Multiple sequence alignment - TraesCS3D01G470700

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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 TraesCS3D01G470700 chr3D 100.000 5986 0 0 1 5986 572738730 572744715 0.000000e+00 11055.0
1 TraesCS3D01G470700 chr3D 86.833 1200 110 25 1108 2267 419551386 419550195 0.000000e+00 1297.0
2 TraesCS3D01G470700 chr3D 84.842 884 92 26 4682 5542 572762903 572763767 0.000000e+00 852.0
3 TraesCS3D01G470700 chr3D 84.084 666 85 11 5328 5986 572763907 572764558 1.830000e-174 623.0
4 TraesCS3D01G470700 chr3D 87.324 426 40 14 2968 3384 572766786 572767206 5.430000e-130 475.0
5 TraesCS3D01G470700 chr3D 81.818 330 35 12 3862 4185 572794317 572794627 2.770000e-63 254.0
6 TraesCS3D01G470700 chr3D 82.594 293 36 7 3487 3778 572793529 572793807 1.670000e-60 244.0
7 TraesCS3D01G470700 chr3D 97.619 126 0 1 4181 4306 572742866 572742988 4.700000e-51 213.0
8 TraesCS3D01G470700 chr3D 97.619 126 0 1 4137 4259 572742910 572743035 4.700000e-51 213.0
9 TraesCS3D01G470700 chr3D 89.677 155 11 2 4886 5036 572796766 572796919 6.120000e-45 193.0
10 TraesCS3D01G470700 chr3D 96.203 79 0 1 4228 4306 572742866 572742941 6.300000e-25 126.0
11 TraesCS3D01G470700 chr3D 96.203 79 0 1 4137 4212 572742957 572743035 6.300000e-25 126.0
12 TraesCS3D01G470700 chr3D 98.113 53 1 0 4625 4677 3008655 3008603 6.390000e-15 93.5
13 TraesCS3D01G470700 chr3D 85.714 77 8 3 4602 4677 20348870 20348796 1.790000e-10 78.7
14 TraesCS3D01G470700 chr3D 93.182 44 3 0 4275 4318 572742866 572742909 1.390000e-06 65.8
15 TraesCS3D01G470700 chr3D 93.182 44 3 0 4137 4180 572743004 572743047 1.390000e-06 65.8
16 TraesCS3D01G470700 chr3A 91.156 3788 163 62 481 4176 705601254 705597547 0.000000e+00 4981.0
17 TraesCS3D01G470700 chr3A 95.116 819 30 5 4678 5495 705597124 705596315 0.000000e+00 1282.0
18 TraesCS3D01G470700 chr3A 83.828 606 66 13 5334 5932 705553898 705553318 1.130000e-151 547.0
19 TraesCS3D01G470700 chr3A 88.993 427 37 6 5015 5438 705343322 705342903 2.470000e-143 520.0
20 TraesCS3D01G470700 chr3A 87.603 363 19 7 4870 5229 705577477 705577138 1.210000e-106 398.0
21 TraesCS3D01G470700 chr3A 82.900 462 56 11 5334 5790 705596133 705595690 1.560000e-105 394.0
22 TraesCS3D01G470700 chr3A 81.518 514 42 20 445 931 705642516 705642029 2.040000e-99 374.0
23 TraesCS3D01G470700 chr3A 88.699 292 22 7 5255 5542 705554332 705554048 4.440000e-91 346.0
24 TraesCS3D01G470700 chr3A 81.953 338 41 12 3726 4059 705582477 705582156 9.890000e-68 268.0
25 TraesCS3D01G470700 chr3A 94.444 144 7 1 4275 4417 705597587 705597444 2.810000e-53 220.0
26 TraesCS3D01G470700 chr3A 84.831 178 22 4 4009 4185 705582140 705581967 2.220000e-39 174.0
27 TraesCS3D01G470700 chr3A 98.077 52 1 0 4626 4677 308700552 308700603 2.300000e-14 91.6
28 TraesCS3D01G470700 chr3A 97.561 41 1 0 5946 5986 705593695 705593655 2.990000e-08 71.3
29 TraesCS3D01G470700 chr3B 89.799 2137 122 35 716 2784 760713888 760711780 0.000000e+00 2651.0
30 TraesCS3D01G470700 chr3B 94.876 1171 41 11 4827 5986 760603941 760602779 0.000000e+00 1812.0
31 TraesCS3D01G470700 chr3B 97.183 994 24 3 3227 4217 760711061 760710069 0.000000e+00 1677.0
32 TraesCS3D01G470700 chr3B 94.781 594 23 5 4794 5384 760709606 760709018 0.000000e+00 918.0
33 TraesCS3D01G470700 chr3B 93.128 553 20 8 4228 4767 760710151 760709604 0.000000e+00 795.0
34 TraesCS3D01G470700 chr3B 82.969 640 68 20 2593 3206 760576488 760575864 1.900000e-149 540.0
35 TraesCS3D01G470700 chr3B 84.565 460 61 8 3726 4179 760582424 760581969 1.180000e-121 448.0
36 TraesCS3D01G470700 chr3B 82.960 446 69 6 1 444 760716551 760716111 4.350000e-106 396.0
37 TraesCS3D01G470700 chr3B 81.285 529 57 25 445 960 760778356 760777857 2.020000e-104 390.0
38 TraesCS3D01G470700 chr3B 90.146 274 26 1 3199 3471 760575815 760575542 7.380000e-94 355.0
39 TraesCS3D01G470700 chr3B 86.957 299 33 5 3892 4185 760604676 760604379 1.240000e-86 331.0
40 TraesCS3D01G470700 chr3B 79.213 534 66 26 445 960 760784352 760783846 4.470000e-86 329.0
41 TraesCS3D01G470700 chr3B 80.425 424 72 7 1 419 760719104 760718687 4.500000e-81 313.0
42 TraesCS3D01G470700 chr3B 88.263 213 23 2 3626 3837 760604887 760604676 2.770000e-63 254.0
43 TraesCS3D01G470700 chr3B 92.857 98 6 1 4870 4967 760575530 760575434 2.250000e-29 141.0
44 TraesCS3D01G470700 chr3B 84.892 139 8 6 445 581 760714129 760714002 1.750000e-25 128.0
45 TraesCS3D01G470700 chr3B 91.860 86 2 2 4181 4264 760710151 760710069 1.360000e-21 115.0
46 TraesCS3D01G470700 chr3B 95.455 44 2 0 4275 4318 760710151 760710108 2.990000e-08 71.3
47 TraesCS3D01G470700 chr3B 93.478 46 3 0 2594 2639 760595628 760595583 1.080000e-07 69.4
48 TraesCS3D01G470700 chr2D 86.906 1199 111 28 1108 2267 574801492 574800301 0.000000e+00 1303.0
49 TraesCS3D01G470700 chr2D 86.822 1199 113 28 1108 2267 488418444 488417252 0.000000e+00 1297.0
50 TraesCS3D01G470700 chr5D 86.572 1199 117 27 1108 2267 438277321 438276128 0.000000e+00 1282.0
51 TraesCS3D01G470700 chr4D 86.322 1199 117 30 1108 2267 487242247 487243437 0.000000e+00 1262.0
52 TraesCS3D01G470700 chr1A 93.125 640 34 4 1638 2267 242070089 242069450 0.000000e+00 929.0
