Multiple sequence alignment - TraesCS2D01G544600

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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 TraesCS2D01G544600 chr2D 100.000 3022 0 0 1 3022 621602366 621599345 0.000000e+00 5581
1 TraesCS2D01G544600 chr2D 94.755 591 26 5 2416 3004 7909096 7908509 0.000000e+00 915
2 TraesCS2D01G544600 chr2D 87.379 206 16 5 1876 2079 621669010 621668813 8.430000e-56 228
3 TraesCS2D01G544600 chr2D 79.605 152 26 4 2089 2240 621667873 621667727 1.480000e-18 104
4 TraesCS2D01G544600 chr2D 88.506 87 3 3 1260 1340 621669095 621669010 6.890000e-17 99
5 TraesCS2D01G544600 chr2B 88.203 1441 104 31 677 2100 763446652 763445261 0.000000e+00 1659
6 TraesCS2D01G544600 chr2B 88.022 1077 96 23 989 2041 763406244 763405177 0.000000e+00 1243
7 TraesCS2D01G544600 chr2B 84.397 423 39 11 1 422 763215194 763214798 1.020000e-104 390
8 TraesCS2D01G544600 chr2B 77.532 543 70 32 1876 2414 763476536 763476042 2.290000e-71 279
9 TraesCS2D01G544600 chr2B 90.854 164 11 4 2120 2282 763445271 763445111 1.820000e-52 217
10 TraesCS2D01G544600 chr2B 90.566 159 10 1 759 912 763408006 763407848 3.950000e-49 206
11 TraesCS2D01G544600 chr2B 95.122 123 3 1 2268 2390 763445095 763444976 1.110000e-44 191
12 TraesCS2D01G544600 chr2B 79.528 254 27 16 1099 1340 763476776 763476536 1.120000e-34 158
13 TraesCS2D01G544600 chr2B 77.586 232 25 12 2030 2240 763525277 763525052 6.850000e-22 115
14 TraesCS2D01G544600 chr7D 95.574 610 24 3 2415 3022 519498234 519498842 0.000000e+00 974
15 TraesCS2D01G544600 chr7D 95.431 591 24 3 2416 3004 44287329 44286740 0.000000e+00 939
16 TraesCS2D01G544600 chr7D 95.424 590 23 4 2417 3004 21347596 21347009 0.000000e+00 937
17 TraesCS2D01G544600 chr1D 94.417 609 31 3 2416 3022 29915672 29915065 0.000000e+00 933
18 TraesCS2D01G544600 chr1D 94.407 590 29 4 2417 3004 451242582 451241995 0.000000e+00 904
19 TraesCS2D01G544600 chr3D 94.243 608 31 4 2417 3022 563015365 563014760 0.000000e+00 926
20 TraesCS2D01G544600 chr3D 94.147 598 31 4 2416 3010 421996877 421997473 0.000000e+00 907
21 TraesCS2D01G544600 chr5D 94.576 590 27 5 2417 3004 501458147 501458733 0.000000e+00 907
22 TraesCS2D01G544600 chr5D 82.228 377 63 4 4 377 179785453 179785828 3.760000e-84 322
23 TraesCS2D01G544600 chr2A 94.757 515 26 1 1402 1916 753413697 753413184 0.000000e+00 800
24 TraesCS2D01G544600 chr2A 92.227 476 22 5 1948 2416 753413181 753412714 0.000000e+00 660
25 TraesCS2D01G544600 chr2A 84.300 414 54 7 13 422 753415106 753414700 7.850000e-106 394
26 TraesCS2D01G544600 chr2A 84.000 400 52 9 548 944 753414459 753414069 1.020000e-99 374
27 TraesCS2D01G544600 chr2A 96.053 228 9 0 985 1212 753414069 753413842 3.680000e-99 372
28 TraesCS2D01G544600 chr2A 83.125 320 32 12 1876 2195 753422173 753421876 3.840000e-69 272
29 TraesCS2D01G544600 chr6A 83.619 409 63 4 10 415 124891571 124891164 6.110000e-102 381
30 TraesCS2D01G544600 chr6A 80.630 413 77 2 4 415 291216722 291216312 1.750000e-82 316
31 TraesCS2D01G544600 chr7B 82.324 413 70 3 4 413 384648261 384647849 3.710000e-94 355
32 TraesCS2D01G544600 chr3B 84.438 347 52 2 69 413 418685991 418685645 1.040000e-89 340
33 TraesCS2D01G544600 chr5A 78.914 313 64 2 103 413 547076262 547075950 8.490000e-51 211
34 TraesCS2D01G544600 chr4B 77.670 206 42 3 532 736 672433 672231 4.090000e-24 122


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 TraesCS2D01G544600 chr2D 621599345 621602366 3021 True 5581.0 5581 100.0000 1 3022 1 chr2D.!!$R2 3021
1 TraesCS2D01G544600 chr2D 7908509 7909096 587 True 915.0 915 94.7550 2416 3004 1 chr2D.!!$R1 588
2 TraesCS2D01G544600 chr2B 763405177 763408006 2829 True 724.5 1243 89.2940 759 2041 2 chr2B.!!$R3 1282
3 TraesCS2D01G544600 chr2B 763444976 763446652 1676 True 689.0 1659 91.3930 677 2390 3 chr2B.!!$R4 1713
4 TraesCS2D01G544600 chr2B 763476042 763476776 734 True 218.5 279 78.5300 1099 2414 2 chr2B.!!$R5 1315
5 TraesCS2D01G544600 chr7D 519498234 519498842 608 False 974.0 974 95.5740 2415 3022 1 chr7D.!!$F1 607
