Multiple sequence alignment - TraesCS1D01G161000

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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 TraesCS1D01G161000 chr1D 100.000 7313 0 0 1 7313 227859143 227866455 0.000000e+00 13505.0
1 TraesCS1D01G161000 chr1D 96.566 3990 106 17 2069 6041 208280251 208276276 0.000000e+00 6580.0
2 TraesCS1D01G161000 chr1D 97.227 1262 31 2 811 2072 208281533 208280276 0.000000e+00 2134.0
3 TraesCS1D01G161000 chr1D 94.074 540 21 3 1 529 208282080 208281541 0.000000e+00 809.0
4 TraesCS1D01G161000 chr1D 96.855 477 12 2 6030 6506 208275910 208275437 0.000000e+00 795.0
5 TraesCS1D01G161000 chr1D 95.181 332 10 5 6988 7313 208240209 208239878 3.020000e-143 520.0
6 TraesCS1D01G161000 chr1D 86.916 321 31 6 6522 6837 208275164 208274850 4.200000e-92 350.0
7 TraesCS1D01G161000 chr1D 97.175 177 5 0 530 706 144940776 144940600 4.290000e-77 300.0
8 TraesCS1D01G161000 chr1D 96.667 180 6 0 527 706 332963050 332963229 4.290000e-77 300.0
9 TraesCS1D01G161000 chr1D 81.439 264 38 4 6603 6856 442997879 442998141 9.620000e-49 206.0
10 TraesCS1D01G161000 chr1D 97.938 97 2 0 704 800 419072702 419072798 1.260000e-37 169.0
11 TraesCS1D01G161000 chr1D 84.795 171 7 3 6835 6997 208241628 208241469 3.530000e-33 154.0
12 TraesCS1D01G161000 chr1A 95.888 3599 96 23 1042 4609 295458804 295462381 0.000000e+00 5779.0
13 TraesCS1D01G161000 chr1A 94.767 1930 69 11 4609 6529 295462709 295464615 0.000000e+00 2976.0
14 TraesCS1D01G161000 chr1A 86.294 591 66 9 1115 1702 311808690 311808112 4.820000e-176 628.0
15 TraesCS1D01G161000 chr1A 86.860 586 40 16 6763 7313 295464622 295465205 8.060000e-174 621.0
16 TraesCS1D01G161000 chr1A 95.065 385 8 5 804 1187 295457902 295458276 4.880000e-166 595.0
17 TraesCS1D01G161000 chr1A 84.039 614 83 10 2083 2683 311807458 311806847 1.770000e-160 577.0
18 TraesCS1D01G161000 chr1A 98.953 191 2 0 1235 1425 295458267 295458457 7.030000e-90 342.0
19 TraesCS1D01G161000 chr1A 82.984 382 42 13 130 490 295457485 295457864 2.540000e-84 324.0
20 TraesCS1D01G161000 chr1B 97.249 3090 68 10 811 3889 327478134 327481217 0.000000e+00 5219.0
21 TraesCS1D01G161000 chr1B 95.679 2615 83 12 3888 6495 327481292 327483883 0.000000e+00 4176.0
22 TraesCS1D01G161000 chr1B 92.542 295 16 5 7025 7313 327486154 327486448 1.130000e-112 418.0
23 TraesCS1D01G161000 chr1B 83.988 331 24 8 6708 7012 327484255 327484582 2.580000e-74 291.0
24 TraesCS1D01G161000 chr1B 88.542 192 14 1 6527 6710 327483984 327484175 7.380000e-55 226.0
25 TraesCS1D01G161000 chr1B 78.395 162 31 4 159 318 400585914 400585755 1.300000e-17 102.0
26 TraesCS1D01G161000 chr2D 98.876 178 2 0 529 706 572373105 572372928 1.180000e-82 318.0
27 TraesCS1D01G161000 chr2D 97.714 175 4 0 532 706 102296520 102296346 1.190000e-77 302.0
28 TraesCS1D01G161000 chr2D 84.190 253 30 5 6603 6846 38626957 38627208 3.410000e-58 237.0
29 TraesCS1D01G161000 chr7D 98.324 179 3 0 528 706 586745239 586745417 1.530000e-81 315.0
30 TraesCS1D01G161000 chr7D 97.191 178 5 0 527 704 155375514 155375691 1.190000e-77 302.0
31 TraesCS1D01G161000 chr7D 82.000 250 34 8 6605 6847 16394229 16394474 1.240000e-47 202.0
32 TraesCS1D01G161000 chr7D 97.938 97 2 0 704 800 397988913 397989009 1.260000e-37 169.0
33 TraesCS1D01G161000 chr4D 98.286 175 3 0 532 706 484620636 484620462 2.560000e-79 307.0
34 TraesCS1D01G161000 chr4D 97.938 97 2 0 704 800 484620336 484620240 1.260000e-37 169.0
35 TraesCS1D01G161000 chr6D 97.740 177 4 0 530 706 30010308 30010132 9.220000e-79 305.0
36 TraesCS1D01G161000 chr6D 80.000 190 37 1 157 346 413071369 413071557 9.890000e-29 139.0
37 TraesCS1D01G161000 chr5D 97.191 178 5 0 529 706 255469896 255469719 1.190000e-77 302.0
38 TraesCS1D01G161000 chr5D 81.579 266 33 10 6603 6856 417734619 417734358 9.620000e-49 206.0
39 TraesCS1D01G161000 chr5D 97.938 97 2 0 704 800 255469593 255469497 1.260000e-37 169.0
40 TraesCS1D01G161000 chr5D 97.938 97 2 0 704 800 495022103 495022199 1.260000e-37 169.0
41 TraesCS1D01G161000 chr5D 80.000 190 34 4 160 347 442675291 442675104 3.560000e-28 137.0
42 TraesCS1D01G161000 chr5D 89.362 47 5 0 6603 6649 285837282 285837236 7.920000e-05 60.2
43 TraesCS1D01G161000 chr3B 83.333 252 39 3 6603 6854 354001487 354001735 5.710000e-56 230.0
44 TraesCS1D01G161000 chr3B 82.955 264 31 7 6603 6856 394097762 394098021 7.380000e-55 226.0
45 TraesCS1D01G161000 chr3A 82.197 264 33 7 6603 6856 396620107 396620366 1.600000e-51 215.0
46 TraesCS1D01G161000 chr3A 81.679 262 36 5 6603 6854 91026496 91026755 2.670000e-49 207.0
47 TraesCS1D01G161000 chr3A 86.010 193 21 5 6649 6839 9518661 9518849 1.240000e-47 202.0
48 TraesCS1D01G161000 chr3A 80.645 186 33 2 162 346 382257505 382257322 2.750000e-29 141.0
49 TraesCS1D01G161000 chr3A 83.036 112 19 0 170 281 111822859 111822748 1.300000e-17 102.0
50 TraesCS1D01G161000 chr5B 85.854 205 24 5 6653 6855 438482553 438482352 5.750000e-51 213.0
