Multiple sequence alignment - TraesCS2A01G551500

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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 TraesCS2A01G551500 chr2A 100.000 2360 0 0 1 2360 758281642 758279283 0.000000e+00 4359.0
1 TraesCS2A01G551500 chr2A 97.959 49 1 0 1499 1547 758280097 758280049 4.180000e-13 86.1
2 TraesCS2A01G551500 chr2A 97.959 49 1 0 1546 1594 758280144 758280096 4.180000e-13 86.1
3 TraesCS2A01G551500 chr2D 87.280 739 50 21 697 1396 627824204 627823471 0.000000e+00 804.0
4 TraesCS2A01G551500 chr2D 93.103 348 17 3 1546 1891 627823072 627822730 9.740000e-139 503.0
5 TraesCS2A01G551500 chr2D 92.118 203 13 2 273 472 627826903 627826701 1.380000e-72 283.0
6 TraesCS2A01G551500 chr2D 89.423 208 12 5 1886 2090 627822677 627822477 1.080000e-63 254.0
7 TraesCS2A01G551500 chr2D 92.701 137 8 2 5 140 627832890 627832755 1.850000e-46 196.0
8 TraesCS2A01G551500 chr2D 86.905 168 11 4 471 627 627825514 627825347 6.700000e-41 178.0
9 TraesCS2A01G551500 chr2D 86.905 168 11 4 471 627 627909410 627909577 6.700000e-41 178.0
10 TraesCS2A01G551500 chr2D 85.380 171 4 8 1398 1547 627823194 627823024 8.730000e-35 158.0
11 TraesCS2A01G551500 chr2D 85.315 143 11 5 2161 2301 627820272 627820138 3.160000e-29 139.0
12 TraesCS2A01G551500 chr2D 100.000 29 0 0 1398 1426 627822921 627822893 1.000000e-03 54.7
13 TraesCS2A01G551500 chr2B 85.795 704 49 25 729 1397 770072066 770071379 0.000000e+00 699.0
14 TraesCS2A01G551500 chr2B 86.975 476 39 12 17 472 770086116 770085644 4.500000e-142 514.0
15 TraesCS2A01G551500 chr2B 90.379 343 25 4 1556 1891 770071245 770070904 5.990000e-121 444.0
16 TraesCS2A01G551500 chr2B 89.286 168 7 1 471 627 770655008 770655175 1.430000e-47 200.0
17 TraesCS2A01G551500 chr2B 82.213 253 17 12 1886 2134 770070849 770070621 2.390000e-45 193.0
18 TraesCS2A01G551500 chr2B 92.308 130 8 2 341 469 770649366 770649494 1.440000e-42 183.0
19 TraesCS2A01G551500 chr2B 85.955 178 15 5 2161 2336 770067886 770067717 5.180000e-42 182.0
20 TraesCS2A01G551500 chr2B 86.471 170 10 5 471 627 770072312 770072143 8.670000e-40 174.0
21 TraesCS2A01G551500 chr2B 85.799 169 13 1 470 627 770611170 770611338 4.030000e-38 169.0
22 TraesCS2A01G551500 chr2B 79.630 162 20 8 471 619 770671232 770671393 1.150000e-18 104.0
23 TraesCS2A01G551500 chr2B 95.000 40 1 1 1509 1547 770071245 770071206 7.040000e-06 62.1
24 TraesCS2A01G551500 chr7A 86.957 345 30 8 1041 1373 271723929 271723588 7.960000e-100 374.0
25 TraesCS2A01G551500 chr7A 86.992 123 13 2 1572 1692 643434554 643434433 4.090000e-28 135.0
26 TraesCS2A01G551500 chr7D 86.919 344 30 8 1058 1386 249485517 249485860 2.860000e-99 372.0
27 TraesCS2A01G551500 chr7D 86.861 137 12 1 1032 1162 249485404 249485540 5.260000e-32 148.0
28 TraesCS2A01G551500 chr7D 86.822 129 11 5 1566 1691 557907831 557907706 3.160000e-29 139.0
29 TraesCS2A01G551500 chr7D 85.271 129 15 3 1561 1687 509198904 509199030 1.900000e-26 130.0
30 TraesCS2A01G551500 chr7B 87.591 137 11 4 1032 1162 226441364 226441500 1.130000e-33 154.0
31 TraesCS2A01G551500 chr7B 86.614 127 13 3 1566 1692 606041046 606040924 1.140000e-28 137.0
32 TraesCS2A01G551500 chr4B 84.028 144 21 2 1546 1687 605389834 605389977 1.140000e-28 137.0
33 TraesCS2A01G551500 chr4B 95.082 61 3 0 1483 1543 605389818 605389878 1.930000e-16 97.1


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 TraesCS2A01G551500 chr2A 758279283 758281642 2359 True 1510.4000 4359 98.639333 1 2360 3 chr2A.!!$R1 2359
1 TraesCS2A01G551500 chr2D 627820138 627826903 6765 True 296.7125 804 89.940500 273 2301 8 chr2D.!!$R2 2028
2 TraesCS2A01G551500 chr2B 770067717 770072312 4595 True 292.3500 699 87.635500 471 2336 6 chr2B.!!$R2 1865

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
661 1866 0.022106 CGACGAACGAAATCGAGCAC 59.978 55.0 10.16 0.0 45.48 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 4610 0.108207 CTCTGGCCCAGATGATGTCC 59.892 60.0 15.2 0.0 39.92 4.02 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.123804 GTGTGCCATGTCGATAAGTAGG 58.876 50.000 0.00 0.00 0.00 3.18
22 23 2.135933 GTGCCATGTCGATAAGTAGGC 58.864 52.381 10.05 10.05 40.93 3.93
23 24 2.526304 GCCATGTCGATAAGTAGGCA 57.474 50.000 11.47 0.00 40.29 4.75
24 25 2.135933 GCCATGTCGATAAGTAGGCAC 58.864 52.381 11.47 0.00 40.29 5.01
25 26 2.755650 CCATGTCGATAAGTAGGCACC 58.244 52.381 0.00 0.00 0.00 5.01
26 27 2.102420 CCATGTCGATAAGTAGGCACCA 59.898 50.000 0.00 0.00 0.00 4.17
27 28 3.244215 CCATGTCGATAAGTAGGCACCAT 60.244 47.826 0.00 0.00 0.00 3.55
28 29 3.728076 TGTCGATAAGTAGGCACCATC 57.272 47.619 0.00 0.00 0.00 3.51
29 30 2.364324 TGTCGATAAGTAGGCACCATCC 59.636 50.000 0.00 0.00 0.00 3.51
30 31 2.364324 GTCGATAAGTAGGCACCATCCA 59.636 50.000 0.00 0.00 0.00 3.41
31 32 2.364324 TCGATAAGTAGGCACCATCCAC 59.636 50.000 0.00 0.00 0.00 4.02
32 33 2.102420 CGATAAGTAGGCACCATCCACA 59.898 50.000 0.00 0.00 0.00 4.17
33 34 3.467803 GATAAGTAGGCACCATCCACAC 58.532 50.000 0.00 0.00 0.00 3.82
34 35 1.362224 AAGTAGGCACCATCCACACT 58.638 50.000 0.00 0.00 0.00 3.55
35 36 1.362224 AGTAGGCACCATCCACACTT 58.638 50.000 0.00 0.00 0.00 3.16
