Multiple sequence alignment - TraesCS2B01G456200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G456200 chr2B 100.000 6982 0 0 1 6982 650799566 650792585 0.000000e+00 12894
1 TraesCS2B01G456200 chr2B 95.161 558 25 2 132 688 763964363 763964919 0.000000e+00 880
2 TraesCS2B01G456200 chr2B 89.247 93 10 0 5583 5675 724693099 724693007 4.420000e-22 117
3 TraesCS2B01G456200 chr2A 95.909 2151 67 13 4334 6475 688967642 688969780 0.000000e+00 3465
4 TraesCS2B01G456200 chr2A 93.098 2072 116 14 2273 4335 688965553 688967606 0.000000e+00 3009
5 TraesCS2B01G456200 chr2A 91.934 1525 72 15 700 2188 688964008 688965517 0.000000e+00 2087
6 TraesCS2B01G456200 chr2A 91.762 437 15 3 6481 6915 688969828 688970245 7.800000e-164 588
7 TraesCS2B01G456200 chr2A 91.176 102 9 0 2 103 688963910 688964011 9.440000e-29 139
8 TraesCS2B01G456200 chr2D 94.118 2074 96 14 2273 4338 544788595 544786540 0.000000e+00 3131
9 TraesCS2B01G456200 chr2D 93.221 1785 93 18 4334 6102 544786507 544784735 0.000000e+00 2601
10 TraesCS2B01G456200 chr2D 91.588 1058 45 14 1200 2239 544789633 544788602 0.000000e+00 1421
11 TraesCS2B01G456200 chr2D 94.652 561 28 2 131 690 589910488 589911047 0.000000e+00 869
12 TraesCS2B01G456200 chr2D 89.300 486 15 15 702 1152 544790131 544789648 6.070000e-160 575
13 TraesCS2B01G456200 chr2D 88.372 129 14 1 4 131 544790247 544790119 3.370000e-33 154
14 TraesCS2B01G456200 chr1D 95.504 556 25 0 132 687 250740831 250741386 0.000000e+00 889
15 TraesCS2B01G456200 chr1D 94.849 563 29 0 126 688 19874675 19875237 0.000000e+00 880
16 TraesCS2B01G456200 chr1B 95.504 556 25 0 132 687 305284316 305284871 0.000000e+00 889
17 TraesCS2B01G456200 chr5D 95.153 557 27 0 132 688 342526240 342525684 0.000000e+00 880
18 TraesCS2B01G456200 chr3D 95.153 557 27 0 132 688 579568117 579568673 0.000000e+00 880
19 TraesCS2B01G456200 chr3D 94.803 558 29 0 132 689 161914858 161914301 0.000000e+00 870
20 TraesCS2B01G456200 chr6D 94.982 558 28 0 132 689 47270446 47269889 0.000000e+00 876


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 TraesCS2B01G456200 chr2B 650792585 650799566 6981 True 12894.0 12894 100.0000 1 6982 1 chr2B.!!$R1 6981
1 TraesCS2B01G456200 chr2B 763964363 763964919 556 False 880.0 880 95.1610 132 688 1 chr2B.!!$F1 556
2 TraesCS2B01G456200 chr2A 688963910 688970245 6335 False 1857.6 3465 92.7758 2 6915 5 chr2A.!!$F1 6913
3 TraesCS2B01G456200 chr2D 544784735 544790247 5512 True 1576.4 3131 91.3198 4 6102 5 chr2D.!!$R1 6098
4 TraesCS2B01G456200 chr2D 589910488 589911047 559 False 869.0 869 94.6520 131 690 1 chr2D.!!$F1 559
5 TraesCS2B01G456200 chr1D 250740831 250741386 555 False 889.0 889 95.5040 132 687 1 chr1D.!!$F2 555
6 TraesCS2B01G456200 chr1D 19874675 19875237 562 False 880.0 880 94.8490 126 688 1 chr1D.!!$F1 562
7 TraesCS2B01G456200 chr1B 305284316 305284871 555 False 889.0 889 95.5040 132 687 1 chr1B.!!$F1 555
8 TraesCS2B01G456200 chr5D 342525684 342526240 556 True 880.0 880 95.1530 132 688 1 chr5D.!!$R1 556
9 TraesCS2B01G456200 chr3D 579568117 579568673 556 False 880.0 880 95.1530 132 688 1 chr3D.!!$F1 556
10 TraesCS2B01G456200 chr3D 161914301 161914858 557 True 870.0 870 94.8030 132 689 1 chr3D.!!$R1 557
11 TraesCS2B01G456200 chr6D 47269889 47270446 557 True 876.0 876 94.9820 132 689 1 chr6D.!!$R1 557

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
700 701 0.309302 TTTGCCGGACAAACACGATG 59.691 50.0 16.73 0.0 43.35 3.84 F
1375 1416 0.248336 TTATGTCGTACCGCGCTCTG 60.248 55.0 5.56 0.0 41.07 3.35 F
2457 2520 0.392706 TGAGTTGTGCCATGACGAGT 59.607 50.0 0.00 0.0 0.00 4.18 F
2862 2927 0.535335 TAAGCAGCAAGGTACGGAGG 59.465 55.0 0.00 0.0 0.00 4.30 F
3798 3870 0.721718 GTGTCTGACATAAGGTGCGC 59.278 55.0 14.37 0.0 0.00 6.09 F
4721 4831 1.507140 TCCAGGTCCACAGAAGTGTT 58.493 50.0 0.00 0.0 44.39 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 1799 0.396001 ACCTAGTCCCCTCTCGCTTC 60.396 60.000 0.00 0.0 0.00 3.86 R
3295 3362 0.324275 GCCATACCTGGGGAAAGCAA 60.324 55.000 0.00 0.0 43.36 3.91 R
3355 3422 1.661463 TGGATGACCAGAGAAGGCTT 58.339 50.000 0.00 0.0 41.77 4.35 R
4721 4831 1.167781 GGGTGGAAAACGGAAGCGAA 61.168 55.000 0.00 0.0 0.00 4.70 R
4936 5064 0.249615 ATGTCGCCGATCAGTCCATG 60.250 55.000 0.00 0.0 0.00 3.66 R
6468 6608 1.000866 GCTGGCAGGGGATTTTCCT 59.999 57.895 17.64 0.0 36.57 3.36 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
43 44 1.988293 TGGATTCCTGCGTTCCAAAA 58.012 45.000 3.95 0.00 36.62 2.44
49 50 1.686052 TCCTGCGTTCCAAAAATGCTT 59.314 42.857 3.89 0.00 0.00 3.91
57 58 6.070829 GCGTTCCAAAAATGCTTTAATTCAC 58.929 36.000 0.00 0.00 0.00 3.18
102 103 0.394352 ATCCATGGACAAACCTCGCC 60.394 55.000 18.99 0.00 39.86 5.54
104 105 1.303236 CATGGACAAACCTCGCCCA 60.303 57.895 0.00 0.00 39.86 5.36
128 129 4.155099 CGCCAGTACAAATACATGGACAAA 59.845 41.667 0.00 0.00 36.56 2.83
129 130 5.399013 GCCAGTACAAATACATGGACAAAC 58.601 41.667 0.00 0.00 36.56 2.93
225 226 1.400494 GCTGACCTTTTTGTGTGACGT 59.600 47.619 0.00 0.00 0.00 4.34
254 255 3.676172 CGAAGGCGTCACACTACATTTTA 59.324 43.478 0.55 0.00 0.00 1.52
