Multiple sequence alignment - TraesCS2D01G081400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G081400 chr2D 100.000 5090 0 0 1 5090 35004269 34999180 0.000000e+00 9400.0
1 TraesCS2D01G081400 chr2D 83.782 2713 268 79 1664 4293 35025071 35022448 0.000000e+00 2414.0
2 TraesCS2D01G081400 chr2D 85.803 641 49 18 894 1530 35025830 35025228 4.300000e-180 641.0
3 TraesCS2D01G081400 chr2D 97.222 36 1 0 1302 1337 398670319 398670284 1.530000e-05 62.1
4 TraesCS2D01G081400 chr2B 93.292 3846 159 45 649 4440 57683019 57679219 0.000000e+00 5581.0
5 TraesCS2D01G081400 chr2B 83.607 2684 289 75 1665 4293 57780954 57778367 0.000000e+00 2379.0
6 TraesCS2D01G081400 chr2B 98.954 478 5 0 4613 5090 57677470 57676993 0.000000e+00 856.0
7 TraesCS2D01G081400 chr2B 85.692 643 53 16 891 1533 57781716 57781113 4.300000e-180 641.0
8 TraesCS2D01G081400 chr2B 94.175 206 10 2 4425 4629 57678555 57678351 3.830000e-81 313.0
9 TraesCS2D01G081400 chr2B 97.222 36 1 0 1302 1337 471320431 471320466 1.530000e-05 62.1
10 TraesCS2D01G081400 chr2A 89.482 3613 256 47 1569 5090 38324209 38320630 0.000000e+00 4453.0
11 TraesCS2D01G081400 chr2A 83.483 2676 285 80 1665 4293 38332071 38329506 0.000000e+00 2348.0
12 TraesCS2D01G081400 chr2A 86.595 1298 106 42 253 1530 38325575 38324326 0.000000e+00 1371.0
13 TraesCS2D01G081400 chr2A 88.869 548 34 16 989 1533 38332752 38332229 0.000000e+00 649.0
14 TraesCS2D01G081400 chr2A 82.105 95 12 4 95 186 1378610 1378702 5.460000e-10 76.8
15 TraesCS2D01G081400 chr7D 76.797 918 143 54 1660 2546 8293973 8293095 7.770000e-123 451.0
16 TraesCS2D01G081400 chr7D 80.285 492 71 21 3050 3525 8292658 8292177 1.050000e-91 348.0
17 TraesCS2D01G081400 chr7D 83.442 308 39 8 1234 1532 8333449 8333145 5.020000e-70 276.0
18 TraesCS2D01G081400 chr7D 92.143 140 11 0 994 1133 8333657 8333518 1.120000e-46 198.0
19 TraesCS2D01G081400 chr7D 83.251 203 34 0 3873 4075 8291818 8291616 2.420000e-43 187.0
20 TraesCS2D01G081400 chr7D 88.158 76 6 2 109 182 591010227 591010301 2.520000e-13 87.9
21 TraesCS2D01G081400 chr4A 76.233 892 152 43 1669 2545 731420103 731420949 7.880000e-113 418.0
22 TraesCS2D01G081400 chr7A 74.848 986 179 54 1733 2697 8751531 8750594 2.880000e-102 383.0
23 TraesCS2D01G081400 chr7A 79.400 500 78 19 3050 3531 8750305 8749813 3.800000e-86 329.0
24 TraesCS2D01G081400 chr7A 82.143 308 43 2 1234 1532 8762716 8762412 2.350000e-63 254.0
25 TraesCS2D01G081400 chr7A 91.489 141 12 0 994 1134 8762942 8762802 1.450000e-45 195.0
26 TraesCS2D01G081400 chr7A 87.013 77 9 1 112 188 232745443 232745368 9.080000e-13 86.1
27 TraesCS2D01G081400 chr6D 77.583 629 102 29 3074 3676 396840573 396839958 1.360000e-90 344.0
28 TraesCS2D01G081400 chr6D 72.909 1052 191 58 1665 2700 396841934 396840961 1.400000e-70 278.0
29 TraesCS2D01G081400 chr6D 80.786 229 40 4 3859 4086 396839696 396839471 5.240000e-40 176.0
30 TraesCS2D01G081400 chr6D 90.323 62 6 0 2853 2914 396840839 396840778 1.170000e-11 82.4
31 TraesCS2D01G081400 chr6B 75.455 660 91 37 2058 2700 593356205 593355600 6.540000e-64 255.0
32 TraesCS2D01G081400 chr6B 90.141 142 11 2 991 1129 593358839 593358698 1.130000e-41 182.0
33 TraesCS2D01G081400 chr6B 79.039 229 44 4 3859 4086 593354343 593354118 2.450000e-33 154.0
34 TraesCS2D01G081400 chr6B 87.838 74 8 1 109 182 23637573 23637501 9.080000e-13 86.1
35 TraesCS2D01G081400 chr6A 87.654 162 15 3 991 1147 543210796 543210635 3.130000e-42 183.0
36 TraesCS2D01G081400 chr6A 79.476 229 43 4 3859 4086 543206250 543206025 5.270000e-35 159.0
37 TraesCS2D01G081400 chr6A 90.323 62 5 1 2853 2914 543207397 543207337 4.220000e-11 80.5
38 TraesCS2D01G081400 chr5D 92.405 79 5 1 109 187 47332257 47332334 1.500000e-20 111.0
39 TraesCS2D01G081400 chr5B 90.667 75 6 1 113 187 50469140 50469213 1.170000e-16 99.0
40 TraesCS2D01G081400 chr5B 88.608 79 8 1 109 187 690622005 690622082 1.510000e-15 95.3
41 TraesCS2D01G081400 chr1B 82.759 87 13 1 109 195 681848346 681848430 5.460000e-10 76.8
42 TraesCS2D01G081400 chrUn 83.750 80 10 3 109 188 67093244 67093168 7.070000e-09 73.1


