Multiple sequence alignment - TraesCS7D01G018500

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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 TraesCS7D01G018500 chr7D 100.000 3683 0 0 1 3683 8232614 8236296 0.000000e+00 6802.0
1 TraesCS7D01G018500 chr7D 86.879 2820 348 18 883 3682 8177061 8179878 0.000000e+00 3138.0
2 TraesCS7D01G018500 chr7D 85.983 2875 360 28 834 3682 7749977 7752834 0.000000e+00 3037.0
3 TraesCS7D01G018500 chr7D 85.057 2871 389 20 835 3682 7712562 7715415 0.000000e+00 2889.0
4 TraesCS7D01G018500 chr7D 84.759 2887 363 49 834 3678 7597277 7600128 0.000000e+00 2822.0
5 TraesCS7D01G018500 chr7D 85.335 1091 157 2 2595 3682 8254254 8253164 0.000000e+00 1125.0
6 TraesCS7D01G018500 chr7D 85.211 994 136 7 2597 3583 8225127 8226116 0.000000e+00 1011.0
7 TraesCS7D01G018500 chr7D 84.645 521 49 17 120 631 8256840 8256342 1.190000e-134 490.0
8 TraesCS7D01G018500 chr7D 85.106 376 43 10 263 631 7923671 7924040 4.490000e-99 372.0
9 TraesCS7D01G018500 chr4A 85.219 2882 372 35 835 3682 731875442 731872581 0.000000e+00 2913.0
10 TraesCS7D01G018500 chr4A 85.426 2827 365 31 892 3682 731761212 731758397 0.000000e+00 2894.0
11 TraesCS7D01G018500 chr4A 83.184 2783 379 63 362 3092 732362006 732364751 0.000000e+00 2464.0
12 TraesCS7D01G018500 chr4A 79.501 3610 585 85 185 3676 732057852 732061424 0.000000e+00 2423.0
13 TraesCS7D01G018500 chr4A 85.690 1796 230 16 835 2607 731774370 731772579 0.000000e+00 1868.0
14 TraesCS7D01G018500 chr4A 84.279 1075 156 9 2597 3663 731662332 731661263 0.000000e+00 1037.0
15 TraesCS7D01G018500 chr4A 86.267 517 57 9 119 631 732104661 732105167 1.930000e-152 549.0
16 TraesCS7D01G018500 chr4A 84.774 532 67 11 117 644 731605036 731604515 4.210000e-144 521.0
17 TraesCS7D01G018500 chr4A 88.660 194 15 6 117 308 732361816 732362004 2.860000e-56 230.0
18 TraesCS7D01G018500 chr4A 89.333 75 8 0 550 624 732354409 732354483 1.090000e-15 95.3
19 TraesCS7D01G018500 chr7A 84.986 2884 363 44 834 3678 8653709 8656561 0.000000e+00 2863.0
20 TraesCS7D01G018500 chr7A 83.386 2865 421 37 841 3682 56204892 56207724 0.000000e+00 2603.0
21 TraesCS7D01G018500 chr7A 82.665 2867 446 37 834 3679 8634301 8637137 0.000000e+00 2494.0
22 TraesCS7D01G018500 chr7A 81.449 2884 462 43 834 3682 56174186 56177031 0.000000e+00 2294.0
23 TraesCS7D01G018500 chr7A 85.662 1102 147 8 2586 3682 3430320 3429225 0.000000e+00 1149.0
24 TraesCS7D01G018500 chr7A 84.601 1091 160 6 2595 3682 8693281 8692196 0.000000e+00 1077.0
25 TraesCS7D01G018500 chr7A 83.877 521 52 15 120 631 8695867 8695370 5.570000e-128 468.0
26 TraesCS7D01G018500 chr7A 92.308 52 4 0 13 64 8588341 8588392 1.420000e-09 75.0
27 TraesCS7D01G018500 chr7A 89.655 58 6 0 762 819 8589635 8589692 1.420000e-09 75.0
28 TraesCS7D01G018500 chr5B 84.173 2679 373 38 836 3493 37410250 37412898 0.000000e+00 2551.0
29 TraesCS7D01G018500 chr5B 87.209 430 43 6 209 631 37480972 37481396 2.570000e-131 479.0
30 TraesCS7D01G018500 chr5B 85.014 367 42 7 234 593 37409037 37409397 9.720000e-96 361.0
31 TraesCS7D01G018500 chr3B 84.510 1091 166 2 2595 3682 741464967 741466057 0.000000e+00 1075.0


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 TraesCS7D01G018500 chr7D 8232614 8236296 3682 False 6802.0 6802 100.0000 1 3683 1 chr7D.!!$F7 3682
1 TraesCS7D01G018500 chr7D 8177061 8179878 2817 False 3138.0 3138 86.8790 883 3682 1 chr7D.!!$F5 2799
2 TraesCS7D01G018500 chr7D 7749977 7752834 2857 False 3037.0 3037 85.9830 834 3682 1 chr7D.!!$F3 2848
3 TraesCS7D01G018500 chr7D 7712562 7715415 2853 False 2889.0 2889 85.0570 835 3682 1 chr7D.!!$F2 2847
4 TraesCS7D01G018500 chr7D 7597277 7600128 2851 False 2822.0 2822 84.7590 834 3678 1 chr7D.!!$F1 2844
5 TraesCS7D01G018500 chr7D 8225127 8226116 989 False 1011.0 1011 85.2110 2597 3583 1 chr7D.!!$F6 986
6 TraesCS7D01G018500 chr7D 8253164 8256840 3676 True 807.5 1125 84.9900 120 3682 2 chr7D.!!$R1 3562
7 TraesCS7D01G018500 chr4A 731872581 731875442 2861 True 2913.0 2913 85.2190 835 3682 1 chr4A.!!$R5 2847
8 TraesCS7D01G018500 chr4A 731758397 731761212 2815 True 2894.0 2894 85.4260 892 3682 1 chr4A.!!$R3 2790
9 TraesCS7D01G018500 chr4A 732057852 732061424 3572 False 2423.0 2423 79.5010 185 3676 1 chr4A.!!$F1 3491
10 TraesCS7D01G018500 chr4A 731772579 731774370 1791 True 1868.0 1868 85.6900 835 2607 1 chr4A.!!$R4 1772
11 TraesCS7D01G018500 chr4A 732361816 732364751 2935 False 1347.0 2464 85.9220 117 3092 2 chr4A.!!$F4 2975
