Multiple sequence alignment - TraesCS5A01G305300

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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 TraesCS5A01G305300 chr5A 100.000 2515 0 0 1422 3936 514152554 514150040 0.000000e+00 4645.0
1 TraesCS5A01G305300 chr5A 100.000 1232 0 0 1 1232 514153975 514152744 0.000000e+00 2276.0
2 TraesCS5A01G305300 chr5A 90.678 118 11 0 2540 2657 514151376 514151259 1.460000e-34 158.0
3 TraesCS5A01G305300 chr5A 90.678 118 11 0 2600 2717 514151436 514151319 1.460000e-34 158.0
4 TraesCS5A01G305300 chr5A 91.398 93 7 1 3031 3123 406990605 406990514 4.130000e-25 126.0
5 TraesCS5A01G305300 chr5B 90.831 1625 122 18 1422 3040 489809061 489807458 0.000000e+00 2150.0
6 TraesCS5A01G305300 chr5B 95.050 808 30 5 429 1232 489809891 489809090 0.000000e+00 1262.0
7 TraesCS5A01G305300 chr5B 89.616 443 36 3 1 433 489810368 489809926 4.440000e-154 555.0
8 TraesCS5A01G305300 chr5B 94.860 214 10 1 3118 3331 489807463 489807251 2.270000e-87 333.0
9 TraesCS5A01G305300 chr5B 92.373 118 9 0 2598 2715 489807961 489807844 6.760000e-38 169.0
10 TraesCS5A01G305300 chr5B 92.308 91 6 1 3031 3121 321218045 321218134 1.150000e-25 128.0
11 TraesCS5A01G305300 chr5D 91.780 1545 96 21 1448 2982 408317264 408315741 0.000000e+00 2121.0
12 TraesCS5A01G305300 chr5D 96.283 807 21 5 429 1232 408318513 408317713 0.000000e+00 1315.0
13 TraesCS5A01G305300 chr5D 90.776 477 27 5 3460 3936 408315465 408315006 4.320000e-174 621.0
14 TraesCS5A01G305300 chr5D 91.874 443 26 3 1 433 408318990 408318548 9.350000e-171 610.0
15 TraesCS5A01G305300 chr5D 94.531 256 1 1 3118 3373 408315714 408315472 2.220000e-102 383.0
16 TraesCS5A01G305300 chr5D 92.500 120 9 0 2598 2717 408316186 408316067 5.230000e-39 172.0
17 TraesCS5A01G305300 chr5D 97.674 43 1 0 2998 3040 408315751 408315709 1.520000e-09 75.0
18 TraesCS5A01G305300 chr1D 92.473 93 7 0 3037 3129 93124874 93124782 2.470000e-27 134.0
19 TraesCS5A01G305300 chr1B 80.337 178 34 1 3479 3656 16433051 16433227 2.470000e-27 134.0
20 TraesCS5A01G305300 chr6A 90.816 98 9 0 3029 3126 557970140 557970043 8.870000e-27 132.0
21 TraesCS5A01G305300 chr3B 91.398 93 7 1 3034 3126 157246643 157246734 4.130000e-25 126.0
22 TraesCS5A01G305300 chr3A 91.398 93 6 2 3034 3126 550416262 550416172 4.130000e-25 126.0
23 TraesCS5A01G305300 chr3A 87.037 108 13 1 3023 3130 480969584 480969478 1.920000e-23 121.0
24 TraesCS5A01G305300 chrUn 81.633 147 26 1 3486 3632 63110164 63110309 1.920000e-23 121.0
25 TraesCS5A01G305300 chr2D 87.037 108 12 2 3029 3135 15192874 15192980 1.920000e-23 121.0
26 TraesCS5A01G305300 chr6B 85.124 121 12 6 3016 3134 520089879 520089995 6.910000e-23 119.0
27 TraesCS5A01G305300 chr3D 79.042 167 30 4 3726 3889 30420069 30420233 4.160000e-20 110.0
28 TraesCS5A01G305300 chr1A 100.000 29 0 0 3490 3518 516456472 516456444 2.000000e-03 54.7


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 TraesCS5A01G305300 chr5A 514150040 514153975 3935 True 1809.250000 4645 95.339000 1 3936 4 chr5A.!!$R2 3935
1 TraesCS5A01G305300 chr5B 489807251 489810368 3117 True 893.800000 2150 92.546000 1 3331 5 chr5B.!!$R1 3330
2 TraesCS5A01G305300 chr5D 408315006 408318990 3984 True 756.714286 2121 93.631143 1 3936 7 chr5D.!!$R1 3935

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
265 267 0.521291 CGACAACATCCGCACCATTT 59.479 50.0 0.00 0.0 0.0 2.32 F
1005 1064 0.107993 TGAGCGCCTGAAGAATGGAG 60.108 55.0 2.29 0.0 0.0 3.86 F
2471 2779 0.318107 CACAAAGGCAGCCAAGAACG 60.318 55.0 15.80 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 2523 0.034896 GAGTGGCCGACTTTGAGGAA 59.965 55.0 8.90 0.0 33.83 3.36 R
2476 2784 0.320374 TCTTCATCGCGGGTTTGTCT 59.680 50.0 6.13 0.0 0.00 3.41 R
3582 3891 0.180171 CCGGGCATGGAGATTGTGTA 59.820 55.0 0.00 0.0 0.00 2.90 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
37 38 1.355971 TGCGCATTCTACTTCGGAAC 58.644 50.000 5.66 0.00 0.00 3.62
44 46 5.444218 CGCATTCTACTTCGGAACTGTAAAC 60.444 44.000 0.00 0.00 0.00 2.01
75 77 1.972660 ATACGCAGGTTCAGGAGGGC 61.973 60.000 0.00 0.00 0.00 5.19
78 80 2.900106 GCAGGTTCAGGAGGGCAGT 61.900 63.158 0.00 0.00 0.00 4.40
87 89 1.997874 GGAGGGCAGTGGAGACCAT 60.998 63.158 0.00 0.00 35.28 3.55
117 119 4.159135 GTGGACCTAAACTATCTTCCGTCA 59.841 45.833 0.00 0.00 0.00 4.35
202 204 2.037381 GAGTCGAAGAAAGGGAAGGTGT 59.963 50.000 0.00 0.00 39.69 4.16
203 205 2.143925 GTCGAAGAAAGGGAAGGTGTG 58.856 52.381 0.00 0.00 39.69 3.82
214 216 3.910627 AGGGAAGGTGTGAACTTAGTCAT 59.089 43.478 0.00 0.00 0.00 3.06
265 267 0.521291 CGACAACATCCGCACCATTT 59.479 50.000 0.00 0.00 0.00 2.32
314 316 8.316640 GTTGAATCAACAATCTGTCTAGAAGT 57.683 34.615 20.08 0.00 43.09 3.01
319 321 4.899352 ACAATCTGTCTAGAAGTGGCTT 57.101 40.909 0.00 0.00 36.32 4.35
349 351 4.083908 GCCTAGAATCGTAGAGTACTTCGG 60.084 50.000 0.00 0.00 43.63 4.30
