Multiple sequence alignment - TraesCS3A01G403700

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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 TraesCS3A01G403700 chr3A 100.000 4422 0 0 1 4422 648858859 648863280 0.000000e+00 8167.0
1 TraesCS3A01G403700 chr3D 90.321 2180 107 35 1 2138 513887396 513889513 0.000000e+00 2761.0
2 TraesCS3A01G403700 chr3D 91.740 908 43 10 3184 4071 513890434 513891329 0.000000e+00 1232.0
3 TraesCS3A01G403700 chr3D 92.067 832 27 7 2315 3133 513889630 513890435 0.000000e+00 1134.0
4 TraesCS3A01G403700 chr3D 88.933 253 19 4 4170 4422 513891333 513891576 2.000000e-78 303.0
5 TraesCS3A01G403700 chr3D 91.667 108 5 2 2220 2327 513889512 513889615 3.560000e-31 147.0
6 TraesCS3A01G403700 chr3B 90.876 1666 81 22 2220 3849 676212994 676214624 0.000000e+00 2169.0
7 TraesCS3A01G403700 chr3B 91.096 876 32 16 653 1518 676211575 676212414 0.000000e+00 1144.0
8 TraesCS3A01G403700 chr3B 94.173 635 22 12 1 622 676210939 676211571 0.000000e+00 953.0
9 TraesCS3A01G403700 chr3B 90.803 598 29 9 1551 2138 676212414 676212995 0.000000e+00 776.0
10 TraesCS3A01G403700 chr3B 95.745 235 4 2 3843 4077 676214702 676214930 1.500000e-99 374.0
11 TraesCS3A01G403700 chr3B 90.037 271 10 7 4169 4422 676214927 676215197 7.090000e-88 335.0
12 TraesCS3A01G403700 chr3B 91.765 85 7 0 2137 2221 680423382 680423298 7.770000e-23 119.0
13 TraesCS3A01G403700 chr3B 90.588 85 8 0 2137 2221 126580065 126580149 3.610000e-21 113.0
14 TraesCS3A01G403700 chr3B 97.872 47 0 1 4265 4310 676215097 676215143 3.670000e-11 80.5
15 TraesCS3A01G403700 chrUn 96.396 111 4 0 4072 4182 305213130 305213240 2.720000e-42 183.0
16 TraesCS3A01G403700 chr7B 98.077 104 2 0 4071 4174 217312362 217312259 9.770000e-42 182.0
17 TraesCS3A01G403700 chr2D 99.000 100 1 0 4073 4172 593274242 593274341 3.510000e-41 180.0
18 TraesCS3A01G403700 chr2D 90.000 90 9 0 2136 2225 557267267 557267178 2.790000e-22 117.0
19 TraesCS3A01G403700 chr2D 90.588 85 8 0 2137 2221 299891103 299891019 3.610000e-21 113.0
20 TraesCS3A01G403700 chr1D 85.799 169 24 0 1 169 356141910 356142078 3.510000e-41 180.0
21 TraesCS3A01G403700 chr1D 94.643 112 6 0 4071 4182 472174538 472174427 1.630000e-39 174.0
22 TraesCS3A01G403700 chr1D 90.909 88 5 3 2135 2222 110052555 110052471 1.010000e-21 115.0
23 TraesCS3A01G403700 chr1A 85.799 169 24 0 1 169 456931376 456931544 3.510000e-41 180.0
24 TraesCS3A01G403700 chr5B 95.495 111 4 1 4062 4172 223038351 223038242 4.550000e-40 176.0
25 TraesCS3A01G403700 chr4D 93.277 119 6 2 4074 4191 54412656 54412539 1.630000e-39 174.0
26 TraesCS3A01G403700 chr4D 93.966 116 5 2 4063 4176 230489529 230489644 1.630000e-39 174.0
27 TraesCS3A01G403700 chr1B 85.207 169 25 0 1 169 478715572 478715740 1.630000e-39 174.0
28 TraesCS3A01G403700 chr1B 89.286 84 9 0 2139 2222 120657925 120657842 6.050000e-19 106.0
29 TraesCS3A01G403700 chr6D 91.200 125 8 3 4069 4192 293316568 293316690 2.740000e-37 167.0
30 TraesCS3A01G403700 chr5A 91.200 125 6 4 4074 4196 66095867 66095746 9.840000e-37 165.0
31 TraesCS3A01G403700 chr2A 94.048 84 5 0 2138 2221 376082517 376082434 1.290000e-25 128.0
32 TraesCS3A01G403700 chr2A 91.011 89 7 1 2134 2221 593655906 593655994 7.770000e-23 119.0
33 TraesCS3A01G403700 chr2B 88.764 89 9 1 2134 2221 529265342 529265430 1.680000e-19 108.0


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 TraesCS3A01G403700 chr3A 648858859 648863280 4421 False 8167.000000 8167 100.000000 1 4422 1 chr3A.!!$F1 4421
1 TraesCS3A01G403700 chr3D 513887396 513891576 4180 False 1115.400000 2761 90.945600 1 4422 5 chr3D.!!$F1 4421
2 TraesCS3A01G403700 chr3B 676210939 676215197 4258 False 833.071429 2169 92.943143 1 4422 7 chr3B.!!$F2 4421

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
872 921 0.109723 AGCCCACCAAGTAGCGAAAA 59.890 50.0 0.00 0.0 0.00 2.29 F
975 1026 0.322546 CAACCCCTTCCTTCCTTCCG 60.323 60.0 0.00 0.0 0.00 4.30 F
2553 2680 0.325602 ATGTTGGCAGCCAAATTGGG 59.674 50.0 29.04 0.0 45.73 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 1886 0.248458 AAACACGAACAAGGCAAGCG 60.248 50.000 0.00 0.0 0.00 4.68 R
2896 3023 0.393537 ACCAGTGCTTAGGCTGCATC 60.394 55.000 2.62 0.0 42.69 3.91 R
4154 4410 1.637553 ACTAGTACTCCCTCCGTTCCA 59.362 52.381 0.00 0.0 0.00 3.53 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
42 43 4.740822 GGGACCTGCGGCACCAAT 62.741 66.667 9.92 0.00 0.00 3.16
231 235 1.376037 CGCCGGAGAAGGAAAAGCT 60.376 57.895 5.05 0.00 0.00 3.74
273 277 0.539438 AACCAAGCAATCTTCGCCCA 60.539 50.000 0.00 0.00 0.00 5.36
289 293 2.100584 CGCCCAGCCTCTAGATATCATC 59.899 54.545 5.32 0.00 0.00 2.92
328 332 2.531206 CTTCCTAGTCTGTAAGCGTGC 58.469 52.381 0.00 0.00 0.00 5.34
