Multiple sequence alignment - TraesCS5D01G088300

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 TraesCS5D01G088300 chr5D 100.000 8623 0 0 1 8623 94063423 94072045 0.000000e+00 15924.0
1 TraesCS5D01G088300 chr5D 87.020 963 113 8 3780 4733 9377195 9378154 0.000000e+00 1075.0
2 TraesCS5D01G088300 chr5D 86.102 957 116 8 3951 4898 9371652 9372600 0.000000e+00 1014.0
3 TraesCS5D01G088300 chr5D 85.256 936 105 17 3972 4898 9353900 9354811 0.000000e+00 933.0
4 TraesCS5D01G088300 chr5D 84.018 438 46 18 3125 3559 9376677 9377093 4.850000e-107 399.0
5 TraesCS5D01G088300 chr5D 83.790 438 48 17 3125 3559 9353427 9353844 2.260000e-105 394.0
6 TraesCS5D01G088300 chr5D 90.066 151 12 3 3125 3274 9371508 9371656 8.830000e-45 193.0
7 TraesCS5D01G088300 chr5D 92.969 128 9 0 3059 3186 9353303 9353430 4.110000e-43 187.0
8 TraesCS5D01G088300 chr5D 92.969 128 9 0 3059 3186 9376553 9376680 4.110000e-43 187.0
9 TraesCS5D01G088300 chr5D 92.188 128 10 0 3059 3186 9371384 9371511 1.910000e-41 182.0
10 TraesCS5D01G088300 chr5A 95.330 4582 136 16 478 5042 88023361 88027881 0.000000e+00 7204.0
11 TraesCS5D01G088300 chr5A 95.723 1777 61 12 5842 7613 88028660 88030426 0.000000e+00 2846.0
12 TraesCS5D01G088300 chr5A 93.782 788 24 11 5039 5822 88027907 88028673 0.000000e+00 1160.0
13 TraesCS5D01G088300 chr5A 93.642 519 18 4 7717 8233 88030509 88031014 0.000000e+00 761.0
14 TraesCS5D01G088300 chr5A 86.942 291 20 6 8330 8620 88031341 88031613 2.340000e-80 311.0
15 TraesCS5D01G088300 chr5A 96.364 55 2 0 7596 7650 88030443 88030497 3.310000e-14 91.6
16 TraesCS5D01G088300 chr5A 81.651 109 17 3 223 330 593223474 593223580 4.290000e-13 87.9
17 TraesCS5D01G088300 chr5B 95.494 3595 99 23 355 3918 101414714 101418276 0.000000e+00 5683.0
18 TraesCS5D01G088300 chr5B 92.575 1697 77 25 5842 7513 101420275 101421947 0.000000e+00 2390.0
19 TraesCS5D01G088300 chr5B 96.092 1126 42 1 3916 5041 101418358 101419481 0.000000e+00 1834.0
20 TraesCS5D01G088300 chr5B 95.063 790 24 10 5039 5822 101419508 101420288 0.000000e+00 1229.0
21 TraesCS5D01G088300 chr5B 90.441 680 37 13 7581 8242 101422113 101422782 0.000000e+00 870.0
22 TraesCS5D01G088300 chr5B 87.179 312 38 2 8309 8620 101422983 101423292 3.830000e-93 353.0
23 TraesCS5D01G088300 chr5B 90.654 214 19 1 125 338 101414518 101414730 5.100000e-72 283.0
24 TraesCS5D01G088300 chr6A 87.239 2829 265 50 2260 5039 601223159 601225940 0.000000e+00 3136.0
25 TraesCS5D01G088300 chr6A 82.834 1002 125 29 986 1971 601222179 601223149 0.000000e+00 854.0
26 TraesCS5D01G088300 chr6A 80.458 568 61 21 5854 6388 601226769 601227319 1.050000e-103 388.0
27 TraesCS5D01G088300 chr6A 85.921 277 34 2 5536 5810 601226493 601226766 3.050000e-74 291.0
28 TraesCS5D01G088300 chr6A 79.125 297 44 10 5099 5392 601226127 601226408 1.140000e-43 189.0
29 TraesCS5D01G088300 chr6A 87.179 78 4 4 7310 7381 601228239 601228316 5.550000e-12 84.2
30 TraesCS5D01G088300 chr6B 87.445 2748 251 48 2260 4964 692025794 692028490 0.000000e+00 3077.0
31 TraesCS5D01G088300 chr6B 83.117 1001 120 30 986 1971 692024818 692025784 0.000000e+00 867.0
32 TraesCS5D01G088300 chr6B 82.046 479 57 18 6600 7056 692030280 692030751 1.760000e-101 381.0
33 TraesCS5D01G088300 chr6B 79.528 508 53 20 5906 6388 692029281 692029762 1.810000e-81 315.0
34 TraesCS5D01G088300 chr6B 85.921 277 34 3 5536 5810 692028945 692029218 3.050000e-74 291.0
35 TraesCS5D01G088300 chr6B 85.135 74 6 4 7307 7375 692031000 692031073 4.320000e-08 71.3
36 TraesCS5D01G088300 chr6D 86.650 2824 273 50 2260 5039 454931806 454934569 0.000000e+00 3031.0
37 TraesCS5D01G088300 chr6D 83.234 1002 120 30 986 1971 454930827 454931796 0.000000e+00 876.0
38 TraesCS5D01G088300 chr6D 80.505 554 57 22 5868 6388 454935322 454935857 2.270000e-100 377.0
39 TraesCS5D01G088300 chr6D 86.643 277 32 3 5536 5810 454935039 454935312 1.410000e-77 302.0
40 TraesCS5D01G088300 chr6D 79.239 289 42 7 5099 5384 454934673 454934946 1.480000e-42 185.0
41 TraesCS5D01G088300 chr6D 86.111 108 13 1 8515 8620 471328459 471328566 1.970000e-21 115.0
42 TraesCS5D01G088300 chr6D 87.805 82 3 5 7307 7381 454936774 454936855 1.190000e-13 89.8
43 TraesCS5D01G088300 chr2B 81.664 1647 220 42 3278 4898 371892632 371894222 0.000000e+00 1293.0
44 TraesCS5D01G088300 chr2B 88.312 154 16 2 3125 3278 371878737 371878888 5.320000e-42 183.0
45 TraesCS5D01G088300 chr2B 86.111 108 13 1 8515 8620 30536413 30536306 1.970000e-21 115.0
46 TraesCS5D01G088300 chr3A 83.160 576 65 20 3213 3774 207777239 207776682 1.670000e-136 497.0
47 TraesCS5D01G088300 chr3D 91.603 131 11 0 3059 3189 170178556 170178426 1.910000e-41 182.0
48 TraesCS5D01G088300 chr3D 85.185 108 14 1 8515 8620 37977588 37977695 9.150000e-20 110.0
49 TraesCS5D01G088300 chrUn 84.259 108 15 1 8515 8620 236204869 236204976 4.260000e-18 104.0
50 TraesCS5D01G088300 chr7B 83.333 108 16 2 8515 8620 637486137 637486030 1.980000e-16 99.0
51 TraesCS5D01G088300 chr2D 84.884 86 9 4 8537 8620 99728313 99728396 5.550000e-12 84.2
52 TraesCS5D01G088300 chr1D 91.525 59 5 0 8515 8573 359831482 359831540 2.000000e-11 82.4


