Multiple sequence alignment - TraesCS4A01G268900

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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 TraesCS4A01G268900 chr4A 100.000 3412 0 0 1 3412 581147192 581150603 0.000000e+00 6301.0
1 TraesCS4A01G268900 chr4B 87.449 2191 152 52 1 2126 32492035 32489903 0.000000e+00 2409.0
2 TraesCS4A01G268900 chr4B 94.431 808 35 5 2125 2931 32488451 32487653 0.000000e+00 1234.0
3 TraesCS4A01G268900 chr4B 89.410 831 77 6 3 830 32493012 32492190 0.000000e+00 1037.0
4 TraesCS4A01G268900 chr4B 86.320 519 46 8 2404 2916 394813490 394813989 2.990000e-150 542.0
5 TraesCS4A01G268900 chr4B 87.004 454 34 10 2436 2883 637162794 637163228 3.960000e-134 488.0
6 TraesCS4A01G268900 chr4B 83.391 289 23 10 2601 2883 94044222 94043953 9.460000e-61 244.0
7 TraesCS4A01G268900 chr4B 96.923 65 2 0 3047 3111 32487654 32487590 3.600000e-20 110.0
8 TraesCS4A01G268900 chr4B 92.958 71 5 0 1918 1988 32489994 32490064 1.670000e-18 104.0
9 TraesCS4A01G268900 chr4D 94.034 1056 48 8 750 1803 20540757 20539715 0.000000e+00 1587.0
10 TraesCS4A01G268900 chr4D 91.518 896 54 8 2034 2916 20539651 20538765 0.000000e+00 1214.0
11 TraesCS4A01G268900 chr4D 90.263 760 63 10 3 757 20541732 20540979 0.000000e+00 983.0
12 TraesCS4A01G268900 chr4D 98.438 64 1 0 1856 1919 20539713 20539650 2.780000e-21 113.0
13 TraesCS4A01G268900 chr4D 91.045 67 2 2 3350 3412 20536181 20536115 1.690000e-13 87.9
14 TraesCS4A01G268900 chr4D 96.296 54 1 1 1987 2039 451152205 451152152 1.690000e-13 87.9
15 TraesCS4A01G268900 chr5B 88.108 555 41 10 2335 2883 540795292 540794757 1.340000e-178 636.0
16 TraesCS4A01G268900 chr5B 80.836 287 30 10 2636 2916 431372894 431373161 5.770000e-48 202.0
17 TraesCS4A01G268900 chr5B 95.238 42 2 0 1994 2035 673767959 673768000 2.200000e-07 67.6
18 TraesCS4A01G268900 chr2B 89.328 506 35 6 2335 2840 97328096 97328582 4.840000e-173 617.0
19 TraesCS4A01G268900 chr2B 86.905 168 19 3 3159 3325 529692415 529692250 5.810000e-43 185.0
20 TraesCS4A01G268900 chr2B 97.917 48 1 0 1987 2034 552427081 552427034 2.180000e-12 84.2
21 TraesCS4A01G268900 chr2B 96.774 31 1 0 1829 1859 799576589 799576559 6.000000e-03 52.8
22 TraesCS4A01G268900 chr6B 87.387 555 44 9 2368 2916 208793298 208793832 6.260000e-172 614.0
23 TraesCS4A01G268900 chr6B 87.665 454 31 8 2436 2883 177349754 177350188 3.930000e-139 505.0
24 TraesCS4A01G268900 chr6B 86.564 454 36 10 2436 2883 677106183 677105749 8.570000e-131 477.0
25 TraesCS4A01G268900 chr6B 81.185 287 29 11 2636 2916 2325806 2325539 1.240000e-49 207.0
26 TraesCS4A01G268900 chr7B 86.667 555 49 8 2368 2916 205798648 205799183 2.930000e-165 592.0
27 TraesCS4A01G268900 chr7B 82.524 206 24 5 2717 2916 365276781 365276980 1.630000e-38 171.0
28 TraesCS4A01G268900 chr3B 86.126 555 52 12 2368 2916 246890076 246889541 2.950000e-160 575.0
29 TraesCS4A01G268900 chr3B 82.039 206 25 5 2717 2916 824084983 824085182 7.570000e-37 165.0
30 TraesCS4A01G268900 chr3B 91.045 67 6 0 1920 1986 181287006 181287072 1.300000e-14 91.6
31 TraesCS4A01G268900 chr3B 92.593 54 4 0 1991 2044 181287048 181286995 1.020000e-10 78.7
32 TraesCS4A01G268900 chr1B 87.558 434 33 10 2436 2867 492594356 492593942 1.840000e-132 483.0
33 TraesCS4A01G268900 chr1B 85.185 324 28 9 2548 2870 15195333 15195029 7.110000e-82 315.0
34 TraesCS4A01G268900 chr1B 83.045 289 24 9 2601 2883 603892764 603893033 4.400000e-59 239.0
35 TraesCS4A01G268900 chr1D 89.744 78 7 1 1908 1985 324624119 324624195 7.790000e-17 99.0
36 TraesCS4A01G268900 chr1D 89.655 58 4 2 1982 2037 50709230 50709173 4.720000e-09 73.1
37 TraesCS4A01G268900 chr7A 90.141 71 7 0 1918 1988 82204212 82204142 3.630000e-15 93.5
38 TraesCS4A01G268900 chr7A 92.982 57 4 0 1980 2036 711827685 711827741 2.180000e-12 84.2
39 TraesCS4A01G268900 chr7A 97.059 34 1 0 1828 1861 29834605 29834572 1.320000e-04 58.4
40 TraesCS4A01G268900 chr6D 90.141 71 7 0 1918 1988 437332694 437332624 3.630000e-15 93.5
41 TraesCS4A01G268900 chr6D 95.918 49 2 0 1987 2035 437332649 437332601 2.820000e-11 80.5
42 TraesCS4A01G268900 chr1A 87.654 81 9 1 1908 1988 420380693 420380614 3.630000e-15 93.5
43 TraesCS4A01G268900 chr3D 90.000 70 5 2 1919 1987 126947365 126947297 4.690000e-14 89.8
44 TraesCS4A01G268900 chr6A 88.732 71 8 0 1918 1988 572166262 572166192 1.690000e-13 87.9
45 TraesCS4A01G268900 chr6A 97.222 36 1 0 1822 1857 447628326 447628291 1.020000e-05 62.1
46 TraesCS4A01G268900 chr7D 95.652 46 2 0 1990 2035 468940428 468940473 1.310000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G268900 chr4A 581147192 581150603 3411 False 6301.00 6301 100.00000 1 3412 1 chr4A.!!$F1 3411
1 TraesCS4A01G268900 chr4B 32487590 32493012 5422 True 1197.50 2409 92.05325 1 3111 4 chr4B.!!$R2 3110
2 TraesCS4A01G268900 chr4D 20536115 20541732 5617 True 796.98 1587 93.05960 3 3412 5 chr4D.!!$R2 3409
3 TraesCS4A01G268900 chr5B 540794757 540795292 535 True 636.00 636 88.10800 2335 2883 1 chr5B.!!$R1 548
4 TraesCS4A01G268900 chr6B 208793298 208793832 534 False 614.00 614 87.38700 2368 2916 1 chr6B.!!$F2 548
5 TraesCS4A01G268900 chr7B 205798648 205799183 535 False 592.00 592 86.66700 2368 2916 1 chr7B.!!$F1 548
6 TraesCS4A01G268900 chr3B 246889541 246890076 535 True 575.00 575 86.12600 2368 2916 1 chr3B.!!$R2 548

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
387 390 0.395586 TTGTCCAAAGGTGCTGCTGT 60.396 50.0 0.0 0.0 0.00 4.40 F
