Multiple sequence alignment - TraesCS3B01G203500

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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 TraesCS3B01G203500 chr3B 100.000 5030 0 0 1 5030 237518351 237523380 0.000000e+00 9289.0
1 TraesCS3B01G203500 chr3B 90.269 483 27 5 487 950 690854685 690854204 9.260000e-172 614.0
2 TraesCS3B01G203500 chr3B 85.000 260 18 7 4782 5022 237555198 237555455 1.400000e-60 244.0
3 TraesCS3B01G203500 chr3B 82.553 235 39 2 226 458 41853241 41853475 6.600000e-49 206.0
4 TraesCS3B01G203500 chr3D 94.729 3851 124 18 933 4780 160733904 160737678 0.000000e+00 5914.0
5 TraesCS3B01G203500 chr3D 93.033 244 13 2 4782 5022 160759210 160759452 2.230000e-93 353.0
6 TraesCS3B01G203500 chr3D 88.636 220 14 4 1 220 160733616 160733824 1.800000e-64 257.0
7 TraesCS3B01G203500 chr3D 85.068 221 13 7 4829 5030 160737942 160738161 1.840000e-49 207.0
8 TraesCS3B01G203500 chr3A 94.720 3201 140 18 1158 4354 187438711 187441886 0.000000e+00 4948.0
9 TraesCS3B01G203500 chr3A 91.613 465 20 4 486 931 209408145 209407681 4.280000e-175 625.0
10 TraesCS3B01G203500 chr3A 93.624 298 16 1 4475 4769 187454541 187454838 4.620000e-120 442.0
11 TraesCS3B01G203500 chr3A 89.103 312 26 5 4457 4766 187451946 187452251 1.020000e-101 381.0
12 TraesCS3B01G203500 chr3A 91.509 212 13 2 954 1165 187438008 187438214 2.290000e-73 287.0
13 TraesCS3B01G203500 chr3A 100.000 46 0 0 4399 4444 187451790 187451835 8.970000e-13 86.1
14 TraesCS3B01G203500 chr2B 91.595 464 21 3 486 931 679155457 679154994 4.280000e-175 625.0
15 TraesCS3B01G203500 chr7A 91.577 463 20 4 487 931 301639635 301639174 5.530000e-174 621.0
16 TraesCS3B01G203500 chr7A 89.223 399 22 5 557 935 611541095 611540698 3.520000e-131 479.0
17 TraesCS3B01G203500 chr4B 91.183 465 22 4 485 931 385954109 385954572 9.260000e-172 614.0
18 TraesCS3B01G203500 chr4B 89.631 434 26 4 516 931 76050162 76050594 7.410000e-148 534.0
19 TraesCS3B01G203500 chr4B 78.886 431 66 18 516 934 237948219 237947802 8.300000e-68 268.0
20 TraesCS3B01G203500 chr4B 85.981 214 28 2 229 440 652301022 652300809 1.410000e-55 228.0
21 TraesCS3B01G203500 chr4B 83.898 236 33 5 226 458 479374620 479374853 2.360000e-53 220.0
22 TraesCS3B01G203500 chr4B 82.661 248 31 11 4782 5022 237935549 237935307 5.100000e-50 209.0
23 TraesCS3B01G203500 chr4B 82.645 242 34 8 220 458 412775306 412775070 1.840000e-49 207.0
24 TraesCS3B01G203500 chr6A 90.618 469 25 4 485 934 237919755 237919287 5.570000e-169 604.0
25 TraesCS3B01G203500 chr5A 90.108 465 26 4 487 931 398892211 398892675 2.020000e-163 586.0
26 TraesCS3B01G203500 chr5A 84.034 238 25 9 226 458 17384954 17384725 3.050000e-52 217.0
27 TraesCS3B01G203500 chr5A 83.613 238 26 9 226 458 17387244 17387015 1.420000e-50 211.0
28 TraesCS3B01G203500 chr5A 83.613 238 26 9 226 458 17389534 17389305 1.420000e-50 211.0
29 TraesCS3B01G203500 chr1A 90.086 464 22 4 486 931 60804660 60805117 9.390000e-162 580.0
30 TraesCS3B01G203500 chr1A 80.601 366 59 10 500 860 107093722 107093364 6.420000e-69 272.0
31 TraesCS3B01G203500 chr4A 89.849 463 26 8 487 931 588511432 588511891 4.370000e-160 575.0
32 TraesCS3B01G203500 chr4A 85.659 258 20 11 4782 5022 151315428 151315685 6.460000e-64 255.0
33 TraesCS3B01G203500 chr4A 84.328 268 22 10 4782 5030 151310287 151310553 1.400000e-60 244.0
34 TraesCS3B01G203500 chr4A 85.938 64 7 2 1231 1294 652815317 652815378 3.250000e-07 67.6
35 TraesCS3B01G203500 chr6B 89.195 435 27 4 516 931 653583434 653583001 4.460000e-145 525.0
36 TraesCS3B01G203500 chr6D 87.402 254 18 8 4782 5022 306299734 306299986 3.830000e-71 279.0
37 TraesCS3B01G203500 chr2D 88.393 224 23 2 4783 5005 218379789 218380010 2.990000e-67 267.0
38 TraesCS3B01G203500 chr7B 84.120 233 32 5 226 456 733079888 733080117 2.360000e-53 220.0
39 TraesCS3B01G203500 chr5B 83.012 259 24 7 4782 5021 320446607 320446350 3.050000e-52 217.0
40 TraesCS3B01G203500 chrUn 83.613 238 26 9 226 458 392418209 392417980 1.420000e-50 211.0
41 TraesCS3B01G203500 chr1D 82.186 247 31 12 4782 5022 220593693 220593932 3.070000e-47 200.0
42 TraesCS3B01G203500 chr1D 80.784 255 36 12 4782 5030 220500929 220501176 2.390000e-43 187.0
43 TraesCS3B01G203500 chr2A 80.162 247 39 7 4782 5022 163625959 163626201 5.180000e-40 176.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G203500 chr3B 237518351 237523380 5029 False 9289.000000 9289 100.000000 1 5030 1 chr3B.!!$F2 5029
1 TraesCS3B01G203500 chr3D 160733616 160738161 4545 False 2126.000000 5914 89.477667 1 5030 3 chr3D.!!$F2 5029
2 TraesCS3B01G203500 chr3A 187438008 187441886 3878 False 2617.500000 4948 93.114500 954 4354 2 chr3A.!!$F1 3400
3 TraesCS3B01G203500 chr3A 187451790 187454838 3048 False 303.033333 442 94.242333 4399 4769 3 chr3A.!!$F2 370
4 TraesCS3B01G203500 chr5A 17384725 17389534 4809 True 213.000000 217 83.753333 226 458 3 chr5A.!!$R1 232

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
578 4936 0.033504 CGCCAGGGCACGATTACTAT 59.966 55.0 11.42 0.0 42.06 2.12 F
