Multiple sequence alignment - TraesCS2B01G567800

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 TraesCS2B01G567800 chr2B 100.000 6107 0 0 1 6107 758803375 758797269 0.000000e+00 11278.0
1 TraesCS2B01G567800 chr2B 94.068 2124 92 13 3571 5681 758112054 758114156 0.000000e+00 3193.0
2 TraesCS2B01G567800 chr2B 75.499 551 118 14 4566 5110 707462252 707461713 2.830000e-63 254.0
3 TraesCS2B01G567800 chr2B 85.532 235 34 0 3726 3960 707959550 707959316 4.730000e-61 246.0
4 TraesCS2B01G567800 chr2B 76.535 456 95 9 4566 5017 707630855 707630408 7.910000e-59 239.0
5 TraesCS2B01G567800 chr2B 85.463 227 33 0 3736 3962 758670797 758671023 2.850000e-58 237.0
6 TraesCS2B01G567800 chr2B 76.159 453 97 9 4569 5018 707414796 707414352 1.710000e-55 228.0
7 TraesCS2B01G567800 chr2B 74.261 575 111 26 4560 5112 707620647 707620088 2.230000e-49 207.0
8 TraesCS2B01G567800 chr2B 81.624 234 41 2 3367 3599 707240290 707240058 6.250000e-45 193.0
9 TraesCS2B01G567800 chr2B 81.448 221 37 3 4801 5019 756970183 756970401 1.750000e-40 178.0
10 TraesCS2B01G567800 chr2B 72.637 402 102 5 1870 2267 707464230 707463833 6.430000e-25 126.0
11 TraesCS2B01G567800 chr2B 80.208 96 17 2 3018 3112 707415646 707415552 3.050000e-08 71.3
12 TraesCS2B01G567800 chr2A 93.173 3325 160 38 2350 5660 750555931 750559202 0.000000e+00 4820.0
13 TraesCS2B01G567800 chr2A 95.111 1493 71 1 875 2367 750554335 750555825 0.000000e+00 2351.0
14 TraesCS2B01G567800 chr2A 75.899 556 109 20 4566 5113 721008561 721008023 1.690000e-65 261.0
15 TraesCS2B01G567800 chr2A 76.940 451 97 5 4569 5018 720060017 720059573 3.650000e-62 250.0
16 TraesCS2B01G567800 chr2A 84.190 253 40 0 3709 3961 750208559 750208307 4.730000e-61 246.0
17 TraesCS2B01G567800 chr2A 83.004 253 43 0 3710 3962 751233988 751234240 4.760000e-56 230.0
18 TraesCS2B01G567800 chr2A 84.034 238 36 2 3727 3963 720584072 720583836 1.710000e-55 228.0
19 TraesCS2B01G567800 chr2A 84.906 159 23 1 719 877 750554051 750554208 6.340000e-35 159.0
20 TraesCS2B01G567800 chr2A 75.806 186 36 8 2933 3112 720060953 720060771 1.090000e-12 86.1
21 TraesCS2B01G567800 chr2A 73.980 196 51 0 2072 2267 720520376 720520181 5.070000e-11 80.5
22 TraesCS2B01G567800 chr2A 92.683 41 3 0 3071 3111 52762902 52762862 6.610000e-05 60.2
23 TraesCS2B01G567800 chr2D 91.989 3333 187 35 2650 5970 619404294 619407558 0.000000e+00 4602.0
24 TraesCS2B01G567800 chr2D 96.075 1503 52 5 875 2373 619402424 619403923 0.000000e+00 2442.0
25 TraesCS2B01G567800 chr2D 89.531 277 19 2 2369 2645 619403994 619404260 5.860000e-90 342.0
26 TraesCS2B01G567800 chr2D 86.817 311 23 5 572 877 619402042 619402339 1.270000e-86 331.0
27 TraesCS2B01G567800 chr2D 84.190 253 40 0 3710 3962 619568651 619568903 4.730000e-61 246.0
28 TraesCS2B01G567800 chr2D 76.754 456 93 11 4566 5017 585916364 585916810 6.120000e-60 243.0
29 TraesCS2B01G567800 chr2D 95.105 143 2 4 71 213 619401322 619401459 2.870000e-53 220.0
30 TraesCS2B01G567800 chr2D 84.358 179 28 0 4801 4979 619148488 619148666 6.290000e-40 176.0
31 TraesCS2B01G567800 chr2D 71.939 392 102 5 1880 2267 585914540 585914927 2.330000e-19 108.0
32 TraesCS2B01G567800 chr2D 79.167 96 18 2 3018 3112 585894505 585894411 1.420000e-06 65.8
33 TraesCS2B01G567800 chr7D 72.091 1272 323 24 1004 2265 585556501 585557750 2.710000e-93 353.0
34 TraesCS2B01G567800 chr7D 78.495 186 39 1 2931 3116 585558296 585558480 2.990000e-23 121.0
35 TraesCS2B01G567800 chr6B 71.698 901 232 18 1380 2267 675451738 675450848 4.760000e-56 230.0
36 TraesCS2B01G567800 chr7B 78.495 186 39 1 2931 3116 654917753 654917937 2.990000e-23 121.0
37 TraesCS2B01G567800 chr7B 100.000 28 0 0 5536 5563 96275096 96275123 1.100000e-02 52.8
38 TraesCS2B01G567800 chr7A 78.075 187 38 3 2931 3116 675588886 675589070 1.390000e-21 115.0
39 TraesCS2B01G567800 chr5D 75.887 141 31 1 3429 3569 438443024 438442887 1.100000e-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 TraesCS2B01G567800 chr2B 758797269 758803375 6106 True 11278.000000 11278 100.000000 1 6107 1 chr2B.!!$R5 6106
1 TraesCS2B01G567800 chr2B 758112054 758114156 2102 False 3193.000000 3193 94.068000 3571 5681 1 chr2B.!!$F2 2110
2 TraesCS2B01G567800 chr2B 707620088 707620647 559 True 207.000000 207 74.261000 4560 5112 1 chr2B.!!$R2 552
3 TraesCS2B01G567800 chr2A 750554051 750559202 5151 False 2443.333333 4820 91.063333 719 5660 3 chr2A.!!$F2 4941
4 TraesCS2B01G567800 chr2A 721008023 721008561 538 True 261.000000 261 75.899000 4566 5113 1 chr2A.!!$R4 547
5 TraesCS2B01G567800 chr2D 619401322 619407558 6236 False 1587.400000 4602 91.903400 71 5970 5 chr2D.!!$F4 5899
6 TraesCS2B01G567800 chr7D 585556501 585558480 1979 False 237.000000 353 75.293000 1004 3116 2 chr7D.!!$F1 2112
7 TraesCS2B01G567800 chr6B 675450848 675451738 890 True 230.000000 230 71.698000 1380 2267 1 chr6B.!!$R1 887

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
38 39 0.032678 CTGCTCGTCGCCCATTATCT 59.967 55.000 0.00 0.00 38.05 1.98 F
584 688 0.037697 TAGCAACTGTAGCCACGTGG 60.038 55.000 30.66 30.66 38.53 4.94 F
1202 1612 0.616371 TGGTTCTACAACATCCCGGG 59.384 55.000 16.85 16.85 33.70 5.73 F
2253 2666 0.824759 AGAACCTGTACATCCGCCTC 59.175 55.000 0.00 0.00 0.00 4.70 F
2824 3388 1.739466 CACGTGCATAGCCATTGTCTT 59.261 47.619 0.82 0.00 0.00 3.01 F
3142 3710 2.093306 TCACATCGGCAAGTAAGGTG 57.907 50.000 0.00 0.00 0.00 4.00 F
