Multiple sequence alignment - TraesCS5D01G142500

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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 TraesCS5D01G142500 chr5D 100.000 4658 0 0 1 4658 228550354 228555011 0.000000e+00 8602.0
1 TraesCS5D01G142500 chr5D 75.397 252 34 15 401 652 513510881 513510658 3.840000e-16 97.1
2 TraesCS5D01G142500 chr5A 93.363 1552 74 10 1315 2865 307206108 307207631 0.000000e+00 2268.0
3 TraesCS5D01G142500 chr5A 95.252 674 29 3 3381 4053 307208338 307209009 0.000000e+00 1064.0
4 TraesCS5D01G142500 chr5A 91.837 637 48 4 2753 3386 307207681 307208316 0.000000e+00 885.0
5 TraesCS5D01G142500 chr5A 96.000 525 11 6 4138 4658 307209322 307209840 0.000000e+00 845.0
6 TraesCS5D01G142500 chr5A 92.164 587 20 9 697 1263 307205317 307205897 0.000000e+00 806.0
7 TraesCS5D01G142500 chr5A 80.810 667 57 26 51 659 307204664 307205317 1.530000e-124 457.0
8 TraesCS5D01G142500 chr5A 96.610 59 2 0 1233 1291 307205975 307206033 1.070000e-16 99.0
9 TraesCS5D01G142500 chr5B 91.593 1594 63 16 1315 2865 254494029 254495594 0.000000e+00 2135.0
10 TraesCS5D01G142500 chr5B 89.640 1332 82 22 2751 4043 254495750 254497064 0.000000e+00 1644.0
11 TraesCS5D01G142500 chr5B 97.276 514 11 2 4146 4658 254497061 254497572 0.000000e+00 869.0
12 TraesCS5D01G142500 chr5B 89.649 570 20 14 725 1263 254493252 254493813 0.000000e+00 689.0
13 TraesCS5D01G142500 chr5B 84.675 646 48 17 51 671 254492637 254493256 8.630000e-167 597.0
14 TraesCS5D01G142500 chr5B 91.304 115 10 0 2751 2865 254495588 254495702 1.740000e-34 158.0
15 TraesCS5D01G142500 chr5B 91.150 113 10 0 2753 2865 254495536 254495648 2.240000e-33 154.0
16 TraesCS5D01G142500 chr5B 91.150 113 10 0 2753 2865 254495644 254495756 2.240000e-33 154.0
17 TraesCS5D01G142500 chr5B 79.399 233 33 7 436 658 594738474 594738247 2.900000e-32 150.0
18 TraesCS5D01G142500 chr5B 85.714 133 19 0 3316 3448 98663310 98663178 1.750000e-29 141.0
19 TraesCS5D01G142500 chr5B 79.147 211 23 7 436 635 495825106 495824906 4.890000e-25 126.0
20 TraesCS5D01G142500 chr5B 96.610 59 2 0 1233 1291 254493891 254493949 1.070000e-16 99.0
21 TraesCS5D01G142500 chr5B 94.737 38 2 0 16 53 277605653 277605690 5.030000e-05 60.2
22 TraesCS5D01G142500 chr7B 95.000 120 5 1 4034 4153 523681967 523682085 2.210000e-43 187.0
23 TraesCS5D01G142500 chr7D 92.913 127 7 2 4032 4157 545096032 545095907 2.860000e-42 183.0
24 TraesCS5D01G142500 chr7D 85.906 149 17 3 3300 3448 101735331 101735187 6.240000e-34 156.0
25 TraesCS5D01G142500 chr7D 80.311 193 20 9 436 622 603748529 603748349 3.780000e-26 130.0
26 TraesCS5D01G142500 chr6A 81.818 231 30 8 436 654 606526924 606527154 2.860000e-42 183.0
27 TraesCS5D01G142500 chr6A 81.567 217 21 13 436 633 415722149 415722365 1.340000e-35 161.0
28 TraesCS5D01G142500 chr6A 85.401 137 19 1 3312 3448 175653587 175653722 1.750000e-29 141.0
29 TraesCS5D01G142500 chr6B 83.019 212 24 7 436 635 720837776 720837565 1.030000e-41 182.0
30 TraesCS5D01G142500 chr3B 94.872 117 5 1 4035 4151 70582219 70582104 1.030000e-41 182.0
31 TraesCS5D01G142500 chr3B 93.496 123 6 2 4031 4153 526281128 526281008 1.030000e-41 182.0
32 TraesCS5D01G142500 chr3A 92.913 127 5 4 4042 4167 585500963 585501086 1.030000e-41 182.0
33 TraesCS5D01G142500 chr3A 85.047 107 11 3 436 537 27292383 27292277 2.290000e-18 104.0
34 TraesCS5D01G142500 chr2D 94.872 117 5 1 4033 4149 605368322 605368437 1.030000e-41 182.0
35 TraesCS5D01G142500 chr2D 91.473 129 8 3 4031 4158 155516965 155517091 1.720000e-39 174.0
36 TraesCS5D01G142500 chr1A 94.167 120 5 2 4033 4151 387511471 387511353 1.030000e-41 182.0
37 TraesCS5D01G142500 chr2A 92.742 124 8 1 4034 4157 17612979 17612857 1.330000e-40 178.0
38 TraesCS5D01G142500 chr2A 94.118 51 3 0 3 53 542456285 542456335 1.390000e-10 78.7
39 TraesCS5D01G142500 chr4B 81.356 236 26 7 436 653 494690184 494689949 4.790000e-40 176.0
40 TraesCS5D01G142500 chr4B 93.023 43 3 0 110 152 124929221 124929179 3.890000e-06 63.9
41 TraesCS5D01G142500 chr1B 81.356 236 25 10 436 652 684002975 684002740 1.720000e-39 174.0
42 TraesCS5D01G142500 chr1B 81.279 219 22 12 436 635 72710329 72710111 4.820000e-35 159.0
43 TraesCS5D01G142500 chr1B 93.333 45 2 1 15 58 334316037 334316081 1.080000e-06 65.8
44 TraesCS5D01G142500 chr2B 81.735 219 21 11 436 635 384034096 384033878 1.040000e-36 165.0