1650 6513 0.114560 AGGTCCTCGGTTTCCTCTCA 59.885 55.0 0.00 0.0 0.00 3.27 F
1672 6535 0.322975 GATGCAGACCCAGACACAGT 59.677 55.0 0.00 0.0 0.00 3.55 F
1826 6689 0.790207 GCGCTTCTCGACACAATTCA 59.210 50.0 0.00 0.0 41.67 2.57 F
3553 8427 0.394192 CATCGCTTCCATGCTCCCTA 59.606 55.0 0.00 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2064 6927 0.675837 GGTAGCGGGTTTGGAGGAAC 60.676 60.000 0.0 0.0 0.00 3.62 R
3269 8142 0.111253 ACCTGACCCCTTTCAGCAAG 59.889 55.000 0.0 0.0 41.61 4.01 R
3270 8143 0.178992 CACCTGACCCCTTTCAGCAA 60.179 55.000 0.0 0.0 41.61 3.91 R
3639 8515 1.759445 GCTCTCAACTGCTAGATCCCA 59.241 52.381 0.0 0.0 0.00 4.37 R
4889 12659 0.030399 AGGCGGATAGGGTTTAGGGT 60.030 55.000 0.0 0.0 0.00 4.34 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
40 41 1.404035 GGGTTTTATGCCCATCGTGAC 59.596 52.381 0.00 0.00 45.40 3.67
63 64 3.844090 GCCTCCTCTCACCTCGCC 61.844 72.222 0.00 0.00 0.00 5.54
71 72 1.176619 TCTCACCTCGCCGTCAAGAA 61.177 55.000 0.00 0.00 0.00 2.52
72 73 0.734253 CTCACCTCGCCGTCAAGAAG 60.734 60.000 0.00 0.00 0.00 2.85
73 74 2.048127 ACCTCGCCGTCAAGAAGC 60.048 61.111 0.00 0.00 0.00 3.86
74 75 2.048222 CCTCGCCGTCAAGAAGCA 60.048 61.111 0.00 0.00 0.00 3.91
77 78 1.005037 TCGCCGTCAAGAAGCACAT 60.005 52.632 0.00 0.00 0.00 3.21
79 80 1.421485 GCCGTCAAGAAGCACATCG 59.579 57.895 0.00 0.00 0.00 3.84
80 81 1.014044 GCCGTCAAGAAGCACATCGA 61.014 55.000 0.00 0.00 0.00 3.59
81 82 0.716108 CCGTCAAGAAGCACATCGAC 59.284 55.000 0.00 0.00 0.00 4.20
118 119 5.657302 TCTTAGGGATAGGCGAGGATTTATC 59.343 44.000 0.00 0.00 0.00 1.75
124 125 3.686916 AGGCGAGGATTTATCTAAGGC 57.313 47.619 0.00 0.00 0.00 4.35
139 140 2.603473 GGCTTGGTTGGGGGTTCC 60.603 66.667 0.00 0.00 0.00 3.62
140 141 2.526110 GCTTGGTTGGGGGTTCCT 59.474 61.111 0.00 0.00 36.20 3.36
142 143 1.850549 CTTGGTTGGGGGTTCCTCA 59.149 57.895 0.00 0.00 36.20 3.86
221 222 9.908152 AAAATTAAAGCGGCAAGATTATATACC 57.092 29.630 1.45 0.00 0.00 2.73
222 223 7.625828 ATTAAAGCGGCAAGATTATATACCC 57.374 36.000 1.45 0.00 0.00 3.69
225 226 3.523564 AGCGGCAAGATTATATACCCCAT 59.476 43.478 1.45 0.00 0.00 4.00
226 227 4.719773 AGCGGCAAGATTATATACCCCATA 59.280 41.667 1.45 0.00 0.00 2.74
229 230 6.038271 GCGGCAAGATTATATACCCCATAAAG 59.962 42.308 0.00 0.00 0.00 1.85
240 2307 1.949525 CCCCATAAAGCATCTCCAACG 59.050 52.381 0.00 0.00 0.00 4.10
272 2340 1.651431 GCTCCGCGCGCTAAAATTC 60.651 57.895 30.48 7.62 0.00 2.17
273 2341 1.366494 CTCCGCGCGCTAAAATTCG 60.366 57.895 30.48 10.63 0.00 3.34
281 2349 2.340283 CGCGCTAAAATTCGGGTTTTTC 59.660 45.455 5.56 0.00 33.62 2.29
286 4644 1.041437 AAATTCGGGTTTTTCGGGCA 58.959 45.000 0.00 0.00 0.00 5.36
306 4664 0.391395 CCAGACAGCTCCAGCAGAAG 60.391 60.000 0.48 0.00 45.16 2.85
321 4679 3.091417 GCAGAAGCTGTAAAATAACGCG 58.909 45.455 3.53 3.53 37.91 6.01
322 4680 3.424433 GCAGAAGCTGTAAAATAACGCGT 60.424 43.478 5.58 5.58 37.91 6.01
323 4681 4.081761 CAGAAGCTGTAAAATAACGCGTG 58.918 43.478 14.98 0.00 0.00 5.34
325 4683 1.168588 GCTGTAAAATAACGCGTGCG 58.831 50.000 14.98 13.39 46.03 5.34
327 4685 0.511653 TGTAAAATAACGCGTGCGCA 59.488 45.000 14.98 5.66 44.19 6.09
363 4721 2.828784 CGCTGAAAAACGCTATCGC 58.171 52.632 0.00 0.00 39.84 4.58
364 4722 0.094558 CGCTGAAAAACGCTATCGCA 59.905 50.000 0.00 0.00 39.84 5.10
365 4723 1.463363 CGCTGAAAAACGCTATCGCAA 60.463 47.619 0.00 0.00 39.84 4.85
366 4724 2.169179 GCTGAAAAACGCTATCGCAAG 58.831 47.619 0.00 0.00 39.84 4.01
367 4725 2.412847 GCTGAAAAACGCTATCGCAAGT 60.413 45.455 0.00 0.00 39.84 3.16
408 4766 1.069255 TACGCGCGCTTCACAATTTA 58.931 45.000 32.58 7.62 0.00 1.40
409 4767 0.446222 ACGCGCGCTTCACAATTTAT 59.554 45.000 32.58 1.37 0.00 1.40
415 4773 3.029074 GCGCTTCACAATTTATACTGCG 58.971 45.455 0.00 0.00 43.05 5.18
416 4774 3.485216 GCGCTTCACAATTTATACTGCGT 60.485 43.478 0.00 0.00 42.33 5.24
417 4775 4.260051 GCGCTTCACAATTTATACTGCGTA 60.260 41.667 0.00 0.00 42.33 4.42
440 4798 1.344942 TTTTGCGCGCGTGTTTTTGT 61.345 45.000 32.35 0.00 0.00 2.83
441 4799 2.002963 TTTGCGCGCGTGTTTTTGTG 62.003 50.000 32.35 0.00 0.00 3.33
442 4800 3.677340 GCGCGCGTGTTTTTGTGG 61.677 61.111 32.35 0.00 0.00 4.17
445 4803 0.932585 CGCGCGTGTTTTTGTGGATT 60.933 50.000 24.19 0.00 0.00 3.01
448 4806 1.520590 CGCGTGTTTTTGTGGATTTGG 59.479 47.619 0.00 0.00 0.00 3.28
469 4827 6.404426 TGGTAAACCAATTTATACTCCCCA 57.596 37.500 0.00 0.00 44.35 4.96
470 4828 6.801953 TGGTAAACCAATTTATACTCCCCAA 58.198 36.000 0.00 0.00 44.35 4.12
471 4829 7.246763 TGGTAAACCAATTTATACTCCCCAAA 58.753 34.615 0.00 0.00 44.35 3.28
472 4830 7.901861 TGGTAAACCAATTTATACTCCCCAAAT 59.098 33.333 0.00 0.00 44.35 2.32
473 4831 8.418662 GGTAAACCAATTTATACTCCCCAAATC 58.581 37.037 0.00 0.00 32.91 2.17
474 4832 8.973182 GTAAACCAATTTATACTCCCCAAATCA 58.027 33.333 0.00 0.00 32.91 2.57
475 4833 8.622572 AAACCAATTTATACTCCCCAAATCAT 57.377 30.769 0.00 0.00 0.00 2.45
476 4834 7.839680 ACCAATTTATACTCCCCAAATCATC 57.160 36.000 0.00 0.00 0.00 2.92
477 4835 6.782494 ACCAATTTATACTCCCCAAATCATCC 59.218 38.462 0.00 0.00 0.00 3.51
478 4836 7.012607 CCAATTTATACTCCCCAAATCATCCT 58.987 38.462 0.00 0.00 0.00 3.24