6 TraesCS2D01G544600 chr7D 44286740 44287329 589 True 939.0 939 95.4310 2416 3004 1 chr7D.!!$R2 588
7 TraesCS2D01G544600 chr7D 21347009 21347596 587 True 937.0 937 95.4240 2417 3004 1 chr7D.!!$R1 587
8 TraesCS2D01G544600 chr1D 29915065 29915672 607 True 933.0 933 94.4170 2416 3022 1 chr1D.!!$R1 606
9 TraesCS2D01G544600 chr1D 451241995 451242582 587 True 904.0 904 94.4070 2417 3004 1 chr1D.!!$R2 587
10 TraesCS2D01G544600 chr3D 563014760 563015365 605 True 926.0 926 94.2430 2417 3022 1 chr3D.!!$R1 605
11 TraesCS2D01G544600 chr3D 421996877 421997473 596 False 907.0 907 94.1470 2416 3010 1 chr3D.!!$F1 594
12 TraesCS2D01G544600 chr5D 501458147 501458733 586 False 907.0 907 94.5760 2417 3004 1 chr5D.!!$F2 587
13 TraesCS2D01G544600 chr2A 753412714 753415106 2392 True 520.0 800 90.2674 13 2416 5 chr2A.!!$R2 2403

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
377 382 0.035439 GGTCCAAATTCCTCGAGGCA 60.035 55.0 27.39 17.72 34.44 4.75 F
648 851 0.109319 CGTGCCCCACTGTAATTTGC 60.109 55.0 0.00 0.00 31.34 3.68 F
715 918 0.393448 TGCCACGCACCTAACAAGTA 59.607 50.0 0.00 0.00 31.71 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1215 3006 1.419387 AGAGTGTCAAGCTCAAGCCTT 59.581 47.619 0.0 0.0 43.38 4.35 R
1839 3679 1.445582 GCCCGTCGTACACCTTGAG 60.446 63.158 0.0 0.0 0.00 3.02 R
2482 4381 2.301346 CCAATGCTCACATTAGTCCCC 58.699 52.381 0.0 0.0 44.83 4.81 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
23 24 6.677781 TGGTTTTAGAGGAATGCGATTTAG 57.322 37.500 0.00 0.00 0.00 1.85
28 29 9.439537 GTTTTAGAGGAATGCGATTTAGATTTC 57.560 33.333 0.00 0.00 0.00 2.17
31 32 5.529060 AGAGGAATGCGATTTAGATTTCCAC 59.471 40.000 0.00 0.00 36.03 4.02
37 38 4.328983 TGCGATTTAGATTTCCACGAAGAC 59.671 41.667 0.00 0.00 0.00 3.01
39 40 4.548346 CGATTTAGATTTCCACGAAGACGC 60.548 45.833 0.00 0.00 43.96 5.19
41 42 4.707030 TTAGATTTCCACGAAGACGCTA 57.293 40.909 0.00 0.00 43.96 4.26
48 49 2.159421 TCCACGAAGACGCTATGAAGTC 60.159 50.000 0.00 0.00 43.96 3.01
59 60 4.754618 ACGCTATGAAGTCACAAAACATGA 59.245 37.500 0.00 0.00 0.00 3.07
65 66 5.649557 TGAAGTCACAAAACATGAAACCAG 58.350 37.500 0.00 0.00 0.00 4.00
67 68 3.384467 AGTCACAAAACATGAAACCAGGG 59.616 43.478 0.00 0.00 0.00 4.45
83 84 1.212751 GGGCTTGCGTCATCCAAAC 59.787 57.895 0.00 0.00 0.00 2.93
88 89 1.336440 CTTGCGTCATCCAAACCAACA 59.664 47.619 0.00 0.00 0.00 3.33
95 96 3.754323 GTCATCCAAACCAACATCGGTAA 59.246 43.478 0.00 0.00 38.76 2.85
101 102 3.713826 AACCAACATCGGTAACCTCAT 57.286 42.857 0.00 0.00 38.76 2.90
113 114 0.324943 AACCTCATCAACCGAGTGGG 59.675 55.000 0.00 0.00 40.75 4.61
120 121 3.384789 TCATCAACCGAGTGGGAGATAAG 59.615 47.826 0.00 0.00 40.75 1.73
123 124 0.395311 ACCGAGTGGGAGATAAGCGA 60.395 55.000 0.00 0.00 40.75 4.93
141 142 3.638160 AGCGAACCATCATATTTGGCATT 59.362 39.130 0.00 0.00 37.81 3.56
146 147 5.186996 ACCATCATATTTGGCATTCGTTC 57.813 39.130 0.00 0.00 37.81 3.95
149 150 5.279106 CCATCATATTTGGCATTCGTTCCAT 60.279 40.000 0.00 0.00 31.54 3.41
177 180 2.830321 CTCGGTTTCAGGGTTAGTAGGT 59.170 50.000 0.00 0.00 0.00 3.08
179 182 3.647590 TCGGTTTCAGGGTTAGTAGGTTT 59.352 43.478 0.00 0.00 0.00 3.27
182 185 5.001874 GGTTTCAGGGTTAGTAGGTTTCTG 58.998 45.833 0.00 0.00 0.00 3.02
186 189 6.350629 TCAGGGTTAGTAGGTTTCTGTTAC 57.649 41.667 0.00 0.00 0.00 2.50
192 195 7.212274 GGTTAGTAGGTTTCTGTTACACTTCA 58.788 38.462 0.00 0.00 0.00 3.02
195 198 7.304497 AGTAGGTTTCTGTTACACTTCAGAT 57.696 36.000 0.00 0.00 39.85 2.90
209 212 7.198306 ACACTTCAGATAAACCTTTAAACGG 57.802 36.000 0.00 3.10 0.00 4.44
212 215 6.993902 ACTTCAGATAAACCTTTAAACGGTCA 59.006 34.615 9.02 3.16 32.46 4.02
213 216 7.499895 ACTTCAGATAAACCTTTAAACGGTCAA 59.500 33.333 9.02 3.16 32.46 3.18
215 218 8.036273 TCAGATAAACCTTTAAACGGTCAATC 57.964 34.615 9.02 12.59 32.46 2.67
216 219 7.881232 TCAGATAAACCTTTAAACGGTCAATCT 59.119 33.333 17.15 17.15 36.84 2.40
217 220 8.512138 CAGATAAACCTTTAAACGGTCAATCTT 58.488 33.333 18.61 10.41 35.45 2.40
232 235 9.095065 ACGGTCAATCTTCATATGTTTAAGTAC 57.905 33.333 1.90 0.00 0.00 2.73
237 240 9.184523 CAATCTTCATATGTTTAAGTACCCCAA 57.815 33.333 1.90 0.00 0.00 4.12