36 37 1.279271 AGTAGGCACCATCCACACTTC 59.721 52.381 0.00 0.00 0.00 3.01
37 38 1.279271 GTAGGCACCATCCACACTTCT 59.721 52.381 0.00 0.00 0.00 2.85
38 39 0.773644 AGGCACCATCCACACTTCTT 59.226 50.000 0.00 0.00 0.00 2.52
39 40 1.145738 AGGCACCATCCACACTTCTTT 59.854 47.619 0.00 0.00 0.00 2.52
40 41 1.963515 GGCACCATCCACACTTCTTTT 59.036 47.619 0.00 0.00 0.00 2.27
41 42 2.365293 GGCACCATCCACACTTCTTTTT 59.635 45.455 0.00 0.00 0.00 1.94
42 43 3.383761 GCACCATCCACACTTCTTTTTG 58.616 45.455 0.00 0.00 0.00 2.44
43 44 3.068024 GCACCATCCACACTTCTTTTTGA 59.932 43.478 0.00 0.00 0.00 2.69
44 45 4.441356 GCACCATCCACACTTCTTTTTGAA 60.441 41.667 0.00 0.00 0.00 2.69
63 64 4.659172 CCCTGGGCCGCAGAACAA 62.659 66.667 19.43 0.00 0.00 2.83
64 65 2.361610 CCTGGGCCGCAGAACAAT 60.362 61.111 19.43 0.00 0.00 2.71
65 66 1.978617 CCTGGGCCGCAGAACAATT 60.979 57.895 19.43 0.00 0.00 2.32
66 67 1.213537 CTGGGCCGCAGAACAATTG 59.786 57.895 14.21 3.24 0.00 2.32
67 68 1.526575 CTGGGCCGCAGAACAATTGT 61.527 55.000 14.21 4.92 0.00 2.71
68 69 1.112315 TGGGCCGCAGAACAATTGTT 61.112 50.000 23.49 23.49 41.64 2.83
79 80 3.751479 AACAATTGTTCTTTGGGGCTC 57.249 42.857 18.13 0.00 31.64 4.70
80 81 2.962859 ACAATTGTTCTTTGGGGCTCT 58.037 42.857 4.92 0.00 0.00 4.09
81 82 2.629617 ACAATTGTTCTTTGGGGCTCTG 59.370 45.455 4.92 0.00 0.00 3.35
82 83 2.892852 CAATTGTTCTTTGGGGCTCTGA 59.107 45.455 0.00 0.00 0.00 3.27
83 84 2.276732 TTGTTCTTTGGGGCTCTGAG 57.723 50.000 0.00 0.00 0.00 3.35
84 85 0.250901 TGTTCTTTGGGGCTCTGAGC 60.251 55.000 21.17 21.17 41.46 4.26
85 86 0.037447 GTTCTTTGGGGCTCTGAGCT 59.963 55.000 27.09 0.00 41.99 4.09
86 87 0.037303 TTCTTTGGGGCTCTGAGCTG 59.963 55.000 27.09 11.77 41.99 4.24
87 88 1.378250 CTTTGGGGCTCTGAGCTGG 60.378 63.158 27.09 9.02 41.99 4.85
88 89 3.574074 TTTGGGGCTCTGAGCTGGC 62.574 63.158 27.09 12.15 41.99 4.85
90 91 3.726144 GGGGCTCTGAGCTGGCTT 61.726 66.667 27.09 0.00 41.99 4.35
91 92 2.438075 GGGCTCTGAGCTGGCTTG 60.438 66.667 27.09 0.00 41.99 4.01
92 93 2.667418 GGCTCTGAGCTGGCTTGA 59.333 61.111 27.09 0.00 41.99 3.02
93 94 1.224039 GGCTCTGAGCTGGCTTGAT 59.776 57.895 27.09 0.00 41.99 2.57
94 95 0.467384 GGCTCTGAGCTGGCTTGATA 59.533 55.000 27.09 0.00 41.99 2.15
95 96 1.540797 GGCTCTGAGCTGGCTTGATAG 60.541 57.143 27.09 0.00 41.99 2.08
96 97 2.140975 GCTCTGAGCTGGCTTGATAGC 61.141 57.143 21.93 1.19 41.60 2.97
162 163 6.992063 ACTGATGCTAAATGTCTTAGTTGG 57.008 37.500 0.00 0.00 0.00 3.77
163 164 6.476378 ACTGATGCTAAATGTCTTAGTTGGT 58.524 36.000 0.00 0.00 0.00 3.67
164 165 6.942576 ACTGATGCTAAATGTCTTAGTTGGTT 59.057 34.615 0.00 0.00 0.00 3.67
165 166 7.448469 ACTGATGCTAAATGTCTTAGTTGGTTT 59.552 33.333 0.00 0.00 0.00 3.27
166 167 7.592938 TGATGCTAAATGTCTTAGTTGGTTTG 58.407 34.615 0.00 0.00 0.00 2.93
167 168 7.446931 TGATGCTAAATGTCTTAGTTGGTTTGA 59.553 33.333 0.00 0.00 0.00 2.69
168 169 7.575414 TGCTAAATGTCTTAGTTGGTTTGAA 57.425 32.000 0.00 0.00 0.00 2.69
169 170 8.001881 TGCTAAATGTCTTAGTTGGTTTGAAA 57.998 30.769 0.00 0.00 0.00 2.69
170 171 8.637986 TGCTAAATGTCTTAGTTGGTTTGAAAT 58.362 29.630 0.00 0.00 0.00 2.17
171 172 9.476202 GCTAAATGTCTTAGTTGGTTTGAAATT 57.524 29.630 0.00 0.00 0.00 1.82
174 175 9.533253 AAATGTCTTAGTTGGTTTGAAATTCAG 57.467 29.630 0.00 0.00 0.00 3.02
175 176 7.873719 TGTCTTAGTTGGTTTGAAATTCAGA 57.126 32.000 0.00 0.00 0.00 3.27
176 177 8.287439 TGTCTTAGTTGGTTTGAAATTCAGAA 57.713 30.769 0.00 0.00 0.00 3.02
177 178 8.744652 TGTCTTAGTTGGTTTGAAATTCAGAAA 58.255 29.630 0.00 0.00 0.00 2.52
178 179 9.581099 GTCTTAGTTGGTTTGAAATTCAGAAAA 57.419 29.630 0.00 0.00 0.00 2.29
209 210 5.989551 GTCACATGGACTTGCAAATTTTT 57.010 34.783 0.00 0.00 43.46 1.94
210 211 5.977731 GTCACATGGACTTGCAAATTTTTC 58.022 37.500 0.00 0.00 43.46 2.29
211 212 5.754890 GTCACATGGACTTGCAAATTTTTCT 59.245 36.000 0.00 0.00 43.46 2.52
212 213 6.258507 GTCACATGGACTTGCAAATTTTTCTT 59.741 34.615 0.00 0.00 43.46 2.52
213 214 7.437862 GTCACATGGACTTGCAAATTTTTCTTA 59.562 33.333 0.00 0.00 43.46 2.10
214 215 7.984050 TCACATGGACTTGCAAATTTTTCTTAA 59.016 29.630 0.00 0.00 0.00 1.85
215 216 8.277713 CACATGGACTTGCAAATTTTTCTTAAG 58.722 33.333 0.00 0.00 0.00 1.85
216 217 6.843069 TGGACTTGCAAATTTTTCTTAAGC 57.157 33.333 0.00 0.00 0.00 3.09
217 218 6.581712 TGGACTTGCAAATTTTTCTTAAGCT 58.418 32.000 0.00 0.00 0.00 3.74
218 219 7.721402 TGGACTTGCAAATTTTTCTTAAGCTA 58.279 30.769 0.00 0.00 0.00 3.32
219 220 8.367156 TGGACTTGCAAATTTTTCTTAAGCTAT 58.633 29.630 0.00 0.00 0.00 2.97
220 221 9.208022 GGACTTGCAAATTTTTCTTAAGCTATT 57.792 29.630 0.00 0.00 0.00 1.73
222 223 9.987272 ACTTGCAAATTTTTCTTAAGCTATTCT 57.013 25.926 0.00 0.00 0.00 2.40
225 226 9.979578 TGCAAATTTTTCTTAAGCTATTCTTCA 57.020 25.926 0.00 0.00 36.25 3.02
297 298 6.930475 AGTAATAACCTGGAGACCACCTATA 58.070 40.000 0.00 0.00 0.00 1.31
298 299 7.011382 AGTAATAACCTGGAGACCACCTATAG 58.989 42.308 0.00 0.00 0.00 1.31
301 302 0.962489 CTGGAGACCACCTATAGGCG 59.038 60.000 19.25 9.43 39.32 5.52
315 316 2.234913 TAGGCGTCGAAAGGGGAAGC 62.235 60.000 0.00 0.00 38.03 3.86
328 329 1.620259 GGAAGCCATGATTCCCCCA 59.380 57.895 15.29 0.00 41.66 4.96
336 337 0.693049 ATGATTCCCCCATACGCTCC 59.307 55.000 0.00 0.00 0.00 4.70
