Multiple sequence alignment - TraesCS2D01G537300

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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 TraesCS2D01G537300 chr2D 100.000 2246 0 0 1 2246 619313594 619311349 0.000000e+00 4148.0
1 TraesCS2D01G537300 chr2D 79.103 847 95 44 804 1615 610757589 610756790 1.990000e-140 508.0
2 TraesCS2D01G537300 chr2A 88.870 1204 87 26 457 1632 750425673 750424489 0.000000e+00 1437.0
3 TraesCS2D01G537300 chr2A 88.028 426 35 7 1830 2246 750331354 750330936 7.210000e-135 490.0
4 TraesCS2D01G537300 chr2A 77.423 939 117 51 715 1588 750365730 750364822 2.610000e-129 472.0
5 TraesCS2D01G537300 chr2A 81.058 586 67 20 772 1335 750334582 750334019 5.730000e-116 427.0
6 TraesCS2D01G537300 chr2A 87.336 229 19 7 1344 1570 750332736 750332516 1.030000e-63 254.0
7 TraesCS2D01G537300 chr2A 83.523 176 23 3 1407 1576 750189339 750189514 2.310000e-35 159.0
8 TraesCS2D01G537300 chr2A 80.408 245 19 11 1534 1754 750332326 750332087 2.310000e-35 159.0
9 TraesCS2D01G537300 chr2A 88.350 103 12 0 13 115 519049568 519049466 8.420000e-25 124.0
10 TraesCS2D01G537300 chr2A 94.872 78 4 0 1756 1833 750190117 750190194 3.030000e-24 122.0
11 TraesCS2D01G537300 chr2A 97.143 35 1 0 457 491 686813860 686813826 2.410000e-05 60.2
12 TraesCS2D01G537300 chr2A 100.000 32 0 0 219 250 750366196 750366165 2.410000e-05 60.2
13 TraesCS2D01G537300 chr2B 89.192 879 55 19 713 1570 757567345 757566486 0.000000e+00 1061.0
14 TraesCS2D01G537300 chr2B 81.435 878 113 35 772 1615 757453372 757452511 0.000000e+00 673.0
15 TraesCS2D01G537300 chr2B 92.566 417 31 0 1830 2246 757231772 757231356 1.150000e-167 599.0
16 TraesCS2D01G537300 chr2B 78.442 937 131 48 710 1616 757394805 757393910 1.520000e-151 545.0
17 TraesCS2D01G537300 chr2B 77.825 938 106 61 646 1544 757241938 757241064 9.320000e-134 486.0
18 TraesCS2D01G537300 chr2B 78.230 836 104 41 767 1555 757433883 757433079 4.370000e-127 464.0
19 TraesCS2D01G537300 chr2B 87.402 381 40 4 1830 2210 757078693 757078321 4.430000e-117 431.0
20 TraesCS2D01G537300 chr2B 87.402 381 41 4 1830 2210 757396353 757395980 4.430000e-117 431.0
21 TraesCS2D01G537300 chr2B 83.191 351 41 11 1043 1390 757294079 757293744 2.800000e-79 305.0
22 TraesCS2D01G537300 chr2B 77.202 579 79 26 750 1307 757016159 757015613 2.820000e-74 289.0
23 TraesCS2D01G537300 chr2B 82.303 356 33 19 851 1191 757561914 757561574 4.720000e-72 281.0
24 TraesCS2D01G537300 chr2B 83.178 214 28 5 1405 1615 757015567 757015359 2.940000e-44 189.0
25 TraesCS2D01G537300 chr2B 82.447 188 20 9 1339 1524 757561575 757561399 3.860000e-33 152.0
26 TraesCS2D01G537300 chr2B 89.623 106 11 0 1643 1748 757391572 757391467 3.890000e-28 135.0
27 TraesCS2D01G537300 chr2B 83.810 105 15 2 1645 1748 757452378 757452275 5.100000e-17 99.0
28 TraesCS2D01G537300 chr2B 92.727 55 4 0 495 549 757563576 757563522 1.850000e-11 80.5
29 TraesCS2D01G537300 chr2B 97.222 36 1 0 457 492 793458315 793458350 6.700000e-06 62.1
30 TraesCS2D01G537300 chr1D 90.625 416 32 3 1830 2245 77451818 77452226 1.520000e-151 545.0
31 TraesCS2D01G537300 chr1D 83.429 175 22 6 1443 1614 77450641 77450811 2.990000e-34 156.0
32 TraesCS2D01G537300 chr1A 90.215 419 34 3 1827 2245 108779610 108780021 7.060000e-150 540.0
33 TraesCS2D01G537300 chr7A 90.144 416 34 3 1830 2245 477183869 477184277 3.280000e-148 534.0
34 TraesCS2D01G537300 chr7A 91.753 97 8 0 294 390 207295682 207295778 3.890000e-28 135.0
35 TraesCS2D01G537300 chr1B 88.942 416 39 3 1830 2245 121013427 121013835 7.160000e-140 507.0
36 TraesCS2D01G537300 chr1B 86.982 169 20 2 1394 1560 121012013 121012181 2.940000e-44 189.0
37 TraesCS2D01G537300 chr1B 87.850 107 8 2 1646 1751 121012496 121012598 1.090000e-23 121.0
38 TraesCS2D01G537300 chr1B 83.478 115 19 0 1 115 161578753 161578867 8.480000e-20 108.0
39 TraesCS2D01G537300 chr7D 76.379 1088 135 60 520 1548 498285706 498284682 7.260000e-130 473.0
40 TraesCS2D01G537300 chr7D 86.288 299 34 4 1831 2129 498279945 498279654 3.600000e-83 318.0
41 TraesCS2D01G537300 chr7D 77.449 541 74 29 735 1252 498252524 498252009 1.700000e-71 279.0
42 TraesCS2D01G537300 chr7D 94.872 78 4 0 1756 1833 498243959 498243882 3.030000e-24 122.0
43 TraesCS2D01G537300 chrUn 76.709 395 44 22 750 1127 291048366 291048003 2.290000e-40 176.0
44 TraesCS2D01G537300 chrUn 88.393 112 13 0 4 115 76751987 76751876 3.890000e-28 135.0
45 TraesCS2D01G537300 chrUn 85.714 112 16 0 4 115 321293832 321293721 3.920000e-23 119.0
46 TraesCS2D01G537300 chrUn 85.714 112 16 0 4 115 321300448 321300337 3.920000e-23 119.0
47 TraesCS2D01G537300 chr7B 91.379 116 9 1 1 115 71815026 71815141 8.300000e-35 158.0
48 TraesCS2D01G537300 chr4A 85.714 112 16 0 4 115 708411415 708411304 3.920000e-23 119.0
49 TraesCS2D01G537300 chr3B 85.217 115 17 0 1 115 811078260 811078374 3.920000e-23 119.0
50 TraesCS2D01G537300 chr3B 88.421 95 11 0 296 390 169359864 169359770 5.070000e-22 115.0
51 TraesCS2D01G537300 chr6A 84.615 117 17 1 1 116 588611165 588611281 5.070000e-22 115.0
