Multiple sequence alignment - TraesCS2D01G390600

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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 TraesCS2D01G390600 chr2D 100.000 3017 0 0 1 3017 498055330 498052314 0.000000e+00 5572
1 TraesCS2D01G390600 chr2D 82.553 235 31 7 1543 1772 498053743 498053514 6.600000e-47 198
2 TraesCS2D01G390600 chr2D 82.553 235 31 7 1588 1817 498053788 498053559 6.600000e-47 198
3 TraesCS2D01G390600 chr2B 90.776 2190 130 30 2 2151 584135967 584133810 0.000000e+00 2859
4 TraesCS2D01G390600 chr2B 89.655 290 25 2 2718 3003 584132920 584132632 6.150000e-97 364
5 TraesCS2D01G390600 chr2B 84.188 234 25 9 1588 1815 584134431 584134204 1.820000e-52 217
6 TraesCS2D01G390600 chr2A 88.353 1803 101 38 417 2151 642715165 642713404 0.000000e+00 2065
7 TraesCS2D01G390600 chr2A 84.000 400 38 14 2622 3006 642713034 642712646 7.950000e-96 361
8 TraesCS2D01G390600 chr2A 92.308 195 11 1 158 352 642715385 642715195 1.070000e-69 274


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 TraesCS2D01G390600 chr2D 498052314 498055330 3016 True 1989.333333 5572 88.368667 1 3017 3 chr2D.!!$R1 3016
1 TraesCS2D01G390600 chr2B 584132632 584135967 3335 True 1146.666667 2859 88.206333 2 3003 3 chr2B.!!$R1 3001
2 TraesCS2D01G390600 chr2A 642712646 642715385 2739 True 900.000000 2065 88.220333 158 3006 3 chr2A.!!$R1 2848

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
518 535 0.034756 CCGTGTCCATTCCACACAGA 59.965 55.0 4.01 0.0 43.79 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2353 2462 0.109689 TGCCGTTTTAAATTCGGGCG 60.11 50.0 23.83 8.98 43.77 6.13 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
28 29 2.520500 TGGTGCGGTGTTGCCATT 60.521 55.556 0.00 0.00 36.97 3.16
29 30 1.228276 TGGTGCGGTGTTGCCATTA 60.228 52.632 0.00 0.00 36.97 1.90
45 46 4.199310 GCCATTATTAACTCTGGAGTGCA 58.801 43.478 3.88 0.00 41.58 4.57
46 47 4.274459 GCCATTATTAACTCTGGAGTGCAG 59.726 45.833 5.07 5.07 41.58 4.41
123 124 3.047280 CGCTACCGGTGCAGCAAA 61.047 61.111 25.16 0.41 37.66 3.68
130 131 2.355009 GGTGCAGCAAAACGCCAG 60.355 61.111 11.86 0.00 44.04 4.85
133 134 1.902918 TGCAGCAAAACGCCAGGAT 60.903 52.632 0.00 0.00 44.04 3.24
375 390 4.344865 ATTTGCCCCGGAGCGTGT 62.345 61.111 0.73 0.00 34.65 4.49
402 417 3.874394 GCGTGATGCGTAATTGCG 58.126 55.556 11.89 11.89 43.66 4.85
403 418 1.060308 GCGTGATGCGTAATTGCGT 59.940 52.632 17.26 0.00 43.66 5.24
404 419 0.299300 GCGTGATGCGTAATTGCGTA 59.701 50.000 17.26 13.49 43.66 4.42
405 420 1.070843 GCGTGATGCGTAATTGCGTAT 60.071 47.619 18.31 18.31 43.66 3.06
406 421 2.549695 CGTGATGCGTAATTGCGTATG 58.450 47.619 22.51 6.37 37.32 2.39
407 422 2.659023 CGTGATGCGTAATTGCGTATGG 60.659 50.000 22.51 9.03 37.32 2.74
431 446 0.730265 TGCTGTGTGAACCGTGAAAC 59.270 50.000 0.00 0.00 0.00 2.78
511 528 3.134127 GCCTGCCGTGTCCATTCC 61.134 66.667 0.00 0.00 0.00 3.01
512 529 2.350895 CCTGCCGTGTCCATTCCA 59.649 61.111 0.00 0.00 0.00 3.53
518 535 0.034756 CCGTGTCCATTCCACACAGA 59.965 55.000 4.01 0.00 43.79 3.41
532 549 3.100545 ACAGACTTTGTGGGTGCAG 57.899 52.632 0.00 0.00 38.99 4.41
617 649 2.732094 GGTCGTACACGCGCTGTT 60.732 61.111 17.12 5.45 39.60 3.16
658 691 2.792290 CGCGCATCTCAGGTGTTCG 61.792 63.158 8.75 0.00 0.00 3.95
678 711 3.994392 TCGAGCTACTGAACCACAATTTC 59.006 43.478 0.00 0.00 0.00 2.17
774 810 0.527565 AATGCGCAACCACCTGAATC 59.472 50.000 17.11 0.00 0.00 2.52
782 818 3.595173 CAACCACCTGAATCGTACATGA 58.405 45.455 0.00 0.00 0.00 3.07
783 819 3.973206 ACCACCTGAATCGTACATGAA 57.027 42.857 0.00 0.00 0.00 2.57
796 842 8.581057 AATCGTACATGAAACATCTGAGATAC 57.419 34.615 0.00 0.00 0.00 2.24
1191 1238 3.834799 GTCGGGGCGAAGATCGGT 61.835 66.667 1.64 0.00 40.84 4.69
1431 1484 2.529389 AGAGGGGGTGCGGAAACT 60.529 61.111 0.00 0.00 0.00 2.66
1932 1985 4.200283 GCGCAGGAGACGAGGAGG 62.200 72.222 0.30 0.00 0.00 4.30
1938 1991 2.474612 GGAGACGAGGAGGAGCGAC 61.475 68.421 0.00 0.00 0.00 5.19
1950 2003 2.043450 AGCGACAGGAGGAGAGGG 60.043 66.667 0.00 0.00 0.00 4.30
2001 2067 1.557371 CCCTCTCTCTTCTTCCCAACC 59.443 57.143 0.00 0.00 0.00 3.77
2035 2102 2.801483 AGCTTGCTCTCTGTGACTCTA 58.199 47.619 0.00 0.00 0.00 2.43
2066 2133 1.389609 GCTGGCAATGGTGGATGGAG 61.390 60.000 0.00 0.00 0.00 3.86
2069 2136 0.550914 GGCAATGGTGGATGGAGGTA 59.449 55.000 0.00 0.00 0.00 3.08
2109 2179 4.318618 CGTTATATATAGCGCGACGATCCT 60.319 45.833 12.10 0.00 30.73 3.24