350 353 5.333339 CCATACGCTCCATCAATAAAGAACG 60.333 44.000 0.00 0.00 0.00 3.95
382 386 7.910683 GCAATATTACTGCTACAAAGAGGAAAC 59.089 37.037 0.00 0.00 36.84 2.78
482 1674 2.893637 GTGTTGATACACGCTGGAGAT 58.106 47.619 0.00 0.00 44.66 2.75
568 1773 1.377202 GTCGGGCTTGCAATCCTCA 60.377 57.895 18.33 3.23 0.00 3.86
642 1847 3.502572 GGTTGCTCCGATGAAGCC 58.497 61.111 0.00 0.00 0.00 4.35
644 1849 1.447838 GTTGCTCCGATGAAGCCGA 60.448 57.895 0.00 0.00 0.00 5.54
645 1850 1.447838 TTGCTCCGATGAAGCCGAC 60.448 57.895 0.00 0.00 0.00 4.79
649 1854 1.140407 CTCCGATGAAGCCGACGAAC 61.140 60.000 0.00 0.00 0.00 3.95
651 1856 1.513373 CGATGAAGCCGACGAACGA 60.513 57.895 0.00 0.00 45.77 3.85
652 1857 1.068832 CGATGAAGCCGACGAACGAA 61.069 55.000 0.00 0.00 45.77 3.85
653 1858 1.065358 GATGAAGCCGACGAACGAAA 58.935 50.000 0.00 0.00 45.77 3.46
654 1859 1.659098 GATGAAGCCGACGAACGAAAT 59.341 47.619 0.00 0.00 45.77 2.17
655 1860 1.065358 TGAAGCCGACGAACGAAATC 58.935 50.000 0.00 4.39 45.77 2.17
657 1862 0.387622 AAGCCGACGAACGAAATCGA 60.388 50.000 10.16 0.00 45.48 3.59
659 1864 1.624323 CCGACGAACGAAATCGAGC 59.376 57.895 10.16 0.10 45.48 5.03
660 1865 1.068832 CCGACGAACGAAATCGAGCA 61.069 55.000 10.16 0.00 45.48 4.26
661 1866 0.022106 CGACGAACGAAATCGAGCAC 59.978 55.000 10.16 0.00 45.48 4.40
662 1867 0.022106 GACGAACGAAATCGAGCACG 59.978 55.000 10.16 10.86 45.48 5.34
671 1876 4.816990 TCGAGCACGACACAAACA 57.183 50.000 0.88 0.00 43.81 2.83
672 1877 3.052181 TCGAGCACGACACAAACAA 57.948 47.368 0.88 0.00 43.81 2.83
673 1878 1.577468 TCGAGCACGACACAAACAAT 58.423 45.000 0.88 0.00 43.81 2.71
674 1879 1.937223 TCGAGCACGACACAAACAATT 59.063 42.857 0.88 0.00 43.81 2.32
675 1880 2.353269 TCGAGCACGACACAAACAATTT 59.647 40.909 0.88 0.00 43.81 1.82
678 1883 4.783764 CGAGCACGACACAAACAATTTGTA 60.784 41.667 6.62 0.00 46.02 2.41
694 2961 8.456904 ACAATTTGTATATATAGGCACGTACG 57.543 34.615 15.01 15.01 0.00 3.67
695 2962 7.062605 ACAATTTGTATATATAGGCACGTACGC 59.937 37.037 16.72 0.00 0.00 4.42
696 2963 4.263139 TGTATATATAGGCACGTACGCG 57.737 45.455 16.72 3.53 44.93 6.01
697 2964 2.838386 ATATATAGGCACGTACGCGG 57.162 50.000 16.72 9.29 43.45 6.46
698 2965 1.807139 TATATAGGCACGTACGCGGA 58.193 50.000 16.72 0.00 43.45 5.54
699 2966 0.520404 ATATAGGCACGTACGCGGAG 59.480 55.000 16.72 3.25 43.45 4.63
700 2967 0.532640 TATAGGCACGTACGCGGAGA 60.533 55.000 16.72 0.00 43.45 3.71
701 2968 1.170919 ATAGGCACGTACGCGGAGAT 61.171 55.000 16.72 0.69 43.45 2.75
767 3047 9.098355 TGTTAATGACTAGGAAAATCTTGATCG 57.902 33.333 0.00 0.00 0.00 3.69
768 3048 9.099454 GTTAATGACTAGGAAAATCTTGATCGT 57.901 33.333 0.00 0.00 0.00 3.73
771 3051 5.805486 TGACTAGGAAAATCTTGATCGTTCG 59.195 40.000 0.00 0.00 0.00 3.95
772 3052 5.962433 ACTAGGAAAATCTTGATCGTTCGA 58.038 37.500 0.00 0.00 0.00 3.71
811 3091 5.450688 CGACTAGGAATAGAAACCCAGACTG 60.451 48.000 0.00 0.00 0.00 3.51
869 3170 3.309675 CGTTTCGGCCGCTCTATG 58.690 61.111 23.51 6.86 0.00 2.23
879 3180 3.060602 GGCCGCTCTATGTAATCTCAAC 58.939 50.000 0.00 0.00 0.00 3.18
887 3188 2.933495 TGTAATCTCAACGGGACTCG 57.067 50.000 0.00 0.00 45.88 4.18
888 3189 2.439409 TGTAATCTCAACGGGACTCGA 58.561 47.619 0.00 0.00 42.43 4.04
893 3194 0.818296 CTCAACGGGACTCGATTCCT 59.182 55.000 19.99 0.00 42.43 3.36
914 3217 8.846423 TTCCTCTCCTTAATTCTGTATTCTCT 57.154 34.615 0.00 0.00 0.00 3.10
1034 3345 4.175489 CGTCCAGATCGTCGGCGT 62.175 66.667 10.18 0.00 39.49 5.68
1170 3490 0.250338 ACGTCCTGGCCAACTTTCTC 60.250 55.000 7.01 0.00 0.00 2.87
1269 3589 2.114051 GGAGGAGGAGGACGACGAC 61.114 68.421 0.00 0.00 0.00 4.34
1292 3615 2.099062 GATGGCGTTTCTGCTGCG 59.901 61.111 0.00 0.00 34.52 5.18
1360 3683 1.737793 CCACCTCGGTGCAAGATTAAC 59.262 52.381 10.59 0.00 44.16 2.01
1361 3684 2.422597 CACCTCGGTGCAAGATTAACA 58.577 47.619 2.72 0.00 39.39 2.41
1377 3704 3.322466 CAGGGACGGCCTGGTTCT 61.322 66.667 7.57 0.00 0.00 3.01
1391 3718 5.879223 GGCCTGGTTCTGATCAAGATATATG 59.121 44.000 0.00 0.00 33.93 1.78
1392 3719 5.353678 GCCTGGTTCTGATCAAGATATATGC 59.646 44.000 0.00 0.00 33.93 3.14
1393 3720 6.709281 CCTGGTTCTGATCAAGATATATGCT 58.291 40.000 0.00 0.00 33.93 3.79
1394 3721 7.580302 GCCTGGTTCTGATCAAGATATATGCTA 60.580 40.741 0.00 0.00 33.93 3.49
1395 3722 7.980662 CCTGGTTCTGATCAAGATATATGCTAG 59.019 40.741 0.00 0.00 33.93 3.42
1396 3723 7.326454 TGGTTCTGATCAAGATATATGCTAGC 58.674 38.462 8.10 8.10 33.93 3.42
1445 4047 2.603075 AAGGGTTGCAATGGAAGCTA 57.397 45.000 15.68 0.00 0.00 3.32
1462 4064 5.578727 GGAAGCTATGGTCAGATTATAAGCG 59.421 44.000 0.00 0.00 0.00 4.68
1465 4067 6.159988 AGCTATGGTCAGATTATAAGCGAAC 58.840 40.000 0.00 0.00 0.00 3.95
1467 4069 7.176865 AGCTATGGTCAGATTATAAGCGAACTA 59.823 37.037 10.41 5.14 0.00 2.24
1473 4075 8.917655 GGTCAGATTATAAGCGAACTAAATCTC 58.082 37.037 7.96 0.00 32.14 2.75
1474 4076 9.685828 GTCAGATTATAAGCGAACTAAATCTCT 57.314 33.333 0.00 0.00 32.14 3.10
1506 4129 6.877611 TTTGAAGGTCGAGCTTCTAATTTT 57.122 33.333 40.93 17.84 0.00 1.82
1520 4143 8.675040 GCTTCTAATTTTAAAGCTCATTCGTT 57.325 30.769 10.29 0.00 41.66 3.85
1521 4144 9.769093 GCTTCTAATTTTAAAGCTCATTCGTTA 57.231 29.630 10.29 0.00 41.66 3.18