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 TraesCS2D01G081400 chr2D 34999180 35004269 5089 True 9400.000000 9400 100.000000 1 5090 1 chr2D.!!$R1 5089
1 TraesCS2D01G081400 chr2D 35022448 35025830 3382 True 1527.500000 2414 84.792500 894 4293 2 chr2D.!!$R3 3399
2 TraesCS2D01G081400 chr2B 57676993 57683019 6026 True 2250.000000 5581 95.473667 649 5090 3 chr2B.!!$R1 4441
3 TraesCS2D01G081400 chr2B 57778367 57781716 3349 True 1510.000000 2379 84.649500 891 4293 2 chr2B.!!$R2 3402
4 TraesCS2D01G081400 chr2A 38320630 38332752 12122 True 2205.250000 4453 87.107250 253 5090 4 chr2A.!!$R1 4837
5 TraesCS2D01G081400 chr7D 8291616 8293973 2357 True 328.666667 451 80.111000 1660 4075 3 chr7D.!!$R1 2415
6 TraesCS2D01G081400 chr7D 8333145 8333657 512 True 237.000000 276 87.792500 994 1532 2 chr7D.!!$R2 538
7 TraesCS2D01G081400 chr4A 731420103 731420949 846 False 418.000000 418 76.233000 1669 2545 1 chr4A.!!$F1 876
8 TraesCS2D01G081400 chr7A 8749813 8751531 1718 True 356.000000 383 77.124000 1733 3531 2 chr7A.!!$R2 1798
9 TraesCS2D01G081400 chr7A 8762412 8762942 530 True 224.500000 254 86.816000 994 1532 2 chr7A.!!$R3 538
10 TraesCS2D01G081400 chr6D 396839471 396841934 2463 True 220.100000 344 80.400250 1665 4086 4 chr6D.!!$R1 2421

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
45 46 0.102120 CTGCTTTGTTTGGGAACGCA 59.898 50.000 0.00 0.00 38.65 5.24 F
595 7528 0.109723 TCCGGGTTTCCAGTTTCCTG 59.890 55.000 0.00 0.00 38.50 3.86 F
1156 8164 0.176449 CATCCACCATGAGAGACGCA 59.824 55.000 0.00 0.00 33.80 5.24 F
1157 8165 0.463204 ATCCACCATGAGAGACGCAG 59.537 55.000 0.00 0.00 0.00 5.18 F
1162 8170 0.597118 CCATGAGAGACGCAGCTAGC 60.597 60.000 6.62 6.62 40.87 3.42 F
1226 8245 1.577328 ATGAGCTGAACGTTTGGGCG 61.577 55.000 0.46 0.00 37.94 6.13 F
2384 9645 3.302699 GTCGCGTCTATGTTTCTTGGTAC 59.697 47.826 5.77 0.00 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 8169 0.101579 GCTTCCTGGTCTCTCTACGC 59.898 60.000 0.00 0.0 0.00 4.42 R
1542 8570 1.001764 TCCCATGCCAGTTGAGCTG 60.002 57.895 0.00 0.0 44.63 4.24 R
2817 10118 4.398319 AGAGTGGGGTTACTTTTCACATG 58.602 43.478 0.00 0.0 0.00 3.21 R
3008 10335 9.539825 TTTTGCATAATGCTTAGTTTGAAAGAA 57.460 25.926 0.00 0.0 45.31 2.52 R
3386 10751 8.593945 TCCTATTTGAAACTAGCAAATCCATT 57.406 30.769 9.29 0.0 42.95 3.16 R
3429 10806 5.408909 CACCTGCAACATTGATAAATGCAAA 59.591 36.000 2.36 0.0 45.37 3.68 R
4505 12693 4.466370 TGGGGTTATCTCGCTAGAATATGG 59.534 45.833 0.00 0.0 34.73 2.74 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
23 24 6.530913 CATATCCAATCTGAAACGACGATT 57.469 37.500 0.00 0.00 0.00 3.34
25 26 3.659786 TCCAATCTGAAACGACGATTGT 58.340 40.909 0.00 0.00 41.32 2.71
26 27 3.678072 TCCAATCTGAAACGACGATTGTC 59.322 43.478 0.00 2.65 41.32 3.18
27 28 3.679980 CCAATCTGAAACGACGATTGTCT 59.320 43.478 11.37 0.00 43.21 3.41
29 30 2.058798 TCTGAAACGACGATTGTCTGC 58.941 47.619 11.37 0.00 43.21 4.26
30 31 2.061773 CTGAAACGACGATTGTCTGCT 58.938 47.619 11.37 0.00 43.21 4.24
31 32 2.476619 CTGAAACGACGATTGTCTGCTT 59.523 45.455 11.37 3.00 43.21 3.91
32 33 2.869801 TGAAACGACGATTGTCTGCTTT 59.130 40.909 11.37 5.89 43.21 3.51
34 35 1.865865 ACGACGATTGTCTGCTTTGT 58.134 45.000 11.37 0.00 43.21 2.83
35 36 2.210116 ACGACGATTGTCTGCTTTGTT 58.790 42.857 11.37 0.00 43.21 2.83
36 37 2.612212 ACGACGATTGTCTGCTTTGTTT 59.388 40.909 11.37 0.00 43.21 2.83
37 38 2.966708 CGACGATTGTCTGCTTTGTTTG 59.033 45.455 11.37 0.00 43.21 2.93
39 40 2.034558 ACGATTGTCTGCTTTGTTTGGG 59.965 45.455 0.00 0.00 0.00 4.12
40 41 2.293122 CGATTGTCTGCTTTGTTTGGGA 59.707 45.455 0.00 0.00 0.00 4.37
41 42 3.243367 CGATTGTCTGCTTTGTTTGGGAA 60.243 43.478 0.00 0.00 0.00 3.97
43 44 1.403679 TGTCTGCTTTGTTTGGGAACG 59.596 47.619 0.00 0.00 38.65 3.95
45 46 0.102120 CTGCTTTGTTTGGGAACGCA 59.898 50.000 0.00 0.00 38.65 5.24
47 48 1.066858 TGCTTTGTTTGGGAACGCAAA 60.067 42.857 11.81 11.81 38.65 3.68
49 50 3.181475 TGCTTTGTTTGGGAACGCAAATA 60.181 39.130 17.19 13.06 38.65 1.40
50 51 3.428534 GCTTTGTTTGGGAACGCAAATAG 59.571 43.478 17.19 15.13 38.65 1.73