4555 5147 0.748005 ACGTGCACTGAGGCAAACTT 60.748 50.000 16.19 0.00 46.93 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 2026 1.003355 ATGCGGCAGTACAGCTTGT 60.003 52.632 9.25 0.0 40.54 3.16 R
2209 2622 0.038892 TAGTTGACGGTCTTCCACGC 60.039 55.000 9.88 0.0 0.00 5.34 R
3124 3692 0.447801 GCACCTTACTTGCCGATGTG 59.552 55.000 0.00 0.0 33.58 3.21 R
3138 3706 1.561076 TCTGGCAGACATATTGCACCT 59.439 47.619 14.43 0.0 43.28 4.00 R
4418 5010 0.401356 TGACTTGCAGGGAAGCATGA 59.599 50.000 0.00 0.0 45.19 3.07 R
4596 5188 1.007387 CAGAAAAAGCGCCACCCAC 60.007 57.895 2.29 0.0 0.00 4.61 R
6064 6717 0.176910 GGGAGAGAAAGGCGAGGAAG 59.823 60.000 0.00 0.0 0.00 3.46 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 2.029838 GATATCCATCCGCCACATCC 57.970 55.000 0.00 0.00 0.00 3.51
20 21 1.556911 GATATCCATCCGCCACATCCT 59.443 52.381 0.00 0.00 0.00 3.24
21 22 0.686789 TATCCATCCGCCACATCCTG 59.313 55.000 0.00 0.00 0.00 3.86
22 23 2.687418 ATCCATCCGCCACATCCTGC 62.687 60.000 0.00 0.00 0.00 4.85
23 24 2.191375 CATCCGCCACATCCTGCT 59.809 61.111 0.00 0.00 0.00 4.24
24 25 1.890979 CATCCGCCACATCCTGCTC 60.891 63.158 0.00 0.00 0.00 4.26
25 26 3.451556 ATCCGCCACATCCTGCTCG 62.452 63.158 0.00 0.00 0.00 5.03
26 27 4.457496 CCGCCACATCCTGCTCGT 62.457 66.667 0.00 0.00 0.00 4.18
27 28 2.887568 CGCCACATCCTGCTCGTC 60.888 66.667 0.00 0.00 0.00 4.20
28 29 2.887568 GCCACATCCTGCTCGTCG 60.888 66.667 0.00 0.00 0.00 5.12
29 30 2.887568 CCACATCCTGCTCGTCGC 60.888 66.667 0.00 0.00 39.77 5.19
30 31 2.887568 CACATCCTGCTCGTCGCC 60.888 66.667 0.00 0.00 38.05 5.54
31 32 4.148825 ACATCCTGCTCGTCGCCC 62.149 66.667 0.00 0.00 38.05 6.13
32 33 4.147449 CATCCTGCTCGTCGCCCA 62.147 66.667 0.00 0.00 38.05 5.36
33 34 3.157252 ATCCTGCTCGTCGCCCAT 61.157 61.111 0.00 0.00 38.05 4.00
34 35 2.735772 ATCCTGCTCGTCGCCCATT 61.736 57.895 0.00 0.00 38.05 3.16
35 36 1.399744 ATCCTGCTCGTCGCCCATTA 61.400 55.000 0.00 0.00 38.05 1.90
36 37 1.069765 CCTGCTCGTCGCCCATTAT 59.930 57.895 0.00 0.00 38.05 1.28
37 38 0.946221 CCTGCTCGTCGCCCATTATC 60.946 60.000 0.00 0.00 38.05 1.75
38 39 0.032678 CTGCTCGTCGCCCATTATCT 59.967 55.000 0.00 0.00 38.05 1.98
39 40 0.464036 TGCTCGTCGCCCATTATCTT 59.536 50.000 0.00 0.00 38.05 2.40
40 41 1.134521 TGCTCGTCGCCCATTATCTTT 60.135 47.619 0.00 0.00 38.05 2.52
41 42 1.940613 GCTCGTCGCCCATTATCTTTT 59.059 47.619 0.00 0.00 0.00 2.27
42 43 2.286418 GCTCGTCGCCCATTATCTTTTG 60.286 50.000 0.00 0.00 0.00 2.44
43 44 2.936498 CTCGTCGCCCATTATCTTTTGT 59.064 45.455 0.00 0.00 0.00 2.83
44 45 3.340034 TCGTCGCCCATTATCTTTTGTT 58.660 40.909 0.00 0.00 0.00 2.83
45 46 3.372822 TCGTCGCCCATTATCTTTTGTTC 59.627 43.478 0.00 0.00 0.00 3.18
46 47 3.374058 CGTCGCCCATTATCTTTTGTTCT 59.626 43.478 0.00 0.00 0.00 3.01
47 48 4.569162 CGTCGCCCATTATCTTTTGTTCTA 59.431 41.667 0.00 0.00 0.00 2.10
48 49 5.064198 CGTCGCCCATTATCTTTTGTTCTAA 59.936 40.000 0.00 0.00 0.00 2.10
49 50 6.238374 CGTCGCCCATTATCTTTTGTTCTAAT 60.238 38.462 0.00 0.00 0.00 1.73
50 51 7.480810 GTCGCCCATTATCTTTTGTTCTAATT 58.519 34.615 0.00 0.00 0.00 1.40
51 52 7.973944 GTCGCCCATTATCTTTTGTTCTAATTT 59.026 33.333 0.00 0.00 0.00 1.82
52 53 8.527810 TCGCCCATTATCTTTTGTTCTAATTTT 58.472 29.630 0.00 0.00 0.00 1.82
53 54 9.150348 CGCCCATTATCTTTTGTTCTAATTTTT 57.850 29.630 0.00 0.00 0.00 1.94
83 84 9.855021 CCTTGTTAAATTTAGAATCGTGGAAAT 57.145 29.630 0.00 0.00 0.00 2.17
191 192 1.697432 TCCCTGTCTTGACCATTCGTT 59.303 47.619 0.00 0.00 0.00 3.85
195 196 4.562757 CCCTGTCTTGACCATTCGTTTCTA 60.563 45.833 0.00 0.00 0.00 2.10
196 197 5.178797 CCTGTCTTGACCATTCGTTTCTAT 58.821 41.667 0.00 0.00 0.00 1.98
197 198 5.292101 CCTGTCTTGACCATTCGTTTCTATC 59.708 44.000 0.00 0.00 0.00 2.08
198 199 5.175859 TGTCTTGACCATTCGTTTCTATCC 58.824 41.667 0.00 0.00 0.00 2.59
258 326 3.520290 AAGACCATTCGCGATACTCAA 57.480 42.857 10.88 0.00 0.00 3.02
268 336 2.464865 GCGATACTCAACGAGCAATCT 58.535 47.619 0.00 0.00 32.04 2.40
289 393 0.918983 ATCCCAATCGACCATGGTGT 59.081 50.000 25.52 5.01 34.79 4.16
384 488 4.112341 GCCTACGTCGACGGCTGT 62.112 66.667 37.89 21.75 44.95 4.40
399 503 3.605749 CTGTGGTAGGTGGCCGTGG 62.606 68.421 0.00 0.00 0.00 4.94
427 531 3.785499 TCCGCTGACTCGTCGTCG 61.785 66.667 0.00 0.00 45.87 5.12
458 562 3.484806 AACCACGGCTGTCCCACA 61.485 61.111 0.00 0.00 0.00 4.17
468 572 0.532862 CTGTCCCACAACAAGCGACT 60.533 55.000 0.00 0.00 0.00 4.18
469 573 0.107410 TGTCCCACAACAAGCGACTT 60.107 50.000 0.00 0.00 0.00 3.01
496 600 2.032681 GGCACAGCGAGGTTTCCT 59.967 61.111 0.00 0.00 36.03 3.36
507 611 0.318762 AGGTTTCCTCTGTCGCACTC 59.681 55.000 0.00 0.00 0.00 3.51
525 629 5.124645 GCACTCTCCAATCTGAATCTGAAT 58.875 41.667 0.00 0.00 0.00 2.57
526 630 5.236911 GCACTCTCCAATCTGAATCTGAATC 59.763 44.000 0.00 0.00 0.00 2.52
527 631 6.584488 CACTCTCCAATCTGAATCTGAATCT 58.416 40.000 0.00 0.00 0.00 2.40
528 632 6.480651 CACTCTCCAATCTGAATCTGAATCTG 59.519 42.308 0.00 0.00 0.00 2.90
529 633 6.383436 ACTCTCCAATCTGAATCTGAATCTGA 59.617 38.462 5.01 5.01 0.00 3.27
530 634 7.092979 ACTCTCCAATCTGAATCTGAATCTGAA 60.093 37.037 6.43 0.00 0.00 3.02
531 635 7.803131 TCTCCAATCTGAATCTGAATCTGAAT 58.197 34.615 6.43 0.00 0.00 2.57
532 636 7.715686 TCTCCAATCTGAATCTGAATCTGAATG 59.284 37.037 6.43 8.11 0.00 2.67
533 637 6.262496 TCCAATCTGAATCTGAATCTGAATGC 59.738 38.462 10.49 0.00 29.37 3.56
534 638 6.439599 CAATCTGAATCTGAATCTGAATGCC 58.560 40.000 6.43 0.00 0.00 4.40
535 639 5.369409 TCTGAATCTGAATCTGAATGCCT 57.631 39.130 0.44 0.00 0.00 4.75
536 640 6.490241 TCTGAATCTGAATCTGAATGCCTA 57.510 37.500 0.44 0.00 0.00 3.93