53 TraesCS3D01G470700 chr1A 91.549 639 43 4 1638 2267 240953372 240952736 0.000000e+00 870.0
54 TraesCS3D01G470700 chr2A 91.930 632 47 4 1638 2267 22436146 22436775 0.000000e+00 881.0
55 TraesCS3D01G470700 chr7B 84.000 775 99 19 1278 2032 64605781 64605012 0.000000e+00 721.0
56 TraesCS3D01G470700 chrUn 80.776 593 69 24 4853 5433 132017539 132018098 7.170000e-114 422.0
57 TraesCS3D01G470700 chrUn 94.915 59 3 0 4619 4677 62663393 62663451 6.390000e-15 93.5
58 TraesCS3D01G470700 chr5B 96.667 60 1 1 4618 4677 367775235 367775293 1.370000e-16 99.0
59 TraesCS3D01G470700 chr6D 100.000 51 0 0 4627 4677 367314859 367314809 1.780000e-15 95.3
60 TraesCS3D01G470700 chr4B 98.113 53 1 0 4625 4677 63895210 63895262 6.390000e-15 93.5
61 TraesCS3D01G470700 chr4B 98.113 53 1 0 4625 4677 195462563 195462615 6.390000e-15 93.5


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 TraesCS3D01G470700 chr3D 572738730 572744715 5985 False 1694.942857 11055 96.286857 1 5986 7 chr3D.!!$F1 5985
1 TraesCS3D01G470700 chr3D 419550195 419551386 1191 True 1297.000000 1297 86.833000 1108 2267 1 chr3D.!!$R3 1159
2 TraesCS3D01G470700 chr3D 572762903 572767206 4303 False 650.000000 852 85.416667 2968 5986 3 chr3D.!!$F2 3018
3 TraesCS3D01G470700 chr3D 572793529 572796919 3390 False 230.333333 254 84.696333 3487 5036 3 chr3D.!!$F3 1549
4 TraesCS3D01G470700 chr3A 705593655 705601254 7599 True 1389.660000 4981 92.235400 481 5986 5 chr3A.!!$R6 5505
5 TraesCS3D01G470700 chr3A 705553318 705554332 1014 True 446.500000 547 86.263500 5255 5932 2 chr3A.!!$R4 677
6 TraesCS3D01G470700 chr3A 705581967 705582477 510 True 221.000000 268 83.392000 3726 4185 2 chr3A.!!$R5 459
7 TraesCS3D01G470700 chr3B 760602779 760604887 2108 True 799.000000 1812 90.032000 3626 5986 3 chr3B.!!$R6 2360
8 TraesCS3D01G470700 chr3B 760709018 760719104 10086 True 784.922222 2651 90.053667 1 5384 9 chr3B.!!$R7 5383
9 TraesCS3D01G470700 chr3B 760575434 760576488 1054 True 345.333333 540 88.657333 2593 4967 3 chr3B.!!$R5 2374
10 TraesCS3D01G470700 chr3B 760783846 760784352 506 True 329.000000 329 79.213000 445 960 1 chr3B.!!$R4 515
11 TraesCS3D01G470700 chr2D 574800301 574801492 1191 True 1303.000000 1303 86.906000 1108 2267 1 chr2D.!!$R2 1159
12 TraesCS3D01G470700 chr2D 488417252 488418444 1192 True 1297.000000 1297 86.822000 1108 2267 1 chr2D.!!$R1 1159
13 TraesCS3D01G470700 chr5D 438276128 438277321 1193 True 1282.000000 1282 86.572000 1108 2267 1 chr5D.!!$R1 1159
14 TraesCS3D01G470700 chr4D 487242247 487243437 1190 False 1262.000000 1262 86.322000 1108 2267 1 chr4D.!!$F1 1159
15 TraesCS3D01G470700 chr1A 242069450 242070089 639 True 929.000000 929 93.125000 1638 2267 1 chr1A.!!$R2 629
16 TraesCS3D01G470700 chr1A 240952736 240953372 636 True 870.000000 870 91.549000 1638 2267 1 chr1A.!!$R1 629
17 TraesCS3D01G470700 chr2A 22436146 22436775 629 False 881.000000 881 91.930000 1638 2267 1 chr2A.!!$F1 629
18 TraesCS3D01G470700 chr7B 64605012 64605781 769 True 721.000000 721 84.000000 1278 2032 1 chr7B.!!$R1 754
19 TraesCS3D01G470700 chrUn 132017539 132018098 559 False 422.000000 422 80.776000 4853 5433 1 chrUn.!!$F2 580

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
373 2928 0.038343 CTGGGATTTTTGGCACGGTG 60.038 55.000 3.15 3.15 0.00 4.94 F
396 2951 0.529337 AGATGGCGCGAGTGATCAAG 60.529 55.000 12.10 0.00 0.00 3.02 F
641 5186 0.541063 TCCGACTGTACCAGCTGGAA 60.541 55.000 39.19 21.56 35.91 3.53 F
1970 6614 0.618458 TGGCACTATTGGAGGGTCAC 59.382 55.000 0.00 0.00 38.66 3.67 F
3463 8660 1.609555 GAACCACACCGTATTTGGCAA 59.390 47.619 0.00 0.00 33.25 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1381 5978 0.310854 CAAAAACTCCACCGACAGCC 59.689 55.000 0.00 0.0 0.00 4.85 R
1895 6539 1.003580 TCTTGCTTTAGCCCACTGGAG 59.996 52.381 0.00 0.0 41.18 3.86 R
2400 7058 1.580942 CCGCACAACCAAGGACATG 59.419 57.895 0.00 0.0 0.00 3.21 R
3745 8948 0.901827 TGAAGCGGCAGGATGAGTAA 59.098 50.000 1.45 0.0 39.69 2.24 R
5097 12570 0.820891 CTGCCTTGTGCTTCACCACT 60.821 55.000 0.00 0.0 42.00 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.071892 TCCTTGGTGTAAACAAGATCGGT 59.928 43.478 6.61 0.00 46.27 4.69
62 63 2.934553 GGTCCTTATAAACGGCACACTC 59.065 50.000 0.00 0.00 0.00 3.51
65 66 3.262405 TCCTTATAAACGGCACACTCCTT 59.738 43.478 0.00 0.00 0.00 3.36
106 107 4.141711 GCCTCTGACCATGTTACCAAGATA 60.142 45.833 0.00 0.00 0.00 1.98
107 108 5.605534 CCTCTGACCATGTTACCAAGATAG 58.394 45.833 0.00 0.00 0.00 2.08
108 109 5.453903 CCTCTGACCATGTTACCAAGATAGG 60.454 48.000 0.00 0.00 0.00 2.57
109 110 5.030147 TCTGACCATGTTACCAAGATAGGT 58.970 41.667 0.00 0.00 45.72 3.08
118 119 9.314321 CATGTTACCAAGATAGGTAGTACAAAG 57.686 37.037 2.06 0.00 44.48 2.77
132 133 6.748658 GGTAGTACAAAGAACCAAACAAACAC 59.251 38.462 2.06 0.00 32.04 3.32
135 136 2.287393 AAGAACCAAACAAACACGGC 57.713 45.000 0.00 0.00 0.00 5.68
165 2719 4.154347 CCCCGAGCCAGAGAGCAC 62.154 72.222 0.00 0.00 34.23 4.40
185 2740 4.629200 GCACTGAAAACAAAACAATGTGGA 59.371 37.500 0.00 0.00 32.81 4.02
187 2742 6.183360 GCACTGAAAACAAAACAATGTGGATT 60.183 34.615 0.00 0.00 32.81 3.01
