Multiple sequence alignment - TraesCS6A01G099600

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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 TraesCS6A01G099600 chr6A 100.000 3916 0 0 1 3916 67132780 67128865 0.000000e+00 7232.0
1 TraesCS6A01G099600 chr6A 100.000 2924 0 0 4157 7080 67128624 67125701 0.000000e+00 5400.0
2 TraesCS6A01G099600 chr6A 100.000 31 0 0 6691 6721 557926699 557926669 2.760000e-04 58.4
3 TraesCS6A01G099600 chr6B 94.959 2440 99 15 1 2437 123715322 123712904 0.000000e+00 3803.0
4 TraesCS6A01G099600 chr6B 92.397 2157 119 22 4186 6314 123704794 123702655 0.000000e+00 3033.0
5 TraesCS6A01G099600 chr6B 91.723 1027 70 10 2446 3469 123712823 123711809 0.000000e+00 1411.0
6 TraesCS6A01G099600 chr6B 94.000 400 15 3 3465 3860 123705190 123704796 1.310000e-166 597.0
7 TraesCS6A01G099600 chr6B 90.654 321 12 7 6342 6644 123702658 123702338 1.840000e-110 411.0
8 TraesCS6A01G099600 chr6B 92.241 116 7 2 6849 6962 123702200 123702085 5.680000e-36 163.0
9 TraesCS6A01G099600 chr6B 87.755 49 3 1 6720 6765 408680860 408680812 4.000000e-03 54.7
10 TraesCS6A01G099600 chr6D 97.212 2080 51 7 358 2437 47938346 47940418 0.000000e+00 3513.0
11 TraesCS6A01G099600 chr6D 96.026 1409 38 5 4160 5554 47941946 47943350 0.000000e+00 2276.0
12 TraesCS6A01G099600 chr6D 91.520 1474 82 10 2446 3916 47940487 47941920 0.000000e+00 1989.0
13 TraesCS6A01G099600 chr6D 94.671 638 19 3 5538 6162 47943368 47944003 0.000000e+00 976.0
14 TraesCS6A01G099600 chr6D 95.028 362 18 0 1 362 47937862 47938223 2.870000e-158 569.0
15 TraesCS6A01G099600 chr6D 91.946 298 13 6 6343 6639 47944186 47944473 2.380000e-109 407.0
16 TraesCS6A01G099600 chr6D 91.975 162 13 0 6187 6348 47944000 47944161 1.990000e-55 228.0
17 TraesCS6A01G099600 chr6D 79.377 257 38 10 1844 2087 149166877 149167131 4.390000e-37 167.0
18 TraesCS6A01G099600 chr6D 81.529 157 26 3 1847 2001 209103292 209103137 7.460000e-25 126.0
19 TraesCS6A01G099600 chr6D 96.154 52 2 0 6749 6800 47944630 47944681 1.270000e-12 86.1
20 TraesCS6A01G099600 chr6D 100.000 27 0 0 6800 6826 47944698 47944724 4.600000e-02 51.0
21 TraesCS6A01G099600 chr1D 82.803 157 24 3 1847 2001 127859202 127859047 3.440000e-28 137.0
22 TraesCS6A01G099600 chr1D 82.166 157 25 3 1847 2001 105731453 105731298 1.600000e-26 132.0
23 TraesCS6A01G099600 chr4D 81.875 160 26 3 1844 2001 106259449 106259607 1.600000e-26 132.0
24 TraesCS6A01G099600 chr3D 81.875 160 26 3 1844 2001 345804299 345804457 1.600000e-26 132.0
25 TraesCS6A01G099600 chr3D 77.733 247 27 11 1866 2096 468943847 468944081 7.460000e-25 126.0
26 TraesCS6A01G099600 chr3D 78.495 93 14 6 6676 6764 292887830 292887740 1.000000e-03 56.5
27 TraesCS6A01G099600 chr2D 81.098 164 27 4 1841 2001 521813896 521814058 2.070000e-25 128.0
28 TraesCS6A01G099600 chr2D 83.784 111 12 4 6659 6765 513458552 513458660 4.520000e-17 100.0
29 TraesCS6A01G099600 chr2A 88.182 110 9 2 6659 6765 657520729 657520837 2.070000e-25 128.0
30 TraesCS6A01G099600 chr2A 76.446 242 29 11 1866 2091 154095899 154095670 9.710000e-19 106.0
31 TraesCS6A01G099600 chr1A 72.658 395 102 6 1002 1393 577469438 577469829 7.460000e-25 126.0
32 TraesCS6A01G099600 chr1A 77.165 254 29 12 1866 2103 108409173 108409413 3.470000e-23 121.0
33 TraesCS6A01G099600 chr3B 77.551 245 26 11 1866 2093 476218560 476218792 3.470000e-23 121.0
34 TraesCS6A01G099600 chr7A 77.016 248 26 13 1866 2096 273269151 273268918 5.800000e-21 113.0
35 TraesCS6A01G099600 chr7A 89.011 91 7 3 2005 2094 364025239 364025151 7.510000e-20 110.0
36 TraesCS6A01G099600 chr7A 80.519 154 12 7 1956 2093 668815974 668815823 1.260000e-17 102.0
37 TraesCS6A01G099600 chr7A 72.840 324 70 15 4925 5237 598217971 598217655 2.100000e-15 95.3
38 TraesCS6A01G099600 chr7D 72.468 316 73 12 4929 5237 520828856 520828548 9.780000e-14 89.8
39 TraesCS6A01G099600 chr7B 72.152 316 74 12 4929 5237 553884951 553884643 4.550000e-12 84.2
40 TraesCS6A01G099600 chr7B 81.481 108 12 8 6662 6764 734291103 734290999 1.640000e-11 82.4
41 TraesCS6A01G099600 chr7B 78.761 113 18 6 6662 6770 613255692 613255802 3.540000e-08 71.3
42 TraesCS6A01G099600 chr5D 80.000 95 15 3 6671 6762 498715972 498715879 4.580000e-07 67.6
43 TraesCS6A01G099600 chr5B 78.788 99 13 7 6671 6764 582392661 582392566 7.670000e-05 60.2
44 TraesCS6A01G099600 chr1B 84.483 58 5 4 6710 6764 114434164 114434108 4.000000e-03 54.7


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 TraesCS6A01G099600 chr6A 67125701 67132780 7079 True 6316.000000 7232 100.000 1 7080 2 chr6A.!!$R2 7079
1 TraesCS6A01G099600 chr6B 123711809 123715322 3513 True 2607.000000 3803 93.341 1 3469 2 chr6B.!!$R3 3468
2 TraesCS6A01G099600 chr6B 123702085 123705190 3105 True 1051.000000 3033 92.323 3465 6962 4 chr6B.!!$R2 3497
3 TraesCS6A01G099600 chr6D 47937862 47944724 6862 False 1121.677778 3513 94.948 1 6826 9 chr6D.!!$F2 6825


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
466 594 1.189752 TGCTCAAAGTTTGTTGGCCA 58.810 45.000 15.08 0.0 0.00 5.36 F
1418 1550 0.675083 TAGTTCAGAAACCGTCGGCA 59.325 50.000 12.28 0.0 35.92 5.69 F
3194 3410 0.104304 AAACTGTCGACGTGCCTTCT 59.896 50.000 11.62 0.0 0.00 2.85 F
3270 3486 0.639392 ACCTAGTCCTCAGAGCCCAT 59.361 55.000 0.00 0.0 0.00 4.00 F
4706 4954 2.398588 TCGTAATGAGAAGGCCAGGAT 58.601 47.619 5.01 0.0 0.00 3.24 F
5200 5452 5.579904 CCACAGATGCTTCAGGATTATATCG 59.420 44.000 2.07 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2241 2378 0.250553 ATGTGCCCGTTCGGAAAGAA 60.251 50.000 13.08 0.00 36.31 2.52 R