241 244 5.189342 TCATATGTTTAAGTACCCCAACCGA 59.811 40.000 1.90 0.00 0.00 4.69
242 245 4.579647 ATGTTTAAGTACCCCAACCGAT 57.420 40.909 0.00 0.00 0.00 4.18
260 265 8.936864 CCAACCGATAGATTAATTTCACTATCC 58.063 37.037 12.74 1.74 38.41 2.59
261 266 9.489084 CAACCGATAGATTAATTTCACTATCCA 57.511 33.333 12.74 0.00 38.41 3.41
272 277 9.540538 TTAATTTCACTATCCATCTTTCCCAAA 57.459 29.630 0.00 0.00 0.00 3.28
302 307 5.222048 ACCAATGTTCTTTAGGCTAGTGGAA 60.222 40.000 4.82 3.86 0.00 3.53
323 328 5.470845 AAATGCGAGTATCCGAAAAAGAG 57.529 39.130 0.00 0.00 0.00 2.85
330 335 6.128634 GCGAGTATCCGAAAAAGAGAGAAAAA 60.129 38.462 0.00 0.00 0.00 1.94
377 382 0.035439 GGTCCAAATTCCTCGAGGCA 60.035 55.000 27.39 17.72 34.44 4.75
378 383 1.408822 GGTCCAAATTCCTCGAGGCAT 60.409 52.381 27.39 19.44 34.44 4.40
379 384 1.672881 GTCCAAATTCCTCGAGGCATG 59.327 52.381 27.39 19.75 34.44 4.06
380 385 1.027357 CCAAATTCCTCGAGGCATGG 58.973 55.000 27.39 24.04 34.44 3.66
392 397 4.137872 GCATGGTGGCGCATTGCT 62.138 61.111 10.83 0.00 45.43 3.91
393 398 2.574929 CATGGTGGCGCATTGCTT 59.425 55.556 10.83 0.00 45.43 3.91
402 407 2.271957 CGCATTGCTTTTGCTAGCG 58.728 52.632 10.77 0.00 46.56 4.26
418 423 2.977700 GCGAATGCTCATCGGAAGA 58.022 52.632 8.11 0.00 40.54 2.87
422 427 4.350007 GCGAATGCTCATCGGAAGAAGAT 61.350 47.826 8.11 0.00 40.59 2.40
423 428 5.088445 GCGAATGCTCATCGGAAGAAGATA 61.088 45.833 8.11 0.00 40.59 1.98
424 429 6.360305 GCGAATGCTCATCGGAAGAAGATAT 61.360 44.000 8.11 0.00 40.59 1.63
437 639 7.335924 TCGGAAGAAGATATTTTTGTTTCGGAT 59.664 33.333 9.88 0.00 37.03 4.18
439 641 7.220875 GGAAGAAGATATTTTTGTTTCGGATGC 59.779 37.037 0.00 0.00 0.00 3.91
442 644 8.306761 AGAAGATATTTTTGTTTCGGATGCTTT 58.693 29.630 0.00 0.00 0.00 3.51
443 645 9.567848 GAAGATATTTTTGTTTCGGATGCTTTA 57.432 29.630 0.00 0.00 0.00 1.85
451 653 5.649557 TGTTTCGGATGCTTTAATTCATGG 58.350 37.500 0.00 0.00 0.00 3.66
452 654 5.184864 TGTTTCGGATGCTTTAATTCATGGT 59.815 36.000 0.00 0.00 0.00 3.55
453 655 4.898829 TCGGATGCTTTAATTCATGGTG 57.101 40.909 0.00 0.00 0.00 4.17
484 686 9.840427 ATTTTAGATGTTTTCCTTTATGTGTCG 57.160 29.630 0.00 0.00 0.00 4.35
485 687 8.610248 TTTAGATGTTTTCCTTTATGTGTCGA 57.390 30.769 0.00 0.00 0.00 4.20
486 688 8.610248 TTAGATGTTTTCCTTTATGTGTCGAA 57.390 30.769 0.00 0.00 0.00 3.71
487 689 7.504924 AGATGTTTTCCTTTATGTGTCGAAA 57.495 32.000 0.00 0.00 0.00 3.46
488 690 8.110860 AGATGTTTTCCTTTATGTGTCGAAAT 57.889 30.769 0.00 0.00 0.00 2.17
489 691 8.237267 AGATGTTTTCCTTTATGTGTCGAAATC 58.763 33.333 0.00 0.00 0.00 2.17
490 692 7.504924 TGTTTTCCTTTATGTGTCGAAATCT 57.495 32.000 0.00 0.00 0.00 2.40
491 693 7.936584 TGTTTTCCTTTATGTGTCGAAATCTT 58.063 30.769 0.00 0.00 0.00 2.40
492 694 8.410141 TGTTTTCCTTTATGTGTCGAAATCTTT 58.590 29.630 0.00 0.00 0.00 2.52
493 695 9.244799 GTTTTCCTTTATGTGTCGAAATCTTTT 57.755 29.630 0.00 0.00 0.00 2.27
494 696 9.810545 TTTTCCTTTATGTGTCGAAATCTTTTT 57.189 25.926 0.00 0.00 0.00 1.94
495 697 9.458374 TTTCCTTTATGTGTCGAAATCTTTTTC 57.542 29.630 0.00 0.00 38.29 2.29
496 698 8.391075 TCCTTTATGTGTCGAAATCTTTTTCT 57.609 30.769 0.00 0.00 39.30 2.52
497 699 9.496873 TCCTTTATGTGTCGAAATCTTTTTCTA 57.503 29.630 0.00 0.00 39.30 2.10
501 703 7.921786 ATGTGTCGAAATCTTTTTCTATGGA 57.078 32.000 0.00 0.00 39.30 3.41
502 704 7.129109 TGTGTCGAAATCTTTTTCTATGGAC 57.871 36.000 0.00 0.00 39.30 4.02
503 705 6.148811 TGTGTCGAAATCTTTTTCTATGGACC 59.851 38.462 0.00 0.00 39.30 4.46
504 706 5.646360 TGTCGAAATCTTTTTCTATGGACCC 59.354 40.000 0.00 0.00 39.30 4.46
505 707 5.880887 GTCGAAATCTTTTTCTATGGACCCT 59.119 40.000 0.00 0.00 39.30 4.34
506 708 5.880332 TCGAAATCTTTTTCTATGGACCCTG 59.120 40.000 0.00 0.00 39.30 4.45
507 709 5.880332 CGAAATCTTTTTCTATGGACCCTGA 59.120 40.000 0.00 0.00 39.30 3.86
508 710 6.543831 CGAAATCTTTTTCTATGGACCCTGAT 59.456 38.462 0.00 0.00 39.30 2.90
509 711 7.715249 CGAAATCTTTTTCTATGGACCCTGATA 59.285 37.037 0.00 0.00 39.30 2.15
510 712 9.408648 GAAATCTTTTTCTATGGACCCTGATAA 57.591 33.333 0.00 0.00 38.56 1.75
511 713 8.753497 AATCTTTTTCTATGGACCCTGATAAC 57.247 34.615 0.00 0.00 0.00 1.89