335 342 1.321743 GTCTGTAAGCGTGCTTCATCG 59.678 52.381 10.88 0.00 37.47 3.84
486 497 2.123988 TTGCCGTCATTCGTGTTGGC 62.124 55.000 0.00 0.00 42.76 4.52
509 524 1.001641 GCACTGATCCTGGGTTGCT 60.002 57.895 0.00 0.00 0.00 3.91
510 525 0.610232 GCACTGATCCTGGGTTGCTT 60.610 55.000 0.00 0.00 0.00 3.91
511 526 1.171308 CACTGATCCTGGGTTGCTTG 58.829 55.000 0.00 0.00 0.00 4.01
512 527 0.610232 ACTGATCCTGGGTTGCTTGC 60.610 55.000 0.00 0.00 0.00 4.01
537 552 2.424557 AGCTGTCTTGCTCTGTTGATG 58.575 47.619 0.00 0.00 39.34 3.07
587 606 9.349713 TGGTTAATACTACAATTCCATCATTCC 57.650 33.333 0.00 0.00 0.00 3.01
612 631 7.711339 CCTAGTAGTATTGACCAAACATCCTTC 59.289 40.741 0.00 0.00 0.00 3.46
636 655 5.592688 CCAAATATGGGGTACTACTTTGGTG 59.407 44.000 0.00 0.00 43.51 4.17
645 664 1.567175 ACTACTTTGGTGGTTGGGTGT 59.433 47.619 0.00 0.00 33.31 4.16
647 666 1.945580 ACTTTGGTGGTTGGGTGTTT 58.054 45.000 0.00 0.00 0.00 2.83
648 667 2.261729 ACTTTGGTGGTTGGGTGTTTT 58.738 42.857 0.00 0.00 0.00 2.43
649 668 2.640332 ACTTTGGTGGTTGGGTGTTTTT 59.360 40.909 0.00 0.00 0.00 1.94
690 709 6.015434 ACACTGGAATAGTTGGGTGATTTTTC 60.015 38.462 0.00 0.00 37.60 2.29
711 730 0.610174 CCCTGCTGTCTGTCTTGCTA 59.390 55.000 0.00 0.00 0.00 3.49
712 731 1.002430 CCCTGCTGTCTGTCTTGCTAA 59.998 52.381 0.00 0.00 0.00 3.09
713 732 2.550855 CCCTGCTGTCTGTCTTGCTAAA 60.551 50.000 0.00 0.00 0.00 1.85
714 733 2.740981 CCTGCTGTCTGTCTTGCTAAAG 59.259 50.000 0.00 0.00 34.45 1.85
715 734 3.397482 CTGCTGTCTGTCTTGCTAAAGT 58.603 45.455 0.00 0.00 34.78 2.66
749 768 5.420725 ACAGCAATGACTTACAGGATACA 57.579 39.130 0.00 0.00 41.41 2.29
872 921 0.109723 AGCCCACCAAGTAGCGAAAA 59.890 50.000 0.00 0.00 0.00 2.29
882 931 1.071814 TAGCGAAAACCGGCCACTT 59.928 52.632 0.00 0.00 39.04 3.16
895 944 1.460273 GCCACTTTCGGAGCCCAAAA 61.460 55.000 0.00 0.00 0.00 2.44
905 954 2.536066 GGAGCCCAAAACTAAACCCAT 58.464 47.619 0.00 0.00 0.00 4.00
926 975 1.004200 AAAAATCTCGTCCGGCCGT 60.004 52.632 26.12 0.00 0.00 5.68
937 986 3.751246 CGGCCGTAGACGACCCAA 61.751 66.667 19.50 0.00 38.75 4.12
938 987 2.658422 GGCCGTAGACGACCCAAA 59.342 61.111 3.07 0.00 43.02 3.28
975 1026 0.322546 CAACCCCTTCCTTCCTTCCG 60.323 60.000 0.00 0.00 0.00 4.30
976 1027 0.770948 AACCCCTTCCTTCCTTCCGT 60.771 55.000 0.00 0.00 0.00 4.69
1299 1353 1.296715 CACCTTCAAGTCCTCCGGG 59.703 63.158 0.00 0.00 0.00 5.73
1388 1442 1.034292 GCCCAGGTCAGCTTCCATTC 61.034 60.000 7.36 0.00 0.00 2.67
1398 1452 1.005215 AGCTTCCATTCTCCAGTTGGG 59.995 52.381 0.00 0.00 35.41 4.12
1425 1489 1.110442 TGCCCAAAACAGAGTGGTTG 58.890 50.000 0.00 0.00 32.60 3.77
1486 1550 2.610976 CGGATGTTGGTTCTAACGGTGA 60.611 50.000 0.00 0.00 33.28 4.02
1496 1560 3.308438 TCTAACGGTGAACTTGTAGCC 57.692 47.619 0.00 0.00 0.00 3.93
1536 1623 2.092429 TGGCACTTCCCAGAATATCCAC 60.092 50.000 0.00 0.00 0.00 4.02
1543 1630 4.169059 TCCCAGAATATCCACACCATTG 57.831 45.455 0.00 0.00 0.00 2.82
1560 1647 5.239306 CACCATTGTCAGTTGAGCTTTAGAA 59.761 40.000 0.00 0.00 0.00 2.10
1599 1686 8.571461 TTGAGAGATTTATGCTTCAAGTCAAT 57.429 30.769 0.00 0.00 0.00 2.57
1608 1695 9.787532 TTTATGCTTCAAGTCAATTAACATAGC 57.212 29.630 0.00 0.00 0.00 2.97
1609 1696 5.868257 TGCTTCAAGTCAATTAACATAGCG 58.132 37.500 0.00 0.00 0.00 4.26
1610 1697 5.641636 TGCTTCAAGTCAATTAACATAGCGA 59.358 36.000 0.00 0.00 0.00 4.93
1611 1698 6.316140 TGCTTCAAGTCAATTAACATAGCGAT 59.684 34.615 0.00 0.00 0.00 4.58
1612 1699 7.148255 TGCTTCAAGTCAATTAACATAGCGATT 60.148 33.333 0.00 0.00 0.00 3.34
1635 1722 7.994425 TTATTAGTGTGTCCACAACATCAAT 57.006 32.000 0.93 1.33 44.39 2.57
1648 1735 8.136800 TCCACAACATCAATCAACAATATATGC 58.863 33.333 0.00 0.00 0.00 3.14
1669 1756 0.394216 CCCATCATGGCGGACAGAAA 60.394 55.000 0.00 0.00 35.79 2.52
1756 1846 3.948473 TCGATGTCTTTGAACCCAAACAA 59.052 39.130 0.00 0.00 37.36 2.83
1796 1886 7.917505 CCCTCTTAAATGAACATTCTATGCAAC 59.082 37.037 0.00 0.00 0.00 4.17
1841 1931 4.019174 CAGTATGGAATGTTGCTTTCCCT 58.981 43.478 10.11 4.75 41.68 4.20
1856 1946 4.511826 GCTTTCCCTACTGAATTCATACGG 59.488 45.833 8.96 9.03 0.00 4.02
1857 1947 3.746045 TCCCTACTGAATTCATACGGC 57.254 47.619 8.96 0.00 0.00 5.68
1989 2087 8.985315 TCCTTTGCATGATAGTTTATCTCATT 57.015 30.769 0.00 0.00 36.17 2.57
2039 2137 5.043903 AGGTCACAACATAAGAATCGATCG 58.956 41.667 9.36 9.36 0.00 3.69
2161 2259 7.934855 ACTCCGTCTGTAACTTTCTAATAGA 57.065 36.000 0.00 0.00 0.00 1.98
2162 2260 7.760437 ACTCCGTCTGTAACTTTCTAATAGAC 58.240 38.462 0.00 0.00 0.00 2.59
2166 2264 8.445193 CGTCTGTAACTTTCTAATAGACGTTT 57.555 34.615 13.75 0.00 46.26 3.60
2167 2265 8.909671 CGTCTGTAACTTTCTAATAGACGTTTT 58.090 33.333 13.75 0.00 46.26 2.43
2175 2273 9.636879 ACTTTCTAATAGACGTTTTTAGAGTCC 57.363 33.333 12.54 0.00 34.44 3.85