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 TraesCS5D01G088300 chr5D 94063423 94072045 8622 False 15924.000000 15924 100.000000 1 8623 1 chr5D.!!$F1 8622
1 TraesCS5D01G088300 chr5D 9371384 9378154 6770 False 508.333333 1075 88.727167 3059 4898 6 chr5D.!!$F3 1839
2 TraesCS5D01G088300 chr5D 9353303 9354811 1508 False 504.666667 933 87.338333 3059 4898 3 chr5D.!!$F2 1839
3 TraesCS5D01G088300 chr5A 88023361 88031613 8252 False 2062.266667 7204 93.630500 478 8620 6 chr5A.!!$F2 8142
4 TraesCS5D01G088300 chr5B 101414518 101423292 8774 False 1806.000000 5683 92.499714 125 8620 7 chr5B.!!$F1 8495
5 TraesCS5D01G088300 chr6A 601222179 601228316 6137 False 823.700000 3136 83.792667 986 7381 6 chr6A.!!$F1 6395
6 TraesCS5D01G088300 chr6B 692024818 692031073 6255 False 833.716667 3077 83.865333 986 7375 6 chr6B.!!$F1 6389
7 TraesCS5D01G088300 chr6D 454930827 454936855 6028 False 810.133333 3031 84.012667 986 7381 6 chr6D.!!$F2 6395
8 TraesCS5D01G088300 chr2B 371892632 371894222 1590 False 1293.000000 1293 81.664000 3278 4898 1 chr2B.!!$F2 1620
9 TraesCS5D01G088300 chr3A 207776682 207777239 557 True 497.000000 497 83.160000 3213 3774 1 chr3A.!!$R1 561

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
60 61 0.037975 GAACTGCCCTTTGTGCCATG 60.038 55.000 0.00 0.00 0.00 3.66 F
130 131 0.043334 CCCCAAGGAGGAGAAGGAGA 59.957 60.000 0.00 0.00 41.22 3.71 F
182 183 0.249657 GAGCAAATCCGCCTCGATCT 60.250 55.000 0.00 0.00 0.00 2.75 F
201 202 0.302288 TGTTTTTGCGTCTTCGACCG 59.698 50.000 0.00 0.00 39.71 4.79 F
2443 2511 0.109272 TCGTTCTCATCAGCGGTGAC 60.109 55.000 21.19 5.59 34.75 3.67 F
2580 2648 1.822186 ACCAGACACGTTTGGGCAC 60.822 57.895 11.11 0.00 39.00 5.01 F
3889 6447 2.092484 TGTTGAGCCTGGCTGCATATTA 60.092 45.455 28.82 6.08 39.88 0.98 F
5503 8302 0.820482 TCGATGGAGCATGCCCATTG 60.820 55.000 30.84 30.84 43.96 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 2104 2.403259 TGCTATGTGTGTCGTCAGTTG 58.597 47.619 0.00 0.0 0.00 3.16 R
2425 2493 0.388520 TGTCACCGCTGATGAGAACG 60.389 55.000 0.00 0.0 0.00 3.95 R
2443 2511 3.570926 AAGCTCATGTTGCTGATTGTG 57.429 42.857 14.55 0.0 41.03 3.33 R
2503 2571 2.639839 AGTCATAACAGCAAGTGGGTCT 59.360 45.455 0.00 0.0 0.00 3.85 R
4288 6937 0.179065 GTAGGGTGGTCGGCATTACC 60.179 60.000 0.00 0.0 37.53 2.85 R
4502 7158 1.348064 CCAAGGACACCAGAGGTACA 58.652 55.000 0.00 0.0 32.11 2.90 R
5932 8748 1.203162 TGCATGACCCCAAAGTTCCAT 60.203 47.619 0.00 0.0 0.00 3.41 R
7713 11175 0.105593 AGCACTGGATATGCACTCCG 59.894 55.000 11.48 9.1 45.92 4.63 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
19 20 2.168326 CCATGGCAAAAGACCAAACC 57.832 50.000 0.00 0.00 41.49 3.27
20 21 1.415659 CCATGGCAAAAGACCAAACCA 59.584 47.619 0.00 0.00 41.49 3.67
21 22 2.548493 CCATGGCAAAAGACCAAACCAG 60.548 50.000 0.00 0.00 41.49 4.00
22 23 1.118838 TGGCAAAAGACCAAACCAGG 58.881 50.000 0.00 0.00 33.12 4.45
23 24 0.392706 GGCAAAAGACCAAACCAGGG 59.607 55.000 0.00 0.00 0.00 4.45
26 27 1.069049 CAAAAGACCAAACCAGGGCAG 59.931 52.381 0.00 0.00 40.05 4.85
27 28 1.115326 AAAGACCAAACCAGGGCAGC 61.115 55.000 0.00 0.00 40.05 5.25
28 29 2.991540 GACCAAACCAGGGCAGCC 60.992 66.667 1.26 1.26 36.38 4.85
45 46 2.440796 CCATGCCATGCCCGAACT 60.441 61.111 0.00 0.00 0.00 3.01
46 47 2.777972 CCATGCCATGCCCGAACTG 61.778 63.158 0.00 0.00 0.00 3.16
47 48 3.142838 ATGCCATGCCCGAACTGC 61.143 61.111 0.00 0.00 0.00 4.40
50 51 4.431131 CCATGCCCGAACTGCCCT 62.431 66.667 0.00 0.00 0.00 5.19
51 52 2.361610 CATGCCCGAACTGCCCTT 60.362 61.111 0.00 0.00 0.00 3.95
52 53 1.978617 CATGCCCGAACTGCCCTTT 60.979 57.895 0.00 0.00 0.00 3.11
53 54 1.978617 ATGCCCGAACTGCCCTTTG 60.979 57.895 0.00 0.00 0.00 2.77
54 55 2.597510 GCCCGAACTGCCCTTTGT 60.598 61.111 0.00 0.00 0.00 2.83
55 56 2.919494 GCCCGAACTGCCCTTTGTG 61.919 63.158 0.00 0.00 0.00 3.33
57 58 2.644992 CGAACTGCCCTTTGTGCC 59.355 61.111 0.00 0.00 0.00 5.01
60 61 0.037975 GAACTGCCCTTTGTGCCATG 60.038 55.000 0.00 0.00 0.00 3.66
61 62 1.474332 AACTGCCCTTTGTGCCATGG 61.474 55.000 7.63 7.63 0.00 3.66
62 63 3.305177 CTGCCCTTTGTGCCATGGC 62.305 63.158 30.54 30.54 42.49 4.40
73 74 3.393472 GCCATGGCAAAACACCAAA 57.607 47.368 32.08 0.00 41.49 3.28
74 75 0.943673 GCCATGGCAAAACACCAAAC 59.056 50.000 32.08 0.00 41.49 2.93
75 76 1.592064 CCATGGCAAAACACCAAACC 58.408 50.000 0.00 0.00 41.49 3.27
76 77 1.134280 CCATGGCAAAACACCAAACCA 60.134 47.619 0.00 0.00 41.49 3.67
77 78 2.211806 CATGGCAAAACACCAAACCAG 58.788 47.619 0.00 0.00 41.49 4.00
78 79 0.539051 TGGCAAAACACCAAACCAGG 59.461 50.000 0.00 0.00 33.12 4.45
80 81 0.813610 GCAAAACACCAAACCAGGGC 60.814 55.000 0.00 0.00 0.00 5.19
82 83 0.829990 AAAACACCAAACCAGGGCAG 59.170 50.000 0.00 0.00 0.00 4.85
83 84 0.325203 AAACACCAAACCAGGGCAGT 60.325 50.000 0.00 0.00 0.00 4.40
84 85 0.755327 AACACCAAACCAGGGCAGTC 60.755 55.000 0.00 0.00 0.00 3.51
86 87 2.391130 ACCAAACCAGGGCAGTCCA 61.391 57.895 0.00 0.00 38.24 4.02
87 88 1.077265 CCAAACCAGGGCAGTCCAT 59.923 57.895 0.00 0.00 38.24 3.41
97 98 3.214123 CAGTCCATGCCATGCCCG 61.214 66.667 0.00 0.00 0.00 6.13
98 99 4.511246 AGTCCATGCCATGCCCGG 62.511 66.667 0.00 0.00 0.00 5.73
99 100 4.504596 GTCCATGCCATGCCCGGA 62.505 66.667 0.73 0.00 0.00 5.14
