTAGTATAA 57.173 33.333 0.00 0.00 0.00 0.98
149 150 9.429109 TGAGTTGTATCACCCATTAGTATAAGA 57.571 33.333 0.00 0.00 0.00 2.10
171 172 7.059202 AGAATATGGATTTTCATTTCAGCCC 57.941 36.000 0.00 0.00 0.00 5.19
172 173 6.612456 AGAATATGGATTTTCATTTCAGCCCA 59.388 34.615 0.00 0.00 0.00 5.36
173 174 7.291651 AGAATATGGATTTTCATTTCAGCCCAT 59.708 33.333 0.00 0.00 37.05 4.00
174 175 8.495160 AATATGGATTTTCATTTCAGCCCATA 57.505 30.769 0.00 0.00 39.04 2.74
175 176 5.596836 TGGATTTTCATTTCAGCCCATAC 57.403 39.130 0.00 0.00 0.00 2.39
176 177 5.271598 TGGATTTTCATTTCAGCCCATACT 58.728 37.500 0.00 0.00 0.00 2.12
177 178 6.430864 TGGATTTTCATTTCAGCCCATACTA 58.569 36.000 0.00 0.00 0.00 1.82
178 179 6.894654 TGGATTTTCATTTCAGCCCATACTAA 59.105 34.615 0.00 0.00 0.00 2.24
179 180 7.147915 TGGATTTTCATTTCAGCCCATACTAAC 60.148 37.037 0.00 0.00 0.00 2.34
180 181 5.811399 TTTCATTTCAGCCCATACTAACG 57.189 39.130 0.00 0.00 0.00 3.18
181 182 4.746535 TCATTTCAGCCCATACTAACGA 57.253 40.909 0.00 0.00 0.00 3.85
182 183 5.290493 TCATTTCAGCCCATACTAACGAT 57.710 39.130 0.00 0.00 0.00 3.73
183 184 5.680619 TCATTTCAGCCCATACTAACGATT 58.319 37.500 0.00 0.00 0.00 3.34
184 185 5.527214 TCATTTCAGCCCATACTAACGATTG 59.473 40.000 0.00 0.00 0.00 2.67
185 186 2.833794 TCAGCCCATACTAACGATTGC 58.166 47.619 0.00 0.00 0.00 3.56
186 187 1.873591 CAGCCCATACTAACGATTGCC 59.126 52.381 0.00 0.00 0.00 4.52
187 188 1.488812 AGCCCATACTAACGATTGCCA 59.511 47.619 0.00 0.00 0.00 4.92
188 189 2.092646 AGCCCATACTAACGATTGCCAA 60.093 45.455 0.00 0.00 0.00 4.52
189 190 2.685897 GCCCATACTAACGATTGCCAAA 59.314 45.455 0.00 0.00 0.00 3.28
190 191 3.317993 GCCCATACTAACGATTGCCAAAT 59.682 43.478 0.00 0.00 0.00 2.32
191 192 4.202111 GCCCATACTAACGATTGCCAAATT 60.202 41.667 0.00 0.00 0.00 1.82
192 193 5.681179 GCCCATACTAACGATTGCCAAATTT 60.681 40.000 0.00 0.00 0.00 1.82
193 194 6.460399 GCCCATACTAACGATTGCCAAATTTA 60.460 38.462 0.00 0.00 0.00 1.40
194 195 7.484975 CCCATACTAACGATTGCCAAATTTAA 58.515 34.615 0.00 0.00 0.00 1.52
195 196 7.976734 CCCATACTAACGATTGCCAAATTTAAA 59.023 33.333 0.00 0.00 0.00 1.52
196 197 9.528018 CCATACTAACGATTGCCAAATTTAAAT 57.472 29.630 0.00 0.00 0.00 1.40
200 201 9.915629 ACTAACGATTGCCAAATTTAAATAACA 57.084 25.926 0.01 0.00 0.00 2.41
203 204 9.871299 AACGATTGCCAAATTTAAATAACAAAC 57.129 25.926 0.01 2.80 0.00 2.93
204 205 9.046296 ACGATTGCCAAATTTAAATAACAAACA 57.954 25.926 0.01 0.00 0.00 2.83
205 206 9.312146 CGATTGCCAAATTTAAATAACAAACAC 57.688 29.630 0.01 1.40 0.00 3.32
208 209 9.994432 TTGCCAAATTTAAATAACAAACACAAG 57.006 25.926 0.01 0.00 0.00 3.16
209 210 9.167311 TGCCAAATTTAAATAACAAACACAAGT 57.833 25.926 0.01 0.00 0.00 3.16
233 234 7.954447 GTAGAATACTCAGTGTAAGCAAACTG 58.046 38.462 0.00 0.00 44.23 3.16
239 240 4.380531 TCAGTGTAAGCAAACTGAGAAGG 58.619 43.478 1.50 0.00 45.97 3.46
240 241 3.058639 CAGTGTAAGCAAACTGAGAAGGC 60.059 47.826 0.00 0.00 45.43 4.35
241 242 2.096218 GTGTAAGCAAACTGAGAAGGCG 60.096 50.000 0.00 0.00 0.00 5.52
242 243 2.143925 GTAAGCAAACTGAGAAGGCGT 58.856 47.619 0.00 0.00 0.00 5.68
243 244 0.947244 AAGCAAACTGAGAAGGCGTG 59.053 50.000 0.00 0.00 0.00 5.34
244 245 0.106708 AGCAAACTGAGAAGGCGTGA 59.893 50.000 0.00 0.00 0.00 4.35