379 390 4.202202 GCAGGCAGAGATGTGTACTAATCT 60.202 45.833 9.73 9.73 35.84 2.40
390 401 2.426024 TGTACTAATCTGGGAGCGACAC 59.574 50.000 0.00 0.00 0.00 3.67
474 524 2.042026 TGGCCCTGTAGACACTGTACTA 59.958 50.000 0.00 0.00 0.00 1.82
523 573 0.614812 TGCTCTGCATAGACCAGCAA 59.385 50.000 2.78 0.00 40.73 3.91
538 588 2.169842 GCAACCTGCTTCTCTCTGC 58.830 57.895 0.00 0.00 40.96 4.26
559 609 7.038048 TCTGCATCTACTCTGTTCTTTGTATG 58.962 38.462 0.00 0.00 0.00 2.39
756 814 2.639065 ACGGTACTGCCCAATGTAATG 58.361 47.619 0.23 0.00 0.00 1.90
757 815 2.026636 ACGGTACTGCCCAATGTAATGT 60.027 45.455 0.23 0.00 0.00 2.71
758 816 3.198200 ACGGTACTGCCCAATGTAATGTA 59.802 43.478 0.23 0.00 0.00 2.29
759 817 4.193090 CGGTACTGCCCAATGTAATGTAA 58.807 43.478 0.00 0.00 0.00 2.41
760 818 4.819630 CGGTACTGCCCAATGTAATGTAAT 59.180 41.667 0.00 0.00 0.00 1.89
798 856 2.353889 CTGCATCTTGATGTCCCTTTCG 59.646 50.000 11.61 0.00 0.00 3.46
880 938 1.298602 GGCACAGTTTTGGCCTTTTG 58.701 50.000 3.32 0.00 44.32 2.44
890 948 3.676291 TTGGCCTTTTGTTATTCAGGC 57.324 42.857 3.32 0.06 41.32 4.85
963 1022 1.197036 GTCTCGGCACCTTTAGTTTGC 59.803 52.381 0.00 0.00 35.40 3.68
1005 1064 0.107993 TGAGCGCCTGAAGAATGGAG 60.108 55.000 2.29 0.00 0.00 3.86
1084 1143 1.515304 GACGAAGACGAGAGCCTGC 60.515 63.158 0.00 0.00 42.66 4.85
1221 1280 5.406649 TCACTTCTTTGCGTGTTCATTTTT 58.593 33.333 0.00 0.00 33.07 1.94
1446 1746 5.136105 GGGGCTAAGATGATGAGATTTTGT 58.864 41.667 0.00 0.00 0.00 2.83
1460 1760 6.295249 TGAGATTTTGTGTCACTGGTATCAA 58.705 36.000 4.27 0.00 0.00 2.57
1501 1802 8.603898 TCTAGGGAAGTTGATACACATCTTTA 57.396 34.615 0.00 0.00 38.26 1.85
1695 1998 8.723942 ATTCTCTCTACTGCGTATTTTGAAAT 57.276 30.769 0.00 0.00 0.00 2.17
1734 2037 0.411452 TCAGGCTCAAGACTCCTCCT 59.589 55.000 0.00 0.00 0.00 3.69
1847 2150 5.234466 ACTTCAAGGGTATGATGGCTATC 57.766 43.478 2.55 2.55 0.00 2.08
1865 2168 6.017026 TGGCTATCGAGTCTTCACAGTAATAG 60.017 42.308 0.00 0.00 0.00 1.73
1879 2183 6.423905 TCACAGTAATAGCAACACTTTCACTC 59.576 38.462 0.00 0.00 0.00 3.51
1883 2187 7.815068 CAGTAATAGCAACACTTTCACTCTACT 59.185 37.037 0.00 0.00 0.00 2.57
1890 2194 6.927381 GCAACACTTTCACTCTACTTACCTTA 59.073 38.462 0.00 0.00 0.00 2.69
1893 2200 8.474710 ACACTTTCACTCTACTTACCTTAGAA 57.525 34.615 0.00 0.00 0.00 2.10
1903 2210 7.903145 TCTACTTACCTTAGAAAAGACATGCA 58.097 34.615 0.00 0.00 34.37 3.96
1904 2211 6.803154 ACTTACCTTAGAAAAGACATGCAC 57.197 37.500 0.00 0.00 34.37 4.57
1909 2216 5.006386 CCTTAGAAAAGACATGCACCTCTT 58.994 41.667 0.00 0.00 34.37 2.85
1913 2220 0.674895 AAGACATGCACCTCTTCCGC 60.675 55.000 0.00 0.00 0.00 5.54
1914 2221 1.375908 GACATGCACCTCTTCCGCA 60.376 57.895 0.00 0.00 40.50 5.69
1916 2223 1.672030 CATGCACCTCTTCCGCACA 60.672 57.895 0.00 0.00 38.73 4.57
1918 2225 0.745845 ATGCACCTCTTCCGCACATC 60.746 55.000 0.00 0.00 38.73 3.06
1919 2226 1.375908 GCACCTCTTCCGCACATCA 60.376 57.895 0.00 0.00 0.00 3.07
1922 2229 2.905075 CACCTCTTCCGCACATCATAA 58.095 47.619 0.00 0.00 0.00 1.90
1926 2233 4.949856 ACCTCTTCCGCACATCATAAAAAT 59.050 37.500 0.00 0.00 0.00 1.82
1927 2234 5.418840 ACCTCTTCCGCACATCATAAAAATT 59.581 36.000 0.00 0.00 0.00 1.82
1928 2235 6.071391 ACCTCTTCCGCACATCATAAAAATTT 60.071 34.615 0.00 0.00 0.00 1.82
1929 2236 6.813152 CCTCTTCCGCACATCATAAAAATTTT 59.187 34.615 0.00 0.00 0.00 1.82
1930 2237 7.331687 CCTCTTCCGCACATCATAAAAATTTTT 59.668 33.333 19.44 19.44 0.00 1.94
1931 2238 9.352784 CTCTTCCGCACATCATAAAAATTTTTA 57.647 29.630 22.20 22.20 37.08 1.52
1932 2239 9.698309 TCTTCCGCACATCATAAAAATTTTTAA 57.302 25.926 23.39 11.43 36.35 1.52
1960 2267 7.688372 ACAATCATGACACATCGAAGTAATTC 58.312 34.615 0.00 0.00 0.00 2.17
1975 2282 6.293955 CGAAGTAATTCACCATTCACCAAGTT 60.294 38.462 3.55 0.00 0.00 2.66
1983 2290 5.242838 TCACCATTCACCAAGTTGAAATACC 59.757 40.000 3.87 0.00 38.95 2.73
1988 2295 3.190327 TCACCAAGTTGAAATACCGCATG 59.810 43.478 3.87 0.00 0.00 4.06
1996 2303 2.618241 TGAAATACCGCATGAGGATTGC 59.382 45.455 23.45 15.16 36.74 3.56
2006 2313 4.501071 GCATGAGGATTGCAGAACATTTT 58.499 39.130 0.00 0.00 39.90 1.82
2008 2315 6.278363 GCATGAGGATTGCAGAACATTTTAT 58.722 36.000 0.00 0.00 39.90 1.40
2009 2316 7.428020 GCATGAGGATTGCAGAACATTTTATA 58.572 34.615 0.00 0.00 39.90 0.98
2011 2318 9.976511 CATGAGGATTGCAGAACATTTTATAAT 57.023 29.630 0.00 0.00 0.00 1.28
2059 2366 2.353323 GGGTGACCGTCAAAGTTATCC 58.647 52.381 1.88 0.00 43.64 2.59
2060 2367 2.289819 GGGTGACCGTCAAAGTTATCCA 60.290 50.000 1.88 0.00 43.64 3.41
2061 2368 2.740447 GGTGACCGTCAAAGTTATCCAC 59.260 50.000 1.88 0.00 0.00 4.02
2065 2372 3.816523 GACCGTCAAAGTTATCCACCAAA 59.183 43.478 0.00 0.00 0.00 3.28
2067 2374 3.057806 CCGTCAAAGTTATCCACCAAACC 60.058 47.826 0.00 0.00 0.00 3.27
2071 2378 5.983118 GTCAAAGTTATCCACCAAACCAAAG 59.017 40.000 0.00 0.00 0.00 2.77
2076 2383 5.535030 AGTTATCCACCAAACCAAAGAAGAC 59.465 40.000 0.00 0.00 0.00 3.01
2077 2384 3.662759 TCCACCAAACCAAAGAAGACT 57.337 42.857 0.00 0.00 0.00 3.24