52 TraesCS2D01G537300 chr5B 87.629 97 12 0 294 390 314298454 314298550 1.820000e-21 113.0
53 TraesCS2D01G537300 chr4B 97.368 38 1 0 456 493 476183803 476183766 5.180000e-07 65.8


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 TraesCS2D01G537300 chr2D 619311349 619313594 2245 True 4148.000000 4148 100.000000 1 2246 1 chr2D.!!$R2 2245
1 TraesCS2D01G537300 chr2D 610756790 610757589 799 True 508.000000 508 79.103000 804 1615 1 chr2D.!!$R1 811
2 TraesCS2D01G537300 chr2A 750424489 750425673 1184 True 1437.000000 1437 88.870000 457 1632 1 chr2A.!!$R3 1175
3 TraesCS2D01G537300 chr2A 750330936 750334582 3646 True 332.500000 490 84.207500 772 2246 4 chr2A.!!$R4 1474
4 TraesCS2D01G537300 chr2A 750364822 750366196 1374 True 266.100000 472 88.711500 219 1588 2 chr2A.!!$R5 1369
5 TraesCS2D01G537300 chr2B 757241064 757241938 874 True 486.000000 486 77.825000 646 1544 1 chr2B.!!$R3 898
6 TraesCS2D01G537300 chr2B 757433079 757433883 804 True 464.000000 464 78.230000 767 1555 1 chr2B.!!$R5 788
7 TraesCS2D01G537300 chr2B 757561399 757567345 5946 True 393.625000 1061 86.667250 495 1570 4 chr2B.!!$R9 1075
8 TraesCS2D01G537300 chr2B 757452275 757453372 1097 True 386.000000 673 82.622500 772 1748 2 chr2B.!!$R8 976
9 TraesCS2D01G537300 chr2B 757391467 757396353 4886 True 370.333333 545 85.155667 710 2210 3 chr2B.!!$R7 1500
10 TraesCS2D01G537300 chr2B 757015359 757016159 800 True 239.000000 289 80.190000 750 1615 2 chr2B.!!$R6 865
11 TraesCS2D01G537300 chr1D 77450641 77452226 1585 False 350.500000 545 87.027000 1443 2245 2 chr1D.!!$F1 802
12 TraesCS2D01G537300 chr1B 121012013 121013835 1822 False 272.333333 507 87.924667 1394 2245 3 chr1B.!!$F2 851
13 TraesCS2D01G537300 chr7D 498284682 498285706 1024 True 473.000000 473 76.379000 520 1548 1 chr7D.!!$R4 1028
14 TraesCS2D01G537300 chr7D 498252009 498252524 515 True 279.000000 279 77.449000 735 1252 1 chr7D.!!$R2 517

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
286 287 0.030235 GAACGTTTTGGTGACCAGGC 59.97 55.0 3.77 0.0 33.81 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2197 12015 0.038166 TGGGACTGCTTTGGTGGATC 59.962 55.0 0.0 0.0 0.0 3.36 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
28 29 3.712016 TTTCATGAAATGGGAGTCGGA 57.288 42.857 16.91 0.00 46.73 4.55
29 30 3.931907 TTCATGAAATGGGAGTCGGAT 57.068 42.857 5.45 0.00 46.73 4.18
30 31 3.198409 TCATGAAATGGGAGTCGGATG 57.802 47.619 0.00 0.00 46.73 3.51
31 32 2.505407 TCATGAAATGGGAGTCGGATGT 59.495 45.455 0.00 0.00 46.73 3.06
32 33 3.709141 TCATGAAATGGGAGTCGGATGTA 59.291 43.478 0.00 0.00 46.73 2.29
33 34 3.536956 TGAAATGGGAGTCGGATGTAC 57.463 47.619 0.00 0.00 0.00 2.90
34 35 2.169769 TGAAATGGGAGTCGGATGTACC 59.830 50.000 0.00 0.00 0.00 3.34
35 36 1.874129 AATGGGAGTCGGATGTACCA 58.126 50.000 0.00 0.00 38.90 3.25
36 37 1.414158 ATGGGAGTCGGATGTACCAG 58.586 55.000 1.29 0.00 38.90 4.00
38 39 1.442148 GGAGTCGGATGTACCAGCC 59.558 63.158 0.00 0.00 36.46 4.85
39 40 1.442148 GAGTCGGATGTACCAGCCC 59.558 63.158 0.00 0.00 36.45 5.19
40 41 2.106332 GTCGGATGTACCAGCCCG 59.894 66.667 0.00 0.00 36.45 6.13
41 42 3.151710 TCGGATGTACCAGCCCGG 61.152 66.667 0.00 0.00 42.03 5.73
42 43 4.235762 CGGATGTACCAGCCCGGG 62.236 72.222 19.09 19.09 36.45 5.73
43 44 4.564110 GGATGTACCAGCCCGGGC 62.564 72.222 39.29 39.29 40.22 6.13
57 58 4.699522 GGGCGGGCGTTTCTGTCT 62.700 66.667 0.00 0.00 0.00 3.41
58 59 2.668550 GGCGGGCGTTTCTGTCTT 60.669 61.111 0.00 0.00 0.00 3.01
59 60 2.556287 GCGGGCGTTTCTGTCTTG 59.444 61.111 0.00 0.00 0.00 3.02
60 61 2.966309 GCGGGCGTTTCTGTCTTGG 61.966 63.158 0.00 0.00 0.00 3.61
61 62 2.325082 CGGGCGTTTCTGTCTTGGG 61.325 63.158 0.00 0.00 0.00 4.12
62 63 2.626780 GGGCGTTTCTGTCTTGGGC 61.627 63.158 0.00 0.00 0.00 5.36
63 64 2.556287 GCGTTTCTGTCTTGGGCG 59.444 61.111 0.00 0.00 0.00 6.13
64 65 1.959226 GCGTTTCTGTCTTGGGCGA 60.959 57.895 0.00 0.00 0.00 5.54
65 66 1.298859 GCGTTTCTGTCTTGGGCGAT 61.299 55.000 0.00 0.00 0.00 4.58
66 67 2.004583 CGTTTCTGTCTTGGGCGATA 57.995 50.000 0.00 0.00 0.00 2.92
67 68 2.550978 CGTTTCTGTCTTGGGCGATAT 58.449 47.619 0.00 0.00 0.00 1.63
69 70 1.953559 TTCTGTCTTGGGCGATATGC 58.046 50.000 0.00 0.00 45.38 3.14
80 81 2.447244 GCGATATGCCTAAGCTCAGT 57.553 50.000 0.00 0.00 40.80 3.41
82 83 3.914312 GCGATATGCCTAAGCTCAGTTA 58.086 45.455 0.00 0.00 40.80 2.24
83 84 4.307432 GCGATATGCCTAAGCTCAGTTAA 58.693 43.478 0.00 0.00 40.80 2.01
85 86 5.533482 CGATATGCCTAAGCTCAGTTAAGT 58.467 41.667 0.00 0.00 40.80 2.24
88 89 7.815068 CGATATGCCTAAGCTCAGTTAAGTAAT 59.185 37.037 0.00 0.00 40.80 1.89
92 93 8.718102 TGCCTAAGCTCAGTTAAGTAATAAAG 57.282 34.615 0.00 0.00 40.80 1.85
93 94 7.280205 TGCCTAAGCTCAGTTAAGTAATAAAGC 59.720 37.037 0.00 0.00 40.80 3.51
94 95 7.496263 GCCTAAGCTCAGTTAAGTAATAAAGCT 59.504 37.037 0.00 0.00 40.37 3.74
95 96 9.384764 CCTAAGCTCAGTTAAGTAATAAAGCTT 57.615 33.333 10.65 10.65 46.98 3.74
127 128 3.515611 AAAAAGTCGCGGTTGCCA 58.484 50.000 6.13 0.00 38.08 4.92
129 130 1.381165 AAAAAGTCGCGGTTGCCAGT 61.381 50.000 6.13 0.00 38.08 4.00