1523 4146 9.769093 TTCTAATTTTAAAGCTCATTCGTTAGC 57.231 29.630 0.00 0.00 39.08 3.09
1524 4147 8.395633 TCTAATTTTAAAGCTCATTCGTTAGCC 58.604 33.333 0.00 0.00 39.64 3.93
1525 4148 5.950758 TTTTAAAGCTCATTCGTTAGCCA 57.049 34.783 0.00 0.00 39.64 4.75
1526 4149 5.950758 TTTAAAGCTCATTCGTTAGCCAA 57.049 34.783 0.00 0.00 39.64 4.52
1527 4150 5.545658 TTAAAGCTCATTCGTTAGCCAAG 57.454 39.130 0.00 0.00 39.64 3.61
1528 4151 2.770164 AGCTCATTCGTTAGCCAAGT 57.230 45.000 0.00 0.00 39.64 3.16
1529 4152 3.887621 AGCTCATTCGTTAGCCAAGTA 57.112 42.857 0.00 0.00 39.64 2.24
1530 4153 3.522553 AGCTCATTCGTTAGCCAAGTAC 58.477 45.455 0.00 0.00 39.64 2.73
1531 4154 3.195825 AGCTCATTCGTTAGCCAAGTACT 59.804 43.478 0.00 0.00 39.64 2.73
1532 4155 3.552294 GCTCATTCGTTAGCCAAGTACTC 59.448 47.826 0.00 0.00 32.40 2.59
1533 4156 4.678309 GCTCATTCGTTAGCCAAGTACTCT 60.678 45.833 0.00 0.00 32.40 3.24
1534 4157 4.995124 TCATTCGTTAGCCAAGTACTCTC 58.005 43.478 0.00 0.00 0.00 3.20
1535 4158 4.461431 TCATTCGTTAGCCAAGTACTCTCA 59.539 41.667 0.00 0.00 0.00 3.27
1536 4159 4.859304 TTCGTTAGCCAAGTACTCTCAA 57.141 40.909 0.00 0.00 0.00 3.02
1537 4160 5.401531 TTCGTTAGCCAAGTACTCTCAAT 57.598 39.130 0.00 0.00 0.00 2.57
1538 4161 4.995124 TCGTTAGCCAAGTACTCTCAATC 58.005 43.478 0.00 0.00 0.00 2.67
1539 4162 4.705507 TCGTTAGCCAAGTACTCTCAATCT 59.294 41.667 0.00 0.00 0.00 2.40
1540 4163 5.185249 TCGTTAGCCAAGTACTCTCAATCTT 59.815 40.000 0.00 0.00 0.00 2.40
1541 4164 5.869888 CGTTAGCCAAGTACTCTCAATCTTT 59.130 40.000 0.00 0.00 0.00 2.52
1542 4165 7.033791 CGTTAGCCAAGTACTCTCAATCTTTA 58.966 38.462 0.00 0.00 0.00 1.85
1543 4166 7.221067 CGTTAGCCAAGTACTCTCAATCTTTAG 59.779 40.741 0.00 0.00 0.00 1.85
1544 4167 6.859112 AGCCAAGTACTCTCAATCTTTAGA 57.141 37.500 0.00 0.00 0.00 2.10
1545 4168 7.430760 AGCCAAGTACTCTCAATCTTTAGAT 57.569 36.000 0.00 0.00 36.07 1.98
1546 4169 7.496747 AGCCAAGTACTCTCAATCTTTAGATC 58.503 38.462 0.00 0.00 32.75 2.75
1547 4170 7.344352 AGCCAAGTACTCTCAATCTTTAGATCT 59.656 37.037 0.00 0.00 32.75 2.75
1548 4171 8.634444 GCCAAGTACTCTCAATCTTTAGATCTA 58.366 37.037 0.00 0.00 32.75 1.98
1599 4222 3.309296 TCTCAATCTTTAGATCGGGGCT 58.691 45.455 0.00 0.00 32.75 5.19
1623 4246 1.228154 GTTTGGCTCGGACAACCCT 60.228 57.895 0.00 0.00 26.20 4.34
1688 4313 3.117512 AGACTTGGCTTCCCTCAAAAAGA 60.118 43.478 0.00 0.00 0.00 2.52
1767 4392 5.127845 CACGGTGGGATATGAAGAGCTATAT 59.872 44.000 0.00 0.00 0.00 0.86
1859 4488 7.012232 CCACATTTCACAGCTTAAAAATGGTTT 59.988 33.333 20.28 5.43 41.29 3.27
1906 4595 9.308000 AGATGAAAATTAAGTGTTACAATCCCA 57.692 29.630 0.00 0.00 0.00 4.37
1921 4610 4.223477 ACAATCCCATCCAACAATTTCCAG 59.777 41.667 0.00 0.00 0.00 3.86
1922 4611 2.818921 TCCCATCCAACAATTTCCAGG 58.181 47.619 0.00 0.00 0.00 4.45
1938 4627 0.179026 CAGGACATCATCTGGGCCAG 60.179 60.000 28.01 28.01 0.00 4.85
1962 4651 2.507110 TAGCCAGACAGCTGTTCGGC 62.507 60.000 35.78 35.78 44.67 5.54
1988 4677 3.120234 GCAACCTACCAAAATTGCAATGC 60.120 43.478 13.82 5.05 45.38 3.56
1989 4678 4.063689 CAACCTACCAAAATTGCAATGCA 58.936 39.130 13.82 2.72 36.47 3.96
2069 4761 5.996513 CCCAAACTGATATTGATCTCTCTGG 59.003 44.000 0.00 0.00 32.79 3.86
2090 4782 9.167311 CTCTGGTAATAAAAGCATACTTTGACT 57.833 33.333 0.00 0.00 45.48 3.41
2104 4796 7.577807 GCATACTTTGACTTGTTCTCCTCTCTA 60.578 40.741 0.00 0.00 0.00 2.43
2146 7710 4.677250 GCCTCCTTGCAATGAGAAGAATTG 60.677 45.833 27.33 13.23 37.94 2.32
2154 7718 4.894937 CAATGAGAAGAATTGCTCGAGTG 58.105 43.478 15.13 0.00 33.89 3.51
2155 7719 3.667497 TGAGAAGAATTGCTCGAGTGT 57.333 42.857 15.13 0.00 33.89 3.55
2156 7720 3.320626 TGAGAAGAATTGCTCGAGTGTG 58.679 45.455 15.13 0.00 33.89 3.82
2157 7721 2.670414 GAGAAGAATTGCTCGAGTGTGG 59.330 50.000 15.13 0.00 0.00 4.17
2158 7722 2.300152 AGAAGAATTGCTCGAGTGTGGA 59.700 45.455 15.13 0.00 0.00 4.02
2159 7723 2.086054 AGAATTGCTCGAGTGTGGAC 57.914 50.000 15.13 2.22 0.00 4.02
2160 7724 1.620819 AGAATTGCTCGAGTGTGGACT 59.379 47.619 15.13 4.51 33.98 3.85
2177 7741 5.363868 TGTGGACTCTGGAGTATTTATCCTG 59.636 44.000 3.03 0.00 42.66 3.86
2221 7785 2.307098 CTCCACTCTTCCATTCCCACTT 59.693 50.000 0.00 0.00 0.00 3.16
2223 7787 3.913799 TCCACTCTTCCATTCCCACTTTA 59.086 43.478 0.00 0.00 0.00 1.85
2224 7788 4.010349 CCACTCTTCCATTCCCACTTTAC 58.990 47.826 0.00 0.00 0.00 2.01
2225 7789 4.506625 CCACTCTTCCATTCCCACTTTACA 60.507 45.833 0.00 0.00 0.00 2.41
2228 7792 6.040391 CACTCTTCCATTCCCACTTTACAAAA 59.960 38.462 0.00 0.00 0.00 2.44
2229 7793 6.265422 ACTCTTCCATTCCCACTTTACAAAAG 59.735 38.462 0.00 0.00 0.00 2.27
2230 7794 5.538433 TCTTCCATTCCCACTTTACAAAAGG 59.462 40.000 4.56 0.00 0.00 3.11
2231 7795 5.068215 TCCATTCCCACTTTACAAAAGGA 57.932 39.130 4.56 0.00 0.00 3.36
2233 7797 6.081356 TCCATTCCCACTTTACAAAAGGAAT 58.919 36.000 4.56 0.00 43.23 3.01
2234 7798 6.556874 TCCATTCCCACTTTACAAAAGGAATT 59.443 34.615 0.00 0.00 41.10 2.17
2235 7799 6.873605 CCATTCCCACTTTACAAAAGGAATTC 59.126 38.462 0.00 0.00 41.10 2.17
2236 7800 7.441017 CATTCCCACTTTACAAAAGGAATTCA 58.559 34.615 7.93 0.00 41.10 2.57
2237 7801 6.399639 TCCCACTTTACAAAAGGAATTCAC 57.600 37.500 7.93 0.00 0.00 3.18
2238 7802 5.894393 TCCCACTTTACAAAAGGAATTCACA 59.106 36.000 7.93 0.00 0.00 3.58