100 101 3.500949 TCCATGCCATGCCCGGAT 61.501 61.111 0.73 0.00 0.00 4.18
101 102 2.522436 CCATGCCATGCCCGGATT 60.522 61.111 0.73 0.00 0.00 3.01
129 130 0.985490 CCCCCAAGGAGGAGAAGGAG 60.985 65.000 0.00 0.00 41.22 3.69
130 131 0.043334 CCCCAAGGAGGAGAAGGAGA 59.957 60.000 0.00 0.00 41.22 3.71
135 136 2.499693 CAAGGAGGAGAAGGAGAAGGAC 59.500 54.545 0.00 0.00 0.00 3.85
148 149 0.815734 GAAGGACGAGGACGGATCAA 59.184 55.000 0.00 0.00 44.46 2.57
149 150 1.203994 GAAGGACGAGGACGGATCAAA 59.796 52.381 0.00 0.00 44.46 2.69
155 156 2.233922 ACGAGGACGGATCAAACATCTT 59.766 45.455 0.00 0.00 44.46 2.40
157 158 2.860735 GAGGACGGATCAAACATCTTCG 59.139 50.000 0.00 0.00 0.00 3.79
182 183 0.249657 GAGCAAATCCGCCTCGATCT 60.250 55.000 0.00 0.00 0.00 2.75
201 202 0.302288 TGTTTTTGCGTCTTCGACCG 59.698 50.000 0.00 0.00 39.71 4.79
207 208 0.524816 TGCGTCTTCGACCGCTATTC 60.525 55.000 19.81 0.00 39.71 1.75
275 276 8.385898 TCTTTCATTACGGTTTCATTTGTAGT 57.614 30.769 0.00 0.00 0.00 2.73
338 339 8.649841 TGTATGTTTAACTACGTATGCAACTTC 58.350 33.333 0.00 0.00 0.00 3.01
342 343 6.956299 TTAACTACGTATGCAACTTCTTCC 57.044 37.500 0.00 0.00 0.00 3.46
344 345 1.076332 ACGTATGCAACTTCTTCCGC 58.924 50.000 0.00 0.00 0.00 5.54
345 346 1.075542 CGTATGCAACTTCTTCCGCA 58.924 50.000 0.00 0.00 39.01 5.69
346 347 1.463056 CGTATGCAACTTCTTCCGCAA 59.537 47.619 0.00 0.00 38.01 4.85
374 375 5.964887 AAAACTACGTACGCAACTTAACA 57.035 34.783 16.72 0.00 0.00 2.41
413 414 9.100197 AGTATAAATTTGAGGATTTGGTTTGGT 57.900 29.630 0.00 0.00 31.96 3.67
416 417 7.610580 AAATTTGAGGATTTGGTTTGGTAGA 57.389 32.000 0.00 0.00 0.00 2.59
417 418 6.840780 ATTTGAGGATTTGGTTTGGTAGAG 57.159 37.500 0.00 0.00 0.00 2.43
418 419 4.301072 TGAGGATTTGGTTTGGTAGAGG 57.699 45.455 0.00 0.00 0.00 3.69
419 420 3.017442 GAGGATTTGGTTTGGTAGAGGC 58.983 50.000 0.00 0.00 0.00 4.70
420 421 2.378547 AGGATTTGGTTTGGTAGAGGCA 59.621 45.455 0.00 0.00 0.00 4.75
421 422 2.755103 GGATTTGGTTTGGTAGAGGCAG 59.245 50.000 0.00 0.00 0.00 4.85
422 423 3.421844 GATTTGGTTTGGTAGAGGCAGT 58.578 45.455 0.00 0.00 0.00 4.40
423 424 3.306472 TTTGGTTTGGTAGAGGCAGTT 57.694 42.857 0.00 0.00 0.00 3.16
424 425 2.270352 TGGTTTGGTAGAGGCAGTTG 57.730 50.000 0.00 0.00 0.00 3.16
435 436 3.050275 GCAGTTGTGGAGGCGGAC 61.050 66.667 0.00 0.00 0.00 4.79
445 446 1.004277 TGGAGGCGGACTTTTAATGCT 59.996 47.619 0.00 0.00 0.00 3.79
449 450 1.202348 GGCGGACTTTTAATGCTTGCT 59.798 47.619 0.00 0.00 0.00 3.91
458 459 5.414454 ACTTTTAATGCTTGCTCGGTCATTA 59.586 36.000 0.00 0.00 32.20 1.90
541 552 6.053005 TGCTCTAATAAACGATCCGGATTTT 58.947 36.000 20.22 17.89 0.00 1.82
546 571 6.503589 AATAAACGATCCGGATTTTCAACA 57.496 33.333 20.22 1.45 0.00 3.33
559 584 6.074888 CGGATTTTCAACAGTTGTGAATGTTC 60.075 38.462 13.14 4.67 37.54 3.18
743 768 1.809619 GGTTCGCAGCGCTATGTCA 60.810 57.895 10.99 0.00 0.00 3.58
1490 1519 1.202651 CCTTGTGAGTTTCTGACCCGT 60.203 52.381 0.00 0.00 0.00 5.28
1628 1664 2.158325 TGAAGCCTGGGGAGATTTTTGT 60.158 45.455 0.00 0.00 0.00 2.83
1663 1699 7.229707 TCCAGTTCATTCAACGAAGGAAAATAA 59.770 33.333 5.49 0.00 42.47 1.40
1728 1764 4.179298 GTCGTCCAATTAGGTACTGGTTC 58.821 47.826 0.00 0.00 41.52 3.62
1921 1965 7.708752 AGCATTAGTTCTGCTCAGTTTAGATAC 59.291 37.037 0.00 0.00 46.79 2.24
1927 1971 6.727824 TCTGCTCAGTTTAGATACTTTTGC 57.272 37.500 0.00 0.00 0.00 3.68
2014 2067 6.885952 TCAATCGGTTAAAAATTCCAGTGA 57.114 33.333 0.00 0.00 0.00 3.41
2015 2068 6.908825 TCAATCGGTTAAAAATTCCAGTGAG 58.091 36.000 0.00 0.00 0.00 3.51
2034 2087 7.202038 CCAGTGAGATTCTTCATATAGGGTTGA 60.202 40.741 0.00 0.00 0.00 3.18
2037 2090 7.987458 GTGAGATTCTTCATATAGGGTTGACAA 59.013 37.037 0.00 0.00 0.00 3.18
2051 2104 5.938125 AGGGTTGACAAATACTGTATCACAC 59.062 40.000 0.00 0.00 38.84 3.82
2160 2213 5.366460 CATGAACCTAGTCTCAGCATCAAT 58.634 41.667 0.00 0.00 0.00 2.57
2357 2410 7.014326 GTCCTGTCCTCATATGTTCACATACTA 59.986 40.741 1.90 0.00 41.15 1.82
2379 2435 2.683447 ACACAGTGTGTCTGCCATTTCA 60.683 45.455 23.27 0.00 43.92 2.69
2422 2490 7.681939 TCCTTTTGTGTAGATAAATGGTGAC 57.318 36.000 11.78 0.00 34.49 3.67
2425 2493 8.237267 CCTTTTGTGTAGATAAATGGTGACTTC 58.763 37.037 6.04 0.00 0.00 3.01
2443 2511 0.109272 TCGTTCTCATCAGCGGTGAC 60.109 55.000 21.19 5.59 34.75 3.67
2559 2627 5.482878 AGCATTCAAAACCTTCAATCCTGAT 59.517 36.000 0.00 0.00 0.00 2.90
2580 2648 1.822186 ACCAGACACGTTTGGGCAC 60.822 57.895 11.11 0.00 39.00 5.01
2864 2937 7.865820 TGTTTTATTGATCTTCATCTCCCTCT 58.134 34.615 0.00 0.00 0.00 3.69
3351 5521 7.750229 AGTTGCATACTGAAAAGAGAATTCA 57.250 32.000 8.44 0.00 35.19 2.57
3521 5703 4.391155 AGGTACATCGGCTGTTTTAAACA 58.609 39.130 10.26 10.26 39.39 2.83
3522 5704 4.214758 AGGTACATCGGCTGTTTTAAACAC 59.785 41.667 6.41 4.45 39.39 3.32
3720 6278 3.920231 TGGAGAGCAGTGCAAGATATT 57.080 42.857 19.20 0.00 0.00 1.28
3889 6447 2.092484 TGTTGAGCCTGGCTGCATATTA 60.092 45.455 28.82 6.08 39.88 0.98
3966 6608 8.197592 TCTAGGAACAGATTGTAAACCAGTTA 57.802 34.615 0.00 0.00 0.00 2.24
4151 6800 3.179830 GGAGTTACAGATAGTGCACGTG 58.820 50.000 12.28 12.28 0.00 4.49
4178 6827 5.748152 CCTGCATACCGTAAAATTTCCATTG 59.252 40.000 0.00 0.00 0.00 2.82
4205 6854 4.757594 TCATACATGCCTTTCCAATTTGC 58.242 39.130 0.00 0.00 0.00 3.68
