Multiple sequence alignment - TraesCS4B01G339000

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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 TraesCS4B01G339000 chr4B 100.000 5415 0 0 774 6188 632125905 632120491 0.000000e+00 10000.0
1 TraesCS4B01G339000 chr4B 91.412 1537 79 15 800 2307 631837393 631838905 0.000000e+00 2058.0
2 TraesCS4B01G339000 chr4B 87.377 1529 127 26 3906 5417 632128798 632130277 0.000000e+00 1694.0
3 TraesCS4B01G339000 chr4B 84.505 1323 152 31 3560 4848 631896893 631895590 0.000000e+00 1258.0
4 TraesCS4B01G339000 chr4B 82.130 1343 124 54 1025 2319 631899433 631898159 0.000000e+00 1044.0
5 TraesCS4B01G339000 chr4B 79.666 1318 162 45 2325 3577 631898183 631896907 0.000000e+00 852.0
6 TraesCS4B01G339000 chr4B 100.000 431 0 0 1 431 632126678 632126248 0.000000e+00 797.0
7 TraesCS4B01G339000 chr4B 90.826 109 9 1 324 431 631837263 631837371 1.800000e-30 145.0
8 TraesCS4B01G339000 chr4B 85.057 87 8 1 4865 4946 631895408 631895322 3.970000e-12 84.2
9 TraesCS4B01G339000 chr4D 92.914 3133 134 38 2325 5417 493908751 493911835 0.000000e+00 4475.0
10 TraesCS4B01G339000 chr4D 93.739 1166 48 15 804 1961 493907327 493908475 0.000000e+00 1725.0
11 TraesCS4B01G339000 chr4D 88.432 778 74 7 5414 6188 416644973 416645737 0.000000e+00 924.0
12 TraesCS4B01G339000 chr4D 89.625 694 46 17 958 1637 493924195 493923514 0.000000e+00 859.0
13 TraesCS4B01G339000 chr4D 83.836 464 53 9 2325 2783 493922889 493922443 7.420000e-114 422.0
14 TraesCS4B01G339000 chr4D 90.541 296 12 3 2006 2300 493908478 493908758 1.630000e-100 377.0
15 TraesCS4B01G339000 chr4D 86.728 324 19 9 2002 2319 493923170 493922865 7.680000e-89 339.0
16 TraesCS4B01G339000 chr4D 85.271 258 31 2 1723 1980 493923467 493923217 6.150000e-65 259.0
17 TraesCS4B01G339000 chr4D 82.879 257 22 9 189 431 493907064 493907312 1.750000e-50 211.0
18 TraesCS4B01G339000 chr5A 91.333 1846 72 24 930 2759 673184966 673186739 0.000000e+00 2442.0
19 TraesCS4B01G339000 chr5A 81.681 1321 146 42 3569 4848 673235335 673234070 0.000000e+00 1011.0
20 TraesCS4B01G339000 chr5A 81.231 1300 156 39 2325 3577 673236614 673235356 0.000000e+00 968.0
21 TraesCS4B01G339000 chr5A 82.922 972 104 32 1012 1980 673237854 673236942 0.000000e+00 819.0
22 TraesCS4B01G339000 chr5A 86.503 326 20 6 2000 2319 673236897 673236590 2.760000e-88 337.0
23 TraesCS4B01G339000 chr5A 84.694 196 14 9 245 431 673184694 673184882 1.370000e-41 182.0
24 TraesCS4B01G339000 chr3A 91.355 775 55 9 5419 6188 492328062 492327295 0.000000e+00 1050.0
25 TraesCS4B01G339000 chr6D 88.903 775 79 7 5417 6188 367152873 367153643 0.000000e+00 948.0
26 TraesCS4B01G339000 chr6D 88.648 784 67 13 5417 6188 463196916 463197689 0.000000e+00 935.0
27 TraesCS4B01G339000 chr1D 89.018 774 71 10 5417 6188 204887328 204888089 0.000000e+00 946.0
28 TraesCS4B01G339000 chr1D 88.903 775 77 5 5416 6188 491944668 491945435 0.000000e+00 946.0
29 TraesCS4B01G339000 chr1A 89.879 741 68 3 5449 6188 583945502 583946236 0.000000e+00 946.0
30 TraesCS4B01G339000 chr6A 88.803 777 74 7 5415 6188 564890475 564891241 0.000000e+00 941.0
31 TraesCS4B01G339000 chr5D 88.476 781 77 9 5413 6188 519335245 519334473 0.000000e+00 931.0
32 TraesCS4B01G339000 chr2B 86.767 529 65 3 1056 1579 540255851 540256379 8.940000e-163 584.0
33 TraesCS4B01G339000 chr2B 88.068 176 12 4 1631 1805 220520360 220520527 3.780000e-47 200.0
34 TraesCS4B01G339000 chr2B 90.647 139 13 0 1441 1579 220520212 220520350 1.060000e-42 185.0
35 TraesCS4B01G339000 chr2B 88.889 54 5 1 4172 4224 666484282 666484229 1.440000e-06 65.8
36 TraesCS4B01G339000 chr2B 91.489 47 3 1 4179 4224 666630770 666630816 5.180000e-06 63.9
37 TraesCS4B01G339000 chr2D 92.405 316 16 4 1631 1946 459045449 459045756 1.580000e-120 444.0
38 TraesCS4B01G339000 chr2D 88.187 364 25 8 1930 2289 459045887 459046236 9.590000e-113 418.0
39 TraesCS4B01G339000 chr2D 91.667 108 6 1 2325 2432 459046409 459046513 5.000000e-31 147.0
40 TraesCS4B01G339000 chr2D 90.566 106 9 1 1080 1184 459038080 459038185 8.360000e-29 139.0
41 TraesCS4B01G339000 chr2D 91.489 47 3 1 4179 4224 558201635 558201681 5.180000e-06 63.9
42 TraesCS4B01G339000 chr2D 97.143 35 1 0 4192 4226 557956120 557956086 6.700000e-05 60.2
43 TraesCS4B01G339000 chr2A 95.349 43 2 0 4179 4221 698784103 698784145 1.110000e-07 69.4


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 TraesCS4B01G339000 chr4B 632120491 632126678 6187 True 5398.500000 10000 100.00000 1 6188 2 chr4B.!!$R2 6187
