Multiple sequence alignment - TraesCS1D01G392300

Loading Multiple Alignment...

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 TraesCS1D01G392300 chr1D 100.000 6766 0 0 1 6766 462380584 462387349 0.000000e+00 12495.0
1 TraesCS1D01G392300 chr1A 96.953 3741 88 14 2335 6055 554205037 554208771 0.000000e+00 6253.0
2 TraesCS1D01G392300 chr1A 91.489 1081 45 10 1100 2144 554203927 554204996 0.000000e+00 1443.0
3 TraesCS1D01G392300 chr1A 91.026 702 42 8 6081 6764 554209396 554210094 0.000000e+00 928.0
4 TraesCS1D01G392300 chr1A 87.656 802 71 18 234 1024 554202859 554203643 0.000000e+00 907.0
5 TraesCS1D01G392300 chr1A 95.833 48 0 1 2273 2320 554204994 554205039 7.280000e-10 76.8
6 TraesCS1D01G392300 chr1B 88.289 2391 203 40 3587 5958 637497529 637499861 0.000000e+00 2793.0
7 TraesCS1D01G392300 chr1B 83.072 2233 186 79 2 2144 637494123 637496253 0.000000e+00 1853.0
8 TraesCS1D01G392300 chr1B 87.701 374 43 2 2781 3152 637496612 637496984 3.750000e-117 433.0
9 TraesCS1D01G392300 chr1B 81.437 167 23 6 2548 2711 637496426 637496587 5.510000e-26 130.0
10 TraesCS1D01G392300 chrUn 99.851 673 1 0 1 673 307102512 307101840 0.000000e+00 1238.0
11 TraesCS1D01G392300 chrUn 78.147 421 55 18 1384 1794 34454524 34454917 4.080000e-57 233.0
12 TraesCS1D01G392300 chrUn 88.350 103 12 0 2137 2239 112023702 112023804 2.560000e-24 124.0
13 TraesCS1D01G392300 chr4B 75.532 282 42 15 1385 1661 20334671 20334412 5.550000e-21 113.0
14 TraesCS1D01G392300 chr4A 75.532 282 42 15 1385 1661 591526408 591526149 5.550000e-21 113.0
15 TraesCS1D01G392300 chr4A 80.769 156 21 6 1385 1535 592517893 592518044 5.550000e-21 113.0
16 TraesCS1D01G392300 chr2D 93.421 76 5 0 2141 2216 608481477 608481552 5.550000e-21 113.0
17 TraesCS1D01G392300 chr7B 90.476 63 6 0 2144 2206 260516583 260516645 4.350000e-12 84.2


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 TraesCS1D01G392300 chr1D 462380584 462387349 6765 False 12495.00 12495 100.00000 1 6766 1 chr1D.!!$F1 6765
1 TraesCS1D01G392300 chr1A 554202859 554210094 7235 False 1921.56 6253 92.59140 234 6764 5 chr1A.!!$F1 6530
2 TraesCS1D01G392300 chr1B 637494123 637499861 5738 False 1302.25 2793 85.12475 2 5958 4 chr1B.!!$F1 5956
3 TraesCS1D01G392300 chrUn 307101840 307102512 672 True 1238.00 1238 99.85100 1 673 1 chrUn.!!$R1 672

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
795 817 3.449095 GATAACAAAGGCGGCGGCG 62.449 63.158 28.70 28.70 41.24 6.46 F
1525 1836 0.040058 TACGTGTCTCTGGCCCCTAA 59.960 55.000 0.00 0.00 0.00 2.69 F
2177 2500 0.178987 ATCCACCGCTCCTACGATCT 60.179 55.000 0.00 0.00 34.06 2.75 F
2180 2503 0.248661 CACCGCTCCTACGATCTGTG 60.249 60.000 0.00 0.00 34.06 3.66 F
2183 2506 0.309302 CGCTCCTACGATCTGTGGAG 59.691 60.000 19.35 19.35 43.26 3.86 F
2226 2549 0.320421 TTTGCACTACTGCTCCGTCC 60.320 55.000 0.00 0.00 44.57 4.79 F
3245 3620 0.482446 TTGTGGAGGAAATGGCCAGT 59.518 50.000 13.05 5.37 31.18 4.00 F
4617 5100 0.381801 CTGTGTTGACACCTGTTGGC 59.618 55.000 11.42 0.00 45.88 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 2481 0.178987 AGATCGTAGGAGCGGTGGAT 60.179 55.000 0.00 0.0 32.66 3.41 R
2538 2862 0.324943 ACAAAGACATCGACTGGGGG 59.675 55.000 0.00 0.0 0.00 5.40 R
3614 4085 4.168101 AGGCCGAGAATTAATATGGAGGA 58.832 43.478 0.00 0.0 0.00 3.71 R
4117 4598 6.486320 TCTTCTTTTTGTGTGCTGTCATATGA 59.514 34.615 0.00 0.0 0.00 2.15 R
4197 4678 3.324846 TCCAGATAAGATGCGCATTACCT 59.675 43.478 26.12 14.5 0.00 3.08 R
4556 5039 2.932234 CGAGGAACACAGCCGGTCT 61.932 63.158 1.90 0.0 0.00 3.85 R
5559 6045 0.112412 TTCACAGGGGCCTTTTCTCC 59.888 55.000 0.84 0.0 0.00 3.71 R
5782 6271 0.034337 TCCGTGCACAAGTTAGGACC 59.966 55.000 18.64 0.0 0.00 4.46 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
673 689 8.792830 TTCTGTTTCTGTAAGGATAATCTTGG 57.207 34.615 0.00 0.00 0.00 3.61
674 690 7.918076 TCTGTTTCTGTAAGGATAATCTTGGT 58.082 34.615 0.00 0.00 0.00 3.67
676 692 9.667107 CTGTTTCTGTAAGGATAATCTTGGTAA 57.333 33.333 0.00 0.00 0.00 2.85
683 699 5.297569 AGGATAATCTTGGTAAGACTGGC 57.702 43.478 0.00 0.00 41.01 4.85
696 712 6.206634 TGGTAAGACTGGCTTTGACTTTAATG 59.793 38.462 0.00 0.00 38.05 1.90
719 741 5.602978 TGTTTTACTATTTGGCCTTTTCCCA 59.397 36.000 3.32 0.00 0.00 4.37
795 817 3.449095 GATAACAAAGGCGGCGGCG 62.449 63.158 28.70 28.70 41.24 6.46
1007 1048 2.023888 CGAGGGGGATATAGATGGAGGT 60.024 54.545 0.00 0.00 0.00 3.85
1016 1057 0.252696 TAGATGGAGGTGGGCAGTGT 60.253 55.000 0.00 0.00 0.00 3.55
1517 1828 5.441543 CCGAAGTATGTATACGTGTCTCTG 58.558 45.833 7.89 3.34 38.28 3.35
1524 1835 0.260816 ATACGTGTCTCTGGCCCCTA 59.739 55.000 0.00 0.00 0.00 3.53