131 132 4.681978 AGTCGCGGTTGCCAGTCC 62.682 66.667 6.13 0.00 38.08 3.85
132 133 4.980805 GTCGCGGTTGCCAGTCCA 62.981 66.667 6.13 0.00 38.08 4.02
133 134 4.015406 TCGCGGTTGCCAGTCCAT 62.015 61.111 6.13 0.00 38.08 3.41
134 135 3.803082 CGCGGTTGCCAGTCCATG 61.803 66.667 0.00 0.00 38.08 3.66
135 136 4.120331 GCGGTTGCCAGTCCATGC 62.120 66.667 0.00 0.00 33.98 4.06
136 137 3.443045 CGGTTGCCAGTCCATGCC 61.443 66.667 0.00 0.00 0.00 4.40
137 138 3.070576 GGTTGCCAGTCCATGCCC 61.071 66.667 0.00 0.00 0.00 5.36
138 139 2.283101 GTTGCCAGTCCATGCCCA 60.283 61.111 0.00 0.00 0.00 5.36
139 140 1.683365 GTTGCCAGTCCATGCCCAT 60.683 57.895 0.00 0.00 0.00 4.00
140 141 0.395586 GTTGCCAGTCCATGCCCATA 60.396 55.000 0.00 0.00 0.00 2.74
141 142 0.395586 TTGCCAGTCCATGCCCATAC 60.396 55.000 0.00 0.00 0.00 2.39
142 143 1.529244 GCCAGTCCATGCCCATACC 60.529 63.158 0.00 0.00 0.00 2.73
143 144 1.922057 CCAGTCCATGCCCATACCA 59.078 57.895 0.00 0.00 0.00 3.25
144 145 0.258484 CCAGTCCATGCCCATACCAA 59.742 55.000 0.00 0.00 0.00 3.67
146 147 0.107214 AGTCCATGCCCATACCAACG 60.107 55.000 0.00 0.00 0.00 4.10
147 148 0.107410 GTCCATGCCCATACCAACGA 60.107 55.000 0.00 0.00 0.00 3.85
148 149 0.107410 TCCATGCCCATACCAACGAC 60.107 55.000 0.00 0.00 0.00 4.34
149 150 1.101049 CCATGCCCATACCAACGACC 61.101 60.000 0.00 0.00 0.00 4.79
150 151 1.153249 ATGCCCATACCAACGACCG 60.153 57.895 0.00 0.00 0.00 4.79
155 156 3.766691 ATACCAACGACCGGCGCT 61.767 61.111 16.48 3.50 46.04 5.92
156 157 3.305177 ATACCAACGACCGGCGCTT 62.305 57.895 16.48 8.60 46.04 4.68
157 158 3.919973 TACCAACGACCGGCGCTTC 62.920 63.158 16.48 0.00 46.04 3.86
162 163 4.124351 CGACCGGCGCTTCCACTA 62.124 66.667 7.64 0.00 34.01 2.74
163 164 2.202756 GACCGGCGCTTCCACTAG 60.203 66.667 7.64 0.00 34.01 2.57
164 165 4.452733 ACCGGCGCTTCCACTAGC 62.453 66.667 7.64 0.00 37.80 3.42
168 169 4.452733 GCGCTTCCACTAGCCGGT 62.453 66.667 1.90 0.00 37.90 5.28
169 170 2.264794 CGCTTCCACTAGCCGGTT 59.735 61.111 1.90 0.00 37.90 4.44
170 171 2.100631 CGCTTCCACTAGCCGGTTG 61.101 63.158 1.90 0.00 37.90 3.77
171 172 1.003718 GCTTCCACTAGCCGGTTGT 60.004 57.895 1.90 0.00 35.06 3.32
172 173 0.605589 GCTTCCACTAGCCGGTTGTT 60.606 55.000 1.90 0.00 35.06 2.83
174 175 1.804748 CTTCCACTAGCCGGTTGTTTC 59.195 52.381 1.90 0.00 0.00 2.78
175 176 0.035739 TCCACTAGCCGGTTGTTTCC 59.964 55.000 1.90 0.00 0.00 3.13
176 177 0.250553 CCACTAGCCGGTTGTTTCCA 60.251 55.000 1.90 0.00 0.00 3.53
177 178 0.872388 CACTAGCCGGTTGTTTCCAC 59.128 55.000 1.90 0.00 0.00 4.02
179 180 1.073284 ACTAGCCGGTTGTTTCCACAT 59.927 47.619 1.90 0.00 31.06 3.21
180 181 2.159382 CTAGCCGGTTGTTTCCACATT 58.841 47.619 1.90 0.00 31.06 2.71
181 182 1.408969 AGCCGGTTGTTTCCACATTT 58.591 45.000 1.90 0.00 31.06 2.32
182 183 1.760029 AGCCGGTTGTTTCCACATTTT 59.240 42.857 1.90 0.00 31.06 1.82
183 184 2.169561 AGCCGGTTGTTTCCACATTTTT 59.830 40.909 1.90 0.00 31.06 1.94
184 185 2.542178 GCCGGTTGTTTCCACATTTTTC 59.458 45.455 1.90 0.00 31.06 2.29
185 186 3.739830 GCCGGTTGTTTCCACATTTTTCT 60.740 43.478 1.90 0.00 31.06 2.52
186 187 4.048504 CCGGTTGTTTCCACATTTTTCTC 58.951 43.478 0.00 0.00 31.06 2.87
188 189 4.377021 GGTTGTTTCCACATTTTTCTCCC 58.623 43.478 0.00 0.00 31.06 4.30
190 191 4.935352 TGTTTCCACATTTTTCTCCCTG 57.065 40.909 0.00 0.00 0.00 4.45
191 192 4.285863 TGTTTCCACATTTTTCTCCCTGT 58.714 39.130 0.00 0.00 0.00 4.00
192 193 4.714308 TGTTTCCACATTTTTCTCCCTGTT 59.286 37.500 0.00 0.00 0.00 3.16
195 196 2.364970 CCACATTTTTCTCCCTGTTGCA 59.635 45.455 0.00 0.00 0.00 4.08
196 197 3.383761 CACATTTTTCTCCCTGTTGCAC 58.616 45.455 0.00 0.00 0.00 4.57
197 198 3.030291 ACATTTTTCTCCCTGTTGCACA 58.970 40.909 0.00 0.00 0.00 4.57
198 199 3.068590 ACATTTTTCTCCCTGTTGCACAG 59.931 43.478 8.73 8.73 45.53 3.66
199 200 2.435372 TTTTCTCCCTGTTGCACAGT 57.565 45.000 13.06 0.00 44.50 3.55
200 201 1.679139 TTTCTCCCTGTTGCACAGTG 58.321 50.000 13.06 0.00 44.50 3.66
201 202 0.546122 TTCTCCCTGTTGCACAGTGT 59.454 50.000 13.06 0.00 44.50 3.55
203 204 0.886490 CTCCCTGTTGCACAGTGTCC 60.886 60.000 13.06 0.00 44.50 4.02
204 205 1.152984 CCCTGTTGCACAGTGTCCA 60.153 57.895 13.06 0.00 44.50 4.02
207 208 1.775039 CTGTTGCACAGTGTCCACCG 61.775 60.000 1.61 0.00 41.19 4.94
209 210 3.399105 TTGCACAGTGTCCACCGCT 62.399 57.895 1.61 0.00 0.00 5.52
213 214 4.320456 CAGTGTCCACCGCTGCCT 62.320 66.667 0.00 0.00 44.18 4.75
214 215 2.603473 AGTGTCCACCGCTGCCTA 60.603 61.111 0.00 0.00 31.06 3.93
215 216 2.434359 GTGTCCACCGCTGCCTAC 60.434 66.667 0.00 0.00 0.00 3.18
216 217 2.603473 TGTCCACCGCTGCCTACT 60.603 61.111 0.00 0.00 0.00 2.57
217 218 1.304630 TGTCCACCGCTGCCTACTA 60.305 57.895 0.00 0.00 0.00 1.82
250 251 6.762702 AGTCTTGAGTCTAAACTACCTAGC 57.237 41.667 0.00 0.00 35.28 3.42
252 253 5.123661 GTCTTGAGTCTAAACTACCTAGCGT 59.876 44.000 0.00 0.00 35.28 5.07
254 255 3.944015 TGAGTCTAAACTACCTAGCGTCC 59.056 47.826 0.00 0.00 35.28 4.79
256 257 4.198530 AGTCTAAACTACCTAGCGTCCTC 58.801 47.826 0.00 0.00 32.59 3.71
257 258 3.314913 GTCTAAACTACCTAGCGTCCTCC 59.685 52.174 0.00 0.00 0.00 4.30
258 259 2.528673 AAACTACCTAGCGTCCTCCT 57.471 50.000 0.00 0.00 0.00 3.69
