Multiple sequence alignment - TraesCS5B01G417400

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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 TraesCS5B01G417400 chr5B 100.000 2696 0 0 1 2696 591837754 591835059 0.000000e+00 4979
1 TraesCS5B01G417400 chr5B 85.921 483 50 6 1 483 592191535 592191071 1.440000e-137 499
2 TraesCS5B01G417400 chr5B 84.344 511 62 9 6 498 592206881 592206371 4.040000e-133 484
3 TraesCS5B01G417400 chr5D 94.922 1418 53 12 711 2121 482598633 482597228 0.000000e+00 2202
4 TraesCS5B01G417400 chr5D 86.640 509 56 5 1 500 482599681 482599176 1.090000e-153 553
5 TraesCS5B01G417400 chr5D 90.461 304 21 2 2381 2677 482597030 482596728 7.000000e-106 394
6 TraesCS5B01G417400 chr5A 93.950 1157 54 9 995 2146 602357090 602355945 0.000000e+00 1735
7 TraesCS5B01G417400 chr5A 83.297 461 56 9 1 442 602358446 602357988 3.230000e-109 405
8 TraesCS5B01G417400 chr5A 87.338 308 20 9 2381 2677 602355930 602355631 4.300000e-88 335
9 TraesCS5B01G417400 chr5A 79.747 395 64 12 6 393 602379144 602378759 3.420000e-69 272
10 TraesCS5B01G417400 chr6B 93.434 198 12 1 2155 2352 579885960 579885764 2.630000e-75 292
11 TraesCS5B01G417400 chr7B 91.827 208 17 0 2155 2362 385068977 385068770 9.440000e-75 291
12 TraesCS5B01G417400 chr4B 90.090 222 18 4 2140 2358 171652291 171652511 4.390000e-73 285
13 TraesCS5B01G417400 chr1D 91.388 209 16 2 2151 2359 46330830 46331036 4.390000e-73 285
14 TraesCS5B01G417400 chr1D 90.995 211 18 1 2152 2362 422682697 422682906 1.580000e-72 283
15 TraesCS5B01G417400 chr1D 88.696 230 22 3 2134 2360 64887437 64887665 7.350000e-71 278
16 TraesCS5B01G417400 chr3D 91.346 208 17 1 2151 2358 108290855 108291061 1.580000e-72 283
17 TraesCS5B01G417400 chr2B 89.954 219 19 3 2144 2362 621058581 621058366 2.040000e-71 279
18 TraesCS5B01G417400 chr7A 91.176 204 18 0 2155 2358 50426937 50427140 7.350000e-71 278


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 TraesCS5B01G417400 chr5B 591835059 591837754 2695 True 4979.000000 4979 100.000000 1 2696 1 chr5B.!!$R1 2695
1 TraesCS5B01G417400 chr5B 592206371 592206881 510 True 484.000000 484 84.344000 6 498 1 chr5B.!!$R3 492
2 TraesCS5B01G417400 chr5D 482596728 482599681 2953 True 1049.666667 2202 90.674333 1 2677 3 chr5D.!!$R1 2676
3 TraesCS5B01G417400 chr5A 602355631 602358446 2815 True 825.000000 1735 88.195000 1 2677 3 chr5A.!!$R2 2676

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
278 286 0.035458 AGCTGCACTACCTTGTCCAC 59.965 55.0 1.02 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1795 2647 0.321919 TCAGTCAGTTGAGCCATGCC 60.322 55.0 0.0 0.0 0.0 4.4 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
31 32 5.344743 GAGCATTCCTCGGGATGAATATA 57.655 43.478 8.44 0.00 30.31 0.86
87 88 1.134699 GGCATGACGGATCTGAGACAA 60.135 52.381 9.00 0.00 0.00 3.18
159 160 9.302345 ACATTGATAGTCATGTCTAGTTTAACG 57.698 33.333 5.90 0.00 0.00 3.18
195 196 4.250305 ACCCACGTGGACAGTGCC 62.250 66.667 36.07 0.00 38.22 5.01
217 218 4.690280 CCACATGTAAAATTGCAAACCCTC 59.310 41.667 1.71 0.00 0.00 4.30
219 220 3.651803 TGTAAAATTGCAAACCCTCGG 57.348 42.857 1.71 0.00 0.00 4.63
230 231 3.491792 GCAAACCCTCGGACAAAATTCAA 60.492 43.478 0.00 0.00 0.00 2.69
232 233 5.296748 CAAACCCTCGGACAAAATTCAATT 58.703 37.500 0.00 0.00 0.00 2.32
260 261 0.886490 GTGGTGAGGTGTTGGAGCAG 60.886 60.000 0.00 0.00 0.00 4.24
261 262 1.968540 GGTGAGGTGTTGGAGCAGC 60.969 63.158 0.00 0.00 37.16 5.25
266 267 2.641559 GTGTTGGAGCAGCTGCAC 59.358 61.111 38.24 32.03 45.16 4.57
272 280 1.298014 GGAGCAGCTGCACTACCTT 59.702 57.895 38.24 17.87 45.16 3.50
278 286 0.035458 AGCTGCACTACCTTGTCCAC 59.965 55.000 1.02 0.00 0.00 4.02
307 328 3.057104 GGTATTTCCCCTTGTTGTTTCGG 60.057 47.826 0.00 0.00 0.00 4.30
325 346 1.597445 CGGTCGTCTCTAGAAATCGCC 60.597 57.143 0.00 4.61 0.00 5.54
372 397 4.454678 CCACACTATGTATGTGCCATCTT 58.545 43.478 0.00 0.00 45.05 2.40
394 419 9.801873 ATCTTACAAAAATTCAAACCCATATCG 57.198 29.630 0.00 0.00 0.00 2.92
420 445 3.852572 GCAGAGCTCAAGAAACAAGCAAG 60.853 47.826 17.77 0.00 38.51 4.01
425 451 1.946768 TCAAGAAACAAGCAAGACGGG 59.053 47.619 0.00 0.00 0.00 5.28
434 460 0.321653 AGCAAGACGGGTCCAATGTC 60.322 55.000 0.00 0.00 0.00 3.06
449 717 3.120546 CCAATGTCGAACAGTAGCAAGTG 60.121 47.826 0.00 0.00 0.00 3.16
465 733 6.246420 AGCAAGTGATTCAAATCAGTACAC 57.754 37.500 12.28 6.45 45.74 2.90
495 766 2.151202 CTACCATCACCACCAACACAC 58.849 52.381 0.00 0.00 0.00 3.82
500 771 1.304254 TCACCACCAACACACGATTG 58.696 50.000 0.00 0.00 0.00 2.67
507 860 3.708563 CCAACACACGATTGGTTTCTT 57.291 42.857 0.00 0.00 41.55 2.52
509 862 4.429108 CCAACACACGATTGGTTTCTTTT 58.571 39.130 0.00 0.00 41.55 2.27
561 914 3.831715 AACACGATTTTTGCTAGGCTC 57.168 42.857 0.00 0.00 0.00 4.70