404 405 1.300971 CGCTGCACTAGTGGTTGCAT 61.301 55.000 23.95 0.00 33.83 3.96
443 444 0.606096 TAGTGCAACGCCTAGAAGCA 59.394 50.000 0.00 0.00 45.86 3.91
517 518 7.156000 TGACTTAGTAATTTTCGGATCACACA 58.844 34.615 0.00 0.00 0.00 3.72
518 519 7.822334 TGACTTAGTAATTTTCGGATCACACAT 59.178 33.333 0.00 0.00 0.00 3.21
519 520 9.309516 GACTTAGTAATTTTCGGATCACACATA 57.690 33.333 0.00 0.00 0.00 2.29
567 568 0.321919 ATCTGTGAGGCGTTGCACAT 60.322 50.000 0.00 0.00 43.34 3.21
689 690 4.509600 GTCAAATTTGTCAATTTTGCCGGA 59.490 37.500 20.61 7.56 40.09 5.14
690 691 4.509600 TCAAATTTGTCAATTTTGCCGGAC 59.490 37.500 20.61 0.00 40.09 4.79
691 692 3.742433 ATTTGTCAATTTTGCCGGACA 57.258 38.095 5.05 0.00 38.41 4.02
692 693 3.526931 TTTGTCAATTTTGCCGGACAA 57.473 38.095 5.05 6.40 45.49 3.18
693 694 3.526931 TTGTCAATTTTGCCGGACAAA 57.473 38.095 16.73 16.73 44.56 2.83
698 699 4.220413 TTTGCCGGACAAACACGA 57.780 50.000 16.73 0.00 43.35 4.35
699 700 2.709170 TTTGCCGGACAAACACGAT 58.291 47.368 16.73 0.00 43.35 3.73
700 701 0.309302 TTTGCCGGACAAACACGATG 59.691 50.000 16.73 0.00 43.35 3.84
701 702 0.533085 TTGCCGGACAAACACGATGA 60.533 50.000 5.05 0.00 34.56 2.92
784 787 2.596851 GCCCTTGAGCCCAGTCAGA 61.597 63.158 0.00 0.00 0.00 3.27
788 791 0.668706 CTTGAGCCCAGTCAGACACG 60.669 60.000 2.66 0.00 0.00 4.49
789 792 2.099652 TTGAGCCCAGTCAGACACGG 62.100 60.000 2.66 2.61 0.00 4.94
945 975 1.671901 CCCTTCCACTCGCTCTCTCC 61.672 65.000 0.00 0.00 0.00 3.71
958 988 2.039624 TCTCCCTCTCCACCAGGC 59.960 66.667 0.00 0.00 33.74 4.85
962 992 3.775654 CCTCTCCACCAGGCGGAC 61.776 72.222 0.00 0.00 35.59 4.79
981 1020 2.671963 AAAAGGAAGGCGCGGGAC 60.672 61.111 8.83 0.00 0.00 4.46
1299 1340 3.195698 GAATCACAGGCGTCCGGC 61.196 66.667 4.96 4.96 42.51 6.13
1374 1415 0.666913 ATTATGTCGTACCGCGCTCT 59.333 50.000 5.56 0.00 41.07 4.09
1375 1416 0.248336 TTATGTCGTACCGCGCTCTG 60.248 55.000 5.56 0.00 41.07 3.35
1376 1417 1.091197 TATGTCGTACCGCGCTCTGA 61.091 55.000 5.56 0.00 41.07 3.27
1377 1418 1.725557 ATGTCGTACCGCGCTCTGAT 61.726 55.000 5.56 0.00 41.07 2.90
1473 1515 1.300620 CTCCCGTCAGTCAAACGCA 60.301 57.895 0.00 0.00 38.77 5.24
1540 1588 5.983540 TGGCTCAAACCAAAATACTTTTGT 58.016 33.333 10.47 0.00 46.53 2.83
1558 1606 1.669437 TGTGCGCGCAAATCCTGTA 60.669 52.632 38.24 6.62 0.00 2.74
1743 1794 1.035932 ACGCACCGACTATGCTACCT 61.036 55.000 0.00 0.00 41.10 3.08
1748 1799 0.875728 CCGACTATGCTACCTCTCGG 59.124 60.000 0.00 0.00 35.15 4.63
2048 2109 1.209019 CTGCTTAGCATGACAGGGTCT 59.791 52.381 7.58 0.00 38.13 3.85
2060 2121 4.388499 GGGTCTTGCTCGCCCGAA 62.388 66.667 0.00 0.00 32.16 4.30
2106 2167 8.770828 GTGTTTCAACTTGTGAACTTAGCTATA 58.229 33.333 0.00 0.00 46.09 1.31
2108 2169 7.900782 TTCAACTTGTGAACTTAGCTATACC 57.099 36.000 0.00 0.00 41.47 2.73
2188 2249 2.961510 TGCATTATTGGAATGGAGGGG 58.038 47.619 0.00 0.00 0.00 4.79
2190 2251 2.961510 CATTATTGGAATGGAGGGGCA 58.038 47.619 0.00 0.00 0.00 5.36
2193 2254 1.953100 ATTGGAATGGAGGGGCAGGG 61.953 60.000 0.00 0.00 0.00 4.45
2209 2270 2.288213 GCAGGGACTAGCAAACAAAACC 60.288 50.000 0.00 0.00 36.02 3.27
2224 2285 3.244318 ACAAAACCCCAGTAGTCTTACCG 60.244 47.826 0.00 0.00 0.00 4.02
2243 2304 3.600388 CCGAAGGCATCTACTTTTGTCT 58.400 45.455 0.00 0.00 46.14 3.41
2244 2305 4.755411 CCGAAGGCATCTACTTTTGTCTA 58.245 43.478 0.00 0.00 46.14 2.59
2245 2306 4.567159 CCGAAGGCATCTACTTTTGTCTAC 59.433 45.833 0.00 0.00 46.14 2.59
2246 2307 4.567159 CGAAGGCATCTACTTTTGTCTACC 59.433 45.833 0.00 0.00 0.00 3.18
2247 2308 5.624738 CGAAGGCATCTACTTTTGTCTACCT 60.625 44.000 0.00 0.00 0.00 3.08
2248 2309 5.346181 AGGCATCTACTTTTGTCTACCTC 57.654 43.478 0.00 0.00 0.00 3.85
2249 2310 5.026790 AGGCATCTACTTTTGTCTACCTCT 58.973 41.667 0.00 0.00 0.00 3.69
2250 2311 5.128008 AGGCATCTACTTTTGTCTACCTCTC 59.872 44.000 0.00 0.00 0.00 3.20
2251 2312 5.105310 GGCATCTACTTTTGTCTACCTCTCA 60.105 44.000 0.00 0.00 0.00 3.27
2252 2313 6.039616 GCATCTACTTTTGTCTACCTCTCAG 58.960 44.000 0.00 0.00 0.00 3.35
2253 2314 6.350612 GCATCTACTTTTGTCTACCTCTCAGT 60.351 42.308 0.00 0.00 0.00 3.41
2254 2315 6.821031 TCTACTTTTGTCTACCTCTCAGTC 57.179 41.667 0.00 0.00 0.00 3.51
2255 2316 6.544650 TCTACTTTTGTCTACCTCTCAGTCT 58.455 40.000 0.00 0.00 0.00 3.24
2256 2317 5.715434 ACTTTTGTCTACCTCTCAGTCTC 57.285 43.478 0.00 0.00 0.00 3.36
2257 2318 5.390387 ACTTTTGTCTACCTCTCAGTCTCT 58.610 41.667 0.00 0.00 0.00 3.10
2258 2319 5.242838 ACTTTTGTCTACCTCTCAGTCTCTG 59.757 44.000 0.00 0.00 0.00 3.35
2259 2320 4.642466 TTGTCTACCTCTCAGTCTCTGA 57.358 45.455 0.00 0.00 38.25 3.27
2269 2330 3.458044 TCAGTCTCTGAGGAGCCTTTA 57.542 47.619 4.59 0.00 35.39 1.85
2271 2332 5.130705 TCAGTCTCTGAGGAGCCTTTATA 57.869 43.478 4.59 0.00 35.39 0.98
2279 2340 7.950684 TCTCTGAGGAGCCTTTATAGCTTATTA 59.049 37.037 4.59 0.00 41.75 0.98
2285 2346 8.158132 AGGAGCCTTTATAGCTTATTAAGAACC 58.842 37.037 7.63 0.00 41.75 3.62
2315 2376 8.212995 AGGTTGAAAAATGGTGAAATTTGATCT 58.787 29.630 0.00 0.00 30.21 2.75
2353 2414 4.220382 TGCCACCATATGCCATTTATAAGC 59.780 41.667 0.00 0.00 0.00 3.09
2381 2444 2.035449 GTGCCAACTGGTAAGGAAAACC 59.965 50.000 0.00 0.00 37.57 3.27