12 TraesCS7D01G018500 chr4A 731661263 731662332 1069 True 1037.0 1037 84.2790 2597 3663 1 chr4A.!!$R2 1066
13 TraesCS7D01G018500 chr4A 732104661 732105167 506 False 549.0 549 86.2670 119 631 1 chr4A.!!$F2 512
14 TraesCS7D01G018500 chr4A 731604515 731605036 521 True 521.0 521 84.7740 117 644 1 chr4A.!!$R1 527
15 TraesCS7D01G018500 chr7A 8653709 8656561 2852 False 2863.0 2863 84.9860 834 3678 1 chr7A.!!$F2 2844
16 TraesCS7D01G018500 chr7A 56204892 56207724 2832 False 2603.0 2603 83.3860 841 3682 1 chr7A.!!$F4 2841
17 TraesCS7D01G018500 chr7A 8634301 8637137 2836 False 2494.0 2494 82.6650 834 3679 1 chr7A.!!$F1 2845
18 TraesCS7D01G018500 chr7A 56174186 56177031 2845 False 2294.0 2294 81.4490 834 3682 1 chr7A.!!$F3 2848
19 TraesCS7D01G018500 chr7A 3429225 3430320 1095 True 1149.0 1149 85.6620 2586 3682 1 chr7A.!!$R1 1096
20 TraesCS7D01G018500 chr7A 8692196 8695867 3671 True 772.5 1077 84.2390 120 3682 2 chr7A.!!$R2 3562
21 TraesCS7D01G018500 chr5B 37409037 37412898 3861 False 1456.0 2551 84.5935 234 3493 2 chr5B.!!$F2 3259
22 TraesCS7D01G018500 chr3B 741464967 741466057 1090 False 1075.0 1075 84.5100 2595 3682 1 chr3B.!!$F1 1087

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
73 74 0.036010 CCGATCTTTCCTGGTGCAGT 60.036 55.0 0.00 0.00 0.0 4.40 F
648 1227 0.318699 TTCACGCGTGAAGAGGTCTG 60.319 55.0 42.01 14.67 43.9 3.51 F
1203 1905 0.462759 GCCGCCAGTCTAAGAGCAAT 60.463 55.0 0.00 0.00 0.0 3.56 F
1220 1922 0.620556 AATGAGTCCACTTCCCGCAT 59.379 50.0 0.00 0.00 0.0 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1202 1904 0.107508 CATGCGGGAAGTGGACTCAT 60.108 55.000 0.00 0.0 0.00 2.90 R
1834 2537 0.318699 TGGCTTCGAGTTGTGACGAG 60.319 55.000 0.00 0.0 39.59 4.18 R
2033 2749 0.465460 TAGCAATCCGCCCATTGTCC 60.465 55.000 4.62 0.0 44.04 4.02 R
2784 3574 1.448540 CTGTTGCAGCTCCCGGTAG 60.449 63.158 0.00 0.0 0.00 3.18 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
22 23 4.872664 CTCCGGTAGTGAATTATGTCTCC 58.127 47.826 0.00 0.00 0.00 3.71
23 24 4.543689 TCCGGTAGTGAATTATGTCTCCT 58.456 43.478 0.00 0.00 0.00 3.69
24 25 4.583489 TCCGGTAGTGAATTATGTCTCCTC 59.417 45.833 0.00 0.00 0.00 3.71
25 26 4.537965 CGGTAGTGAATTATGTCTCCTCG 58.462 47.826 0.00 0.00 0.00 4.63
26 27 4.036498 CGGTAGTGAATTATGTCTCCTCGT 59.964 45.833 0.00 0.00 0.00 4.18
27 28 5.237996 CGGTAGTGAATTATGTCTCCTCGTA 59.762 44.000 0.00 0.00 0.00 3.43
28 29 6.437094 GGTAGTGAATTATGTCTCCTCGTAC 58.563 44.000 0.00 0.00 0.00 3.67
29 30 6.039047 GGTAGTGAATTATGTCTCCTCGTACA 59.961 42.308 0.00 0.00 0.00 2.90
30 31 6.716934 AGTGAATTATGTCTCCTCGTACAT 57.283 37.500 0.00 0.00 39.56 2.29
31 32 7.818997 AGTGAATTATGTCTCCTCGTACATA 57.181 36.000 0.00 0.00 37.50 2.29
32 33 7.649973 AGTGAATTATGTCTCCTCGTACATAC 58.350 38.462 0.00 0.00 38.09 2.39
33 34 7.502895 AGTGAATTATGTCTCCTCGTACATACT 59.497 37.037 0.00 0.00 38.09 2.12
34 35 7.804129 GTGAATTATGTCTCCTCGTACATACTC 59.196 40.741 0.00 0.00 38.09 2.59
35 36 7.720074 TGAATTATGTCTCCTCGTACATACTCT 59.280 37.037 0.00 0.00 38.09 3.24
36 37 8.466617 AATTATGTCTCCTCGTACATACTCTT 57.533 34.615 0.00 0.00 38.09 2.85
37 38 5.759506 ATGTCTCCTCGTACATACTCTTG 57.240 43.478 0.00 0.00 34.61 3.02
38 39 4.586884 TGTCTCCTCGTACATACTCTTGT 58.413 43.478 0.00 0.00 0.00 3.16
39 40 4.634883 TGTCTCCTCGTACATACTCTTGTC 59.365 45.833 0.00 0.00 0.00 3.18
40 41 4.877251 GTCTCCTCGTACATACTCTTGTCT 59.123 45.833 0.00 0.00 0.00 3.41
41 42 6.047870 GTCTCCTCGTACATACTCTTGTCTA 58.952 44.000 0.00 0.00 0.00 2.59
42 43 6.201425 GTCTCCTCGTACATACTCTTGTCTAG 59.799 46.154 0.00 0.00 0.00 2.43
43 44 4.815308 TCCTCGTACATACTCTTGTCTAGC 59.185 45.833 0.00 0.00 0.00 3.42
44 45 4.318903 CCTCGTACATACTCTTGTCTAGCG 60.319 50.000 0.00 0.00 0.00 4.26
45 46 4.186926 TCGTACATACTCTTGTCTAGCGT 58.813 43.478 0.00 0.00 0.00 5.07
46 47 4.633126 TCGTACATACTCTTGTCTAGCGTT 59.367 41.667 0.00 0.00 0.00 4.84
47 48 5.812127 TCGTACATACTCTTGTCTAGCGTTA 59.188 40.000 0.00 0.00 0.00 3.18
48 49 6.019237 TCGTACATACTCTTGTCTAGCGTTAG 60.019 42.308 0.00 0.00 0.00 2.34
49 50 5.502153 ACATACTCTTGTCTAGCGTTAGG 57.498 43.478 6.45 0.00 0.00 2.69
50 51 4.338682 ACATACTCTTGTCTAGCGTTAGGG 59.661 45.833 6.45 0.00 0.00 3.53
51 52 2.805194 ACTCTTGTCTAGCGTTAGGGT 58.195 47.619 6.45 0.00 0.00 4.34
52 53 2.754002 ACTCTTGTCTAGCGTTAGGGTC 59.246 50.000 6.45 0.00 0.00 4.46
53 54 3.018149 CTCTTGTCTAGCGTTAGGGTCT 58.982 50.000 6.45 0.00 0.00 3.85