2081 2388 4.137543 CACCAAACCAAAGAAGACTAGCT 58.862 43.478 0.00 0.00 0.00 3.32
2082 2389 4.023707 CACCAAACCAAAGAAGACTAGCTG 60.024 45.833 0.00 0.00 0.00 4.24
2083 2390 4.137543 CCAAACCAAAGAAGACTAGCTGT 58.862 43.478 0.00 0.00 0.00 4.40
2141 2449 9.897744 TGATCTTATTTCTTGACATTGTGAAAC 57.102 29.630 0.00 0.00 32.32 2.78
2162 2470 3.879892 ACTTTGACAGTTCTCAGGAAAGC 59.120 43.478 0.00 0.00 32.81 3.51
2167 2475 2.564947 ACAGTTCTCAGGAAAGCTCGAT 59.435 45.455 0.00 0.00 32.81 3.59
2172 2480 0.610174 TCAGGAAAGCTCGATGCACT 59.390 50.000 9.09 0.60 45.94 4.40
2176 2484 1.674221 GGAAAGCTCGATGCACTCAGT 60.674 52.381 9.09 0.00 45.94 3.41
2185 2493 1.857217 GATGCACTCAGTAGCACATCG 59.143 52.381 4.33 0.00 44.49 3.84
2191 2499 2.228103 ACTCAGTAGCACATCGACGAAA 59.772 45.455 0.00 0.00 0.00 3.46
2194 2502 3.128764 TCAGTAGCACATCGACGAAATCT 59.871 43.478 0.00 0.00 0.00 2.40
2206 2514 3.969352 CGACGAAATCTGAATCTCCTACG 59.031 47.826 0.00 0.00 0.00 3.51
2215 2523 2.015587 GAATCTCCTACGACGTCCAGT 58.984 52.381 10.58 5.62 0.00 4.00
2227 2535 1.269621 ACGTCCAGTTCCTCAAAGTCG 60.270 52.381 0.00 0.00 0.00 4.18
2240 2548 3.530910 AAGTCGGCCACTCCAACGG 62.531 63.158 2.24 0.00 32.30 4.44
2287 2595 2.575993 CTCAGCACCAGAGGACCG 59.424 66.667 0.00 0.00 0.00 4.79
2471 2779 0.318107 CACAAAGGCAGCCAAGAACG 60.318 55.000 15.80 0.00 0.00 3.95
2476 2784 3.345808 GCAGCCAAGAACGTCGCA 61.346 61.111 0.00 0.00 0.00 5.10
2497 2805 1.737793 GACAAACCCGCGATGAAGAAT 59.262 47.619 8.23 0.00 0.00 2.40
2538 2846 0.253327 GCTCGGACCAAGGATCCTTT 59.747 55.000 24.93 11.58 33.42 3.11
2551 2859 2.103941 GGATCCTTTGGTTGGTGCAAAA 59.896 45.455 3.84 0.00 0.00 2.44
2628 2936 3.866651 CAAAGGATCTGAAGGTCGATGT 58.133 45.455 0.00 0.00 0.00 3.06
2763 3071 0.698818 ATCGGCAAAGACCCCTCTTT 59.301 50.000 0.00 0.00 46.01 2.52
2765 3073 1.002773 TCGGCAAAGACCCCTCTTTAC 59.997 52.381 0.00 0.00 43.70 2.01
2834 3142 1.079681 GGTAACGGTGTCGATGCCA 60.080 57.895 8.59 0.00 41.89 4.92
2943 3251 1.151677 TGGTTGGGTAGCTTCCCCT 60.152 57.895 24.44 0.00 46.48 4.79
3026 3335 4.766404 AGAACTTTCCGTTGCCTAAATG 57.234 40.909 0.00 0.00 35.56 2.32
3040 3349 6.677781 TGCCTAAATGTATGCAAAGTACTC 57.322 37.500 0.00 0.00 29.11 2.59
3041 3350 5.588648 TGCCTAAATGTATGCAAAGTACTCC 59.411 40.000 0.00 0.00 29.11 3.85
3042 3351 5.008712 GCCTAAATGTATGCAAAGTACTCCC 59.991 44.000 0.00 0.00 0.00 4.30
3043 3352 6.357367 CCTAAATGTATGCAAAGTACTCCCT 58.643 40.000 0.00 0.00 0.00 4.20
3044 3353 6.483640 CCTAAATGTATGCAAAGTACTCCCTC 59.516 42.308 0.00 0.00 0.00 4.30
3045 3354 3.906720 TGTATGCAAAGTACTCCCTCC 57.093 47.619 0.00 0.00 0.00 4.30
3046 3355 2.167693 TGTATGCAAAGTACTCCCTCCG 59.832 50.000 0.00 0.00 0.00 4.63
3047 3356 1.276622 ATGCAAAGTACTCCCTCCGT 58.723 50.000 0.00 0.00 0.00 4.69
3048 3357 0.606604 TGCAAAGTACTCCCTCCGTC 59.393 55.000 0.00 0.00 0.00 4.79
3049 3358 0.896226 GCAAAGTACTCCCTCCGTCT 59.104 55.000 0.00 0.00 0.00 4.18
3050 3359 1.135053 GCAAAGTACTCCCTCCGTCTC 60.135 57.143 0.00 0.00 0.00 3.36
3051 3360 2.168496 CAAAGTACTCCCTCCGTCTCA 58.832 52.381 0.00 0.00 0.00 3.27
3052 3361 2.761208 CAAAGTACTCCCTCCGTCTCAT 59.239 50.000 0.00 0.00 0.00 2.90
3053 3362 3.947612 AAGTACTCCCTCCGTCTCATA 57.052 47.619 0.00 0.00 0.00 2.15
3054 3363 3.947612 AGTACTCCCTCCGTCTCATAA 57.052 47.619 0.00 0.00 0.00 1.90
3055 3364 4.456662 AGTACTCCCTCCGTCTCATAAT 57.543 45.455 0.00 0.00 0.00 1.28
3056 3365 5.579753 AGTACTCCCTCCGTCTCATAATA 57.420 43.478 0.00 0.00 0.00 0.98
3057 3366 6.142259 AGTACTCCCTCCGTCTCATAATAT 57.858 41.667 0.00 0.00 0.00 1.28
3058 3367 7.268212 AGTACTCCCTCCGTCTCATAATATA 57.732 40.000 0.00 0.00 0.00 0.86
3059 3368 7.874252 AGTACTCCCTCCGTCTCATAATATAT 58.126 38.462 0.00 0.00 0.00 0.86
3060 3369 7.776030 AGTACTCCCTCCGTCTCATAATATATG 59.224 40.741 0.00 0.00 0.00 1.78
3061 3370 6.732487 ACTCCCTCCGTCTCATAATATATGA 58.268 40.000 0.58 0.58 0.00 2.15
3062 3371 6.831353 ACTCCCTCCGTCTCATAATATATGAG 59.169 42.308 17.39 17.39 45.08 2.90
3063 3372 6.732487 TCCCTCCGTCTCATAATATATGAGT 58.268 40.000 20.86 0.00 44.30 3.41
3064 3373 6.603599 TCCCTCCGTCTCATAATATATGAGTG 59.396 42.308 20.86 15.93 44.30 3.51
3065 3374 6.378564 CCCTCCGTCTCATAATATATGAGTGT 59.621 42.308 20.86 0.00 44.30 3.55
3066 3375 7.093727 CCCTCCGTCTCATAATATATGAGTGTT 60.094 40.741 20.86 0.00 44.30 3.32
3067 3376 8.307483 CCTCCGTCTCATAATATATGAGTGTTT 58.693 37.037 20.86 0.00 44.30 2.83
3068 3377 9.698309 CTCCGTCTCATAATATATGAGTGTTTT 57.302 33.333 20.86 0.00 44.30 2.43
3116 3425 8.350852 ACGTTCTTATATTATGGTAGAGAGGG 57.649 38.462 0.00 0.00 0.00 4.30
3117 3426 8.168725 ACGTTCTTATATTATGGTAGAGAGGGA 58.831 37.037 0.00 0.00 0.00 4.20
3118 3427 8.679100 CGTTCTTATATTATGGTAGAGAGGGAG 58.321 40.741 0.00 0.00 0.00 4.30
3119 3428 9.536510 GTTCTTATATTATGGTAGAGAGGGAGT 57.463 37.037 0.00 0.00 0.00 3.85
3332 3641 0.303493 GTTCGCTGAAACAACTCGCA 59.697 50.000 0.00 0.00 0.00 5.10