4240 6889 4.206477 TGGACCTGTATCACTCATGTTG 57.794 45.455 0.00 0.00 0.00 3.33
4288 6937 2.335712 GCCTTTTCCAGCACGAGGG 61.336 63.158 0.00 0.00 0.00 4.30
4424 7078 5.416083 TGTGTTAGTTGTCGGGATTATCTG 58.584 41.667 0.00 0.00 0.00 2.90
4502 7158 6.881065 TGCTGTCTTTGATATTGCTTAGACTT 59.119 34.615 0.00 0.00 34.56 3.01
4703 7359 4.633126 ACCGTGACAATGATTCTGAGATTG 59.367 41.667 0.00 0.00 33.99 2.67
4902 7558 2.161486 GCGCTCAGGTGTAAGCTCG 61.161 63.158 0.00 0.00 44.61 5.03
4918 7574 2.039084 AGCTCGTTTCTTTCCCACTGAT 59.961 45.455 0.00 0.00 0.00 2.90
5238 8034 0.929824 CAAACTGTTTCGCACTGCCG 60.930 55.000 2.13 0.00 0.00 5.69
5265 8061 9.793252 ATGTTCATTAAGCATGTGAATTTAGAC 57.207 29.630 0.00 0.00 34.71 2.59
5503 8302 0.820482 TCGATGGAGCATGCCCATTG 60.820 55.000 30.84 30.84 43.96 2.82
5673 8472 2.579207 TAGTCGCTGCACAATCTACC 57.421 50.000 0.00 0.00 0.00 3.18
5732 8533 4.746466 ACCATGGTGGACTTAAAATTGGA 58.254 39.130 18.99 0.00 40.96 3.53
5798 8599 6.068931 CGTAACAGAAATGAACCAGTTTACG 58.931 40.000 0.00 0.00 0.00 3.18
5817 8618 1.964223 CGGAGGAGCTTAGCTTGGATA 59.036 52.381 8.58 0.00 39.88 2.59
5818 8619 2.564947 CGGAGGAGCTTAGCTTGGATAT 59.435 50.000 8.58 0.00 39.88 1.63
5819 8620 3.007398 CGGAGGAGCTTAGCTTGGATATT 59.993 47.826 8.58 0.00 39.88 1.28
5820 8621 4.503991 CGGAGGAGCTTAGCTTGGATATTT 60.504 45.833 8.58 0.00 39.88 1.40
5821 8622 4.759183 GGAGGAGCTTAGCTTGGATATTTG 59.241 45.833 8.58 0.00 39.88 2.32
5822 8623 5.372373 GAGGAGCTTAGCTTGGATATTTGT 58.628 41.667 8.58 0.00 39.88 2.83
5823 8624 5.760131 AGGAGCTTAGCTTGGATATTTGTT 58.240 37.500 8.58 0.00 39.88 2.83
5824 8625 6.190587 AGGAGCTTAGCTTGGATATTTGTTT 58.809 36.000 8.58 0.00 39.88 2.83
5825 8626 6.665248 AGGAGCTTAGCTTGGATATTTGTTTT 59.335 34.615 8.58 0.00 39.88 2.43
5826 8627 7.179160 AGGAGCTTAGCTTGGATATTTGTTTTT 59.821 33.333 8.58 0.00 39.88 1.94
5847 8648 6.976636 TTTTGTTTTTACCAGAAAGCTTGG 57.023 33.333 0.00 0.00 0.00 3.61
5848 8649 5.923733 TTGTTTTTACCAGAAAGCTTGGA 57.076 34.783 9.96 0.00 0.00 3.53
5849 8650 6.478512 TTGTTTTTACCAGAAAGCTTGGAT 57.521 33.333 9.96 0.00 0.00 3.41
5932 8748 8.783093 CCAAACATGACAGTTTCATTCTTACTA 58.217 33.333 0.00 0.00 42.87 1.82
6002 8831 7.470424 GCTGTTAGATTTGATATGGGATGCAAA 60.470 37.037 0.00 0.00 35.07 3.68
6087 8916 5.167303 ACTTACCAAGTGGAAGGATCTTC 57.833 43.478 3.83 0.00 41.01 2.87
6395 9265 9.507329 GATATTGATCTACACAATGGGTATGTT 57.493 33.333 0.00 0.00 38.25 2.71
6477 9713 3.097614 GACTGTTGGAAGGCCTCTACTA 58.902 50.000 5.23 0.00 34.31 1.82
6527 9763 6.730447 TGAAAACAGGATTTCCTCATGGATA 58.270 36.000 0.00 0.00 46.65 2.59
6823 10087 5.163131 ACTGGGTGGTGTGTACTCTATTTTT 60.163 40.000 0.00 0.00 0.00 1.94
6846 10110 6.957920 TGAATTGATGAAGTCCTGTTTTGA 57.042 33.333 0.00 0.00 0.00 2.69
6859 10123 6.431234 AGTCCTGTTTTGATTGGTTCTGATAC 59.569 38.462 0.00 0.00 0.00 2.24
6866 10130 4.763073 TGATTGGTTCTGATACTCTGCTG 58.237 43.478 0.00 0.00 0.00 4.41
6945 10209 2.113860 TGAGATGGGCGGAAGAAAAG 57.886 50.000 0.00 0.00 0.00 2.27
7031 10295 0.583438 CTGCACTTGGTCGAGTTGTG 59.417 55.000 0.00 0.00 0.00 3.33
7229 10514 0.184451 ATGATGGCAGGGCTTGTAGG 59.816 55.000 0.00 0.00 0.00 3.18
7246 10531 1.039856 AGGATGTGTTTGGTTGGCAC 58.960 50.000 0.00 0.00 0.00 5.01
7249 10534 1.269448 GATGTGTTTGGTTGGCACGAT 59.731 47.619 0.00 0.00 36.04 3.73
7250 10535 0.383590 TGTGTTTGGTTGGCACGATG 59.616 50.000 0.00 0.00 36.04 3.84
7359 10676 5.185828 TGAAGAGGAAGATGAAGATGACGAA 59.814 40.000 0.00 0.00 0.00 3.85
7503 10821 7.309990 CCAGTTTTGTTCCTAACCAATCATCAT 60.310 37.037 0.00 0.00 0.00 2.45
7529 10847 0.606673 AAAAGGGAGAACAGAGCCGC 60.607 55.000 0.00 0.00 0.00 6.53
7539 10857 3.077556 AGAGCCGCGGGATGAACT 61.078 61.111 29.38 14.47 0.00 3.01
7557 10967 1.135083 ACTACCGCAGAGTGTGTATGC 60.135 52.381 0.00 0.00 40.22 3.14
7634 11084 0.884259 TGTCCATGCGTGTGTTCCTG 60.884 55.000 4.96 0.00 0.00 3.86
7677 11139 2.751837 GGGGAAGGAAAGCAGCGG 60.752 66.667 0.00 0.00 0.00 5.52
7679 11141 3.443925 GGAAGGAAAGCAGCGGGC 61.444 66.667 0.00 0.00 45.30 6.13
7694 11156 3.302344 GGCGGGTGTGCAAATGGT 61.302 61.111 0.00 0.00 36.28 3.55
7713 11175 2.498167 GTGGATCATGTGGGTAGCATC 58.502 52.381 0.00 0.00 0.00 3.91
7787 11249 2.814336 GAGCCTTGACCGTTTGATCTTT 59.186 45.455 0.00 0.00 0.00 2.52
7893 11355 4.299586 TGATGTTCATGACCCAAGCTTA 57.700 40.909 0.00 0.00 0.00 3.09
7933 11397 3.093814 TGACTTTCGGTAGCACTGGATA 58.906 45.455 0.00 0.00 0.00 2.59
7934 11398 3.704566 TGACTTTCGGTAGCACTGGATAT 59.295 43.478 0.00 0.00 0.00 1.63
7992 11456 0.824109 CTTGAGCTCATGGGTCCGTA 59.176 55.000 19.04 0.00 41.34 4.02
8051 11515 8.322906 TGGCACACTATACATATTAATTCTGC 57.677 34.615 0.00 0.00 0.00 4.26
8099 11563 4.494855 GGCGTATTTTTCAGAGATGACAGC 60.495 45.833 0.00 0.00 0.00 4.40
8101 11565 4.259970 CGTATTTTTCAGAGATGACAGCGG 60.260 45.833 0.00 0.00 0.00 5.52
8102 11566 2.839486 TTTTCAGAGATGACAGCGGT 57.161 45.000 0.00 0.00 0.00 5.68
8103 11567 2.839486 TTTCAGAGATGACAGCGGTT 57.161 45.000 0.00 0.00 0.00 4.44
8105 11569 3.953712 TTCAGAGATGACAGCGGTTTA 57.046 42.857 0.00 0.00 0.00 2.01
8106 11570 3.232213 TCAGAGATGACAGCGGTTTAC 57.768 47.619 0.00 0.00 0.00 2.01
8107 11571 2.826128 TCAGAGATGACAGCGGTTTACT 59.174 45.455 0.00 0.00 0.00 2.24