924 2154 0.673956 TCTCCACGTGACCTCTCTCG 60.674 60.0 19.3 0.0 38.95 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1315 2560 1.592223 CGAGGACCTCCCAGTTGTC 59.408 63.158 16.13 0.0 37.41 3.18 R
2698 5426 1.880027 GCAAACCACTGGAGTACCAAG 59.120 52.381 0.71 0.0 46.32 3.61 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
35 36 1.117994 CTGATGAGCAGGAGTAGCCA 58.882 55.000 0.00 0.00 41.07 4.75
39 40 0.898320 TGAGCAGGAGTAGCCACTTC 59.102 55.000 0.00 0.00 40.02 3.01
53 54 6.768381 AGTAGCCACTTCATAGAAAATAAGCC 59.232 38.462 0.00 0.00 0.00 4.35
82 83 0.908198 CTAACCCTGCTCTGCCTTCT 59.092 55.000 0.00 0.00 0.00 2.85
115 117 9.973450 TGCTCTATTTCTACAGATCTTATTGTC 57.027 33.333 0.00 0.00 0.00 3.18
127 129 4.764050 TCTTATTGTCGGGCCAAAGATA 57.236 40.909 4.39 0.00 0.00 1.98
132 135 4.712122 TTGTCGGGCCAAAGATATTTTC 57.288 40.909 4.39 0.00 0.00 2.29
133 136 3.691575 TGTCGGGCCAAAGATATTTTCA 58.308 40.909 4.39 0.00 0.00 2.69
138 141 4.339247 CGGGCCAAAGATATTTTCAGATGT 59.661 41.667 4.39 0.00 0.00 3.06
193 196 3.696051 TGCACCTTCCAGCAATAAGATTC 59.304 43.478 0.00 0.00 37.90 2.52
194 197 3.696051 GCACCTTCCAGCAATAAGATTCA 59.304 43.478 0.00 0.00 0.00 2.57
195 198 4.158394 GCACCTTCCAGCAATAAGATTCAA 59.842 41.667 0.00 0.00 0.00 2.69
197 200 5.183713 CACCTTCCAGCAATAAGATTCAACA 59.816 40.000 0.00 0.00 0.00 3.33
273 276 5.709164 CCACAATGGATCAAACTTCTTCTCT 59.291 40.000 0.00 0.00 40.96 3.10
290 293 2.368548 TCTCTGCTTGTGGTTGAAGCTA 59.631 45.455 0.00 0.00 45.14 3.32
381 384 3.421844 ACCTATCTTTGTCCAAAGGTGC 58.578 45.455 17.25 0.00 45.80 5.01
387 390 0.395586 TTGTCCAAAGGTGCTGCTGT 60.396 50.000 0.00 0.00 0.00 4.40
392 395 1.027357 CAAAGGTGCTGCTGTCAAGT 58.973 50.000 0.00 0.00 0.00 3.16
424 427 1.798079 GCTCGTACTCGTTGGGACATC 60.798 57.143 0.00 0.00 38.33 3.06
436 439 2.765276 TTGGGACATCAGGGAACACCTA 60.765 50.000 0.00 0.00 44.89 3.08
444 447 2.836944 GGGAACACCTACTTGCGTC 58.163 57.895 0.00 0.00 35.85 5.19
514 517 3.285484 GGATCTCAATGGAGTTGTGCAT 58.715 45.455 0.00 0.00 42.05 3.96
516 519 3.144657 TCTCAATGGAGTTGTGCATGT 57.855 42.857 0.00 0.00 42.05 3.21
538 541 3.007506 TCTGTGCTCATCGGGTTCTAAAA 59.992 43.478 0.00 0.00 0.00 1.52
540 543 3.500680 TGTGCTCATCGGGTTCTAAAAAC 59.499 43.478 0.00 0.00 0.00 2.43
541 544 3.500680 GTGCTCATCGGGTTCTAAAAACA 59.499 43.478 0.00 0.00 0.00 2.83
542 545 3.751175 TGCTCATCGGGTTCTAAAAACAG 59.249 43.478 0.00 0.00 0.00 3.16
548 551 4.773013 TCGGGTTCTAAAAACAGAAGTGT 58.227 39.130 0.00 0.00 39.19 3.55
550 553 4.573201 CGGGTTCTAAAAACAGAAGTGTGA 59.427 41.667 0.00 0.00 36.84 3.58
555 558 7.309920 GTTCTAAAAACAGAAGTGTGAAACCA 58.690 34.615 0.00 0.00 36.84 3.67
586 589 5.814188 TGCATCAAACTAGCTCATAGACAAG 59.186 40.000 0.00 0.00 35.30 3.16
648 652 3.119495 GCCCAGGTGTTGTTATTCATGTC 60.119 47.826 0.00 0.00 0.00 3.06
704 709 3.775654 CCTCGTGCACCCCCTCTC 61.776 72.222 12.15 0.00 0.00 3.20
791 1024 7.342769 CCCTCTATATGGGGTAAAACAAAAC 57.657 40.000 3.63 0.00 40.97 2.43
792 1025 6.893005 CCCTCTATATGGGGTAAAACAAAACA 59.107 38.462 3.63 0.00 40.97 2.83
793 1026 7.397761 CCCTCTATATGGGGTAAAACAAAACAA 59.602 37.037 3.63 0.00 40.97 2.83
794 1027 8.808092 CCTCTATATGGGGTAAAACAAAACAAA 58.192 33.333 0.00 0.00 0.00 2.83
799 1032 6.759497 TGGGGTAAAACAAAACAAAAATGG 57.241 33.333 0.00 0.00 0.00 3.16
811 1044 2.632028 ACAAAAATGGCCTATGTGCACA 59.368 40.909 24.08 24.08 0.00 4.57
831 2060 7.749126 GTGCACATGTAAATACTTCACTTAACC 59.251 37.037 13.17 0.00 0.00 2.85
832 2061 7.094549 TGCACATGTAAATACTTCACTTAACCC 60.095 37.037 0.00 0.00 0.00 4.11
843 2072 9.945904 ATACTTCACTTAACCCAAAAACAAAAA 57.054 25.926 0.00 0.00 0.00 1.94
848 2077 6.655425 CACTTAACCCAAAAACAAAAAGGGAA 59.345 34.615 2.29 0.00 42.25 3.97
849 2078 6.882140 ACTTAACCCAAAAACAAAAAGGGAAG 59.118 34.615 2.29 0.00 42.25 3.46
850 2079 5.506730 AACCCAAAAACAAAAAGGGAAGA 57.493 34.783 2.29 0.00 42.25 2.87
924 2154 0.673956 TCTCCACGTGACCTCTCTCG 60.674 60.000 19.30 0.00 38.95 4.04
978 2208 3.996124 AGTCGCGCAGAGCCACTT 61.996 61.111 8.75 0.00 44.96 3.16
1315 2560 3.083997 CCGACTTCTGGGAGGGGG 61.084 72.222 0.00 0.00 0.00 5.40
1316 2561 2.038975 CGACTTCTGGGAGGGGGA 59.961 66.667 0.00 0.00 0.00 4.81
1321 2566 0.842467 CTTCTGGGAGGGGGACAACT 60.842 60.000 0.00 0.00 0.00 3.16
1322 2567 1.133809 TTCTGGGAGGGGGACAACTG 61.134 60.000 0.00 0.00 0.00 3.16
1387 2632 0.605589 CTTCTTCTCCGTGAGCACCT 59.394 55.000 0.00 0.00 0.00 4.00
1409 2654 3.014110 TCCTCCTCCTCCTCCATTACTTT 59.986 47.826 0.00 0.00 0.00 2.66
1676 2931 0.609131 AAACAGCGAGGGTTCCATGG 60.609 55.000 4.97 4.97 0.00 3.66
1677 2932 2.825836 CAGCGAGGGTTCCATGGC 60.826 66.667 6.96 2.51 0.00 4.40
1716 2971 4.436242 TTGTAGTACACTGAGCTACTGC 57.564 45.455 1.43 0.00 36.84 4.40
1736 2991 7.330900 ACTGCATTATTTTCCTCATCTGAAG 57.669 36.000 0.00 0.00 0.00 3.02
1748 3003 4.942483 CCTCATCTGAAGCAAAAGAGTGAT 59.058 41.667 0.00 0.00 0.00 3.06
1785 3047 3.497332 AGAACTCTACTGGTACTGTGCA 58.503 45.455 0.00 0.00 41.61 4.57
1809 3071 8.752766 CATAGATTGCTGAAAACATTGAACTT 57.247 30.769 0.00 0.00 0.00 2.66
1826 3089 6.389830 TGAACTTTCTACTGGTACGTGTAA 57.610 37.500 0.00 0.00 0.00 2.41
1849 3112 0.462047 CATCCGGGAGCTGTTACACC 60.462 60.000 0.00 0.00 0.00 4.16
1852 3115 0.036306 CCGGGAGCTGTTACACCTTT 59.964 55.000 0.00 0.00 0.00 3.11
1926 3189 2.806244 CCACTTCTTTGTTACTCCCACG 59.194 50.000 0.00 0.00 0.00 4.94
1943 3206 5.347124 TCCCACGGTCCCATAATATAAGAT 58.653 41.667 0.00 0.00 0.00 2.40