3339 3556 0.037590 AAGGTGGCAATTGCTCCGTA 59.962 50.000 28.42 8.75 41.70 4.02 R
4532 4768 0.928229 GAAGTCGTGCGTTTGTGAGT 59.072 50.000 0.00 0.00 0.00 3.41 R
5200 5452 1.341581 ACTAGTCTGTCCTCCAGCTCC 60.342 57.143 0.00 0.00 41.25 4.70 R
5640 5926 1.070758 GTGCACAGACTCTTTCCCTGA 59.929 52.381 13.17 0.00 0.00 3.86 R
6973 7445 0.038744 CCCAACCAGACTTGAGCCAT 59.961 55.000 0.00 0.00 0.00 4.40 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
145 146 4.142315 GCAATCATGTGCTGTGGAGTATTT 60.142 41.667 1.20 0.00 41.51 1.40
196 197 7.568349 ACTGAATAATTCTCCATTCTAGCACA 58.432 34.615 1.49 0.00 33.26 4.57
197 198 7.497249 ACTGAATAATTCTCCATTCTAGCACAC 59.503 37.037 1.49 0.00 33.26 3.82
220 221 7.560262 ACACCTCATACTTGTATGTCTAGCTTA 59.440 37.037 17.14 0.00 0.00 3.09
332 333 6.866770 CCATTCTGAACATTGATTATGATGGC 59.133 38.462 0.00 0.00 37.69 4.40
355 483 5.674318 GCCATTTGCTTCAAATTATGTTGCC 60.674 40.000 2.35 0.00 40.60 4.52
462 590 2.283351 GCTGCTTGCTCAAAGTTTGTTG 59.717 45.455 15.08 10.42 38.25 3.33
466 594 1.189752 TGCTCAAAGTTTGTTGGCCA 58.810 45.000 15.08 0.00 0.00 5.36
652 782 7.094508 TCTGTTGTAAATTTGCTTCTTCACA 57.905 32.000 7.80 0.00 0.00 3.58
742 872 7.947782 TCATTTGGTAATCCCTCTTAGGTAT 57.052 36.000 0.00 0.00 31.93 2.73
875 1007 9.682465 GTAATTGACTACCTAGAATTTTCCCTT 57.318 33.333 0.00 0.00 0.00 3.95
1223 1355 2.488153 GCCACCCAAACATAGTTGAGAC 59.512 50.000 0.00 0.00 0.00 3.36
1305 1437 1.678627 CTCATGGAGTCGGACCTACAG 59.321 57.143 4.14 0.00 0.00 2.74
1319 1451 3.935828 GACCTACAGAAAGTGATCCAAGC 59.064 47.826 0.00 0.00 0.00 4.01
1350 1482 3.640407 ACTGCAGGGCATCACCGT 61.640 61.111 19.93 0.00 38.13 4.83
1352 1484 1.973281 CTGCAGGGCATCACCGTTT 60.973 57.895 5.57 0.00 38.13 3.60
1418 1550 0.675083 TAGTTCAGAAACCGTCGGCA 59.325 50.000 12.28 0.00 35.92 5.69
1514 1646 7.741785 TCTCATGAAACCCTGTCTTACTTTTA 58.258 34.615 0.00 0.00 0.00 1.52
1518 1650 6.065374 TGAAACCCTGTCTTACTTTTATGCA 58.935 36.000 0.00 0.00 0.00 3.96
1524 1656 8.220559 ACCCTGTCTTACTTTTATGCATATGAT 58.779 33.333 7.36 0.02 0.00 2.45
1588 1721 4.154015 CCGAGCAACATACTTGTCAATTCA 59.846 41.667 0.00 0.00 34.06 2.57
1884 2017 1.247567 CACACCTAAGGTTGGGCAAG 58.752 55.000 0.00 0.00 31.02 4.01
2006 2139 4.540715 CAAGATTCCCTTAGGCTCCAATT 58.459 43.478 0.00 0.00 32.86 2.32
2007 2140 4.888626 AGATTCCCTTAGGCTCCAATTT 57.111 40.909 0.00 0.00 0.00 1.82
2008 2141 4.797743 AGATTCCCTTAGGCTCCAATTTC 58.202 43.478 0.00 0.00 0.00 2.17
2009 2142 2.710096 TCCCTTAGGCTCCAATTTCG 57.290 50.000 0.00 0.00 0.00 3.46
2073 2210 6.017440 GCAAAGTGTGACATTGTTAGTCCTAA 60.017 38.462 1.46 0.00 35.15 2.69
2103 2240 4.195416 CAGCCCCTTAGTCTTCAATTCTC 58.805 47.826 0.00 0.00 0.00 2.87
2119 2256 4.655762 ATTCTCAGCGCACTATAGTCAA 57.344 40.909 11.47 0.00 0.00 3.18
2130 2267 6.579292 GCGCACTATAGTCAAATAGTACAGAG 59.421 42.308 0.30 0.00 40.02 3.35
2160 2297 6.098982 AGCCTCTTGCAGTACTAAATCTGTAT 59.901 38.462 0.00 0.00 44.83 2.29
2280 2417 4.937620 ACATAAGTGCTGGTCATTGTAGTG 59.062 41.667 0.00 0.00 0.00 2.74
2294 2431 4.497473 TTGTAGTGGAAGAAAAATGCCG 57.503 40.909 0.00 0.00 0.00 5.69
2328 2465 1.369209 CACACTGCCAAGAAACGCG 60.369 57.895 3.53 3.53 0.00 6.01
2329 2466 1.522806 ACACTGCCAAGAAACGCGA 60.523 52.632 15.93 0.00 0.00 5.87
2437 2576 2.433446 CTCAGCACCTTGGCACCT 59.567 61.111 0.00 0.00 35.83 4.00
2438 2577 1.228367 CTCAGCACCTTGGCACCTT 60.228 57.895 0.00 0.00 35.83 3.50
2440 2579 2.203538 AGCACCTTGGCACCTTGG 60.204 61.111 0.00 0.00 35.83 3.61
2441 2580 3.994853 GCACCTTGGCACCTTGGC 61.995 66.667 0.00 0.00 44.03 4.52
2497 2708 0.788995 GAGGATGATGATTGAGCGCG 59.211 55.000 0.00 0.00 0.00 6.86
2597 2810 0.175302 AGATGCTGGAGCGAGAAGTG 59.825 55.000 0.00 0.00 45.83 3.16
2625 2838 1.812922 CGAGTGCCAGACCTGATGC 60.813 63.158 0.00 0.00 0.00 3.91
2632 2845 1.153765 CAGACCTGATGCGCGAAGA 60.154 57.895 12.10 0.00 0.00 2.87
2634 2847 1.446099 GACCTGATGCGCGAAGACA 60.446 57.895 12.10 2.95 0.00 3.41
2665 2878 0.445436 CAGATGCGAGTTTGTCCTGC 59.555 55.000 0.00 0.00 0.00 4.85
2667 2880 1.648467 GATGCGAGTTTGTCCTGCCC 61.648 60.000 0.00 0.00 0.00 5.36
2676 2889 3.403558 GTCCTGCCCTCCTGGTCC 61.404 72.222 0.00 0.00 36.04 4.46
2682 2895 2.365635 CCCTCCTGGTCCCACGAT 60.366 66.667 0.00 0.00 0.00 3.73
2694 2907 3.951115 CCACGATGGGCATTGATTG 57.049 52.632 0.00 0.00 32.67 2.67
2698 2911 0.756442 CGATGGGCATTGATTGGGGT 60.756 55.000 0.00 0.00 0.00 4.95
2699 2912 1.043022 GATGGGCATTGATTGGGGTC 58.957 55.000 0.00 0.00 0.00 4.46
2726 2939 1.446272 CTCGCCTTTGGAGACGGTC 60.446 63.158 0.00 0.00 33.27 4.79
2727 2940 2.154798 CTCGCCTTTGGAGACGGTCA 62.155 60.000 11.27 0.00 33.27 4.02
2728 2941 1.738099 CGCCTTTGGAGACGGTCAG 60.738 63.158 11.27 0.00 0.00 3.51
2729 2942 2.035442 GCCTTTGGAGACGGTCAGC 61.035 63.158 11.27 1.69 0.00 4.26
2730 2943 1.376037 CCTTTGGAGACGGTCAGCC 60.376 63.158 11.27 11.52 0.00 4.85
3002 3218 4.019501 GGGTGCTTGAGATATCATGGATCT 60.020 45.833 5.32 9.91 36.33 2.75
3004 3220 6.126825 GGGTGCTTGAGATATCATGGATCTAT 60.127 42.308 5.32 0.00 33.71 1.98
3007 3223 7.280428 GTGCTTGAGATATCATGGATCTATTGG 59.720 40.741 5.32 4.53 33.71 3.16
3039 3255 4.600576 TTCGCTCACCGTGCAGCA 62.601 61.111 17.51 0.00 35.15 4.41
3046 3262 2.009051 CTCACCGTGCAGCAATTGATA 58.991 47.619 10.34 0.00 0.00 2.15
3051 3267 2.095314 CCGTGCAGCAATTGATAACACA 60.095 45.455 21.72 6.77 0.00 3.72
3076 3292 1.482182 CTGACTGCAGCAGGTACCATA 59.518 52.381 26.38 3.72 35.51 2.74
