Multiple sequence alignment - TraesCS5D01G091500

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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 TraesCS5D01G091500 chr5D 100.000 2930 0 0 1 2930 98670500 98667571 0.000000e+00 5411.0
1 TraesCS5D01G091500 chr5D 90.683 322 11 10 2105 2409 121073088 121073407 7.560000e-111 411.0
2 TraesCS5D01G091500 chr5A 96.418 1619 42 6 501 2104 104228647 104230264 0.000000e+00 2654.0
3 TraesCS5D01G091500 chr5A 91.923 520 23 4 1 507 104227715 104228228 0.000000e+00 710.0
4 TraesCS5D01G091500 chr5B 93.995 1149 39 14 1 1133 107910099 107908965 0.000000e+00 1712.0
5 TraesCS5D01G091500 chr5B 93.501 954 33 9 1178 2104 107908965 107908014 0.000000e+00 1391.0
6 TraesCS5D01G091500 chr7D 91.697 542 24 1 2410 2930 568394425 568394966 0.000000e+00 732.0
7 TraesCS5D01G091500 chr7D 94.678 451 24 0 2410 2860 76972636 76973086 0.000000e+00 701.0
8 TraesCS5D01G091500 chr7D 94.872 195 10 0 2104 2298 610560380 610560574 3.670000e-79 305.0
9 TraesCS5D01G091500 chr2A 89.299 542 37 1 2410 2930 470052604 470053145 0.000000e+00 660.0
10 TraesCS5D01G091500 chr6D 91.489 329 10 1 2099 2409 283809921 283810249 1.250000e-118 436.0
11 TraesCS5D01G091500 chr3D 90.712 323 12 1 2105 2409 462046668 462046346 5.840000e-112 414.0
12 TraesCS5D01G091500 chr3D 90.093 323 14 1 2105 2409 351018071 351017749 1.260000e-108 403.0
13 TraesCS5D01G091500 chr3D 90.438 251 23 1 2596 2846 15412607 15412856 2.180000e-86 329.0
14 TraesCS5D01G091500 chr3D 93.000 100 7 0 2460 2559 15412510 15412609 2.350000e-31 147.0
15 TraesCS5D01G091500 chr3A 86.458 384 32 1 2463 2846 412934610 412934247 1.260000e-108 403.0
16 TraesCS5D01G091500 chr3A 94.000 100 6 0 2460 2559 123291821 123291920 5.060000e-33 152.0
17 TraesCS5D01G091500 chr1D 91.639 299 6 1 2105 2384 430065852 430066150 2.120000e-106 396.0
18 TraesCS5D01G091500 chr1D 91.148 305 6 4 2105 2389 442450784 442450481 7.610000e-106 394.0
19 TraesCS5D01G091500 chr1D 88.854 323 19 1 2104 2409 76964989 76965311 5.930000e-102 381.0
20 TraesCS5D01G091500 chr1D 88.040 301 15 4 2103 2384 38791165 38791463 1.300000e-88 337.0
21 TraesCS5D01G091500 chr2B 89.198 324 15 5 2105 2409 5721682 5721360 1.270000e-103 387.0
22 TraesCS5D01G091500 chr4D 88.294 299 14 4 2105 2384 456275958 456276254 3.620000e-89 339.0
23 TraesCS5D01G091500 chr4D 86.942 291 18 11 2105 2378 307235548 307235835 2.840000e-80 309.0
24 TraesCS5D01G091500 chr3B 90.438 251 24 0 2596 2846 655317243 655317493 6.050000e-87 331.0
25 TraesCS5D01G091500 chr3B 93.000 100 7 0 2460 2559 655317146 655317245 2.350000e-31 147.0
26 TraesCS5D01G091500 chr6B 82.263 327 27 12 2105 2409 92059272 92058955 1.350000e-63 254.0
27 TraesCS5D01G091500 chr1B 90.476 63 6 0 2846 2908 9644699 9644637 1.870000e-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 TraesCS5D01G091500 chr5D 98667571 98670500 2929 True 5411.0 5411 100.0000 1 2930 1 chr5D.!!$R1 2929
1 TraesCS5D01G091500 chr5A 104227715 104230264 2549 False 1682.0 2654 94.1705 1 2104 2 chr5A.!!$F1 2103
2 TraesCS5D01G091500 chr5B 107908014 107910099 2085 True 1551.5 1712 93.7480 1 2104 2 chr5B.!!$R1 2103
3 TraesCS5D01G091500 chr7D 568394425 568394966 541 False 732.0 732 91.6970 2410 2930 1 chr7D.!!$F2 520
4 TraesCS5D01G091500 chr2A 470052604 470053145 541 False 660.0 660 89.2990 2410 2930 1 chr2A.!!$F1 520

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
994 1435 0.108615 AGGAAGAGCATCCACGAACG 60.109 55.0 6.07 0.0 42.27 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2218 2696 0.106719 AACGGGCCAAATCATCCGAT 60.107 50.0 4.39 0.0 44.69 4.18 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
118 119 8.137745 ACATTCACCATGATGTTCCTTTTATT 57.862 30.769 0.00 0.00 36.24 1.40
330 344 8.526147 CAAGTTAATTCCAACATTCAGGAAGAT 58.474 33.333 0.00 0.00 46.25 2.40
331 345 8.059798 AGTTAATTCCAACATTCAGGAAGATG 57.940 34.615 0.00 0.00 46.25 2.90
407 421 9.875708 ATTTTATGGTATATGGTTCCAGCTTAA 57.124 29.630 0.00 0.00 34.62 1.85
994 1435 0.108615 AGGAAGAGCATCCACGAACG 60.109 55.000 6.07 0.00 42.27 3.95
1026 1467 2.621070 ACCGGCATTCTGGAGGTATAT 58.379 47.619 0.00 0.00 41.45 0.86
1144 1586 2.939103 GTTATACCAGCTCCAGTTGCAG 59.061 50.000 0.00 0.00 0.00 4.41
1208 1650 2.408271 ACATGTGTCGAAGCCATCAT 57.592 45.000 0.00 0.00 0.00 2.45
1339 1781 3.731216 CGTAATAGAAGTCACAGATGGCG 59.269 47.826 0.00 0.00 34.75 5.69
1488 1930 3.841845 ACACTACTGGCATGTACCCTAAA 59.158 43.478 0.00 0.00 0.00 1.85
1781 2237 4.024641 GGGTTTTTATCGACACGTGAAAGT 60.025 41.667 25.01 7.98 0.00 2.66
1822 2290 5.012328 AGACGGAAATACACCAGAGAATC 57.988 43.478 0.00 0.00 0.00 2.52
1863 2331 5.355350 CACCTTAAGAATCATGTCCAGAACC 59.645 44.000 3.36 0.00 0.00 3.62