45 TraesCS5D01G142500 chr2B 78.302 212 33 5 436 637 794996470 794996262 1.760000e-24 124.0
46 TraesCS5D01G142500 chr7A 86.395 147 19 1 3302 3448 701301365 701301510 4.820000e-35 159.0
47 TraesCS5D01G142500 chr7A 83.221 149 25 0 3301 3449 609383417 609383565 2.260000e-28 137.0
48 TraesCS5D01G142500 chr3D 83.660 153 19 4 489 635 87401097 87400945 6.280000e-29 139.0
49 TraesCS5D01G142500 chr1D 82.500 160 24 4 3292 3449 111003369 111003526 2.260000e-28 137.0
50 TraesCS5D01G142500 chr6D 83.562 146 23 1 3300 3445 134288964 134289108 8.130000e-28 135.0
51 TraesCS5D01G142500 chr4A 88.889 108 11 1 547 654 170421904 170421798 1.050000e-26 132.0
52 TraesCS5D01G142500 chr4A 100.000 28 0 0 30 57 97258727 97258700 8.000000e-03 52.8
53 TraesCS5D01G142500 chr4D 93.878 49 3 0 5 53 421087775 421087727 1.800000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G142500 chr5D 228550354 228555011 4657 False 8602.000000 8602 100.000000 1 4658 1 chr5D.!!$F1 4657
1 TraesCS5D01G142500 chr5A 307204664 307209840 5176 False 917.714286 2268 92.290857 51 4658 7 chr5A.!!$F1 4607
2 TraesCS5D01G142500 chr5B 254492637 254497572 4935 False 722.111111 2135 91.449667 51 4658 9 chr5B.!!$F2 4607

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
426 500 0.039165 GCCTGAAAAAGCTCAACCCG 60.039 55.0 0.00 0.0 0.00 5.28 F
1263 1502 0.029834 CGCCCTGCAACAATAGATGC 59.970 55.0 0.00 0.0 43.17 3.91 F
1471 1769 0.250038 GGATGCCTATGCTTCAGCGA 60.250 55.0 7.91 0.0 45.83 4.93 F
1688 2011 0.750249 CGAAGGGGTTGGCAAGTTTT 59.250 50.0 0.00 0.0 0.00 2.43 F
2997 3768 0.173708 AAGAGGTTCGTCGATCTGGC 59.826 55.0 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2344 2682 0.463295 CAGAGGGTGCCATAGTGCAG 60.463 60.000 0.00 0.00 43.02 4.41 R
2710 3048 0.172352 GAGGAAGAGCAGGAGTGACG 59.828 60.000 0.00 0.00 0.00 4.35 R
2894 3664 1.755179 ATCCTCACAAGCCAAATCGG 58.245 50.000 0.00 0.00 38.11 4.18 R
3487 4287 1.339727 GCCTATTCGACAAGTTGGGGT 60.340 52.381 7.96 0.00 0.00 4.95 R
4132 4943 0.256752 TCATACTCCCTCCGTTCGGA 59.743 55.000 13.34 13.34 0.00 4.55 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
43 44 9.389570 CAAAGTTAAGTTACTTATTTTGGGACG 57.610 33.333 21.71 7.77 37.37 4.79
44 45 7.677454 AGTTAAGTTACTTATTTTGGGACGG 57.323 36.000 5.60 0.00 0.00 4.79
45 46 7.452562 AGTTAAGTTACTTATTTTGGGACGGA 58.547 34.615 5.60 0.00 0.00 4.69
46 47 7.605309 AGTTAAGTTACTTATTTTGGGACGGAG 59.395 37.037 5.60 0.00 0.00 4.63
47 48 4.840271 AGTTACTTATTTTGGGACGGAGG 58.160 43.478 0.00 0.00 0.00 4.30
48 49 4.533311 AGTTACTTATTTTGGGACGGAGGA 59.467 41.667 0.00 0.00 0.00 3.71
49 50 5.013391 AGTTACTTATTTTGGGACGGAGGAA 59.987 40.000 0.00 0.00 0.00 3.36
131 132 7.108847 AGTTTAGCATCTCATCTAAGCACTTT 58.891 34.615 0.00 0.00 31.25 2.66
149 150 5.936054 CACTTTTGCATTAGAAGAGACCTG 58.064 41.667 2.88 0.00 0.00 4.00
160 161 2.317371 AGAGACCTGAGCTTCAAGGA 57.683 50.000 15.72 0.00 0.00 3.36
181 201 4.382685 GGATGTCAAGTTCATCTTACCCGA 60.383 45.833 4.96 0.00 40.76 5.14
373 422 8.492673 AACATAAGAGCGTATGAATGAAAAGA 57.507 30.769 9.79 0.00 35.74 2.52
398 447 1.522092 CGCTTAGTCCTGGCCATGA 59.478 57.895 5.51 6.16 0.00 3.07
399 448 0.107703 CGCTTAGTCCTGGCCATGAA 60.108 55.000 12.76 0.00 0.00 2.57
402 451 2.879756 GCTTAGTCCTGGCCATGAACAA 60.880 50.000 12.76 8.54 0.00 2.83
405 454 0.251341 GTCCTGGCCATGAACAACCT 60.251 55.000 12.76 0.00 0.00 3.50
410 459 4.850193 CCATGAACAACCTGGCCT 57.150 55.556 3.32 0.00 0.00 5.19
413 487 1.619654 CATGAACAACCTGGCCTGAA 58.380 50.000 11.88 0.00 0.00 3.02
414 488 1.962807 CATGAACAACCTGGCCTGAAA 59.037 47.619 11.88 0.00 0.00 2.69
415 489 2.151502 TGAACAACCTGGCCTGAAAA 57.848 45.000 11.88 0.00 0.00 2.29
416 490 2.461695 TGAACAACCTGGCCTGAAAAA 58.538 42.857 11.88 0.00 0.00 1.94
421 495 0.185901 ACCTGGCCTGAAAAAGCTCA 59.814 50.000 11.88 0.00 0.00 4.26
422 496 1.331214 CCTGGCCTGAAAAAGCTCAA 58.669 50.000 11.88 0.00 0.00 3.02
423 497 1.000171 CCTGGCCTGAAAAAGCTCAAC 60.000 52.381 11.88 0.00 0.00 3.18
424 498 1.000171 CTGGCCTGAAAAAGCTCAACC 60.000 52.381 3.32 0.00 0.00 3.77
425 499 0.318441 GGCCTGAAAAAGCTCAACCC 59.682 55.000 0.00 0.00 0.00 4.11
426 500 0.039165 GCCTGAAAAAGCTCAACCCG 60.039 55.000 0.00 0.00 0.00 5.28
427 501 0.598065 CCTGAAAAAGCTCAACCCGG 59.402 55.000 0.00 0.00 0.00 5.73
428 502 0.039165 CTGAAAAAGCTCAACCCGGC 60.039 55.000 0.00 0.00 0.00 6.13