1 TraesCS4B01G339000 chr4B 632128798 632130277 1479 False 1694.000000 1694 87.37700 3906 5417 1 chr4B.!!$F1 1511
2 TraesCS4B01G339000 chr4B 631837263 631838905 1642 False 1101.500000 2058 91.11900 324 2307 2 chr4B.!!$F2 1983
3 TraesCS4B01G339000 chr4B 631895322 631899433 4111 True 809.550000 1258 82.83950 1025 4946 4 chr4B.!!$R1 3921
4 TraesCS4B01G339000 chr4D 493907064 493911835 4771 False 1697.000000 4475 90.01825 189 5417 4 chr4D.!!$F2 5228
5 TraesCS4B01G339000 chr4D 416644973 416645737 764 False 924.000000 924 88.43200 5414 6188 1 chr4D.!!$F1 774
6 TraesCS4B01G339000 chr4D 493922443 493924195 1752 True 469.750000 859 86.36500 958 2783 4 chr4D.!!$R1 1825
7 TraesCS4B01G339000 chr5A 673184694 673186739 2045 False 1312.000000 2442 88.01350 245 2759 2 chr5A.!!$F1 2514
8 TraesCS4B01G339000 chr5A 673234070 673237854 3784 True 783.750000 1011 83.08425 1012 4848 4 chr5A.!!$R1 3836
9 TraesCS4B01G339000 chr3A 492327295 492328062 767 True 1050.000000 1050 91.35500 5419 6188 1 chr3A.!!$R1 769
10 TraesCS4B01G339000 chr6D 367152873 367153643 770 False 948.000000 948 88.90300 5417 6188 1 chr6D.!!$F1 771
11 TraesCS4B01G339000 chr6D 463196916 463197689 773 False 935.000000 935 88.64800 5417 6188 1 chr6D.!!$F2 771
12 TraesCS4B01G339000 chr1D 204887328 204888089 761 False 946.000000 946 89.01800 5417 6188 1 chr1D.!!$F1 771
13 TraesCS4B01G339000 chr1D 491944668 491945435 767 False 946.000000 946 88.90300 5416 6188 1 chr1D.!!$F2 772
14 TraesCS4B01G339000 chr1A 583945502 583946236 734 False 946.000000 946 89.87900 5449 6188 1 chr1A.!!$F1 739
15 TraesCS4B01G339000 chr6A 564890475 564891241 766 False 941.000000 941 88.80300 5415 6188 1 chr6A.!!$F1 773
16 TraesCS4B01G339000 chr5D 519334473 519335245 772 True 931.000000 931 88.47600 5413 6188 1 chr5D.!!$R1 775
17 TraesCS4B01G339000 chr2B 540255851 540256379 528 False 584.000000 584 86.76700 1056 1579 1 chr2B.!!$F1 523
18 TraesCS4B01G339000 chr2D 459045449 459046513 1064 False 336.333333 444 90.75300 1631 2432 3 chr2D.!!$F3 801

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
149 150 0.037697 TGTTCGAACCGGATGGAGTG 60.038 55.0 24.78 0.0 39.21 3.51 F
153 154 0.249073 CGAACCGGATGGAGTGCTAG 60.249 60.0 9.46 0.0 39.21 3.42 F
158 159 0.313672 CGGATGGAGTGCTAGCTCTC 59.686 60.0 30.10 30.1 35.89 3.20 F
1622 1704 0.673437 TCATGTCTGCGTGTCTGTCA 59.327 50.0 0.00 0.0 33.51 3.58 F
2655 3130 1.528129 CAAGCTGGTCTGGAACTTCC 58.472 55.0 0.20 0.2 36.96 3.46 F
3898 4521 0.250295 TCCTGTTGCTCCAGTTTCGG 60.250 55.0 3.13 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 2278 0.035820 CGGTACCTAGGCCAAGCAAA 60.036 55.000 9.30 0.00 0.00 3.68 R
2134 2431 0.457851 AAGAGCAGAATCGAGGGACG 59.542 55.000 0.00 0.00 44.09 4.79 R
2196 2500 2.042259 CGATGAAGGCAGCCTGCAA 61.042 57.895 27.23 10.12 43.33 4.08 R
3147 3717 1.067295 ATCAAGCCTGACAGGGACAA 58.933 50.000 23.09 0.00 35.37 3.18 R
4146 4776 0.107263 TGTCAACTTCACTGCCTGCA 60.107 50.000 0.00 0.00 0.00 4.41 R
5864 6752 0.400213 AGGCAAATCTCGGAACACCA 59.600 50.000 0.00 0.00 0.00 4.17 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
48 49 9.171877 TGCAAATTTAAATACCAAATTCCATCC 57.828 29.630 0.01 0.00 35.15 3.51
49 50 8.620416 GCAAATTTAAATACCAAATTCCATCCC 58.380 33.333 0.01 0.00 35.15 3.85
50 51 9.678260 CAAATTTAAATACCAAATTCCATCCCA 57.322 29.630 0.01 0.00 35.15 4.37
53 54 9.679661 ATTTAAATACCAAATTCCATCCCAAAC 57.320 29.630 0.00 0.00 0.00 2.93
54 55 5.692115 AATACCAAATTCCATCCCAAACC 57.308 39.130 0.00 0.00 0.00 3.27
55 56 2.983296 ACCAAATTCCATCCCAAACCA 58.017 42.857 0.00 0.00 0.00 3.67
56 57 2.905736 ACCAAATTCCATCCCAAACCAG 59.094 45.455 0.00 0.00 0.00 4.00
57 58 3.172339 CCAAATTCCATCCCAAACCAGA 58.828 45.455 0.00 0.00 0.00 3.86
58 59 3.055891 CCAAATTCCATCCCAAACCAGAC 60.056 47.826 0.00 0.00 0.00 3.51
59 60 2.128771 ATTCCATCCCAAACCAGACG 57.871 50.000 0.00 0.00 0.00 4.18
60 61 1.060729 TTCCATCCCAAACCAGACGA 58.939 50.000 0.00 0.00 0.00 4.20
61 62 0.613260 TCCATCCCAAACCAGACGAG 59.387 55.000 0.00 0.00 0.00 4.18
62 63 0.613260 CCATCCCAAACCAGACGAGA 59.387 55.000 0.00 0.00 0.00 4.04
63 64 1.003118 CCATCCCAAACCAGACGAGAA 59.997 52.381 0.00 0.00 0.00 2.87
64 65 2.552155 CCATCCCAAACCAGACGAGAAA 60.552 50.000 0.00 0.00 0.00 2.52
65 66 3.347216 CATCCCAAACCAGACGAGAAAT 58.653 45.455 0.00 0.00 0.00 2.17
66 67 3.502123 TCCCAAACCAGACGAGAAATT 57.498 42.857 0.00 0.00 0.00 1.82
67 68 3.827722 TCCCAAACCAGACGAGAAATTT 58.172 40.909 0.00 0.00 0.00 1.82
68 69 3.818773 TCCCAAACCAGACGAGAAATTTC 59.181 43.478 10.33 10.33 0.00 2.17