51 52 4.616953 CTTTGTTTGGGAACGCAAATAGT 58.383 39.130 17.19 0.00 38.65 2.12
52 53 5.764131 CTTTGTTTGGGAACGCAAATAGTA 58.236 37.500 17.19 8.26 38.65 1.82
53 54 5.968528 TTGTTTGGGAACGCAAATAGTAT 57.031 34.783 17.19 0.00 38.65 2.12
54 55 7.450124 TTTGTTTGGGAACGCAAATAGTATA 57.550 32.000 17.19 1.26 38.65 1.47
55 56 7.633193 TTGTTTGGGAACGCAAATAGTATAT 57.367 32.000 17.19 0.00 38.65 0.86
56 57 7.633193 TGTTTGGGAACGCAAATAGTATATT 57.367 32.000 17.19 0.00 38.65 1.28
57 58 8.057536 TGTTTGGGAACGCAAATAGTATATTT 57.942 30.769 17.19 0.00 38.65 1.40
58 59 8.524487 TGTTTGGGAACGCAAATAGTATATTTT 58.476 29.630 17.19 0.00 38.65 1.82
62 63 8.623030 TGGGAACGCAAATAGTATATTTTAACC 58.377 33.333 0.00 0.00 0.00 2.85
202 203 8.476447 CAGAGGAAGTATATATCAGTGATGCAT 58.524 37.037 16.15 0.00 0.00 3.96
203 204 9.044646 AGAGGAAGTATATATCAGTGATGCATT 57.955 33.333 16.15 2.26 0.00 3.56
216 217 9.836864 ATCAGTGATGCATTTACTTACAGATTA 57.163 29.630 4.39 0.00 0.00 1.75
217 218 9.665719 TCAGTGATGCATTTACTTACAGATTAA 57.334 29.630 13.10 0.00 0.00 1.40
220 221 8.616076 GTGATGCATTTACTTACAGATTAAGCT 58.384 33.333 0.00 0.00 0.00 3.74
221 222 8.615211 TGATGCATTTACTTACAGATTAAGCTG 58.385 33.333 18.88 18.88 41.63 4.24
222 223 8.737168 ATGCATTTACTTACAGATTAAGCTGA 57.263 30.769 26.59 8.11 39.20 4.26
223 224 8.560355 TGCATTTACTTACAGATTAAGCTGAA 57.440 30.769 26.59 14.64 39.20 3.02
224 225 9.008965 TGCATTTACTTACAGATTAAGCTGAAA 57.991 29.630 26.59 15.69 39.20 2.69
243 244 9.103861 AGCTGAAATAATACTAGTGAAGAAAGC 57.896 33.333 5.39 5.52 0.00 3.51
244 245 9.103861 GCTGAAATAATACTAGTGAAGAAAGCT 57.896 33.333 5.39 0.00 0.00 3.74
273 7199 0.180642 TGCTTTTCACCGGTACCACA 59.819 50.000 6.87 0.00 0.00 4.17
276 7202 2.500229 CTTTTCACCGGTACCACATGT 58.500 47.619 6.87 0.00 0.00 3.21
299 7229 8.773404 TGTGCTAGGTCTAGAATTCTTTTTAC 57.227 34.615 14.36 6.91 35.21 2.01
301 7231 8.041919 GTGCTAGGTCTAGAATTCTTTTTACCT 58.958 37.037 23.16 23.16 39.38 3.08
302 7232 8.258708 TGCTAGGTCTAGAATTCTTTTTACCTC 58.741 37.037 23.24 15.52 37.32 3.85
344 7277 7.976734 ACCAAAACAATGACTACAAATTCGAAA 59.023 29.630 0.00 0.00 0.00 3.46
361 7294 3.065233 TCGAAAATTTCAGATCCATGGCG 59.935 43.478 6.96 0.00 0.00 5.69
367 7300 0.460109 TCAGATCCATGGCGTTGTCG 60.460 55.000 6.96 0.00 40.37 4.35
401 7334 6.035542 GGCAACGACAAATTTGAAAGAAAAGA 59.964 34.615 24.64 0.00 0.00 2.52
405 7338 6.972901 ACGACAAATTTGAAAGAAAAGAGGAC 59.027 34.615 24.64 0.00 0.00 3.85
411 7344 4.351874 TGAAAGAAAAGAGGACCATCGT 57.648 40.909 0.00 0.00 0.00 3.73
413 7346 4.202315 TGAAAGAAAAGAGGACCATCGTCA 60.202 41.667 0.00 0.00 41.13 4.35
417 7350 2.029838 AAGAGGACCATCGTCATTGC 57.970 50.000 0.00 0.00 41.13 3.56
422 7355 1.079197 ACCATCGTCATTGCGAGCA 60.079 52.632 8.64 0.00 44.43 4.26
423 7356 1.349627 CCATCGTCATTGCGAGCAC 59.650 57.895 0.00 0.00 44.43 4.40
432 7365 2.613595 TCATTGCGAGCACCATTACATC 59.386 45.455 0.00 0.00 0.00 3.06
436 7369 2.161410 TGCGAGCACCATTACATCAAAC 59.839 45.455 0.00 0.00 0.00 2.93
437 7370 2.161410 GCGAGCACCATTACATCAAACA 59.839 45.455 0.00 0.00 0.00 2.83
438 7371 3.365868 GCGAGCACCATTACATCAAACAA 60.366 43.478 0.00 0.00 0.00 2.83
440 7373 4.853196 CGAGCACCATTACATCAAACAAAG 59.147 41.667 0.00 0.00 0.00 2.77
441 7374 5.562696 CGAGCACCATTACATCAAACAAAGT 60.563 40.000 0.00 0.00 0.00 2.66
442 7375 6.160576 AGCACCATTACATCAAACAAAGTT 57.839 33.333 0.00 0.00 0.00 2.66
457 7390 5.606348 ACAAAGTTCCAAAAGCCACATTA 57.394 34.783 0.00 0.00 0.00 1.90
460 7393 4.584327 AGTTCCAAAAGCCACATTACAC 57.416 40.909 0.00 0.00 0.00 2.90
461 7394 3.004315 AGTTCCAAAAGCCACATTACACG 59.996 43.478 0.00 0.00 0.00 4.49
464 7397 3.823873 TCCAAAAGCCACATTACACGAAT 59.176 39.130 0.00 0.00 0.00 3.34
500 7433 4.142138 ACAAATTTACCAAACAGCGACCAA 60.142 37.500 0.00 0.00 0.00 3.67
503 7436 4.657436 TTTACCAAACAGCGACCAAATT 57.343 36.364 0.00 0.00 0.00 1.82
514 7447 6.512297 ACAGCGACCAAATTTAATCAAAGTT 58.488 32.000 0.00 0.00 32.42 2.66
515 7448 7.653647 ACAGCGACCAAATTTAATCAAAGTTA 58.346 30.769 0.00 0.00 31.15 2.24
516 7449 7.593644 ACAGCGACCAAATTTAATCAAAGTTAC 59.406 33.333 0.00 0.00 31.15 2.50
