Multiple sequence alignment - TraesCS7D01G421700

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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 TraesCS7D01G421700 chr7D 100.000 2505 0 0 1 2505 541243076 541240572 0.000000e+00 4626.0
1 TraesCS7D01G421700 chr7D 100.000 2090 0 0 4058 6147 541239019 541236930 0.000000e+00 3860.0
2 TraesCS7D01G421700 chr7D 100.000 753 0 0 3008 3760 541240069 541239317 0.000000e+00 1391.0
3 TraesCS7D01G421700 chr7D 86.882 465 57 2 1343 1807 541261028 541260568 9.130000e-143 518.0
4 TraesCS7D01G421700 chr7D 83.735 332 53 1 1803 2134 541250089 541249759 4.630000e-81 313.0
5 TraesCS7D01G421700 chr7D 83.434 332 54 1 1803 2134 541258848 541258518 2.150000e-79 307.0
6 TraesCS7D01G421700 chr7D 96.689 151 5 0 303 453 267557919 267558069 1.020000e-62 252.0
7 TraesCS7D01G421700 chr7D 96.667 60 2 0 454 513 267558092 267558151 3.920000e-17 100.0
8 TraesCS7D01G421700 chr7D 97.297 37 1 0 2239 2275 541240807 541240771 5.140000e-06 63.9
9 TraesCS7D01G421700 chr7D 97.297 37 1 0 2270 2306 541240838 541240802 5.140000e-06 63.9
10 TraesCS7D01G421700 chr7B 98.152 1894 27 3 615 2505 584814297 584812409 0.000000e+00 3297.0
11 TraesCS7D01G421700 chr7B 97.635 1184 22 3 4554 5737 584806913 584805736 0.000000e+00 2026.0
12 TraesCS7D01G421700 chr7B 96.345 766 9 8 3014 3760 584811941 584811176 0.000000e+00 1242.0
13 TraesCS7D01G421700 chr7B 95.951 494 8 4 4061 4554 584811049 584810568 0.000000e+00 791.0
14 TraesCS7D01G421700 chr7B 95.225 377 16 1 5769 6145 584798593 584798219 4.100000e-166 595.0
15 TraesCS7D01G421700 chr7B 92.810 153 11 0 303 455 33380837 33380989 8.020000e-54 222.0
16 TraesCS7D01G421700 chr7B 94.286 140 7 1 143 281 584817042 584816903 4.830000e-51 213.0
17 TraesCS7D01G421700 chr7B 100.000 91 0 0 5683 5773 584805738 584805648 1.060000e-37 169.0
18 TraesCS7D01G421700 chr7B 95.775 71 3 0 535 605 584814420 584814350 1.400000e-21 115.0
19 TraesCS7D01G421700 chr7A 97.146 1892 44 3 615 2505 624644368 624642486 0.000000e+00 3186.0
20 TraesCS7D01G421700 chr7A 96.198 1052 22 5 4453 5502 624641163 624640128 0.000000e+00 1705.0
21 TraesCS7D01G421700 chr7A 98.400 625 8 2 3008 3631 624642147 624641524 0.000000e+00 1098.0
22 TraesCS7D01G421700 chr7A 94.819 637 14 7 5527 6147 624640133 624639500 0.000000e+00 976.0
23 TraesCS7D01G421700 chr7A 93.803 355 6 3 4058 4399 624641513 624641162 2.540000e-143 520.0
24 TraesCS7D01G421700 chr7A 93.514 185 11 1 130 313 624645344 624645160 2.180000e-69 274.0
25 TraesCS7D01G421700 chr7A 94.186 86 5 0 1 86 624645436 624645351 1.390000e-26 132.0
26 TraesCS7D01G421700 chr7A 94.366 71 4 0 535 605 624644491 624644421 6.510000e-20 110.0
27 TraesCS7D01G421700 chr7A 97.297 37 1 0 2239 2275 624642721 624642685 5.140000e-06 63.9
28 TraesCS7D01G421700 chr7A 97.297 37 1 0 2270 2306 624642752 624642716 5.140000e-06 63.9
29 TraesCS7D01G421700 chr3B 96.815 157 5 0 299 455 828797293 828797137 4.730000e-66 263.0
30 TraesCS7D01G421700 chr3D 87.931 232 7 2 301 512 84502604 84502834 2.840000e-63 254.0
31 TraesCS7D01G421700 chr5D 95.597 159 4 1 300 455 504155006 504155164 1.020000e-62 252.0
32 TraesCS7D01G421700 chr5D 72.444 450 94 25 1292 1724 437530674 437530238 3.890000e-22 117.0
33 TraesCS7D01G421700 chr5D 96.610 59 2 0 454 512 504155185 504155243 1.410000e-16 99.0
34 TraesCS7D01G421700 chr5A 95.425 153 7 0 303 455 568697969 568697817 1.710000e-60 244.0
35 TraesCS7D01G421700 chr5A 94.805 154 7 1 302 455 230807046 230806894 7.960000e-59 239.0
36 TraesCS7D01G421700 chr5A 85.903 227 9 4 307 510 83638804 83638578 2.880000e-53 220.0
37 TraesCS7D01G421700 chr5A 91.045 67 5 1 454 519 568697796 568697730 8.490000e-14 89.8
38 TraesCS7D01G421700 chr2D 94.904 157 7 1 296 452 347816076 347816231 1.710000e-60 244.0
39 TraesCS7D01G421700 chr2D 96.599 147 4 1 307 453 532187942 532188087 6.160000e-60 243.0
40 TraesCS7D01G421700 chr6D 93.333 165 8 3 292 455 47023199 47023361 2.210000e-59 241.0
41 TraesCS7D01G421700 chr6D 71.568 925 224 32 1312 2212 466130869 466129960 1.340000e-51 215.0
42 TraesCS7D01G421700 chr1D 71.286 1003 246 35 1286 2263 52681743 52682728 1.040000e-52 219.0
43 TraesCS7D01G421700 chr1D 92.414 145 5 1 311 455 136502530 136502668 1.040000e-47 202.0
44 TraesCS7D01G421700 chr2A 88.889 153 17 0 303 455 647882907 647883059 8.130000e-44 189.0
45 TraesCS7D01G421700 chr6A 84.615 91 14 0 4876 4966 125261803 125261893 2.360000e-14 91.6