1525 1836 0.040058 TACGTGTCTCTGGCCCCTAA 59.960 55.000 0.00 0.00 0.00 2.69
1561 1872 1.080569 GTTCAGTGCCCAAATGCGG 60.081 57.895 0.00 0.00 0.00 5.69
1593 1907 3.019564 ACATCTGTCCCTTATTTGCTGC 58.980 45.455 0.00 0.00 0.00 5.25
1666 1980 4.139786 CCGGACAGCAGGTAGTATTAGTA 58.860 47.826 0.00 0.00 0.00 1.82
1675 1989 6.039829 AGCAGGTAGTATTAGTAACCGGTTAC 59.960 42.308 38.89 38.89 44.22 2.50
1678 1992 7.864379 CAGGTAGTATTAGTAACCGGTTACATG 59.136 40.741 43.23 27.75 45.79 3.21
1692 2006 5.279056 CCGGTTACATGGTTATGTGGTTTTT 60.279 40.000 0.00 0.00 46.63 1.94
1713 2027 5.499139 TTCCATCAAGAATTCGGTTATGC 57.501 39.130 0.00 0.00 0.00 3.14
1786 2100 4.201940 TGTGCTTCTGTTCATGTCAAGTTG 60.202 41.667 0.00 0.00 0.00 3.16
1864 2185 9.453572 AGATCACTAGCTTAAAATGATTTGTGA 57.546 29.630 7.22 7.22 32.19 3.58
1866 2187 9.846248 ATCACTAGCTTAAAATGATTTGTGAAC 57.154 29.630 8.41 0.00 31.73 3.18
1868 2189 9.121517 CACTAGCTTAAAATGATTTGTGAACTG 57.878 33.333 0.00 0.00 0.00 3.16
1949 2270 4.069304 CTGGGAAACTCGGTAAACATTCA 58.931 43.478 0.00 0.00 0.00 2.57
1958 2279 4.317488 TCGGTAAACATTCACCCTTGTAC 58.683 43.478 0.00 0.00 0.00 2.90
2050 2372 7.093814 TGGATATTGTTGAACTTCATTCCCAAG 60.094 37.037 0.00 0.00 36.36 3.61
2146 2469 8.822652 AGCTATTGCATTTATGAAATTAAGGC 57.177 30.769 1.12 3.02 42.22 4.35
2147 2470 7.874528 AGCTATTGCATTTATGAAATTAAGGCC 59.125 33.333 0.00 0.00 41.33 5.19
2148 2471 7.118245 GCTATTGCATTTATGAAATTAAGGCCC 59.882 37.037 0.00 0.00 41.33 5.80
2149 2472 5.289083 TGCATTTATGAAATTAAGGCCCC 57.711 39.130 0.00 0.00 41.33 5.80
2150 2473 4.718774 TGCATTTATGAAATTAAGGCCCCA 59.281 37.500 0.00 0.00 41.33 4.96
2151 2474 5.369110 TGCATTTATGAAATTAAGGCCCCAT 59.631 36.000 0.00 0.00 41.33 4.00
2152 2475 6.126536 TGCATTTATGAAATTAAGGCCCCATT 60.127 34.615 0.00 0.00 41.33 3.16
2153 2476 6.427853 GCATTTATGAAATTAAGGCCCCATTC 59.572 38.462 0.00 0.00 36.74 2.67
2154 2477 5.782893 TTATGAAATTAAGGCCCCATTCG 57.217 39.130 0.00 0.00 0.00 3.34
2155 2478 2.383855 TGAAATTAAGGCCCCATTCGG 58.616 47.619 0.00 0.00 0.00 4.30
2170 2493 3.470888 CGGGAATCCACCGCTCCT 61.471 66.667 0.09 0.00 45.34 3.69
2171 2494 2.131709 CGGGAATCCACCGCTCCTA 61.132 63.158 0.09 0.00 45.34 2.94
2172 2495 1.446366 GGGAATCCACCGCTCCTAC 59.554 63.158 0.09 0.00 0.00 3.18
2173 2496 1.067582 GGAATCCACCGCTCCTACG 59.932 63.158 0.00 0.00 0.00 3.51
2174 2497 1.389609 GGAATCCACCGCTCCTACGA 61.390 60.000 0.00 0.00 34.06 3.43
2175 2498 0.674534 GAATCCACCGCTCCTACGAT 59.325 55.000 0.00 0.00 34.06 3.73
2176 2499 0.674534 AATCCACCGCTCCTACGATC 59.325 55.000 0.00 0.00 34.06 3.69
2177 2500 0.178987 ATCCACCGCTCCTACGATCT 60.179 55.000 0.00 0.00 34.06 2.75
2178 2501 1.101635 TCCACCGCTCCTACGATCTG 61.102 60.000 0.00 0.00 34.06 2.90
2179 2502 1.384989 CCACCGCTCCTACGATCTGT 61.385 60.000 0.00 0.00 34.06 3.41
2180 2503 0.248661 CACCGCTCCTACGATCTGTG 60.249 60.000 0.00 0.00 34.06 3.66
2181 2504 1.360551 CCGCTCCTACGATCTGTGG 59.639 63.158 0.00 0.00 34.06 4.17
2182 2505 1.101635 CCGCTCCTACGATCTGTGGA 61.102 60.000 0.00 5.97 34.06 4.02
2183 2506 0.309302 CGCTCCTACGATCTGTGGAG 59.691 60.000 19.35 19.35 43.26 3.86
2189 2512 2.584418 CGATCTGTGGAGCGGCTG 60.584 66.667 7.50 0.00 46.01 4.85
2190 2513 2.581354 GATCTGTGGAGCGGCTGT 59.419 61.111 7.50 0.00 0.00 4.40
2191 2514 1.078848 GATCTGTGGAGCGGCTGTT 60.079 57.895 7.50 0.00 0.00 3.16
2192 2515 0.674895 GATCTGTGGAGCGGCTGTTT 60.675 55.000 7.50 0.00 0.00 2.83
2193 2516 0.957395 ATCTGTGGAGCGGCTGTTTG 60.957 55.000 7.50 0.00 0.00 2.93
2194 2517 3.259425 CTGTGGAGCGGCTGTTTGC 62.259 63.158 7.50 0.00 41.94 3.68
2195 2518 2.980233 GTGGAGCGGCTGTTTGCT 60.980 61.111 7.50 0.00 45.90 3.91
2201 2524 3.741476 CGGCTGTTTGCTGGCTCC 61.741 66.667 0.00 0.00 44.06 4.70
2202 2525 2.598394 GGCTGTTTGCTGGCTCCA 60.598 61.111 0.00 0.00 42.39 3.86
2203 2526 2.202395 GGCTGTTTGCTGGCTCCAA 61.202 57.895 0.00 0.00 42.39 3.53
2204 2527 1.288127 GCTGTTTGCTGGCTCCAAG 59.712 57.895 0.00 0.00 38.95 3.61
2205 2528 1.174712 GCTGTTTGCTGGCTCCAAGA 61.175 55.000 0.00 0.00 38.95 3.02
2206 2529 1.542492 CTGTTTGCTGGCTCCAAGAT 58.458 50.000 0.00 0.00 0.00 2.40
2207 2530 1.891150 CTGTTTGCTGGCTCCAAGATT 59.109 47.619 0.00 0.00 0.00 2.40
2208 2531 2.298163 CTGTTTGCTGGCTCCAAGATTT 59.702 45.455 0.00 0.00 0.00 2.17
2209 2532 2.699846 TGTTTGCTGGCTCCAAGATTTT 59.300 40.909 0.00 0.00 0.00 1.82
2210 2533 3.062042 GTTTGCTGGCTCCAAGATTTTG 58.938 45.455 0.00 0.00 0.00 2.44
2211 2534 0.604578 TGCTGGCTCCAAGATTTTGC 59.395 50.000 0.00 0.00 32.79 3.68
2212 2535 0.604578 GCTGGCTCCAAGATTTTGCA 59.395 50.000 0.00 0.00 32.79 4.08
2213 2536 1.670967 GCTGGCTCCAAGATTTTGCAC 60.671 52.381 0.00 0.00 32.79 4.57