260 261 0.917533 ACTACCTAGCGTCCTCCTGA 59.082 55.000 0.00 0.00 0.00 3.86
262 263 1.883275 CTACCTAGCGTCCTCCTGATG 59.117 57.143 0.00 0.00 0.00 3.07
264 265 0.958091 CCTAGCGTCCTCCTGATGAG 59.042 60.000 0.00 0.00 41.07 2.90
265 266 1.686355 CTAGCGTCCTCCTGATGAGT 58.314 55.000 0.00 0.00 39.65 3.41
266 267 1.336440 CTAGCGTCCTCCTGATGAGTG 59.664 57.143 0.00 0.00 39.65 3.51
267 268 1.142748 GCGTCCTCCTGATGAGTGG 59.857 63.158 0.00 0.00 39.65 4.00
268 269 1.323271 GCGTCCTCCTGATGAGTGGA 61.323 60.000 0.00 0.00 39.65 4.02
271 272 1.134965 GTCCTCCTGATGAGTGGAACG 60.135 57.143 0.00 0.00 45.86 3.95
273 274 1.276421 CCTCCTGATGAGTGGAACGTT 59.724 52.381 0.00 0.00 45.86 3.99
276 277 3.138304 TCCTGATGAGTGGAACGTTTTG 58.862 45.455 0.46 0.00 45.86 2.44
278 279 2.878406 CTGATGAGTGGAACGTTTTGGT 59.122 45.455 0.46 0.00 45.86 3.67
280 281 2.404923 TGAGTGGAACGTTTTGGTGA 57.595 45.000 0.46 0.00 45.86 4.02
281 282 2.011222 TGAGTGGAACGTTTTGGTGAC 58.989 47.619 0.46 0.00 45.86 3.67
282 283 1.332686 GAGTGGAACGTTTTGGTGACC 59.667 52.381 0.46 0.00 45.86 4.02
283 284 1.096416 GTGGAACGTTTTGGTGACCA 58.904 50.000 0.00 0.00 0.00 4.02
284 285 1.064952 GTGGAACGTTTTGGTGACCAG 59.935 52.381 3.77 0.00 33.81 4.00
286 287 0.030235 GAACGTTTTGGTGACCAGGC 59.970 55.000 3.77 0.00 33.81 4.85
288 289 0.818040 ACGTTTTGGTGACCAGGCTC 60.818 55.000 3.77 0.00 33.81 4.70
290 291 0.467290 GTTTTGGTGACCAGGCTCCA 60.467 55.000 3.77 0.00 33.81 3.86
291 292 0.482446 TTTTGGTGACCAGGCTCCAT 59.518 50.000 3.77 0.00 33.81 3.41
292 293 1.367346 TTTGGTGACCAGGCTCCATA 58.633 50.000 3.77 0.00 33.81 2.74
294 295 0.982852 TGGTGACCAGGCTCCATAGG 60.983 60.000 0.00 0.00 0.00 2.57
295 296 1.700042 GGTGACCAGGCTCCATAGGG 61.700 65.000 0.00 0.00 0.00 3.53
296 297 1.384502 TGACCAGGCTCCATAGGGG 60.385 63.158 0.00 0.00 38.37 4.79
297 298 1.074471 GACCAGGCTCCATAGGGGA 60.074 63.158 0.00 0.00 45.89 4.81
299 300 2.511452 CCAGGCTCCATAGGGGACG 61.511 68.421 0.00 0.00 42.15 4.79
300 301 1.457643 CAGGCTCCATAGGGGACGA 60.458 63.158 0.00 0.00 42.15 4.20
301 302 1.152440 AGGCTCCATAGGGGACGAG 60.152 63.158 0.00 0.00 42.15 4.18
303 304 1.152525 GCTCCATAGGGGACGAGGA 60.153 63.158 0.00 0.00 42.15 3.71
309 310 3.777075 AGGGGACGAGGATCCTCT 58.223 61.111 33.70 22.77 45.53 3.69
312 313 2.503382 GGGACGAGGATCCTCTGCC 61.503 68.421 33.70 30.91 40.69 4.85
313 314 2.725008 GACGAGGATCCTCTGCCG 59.275 66.667 33.70 25.21 40.69 5.69
315 316 1.668101 GACGAGGATCCTCTGCCGTT 61.668 60.000 33.70 15.24 40.69 4.44
317 318 1.066587 GAGGATCCTCTGCCGTTCG 59.933 63.158 31.11 0.00 39.80 3.95
318 319 2.107141 GGATCCTCTGCCGTTCGG 59.893 66.667 3.84 6.90 0.00 4.30
336 337 2.280524 CAAGGTGCCGTTCGACCA 60.281 61.111 6.01 0.00 34.36 4.02
337 338 2.280592 AAGGTGCCGTTCGACCAC 60.281 61.111 6.01 6.63 34.36 4.16
338 339 2.803817 AAGGTGCCGTTCGACCACT 61.804 57.895 12.56 0.00 34.36 4.00
339 340 2.989055 AAGGTGCCGTTCGACCACTG 62.989 60.000 12.56 0.00 34.36 3.66
340 341 2.028484 GTGCCGTTCGACCACTGA 59.972 61.111 0.00 0.00 0.00 3.41
341 342 1.374252 GTGCCGTTCGACCACTGAT 60.374 57.895 0.00 0.00 0.00 2.90
342 343 0.108992 GTGCCGTTCGACCACTGATA 60.109 55.000 0.00 0.00 0.00 2.15
345 346 0.815734 CCGTTCGACCACTGATAGGT 59.184 55.000 0.00 0.00 43.46 3.08
352 353 3.739922 CACTGATAGGTGGGCCCA 58.260 61.111 24.45 24.45 34.66 5.36
353 354 2.234586 CACTGATAGGTGGGCCCAT 58.765 57.895 31.45 16.64 34.66 4.00
354 355 1.434188 CACTGATAGGTGGGCCCATA 58.566 55.000 31.45 18.61 34.66 2.74
355 356 1.349026 CACTGATAGGTGGGCCCATAG 59.651 57.143 31.45 20.27 34.66 2.23
357 358 0.570727 TGATAGGTGGGCCCATAGGA 59.429 55.000 31.45 14.64 34.66 2.94
359 360 2.062636 GATAGGTGGGCCCATAGGAAA 58.937 52.381 31.45 11.25 34.66 3.13
361 362 0.335019 AGGTGGGCCCATAGGAAAAC 59.665 55.000 31.45 12.49 34.66 2.43
363 364 1.474330 GTGGGCCCATAGGAAAACAG 58.526 55.000 31.45 0.00 33.47 3.16
364 365 0.334676 TGGGCCCATAGGAAAACAGG 59.665 55.000 24.45 0.00 33.47 4.00
369 370 1.474330 CCATAGGAAAACAGGCCCAC 58.526 55.000 0.00 0.00 0.00 4.61
371 372 2.624029 CCATAGGAAAACAGGCCCACAT 60.624 50.000 0.00 0.00 0.00 3.21
401 402 4.493547 CCACAACGGCATTCATATTTGTT 58.506 39.130 0.00 0.00 0.00 2.83
402 403 4.928615 CCACAACGGCATTCATATTTGTTT 59.071 37.500 0.00 0.00 0.00 2.83
427 428 5.890424 TTTTCCATATCCCTCGTTTCAAC 57.110 39.130 0.00 0.00 0.00 3.18
467 468 0.110486 ACAAACGGAGGCCTTCATGT 59.890 50.000 12.82 10.04 0.00 3.21
470 471 0.107654 AACGGAGGCCTTCATGTAGC 60.108 55.000 12.82 0.00 0.00 3.58
493 494 2.547642 CGGCCTCCAAAAGCAATTTTCA 60.548 45.455 0.00 0.00 0.00 2.69
494 495 2.807967 GGCCTCCAAAAGCAATTTTCAC 59.192 45.455 0.00 0.00 0.00 3.18
496 497 3.494924 GCCTCCAAAAGCAATTTTCACCT 60.495 43.478 0.00 0.00 0.00 4.00
497 498 4.309933 CCTCCAAAAGCAATTTTCACCTC 58.690 43.478 0.00 0.00 0.00 3.85
499 500 5.511888 CCTCCAAAAGCAATTTTCACCTCAT 60.512 40.000 0.00 0.00 0.00 2.90
611 691 7.985634 TGAGTTGCTTTCATCAAAAAGTTAC 57.014 32.000 0.00 0.00 38.30 2.50
627 707 4.866508 AGTTACACAGCTACTTGCAGTA 57.133 40.909 0.00 0.00 45.94 2.74
654 734 5.011738 AGTTTATATATGGACCCGACTGTGG 59.988 44.000 0.00 0.00 0.00 4.17