562 915 1.732259 ACACGATTTTTGCTAGGCTCG 59.268 47.619 0.00 0.00 0.00 5.03
568 921 1.961793 TTTTGCTAGGCTCGTGTGTT 58.038 45.000 0.00 0.00 0.00 3.32
572 925 4.459390 TTGCTAGGCTCGTGTGTTTATA 57.541 40.909 0.00 0.00 0.00 0.98
582 935 6.349033 GGCTCGTGTGTTTATATTCCTTGTTT 60.349 38.462 0.00 0.00 0.00 2.83
583 936 7.148373 GGCTCGTGTGTTTATATTCCTTGTTTA 60.148 37.037 0.00 0.00 0.00 2.01
584 937 7.691050 GCTCGTGTGTTTATATTCCTTGTTTAC 59.309 37.037 0.00 0.00 0.00 2.01
585 938 8.604640 TCGTGTGTTTATATTCCTTGTTTACA 57.395 30.769 0.00 0.00 0.00 2.41
586 939 8.714179 TCGTGTGTTTATATTCCTTGTTTACAG 58.286 33.333 0.00 0.00 0.00 2.74
595 948 8.706322 ATATTCCTTGTTTACAGTTTCCAACT 57.294 30.769 0.00 0.00 44.06 3.16
616 969 3.325870 TGATAGAGGCAAACTTGTCACG 58.674 45.455 0.00 0.00 34.61 4.35
618 971 0.180406 AGAGGCAAACTTGTCACGGT 59.820 50.000 0.00 0.00 34.61 4.83
641 994 7.797123 CGGTTGACTGAATAAAACAGTAGAAAC 59.203 37.037 0.00 0.00 46.57 2.78
642 995 8.074370 GGTTGACTGAATAAAACAGTAGAAACC 58.926 37.037 16.32 16.32 46.57 3.27
646 999 6.145048 ACTGAATAAAACAGTAGAAACCGACG 59.855 38.462 0.00 0.00 45.10 5.12
648 1001 6.144402 TGAATAAAACAGTAGAAACCGACGTC 59.856 38.462 5.18 5.18 0.00 4.34
661 1033 3.358076 GACGTCCCCGGAGCTTCTG 62.358 68.421 0.73 0.00 38.78 3.02
670 1042 2.226674 CCCGGAGCTTCTGTTTTCTTTC 59.773 50.000 0.73 0.00 0.00 2.62
671 1043 3.142174 CCGGAGCTTCTGTTTTCTTTCT 58.858 45.455 0.00 0.00 0.00 2.52
674 1046 5.238650 CCGGAGCTTCTGTTTTCTTTCTTTA 59.761 40.000 0.00 0.00 0.00 1.85
675 1047 6.072452 CCGGAGCTTCTGTTTTCTTTCTTTAT 60.072 38.462 0.00 0.00 0.00 1.40
676 1048 7.363431 CGGAGCTTCTGTTTTCTTTCTTTATT 58.637 34.615 0.00 0.00 0.00 1.40
677 1049 7.862873 CGGAGCTTCTGTTTTCTTTCTTTATTT 59.137 33.333 0.00 0.00 0.00 1.40
679 1051 8.357796 AGCTTCTGTTTTCTTTCTTTATTTGC 57.642 30.769 0.00 0.00 0.00 3.68
681 1053 8.820933 GCTTCTGTTTTCTTTCTTTATTTGCTT 58.179 29.630 0.00 0.00 0.00 3.91
723 1331 4.011966 AGACTGACACATGAAATCTGCA 57.988 40.909 0.00 0.00 0.00 4.41
729 1337 4.037089 TGACACATGAAATCTGCATATGGC 59.963 41.667 4.56 0.00 45.13 4.40
1103 1955 4.069232 CTCCTGCTCCGCGTCCAA 62.069 66.667 4.92 0.00 0.00 3.53
1500 2352 0.382158 TGCTCTTCCTCTACATCGCG 59.618 55.000 0.00 0.00 0.00 5.87
1503 2355 1.107538 TCTTCCTCTACATCGCGGGG 61.108 60.000 6.13 0.36 0.00 5.73
1734 2586 1.218316 GTTGGCTAGTCGGTCCCAG 59.782 63.158 0.00 0.00 0.00 4.45
1735 2587 1.987855 TTGGCTAGTCGGTCCCAGG 60.988 63.158 0.00 0.00 0.00 4.45
1768 2620 1.430632 CATCCATGCCTGAACGTGC 59.569 57.895 0.00 0.00 0.00 5.34
1769 2621 1.028330 CATCCATGCCTGAACGTGCT 61.028 55.000 0.00 0.00 0.00 4.40
1770 2622 0.745845 ATCCATGCCTGAACGTGCTC 60.746 55.000 0.00 0.00 0.00 4.26
1771 2623 1.376424 CCATGCCTGAACGTGCTCT 60.376 57.895 0.00 0.00 0.00 4.09
1772 2624 1.642037 CCATGCCTGAACGTGCTCTG 61.642 60.000 0.00 0.00 0.00 3.35
1773 2625 2.037136 ATGCCTGAACGTGCTCTGC 61.037 57.895 0.00 0.00 0.00 4.26
1774 2626 2.358003 GCCTGAACGTGCTCTGCT 60.358 61.111 0.00 0.00 0.00 4.24
1775 2627 2.386660 GCCTGAACGTGCTCTGCTC 61.387 63.158 0.00 0.00 0.00 4.26
1776 2628 1.291588 CCTGAACGTGCTCTGCTCT 59.708 57.895 0.00 0.00 0.00 4.09
1777 2629 1.013005 CCTGAACGTGCTCTGCTCTG 61.013 60.000 0.00 0.00 0.00 3.35
1779 2631 1.665916 GAACGTGCTCTGCTCTGCA 60.666 57.895 0.00 0.00 36.92 4.41
1780 2632 1.004080 AACGTGCTCTGCTCTGCAT 60.004 52.632 0.00 0.00 41.45 3.96
1781 2633 1.018226 AACGTGCTCTGCTCTGCATC 61.018 55.000 0.00 0.00 41.45 3.91
1782 2634 1.153608 CGTGCTCTGCTCTGCATCT 60.154 57.895 0.00 0.00 41.45 2.90
1783 2635 1.422179 CGTGCTCTGCTCTGCATCTG 61.422 60.000 0.00 0.00 41.45 2.90
1784 2636 0.391395 GTGCTCTGCTCTGCATCTGT 60.391 55.000 0.00 0.00 41.45 3.41
1785 2637 0.391263 TGCTCTGCTCTGCATCTGTG 60.391 55.000 0.00 0.00 38.13 3.66
1786 2638 0.391395 GCTCTGCTCTGCATCTGTGT 60.391 55.000 0.00 0.00 38.13 3.72
1787 2639 1.642728 CTCTGCTCTGCATCTGTGTC 58.357 55.000 0.00 0.00 38.13 3.67
1788 2640 0.971386 TCTGCTCTGCATCTGTGTCA 59.029 50.000 0.00 0.00 38.13 3.58
1789 2641 1.553704 TCTGCTCTGCATCTGTGTCAT 59.446 47.619 0.00 0.00 38.13 3.06
1790 2642 2.762327 TCTGCTCTGCATCTGTGTCATA 59.238 45.455 0.00 0.00 38.13 2.15
1791 2643 2.864946 CTGCTCTGCATCTGTGTCATAC 59.135 50.000 0.00 0.00 38.13 2.39
1792 2644 2.208431 GCTCTGCATCTGTGTCATACC 58.792 52.381 0.00 0.00 0.00 2.73
1793 2645 2.419159 GCTCTGCATCTGTGTCATACCA 60.419 50.000 0.00 0.00 0.00 3.25
1794 2646 3.743584 GCTCTGCATCTGTGTCATACCAT 60.744 47.826 0.00 0.00 0.00 3.55
1795 2647 3.800531 TCTGCATCTGTGTCATACCATG 58.199 45.455 0.00 0.00 0.00 3.66
1796 2648 2.876550 CTGCATCTGTGTCATACCATGG 59.123 50.000 11.19 11.19 0.00 3.66
1808 2660 4.349682 CCATGGCATGGCTCAACT 57.650 55.556 31.96 0.00 44.70 3.16
1811 2677 0.454600 CATGGCATGGCTCAACTGAC 59.545 55.000 19.80 0.00 0.00 3.51
1813 2679 0.607217 TGGCATGGCTCAACTGACTG 60.607 55.000 21.08 0.00 0.00 3.51