2412 2475 5.001232 GGTCTGTGGAGCTATTGTTACAAA 58.999 41.667 0.66 0.00 37.05 2.83
2423 2486 2.319136 TGTTACAAAGACGGCAGTGT 57.681 45.000 0.00 2.16 0.00 3.55
2425 2488 2.206750 GTTACAAAGACGGCAGTGTCA 58.793 47.619 0.00 0.00 41.41 3.58
2428 2491 2.297701 ACAAAGACGGCAGTGTCATTT 58.702 42.857 0.00 0.00 41.41 2.32
2429 2492 2.033299 ACAAAGACGGCAGTGTCATTTG 59.967 45.455 12.83 12.83 41.41 2.32
2449 2512 4.284829 TGTAGATGAATGAGTTGTGCCA 57.715 40.909 0.00 0.00 0.00 4.92
2451 2514 4.637091 TGTAGATGAATGAGTTGTGCCATG 59.363 41.667 0.00 0.00 0.00 3.66
2452 2515 3.959293 AGATGAATGAGTTGTGCCATGA 58.041 40.909 0.00 0.00 0.00 3.07
2453 2516 3.693085 AGATGAATGAGTTGTGCCATGAC 59.307 43.478 0.00 0.00 0.00 3.06
2454 2517 1.805943 TGAATGAGTTGTGCCATGACG 59.194 47.619 0.00 0.00 0.00 4.35
2455 2518 2.076100 GAATGAGTTGTGCCATGACGA 58.924 47.619 0.00 0.00 0.00 4.20
2456 2519 1.730501 ATGAGTTGTGCCATGACGAG 58.269 50.000 0.00 0.00 0.00 4.18
2457 2520 0.392706 TGAGTTGTGCCATGACGAGT 59.607 50.000 0.00 0.00 0.00 4.18
2458 2521 1.616374 TGAGTTGTGCCATGACGAGTA 59.384 47.619 0.00 0.00 0.00 2.59
2472 2535 6.201044 CCATGACGAGTAGGTTAGCATTTTAG 59.799 42.308 0.00 0.00 0.00 1.85
2473 2536 6.276832 TGACGAGTAGGTTAGCATTTTAGT 57.723 37.500 0.00 0.00 0.00 2.24
2485 2548 7.094377 GGTTAGCATTTTAGTCAGATGTTTGGA 60.094 37.037 0.00 0.00 0.00 3.53
2559 2623 6.535150 GCAAAAAGGCTCTAAACTTCTGTTTT 59.465 34.615 0.00 0.00 43.13 2.43
2573 2637 0.590984 TGTTTTGTGTCATGCGTGCG 60.591 50.000 0.00 0.00 0.00 5.34
2577 2641 0.876342 TTGTGTCATGCGTGCGTACA 60.876 50.000 4.09 3.47 0.00 2.90
2594 2658 5.105513 TGCGTACAAGTAGGATTCAGATCAA 60.106 40.000 4.27 0.00 33.77 2.57
2600 2664 6.825721 ACAAGTAGGATTCAGATCAACCATTC 59.174 38.462 0.00 0.00 33.77 2.67
2641 2706 3.109928 GCTACCTAACCTTCCACCCTTA 58.890 50.000 0.00 0.00 0.00 2.69
2642 2707 3.715315 GCTACCTAACCTTCCACCCTTAT 59.285 47.826 0.00 0.00 0.00 1.73
2738 2803 7.615365 TGCCAATTATCATCACCTTTTTAGACT 59.385 33.333 0.00 0.00 0.00 3.24
2796 2861 3.308259 GCTAGGTCCGTCTATATGGAGGA 60.308 52.174 10.05 6.74 41.64 3.71
2858 2923 3.889196 TTTTGTAAGCAGCAAGGTACG 57.111 42.857 0.00 0.00 0.00 3.67
2862 2927 0.535335 TAAGCAGCAAGGTACGGAGG 59.465 55.000 0.00 0.00 0.00 4.30
2894 2959 3.657398 TCATGGATGACTTCATTGGCT 57.343 42.857 0.00 0.00 36.57 4.75
3006 3072 2.624029 CCCCATTTGACCACAAGCCTAT 60.624 50.000 0.00 0.00 37.32 2.57
3010 3076 3.500448 TTTGACCACAAGCCTATCACA 57.500 42.857 0.00 0.00 37.32 3.58
3037 3103 5.559770 TGATCAAGTGTCCTTTTGAGCATA 58.440 37.500 0.00 0.00 42.67 3.14
3061 3127 3.304928 CCACAAACAACTGCCTCATCTTC 60.305 47.826 0.00 0.00 0.00 2.87
3097 3163 6.405538 CAATTTTGGCCATGTTAGGTGTTAT 58.594 36.000 6.09 0.00 0.00 1.89
3102 3168 8.824756 TTTGGCCATGTTAGGTGTTATATTTA 57.175 30.769 6.09 0.00 0.00 1.40
3112 3178 9.228636 GTTAGGTGTTATATTTATTTTGCACCG 57.771 33.333 0.00 0.00 46.75 4.94
3124 3190 3.701532 TTTGCACCGTTGGAAGTTTAG 57.298 42.857 0.00 0.00 34.12 1.85
3137 3204 7.262772 GTTGGAAGTTTAGCCCCATTAATTAC 58.737 38.462 0.00 0.00 0.00 1.89
3163 3230 5.560724 AGTTTCACACTGTAATACTGGCAT 58.439 37.500 2.50 0.00 32.83 4.40
3222 3289 8.373981 ACTGCAGTAATTATAGCATCTCTGAAT 58.626 33.333 20.16 0.00 36.28 2.57
3227 3294 9.499479 AGTAATTATAGCATCTCTGAATTGTGG 57.501 33.333 0.00 0.00 0.00 4.17
3244 3311 8.428063 TGAATTGTGGTTTCAAAATACAATCCT 58.572 29.630 11.59 1.25 37.46 3.24
3265 3332 4.751600 CCTTTTCAGGCAATTTTCAAGTCC 59.248 41.667 0.00 0.00 31.53 3.85
3268 3335 1.067635 CAGGCAATTTTCAAGTCCCCG 60.068 52.381 0.00 0.00 0.00 5.73
3324 3391 1.142465 CCAGGTATGGCAGCTTCATCT 59.858 52.381 2.87 0.00 40.52 2.90
3486 3554 1.418637 TCCACCACTCCCAGTAAACAC 59.581 52.381 0.00 0.00 0.00 3.32
3487 3555 1.420138 CCACCACTCCCAGTAAACACT 59.580 52.381 0.00 0.00 0.00 3.55
3508 3576 8.040716 ACACTGGTATTAAAACTTATGCAGAC 57.959 34.615 0.00 0.00 0.00 3.51
3566 3634 1.608717 GCCTCACAGGTCCGTGATCT 61.609 60.000 14.30 0.00 44.61 2.75
3798 3870 0.721718 GTGTCTGACATAAGGTGCGC 59.278 55.000 14.37 0.00 0.00 6.09
3835 3907 3.327439 TCTTTTCCTCCCTTTCCTCAGT 58.673 45.455 0.00 0.00 0.00 3.41
3995 4067 2.305927 AGACACCGATCCACCTTTCAAT 59.694 45.455 0.00 0.00 0.00 2.57
4123 4195 6.330278 GTTTTCTACCCTGGTTTCATATTGC 58.670 40.000 0.00 0.00 0.00 3.56
4163 4235 3.130633 TCATGTATGTGATAGTTGCGGC 58.869 45.455 0.00 0.00 0.00 6.53
4184 4256 3.375922 GCGCTTGTATTAAACCAAGGCTA 59.624 43.478 15.34 0.00 38.76 3.93
4262 4334 3.469008 TCTCATATTGTTAGTGCCGGG 57.531 47.619 2.18 0.00 0.00 5.73
4570 4679 4.777896 ACCCAGAGTGCTTATCTCAGTTAA 59.222 41.667 0.00 0.00 34.73 2.01
4575 4684 6.529829 CAGAGTGCTTATCTCAGTTAAGACAC 59.470 42.308 15.35 15.35 35.85 3.67
4708 4818 3.708451 ACTGAAAACCAAAGTTCCAGGT 58.292 40.909 10.80 0.00 34.19 4.00
4721 4831 1.507140 TCCAGGTCCACAGAAGTGTT 58.493 50.000 0.00 0.00 44.39 3.32
4855 4976 1.784525 GCTGTAGCGACTCAACTTGT 58.215 50.000 0.00 0.00 0.00 3.16
4917 5045 5.435291 TCTAGTCTAGCCTGTAGGTTGTAC 58.565 45.833 1.60 0.00 37.57 2.90
4936 5064 1.591248 CGCTTGTTATTGCGTGTGTC 58.409 50.000 0.00 0.00 46.09 3.67
5012 5140 3.576118 CTGATCAATCTGAGTATCCGGGT 59.424 47.826 0.00 0.00 0.00 5.28