1973 3236 9.912634 ATTACATCCAGTTTACTCACAAATTTG 57.087 29.630 16.67 16.67 0.00 2.32
1974 3237 7.581213 ACATCCAGTTTACTCACAAATTTGA 57.419 32.000 24.64 2.21 0.00 2.69
1975 3238 8.181904 ACATCCAGTTTACTCACAAATTTGAT 57.818 30.769 24.64 6.33 0.00 2.57
1976 3239 8.084073 ACATCCAGTTTACTCACAAATTTGATG 58.916 33.333 24.64 17.26 31.56 3.07
1977 3240 7.581213 TCCAGTTTACTCACAAATTTGATGT 57.419 32.000 24.64 18.96 0.00 3.06
1978 3241 8.684386 TCCAGTTTACTCACAAATTTGATGTA 57.316 30.769 24.64 18.09 0.00 2.29
1979 3242 9.126151 TCCAGTTTACTCACAAATTTGATGTAA 57.874 29.630 24.64 21.77 0.00 2.41
1980 3243 9.912634 CCAGTTTACTCACAAATTTGATGTAAT 57.087 29.630 24.64 11.92 0.00 1.89
2077 3344 3.524095 TCCTGGTGTTTGATCATTGGT 57.476 42.857 0.00 0.00 0.00 3.67
2081 3348 5.418524 TCCTGGTGTTTGATCATTGGTATTG 59.581 40.000 0.00 0.00 0.00 1.90
2131 4851 7.199766 CAGATGTCCACTCAATAAGTAGAGAC 58.800 42.308 0.00 0.00 36.07 3.36
2149 4869 5.606348 GAGACAACTCTCCATGTTATCCT 57.394 43.478 0.00 0.00 37.56 3.24
2153 4873 6.841229 AGACAACTCTCCATGTTATCCTATCA 59.159 38.462 0.00 0.00 0.00 2.15
2195 4915 6.959639 ATCCATCCATGTAACCATGTTAAC 57.040 37.500 0.00 0.00 45.83 2.01
2206 4926 1.942657 CCATGTTAACTCCCATGCGAG 59.057 52.381 7.22 5.82 37.67 5.03
2357 5085 2.224161 CCCCGAAGAGTCAGAATCATCC 60.224 54.545 0.00 0.00 0.00 3.51
2517 5245 6.877236 ACAACATTCAGTGGAAACTTGAAAT 58.123 32.000 0.00 0.00 37.86 2.17
2567 5295 4.830600 TGGTTCGGAAAAGGAAATTAGCTT 59.169 37.500 0.00 0.00 0.00 3.74
2570 5298 3.823873 TCGGAAAAGGAAATTAGCTTGCA 59.176 39.130 0.00 0.00 0.00 4.08
2576 5304 4.725790 AGGAAATTAGCTTGCAATCACC 57.274 40.909 0.00 0.00 0.00 4.02
2728 5456 3.072330 TCCAGTGGTTTGCTTAGATGTCA 59.928 43.478 9.54 0.00 0.00 3.58
2765 5493 1.872952 TGTGTGATTTGACTGCTTCCG 59.127 47.619 0.00 0.00 0.00 4.30
2906 5646 6.263754 AGGGTTAGTTGGGATTCAATTCAAT 58.736 36.000 0.00 0.00 37.73 2.57
2952 5701 5.922739 TTACGCATATCAATCCATGACAC 57.077 39.130 0.00 0.00 41.93 3.67
2955 5704 4.274214 ACGCATATCAATCCATGACACAAG 59.726 41.667 0.00 0.00 41.93 3.16
2959 5708 6.474427 GCATATCAATCCATGACACAAGTTTG 59.526 38.462 0.00 0.00 41.93 2.93
2961 5710 8.676401 CATATCAATCCATGACACAAGTTTGTA 58.324 33.333 0.00 0.00 41.93 2.41
2962 5711 7.707624 ATCAATCCATGACACAAGTTTGTAT 57.292 32.000 0.00 0.00 41.93 2.29
2963 5712 6.912082 TCAATCCATGACACAAGTTTGTATG 58.088 36.000 0.00 0.00 34.42 2.39
2964 5713 6.714356 TCAATCCATGACACAAGTTTGTATGA 59.286 34.615 0.00 0.00 34.42 2.15
2966 5715 7.707624 ATCCATGACACAAGTTTGTATGATT 57.292 32.000 0.00 0.00 39.91 2.57
2967 5716 7.523293 TCCATGACACAAGTTTGTATGATTT 57.477 32.000 0.00 0.00 39.91 2.17
2968 5717 7.592938 TCCATGACACAAGTTTGTATGATTTC 58.407 34.615 0.00 0.00 39.91 2.17
2969 5718 7.448161 TCCATGACACAAGTTTGTATGATTTCT 59.552 33.333 0.00 0.00 39.91 2.52
2970 5719 7.539710 CCATGACACAAGTTTGTATGATTTCTG 59.460 37.037 0.00 0.00 39.91 3.02
2971 5720 7.800155 TGACACAAGTTTGTATGATTTCTGA 57.200 32.000 0.00 0.00 39.91 3.27
2972 5721 7.639039 TGACACAAGTTTGTATGATTTCTGAC 58.361 34.615 0.00 0.00 39.91 3.51
2975 5724 8.077991 ACACAAGTTTGTATGATTTCTGACATG 58.922 33.333 0.00 0.00 39.91 3.21
2976 5725 8.077991 CACAAGTTTGTATGATTTCTGACATGT 58.922 33.333 0.00 0.00 39.91 3.21
2977 5726 8.632679 ACAAGTTTGTATGATTTCTGACATGTT 58.367 29.630 0.00 0.00 40.16 2.71
2978 5727 9.467258 CAAGTTTGTATGATTTCTGACATGTTT 57.533 29.630 0.00 0.00 0.00 2.83
2979 5728 9.683069 AAGTTTGTATGATTTCTGACATGTTTC 57.317 29.630 0.00 0.00 0.00 2.78
2981 5730 9.121517 GTTTGTATGATTTCTGACATGTTTCTG 57.878 33.333 0.00 0.00 0.00 3.02
2982 5731 6.845302 TGTATGATTTCTGACATGTTTCTGC 58.155 36.000 0.00 0.00 0.00 4.26
2983 5732 4.771590 TGATTTCTGACATGTTTCTGCC 57.228 40.909 0.00 0.00 0.00 4.85
2984 5733 4.143543 TGATTTCTGACATGTTTCTGCCA 58.856 39.130 0.00 0.00 0.00 4.92
2985 5734 4.583907 TGATTTCTGACATGTTTCTGCCAA 59.416 37.500 0.00 0.00 0.00 4.52
2986 5735 5.244402 TGATTTCTGACATGTTTCTGCCAAT 59.756 36.000 0.00 0.00 0.00 3.16
2990 5739 4.696877 TCTGACATGTTTCTGCCAATGTAG 59.303 41.667 0.00 0.00 0.00 2.74
2991 5740 3.191162 TGACATGTTTCTGCCAATGTAGC 59.809 43.478 0.00 0.00 0.00 3.58
2993 5742 3.765511 ACATGTTTCTGCCAATGTAGCAT 59.234 39.130 0.00 0.00 40.04 3.79
2994 5743 3.853831 TGTTTCTGCCAATGTAGCATG 57.146 42.857 0.00 0.00 40.04 4.06
2996 5745 3.191162 TGTTTCTGCCAATGTAGCATGTC 59.809 43.478 0.00 0.00 40.04 3.06
2997 5746 2.785540 TCTGCCAATGTAGCATGTCA 57.214 45.000 0.00 0.00 40.04 3.58
2998 5747 3.286329 TCTGCCAATGTAGCATGTCAT 57.714 42.857 0.00 0.00 40.04 3.06
2999 5748 3.623703 TCTGCCAATGTAGCATGTCATT 58.376 40.909 0.00 1.12 40.04 2.57
3000 5749 4.018490 TCTGCCAATGTAGCATGTCATTT 58.982 39.130 9.12 0.00 40.04 2.32
3001 5750 4.463539 TCTGCCAATGTAGCATGTCATTTT 59.536 37.500 9.12 0.00 40.04 1.82
3003 5752 4.021280 TGCCAATGTAGCATGTCATTTTGT 60.021 37.500 9.12 0.00 34.69 2.83
3004 5753 4.327898 GCCAATGTAGCATGTCATTTTGTG 59.672 41.667 9.12 2.27 32.85 3.33
3005 5754 5.712004 CCAATGTAGCATGTCATTTTGTGA 58.288 37.500 9.12 0.00 32.85 3.58
3006 5755 6.157904 CCAATGTAGCATGTCATTTTGTGAA 58.842 36.000 9.12 0.00 38.90 3.18
3009 5758 8.549548 CAATGTAGCATGTCATTTTGTGAAAAA 58.450 29.630 9.12 0.00 38.90 1.94
3010 5759 7.697352 TGTAGCATGTCATTTTGTGAAAAAG 57.303 32.000 0.00 0.00 38.90 2.27
3013 5762 9.410556 GTAGCATGTCATTTTGTGAAAAAGTAT 57.589 29.630 0.00 0.00 38.90 2.12
3014 5763 8.891671 AGCATGTCATTTTGTGAAAAAGTATT 57.108 26.923 0.00 0.00 38.90 1.89
3036 5785 3.746045 TGACAGTTTCTACAGTCACCC 57.254 47.619 0.00 0.00 43.30 4.61
