Multiple sequence alignment - TraesCS5A01G435800

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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 TraesCS5A01G435800 chr5A 100.000 3836 0 0 1 3836 618969002 618965167 0.000000e+00 7084
1 TraesCS5A01G435800 chr5A 92.174 115 8 1 3394 3508 69844898 69844785 1.100000e-35 161
2 TraesCS5A01G435800 chr5D 90.163 2084 62 48 94 2108 494818564 494816555 0.000000e+00 2580
3 TraesCS5A01G435800 chr5D 94.177 1185 43 13 2213 3392 494816491 494815328 0.000000e+00 1783
4 TraesCS5A01G435800 chr5D 92.683 246 11 3 3597 3836 494815276 494815032 7.890000e-92 348
5 TraesCS5A01G435800 chr5D 92.079 101 8 0 1 101 431881370 431881270 3.990000e-30 143
6 TraesCS5A01G435800 chr5B 89.567 1572 57 45 579 2108 611389239 611387733 0.000000e+00 1895
7 TraesCS5A01G435800 chr5B 92.691 1204 51 17 2215 3397 611387659 611386472 0.000000e+00 1701
8 TraesCS5A01G435800 chr5B 86.957 345 35 7 3499 3836 611386466 611386125 2.800000e-101 379
9 TraesCS5A01G435800 chr5B 81.535 482 30 35 100 533 611389710 611389240 3.670000e-90 342
10 TraesCS5A01G435800 chr5B 93.814 97 5 1 1 96 525203188 525203092 1.110000e-30 145
11 TraesCS5A01G435800 chr4A 93.636 110 7 0 3395 3504 86810031 86810140 8.530000e-37 165
12 TraesCS5A01G435800 chr4A 93.814 97 5 1 1 97 118952351 118952446 1.110000e-30 145
13 TraesCS5A01G435800 chr3D 93.636 110 7 0 3396 3505 308274905 308275014 8.530000e-37 165
14 TraesCS5A01G435800 chr3A 93.694 111 6 1 3398 3508 147557942 147557833 8.530000e-37 165
15 TraesCS5A01G435800 chr3A 93.814 97 5 1 1 97 459080631 459080726 1.110000e-30 145
16 TraesCS5A01G435800 chr6A 88.806 134 13 2 3373 3505 108925766 108925898 3.070000e-36 163
17 TraesCS5A01G435800 chr6A 92.105 114 9 0 3395 3508 109490406 109490293 1.100000e-35 161
18 TraesCS5A01G435800 chr2A 92.174 115 9 0 3398 3512 475555296 475555182 3.070000e-36 163
19 TraesCS5A01G435800 chr2A 92.079 101 7 1 1 101 398875625 398875526 1.440000e-29 141
20 TraesCS5A01G435800 chr1A 92.174 115 9 0 3396 3510 76497797 76497683 3.070000e-36 163
21 TraesCS5A01G435800 chr2D 89.600 125 12 1 3390 3513 592790311 592790435 1.430000e-34 158
22 TraesCS5A01G435800 chr3B 95.876 97 3 1 1 97 206169884 206169789 5.130000e-34 156
23 TraesCS5A01G435800 chr3B 93.814 97 5 1 1 97 206167401 206167306 1.110000e-30 145
24 TraesCS5A01G435800 chr6B 93.878 98 5 1 1 98 557939752 557939848 3.090000e-31 147
25 TraesCS5A01G435800 chr7B 93.814 97 5 1 1 97 6171024 6171119 1.110000e-30 145


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 TraesCS5A01G435800 chr5A 618965167 618969002 3835 True 7084.000000 7084 100.0000 1 3836 1 chr5A.!!$R2 3835
1 TraesCS5A01G435800 chr5D 494815032 494818564 3532 True 1570.333333 2580 92.3410 94 3836 3 chr5D.!!$R2 3742
2 TraesCS5A01G435800 chr5B 611386125 611389710 3585 True 1079.250000 1895 87.6875 100 3836 4 chr5B.!!$R2 3736

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
470 530 0.034089 GCCTGTGGGGTAGCAAGAAT 60.034 55.0 0.00 0.0 37.43 2.40 F
1383 1482 0.107848 AGCCAAGGTATACACACCGC 60.108 55.0 5.01 0.0 43.84 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1385 1484 0.035056 GAGGAAGATGGTGGTGTGGG 60.035 60.0 0.0 0.0 0.00 4.61 R
2981 3141 0.378962 CCACGACGGATCTGAGACTC 59.621 60.0 9.0 0.0 36.56 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
26 27 8.888716 AGAGTACGCTCATATATCAAGATACTG 58.111 37.037 0.00 0.00 44.00 2.74
27 28 8.794335 AGTACGCTCATATATCAAGATACTGA 57.206 34.615 0.00 0.00 0.00 3.41
28 29 8.888716 AGTACGCTCATATATCAAGATACTGAG 58.111 37.037 18.27 18.27 38.33 3.35
29 30 7.695480 ACGCTCATATATCAAGATACTGAGT 57.305 36.000 20.91 0.00 37.98 3.41
30 31 7.757526 ACGCTCATATATCAAGATACTGAGTC 58.242 38.462 20.91 15.76 37.98 3.36
31 32 7.391833 ACGCTCATATATCAAGATACTGAGTCA 59.608 37.037 20.91 0.00 37.98 3.41
32 33 8.404765 CGCTCATATATCAAGATACTGAGTCAT 58.595 37.037 20.91 0.00 37.98 3.06
43 44 9.823647 CAAGATACTGAGTCATACTTATTTGGT 57.176 33.333 0.00 0.00 0.00 3.67
47 48 9.765795 ATACTGAGTCATACTTATTTGGTTAGC 57.234 33.333 0.00 0.00 0.00 3.09
48 49 7.048512 ACTGAGTCATACTTATTTGGTTAGCC 58.951 38.462 0.00 0.00 0.00 3.93
49 50 6.953101 TGAGTCATACTTATTTGGTTAGCCA 58.047 36.000 0.00 0.00 44.38 4.75
50 51 7.573710 TGAGTCATACTTATTTGGTTAGCCAT 58.426 34.615 0.00 0.00 45.56 4.40
51 52 8.710239 TGAGTCATACTTATTTGGTTAGCCATA 58.290 33.333 0.00 0.00 45.56 2.74
52 53 9.555727 GAGTCATACTTATTTGGTTAGCCATAA 57.444 33.333 0.00 0.00 45.56 1.90
83 84 3.258931 CGTTACAACGCATGGGCA 58.741 55.556 10.10 0.00 46.06 5.36
84 85 1.800032 CGTTACAACGCATGGGCAT 59.200 52.632 10.10 0.00 46.06 4.40