190 2745 7.224557 ACTGAAAACAAAACAATGTGGATTAGC 59.775 33.333 0.00 0.00 32.81 3.09
203 2758 4.541250 TGGATTAGCCAATCAATCCCTT 57.459 40.909 7.19 0.00 46.51 3.95
254 2809 5.698741 ACACATGATCTCCAGAAACCATA 57.301 39.130 0.00 0.00 0.00 2.74
257 2812 3.819564 TGATCTCCAGAAACCATACGG 57.180 47.619 0.00 0.00 38.77 4.02
259 2814 1.200519 TCTCCAGAAACCATACGGGG 58.799 55.000 0.00 0.00 42.91 5.73
264 2819 2.218603 CAGAAACCATACGGGGCATAC 58.781 52.381 0.00 0.00 42.91 2.39
268 2823 0.472471 ACCATACGGGGCATACCAAG 59.528 55.000 0.00 0.00 42.91 3.61
270 2825 1.270839 CCATACGGGGCATACCAAGAG 60.271 57.143 0.00 0.00 42.91 2.85
271 2826 1.056660 ATACGGGGCATACCAAGAGG 58.943 55.000 0.00 0.00 42.91 3.69
276 2831 2.379005 GGGGCATACCAAGAGGAAAAG 58.621 52.381 0.00 0.00 42.91 2.27
279 2834 1.751351 GCATACCAAGAGGAAAAGGGC 59.249 52.381 0.00 0.00 38.69 5.19
281 2836 0.702316 TACCAAGAGGAAAAGGGCCC 59.298 55.000 16.46 16.46 38.69 5.80
297 2852 1.035139 GCCCGTATTCGTTAGGAGGA 58.965 55.000 0.00 0.00 35.01 3.71
304 2859 4.196965 CGTTAGGAGGAAACGGGC 57.803 61.111 0.63 0.00 44.49 6.13
320 2875 1.671742 GGCACCAGAAGAGGTCGAA 59.328 57.895 0.00 0.00 40.77 3.71
321 2876 0.390472 GGCACCAGAAGAGGTCGAAG 60.390 60.000 0.00 0.00 40.77 3.79
323 2878 0.390472 CACCAGAAGAGGTCGAAGCC 60.390 60.000 0.00 0.00 40.77 4.35
325 2880 1.153745 CAGAAGAGGTCGAAGCCCG 60.154 63.158 0.00 0.00 40.25 6.13
326 2881 1.304217 AGAAGAGGTCGAAGCCCGA 60.304 57.895 0.00 0.00 46.35 5.14
338 2893 0.686769 AAGCCCGAAGAGTATCCCGT 60.687 55.000 0.00 0.00 33.66 5.28
340 2895 0.597072 GCCCGAAGAGTATCCCGTAG 59.403 60.000 0.00 0.00 33.66 3.51
354 2909 1.299468 CGTAGCGGGAGAGATGCAC 60.299 63.158 0.00 0.00 0.00 4.57
355 2910 1.729470 CGTAGCGGGAGAGATGCACT 61.729 60.000 0.00 0.00 0.00 4.40
356 2911 0.249238 GTAGCGGGAGAGATGCACTG 60.249 60.000 0.00 0.00 0.00 3.66
357 2912 1.395045 TAGCGGGAGAGATGCACTGG 61.395 60.000 0.00 0.00 0.00 4.00
358 2913 2.503061 CGGGAGAGATGCACTGGG 59.497 66.667 0.00 0.00 0.00 4.45
362 2917 1.213926 GGGAGAGATGCACTGGGATTT 59.786 52.381 0.00 0.00 0.00 2.17
363 2918 2.357569 GGGAGAGATGCACTGGGATTTT 60.358 50.000 0.00 0.00 0.00 1.82
372 2927 0.469144 ACTGGGATTTTTGGCACGGT 60.469 50.000 0.00 0.00 0.00 4.83
373 2928 0.038343 CTGGGATTTTTGGCACGGTG 60.038 55.000 3.15 3.15 0.00 4.94
375 2930 1.374125 GGATTTTTGGCACGGTGGC 60.374 57.895 25.93 25.93 44.03 5.01
382 2937 3.443045 GGCACGGTGGCAAGATGG 61.443 66.667 27.39 0.00 43.14 3.51
390 2945 3.869272 GGCAAGATGGCGCGAGTG 61.869 66.667 12.10 0.00 31.79 3.51
391 2946 2.815211 GCAAGATGGCGCGAGTGA 60.815 61.111 12.10 0.00 0.00 3.41
396 2951 0.529337 AGATGGCGCGAGTGATCAAG 60.529 55.000 12.10 0.00 0.00 3.02
398 2953 3.567797 GGCGCGAGTGATCAAGCC 61.568 66.667 12.10 4.33 37.61 4.35
400 2955 2.507102 CGCGAGTGATCAAGCCGT 60.507 61.111 0.00 0.00 0.00 5.68
403 2958 1.571919 GCGAGTGATCAAGCCGTTAT 58.428 50.000 0.00 0.00 0.00 1.89
418 2973 1.799917 CGTTATTCGCCGGCTAGAACA 60.800 52.381 26.68 8.04 0.00 3.18
420 2975 2.218953 TATTCGCCGGCTAGAACAAG 57.781 50.000 26.68 6.06 0.00 3.16
422 2977 2.125512 CGCCGGCTAGAACAAGCT 60.126 61.111 26.68 0.00 42.37 3.74
426 2981 1.639298 CCGGCTAGAACAAGCTGCAC 61.639 60.000 1.02 0.00 45.78 4.57
427 2982 0.671781 CGGCTAGAACAAGCTGCACT 60.672 55.000 1.02 0.00 41.71 4.40
463 3018 3.336138 AAAAACGGAACCAGCCAAAAA 57.664 38.095 0.00 0.00 0.00 1.94
487 3253 2.594592 GCGACAAAGCCCACCACT 60.595 61.111 0.00 0.00 0.00 4.00
536 5065 1.960689 ACACAAAATTAGCCCGCACTT 59.039 42.857 0.00 0.00 0.00 3.16
625 5170 1.332997 CTAACCCAGCGTACTACTCCG 59.667 57.143 0.00 0.00 0.00 4.63
641 5186 0.541063 TCCGACTGTACCAGCTGGAA 60.541 55.000 39.19 21.56 35.91 3.53
643 5188 0.888619 CGACTGTACCAGCTGGAAGA 59.111 55.000 39.19 20.20 38.94 2.87
644 5189 1.135257 CGACTGTACCAGCTGGAAGAG 60.135 57.143 39.19 28.26 38.94 2.85
1263 5856 1.979693 GGATCTCCCCTCCGGATCG 60.980 68.421 3.57 0.00 41.00 3.69
1372 5966 2.351336 GATCTGGCTGTACGGACCGG 62.351 65.000 20.00 10.92 0.00 5.28
1373 5967 2.849096 ATCTGGCTGTACGGACCGGA 62.849 60.000 20.00 21.57 42.89 5.14
1406 6003 2.882137 GTCGGTGGAGTTTTTGAATCCA 59.118 45.455 0.00 0.00 40.80 3.41
1435 6033 1.063867 GGGGAGAGTGGTCTGCTAGTA 60.064 57.143 0.00 0.00 40.90 1.82
1466 6067 9.733556 TTGTTATTCTCACCTGCTAATTTTAGA 57.266 29.630 1.52 0.00 32.47 2.10
1482 6083 3.895232 TTAGACTCATCTGGCTGGTTC 57.105 47.619 0.00 0.00 36.29 3.62
1504 6133 3.401243 GATCCGCGCTGCTTTTGGG 62.401 63.158 5.56 0.00 0.00 4.12
1553 6183 5.696724 ACAGTGAATTTGCTACAGTCAGTAC 59.303 40.000 0.00 0.00 0.00 2.73
1559 6189 1.134367 TGCTACAGTCAGTACGGATGC 59.866 52.381 0.00 0.90 0.00 3.91
1611 6242 0.931005 GATTCGGTTCGATGCCAGTC 59.069 55.000 7.23 0.00 35.23 3.51
1661 6305 5.927954 TGATTTTGTACCGTTGTTAGTCC 57.072 39.130 0.00 0.00 0.00 3.85
1792 6436 4.763073 TGTGATGAAGGATTGAGCAGTAG 58.237 43.478 0.00 0.00 20.54 2.57
1833 6477 7.174253 TGAATTTTAGGCGTGATATATTCCCAC 59.826 37.037 0.00 0.00 0.00 4.61
1843 6487 9.109393 GCGTGATATATTCCCACACAATATATT 57.891 33.333 0.00 0.00 38.60 1.28
1895 6539 9.319143 CTATTCCCAAACGATATATGAATCCTC 57.681 37.037 0.00 0.00 0.00 3.71
1904 6548 5.163468 CGATATATGAATCCTCTCCAGTGGG 60.163 48.000 9.92 0.00 0.00 4.61