54 55 3.015327 TCTTGTCTAGCGTTAGGGTCTC 58.985 50.000 6.45 0.00 0.00 3.36
55 56 1.760192 TGTCTAGCGTTAGGGTCTCC 58.240 55.000 6.45 0.00 0.00 3.71
56 57 0.662085 GTCTAGCGTTAGGGTCTCCG 59.338 60.000 6.45 0.00 38.33 4.63
57 58 0.543277 TCTAGCGTTAGGGTCTCCGA 59.457 55.000 6.45 0.00 38.33 4.55
58 59 1.142465 TCTAGCGTTAGGGTCTCCGAT 59.858 52.381 6.45 0.00 38.33 4.18
59 60 1.536331 CTAGCGTTAGGGTCTCCGATC 59.464 57.143 0.00 0.00 38.33 3.69
60 61 0.106619 AGCGTTAGGGTCTCCGATCT 60.107 55.000 0.00 0.00 38.33 2.75
61 62 0.745468 GCGTTAGGGTCTCCGATCTT 59.255 55.000 0.00 0.00 38.33 2.40
62 63 1.136500 GCGTTAGGGTCTCCGATCTTT 59.864 52.381 0.00 0.00 38.33 2.52
63 64 2.798853 GCGTTAGGGTCTCCGATCTTTC 60.799 54.545 0.00 0.00 38.33 2.62
64 65 2.223758 CGTTAGGGTCTCCGATCTTTCC 60.224 54.545 0.00 0.00 38.33 3.13
65 66 3.032459 GTTAGGGTCTCCGATCTTTCCT 58.968 50.000 0.00 0.00 38.33 3.36
66 67 1.490574 AGGGTCTCCGATCTTTCCTG 58.509 55.000 0.00 0.00 38.33 3.86
67 68 0.466124 GGGTCTCCGATCTTTCCTGG 59.534 60.000 0.00 0.00 0.00 4.45
68 69 1.196012 GGTCTCCGATCTTTCCTGGT 58.804 55.000 0.00 0.00 0.00 4.00
69 70 1.134670 GGTCTCCGATCTTTCCTGGTG 60.135 57.143 0.00 0.00 0.00 4.17
70 71 0.537188 TCTCCGATCTTTCCTGGTGC 59.463 55.000 0.00 0.00 0.00 5.01
71 72 0.250234 CTCCGATCTTTCCTGGTGCA 59.750 55.000 0.00 0.00 0.00 4.57
72 73 0.250234 TCCGATCTTTCCTGGTGCAG 59.750 55.000 0.00 0.00 0.00 4.41
73 74 0.036010 CCGATCTTTCCTGGTGCAGT 60.036 55.000 0.00 0.00 0.00 4.40
74 75 1.081892 CGATCTTTCCTGGTGCAGTG 58.918 55.000 0.00 0.00 0.00 3.66
75 76 1.457346 GATCTTTCCTGGTGCAGTGG 58.543 55.000 0.00 0.00 0.00 4.00
76 77 0.610232 ATCTTTCCTGGTGCAGTGGC 60.610 55.000 0.00 0.00 41.68 5.01
90 91 4.908966 GCAGTGGCAATTGTTTATTGTC 57.091 40.909 7.40 0.00 46.73 3.18
91 92 3.679502 GCAGTGGCAATTGTTTATTGTCC 59.320 43.478 7.40 0.00 46.14 4.02
92 93 4.561326 GCAGTGGCAATTGTTTATTGTCCT 60.561 41.667 7.40 0.00 46.14 3.85
93 94 5.336372 GCAGTGGCAATTGTTTATTGTCCTA 60.336 40.000 7.40 0.00 46.14 2.94
94 95 6.627953 GCAGTGGCAATTGTTTATTGTCCTAT 60.628 38.462 7.40 0.00 46.14 2.57
95 96 6.974622 CAGTGGCAATTGTTTATTGTCCTATC 59.025 38.462 7.40 0.00 46.14 2.08
96 97 5.971202 GTGGCAATTGTTTATTGTCCTATCG 59.029 40.000 7.40 0.00 46.14 2.92
97 98 5.883115 TGGCAATTGTTTATTGTCCTATCGA 59.117 36.000 7.40 0.00 46.14 3.59
98 99 6.183360 TGGCAATTGTTTATTGTCCTATCGAC 60.183 38.462 7.40 0.00 46.14 4.20
112 113 6.570692 GTCCTATCGACAAGTAGGAAAATCA 58.429 40.000 12.94 0.00 45.89 2.57
113 114 7.039882 GTCCTATCGACAAGTAGGAAAATCAA 58.960 38.462 12.94 0.00 45.89 2.57
114 115 7.222999 GTCCTATCGACAAGTAGGAAAATCAAG 59.777 40.741 12.94 0.00 45.89 3.02
115 116 7.042335 CCTATCGACAAGTAGGAAAATCAAGT 58.958 38.462 4.08 0.00 39.91 3.16
129 130 6.183360 GGAAAATCAAGTGGCAATTGTTTGTT 60.183 34.615 24.81 17.92 35.17 2.83
158 159 3.193267 AGTTGCAGAACAAACTCAAAGCA 59.807 39.130 0.00 0.00 40.82 3.91
175 178 7.011482 ACTCAAAGCACTTGAATATCGGTATTC 59.989 37.037 19.51 19.51 43.54 1.75
218 222 5.189145 AGGGAAGTGTTGTCGACCTAAATAT 59.811 40.000 14.12 0.00 0.00 1.28
224 228 8.644318 AGTGTTGTCGACCTAAATATAACATC 57.356 34.615 14.12 8.74 0.00 3.06
303 308 7.662897 TGTTTCCTTCCACAATTATTTGTACC 58.337 34.615 2.82 0.00 44.24 3.34
311 316 7.881142 TCCACAATTATTTGTACCAACTGAAG 58.119 34.615 2.82 0.00 44.24 3.02
325 334 5.707298 ACCAACTGAAGAATTAGACACCATG 59.293 40.000 0.00 0.00 0.00 3.66
334 343 3.973206 TTAGACACCATGTACACTGGG 57.027 47.619 21.11 15.44 38.14 4.45
346 355 3.576982 TGTACACTGGGTGGTCTTAAGAG 59.423 47.826 5.12 0.00 37.94 2.85
355 364 6.423182 TGGGTGGTCTTAAGAGGATTAAATG 58.577 40.000 5.12 0.00 0.00 2.32
403 412 5.574055 CACTAACACAATGGCAATGCTAAAG 59.426 40.000 4.82 0.00 0.00 1.85
405 414 4.605640 ACACAATGGCAATGCTAAAGTT 57.394 36.364 4.82 0.00 0.00 2.66
412 421 8.408601 ACAATGGCAATGCTAAAGTTATCTAAG 58.591 33.333 4.82 0.00 0.00 2.18
414 423 8.752005 ATGGCAATGCTAAAGTTATCTAAGAA 57.248 30.769 4.82 0.00 0.00 2.52
427 436 7.352739 AGTTATCTAAGAAAAACAGTTGCGTG 58.647 34.615 0.00 0.00 0.00 5.34
441 452 4.510340 CAGTTGCGTGTAGGTAAAAGAGTT 59.490 41.667 0.00 0.00 0.00 3.01
534 553 1.487558 GGGACCACCGGTACATGTATT 59.512 52.381 6.87 0.00 38.55 1.89
561 580 7.558081 AGTCAGTCAGTCAATATACAGCTCTTA 59.442 37.037 0.00 0.00 0.00 2.10
577 596 7.496747 ACAGCTCTTAGATTCCTTGATCTTAC 58.503 38.462 0.00 0.00 37.54 2.34
584 603 6.185114 AGATTCCTTGATCTTACCTCCATG 57.815 41.667 0.00 0.00 32.54 3.66
624 1203 3.758023 CAGCAACCACACAATTCCATAGA 59.242 43.478 0.00 0.00 0.00 1.98