2111 2181 0.179161 ATATAGCGCGACGATCCTGC 60.179 55.000 12.10 0.00 0.00 4.85
2117 2187 4.829518 CGACGATCCTGCGTGCGA 62.830 66.667 0.00 0.00 45.72 5.10
2118 2188 2.506217 GACGATCCTGCGTGCGAA 60.506 61.111 0.00 0.00 45.72 4.70
2119 2189 2.048597 ACGATCCTGCGTGCGAAA 60.049 55.556 0.00 0.00 43.79 3.46
2121 2191 2.094659 CGATCCTGCGTGCGAAACT 61.095 57.895 0.00 0.00 0.00 2.66
2122 2192 1.421485 GATCCTGCGTGCGAAACTG 59.579 57.895 0.00 0.00 0.00 3.16
2124 2194 4.389576 CCTGCGTGCGAAACTGGC 62.390 66.667 0.00 0.00 0.00 4.85
2151 2234 1.599419 GCCAACACGTGACCAAATGAC 60.599 52.381 25.01 0.00 0.00 3.06
2152 2235 1.001815 CCAACACGTGACCAAATGACC 60.002 52.381 25.01 0.00 0.00 4.02
2153 2236 1.946768 CAACACGTGACCAAATGACCT 59.053 47.619 25.01 0.00 0.00 3.85
2154 2237 2.341846 ACACGTGACCAAATGACCTT 57.658 45.000 25.01 0.00 0.00 3.50
2155 2238 2.218603 ACACGTGACCAAATGACCTTC 58.781 47.619 25.01 0.00 0.00 3.46
2156 2239 2.217750 CACGTGACCAAATGACCTTCA 58.782 47.619 10.90 0.00 0.00 3.02
2159 2242 2.480419 CGTGACCAAATGACCTTCACTC 59.520 50.000 0.00 0.00 35.46 3.51
2160 2243 3.744660 GTGACCAAATGACCTTCACTCT 58.255 45.455 0.00 0.00 34.89 3.24
2161 2244 3.499918 GTGACCAAATGACCTTCACTCTG 59.500 47.826 0.00 0.00 34.89 3.35
2162 2245 2.485814 GACCAAATGACCTTCACTCTGC 59.514 50.000 0.00 0.00 0.00 4.26
2163 2246 2.158623 ACCAAATGACCTTCACTCTGCA 60.159 45.455 0.00 0.00 0.00 4.41
2164 2247 2.227388 CCAAATGACCTTCACTCTGCAC 59.773 50.000 0.00 0.00 0.00 4.57
2165 2248 2.880268 CAAATGACCTTCACTCTGCACA 59.120 45.455 0.00 0.00 0.00 4.57
2166 2249 2.469274 ATGACCTTCACTCTGCACAG 57.531 50.000 0.00 0.00 0.00 3.66
2167 2250 1.413118 TGACCTTCACTCTGCACAGA 58.587 50.000 0.00 0.00 35.85 3.41
2168 2251 1.762370 TGACCTTCACTCTGCACAGAA 59.238 47.619 1.42 0.00 36.94 3.02
2169 2252 2.170397 TGACCTTCACTCTGCACAGAAA 59.830 45.455 1.42 0.00 36.94 2.52
2170 2253 3.206150 GACCTTCACTCTGCACAGAAAA 58.794 45.455 1.42 0.00 36.94 2.29
2171 2254 3.817647 GACCTTCACTCTGCACAGAAAAT 59.182 43.478 1.42 0.00 36.94 1.82
2172 2255 3.567164 ACCTTCACTCTGCACAGAAAATG 59.433 43.478 1.42 1.53 36.94 2.32
2173 2256 3.817084 CCTTCACTCTGCACAGAAAATGA 59.183 43.478 1.42 3.76 36.94 2.57
2174 2257 4.320057 CCTTCACTCTGCACAGAAAATGAC 60.320 45.833 1.42 0.00 36.94 3.06
2175 2258 3.141398 TCACTCTGCACAGAAAATGACC 58.859 45.455 1.42 0.00 36.94 4.02
2176 2259 2.227388 CACTCTGCACAGAAAATGACCC 59.773 50.000 1.42 0.00 36.94 4.46
2177 2260 2.107204 ACTCTGCACAGAAAATGACCCT 59.893 45.455 1.42 0.00 36.94 4.34
2178 2261 3.152341 CTCTGCACAGAAAATGACCCTT 58.848 45.455 1.42 0.00 36.94 3.95
2179 2262 3.149196 TCTGCACAGAAAATGACCCTTC 58.851 45.455 0.00 0.00 33.91 3.46
2180 2263 3.152341 CTGCACAGAAAATGACCCTTCT 58.848 45.455 0.00 0.00 31.99 2.85
2181 2264 3.565307 TGCACAGAAAATGACCCTTCTT 58.435 40.909 0.00 0.00 29.29 2.52
2182 2265 4.724399 TGCACAGAAAATGACCCTTCTTA 58.276 39.130 0.00 0.00 29.29 2.10
2183 2266 4.518970 TGCACAGAAAATGACCCTTCTTAC 59.481 41.667 0.00 0.00 29.29 2.34
2184 2267 4.518970 GCACAGAAAATGACCCTTCTTACA 59.481 41.667 0.00 0.00 29.29 2.41
2185 2268 5.335191 GCACAGAAAATGACCCTTCTTACAG 60.335 44.000 0.00 0.00 29.29 2.74
2186 2269 5.182001 CACAGAAAATGACCCTTCTTACAGG 59.818 44.000 0.00 0.00 29.29 4.00
2224 2312 2.110721 GGGCCCTCTCCCAATTATGATT 59.889 50.000 17.04 0.00 45.82 2.57
2225 2313 3.425659 GGCCCTCTCCCAATTATGATTC 58.574 50.000 0.00 0.00 0.00 2.52
2227 2315 4.077822 GCCCTCTCCCAATTATGATTCAG 58.922 47.826 0.00 0.00 0.00 3.02
2229 2317 4.352001 CCCTCTCCCAATTATGATTCAGGA 59.648 45.833 0.00 0.17 0.00 3.86
2230 2318 5.014966 CCCTCTCCCAATTATGATTCAGGAT 59.985 44.000 0.00 0.00 29.01 3.24
2231 2319 6.179040 CCTCTCCCAATTATGATTCAGGATC 58.821 44.000 0.00 0.00 35.21 3.36
2232 2320 5.798132 TCTCCCAATTATGATTCAGGATCG 58.202 41.667 0.00 0.00 37.60 3.69
2233 2321 5.543790 TCTCCCAATTATGATTCAGGATCGA 59.456 40.000 0.00 0.00 37.60 3.59
2234 2322 6.214208 TCTCCCAATTATGATTCAGGATCGAT 59.786 38.462 0.00 0.00 37.60 3.59
2235 2323 6.175471 TCCCAATTATGATTCAGGATCGATG 58.825 40.000 0.54 0.00 37.60 3.84
2236 2324 5.163683 CCCAATTATGATTCAGGATCGATGC 60.164 44.000 9.16 9.16 37.60 3.91
2237 2325 5.413523 CCAATTATGATTCAGGATCGATGCA 59.586 40.000 19.67 0.00 37.60 3.96
2238 2326 6.403309 CCAATTATGATTCAGGATCGATGCAG 60.403 42.308 19.67 11.46 37.60 4.41
2239 2327 2.538512 TGATTCAGGATCGATGCAGG 57.461 50.000 19.67 10.68 37.60 4.85
2240 2328 1.155042 GATTCAGGATCGATGCAGGC 58.845 55.000 19.67 1.37 0.00 4.85