2176 2274 9.635520 CTTTCTAATAGACGTTTTTAGAGTCCA 57.364 33.333 12.54 1.19 34.44 4.02
2178 2276 9.582431 TTCTAATAGACGTTTTTAGAGTCCATG 57.418 33.333 12.54 0.00 34.44 3.66
2179 2277 8.963725 TCTAATAGACGTTTTTAGAGTCCATGA 58.036 33.333 10.12 0.00 35.65 3.07
2180 2278 7.829378 AATAGACGTTTTTAGAGTCCATGAC 57.171 36.000 0.00 0.00 35.65 3.06
2181 2279 5.209818 AGACGTTTTTAGAGTCCATGACA 57.790 39.130 0.00 0.00 34.60 3.58
2182 2280 5.230942 AGACGTTTTTAGAGTCCATGACAG 58.769 41.667 0.00 0.00 34.60 3.51
2183 2281 4.957296 ACGTTTTTAGAGTCCATGACAGT 58.043 39.130 0.00 0.00 34.60 3.55
2184 2282 4.750098 ACGTTTTTAGAGTCCATGACAGTG 59.250 41.667 0.00 0.00 34.60 3.66
2185 2283 4.750098 CGTTTTTAGAGTCCATGACAGTGT 59.250 41.667 0.00 0.00 34.60 3.55
2186 2284 5.107453 CGTTTTTAGAGTCCATGACAGTGTC 60.107 44.000 16.68 16.68 34.60 3.67
2187 2285 5.545063 TTTTAGAGTCCATGACAGTGTCA 57.455 39.130 27.35 27.35 46.90 3.58
2188 2286 5.545063 TTTAGAGTCCATGACAGTGTCAA 57.455 39.130 28.70 11.00 45.96 3.18
2189 2287 5.545063 TTAGAGTCCATGACAGTGTCAAA 57.455 39.130 28.70 14.94 45.96 2.69
2190 2288 4.422073 AGAGTCCATGACAGTGTCAAAA 57.578 40.909 28.70 14.59 45.96 2.44
2191 2289 4.780815 AGAGTCCATGACAGTGTCAAAAA 58.219 39.130 28.70 14.25 45.96 1.94
2216 2314 9.449719 AAATGTCTTGTATTAAGTTACAGAGGG 57.550 33.333 0.00 0.00 33.81 4.30
2217 2315 7.786046 TGTCTTGTATTAAGTTACAGAGGGA 57.214 36.000 0.00 0.00 33.81 4.20
2218 2316 7.837863 TGTCTTGTATTAAGTTACAGAGGGAG 58.162 38.462 0.00 0.00 33.81 4.30
2228 2326 4.904251 AGTTACAGAGGGAGTATCATGCAT 59.096 41.667 0.00 0.00 36.25 3.96
2241 2339 3.941704 TCATGCATACCCAATACCACA 57.058 42.857 0.00 0.00 0.00 4.17
2296 2394 5.461032 TGTTAGTTGCAAATAACCCCAAG 57.539 39.130 34.22 0.00 32.11 3.61
2366 2492 8.236586 CACTTACTCATAATTTACAGCAGCAAA 58.763 33.333 0.00 0.00 0.00 3.68
2541 2668 3.489738 CCATTCGATCAAAGGATGTTGGC 60.490 47.826 0.00 0.00 32.67 4.52
2553 2680 0.325602 ATGTTGGCAGCCAAATTGGG 59.674 50.000 29.04 0.00 45.73 4.12
2595 2722 6.458232 TCTCCAGTATGCTTCTCTTCTTAC 57.542 41.667 0.00 0.00 31.97 2.34
2596 2723 5.361285 TCTCCAGTATGCTTCTCTTCTTACC 59.639 44.000 0.00 0.00 31.97 2.85
2597 2724 5.273208 TCCAGTATGCTTCTCTTCTTACCT 58.727 41.667 0.00 0.00 31.97 3.08
2598 2725 5.721960 TCCAGTATGCTTCTCTTCTTACCTT 59.278 40.000 0.00 0.00 31.97 3.50
2599 2726 6.895756 TCCAGTATGCTTCTCTTCTTACCTTA 59.104 38.462 0.00 0.00 31.97 2.69
2600 2727 7.399191 TCCAGTATGCTTCTCTTCTTACCTTAA 59.601 37.037 0.00 0.00 31.97 1.85
2601 2728 8.041323 CCAGTATGCTTCTCTTCTTACCTTAAA 58.959 37.037 0.00 0.00 31.97 1.52
2602 2729 9.606631 CAGTATGCTTCTCTTCTTACCTTAAAT 57.393 33.333 0.00 0.00 0.00 1.40
2606 2733 8.438676 TGCTTCTCTTCTTACCTTAAATATGC 57.561 34.615 0.00 0.00 0.00 3.14
2607 2734 7.499232 TGCTTCTCTTCTTACCTTAAATATGCC 59.501 37.037 0.00 0.00 0.00 4.40
2608 2735 7.499232 GCTTCTCTTCTTACCTTAAATATGCCA 59.501 37.037 0.00 0.00 0.00 4.92
2609 2736 9.396022 CTTCTCTTCTTACCTTAAATATGCCAA 57.604 33.333 0.00 0.00 0.00 4.52
2610 2737 8.964476 TCTCTTCTTACCTTAAATATGCCAAG 57.036 34.615 0.00 0.00 0.00 3.61
2611 2738 8.548877 TCTCTTCTTACCTTAAATATGCCAAGT 58.451 33.333 0.00 0.00 0.00 3.16
2612 2739 8.506168 TCTTCTTACCTTAAATATGCCAAGTG 57.494 34.615 0.00 0.00 0.00 3.16
2613 2740 8.107095 TCTTCTTACCTTAAATATGCCAAGTGT 58.893 33.333 0.00 0.00 0.00 3.55
2614 2741 7.624360 TCTTACCTTAAATATGCCAAGTGTG 57.376 36.000 0.00 0.00 0.00 3.82
2615 2742 7.172342 TCTTACCTTAAATATGCCAAGTGTGT 58.828 34.615 0.00 0.00 0.00 3.72
2616 2743 7.668052 TCTTACCTTAAATATGCCAAGTGTGTT 59.332 33.333 0.00 0.00 0.00 3.32
2617 2744 6.664428 ACCTTAAATATGCCAAGTGTGTTT 57.336 33.333 0.00 0.00 0.00 2.83
2618 2745 7.061566 ACCTTAAATATGCCAAGTGTGTTTT 57.938 32.000 0.00 0.00 0.00 2.43
2619 2746 7.505258 ACCTTAAATATGCCAAGTGTGTTTTT 58.495 30.769 0.00 0.00 0.00 1.94
2620 2747 8.643324 ACCTTAAATATGCCAAGTGTGTTTTTA 58.357 29.630 0.00 0.00 0.00 1.52
2637 2764 8.791675 TGTGTTTTTATCTCATGCTCAATGTTA 58.208 29.630 0.00 0.00 37.56 2.41
2651 2778 5.870978 GCTCAATGTTACCAATTTGAATGCT 59.129 36.000 0.00 0.00 0.00 3.79
2655 2782 5.798125 TGTTACCAATTTGAATGCTTCCA 57.202 34.783 0.00 0.00 0.00 3.53
2674 2801 6.579666 TTCCATTTCCAATGTTCTCTTCTG 57.420 37.500 0.00 0.00 0.00 3.02
2841 2968 5.009210 GGGTGCTAGTTTACAACATGTTCAA 59.991 40.000 8.48 3.00 0.00 2.69
3296 3438 3.424703 CCCATCACATCCAAGTTTGAGT 58.575 45.455 0.00 0.00 0.00 3.41
3300 3443 5.242393 CCATCACATCCAAGTTTGAGTCTTT 59.758 40.000 0.00 0.00 0.00 2.52
3344 3487 5.549742 TCAGTCCCAAATTCTGCAATTTT 57.450 34.783 0.00 0.00 39.75 1.82
3345 3488 5.927819 TCAGTCCCAAATTCTGCAATTTTT 58.072 33.333 0.00 0.00 39.75 1.94
3346 3489 5.759273 TCAGTCCCAAATTCTGCAATTTTTG 59.241 36.000 7.56 7.56 39.75 2.44
3347 3490 5.759273 CAGTCCCAAATTCTGCAATTTTTGA 59.241 36.000 13.55 3.43 39.75 2.69