5035 5163 4.699735 TGTTGACTATTCAATCCGCATTGT 59.300 37.500 0.00 0.00 43.72 2.71
5062 5190 8.965172 GCATAACAAGCTTGAAATATTCAGATG 58.035 33.333 32.50 15.80 41.38 2.90
5285 5414 8.262227 ACTAATGATGATTTCCAATGCACATTT 58.738 29.630 0.00 0.00 0.00 2.32
5311 5440 7.546358 TGGTGATAACATTGAGCAATTTTAGG 58.454 34.615 7.58 0.00 29.70 2.69
5331 5460 8.756486 TTTAGGTTTACTTTTTGTAGCTTCCT 57.244 30.769 0.00 0.00 32.08 3.36
5767 5900 2.752354 CCGTTATCATGTTGCCCTTTGA 59.248 45.455 0.00 0.00 0.00 2.69
5770 5903 4.176271 GTTATCATGTTGCCCTTTGAAGC 58.824 43.478 0.00 0.00 0.00 3.86
5880 6013 2.369394 CTGTTGAGAAGCCCATTACCC 58.631 52.381 0.00 0.00 0.00 3.69
6106 6239 2.235155 TGCCGTAACTGTATGGACACAT 59.765 45.455 0.00 0.00 38.53 3.21
6107 6240 3.447944 TGCCGTAACTGTATGGACACATA 59.552 43.478 0.00 0.00 38.53 2.29
6158 6291 8.242053 ACTTTGAGAATTCTGCATCATTTACAG 58.758 33.333 14.00 0.10 0.00 2.74
6201 6334 7.610305 TCTTGGAATAGTTGGTTTAGGAATGTC 59.390 37.037 0.00 0.00 0.00 3.06
6265 6398 3.387699 AGTTTTGATTTCAACACTGGGGG 59.612 43.478 10.46 0.00 43.03 5.40
6301 6435 1.407258 TCTTTTCTTGCCAAACCCACG 59.593 47.619 0.00 0.00 0.00 4.94
6309 6443 0.887387 GCCAAACCCACGCTCTAACA 60.887 55.000 0.00 0.00 0.00 2.41
6310 6444 1.821216 CCAAACCCACGCTCTAACAT 58.179 50.000 0.00 0.00 0.00 2.71
6331 6471 5.187381 ACATAATGCATGGTGATTGTTTGGA 59.813 36.000 16.04 0.00 39.13 3.53
6333 6473 1.273048 TGCATGGTGATTGTTTGGAGC 59.727 47.619 0.00 0.00 0.00 4.70
6339 6479 2.612972 GGTGATTGTTTGGAGCGAGAGA 60.613 50.000 0.00 0.00 0.00 3.10
6379 6519 3.711842 GCACGTGCGCAGTAAGCA 61.712 61.111 26.77 0.00 46.13 3.91
6439 6579 8.734386 CATTATACTGATAAGCCAGGAAAATCC 58.266 37.037 0.00 0.00 38.44 3.01
6447 6587 2.583472 CAGGAAAATCCCCTGCCAC 58.417 57.895 0.00 0.00 43.93 5.01
6463 6603 2.103263 TGCCACCAAAATGGGTTACAAC 59.897 45.455 0.87 0.00 43.37 3.32
6468 6608 4.515944 CACCAAAATGGGTTACAACGTCTA 59.484 41.667 0.87 0.00 43.37 2.59
6475 6615 5.231702 TGGGTTACAACGTCTAGGAAAAT 57.768 39.130 0.00 0.00 0.00 1.82
6476 6616 5.240121 TGGGTTACAACGTCTAGGAAAATC 58.760 41.667 0.00 0.00 0.00 2.17
6477 6617 4.633126 GGGTTACAACGTCTAGGAAAATCC 59.367 45.833 0.00 0.00 36.58 3.01
6478 6618 4.633126 GGTTACAACGTCTAGGAAAATCCC 59.367 45.833 0.00 0.00 37.19 3.85
6479 6619 3.345508 ACAACGTCTAGGAAAATCCCC 57.654 47.619 0.00 0.00 37.19 4.81
6480 6620 2.910977 ACAACGTCTAGGAAAATCCCCT 59.089 45.455 0.00 0.00 37.19 4.79
6481 6621 3.270877 CAACGTCTAGGAAAATCCCCTG 58.729 50.000 0.00 0.00 37.19 4.45
6560 6744 9.877178 GCTAATTGCATATGACTAGGTATAAGT 57.123 33.333 6.97 0.00 42.31 2.24
6567 6751 7.704472 GCATATGACTAGGTATAAGTCTCATGC 59.296 40.741 6.97 18.08 44.62 4.06
6571 6755 8.941995 TGACTAGGTATAAGTCTCATGCTTAT 57.058 34.615 8.53 8.53 43.13 1.73
6579 6763 9.119329 GTATAAGTCTCATGCTTATAAGTCACG 57.881 37.037 13.91 5.66 40.75 4.35
6588 6772 3.679083 GCTTATAAGTCACGGCCAGAAGT 60.679 47.826 13.91 0.00 0.00 3.01
6589 6773 4.504858 CTTATAAGTCACGGCCAGAAGTT 58.495 43.478 2.24 0.00 0.00 2.66
6676 6860 9.941664 CATACTTTGACAGATAAGGCATAAAAG 57.058 33.333 0.00 0.00 0.00 2.27
6750 6934 2.240160 ACACACTCCCCTAAAACACACA 59.760 45.455 0.00 0.00 0.00 3.72
6751 6935 2.616842 CACACTCCCCTAAAACACACAC 59.383 50.000 0.00 0.00 0.00 3.82
6752 6936 2.240160 ACACTCCCCTAAAACACACACA 59.760 45.455 0.00 0.00 0.00 3.72
6753 6937 2.616842 CACTCCCCTAAAACACACACAC 59.383 50.000 0.00 0.00 0.00 3.82
6754 6938 2.240160 ACTCCCCTAAAACACACACACA 59.760 45.455 0.00 0.00 0.00 3.72
6755 6939 2.616842 CTCCCCTAAAACACACACACAC 59.383 50.000 0.00 0.00 0.00 3.82
6756 6940 2.026169 TCCCCTAAAACACACACACACA 60.026 45.455 0.00 0.00 0.00 3.72
6757 6941 2.098443 CCCCTAAAACACACACACACAC 59.902 50.000 0.00 0.00 0.00 3.82
6758 6942 2.750166 CCCTAAAACACACACACACACA 59.250 45.455 0.00 0.00 0.00 3.72
6759 6943 3.426963 CCCTAAAACACACACACACACAC 60.427 47.826 0.00 0.00 0.00 3.82
6760 6944 3.189495 CCTAAAACACACACACACACACA 59.811 43.478 0.00 0.00 0.00 3.72
6761 6945 2.697431 AAACACACACACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
6762 6946 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
6763 6947 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6764 6948 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6765 6949 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6785 6969 4.278170 ACACACACACACAAATAATGAGGG 59.722 41.667 0.00 0.00 0.00 4.30
6802 6986 5.171541 TGAGGGATAAAGAATAGGAGGGT 57.828 43.478 0.00 0.00 0.00 4.34
6935 7119 6.548441 ACATCTGACTAGTTCTAGATACGC 57.452 41.667 12.97 0.00 0.00 4.42
6936 7120 6.056236 ACATCTGACTAGTTCTAGATACGCA 58.944 40.000 12.97 0.00 0.00 5.24
6937 7121 6.712998 ACATCTGACTAGTTCTAGATACGCAT 59.287 38.462 12.97 0.00 0.00 4.73
6938 7122 7.229707 ACATCTGACTAGTTCTAGATACGCATT 59.770 37.037 12.97 0.00 0.00 3.56
6939 7123 7.569639 TCTGACTAGTTCTAGATACGCATTT 57.430 36.000 12.97 0.00 0.00 2.32
6940 7124 7.640852 TCTGACTAGTTCTAGATACGCATTTC 58.359 38.462 12.97 0.00 0.00 2.17
6941 7125 7.499563 TCTGACTAGTTCTAGATACGCATTTCT 59.500 37.037 12.97 0.00 0.00 2.52
6942 7126 7.418408 TGACTAGTTCTAGATACGCATTTCTG 58.582 38.462 12.97 0.00 0.00 3.02