3380 3689 3.220222 CTGCCATAGCCGGTCAGA 58.780 61.111 1.90 0.00 38.69 3.27
3381 3690 1.068753 CTGCCATAGCCGGTCAGAG 59.931 63.158 1.90 0.00 38.69 3.35
3382 3691 1.381191 TGCCATAGCCGGTCAGAGA 60.381 57.895 1.90 0.00 38.69 3.10
3383 3692 0.975556 TGCCATAGCCGGTCAGAGAA 60.976 55.000 1.90 0.00 38.69 2.87
3384 3693 0.178068 GCCATAGCCGGTCAGAGAAA 59.822 55.000 1.90 0.00 0.00 2.52
3385 3694 1.406887 GCCATAGCCGGTCAGAGAAAA 60.407 52.381 1.90 0.00 0.00 2.29
3386 3695 2.555199 CCATAGCCGGTCAGAGAAAAG 58.445 52.381 1.90 0.00 0.00 2.27
3387 3696 2.093447 CCATAGCCGGTCAGAGAAAAGT 60.093 50.000 1.90 0.00 0.00 2.66
3388 3697 3.600388 CATAGCCGGTCAGAGAAAAGTT 58.400 45.455 1.90 0.00 0.00 2.66
3389 3698 2.640316 AGCCGGTCAGAGAAAAGTTT 57.360 45.000 1.90 0.00 0.00 2.66
3390 3699 3.764237 AGCCGGTCAGAGAAAAGTTTA 57.236 42.857 1.90 0.00 0.00 2.01
3391 3700 3.665190 AGCCGGTCAGAGAAAAGTTTAG 58.335 45.455 1.90 0.00 0.00 1.85
3392 3701 3.071167 AGCCGGTCAGAGAAAAGTTTAGT 59.929 43.478 1.90 0.00 0.00 2.24
3393 3702 3.432592 GCCGGTCAGAGAAAAGTTTAGTC 59.567 47.826 1.90 0.00 0.00 2.59
3394 3703 3.673809 CCGGTCAGAGAAAAGTTTAGTCG 59.326 47.826 0.00 0.00 0.00 4.18
3395 3704 3.121445 CGGTCAGAGAAAAGTTTAGTCGC 59.879 47.826 0.00 0.00 0.00 5.19
3396 3705 3.121445 GGTCAGAGAAAAGTTTAGTCGCG 59.879 47.826 0.00 0.00 0.00 5.87
3397 3706 3.979495 GTCAGAGAAAAGTTTAGTCGCGA 59.021 43.478 3.71 3.71 0.00 5.87
3398 3707 4.621886 GTCAGAGAAAAGTTTAGTCGCGAT 59.378 41.667 14.06 3.98 0.00 4.58
3399 3708 5.118817 GTCAGAGAAAAGTTTAGTCGCGATT 59.881 40.000 14.06 11.66 0.00 3.34
3400 3709 5.345202 TCAGAGAAAAGTTTAGTCGCGATTC 59.655 40.000 14.06 9.52 0.00 2.52
3401 3710 5.346281 CAGAGAAAAGTTTAGTCGCGATTCT 59.654 40.000 14.06 14.69 0.00 2.40
3402 3711 5.346281 AGAGAAAAGTTTAGTCGCGATTCTG 59.654 40.000 18.83 0.00 0.00 3.02
3403 3712 3.724295 AAAGTTTAGTCGCGATTCTGC 57.276 42.857 14.06 0.00 0.00 4.26
3404 3713 1.641577 AGTTTAGTCGCGATTCTGCC 58.358 50.000 14.06 0.00 0.00 4.85
3405 3714 1.204941 AGTTTAGTCGCGATTCTGCCT 59.795 47.619 14.06 5.92 0.00 4.75
3406 3715 2.426024 AGTTTAGTCGCGATTCTGCCTA 59.574 45.455 14.06 4.75 0.00 3.93
3407 3716 3.119245 AGTTTAGTCGCGATTCTGCCTAA 60.119 43.478 14.06 11.31 0.00 2.69
3408 3717 3.728076 TTAGTCGCGATTCTGCCTAAT 57.272 42.857 14.06 0.00 0.00 1.73
3409 3718 4.841443 TTAGTCGCGATTCTGCCTAATA 57.159 40.909 14.06 0.00 0.00 0.98
3410 3719 3.728076 AGTCGCGATTCTGCCTAATAA 57.272 42.857 14.06 0.00 0.00 1.40
3411 3720 3.643763 AGTCGCGATTCTGCCTAATAAG 58.356 45.455 14.06 0.00 0.00 1.73
3412 3721 3.318275 AGTCGCGATTCTGCCTAATAAGA 59.682 43.478 14.06 0.00 0.00 2.10
3413 3722 3.670991 GTCGCGATTCTGCCTAATAAGAG 59.329 47.826 14.06 0.00 0.00 2.85
3414 3723 2.410053 CGCGATTCTGCCTAATAAGAGC 59.590 50.000 0.00 0.00 0.00 4.09
3415 3724 3.393800 GCGATTCTGCCTAATAAGAGCA 58.606 45.455 0.00 0.00 34.79 4.26
3416 3725 3.999663 GCGATTCTGCCTAATAAGAGCAT 59.000 43.478 0.00 0.00 35.64 3.79
3417 3726 4.092675 GCGATTCTGCCTAATAAGAGCATC 59.907 45.833 0.00 0.00 35.64 3.91
3430 3739 2.674796 GAGCATCTACAACCGGAAGT 57.325 50.000 9.46 8.83 0.00 3.01
3431 3740 3.795623 GAGCATCTACAACCGGAAGTA 57.204 47.619 9.46 9.62 0.00 2.24
3432 3741 3.445857 GAGCATCTACAACCGGAAGTAC 58.554 50.000 9.46 0.00 0.00 2.73
3433 3742 2.167900 AGCATCTACAACCGGAAGTACC 59.832 50.000 9.46 0.00 0.00 3.34
3434 3743 2.093869 GCATCTACAACCGGAAGTACCA 60.094 50.000 9.46 0.00 38.90 3.25
3435 3744 3.618019 GCATCTACAACCGGAAGTACCAA 60.618 47.826 9.46 0.00 38.90 3.67
3436 3745 4.571919 CATCTACAACCGGAAGTACCAAA 58.428 43.478 9.46 0.00 38.90 3.28
3437 3746 4.686191 TCTACAACCGGAAGTACCAAAA 57.314 40.909 9.46 0.00 38.90 2.44
3438 3747 5.231702 TCTACAACCGGAAGTACCAAAAT 57.768 39.130 9.46 0.00 38.90 1.82
3439 3748 5.623169 TCTACAACCGGAAGTACCAAAATT 58.377 37.500 9.46 0.00 38.90 1.82
3440 3749 4.841443 ACAACCGGAAGTACCAAAATTC 57.159 40.909 9.46 0.00 38.90 2.17
3441 3750 4.208746 ACAACCGGAAGTACCAAAATTCA 58.791 39.130 9.46 0.00 38.90 2.57
3442 3751 4.037089 ACAACCGGAAGTACCAAAATTCAC 59.963 41.667 9.46 0.00 38.90 3.18
3443 3752 3.151554 ACCGGAAGTACCAAAATTCACC 58.848 45.455 9.46 0.00 38.90 4.02
3444 3753 2.490509 CCGGAAGTACCAAAATTCACCC 59.509 50.000 0.00 0.00 38.90 4.61
3445 3754 3.418047 CGGAAGTACCAAAATTCACCCT 58.582 45.455 0.00 0.00 38.90 4.34
3446 3755 3.824443 CGGAAGTACCAAAATTCACCCTT 59.176 43.478 0.00 0.00 38.90 3.95
3447 3756 4.082949 CGGAAGTACCAAAATTCACCCTTC 60.083 45.833 0.00 0.00 38.90 3.46
3448 3757 4.830600 GGAAGTACCAAAATTCACCCTTCA 59.169 41.667 0.00 0.00 38.79 3.02
3449 3758 5.303333 GGAAGTACCAAAATTCACCCTTCAA 59.697 40.000 0.00 0.00 38.79 2.69
3450 3759 6.183360 GGAAGTACCAAAATTCACCCTTCAAA 60.183 38.462 0.00 0.00 38.79 2.69
3451 3760 6.156748 AGTACCAAAATTCACCCTTCAAAC 57.843 37.500 0.00 0.00 0.00 2.93
3452 3761 4.053469 ACCAAAATTCACCCTTCAAACG 57.947 40.909 0.00 0.00 0.00 3.60
3453 3762 2.799978 CCAAAATTCACCCTTCAAACGC 59.200 45.455 0.00 0.00 0.00 4.84