51 TraesCS1D01G161000 chr5B 79.787 188 35 3 161 347 493924537 493924352 4.600000e-27 134.0
52 TraesCS1D01G161000 chr5B 78.571 168 20 12 159 324 551228900 551229053 6.040000e-16 97.1
53 TraesCS1D01G161000 chr5B 96.875 32 1 0 195 226 147474167 147474198 4.000000e-03 54.7
54 TraesCS1D01G161000 chr4A 82.213 253 40 5 6605 6853 718416404 718416153 5.750000e-51 213.0
55 TraesCS1D01G161000 chr4A 81.423 253 32 8 6605 6846 437487876 437488124 7.490000e-45 193.0
56 TraesCS1D01G161000 chr4A 81.197 117 15 6 173 287 147366777 147366888 3.630000e-13 87.9
57 TraesCS1D01G161000 chr3D 99.000 100 1 0 704 803 13436625 13436526 5.830000e-41 180.0
58 TraesCS1D01G161000 chr3D 97.938 97 2 0 704 800 380952312 380952216 1.260000e-37 169.0
59 TraesCS1D01G161000 chr3D 96.970 99 3 0 702 800 459090499 459090401 4.540000e-37 167.0
60 TraesCS1D01G161000 chr3D 96.970 99 3 0 702 800 504042945 504043043 4.540000e-37 167.0
61 TraesCS1D01G161000 chr4B 81.183 186 32 3 161 345 553611335 553611152 5.910000e-31 147.0
62 TraesCS1D01G161000 chr7B 81.481 162 27 3 185 344 129965695 129965855 5.950000e-26 130.0
63 TraesCS1D01G161000 chr6A 89.583 48 4 1 6603 6649 581751038 581751085 7.920000e-05 60.2


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 TraesCS1D01G161000 chr1D 227859143 227866455 7312 False 13505.000000 13505 100.0000 1 7313 1 chr1D.!!$F1 7312
1 TraesCS1D01G161000 chr1D 208274850 208282080 7230 True 2133.600000 6580 94.3276 1 6837 5 chr1D.!!$R3 6836
2 TraesCS1D01G161000 chr1D 208239878 208241628 1750 True 337.000000 520 89.9880 6835 7313 2 chr1D.!!$R2 478
3 TraesCS1D01G161000 chr1A 295457485 295465205 7720 False 1772.833333 5779 92.4195 130 7313 6 chr1A.!!$F1 7183
4 TraesCS1D01G161000 chr1A 311806847 311808690 1843 True 602.500000 628 85.1665 1115 2683 2 chr1A.!!$R1 1568
5 TraesCS1D01G161000 chr1B 327478134 327486448 8314 False 2066.000000 5219 91.6000 811 7313 5 chr1B.!!$F1 6502

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
805 842 0.033228 TTGTCAAATTTGCCAGCCCG 59.967 50.000 13.54 0.00 0.00 6.13 F
807 844 0.033366 GTCAAATTTGCCAGCCCGTT 59.967 50.000 13.54 0.00 0.00 4.44 F
1973 3038 0.034337 GAACCTGGTAACTCGTGCCA 59.966 55.000 0.00 0.00 37.61 4.92 F
3561 4681 1.747709 CAGGCCTTGAAGACCATCTG 58.252 55.000 0.00 0.00 0.00 2.90 F
3957 5160 0.252197 GTTACTGCCCCGATGGAGTT 59.748 55.000 3.88 0.00 35.39 3.01 F
5112 6649 1.340114 ACTTAAAGTGGCAGGCTAGGC 60.340 52.381 8.55 8.55 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1675 2393 1.221840 CGCCACCTTGGAGCATAGT 59.778 57.895 0.0 0.0 40.96 2.12 R
2016 3094 3.002791 CGGGGAAATCGATCATACATGG 58.997 50.000 0.0 0.0 0.00 3.66 R
3585 4705 1.707427 AGCCTCACAACAGGAAAGGAT 59.293 47.619 0.0 0.0 35.20 3.24 R
4858 6394 0.672342 GGACATCTGCCATCCATTGC 59.328 55.000 0.0 0.0 32.35 3.56 R
5729 7277 1.003839 GTGCTGATCCGGTGGAACA 60.004 57.895 0.0 0.0 39.98 3.18 R
6825 9102 2.016318 TCCCTTTCATAATGCAGTGCG 58.984 47.619 11.2 0.0 0.00 5.34 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
51 60 2.886523 AGCCGGGTTACACCTTTTTAAC 59.113 45.455 0.00 0.00 38.64 2.01
59 68 7.534918 CGGGTTACACCTTTTTAACGAATAAAG 59.465 37.037 0.00 0.00 38.64 1.85
146 155 2.386661 ATAACTTGACCGACCAGCTG 57.613 50.000 6.78 6.78 0.00 4.24
218 231 1.194781 TCCTCAGCTCACCAGGGTTC 61.195 60.000 0.00 0.00 0.00 3.62
245 258 2.400399 TCGACTTGACATCGGTGTTTC 58.600 47.619 1.13 0.00 39.09 2.78
296 310 1.626654 CGATGTGCGTTCAGTGGGAC 61.627 60.000 0.00 0.00 34.64 4.46
364 389 2.501723 TCTTCCAAGTGCTCATAGGGTC 59.498 50.000 0.00 0.00 0.00 4.46
529 566 2.162754 ATCGCGTTAAGCCCGTTCG 61.163 57.895 5.77 0.00 44.76 3.95
540 577 3.101019 CCCGTTCGGCAAATTTGAC 57.899 52.632 22.31 18.50 0.00 3.18
541 578 0.312416 CCCGTTCGGCAAATTTGACA 59.688 50.000 23.49 8.31 35.35 3.58
542 579 1.269309 CCCGTTCGGCAAATTTGACAA 60.269 47.619 23.49 13.56 35.35 3.18
543 580 2.464865 CCGTTCGGCAAATTTGACAAA 58.535 42.857 23.49 9.26 35.35 2.83
544 581 3.056304 CCGTTCGGCAAATTTGACAAAT 58.944 40.909 23.49 7.62 35.35 2.32
545 582 3.492756 CCGTTCGGCAAATTTGACAAATT 59.507 39.130 23.49 18.41 42.62 1.82
547 584 5.175856 CCGTTCGGCAAATTTGACAAATTTA 59.824 36.000 29.34 16.77 46.34 1.40
548 585 6.292381 CCGTTCGGCAAATTTGACAAATTTAA 60.292 34.615 29.34 20.44 46.34 1.52
549 586 6.568238 CGTTCGGCAAATTTGACAAATTTAAC 59.432 34.615 29.34 26.39 46.34 2.01
550 587 6.532365 TCGGCAAATTTGACAAATTTAACC 57.468 33.333 29.34 28.65 46.34 2.85
551 588 6.284459 TCGGCAAATTTGACAAATTTAACCT 58.716 32.000 30.99 16.64 46.34 3.50
552 589 7.434492 TCGGCAAATTTGACAAATTTAACCTA 58.566 30.769 30.99 25.08 46.34 3.08
553 590 8.091449 TCGGCAAATTTGACAAATTTAACCTAT 58.909 29.630 30.99 15.65 46.34 2.57
554 591 9.360093 CGGCAAATTTGACAAATTTAACCTATA 57.640 29.630 30.99 4.05 46.34 1.31
571 608 9.878667 TTAACCTATAGACGAAATCAAATCACA 57.121 29.630 0.00 0.00 0.00 3.58
572 609 8.425577 AACCTATAGACGAAATCAAATCACAG 57.574 34.615 0.00 0.00 0.00 3.66
573 610 7.782049 ACCTATAGACGAAATCAAATCACAGA 58.218 34.615 0.00 0.00 0.00 3.41