69 70 3.821033 CCCAAACCAGACGAGAAATTTCT 59.179 43.478 20.60 20.60 41.00 2.52
130 131 5.975693 TTTTGGCGGACATTTTTCTATCT 57.024 34.783 0.00 0.00 0.00 1.98
131 132 4.963276 TTGGCGGACATTTTTCTATCTG 57.037 40.909 0.00 0.00 0.00 2.90
132 133 3.950397 TGGCGGACATTTTTCTATCTGT 58.050 40.909 0.00 0.00 0.00 3.41
133 134 4.331968 TGGCGGACATTTTTCTATCTGTT 58.668 39.130 0.00 0.00 0.00 3.16
134 135 4.394920 TGGCGGACATTTTTCTATCTGTTC 59.605 41.667 0.00 0.00 0.00 3.18
135 136 4.494199 GGCGGACATTTTTCTATCTGTTCG 60.494 45.833 0.00 0.00 42.20 3.95
136 137 4.328983 GCGGACATTTTTCTATCTGTTCGA 59.671 41.667 6.42 0.00 41.94 3.71
137 138 5.163893 GCGGACATTTTTCTATCTGTTCGAA 60.164 40.000 6.42 0.00 41.94 3.71
138 139 6.241385 CGGACATTTTTCTATCTGTTCGAAC 58.759 40.000 21.42 21.42 41.94 3.95
139 140 6.543736 GGACATTTTTCTATCTGTTCGAACC 58.456 40.000 24.78 8.19 0.00 3.62
140 141 6.165659 ACATTTTTCTATCTGTTCGAACCG 57.834 37.500 24.78 18.85 0.00 4.44
141 142 5.121768 ACATTTTTCTATCTGTTCGAACCGG 59.878 40.000 24.78 17.07 0.00 5.28
142 143 4.524316 TTTTCTATCTGTTCGAACCGGA 57.476 40.909 24.78 21.28 0.00 5.14
143 144 4.730949 TTTCTATCTGTTCGAACCGGAT 57.269 40.909 24.78 25.43 0.00 4.18
144 145 3.710326 TCTATCTGTTCGAACCGGATG 57.290 47.619 28.42 21.58 0.00 3.51
145 146 2.361119 TCTATCTGTTCGAACCGGATGG 59.639 50.000 28.42 26.53 42.84 3.51
146 147 1.191535 ATCTGTTCGAACCGGATGGA 58.808 50.000 24.78 13.02 39.21 3.41
147 148 0.530744 TCTGTTCGAACCGGATGGAG 59.469 55.000 24.78 13.61 39.21 3.86
148 149 0.246635 CTGTTCGAACCGGATGGAGT 59.753 55.000 24.78 0.00 39.21 3.85
149 150 0.037697 TGTTCGAACCGGATGGAGTG 60.038 55.000 24.78 0.00 39.21 3.51
150 151 1.079405 TTCGAACCGGATGGAGTGC 60.079 57.895 9.46 0.00 39.21 4.40
151 152 1.541310 TTCGAACCGGATGGAGTGCT 61.541 55.000 9.46 0.00 39.21 4.40
152 153 0.681887 TCGAACCGGATGGAGTGCTA 60.682 55.000 9.46 0.00 39.21 3.49
153 154 0.249073 CGAACCGGATGGAGTGCTAG 60.249 60.000 9.46 0.00 39.21 3.42
154 155 0.530870 GAACCGGATGGAGTGCTAGC 60.531 60.000 9.46 8.10 39.21 3.42
155 156 0.978146 AACCGGATGGAGTGCTAGCT 60.978 55.000 17.23 0.00 39.21 3.32
156 157 1.365633 CCGGATGGAGTGCTAGCTC 59.634 63.158 17.23 12.88 37.49 4.09
157 158 1.112315 CCGGATGGAGTGCTAGCTCT 61.112 60.000 18.82 18.82 37.49 4.09
158 159 0.313672 CGGATGGAGTGCTAGCTCTC 59.686 60.000 30.10 30.10 35.89 3.20
164 165 1.318576 GAGTGCTAGCTCTCCTCTCC 58.681 60.000 28.57 9.70 32.32 3.71
165 166 0.926293 AGTGCTAGCTCTCCTCTCCT 59.074 55.000 17.23 0.00 0.00 3.69
166 167 1.287739 AGTGCTAGCTCTCCTCTCCTT 59.712 52.381 17.23 0.00 0.00 3.36
167 168 1.681264 GTGCTAGCTCTCCTCTCCTTC 59.319 57.143 17.23 0.00 0.00 3.46
168 169 1.568597 TGCTAGCTCTCCTCTCCTTCT 59.431 52.381 17.23 0.00 0.00 2.85
169 170 2.780592 TGCTAGCTCTCCTCTCCTTCTA 59.219 50.000 17.23 0.00 0.00 2.10
170 171 3.203263 TGCTAGCTCTCCTCTCCTTCTAA 59.797 47.826 17.23 0.00 0.00 2.10
171 172 3.821033 GCTAGCTCTCCTCTCCTTCTAAG 59.179 52.174 7.70 0.00 0.00 2.18
172 173 4.688874 GCTAGCTCTCCTCTCCTTCTAAGT 60.689 50.000 7.70 0.00 0.00 2.24
173 174 4.331159 AGCTCTCCTCTCCTTCTAAGTT 57.669 45.455 0.00 0.00 0.00 2.66
174 175 4.278310 AGCTCTCCTCTCCTTCTAAGTTC 58.722 47.826 0.00 0.00 0.00 3.01
175 176 4.017499 AGCTCTCCTCTCCTTCTAAGTTCT 60.017 45.833 0.00 0.00 0.00 3.01
176 177 5.192923 AGCTCTCCTCTCCTTCTAAGTTCTA 59.807 44.000 0.00 0.00 0.00 2.10
177 178 5.889289 GCTCTCCTCTCCTTCTAAGTTCTAA 59.111 44.000 0.00 0.00 0.00 2.10
178 179 6.183360 GCTCTCCTCTCCTTCTAAGTTCTAAC 60.183 46.154 0.00 0.00 0.00 2.34
179 180 7.034967 TCTCCTCTCCTTCTAAGTTCTAACT 57.965 40.000 0.00 0.00 42.04 2.24
180 181 7.114095 TCTCCTCTCCTTCTAAGTTCTAACTC 58.886 42.308 0.00 0.00 38.57 3.01
181 182 6.791371 TCCTCTCCTTCTAAGTTCTAACTCA 58.209 40.000 0.00 0.00 38.57 3.41
182 183 7.239438 TCCTCTCCTTCTAAGTTCTAACTCAA 58.761 38.462 0.00 0.00 38.57 3.02
183 184 7.728981 TCCTCTCCTTCTAAGTTCTAACTCAAA 59.271 37.037 0.00 0.00 38.57 2.69
184 185 8.536175 CCTCTCCTTCTAAGTTCTAACTCAAAT 58.464 37.037 0.00 0.00 38.57 2.32
185 186 9.936759 CTCTCCTTCTAAGTTCTAACTCAAATT 57.063 33.333 0.00 0.00 38.57 1.82
221 225 8.786937 AAAACAATATGATCATGTAACATCGC 57.213 30.769 18.72 0.00 0.00 4.58
228 232 6.434018 TGATCATGTAACATCGCAAAATCA 57.566 33.333 0.00 0.00 0.00 2.57
229 233 6.850555 TGATCATGTAACATCGCAAAATCAA 58.149 32.000 0.00 0.00 0.00 2.57
230 234 7.482474 TGATCATGTAACATCGCAAAATCAAT 58.518 30.769 0.00 0.00 0.00 2.57
233 237 7.537715 TCATGTAACATCGCAAAATCAATCTT 58.462 30.769 0.00 0.00 0.00 2.40