245 246 0.944386 GCAAACTGAGAAGGCGTGAA 59.056 50.000 0.00 0.00 0.00 3.18
246 247 1.069636 GCAAACTGAGAAGGCGTGAAG 60.070 52.381 0.00 0.00 0.00 3.02
260 261 2.858839 CGTGAAGCACTATACGTCACA 58.141 47.619 9.76 0.00 43.81 3.58
261 262 2.846550 CGTGAAGCACTATACGTCACAG 59.153 50.000 9.76 0.00 43.81 3.66
262 263 3.669824 CGTGAAGCACTATACGTCACAGT 60.670 47.826 9.76 0.00 43.81 3.55
263 264 4.436451 CGTGAAGCACTATACGTCACAGTA 60.436 45.833 9.76 0.00 43.81 2.74
264 265 5.029014 GTGAAGCACTATACGTCACAGTAG 58.971 45.833 0.00 0.00 43.32 2.57
265 266 4.698780 TGAAGCACTATACGTCACAGTAGT 59.301 41.667 0.00 0.00 0.00 2.73
266 267 5.876460 TGAAGCACTATACGTCACAGTAGTA 59.124 40.000 0.00 0.00 0.00 1.82
267 268 5.731599 AGCACTATACGTCACAGTAGTAC 57.268 43.478 0.00 0.00 0.00 2.73
268 269 5.426504 AGCACTATACGTCACAGTAGTACT 58.573 41.667 0.00 0.00 0.00 2.73
269 270 5.879223 AGCACTATACGTCACAGTAGTACTT 59.121 40.000 0.00 0.00 0.00 2.24
270 271 7.044181 AGCACTATACGTCACAGTAGTACTTA 58.956 38.462 0.00 0.00 0.00 2.24
271 272 7.010923 AGCACTATACGTCACAGTAGTACTTAC 59.989 40.741 0.00 0.00 0.00 2.34
272 273 7.201556 GCACTATACGTCACAGTAGTACTTACA 60.202 40.741 0.00 0.00 34.56 2.41
273 274 8.659491 CACTATACGTCACAGTAGTACTTACAA 58.341 37.037 0.00 0.00 34.56 2.41
274 275 9.388506 ACTATACGTCACAGTAGTACTTACAAT 57.611 33.333 0.00 0.20 34.56 2.71
277 278 7.678947 ACGTCACAGTAGTACTTACAATAGT 57.321 36.000 0.00 0.00 34.56 2.12
278 279 8.103948 ACGTCACAGTAGTACTTACAATAGTT 57.896 34.615 0.00 0.00 34.56 2.24
279 280 8.571336 ACGTCACAGTAGTACTTACAATAGTTT 58.429 33.333 0.00 0.00 34.56 2.66
280 281 9.059485 CGTCACAGTAGTACTTACAATAGTTTC 57.941 37.037 0.00 0.00 34.56 2.78
281 282 9.903682 GTCACAGTAGTACTTACAATAGTTTCA 57.096 33.333 0.00 0.00 34.56 2.69
289 290 9.804758 AGTACTTACAATAGTTTCAGATACTGC 57.195 33.333 3.89 0.00 0.00 4.40
290 291 9.582431 GTACTTACAATAGTTTCAGATACTGCA 57.418 33.333 3.89 0.00 0.00 4.41
292 293 9.319143 ACTTACAATAGTTTCAGATACTGCATC 57.681 33.333 3.89 0.00 0.00 3.91
293 294 9.539825 CTTACAATAGTTTCAGATACTGCATCT 57.460 33.333 3.89 0.00 45.35 2.90
301 302 1.612950 AGATACTGCATCTGAGCGAGG 59.387 52.381 0.00 0.00 42.69 4.63
302 303 1.339610 GATACTGCATCTGAGCGAGGT 59.660 52.381 0.00 0.00 37.31 3.85
303 304 2.052782 TACTGCATCTGAGCGAGGTA 57.947 50.000 0.00 0.00 37.31 3.08
304 305 1.186200 ACTGCATCTGAGCGAGGTAA 58.814 50.000 0.00 0.00 37.31 2.85
305 306 1.135915 ACTGCATCTGAGCGAGGTAAG 59.864 52.381 0.00 0.00 37.31 2.34
306 307 0.179100 TGCATCTGAGCGAGGTAAGC 60.179 55.000 0.00 0.00 37.31 3.09
307 308 0.179100 GCATCTGAGCGAGGTAAGCA 60.179 55.000 0.00 0.00 37.01 3.91
308 309 1.850377 CATCTGAGCGAGGTAAGCAG 58.150 55.000 0.00 0.00 37.01 4.24
309 310 0.749649 ATCTGAGCGAGGTAAGCAGG 59.250 55.000 0.00 0.00 37.01 4.85
310 311 0.612174 TCTGAGCGAGGTAAGCAGGT 60.612 55.000 0.00 0.00 37.01 4.00
311 312 0.247736 CTGAGCGAGGTAAGCAGGTT 59.752 55.000 0.00 0.00 37.01 3.50
312 313 0.685097 TGAGCGAGGTAAGCAGGTTT 59.315 50.000 0.00 0.00 37.01 3.27
313 314 1.337823 TGAGCGAGGTAAGCAGGTTTC 60.338 52.381 0.00 0.00 37.01 2.78
314 315 0.977395 AGCGAGGTAAGCAGGTTTCT 59.023 50.000 0.00 0.00 37.01 2.52
315 316 1.066787 AGCGAGGTAAGCAGGTTTCTC 60.067 52.381 0.00 0.00 37.01 2.87