574 611 8.258007 ACCTATAGACGAAATCAAATCACAGAA 58.742 33.333 0.00 0.00 0.00 3.02
575 612 9.265901 CCTATAGACGAAATCAAATCACAGAAT 57.734 33.333 0.00 0.00 0.00 2.40
577 614 8.722480 ATAGACGAAATCAAATCACAGAATGA 57.278 30.769 0.00 0.00 43.13 2.57
578 615 7.439157 AGACGAAATCAAATCACAGAATGAA 57.561 32.000 0.00 0.00 41.93 2.57
579 616 7.301054 AGACGAAATCAAATCACAGAATGAAC 58.699 34.615 0.00 0.00 41.93 3.18
580 617 7.173907 AGACGAAATCAAATCACAGAATGAACT 59.826 33.333 0.00 0.00 41.93 3.01
581 618 8.322906 ACGAAATCAAATCACAGAATGAACTA 57.677 30.769 0.00 0.00 41.93 2.24
582 619 8.950210 ACGAAATCAAATCACAGAATGAACTAT 58.050 29.630 0.00 0.00 41.93 2.12
583 620 9.430838 CGAAATCAAATCACAGAATGAACTATC 57.569 33.333 0.00 0.00 41.93 2.08
584 621 9.727627 GAAATCAAATCACAGAATGAACTATCC 57.272 33.333 0.00 0.00 41.93 2.59
585 622 6.908870 TCAAATCACAGAATGAACTATCCG 57.091 37.500 0.00 0.00 41.93 4.18
586 623 6.406370 TCAAATCACAGAATGAACTATCCGT 58.594 36.000 0.00 0.00 41.93 4.69
587 624 6.313658 TCAAATCACAGAATGAACTATCCGTG 59.686 38.462 0.00 0.00 41.93 4.94
588 625 5.598416 ATCACAGAATGAACTATCCGTGA 57.402 39.130 0.00 0.00 41.93 4.35
589 626 5.400066 TCACAGAATGAACTATCCGTGAA 57.600 39.130 0.00 0.00 39.69 3.18
590 627 5.789521 TCACAGAATGAACTATCCGTGAAA 58.210 37.500 0.00 0.00 39.69 2.69
591 628 5.637810 TCACAGAATGAACTATCCGTGAAAC 59.362 40.000 0.00 0.00 39.69 2.78
592 629 5.639506 CACAGAATGAACTATCCGTGAAACT 59.360 40.000 0.00 0.00 39.69 2.66
593 630 6.811665 CACAGAATGAACTATCCGTGAAACTA 59.188 38.462 0.00 0.00 39.69 2.24
594 631 7.492669 CACAGAATGAACTATCCGTGAAACTAT 59.507 37.037 0.00 0.00 39.69 2.12
595 632 8.041323 ACAGAATGAACTATCCGTGAAACTATT 58.959 33.333 0.00 0.00 39.69 1.73
596 633 8.883731 CAGAATGAACTATCCGTGAAACTATTT 58.116 33.333 0.00 0.00 39.69 1.40
597 634 9.099454 AGAATGAACTATCCGTGAAACTATTTC 57.901 33.333 0.00 0.00 40.08 2.17
598 635 8.786826 AATGAACTATCCGTGAAACTATTTCA 57.213 30.769 0.00 0.00 46.68 2.69
605 642 1.803334 TGAAACTATTTCACGCGCCT 58.197 45.000 5.73 0.00 44.21 5.52
606 643 1.463056 TGAAACTATTTCACGCGCCTG 59.537 47.619 5.73 0.00 44.21 4.85
607 644 1.730064 GAAACTATTTCACGCGCCTGA 59.270 47.619 5.73 4.90 39.45 3.86
608 645 1.076332 AACTATTTCACGCGCCTGAC 58.924 50.000 5.73 0.00 0.00 3.51
609 646 0.739813 ACTATTTCACGCGCCTGACC 60.740 55.000 5.73 0.00 0.00 4.02
610 647 0.460284 CTATTTCACGCGCCTGACCT 60.460 55.000 5.73 2.38 0.00 3.85
611 648 0.036765 TATTTCACGCGCCTGACCTT 60.037 50.000 5.73 0.22 0.00 3.50
612 649 0.889186 ATTTCACGCGCCTGACCTTT 60.889 50.000 5.73 0.00 0.00 3.11
613 650 1.098712 TTTCACGCGCCTGACCTTTT 61.099 50.000 5.73 0.00 0.00 2.27
614 651 1.098712 TTCACGCGCCTGACCTTTTT 61.099 50.000 5.73 0.00 0.00 1.94
615 652 1.370414 CACGCGCCTGACCTTTTTG 60.370 57.895 5.73 0.00 0.00 2.44
616 653 1.822186 ACGCGCCTGACCTTTTTGT 60.822 52.632 5.73 0.00 0.00 2.83
617 654 1.370414 CGCGCCTGACCTTTTTGTG 60.370 57.895 0.00 0.00 0.00 3.33
618 655 1.661509 GCGCCTGACCTTTTTGTGC 60.662 57.895 0.00 0.00 0.00 4.57
619 656 1.370414 CGCCTGACCTTTTTGTGCG 60.370 57.895 0.00 0.00 0.00 5.34
620 657 1.781025 CGCCTGACCTTTTTGTGCGA 61.781 55.000 0.00 0.00 42.84 5.10
621 658 0.317854 GCCTGACCTTTTTGTGCGAC 60.318 55.000 0.00 0.00 0.00 5.19
622 659 0.041312 CCTGACCTTTTTGTGCGACG 60.041 55.000 0.00 0.00 0.00 5.12
623 660 0.657368 CTGACCTTTTTGTGCGACGC 60.657 55.000 14.19 14.19 0.00 5.19
624 661 1.370051 GACCTTTTTGTGCGACGCC 60.370 57.895 18.69 9.37 0.00 5.68
625 662 2.050442 CCTTTTTGTGCGACGCCC 60.050 61.111 18.69 6.32 0.00 6.13
626 663 2.426752 CTTTTTGTGCGACGCCCG 60.427 61.111 18.69 0.00 42.21 6.13
627 664 2.887889 CTTTTTGTGCGACGCCCGA 61.888 57.895 18.69 1.87 41.76 5.14
628 665 3.170810 TTTTTGTGCGACGCCCGAC 62.171 57.895 18.69 9.69 41.76 4.79
629 666 4.893601 TTTGTGCGACGCCCGACA 62.894 61.111 18.69 12.47 41.76 4.35
643 680 3.712881 GACACGAAGGCGCCACAC 61.713 66.667 31.54 17.81 42.48 3.82
644 681 4.235762 ACACGAAGGCGCCACACT 62.236 61.111 31.54 9.96 42.48 3.55
645 682 2.048597 CACGAAGGCGCCACACTA 60.049 61.111 31.54 0.00 42.48 2.74
646 683 2.048503 ACGAAGGCGCCACACTAC 60.049 61.111 31.54 11.50 42.48 2.73
647 684 2.048597 CGAAGGCGCCACACTACA 60.049 61.111 31.54 0.00 0.00 2.74
648 685 1.447838 CGAAGGCGCCACACTACAT 60.448 57.895 31.54 0.76 0.00 2.29
649 686 1.019278 CGAAGGCGCCACACTACATT 61.019 55.000 31.54 11.63 0.00 2.71
650 687 0.447801 GAAGGCGCCACACTACATTG 59.552 55.000 31.54 0.00 0.00 2.82
651 688 0.250727 AAGGCGCCACACTACATTGT 60.251 50.000 31.54 0.00 0.00 2.71
652 689 0.955428 AGGCGCCACACTACATTGTG 60.955 55.000 31.54 0.00 45.57 3.33
653 690 1.154225 GCGCCACACTACATTGTGC 60.154 57.895 0.00 0.00 44.79 4.57
654 691 1.851021 GCGCCACACTACATTGTGCA 61.851 55.000 0.00 0.00 44.79 4.57
655 692 0.590682 CGCCACACTACATTGTGCAA 59.409 50.000 0.00 0.00 44.79 4.08
656 693 1.662876 CGCCACACTACATTGTGCAAC 60.663 52.381 0.00 0.00 44.79 4.17
657 694 1.662876 GCCACACTACATTGTGCAACG 60.663 52.381 0.00 0.00 44.79 4.10
658 695 1.662876 CCACACTACATTGTGCAACGC 60.663 52.381 0.00 0.00 44.79 4.84
659 696 0.591170 ACACTACATTGTGCAACGCC 59.409 50.000 0.00 0.00 42.39 5.68