537 641 6.522946 TCTGAATCTGAATCTGAATGCCTAG 58.477 40.000 0.44 0.00 0.00 3.02
538 642 5.061853 TGAATCTGAATCTGAATGCCTAGC 58.938 41.667 0.00 0.00 0.00 3.42
539 643 4.701651 ATCTGAATCTGAATGCCTAGCA 57.298 40.909 0.00 0.00 44.86 3.49
540 644 4.492494 TCTGAATCTGAATGCCTAGCAA 57.508 40.909 0.00 0.00 43.62 3.91
541 645 4.194640 TCTGAATCTGAATGCCTAGCAAC 58.805 43.478 0.00 0.00 43.62 4.17
542 646 2.938451 TGAATCTGAATGCCTAGCAACG 59.062 45.455 0.00 0.00 43.62 4.10
543 647 2.988010 ATCTGAATGCCTAGCAACGA 57.012 45.000 0.00 0.00 43.62 3.85
544 648 2.760634 TCTGAATGCCTAGCAACGAA 57.239 45.000 0.00 0.00 43.62 3.85
545 649 3.266510 TCTGAATGCCTAGCAACGAAT 57.733 42.857 0.00 0.00 43.62 3.34
546 650 3.609853 TCTGAATGCCTAGCAACGAATT 58.390 40.909 0.00 0.00 43.62 2.17
547 651 4.009675 TCTGAATGCCTAGCAACGAATTT 58.990 39.130 0.00 0.00 43.62 1.82
548 652 4.458989 TCTGAATGCCTAGCAACGAATTTT 59.541 37.500 0.00 0.00 43.62 1.82
549 653 4.732784 TGAATGCCTAGCAACGAATTTTC 58.267 39.130 0.00 0.00 43.62 2.29
550 654 4.458989 TGAATGCCTAGCAACGAATTTTCT 59.541 37.500 0.00 0.00 43.62 2.52
551 655 5.048083 TGAATGCCTAGCAACGAATTTTCTT 60.048 36.000 0.00 0.00 43.62 2.52
552 656 4.846779 TGCCTAGCAACGAATTTTCTTT 57.153 36.364 0.00 0.00 34.76 2.52
553 657 4.794169 TGCCTAGCAACGAATTTTCTTTC 58.206 39.130 0.00 0.00 34.76 2.62
554 658 4.166523 GCCTAGCAACGAATTTTCTTTCC 58.833 43.478 0.00 0.00 0.00 3.13
555 659 4.733850 CCTAGCAACGAATTTTCTTTCCC 58.266 43.478 0.00 0.00 0.00 3.97
556 660 4.459337 CCTAGCAACGAATTTTCTTTCCCT 59.541 41.667 0.00 0.00 0.00 4.20
580 684 1.068474 CGTGTAGCAACTGTAGCCAC 58.932 55.000 0.00 0.00 0.00 5.01
584 688 0.037697 TAGCAACTGTAGCCACGTGG 60.038 55.000 30.66 30.66 38.53 4.94
595 699 3.015516 CCACGTGGCAGTTAACCTT 57.984 52.632 24.02 0.00 0.00 3.50
596 700 2.172851 CCACGTGGCAGTTAACCTTA 57.827 50.000 24.02 0.00 0.00 2.69
598 702 1.802365 CACGTGGCAGTTAACCTTACC 59.198 52.381 7.95 0.00 0.00 2.85
599 703 1.073177 CGTGGCAGTTAACCTTACCG 58.927 55.000 0.88 0.00 0.00 4.02
600 704 1.337074 CGTGGCAGTTAACCTTACCGA 60.337 52.381 0.88 0.00 0.00 4.69
609 886 4.458642 AGTTAACCTTACCGACTCAGTCTC 59.541 45.833 2.61 0.00 0.00 3.36
611 888 3.996921 ACCTTACCGACTCAGTCTCTA 57.003 47.619 2.61 0.00 0.00 2.43
619 896 4.102838 ACCGACTCAGTCTCTATAGGCTTA 59.897 45.833 2.61 0.00 34.68 3.09
645 922 7.920738 TCTCTTTCTTTGTTCTAGTCTTTTGC 58.079 34.615 0.00 0.00 0.00 3.68
700 981 8.054152 ACATCTGCAGTAGAGATGACTATATG 57.946 38.462 14.67 7.13 46.73 1.78
702 983 8.905850 CATCTGCAGTAGAGATGACTATATGAT 58.094 37.037 14.67 0.00 46.73 2.45
717 998 2.824041 GATGTGGCGCATCCGGTT 60.824 61.111 26.65 0.00 46.26 4.44
797 1078 5.045432 TGTGGATTCCTAGTACCGGATTTTT 60.045 40.000 9.46 0.00 0.00 1.94
814 1095 3.648339 TTTTCTTCTGGCTTGCATCAC 57.352 42.857 0.00 0.00 0.00 3.06
819 1100 0.991146 TCTGGCTTGCATCACCCTTA 59.009 50.000 0.00 0.00 0.00 2.69
827 1108 2.888212 TGCATCACCCTTAAAGGCTTT 58.112 42.857 17.76 17.76 32.73 3.51
834 1115 3.259123 CACCCTTAAAGGCTTTGAGCAAT 59.741 43.478 22.43 9.67 44.75 3.56
894 1304 2.277084 CTTCCAACCATACACGTAGCC 58.723 52.381 0.00 0.00 0.00 3.93
1008 1418 4.821805 CACAAAGGAGGCGTAATGGATATT 59.178 41.667 0.00 0.00 0.00 1.28
1013 1423 5.091552 AGGAGGCGTAATGGATATTTCCTA 58.908 41.667 3.72 0.00 43.07 2.94
1202 1612 0.616371 TGGTTCTACAACATCCCGGG 59.384 55.000 16.85 16.85 33.70 5.73
1209 1619 2.610859 AACATCCCGGGGAGCAGT 60.611 61.111 23.50 16.29 34.05 4.40
1467 1877 1.219124 CCCGACAGACACCATCCTG 59.781 63.158 0.00 0.00 36.53 3.86
1470 1880 1.078143 GACAGACACCATCCTGCCC 60.078 63.158 0.00 0.00 33.90 5.36
1613 2026 2.050836 ATGGTCACTTGGCACGGTGA 62.051 55.000 13.29 15.57 40.20 4.02
1830 2243 1.751351 TGGAACAGCTACTCCTCATCG 59.249 52.381 13.09 0.00 32.51 3.84
2209 2622 2.125912 CAGGGGAGCTTGTCGACG 60.126 66.667 11.62 0.00 0.00 5.12
2221 2634 4.394078 TCGACGCGTGGAAGACCG 62.394 66.667 22.04 14.48 39.42 4.79
2222 2635 4.695231 CGACGCGTGGAAGACCGT 62.695 66.667 20.70 0.00 39.42 4.83
2253 2666 0.824759 AGAACCTGTACATCCGCCTC 59.175 55.000 0.00 0.00 0.00 4.70
2277 2690 2.324541 GACTCTCCTGCTGGTATGGAT 58.675 52.381 9.73 0.00 34.23 3.41
2327 2740 7.769272 TTTTCTTTTGTTTACTTGGATGCAG 57.231 32.000 0.00 0.00 0.00 4.41
2329 2742 6.072112 TCTTTTGTTTACTTGGATGCAGAC 57.928 37.500 0.00 0.00 0.00 3.51
2332 2745 3.826524 TGTTTACTTGGATGCAGACCAA 58.173 40.909 21.44 21.44 43.84 3.67
2379 2913 6.017852 CAGAGAGAAGTACAAAACAGGGAAAC 60.018 42.308 0.00 0.00 0.00 2.78
2586 3120 4.575885 TGTACTAATGCACCCTCAGTTTC 58.424 43.478 0.00 0.00 0.00 2.78
2777 3341 3.853671 GCAATTTAGTGAAGATTGTGCCG 59.146 43.478 0.00 0.00 34.19 5.69
2824 3388 1.739466 CACGTGCATAGCCATTGTCTT 59.261 47.619 0.82 0.00 0.00 3.01
2954 3522 5.124617 GGCGAAAGAAGGAAATCAAGAAGAT 59.875 40.000 0.00 0.00 39.09 2.40
3015 3583 5.071519 TGGAGGCAAAAATTCAGATTTTCCA 59.928 36.000 0.00 0.00 42.97 3.53
3016 3584 5.640783 GGAGGCAAAAATTCAGATTTTCCAG 59.359 40.000 0.00 0.00 42.97 3.86
3043 3611 3.950397 AGTTTCGAAGATATTGTGGCCA 58.050 40.909 0.00 0.00 35.04 5.36
3138 3706 4.941263 AGCTTAATTCACATCGGCAAGTAA 59.059 37.500 0.00 0.00 0.00 2.24
3142 3710 2.093306 TCACATCGGCAAGTAAGGTG 57.907 50.000 0.00 0.00 0.00 4.00
3241 3810 9.104713 ACATCATAATGGTCCTGTCAATCTATA 57.895 33.333 0.00 0.00 37.19 1.31
3330 3902 6.564709 TCATTGTTTCTCAGTTCAGAATGG 57.435 37.500 0.00 0.00 36.16 3.16
3340 3912 6.655003 TCTCAGTTCAGAATGGTGGAATTAAC 59.345 38.462 0.00 0.00 36.16 2.01
3384 3956 7.518188 ACAATTATGTAGGGAATACTGGAAGG 58.482 38.462 0.00 0.00 38.24 3.46