316 317 2.007547 GCGAGGTAAGCAGGTTTCTCC 61.008 57.143 0.00 0.00 34.19 3.71
317 318 1.405661 CGAGGTAAGCAGGTTTCTCCC 60.406 57.143 0.00 0.00 36.75 4.30
318 319 0.992695 AGGTAAGCAGGTTTCTCCCC 59.007 55.000 0.00 0.00 36.75 4.81
319 320 0.696501 GGTAAGCAGGTTTCTCCCCA 59.303 55.000 0.00 0.00 36.75 4.96
320 321 1.285078 GGTAAGCAGGTTTCTCCCCAT 59.715 52.381 0.00 0.00 36.75 4.00
321 322 2.508300 GGTAAGCAGGTTTCTCCCCATA 59.492 50.000 0.00 0.00 36.75 2.74
322 323 3.138468 GGTAAGCAGGTTTCTCCCCATAT 59.862 47.826 0.00 0.00 36.75 1.78
323 324 4.349930 GGTAAGCAGGTTTCTCCCCATATA 59.650 45.833 0.00 0.00 36.75 0.86
324 325 5.014228 GGTAAGCAGGTTTCTCCCCATATAT 59.986 44.000 0.00 0.00 36.75 0.86
325 326 4.647564 AGCAGGTTTCTCCCCATATATG 57.352 45.455 5.68 5.68 36.75 1.78
326 327 4.242811 AGCAGGTTTCTCCCCATATATGA 58.757 43.478 14.54 0.00 36.75 2.15
327 328 4.665009 AGCAGGTTTCTCCCCATATATGAA 59.335 41.667 14.54 0.00 36.75 2.57
328 329 5.314306 AGCAGGTTTCTCCCCATATATGAAT 59.686 40.000 14.54 0.00 36.75 2.57
378 379 2.086869 CATGCGAATTGGAAGGAGTGT 58.913 47.619 0.00 0.00 0.00 3.55
1179 1204 1.616865 CGAATTAGGGCGGTGGATCTA 59.383 52.381 0.00 0.00 0.00 1.98
1180 1205 2.036733 CGAATTAGGGCGGTGGATCTAA 59.963 50.000 0.00 0.00 0.00 2.10
1249 1300 2.288666 GGCATTTTGAGTGGCTCGATA 58.711 47.619 0.00 0.00 38.91 2.92
1411 1466 6.487331 TGAATTGAAGAAAATTGGCAAGCAAT 59.513 30.769 5.96 4.26 29.89 3.56
1524 1579 7.988737 TGATGTTCATCAATCGCTAGAATTTT 58.011 30.769 12.29 0.00 0.00 1.82
1686 1771 8.980143 TCCTCTGTTTTTGTTTTTCAGTTAAG 57.020 30.769 0.00 0.00 0.00 1.85
1717 1803 8.387190 ACACACCCAAATTTAGTTTCTAGTAC 57.613 34.615 0.00 0.00 0.00 2.73
2135 2276 2.081462 GTGATTGGGGTGTAGAAACCG 58.919 52.381 0.00 0.00 41.52 4.44
2213 2356 7.697691 AGCAATCCACAAATAATAGACGAAAG 58.302 34.615 0.00 0.00 0.00 2.62
2409 2553 5.333566 AGCTAGATAGATAGATAGGGGGC 57.666 47.826 0.00 0.00 0.00 5.80
2418 2563 0.849094 AGATAGGGGGCCACCAAACA 60.849 55.000 30.24 8.70 42.91 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.808656 GAAAGGCTGCCTGCTCGC 61.809 66.667 24.16 6.37 42.39 5.03
3 4 3.130160 GGAAAGGCTGCCTGCTCG 61.130 66.667 24.16 0.00 42.39 5.03
6 7 3.741476 CACGGAAAGGCTGCCTGC 61.741 66.667 24.16 17.11 41.94 4.85
7 8 3.058160 CCACGGAAAGGCTGCCTG 61.058 66.667 24.16 12.26 32.13 4.85
14 15 2.644992 GCTTGTGCCACGGAAAGG 59.355 61.111 0.00 0.00 0.00 3.11
15 16 2.175184 CTCGCTTGTGCCACGGAAAG 62.175 60.000 0.00 0.00 35.36 2.62
16 17 2.203084 TCGCTTGTGCCACGGAAA 60.203 55.556 0.00 0.00 35.36 3.13
17 18 2.664851 CTCGCTTGTGCCACGGAA 60.665 61.111 0.00 0.00 35.36 4.30
18 19 4.680237 CCTCGCTTGTGCCACGGA 62.680 66.667 0.00 0.00 35.36 4.69
19 20 4.680237 TCCTCGCTTGTGCCACGG 62.680 66.667 0.00 0.00 35.36 4.94
20 21 3.414700 GTCCTCGCTTGTGCCACG 61.415 66.667 0.00 0.00 35.36 4.94
21 22 3.050275 GGTCCTCGCTTGTGCCAC 61.050 66.667 0.00 0.00 35.36 5.01
22 23 2.731691 GAAGGTCCTCGCTTGTGCCA 62.732 60.000 0.00 0.00 35.36 4.92
23 24 2.032681 AAGGTCCTCGCTTGTGCC 59.967 61.111 0.00 0.00 35.36 5.01
24 25 1.294659 CTGAAGGTCCTCGCTTGTGC 61.295 60.000 0.00 0.00 0.00 4.57
25 26 0.671781 CCTGAAGGTCCTCGCTTGTG 60.672 60.000 0.00 0.00 0.00 3.33