2214 2537 1.891150 CTGGCTCCAAGATTTTGCACT 59.109 47.619 0.00 0.00 32.79 4.40
2215 2538 3.084039 CTGGCTCCAAGATTTTGCACTA 58.916 45.455 0.00 0.00 32.79 2.74
2216 2539 2.819608 TGGCTCCAAGATTTTGCACTAC 59.180 45.455 0.00 0.00 32.79 2.73
2217 2540 3.084786 GGCTCCAAGATTTTGCACTACT 58.915 45.455 0.00 0.00 32.79 2.57
2218 2541 3.119708 GGCTCCAAGATTTTGCACTACTG 60.120 47.826 0.00 0.00 32.79 2.74
2219 2542 3.671702 GCTCCAAGATTTTGCACTACTGC 60.672 47.826 0.00 0.00 44.52 4.40
2220 2543 3.754965 TCCAAGATTTTGCACTACTGCT 58.245 40.909 0.00 0.00 44.57 4.24
2221 2544 3.753272 TCCAAGATTTTGCACTACTGCTC 59.247 43.478 0.00 0.00 44.57 4.26
2222 2545 3.119708 CCAAGATTTTGCACTACTGCTCC 60.120 47.826 0.00 0.00 44.57 4.70
2223 2546 2.350522 AGATTTTGCACTACTGCTCCG 58.649 47.619 0.00 0.00 44.57 4.63
2224 2547 2.076863 GATTTTGCACTACTGCTCCGT 58.923 47.619 0.00 0.00 44.57 4.69
2225 2548 1.508632 TTTTGCACTACTGCTCCGTC 58.491 50.000 0.00 0.00 44.57 4.79
2226 2549 0.320421 TTTGCACTACTGCTCCGTCC 60.320 55.000 0.00 0.00 44.57 4.79
2227 2550 2.202623 GCACTACTGCTCCGTCCG 60.203 66.667 0.00 0.00 40.63 4.79
2228 2551 2.202623 CACTACTGCTCCGTCCGC 60.203 66.667 0.00 0.00 0.00 5.54
2229 2552 2.361357 ACTACTGCTCCGTCCGCT 60.361 61.111 0.00 0.00 0.00 5.52
2230 2553 2.408241 ACTACTGCTCCGTCCGCTC 61.408 63.158 0.00 0.00 0.00 5.03
2231 2554 3.127352 CTACTGCTCCGTCCGCTCC 62.127 68.421 0.00 0.00 0.00 4.70
2254 2577 2.125912 CGAAGCCGTGGAGTGGAG 60.126 66.667 0.00 0.00 0.00 3.86
2255 2578 2.932234 CGAAGCCGTGGAGTGGAGT 61.932 63.158 0.00 0.00 0.00 3.85
2256 2579 1.374758 GAAGCCGTGGAGTGGAGTG 60.375 63.158 0.00 0.00 0.00 3.51
2257 2580 1.816863 GAAGCCGTGGAGTGGAGTGA 61.817 60.000 0.00 0.00 0.00 3.41
2258 2581 1.407656 AAGCCGTGGAGTGGAGTGAA 61.408 55.000 0.00 0.00 0.00 3.18
2259 2582 1.374758 GCCGTGGAGTGGAGTGAAG 60.375 63.158 0.00 0.00 0.00 3.02
2260 2583 1.374758 CCGTGGAGTGGAGTGAAGC 60.375 63.158 0.00 0.00 0.00 3.86
2261 2584 1.374758 CGTGGAGTGGAGTGAAGCC 60.375 63.158 0.00 0.00 0.00 4.35
2262 2585 1.374758 GTGGAGTGGAGTGAAGCCG 60.375 63.158 0.00 0.00 0.00 5.52
2263 2586 1.533033 TGGAGTGGAGTGAAGCCGA 60.533 57.895 0.00 0.00 0.00 5.54
2264 2587 1.216710 GGAGTGGAGTGAAGCCGAG 59.783 63.158 0.00 0.00 0.00 4.63
2265 2588 1.446966 GAGTGGAGTGAAGCCGAGC 60.447 63.158 0.00 0.00 0.00 5.03
2266 2589 2.811317 GTGGAGTGAAGCCGAGCG 60.811 66.667 0.00 0.00 0.00 5.03
2267 2590 4.069232 TGGAGTGAAGCCGAGCGG 62.069 66.667 4.20 4.20 38.57 5.52
2268 2591 4.821589 GGAGTGAAGCCGAGCGGG 62.822 72.222 11.30 0.00 39.58 6.13
2269 2592 4.821589 GAGTGAAGCCGAGCGGGG 62.822 72.222 11.30 0.00 35.78 5.73
2313 2636 9.517609 ACTATTATAGTGAACGCAAAAGAGTAG 57.482 33.333 3.83 0.00 37.69 2.57
2315 2638 8.773404 ATTATAGTGAACGCAAAAGAGTAGTT 57.227 30.769 0.00 0.00 0.00 2.24
2318 2641 6.190954 AGTGAACGCAAAAGAGTAGTTTTT 57.809 33.333 0.00 0.00 0.00 1.94
2542 2866 4.706842 TTTAGTCTATGAGATTGCCCCC 57.293 45.455 0.00 0.00 0.00 5.40
2646 2971 5.624159 TGAGATTGCCCCAAGTCTAATATG 58.376 41.667 0.00 0.00 0.00 1.78
2904 3233 1.172812 GCCGACCAAATATCTGGCCC 61.173 60.000 0.00 0.00 40.45 5.80
2936 3265 3.873910 TGCCTGAGCTTGAAATAGGTAC 58.126 45.455 0.00 0.00 40.80 3.34
3105 3434 3.638627 TGGCTCGTCATTGTGATCTCTAT 59.361 43.478 0.00 0.00 0.00 1.98
3182 3519 5.732247 GCCACACAGTAAATTTGTTTCTCGT 60.732 40.000 0.00 0.00 0.00 4.18
3245 3620 0.482446 TTGTGGAGGAAATGGCCAGT 59.518 50.000 13.05 5.37 31.18 4.00
3317 3692 5.633830 AACTCTGTTATGAATTGCCAGTG 57.366 39.130 0.00 0.00 0.00 3.66
3398 3775 8.568732 TTTCTTAAGCTTTTAATGGACAAACG 57.431 30.769 3.20 0.00 0.00 3.60
3614 4085 6.204108 CCGTAAGTGTCTTTTGGAAATAGTGT 59.796 38.462 0.00 0.00 0.00 3.55
4556 5039 4.323485 CCTGCACAGGGAAATAGACACTAA 60.323 45.833 8.93 0.00 44.87 2.24
4617 5100 0.381801 CTGTGTTGACACCTGTTGGC 59.618 55.000 11.42 0.00 45.88 4.52
4856 5339 2.765689 AGTGTCCCAAATTTCCCACA 57.234 45.000 0.00 0.00 0.00 4.17
4888 5371 5.193663 TCTCATACTGATGCTGCTACTTC 57.806 43.478 0.00 0.00 32.62 3.01
5191 5675 8.587608 TGTACGGTATTAATTAATCCGGAAGAT 58.412 33.333 30.66 20.93 38.97 2.40
5357 5841 4.206375 TCACAAAATCTTGCCTCACTTCA 58.794 39.130 0.00 0.00 35.84 3.02
5362 5846 6.183360 ACAAAATCTTGCCTCACTTCATTTCA 60.183 34.615 0.00 0.00 35.84 2.69
5370 5854 6.449698 TGCCTCACTTCATTTCATCTTTTTC 58.550 36.000 0.00 0.00 0.00 2.29
5535 6021 0.460284 CCAGGGGAAGACGTGATTCG 60.460 60.000 0.00 0.00 46.00 3.34
5537 6023 1.079405 GGGGAAGACGTGATTCGCA 60.079 57.895 21.34 0.00 44.19 5.10
5556 6042 1.600957 CATGGATTGTCACGATGAGGC 59.399 52.381 0.00 0.00 0.00 4.70
5559 6045 2.082437 GATTGTCACGATGAGGCGCG 62.082 60.000 0.00 0.00 33.86 6.86