2240 7804 6.646240 CCCACTTTACAAAAGGAATTCACATG 59.354 38.462 7.93 3.28 0.00 3.21
2241 7805 6.646240 CCACTTTACAAAAGGAATTCACATGG 59.354 38.462 7.93 0.00 0.00 3.66
2243 7807 8.090214 CACTTTACAAAAGGAATTCACATGGAT 58.910 33.333 7.93 0.00 0.00 3.41
2248 7812 8.237811 ACAAAAGGAATTCACATGGATATACC 57.762 34.615 7.93 0.00 39.54 2.73
2311 7875 3.355378 AGATGACTCTCTGGTCTGTCTG 58.645 50.000 0.00 0.00 37.16 3.51
2336 7900 0.037232 AGGCGGACTAGTGAGTTTGC 60.037 55.000 0.00 0.00 35.45 3.68
2337 7901 0.320421 GGCGGACTAGTGAGTTTGCA 60.320 55.000 0.00 0.00 37.66 4.08
2338 7902 1.071605 GCGGACTAGTGAGTTTGCAG 58.928 55.000 0.00 0.00 35.45 4.41
2339 7903 1.336887 GCGGACTAGTGAGTTTGCAGA 60.337 52.381 0.00 0.00 35.45 4.26
2340 7904 2.866460 GCGGACTAGTGAGTTTGCAGAA 60.866 50.000 0.00 0.00 35.45 3.02
2341 7905 3.589988 CGGACTAGTGAGTTTGCAGAAT 58.410 45.455 0.00 0.00 35.45 2.40
2342 7906 3.614616 CGGACTAGTGAGTTTGCAGAATC 59.385 47.826 0.00 0.00 35.45 2.52
2343 7907 4.619394 CGGACTAGTGAGTTTGCAGAATCT 60.619 45.833 0.00 0.00 35.45 2.40
2344 7908 4.629200 GGACTAGTGAGTTTGCAGAATCTG 59.371 45.833 5.78 5.78 35.45 2.90
2345 7909 5.220710 ACTAGTGAGTTTGCAGAATCTGT 57.779 39.130 12.29 0.00 29.88 3.41
2346 7910 5.233988 ACTAGTGAGTTTGCAGAATCTGTC 58.766 41.667 12.29 5.05 29.88 3.51
2347 7911 4.077300 AGTGAGTTTGCAGAATCTGTCA 57.923 40.909 12.29 7.61 33.43 3.58
2348 7912 4.063689 AGTGAGTTTGCAGAATCTGTCAG 58.936 43.478 12.29 0.00 33.43 3.51
2349 7913 3.188048 GTGAGTTTGCAGAATCTGTCAGG 59.812 47.826 12.29 0.00 33.43 3.86
2350 7914 2.157738 AGTTTGCAGAATCTGTCAGGC 58.842 47.619 12.29 7.13 33.43 4.85
2351 7915 2.157738 GTTTGCAGAATCTGTCAGGCT 58.842 47.619 12.29 0.00 33.43 4.58
2352 7916 1.817357 TTGCAGAATCTGTCAGGCTG 58.183 50.000 12.29 8.58 33.43 4.85
2353 7917 0.689055 TGCAGAATCTGTCAGGCTGT 59.311 50.000 15.27 0.00 33.43 4.40
2354 7918 1.338484 TGCAGAATCTGTCAGGCTGTC 60.338 52.381 15.27 9.82 33.43 3.51
2355 7919 1.338484 GCAGAATCTGTCAGGCTGTCA 60.338 52.381 15.27 14.36 33.43 3.58
2356 7920 2.344950 CAGAATCTGTCAGGCTGTCAC 58.655 52.381 15.27 6.90 0.00 3.67
2357 7921 2.028294 CAGAATCTGTCAGGCTGTCACT 60.028 50.000 15.27 5.63 0.00 3.41
2358 7922 2.233431 AGAATCTGTCAGGCTGTCACTC 59.767 50.000 15.27 9.47 0.00 3.51
2359 7923 1.935799 ATCTGTCAGGCTGTCACTCT 58.064 50.000 15.27 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.001576 TGCCTACTTATCGACATGGCACA 62.002 47.826 0.00 0.00 43.09 4.57
2 3 2.135933 GCCTACTTATCGACATGGCAC 58.864 52.381 0.00 0.00 38.79 5.01
3 4 1.760029 TGCCTACTTATCGACATGGCA 59.240 47.619 0.00 10.81 45.31 4.92
4 5 2.135933 GTGCCTACTTATCGACATGGC 58.864 52.381 0.00 0.00 39.33 4.40
5 6 2.102420 TGGTGCCTACTTATCGACATGG 59.898 50.000 0.00 0.00 0.00 3.66
6 7 3.452755 TGGTGCCTACTTATCGACATG 57.547 47.619 0.00 0.00 0.00 3.21
7 8 3.006967 GGATGGTGCCTACTTATCGACAT 59.993 47.826 0.00 0.00 0.00 3.06
8 9 2.364324 GGATGGTGCCTACTTATCGACA 59.636 50.000 0.00 0.00 0.00 4.35
9 10 2.364324 TGGATGGTGCCTACTTATCGAC 59.636 50.000 0.00 0.00 0.00 4.20
10 11 2.364324 GTGGATGGTGCCTACTTATCGA 59.636 50.000 0.00 0.00 0.00 3.59
11 12 2.102420 TGTGGATGGTGCCTACTTATCG 59.898 50.000 0.00 0.00 0.00 2.92
12 13 3.134804 AGTGTGGATGGTGCCTACTTATC 59.865 47.826 0.00 0.00 0.00 1.75
13 14 3.115390 AGTGTGGATGGTGCCTACTTAT 58.885 45.455 0.00 0.00 0.00 1.73
14 15 2.546899 AGTGTGGATGGTGCCTACTTA 58.453 47.619 0.00 0.00 0.00 2.24
15 16 1.362224 AGTGTGGATGGTGCCTACTT 58.638 50.000 0.00 0.00 0.00 2.24
16 17 1.279271 GAAGTGTGGATGGTGCCTACT 59.721 52.381 0.00 0.00 0.00 2.57
17 18 1.279271 AGAAGTGTGGATGGTGCCTAC 59.721 52.381 0.00 0.00 0.00 3.18
18 19 1.656587 AGAAGTGTGGATGGTGCCTA 58.343 50.000 0.00 0.00 0.00 3.93
19 20 0.773644 AAGAAGTGTGGATGGTGCCT 59.226 50.000 0.00 0.00 0.00 4.75
20 21 1.620822 AAAGAAGTGTGGATGGTGCC 58.379 50.000 0.00 0.00 0.00 5.01
21 22 3.068024 TCAAAAAGAAGTGTGGATGGTGC 59.932 43.478 0.00 0.00 0.00 5.01
22 23 4.916983 TCAAAAAGAAGTGTGGATGGTG 57.083 40.909 0.00 0.00 0.00 4.17
23 24 5.520376 CTTCAAAAAGAAGTGTGGATGGT 57.480 39.130 0.00 0.00 46.97 3.55
34 35 1.047801 GCCCAGGGCTTCAAAAAGAA 58.952 50.000 24.99 0.00 46.69 2.52
35 36 2.745379 GCCCAGGGCTTCAAAAAGA 58.255 52.632 24.99 0.00 46.69 2.52
46 47 3.944250 ATTGTTCTGCGGCCCAGGG 62.944 63.158 17.89 0.00 42.05 4.45
47 48 1.978617 AATTGTTCTGCGGCCCAGG 60.979 57.895 17.89 0.00 42.05 4.45
48 49 1.213537 CAATTGTTCTGCGGCCCAG 59.786 57.895 13.43 13.43 43.17 4.45
49 50 1.112315 AACAATTGTTCTGCGGCCCA 61.112 50.000 18.13 0.00 31.64 5.36
50 51 1.665442 AACAATTGTTCTGCGGCCC 59.335 52.632 18.13 0.00 31.64 5.80
59 60 3.070015 CAGAGCCCCAAAGAACAATTGTT 59.930 43.478 23.49 23.49 41.64 2.83
60 61 2.629617 CAGAGCCCCAAAGAACAATTGT 59.370 45.455 4.92 4.92 0.00 2.71
61 62 2.892852 TCAGAGCCCCAAAGAACAATTG 59.107 45.455 3.24 3.24 0.00 2.32
62 63 3.160269 CTCAGAGCCCCAAAGAACAATT 58.840 45.455 0.00 0.00 0.00 2.32
63 64 2.800250 CTCAGAGCCCCAAAGAACAAT 58.200 47.619 0.00 0.00 0.00 2.71
64 65 1.819305 GCTCAGAGCCCCAAAGAACAA 60.819 52.381 11.84 0.00 34.48 2.83
65 66 0.250901 GCTCAGAGCCCCAAAGAACA 60.251 55.000 11.84 0.00 34.48 3.18
66 67 0.037447 AGCTCAGAGCCCCAAAGAAC 59.963 55.000 19.40 0.00 43.77 3.01