512 714 6.346096 TCTTTTTCTATGGACCCTGATAACG 58.654 40.000 0.00 0.00 0.00 3.18
513 715 5.687166 TTTTCTATGGACCCTGATAACGT 57.313 39.130 0.00 0.00 0.00 3.99
514 716 4.931661 TTCTATGGACCCTGATAACGTC 57.068 45.455 0.00 0.00 0.00 4.34
515 717 3.905968 TCTATGGACCCTGATAACGTCA 58.094 45.455 0.00 0.00 35.05 4.35
516 718 4.283337 TCTATGGACCCTGATAACGTCAA 58.717 43.478 0.00 0.00 36.14 3.18
517 719 3.543680 ATGGACCCTGATAACGTCAAG 57.456 47.619 0.00 0.00 36.14 3.02
518 720 2.253610 TGGACCCTGATAACGTCAAGT 58.746 47.619 0.00 0.00 36.14 3.16
519 721 3.433343 TGGACCCTGATAACGTCAAGTA 58.567 45.455 0.00 0.00 36.14 2.24
520 722 3.194116 TGGACCCTGATAACGTCAAGTAC 59.806 47.826 0.00 0.00 36.14 2.73
531 733 0.721718 GTCAAGTACGAGCACATGGC 59.278 55.000 0.00 0.00 45.30 4.40
537 739 1.468520 GTACGAGCACATGGCAATGTT 59.531 47.619 3.20 0.00 44.94 2.71
538 740 0.961019 ACGAGCACATGGCAATGTTT 59.039 45.000 3.20 0.00 44.94 2.83
539 741 1.340889 ACGAGCACATGGCAATGTTTT 59.659 42.857 3.20 0.00 44.94 2.43
540 742 2.224018 ACGAGCACATGGCAATGTTTTT 60.224 40.909 3.20 0.00 44.94 1.94
562 764 1.868469 TGGCAAGTTTAGTTACGCGT 58.132 45.000 19.17 19.17 0.00 6.01
565 767 1.794116 GCAAGTTTAGTTACGCGTGGA 59.206 47.619 24.59 7.64 0.00 4.02
568 770 3.581024 AGTTTAGTTACGCGTGGATGA 57.419 42.857 24.59 0.00 0.00 2.92
569 771 4.119442 AGTTTAGTTACGCGTGGATGAT 57.881 40.909 24.59 4.22 0.00 2.45
572 774 6.278363 AGTTTAGTTACGCGTGGATGATAAT 58.722 36.000 24.59 0.00 0.00 1.28
576 778 6.431198 AGTTACGCGTGGATGATAATTTTT 57.569 33.333 24.59 0.00 0.00 1.94
581 783 4.856487 CGCGTGGATGATAATTTTTGTTGT 59.144 37.500 0.00 0.00 0.00 3.32
582 784 5.220006 CGCGTGGATGATAATTTTTGTTGTG 60.220 40.000 0.00 0.00 0.00 3.33
587 789 7.275560 GTGGATGATAATTTTTGTTGTGTAGCC 59.724 37.037 0.00 0.00 0.00 3.93
590 792 6.686630 TGATAATTTTTGTTGTGTAGCCTGG 58.313 36.000 0.00 0.00 0.00 4.45
598 800 3.133721 TGTTGTGTAGCCTGGCAATTTTT 59.866 39.130 22.65 0.61 0.00 1.94
601 803 3.891977 TGTGTAGCCTGGCAATTTTTGTA 59.108 39.130 22.65 0.00 0.00 2.41
603 805 3.257127 TGTAGCCTGGCAATTTTTGTACC 59.743 43.478 22.65 0.00 0.00 3.34
606 808 2.671070 GCCTGGCAATTTTTGTACCTCG 60.671 50.000 15.17 0.00 0.00 4.63
610 812 3.385111 TGGCAATTTTTGTACCTCGGTTT 59.615 39.130 0.00 0.00 0.00 3.27
611 813 4.583489 TGGCAATTTTTGTACCTCGGTTTA 59.417 37.500 0.00 0.00 0.00 2.01
618 821 9.990360 AATTTTTGTACCTCGGTTTATTTTGAT 57.010 25.926 0.00 0.00 0.00 2.57
628 831 8.512138 CCTCGGTTTATTTTGATAGAAACTTGT 58.488 33.333 0.00 0.00 33.31 3.16
633 836 8.627428 GTTTATTTTGATAGAAACTTGTCGTGC 58.373 33.333 0.00 0.00 0.00 5.34
634 837 4.742438 TTTGATAGAAACTTGTCGTGCC 57.258 40.909 0.00 0.00 0.00 5.01
635 838 2.695359 TGATAGAAACTTGTCGTGCCC 58.305 47.619 0.00 0.00 0.00 5.36
641 844 2.111043 CTTGTCGTGCCCCACTGT 59.889 61.111 0.00 0.00 31.34 3.55
648 851 0.109319 CGTGCCCCACTGTAATTTGC 60.109 55.000 0.00 0.00 31.34 3.68
652 855 1.136891 GCCCCACTGTAATTTGCCATC 59.863 52.381 0.00 0.00 0.00 3.51
656 859 3.119029 CCCACTGTAATTTGCCATCCTTG 60.119 47.826 0.00 0.00 0.00 3.61
657 860 3.763360 CCACTGTAATTTGCCATCCTTGA 59.237 43.478 0.00 0.00 0.00 3.02
660 863 4.460382 ACTGTAATTTGCCATCCTTGAGTG 59.540 41.667 0.00 0.00 0.00 3.51
671 874 4.330250 CATCCTTGAGTGAGTGGAATTGT 58.670 43.478 0.00 0.00 31.87 2.71
682 885 5.625311 GTGAGTGGAATTGTCATCGAAAAAC 59.375 40.000 0.00 0.00 0.00 2.43
689 892 6.349280 GGAATTGTCATCGAAAAACATCAGGA 60.349 38.462 0.00 0.00 0.00 3.86
696 899 2.723273 GAAAAACATCAGGACCGGGAT 58.277 47.619 6.32 0.00 0.00 3.85
712 915 0.958382 GGATGCCACGCACCTAACAA 60.958 55.000 0.00 0.00 43.04 2.83
715 918 0.393448 TGCCACGCACCTAACAAGTA 59.607 50.000 0.00 0.00 31.71 2.24
716 919 0.794473 GCCACGCACCTAACAAGTAC 59.206 55.000 0.00 0.00 0.00 2.73
717 920 1.607251 GCCACGCACCTAACAAGTACT 60.607 52.381 0.00 0.00 0.00 2.73
718 921 2.353011 GCCACGCACCTAACAAGTACTA 60.353 50.000 0.00 0.00 0.00 1.82
807 1011 2.102588 ACCGAATAATTGGAGGAGACGG 59.897 50.000 0.00 0.00 42.78 4.79
828 1037 7.604927 AGACGGCACTATTATTCTTTGTTGTTA 59.395 33.333 0.00 0.00 0.00 2.41
846 1055 3.270877 GTTAGATCTTGACCGTGGCATT 58.729 45.455 0.00 0.00 0.00 3.56