3350 3493 6.928492 GTCCCAAATTCTGCAATTTTTGAGTA 59.072 34.615 13.55 0.81 39.75 2.59
3358 3501 4.239304 TGCAATTTTTGAGTAGCATGCTG 58.761 39.130 30.42 10.50 30.72 4.41
3396 3539 7.296628 AGATCTTAACCACATATCTGTCTCC 57.703 40.000 0.00 0.00 31.62 3.71
3397 3540 6.841229 AGATCTTAACCACATATCTGTCTCCA 59.159 38.462 0.00 0.00 31.62 3.86
3595 3753 1.985473 TCATGCCTGCTTGTTTGTCT 58.015 45.000 5.12 0.00 0.00 3.41
3693 3860 8.303876 TCAACAAATTGGATCTACTTTTAAGCC 58.696 33.333 0.00 0.00 36.39 4.35
3702 3869 8.934697 TGGATCTACTTTTAAGCCATATAGTGT 58.065 33.333 0.00 0.00 0.00 3.55
3750 3917 1.109609 TTGTGTGTCCATTTGCTGCA 58.890 45.000 0.00 0.00 0.00 4.41
3761 3934 1.855513 TTTGCTGCATTGCTGTCAAC 58.144 45.000 15.71 1.55 34.60 3.18
3792 3965 6.719370 ACTCAAACAGAAAACCTTGCCATATA 59.281 34.615 0.00 0.00 0.00 0.86
3800 3973 7.170320 CAGAAAACCTTGCCATATATTCATTGC 59.830 37.037 0.00 0.00 0.00 3.56
3804 3977 4.478699 CTTGCCATATATTCATTGCCACG 58.521 43.478 0.00 0.00 0.00 4.94
4034 4290 2.358582 TCACCTGCAACAAGTTCACATG 59.641 45.455 0.00 0.00 0.00 3.21
4036 4292 2.358898 ACCTGCAACAAGTTCACATGTC 59.641 45.455 0.00 0.00 0.00 3.06
4082 4338 9.549078 CTTAAAAGTTCAGAATATACTCCCTCC 57.451 37.037 0.00 0.00 0.00 4.30
4083 4339 5.793030 AAGTTCAGAATATACTCCCTCCG 57.207 43.478 0.00 0.00 0.00 4.63
4084 4340 4.805744 AGTTCAGAATATACTCCCTCCGT 58.194 43.478 0.00 0.00 0.00 4.69
4085 4341 5.209659 AGTTCAGAATATACTCCCTCCGTT 58.790 41.667 0.00 0.00 0.00 4.44
4086 4342 5.302313 AGTTCAGAATATACTCCCTCCGTTC 59.698 44.000 0.00 0.00 0.00 3.95
4087 4343 4.150359 TCAGAATATACTCCCTCCGTTCC 58.850 47.826 0.00 0.00 0.00 3.62
4088 4344 3.895656 CAGAATATACTCCCTCCGTTCCA 59.104 47.826 0.00 0.00 0.00 3.53
4089 4345 4.344102 CAGAATATACTCCCTCCGTTCCAA 59.656 45.833 0.00 0.00 0.00 3.53
4090 4346 4.966805 AGAATATACTCCCTCCGTTCCAAA 59.033 41.667 0.00 0.00 0.00 3.28
4091 4347 5.427481 AGAATATACTCCCTCCGTTCCAAAA 59.573 40.000 0.00 0.00 0.00 2.44
4092 4348 5.906772 ATATACTCCCTCCGTTCCAAAAT 57.093 39.130 0.00 0.00 0.00 1.82
4093 4349 7.291651 AGAATATACTCCCTCCGTTCCAAAATA 59.708 37.037 0.00 0.00 0.00 1.40
4094 4350 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
4095 4351 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
4096 4352 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
4097 4353 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
4098 4354 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
4099 4355 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
4100 4356 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
4101 4357 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
4102 4358 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
4103 4359 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
4104 4360 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
4105 4361 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
4106 4362 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
4107 4363 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
4108 4364 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
4109 4365 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
4110 4366 7.874940 TCCAAAATAGATGACTCAACTTTGTG 58.125 34.615 0.00 0.00 0.00 3.33
4111 4367 6.583806 CCAAAATAGATGACTCAACTTTGTGC 59.416 38.462 0.00 0.00 0.00 4.57
4112 4368 7.365741 CAAAATAGATGACTCAACTTTGTGCT 58.634 34.615 0.00 0.00 0.00 4.40
4113 4369 8.506437 CAAAATAGATGACTCAACTTTGTGCTA 58.494 33.333 0.00 0.00 0.00 3.49
4114 4370 8.621532 AAATAGATGACTCAACTTTGTGCTAA 57.378 30.769 0.00 0.00 0.00 3.09
4115 4371 5.931441 AGATGACTCAACTTTGTGCTAAC 57.069 39.130 0.00 0.00 0.00 2.34
4116 4372 5.615289 AGATGACTCAACTTTGTGCTAACT 58.385 37.500 0.00 0.00 0.00 2.24
4117 4373 6.058183 AGATGACTCAACTTTGTGCTAACTT 58.942 36.000 0.00 0.00 0.00 2.66
4118 4374 6.543831 AGATGACTCAACTTTGTGCTAACTTT 59.456 34.615 0.00 0.00 0.00 2.66
4119 4375 7.715249 AGATGACTCAACTTTGTGCTAACTTTA 59.285 33.333 0.00 0.00 0.00 1.85
4120 4376 7.246674 TGACTCAACTTTGTGCTAACTTTAG 57.753 36.000 0.00 0.00 0.00 1.85
4121 4377 6.821665 TGACTCAACTTTGTGCTAACTTTAGT 59.178 34.615 0.00 0.00 33.32 2.24
4122 4378 7.982919 TGACTCAACTTTGTGCTAACTTTAGTA 59.017 33.333 0.00 0.00 33.32 1.82
4123 4379 8.139521 ACTCAACTTTGTGCTAACTTTAGTAC 57.860 34.615 9.56 9.56 43.76 2.73
4145 4401 9.716531 AGTACAAAGTTAGTATAAAGTTGGGTC 57.283 33.333 0.00 0.00 0.00 4.46
4146 4402 9.492973 GTACAAAGTTAGTATAAAGTTGGGTCA 57.507 33.333 0.00 0.00 0.00 4.02
4148 4404 9.227777 ACAAAGTTAGTATAAAGTTGGGTCATC 57.772 33.333 0.00 0.00 0.00 2.92
4149 4405 9.449719 CAAAGTTAGTATAAAGTTGGGTCATCT 57.550 33.333 0.00 0.00 0.00 2.90
4156 4412 9.408648 AGTATAAAGTTGGGTCATCTATTTTGG 57.591 33.333 0.00 0.00 0.00 3.28