67 68 0.037303 CAGCTCAGAGCCCCAAAGAA 59.963 55.000 19.40 0.00 43.77 2.52
68 69 1.681666 CAGCTCAGAGCCCCAAAGA 59.318 57.895 19.40 0.00 43.77 2.52
69 70 1.378250 CCAGCTCAGAGCCCCAAAG 60.378 63.158 19.40 2.56 43.77 2.77
70 71 2.759114 CCAGCTCAGAGCCCCAAA 59.241 61.111 19.40 0.00 43.77 3.28
71 72 4.039092 GCCAGCTCAGAGCCCCAA 62.039 66.667 19.40 0.00 43.77 4.12
73 74 3.726144 AAGCCAGCTCAGAGCCCC 61.726 66.667 19.40 7.57 43.77 5.80
74 75 2.268167 ATCAAGCCAGCTCAGAGCCC 62.268 60.000 19.40 7.94 43.77 5.19
75 76 0.467384 TATCAAGCCAGCTCAGAGCC 59.533 55.000 19.40 3.83 43.77 4.70
76 77 1.868469 CTATCAAGCCAGCTCAGAGC 58.132 55.000 15.25 15.25 42.84 4.09
77 78 1.868469 GCTATCAAGCCAGCTCAGAG 58.132 55.000 0.00 0.00 43.40 3.35
136 137 9.764363 CCAACTAAGACATTTAGCATCAGTATA 57.236 33.333 0.00 0.00 0.00 1.47
137 138 8.267894 ACCAACTAAGACATTTAGCATCAGTAT 58.732 33.333 0.00 0.00 0.00 2.12
138 139 7.620880 ACCAACTAAGACATTTAGCATCAGTA 58.379 34.615 0.00 0.00 0.00 2.74
139 140 6.476378 ACCAACTAAGACATTTAGCATCAGT 58.524 36.000 0.00 0.00 0.00 3.41
140 141 6.992063 ACCAACTAAGACATTTAGCATCAG 57.008 37.500 0.00 0.00 0.00 2.90
141 142 7.446931 TCAAACCAACTAAGACATTTAGCATCA 59.553 33.333 0.00 0.00 0.00 3.07
142 143 7.816640 TCAAACCAACTAAGACATTTAGCATC 58.183 34.615 0.00 0.00 0.00 3.91
143 144 7.759489 TCAAACCAACTAAGACATTTAGCAT 57.241 32.000 0.00 0.00 0.00 3.79
144 145 7.575414 TTCAAACCAACTAAGACATTTAGCA 57.425 32.000 0.00 0.00 0.00 3.49
145 146 9.476202 AATTTCAAACCAACTAAGACATTTAGC 57.524 29.630 0.00 0.00 0.00 3.09
148 149 9.533253 CTGAATTTCAAACCAACTAAGACATTT 57.467 29.630 0.01 0.00 0.00 2.32
149 150 8.912988 TCTGAATTTCAAACCAACTAAGACATT 58.087 29.630 0.01 0.00 0.00 2.71
150 151 8.463930 TCTGAATTTCAAACCAACTAAGACAT 57.536 30.769 0.01 0.00 0.00 3.06
151 152 7.873719 TCTGAATTTCAAACCAACTAAGACA 57.126 32.000 0.01 0.00 0.00 3.41
152 153 9.581099 TTTTCTGAATTTCAAACCAACTAAGAC 57.419 29.630 0.01 0.00 0.00 3.01
187 188 5.754890 AGAAAAATTTGCAAGTCCATGTGAC 59.245 36.000 0.00 6.29 44.82 3.67
188 189 5.916318 AGAAAAATTTGCAAGTCCATGTGA 58.084 33.333 0.00 0.00 0.00 3.58
189 190 6.607735 AAGAAAAATTTGCAAGTCCATGTG 57.392 33.333 0.00 0.00 0.00 3.21
190 191 7.041848 GCTTAAGAAAAATTTGCAAGTCCATGT 60.042 33.333 6.67 0.00 0.00 3.21
191 192 7.172019 AGCTTAAGAAAAATTTGCAAGTCCATG 59.828 33.333 6.67 0.00 0.00 3.66
192 193 7.219322 AGCTTAAGAAAAATTTGCAAGTCCAT 58.781 30.769 6.67 0.00 0.00 3.41
193 194 6.581712 AGCTTAAGAAAAATTTGCAAGTCCA 58.418 32.000 6.67 0.00 0.00 4.02
194 195 8.763049 ATAGCTTAAGAAAAATTTGCAAGTCC 57.237 30.769 6.67 0.00 0.00 3.85
196 197 9.987272 AGAATAGCTTAAGAAAAATTTGCAAGT 57.013 25.926 6.67 0.00 0.00 3.16
199 200 9.979578 TGAAGAATAGCTTAAGAAAAATTTGCA 57.020 25.926 6.67 0.00 36.83 4.08
261 262 9.907229 CTCCAGGTTATTACTAGAAGGAAATTT 57.093 33.333 0.00 0.00 0.00 1.82
262 263 9.280456 TCTCCAGGTTATTACTAGAAGGAAATT 57.720 33.333 0.00 0.00 0.00 1.82
263 264 8.706521 GTCTCCAGGTTATTACTAGAAGGAAAT 58.293 37.037 0.00 0.00 0.00 2.17
264 265 7.125356 GGTCTCCAGGTTATTACTAGAAGGAAA 59.875 40.741 0.00 0.00 0.00 3.13
265 266 6.610425 GGTCTCCAGGTTATTACTAGAAGGAA 59.390 42.308 0.00 0.00 0.00 3.36
266 267 6.134754 GGTCTCCAGGTTATTACTAGAAGGA 58.865 44.000 0.00 0.00 0.00 3.36
267 268 5.897824 TGGTCTCCAGGTTATTACTAGAAGG 59.102 44.000 0.00 0.00 0.00 3.46
268 269 6.183360 GGTGGTCTCCAGGTTATTACTAGAAG 60.183 46.154 0.00 0.00 32.34 2.85
269 270 5.659971 GGTGGTCTCCAGGTTATTACTAGAA 59.340 44.000 0.00 0.00 32.34 2.10
270 271 5.043582 AGGTGGTCTCCAGGTTATTACTAGA 60.044 44.000 0.00 0.00 32.34 2.43
271 272 5.209659 AGGTGGTCTCCAGGTTATTACTAG 58.790 45.833 0.00 0.00 32.34 2.57
297 298 2.663196 CTTCCCCTTTCGACGCCT 59.337 61.111 0.00 0.00 0.00 5.52
298 299 3.125573 GCTTCCCCTTTCGACGCC 61.126 66.667 0.00 0.00 0.00 5.68
301 302 0.035439 TCATGGCTTCCCCTTTCGAC 60.035 55.000 0.00 0.00 0.00 4.20
315 316 0.401738 AGCGTATGGGGGAATCATGG 59.598 55.000 0.00 0.00 0.00 3.66
325 326 4.641396 TCTTTATTGATGGAGCGTATGGG 58.359 43.478 0.00 0.00 0.00 4.00
328 329 4.750098 CCGTTCTTTATTGATGGAGCGTAT 59.250 41.667 0.00 0.00 32.25 3.06
336 337 5.484173 TGCTTAGCCGTTCTTTATTGATG 57.516 39.130 0.29 0.00 0.00 3.07
372 376 7.881232 TCAATGTTACTTATCGGTTTCCTCTTT 59.119 33.333 0.00 0.00 0.00 2.52
375 379 7.630924 CATCAATGTTACTTATCGGTTTCCTC 58.369 38.462 0.00 0.00 0.00 3.71
382 386 5.741425 CACTGCATCAATGTTACTTATCGG 58.259 41.667 0.00 0.00 0.00 4.18
411 415 7.502561 GCCATAACATAACATTCCTACTTTCCT 59.497 37.037 0.00 0.00 0.00 3.36
413 417 8.220755 TGCCATAACATAACATTCCTACTTTC 57.779 34.615 0.00 0.00 0.00 2.62
525 1719 1.341606 CAGTTTCCTCGTCGAAGCTC 58.658 55.000 0.00 0.00 31.71 4.09
526 1720 0.038159 CCAGTTTCCTCGTCGAAGCT 60.038 55.000 0.00 0.00 34.06 3.74
527 1721 1.627550 GCCAGTTTCCTCGTCGAAGC 61.628 60.000 0.00 0.00 0.00 3.86
531 1725 1.446272 GAGGCCAGTTTCCTCGTCG 60.446 63.158 5.01 0.00 40.51 5.12
568 1773 2.711922 GCTCGTCATGGAGACCCGT 61.712 63.158 3.41 0.00 44.66 5.28
627 1832 1.447838 GTCGGCTTCATCGGAGCAA 60.448 57.895 0.00 0.00 0.00 3.91
628 1833 2.184322 GTCGGCTTCATCGGAGCA 59.816 61.111 0.00 0.00 0.00 4.26