631 1210 4.096984 CCACACAATTCCATAGAAGCCTTC 59.903 45.833 0.00 0.00 34.86 3.46
632 1211 4.701651 CACACAATTCCATAGAAGCCTTCA 59.298 41.667 7.29 0.00 34.86 3.02
646 1225 4.647654 TTCACGCGTGAAGAGGTC 57.352 55.556 42.01 0.00 43.90 3.85
647 1226 2.038690 TTCACGCGTGAAGAGGTCT 58.961 52.632 42.01 1.00 43.90 3.85
648 1227 0.318699 TTCACGCGTGAAGAGGTCTG 60.319 55.000 42.01 14.67 43.90 3.51
649 1228 2.049063 ACGCGTGAAGAGGTCTGC 60.049 61.111 12.93 0.00 0.00 4.26
687 1295 6.538021 CACCAATTTGGACAAGTCAAATTTGA 59.462 34.615 22.19 16.91 46.42 2.69
693 1301 3.975035 GGACAAGTCAAATTTGAGCGTTC 59.025 43.478 21.05 12.86 37.98 3.95
705 1313 2.688507 TGAGCGTTCTTGAGGTGAATC 58.311 47.619 0.00 0.00 0.00 2.52
707 1315 1.087501 GCGTTCTTGAGGTGAATCCC 58.912 55.000 0.00 0.00 36.75 3.85
710 1318 2.500098 CGTTCTTGAGGTGAATCCCCTA 59.500 50.000 0.00 0.00 36.75 3.53
717 1325 4.890988 TGAGGTGAATCCCCTACTCAATA 58.109 43.478 0.00 0.00 36.75 1.90
718 1326 4.901849 TGAGGTGAATCCCCTACTCAATAG 59.098 45.833 0.00 0.00 36.75 1.73
719 1327 4.897051 AGGTGAATCCCCTACTCAATAGT 58.103 43.478 0.00 0.00 36.98 2.12
720 1328 4.902448 AGGTGAATCCCCTACTCAATAGTC 59.098 45.833 0.00 0.00 35.44 2.59
721 1329 4.654262 GGTGAATCCCCTACTCAATAGTCA 59.346 45.833 0.00 0.00 37.15 3.41
722 1330 5.130477 GGTGAATCCCCTACTCAATAGTCAA 59.870 44.000 0.00 0.00 37.15 3.18
723 1331 6.183361 GGTGAATCCCCTACTCAATAGTCAAT 60.183 42.308 0.00 0.00 37.15 2.57
724 1332 7.283329 GTGAATCCCCTACTCAATAGTCAATT 58.717 38.462 0.00 0.00 37.15 2.32
730 1338 6.058183 CCCTACTCAATAGTCAATTCTTGGG 58.942 44.000 0.00 0.00 37.15 4.12
731 1339 6.353082 CCCTACTCAATAGTCAATTCTTGGGT 60.353 42.308 0.00 0.00 37.15 4.51
740 1348 6.293004 AGTCAATTCTTGGGTTTGTTTTGA 57.707 33.333 0.00 0.00 0.00 2.69
753 1361 7.710475 TGGGTTTGTTTTGATCTTCTTTGATTC 59.290 33.333 0.00 0.00 0.00 2.52
880 1573 7.396339 TCTGTCAGTGCTTAACCTCTCTTATTA 59.604 37.037 0.00 0.00 0.00 0.98
890 1588 5.606348 ACCTCTCTTATTACTTCTGCTGG 57.394 43.478 0.00 0.00 0.00 4.85
899 1601 8.812972 TCTTATTACTTCTGCTGGAGTTTCTTA 58.187 33.333 10.13 0.00 0.00 2.10
949 1651 4.133078 GTCATTGCTTCTCCCTCTATTGG 58.867 47.826 0.00 0.00 0.00 3.16
1004 1706 1.335964 CGAGACGGTGACTCACATGTT 60.336 52.381 11.34 1.32 35.86 2.71
1134 1836 3.307339 GGATGAAGGAGCTCAAGTCTGTT 60.307 47.826 17.19 0.00 0.00 3.16
1199 1901 2.583593 GCGCCGCCAGTCTAAGAG 60.584 66.667 0.00 0.00 0.00 2.85
1202 1904 1.079127 GCCGCCAGTCTAAGAGCAA 60.079 57.895 0.00 0.00 0.00 3.91
1203 1905 0.462759 GCCGCCAGTCTAAGAGCAAT 60.463 55.000 0.00 0.00 0.00 3.56
1220 1922 0.620556 AATGAGTCCACTTCCCGCAT 59.379 50.000 0.00 0.00 0.00 4.73
1239 1941 3.872696 CATGGTACTTGGCTACATCACA 58.127 45.455 0.00 0.00 0.00 3.58
1334 2036 2.038952 TGGTTGAGGAGATGAACAGGTG 59.961 50.000 0.00 0.00 0.00 4.00
1413 2115 5.335035 GCACTCAAAACTAGACGAGACTACT 60.335 44.000 0.00 0.00 0.00 2.57
1467 2169 1.956477 GTGGTGAAGTTGCTGTTGGAT 59.044 47.619 0.00 0.00 0.00 3.41
1524 2226 1.214305 TTGGGATGGGAGGTCTTGGG 61.214 60.000 0.00 0.00 0.00 4.12
1728 2431 3.509442 TGAGAAGGTCATTGGCCAAAAT 58.491 40.909 24.71 3.41 0.00 1.82
1803 2506 5.491982 GAGGATGTCTTGAAGCCTCTTTTA 58.508 41.667 8.71 0.00 41.44 1.52
1819 2522 6.547510 GCCTCTTTTATGTTCTATTGGTGGAT 59.452 38.462 0.00 0.00 0.00 3.41
1834 2537 5.353394 TGGTGGATCAGGAAGTGTAATAC 57.647 43.478 0.00 0.00 0.00 1.89
1889 2592 4.452733 GCAGACCCTTCGACCCCG 62.453 72.222 0.00 0.00 37.07 5.73
1894 2597 0.967380 GACCCTTCGACCCCGTAAGA 60.967 60.000 0.00 0.00 43.02 2.10
1897 2600 2.034124 CCCTTCGACCCCGTAAGATAA 58.966 52.381 0.00 0.00 43.02 1.75
1903 2606 3.448301 TCGACCCCGTAAGATAACATGTT 59.552 43.478 16.68 16.68 43.02 2.71
1907 2610 5.562635 ACCCCGTAAGATAACATGTTTGAA 58.437 37.500 17.78 0.00 43.02 2.69
1927 2631 6.519679 TGAATGAACAAGATTCATGGGAAG 57.480 37.500 3.03 0.00 38.96 3.46
1960 2664 1.949257 GCATATAGCAACGGTGGGC 59.051 57.895 0.90 0.00 44.79 5.36
1968 2678 2.852075 AACGGTGGGCAGGAGGAA 60.852 61.111 0.00 0.00 0.00 3.36
1970 2680 1.789576 AACGGTGGGCAGGAGGAAAT 61.790 55.000 0.00 0.00 0.00 2.17
1974 2687 1.564348 GGTGGGCAGGAGGAAATAGAA 59.436 52.381 0.00 0.00 0.00 2.10
2033 2749 1.449956 GGCTGCCTCTTGCTCTCAG 60.450 63.158 12.43 0.00 42.00 3.35
2106 2822 7.736893 AGGCCATCGAAGAAAGTAATATTAGT 58.263 34.615 5.01 0.00 43.58 2.24
2109 2825 9.042008 GCCATCGAAGAAAGTAATATTAGTGAA 57.958 33.333 3.54 0.00 43.58 3.18
2171 2890 7.182817 AGTTGAGCTACAAACACCTATCATA 57.817 36.000 8.60 0.00 40.36 2.15