1932 6576 3.305608 GCAAGAACTTTGACCTCCAATGG 60.306 47.826 0.00 0.00 35.07 3.16
1965 6609 3.644966 TTTAGGTGGCACTATTGGAGG 57.355 47.619 18.45 0.00 0.00 4.30
1970 6614 0.618458 TGGCACTATTGGAGGGTCAC 59.382 55.000 0.00 0.00 38.66 3.67
2292 6950 2.086869 CAGGTGGCTGTGGATTTACTG 58.913 52.381 0.00 0.00 0.00 2.74
2400 7058 7.255277 GGGTTGAGCATTATTAGGTCATCTTTC 60.255 40.741 0.00 0.00 42.35 2.62
2514 7172 6.385649 GGAATAACAATAATTCCTCCGCAA 57.614 37.500 7.45 0.00 45.99 4.85
2517 7175 6.959639 ATAACAATAATTCCTCCGCAACAT 57.040 33.333 0.00 0.00 0.00 2.71
2625 7283 9.591792 GAATTAAAGGATCAAATGAAGAAAGGG 57.408 33.333 0.00 0.00 0.00 3.95
2916 8046 4.402155 CAGCCCTATGAGTATGAGAGATCC 59.598 50.000 0.00 0.00 0.00 3.36
2939 8069 6.839134 TCCTTCATGCAGTAGAACTTATAGGA 59.161 38.462 0.00 0.00 0.00 2.94
3015 8145 6.640907 GGAAACTGGTTGTTATGCTTAGTTTG 59.359 38.462 0.00 0.00 37.11 2.93
3064 8196 5.814705 ACATGCTAGCAAGTCTATGTTTCTC 59.185 40.000 23.54 0.00 0.00 2.87
3121 8256 4.096833 TCGAATGCATTTCTCCCATTCTTG 59.903 41.667 14.33 0.00 41.48 3.02
3145 8280 4.462834 TGTCCCACTCTACTAGACACAATG 59.537 45.833 0.00 0.00 32.75 2.82
3146 8281 4.705507 GTCCCACTCTACTAGACACAATGA 59.294 45.833 0.00 0.00 0.00 2.57
3147 8282 5.185249 GTCCCACTCTACTAGACACAATGAA 59.815 44.000 0.00 0.00 0.00 2.57
3218 8413 3.393089 TTGTGCAAAAAGTTGGTGTGT 57.607 38.095 0.00 0.00 35.10 3.72
3219 8414 4.521130 TTGTGCAAAAAGTTGGTGTGTA 57.479 36.364 0.00 0.00 35.10 2.90
3332 8529 4.766891 GGATCAACAATTCTTCCTCCAACA 59.233 41.667 0.00 0.00 0.00 3.33
3463 8660 1.609555 GAACCACACCGTATTTGGCAA 59.390 47.619 0.00 0.00 33.25 4.52
3500 8697 3.997681 GCCTTTCCTCCTATCTTAATCGC 59.002 47.826 0.00 0.00 0.00 4.58
3745 8948 3.009723 CTGTAGCCAATGATCACCGTTT 58.990 45.455 0.00 0.00 0.00 3.60
3831 9034 5.859114 CGTGATCCTAATATGCACAGTAGAC 59.141 44.000 0.05 0.00 0.00 2.59
3877 9527 4.729918 AGAGCCGCCTTTGCCCAG 62.730 66.667 0.00 0.00 0.00 4.45
3913 9563 1.451504 CACACCCTCCAAGTGAGCA 59.548 57.895 0.00 0.00 39.98 4.26
3916 9566 0.679002 CACCCTCCAAGTGAGCATGG 60.679 60.000 0.00 0.00 39.98 3.66
4173 9890 3.055385 TCTGCTCCTGTGGGTAATACAAC 60.055 47.826 0.00 0.00 0.00 3.32
4174 9891 2.640332 TGCTCCTGTGGGTAATACAACA 59.360 45.455 0.00 0.00 0.00 3.33
4175 9892 3.073209 TGCTCCTGTGGGTAATACAACAA 59.927 43.478 0.00 0.00 0.00 2.83
4176 9893 3.689649 GCTCCTGTGGGTAATACAACAAG 59.310 47.826 0.00 0.00 0.00 3.16
4177 9894 4.806286 GCTCCTGTGGGTAATACAACAAGT 60.806 45.833 0.00 0.00 0.00 3.16
4178 9895 4.901868 TCCTGTGGGTAATACAACAAGTC 58.098 43.478 0.00 0.00 0.00 3.01
4179 9896 4.007659 CCTGTGGGTAATACAACAAGTCC 58.992 47.826 0.00 0.00 0.00 3.85
4180 9897 4.263331 CCTGTGGGTAATACAACAAGTCCT 60.263 45.833 0.00 0.00 0.00 3.85
4181 9898 4.647611 TGTGGGTAATACAACAAGTCCTG 58.352 43.478 0.00 0.00 0.00 3.86
4182 9899 4.103469 TGTGGGTAATACAACAAGTCCTGT 59.897 41.667 0.00 0.00 41.27 4.00
4184 9901 5.180680 GTGGGTAATACAACAAGTCCTGTTC 59.819 44.000 0.00 0.00 45.50 3.18
4185 9902 5.072600 TGGGTAATACAACAAGTCCTGTTCT 59.927 40.000 0.00 0.00 45.50 3.01
4186 9903 6.270463 TGGGTAATACAACAAGTCCTGTTCTA 59.730 38.462 0.00 0.00 45.50 2.10
4187 9904 6.817140 GGGTAATACAACAAGTCCTGTTCTAG 59.183 42.308 0.00 0.00 45.50 2.43
4188 9905 7.384477 GGTAATACAACAAGTCCTGTTCTAGT 58.616 38.462 0.00 0.00 45.50 2.57
4189 9906 7.544915 GGTAATACAACAAGTCCTGTTCTAGTC 59.455 40.741 0.00 0.00 45.50 2.59
4190 9907 6.665992 ATACAACAAGTCCTGTTCTAGTCA 57.334 37.500 0.00 0.00 45.50 3.41
4191 9908 5.552870 ACAACAAGTCCTGTTCTAGTCAT 57.447 39.130 0.00 0.00 45.50 3.06
4192 9909 6.665992 ACAACAAGTCCTGTTCTAGTCATA 57.334 37.500 0.00 0.00 45.50 2.15
4193 9910 7.246171 ACAACAAGTCCTGTTCTAGTCATAT 57.754 36.000 0.00 0.00 45.50 1.78
4194 9911 8.362464 ACAACAAGTCCTGTTCTAGTCATATA 57.638 34.615 0.00 0.00 45.50 0.86
4195 9912 8.982723 ACAACAAGTCCTGTTCTAGTCATATAT 58.017 33.333 0.00 0.00 45.50 0.86
4196 9913 9.469807 CAACAAGTCCTGTTCTAGTCATATATC 57.530 37.037 0.00 0.00 45.50 1.63
4197 9914 9.427821 AACAAGTCCTGTTCTAGTCATATATCT 57.572 33.333 0.00 0.00 45.50 1.98
4198 9915 8.855110 ACAAGTCCTGTTCTAGTCATATATCTG 58.145 37.037 0.00 0.00 32.99 2.90
4199 9916 7.461182 AGTCCTGTTCTAGTCATATATCTGC 57.539 40.000 0.00 0.00 0.00 4.26
4200 9917 7.237982 AGTCCTGTTCTAGTCATATATCTGCT 58.762 38.462 0.00 0.00 0.00 4.24
4201 9918 7.393234 AGTCCTGTTCTAGTCATATATCTGCTC 59.607 40.741 0.00 0.00 0.00 4.26
4202 9919 6.661377 TCCTGTTCTAGTCATATATCTGCTCC 59.339 42.308 0.00 0.00 0.00 4.70
4203 9920 6.663093 CCTGTTCTAGTCATATATCTGCTCCT 59.337 42.308 0.00 0.00 0.00 3.69
4204 9921 7.362834 CCTGTTCTAGTCATATATCTGCTCCTG 60.363 44.444 0.00 0.00 0.00 3.86
4205 9922 7.007116 TGTTCTAGTCATATATCTGCTCCTGT 58.993 38.462 0.00 0.00 0.00 4.00
4206 9923 7.040132 TGTTCTAGTCATATATCTGCTCCTGTG 60.040 40.741 0.00 0.00 0.00 3.66
4207 9924 5.948758 TCTAGTCATATATCTGCTCCTGTGG 59.051 44.000 0.00 0.00 0.00 4.17
4208 9925 3.837146 AGTCATATATCTGCTCCTGTGGG 59.163 47.826 0.00 0.00 0.00 4.61
4209 9926 3.580458 GTCATATATCTGCTCCTGTGGGT 59.420 47.826 0.00 0.00 0.00 4.51
4210 9927 4.772624 GTCATATATCTGCTCCTGTGGGTA 59.227 45.833 0.00 0.00 0.00 3.69
4211 9928 5.246203 GTCATATATCTGCTCCTGTGGGTAA 59.754 44.000 0.00 0.00 0.00 2.85