660 697 0.874390 CACTACATTGTGCAACGCCT 59.126 50.000 0.00 0.00 42.39 5.52
661 698 1.135972 CACTACATTGTGCAACGCCTC 60.136 52.381 0.00 0.00 42.39 4.70
662 699 1.155889 CTACATTGTGCAACGCCTCA 58.844 50.000 0.00 0.00 42.39 3.86
663 700 0.871722 TACATTGTGCAACGCCTCAC 59.128 50.000 0.00 0.00 42.39 3.51
664 701 1.100463 ACATTGTGCAACGCCTCACA 61.100 50.000 0.00 0.86 42.39 3.58
665 702 0.386352 CATTGTGCAACGCCTCACAG 60.386 55.000 0.00 0.00 43.15 3.66
666 703 0.534877 ATTGTGCAACGCCTCACAGA 60.535 50.000 0.00 0.00 43.15 3.41
667 704 0.534877 TTGTGCAACGCCTCACAGAT 60.535 50.000 0.00 0.00 43.15 2.90
668 705 0.320050 TGTGCAACGCCTCACAGATA 59.680 50.000 0.00 0.00 42.39 1.98
669 706 1.002366 GTGCAACGCCTCACAGATAG 58.998 55.000 0.00 0.00 33.63 2.08
670 707 0.108186 TGCAACGCCTCACAGATAGG 60.108 55.000 0.00 0.00 37.17 2.57
676 713 3.875838 CCTCACAGATAGGCGCTAC 57.124 57.895 7.64 0.00 0.00 3.58
677 714 1.032794 CCTCACAGATAGGCGCTACA 58.967 55.000 7.64 0.00 0.00 2.74
678 715 1.269309 CCTCACAGATAGGCGCTACAC 60.269 57.143 7.64 0.00 0.00 2.90
680 717 0.595053 CACAGATAGGCGCTACACGG 60.595 60.000 7.64 0.58 43.93 4.94
704 741 2.261361 TCGCACCCGTGTGATCAG 59.739 61.111 0.90 0.00 45.76 2.90
705 742 2.261361 CGCACCCGTGTGATCAGA 59.739 61.111 0.90 0.00 45.76 3.27
706 743 1.807165 CGCACCCGTGTGATCAGAG 60.807 63.158 0.90 0.00 45.76 3.35
707 744 2.103042 GCACCCGTGTGATCAGAGC 61.103 63.158 0.90 0.00 45.76 4.09
708 745 1.593787 CACCCGTGTGATCAGAGCT 59.406 57.895 0.00 0.00 45.76 4.09
709 746 0.817654 CACCCGTGTGATCAGAGCTA 59.182 55.000 0.00 0.00 45.76 3.32
710 747 1.107114 ACCCGTGTGATCAGAGCTAG 58.893 55.000 0.00 0.00 0.00 3.42
711 748 0.387202 CCCGTGTGATCAGAGCTAGG 59.613 60.000 0.00 0.00 0.00 3.02
712 749 0.249238 CCGTGTGATCAGAGCTAGGC 60.249 60.000 0.00 0.00 0.00 3.93
713 750 0.593518 CGTGTGATCAGAGCTAGGCG 60.594 60.000 0.00 0.00 0.00 5.52
714 751 0.873743 GTGTGATCAGAGCTAGGCGC 60.874 60.000 0.00 0.00 39.57 6.53
715 752 1.300542 GTGATCAGAGCTAGGCGCC 60.301 63.158 21.89 21.89 40.39 6.53
716 753 1.758122 TGATCAGAGCTAGGCGCCA 60.758 57.895 31.54 14.00 40.39 5.69
717 754 1.300542 GATCAGAGCTAGGCGCCAC 60.301 63.158 31.54 17.93 40.39 5.01
718 755 3.144120 ATCAGAGCTAGGCGCCACG 62.144 63.158 31.54 19.97 40.39 4.94
719 756 4.880537 CAGAGCTAGGCGCCACGG 62.881 72.222 31.54 18.60 40.39 4.94
724 761 4.514577 CTAGGCGCCACGGGTCAG 62.515 72.222 31.54 9.46 0.00 3.51
735 772 2.746277 GGGTCAGCCGCGTGAAAT 60.746 61.111 4.92 0.00 34.97 2.17
736 773 1.448893 GGGTCAGCCGCGTGAAATA 60.449 57.895 4.92 0.00 34.97 1.40
737 774 1.429148 GGGTCAGCCGCGTGAAATAG 61.429 60.000 4.92 0.00 34.97 1.73
738 775 0.739813 GGTCAGCCGCGTGAAATAGT 60.740 55.000 4.92 0.00 0.00 2.12
739 776 1.076332 GTCAGCCGCGTGAAATAGTT 58.924 50.000 4.92 0.00 0.00 2.24
740 777 1.463444 GTCAGCCGCGTGAAATAGTTT 59.537 47.619 4.92 0.00 0.00 2.66
741 778 1.730064 TCAGCCGCGTGAAATAGTTTC 59.270 47.619 4.92 0.00 40.08 2.78
742 779 1.463056 CAGCCGCGTGAAATAGTTTCA 59.537 47.619 4.92 1.24 46.68 2.69
753 790 5.849510 TGAAATAGTTTCACGGAGAGTTCA 58.150 37.500 1.24 0.00 44.21 3.18
754 791 6.464222 TGAAATAGTTTCACGGAGAGTTCAT 58.536 36.000 1.24 0.00 44.21 2.57
755 792 6.934645 TGAAATAGTTTCACGGAGAGTTCATT 59.065 34.615 1.24 0.00 44.21 2.57
756 793 6.969828 AATAGTTTCACGGAGAGTTCATTC 57.030 37.500 0.00 0.00 0.00 2.67
757 794 4.608948 AGTTTCACGGAGAGTTCATTCT 57.391 40.909 0.00 0.00 0.00 2.40
758 795 4.310769 AGTTTCACGGAGAGTTCATTCTG 58.689 43.478 0.00 0.00 0.00 3.02
759 796 4.058817 GTTTCACGGAGAGTTCATTCTGT 58.941 43.478 0.00 0.00 33.29 3.41
760 797 3.303881 TCACGGAGAGTTCATTCTGTG 57.696 47.619 7.03 7.03 46.96 3.66
763 800 4.543590 ACGGAGAGTTCATTCTGTGATT 57.456 40.909 0.00 0.00 36.54 2.57
764 801 4.899502 ACGGAGAGTTCATTCTGTGATTT 58.100 39.130 0.00 0.00 36.54 2.17
765 802 4.692625 ACGGAGAGTTCATTCTGTGATTTG 59.307 41.667 0.00 0.00 36.54 2.32
766 803 4.931601 CGGAGAGTTCATTCTGTGATTTGA 59.068 41.667 0.00 0.00 36.54 2.69
767 804 5.583854 CGGAGAGTTCATTCTGTGATTTGAT 59.416 40.000 0.00 0.00 36.54 2.57
768 805 6.093219 CGGAGAGTTCATTCTGTGATTTGATT 59.907 38.462 0.00 0.00 36.54 2.57
769 806 7.361542 CGGAGAGTTCATTCTGTGATTTGATTT 60.362 37.037 0.00 0.00 36.54 2.17
770 807 8.302438 GGAGAGTTCATTCTGTGATTTGATTTT 58.698 33.333 0.00 0.00 36.54 1.82
771 808 9.125906 GAGAGTTCATTCTGTGATTTGATTTTG 57.874 33.333 0.00 0.00 36.54 2.44
772 809 8.636213 AGAGTTCATTCTGTGATTTGATTTTGT 58.364 29.630 0.00 0.00 36.54 2.83
773 810 9.252962 GAGTTCATTCTGTGATTTGATTTTGTT 57.747 29.630 0.00 0.00 36.54 2.83
774 811 9.603921 AGTTCATTCTGTGATTTGATTTTGTTT 57.396 25.926 0.00 0.00 36.54 2.83
803 840 4.834357 AAATTTGTCAAATTTGCCAGCC 57.166 36.364 27.61 0.00 46.30 4.85
804 841 2.252976 TTTGTCAAATTTGCCAGCCC 57.747 45.000 13.54 0.00 0.00 5.19
805 842 0.033228 TTGTCAAATTTGCCAGCCCG 59.967 50.000 13.54 0.00 0.00 6.13
806 843 1.112315 TGTCAAATTTGCCAGCCCGT 61.112 50.000 13.54 0.00 0.00 5.28
807 844 0.033366 GTCAAATTTGCCAGCCCGTT 59.967 50.000 13.54 0.00 0.00 4.44