531 7464 5.823570 TCAAAGTTACCAAATTTCGGTCAGA 59.176 36.000 13.43 2.64 37.99 3.27
534 7467 4.514066 AGTTACCAAATTTCGGTCAGACAC 59.486 41.667 13.43 6.69 37.99 3.67
545 7478 1.611673 GGTCAGACACTTGGGGACATG 60.612 57.143 2.17 0.00 42.32 3.21
550 7483 3.198635 CAGACACTTGGGGACATGATACT 59.801 47.826 0.00 0.00 42.32 2.12
551 7484 4.405680 CAGACACTTGGGGACATGATACTA 59.594 45.833 0.00 0.00 42.32 1.82
552 7485 5.070981 CAGACACTTGGGGACATGATACTAT 59.929 44.000 0.00 0.00 42.32 2.12
558 7491 7.773224 CACTTGGGGACATGATACTATAAACAA 59.227 37.037 0.00 0.00 42.32 2.83
565 7498 8.621286 GGACATGATACTATAAACAACCCAAAG 58.379 37.037 0.00 0.00 0.00 2.77
566 7499 9.174166 GACATGATACTATAAACAACCCAAAGT 57.826 33.333 0.00 0.00 0.00 2.66
579 7512 6.579865 ACAACCCAAAGTAGACTAATATCCG 58.420 40.000 0.00 0.00 0.00 4.18
580 7513 5.803237 ACCCAAAGTAGACTAATATCCGG 57.197 43.478 0.00 0.00 0.00 5.14
591 7524 5.191124 AGACTAATATCCGGGTTTCCAGTTT 59.809 40.000 0.00 0.00 0.00 2.66
594 7527 1.073098 ATCCGGGTTTCCAGTTTCCT 58.927 50.000 0.00 0.00 0.00 3.36
595 7528 0.109723 TCCGGGTTTCCAGTTTCCTG 59.890 55.000 0.00 0.00 38.50 3.86
597 7530 1.687563 CGGGTTTCCAGTTTCCTGTT 58.312 50.000 0.00 0.00 36.95 3.16
598 7531 1.607148 CGGGTTTCCAGTTTCCTGTTC 59.393 52.381 0.00 0.00 36.95 3.18
599 7532 2.661718 GGGTTTCCAGTTTCCTGTTCA 58.338 47.619 0.00 0.00 36.95 3.18
601 7534 3.005791 GGGTTTCCAGTTTCCTGTTCATG 59.994 47.826 0.00 0.00 36.95 3.07
602 7535 3.888930 GGTTTCCAGTTTCCTGTTCATGA 59.111 43.478 0.00 0.00 36.95 3.07
603 7536 4.340950 GGTTTCCAGTTTCCTGTTCATGAA 59.659 41.667 3.38 3.38 36.95 2.57
604 7537 5.281727 GTTTCCAGTTTCCTGTTCATGAAC 58.718 41.667 28.10 28.10 41.50 3.18
606 7539 3.882888 TCCAGTTTCCTGTTCATGAACAC 59.117 43.478 32.36 23.05 45.42 3.32
607 7540 3.885297 CCAGTTTCCTGTTCATGAACACT 59.115 43.478 32.36 24.64 45.42 3.55
608 7541 5.063204 CCAGTTTCCTGTTCATGAACACTA 58.937 41.667 32.36 21.59 45.42 2.74
609 7542 5.180117 CCAGTTTCCTGTTCATGAACACTAG 59.820 44.000 32.36 23.45 45.42 2.57
610 7543 5.180117 CAGTTTCCTGTTCATGAACACTAGG 59.820 44.000 32.36 29.67 45.42 3.02
611 7544 4.974645 TTCCTGTTCATGAACACTAGGT 57.025 40.909 32.36 0.00 45.42 3.08
612 7545 6.042781 AGTTTCCTGTTCATGAACACTAGGTA 59.957 38.462 32.36 23.29 45.42 3.08
613 7546 5.661056 TCCTGTTCATGAACACTAGGTAG 57.339 43.478 32.36 21.57 45.42 3.18
614 7547 5.084519 TCCTGTTCATGAACACTAGGTAGT 58.915 41.667 32.36 0.00 45.42 2.73
623 7556 2.831685 CACTAGGTAGTGTGGTGCAA 57.168 50.000 8.73 0.00 46.51 4.08
624 7557 3.334583 CACTAGGTAGTGTGGTGCAAT 57.665 47.619 8.73 0.00 46.51 3.56
625 7558 3.674997 CACTAGGTAGTGTGGTGCAATT 58.325 45.455 8.73 0.00 46.51 2.32
626 7559 3.684788 CACTAGGTAGTGTGGTGCAATTC 59.315 47.826 8.73 0.00 46.51 2.17
627 7560 2.200373 AGGTAGTGTGGTGCAATTCC 57.800 50.000 0.00 0.00 33.62 3.01
628 7561 1.423541 AGGTAGTGTGGTGCAATTCCA 59.576 47.619 0.00 0.00 35.48 3.53
629 7562 2.158534 AGGTAGTGTGGTGCAATTCCAA 60.159 45.455 0.00 0.00 35.48 3.53
630 7563 2.625790 GGTAGTGTGGTGCAATTCCAAA 59.374 45.455 0.00 0.00 36.68 3.28
636 7569 4.152223 GTGTGGTGCAATTCCAAAAATAGC 59.848 41.667 0.00 0.00 36.68 2.97
648 7581 3.069443 CCAAAAATAGCAGTGTGGTGGTT 59.931 43.478 0.00 0.00 0.00 3.67
649 7582 4.050553 CAAAAATAGCAGTGTGGTGGTTG 58.949 43.478 0.00 0.00 0.00 3.77
650 7583 1.909700 AATAGCAGTGTGGTGGTTGG 58.090 50.000 0.00 0.00 0.00 3.77
651 7584 0.771127 ATAGCAGTGTGGTGGTTGGT 59.229 50.000 0.00 0.00 0.00 3.67
653 7586 2.489275 GCAGTGTGGTGGTTGGTGG 61.489 63.158 0.00 0.00 0.00 4.61
722 7675 1.831736 ACTGCCAGCGGAATACTAGTT 59.168 47.619 0.00 0.00 0.00 2.24
743 7699 9.227490 CTAGTTGTAGTATTGTTCGAGAATGAG 57.773 37.037 2.78 0.00 0.00 2.90
749 7709 9.866936 GTAGTATTGTTCGAGAATGAGTACTAG 57.133 37.037 0.00 0.00 0.00 2.57
750 7710 8.508883 AGTATTGTTCGAGAATGAGTACTAGT 57.491 34.615 0.00 0.00 0.00 2.57
751 7711 9.610705 AGTATTGTTCGAGAATGAGTACTAGTA 57.389 33.333 0.00 0.00 0.00 1.82
752 7712 9.649024 GTATTGTTCGAGAATGAGTACTAGTAC 57.351 37.037 23.03 23.03 36.35 2.73
876 7846 1.596260 CGTGATGACTGATGACCATGC 59.404 52.381 0.00 0.00 0.00 4.06