85 86 1.010580 CGTTACAACGCATGGGCATA 58.989 50.000 10.10 0.00 46.06 3.14
86 87 1.601903 CGTTACAACGCATGGGCATAT 59.398 47.619 10.10 0.00 46.06 1.78
87 88 2.032799 CGTTACAACGCATGGGCATATT 59.967 45.455 10.10 0.00 46.06 1.28
88 89 3.488384 CGTTACAACGCATGGGCATATTT 60.488 43.478 10.10 0.00 46.06 1.40
89 90 2.582728 ACAACGCATGGGCATATTTG 57.417 45.000 10.10 8.88 41.24 2.32
110 115 8.887036 ATTTGCTAGTAATCATCGAATACACA 57.113 30.769 0.00 0.00 0.00 3.72
147 152 0.321919 AACTGCGTGGCTGTCATCAT 60.322 50.000 0.61 0.00 39.66 2.45
151 157 2.009051 TGCGTGGCTGTCATCATAAAG 58.991 47.619 0.00 0.00 0.00 1.85
179 189 3.937079 ACTCTAAAATAAAACCCGGCGAG 59.063 43.478 9.30 0.00 0.00 5.03
180 190 4.186159 CTCTAAAATAAAACCCGGCGAGA 58.814 43.478 9.30 0.00 0.00 4.04
181 191 4.577875 TCTAAAATAAAACCCGGCGAGAA 58.422 39.130 9.30 0.00 0.00 2.87
182 192 3.842732 AAAATAAAACCCGGCGAGAAG 57.157 42.857 9.30 0.00 0.00 2.85
187 197 0.320508 AAACCCGGCGAGAAGAGAAC 60.321 55.000 9.30 0.00 0.00 3.01
223 233 2.032681 GACTCCAGTGTGGTGGCC 59.967 66.667 0.00 0.00 39.03 5.36
285 310 0.906775 TAAATCCCCCGTCTCCACAC 59.093 55.000 0.00 0.00 0.00 3.82
397 454 1.709578 TTATCTCCCTCTCATGCGCT 58.290 50.000 9.73 0.00 0.00 5.92
400 457 2.124983 TCCCTCTCATGCGCTTGC 60.125 61.111 17.84 0.00 39.78 4.01
406 463 3.109612 CTCATGCGCTTGCTGCCTC 62.110 63.158 17.84 0.00 40.12 4.70
436 493 3.244318 GGATGCATTTGATTTGATCCCCC 60.244 47.826 0.00 0.00 0.00 5.40
470 530 0.034089 GCCTGTGGGGTAGCAAGAAT 60.034 55.000 0.00 0.00 37.43 2.40
480 540 5.724854 TGGGGTAGCAAGAATAAGTAGAAGT 59.275 40.000 0.00 0.00 0.00 3.01
544 610 1.133853 GCTGGCTGGATTCCTCATCTT 60.134 52.381 3.95 0.00 31.67 2.40
547 613 2.437281 TGGCTGGATTCCTCATCTTCTC 59.563 50.000 3.95 0.00 31.67 2.87
549 615 2.224499 GCTGGATTCCTCATCTTCTCCC 60.224 54.545 3.95 0.00 31.67 4.30
550 616 3.316501 CTGGATTCCTCATCTTCTCCCT 58.683 50.000 3.95 0.00 31.67 4.20
551 617 3.715834 CTGGATTCCTCATCTTCTCCCTT 59.284 47.826 3.95 0.00 31.67 3.95
552 618 3.713764 TGGATTCCTCATCTTCTCCCTTC 59.286 47.826 3.95 0.00 31.67 3.46
553 619 3.072330 GGATTCCTCATCTTCTCCCTTCC 59.928 52.174 0.00 0.00 31.67 3.46
554 620 3.498614 TTCCTCATCTTCTCCCTTCCT 57.501 47.619 0.00 0.00 0.00 3.36
555 621 3.498614 TCCTCATCTTCTCCCTTCCTT 57.501 47.619 0.00 0.00 0.00 3.36
559 625 3.779738 CTCATCTTCTCCCTTCCTTTCCT 59.220 47.826 0.00 0.00 0.00 3.36
562 628 4.642466 TCTTCTCCCTTCCTTTCCTTTC 57.358 45.455 0.00 0.00 0.00 2.62
571 637 4.281941 CCTTCCTTTCCTTTCCTTTCCTTG 59.718 45.833 0.00 0.00 0.00 3.61
601 671 4.500116 GAGAGACCCACCTCGCGC 62.500 72.222 0.00 0.00 38.19 6.86
617 687 3.773154 GCCCTCCCTCCCTCCTCT 61.773 72.222 0.00 0.00 0.00 3.69
618 688 2.612251 CCCTCCCTCCCTCCTCTC 59.388 72.222 0.00 0.00 0.00 3.20
619 689 2.018086 CCCTCCCTCCCTCCTCTCT 61.018 68.421 0.00 0.00 0.00 3.10
620 690 1.541672 CCTCCCTCCCTCCTCTCTC 59.458 68.421 0.00 0.00 0.00 3.20
621 691 0.998945 CCTCCCTCCCTCCTCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
622 692 0.185901 CTCCCTCCCTCCTCTCTCTG 59.814 65.000 0.00 0.00 0.00 3.35
623 693 1.232792 CCCTCCCTCCTCTCTCTGG 59.767 68.421 0.00 0.00 0.00 3.86
743 813 1.955458 ATTCGCCTCCCTCCTCCTCT 61.955 60.000 0.00 0.00 0.00 3.69
776 846 2.890474 CGGCGGTTCTTGATCCGG 60.890 66.667 18.13 0.00 45.85 5.14
1163 1256 3.255379 GATTGAGGTCGTCGCGCC 61.255 66.667 0.00 0.00 0.00 6.53
1196 1289 1.084370 GCCGACAAGGATGAAGACGG 61.084 60.000 0.00 0.00 45.00 4.79
1380 1479 2.928116 GTTCGAGCCAAGGTATACACAC 59.072 50.000 5.01 0.00 0.00 3.82
1381 1480 1.479323 TCGAGCCAAGGTATACACACC 59.521 52.381 5.01 0.00 39.02 4.16
1382 1481 1.801395 CGAGCCAAGGTATACACACCG 60.801 57.143 5.01 0.00 43.84 4.94
1383 1482 0.107848 AGCCAAGGTATACACACCGC 60.108 55.000 5.01 0.00 43.84 5.68
1384 1483 0.391927 GCCAAGGTATACACACCGCA 60.392 55.000 5.01 0.00 43.84 5.69
1385 1484 1.365699 CCAAGGTATACACACCGCAC 58.634 55.000 5.01 0.00 43.84 5.34
1400 1499 1.228552 GCACCCACACCACCATCTT 60.229 57.895 0.00 0.00 0.00 2.40
1651 1765 7.016563 TGCCAGATGCTTTCCTTAATCTATCTA 59.983 37.037 0.00 0.00 42.00 1.98
1716 1830 1.497161 CTTCTTGATACGGGGAGGGT 58.503 55.000 0.00 0.00 0.00 4.34
1720 1834 1.687123 CTTGATACGGGGAGGGTACAG 59.313 57.143 0.00 0.00 0.00 2.74
1721 1835 0.105862 TGATACGGGGAGGGTACAGG 60.106 60.000 0.00 0.00 0.00 4.00
1722 1836 0.105811 GATACGGGGAGGGTACAGGT 60.106 60.000 0.00 0.00 0.00 4.00
1723 1837 0.105811 ATACGGGGAGGGTACAGGTC 60.106 60.000 0.00 0.00 0.00 3.85
1780 1894 6.453092 ACTCGGTCATAATATTTACTTCGGG 58.547 40.000 0.00 0.00 0.00 5.14
1888 2006 3.309296 GGGGAGTAGATGACAGGATCAA 58.691 50.000 0.00 0.00 41.93 2.57
1919 2042 7.589958 ACATGTGTTGGACTTGGTATTTAAA 57.410 32.000 0.00 0.00 34.66 1.52