479 4837 7.177392 CCAATTTATACTCCCCAAATCATCCTC 59.823 40.741 0.00 0.00 0.00 3.71
480 4838 7.654287 ATTTATACTCCCCAAATCATCCTCT 57.346 36.000 0.00 0.00 0.00 3.69
481 4839 6.688073 TTATACTCCCCAAATCATCCTCTC 57.312 41.667 0.00 0.00 0.00 3.20
482 4840 2.131023 ACTCCCCAAATCATCCTCTCC 58.869 52.381 0.00 0.00 0.00 3.71
483 4841 2.294127 ACTCCCCAAATCATCCTCTCCT 60.294 50.000 0.00 0.00 0.00 3.69
484 4842 2.371510 CTCCCCAAATCATCCTCTCCTC 59.628 54.545 0.00 0.00 0.00 3.71
485 4843 2.021639 TCCCCAAATCATCCTCTCCTCT 60.022 50.000 0.00 0.00 0.00 3.69
486 4844 3.209843 TCCCCAAATCATCCTCTCCTCTA 59.790 47.826 0.00 0.00 0.00 2.43
487 4845 4.140350 TCCCCAAATCATCCTCTCCTCTAT 60.140 45.833 0.00 0.00 0.00 1.98
488 4846 5.077864 TCCCCAAATCATCCTCTCCTCTATA 59.922 44.000 0.00 0.00 0.00 1.31
489 4847 5.188751 CCCCAAATCATCCTCTCCTCTATAC 59.811 48.000 0.00 0.00 0.00 1.47
490 4848 5.188751 CCCAAATCATCCTCTCCTCTATACC 59.811 48.000 0.00 0.00 0.00 2.73
491 4849 6.022315 CCAAATCATCCTCTCCTCTATACCT 58.978 44.000 0.00 0.00 0.00 3.08
492 4850 6.070881 CCAAATCATCCTCTCCTCTATACCTG 60.071 46.154 0.00 0.00 0.00 4.00
493 4851 4.666412 TCATCCTCTCCTCTATACCTGG 57.334 50.000 0.00 0.00 0.00 4.45
494 4852 2.982339 TCCTCTCCTCTATACCTGGC 57.018 55.000 0.00 0.00 0.00 4.85
495 4853 1.429687 TCCTCTCCTCTATACCTGGCC 59.570 57.143 0.00 0.00 0.00 5.36
496 4854 1.148027 CCTCTCCTCTATACCTGGCCA 59.852 57.143 4.71 4.71 0.00 5.36
497 4855 2.426414 CCTCTCCTCTATACCTGGCCAA 60.426 54.545 7.01 0.00 0.00 4.52
498 4856 3.309296 CTCTCCTCTATACCTGGCCAAA 58.691 50.000 7.01 0.00 0.00 3.28
499 4857 3.039011 TCTCCTCTATACCTGGCCAAAC 58.961 50.000 7.01 0.00 0.00 2.93
500 4858 1.760613 TCCTCTATACCTGGCCAAACG 59.239 52.381 7.01 0.00 0.00 3.60
501 4859 1.202651 CCTCTATACCTGGCCAAACGG 60.203 57.143 7.01 7.56 0.00 4.44
502 4860 0.834612 TCTATACCTGGCCAAACGGG 59.165 55.000 7.01 7.12 42.81 5.28
542 4900 2.213483 CGACCCATCGTAATCGTGC 58.787 57.895 0.00 0.00 43.66 5.34
543 4901 1.213094 CGACCCATCGTAATCGTGCC 61.213 60.000 0.00 0.00 43.66 5.01
544 4902 0.104304 GACCCATCGTAATCGTGCCT 59.896 55.000 0.00 0.00 38.33 4.75
545 4903 0.179084 ACCCATCGTAATCGTGCCTG 60.179 55.000 0.00 0.00 38.33 4.85
546 4904 0.880278 CCCATCGTAATCGTGCCTGG 60.880 60.000 0.00 0.00 38.33 4.45
547 4905 1.498865 CCATCGTAATCGTGCCTGGC 61.499 60.000 12.87 12.87 38.33 4.85
548 4906 1.227556 ATCGTAATCGTGCCTGGCC 60.228 57.895 17.53 6.66 38.33 5.36
549 4907 2.660258 ATCGTAATCGTGCCTGGCCC 62.660 60.000 17.53 2.94 38.33 5.80
550 4908 2.516225 GTAATCGTGCCTGGCCCC 60.516 66.667 17.53 5.77 0.00 5.80
551 4909 4.169696 TAATCGTGCCTGGCCCCG 62.170 66.667 17.53 18.04 0.00 5.73
575 4933 2.895372 CCGCCAGGGCACGATTAC 60.895 66.667 11.42 0.00 42.06 1.89
576 4934 2.186903 CGCCAGGGCACGATTACT 59.813 61.111 11.42 0.00 42.06 2.24
577 4935 1.440060 CGCCAGGGCACGATTACTA 59.560 57.895 11.42 0.00 42.06 1.82
578 4936 0.033504 CGCCAGGGCACGATTACTAT 59.966 55.000 11.42 0.00 42.06 2.12
579 4937 1.271379 CGCCAGGGCACGATTACTATA 59.729 52.381 11.42 0.00 42.06 1.31
580 4938 2.685100 GCCAGGGCACGATTACTATAC 58.315 52.381 5.20 0.00 41.49 1.47
581 4939 2.925306 GCCAGGGCACGATTACTATACG 60.925 54.545 5.20 0.00 41.49 3.06
582 4940 2.352421 CCAGGGCACGATTACTATACGG 60.352 54.545 0.00 0.00 0.00 4.02
583 4941 1.891150 AGGGCACGATTACTATACGGG 59.109 52.381 0.00 0.00 0.00 5.28
586 4944 1.973138 CACGATTACTATACGGGCCG 58.027 55.000 27.06 27.06 0.00 6.13
587 4945 1.267806 CACGATTACTATACGGGCCGT 59.732 52.381 35.91 35.91 44.35 5.68
588 4946 1.267806 ACGATTACTATACGGGCCGTG 59.732 52.381 39.80 26.05 41.39 4.94
589 4947 1.706443 GATTACTATACGGGCCGTGC 58.294 55.000 39.80 15.03 41.39 5.34
640 4998 2.983791 GGCACGGCCCAGTTAGTA 59.016 61.111 0.00 0.00 44.06 1.82
641 4999 1.297364 GGCACGGCCCAGTTAGTAA 59.703 57.895 0.00 0.00 44.06 2.24
642 5000 0.321830 GGCACGGCCCAGTTAGTAAA 60.322 55.000 0.00 0.00 44.06 2.01
643 5001 1.680860 GGCACGGCCCAGTTAGTAAAT 60.681 52.381 0.00 0.00 44.06 1.40
644 5002 1.400494 GCACGGCCCAGTTAGTAAATG 59.600 52.381 3.33 3.33 0.00 2.32
645 5003 2.014128 CACGGCCCAGTTAGTAAATGG 58.986 52.381 20.17 20.17 0.00 3.16
649 5007 1.675552 CCCAGTTAGTAAATGGGCCG 58.324 55.000 30.03 11.64 46.86 6.13
650 5008 1.675552 CCAGTTAGTAAATGGGCCGG 58.324 55.000 19.51 0.00 0.00 6.13
651 5009 1.021968 CAGTTAGTAAATGGGCCGGC 58.978 55.000 21.18 21.18 0.00 6.13
652 5010 0.621609 AGTTAGTAAATGGGCCGGCA 59.378 50.000 30.85 9.36 0.00 5.69
653 5011 0.736636 GTTAGTAAATGGGCCGGCAC 59.263 55.000 30.85 28.40 0.00 5.01
667 5025 2.105328 GCACGTTGGCCCGTTTTT 59.895 55.556 4.13 0.00 39.45 1.94
687 5045 3.296322 TTTTCAGCCTGTTATTTGCCG 57.704 42.857 0.00 0.00 0.00 5.69
688 5046 0.525761 TTCAGCCTGTTATTTGCCGC 59.474 50.000 0.00 0.00 0.00 6.53
689 5047 0.607762 TCAGCCTGTTATTTGCCGCA 60.608 50.000 0.00 0.00 0.00 5.69
690 5048 0.456653 CAGCCTGTTATTTGCCGCAC 60.457 55.000 0.00 0.00 0.00 5.34
691 5049 0.609131 AGCCTGTTATTTGCCGCACT 60.609 50.000 0.00 0.00 0.00 4.40
692 5050 0.456653 GCCTGTTATTTGCCGCACTG 60.457 55.000 0.00 0.00 0.00 3.66
693 5051 1.164411 CCTGTTATTTGCCGCACTGA 58.836 50.000 0.00 0.00 0.00 3.41