1916 2394 2.671963 CCAGAGCAGCAGCAGCAA 60.672 61.111 12.92 0.00 45.49 3.91
1944 2422 4.536489 AGGTGTTAGGCTCCTTCATTAAGT 59.464 41.667 0.00 0.00 37.81 2.24
2033 2511 5.878332 TGTACTCCACATTTGCATTACAG 57.122 39.130 0.00 0.00 30.04 2.74
2036 2514 5.789643 ACTCCACATTTGCATTACAGTTT 57.210 34.783 0.00 0.00 0.00 2.66
2104 2582 4.433186 TTTGTATTCCATCAGCAAACCG 57.567 40.909 0.00 0.00 0.00 4.44
2105 2583 3.342377 TGTATTCCATCAGCAAACCGA 57.658 42.857 0.00 0.00 0.00 4.69
2106 2584 3.270027 TGTATTCCATCAGCAAACCGAG 58.730 45.455 0.00 0.00 0.00 4.63
2107 2585 2.496899 ATTCCATCAGCAAACCGAGT 57.503 45.000 0.00 0.00 0.00 4.18
2108 2586 1.808411 TTCCATCAGCAAACCGAGTC 58.192 50.000 0.00 0.00 0.00 3.36
2109 2587 0.684535 TCCATCAGCAAACCGAGTCA 59.315 50.000 0.00 0.00 0.00 3.41
2110 2588 1.071542 TCCATCAGCAAACCGAGTCAA 59.928 47.619 0.00 0.00 0.00 3.18
2111 2589 2.086869 CCATCAGCAAACCGAGTCAAT 58.913 47.619 0.00 0.00 0.00 2.57
2112 2590 2.489329 CCATCAGCAAACCGAGTCAATT 59.511 45.455 0.00 0.00 0.00 2.32
2113 2591 3.495193 CATCAGCAAACCGAGTCAATTG 58.505 45.455 0.00 0.00 0.00 2.32
2114 2592 1.266718 TCAGCAAACCGAGTCAATTGC 59.733 47.619 13.70 13.70 46.43 3.56
2115 2593 3.863681 GCAAACCGAGTCAATTGCA 57.136 47.368 15.68 0.00 45.61 4.08
2116 2594 2.132740 GCAAACCGAGTCAATTGCAA 57.867 45.000 15.68 0.00 45.61 4.08
2117 2595 2.053627 GCAAACCGAGTCAATTGCAAG 58.946 47.619 15.68 0.00 45.61 4.01
2118 2596 2.287547 GCAAACCGAGTCAATTGCAAGA 60.288 45.455 15.68 0.00 45.61 3.02
2119 2597 3.795150 GCAAACCGAGTCAATTGCAAGAA 60.795 43.478 15.68 0.00 45.61 2.52
2120 2598 4.358851 CAAACCGAGTCAATTGCAAGAAA 58.641 39.130 4.94 0.00 0.00 2.52
2121 2599 3.626028 ACCGAGTCAATTGCAAGAAAC 57.374 42.857 4.94 2.49 0.00 2.78
2122 2600 2.293399 ACCGAGTCAATTGCAAGAAACC 59.707 45.455 4.94 0.00 0.00 3.27
2123 2601 2.293122 CCGAGTCAATTGCAAGAAACCA 59.707 45.455 4.94 0.00 0.00 3.67
2124 2602 3.300009 CGAGTCAATTGCAAGAAACCAC 58.700 45.455 4.94 0.00 0.00 4.16
2125 2603 3.642705 GAGTCAATTGCAAGAAACCACC 58.357 45.455 4.94 0.00 0.00 4.61
2126 2604 3.030291 AGTCAATTGCAAGAAACCACCA 58.970 40.909 4.94 0.00 0.00 4.17
2127 2605 3.123050 GTCAATTGCAAGAAACCACCAC 58.877 45.455 4.94 0.00 0.00 4.16
2128 2606 2.762887 TCAATTGCAAGAAACCACCACA 59.237 40.909 4.94 0.00 0.00 4.17
2129 2607 3.387374 TCAATTGCAAGAAACCACCACAT 59.613 39.130 4.94 0.00 0.00 3.21
2130 2608 4.128643 CAATTGCAAGAAACCACCACATT 58.871 39.130 4.94 0.00 0.00 2.71
2131 2609 3.902881 TTGCAAGAAACCACCACATTT 57.097 38.095 0.00 0.00 0.00 2.32
2132 2610 3.176552 TGCAAGAAACCACCACATTTG 57.823 42.857 0.00 0.00 0.00 2.32
2133 2611 1.866601 GCAAGAAACCACCACATTTGC 59.133 47.619 0.00 0.00 33.64 3.68
2134 2612 2.126467 CAAGAAACCACCACATTTGCG 58.874 47.619 0.00 0.00 0.00 4.85
2135 2613 0.673437 AGAAACCACCACATTTGCGG 59.327 50.000 0.00 0.00 0.00 5.69
2136 2614 0.943835 GAAACCACCACATTTGCGGC 60.944 55.000 0.00 0.00 0.00 6.53
2137 2615 1.398958 AAACCACCACATTTGCGGCT 61.399 50.000 0.00 0.00 0.00 5.52
2138 2616 0.538516 AACCACCACATTTGCGGCTA 60.539 50.000 0.00 0.00 0.00 3.93
2139 2617 0.960364 ACCACCACATTTGCGGCTAG 60.960 55.000 0.00 0.00 0.00 3.42
2140 2618 1.656818 CCACCACATTTGCGGCTAGG 61.657 60.000 0.00 0.00 0.00 3.02
2141 2619 0.960364 CACCACATTTGCGGCTAGGT 60.960 55.000 0.00 0.00 0.00 3.08
2142 2620 0.251165 ACCACATTTGCGGCTAGGTT 60.251 50.000 0.00 0.00 0.00 3.50
2143 2621 0.887933 CCACATTTGCGGCTAGGTTT 59.112 50.000 0.00 0.00 0.00 3.27
2144 2622 1.402720 CCACATTTGCGGCTAGGTTTG 60.403 52.381 0.00 0.00 0.00 2.93
2145 2623 0.243636 ACATTTGCGGCTAGGTTTGC 59.756 50.000 0.00 0.00 0.00 3.68
2146 2624 0.798009 CATTTGCGGCTAGGTTTGCG 60.798 55.000 0.00 0.00 0.00 4.85
2147 2625 1.933115 ATTTGCGGCTAGGTTTGCGG 61.933 55.000 0.00 0.00 0.00 5.69
2148 2626 3.538785 TTGCGGCTAGGTTTGCGGA 62.539 57.895 0.00 0.00 33.45 5.54
2149 2627 2.744709 GCGGCTAGGTTTGCGGAA 60.745 61.111 0.00 0.00 33.45 4.30
2150 2628 2.329614 GCGGCTAGGTTTGCGGAAA 61.330 57.895 0.00 0.00 33.45 3.13
2151 2629 1.858372 GCGGCTAGGTTTGCGGAAAA 61.858 55.000 2.79 0.00 33.45 2.29
2152 2630 0.109919 CGGCTAGGTTTGCGGAAAAC 60.110 55.000 9.72 9.72 46.32 2.43
2158 2636 3.742983 GTTTGCGGAAAACCACCAA 57.257 47.368 2.79 0.00 42.06 3.67
2159 2637 1.566404 GTTTGCGGAAAACCACCAAG 58.434 50.000 2.79 0.00 42.06 3.61
2160 2638 1.134936 GTTTGCGGAAAACCACCAAGT 60.135 47.619 2.79 0.00 42.06 3.16
2161 2639 0.741915 TTGCGGAAAACCACCAAGTC 59.258 50.000 0.00 0.00 0.00 3.01
2162 2640 1.281656 GCGGAAAACCACCAAGTCG 59.718 57.895 0.00 0.00 0.00 4.18
2163 2641 1.441732 GCGGAAAACCACCAAGTCGT 61.442 55.000 0.00 0.00 0.00 4.34
2164 2642 1.018910 CGGAAAACCACCAAGTCGTT 58.981 50.000 0.00 0.00 0.00 3.85
2165 2643 2.211806 CGGAAAACCACCAAGTCGTTA 58.788 47.619 0.00 0.00 0.00 3.18