2241 2329 0.250640 ATTCAGGATCGATGCAGGCC 60.251 55.000 19.67 5.82 0.00 5.19
2242 2330 1.625417 TTCAGGATCGATGCAGGCCA 61.625 55.000 19.67 0.00 0.00 5.36
2243 2331 1.597302 CAGGATCGATGCAGGCCAG 60.597 63.158 19.67 0.00 0.00 4.85
2244 2332 1.763655 AGGATCGATGCAGGCCAGA 60.764 57.895 19.67 0.00 0.00 3.86
2245 2333 1.596477 GGATCGATGCAGGCCAGAC 60.596 63.158 12.54 0.00 0.00 3.51
2248 2336 0.182061 ATCGATGCAGGCCAGACATT 59.818 50.000 5.01 0.00 0.00 2.71
2251 2349 1.022735 GATGCAGGCCAGACATTCAG 58.977 55.000 5.01 0.00 0.00 3.02
2256 2354 0.607489 AGGCCAGACATTCAGTGCAC 60.607 55.000 9.40 9.40 0.00 4.57
2283 2381 4.796231 ACTCGCATCGCACGGGAC 62.796 66.667 0.00 0.00 34.34 4.46
2299 2397 2.124151 ACGATTCATGGCAGGGGC 60.124 61.111 0.00 0.00 40.13 5.80
2304 2402 2.215451 ATTCATGGCAGGGGCTCGTT 62.215 55.000 0.00 0.00 40.87 3.85
2308 2406 4.699522 GGCAGGGGCTCGTTCGTT 62.700 66.667 0.00 0.00 40.87 3.85
2320 2418 3.978764 TTCGTTCGTGCGTGCGTG 61.979 61.111 9.23 0.00 0.00 5.34
2353 2462 2.473376 GCGTATACGTGCAAGGTTTCAC 60.473 50.000 25.04 1.37 42.22 3.18
2405 2519 2.159099 TCCTACATGCAATCGTCAGACC 60.159 50.000 0.00 0.00 0.00 3.85
2417 2531 3.450115 CAGACCCCGGACCTCGTC 61.450 72.222 0.73 0.00 37.11 4.20
2420 2534 3.976701 GACCCCGGACCTCGTCGTA 62.977 68.421 0.73 0.00 37.11 3.43
2421 2535 3.512516 CCCCGGACCTCGTCGTAC 61.513 72.222 0.73 0.00 37.11 3.67
2422 2536 3.869272 CCCGGACCTCGTCGTACG 61.869 72.222 9.53 9.53 44.19 3.67
2423 2537 3.121030 CCGGACCTCGTCGTACGT 61.121 66.667 16.05 0.00 43.14 3.57
2424 2538 1.809619 CCGGACCTCGTCGTACGTA 60.810 63.158 16.05 0.00 43.14 3.57
2440 2554 2.790433 ACGTACGTACCCTTCACCTTA 58.210 47.619 21.41 0.00 0.00 2.69
2445 2559 3.771216 ACGTACCCTTCACCTTAGAGAA 58.229 45.455 0.00 0.00 0.00 2.87
2448 2562 4.220163 CGTACCCTTCACCTTAGAGAAACT 59.780 45.833 0.00 0.00 0.00 2.66
2457 2574 4.394300 CACCTTAGAGAAACTCCTTGCATG 59.606 45.833 0.00 0.00 0.00 4.06
2470 2587 2.413239 CCTTGCATGAACAAGCTACGTG 60.413 50.000 0.00 0.00 44.66 4.49
2476 2593 1.202325 TGAACAAGCTACGTGACGTGT 60.202 47.619 22.16 6.62 41.39 4.49
2511 2630 2.748647 GGTACGGGTTGCGCCATT 60.749 61.111 4.18 0.00 39.65 3.16
2522 2641 2.807895 CGCCATTGCTTGCACTGC 60.808 61.111 7.33 4.10 34.43 4.40
2533 2652 2.477845 GCACTGCTGCACACGATC 59.522 61.111 0.00 0.00 43.62 3.69
2534 2653 2.774126 CACTGCTGCACACGATCG 59.226 61.111 14.88 14.88 0.00 3.69
2535 2654 1.734117 CACTGCTGCACACGATCGA 60.734 57.895 24.34 0.00 0.00 3.59
2536 2655 1.445066 ACTGCTGCACACGATCGAG 60.445 57.895 24.34 17.42 0.00 4.04
2547 2666 0.108662 ACGATCGAGTGCATGCAGAA 60.109 50.000 23.41 7.18 0.00 3.02
2548 2667 1.215244 CGATCGAGTGCATGCAGAAT 58.785 50.000 23.41 10.44 0.00 2.40
2550 2669 2.207590 GATCGAGTGCATGCAGAATCA 58.792 47.619 23.41 10.56 0.00 2.57
2551 2670 2.097680 TCGAGTGCATGCAGAATCAA 57.902 45.000 23.41 1.94 0.00 2.57
2552 2671 2.425539 TCGAGTGCATGCAGAATCAAA 58.574 42.857 23.41 7.89 0.00 2.69
2553 2672 2.417586 TCGAGTGCATGCAGAATCAAAG 59.582 45.455 23.41 7.46 0.00 2.77
2554 2673 2.477357 CGAGTGCATGCAGAATCAAAGG 60.477 50.000 23.41 3.46 0.00 3.11
2555 2674 1.822990 AGTGCATGCAGAATCAAAGGG 59.177 47.619 23.41 0.00 0.00 3.95
2556 2675 1.820519 GTGCATGCAGAATCAAAGGGA 59.179 47.619 23.41 0.00 0.00 4.20
2557 2676 2.429610 GTGCATGCAGAATCAAAGGGAT 59.570 45.455 23.41 0.00 38.05 3.85
2558 2677 2.691526 TGCATGCAGAATCAAAGGGATC 59.308 45.455 18.46 0.00 34.28 3.36
2559 2678 2.287427 GCATGCAGAATCAAAGGGATCG 60.287 50.000 14.21 0.00 34.28 3.69
2560 2679 3.208594 CATGCAGAATCAAAGGGATCGA 58.791 45.455 0.00 0.00 34.28 3.59
2561 2680 3.348647 TGCAGAATCAAAGGGATCGAA 57.651 42.857 0.00 0.00 34.28 3.71
2562 2681 3.273434 TGCAGAATCAAAGGGATCGAAG 58.727 45.455 0.00 0.00 34.28 3.79
2563 2682 3.274288 GCAGAATCAAAGGGATCGAAGT 58.726 45.455 0.00 0.00 34.28 3.01
2564 2683 3.064545 GCAGAATCAAAGGGATCGAAGTG 59.935 47.826 0.00 0.00 34.28 3.16
2565 2684 3.624861 CAGAATCAAAGGGATCGAAGTGG 59.375 47.826 0.00 0.00 34.28 4.00
2566 2685 2.044123 ATCAAAGGGATCGAAGTGGC 57.956 50.000 0.00 0.00 0.00 5.01
2567 2686 0.035439 TCAAAGGGATCGAAGTGGCC 60.035 55.000 0.00 0.00 0.00 5.36
2571 2690 1.144936 GGGATCGAAGTGGCCAGAG 59.855 63.158 5.11 0.00 0.00 3.35
2572 2691 1.330655 GGGATCGAAGTGGCCAGAGA 61.331 60.000 5.11 3.38 0.00 3.10
2573 2692 0.755686 GGATCGAAGTGGCCAGAGAT 59.244 55.000 5.11 8.91 0.00 2.75
2574 2693 1.539929 GGATCGAAGTGGCCAGAGATG 60.540 57.143 5.11 0.00 0.00 2.90
2575 2694 1.137872 GATCGAAGTGGCCAGAGATGT 59.862 52.381 5.11 0.00 0.00 3.06