3454 3763 3.452474 CAAAATTCACCCTTCAAACGCA 58.548 40.909 0.00 0.00 0.00 5.24
3455 3764 3.369546 AAATTCACCCTTCAAACGCAG 57.630 42.857 0.00 0.00 0.00 5.18
3456 3765 0.598065 ATTCACCCTTCAAACGCAGC 59.402 50.000 0.00 0.00 0.00 5.25
3457 3766 0.749818 TTCACCCTTCAAACGCAGCA 60.750 50.000 0.00 0.00 0.00 4.41
3458 3767 0.537143 TCACCCTTCAAACGCAGCAT 60.537 50.000 0.00 0.00 0.00 3.79
3491 3800 3.559069 ACATCCATCACATCCATGAACC 58.441 45.455 0.00 0.00 30.82 3.62
3546 3855 7.201732 GCAATGCAGATAAACAACCTACATACT 60.202 37.037 0.00 0.00 0.00 2.12
3547 3856 8.677300 CAATGCAGATAAACAACCTACATACTT 58.323 33.333 0.00 0.00 0.00 2.24
3548 3857 8.807948 ATGCAGATAAACAACCTACATACTTT 57.192 30.769 0.00 0.00 0.00 2.66
3582 3891 9.367444 CCTAAAACTACTTATTGTCGAAGATGT 57.633 33.333 0.00 0.00 40.67 3.06
3594 3903 4.219725 TGTCGAAGATGTACACAATCTCCA 59.780 41.667 0.00 0.00 40.67 3.86
3597 3906 4.025396 CGAAGATGTACACAATCTCCATGC 60.025 45.833 0.00 0.00 0.00 4.06
3598 3907 3.813443 AGATGTACACAATCTCCATGCC 58.187 45.455 0.00 0.00 0.00 4.40
3599 3908 2.418368 TGTACACAATCTCCATGCCC 57.582 50.000 0.00 0.00 0.00 5.36
3600 3909 1.299541 GTACACAATCTCCATGCCCG 58.700 55.000 0.00 0.00 0.00 6.13
3601 3910 0.180171 TACACAATCTCCATGCCCGG 59.820 55.000 0.00 0.00 0.00 5.73
3602 3911 2.124151 ACAATCTCCATGCCCGGC 60.124 61.111 1.04 1.04 0.00 6.13
3603 3912 3.282157 CAATCTCCATGCCCGGCG 61.282 66.667 4.58 0.00 0.00 6.46
3641 3950 3.917760 GGCAGCTCCGACGCCTAT 61.918 66.667 4.80 0.00 42.78 2.57
3642 3951 2.659897 GCAGCTCCGACGCCTATG 60.660 66.667 0.00 0.00 0.00 2.23
3643 3952 3.120105 CAGCTCCGACGCCTATGA 58.880 61.111 0.00 0.00 0.00 2.15
3644 3953 1.007964 CAGCTCCGACGCCTATGAG 60.008 63.158 0.00 0.00 0.00 2.90
3678 3987 1.572085 CTTGCGGTGTCTCCTGCTTG 61.572 60.000 8.50 0.75 36.93 4.01
3689 3998 1.077429 CCTGCTTGCTTAGGGGGAC 60.077 63.158 0.00 0.00 0.00 4.46
3693 4002 2.074967 CTTGCTTAGGGGGACACCA 58.925 57.895 0.00 0.00 42.91 4.17
3715 4024 2.743928 CTGCTTGCCGTGTCTCCC 60.744 66.667 0.00 0.00 0.00 4.30
3734 4043 2.632544 ATCTGGTCGCGTCGGTCAA 61.633 57.895 5.77 0.00 0.00 3.18
3769 4078 0.500178 CGATCACATCGCACGACATC 59.500 55.000 0.00 0.00 46.55 3.06
3844 4153 2.046292 GGAGAGAAAGGATGGGAGAGG 58.954 57.143 0.00 0.00 0.00 3.69
3852 4161 0.999712 GGATGGGAGAGGGTTTTGGA 59.000 55.000 0.00 0.00 0.00 3.53
3867 4176 4.129148 GGATGGGCCAGGGGTGTC 62.129 72.222 13.78 2.73 36.34 3.67
3872 4181 3.315949 GGCCAGGGGTGTCGTACA 61.316 66.667 0.00 0.00 0.00 2.90
3879 4188 2.736682 GGGTGTCGTACATGTGCGC 61.737 63.158 28.51 22.82 38.56 6.09
3920 4229 0.179040 ACCGGTTCACAAACGGATGT 60.179 50.000 19.33 0.00 37.79 3.06
3926 4235 3.322514 CACAAACGGATGTGGGACT 57.677 52.632 13.29 0.00 45.47 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.495939 CGAAGTAGAATGCGCAACAAC 58.504 47.619 17.11 10.88 0.00 3.32
14 15 1.463056 CCGAAGTAGAATGCGCAACAA 59.537 47.619 17.11 0.00 0.00 2.83
20 21 2.607187 ACAGTTCCGAAGTAGAATGCG 58.393 47.619 0.00 0.00 0.00 4.73
37 38 6.183360 TGCGTATTCAAAGGCTATGTTTACAG 60.183 38.462 0.00 0.00 0.00 2.74
44 46 3.206150 ACCTGCGTATTCAAAGGCTATG 58.794 45.455 0.00 0.00 32.73 2.23
75 77 3.431346 CCACTATGACATGGTCTCCACTG 60.431 52.174 0.74 0.00 35.80 3.66
78 80 2.766263 GTCCACTATGACATGGTCTCCA 59.234 50.000 0.74 0.00 37.27 3.86
87 89 7.069578 GGAAGATAGTTTAGGTCCACTATGACA 59.930 40.741 5.33 0.00 36.52 3.58
117 119 4.040461 TCGGAGTCAGGAACTTCTTTGAAT 59.960 41.667 0.00 0.00 38.74 2.57
202 204 2.565391 TCGAGGCCAATGACTAAGTTCA 59.435 45.455 5.01 0.00 0.00 3.18
203 205 3.119101 TCTCGAGGCCAATGACTAAGTTC 60.119 47.826 13.56 0.00 0.00 3.01
230 232 5.110598 TGTTGTCGCCGTTATTGTATATGT 58.889 37.500 0.00 0.00 0.00 2.29
319 321 3.538591 TCTACGATTCTAGGCGACAAGA 58.461 45.455 0.00 5.01 0.00 3.02
349 351 2.095364 CACATCTCTGCCTGCAAAGTTC 60.095 50.000 0.00 0.00 0.00 3.01
390 401 2.163818 TTAACTCCACAGTTGAGCGG 57.836 50.000 1.42 0.00 43.17 5.52
474 524 5.434408 AGCATATCATGTCACTCACATTGT 58.566 37.500 0.00 0.00 43.89 2.71
523 573 1.570803 AGATGCAGAGAGAAGCAGGT 58.429 50.000 0.00 0.00 44.94 4.00
538 588 8.763049 TTCACATACAAAGAACAGAGTAGATG 57.237 34.615 0.00 0.00 0.00 2.90
559 609 7.934457 ACAGGCTTTCACATGATATAATTCAC 58.066 34.615 0.00 0.00 0.00 3.18
756 814 6.017440 TGCAGCCGAATGGAAAGTATTATTAC 60.017 38.462 0.00 0.00 37.49 1.89
757 815 6.058833 TGCAGCCGAATGGAAAGTATTATTA 58.941 36.000 0.00 0.00 37.49 0.98
758 816 4.887071 TGCAGCCGAATGGAAAGTATTATT 59.113 37.500 0.00 0.00 37.49 1.40
759 817 4.460263 TGCAGCCGAATGGAAAGTATTAT 58.540 39.130 0.00 0.00 37.49 1.28
760 818 3.879998 TGCAGCCGAATGGAAAGTATTA 58.120 40.909 0.00 0.00 37.49 0.98
880 938 2.084546 ACGGAAGCTTGCCTGAATAAC 58.915 47.619 12.80 0.00 0.00 1.89
890 948 1.394917 GCATACAGTGACGGAAGCTTG 59.605 52.381 2.10 0.00 0.00 4.01
963 1022 1.677217 GCAGGGAGCAGAGTAAACAGG 60.677 57.143 0.00 0.00 44.79 4.00
984 1043 1.065199 TCCATTCTTCAGGCGCTCAAT 60.065 47.619 7.64 0.00 0.00 2.57