1824 2690 5.174395 GCTCAACTGACTGATGTATCTTGT 58.826 41.667 0.00 0.00 0.00 3.16
1829 2695 6.352016 ACTGACTGATGTATCTTGTGTTCT 57.648 37.500 0.00 0.00 0.00 3.01
1865 2734 1.713005 ATGGGCAGCGGAGGATTGAT 61.713 55.000 0.00 0.00 0.00 2.57
1866 2735 1.895707 GGGCAGCGGAGGATTGATG 60.896 63.158 0.00 0.00 0.00 3.07
1867 2736 1.146930 GGCAGCGGAGGATTGATGA 59.853 57.895 0.00 0.00 0.00 2.92
1916 2785 3.398318 TGGTGTAGGAGCTGATAGGAA 57.602 47.619 0.00 0.00 0.00 3.36
1994 2867 7.664082 AACTATTGTGTTCTCTCTTCACATG 57.336 36.000 0.00 0.00 40.85 3.21
2074 2947 3.979948 TGAGTGAAAATGTGCCAACATG 58.020 40.909 0.00 0.00 46.58 3.21
2147 3178 7.916077 AGGTATAAGCCAAATGTCTACTACT 57.084 36.000 0.00 0.00 0.00 2.57
2148 3179 7.953752 AGGTATAAGCCAAATGTCTACTACTC 58.046 38.462 0.00 0.00 0.00 2.59
2149 3180 7.015389 AGGTATAAGCCAAATGTCTACTACTCC 59.985 40.741 0.00 0.00 0.00 3.85
2150 3181 4.489306 AAGCCAAATGTCTACTACTCCC 57.511 45.455 0.00 0.00 0.00 4.30
2151 3182 3.725634 AGCCAAATGTCTACTACTCCCT 58.274 45.455 0.00 0.00 0.00 4.20
2152 3183 3.707102 AGCCAAATGTCTACTACTCCCTC 59.293 47.826 0.00 0.00 0.00 4.30
2153 3184 3.181464 GCCAAATGTCTACTACTCCCTCC 60.181 52.174 0.00 0.00 0.00 4.30
2154 3185 3.068307 CCAAATGTCTACTACTCCCTCCG 59.932 52.174 0.00 0.00 0.00 4.63
2155 3186 3.666345 AATGTCTACTACTCCCTCCGT 57.334 47.619 0.00 0.00 0.00 4.69
2156 3187 3.666345 ATGTCTACTACTCCCTCCGTT 57.334 47.619 0.00 0.00 0.00 4.44
2157 3188 3.446442 TGTCTACTACTCCCTCCGTTT 57.554 47.619 0.00 0.00 0.00 3.60
2158 3189 4.574674 TGTCTACTACTCCCTCCGTTTA 57.425 45.455 0.00 0.00 0.00 2.01
2159 3190 4.265073 TGTCTACTACTCCCTCCGTTTAC 58.735 47.826 0.00 0.00 0.00 2.01
2160 3191 4.263462 TGTCTACTACTCCCTCCGTTTACA 60.263 45.833 0.00 0.00 0.00 2.41
2161 3192 4.702131 GTCTACTACTCCCTCCGTTTACAA 59.298 45.833 0.00 0.00 0.00 2.41
2162 3193 4.946157 TCTACTACTCCCTCCGTTTACAAG 59.054 45.833 0.00 0.00 0.00 3.16
2163 3194 3.504375 ACTACTCCCTCCGTTTACAAGT 58.496 45.455 0.00 0.00 0.00 3.16
2164 3195 3.509184 ACTACTCCCTCCGTTTACAAGTC 59.491 47.826 0.00 0.00 0.00 3.01
2165 3196 1.622312 ACTCCCTCCGTTTACAAGTCC 59.378 52.381 0.00 0.00 0.00 3.85
2166 3197 1.900486 CTCCCTCCGTTTACAAGTCCT 59.100 52.381 0.00 0.00 0.00 3.85
2167 3198 3.094572 CTCCCTCCGTTTACAAGTCCTA 58.905 50.000 0.00 0.00 0.00 2.94
2168 3199 2.827921 TCCCTCCGTTTACAAGTCCTAC 59.172 50.000 0.00 0.00 0.00 3.18
2169 3200 2.416431 CCCTCCGTTTACAAGTCCTACG 60.416 54.545 0.00 0.00 0.00 3.51
2170 3201 2.257034 CTCCGTTTACAAGTCCTACGC 58.743 52.381 0.00 0.00 0.00 4.42
2171 3202 1.612950 TCCGTTTACAAGTCCTACGCA 59.387 47.619 0.00 0.00 0.00 5.24
2172 3203 2.231964 TCCGTTTACAAGTCCTACGCAT 59.768 45.455 0.00 0.00 0.00 4.73
2173 3204 3.443329 TCCGTTTACAAGTCCTACGCATA 59.557 43.478 0.00 0.00 0.00 3.14
2174 3205 4.098349 TCCGTTTACAAGTCCTACGCATAT 59.902 41.667 0.00 0.00 0.00 1.78
2175 3206 5.299028 TCCGTTTACAAGTCCTACGCATATA 59.701 40.000 0.00 0.00 0.00 0.86
2176 3207 5.400485 CCGTTTACAAGTCCTACGCATATAC 59.600 44.000 0.00 0.00 0.00 1.47
2177 3208 5.400485 CGTTTACAAGTCCTACGCATATACC 59.600 44.000 0.00 0.00 0.00 2.73
2178 3209 6.510536 GTTTACAAGTCCTACGCATATACCT 58.489 40.000 0.00 0.00 0.00 3.08
2179 3210 7.520453 CGTTTACAAGTCCTACGCATATACCTA 60.520 40.741 0.00 0.00 0.00 3.08
2180 3211 7.822161 TTACAAGTCCTACGCATATACCTAA 57.178 36.000 0.00 0.00 0.00 2.69
2181 3212 6.328641 ACAAGTCCTACGCATATACCTAAG 57.671 41.667 0.00 0.00 0.00 2.18
2182 3213 5.832060 ACAAGTCCTACGCATATACCTAAGT 59.168 40.000 0.00 0.00 0.00 2.24
2183 3214 6.323225 ACAAGTCCTACGCATATACCTAAGTT 59.677 38.462 0.00 0.00 0.00 2.66
2184 3215 6.328641 AGTCCTACGCATATACCTAAGTTG 57.671 41.667 0.00 0.00 0.00 3.16
2185 3216 5.832060 AGTCCTACGCATATACCTAAGTTGT 59.168 40.000 0.00 0.00 0.00 3.32
2186 3217 6.016443 AGTCCTACGCATATACCTAAGTTGTC 60.016 42.308 0.00 0.00 0.00 3.18
2187 3218 5.829391 TCCTACGCATATACCTAAGTTGTCA 59.171 40.000 0.00 0.00 0.00 3.58
2188 3219 6.321945 TCCTACGCATATACCTAAGTTGTCAA 59.678 38.462 0.00 0.00 0.00 3.18
2189 3220 7.014905 TCCTACGCATATACCTAAGTTGTCAAT 59.985 37.037 0.00 0.00 0.00 2.57
2190 3221 7.656137 CCTACGCATATACCTAAGTTGTCAATT 59.344 37.037 0.00 0.00 0.00 2.32
2191 3222 7.859325 ACGCATATACCTAAGTTGTCAATTT 57.141 32.000 0.00 0.00 0.00 1.82
2192 3223 8.276252 ACGCATATACCTAAGTTGTCAATTTT 57.724 30.769 0.00 0.00 0.00 1.82
2193 3224 9.386010 ACGCATATACCTAAGTTGTCAATTTTA 57.614 29.630 0.00 0.00 0.00 1.52
2199 3230 7.462571 ACCTAAGTTGTCAATTTTATCACCC 57.537 36.000 0.00 0.00 0.00 4.61
2200 3231 7.238710 ACCTAAGTTGTCAATTTTATCACCCT 58.761 34.615 0.00 0.00 0.00 4.34
2201 3232 7.176690 ACCTAAGTTGTCAATTTTATCACCCTG 59.823 37.037 0.00 0.00 0.00 4.45
2202 3233 7.393234 CCTAAGTTGTCAATTTTATCACCCTGA 59.607 37.037 0.00 0.00 0.00 3.86
2203 3234 7.781324 AAGTTGTCAATTTTATCACCCTGAT 57.219 32.000 0.00 0.00 40.72 2.90