26 27 1.674057 CCTGAAGGTCCTCGCTTGT 59.326 57.895 0.00 0.00 0.00 3.16
27 28 4.606071 CCTGAAGGTCCTCGCTTG 57.394 61.111 0.00 0.00 0.00 4.01
36 37 5.042533 AAGGGCTTCTTTGACCTGAAGGT 62.043 47.826 0.38 0.38 46.66 3.50
37 38 1.074566 AGGGCTTCTTTGACCTGAAGG 59.925 52.381 0.00 0.00 45.36 3.46
38 39 2.555757 CAAGGGCTTCTTTGACCTGAAG 59.444 50.000 0.00 0.00 46.66 3.02
39 40 2.174639 TCAAGGGCTTCTTTGACCTGAA 59.825 45.455 0.00 0.00 46.66 3.02
40 41 1.774254 TCAAGGGCTTCTTTGACCTGA 59.226 47.619 0.00 0.00 46.66 3.86
41 42 2.276732 TCAAGGGCTTCTTTGACCTG 57.723 50.000 0.00 0.00 46.66 4.00
43 44 1.821136 CCATCAAGGGCTTCTTTGACC 59.179 52.381 0.00 0.00 32.41 4.02
44 45 2.795329 TCCATCAAGGGCTTCTTTGAC 58.205 47.619 0.00 0.00 38.24 3.18
45 46 3.744940 ATCCATCAAGGGCTTCTTTGA 57.255 42.857 0.00 0.00 38.24 2.69
46 47 3.181493 CGAATCCATCAAGGGCTTCTTTG 60.181 47.826 0.00 0.00 38.24 2.77
47 48 3.019564 CGAATCCATCAAGGGCTTCTTT 58.980 45.455 0.00 0.00 38.24 2.52
48 49 2.239654 TCGAATCCATCAAGGGCTTCTT 59.760 45.455 0.00 0.00 38.24 2.52
49 50 1.839994 TCGAATCCATCAAGGGCTTCT 59.160 47.619 0.00 0.00 38.24 2.85
50 51 2.332063 TCGAATCCATCAAGGGCTTC 57.668 50.000 0.00 0.00 38.24 3.86
51 52 2.579873 CATCGAATCCATCAAGGGCTT 58.420 47.619 0.00 0.00 38.24 4.35
52 53 1.202855 CCATCGAATCCATCAAGGGCT 60.203 52.381 0.00 0.00 38.24 5.19
53 54 1.242076 CCATCGAATCCATCAAGGGC 58.758 55.000 0.00 0.00 38.24 5.19
54 55 1.242076 GCCATCGAATCCATCAAGGG 58.758 55.000 0.00 0.00 38.24 3.95
55 56 1.971481 TGCCATCGAATCCATCAAGG 58.029 50.000 0.00 0.00 39.47 3.61
56 57 2.351447 GCATGCCATCGAATCCATCAAG 60.351 50.000 6.36 0.00 0.00 3.02
57 58 1.610038 GCATGCCATCGAATCCATCAA 59.390 47.619 6.36 0.00 0.00 2.57
58 59 1.202842 AGCATGCCATCGAATCCATCA 60.203 47.619 15.66 0.00 0.00 3.07
59 60 1.467734 GAGCATGCCATCGAATCCATC 59.532 52.381 15.66 0.00 0.00 3.51
60 61 1.202842 TGAGCATGCCATCGAATCCAT 60.203 47.619 15.66 0.00 0.00 3.41
61 62 0.180878 TGAGCATGCCATCGAATCCA 59.819 50.000 15.66 0.00 0.00 3.41
62 63 1.311859 TTGAGCATGCCATCGAATCC 58.688 50.000 15.66 0.00 0.00 3.01
63 64 2.812591 AGATTGAGCATGCCATCGAATC 59.187 45.455 15.66 15.89 0.00 2.52
64 65 2.552743 CAGATTGAGCATGCCATCGAAT 59.447 45.455 15.66 8.80 0.00 3.34
65 66 1.944709 CAGATTGAGCATGCCATCGAA 59.055 47.619 15.66 4.42 0.00 3.71
66 67 1.589803 CAGATTGAGCATGCCATCGA 58.410 50.000 15.66 6.71 0.00 3.59
67 68 0.040336 GCAGATTGAGCATGCCATCG 60.040 55.000 15.66 10.76 33.81 3.84
68 69 1.001268 CTGCAGATTGAGCATGCCATC 60.001 52.381 15.66 13.56 41.82 3.51
69 70 1.032794 CTGCAGATTGAGCATGCCAT 58.967 50.000 15.66 3.96 41.82 4.40
70 71 1.663379 GCTGCAGATTGAGCATGCCA 61.663 55.000 20.43 9.53 41.82 4.92
71 72 1.065928 GCTGCAGATTGAGCATGCC 59.934 57.895 20.43 6.65 41.82 4.40
72 73 1.807226 TGCTGCAGATTGAGCATGC 59.193 52.632 20.43 10.51 40.30 4.06
76 77 1.002684 GCACTATGCTGCAGATTGAGC 60.003 52.381 20.43 14.33 40.96 4.26
77 78 2.285977 TGCACTATGCTGCAGATTGAG 58.714 47.619 20.43 10.68 45.31 3.02
78 79 2.406596 TGCACTATGCTGCAGATTGA 57.593 45.000 20.43 0.00 45.31 2.57
84 85 1.725641 GTGTAGTGCACTATGCTGCA 58.274 50.000 28.37 18.24 45.31 4.41
94 95 8.278729 TGAATATGAAAATCATGTGTAGTGCA 57.721 30.769 3.17 0.00 37.70 4.57