2166 2644 2.613133 CGGAAAACCACCAAGTCGTTAA 59.387 45.455 0.00 0.00 0.00 2.01
2167 2645 3.251487 CGGAAAACCACCAAGTCGTTAAT 59.749 43.478 0.00 0.00 0.00 1.40
2168 2646 4.612033 CGGAAAACCACCAAGTCGTTAATC 60.612 45.833 0.00 0.00 0.00 1.75
2169 2647 4.320714 GGAAAACCACCAAGTCGTTAATCC 60.321 45.833 0.00 0.00 0.00 3.01
2170 2648 2.088950 ACCACCAAGTCGTTAATCCG 57.911 50.000 0.00 0.00 0.00 4.18
2171 2649 1.345415 ACCACCAAGTCGTTAATCCGT 59.655 47.619 0.00 0.00 0.00 4.69
2172 2650 2.224354 ACCACCAAGTCGTTAATCCGTT 60.224 45.455 0.00 0.00 0.00 4.44
2173 2651 2.158841 CCACCAAGTCGTTAATCCGTTG 59.841 50.000 0.00 0.00 0.00 4.10
2174 2652 1.802365 ACCAAGTCGTTAATCCGTTGC 59.198 47.619 0.00 0.00 0.00 4.17
2175 2653 1.801771 CCAAGTCGTTAATCCGTTGCA 59.198 47.619 0.00 0.00 0.00 4.08
2176 2654 2.159707 CCAAGTCGTTAATCCGTTGCAG 60.160 50.000 0.00 0.00 0.00 4.41
2177 2655 2.734606 CAAGTCGTTAATCCGTTGCAGA 59.265 45.455 0.00 0.00 0.00 4.26
2178 2656 3.034721 AGTCGTTAATCCGTTGCAGAA 57.965 42.857 0.00 0.00 0.00 3.02
2179 2657 3.395639 AGTCGTTAATCCGTTGCAGAAA 58.604 40.909 0.00 0.00 0.00 2.52
2180 2658 3.810941 AGTCGTTAATCCGTTGCAGAAAA 59.189 39.130 0.00 0.00 0.00 2.29
2181 2659 3.904234 GTCGTTAATCCGTTGCAGAAAAC 59.096 43.478 0.00 0.00 0.00 2.43
2182 2660 3.560481 TCGTTAATCCGTTGCAGAAAACA 59.440 39.130 0.00 0.00 0.00 2.83
2183 2661 4.214545 TCGTTAATCCGTTGCAGAAAACAT 59.785 37.500 0.00 0.00 0.00 2.71
2184 2662 4.553429 CGTTAATCCGTTGCAGAAAACATC 59.447 41.667 0.00 0.00 0.00 3.06
2185 2663 2.900122 ATCCGTTGCAGAAAACATCG 57.100 45.000 0.00 0.00 0.00 3.84
2186 2664 0.871722 TCCGTTGCAGAAAACATCGG 59.128 50.000 6.87 6.87 46.75 4.18
2188 2666 2.679355 CGTTGCAGAAAACATCGGAA 57.321 45.000 0.00 0.00 0.00 4.30
2189 2667 2.993545 CGTTGCAGAAAACATCGGAAA 58.006 42.857 0.00 0.00 0.00 3.13
2190 2668 3.367607 CGTTGCAGAAAACATCGGAAAA 58.632 40.909 0.00 0.00 0.00 2.29
2191 2669 3.980775 CGTTGCAGAAAACATCGGAAAAT 59.019 39.130 0.00 0.00 0.00 1.82
2192 2670 4.444056 CGTTGCAGAAAACATCGGAAAATT 59.556 37.500 0.00 0.00 0.00 1.82
2193 2671 5.051106 CGTTGCAGAAAACATCGGAAAATTT 60.051 36.000 0.00 0.00 0.00 1.82
2194 2672 5.903764 TGCAGAAAACATCGGAAAATTTG 57.096 34.783 0.00 0.00 0.00 2.32
2195 2673 5.355596 TGCAGAAAACATCGGAAAATTTGT 58.644 33.333 0.00 0.00 0.00 2.83
2196 2674 5.814705 TGCAGAAAACATCGGAAAATTTGTT 59.185 32.000 0.00 0.00 33.93 2.83
2197 2675 6.980978 TGCAGAAAACATCGGAAAATTTGTTA 59.019 30.769 0.00 0.00 32.31 2.41
2198 2676 7.492669 TGCAGAAAACATCGGAAAATTTGTTAA 59.507 29.630 0.00 0.00 32.31 2.01
2199 2677 8.003784 GCAGAAAACATCGGAAAATTTGTTAAG 58.996 33.333 0.00 0.00 32.31 1.85
2200 2678 9.030301 CAGAAAACATCGGAAAATTTGTTAAGT 57.970 29.630 0.00 0.00 32.31 2.24
2201 2679 9.244799 AGAAAACATCGGAAAATTTGTTAAGTC 57.755 29.630 0.00 0.00 32.31 3.01
2202 2680 7.617533 AAACATCGGAAAATTTGTTAAGTCG 57.382 32.000 0.00 0.00 32.31 4.18
2203 2681 6.308371 ACATCGGAAAATTTGTTAAGTCGT 57.692 33.333 0.00 0.00 0.00 4.34
2204 2682 6.731164 ACATCGGAAAATTTGTTAAGTCGTT 58.269 32.000 0.00 0.00 0.00 3.85
2205 2683 6.635239 ACATCGGAAAATTTGTTAAGTCGTTG 59.365 34.615 0.00 0.00 0.00 4.10
2206 2684 4.971220 TCGGAAAATTTGTTAAGTCGTTGC 59.029 37.500 0.00 0.00 0.00 4.17
2207 2685 4.735822 CGGAAAATTTGTTAAGTCGTTGCA 59.264 37.500 0.00 0.00 0.00 4.08
2208 2686 5.230306 CGGAAAATTTGTTAAGTCGTTGCAA 59.770 36.000 0.00 0.00 0.00 4.08
2209 2687 6.237595 CGGAAAATTTGTTAAGTCGTTGCAAA 60.238 34.615 0.00 0.00 34.25 3.68
2210 2688 7.457060 GGAAAATTTGTTAAGTCGTTGCAAAA 58.543 30.769 0.00 0.00 33.60 2.44
2211 2689 7.958025 GGAAAATTTGTTAAGTCGTTGCAAAAA 59.042 29.630 0.00 0.00 33.60 1.94
2231 2709 4.970662 AAACACTGATCGGATGATTTGG 57.029 40.909 9.00 0.00 34.09 3.28
2232 2710 2.292267 ACACTGATCGGATGATTTGGC 58.708 47.619 9.00 0.00 34.09 4.52
2233 2711 1.605710 CACTGATCGGATGATTTGGCC 59.394 52.381 9.00 0.00 34.09 5.36
2234 2712 1.242076 CTGATCGGATGATTTGGCCC 58.758 55.000 0.00 0.00 34.09 5.80
2235 2713 0.534877 TGATCGGATGATTTGGCCCG 60.535 55.000 0.00 0.00 43.02 6.13
2236 2714 0.535102 GATCGGATGATTTGGCCCGT 60.535 55.000 0.00 0.00 42.34 5.28
2237 2715 0.106719 ATCGGATGATTTGGCCCGTT 60.107 50.000 0.00 0.00 42.34 4.44
2238 2716 0.322997 TCGGATGATTTGGCCCGTTT 60.323 50.000 0.00 0.00 42.34 3.60
2239 2717 1.065345 TCGGATGATTTGGCCCGTTTA 60.065 47.619 0.00 0.00 42.34 2.01
2240 2718 1.746220 CGGATGATTTGGCCCGTTTAA 59.254 47.619 0.00 0.00 37.40 1.52
2241 2719 2.360801 CGGATGATTTGGCCCGTTTAAT 59.639 45.455 0.00 0.00 37.40 1.40
2242 2720 3.550030 CGGATGATTTGGCCCGTTTAATC 60.550 47.826 0.00 2.65 37.40 1.75
2243 2721 3.383185 GGATGATTTGGCCCGTTTAATCA 59.617 43.478 0.00 8.39 40.21 2.57
2244 2722 3.859411 TGATTTGGCCCGTTTAATCAC 57.141 42.857 0.00 0.00 33.41 3.06