8108 11572 3.258372 TCAGAGATGACAGCGGTTTACTT 59.742 43.478 0.00 0.00 0.00 2.24
8109 11573 3.369147 CAGAGATGACAGCGGTTTACTTG 59.631 47.826 0.00 0.00 0.00 3.16
8112 11577 1.873698 TGACAGCGGTTTACTTGACC 58.126 50.000 0.00 0.00 0.00 4.02
8199 11668 4.952460 CCAAAGCTGGGATTGATAATTGG 58.048 43.478 0.00 0.00 39.30 3.16
8228 11697 2.252714 AGATATTTCCCCTCGCTCCTC 58.747 52.381 0.00 0.00 0.00 3.71
8242 11711 2.183811 CCTCTGCTGCTCGGTGAG 59.816 66.667 0.00 1.30 0.00 3.51
8270 11739 4.191015 GTGCCCCGAATCCCCCTC 62.191 72.222 0.00 0.00 0.00 4.30
8299 11768 4.504916 CCCTCGACGGCAGCTGAG 62.505 72.222 20.43 13.14 0.00 3.35
8300 11769 4.504916 CCTCGACGGCAGCTGAGG 62.505 72.222 20.43 10.42 41.82 3.86
8301 11770 3.753434 CTCGACGGCAGCTGAGGT 61.753 66.667 20.43 14.18 0.00 3.85
8302 11771 3.288308 CTCGACGGCAGCTGAGGTT 62.288 63.158 20.43 0.00 0.00 3.50
8303 11772 3.114616 CGACGGCAGCTGAGGTTG 61.115 66.667 20.43 13.79 0.00 3.77
8304 11773 3.426568 GACGGCAGCTGAGGTTGC 61.427 66.667 20.43 0.23 46.58 4.17
8326 11929 0.771127 TAAGAGGCTGCTTGGTGGTT 59.229 50.000 0.00 0.00 0.00 3.67
8464 12163 0.104487 TCGTCGGGTTGTGCTGTTTA 59.896 50.000 0.00 0.00 0.00 2.01
8474 12173 5.066505 GGGTTGTGCTGTTTATCCTATTCTG 59.933 44.000 0.00 0.00 0.00 3.02
8492 12191 1.753463 GGTCTCCGGTCGGTGAGAT 60.753 63.158 13.47 0.00 39.63 2.75
8495 12194 0.748367 TCTCCGGTCGGTGAGATCAG 60.748 60.000 9.36 0.00 32.84 2.90
8506 12205 0.764271 TGAGATCAGTGGTGGTTGCA 59.236 50.000 0.00 0.00 0.00 4.08
8562 12261 1.227853 GGCTTCGTGGAAGGTGTGT 60.228 57.895 7.42 0.00 39.76 3.72
8577 12276 2.118732 TGTGGGTCAGCGGAGGTA 59.881 61.111 0.00 0.00 35.08 3.08
8584 12283 0.391130 GTCAGCGGAGGTACAATGCA 60.391 55.000 0.00 0.00 35.08 3.96
8610 12309 2.115052 TGGTGTTGGGCGATGCTT 59.885 55.556 0.00 0.00 0.00 3.91
8620 12319 3.034370 GCGATGCTTCGGGCGAAAA 62.034 57.895 21.74 0.00 45.59 2.29
8621 12320 1.499949 CGATGCTTCGGGCGAAAAA 59.500 52.632 13.82 0.00 45.43 1.94
8622 12321 0.098728 CGATGCTTCGGGCGAAAAAT 59.901 50.000 13.82 0.00 45.43 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.693606 CCTGGTTTGGTCTTTTGCCAT 59.306 47.619 0.00 0.00 35.71 4.40
5 6 0.249868 GCCCTGGTTTGGTCTTTTGC 60.250 55.000 0.00 0.00 0.00 3.68
8 9 1.115326 GCTGCCCTGGTTTGGTCTTT 61.115 55.000 0.00 0.00 0.00 2.52
9 10 1.531602 GCTGCCCTGGTTTGGTCTT 60.532 57.895 0.00 0.00 0.00 3.01
10 11 2.116125 GCTGCCCTGGTTTGGTCT 59.884 61.111 0.00 0.00 0.00 3.85
11 12 2.991540 GGCTGCCCTGGTTTGGTC 60.992 66.667 7.66 0.00 0.00 4.02
12 13 4.621087 GGGCTGCCCTGGTTTGGT 62.621 66.667 30.42 0.00 41.34 3.67
13 14 3.910784 ATGGGCTGCCCTGGTTTGG 62.911 63.158 35.80 0.00 45.70 3.28
14 15 2.284112 ATGGGCTGCCCTGGTTTG 60.284 61.111 35.80 0.00 45.70 2.93
15 16 2.284112 CATGGGCTGCCCTGGTTT 60.284 61.111 35.80 14.43 45.70 3.27
27 28 3.530260 GTTCGGGCATGGCATGGG 61.530 66.667 27.48 4.98 0.00 4.00
28 29 2.440796 AGTTCGGGCATGGCATGG 60.441 61.111 27.48 12.26 0.00 3.66
30 31 3.142838 GCAGTTCGGGCATGGCAT 61.143 61.111 22.06 0.00 0.00 4.40
33 34 3.944250 AAGGGCAGTTCGGGCATGG 62.944 63.158 0.00 0.00 34.52 3.66
35 36 1.978617 CAAAGGGCAGTTCGGGCAT 60.979 57.895 0.00 0.00 34.52 4.40
36 37 2.597217 CAAAGGGCAGTTCGGGCA 60.597 61.111 0.00 0.00 34.52 5.36
37 38 2.597510 ACAAAGGGCAGTTCGGGC 60.598 61.111 0.00 0.00 0.00 6.13
38 39 2.919494 GCACAAAGGGCAGTTCGGG 61.919 63.158 0.00 0.00 0.00 5.14
39 40 2.644992 GCACAAAGGGCAGTTCGG 59.355 61.111 0.00 0.00 0.00 4.30
41 42 3.854856 TGGCACAAAGGGCAGTTC 58.145 55.556 0.00 0.00 38.55 3.01
55 56 0.943673 GTTTGGTGTTTTGCCATGGC 59.056 50.000 30.54 30.54 42.35 4.40
57 58 2.211806 CTGGTTTGGTGTTTTGCCATG 58.788 47.619 0.00 0.00 35.71 3.66
60 61 0.179059 CCCTGGTTTGGTGTTTTGCC 60.179 55.000 0.00 0.00 0.00 4.52
61 62 0.813610 GCCCTGGTTTGGTGTTTTGC 60.814 55.000 0.00 0.00 0.00 3.68
62 63 0.539051 TGCCCTGGTTTGGTGTTTTG 59.461 50.000 0.00 0.00 0.00 2.44
63 64 0.829990 CTGCCCTGGTTTGGTGTTTT 59.170 50.000 0.00 0.00 0.00 2.43
64 65 0.325203 ACTGCCCTGGTTTGGTGTTT 60.325 50.000 0.00 0.00 0.00 2.83
65 66 0.755327 GACTGCCCTGGTTTGGTGTT 60.755 55.000 0.00 0.00 0.00 3.32
67 68 1.903404 GGACTGCCCTGGTTTGGTG 60.903 63.158 0.00 0.00 0.00 4.17
69 70 1.077265 ATGGACTGCCCTGGTTTGG 59.923 57.895 0.00 0.00 35.38 3.28
70 71 1.880819 GCATGGACTGCCCTGGTTTG 61.881 60.000 0.00 0.00 45.66 2.93
72 73 2.036256 GCATGGACTGCCCTGGTT 59.964 61.111 0.00 0.00 45.66 3.67
80 81 3.214123 CGGGCATGGCATGGACTG 61.214 66.667 27.48 12.63 0.00 3.51
82 83 3.797507 ATCCGGGCATGGCATGGAC 62.798 63.158 27.54 12.58 36.49 4.02
83 84 3.072292 AATCCGGGCATGGCATGGA 62.072 57.895 27.28 27.28 37.66 3.41
84 85 2.522436 AATCCGGGCATGGCATGG 60.522 61.111 27.48 20.86 0.00 3.66
86 87 3.228759 GCAATCCGGGCATGGCAT 61.229 61.111 22.06 2.92 0.00 4.40
110 111 0.985490 CTCCTTCTCCTCCTTGGGGG 60.985 65.000 0.00 0.00 36.78 5.40
111 112 0.043334 TCTCCTTCTCCTCCTTGGGG 59.957 60.000 0.00 0.00 37.77 4.96
112 113 1.836802 CTTCTCCTTCTCCTCCTTGGG 59.163 57.143 0.00 0.00 36.20 4.12
113 114 1.836802 CCTTCTCCTTCTCCTCCTTGG 59.163 57.143 0.00 0.00 37.10 3.61
115 116 2.827755 GTCCTTCTCCTTCTCCTCCTT 58.172 52.381 0.00 0.00 0.00 3.36
116 117 1.341581 CGTCCTTCTCCTTCTCCTCCT 60.342 57.143 0.00 0.00 0.00 3.69
117 118 1.107945 CGTCCTTCTCCTTCTCCTCC 58.892 60.000 0.00 0.00 0.00 4.30