679 759 1.133606 ACCCATCTTTTCCACGTTGGT 60.134 47.619 0.00 0.00 39.03 3.67
681 761 1.953686 CCATCTTTTCCACGTTGGTGT 59.046 47.619 0.00 0.00 42.80 4.16
683 763 1.292061 TCTTTTCCACGTTGGTGTCG 58.708 50.000 0.00 0.00 42.80 4.35
687 767 2.981977 TTCCACGTTGGTGTCGGCTC 62.982 60.000 0.00 0.00 42.80 4.70
699 779 1.805539 TCGGCTCGAATGAACGCAG 60.806 57.895 0.00 0.00 31.06 5.18
700 780 2.401195 GGCTCGAATGAACGCAGC 59.599 61.111 0.00 0.00 36.51 5.25
701 781 2.401195 GCTCGAATGAACGCAGCC 59.599 61.111 0.00 0.00 33.75 4.85
702 782 2.390599 GCTCGAATGAACGCAGCCA 61.391 57.895 0.00 0.00 33.75 4.75
703 783 1.712081 CTCGAATGAACGCAGCCAG 59.288 57.895 0.00 0.00 0.00 4.85
705 785 2.486966 GAATGAACGCAGCCAGCC 59.513 61.111 0.00 0.00 41.38 4.85
706 786 3.056313 GAATGAACGCAGCCAGCCC 62.056 63.158 0.00 0.00 41.38 5.19
713 793 3.402681 GCAGCCAGCCCCTGAGTA 61.403 66.667 0.54 0.00 37.23 2.59
923 1849 3.244735 GCAGACCTTCTCCCTTTCTTCTT 60.245 47.826 0.00 0.00 0.00 2.52
1301 2321 9.168451 TGGATGTATAGATCTCTAGAAATCGTC 57.832 37.037 9.53 0.00 35.99 4.20
1321 2376 2.103094 TCAGGCATACAGTGGTAGATGC 59.897 50.000 11.14 11.14 35.64 3.91
1391 3731 5.908831 TGGGAAATGGACATATAGTGTAGGT 59.091 40.000 0.00 0.00 42.36 3.08
1392 3732 6.042781 TGGGAAATGGACATATAGTGTAGGTC 59.957 42.308 3.36 3.36 42.36 3.85
1451 3797 4.069304 CGTTTGTCCCTCCAAGTATTTGA 58.931 43.478 0.00 0.00 36.36 2.69
1456 3802 7.938140 TTGTCCCTCCAAGTATTTGATTAAG 57.062 36.000 0.00 0.00 36.36 1.85
1463 3814 9.025041 CCTCCAAGTATTTGATTAAGGAGTTTT 57.975 33.333 0.00 0.00 39.73 2.43
1524 3880 3.389329 ACCGATTCAAGATGATACTGGCT 59.611 43.478 0.00 0.00 0.00 4.75
1637 8298 7.806680 AACCCATAAGAATTTACCCAAACAT 57.193 32.000 0.00 0.00 0.00 2.71
1693 10659 3.382546 CCACCTGGGATGCTATTTTTCTG 59.617 47.826 0.00 0.00 40.01 3.02
1733 10700 3.998341 CAGGTGCCAATTCATTTTCCTTG 59.002 43.478 0.00 0.00 0.00 3.61
1751 10735 5.888901 TCCTTGTAGACTAGAGTCCTGAAA 58.111 41.667 6.05 0.00 45.85 2.69
1754 10738 7.455008 TCCTTGTAGACTAGAGTCCTGAAAATT 59.545 37.037 6.05 0.00 45.85 1.82
1757 11168 7.963532 TGTAGACTAGAGTCCTGAAAATTTGT 58.036 34.615 6.05 0.00 45.85 2.83
1759 11170 6.159988 AGACTAGAGTCCTGAAAATTTGTCG 58.840 40.000 6.05 0.00 45.85 4.35
1785 11196 5.398353 CCTCCTTGACATGAATACCAATCCT 60.398 44.000 0.00 0.00 0.00 3.24
1793 11204 5.359009 ACATGAATACCAATCCTGAAAGCAG 59.641 40.000 0.00 0.00 41.93 4.24
1817 11228 5.862924 TTTCAGTAAGACTGCAATACTGC 57.137 39.130 17.34 0.00 45.54 4.40
1837 11646 2.471818 CAGTTGATCTGCATCTCCTCG 58.528 52.381 0.00 0.00 37.36 4.63
1917 11726 0.606604 TAGTGCTCGACCTTGGGAAC 59.393 55.000 0.00 0.00 0.00 3.62
1930 11739 1.803334 TGGGAACGATTTGGAACTCG 58.197 50.000 0.00 0.00 40.62 4.18
1934 11743 3.431207 GGGAACGATTTGGAACTCGGATA 60.431 47.826 4.45 0.00 39.16 2.59
1940 11749 4.501571 CGATTTGGAACTCGGATATCAGGT 60.502 45.833 4.83 0.00 0.00 4.00
1943 11752 4.931661 TGGAACTCGGATATCAGGTAAC 57.068 45.455 4.83 0.00 0.00 2.50
1996 11813 0.931662 CGTGCACACAAGCAGAAAGC 60.932 55.000 18.64 0.00 46.69 3.51
2029 11846 1.970114 GATATCGTCCGGCCGGAGA 60.970 63.158 46.28 38.72 46.16 3.71
2050 11867 3.454082 GACCTTCCTCATTCCTCATCAGT 59.546 47.826 0.00 0.00 0.00 3.41
2051 11868 3.848975 ACCTTCCTCATTCCTCATCAGTT 59.151 43.478 0.00 0.00 0.00 3.16
2052 11869 5.032846 ACCTTCCTCATTCCTCATCAGTTA 58.967 41.667 0.00 0.00 0.00 2.24
2072 11889 6.257849 CAGTTATTCAAACTGCCGAATAGCTA 59.742 38.462 5.06 0.00 41.12 3.32
2073 11890 6.480320 AGTTATTCAAACTGCCGAATAGCTAG 59.520 38.462 0.00 0.00 41.20 3.42
2074 11891 2.550978 TCAAACTGCCGAATAGCTAGC 58.449 47.619 6.62 6.62 0.00 3.42
2075 11892 2.168521 TCAAACTGCCGAATAGCTAGCT 59.831 45.455 23.12 23.12 0.00 3.32
2076 11893 2.517650 AACTGCCGAATAGCTAGCTC 57.482 50.000 23.26 6.43 0.00 4.09
2079 11896 0.676184 TGCCGAATAGCTAGCTCCAG 59.324 55.000 23.26 11.21 0.00 3.86
2082 11899 1.333177 CGAATAGCTAGCTCCAGGGT 58.667 55.000 23.26 0.68 0.00 4.34
2170 11987 2.107378 TCCCAAACACTTGTATGGCTCA 59.893 45.455 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.235079 TCCGACTCCCATTTCATGAAAT 57.765 40.909 24.83 24.83 41.33 2.17
8 9 3.712016 TCCGACTCCCATTTCATGAAA 57.288 42.857 22.52 22.52 34.46 2.69
9 10 3.054434 ACATCCGACTCCCATTTCATGAA 60.054 43.478 3.38 3.38 0.00 2.57
10 11 2.505407 ACATCCGACTCCCATTTCATGA 59.495 45.455 0.00 0.00 0.00 3.07
11 12 2.923121 ACATCCGACTCCCATTTCATG 58.077 47.619 0.00 0.00 0.00 3.07
13 14 2.169769 GGTACATCCGACTCCCATTTCA 59.830 50.000 0.00 0.00 0.00 2.69
14 15 2.169769 TGGTACATCCGACTCCCATTTC 59.830 50.000 0.00 0.00 39.52 2.17
15 16 2.170607 CTGGTACATCCGACTCCCATTT 59.829 50.000 0.00 0.00 38.20 2.32
16 17 1.762957 CTGGTACATCCGACTCCCATT 59.237 52.381 0.00 0.00 38.20 3.16
17 18 1.414158 CTGGTACATCCGACTCCCAT 58.586 55.000 0.00 0.00 38.20 4.00
18 19 1.327690 GCTGGTACATCCGACTCCCA 61.328 60.000 0.00 0.00 38.20 4.37
19 20 1.442148 GCTGGTACATCCGACTCCC 59.558 63.158 0.00 0.00 38.20 4.30
20 21 1.442148 GGCTGGTACATCCGACTCC 59.558 63.158 0.00 0.00 33.85 3.85
26 27 4.564110 GCCCGGGCTGGTACATCC 62.564 72.222 38.76 4.71 45.18 3.51