2245 2723 3.426615 TGATTTGGCCCGTTTAATCACT 58.573 40.909 0.00 0.00 33.41 3.41
2246 2724 3.829601 TGATTTGGCCCGTTTAATCACTT 59.170 39.130 0.00 0.00 33.41 3.16
2247 2725 4.282195 TGATTTGGCCCGTTTAATCACTTT 59.718 37.500 0.00 0.00 33.41 2.66
2248 2726 3.926821 TTGGCCCGTTTAATCACTTTC 57.073 42.857 0.00 0.00 0.00 2.62
2249 2727 3.149005 TGGCCCGTTTAATCACTTTCT 57.851 42.857 0.00 0.00 0.00 2.52
2250 2728 3.492337 TGGCCCGTTTAATCACTTTCTT 58.508 40.909 0.00 0.00 0.00 2.52
2251 2729 4.653868 TGGCCCGTTTAATCACTTTCTTA 58.346 39.130 0.00 0.00 0.00 2.10
2252 2730 4.456566 TGGCCCGTTTAATCACTTTCTTAC 59.543 41.667 0.00 0.00 0.00 2.34
2253 2731 4.456566 GGCCCGTTTAATCACTTTCTTACA 59.543 41.667 0.00 0.00 0.00 2.41
2254 2732 5.391629 GGCCCGTTTAATCACTTTCTTACAG 60.392 44.000 0.00 0.00 0.00 2.74
2255 2733 5.391629 GCCCGTTTAATCACTTTCTTACAGG 60.392 44.000 0.00 0.00 0.00 4.00
2256 2734 5.704053 CCCGTTTAATCACTTTCTTACAGGT 59.296 40.000 0.00 0.00 0.00 4.00
2257 2735 6.348213 CCCGTTTAATCACTTTCTTACAGGTG 60.348 42.308 0.00 0.00 0.00 4.00
2258 2736 6.348213 CCGTTTAATCACTTTCTTACAGGTGG 60.348 42.308 0.00 0.00 0.00 4.61
2259 2737 6.348213 CGTTTAATCACTTTCTTACAGGTGGG 60.348 42.308 0.00 0.00 0.00 4.61
2260 2738 3.721087 ATCACTTTCTTACAGGTGGGG 57.279 47.619 0.00 0.00 0.00 4.96
2261 2739 1.073284 TCACTTTCTTACAGGTGGGGC 59.927 52.381 0.00 0.00 0.00 5.80
2262 2740 0.404426 ACTTTCTTACAGGTGGGGCC 59.596 55.000 0.00 0.00 37.58 5.80
2263 2741 0.404040 CTTTCTTACAGGTGGGGCCA 59.596 55.000 4.39 0.00 40.61 5.36
2264 2742 0.404040 TTTCTTACAGGTGGGGCCAG 59.596 55.000 4.39 0.00 40.61 4.85
2265 2743 1.497309 TTCTTACAGGTGGGGCCAGG 61.497 60.000 4.39 0.00 40.61 4.45
2266 2744 2.121689 TTACAGGTGGGGCCAGGT 60.122 61.111 4.39 0.00 40.61 4.00
2267 2745 1.776710 TTACAGGTGGGGCCAGGTT 60.777 57.895 4.39 0.00 40.61 3.50
2268 2746 2.075355 TTACAGGTGGGGCCAGGTTG 62.075 60.000 4.39 0.34 40.61 3.77
2269 2747 3.902112 CAGGTGGGGCCAGGTTGT 61.902 66.667 4.39 0.00 40.61 3.32
2270 2748 2.121689 AGGTGGGGCCAGGTTGTA 60.122 61.111 4.39 0.00 40.61 2.41
2271 2749 1.776710 AGGTGGGGCCAGGTTGTAA 60.777 57.895 4.39 0.00 40.61 2.41
2272 2750 1.304134 GGTGGGGCCAGGTTGTAAG 60.304 63.158 4.39 0.00 37.17 2.34
2273 2751 1.304134 GTGGGGCCAGGTTGTAAGG 60.304 63.158 4.39 0.00 0.00 2.69
2274 2752 1.464395 TGGGGCCAGGTTGTAAGGA 60.464 57.895 4.39 0.00 0.00 3.36
2275 2753 1.068943 TGGGGCCAGGTTGTAAGGAA 61.069 55.000 4.39 0.00 0.00 3.36
2276 2754 0.335019 GGGGCCAGGTTGTAAGGAAT 59.665 55.000 4.39 0.00 0.00 3.01
2277 2755 1.273041 GGGGCCAGGTTGTAAGGAATT 60.273 52.381 4.39 0.00 0.00 2.17
2278 2756 1.824852 GGGCCAGGTTGTAAGGAATTG 59.175 52.381 4.39 0.00 0.00 2.32
2279 2757 2.556559 GGGCCAGGTTGTAAGGAATTGA 60.557 50.000 4.39 0.00 0.00 2.57
2280 2758 2.492088 GGCCAGGTTGTAAGGAATTGAC 59.508 50.000 0.00 0.00 0.00 3.18
2281 2759 3.421844 GCCAGGTTGTAAGGAATTGACT 58.578 45.455 0.00 0.00 0.00 3.41
2282 2760 3.826729 GCCAGGTTGTAAGGAATTGACTT 59.173 43.478 0.00 0.00 0.00 3.01
2283 2761 5.007682 GCCAGGTTGTAAGGAATTGACTTA 58.992 41.667 0.00 0.00 0.00 2.24
2284 2762 5.123979 GCCAGGTTGTAAGGAATTGACTTAG 59.876 44.000 0.66 0.00 31.57 2.18
2285 2763 5.123979 CCAGGTTGTAAGGAATTGACTTAGC 59.876 44.000 0.66 0.00 31.57 3.09
2286 2764 5.705441 CAGGTTGTAAGGAATTGACTTAGCA 59.295 40.000 0.66 1.05 31.57 3.49
2287 2765 6.206634 CAGGTTGTAAGGAATTGACTTAGCAA 59.793 38.462 0.66 5.52 31.57 3.91
2288 2766 6.775629 AGGTTGTAAGGAATTGACTTAGCAAA 59.224 34.615 11.55 3.16 31.57 3.68
2289 2767 7.286775 AGGTTGTAAGGAATTGACTTAGCAAAA 59.713 33.333 11.55 0.00 31.57 2.44
2290 2768 7.923878 GGTTGTAAGGAATTGACTTAGCAAAAA 59.076 33.333 11.55 0.00 31.57 1.94
2320 2798 5.357742 AAAAACAAAAGCAATCAGACCCT 57.642 34.783 0.00 0.00 0.00 4.34
2321 2799 4.590850 AAACAAAAGCAATCAGACCCTC 57.409 40.909 0.00 0.00 0.00 4.30
2322 2800 2.519013 ACAAAAGCAATCAGACCCTCC 58.481 47.619 0.00 0.00 0.00 4.30
2323 2801 1.821136 CAAAAGCAATCAGACCCTCCC 59.179 52.381 0.00 0.00 0.00 4.30
2324 2802 0.332972 AAAGCAATCAGACCCTCCCC 59.667 55.000 0.00 0.00 0.00 4.81
2325 2803 0.846427 AAGCAATCAGACCCTCCCCA 60.846 55.000 0.00 0.00 0.00 4.96
2326 2804 0.625683 AGCAATCAGACCCTCCCCAT 60.626 55.000 0.00 0.00 0.00 4.00
2327 2805 1.140312 GCAATCAGACCCTCCCCATA 58.860 55.000 0.00 0.00 0.00 2.74
2328 2806 1.072965 GCAATCAGACCCTCCCCATAG 59.927 57.143 0.00 0.00 0.00 2.23
2329 2807 2.694397 CAATCAGACCCTCCCCATAGA 58.306 52.381 0.00 0.00 0.00 1.98
2330 2808 3.048600 CAATCAGACCCTCCCCATAGAA 58.951 50.000 0.00 0.00 0.00 2.10
2331 2809 2.176247 TCAGACCCTCCCCATAGAAC 57.824 55.000 0.00 0.00 0.00 3.01
2332 2810 1.364678 TCAGACCCTCCCCATAGAACA 59.635 52.381 0.00 0.00 0.00 3.18
2333 2811 1.486726 CAGACCCTCCCCATAGAACAC 59.513 57.143 0.00 0.00 0.00 3.32