4157 4413 9.403583 GTATAAAGTTGGGTCATCTATTTTGGA 57.596 33.333 0.00 0.00 0.00 3.53
4158 4414 8.893563 ATAAAGTTGGGTCATCTATTTTGGAA 57.106 30.769 0.00 0.00 0.00 3.53
4159 4415 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
4160 4416 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
4161 4417 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
4162 4418 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
4163 4419 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
4164 4420 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
4165 4421 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
4166 4422 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
4167 4423 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
4168 4424 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
4335 4591 8.876790 CAAGAAGAAAATGAAATGGGAATTAGC 58.123 33.333 0.00 0.00 0.00 3.09
4347 4603 5.848286 TGGGAATTAGCATATCAGTGGAT 57.152 39.130 0.00 0.00 37.55 3.41
4359 4615 7.886970 AGCATATCAGTGGATTATATTTGCTGT 59.113 33.333 4.97 0.00 34.89 4.40
4360 4616 7.966753 GCATATCAGTGGATTATATTTGCTGTG 59.033 37.037 0.00 0.00 34.89 3.66
4410 4683 4.725790 ACCATCTTTGAGCAAATTAGGC 57.274 40.909 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.006571 GAACTCGTCCTTGCCGTCA 60.007 57.895 0.00 0.00 0.00 4.35
273 277 7.015487 GCCATGAATAGATGATATCTAGAGGCT 59.985 40.741 3.98 0.00 44.44 4.58
289 293 6.360618 AGGAAGGAAACTAAGCCATGAATAG 58.639 40.000 0.00 0.00 42.68 1.73
349 356 5.755861 TGTCAACACACACGAAAATCTCATA 59.244 36.000 0.00 0.00 0.00 2.15
350 357 4.574421 TGTCAACACACACGAAAATCTCAT 59.426 37.500 0.00 0.00 0.00 2.90
486 497 1.843368 ACCCAGGATCAGTGCAAATG 58.157 50.000 0.00 0.00 0.00 2.32
509 524 1.605710 GAGCAAGACAGCTTCAAGCAA 59.394 47.619 13.10 0.00 46.75 3.91
510 525 1.202734 AGAGCAAGACAGCTTCAAGCA 60.203 47.619 13.10 0.00 46.75 3.91
511 526 1.197264 CAGAGCAAGACAGCTTCAAGC 59.803 52.381 0.00 0.00 46.75 4.01
512 527 2.492012 ACAGAGCAAGACAGCTTCAAG 58.508 47.619 0.00 0.00 46.75 3.02
520 535 3.141398 GTTCCATCAACAGAGCAAGACA 58.859 45.455 0.00 0.00 34.76 3.41
537 552 6.515272 AACATCCTGACAAATATGTGTTCC 57.485 37.500 0.00 0.00 40.74 3.62
587 606 7.711339 GGAAGGATGTTTGGTCAATACTACTAG 59.289 40.741 0.00 0.00 0.00 2.57
612 631 5.592688 CACCAAAGTAGTACCCCATATTTGG 59.407 44.000 20.02 20.02 46.70 3.28
622 641 2.107031 ACCCAACCACCAAAGTAGTACC 59.893 50.000 0.00 0.00 0.00 3.34
650 669 7.736447 ATTCCAGTGTCAAACAAAACAAAAA 57.264 28.000 0.00 0.00 0.00 1.94
651 670 8.091449 ACTATTCCAGTGTCAAACAAAACAAAA 58.909 29.630 0.00 0.00 35.62 2.44
652 671 7.607250 ACTATTCCAGTGTCAAACAAAACAAA 58.393 30.769 0.00 0.00 35.62 2.83
655 674 6.475402 CCAACTATTCCAGTGTCAAACAAAAC 59.525 38.462 0.00 0.00 37.63 2.43
690 709 0.673022 GCAAGACAGACAGCAGGGAG 60.673 60.000 0.00 0.00 0.00 4.30
711 730 3.397482 TGCTGTTTTGCAACACAACTTT 58.603 36.364 18.38 0.00 38.03 2.66
712 731 3.037431 TGCTGTTTTGCAACACAACTT 57.963 38.095 18.38 0.00 38.03 2.66
713 732 2.739885 TGCTGTTTTGCAACACAACT 57.260 40.000 18.38 0.00 38.03 3.16
760 779 4.467438 TGTATCCTGCAAGTGATTCTCAGA 59.533 41.667 0.00 0.00 0.00 3.27
761 780 4.569966 GTGTATCCTGCAAGTGATTCTCAG 59.430 45.833 0.00 0.00 0.00 3.35
762 781 4.507710 GTGTATCCTGCAAGTGATTCTCA 58.492 43.478 0.00 0.00 0.00 3.27
763 782 3.553511 CGTGTATCCTGCAAGTGATTCTC 59.446 47.826 0.00 0.00 0.00 2.87
795 814 2.664081 GGCCCAGACCTGTGAGGAG 61.664 68.421 0.00 0.00 37.67 3.69
796 815 1.811025 TAGGCCCAGACCTGTGAGGA 61.811 60.000 0.00 0.00 41.34 3.71
797 816 1.306141 TAGGCCCAGACCTGTGAGG 60.306 63.158 0.00 0.00 41.34 3.86
798 817 1.901085 GTAGGCCCAGACCTGTGAG 59.099 63.158 0.00 0.00 41.34 3.51
872 921 4.699522 GCTCCGAAAGTGGCCGGT 62.700 66.667 1.90 0.00 45.48 5.28
882 931 2.232399 GGTTTAGTTTTGGGCTCCGAA 58.768 47.619 0.00 0.00 0.00 4.30
913 962 2.821366 GTCTACGGCCGGACGAGA 60.821 66.667 41.17 30.06 37.61 4.04
922 971 1.004595 GATTTTGGGTCGTCTACGGC 58.995 55.000 2.24 0.00 44.28 5.68
926 975 0.108041 GGCGGATTTTGGGTCGTCTA 60.108 55.000 0.00 0.00 0.00 2.59
962 1011 1.066071 GGAGGAACGGAAGGAAGGAAG 60.066 57.143 0.00 0.00 0.00 3.46
1140 1191 3.771160 GCGGAGGCGGAGAAGGAA 61.771 66.667 0.00 0.00 0.00 3.36
1160 1211 4.662961 CGTGCGAGCTGGTGGACA 62.663 66.667 0.00 0.00 0.00 4.02
1398 1452 2.050077 GTTTTGGGCACTCGCAGC 60.050 61.111 0.00 0.00 41.24 5.25
1425 1489 1.599542 GCTGGACATCACGGCTAAATC 59.400 52.381 0.00 0.00 37.26 2.17
1486 1550 2.327325 TCTCCCAGAGGCTACAAGTT 57.673 50.000 0.00 0.00 0.00 2.66
1496 1560 2.697751 CCAAGTACTCCATCTCCCAGAG 59.302 54.545 0.00 0.00 0.00 3.35
1536 1623 3.996150 AAAGCTCAACTGACAATGGTG 57.004 42.857 0.00 0.00 0.00 4.17