46 TraesCS7D01G421700 chr6A 84.615 91 14 0 4876 4966 611903573 611903663 2.360000e-14 91.6
47 TraesCS7D01G421700 chr1A 77.333 150 32 2 1286 1435 52471878 52472025 3.050000e-13 87.9
48 TraesCS7D01G421700 chr6B 94.444 54 1 2 6096 6147 21091249 21091196 1.420000e-11 82.4
49 TraesCS7D01G421700 chr2B 94.545 55 0 3 6095 6147 425794098 425794045 1.420000e-11 82.4
50 TraesCS7D01G421700 chr1B 94.118 51 3 0 6096 6146 649027485 649027535 1.840000e-10 78.7
51 TraesCS7D01G421700 chr5B 92.453 53 2 1 6097 6147 709190477 709190529 2.380000e-09 75.0
52 TraesCS7D01G421700 chrUn 92.308 52 2 1 6098 6147 252895646 252895595 8.550000e-09 73.1
53 TraesCS7D01G421700 chrUn 92.308 52 2 1 6098 6147 281107203 281107254 8.550000e-09 73.1
54 TraesCS7D01G421700 chr4A 87.302 63 4 3 6088 6147 665731214 665731275 1.110000e-07 69.4


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 TraesCS7D01G421700 chr7D 541236930 541243076 6146 True 2000.960000 4626 98.918800 1 6147 5 chr7D.!!$R2 6146
1 TraesCS7D01G421700 chr7D 541258518 541261028 2510 True 412.500000 518 85.158000 1343 2134 2 chr7D.!!$R3 791
2 TraesCS7D01G421700 chr7B 584805648 584817042 11394 True 1121.857143 3297 96.877714 143 5773 7 chr7B.!!$R2 5630
3 TraesCS7D01G421700 chr7A 624639500 624645436 5936 True 812.880000 3186 95.702600 1 6147 10 chr7A.!!$R1 6146
4 TraesCS7D01G421700 chr6D 466129960 466130869 909 True 215.000000 215 71.568000 1312 2212 1 chr6D.!!$R1 900
5 TraesCS7D01G421700 chr1D 52681743 52682728 985 False 219.000000 219 71.286000 1286 2263 1 chr1D.!!$F1 977

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
611 3535 0.453390 GGCAGCCCATCTCTTTTTCG 59.547 55.000 0.0 0.0 0.00 3.46 F
1448 4419 0.458025 GGTGGAGTCGGCTTTCTACG 60.458 60.000 0.0 0.0 0.00 3.51 F
1492 4463 1.826385 ATTTTGGACTTCCTGCCTCG 58.174 50.000 0.0 0.0 36.82 4.63 F
3622 8351 1.412343 GGCTTTTTGGGTGAGCTTTGA 59.588 47.619 0.0 0.0 36.66 2.69 F
4361 9103 0.620030 CATGTCCCATGTCCCTGACA 59.380 55.000 0.0 0.0 46.90 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 4660 1.538047 TTCAGCCATCTCAACCTTGC 58.462 50.000 0.00 0.0 0.00 4.01 R
3446 8174 2.171448 AGGAGACACAAGAAACACTGCT 59.829 45.455 0.00 0.0 0.00 4.24 R
4090 8819 5.368145 GACATACCTAAATGGCATCTGACA 58.632 41.667 0.00 0.0 40.22 3.58 R
4423 9220 1.482593 CGCATATCCCCAGAGTATCCC 59.517 57.143 0.00 0.0 33.66 3.85 R
5625 14085 1.879380 CATTGACGTCCCTTGCTCAAA 59.121 47.619 14.12 0.0 0.00 2.69 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
44 45 3.664551 ATTTTTAGGGGTAGCAGGACC 57.335 47.619 0.00 0.00 38.93 4.46
58 59 2.388735 CAGGACCATGCTAGGTAGACA 58.611 52.381 0.46 0.00 43.38 3.41
115 116 6.633668 TTTTTGCGAACTCGAAAATTTGAA 57.366 29.167 6.11 0.00 45.27 2.69
116 117 6.633668 TTTTGCGAACTCGAAAATTTGAAA 57.366 29.167 6.11 0.00 45.27 2.69
117 118 6.633668 TTTGCGAACTCGAAAATTTGAAAA 57.366 29.167 2.69 0.00 41.53 2.29
118 119 6.633668 TTGCGAACTCGAAAATTTGAAAAA 57.366 29.167 2.69 0.00 43.02 1.94
151 152 8.606602 AGATTTGAAAATTTGACTTTTGTGAGC 58.393 29.630 0.00 0.00 0.00 4.26
191 193 3.119637 ACTGAATATTTTCCCAAACCGCG 60.120 43.478 0.00 0.00 0.00 6.46
249 251 5.178252 GCGCAGGCCATATAATAGTATCATG 59.822 44.000 5.01 0.00 0.00 3.07
257 259 7.170965 CCATATAATAGTATCATGCCCATCCC 58.829 42.308 0.00 0.00 0.00 3.85
290 2749 1.152777 CCAGCTCCAACCAACCACA 60.153 57.895 0.00 0.00 0.00 4.17
301 2760 1.002624 CAACCACACCGCCACCTAT 60.003 57.895 0.00 0.00 0.00 2.57
313 2772 1.014352 CCACCTATAGCGTGTTTGGC 58.986 55.000 15.76 0.00 0.00 4.52
314 2773 1.677518 CCACCTATAGCGTGTTTGGCA 60.678 52.381 15.76 0.00 0.00 4.92
315 2774 2.080693 CACCTATAGCGTGTTTGGCAA 58.919 47.619 0.00 0.00 0.00 4.52
316 2775 2.486203 CACCTATAGCGTGTTTGGCAAA 59.514 45.455 8.93 8.93 0.00 3.68
317 2776 2.486592 ACCTATAGCGTGTTTGGCAAAC 59.513 45.455 30.99 30.99 41.73 2.93
321 2780 2.485266 AGCGTGTTTGGCAAACTAAC 57.515 45.000 35.03 26.54 41.90 2.34
323 2782 1.749153 CGTGTTTGGCAAACTAACGG 58.251 50.000 35.03 20.76 41.90 4.44
326 2785 3.368495 GTGTTTGGCAAACTAACGGAAG 58.632 45.455 35.03 0.00 41.90 3.46
331 2790 1.546099 GGCAAACTAACGGAAGGGGAA 60.546 52.381 0.00 0.00 0.00 3.97
337 2796 1.141053 CTAACGGAAGGGGAATGGGAG 59.859 57.143 0.00 0.00 0.00 4.30
342 2801 2.025699 CGGAAGGGGAATGGGAGTTTAA 60.026 50.000 0.00 0.00 0.00 1.52
343 2802 3.362706 GGAAGGGGAATGGGAGTTTAAC 58.637 50.000 0.00 0.00 0.00 2.01
344 2803 3.011369 GGAAGGGGAATGGGAGTTTAACT 59.989 47.826 0.00 0.00 0.00 2.24
345 2804 4.270834 GAAGGGGAATGGGAGTTTAACTC 58.729 47.826 16.07 16.07 44.32 3.01