934 1145 6.661377 TCCTATAGCTAGTCAGATTCCATGTC 59.339 42.308 0.00 0.00 0.00 3.06
943 1154 2.615227 GATTCCATGTCTGGCCCGCT 62.615 60.000 0.00 0.00 42.80 5.52
944 1155 2.898920 ATTCCATGTCTGGCCCGCTG 62.899 60.000 0.00 0.00 42.80 5.18
965 1176 1.644337 ACCATTAACTTTCCCCTCCCC 59.356 52.381 0.00 0.00 0.00 4.81
966 1177 1.930204 CCATTAACTTTCCCCTCCCCT 59.070 52.381 0.00 0.00 0.00 4.79
967 1178 3.128049 CCATTAACTTTCCCCTCCCCTA 58.872 50.000 0.00 0.00 0.00 3.53
1179 2970 3.779271 TGCAACCGTACGTATACATCA 57.221 42.857 15.21 0.00 0.00 3.07
1207 2998 3.314553 CTTGACTTCCATTGCTTGCTTG 58.685 45.455 0.00 0.00 0.00 4.01
1208 2999 1.000060 TGACTTCCATTGCTTGCTTGC 60.000 47.619 0.00 0.00 0.00 4.01
1215 3006 2.610976 CCATTGCTTGCTTGCTTGCTTA 60.611 45.455 10.35 2.19 0.00 3.09
1217 3008 2.427232 TGCTTGCTTGCTTGCTTAAG 57.573 45.000 0.00 0.00 0.00 1.85
1251 3059 3.870419 ACACTCTCGTCTCTAATCCGTAC 59.130 47.826 0.00 0.00 0.00 3.67
1410 3246 9.812347 TTAAATCATATATGTGGGCAGAAATCT 57.188 29.630 12.42 0.00 0.00 2.40
1577 3413 7.967890 GTAGTACTCCTACATCCTCTAGAAC 57.032 44.000 0.00 0.00 44.65 3.01
1594 3430 7.312657 TCTAGAACACTGTAACATACTACGG 57.687 40.000 0.00 0.00 34.79 4.02
1811 3651 2.019807 AAGACGGGACCAAGTTCCTA 57.980 50.000 0.00 0.00 35.76 2.94
1812 3652 2.019807 AGACGGGACCAAGTTCCTAA 57.980 50.000 0.00 0.00 35.76 2.69
2018 3860 0.322636 TCGGCTTCTTCTCTCGGTCT 60.323 55.000 0.00 0.00 0.00 3.85
2077 3919 4.546224 TTTTCCCTTTCCCTTTGGTACT 57.454 40.909 0.00 0.00 0.00 2.73
2078 3920 3.518992 TTCCCTTTCCCTTTGGTACTG 57.481 47.619 0.00 0.00 0.00 2.74
2095 3937 6.472016 TGGTACTGCTGATTACTGAAAATGA 58.528 36.000 0.00 0.00 0.00 2.57
2203 4046 0.583438 CTACATGCATTTCTCGCCGG 59.417 55.000 0.00 0.00 0.00 6.13
2240 4089 3.000925 GGTGCACGGATAACATTTCTACG 59.999 47.826 11.45 0.00 0.00 3.51
2378 4277 5.529430 TGAAAATACCAAACTCACGTGATGT 59.471 36.000 20.40 15.89 0.00 3.06
2409 4308 3.071602 ACTTCCGGAATGACATCCATAGG 59.928 47.826 19.21 3.40 39.61 2.57
2482 4381 2.019951 CCCGGTTCAGTCACGAACG 61.020 63.158 0.00 0.00 45.12 3.95
2559 4459 2.034999 GGCATTGGTCCCGGTTCA 59.965 61.111 0.00 0.00 0.00 3.18
2632 4532 2.283173 CTGGCCCACCACCCTTTC 60.283 66.667 0.00 0.00 42.67 2.62
2759 4659 1.072331 GTCCCTCTCTGCCTTGTTGAA 59.928 52.381 0.00 0.00 0.00 2.69
2762 4662 2.487986 CCCTCTCTGCCTTGTTGAACTT 60.488 50.000 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.411376 TCTAAATCGCATTCCTCTAAAACCA 58.589 36.000 0.00 0.00 0.00 3.67
1 2 6.920569 TCTAAATCGCATTCCTCTAAAACC 57.079 37.500 0.00 0.00 0.00 3.27
2 3 9.439537 GAAATCTAAATCGCATTCCTCTAAAAC 57.560 33.333 0.00 0.00 0.00 2.43
3 4 8.621286 GGAAATCTAAATCGCATTCCTCTAAAA 58.379 33.333 0.00 0.00 34.79 1.52
4 5 7.773224 TGGAAATCTAAATCGCATTCCTCTAAA 59.227 33.333 0.00 0.00 37.73 1.85
5 6 7.226720 GTGGAAATCTAAATCGCATTCCTCTAA 59.773 37.037 0.00 0.00 37.73 2.10
6 7 6.706270 GTGGAAATCTAAATCGCATTCCTCTA 59.294 38.462 0.00 0.00 37.73 2.43
7 8 5.529060 GTGGAAATCTAAATCGCATTCCTCT 59.471 40.000 0.00 0.00 37.73 3.69
8 9 5.559035 CGTGGAAATCTAAATCGCATTCCTC 60.559 44.000 0.00 0.00 37.73 3.71
9 10 4.273480 CGTGGAAATCTAAATCGCATTCCT 59.727 41.667 0.00 0.00 37.73 3.36
10 11 4.272504 TCGTGGAAATCTAAATCGCATTCC 59.727 41.667 0.00 0.00 37.44 3.01
11 12 5.403897 TCGTGGAAATCTAAATCGCATTC 57.596 39.130 0.00 0.00 0.00 2.67
23 24 3.444916 TCATAGCGTCTTCGTGGAAATC 58.555 45.455 0.00 0.00 39.49 2.17
28 29 2.186076 GACTTCATAGCGTCTTCGTGG 58.814 52.381 0.00 0.00 39.49 4.94
31 32 2.863739 TGTGACTTCATAGCGTCTTCG 58.136 47.619 0.00 0.00 40.37 3.79
37 38 5.281693 TCATGTTTTGTGACTTCATAGCG 57.718 39.130 0.00 0.00 0.00 4.26
39 40 7.424803 TGGTTTCATGTTTTGTGACTTCATAG 58.575 34.615 0.00 0.00 0.00 2.23
41 42 6.219417 TGGTTTCATGTTTTGTGACTTCAT 57.781 33.333 0.00 0.00 0.00 2.57
48 49 2.102925 AGCCCTGGTTTCATGTTTTGTG 59.897 45.455 0.00 0.00 0.00 3.33
59 60 1.228552 ATGACGCAAGCCCTGGTTT 60.229 52.632 0.00 0.00 45.62 3.27
65 66 1.212751 GTTTGGATGACGCAAGCCC 59.787 57.895 0.00 0.00 45.62 5.19
67 68 0.313672 TTGGTTTGGATGACGCAAGC 59.686 50.000 0.00 0.00 45.62 4.01
83 84 3.260475 TGATGAGGTTACCGATGTTGG 57.740 47.619 0.00 0.00 0.00 3.77