2187 2906 7.541091 CACCTATCATATGAAATGAAGCAATGC 59.459 37.037 9.99 0.00 0.00 3.56
2316 3036 6.737254 TTAACACGGAAAGGAGAAATCATC 57.263 37.500 0.00 0.00 0.00 2.92
2578 3323 4.216411 ACATACCTCCGCACTTTGTTAT 57.784 40.909 0.00 0.00 0.00 1.89
2591 3339 6.535150 CGCACTTTGTTATCTCCTTCAGAATA 59.465 38.462 0.00 0.00 33.62 1.75
2592 3340 7.464710 CGCACTTTGTTATCTCCTTCAGAATAC 60.465 40.741 0.00 0.00 33.62 1.89
2616 3400 8.494016 ACTACAAGGATTATAAAGTGTTGCTC 57.506 34.615 0.00 0.00 0.00 4.26
2670 3455 3.026694 CCCCCTCCTTCAATTGTCATTC 58.973 50.000 5.13 0.00 0.00 2.67
2691 3479 2.349275 CGCAAGGCCATAAATGCAAAAG 59.651 45.455 5.01 0.00 38.69 2.27
2751 3541 4.415881 ACCGCCAGATTCAATATGTGTA 57.584 40.909 0.00 0.00 0.00 2.90
2784 3574 2.164422 GCAAACCTTAAGGCTCATGGAC 59.836 50.000 21.92 0.00 39.32 4.02
2786 3576 4.843728 CAAACCTTAAGGCTCATGGACTA 58.156 43.478 21.92 0.00 39.32 2.59
2882 3672 9.737427 ATGTTATAGTCTCAAAAGTATGTCTCG 57.263 33.333 0.00 0.00 0.00 4.04
2907 3697 6.204301 GGAACTTTGGTCTACTAAACAACCTC 59.796 42.308 0.00 0.00 32.82 3.85
2912 3702 6.336842 TGGTCTACTAAACAACCTCTACAC 57.663 41.667 0.00 0.00 32.82 2.90
3002 3792 4.396166 CCTTAGCAATAGGTTGGAACTGTG 59.604 45.833 0.00 0.00 35.83 3.66
3070 3860 5.489792 TCTCAGTCAGAAGCAAAACCTAT 57.510 39.130 0.00 0.00 0.00 2.57
3096 3890 2.618709 GTTGTTGTTCTCTTGGGACCAG 59.381 50.000 0.00 0.00 0.00 4.00
3103 3897 4.352595 TGTTCTCTTGGGACCAGGAAATAA 59.647 41.667 4.66 0.00 31.71 1.40
3141 3950 2.859165 TGGCTTGTAAGGTGGAAGAG 57.141 50.000 0.00 0.00 0.00 2.85
3236 4046 1.066573 ACAGTGGATGAGAAAGCCTCG 60.067 52.381 0.00 0.00 44.92 4.63
3275 4085 4.008330 AGAGAACTCGAAATGTCCGACTA 58.992 43.478 0.00 0.00 34.09 2.59
3278 4088 2.444421 ACTCGAAATGTCCGACTACCT 58.556 47.619 0.00 0.00 32.18 3.08
3280 4090 3.626670 ACTCGAAATGTCCGACTACCTAG 59.373 47.826 0.00 0.00 32.18 3.02
3313 4123 6.835174 AGTATACCTGTAGTATGGTTCTCGA 58.165 40.000 0.00 0.00 41.89 4.04
3314 4124 6.709846 AGTATACCTGTAGTATGGTTCTCGAC 59.290 42.308 0.00 0.00 41.89 4.20
3384 4194 9.120538 ACATTATGTAATAACCTTGATGTGGAC 57.879 33.333 0.00 0.00 42.43 4.02
3392 4205 1.364626 CTTGATGTGGACGCTGGAGC 61.365 60.000 0.00 0.00 37.78 4.70
3443 4256 5.825593 AGGTTGAAGAGGATGTACTTGAA 57.174 39.130 0.00 0.00 0.00 2.69
3502 4315 0.833287 GGGAGAGCCTTGTGATAGCA 59.167 55.000 0.00 0.00 0.00 3.49
3533 4346 3.950397 TCCCGATGTTTGAAGTGCTAAT 58.050 40.909 0.00 0.00 0.00 1.73
3538 4351 5.504665 CCGATGTTTGAAGTGCTAATGATCC 60.505 44.000 0.00 0.00 0.00 3.36
3543 4356 7.495901 TGTTTGAAGTGCTAATGATCCAAAAA 58.504 30.769 0.00 0.00 0.00 1.94
3583 4396 2.435938 CGGTGACCCCCAATGTCG 60.436 66.667 0.00 0.00 35.46 4.35
3584 4397 2.949909 CGGTGACCCCCAATGTCGA 61.950 63.158 0.00 0.00 35.46 4.20
3606 4419 5.803461 CGACGAGTTGACAATAATTGGAGTA 59.197 40.000 0.00 0.00 34.12 2.59
3652 4466 6.719370 AGTTTTTATGAGTATCTGTTTGGGCA 59.281 34.615 0.00 0.00 34.92 5.36
3682 4496 5.701290 CCATTTCTCGTCAGGTTAACTCTTT 59.299 40.000 5.42 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.543689 AGGAGACATAATTCACTACCGGA 58.456 43.478 9.46 0.00 0.00 5.14
2 3 4.556898 CGAGGAGACATAATTCACTACCGG 60.557 50.000 0.00 0.00 0.00 5.28
3 4 4.036498 ACGAGGAGACATAATTCACTACCG 59.964 45.833 0.00 0.00 0.00 4.02
4 5 5.517322 ACGAGGAGACATAATTCACTACC 57.483 43.478 0.00 0.00 0.00 3.18
5 6 7.024340 TGTACGAGGAGACATAATTCACTAC 57.976 40.000 0.00 0.00 0.00 2.73
6 7 7.818997 ATGTACGAGGAGACATAATTCACTA 57.181 36.000 0.00 0.00 34.52 2.74
7 8 6.716934 ATGTACGAGGAGACATAATTCACT 57.283 37.500 0.00 0.00 34.52 3.41
8 9 7.649973 AGTATGTACGAGGAGACATAATTCAC 58.350 38.462 0.00 0.00 39.58 3.18
9 10 7.720074 AGAGTATGTACGAGGAGACATAATTCA 59.280 37.037 0.00 0.00 39.58 2.57
10 11 8.101654 AGAGTATGTACGAGGAGACATAATTC 57.898 38.462 0.00 0.00 39.58 2.17
11 12 8.353684 CAAGAGTATGTACGAGGAGACATAATT 58.646 37.037 0.00 0.00 39.58 1.40
12 13 7.502895 ACAAGAGTATGTACGAGGAGACATAAT 59.497 37.037 0.00 0.00 39.58 1.28
13 14 6.827251 ACAAGAGTATGTACGAGGAGACATAA 59.173 38.462 0.00 0.00 39.58 1.90
14 15 6.354938 ACAAGAGTATGTACGAGGAGACATA 58.645 40.000 0.00 0.00 37.47 2.29
15 16 5.194432 ACAAGAGTATGTACGAGGAGACAT 58.806 41.667 0.00 0.00 39.57 3.06
16 17 4.586884 ACAAGAGTATGTACGAGGAGACA 58.413 43.478 0.00 0.00 0.00 3.41
17 18 4.877251 AGACAAGAGTATGTACGAGGAGAC 59.123 45.833 0.00 0.00 32.57 3.36
18 19 5.100344 AGACAAGAGTATGTACGAGGAGA 57.900 43.478 0.00 0.00 32.57 3.71
19 20 5.049954 GCTAGACAAGAGTATGTACGAGGAG 60.050 48.000 0.00 0.00 32.57 3.69