27 28 4.910585 CGCCCGGGCTGGTACATC 62.911 72.222 41.01 11.53 38.20 3.06
40 41 4.699522 AGACAGAAACGCCCGCCC 62.700 66.667 0.00 0.00 0.00 6.13
41 42 2.668550 AAGACAGAAACGCCCGCC 60.669 61.111 0.00 0.00 0.00 6.13
42 43 2.556287 CAAGACAGAAACGCCCGC 59.444 61.111 0.00 0.00 0.00 6.13
43 44 2.325082 CCCAAGACAGAAACGCCCG 61.325 63.158 0.00 0.00 0.00 6.13
44 45 2.626780 GCCCAAGACAGAAACGCCC 61.627 63.158 0.00 0.00 0.00 6.13
46 47 1.298859 ATCGCCCAAGACAGAAACGC 61.299 55.000 0.00 0.00 0.00 4.84
48 49 2.032178 GCATATCGCCCAAGACAGAAAC 59.968 50.000 0.00 0.00 32.94 2.78
49 50 2.288666 GCATATCGCCCAAGACAGAAA 58.711 47.619 0.00 0.00 32.94 2.52
51 52 3.686622 GCATATCGCCCAAGACAGA 57.313 52.632 0.00 0.00 32.94 3.41
61 62 2.447244 ACTGAGCTTAGGCATATCGC 57.553 50.000 10.64 0.00 41.70 4.58
62 63 5.533482 ACTTAACTGAGCTTAGGCATATCG 58.467 41.667 10.64 0.00 41.70 2.92
66 67 9.331282 CTTTATTACTTAACTGAGCTTAGGCAT 57.669 33.333 10.64 0.00 41.70 4.40
67 68 7.280205 GCTTTATTACTTAACTGAGCTTAGGCA 59.720 37.037 10.64 0.00 41.70 4.75
69 70 8.950208 AGCTTTATTACTTAACTGAGCTTAGG 57.050 34.615 10.64 0.00 35.89 2.69
73 74 7.391833 AGCAAAGCTTTATTACTTAACTGAGCT 59.608 33.333 12.25 8.14 40.64 4.09
74 75 7.530863 AGCAAAGCTTTATTACTTAACTGAGC 58.469 34.615 12.25 5.85 33.89 4.26
110 111 1.358759 CTGGCAACCGCGACTTTTT 59.641 52.632 8.23 0.00 39.92 1.94
111 112 1.782028 GACTGGCAACCGCGACTTTT 61.782 55.000 8.23 0.00 39.92 2.27
114 115 4.681978 GGACTGGCAACCGCGACT 62.682 66.667 8.23 0.00 39.92 4.18
115 116 4.980805 TGGACTGGCAACCGCGAC 62.981 66.667 8.23 0.00 39.92 5.19
116 117 4.015406 ATGGACTGGCAACCGCGA 62.015 61.111 8.23 0.00 39.92 5.87
117 118 3.803082 CATGGACTGGCAACCGCG 61.803 66.667 0.00 0.00 39.92 6.46
118 119 4.120331 GCATGGACTGGCAACCGC 62.120 66.667 0.00 1.54 37.44 5.68
126 127 1.392589 GTTGGTATGGGCATGGACTG 58.607 55.000 0.00 0.00 0.00 3.51
127 128 0.107214 CGTTGGTATGGGCATGGACT 60.107 55.000 0.00 0.00 0.00 3.85
129 130 0.107410 GTCGTTGGTATGGGCATGGA 60.107 55.000 0.00 0.00 0.00 3.41
131 132 1.436195 CGGTCGTTGGTATGGGCATG 61.436 60.000 0.00 0.00 0.00 4.06
132 133 1.153249 CGGTCGTTGGTATGGGCAT 60.153 57.895 0.00 0.00 0.00 4.40
133 134 2.266372 CGGTCGTTGGTATGGGCA 59.734 61.111 0.00 0.00 0.00 5.36
134 135 2.512974 CCGGTCGTTGGTATGGGC 60.513 66.667 0.00 0.00 0.00 5.36
135 136 2.512974 GCCGGTCGTTGGTATGGG 60.513 66.667 1.90 0.00 0.00 4.00
136 137 2.888534 CGCCGGTCGTTGGTATGG 60.889 66.667 1.90 0.00 0.00 2.74
137 138 3.560278 GCGCCGGTCGTTGGTATG 61.560 66.667 17.38 0.00 41.07 2.39
138 139 3.305177 AAGCGCCGGTCGTTGGTAT 62.305 57.895 17.38 0.00 41.07 2.73
139 140 3.919973 GAAGCGCCGGTCGTTGGTA 62.920 63.158 17.38 0.00 41.07 3.25
146 147 2.202756 CTAGTGGAAGCGCCGGTC 60.203 66.667 2.29 0.00 40.66 4.79
147 148 4.452733 GCTAGTGGAAGCGCCGGT 62.453 66.667 2.29 0.00 40.66 5.28
153 154 0.605589 AACAACCGGCTAGTGGAAGC 60.606 55.000 0.00 0.00 41.99 3.86
155 156 1.543871 GGAAACAACCGGCTAGTGGAA 60.544 52.381 0.00 0.00 0.00 3.53
156 157 0.035739 GGAAACAACCGGCTAGTGGA 59.964 55.000 0.00 0.00 0.00 4.02
157 158 0.250553 TGGAAACAACCGGCTAGTGG 60.251 55.000 0.00 2.01 37.44 4.00
158 159 0.872388 GTGGAAACAACCGGCTAGTG 59.128 55.000 0.00 0.00 46.06 2.74
161 162 2.279935 AATGTGGAAACAACCGGCTA 57.720 45.000 0.00 0.00 46.06 3.93
162 163 1.408969 AAATGTGGAAACAACCGGCT 58.591 45.000 0.00 0.00 46.06 5.52
163 164 2.232756 AAAATGTGGAAACAACCGGC 57.767 45.000 0.00 0.00 46.06 6.13
164 165 4.048504 GAGAAAAATGTGGAAACAACCGG 58.951 43.478 0.00 0.00 46.06 5.28
165 166 4.048504 GGAGAAAAATGTGGAAACAACCG 58.951 43.478 0.00 0.00 46.06 4.44
167 168 5.049828 CAGGGAGAAAAATGTGGAAACAAC 58.950 41.667 0.00 0.00 46.06 3.32
168 169 4.714308 ACAGGGAGAAAAATGTGGAAACAA 59.286 37.500 0.00 0.00 46.06 2.83
169 170 4.285863 ACAGGGAGAAAAATGTGGAAACA 58.714 39.130 0.00 0.00 38.70 2.83
170 171 4.937201 ACAGGGAGAAAAATGTGGAAAC 57.063 40.909 0.00 0.00 0.00 2.78
171 172 4.442753 GCAACAGGGAGAAAAATGTGGAAA 60.443 41.667 0.00 0.00 0.00 3.13
172 173 3.069443 GCAACAGGGAGAAAAATGTGGAA 59.931 43.478 0.00 0.00 0.00 3.53
174 175 2.364970 TGCAACAGGGAGAAAAATGTGG 59.635 45.455 0.00 0.00 0.00 4.17
175 176 3.181477 TGTGCAACAGGGAGAAAAATGTG 60.181 43.478 0.00 0.00 45.67 3.21
176 177 3.030291 TGTGCAACAGGGAGAAAAATGT 58.970 40.909 0.00 0.00 45.67 2.71
177 178 3.731652 TGTGCAACAGGGAGAAAAATG 57.268 42.857 0.00 0.00 45.67 2.32
190 191 3.022287 CGGTGGACACTGTGCAAC 58.978 61.111 8.62 8.62 38.21 4.17
191 192 2.899838 GCGGTGGACACTGTGCAA 60.900 61.111 7.90 0.00 39.81 4.08
192 193 3.860605 AGCGGTGGACACTGTGCA 61.861 61.111 7.90 0.00 39.81 4.57
195 196 4.626081 GGCAGCGGTGGACACTGT 62.626 66.667 17.54 0.00 39.81 3.55
196 197 2.942796 TAGGCAGCGGTGGACACTG 61.943 63.158 17.54 6.91 40.59 3.66
197 198 2.603473 TAGGCAGCGGTGGACACT 60.603 61.111 17.54 3.13 0.00 3.55
198 199 1.601419 TAGTAGGCAGCGGTGGACAC 61.601 60.000 17.54 0.00 0.00 3.67
199 200 1.304630 TAGTAGGCAGCGGTGGACA 60.305 57.895 17.54 0.00 0.00 4.02
200 201 1.437986 CTAGTAGGCAGCGGTGGAC 59.562 63.158 17.54 0.00 0.00 4.02
201 202 2.423898 GCTAGTAGGCAGCGGTGGA 61.424 63.158 17.54 0.00 0.00 4.02