95 96 0.544357 TCCCACTCGGTTGATGAGGT 60.544 55.000 0.00 0.00 37.79 3.85
101 102 1.480954 GCTTATCTCCCACTCGGTTGA 59.519 52.381 0.00 0.00 0.00 3.18
107 108 1.480954 TGGTTCGCTTATCTCCCACTC 59.519 52.381 0.00 0.00 0.00 3.51
113 114 6.621596 GCCAAATATGATGGTTCGCTTATCTC 60.622 42.308 9.02 0.00 40.23 2.75
120 121 3.648339 ATGCCAAATATGATGGTTCGC 57.352 42.857 9.02 0.00 40.23 4.70
123 124 5.451798 GGAACGAATGCCAAATATGATGGTT 60.452 40.000 9.02 0.00 40.23 3.67
141 142 1.032794 CCGAGGAGATGATGGAACGA 58.967 55.000 0.00 0.00 0.00 3.85
146 147 2.484417 CCTGAAACCGAGGAGATGATGG 60.484 54.545 0.00 0.00 31.48 3.51
149 150 1.195115 CCCTGAAACCGAGGAGATGA 58.805 55.000 0.00 0.00 31.48 2.92
177 180 8.974060 AAGGTTTATCTGAAGTGTAACAGAAA 57.026 30.769 0.00 0.00 44.47 2.52
182 185 9.590088 CGTTTAAAGGTTTATCTGAAGTGTAAC 57.410 33.333 0.00 0.00 0.00 2.50
186 189 7.041644 TGACCGTTTAAAGGTTTATCTGAAGTG 60.042 37.037 3.79 0.00 43.01 3.16
192 195 8.631480 AAGATTGACCGTTTAAAGGTTTATCT 57.369 30.769 15.95 15.95 43.01 1.98
195 198 7.804843 TGAAGATTGACCGTTTAAAGGTTTA 57.195 32.000 3.79 0.00 43.01 2.01
205 208 8.561738 ACTTAAACATATGAAGATTGACCGTT 57.438 30.769 10.38 0.00 0.00 4.44
207 210 8.548721 GGTACTTAAACATATGAAGATTGACCG 58.451 37.037 10.38 0.00 0.00 4.79
209 212 8.837389 GGGGTACTTAAACATATGAAGATTGAC 58.163 37.037 10.38 0.05 0.00 3.18
212 215 9.185680 GTTGGGGTACTTAAACATATGAAGATT 57.814 33.333 10.38 1.80 0.00 2.40
213 216 7.778382 GGTTGGGGTACTTAAACATATGAAGAT 59.222 37.037 10.38 0.00 0.00 2.40
215 218 6.037830 CGGTTGGGGTACTTAAACATATGAAG 59.962 42.308 10.38 5.42 0.00 3.02
216 219 5.881443 CGGTTGGGGTACTTAAACATATGAA 59.119 40.000 10.38 0.00 0.00 2.57
217 220 5.189342 TCGGTTGGGGTACTTAAACATATGA 59.811 40.000 10.38 0.00 0.00 2.15
232 235 6.062095 AGTGAAATTAATCTATCGGTTGGGG 58.938 40.000 0.00 0.00 0.00 4.96
237 240 9.877178 GATGGATAGTGAAATTAATCTATCGGT 57.123 33.333 12.36 6.60 39.41 4.69
260 265 4.935352 TGGTGTTTCTTTGGGAAAGATG 57.065 40.909 0.00 0.00 46.15 2.90
261 266 5.366477 ACATTGGTGTTTCTTTGGGAAAGAT 59.634 36.000 0.00 0.00 46.15 2.40
281 286 6.127619 GCATTTCCACTAGCCTAAAGAACATT 60.128 38.462 0.00 0.00 0.00 2.71
283 288 4.700213 GCATTTCCACTAGCCTAAAGAACA 59.300 41.667 0.00 0.00 0.00 3.18
294 299 3.004419 TCGGATACTCGCATTTCCACTAG 59.996 47.826 0.00 0.00 0.00 2.57
302 307 4.755411 TCTCTTTTTCGGATACTCGCATT 58.245 39.130 0.00 0.00 0.00 3.56
330 335 4.644685 GCCAGGTACCACATATGTTCAATT 59.355 41.667 15.94 0.00 0.00 2.32
331 336 4.207165 GCCAGGTACCACATATGTTCAAT 58.793 43.478 15.94 0.00 0.00 2.57
333 338 2.419436 CGCCAGGTACCACATATGTTCA 60.419 50.000 15.94 0.00 0.00 3.18
338 343 0.468226 CCACGCCAGGTACCACATAT 59.532 55.000 15.94 0.00 0.00 1.78
339 344 1.618876 CCCACGCCAGGTACCACATA 61.619 60.000 15.94 0.00 0.00 2.29
377 382 0.671163 CAAAAGCAATGCGCCACCAT 60.671 50.000 4.18 0.00 44.04 3.55
378 383 1.300775 CAAAAGCAATGCGCCACCA 60.301 52.632 4.18 0.00 44.04 4.17
379 384 2.670210 GCAAAAGCAATGCGCCACC 61.670 57.895 4.18 0.00 44.04 4.61
380 385 2.855325 GCAAAAGCAATGCGCCAC 59.145 55.556 4.18 0.00 44.04 5.01
402 407 7.432350 AAATATCTTCTTCCGATGAGCATTC 57.568 36.000 0.00 0.00 0.00 2.67
413 418 7.220875 GCATCCGAAACAAAAATATCTTCTTCC 59.779 37.037 0.00 0.00 0.00 3.46
416 421 7.396540 AGCATCCGAAACAAAAATATCTTCT 57.603 32.000 0.00 0.00 0.00 2.85
418 423 9.921637 TTAAAGCATCCGAAACAAAAATATCTT 57.078 25.926 0.00 0.00 0.00 2.40
422 427 9.698309 TGAATTAAAGCATCCGAAACAAAAATA 57.302 25.926 0.00 0.00 0.00 1.40
423 428 8.600449 TGAATTAAAGCATCCGAAACAAAAAT 57.400 26.923 0.00 0.00 0.00 1.82
424 429 8.494347 CATGAATTAAAGCATCCGAAACAAAAA 58.506 29.630 0.00 0.00 0.00 1.94
434 636 8.947055 ATAAAACACCATGAATTAAAGCATCC 57.053 30.769 0.00 0.00 0.00 3.51
462 664 8.610248 TTTCGACACATAAAGGAAAACATCTA 57.390 30.769 0.00 0.00 0.00 1.98
465 667 8.110860 AGATTTCGACACATAAAGGAAAACAT 57.889 30.769 0.00 0.00 31.24 2.71
466 668 7.504924 AGATTTCGACACATAAAGGAAAACA 57.495 32.000 0.00 0.00 31.24 2.83
467 669 8.797266 AAAGATTTCGACACATAAAGGAAAAC 57.203 30.769 0.00 0.00 31.24 2.43
468 670 9.810545 AAAAAGATTTCGACACATAAAGGAAAA 57.189 25.926 0.00 0.00 31.24 2.29