2576 2695 1.847328 TCGAAGTGGCCAGAGATGTA 58.153 50.000 5.11 0.00 0.00 2.29
2577 2696 2.388735 TCGAAGTGGCCAGAGATGTAT 58.611 47.619 5.11 0.00 0.00 2.29
2578 2697 2.101415 TCGAAGTGGCCAGAGATGTATG 59.899 50.000 5.11 0.00 0.00 2.39
2579 2698 2.804572 CGAAGTGGCCAGAGATGTATGG 60.805 54.545 5.11 0.00 38.19 2.74
2580 2699 2.180946 AGTGGCCAGAGATGTATGGA 57.819 50.000 5.11 0.00 37.20 3.41
2581 2700 2.699160 AGTGGCCAGAGATGTATGGAT 58.301 47.619 5.11 0.00 37.20 3.41
2582 2701 2.636893 AGTGGCCAGAGATGTATGGATC 59.363 50.000 5.11 0.00 37.20 3.36
2583 2702 1.980765 TGGCCAGAGATGTATGGATCC 59.019 52.381 7.87 4.20 37.20 3.36
2584 2703 1.980765 GGCCAGAGATGTATGGATCCA 59.019 52.381 18.88 18.88 37.20 3.41
2585 2704 2.373169 GGCCAGAGATGTATGGATCCAA 59.627 50.000 20.67 2.02 37.20 3.53
2586 2705 3.406764 GCCAGAGATGTATGGATCCAAC 58.593 50.000 20.67 17.69 37.20 3.77
2587 2706 3.808618 GCCAGAGATGTATGGATCCAACC 60.809 52.174 20.67 12.70 37.20 3.77
2588 2707 3.244700 CCAGAGATGTATGGATCCAACCC 60.245 52.174 20.67 10.03 37.20 4.11
2589 2708 3.392285 CAGAGATGTATGGATCCAACCCA 59.608 47.826 20.67 15.55 38.19 4.51
2590 2709 4.047166 AGAGATGTATGGATCCAACCCAA 58.953 43.478 20.67 3.41 37.22 4.12
2591 2710 4.103785 AGAGATGTATGGATCCAACCCAAG 59.896 45.833 20.67 0.00 37.22 3.61
2592 2711 2.435372 TGTATGGATCCAACCCAAGC 57.565 50.000 20.67 4.72 37.22 4.01
2593 2712 1.638070 TGTATGGATCCAACCCAAGCA 59.362 47.619 20.67 7.26 37.22 3.91
2594 2713 2.024414 GTATGGATCCAACCCAAGCAC 58.976 52.381 20.67 3.26 37.22 4.40
2595 2714 0.409092 ATGGATCCAACCCAAGCACA 59.591 50.000 20.67 0.00 37.22 4.57
2596 2715 0.409092 TGGATCCAACCCAAGCACAT 59.591 50.000 13.46 0.00 0.00 3.21
2597 2716 1.106285 GGATCCAACCCAAGCACATC 58.894 55.000 6.95 0.00 0.00 3.06
2598 2717 1.616725 GGATCCAACCCAAGCACATCA 60.617 52.381 6.95 0.00 0.00 3.07
2599 2718 1.474077 GATCCAACCCAAGCACATCAC 59.526 52.381 0.00 0.00 0.00 3.06
2600 2719 0.184692 TCCAACCCAAGCACATCACA 59.815 50.000 0.00 0.00 0.00 3.58
2601 2720 0.599558 CCAACCCAAGCACATCACAG 59.400 55.000 0.00 0.00 0.00 3.66
2602 2721 0.599558 CAACCCAAGCACATCACAGG 59.400 55.000 0.00 0.00 0.00 4.00
2603 2722 1.181098 AACCCAAGCACATCACAGGC 61.181 55.000 0.00 0.00 0.00 4.85
2604 2723 1.604308 CCCAAGCACATCACAGGCA 60.604 57.895 0.00 0.00 0.00 4.75
2605 2724 1.592400 CCCAAGCACATCACAGGCAG 61.592 60.000 0.00 0.00 0.00 4.85
2606 2725 0.892358 CCAAGCACATCACAGGCAGT 60.892 55.000 0.00 0.00 0.00 4.40
2607 2726 0.956633 CAAGCACATCACAGGCAGTT 59.043 50.000 0.00 0.00 0.00 3.16
2608 2727 0.956633 AAGCACATCACAGGCAGTTG 59.043 50.000 0.00 0.00 0.00 3.16
2609 2728 0.179009 AGCACATCACAGGCAGTTGT 60.179 50.000 0.00 0.00 0.00 3.32
2610 2729 0.670162 GCACATCACAGGCAGTTGTT 59.330 50.000 0.00 0.00 0.00 2.83
2611 2730 1.067516 GCACATCACAGGCAGTTGTTT 59.932 47.619 0.00 0.00 0.00 2.83
2612 2731 2.859806 GCACATCACAGGCAGTTGTTTC 60.860 50.000 0.00 0.00 0.00 2.78
2613 2732 2.620115 CACATCACAGGCAGTTGTTTCT 59.380 45.455 0.00 0.00 0.00 2.52
2614 2733 2.620115 ACATCACAGGCAGTTGTTTCTG 59.380 45.455 0.00 0.00 38.35 3.02
2615 2734 2.708216 TCACAGGCAGTTGTTTCTGA 57.292 45.000 0.00 0.00 37.61 3.27
2616 2735 2.997980 TCACAGGCAGTTGTTTCTGAA 58.002 42.857 0.00 0.00 37.61 3.02
2617 2736 2.682856 TCACAGGCAGTTGTTTCTGAAC 59.317 45.455 0.00 0.00 37.61 3.18
2618 2737 2.024414 ACAGGCAGTTGTTTCTGAACC 58.976 47.619 0.00 0.00 37.61 3.62
2619 2738 2.023673 CAGGCAGTTGTTTCTGAACCA 58.976 47.619 0.00 0.00 37.61 3.67
2620 2739 2.624838 CAGGCAGTTGTTTCTGAACCAT 59.375 45.455 0.00 0.00 37.61 3.55
2637 2756 4.961511 TGCGTGCACGTGAGGACC 62.962 66.667 36.80 20.52 42.22 4.46
2643 2762 1.668151 GCACGTGAGGACCAAGGAC 60.668 63.158 22.23 0.00 0.00 3.85
2686 2805 1.080434 GCTTGAAGCGAGGTCGACT 60.080 57.895 16.46 0.90 43.02 4.18
2690 2809 2.035940 AAGCGAGGTCGACTCCCT 59.964 61.111 16.46 3.77 43.57 4.20
2711 2830 4.849329 CCGTACGCTCAGGCCGAC 62.849 72.222 10.49 0.00 34.44 4.79
2755 3292 3.614150 CGAAGAGGTTGGTCGAAATCTCA 60.614 47.826 11.67 0.00 36.92 3.27
2809 3346 3.050703 GTGTCGTGACAGCTATGGG 57.949 57.895 2.31 0.00 42.74 4.00
2922 3459 2.093890 CATTACTGCCAATGTCCTGCA 58.906 47.619 0.00 0.00 32.33 4.41
2934 3471 1.202687 TGTCCTGCACTTCTCTGTTGG 60.203 52.381 0.00 0.00 0.00 3.77
2935 3472 1.131638 TCCTGCACTTCTCTGTTGGT 58.868 50.000 0.00 0.00 0.00 3.67
2957 3494 5.105473 GGTACAGTACAGCTTAATCACTCCA 60.105 44.000 12.89 0.00 0.00 3.86
2958 3495 5.683876 ACAGTACAGCTTAATCACTCCAT 57.316 39.130 0.00 0.00 0.00 3.41