5563 6049 4.193334 CACGATGAGGCGCGGAGA 62.193 66.667 8.83 0.00 33.86 3.71
5565 6051 2.202743 CGATGAGGCGCGGAGAAA 60.203 61.111 8.83 0.00 0.00 2.52
5573 6059 4.410400 CGCGGAGAAAAGGCCCCT 62.410 66.667 0.00 0.00 0.00 4.79
5581 6070 1.713078 AGAAAAGGCCCCTGTGAAGAT 59.287 47.619 0.00 0.00 0.00 2.40
5655 6144 3.634397 TCCAAGTCCCTAGAAAGCATG 57.366 47.619 0.00 0.00 0.00 4.06
5656 6145 2.912956 TCCAAGTCCCTAGAAAGCATGT 59.087 45.455 0.00 0.00 0.00 3.21
5658 6147 4.534500 TCCAAGTCCCTAGAAAGCATGTAA 59.466 41.667 0.00 0.00 0.00 2.41
5749 6238 8.335532 TGACCTCCTGAAAACTGTATAAAATG 57.664 34.615 0.00 0.00 0.00 2.32
5763 6252 9.793252 ACTGTATAAAATGAGATGAAATTGTGC 57.207 29.630 0.00 0.00 0.00 4.57
5782 6271 9.571810 AATTGTGCACATGTAGTTTGTTATATG 57.428 29.630 22.39 0.00 0.00 1.78
5790 6279 9.609346 ACATGTAGTTTGTTATATGGTCCTAAC 57.391 33.333 0.00 0.00 0.00 2.34
5798 6287 5.878116 TGTTATATGGTCCTAACTTGTGCAC 59.122 40.000 10.75 10.75 0.00 4.57
5862 6351 3.805108 GCTCTTGCACGAGGGATATCAAT 60.805 47.826 20.56 0.00 39.41 2.57
5869 6358 4.578871 CACGAGGGATATCAATGCCAATA 58.421 43.478 4.83 0.00 45.78 1.90
5947 6437 6.264841 AGTTTGCCTGAATCTCTTGATTTC 57.735 37.500 0.00 0.00 42.43 2.17
5948 6438 5.771666 AGTTTGCCTGAATCTCTTGATTTCA 59.228 36.000 0.00 0.00 42.43 2.69
5949 6439 5.633830 TTGCCTGAATCTCTTGATTTCAC 57.366 39.130 0.00 0.00 42.43 3.18
5950 6440 4.914983 TGCCTGAATCTCTTGATTTCACT 58.085 39.130 0.00 0.00 42.43 3.41
5951 6441 4.698780 TGCCTGAATCTCTTGATTTCACTG 59.301 41.667 0.00 0.00 42.43 3.66
5952 6442 4.438472 GCCTGAATCTCTTGATTTCACTGC 60.438 45.833 0.00 0.00 42.43 4.40
5953 6443 4.698780 CCTGAATCTCTTGATTTCACTGCA 59.301 41.667 0.00 0.00 42.43 4.41
5954 6444 5.163744 CCTGAATCTCTTGATTTCACTGCAG 60.164 44.000 13.48 13.48 42.43 4.41
5955 6445 5.554070 TGAATCTCTTGATTTCACTGCAGA 58.446 37.500 23.35 0.00 42.43 4.26
5956 6446 5.410746 TGAATCTCTTGATTTCACTGCAGAC 59.589 40.000 23.35 4.93 42.43 3.51
5958 6448 2.414481 CTCTTGATTTCACTGCAGACCG 59.586 50.000 23.35 8.50 0.00 4.79
5959 6449 1.466167 CTTGATTTCACTGCAGACCGG 59.534 52.381 23.35 0.00 0.00 5.28
5967 6467 0.036164 ACTGCAGACCGGCACATTAA 59.964 50.000 23.35 0.00 39.25 1.40
5975 6475 2.415512 GACCGGCACATTAACAACTCTC 59.584 50.000 0.00 0.00 0.00 3.20
5977 6477 2.416547 CCGGCACATTAACAACTCTCTG 59.583 50.000 0.00 0.00 0.00 3.35
5992 6492 8.453238 ACAACTCTCTGTGATATTAGATACGT 57.547 34.615 0.00 0.00 0.00 3.57
5993 6493 9.557061 ACAACTCTCTGTGATATTAGATACGTA 57.443 33.333 0.00 0.00 0.00 3.57
6011 6511 9.737427 AGATACGTATTGAAGTTCACATAGAAG 57.263 33.333 9.92 0.00 36.78 2.85
6015 6515 8.926710 ACGTATTGAAGTTCACATAGAAGAAAG 58.073 33.333 4.68 0.00 36.78 2.62
6024 6524 3.944015 CACATAGAAGAAAGGAAGGCCAG 59.056 47.826 5.01 0.00 36.29 4.85
6029 6529 3.262151 AGAAGAAAGGAAGGCCAGTCTAC 59.738 47.826 5.01 0.00 36.29 2.59
6039 6539 1.291877 GCCAGTCTACCAGTGCAACG 61.292 60.000 0.00 0.00 45.86 4.10
6049 6549 2.552315 ACCAGTGCAACGAAATACCAAG 59.448 45.455 0.00 0.00 45.86 3.61
6055 6555 5.240623 AGTGCAACGAAATACCAAGAATGAA 59.759 36.000 0.00 0.00 45.86 2.57
6056 6556 6.071952 AGTGCAACGAAATACCAAGAATGAAT 60.072 34.615 0.00 0.00 45.86 2.57
6057 6557 6.251376 GTGCAACGAAATACCAAGAATGAATC 59.749 38.462 0.00 0.00 0.00 2.52
6058 6558 5.743872 GCAACGAAATACCAAGAATGAATCC 59.256 40.000 0.00 0.00 0.00 3.01
6059 6559 5.734855 ACGAAATACCAAGAATGAATCCG 57.265 39.130 0.00 0.00 0.00 4.18
6060 6560 4.574828 ACGAAATACCAAGAATGAATCCGG 59.425 41.667 0.00 0.00 0.00 5.14
6061 6561 4.814234 CGAAATACCAAGAATGAATCCGGA 59.186 41.667 6.61 6.61 0.00 5.14
6062 6562 5.295787 CGAAATACCAAGAATGAATCCGGAA 59.704 40.000 9.01 0.00 0.00 4.30
6063 6563 6.183360 CGAAATACCAAGAATGAATCCGGAAA 60.183 38.462 9.01 0.00 0.00 3.13
6064 6564 7.468631 CGAAATACCAAGAATGAATCCGGAAAT 60.469 37.037 9.01 0.00 0.00 2.17
6065 6565 8.760980 AAATACCAAGAATGAATCCGGAAATA 57.239 30.769 9.01 0.00 0.00 1.40
6066 6566 7.745620 ATACCAAGAATGAATCCGGAAATAC 57.254 36.000 9.01 0.48 0.00 1.89
6067 6567 5.505780 ACCAAGAATGAATCCGGAAATACA 58.494 37.500 9.01 6.98 0.00 2.29
6069 6569 7.287061 ACCAAGAATGAATCCGGAAATACATA 58.713 34.615 9.01 0.00 0.00 2.29
6070 6570 7.944554 ACCAAGAATGAATCCGGAAATACATAT 59.055 33.333 9.01 2.36 0.00 1.78
6079 6579 9.798994 GAATCCGGAAATACATATTAGATACGT 57.201 33.333 9.01 0.00 0.00 3.57
6134 7233 6.410157 CCATTCCTCTGAATCCAAATACTCCT 60.410 42.308 0.00 0.00 39.20 3.69
6180 7279 1.303561 AAAATGAGGCGGCAGCTCA 60.304 52.632 13.08 10.75 44.37 4.26
6198 7297 3.399330 CTCAGCCTTCGAAAACAAGGTA 58.601 45.455 0.00 0.00 42.35 3.08
6209 7308 8.850454 TTCGAAAACAAGGTATCTTCAAAAAG 57.150 30.769 0.00 0.00 0.00 2.27