118 119 2.021457 CTCGTCCTTCTCCTTCTCCTC 58.979 57.143 0.00 0.00 0.00 3.71
121 122 1.746787 GTCCTCGTCCTTCTCCTTCTC 59.253 57.143 0.00 0.00 0.00 2.87
122 123 1.842052 GTCCTCGTCCTTCTCCTTCT 58.158 55.000 0.00 0.00 0.00 2.85
123 124 0.452585 CGTCCTCGTCCTTCTCCTTC 59.547 60.000 0.00 0.00 0.00 3.46
129 130 0.815734 TTGATCCGTCCTCGTCCTTC 59.184 55.000 0.00 0.00 35.01 3.46
130 131 1.067071 GTTTGATCCGTCCTCGTCCTT 60.067 52.381 0.00 0.00 35.01 3.36
135 136 2.586258 AGATGTTTGATCCGTCCTCG 57.414 50.000 0.00 0.00 0.00 4.63
148 149 2.254546 TGCTCACAACCGAAGATGTT 57.745 45.000 0.00 0.00 0.00 2.71
149 150 2.254546 TTGCTCACAACCGAAGATGT 57.745 45.000 0.00 0.00 0.00 3.06
155 156 1.573829 GCGGATTTGCTCACAACCGA 61.574 55.000 8.57 0.00 44.20 4.69
157 158 1.212751 GGCGGATTTGCTCACAACC 59.787 57.895 0.00 0.00 34.87 3.77
201 202 2.024176 TGTCTCTTTGCGGGAATAGC 57.976 50.000 0.00 0.00 0.00 2.97
207 208 0.593128 CCTTGTTGTCTCTTTGCGGG 59.407 55.000 0.00 0.00 0.00 6.13
325 326 1.076332 GCGGAAGAAGTTGCATACGT 58.924 50.000 0.00 0.00 0.00 3.57
326 327 1.075542 TGCGGAAGAAGTTGCATACG 58.924 50.000 0.00 0.00 31.31 3.06
351 352 6.343226 TGTTAAGTTGCGTACGTAGTTTTT 57.657 33.333 17.90 7.83 37.78 1.94
352 353 5.964887 TGTTAAGTTGCGTACGTAGTTTT 57.035 34.783 17.90 10.13 37.78 2.43
353 354 6.018832 ACAATGTTAAGTTGCGTACGTAGTTT 60.019 34.615 17.90 12.47 37.78 2.66
354 355 5.463061 ACAATGTTAAGTTGCGTACGTAGTT 59.537 36.000 17.90 15.60 37.78 2.24
356 357 5.505165 ACAATGTTAAGTTGCGTACGTAG 57.495 39.130 17.90 0.00 0.00 3.51
357 358 6.805760 TCATACAATGTTAAGTTGCGTACGTA 59.194 34.615 17.90 10.06 0.00 3.57
358 359 5.634439 TCATACAATGTTAAGTTGCGTACGT 59.366 36.000 17.90 0.00 0.00 3.57
359 360 6.034150 TCTCATACAATGTTAAGTTGCGTACG 59.966 38.462 11.84 11.84 0.00 3.67
360 361 7.063074 AGTCTCATACAATGTTAAGTTGCGTAC 59.937 37.037 0.00 0.00 0.00 3.67
362 363 5.932303 AGTCTCATACAATGTTAAGTTGCGT 59.068 36.000 0.00 0.00 0.00 5.24
363 364 6.408858 AGTCTCATACAATGTTAAGTTGCG 57.591 37.500 0.00 0.00 0.00 4.85
364 365 8.480643 ACTAGTCTCATACAATGTTAAGTTGC 57.519 34.615 0.00 0.00 0.00 4.17
393 394 6.211384 CCTCTACCAAACCAAATCCTCAAATT 59.789 38.462 0.00 0.00 0.00 1.82
407 408 1.880027 CCACAACTGCCTCTACCAAAC 59.120 52.381 0.00 0.00 0.00 2.93
412 413 0.391793 GCCTCCACAACTGCCTCTAC 60.392 60.000 0.00 0.00 0.00 2.59
413 414 1.888436 CGCCTCCACAACTGCCTCTA 61.888 60.000 0.00 0.00 0.00 2.43
415 416 2.743928 CGCCTCCACAACTGCCTC 60.744 66.667 0.00 0.00 0.00 4.70
416 417 4.335647 CCGCCTCCACAACTGCCT 62.336 66.667 0.00 0.00 0.00 4.75
417 418 4.329545 TCCGCCTCCACAACTGCC 62.330 66.667 0.00 0.00 0.00 4.85
418 419 3.050275 GTCCGCCTCCACAACTGC 61.050 66.667 0.00 0.00 0.00 4.40
419 420 0.535102 AAAGTCCGCCTCCACAACTG 60.535 55.000 0.00 0.00 0.00 3.16
420 421 0.182775 AAAAGTCCGCCTCCACAACT 59.817 50.000 0.00 0.00 0.00 3.16
421 422 1.886886 TAAAAGTCCGCCTCCACAAC 58.113 50.000 0.00 0.00 0.00 3.32
422 423 2.642154 TTAAAAGTCCGCCTCCACAA 57.358 45.000 0.00 0.00 0.00 3.33
423 424 2.432444 CATTAAAAGTCCGCCTCCACA 58.568 47.619 0.00 0.00 0.00 4.17
424 425 1.132453 GCATTAAAAGTCCGCCTCCAC 59.868 52.381 0.00 0.00 0.00 4.02
435 436 3.829886 TGACCGAGCAAGCATTAAAAG 57.170 42.857 0.00 0.00 0.00 2.27
486 497 1.995376 AAGTTGCCAAATCCGAACCT 58.005 45.000 0.00 0.00 0.00 3.50
541 552 5.749596 ATTCGAACATTCACAACTGTTGA 57.250 34.783 26.00 5.21 35.80 3.18
546 571 4.821805 ACTCCAATTCGAACATTCACAACT 59.178 37.500 0.00 0.00 0.00 3.16
559 584 2.620251 TCATAGGCCACTCCAATTCG 57.380 50.000 5.01 0.00 37.29 3.34
650 675 1.133606 TCCCCACCTCCTCACAAAAAC 60.134 52.381 0.00 0.00 0.00 2.43
743 768 0.620556 AATGGTGAACGGGCAGAGAT 59.379 50.000 0.00 0.00 0.00 2.75
938 963 4.921515 TCTTCTCCGATTTTTCTGTGTACG 59.078 41.667 0.00 0.00 0.00 3.67
1390 1419 2.745308 CCATGACGGCCATCTCCCA 61.745 63.158 2.24 0.00 31.94 4.37
1490 1519 2.640332 TGCACAATCCACAGTAAGGGTA 59.360 45.455 0.00 0.00 0.00 3.69
1628 1664 5.408299 CGTTGAATGAACTGGAATGACACTA 59.592 40.000 0.00 0.00 31.70 2.74
1728 1764 2.700897 CCCAAGTCCACAGTATAGAGGG 59.299 54.545 0.00 0.00 0.00 4.30
1921 1965 3.198863 CAGAGCTAAGCACTGCAAAAG 57.801 47.619 3.30 0.00 39.93 2.27
2034 2087 6.145534 CGTCAGTTGTGTGATACAGTATTTGT 59.854 38.462 0.00 0.00 41.10 2.83
2037 2090 5.862323 GTCGTCAGTTGTGTGATACAGTATT 59.138 40.000 0.00 0.00 41.10 1.89
2051 2104 2.403259 TGCTATGTGTGTCGTCAGTTG 58.597 47.619 0.00 0.00 0.00 3.16
2422 2490 0.994995 CACCGCTGATGAGAACGAAG 59.005 55.000 0.00 0.00 0.00 3.79
2425 2493 0.388520 TGTCACCGCTGATGAGAACG 60.389 55.000 0.00 0.00 0.00 3.95
2443 2511 3.570926 AAGCTCATGTTGCTGATTGTG 57.429 42.857 14.55 0.00 41.03 3.33
2503 2571 2.639839 AGTCATAACAGCAAGTGGGTCT 59.360 45.455 0.00 0.00 0.00 3.85
2559 2627 1.821759 CCCAAACGTGTCTGGTGCA 60.822 57.895 9.90 0.00 0.00 4.57
2580 2648 4.297299 AGCGCCATAACAATTTCATCAG 57.703 40.909 2.29 0.00 0.00 2.90
2777 2846 7.611467 TGGTCTCAGTAACATAGCAAAAATGAT 59.389 33.333 0.00 0.00 0.00 2.45
2906 2979 7.031975 AGTTATCGGTAAAAAGACTAAGGACG 58.968 38.462 0.00 0.00 0.00 4.79
3351 5521 7.398024 ACAAGGTACAGAAATAGATCTTTGCT 58.602 34.615 0.00 0.00 0.00 3.91
3720 6278 3.010808 ACCTTCCCCAATTACCGAATTCA 59.989 43.478 6.22 0.00 32.73 2.57