1925 2048 6.203338 TGTTGGACTTGGTATTTAAACGAGTC 59.797 38.462 12.94 12.94 34.79 3.36
2002 2126 5.411361 TGTAGATTGTGTTGGCATCAGTAAC 59.589 40.000 0.00 0.00 0.00 2.50
2084 2208 5.835257 TCCACCTGTGTATAATAGCGTAAC 58.165 41.667 0.00 0.00 0.00 2.50
2108 2233 7.547227 ACTTGTATGGTCAATAATTTTGGAGC 58.453 34.615 0.00 0.00 0.00 4.70
2109 2234 7.397192 ACTTGTATGGTCAATAATTTTGGAGCT 59.603 33.333 4.45 0.00 0.00 4.09
2110 2235 8.815565 TTGTATGGTCAATAATTTTGGAGCTA 57.184 30.769 4.45 0.00 0.00 3.32
2111 2236 8.815565 TGTATGGTCAATAATTTTGGAGCTAA 57.184 30.769 4.45 0.00 0.00 3.09
2112 2237 9.420118 TGTATGGTCAATAATTTTGGAGCTAAT 57.580 29.630 4.45 0.00 0.00 1.73
2113 2238 9.899226 GTATGGTCAATAATTTTGGAGCTAATC 57.101 33.333 4.45 0.00 0.00 1.75
2114 2239 8.773033 ATGGTCAATAATTTTGGAGCTAATCT 57.227 30.769 4.45 0.00 0.00 2.40
2115 2240 9.866655 ATGGTCAATAATTTTGGAGCTAATCTA 57.133 29.630 4.45 0.00 0.00 1.98
2116 2241 9.120538 TGGTCAATAATTTTGGAGCTAATCTAC 57.879 33.333 4.45 0.00 0.00 2.59
2117 2242 8.568794 GGTCAATAATTTTGGAGCTAATCTACC 58.431 37.037 0.00 0.00 0.00 3.18
2118 2243 9.120538 GTCAATAATTTTGGAGCTAATCTACCA 57.879 33.333 0.00 0.00 0.00 3.25
2119 2244 9.120538 TCAATAATTTTGGAGCTAATCTACCAC 57.879 33.333 0.00 0.00 31.87 4.16
2120 2245 9.125026 CAATAATTTTGGAGCTAATCTACCACT 57.875 33.333 0.00 0.00 31.87 4.00
2123 2248 7.676683 ATTTTGGAGCTAATCTACCACTAGA 57.323 36.000 0.00 0.00 33.32 2.43
2124 2249 7.676683 TTTTGGAGCTAATCTACCACTAGAT 57.323 36.000 0.00 0.00 40.90 1.98
2125 2250 7.676683 TTTGGAGCTAATCTACCACTAGATT 57.323 36.000 0.00 7.85 46.96 2.40
2126 2251 8.777578 TTTGGAGCTAATCTACCACTAGATTA 57.222 34.615 0.00 9.00 44.66 1.75
2127 2252 8.958060 TTGGAGCTAATCTACCACTAGATTAT 57.042 34.615 9.57 0.00 45.15 1.28
2128 2253 8.582657 TGGAGCTAATCTACCACTAGATTATC 57.417 38.462 9.57 6.84 45.15 1.75
2129 2254 7.616150 TGGAGCTAATCTACCACTAGATTATCC 59.384 40.741 15.70 15.70 45.15 2.59
2130 2255 7.837187 GGAGCTAATCTACCACTAGATTATCCT 59.163 40.741 15.48 12.23 45.15 3.24
2131 2256 8.817092 AGCTAATCTACCACTAGATTATCCTC 57.183 38.462 9.57 2.94 45.15 3.71
2132 2257 7.837187 AGCTAATCTACCACTAGATTATCCTCC 59.163 40.741 9.57 0.71 45.15 4.30
2133 2258 7.837187 GCTAATCTACCACTAGATTATCCTCCT 59.163 40.741 9.57 0.00 45.15 3.69
2134 2259 9.762381 CTAATCTACCACTAGATTATCCTCCTT 57.238 37.037 9.57 0.00 45.15 3.36
2136 2261 9.453830 AATCTACCACTAGATTATCCTCCTTTT 57.546 33.333 0.00 0.00 44.66 2.27
2137 2262 8.855804 TCTACCACTAGATTATCCTCCTTTTT 57.144 34.615 0.00 0.00 0.00 1.94
2138 2263 9.947189 TCTACCACTAGATTATCCTCCTTTTTA 57.053 33.333 0.00 0.00 0.00 1.52
2201 2326 3.876309 TCAAAAAGTAGTTCTGGGGCT 57.124 42.857 0.00 0.00 0.00 5.19
2205 2330 7.208064 TCAAAAAGTAGTTCTGGGGCTATAT 57.792 36.000 0.00 0.00 0.00 0.86
2209 2334 7.541916 AAAGTAGTTCTGGGGCTATATCTAC 57.458 40.000 0.00 0.00 0.00 2.59
2211 2336 6.486941 AGTAGTTCTGGGGCTATATCTACTC 58.513 44.000 0.00 0.00 33.94 2.59
2266 2412 7.308435 CCACATGATTTCAGTAGTCTTTTTCC 58.692 38.462 0.00 0.00 0.00 3.13
2271 2417 8.665643 TGATTTCAGTAGTCTTTTTCCGTTTA 57.334 30.769 0.00 0.00 0.00 2.01
2300 2446 1.348696 TGAAATGACAGCAGCTCTCCA 59.651 47.619 0.00 0.00 0.00 3.86
2307 2453 1.155042 CAGCAGCTCTCCACAGAAAC 58.845 55.000 0.00 0.00 0.00 2.78
2316 2462 3.728845 TCTCCACAGAAACTTGTAGTGC 58.271 45.455 0.00 0.00 0.00 4.40
2326 2472 2.154462 ACTTGTAGTGCAGCATTGTCC 58.846 47.619 0.00 0.00 0.00 4.02
2335 2481 2.275318 GCAGCATTGTCCTAGTCTCAC 58.725 52.381 0.00 0.00 0.00 3.51
2403 2554 7.049133 CACTGGTCATCACTACTACTACTACT 58.951 42.308 0.00 0.00 0.00 2.57
2714 2868 2.799017 TGTTCTCATTGCTGGCTGATT 58.201 42.857 0.00 0.00 0.00 2.57
2723 2877 3.138884 TGCTGGCTGATTGTTGACTTA 57.861 42.857 0.00 0.00 0.00 2.24
2735 2890 6.318648 TGATTGTTGACTTACTTGACTGCTTT 59.681 34.615 0.00 0.00 0.00 3.51
2753 2908 6.019779 TGCTTTTTAAACTCACAGTGTGTT 57.980 33.333 22.29 14.05 35.84 3.32
2755 2910 6.584563 TGCTTTTTAAACTCACAGTGTGTTTC 59.415 34.615 28.51 17.52 41.40 2.78
2790 2945 0.679960 TCAGCGAATCCGGAGACTCA 60.680 55.000 11.34 0.00 36.06 3.41
2935 3095 3.643978 CGCCGCCATAGCTGCTTC 61.644 66.667 7.79 0.00 46.08 3.86
2956 3116 3.147629 CGTAGATGTAGTAGAGGGGTGG 58.852 54.545 0.00 0.00 0.00 4.61
2981 3141 4.202305 TGGGGGTTTTCTGCTGTTTTTATG 60.202 41.667 0.00 0.00 0.00 1.90
3013 3173 1.593209 TCGTGGGTGCGTGTTCTTC 60.593 57.895 0.00 0.00 0.00 2.87
3034 3195 1.150536 TGTGGGGTGGAGCTTTGTC 59.849 57.895 0.00 0.00 0.00 3.18
3045 3206 0.036022 AGCTTTGTCCTGCTGGAGTC 59.964 55.000 13.36 2.85 44.16 3.36
3054 3215 2.092592 TCCTGCTGGAGTCGATACAGTA 60.093 50.000 8.48 9.23 42.55 2.74
3109 3270 2.370189 AGTTCAGGGTTGAGACTTGAGG 59.630 50.000 0.00 0.00 34.15 3.86