346 2805 3.542604 AGGGGAATGGGAGTTTAACTCT 58.457 45.455 22.26 4.80 44.46 3.24
349 3250 5.736616 AGGGGAATGGGAGTTTAACTCTAAT 59.263 40.000 22.26 14.04 44.46 1.73
354 3255 6.910259 ATGGGAGTTTAACTCTAATTCCCT 57.090 37.500 22.26 7.08 44.46 4.20
359 3260 6.602406 GGAGTTTAACTCTAATTCCCTTTCCC 59.398 42.308 22.26 0.13 44.46 3.97
360 3261 6.491383 AGTTTAACTCTAATTCCCTTTCCCC 58.509 40.000 0.00 0.00 0.00 4.81
361 3262 6.046286 AGTTTAACTCTAATTCCCTTTCCCCA 59.954 38.462 0.00 0.00 0.00 4.96
362 3263 6.668133 TTAACTCTAATTCCCTTTCCCCAT 57.332 37.500 0.00 0.00 0.00 4.00
363 3264 4.797912 ACTCTAATTCCCTTTCCCCATC 57.202 45.455 0.00 0.00 0.00 3.51
364 3265 4.384465 ACTCTAATTCCCTTTCCCCATCT 58.616 43.478 0.00 0.00 0.00 2.90
365 3266 4.413851 ACTCTAATTCCCTTTCCCCATCTC 59.586 45.833 0.00 0.00 0.00 2.75
375 3276 3.297134 TTCCCCATCTCAATTACCAGC 57.703 47.619 0.00 0.00 0.00 4.85
376 3277 1.494721 TCCCCATCTCAATTACCAGCC 59.505 52.381 0.00 0.00 0.00 4.85
377 3278 1.479389 CCCCATCTCAATTACCAGCCC 60.479 57.143 0.00 0.00 0.00 5.19
378 3279 1.496429 CCCATCTCAATTACCAGCCCT 59.504 52.381 0.00 0.00 0.00 5.19
383 3284 1.230212 CAATTACCAGCCCTCCCCC 59.770 63.158 0.00 0.00 0.00 5.40
387 3288 2.208562 TTACCAGCCCTCCCCCAGAT 62.209 60.000 0.00 0.00 0.00 2.90
390 3291 0.773700 CCAGCCCTCCCCCAGATAAT 60.774 60.000 0.00 0.00 0.00 1.28
391 3292 1.486943 CCAGCCCTCCCCCAGATAATA 60.487 57.143 0.00 0.00 0.00 0.98
392 3293 1.912043 CAGCCCTCCCCCAGATAATAG 59.088 57.143 0.00 0.00 0.00 1.73
393 3294 1.802117 AGCCCTCCCCCAGATAATAGA 59.198 52.381 0.00 0.00 0.00 1.98
394 3295 2.392100 AGCCCTCCCCCAGATAATAGAT 59.608 50.000 0.00 0.00 0.00 1.98
395 3296 3.607575 AGCCCTCCCCCAGATAATAGATA 59.392 47.826 0.00 0.00 0.00 1.98
396 3297 4.238731 AGCCCTCCCCCAGATAATAGATAT 59.761 45.833 0.00 0.00 0.00 1.63
397 3298 4.349342 GCCCTCCCCCAGATAATAGATATG 59.651 50.000 0.00 0.00 0.00 1.78
398 3299 5.542743 CCCTCCCCCAGATAATAGATATGT 58.457 45.833 0.00 0.00 0.00 2.29
399 3300 5.367937 CCCTCCCCCAGATAATAGATATGTG 59.632 48.000 0.00 0.00 35.55 3.21
406 3307 7.840342 CCAGATAATAGATATGTGGCACTTC 57.160 40.000 19.83 12.66 45.41 3.01
407 3308 7.619050 CCAGATAATAGATATGTGGCACTTCT 58.381 38.462 19.83 18.58 45.41 2.85
408 3309 8.753133 CCAGATAATAGATATGTGGCACTTCTA 58.247 37.037 19.83 19.94 45.41 2.10
410 3311 9.314133 AGATAATAGATATGTGGCACTTCTACA 57.686 33.333 19.83 12.98 40.54 2.74
412 3313 4.046938 AGATATGTGGCACTTCTACACG 57.953 45.455 19.83 0.00 39.04 4.49
414 3315 1.795768 ATGTGGCACTTCTACACGTG 58.204 50.000 19.83 15.48 39.04 4.49
422 3323 3.864921 GCACTTCTACACGTGAATTCCCT 60.865 47.826 25.01 0.00 33.04 4.20
425 3326 4.995487 ACTTCTACACGTGAATTCCCTTTC 59.005 41.667 25.01 0.00 0.00 2.62
427 3328 2.649531 ACACGTGAATTCCCTTTCCA 57.350 45.000 25.01 0.00 0.00 3.53
435 3336 2.907458 ATTCCCTTTCCACTTCCCTG 57.093 50.000 0.00 0.00 0.00 4.45
436 3337 1.529744 TTCCCTTTCCACTTCCCTGT 58.470 50.000 0.00 0.00 0.00 4.00
438 3339 1.144913 TCCCTTTCCACTTCCCTGTTG 59.855 52.381 0.00 0.00 0.00 3.33
447 3348 3.434309 CACTTCCCTGTTGAATTCCCAT 58.566 45.455 2.27 0.00 0.00 4.00
448 3349 3.834231 CACTTCCCTGTTGAATTCCCATT 59.166 43.478 2.27 0.00 0.00 3.16
449 3350 4.082026 CACTTCCCTGTTGAATTCCCATTC 60.082 45.833 2.27 0.00 39.58 2.67
451 3352 2.381618 TCCCTGTTGAATTCCCATTCCA 59.618 45.455 2.27 0.00 38.50 3.53
452 3353 2.497273 CCCTGTTGAATTCCCATTCCAC 59.503 50.000 2.27 0.00 38.50 4.02
453 3354 2.497273 CCTGTTGAATTCCCATTCCACC 59.503 50.000 2.27 0.00 38.50 4.61
454 3355 3.434309 CTGTTGAATTCCCATTCCACCT 58.566 45.455 2.27 0.00 38.50 4.00
455 3356 3.430453 TGTTGAATTCCCATTCCACCTC 58.570 45.455 2.27 0.00 38.50 3.85
456 3357 3.075882 TGTTGAATTCCCATTCCACCTCT 59.924 43.478 2.27 0.00 38.50 3.69
458 3359 3.192944 TGAATTCCCATTCCACCTCTCT 58.807 45.455 2.27 0.00 38.50 3.10
460 3361 4.977739 TGAATTCCCATTCCACCTCTCTAT 59.022 41.667 2.27 0.00 38.50 1.98
461 3362 4.989875 ATTCCCATTCCACCTCTCTATG 57.010 45.455 0.00 0.00 0.00 2.23
463 3364 1.072965 CCCATTCCACCTCTCTATGCC 59.927 57.143 0.00 0.00 0.00 4.40
464 3365 2.053244 CCATTCCACCTCTCTATGCCT 58.947 52.381 0.00 0.00 0.00 4.75
465 3366 2.038295 CCATTCCACCTCTCTATGCCTC 59.962 54.545 0.00 0.00 0.00 4.70
467 3368 2.550277 TCCACCTCTCTATGCCTCAA 57.450 50.000 0.00 0.00 0.00 3.02
469 3370 2.501723 TCCACCTCTCTATGCCTCAAAC 59.498 50.000 0.00 0.00 0.00 2.93
481 3405 1.683319 GCCTCAAACTCCCATTCCCTC 60.683 57.143 0.00 0.00 0.00 4.30
482 3406 1.918957 CCTCAAACTCCCATTCCCTCT 59.081 52.381 0.00 0.00 0.00 3.69