3087 3303 1.060561 AGGTACCATAGGGGCCAGATT 60.061 52.381 15.94 0.00 42.05 2.40
3186 3402 0.776451 CACGAAGGAAACTGTCGACG 59.224 55.000 11.62 8.41 42.68 5.12
3194 3410 0.104304 AAACTGTCGACGTGCCTTCT 59.896 50.000 11.62 0.00 0.00 2.85
3270 3486 0.639392 ACCTAGTCCTCAGAGCCCAT 59.361 55.000 0.00 0.00 0.00 4.00
3339 3556 3.022287 CACACGTTTCGCCAAGCT 58.978 55.556 0.00 0.00 0.00 3.74
3368 3585 3.423154 GCCACCTTTCGCCTCACG 61.423 66.667 0.00 0.00 45.62 4.35
3517 3734 3.069586 CCACCACATATCGCTCTTAAGGA 59.930 47.826 1.85 0.00 0.00 3.36
3541 3759 7.559897 GGAGGTTAGAAATTCCCACATTAATCA 59.440 37.037 0.00 0.00 0.00 2.57
3564 3782 3.476552 AGAGGAAAGCGACATTTCAACA 58.523 40.909 9.46 0.00 40.29 3.33
3660 3878 9.674068 TGTATAAGGATTACAACTGCATTTGTA 57.326 29.630 21.73 21.73 40.29 2.41
3661 3879 9.931210 GTATAAGGATTACAACTGCATTTGTAC 57.069 33.333 24.39 15.86 40.80 2.90
3662 3880 5.545658 AGGATTACAACTGCATTTGTACG 57.454 39.130 24.39 0.29 40.80 3.67
3663 3881 5.001232 AGGATTACAACTGCATTTGTACGT 58.999 37.500 24.39 17.48 40.80 3.57
3762 3984 9.093458 ACCACTCAGGAAATATCTTTGAAAAAT 57.907 29.630 0.00 0.00 41.22 1.82
3788 4010 5.243060 ACCTTTAGAAAGTACCCAAATGCAC 59.757 40.000 0.00 0.00 34.20 4.57
3790 4012 3.237268 AGAAAGTACCCAAATGCACCA 57.763 42.857 0.00 0.00 0.00 4.17
3821 4043 6.134061 GGCGAAAACTGAAGTAGTAAAGTTG 58.866 40.000 0.00 0.00 39.18 3.16
3834 4056 7.949434 AGTAGTAAAGTTGTAAGCAGTACAGT 58.051 34.615 0.00 0.00 43.61 3.55
3862 4084 6.147656 GCACCAATTTTCCTTTCTAAACATGG 59.852 38.462 0.00 0.00 33.28 3.66
3879 4101 6.849588 AACATGGAAATTTTGCTGAACTTC 57.150 33.333 0.00 0.00 0.00 3.01
4184 4406 3.973206 TTCCTACATCACCATGAACGT 57.027 42.857 0.00 0.00 33.72 3.99
4288 4510 3.617284 ACCATTATTTCCTGGGACGAAC 58.383 45.455 0.00 0.00 36.82 3.95
4361 4583 3.458118 TGAAACCCTATCCCAGGTATGTG 59.542 47.826 0.00 0.00 43.80 3.21
4367 4589 4.597507 CCCTATCCCAGGTATGTGTACATT 59.402 45.833 0.00 0.00 43.80 2.71
4381 4603 6.061022 TGTGTACATTATCACCCATTCACT 57.939 37.500 0.00 0.00 34.14 3.41
4482 4718 5.045286 AGACTTGGCCACAGATAGAATTCTT 60.045 40.000 14.36 1.45 0.00 2.52
4532 4768 2.637872 CAGAACTACTTCCCCAACCTGA 59.362 50.000 0.00 0.00 0.00 3.86
4577 4813 7.057894 TGTGTGGTTGGTTCTCTAAGTAAATT 58.942 34.615 0.00 0.00 0.00 1.82
4706 4954 2.398588 TCGTAATGAGAAGGCCAGGAT 58.601 47.619 5.01 0.00 0.00 3.24
4881 5130 6.749923 AGAGTTCTTGCTTTTATGATGACC 57.250 37.500 0.00 0.00 0.00 4.02
5077 5326 8.988060 AGAGATCTGATATATCGAGAGGTAGAA 58.012 37.037 0.00 0.00 0.00 2.10
5116 5365 8.924303 AGTGTATGTTTTAGGCTGACTATATCA 58.076 33.333 0.00 0.00 35.45 2.15
5200 5452 5.579904 CCACAGATGCTTCAGGATTATATCG 59.420 44.000 2.07 0.00 0.00 2.92
5351 5603 7.009083 TCACATTTTGTTTTCACACAGAAATCG 59.991 33.333 0.00 0.00 45.15 3.34
5640 5926 3.758755 TCTGCACTCTTCTTCATGTGT 57.241 42.857 0.00 0.00 33.44 3.72
5665 5951 2.687935 GGAAAGAGTCTGTGCACCAAAA 59.312 45.455 15.69 0.00 0.00 2.44
5671 5957 1.266989 GTCTGTGCACCAAAAGGTAGC 59.733 52.381 15.69 0.00 0.00 3.58
5698 5984 9.809096 GATAATCAAGACTGTAACAATGAGAGA 57.191 33.333 0.00 0.00 0.00 3.10
5806 6092 1.277557 AGCATTCCGAACTTCTGCTCT 59.722 47.619 1.80 0.00 38.78 4.09
5873 6159 1.164662 CGATGAGCATGAAGGCCTGG 61.165 60.000 5.69 0.00 0.00 4.45
5896 6182 0.176219 TACTCCCGGCACCAATTACG 59.824 55.000 0.00 0.00 0.00 3.18
5945 6231 8.933807 CAGGATCTTATAATTATCAGTGCACAG 58.066 37.037 21.04 11.93 0.00 3.66
5965 6251 1.880271 TCACTCTTCTCGTGACGACT 58.120 50.000 2.39 0.00 36.54 4.18
5970 6256 1.060726 CTTCTCGTGACGACTCGTGC 61.061 60.000 9.27 0.84 41.37 5.34
6010 6300 6.245408 ACCAATAGCCAATCTGTTTTCTGTA 58.755 36.000 0.00 0.00 0.00 2.74
6133 6440 1.706443 GCAGCTCCAAATTTCAGCAC 58.294 50.000 17.21 8.08 35.46 4.40
6134 6441 1.000060 GCAGCTCCAAATTTCAGCACA 60.000 47.619 17.21 0.00 35.46 4.57
6135 6442 2.546373 GCAGCTCCAAATTTCAGCACAA 60.546 45.455 17.21 0.00 35.46 3.33
6172 6479 2.947938 CTTATGGGTCCCGGCAGCAG 62.948 65.000 2.65 0.00 0.00 4.24
6175 6482 4.115199 GGGTCCCGGCAGCAGAAT 62.115 66.667 0.00 0.00 0.00 2.40
6177 6484 1.223487 GGTCCCGGCAGCAGAATAA 59.777 57.895 0.00 0.00 0.00 1.40
6179 6486 0.733150 GTCCCGGCAGCAGAATAAAC 59.267 55.000 0.00 0.00 0.00 2.01
6211 6521 0.463654 AGGTGCTGCGAACTTCACAA 60.464 50.000 0.00 0.00 0.00 3.33
6221 6531 3.242712 GCGAACTTCACAACAACCATTTG 59.757 43.478 0.00 0.00 38.83 2.32
6222 6532 3.796178 CGAACTTCACAACAACCATTTGG 59.204 43.478 0.00 0.00 37.00 3.28
6229 6539 6.279513 TCACAACAACCATTTGGATTATCC 57.720 37.500 3.91 3.91 37.00 2.59
6323 6633 3.926289 GGTACCGTACCGTAAGAGC 57.074 57.895 12.01 0.00 39.39 4.09
6329 6639 1.601430 CCGTACCGTAAGAGCCTAGAC 59.399 57.143 0.00 0.00 43.02 2.59
6330 6640 1.601430 CGTACCGTAAGAGCCTAGACC 59.399 57.143 0.00 0.00 43.02 3.85
6348 6658 1.614903 ACCCGAAGAACATCGTGTGTA 59.385 47.619 0.00 0.00 41.14 2.90
6360 6700 4.983538 ACATCGTGTGTAATGTCGTAACAA 59.016 37.500 0.00 0.00 39.91 2.83
6489 6829 2.037847 AAGGGGCCCATGCTGAAC 59.962 61.111 27.72 2.59 37.74 3.18
6588 6928 3.616956 CATAACTGCAAGAGAGGGACA 57.383 47.619 0.00 0.00 37.43 4.02
6589 6929 3.529533 CATAACTGCAAGAGAGGGACAG 58.470 50.000 0.00 0.00 37.43 3.51
6639 6996 3.480470 ACTGAACAACCACTCCATCAAG 58.520 45.455 0.00 0.00 0.00 3.02
6643 7000 4.102524 TGAACAACCACTCCATCAAGTACT 59.897 41.667 0.00 0.00 0.00 2.73
6644 7001 4.706842 ACAACCACTCCATCAAGTACTT 57.293 40.909 1.12 1.12 0.00 2.24
6645 7002 5.048846 ACAACCACTCCATCAAGTACTTT 57.951 39.130 5.07 0.00 0.00 2.66
6646 7003 5.445964 ACAACCACTCCATCAAGTACTTTT 58.554 37.500 5.07 0.00 0.00 2.27