95 96 9.177304 CATGAATATGAAAATCATGTGTAGTGC 57.823 33.333 3.17 0.00 43.36 4.40
110 111 8.892723 GGTGATACAACTCAACATGAATATGAA 58.107 33.333 0.00 0.00 37.73 2.57
111 112 7.498900 GGGTGATACAACTCAACATGAATATGA 59.501 37.037 0.00 0.00 34.39 2.15
112 113 7.282901 TGGGTGATACAACTCAACATGAATATG 59.717 37.037 0.00 0.00 34.39 1.78
113 114 7.345691 TGGGTGATACAACTCAACATGAATAT 58.654 34.615 0.00 0.00 34.39 1.28
114 115 6.716284 TGGGTGATACAACTCAACATGAATA 58.284 36.000 0.00 0.00 34.39 1.75
115 116 5.569355 TGGGTGATACAACTCAACATGAAT 58.431 37.500 0.00 0.00 34.39 2.57
116 117 4.979335 TGGGTGATACAACTCAACATGAA 58.021 39.130 0.00 0.00 34.39 2.57
117 118 4.632327 TGGGTGATACAACTCAACATGA 57.368 40.909 0.00 0.00 34.39 3.07
118 119 5.902613 AATGGGTGATACAACTCAACATG 57.097 39.130 0.00 0.00 33.29 3.21
119 120 6.721318 ACTAATGGGTGATACAACTCAACAT 58.279 36.000 0.00 0.00 33.29 2.71
120 121 6.121776 ACTAATGGGTGATACAACTCAACA 57.878 37.500 0.00 0.00 33.29 3.33
121 122 9.826574 TTATACTAATGGGTGATACAACTCAAC 57.173 33.333 0.00 0.00 33.29 3.18
123 124 9.429109 TCTTATACTAATGGGTGATACAACTCA 57.571 33.333 0.00 0.00 34.32 3.41
145 146 8.641541 GGGCTGAAATGAAAATCCATATTCTTA 58.358 33.333 0.00 0.00 0.00 2.10
146 147 7.126115 TGGGCTGAAATGAAAATCCATATTCTT 59.874 33.333 0.00 0.00 0.00 2.52
147 148 6.612456 TGGGCTGAAATGAAAATCCATATTCT 59.388 34.615 0.00 0.00 0.00 2.40
148 149 6.819284 TGGGCTGAAATGAAAATCCATATTC 58.181 36.000 0.00 0.00 0.00 1.75
149 150 6.811634 TGGGCTGAAATGAAAATCCATATT 57.188 33.333 0.00 0.00 0.00 1.28
150 151 7.731688 AGTATGGGCTGAAATGAAAATCCATAT 59.268 33.333 0.00 0.00 38.01 1.78
151 152 7.068702 AGTATGGGCTGAAATGAAAATCCATA 58.931 34.615 0.00 0.00 35.62 2.74
152 153 5.901276 AGTATGGGCTGAAATGAAAATCCAT 59.099 36.000 0.00 0.00 37.50 3.41
153 154 5.271598 AGTATGGGCTGAAATGAAAATCCA 58.728 37.500 0.00 0.00 0.00 3.41
154 155 5.859205 AGTATGGGCTGAAATGAAAATCC 57.141 39.130 0.00 0.00 0.00 3.01
155 156 6.912591 CGTTAGTATGGGCTGAAATGAAAATC 59.087 38.462 0.00 0.00 0.00 2.17
156 157 6.601613 TCGTTAGTATGGGCTGAAATGAAAAT 59.398 34.615 0.00 0.00 0.00 1.82
157 158 5.941058 TCGTTAGTATGGGCTGAAATGAAAA 59.059 36.000 0.00 0.00 0.00 2.29
158 159 5.492895 TCGTTAGTATGGGCTGAAATGAAA 58.507 37.500 0.00 0.00 0.00 2.69
159 160 5.092554 TCGTTAGTATGGGCTGAAATGAA 57.907 39.130 0.00 0.00 0.00 2.57
160 161 4.746535 TCGTTAGTATGGGCTGAAATGA 57.253 40.909 0.00 0.00 0.00 2.57
161 162 5.751680 CAATCGTTAGTATGGGCTGAAATG 58.248 41.667 0.00 0.00 0.00 2.32
162 163 4.275936 GCAATCGTTAGTATGGGCTGAAAT 59.724 41.667 0.00 0.00 0.00 2.17
163 164 3.625764 GCAATCGTTAGTATGGGCTGAAA 59.374 43.478 0.00 0.00 0.00 2.69
164 165 3.202906 GCAATCGTTAGTATGGGCTGAA 58.797 45.455 0.00 0.00 0.00 3.02
165 166 2.484770 GGCAATCGTTAGTATGGGCTGA 60.485 50.000 0.00 0.00 0.00 4.26
166 167 1.873591 GGCAATCGTTAGTATGGGCTG 59.126 52.381 0.00 0.00 0.00 4.85
167 168 1.488812 TGGCAATCGTTAGTATGGGCT 59.511 47.619 0.00 0.00 0.00 5.19
168 169 1.961793 TGGCAATCGTTAGTATGGGC 58.038 50.000 0.00 0.00 0.00 5.36
169 170 5.514274 AATTTGGCAATCGTTAGTATGGG 57.486 39.130 0.00 0.00 0.00 4.00
170 171 8.918961 TTTAAATTTGGCAATCGTTAGTATGG 57.081 30.769 0.00 0.00 0.00 2.74