991 1050 1.404391 CATGTGCTCCATTCTTCAGGC 59.596 52.381 0.00 0.00 0.00 4.85
1005 1064 1.363744 CGGAGAACCTCTTCATGTGC 58.636 55.000 0.00 0.00 0.00 4.57
1084 1143 4.319177 CTGTACAGTTCCCCAAAGAGAAG 58.681 47.826 15.06 0.00 0.00 2.85
1446 1746 6.429692 CCAACAGTTTATTGATACCAGTGACA 59.570 38.462 0.00 0.00 0.00 3.58
1460 1760 7.182930 ACTTCCCTAGATCTTCCAACAGTTTAT 59.817 37.037 0.00 0.00 0.00 1.40
1695 1998 0.322997 AATCAAATGAACCGCCCCGA 60.323 50.000 0.00 0.00 0.00 5.14
1847 2150 5.061064 GTGTTGCTATTACTGTGAAGACTCG 59.939 44.000 0.00 0.00 0.00 4.18
1865 2168 5.298347 AGGTAAGTAGAGTGAAAGTGTTGC 58.702 41.667 0.00 0.00 0.00 4.17
1879 2183 7.064728 GGTGCATGTCTTTTCTAAGGTAAGTAG 59.935 40.741 0.00 0.00 32.02 2.57
1883 2187 5.876357 AGGTGCATGTCTTTTCTAAGGTAA 58.124 37.500 0.00 0.00 32.02 2.85
1890 2194 3.416156 GGAAGAGGTGCATGTCTTTTCT 58.584 45.455 13.15 0.00 33.04 2.52
1893 2200 1.813513 CGGAAGAGGTGCATGTCTTT 58.186 50.000 13.15 0.61 33.04 2.52
1903 2210 3.627395 TTTATGATGTGCGGAAGAGGT 57.373 42.857 0.00 0.00 0.00 3.85
1904 2211 4.963276 TTTTTATGATGTGCGGAAGAGG 57.037 40.909 0.00 0.00 0.00 3.69
1926 2233 9.521503 TCGATGTGTCATGATTGTTTTTAAAAA 57.478 25.926 9.31 9.31 0.00 1.94
1927 2234 9.521503 TTCGATGTGTCATGATTGTTTTTAAAA 57.478 25.926 0.00 0.00 0.00 1.52
1928 2235 9.179552 CTTCGATGTGTCATGATTGTTTTTAAA 57.820 29.630 0.00 0.00 0.00 1.52
1929 2236 8.349245 ACTTCGATGTGTCATGATTGTTTTTAA 58.651 29.630 0.00 0.00 0.00 1.52
1930 2237 7.870826 ACTTCGATGTGTCATGATTGTTTTTA 58.129 30.769 0.00 0.00 0.00 1.52
1931 2238 6.738114 ACTTCGATGTGTCATGATTGTTTTT 58.262 32.000 0.00 0.00 0.00 1.94
1932 2239 6.317789 ACTTCGATGTGTCATGATTGTTTT 57.682 33.333 0.00 0.00 0.00 2.43
1933 2240 5.947228 ACTTCGATGTGTCATGATTGTTT 57.053 34.783 0.00 0.00 0.00 2.83
1934 2241 7.615582 ATTACTTCGATGTGTCATGATTGTT 57.384 32.000 13.80 0.00 0.00 2.83
1935 2242 7.334171 TGAATTACTTCGATGTGTCATGATTGT 59.666 33.333 13.80 0.00 33.86 2.71
1936 2243 7.637519 GTGAATTACTTCGATGTGTCATGATTG 59.362 37.037 13.80 0.00 33.86 2.67
1937 2244 7.201644 GGTGAATTACTTCGATGTGTCATGATT 60.202 37.037 13.80 4.98 33.86 2.57
1938 2245 6.258727 GGTGAATTACTTCGATGTGTCATGAT 59.741 38.462 13.80 0.00 33.86 2.45
1939 2246 5.580691 GGTGAATTACTTCGATGTGTCATGA 59.419 40.000 13.80 0.00 33.86 3.07
1940 2247 5.351189 TGGTGAATTACTTCGATGTGTCATG 59.649 40.000 13.80 0.00 33.86 3.07
1941 2248 5.487433 TGGTGAATTACTTCGATGTGTCAT 58.513 37.500 13.80 1.32 33.86 3.06
1942 2249 4.888917 TGGTGAATTACTTCGATGTGTCA 58.111 39.130 13.80 11.00 33.86 3.58
1943 2250 6.092122 TGAATGGTGAATTACTTCGATGTGTC 59.908 38.462 13.80 8.84 33.86 3.67
1947 2254 5.353956 TGGTGAATGGTGAATTACTTCGATG 59.646 40.000 0.00 0.00 33.86 3.84
1960 2267 5.469479 GGTATTTCAACTTGGTGAATGGTG 58.531 41.667 1.70 0.00 37.36 4.17
1975 2282 2.618241 GCAATCCTCATGCGGTATTTCA 59.382 45.455 0.77 0.00 33.57 2.69
1983 2290 1.089112 TGTTCTGCAATCCTCATGCG 58.911 50.000 0.00 0.00 46.76 4.73
2016 2323 8.469309 CCCATGTGGTATTAGAAGATGATTTT 57.531 34.615 0.00 0.00 0.00 1.82
2034 2341 0.874390 CTTTGACGGTCACCCATGTG 59.126 55.000 10.97 0.00 44.18 3.21
2038 2345 2.289819 GGATAACTTTGACGGTCACCCA 60.290 50.000 10.97 0.00 0.00 4.51
2039 2346 2.289819 TGGATAACTTTGACGGTCACCC 60.290 50.000 10.97 4.58 0.00 4.61
2042 2349 2.369203 TGGTGGATAACTTTGACGGTCA 59.631 45.455 6.76 6.76 0.00 4.02
2043 2350 3.048337 TGGTGGATAACTTTGACGGTC 57.952 47.619 0.00 0.00 0.00 4.79
2049 2356 6.155475 TCTTTGGTTTGGTGGATAACTTTG 57.845 37.500 0.00 0.00 0.00 2.77
2059 2366 4.023707 CAGCTAGTCTTCTTTGGTTTGGTG 60.024 45.833 0.00 0.00 0.00 4.17
2060 2367 4.137543 CAGCTAGTCTTCTTTGGTTTGGT 58.862 43.478 0.00 0.00 0.00 3.67
2061 2368 4.137543 ACAGCTAGTCTTCTTTGGTTTGG 58.862 43.478 0.00 0.00 0.00 3.28
2123 2431 7.374272 TGTCAAAGTTTCACAATGTCAAGAAA 58.626 30.769 0.00 0.00 0.00 2.52
2125 2433 6.150976 ACTGTCAAAGTTTCACAATGTCAAGA 59.849 34.615 0.00 0.00 34.57 3.02
2126 2434 6.324819 ACTGTCAAAGTTTCACAATGTCAAG 58.675 36.000 0.00 0.00 34.57 3.02
2141 2449 4.133078 AGCTTTCCTGAGAACTGTCAAAG 58.867 43.478 0.00 0.00 0.00 2.77
2144 2452 2.288457 CGAGCTTTCCTGAGAACTGTCA 60.288 50.000 0.00 0.00 0.00 3.58
2145 2453 2.029828 TCGAGCTTTCCTGAGAACTGTC 60.030 50.000 0.00 0.00 0.00 3.51
2162 2470 1.135286 TGTGCTACTGAGTGCATCGAG 60.135 52.381 11.64 0.00 41.45 4.04
2167 2475 0.887933 TCGATGTGCTACTGAGTGCA 59.112 50.000 0.00 0.02 36.79 4.57
2172 2480 3.128764 AGATTTCGTCGATGTGCTACTGA 59.871 43.478 4.21 0.00 0.00 3.41
2176 2484 3.775661 TCAGATTTCGTCGATGTGCTA 57.224 42.857 4.21 0.00 0.00 3.49
2185 2493 4.971220 GTCGTAGGAGATTCAGATTTCGTC 59.029 45.833 0.00 0.00 0.00 4.20
2191 2499 2.879646 GGACGTCGTAGGAGATTCAGAT 59.120 50.000 9.92 0.00 0.00 2.90
2194 2502 2.014857 CTGGACGTCGTAGGAGATTCA 58.985 52.381 9.92 0.00 0.00 2.57
2206 2514 2.405172 GACTTTGAGGAACTGGACGTC 58.595 52.381 7.13 7.13 41.55 4.34
2215 2523 0.034896 GAGTGGCCGACTTTGAGGAA 59.965 55.000 8.90 0.00 33.83 3.36