6647 7004 5.891551 ACAACCACTCCATCAAGTACTTTTT 59.108 36.000 5.07 0.00 0.00 1.94
6676 7033 6.380095 ACATCAAGTACTATTCTCTCCGTC 57.620 41.667 0.00 0.00 0.00 4.79
6678 7035 4.205587 TCAAGTACTATTCTCTCCGTCCC 58.794 47.826 0.00 0.00 0.00 4.46
6679 7036 3.947612 AGTACTATTCTCTCCGTCCCA 57.052 47.619 0.00 0.00 0.00 4.37
6685 7042 6.555463 ACTATTCTCTCCGTCCCAAAATAA 57.445 37.500 0.00 0.00 0.00 1.40
6686 7043 6.583562 ACTATTCTCTCCGTCCCAAAATAAG 58.416 40.000 0.00 0.00 0.00 1.73
6687 7044 4.903045 TTCTCTCCGTCCCAAAATAAGT 57.097 40.909 0.00 0.00 0.00 2.24
6688 7045 4.903045 TCTCTCCGTCCCAAAATAAGTT 57.097 40.909 0.00 0.00 0.00 2.66
6690 7047 5.627135 TCTCTCCGTCCCAAAATAAGTTTT 58.373 37.500 0.00 0.00 38.03 2.43
6750 7173 4.654091 ATCAATGCTTATTTTGGGACGG 57.346 40.909 0.00 0.00 0.00 4.79
6762 7185 0.928505 TGGGACGGAGGGAGTACATA 59.071 55.000 0.00 0.00 0.00 2.29
6842 7283 1.911766 GGAGACGGGGACAAGTGGA 60.912 63.158 0.00 0.00 0.00 4.02
6843 7284 1.292541 GAGACGGGGACAAGTGGAC 59.707 63.158 0.00 0.00 0.00 4.02
6845 7286 1.004918 GACGGGGACAAGTGGACTG 60.005 63.158 0.00 0.00 0.00 3.51
6847 7288 2.757077 GGGGACAAGTGGACTGGG 59.243 66.667 0.00 0.00 0.00 4.45
6941 7412 3.759581 CCAGTCCCATATTAATGCAGCT 58.240 45.455 0.00 0.00 0.00 4.24
6962 7434 7.597386 CAGCTAGATGCAGATAACTACATACA 58.403 38.462 0.00 0.00 45.94 2.29
6963 7435 8.249638 CAGCTAGATGCAGATAACTACATACAT 58.750 37.037 0.00 0.00 45.94 2.29
6964 7436 9.467796 AGCTAGATGCAGATAACTACATACATA 57.532 33.333 0.00 0.00 45.94 2.29
6969 7441 8.917415 ATGCAGATAACTACATACATATGACG 57.083 34.615 10.38 0.00 37.15 4.35
6970 7442 8.106247 TGCAGATAACTACATACATATGACGA 57.894 34.615 10.38 0.00 37.15 4.20
6971 7443 8.573035 TGCAGATAACTACATACATATGACGAA 58.427 33.333 10.38 0.00 37.15 3.85
6972 7444 9.406828 GCAGATAACTACATACATATGACGAAA 57.593 33.333 10.38 0.00 37.15 3.46
6977 7449 7.421530 ACTACATACATATGACGAAAATGGC 57.578 36.000 10.38 0.00 37.15 4.40
6978 7450 7.217200 ACTACATACATATGACGAAAATGGCT 58.783 34.615 10.38 0.00 37.15 4.75
6979 7451 6.545504 ACATACATATGACGAAAATGGCTC 57.454 37.500 10.38 0.00 37.15 4.70
6980 7452 6.054941 ACATACATATGACGAAAATGGCTCA 58.945 36.000 10.38 0.00 37.15 4.26
6981 7453 6.542005 ACATACATATGACGAAAATGGCTCAA 59.458 34.615 10.38 0.00 37.15 3.02
6982 7454 5.490139 ACATATGACGAAAATGGCTCAAG 57.510 39.130 10.38 0.00 0.00 3.02
6983 7455 4.943705 ACATATGACGAAAATGGCTCAAGT 59.056 37.500 10.38 0.00 0.00 3.16
6984 7456 5.065218 ACATATGACGAAAATGGCTCAAGTC 59.935 40.000 10.38 0.00 0.00 3.01
6985 7457 3.126001 TGACGAAAATGGCTCAAGTCT 57.874 42.857 0.00 0.00 0.00 3.24
6986 7458 2.807967 TGACGAAAATGGCTCAAGTCTG 59.192 45.455 0.00 0.00 0.00 3.51
6987 7459 2.154462 ACGAAAATGGCTCAAGTCTGG 58.846 47.619 0.00 0.00 0.00 3.86
6988 7460 2.154462 CGAAAATGGCTCAAGTCTGGT 58.846 47.619 0.00 0.00 0.00 4.00
6989 7461 2.554032 CGAAAATGGCTCAAGTCTGGTT 59.446 45.455 0.00 0.00 0.00 3.67
6990 7462 3.610114 CGAAAATGGCTCAAGTCTGGTTG 60.610 47.826 0.00 0.00 0.00 3.77
6991 7463 1.915141 AATGGCTCAAGTCTGGTTGG 58.085 50.000 0.00 0.00 0.00 3.77
6992 7464 0.038744 ATGGCTCAAGTCTGGTTGGG 59.961 55.000 0.00 0.00 0.00 4.12
6993 7465 1.352622 TGGCTCAAGTCTGGTTGGGT 61.353 55.000 0.00 0.00 29.81 4.51
6994 7466 0.890996 GGCTCAAGTCTGGTTGGGTG 60.891 60.000 0.00 0.00 29.81 4.61
6995 7467 0.179018 GCTCAAGTCTGGTTGGGTGT 60.179 55.000 0.00 0.00 29.81 4.16
6996 7468 1.597742 CTCAAGTCTGGTTGGGTGTG 58.402 55.000 0.00 0.00 0.00 3.82
6997 7469 0.916086 TCAAGTCTGGTTGGGTGTGT 59.084 50.000 0.00 0.00 0.00 3.72
6998 7470 1.024271 CAAGTCTGGTTGGGTGTGTG 58.976 55.000 0.00 0.00 0.00 3.82
6999 7471 0.751643 AAGTCTGGTTGGGTGTGTGC 60.752 55.000 0.00 0.00 0.00 4.57
7000 7472 2.203139 TCTGGTTGGGTGTGTGCG 60.203 61.111 0.00 0.00 0.00 5.34
7001 7473 3.286751 CTGGTTGGGTGTGTGCGG 61.287 66.667 0.00 0.00 0.00 5.69
7002 7474 3.765894 CTGGTTGGGTGTGTGCGGA 62.766 63.158 0.00 0.00 0.00 5.54
7003 7475 2.282180 GGTTGGGTGTGTGCGGAT 60.282 61.111 0.00 0.00 0.00 4.18
7004 7476 1.003112 GGTTGGGTGTGTGCGGATA 60.003 57.895 0.00 0.00 0.00 2.59
7005 7477 0.393808 GGTTGGGTGTGTGCGGATAT 60.394 55.000 0.00 0.00 0.00 1.63
7006 7478 0.732571 GTTGGGTGTGTGCGGATATG 59.267 55.000 0.00 0.00 0.00 1.78
7007 7479 0.393673 TTGGGTGTGTGCGGATATGG 60.394 55.000 0.00 0.00 0.00 2.74
7008 7480 1.223487 GGGTGTGTGCGGATATGGT 59.777 57.895 0.00 0.00 0.00 3.55
7009 7481 0.814010 GGGTGTGTGCGGATATGGTC 60.814 60.000 0.00 0.00 0.00 4.02
7010 7482 0.178068 GGTGTGTGCGGATATGGTCT 59.822 55.000 0.00 0.00 0.00 3.85
7011 7483 1.406887 GGTGTGTGCGGATATGGTCTT 60.407 52.381 0.00 0.00 0.00 3.01
7012 7484 2.159014 GGTGTGTGCGGATATGGTCTTA 60.159 50.000 0.00 0.00 0.00 2.10
7013 7485 3.123804 GTGTGTGCGGATATGGTCTTAG 58.876 50.000 0.00 0.00 0.00 2.18
7014 7486 2.764010 TGTGTGCGGATATGGTCTTAGT 59.236 45.455 0.00 0.00 0.00 2.24
7015 7487 3.196901 TGTGTGCGGATATGGTCTTAGTT 59.803 43.478 0.00 0.00 0.00 2.24
7016 7488 4.189231 GTGTGCGGATATGGTCTTAGTTT 58.811 43.478 0.00 0.00 0.00 2.66
7017 7489 4.634443 GTGTGCGGATATGGTCTTAGTTTT 59.366 41.667 0.00 0.00 0.00 2.43
7018 7490 5.813672 GTGTGCGGATATGGTCTTAGTTTTA 59.186 40.000 0.00 0.00 0.00 1.52
7019 7491 6.018994 GTGTGCGGATATGGTCTTAGTTTTAG 60.019 42.308 0.00 0.00 0.00 1.85
7020 7492 6.047231 GTGCGGATATGGTCTTAGTTTTAGT 58.953 40.000 0.00 0.00 0.00 2.24
7021 7493 6.537660 GTGCGGATATGGTCTTAGTTTTAGTT 59.462 38.462 0.00 0.00 0.00 2.24
7022 7494 6.759827 TGCGGATATGGTCTTAGTTTTAGTTC 59.240 38.462 0.00 0.00 0.00 3.01