6943 7127 7.282450 TGACTAGTTCTAGATACGCATTTCTGA 59.718 37.037 12.97 0.00 0.00 3.27
6944 7128 8.172352 ACTAGTTCTAGATACGCATTTCTGAT 57.828 34.615 12.97 0.00 0.00 2.90
6945 7129 8.079203 ACTAGTTCTAGATACGCATTTCTGATG 58.921 37.037 12.97 0.00 0.00 3.07
6946 7130 6.810911 AGTTCTAGATACGCATTTCTGATGT 58.189 36.000 0.00 0.00 0.00 3.06
6947 7131 6.699204 AGTTCTAGATACGCATTTCTGATGTG 59.301 38.462 0.00 0.00 35.78 3.21
6948 7132 4.984785 TCTAGATACGCATTTCTGATGTGC 59.015 41.667 0.00 5.10 33.15 4.57
6952 7136 3.635433 GCATTTCTGATGTGCGCAT 57.365 47.368 15.91 13.71 38.18 4.73
6953 7137 1.197055 GCATTTCTGATGTGCGCATG 58.803 50.000 19.33 5.26 35.07 4.06
6954 7138 1.835121 CATTTCTGATGTGCGCATGG 58.165 50.000 19.33 10.30 35.07 3.66
6955 7139 0.101759 ATTTCTGATGTGCGCATGGC 59.898 50.000 19.33 6.36 43.96 4.40
6956 7140 0.961857 TTTCTGATGTGCGCATGGCT 60.962 50.000 19.33 0.00 44.05 4.75
6957 7141 1.650314 TTCTGATGTGCGCATGGCTG 61.650 55.000 19.33 9.97 44.05 4.85
6958 7142 3.751401 CTGATGTGCGCATGGCTGC 62.751 63.158 19.33 2.99 45.31 5.25
6959 7143 3.515286 GATGTGCGCATGGCTGCT 61.515 61.111 19.33 0.00 46.65 4.24
6960 7144 3.751401 GATGTGCGCATGGCTGCTG 62.751 63.158 19.33 0.00 46.65 4.41
6965 7149 3.744719 CGCATGGCTGCTGCTGTT 61.745 61.111 15.64 0.00 46.65 3.16
6966 7150 2.126071 GCATGGCTGCTGCTGTTG 60.126 61.111 15.64 11.13 45.32 3.33
6967 7151 2.126071 CATGGCTGCTGCTGTTGC 60.126 61.111 15.64 4.04 39.59 4.17
6968 7152 2.282958 ATGGCTGCTGCTGTTGCT 60.283 55.556 15.64 0.00 40.48 3.91
6969 7153 1.906824 ATGGCTGCTGCTGTTGCTT 60.907 52.632 15.64 0.00 40.48 3.91
6970 7154 1.469335 ATGGCTGCTGCTGTTGCTTT 61.469 50.000 15.64 0.00 40.48 3.51
6971 7155 1.068585 GGCTGCTGCTGTTGCTTTT 59.931 52.632 15.64 0.00 40.48 2.27
6972 7156 0.531311 GGCTGCTGCTGTTGCTTTTT 60.531 50.000 15.64 0.00 40.48 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.682234 TCCAAAGACAGAAGCATCATAGA 57.318 39.130 0.00 0.00 0.00 1.98
6 7 6.017275 GGAATCCAAAGACAGAAGCATCATAG 60.017 42.308 0.00 0.00 0.00 2.23
7 8 5.824624 GGAATCCAAAGACAGAAGCATCATA 59.175 40.000 0.00 0.00 0.00 2.15
8 9 4.643784 GGAATCCAAAGACAGAAGCATCAT 59.356 41.667 0.00 0.00 0.00 2.45
10 11 4.096081 CAGGAATCCAAAGACAGAAGCATC 59.904 45.833 0.61 0.00 0.00 3.91
11 12 4.015084 CAGGAATCCAAAGACAGAAGCAT 58.985 43.478 0.61 0.00 0.00 3.79
13 14 2.163211 GCAGGAATCCAAAGACAGAAGC 59.837 50.000 0.61 0.00 0.00 3.86
14 15 2.417933 CGCAGGAATCCAAAGACAGAAG 59.582 50.000 0.61 0.00 0.00 2.85
15 16 2.224523 ACGCAGGAATCCAAAGACAGAA 60.225 45.455 0.61 0.00 0.00 3.02
16 17 1.347707 ACGCAGGAATCCAAAGACAGA 59.652 47.619 0.61 0.00 0.00 3.41
43 44 4.485163 GTCGCCAAGTGAATTAAAGCATT 58.515 39.130 0.00 0.00 0.00 3.56
49 50 0.800012 GCCGTCGCCAAGTGAATTAA 59.200 50.000 0.00 0.00 0.00 1.40
57 58 3.709880 TATGGTCGCCGTCGCCAAG 62.710 63.158 6.14 0.00 42.14 3.61
99 100 0.741574 TATTTGTACTGGCGTGGGCG 60.742 55.000 0.00 0.00 41.24 6.13
102 103 2.354510 CCATGTATTTGTACTGGCGTGG 59.645 50.000 0.00 0.00 0.00 4.94
104 105 3.267483 GTCCATGTATTTGTACTGGCGT 58.733 45.455 0.00 0.00 0.00 5.68
404 405 6.734137 CACTAGTGGTTGCTTCATTTTGTAA 58.266 36.000 15.49 0.00 0.00 2.41
443 444 0.966920 ACTGTACAGTGTAGCGCCTT 59.033 50.000 27.41 0.00 40.75 4.35
517 518 2.280389 CTGGCCAGCGTCGCATAT 60.280 61.111 22.33 0.00 0.00 1.78
518 519 4.529219 CCTGGCCAGCGTCGCATA 62.529 66.667 28.39 0.00 0.00 3.14
547 548 1.229975 TGTGCAACGCCTCACAGATG 61.230 55.000 0.00 0.00 42.39 2.90
567 568 1.666553 CGAAGGCGCCACACTACAA 60.667 57.895 31.54 0.00 0.00 2.41
689 690 3.436704 GTCATCCATGTCATCGTGTTTGT 59.563 43.478 0.00 0.00 0.00 2.83
690 691 3.436359 TGTCATCCATGTCATCGTGTTTG 59.564 43.478 0.00 0.00 0.00 2.93
691 692 3.436704 GTGTCATCCATGTCATCGTGTTT 59.563 43.478 0.00 0.00 0.00 2.83
692 693 3.002791 GTGTCATCCATGTCATCGTGTT 58.997 45.455 0.00 0.00 0.00 3.32
693 694 2.621338 GTGTCATCCATGTCATCGTGT 58.379 47.619 0.00 0.00 0.00 4.49
694 695 1.935873 GGTGTCATCCATGTCATCGTG 59.064 52.381 0.00 0.00 0.00 4.35
695 696 1.471501 CGGTGTCATCCATGTCATCGT 60.472 52.381 10.22 0.00 42.54 3.73
696 697 1.202405 TCGGTGTCATCCATGTCATCG 60.202 52.381 11.70 11.70 46.55 3.84
697 698 2.477825 CTCGGTGTCATCCATGTCATC 58.522 52.381 0.00 0.00 0.00 2.92
698 699 1.139654 CCTCGGTGTCATCCATGTCAT 59.860 52.381 0.00 0.00 0.00 3.06
699 700 0.536724 CCTCGGTGTCATCCATGTCA 59.463 55.000 0.00 0.00 0.00 3.58
700 701 0.811616 GCCTCGGTGTCATCCATGTC 60.812 60.000 0.00 0.00 0.00 3.06
701 702 1.221840 GCCTCGGTGTCATCCATGT 59.778 57.895 0.00 0.00 0.00 3.21
758 759 2.592308 GCTCAAGGGCCTACAGGG 59.408 66.667 6.41 0.36 35.18 4.45
945 975 3.775654 GTCCGCCTGGTGGAGAGG 61.776 72.222 28.69 6.67 43.30 3.69
958 988 3.023591 GCGCCTTCCTTTTCGTCCG 62.024 63.158 0.00 0.00 0.00 4.79
962 992 3.799755 CCCGCGCCTTCCTTTTCG 61.800 66.667 0.00 0.00 0.00 3.46
988 1027 3.991318 GGCCATTCCCCACCACCA 61.991 66.667 0.00 0.00 0.00 4.17
1277 1318 1.363744 GGACGCCTGTGATTCTGAAG 58.636 55.000 0.00 0.00 0.00 3.02
1374 1415 7.506114 ACGCTAAGAATTAAACCCTATCATCA 58.494 34.615 0.00 0.00 0.00 3.07
1375 1416 7.873505 AGACGCTAAGAATTAAACCCTATCATC 59.126 37.037 0.00 0.00 0.00 2.92