234 238 8.672815 TCATGTAACATCGCAAAATCAATCTTA 58.327 29.630 0.00 0.00 0.00 2.10
235 239 8.736742 CATGTAACATCGCAAAATCAATCTTAC 58.263 33.333 0.00 0.00 0.00 2.34
236 240 8.039603 TGTAACATCGCAAAATCAATCTTACT 57.960 30.769 0.00 0.00 0.00 2.24
237 241 9.157104 TGTAACATCGCAAAATCAATCTTACTA 57.843 29.630 0.00 0.00 0.00 1.82
289 298 5.731686 GCACATGAAAATAGCCTGAGTTAGC 60.732 44.000 0.00 0.00 0.00 3.09
312 321 1.889829 GCGGTGCTCATATCTAGTCCT 59.110 52.381 0.00 0.00 0.00 3.85
315 324 4.072839 CGGTGCTCATATCTAGTCCTGTA 58.927 47.826 0.00 0.00 0.00 2.74
331 340 6.289064 AGTCCTGTAAACGAAAGAAAGACAT 58.711 36.000 0.00 0.00 0.00 3.06
337 346 4.635699 AACGAAAGAAAGACATAGGGGT 57.364 40.909 0.00 0.00 0.00 4.95
354 364 2.675844 GGGGTGTTTTCAAAAAGTGCAC 59.324 45.455 9.40 9.40 0.00 4.57
356 366 3.124466 GGGTGTTTTCAAAAAGTGCACAC 59.876 43.478 21.04 5.39 34.26 3.82
369 379 2.666190 CACACGACACCTGGCCAG 60.666 66.667 26.87 26.87 0.00 4.85
945 972 3.073735 CTGTCTGCTCGCTCCCCT 61.074 66.667 0.00 0.00 0.00 4.79
1160 1191 2.048503 GCGAGGGTACGTGCTTGT 60.049 61.111 3.01 0.00 35.59 3.16
1161 1192 2.092882 GCGAGGGTACGTGCTTGTC 61.093 63.158 3.01 0.00 35.59 3.18
1162 1193 1.585006 CGAGGGTACGTGCTTGTCT 59.415 57.895 3.01 0.00 0.00 3.41
1292 1354 2.261361 CGTCATCCACCTGTCGCA 59.739 61.111 0.00 0.00 0.00 5.10
1468 1530 3.305813 CCGTAACCTCAGCTACTTCAACA 60.306 47.826 0.00 0.00 0.00 3.33
1482 1544 4.965062 ACTTCAACAACAAGTACAACACG 58.035 39.130 0.00 0.00 32.08 4.49
1613 1695 2.998670 ACATCTTCAGTTCATGTCTGCG 59.001 45.455 13.07 8.54 33.48 5.18
1622 1704 0.673437 TCATGTCTGCGTGTCTGTCA 59.327 50.000 0.00 0.00 33.51 3.58
1823 1917 1.544246 GAAAAACGTGGCCCTATTGCT 59.456 47.619 0.00 0.00 0.00 3.91
2134 2431 3.401182 TGAAACATGGCAAATTCAAGGC 58.599 40.909 9.59 0.00 0.00 4.35
2196 2500 4.099881 ACTCAGCACATGTTCCATGTTTTT 59.900 37.500 7.11 0.00 0.00 1.94
2211 2515 2.514129 TTTTTGCAGGCTGCCTTCA 58.486 47.368 34.58 18.83 44.23 3.02
2308 2781 6.471233 TCCTTGTAGATTCTATGTCTGTGG 57.529 41.667 0.00 0.00 0.00 4.17
2309 2782 6.194967 TCCTTGTAGATTCTATGTCTGTGGA 58.805 40.000 0.00 0.00 0.00 4.02
2310 2783 6.841229 TCCTTGTAGATTCTATGTCTGTGGAT 59.159 38.462 0.00 0.00 0.00 3.41
2311 2784 7.014711 TCCTTGTAGATTCTATGTCTGTGGATC 59.985 40.741 0.00 0.00 0.00 3.36
2312 2785 6.656632 TGTAGATTCTATGTCTGTGGATCC 57.343 41.667 4.20 4.20 0.00 3.36
2313 2786 6.377080 TGTAGATTCTATGTCTGTGGATCCT 58.623 40.000 14.23 0.00 0.00 3.24
2314 2787 6.491745 TGTAGATTCTATGTCTGTGGATCCTC 59.508 42.308 14.23 10.39 0.00 3.71
2315 2788 5.462240 AGATTCTATGTCTGTGGATCCTCA 58.538 41.667 14.23 14.93 0.00 3.86
2316 2789 5.901853 AGATTCTATGTCTGTGGATCCTCAA 59.098 40.000 16.89 3.73 0.00 3.02
2317 2790 6.385176 AGATTCTATGTCTGTGGATCCTCAAA 59.615 38.462 16.89 1.56 0.00 2.69
2318 2791 6.373005 TTCTATGTCTGTGGATCCTCAAAA 57.627 37.500 16.89 6.26 0.00 2.44
2319 2792 6.373005 TCTATGTCTGTGGATCCTCAAAAA 57.627 37.500 16.89 0.00 0.00 1.94
2446 2919 1.943507 GCCTCTGCTCTTGTGTCCTTC 60.944 57.143 0.00 0.00 33.53 3.46
2461 2934 6.411376 TGTGTCCTTCTCTTGTTTACTTTGA 58.589 36.000 0.00 0.00 0.00 2.69
2488 2961 3.341823 ACGTATCTAGACCTGTGTTCGT 58.658 45.455 0.00 0.00 0.00 3.85
2489 2962 3.755378 ACGTATCTAGACCTGTGTTCGTT 59.245 43.478 0.00 0.00 0.00 3.85
2655 3130 1.528129 CAAGCTGGTCTGGAACTTCC 58.472 55.000 0.20 0.20 36.96 3.46
2761 3246 5.832595 TGTCTCATTGGTTGAATCCTTTTGA 59.167 36.000 0.00 0.00 32.78 2.69
2789 3274 7.557358 ACACATCTGCATAATATCTTTGACCAA 59.443 33.333 0.00 0.00 0.00 3.67
2791 3276 8.790718 ACATCTGCATAATATCTTTGACCAATC 58.209 33.333 0.00 0.00 0.00 2.67
2880 3384 9.463443 GCCCTGTTGATTAATTATATGTCAAAC 57.537 33.333 0.00 0.00 31.38 2.93
2911 3415 5.880054 ACTAATTCTTGTTGCGCTAATGT 57.120 34.783 9.73 0.00 0.00 2.71
2912 3416 5.631026 ACTAATTCTTGTTGCGCTAATGTG 58.369 37.500 9.73 0.00 0.00 3.21
2913 3417 4.503741 AATTCTTGTTGCGCTAATGTGT 57.496 36.364 9.73 0.00 0.00 3.72
2914 3418 3.980646 TTCTTGTTGCGCTAATGTGTT 57.019 38.095 9.73 0.00 0.00 3.32
3043 3586 4.475028 CGTTGCAGCACATATCTTTGAAA 58.525 39.130 0.00 0.00 0.00 2.69
3125 3673 6.876257 AGTTGTTTTCCATGTGTTTGCTTTTA 59.124 30.769 0.00 0.00 0.00 1.52
3232 3810 6.035217 GCTGCTTACTACCAGTTCTAACTAC 58.965 44.000 0.00 0.00 37.08 2.73
3237 3815 8.302438 GCTTACTACCAGTTCTAACTACTGAAA 58.698 37.037 4.66 0.00 44.52 2.69
3250 3828 0.316204 ACTGAAAGCATTGCAGGTGC 59.684 50.000 15.90 15.90 42.81 5.01
3316 3894 7.836183 AGCACATCTTACTAAAAATTCTGGGAT 59.164 33.333 0.00 0.00 0.00 3.85
3320 3898 9.618890 CATCTTACTAAAAATTCTGGGATCTCA 57.381 33.333 0.00 0.00 0.00 3.27