808 845 0.316841 TCAAATTTGCCAGCCCGTTC 59.683 50.000 13.54 0.00 0.00 3.95
809 846 0.670239 CAAATTTGCCAGCCCGTTCC 60.670 55.000 5.01 0.00 0.00 3.62
1961 3026 5.468540 TCCTGATATTATGACGAACCTGG 57.531 43.478 0.00 0.00 0.00 4.45
1973 3038 0.034337 GAACCTGGTAACTCGTGCCA 59.966 55.000 0.00 0.00 37.61 4.92
1991 3069 5.512788 CGTGCCATGATTAAGTCATTTGTTC 59.487 40.000 0.00 0.00 45.25 3.18
2016 3094 8.128582 TCTACAACACATTTTGATGAAGACAAC 58.871 33.333 0.00 0.00 32.37 3.32
2058 3136 5.105756 CCCGCTTTCCTTTGTCTCATATTTT 60.106 40.000 0.00 0.00 0.00 1.82
2059 3137 5.801947 CCGCTTTCCTTTGTCTCATATTTTG 59.198 40.000 0.00 0.00 0.00 2.44
2060 3138 5.287035 CGCTTTCCTTTGTCTCATATTTTGC 59.713 40.000 0.00 0.00 0.00 3.68
2061 3139 6.158598 GCTTTCCTTTGTCTCATATTTTGCA 58.841 36.000 0.00 0.00 0.00 4.08
2062 3140 6.309737 GCTTTCCTTTGTCTCATATTTTGCAG 59.690 38.462 0.00 0.00 0.00 4.41
2063 3141 6.899393 TTCCTTTGTCTCATATTTTGCAGT 57.101 33.333 0.00 0.00 0.00 4.40
2064 3142 7.994425 TTCCTTTGTCTCATATTTTGCAGTA 57.006 32.000 0.00 0.00 0.00 2.74
2065 3143 7.615582 TCCTTTGTCTCATATTTTGCAGTAG 57.384 36.000 0.00 0.00 0.00 2.57
2066 3144 7.394016 TCCTTTGTCTCATATTTTGCAGTAGA 58.606 34.615 0.00 0.00 0.00 2.59
2067 3145 7.550551 TCCTTTGTCTCATATTTTGCAGTAGAG 59.449 37.037 0.00 0.00 0.00 2.43
2166 3279 6.947733 TCAACTTCATGATACCACATTCCTTT 59.052 34.615 0.00 0.00 0.00 3.11
2733 3850 5.046591 GGTAGATGATATCATTCGGACCCAA 60.047 44.000 19.11 0.00 36.57 4.12
3266 4383 5.067674 GCAATGAACTGCACCCTATTATTCA 59.932 40.000 0.00 0.00 42.17 2.57
3278 4398 8.531982 GCACCCTATTATTCATCACTATCAGTA 58.468 37.037 0.00 0.00 0.00 2.74
3561 4681 1.747709 CAGGCCTTGAAGACCATCTG 58.252 55.000 0.00 0.00 0.00 2.90
3585 4705 7.287061 TGAAGGAAATGAAGAGAAAGGTACAA 58.713 34.615 0.00 0.00 0.00 2.41
3693 4814 5.068460 TGGTGCTGTATTTTGTTTGCTAACT 59.932 36.000 12.20 0.00 35.24 2.24
3696 4817 7.136119 GTGCTGTATTTTGTTTGCTAACTGTA 58.864 34.615 12.20 0.00 35.24 2.74
3745 4866 2.618816 GGTGCCTGATCTTGGTGATGAA 60.619 50.000 0.00 0.00 35.14 2.57
3823 4944 2.083774 GAATCCGTGTGCAATCCTTCA 58.916 47.619 0.00 0.00 0.00 3.02
3824 4945 2.198827 ATCCGTGTGCAATCCTTCAA 57.801 45.000 0.00 0.00 0.00 2.69
3825 4946 1.522668 TCCGTGTGCAATCCTTCAAG 58.477 50.000 0.00 0.00 0.00 3.02
3826 4947 1.202758 TCCGTGTGCAATCCTTCAAGT 60.203 47.619 0.00 0.00 0.00 3.16
3901 5104 6.095440 ACATTTGCACCTAGTATTTTAGGCAG 59.905 38.462 0.00 0.00 43.36 4.85
3918 5121 1.267087 GCAGTTTAAGAAGCTAGCGCG 60.267 52.381 9.55 0.00 42.32 6.86
3920 5123 2.028165 CAGTTTAAGAAGCTAGCGCGTC 59.972 50.000 9.55 8.47 43.71 5.19
3957 5160 0.252197 GTTACTGCCCCGATGGAGTT 59.748 55.000 3.88 0.00 35.39 3.01
3997 5201 5.577945 CGCAAGCAATTTTCCAGTTATCATT 59.422 36.000 0.00 0.00 0.00 2.57
4043 5247 6.298361 TGTATGAGATGTTATGTTCATGGGG 58.702 40.000 0.00 0.00 32.83 4.96
4091 5295 7.870445 GTGATAACCTTTAATGAAAACCTTGCA 59.130 33.333 0.00 0.00 0.00 4.08
4235 5439 7.599998 GTCCTTGCATAACTGAATTTGATGTTT 59.400 33.333 0.00 0.00 0.00 2.83
4240 5444 7.095565 TGCATAACTGAATTTGATGTTTGCAAG 60.096 33.333 0.00 0.00 35.63 4.01
4302 5506 9.990360 TGTCTACAACTCTACATTGATTTTGTA 57.010 29.630 0.00 0.00 0.00 2.41
4650 6186 6.864685 AGCATTAACGATTTGCATCCAATATG 59.135 34.615 0.00 0.00 38.84 1.78
4658 6194 5.422666 TTTGCATCCAATATGTAGAAGCG 57.577 39.130 0.00 0.00 0.00 4.68
4869 6405 3.814005 ATTTCTTCAGCAATGGATGGC 57.186 42.857 0.00 0.00 0.00 4.40
4874 6410 1.687563 TCAGCAATGGATGGCAGATG 58.312 50.000 0.00 0.00 0.00 2.90
4924 6460 7.066163 TGGCTTGATACAATCTTGAATGTACTG 59.934 37.037 1.21 0.00 35.05 2.74
4956 6492 4.762765 ACGGTTGTACCAGCAAATGATTTA 59.237 37.500 0.00 0.00 38.47 1.40
4961 6497 6.509418 TGTACCAGCAAATGATTTAGGAAC 57.491 37.500 9.33 0.00 0.00 3.62
5002 6538 7.639113 TTCCTTGTACAATTGGATTGGATAC 57.361 36.000 15.26 2.02 44.42 2.24
5020 6556 6.518493 TGGATACCTATTGTTTCGGTCATAC 58.482 40.000 0.00 0.00 32.36 2.39
5089 6626 5.118729 TGTTCTCCCTTTGACCACTTTAA 57.881 39.130 0.00 0.00 0.00 1.52
5112 6649 1.340114 ACTTAAAGTGGCAGGCTAGGC 60.340 52.381 8.55 8.55 0.00 3.93
5124 6661 2.754552 CAGGCTAGGCATTTGCTTGTAA 59.245 45.455 19.70 0.00 41.70 2.41
5126 6663 2.755103 GGCTAGGCATTTGCTTGTAAGT 59.245 45.455 12.16 0.00 41.70 2.24
5129 6666 4.636206 GCTAGGCATTTGCTTGTAAGTACT 59.364 41.667 2.12 0.00 41.70 2.73
5258 6795 3.430218 GCTTCGAAATGATATCCCAGTCG 59.570 47.826 0.00 4.77 0.00 4.18
5288 6825 8.560355 TCTTTATGTGCAGTATTTATGTGTGT 57.440 30.769 0.00 0.00 0.00 3.72
5290 6827 9.277565 CTTTATGTGCAGTATTTATGTGTGTTC 57.722 33.333 0.00 0.00 0.00 3.18
5295 6832 7.647318 TGTGCAGTATTTATGTGTGTTCTTTTG 59.353 33.333 0.00 0.00 0.00 2.44
5499 7037 4.268405 CAGGTTTGTGTGACTGCATTTTTC 59.732 41.667 0.00 0.00 0.00 2.29
5729 7277 2.361865 ACGCCGAGGAGCTCTTCT 60.362 61.111 22.00 8.21 0.00 2.85
6233 8158 0.527565 TACTGGTTACGAGTTCCGGC 59.472 55.000 5.19 0.00 43.93 6.13
6393 8320 2.986479 CCGCTTGGATGCTTTGTTTAAC 59.014 45.455 0.00 0.00 33.02 2.01
6506 8433 4.626042 AGAGAACCAATGCATATCTCGTC 58.374 43.478 18.32 6.87 41.04 4.20