694 5052 1.131126 CCTGTTATTTGCCGCACTGAG 59.869 52.381 0.00 0.00 0.00 3.35
695 5053 0.521291 TGTTATTTGCCGCACTGAGC 59.479 50.000 0.00 0.00 40.87 4.26
696 5054 0.521291 GTTATTTGCCGCACTGAGCA 59.479 50.000 0.00 0.00 46.13 4.26
697 5055 1.133025 GTTATTTGCCGCACTGAGCAT 59.867 47.619 0.00 0.00 46.13 3.79
698 5056 1.462616 TATTTGCCGCACTGAGCATT 58.537 45.000 0.00 0.00 46.13 3.56
699 5057 0.604578 ATTTGCCGCACTGAGCATTT 59.395 45.000 0.00 0.00 46.13 2.32
700 5058 0.388659 TTTGCCGCACTGAGCATTTT 59.611 45.000 0.00 0.00 46.13 1.82
701 5059 0.388659 TTGCCGCACTGAGCATTTTT 59.611 45.000 0.00 0.00 46.13 1.94
726 5084 9.830186 TTTAGCCTATTTTTATATATTGGGCCA 57.170 29.630 0.00 0.00 37.98 5.36
767 5125 3.955775 AAAAACGTAGTCGGGCCG 58.044 55.556 22.51 22.51 45.00 6.13
768 5126 1.069596 AAAAACGTAGTCGGGCCGT 59.930 52.632 27.32 10.46 45.00 5.68
769 5127 1.223417 AAAAACGTAGTCGGGCCGTG 61.223 55.000 27.32 13.82 45.00 4.94
770 5128 4.729856 AACGTAGTCGGGCCGTGC 62.730 66.667 27.32 19.49 45.00 5.34
848 5206 2.437895 GGCCTGGCCCGTTTAGAC 60.438 66.667 27.77 0.00 44.06 2.59
849 5207 2.437895 GCCTGGCCCGTTTAGACC 60.438 66.667 7.66 0.00 0.00 3.85
850 5208 2.125269 CCTGGCCCGTTTAGACCG 60.125 66.667 0.00 0.00 0.00 4.79
851 5209 2.660802 CTGGCCCGTTTAGACCGT 59.339 61.111 0.00 0.00 0.00 4.83
852 5210 1.740296 CTGGCCCGTTTAGACCGTG 60.740 63.158 0.00 0.00 0.00 4.94
853 5211 3.122971 GGCCCGTTTAGACCGTGC 61.123 66.667 0.00 0.00 0.00 5.34
854 5212 3.122971 GCCCGTTTAGACCGTGCC 61.123 66.667 0.00 0.00 0.00 5.01
855 5213 2.812178 CCCGTTTAGACCGTGCCG 60.812 66.667 0.00 0.00 0.00 5.69
856 5214 2.048877 CCGTTTAGACCGTGCCGT 60.049 61.111 0.00 0.00 0.00 5.68
857 5215 2.377310 CCGTTTAGACCGTGCCGTG 61.377 63.158 0.00 0.00 0.00 4.94
858 5216 2.858158 GTTTAGACCGTGCCGTGC 59.142 61.111 0.00 0.00 0.00 5.34
859 5217 2.357760 TTTAGACCGTGCCGTGCC 60.358 61.111 0.00 0.00 0.00 5.01
860 5218 2.874664 TTTAGACCGTGCCGTGCCT 61.875 57.895 0.00 0.00 0.00 4.75
861 5219 3.583276 TTAGACCGTGCCGTGCCTG 62.583 63.158 0.00 0.00 0.00 4.85
908 5266 4.548513 ACAGGCCGGCCCCAAAAA 62.549 61.111 41.72 0.00 36.58 1.94
941 5299 0.319469 GCCAGCTATTCTCTCCTCGC 60.319 60.000 0.00 0.00 0.00 5.03
1298 6161 2.675423 CCTCGTCACCTCCGACCA 60.675 66.667 0.00 0.00 31.91 4.02
1299 6162 2.273179 CCTCGTCACCTCCGACCAA 61.273 63.158 0.00 0.00 31.91 3.67
1408 6271 3.010200 TCTACTTCTTCCCGTACCTCC 57.990 52.381 0.00 0.00 0.00 4.30
1512 6375 1.141234 GACGGGGTTCTCGGTCATC 59.859 63.158 5.68 0.00 37.09 2.92
1650 6513 0.114560 AGGTCCTCGGTTTCCTCTCA 59.885 55.000 0.00 0.00 0.00 3.27
1672 6535 0.322975 GATGCAGACCCAGACACAGT 59.677 55.000 0.00 0.00 0.00 3.55
1688 6551 5.470098 AGACACAGTGTATGAACATCCAAAC 59.530 40.000 6.06 0.00 38.08 2.93
1740 6603 1.332195 GGAAAGCTTGGAACCTTGCT 58.668 50.000 0.00 0.00 37.37 3.91
1826 6689 0.790207 GCGCTTCTCGACACAATTCA 59.210 50.000 0.00 0.00 41.67 2.57
1829 6692 2.159920 CGCTTCTCGACACAATTCACAG 60.160 50.000 0.00 0.00 41.67 3.66
2064 6927 2.939103 CTCCTTTTATGGTCTTGCCTCG 59.061 50.000 0.00 0.00 38.35 4.63
2101 6964 1.416049 CACGATTTGTCGGAGCACG 59.584 57.895 2.76 0.00 46.11 5.34
2168 7031 1.818060 TGATCCAAACTTTGATGCGGG 59.182 47.619 2.87 0.00 0.00 6.13
2185 7048 1.763968 GGGGTTTGCTTACCATCCTC 58.236 55.000 9.54 0.00 40.09 3.71
2447 7310 1.221293 CCTTCCTCCTGCTGCAGAG 59.779 63.158 30.10 22.35 32.44 3.35
2642 7505 5.926542 TGGATAAATACTTGCTACGAGATGC 59.073 40.000 0.00 0.00 0.00 3.91
2692 7555 5.763204 CCTTATTGTAACCGATAATGGCAGT 59.237 40.000 0.00 0.00 0.00 4.40
2957 7820 5.305644 TCTGCAGAAAGATATCCCTTACTCC 59.694 44.000 15.67 0.00 0.00 3.85
3168 8041 7.067615 TGAGTAAATTTGTAGACACCTTGCAAA 59.932 33.333 0.00 0.00 33.75 3.68
3169 8042 7.777095 AGTAAATTTGTAGACACCTTGCAAAA 58.223 30.769 0.00 0.00 33.32 2.44
3170 8043 6.902224 AAATTTGTAGACACCTTGCAAAAC 57.098 33.333 0.00 0.00 33.32 2.43
3171 8044 4.379339 TTTGTAGACACCTTGCAAAACC 57.621 40.909 0.00 0.00 0.00 3.27
3172 8045 3.290948 TGTAGACACCTTGCAAAACCT 57.709 42.857 0.00 0.00 0.00 3.50
3173 8046 3.626930 TGTAGACACCTTGCAAAACCTT 58.373 40.909 0.00 0.00 0.00 3.50
3174 8047 3.380004 TGTAGACACCTTGCAAAACCTTG 59.620 43.478 0.00 0.00 35.49 3.61
3236 8109 7.173907 ACACACAAAAATCTTCTACAGGATCTG 59.826 37.037 0.00 0.00 37.52 2.90
3260 8133 7.450074 TGAAGTATTTTGTCTGTGTCTATGGT 58.550 34.615 0.00 0.00 0.00 3.55
3261 8134 7.602644 TGAAGTATTTTGTCTGTGTCTATGGTC 59.397 37.037 0.00 0.00 0.00 4.02
3262 8135 7.004555 AGTATTTTGTCTGTGTCTATGGTCA 57.995 36.000 0.00 0.00 0.00 4.02
3263 8136 7.099764 AGTATTTTGTCTGTGTCTATGGTCAG 58.900 38.462 0.00 0.00 0.00 3.51
3264 8137 5.545063 TTTTGTCTGTGTCTATGGTCAGA 57.455 39.130 0.00 0.00 35.06 3.27
3265 8138 4.790765 TTGTCTGTGTCTATGGTCAGAG 57.209 45.455 0.00 0.00 37.56 3.35
3267 8140 3.093057 GTCTGTGTCTATGGTCAGAGGT 58.907 50.000 1.30 0.00 37.56 3.85
3268 8141 3.092301 TCTGTGTCTATGGTCAGAGGTG 58.908 50.000 1.30 0.00 33.77 4.00
3269 8142 1.550524 TGTGTCTATGGTCAGAGGTGC 59.449 52.381 0.00 0.00 0.00 5.01
3270 8143 1.827969 GTGTCTATGGTCAGAGGTGCT 59.172 52.381 0.00 0.00 0.00 4.40