485 3409 2.840651 TCAAACTCCCATTCCCTCTCTC 59.159 50.000 0.00 0.00 0.00 3.20
489 3413 2.294127 ACTCCCATTCCCTCTCTCCAAT 60.294 50.000 0.00 0.00 0.00 3.16
493 3417 2.511218 CCATTCCCTCTCTCCAATTCCA 59.489 50.000 0.00 0.00 0.00 3.53
494 3418 3.139770 CCATTCCCTCTCTCCAATTCCAT 59.860 47.826 0.00 0.00 0.00 3.41
496 3420 2.042464 TCCCTCTCTCCAATTCCATCG 58.958 52.381 0.00 0.00 0.00 3.84
499 3423 3.462021 CCTCTCTCCAATTCCATCGAAC 58.538 50.000 0.00 0.00 0.00 3.95
510 3434 0.523072 CCATCGAACCAAACAGGCTG 59.477 55.000 14.16 14.16 43.14 4.85
511 3435 1.238439 CATCGAACCAAACAGGCTGT 58.762 50.000 15.88 15.88 43.14 4.40
512 3436 2.422597 CATCGAACCAAACAGGCTGTA 58.577 47.619 22.37 2.28 43.14 2.74
515 3439 1.534729 GAACCAAACAGGCTGTAGGG 58.465 55.000 30.73 28.86 43.14 3.53
517 3441 0.850784 ACCAAACAGGCTGTAGGGTT 59.149 50.000 30.73 17.29 43.14 4.11
518 3442 2.059490 ACCAAACAGGCTGTAGGGTTA 58.941 47.619 30.73 0.00 43.14 2.85
519 3443 2.039879 ACCAAACAGGCTGTAGGGTTAG 59.960 50.000 30.73 15.67 43.14 2.34
520 3444 2.304761 CCAAACAGGCTGTAGGGTTAGA 59.695 50.000 22.37 0.00 0.00 2.10
521 3445 3.600388 CAAACAGGCTGTAGGGTTAGAG 58.400 50.000 22.37 0.00 0.00 2.43
522 3446 2.921834 ACAGGCTGTAGGGTTAGAGA 57.078 50.000 20.61 0.00 0.00 3.10
523 3447 2.741145 ACAGGCTGTAGGGTTAGAGAG 58.259 52.381 20.61 0.00 0.00 3.20
524 3448 2.035632 CAGGCTGTAGGGTTAGAGAGG 58.964 57.143 6.28 0.00 0.00 3.69
525 3449 1.062810 AGGCTGTAGGGTTAGAGAGGG 60.063 57.143 0.00 0.00 0.00 4.30
526 3450 1.063114 GGCTGTAGGGTTAGAGAGGGA 60.063 57.143 0.00 0.00 0.00 4.20
527 3451 2.312390 GCTGTAGGGTTAGAGAGGGAG 58.688 57.143 0.00 0.00 0.00 4.30
528 3452 2.091775 GCTGTAGGGTTAGAGAGGGAGA 60.092 54.545 0.00 0.00 0.00 3.71
529 3453 3.827722 CTGTAGGGTTAGAGAGGGAGAG 58.172 54.545 0.00 0.00 0.00 3.20
530 3454 3.460340 CTGTAGGGTTAGAGAGGGAGAGA 59.540 52.174 0.00 0.00 0.00 3.10
531 3455 3.460340 TGTAGGGTTAGAGAGGGAGAGAG 59.540 52.174 0.00 0.00 0.00 3.20
532 3456 2.866515 AGGGTTAGAGAGGGAGAGAGA 58.133 52.381 0.00 0.00 0.00 3.10
533 3457 2.783510 AGGGTTAGAGAGGGAGAGAGAG 59.216 54.545 0.00 0.00 0.00 3.20
540 3464 3.051803 AGAGAGGGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
548 3472 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
591 3515 4.778415 CCGCCGGTCGAGTGTCAG 62.778 72.222 17.96 0.00 41.67 3.51
608 3532 4.772678 GGGCAGCCCATCTCTTTT 57.227 55.556 27.33 0.00 44.65 2.27
610 3534 0.820226 GGGCAGCCCATCTCTTTTTC 59.180 55.000 27.33 0.00 44.65 2.29
611 3535 0.453390 GGCAGCCCATCTCTTTTTCG 59.547 55.000 0.00 0.00 0.00 3.46
612 3536 1.453155 GCAGCCCATCTCTTTTTCGA 58.547 50.000 0.00 0.00 0.00 3.71
613 3537 1.399791 GCAGCCCATCTCTTTTTCGAG 59.600 52.381 0.00 0.00 0.00 4.04
910 3880 4.004348 TCTCAGACGAGACCAGCC 57.996 61.111 0.00 0.00 43.55 4.85
927 3897 1.452108 CCATTCCCGAGCCAGGTTC 60.452 63.158 0.00 0.00 0.00 3.62
1037 4007 6.886459 TCCTTGTCCTTTTATTCTTCTGATGG 59.114 38.462 0.00 0.00 0.00 3.51
1039 4009 7.066766 CCTTGTCCTTTTATTCTTCTGATGGAG 59.933 40.741 0.00 0.00 0.00 3.86
1120 4091 6.054941 CCAAAAATTGACACCTTTTAGCCTT 58.945 36.000 0.00 0.00 0.00 4.35
1289 4260 5.777802 ACTGCATCTTTCCGACTATATCAG 58.222 41.667 0.00 0.00 0.00 2.90
1448 4419 0.458025 GGTGGAGTCGGCTTTCTACG 60.458 60.000 0.00 0.00 0.00 3.51
1473 4444 6.268825 AGCTTTCTCGACTGACAATAAGTA 57.731 37.500 0.00 0.00 0.00 2.24
1492 4463 1.826385 ATTTTGGACTTCCTGCCTCG 58.174 50.000 0.00 0.00 36.82 4.63
1610 4587 4.394729 GAAAAACCATCCACCTACTGTCA 58.605 43.478 0.00 0.00 0.00 3.58
3202 7930 7.007367 CGCAATTGTATGTTGACTGATGTTTAC 59.993 37.037 7.40 0.00 0.00 2.01
3622 8351 1.412343 GGCTTTTTGGGTGAGCTTTGA 59.588 47.619 0.00 0.00 36.66 2.69
4090 8819 1.669115 CTGCTTGTGCTACGTGCCT 60.669 57.895 0.00 0.00 42.00 4.75
4361 9103 0.620030 CATGTCCCATGTCCCTGACA 59.380 55.000 0.00 0.00 46.90 3.58
4402 9199 4.725790 GCATATCAGCCTTTTGGTTCTT 57.274 40.909 0.00 0.00 42.99 2.52
4403 9200 5.077134 GCATATCAGCCTTTTGGTTCTTT 57.923 39.130 0.00 0.00 42.99 2.52
4404 9201 5.105063 GCATATCAGCCTTTTGGTTCTTTC 58.895 41.667 0.00 0.00 42.99 2.62
4405 9202 5.654497 CATATCAGCCTTTTGGTTCTTTCC 58.346 41.667 0.00 0.00 42.99 3.13
4406 9203 3.312736 TCAGCCTTTTGGTTCTTTCCT 57.687 42.857 0.00 0.00 42.99 3.36
4407 9204 3.642141 TCAGCCTTTTGGTTCTTTCCTT 58.358 40.909 0.00 0.00 42.99 3.36
4408 9205 4.030216 TCAGCCTTTTGGTTCTTTCCTTT 58.970 39.130 0.00 0.00 42.99 3.11
4409 9206 4.469586 TCAGCCTTTTGGTTCTTTCCTTTT 59.530 37.500 0.00 0.00 42.99 2.27