3398 3970 3.142174 CTGGAAGGTGACAAGGAAGTTC 58.858 50.000 0.00 0.00 0.00 3.01
3399 3971 2.507886 TGGAAGGTGACAAGGAAGTTCA 59.492 45.455 5.01 0.00 0.00 3.18
3442 4014 2.964209 TCTGGGCAAGGTATAGAGGAG 58.036 52.381 0.00 0.00 0.00 3.69
3640 4216 9.696917 AAATTCTCAATGTTGACCATAAAGTTC 57.303 29.630 0.00 0.00 31.97 3.01
3641 4217 8.641498 ATTCTCAATGTTGACCATAAAGTTCT 57.359 30.769 0.00 0.00 31.97 3.01
3642 4218 8.463930 TTCTCAATGTTGACCATAAAGTTCTT 57.536 30.769 0.00 0.00 31.97 2.52
3684 4260 8.008279 CGAAAGAATATGCATGATGACTAACAG 58.992 37.037 10.16 0.00 0.00 3.16
3708 4284 7.920151 CAGTTGGTTTTATTGAACTGTTCATGA 59.080 33.333 22.60 10.41 40.19 3.07
4037 4614 2.364970 TGGGCAGGAATGAACACTTTTG 59.635 45.455 0.00 0.00 0.00 2.44
4060 4637 5.068987 TGCTCCCATTGCCTGTTATATTTTC 59.931 40.000 0.00 0.00 0.00 2.29
4240 4824 3.621892 CTTTGCTTCGCTGCCCTGC 62.622 63.158 0.00 0.00 0.00 4.85
4262 4846 5.587043 TGCCGGATGAAAGTTACGAAATTAT 59.413 36.000 5.05 0.00 0.00 1.28
4362 4946 7.090173 TCTCTATTATTTTTGCAACTGCCAAC 58.910 34.615 0.00 0.00 41.18 3.77
4384 4968 5.660533 ACTCCAATTTAAATCCCCCAAAGA 58.339 37.500 0.10 0.00 0.00 2.52
4418 5010 5.995282 TCACTCGTGTTTGATTAGGATGTTT 59.005 36.000 0.00 0.00 0.00 2.83
4424 5016 6.623549 CGTGTTTGATTAGGATGTTTCATGCT 60.624 38.462 8.60 8.60 0.00 3.79
4425 5017 7.092716 GTGTTTGATTAGGATGTTTCATGCTT 58.907 34.615 8.83 0.00 0.00 3.91
4426 5018 7.274250 GTGTTTGATTAGGATGTTTCATGCTTC 59.726 37.037 8.83 3.32 0.00 3.86
4427 5019 6.455360 TTGATTAGGATGTTTCATGCTTCC 57.545 37.500 8.83 0.00 0.00 3.46
4428 5020 4.889409 TGATTAGGATGTTTCATGCTTCCC 59.111 41.667 8.83 1.06 32.48 3.97
4429 5021 4.591321 TTAGGATGTTTCATGCTTCCCT 57.409 40.909 8.83 1.65 32.48 4.20
4430 5022 2.731572 AGGATGTTTCATGCTTCCCTG 58.268 47.619 0.00 0.00 32.48 4.45
4431 5023 1.135721 GGATGTTTCATGCTTCCCTGC 59.864 52.381 0.00 0.00 0.00 4.85
4555 5147 0.748005 ACGTGCACTGAGGCAAACTT 60.748 50.000 16.19 0.00 46.93 2.66
4556 5148 1.225855 CGTGCACTGAGGCAAACTTA 58.774 50.000 16.19 0.00 46.93 2.24
4596 5188 5.760253 GGTTACATGTCTCCAGAATATGTGG 59.240 44.000 0.00 0.00 35.92 4.17
4607 5199 2.210144 AATATGTGGTGGGTGGCGCT 62.210 55.000 7.64 0.00 0.00 5.92
4876 5508 0.108186 TGCTGGTAGCTGTCCAATCG 60.108 55.000 12.37 4.27 42.97 3.34
4982 5614 8.805175 TGTGTTTATGTTGGAGAATGAAATCAT 58.195 29.630 0.00 0.00 38.41 2.45
5226 5858 7.093156 GGTGGTAGTAACCTCTGGTAGTTTAAT 60.093 40.741 0.00 0.00 46.91 1.40
5335 5968 6.539649 TTTCAGACAAGGTGTTTCTATTCG 57.460 37.500 0.00 0.00 0.00 3.34
5347 5980 6.704493 GGTGTTTCTATTCGGATATGCTTGTA 59.296 38.462 0.00 0.00 0.00 2.41
5398 6036 8.007788 GCTTTCCATCATAGCATCTCAGTATGA 61.008 40.741 0.00 0.00 37.57 2.15
5403 6041 4.525874 TCATAGCATCTCAGTATGACCTGG 59.474 45.833 0.00 0.00 42.56 4.45
5409 6047 5.873712 GCATCTCAGTATGACCTGGATTATG 59.126 44.000 0.00 0.00 42.56 1.90
5443 6083 0.737019 GCTCTGTGTCAGCTGCTCTC 60.737 60.000 9.47 6.37 33.75 3.20
5491 6135 5.982890 AAAAATCCAACCTCAGTGTATGG 57.017 39.130 0.00 0.00 0.00 2.74
5499 6143 1.003580 CCTCAGTGTATGGCCAAGTGT 59.996 52.381 10.96 0.00 0.00 3.55
5553 6206 6.085416 TGGGGGAAATATGTAAACACCTTTT 58.915 36.000 0.00 0.00 0.00 2.27
5883 6536 0.390340 CTAGTGGCGAGCTTTGAGCA 60.390 55.000 2.47 0.00 45.56 4.26
5886 6539 1.227943 TGGCGAGCTTTGAGCAGTT 60.228 52.632 2.47 0.00 45.56 3.16
5887 6540 0.819259 TGGCGAGCTTTGAGCAGTTT 60.819 50.000 2.47 0.00 45.56 2.66
5888 6541 0.312102 GGCGAGCTTTGAGCAGTTTT 59.688 50.000 2.47 0.00 45.56 2.43
5889 6542 1.535462 GGCGAGCTTTGAGCAGTTTTA 59.465 47.619 2.47 0.00 45.56 1.52
5890 6543 2.031157 GGCGAGCTTTGAGCAGTTTTAA 60.031 45.455 2.47 0.00 45.56 1.52
5891 6544 3.229552 GCGAGCTTTGAGCAGTTTTAAG 58.770 45.455 2.47 0.00 45.56 1.85
5892 6545 3.304057 GCGAGCTTTGAGCAGTTTTAAGT 60.304 43.478 2.47 0.00 45.56 2.24
5893 6546 4.458708 CGAGCTTTGAGCAGTTTTAAGTC 58.541 43.478 2.47 0.00 45.56 3.01
5894 6547 4.611581 CGAGCTTTGAGCAGTTTTAAGTCC 60.612 45.833 2.47 0.00 45.56 3.85
5924 6577 0.463654 CTGCAGCCCGCTTGGTATTA 60.464 55.000 0.00 0.00 43.06 0.98
5925 6578 0.182537 TGCAGCCCGCTTGGTATTAT 59.817 50.000 0.00 0.00 43.06 1.28
5926 6579 1.318576 GCAGCCCGCTTGGTATTATT 58.681 50.000 0.00 0.00 37.77 1.40
5927 6580 1.681264 GCAGCCCGCTTGGTATTATTT 59.319 47.619 0.00 0.00 37.77 1.40
5928 6581 2.100749 GCAGCCCGCTTGGTATTATTTT 59.899 45.455 0.00 0.00 37.77 1.82
5929 6582 3.316868 GCAGCCCGCTTGGTATTATTTTA 59.683 43.478 0.00 0.00 37.77 1.52
5963 6616 0.676151 CTCCAGCCCAGAAGCAAGTC 60.676 60.000 0.00 0.00 34.23 3.01
5966 6619 3.435186 GCCCAGAAGCAAGTCGCC 61.435 66.667 0.00 0.00 44.04 5.54
5968 6621 3.121030 CCAGAAGCAAGTCGCCGG 61.121 66.667 0.00 0.00 44.04 6.13
5969 6622 3.793144 CAGAAGCAAGTCGCCGGC 61.793 66.667 19.07 19.07 44.04 6.13
5970 6623 4.008933 AGAAGCAAGTCGCCGGCT 62.009 61.111 26.68 1.82 44.04 5.52
5971 6624 3.491652 GAAGCAAGTCGCCGGCTC 61.492 66.667 26.68 17.37 44.04 4.70
6029 6682 2.514592 CGCAGGTCCGCCAATCAT 60.515 61.111 0.95 0.00 37.19 2.45
6030 6683 2.827051 CGCAGGTCCGCCAATCATG 61.827 63.158 0.00 0.00 37.19 3.07
6046 6699 2.124362 TGGCGCCACCACCATATG 60.124 61.111 29.03 0.00 46.36 1.78
6047 6700 3.595758 GGCGCCACCACCATATGC 61.596 66.667 24.80 0.00 38.86 3.14
6049 6702 2.513666 CGCCACCACCATATGCGT 60.514 61.111 0.00 0.00 40.33 5.24
6050 6703 2.534019 CGCCACCACCATATGCGTC 61.534 63.158 0.00 0.00 40.33 5.19
6051 6704 1.153168 GCCACCACCATATGCGTCT 60.153 57.895 0.00 0.00 0.00 4.18
6052 6705 1.160329 GCCACCACCATATGCGTCTC 61.160 60.000 0.00 0.00 0.00 3.36