3037 5786 2.367567 TGACAGTTTCTACAGTCACCCC 59.632 50.000 0.00 0.00 43.30 4.95
3038 5787 1.697982 ACAGTTTCTACAGTCACCCCC 59.302 52.381 0.00 0.00 0.00 5.40
3039 5788 1.697432 CAGTTTCTACAGTCACCCCCA 59.303 52.381 0.00 0.00 0.00 4.96
3040 5789 1.978580 AGTTTCTACAGTCACCCCCAG 59.021 52.381 0.00 0.00 0.00 4.45
3041 5790 1.975680 GTTTCTACAGTCACCCCCAGA 59.024 52.381 0.00 0.00 0.00 3.86
3042 5791 2.572104 GTTTCTACAGTCACCCCCAGAT 59.428 50.000 0.00 0.00 0.00 2.90
3045 5794 4.069312 TCTACAGTCACCCCCAGATTAA 57.931 45.455 0.00 0.00 0.00 1.40
3082 5831 3.325870 TGATAACAAGCTTGAGACGGTG 58.674 45.455 32.50 4.69 0.00 4.94
3112 5861 4.343526 TCAGCTTGCTCCTATTCCTAAGAG 59.656 45.833 0.00 0.00 0.00 2.85
3127 5876 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
3128 5877 2.437359 AGCATCTCCAGCCGTTGC 60.437 61.111 0.00 0.00 37.95 4.17
3129 5878 2.747460 GCATCTCCAGCCGTTGCA 60.747 61.111 0.00 0.00 41.13 4.08
3131 5880 2.437359 ATCTCCAGCCGTTGCAGC 60.437 61.111 0.00 0.00 41.13 5.25
3132 5881 3.984193 ATCTCCAGCCGTTGCAGCC 62.984 63.158 0.00 0.00 41.13 4.85
3141 5890 2.116125 GTTGCAGCCCCCAAGAGT 59.884 61.111 0.00 0.00 0.00 3.24
3142 5891 1.378762 GTTGCAGCCCCCAAGAGTA 59.621 57.895 0.00 0.00 0.00 2.59
3143 5892 0.960861 GTTGCAGCCCCCAAGAGTAC 60.961 60.000 0.00 0.00 0.00 2.73
3145 5894 0.252513 TGCAGCCCCCAAGAGTACTA 60.253 55.000 0.00 0.00 0.00 1.82
3147 5896 0.831307 CAGCCCCCAAGAGTACTACC 59.169 60.000 0.00 0.00 0.00 3.18
3149 5898 1.203389 AGCCCCCAAGAGTACTACCAA 60.203 52.381 0.00 0.00 0.00 3.67
3150 5899 1.209747 GCCCCCAAGAGTACTACCAAG 59.790 57.143 0.00 0.00 0.00 3.61
3151 5900 1.209747 CCCCCAAGAGTACTACCAAGC 59.790 57.143 0.00 0.00 0.00 4.01
3154 5903 2.304761 CCCAAGAGTACTACCAAGCCAA 59.695 50.000 0.00 0.00 0.00 4.52
3155 5904 3.244770 CCCAAGAGTACTACCAAGCCAAA 60.245 47.826 0.00 0.00 0.00 3.28
3157 5906 3.336138 AGAGTACTACCAAGCCAAAGC 57.664 47.619 0.00 0.00 40.32 3.51
3158 5907 2.000447 GAGTACTACCAAGCCAAAGCG 59.000 52.381 0.00 0.00 46.67 4.68
3159 5908 1.621814 AGTACTACCAAGCCAAAGCGA 59.378 47.619 0.00 0.00 46.67 4.93
3160 5909 2.038033 AGTACTACCAAGCCAAAGCGAA 59.962 45.455 0.00 0.00 46.67 4.70
3161 5910 1.975660 ACTACCAAGCCAAAGCGAAA 58.024 45.000 0.00 0.00 46.67 3.46
3164 5913 3.689649 ACTACCAAGCCAAAGCGAAATAG 59.310 43.478 0.00 0.00 46.67 1.73
3167 5916 3.191371 ACCAAGCCAAAGCGAAATAGAAG 59.809 43.478 0.00 0.00 46.67 2.85
3168 5917 3.191371 CCAAGCCAAAGCGAAATAGAAGT 59.809 43.478 0.00 0.00 46.67 3.01
3169 5918 4.161333 CAAGCCAAAGCGAAATAGAAGTG 58.839 43.478 0.00 0.00 46.67 3.16
3170 5919 2.162408 AGCCAAAGCGAAATAGAAGTGC 59.838 45.455 0.00 0.00 46.67 4.40
3171 5920 2.095263 GCCAAAGCGAAATAGAAGTGCA 60.095 45.455 0.00 0.00 0.00 4.57
3173 5922 4.100529 CCAAAGCGAAATAGAAGTGCATG 58.899 43.478 0.00 0.00 0.00 4.06
3175 5924 4.871993 AAGCGAAATAGAAGTGCATGAG 57.128 40.909 0.00 0.00 0.00 2.90
3176 5925 3.201290 AGCGAAATAGAAGTGCATGAGG 58.799 45.455 0.00 0.00 0.00 3.86
3179 5928 3.806521 CGAAATAGAAGTGCATGAGGAGG 59.193 47.826 0.00 0.00 0.00 4.30
3180 5929 3.853355 AATAGAAGTGCATGAGGAGGG 57.147 47.619 0.00 0.00 0.00 4.30
3182 5931 1.203441 AGAAGTGCATGAGGAGGGCA 61.203 55.000 0.00 0.00 34.70 5.36
3183 5932 0.106819 GAAGTGCATGAGGAGGGCAT 60.107 55.000 0.00 0.00 40.05 4.40
3185 5934 0.987081 AGTGCATGAGGAGGGCATCT 60.987 55.000 0.00 0.00 40.05 2.90
3186 5935 0.106819 GTGCATGAGGAGGGCATCTT 60.107 55.000 0.00 0.00 40.05 2.40
3187 5936 0.627451 TGCATGAGGAGGGCATCTTT 59.373 50.000 0.00 0.00 31.58 2.52
3188 5937 1.316651 GCATGAGGAGGGCATCTTTC 58.683 55.000 0.00 0.00 0.00 2.62
3190 5939 1.213678 CATGAGGAGGGCATCTTTCCA 59.786 52.381 0.00 0.00 33.32 3.53
3191 5940 0.914644 TGAGGAGGGCATCTTTCCAG 59.085 55.000 0.00 0.00 33.32 3.86
3192 5941 0.465278 GAGGAGGGCATCTTTCCAGC 60.465 60.000 0.00 0.00 33.32 4.85
3198 5947 1.885871 GCATCTTTCCAGCCACACC 59.114 57.895 0.00 0.00 0.00 4.16
3199 5948 1.598701 GCATCTTTCCAGCCACACCC 61.599 60.000 0.00 0.00 0.00 4.61
3200 5949 0.038744 CATCTTTCCAGCCACACCCT 59.961 55.000 0.00 0.00 0.00 4.34
3201 5950 1.281867 CATCTTTCCAGCCACACCCTA 59.718 52.381 0.00 0.00 0.00 3.53
3202 5951 1.668826 TCTTTCCAGCCACACCCTAT 58.331 50.000 0.00 0.00 0.00 2.57
3203 5952 1.559682 TCTTTCCAGCCACACCCTATC 59.440 52.381 0.00 0.00 0.00 2.08
3204 5953 0.623723 TTTCCAGCCACACCCTATCC 59.376 55.000 0.00 0.00 0.00 2.59
3205 5954 1.279025 TTCCAGCCACACCCTATCCC 61.279 60.000 0.00 0.00 0.00 3.85
3208 5957 0.394352 CAGCCACACCCTATCCCAAC 60.394 60.000 0.00 0.00 0.00 3.77
3209 5958 1.076995 GCCACACCCTATCCCAACC 60.077 63.158 0.00 0.00 0.00 3.77
3210 5959 1.858739 GCCACACCCTATCCCAACCA 61.859 60.000 0.00 0.00 0.00 3.67
3211 5960 0.701731 CCACACCCTATCCCAACCAA 59.298 55.000 0.00 0.00 0.00 3.67
3213 5962 2.491825 CCACACCCTATCCCAACCAAAA 60.492 50.000 0.00 0.00 0.00 2.44
3214 5963 3.235200 CACACCCTATCCCAACCAAAAA 58.765 45.455 0.00 0.00 0.00 1.94
3218 5967 5.221823 ACACCCTATCCCAACCAAAAATTTG 60.222 40.000 0.00 0.00 37.90 2.32
3220 5969 6.014156 CACCCTATCCCAACCAAAAATTTGTA 60.014 38.462 5.27 0.00 36.45 2.41
3221 5970 6.559157 ACCCTATCCCAACCAAAAATTTGTAA 59.441 34.615 5.27 0.00 36.45 2.41
3222 5971 7.072581 ACCCTATCCCAACCAAAAATTTGTAAA 59.927 33.333 5.27 0.00 36.45 2.01
3223 5972 7.606073 CCCTATCCCAACCAAAAATTTGTAAAG 59.394 37.037 5.27 0.00 36.45 1.85
3224 5973 7.606073 CCTATCCCAACCAAAAATTTGTAAAGG 59.394 37.037 5.27 1.74 36.45 3.11
3225 5974 6.561519 TCCCAACCAAAAATTTGTAAAGGA 57.438 33.333 5.27 3.77 36.45 3.36