429 503 1.289066 GAAAAAGCTCAACCCGGCC 59.711 57.895 0.00 0.00 0.00 6.13
430 504 1.152546 AAAAAGCTCAACCCGGCCT 60.153 52.632 0.00 0.00 0.00 5.19
431 505 1.463553 AAAAAGCTCAACCCGGCCTG 61.464 55.000 0.00 0.00 0.00 4.85
432 506 3.868200 AAAGCTCAACCCGGCCTGG 62.868 63.158 12.40 12.40 37.55 4.45
462 536 1.749258 GGCCTAGGTTTTGAGCCCG 60.749 63.158 11.31 0.00 37.66 6.13
465 539 1.450025 CCTAGGTTTTGAGCCCGAAC 58.550 55.000 0.00 0.00 0.00 3.95
466 540 1.271163 CCTAGGTTTTGAGCCCGAACA 60.271 52.381 0.00 0.00 0.00 3.18
469 543 0.168128 GGTTTTGAGCCCGAACATCG 59.832 55.000 0.00 0.00 40.07 3.84
479 553 4.090588 GAACATCGGGCCCGGTCA 62.091 66.667 42.36 25.80 40.25 4.02
511 585 4.095782 TGTTTTTGCGCTTTACTGAAGAGT 59.904 37.500 9.73 0.00 37.47 3.24
516 590 1.201647 CGCTTTACTGAAGAGTCCCGA 59.798 52.381 0.00 0.00 37.57 5.14
517 591 2.608268 GCTTTACTGAAGAGTCCCGAC 58.392 52.381 0.00 0.00 37.57 4.79
518 592 2.674462 GCTTTACTGAAGAGTCCCGACC 60.674 54.545 0.00 0.00 37.57 4.79
519 593 1.553706 TTACTGAAGAGTCCCGACCC 58.446 55.000 0.00 0.00 33.21 4.46
520 594 0.406750 TACTGAAGAGTCCCGACCCA 59.593 55.000 0.00 0.00 33.21 4.51
521 595 0.471211 ACTGAAGAGTCCCGACCCAA 60.471 55.000 0.00 0.00 0.00 4.12
522 596 0.247736 CTGAAGAGTCCCGACCCAAG 59.752 60.000 0.00 0.00 0.00 3.61
523 597 1.192146 TGAAGAGTCCCGACCCAAGG 61.192 60.000 0.00 0.00 0.00 3.61
524 598 2.523453 GAAGAGTCCCGACCCAAGGC 62.523 65.000 0.00 0.00 0.00 4.35
525 599 4.097361 GAGTCCCGACCCAAGGCC 62.097 72.222 0.00 0.00 0.00 5.19
540 614 0.109723 AGGCCCGCTGACTTTTGTAA 59.890 50.000 0.00 0.00 0.00 2.41
543 617 1.810151 GCCCGCTGACTTTTGTAATGA 59.190 47.619 0.00 0.00 0.00 2.57
544 618 2.423538 GCCCGCTGACTTTTGTAATGAT 59.576 45.455 0.00 0.00 0.00 2.45
624 703 0.543410 TCTACCTCGGGCTTGGTCAA 60.543 55.000 0.00 0.00 37.74 3.18
671 771 6.237996 CGTATAATTTGCGCTAGACAAGGAAA 60.238 38.462 9.73 0.00 0.00 3.13
672 772 3.831715 ATTTGCGCTAGACAAGGAAAC 57.168 42.857 9.73 0.00 0.00 2.78
673 773 2.248280 TTGCGCTAGACAAGGAAACA 57.752 45.000 9.73 0.00 0.00 2.83
674 774 1.508632 TGCGCTAGACAAGGAAACAC 58.491 50.000 9.73 0.00 0.00 3.32
675 775 0.796927 GCGCTAGACAAGGAAACACC 59.203 55.000 0.00 0.00 39.35 4.16
676 776 1.876416 GCGCTAGACAAGGAAACACCA 60.876 52.381 0.00 0.00 42.04 4.17
677 777 2.069273 CGCTAGACAAGGAAACACCAG 58.931 52.381 0.00 0.00 42.04 4.00
678 778 1.807142 GCTAGACAAGGAAACACCAGC 59.193 52.381 0.00 0.00 42.04 4.85
679 779 2.810400 GCTAGACAAGGAAACACCAGCA 60.810 50.000 0.00 0.00 42.04 4.41
680 780 1.972872 AGACAAGGAAACACCAGCAG 58.027 50.000 0.00 0.00 42.04 4.24
681 781 1.490490 AGACAAGGAAACACCAGCAGA 59.510 47.619 0.00 0.00 42.04 4.26
682 782 2.107204 AGACAAGGAAACACCAGCAGAT 59.893 45.455 0.00 0.00 42.04 2.90
683 783 2.485814 GACAAGGAAACACCAGCAGATC 59.514 50.000 0.00 0.00 42.04 2.75
684 784 1.815003 CAAGGAAACACCAGCAGATCC 59.185 52.381 0.00 0.00 42.04 3.36
685 785 1.366319 AGGAAACACCAGCAGATCCT 58.634 50.000 0.00 0.00 42.04 3.24
686 786 2.551270 AGGAAACACCAGCAGATCCTA 58.449 47.619 0.00 0.00 42.04 2.94
687 787 2.912956 AGGAAACACCAGCAGATCCTAA 59.087 45.455 0.00 0.00 42.04 2.69
688 788 3.330701 AGGAAACACCAGCAGATCCTAAA 59.669 43.478 0.00 0.00 42.04 1.85
689 789 4.079253 GGAAACACCAGCAGATCCTAAAA 58.921 43.478 0.00 0.00 38.79 1.52
690 790 4.522789 GGAAACACCAGCAGATCCTAAAAA 59.477 41.667 0.00 0.00 38.79 1.94
711 811 3.801114 AAAAAGGAAACACCAGCAGTC 57.199 42.857 0.00 0.00 42.04 3.51
712 812 1.692411 AAAGGAAACACCAGCAGTCC 58.308 50.000 0.00 0.00 42.04 3.85
713 813 0.178990 AAGGAAACACCAGCAGTCCC 60.179 55.000 0.00 0.00 42.04 4.46
714 814 1.966451 GGAAACACCAGCAGTCCCG 60.966 63.158 0.00 0.00 38.79 5.14
715 815 1.070786 GAAACACCAGCAGTCCCGA 59.929 57.895 0.00 0.00 0.00 5.14
716 816 1.227853 AAACACCAGCAGTCCCGAC 60.228 57.895 0.00 0.00 0.00 4.79
717 817 2.676163 AAACACCAGCAGTCCCGACC 62.676 60.000 0.00 0.00 0.00 4.79
718 818 4.394712 CACCAGCAGTCCCGACCC 62.395 72.222 0.00 0.00 0.00 4.46
721 821 4.135153 CAGCAGTCCCGACCCGAG 62.135 72.222 0.00 0.00 0.00 4.63
722 822 4.361971 AGCAGTCCCGACCCGAGA 62.362 66.667 0.00 0.00 0.00 4.04
723 823 3.827898 GCAGTCCCGACCCGAGAG 61.828 72.222 0.00 0.00 0.00 3.20
724 824 2.045242 CAGTCCCGACCCGAGAGA 60.045 66.667 0.00 0.00 0.00 3.10
725 825 2.115911 CAGTCCCGACCCGAGAGAG 61.116 68.421 0.00 0.00 0.00 3.20
726 826 2.271497 GTCCCGACCCGAGAGAGA 59.729 66.667 0.00 0.00 0.00 3.10