2334 2812 1.080498 AGACCCTCCCCATAGAACACA 59.920 52.381 0.00 0.00 0.00 3.72
2335 2813 1.486726 GACCCTCCCCATAGAACACAG 59.513 57.143 0.00 0.00 0.00 3.66
2336 2814 1.080498 ACCCTCCCCATAGAACACAGA 59.920 52.381 0.00 0.00 0.00 3.41
2337 2815 1.486726 CCCTCCCCATAGAACACAGAC 59.513 57.143 0.00 0.00 0.00 3.51
2338 2816 1.137086 CCTCCCCATAGAACACAGACG 59.863 57.143 0.00 0.00 0.00 4.18
2339 2817 0.535335 TCCCCATAGAACACAGACGC 59.465 55.000 0.00 0.00 0.00 5.19
2340 2818 0.462047 CCCCATAGAACACAGACGCC 60.462 60.000 0.00 0.00 0.00 5.68
2341 2819 0.462047 CCCATAGAACACAGACGCCC 60.462 60.000 0.00 0.00 0.00 6.13
2342 2820 0.537188 CCATAGAACACAGACGCCCT 59.463 55.000 0.00 0.00 0.00 5.19
2343 2821 1.754803 CCATAGAACACAGACGCCCTA 59.245 52.381 0.00 0.00 0.00 3.53
2344 2822 2.365617 CCATAGAACACAGACGCCCTAT 59.634 50.000 0.00 0.00 0.00 2.57
2345 2823 3.553096 CCATAGAACACAGACGCCCTATC 60.553 52.174 0.00 0.00 0.00 2.08
2346 2824 0.824759 AGAACACAGACGCCCTATCC 59.175 55.000 0.00 0.00 0.00 2.59
2347 2825 0.535335 GAACACAGACGCCCTATCCA 59.465 55.000 0.00 0.00 0.00 3.41
2348 2826 0.249398 AACACAGACGCCCTATCCAC 59.751 55.000 0.00 0.00 0.00 4.02
2349 2827 0.614979 ACACAGACGCCCTATCCACT 60.615 55.000 0.00 0.00 0.00 4.00
2350 2828 1.341679 ACACAGACGCCCTATCCACTA 60.342 52.381 0.00 0.00 0.00 2.74
2351 2829 1.067212 CACAGACGCCCTATCCACTAC 59.933 57.143 0.00 0.00 0.00 2.73
2352 2830 0.311165 CAGACGCCCTATCCACTACG 59.689 60.000 0.00 0.00 0.00 3.51
2353 2831 1.007618 GACGCCCTATCCACTACGC 60.008 63.158 0.00 0.00 0.00 4.42
2354 2832 2.050351 CGCCCTATCCACTACGCG 60.050 66.667 3.53 3.53 0.00 6.01
2355 2833 2.355956 GCCCTATCCACTACGCGC 60.356 66.667 5.73 0.00 0.00 6.86
2356 2834 2.338984 CCCTATCCACTACGCGCC 59.661 66.667 5.73 0.00 0.00 6.53
2357 2835 2.338984 CCTATCCACTACGCGCCC 59.661 66.667 5.73 0.00 0.00 6.13
2358 2836 2.050351 CTATCCACTACGCGCCCG 60.050 66.667 5.73 0.00 41.14 6.13
2359 2837 4.274700 TATCCACTACGCGCCCGC 62.275 66.667 5.73 1.98 38.22 6.13
2457 2935 1.677300 CTGTGTTATGGGGCGGCAA 60.677 57.895 12.47 0.00 0.00 4.52
2477 2955 0.719465 CATTCGTCGGGAAGGAAACG 59.281 55.000 0.00 0.00 38.70 3.60
2564 3042 2.361104 GGCCGCCATTCCTGTTGA 60.361 61.111 3.91 0.00 0.00 3.18
2669 3147 2.038837 ATCGTCGACGTGCTCTCCA 61.039 57.895 34.40 15.55 40.80 3.86
2801 3279 2.049433 GGATATGCGGTCCGTCGG 60.049 66.667 13.94 4.39 0.00 4.79
2826 3304 0.752054 CAAAAGTTGCTGGCCCAGAA 59.248 50.000 16.85 0.00 32.44 3.02
2887 3386 3.151710 CATGGACGGAGGGCGGTA 61.152 66.667 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 2.290260 ACAGCCATGAGAATTCAACCGA 60.290 45.455 8.44 0.00 36.78 4.69
468 723 2.036733 TCCCTGTGGACACGTTAAAGAG 59.963 50.000 0.00 0.00 35.03 2.85
473 728 1.342174 GAACTCCCTGTGGACACGTTA 59.658 52.381 0.00 0.00 35.03 3.18
477 732 0.693049 ATGGAACTCCCTGTGGACAC 59.307 55.000 0.00 0.00 35.03 3.67
634 1075 4.219725 TGGAGTGGCAGGTAAAAATAAAGC 59.780 41.667 0.00 0.00 0.00 3.51
719 1160 9.646427 GCCTAGATAGTTAATTATCAGTTCTGG 57.354 37.037 17.36 11.16 33.41 3.86
994 1435 1.394266 ATGCCGGTTGCCATGGAATC 61.394 55.000 18.40 3.54 40.16 2.52
1026 1467 7.984617 TCAGTGTGCTGTATAGTAATAATTGCA 59.015 33.333 0.00 0.00 43.05 4.08
1049 1490 6.600822 ACATCTTTGGGTGATAAACTCATCAG 59.399 38.462 0.00 0.00 39.67 2.90
1138 1580 2.984471 CACTGATGTCAAATGCTGCAAC 59.016 45.455 6.36 0.02 0.00 4.17
1144 1586 4.690184 TGTCATCACTGATGTCAAATGC 57.310 40.909 16.96 3.53 40.55 3.56
1208 1650 3.185594 CGTTTCTTTCGCCATGTGACTTA 59.814 43.478 0.00 0.00 0.00 2.24
1339 1781 2.682836 GACCAGTTGCAGACTCTTCTC 58.317 52.381 0.00 0.00 36.10 2.87
1781 2237 7.678837 TCCGTCTAGGGTAAAACTCATTTTTA 58.321 34.615 0.00 0.00 38.63 1.52
1822 2290 0.107945 GTGGTAGCAGCCTTCCTGAG 60.108 60.000 0.00 0.00 44.64 3.35
1863 2331 1.488812 TCCACCCACTTATCCCATTCG 59.511 52.381 0.00 0.00 0.00 3.34
1916 2394 0.838122 AGGAGCCTAACACCTGCTGT 60.838 55.000 0.00 0.00 38.05 4.40
1944 2422 7.444299 ACGGGTAGTAGAAATTACTTTTCACA 58.556 34.615 1.41 0.00 45.19 3.58
1966 2444 1.996798 TAGAGGCTAGGGAATGACGG 58.003 55.000 0.00 0.00 0.00 4.79
2104 2582 3.068024 TGGTGGTTTCTTGCAATTGACTC 59.932 43.478 10.34 0.00 0.00 3.36
2105 2583 3.030291 TGGTGGTTTCTTGCAATTGACT 58.970 40.909 10.34 0.00 0.00 3.41
2106 2584 3.123050 GTGGTGGTTTCTTGCAATTGAC 58.877 45.455 10.34 1.02 0.00 3.18
2107 2585 2.762887 TGTGGTGGTTTCTTGCAATTGA 59.237 40.909 10.34 0.00 0.00 2.57
2108 2586 3.176552 TGTGGTGGTTTCTTGCAATTG 57.823 42.857 0.00 0.00 0.00 2.32
2109 2587 4.420522 AATGTGGTGGTTTCTTGCAATT 57.579 36.364 0.00 0.00 0.00 2.32
2110 2588 4.128643 CAAATGTGGTGGTTTCTTGCAAT 58.871 39.130 0.00 0.00 0.00 3.56
2111 2589 3.529533 CAAATGTGGTGGTTTCTTGCAA 58.470 40.909 0.00 0.00 0.00 4.08