3421 3999 7.591057 TCTGAAATTGTTTGTTTCTAGCAATCG 59.409 33.333 0.00 0.00 36.71 3.34
3449 4027 1.563924 ACGTGTGAAGGGGCTATGTA 58.436 50.000 0.00 0.00 0.00 2.29
3641 4254 1.630878 AGAGGAAGTTGATTCGGCCTT 59.369 47.619 0.00 0.00 38.95 4.35
3670 4284 5.163343 ACCTTGTAGTGCTAAGTTCTGTTCA 60.163 40.000 0.00 0.00 0.00 3.18
3744 4367 4.040952 GGGCCTATCTCTAAAAGATCTGCA 59.959 45.833 0.84 0.00 43.90 4.41
3835 4458 3.044305 GCACTTCGTCAGCGCCTT 61.044 61.111 2.29 0.00 38.14 4.35
3898 4521 0.250295 TCCTGTTGCTCCAGTTTCGG 60.250 55.000 3.13 0.00 0.00 4.30
3946 4569 5.129320 ACATGTGCTGAAGTATCTGGTATCA 59.871 40.000 0.00 0.00 0.00 2.15
4071 4701 3.266510 TCAAGCTTTGATAGTCCGCAT 57.733 42.857 0.00 0.00 34.08 4.73
4072 4702 4.400529 TCAAGCTTTGATAGTCCGCATA 57.599 40.909 0.00 0.00 34.08 3.14
4145 4775 0.898320 TGCTCCTGCTACTTCAGTCC 59.102 55.000 0.00 0.00 40.48 3.85
4146 4776 1.190643 GCTCCTGCTACTTCAGTCCT 58.809 55.000 0.00 0.00 36.03 3.85
4270 4920 4.540824 GAAACTCCATTTGCTCAGTTGAC 58.459 43.478 0.00 0.00 0.00 3.18
4284 4934 5.629133 GCTCAGTTGACCCCTGATATTGTTA 60.629 44.000 0.00 0.00 38.23 2.41
4337 4990 9.294030 GCCTGCTTCATTGTTAATATAATATGC 57.706 33.333 0.00 0.00 0.00 3.14
4358 5011 3.489785 GCGATGTCCGTATTTCGATTTCT 59.510 43.478 0.00 0.00 42.86 2.52
4415 5068 2.223805 CCTGTCCTTTTGGCACTTGTTC 60.224 50.000 0.00 0.00 40.12 3.18
4416 5069 1.403679 TGTCCTTTTGGCACTTGTTCG 59.596 47.619 0.00 0.00 40.12 3.95
4425 5078 0.040958 GCACTTGTTCGCTGTGGAAG 60.041 55.000 0.00 0.00 32.85 3.46
4486 5147 8.097038 TCTGAGTCTGCATTTGTTATCTACTTT 58.903 33.333 0.00 0.00 0.00 2.66
4488 5149 8.506437 TGAGTCTGCATTTGTTATCTACTTTTG 58.494 33.333 0.00 0.00 0.00 2.44
4531 5200 6.360370 TGGTATATCCAGGATAGTTTCAGC 57.640 41.667 14.78 7.43 41.93 4.26
4556 5225 3.091545 ACATTTGCATTGTGGAGGGTAG 58.908 45.455 2.26 0.00 0.00 3.18
4667 5338 5.931441 AATGAAAGTCGGACTCTTTCTTG 57.069 39.130 18.43 0.00 46.08 3.02
4695 5366 2.749044 CAAGCCGCTGCCATCACT 60.749 61.111 0.00 0.00 38.69 3.41
4734 5405 5.647658 TGATCATTGTTAAGAAAGCATCGGT 59.352 36.000 0.00 0.00 0.00 4.69
4735 5406 5.545658 TCATTGTTAAGAAAGCATCGGTC 57.454 39.130 0.00 0.00 0.00 4.79
4736 5407 5.000591 TCATTGTTAAGAAAGCATCGGTCA 58.999 37.500 0.00 0.00 0.00 4.02
4737 5408 5.647658 TCATTGTTAAGAAAGCATCGGTCAT 59.352 36.000 0.00 0.00 0.00 3.06
4738 5409 6.821160 TCATTGTTAAGAAAGCATCGGTCATA 59.179 34.615 0.00 0.00 0.00 2.15
4739 5410 6.417191 TTGTTAAGAAAGCATCGGTCATAC 57.583 37.500 0.00 0.00 0.00 2.39
4794 5465 7.123997 TGAAAATATTGTCTATTGGGCACACAT 59.876 33.333 7.16 0.00 0.00 3.21
5081 5927 1.202891 GGGTGCACTTGGTAAAGAGGT 60.203 52.381 17.98 0.00 36.84 3.85
5098 5944 0.548510 GGTAGGAAGGAGGCATTGCT 59.451 55.000 8.82 0.00 32.66 3.91
5169 6030 6.681729 AGAAGAGGTGGTGTACTTAATTGA 57.318 37.500 0.00 0.00 0.00 2.57
5207 6068 1.196766 AACTTGGGGAGGGTCGGTAC 61.197 60.000 0.00 0.00 0.00 3.34
5272 6133 0.396417 TGGTGGTGTTTCCTTGTGGG 60.396 55.000 0.00 0.00 37.07 4.61
5333 6195 5.243507 TGATGTTGTTACTGATGCATGGTTT 59.756 36.000 2.46 0.00 0.00 3.27
5360 6223 2.208132 TGTAATGGCCACCGATTTGT 57.792 45.000 8.16 0.00 0.00 2.83
5399 6269 5.688807 AGTTATGGTCAAATATCAGCAGCT 58.311 37.500 0.00 0.00 0.00 4.24
5408 6278 7.540055 GGTCAAATATCAGCAGCTAATAAATGC 59.460 37.037 0.00 0.00 40.29 3.56
5767 6653 2.885266 GCCGGAAAAGAGAAGAGGTTTT 59.115 45.455 5.05 0.00 0.00 2.43
5864 6752 4.524318 CGCCTACCACGCCCGAAT 62.524 66.667 0.00 0.00 0.00 3.34
5887 6777 1.168714 GTTCCGAGATTTGCCTGCTT 58.831 50.000 0.00 0.00 0.00 3.91
6110 7000 2.424246 GCTCTACTCCAACTACTTCGCT 59.576 50.000 0.00 0.00 0.00 4.93
6111 7001 3.487879 GCTCTACTCCAACTACTTCGCTC 60.488 52.174 0.00 0.00 0.00 5.03
6112 7002 2.676839 TCTACTCCAACTACTTCGCTCG 59.323 50.000 0.00 0.00 0.00 5.03
6146 7036 1.787012 ACGACAAAGTATTTCGGCGT 58.213 45.000 6.85 0.00 42.77 5.68
6163 7053 0.030235 CGTCGTTATCGGATGAGCCA 59.970 55.000 0.00 0.00 37.69 4.75
6181 7071 2.365293 GCCAAAAGCTTTTCCTCAGGAA 59.635 45.455 21.45 0.34 38.07 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 9.171877 GGATGGAATTTGGTATTTAAATTTGCA 57.828 29.630 5.91 5.46 37.73 4.08
23 24 8.620416 GGGATGGAATTTGGTATTTAAATTTGC 58.380 33.333 5.91 0.00 37.73 3.68
24 25 9.678260 TGGGATGGAATTTGGTATTTAAATTTG 57.322 29.630 5.91 0.00 37.73 2.32
27 28 9.679661 GTTTGGGATGGAATTTGGTATTTAAAT 57.320 29.630 5.89 5.89 0.00 1.40
28 29 8.103935 GGTTTGGGATGGAATTTGGTATTTAAA 58.896 33.333 0.00 0.00 0.00 1.52
29 30 7.237679 TGGTTTGGGATGGAATTTGGTATTTAA 59.762 33.333 0.00 0.00 0.00 1.52
30 31 6.730977 TGGTTTGGGATGGAATTTGGTATTTA 59.269 34.615 0.00 0.00 0.00 1.40