6518 8453 1.933021 ATCTCGTCAGGTACAACCCA 58.067 50.000 0.00 0.00 39.75 4.51
6558 8742 2.290464 TCATGCATGCATTGATCGACA 58.710 42.857 30.32 6.64 33.90 4.35
6613 8797 0.115745 TGTACTCCCTCCCTCCGTTT 59.884 55.000 0.00 0.00 0.00 3.60
6678 8873 9.515226 TTTGCACCAAGTTTATAGAGAAACTAT 57.485 29.630 2.90 0.00 46.52 2.12
7027 12155 9.950496 AAACTACTTCATCAGTTCATCTACAAT 57.050 29.630 0.00 0.00 36.88 2.71
7098 12227 1.895798 GCCTCATCCGTCCATCTATGA 59.104 52.381 0.00 0.00 0.00 2.15
7236 12369 6.593268 TTCCAAATGAGATTCAATTGCAGA 57.407 33.333 0.00 0.00 36.28 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.424061 AACCCGGCTAATTAACGAAAAC 57.576 40.909 0.00 0.00 0.00 2.43
51 60 4.770795 ACAACCATCTCCTCCTTTATTCG 58.229 43.478 0.00 0.00 0.00 3.34
146 155 2.174319 GGTTCGCCGCAATCTCTCC 61.174 63.158 0.00 0.00 0.00 3.71
344 358 2.420687 GGACCCTATGAGCACTTGGAAG 60.421 54.545 0.00 0.00 0.00 3.46
364 389 0.034896 ACAGTACAAAGCACTCCCGG 59.965 55.000 0.00 0.00 0.00 5.73
434 462 5.930569 GCTCGGAGTAGTAGGAAAAGAAAAA 59.069 40.000 6.90 0.00 0.00 1.94
545 582 9.878667 TGTGATTTGATTTCGTCTATAGGTTAA 57.121 29.630 0.00 0.00 0.00 2.01
546 583 9.529325 CTGTGATTTGATTTCGTCTATAGGTTA 57.471 33.333 0.00 0.00 0.00 2.85
547 584 8.258007 TCTGTGATTTGATTTCGTCTATAGGTT 58.742 33.333 0.00 0.00 0.00 3.50
548 585 7.782049 TCTGTGATTTGATTTCGTCTATAGGT 58.218 34.615 0.00 0.00 0.00 3.08
549 586 8.648557 TTCTGTGATTTGATTTCGTCTATAGG 57.351 34.615 0.00 0.00 0.00 2.57
551 588 9.816354 TCATTCTGTGATTTGATTTCGTCTATA 57.184 29.630 0.00 0.00 0.00 1.31
552 589 8.722480 TCATTCTGTGATTTGATTTCGTCTAT 57.278 30.769 0.00 0.00 0.00 1.98
553 590 8.443160 GTTCATTCTGTGATTTGATTTCGTCTA 58.557 33.333 0.00 0.00 36.54 2.59
554 591 7.173907 AGTTCATTCTGTGATTTGATTTCGTCT 59.826 33.333 0.00 0.00 36.54 4.18
555 592 7.301054 AGTTCATTCTGTGATTTGATTTCGTC 58.699 34.615 0.00 0.00 36.54 4.20
556 593 7.206981 AGTTCATTCTGTGATTTGATTTCGT 57.793 32.000 0.00 0.00 36.54 3.85
557 594 9.430838 GATAGTTCATTCTGTGATTTGATTTCG 57.569 33.333 0.00 0.00 36.54 3.46
558 595 9.727627 GGATAGTTCATTCTGTGATTTGATTTC 57.272 33.333 0.00 0.00 36.54 2.17
559 596 8.400947 CGGATAGTTCATTCTGTGATTTGATTT 58.599 33.333 0.00 0.00 36.54 2.17
560 597 7.554118 ACGGATAGTTCATTCTGTGATTTGATT 59.446 33.333 0.00 0.00 36.54 2.57
561 598 7.050377 ACGGATAGTTCATTCTGTGATTTGAT 58.950 34.615 0.00 0.00 36.54 2.57
562 599 6.406370 ACGGATAGTTCATTCTGTGATTTGA 58.594 36.000 0.00 0.00 36.54 2.69
563 600 6.668541 ACGGATAGTTCATTCTGTGATTTG 57.331 37.500 0.00 0.00 36.54 2.32
568 605 5.639506 AGTTTCACGGATAGTTCATTCTGTG 59.360 40.000 5.70 5.70 46.17 3.66
569 606 5.794894 AGTTTCACGGATAGTTCATTCTGT 58.205 37.500 0.00 0.00 31.63 3.41
570 607 8.425577 AATAGTTTCACGGATAGTTCATTCTG 57.574 34.615 0.00 0.00 0.00 3.02
571 608 9.099454 GAAATAGTTTCACGGATAGTTCATTCT 57.901 33.333 0.00 0.00 39.45 2.40
572 609 8.879759 TGAAATAGTTTCACGGATAGTTCATTC 58.120 33.333 1.24 0.00 44.21 2.67
573 610 8.786826 TGAAATAGTTTCACGGATAGTTCATT 57.213 30.769 1.24 0.00 44.21 2.57
586 623 1.463056 CAGGCGCGTGAAATAGTTTCA 59.537 47.619 25.09 1.24 46.68 2.69
587 624 1.730064 TCAGGCGCGTGAAATAGTTTC 59.270 47.619 28.85 0.00 40.08 2.78
588 625 1.463444 GTCAGGCGCGTGAAATAGTTT 59.537 47.619 31.98 0.00 0.00 2.66
589 626 1.076332 GTCAGGCGCGTGAAATAGTT 58.924 50.000 31.98 0.00 0.00 2.24
590 627 0.739813 GGTCAGGCGCGTGAAATAGT 60.740 55.000 31.98 0.00 0.00 2.12
591 628 0.460284 AGGTCAGGCGCGTGAAATAG 60.460 55.000 31.98 5.41 0.00 1.73
592 629 0.036765 AAGGTCAGGCGCGTGAAATA 60.037 50.000 31.98 9.75 0.00 1.40
593 630 0.889186 AAAGGTCAGGCGCGTGAAAT 60.889 50.000 31.98 20.97 0.00 2.17
594 631 1.098712 AAAAGGTCAGGCGCGTGAAA 61.099 50.000 31.98 10.91 0.00 2.69
595 632 1.098712 AAAAAGGTCAGGCGCGTGAA 61.099 50.000 31.98 15.14 0.00 3.18
596 633 1.525077 AAAAAGGTCAGGCGCGTGA 60.525 52.632 27.51 27.51 0.00 4.35
597 634 1.370414 CAAAAAGGTCAGGCGCGTG 60.370 57.895 23.52 23.52 0.00 5.34
598 635 1.822186 ACAAAAAGGTCAGGCGCGT 60.822 52.632 8.43 0.00 0.00 6.01
599 636 1.370414 CACAAAAAGGTCAGGCGCG 60.370 57.895 0.00 0.00 0.00 6.86
600 637 1.661509 GCACAAAAAGGTCAGGCGC 60.662 57.895 0.00 0.00 0.00 6.53
601 638 1.370414 CGCACAAAAAGGTCAGGCG 60.370 57.895 0.00 0.00 36.93 5.52
602 639 0.317854 GTCGCACAAAAAGGTCAGGC 60.318 55.000 0.00 0.00 0.00 4.85
603 640 0.041312 CGTCGCACAAAAAGGTCAGG 60.041 55.000 0.00 0.00 0.00 3.86
604 641 0.657368 GCGTCGCACAAAAAGGTCAG 60.657 55.000 13.44 0.00 0.00 3.51
605 642 1.353804 GCGTCGCACAAAAAGGTCA 59.646 52.632 13.44 0.00 0.00 4.02
606 643 1.370051 GGCGTCGCACAAAAAGGTC 60.370 57.895 20.50 0.00 0.00 3.85
607 644 2.719354 GGCGTCGCACAAAAAGGT 59.281 55.556 20.50 0.00 0.00 3.50
608 645 2.050442 GGGCGTCGCACAAAAAGG 60.050 61.111 20.50 0.00 0.00 3.11
609 646 2.426752 CGGGCGTCGCACAAAAAG 60.427 61.111 21.18 0.00 0.00 2.27
610 647 2.895865 TCGGGCGTCGCACAAAAA 60.896 55.556 21.18 0.00 39.05 1.94
611 648 3.641986 GTCGGGCGTCGCACAAAA 61.642 61.111 21.18 0.61 39.05 2.44
612 649 4.893601 TGTCGGGCGTCGCACAAA 62.894 61.111 21.18 3.54 39.05 2.83