4212 9929 6.025539 TCATATATCTGCTCCTGTGGGTAAT 58.974 40.000 0.00 0.00 0.00 1.89
4213 9930 7.124298 GTCATATATCTGCTCCTGTGGGTAATA 59.876 40.741 0.00 0.00 0.00 0.98
4214 9931 7.678171 TCATATATCTGCTCCTGTGGGTAATAA 59.322 37.037 0.00 0.00 0.00 1.40
4215 9932 6.959606 ATATCTGCTCCTGTGGGTAATAAT 57.040 37.500 0.00 0.00 0.00 1.28
4216 9933 9.729550 ATATATCTGCTCCTGTGGGTAATAATA 57.270 33.333 0.00 0.00 0.00 0.98
4217 9934 5.546621 TCTGCTCCTGTGGGTAATAATAC 57.453 43.478 0.00 0.00 0.00 1.89
4218 9935 4.966168 TCTGCTCCTGTGGGTAATAATACA 59.034 41.667 0.00 0.00 33.45 2.29
4219 9936 5.427157 TCTGCTCCTGTGGGTAATAATACAA 59.573 40.000 0.00 0.00 33.45 2.41
4220 9937 5.433526 TGCTCCTGTGGGTAATAATACAAC 58.566 41.667 0.00 0.00 33.45 3.32
4221 9938 5.045505 TGCTCCTGTGGGTAATAATACAACA 60.046 40.000 0.00 0.00 33.45 3.33
4222 9939 5.883673 GCTCCTGTGGGTAATAATACAACAA 59.116 40.000 0.00 0.00 32.81 2.83
4223 9940 6.038271 GCTCCTGTGGGTAATAATACAACAAG 59.962 42.308 0.00 0.00 32.81 3.16
4224 9941 7.023171 TCCTGTGGGTAATAATACAACAAGT 57.977 36.000 0.00 0.00 32.81 3.16
4225 9942 7.107542 TCCTGTGGGTAATAATACAACAAGTC 58.892 38.462 0.00 0.00 32.81 3.01
4226 9943 6.317893 CCTGTGGGTAATAATACAACAAGTCC 59.682 42.308 0.00 0.00 32.81 3.85
4227 9944 7.023171 TGTGGGTAATAATACAACAAGTCCT 57.977 36.000 0.00 0.00 33.45 3.85
4228 9945 6.882140 TGTGGGTAATAATACAACAAGTCCTG 59.118 38.462 0.00 0.00 33.45 3.86
4229 9946 6.882678 GTGGGTAATAATACAACAAGTCCTGT 59.117 38.462 0.00 0.00 41.27 4.00
4231 9948 7.608761 TGGGTAATAATACAACAAGTCCTGTTC 59.391 37.037 0.00 0.00 45.50 3.18
4232 9949 7.827729 GGGTAATAATACAACAAGTCCTGTTCT 59.172 37.037 0.00 0.00 45.50 3.01
4233 9950 9.880157 GGTAATAATACAACAAGTCCTGTTCTA 57.120 33.333 0.00 0.00 45.50 2.10
4236 9953 9.654663 AATAATACAACAAGTCCTGTTCTAGTC 57.345 33.333 0.00 0.00 45.50 2.59
4237 9954 6.665992 ATACAACAAGTCCTGTTCTAGTCA 57.334 37.500 0.00 0.00 45.50 3.41
4238 9955 5.552870 ACAACAAGTCCTGTTCTAGTCAT 57.447 39.130 0.00 0.00 45.50 3.06
4239 9956 6.665992 ACAACAAGTCCTGTTCTAGTCATA 57.334 37.500 0.00 0.00 45.50 2.15
4240 9957 7.246171 ACAACAAGTCCTGTTCTAGTCATAT 57.754 36.000 0.00 0.00 45.50 1.78
4241 9958 8.362464 ACAACAAGTCCTGTTCTAGTCATATA 57.638 34.615 0.00 0.00 45.50 0.86
4242 9959 8.982723 ACAACAAGTCCTGTTCTAGTCATATAT 58.017 33.333 0.00 0.00 45.50 0.86
4243 9960 9.469807 CAACAAGTCCTGTTCTAGTCATATATC 57.530 37.037 0.00 0.00 45.50 1.63
4244 9961 9.427821 AACAAGTCCTGTTCTAGTCATATATCT 57.572 33.333 0.00 0.00 45.50 1.98
4245 9962 8.855110 ACAAGTCCTGTTCTAGTCATATATCTG 58.145 37.037 0.00 0.00 32.99 2.90
4246 9963 7.461182 AGTCCTGTTCTAGTCATATATCTGC 57.539 40.000 0.00 0.00 0.00 4.26
4247 9964 7.237982 AGTCCTGTTCTAGTCATATATCTGCT 58.762 38.462 0.00 0.00 0.00 4.24
4248 9965 7.393234 AGTCCTGTTCTAGTCATATATCTGCTC 59.607 40.741 0.00 0.00 0.00 4.26
4249 9966 6.661377 TCCTGTTCTAGTCATATATCTGCTCC 59.339 42.308 0.00 0.00 0.00 4.70
4250 9967 6.663093 CCTGTTCTAGTCATATATCTGCTCCT 59.337 42.308 0.00 0.00 0.00 3.69
4251 9968 7.362834 CCTGTTCTAGTCATATATCTGCTCCTG 60.363 44.444 0.00 0.00 0.00 3.86
4252 9969 7.007116 TGTTCTAGTCATATATCTGCTCCTGT 58.993 38.462 0.00 0.00 0.00 4.00
4253 9970 7.040132 TGTTCTAGTCATATATCTGCTCCTGTG 60.040 40.741 0.00 0.00 0.00 3.66
4254 9971 5.948758 TCTAGTCATATATCTGCTCCTGTGG 59.051 44.000 0.00 0.00 0.00 4.17
4255 9972 3.837146 AGTCATATATCTGCTCCTGTGGG 59.163 47.826 0.00 0.00 0.00 4.61
4256 9973 3.580458 GTCATATATCTGCTCCTGTGGGT 59.420 47.826 0.00 0.00 0.00 4.51
4257 9974 4.772624 GTCATATATCTGCTCCTGTGGGTA 59.227 45.833 0.00 0.00 0.00 3.69
4258 9975 5.246203 GTCATATATCTGCTCCTGTGGGTAA 59.754 44.000 0.00 0.00 0.00 2.85
4259 9976 6.025539 TCATATATCTGCTCCTGTGGGTAAT 58.974 40.000 0.00 0.00 0.00 1.89
4260 9977 7.124298 GTCATATATCTGCTCCTGTGGGTAATA 59.876 40.741 0.00 0.00 0.00 0.98
4261 9978 7.678171 TCATATATCTGCTCCTGTGGGTAATAA 59.322 37.037 0.00 0.00 0.00 1.40
4262 9979 6.959606 ATATCTGCTCCTGTGGGTAATAAT 57.040 37.500 0.00 0.00 0.00 1.28
4263 9980 9.729550 ATATATCTGCTCCTGTGGGTAATAATA 57.270 33.333 0.00 0.00 0.00 0.98
4264 9981 5.546621 TCTGCTCCTGTGGGTAATAATAC 57.453 43.478 0.00 0.00 0.00 1.89
4265 9982 4.966168 TCTGCTCCTGTGGGTAATAATACA 59.034 41.667 0.00 0.00 33.45 2.29
4266 9983 5.427157 TCTGCTCCTGTGGGTAATAATACAA 59.573 40.000 0.00 0.00 33.45 2.41
4267 9984 5.433526 TGCTCCTGTGGGTAATAATACAAC 58.566 41.667 0.00 0.00 33.45 3.32
4466 10225 2.634453 TGAGTTCCAAGATGAGCTCACA 59.366 45.455 20.97 5.33 44.44 3.58
4532 10316 8.362639 AGCAAAGATAACAGTCAAATTGAACAT 58.637 29.630 0.00 0.00 0.00 2.71
4571 10355 5.541845 TGGCTTTCCATCTGTAATATCTCG 58.458 41.667 0.00 0.00 37.47 4.04
4653 10444 3.583086 CCCTCCGTCCCATAATGTAAGAT 59.417 47.826 0.00 0.00 0.00 2.40
4868 10721 2.099921 CTCCGAAGAATCATGTCCTCGT 59.900 50.000 4.29 0.00 0.00 4.18
5220 12700 0.390735 GCAAGGCAAAGAATGGGCAG 60.391 55.000 0.00 0.00 0.00 4.85
5332 12812 5.227569 TGCTGTTCAGAAGAGGATTGTTA 57.772 39.130 9.29 0.00 0.00 2.41
5455 13298 4.498009 CGTTGTTGCCTCTGAAATTCTGTT 60.498 41.667 0.00 0.00 0.00 3.16
5519 14038 1.529865 GTTGTTGCCTACGGAGTTGTC 59.470 52.381 0.00 0.00 37.78 3.18
5663 14184 4.751767 TTGCACAAAATGGTTCCTTCTT 57.248 36.364 0.00 0.00 0.00 2.52