7023 7495 6.074463 GCGGATATGGTCTTAGTTTTAGTTCG 60.074 42.308 0.00 0.00 0.00 3.95
7024 7496 6.976925 CGGATATGGTCTTAGTTTTAGTTCGT 59.023 38.462 0.00 0.00 0.00 3.85
7025 7497 8.131100 CGGATATGGTCTTAGTTTTAGTTCGTA 58.869 37.037 0.00 0.00 0.00 3.43
7026 7498 9.460906 GGATATGGTCTTAGTTTTAGTTCGTAG 57.539 37.037 0.00 0.00 0.00 3.51
7030 7502 8.621532 TGGTCTTAGTTTTAGTTCGTAGTAGA 57.378 34.615 0.00 0.00 0.00 2.59
7031 7503 9.236006 TGGTCTTAGTTTTAGTTCGTAGTAGAT 57.764 33.333 0.00 0.00 0.00 1.98
7032 7504 9.715123 GGTCTTAGTTTTAGTTCGTAGTAGATC 57.285 37.037 0.00 0.00 0.00 2.75
7037 7509 8.332996 AGTTTTAGTTCGTAGTAGATCACTGA 57.667 34.615 0.00 0.00 38.24 3.41
7038 7510 8.958506 AGTTTTAGTTCGTAGTAGATCACTGAT 58.041 33.333 0.00 0.00 38.24 2.90
7039 7511 9.224058 GTTTTAGTTCGTAGTAGATCACTGATC 57.776 37.037 10.65 10.65 38.24 2.92
7051 7523 5.375417 GATCACTGATCTGATCTGATCGT 57.625 43.478 27.54 24.60 44.12 3.73
7052 7524 5.771469 GATCACTGATCTGATCTGATCGTT 58.229 41.667 27.54 18.45 44.12 3.85
7053 7525 6.890979 ATCACTGATCTGATCTGATCGTTA 57.109 37.500 27.54 21.20 44.12 3.18
7054 7526 6.066054 TCACTGATCTGATCTGATCGTTAC 57.934 41.667 27.54 12.46 44.12 2.50
7055 7527 4.908730 CACTGATCTGATCTGATCGTTACG 59.091 45.833 27.54 18.52 44.12 3.18
7056 7528 4.023622 ACTGATCTGATCTGATCGTTACGG 60.024 45.833 27.54 16.86 44.12 4.02
7057 7529 3.253432 TGATCTGATCTGATCGTTACGGG 59.747 47.826 27.54 0.00 44.12 5.28
7058 7530 1.954382 TCTGATCTGATCGTTACGGGG 59.046 52.381 12.65 0.00 0.00 5.73
7059 7531 1.681793 CTGATCTGATCGTTACGGGGT 59.318 52.381 12.65 0.00 0.00 4.95
7060 7532 2.100916 CTGATCTGATCGTTACGGGGTT 59.899 50.000 12.65 0.00 0.00 4.11
7061 7533 2.498481 TGATCTGATCGTTACGGGGTTT 59.502 45.455 12.65 0.00 0.00 3.27
7062 7534 3.055675 TGATCTGATCGTTACGGGGTTTT 60.056 43.478 12.65 0.00 0.00 2.43
7063 7535 3.405823 TCTGATCGTTACGGGGTTTTT 57.594 42.857 4.53 0.00 0.00 1.94
7064 7536 3.328505 TCTGATCGTTACGGGGTTTTTC 58.671 45.455 4.53 0.00 0.00 2.29
7065 7537 3.007182 TCTGATCGTTACGGGGTTTTTCT 59.993 43.478 4.53 0.00 0.00 2.52
7066 7538 3.742385 TGATCGTTACGGGGTTTTTCTT 58.258 40.909 4.53 0.00 0.00 2.52
7067 7539 4.136051 TGATCGTTACGGGGTTTTTCTTT 58.864 39.130 4.53 0.00 0.00 2.52
7068 7540 4.579753 TGATCGTTACGGGGTTTTTCTTTT 59.420 37.500 4.53 0.00 0.00 2.27
7069 7541 4.979943 TCGTTACGGGGTTTTTCTTTTT 57.020 36.364 4.53 0.00 0.00 1.94
7070 7542 4.919206 TCGTTACGGGGTTTTTCTTTTTC 58.081 39.130 4.53 0.00 0.00 2.29
7071 7543 4.639755 TCGTTACGGGGTTTTTCTTTTTCT 59.360 37.500 4.53 0.00 0.00 2.52
7072 7544 5.125257 TCGTTACGGGGTTTTTCTTTTTCTT 59.875 36.000 4.53 0.00 0.00 2.52
7073 7545 5.806502 CGTTACGGGGTTTTTCTTTTTCTTT 59.193 36.000 0.00 0.00 0.00 2.52
7074 7546 6.310956 CGTTACGGGGTTTTTCTTTTTCTTTT 59.689 34.615 0.00 0.00 0.00 2.27
7075 7547 7.148606 CGTTACGGGGTTTTTCTTTTTCTTTTT 60.149 33.333 0.00 0.00 0.00 1.94
7076 7548 6.730960 ACGGGGTTTTTCTTTTTCTTTTTC 57.269 33.333 0.00 0.00 0.00 2.29
7077 7549 5.644636 ACGGGGTTTTTCTTTTTCTTTTTCC 59.355 36.000 0.00 0.00 0.00 3.13
7078 7550 5.878116 CGGGGTTTTTCTTTTTCTTTTTCCT 59.122 36.000 0.00 0.00 0.00 3.36
7079 7551 6.036735 CGGGGTTTTTCTTTTTCTTTTTCCTC 59.963 38.462 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
187 188 6.154534 ACATACAAGTATGAGGTGTGCTAGAA 59.845 38.462 23.02 0.00 44.22 2.10
196 197 8.534954 TTAAGCTAGACATACAAGTATGAGGT 57.465 34.615 23.02 14.09 44.22 3.85
197 198 9.250624 GTTTAAGCTAGACATACAAGTATGAGG 57.749 37.037 23.02 12.08 44.22 3.86
220 221 4.819630 TCCGAATGAAGCACTGTTAAGTTT 59.180 37.500 0.00 0.00 32.98 2.66
275 276 2.287009 GCTCCGTGTCAACTTTCAAAGG 60.287 50.000 1.31 0.00 0.00 3.11
332 333 5.411977 TGGCAACATAATTTGAAGCAAATGG 59.588 36.000 6.19 3.07 41.87 3.16
355 483 6.741992 ACTACCATCACACACAACAATATG 57.258 37.500 0.00 0.00 0.00 1.78
462 590 6.639632 TGATAGAAAAGCATTAGATTGGCC 57.360 37.500 0.00 0.00 0.00 5.36
630 758 6.862209 ACTGTGAAGAAGCAAATTTACAACA 58.138 32.000 0.00 0.00 0.00 3.33
663 793 7.542025 AGCAAGTTCAGAAATAATTAAGCCAG 58.458 34.615 0.00 0.00 0.00 4.85
742 872 2.224992 TGCAAAAGTTGGAGGGCAGATA 60.225 45.455 0.00 0.00 0.00 1.98
1156 1288 1.656818 CGAAGAATGCGGGTGCCATT 61.657 55.000 0.00 0.00 41.78 3.16
1223 1355 0.890683 GGGAAGCAGGATGTGTTTGG 59.109 55.000 0.00 0.00 39.31 3.28
1305 1437 5.633830 TCTCATTTGCTTGGATCACTTTC 57.366 39.130 0.00 0.00 0.00 2.62
1319 1451 2.486982 CCTGCAGTGAGGTTCTCATTTG 59.513 50.000 13.81 4.88 42.73 2.32
1352 1484 7.370383 GGCATGAAGAAGTTGATACAAGAAAA 58.630 34.615 0.00 0.00 0.00 2.29
1514 1646 6.622245 GCTGCGACAAGATAAATCATATGCAT 60.622 38.462 3.79 3.79 0.00 3.96
1518 1650 8.663025 CATTAGCTGCGACAAGATAAATCATAT 58.337 33.333 0.00 0.00 32.23 1.78
1524 1656 7.786178 AATACATTAGCTGCGACAAGATAAA 57.214 32.000 0.00 0.00 32.23 1.40
1588 1721 6.543831 AGTCACAGATCTTTAGTTTGCAGTTT 59.456 34.615 0.00 0.00 0.00 2.66
1884 2017 5.069501 AGACCTACCTACGTCAATCAAAC 57.930 43.478 0.00 0.00 0.00 2.93
2006 2139 4.339872 TGCCTAAGGTTAGTTCAACGAA 57.660 40.909 0.00 0.00 38.09 3.85
2007 2140 4.202284 ACTTGCCTAAGGTTAGTTCAACGA 60.202 41.667 0.00 0.00 38.09 3.85
2008 2141 4.062991 ACTTGCCTAAGGTTAGTTCAACG 58.937 43.478 0.00 0.00 38.09 4.10
2009 2142 6.206498 CAAACTTGCCTAAGGTTAGTTCAAC 58.794 40.000 0.00 0.00 41.80 3.18
2041 2178 5.900425 ACAATGTCACACTTTGCACAATTA 58.100 33.333 0.00 0.00 36.91 1.40
2073 2210 2.177016 AGACTAAGGGGCTGTTTGGTTT 59.823 45.455 0.00 0.00 0.00 3.27
2103 2240 6.206498 TGTACTATTTGACTATAGTGCGCTG 58.794 40.000 10.90 0.00 42.87 5.18