3332 3500 9.937175 GGTTCTAAAAGAATACTATGCACATTC 57.063 33.333 0.00 0.00 36.50 2.67
3366 3534 4.537751 TGATACTCCCTCCGATCCATATC 58.462 47.826 0.00 0.00 0.00 1.63
3392 3560 7.119699 CACTTGTTTCAGATTTGCCTAGATACA 59.880 37.037 0.00 0.00 0.00 2.29
3397 3565 6.737720 TCAGATTTGCCTAGATACAGATGT 57.262 37.500 0.00 0.00 0.00 3.06
3399 3567 7.661968 TCAGATTTGCCTAGATACAGATGTAC 58.338 38.462 0.00 0.00 32.72 2.90
3400 3568 7.507277 TCAGATTTGCCTAGATACAGATGTACT 59.493 37.037 0.00 0.00 32.72 2.73
3402 3570 6.406692 TTTGCCTAGATACAGATGTACTCC 57.593 41.667 0.00 0.00 32.72 3.85
3403 3571 4.408276 TGCCTAGATACAGATGTACTCCC 58.592 47.826 0.00 0.00 32.72 4.30
3404 3572 4.106502 TGCCTAGATACAGATGTACTCCCT 59.893 45.833 0.00 0.00 32.72 4.20
3405 3573 4.703093 GCCTAGATACAGATGTACTCCCTC 59.297 50.000 0.00 0.00 32.72 4.30
3406 3574 5.258051 CCTAGATACAGATGTACTCCCTCC 58.742 50.000 0.00 0.00 32.72 4.30
3407 3575 3.757270 AGATACAGATGTACTCCCTCCG 58.243 50.000 0.00 0.00 32.72 4.63
3409 3577 2.233305 ACAGATGTACTCCCTCCGTT 57.767 50.000 0.00 0.00 0.00 4.44
3411 3579 2.496470 ACAGATGTACTCCCTCCGTTTC 59.504 50.000 0.00 0.00 0.00 2.78
3412 3580 2.496070 CAGATGTACTCCCTCCGTTTCA 59.504 50.000 0.00 0.00 0.00 2.69
3413 3581 3.056107 CAGATGTACTCCCTCCGTTTCAA 60.056 47.826 0.00 0.00 0.00 2.69
3414 3582 3.581332 AGATGTACTCCCTCCGTTTCAAA 59.419 43.478 0.00 0.00 0.00 2.69
3415 3583 3.116079 TGTACTCCCTCCGTTTCAAAC 57.884 47.619 0.00 0.00 0.00 2.93
3416 3584 2.701951 TGTACTCCCTCCGTTTCAAACT 59.298 45.455 0.00 0.00 0.00 2.66
3417 3585 3.896888 TGTACTCCCTCCGTTTCAAACTA 59.103 43.478 0.00 0.00 0.00 2.24
3418 3586 3.397849 ACTCCCTCCGTTTCAAACTAC 57.602 47.619 0.00 0.00 0.00 2.73
3419 3587 2.970640 ACTCCCTCCGTTTCAAACTACT 59.029 45.455 0.00 0.00 0.00 2.57
3420 3588 3.390311 ACTCCCTCCGTTTCAAACTACTT 59.610 43.478 0.00 0.00 0.00 2.24
3421 3589 3.735591 TCCCTCCGTTTCAAACTACTTG 58.264 45.455 0.00 0.00 36.25 3.16
3422 3590 3.135167 TCCCTCCGTTTCAAACTACTTGT 59.865 43.478 0.00 0.00 36.34 3.16
3423 3591 3.497262 CCCTCCGTTTCAAACTACTTGTC 59.503 47.826 0.00 0.00 36.34 3.18
3424 3592 3.183775 CCTCCGTTTCAAACTACTTGTCG 59.816 47.826 0.00 0.00 36.34 4.35
3425 3593 2.540931 TCCGTTTCAAACTACTTGTCGC 59.459 45.455 0.00 0.00 36.34 5.19
3426 3594 2.285756 CCGTTTCAAACTACTTGTCGCA 59.714 45.455 0.00 0.00 36.34 5.10
3427 3595 3.531982 CGTTTCAAACTACTTGTCGCAG 58.468 45.455 0.00 0.00 36.34 5.18
3428 3596 3.244345 CGTTTCAAACTACTTGTCGCAGA 59.756 43.478 0.00 0.00 36.34 4.26
3429 3597 4.260051 CGTTTCAAACTACTTGTCGCAGAA 60.260 41.667 0.00 0.00 39.69 3.02
3430 3598 5.565695 GTTTCAAACTACTTGTCGCAGAAA 58.434 37.500 0.00 0.00 39.69 2.52
3431 3599 6.199393 GTTTCAAACTACTTGTCGCAGAAAT 58.801 36.000 0.00 0.00 39.69 2.17
3432 3600 5.342806 TCAAACTACTTGTCGCAGAAATG 57.657 39.130 0.00 0.00 39.69 2.32
3433 3601 4.213270 TCAAACTACTTGTCGCAGAAATGG 59.787 41.667 0.00 0.00 39.69 3.16
3434 3602 3.678056 ACTACTTGTCGCAGAAATGGA 57.322 42.857 0.00 0.00 39.69 3.41
3435 3603 4.207891 ACTACTTGTCGCAGAAATGGAT 57.792 40.909 0.00 0.00 39.69 3.41
3436 3604 5.339008 ACTACTTGTCGCAGAAATGGATA 57.661 39.130 0.00 0.00 39.69 2.59
3437 3605 5.918608 ACTACTTGTCGCAGAAATGGATAT 58.081 37.500 0.00 0.00 39.69 1.63
3438 3606 7.050970 ACTACTTGTCGCAGAAATGGATATA 57.949 36.000 0.00 0.00 39.69 0.86
3439 3607 7.671302 ACTACTTGTCGCAGAAATGGATATAT 58.329 34.615 0.00 0.00 39.69 0.86
3440 3608 7.815068 ACTACTTGTCGCAGAAATGGATATATC 59.185 37.037 3.96 3.96 39.69 1.63
3441 3609 6.763355 ACTTGTCGCAGAAATGGATATATCT 58.237 36.000 12.42 0.00 39.69 1.98
3442 3610 7.896811 ACTTGTCGCAGAAATGGATATATCTA 58.103 34.615 12.42 6.97 39.69 1.98
3443 3611 8.031864 ACTTGTCGCAGAAATGGATATATCTAG 58.968 37.037 12.42 0.00 39.69 2.43
3444 3612 7.703058 TGTCGCAGAAATGGATATATCTAGA 57.297 36.000 12.42 0.00 39.69 2.43
3445 3613 8.122472 TGTCGCAGAAATGGATATATCTAGAA 57.878 34.615 12.42 0.00 39.69 2.10
3446 3614 8.029522 TGTCGCAGAAATGGATATATCTAGAAC 58.970 37.037 12.42 2.68 39.69 3.01
3447 3615 8.247562 GTCGCAGAAATGGATATATCTAGAACT 58.752 37.037 12.42 4.71 39.69 3.01
3448 3616 9.462606 TCGCAGAAATGGATATATCTAGAACTA 57.537 33.333 12.42 0.00 0.00 2.24
3476 3644 8.824756 ATACATCTAGATACATCAATACCCGT 57.175 34.615 4.54 0.00 0.00 5.28
3477 3645 6.925211 ACATCTAGATACATCAATACCCGTG 58.075 40.000 4.54 0.00 0.00 4.94
3478 3646 6.719829 ACATCTAGATACATCAATACCCGTGA 59.280 38.462 4.54 0.00 0.00 4.35
3479 3647 6.570672 TCTAGATACATCAATACCCGTGAC 57.429 41.667 0.00 0.00 0.00 3.67
3480 3648 6.066032 TCTAGATACATCAATACCCGTGACA 58.934 40.000 0.00 0.00 0.00 3.58
3481 3649 5.607939 AGATACATCAATACCCGTGACAA 57.392 39.130 0.00 0.00 0.00 3.18
3482 3650 5.601662 AGATACATCAATACCCGTGACAAG 58.398 41.667 0.00 0.00 0.00 3.16