1560 1647 1.945394 CTCTCAATTAGGCAATGCGCT 59.055 47.619 9.73 0.01 41.91 5.92
1599 1686 8.198778 TGGACACACTAATAATCGCTATGTTAA 58.801 33.333 0.00 0.00 0.00 2.01
1635 1722 5.477637 CCATGATGGGTGCATATATTGTTGA 59.522 40.000 2.79 0.00 32.67 3.18
1648 1735 1.820906 CTGTCCGCCATGATGGGTG 60.821 63.158 14.26 0.66 38.19 4.61
1756 1846 5.499004 TTAAGAGGGTTAGTGCAAGATGT 57.501 39.130 0.00 0.00 0.00 3.06
1796 1886 0.248458 AAACACGAACAAGGCAAGCG 60.248 50.000 0.00 0.00 0.00 4.68
1804 1894 5.301555 TCCATACTGATCAAACACGAACAA 58.698 37.500 0.00 0.00 0.00 2.83
1841 1931 4.141824 TGTGATGGCCGTATGAATTCAGTA 60.142 41.667 14.54 4.18 0.00 2.74
1856 1946 3.316308 ACTTTGAAGTTCAGTGTGATGGC 59.684 43.478 5.56 0.00 35.21 4.40
1857 1947 5.505173 AACTTTGAAGTTCAGTGTGATGG 57.495 39.130 5.56 0.00 45.65 3.51
1989 2087 3.177884 AGCCTGTGGGGAAGCACA 61.178 61.111 0.00 0.00 37.23 4.57
2039 2137 1.855360 CGAAGCCGAGATAAAGCAGAC 59.145 52.381 0.00 0.00 38.22 3.51
2138 2236 6.906143 CGTCTATTAGAAAGTTACAGACGGAG 59.094 42.308 12.12 0.00 46.07 4.63
2139 2237 6.779117 CGTCTATTAGAAAGTTACAGACGGA 58.221 40.000 12.12 0.00 46.07 4.69
2149 2247 9.636879 GGACTCTAAAAACGTCTATTAGAAAGT 57.363 33.333 14.64 11.39 35.78 2.66
2150 2248 9.635520 TGGACTCTAAAAACGTCTATTAGAAAG 57.364 33.333 14.64 9.26 35.78 2.62
2152 2250 9.582431 CATGGACTCTAAAAACGTCTATTAGAA 57.418 33.333 14.64 5.10 35.78 2.10
2153 2251 8.963725 TCATGGACTCTAAAAACGTCTATTAGA 58.036 33.333 13.64 13.64 35.14 2.10
2154 2252 9.021863 GTCATGGACTCTAAAAACGTCTATTAG 57.978 37.037 0.00 0.00 28.16 1.73
2155 2253 8.525316 TGTCATGGACTCTAAAAACGTCTATTA 58.475 33.333 0.00 0.00 33.15 0.98
2156 2254 7.383687 TGTCATGGACTCTAAAAACGTCTATT 58.616 34.615 0.00 0.00 33.15 1.73
2157 2255 6.931838 TGTCATGGACTCTAAAAACGTCTAT 58.068 36.000 0.00 0.00 33.15 1.98
2158 2256 6.015688 ACTGTCATGGACTCTAAAAACGTCTA 60.016 38.462 0.00 0.00 33.15 2.59
2159 2257 5.209818 TGTCATGGACTCTAAAAACGTCT 57.790 39.130 0.00 0.00 33.15 4.18
2160 2258 4.989168 ACTGTCATGGACTCTAAAAACGTC 59.011 41.667 0.00 0.00 33.15 4.34
2161 2259 4.750098 CACTGTCATGGACTCTAAAAACGT 59.250 41.667 0.00 0.00 33.15 3.99
2162 2260 4.750098 ACACTGTCATGGACTCTAAAAACG 59.250 41.667 0.00 0.00 33.15 3.60
2163 2261 5.758296 TGACACTGTCATGGACTCTAAAAAC 59.242 40.000 7.84 0.00 37.67 2.43
2164 2262 5.924356 TGACACTGTCATGGACTCTAAAAA 58.076 37.500 7.84 0.00 37.67 1.94
2165 2263 5.545063 TGACACTGTCATGGACTCTAAAA 57.455 39.130 7.84 0.00 37.67 1.52
2166 2264 5.545063 TTGACACTGTCATGGACTCTAAA 57.455 39.130 12.71 0.00 42.40 1.85
2167 2265 5.545063 TTTGACACTGTCATGGACTCTAA 57.455 39.130 12.71 0.00 42.40 2.10
2168 2266 5.545063 TTTTGACACTGTCATGGACTCTA 57.455 39.130 12.71 0.00 42.40 2.43
2169 2267 4.422073 TTTTGACACTGTCATGGACTCT 57.578 40.909 12.71 0.00 42.40 3.24
2190 2288 9.449719 CCCTCTGTAACTTAATACAAGACATTT 57.550 33.333 0.00 0.00 35.48 2.32
2191 2289 8.822805 TCCCTCTGTAACTTAATACAAGACATT 58.177 33.333 0.00 0.00 35.48 2.71
2192 2290 8.375493 TCCCTCTGTAACTTAATACAAGACAT 57.625 34.615 0.00 0.00 35.48 3.06
2193 2291 7.453752 ACTCCCTCTGTAACTTAATACAAGACA 59.546 37.037 0.00 0.00 35.48 3.41
2194 2292 7.838884 ACTCCCTCTGTAACTTAATACAAGAC 58.161 38.462 0.00 0.00 35.48 3.01
2195 2293 9.710818 ATACTCCCTCTGTAACTTAATACAAGA 57.289 33.333 0.00 0.00 35.48 3.02
2196 2294 9.968870 GATACTCCCTCTGTAACTTAATACAAG 57.031 37.037 0.00 0.00 35.48 3.16
2197 2295 9.483489 TGATACTCCCTCTGTAACTTAATACAA 57.517 33.333 0.00 0.00 35.48 2.41
2198 2296 9.656323 ATGATACTCCCTCTGTAACTTAATACA 57.344 33.333 0.00 0.00 34.72 2.29
2199 2297 9.915629 CATGATACTCCCTCTGTAACTTAATAC 57.084 37.037 0.00 0.00 0.00 1.89
2200 2298 8.585881 GCATGATACTCCCTCTGTAACTTAATA 58.414 37.037 0.00 0.00 0.00 0.98
2201 2299 7.071196 TGCATGATACTCCCTCTGTAACTTAAT 59.929 37.037 0.00 0.00 0.00 1.40
2202 2300 6.382859 TGCATGATACTCCCTCTGTAACTTAA 59.617 38.462 0.00 0.00 0.00 1.85
2203 2301 5.897250 TGCATGATACTCCCTCTGTAACTTA 59.103 40.000 0.00 0.00 0.00 2.24
2204 2302 4.716784 TGCATGATACTCCCTCTGTAACTT 59.283 41.667 0.00 0.00 0.00 2.66
2205 2303 4.290093 TGCATGATACTCCCTCTGTAACT 58.710 43.478 0.00 0.00 0.00 2.24
2206 2304 4.672587 TGCATGATACTCCCTCTGTAAC 57.327 45.455 0.00 0.00 0.00 2.50
2207 2305 5.246203 GGTATGCATGATACTCCCTCTGTAA 59.754 44.000 10.16 0.00 37.64 2.41
2208 2306 4.772624 GGTATGCATGATACTCCCTCTGTA 59.227 45.833 10.16 0.00 37.64 2.74
2209 2307 3.580458 GGTATGCATGATACTCCCTCTGT 59.420 47.826 10.16 0.00 37.64 3.41
2210 2308 3.055530 GGGTATGCATGATACTCCCTCTG 60.056 52.174 10.16 0.00 37.64 3.35
2211 2309 3.177228 GGGTATGCATGATACTCCCTCT 58.823 50.000 10.16 0.00 37.64 3.69
2212 2310 2.906389 TGGGTATGCATGATACTCCCTC 59.094 50.000 10.16 0.00 37.23 4.30
2213 2311 2.990195 TGGGTATGCATGATACTCCCT 58.010 47.619 10.16 0.00 37.23 4.20