203 204 2.107141 GGCTAGTAGGCAGCGGTG 59.893 66.667 18.34 10.98 40.97 4.94
204 205 2.363795 TGGCTAGTAGGCAGCGGT 60.364 61.111 21.67 0.00 46.47 5.68
210 211 6.994221 TCAAGACTAATTATGGCTAGTAGGC 58.006 40.000 16.57 16.57 41.77 3.93
211 212 8.184304 ACTCAAGACTAATTATGGCTAGTAGG 57.816 38.462 0.00 0.00 0.00 3.18
212 213 9.073475 AGACTCAAGACTAATTATGGCTAGTAG 57.927 37.037 0.00 0.00 0.00 2.57
213 214 8.998277 AGACTCAAGACTAATTATGGCTAGTA 57.002 34.615 0.00 0.00 0.00 1.82
214 215 7.906199 AGACTCAAGACTAATTATGGCTAGT 57.094 36.000 0.00 0.00 0.00 2.57
217 218 8.763601 AGTTTAGACTCAAGACTAATTATGGCT 58.236 33.333 3.43 0.00 33.68 4.75
256 257 2.226437 CCAAAACGTTCCACTCATCAGG 59.774 50.000 0.00 0.00 0.00 3.86
257 258 2.878406 ACCAAAACGTTCCACTCATCAG 59.122 45.455 0.00 0.00 0.00 2.90
258 259 2.616376 CACCAAAACGTTCCACTCATCA 59.384 45.455 0.00 0.00 0.00 3.07
260 261 2.616842 GTCACCAAAACGTTCCACTCAT 59.383 45.455 0.00 0.00 0.00 2.90
262 263 1.332686 GGTCACCAAAACGTTCCACTC 59.667 52.381 0.00 0.00 0.00 3.51
264 265 1.064952 CTGGTCACCAAAACGTTCCAC 59.935 52.381 0.00 0.00 30.80 4.02
265 266 1.384525 CTGGTCACCAAAACGTTCCA 58.615 50.000 0.00 1.45 30.80 3.53
266 267 0.666374 CCTGGTCACCAAAACGTTCC 59.334 55.000 0.00 0.00 30.80 3.62
267 268 0.030235 GCCTGGTCACCAAAACGTTC 59.970 55.000 0.00 0.00 30.80 3.95
268 269 0.395173 AGCCTGGTCACCAAAACGTT 60.395 50.000 0.00 0.00 30.80 3.99
271 272 0.467290 TGGAGCCTGGTCACCAAAAC 60.467 55.000 0.00 0.00 30.80 2.43
273 274 1.281867 CTATGGAGCCTGGTCACCAAA 59.718 52.381 0.00 0.00 36.00 3.28
276 277 1.700042 CCCTATGGAGCCTGGTCACC 61.700 65.000 0.00 0.00 0.00 4.02
278 279 1.384502 CCCCTATGGAGCCTGGTCA 60.385 63.158 0.00 0.00 35.39 4.02
280 281 1.384643 GTCCCCTATGGAGCCTGGT 60.385 63.158 0.00 0.00 46.38 4.00
281 282 2.511452 CGTCCCCTATGGAGCCTGG 61.511 68.421 0.00 0.00 46.38 4.45
282 283 1.457643 TCGTCCCCTATGGAGCCTG 60.458 63.158 0.00 0.00 46.38 4.85
283 284 1.152440 CTCGTCCCCTATGGAGCCT 60.152 63.158 0.00 0.00 46.38 4.58
284 285 2.210711 CCTCGTCCCCTATGGAGCC 61.211 68.421 0.00 0.00 46.38 4.70
286 287 1.551452 GATCCTCGTCCCCTATGGAG 58.449 60.000 0.00 0.00 46.38 3.86
288 289 0.115349 AGGATCCTCGTCCCCTATGG 59.885 60.000 9.02 0.00 39.17 2.74
290 291 1.076350 CAGAGGATCCTCGTCCCCTAT 59.924 57.143 31.51 12.52 46.90 2.57
291 292 0.478942 CAGAGGATCCTCGTCCCCTA 59.521 60.000 31.51 0.00 46.90 3.53
292 293 1.231641 CAGAGGATCCTCGTCCCCT 59.768 63.158 31.51 13.95 46.90 4.79
294 295 2.503382 GGCAGAGGATCCTCGTCCC 61.503 68.421 31.51 27.06 46.90 4.46
295 296 2.851071 CGGCAGAGGATCCTCGTCC 61.851 68.421 31.51 30.77 46.90 4.79
296 297 1.668101 AACGGCAGAGGATCCTCGTC 61.668 60.000 31.51 25.76 46.90 4.20
297 298 1.668101 GAACGGCAGAGGATCCTCGT 61.668 60.000 31.51 24.57 46.90 4.18
299 300 1.066587 CGAACGGCAGAGGATCCTC 59.933 63.158 31.27 31.27 43.03 3.71
300 301 2.427245 CCGAACGGCAGAGGATCCT 61.427 63.158 16.13 16.13 33.66 3.24
301 302 2.107141 CCGAACGGCAGAGGATCC 59.893 66.667 2.48 2.48 33.66 3.36
318 319 3.723348 GGTCGAACGGCACCTTGC 61.723 66.667 0.61 0.00 44.08 4.01
319 320 2.280524 TGGTCGAACGGCACCTTG 60.281 61.111 0.00 0.00 33.36 3.61
320 321 2.280592 GTGGTCGAACGGCACCTT 60.281 61.111 0.00 0.00 33.36 3.50
321 322 3.231736 AGTGGTCGAACGGCACCT 61.232 61.111 0.00 0.00 33.36 4.00
322 323 2.781595 ATCAGTGGTCGAACGGCACC 62.782 60.000 0.00 0.00 0.00 5.01
336 337 1.734655 CTATGGGCCCACCTATCAGT 58.265 55.000 31.51 11.72 38.31 3.41
337 338 0.987294 CCTATGGGCCCACCTATCAG 59.013 60.000 31.51 16.60 38.31 2.90
338 339 0.570727 TCCTATGGGCCCACCTATCA 59.429 55.000 31.51 6.20 38.31 2.15
339 340 1.742308 TTCCTATGGGCCCACCTATC 58.258 55.000 31.51 0.00 38.31 2.08
340 341 2.177016 GTTTTCCTATGGGCCCACCTAT 59.823 50.000 31.51 14.89 40.82 2.57
341 342 1.567175 GTTTTCCTATGGGCCCACCTA 59.433 52.381 31.51 16.57 41.11 3.08
342 343 0.335019 GTTTTCCTATGGGCCCACCT 59.665 55.000 31.51 16.26 41.11 4.00
345 346 0.334676 CCTGTTTTCCTATGGGCCCA 59.665 55.000 30.92 30.92 0.00 5.36
347 348 2.504920 GCCTGTTTTCCTATGGGCC 58.495 57.895 0.00 0.00 34.19 5.80
348 349 1.043116 GGGCCTGTTTTCCTATGGGC 61.043 60.000 0.84 0.00 41.79 5.36
349 350 0.334676 TGGGCCTGTTTTCCTATGGG 59.665 55.000 4.53 0.00 0.00 4.00
351 352 2.214376 TGTGGGCCTGTTTTCCTATG 57.786 50.000 4.53 0.00 0.00 2.23
352 353 2.624029 CCATGTGGGCCTGTTTTCCTAT 60.624 50.000 4.53 0.00 0.00 2.57
353 354 1.272425 CCATGTGGGCCTGTTTTCCTA 60.272 52.381 4.53 0.00 0.00 2.94
354 355 0.542702 CCATGTGGGCCTGTTTTCCT 60.543 55.000 4.53 0.00 0.00 3.36
355 356 1.974543 CCATGTGGGCCTGTTTTCC 59.025 57.895 4.53 0.00 0.00 3.13
379 380 4.108699 ACAAATATGAATGCCGTTGTGG 57.891 40.909 0.00 0.00 42.50 4.17
380 381 6.464895 AAAACAAATATGAATGCCGTTGTG 57.535 33.333 0.00 0.00 30.06 3.33
443 444 3.288964 TGAAGGCCTCCGTTTGTAAAAA 58.711 40.909 5.23 0.00 0.00 1.94
445 446 2.642154 TGAAGGCCTCCGTTTGTAAA 57.358 45.000 5.23 0.00 0.00 2.01
447 448 1.349688 ACATGAAGGCCTCCGTTTGTA 59.650 47.619 5.23 0.00 0.00 2.41
448 449 0.110486 ACATGAAGGCCTCCGTTTGT 59.890 50.000 5.23 3.14 0.00 2.83
450 451 1.679032 GCTACATGAAGGCCTCCGTTT 60.679 52.381 5.23 0.00 0.00 3.60