174 175 9.915629 TGTTATTTAAATTTGGCAATCGTTAGT 57.084 25.926 5.91 0.00 0.00 2.24
177 178 9.871299 GTTTGTTATTTAAATTTGGCAATCGTT 57.129 25.926 5.91 0.00 0.00 3.85
178 179 9.046296 TGTTTGTTATTTAAATTTGGCAATCGT 57.954 25.926 5.91 0.00 0.00 3.73
179 180 9.312146 GTGTTTGTTATTTAAATTTGGCAATCG 57.688 29.630 5.91 0.00 0.00 3.34
182 183 9.994432 CTTGTGTTTGTTATTTAAATTTGGCAA 57.006 25.926 5.91 0.00 0.00 4.52
183 184 9.167311 ACTTGTGTTTGTTATTTAAATTTGGCA 57.833 25.926 5.91 0.00 0.00 4.92
195 196 9.998106 ACTGAGTATTCTACTTGTGTTTGTTAT 57.002 29.630 0.00 0.00 39.59 1.89
196 197 9.256477 CACTGAGTATTCTACTTGTGTTTGTTA 57.744 33.333 0.00 0.00 39.59 2.41
197 198 7.769044 ACACTGAGTATTCTACTTGTGTTTGTT 59.231 33.333 15.12 1.61 45.41 2.83
198 199 7.272978 ACACTGAGTATTCTACTTGTGTTTGT 58.727 34.615 15.12 0.00 45.41 2.83
199 200 7.715265 ACACTGAGTATTCTACTTGTGTTTG 57.285 36.000 15.12 2.12 45.41 2.93
200 201 9.477484 CTTACACTGAGTATTCTACTTGTGTTT 57.523 33.333 20.92 9.13 45.41 2.83
201 202 7.599245 GCTTACACTGAGTATTCTACTTGTGTT 59.401 37.037 20.92 12.10 45.41 3.32
203 204 7.090808 TGCTTACACTGAGTATTCTACTTGTG 58.909 38.462 14.28 14.28 43.08 3.33
204 205 7.228314 TGCTTACACTGAGTATTCTACTTGT 57.772 36.000 0.00 0.00 39.59 3.16
205 206 8.436200 GTTTGCTTACACTGAGTATTCTACTTG 58.564 37.037 0.00 0.00 39.59 3.16
206 207 8.368668 AGTTTGCTTACACTGAGTATTCTACTT 58.631 33.333 0.00 0.00 39.59 2.24
207 208 7.815068 CAGTTTGCTTACACTGAGTATTCTACT 59.185 37.037 0.00 0.00 42.74 2.57
208 209 7.813148 TCAGTTTGCTTACACTGAGTATTCTAC 59.187 37.037 0.00 0.00 43.63 2.59
209 210 7.892609 TCAGTTTGCTTACACTGAGTATTCTA 58.107 34.615 0.00 0.00 43.63 2.10
210 211 6.759272 TCAGTTTGCTTACACTGAGTATTCT 58.241 36.000 0.00 0.00 43.63 2.40
217 218 4.380531 CCTTCTCAGTTTGCTTACACTGA 58.619 43.478 2.23 2.23 45.77 3.41
218 219 3.058639 GCCTTCTCAGTTTGCTTACACTG 60.059 47.826 0.00 0.00 41.65 3.66
219 220 3.142174 GCCTTCTCAGTTTGCTTACACT 58.858 45.455 0.00 0.00 0.00 3.55
220 221 2.096218 CGCCTTCTCAGTTTGCTTACAC 60.096 50.000 0.00 0.00 0.00 2.90
221 222 2.143122 CGCCTTCTCAGTTTGCTTACA 58.857 47.619 0.00 0.00 0.00 2.41
222 223 2.096218 CACGCCTTCTCAGTTTGCTTAC 60.096 50.000 0.00 0.00 0.00 2.34
223 224 2.143122 CACGCCTTCTCAGTTTGCTTA 58.857 47.619 0.00 0.00 0.00 3.09
224 225 0.947244 CACGCCTTCTCAGTTTGCTT 59.053 50.000 0.00 0.00 0.00 3.91
225 226 0.106708 TCACGCCTTCTCAGTTTGCT 59.893 50.000 0.00 0.00 0.00 3.91
226 227 0.944386 TTCACGCCTTCTCAGTTTGC 59.056 50.000 0.00 0.00 0.00 3.68
227 228 1.069636 GCTTCACGCCTTCTCAGTTTG 60.070 52.381 0.00 0.00 0.00 2.93
228 229 1.230324 GCTTCACGCCTTCTCAGTTT 58.770 50.000 0.00 0.00 0.00 2.66
229 230 0.106708 TGCTTCACGCCTTCTCAGTT 59.893 50.000 0.00 0.00 38.05 3.16
230 231 0.601311 GTGCTTCACGCCTTCTCAGT 60.601 55.000 0.00 0.00 38.05 3.41
231 232 0.320247 AGTGCTTCACGCCTTCTCAG 60.320 55.000 0.00 0.00 39.64 3.35
232 233 0.966179 TAGTGCTTCACGCCTTCTCA 59.034 50.000 0.00 0.00 39.64 3.27
233 234 2.301577 ATAGTGCTTCACGCCTTCTC 57.698 50.000 0.00 0.00 39.64 2.87
234 235 2.479730 CGTATAGTGCTTCACGCCTTCT 60.480 50.000 0.00 0.00 39.64 2.85
235 236 1.852895 CGTATAGTGCTTCACGCCTTC 59.147 52.381 0.00 0.00 39.64 3.46
236 237 1.203994 ACGTATAGTGCTTCACGCCTT 59.796 47.619 0.00 0.00 39.64 4.35