6053 6706 0.532862 CCACCACCATATGCGTCTCC 60.533 60.000 0.00 0.00 0.00 3.71
6054 6707 0.875908 CACCACCATATGCGTCTCCG 60.876 60.000 0.00 0.00 37.07 4.63
6055 6708 1.300931 CCACCATATGCGTCTCCGG 60.301 63.158 0.00 0.00 33.68 5.14
6056 6709 1.956170 CACCATATGCGTCTCCGGC 60.956 63.158 0.00 0.00 33.68 6.13
6057 6710 2.734723 CCATATGCGTCTCCGGCG 60.735 66.667 0.00 0.00 33.68 6.46
6067 6720 4.856607 CTCCGGCGCCTCGTCTTC 62.857 72.222 26.68 0.00 0.00 2.87
6070 6723 4.856607 CGGCGCCTCGTCTTCCTC 62.857 72.222 26.68 0.00 0.00 3.71
6071 6724 4.856607 GGCGCCTCGTCTTCCTCG 62.857 72.222 22.15 0.00 0.00 4.63
6073 6726 4.856607 CGCCTCGTCTTCCTCGCC 62.857 72.222 0.00 0.00 0.00 5.54
6074 6727 3.453679 GCCTCGTCTTCCTCGCCT 61.454 66.667 0.00 0.00 0.00 5.52
6075 6728 3.007973 GCCTCGTCTTCCTCGCCTT 62.008 63.158 0.00 0.00 0.00 4.35
6076 6729 1.592223 CCTCGTCTTCCTCGCCTTT 59.408 57.895 0.00 0.00 0.00 3.11
6077 6730 0.458716 CCTCGTCTTCCTCGCCTTTC 60.459 60.000 0.00 0.00 0.00 2.62
6078 6731 0.528470 CTCGTCTTCCTCGCCTTTCT 59.472 55.000 0.00 0.00 0.00 2.52
6079 6732 0.526662 TCGTCTTCCTCGCCTTTCTC 59.473 55.000 0.00 0.00 0.00 2.87
6080 6733 0.528470 CGTCTTCCTCGCCTTTCTCT 59.472 55.000 0.00 0.00 0.00 3.10
6081 6734 1.468395 CGTCTTCCTCGCCTTTCTCTC 60.468 57.143 0.00 0.00 0.00 3.20
6082 6735 1.134936 GTCTTCCTCGCCTTTCTCTCC 60.135 57.143 0.00 0.00 0.00 3.71
6083 6736 0.176910 CTTCCTCGCCTTTCTCTCCC 59.823 60.000 0.00 0.00 0.00 4.30
6084 6737 1.265454 TTCCTCGCCTTTCTCTCCCC 61.265 60.000 0.00 0.00 0.00 4.81
6085 6738 1.687493 CCTCGCCTTTCTCTCCCCT 60.687 63.158 0.00 0.00 0.00 4.79
6086 6739 1.268283 CCTCGCCTTTCTCTCCCCTT 61.268 60.000 0.00 0.00 0.00 3.95
6087 6740 0.176910 CTCGCCTTTCTCTCCCCTTC 59.823 60.000 0.00 0.00 0.00 3.46
6088 6741 1.222113 CGCCTTTCTCTCCCCTTCC 59.778 63.158 0.00 0.00 0.00 3.46
6089 6742 1.553690 CGCCTTTCTCTCCCCTTCCA 61.554 60.000 0.00 0.00 0.00 3.53
6090 6743 0.254462 GCCTTTCTCTCCCCTTCCAG 59.746 60.000 0.00 0.00 0.00 3.86
6091 6744 0.915364 CCTTTCTCTCCCCTTCCAGG 59.085 60.000 0.00 0.00 34.30 4.45
6092 6745 0.254462 CTTTCTCTCCCCTTCCAGGC 59.746 60.000 0.00 0.00 32.73 4.85
6093 6746 1.553690 TTTCTCTCCCCTTCCAGGCG 61.554 60.000 0.00 0.00 32.73 5.52
6094 6747 3.474570 CTCTCCCCTTCCAGGCGG 61.475 72.222 0.00 0.00 32.73 6.13
6099 6752 3.488569 CCCTTCCAGGCGGCCATA 61.489 66.667 23.09 2.47 32.73 2.74
6100 6753 2.111878 CCTTCCAGGCGGCCATAG 59.888 66.667 23.09 10.42 0.00 2.23
6101 6754 2.592861 CTTCCAGGCGGCCATAGC 60.593 66.667 23.09 0.00 38.76 2.97
6102 6755 3.405093 CTTCCAGGCGGCCATAGCA 62.405 63.158 23.09 0.00 42.56 3.49
6103 6756 2.891941 CTTCCAGGCGGCCATAGCAA 62.892 60.000 23.09 1.95 42.56 3.91
6104 6757 2.891941 TTCCAGGCGGCCATAGCAAG 62.892 60.000 23.09 1.27 42.56 4.01
6105 6758 3.589881 CAGGCGGCCATAGCAAGC 61.590 66.667 23.09 0.00 42.56 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.556911 AGGATGTGGCGGATGGATATC 59.443 52.381 0.00 0.00 0.00 1.63
1 2 1.280133 CAGGATGTGGCGGATGGATAT 59.720 52.381 0.00 0.00 0.00 1.63
2 3 0.686789 CAGGATGTGGCGGATGGATA 59.313 55.000 0.00 0.00 0.00 2.59
3 4 1.453235 CAGGATGTGGCGGATGGAT 59.547 57.895 0.00 0.00 0.00 3.41
5 6 2.903855 GCAGGATGTGGCGGATGG 60.904 66.667 0.00 0.00 39.31 3.51
6 7 1.890979 GAGCAGGATGTGGCGGATG 60.891 63.158 0.00 0.00 39.31 3.51
7 8 2.507944 GAGCAGGATGTGGCGGAT 59.492 61.111 0.00 0.00 39.31 4.18
8 9 4.147449 CGAGCAGGATGTGGCGGA 62.147 66.667 0.00 0.00 39.31 5.54
9 10 4.457496 ACGAGCAGGATGTGGCGG 62.457 66.667 0.00 0.00 39.31 6.13
10 11 2.887568 GACGAGCAGGATGTGGCG 60.888 66.667 0.00 0.00 39.31 5.69
11 12 2.887568 CGACGAGCAGGATGTGGC 60.888 66.667 0.00 0.00 39.31 5.01
22 23 2.936498 ACAAAAGATAATGGGCGACGAG 59.064 45.455 0.00 0.00 0.00 4.18
23 24 2.980568 ACAAAAGATAATGGGCGACGA 58.019 42.857 0.00 0.00 0.00 4.20
24 25 3.374058 AGAACAAAAGATAATGGGCGACG 59.626 43.478 0.00 0.00 0.00 5.12
25 26 4.965119 AGAACAAAAGATAATGGGCGAC 57.035 40.909 0.00 0.00 0.00 5.19
26 27 7.639113 AATTAGAACAAAAGATAATGGGCGA 57.361 32.000 0.00 0.00 0.00 5.54
27 28 8.702163 AAAATTAGAACAAAAGATAATGGGCG 57.298 30.769 0.00 0.00 0.00 6.13
52 53 9.685828 CACGATTCTAAATTTAACAAGGGAAAA 57.314 29.630 0.00 0.00 0.00 2.29
53 54 8.301002 CCACGATTCTAAATTTAACAAGGGAAA 58.699 33.333 0.00 0.00 0.00 3.13
54 55 7.666388 TCCACGATTCTAAATTTAACAAGGGAA 59.334 33.333 0.00 0.00 0.00 3.97
55 56 7.169591 TCCACGATTCTAAATTTAACAAGGGA 58.830 34.615 0.00 0.00 0.00 4.20
56 57 7.385778 TCCACGATTCTAAATTTAACAAGGG 57.614 36.000 0.00 0.00 0.00 3.95
57 58 9.855021 ATTTCCACGATTCTAAATTTAACAAGG 57.145 29.630 0.00 0.00 0.00 3.61
60 61 9.834628 GTCATTTCCACGATTCTAAATTTAACA 57.165 29.630 0.00 0.00 0.00 2.41
61 62 9.834628 TGTCATTTCCACGATTCTAAATTTAAC 57.165 29.630 0.00 0.00 0.00 2.01
62 63 9.834628 GTGTCATTTCCACGATTCTAAATTTAA 57.165 29.630 0.00 0.00 0.00 1.52
63 64 8.455682 GGTGTCATTTCCACGATTCTAAATTTA 58.544 33.333 0.00 0.00 33.56 1.40
64 65 7.040062 TGGTGTCATTTCCACGATTCTAAATTT 60.040 33.333 0.00 0.00 33.56 1.82
65 66 6.432783 TGGTGTCATTTCCACGATTCTAAATT 59.567 34.615 0.00 0.00 33.56 1.82
66 67 5.943416 TGGTGTCATTTCCACGATTCTAAAT 59.057 36.000 0.00 0.00 33.56 1.40
67 68 5.180492 GTGGTGTCATTTCCACGATTCTAAA 59.820 40.000 0.00 0.00 43.34 1.85
68 69 4.693566 GTGGTGTCATTTCCACGATTCTAA 59.306 41.667 0.00 0.00 43.34 2.10
69 70 4.250464 GTGGTGTCATTTCCACGATTCTA 58.750 43.478 0.00 0.00 43.34 2.10
114 115 4.870426 CCGTTATGTGCACTTCAGACTTAT 59.130 41.667 19.41 1.95 0.00 1.73