3483 3651 3.695830 ACATCAATACCCGTGACAAGT 57.304 42.857 0.00 0.00 0.00 3.16
3484 3652 4.811969 ACATCAATACCCGTGACAAGTA 57.188 40.909 0.00 0.00 0.00 2.24
3485 3653 5.155278 ACATCAATACCCGTGACAAGTAA 57.845 39.130 0.00 0.00 0.00 2.24
3486 3654 5.741011 ACATCAATACCCGTGACAAGTAAT 58.259 37.500 0.00 0.00 0.00 1.89
3487 3655 6.177610 ACATCAATACCCGTGACAAGTAATT 58.822 36.000 0.00 0.00 0.00 1.40
3488 3656 6.315393 ACATCAATACCCGTGACAAGTAATTC 59.685 38.462 0.00 0.00 0.00 2.17
3489 3657 4.865925 TCAATACCCGTGACAAGTAATTCG 59.134 41.667 0.00 0.00 0.00 3.34
3490 3658 2.088950 ACCCGTGACAAGTAATTCGG 57.911 50.000 0.00 0.00 38.05 4.30
3491 3659 1.619827 ACCCGTGACAAGTAATTCGGA 59.380 47.619 2.71 0.00 40.29 4.55
3492 3660 2.037511 ACCCGTGACAAGTAATTCGGAA 59.962 45.455 2.71 0.00 40.29 4.30
3493 3661 2.414138 CCCGTGACAAGTAATTCGGAAC 59.586 50.000 2.71 0.00 40.29 3.62
3535 3703 5.994054 TGTGTCTAGGTACATCCGTATCTAC 59.006 44.000 0.00 0.00 39.80 2.59
3539 3707 7.722728 TGTCTAGGTACATCCGTATCTACAAAT 59.277 37.037 0.00 0.00 39.80 2.32
3588 3758 1.277842 TGATAAAAGGAGTCGGCAGCA 59.722 47.619 0.00 0.00 0.00 4.41
3613 3783 2.354328 TGGAAGGAGGGTATGTTTGGT 58.646 47.619 0.00 0.00 0.00 3.67
3621 3791 3.886505 GAGGGTATGTTTGGTTTGTGTCA 59.113 43.478 0.00 0.00 0.00 3.58
3674 3845 4.579647 TTTGTATGGGAAGGAGGGTTAC 57.420 45.455 0.00 0.00 0.00 2.50
3721 3896 6.825610 TCTTGTTTAGATGGTTGGCAAAATT 58.174 32.000 0.00 0.00 0.00 1.82
3724 3899 7.256756 TGTTTAGATGGTTGGCAAAATTTTG 57.743 32.000 23.74 23.74 41.03 2.44
3750 3927 2.165998 GCCAACCTTGCTCTCTCATTT 58.834 47.619 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.884726 TCAGTATCTTGATATATGAGCGTACTC 58.115 37.037 0.00 0.00 43.76 2.59
2 3 8.794335 TCAGTATCTTGATATATGAGCGTACT 57.206 34.615 0.00 0.00 0.00 2.73
3 4 8.670135 ACTCAGTATCTTGATATATGAGCGTAC 58.330 37.037 22.08 0.00 36.92 3.67
4 5 8.794335 ACTCAGTATCTTGATATATGAGCGTA 57.206 34.615 22.08 0.00 36.92 4.42
17 18 9.823647 ACCAAATAAGTATGACTCAGTATCTTG 57.176 33.333 0.00 0.00 0.00 3.02
21 22 9.765795 GCTAACCAAATAAGTATGACTCAGTAT 57.234 33.333 0.00 0.00 0.00 2.12
22 23 8.202137 GGCTAACCAAATAAGTATGACTCAGTA 58.798 37.037 0.00 0.00 35.26 2.74
23 24 7.048512 GGCTAACCAAATAAGTATGACTCAGT 58.951 38.462 0.00 0.00 35.26 3.41
24 25 7.047891 TGGCTAACCAAATAAGTATGACTCAG 58.952 38.462 0.00 0.00 45.37 3.35
25 26 6.953101 TGGCTAACCAAATAAGTATGACTCA 58.047 36.000 0.00 0.00 45.37 3.41
67 68 3.708563 AATATGCCCATGCGTTGTAAC 57.291 42.857 0.00 0.00 41.78 2.50
68 69 4.039151 CAAATATGCCCATGCGTTGTAA 57.961 40.909 0.00 0.00 41.78 2.41
69 70 3.706802 CAAATATGCCCATGCGTTGTA 57.293 42.857 0.00 0.00 41.78 2.41
70 71 2.582728 CAAATATGCCCATGCGTTGT 57.417 45.000 0.00 0.00 41.78 3.32
84 85 9.974980 TGTGTATTCGATGATTACTAGCAAATA 57.025 29.630 0.00 0.00 0.00 1.40
85 86 8.887036 TGTGTATTCGATGATTACTAGCAAAT 57.113 30.769 0.00 0.00 0.00 2.32
86 87 7.979537 ACTGTGTATTCGATGATTACTAGCAAA 59.020 33.333 0.00 0.00 0.00 3.68
87 88 7.489160 ACTGTGTATTCGATGATTACTAGCAA 58.511 34.615 0.00 0.00 0.00 3.91
88 89 7.039313 ACTGTGTATTCGATGATTACTAGCA 57.961 36.000 0.00 0.00 0.00 3.49
89 90 7.648112 TCAACTGTGTATTCGATGATTACTAGC 59.352 37.037 0.00 0.00 0.00 3.42
90 91 9.516314 TTCAACTGTGTATTCGATGATTACTAG 57.484 33.333 0.00 0.00 0.00 2.57
91 92 9.863845 TTTCAACTGTGTATTCGATGATTACTA 57.136 29.630 0.00 0.00 0.00 1.82
92 93 8.771920 TTTCAACTGTGTATTCGATGATTACT 57.228 30.769 0.00 0.00 0.00 2.24
102 103 7.642194 TGTCATTTCGTTTTCAACTGTGTATTC 59.358 33.333 0.00 0.00 0.00 1.75
110 115 4.798387 GCAGTTGTCATTTCGTTTTCAACT 59.202 37.500 0.00 0.00 43.67 3.16
130 135 1.655484 TTATGATGACAGCCACGCAG 58.345 50.000 0.00 0.00 0.00 5.18
151 157 7.430211 CGCCGGGTTTTATTTTAGAGTATTTTC 59.570 37.037 2.18 0.00 0.00 2.29
179 189 1.066787 CCAGGAAGACGGGTTCTCTTC 60.067 57.143 4.56 4.56 42.03 2.87
180 190 0.977395 CCAGGAAGACGGGTTCTCTT 59.023 55.000 0.00 0.00 31.02 2.85
181 191 0.905337 CCCAGGAAGACGGGTTCTCT 60.905 60.000 0.00 0.00 37.70 3.10
182 192 0.903454 TCCCAGGAAGACGGGTTCTC 60.903 60.000 0.00 0.00 43.57 2.87
187 197 2.982130 CTGTCCCAGGAAGACGGG 59.018 66.667 0.00 0.00 44.60 5.28
223 233 3.957497 CTCCGGGAGAGGGATAATCTATG 59.043 52.174 19.57 0.00 39.13 2.23
337 388 2.094762 AAGAAGGGAATTCGTCACGG 57.905 50.000 0.00 0.00 43.16 4.94
338 389 5.220605 GGATAAAAGAAGGGAATTCGTCACG 60.221 44.000 0.00 0.00 43.16 4.35
339 390 5.646360 TGGATAAAAGAAGGGAATTCGTCAC 59.354 40.000 0.00 0.00 43.16 3.67
340 391 5.646360 GTGGATAAAAGAAGGGAATTCGTCA 59.354 40.000 0.00 0.00 43.16 4.35
341 392 5.220605 CGTGGATAAAAGAAGGGAATTCGTC 60.221 44.000 0.00 0.00 43.16 4.20
342 393 4.634443 CGTGGATAAAAGAAGGGAATTCGT 59.366 41.667 0.00 0.00 43.16 3.85