2112 2590 2.741228 GCAAATGTGGTGGTTTCTTGCA 60.741 45.455 0.00 0.00 38.03 4.08
2113 2591 1.866601 GCAAATGTGGTGGTTTCTTGC 59.133 47.619 0.00 0.00 0.00 4.01
2114 2592 2.126467 CGCAAATGTGGTGGTTTCTTG 58.874 47.619 0.00 0.00 0.00 3.02
2115 2593 1.068434 CCGCAAATGTGGTGGTTTCTT 59.932 47.619 4.82 0.00 40.69 2.52
2116 2594 0.673437 CCGCAAATGTGGTGGTTTCT 59.327 50.000 4.82 0.00 40.69 2.52
2117 2595 0.943835 GCCGCAAATGTGGTGGTTTC 60.944 55.000 14.07 0.00 46.99 2.78
2118 2596 1.068921 GCCGCAAATGTGGTGGTTT 59.931 52.632 14.07 0.00 46.99 3.27
2119 2597 0.538516 TAGCCGCAAATGTGGTGGTT 60.539 50.000 14.07 1.84 46.99 3.67
2120 2598 0.960364 CTAGCCGCAAATGTGGTGGT 60.960 55.000 14.07 3.04 46.99 4.16
2121 2599 1.656818 CCTAGCCGCAAATGTGGTGG 61.657 60.000 14.07 10.16 46.99 4.61
2122 2600 0.960364 ACCTAGCCGCAAATGTGGTG 60.960 55.000 14.07 5.59 46.99 4.17
2123 2601 0.251165 AACCTAGCCGCAAATGTGGT 60.251 50.000 14.07 4.51 46.99 4.16
2125 2603 1.981254 CAAACCTAGCCGCAAATGTG 58.019 50.000 0.00 0.00 0.00 3.21
2126 2604 0.243636 GCAAACCTAGCCGCAAATGT 59.756 50.000 0.00 0.00 0.00 2.71
2127 2605 0.798009 CGCAAACCTAGCCGCAAATG 60.798 55.000 0.00 0.00 0.00 2.32
2128 2606 1.506262 CGCAAACCTAGCCGCAAAT 59.494 52.632 0.00 0.00 0.00 2.32
2129 2607 2.622011 CCGCAAACCTAGCCGCAAA 61.622 57.895 0.00 0.00 0.00 3.68
2130 2608 3.053291 CCGCAAACCTAGCCGCAA 61.053 61.111 0.00 0.00 0.00 4.85
2131 2609 3.538785 TTCCGCAAACCTAGCCGCA 62.539 57.895 0.00 0.00 0.00 5.69
2132 2610 1.858372 TTTTCCGCAAACCTAGCCGC 61.858 55.000 0.00 0.00 0.00 6.53
2133 2611 0.109919 GTTTTCCGCAAACCTAGCCG 60.110 55.000 0.00 0.00 39.22 5.52
2134 2612 3.786809 GTTTTCCGCAAACCTAGCC 57.213 52.632 0.00 0.00 39.22 3.93
2145 2623 1.018910 AACGACTTGGTGGTTTTCCG 58.981 50.000 0.00 0.00 44.36 4.30
2146 2624 4.320714 GGATTAACGACTTGGTGGTTTTCC 60.321 45.833 3.70 7.19 36.09 3.13
2147 2625 4.612033 CGGATTAACGACTTGGTGGTTTTC 60.612 45.833 3.70 2.86 36.09 2.29
2148 2626 3.251487 CGGATTAACGACTTGGTGGTTTT 59.749 43.478 3.70 0.00 36.09 2.43
2149 2627 2.809696 CGGATTAACGACTTGGTGGTTT 59.190 45.455 3.70 0.00 36.09 3.27
2150 2628 2.224354 ACGGATTAACGACTTGGTGGTT 60.224 45.455 0.00 3.85 38.05 3.67
2151 2629 1.345415 ACGGATTAACGACTTGGTGGT 59.655 47.619 0.00 0.00 37.61 4.16
2152 2630 2.088950 ACGGATTAACGACTTGGTGG 57.911 50.000 0.00 0.00 37.61 4.61
2153 2631 2.412325 GCAACGGATTAACGACTTGGTG 60.412 50.000 0.00 0.00 37.61 4.17
2154 2632 1.802365 GCAACGGATTAACGACTTGGT 59.198 47.619 0.00 0.00 37.61 3.67
2155 2633 1.801771 TGCAACGGATTAACGACTTGG 59.198 47.619 0.00 0.00 37.61 3.61
2156 2634 2.734606 TCTGCAACGGATTAACGACTTG 59.265 45.455 0.00 0.00 37.61 3.16
2157 2635 3.034721 TCTGCAACGGATTAACGACTT 57.965 42.857 0.00 0.00 37.61 3.01
2158 2636 2.736144 TCTGCAACGGATTAACGACT 57.264 45.000 0.00 0.00 37.61 4.18
2159 2637 3.799137 TTTCTGCAACGGATTAACGAC 57.201 42.857 0.00 0.00 37.61 4.34
2160 2638 3.560481 TGTTTTCTGCAACGGATTAACGA 59.440 39.130 0.00 0.00 37.61 3.85
2161 2639 3.879427 TGTTTTCTGCAACGGATTAACG 58.121 40.909 0.00 0.00 40.31 3.18
2162 2640 4.553429 CGATGTTTTCTGCAACGGATTAAC 59.447 41.667 0.00 0.00 0.00 2.01
2163 2641 4.717991 CGATGTTTTCTGCAACGGATTAA 58.282 39.130 0.00 0.00 0.00 1.40
2164 2642 4.335082 CGATGTTTTCTGCAACGGATTA 57.665 40.909 0.00 0.00 0.00 1.75
2165 2643 3.201726 CGATGTTTTCTGCAACGGATT 57.798 42.857 0.00 0.00 0.00 3.01
2166 2644 2.900122 CGATGTTTTCTGCAACGGAT 57.100 45.000 0.00 0.00 0.00 4.18
2168 2646 3.383026 CCGATGTTTTCTGCAACGG 57.617 52.632 0.00 0.00 43.64 4.44
2169 2647 2.679355 TTCCGATGTTTTCTGCAACG 57.321 45.000 0.00 0.00 33.04 4.10
2170 2648 5.905480 AATTTTCCGATGTTTTCTGCAAC 57.095 34.783 0.00 0.00 0.00 4.17
2171 2649 5.814705 ACAAATTTTCCGATGTTTTCTGCAA 59.185 32.000 0.00 0.00 0.00 4.08
2172 2650 5.355596 ACAAATTTTCCGATGTTTTCTGCA 58.644 33.333 0.00 0.00 0.00 4.41
2173 2651 5.905480 ACAAATTTTCCGATGTTTTCTGC 57.095 34.783 0.00 0.00 0.00 4.26
2174 2652 9.030301 ACTTAACAAATTTTCCGATGTTTTCTG 57.970 29.630 0.00 0.00 37.25 3.02
2175 2653 9.244799 GACTTAACAAATTTTCCGATGTTTTCT 57.755 29.630 0.00 0.00 37.25 2.52
2176 2654 8.205297 CGACTTAACAAATTTTCCGATGTTTTC 58.795 33.333 0.00 0.00 37.25 2.29
2177 2655 7.703197 ACGACTTAACAAATTTTCCGATGTTTT 59.297 29.630 0.00 0.00 37.25 2.43
2178 2656 7.197703 ACGACTTAACAAATTTTCCGATGTTT 58.802 30.769 0.00 0.00 37.25 2.83
2179 2657 6.731164 ACGACTTAACAAATTTTCCGATGTT 58.269 32.000 0.00 0.00 39.23 2.71
2180 2658 6.308371 ACGACTTAACAAATTTTCCGATGT 57.692 33.333 0.00 0.00 0.00 3.06
2181 2659 6.398517 GCAACGACTTAACAAATTTTCCGATG 60.399 38.462 0.00 0.00 0.00 3.84
2182 2660 5.627780 GCAACGACTTAACAAATTTTCCGAT 59.372 36.000 0.00 0.00 0.00 4.18
2183 2661 4.971220 GCAACGACTTAACAAATTTTCCGA 59.029 37.500 0.00 0.00 0.00 4.55