2160 2297 1.000827 CAATAACAAGCAACACCGGCA 60.001 47.619 0.00 0.00 0.00 5.69
2241 2378 0.250553 ATGTGCCCGTTCGGAAAGAA 60.251 50.000 13.08 0.00 36.31 2.52
2280 2417 3.494045 CCTTCTCGGCATTTTTCTTCC 57.506 47.619 0.00 0.00 0.00 3.46
2294 2431 2.233431 AGTGTGAGACATCTGCCTTCTC 59.767 50.000 0.00 0.00 36.99 2.87
2441 2580 4.332637 GGCTGCACAACGCTGGTG 62.333 66.667 0.50 0.00 43.06 4.17
2442 2581 4.569180 AGGCTGCACAACGCTGGT 62.569 61.111 0.50 0.00 43.06 4.00
2444 2583 3.730761 GGAGGCTGCACAACGCTG 61.731 66.667 0.00 0.00 43.06 5.18
2445 2584 2.184020 TATGGAGGCTGCACAACGCT 62.184 55.000 12.06 0.00 43.06 5.07
2446 2585 1.709147 CTATGGAGGCTGCACAACGC 61.709 60.000 12.06 0.00 42.89 4.84
2497 2708 1.487976 TGGTCAGAGATCCAATGGAGC 59.512 52.381 9.93 9.93 38.56 4.70
2578 2791 0.175302 CACTTCTCGCTCCAGCATCT 59.825 55.000 0.00 0.00 42.21 2.90
2579 2792 0.809241 CCACTTCTCGCTCCAGCATC 60.809 60.000 0.00 0.00 42.21 3.91
2597 2810 2.187163 GGCACTCGGTCCTAAGCC 59.813 66.667 0.00 0.00 34.71 4.35
2625 2838 0.319211 TAACAGGGTGTGTCTTCGCG 60.319 55.000 0.00 0.00 39.03 5.87
2632 2845 2.504367 GCATCTGTTAACAGGGTGTGT 58.496 47.619 30.35 10.95 43.91 3.72
2634 2847 1.346395 TCGCATCTGTTAACAGGGTGT 59.654 47.619 30.35 14.58 43.91 4.16
2665 2878 2.365635 ATCGTGGGACCAGGAGGG 60.366 66.667 17.45 0.00 42.82 4.30
2667 2880 2.903357 CCATCGTGGGACCAGGAG 59.097 66.667 17.45 10.34 42.82 3.69
2676 2889 0.386476 CCAATCAATGCCCATCGTGG 59.614 55.000 0.00 0.00 37.25 4.94
2680 2893 1.043022 GACCCCAATCAATGCCCATC 58.957 55.000 0.00 0.00 0.00 3.51
2682 2895 1.379710 CGACCCCAATCAATGCCCA 60.380 57.895 0.00 0.00 0.00 5.36
2726 2939 3.672293 AACTGATGTTGGCGGCTG 58.328 55.556 11.43 0.00 34.71 4.85
2763 2976 3.126686 GCTCCTCTGAAATGCAAAGTCTC 59.873 47.826 0.00 0.00 0.00 3.36
2982 3198 7.336396 CCAATAGATCCATGATATCTCAAGCA 58.664 38.462 12.24 0.00 35.36 3.91
3002 3218 1.375853 GCATGCACTGACGGCCAATA 61.376 55.000 14.21 0.00 0.00 1.90
3004 3220 3.364441 GCATGCACTGACGGCCAA 61.364 61.111 14.21 0.00 0.00 4.52
3007 3223 2.482374 GAAGCATGCACTGACGGC 59.518 61.111 21.98 0.00 0.00 5.68
3039 3255 5.620654 GCAGTCAGCATGTGTGTTATCAATT 60.621 40.000 0.00 0.00 44.79 2.32
3144 3360 1.800805 CGAGCAAGGTCATGTTGAGT 58.199 50.000 0.00 0.00 0.00 3.41
3176 3392 0.956633 TAGAAGGCACGTCGACAGTT 59.043 50.000 17.16 0.41 42.91 3.16
3186 3402 6.267928 TCACTCCCTATTAAGATAGAAGGCAC 59.732 42.308 0.00 0.00 37.97 5.01
3194 3410 5.087923 TGGGCTCACTCCCTATTAAGATA 57.912 43.478 0.12 0.00 46.67 1.98
3270 3486 1.964223 GCAGATACGAGGAAGATGGGA 59.036 52.381 0.00 0.00 0.00 4.37
3339 3556 0.037590 AAGGTGGCAATTGCTCCGTA 59.962 50.000 28.42 8.75 41.70 4.02
3348 3565 1.074775 TGAGGCGAAAGGTGGCAAT 59.925 52.632 0.00 0.00 0.00 3.56
3368 3585 4.090498 GCAATTTCTTTTGGCGAGTTCATC 59.910 41.667 0.00 0.00 0.00 2.92
3430 3647 0.694444 ACTATGACGGCTGGGGGATT 60.694 55.000 0.00 0.00 0.00 3.01
3517 3734 8.336235 TCTGATTAATGTGGGAATTTCTAACCT 58.664 33.333 0.00 0.00 0.00 3.50
3541 3759 3.685139 TGAAATGTCGCTTTCCTCTCT 57.315 42.857 0.00 0.00 34.83 3.10
3652 3870 6.219302 ACACTTGTTAGTACGTACAAATGC 57.781 37.500 26.55 12.33 35.54 3.56
3660 3878 9.403110 CATAACTCTTAACACTTGTTAGTACGT 57.597 33.333 0.00 0.00 41.03 3.57
3661 3879 8.371053 GCATAACTCTTAACACTTGTTAGTACG 58.629 37.037 2.25 0.00 41.03 3.67
3662 3880 9.199982 TGCATAACTCTTAACACTTGTTAGTAC 57.800 33.333 2.25 0.00 41.03 2.73
3663 3881 9.419297 CTGCATAACTCTTAACACTTGTTAGTA 57.581 33.333 2.25 0.00 41.03 1.82
3704 3926 3.715495 AGCGCATGTTCACATTTGAAAA 58.285 36.364 11.47 0.00 43.52 2.29
3762 3984 5.475564 GCATTTGGGTACTTTCTAAAGGTGA 59.524 40.000 7.34 0.00 40.31 4.02
3778 4000 3.738830 CCATAATCTGGTGCATTTGGG 57.261 47.619 0.00 0.00 40.49 4.12
3788 4010 8.537466 ACTACTTCAGTTTTCGCCATAATCTGG 61.537 40.741 0.00 0.00 40.71 3.86
3790 4012 6.407202 ACTACTTCAGTTTTCGCCATAATCT 58.593 36.000 0.00 0.00 31.59 2.40
3821 4043 1.804748 GGTGCCAACTGTACTGCTTAC 59.195 52.381 0.00 0.00 0.00 2.34
3834 4056 5.878406 TTAGAAAGGAAAATTGGTGCCAA 57.122 34.783 6.08 6.08 40.47 4.52
3862 4084 7.306457 GCAAGAAGAGAAGTTCAGCAAAATTTC 60.306 37.037 5.50 0.00 32.83 2.17
3879 4101 2.540265 AGTGTCCACTGCAAGAAGAG 57.460 50.000 0.00 0.00 40.75 2.85
4156 4378 4.365514 TGGTGATGTAGGAAATGTGTGT 57.634 40.909 0.00 0.00 0.00 3.72
4157 4379 4.943093 TCATGGTGATGTAGGAAATGTGTG 59.057 41.667 0.00 0.00 0.00 3.82
4158 4380 5.178096 TCATGGTGATGTAGGAAATGTGT 57.822 39.130 0.00 0.00 0.00 3.72
4159 4381 5.447683 CGTTCATGGTGATGTAGGAAATGTG 60.448 44.000 0.00 0.00 0.00 3.21
4160 4382 4.635765 CGTTCATGGTGATGTAGGAAATGT 59.364 41.667 0.00 0.00 0.00 2.71
4161 4383 4.635765 ACGTTCATGGTGATGTAGGAAATG 59.364 41.667 0.00 0.00 0.00 2.32
4184 4406 6.423905 GTGTACTGTACAGAGAAAATCAGCAA 59.576 38.462 29.30 0.00 39.77 3.91
4288 4510 2.926200 CAGATCTAGTTGGTGCTTGACG 59.074 50.000 0.00 0.00 0.00 4.35
4361 4583 6.706270 CCACTAGTGAATGGGTGATAATGTAC 59.294 42.308 24.68 0.00 31.83 2.90
4367 4589 4.358214 TGTCCACTAGTGAATGGGTGATA 58.642 43.478 24.68 6.43 36.56 2.15
4381 4603 7.201785 GGAAAACAGTGAAATCTTTGTCCACTA 60.202 37.037 0.00 0.00 36.44 2.74
4482 4718 7.871973 ACATTGTATTGCATTTTACAGAAAGCA 59.128 29.630 0.00 0.00 30.53 3.91
4532 4768 0.928229 GAAGTCGTGCGTTTGTGAGT 59.072 50.000 0.00 0.00 0.00 3.41
4577 4813 9.667107 CTCAAACAGGTTATTATCTAGGAAACA 57.333 33.333 0.00 0.00 0.00 2.83
4647 4883 6.290294 AGCCATGTTAAGAAATTCATTGCT 57.710 33.333 0.00 0.00 35.49 3.91
4706 4954 6.499106 TCCTCTTCATGCCAGTCAAATATA 57.501 37.500 0.00 0.00 0.00 0.86