727 827 1.378250 GTCCCGACCCGAGAGAGAA 60.378 63.158 0.00 0.00 0.00 2.87
728 828 0.964358 GTCCCGACCCGAGAGAGAAA 60.964 60.000 0.00 0.00 0.00 2.52
917 1047 2.413765 GAGGCGACGAGGATGACC 59.586 66.667 0.00 0.00 0.00 4.02
1108 1238 1.592743 CACCACGGTCGGTAATCCA 59.407 57.895 2.63 0.00 37.07 3.41
1109 1239 0.037139 CACCACGGTCGGTAATCCAA 60.037 55.000 2.63 0.00 37.07 3.53
1110 1240 0.906775 ACCACGGTCGGTAATCCAAT 59.093 50.000 1.18 0.00 37.57 3.16
1111 1241 1.134610 ACCACGGTCGGTAATCCAATC 60.135 52.381 1.18 0.00 37.57 2.67
1112 1242 1.578583 CACGGTCGGTAATCCAATCC 58.421 55.000 0.00 0.00 0.00 3.01
1124 1254 4.886755 AATCCAATCCCCTCATTCTTCA 57.113 40.909 0.00 0.00 0.00 3.02
1125 1255 4.886755 ATCCAATCCCCTCATTCTTCAA 57.113 40.909 0.00 0.00 0.00 2.69
1126 1256 4.886755 TCCAATCCCCTCATTCTTCAAT 57.113 40.909 0.00 0.00 0.00 2.57
1127 1257 4.539726 TCCAATCCCCTCATTCTTCAATG 58.460 43.478 0.00 0.00 40.91 2.82
1140 1270 1.207811 CTTCAATGCCCCAACCAATCC 59.792 52.381 0.00 0.00 0.00 3.01
1171 1301 7.952671 AGCTATCTCTATCAATTGGTTCGTTA 58.047 34.615 5.42 0.00 0.00 3.18
1172 1302 8.421784 AGCTATCTCTATCAATTGGTTCGTTAA 58.578 33.333 5.42 0.00 0.00 2.01
1214 1344 1.134098 ACCCTGCCACCATTAATCTCG 60.134 52.381 0.00 0.00 0.00 4.04
1263 1502 0.029834 CGCCCTGCAACAATAGATGC 59.970 55.000 0.00 0.00 43.17 3.91
1287 1526 6.210385 GCCCTCATCTCTGAATCAGACTATTA 59.790 42.308 9.18 0.00 35.39 0.98
1298 1563 8.034313 TGAATCAGACTATTAGGCTAAATGGT 57.966 34.615 11.59 9.99 26.27 3.55
1299 1564 8.494433 TGAATCAGACTATTAGGCTAAATGGTT 58.506 33.333 11.59 7.80 26.27 3.67
1300 1565 9.343539 GAATCAGACTATTAGGCTAAATGGTTT 57.656 33.333 11.59 3.42 26.27 3.27
1307 1572 6.961360 ATTAGGCTAAATGGTTTCTTAGGC 57.039 37.500 11.59 7.17 46.01 3.93
1313 1578 1.852633 ATGGTTTCTTAGGCTTGCCC 58.147 50.000 8.17 0.00 0.00 5.36
1383 1678 3.565307 TCCCAATAACCATGATCTTGCC 58.435 45.455 3.07 0.00 0.00 4.52
1393 1688 2.857186 TGATCTTGCCAGTGTTGCTA 57.143 45.000 0.00 0.00 0.00 3.49
1471 1769 0.250038 GGATGCCTATGCTTCAGCGA 60.250 55.000 7.91 0.00 45.83 4.93
1496 1794 1.618343 CGATTGGCCACCTTTCCTTTT 59.382 47.619 3.88 0.00 0.00 2.27
1667 1990 2.587247 GCACTCAGGTCAGGCTGGA 61.587 63.158 15.73 2.67 0.00 3.86
1688 2011 0.750249 CGAAGGGGTTGGCAAGTTTT 59.250 50.000 0.00 0.00 0.00 2.43
1689 2012 1.957877 CGAAGGGGTTGGCAAGTTTTA 59.042 47.619 0.00 0.00 0.00 1.52
1690 2013 2.560981 CGAAGGGGTTGGCAAGTTTTAT 59.439 45.455 0.00 0.00 0.00 1.40
1691 2014 3.366985 CGAAGGGGTTGGCAAGTTTTATC 60.367 47.826 0.00 0.00 0.00 1.75
1692 2015 3.542969 AGGGGTTGGCAAGTTTTATCT 57.457 42.857 0.00 0.00 0.00 1.98
1693 2016 3.856900 AGGGGTTGGCAAGTTTTATCTT 58.143 40.909 0.00 0.00 0.00 2.40
1694 2017 4.231273 AGGGGTTGGCAAGTTTTATCTTT 58.769 39.130 0.00 0.00 0.00 2.52
1714 2037 8.978564 ATCTTTTATGTGACTCAGATATAGCG 57.021 34.615 0.00 0.00 0.00 4.26
1725 2048 3.384789 TCAGATATAGCGGAAGTTGTGCT 59.615 43.478 4.09 4.09 42.58 4.40
1730 2053 1.954146 GCGGAAGTTGTGCTCGTGA 60.954 57.895 0.00 0.00 0.00 4.35
1800 2131 5.929415 CCCGTACATTTGTAATTTGGCTTTT 59.071 36.000 0.00 0.00 31.52 2.27
1804 2135 7.381139 CGTACATTTGTAATTTGGCTTTTGACT 59.619 33.333 0.00 0.00 31.52 3.41
1987 2325 4.515191 ACTGCAATACTTGTTCGTGATGTT 59.485 37.500 0.00 0.00 0.00 2.71
2146 2484 2.102578 GGACATGAAATTGGGACAGGG 58.897 52.381 0.00 0.00 42.39 4.45
2152 2490 3.855668 TGAAATTGGGACAGGGACATTT 58.144 40.909 0.00 0.00 42.39 2.32
2206 2544 4.115199 GCGGATGGCCCTCCTTGT 62.115 66.667 23.03 0.00 34.80 3.16
2323 2661 1.379146 GTCGCCCCCTTTCTTCCTT 59.621 57.895 0.00 0.00 0.00 3.36
2344 2682 1.515521 CCAAAGCACGTGGAGGAACC 61.516 60.000 18.88 0.00 38.54 3.62
2482 2820 1.670406 CTGCAAGACGGAGCTGCTT 60.670 57.895 2.53 0.00 34.07 3.91
2710 3048 2.143925 GTAGAGCACTGGGTGAACAAC 58.856 52.381 1.57 0.00 35.23 3.32
2817 3479 0.948678 GCTAAAACGGCAACACCAGA 59.051 50.000 0.00 0.00 39.03 3.86
2847 3617 3.081409 GCTACCAGGCGAAGGGGA 61.081 66.667 0.00 0.00 0.00 4.81
2862 3632 2.248248 AGGGGAACTTGCTAAAAAGGC 58.752 47.619 0.00 0.00 0.00 4.35
2894 3664 1.343821 CTGCGGTATTGTCGTTCGC 59.656 57.895 0.00 0.00 45.60 4.70
2915 3686 3.278574 CCGATTTGGCTTGTGAGGATTA 58.721 45.455 0.00 0.00 0.00 1.75
2969 3740 9.288124 CACGCAATTCTTCATGTAAATTAATCA 57.712 29.630 0.00 0.00 0.00 2.57
2997 3768 0.173708 AAGAGGTTCGTCGATCTGGC 59.826 55.000 0.00 0.00 0.00 4.85