1376 1417 7.736893 AGACGCTAAGAATTAAACCCTATCAT 58.263 34.615 0.00 0.00 0.00 2.45
1377 1418 7.069578 AGAGACGCTAAGAATTAAACCCTATCA 59.930 37.037 0.00 0.00 0.00 2.15
1473 1515 1.153229 GCTCCCCGGCGATTAAACT 60.153 57.895 9.30 0.00 0.00 2.66
1494 1536 0.097499 CGCGAAATCTGATTGCAGCA 59.903 50.000 18.51 0.00 42.01 4.41
1496 1538 1.662629 ACTCGCGAAATCTGATTGCAG 59.337 47.619 11.33 8.93 43.67 4.41
1540 1588 1.231296 TTACAGGATTTGCGCGCACA 61.231 50.000 36.72 29.94 0.00 4.57
1593 1641 2.403259 TGTGAATGCTACAGTGACGTG 58.597 47.619 0.00 0.00 0.00 4.49
1748 1799 0.396001 ACCTAGTCCCCTCTCGCTTC 60.396 60.000 0.00 0.00 0.00 3.86
1815 1870 2.130821 TATGGGACCAAACGCCAGCA 62.131 55.000 0.00 0.00 0.00 4.41
2048 2109 2.443260 TTAGTGCTTCGGGCGAGCAA 62.443 55.000 9.85 0.00 45.43 3.91
2106 2167 9.403583 TCTTGTAATTCTAAAGTTGTCTTTGGT 57.596 29.630 3.85 0.00 42.86 3.67
2147 2208 1.566018 GACCGGGAAACAGAGCAACG 61.566 60.000 6.32 0.00 0.00 4.10
2188 2249 2.288213 GGTTTTGTTTGCTAGTCCCTGC 60.288 50.000 0.00 0.00 0.00 4.85
2190 2251 2.594131 GGGTTTTGTTTGCTAGTCCCT 58.406 47.619 0.00 0.00 0.00 4.20
2193 2254 2.956333 ACTGGGGTTTTGTTTGCTAGTC 59.044 45.455 0.00 0.00 0.00 2.59
2209 2270 1.136500 GCCTTCGGTAAGACTACTGGG 59.864 57.143 0.00 0.00 35.41 4.45
2224 2285 5.735766 AGGTAGACAAAAGTAGATGCCTTC 58.264 41.667 0.00 0.00 0.00 3.46
2235 2296 5.475220 TCAGAGACTGAGAGGTAGACAAAAG 59.525 44.000 0.00 0.00 35.39 2.27
2253 2314 4.191804 AGCTATAAAGGCTCCTCAGAGA 57.808 45.455 0.00 0.00 43.39 3.10
2254 2315 4.953940 AAGCTATAAAGGCTCCTCAGAG 57.046 45.455 0.00 0.00 43.57 3.35
2255 2316 8.492415 TTAATAAGCTATAAAGGCTCCTCAGA 57.508 34.615 0.00 0.00 39.30 3.27
2256 2317 8.589338 TCTTAATAAGCTATAAAGGCTCCTCAG 58.411 37.037 0.00 0.00 39.30 3.35
2257 2318 8.492415 TCTTAATAAGCTATAAAGGCTCCTCA 57.508 34.615 0.00 0.00 39.30 3.86
2258 2319 9.210329 GTTCTTAATAAGCTATAAAGGCTCCTC 57.790 37.037 0.00 0.00 39.30 3.71
2259 2320 8.158132 GGTTCTTAATAAGCTATAAAGGCTCCT 58.842 37.037 0.00 0.00 39.30 3.69
2260 2321 7.117956 CGGTTCTTAATAAGCTATAAAGGCTCC 59.882 40.741 0.00 0.00 39.30 4.70
2261 2322 7.656542 ACGGTTCTTAATAAGCTATAAAGGCTC 59.343 37.037 0.00 0.00 39.30 4.70
2262 2323 7.506971 ACGGTTCTTAATAAGCTATAAAGGCT 58.493 34.615 0.00 0.00 42.31 4.58
2263 2324 7.725818 ACGGTTCTTAATAAGCTATAAAGGC 57.274 36.000 0.00 0.00 0.00 4.35
2285 2346 7.707774 AATTTCACCATTTTTCAACCTTACG 57.292 32.000 0.00 0.00 0.00 3.18
2291 2352 9.044150 TGAGATCAAATTTCACCATTTTTCAAC 57.956 29.630 0.00 0.00 0.00 3.18
2293 2354 9.781633 AATGAGATCAAATTTCACCATTTTTCA 57.218 25.926 0.00 0.00 0.00 2.69
2315 2376 9.814899 CATATGGTGGCAAACTAATTTTAATGA 57.185 29.630 0.00 0.00 0.00 2.57
2374 2437 2.758423 ACAGACCACAAACAGGTTTTCC 59.242 45.455 0.00 0.00 40.09 3.13
2381 2444 0.947244 GCTCCACAGACCACAAACAG 59.053 55.000 0.00 0.00 0.00 3.16
2412 2475 2.299013 TCTACAAATGACACTGCCGTCT 59.701 45.455 0.00 0.00 36.82 4.18
2423 2486 6.127925 GGCACAACTCATTCATCTACAAATGA 60.128 38.462 0.00 0.00 39.06 2.57
2425 2488 5.711506 TGGCACAACTCATTCATCTACAAAT 59.288 36.000 0.00 0.00 31.92 2.32
2428 2491 4.284829 TGGCACAACTCATTCATCTACA 57.715 40.909 0.00 0.00 31.92 2.74
2449 2512 6.875076 ACTAAAATGCTAACCTACTCGTCAT 58.125 36.000 0.00 0.00 0.00 3.06
2451 2514 6.327934 TGACTAAAATGCTAACCTACTCGTC 58.672 40.000 0.00 0.00 0.00 4.20
2452 2515 6.152323 TCTGACTAAAATGCTAACCTACTCGT 59.848 38.462 0.00 0.00 0.00 4.18
2453 2516 6.561614 TCTGACTAAAATGCTAACCTACTCG 58.438 40.000 0.00 0.00 0.00 4.18
2454 2517 7.982354 ACATCTGACTAAAATGCTAACCTACTC 59.018 37.037 0.00 0.00 0.00 2.59
2455 2518 7.852263 ACATCTGACTAAAATGCTAACCTACT 58.148 34.615 0.00 0.00 0.00 2.57
2456 2519 8.494016 AACATCTGACTAAAATGCTAACCTAC 57.506 34.615 0.00 0.00 0.00 3.18
2457 2520 8.946085 CAAACATCTGACTAAAATGCTAACCTA 58.054 33.333 0.00 0.00 0.00 3.08
2458 2521 7.094205 CCAAACATCTGACTAAAATGCTAACCT 60.094 37.037 0.00 0.00 0.00 3.50
2542 2605 6.119144 TGACACAAAACAGAAGTTTAGAGC 57.881 37.500 0.00 0.00 46.79 4.09
2543 2606 6.634436 GCATGACACAAAACAGAAGTTTAGAG 59.366 38.462 0.00 0.00 46.79 2.43
2559 2623 0.876342 TTGTACGCACGCATGACACA 60.876 50.000 0.00 0.00 0.00 3.72
2573 2637 6.640518 TGGTTGATCTGAATCCTACTTGTAC 58.359 40.000 0.00 0.00 0.00 2.90
2577 2641 7.052873 CAGAATGGTTGATCTGAATCCTACTT 58.947 38.462 0.00 0.00 44.64 2.24
2594 2658 3.726557 TGCAGGAGAATTCAGAATGGT 57.273 42.857 8.44 0.00 36.16 3.55
2623 2687 4.227527 CAGAATAAGGGTGGAAGGTTAGGT 59.772 45.833 0.00 0.00 0.00 3.08
2641 2706 7.255381 CGGATAATTCTTGAGATTTGGCAGAAT 60.255 37.037 0.00 0.00 0.00 2.40
2642 2707 6.038603 CGGATAATTCTTGAGATTTGGCAGAA 59.961 38.462 0.00 0.00 0.00 3.02
2738 2803 4.890158 TTGATTAGCAAGACTGGTCTGA 57.110 40.909 3.88 0.00 40.36 3.27
2858 2923 2.653234 ATGACCTCATGAATGCCTCC 57.347 50.000 0.00 0.00 34.83 4.30
2885 2950 9.421806 CAACAAAATAATGACTTAGCCAATGAA 57.578 29.630 0.00 0.00 0.00 2.57
3006 3072 4.897509 AGGACACTTGATCAGAATGTGA 57.102 40.909 19.61 0.00 40.38 3.58
3010 3076 5.182760 GCTCAAAAGGACACTTGATCAGAAT 59.817 40.000 0.00 0.00 36.93 2.40
3037 3103 1.846007 TGAGGCAGTTGTTTGTGGTT 58.154 45.000 0.00 0.00 0.00 3.67