237 238 0.815734 ACGTATAGTGCTTCACGCCT 59.184 50.000 0.00 0.00 39.64 5.52
238 239 1.197910 GACGTATAGTGCTTCACGCC 58.802 55.000 0.00 0.00 39.64 5.68
239 240 1.582502 GTGACGTATAGTGCTTCACGC 59.417 52.381 0.00 0.00 39.64 5.34
240 241 2.846550 CTGTGACGTATAGTGCTTCACG 59.153 50.000 0.00 0.00 39.64 4.35
241 242 3.834610 ACTGTGACGTATAGTGCTTCAC 58.165 45.455 0.00 0.00 36.20 3.18
242 243 4.698780 ACTACTGTGACGTATAGTGCTTCA 59.301 41.667 8.57 0.00 32.53 3.02
243 244 5.232610 ACTACTGTGACGTATAGTGCTTC 57.767 43.478 8.57 0.00 32.53 3.86
244 245 5.879223 AGTACTACTGTGACGTATAGTGCTT 59.121 40.000 0.00 0.00 37.32 3.91
245 246 5.426504 AGTACTACTGTGACGTATAGTGCT 58.573 41.667 0.00 8.06 36.25 4.40
246 247 5.731599 AGTACTACTGTGACGTATAGTGC 57.268 43.478 0.00 6.34 32.53 4.40
247 248 8.189709 TGTAAGTACTACTGTGACGTATAGTG 57.810 38.462 0.00 3.12 32.53 2.74
248 249 8.777865 TTGTAAGTACTACTGTGACGTATAGT 57.222 34.615 0.00 0.00 34.81 2.12
251 252 9.388506 ACTATTGTAAGTACTACTGTGACGTAT 57.611 33.333 0.00 0.00 0.00 3.06
252 253 8.777865 ACTATTGTAAGTACTACTGTGACGTA 57.222 34.615 0.00 0.00 0.00 3.57
253 254 7.678947 ACTATTGTAAGTACTACTGTGACGT 57.321 36.000 0.00 0.00 0.00 4.34
254 255 8.961294 AAACTATTGTAAGTACTACTGTGACG 57.039 34.615 0.00 0.00 0.00 4.35
255 256 9.903682 TGAAACTATTGTAAGTACTACTGTGAC 57.096 33.333 0.00 0.00 0.00 3.67
263 264 9.804758 GCAGTATCTGAAACTATTGTAAGTACT 57.195 33.333 0.66 0.00 32.44 2.73
264 265 9.582431 TGCAGTATCTGAAACTATTGTAAGTAC 57.418 33.333 0.66 0.00 32.44 2.73
266 267 9.319143 GATGCAGTATCTGAAACTATTGTAAGT 57.681 33.333 0.00 0.00 32.44 2.24
267 268 9.539825 AGATGCAGTATCTGAAACTATTGTAAG 57.460 33.333 0.00 0.00 44.46 2.34
282 283 1.339610 ACCTCGCTCAGATGCAGTATC 59.660 52.381 0.00 0.00 35.97 2.24
283 284 1.407936 ACCTCGCTCAGATGCAGTAT 58.592 50.000 0.00 0.00 0.00 2.12
284 285 2.052782 TACCTCGCTCAGATGCAGTA 57.947 50.000 0.00 0.00 0.00 2.74
285 286 1.135915 CTTACCTCGCTCAGATGCAGT 59.864 52.381 0.00 0.00 0.00 4.40
286 287 1.850377 CTTACCTCGCTCAGATGCAG 58.150 55.000 0.00 0.00 0.00 4.41
287 288 0.179100 GCTTACCTCGCTCAGATGCA 60.179 55.000 0.00 0.00 0.00 3.96
288 289 0.179100 TGCTTACCTCGCTCAGATGC 60.179 55.000 0.00 0.00 0.00 3.91
289 290 1.537776 CCTGCTTACCTCGCTCAGATG 60.538 57.143 0.00 0.00 0.00 2.90
290 291 0.749649 CCTGCTTACCTCGCTCAGAT 59.250 55.000 0.00 0.00 0.00 2.90
291 292 0.612174 ACCTGCTTACCTCGCTCAGA 60.612 55.000 0.00 0.00 0.00 3.27
292 293 0.247736 AACCTGCTTACCTCGCTCAG 59.752 55.000 0.00 0.00 0.00 3.35
293 294 0.685097 AAACCTGCTTACCTCGCTCA 59.315 50.000 0.00 0.00 0.00 4.26
294 295 1.066787 AGAAACCTGCTTACCTCGCTC 60.067 52.381 0.00 0.00 0.00 5.03
295 296 0.977395 AGAAACCTGCTTACCTCGCT 59.023 50.000 0.00 0.00 0.00 4.93
296 297 1.360820 GAGAAACCTGCTTACCTCGC 58.639 55.000 0.00 0.00 0.00 5.03
297 298 1.405661 GGGAGAAACCTGCTTACCTCG 60.406 57.143 0.00 0.00 38.98 4.63
298 299 1.065345 GGGGAGAAACCTGCTTACCTC 60.065 57.143 0.00 0.00 38.98 3.85
299 300 0.992695 GGGGAGAAACCTGCTTACCT 59.007 55.000 0.00 0.00 38.98 3.08
300 301 0.696501 TGGGGAGAAACCTGCTTACC 59.303 55.000 0.00 0.00 38.98 2.85
301 302 2.808906 ATGGGGAGAAACCTGCTTAC 57.191 50.000 0.00 0.00 38.98 2.34