2204 3235 8.877864 AAGTTGTCAATTTTATCACCCTGATA 57.122 30.769 0.00 0.00 38.26 2.15
2205 3236 9.479549 AAGTTGTCAATTTTATCACCCTGATAT 57.520 29.630 0.00 0.00 38.94 1.63
2209 3240 9.778741 TGTCAATTTTATCACCCTGATATAGAC 57.221 33.333 0.00 0.00 38.94 2.59
2253 3284 7.921786 ACGGTTTGAAAATAGATCATCTGAA 57.078 32.000 0.00 0.00 0.00 3.02
2254 3285 7.978982 ACGGTTTGAAAATAGATCATCTGAAG 58.021 34.615 0.00 0.00 0.00 3.02
2255 3286 7.607991 ACGGTTTGAAAATAGATCATCTGAAGT 59.392 33.333 0.00 0.00 0.00 3.01
2256 3287 8.454106 CGGTTTGAAAATAGATCATCTGAAGTT 58.546 33.333 0.00 0.00 0.00 2.66
2307 3338 9.920946 ATATGACTTGTATTAGGTTGGTCAAAT 57.079 29.630 0.00 0.00 36.16 2.32
2308 3339 8.650143 ATGACTTGTATTAGGTTGGTCAAATT 57.350 30.769 0.00 0.00 36.16 1.82
2309 3340 7.881142 TGACTTGTATTAGGTTGGTCAAATTG 58.119 34.615 0.00 0.00 30.81 2.32
2310 3341 7.721842 TGACTTGTATTAGGTTGGTCAAATTGA 59.278 33.333 0.00 0.00 30.81 2.57
2311 3342 7.882179 ACTTGTATTAGGTTGGTCAAATTGAC 58.118 34.615 17.16 17.16 46.23 3.18
2326 3357 8.281212 GTCAAATTGACAACTTAGGGATATGT 57.719 34.615 20.08 0.00 46.22 2.29
2327 3358 8.184192 GTCAAATTGACAACTTAGGGATATGTG 58.816 37.037 20.08 0.00 46.22 3.21
2328 3359 6.699575 AATTGACAACTTAGGGATATGTGC 57.300 37.500 0.00 0.00 0.00 4.57
2329 3360 4.835284 TGACAACTTAGGGATATGTGCA 57.165 40.909 0.00 0.00 0.00 4.57
2330 3361 4.513442 TGACAACTTAGGGATATGTGCAC 58.487 43.478 10.75 10.75 0.00 4.57
2331 3362 3.531538 ACAACTTAGGGATATGTGCACG 58.468 45.455 13.13 0.00 0.00 5.34
2332 3363 2.240493 ACTTAGGGATATGTGCACGC 57.760 50.000 13.13 1.21 0.00 5.34
2333 3364 1.202651 ACTTAGGGATATGTGCACGCC 60.203 52.381 13.13 10.56 0.00 5.68
2334 3365 0.107831 TTAGGGATATGTGCACGCCC 59.892 55.000 22.22 22.22 39.12 6.13
2335 3366 2.072487 AGGGATATGTGCACGCCCT 61.072 57.895 25.08 25.08 44.17 5.19
2336 3367 0.762842 AGGGATATGTGCACGCCCTA 60.763 55.000 27.75 12.41 47.00 3.53
2337 3368 0.324943 GGGATATGTGCACGCCCTAT 59.675 55.000 22.36 12.90 35.86 2.57
2338 3369 1.553248 GGGATATGTGCACGCCCTATA 59.447 52.381 22.36 11.60 35.86 1.31
2339 3370 2.027561 GGGATATGTGCACGCCCTATAA 60.028 50.000 22.36 1.21 35.86 0.98
2340 3371 3.558321 GGGATATGTGCACGCCCTATAAA 60.558 47.826 22.36 0.53 35.86 1.40
2341 3372 3.435671 GGATATGTGCACGCCCTATAAAC 59.564 47.826 13.13 3.41 0.00 2.01
2342 3373 2.710096 ATGTGCACGCCCTATAAACT 57.290 45.000 13.13 0.00 0.00 2.66
2343 3374 1.732941 TGTGCACGCCCTATAAACTG 58.267 50.000 13.13 0.00 0.00 3.16
2344 3375 1.276705 TGTGCACGCCCTATAAACTGA 59.723 47.619 13.13 0.00 0.00 3.41
2345 3376 1.933853 GTGCACGCCCTATAAACTGAG 59.066 52.381 0.00 0.00 0.00 3.35
2346 3377 1.828595 TGCACGCCCTATAAACTGAGA 59.171 47.619 0.00 0.00 0.00 3.27
2347 3378 2.159099 TGCACGCCCTATAAACTGAGAG 60.159 50.000 0.00 0.00 0.00 3.20
2348 3379 2.100916 GCACGCCCTATAAACTGAGAGA 59.899 50.000 0.00 0.00 0.00 3.10
2349 3380 3.797184 GCACGCCCTATAAACTGAGAGAG 60.797 52.174 0.00 0.00 0.00 3.20
2350 3381 3.632604 CACGCCCTATAAACTGAGAGAGA 59.367 47.826 0.00 0.00 0.00 3.10
2351 3382 3.886505 ACGCCCTATAAACTGAGAGAGAG 59.113 47.826 0.00 0.00 0.00 3.20
2352 3383 3.254657 CGCCCTATAAACTGAGAGAGAGG 59.745 52.174 0.00 0.00 0.00 3.69
2353 3384 3.576550 GCCCTATAAACTGAGAGAGAGGG 59.423 52.174 7.90 7.90 44.52 4.30
2354 3385 4.693058 GCCCTATAAACTGAGAGAGAGGGA 60.693 50.000 14.02 0.00 44.48 4.20
2355 3386 5.076873 CCCTATAAACTGAGAGAGAGGGAG 58.923 50.000 6.82 0.00 44.48 4.30
2356 3387 5.399727 CCCTATAAACTGAGAGAGAGGGAGT 60.400 48.000 6.82 0.00 44.48 3.85
2357 3388 6.183361 CCCTATAAACTGAGAGAGAGGGAGTA 60.183 46.154 6.82 0.00 44.48 2.59
2378 3409 7.377766 AGTAGCAAACTTAACATACATGGTG 57.622 36.000 0.00 0.00 33.35 4.17
2379 3410 6.940298 AGTAGCAAACTTAACATACATGGTGT 59.060 34.615 0.00 0.00 33.35 4.16
2380 3411 6.254281 AGCAAACTTAACATACATGGTGTC 57.746 37.500 6.48 0.00 0.00 3.67
2381 3412 5.767665 AGCAAACTTAACATACATGGTGTCA 59.232 36.000 6.48 0.00 0.00 3.58
2382 3413 6.434028 AGCAAACTTAACATACATGGTGTCAT 59.566 34.615 6.48 0.00 0.00 3.06
2427 3458 2.105006 ATGACAGATCTGCGTTGCTT 57.895 45.000 22.83 0.53 0.00 3.91
2450 3481 6.474140 TCTCAGAAACACTACACCAACTTA 57.526 37.500 0.00 0.00 0.00 2.24
2479 3528 8.567948 CACACTGAAATACTTAAATCACTGGTT 58.432 33.333 0.00 0.00 0.00 3.67
2480 3529 8.567948 ACACTGAAATACTTAAATCACTGGTTG 58.432 33.333 0.00 0.00 0.00 3.77
2481 3530 7.538678 CACTGAAATACTTAAATCACTGGTTGC 59.461 37.037 0.00 0.00 0.00 4.17
2482 3531 6.919721 TGAAATACTTAAATCACTGGTTGCC 58.080 36.000 0.00 0.00 0.00 4.52
2483 3532 6.491745 TGAAATACTTAAATCACTGGTTGCCA 59.508 34.615 0.00 0.00 0.00 4.92
2484 3533 5.897377 ATACTTAAATCACTGGTTGCCAC 57.103 39.130 0.00 0.00 0.00 5.01
2485 3534 3.832527 ACTTAAATCACTGGTTGCCACT 58.167 40.909 0.00 0.00 0.00 4.00
2513 3562 7.259161 CCACCATCTTGTTTAGTCTAGTAGAC 58.741 42.308 20.73 20.73 45.38 2.59