886 7856 4.256110 CTGATGACCATGCAACTGAGTAA 58.744 43.478 0.00 0.00 0.00 2.24
956 7932 0.320073 TTCTTACGACAAGGGGCGTG 60.320 55.000 5.75 0.00 41.35 5.34
958 7934 3.887335 TTACGACAAGGGGCGTGGC 62.887 63.158 5.75 0.00 41.35 5.01
980 7956 2.029020 TGTGGTCTGGATTCTTGACGAG 60.029 50.000 0.00 0.00 0.00 4.18
981 7957 2.028930 GTGGTCTGGATTCTTGACGAGT 60.029 50.000 0.00 0.00 0.00 4.18
982 7958 3.192844 GTGGTCTGGATTCTTGACGAGTA 59.807 47.826 0.00 0.00 0.00 2.59
983 7959 3.192844 TGGTCTGGATTCTTGACGAGTAC 59.807 47.826 0.00 0.00 0.00 2.73
1156 8164 0.176449 CATCCACCATGAGAGACGCA 59.824 55.000 0.00 0.00 33.80 5.24
1157 8165 0.463204 ATCCACCATGAGAGACGCAG 59.537 55.000 0.00 0.00 0.00 5.18
1158 8166 1.812922 CCACCATGAGAGACGCAGC 60.813 63.158 0.00 0.00 0.00 5.25
1159 8167 1.217511 CACCATGAGAGACGCAGCT 59.782 57.895 0.00 0.00 0.00 4.24
1161 8169 0.743688 ACCATGAGAGACGCAGCTAG 59.256 55.000 0.00 0.00 0.00 3.42
1162 8170 0.597118 CCATGAGAGACGCAGCTAGC 60.597 60.000 6.62 6.62 40.87 3.42
1185 8193 2.125350 GAGACCAGGAAGCTGCCG 60.125 66.667 4.63 0.00 0.00 5.69
1209 8221 3.393800 GGTATCTGTCCAATCGACCATG 58.606 50.000 0.00 0.00 41.18 3.66
1226 8245 1.577328 ATGAGCTGAACGTTTGGGCG 61.577 55.000 0.46 0.00 37.94 6.13
1228 8247 3.959975 GCTGAACGTTTGGGCGCA 61.960 61.111 10.83 0.00 34.88 6.09
1541 8569 8.156994 CCTCAAGAAGGTACTACATACTACTC 57.843 42.308 0.00 0.00 38.49 2.59
1542 8570 7.229106 CCTCAAGAAGGTACTACATACTACTCC 59.771 44.444 0.00 0.00 38.49 3.85
1999 9234 6.966632 CGATGACTTCACAAGTTTTCTTCAAA 59.033 34.615 0.00 0.00 43.03 2.69
2378 9639 3.851976 AGAAGTCGCGTCTATGTTTCT 57.148 42.857 6.24 2.48 0.00 2.52
2384 9645 3.302699 GTCGCGTCTATGTTTCTTGGTAC 59.697 47.826 5.77 0.00 0.00 3.34
2546 9812 4.559862 AGGTAAGTGCTCAATGCTACTT 57.440 40.909 0.00 0.00 41.84 2.24
2550 9816 7.112779 AGGTAAGTGCTCAATGCTACTTTTAT 58.887 34.615 0.00 0.00 40.61 1.40
2691 9983 7.921786 TTCCTACTATTGAATGTTGAAGGTG 57.078 36.000 0.00 0.00 0.00 4.00
2734 10026 9.965824 AAAAGTTTTGATCCACTTGTATAACTG 57.034 29.630 0.00 0.00 33.38 3.16
2817 10118 8.114905 GCTAACCGTCACTAGACAATATTTTTC 58.885 37.037 0.00 0.00 45.23 2.29
3026 10353 9.683069 CTACAATGTTCTTTCAAACTAAGCATT 57.317 29.630 0.00 0.00 0.00 3.56
3242 10604 9.739276 AAATTAGTTCTTCTGTTGATCCACATA 57.261 29.630 0.00 0.00 0.00 2.29
3560 10950 4.095932 CAGCTGCAACATCATATTGTGACT 59.904 41.667 0.00 0.00 40.28 3.41
3671 11079 3.691609 GTCTCCCATGTGAGTTCAATTCC 59.308 47.826 5.05 0.00 33.93 3.01
3681 11090 5.763204 TGTGAGTTCAATTCCTAAAGTGGAC 59.237 40.000 0.00 0.00 38.89 4.02
3740 11154 8.610248 TTTTACTTGAACTTTACCGATGATCA 57.390 30.769 0.00 0.00 0.00 2.92
3752 11167 5.398603 ACCGATGATCAGTATCCATTCTC 57.601 43.478 0.09 0.00 0.00 2.87
3753 11168 5.083122 ACCGATGATCAGTATCCATTCTCT 58.917 41.667 0.09 0.00 0.00 3.10
4119 11615 6.451064 ACATTAGTTGCTAATACAAAGGGC 57.549 37.500 1.62 0.00 34.83 5.19
4136 11632 3.994317 AGGGCCCTATAGCAACAATTTT 58.006 40.909 27.42 0.00 0.00 1.82
4423 12611 8.908903 TCACTGTTTTAATCACATTAACCTTGT 58.091 29.630 0.00 0.00 34.68 3.16
4477 12665 2.723209 GCCAACACCGACAAACTTAAC 58.277 47.619 0.00 0.00 0.00 2.01
4487 12675 6.849305 CACCGACAAACTTAACTACAATTGTC 59.151 38.462 15.85 6.42 41.81 3.18
4489 12677 7.066043 ACCGACAAACTTAACTACAATTGTCAA 59.934 33.333 15.85 4.69 44.11 3.18
4505 12693 9.113838 ACAATTGTCAATAGGTCATTATGAGAC 57.886 33.333 4.92 0.00 35.29 3.36
4574 12765 1.337118 TGCCAAACCCTAAAAGCCTG 58.663 50.000 0.00 0.00 0.00 4.85
4935 14031 5.988287 TGATCTGTGGTTAGCATTACATCA 58.012 37.500 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.357980 CAATCGTCGTTTCAGATTGGATATG 58.642 40.000 8.93 0.00 44.29 1.78
1 2 6.530913 CAATCGTCGTTTCAGATTGGATAT 57.469 37.500 8.93 0.00 44.29 1.63
3 4 4.864916 CAATCGTCGTTTCAGATTGGAT 57.135 40.909 8.93 0.00 44.29 3.41
17 18 3.300009 CCAAACAAAGCAGACAATCGTC 58.700 45.455 0.00 0.00 42.95 4.20
18 19 2.034558 CCCAAACAAAGCAGACAATCGT 59.965 45.455 0.00 0.00 0.00 3.73
19 20 2.293122 TCCCAAACAAAGCAGACAATCG 59.707 45.455 0.00 0.00 0.00 3.34
20 21 4.051237 GTTCCCAAACAAAGCAGACAATC 58.949 43.478 0.00 0.00 35.36 2.67