3308 8181 5.644636 CAGGTGCAAATGGAAGCAAAATAAT 59.355 36.000 0.00 0.00 43.20 1.28
3309 8182 6.817641 CAGGTGCAAATGGAAGCAAAATAATA 59.182 34.615 0.00 0.00 43.20 0.98
3310 8183 7.496591 CAGGTGCAAATGGAAGCAAAATAATAT 59.503 33.333 0.00 0.00 43.20 1.28
3376 8249 4.098501 CCATAGGTTGAAAAGGCAGGAATC 59.901 45.833 0.00 0.00 0.00 2.52
3377 8250 3.243359 AGGTTGAAAAGGCAGGAATCA 57.757 42.857 0.00 0.00 0.00 2.57
3415 8288 8.749354 ACAATTAACCTTAAAATCCATGGAGAC 58.251 33.333 21.33 0.00 0.00 3.36
3434 8307 6.573289 TGGAGACAGTAGAGAATTGCTCTTTC 60.573 42.308 0.00 0.00 43.33 2.62
3471 8344 6.238648 AGTCTATGTGGTTAAACAGAAAGGG 58.761 40.000 0.00 0.00 32.52 3.95
3488 8361 6.758416 CAGAAAGGGAAGGAAAACAAAGAAAG 59.242 38.462 0.00 0.00 0.00 2.62
3552 8426 1.147824 CATCGCTTCCATGCTCCCT 59.852 57.895 0.00 0.00 0.00 4.20
3553 8427 0.394192 CATCGCTTCCATGCTCCCTA 59.606 55.000 0.00 0.00 0.00 3.53
3581 8455 4.202599 TGAATAATATGAGCCACAGCCCAT 60.203 41.667 0.00 0.00 40.95 4.00
3639 8515 3.004734 GCACAGTACCAGCATTTTCTGTT 59.995 43.478 0.00 0.00 34.57 3.16
4042 8918 5.096954 CATCAGTTAGATGCTCTGCAATG 57.903 43.478 0.00 0.00 46.90 2.82
4046 8922 5.474532 TCAGTTAGATGCTCTGCAATGTTTT 59.525 36.000 0.00 0.00 43.62 2.43
4048 8924 5.709164 AGTTAGATGCTCTGCAATGTTTTCT 59.291 36.000 0.00 0.00 43.62 2.52
4096 8972 0.255890 AAGGCCACCGTATCATGCTT 59.744 50.000 5.01 0.00 0.00 3.91
4382 9259 7.447594 TGGTTTAATTTACCCCGCAAATAAAA 58.552 30.769 6.90 0.00 34.66 1.52
4504 12056 2.676748 TGTTGAAGGCCCTGATTGTTT 58.323 42.857 0.00 0.00 0.00 2.83
4713 12268 7.442062 TCATTCAAAGAAAGCCTTGGATTTTTC 59.558 33.333 4.33 4.50 34.89 2.29
4780 12335 7.656137 TCCTCAGAACAACTCAATAACTGTTAC 59.344 37.037 1.73 0.00 32.31 2.50
4820 12480 7.843490 TTAGCATCGGGATTATATAAACAGC 57.157 36.000 0.00 0.00 0.00 4.40
4821 12481 6.054860 AGCATCGGGATTATATAAACAGCT 57.945 37.500 0.00 0.69 0.00 4.24
4822 12482 5.877012 AGCATCGGGATTATATAAACAGCTG 59.123 40.000 13.48 13.48 0.00 4.24
4823 12483 5.643777 GCATCGGGATTATATAAACAGCTGT 59.356 40.000 15.25 15.25 0.00 4.40
4824 12484 6.816640 GCATCGGGATTATATAAACAGCTGTA 59.183 38.462 22.01 5.63 0.00 2.74
4825 12485 7.333423 GCATCGGGATTATATAAACAGCTGTAA 59.667 37.037 22.01 12.23 0.00 2.41
4826 12486 9.214957 CATCGGGATTATATAAACAGCTGTAAA 57.785 33.333 22.01 11.83 0.00 2.01
4868 12638 5.009010 AGCAATAAGACAATTCTATTGCCCG 59.991 40.000 17.82 0.00 42.48 6.13
4872 12642 2.438021 AGACAATTCTATTGCCCGGCTA 59.562 45.455 11.61 2.84 0.00 3.93
4875 12645 0.400594 ATTCTATTGCCCGGCTACCC 59.599 55.000 11.61 0.00 0.00 3.69
4892 12662 2.436115 CGAGGAGCCGGAAAACCC 60.436 66.667 5.05 0.00 0.00 4.11
4893 12663 2.955881 CGAGGAGCCGGAAAACCCT 61.956 63.158 5.05 2.46 0.00 4.34
4896 12666 1.003928 GAGGAGCCGGAAAACCCTAAA 59.996 52.381 5.05 0.00 0.00 1.85
4899 12669 0.251474 AGCCGGAAAACCCTAAACCC 60.251 55.000 5.05 0.00 0.00 4.11
4900 12670 0.251474 GCCGGAAAACCCTAAACCCT 60.251 55.000 5.05 0.00 0.00 4.34
4901 12671 1.004628 GCCGGAAAACCCTAAACCCTA 59.995 52.381 5.05 0.00 0.00 3.53
4902 12672 2.357465 GCCGGAAAACCCTAAACCCTAT 60.357 50.000 5.05 0.00 0.00 2.57
4916 12704 1.188871 CCCTATCCGCCTCCTCTTCC 61.189 65.000 0.00 0.00 0.00 3.46
4919 12707 2.642183 TATCCGCCTCCTCTTCCGCT 62.642 60.000 0.00 0.00 0.00 5.52
4983 12771 1.043673 CACCTCCCTCCTTCCCGTAG 61.044 65.000 0.00 0.00 0.00 3.51
4999 12787 1.031235 GTAGAACCTCCGGCCTAGAC 58.969 60.000 0.00 0.00 0.00 2.59
5011 12799 1.398174 GCCTAGACCCGGTAGAACCC 61.398 65.000 0.00 0.00 33.75 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.177373 AAACCCGATACTCGAAGCCC 59.823 55.000 0.00 0.00 43.74 5.19
11 12 2.224113 GGGCATAAAACCCGATACTCGA 60.224 50.000 0.00 0.00 43.74 4.04
40 41 2.583520 GTGAGAGGAGGCAGCAGG 59.416 66.667 0.00 0.00 0.00 4.85
63 64 0.716108 GGTCGATGTGCTTCTTGACG 59.284 55.000 0.00 0.00 0.00 4.35
79 80 1.611491 CTAAGAGAGCCCGATGAGGTC 59.389 57.143 0.00 0.00 38.74 3.85
80 81 1.698506 CTAAGAGAGCCCGATGAGGT 58.301 55.000 0.00 0.00 38.74 3.85
81 82 0.965439 CCTAAGAGAGCCCGATGAGG 59.035 60.000 0.00 0.00 40.63 3.86
118 119 0.114364 AACCCCCAACCAAGCCTTAG 59.886 55.000 0.00 0.00 0.00 2.18
124 125 0.251341 CTGAGGAACCCCCAACCAAG 60.251 60.000 0.00 0.00 37.41 3.61
165 166 6.660521 AGCTATCAAAGGTTGAAATGTCATCA 59.339 34.615 0.00 0.00 43.95 3.07
199 200 5.941647 GGGGTATATAATCTTGCCGCTTTAA 59.058 40.000 0.00 0.00 0.00 1.52
221 222 1.949525 CCGTTGGAGATGCTTTATGGG 59.050 52.381 0.00 0.00 0.00 4.00
222 223 1.949525 CCCGTTGGAGATGCTTTATGG 59.050 52.381 0.00 0.00 0.00 2.74
225 226 0.742990 CGCCCGTTGGAGATGCTTTA 60.743 55.000 0.00 0.00 32.25 1.85
226 227 2.040544 CGCCCGTTGGAGATGCTTT 61.041 57.895 0.00 0.00 32.25 3.51
240 2307 4.056125 GAGCAGTTTTGGGCGCCC 62.056 66.667 39.40 39.40 34.54 6.13
272 2340 2.907917 TGGTGCCCGAAAAACCCG 60.908 61.111 0.00 0.00 32.70 5.28
273 2341 1.529713 TCTGGTGCCCGAAAAACCC 60.530 57.895 0.00 0.00 32.70 4.11
281 2349 4.767255 GGAGCTGTCTGGTGCCCG 62.767 72.222 0.00 0.00 0.00 6.13
286 4644 1.123861 TTCTGCTGGAGCTGTCTGGT 61.124 55.000 0.00 0.00 42.66 4.00
289 4647 1.296068 GCTTCTGCTGGAGCTGTCT 59.704 57.895 16.22 0.00 42.66 3.41