31 32 5.549619 TGGTTTGGGATGGAATTTGGTATTT 59.450 36.000 0.00 0.00 0.00 1.40
32 33 5.097234 TGGTTTGGGATGGAATTTGGTATT 58.903 37.500 0.00 0.00 0.00 1.89
33 34 4.693420 TGGTTTGGGATGGAATTTGGTAT 58.307 39.130 0.00 0.00 0.00 2.73
34 35 4.093011 CTGGTTTGGGATGGAATTTGGTA 58.907 43.478 0.00 0.00 0.00 3.25
35 36 2.905736 CTGGTTTGGGATGGAATTTGGT 59.094 45.455 0.00 0.00 0.00 3.67
36 37 3.055891 GTCTGGTTTGGGATGGAATTTGG 60.056 47.826 0.00 0.00 0.00 3.28
37 38 3.367292 CGTCTGGTTTGGGATGGAATTTG 60.367 47.826 0.00 0.00 0.00 2.32
38 39 2.825532 CGTCTGGTTTGGGATGGAATTT 59.174 45.455 0.00 0.00 0.00 1.82
39 40 2.041081 TCGTCTGGTTTGGGATGGAATT 59.959 45.455 0.00 0.00 0.00 2.17
40 41 1.633432 TCGTCTGGTTTGGGATGGAAT 59.367 47.619 0.00 0.00 0.00 3.01
41 42 1.003118 CTCGTCTGGTTTGGGATGGAA 59.997 52.381 0.00 0.00 0.00 3.53
42 43 0.613260 CTCGTCTGGTTTGGGATGGA 59.387 55.000 0.00 0.00 0.00 3.41
43 44 0.613260 TCTCGTCTGGTTTGGGATGG 59.387 55.000 0.00 0.00 0.00 3.51
44 45 2.472695 TTCTCGTCTGGTTTGGGATG 57.527 50.000 0.00 0.00 0.00 3.51
45 46 3.721087 ATTTCTCGTCTGGTTTGGGAT 57.279 42.857 0.00 0.00 0.00 3.85
46 47 3.502123 AATTTCTCGTCTGGTTTGGGA 57.498 42.857 0.00 0.00 0.00 4.37
47 48 3.821033 AGAAATTTCTCGTCTGGTTTGGG 59.179 43.478 15.11 0.00 29.94 4.12
48 49 5.035784 GAGAAATTTCTCGTCTGGTTTGG 57.964 43.478 27.70 0.00 43.63 3.28
104 105 9.349713 AGATAGAAAAATGTCCGCCAAAATATA 57.650 29.630 0.00 0.00 0.00 0.86
105 106 8.137437 CAGATAGAAAAATGTCCGCCAAAATAT 58.863 33.333 0.00 0.00 0.00 1.28
106 107 7.122055 ACAGATAGAAAAATGTCCGCCAAAATA 59.878 33.333 0.00 0.00 0.00 1.40
107 108 6.071391 ACAGATAGAAAAATGTCCGCCAAAAT 60.071 34.615 0.00 0.00 0.00 1.82
108 109 5.242838 ACAGATAGAAAAATGTCCGCCAAAA 59.757 36.000 0.00 0.00 0.00 2.44
109 110 4.764823 ACAGATAGAAAAATGTCCGCCAAA 59.235 37.500 0.00 0.00 0.00 3.28
110 111 4.331968 ACAGATAGAAAAATGTCCGCCAA 58.668 39.130 0.00 0.00 0.00 4.52
111 112 3.950397 ACAGATAGAAAAATGTCCGCCA 58.050 40.909 0.00 0.00 0.00 5.69
112 113 4.494199 CGAACAGATAGAAAAATGTCCGCC 60.494 45.833 0.00 0.00 0.00 6.13
113 114 4.328983 TCGAACAGATAGAAAAATGTCCGC 59.671 41.667 0.00 0.00 0.00 5.54
114 115 6.241385 GTTCGAACAGATAGAAAAATGTCCG 58.759 40.000 23.12 0.00 0.00 4.79
115 116 6.543736 GGTTCGAACAGATAGAAAAATGTCC 58.456 40.000 28.24 2.29 0.00 4.02
116 117 6.241385 CGGTTCGAACAGATAGAAAAATGTC 58.759 40.000 28.24 5.43 0.00 3.06
117 118 5.121768 CCGGTTCGAACAGATAGAAAAATGT 59.878 40.000 28.24 0.00 0.00 2.71
118 119 5.350365 TCCGGTTCGAACAGATAGAAAAATG 59.650 40.000 28.24 8.78 0.00 2.32
119 120 5.484715 TCCGGTTCGAACAGATAGAAAAAT 58.515 37.500 28.24 0.00 0.00 1.82
120 121 4.885413 TCCGGTTCGAACAGATAGAAAAA 58.115 39.130 28.24 0.00 0.00 1.94
121 122 4.524316 TCCGGTTCGAACAGATAGAAAA 57.476 40.909 28.24 3.77 0.00 2.29
122 123 4.430007 CATCCGGTTCGAACAGATAGAAA 58.570 43.478 28.24 8.01 0.00 2.52
123 124 3.181479 CCATCCGGTTCGAACAGATAGAA 60.181 47.826 28.24 9.57 0.00 2.10
124 125 2.361119 CCATCCGGTTCGAACAGATAGA 59.639 50.000 28.24 17.27 0.00 1.98
125 126 2.361119 TCCATCCGGTTCGAACAGATAG 59.639 50.000 28.24 20.70 0.00 2.08
126 127 2.361119 CTCCATCCGGTTCGAACAGATA 59.639 50.000 28.24 16.31 0.00 1.98
127 128 1.137086 CTCCATCCGGTTCGAACAGAT 59.863 52.381 28.24 24.21 0.00 2.90
128 129 0.530744 CTCCATCCGGTTCGAACAGA 59.469 55.000 28.24 23.18 0.00 3.41
129 130 0.246635 ACTCCATCCGGTTCGAACAG 59.753 55.000 28.24 24.02 0.00 3.16
130 131 0.037697 CACTCCATCCGGTTCGAACA 60.038 55.000 28.24 9.90 0.00 3.18
131 132 1.359459 GCACTCCATCCGGTTCGAAC 61.359 60.000 20.14 20.14 0.00 3.95
132 133 1.079405 GCACTCCATCCGGTTCGAA 60.079 57.895 0.00 0.00 0.00 3.71
133 134 0.681887 TAGCACTCCATCCGGTTCGA 60.682 55.000 0.00 0.00 0.00 3.71
134 135 0.249073 CTAGCACTCCATCCGGTTCG 60.249 60.000 0.00 0.00 0.00 3.95
135 136 0.530870 GCTAGCACTCCATCCGGTTC 60.531 60.000 10.63 0.00 0.00 3.62
136 137 0.978146 AGCTAGCACTCCATCCGGTT 60.978 55.000 18.83 0.00 0.00 4.44
137 138 1.381872 AGCTAGCACTCCATCCGGT 60.382 57.895 18.83 0.00 0.00 5.28
138 139 1.112315 AGAGCTAGCACTCCATCCGG 61.112 60.000 18.83 0.00 37.39 5.14
139 140 0.313672 GAGAGCTAGCACTCCATCCG 59.686 60.000 26.35 0.00 37.39 4.18
145 146 1.133792 AGGAGAGGAGAGCTAGCACTC 60.134 57.143 28.04 28.04 36.91 3.51
146 147 0.926293 AGGAGAGGAGAGCTAGCACT 59.074 55.000 18.83 16.86 0.00 4.40
147 148 1.681264 GAAGGAGAGGAGAGCTAGCAC 59.319 57.143 18.83 11.32 0.00 4.40
148 149 1.568597 AGAAGGAGAGGAGAGCTAGCA 59.431 52.381 18.83 0.00 0.00 3.49
149 150 2.364972 AGAAGGAGAGGAGAGCTAGC 57.635 55.000 6.62 6.62 0.00 3.42