2240 2548 1.004440 ACGAAGAGCTGGGTCTTGC 60.004 57.895 17.91 9.69 36.89 4.01
2242 2550 0.605589 CTGACGAAGAGCTGGGTCTT 59.394 55.000 13.79 13.79 39.59 3.01
2285 2593 4.785453 GCAGAAGGCAGGGGACGG 62.785 72.222 0.00 0.00 43.97 4.79
2305 2613 4.993705 TTTGTAAGATGGGGACTCTTGT 57.006 40.909 0.00 0.00 34.81 3.16
2476 2784 0.320374 TCTTCATCGCGGGTTTGTCT 59.680 50.000 6.13 0.00 0.00 3.41
2538 2846 2.942804 TCAGATCTTTTGCACCAACCA 58.057 42.857 0.00 0.00 0.00 3.67
2551 2859 1.411977 CCAGCATCGACCTTCAGATCT 59.588 52.381 0.00 0.00 0.00 2.75
2743 3051 1.580059 AAGAGGGGTCTTTGCCGATA 58.420 50.000 0.00 0.00 0.00 2.92
2834 3142 3.941188 CACCACAGCCCCGTCAGT 61.941 66.667 0.00 0.00 0.00 3.41
2847 3155 1.081092 CTCCTCCTCCCCTTCACCA 59.919 63.158 0.00 0.00 0.00 4.17
3026 3335 2.167900 ACGGAGGGAGTACTTTGCATAC 59.832 50.000 0.00 0.00 0.00 2.39
3040 3349 6.378564 ACACTCATATATTATGAGACGGAGGG 59.621 42.308 24.24 5.93 46.25 4.30
3041 3350 7.397892 ACACTCATATATTATGAGACGGAGG 57.602 40.000 24.24 12.12 46.25 4.30
3042 3351 9.698309 AAAACACTCATATATTATGAGACGGAG 57.302 33.333 24.24 13.55 46.25 4.63
3090 3399 8.804204 CCCTCTCTACCATAATATAAGAACGTT 58.196 37.037 0.00 0.00 0.00 3.99
3091 3400 8.168725 TCCCTCTCTACCATAATATAAGAACGT 58.831 37.037 0.00 0.00 0.00 3.99
3092 3401 8.577048 TCCCTCTCTACCATAATATAAGAACG 57.423 38.462 0.00 0.00 0.00 3.95
3093 3402 9.536510 ACTCCCTCTCTACCATAATATAAGAAC 57.463 37.037 0.00 0.00 0.00 3.01
3099 3408 9.900112 AAAAGTACTCCCTCTCTACCATAATAT 57.100 33.333 0.00 0.00 0.00 1.28
3100 3409 9.144298 CAAAAGTACTCCCTCTCTACCATAATA 57.856 37.037 0.00 0.00 0.00 0.98
3101 3410 7.844779 TCAAAAGTACTCCCTCTCTACCATAAT 59.155 37.037 0.00 0.00 0.00 1.28
3102 3411 7.186972 TCAAAAGTACTCCCTCTCTACCATAA 58.813 38.462 0.00 0.00 0.00 1.90
3103 3412 6.738635 TCAAAAGTACTCCCTCTCTACCATA 58.261 40.000 0.00 0.00 0.00 2.74
3104 3413 5.590818 TCAAAAGTACTCCCTCTCTACCAT 58.409 41.667 0.00 0.00 0.00 3.55
3105 3414 5.006896 TCAAAAGTACTCCCTCTCTACCA 57.993 43.478 0.00 0.00 0.00 3.25
3106 3415 6.154706 TCAATCAAAAGTACTCCCTCTCTACC 59.845 42.308 0.00 0.00 0.00 3.18
3107 3416 7.171630 TCAATCAAAAGTACTCCCTCTCTAC 57.828 40.000 0.00 0.00 0.00 2.59
3108 3417 7.792364 TTCAATCAAAAGTACTCCCTCTCTA 57.208 36.000 0.00 0.00 0.00 2.43
3109 3418 6.688073 TTCAATCAAAAGTACTCCCTCTCT 57.312 37.500 0.00 0.00 0.00 3.10
3110 3419 6.372937 CCTTTCAATCAAAAGTACTCCCTCTC 59.627 42.308 0.00 0.00 34.99 3.20
3111 3420 6.183361 ACCTTTCAATCAAAAGTACTCCCTCT 60.183 38.462 0.00 0.00 34.99 3.69
3112 3421 6.004574 ACCTTTCAATCAAAAGTACTCCCTC 58.995 40.000 0.00 0.00 34.99 4.30
3113 3422 5.953571 ACCTTTCAATCAAAAGTACTCCCT 58.046 37.500 0.00 0.00 34.99 4.20
3114 3423 6.040504 ACAACCTTTCAATCAAAAGTACTCCC 59.959 38.462 0.00 0.00 34.99 4.30
3115 3424 7.039313 ACAACCTTTCAATCAAAAGTACTCC 57.961 36.000 0.00 0.00 34.99 3.85
3116 3425 8.188139 TGAACAACCTTTCAATCAAAAGTACTC 58.812 33.333 0.00 0.00 34.99 2.59
3117 3426 8.062065 TGAACAACCTTTCAATCAAAAGTACT 57.938 30.769 0.00 0.00 34.99 2.73
3118 3427 8.871686 ATGAACAACCTTTCAATCAAAAGTAC 57.128 30.769 0.00 0.00 38.95 2.73
3280 3589 6.696411 TCATAGAAATGAACCCGCAATTTTT 58.304 32.000 0.00 0.00 39.20 1.94
3332 3641 6.044871 CCCCTCCTTTTGATTAGTCTATCCAT 59.955 42.308 0.00 0.00 0.00 3.41
3373 3682 3.121445 GCGACTAAACTTTTCTCTGACCG 59.879 47.826 0.00 0.00 0.00 4.79
3375 3684 3.979495 TCGCGACTAAACTTTTCTCTGAC 59.021 43.478 3.71 0.00 0.00 3.51
3376 3685 4.233123 TCGCGACTAAACTTTTCTCTGA 57.767 40.909 3.71 0.00 0.00 3.27
3379 3688 5.542813 CAGAATCGCGACTAAACTTTTCTC 58.457 41.667 12.93 0.00 0.00 2.87
3380 3689 4.143094 GCAGAATCGCGACTAAACTTTTCT 60.143 41.667 12.93 11.46 0.00 2.52
3381 3690 4.082447 GCAGAATCGCGACTAAACTTTTC 58.918 43.478 12.93 8.99 0.00 2.29
3382 3691 3.120304 GGCAGAATCGCGACTAAACTTTT 60.120 43.478 12.93 0.00 0.00 2.27
3383 3692 2.415512 GGCAGAATCGCGACTAAACTTT 59.584 45.455 12.93 0.00 0.00 2.66
3384 3693 2.000447 GGCAGAATCGCGACTAAACTT 59.000 47.619 12.93 0.00 0.00 2.66
3385 3694 1.204941 AGGCAGAATCGCGACTAAACT 59.795 47.619 12.93 2.71 0.00 2.66
3386 3695 1.641577 AGGCAGAATCGCGACTAAAC 58.358 50.000 12.93 0.50 0.00 2.01
3387 3696 3.513680 TTAGGCAGAATCGCGACTAAA 57.486 42.857 12.93 0.00 0.00 1.85
3388 3697 3.728076 ATTAGGCAGAATCGCGACTAA 57.272 42.857 12.93 13.97 0.00 2.24
3389 3698 4.517832 TCTTATTAGGCAGAATCGCGACTA 59.482 41.667 12.93 4.05 0.00 2.59
3390 3699 3.318275 TCTTATTAGGCAGAATCGCGACT 59.682 43.478 12.93 0.00 0.00 4.18
3391 3700 3.639538 TCTTATTAGGCAGAATCGCGAC 58.360 45.455 12.93 0.00 0.00 5.19
3392 3701 3.857383 GCTCTTATTAGGCAGAATCGCGA 60.857 47.826 13.09 13.09 0.00 5.87
3393 3702 2.410053 GCTCTTATTAGGCAGAATCGCG 59.590 50.000 0.00 0.00 0.00 5.87
3394 3703 3.393800 TGCTCTTATTAGGCAGAATCGC 58.606 45.455 0.00 0.00 0.00 4.58
3395 3704 5.477510 AGATGCTCTTATTAGGCAGAATCG 58.522 41.667 0.00 0.00 39.38 3.34