20 21 4.815308 GCTAGACAAGAGTATGTACGAGGA 59.185 45.833 0.00 0.00 32.57 3.71
21 22 4.318903 CGCTAGACAAGAGTATGTACGAGG 60.319 50.000 0.00 0.00 32.57 4.63
22 23 4.270566 ACGCTAGACAAGAGTATGTACGAG 59.729 45.833 0.00 0.00 36.35 4.18
23 24 4.186926 ACGCTAGACAAGAGTATGTACGA 58.813 43.478 0.00 0.00 36.35 3.43
24 25 4.533225 ACGCTAGACAAGAGTATGTACG 57.467 45.455 0.00 0.00 36.35 3.67
25 26 6.428799 CCTAACGCTAGACAAGAGTATGTAC 58.571 44.000 0.00 0.00 37.23 2.90
26 27 5.530171 CCCTAACGCTAGACAAGAGTATGTA 59.470 44.000 0.00 0.00 37.23 2.29
27 28 4.338682 CCCTAACGCTAGACAAGAGTATGT 59.661 45.833 0.00 0.00 37.23 2.29
28 29 4.338682 ACCCTAACGCTAGACAAGAGTATG 59.661 45.833 0.00 0.00 37.23 2.39
29 30 4.534797 ACCCTAACGCTAGACAAGAGTAT 58.465 43.478 0.00 0.00 37.23 2.12
30 31 3.944015 GACCCTAACGCTAGACAAGAGTA 59.056 47.826 0.00 0.00 37.23 2.59
31 32 2.754002 GACCCTAACGCTAGACAAGAGT 59.246 50.000 0.00 0.00 40.33 3.24
32 33 3.018149 AGACCCTAACGCTAGACAAGAG 58.982 50.000 0.00 0.00 0.00 2.85
33 34 3.015327 GAGACCCTAACGCTAGACAAGA 58.985 50.000 0.00 0.00 0.00 3.02
34 35 2.099427 GGAGACCCTAACGCTAGACAAG 59.901 54.545 0.00 0.00 0.00 3.16
35 36 2.097825 GGAGACCCTAACGCTAGACAA 58.902 52.381 0.00 0.00 0.00 3.18
36 37 1.760192 GGAGACCCTAACGCTAGACA 58.240 55.000 0.00 0.00 0.00 3.41
37 38 0.662085 CGGAGACCCTAACGCTAGAC 59.338 60.000 0.00 0.00 0.00 2.59
38 39 0.543277 TCGGAGACCCTAACGCTAGA 59.457 55.000 0.00 0.00 0.00 2.43
39 40 1.536331 GATCGGAGACCCTAACGCTAG 59.464 57.143 0.00 0.00 42.51 3.42
40 41 1.142465 AGATCGGAGACCCTAACGCTA 59.858 52.381 0.00 0.00 42.51 4.26
41 42 0.106619 AGATCGGAGACCCTAACGCT 60.107 55.000 0.00 0.00 42.51 5.07
42 43 0.745468 AAGATCGGAGACCCTAACGC 59.255 55.000 0.00 0.00 42.51 4.84
43 44 2.223758 GGAAAGATCGGAGACCCTAACG 60.224 54.545 0.00 0.00 42.51 3.18
44 45 3.032459 AGGAAAGATCGGAGACCCTAAC 58.968 50.000 0.00 0.00 42.51 2.34
45 46 3.031736 CAGGAAAGATCGGAGACCCTAA 58.968 50.000 0.00 0.00 42.51 2.69
46 47 2.667470 CAGGAAAGATCGGAGACCCTA 58.333 52.381 0.00 0.00 42.51 3.53
47 48 1.490574 CAGGAAAGATCGGAGACCCT 58.509 55.000 0.00 0.00 42.51 4.34
48 49 0.466124 CCAGGAAAGATCGGAGACCC 59.534 60.000 0.00 0.00 42.51 4.46
49 50 1.134670 CACCAGGAAAGATCGGAGACC 60.135 57.143 0.00 0.00 42.51 3.85
50 51 1.740718 GCACCAGGAAAGATCGGAGAC 60.741 57.143 0.00 0.00 42.51 3.36
51 52 0.537188 GCACCAGGAAAGATCGGAGA 59.463 55.000 0.00 0.00 45.75 3.71
52 53 0.250234 TGCACCAGGAAAGATCGGAG 59.750 55.000 0.00 0.00 0.00 4.63
53 54 0.250234 CTGCACCAGGAAAGATCGGA 59.750 55.000 0.00 0.00 0.00 4.55
54 55 0.036010 ACTGCACCAGGAAAGATCGG 60.036 55.000 0.00 0.00 35.51 4.18
55 56 1.081892 CACTGCACCAGGAAAGATCG 58.918 55.000 0.00 0.00 35.51 3.69
56 57 1.457346 CCACTGCACCAGGAAAGATC 58.543 55.000 0.00 0.00 35.51 2.75
57 58 0.610232 GCCACTGCACCAGGAAAGAT 60.610 55.000 0.00 0.00 35.51 2.40
58 59 1.228245 GCCACTGCACCAGGAAAGA 60.228 57.895 0.00 0.00 35.51 2.52
59 60 1.529010 TGCCACTGCACCAGGAAAG 60.529 57.895 0.00 0.00 44.23 2.62
60 61 2.600164 TGCCACTGCACCAGGAAA 59.400 55.556 0.00 0.00 44.23 3.13
88 89 6.570692 TGATTTTCCTACTTGTCGATAGGAC 58.429 40.000 11.27 2.63 45.37 3.85
89 90 6.785337 TGATTTTCCTACTTGTCGATAGGA 57.215 37.500 8.19 8.19 44.29 2.94
90 91 7.010552 CACTTGATTTTCCTACTTGTCGATAGG 59.989 40.741 3.77 3.77 39.58 2.57
91 92 7.010552 CCACTTGATTTTCCTACTTGTCGATAG 59.989 40.741 0.00 0.00 0.00 2.08
92 93 6.816640 CCACTTGATTTTCCTACTTGTCGATA 59.183 38.462 0.00 0.00 0.00 2.92
93 94 5.643777 CCACTTGATTTTCCTACTTGTCGAT 59.356 40.000 0.00 0.00 0.00 3.59
94 95 4.994852 CCACTTGATTTTCCTACTTGTCGA 59.005 41.667 0.00 0.00 0.00 4.20
95 96 4.378459 GCCACTTGATTTTCCTACTTGTCG 60.378 45.833 0.00 0.00 0.00 4.35
96 97 4.518970 TGCCACTTGATTTTCCTACTTGTC 59.481 41.667 0.00 0.00 0.00 3.18
97 98 4.469657 TGCCACTTGATTTTCCTACTTGT 58.530 39.130 0.00 0.00 0.00 3.16
98 99 5.452078 TTGCCACTTGATTTTCCTACTTG 57.548 39.130 0.00 0.00 0.00 3.16
99 100 6.041979 ACAATTGCCACTTGATTTTCCTACTT 59.958 34.615 5.05 0.00 0.00 2.24
100 101 5.539955 ACAATTGCCACTTGATTTTCCTACT 59.460 36.000 5.05 0.00 0.00 2.57
101 102 5.783111 ACAATTGCCACTTGATTTTCCTAC 58.217 37.500 5.05 0.00 0.00 3.18
102 103 6.418057 AACAATTGCCACTTGATTTTCCTA 57.582 33.333 5.05 0.00 0.00 2.94
103 104 4.961438 ACAATTGCCACTTGATTTTCCT 57.039 36.364 5.05 0.00 0.00 3.36
104 105 5.296531 ACAAACAATTGCCACTTGATTTTCC 59.703 36.000 5.05 0.00 40.34 3.13
105 106 6.362210 ACAAACAATTGCCACTTGATTTTC 57.638 33.333 5.05 0.00 40.34 2.29
106 107 6.756299 AACAAACAATTGCCACTTGATTTT 57.244 29.167 5.05 0.00 40.34 1.82