6250 7349 0.332972 AGGGATCAAAGAGGCCCAAC 59.667 55.000 0.00 0.00 43.20 3.77
6255 7354 4.023291 GGATCAAAGAGGCCCAACATTTA 58.977 43.478 0.00 0.00 0.00 1.40
6279 7395 2.358939 CAAAGTTGCAATCCCAGAGC 57.641 50.000 0.59 0.00 0.00 4.09
6302 7418 2.880890 GGTGCATGAGTGTTTCTTCAGT 59.119 45.455 0.00 0.00 0.00 3.41
6311 7427 4.698575 AGTGTTTCTTCAGTCTCTTGGTC 58.301 43.478 0.00 0.00 0.00 4.02
6330 7446 2.558359 GTCACAATTTGGACAGAAGGGG 59.442 50.000 0.78 0.00 34.22 4.79
6335 7451 2.584835 TTTGGACAGAAGGGGTCATG 57.415 50.000 0.00 0.00 37.00 3.07
6338 7454 0.393537 GGACAGAAGGGGTCATGCAG 60.394 60.000 0.00 0.00 37.00 4.41
6370 7486 5.152623 TCTTCGAATCAAGGATCTTGTGT 57.847 39.130 0.00 0.00 0.00 3.72
6376 7492 7.608153 TCGAATCAAGGATCTTGTGTTAACTA 58.392 34.615 7.22 0.00 0.00 2.24
6387 7503 3.616219 TGTGTTAACTATGTCATGGGCC 58.384 45.455 7.22 0.00 0.00 5.80
6426 7542 7.510549 AAAATTGTGCTTTAGTCTGCTAGAA 57.489 32.000 0.00 0.00 0.00 2.10
6427 7543 6.734104 AATTGTGCTTTAGTCTGCTAGAAG 57.266 37.500 0.00 0.00 0.00 2.85
6428 7544 4.873746 TGTGCTTTAGTCTGCTAGAAGT 57.126 40.909 0.00 0.00 0.00 3.01
6429 7545 4.560128 TGTGCTTTAGTCTGCTAGAAGTG 58.440 43.478 0.00 0.00 0.00 3.16
6430 7546 3.369451 GTGCTTTAGTCTGCTAGAAGTGC 59.631 47.826 0.00 0.00 0.00 4.40
6431 7547 3.259374 TGCTTTAGTCTGCTAGAAGTGCT 59.741 43.478 0.00 0.50 0.00 4.40
6434 7550 4.710423 TTAGTCTGCTAGAAGTGCTCAG 57.290 45.455 0.00 0.00 0.00 3.35
6437 7553 3.130869 AGTCTGCTAGAAGTGCTCAGATG 59.869 47.826 0.00 0.00 36.37 2.90
6446 7562 4.936411 AGAAGTGCTCAGATGTGATTGAAG 59.064 41.667 0.00 0.00 30.18 3.02
6466 7582 1.073284 GAAAGTGTGCCCCTCTTGGTA 59.927 52.381 0.00 0.00 0.00 3.25
6503 7619 8.289618 TGCTTGTACATTTTCATTGAAGAGTAC 58.710 33.333 19.96 19.96 31.79 2.73
6562 7678 3.945285 TCTGAAGGTGTCAAAACAGGAAC 59.055 43.478 0.00 0.00 35.64 3.62
6578 7694 4.074259 CAGGAACAATGTCATGGAGTTGA 58.926 43.478 10.44 0.00 0.00 3.18
6581 7697 4.082571 GGAACAATGTCATGGAGTTGAAGG 60.083 45.833 10.44 0.00 0.00 3.46
6611 7727 2.378038 TGTGCTTGGTTTGAAAGAGCT 58.622 42.857 8.62 0.00 34.56 4.09
6620 7736 5.003804 TGGTTTGAAAGAGCTAGATGGAAC 58.996 41.667 0.00 0.00 0.00 3.62
6636 7752 0.398318 GAACTGCTCAACCCAGTCCT 59.602 55.000 0.00 0.00 42.37 3.85
6642 7758 1.066787 GCTCAACCCAGTCCTAGTGTC 60.067 57.143 0.00 0.00 0.00 3.67
6658 7774 3.744660 AGTGTCCAGCAAAGTCCTTAAG 58.255 45.455 0.00 0.00 0.00 1.85
6665 7781 6.430000 GTCCAGCAAAGTCCTTAAGTGAAATA 59.570 38.462 0.97 0.00 0.00 1.40
6725 7841 1.347378 TGTTGCAGTGGCTCATCAGTA 59.653 47.619 0.00 0.00 41.91 2.74
6729 7845 2.026915 TGCAGTGGCTCATCAGTACAAT 60.027 45.455 0.00 0.00 41.91 2.71
6738 7854 6.098838 TGGCTCATCAGTACAATTATCAGTCT 59.901 38.462 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
673 689 7.203255 ACATTAAAGTCAAAGCCAGTCTTAC 57.797 36.000 0.00 0.00 33.88 2.34
674 690 7.817418 AACATTAAAGTCAAAGCCAGTCTTA 57.183 32.000 0.00 0.00 33.88 2.10
676 692 6.715347 AAACATTAAAGTCAAAGCCAGTCT 57.285 33.333 0.00 0.00 0.00 3.24
696 712 6.104146 TGGGAAAAGGCCAAATAGTAAAAC 57.896 37.500 5.01 0.00 0.00 2.43
716 738 6.348498 ACTGAATCTTGTTTTTCCTTTTGGG 58.652 36.000 0.00 0.00 40.87 4.12
719 741 8.935844 GTGAAACTGAATCTTGTTTTTCCTTTT 58.064 29.630 6.45 0.00 36.64 2.27
1057 1098 4.097361 GTCTTGGCCCCGGTCTCC 62.097 72.222 0.00 0.00 0.00 3.71
1218 1470 1.620819 TCTGTCAGAACCAGAGGAAGC 59.379 52.381 0.00 0.00 34.12 3.86
1371 1681 3.145551 CCCATGGCTTGGCTCTGC 61.146 66.667 13.72 0.00 44.97 4.26
1431 1741 2.606961 CCTGAACGCGCAGAAAGCA 61.607 57.895 14.33 0.00 46.13 3.91
1454 1765 0.826715 TCCTCAGAGCTGGGAAATCG 59.173 55.000 0.00 0.00 31.13 3.34
1517 1828 1.106285 CTGCACTGAAATTAGGGGCC 58.894 55.000 0.00 0.00 0.00 5.80
1524 1835 4.828939 TGAACTGAATCCTGCACTGAAATT 59.171 37.500 0.00 0.00 0.00 1.82
1525 1836 4.401022 TGAACTGAATCCTGCACTGAAAT 58.599 39.130 0.00 0.00 0.00 2.17
1581 1895 2.681848 CTCTGACAGGCAGCAAATAAGG 59.318 50.000 0.00 0.00 44.52 2.69
1593 1907 1.876156 GAGGTTTGCAACTCTGACAGG 59.124 52.381 0.00 0.00 0.00 4.00
1666 1980 3.244981 ACCACATAACCATGTAACCGGTT 60.245 43.478 25.64 25.64 43.73 4.44
1692 2006 3.882888 GGCATAACCGAATTCTTGATGGA 59.117 43.478 3.52 0.00 0.00 3.41
1713 2027 2.462456 TAAGTCTGAAGTGCAGCAGG 57.538 50.000 0.00 0.00 44.52 4.85
1786 2100 3.445450 TCACTGCTCACTGAGAACTATCC 59.555 47.826 10.45 0.00 0.00 2.59
1861 2182 1.264288 GCAGTAGCCACAACAGTTCAC 59.736 52.381 0.00 0.00 33.58 3.18
1864 2185 1.308998 GTGCAGTAGCCACAACAGTT 58.691 50.000 0.00 0.00 41.13 3.16
1866 2187 0.870393 CTGTGCAGTAGCCACAACAG 59.130 55.000 0.00 0.08 41.13 3.16
1868 2189 0.535102 ACCTGTGCAGTAGCCACAAC 60.535 55.000 0.00 0.00 41.13 3.32