21 22 3.490761 CGTTCCCAAACAAAGCAGACAAT 60.491 43.478 0.00 0.00 34.93 2.71
22 23 2.159310 CGTTCCCAAACAAAGCAGACAA 60.159 45.455 0.00 0.00 34.93 3.18
23 24 1.403679 CGTTCCCAAACAAAGCAGACA 59.596 47.619 0.00 0.00 34.93 3.41
25 26 0.383949 GCGTTCCCAAACAAAGCAGA 59.616 50.000 0.00 0.00 34.93 4.26
26 27 0.102120 TGCGTTCCCAAACAAAGCAG 59.898 50.000 0.00 0.00 34.93 4.24
27 28 0.532573 TTGCGTTCCCAAACAAAGCA 59.467 45.000 0.00 0.00 34.93 3.91
29 30 4.616953 ACTATTTGCGTTCCCAAACAAAG 58.383 39.130 0.00 0.00 37.51 2.77
30 31 4.657436 ACTATTTGCGTTCCCAAACAAA 57.343 36.364 0.00 0.00 37.51 2.83
31 32 5.968528 ATACTATTTGCGTTCCCAAACAA 57.031 34.783 0.00 0.00 37.51 2.83
32 33 7.633193 AATATACTATTTGCGTTCCCAAACA 57.367 32.000 0.00 0.00 37.51 2.83
36 37 8.623030 GGTTAAAATATACTATTTGCGTTCCCA 58.377 33.333 0.00 0.00 0.00 4.37
37 38 8.623030 TGGTTAAAATATACTATTTGCGTTCCC 58.377 33.333 0.00 0.00 0.00 3.97
174 175 8.961634 GCATCACTGATATATACTTCCTCTGTA 58.038 37.037 0.00 0.00 0.00 2.74
175 176 7.452813 TGCATCACTGATATATACTTCCTCTGT 59.547 37.037 0.00 0.00 0.00 3.41
176 177 7.834803 TGCATCACTGATATATACTTCCTCTG 58.165 38.462 0.00 0.00 0.00 3.35
177 178 8.606754 ATGCATCACTGATATATACTTCCTCT 57.393 34.615 0.00 0.00 0.00 3.69
178 179 9.664332 AAATGCATCACTGATATATACTTCCTC 57.336 33.333 0.00 0.00 0.00 3.71
189 190 9.836864 AATCTGTAAGTAAATGCATCACTGATA 57.163 29.630 13.11 5.24 33.76 2.15
191 192 9.665719 TTAATCTGTAAGTAAATGCATCACTGA 57.334 29.630 13.11 4.84 33.76 3.41
192 193 9.926751 CTTAATCTGTAAGTAAATGCATCACTG 57.073 33.333 13.11 3.39 33.76 3.66
193 194 8.616076 GCTTAATCTGTAAGTAAATGCATCACT 58.384 33.333 0.00 3.66 33.76 3.41
195 196 8.615211 CAGCTTAATCTGTAAGTAAATGCATCA 58.385 33.333 0.00 0.00 33.76 3.07
196 197 8.830580 TCAGCTTAATCTGTAAGTAAATGCATC 58.169 33.333 0.00 0.00 35.63 3.91
197 198 8.737168 TCAGCTTAATCTGTAAGTAAATGCAT 57.263 30.769 6.23 0.00 35.63 3.96
198 199 8.560355 TTCAGCTTAATCTGTAAGTAAATGCA 57.440 30.769 6.23 0.00 35.63 3.96
217 218 9.103861 GCTTTCTTCACTAGTATTATTTCAGCT 57.896 33.333 0.00 0.00 0.00 4.24
225 226 8.842280 GCTCTCTAGCTTTCTTCACTAGTATTA 58.158 37.037 0.00 0.00 45.85 0.98
226 227 7.712797 GCTCTCTAGCTTTCTTCACTAGTATT 58.287 38.462 0.00 0.00 45.85 1.89
227 228 7.272037 GCTCTCTAGCTTTCTTCACTAGTAT 57.728 40.000 0.00 0.00 45.85 2.12
229 230 5.576447 GCTCTCTAGCTTTCTTCACTAGT 57.424 43.478 0.00 0.00 45.85 2.57
242 243 2.414825 GTGAAAAGCACAGCTCTCTAGC 59.585 50.000 0.00 0.00 46.91 3.42
253 254 0.589708 GTGGTACCGGTGAAAAGCAC 59.410 55.000 19.93 19.13 46.98 4.40
254 255 0.180642 TGTGGTACCGGTGAAAAGCA 59.819 50.000 19.93 10.49 0.00 3.91
255 256 1.199097 CATGTGGTACCGGTGAAAAGC 59.801 52.381 19.93 7.43 0.00 3.51
256 257 2.225491 CACATGTGGTACCGGTGAAAAG 59.775 50.000 19.93 3.49 0.00 2.27
261 7187 0.248012 TAGCACATGTGGTACCGGTG 59.752 55.000 29.05 16.85 41.96 4.94
273 7199 9.384764 GTAAAAAGAATTCTAGACCTAGCACAT 57.615 33.333 8.75 0.00 33.32 3.21
276 7202 8.147244 AGGTAAAAAGAATTCTAGACCTAGCA 57.853 34.615 20.65 0.00 34.30 3.49
305 7235 9.670719 GTCATTGTTTTGGTTTTCTTTCAAAAA 57.329 25.926 0.00 0.00 40.54 1.94
319 7251 7.922505 TTCGAATTTGTAGTCATTGTTTTGG 57.077 32.000 0.00 0.00 0.00 3.28
344 7277 3.091545 ACAACGCCATGGATCTGAAATT 58.908 40.909 18.40 0.00 0.00 1.82
382 7315 7.264947 TGGTCCTCTTTTCTTTCAAATTTGTC 58.735 34.615 17.47 0.00 0.00 3.18
401 7334 0.179100 CTCGCAATGACGATGGTCCT 60.179 55.000 5.33 0.00 42.73 3.85
405 7338 1.349627 GTGCTCGCAATGACGATGG 59.650 57.895 0.00 0.00 42.02 3.51
411 7344 2.106477 TGTAATGGTGCTCGCAATGA 57.894 45.000 0.00 0.00 0.00 2.57
413 7346 2.642427 TGATGTAATGGTGCTCGCAAT 58.358 42.857 0.00 0.00 0.00 3.56
417 7350 4.418013 TTGTTTGATGTAATGGTGCTCG 57.582 40.909 0.00 0.00 0.00 5.03
422 7355 6.723298 TGGAACTTTGTTTGATGTAATGGT 57.277 33.333 0.00 0.00 0.00 3.55
423 7356 8.430801 TTTTGGAACTTTGTTTGATGTAATGG 57.569 30.769 0.00 0.00 0.00 3.16
432 7365 3.999663 TGTGGCTTTTGGAACTTTGTTTG 59.000 39.130 0.00 0.00 0.00 2.93
436 7369 5.234116 GTGTAATGTGGCTTTTGGAACTTTG 59.766 40.000 0.00 0.00 0.00 2.77
437 7370 5.356426 GTGTAATGTGGCTTTTGGAACTTT 58.644 37.500 0.00 0.00 0.00 2.66