240 241 1.517276 CGTTGAGTATCGCGAATGGTC 59.483 52.381 15.24 8.56 38.13 4.02
258 326 2.804572 CGATTGGGATCAGATTGCTCGT 60.805 50.000 0.00 0.00 32.33 4.18
268 336 1.134128 CACCATGGTCGATTGGGATCA 60.134 52.381 16.53 0.00 37.32 2.92
370 474 1.638388 CTACCACAGCCGTCGACGTA 61.638 60.000 33.49 17.70 37.74 3.57
371 475 2.974489 CTACCACAGCCGTCGACGT 61.974 63.158 33.49 16.10 37.74 4.34
377 481 4.016706 GCCACCTACCACAGCCGT 62.017 66.667 0.00 0.00 0.00 5.68
382 486 3.632080 CCACGGCCACCTACCACA 61.632 66.667 2.24 0.00 0.00 4.17
427 531 1.235724 GTGGTTGGCTAGTTGGTGTC 58.764 55.000 0.00 0.00 0.00 3.67
454 558 1.596954 CGGAAAAGTCGCTTGTTGTGG 60.597 52.381 0.00 0.00 0.00 4.17
468 572 3.659092 CTGTGCCTGCGCGGAAAA 61.659 61.111 20.25 3.05 38.08 2.29
496 600 1.203287 CAGATTGGAGAGTGCGACAGA 59.797 52.381 0.00 0.00 0.00 3.41
507 611 7.520776 GCATTCAGATTCAGATTCAGATTGGAG 60.521 40.741 9.69 0.00 0.00 3.86
525 629 2.760634 TTCGTTGCTAGGCATTCAGA 57.239 45.000 0.00 0.00 38.76 3.27
526 630 4.361451 AAATTCGTTGCTAGGCATTCAG 57.639 40.909 0.00 0.00 38.76 3.02
527 631 4.458989 AGAAAATTCGTTGCTAGGCATTCA 59.541 37.500 0.00 0.00 38.76 2.57
528 632 4.986622 AGAAAATTCGTTGCTAGGCATTC 58.013 39.130 0.00 0.00 38.76 2.67
529 633 5.391312 AAGAAAATTCGTTGCTAGGCATT 57.609 34.783 0.00 0.00 38.76 3.56
530 634 5.391312 AAAGAAAATTCGTTGCTAGGCAT 57.609 34.783 0.00 0.00 38.76 4.40
531 635 4.320935 GGAAAGAAAATTCGTTGCTAGGCA 60.321 41.667 6.19 0.00 35.03 4.75
532 636 4.166523 GGAAAGAAAATTCGTTGCTAGGC 58.833 43.478 6.19 0.00 35.03 3.93
533 637 4.459337 AGGGAAAGAAAATTCGTTGCTAGG 59.541 41.667 11.59 0.00 37.23 3.02
534 638 5.629079 AGGGAAAGAAAATTCGTTGCTAG 57.371 39.130 11.59 0.00 37.23 3.42
535 639 5.768317 CAAGGGAAAGAAAATTCGTTGCTA 58.232 37.500 11.59 0.00 37.23 3.49
536 640 4.620982 CAAGGGAAAGAAAATTCGTTGCT 58.379 39.130 11.59 0.00 37.23 3.91
537 641 3.184379 GCAAGGGAAAGAAAATTCGTTGC 59.816 43.478 5.11 5.11 40.06 4.17
538 642 3.425193 CGCAAGGGAAAGAAAATTCGTTG 59.575 43.478 0.00 0.00 31.81 4.10
539 643 3.638484 CGCAAGGGAAAGAAAATTCGTT 58.362 40.909 0.00 0.00 0.00 3.85
540 644 2.607038 GCGCAAGGGAAAGAAAATTCGT 60.607 45.455 0.30 0.00 38.28 3.85
541 645 1.985684 GCGCAAGGGAAAGAAAATTCG 59.014 47.619 0.30 0.00 38.28 3.34
554 658 2.173382 GTTGCTACACGCGCAAGG 59.827 61.111 5.73 0.00 46.81 3.61
555 659 1.154599 CAGTTGCTACACGCGCAAG 60.155 57.895 5.73 1.61 46.81 4.01
556 660 0.597898 TACAGTTGCTACACGCGCAA 60.598 50.000 5.73 0.00 44.36 4.85
580 684 1.073177 CGGTAAGGTTAACTGCCACG 58.927 55.000 5.42 2.23 0.00 4.94
584 688 3.251571 CTGAGTCGGTAAGGTTAACTGC 58.748 50.000 5.42 0.00 0.00 4.40
588 692 4.660168 AGAGACTGAGTCGGTAAGGTTAA 58.340 43.478 4.10 0.00 37.67 2.01
590 694 3.157750 AGAGACTGAGTCGGTAAGGTT 57.842 47.619 4.10 0.00 37.67 3.50
591 695 2.883122 AGAGACTGAGTCGGTAAGGT 57.117 50.000 4.10 0.00 37.67 3.50
592 696 4.998672 CCTATAGAGACTGAGTCGGTAAGG 59.001 50.000 4.10 8.08 37.67 2.69
595 699 3.647113 AGCCTATAGAGACTGAGTCGGTA 59.353 47.826 4.10 3.29 37.67 4.02
596 700 2.440253 AGCCTATAGAGACTGAGTCGGT 59.560 50.000 3.66 3.66 37.67 4.69
598 702 6.170506 AGATAAGCCTATAGAGACTGAGTCG 58.829 44.000 6.99 0.00 37.67 4.18
599 703 7.394816 AGAGATAAGCCTATAGAGACTGAGTC 58.605 42.308 3.98 3.98 0.00 3.36
600 704 7.329746 AGAGATAAGCCTATAGAGACTGAGT 57.670 40.000 0.00 0.00 0.00 3.41
619 896 8.563732 GCAAAAGACTAGAACAAAGAAAGAGAT 58.436 33.333 0.00 0.00 0.00 2.75
634 911 9.515020 TTTTCAAAAGTATGTGCAAAAGACTAG 57.485 29.630 0.00 0.00 0.00 2.57
678 959 7.887495 ACATCATATAGTCATCTCTACTGCAGA 59.113 37.037 23.35 2.95 0.00 4.26
679 960 7.969508 CACATCATATAGTCATCTCTACTGCAG 59.030 40.741 13.48 13.48 0.00 4.41
680 961 7.094032 CCACATCATATAGTCATCTCTACTGCA 60.094 40.741 0.00 0.00 0.00 4.41
681 962 7.257003 CCACATCATATAGTCATCTCTACTGC 58.743 42.308 0.00 0.00 0.00 4.40
682 963 7.257003 GCCACATCATATAGTCATCTCTACTG 58.743 42.308 0.00 0.00 0.00 2.74
683 964 6.094742 CGCCACATCATATAGTCATCTCTACT 59.905 42.308 0.00 0.00 0.00 2.57
684 965 6.261859 CGCCACATCATATAGTCATCTCTAC 58.738 44.000 0.00 0.00 0.00 2.59
685 966 5.163612 GCGCCACATCATATAGTCATCTCTA 60.164 44.000 0.00 0.00 0.00 2.43
686 967 4.381398 GCGCCACATCATATAGTCATCTCT 60.381 45.833 0.00 0.00 0.00 3.10
687 968 3.862267 GCGCCACATCATATAGTCATCTC 59.138 47.826 0.00 0.00 0.00 2.75
688 969 3.259123 TGCGCCACATCATATAGTCATCT 59.741 43.478 4.18 0.00 0.00 2.90
689 970 3.588955 TGCGCCACATCATATAGTCATC 58.411 45.455 4.18 0.00 0.00 2.92
702 983 3.361158 CAAACCGGATGCGCCACA 61.361 61.111 9.46 0.00 35.94 4.17
713 994 1.831389 CGACACCTCACTGCAAACCG 61.831 60.000 0.00 0.00 0.00 4.44
715 996 1.279840 GCGACACCTCACTGCAAAC 59.720 57.895 0.00 0.00 0.00 2.93
717 998 2.280797 GGCGACACCTCACTGCAA 60.281 61.111 0.00 0.00 34.51 4.08
782 1063 4.571176 GCCAGAAGAAAAATCCGGTACTAG 59.429 45.833 0.00 0.00 0.00 2.57
797 1078 0.322816 GGGTGATGCAAGCCAGAAGA 60.323 55.000 1.67 0.00 37.66 2.87
814 1095 5.859205 ATATTGCTCAAAGCCTTTAAGGG 57.141 39.130 13.42 0.00 41.51 3.95
819 1100 6.594788 TCTCAAATATTGCTCAAAGCCTTT 57.405 33.333 0.00 0.00 41.51 3.11
827 1108 4.240881 AGGCCTTCTCAAATATTGCTCA 57.759 40.909 0.00 0.00 0.00 4.26
834 1115 3.244875 TGCTGACAAGGCCTTCTCAAATA 60.245 43.478 21.96 10.14 0.00 1.40
894 1304 3.262420 CGGTTCTCCATAACAGGAAGTG 58.738 50.000 0.00 0.00 37.20 3.16
988 1398 5.070685 GGAAATATCCATTACGCCTCCTTT 58.929 41.667 0.00 0.00 45.79 3.11
1008 1418 4.544152 AGGATGAAAATGGGGAAGTAGGAA 59.456 41.667 0.00 0.00 0.00 3.36
1013 1423 2.929043 AGGAGGATGAAAATGGGGAAGT 59.071 45.455 0.00 0.00 0.00 3.01