302 303 5.849475 TCATATATGGGGAGAAACCTGCTTA 59.151 40.000 12.78 0.00 38.98 3.09
303 304 4.665009 TCATATATGGGGAGAAACCTGCTT 59.335 41.667 12.78 0.00 38.98 3.91
304 305 4.242811 TCATATATGGGGAGAAACCTGCT 58.757 43.478 12.78 0.00 38.98 4.24
305 306 4.640771 TCATATATGGGGAGAAACCTGC 57.359 45.455 12.78 0.00 38.98 4.85
306 307 5.877012 CGATTCATATATGGGGAGAAACCTG 59.123 44.000 12.78 0.00 38.98 4.00
307 308 5.045578 CCGATTCATATATGGGGAGAAACCT 60.046 44.000 12.78 0.00 38.98 3.50
308 309 5.186198 CCGATTCATATATGGGGAGAAACC 58.814 45.833 12.78 0.00 38.08 3.27
309 310 5.186198 CCCGATTCATATATGGGGAGAAAC 58.814 45.833 16.06 1.49 44.05 2.78
310 311 4.324254 GCCCGATTCATATATGGGGAGAAA 60.324 45.833 22.32 6.80 44.05 2.52
311 312 3.199946 GCCCGATTCATATATGGGGAGAA 59.800 47.826 22.32 7.41 44.05 2.87
312 313 2.771943 GCCCGATTCATATATGGGGAGA 59.228 50.000 22.32 0.00 44.05 3.71
313 314 2.158755 GGCCCGATTCATATATGGGGAG 60.159 54.545 22.32 9.48 44.05 4.30
314 315 1.843851 GGCCCGATTCATATATGGGGA 59.156 52.381 22.32 7.59 44.05 4.81
315 316 1.563879 TGGCCCGATTCATATATGGGG 59.436 52.381 16.54 16.54 44.12 4.96
316 317 3.364460 TTGGCCCGATTCATATATGGG 57.636 47.619 12.78 6.78 43.02 4.00
317 318 4.516698 GCTATTGGCCCGATTCATATATGG 59.483 45.833 12.78 0.00 34.27 2.74
318 319 5.371526 AGCTATTGGCCCGATTCATATATG 58.628 41.667 6.36 6.36 43.05 1.78
319 320 5.455326 GGAGCTATTGGCCCGATTCATATAT 60.455 44.000 0.00 0.00 43.05 0.86
320 321 4.141711 GGAGCTATTGGCCCGATTCATATA 60.142 45.833 0.00 0.00 43.05 0.86
321 322 3.370953 GGAGCTATTGGCCCGATTCATAT 60.371 47.826 0.00 0.00 43.05 1.78
322 323 2.027192 GGAGCTATTGGCCCGATTCATA 60.027 50.000 0.00 0.00 43.05 2.15
323 324 1.271597 GGAGCTATTGGCCCGATTCAT 60.272 52.381 0.00 0.00 43.05 2.57
324 325 0.108585 GGAGCTATTGGCCCGATTCA 59.891 55.000 0.00 0.00 43.05 2.57
325 326 0.398318 AGGAGCTATTGGCCCGATTC 59.602 55.000 0.00 0.00 43.05 2.52
326 327 0.109342 CAGGAGCTATTGGCCCGATT 59.891 55.000 0.00 0.00 43.05 3.34
327 328 1.056700 ACAGGAGCTATTGGCCCGAT 61.057 55.000 0.00 0.00 43.05 4.18
328 329 1.689233 ACAGGAGCTATTGGCCCGA 60.689 57.895 0.00 0.00 43.05 5.14
378 379 2.030363 GCCATTCATTCCAACAACGTCA 60.030 45.455 0.00 0.00 0.00 4.35
1179 1204 3.576356 CGGCGGCGCATGAATCTT 61.576 61.111 34.36 0.00 0.00 2.40
1249 1300 8.017418 TCCAATTTCAACCTTTCAACATAGTT 57.983 30.769 0.00 0.00 0.00 2.24
1411 1466 6.093909 TGCTTCAAATCGATCAGATGCTTTAA 59.906 34.615 24.84 11.95 40.02 1.52
1524 1579 8.038944 AGTTGACACACTAACTGAAACTCTAAA 58.961 33.333 0.00 0.00 35.91 1.85
1650 1735 5.827797 ACAAAAACAGAGGAAACAGAGCATA 59.172 36.000 0.00 0.00 0.00 3.14
1686 1771 7.444487 AGAAACTAAATTTGGGTGTGTACTCTC 59.556 37.037 6.50 0.00 0.00 3.20
1717 1803 0.032540 GGCAGCCCAGTCTTGTTTTG 59.967 55.000 0.00 0.00 0.00 2.44
1725 1812 0.394565 ATCTATTCGGCAGCCCAGTC 59.605 55.000 5.63 0.00 0.00 3.51
2099 2240 2.727123 TCACCACACACACCATCTTT 57.273 45.000 0.00 0.00 0.00 2.52
2183 2324 7.387673 CGTCTATTATTTGTGGATTGCTATGGA 59.612 37.037 0.00 0.00 0.00 3.41
2409 2553 0.666374 GAAGAACCCGTGTTTGGTGG 59.334 55.000 0.00 0.00 35.88 4.61
2418 2563 0.034476 GAAGAACCCGAAGAACCCGT 59.966 55.000 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.