3966 6608 5.010415 GCAAGGCTGCTGGATAGAAAATTAT 59.990 40.000 0.00 0.00 45.74 1.28
4151 6800 4.497507 GGAAATTTTACGGTATGCAGGCTC 60.498 45.833 0.00 0.00 0.00 4.70
4178 6827 4.782019 TGGAAAGGCATGTATGAACAAC 57.218 40.909 0.00 0.00 39.58 3.32
4205 6854 8.210946 TGATACAGGTCCAAATAACCATAAGAG 58.789 37.037 0.00 0.00 39.39 2.85
4240 6889 6.803154 ACAGAAATCCAGTTTGCTAAGTAC 57.197 37.500 0.00 0.00 0.00 2.73
4288 6937 0.179065 GTAGGGTGGTCGGCATTACC 60.179 60.000 0.00 0.00 37.53 2.85
4320 6969 2.641815 AGATGCCCCTAACTCATCATCC 59.358 50.000 0.00 0.00 39.12 3.51
4329 6978 3.648545 AGAATACCTCAGATGCCCCTAAC 59.351 47.826 0.00 0.00 0.00 2.34
4502 7158 1.348064 CCAAGGACACCAGAGGTACA 58.652 55.000 0.00 0.00 32.11 2.90
4703 7359 8.099537 AGTATAATCATCATCCTCAATCACACC 58.900 37.037 0.00 0.00 0.00 4.16
4902 7558 5.473504 ACACATACATCAGTGGGAAAGAAAC 59.526 40.000 0.00 0.00 39.99 2.78
4918 7574 9.797556 GTATACATTTAGACAGTCACACATACA 57.202 33.333 2.66 0.00 0.00 2.29
4955 7614 4.532126 ACCATACTCAAAGGATGACTGACA 59.468 41.667 0.57 0.00 33.47 3.58
5265 8061 3.251004 GTGCTTGGGAAACAGAGTGTTAG 59.749 47.826 0.00 0.00 40.14 2.34
5673 8472 6.949352 AAGTGCCTAGAAATCATACCATTG 57.051 37.500 0.00 0.00 0.00 2.82
5750 8551 7.069569 CGATTAAACACCCAAATATCTTAGCG 58.930 38.462 0.00 0.00 0.00 4.26
5798 8599 4.632327 AATATCCAAGCTAAGCTCCTCC 57.368 45.455 0.00 0.00 38.25 4.30
5823 8624 7.162082 TCCAAGCTTTCTGGTAAAAACAAAAA 58.838 30.769 0.00 0.00 0.00 1.94
5824 8625 6.702329 TCCAAGCTTTCTGGTAAAAACAAAA 58.298 32.000 0.00 0.00 0.00 2.44
5825 8626 6.287589 TCCAAGCTTTCTGGTAAAAACAAA 57.712 33.333 0.00 0.00 0.00 2.83
5826 8627 5.923733 TCCAAGCTTTCTGGTAAAAACAA 57.076 34.783 0.00 0.00 0.00 2.83
5827 8628 7.775053 ATATCCAAGCTTTCTGGTAAAAACA 57.225 32.000 0.00 0.00 0.00 2.83
5828 8629 8.925700 CAAATATCCAAGCTTTCTGGTAAAAAC 58.074 33.333 0.00 0.00 0.00 2.43
5829 8630 8.093927 CCAAATATCCAAGCTTTCTGGTAAAAA 58.906 33.333 0.00 0.00 0.00 1.94
5830 8631 7.234577 ACCAAATATCCAAGCTTTCTGGTAAAA 59.765 33.333 0.00 0.00 0.00 1.52
5831 8632 6.723977 ACCAAATATCCAAGCTTTCTGGTAAA 59.276 34.615 0.00 0.00 0.00 2.01
5832 8633 6.252995 ACCAAATATCCAAGCTTTCTGGTAA 58.747 36.000 0.00 0.00 0.00 2.85
5833 8634 5.826643 ACCAAATATCCAAGCTTTCTGGTA 58.173 37.500 0.00 0.00 0.00 3.25
5834 8635 4.677182 ACCAAATATCCAAGCTTTCTGGT 58.323 39.130 0.00 0.00 0.00 4.00
5835 8636 5.665916 AACCAAATATCCAAGCTTTCTGG 57.334 39.130 0.00 0.00 0.00 3.86
5836 8637 6.698766 GCATAACCAAATATCCAAGCTTTCTG 59.301 38.462 0.00 0.00 0.00 3.02
5837 8638 6.380846 TGCATAACCAAATATCCAAGCTTTCT 59.619 34.615 0.00 0.00 0.00 2.52
5838 8639 6.572519 TGCATAACCAAATATCCAAGCTTTC 58.427 36.000 0.00 0.00 0.00 2.62
5839 8640 6.407299 CCTGCATAACCAAATATCCAAGCTTT 60.407 38.462 0.00 0.00 0.00 3.51
5840 8641 5.069516 CCTGCATAACCAAATATCCAAGCTT 59.930 40.000 0.00 0.00 0.00 3.74
5841 8642 4.586001 CCTGCATAACCAAATATCCAAGCT 59.414 41.667 0.00 0.00 0.00 3.74
5842 8643 4.584325 TCCTGCATAACCAAATATCCAAGC 59.416 41.667 0.00 0.00 0.00 4.01
5843 8644 6.266103 ACATCCTGCATAACCAAATATCCAAG 59.734 38.462 0.00 0.00 0.00 3.61
5844 8645 6.135454 ACATCCTGCATAACCAAATATCCAA 58.865 36.000 0.00 0.00 0.00 3.53
5845 8646 5.704354 ACATCCTGCATAACCAAATATCCA 58.296 37.500 0.00 0.00 0.00 3.41
5846 8647 6.265196 TGAACATCCTGCATAACCAAATATCC 59.735 38.462 0.00 0.00 0.00 2.59
5847 8648 7.275888 TGAACATCCTGCATAACCAAATATC 57.724 36.000 0.00 0.00 0.00 1.63
5848 8649 7.844493 ATGAACATCCTGCATAACCAAATAT 57.156 32.000 0.00 0.00 0.00 1.28
5849 8650 7.448161 CCTATGAACATCCTGCATAACCAAATA 59.552 37.037 0.00 0.00 0.00 1.40
5932 8748 1.203162 TGCATGACCCCAAAGTTCCAT 60.203 47.619 0.00 0.00 0.00 3.41
6002 8831 1.827344 GGGAAGCAAGGCAAATAAGCT 59.173 47.619 0.00 0.00 37.08 3.74
6087 8916 3.994392 ACTGTCTTGGTGTAATTGCGTAG 59.006 43.478 0.00 0.00 0.00 3.51
6395 9265 4.081142 CACAACCACCATACTACATGGAGA 60.081 45.833 13.29 0.00 41.64 3.71
6477 9713 8.706322 AACTGGACCTAAAACTTAACAATCAT 57.294 30.769 0.00 0.00 0.00 2.45
6527 9763 4.516698 AGAGTGCATGTTTCTTTCGTGAAT 59.483 37.500 0.00 0.00 0.00 2.57
6634 9870 6.038161 TCACCATCACGGAATGATTCATTTAC 59.962 38.462 12.96 8.66 46.54 2.01
6823 10087 6.957920 TCAAAACAGGACTTCATCAATTCA 57.042 33.333 0.00 0.00 0.00 2.57
6846 10110 4.833478 ACAGCAGAGTATCAGAACCAAT 57.167 40.909 0.00 0.00 37.82 3.16
6917 10181 1.067000 CCGCCCATCTCAAAATTGCAA 60.067 47.619 0.00 0.00 0.00 4.08
6945 10209 2.791927 GGCTCGTCGGCATTTTCC 59.208 61.111 7.78 0.00 38.25 3.13
7031 10295 2.253392 CTCACGCAAAATGAGAAGGC 57.747 50.000 0.00 0.00 45.46 4.35
7078 10342 8.141909 AGGGAAAGCAACTACAGAAATAAAAAC 58.858 33.333 0.00 0.00 0.00 2.43
7229 10514 0.665835 TCGTGCCAACCAAACACATC 59.334 50.000 0.00 0.00 33.89 3.06
7359 10676 5.656416 CCATCTCCAACTCTACTCTTCTTCT 59.344 44.000 0.00 0.00 0.00 2.85
7513 10831 3.764466 CGCGGCTCTGTTCTCCCT 61.764 66.667 0.00 0.00 0.00 4.20
7514 10832 4.821589 CCGCGGCTCTGTTCTCCC 62.822 72.222 14.67 0.00 0.00 4.30
7515 10833 4.821589 CCCGCGGCTCTGTTCTCC 62.822 72.222 22.85 0.00 0.00 3.71
7529 10847 0.249073 CTCTGCGGTAGTTCATCCCG 60.249 60.000 0.00 0.00 44.46 5.14
7539 10857 1.182667 AGCATACACACTCTGCGGTA 58.817 50.000 0.00 0.00 40.78 4.02