1467 1877 2.028130 CAGAAATCTCATGCCGGGC 58.972 57.895 13.32 13.32 0.00 6.13
1470 1880 1.598132 CTCAGCAGAAATCTCATGCCG 59.402 52.381 0.00 0.00 40.89 5.69
1613 2026 1.003355 ATGCGGCAGTACAGCTTGT 60.003 52.632 9.25 0.00 40.54 3.16
2209 2622 0.038892 TAGTTGACGGTCTTCCACGC 60.039 55.000 9.88 0.00 0.00 5.34
2221 2634 2.271800 CAGGTTCTCGCCATAGTTGAC 58.728 52.381 0.00 0.00 0.00 3.18
2222 2635 1.899814 ACAGGTTCTCGCCATAGTTGA 59.100 47.619 0.00 0.00 0.00 3.18
2253 2666 2.856039 TACCAGCAGGAGAGTCCCCG 62.856 65.000 0.35 0.00 37.19 5.73
2277 2690 7.327975 ACTATTGATCCGAAACAGTAATGTCA 58.672 34.615 0.00 0.00 0.00 3.58
2342 2755 5.789643 ACTTCTCTCTGCTAGATGATTCC 57.210 43.478 0.00 0.00 32.41 3.01
2351 2764 5.279506 CCCTGTTTTGTACTTCTCTCTGCTA 60.280 44.000 0.00 0.00 0.00 3.49
2360 2773 8.127327 GTCTAAAGTTTCCCTGTTTTGTACTTC 58.873 37.037 0.00 0.00 0.00 3.01
2379 2913 4.579340 TCGCCTACAGTCCTATGTCTAAAG 59.421 45.833 0.00 0.00 34.56 1.85
2571 3105 0.478072 TGGTGAAACTGAGGGTGCAT 59.522 50.000 0.00 0.00 36.74 3.96
2586 3120 1.656652 GTACTGCTAGGCATGTGGTG 58.343 55.000 0.00 0.00 38.13 4.17
2645 3179 4.510711 GCATGAAGTACCATGACTGATCTG 59.489 45.833 14.19 0.00 44.98 2.90
2714 3277 9.624697 GCTGAAATGTATCACAACAGAATTTAA 57.375 29.630 0.00 0.00 33.28 1.52
2715 3278 8.791675 TGCTGAAATGTATCACAACAGAATTTA 58.208 29.630 0.00 0.00 33.28 1.40
2716 3279 7.660112 TGCTGAAATGTATCACAACAGAATTT 58.340 30.769 0.00 0.00 33.28 1.82
2717 3280 7.040201 ACTGCTGAAATGTATCACAACAGAATT 60.040 33.333 0.00 0.00 33.28 2.17
2777 3341 2.438434 AGGCATGCTACAACCGGC 60.438 61.111 18.92 0.00 0.00 6.13
2824 3388 9.554395 TTGTTCTATCTTTGTACTCACATTTCA 57.446 29.630 0.00 0.00 33.76 2.69
2954 3522 5.505819 GCACTCAAGTATCGTAGCATCAGTA 60.506 44.000 0.00 0.00 0.00 2.74
3015 3583 7.360946 GCCACAATATCTTCGAAACTAACAACT 60.361 37.037 0.00 0.00 0.00 3.16
3016 3584 6.741358 GCCACAATATCTTCGAAACTAACAAC 59.259 38.462 0.00 0.00 0.00 3.32
3124 3692 0.447801 GCACCTTACTTGCCGATGTG 59.552 55.000 0.00 0.00 33.58 3.21
3138 3706 1.561076 TCTGGCAGACATATTGCACCT 59.439 47.619 14.43 0.00 43.28 4.00
3142 3710 4.357142 CACAATTCTGGCAGACATATTGC 58.643 43.478 27.96 0.00 40.80 3.56
3193 3761 9.912634 GATGTCAAATGTCAATTAAGAAGGAAA 57.087 29.630 0.00 0.00 0.00 3.13
3194 3762 9.076781 TGATGTCAAATGTCAATTAAGAAGGAA 57.923 29.630 0.00 0.00 0.00 3.36
3272 3841 3.410631 TTTCTCCACGGAATTACTGCA 57.589 42.857 0.00 0.00 0.00 4.41
3273 3842 4.759516 TTTTTCTCCACGGAATTACTGC 57.240 40.909 0.00 0.00 0.00 4.40
3384 3956 7.308435 CCTTTTGATATGAACTTCCTTGTCAC 58.692 38.462 0.00 0.00 0.00 3.67
3398 3970 3.429822 CCACTGCCAAGCCTTTTGATATG 60.430 47.826 0.00 0.00 0.00 1.78
3399 3971 2.762327 CCACTGCCAAGCCTTTTGATAT 59.238 45.455 0.00 0.00 0.00 1.63
3442 4014 7.748241 GCAATTAGAGTCACTTCATTTCTGAAC 59.252 37.037 0.00 0.00 36.46 3.18
3684 4260 8.702438 CATCATGAACAGTTCAATAAAACCAAC 58.298 33.333 19.92 0.00 43.95 3.77
3708 4284 8.798859 ACATCTTTTCTTGTACTATCTTGCAT 57.201 30.769 0.00 0.00 0.00 3.96
3963 4539 4.973168 TCCTAGACACTTTTCAGCACATT 58.027 39.130 0.00 0.00 0.00 2.71
4037 4614 5.532557 GAAAATATAACAGGCAATGGGAGC 58.467 41.667 0.00 0.00 0.00 4.70
4060 4637 7.242914 AGACAAGTTGAACTTAACTAAACCG 57.757 36.000 10.63 0.00 39.86 4.44
4240 4824 9.807386 GATTATAATTTCGTAACTTTCATCCGG 57.193 33.333 0.00 0.00 0.00 5.14
4262 4846 9.219603 CTGAACCTCTGAACAAACATAAGATTA 57.780 33.333 0.00 0.00 0.00 1.75
4362 4946 5.483583 TGTCTTTGGGGGATTTAAATTGGAG 59.516 40.000 1.43 0.00 0.00 3.86
4384 4968 3.735237 AACACGAGTGAAGATCTGTGT 57.265 42.857 10.50 8.11 41.89 3.72
4418 5010 0.401356 TGACTTGCAGGGAAGCATGA 59.599 50.000 0.00 0.00 45.19 3.07
4424 5016 3.072915 TCTCTTTCATGACTTGCAGGGAA 59.927 43.478 0.00 0.00 0.00 3.97
4425 5017 2.639347 TCTCTTTCATGACTTGCAGGGA 59.361 45.455 0.00 0.00 0.00 4.20
4426 5018 3.063510 TCTCTTTCATGACTTGCAGGG 57.936 47.619 0.00 0.00 0.00 4.45
4427 5019 7.440198 TCTATATCTCTTTCATGACTTGCAGG 58.560 38.462 0.00 0.00 0.00 4.85
4428 5020 8.927721 CATCTATATCTCTTTCATGACTTGCAG 58.072 37.037 0.00 0.00 0.00 4.41
4429 5021 7.876582 CCATCTATATCTCTTTCATGACTTGCA 59.123 37.037 0.00 0.00 0.00 4.08
4430 5022 7.877097 ACCATCTATATCTCTTTCATGACTTGC 59.123 37.037 0.00 0.00 0.00 4.01
4431 5023 9.775854 AACCATCTATATCTCTTTCATGACTTG 57.224 33.333 0.00 0.00 0.00 3.16
4537 5129 1.225855 TAAGTTTGCCTCAGTGCACG 58.774 50.000 12.01 6.78 41.88 5.34
4555 5147 8.948145 ACATGTAACCGCTGTTTAAACATTATA 58.052 29.630 20.83 14.30 38.41 0.98
4556 5148 7.822658 ACATGTAACCGCTGTTTAAACATTAT 58.177 30.769 20.83 8.93 38.41 1.28
4596 5188 1.007387 CAGAAAAAGCGCCACCCAC 60.007 57.895 2.29 0.00 0.00 4.61
4607 5199 7.211573 TGTAGATGTCCGACTTAACAGAAAAA 58.788 34.615 0.00 0.00 0.00 1.94
4876 5508 3.932710 TGAATGCACCGTAGAACTTCATC 59.067 43.478 0.00 0.00 0.00 2.92
5226 5858 3.007074 TCCACTTCGGTGCTTTACATACA 59.993 43.478 0.00 0.00 44.05 2.29
5300 5933 6.639686 CACCTTGTCTGAAATGAGAAACAATG 59.360 38.462 0.00 0.00 0.00 2.82
5356 5990 7.450014 TGATGGAAAGCTTATTCTTACCAAACA 59.550 33.333 0.00 4.40 0.00 2.83
5357 5991 7.826690 TGATGGAAAGCTTATTCTTACCAAAC 58.173 34.615 0.00 2.25 0.00 2.93
5362 5996 8.383318 TGCTATGATGGAAAGCTTATTCTTAC 57.617 34.615 0.00 0.00 37.16 2.34
5373 6007 7.331440 GTCATACTGAGATGCTATGATGGAAAG 59.669 40.741 0.00 0.00 31.26 2.62
5398 6036 5.036916 TCTCAGGGTAAACATAATCCAGGT 58.963 41.667 0.00 0.00 0.00 4.00
5403 6041 6.995091 AGAGCAATCTCAGGGTAAACATAATC 59.005 38.462 0.00 0.00 41.81 1.75