4881 5130 5.966636 TGTACTCATCAATTTCGGAATCG 57.033 39.130 0.00 0.00 37.82 3.34
4969 5218 2.238521 GGTGAAGGCTCATGTTCCAAA 58.761 47.619 8.32 0.00 33.05 3.28
5200 5452 1.341581 ACTAGTCTGTCCTCCAGCTCC 60.342 57.143 0.00 0.00 41.25 4.70
5293 5545 7.614908 CATACAAAGCATACAATTTCATGTGC 58.385 34.615 0.00 0.00 34.75 4.57
5351 5603 3.197333 GGTTAGACCTCCTAAGTCCCAAC 59.803 52.174 0.00 0.00 37.98 3.77
5640 5926 1.070758 GTGCACAGACTCTTTCCCTGA 59.929 52.381 13.17 0.00 0.00 3.86
5665 5951 6.096423 TGTTACAGTCTTGATTATCGCTACCT 59.904 38.462 0.00 0.00 0.00 3.08
5671 5957 8.634475 TCTCATTGTTACAGTCTTGATTATCG 57.366 34.615 0.00 0.00 0.00 2.92
5806 6092 4.584638 ACCATTCTGCAAGTAATACCCA 57.415 40.909 0.00 0.00 33.76 4.51
5873 6159 1.623542 ATTGGTGCCGGGAGTACCTC 61.624 60.000 2.18 0.00 36.49 3.85
5896 6182 3.879892 GGAGGAATTTAGGCAGTGTCATC 59.120 47.826 0.00 0.00 0.00 2.92
5965 6251 1.992667 CAGTTTCTCGCATAAGCACGA 59.007 47.619 0.00 0.00 42.27 4.35
5970 6256 5.277058 GCTATTGGTCAGTTTCTCGCATAAG 60.277 44.000 0.00 0.00 0.00 1.73
5981 6267 4.307032 ACAGATTGGCTATTGGTCAGTT 57.693 40.909 0.00 0.00 0.00 3.16
6010 6300 2.963371 GAGACGCCGTTCTCCTGT 59.037 61.111 0.00 0.00 36.74 4.00
6211 6521 6.015010 TGTTTTCGGATAATCCAAATGGTTGT 60.015 34.615 0.00 0.00 35.91 3.32
6315 6625 1.334243 CTTCGGGTCTAGGCTCTTACG 59.666 57.143 0.00 0.00 0.00 3.18
6323 6633 1.749634 ACGATGTTCTTCGGGTCTAGG 59.250 52.381 11.53 0.00 43.33 3.02
6330 6640 3.678072 ACATTACACACGATGTTCTTCGG 59.322 43.478 11.53 4.78 43.19 4.30
6348 6658 6.269315 TGTCTGCAATTTTTGTTACGACATT 58.731 32.000 0.00 0.00 35.29 2.71
6360 6700 6.339730 TCACAAACTGAATGTCTGCAATTTT 58.660 32.000 0.00 0.00 0.00 1.82
6453 6793 3.998672 TTCGTCCGTCACTGGCCC 61.999 66.667 0.00 0.00 0.00 5.80
6468 6808 2.037847 AGCATGGGCCCCTTGTTC 59.962 61.111 22.27 5.35 42.56 3.18
6489 6829 4.019174 AGAAATGCTGTGGATTAACTGGG 58.981 43.478 0.00 0.00 0.00 4.45
6587 6927 1.673665 GCTTGACTGACTGGGCCTG 60.674 63.158 9.11 9.11 0.00 4.85
6588 6928 2.753029 GCTTGACTGACTGGGCCT 59.247 61.111 4.53 0.00 0.00 5.19
6589 6929 2.360475 GGCTTGACTGACTGGGCC 60.360 66.667 0.00 0.00 0.00 5.80
6647 7004 9.436957 GGAGAGAATAGTACTTGATGTTCAAAA 57.563 33.333 0.00 0.00 35.73 2.44
6648 7005 7.759886 CGGAGAGAATAGTACTTGATGTTCAAA 59.240 37.037 0.00 0.00 35.73 2.69
6649 7006 7.093902 ACGGAGAGAATAGTACTTGATGTTCAA 60.094 37.037 0.00 0.00 34.79 2.69
6650 7007 6.377429 ACGGAGAGAATAGTACTTGATGTTCA 59.623 38.462 0.00 0.00 0.00 3.18
6651 7008 6.797454 ACGGAGAGAATAGTACTTGATGTTC 58.203 40.000 0.00 0.00 0.00 3.18
6652 7009 6.183360 GGACGGAGAGAATAGTACTTGATGTT 60.183 42.308 0.00 0.00 0.00 2.71
6653 7010 5.299782 GGACGGAGAGAATAGTACTTGATGT 59.700 44.000 0.00 0.00 0.00 3.06
6654 7011 5.278561 GGGACGGAGAGAATAGTACTTGATG 60.279 48.000 0.00 0.00 0.00 3.07
6655 7012 4.828387 GGGACGGAGAGAATAGTACTTGAT 59.172 45.833 0.00 0.00 0.00 2.57
6656 7013 4.205587 GGGACGGAGAGAATAGTACTTGA 58.794 47.826 0.00 0.00 0.00 3.02
6657 7014 3.952323 TGGGACGGAGAGAATAGTACTTG 59.048 47.826 0.00 0.00 0.00 3.16
6658 7015 4.246712 TGGGACGGAGAGAATAGTACTT 57.753 45.455 0.00 0.00 0.00 2.24
6659 7016 3.947612 TGGGACGGAGAGAATAGTACT 57.052 47.619 0.00 0.00 0.00 2.73
6660 7017 4.996788 TTTGGGACGGAGAGAATAGTAC 57.003 45.455 0.00 0.00 0.00 2.73
6666 7023 4.903045 ACTTATTTTGGGACGGAGAGAA 57.097 40.909 0.00 0.00 0.00 2.87
6723 7080 8.402472 CGTCCCAAAATAAGCATTGATTTAGTA 58.598 33.333 0.00 0.00 0.00 1.82
6725 7082 6.697019 CCGTCCCAAAATAAGCATTGATTTAG 59.303 38.462 0.00 0.00 0.00 1.85
6726 7083 6.378564 TCCGTCCCAAAATAAGCATTGATTTA 59.621 34.615 0.00 0.00 0.00 1.40
6730 7087 3.691575 TCCGTCCCAAAATAAGCATTGA 58.308 40.909 0.00 0.00 0.00 2.57
6732 7089 3.023832 CCTCCGTCCCAAAATAAGCATT 58.976 45.455 0.00 0.00 0.00 3.56
6734 7091 1.340600 CCCTCCGTCCCAAAATAAGCA 60.341 52.381 0.00 0.00 0.00 3.91
6735 7092 1.064979 TCCCTCCGTCCCAAAATAAGC 60.065 52.381 0.00 0.00 0.00 3.09
6737 7094 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
6743 7166 0.928505 TATGTACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
6745 7168 2.361438 CTGTTATGTACTCCCTCCGTCC 59.639 54.545 0.00 0.00 0.00 4.79
6746 7169 3.285484 TCTGTTATGTACTCCCTCCGTC 58.715 50.000 0.00 0.00 0.00 4.79
6747 7170 3.377253 TCTGTTATGTACTCCCTCCGT 57.623 47.619 0.00 0.00 0.00 4.69
6750 7173 5.294552 GCATGTTTCTGTTATGTACTCCCTC 59.705 44.000 0.00 0.00 0.00 4.30
6847 7288 4.980805 TCACCCTTGTGGCGACGC 62.981 66.667 12.43 12.43 42.98 5.19
6893 7364 2.150014 TAAGTTGCCCTGCCTTCCCC 62.150 60.000 0.00 0.00 0.00 4.81
6954 7426 7.384932 TGAGCCATTTTCGTCATATGTATGTAG 59.615 37.037 1.90 0.00 35.26 2.74
6956 7428 6.054941 TGAGCCATTTTCGTCATATGTATGT 58.945 36.000 1.90 0.00 35.26 2.29
6962 7434 5.295292 CAGACTTGAGCCATTTTCGTCATAT 59.705 40.000 0.00 0.00 0.00 1.78
6963 7435 4.631377 CAGACTTGAGCCATTTTCGTCATA 59.369 41.667 0.00 0.00 0.00 2.15
6964 7436 3.438087 CAGACTTGAGCCATTTTCGTCAT 59.562 43.478 0.00 0.00 0.00 3.06
6965 7437 2.807967 CAGACTTGAGCCATTTTCGTCA 59.192 45.455 0.00 0.00 0.00 4.35
6966 7438 2.160417 CCAGACTTGAGCCATTTTCGTC 59.840 50.000 0.00 0.00 0.00 4.20
6967 7439 2.154462 CCAGACTTGAGCCATTTTCGT 58.846 47.619 0.00 0.00 0.00 3.85
6968 7440 2.154462 ACCAGACTTGAGCCATTTTCG 58.846 47.619 0.00 0.00 0.00 3.46
6969 7441 3.305608 CCAACCAGACTTGAGCCATTTTC 60.306 47.826 0.00 0.00 0.00 2.29
6970 7442 2.629617 CCAACCAGACTTGAGCCATTTT 59.370 45.455 0.00 0.00 0.00 1.82
6971 7443 2.242043 CCAACCAGACTTGAGCCATTT 58.758 47.619 0.00 0.00 0.00 2.32
6972 7444 1.548582 CCCAACCAGACTTGAGCCATT 60.549 52.381 0.00 0.00 0.00 3.16