3226 5975 6.958767 TCCCAACCAAAAATTTGTAAAGGAA 58.041 32.000 5.27 0.00 36.45 3.36
3227 5976 7.402862 TCCCAACCAAAAATTTGTAAAGGAAA 58.597 30.769 5.27 0.00 36.45 3.13
3228 5977 8.055790 TCCCAACCAAAAATTTGTAAAGGAAAT 58.944 29.630 5.27 0.00 36.45 2.17
3230 5979 8.897752 CCAACCAAAAATTTGTAAAGGAAATGA 58.102 29.630 5.27 0.00 36.45 2.57
3238 5987 9.435688 AAATTTGTAAAGGAAATGATTAGGTGC 57.564 29.630 0.00 0.00 0.00 5.01
3239 5988 5.811399 TGTAAAGGAAATGATTAGGTGCG 57.189 39.130 0.00 0.00 0.00 5.34
3240 5989 3.782889 AAAGGAAATGATTAGGTGCGC 57.217 42.857 0.00 0.00 0.00 6.09
3241 5990 1.680338 AGGAAATGATTAGGTGCGCC 58.320 50.000 8.71 8.71 0.00 6.53
3243 5992 1.748493 GGAAATGATTAGGTGCGCCAA 59.252 47.619 20.59 11.20 37.19 4.52
3245 5994 2.418368 AATGATTAGGTGCGCCAAGA 57.582 45.000 20.59 3.70 37.19 3.02
3246 5995 2.418368 ATGATTAGGTGCGCCAAGAA 57.582 45.000 20.59 9.91 37.19 2.52
3268 6017 3.543680 AAAGATATGTGGGGAGACACG 57.456 47.619 0.00 0.00 44.21 4.49
3269 6018 2.160721 AGATATGTGGGGAGACACGT 57.839 50.000 0.00 0.00 44.21 4.49
3270 6019 2.467880 AGATATGTGGGGAGACACGTT 58.532 47.619 0.00 0.00 44.21 3.99
3272 6021 2.754946 TATGTGGGGAGACACGTTTC 57.245 50.000 0.00 0.00 44.21 2.78
3273 6022 0.320421 ATGTGGGGAGACACGTTTCG 60.320 55.000 0.00 0.00 44.21 3.46
3274 6023 2.029964 TGGGGAGACACGTTTCGC 59.970 61.111 0.00 0.00 35.32 4.70
3275 6024 2.741211 GGGGAGACACGTTTCGCC 60.741 66.667 15.28 15.28 39.07 5.54
3276 6025 3.110178 GGGAGACACGTTTCGCCG 61.110 66.667 16.74 0.00 36.36 6.46
3277 6026 2.049802 GGAGACACGTTTCGCCGA 60.050 61.111 8.77 0.00 0.00 5.54
3278 6027 1.662446 GGAGACACGTTTCGCCGAA 60.662 57.895 8.77 0.00 0.00 4.30
3282 6031 0.302589 GACACGTTTCGCCGAAACTT 59.697 50.000 32.28 24.42 46.55 2.66
3283 6032 0.302589 ACACGTTTCGCCGAAACTTC 59.697 50.000 32.28 13.50 46.55 3.01
3307 6345 3.646715 CGTTCCCAAGAGCCCCCA 61.647 66.667 0.00 0.00 0.00 4.96
3308 6346 2.851045 GTTCCCAAGAGCCCCCAA 59.149 61.111 0.00 0.00 0.00 4.12
3322 6360 4.383602 CCAACGCGCTGGGTTTCG 62.384 66.667 20.85 0.00 36.59 3.46
3328 6366 4.697756 CGCTGGGTTTCGCCTGGA 62.698 66.667 0.00 0.00 37.43 3.86
3329 6367 2.044946 GCTGGGTTTCGCCTGGAT 60.045 61.111 0.00 0.00 37.43 3.41
3330 6368 1.678970 GCTGGGTTTCGCCTGGATT 60.679 57.895 0.00 0.00 37.43 3.01
3331 6369 1.250840 GCTGGGTTTCGCCTGGATTT 61.251 55.000 0.00 0.00 37.43 2.17
3332 6370 0.527565 CTGGGTTTCGCCTGGATTTG 59.472 55.000 0.00 0.00 37.43 2.32
3333 6371 1.215382 GGGTTTCGCCTGGATTTGC 59.785 57.895 0.00 0.00 37.43 3.68
3334 6372 1.215382 GGTTTCGCCTGGATTTGCC 59.785 57.895 0.00 0.00 37.10 4.52
3335 6373 1.154035 GTTTCGCCTGGATTTGCCG 60.154 57.895 0.00 0.00 40.66 5.69
3336 6374 2.339556 TTTCGCCTGGATTTGCCGG 61.340 57.895 0.00 0.00 43.18 6.13
3340 6378 3.619938 CCTGGATTTGCCGGCATT 58.380 55.556 33.25 21.61 42.12 3.56
3341 6379 2.805897 CCTGGATTTGCCGGCATTA 58.194 52.632 33.25 22.14 42.12 1.90
3342 6380 1.331214 CCTGGATTTGCCGGCATTAT 58.669 50.000 33.25 25.94 42.12 1.28
3344 6382 2.102925 CCTGGATTTGCCGGCATTATTT 59.897 45.455 33.25 13.46 42.12 1.40
3345 6383 3.432046 CCTGGATTTGCCGGCATTATTTT 60.432 43.478 33.25 11.50 42.12 1.82
3346 6384 3.529533 TGGATTTGCCGGCATTATTTTG 58.470 40.909 33.25 0.00 40.66 2.44
3348 6386 3.555547 GGATTTGCCGGCATTATTTTGAC 59.444 43.478 33.25 13.53 0.00 3.18
3360 8250 5.622856 GCATTATTTTGACGATGCTCTAAGC 59.377 40.000 0.00 0.00 41.16 3.09
3393 8283 2.935481 TGGCTTCTGTGGAGGGGG 60.935 66.667 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 6.017026 GGGCTTATTTTCTATGAAGTGGCTAC 60.017 42.308 0.00 0.00 0.00 3.58
30 31 6.062095 GGGCTTATTTTCTATGAAGTGGCTA 58.938 40.000 0.00 0.00 0.00 3.93
32 33 4.889995 AGGGCTTATTTTCTATGAAGTGGC 59.110 41.667 0.00 0.00 0.00 5.01
35 36 9.343539 GTCATTAGGGCTTATTTTCTATGAAGT 57.656 33.333 0.00 0.00 0.00 3.01
53 54 3.964031 AGAGCAGGGTTAGAGTCATTAGG 59.036 47.826 0.00 0.00 0.00 2.69
82 83 8.481314 AGATCTGTAGAAATAGAGCAACATTGA 58.519 33.333 0.00 0.00 32.19 2.57
115 117 4.339247 ACATCTGAAAATATCTTTGGCCCG 59.661 41.667 0.00 0.00 0.00 6.13
127 129 6.492772 AGCTCTTCCAAGAAACATCTGAAAAT 59.507 34.615 0.00 0.00 34.03 1.82
132 135 3.688673 GGAGCTCTTCCAAGAAACATCTG 59.311 47.826 14.64 0.00 46.01 2.90
133 136 3.949132 GGAGCTCTTCCAAGAAACATCT 58.051 45.455 14.64 0.00 46.01 2.90
290 293 1.595466 GCAGCTAGATGCAATGCTCT 58.405 50.000 27.32 9.37 45.77 4.09
337 340 5.733620 TGTCCGTATGAAAAGTAGGTCTT 57.266 39.130 0.00 0.00 38.10 3.01
381 384 6.093219 AGCAGAATTGTTATACTTGACAGCAG 59.907 38.462 0.00 0.00 0.00 4.24
387 390 7.544622 AGTACGAGCAGAATTGTTATACTTGA 58.455 34.615 0.00 0.00 0.00 3.02
392 395 6.127810 ACGAGTACGAGCAGAATTGTTATA 57.872 37.500 0.00 0.00 42.66 0.98
424 427 2.840974 CGCAAGTAGGTGTTCCCTG 58.159 57.895 0.00 0.00 45.81 4.45
444 447 1.750778 ACTGTGTGGAGTTGCAAAAGG 59.249 47.619 0.00 0.00 0.00 3.11
514 517 0.037326 GAACCCGATGAGCACAGACA 60.037 55.000 0.00 0.00 0.00 3.41
516 519 1.847328 TAGAACCCGATGAGCACAGA 58.153 50.000 0.00 0.00 0.00 3.41
538 541 4.142687 CGAAACTGGTTTCACACTTCTGTT 60.143 41.667 21.13 0.00 46.84 3.16
540 543 3.374058 ACGAAACTGGTTTCACACTTCTG 59.626 43.478 21.13 8.63 46.84 3.02
541 544 3.374058 CACGAAACTGGTTTCACACTTCT 59.626 43.478 21.13 0.00 46.84 2.85
542 545 3.680789 CACGAAACTGGTTTCACACTTC 58.319 45.455 21.13 0.00 46.84 3.01
548 551 2.293170 TGATGCACGAAACTGGTTTCA 58.707 42.857 21.13 7.21 46.84 2.69
550 553 3.130340 AGTTTGATGCACGAAACTGGTTT 59.870 39.130 19.31 0.00 40.19 3.27