626 663 2.758770 TAGTGTGGCGCCTTCGTGTC 62.759 60.000 29.70 10.72 38.14 3.67
627 664 2.863346 TAGTGTGGCGCCTTCGTGT 61.863 57.895 29.70 9.85 38.14 4.49
628 665 2.048597 TAGTGTGGCGCCTTCGTG 60.049 61.111 29.70 0.00 38.14 4.35
629 666 2.048503 GTAGTGTGGCGCCTTCGT 60.049 61.111 29.70 12.53 38.14 3.85
630 667 1.019278 AATGTAGTGTGGCGCCTTCG 61.019 55.000 29.70 0.00 39.07 3.79
631 668 0.447801 CAATGTAGTGTGGCGCCTTC 59.552 55.000 29.70 20.58 0.00 3.46
632 669 0.250727 ACAATGTAGTGTGGCGCCTT 60.251 50.000 29.70 13.03 0.00 4.35
633 670 0.955428 CACAATGTAGTGTGGCGCCT 60.955 55.000 29.70 9.99 44.29 5.52
634 671 1.501741 CACAATGTAGTGTGGCGCC 59.498 57.895 22.73 22.73 44.29 6.53
640 677 0.591170 GGCGTTGCACAATGTAGTGT 59.409 50.000 4.63 0.00 41.52 3.55
641 678 0.874390 AGGCGTTGCACAATGTAGTG 59.126 50.000 4.63 0.00 42.37 2.74
642 679 1.156736 GAGGCGTTGCACAATGTAGT 58.843 50.000 4.63 0.00 0.00 2.73
643 680 1.135972 GTGAGGCGTTGCACAATGTAG 60.136 52.381 4.63 0.00 35.19 2.74
644 681 0.871722 GTGAGGCGTTGCACAATGTA 59.128 50.000 4.63 0.00 35.19 2.29
645 682 1.100463 TGTGAGGCGTTGCACAATGT 61.100 50.000 4.63 0.00 41.61 2.71
646 683 0.386352 CTGTGAGGCGTTGCACAATG 60.386 55.000 0.00 0.00 43.65 2.82
647 684 0.534877 TCTGTGAGGCGTTGCACAAT 60.535 50.000 0.00 0.00 43.65 2.71
648 685 0.534877 ATCTGTGAGGCGTTGCACAA 60.535 50.000 0.00 0.00 43.65 3.33
649 686 0.320050 TATCTGTGAGGCGTTGCACA 59.680 50.000 0.00 0.00 42.25 4.57
650 687 1.002366 CTATCTGTGAGGCGTTGCAC 58.998 55.000 0.00 0.00 35.63 4.57
651 688 0.108186 CCTATCTGTGAGGCGTTGCA 60.108 55.000 0.00 0.00 0.00 4.08
652 689 2.682893 CCTATCTGTGAGGCGTTGC 58.317 57.895 0.00 0.00 0.00 4.17
658 695 1.032794 TGTAGCGCCTATCTGTGAGG 58.967 55.000 2.29 0.00 37.12 3.86
659 696 1.598183 CGTGTAGCGCCTATCTGTGAG 60.598 57.143 2.29 0.00 0.00 3.51
660 697 0.380733 CGTGTAGCGCCTATCTGTGA 59.619 55.000 2.29 0.00 0.00 3.58
661 698 0.595053 CCGTGTAGCGCCTATCTGTG 60.595 60.000 2.29 0.00 39.71 3.66
662 699 1.734137 CCGTGTAGCGCCTATCTGT 59.266 57.895 2.29 0.00 39.71 3.41
663 700 1.661821 GCCGTGTAGCGCCTATCTG 60.662 63.158 2.29 0.00 39.71 2.90
664 701 2.728817 GCCGTGTAGCGCCTATCT 59.271 61.111 2.29 0.00 39.71 1.98
665 702 2.355956 GGCCGTGTAGCGCCTATC 60.356 66.667 2.29 0.00 39.71 2.08
666 703 3.151710 TGGCCGTGTAGCGCCTAT 61.152 61.111 2.29 0.00 39.71 2.57
667 704 3.833645 CTGGCCGTGTAGCGCCTA 61.834 66.667 2.29 0.00 39.71 3.93
685 722 3.179265 GATCACACGGGTGCGACG 61.179 66.667 14.50 0.00 44.87 5.12
686 723 2.048597 TGATCACACGGGTGCGAC 60.049 61.111 14.50 7.33 44.87 5.19
687 724 2.212900 CTCTGATCACACGGGTGCGA 62.213 60.000 14.50 5.87 44.87 5.10
688 725 1.807165 CTCTGATCACACGGGTGCG 60.807 63.158 14.50 1.20 44.87 5.34
689 726 2.103042 GCTCTGATCACACGGGTGC 61.103 63.158 14.50 0.00 44.87 5.01
690 727 0.817654 TAGCTCTGATCACACGGGTG 59.182 55.000 12.84 12.84 46.66 4.61
691 728 1.107114 CTAGCTCTGATCACACGGGT 58.893 55.000 0.00 0.00 0.00 5.28
692 729 0.387202 CCTAGCTCTGATCACACGGG 59.613 60.000 0.00 0.00 0.00 5.28
693 730 0.249238 GCCTAGCTCTGATCACACGG 60.249 60.000 0.00 0.00 0.00 4.94
694 731 0.593518 CGCCTAGCTCTGATCACACG 60.594 60.000 0.00 0.00 0.00 4.49
695 732 0.873743 GCGCCTAGCTCTGATCACAC 60.874 60.000 0.00 0.00 44.04 3.82
696 733 1.439228 GCGCCTAGCTCTGATCACA 59.561 57.895 0.00 0.00 44.04 3.58
697 734 4.334837 GCGCCTAGCTCTGATCAC 57.665 61.111 0.00 0.00 44.04 3.06
707 744 4.514577 CTGACCCGTGGCGCCTAG 62.515 72.222 29.70 20.71 0.00 3.02
718 755 1.429148 CTATTTCACGCGGCTGACCC 61.429 60.000 12.47 0.00 0.00 4.46
719 756 0.739813 ACTATTTCACGCGGCTGACC 60.740 55.000 12.47 0.00 0.00 4.02
720 757 1.076332 AACTATTTCACGCGGCTGAC 58.924 50.000 12.47 0.00 0.00 3.51
721 758 1.730064 GAAACTATTTCACGCGGCTGA 59.270 47.619 12.47 2.44 39.45 4.26
722 759 1.463056 TGAAACTATTTCACGCGGCTG 59.537 47.619 12.47 0.00 44.21 4.85
723 760 1.803334 TGAAACTATTTCACGCGGCT 58.197 45.000 12.47 0.00 44.21 5.52
730 767 5.849510 TGAACTCTCCGTGAAACTATTTCA 58.150 37.500 0.00 0.00 46.68 2.69
731 768 6.969828 ATGAACTCTCCGTGAAACTATTTC 57.030 37.500 0.00 0.00 40.08 2.17
732 769 7.118390 CAGAATGAACTCTCCGTGAAACTATTT 59.882 37.037 0.00 0.00 39.69 1.40
733 770 6.591834 CAGAATGAACTCTCCGTGAAACTATT 59.408 38.462 0.00 0.00 39.69 1.73
734 771 6.102663 CAGAATGAACTCTCCGTGAAACTAT 58.897 40.000 0.00 0.00 39.69 2.12
735 772 5.010719 ACAGAATGAACTCTCCGTGAAACTA 59.989 40.000 0.00 0.00 39.69 2.24
736 773 4.202264 ACAGAATGAACTCTCCGTGAAACT 60.202 41.667 0.00 0.00 39.69 2.66
737 774 4.058817 ACAGAATGAACTCTCCGTGAAAC 58.941 43.478 0.00 0.00 39.69 2.78
738 775 4.058124 CACAGAATGAACTCTCCGTGAAA 58.942 43.478 0.00 0.00 39.69 2.69
739 776 3.320826 TCACAGAATGAACTCTCCGTGAA 59.679 43.478 0.00 0.00 39.69 3.18
740 777 2.890945 TCACAGAATGAACTCTCCGTGA 59.109 45.455 0.00 0.00 39.69 4.35
741 778 3.303881 TCACAGAATGAACTCTCCGTG 57.696 47.619 0.00 0.00 39.69 4.94
742 779 4.543590 AATCACAGAATGAACTCTCCGT 57.456 40.909 0.00 0.00 41.93 4.69
743 780 4.931601 TCAAATCACAGAATGAACTCTCCG 59.068 41.667 0.00 0.00 41.93 4.63