3039 3811 4.301072 TCCACTTATTAACTTGCTGCCT 57.699 40.909 0.00 0.00 0.00 4.75
3047 3819 1.458639 AACTTGCTGCCTGAACCTGC 61.459 55.000 0.00 0.00 0.00 4.85
3147 3920 4.093556 GGAACTTCTAGCCAAGATTTGTCG 59.906 45.833 0.00 0.00 33.05 4.35
3239 4012 1.075601 TGCTCTTCCCCTTCCACAAT 58.924 50.000 0.00 0.00 0.00 2.71
3287 4060 3.009723 TGAAGCCTTTTCCTCGCAATAG 58.990 45.455 0.00 0.00 0.00 1.73
3296 4069 5.401531 TTTCCTCGCAATAGTGTCTAGTT 57.598 39.130 0.00 0.00 0.00 2.24
3309 4082 4.896482 AGTGTCTAGTTTCACCTCTGTTCT 59.104 41.667 10.17 0.00 35.45 3.01
3321 4094 6.634805 TCACCTCTGTTCTGAATCATAAGAC 58.365 40.000 0.00 0.00 0.00 3.01
3371 4144 4.151258 ACGTGCTGAAATGAATGAACAG 57.849 40.909 0.00 0.00 0.00 3.16
3388 4188 4.036262 TGAACAGGCACACTAAAACACATC 59.964 41.667 0.00 0.00 0.00 3.06
3391 4191 5.373222 ACAGGCACACTAAAACACATCTAA 58.627 37.500 0.00 0.00 0.00 2.10
3396 4196 6.959311 GGCACACTAAAACACATCTAAATACG 59.041 38.462 0.00 0.00 0.00 3.06
3398 4198 8.649841 GCACACTAAAACACATCTAAATACGTA 58.350 33.333 0.00 0.00 0.00 3.57
3467 4267 8.861086 GGGAGTAACTCTTATGTTCTATCATCA 58.139 37.037 0.00 0.00 0.00 3.07
3487 4287 8.956533 TCATCATACAATTCACGAATTCCTTA 57.043 30.769 2.00 0.00 38.84 2.69
3491 4291 4.014406 ACAATTCACGAATTCCTTACCCC 58.986 43.478 2.00 0.00 38.84 4.95
3505 4305 4.081309 TCCTTACCCCAACTTGTCGAATAG 60.081 45.833 0.00 0.00 0.00 1.73
3545 4345 6.262049 TCTCAGTTGCAGTTTTGTAATGCTAA 59.738 34.615 0.00 0.00 40.62 3.09
3548 4348 7.381948 TCAGTTGCAGTTTTGTAATGCTAAATG 59.618 33.333 0.00 0.00 40.62 2.32
3656 4456 5.410439 ACCGTACTAATTGTGGCTACTTTTG 59.590 40.000 0.64 0.00 0.00 2.44
3683 4483 5.127356 CCTCGGTAATAACTCCAGAACTTCT 59.873 44.000 0.00 0.00 0.00 2.85
3769 4579 7.581011 ATTCAACTGTGTGTGTTTCTTTTTC 57.419 32.000 0.00 0.00 0.00 2.29
3845 4655 1.107538 CATCCATGAAGGCCTGCCAG 61.108 60.000 5.69 0.00 38.92 4.85
3918 4729 7.094549 CCACTTAAATTGTGAAATCGGGTAGAA 60.095 37.037 0.00 0.00 37.60 2.10
3959 4770 3.317993 CGAAGTTTGTTGTTCCTTGGGAT 59.682 43.478 0.00 0.00 0.00 3.85
4053 4864 4.670765 TCTTAGAAAGTACTCCCTCCGTT 58.329 43.478 0.00 0.00 0.00 4.44
4054 4865 4.704057 TCTTAGAAAGTACTCCCTCCGTTC 59.296 45.833 0.00 0.00 0.00 3.95
4055 4866 1.817447 AGAAAGTACTCCCTCCGTTCG 59.183 52.381 0.00 0.00 0.00 3.95
4059 4870 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
4062 4873 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
4063 4874 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
4064 4875 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
4066 4877 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
4068 4879 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
4069 4880 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
4070 4881 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
4071 4882 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
4072 4883 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
4073 4884 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
4074 4885 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
4075 4886 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
4077 4888 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
4078 4889 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
4081 4892 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
4083 4894 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
4084 4895 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
4085 4896 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
4086 4897 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
4087 4898 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
4088 4899 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
4089 4900 6.016192 TGTCTCGGAAATGGATGTATCTAGAC 60.016 42.308 0.00 0.00 0.00 2.59
4090 4901 5.181433 TCTCGGAAATGGATGTATCTAGACG 59.819 44.000 0.00 0.00 0.00 4.18
4091 4902 4.825634 TCGGAAATGGATGTATCTAGACGT 59.174 41.667 0.00 0.00 0.00 4.34
4092 4903 5.999600 TCGGAAATGGATGTATCTAGACGTA 59.000 40.000 0.00 0.00 0.00 3.57
4093 4904 6.657966 TCGGAAATGGATGTATCTAGACGTAT 59.342 38.462 0.00 0.00 0.00 3.06
4094 4905 7.176165 TCGGAAATGGATGTATCTAGACGTATT 59.824 37.037 0.00 0.00 0.00 1.89
4095 4906 7.813148 CGGAAATGGATGTATCTAGACGTATTT 59.187 37.037 0.00 0.00 0.00 1.40
4096 4907 9.490379 GGAAATGGATGTATCTAGACGTATTTT 57.510 33.333 0.00 0.00 0.00 1.82