555 558 3.403038 AGCTAGTTTGATGCACGAAACT 58.597 40.909 22.12 22.12 43.28 2.66
586 589 0.109735 GCTAAAGTTGGACAAGCGGC 60.110 55.000 0.00 0.00 0.00 6.53
743 749 7.287810 GGGTGGGATTAGCTTATTTTCTTCTA 58.712 38.462 0.00 0.00 0.00 2.10
745 751 5.302059 GGGGTGGGATTAGCTTATTTTCTTC 59.698 44.000 0.00 0.00 0.00 2.87
747 753 4.482398 AGGGGTGGGATTAGCTTATTTTCT 59.518 41.667 0.00 0.00 0.00 2.52
748 754 4.804597 AGGGGTGGGATTAGCTTATTTTC 58.195 43.478 0.00 0.00 0.00 2.29
753 759 2.889522 AGAGGGGTGGGATTAGCTTA 57.110 50.000 0.00 0.00 0.00 3.09
791 1024 3.316071 TGTGCACATAGGCCATTTTTG 57.684 42.857 17.42 0.00 0.00 2.44
792 1025 3.261390 ACATGTGCACATAGGCCATTTTT 59.739 39.130 30.92 3.48 34.26 1.94
793 1026 2.833338 ACATGTGCACATAGGCCATTTT 59.167 40.909 30.92 4.06 34.26 1.82
794 1027 2.459644 ACATGTGCACATAGGCCATTT 58.540 42.857 30.92 4.88 34.26 2.32
795 1028 2.148446 ACATGTGCACATAGGCCATT 57.852 45.000 30.92 5.69 34.26 3.16
799 1032 6.038161 TGAAGTATTTACATGTGCACATAGGC 59.962 38.462 30.92 16.20 34.26 3.93
831 2060 4.163268 TCCCTCTTCCCTTTTTGTTTTTGG 59.837 41.667 0.00 0.00 0.00 3.28
832 2061 5.351948 TCCCTCTTCCCTTTTTGTTTTTG 57.648 39.130 0.00 0.00 0.00 2.44
1315 2560 1.592223 CGAGGACCTCCCAGTTGTC 59.408 63.158 16.13 0.00 37.41 3.18
1316 2561 1.913762 CCGAGGACCTCCCAGTTGT 60.914 63.158 16.13 0.00 37.41 3.32
1321 2566 2.683933 GAAGCCGAGGACCTCCCA 60.684 66.667 16.13 0.00 37.41 4.37
1322 2567 1.962321 GAAGAAGCCGAGGACCTCCC 61.962 65.000 16.13 7.27 36.42 4.30
1387 2632 2.227703 AGTAATGGAGGAGGAGGAGGA 58.772 52.381 0.00 0.00 0.00 3.71
1569 2821 3.440173 GCTTGTCGAATTCAAGGGATTGA 59.560 43.478 14.08 0.00 41.50 2.57
1676 2931 3.382546 ACAAAGAGTGATTATGCCATGGC 59.617 43.478 30.54 30.54 42.35 4.40
1677 2932 5.824624 ACTACAAAGAGTGATTATGCCATGG 59.175 40.000 7.63 7.63 0.00 3.66
1682 2937 7.759886 TCAGTGTACTACAAAGAGTGATTATGC 59.240 37.037 0.00 0.00 0.00 3.14
1683 2938 9.295214 CTCAGTGTACTACAAAGAGTGATTATG 57.705 37.037 9.50 0.00 30.96 1.90
1688 2943 4.827835 AGCTCAGTGTACTACAAAGAGTGA 59.172 41.667 15.42 2.93 35.19 3.41
1716 2971 8.991243 TTTTGCTTCAGATGAGGAAAATAATG 57.009 30.769 0.00 0.00 30.10 1.90
1736 2991 4.853924 TGGAAAGGAATCACTCTTTTGC 57.146 40.909 0.00 0.00 40.52 3.68
1748 3003 4.289672 AGAGTTCTAGGCATTGGAAAGGAA 59.710 41.667 0.00 0.00 0.00 3.36
1785 3047 9.415544 GAAAGTTCAATGTTTTCAGCAATCTAT 57.584 29.630 0.00 0.00 32.49 1.98
1809 3071 2.493278 GCCCTTACACGTACCAGTAGAA 59.507 50.000 0.00 0.00 0.00 2.10
2077 3344 7.940137 ACAATAGGTGGTTAAGTTGTCACAATA 59.060 33.333 0.00 0.00 32.29 1.90
2081 3348 6.435428 CAACAATAGGTGGTTAAGTTGTCAC 58.565 40.000 0.00 0.00 32.52 3.67
2131 4851 7.504403 AGTTGATAGGATAACATGGAGAGTTG 58.496 38.462 0.00 0.00 0.00 3.16
2153 4873 9.512588 GGATGGATTAATGTGATGATCTAAGTT 57.487 33.333 0.00 0.00 0.00 2.66
2357 5085 2.832818 CTTCAAACACATCGGCGCCG 62.833 60.000 42.13 42.13 41.35 6.46
2469 5197 4.065088 CAAGTTTACTGGCTACTGCAGAA 58.935 43.478 23.35 0.00 41.91 3.02
2517 5245 5.125417 GCAGCCAATTTCCTTAACACTATCA 59.875 40.000 0.00 0.00 0.00 2.15
2567 5295 7.056006 AGATAATTCAGTACATGGTGATTGCA 58.944 34.615 0.00 0.00 0.00 4.08
2570 5298 9.334947 CAAGAGATAATTCAGTACATGGTGATT 57.665 33.333 0.00 0.00 0.00 2.57
2695 5423 4.062991 CAAACCACTGGAGTACCAAGTAC 58.937 47.826 0.71 0.00 46.32 2.73
2696 5424 3.495453 GCAAACCACTGGAGTACCAAGTA 60.495 47.826 0.71 0.00 46.32 2.24
2697 5425 2.748465 GCAAACCACTGGAGTACCAAGT 60.748 50.000 0.71 0.00 46.32 3.16
2698 5426 1.880027 GCAAACCACTGGAGTACCAAG 59.120 52.381 0.71 0.00 46.32 3.61
2728 5456 4.941263 TCACACAAGTTTGCTTCTTACACT 59.059 37.500 0.00 0.00 31.49 3.55
2883 5623 5.993748 TTGAATTGAATCCCAACTAACCC 57.006 39.130 0.00 0.00 37.63 4.11
2893 5633 9.090692 CAACTAACCATTGATTGAATTGAATCC 57.909 33.333 14.05 0.00 32.20 3.01
2933 5682 4.274214 ACTTGTGTCATGGATTGATATGCG 59.726 41.667 0.00 0.00 36.54 4.73
2936 5685 7.707624 ACAAACTTGTGTCATGGATTGATAT 57.292 32.000 0.00 0.00 40.49 1.63
2940 5689 6.912082 TCATACAAACTTGTGTCATGGATTG 58.088 36.000 5.34 0.00 42.31 2.67
2942 5691 7.707624 AATCATACAAACTTGTGTCATGGAT 57.292 32.000 5.34 0.00 42.31 3.41
2943 5692 7.448161 AGAAATCATACAAACTTGTGTCATGGA 59.552 33.333 5.34 0.00 42.31 3.41
2944 5693 7.539710 CAGAAATCATACAAACTTGTGTCATGG 59.460 37.037 5.34 0.00 42.31 3.66
2945 5694 8.291740 TCAGAAATCATACAAACTTGTGTCATG 58.708 33.333 5.34 2.06 42.31 3.07
2946 5695 8.292448 GTCAGAAATCATACAAACTTGTGTCAT 58.708 33.333 5.34 0.00 42.31 3.06
2949 5698 7.566760 TGTCAGAAATCATACAAACTTGTGT 57.433 32.000 5.34 0.00 42.31 3.72
2950 5699 8.077991 ACATGTCAGAAATCATACAAACTTGTG 58.922 33.333 5.34 0.00 42.31 3.33
2952 5701 9.467258 AAACATGTCAGAAATCATACAAACTTG 57.533 29.630 0.00 0.00 0.00 3.16
2955 5704 9.121517 CAGAAACATGTCAGAAATCATACAAAC 57.878 33.333 0.00 0.00 0.00 2.93
2959 5708 6.127925 TGGCAGAAACATGTCAGAAATCATAC 60.128 38.462 0.00 0.00 29.73 2.39
2961 5710 4.768448 TGGCAGAAACATGTCAGAAATCAT 59.232 37.500 0.00 0.00 29.73 2.45
2962 5711 4.143543 TGGCAGAAACATGTCAGAAATCA 58.856 39.130 0.00 0.00 29.73 2.57
2963 5712 4.771590 TGGCAGAAACATGTCAGAAATC 57.228 40.909 0.00 0.00 29.73 2.17
2964 5713 5.011329 ACATTGGCAGAAACATGTCAGAAAT 59.989 36.000 0.00 0.00 35.92 2.17
2966 5715 3.890756 ACATTGGCAGAAACATGTCAGAA 59.109 39.130 0.00 0.00 35.92 3.02
2967 5716 3.489355 ACATTGGCAGAAACATGTCAGA 58.511 40.909 0.00 0.00 35.92 3.27
2968 5717 3.928727 ACATTGGCAGAAACATGTCAG 57.071 42.857 0.00 0.00 35.92 3.51
2969 5718 3.191162 GCTACATTGGCAGAAACATGTCA 59.809 43.478 0.00 0.00 31.66 3.58