306 4664 1.168588 CGCACGCGTTATTTTACAGC 58.831 50.000 10.22 5.55 34.35 4.40
309 4667 1.593426 TTGCGCACGCGTTATTTTAC 58.407 45.000 11.12 0.00 45.51 2.01
335 4693 2.945398 TTTTTCAGCGCACGCCCAAC 62.945 55.000 11.47 0.00 43.17 3.77
362 4720 1.192980 CGCCTCAAATTTGCAACTTGC 59.807 47.619 13.54 6.82 45.29 4.01
363 4721 1.192980 GCGCCTCAAATTTGCAACTTG 59.807 47.619 13.54 12.34 0.00 3.16
364 4722 1.069049 AGCGCCTCAAATTTGCAACTT 59.931 42.857 13.54 0.00 0.00 2.66
365 4723 0.675633 AGCGCCTCAAATTTGCAACT 59.324 45.000 13.54 3.66 0.00 3.16
366 4724 0.785979 CAGCGCCTCAAATTTGCAAC 59.214 50.000 13.54 3.98 0.00 4.17
367 4725 0.319727 CCAGCGCCTCAAATTTGCAA 60.320 50.000 13.54 0.00 0.00 4.08
425 4783 3.677340 CCACAAAAACACGCGCGC 61.677 61.111 32.58 23.91 0.00 6.86
426 4784 0.932585 AATCCACAAAAACACGCGCG 60.933 50.000 30.96 30.96 0.00 6.86
448 4806 8.973182 TGATTTGGGGAGTATAAATTGGTTTAC 58.027 33.333 0.00 0.00 32.91 2.01
458 4816 5.548056 GGAGAGGATGATTTGGGGAGTATAA 59.452 44.000 0.00 0.00 0.00 0.98
459 4817 5.094387 GGAGAGGATGATTTGGGGAGTATA 58.906 45.833 0.00 0.00 0.00 1.47
460 4818 3.913163 GGAGAGGATGATTTGGGGAGTAT 59.087 47.826 0.00 0.00 0.00 2.12
461 4819 3.051032 AGGAGAGGATGATTTGGGGAGTA 60.051 47.826 0.00 0.00 0.00 2.59
462 4820 2.131023 GGAGAGGATGATTTGGGGAGT 58.869 52.381 0.00 0.00 0.00 3.85
463 4821 2.371510 GAGGAGAGGATGATTTGGGGAG 59.628 54.545 0.00 0.00 0.00 4.30
464 4822 2.021639 AGAGGAGAGGATGATTTGGGGA 60.022 50.000 0.00 0.00 0.00 4.81
465 4823 2.416638 AGAGGAGAGGATGATTTGGGG 58.583 52.381 0.00 0.00 0.00 4.96
466 4824 5.188751 GGTATAGAGGAGAGGATGATTTGGG 59.811 48.000 0.00 0.00 0.00 4.12
467 4825 6.022315 AGGTATAGAGGAGAGGATGATTTGG 58.978 44.000 0.00 0.00 0.00 3.28
468 4826 6.070881 CCAGGTATAGAGGAGAGGATGATTTG 60.071 46.154 0.00 0.00 0.00 2.32
469 4827 6.022315 CCAGGTATAGAGGAGAGGATGATTT 58.978 44.000 0.00 0.00 0.00 2.17
470 4828 5.588845 CCAGGTATAGAGGAGAGGATGATT 58.411 45.833 0.00 0.00 0.00 2.57
471 4829 4.571792 GCCAGGTATAGAGGAGAGGATGAT 60.572 50.000 0.00 0.00 0.00 2.45
472 4830 3.245443 GCCAGGTATAGAGGAGAGGATGA 60.245 52.174 0.00 0.00 0.00 2.92
473 4831 3.096092 GCCAGGTATAGAGGAGAGGATG 58.904 54.545 0.00 0.00 0.00 3.51
474 4832 2.043801 GGCCAGGTATAGAGGAGAGGAT 59.956 54.545 0.00 0.00 0.00 3.24
475 4833 1.429687 GGCCAGGTATAGAGGAGAGGA 59.570 57.143 0.00 0.00 0.00 3.71
476 4834 1.148027 TGGCCAGGTATAGAGGAGAGG 59.852 57.143 0.00 0.00 0.00 3.69
477 4835 2.685106 TGGCCAGGTATAGAGGAGAG 57.315 55.000 0.00 0.00 0.00 3.20
478 4836 3.039011 GTTTGGCCAGGTATAGAGGAGA 58.961 50.000 5.11 0.00 0.00 3.71
479 4837 2.224066 CGTTTGGCCAGGTATAGAGGAG 60.224 54.545 5.11 0.00 0.00 3.69
480 4838 1.760613 CGTTTGGCCAGGTATAGAGGA 59.239 52.381 5.11 0.00 0.00 3.71
481 4839 1.202651 CCGTTTGGCCAGGTATAGAGG 60.203 57.143 5.11 0.00 0.00 3.69
482 4840 1.202651 CCCGTTTGGCCAGGTATAGAG 60.203 57.143 5.11 0.00 0.00 2.43
483 4841 0.834612 CCCGTTTGGCCAGGTATAGA 59.165 55.000 5.11 0.00 0.00 1.98
484 4842 3.396951 CCCGTTTGGCCAGGTATAG 57.603 57.895 5.11 0.00 0.00 1.31
525 4883 0.104304 AGGCACGATTACGATGGGTC 59.896 55.000 0.00 0.00 42.66 4.46
526 4884 0.179084 CAGGCACGATTACGATGGGT 60.179 55.000 0.00 0.00 42.66 4.51
527 4885 0.880278 CCAGGCACGATTACGATGGG 60.880 60.000 0.00 0.00 42.66 4.00
528 4886 1.498865 GCCAGGCACGATTACGATGG 61.499 60.000 6.55 0.00 42.66 3.51
529 4887 1.498865 GGCCAGGCACGATTACGATG 61.499 60.000 15.19 0.00 42.66 3.84
530 4888 1.227556 GGCCAGGCACGATTACGAT 60.228 57.895 15.19 0.00 42.66 3.73
531 4889 2.185867 GGCCAGGCACGATTACGA 59.814 61.111 15.19 0.00 42.66 3.43
532 4890 2.895372 GGGCCAGGCACGATTACG 60.895 66.667 15.19 0.00 45.75 3.18
533 4891 2.516225 GGGGCCAGGCACGATTAC 60.516 66.667 15.19 0.00 29.41 1.89
534 4892 4.169696 CGGGGCCAGGCACGATTA 62.170 66.667 19.92 0.00 33.62 1.75
558 4916 2.023414 TAGTAATCGTGCCCTGGCGG 62.023 60.000 3.32 0.00 45.51 6.13
559 4917 0.033504 ATAGTAATCGTGCCCTGGCG 59.966 55.000 3.32 0.00 45.51 5.69
560 4918 2.685100 GTATAGTAATCGTGCCCTGGC 58.315 52.381 0.00 0.00 42.35 4.85
561 4919 2.352421 CCGTATAGTAATCGTGCCCTGG 60.352 54.545 0.00 0.00 0.00 4.45
562 4920 2.352421 CCCGTATAGTAATCGTGCCCTG 60.352 54.545 0.00 0.00 0.00 4.45
563 4921 1.891150 CCCGTATAGTAATCGTGCCCT 59.109 52.381 0.00 0.00 0.00 5.19
564 4922 1.670967 GCCCGTATAGTAATCGTGCCC 60.671 57.143 0.00 0.00 0.00 5.36
565 4923 1.670967 GGCCCGTATAGTAATCGTGCC 60.671 57.143 7.70 7.70 40.23 5.01
566 4924 1.706443 GGCCCGTATAGTAATCGTGC 58.294 55.000 0.00 0.00 0.00 5.34
567 4925 1.267806 ACGGCCCGTATAGTAATCGTG 59.732 52.381 7.20 0.00 38.73 4.35
568 4926 1.267806 CACGGCCCGTATAGTAATCGT 59.732 52.381 9.25 0.00 38.32 3.73
569 4927 1.973138 CACGGCCCGTATAGTAATCG 58.027 55.000 9.25 0.00 38.32 3.34
570 4928 1.670967 GGCACGGCCCGTATAGTAATC 60.671 57.143 9.25 0.00 44.06 1.75
571 4929 0.319405 GGCACGGCCCGTATAGTAAT 59.681 55.000 9.25 0.00 44.06 1.89
572 4930 1.741525 GGCACGGCCCGTATAGTAA 59.258 57.895 9.25 0.00 44.06 2.24
573 4931 3.447040 GGCACGGCCCGTATAGTA 58.553 61.111 9.25 0.00 44.06 1.82
624 4982 1.400494 CATTTACTAACTGGGCCGTGC 59.600 52.381 0.00 0.00 0.00 5.34