2027 2349 7.781324 ACTTGGGAATGAAGTTCAACAATAT 57.219 32.000 10.14 2.85 38.64 1.28
2050 2372 1.070758 TCTTGGAGGTGCAGAGTGAAC 59.929 52.381 0.00 0.00 0.00 3.18
2154 2477 1.446366 GTAGGAGCGGTGGATTCCC 59.554 63.158 0.00 0.00 0.00 3.97
2155 2478 1.067582 CGTAGGAGCGGTGGATTCC 59.932 63.158 0.00 0.00 0.00 3.01
2156 2479 0.674534 ATCGTAGGAGCGGTGGATTC 59.325 55.000 0.00 0.00 0.00 2.52
2157 2480 0.674534 GATCGTAGGAGCGGTGGATT 59.325 55.000 0.00 0.00 0.00 3.01
2158 2481 0.178987 AGATCGTAGGAGCGGTGGAT 60.179 55.000 0.00 0.00 32.66 3.41
2159 2482 1.101635 CAGATCGTAGGAGCGGTGGA 61.102 60.000 0.00 0.00 32.66 4.02
2160 2483 1.360551 CAGATCGTAGGAGCGGTGG 59.639 63.158 0.00 0.00 32.66 4.61
2161 2484 0.248661 CACAGATCGTAGGAGCGGTG 60.249 60.000 17.03 17.03 45.45 4.94
2162 2485 1.384989 CCACAGATCGTAGGAGCGGT 61.385 60.000 0.57 0.57 37.47 5.68
2163 2486 1.101635 TCCACAGATCGTAGGAGCGG 61.102 60.000 0.00 0.00 32.66 5.52
2164 2487 0.309302 CTCCACAGATCGTAGGAGCG 59.691 60.000 14.57 0.00 36.65 5.03
2166 2489 0.309302 CGCTCCACAGATCGTAGGAG 59.691 60.000 19.73 19.73 41.84 3.69
2167 2490 1.101635 CCGCTCCACAGATCGTAGGA 61.102 60.000 3.58 3.58 29.66 2.94
2168 2491 1.360551 CCGCTCCACAGATCGTAGG 59.639 63.158 0.00 0.00 29.66 3.18
2169 2492 1.299468 GCCGCTCCACAGATCGTAG 60.299 63.158 0.00 0.00 29.66 3.51
2170 2493 1.753078 AGCCGCTCCACAGATCGTA 60.753 57.895 0.00 0.00 29.66 3.43
2171 2494 3.071206 AGCCGCTCCACAGATCGT 61.071 61.111 0.00 0.00 29.66 3.73
2172 2495 2.584418 CAGCCGCTCCACAGATCG 60.584 66.667 0.00 0.00 0.00 3.69
2173 2496 0.674895 AAACAGCCGCTCCACAGATC 60.675 55.000 0.00 0.00 0.00 2.75
2174 2497 0.957395 CAAACAGCCGCTCCACAGAT 60.957 55.000 0.00 0.00 0.00 2.90
2175 2498 1.597854 CAAACAGCCGCTCCACAGA 60.598 57.895 0.00 0.00 0.00 3.41
2176 2499 2.949106 CAAACAGCCGCTCCACAG 59.051 61.111 0.00 0.00 0.00 3.66
2177 2500 3.286751 GCAAACAGCCGCTCCACA 61.287 61.111 0.00 0.00 37.23 4.17
2186 2509 1.174712 TCTTGGAGCCAGCAAACAGC 61.175 55.000 0.00 0.00 46.19 4.40
2187 2510 1.542492 ATCTTGGAGCCAGCAAACAG 58.458 50.000 0.00 0.00 0.00 3.16
2188 2511 1.999648 AATCTTGGAGCCAGCAAACA 58.000 45.000 0.00 0.00 0.00 2.83
2189 2512 3.062042 CAAAATCTTGGAGCCAGCAAAC 58.938 45.455 0.00 0.00 0.00 2.93
2190 2513 2.548493 GCAAAATCTTGGAGCCAGCAAA 60.548 45.455 0.00 0.00 32.76 3.68
2191 2514 1.001181 GCAAAATCTTGGAGCCAGCAA 59.999 47.619 0.00 0.00 32.76 3.91
2192 2515 0.604578 GCAAAATCTTGGAGCCAGCA 59.395 50.000 0.00 0.00 32.76 4.41
2193 2516 0.604578 TGCAAAATCTTGGAGCCAGC 59.395 50.000 0.00 0.00 32.76 4.85
2194 2517 1.891150 AGTGCAAAATCTTGGAGCCAG 59.109 47.619 0.00 0.00 32.99 4.85
2195 2518 1.999648 AGTGCAAAATCTTGGAGCCA 58.000 45.000 0.00 0.00 32.99 4.75
2196 2519 3.084786 AGTAGTGCAAAATCTTGGAGCC 58.915 45.455 0.00 0.00 32.99 4.70
2197 2520 4.088823 CAGTAGTGCAAAATCTTGGAGC 57.911 45.455 0.00 0.00 32.99 4.70
2211 2534 2.202623 GCGGACGGAGCAGTAGTG 60.203 66.667 0.00 0.00 34.19 2.74
2212 2535 2.361357 AGCGGACGGAGCAGTAGT 60.361 61.111 2.17 0.00 37.01 2.73
2213 2536 2.409651 GAGCGGACGGAGCAGTAG 59.590 66.667 2.17 0.00 37.01 2.57
2214 2537 3.138798 GGAGCGGACGGAGCAGTA 61.139 66.667 2.17 0.00 37.01 2.74
2233 2556 4.070552 ACTCCACGGCTTCGCTCC 62.071 66.667 0.00 0.00 37.41 4.70
2234 2557 2.811317 CACTCCACGGCTTCGCTC 60.811 66.667 0.00 0.00 37.41 5.03
2235 2558 4.379243 CCACTCCACGGCTTCGCT 62.379 66.667 0.00 0.00 37.41 4.93
2236 2559 4.373116 TCCACTCCACGGCTTCGC 62.373 66.667 0.00 0.00 37.41 4.70
2237 2560 2.125912 CTCCACTCCACGGCTTCG 60.126 66.667 0.00 0.00 40.22 3.79
2238 2561 1.374758 CACTCCACTCCACGGCTTC 60.375 63.158 0.00 0.00 0.00 3.86
2239 2562 1.407656 TTCACTCCACTCCACGGCTT 61.408 55.000 0.00 0.00 0.00 4.35
2240 2563 1.821061 CTTCACTCCACTCCACGGCT 61.821 60.000 0.00 0.00 0.00 5.52
2241 2564 1.374758 CTTCACTCCACTCCACGGC 60.375 63.158 0.00 0.00 0.00 5.68
2242 2565 1.374758 GCTTCACTCCACTCCACGG 60.375 63.158 0.00 0.00 0.00 4.94
2243 2566 1.374758 GGCTTCACTCCACTCCACG 60.375 63.158 0.00 0.00 0.00 4.94
2244 2567 1.374758 CGGCTTCACTCCACTCCAC 60.375 63.158 0.00 0.00 0.00 4.02
2245 2568 1.533033 TCGGCTTCACTCCACTCCA 60.533 57.895 0.00 0.00 0.00 3.86
2246 2569 1.216710 CTCGGCTTCACTCCACTCC 59.783 63.158 0.00 0.00 0.00 3.85
2247 2570 1.446966 GCTCGGCTTCACTCCACTC 60.447 63.158 0.00 0.00 0.00 3.51
2248 2571 2.659610 GCTCGGCTTCACTCCACT 59.340 61.111 0.00 0.00 0.00 4.00
2249 2572 2.811317 CGCTCGGCTTCACTCCAC 60.811 66.667 0.00 0.00 0.00 4.02
2250 2573 4.069232 CCGCTCGGCTTCACTCCA 62.069 66.667 0.00 0.00 0.00 3.86
2251 2574 4.821589 CCCGCTCGGCTTCACTCC 62.822 72.222 2.18 0.00 0.00 3.85
2252 2575 4.821589 CCCCGCTCGGCTTCACTC 62.822 72.222 2.18 0.00 0.00 3.51