107 108 6.756299 AAACAAACAATTGCCACTTGATTT 57.244 29.167 5.05 5.52 40.34 2.17
108 109 7.520292 GCATAAACAAACAATTGCCACTTGATT 60.520 33.333 5.05 7.84 40.34 2.57
109 110 6.073112 GCATAAACAAACAATTGCCACTTGAT 60.073 34.615 5.05 0.00 40.34 2.57
110 111 5.236047 GCATAAACAAACAATTGCCACTTGA 59.764 36.000 5.05 0.00 40.34 3.02
111 112 5.007430 TGCATAAACAAACAATTGCCACTTG 59.993 36.000 5.05 6.95 40.34 3.16
112 113 5.121811 TGCATAAACAAACAATTGCCACTT 58.878 33.333 5.05 0.00 40.34 3.16
113 114 4.701765 TGCATAAACAAACAATTGCCACT 58.298 34.783 5.05 0.00 40.34 4.00
114 115 5.007528 ACTTGCATAAACAAACAATTGCCAC 59.992 36.000 5.05 0.00 40.34 5.01
115 116 5.121811 ACTTGCATAAACAAACAATTGCCA 58.878 33.333 5.05 0.00 40.34 4.92
146 147 5.796935 CCGATATTCAAGTGCTTTGAGTTTG 59.203 40.000 5.24 0.00 46.01 2.93
175 178 7.611855 ACTTCCCTTTCACTCAATAAATACTGG 59.388 37.037 0.00 0.00 0.00 4.00
218 222 1.065709 GGAAAGGGCGTGGAGATGTTA 60.066 52.381 0.00 0.00 0.00 2.41
224 228 0.035056 AAGATGGAAAGGGCGTGGAG 60.035 55.000 0.00 0.00 0.00 3.86
267 271 2.888414 GGAAGGAAACATTTTGGTCCGA 59.112 45.455 0.00 0.00 32.74 4.55
303 308 6.808008 ACATGGTGTCTAATTCTTCAGTTG 57.192 37.500 0.00 0.00 0.00 3.16
311 316 4.876107 CCCAGTGTACATGGTGTCTAATTC 59.124 45.833 17.62 0.00 35.96 2.17
325 334 3.056035 CCTCTTAAGACCACCCAGTGTAC 60.056 52.174 0.00 0.00 0.00 2.90
334 343 8.561738 TGTTCATTTAATCCTCTTAAGACCAC 57.438 34.615 0.00 0.00 0.00 4.16
403 412 7.130269 ACACGCAACTGTTTTTCTTAGATAAC 58.870 34.615 0.00 2.16 0.00 1.89
405 414 6.854496 ACACGCAACTGTTTTTCTTAGATA 57.146 33.333 0.00 0.00 0.00 1.98
412 421 3.685836 ACCTACACGCAACTGTTTTTC 57.314 42.857 0.00 0.00 0.00 2.29
414 423 5.354792 TCTTTTACCTACACGCAACTGTTTT 59.645 36.000 0.00 0.00 0.00 2.43
534 553 7.057264 AGAGCTGTATATTGACTGACTGACTA 58.943 38.462 0.00 0.00 0.00 2.59
561 580 5.669447 ACATGGAGGTAAGATCAAGGAATCT 59.331 40.000 0.00 0.00 37.61 2.40
577 596 0.549950 AGGATGGAAGCACATGGAGG 59.450 55.000 0.00 0.00 0.00 4.30
584 603 1.138661 CTGGAGAGAGGATGGAAGCAC 59.861 57.143 0.00 0.00 0.00 4.40
631 1210 2.375766 GCAGACCTCTTCACGCGTG 61.376 63.158 32.76 32.76 0.00 5.34
632 1211 2.049063 GCAGACCTCTTCACGCGT 60.049 61.111 5.58 5.58 0.00 6.01
648 1227 1.785041 TTGGTGAAAGAGCAGCGTGC 61.785 55.000 2.28 2.28 45.46 5.34
649 1228 0.877071 ATTGGTGAAAGAGCAGCGTG 59.123 50.000 0.00 0.00 39.04 5.34
687 1295 1.339151 GGGATTCACCTCAAGAACGCT 60.339 52.381 0.00 0.00 38.98 5.07
693 1301 3.107601 TGAGTAGGGGATTCACCTCAAG 58.892 50.000 11.73 0.00 42.78 3.02
721 1329 7.795047 AGAAGATCAAAACAAACCCAAGAATT 58.205 30.769 0.00 0.00 0.00 2.17
722 1330 7.365497 AGAAGATCAAAACAAACCCAAGAAT 57.635 32.000 0.00 0.00 0.00 2.40
723 1331 6.790232 AGAAGATCAAAACAAACCCAAGAA 57.210 33.333 0.00 0.00 0.00 2.52
724 1332 6.790232 AAGAAGATCAAAACAAACCCAAGA 57.210 33.333 0.00 0.00 0.00 3.02
740 1348 7.394641 GGGGTTGAGTAAAGAATCAAAGAAGAT 59.605 37.037 0.00 0.00 37.19 2.40
753 1361 3.502123 TTCCAGTGGGGTTGAGTAAAG 57.498 47.619 9.92 0.00 38.11 1.85
756 1364 4.463050 AAAATTCCAGTGGGGTTGAGTA 57.537 40.909 9.92 0.00 38.11 2.59
758 1366 5.245977 ACATAAAAATTCCAGTGGGGTTGAG 59.754 40.000 9.92 0.00 38.11 3.02
759 1367 5.151454 ACATAAAAATTCCAGTGGGGTTGA 58.849 37.500 9.92 0.00 38.11 3.18
760 1368 5.482163 ACATAAAAATTCCAGTGGGGTTG 57.518 39.130 9.92 0.00 38.11 3.77
880 1573 4.534103 AGGATAAGAAACTCCAGCAGAAGT 59.466 41.667 0.00 0.00 33.75 3.01
890 1588 3.738590 GCAGGTCGGAGGATAAGAAACTC 60.739 52.174 0.00 0.00 0.00 3.01
899 1601 0.755686 GATCTTGCAGGTCGGAGGAT 59.244 55.000 0.00 0.00 34.29 3.24
1004 1706 2.654877 GGTCGTTCTCGAGGCCAA 59.345 61.111 13.56 0.00 46.96 4.52
1199 1901 1.648467 GCGGGAAGTGGACTCATTGC 61.648 60.000 0.00 0.00 0.00 3.56
1202 1904 0.107508 CATGCGGGAAGTGGACTCAT 60.108 55.000 0.00 0.00 0.00 2.90
1203 1905 1.296392 CATGCGGGAAGTGGACTCA 59.704 57.895 0.00 0.00 0.00 3.41
1220 1922 2.353307 CGTGTGATGTAGCCAAGTACCA 60.353 50.000 0.00 0.00 0.00 3.25
1257 1959 3.634448 TCCTGCTCATTTCAAAACGGAAA 59.366 39.130 0.00 0.00 40.72 3.13
1334 2036 3.685139 TGACAGAATTCTCCAGGTCAC 57.315 47.619 17.78 0.65 30.99 3.67
1413 2115 7.868792 ATCATCATCTCTCCCAAAGATCTTA 57.131 36.000 8.75 0.00 31.05 2.10
1467 2169 2.429767 CCTCCGCTGATCCTGCTGA 61.430 63.158 6.30 4.55 0.00 4.26
1524 2226 6.096282 AGACCATCTTAGCAAGAGTAGTCTTC 59.904 42.308 9.98 5.88 41.40 2.87
1530 2232 9.588096 TCATTATAGACCATCTTAGCAAGAGTA 57.412 33.333 5.15 0.00 41.61 2.59