469 671 9.458374 GAAAAAGATTTCGACACATAAAGGAAA 57.542 29.630 0.00 0.00 35.94 3.13
484 686 7.888250 ATCAGGGTCCATAGAAAAAGATTTC 57.112 36.000 0.00 0.00 44.34 2.17
485 687 9.190317 GTTATCAGGGTCCATAGAAAAAGATTT 57.810 33.333 0.00 0.00 0.00 2.17
486 688 7.499232 CGTTATCAGGGTCCATAGAAAAAGATT 59.501 37.037 0.00 0.00 0.00 2.40
487 689 6.992715 CGTTATCAGGGTCCATAGAAAAAGAT 59.007 38.462 0.00 0.00 0.00 2.40
488 690 6.070424 ACGTTATCAGGGTCCATAGAAAAAGA 60.070 38.462 0.00 0.00 0.00 2.52
489 691 6.113411 ACGTTATCAGGGTCCATAGAAAAAG 58.887 40.000 0.00 0.00 0.00 2.27
490 692 6.057321 ACGTTATCAGGGTCCATAGAAAAA 57.943 37.500 0.00 0.00 0.00 1.94
491 693 5.188163 TGACGTTATCAGGGTCCATAGAAAA 59.812 40.000 0.00 0.00 31.91 2.29
492 694 4.712829 TGACGTTATCAGGGTCCATAGAAA 59.287 41.667 0.00 0.00 31.91 2.52
493 695 4.283337 TGACGTTATCAGGGTCCATAGAA 58.717 43.478 0.00 0.00 31.91 2.10
494 696 3.905968 TGACGTTATCAGGGTCCATAGA 58.094 45.455 0.00 0.00 31.91 1.98
495 697 4.099573 ACTTGACGTTATCAGGGTCCATAG 59.900 45.833 0.00 0.00 38.74 2.23
496 698 4.028131 ACTTGACGTTATCAGGGTCCATA 58.972 43.478 0.00 0.00 38.74 2.74
497 699 2.838202 ACTTGACGTTATCAGGGTCCAT 59.162 45.455 0.00 0.00 38.74 3.41
498 700 2.253610 ACTTGACGTTATCAGGGTCCA 58.746 47.619 0.00 0.00 38.74 4.02
499 701 3.733077 CGTACTTGACGTTATCAGGGTCC 60.733 52.174 0.00 0.00 46.86 4.46
500 702 3.432782 CGTACTTGACGTTATCAGGGTC 58.567 50.000 0.00 0.00 46.86 4.46
501 703 3.498927 CGTACTTGACGTTATCAGGGT 57.501 47.619 0.00 0.00 46.86 4.34
512 714 0.721718 GCCATGTGCTCGTACTTGAC 59.278 55.000 0.00 0.00 36.87 3.18
513 715 0.320050 TGCCATGTGCTCGTACTTGA 59.680 50.000 7.54 0.00 42.00 3.02
514 716 1.155889 TTGCCATGTGCTCGTACTTG 58.844 50.000 7.54 0.00 42.00 3.16
515 717 1.739466 CATTGCCATGTGCTCGTACTT 59.261 47.619 7.54 0.00 42.00 2.24
516 718 1.339055 ACATTGCCATGTGCTCGTACT 60.339 47.619 2.00 0.00 42.46 2.73
517 719 1.086696 ACATTGCCATGTGCTCGTAC 58.913 50.000 2.00 0.00 42.46 3.67
518 720 1.819928 AACATTGCCATGTGCTCGTA 58.180 45.000 3.86 0.00 43.34 3.43
519 721 0.961019 AAACATTGCCATGTGCTCGT 59.039 45.000 3.86 0.00 43.34 4.18
520 722 2.068837 AAAACATTGCCATGTGCTCG 57.931 45.000 3.86 0.14 43.34 5.03
537 739 5.852229 CGCGTAACTAAACTTGCCATAAAAA 59.148 36.000 0.00 0.00 0.00 1.94
538 740 5.049543 ACGCGTAACTAAACTTGCCATAAAA 60.050 36.000 11.67 0.00 0.00 1.52
539 741 4.451774 ACGCGTAACTAAACTTGCCATAAA 59.548 37.500 11.67 0.00 0.00 1.40
540 742 3.995705 ACGCGTAACTAAACTTGCCATAA 59.004 39.130 11.67 0.00 0.00 1.90
541 743 3.368539 CACGCGTAACTAAACTTGCCATA 59.631 43.478 13.44 0.00 0.00 2.74
542 744 2.158841 CACGCGTAACTAAACTTGCCAT 59.841 45.455 13.44 0.00 0.00 4.40
543 745 1.527736 CACGCGTAACTAAACTTGCCA 59.472 47.619 13.44 0.00 0.00 4.92
544 746 1.136169 CCACGCGTAACTAAACTTGCC 60.136 52.381 13.44 0.00 0.00 4.52
545 747 1.794116 TCCACGCGTAACTAAACTTGC 59.206 47.619 13.44 0.00 0.00 4.01
546 748 3.676172 TCATCCACGCGTAACTAAACTTG 59.324 43.478 13.44 0.00 0.00 3.16
559 761 5.633182 ACACAACAAAAATTATCATCCACGC 59.367 36.000 0.00 0.00 0.00 5.34
562 764 7.178274 AGGCTACACAACAAAAATTATCATCCA 59.822 33.333 0.00 0.00 0.00 3.41
565 767 7.322664 CCAGGCTACACAACAAAAATTATCAT 58.677 34.615 0.00 0.00 0.00 2.45
568 770 5.011533 TGCCAGGCTACACAACAAAAATTAT 59.988 36.000 14.15 0.00 0.00 1.28
569 771 4.342378 TGCCAGGCTACACAACAAAAATTA 59.658 37.500 14.15 0.00 0.00 1.40
572 774 2.103373 TGCCAGGCTACACAACAAAAA 58.897 42.857 14.15 0.00 0.00 1.94
576 778 1.993956 AATTGCCAGGCTACACAACA 58.006 45.000 14.15 0.00 0.00 3.33
581 783 3.257127 GGTACAAAAATTGCCAGGCTACA 59.743 43.478 14.15 0.00 0.00 2.74
582 784 3.509967 AGGTACAAAAATTGCCAGGCTAC 59.490 43.478 14.15 3.80 0.00 3.58
587 789 2.556622 ACCGAGGTACAAAAATTGCCAG 59.443 45.455 0.00 0.00 0.00 4.85
590 792 7.646446 AAATAAACCGAGGTACAAAAATTGC 57.354 32.000 0.00 0.00 0.00 3.56
598 800 8.938906 GTTTCTATCAAAATAAACCGAGGTACA 58.061 33.333 0.00 0.00 0.00 2.90
601 803 8.512138 CAAGTTTCTATCAAAATAAACCGAGGT 58.488 33.333 0.00 0.00 33.33 3.85
603 805 9.543018 GACAAGTTTCTATCAAAATAAACCGAG 57.457 33.333 0.00 0.00 33.33 4.63