4410 9207 5.045942 TCAGCCTTTTGGTTCTTTCCTTTTT 60.046 36.000 0.00 0.00 42.99 1.94
4429 9226 4.417426 TTTTGATCGGAGAAGGGGATAC 57.583 45.455 0.00 0.00 43.58 2.24
4430 9227 3.330126 TTGATCGGAGAAGGGGATACT 57.670 47.619 0.00 0.00 43.58 2.12
4431 9228 2.877866 TGATCGGAGAAGGGGATACTC 58.122 52.381 0.00 0.00 43.58 2.59
4442 9239 1.840635 GGGGATACTCTGGGGATATGC 59.159 57.143 0.00 0.00 0.00 3.14
4443 9240 1.482593 GGGATACTCTGGGGATATGCG 59.517 57.143 0.00 0.00 0.00 4.73
4444 9241 2.180276 GGATACTCTGGGGATATGCGT 58.820 52.381 0.00 0.00 0.00 5.24
4445 9242 3.362706 GGATACTCTGGGGATATGCGTA 58.637 50.000 0.00 0.00 0.00 4.42
4446 9243 3.961408 GGATACTCTGGGGATATGCGTAT 59.039 47.826 0.00 0.00 0.00 3.06
4447 9244 4.406003 GGATACTCTGGGGATATGCGTATT 59.594 45.833 0.00 0.00 0.00 1.89
4448 9245 3.685139 ACTCTGGGGATATGCGTATTG 57.315 47.619 0.00 0.00 0.00 1.90
4449 9246 2.289694 ACTCTGGGGATATGCGTATTGC 60.290 50.000 0.00 0.00 46.70 3.56
4494 9298 2.025727 CGCCGACCTGGACGTATC 59.974 66.667 16.67 5.47 42.00 2.24
4495 9299 2.025727 GCCGACCTGGACGTATCG 59.974 66.667 16.67 7.19 42.00 2.92
4497 9301 3.506108 CGACCTGGACGTATCGGT 58.494 61.111 10.37 2.15 0.00 4.69
4498 9302 1.063649 CGACCTGGACGTATCGGTG 59.936 63.158 10.37 0.00 0.00 4.94
4499 9303 1.226888 GACCTGGACGTATCGGTGC 60.227 63.158 0.00 0.00 0.00 5.01
4500 9304 1.664321 GACCTGGACGTATCGGTGCT 61.664 60.000 0.00 0.00 0.00 4.40
4510 9314 3.119245 ACGTATCGGTGCTTTGTAGTCAT 60.119 43.478 0.00 0.00 0.00 3.06
4582 13041 4.112634 GAGATGTGTAGTTTCATAGCGCA 58.887 43.478 11.47 0.00 0.00 6.09
4587 13046 5.448438 TGTGTAGTTTCATAGCGCAAAAAG 58.552 37.500 11.47 0.00 0.00 2.27
4931 13390 1.358725 GCGTGTAATGGAAGCAGCGA 61.359 55.000 0.00 0.00 0.00 4.93
4933 13392 1.438651 GTGTAATGGAAGCAGCGACA 58.561 50.000 0.00 0.00 0.00 4.35
5123 13582 3.209410 GCTGGATTAAGGTCTGACCATG 58.791 50.000 27.48 5.16 41.95 3.66
5241 13700 7.835682 TGGTAGTAGTAGTAGGCTGTTTGATAA 59.164 37.037 0.00 0.00 0.00 1.75
5321 13780 5.860182 CCTCAGCAAGATATTGTTTGTGTTG 59.140 40.000 1.46 0.00 0.00 3.33
5359 13819 7.120579 TGAGTGGTTTTTGGTGATGTATGTATC 59.879 37.037 0.00 0.00 0.00 2.24
5521 13981 3.629142 ACAAGTAAGGATACAGGCACC 57.371 47.619 0.00 0.00 41.41 5.01
5821 14333 0.831966 CAGCAGCAGAGAAGGGAGAT 59.168 55.000 0.00 0.00 0.00 2.75
5900 14412 9.111519 TGCATAAAGGATAAGAACCCTATGATA 57.888 33.333 0.00 0.00 31.19 2.15
5922 14434 1.416772 GTTATGTACTCCCTCTGCCCC 59.583 57.143 0.00 0.00 0.00 5.80
5930 14442 2.024941 ACTCCCTCTGCCCCAAAATAAG 60.025 50.000 0.00 0.00 0.00 1.73
5934 14446 1.401905 CTCTGCCCCAAAATAAGCGTC 59.598 52.381 0.00 0.00 0.00 5.19
6006 14518 9.213799 CTAGGTCTTTGGCTATGAGATTTTATC 57.786 37.037 0.00 0.00 0.00 1.75
6009 14521 7.389053 GGTCTTTGGCTATGAGATTTTATCGAT 59.611 37.037 2.16 2.16 0.00 3.59
6014 14526 8.484641 TGGCTATGAGATTTTATCGATCAATC 57.515 34.615 17.08 17.08 0.00 2.67
6095 14623 8.094548 TGCAACTAAACATGATGACTACTTACT 58.905 33.333 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.543749 ACTAGCATGGTCCTGCCTTC 59.456 55.000 0.00 0.00 43.33 3.46
44 45 4.330894 CACAACATGTGTCTACCTAGCATG 59.669 45.833 0.00 0.00 43.08 4.06
92 93 6.633668 TTCAAATTTTCGAGTTCGCAAAAA 57.366 29.167 3.69 4.07 37.92 1.94
93 94 6.633668 TTTCAAATTTTCGAGTTCGCAAAA 57.366 29.167 3.69 8.29 37.92 2.44
94 95 6.633668 TTTTCAAATTTTCGAGTTCGCAAA 57.366 29.167 2.16 2.16 38.64 3.68
95 96 6.633668 TTTTTCAAATTTTCGAGTTCGCAA 57.366 29.167 0.00 0.00 39.60 4.85
123 124 9.650539 TCACAAAAGTCAAATTTTCAAATCTCA 57.349 25.926 0.00 0.00 30.01 3.27
125 126 8.606602 GCTCACAAAAGTCAAATTTTCAAATCT 58.393 29.630 0.00 0.00 30.01 2.40
126 127 8.606602 AGCTCACAAAAGTCAAATTTTCAAATC 58.393 29.630 0.00 0.00 30.01 2.17
127 128 8.496707 AGCTCACAAAAGTCAAATTTTCAAAT 57.503 26.923 0.00 0.00 30.01 2.32
128 129 7.903995 AGCTCACAAAAGTCAAATTTTCAAA 57.096 28.000 0.00 0.00 30.01 2.69
141 142 1.268899 CCTGCTCCAAGCTCACAAAAG 59.731 52.381 0.11 0.00 42.97 2.27
151 152 2.045536 GCTCCCACCTGCTCCAAG 60.046 66.667 0.00 0.00 0.00 3.61
301 2760 2.032722 CGTTAGTTTGCCAAACACGCTA 60.033 45.455 21.45 3.26 43.79 4.26
306 2765 2.359531 CCTTCCGTTAGTTTGCCAAACA 59.640 45.455 21.45 5.81 43.79 2.83
313 2772 2.752903 CCATTCCCCTTCCGTTAGTTTG 59.247 50.000 0.00 0.00 0.00 2.93
314 2773 2.291346 CCCATTCCCCTTCCGTTAGTTT 60.291 50.000 0.00 0.00 0.00 2.66
315 2774 1.283905 CCCATTCCCCTTCCGTTAGTT 59.716 52.381 0.00 0.00 0.00 2.24
316 2775 0.916809 CCCATTCCCCTTCCGTTAGT 59.083 55.000 0.00 0.00 0.00 2.24
317 2776 1.141053 CTCCCATTCCCCTTCCGTTAG 59.859 57.143 0.00 0.00 0.00 2.34