4123 4934 6.778069 AGTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
4124 4935 7.453126 AGTTCTAGATACATCCATTTCCGAGAT 59.547 37.037 0.00 0.00 0.00 2.75
4125 4936 7.163001 TCTAGATACATCCATTTCCGAGATG 57.837 40.000 0.00 0.00 42.49 2.90
4127 4938 6.035368 AGATACATCCATTTCCGAGATGAG 57.965 41.667 6.25 0.00 39.84 2.90
4129 4940 6.721668 AGATACATCCATTTCCGAGATGAGTA 59.278 38.462 6.25 2.14 39.84 2.59
4130 4941 5.614324 ACATCCATTTCCGAGATGAGTAA 57.386 39.130 6.25 0.00 39.84 2.24
4131 4942 6.179906 ACATCCATTTCCGAGATGAGTAAT 57.820 37.500 6.25 0.00 39.84 1.89
4132 4943 6.595682 ACATCCATTTCCGAGATGAGTAATT 58.404 36.000 6.25 0.00 39.84 1.40
4133 4944 6.708054 ACATCCATTTCCGAGATGAGTAATTC 59.292 38.462 6.25 0.00 39.84 2.17
4134 4945 5.611374 TCCATTTCCGAGATGAGTAATTCC 58.389 41.667 0.45 0.00 0.00 3.01
4135 4946 4.449068 CCATTTCCGAGATGAGTAATTCCG 59.551 45.833 0.45 0.00 0.00 4.30
4139 5178 3.043586 CCGAGATGAGTAATTCCGAACG 58.956 50.000 0.00 0.00 0.00 3.95
4157 5196 4.743644 CGAACGGAGGGAGTATGAATTAAC 59.256 45.833 0.00 0.00 0.00 2.01
4191 5231 0.521291 TGAGGCGCGAAGGAATTTTG 59.479 50.000 12.10 0.00 0.00 2.44
4350 5390 7.637229 CAAGTCCAACATAAGATGCTTAGATG 58.363 38.462 0.00 0.00 0.00 2.90
4351 5391 7.129457 AGTCCAACATAAGATGCTTAGATGA 57.871 36.000 0.00 0.00 0.00 2.92
4405 5445 5.123227 TGGGTACTTCTGAACTGAAAAGTG 58.877 41.667 0.00 0.00 34.09 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 9.389570 CGTCCCAAAATAAGTAACTTAACTTTG 57.610 33.333 1.12 1.12 40.20 2.77
18 19 8.570488 CCGTCCCAAAATAAGTAACTTAACTTT 58.430 33.333 0.00 0.00 40.20 2.66
19 20 7.938490 TCCGTCCCAAAATAAGTAACTTAACTT 59.062 33.333 0.00 0.00 42.31 2.66
20 21 7.452562 TCCGTCCCAAAATAAGTAACTTAACT 58.547 34.615 0.00 0.00 29.35 2.24
21 22 7.148356 CCTCCGTCCCAAAATAAGTAACTTAAC 60.148 40.741 0.00 0.00 29.35 2.01
22 23 6.880529 CCTCCGTCCCAAAATAAGTAACTTAA 59.119 38.462 0.00 0.00 29.35 1.85
23 24 6.213195 TCCTCCGTCCCAAAATAAGTAACTTA 59.787 38.462 0.00 0.00 0.00 2.24
24 25 5.013391 TCCTCCGTCCCAAAATAAGTAACTT 59.987 40.000 0.00 0.00 0.00 2.66
25 26 4.533311 TCCTCCGTCCCAAAATAAGTAACT 59.467 41.667 0.00 0.00 0.00 2.24
26 27 4.835678 TCCTCCGTCCCAAAATAAGTAAC 58.164 43.478 0.00 0.00 0.00 2.50
27 28 5.013391 ACTTCCTCCGTCCCAAAATAAGTAA 59.987 40.000 0.00 0.00 0.00 2.24
28 29 4.533311 ACTTCCTCCGTCCCAAAATAAGTA 59.467 41.667 0.00 0.00 0.00 2.24
29 30 3.329814 ACTTCCTCCGTCCCAAAATAAGT 59.670 43.478 0.00 0.00 0.00 2.24
30 31 3.951663 ACTTCCTCCGTCCCAAAATAAG 58.048 45.455 0.00 0.00 0.00 1.73
31 32 4.286549 TGTACTTCCTCCGTCCCAAAATAA 59.713 41.667 0.00 0.00 0.00 1.40
32 33 3.839490 TGTACTTCCTCCGTCCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
33 34 2.640826 TGTACTTCCTCCGTCCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
34 35 2.048601 TGTACTTCCTCCGTCCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
35 36 1.719529 TGTACTTCCTCCGTCCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
36 37 1.345415 GTTGTACTTCCTCCGTCCCAA 59.655 52.381 0.00 0.00 0.00 4.12
37 38 0.971386 GTTGTACTTCCTCCGTCCCA 59.029 55.000 0.00 0.00 0.00 4.37
38 39 0.971386 TGTTGTACTTCCTCCGTCCC 59.029 55.000 0.00 0.00 0.00 4.46
39 40 2.036862 ACTTGTTGTACTTCCTCCGTCC 59.963 50.000 0.00 0.00 0.00 4.79
40 41 3.382048 ACTTGTTGTACTTCCTCCGTC 57.618 47.619 0.00 0.00 0.00 4.79
41 42 3.832615 AACTTGTTGTACTTCCTCCGT 57.167 42.857 0.00 0.00 0.00 4.69
42 43 4.151867 GCTTAACTTGTTGTACTTCCTCCG 59.848 45.833 0.00 0.00 0.00 4.63
43 44 5.061179 TGCTTAACTTGTTGTACTTCCTCC 58.939 41.667 0.00 0.00 0.00 4.30
44 45 6.803154 ATGCTTAACTTGTTGTACTTCCTC 57.197 37.500 0.00 0.00 0.00 3.71
45 46 9.379791 GTATATGCTTAACTTGTTGTACTTCCT 57.620 33.333 0.00 0.00 0.00 3.36
46 47 9.158233 TGTATATGCTTAACTTGTTGTACTTCC 57.842 33.333 0.00 0.00 0.00 3.46
47 48 9.968743 GTGTATATGCTTAACTTGTTGTACTTC 57.031 33.333 0.00 0.00 0.00 3.01
48 49 9.496873 TGTGTATATGCTTAACTTGTTGTACTT 57.503 29.630 0.00 0.00 0.00 2.24
49 50 9.667107 ATGTGTATATGCTTAACTTGTTGTACT 57.333 29.630 0.00 0.00 0.00 2.73
131 132 3.517100 AGCTCAGGTCTCTTCTAATGCAA 59.483 43.478 0.00 0.00 0.00 4.08
149 150 4.067896 TGAACTTGACATCCTTGAAGCTC 58.932 43.478 0.00 0.00 0.00 4.09
160 161 4.504858 GTCGGGTAAGATGAACTTGACAT 58.495 43.478 0.00 0.00 39.38 3.06
330 379 7.929785 TCTTATGTTTCCTTACGAACAGAGTTT 59.070 33.333 0.00 0.00 38.95 2.66
331 380 7.439381 TCTTATGTTTCCTTACGAACAGAGTT 58.561 34.615 0.00 0.00 38.95 3.01