2214 2312 3.788227 TTGGGTATGCATGATACTCCC 57.212 47.619 10.16 11.33 37.23 4.30
2215 2313 5.186198 GGTATTGGGTATGCATGATACTCC 58.814 45.833 10.16 4.29 37.23 3.85
2216 2314 5.643777 GTGGTATTGGGTATGCATGATACTC 59.356 44.000 10.16 0.00 38.40 2.59
2217 2315 5.073008 TGTGGTATTGGGTATGCATGATACT 59.927 40.000 10.16 0.00 37.64 2.12
2218 2316 5.312895 TGTGGTATTGGGTATGCATGATAC 58.687 41.667 10.16 9.34 36.87 2.24
2257 2355 8.119226 GCAACTAACATAATAAGTTCTGAGCTG 58.881 37.037 0.00 0.00 31.21 4.24
2258 2356 7.824289 TGCAACTAACATAATAAGTTCTGAGCT 59.176 33.333 0.00 0.00 31.21 4.09
2296 2394 3.658757 TTGAAACATTAGGTTGCTGCC 57.341 42.857 0.00 0.00 40.35 4.85
2327 2425 4.847198 TGAGTAAGTGCATGGTGATCAAT 58.153 39.130 0.00 0.00 0.00 2.57
2366 2492 7.639113 ATGATGTAAACATAACCCGACATTT 57.361 32.000 0.00 0.00 36.57 2.32
2417 2544 4.929808 AGATGTGAACGACCAAGATGTTAC 59.070 41.667 0.00 0.00 0.00 2.50
2424 2551 5.171476 ACTGATAAGATGTGAACGACCAAG 58.829 41.667 0.00 0.00 0.00 3.61
2553 2680 6.000840 TGGAGAAAATTTTGGGTTATTTGGC 58.999 36.000 8.47 0.00 0.00 4.52
2595 2722 7.961325 AAAAACACACTTGGCATATTTAAGG 57.039 32.000 0.00 0.00 0.00 2.69
2599 2726 8.584157 TGAGATAAAAACACACTTGGCATATTT 58.416 29.630 0.00 0.00 0.00 1.40
2600 2727 8.121305 TGAGATAAAAACACACTTGGCATATT 57.879 30.769 0.00 0.00 0.00 1.28
2601 2728 7.701539 TGAGATAAAAACACACTTGGCATAT 57.298 32.000 0.00 0.00 0.00 1.78
2602 2729 7.537715 CATGAGATAAAAACACACTTGGCATA 58.462 34.615 0.00 0.00 0.00 3.14
2603 2730 6.392354 CATGAGATAAAAACACACTTGGCAT 58.608 36.000 0.00 0.00 0.00 4.40
2604 2731 5.771469 CATGAGATAAAAACACACTTGGCA 58.229 37.500 0.00 0.00 0.00 4.92
2605 2732 4.622740 GCATGAGATAAAAACACACTTGGC 59.377 41.667 0.00 0.00 0.00 4.52
2606 2733 6.017400 AGCATGAGATAAAAACACACTTGG 57.983 37.500 0.00 0.00 0.00 3.61
2607 2734 6.671190 TGAGCATGAGATAAAAACACACTTG 58.329 36.000 0.00 0.00 0.00 3.16
2608 2735 6.882610 TGAGCATGAGATAAAAACACACTT 57.117 33.333 0.00 0.00 0.00 3.16
2609 2736 6.882610 TTGAGCATGAGATAAAAACACACT 57.117 33.333 0.00 0.00 0.00 3.55
2610 2737 7.086376 ACATTGAGCATGAGATAAAAACACAC 58.914 34.615 0.00 0.00 36.24 3.82
2611 2738 7.218228 ACATTGAGCATGAGATAAAAACACA 57.782 32.000 0.00 0.00 36.24 3.72
2612 2739 9.065871 GTAACATTGAGCATGAGATAAAAACAC 57.934 33.333 0.00 0.00 36.24 3.32
2613 2740 8.243426 GGTAACATTGAGCATGAGATAAAAACA 58.757 33.333 0.00 0.00 36.24 2.83
2614 2741 8.243426 TGGTAACATTGAGCATGAGATAAAAAC 58.757 33.333 0.00 0.00 46.17 2.43
2615 2742 8.347004 TGGTAACATTGAGCATGAGATAAAAA 57.653 30.769 0.00 0.00 46.17 1.94
2616 2743 7.936496 TGGTAACATTGAGCATGAGATAAAA 57.064 32.000 0.00 0.00 46.17 1.52
2651 2778 6.070656 ACAGAAGAGAACATTGGAAATGGAA 58.929 36.000 5.08 0.00 0.00 3.53
2655 2782 5.835280 ACCAACAGAAGAGAACATTGGAAAT 59.165 36.000 7.77 0.00 39.15 2.17
2780 2907 6.019640 CAGATTGTTTTGTTACACTTGCCAAG 60.020 38.462 2.11 2.11 0.00 3.61
2896 3023 0.393537 ACCAGTGCTTAGGCTGCATC 60.394 55.000 2.62 0.00 42.69 3.91
3214 3353 8.579863 ACCCATGATTTAGCTAGCATAAATTTC 58.420 33.333 18.83 13.12 33.94 2.17
3296 3438 2.158769 TGGCTTCAGAGTTCAGCAAAGA 60.159 45.455 0.00 0.00 35.05 2.52
3300 3443 0.469494 TGTGGCTTCAGAGTTCAGCA 59.531 50.000 0.00 0.00 35.05 4.41
3350 3493 2.022195 CATTTGAGTAGCCAGCATGCT 58.978 47.619 16.30 16.30 45.38 3.79
3358 3501 6.823689 TGGTTAAGATCTTCATTTGAGTAGCC 59.176 38.462 12.24 3.22 0.00 3.93
3396 3539 2.787473 TAATGGCTTCAGTCCCTGTG 57.213 50.000 0.00 0.00 32.61 3.66
3397 3540 2.912956 TCTTAATGGCTTCAGTCCCTGT 59.087 45.455 0.00 0.00 32.61 4.00
3413 3556 6.194235 ACATTGTAAAGGGGCATCATCTTAA 58.806 36.000 0.00 0.00 0.00 1.85
3544 3687 5.909621 TGTATAAGACAGACCCTGTGTAC 57.090 43.478 4.14 3.80 45.44 2.90
3595 3753 4.274147 ACAACAAGGTTACAATGGTGTGA 58.726 39.130 9.02 0.00 43.01 3.58
3750 3917 6.262944 TGTTTGAGTTCATAGTTGACAGCAAT 59.737 34.615 0.00 0.00 36.22 3.56
3761 3934 6.638468 GCAAGGTTTTCTGTTTGAGTTCATAG 59.362 38.462 0.00 0.00 0.00 2.23
3792 3965 3.511146 ACATTCTTTCCGTGGCAATGAAT 59.489 39.130 0.00 0.00 31.23 2.57
3800 3973 5.064707 CCTGTATGTAACATTCTTTCCGTGG 59.935 44.000 0.00 0.00 37.50 4.94
3804 3977 9.614792 AGATAACCTGTATGTAACATTCTTTCC 57.385 33.333 0.00 0.00 37.50 3.13
4034 4290 6.541111 AGTTTGAATTAACTGAACCTCGAC 57.459 37.500 0.00 0.00 37.00 4.20
4036 4292 9.724839 TTTTAAGTTTGAATTAACTGAACCTCG 57.275 29.630 0.00 0.00 38.33 4.63
4074 4330 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
4075 4331 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
4076 4332 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
4077 4333 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
4078 4334 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
4079 4335 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