5699 14220 3.813166 AGGTATTTTCCACACAACACTCG 59.187 43.478 0.00 0.00 0.00 4.18
5764 14443 0.253327 CTTTGTCCCTCTGCTACCCC 59.747 60.000 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.690122 CCGTTTATAAGGACCGATCTTGT 58.310 43.478 0.00 0.00 0.00 3.16
43 44 2.835764 AGGAGTGTGCCGTTTATAAGGA 59.164 45.455 0.00 0.00 0.00 3.36
62 63 4.405404 CTACAAGTAGACGCCCCGAAGG 62.405 59.091 0.93 0.00 41.03 3.46
65 66 1.660560 GCTACAAGTAGACGCCCCGA 61.661 60.000 11.25 0.00 35.21 5.14
106 107 6.660094 TGTTTGTTTGGTTCTTTGTACTACCT 59.340 34.615 0.00 0.00 0.00 3.08
107 108 6.748658 GTGTTTGTTTGGTTCTTTGTACTACC 59.251 38.462 0.00 0.00 0.00 3.18
108 109 6.466730 CGTGTTTGTTTGGTTCTTTGTACTAC 59.533 38.462 0.00 0.00 0.00 2.73
109 110 6.403418 CCGTGTTTGTTTGGTTCTTTGTACTA 60.403 38.462 0.00 0.00 0.00 1.82
118 119 0.868177 CCGCCGTGTTTGTTTGGTTC 60.868 55.000 0.00 0.00 0.00 3.62
163 2717 6.907206 ATCCACATTGTTTTGTTTTCAGTG 57.093 33.333 0.00 0.00 0.00 3.66
165 2719 7.307337 GGCTAATCCACATTGTTTTGTTTTCAG 60.307 37.037 0.00 0.00 34.01 3.02
185 2740 6.218195 TCCATAAGGGATTGATTGGCTAAT 57.782 37.500 0.00 0.00 42.15 1.73
201 2756 7.756395 ATGCCTCACATTCTTATTCCATAAG 57.244 36.000 0.00 0.00 42.78 1.73
203 2758 7.830697 CCATATGCCTCACATTCTTATTCCATA 59.169 37.037 0.00 0.00 40.38 2.74
254 2809 0.912487 TTCCTCTTGGTATGCCCCGT 60.912 55.000 0.00 0.00 34.23 5.28
257 2812 2.379005 CCTTTTCCTCTTGGTATGCCC 58.621 52.381 0.00 0.00 34.23 5.36
259 2814 1.751351 GCCCTTTTCCTCTTGGTATGC 59.249 52.381 0.00 0.00 34.23 3.14
264 2819 1.678970 CGGGCCCTTTTCCTCTTGG 60.679 63.158 22.43 0.00 0.00 3.61
268 2823 1.676746 GAATACGGGCCCTTTTCCTC 58.323 55.000 22.43 4.93 0.00 3.71
270 2825 0.393402 ACGAATACGGGCCCTTTTCC 60.393 55.000 22.43 5.20 44.46 3.13
271 2826 1.456296 AACGAATACGGGCCCTTTTC 58.544 50.000 22.43 17.79 44.46 2.29
276 2831 0.033090 CTCCTAACGAATACGGGCCC 59.967 60.000 13.57 13.57 44.46 5.80
279 2834 3.451526 GTTTCCTCCTAACGAATACGGG 58.548 50.000 0.00 0.00 44.46 5.28
297 2852 1.073199 CCTCTTCTGGTGCCCGTTT 59.927 57.895 0.00 0.00 0.00 3.60
303 2858 1.016653 GCTTCGACCTCTTCTGGTGC 61.017 60.000 0.00 0.00 41.00 5.01
304 2859 0.390472 GGCTTCGACCTCTTCTGGTG 60.390 60.000 0.00 0.00 41.00 4.17
317 2872 0.032267 GGGATACTCTTCGGGCTTCG 59.968 60.000 0.00 0.00 40.90 3.79
320 2875 0.184451 TACGGGATACTCTTCGGGCT 59.816 55.000 0.00 0.00 0.00 5.19
321 2876 0.597072 CTACGGGATACTCTTCGGGC 59.403 60.000 0.00 0.00 0.00 6.13
323 2878 0.237761 CGCTACGGGATACTCTTCGG 59.762 60.000 0.00 0.00 0.00 4.30
338 2893 1.395045 CCAGTGCATCTCTCCCGCTA 61.395 60.000 0.00 0.00 0.00 4.26
340 2895 2.202987 CCAGTGCATCTCTCCCGC 60.203 66.667 0.00 0.00 0.00 6.13
343 2898 2.725221 AAATCCCAGTGCATCTCTCC 57.275 50.000 0.00 0.00 0.00 3.71
349 2904 1.002315 GTGCCAAAAATCCCAGTGCAT 59.998 47.619 0.00 0.00 0.00 3.96
354 2909 0.038343 CACCGTGCCAAAAATCCCAG 60.038 55.000 0.00 0.00 0.00 4.45
355 2910 1.467678 CCACCGTGCCAAAAATCCCA 61.468 55.000 0.00 0.00 0.00 4.37
356 2911 1.291906 CCACCGTGCCAAAAATCCC 59.708 57.895 0.00 0.00 0.00 3.85
357 2912 1.374125 GCCACCGTGCCAAAAATCC 60.374 57.895 0.00 0.00 0.00 3.01
358 2913 0.249657 TTGCCACCGTGCCAAAAATC 60.250 50.000 0.00 0.00 0.00 2.17
362 2917 1.530419 ATCTTGCCACCGTGCCAAA 60.530 52.632 0.00 0.00 0.00 3.28
363 2918 2.115052 ATCTTGCCACCGTGCCAA 59.885 55.556 0.00 0.00 0.00 4.52
372 2927 4.393155 ACTCGCGCCATCTTGCCA 62.393 61.111 0.00 0.00 0.00 4.92
373 2928 3.869272 CACTCGCGCCATCTTGCC 61.869 66.667 0.00 0.00 0.00 4.52
375 2930 0.807275 TGATCACTCGCGCCATCTTG 60.807 55.000 0.00 0.00 0.00 3.02
380 2935 2.815211 GCTTGATCACTCGCGCCA 60.815 61.111 0.00 0.00 0.00 5.69
381 2936 3.567797 GGCTTGATCACTCGCGCC 61.568 66.667 0.00 0.00 33.82 6.53
382 2937 3.918220 CGGCTTGATCACTCGCGC 61.918 66.667 0.00 0.00 0.00 6.86
384 2939 1.571919 ATAACGGCTTGATCACTCGC 58.428 50.000 0.00 0.00 0.00 5.03
398 2953 0.850856 GTTCTAGCCGGCGAATAACG 59.149 55.000 23.20 3.22 45.66 3.18
400 2955 2.546778 CTTGTTCTAGCCGGCGAATAA 58.453 47.619 23.20 20.96 0.00 1.40
403 2958 1.740296 GCTTGTTCTAGCCGGCGAA 60.740 57.895 23.20 16.99 35.06 4.70
420 2975 0.947244 ACAAGTGTAAGCAGTGCAGC 59.053 50.000 19.20 7.25 0.00 5.25
422 2977 1.134250 TGGACAAGTGTAAGCAGTGCA 60.134 47.619 19.20 0.00 0.00 4.57
463 3018 4.716003 GGCTTTGTCGCCTAGGTT 57.284 55.556 11.31 0.00 46.63 3.50
471 3237 0.817634 TTCAGTGGTGGGCTTTGTCG 60.818 55.000 0.00 0.00 0.00 4.35
487 3253 2.808244 CGCTTTTGGTGCTTTTCTTCA 58.192 42.857 0.00 0.00 0.00 3.02
520 5049 1.131693 GCGTAAGTGCGGGCTAATTTT 59.868 47.619 0.00 0.00 41.68 1.82
521 5050 0.730840 GCGTAAGTGCGGGCTAATTT 59.269 50.000 0.00 0.00 41.68 1.82
556 5085 5.276461 TCGGATCGGAATATGGGATTATG 57.724 43.478 0.00 0.00 0.00 1.90
652 5197 2.049802 TGGACGAGCGAACGGAAC 60.050 61.111 0.00 0.00 37.61 3.62
653 5198 2.049802 GTGGACGAGCGAACGGAA 60.050 61.111 0.00 0.00 37.61 4.30
654 5199 4.047059 GGTGGACGAGCGAACGGA 62.047 66.667 0.00 0.00 37.61 4.69
655 5200 4.351938 TGGTGGACGAGCGAACGG 62.352 66.667 0.00 0.00 37.61 4.44
656 5201 2.805353 CTGGTGGACGAGCGAACG 60.805 66.667 0.00 0.00 39.31 3.95
872 5450 2.610859 CTGCTAGGTGGTGGGGGT 60.611 66.667 0.00 0.00 0.00 4.95