625 4983 2.014128 CCATTTACTAACTGGGCCGTG 58.986 52.381 0.00 0.00 0.00 4.94
626 4984 1.064979 CCCATTTACTAACTGGGCCGT 60.065 52.381 10.50 0.00 43.02 5.68
627 4985 1.675552 CCCATTTACTAACTGGGCCG 58.324 55.000 10.50 0.00 43.02 6.13
631 4989 1.675552 CCGGCCCATTTACTAACTGG 58.324 55.000 0.00 0.00 0.00 4.00
632 4990 1.021968 GCCGGCCCATTTACTAACTG 58.978 55.000 18.11 0.00 0.00 3.16
633 4991 0.621609 TGCCGGCCCATTTACTAACT 59.378 50.000 26.77 0.00 0.00 2.24
634 4992 0.736636 GTGCCGGCCCATTTACTAAC 59.263 55.000 26.77 7.29 0.00 2.34
635 4993 0.745128 CGTGCCGGCCCATTTACTAA 60.745 55.000 26.77 0.00 0.00 2.24
636 4994 1.153329 CGTGCCGGCCCATTTACTA 60.153 57.895 26.77 0.00 0.00 1.82
637 4995 2.437716 CGTGCCGGCCCATTTACT 60.438 61.111 26.77 0.00 0.00 2.24
638 4996 2.337246 AACGTGCCGGCCCATTTAC 61.337 57.895 26.77 13.53 0.00 2.01
639 4997 2.034376 AACGTGCCGGCCCATTTA 59.966 55.556 26.77 0.00 0.00 1.40
640 4998 3.679738 CAACGTGCCGGCCCATTT 61.680 61.111 26.77 9.04 0.00 2.32
666 5024 3.648009 CGGCAAATAACAGGCTGAAAAA 58.352 40.909 23.66 3.34 35.98 1.94
667 5025 2.609244 GCGGCAAATAACAGGCTGAAAA 60.609 45.455 23.66 6.07 35.98 2.29
668 5026 1.067915 GCGGCAAATAACAGGCTGAAA 60.068 47.619 23.66 8.84 35.98 2.69
669 5027 0.525761 GCGGCAAATAACAGGCTGAA 59.474 50.000 23.66 9.24 35.98 3.02
670 5028 0.607762 TGCGGCAAATAACAGGCTGA 60.608 50.000 23.66 0.00 35.98 4.26
671 5029 0.456653 GTGCGGCAAATAACAGGCTG 60.457 55.000 14.16 14.16 36.99 4.85
672 5030 0.609131 AGTGCGGCAAATAACAGGCT 60.609 50.000 3.23 0.00 0.00 4.58
673 5031 0.456653 CAGTGCGGCAAATAACAGGC 60.457 55.000 3.23 0.00 0.00 4.85
674 5032 1.131126 CTCAGTGCGGCAAATAACAGG 59.869 52.381 3.23 0.00 0.00 4.00
675 5033 1.466360 GCTCAGTGCGGCAAATAACAG 60.466 52.381 3.23 0.00 0.00 3.16
676 5034 0.521291 GCTCAGTGCGGCAAATAACA 59.479 50.000 3.23 0.00 0.00 2.41
677 5035 0.521291 TGCTCAGTGCGGCAAATAAC 59.479 50.000 3.23 0.00 46.63 1.89
678 5036 1.462616 ATGCTCAGTGCGGCAAATAA 58.537 45.000 3.23 0.00 46.63 1.40
679 5037 1.462616 AATGCTCAGTGCGGCAAATA 58.537 45.000 3.23 0.00 46.63 1.40
680 5038 0.604578 AAATGCTCAGTGCGGCAAAT 59.395 45.000 3.23 0.00 46.63 2.32
681 5039 0.388659 AAAATGCTCAGTGCGGCAAA 59.611 45.000 3.23 0.00 46.63 3.68
682 5040 0.388659 AAAAATGCTCAGTGCGGCAA 59.611 45.000 3.23 0.00 46.63 4.52
683 5041 2.040330 AAAAATGCTCAGTGCGGCA 58.960 47.368 11.78 11.78 46.63 5.69
684 5042 4.972591 AAAAATGCTCAGTGCGGC 57.027 50.000 0.00 0.00 46.63 6.53
700 5058 9.830186 TGGCCCAATATATAAAAATAGGCTAAA 57.170 29.630 0.00 0.00 37.98 1.85
750 5108 1.069596 ACGGCCCGACTACGTTTTT 59.930 52.632 11.71 0.00 37.61 1.94
751 5109 1.665599 CACGGCCCGACTACGTTTT 60.666 57.895 11.71 0.00 39.02 2.43
752 5110 2.048877 CACGGCCCGACTACGTTT 60.049 61.111 11.71 0.00 39.02 3.60
753 5111 4.729856 GCACGGCCCGACTACGTT 62.730 66.667 11.71 0.00 39.02 3.99
832 5190 2.437895 GGTCTAAACGGGCCAGGC 60.438 66.667 8.08 1.26 0.00 4.85
833 5191 2.125269 CGGTCTAAACGGGCCAGG 60.125 66.667 8.08 0.00 0.00 4.45
834 5192 1.740296 CACGGTCTAAACGGGCCAG 60.740 63.158 4.39 1.85 35.23 4.85
835 5193 2.344500 CACGGTCTAAACGGGCCA 59.656 61.111 4.39 0.00 35.23 5.36
891 5249 4.548513 TTTTTGGGGCCGGCCTGT 62.549 61.111 42.70 0.00 36.10 4.00
914 5272 2.019984 GAGAATAGCTGGCCAAACAGG 58.980 52.381 7.01 0.00 38.90 4.00
915 5273 2.941720 GAGAGAATAGCTGGCCAAACAG 59.058 50.000 7.01 0.00 41.41 3.16
916 5274 2.356125 GGAGAGAATAGCTGGCCAAACA 60.356 50.000 7.01 0.00 0.00 2.83
917 5275 2.092699 AGGAGAGAATAGCTGGCCAAAC 60.093 50.000 7.01 1.16 0.00 2.93
918 5276 2.171448 GAGGAGAGAATAGCTGGCCAAA 59.829 50.000 7.01 0.00 0.00 3.28
919 5277 1.765314 GAGGAGAGAATAGCTGGCCAA 59.235 52.381 7.01 0.00 0.00 4.52
920 5278 1.418334 GAGGAGAGAATAGCTGGCCA 58.582 55.000 4.71 4.71 0.00 5.36
921 5279 0.316841 CGAGGAGAGAATAGCTGGCC 59.683 60.000 0.00 0.00 0.00 5.36
922 5280 0.319469 GCGAGGAGAGAATAGCTGGC 60.319 60.000 0.00 0.00 0.00 4.85
923 5281 0.316841 GGCGAGGAGAGAATAGCTGG 59.683 60.000 0.00 0.00 0.00 4.85
924 5282 0.039617 CGGCGAGGAGAGAATAGCTG 60.040 60.000 0.00 0.00 0.00 4.24
925 5283 1.801309 GCGGCGAGGAGAGAATAGCT 61.801 60.000 12.98 0.00 0.00 3.32
926 5284 1.372375 GCGGCGAGGAGAGAATAGC 60.372 63.158 12.98 0.00 0.00 2.97
927 5285 1.287503 GGCGGCGAGGAGAGAATAG 59.712 63.158 12.98 0.00 0.00 1.73
928 5286 2.552819 CGGCGGCGAGGAGAGAATA 61.553 63.158 29.19 0.00 0.00 1.75
929 5287 3.905678 CGGCGGCGAGGAGAGAAT 61.906 66.667 29.19 0.00 0.00 2.40
995 5354 2.154462 GGGTCTTGGACAACATCACTG 58.846 52.381 0.14 0.00 33.68 3.66
1004 5363 1.884075 CGTCGATGGGGTCTTGGACA 61.884 60.000 0.00 0.00 33.68 4.02
1267 6130 2.040544 CGAGGGTGTTGGCCATGAC 61.041 63.158 6.09 2.62 0.00 3.06
1314 6177 0.816825 TATCCTCGGGGACTTCGTCG 60.817 60.000 5.91 0.00 45.43 5.12
1318 6181 1.413077 CTTGGTATCCTCGGGGACTTC 59.587 57.143 5.91 0.00 45.43 3.01
1326 6189 2.088674 CTCCCGGCTTGGTATCCTCG 62.089 65.000 0.00 0.00 35.15 4.63
1496 6359 1.320344 TGAGATGACCGAGAACCCCG 61.320 60.000 0.00 0.00 0.00 5.73
1512 6375 2.821366 GCCACCGATGCCAGTGAG 60.821 66.667 0.00 0.00 36.01 3.51
1533 6396 3.854669 CTGAGGGCCGCCTCGAAT 61.855 66.667 9.86 0.00 39.49 3.34