2542 3591 7.593825 AGTCTGTATTGCTGAAATTTAACCAC 58.406 34.615 0.00 0.00 0.00 4.16
2625 3680 8.306761 GCAAGGAAAGGAAGATCTTAAATTCAA 58.693 33.333 8.25 0.00 0.00 2.69
2631 3686 5.654209 AGGAAGATCTTAAATTCAAGCCCAC 59.346 40.000 8.25 0.00 0.00 4.61
2640 3695 5.622346 AAATTCAAGCCCACTTTTAACCA 57.378 34.783 0.00 0.00 32.29 3.67
2677 3732 5.049267 GGTTTCAACAGCTTGGTACGATTAA 60.049 40.000 0.00 0.00 0.00 1.40
2678 3733 6.349033 GGTTTCAACAGCTTGGTACGATTAAT 60.349 38.462 0.00 0.00 0.00 1.40
2679 3734 6.811253 TTCAACAGCTTGGTACGATTAATT 57.189 33.333 0.00 0.00 0.00 1.40
2680 3735 6.811253 TCAACAGCTTGGTACGATTAATTT 57.189 33.333 0.00 0.00 0.00 1.82
2681 3736 7.209471 TCAACAGCTTGGTACGATTAATTTT 57.791 32.000 0.00 0.00 0.00 1.82
2682 3737 7.653647 TCAACAGCTTGGTACGATTAATTTTT 58.346 30.769 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 5.402630 ACCACCCATTCCAAAGTAGAAAAT 58.597 37.500 0.00 0.00 0.00 1.82
49 50 4.164843 TGCCTAATTTCCAGATACCACC 57.835 45.455 0.00 0.00 0.00 4.61
142 143 6.388278 AGGAAGTCGTTAAACTAGACATGAC 58.612 40.000 0.00 0.00 37.36 3.06
195 196 4.385447 CGAGGGTTTGCAATTTTACATGTG 59.615 41.667 9.11 0.00 0.00 3.21
217 218 4.507388 ACAGCAACAATTGAATTTTGTCCG 59.493 37.500 13.59 2.25 36.32 4.79
219 220 6.186785 CACACAGCAACAATTGAATTTTGTC 58.813 36.000 13.59 3.20 36.32 3.18
230 231 1.321474 CCTCACCACACAGCAACAAT 58.679 50.000 0.00 0.00 0.00 2.71
232 233 0.747644 CACCTCACCACACAGCAACA 60.748 55.000 0.00 0.00 0.00 3.33
260 261 1.291877 CGTGGACAAGGTAGTGCAGC 61.292 60.000 0.00 0.00 40.60 5.25
261 262 0.033504 ACGTGGACAAGGTAGTGCAG 59.966 55.000 0.00 0.00 40.60 4.41
266 267 1.497991 CACACACGTGGACAAGGTAG 58.502 55.000 21.57 0.56 39.64 3.18
278 286 1.810151 CAAGGGGAAATACCACACACG 59.190 52.381 0.00 0.00 46.31 4.49
307 328 2.846039 TGGCGATTTCTAGAGACGAC 57.154 50.000 15.65 13.92 0.00 4.34
372 397 9.579768 CAATCGATATGGGTTTGAATTTTTGTA 57.420 29.630 0.00 0.00 0.00 2.41
394 419 4.474113 CTTGTTTCTTGAGCTCTGCAATC 58.526 43.478 16.19 4.58 0.00 2.67
397 422 1.605710 GCTTGTTTCTTGAGCTCTGCA 59.394 47.619 16.19 2.16 33.72 4.41
420 445 0.320073 TGTTCGACATTGGACCCGTC 60.320 55.000 0.00 0.00 0.00 4.79
425 451 2.683968 TGCTACTGTTCGACATTGGAC 58.316 47.619 0.00 0.00 0.00 4.02
434 460 4.990543 TTGAATCACTTGCTACTGTTCG 57.009 40.909 0.00 0.00 0.00 3.95
449 717 5.618561 GGTGTTCGTGTACTGATTTGAATC 58.381 41.667 0.00 0.00 35.97 2.52
461 729 1.177895 TGGTAGGCGGTGTTCGTGTA 61.178 55.000 0.00 0.00 41.72 2.90
465 733 1.082117 GTGATGGTAGGCGGTGTTCG 61.082 60.000 0.00 0.00 42.76 3.95
547 900 2.504367 ACACACGAGCCTAGCAAAAAT 58.496 42.857 0.00 0.00 0.00 1.82
548 901 1.961793 ACACACGAGCCTAGCAAAAA 58.038 45.000 0.00 0.00 0.00 1.94
561 914 8.500773 ACTGTAAACAAGGAATATAAACACACG 58.499 33.333 0.00 0.00 0.00 4.49
588 941 4.640771 AGTTTGCCTCTATCAGTTGGAA 57.359 40.909 0.00 0.00 0.00 3.53
589 942 4.202461 ACAAGTTTGCCTCTATCAGTTGGA 60.202 41.667 0.00 0.00 0.00 3.53
590 943 4.074970 ACAAGTTTGCCTCTATCAGTTGG 58.925 43.478 0.00 0.00 0.00 3.77
591 944 4.756642 TGACAAGTTTGCCTCTATCAGTTG 59.243 41.667 0.00 0.00 0.00 3.16
592 945 4.757149 GTGACAAGTTTGCCTCTATCAGTT 59.243 41.667 0.00 0.00 0.00 3.16
593 946 4.319177 GTGACAAGTTTGCCTCTATCAGT 58.681 43.478 0.00 0.00 0.00 3.41
594 947 3.369147 CGTGACAAGTTTGCCTCTATCAG 59.631 47.826 0.00 0.00 0.00 2.90
595 948 3.325870 CGTGACAAGTTTGCCTCTATCA 58.674 45.455 0.00 0.00 0.00 2.15
596 949 2.673368 CCGTGACAAGTTTGCCTCTATC 59.327 50.000 0.00 0.00 0.00 2.08
598 951 1.414919 ACCGTGACAAGTTTGCCTCTA 59.585 47.619 0.00 0.00 0.00 2.43
616 969 8.074370 GGTTTCTACTGTTTTATTCAGTCAACC 58.926 37.037 13.65 13.65 43.76 3.77
618 971 7.711772 TCGGTTTCTACTGTTTTATTCAGTCAA 59.288 33.333 1.82 0.00 43.76 3.18
626 979 4.925646 GGACGTCGGTTTCTACTGTTTTAT 59.074 41.667 9.92 0.00 32.23 1.40
629 982 2.546584 GGGACGTCGGTTTCTACTGTTT 60.547 50.000 9.92 0.00 32.23 2.83
646 999 0.250770 AAAACAGAAGCTCCGGGGAC 60.251 55.000 4.80 0.00 0.00 4.46
648 1001 0.036875 AGAAAACAGAAGCTCCGGGG 59.963 55.000 0.00 0.00 0.00 5.73
653 1025 8.483218 GCAAATAAAGAAAGAAAACAGAAGCTC 58.517 33.333 0.00 0.00 0.00 4.09
687 1059 8.918202 TGTGTCAGTCTTAACAAATAAATCCT 57.082 30.769 0.00 0.00 0.00 3.24
688 1060 9.559958 CATGTGTCAGTCTTAACAAATAAATCC 57.440 33.333 0.00 0.00 0.00 3.01
694 1066 9.071276 AGATTTCATGTGTCAGTCTTAACAAAT 57.929 29.630 0.00 0.00 0.00 2.32
695 1067 8.344831 CAGATTTCATGTGTCAGTCTTAACAAA 58.655 33.333 0.00 0.00 0.00 2.83
697 1069 6.073058 GCAGATTTCATGTGTCAGTCTTAACA 60.073 38.462 0.00 0.00 0.00 2.41
698 1070 6.073058 TGCAGATTTCATGTGTCAGTCTTAAC 60.073 38.462 0.00 0.00 0.00 2.01
699 1071 5.997129 TGCAGATTTCATGTGTCAGTCTTAA 59.003 36.000 0.00 0.00 0.00 1.85
700 1072 5.550290 TGCAGATTTCATGTGTCAGTCTTA 58.450 37.500 0.00 0.00 0.00 2.10