744 781 6.998968 ATCAAATCACAGAATGAACTCTCC 57.001 37.500 0.00 0.00 41.93 3.71
745 782 9.125906 CAAAATCAAATCACAGAATGAACTCTC 57.874 33.333 0.00 0.00 41.93 3.20
746 783 8.636213 ACAAAATCAAATCACAGAATGAACTCT 58.364 29.630 0.00 0.00 41.93 3.24
747 784 8.807667 ACAAAATCAAATCACAGAATGAACTC 57.192 30.769 0.00 0.00 41.93 3.01
748 785 9.603921 AAACAAAATCAAATCACAGAATGAACT 57.396 25.926 0.00 0.00 41.93 3.01
787 824 1.112315 ACGGGCTGGCAAATTTGACA 61.112 50.000 24.92 24.92 45.70 3.58
788 825 0.033366 AACGGGCTGGCAAATTTGAC 59.967 50.000 22.31 19.99 36.50 3.18
789 826 0.316841 GAACGGGCTGGCAAATTTGA 59.683 50.000 22.31 0.69 0.00 2.69
790 827 0.670239 GGAACGGGCTGGCAAATTTG 60.670 55.000 14.03 14.03 0.00 2.32
791 828 1.671166 GGAACGGGCTGGCAAATTT 59.329 52.632 2.88 0.00 0.00 1.82
792 829 3.376546 GGAACGGGCTGGCAAATT 58.623 55.556 2.88 0.00 0.00 1.82
1675 2393 1.221840 CGCCACCTTGGAGCATAGT 59.778 57.895 0.00 0.00 40.96 2.12
1855 2914 5.243207 ACTAGACAAATTCCCCAAACTACG 58.757 41.667 0.00 0.00 0.00 3.51
1961 3026 4.868171 TGACTTAATCATGGCACGAGTTAC 59.132 41.667 0.00 0.00 29.99 2.50
1991 3069 7.379529 GGTTGTCTTCATCAAAATGTGTTGTAG 59.620 37.037 0.00 0.00 34.32 2.74
2016 3094 3.002791 CGGGGAAATCGATCATACATGG 58.997 50.000 0.00 0.00 0.00 3.66
2166 3279 8.939201 TTTGAAATCAAAGTTACAGAAATGCA 57.061 26.923 4.52 0.00 40.55 3.96
2733 3850 4.018484 AGATTGCTGAAGTTTCTCTGCT 57.982 40.909 4.47 0.00 40.04 4.24
2913 4030 6.709846 CCTGATTGACCCTATTCAAATCTCTC 59.290 42.308 0.00 0.00 38.95 3.20
3220 4337 5.118664 TGCGAAGTAGATCAAGAAAGTTTCG 59.881 40.000 9.91 0.00 38.23 3.46
3266 4383 8.056400 ACTAAGAGGTGAAGTACTGATAGTGAT 58.944 37.037 0.00 0.00 0.00 3.06
3561 4681 7.745620 TTGTACCTTTCTCTTCATTTCCTTC 57.254 36.000 0.00 0.00 0.00 3.46
3585 4705 1.707427 AGCCTCACAACAGGAAAGGAT 59.293 47.619 0.00 0.00 35.20 3.24
3693 4814 9.188588 GTTCGCTACTATAGTATTTGCAATACA 57.811 33.333 12.98 0.00 0.00 2.29
3696 4817 8.833231 ATGTTCGCTACTATAGTATTTGCAAT 57.167 30.769 12.98 2.13 0.00 3.56
3811 4932 8.462016 ACAATTAGAATACTTGAAGGATTGCAC 58.538 33.333 7.50 0.00 35.12 4.57
3901 5104 1.990563 TGACGCGCTAGCTTCTTAAAC 59.009 47.619 13.93 0.00 41.59 2.01
3957 5160 6.201226 TGCTTGCGATTATTCAATTACCAA 57.799 33.333 0.00 0.00 0.00 3.67
4043 5247 8.378172 TCACAAATTAGTATTAGCATAGCACC 57.622 34.615 0.00 0.00 0.00 5.01
4082 5286 6.040391 TGAGTAGCAAACTAAATGCAAGGTTT 59.960 34.615 0.00 0.00 46.22 3.27
4091 5295 5.500234 TCCAGCATGAGTAGCAAACTAAAT 58.500 37.500 0.00 0.00 39.07 1.40
4302 5506 4.524802 TGAATGCCCCAAATCTCAGTAT 57.475 40.909 0.00 0.00 0.00 2.12
4650 6186 4.340894 TGCAAATCATTGACGCTTCTAC 57.659 40.909 6.23 0.00 38.94 2.59
4658 6194 7.007313 CCAATATTGGTTGCAAATCATTGAC 57.993 36.000 24.12 0.00 36.42 3.18
4721 6257 6.795098 AAGAACGTCAAATGTAGCATTGTA 57.205 33.333 0.00 0.00 0.00 2.41
4858 6394 0.672342 GGACATCTGCCATCCATTGC 59.328 55.000 0.00 0.00 32.35 3.56
4869 6405 1.802960 GTCACAAGTGCTGGACATCTG 59.197 52.381 1.24 0.00 0.00 2.90
4874 6410 3.728845 TCTAAAGTCACAAGTGCTGGAC 58.271 45.455 0.00 0.00 0.00 4.02
4956 6492 8.440771 AGGAATATAAATGGAGAAATCGTTCCT 58.559 33.333 0.00 0.00 36.62 3.36
5002 6538 4.570772 CACAGGTATGACCGAAACAATAGG 59.429 45.833 0.00 0.00 44.90 2.57
5020 6556 3.996150 AATTGCTGAAACTGTCACAGG 57.004 42.857 10.28 0.00 35.51 4.00
5089 6626 3.197983 CCTAGCCTGCCACTTTAAGTACT 59.802 47.826 0.00 0.00 0.00 2.73
5258 6795 8.893727 ACATAAATACTGCACATAAAGAACTCC 58.106 33.333 0.00 0.00 0.00 3.85
5288 6825 7.787028 ACAGGCCTATAAACAAAACAAAAGAA 58.213 30.769 3.98 0.00 0.00 2.52
5290 6827 9.705290 ATTACAGGCCTATAAACAAAACAAAAG 57.295 29.630 7.75 0.00 0.00 2.27
5295 6832 9.783256 CTTGTATTACAGGCCTATAAACAAAAC 57.217 33.333 21.38 11.72 0.00 2.43
5346 6884 7.781324 AAAGTTATGTTCCACAAATCAGGAT 57.219 32.000 0.00 0.00 33.10 3.24
5729 7277 1.003839 GTGCTGATCCGGTGGAACA 60.004 57.895 0.00 0.00 39.98 3.18
5810 7358 1.447314 GTAAACTGGCCTCGGGTCG 60.447 63.158 3.32 0.00 0.00 4.79
6233 8158 3.242091 CGAGCACAATTGACATTACTCCG 60.242 47.826 13.59 0.00 0.00 4.63
6393 8320 3.646715 TTCCCCTCGCCAGGTTGG 61.647 66.667 0.00 0.00 38.30 3.77
6425 8352 3.585862 AGATACGCAGTGTACCAAAGTG 58.414 45.455 0.00 0.00 45.73 3.16
6518 8453 8.428852 TGCATGAATGTAGGTAGTATGTACAAT 58.571 33.333 0.00 0.00 30.70 2.71
6613 8797 9.758651 AACAATTCTATACGCACTACATTATGA 57.241 29.630 0.00 0.00 0.00 2.15
6637 8824 3.245990 GGTGCAAAGCATGACTTTTCAAC 59.754 43.478 13.27 12.57 46.73 3.18
6819 9096 6.072508 CCCTTTCATAATGCAGTGCGTATATT 60.073 38.462 10.95 6.94 0.00 1.28
6820 9097 5.412594 CCCTTTCATAATGCAGTGCGTATAT 59.587 40.000 10.95 8.02 0.00 0.86
6825 9102 2.016318 TCCCTTTCATAATGCAGTGCG 58.984 47.619 11.20 0.00 0.00 5.34
7027 12155 2.108168 GACTGGCAGTGTACAGGGATA 58.892 52.381 27.45 0.00 39.00 2.59
7098 12227 8.461222 CAGACACCATACAACAATAATCAATGT 58.539 33.333 0.00 0.00 0.00 2.71
7236 12369 8.908903 TGCCGAATAAACCAGACATATTATTTT 58.091 29.630 0.00 0.00 30.36 1.82


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

AutoCloner maintained by Alex Coulton.