332 381 6.989659 TCTTATGTTTCCTTACGAACAGAGT 58.010 36.000 0.00 0.00 38.95 3.24
337 386 4.624452 ACGCTCTTATGTTTCCTTACGAAC 59.376 41.667 0.00 0.00 0.00 3.95
345 394 6.844696 TCATTCATACGCTCTTATGTTTCC 57.155 37.500 0.00 0.00 32.17 3.13
373 422 1.959042 CCAGGACTAAGCGCAATCAT 58.041 50.000 11.47 0.00 0.00 2.45
398 447 1.138859 GCTTTTTCAGGCCAGGTTGTT 59.861 47.619 5.01 0.00 0.00 2.83
399 448 0.752658 GCTTTTTCAGGCCAGGTTGT 59.247 50.000 5.01 0.00 0.00 3.32
402 451 0.185901 TGAGCTTTTTCAGGCCAGGT 59.814 50.000 5.01 0.00 0.00 4.00
405 454 1.039856 GGTTGAGCTTTTTCAGGCCA 58.960 50.000 5.01 0.00 0.00 5.36
410 459 1.460273 GGCCGGGTTGAGCTTTTTCA 61.460 55.000 2.18 0.00 0.00 2.69
413 487 1.903404 CAGGCCGGGTTGAGCTTTT 60.903 57.895 2.18 0.00 0.00 2.27
414 488 2.282462 CAGGCCGGGTTGAGCTTT 60.282 61.111 2.18 0.00 0.00 3.51
415 489 4.351054 CCAGGCCGGGTTGAGCTT 62.351 66.667 14.74 0.00 0.00 3.74
462 536 4.090588 TGACCGGGCCCGATGTTC 62.091 66.667 45.44 31.29 42.83 3.18
477 551 2.197324 AAAAACAGCGGGCCCTGA 59.803 55.556 22.43 0.00 36.67 3.86
479 553 3.615709 GCAAAAACAGCGGGCCCT 61.616 61.111 22.43 0.00 0.00 5.19
517 591 3.868200 AAAGTCAGCGGGCCTTGGG 62.868 63.158 0.84 0.00 0.00 4.12
518 592 1.903404 AAAAGTCAGCGGGCCTTGG 60.903 57.895 0.84 0.00 0.00 3.61
519 593 1.286880 CAAAAGTCAGCGGGCCTTG 59.713 57.895 0.84 0.00 0.00 3.61
520 594 0.109723 TACAAAAGTCAGCGGGCCTT 59.890 50.000 0.84 0.00 0.00 4.35
521 595 0.109723 TTACAAAAGTCAGCGGGCCT 59.890 50.000 0.84 0.00 0.00 5.19
522 596 1.135402 CATTACAAAAGTCAGCGGGCC 60.135 52.381 0.00 0.00 0.00 5.80
523 597 1.810151 TCATTACAAAAGTCAGCGGGC 59.190 47.619 0.00 0.00 0.00 6.13
524 598 3.181497 CCATCATTACAAAAGTCAGCGGG 60.181 47.826 0.00 0.00 0.00 6.13
525 599 3.181497 CCCATCATTACAAAAGTCAGCGG 60.181 47.826 0.00 0.00 0.00 5.52
526 600 3.731867 GCCCATCATTACAAAAGTCAGCG 60.732 47.826 0.00 0.00 0.00 5.18
529 603 4.220382 CCAAGCCCATCATTACAAAAGTCA 59.780 41.667 0.00 0.00 0.00 3.41
593 672 1.550976 CGAGGTAGAAAACTCAGGCCT 59.449 52.381 0.00 0.00 33.36 5.19
646 725 4.743151 TCCTTGTCTAGCGCAAATTATACG 59.257 41.667 11.47 0.00 0.00 3.06
691 791 2.430694 GGACTGCTGGTGTTTCCTTTTT 59.569 45.455 0.00 0.00 37.07 1.94
692 792 2.031870 GGACTGCTGGTGTTTCCTTTT 58.968 47.619 0.00 0.00 37.07 2.27
693 793 1.692411 GGACTGCTGGTGTTTCCTTT 58.308 50.000 0.00 0.00 37.07 3.11
694 794 0.178990 GGGACTGCTGGTGTTTCCTT 60.179 55.000 0.00 0.00 37.07 3.36
695 795 1.456287 GGGACTGCTGGTGTTTCCT 59.544 57.895 0.00 0.00 37.07 3.36
696 796 1.966451 CGGGACTGCTGGTGTTTCC 60.966 63.158 0.00 0.00 0.00 3.13
697 797 1.070786 TCGGGACTGCTGGTGTTTC 59.929 57.895 0.00 0.00 0.00 2.78
698 798 1.227853 GTCGGGACTGCTGGTGTTT 60.228 57.895 0.00 0.00 0.00 2.83
699 799 2.426023 GTCGGGACTGCTGGTGTT 59.574 61.111 0.00 0.00 0.00 3.32
700 800 3.626924 GGTCGGGACTGCTGGTGT 61.627 66.667 0.00 0.00 0.00 4.16
701 801 4.394712 GGGTCGGGACTGCTGGTG 62.395 72.222 0.00 0.00 0.00 4.17
704 804 4.135153 CTCGGGTCGGGACTGCTG 62.135 72.222 0.00 0.00 0.00 4.41
705 805 4.361971 TCTCGGGTCGGGACTGCT 62.362 66.667 0.00 0.00 28.48 4.24
706 806 3.827898 CTCTCGGGTCGGGACTGC 61.828 72.222 0.00 0.00 31.17 4.40
707 807 2.045242 TCTCTCGGGTCGGGACTG 60.045 66.667 0.00 0.00 31.17 3.51
708 808 1.849975 TTCTCTCTCGGGTCGGGACT 61.850 60.000 0.00 0.00 31.17 3.85
709 809 0.964358 TTTCTCTCTCGGGTCGGGAC 60.964 60.000 0.00 0.00 31.17 4.46
710 810 0.680280 CTTTCTCTCTCGGGTCGGGA 60.680 60.000 0.00 0.00 34.26 5.14
711 811 0.680280 TCTTTCTCTCTCGGGTCGGG 60.680 60.000 0.00 0.00 0.00 5.14
712 812 0.736053 CTCTTTCTCTCTCGGGTCGG 59.264 60.000 0.00 0.00 0.00 4.79
713 813 1.668751 CTCTCTTTCTCTCTCGGGTCG 59.331 57.143 0.00 0.00 0.00 4.79
714 814 2.681344 GACTCTCTTTCTCTCTCGGGTC 59.319 54.545 0.00 0.00 0.00 4.46
715 815 2.718563 GACTCTCTTTCTCTCTCGGGT 58.281 52.381 0.00 0.00 0.00 5.28
716 816 1.668751 CGACTCTCTTTCTCTCTCGGG 59.331 57.143 0.00 0.00 0.00 5.14
717 817 2.095213 CACGACTCTCTTTCTCTCTCGG 59.905 54.545 0.00 0.00 0.00 4.63
718 818 2.095213 CCACGACTCTCTTTCTCTCTCG 59.905 54.545 0.00 0.00 0.00 4.04
719 819 3.078837 ACCACGACTCTCTTTCTCTCTC 58.921 50.000 0.00 0.00 0.00 3.20
720 820 3.078837 GACCACGACTCTCTTTCTCTCT 58.921 50.000 0.00 0.00 0.00 3.10
721 821 2.159626 CGACCACGACTCTCTTTCTCTC 60.160 54.545 0.00 0.00 42.66 3.20
722 822 1.807742 CGACCACGACTCTCTTTCTCT 59.192 52.381 0.00 0.00 42.66 3.10