150 151 5.048846 ACTTAGAAGGAGAGGAGAGCTAG 57.951 47.826 0.00 0.00 0.00 3.42
151 152 5.192923 AGAACTTAGAAGGAGAGGAGAGCTA 59.807 44.000 0.00 0.00 0.00 3.32
152 153 4.017499 AGAACTTAGAAGGAGAGGAGAGCT 60.017 45.833 0.00 0.00 0.00 4.09
153 154 4.278310 AGAACTTAGAAGGAGAGGAGAGC 58.722 47.826 0.00 0.00 0.00 4.09
154 155 7.116736 AGTTAGAACTTAGAAGGAGAGGAGAG 58.883 42.308 0.00 0.00 35.21 3.20
155 156 7.034967 AGTTAGAACTTAGAAGGAGAGGAGA 57.965 40.000 0.00 0.00 35.21 3.71
156 157 6.887545 TGAGTTAGAACTTAGAAGGAGAGGAG 59.112 42.308 0.00 0.00 39.88 3.69
157 158 6.791371 TGAGTTAGAACTTAGAAGGAGAGGA 58.209 40.000 0.00 0.00 39.88 3.71
158 159 7.469537 TTGAGTTAGAACTTAGAAGGAGAGG 57.530 40.000 0.00 0.00 39.88 3.69
159 160 9.936759 AATTTGAGTTAGAACTTAGAAGGAGAG 57.063 33.333 0.00 0.00 39.88 3.20
265 274 4.708726 AACTCAGGCTATTTTCATGTGC 57.291 40.909 0.00 0.00 0.00 4.57
271 280 4.553547 CGCATGCTAACTCAGGCTATTTTC 60.554 45.833 17.13 0.00 41.12 2.29
289 298 3.249091 GACTAGATATGAGCACCGCATG 58.751 50.000 0.00 0.00 0.00 4.06
300 309 9.582431 TTTCTTTCGTTTACAGGACTAGATATG 57.418 33.333 0.00 0.00 0.00 1.78
312 321 5.935789 CCCCTATGTCTTTCTTTCGTTTACA 59.064 40.000 0.00 0.00 0.00 2.41
315 324 4.760204 CACCCCTATGTCTTTCTTTCGTTT 59.240 41.667 0.00 0.00 0.00 3.60
331 340 3.769844 TGCACTTTTTGAAAACACCCCTA 59.230 39.130 0.00 0.00 0.00 3.53
337 346 3.670991 GTCGTGTGCACTTTTTGAAAACA 59.329 39.130 19.41 0.00 0.00 2.83
354 364 4.320456 AGCTGGCCAGGTGTCGTG 62.320 66.667 35.74 8.45 37.82 4.35
369 379 4.351054 CACCCCACTCCACCCAGC 62.351 72.222 0.00 0.00 0.00 4.85
773 791 2.727544 CCAAACCCCTGTGCGTTG 59.272 61.111 0.00 0.00 0.00 4.10
907 930 6.648192 ACAGAATTTGTTTGTTTTGGATGGA 58.352 32.000 0.00 0.00 36.31 3.41
945 972 4.440829 GGCGGGCTGGGGATTTGA 62.441 66.667 0.00 0.00 0.00 2.69
1160 1191 1.320512 GGGGTGGGGATTAGGGAGA 59.679 63.158 0.00 0.00 0.00 3.71
1161 1192 1.774631 GGGGGTGGGGATTAGGGAG 60.775 68.421 0.00 0.00 0.00 4.30
1162 1193 2.276899 AGGGGGTGGGGATTAGGGA 61.277 63.158 0.00 0.00 0.00 4.20
1323 1385 3.129502 CGGGAGACGTAGGCGACA 61.130 66.667 0.00 0.00 42.00 4.35
1449 1511 5.284861 TGTTGTTGAAGTAGCTGAGGTTA 57.715 39.130 0.00 0.00 0.00 2.85
1468 1530 1.860326 GTACCGCGTGTTGTACTTGTT 59.140 47.619 13.85 0.00 35.55 2.83
1482 1544 2.092882 GTCGTGCTTGAGGTACCGC 61.093 63.158 8.97 8.97 0.00 5.68
1613 1695 4.510038 AATTGCAGGAATTGACAGACAC 57.490 40.909 0.00 0.00 32.69 3.67
1622 1704 4.354893 TGGCTTGAAAATTGCAGGAATT 57.645 36.364 0.00 0.00 35.65 2.17
1823 1917 4.545706 GCATCATCGGACCGCCCA 62.546 66.667 9.66 0.00 34.14 5.36
1830 1924 2.140138 ATCGTGGGGCATCATCGGA 61.140 57.895 0.00 0.00 0.00 4.55
1998 2276 2.521126 GGTACCTAGGCCAAGCAAAAA 58.479 47.619 9.30 0.00 0.00 1.94
1999 2277 1.612199 CGGTACCTAGGCCAAGCAAAA 60.612 52.381 9.30 0.00 0.00 2.44
2000 2278 0.035820 CGGTACCTAGGCCAAGCAAA 60.036 55.000 9.30 0.00 0.00 3.68
2134 2431 0.457851 AAGAGCAGAATCGAGGGACG 59.542 55.000 0.00 0.00 44.09 4.79
2196 2500 2.042259 CGATGAAGGCAGCCTGCAA 61.042 57.895 27.23 10.12 43.33 4.08
2211 2515 0.452184 ATTCGTGTCTGCGAGTCGAT 59.548 50.000 18.61 0.00 42.10 3.59
2320 2793 9.739276 TTACCATCACAGACATAGAATCTTTTT 57.261 29.630 0.00 0.00 0.00 1.94
2321 2794 9.739276 TTTACCATCACAGACATAGAATCTTTT 57.261 29.630 0.00 0.00 0.00 2.27
2322 2795 9.739276 TTTTACCATCACAGACATAGAATCTTT 57.261 29.630 0.00 0.00 0.00 2.52
2323 2796 9.388506 CTTTTACCATCACAGACATAGAATCTT 57.611 33.333 0.00 0.00 0.00 2.40
2324 2797 7.497249 GCTTTTACCATCACAGACATAGAATCT 59.503 37.037 0.00 0.00 0.00 2.40
2325 2798 7.254932 GGCTTTTACCATCACAGACATAGAATC 60.255 40.741 0.00 0.00 0.00 2.52
2326 2799 6.543831 GGCTTTTACCATCACAGACATAGAAT 59.456 38.462 0.00 0.00 0.00 2.40
2327 2800 5.880332 GGCTTTTACCATCACAGACATAGAA 59.120 40.000 0.00 0.00 0.00 2.10
2328 2801 5.045942 TGGCTTTTACCATCACAGACATAGA 60.046 40.000 0.00 0.00 33.75 1.98
2329 2802 5.185454 TGGCTTTTACCATCACAGACATAG 58.815 41.667 0.00 0.00 33.75 2.23
2330 2803 5.172687 TGGCTTTTACCATCACAGACATA 57.827 39.130 0.00 0.00 33.75 2.29
2331 2804 4.032960 TGGCTTTTACCATCACAGACAT 57.967 40.909 0.00 0.00 33.75 3.06
2332 2805 3.500448 TGGCTTTTACCATCACAGACA 57.500 42.857 0.00 0.00 33.75 3.41
2343 2816 6.143278 CCAAAAACAGTAACGATGGCTTTTAC 59.857 38.462 0.00 0.00 0.00 2.01
2461 2934 7.487189 CGAACACAGGTCTAGATACGTAAAATT 59.513 37.037 0.00 0.00 0.00 1.82
2488 2961 9.184523 CCAAATATATCTGGGTTGACAGTAAAA 57.815 33.333 0.00 0.00 39.48 1.52
2489 2962 7.284489 GCCAAATATATCTGGGTTGACAGTAAA 59.716 37.037 7.20 0.00 39.48 2.01