629 1834 2.884087 TTCGTCGGCTTCATCGGAGC 62.884 60.000 0.00 0.00 0.00 4.70
631 1836 1.153901 GTTCGTCGGCTTCATCGGA 60.154 57.895 0.00 0.00 0.00 4.55
632 1837 2.505498 CGTTCGTCGGCTTCATCGG 61.505 63.158 0.00 0.00 35.71 4.18
635 1840 1.659098 GATTTCGTTCGTCGGCTTCAT 59.341 47.619 0.00 0.00 40.32 2.57
636 1841 1.065358 GATTTCGTTCGTCGGCTTCA 58.935 50.000 0.00 0.00 40.32 3.02
639 1844 0.797249 CTCGATTTCGTTCGTCGGCT 60.797 55.000 0.00 0.00 40.03 5.52
640 1845 1.624323 CTCGATTTCGTTCGTCGGC 59.376 57.895 0.00 0.00 40.03 5.54
642 1847 0.022106 GTGCTCGATTTCGTTCGTCG 59.978 55.000 0.00 0.00 40.03 5.12
644 1849 0.386352 TCGTGCTCGATTTCGTTCGT 60.386 50.000 6.80 0.00 41.35 3.85
645 1850 2.345900 TCGTGCTCGATTTCGTTCG 58.654 52.632 6.80 2.20 41.35 3.95
651 1856 7.911595 CAAATTGTTTGTGTCGTGCTCGATTT 61.912 38.462 14.59 4.66 40.66 2.17
652 1857 6.510143 CAAATTGTTTGTGTCGTGCTCGATT 61.510 40.000 14.59 0.00 40.66 3.34
653 1858 5.076566 CAAATTGTTTGTGTCGTGCTCGAT 61.077 41.667 14.59 0.00 40.66 3.59
654 1859 1.577468 ATTGTTTGTGTCGTGCTCGA 58.423 45.000 6.80 6.80 44.12 4.04
655 1860 2.383298 AATTGTTTGTGTCGTGCTCG 57.617 45.000 0.81 0.81 38.55 5.03
668 1873 8.918658 CGTACGTGCCTATATATACAAATTGTT 58.081 33.333 7.22 0.00 0.00 2.83
669 1874 7.062605 GCGTACGTGCCTATATATACAAATTGT 59.937 37.037 17.90 3.43 0.00 2.71
670 1875 7.388712 GCGTACGTGCCTATATATACAAATTG 58.611 38.462 17.90 0.00 0.00 2.32
671 1876 6.252015 CGCGTACGTGCCTATATATACAAATT 59.748 38.462 16.78 0.00 33.53 1.82
672 1877 5.740569 CGCGTACGTGCCTATATATACAAAT 59.259 40.000 16.78 0.00 33.53 2.32
673 1878 5.088068 CGCGTACGTGCCTATATATACAAA 58.912 41.667 16.78 0.00 33.53 2.83
674 1879 4.437255 CCGCGTACGTGCCTATATATACAA 60.437 45.833 23.00 0.00 37.70 2.41
675 1880 3.063861 CCGCGTACGTGCCTATATATACA 59.936 47.826 23.00 0.00 37.70 2.29
677 1882 3.530535 TCCGCGTACGTGCCTATATATA 58.469 45.455 23.00 0.00 37.70 0.86
678 1883 2.353889 CTCCGCGTACGTGCCTATATAT 59.646 50.000 23.00 0.00 37.70 0.86
696 2963 4.838152 TCCAAGCCGCGCATCTCC 62.838 66.667 8.75 0.00 0.00 3.71
697 2964 3.567797 GTCCAAGCCGCGCATCTC 61.568 66.667 8.75 0.00 0.00 2.75
800 3080 2.102925 CACCAAAATGCAGTCTGGGTTT 59.897 45.455 11.81 0.00 32.94 3.27
811 3091 1.444895 CAGCTCGGCACCAAAATGC 60.445 57.895 0.00 0.00 45.34 3.56
869 3170 3.712091 ATCGAGTCCCGTTGAGATTAC 57.288 47.619 0.00 0.00 39.75 1.89
879 3180 0.466555 AGGAGAGGAATCGAGTCCCG 60.467 60.000 27.27 0.00 38.59 5.14
887 3188 9.705290 GAGAATACAGAATTAAGGAGAGGAATC 57.295 37.037 0.00 0.00 0.00 2.52
888 3189 9.445973 AGAGAATACAGAATTAAGGAGAGGAAT 57.554 33.333 0.00 0.00 0.00 3.01
893 3194 7.284716 TGCGTAGAGAATACAGAATTAAGGAGA 59.715 37.037 0.00 0.00 0.00 3.71
914 3217 0.314618 TAGGTGTTTGAGCGTGCGTA 59.685 50.000 0.00 0.00 0.00 4.42
1070 3381 4.509737 GGTACTCGGCCAGGACGC 62.510 72.222 11.03 0.00 36.68 5.19
1122 3442 2.742372 CACTTGACGCCGGGAAGG 60.742 66.667 2.18 0.00 44.97 3.46
1212 3532 4.099170 CCGCTGCTGCTGTTGCTC 62.099 66.667 14.03 0.00 40.48 4.26
1214 3534 3.606065 CTTCCGCTGCTGCTGTTGC 62.606 63.158 14.03 3.39 36.97 4.17
1269 3589 1.424493 GCAGAAACGCCATCTCCTCG 61.424 60.000 0.00 0.00 0.00 4.63
1292 3615 2.512515 GGAGGCTCGTGATGTGGC 60.513 66.667 8.69 0.00 36.93 5.01
1293 3616 2.187946 GGGAGGCTCGTGATGTGG 59.812 66.667 8.69 0.00 0.00 4.17
1377 3704 8.355913 CGAATAGGCTAGCATATATCTTGATCA 58.644 37.037 21.29 0.00 0.00 2.92
1391 3718 0.885150 GCAACCCCGAATAGGCTAGC 60.885 60.000 6.04 6.04 39.21 3.42
1392 3719 0.759346 AGCAACCCCGAATAGGCTAG 59.241 55.000 0.00 0.00 39.21 3.42
1393 3720 1.140252 GAAGCAACCCCGAATAGGCTA 59.860 52.381 0.00 0.00 39.21 3.93
1394 3721 0.107165 GAAGCAACCCCGAATAGGCT 60.107 55.000 0.00 0.00 39.21 4.58
1395 3722 0.107165 AGAAGCAACCCCGAATAGGC 60.107 55.000 0.00 0.00 39.21 3.93
1396 3723 2.420058 AAGAAGCAACCCCGAATAGG 57.580 50.000 0.00 0.00 40.63 2.57
1445 4047 9.209175 GATTTAGTTCGCTTATAATCTGACCAT 57.791 33.333 0.00 0.00 0.00 3.55
1467 4069 9.372369 CGACCTTCAAAAATAGAGTAGAGATTT 57.628 33.333 0.00 0.00 0.00 2.17
1470 4072 7.628794 GCTCGACCTTCAAAAATAGAGTAGAGA 60.629 40.741 0.00 0.00 30.13 3.10
1473 4075 6.334202 AGCTCGACCTTCAAAAATAGAGTAG 58.666 40.000 0.00 0.00 0.00 2.57
1474 4076 6.282199 AGCTCGACCTTCAAAAATAGAGTA 57.718 37.500 0.00 0.00 0.00 2.59
1475 4077 5.153950 AGCTCGACCTTCAAAAATAGAGT 57.846 39.130 0.00 0.00 0.00 3.24
1506 4129 4.575885 ACTTGGCTAACGAATGAGCTTTA 58.424 39.130 0.00 0.00 38.79 1.85
1515 4138 4.859304 TTGAGAGTACTTGGCTAACGAA 57.141 40.909 0.00 0.00 0.00 3.85
1516 4139 4.705507 AGATTGAGAGTACTTGGCTAACGA 59.294 41.667 0.00 0.00 0.00 3.85
1517 4140 5.000012 AGATTGAGAGTACTTGGCTAACG 58.000 43.478 0.00 0.00 0.00 3.18
1518 4141 8.251721 TCTAAAGATTGAGAGTACTTGGCTAAC 58.748 37.037 0.00 0.00 0.00 2.34
1519 4142 8.362464 TCTAAAGATTGAGAGTACTTGGCTAA 57.638 34.615 0.00 0.00 0.00 3.09
1520 4143 7.956328 TCTAAAGATTGAGAGTACTTGGCTA 57.044 36.000 0.00 0.00 0.00 3.93
1521 4144 6.859112 TCTAAAGATTGAGAGTACTTGGCT 57.141 37.500 0.00 0.00 0.00 4.75
1522 4145 7.496747 AGATCTAAAGATTGAGAGTACTTGGC 58.503 38.462 0.00 0.00 34.37 4.52
1540 4163 9.383519 ACGAATGAGCTTTGAAATTAGATCTAA 57.616 29.630 17.32 17.32 0.00 2.10
1541 4164 8.948631 ACGAATGAGCTTTGAAATTAGATCTA 57.051 30.769 0.00 0.00 0.00 1.98