2959 3496 5.423015 ACAGTACAGCTTAATCACTCCATG 58.577 41.667 0.00 0.00 0.00 3.66
2960 3497 4.813161 CAGTACAGCTTAATCACTCCATGG 59.187 45.833 4.97 4.97 0.00 3.66
2962 3499 3.614092 ACAGCTTAATCACTCCATGGTG 58.386 45.455 12.58 12.42 38.44 4.17
2964 3501 1.331756 GCTTAATCACTCCATGGTGCG 59.668 52.381 12.58 3.21 37.16 5.34
2966 3503 3.792401 CTTAATCACTCCATGGTGCGTA 58.208 45.455 12.58 0.00 37.16 4.42
2973 3510 0.821517 TCCATGGTGCGTAGTAGGTG 59.178 55.000 12.58 0.00 0.00 4.00
2992 3537 3.514645 GTGTCTTATGCCAATGCCAAAG 58.485 45.455 0.00 0.00 36.33 2.77
3006 3551 4.543590 TGCCAAAGTTTTCACCAAAGAA 57.456 36.364 0.00 0.00 0.00 2.52
3007 3552 4.249661 TGCCAAAGTTTTCACCAAAGAAC 58.750 39.130 0.00 0.00 0.00 3.01
3008 3553 3.621268 GCCAAAGTTTTCACCAAAGAACC 59.379 43.478 0.00 0.00 0.00 3.62
3009 3554 4.826556 CCAAAGTTTTCACCAAAGAACCA 58.173 39.130 0.00 0.00 0.00 3.67
3010 3555 4.629634 CCAAAGTTTTCACCAAAGAACCAC 59.370 41.667 0.00 0.00 0.00 4.16
3011 3556 4.465632 AAGTTTTCACCAAAGAACCACC 57.534 40.909 0.00 0.00 0.00 4.61
3012 3557 2.425668 AGTTTTCACCAAAGAACCACCG 59.574 45.455 0.00 0.00 0.00 4.94
3013 3558 2.421751 TTTCACCAAAGAACCACCGA 57.578 45.000 0.00 0.00 0.00 4.69
3014 3559 1.961793 TTCACCAAAGAACCACCGAG 58.038 50.000 0.00 0.00 0.00 4.63
3015 3560 1.124780 TCACCAAAGAACCACCGAGA 58.875 50.000 0.00 0.00 0.00 4.04
3016 3561 1.202604 TCACCAAAGAACCACCGAGAC 60.203 52.381 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.625823 CCGCACCACCGCTGAATTT 61.626 57.895 0.00 0.00 0.00 1.82
21 22 4.640201 GCACTCCAGAGTTAATAATGGCAA 59.360 41.667 0.00 0.00 40.20 4.52
26 27 4.878397 GCACTGCACTCCAGAGTTAATAAT 59.122 41.667 0.00 0.00 44.64 1.28
28 29 3.260632 TGCACTGCACTCCAGAGTTAATA 59.739 43.478 0.00 0.00 44.64 0.98
29 30 2.038952 TGCACTGCACTCCAGAGTTAAT 59.961 45.455 0.00 0.00 44.64 1.40
96 97 0.822532 ACCGGTAGCGGTAGGATCTG 60.823 60.000 35.91 8.52 40.96 2.90
115 116 1.902918 ATCCTGGCGTTTTGCTGCA 60.903 52.632 0.00 0.00 45.43 4.41
118 119 2.964978 GCATCCTGGCGTTTTGCT 59.035 55.556 0.00 0.00 45.43 3.91
354 359 2.750237 GCTCCGGGGCAAATCGTT 60.750 61.111 24.98 0.00 0.00 3.85
358 373 2.472414 TTACACGCTCCGGGGCAAAT 62.472 55.000 29.20 13.12 32.94 2.32
361 376 3.379865 GATTACACGCTCCGGGGCA 62.380 63.158 29.20 6.39 32.94 5.36
400 415 1.091771 ACACAGCAGATGCCATACGC 61.092 55.000 0.14 0.00 43.38 4.42
401 416 0.654160 CACACAGCAGATGCCATACG 59.346 55.000 0.14 0.00 43.38 3.06
402 417 2.028420 TCACACAGCAGATGCCATAC 57.972 50.000 0.14 0.00 43.38 2.39
403 418 2.358957 GTTCACACAGCAGATGCCATA 58.641 47.619 0.14 0.00 43.38 2.74
404 419 1.171308 GTTCACACAGCAGATGCCAT 58.829 50.000 0.14 0.00 43.38 4.40
405 420 0.890542 GGTTCACACAGCAGATGCCA 60.891 55.000 0.14 0.00 43.38 4.92
406 421 1.878775 GGTTCACACAGCAGATGCC 59.121 57.895 0.14 0.00 43.38 4.40
407 422 1.230635 ACGGTTCACACAGCAGATGC 61.231 55.000 0.00 0.00 42.49 3.91
431 446 1.600485 AGGGAAAAAGTTACGTGTGCG 59.400 47.619 0.00 0.00 44.93 5.34
437 452 4.769215 CTGACGAAAGGGAAAAAGTTACG 58.231 43.478 0.00 0.00 0.00 3.18
447 462 2.646175 CGGAGGCTGACGAAAGGGA 61.646 63.158 0.00 0.00 0.00 4.20
518 535 1.829533 CAGCCTGCACCCACAAAGT 60.830 57.895 0.00 0.00 0.00 2.66
527 544 1.078848 CTGTAGGGTCAGCCTGCAC 60.079 63.158 9.98 0.00 34.45 4.57
532 549 0.103208 CGTGATCTGTAGGGTCAGCC 59.897 60.000 0.00 0.00 35.63 4.85
658 691 4.072131 TGGAAATTGTGGTTCAGTAGCTC 58.928 43.478 0.00 0.00 0.00 4.09
678 711 5.457799 CGTTGTATACTATTCTTGTCGGTGG 59.542 44.000 4.17 0.00 0.00 4.61
759 794 0.719465 GTACGATTCAGGTGGTTGCG 59.281 55.000 0.00 0.00 0.00 4.85
769 805 6.630071 TCTCAGATGTTTCATGTACGATTCA 58.370 36.000 0.00 0.00 0.00 2.57
774 810 6.273071 TGGTATCTCAGATGTTTCATGTACG 58.727 40.000 0.00 0.00 0.00 3.67
782 818 5.370584 TGGATGGATGGTATCTCAGATGTTT 59.629 40.000 0.00 0.00 0.00 2.83
783 819 4.909695 TGGATGGATGGTATCTCAGATGTT 59.090 41.667 0.00 0.00 0.00 2.71
926 973 3.831715 ACTTTGGCGATCTTGTTTAGC 57.168 42.857 0.00 0.00 0.00 3.09
1247 1300 2.350458 ATCGCCCCACCAACAATGC 61.350 57.895 0.00 0.00 0.00 3.56
1425 1478 1.376037 CTCCTCGCCACCAGTTTCC 60.376 63.158 0.00 0.00 0.00 3.13
1428 1481 2.526873 ACCTCCTCGCCACCAGTT 60.527 61.111 0.00 0.00 0.00 3.16
1715 1768 2.513204 CTGCAGCACCTCCGATGG 60.513 66.667 0.00 0.00 0.00 3.51
1717 1770 2.285773 TGTCTGCAGCACCTCCGAT 61.286 57.895 9.47 0.00 0.00 4.18
1806 1859 2.480555 GTCAAATCACCGCCGCAG 59.519 61.111 0.00 0.00 0.00 5.18