321 2780 0.331616 AAACTCCCATTCCCCTTCCG 59.668 55.000 0.00 0.00 0.00 4.30
323 2782 4.018324 AGAGTTAAACTCCCATTCCCCTTC 60.018 45.833 0.00 0.00 46.18 3.46
326 2785 5.446260 TTAGAGTTAAACTCCCATTCCCC 57.554 43.478 0.00 0.00 46.18 4.81
331 2790 6.910259 AGGGAATTAGAGTTAAACTCCCAT 57.090 37.500 15.00 0.00 46.18 4.00
337 2796 6.250711 TGGGGAAAGGGAATTAGAGTTAAAC 58.749 40.000 0.00 0.00 0.00 2.01
342 2801 4.384465 AGATGGGGAAAGGGAATTAGAGT 58.616 43.478 0.00 0.00 0.00 3.24
343 2802 4.413520 TGAGATGGGGAAAGGGAATTAGAG 59.586 45.833 0.00 0.00 0.00 2.43
344 2803 4.379875 TGAGATGGGGAAAGGGAATTAGA 58.620 43.478 0.00 0.00 0.00 2.10
345 2804 4.796110 TGAGATGGGGAAAGGGAATTAG 57.204 45.455 0.00 0.00 0.00 1.73
346 2805 5.749422 ATTGAGATGGGGAAAGGGAATTA 57.251 39.130 0.00 0.00 0.00 1.40
349 3250 4.325816 GGTAATTGAGATGGGGAAAGGGAA 60.326 45.833 0.00 0.00 0.00 3.97
354 3255 3.627237 GGCTGGTAATTGAGATGGGGAAA 60.627 47.826 0.00 0.00 0.00 3.13
359 3260 2.487986 GGAGGGCTGGTAATTGAGATGG 60.488 54.545 0.00 0.00 0.00 3.51
360 3261 2.487986 GGGAGGGCTGGTAATTGAGATG 60.488 54.545 0.00 0.00 0.00 2.90
361 3262 1.777272 GGGAGGGCTGGTAATTGAGAT 59.223 52.381 0.00 0.00 0.00 2.75
362 3263 1.213296 GGGAGGGCTGGTAATTGAGA 58.787 55.000 0.00 0.00 0.00 3.27
363 3264 0.183731 GGGGAGGGCTGGTAATTGAG 59.816 60.000 0.00 0.00 0.00 3.02
364 3265 1.286305 GGGGGAGGGCTGGTAATTGA 61.286 60.000 0.00 0.00 0.00 2.57
365 3266 1.230212 GGGGGAGGGCTGGTAATTG 59.770 63.158 0.00 0.00 0.00 2.32
375 3276 5.367937 CACATATCTATTATCTGGGGGAGGG 59.632 48.000 0.00 0.00 0.00 4.30
376 3277 5.367937 CCACATATCTATTATCTGGGGGAGG 59.632 48.000 0.00 0.00 0.00 4.30
377 3278 5.163258 GCCACATATCTATTATCTGGGGGAG 60.163 48.000 0.00 0.00 29.47 4.30
378 3279 4.721776 GCCACATATCTATTATCTGGGGGA 59.278 45.833 0.00 0.00 29.47 4.81
383 3284 9.579768 GTAGAAGTGCCACATATCTATTATCTG 57.420 37.037 0.00 0.00 0.00 2.90
387 3288 7.013942 ACGTGTAGAAGTGCCACATATCTATTA 59.986 37.037 0.00 0.00 0.00 0.98
390 3291 4.643334 ACGTGTAGAAGTGCCACATATCTA 59.357 41.667 0.00 0.00 0.00 1.98
391 3292 3.447586 ACGTGTAGAAGTGCCACATATCT 59.552 43.478 0.00 0.29 0.00 1.98
392 3293 3.551890 CACGTGTAGAAGTGCCACATATC 59.448 47.826 7.58 0.00 0.00 1.63
393 3294 3.194755 TCACGTGTAGAAGTGCCACATAT 59.805 43.478 16.51 0.00 38.19 1.78
394 3295 2.559231 TCACGTGTAGAAGTGCCACATA 59.441 45.455 16.51 0.00 38.19 2.29
395 3296 1.343142 TCACGTGTAGAAGTGCCACAT 59.657 47.619 16.51 0.00 38.19 3.21
396 3297 0.747852 TCACGTGTAGAAGTGCCACA 59.252 50.000 16.51 0.00 38.19 4.17
397 3298 1.860676 TTCACGTGTAGAAGTGCCAC 58.139 50.000 16.51 0.00 38.19 5.01
398 3299 2.831685 ATTCACGTGTAGAAGTGCCA 57.168 45.000 16.51 0.00 38.19 4.92
399 3300 2.415512 GGAATTCACGTGTAGAAGTGCC 59.584 50.000 16.51 0.00 38.19 5.01
401 3302 3.926616 AGGGAATTCACGTGTAGAAGTG 58.073 45.455 16.51 0.00 39.55 3.16
402 3303 4.618920 AAGGGAATTCACGTGTAGAAGT 57.381 40.909 16.51 1.27 0.00 3.01
403 3304 4.392138 GGAAAGGGAATTCACGTGTAGAAG 59.608 45.833 16.51 0.00 0.00 2.85
405 3306 3.325425 TGGAAAGGGAATTCACGTGTAGA 59.675 43.478 16.51 3.42 0.00 2.59
406 3307 3.435671 GTGGAAAGGGAATTCACGTGTAG 59.564 47.826 16.51 0.00 0.00 2.74
407 3308 3.071892 AGTGGAAAGGGAATTCACGTGTA 59.928 43.478 16.51 6.35 0.00 2.90
408 3309 2.158667 AGTGGAAAGGGAATTCACGTGT 60.159 45.455 16.51 0.00 0.00 4.49
410 3311 2.951229 AGTGGAAAGGGAATTCACGT 57.049 45.000 7.93 0.00 0.00 4.49
412 3313 2.826128 GGGAAGTGGAAAGGGAATTCAC 59.174 50.000 7.93 3.01 0.00 3.18
414 3315 3.092301 CAGGGAAGTGGAAAGGGAATTC 58.908 50.000 0.00 0.00 0.00 2.17
422 3323 3.895041 GGAATTCAACAGGGAAGTGGAAA 59.105 43.478 7.93 0.00 35.23 3.13
425 3326 2.171003 GGGAATTCAACAGGGAAGTGG 58.829 52.381 7.93 0.00 0.00 4.00
427 3328 3.833559 ATGGGAATTCAACAGGGAAGT 57.166 42.857 7.93 0.00 0.00 3.01
435 3336 3.696548 GAGAGGTGGAATGGGAATTCAAC 59.303 47.826 7.93 0.00 34.51 3.18
436 3337 3.593328 AGAGAGGTGGAATGGGAATTCAA 59.407 43.478 7.93 0.00 32.39 2.69
438 3339 3.941704 AGAGAGGTGGAATGGGAATTC 57.058 47.619 0.00 0.00 0.00 2.17
447 3348 2.550277 TGAGGCATAGAGAGGTGGAA 57.450 50.000 0.00 0.00 0.00 3.53
448 3349 2.501723 GTTTGAGGCATAGAGAGGTGGA 59.498 50.000 0.00 0.00 0.00 4.02
449 3350 2.503356 AGTTTGAGGCATAGAGAGGTGG 59.497 50.000 0.00 0.00 0.00 4.61
451 3352 2.769095 GGAGTTTGAGGCATAGAGAGGT 59.231 50.000 0.00 0.00 0.00 3.85
452 3353 2.103941 GGGAGTTTGAGGCATAGAGAGG 59.896 54.545 0.00 0.00 0.00 3.69
453 3354 2.768527 TGGGAGTTTGAGGCATAGAGAG 59.231 50.000 0.00 0.00 0.00 3.20