6973 7445 0.038744 CCCAACCAGACTTGAGCCAT 59.961 55.000 0.00 0.00 0.00 4.40
6974 7446 1.352622 ACCCAACCAGACTTGAGCCA 61.353 55.000 0.00 0.00 0.00 4.75
6975 7447 0.890996 CACCCAACCAGACTTGAGCC 60.891 60.000 0.00 0.00 0.00 4.70
6976 7448 0.179018 ACACCCAACCAGACTTGAGC 60.179 55.000 0.00 0.00 0.00 4.26
6977 7449 1.134098 ACACACCCAACCAGACTTGAG 60.134 52.381 0.00 0.00 0.00 3.02
6978 7450 0.916086 ACACACCCAACCAGACTTGA 59.084 50.000 0.00 0.00 0.00 3.02
6979 7451 1.024271 CACACACCCAACCAGACTTG 58.976 55.000 0.00 0.00 0.00 3.16
6980 7452 0.751643 GCACACACCCAACCAGACTT 60.752 55.000 0.00 0.00 0.00 3.01
6981 7453 1.152963 GCACACACCCAACCAGACT 60.153 57.895 0.00 0.00 0.00 3.24
6982 7454 2.542907 CGCACACACCCAACCAGAC 61.543 63.158 0.00 0.00 0.00 3.51
6983 7455 2.203139 CGCACACACCCAACCAGA 60.203 61.111 0.00 0.00 0.00 3.86
6984 7456 3.286751 CCGCACACACCCAACCAG 61.287 66.667 0.00 0.00 0.00 4.00
6985 7457 1.769716 TATCCGCACACACCCAACCA 61.770 55.000 0.00 0.00 0.00 3.67
6986 7458 0.393808 ATATCCGCACACACCCAACC 60.394 55.000 0.00 0.00 0.00 3.77
6987 7459 0.732571 CATATCCGCACACACCCAAC 59.267 55.000 0.00 0.00 0.00 3.77
6988 7460 0.393673 CCATATCCGCACACACCCAA 60.394 55.000 0.00 0.00 0.00 4.12
6989 7461 1.223211 CCATATCCGCACACACCCA 59.777 57.895 0.00 0.00 0.00 4.51
6990 7462 0.814010 GACCATATCCGCACACACCC 60.814 60.000 0.00 0.00 0.00 4.61
6991 7463 0.178068 AGACCATATCCGCACACACC 59.822 55.000 0.00 0.00 0.00 4.16
6992 7464 2.024176 AAGACCATATCCGCACACAC 57.976 50.000 0.00 0.00 0.00 3.82
6993 7465 2.764010 ACTAAGACCATATCCGCACACA 59.236 45.455 0.00 0.00 0.00 3.72
6994 7466 3.454371 ACTAAGACCATATCCGCACAC 57.546 47.619 0.00 0.00 0.00 3.82
6995 7467 4.481368 AAACTAAGACCATATCCGCACA 57.519 40.909 0.00 0.00 0.00 4.57
6996 7468 6.047231 ACTAAAACTAAGACCATATCCGCAC 58.953 40.000 0.00 0.00 0.00 5.34
6997 7469 6.229936 ACTAAAACTAAGACCATATCCGCA 57.770 37.500 0.00 0.00 0.00 5.69
6998 7470 6.074463 CGAACTAAAACTAAGACCATATCCGC 60.074 42.308 0.00 0.00 0.00 5.54
6999 7471 6.976925 ACGAACTAAAACTAAGACCATATCCG 59.023 38.462 0.00 0.00 0.00 4.18
7000 7472 9.460906 CTACGAACTAAAACTAAGACCATATCC 57.539 37.037 0.00 0.00 0.00 2.59
7004 7476 9.236006 TCTACTACGAACTAAAACTAAGACCAT 57.764 33.333 0.00 0.00 0.00 3.55
7005 7477 8.621532 TCTACTACGAACTAAAACTAAGACCA 57.378 34.615 0.00 0.00 0.00 4.02
7006 7478 9.715123 GATCTACTACGAACTAAAACTAAGACC 57.285 37.037 0.00 0.00 0.00 3.85
7011 7483 9.440773 TCAGTGATCTACTACGAACTAAAACTA 57.559 33.333 0.00 0.00 37.60 2.24
7012 7484 8.332996 TCAGTGATCTACTACGAACTAAAACT 57.667 34.615 0.00 0.00 37.60 2.66
7013 7485 9.224058 GATCAGTGATCTACTACGAACTAAAAC 57.776 37.037 23.33 0.00 37.60 2.43
7014 7486 9.175312 AGATCAGTGATCTACTACGAACTAAAA 57.825 33.333 30.16 0.00 46.15 1.52
7015 7487 8.613482 CAGATCAGTGATCTACTACGAACTAAA 58.387 37.037 30.54 0.00 46.25 1.85
7016 7488 7.985752 TCAGATCAGTGATCTACTACGAACTAA 59.014 37.037 30.54 4.03 46.25 2.24
7017 7489 7.498443 TCAGATCAGTGATCTACTACGAACTA 58.502 38.462 30.54 4.35 46.25 2.24
7018 7490 6.350103 TCAGATCAGTGATCTACTACGAACT 58.650 40.000 30.54 6.82 46.25 3.01
7019 7491 6.606234 TCAGATCAGTGATCTACTACGAAC 57.394 41.667 30.54 4.37 46.25 3.95
7020 7492 7.428282 GATCAGATCAGTGATCTACTACGAA 57.572 40.000 30.54 13.35 46.25 3.85
7030 7502 5.787953 AACGATCAGATCAGATCAGTGAT 57.212 39.130 23.21 12.94 43.61 3.06
7031 7503 5.277538 CGTAACGATCAGATCAGATCAGTGA 60.278 44.000 23.21 14.19 43.61 3.41
7032 7504 4.908730 CGTAACGATCAGATCAGATCAGTG 59.091 45.833 23.21 12.44 43.61 3.66
7033 7505 4.023622 CCGTAACGATCAGATCAGATCAGT 60.024 45.833 23.21 18.72 43.61 3.41
7034 7506 4.471373 CCGTAACGATCAGATCAGATCAG 58.529 47.826 23.21 18.22 43.61 2.90
7035 7507 3.253432 CCCGTAACGATCAGATCAGATCA 59.747 47.826 23.21 5.87 43.61 2.92
7036 7508 3.366476 CCCCGTAACGATCAGATCAGATC 60.366 52.174 16.10 16.10 40.76 2.75
7037 7509 2.558795 CCCCGTAACGATCAGATCAGAT 59.441 50.000 11.12 0.00 0.00 2.90
7038 7510 1.954382 CCCCGTAACGATCAGATCAGA 59.046 52.381 11.12 0.00 0.00 3.27
7039 7511 1.681793 ACCCCGTAACGATCAGATCAG 59.318 52.381 11.12 6.05 0.00 2.90
7040 7512 1.771565 ACCCCGTAACGATCAGATCA 58.228 50.000 11.12 0.00 0.00 2.92
7041 7513 2.884894 AACCCCGTAACGATCAGATC 57.115 50.000 0.00 0.00 0.00 2.75
7042 7514 3.622166 AAAACCCCGTAACGATCAGAT 57.378 42.857 0.00 0.00 0.00 2.90
7043 7515 3.007182 AGAAAAACCCCGTAACGATCAGA 59.993 43.478 0.00 0.00 0.00 3.27
7044 7516 3.332034 AGAAAAACCCCGTAACGATCAG 58.668 45.455 0.00 0.00 0.00 2.90
7045 7517 3.405823 AGAAAAACCCCGTAACGATCA 57.594 42.857 0.00 0.00 0.00 2.92
7046 7518 4.754372 AAAGAAAAACCCCGTAACGATC 57.246 40.909 0.00 0.00 0.00 3.69
7047 7519 5.300034 AGAAAAAGAAAAACCCCGTAACGAT 59.700 36.000 0.00 0.00 0.00 3.73
7048 7520 4.639755 AGAAAAAGAAAAACCCCGTAACGA 59.360 37.500 0.00 0.00 0.00 3.85
7049 7521 4.923893 AGAAAAAGAAAAACCCCGTAACG 58.076 39.130 0.00 0.00 0.00 3.18
7050 7522 7.599630 AAAAGAAAAAGAAAAACCCCGTAAC 57.400 32.000 0.00 0.00 0.00 2.50
7051 7523 7.333921 GGAAAAAGAAAAAGAAAAACCCCGTAA 59.666 33.333 0.00 0.00 0.00 3.18
7052 7524 6.817641 GGAAAAAGAAAAAGAAAAACCCCGTA 59.182 34.615 0.00 0.00 0.00 4.02
7053 7525 5.644636 GGAAAAAGAAAAAGAAAAACCCCGT 59.355 36.000 0.00 0.00 0.00 5.28
7054 7526 5.878116 AGGAAAAAGAAAAAGAAAAACCCCG 59.122 36.000 0.00 0.00 0.00 5.73
7055 7527 7.316544 GAGGAAAAAGAAAAAGAAAAACCCC 57.683 36.000 0.00 0.00 0.00 4.95



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

AutoCloner maintained by Alex Coulton.