2970 5719 3.191162 TGCTACATTGGCAGAAACATGTC 59.809 43.478 0.00 0.00 34.56 3.06
2971 5720 3.156293 TGCTACATTGGCAGAAACATGT 58.844 40.909 6.93 6.93 34.56 3.21
2972 5721 3.853831 TGCTACATTGGCAGAAACATG 57.146 42.857 0.00 0.00 34.56 3.21
2975 5724 3.191162 TGACATGCTACATTGGCAGAAAC 59.809 43.478 0.00 0.00 43.15 2.78
2976 5725 3.419943 TGACATGCTACATTGGCAGAAA 58.580 40.909 0.00 0.00 43.15 2.52
2977 5726 3.070476 TGACATGCTACATTGGCAGAA 57.930 42.857 0.00 0.00 43.15 3.02
2978 5727 2.785540 TGACATGCTACATTGGCAGA 57.214 45.000 0.00 0.00 43.15 4.26
2979 5728 4.380841 AAATGACATGCTACATTGGCAG 57.619 40.909 12.00 0.00 43.15 4.85
2981 5730 4.327898 CACAAAATGACATGCTACATTGGC 59.672 41.667 12.00 0.00 36.92 4.52
2982 5731 5.712004 TCACAAAATGACATGCTACATTGG 58.288 37.500 12.00 10.43 36.92 3.16
2983 5732 7.640616 TTTCACAAAATGACATGCTACATTG 57.359 32.000 12.00 6.80 36.92 2.82
2984 5733 8.659925 TTTTTCACAAAATGACATGCTACATT 57.340 26.923 0.00 0.00 36.92 2.71
2985 5734 7.927629 ACTTTTTCACAAAATGACATGCTACAT 59.072 29.630 0.00 0.00 36.92 2.29
2986 5735 7.264221 ACTTTTTCACAAAATGACATGCTACA 58.736 30.769 0.00 0.00 36.92 2.74
3018 5767 1.697982 GGGGGTGACTGTAGAAACTGT 59.302 52.381 0.00 0.00 40.14 3.55
3019 5768 1.697432 TGGGGGTGACTGTAGAAACTG 59.303 52.381 0.00 0.00 0.00 3.16
3021 5770 1.975680 TCTGGGGGTGACTGTAGAAAC 59.024 52.381 0.00 0.00 0.00 2.78
3022 5771 2.409064 TCTGGGGGTGACTGTAGAAA 57.591 50.000 0.00 0.00 0.00 2.52
3024 5773 2.642171 AATCTGGGGGTGACTGTAGA 57.358 50.000 0.00 0.00 0.00 2.59
3025 5774 5.373812 AATTAATCTGGGGGTGACTGTAG 57.626 43.478 0.00 0.00 0.00 2.74
3027 5776 5.789574 TTAATTAATCTGGGGGTGACTGT 57.210 39.130 0.00 0.00 0.00 3.55
3028 5777 6.095440 CAGTTTAATTAATCTGGGGGTGACTG 59.905 42.308 21.27 13.53 32.21 3.51
3029 5778 6.187682 CAGTTTAATTAATCTGGGGGTGACT 58.812 40.000 21.27 7.06 32.21 3.41
3030 5779 5.163550 GCAGTTTAATTAATCTGGGGGTGAC 60.164 44.000 26.44 12.17 34.92 3.67
3031 5780 4.953579 GCAGTTTAATTAATCTGGGGGTGA 59.046 41.667 26.44 0.00 34.92 4.02
3032 5781 4.709397 TGCAGTTTAATTAATCTGGGGGTG 59.291 41.667 26.44 10.57 34.92 4.61
3034 5783 5.656416 TCTTGCAGTTTAATTAATCTGGGGG 59.344 40.000 26.44 10.74 34.92 5.40
3035 5784 6.773976 TCTTGCAGTTTAATTAATCTGGGG 57.226 37.500 26.44 11.00 34.92 4.96
3036 5785 9.090692 CAAATCTTGCAGTTTAATTAATCTGGG 57.909 33.333 26.44 11.52 34.92 4.45
3037 5786 9.859427 TCAAATCTTGCAGTTTAATTAATCTGG 57.141 29.630 26.44 16.02 34.92 3.86
3045 5794 9.143631 GCTTGTTATCAAATCTTGCAGTTTAAT 57.856 29.630 0.00 0.00 32.87 1.40
3082 5831 5.468409 GGAATAGGAGCAAGCTGAATCTAAC 59.532 44.000 0.00 0.00 0.00 2.34
3112 5861 2.747460 TGCAACGGCTGGAGATGC 60.747 61.111 0.00 2.67 41.91 3.91
3113 5862 2.758089 GCTGCAACGGCTGGAGATG 61.758 63.158 11.62 0.00 46.07 2.90
3114 5863 2.437359 GCTGCAACGGCTGGAGAT 60.437 61.111 11.62 0.00 46.07 2.75
3122 5871 4.659172 TCTTGGGGGCTGCAACGG 62.659 66.667 0.50 0.00 0.00 4.44
3123 5872 2.463589 TACTCTTGGGGGCTGCAACG 62.464 60.000 0.50 0.00 0.00 4.10
3124 5873 0.960861 GTACTCTTGGGGGCTGCAAC 60.961 60.000 0.50 0.00 0.00 4.17
3127 5876 0.178301 GTAGTACTCTTGGGGGCTGC 59.822 60.000 0.00 0.00 0.00 5.25
3128 5877 0.831307 GGTAGTACTCTTGGGGGCTG 59.169 60.000 0.00 0.00 0.00 4.85
3129 5878 0.416231 TGGTAGTACTCTTGGGGGCT 59.584 55.000 0.00 0.00 0.00 5.19
3131 5880 1.209747 GCTTGGTAGTACTCTTGGGGG 59.790 57.143 0.00 0.00 0.00 5.40
3132 5881 1.209747 GGCTTGGTAGTACTCTTGGGG 59.790 57.143 0.00 0.00 0.00 4.96
3134 5883 3.695830 TTGGCTTGGTAGTACTCTTGG 57.304 47.619 0.00 0.00 0.00 3.61
3138 5887 2.000447 CGCTTTGGCTTGGTAGTACTC 59.000 52.381 0.00 0.00 36.09 2.59
3141 5890 2.843401 TTCGCTTTGGCTTGGTAGTA 57.157 45.000 0.00 0.00 36.09 1.82
3142 5891 1.975660 TTTCGCTTTGGCTTGGTAGT 58.024 45.000 0.00 0.00 36.09 2.73
3143 5892 3.938963 TCTATTTCGCTTTGGCTTGGTAG 59.061 43.478 0.00 0.00 36.09 3.18
3145 5894 2.790433 TCTATTTCGCTTTGGCTTGGT 58.210 42.857 0.00 0.00 36.09 3.67
3147 5896 4.161333 CACTTCTATTTCGCTTTGGCTTG 58.839 43.478 0.00 0.00 36.09 4.01
3149 5898 2.162408 GCACTTCTATTTCGCTTTGGCT 59.838 45.455 0.00 0.00 36.09 4.75
3150 5899 2.095263 TGCACTTCTATTTCGCTTTGGC 60.095 45.455 0.00 0.00 0.00 4.52
3151 5900 3.829886 TGCACTTCTATTTCGCTTTGG 57.170 42.857 0.00 0.00 0.00 3.28
3154 5903 3.624861 CCTCATGCACTTCTATTTCGCTT 59.375 43.478 0.00 0.00 0.00 4.68
3155 5904 3.118629 TCCTCATGCACTTCTATTTCGCT 60.119 43.478 0.00 0.00 0.00 4.93
3157 5906 3.806521 CCTCCTCATGCACTTCTATTTCG 59.193 47.826 0.00 0.00 0.00 3.46
3158 5907 4.133078 CCCTCCTCATGCACTTCTATTTC 58.867 47.826 0.00 0.00 0.00 2.17
3159 5908 3.686691 GCCCTCCTCATGCACTTCTATTT 60.687 47.826 0.00 0.00 0.00 1.40
3160 5909 2.158696 GCCCTCCTCATGCACTTCTATT 60.159 50.000 0.00 0.00 0.00 1.73
3161 5910 1.419387 GCCCTCCTCATGCACTTCTAT 59.581 52.381 0.00 0.00 0.00 1.98
3164 5913 0.106819 ATGCCCTCCTCATGCACTTC 60.107 55.000 0.00 0.00 37.92 3.01
3167 5916 0.106819 AAGATGCCCTCCTCATGCAC 60.107 55.000 0.00 0.00 37.92 4.57
3168 5917 0.627451 AAAGATGCCCTCCTCATGCA 59.373 50.000 0.00 0.00 39.68 3.96
3169 5918 1.316651 GAAAGATGCCCTCCTCATGC 58.683 55.000 0.00 0.00 0.00 4.06
3170 5919 1.213678 TGGAAAGATGCCCTCCTCATG 59.786 52.381 0.00 0.00 0.00 3.07
3171 5920 1.493871 CTGGAAAGATGCCCTCCTCAT 59.506 52.381 0.00 0.00 0.00 2.90
3173 5922 0.465278 GCTGGAAAGATGCCCTCCTC 60.465 60.000 0.00 0.00 0.00 3.71
3175 5924 1.454663 GGCTGGAAAGATGCCCTCC 60.455 63.158 0.00 0.00 40.71 4.30