1932 1985 2.124693 CCCTCTCCTCCTGTCGCTC 61.125 68.421 0.00 0.00 0.00 5.03
1938 1991 2.124693 GCTCGTCCCTCTCCTCCTG 61.125 68.421 0.00 0.00 0.00 3.86
2001 2067 2.094286 AGCAAGCTAGAGCACTGTACTG 60.094 50.000 4.01 0.00 45.16 2.74
2066 2133 2.202810 GCCACAGCTCTCGCTACC 60.203 66.667 0.00 0.00 46.99 3.18
2080 2150 2.788750 CGCGCTATATATAACGTCGCCA 60.789 50.000 15.03 0.00 38.10 5.69
2113 2183 2.745884 CATCGGGCCAGTTTCGCA 60.746 61.111 4.39 0.00 0.00 5.10
2114 2184 3.508840 CCATCGGGCCAGTTTCGC 61.509 66.667 4.39 0.00 0.00 4.70
2124 2194 3.430862 CACGTGTTGGCCATCGGG 61.431 66.667 22.64 17.80 37.18 5.14
2151 2234 3.817084 TCATTTTCTGTGCAGAGTGAAGG 59.183 43.478 11.09 8.67 38.88 3.46
2152 2235 4.320057 GGTCATTTTCTGTGCAGAGTGAAG 60.320 45.833 11.09 0.00 38.88 3.02
2153 2236 3.565482 GGTCATTTTCTGTGCAGAGTGAA 59.435 43.478 11.09 7.36 38.88 3.18
2154 2237 3.141398 GGTCATTTTCTGTGCAGAGTGA 58.859 45.455 11.09 4.29 38.88 3.41
2155 2238 2.227388 GGGTCATTTTCTGTGCAGAGTG 59.773 50.000 11.09 1.73 38.88 3.51
2156 2239 2.107204 AGGGTCATTTTCTGTGCAGAGT 59.893 45.455 11.09 0.00 38.88 3.24
2159 2242 3.152341 AGAAGGGTCATTTTCTGTGCAG 58.848 45.455 0.00 0.00 32.65 4.41
2160 2243 3.228188 AGAAGGGTCATTTTCTGTGCA 57.772 42.857 0.00 0.00 32.65 4.57
2161 2244 4.518970 TGTAAGAAGGGTCATTTTCTGTGC 59.481 41.667 0.00 0.00 34.09 4.57
2162 2245 5.182001 CCTGTAAGAAGGGTCATTTTCTGTG 59.818 44.000 0.00 0.00 34.09 3.66
2163 2246 5.316987 CCTGTAAGAAGGGTCATTTTCTGT 58.683 41.667 0.00 0.00 34.09 3.41
2164 2247 4.156739 GCCTGTAAGAAGGGTCATTTTCTG 59.843 45.833 0.00 0.00 37.84 3.02
2165 2248 4.043435 AGCCTGTAAGAAGGGTCATTTTCT 59.957 41.667 0.00 0.00 44.89 2.52
2166 2249 4.336280 AGCCTGTAAGAAGGGTCATTTTC 58.664 43.478 0.00 0.00 44.89 2.29
2167 2250 4.388577 AGCCTGTAAGAAGGGTCATTTT 57.611 40.909 0.00 0.00 44.89 1.82
2205 2288 4.077822 CTGAATCATAATTGGGAGAGGGC 58.922 47.826 0.00 0.00 0.00 5.19
2209 2292 5.543790 TCGATCCTGAATCATAATTGGGAGA 59.456 40.000 0.00 0.00 33.65 3.71
2210 2293 5.798132 TCGATCCTGAATCATAATTGGGAG 58.202 41.667 0.00 0.00 33.65 4.30
2211 2294 5.823861 TCGATCCTGAATCATAATTGGGA 57.176 39.130 0.00 0.00 33.65 4.37
2218 2306 3.618263 GCCTGCATCGATCCTGAATCATA 60.618 47.826 0.00 0.00 33.65 2.15
2224 2312 2.036428 CTGGCCTGCATCGATCCTGA 62.036 60.000 3.32 0.00 0.00 3.86
2225 2313 1.597302 CTGGCCTGCATCGATCCTG 60.597 63.158 3.32 0.00 0.00 3.86
2227 2315 1.596477 GTCTGGCCTGCATCGATCC 60.596 63.158 3.32 0.00 0.00 3.36
2229 2317 0.182061 AATGTCTGGCCTGCATCGAT 59.818 50.000 15.98 0.00 0.00 3.59
2230 2318 0.462581 GAATGTCTGGCCTGCATCGA 60.463 55.000 15.98 0.00 0.00 3.59
2231 2319 0.745486 TGAATGTCTGGCCTGCATCG 60.745 55.000 15.98 0.00 0.00 3.84
2232 2320 1.022735 CTGAATGTCTGGCCTGCATC 58.977 55.000 15.98 11.59 0.00 3.91
2233 2321 0.330604 ACTGAATGTCTGGCCTGCAT 59.669 50.000 3.32 8.93 0.00 3.96
2234 2322 0.607217 CACTGAATGTCTGGCCTGCA 60.607 55.000 3.32 6.76 0.00 4.41
2235 2323 1.930908 GCACTGAATGTCTGGCCTGC 61.931 60.000 3.32 0.00 0.00 4.85
2236 2324 0.607217 TGCACTGAATGTCTGGCCTG 60.607 55.000 3.32 2.92 0.00 4.85
2237 2325 0.607489 GTGCACTGAATGTCTGGCCT 60.607 55.000 10.32 0.00 0.00 5.19
2238 2326 1.878775 GTGCACTGAATGTCTGGCC 59.121 57.895 10.32 0.00 0.00 5.36
2239 2327 1.499056 CGTGCACTGAATGTCTGGC 59.501 57.895 16.19 0.00 0.00 4.85
2240 2328 1.499056 GCGTGCACTGAATGTCTGG 59.501 57.895 16.19 0.00 0.00 3.86
2241 2329 1.499056 GGCGTGCACTGAATGTCTG 59.501 57.895 16.19 0.00 0.00 3.51
2242 2330 2.029288 CGGCGTGCACTGAATGTCT 61.029 57.895 16.19 0.00 0.00 3.41
2243 2331 2.476051 CGGCGTGCACTGAATGTC 59.524 61.111 16.19 0.00 0.00 3.06
2244 2332 3.726517 GCGGCGTGCACTGAATGT 61.727 61.111 16.19 0.00 45.45 2.71
2245 2333 4.799473 CGCGGCGTGCACTGAATG 62.799 66.667 15.36 0.00 46.97 2.67
2265 2363 4.794439 TCCCGTGCGATGCGAGTG 62.794 66.667 0.00 0.00 0.00 3.51
2270 2368 2.871427 GAATCGTCCCGTGCGATGC 61.871 63.158 6.74 2.14 46.68 3.91
2271 2369 0.875908 ATGAATCGTCCCGTGCGATG 60.876 55.000 6.74 0.00 46.68 3.84
2283 2381 1.895707 GAGCCCCTGCCATGAATCG 60.896 63.158 0.00 0.00 38.69 3.34
2285 2383 2.194056 CGAGCCCCTGCCATGAAT 59.806 61.111 0.00 0.00 38.69 2.57
2299 2397 2.459904 CACGCACGAACGAACGAG 59.540 61.111 16.45 6.15 36.70 4.18
2324 2422 3.277133 ACGTATACGCGTGTGGGT 58.723 55.556 24.59 14.68 43.99 4.51
2344 2453 1.324383 AAATTCGGGCGTGAAACCTT 58.676 45.000 0.00 0.00 0.00 3.50
2353 2462 0.109689 TGCCGTTTTAAATTCGGGCG 60.110 50.000 23.83 8.98 43.77 6.13