5409 6047 3.686726 CACAGAGCAATCTCAGGGTAAAC 59.313 47.826 0.00 0.00 41.81 2.01
5491 6135 4.009675 TCCTGTTAATGATGACACTTGGC 58.990 43.478 0.00 0.00 0.00 4.52
5563 6216 5.831702 TGCACATGGAAAAATTTGCTTTT 57.168 30.435 0.00 0.00 38.73 2.27
5564 6217 6.394025 AATGCACATGGAAAAATTTGCTTT 57.606 29.167 0.00 0.00 34.90 3.51
5567 6220 8.745464 AAAATAATGCACATGGAAAAATTTGC 57.255 26.923 0.00 0.00 34.51 3.68
5825 6478 7.657336 TGTGTTTTTCCCATAGAGAATCAAAC 58.343 34.615 0.00 0.00 37.82 2.93
5828 6481 9.527157 TTAATGTGTTTTTCCCATAGAGAATCA 57.473 29.630 0.00 0.00 37.82 2.57
5832 6485 7.341769 CCCATTAATGTGTTTTTCCCATAGAGA 59.658 37.037 14.25 0.00 0.00 3.10
5833 6486 7.491682 CCCATTAATGTGTTTTTCCCATAGAG 58.508 38.462 14.25 0.00 0.00 2.43
5835 6488 6.048509 GCCCATTAATGTGTTTTTCCCATAG 58.951 40.000 14.25 0.00 0.00 2.23
5836 6489 5.104735 GGCCCATTAATGTGTTTTTCCCATA 60.105 40.000 14.25 0.00 0.00 2.74
5837 6490 4.324176 GGCCCATTAATGTGTTTTTCCCAT 60.324 41.667 14.25 0.00 0.00 4.00
5838 6491 3.008485 GGCCCATTAATGTGTTTTTCCCA 59.992 43.478 14.25 0.00 0.00 4.37
5840 6493 3.258228 CGGCCCATTAATGTGTTTTTCC 58.742 45.455 14.25 0.00 0.00 3.13
5841 6494 2.670905 GCGGCCCATTAATGTGTTTTTC 59.329 45.455 14.25 0.00 0.00 2.29
5871 6524 4.458708 GACTTAAAACTGCTCAAAGCTCG 58.541 43.478 0.11 0.00 42.97 5.03
5883 6536 5.831525 CAGGTTTACTTGGGGACTTAAAACT 59.168 40.000 0.00 0.00 32.78 2.66
5886 6539 4.146564 GCAGGTTTACTTGGGGACTTAAA 58.853 43.478 0.00 0.00 0.00 1.52
5887 6540 3.138653 TGCAGGTTTACTTGGGGACTTAA 59.861 43.478 0.00 0.00 0.00 1.85
5888 6541 2.712087 TGCAGGTTTACTTGGGGACTTA 59.288 45.455 0.00 0.00 0.00 2.24
5889 6542 1.497286 TGCAGGTTTACTTGGGGACTT 59.503 47.619 0.00 0.00 0.00 3.01
5890 6543 1.073923 CTGCAGGTTTACTTGGGGACT 59.926 52.381 5.57 0.00 0.00 3.85
5891 6544 1.534729 CTGCAGGTTTACTTGGGGAC 58.465 55.000 5.57 0.00 0.00 4.46
5892 6545 0.251165 GCTGCAGGTTTACTTGGGGA 60.251 55.000 17.12 0.00 0.00 4.81
5893 6546 1.250840 GGCTGCAGGTTTACTTGGGG 61.251 60.000 17.12 0.00 0.00 4.96
5894 6547 1.250840 GGGCTGCAGGTTTACTTGGG 61.251 60.000 17.12 0.00 0.00 4.12
5924 6577 6.151049 TGGAGGCCCTTCTATCTAGTAAAAT 58.849 40.000 0.00 0.00 0.00 1.82
5925 6578 5.535029 TGGAGGCCCTTCTATCTAGTAAAA 58.465 41.667 0.00 0.00 0.00 1.52
5926 6579 5.148502 CTGGAGGCCCTTCTATCTAGTAAA 58.851 45.833 0.00 0.00 0.00 2.01
5927 6580 4.742012 CTGGAGGCCCTTCTATCTAGTAA 58.258 47.826 0.00 0.00 0.00 2.24
5928 6581 3.500654 GCTGGAGGCCCTTCTATCTAGTA 60.501 52.174 0.00 0.00 34.27 1.82
5929 6582 2.758295 GCTGGAGGCCCTTCTATCTAGT 60.758 54.545 0.00 0.00 34.27 2.57
5954 6607 3.491652 GAGCCGGCGACTTGCTTC 61.492 66.667 23.20 6.54 45.43 3.86
6010 6663 4.778143 GATTGGCGGACCTGCGGT 62.778 66.667 0.00 0.00 39.44 5.68
6011 6664 4.776322 TGATTGGCGGACCTGCGG 62.776 66.667 2.88 0.00 36.63 5.69
6012 6665 2.514592 ATGATTGGCGGACCTGCG 60.515 61.111 2.88 0.00 36.63 5.18
6013 6666 2.484062 CCATGATTGGCGGACCTGC 61.484 63.158 0.00 0.32 35.85 4.85
6014 6667 3.831883 CCATGATTGGCGGACCTG 58.168 61.111 0.00 0.00 35.85 4.00
6022 6675 2.755064 TGGTGGCGCCATGATTGG 60.755 61.111 35.23 0.00 43.61 3.16
6029 6682 2.124362 CATATGGTGGTGGCGCCA 60.124 61.111 29.03 29.03 46.95 5.69
6030 6683 3.595758 GCATATGGTGGTGGCGCC 61.596 66.667 22.73 22.73 37.90 6.53
6031 6684 3.952675 CGCATATGGTGGTGGCGC 61.953 66.667 0.00 0.00 41.27 6.53
6033 6686 1.153168 AGACGCATATGGTGGTGGC 60.153 57.895 4.56 0.00 0.00 5.01
6034 6687 0.532862 GGAGACGCATATGGTGGTGG 60.533 60.000 4.56 0.00 0.00 4.61
6035 6688 2.992089 GGAGACGCATATGGTGGTG 58.008 57.895 4.56 0.00 0.00 4.17
6050 6703 4.856607 GAAGACGAGGCGCCGGAG 62.857 72.222 23.20 18.64 0.00 4.63
6053 6706 4.856607 GAGGAAGACGAGGCGCCG 62.857 72.222 23.20 13.22 0.00 6.46
6054 6707 4.856607 CGAGGAAGACGAGGCGCC 62.857 72.222 21.89 21.89 0.00 6.53
6056 6709 4.856607 GGCGAGGAAGACGAGGCG 62.857 72.222 0.00 0.00 0.00 5.52
6057 6710 2.508586 AAAGGCGAGGAAGACGAGGC 62.509 60.000 0.00 0.00 0.00 4.70
6058 6711 0.458716 GAAAGGCGAGGAAGACGAGG 60.459 60.000 0.00 0.00 0.00 4.63
6059 6712 0.528470 AGAAAGGCGAGGAAGACGAG 59.472 55.000 0.00 0.00 0.00 4.18
6060 6713 0.526662 GAGAAAGGCGAGGAAGACGA 59.473 55.000 0.00 0.00 0.00 4.20
6061 6714 0.528470 AGAGAAAGGCGAGGAAGACG 59.472 55.000 0.00 0.00 0.00 4.18
6062 6715 1.134936 GGAGAGAAAGGCGAGGAAGAC 60.135 57.143 0.00 0.00 0.00 3.01
6063 6716 1.187087 GGAGAGAAAGGCGAGGAAGA 58.813 55.000 0.00 0.00 0.00 2.87
6064 6717 0.176910 GGGAGAGAAAGGCGAGGAAG 59.823 60.000 0.00 0.00 0.00 3.46
6065 6718 1.265454 GGGGAGAGAAAGGCGAGGAA 61.265 60.000 0.00 0.00 0.00 3.36
6066 6719 1.686110 GGGGAGAGAAAGGCGAGGA 60.686 63.158 0.00 0.00 0.00 3.71
6067 6720 1.268283 AAGGGGAGAGAAAGGCGAGG 61.268 60.000 0.00 0.00 0.00 4.63
6068 6721 0.176910 GAAGGGGAGAGAAAGGCGAG 59.823 60.000 0.00 0.00 0.00 5.03
6069 6722 1.265454 GGAAGGGGAGAGAAAGGCGA 61.265 60.000 0.00 0.00 0.00 5.54
6070 6723 1.222113 GGAAGGGGAGAGAAAGGCG 59.778 63.158 0.00 0.00 0.00 5.52
6071 6724 0.254462 CTGGAAGGGGAGAGAAAGGC 59.746 60.000 0.00 0.00 0.00 4.35
6084 6737 2.592861 GCTATGGCCGCCTGGAAG 60.593 66.667 11.61 3.93 37.49 3.46
6085 6738 2.891941 CTTGCTATGGCCGCCTGGAA 62.892 60.000 11.61 7.56 37.49 3.53
6086 6739 3.405093 CTTGCTATGGCCGCCTGGA 62.405 63.158 11.61 0.00 37.49 3.86
6087 6740 2.903855 CTTGCTATGGCCGCCTGG 60.904 66.667 11.61 1.82 37.74 4.45
6088 6741 3.589881 GCTTGCTATGGCCGCCTG 61.590 66.667 11.61 2.17 37.74 4.85


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

AutoCloner maintained by Alex Coulton.