701 1073 4.392047 TGCAGATTTCATGTGTCAGTCTT 58.608 39.130 0.00 0.00 0.00 3.01
702 1074 4.011966 TGCAGATTTCATGTGTCAGTCT 57.988 40.909 0.00 0.00 0.00 3.24
703 1075 4.959596 ATGCAGATTTCATGTGTCAGTC 57.040 40.909 0.00 0.00 0.00 3.51
704 1076 5.298527 CCATATGCAGATTTCATGTGTCAGT 59.701 40.000 0.00 0.00 33.11 3.41
706 1078 4.037089 GCCATATGCAGATTTCATGTGTCA 59.963 41.667 0.00 0.00 40.77 3.58
707 1079 4.543692 GCCATATGCAGATTTCATGTGTC 58.456 43.478 0.00 0.00 40.77 3.67
723 1331 1.524621 GGCTGTGTGCTCGCCATAT 60.525 57.895 0.00 0.00 43.25 1.78
1103 1955 2.898343 GGGTGTTGTTGTCGCCGT 60.898 61.111 0.00 0.00 36.45 5.68
1134 1986 1.066143 GCCGAGAAGGTCTTGATGGAA 60.066 52.381 0.00 0.00 43.70 3.53
1170 2022 1.539665 GGAGGAGAGGAGGACGGAT 59.460 63.158 0.00 0.00 0.00 4.18
1503 2355 4.157120 CCGACCCACCCGATCCAC 62.157 72.222 0.00 0.00 0.00 4.02
1734 2586 0.461693 GATGCAGAGCTCACCTGACC 60.462 60.000 17.77 0.00 33.65 4.02
1735 2587 0.461693 GGATGCAGAGCTCACCTGAC 60.462 60.000 17.77 2.53 33.65 3.51
1758 2610 1.013005 CAGAGCAGAGCACGTTCAGG 61.013 60.000 0.00 0.00 0.00 3.86
1764 2616 1.153608 AGATGCAGAGCAGAGCACG 60.154 57.895 0.00 0.00 43.65 5.34
1765 2617 0.391395 ACAGATGCAGAGCAGAGCAC 60.391 55.000 0.00 0.00 43.65 4.40
1766 2618 0.391263 CACAGATGCAGAGCAGAGCA 60.391 55.000 0.00 0.00 43.65 4.26
1767 2619 0.391395 ACACAGATGCAGAGCAGAGC 60.391 55.000 0.00 0.00 43.65 4.09
1768 2620 1.067071 TGACACAGATGCAGAGCAGAG 60.067 52.381 0.00 0.00 43.65 3.35
1769 2621 0.971386 TGACACAGATGCAGAGCAGA 59.029 50.000 0.00 0.00 43.65 4.26
1770 2622 2.025589 ATGACACAGATGCAGAGCAG 57.974 50.000 0.00 0.00 43.65 4.24
1771 2623 2.419159 GGTATGACACAGATGCAGAGCA 60.419 50.000 0.00 0.00 44.86 4.26
1772 2624 2.208431 GGTATGACACAGATGCAGAGC 58.792 52.381 0.00 0.00 0.00 4.09
1773 2625 3.531934 TGGTATGACACAGATGCAGAG 57.468 47.619 0.00 0.00 0.00 3.35
1774 2626 3.432608 CCATGGTATGACACAGATGCAGA 60.433 47.826 2.57 0.00 0.00 4.26
1775 2627 2.876550 CCATGGTATGACACAGATGCAG 59.123 50.000 2.57 0.00 0.00 4.41
1776 2628 2.921821 CCATGGTATGACACAGATGCA 58.078 47.619 2.57 0.00 0.00 3.96
1777 2629 1.605710 GCCATGGTATGACACAGATGC 59.394 52.381 14.67 0.00 0.00 3.91
1779 2631 3.483421 CATGCCATGGTATGACACAGAT 58.517 45.455 32.50 0.00 39.96 2.90
1780 2632 2.421811 CCATGCCATGGTATGACACAGA 60.422 50.000 36.14 0.00 45.54 3.41
1781 2633 1.951602 CCATGCCATGGTATGACACAG 59.048 52.381 36.14 19.65 45.54 3.66
1782 2634 2.055684 CCATGCCATGGTATGACACA 57.944 50.000 36.14 15.40 45.54 3.72
1792 2644 0.454600 GTCAGTTGAGCCATGCCATG 59.545 55.000 0.00 0.00 0.00 3.66
1793 2645 0.330604 AGTCAGTTGAGCCATGCCAT 59.669 50.000 0.00 0.00 0.00 4.40
1794 2646 0.607217 CAGTCAGTTGAGCCATGCCA 60.607 55.000 0.00 0.00 0.00 4.92
1795 2647 0.321919 TCAGTCAGTTGAGCCATGCC 60.322 55.000 0.00 0.00 0.00 4.40
1796 2648 1.400846 CATCAGTCAGTTGAGCCATGC 59.599 52.381 0.00 0.00 0.00 4.06
1807 2659 7.172190 ACAAAGAACACAAGATACATCAGTCAG 59.828 37.037 0.00 0.00 0.00 3.51
1808 2660 6.992123 ACAAAGAACACAAGATACATCAGTCA 59.008 34.615 0.00 0.00 0.00 3.41
1811 2677 7.113965 GCAAACAAAGAACACAAGATACATCAG 59.886 37.037 0.00 0.00 0.00 2.90
1813 2679 7.141363 AGCAAACAAAGAACACAAGATACATC 58.859 34.615 0.00 0.00 0.00 3.06
1865 2734 1.480212 ATCGACACCACAAGCCCTCA 61.480 55.000 0.00 0.00 0.00 3.86
1866 2735 0.741221 GATCGACACCACAAGCCCTC 60.741 60.000 0.00 0.00 0.00 4.30
1867 2736 1.194781 AGATCGACACCACAAGCCCT 61.195 55.000 0.00 0.00 0.00 5.19
1916 2785 3.522750 AGAGAGCTTCCATTTCTCCATGT 59.477 43.478 0.00 0.00 38.45 3.21
2122 2995 9.075678 GAGTAGTAGACATTTGGCTTATACCTA 57.924 37.037 0.00 0.00 33.72 3.08
2123 2996 7.015389 GGAGTAGTAGACATTTGGCTTATACCT 59.985 40.741 0.00 0.00 33.72 3.08
2124 2997 7.153315 GGAGTAGTAGACATTTGGCTTATACC 58.847 42.308 0.00 0.00 33.72 2.73
2146 3177 1.900486 AGGACTTGTAAACGGAGGGAG 59.100 52.381 0.00 0.00 0.00 4.30
2147 3178 2.019807 AGGACTTGTAAACGGAGGGA 57.980 50.000 0.00 0.00 0.00 4.20
2148 3179 2.416431 CGTAGGACTTGTAAACGGAGGG 60.416 54.545 0.00 0.00 0.00 4.30
2149 3180 2.872370 CGTAGGACTTGTAAACGGAGG 58.128 52.381 0.00 0.00 0.00 4.30
2150 3181 2.257034 GCGTAGGACTTGTAAACGGAG 58.743 52.381 0.00 0.00 34.29 4.63
2151 3182 1.612950 TGCGTAGGACTTGTAAACGGA 59.387 47.619 0.00 0.00 34.29 4.69
2152 3183 2.068837 TGCGTAGGACTTGTAAACGG 57.931 50.000 0.00 0.00 34.29 4.44
2153 3184 5.400485 GGTATATGCGTAGGACTTGTAAACG 59.600 44.000 0.00 0.00 36.67 3.60
2154 3185 6.510536 AGGTATATGCGTAGGACTTGTAAAC 58.489 40.000 0.00 0.00 0.00 2.01
2155 3186 6.720112 AGGTATATGCGTAGGACTTGTAAA 57.280 37.500 0.00 0.00 0.00 2.01
2156 3187 7.503566 ACTTAGGTATATGCGTAGGACTTGTAA 59.496 37.037 9.10 0.00 0.00 2.41
2157 3188 7.000472 ACTTAGGTATATGCGTAGGACTTGTA 59.000 38.462 9.10 0.00 0.00 2.41
2158 3189 5.832060 ACTTAGGTATATGCGTAGGACTTGT 59.168 40.000 9.10 0.00 0.00 3.16