2184 2662 4.735822 TGCAACGACTTAACAAATTTTCCG 59.264 37.500 0.00 0.00 0.00 4.30
2185 2663 6.576551 TTGCAACGACTTAACAAATTTTCC 57.423 33.333 0.00 0.00 0.00 3.13
2186 2664 8.867248 TTTTTGCAACGACTTAACAAATTTTC 57.133 26.923 0.00 0.00 30.95 2.29
2208 2686 5.713025 CCAAATCATCCGATCAGTGTTTTT 58.287 37.500 0.00 0.00 0.00 1.94
2209 2687 4.380867 GCCAAATCATCCGATCAGTGTTTT 60.381 41.667 0.00 0.00 0.00 2.43
2210 2688 3.129287 GCCAAATCATCCGATCAGTGTTT 59.871 43.478 0.00 0.00 0.00 2.83
2211 2689 2.684881 GCCAAATCATCCGATCAGTGTT 59.315 45.455 0.00 0.00 0.00 3.32
2212 2690 2.292267 GCCAAATCATCCGATCAGTGT 58.708 47.619 0.00 0.00 0.00 3.55
2213 2691 1.605710 GGCCAAATCATCCGATCAGTG 59.394 52.381 0.00 0.00 0.00 3.66
2214 2692 1.477558 GGGCCAAATCATCCGATCAGT 60.478 52.381 4.39 0.00 0.00 3.41
2215 2693 1.242076 GGGCCAAATCATCCGATCAG 58.758 55.000 4.39 0.00 0.00 2.90
2216 2694 0.534877 CGGGCCAAATCATCCGATCA 60.535 55.000 4.39 0.00 44.69 2.92
2217 2695 0.535102 ACGGGCCAAATCATCCGATC 60.535 55.000 4.39 0.00 44.69 3.69
2218 2696 0.106719 AACGGGCCAAATCATCCGAT 60.107 50.000 4.39 0.00 44.69 4.18
2219 2697 0.322997 AAACGGGCCAAATCATCCGA 60.323 50.000 4.39 0.00 44.69 4.55
2220 2698 1.384525 TAAACGGGCCAAATCATCCG 58.615 50.000 4.39 0.00 46.95 4.18
2221 2699 3.383185 TGATTAAACGGGCCAAATCATCC 59.617 43.478 4.39 0.00 34.34 3.51
2222 2700 4.097892 AGTGATTAAACGGGCCAAATCATC 59.902 41.667 17.99 13.38 39.70 2.92
2223 2701 4.023291 AGTGATTAAACGGGCCAAATCAT 58.977 39.130 17.99 8.97 39.70 2.45
2224 2702 3.426615 AGTGATTAAACGGGCCAAATCA 58.573 40.909 4.39 10.13 36.32 2.57
2225 2703 4.450082 AAGTGATTAAACGGGCCAAATC 57.550 40.909 4.39 7.58 0.00 2.17
2226 2704 4.526650 AGAAAGTGATTAAACGGGCCAAAT 59.473 37.500 4.39 0.00 0.00 2.32
2227 2705 3.892588 AGAAAGTGATTAAACGGGCCAAA 59.107 39.130 4.39 0.00 0.00 3.28
2228 2706 3.492337 AGAAAGTGATTAAACGGGCCAA 58.508 40.909 4.39 0.00 0.00 4.52
2229 2707 3.149005 AGAAAGTGATTAAACGGGCCA 57.851 42.857 4.39 0.00 0.00 5.36
2230 2708 4.456566 TGTAAGAAAGTGATTAAACGGGCC 59.543 41.667 0.00 0.00 0.00 5.80
2231 2709 5.391629 CCTGTAAGAAAGTGATTAAACGGGC 60.392 44.000 0.00 0.00 34.07 6.13
2232 2710 5.704053 ACCTGTAAGAAAGTGATTAAACGGG 59.296 40.000 0.00 0.00 37.98 5.28
2233 2711 6.348213 CCACCTGTAAGAAAGTGATTAAACGG 60.348 42.308 0.00 0.00 34.07 4.44
2234 2712 6.348213 CCCACCTGTAAGAAAGTGATTAAACG 60.348 42.308 0.00 0.00 34.07 3.60
2235 2713 6.072119 CCCCACCTGTAAGAAAGTGATTAAAC 60.072 42.308 0.00 0.00 34.07 2.01
2236 2714 6.007703 CCCCACCTGTAAGAAAGTGATTAAA 58.992 40.000 0.00 0.00 34.07 1.52
2237 2715 5.566469 CCCCACCTGTAAGAAAGTGATTAA 58.434 41.667 0.00 0.00 34.07 1.40
2238 2716 4.566907 GCCCCACCTGTAAGAAAGTGATTA 60.567 45.833 0.00 0.00 34.07 1.75
2239 2717 3.814316 GCCCCACCTGTAAGAAAGTGATT 60.814 47.826 0.00 0.00 34.07 2.57
2240 2718 2.290960 GCCCCACCTGTAAGAAAGTGAT 60.291 50.000 0.00 0.00 34.07 3.06
2241 2719 1.073284 GCCCCACCTGTAAGAAAGTGA 59.927 52.381 0.00 0.00 34.07 3.41
2242 2720 1.534729 GCCCCACCTGTAAGAAAGTG 58.465 55.000 0.00 0.00 34.07 3.16
2243 2721 0.404426 GGCCCCACCTGTAAGAAAGT 59.596 55.000 0.00 0.00 34.07 2.66
2244 2722 0.404040 TGGCCCCACCTGTAAGAAAG 59.596 55.000 0.00 0.00 40.22 2.62
2245 2723 0.404040 CTGGCCCCACCTGTAAGAAA 59.596 55.000 0.00 0.00 40.22 2.52
2246 2724 1.497309 CCTGGCCCCACCTGTAAGAA 61.497 60.000 0.00 0.00 40.22 2.52
2247 2725 1.923395 CCTGGCCCCACCTGTAAGA 60.923 63.158 0.00 0.00 40.22 2.10
2248 2726 1.789576 AACCTGGCCCCACCTGTAAG 61.790 60.000 0.00 0.00 40.22 2.34
2249 2727 1.776710 AACCTGGCCCCACCTGTAA 60.777 57.895 0.00 0.00 40.22 2.41
2250 2728 2.121689 AACCTGGCCCCACCTGTA 60.122 61.111 0.00 0.00 40.22 2.74
2251 2729 3.902112 CAACCTGGCCCCACCTGT 61.902 66.667 0.00 0.00 40.22 4.00
2252 2730 2.075355 TTACAACCTGGCCCCACCTG 62.075 60.000 0.00 0.00 40.22 4.00
2253 2731 1.776710 TTACAACCTGGCCCCACCT 60.777 57.895 0.00 0.00 40.22 4.00
2254 2732 1.304134 CTTACAACCTGGCCCCACC 60.304 63.158 0.00 0.00 39.84 4.61
2255 2733 1.304134 CCTTACAACCTGGCCCCAC 60.304 63.158 0.00 0.00 0.00 4.61
2256 2734 1.068943 TTCCTTACAACCTGGCCCCA 61.069 55.000 0.00 0.00 0.00 4.96
2257 2735 0.335019 ATTCCTTACAACCTGGCCCC 59.665 55.000 0.00 0.00 0.00 5.80
2258 2736 1.824852 CAATTCCTTACAACCTGGCCC 59.175 52.381 0.00 0.00 0.00 5.80
2259 2737 2.492088 GTCAATTCCTTACAACCTGGCC 59.508 50.000 0.00 0.00 0.00 5.36
2260 2738 3.421844 AGTCAATTCCTTACAACCTGGC 58.578 45.455 0.00 0.00 0.00 4.85
2261 2739 5.123979 GCTAAGTCAATTCCTTACAACCTGG 59.876 44.000 0.00 0.00 0.00 4.45
2262 2740 5.705441 TGCTAAGTCAATTCCTTACAACCTG 59.295 40.000 0.00 0.00 0.00 4.00
2263 2741 5.876357 TGCTAAGTCAATTCCTTACAACCT 58.124 37.500 0.00 0.00 0.00 3.50
2264 2742 6.569179 TTGCTAAGTCAATTCCTTACAACC 57.431 37.500 0.00 0.00 0.00 3.77