451 452 0.107654 GCTACATGAAGGCCTCCGTT 60.108 55.000 5.23 0.00 0.00 4.44
452 453 0.978146 AGCTACATGAAGGCCTCCGT 60.978 55.000 5.23 3.38 0.00 4.69
453 454 0.249657 GAGCTACATGAAGGCCTCCG 60.250 60.000 5.23 0.00 0.00 4.63
454 455 0.249657 CGAGCTACATGAAGGCCTCC 60.250 60.000 5.23 0.00 0.00 4.30
455 456 0.249657 CCGAGCTACATGAAGGCCTC 60.250 60.000 5.23 0.00 0.00 4.70
462 463 0.975556 TTGGAGGCCGAGCTACATGA 60.976 55.000 0.00 0.00 0.00 3.07
467 468 1.078426 GCTTTTGGAGGCCGAGCTA 60.078 57.895 0.00 0.00 0.00 3.32
470 471 0.890683 AATTGCTTTTGGAGGCCGAG 59.109 50.000 0.00 0.00 0.00 4.63
493 494 2.820787 GCTAGATAGGCGTACATGAGGT 59.179 50.000 0.00 0.00 0.00 3.85
494 495 3.085533 AGCTAGATAGGCGTACATGAGG 58.914 50.000 0.00 0.00 34.52 3.86
496 497 4.096532 GCATAGCTAGATAGGCGTACATGA 59.903 45.833 9.07 0.00 34.52 3.07
497 498 4.142381 TGCATAGCTAGATAGGCGTACATG 60.142 45.833 18.55 0.00 35.26 3.21
499 500 3.190744 GTGCATAGCTAGATAGGCGTACA 59.809 47.826 18.55 0.00 35.26 2.90
602 682 5.821204 CTGCAAGTAGCTGTGTAACTTTTT 58.179 37.500 0.00 0.00 45.94 1.94
627 707 6.099269 ACAGTCGGGTCCATATATAAACTTGT 59.901 38.462 0.00 0.00 0.00 3.16
639 719 1.125093 TGTTCCACAGTCGGGTCCAT 61.125 55.000 0.00 0.00 0.00 3.41
641 721 0.883370 GTTGTTCCACAGTCGGGTCC 60.883 60.000 0.00 0.00 0.00 4.46
642 722 0.883370 GGTTGTTCCACAGTCGGGTC 60.883 60.000 0.00 0.00 35.97 4.46
643 723 1.147600 GGTTGTTCCACAGTCGGGT 59.852 57.895 0.00 0.00 35.97 5.28
654 734 2.621526 ACGTGGAAAAGATGGGTTGTTC 59.378 45.455 0.00 0.00 0.00 3.18
679 759 2.092291 GCGTTCATTCGAGCCGACA 61.092 57.895 0.00 0.00 34.89 4.35
681 761 1.805539 CTGCGTTCATTCGAGCCGA 60.806 57.895 0.00 0.00 0.00 5.54
683 763 2.401195 GCTGCGTTCATTCGAGCC 59.599 61.111 0.00 0.00 32.43 4.70
687 767 2.099062 GCTGGCTGCGTTCATTCG 59.901 61.111 0.00 0.00 0.00 3.34
699 779 3.100503 GCTCTACTCAGGGGCTGGC 62.101 68.421 0.00 0.00 31.51 4.85
700 780 2.790791 CGCTCTACTCAGGGGCTGG 61.791 68.421 0.00 0.00 31.51 4.85
701 781 2.790791 CCGCTCTACTCAGGGGCTG 61.791 68.421 0.00 0.00 39.47 4.85
702 782 2.443016 CCGCTCTACTCAGGGGCT 60.443 66.667 0.00 0.00 39.47 5.19
703 783 2.022240 CTTCCGCTCTACTCAGGGGC 62.022 65.000 0.00 0.00 44.49 5.80
705 785 1.407258 CTTCTTCCGCTCTACTCAGGG 59.593 57.143 0.00 0.00 0.00 4.45
706 786 1.202359 GCTTCTTCCGCTCTACTCAGG 60.202 57.143 0.00 0.00 0.00 3.86
708 788 1.474478 CTGCTTCTTCCGCTCTACTCA 59.526 52.381 0.00 0.00 0.00 3.41
709 789 1.746220 TCTGCTTCTTCCGCTCTACTC 59.254 52.381 0.00 0.00 0.00 2.59
711 791 1.474879 ACTCTGCTTCTTCCGCTCTAC 59.525 52.381 0.00 0.00 0.00 2.59
713 793 0.530288 GACTCTGCTTCTTCCGCTCT 59.470 55.000 0.00 0.00 0.00 4.09
923 1849 2.495270 AGCAGCGAGAGATCTTTCTTGA 59.505 45.455 11.20 0.00 31.34 3.02
1301 2321 2.103771 AGCATCTACCACTGTATGCCTG 59.896 50.000 8.45 0.00 34.79 4.85
1417 3760 4.461198 AGGGACAAACGAAAGAATGAAGT 58.539 39.130 0.00 0.00 0.00 3.01
1524 3880 2.237143 CAGGAGCTGGGACATTCTTACA 59.763 50.000 0.00 0.00 38.20 2.41
1584 7763 4.764050 TTTCCCCTCGTAATTATCTGCA 57.236 40.909 0.00 0.00 0.00 4.41
1637 8298 3.414759 TCCAAAGGAGCTACATCCCTA 57.585 47.619 0.00 0.00 40.53 3.53
1693 10659 5.170748 CACCTGCCTAATGTTGGAATTTTC 58.829 41.667 0.00 0.00 0.00 2.29
1733 10700 7.273815 CGACAAATTTTCAGGACTCTAGTCTAC 59.726 40.741 9.84 0.00 44.20 2.59
1751 10735 1.202879 TGTCAAGGAGGCCGACAAATT 60.203 47.619 7.84 0.00 36.75 1.82
1754 10738 0.321564 CATGTCAAGGAGGCCGACAA 60.322 55.000 13.44 0.00 42.53 3.18
1757 11168 0.911769 ATTCATGTCAAGGAGGCCGA 59.088 50.000 0.00 0.00 0.00 5.54
1759 11170 2.092429 TGGTATTCATGTCAAGGAGGCC 60.092 50.000 0.00 0.00 0.00 5.19
1817 11228 3.243805 ATCGAGGAGATGCAGATCAACTG 60.244 47.826 0.00 0.00 39.71 3.16
1833 11244 2.267174 AGCATGGGATTTCATCGAGG 57.733 50.000 0.00 0.00 0.00 4.63
1837 11646 6.949352 TTAGAAGAAGCATGGGATTTCATC 57.051 37.500 0.00 0.00 0.00 2.92
1917 11726 3.990469 CCTGATATCCGAGTTCCAAATCG 59.010 47.826 0.00 2.25 45.04 3.34
1930 11739 4.809426 CGTTGGTTCAGTTACCTGATATCC 59.191 45.833 0.00 0.00 46.80 2.59
1934 11743 2.038557 AGCGTTGGTTCAGTTACCTGAT 59.961 45.455 0.00 0.00 46.80 2.90
1940 11749 0.887387 GGCCAGCGTTGGTTCAGTTA 60.887 55.000 20.17 0.00 46.80 2.24
1943 11752 3.726517 CGGCCAGCGTTGGTTCAG 61.727 66.667 20.17 5.23 46.80 3.02
1978 11787 0.101040 TGCTTTCTGCTTGTGTGCAC 59.899 50.000 10.75 10.75 43.37 4.57
1996 11813 6.153067 GGACGATATCACTTTCATAGGAGTG 58.847 44.000 3.12 0.00 43.54 3.51
2029 11846 3.458831 ACTGATGAGGAATGAGGAAGGT 58.541 45.455 0.00 0.00 0.00 3.50
2050 11867 5.236478 GCTAGCTATTCGGCAGTTTGAATAA 59.764 40.000 7.70 0.00 36.81 1.40
2051 11868 4.750098 GCTAGCTATTCGGCAGTTTGAATA 59.250 41.667 7.70 0.00 36.32 1.75
2052 11869 3.561725 GCTAGCTATTCGGCAGTTTGAAT 59.438 43.478 7.70 0.00 38.34 2.57
2106 11923 2.098117 CCTCATGGAACGCCTTGATTTC 59.902 50.000 0.00 0.00 44.52 2.17
2170 11987 2.632996 TCGAAGTGTGGAAATCTCACCT 59.367 45.455 0.00 0.00 34.46 4.00
2194 12012 0.807496 GACTGCTTTGGTGGATCTGC 59.193 55.000 0.00 0.00 0.00 4.26
2197 12015 0.038166 TGGGACTGCTTTGGTGGATC 59.962 55.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.