3396 3705 7.382110 TGTAGATGCTCTTATTAGGCAGAATC 58.618 38.462 0.00 0.00 39.38 2.52
3397 3706 7.308450 TGTAGATGCTCTTATTAGGCAGAAT 57.692 36.000 0.00 0.00 39.38 2.40
3398 3707 6.731292 TGTAGATGCTCTTATTAGGCAGAA 57.269 37.500 0.00 0.00 39.38 3.02
3399 3708 6.463049 GGTTGTAGATGCTCTTATTAGGCAGA 60.463 42.308 0.00 0.00 39.38 4.26
3400 3709 5.698545 GGTTGTAGATGCTCTTATTAGGCAG 59.301 44.000 0.00 0.00 39.38 4.85
3401 3710 5.611374 GGTTGTAGATGCTCTTATTAGGCA 58.389 41.667 0.00 0.00 40.32 4.75
3402 3711 4.686554 CGGTTGTAGATGCTCTTATTAGGC 59.313 45.833 0.00 0.00 0.00 3.93
3403 3712 5.010719 TCCGGTTGTAGATGCTCTTATTAGG 59.989 44.000 0.00 0.00 0.00 2.69
3404 3713 6.085555 TCCGGTTGTAGATGCTCTTATTAG 57.914 41.667 0.00 0.00 0.00 1.73
3405 3714 6.097839 ACTTCCGGTTGTAGATGCTCTTATTA 59.902 38.462 0.00 0.00 0.00 0.98
3406 3715 5.104900 ACTTCCGGTTGTAGATGCTCTTATT 60.105 40.000 0.00 0.00 0.00 1.40
3407 3716 4.406003 ACTTCCGGTTGTAGATGCTCTTAT 59.594 41.667 0.00 0.00 0.00 1.73
3408 3717 3.767673 ACTTCCGGTTGTAGATGCTCTTA 59.232 43.478 0.00 0.00 0.00 2.10
3409 3718 2.567615 ACTTCCGGTTGTAGATGCTCTT 59.432 45.455 0.00 0.00 0.00 2.85
3410 3719 2.180276 ACTTCCGGTTGTAGATGCTCT 58.820 47.619 0.00 0.00 0.00 4.09
3411 3720 2.674796 ACTTCCGGTTGTAGATGCTC 57.325 50.000 0.00 0.00 0.00 4.26
3412 3721 2.167900 GGTACTTCCGGTTGTAGATGCT 59.832 50.000 0.00 0.00 0.00 3.79
3413 3722 2.093869 TGGTACTTCCGGTTGTAGATGC 60.094 50.000 0.00 0.00 39.52 3.91
3414 3723 3.880047 TGGTACTTCCGGTTGTAGATG 57.120 47.619 0.00 0.00 39.52 2.90
3415 3724 4.895668 TTTGGTACTTCCGGTTGTAGAT 57.104 40.909 0.00 0.00 39.52 1.98
3416 3725 4.686191 TTTTGGTACTTCCGGTTGTAGA 57.314 40.909 0.00 0.00 39.52 2.59
3417 3726 5.470777 TGAATTTTGGTACTTCCGGTTGTAG 59.529 40.000 0.00 0.00 39.52 2.74
3418 3727 5.239087 GTGAATTTTGGTACTTCCGGTTGTA 59.761 40.000 0.00 3.09 39.52 2.41
3419 3728 4.037089 GTGAATTTTGGTACTTCCGGTTGT 59.963 41.667 0.00 4.19 39.52 3.32
3420 3729 4.542735 GTGAATTTTGGTACTTCCGGTTG 58.457 43.478 0.00 0.00 39.52 3.77
3421 3730 3.570975 GGTGAATTTTGGTACTTCCGGTT 59.429 43.478 0.00 0.00 39.52 4.44
3422 3731 3.151554 GGTGAATTTTGGTACTTCCGGT 58.848 45.455 0.00 0.00 39.52 5.28
3423 3732 2.490509 GGGTGAATTTTGGTACTTCCGG 59.509 50.000 0.00 0.00 39.52 5.14
3424 3733 3.418047 AGGGTGAATTTTGGTACTTCCG 58.582 45.455 0.00 0.00 39.52 4.30
3425 3734 4.830600 TGAAGGGTGAATTTTGGTACTTCC 59.169 41.667 0.00 0.00 33.91 3.46
3426 3735 6.399639 TTGAAGGGTGAATTTTGGTACTTC 57.600 37.500 0.00 0.00 35.05 3.01
3427 3736 6.578944 GTTTGAAGGGTGAATTTTGGTACTT 58.421 36.000 0.00 0.00 0.00 2.24
3428 3737 5.221165 CGTTTGAAGGGTGAATTTTGGTACT 60.221 40.000 0.00 0.00 0.00 2.73
3429 3738 4.979815 CGTTTGAAGGGTGAATTTTGGTAC 59.020 41.667 0.00 0.00 0.00 3.34
3430 3739 4.500035 GCGTTTGAAGGGTGAATTTTGGTA 60.500 41.667 0.00 0.00 0.00 3.25
3431 3740 3.739830 GCGTTTGAAGGGTGAATTTTGGT 60.740 43.478 0.00 0.00 0.00 3.67
3432 3741 2.799978 GCGTTTGAAGGGTGAATTTTGG 59.200 45.455 0.00 0.00 0.00 3.28
3433 3742 3.452474 TGCGTTTGAAGGGTGAATTTTG 58.548 40.909 0.00 0.00 0.00 2.44
3434 3743 3.716601 CTGCGTTTGAAGGGTGAATTTT 58.283 40.909 0.00 0.00 0.00 1.82
3435 3744 2.545742 GCTGCGTTTGAAGGGTGAATTT 60.546 45.455 0.00 0.00 0.00 1.82
3436 3745 1.000274 GCTGCGTTTGAAGGGTGAATT 60.000 47.619 0.00 0.00 0.00 2.17
3437 3746 0.598065 GCTGCGTTTGAAGGGTGAAT 59.402 50.000 0.00 0.00 0.00 2.57
3438 3747 0.749818 TGCTGCGTTTGAAGGGTGAA 60.750 50.000 0.00 0.00 0.00 3.18
3439 3748 0.537143 ATGCTGCGTTTGAAGGGTGA 60.537 50.000 0.00 0.00 0.00 4.02
3440 3749 1.164411 TATGCTGCGTTTGAAGGGTG 58.836 50.000 0.00 0.00 0.00 4.61
3441 3750 1.904287 TTATGCTGCGTTTGAAGGGT 58.096 45.000 0.00 0.00 0.00 4.34
3442 3751 3.296322 TTTTATGCTGCGTTTGAAGGG 57.704 42.857 0.00 0.00 0.00 3.95
3476 3785 4.927049 AGTTTGAGGTTCATGGATGTGAT 58.073 39.130 0.00 0.00 0.00 3.06
3491 3800 7.636150 ATGGATTTGAGGTATGAAGTTTGAG 57.364 36.000 0.00 0.00 0.00 3.02
3556 3865 9.367444 ACATCTTCGACAATAAGTAGTTTTAGG 57.633 33.333 0.00 0.00 0.00 2.69
3571 3880 4.219725 TGGAGATTGTGTACATCTTCGACA 59.780 41.667 0.00 0.00 0.00 4.35
3582 3891 0.180171 CCGGGCATGGAGATTGTGTA 59.820 55.000 0.00 0.00 0.00 2.90
3584 3893 2.484062 GCCGGGCATGGAGATTGTG 61.484 63.158 15.62 0.00 0.00 3.33
3678 3987 2.258748 GAGCTGGTGTCCCCCTAAGC 62.259 65.000 0.00 0.00 31.42 3.09
3706 4015 1.139734 CGACCAGATGGGAGACACG 59.860 63.158 3.48 0.00 41.15 4.49
3715 4024 2.579787 GACCGACGCGACCAGATG 60.580 66.667 15.93 0.00 0.00 2.90
3752 4061 2.008752 TTGATGTCGTGCGATGTGAT 57.991 45.000 0.00 0.00 0.00 3.06
3769 4078 4.170062 CCGCAGCAGCCGACATTG 62.170 66.667 0.00 0.00 37.52 2.82
3844 4153 1.989508 CCCTGGCCCATCCAAAACC 60.990 63.158 0.00 0.00 46.01 3.27
3852 4161 3.935456 TACGACACCCCTGGCCCAT 62.935 63.158 0.00 0.00 0.00 4.00
3867 4176 4.208948 CTGCCGCGCACATGTACG 62.209 66.667 14.22 14.22 33.79 3.67
3912 4221 0.472471 AACACAGTCCCACATCCGTT 59.528 50.000 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.