606 808 9.113876 CACGACAAGTTTCTATCAAAATAAACC 57.886 33.333 0.00 0.00 33.33 3.27
610 812 6.128117 GGGCACGACAAGTTTCTATCAAAATA 60.128 38.462 0.00 0.00 0.00 1.40
611 813 5.335661 GGGCACGACAAGTTTCTATCAAAAT 60.336 40.000 0.00 0.00 0.00 1.82
618 821 0.759959 TGGGGCACGACAAGTTTCTA 59.240 50.000 0.00 0.00 0.00 2.10
628 831 1.529226 CAAATTACAGTGGGGCACGA 58.471 50.000 0.00 0.00 39.64 4.35
633 836 1.756538 GGATGGCAAATTACAGTGGGG 59.243 52.381 0.00 0.00 0.00 4.96
634 837 2.738743 AGGATGGCAAATTACAGTGGG 58.261 47.619 0.00 0.00 0.00 4.61
635 838 3.763360 TCAAGGATGGCAAATTACAGTGG 59.237 43.478 0.00 0.00 0.00 4.00
641 844 4.701651 CACTCACTCAAGGATGGCAAATTA 59.298 41.667 0.00 0.00 0.00 1.40
648 851 3.641434 ATTCCACTCACTCAAGGATGG 57.359 47.619 0.00 0.00 0.00 3.51
652 855 3.743521 TGACAATTCCACTCACTCAAGG 58.256 45.455 0.00 0.00 0.00 3.61
656 859 3.849911 TCGATGACAATTCCACTCACTC 58.150 45.455 0.00 0.00 0.00 3.51
657 860 3.961480 TCGATGACAATTCCACTCACT 57.039 42.857 0.00 0.00 0.00 3.41
660 863 5.757886 TGTTTTTCGATGACAATTCCACTC 58.242 37.500 0.00 0.00 0.00 3.51
671 874 3.000041 CGGTCCTGATGTTTTTCGATGA 59.000 45.455 0.00 0.00 0.00 2.92
682 885 2.111878 GGCATCCCGGTCCTGATG 59.888 66.667 12.56 12.56 41.02 3.07
696 899 0.393448 TACTTGTTAGGTGCGTGGCA 59.607 50.000 0.00 0.00 35.60 4.92
712 915 8.823220 AAACCCAAATGATAAATGCTAGTACT 57.177 30.769 0.00 0.00 0.00 2.73
715 918 8.366359 AGAAAACCCAAATGATAAATGCTAGT 57.634 30.769 0.00 0.00 0.00 2.57
718 921 9.822185 GAATAGAAAACCCAAATGATAAATGCT 57.178 29.630 0.00 0.00 0.00 3.79
754 957 6.218019 CCAAGCATTTTCTGAATTCAACAGA 58.782 36.000 9.88 0.48 41.70 3.41
828 1037 1.407437 GGAATGCCACGGTCAAGATCT 60.407 52.381 0.00 0.00 0.00 2.75
838 1047 1.586154 GGTTGACCTGGAATGCCACG 61.586 60.000 0.00 0.00 39.92 4.94
846 1055 1.911766 GACGAGGGGTTGACCTGGA 60.912 63.158 0.00 0.00 42.10 3.86
934 1145 1.077787 TTAATGGTCAGCGGGCCAG 60.078 57.895 17.04 0.00 38.27 4.85
943 1154 2.310647 GGGAGGGGAAAGTTAATGGTCA 59.689 50.000 0.00 0.00 0.00 4.02
944 1155 2.357881 GGGGAGGGGAAAGTTAATGGTC 60.358 54.545 0.00 0.00 0.00 4.02
965 1176 2.754552 AGAACAGAGCAGAGCAGAGTAG 59.245 50.000 0.00 0.00 0.00 2.57
966 1177 2.491298 CAGAACAGAGCAGAGCAGAGTA 59.509 50.000 0.00 0.00 0.00 2.59
967 1178 1.273048 CAGAACAGAGCAGAGCAGAGT 59.727 52.381 0.00 0.00 0.00 3.24
1179 2970 2.290577 GCAATGGAAGTCAAGGAGGTCT 60.291 50.000 0.00 0.00 0.00 3.85
1215 3006 1.419387 AGAGTGTCAAGCTCAAGCCTT 59.581 47.619 0.00 0.00 43.38 4.35
1217 3008 1.437625 GAGAGTGTCAAGCTCAAGCC 58.562 55.000 0.00 0.00 43.38 4.35
1568 3404 7.408123 CGTAGTATGTTACAGTGTTCTAGAGG 58.592 42.308 0.00 0.00 0.00 3.69
1577 3413 4.604843 TCGTCCGTAGTATGTTACAGTG 57.395 45.455 0.00 0.00 0.00 3.66
1594 3430 1.930100 CCTGCTCATGCGATTCGTC 59.070 57.895 8.03 0.94 43.34 4.20
1839 3679 1.445582 GCCCGTCGTACACCTTGAG 60.446 63.158 0.00 0.00 0.00 3.02
2018 3860 2.881827 CGATCCACGGCGCGTTAA 60.882 61.111 6.90 0.00 38.32 2.01
2076 3918 6.688637 TGGATCATTTTCAGTAATCAGCAG 57.311 37.500 0.00 0.00 0.00 4.24
2077 3919 7.339976 TGATTGGATCATTTTCAGTAATCAGCA 59.660 33.333 0.00 0.00 33.59 4.41
2078 3920 7.709947 TGATTGGATCATTTTCAGTAATCAGC 58.290 34.615 0.00 0.00 33.59 4.26
2125 3967 5.067805 GTCTCCACCATTTGAAATATGGACC 59.932 44.000 15.40 8.35 44.36 4.46
2126 3968 5.888161 AGTCTCCACCATTTGAAATATGGAC 59.112 40.000 15.40 9.91 44.36 4.02
2203 4046 3.680789 GTGCACCGTGCTTAATGTTATC 58.319 45.455 23.52 0.00 45.31 1.75
2240 4089 5.275494 GTGAATAGGACTACTCTCGAAAGC 58.725 45.833 0.00 0.00 0.00 3.51
2327 4210 9.716531 TTCATTTTGCAAATCATGTACCAATAA 57.283 25.926 13.65 0.99 0.00 1.40
2378 4277 4.202274 TGTCATTCCGGAAGTGTGAACTTA 60.202 41.667 23.47 6.40 0.00 2.24
2409 4308 5.453480 CCCAGTTTTCTACTAGTGATAGGGC 60.453 48.000 5.39 0.00 34.56 5.19
2482 4381 2.301346 CCAATGCTCACATTAGTCCCC 58.699 52.381 0.00 0.00 44.83 4.81
2717 4617 3.369052 CGGGCTTATAAACTGGTGTGAGA 60.369 47.826 0.00 0.00 0.00 3.27
2759 4659 7.120432 GGCATCTATTTTCACTTTGAGAGAAGT 59.880 37.037 0.00 0.00 40.37 3.01
2762 4662 5.882557 GGGCATCTATTTTCACTTTGAGAGA 59.117 40.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.