3176 5925 1.034292 GTGGCTGGAAAGATGCCCTC 61.034 60.000 0.00 0.00 45.56 4.30
3179 5928 1.598701 GGTGTGGCTGGAAAGATGCC 61.599 60.000 0.00 0.00 46.26 4.40
3180 5929 1.598701 GGGTGTGGCTGGAAAGATGC 61.599 60.000 0.00 0.00 0.00 3.91
3182 5931 1.668826 TAGGGTGTGGCTGGAAAGAT 58.331 50.000 0.00 0.00 0.00 2.40
3183 5932 1.559682 GATAGGGTGTGGCTGGAAAGA 59.440 52.381 0.00 0.00 0.00 2.52
3185 5934 0.623723 GGATAGGGTGTGGCTGGAAA 59.376 55.000 0.00 0.00 0.00 3.13
3186 5935 1.279025 GGGATAGGGTGTGGCTGGAA 61.279 60.000 0.00 0.00 0.00 3.53
3187 5936 1.692749 GGGATAGGGTGTGGCTGGA 60.693 63.158 0.00 0.00 0.00 3.86
3188 5937 1.570857 TTGGGATAGGGTGTGGCTGG 61.571 60.000 0.00 0.00 0.00 4.85
3190 5939 1.571773 GGTTGGGATAGGGTGTGGCT 61.572 60.000 0.00 0.00 0.00 4.75
3191 5940 1.076995 GGTTGGGATAGGGTGTGGC 60.077 63.158 0.00 0.00 0.00 5.01
3192 5941 0.701731 TTGGTTGGGATAGGGTGTGG 59.298 55.000 0.00 0.00 0.00 4.17
3193 5942 2.595750 TTTGGTTGGGATAGGGTGTG 57.404 50.000 0.00 0.00 0.00 3.82
3194 5943 3.621682 TTTTTGGTTGGGATAGGGTGT 57.378 42.857 0.00 0.00 0.00 4.16
3195 5944 5.221823 ACAAATTTTTGGTTGGGATAGGGTG 60.222 40.000 7.85 0.00 42.34 4.61
3196 5945 4.910913 ACAAATTTTTGGTTGGGATAGGGT 59.089 37.500 7.85 0.00 42.34 4.34
3197 5946 5.497464 ACAAATTTTTGGTTGGGATAGGG 57.503 39.130 7.85 0.00 42.34 3.53
3198 5947 7.606073 CCTTTACAAATTTTTGGTTGGGATAGG 59.394 37.037 7.85 0.00 42.34 2.57
3199 5948 8.371699 TCCTTTACAAATTTTTGGTTGGGATAG 58.628 33.333 7.85 0.00 42.34 2.08
3200 5949 8.263854 TCCTTTACAAATTTTTGGTTGGGATA 57.736 30.769 7.85 0.00 42.34 2.59
3201 5950 7.142995 TCCTTTACAAATTTTTGGTTGGGAT 57.857 32.000 7.85 0.00 42.34 3.85
3202 5951 6.561519 TCCTTTACAAATTTTTGGTTGGGA 57.438 33.333 7.85 6.89 42.34 4.37
3203 5952 7.631717 TTTCCTTTACAAATTTTTGGTTGGG 57.368 32.000 7.85 5.02 42.34 4.12
3204 5953 8.897752 TCATTTCCTTTACAAATTTTTGGTTGG 58.102 29.630 7.85 4.73 42.34 3.77
3213 5962 7.759433 CGCACCTAATCATTTCCTTTACAAATT 59.241 33.333 0.00 0.00 0.00 1.82
3214 5963 7.257722 CGCACCTAATCATTTCCTTTACAAAT 58.742 34.615 0.00 0.00 0.00 2.32
3218 5967 4.497507 GGCGCACCTAATCATTTCCTTTAC 60.498 45.833 10.83 0.00 0.00 2.01
3220 5969 2.427095 GGCGCACCTAATCATTTCCTTT 59.573 45.455 10.83 0.00 0.00 3.11
3221 5970 2.024414 GGCGCACCTAATCATTTCCTT 58.976 47.619 10.83 0.00 0.00 3.36
3222 5971 1.064758 TGGCGCACCTAATCATTTCCT 60.065 47.619 10.83 0.00 36.63 3.36
3223 5972 1.388547 TGGCGCACCTAATCATTTCC 58.611 50.000 10.83 0.00 36.63 3.13
3224 5973 2.682856 TCTTGGCGCACCTAATCATTTC 59.317 45.455 10.83 0.00 36.63 2.17
3225 5974 2.722094 TCTTGGCGCACCTAATCATTT 58.278 42.857 10.83 0.00 36.63 2.32
3226 5975 2.418368 TCTTGGCGCACCTAATCATT 57.582 45.000 10.83 0.00 36.63 2.57
3227 5976 2.418368 TTCTTGGCGCACCTAATCAT 57.582 45.000 10.83 0.00 36.63 2.45
3228 5977 2.192664 TTTCTTGGCGCACCTAATCA 57.807 45.000 10.83 0.00 36.63 2.57
3246 5995 4.261801 CGTGTCTCCCCACATATCTTTTT 58.738 43.478 0.00 0.00 34.98 1.94
3251 6000 2.981859 AACGTGTCTCCCCACATATC 57.018 50.000 0.00 0.00 34.98 1.63
3253 6002 1.067425 CGAAACGTGTCTCCCCACATA 60.067 52.381 3.82 0.00 34.98 2.29
3255 6004 1.068417 CGAAACGTGTCTCCCCACA 59.932 57.895 3.82 0.00 34.98 4.17
3256 6005 2.315386 GCGAAACGTGTCTCCCCAC 61.315 63.158 3.82 0.00 0.00 4.61
3257 6006 2.029964 GCGAAACGTGTCTCCCCA 59.970 61.111 3.82 0.00 0.00 4.96
3259 6008 3.110178 CGGCGAAACGTGTCTCCC 61.110 66.667 9.18 5.78 0.00 4.30
3260 6009 1.216941 TTTCGGCGAAACGTGTCTCC 61.217 55.000 29.31 4.55 34.94 3.71
3261 6010 0.111398 GTTTCGGCGAAACGTGTCTC 60.111 55.000 39.13 21.64 41.59 3.36
3263 6012 4.484297 GTTTCGGCGAAACGTGTC 57.516 55.556 39.13 22.92 41.59 3.67
3269 6018 2.940561 GCGGAAGTTTCGGCGAAA 59.059 55.556 29.31 29.31 42.30 3.46
3324 6362 3.457610 AAATAATGCCGGCAAATCCAG 57.542 42.857 36.33 0.00 34.01 3.86
3325 6363 3.196469 TCAAAATAATGCCGGCAAATCCA 59.804 39.130 36.33 16.96 34.01 3.41
3328 6366 3.119316 TCGTCAAAATAATGCCGGCAAAT 60.119 39.130 36.33 26.37 0.00 2.32
3329 6367 2.229062 TCGTCAAAATAATGCCGGCAAA 59.771 40.909 36.33 25.24 0.00 3.68
3330 6368 1.813178 TCGTCAAAATAATGCCGGCAA 59.187 42.857 36.33 19.92 0.00 4.52
3331 6369 1.454201 TCGTCAAAATAATGCCGGCA 58.546 45.000 34.80 34.80 0.00 5.69
3332 6370 2.384382 CATCGTCAAAATAATGCCGGC 58.616 47.619 22.73 22.73 0.00 6.13
3333 6371 2.033299 AGCATCGTCAAAATAATGCCGG 59.967 45.455 0.00 0.00 44.34 6.13
3334 6372 3.002656 AGAGCATCGTCAAAATAATGCCG 59.997 43.478 2.78 0.00 44.34 5.69
3335 6373 4.558538 AGAGCATCGTCAAAATAATGCC 57.441 40.909 2.78 0.00 44.34 4.40
3336 6374 5.622856 GCTTAGAGCATCGTCAAAATAATGC 59.377 40.000 0.00 0.00 41.89 3.56
3337 6375 6.138761 GGCTTAGAGCATCGTCAAAATAATG 58.861 40.000 2.04 0.00 44.75 1.90
3338 6376 5.239525 GGGCTTAGAGCATCGTCAAAATAAT 59.760 40.000 2.04 0.00 44.75 1.28
3339 6377 4.574828 GGGCTTAGAGCATCGTCAAAATAA 59.425 41.667 2.04 0.00 44.75 1.40
3340 6378 4.127171 GGGCTTAGAGCATCGTCAAAATA 58.873 43.478 2.04 0.00 44.75 1.40
3341 6379 2.945668 GGGCTTAGAGCATCGTCAAAAT 59.054 45.455 2.04 0.00 44.75 1.82
3342 6380 2.290008 TGGGCTTAGAGCATCGTCAAAA 60.290 45.455 2.04 0.00 44.75 2.44
3344 6382 0.901827 TGGGCTTAGAGCATCGTCAA 59.098 50.000 2.04 0.00 44.75 3.18
3345 6383 0.901827 TTGGGCTTAGAGCATCGTCA 59.098 50.000 2.04 0.00 44.75 4.35
3346 6384 1.936547 CTTTGGGCTTAGAGCATCGTC 59.063 52.381 2.04 0.00 44.75 4.20
3348 6386 1.303309 CCTTTGGGCTTAGAGCATCG 58.697 55.000 2.04 0.00 44.75 3.84


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

AutoCloner maintained by Alex Coulton.