3078 3144 9.427821 AATAAATATAACACCTAACATGGCCAA 57.572 29.630 10.96 0.00 0.00 4.52
3091 3157 7.755822 TCCAACGGTGCAAAATAAATATAACAC 59.244 33.333 0.00 0.00 0.00 3.32
3097 3163 6.334102 ACTTCCAACGGTGCAAAATAAATA 57.666 33.333 0.00 0.00 0.00 1.40
3102 3168 3.535280 AAACTTCCAACGGTGCAAAAT 57.465 38.095 0.00 0.00 0.00 1.82
3112 3178 5.932619 ATTAATGGGGCTAAACTTCCAAC 57.067 39.130 0.00 0.00 32.56 3.77
3124 3190 5.106078 TGTGAAACTTCGTAATTAATGGGGC 60.106 40.000 0.00 0.00 38.04 5.80
3137 3204 5.389516 GCCAGTATTACAGTGTGAAACTTCG 60.390 44.000 5.88 0.70 36.83 3.79
3176 3243 7.862648 TGCAGTAACACGTAACAAATCAAATA 58.137 30.769 0.00 0.00 0.00 1.40
3177 3244 6.730175 TGCAGTAACACGTAACAAATCAAAT 58.270 32.000 0.00 0.00 0.00 2.32
3185 3252 9.292846 CTATAATTACTGCAGTAACACGTAACA 57.707 33.333 35.31 15.35 42.55 2.41
3186 3253 8.264632 GCTATAATTACTGCAGTAACACGTAAC 58.735 37.037 35.31 20.56 42.55 2.50
3187 3254 7.975058 TGCTATAATTACTGCAGTAACACGTAA 59.025 33.333 35.31 18.39 42.55 3.18
3222 3289 9.103861 GAAAAGGATTGTATTTTGAAACCACAA 57.896 29.630 6.12 6.12 33.44 3.33
3226 3293 7.095229 GCCTGAAAAGGATTGTATTTTGAAACC 60.095 37.037 0.00 0.00 0.00 3.27
3227 3294 7.440856 TGCCTGAAAAGGATTGTATTTTGAAAC 59.559 33.333 0.00 0.00 0.00 2.78
3244 3311 4.444164 GGGGACTTGAAAATTGCCTGAAAA 60.444 41.667 0.00 0.00 37.16 2.29
3265 3332 2.824041 CCACGAATTGCTCCCGGG 60.824 66.667 16.85 16.85 0.00 5.73
3268 3335 2.700773 GCCACCACGAATTGCTCCC 61.701 63.158 0.00 0.00 0.00 4.30
3292 3359 3.106827 CCATACCTGGGGAAAGCAAATT 58.893 45.455 0.00 0.00 39.04 1.82
3295 3362 0.324275 GCCATACCTGGGGAAAGCAA 60.324 55.000 0.00 0.00 43.36 3.91
3313 3380 7.969536 TGGAAGTAAATATAGATGAAGCTGC 57.030 36.000 0.00 0.00 0.00 5.25
3345 3412 5.491982 ACCAGAGAAGGCTTACATTACAAG 58.508 41.667 0.00 0.00 0.00 3.16
3355 3422 1.661463 TGGATGACCAGAGAAGGCTT 58.339 50.000 0.00 0.00 41.77 4.35
3356 3423 3.406442 TGGATGACCAGAGAAGGCT 57.594 52.632 0.00 0.00 41.77 4.58
3387 3455 4.148079 TCCATGTGTTCCAAACTGCATTA 58.852 39.130 0.00 0.00 0.00 1.90
3486 3554 7.552687 TGAGGTCTGCATAAGTTTTAATACCAG 59.447 37.037 0.00 0.00 0.00 4.00
3487 3555 7.398829 TGAGGTCTGCATAAGTTTTAATACCA 58.601 34.615 0.00 0.00 0.00 3.25
3508 3576 7.566945 CTTCTTCAGAAGGCTTCAGAATGAGG 61.567 46.154 28.13 21.65 46.24 3.86
3544 3612 2.847234 ACGGACCTGTGAGGCCAA 60.847 61.111 5.01 0.00 39.63 4.52
3566 3634 4.971282 AGGAAACATGATCTCTGGATGGTA 59.029 41.667 0.00 0.00 31.46 3.25
3798 3870 6.168389 AGGAAAAGAAATTGCAAAGCATAGG 58.832 36.000 1.71 0.00 38.76 2.57
3995 4067 9.938280 GACACAAATACCATGTATATAAGCCTA 57.062 33.333 0.00 0.00 0.00 3.93
4123 4195 4.955811 TGAGCCTGTACCATGGTATTAG 57.044 45.455 27.03 24.46 32.82 1.73
4163 4235 4.634443 ACTAGCCTTGGTTTAATACAAGCG 59.366 41.667 11.97 8.12 42.01 4.68
4184 4256 8.084684 GCTCCAAGAAAATGTTCTGAATTTACT 58.915 33.333 0.00 0.00 43.59 2.24
4195 4267 3.366679 CGCATCTGCTCCAAGAAAATGTT 60.367 43.478 0.09 0.00 39.32 2.71
4373 4482 4.277423 ACAACTTAACACCCAAGCATACAC 59.723 41.667 0.00 0.00 0.00 2.90
4374 4483 4.465886 ACAACTTAACACCCAAGCATACA 58.534 39.130 0.00 0.00 0.00 2.29
4570 4679 7.661437 TCAGTTCAGTTTTAATATGCAGTGTCT 59.339 33.333 0.00 0.00 0.00 3.41
4575 4684 7.592938 TGGTTCAGTTCAGTTTTAATATGCAG 58.407 34.615 0.00 0.00 0.00 4.41
4635 4744 5.995897 GGCTAAAACGGTACCAGATATTGAT 59.004 40.000 13.54 0.00 0.00 2.57
4636 4745 5.129815 AGGCTAAAACGGTACCAGATATTGA 59.870 40.000 13.54 0.00 0.00 2.57
4644 4753 1.420891 ACCAAGGCTAAAACGGTACCA 59.579 47.619 13.54 0.00 0.00 3.25
4721 4831 1.167781 GGGTGGAAAACGGAAGCGAA 61.168 55.000 0.00 0.00 0.00 4.70
4855 4976 2.807967 GCATCACACAAGCTGACAAGTA 59.192 45.455 0.00 0.00 0.00 2.24
4936 5064 0.249615 ATGTCGCCGATCAGTCCATG 60.250 55.000 0.00 0.00 0.00 3.66
5012 5140 4.699735 ACAATGCGGATTGAATAGTCAACA 59.300 37.500 32.67 2.11 46.40 3.33
5035 5163 8.054152 TCTGAATATTTCAAGCTTGTTATGCA 57.946 30.769 25.19 20.84 39.58 3.96
5062 5190 7.675637 GCCACCATATTTTACTTCTGTTCGTAC 60.676 40.741 0.00 0.00 0.00 3.67
5189 5317 5.106712 GCATTCGGTTAATTCAGTCAGTTCA 60.107 40.000 0.00 0.00 0.00 3.18
5285 5414 8.034215 CCTAAAATTGCTCAATGTTATCACCAA 58.966 33.333 5.87 0.00 31.96 3.67
5311 5440 7.434307 GGAACAAGGAAGCTACAAAAAGTAAAC 59.566 37.037 0.00 0.00 30.92 2.01
5542 5671 4.338118 AGCAAAGTTTACAAGTTAGCAGCA 59.662 37.500 0.00 0.00 0.00 4.41
5549 5678 6.509418 TCTTCACAGCAAAGTTTACAAGTT 57.491 33.333 0.00 0.00 0.00 2.66
5756 5889 2.094545 CCATACAGCTTCAAAGGGCAAC 60.095 50.000 0.00 0.00 0.00 4.17
5767 5900 1.063717 CCCATGGGTTCCATACAGCTT 60.064 52.381 23.93 0.00 43.15 3.74
5770 5903 2.105477 CTCTCCCATGGGTTCCATACAG 59.895 54.545 30.28 17.25 43.15 2.74
5880 6013 1.610102 CCACTCTTCACCAGGCTTCAG 60.610 57.143 0.00 0.00 0.00 3.02
6062 6195 9.586435 GGCAGCATTATTTAAGAAATGTACTTT 57.414 29.630 11.36 0.00 35.86 2.66
6065 6198 7.193595 ACGGCAGCATTATTTAAGAAATGTAC 58.806 34.615 11.36 0.00 35.86 2.90
6124 6257 7.566760 TGCAGAATTCTCAAAGTTAACTTCA 57.433 32.000 20.78 10.04 34.61 3.02
6163 6296 7.710475 CCAACTATTCCAAGAACACAAACAAAT 59.290 33.333 0.00 0.00 0.00 2.32