438 7371 4.499019 CGTGTAATGTGGCTTTTGGAACTT 60.499 41.667 0.00 0.00 0.00 2.66
440 7373 3.003897 TCGTGTAATGTGGCTTTTGGAAC 59.996 43.478 0.00 0.00 0.00 3.62
441 7374 3.215151 TCGTGTAATGTGGCTTTTGGAA 58.785 40.909 0.00 0.00 0.00 3.53
442 7375 2.852449 TCGTGTAATGTGGCTTTTGGA 58.148 42.857 0.00 0.00 0.00 3.53
457 7390 3.181471 TGTTGCCAAAATTCCATTCGTGT 60.181 39.130 0.00 0.00 0.00 4.49
460 7393 5.610235 ATTTGTTGCCAAAATTCCATTCG 57.390 34.783 0.00 0.00 43.43 3.34
461 7394 7.807433 GGTAAATTTGTTGCCAAAATTCCATTC 59.193 33.333 0.00 0.00 43.43 2.67
464 7397 6.122277 TGGTAAATTTGTTGCCAAAATTCCA 58.878 32.000 0.00 4.28 43.43 3.53
474 7407 3.799420 TCGCTGTTTGGTAAATTTGTTGC 59.201 39.130 0.00 0.00 0.00 4.17
493 7426 6.864165 TGGTAACTTTGATTAAATTTGGTCGC 59.136 34.615 0.00 0.00 37.61 5.19
503 7436 8.630917 TGACCGAAATTTGGTAACTTTGATTAA 58.369 29.630 4.61 0.00 40.63 1.40
514 7447 4.345859 AGTGTCTGACCGAAATTTGGTA 57.654 40.909 4.61 0.00 40.63 3.25
515 7448 3.208747 AGTGTCTGACCGAAATTTGGT 57.791 42.857 4.21 4.21 44.10 3.67
516 7449 3.304659 CCAAGTGTCTGACCGAAATTTGG 60.305 47.826 5.17 5.66 39.49 3.28
526 7459 1.347707 TCATGTCCCCAAGTGTCTGAC 59.652 52.381 0.00 0.00 0.00 3.51
531 7464 7.092623 TGTTTATAGTATCATGTCCCCAAGTGT 60.093 37.037 0.00 0.00 0.00 3.55
534 7467 7.228706 GGTTGTTTATAGTATCATGTCCCCAAG 59.771 40.741 0.00 0.00 0.00 3.61
552 7485 9.895138 GGATATTAGTCTACTTTGGGTTGTTTA 57.105 33.333 0.00 0.00 0.00 2.01
558 7491 4.591924 CCCGGATATTAGTCTACTTTGGGT 59.408 45.833 0.73 0.00 0.00 4.51
565 7498 5.303845 ACTGGAAACCCGGATATTAGTCTAC 59.696 44.000 0.73 0.00 34.16 2.59
566 7499 5.461327 ACTGGAAACCCGGATATTAGTCTA 58.539 41.667 0.73 0.00 34.16 2.59
573 7506 2.850568 AGGAAACTGGAAACCCGGATAT 59.149 45.455 0.73 0.00 41.13 1.63
605 7538 3.307480 GGAATTGCACCACACTACCTAGT 60.307 47.826 0.00 0.00 36.90 2.57
606 7539 3.270877 GGAATTGCACCACACTACCTAG 58.729 50.000 0.00 0.00 0.00 3.02
607 7540 2.640332 TGGAATTGCACCACACTACCTA 59.360 45.455 0.00 0.00 32.03 3.08
608 7541 1.423541 TGGAATTGCACCACACTACCT 59.576 47.619 0.00 0.00 32.03 3.08
609 7542 1.904287 TGGAATTGCACCACACTACC 58.096 50.000 0.00 0.00 32.03 3.18
610 7543 4.314740 TTTTGGAATTGCACCACACTAC 57.685 40.909 0.00 0.00 37.13 2.73
611 7544 5.543507 ATTTTTGGAATTGCACCACACTA 57.456 34.783 0.00 0.00 37.13 2.74
612 7545 3.902881 TTTTTGGAATTGCACCACACT 57.097 38.095 0.00 0.00 37.13 3.55
613 7546 4.152223 GCTATTTTTGGAATTGCACCACAC 59.848 41.667 0.00 0.00 37.13 3.82
614 7547 4.202295 TGCTATTTTTGGAATTGCACCACA 60.202 37.500 0.00 0.00 37.13 4.17
615 7548 4.314121 TGCTATTTTTGGAATTGCACCAC 58.686 39.130 0.00 0.00 37.13 4.16
616 7549 4.040217 ACTGCTATTTTTGGAATTGCACCA 59.960 37.500 0.00 0.00 34.46 4.17
617 7550 4.389687 CACTGCTATTTTTGGAATTGCACC 59.610 41.667 0.00 0.00 34.46 5.01
618 7551 4.990426 ACACTGCTATTTTTGGAATTGCAC 59.010 37.500 0.00 0.00 34.46 4.57
619 7552 4.989797 CACACTGCTATTTTTGGAATTGCA 59.010 37.500 0.00 0.00 36.38 4.08
620 7553 4.389687 CCACACTGCTATTTTTGGAATTGC 59.610 41.667 0.00 0.00 0.00 3.56
621 7554 5.406175 CACCACACTGCTATTTTTGGAATTG 59.594 40.000 0.00 0.00 0.00 2.32
622 7555 5.511202 CCACCACACTGCTATTTTTGGAATT 60.511 40.000 0.00 0.00 0.00 2.17
623 7556 4.021192 CCACCACACTGCTATTTTTGGAAT 60.021 41.667 0.00 0.00 0.00 3.01
624 7557 3.320541 CCACCACACTGCTATTTTTGGAA 59.679 43.478 0.00 0.00 0.00 3.53
625 7558 2.890311 CCACCACACTGCTATTTTTGGA 59.110 45.455 0.00 0.00 0.00 3.53
626 7559 2.627699 ACCACCACACTGCTATTTTTGG 59.372 45.455 0.00 0.00 0.00 3.28
627 7560 4.050553 CAACCACCACACTGCTATTTTTG 58.949 43.478 0.00 0.00 0.00 2.44
628 7561 3.069443 CCAACCACCACACTGCTATTTTT 59.931 43.478 0.00 0.00 0.00 1.94
629 7562 2.627699 CCAACCACCACACTGCTATTTT 59.372 45.455 0.00 0.00 0.00 1.82
630 7563 2.238521 CCAACCACCACACTGCTATTT 58.761 47.619 0.00 0.00 0.00 1.40
636 7569 1.077068 ACCACCAACCACCACACTG 60.077 57.895 0.00 0.00 0.00 3.66
653 7586 1.080025 GCAGTCTACGGTCCACCAC 60.080 63.158 0.00 0.00 35.14 4.16
722 7675 8.277490 AGTACTCATTCTCGAACAATACTACA 57.723 34.615 0.00 0.00 0.00 2.74