2265 2743 8.865590 TTTTTGCTAAGTCAATTCCTTACAAC 57.134 30.769 0.00 0.00 0.00 3.32
2298 2776 5.357742 AGGGTCTGATTGCTTTTGTTTTT 57.642 34.783 0.00 0.00 0.00 1.94
2299 2777 4.202253 GGAGGGTCTGATTGCTTTTGTTTT 60.202 41.667 0.00 0.00 0.00 2.43
2300 2778 3.321968 GGAGGGTCTGATTGCTTTTGTTT 59.678 43.478 0.00 0.00 0.00 2.83
2301 2779 2.893489 GGAGGGTCTGATTGCTTTTGTT 59.107 45.455 0.00 0.00 0.00 2.83
2302 2780 2.519013 GGAGGGTCTGATTGCTTTTGT 58.481 47.619 0.00 0.00 0.00 2.83
2303 2781 1.821136 GGGAGGGTCTGATTGCTTTTG 59.179 52.381 0.00 0.00 0.00 2.44
2304 2782 1.272704 GGGGAGGGTCTGATTGCTTTT 60.273 52.381 0.00 0.00 0.00 2.27
2305 2783 0.332972 GGGGAGGGTCTGATTGCTTT 59.667 55.000 0.00 0.00 0.00 3.51
2306 2784 0.846427 TGGGGAGGGTCTGATTGCTT 60.846 55.000 0.00 0.00 0.00 3.91
2307 2785 0.625683 ATGGGGAGGGTCTGATTGCT 60.626 55.000 0.00 0.00 0.00 3.91
2308 2786 1.072965 CTATGGGGAGGGTCTGATTGC 59.927 57.143 0.00 0.00 0.00 3.56
2309 2787 2.694397 TCTATGGGGAGGGTCTGATTG 58.306 52.381 0.00 0.00 0.00 2.67
2310 2788 3.049344 GTTCTATGGGGAGGGTCTGATT 58.951 50.000 0.00 0.00 0.00 2.57
2311 2789 2.022035 TGTTCTATGGGGAGGGTCTGAT 60.022 50.000 0.00 0.00 0.00 2.90
2312 2790 1.364678 TGTTCTATGGGGAGGGTCTGA 59.635 52.381 0.00 0.00 0.00 3.27
2313 2791 1.486726 GTGTTCTATGGGGAGGGTCTG 59.513 57.143 0.00 0.00 0.00 3.51
2314 2792 1.080498 TGTGTTCTATGGGGAGGGTCT 59.920 52.381 0.00 0.00 0.00 3.85
2315 2793 1.486726 CTGTGTTCTATGGGGAGGGTC 59.513 57.143 0.00 0.00 0.00 4.46
2316 2794 1.080498 TCTGTGTTCTATGGGGAGGGT 59.920 52.381 0.00 0.00 0.00 4.34
2317 2795 1.486726 GTCTGTGTTCTATGGGGAGGG 59.513 57.143 0.00 0.00 0.00 4.30
2318 2796 1.137086 CGTCTGTGTTCTATGGGGAGG 59.863 57.143 0.00 0.00 0.00 4.30
2319 2797 1.471676 GCGTCTGTGTTCTATGGGGAG 60.472 57.143 0.00 0.00 0.00 4.30
2320 2798 0.535335 GCGTCTGTGTTCTATGGGGA 59.465 55.000 0.00 0.00 0.00 4.81
2321 2799 0.462047 GGCGTCTGTGTTCTATGGGG 60.462 60.000 0.00 0.00 0.00 4.96
2322 2800 0.462047 GGGCGTCTGTGTTCTATGGG 60.462 60.000 0.00 0.00 0.00 4.00
2323 2801 0.537188 AGGGCGTCTGTGTTCTATGG 59.463 55.000 0.00 0.00 0.00 2.74
2324 2802 3.553096 GGATAGGGCGTCTGTGTTCTATG 60.553 52.174 0.00 0.00 0.00 2.23
2325 2803 2.628657 GGATAGGGCGTCTGTGTTCTAT 59.371 50.000 0.00 0.00 0.00 1.98
2326 2804 2.029623 GGATAGGGCGTCTGTGTTCTA 58.970 52.381 0.00 0.00 0.00 2.10
2327 2805 0.824759 GGATAGGGCGTCTGTGTTCT 59.175 55.000 0.00 0.00 0.00 3.01
2328 2806 0.535335 TGGATAGGGCGTCTGTGTTC 59.465 55.000 0.00 0.00 0.00 3.18
2329 2807 0.249398 GTGGATAGGGCGTCTGTGTT 59.751 55.000 0.00 0.00 0.00 3.32
2330 2808 0.614979 AGTGGATAGGGCGTCTGTGT 60.615 55.000 0.00 0.00 0.00 3.72
2331 2809 1.067212 GTAGTGGATAGGGCGTCTGTG 59.933 57.143 0.00 0.00 0.00 3.66
2332 2810 1.400737 GTAGTGGATAGGGCGTCTGT 58.599 55.000 0.00 0.00 0.00 3.41
2333 2811 0.311165 CGTAGTGGATAGGGCGTCTG 59.689 60.000 0.00 0.00 0.00 3.51
2334 2812 1.453762 GCGTAGTGGATAGGGCGTCT 61.454 60.000 0.00 0.00 0.00 4.18
2335 2813 1.007618 GCGTAGTGGATAGGGCGTC 60.008 63.158 0.00 0.00 0.00 5.19
2336 2814 2.842256 CGCGTAGTGGATAGGGCGT 61.842 63.158 0.00 0.00 0.00 5.68
2337 2815 2.050351 CGCGTAGTGGATAGGGCG 60.050 66.667 0.00 0.00 0.00 6.13
2338 2816 2.355956 GCGCGTAGTGGATAGGGC 60.356 66.667 8.43 0.00 39.19 5.19
2339 2817 2.338984 GGCGCGTAGTGGATAGGG 59.661 66.667 8.43 0.00 39.19 3.53
2340 2818 2.338984 GGGCGCGTAGTGGATAGG 59.661 66.667 8.43 0.00 39.19 2.57
2341 2819 2.050351 CGGGCGCGTAGTGGATAG 60.050 66.667 15.94 0.00 39.19 2.08
2342 2820 4.274700 GCGGGCGCGTAGTGGATA 62.275 66.667 24.70 0.00 39.19 2.59
2396 2874 4.489771 GTGACCATCCCGGCCTGG 62.490 72.222 16.63 16.63 39.03 4.45
2397 2875 4.838152 CGTGACCATCCCGGCCTG 62.838 72.222 0.00 0.00 39.03 4.85
2401 2879 4.530857 GGAGCGTGACCATCCCGG 62.531 72.222 0.00 0.00 42.50 5.73
2402 2880 3.432051 GAGGAGCGTGACCATCCCG 62.432 68.421 0.00 0.00 33.30 5.14
2403 2881 2.501610 GAGGAGCGTGACCATCCC 59.498 66.667 0.00 0.00 33.30 3.85
2404 2882 2.022240 GAGGAGGAGCGTGACCATCC 62.022 65.000 0.00 0.00 0.00 3.51
2405 2883 1.040339 AGAGGAGGAGCGTGACCATC 61.040 60.000 0.00 0.00 0.00 3.51
2406 2884 1.000993 AGAGGAGGAGCGTGACCAT 59.999 57.895 0.00 0.00 0.00 3.55
2407 2885 1.679305 GAGAGGAGGAGCGTGACCA 60.679 63.158 0.00 0.00 0.00 4.02
2408 2886 2.419739 GGAGAGGAGGAGCGTGACC 61.420 68.421 0.00 0.00 0.00 4.02
2457 2935 1.804601 GTTTCCTTCCCGACGAATGT 58.195 50.000 0.00 0.00 0.00 2.71
2477 2955 1.674651 GCAACCCTTCGTCCCTTCC 60.675 63.158 0.00 0.00 0.00 3.46
2564 3042 1.678627 CATGGTCTCTCCGACGAGAAT 59.321 52.381 0.00 0.00 44.62 2.40
2648 3126 1.978712 GAGAGCACGTCGACGATGGA 61.979 60.000 41.52 0.00 43.02 3.41
2826 3304 2.003548 GCAATCCAGTCCCTCCCCT 61.004 63.158 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.