1650 6513 2.285773 TGTCTGGGTCTGCATCGCT 61.286 57.895 0.00 0.00 0.00 4.93
1672 6535 3.818210 AGCAACGTTTGGATGTTCATACA 59.182 39.130 0.00 0.00 38.95 2.29
1688 6551 4.657824 ACCGTCCACCGAGCAACG 62.658 66.667 0.00 0.00 39.56 4.10
1740 6603 1.295423 GTAAGGTGGCCGAGAAGCA 59.705 57.895 0.00 0.00 0.00 3.91
1826 6689 1.216710 GCTCGCAGGTAGAAGCTGT 59.783 57.895 7.83 0.00 44.96 4.40
1829 6692 2.202946 GGGCTCGCAGGTAGAAGC 60.203 66.667 0.00 0.00 0.00 3.86
2064 6927 0.675837 GGTAGCGGGTTTGGAGGAAC 60.676 60.000 0.00 0.00 0.00 3.62
2101 6964 1.826385 ACTAGGCATTGCACCAGTTC 58.174 50.000 11.39 0.00 0.00 3.01
2168 7031 3.421844 ACAAGAGGATGGTAAGCAAACC 58.578 45.455 0.65 0.65 40.19 3.27
2642 7505 4.155644 AGAGAGAAAACTAGTTACCGACCG 59.844 45.833 8.92 0.00 0.00 4.79
2957 7820 7.475015 TCCTCATTATCGAATTCAGCAAAAAG 58.525 34.615 6.22 0.00 0.00 2.27
3168 8041 2.562296 TCCTCCTCCTATTGCAAGGTT 58.438 47.619 4.94 0.00 37.91 3.50
3169 8042 2.270434 TCCTCCTCCTATTGCAAGGT 57.730 50.000 4.94 0.00 37.91 3.50
3170 8043 3.872459 AATCCTCCTCCTATTGCAAGG 57.128 47.619 4.94 0.80 38.06 3.61
3171 8044 4.785301 TGAAATCCTCCTCCTATTGCAAG 58.215 43.478 4.94 0.00 0.00 4.01
3172 8045 4.860802 TGAAATCCTCCTCCTATTGCAA 57.139 40.909 0.00 0.00 0.00 4.08
3173 8046 4.860802 TTGAAATCCTCCTCCTATTGCA 57.139 40.909 0.00 0.00 0.00 4.08
3174 8047 6.322201 TCAAATTGAAATCCTCCTCCTATTGC 59.678 38.462 0.00 0.00 0.00 3.56
3175 8048 7.886629 TCAAATTGAAATCCTCCTCCTATTG 57.113 36.000 0.00 0.00 0.00 1.90
3176 8049 8.921205 CATTCAAATTGAAATCCTCCTCCTATT 58.079 33.333 12.75 0.00 40.12 1.73
3177 8050 8.063770 ACATTCAAATTGAAATCCTCCTCCTAT 58.936 33.333 12.75 0.00 40.12 2.57
3183 8056 5.481105 TGCACATTCAAATTGAAATCCTCC 58.519 37.500 12.75 0.95 40.12 4.30
3236 8109 7.602644 TGACCATAGACACAGACAAAATACTTC 59.397 37.037 0.00 0.00 0.00 3.01
3260 8133 1.544093 CCTTTCAGCAAGCACCTCTGA 60.544 52.381 0.00 0.00 35.30 3.27
3261 8134 0.879765 CCTTTCAGCAAGCACCTCTG 59.120 55.000 0.00 0.00 0.00 3.35
3262 8135 0.251077 CCCTTTCAGCAAGCACCTCT 60.251 55.000 0.00 0.00 0.00 3.69
3263 8136 1.246737 CCCCTTTCAGCAAGCACCTC 61.247 60.000 0.00 0.00 0.00 3.85
3264 8137 1.228675 CCCCTTTCAGCAAGCACCT 60.229 57.895 0.00 0.00 0.00 4.00
3265 8138 1.527433 GACCCCTTTCAGCAAGCACC 61.527 60.000 0.00 0.00 0.00 5.01
3267 8140 0.538057 CTGACCCCTTTCAGCAAGCA 60.538 55.000 0.00 0.00 36.83 3.91
3268 8141 1.246737 CCTGACCCCTTTCAGCAAGC 61.247 60.000 0.00 0.00 41.61 4.01
3269 8142 0.111253 ACCTGACCCCTTTCAGCAAG 59.889 55.000 0.00 0.00 41.61 4.01
3270 8143 0.178992 CACCTGACCCCTTTCAGCAA 60.179 55.000 0.00 0.00 41.61 3.91
3376 8249 6.300354 AGGTTAATTGTGACGAGTTTTCTG 57.700 37.500 0.00 0.00 0.00 3.02
3377 8250 6.937436 AAGGTTAATTGTGACGAGTTTTCT 57.063 33.333 0.00 0.00 0.00 2.52
3434 8307 7.086230 ACCACATAGACTCTTACTTTCTACG 57.914 40.000 0.00 0.00 0.00 3.51
3471 8344 5.508153 GCTCTCCCTTTCTTTGTTTTCCTTC 60.508 44.000 0.00 0.00 0.00 3.46
3552 8426 7.770433 GGCTGTGGCTCATATTATTCATGTATA 59.230 37.037 0.00 0.00 38.73 1.47
3553 8427 6.600822 GGCTGTGGCTCATATTATTCATGTAT 59.399 38.462 0.00 0.00 38.73 2.29
3581 8455 2.570302 GGCCTTTGGACACTAACTAGGA 59.430 50.000 0.00 0.00 0.00 2.94
3620 8496 3.057315 CCCAACAGAAAATGCTGGTACTG 60.057 47.826 0.00 0.00 42.69 2.74
3639 8515 1.759445 GCTCTCAACTGCTAGATCCCA 59.241 52.381 0.00 0.00 0.00 4.37
3737 8613 2.022195 CAAGAGAACTGCATCCATGGG 58.978 52.381 13.02 0.00 0.00 4.00
4382 9259 5.971763 TGCATTTAAGTTGAACCAAACAGT 58.028 33.333 0.00 0.00 32.21 3.55
4569 12124 8.618702 TGTGGAACCGAGTTAAATTGTATTAA 57.381 30.769 0.00 0.00 34.36 1.40
4713 12268 5.605534 AGTGAGATAATTCCGGTCATCAAG 58.394 41.667 0.00 0.00 0.00 3.02
4780 12335 9.755064 CCCGATGCTAATAAAAATAAGATAACG 57.245 33.333 0.00 0.00 0.00 3.18
4816 12476 5.036117 TCCAAAAGAGTCTTTACAGCTGT 57.964 39.130 25.12 25.12 0.00 4.40
4817 12477 6.377327 TTTCCAAAAGAGTCTTTACAGCTG 57.623 37.500 18.31 13.48 0.00 4.24
4818 12478 7.588497 AATTTCCAAAAGAGTCTTTACAGCT 57.412 32.000 18.31 0.00 0.00 4.24
4819 12479 9.399403 CTTAATTTCCAAAAGAGTCTTTACAGC 57.601 33.333 18.31 0.00 0.00 4.40
4820 12480 9.399403 GCTTAATTTCCAAAAGAGTCTTTACAG 57.601 33.333 18.31 11.16 0.00 2.74
4821 12481 8.908903 TGCTTAATTTCCAAAAGAGTCTTTACA 58.091 29.630 18.31 3.07 0.00 2.41
4822 12482 9.744468 TTGCTTAATTTCCAAAAGAGTCTTTAC 57.256 29.630 18.31 0.00 0.00 2.01
4875 12645 1.610554 TAGGGTTTTCCGGCTCCTCG 61.611 60.000 0.00 0.00 41.82 4.63
4889 12659 0.030399 AGGCGGATAGGGTTTAGGGT 60.030 55.000 0.00 0.00 0.00 4.34
4892 12662 1.619332 GAGGAGGCGGATAGGGTTTAG 59.381 57.143 0.00 0.00 0.00 1.85
4893 12663 1.219724 AGAGGAGGCGGATAGGGTTTA 59.780 52.381 0.00 0.00 0.00 2.01
4896 12666 0.470268 GAAGAGGAGGCGGATAGGGT 60.470 60.000 0.00 0.00 0.00 4.34
4899 12669 1.960612 CGGAAGAGGAGGCGGATAG 59.039 63.158 0.00 0.00 0.00 2.08
4900 12670 2.201022 GCGGAAGAGGAGGCGGATA 61.201 63.158 0.00 0.00 0.00 2.59
4901 12671 3.541713 GCGGAAGAGGAGGCGGAT 61.542 66.667 0.00 0.00 0.00 4.18
4902 12672 4.761058 AGCGGAAGAGGAGGCGGA 62.761 66.667 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.