2405 2519 3.869272 CGTACGACGAGGTCCGGG 61.869 72.222 10.44 0.00 46.05 5.73
2419 2533 2.489938 AGGTGAAGGGTACGTACGTA 57.510 50.000 23.60 23.60 0.00 3.57
2420 2534 1.620822 AAGGTGAAGGGTACGTACGT 58.379 50.000 25.98 25.98 0.00 3.57
2421 2535 3.009723 TCTAAGGTGAAGGGTACGTACG 58.990 50.000 18.98 15.01 0.00 3.67
2422 2536 4.265073 TCTCTAAGGTGAAGGGTACGTAC 58.735 47.826 17.56 17.56 0.00 3.67
2423 2537 4.574674 TCTCTAAGGTGAAGGGTACGTA 57.425 45.455 0.00 0.00 0.00 3.57
2424 2538 3.446442 TCTCTAAGGTGAAGGGTACGT 57.554 47.619 0.00 0.00 0.00 3.57
2440 2554 4.090761 TGTTCATGCAAGGAGTTTCTCT 57.909 40.909 0.00 0.00 0.00 3.10
2445 2559 2.590821 AGCTTGTTCATGCAAGGAGTT 58.409 42.857 13.03 0.00 44.29 3.01
2448 2562 2.076100 CGTAGCTTGTTCATGCAAGGA 58.924 47.619 13.03 0.00 44.29 3.36
2457 2574 1.450905 GACACGTCACGTAGCTTGTTC 59.549 52.381 0.41 0.00 38.32 3.18
2470 2587 1.154263 CCCTCGAACTCGACACGTC 60.154 63.158 0.00 0.00 44.22 4.34
2489 2606 2.447070 GCGCAACCCGTACCGTTAG 61.447 63.158 0.30 0.00 39.71 2.34
2506 2624 1.736645 CAGCAGTGCAAGCAATGGC 60.737 57.895 21.79 14.49 41.62 4.40
2529 2648 1.191868 GATTCTGCATGCACTCGATCG 59.808 52.381 18.46 9.36 0.00 3.69
2532 2651 2.097680 TTGATTCTGCATGCACTCGA 57.902 45.000 18.46 10.42 0.00 4.04
2533 2652 2.477357 CCTTTGATTCTGCATGCACTCG 60.477 50.000 18.46 7.79 0.00 4.18
2534 2653 2.159282 CCCTTTGATTCTGCATGCACTC 60.159 50.000 18.46 14.08 0.00 3.51
2535 2654 1.822990 CCCTTTGATTCTGCATGCACT 59.177 47.619 18.46 4.11 0.00 4.40
2536 2655 1.820519 TCCCTTTGATTCTGCATGCAC 59.179 47.619 18.46 7.77 0.00 4.57
2539 2658 3.208594 TCGATCCCTTTGATTCTGCATG 58.791 45.455 0.00 0.00 32.41 4.06
2541 2660 3.273434 CTTCGATCCCTTTGATTCTGCA 58.727 45.455 0.00 0.00 32.41 4.41
2547 2666 1.408822 GGCCACTTCGATCCCTTTGAT 60.409 52.381 0.00 0.00 36.01 2.57
2548 2667 0.035439 GGCCACTTCGATCCCTTTGA 60.035 55.000 0.00 0.00 0.00 2.69
2550 2669 0.035056 CTGGCCACTTCGATCCCTTT 60.035 55.000 0.00 0.00 0.00 3.11
2551 2670 0.909610 TCTGGCCACTTCGATCCCTT 60.910 55.000 0.00 0.00 0.00 3.95
2552 2671 1.306141 TCTGGCCACTTCGATCCCT 60.306 57.895 0.00 0.00 0.00 4.20
2553 2672 1.144936 CTCTGGCCACTTCGATCCC 59.855 63.158 0.00 0.00 0.00 3.85
2554 2673 0.755686 ATCTCTGGCCACTTCGATCC 59.244 55.000 0.00 0.00 0.00 3.36
2555 2674 1.137872 ACATCTCTGGCCACTTCGATC 59.862 52.381 0.00 0.00 0.00 3.69
2556 2675 1.198713 ACATCTCTGGCCACTTCGAT 58.801 50.000 0.00 0.00 0.00 3.59
2557 2676 1.847328 TACATCTCTGGCCACTTCGA 58.153 50.000 0.00 0.00 0.00 3.71
2558 2677 2.477825 CATACATCTCTGGCCACTTCG 58.522 52.381 0.00 0.00 0.00 3.79
2559 2678 2.435805 TCCATACATCTCTGGCCACTTC 59.564 50.000 0.00 0.00 32.30 3.01
2560 2679 2.481441 TCCATACATCTCTGGCCACTT 58.519 47.619 0.00 0.00 32.30 3.16
2561 2680 2.180946 TCCATACATCTCTGGCCACT 57.819 50.000 0.00 0.00 32.30 4.00
2562 2681 2.289945 GGATCCATACATCTCTGGCCAC 60.290 54.545 6.95 0.00 32.30 5.01
2563 2682 1.980765 GGATCCATACATCTCTGGCCA 59.019 52.381 4.71 4.71 32.30 5.36
2564 2683 1.980765 TGGATCCATACATCTCTGGCC 59.019 52.381 11.44 0.00 32.30 5.36
2565 2684 3.406764 GTTGGATCCATACATCTCTGGC 58.593 50.000 17.06 0.00 32.30 4.85
2566 2685 3.244700 GGGTTGGATCCATACATCTCTGG 60.245 52.174 17.06 0.00 0.00 3.86
2567 2686 3.392285 TGGGTTGGATCCATACATCTCTG 59.608 47.826 17.06 0.00 0.00 3.35
2571 2690 2.887152 GCTTGGGTTGGATCCATACATC 59.113 50.000 17.06 12.30 33.82 3.06
2572 2691 2.244510 TGCTTGGGTTGGATCCATACAT 59.755 45.455 17.06 0.00 33.82 2.29
2573 2692 1.638070 TGCTTGGGTTGGATCCATACA 59.362 47.619 17.06 12.14 33.82 2.29
2574 2693 2.024414 GTGCTTGGGTTGGATCCATAC 58.976 52.381 17.06 15.74 33.82 2.39
2575 2694 1.638070 TGTGCTTGGGTTGGATCCATA 59.362 47.619 17.06 3.77 33.82 2.74
2576 2695 0.409092 TGTGCTTGGGTTGGATCCAT 59.591 50.000 17.06 0.00 33.82 3.41
2577 2696 0.409092 ATGTGCTTGGGTTGGATCCA 59.591 50.000 11.44 11.44 0.00 3.41
2578 2697 1.106285 GATGTGCTTGGGTTGGATCC 58.894 55.000 4.20 4.20 0.00 3.36
2579 2698 1.474077 GTGATGTGCTTGGGTTGGATC 59.526 52.381 0.00 0.00 0.00 3.36
2580 2699 1.203038 TGTGATGTGCTTGGGTTGGAT 60.203 47.619 0.00 0.00 0.00 3.41
2581 2700 0.184692 TGTGATGTGCTTGGGTTGGA 59.815 50.000 0.00 0.00 0.00 3.53
2582 2701 0.599558 CTGTGATGTGCTTGGGTTGG 59.400 55.000 0.00 0.00 0.00 3.77
2583 2702 0.599558 CCTGTGATGTGCTTGGGTTG 59.400 55.000 0.00 0.00 0.00 3.77
2584 2703 1.181098 GCCTGTGATGTGCTTGGGTT 61.181 55.000 0.00 0.00 0.00 4.11
2585 2704 1.604593 GCCTGTGATGTGCTTGGGT 60.605 57.895 0.00 0.00 0.00 4.51