731 7687 6.343226 ACGTACTAGTACTCATTCTCGAAC 57.657 41.667 26.36 2.89 34.04 3.95
743 7699 9.549078 ACCTTCCTAAATACTACGTACTAGTAC 57.451 37.037 21.06 21.06 40.18 2.73
749 7709 7.640240 CGTGTTACCTTCCTAAATACTACGTAC 59.360 40.741 0.00 0.00 0.00 3.67
750 7710 7.335924 ACGTGTTACCTTCCTAAATACTACGTA 59.664 37.037 0.00 0.00 36.86 3.57
751 7711 6.151144 ACGTGTTACCTTCCTAAATACTACGT 59.849 38.462 0.00 0.00 34.26 3.57
752 7712 6.555315 ACGTGTTACCTTCCTAAATACTACG 58.445 40.000 0.00 0.00 0.00 3.51
912 7887 1.265365 GTGGCAAGCAAGACTGTTCTC 59.735 52.381 0.00 0.00 0.00 2.87
956 7932 1.003580 TCAAGAATCCAGACCACAGCC 59.996 52.381 0.00 0.00 0.00 4.85
958 7934 2.029020 TCGTCAAGAATCCAGACCACAG 60.029 50.000 0.00 0.00 0.00 3.66
964 7940 3.759527 CGTACTCGTCAAGAATCCAGA 57.240 47.619 0.00 0.00 0.00 3.86
980 7956 2.729675 GCGCCCCAAACGTACGTAC 61.730 63.158 23.12 15.90 0.00 3.67
981 7957 2.432285 GCGCCCCAAACGTACGTA 60.432 61.111 23.12 0.00 0.00 3.57
1011 7987 2.363018 GGCTTGGCTTTCCCTCCC 60.363 66.667 0.00 0.00 0.00 4.30
1156 8164 1.476110 CCTGGTCTCTCTACGCTAGCT 60.476 57.143 13.93 2.46 0.00 3.32
1157 8165 0.948678 CCTGGTCTCTCTACGCTAGC 59.051 60.000 4.06 4.06 0.00 3.42
1158 8166 2.623878 TCCTGGTCTCTCTACGCTAG 57.376 55.000 0.00 0.00 0.00 3.42
1159 8167 2.920524 CTTCCTGGTCTCTCTACGCTA 58.079 52.381 0.00 0.00 0.00 4.26
1161 8169 0.101579 GCTTCCTGGTCTCTCTACGC 59.898 60.000 0.00 0.00 0.00 4.42
1162 8170 1.403679 CAGCTTCCTGGTCTCTCTACG 59.596 57.143 0.00 0.00 35.38 3.51
1163 8171 1.136110 GCAGCTTCCTGGTCTCTCTAC 59.864 57.143 0.00 0.00 39.54 2.59
1164 8172 1.479709 GCAGCTTCCTGGTCTCTCTA 58.520 55.000 0.00 0.00 39.54 2.43
1165 8173 1.264045 GGCAGCTTCCTGGTCTCTCT 61.264 60.000 0.00 0.00 39.54 3.10
1166 8174 1.220477 GGCAGCTTCCTGGTCTCTC 59.780 63.158 0.00 0.00 39.54 3.20
1167 8175 2.654079 CGGCAGCTTCCTGGTCTCT 61.654 63.158 0.00 0.00 39.54 3.10
1185 8193 0.387929 TCGATTGGACAGATACCGCC 59.612 55.000 0.00 0.00 0.00 6.13
1209 8221 2.556287 CGCCCAAACGTTCAGCTC 59.444 61.111 0.00 0.00 0.00 4.09
1226 8245 1.000233 CTCTGCATGCAAACGTGTGC 61.000 55.000 24.10 24.10 45.15 4.57
1228 8247 1.951510 CCTCTGCATGCAAACGTGT 59.048 52.632 22.88 0.00 35.09 4.49
1542 8570 1.001764 TCCCATGCCAGTTGAGCTG 60.002 57.895 0.00 0.00 44.63 4.24
1868 9092 8.522830 CCAATTCCTTGTCTACACAACAATTAT 58.477 33.333 0.00 0.00 37.61 1.28
1885 9112 1.185315 CCCAATGTCGCCAATTCCTT 58.815 50.000 0.00 0.00 0.00 3.36
1944 9172 4.946784 ACTAGGAAACGATTTGCATCAC 57.053 40.909 0.00 0.00 32.92 3.06
2378 9639 6.921486 TCTTCCACTAATAGTGTGTACCAA 57.079 37.500 18.00 2.11 44.50 3.67
2416 9682 6.773976 TTCTGTGAAAAGGAATGAAACACT 57.226 33.333 0.00 0.00 0.00 3.55
2417 9683 6.811170 TGTTTCTGTGAAAAGGAATGAAACAC 59.189 34.615 12.40 0.00 43.39 3.32
2562 9828 7.969536 GCATATGCTTTAGACAAGGATTAGA 57.030 36.000 20.64 0.00 38.21 2.10
2691 9983 4.642429 ACTTTTGACCTCCAGTGATACAC 58.358 43.478 0.00 0.00 34.10 2.90
2817 10118 4.398319 AGAGTGGGGTTACTTTTCACATG 58.602 43.478 0.00 0.00 0.00 3.21
3008 10335 9.539825 TTTTGCATAATGCTTAGTTTGAAAGAA 57.460 25.926 0.00 0.00 45.31 2.52
3386 10751 8.593945 TCCTATTTGAAACTAGCAAATCCATT 57.406 30.769 9.29 0.00 42.95 3.16
3427 10804 5.640357 CCTGCAACATTGATAAATGCAAAGT 59.360 36.000 2.36 0.00 45.37 2.66
3428 10805 5.640357 ACCTGCAACATTGATAAATGCAAAG 59.360 36.000 2.36 0.00 45.37 2.77
3429 10806 5.408909 CACCTGCAACATTGATAAATGCAAA 59.591 36.000 2.36 0.00 45.37 3.68
3716 11130 7.876068 ACTGATCATCGGTAAAGTTCAAGTAAA 59.124 33.333 0.00 0.00 33.46 2.01
3717 11131 7.383687 ACTGATCATCGGTAAAGTTCAAGTAA 58.616 34.615 0.00 0.00 33.46 2.24
3718 11132 6.931838 ACTGATCATCGGTAAAGTTCAAGTA 58.068 36.000 0.00 0.00 33.46 2.24
3762 11177 6.039616 GGTGTCAATTTGTGAAAACAAGCTA 58.960 36.000 0.00 0.00 38.23 3.32
4119 11615 4.734398 TGCCAAAATTGTTGCTATAGGG 57.266 40.909 1.04 0.00 0.00 3.53
4505 12693 4.466370 TGGGGTTATCTCGCTAGAATATGG 59.534 45.833 0.00 0.00 34.73 2.74
4696 13791 8.193250 AGAAAATTGTGCATTTCATAGCATTC 57.807 30.769 11.89 0.00 43.44 2.67
4935 14031 3.263425 CAGGATTATATACGGTGGGGCTT 59.737 47.826 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.