400 457 1.798735 CATCCAACTTGCGAGGCAG 59.201 57.895 5.79 0.00 40.61 4.85
406 463 2.350899 TCAAATGCATCCAACTTGCG 57.649 45.000 0.00 0.00 43.10 4.85
438 495 2.670934 CAGGCACAGCACAGGGAC 60.671 66.667 0.00 0.00 0.00 4.46
439 496 3.170672 ACAGGCACAGCACAGGGA 61.171 61.111 0.00 0.00 0.00 4.20
443 500 4.584518 CCCCACAGGCACAGCACA 62.585 66.667 0.00 0.00 0.00 4.57
444 501 3.190738 TACCCCACAGGCACAGCAC 62.191 63.158 0.00 0.00 40.58 4.40
445 502 2.851588 TACCCCACAGGCACAGCA 60.852 61.111 0.00 0.00 40.58 4.41
446 503 2.045926 CTACCCCACAGGCACAGC 60.046 66.667 0.00 0.00 40.58 4.40
449 506 1.675641 CTTGCTACCCCACAGGCAC 60.676 63.158 0.00 0.00 40.58 5.01
450 507 1.422977 TTCTTGCTACCCCACAGGCA 61.423 55.000 0.00 0.00 40.58 4.75
470 530 9.675464 CTTCCTCTCTTCTTCTACTTCTACTTA 57.325 37.037 0.00 0.00 0.00 2.24
480 540 4.277476 CAGCCTCTTCCTCTCTTCTTCTA 58.723 47.826 0.00 0.00 0.00 2.10
544 610 3.005529 AGGAAAGGAAAGGAAGGGAGA 57.994 47.619 0.00 0.00 0.00 3.71
547 613 3.165875 GGAAAGGAAAGGAAAGGAAGGG 58.834 50.000 0.00 0.00 0.00 3.95
549 615 4.281941 CCAAGGAAAGGAAAGGAAAGGAAG 59.718 45.833 0.00 0.00 0.00 3.46
550 616 4.223144 CCAAGGAAAGGAAAGGAAAGGAA 58.777 43.478 0.00 0.00 0.00 3.36
551 617 3.437931 CCCAAGGAAAGGAAAGGAAAGGA 60.438 47.826 0.00 0.00 0.00 3.36
552 618 2.899900 CCCAAGGAAAGGAAAGGAAAGG 59.100 50.000 0.00 0.00 0.00 3.11
553 619 2.899900 CCCCAAGGAAAGGAAAGGAAAG 59.100 50.000 0.00 0.00 33.47 2.62
554 620 2.970987 CCCCAAGGAAAGGAAAGGAAA 58.029 47.619 0.00 0.00 33.47 3.13
555 621 1.482365 GCCCCAAGGAAAGGAAAGGAA 60.482 52.381 0.00 0.00 33.47 3.36
559 625 1.503347 AGAAGCCCCAAGGAAAGGAAA 59.497 47.619 0.00 0.00 33.47 3.13
562 628 0.323816 GGAGAAGCCCCAAGGAAAGG 60.324 60.000 0.00 0.00 33.47 3.11
571 637 1.076632 TCTCTCTCGGAGAAGCCCC 60.077 63.158 9.32 0.00 46.85 5.80
601 671 2.018086 AGAGAGGAGGGAGGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
611 681 1.042559 GGACCAGCCAGAGAGAGGAG 61.043 65.000 0.00 0.00 36.34 3.69
612 682 1.000993 GGACCAGCCAGAGAGAGGA 59.999 63.158 0.00 0.00 36.34 3.71
819 889 2.045340 AATCTTTGGCCGGACCCG 60.045 61.111 3.83 0.66 37.83 5.28
834 904 3.064324 GACCCCGCAAGCAGCAAT 61.064 61.111 0.00 0.00 46.13 3.56
1196 1289 1.228245 TGCTCCTTGTGGTCCTTGC 60.228 57.895 0.00 0.00 34.23 4.01
1380 1479 4.659172 ATGGTGGTGTGGGTGCGG 62.659 66.667 0.00 0.00 0.00 5.69
1381 1480 3.055719 GATGGTGGTGTGGGTGCG 61.056 66.667 0.00 0.00 0.00 5.34
1382 1481 1.228552 AAGATGGTGGTGTGGGTGC 60.229 57.895 0.00 0.00 0.00 5.01
1383 1482 0.609131 GGAAGATGGTGGTGTGGGTG 60.609 60.000 0.00 0.00 0.00 4.61
1384 1483 0.772124 AGGAAGATGGTGGTGTGGGT 60.772 55.000 0.00 0.00 0.00 4.51
1385 1484 0.035056 GAGGAAGATGGTGGTGTGGG 60.035 60.000 0.00 0.00 0.00 4.61
1400 1499 4.141274 TCAGTTGGAAAAGTTCATGGAGGA 60.141 41.667 0.00 0.00 0.00 3.71
1569 1674 2.980586 GCACAACGCGCAATATGATTA 58.019 42.857 5.73 0.00 0.00 1.75
1651 1765 5.407502 CAATGCAATGTGAGACATCATTGT 58.592 37.500 16.00 0.00 46.97 2.71
1721 1835 8.235154 TTGTAGTACAATACTGGGTGACCGAC 62.235 46.154 11.75 0.00 43.51 4.79
1722 1836 6.272223 TTGTAGTACAATACTGGGTGACCGA 61.272 44.000 11.75 0.00 43.51 4.69
1723 1837 4.082081 TTGTAGTACAATACTGGGTGACCG 60.082 45.833 11.75 0.00 43.51 4.79
1780 1894 8.605746 CAGTAAGACCTATCTATCTATACGTGC 58.394 40.741 0.00 0.00 33.57 5.34
1816 1934 1.769026 TCAGAAGGATGTCTCTCGGG 58.231 55.000 0.00 0.00 0.00 5.14
1888 2006 6.303839 ACCAAGTCCAACACATGTATAAAGT 58.696 36.000 0.00 0.00 0.00 2.66
1919 2042 6.796705 ATTTTCGGAATAAACAAGACTCGT 57.203 33.333 0.00 0.00 0.00 4.18
2002 2126 8.435982 AGATGGTGGAATTTAGAATCTAGAAGG 58.564 37.037 0.00 0.00 0.00 3.46
2046 2170 1.000521 TGGAAAGCATGCCCTGAGG 60.001 57.895 15.66 0.00 0.00 3.86
2084 2208 7.775120 AGCTCCAAAATTATTGACCATACAAG 58.225 34.615 0.00 0.00 33.22 3.16
2111 2236 9.453830 AAAAAGGAGGATAATCTAGTGGTAGAT 57.546 33.333 0.00 0.00 46.36 1.98
2112 2237 8.855804 AAAAAGGAGGATAATCTAGTGGTAGA 57.144 34.615 0.00 0.00 39.70 2.59
2156 2281 4.081917 CAGAAAACTGTAGGGGAGAGACTC 60.082 50.000 0.00 0.00 0.00 3.36
2157 2282 3.835395 CAGAAAACTGTAGGGGAGAGACT 59.165 47.826 0.00 0.00 0.00 3.24
2158 2283 3.833070 TCAGAAAACTGTAGGGGAGAGAC 59.167 47.826 0.00 0.00 0.00 3.36
2159 2284 4.127918 TCAGAAAACTGTAGGGGAGAGA 57.872 45.455 0.00 0.00 0.00 3.10
2160 2285 4.467795 TGATCAGAAAACTGTAGGGGAGAG 59.532 45.833 0.00 0.00 0.00 3.20
2191 2316 4.156373 GTCGAGTAGATATAGCCCCAGAAC 59.844 50.000 0.00 0.00 0.00 3.01
2205 2330 9.243105 TCAATATCATGAATATGGTCGAGTAGA 57.757 33.333 0.00 0.00 34.97 2.59
2266 2412 6.524586 GCTGTCATTTCAATCCTCTTTAAACG 59.475 38.462 0.00 0.00 0.00 3.60
2271 2417 4.082354 GCTGCTGTCATTTCAATCCTCTTT 60.082 41.667 0.00 0.00 0.00 2.52