1623 2325 5.643664 TCAATGATGGATTTCAAAAGAGCG 58.356 37.500 0.00 0.00 0.00 5.03
1713 2416 4.551702 AAACCTATTTTGGCCAATGACC 57.448 40.909 21.26 0.00 0.00 4.02
1728 2431 3.603158 TCAAGCACGAGCATAAACCTA 57.397 42.857 7.77 0.00 45.49 3.08
1803 2506 5.192522 ACTTCCTGATCCACCAATAGAACAT 59.807 40.000 0.00 0.00 0.00 2.71
1819 2522 4.763279 TGTGACGAGTATTACACTTCCTGA 59.237 41.667 0.00 0.00 37.72 3.86
1834 2537 0.318699 TGGCTTCGAGTTGTGACGAG 60.319 55.000 0.00 0.00 39.59 4.18
1897 2600 7.601130 CCATGAATCTTGTTCATTCAAACATGT 59.399 33.333 0.00 0.00 42.23 3.21
1903 2606 6.494491 ACTTCCCATGAATCTTGTTCATTCAA 59.506 34.615 0.00 0.00 42.23 2.69
1907 2610 5.327732 ACACTTCCCATGAATCTTGTTCAT 58.672 37.500 0.00 0.00 39.53 2.57
1958 2662 3.885901 GGTCAATTCTATTTCCTCCTGCC 59.114 47.826 0.00 0.00 0.00 4.85
1960 2664 4.578105 GCTGGTCAATTCTATTTCCTCCTG 59.422 45.833 0.00 0.00 0.00 3.86
1968 2678 4.025360 TGCCAATGCTGGTCAATTCTATT 58.975 39.130 0.00 0.00 45.53 1.73
1970 2680 3.018856 CTGCCAATGCTGGTCAATTCTA 58.981 45.455 0.00 0.00 45.53 2.10
1974 2687 1.754803 CATCTGCCAATGCTGGTCAAT 59.245 47.619 0.00 0.00 45.53 2.57
2033 2749 0.465460 TAGCAATCCGCCCATTGTCC 60.465 55.000 4.62 0.00 44.04 4.02
2187 2906 4.925646 GGGAAAACTGCTAAGAATGCAAAG 59.074 41.667 0.00 0.00 40.13 2.77
2316 3036 3.891366 ACCTCCAAACCAACTCATCAAAG 59.109 43.478 0.00 0.00 0.00 2.77
2372 3101 6.877322 ACAGTTAACAGTCACATAACCATACC 59.123 38.462 8.61 0.00 31.43 2.73
2375 3104 8.372459 TCTTACAGTTAACAGTCACATAACCAT 58.628 33.333 6.95 0.00 31.43 3.55
2457 3199 4.375272 CTTTCTGCTGAGTCAGTTCTTCA 58.625 43.478 21.06 9.29 35.63 3.02
2578 3323 7.979786 AATCCTTGTAGTATTCTGAAGGAGA 57.020 36.000 15.41 1.00 42.04 3.71
2591 3339 7.553044 GGAGCAACACTTTATAATCCTTGTAGT 59.447 37.037 0.00 0.00 0.00 2.73
2592 3340 7.552687 TGGAGCAACACTTTATAATCCTTGTAG 59.447 37.037 0.00 0.00 0.00 2.74
2616 3400 4.798924 GCTCTTAGTGATGCTGATACCTGG 60.799 50.000 0.00 0.00 0.00 4.45
2670 3455 2.007360 TTTGCATTTATGGCCTTGCG 57.993 45.000 3.32 0.00 37.92 4.85
2691 3479 5.903810 AGACAGGTCAAGATACCGTAAATC 58.096 41.667 1.84 0.00 44.77 2.17
2751 3541 7.178451 AGCCTTAAGGTTTGCAAGTTATACAAT 59.822 33.333 22.55 0.00 37.57 2.71
2769 3559 2.224066 CCGGTAGTCCATGAGCCTTAAG 60.224 54.545 0.00 0.00 0.00 1.85
2784 3574 1.448540 CTGTTGCAGCTCCCGGTAG 60.449 63.158 0.00 0.00 0.00 3.18
2803 3593 3.057969 TCTTGCCATGTGTTCTGGTAG 57.942 47.619 0.00 0.00 36.10 3.18
2812 3602 3.192844 AGCTTTCTCAATCTTGCCATGTG 59.807 43.478 0.00 0.00 0.00 3.21
2856 3646 9.737427 CGAGACATACTTTTGAGACTATAACAT 57.263 33.333 0.00 0.00 0.00 2.71
2882 3672 6.060136 AGGTTGTTTAGTAGACCAAAGTTCC 58.940 40.000 0.00 0.00 34.60 3.62
3002 3792 5.123027 CCACTCTTTATCTTGCTCAAGTTCC 59.877 44.000 9.20 0.00 39.38 3.62
3070 3860 3.054728 TCCCAAGAGAACAACAACTCACA 60.055 43.478 0.00 0.00 35.83 3.58
3096 3890 6.916360 TCCTTATGCCCATCATTTATTTCC 57.084 37.500 0.00 0.00 36.63 3.13
3103 3897 4.016851 AGCCATATCCTTATGCCCATCATT 60.017 41.667 0.00 0.00 36.63 2.57
3126 3935 2.054799 AGCACCTCTTCCACCTTACAA 58.945 47.619 0.00 0.00 0.00 2.41
3141 3950 2.160205 GGTTCTAAACCCTGAAGCACC 58.840 52.381 0.00 0.00 46.12 5.01
3236 4046 7.195839 AGTTCTCTCAAGCAGTTAAACATTC 57.804 36.000 0.00 0.00 0.00 2.67
3275 4085 5.900123 ACAGGTATACTCTTGCATTCTAGGT 59.100 40.000 2.25 0.00 0.00 3.08
3278 4088 9.809395 ATACTACAGGTATACTCTTGCATTCTA 57.191 33.333 2.25 0.00 39.15 2.10
3280 4090 7.815068 CCATACTACAGGTATACTCTTGCATTC 59.185 40.741 2.25 0.00 38.92 2.67
3313 4123 7.817440 TGTAAGGACAATATCTCTAGAGAGGT 58.183 38.462 25.86 19.84 36.32 3.85
3314 4124 8.160765 TCTGTAAGGACAATATCTCTAGAGAGG 58.839 40.741 25.86 17.19 37.69 3.69
3384 4194 1.650912 GGTAATGCATGCTCCAGCG 59.349 57.895 20.33 0.00 45.83 5.18
3392 4205 4.526970 ACTTTGTAGAGGGGTAATGCATG 58.473 43.478 0.00 0.00 0.00 4.06
3443 4256 0.835941 CTCCAGGCTTGGTAGCTCAT 59.164 55.000 15.41 0.00 46.90 2.90
3520 4333 7.118101 GCATTTTTGGATCATTAGCACTTCAAA 59.882 33.333 0.00 0.00 0.00 2.69
3533 4346 1.278699 GCTTGGGGCATTTTTGGATCA 59.721 47.619 0.00 0.00 41.35 2.92
3538 4351 0.876399 GCAAGCTTGGGGCATTTTTG 59.124 50.000 27.10 0.00 44.79 2.44
3543 4356 0.251742 TACTTGCAAGCTTGGGGCAT 60.252 50.000 27.10 8.37 44.79 4.40
3583 4396 6.588756 TGTACTCCAATTATTGTCAACTCGTC 59.411 38.462 4.15 0.00 0.00 4.20
3584 4397 6.367969 GTGTACTCCAATTATTGTCAACTCGT 59.632 38.462 4.15 0.00 0.00 4.18
3652 4466 1.611673 CCTGACGAGAAATGGCCAAGT 60.612 52.381 10.96 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.