4080 4336 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
4081 4337 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
4082 4338 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
4083 4339 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
4084 4340 8.352201 CACAAAGTTGAGTCATCTATTTTGGAA 58.648 33.333 14.35 0.00 40.00 3.53
4085 4341 7.522073 GCACAAAGTTGAGTCATCTATTTTGGA 60.522 37.037 14.35 0.00 40.00 3.53
4086 4342 6.583806 GCACAAAGTTGAGTCATCTATTTTGG 59.416 38.462 14.35 7.81 40.00 3.28
4087 4343 7.365741 AGCACAAAGTTGAGTCATCTATTTTG 58.634 34.615 4.14 8.00 40.82 2.44
4088 4344 7.516198 AGCACAAAGTTGAGTCATCTATTTT 57.484 32.000 4.14 0.00 0.00 1.82
4089 4345 8.507249 GTTAGCACAAAGTTGAGTCATCTATTT 58.493 33.333 4.14 0.00 0.00 1.40
4090 4346 7.880195 AGTTAGCACAAAGTTGAGTCATCTATT 59.120 33.333 4.14 0.00 0.00 1.73
4091 4347 7.390027 AGTTAGCACAAAGTTGAGTCATCTAT 58.610 34.615 4.14 0.00 0.00 1.98
4092 4348 6.759272 AGTTAGCACAAAGTTGAGTCATCTA 58.241 36.000 4.14 0.00 0.00 1.98
4093 4349 5.615289 AGTTAGCACAAAGTTGAGTCATCT 58.385 37.500 0.00 0.00 0.00 2.90
4094 4350 5.931441 AGTTAGCACAAAGTTGAGTCATC 57.069 39.130 0.00 0.00 0.00 2.92
4095 4351 6.699575 AAAGTTAGCACAAAGTTGAGTCAT 57.300 33.333 0.00 0.00 0.00 3.06
4096 4352 6.821665 ACTAAAGTTAGCACAAAGTTGAGTCA 59.178 34.615 0.00 0.00 30.60 3.41
4097 4353 7.247929 ACTAAAGTTAGCACAAAGTTGAGTC 57.752 36.000 0.00 0.00 30.60 3.36
4098 4354 7.767198 TGTACTAAAGTTAGCACAAAGTTGAGT 59.233 33.333 2.29 8.36 37.31 3.41
4099 4355 8.138365 TGTACTAAAGTTAGCACAAAGTTGAG 57.862 34.615 2.29 0.00 34.88 3.02
4100 4356 8.495361 TTGTACTAAAGTTAGCACAAAGTTGA 57.505 30.769 12.43 0.00 41.56 3.18
4119 4375 9.716531 GACCCAACTTTATACTAACTTTGTACT 57.283 33.333 0.00 0.00 0.00 2.73
4120 4376 9.492973 TGACCCAACTTTATACTAACTTTGTAC 57.507 33.333 0.00 0.00 0.00 2.90
4122 4378 9.227777 GATGACCCAACTTTATACTAACTTTGT 57.772 33.333 0.00 0.00 0.00 2.83
4123 4379 9.449719 AGATGACCCAACTTTATACTAACTTTG 57.550 33.333 0.00 0.00 0.00 2.77
4130 4386 9.408648 CCAAAATAGATGACCCAACTTTATACT 57.591 33.333 0.00 0.00 0.00 2.12
4131 4387 9.403583 TCCAAAATAGATGACCCAACTTTATAC 57.596 33.333 0.00 0.00 0.00 1.47
4132 4388 9.983024 TTCCAAAATAGATGACCCAACTTTATA 57.017 29.630 0.00 0.00 0.00 0.98
4133 4389 8.749354 GTTCCAAAATAGATGACCCAACTTTAT 58.251 33.333 0.00 0.00 0.00 1.40
4134 4390 7.094549 CGTTCCAAAATAGATGACCCAACTTTA 60.095 37.037 0.00 0.00 0.00 1.85
4135 4391 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
4136 4392 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
4137 4393 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
4138 4394 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
4139 4395 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
4140 4396 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
4141 4397 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
4142 4398 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
4143 4399 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
4144 4400 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
4145 4401 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
4146 4402 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
4147 4403 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
4148 4404 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
4149 4405 4.098894 AGTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
4150 4406 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
4151 4407 2.332117 AGTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
4152 4408 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
4153 4409 2.042162 ACTAGTACTCCCTCCGTTCCAA 59.958 50.000 0.00 0.00 0.00 3.53
4154 4410 1.637553 ACTAGTACTCCCTCCGTTCCA 59.362 52.381 0.00 0.00 0.00 3.53
4155 4411 2.433662 ACTAGTACTCCCTCCGTTCC 57.566 55.000 0.00 0.00 0.00 3.62
4156 4412 5.904362 TTAAACTAGTACTCCCTCCGTTC 57.096 43.478 0.00 0.00 0.00 3.95
4157 4413 6.864151 ATTTAAACTAGTACTCCCTCCGTT 57.136 37.500 0.00 0.00 0.00 4.44
4158 4414 6.040278 GCTATTTAAACTAGTACTCCCTCCGT 59.960 42.308 0.00 0.00 0.00 4.69
4159 4415 6.264970 AGCTATTTAAACTAGTACTCCCTCCG 59.735 42.308 0.00 0.00 0.00 4.63
4160 4416 7.600231 AGCTATTTAAACTAGTACTCCCTCC 57.400 40.000 0.00 0.00 0.00 4.30
4161 4417 9.964303 GTTAGCTATTTAAACTAGTACTCCCTC 57.036 37.037 0.00 0.00 0.00 4.30
4162 4418 9.484806 TGTTAGCTATTTAAACTAGTACTCCCT 57.515 33.333 0.00 0.00 0.00 4.20
4335 4591 9.223099 TCACAGCAAATATAATCCACTGATATG 57.777 33.333 0.00 0.00 0.00 1.78
4359 4615 5.734720 CTTGTTAAGAGGTTAGCTGGATCA 58.265 41.667 0.00 0.00 0.00 2.92
4360 4616 4.572795 GCTTGTTAAGAGGTTAGCTGGATC 59.427 45.833 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.