2586 2705 1.592400 CTGCCTGTGATGTGCTTGGG 61.592 60.000 0.00 0.00 0.00 4.12
2587 2706 0.892358 ACTGCCTGTGATGTGCTTGG 60.892 55.000 0.00 0.00 0.00 3.61
2588 2707 0.956633 AACTGCCTGTGATGTGCTTG 59.043 50.000 0.00 0.00 0.00 4.01
2589 2708 0.956633 CAACTGCCTGTGATGTGCTT 59.043 50.000 0.00 0.00 0.00 3.91
2590 2709 0.179009 ACAACTGCCTGTGATGTGCT 60.179 50.000 0.00 0.00 0.00 4.40
2591 2710 0.670162 AACAACTGCCTGTGATGTGC 59.330 50.000 0.00 0.00 0.00 4.57
2592 2711 2.620115 AGAAACAACTGCCTGTGATGTG 59.380 45.455 0.00 0.00 0.00 3.21
2593 2712 2.620115 CAGAAACAACTGCCTGTGATGT 59.380 45.455 0.00 0.00 0.00 3.06
2594 2713 2.880268 TCAGAAACAACTGCCTGTGATG 59.120 45.455 0.00 0.00 37.75 3.07
2595 2714 3.213206 TCAGAAACAACTGCCTGTGAT 57.787 42.857 0.00 0.00 37.75 3.06
2596 2715 2.682856 GTTCAGAAACAACTGCCTGTGA 59.317 45.455 0.00 0.00 37.75 3.58
2597 2716 2.223572 GGTTCAGAAACAACTGCCTGTG 60.224 50.000 0.00 0.00 37.10 3.66
2598 2717 2.024414 GGTTCAGAAACAACTGCCTGT 58.976 47.619 0.00 0.00 37.10 4.00
2599 2718 2.023673 TGGTTCAGAAACAACTGCCTG 58.976 47.619 0.00 0.00 37.10 4.85
2600 2719 2.435372 TGGTTCAGAAACAACTGCCT 57.565 45.000 0.00 0.00 37.10 4.75
2601 2720 2.863704 GCATGGTTCAGAAACAACTGCC 60.864 50.000 13.79 0.00 37.10 4.85
2602 2721 2.397549 GCATGGTTCAGAAACAACTGC 58.602 47.619 10.36 10.36 37.10 4.40
2603 2722 2.033299 ACGCATGGTTCAGAAACAACTG 59.967 45.455 4.61 0.92 37.10 3.16
2604 2723 2.033299 CACGCATGGTTCAGAAACAACT 59.967 45.455 4.61 0.00 37.10 3.16
2605 2724 2.384382 CACGCATGGTTCAGAAACAAC 58.616 47.619 4.61 0.00 37.10 3.32
2606 2725 1.268999 GCACGCATGGTTCAGAAACAA 60.269 47.619 4.61 0.00 37.10 2.83
2607 2726 0.310543 GCACGCATGGTTCAGAAACA 59.689 50.000 2.56 2.56 37.10 2.83
2608 2727 0.310543 TGCACGCATGGTTCAGAAAC 59.689 50.000 0.00 0.00 34.46 2.78
2609 2728 0.310543 GTGCACGCATGGTTCAGAAA 59.689 50.000 0.00 0.00 0.00 2.52
2610 2729 1.840630 CGTGCACGCATGGTTCAGAA 61.841 55.000 28.16 0.00 0.00 3.02
2611 2730 2.316867 CGTGCACGCATGGTTCAGA 61.317 57.895 28.16 0.00 0.00 3.27
2612 2731 2.174107 CGTGCACGCATGGTTCAG 59.826 61.111 28.16 0.00 0.00 3.02
2613 2732 2.590291 ACGTGCACGCATGGTTCA 60.590 55.556 37.35 0.00 44.43 3.18
2614 2733 2.127270 CACGTGCACGCATGGTTC 60.127 61.111 37.35 0.00 44.43 3.62
2615 2734 2.590291 TCACGTGCACGCATGGTT 60.590 55.556 37.35 15.76 44.43 3.67
2616 2735 3.043713 CTCACGTGCACGCATGGT 61.044 61.111 37.35 16.56 44.43 3.55
2617 2736 3.792047 CCTCACGTGCACGCATGG 61.792 66.667 37.35 29.45 44.43 3.66
2618 2737 2.738139 TCCTCACGTGCACGCATG 60.738 61.111 37.35 28.22 44.43 4.06
2619 2738 2.738521 GTCCTCACGTGCACGCAT 60.739 61.111 37.35 18.20 44.43 4.73
2620 2739 4.961511 GGTCCTCACGTGCACGCA 62.962 66.667 37.35 23.57 44.43 5.24
2637 2756 1.278637 GAACACGTTGCCGTCCTTG 59.721 57.895 0.00 0.00 46.28 3.61
2643 2762 3.558282 GAGCACGAACACGTTGCCG 62.558 63.158 5.57 2.43 38.21 5.69
2680 2799 0.169894 GTACGGTTCAGGGAGTCGAC 59.830 60.000 7.70 7.70 0.00 4.20
2686 2805 1.592400 CTGAGCGTACGGTTCAGGGA 61.592 60.000 22.26 1.27 46.70 4.20
2690 2809 2.260434 GCCTGAGCGTACGGTTCA 59.740 61.111 22.26 18.02 34.46 3.18
2730 2849 2.434359 CGACCAACCTCTTCGGGC 60.434 66.667 0.00 0.00 36.97 6.13
2913 3450 2.551721 CCAACAGAGAAGTGCAGGACAT 60.552 50.000 0.00 0.00 0.00 3.06
2914 3451 1.202687 CCAACAGAGAAGTGCAGGACA 60.203 52.381 0.00 0.00 0.00 4.02
2934 3471 5.962433 TGGAGTGATTAAGCTGTACTGTAC 58.038 41.667 10.98 10.98 0.00 2.90
2935 3472 6.406961 CCATGGAGTGATTAAGCTGTACTGTA 60.407 42.308 5.56 0.00 0.00 2.74
2943 3480 2.648059 GCACCATGGAGTGATTAAGCT 58.352 47.619 21.47 0.00 40.34 3.74
2945 3482 2.632377 ACGCACCATGGAGTGATTAAG 58.368 47.619 26.72 6.69 40.34 1.85
2946 3483 2.779755 ACGCACCATGGAGTGATTAA 57.220 45.000 26.72 0.00 40.34 1.40
2957 3494 1.848652 AGACACCTACTACGCACCAT 58.151 50.000 0.00 0.00 0.00 3.55
2958 3495 1.624336 AAGACACCTACTACGCACCA 58.376 50.000 0.00 0.00 0.00 4.17
2959 3496 3.703420 CATAAGACACCTACTACGCACC 58.297 50.000 0.00 0.00 0.00 5.01
2960 3497 3.114065 GCATAAGACACCTACTACGCAC 58.886 50.000 0.00 0.00 0.00 5.34
2962 3499 2.100252 TGGCATAAGACACCTACTACGC 59.900 50.000 0.00 0.00 0.00 4.42
2964 3501 4.511826 GCATTGGCATAAGACACCTACTAC 59.488 45.833 0.00 0.00 40.72 2.73
2966 3503 3.545703 GCATTGGCATAAGACACCTACT 58.454 45.455 0.00 0.00 40.72 2.57
2973 3510 3.874392 ACTTTGGCATTGGCATAAGAC 57.126 42.857 26.36 0.00 43.71 3.01
2992 3537 2.424246 TCGGTGGTTCTTTGGTGAAAAC 59.576 45.455 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.