6167 6300 6.144078 ACCAACTATTCCAAGAACACAAAC 57.856 37.500 0.00 0.00 0.00 2.93
6201 6334 9.436957 TCTAAACTAGAACTTTTAGGCATCAAG 57.563 33.333 0.00 0.00 36.39 3.02
6265 6398 5.249420 AGAAAAGAGGGCTCAAAGACATAC 58.751 41.667 0.00 0.00 0.00 2.39
6301 6435 5.954296 ATCACCATGCATTATGTTAGAGC 57.046 39.130 0.00 0.00 34.87 4.09
6309 6443 5.682990 GCTCCAAACAATCACCATGCATTAT 60.683 40.000 0.00 0.00 0.00 1.28
6310 6444 4.381825 GCTCCAAACAATCACCATGCATTA 60.382 41.667 0.00 0.00 0.00 1.90
6331 6471 1.551452 AGTTTGTAGCCTCTCTCGCT 58.449 50.000 0.00 0.00 40.45 4.93
6333 6473 5.061920 AGTTTAGTTTGTAGCCTCTCTCG 57.938 43.478 0.00 0.00 0.00 4.04
6339 6479 6.940298 TGCTTTGATAGTTTAGTTTGTAGCCT 59.060 34.615 0.00 0.00 0.00 4.58
6403 6543 9.372369 GGCTTATCAGTATAATGGAATAGTCAC 57.628 37.037 0.00 0.00 0.00 3.67
6417 6557 5.458215 GGGGATTTTCCTGGCTTATCAGTAT 60.458 44.000 0.00 0.00 36.57 2.12
6439 6579 1.126948 AACCCATTTTGGTGGCAGGG 61.127 55.000 4.30 4.30 39.05 4.45
6447 6587 4.155280 CCTAGACGTTGTAACCCATTTTGG 59.845 45.833 0.00 0.00 37.25 3.28
6463 6603 1.475213 GGCAGGGGATTTTCCTAGACG 60.475 57.143 0.00 0.00 36.57 4.18
6468 6608 1.000866 GCTGGCAGGGGATTTTCCT 59.999 57.895 17.64 0.00 36.57 3.36
6475 6615 4.119363 GCATGAGCTGGCAGGGGA 62.119 66.667 17.64 0.00 37.91 4.81
6560 6744 3.492656 GGCCGTGACTTATAAGCATGAGA 60.493 47.826 21.08 0.00 0.00 3.27
6567 6751 4.124851 ACTTCTGGCCGTGACTTATAAG 57.875 45.455 11.05 11.05 0.00 1.73
6571 6755 1.001633 GGAACTTCTGGCCGTGACTTA 59.998 52.381 0.00 0.00 0.00 2.24
6588 6772 6.208599 GGACCAACTGATGATAAGTTTTGGAA 59.791 38.462 7.52 0.00 35.70 3.53
6589 6773 5.710099 GGACCAACTGATGATAAGTTTTGGA 59.290 40.000 7.52 0.00 35.70 3.53
6750 6934 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
6751 6935 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6752 6936 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
6753 6937 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6754 6938 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
6755 6939 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6756 6940 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
6757 6941 2.695613 TTTGTGTGTGTGTGTGTGTG 57.304 45.000 0.00 0.00 0.00 3.82
6758 6942 5.124617 TCATTATTTGTGTGTGTGTGTGTGT 59.875 36.000 0.00 0.00 0.00 3.72
6759 6943 5.576895 TCATTATTTGTGTGTGTGTGTGTG 58.423 37.500 0.00 0.00 0.00 3.82
6760 6944 5.221028 CCTCATTATTTGTGTGTGTGTGTGT 60.221 40.000 0.00 0.00 0.00 3.72
6761 6945 5.214417 CCTCATTATTTGTGTGTGTGTGTG 58.786 41.667 0.00 0.00 0.00 3.82
6762 6946 4.278170 CCCTCATTATTTGTGTGTGTGTGT 59.722 41.667 0.00 0.00 0.00 3.72
6763 6947 4.518590 TCCCTCATTATTTGTGTGTGTGTG 59.481 41.667 0.00 0.00 0.00 3.82
6764 6948 4.724399 TCCCTCATTATTTGTGTGTGTGT 58.276 39.130 0.00 0.00 0.00 3.72
6765 6949 5.902613 ATCCCTCATTATTTGTGTGTGTG 57.097 39.130 0.00 0.00 0.00 3.82
6785 6969 7.829706 ACTTTTCACACCCTCCTATTCTTTATC 59.170 37.037 0.00 0.00 0.00 1.75
6802 6986 4.399618 TGAAATTTCCCACGACTTTTCACA 59.600 37.500 15.48 0.00 30.08 3.58
6915 7099 7.499563 AGAAATGCGTATCTAGAACTAGTCAGA 59.500 37.037 0.00 0.00 34.84 3.27
6916 7100 7.589587 CAGAAATGCGTATCTAGAACTAGTCAG 59.410 40.741 0.00 0.00 34.84 3.51
6917 7101 7.282450 TCAGAAATGCGTATCTAGAACTAGTCA 59.718 37.037 0.00 0.00 34.84 3.41
6918 7102 7.640852 TCAGAAATGCGTATCTAGAACTAGTC 58.359 38.462 0.00 0.00 34.84 2.59
6919 7103 7.569639 TCAGAAATGCGTATCTAGAACTAGT 57.430 36.000 0.00 0.00 34.84 2.57
6920 7104 8.079203 ACATCAGAAATGCGTATCTAGAACTAG 58.921 37.037 0.00 2.77 34.56 2.57
6921 7105 7.862873 CACATCAGAAATGCGTATCTAGAACTA 59.137 37.037 0.00 0.00 0.00 2.24
6922 7106 6.699204 CACATCAGAAATGCGTATCTAGAACT 59.301 38.462 0.00 0.00 0.00 3.01
6923 7107 6.563010 GCACATCAGAAATGCGTATCTAGAAC 60.563 42.308 0.00 0.00 0.00 3.01
6924 7108 5.463392 GCACATCAGAAATGCGTATCTAGAA 59.537 40.000 0.00 0.00 0.00 2.10
6925 7109 4.984785 GCACATCAGAAATGCGTATCTAGA 59.015 41.667 0.00 0.00 0.00 2.43
6926 7110 5.261370 GCACATCAGAAATGCGTATCTAG 57.739 43.478 0.00 0.00 0.00 2.43
6934 7118 1.197055 CATGCGCACATCAGAAATGC 58.803 50.000 14.90 0.00 32.87 3.56
6935 7119 1.835121 CCATGCGCACATCAGAAATG 58.165 50.000 14.90 3.00 32.87 2.32
6936 7120 0.101759 GCCATGCGCACATCAGAAAT 59.898 50.000 14.90 0.00 37.47 2.17
6937 7121 0.961857 AGCCATGCGCACATCAGAAA 60.962 50.000 14.90 0.00 41.38 2.52
6938 7122 1.377594 AGCCATGCGCACATCAGAA 60.378 52.632 14.90 0.00 41.38 3.02
6939 7123 2.110352 CAGCCATGCGCACATCAGA 61.110 57.895 14.90 0.00 41.38 3.27
6940 7124 2.407616 CAGCCATGCGCACATCAG 59.592 61.111 14.90 0.08 41.38 2.90
6941 7125 3.817655 GCAGCCATGCGCACATCA 61.818 61.111 14.90 0.00 43.87 3.07
6950 7134 2.126071 GCAACAGCAGCAGCCATG 60.126 61.111 0.00 0.00 43.56 3.66
6951 7135 1.469335 AAAGCAACAGCAGCAGCCAT 61.469 50.000 0.00 0.00 43.56 4.40
6952 7136 1.678598 AAAAGCAACAGCAGCAGCCA 61.679 50.000 0.00 0.00 43.56 4.75
6953 7137 0.531311 AAAAAGCAACAGCAGCAGCC 60.531 50.000 0.00 0.00 43.56 4.85
6954 7138 2.981997 AAAAAGCAACAGCAGCAGC 58.018 47.368 0.00 0.00 42.56 5.25


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

AutoCloner maintained by Alex Coulton.