2159 3190 6.328641 ACTTAGGTATATGCGTAGGACTTG 57.671 41.667 9.10 0.00 0.00 3.16
2160 3191 6.323225 ACAACTTAGGTATATGCGTAGGACTT 59.677 38.462 9.10 0.00 0.00 3.01
2161 3192 5.832060 ACAACTTAGGTATATGCGTAGGACT 59.168 40.000 9.10 0.00 0.00 3.85
2162 3193 6.081872 ACAACTTAGGTATATGCGTAGGAC 57.918 41.667 9.10 0.00 0.00 3.85
2163 3194 5.829391 TGACAACTTAGGTATATGCGTAGGA 59.171 40.000 9.10 0.00 0.00 2.94
2164 3195 6.080648 TGACAACTTAGGTATATGCGTAGG 57.919 41.667 1.96 1.96 0.00 3.18
2165 3196 8.589335 AATTGACAACTTAGGTATATGCGTAG 57.411 34.615 0.00 0.00 0.00 3.51
2166 3197 8.951787 AAATTGACAACTTAGGTATATGCGTA 57.048 30.769 0.00 0.00 0.00 4.42
2167 3198 7.859325 AAATTGACAACTTAGGTATATGCGT 57.141 32.000 0.00 0.00 0.00 5.24
2173 3204 9.185680 GGGTGATAAAATTGACAACTTAGGTAT 57.814 33.333 0.00 0.00 0.00 2.73
2174 3205 8.387813 AGGGTGATAAAATTGACAACTTAGGTA 58.612 33.333 0.00 0.00 0.00 3.08
2175 3206 7.176690 CAGGGTGATAAAATTGACAACTTAGGT 59.823 37.037 0.00 0.00 0.00 3.08
2176 3207 7.393234 TCAGGGTGATAAAATTGACAACTTAGG 59.607 37.037 0.00 0.00 0.00 2.69
2177 3208 8.335532 TCAGGGTGATAAAATTGACAACTTAG 57.664 34.615 0.00 0.00 0.00 2.18
2178 3209 8.877864 ATCAGGGTGATAAAATTGACAACTTA 57.122 30.769 0.00 0.00 34.88 2.24
2179 3210 7.781324 ATCAGGGTGATAAAATTGACAACTT 57.219 32.000 0.00 0.00 34.88 2.66
2183 3214 9.778741 GTCTATATCAGGGTGATAAAATTGACA 57.221 33.333 0.89 0.00 42.05 3.58
2227 3258 9.613428 TTCAGATGATCTATTTTCAAACCGTAT 57.387 29.630 0.00 0.00 0.00 3.06
2228 3259 9.098355 CTTCAGATGATCTATTTTCAAACCGTA 57.902 33.333 0.00 0.00 0.00 4.02
2229 3260 7.607991 ACTTCAGATGATCTATTTTCAAACCGT 59.392 33.333 0.00 0.00 0.00 4.83
2230 3261 7.978982 ACTTCAGATGATCTATTTTCAAACCG 58.021 34.615 0.00 0.00 0.00 4.44
2281 3312 9.920946 ATTTGACCAACCTAATACAAGTCATAT 57.079 29.630 0.00 0.00 33.21 1.78
2282 3313 9.747898 AATTTGACCAACCTAATACAAGTCATA 57.252 29.630 0.00 0.00 33.21 2.15
2283 3314 8.522830 CAATTTGACCAACCTAATACAAGTCAT 58.477 33.333 0.00 0.00 33.21 3.06
2284 3315 7.721842 TCAATTTGACCAACCTAATACAAGTCA 59.278 33.333 0.00 0.00 0.00 3.41
2285 3316 8.021396 GTCAATTTGACCAACCTAATACAAGTC 58.979 37.037 17.07 0.00 41.37 3.01
2286 3317 7.504238 TGTCAATTTGACCAACCTAATACAAGT 59.496 33.333 23.22 0.00 46.40 3.16
2287 3318 7.881142 TGTCAATTTGACCAACCTAATACAAG 58.119 34.615 23.22 0.00 46.40 3.16
2288 3319 7.825331 TGTCAATTTGACCAACCTAATACAA 57.175 32.000 23.22 1.00 46.40 2.41
2289 3320 7.504238 AGTTGTCAATTTGACCAACCTAATACA 59.496 33.333 23.22 1.78 46.40 2.29
2290 3321 7.882179 AGTTGTCAATTTGACCAACCTAATAC 58.118 34.615 23.22 9.56 46.40 1.89
2291 3322 8.472007 AAGTTGTCAATTTGACCAACCTAATA 57.528 30.769 23.22 2.31 46.40 0.98
2292 3323 6.976934 AGTTGTCAATTTGACCAACCTAAT 57.023 33.333 23.22 10.79 46.40 1.73
2293 3324 6.783708 AAGTTGTCAATTTGACCAACCTAA 57.216 33.333 23.22 9.65 46.40 2.69
2294 3325 6.488683 CCTAAGTTGTCAATTTGACCAACCTA 59.511 38.462 23.22 18.16 46.40 3.08
2295 3326 5.301805 CCTAAGTTGTCAATTTGACCAACCT 59.698 40.000 23.22 18.05 46.40 3.50
2296 3327 5.508994 CCCTAAGTTGTCAATTTGACCAACC 60.509 44.000 23.22 10.61 46.40 3.77
2297 3328 5.300792 TCCCTAAGTTGTCAATTTGACCAAC 59.699 40.000 23.22 23.11 46.40 3.77
2298 3329 5.450453 TCCCTAAGTTGTCAATTTGACCAA 58.550 37.500 23.22 15.47 46.40 3.67
2299 3330 5.055265 TCCCTAAGTTGTCAATTTGACCA 57.945 39.130 23.22 12.38 46.40 4.02
2300 3331 7.339466 ACATATCCCTAAGTTGTCAATTTGACC 59.661 37.037 23.22 11.31 46.40 4.02
2302 3333 7.148086 GCACATATCCCTAAGTTGTCAATTTGA 60.148 37.037 3.71 0.00 0.00 2.69
2303 3334 6.974622 GCACATATCCCTAAGTTGTCAATTTG 59.025 38.462 3.71 0.00 0.00 2.32
2304 3335 6.663093 TGCACATATCCCTAAGTTGTCAATTT 59.337 34.615 0.00 0.00 0.00 1.82
2305 3336 6.095440 GTGCACATATCCCTAAGTTGTCAATT 59.905 38.462 13.17 0.00 0.00 2.32
2306 3337 5.590259 GTGCACATATCCCTAAGTTGTCAAT 59.410 40.000 13.17 0.00 0.00 2.57
2307 3338 4.941263 GTGCACATATCCCTAAGTTGTCAA 59.059 41.667 13.17 0.00 0.00 3.18
2308 3339 4.513442 GTGCACATATCCCTAAGTTGTCA 58.487 43.478 13.17 0.00 0.00 3.58
2309 3340 3.555956 CGTGCACATATCCCTAAGTTGTC 59.444 47.826 18.64 0.00 0.00 3.18
2310 3341 3.531538 CGTGCACATATCCCTAAGTTGT 58.468 45.455 18.64 0.00 0.00 3.32
2311 3342 2.287915 GCGTGCACATATCCCTAAGTTG 59.712 50.000 18.64 0.00 0.00 3.16
2312 3343 2.561569 GCGTGCACATATCCCTAAGTT 58.438 47.619 18.64 0.00 0.00 2.66
2313 3344 1.202651 GGCGTGCACATATCCCTAAGT 60.203 52.381 18.64 0.00 0.00 2.24
2314 3345 1.512926 GGCGTGCACATATCCCTAAG 58.487 55.000 18.64 0.00 0.00 2.18
2315 3346 0.107831 GGGCGTGCACATATCCCTAA 59.892 55.000 18.64 0.00 34.19 2.69
2316 3347 0.762842 AGGGCGTGCACATATCCCTA 60.763 55.000 25.49 0.00 45.03 3.53
2317 3348 2.072487 AGGGCGTGCACATATCCCT 61.072 57.895 22.80 22.80 42.25 4.20
2318 3349 0.324943 ATAGGGCGTGCACATATCCC 59.675 55.000 18.64 19.39 37.24 3.85