875 5453 2.270205 CTGCTGCTAGGTGGTGGG 59.730 66.667 0.00 0.00 0.00 4.61
1149 5733 4.140599 AGCCAGAAGAGCGCGGAG 62.141 66.667 8.83 0.00 34.64 4.63
1201 5785 3.262686 GGGATCCGACGCGCTTTC 61.263 66.667 5.73 0.00 0.00 2.62
1202 5786 3.310860 AAGGGATCCGACGCGCTTT 62.311 57.895 5.73 0.00 34.15 3.51
1203 5790 3.718210 GAAGGGATCCGACGCGCTT 62.718 63.158 5.73 0.00 39.58 4.68
1210 5797 3.524606 GACGGCGAAGGGATCCGA 61.525 66.667 16.62 0.00 45.53 4.55
1381 5978 0.310854 CAAAAACTCCACCGACAGCC 59.689 55.000 0.00 0.00 0.00 4.85
1420 6017 4.158764 ACAAGTCATACTAGCAGACCACTC 59.841 45.833 6.28 0.00 32.82 3.51
1435 6033 5.171339 AGCAGGTGAGAATAACAAGTCAT 57.829 39.130 0.00 0.00 0.00 3.06
1466 6067 1.004044 CAAGGAACCAGCCAGATGAGT 59.996 52.381 0.00 0.00 0.00 3.41
1482 6083 1.926511 AAAAGCAGCGCGGATCAAGG 61.927 55.000 13.03 0.00 0.00 3.61
1504 6133 5.120363 GGACGTTTCTCAACCTACTCAATTC 59.880 44.000 0.00 0.00 0.00 2.17
1611 6242 8.442384 GGCAAAATCAAAACCAAATACTACATG 58.558 33.333 0.00 0.00 0.00 3.21
1661 6305 8.246180 ACAGCCAGATGAAAAATTAACTATGTG 58.754 33.333 0.00 0.00 0.00 3.21
1792 6436 7.433425 GCCTAAAATTCATGAGCAGTAATCAAC 59.567 37.037 0.00 0.00 0.00 3.18
1833 6477 9.537192 AAAATTCATGGACAGCAATATATTGTG 57.463 29.630 23.14 20.49 39.88 3.33
1843 6487 3.193267 GCACCTAAAATTCATGGACAGCA 59.807 43.478 0.00 0.00 0.00 4.41
1844 6488 3.731867 CGCACCTAAAATTCATGGACAGC 60.732 47.826 0.00 0.00 0.00 4.40
1895 6539 1.003580 TCTTGCTTTAGCCCACTGGAG 59.996 52.381 0.00 0.00 41.18 3.86
1904 6548 4.320567 GGAGGTCAAAGTTCTTGCTTTAGC 60.321 45.833 0.00 0.00 36.64 3.09
1932 6576 4.391405 CCACCTAAAATTGGCAAGGATC 57.609 45.455 9.11 0.00 33.16 3.36
1965 6609 4.841443 AAACTAAATTGGAACCGTGACC 57.159 40.909 0.00 0.00 0.00 4.02
1970 6614 5.764131 TGTGCTTAAACTAAATTGGAACCG 58.236 37.500 0.00 0.00 0.00 4.44
2078 6734 6.252599 ACTTGCCACTATATCATCTGGAAA 57.747 37.500 0.00 0.00 0.00 3.13
2141 6797 2.672961 TCCAATACGAGCTTGGACAG 57.327 50.000 5.79 0.00 45.56 3.51
2400 7058 1.580942 CCGCACAACCAAGGACATG 59.419 57.895 0.00 0.00 0.00 3.21
2446 7104 6.441284 TCAAAGGATGATGAATTCCCAAACAT 59.559 34.615 2.27 1.87 31.50 2.71
2514 7172 3.319122 GTGTTTCAGGAGGAAAAGCATGT 59.681 43.478 0.00 0.00 46.53 3.21
2517 7175 3.214328 GAGTGTTTCAGGAGGAAAAGCA 58.786 45.455 0.00 0.00 46.53 3.91
2625 7283 9.685828 CTAACCTCATTAGAATTGAGTAGTAGC 57.314 37.037 0.00 0.00 42.75 3.58
2795 7862 9.398170 CAAGATATCACACAACTAAAAGTTTGG 57.602 33.333 5.32 0.00 36.03 3.28
2916 8046 8.986847 CAATCCTATAAGTTCTACTGCATGAAG 58.013 37.037 0.00 0.00 0.00 3.02
3064 8196 9.107177 AGAATGAGATAGCTTTGTGTTAAGATG 57.893 33.333 0.00 0.00 0.00 2.90
3147 8282 2.739943 GCTCCCAGCCCTATTCTTTTT 58.260 47.619 0.00 0.00 34.48 1.94
3218 8413 2.771943 AGCAGGGCAATGTAAGCTACTA 59.228 45.455 0.00 0.00 0.00 1.82
3219 8414 1.561542 AGCAGGGCAATGTAAGCTACT 59.438 47.619 0.00 0.00 0.00 2.57
3332 8529 5.763204 ACGAACAATGTAGGTCTCAACAATT 59.237 36.000 0.00 0.00 0.00 2.32
3463 8660 5.821097 AGGAAAGGCTTATCTGCTTTACTT 58.179 37.500 0.00 0.00 31.96 2.24
3500 8697 2.171448 ACTGCCCCTGCTATGTAAAGAG 59.829 50.000 0.00 0.00 38.71 2.85
3745 8948 0.901827 TGAAGCGGCAGGATGAGTAA 59.098 50.000 1.45 0.00 39.69 2.24
3877 9527 4.976116 GGTGTGCATGACTAAAAGAAACAC 59.024 41.667 0.00 0.00 35.74 3.32
3913 9563 2.298661 GGACCGGTTCCTGTCCCAT 61.299 63.158 9.42 0.00 44.32 4.00
4101 9818 2.303022 TGAAGCGTCAAAATCCTCCTCT 59.697 45.455 0.00 0.00 0.00 3.69
4173 9890 7.812191 GCAGATATATGACTAGAACAGGACTTG 59.188 40.741 0.39 0.00 0.00 3.16
4174 9891 7.728083 AGCAGATATATGACTAGAACAGGACTT 59.272 37.037 0.39 0.00 0.00 3.01
4175 9892 7.237982 AGCAGATATATGACTAGAACAGGACT 58.762 38.462 0.39 0.00 0.00 3.85
4176 9893 7.362574 GGAGCAGATATATGACTAGAACAGGAC 60.363 44.444 0.39 0.00 0.00 3.85
4177 9894 6.661377 GGAGCAGATATATGACTAGAACAGGA 59.339 42.308 0.39 0.00 0.00 3.86
4178 9895 6.663093 AGGAGCAGATATATGACTAGAACAGG 59.337 42.308 0.39 0.00 0.00 4.00
4179 9896 7.176515 ACAGGAGCAGATATATGACTAGAACAG 59.823 40.741 0.39 0.00 0.00 3.16
4180 9897 7.007116 ACAGGAGCAGATATATGACTAGAACA 58.993 38.462 0.39 0.00 0.00 3.18
4181 9898 7.312154 CACAGGAGCAGATATATGACTAGAAC 58.688 42.308 0.39 0.00 0.00 3.01
4182 9899 6.435591 CCACAGGAGCAGATATATGACTAGAA 59.564 42.308 0.39 0.00 0.00 2.10
4183 9900 5.948758 CCACAGGAGCAGATATATGACTAGA 59.051 44.000 0.39 0.00 0.00 2.43
4184 9901 5.126869 CCCACAGGAGCAGATATATGACTAG 59.873 48.000 0.39 0.00 33.47 2.57
4185 9902 5.019470 CCCACAGGAGCAGATATATGACTA 58.981 45.833 0.39 0.00 33.47 2.59
4186 9903 3.837146 CCCACAGGAGCAGATATATGACT 59.163 47.826 0.39 0.00 33.47 3.41
4187 9904 3.580458 ACCCACAGGAGCAGATATATGAC 59.420 47.826 0.39 0.00 36.73 3.06
4188 9905 3.861846 ACCCACAGGAGCAGATATATGA 58.138 45.455 0.39 0.00 36.73 2.15
4189 9906 5.745312 TTACCCACAGGAGCAGATATATG 57.255 43.478 0.00 0.00 36.73 1.78
4190 9907 8.629821 ATTATTACCCACAGGAGCAGATATAT 57.370 34.615 0.00 0.00 36.73 0.86
4191 9908 8.978472 GTATTATTACCCACAGGAGCAGATATA 58.022 37.037 0.00 0.00 36.73 0.86
4192 9909 6.959606 ATTATTACCCACAGGAGCAGATAT 57.040 37.500 0.00 0.00 36.73 1.63
4193 9910 6.785466 TGTATTATTACCCACAGGAGCAGATA 59.215 38.462 0.00 0.00 36.73 1.98
4194 9911 5.606749 TGTATTATTACCCACAGGAGCAGAT 59.393 40.000 0.00 0.00 36.73 2.90