2300 2446 2.917933 TGCTGCACTACAAGTTTCTGT 58.082 42.857 0.00 0.00 0.00 3.41
2307 2453 2.430465 AGGACAATGCTGCACTACAAG 58.570 47.619 3.57 0.00 0.00 3.16
2316 2462 3.194329 TCTGTGAGACTAGGACAATGCTG 59.806 47.826 0.00 0.00 0.00 4.41
2409 2560 8.635765 ATGAGGAATTTTCTTGTTGCTAAGTA 57.364 30.769 0.00 0.00 0.00 2.24
2414 2565 4.992951 GCAATGAGGAATTTTCTTGTTGCT 59.007 37.500 15.39 0.00 37.16 3.91
2635 2787 1.303091 ATTTCCGTACACGCCAAGGC 61.303 55.000 0.00 0.00 38.18 4.35
2703 2857 1.985473 AAGTCAACAATCAGCCAGCA 58.015 45.000 0.00 0.00 0.00 4.41
2714 2868 6.509418 AAAAAGCAGTCAAGTAAGTCAACA 57.491 33.333 0.00 0.00 0.00 3.33
2723 2877 6.151144 ACTGTGAGTTTAAAAAGCAGTCAAGT 59.849 34.615 8.98 2.71 31.04 3.16
2735 2890 6.315393 GGAGAGAAACACACTGTGAGTTTAAA 59.685 38.462 27.90 0.00 40.33 1.52
2753 2908 5.302823 TCGCTGAAATCATCATAGGAGAGAA 59.697 40.000 0.00 0.00 37.44 2.87
2755 2910 5.131594 TCGCTGAAATCATCATAGGAGAG 57.868 43.478 0.00 0.00 37.44 3.20
2790 2945 0.537188 AGATGCCTTCGTCGTCCATT 59.463 50.000 0.00 0.00 33.49 3.16
2935 3095 3.147629 CCACCCCTCTACTACATCTACG 58.852 54.545 0.00 0.00 0.00 3.51
2956 3116 0.759060 AACAGCAGAAAACCCCCACC 60.759 55.000 0.00 0.00 0.00 4.61
2981 3141 0.378962 CCACGACGGATCTGAGACTC 59.621 60.000 9.00 0.00 36.56 3.36
3013 3173 3.491598 AAAGCTCCACCCCACACCG 62.492 63.158 0.00 0.00 0.00 4.94
3034 3195 1.107114 ACTGTATCGACTCCAGCAGG 58.893 55.000 7.51 0.00 0.00 4.85
3045 3206 2.512885 AGCGTCAAACGTACTGTATCG 58.487 47.619 1.14 7.80 44.73 2.92
3054 3215 1.081376 CGAGAGGAGCGTCAAACGT 60.081 57.895 1.14 0.00 44.73 3.99
3109 3270 5.007682 TGGGAACTTTACAGAAGCAATACC 58.992 41.667 0.00 0.00 0.00 2.73
3154 3315 5.042463 TCATCTCTATGTCTTCCGACTCT 57.958 43.478 0.00 0.00 40.86 3.24
3342 3510 3.260269 TGGATCGGAGGGAGTATCATT 57.740 47.619 0.00 0.00 36.25 2.57
3343 3511 3.481559 ATGGATCGGAGGGAGTATCAT 57.518 47.619 0.00 0.00 36.25 2.45
3366 3534 5.947228 TCTAGGCAAATCTGAAACAAGTG 57.053 39.130 0.00 0.00 0.00 3.16
3392 3560 2.816411 TGAAACGGAGGGAGTACATCT 58.184 47.619 0.00 0.00 0.00 2.90
3397 3565 4.154942 AGTAGTTTGAAACGGAGGGAGTA 58.845 43.478 1.97 0.00 36.23 2.59
3399 3567 3.679824 AGTAGTTTGAAACGGAGGGAG 57.320 47.619 1.97 0.00 36.23 4.30
3400 3568 3.135167 ACAAGTAGTTTGAAACGGAGGGA 59.865 43.478 1.97 0.00 39.21 4.20
3402 3570 3.183775 CGACAAGTAGTTTGAAACGGAGG 59.816 47.826 1.97 0.00 39.21 4.30
3403 3571 3.362693 GCGACAAGTAGTTTGAAACGGAG 60.363 47.826 1.97 0.00 39.21 4.63
3404 3572 2.540931 GCGACAAGTAGTTTGAAACGGA 59.459 45.455 1.97 0.00 39.21 4.69
3405 3573 2.285756 TGCGACAAGTAGTTTGAAACGG 59.714 45.455 1.97 0.00 39.21 4.44
3406 3574 3.244345 TCTGCGACAAGTAGTTTGAAACG 59.756 43.478 1.97 0.00 39.21 3.60
3407 3575 4.789095 TCTGCGACAAGTAGTTTGAAAC 57.211 40.909 0.00 0.00 39.21 2.78
3409 3577 5.277779 CCATTTCTGCGACAAGTAGTTTGAA 60.278 40.000 0.00 0.00 39.21 2.69
3411 3579 4.213270 TCCATTTCTGCGACAAGTAGTTTG 59.787 41.667 0.00 0.00 42.68 2.93
3412 3580 4.385825 TCCATTTCTGCGACAAGTAGTTT 58.614 39.130 0.00 0.00 34.00 2.66
3413 3581 4.002906 TCCATTTCTGCGACAAGTAGTT 57.997 40.909 0.00 0.00 34.00 2.24
3414 3582 3.678056 TCCATTTCTGCGACAAGTAGT 57.322 42.857 0.00 0.00 34.00 2.73
3415 3583 8.031864 AGATATATCCATTTCTGCGACAAGTAG 58.968 37.037 9.18 0.00 0.00 2.57
3416 3584 7.896811 AGATATATCCATTTCTGCGACAAGTA 58.103 34.615 9.18 0.00 0.00 2.24
3417 3585 6.763355 AGATATATCCATTTCTGCGACAAGT 58.237 36.000 9.18 0.00 0.00 3.16
3418 3586 8.246871 TCTAGATATATCCATTTCTGCGACAAG 58.753 37.037 9.18 0.00 0.00 3.16
3419 3587 8.122472 TCTAGATATATCCATTTCTGCGACAA 57.878 34.615 9.18 0.00 0.00 3.18
3420 3588 7.703058 TCTAGATATATCCATTTCTGCGACA 57.297 36.000 9.18 0.00 0.00 4.35
3421 3589 8.247562 AGTTCTAGATATATCCATTTCTGCGAC 58.752 37.037 9.18 0.00 0.00 5.19
3422 3590 8.354711 AGTTCTAGATATATCCATTTCTGCGA 57.645 34.615 9.18 0.00 0.00 5.10
3450 3618 9.256228 ACGGGTATTGATGTATCTAGATGTATT 57.744 33.333 15.79 0.00 0.00 1.89
3451 3619 8.687242 CACGGGTATTGATGTATCTAGATGTAT 58.313 37.037 15.79 9.11 0.00 2.29
3452 3620 7.886446 TCACGGGTATTGATGTATCTAGATGTA 59.114 37.037 15.79 4.44 0.00 2.29
3453 3621 6.719829 TCACGGGTATTGATGTATCTAGATGT 59.280 38.462 15.79 1.25 0.00 3.06
3454 3622 7.030165 GTCACGGGTATTGATGTATCTAGATG 58.970 42.308 15.79 0.00 0.00 2.90
3455 3623 6.719829 TGTCACGGGTATTGATGTATCTAGAT 59.280 38.462 10.73 10.73 0.00 1.98
3456 3624 6.066032 TGTCACGGGTATTGATGTATCTAGA 58.934 40.000 0.00 0.00 0.00 2.43
3457 3625 6.327279 TGTCACGGGTATTGATGTATCTAG 57.673 41.667 0.00 0.00 0.00 2.43
3458 3626 6.322969 ACTTGTCACGGGTATTGATGTATCTA 59.677 38.462 0.00 0.00 0.00 1.98
3459 3627 5.128827 ACTTGTCACGGGTATTGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