7652 11102 2.441035 CTTTCCTTCCCCCACCCCAC 62.441 65.000 0.00 0.00 0.00 4.61
7653 11103 2.037128 TTTCCTTCCCCCACCCCA 60.037 61.111 0.00 0.00 0.00 4.96
7677 11139 3.302344 ACCATTTGCACACCCGCC 61.302 61.111 0.00 0.00 0.00 6.13
7679 11141 1.250154 ATCCACCATTTGCACACCCG 61.250 55.000 0.00 0.00 0.00 5.28
7685 11147 1.826096 CCACATGATCCACCATTTGCA 59.174 47.619 0.00 0.00 0.00 4.08
7688 11150 2.925966 ACCCACATGATCCACCATTT 57.074 45.000 0.00 0.00 0.00 2.32
7694 11156 1.070601 CGATGCTACCCACATGATCCA 59.929 52.381 0.00 0.00 0.00 3.41
7713 11175 0.105593 AGCACTGGATATGCACTCCG 59.894 55.000 11.48 9.10 45.92 4.63
7739 11201 1.285962 AGCACAGGGGCATGTAAATCT 59.714 47.619 0.00 0.00 35.83 2.40
7766 11228 2.100605 AGATCAAACGGTCAAGGCTC 57.899 50.000 0.00 0.00 0.00 4.70
7772 11234 4.014569 TGGATCAAAGATCAAACGGTCA 57.985 40.909 9.02 0.00 0.00 4.02
7773 11235 4.142600 CCTTGGATCAAAGATCAAACGGTC 60.143 45.833 11.72 0.00 0.00 4.79
7787 11249 6.408548 GGACTTCATCTATGTTCCTTGGATCA 60.409 42.308 3.26 3.26 0.00 2.92
7893 11355 0.832135 ATATGATCCCGTGCTCCCGT 60.832 55.000 0.00 0.00 0.00 5.28
7933 11397 7.331026 TCACTCGAATCTATGTCCAAGAAAAT 58.669 34.615 0.00 0.00 0.00 1.82
7934 11398 6.697395 TCACTCGAATCTATGTCCAAGAAAA 58.303 36.000 0.00 0.00 0.00 2.29
7978 11442 2.158957 TGATTTCTACGGACCCATGAGC 60.159 50.000 0.00 0.00 0.00 4.26
7992 11456 4.731313 AGGAGGTCAAGGTTTGATTTCT 57.269 40.909 0.00 0.00 42.47 2.52
8049 11513 5.242171 GCAAGTTTAGGGTTAAGGTTAAGCA 59.758 40.000 7.52 0.00 41.56 3.91
8051 11515 6.008331 AGGCAAGTTTAGGGTTAAGGTTAAG 58.992 40.000 0.00 0.00 0.00 1.85
8099 11563 2.457366 AGCTCTGGTCAAGTAAACCG 57.543 50.000 0.00 0.00 39.81 4.44
8101 11565 3.740115 TCCAAGCTCTGGTCAAGTAAAC 58.260 45.455 12.71 0.00 46.51 2.01
8102 11566 4.640771 ATCCAAGCTCTGGTCAAGTAAA 57.359 40.909 12.71 0.00 46.51 2.01
8103 11567 4.041567 TCAATCCAAGCTCTGGTCAAGTAA 59.958 41.667 12.71 0.00 46.51 2.24
8105 11569 2.373169 TCAATCCAAGCTCTGGTCAAGT 59.627 45.455 12.71 0.00 46.51 3.16
8106 11570 3.063510 TCAATCCAAGCTCTGGTCAAG 57.936 47.619 12.71 4.84 46.51 3.02
8107 11571 3.726557 ATCAATCCAAGCTCTGGTCAA 57.273 42.857 12.71 0.00 46.51 3.18
8108 11572 4.842531 TTATCAATCCAAGCTCTGGTCA 57.157 40.909 12.71 0.00 46.51 4.02
8109 11573 5.824624 TCAATTATCAATCCAAGCTCTGGTC 59.175 40.000 12.71 0.00 46.51 4.02
8112 11577 6.489022 TGGATCAATTATCAATCCAAGCTCTG 59.511 38.462 6.17 0.00 44.53 3.35
8199 11668 3.885901 GAGGGGAAATATCTTGCTTGGAC 59.114 47.826 0.00 0.00 0.00 4.02
8253 11722 4.191015 GAGGGGGATTCGGGGCAC 62.191 72.222 0.00 0.00 0.00 5.01
8282 11751 4.504916 CTCAGCTGCCGTCGAGGG 62.505 72.222 19.82 19.82 41.48 4.30
8283 11752 4.504916 CCTCAGCTGCCGTCGAGG 62.505 72.222 9.47 5.59 44.97 4.63
8284 11753 3.288308 AACCTCAGCTGCCGTCGAG 62.288 63.158 9.47 0.00 0.00 4.04
8285 11754 3.303135 AACCTCAGCTGCCGTCGA 61.303 61.111 9.47 0.00 0.00 4.20
8286 11755 3.114616 CAACCTCAGCTGCCGTCG 61.115 66.667 9.47 0.00 0.00 5.12
8287 11756 3.426568 GCAACCTCAGCTGCCGTC 61.427 66.667 9.47 0.00 32.18 4.79
8290 11759 3.605749 TACCGCAACCTCAGCTGCC 62.606 63.158 9.47 0.00 35.01 4.85
8291 11760 1.639298 CTTACCGCAACCTCAGCTGC 61.639 60.000 9.47 0.00 35.14 5.25
8292 11761 0.037326 TCTTACCGCAACCTCAGCTG 60.037 55.000 7.63 7.63 0.00 4.24
8293 11762 0.247736 CTCTTACCGCAACCTCAGCT 59.752 55.000 0.00 0.00 0.00 4.24
8294 11763 0.741221 CCTCTTACCGCAACCTCAGC 60.741 60.000 0.00 0.00 0.00 4.26
8295 11764 0.741221 GCCTCTTACCGCAACCTCAG 60.741 60.000 0.00 0.00 0.00 3.35
8296 11765 1.192146 AGCCTCTTACCGCAACCTCA 61.192 55.000 0.00 0.00 0.00 3.86
8297 11766 0.741221 CAGCCTCTTACCGCAACCTC 60.741 60.000 0.00 0.00 0.00 3.85
8298 11767 1.296715 CAGCCTCTTACCGCAACCT 59.703 57.895 0.00 0.00 0.00 3.50
8299 11768 2.399356 GCAGCCTCTTACCGCAACC 61.399 63.158 0.00 0.00 0.00 3.77
8300 11769 0.955919 AAGCAGCCTCTTACCGCAAC 60.956 55.000 0.00 0.00 0.00 4.17
8301 11770 0.955428 CAAGCAGCCTCTTACCGCAA 60.955 55.000 0.00 0.00 0.00 4.85
8302 11771 1.375908 CAAGCAGCCTCTTACCGCA 60.376 57.895 0.00 0.00 0.00 5.69
8303 11772 2.109126 CCAAGCAGCCTCTTACCGC 61.109 63.158 0.00 0.00 0.00 5.68
8304 11773 1.021390 CACCAAGCAGCCTCTTACCG 61.021 60.000 0.00 0.00 0.00 4.02
8305 11774 0.678048 CCACCAAGCAGCCTCTTACC 60.678 60.000 0.00 0.00 0.00 2.85
8306 11775 0.036875 ACCACCAAGCAGCCTCTTAC 59.963 55.000 0.00 0.00 0.00 2.34
8307 11776 0.771127 AACCACCAAGCAGCCTCTTA 59.229 50.000 0.00 0.00 0.00 2.10
8326 11929 1.228894 AGAGTCCAAGCCCTGTCGA 60.229 57.895 0.00 0.00 0.00 4.20
8377 12076 4.802051 GCCAGCATCCCGAGGCAA 62.802 66.667 3.98 0.00 46.26 4.52
8464 12163 2.599677 GACCGGAGACCAGAATAGGAT 58.400 52.381 9.46 0.00 0.00 3.24
8474 12173 1.726533 GATCTCACCGACCGGAGACC 61.727 65.000 16.07 0.00 42.49 3.85
8492 12191 0.822944 CACCATGCAACCACCACTGA 60.823 55.000 0.00 0.00 0.00 3.41
8495 12194 1.363443 CACACCATGCAACCACCAC 59.637 57.895 0.00 0.00 0.00 4.16
8506 12205 1.228552 GAAGCCACCACCACACCAT 60.229 57.895 0.00 0.00 0.00 3.55
8562 12261 0.907704 ATTGTACCTCCGCTGACCCA 60.908 55.000 0.00 0.00 0.00 4.51
8577 12276 0.112995 ACCACACCCTCATGCATTGT 59.887 50.000 0.00 0.00 0.00 2.71
8584 12283 1.460255 CCCAACACCACACCCTCAT 59.540 57.895 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.