2260 2583 2.280865 GATTTAGGCCCCGCTCGG 60.281 66.667 0.00 0.48 0.00 4.63
2261 2584 2.436087 ATCGATTTAGGCCCCGCTCG 62.436 60.000 0.00 3.85 0.00 5.03
2262 2585 0.250338 AATCGATTTAGGCCCCGCTC 60.250 55.000 4.39 0.00 0.00 5.03
2263 2586 0.535102 CAATCGATTTAGGCCCCGCT 60.535 55.000 8.21 0.00 0.00 5.52
2264 2587 1.949257 CAATCGATTTAGGCCCCGC 59.051 57.895 8.21 0.00 0.00 6.13
2265 2588 0.817634 TGCAATCGATTTAGGCCCCG 60.818 55.000 8.21 0.00 0.00 5.73
2266 2589 1.067060 GTTGCAATCGATTTAGGCCCC 59.933 52.381 8.21 0.00 0.00 5.80
2267 2590 1.748493 TGTTGCAATCGATTTAGGCCC 59.252 47.619 8.21 3.73 0.00 5.80
2268 2591 2.423538 AGTGTTGCAATCGATTTAGGCC 59.576 45.455 8.21 0.00 0.00 5.19
2269 2592 3.764885 AGTGTTGCAATCGATTTAGGC 57.235 42.857 8.21 9.90 0.00 3.93
2385 2709 5.756833 TGAATGTGTCTGCATAGATGATGAC 59.243 40.000 0.00 1.74 37.82 3.06
2394 2718 3.689347 AGCCTTTGAATGTGTCTGCATA 58.311 40.909 0.00 0.00 0.00 3.14
2538 2862 0.324943 ACAAAGACATCGACTGGGGG 59.675 55.000 0.00 0.00 0.00 5.40
2542 2866 5.710984 ACCTAGTTACAAAGACATCGACTG 58.289 41.667 0.00 0.00 0.00 3.51
2646 2971 9.770097 TTAATATGGACAGAGATCTCATCAAAC 57.230 33.333 24.39 9.78 0.00 2.93
2798 3125 8.516313 GCATAATATTGCAGCTCAAGAAGCATC 61.516 40.741 0.00 0.00 45.19 3.91
2904 3233 1.222766 GCTCAGGCAGATGATCAGCG 61.223 60.000 5.12 1.93 38.54 5.18
3105 3434 9.246670 ACAGTACTATTTACACAGTACATACCA 57.753 33.333 12.84 0.00 46.26 3.25
3614 4085 4.168101 AGGCCGAGAATTAATATGGAGGA 58.832 43.478 0.00 0.00 0.00 3.71
4117 4598 6.486320 TCTTCTTTTTGTGTGCTGTCATATGA 59.514 34.615 0.00 0.00 0.00 2.15
4197 4678 3.324846 TCCAGATAAGATGCGCATTACCT 59.675 43.478 26.12 14.50 0.00 3.08
4556 5039 2.932234 CGAGGAACACAGCCGGTCT 61.932 63.158 1.90 0.00 0.00 3.85
5126 5610 3.187842 GGTTTAGCTTAACTGGTCCAACG 59.812 47.826 14.69 0.00 0.00 4.10
5191 5675 6.086011 ACAAACCCATAATAATCACCCAGA 57.914 37.500 0.00 0.00 0.00 3.86
5357 5841 7.894376 ATGTTCATTGCGAAAAAGATGAAAT 57.106 28.000 0.00 0.00 39.43 2.17
5362 5846 7.329226 CAGGTTTATGTTCATTGCGAAAAAGAT 59.671 33.333 0.00 0.00 34.69 2.40
5370 5854 3.214697 TGCAGGTTTATGTTCATTGCG 57.785 42.857 0.00 0.00 33.03 4.85
5535 6021 1.600957 CCTCATCGTGACAATCCATGC 59.399 52.381 0.00 0.00 0.00 4.06
5537 6023 1.807755 CGCCTCATCGTGACAATCCAT 60.808 52.381 0.00 0.00 0.00 3.41
5556 6042 4.410400 AGGGGCCTTTTCTCCGCG 62.410 66.667 0.84 0.00 39.90 6.46
5559 6045 0.112412 TTCACAGGGGCCTTTTCTCC 59.888 55.000 0.84 0.00 0.00 3.71
5563 6049 1.928868 CATCTTCACAGGGGCCTTTT 58.071 50.000 0.84 0.00 0.00 2.27
5565 6051 1.000396 GCATCTTCACAGGGGCCTT 60.000 57.895 0.84 0.00 0.00 4.35
5573 6059 1.347378 TGGTAGCACAGCATCTTCACA 59.653 47.619 0.00 0.00 0.00 3.58
5581 6070 0.764890 AGTTTCCTGGTAGCACAGCA 59.235 50.000 0.00 0.00 37.16 4.41
5674 6163 6.658831 CACATGGTACGGAAATGATGTAATC 58.341 40.000 0.00 0.00 45.83 1.75
5689 6178 3.546002 TTTTACAAGCGCACATGGTAC 57.454 42.857 11.47 0.00 0.00 3.34
5718 6207 4.580580 ACAGTTTTCAGGAGGTCATGTTTC 59.419 41.667 0.00 0.00 0.00 2.78
5749 6238 6.187125 ACTACATGTGCACAATTTCATCTC 57.813 37.500 25.72 0.00 0.00 2.75
5763 6252 9.607988 TTAGGACCATATAACAAACTACATGTG 57.392 33.333 9.11 0.93 0.00 3.21
5782 6271 0.034337 TCCGTGCACAAGTTAGGACC 59.966 55.000 18.64 0.00 0.00 4.46
5798 6287 6.422776 AGTGTGTAAAAATAGAGCATTCCG 57.577 37.500 0.00 0.00 0.00 4.30
5809 6298 6.723298 TGGATTCCACAAGTGTGTAAAAAT 57.277 33.333 10.40 4.93 44.21 1.82
5862 6351 1.078072 ACGTGGGCGAATATTGGCA 60.078 52.632 21.85 1.86 42.00 4.92
5869 6358 1.808390 GTTAGCGACGTGGGCGAAT 60.808 57.895 0.00 0.00 42.00 3.34
5947 6437 0.673333 TAATGTGCCGGTCTGCAGTG 60.673 55.000 14.67 5.01 43.02 3.66
5948 6438 0.036164 TTAATGTGCCGGTCTGCAGT 59.964 50.000 14.67 0.00 43.02 4.40
5949 6439 0.447801 GTTAATGTGCCGGTCTGCAG 59.552 55.000 7.63 7.63 43.02 4.41
5950 6440 0.250510 TGTTAATGTGCCGGTCTGCA 60.251 50.000 1.90 0.00 39.37 4.41
5951 6441 0.878416 TTGTTAATGTGCCGGTCTGC 59.122 50.000 1.90 0.00 0.00 4.26
5952 6442 2.151202 AGTTGTTAATGTGCCGGTCTG 58.849 47.619 1.90 0.00 0.00 3.51
5953 6443 2.038557 AGAGTTGTTAATGTGCCGGTCT 59.961 45.455 1.90 0.00 0.00 3.85
5954 6444 2.415512 GAGAGTTGTTAATGTGCCGGTC 59.584 50.000 1.90 0.00 0.00 4.79
5955 6445 2.038557 AGAGAGTTGTTAATGTGCCGGT 59.961 45.455 1.90 0.00 0.00 5.28
5956 6446 2.416547 CAGAGAGTTGTTAATGTGCCGG 59.583 50.000 0.00 0.00 0.00 6.13
5958 6448 4.065088 TCACAGAGAGTTGTTAATGTGCC 58.935 43.478 0.00 0.00 38.29 5.01
5959 6449 5.869753 ATCACAGAGAGTTGTTAATGTGC 57.130 39.130 0.00 0.00 38.29 4.57
5967 6467 8.453238 ACGTATCTAATATCACAGAGAGTTGT 57.547 34.615 0.00 0.00 0.00 3.32