2319 3350 3.328382 TTATAGGGCGTGCACATATCC 57.672 47.619 18.64 11.69 0.00 2.59
2320 3351 4.152402 CAGTTTATAGGGCGTGCACATATC 59.848 45.833 18.64 3.01 0.00 1.63
2321 3352 4.065088 CAGTTTATAGGGCGTGCACATAT 58.935 43.478 18.64 11.17 0.00 1.78
2322 3353 3.133183 TCAGTTTATAGGGCGTGCACATA 59.867 43.478 18.64 3.60 0.00 2.29
2323 3354 2.093181 TCAGTTTATAGGGCGTGCACAT 60.093 45.455 18.64 4.67 0.00 3.21
2324 3355 1.276705 TCAGTTTATAGGGCGTGCACA 59.723 47.619 18.64 0.00 0.00 4.57
2325 3356 1.933853 CTCAGTTTATAGGGCGTGCAC 59.066 52.381 6.82 6.82 0.00 4.57
2326 3357 1.828595 TCTCAGTTTATAGGGCGTGCA 59.171 47.619 0.00 0.00 0.00 4.57
2327 3358 2.100916 TCTCTCAGTTTATAGGGCGTGC 59.899 50.000 0.00 0.00 0.00 5.34
2328 3359 3.632604 TCTCTCTCAGTTTATAGGGCGTG 59.367 47.826 0.00 0.00 0.00 5.34
2329 3360 3.886505 CTCTCTCTCAGTTTATAGGGCGT 59.113 47.826 0.00 0.00 0.00 5.68
2330 3361 3.254657 CCTCTCTCTCAGTTTATAGGGCG 59.745 52.174 0.00 0.00 0.00 6.13
2331 3362 3.576550 CCCTCTCTCTCAGTTTATAGGGC 59.423 52.174 0.00 0.00 36.30 5.19
2332 3363 5.068215 TCCCTCTCTCTCAGTTTATAGGG 57.932 47.826 0.00 0.00 43.23 3.53
2333 3364 5.701224 ACTCCCTCTCTCTCAGTTTATAGG 58.299 45.833 0.00 0.00 0.00 2.57
2334 3365 6.430000 GCTACTCCCTCTCTCTCAGTTTATAG 59.570 46.154 0.00 0.00 0.00 1.31
2335 3366 6.126449 TGCTACTCCCTCTCTCTCAGTTTATA 60.126 42.308 0.00 0.00 0.00 0.98
2336 3367 5.137551 GCTACTCCCTCTCTCTCAGTTTAT 58.862 45.833 0.00 0.00 0.00 1.40
2337 3368 4.018324 TGCTACTCCCTCTCTCTCAGTTTA 60.018 45.833 0.00 0.00 0.00 2.01
2338 3369 3.245443 TGCTACTCCCTCTCTCTCAGTTT 60.245 47.826 0.00 0.00 0.00 2.66
2339 3370 2.310349 TGCTACTCCCTCTCTCTCAGTT 59.690 50.000 0.00 0.00 0.00 3.16
2340 3371 1.919654 TGCTACTCCCTCTCTCTCAGT 59.080 52.381 0.00 0.00 0.00 3.41
2341 3372 2.727123 TGCTACTCCCTCTCTCTCAG 57.273 55.000 0.00 0.00 0.00 3.35
2342 3373 3.093057 GTTTGCTACTCCCTCTCTCTCA 58.907 50.000 0.00 0.00 0.00 3.27
2343 3374 3.361786 AGTTTGCTACTCCCTCTCTCTC 58.638 50.000 0.00 0.00 28.23 3.20
2344 3375 3.466395 AGTTTGCTACTCCCTCTCTCT 57.534 47.619 0.00 0.00 28.23 3.10
2345 3376 5.047235 TGTTAAGTTTGCTACTCCCTCTCTC 60.047 44.000 0.00 0.00 35.54 3.20
2346 3377 4.838986 TGTTAAGTTTGCTACTCCCTCTCT 59.161 41.667 0.00 0.00 35.54 3.10
2347 3378 5.148651 TGTTAAGTTTGCTACTCCCTCTC 57.851 43.478 0.00 0.00 35.54 3.20
2348 3379 5.763876 ATGTTAAGTTTGCTACTCCCTCT 57.236 39.130 0.00 0.00 35.54 3.69
2349 3380 6.403878 TGTATGTTAAGTTTGCTACTCCCTC 58.596 40.000 0.00 0.00 35.54 4.30
2350 3381 6.368779 TGTATGTTAAGTTTGCTACTCCCT 57.631 37.500 0.00 0.00 35.54 4.20
2351 3382 6.038271 CCATGTATGTTAAGTTTGCTACTCCC 59.962 42.308 0.00 0.00 35.54 4.30
2352 3383 6.598064 ACCATGTATGTTAAGTTTGCTACTCC 59.402 38.462 0.00 0.00 35.54 3.85
2353 3384 7.119262 ACACCATGTATGTTAAGTTTGCTACTC 59.881 37.037 0.00 0.00 35.54 2.59
2354 3385 6.940298 ACACCATGTATGTTAAGTTTGCTACT 59.060 34.615 0.00 0.00 39.32 2.57
2355 3386 7.094975 TGACACCATGTATGTTAAGTTTGCTAC 60.095 37.037 1.70 0.00 0.00 3.58
2356 3387 6.937465 TGACACCATGTATGTTAAGTTTGCTA 59.063 34.615 1.70 0.00 0.00 3.49
2357 3388 5.767665 TGACACCATGTATGTTAAGTTTGCT 59.232 36.000 1.70 0.00 0.00 3.91
2378 3409 3.976704 TGGACCAATGGACCATGAC 57.023 52.632 19.09 0.00 42.08 3.06
2382 3413 0.039472 CCATGTGGACCAATGGACCA 59.961 55.000 19.09 19.09 44.45 4.02
2383 3414 0.331278 TCCATGTGGACCAATGGACC 59.669 55.000 23.65 13.83 39.78 4.46
2384 3415 1.755179 CTCCATGTGGACCAATGGAC 58.245 55.000 23.65 0.00 39.78 4.02
2385 3416 0.034186 GCTCCATGTGGACCAATGGA 60.034 55.000 24.83 24.83 39.78 3.41
2427 3458 5.353394 AAGTTGGTGTAGTGTTTCTGAGA 57.647 39.130 0.00 0.00 0.00 3.27
2450 3481 6.942576 AGTGATTTAAGTATTTCAGTGTGGCT 59.057 34.615 0.00 0.00 0.00 4.75
2480 3529 1.181098 ACAAGATGGTGGCAAGTGGC 61.181 55.000 0.00 0.00 43.74 5.01
2481 3530 1.331214 AACAAGATGGTGGCAAGTGG 58.669 50.000 0.00 0.00 0.00 4.00
2482 3531 3.569701 ACTAAACAAGATGGTGGCAAGTG 59.430 43.478 0.00 0.00 0.00 3.16
2483 3532 3.821033 GACTAAACAAGATGGTGGCAAGT 59.179 43.478 0.00 0.00 0.00 3.16
2484 3533 4.074970 AGACTAAACAAGATGGTGGCAAG 58.925 43.478 0.00 0.00 0.00 4.01
2485 3534 4.098914 AGACTAAACAAGATGGTGGCAA 57.901 40.909 0.00 0.00 0.00 4.52
2513 3562 8.840867 GTTAAATTTCAGCAATACAGACTTTCG 58.159 33.333 0.00 0.00 0.00 3.46
2559 3608 2.219216 CCTTTTGTTTCAGCAATGCACG 59.781 45.455 8.35 0.00 0.00 5.34
2560 3609 3.456280 TCCTTTTGTTTCAGCAATGCAC 58.544 40.909 8.35 0.00 0.00 4.57
2561 3610 3.815856 TCCTTTTGTTTCAGCAATGCA 57.184 38.095 8.35 0.00 0.00 3.96
2600 3649 9.852091 CTTGAATTTAAGATCTTCCTTTCCTTG 57.148 33.333 12.24 3.47 0.00 3.61
2625 3680 4.156477 TGCTTAATGGTTAAAAGTGGGCT 58.844 39.130 0.00 0.00 0.00 5.19
2631 3686 4.142469 CCCCGACTGCTTAATGGTTAAAAG 60.142 45.833 0.00 0.00 0.00 2.27
2640 3695 2.817844 GTTGAAACCCCGACTGCTTAAT 59.182 45.455 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.