3460 3628 5.357257 ACTTGTCACGGGTATTGATGTATC 58.643 41.667 0.00 0.00 0.00 2.24
3461 3629 5.353394 ACTTGTCACGGGTATTGATGTAT 57.647 39.130 0.00 0.00 0.00 2.29
3462 3630 4.811969 ACTTGTCACGGGTATTGATGTA 57.188 40.909 0.00 0.00 0.00 2.29
3463 3631 3.695830 ACTTGTCACGGGTATTGATGT 57.304 42.857 0.00 0.00 0.00 3.06
3464 3632 6.509517 CGAATTACTTGTCACGGGTATTGATG 60.510 42.308 0.00 0.00 0.00 3.07
3465 3633 5.522460 CGAATTACTTGTCACGGGTATTGAT 59.478 40.000 0.00 0.00 0.00 2.57
3466 3634 4.865925 CGAATTACTTGTCACGGGTATTGA 59.134 41.667 0.00 0.00 0.00 2.57
3467 3635 4.033587 CCGAATTACTTGTCACGGGTATTG 59.966 45.833 0.00 0.00 37.28 1.90
3468 3636 4.081531 TCCGAATTACTTGTCACGGGTATT 60.082 41.667 0.00 0.00 40.59 1.89
3469 3637 3.448301 TCCGAATTACTTGTCACGGGTAT 59.552 43.478 0.00 0.00 40.59 2.73
3470 3638 2.824936 TCCGAATTACTTGTCACGGGTA 59.175 45.455 0.00 0.00 40.59 3.69
3471 3639 1.619827 TCCGAATTACTTGTCACGGGT 59.380 47.619 0.00 0.00 40.59 5.28
3472 3640 2.373540 TCCGAATTACTTGTCACGGG 57.626 50.000 0.00 0.00 40.59 5.28
3473 3641 2.091588 CGTTCCGAATTACTTGTCACGG 59.908 50.000 0.00 0.00 41.39 4.94
3474 3642 2.981805 TCGTTCCGAATTACTTGTCACG 59.018 45.455 0.00 0.00 31.06 4.35
3475 3643 4.143179 CCTTCGTTCCGAATTACTTGTCAC 60.143 45.833 0.00 0.00 44.85 3.67
3476 3644 3.991773 CCTTCGTTCCGAATTACTTGTCA 59.008 43.478 0.00 0.00 44.85 3.58
3477 3645 3.370061 CCCTTCGTTCCGAATTACTTGTC 59.630 47.826 0.00 0.00 44.85 3.18
3478 3646 3.007182 TCCCTTCGTTCCGAATTACTTGT 59.993 43.478 0.00 0.00 44.85 3.16
3479 3647 3.592059 TCCCTTCGTTCCGAATTACTTG 58.408 45.455 0.00 0.00 44.85 3.16
3480 3648 3.260128 ACTCCCTTCGTTCCGAATTACTT 59.740 43.478 0.00 0.00 44.85 2.24
3481 3649 2.830321 ACTCCCTTCGTTCCGAATTACT 59.170 45.455 0.00 0.00 44.85 2.24
3482 3650 3.242549 ACTCCCTTCGTTCCGAATTAC 57.757 47.619 0.00 0.00 44.85 1.89
3483 3651 4.891756 AGATACTCCCTTCGTTCCGAATTA 59.108 41.667 0.00 0.00 44.85 1.40
3484 3652 3.705072 AGATACTCCCTTCGTTCCGAATT 59.295 43.478 0.00 0.00 44.85 2.17
3485 3653 3.297736 AGATACTCCCTTCGTTCCGAAT 58.702 45.455 0.00 0.00 44.85 3.34
3486 3654 2.731572 AGATACTCCCTTCGTTCCGAA 58.268 47.619 0.00 0.00 43.75 4.30
3487 3655 2.431954 AGATACTCCCTTCGTTCCGA 57.568 50.000 0.00 0.00 0.00 4.55
3488 3656 4.644103 TTTAGATACTCCCTTCGTTCCG 57.356 45.455 0.00 0.00 0.00 4.30
3489 3657 6.258068 CACATTTTAGATACTCCCTTCGTTCC 59.742 42.308 0.00 0.00 0.00 3.62
3490 3658 6.817140 ACACATTTTAGATACTCCCTTCGTTC 59.183 38.462 0.00 0.00 0.00 3.95
3491 3659 6.708285 ACACATTTTAGATACTCCCTTCGTT 58.292 36.000 0.00 0.00 0.00 3.85
3492 3660 6.154706 AGACACATTTTAGATACTCCCTTCGT 59.845 38.462 0.00 0.00 0.00 3.85
3493 3661 6.574350 AGACACATTTTAGATACTCCCTTCG 58.426 40.000 0.00 0.00 0.00 3.79
3494 3662 8.145122 CCTAGACACATTTTAGATACTCCCTTC 58.855 40.741 0.00 0.00 0.00 3.46
3495 3663 7.624077 ACCTAGACACATTTTAGATACTCCCTT 59.376 37.037 0.00 0.00 0.00 3.95
3496 3664 7.133483 ACCTAGACACATTTTAGATACTCCCT 58.867 38.462 0.00 0.00 0.00 4.20
3497 3665 7.362802 ACCTAGACACATTTTAGATACTCCC 57.637 40.000 0.00 0.00 0.00 4.30
3498 3666 8.910944 TGTACCTAGACACATTTTAGATACTCC 58.089 37.037 0.00 0.00 0.00 3.85
3501 3669 9.694137 GGATGTACCTAGACACATTTTAGATAC 57.306 37.037 9.65 0.00 35.55 2.24
3502 3670 8.573885 CGGATGTACCTAGACACATTTTAGATA 58.426 37.037 9.65 0.00 35.55 1.98
3503 3671 7.069578 ACGGATGTACCTAGACACATTTTAGAT 59.930 37.037 9.65 0.00 35.55 1.98
3504 3672 6.379133 ACGGATGTACCTAGACACATTTTAGA 59.621 38.462 9.65 0.00 35.55 2.10
3505 3673 6.570692 ACGGATGTACCTAGACACATTTTAG 58.429 40.000 9.65 5.80 35.55 1.85
3506 3674 6.534475 ACGGATGTACCTAGACACATTTTA 57.466 37.500 9.65 0.00 35.55 1.52
3507 3675 5.416271 ACGGATGTACCTAGACACATTTT 57.584 39.130 9.65 0.00 35.55 1.82
3574 3744 1.270550 CAATTTTGCTGCCGACTCCTT 59.729 47.619 0.00 0.00 0.00 3.36
3578 3748 1.270550 CTTCCAATTTTGCTGCCGACT 59.729 47.619 0.00 0.00 0.00 4.18
3580 3750 0.602562 CCTTCCAATTTTGCTGCCGA 59.397 50.000 0.00 0.00 0.00 5.54
3583 3753 1.066645 CCCTCCTTCCAATTTTGCTGC 60.067 52.381 0.00 0.00 0.00 5.25
3585 3755 2.702270 ACCCTCCTTCCAATTTTGCT 57.298 45.000 0.00 0.00 0.00 3.91
3588 3758 5.248248 CCAAACATACCCTCCTTCCAATTTT 59.752 40.000 0.00 0.00 0.00 1.82
3613 3783 3.506455 TCAAGGTCGGTTTTTGACACAAA 59.494 39.130 0.00 0.00 38.10 2.83
3621 3791 7.820386 ACTTTTAAATTGTCAAGGTCGGTTTTT 59.180 29.630 0.00 0.00 0.00 1.94
3628 3798 8.887036 AATGGAACTTTTAAATTGTCAAGGTC 57.113 30.769 0.00 1.75 32.97 3.85
3705 3880 3.148412 GCCAAAATTTTGCCAACCATCT 58.852 40.909 22.90 0.00 36.86 2.90
3750 3927 3.195396 GGCCAATGTCTGCAGGAAAAATA 59.805 43.478 15.13 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.