454 3355 2.832838 TGGGAGTTTGAGGCATAGAGA 58.167 47.619 0.00 0.00 0.00 3.10
455 3356 3.853355 ATGGGAGTTTGAGGCATAGAG 57.147 47.619 0.00 0.00 0.00 2.43
456 3357 3.117888 GGAATGGGAGTTTGAGGCATAGA 60.118 47.826 0.00 0.00 0.00 1.98
458 3359 2.091885 GGGAATGGGAGTTTGAGGCATA 60.092 50.000 0.00 0.00 0.00 3.14
460 3361 0.039618 GGGAATGGGAGTTTGAGGCA 59.960 55.000 0.00 0.00 0.00 4.75
461 3362 0.332972 AGGGAATGGGAGTTTGAGGC 59.667 55.000 0.00 0.00 0.00 4.70
463 3364 2.843113 AGAGAGGGAATGGGAGTTTGAG 59.157 50.000 0.00 0.00 0.00 3.02
464 3365 2.840651 GAGAGAGGGAATGGGAGTTTGA 59.159 50.000 0.00 0.00 0.00 2.69
465 3366 2.092699 GGAGAGAGGGAATGGGAGTTTG 60.093 54.545 0.00 0.00 0.00 2.93
467 3368 1.081174 TGGAGAGAGGGAATGGGAGTT 59.919 52.381 0.00 0.00 0.00 3.01
469 3370 1.885049 TTGGAGAGAGGGAATGGGAG 58.115 55.000 0.00 0.00 0.00 4.30
481 3405 3.266510 TGGTTCGATGGAATTGGAGAG 57.733 47.619 0.00 0.00 34.05 3.20
482 3406 3.712016 TTGGTTCGATGGAATTGGAGA 57.288 42.857 0.00 0.00 34.05 3.71
485 3409 3.367292 CCTGTTTGGTTCGATGGAATTGG 60.367 47.826 0.00 0.00 34.05 3.16
489 3413 1.202879 AGCCTGTTTGGTTCGATGGAA 60.203 47.619 0.00 0.00 38.35 3.53
493 3417 2.615493 CCTACAGCCTGTTTGGTTCGAT 60.615 50.000 1.02 0.00 38.35 3.59
494 3418 1.270625 CCTACAGCCTGTTTGGTTCGA 60.271 52.381 1.02 0.00 38.35 3.71
496 3420 1.202891 ACCCTACAGCCTGTTTGGTTC 60.203 52.381 1.02 0.00 38.35 3.62
499 3423 2.304761 TCTAACCCTACAGCCTGTTTGG 59.695 50.000 1.02 6.73 39.35 3.28
510 3434 3.717913 TCTCTCTCCCTCTCTAACCCTAC 59.282 52.174 0.00 0.00 0.00 3.18
511 3435 3.977999 CTCTCTCTCCCTCTCTAACCCTA 59.022 52.174 0.00 0.00 0.00 3.53
512 3436 2.783510 CTCTCTCTCCCTCTCTAACCCT 59.216 54.545 0.00 0.00 0.00 4.34
515 3439 4.654262 TCTCTCTCTCTCTCCCTCTCTAAC 59.346 50.000 0.00 0.00 0.00 2.34
517 3441 4.170053 TCTCTCTCTCTCTCTCCCTCTCTA 59.830 50.000 0.00 0.00 0.00 2.43
518 3442 3.051803 TCTCTCTCTCTCTCTCCCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
519 3443 3.309296 TCTCTCTCTCTCTCTCCCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
520 3444 3.051803 TCTCTCTCTCTCTCTCTCCCTCT 60.052 52.174 0.00 0.00 0.00 3.69
521 3445 3.309296 TCTCTCTCTCTCTCTCTCCCTC 58.691 54.545 0.00 0.00 0.00 4.30
522 3446 3.051803 TCTCTCTCTCTCTCTCTCTCCCT 60.052 52.174 0.00 0.00 0.00 4.20
523 3447 3.309296 TCTCTCTCTCTCTCTCTCTCCC 58.691 54.545 0.00 0.00 0.00 4.30
524 3448 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
525 3449 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
526 3450 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
527 3451 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
528 3452 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
529 3453 5.335583 CGATCTCTCTCTCTCTCTCTCTCTC 60.336 52.000 0.00 0.00 0.00 3.20
530 3454 4.522405 CGATCTCTCTCTCTCTCTCTCTCT 59.478 50.000 0.00 0.00 0.00 3.10
531 3455 4.321601 CCGATCTCTCTCTCTCTCTCTCTC 60.322 54.167 0.00 0.00 0.00 3.20
532 3456 3.576118 CCGATCTCTCTCTCTCTCTCTCT 59.424 52.174 0.00 0.00 0.00 3.10
533 3457 3.574396 TCCGATCTCTCTCTCTCTCTCTC 59.426 52.174 0.00 0.00 0.00 3.20
540 3464 2.783135 GCATCTCCGATCTCTCTCTCT 58.217 52.381 0.00 0.00 0.00 3.10
591 3515 0.820226 GAAAAAGAGATGGGCTGCCC 59.180 55.000 30.97 30.97 45.71 5.36
605 3529 1.873591 GTGCCTCTTCTGCTCGAAAAA 59.126 47.619 0.00 0.00 0.00 1.94
606 3530 1.202639 TGTGCCTCTTCTGCTCGAAAA 60.203 47.619 0.00 0.00 0.00 2.29
608 3532 0.319900 GTGTGCCTCTTCTGCTCGAA 60.320 55.000 0.00 0.00 0.00 3.71
610 3534 0.601046 TTGTGTGCCTCTTCTGCTCG 60.601 55.000 0.00 0.00 0.00 5.03
611 3535 1.597742 TTTGTGTGCCTCTTCTGCTC 58.402 50.000 0.00 0.00 0.00 4.26
612 3536 2.283145 ATTTGTGTGCCTCTTCTGCT 57.717 45.000 0.00 0.00 0.00 4.24
613 3537 3.671702 GCTTATTTGTGTGCCTCTTCTGC 60.672 47.826 0.00 0.00 0.00 4.26
910 3880 1.026718 GTGAACCTGGCTCGGGAATG 61.027 60.000 7.02 0.00 33.36 2.67
927 3897 1.139095 GAGAAGGTAGGCGTCCGTG 59.861 63.158 0.00 0.00 0.00 4.94
1037 4007 4.167268 ACTAATTCGAGTGCGTTCTTCTC 58.833 43.478 0.00 0.00 38.98 2.87
1039 4009 4.150098 ACAACTAATTCGAGTGCGTTCTTC 59.850 41.667 0.00 0.00 38.98 2.87
1079 4049 6.616774 TTTTTGGCATCTTTGATGAAAACC 57.383 33.333 11.25 3.95 0.00 3.27
1140 4111 6.112058 AGAAGAGATGCAACTTTGATAGTCC 58.888 40.000 0.00 0.00 35.54 3.85
1289 4260 4.051237 GTGGCAAGGAAACAAATCAGAAC 58.949 43.478 0.00 0.00 0.00 3.01
1448 4419 5.635700 ACTTATTGTCAGTCGAGAAAGCTTC 59.364 40.000 0.00 0.00 0.00 3.86
1473 4444 1.826385 CGAGGCAGGAAGTCCAAAAT 58.174 50.000 0.00 0.00 38.89 1.82