5988 6488 9.917129 TTTCTTCTATGTGAACTTCAATACGTA 57.083 29.630 0.00 0.00 0.00 3.57
5991 6491 9.436957 TCCTTTCTTCTATGTGAACTTCAATAC 57.563 33.333 0.00 0.00 0.00 1.89
5993 6493 8.924511 TTCCTTTCTTCTATGTGAACTTCAAT 57.075 30.769 0.00 0.00 0.00 2.57
5994 6494 7.445402 CCTTCCTTTCTTCTATGTGAACTTCAA 59.555 37.037 0.00 0.00 0.00 2.69
6008 6508 2.869101 AGACTGGCCTTCCTTTCTTC 57.131 50.000 3.32 0.00 0.00 2.87
6011 6511 1.628846 TGGTAGACTGGCCTTCCTTTC 59.371 52.381 3.32 0.00 0.00 2.62
6015 6515 0.250513 CACTGGTAGACTGGCCTTCC 59.749 60.000 3.32 0.00 0.00 3.46
6024 6524 3.370061 GGTATTTCGTTGCACTGGTAGAC 59.630 47.826 0.00 0.00 0.00 2.59
6029 6529 2.811431 TCTTGGTATTTCGTTGCACTGG 59.189 45.455 0.00 0.00 0.00 4.00
6039 6539 6.693315 TTCCGGATTCATTCTTGGTATTTC 57.307 37.500 4.15 0.00 0.00 2.17
6070 6570 9.661563 AGAAACATTCAACCAATACGTATCTAA 57.338 29.630 8.86 0.00 0.00 2.10
6072 6572 9.661563 TTAGAAACATTCAACCAATACGTATCT 57.338 29.630 8.86 0.00 0.00 1.98
6104 7203 4.656100 TGGATTCAGAGGAATGGTCAAA 57.344 40.909 0.00 0.00 43.69 2.69
6105 7204 4.656100 TTGGATTCAGAGGAATGGTCAA 57.344 40.909 0.00 0.00 43.69 3.18
6134 7233 3.554934 GAGATAACCATGTTGGGATGCA 58.445 45.455 0.00 0.00 43.37 3.96
6161 7260 1.138247 GAGCTGCCGCCTCATTTTG 59.862 57.895 0.00 0.00 36.60 2.44
6163 7262 1.748122 CTGAGCTGCCGCCTCATTT 60.748 57.895 0.00 0.00 36.60 2.32
6180 7279 4.287766 AGATACCTTGTTTTCGAAGGCT 57.712 40.909 0.00 0.00 43.46 4.58
6186 7285 8.342634 TCTCTTTTTGAAGATACCTTGTTTTCG 58.657 33.333 0.00 0.00 31.62 3.46
6198 7297 4.331108 GAGGCACCTCTCTTTTTGAAGAT 58.669 43.478 9.54 0.00 39.80 2.40
6229 7328 1.454663 GGGCCTCTTTGATCCCTGC 60.455 63.158 0.84 0.00 35.87 4.85
6242 7341 4.202451 ACTTTGCAAATAAATGTTGGGCCT 60.202 37.500 13.23 0.00 0.00 5.19
6279 7395 2.880268 TGAAGAAACACTCATGCACCTG 59.120 45.455 0.00 0.00 0.00 4.00
6302 7418 4.136796 CTGTCCAAATTGTGACCAAGAGA 58.863 43.478 10.53 0.00 33.17 3.10
6311 7427 2.558359 GACCCCTTCTGTCCAAATTGTG 59.442 50.000 0.00 0.00 0.00 3.33
6335 7451 2.178890 CGAAGAGGGATGCAGCTGC 61.179 63.158 31.89 31.89 42.50 5.25
6338 7454 1.224965 GATTCGAAGAGGGATGCAGC 58.775 55.000 3.35 0.00 38.43 5.25
6370 7486 5.433526 GTTAGTGGCCCATGACATAGTTAA 58.566 41.667 0.00 0.00 0.00 2.01
6376 7492 0.998928 TGGTTAGTGGCCCATGACAT 59.001 50.000 0.00 0.00 0.00 3.06
6403 7519 6.712547 ACTTCTAGCAGACTAAAGCACAATTT 59.287 34.615 0.00 0.00 0.00 1.82
6408 7524 3.369451 GCACTTCTAGCAGACTAAAGCAC 59.631 47.826 0.00 0.00 0.00 4.40
6422 7538 5.665916 TCAATCACATCTGAGCACTTCTA 57.334 39.130 0.00 0.00 0.00 2.10
6423 7539 4.548451 TCAATCACATCTGAGCACTTCT 57.452 40.909 0.00 0.00 0.00 2.85
6424 7540 4.934001 TCTTCAATCACATCTGAGCACTTC 59.066 41.667 0.00 0.00 0.00 3.01
6426 7542 4.548451 TCTTCAATCACATCTGAGCACT 57.452 40.909 0.00 0.00 0.00 4.40
6427 7543 5.180868 ACTTTCTTCAATCACATCTGAGCAC 59.819 40.000 0.00 0.00 0.00 4.40
6428 7544 5.180680 CACTTTCTTCAATCACATCTGAGCA 59.819 40.000 0.00 0.00 0.00 4.26
6429 7545 5.180868 ACACTTTCTTCAATCACATCTGAGC 59.819 40.000 0.00 0.00 0.00 4.26
6430 7546 6.600350 CACACTTTCTTCAATCACATCTGAG 58.400 40.000 0.00 0.00 0.00 3.35
6431 7547 5.049198 GCACACTTTCTTCAATCACATCTGA 60.049 40.000 0.00 0.00 0.00 3.27
6434 7550 4.479619 GGCACACTTTCTTCAATCACATC 58.520 43.478 0.00 0.00 0.00 3.06
6437 7553 2.029918 GGGGCACACTTTCTTCAATCAC 60.030 50.000 0.00 0.00 0.00 3.06
6446 7562 0.178990 ACCAAGAGGGGCACACTTTC 60.179 55.000 0.00 0.00 42.91 2.62
6466 7582 2.672098 TGTACAAGCATTTGTTGGGGT 58.328 42.857 0.00 0.00 45.01 4.95
6503 7619 4.074970 AGTGCCTTGGACAACATTAGAAG 58.925 43.478 0.00 0.00 0.00 2.85
6508 7624 0.675633 GCAGTGCCTTGGACAACATT 59.324 50.000 2.85 0.00 0.00 2.71
6510 7626 1.827789 GGCAGTGCCTTGGACAACA 60.828 57.895 27.48 0.00 46.69 3.33
6562 7678 5.909621 ATTCCTTCAACTCCATGACATTG 57.090 39.130 0.00 0.00 0.00 2.82
6578 7694 2.232941 CCAAGCACATGAGCAATTCCTT 59.767 45.455 17.61 0.00 36.85 3.36
6581 7697 3.308438 AACCAAGCACATGAGCAATTC 57.692 42.857 17.61 0.00 36.85 2.17
6611 7727 2.237143 CTGGGTTGAGCAGTTCCATCTA 59.763 50.000 0.00 0.00 0.00 1.98
6620 7736 1.066573 CACTAGGACTGGGTTGAGCAG 60.067 57.143 0.00 0.00 0.00 4.24
6636 7752 4.347000 ACTTAAGGACTTTGCTGGACACTA 59.653 41.667 7.53 0.00 0.00 2.74
6642 7758 5.712152 ATTTCACTTAAGGACTTTGCTGG 57.288 39.130 7.53 0.00 0.00 4.85
6658 7774 9.586435 CCTTTTCCAAATATGAGGTTATTTCAC 57.414 33.333 0.00 0.00 31.08 3.18
6665 7781 6.552008 TCACTCCTTTTCCAAATATGAGGTT 58.448 36.000 0.00 0.00 0.00 3.50
6673 7789 5.302823 CCTGAACTTCACTCCTTTTCCAAAT 59.697 40.000 0.00 0.00 0.00 2.32
6677 7793 3.149981 CCCTGAACTTCACTCCTTTTCC 58.850 50.000 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.