1542 4165 7.856145 ACGAATGAGCTTTGAAATTAGATCT 57.144 32.000 0.00 0.00 0.00 2.75
1543 4166 9.643652 CTAACGAATGAGCTTTGAAATTAGATC 57.356 33.333 0.00 0.00 0.00 2.75
1544 4167 8.125448 GCTAACGAATGAGCTTTGAAATTAGAT 58.875 33.333 0.00 0.00 35.73 1.98
1545 4168 7.414098 GGCTAACGAATGAGCTTTGAAATTAGA 60.414 37.037 0.00 0.00 38.79 2.10
1546 4169 6.688813 GGCTAACGAATGAGCTTTGAAATTAG 59.311 38.462 0.00 0.00 38.79 1.73
1547 4170 6.150307 TGGCTAACGAATGAGCTTTGAAATTA 59.850 34.615 0.00 0.00 38.79 1.40
1548 4171 5.048083 TGGCTAACGAATGAGCTTTGAAATT 60.048 36.000 0.00 0.00 38.79 1.82
1549 4172 4.458989 TGGCTAACGAATGAGCTTTGAAAT 59.541 37.500 0.00 0.00 38.79 2.17
1550 4173 3.818210 TGGCTAACGAATGAGCTTTGAAA 59.182 39.130 0.00 0.00 38.79 2.69
1551 4174 3.407698 TGGCTAACGAATGAGCTTTGAA 58.592 40.909 0.00 0.00 38.79 2.69
1552 4175 3.052455 TGGCTAACGAATGAGCTTTGA 57.948 42.857 0.00 0.00 38.79 2.69
1553 4176 3.189287 ACTTGGCTAACGAATGAGCTTTG 59.811 43.478 0.00 0.00 38.79 2.77
1554 4177 3.412386 ACTTGGCTAACGAATGAGCTTT 58.588 40.909 0.00 0.00 38.79 3.51
1555 4178 3.059352 ACTTGGCTAACGAATGAGCTT 57.941 42.857 0.00 0.00 38.79 3.74
1556 4179 2.770164 ACTTGGCTAACGAATGAGCT 57.230 45.000 0.00 0.00 38.79 4.09
1557 4180 3.522553 AGTACTTGGCTAACGAATGAGC 58.477 45.455 0.00 0.00 38.00 4.26
1558 4181 5.000012 AGAGTACTTGGCTAACGAATGAG 58.000 43.478 0.00 0.00 0.00 2.90
1559 4182 4.461431 TGAGAGTACTTGGCTAACGAATGA 59.539 41.667 0.00 0.00 0.00 2.57
1560 4183 4.744570 TGAGAGTACTTGGCTAACGAATG 58.255 43.478 0.00 0.00 0.00 2.67
1561 4184 5.401531 TTGAGAGTACTTGGCTAACGAAT 57.598 39.130 0.00 0.00 0.00 3.34
1688 4313 9.836864 AAGCAATCCTGAATAGTTTTTCTTTTT 57.163 25.926 0.00 0.00 0.00 1.94
1705 4330 4.631813 GTCGTCATACAAAGAAGCAATCCT 59.368 41.667 0.00 0.00 0.00 3.24
1767 4392 6.991531 TGATAATGTATAGTTGTGATGCAGCA 59.008 34.615 0.00 0.00 0.00 4.41
1904 4593 3.164268 TGTCCTGGAAATTGTTGGATGG 58.836 45.455 0.00 0.00 0.00 3.51
1906 4595 4.676109 TGATGTCCTGGAAATTGTTGGAT 58.324 39.130 0.00 0.00 0.00 3.41
1921 4610 0.108207 CTCTGGCCCAGATGATGTCC 59.892 60.000 15.20 0.00 39.92 4.02
1922 4611 0.534652 GCTCTGGCCCAGATGATGTC 60.535 60.000 15.20 0.00 39.92 3.06
1938 4627 0.177604 ACAGCTGTCTGGCTATGCTC 59.822 55.000 15.25 0.00 44.54 4.26
1949 4638 3.044059 GCATGGCCGAACAGCTGTC 62.044 63.158 21.95 12.65 0.00 3.51
1962 4651 3.002102 GCAATTTTGGTAGGTTGCATGG 58.998 45.455 4.26 0.00 44.63 3.66
1984 4673 2.961062 GGGCTAGTCATTCCATTGCATT 59.039 45.455 0.00 0.00 0.00 3.56
1988 4677 6.206243 CAGAAATAGGGCTAGTCATTCCATTG 59.794 42.308 0.00 0.00 0.00 2.82
1989 4678 6.302269 CAGAAATAGGGCTAGTCATTCCATT 58.698 40.000 0.00 0.00 0.00 3.16
1990 4679 5.747248 GCAGAAATAGGGCTAGTCATTCCAT 60.747 44.000 0.00 0.00 0.00 3.41
1991 4680 4.444876 GCAGAAATAGGGCTAGTCATTCCA 60.445 45.833 0.00 0.00 0.00 3.53
1992 4681 4.068599 GCAGAAATAGGGCTAGTCATTCC 58.931 47.826 0.00 0.00 0.00 3.01
1993 4682 4.967036 AGCAGAAATAGGGCTAGTCATTC 58.033 43.478 0.00 0.00 35.82 2.67
2090 4782 7.303182 TGATCAAAAGTAGAGAGGAGAACAA 57.697 36.000 0.00 0.00 0.00 2.83
2104 4796 2.423538 GGCCGTTGCTATGATCAAAAGT 59.576 45.455 0.00 0.00 37.74 2.66
2154 7718 5.364157 ACAGGATAAATACTCCAGAGTCCAC 59.636 44.000 3.00 0.00 42.54 4.02
2155 7719 5.529289 ACAGGATAAATACTCCAGAGTCCA 58.471 41.667 3.00 0.00 42.54 4.02
2156 7720 7.784470 ATACAGGATAAATACTCCAGAGTCC 57.216 40.000 3.00 0.00 42.54 3.85
2157 7721 9.742144 TCTATACAGGATAAATACTCCAGAGTC 57.258 37.037 3.00 0.00 42.54 3.36
2160 7724 9.702253 GGATCTATACAGGATAAATACTCCAGA 57.298 37.037 0.00 0.00 35.08 3.86
2177 7741 7.201839 GGAGTTCCATTCGATAGGGATCTATAC 60.202 44.444 9.70 2.74 34.72 1.47
2223 7787 7.838696 TGGTATATCCATGTGAATTCCTTTTGT 59.161 33.333 2.27 0.00 41.93 2.83
2224 7788 8.236585 TGGTATATCCATGTGAATTCCTTTTG 57.763 34.615 2.27 0.00 41.93 2.44
2240 7804 4.640771 TTGCCAAGGAGATGGTATATCC 57.359 45.455 0.00 0.00 42.75 2.59
2241 7805 7.714377 CAGATATTGCCAAGGAGATGGTATATC 59.286 40.741 15.31 15.31 42.75 1.63
2243 7807 6.070021 CCAGATATTGCCAAGGAGATGGTATA 60.070 42.308 0.00 0.00 42.75 1.47
2245 7809 4.042062 CCAGATATTGCCAAGGAGATGGTA 59.958 45.833 0.00 0.00 42.75 3.25
2246 7810 3.181436 CCAGATATTGCCAAGGAGATGGT 60.181 47.826 0.00 0.00 42.75 3.55
2247 7811 3.073503 TCCAGATATTGCCAAGGAGATGG 59.926 47.826 0.00 0.00 43.70 3.51
2248 7812 4.362470 TCCAGATATTGCCAAGGAGATG 57.638 45.455 0.00 0.00 0.00 2.90
2249 7813 5.393068 TTTCCAGATATTGCCAAGGAGAT 57.607 39.130 0.00 0.00 0.00 2.75
2250 7814 4.860802 TTTCCAGATATTGCCAAGGAGA 57.139 40.909 0.00 0.00 0.00 3.71
2311 7875 0.465824 TCACTAGTCCGCCTCTAGCC 60.466 60.000 0.00 0.00 38.60 3.93
2336 7900 2.028294 AGTGACAGCCTGACAGATTCTG 60.028 50.000 12.17 12.17 37.52 3.02
2337 7901 2.233431 GAGTGACAGCCTGACAGATTCT 59.767 50.000 3.32 0.00 0.00 2.40
2338 7902 2.233431 AGAGTGACAGCCTGACAGATTC 59.767 50.000 3.32 0.00 0.00 2.52
2339 7903 2.255406 AGAGTGACAGCCTGACAGATT 58.745 47.619 3.32 0.00 0.00 2.40
2340 7904 1.935799 AGAGTGACAGCCTGACAGAT 58.064 50.000 3.32 0.00 0.00 2.90
2341 7905 3.446658 AGAGTGACAGCCTGACAGA 57.553 52.632 3.32 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.