2655 3130 2.887151 ACCTTCCTTCCCACTTGATG 57.113 50.000 0.00 0.00 0.00 3.07
2761 3246 7.012704 GGTCAAAGATATTATGCAGATGTGTGT 59.987 37.037 0.00 0.00 0.00 3.72
2789 3274 5.015178 TGGAAGGGGAATAAACTGTTCAGAT 59.985 40.000 6.83 0.00 0.00 2.90
2791 3276 4.662278 TGGAAGGGGAATAAACTGTTCAG 58.338 43.478 0.00 0.00 0.00 3.02
2844 3348 2.672961 TCAACAGGGCTATTGTCTCG 57.327 50.000 0.00 0.00 0.00 4.04
2880 3384 6.684555 GCGCAACAAGAATTAGTTCAATCTAG 59.315 38.462 0.30 0.00 36.79 2.43
2885 3389 4.829064 AGCGCAACAAGAATTAGTTCAA 57.171 36.364 11.47 0.00 36.79 2.69
3043 3586 3.334583 ACATGTTTCTACCGTGCATCT 57.665 42.857 0.00 0.00 0.00 2.90
3147 3717 1.067295 ATCAAGCCTGACAGGGACAA 58.933 50.000 23.09 0.00 35.37 3.18
3193 3763 2.517959 AGCAGCCAAGCACTAATGAAA 58.482 42.857 0.00 0.00 36.85 2.69
3196 3766 3.012518 AGTAAGCAGCCAAGCACTAATG 58.987 45.455 0.00 0.00 36.85 1.90
3232 3810 3.117589 GCACCTGCAATGCTTTCAG 57.882 52.632 13.99 0.00 40.08 3.02
3316 3894 4.338012 ACCTGCATTTGTCAATGATGAGA 58.662 39.130 2.06 0.00 42.35 3.27
3320 3898 7.879160 ACAAAATTACCTGCATTTGTCAATGAT 59.121 29.630 7.80 0.00 40.85 2.45
3421 3999 1.199097 CCCTTCACACGTACATTTGGC 59.801 52.381 0.00 0.00 0.00 4.52
3449 4027 1.327303 AACCACGGCACAACAATGAT 58.673 45.000 0.00 0.00 0.00 2.45
3582 4191 7.524717 ACTTTGGCTAGTATGTTTTCAATGT 57.475 32.000 0.00 0.00 0.00 2.71
3641 4254 7.097192 CAGAACTTAGCACTACAAGGTATTCA 58.903 38.462 0.00 0.00 0.00 2.57
3670 4284 3.286329 ACGAACCAAACTGTAAGGGTT 57.714 42.857 9.55 9.55 45.82 4.11
3744 4367 3.243602 GGGCAAAATGTTCAAACGGTACT 60.244 43.478 0.00 0.00 0.00 2.73
3898 4521 1.068741 CAAGGTACCGAGCATACTCCC 59.931 57.143 6.18 0.00 40.03 4.30
3946 4569 2.467880 ACCTGGATTAGTCACCGATGT 58.532 47.619 0.00 0.00 0.00 3.06
3983 4606 5.580297 GGAAGTTTTTCATGTGCAGAAAACA 59.420 36.000 10.82 0.00 42.68 2.83
4040 4665 4.209452 TCAAAGCTTGATTGTTGACGTC 57.791 40.909 9.11 9.11 34.08 4.34
4146 4776 0.107263 TGTCAACTTCACTGCCTGCA 60.107 50.000 0.00 0.00 0.00 4.41
4284 4934 9.950496 ACTTGACTATATTTGTTGTTCTCTGAT 57.050 29.630 0.00 0.00 0.00 2.90
4337 4990 5.637104 AAGAAATCGAAATACGGACATCG 57.363 39.130 0.00 0.00 45.88 3.84
4358 5011 5.007682 GGCCACCTCTATAACTGAACAAAA 58.992 41.667 0.00 0.00 0.00 2.44
4425 5078 6.818644 TCTTCCACAATGTTCAGAAGCTATAC 59.181 38.462 10.88 0.00 35.11 1.47
4439 5092 6.095860 TCAGAAAAGGCATATCTTCCACAATG 59.904 38.462 0.00 0.00 0.00 2.82
4486 5147 6.183360 ACCATATGCAAAAAGAAGGAACACAA 60.183 34.615 0.00 0.00 0.00 3.33
4488 5149 5.783111 ACCATATGCAAAAAGAAGGAACAC 58.217 37.500 0.00 0.00 0.00 3.32
4531 5200 3.119388 CCCTCCACAATGCAAATGTAGTG 60.119 47.826 8.04 0.00 0.00 2.74
4556 5225 3.988379 TTCAGTGGAAACATGAACAGC 57.012 42.857 0.00 0.00 46.14 4.40
4794 5465 7.074653 ACCTTCTGGACTCAAATGTTACTTA 57.925 36.000 0.00 0.00 37.04 2.24
4836 5510 2.359850 GCATGCTTCCGTCCACCA 60.360 61.111 11.37 0.00 0.00 4.17
5081 5927 3.456380 AAAAGCAATGCCTCCTTCCTA 57.544 42.857 0.00 0.00 0.00 2.94
5272 6133 1.024271 TGTGTCTTCAACCAGCAAGC 58.976 50.000 0.00 0.00 0.00 4.01
5333 6195 1.618345 GGTGGCCATTACATGAACCCA 60.618 52.381 9.72 0.00 0.00 4.51
5360 6223 8.977412 TGACCATAACTCATCACTGTCTATAAA 58.023 33.333 0.00 0.00 0.00 1.40
5399 6269 5.295540 TGCTCTAACACGCATGCATTTATTA 59.704 36.000 19.57 7.49 0.00 0.98
5408 6278 1.394917 GGAGTTGCTCTAACACGCATG 59.605 52.381 0.00 0.00 41.88 4.06
5447 6318 2.227194 CGTAAAAAGTTGCCTGGAGGT 58.773 47.619 0.00 0.00 37.57 3.85
5726 6611 1.662686 GGGGAATGGCCTATCTAGCT 58.337 55.000 3.32 0.00 36.66 3.32
5851 6739 2.114488 AACACCATTCGGGCGTGGTA 62.114 55.000 0.00 0.00 46.62 3.25
5862 6750 1.818674 GGCAAATCTCGGAACACCATT 59.181 47.619 0.00 0.00 0.00 3.16
5864 6752 0.400213 AGGCAAATCTCGGAACACCA 59.600 50.000 0.00 0.00 0.00 4.17
5887 6777 1.613317 ATCGTCCGAGTCCATTGCCA 61.613 55.000 0.00 0.00 0.00 4.92
5922 6812 2.604686 TTCCTCCTCCAGCAGCGT 60.605 61.111 0.00 0.00 0.00 5.07
5995 6885 0.534877 TTCATTGCTCGTGTGCAGGT 60.535 50.000 0.00 0.00 44.27 4.00
6001 6891 0.238289 CGGCTTTTCATTGCTCGTGT 59.762 50.000 0.00 0.00 0.00 4.49
6003 6893 1.210155 GCGGCTTTTCATTGCTCGT 59.790 52.632 0.00 0.00 0.00 4.18
6036 6926 1.451387 CTTTTATCTGCCCCGGCGT 60.451 57.895 6.01 0.00 45.51 5.68
6050 6940 1.335872 CGATGCCGGTTCTTTGCTTTT 60.336 47.619 1.90 0.00 0.00 2.27
6146 7036 2.971660 TTTGGCTCATCCGATAACGA 57.028 45.000 0.00 0.00 42.66 3.85
6163 7053 4.895297 TCACATTCCTGAGGAAAAGCTTTT 59.105 37.500 24.08 24.08 45.41 2.27


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

AutoCloner maintained by Alex Coulton.