1492 4463 3.557228 TTTCAAATATGGGCCCATTGC 57.443 42.857 41.49 5.65 37.82 3.56
1610 4587 9.396022 TCACTGTCTTTTAAGAAGAAAGTCATT 57.604 29.630 14.97 0.00 41.60 2.57
1681 4660 1.538047 TTCAGCCATCTCAACCTTGC 58.462 50.000 0.00 0.00 0.00 4.01
3057 7765 7.043059 TCCAAATGCGTAGAAAAATGTCAAAAC 60.043 33.333 0.00 0.00 0.00 2.43
3446 8174 2.171448 AGGAGACACAAGAAACACTGCT 59.829 45.455 0.00 0.00 0.00 4.24
4090 8819 5.368145 GACATACCTAAATGGCATCTGACA 58.632 41.667 0.00 0.00 40.22 3.58
4361 9103 1.378514 GCCGGGACACCATCAACAT 60.379 57.895 2.18 0.00 36.13 2.71
4407 9204 4.473559 AGTATCCCCTTCTCCGATCAAAAA 59.526 41.667 0.00 0.00 0.00 1.94
4408 9205 4.037927 AGTATCCCCTTCTCCGATCAAAA 58.962 43.478 0.00 0.00 0.00 2.44
4409 9206 3.641906 GAGTATCCCCTTCTCCGATCAAA 59.358 47.826 0.00 0.00 0.00 2.69
4410 9207 3.117093 AGAGTATCCCCTTCTCCGATCAA 60.117 47.826 0.00 0.00 33.66 2.57
4411 9208 2.447429 AGAGTATCCCCTTCTCCGATCA 59.553 50.000 0.00 0.00 33.66 2.92
4412 9209 2.823154 CAGAGTATCCCCTTCTCCGATC 59.177 54.545 0.00 0.00 33.66 3.69
4413 9210 2.491825 CCAGAGTATCCCCTTCTCCGAT 60.492 54.545 0.00 0.00 33.66 4.18
4414 9211 1.133450 CCAGAGTATCCCCTTCTCCGA 60.133 57.143 0.00 0.00 33.66 4.55
4415 9212 1.333177 CCAGAGTATCCCCTTCTCCG 58.667 60.000 0.00 0.00 33.66 4.63
4416 9213 1.723288 CCCAGAGTATCCCCTTCTCC 58.277 60.000 0.00 0.00 33.66 3.71
4417 9214 1.220750 TCCCCAGAGTATCCCCTTCTC 59.779 57.143 0.00 0.00 33.66 2.87
4418 9215 1.330155 TCCCCAGAGTATCCCCTTCT 58.670 55.000 0.00 0.00 33.66 2.85
4419 9216 2.424684 ATCCCCAGAGTATCCCCTTC 57.575 55.000 0.00 0.00 33.66 3.46
4420 9217 3.808189 CATATCCCCAGAGTATCCCCTT 58.192 50.000 0.00 0.00 33.66 3.95
4421 9218 2.563134 GCATATCCCCAGAGTATCCCCT 60.563 54.545 0.00 0.00 33.66 4.79
4422 9219 1.840635 GCATATCCCCAGAGTATCCCC 59.159 57.143 0.00 0.00 33.66 4.81
4423 9220 1.482593 CGCATATCCCCAGAGTATCCC 59.517 57.143 0.00 0.00 33.66 3.85
4424 9221 2.180276 ACGCATATCCCCAGAGTATCC 58.820 52.381 0.00 0.00 33.66 2.59
4425 9222 5.352284 CAATACGCATATCCCCAGAGTATC 58.648 45.833 0.00 0.00 29.87 2.24
4426 9223 4.383118 GCAATACGCATATCCCCAGAGTAT 60.383 45.833 0.00 0.00 41.79 2.12
4427 9224 3.056107 GCAATACGCATATCCCCAGAGTA 60.056 47.826 0.00 0.00 41.79 2.59
4428 9225 2.289694 GCAATACGCATATCCCCAGAGT 60.290 50.000 0.00 0.00 41.79 3.24
4429 9226 2.350522 GCAATACGCATATCCCCAGAG 58.649 52.381 0.00 0.00 41.79 3.35
4430 9227 2.472695 GCAATACGCATATCCCCAGA 57.527 50.000 0.00 0.00 41.79 3.86
4450 9247 4.201773 CCGCGTACAAAACATGATACACAT 60.202 41.667 4.92 0.00 40.17 3.21
4451 9248 3.123790 CCGCGTACAAAACATGATACACA 59.876 43.478 4.92 0.00 0.00 3.72
4452 9249 3.368539 TCCGCGTACAAAACATGATACAC 59.631 43.478 4.92 0.00 0.00 2.90
4453 9250 3.368539 GTCCGCGTACAAAACATGATACA 59.631 43.478 4.92 0.00 0.00 2.29
4494 9298 3.367932 CACTACATGACTACAAAGCACCG 59.632 47.826 0.00 0.00 0.00 4.94
4495 9299 3.125316 GCACTACATGACTACAAAGCACC 59.875 47.826 0.00 0.00 0.00 5.01
4496 9300 3.125316 GGCACTACATGACTACAAAGCAC 59.875 47.826 0.00 0.00 31.11 4.40
4497 9301 3.244387 TGGCACTACATGACTACAAAGCA 60.244 43.478 0.00 0.00 37.17 3.91
4498 9302 3.125316 GTGGCACTACATGACTACAAAGC 59.875 47.826 11.13 0.00 37.17 3.51
4499 9303 3.684788 GGTGGCACTACATGACTACAAAG 59.315 47.826 18.45 0.00 37.17 2.77
4500 9304 3.326588 AGGTGGCACTACATGACTACAAA 59.673 43.478 18.45 0.00 37.17 2.83
4510 9314 2.940994 TTTGCTTAGGTGGCACTACA 57.059 45.000 18.45 6.08 39.55 2.74
4931 13390 2.040412 GGAACACCTCCTCCAGATTTGT 59.960 50.000 0.00 0.00 41.61 2.83
5123 13582 2.817844 ACGGATAGTTCTTTTTGGCCAC 59.182 45.455 3.88 0.00 0.00 5.01
5288 13747 8.389742 ACAATATCTTGCTGAGGATCATGGCT 62.390 42.308 0.00 0.00 39.19 4.75
5321 13780 5.544136 AAAACCACTCAAATTTGTTGCAC 57.456 34.783 17.47 0.00 0.00 4.57
5359 13819 3.554342 CCTCCTCCATCTGCCGGG 61.554 72.222 2.18 0.00 0.00 5.73
5521 13981 8.559536 GTGTGTGGTATGTAAATTGATATCCTG 58.440 37.037 0.00 0.00 0.00 3.86
5625 14085 1.879380 CATTGACGTCCCTTGCTCAAA 59.121 47.619 14.12 0.00 0.00 2.69
5821 14333 8.640063 ATTTCAGCACCATATCAAATATGCTA 57.360 30.769 0.00 0.00 40.96 3.49
5872 14384 8.278639 TCATAGGGTTCTTATCCTTTATGCAAA 58.721 33.333 0.00 0.00 34.75 3.68
5900 14412 2.772515 GGGCAGAGGGAGTACATAACTT 59.227 50.000 0.00 0.00 39.07 2.66
6006 14518 7.759886 TCTTTAGTTCCTAACACTGATTGATCG 59.240 37.037 0.00 0.00 0.00 3.69
6009 14521 9.793259 ATTTCTTTAGTTCCTAACACTGATTGA 57.207 29.630 0.00 0.00 0.00 2.57
6014 14526 8.833231 TCAGATTTCTTTAGTTCCTAACACTG 57.167 34.615 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.