4195 9912 4.966168 TGTATTATTACCCACAGGAGCAGA 59.034 41.667 0.00 0.00 36.73 4.26
4196 9913 5.290493 TGTATTATTACCCACAGGAGCAG 57.710 43.478 0.00 0.00 36.73 4.24
4197 9914 5.045505 TGTTGTATTATTACCCACAGGAGCA 60.046 40.000 0.00 0.00 36.73 4.26
4198 9915 5.433526 TGTTGTATTATTACCCACAGGAGC 58.566 41.667 0.00 0.00 36.73 4.70
4199 9916 7.110155 ACTTGTTGTATTATTACCCACAGGAG 58.890 38.462 10.66 4.97 36.73 3.69
4200 9917 7.023171 ACTTGTTGTATTATTACCCACAGGA 57.977 36.000 10.66 0.00 36.73 3.86
4201 9918 6.317893 GGACTTGTTGTATTATTACCCACAGG 59.682 42.308 5.48 5.48 40.04 4.00
4202 9919 7.065803 CAGGACTTGTTGTATTATTACCCACAG 59.934 40.741 0.00 0.00 0.00 3.66
4203 9920 6.882140 CAGGACTTGTTGTATTATTACCCACA 59.118 38.462 0.00 0.00 0.00 4.17
4204 9921 6.882678 ACAGGACTTGTTGTATTATTACCCAC 59.117 38.462 0.00 0.00 36.31 4.61
4205 9922 7.023171 ACAGGACTTGTTGTATTATTACCCA 57.977 36.000 0.00 0.00 36.31 4.51
4219 9936 8.855110 CAGATATATGACTAGAACAGGACTTGT 58.145 37.037 0.00 0.00 43.45 3.16
4220 9937 7.812191 GCAGATATATGACTAGAACAGGACTTG 59.188 40.741 0.39 0.00 0.00 3.16
4221 9938 7.728083 AGCAGATATATGACTAGAACAGGACTT 59.272 37.037 0.39 0.00 0.00 3.01
4222 9939 7.237982 AGCAGATATATGACTAGAACAGGACT 58.762 38.462 0.39 0.00 0.00 3.85
4223 9940 7.362574 GGAGCAGATATATGACTAGAACAGGAC 60.363 44.444 0.39 0.00 0.00 3.85
4224 9941 6.661377 GGAGCAGATATATGACTAGAACAGGA 59.339 42.308 0.39 0.00 0.00 3.86
4225 9942 6.663093 AGGAGCAGATATATGACTAGAACAGG 59.337 42.308 0.39 0.00 0.00 4.00
4226 9943 7.176515 ACAGGAGCAGATATATGACTAGAACAG 59.823 40.741 0.39 0.00 0.00 3.16
4227 9944 7.007116 ACAGGAGCAGATATATGACTAGAACA 58.993 38.462 0.39 0.00 0.00 3.18
4228 9945 7.312154 CACAGGAGCAGATATATGACTAGAAC 58.688 42.308 0.39 0.00 0.00 3.01
4229 9946 6.435591 CCACAGGAGCAGATATATGACTAGAA 59.564 42.308 0.39 0.00 0.00 2.10
4230 9947 5.948758 CCACAGGAGCAGATATATGACTAGA 59.051 44.000 0.39 0.00 0.00 2.43
4231 9948 5.126869 CCCACAGGAGCAGATATATGACTAG 59.873 48.000 0.39 0.00 33.47 2.57
4232 9949 5.019470 CCCACAGGAGCAGATATATGACTA 58.981 45.833 0.39 0.00 33.47 2.59
4233 9950 3.837146 CCCACAGGAGCAGATATATGACT 59.163 47.826 0.39 0.00 33.47 3.41
4234 9951 3.580458 ACCCACAGGAGCAGATATATGAC 59.420 47.826 0.39 0.00 36.73 3.06
4235 9952 3.861846 ACCCACAGGAGCAGATATATGA 58.138 45.455 0.39 0.00 36.73 2.15
4236 9953 5.745312 TTACCCACAGGAGCAGATATATG 57.255 43.478 0.00 0.00 36.73 1.78
4237 9954 8.629821 ATTATTACCCACAGGAGCAGATATAT 57.370 34.615 0.00 0.00 36.73 0.86
4238 9955 8.978472 GTATTATTACCCACAGGAGCAGATATA 58.022 37.037 0.00 0.00 36.73 0.86
4239 9956 6.959606 ATTATTACCCACAGGAGCAGATAT 57.040 37.500 0.00 0.00 36.73 1.63
4240 9957 6.785466 TGTATTATTACCCACAGGAGCAGATA 59.215 38.462 0.00 0.00 36.73 1.98
4241 9958 5.606749 TGTATTATTACCCACAGGAGCAGAT 59.393 40.000 0.00 0.00 36.73 2.90
4242 9959 4.966168 TGTATTATTACCCACAGGAGCAGA 59.034 41.667 0.00 0.00 36.73 4.26
4243 9960 5.290493 TGTATTATTACCCACAGGAGCAG 57.710 43.478 0.00 0.00 36.73 4.24
4244 9961 5.045505 TGTTGTATTATTACCCACAGGAGCA 60.046 40.000 0.00 0.00 36.73 4.26
4245 9962 5.433526 TGTTGTATTATTACCCACAGGAGC 58.566 41.667 0.00 0.00 36.73 4.70
4246 9963 7.110155 ACTTGTTGTATTATTACCCACAGGAG 58.890 38.462 10.66 4.97 36.73 3.69
4247 9964 7.023171 ACTTGTTGTATTATTACCCACAGGA 57.977 36.000 10.66 0.00 36.73 3.86
4248 9965 6.317893 GGACTTGTTGTATTATTACCCACAGG 59.682 42.308 5.48 5.48 40.04 4.00
4249 9966 7.065803 CAGGACTTGTTGTATTATTACCCACAG 59.934 40.741 0.00 0.00 0.00 3.66
4250 9967 6.882140 CAGGACTTGTTGTATTATTACCCACA 59.118 38.462 0.00 0.00 0.00 4.17
4251 9968 6.882678 ACAGGACTTGTTGTATTATTACCCAC 59.117 38.462 0.00 0.00 36.31 4.61
4252 9969 7.023171 ACAGGACTTGTTGTATTATTACCCA 57.977 36.000 0.00 0.00 36.31 4.51
4266 9983 8.855110 CAGATATATGACTAGAACAGGACTTGT 58.145 37.037 0.00 0.00 43.45 3.16
4267 9984 7.812191 GCAGATATATGACTAGAACAGGACTTG 59.188 40.741 0.39 0.00 0.00 3.16
4282 9999 3.861846 ACCCACAGGAGCAGATATATGA 58.138 45.455 0.39 0.00 36.73 2.15
4435 10194 5.945784 TCATCTTGGAACTCAAATTACCTGG 59.054 40.000 0.00 0.00 34.56 4.45
4495 10279 9.384764 GACTGTTATCTTTGCTCTAGGTTATTT 57.615 33.333 0.00 0.00 0.00 1.40
4532 10316 5.997129 GGAAAGCCAAAATCCAGAAATGAAA 59.003 36.000 0.00 0.00 33.30 2.69
4571 10355 7.171337 AGGTCAAACATATTTCAAAATGCACAC 59.829 33.333 0.00 0.00 0.00 3.82
4666 10457 9.745018 AGTAATAAACTACTCCACACTAGTGTA 57.255 33.333 27.48 12.95 39.42 2.90
4667 10458 8.521176 CAGTAATAAACTACTCCACACTAGTGT 58.479 37.037 22.95 22.95 39.28 3.55
5097 12570 0.820891 CTGCCTTGTGCTTCACCACT 60.821 55.000 0.00 0.00 42.00 4.00
5220 12700 2.097038 CACTACGAGCACAGCTGCC 61.097 63.158 15.27 5.10 45.53 4.85
5475 13318 3.624410 TCAGCATCAGCATCAACATGTAC 59.376 43.478 0.00 0.00 45.49 2.90
5477 13320 2.718563 TCAGCATCAGCATCAACATGT 58.281 42.857 0.00 0.00 45.49 3.21
5482 13325 3.086282 ACAACATCAGCATCAGCATCAA 58.914 40.909 0.00 0.00 45.49 2.57
5519 14038 3.248602 CAGTTTCTGAACTCTTTCCCACG 59.751 47.826 0.00 0.00 44.14 4.94
5663 14184 5.428253 GAAAATACCTGTGTGCAGATAGGA 58.572 41.667 29.85 15.43 45.28 2.94
5764 14443 4.072839 TCCCGCATGTCTAGAGTATACAG 58.927 47.826 5.50 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.