723 823 1.536331 ACGACCACGACTCTCTTTCTC 59.464 52.381 0.00 0.00 42.66 2.87
724 824 1.536331 GACGACCACGACTCTCTTTCT 59.464 52.381 0.00 0.00 42.66 2.52
725 825 1.725292 CGACGACCACGACTCTCTTTC 60.725 57.143 0.00 0.00 42.66 2.62
726 826 0.237761 CGACGACCACGACTCTCTTT 59.762 55.000 0.00 0.00 42.66 2.52
727 827 1.867615 CGACGACCACGACTCTCTT 59.132 57.895 0.00 0.00 42.66 2.85
728 828 2.678956 GCGACGACCACGACTCTCT 61.679 63.158 0.00 0.00 42.66 3.10
777 883 1.600636 CAAGGGCACGAGGAAAGCA 60.601 57.895 0.00 0.00 0.00 3.91
897 1012 4.933064 CATCCTCGTCGCCTCGGC 62.933 72.222 0.00 0.00 37.85 5.54
898 1013 3.209812 TCATCCTCGTCGCCTCGG 61.210 66.667 0.00 0.00 0.00 4.63
917 1047 1.006102 CCGGGGCTAGAGCATTACG 60.006 63.158 3.54 2.14 44.36 3.18
1108 1238 3.303049 GGCATTGAAGAATGAGGGGATT 58.697 45.455 0.00 0.00 41.49 3.01
1109 1239 2.425392 GGGCATTGAAGAATGAGGGGAT 60.425 50.000 0.00 0.00 41.49 3.85
1110 1240 1.063717 GGGCATTGAAGAATGAGGGGA 60.064 52.381 0.00 0.00 41.49 4.81
1111 1241 1.406903 GGGCATTGAAGAATGAGGGG 58.593 55.000 0.00 0.00 41.49 4.79
1112 1242 1.342275 TGGGGCATTGAAGAATGAGGG 60.342 52.381 0.00 0.00 41.49 4.30
1124 1254 1.306911 GGGGATTGGTTGGGGCATT 60.307 57.895 0.00 0.00 0.00 3.56
1125 1255 2.368188 GGGGATTGGTTGGGGCAT 59.632 61.111 0.00 0.00 0.00 4.40
1126 1256 4.004635 GGGGGATTGGTTGGGGCA 62.005 66.667 0.00 0.00 0.00 5.36
1140 1270 5.130145 CCAATTGATAGAGATAGCTAGGGGG 59.870 48.000 7.12 0.00 0.00 5.40
1147 1277 8.589335 TTAACGAACCAATTGATAGAGATAGC 57.411 34.615 7.12 0.00 0.00 2.97
1152 1282 8.283291 GGCTAATTAACGAACCAATTGATAGAG 58.717 37.037 7.12 0.00 0.00 2.43
1156 1286 5.587043 TCGGCTAATTAACGAACCAATTGAT 59.413 36.000 7.12 0.00 33.21 2.57
1171 1301 6.206829 GGTGCTTAATTAATCCTCGGCTAATT 59.793 38.462 0.00 7.54 0.00 1.40
1172 1302 5.705905 GGTGCTTAATTAATCCTCGGCTAAT 59.294 40.000 0.00 0.00 0.00 1.73
1175 1305 3.477530 GGTGCTTAATTAATCCTCGGCT 58.522 45.455 0.00 0.00 0.00 5.52
1231 1361 0.671781 CAGGGCGTCTTCAAGGTGAG 60.672 60.000 0.00 0.00 0.00 3.51
1263 1502 6.669125 AATAGTCTGATTCAGAGATGAGGG 57.331 41.667 16.62 0.00 41.46 4.30
1287 1526 4.592997 AGCCTAAGAAACCATTTAGCCT 57.407 40.909 0.00 0.00 0.00 4.58
1298 1563 0.960364 CAGCGGGCAAGCCTAAGAAA 60.960 55.000 11.40 0.00 38.01 2.52
1299 1564 1.377202 CAGCGGGCAAGCCTAAGAA 60.377 57.895 11.40 0.00 38.01 2.52
1300 1565 2.268920 CAGCGGGCAAGCCTAAGA 59.731 61.111 11.40 0.00 38.01 2.10
1323 1618 4.865365 ACTCGACGAAAATCTTCCTCAATC 59.135 41.667 0.00 0.00 0.00 2.67
1324 1619 4.627467 CACTCGACGAAAATCTTCCTCAAT 59.373 41.667 0.00 0.00 0.00 2.57
1393 1688 2.203070 GCCGATCCACCGCTGAAT 60.203 61.111 0.00 0.00 0.00 2.57
1401 1696 0.659957 GCAAGAATGAGCCGATCCAC 59.340 55.000 0.00 0.00 0.00 4.02
1402 1697 0.543277 AGCAAGAATGAGCCGATCCA 59.457 50.000 0.00 0.00 0.00 3.41
1471 1769 0.827507 AAAGGTGGCCAATCGTGCTT 60.828 50.000 7.24 0.00 0.00 3.91
1496 1794 3.248418 TGCTGGTGCTGCTGGGTA 61.248 61.111 0.00 0.00 40.48 3.69
1520 1818 2.691732 CCCCATCCACCATGCCTT 59.308 61.111 0.00 0.00 0.00 4.35
1553 1851 4.497507 CGAAAACTCAAGTGTTTCCCTTCC 60.498 45.833 1.32 0.00 38.98 3.46
1560 1858 3.754323 TGGTGTCGAAAACTCAAGTGTTT 59.246 39.130 0.00 0.00 41.32 2.83
1667 1990 2.282462 CTTGCCAACCCCTTCGCT 60.282 61.111 0.00 0.00 0.00 4.93
1689 2012 8.031864 CCGCTATATCTGAGTCACATAAAAGAT 58.968 37.037 0.00 0.00 0.00 2.40
1690 2013 7.230712 TCCGCTATATCTGAGTCACATAAAAGA 59.769 37.037 0.00 0.00 0.00 2.52
1691 2014 7.371159 TCCGCTATATCTGAGTCACATAAAAG 58.629 38.462 0.00 0.00 0.00 2.27
1692 2015 7.284919 TCCGCTATATCTGAGTCACATAAAA 57.715 36.000 0.00 0.00 0.00 1.52
1693 2016 6.894339 TCCGCTATATCTGAGTCACATAAA 57.106 37.500 0.00 0.00 0.00 1.40
1694 2017 6.490381 ACTTCCGCTATATCTGAGTCACATAA 59.510 38.462 0.00 0.00 0.00 1.90
1714 2037 1.873591 ACAATCACGAGCACAACTTCC 59.126 47.619 0.00 0.00 0.00 3.46
1730 2053 8.641498 ATTCTTAACAGTCCAGATTGAACAAT 57.359 30.769 0.00 0.00 0.00 2.71
1800 2131 7.065803 GCCTTTGTATTACATAGAAAGCAGTCA 59.934 37.037 13.80 0.00 41.91 3.41
1804 2135 6.318648 CAGGCCTTTGTATTACATAGAAAGCA 59.681 38.462 0.00 0.00 41.91 3.91
1889 2227 2.134789 AATGCGGCTTGAGAAGGAAT 57.865 45.000 0.00 0.00 0.00 3.01
1987 2325 5.064707 GTGTACAAGCAAACAAGTCAAGAGA 59.935 40.000 0.00 0.00 0.00 3.10
2041 2379 9.736414 AAGATCAAACTAGTCAGTACTACAGTA 57.264 33.333 0.00 0.00 37.15 2.74
2042 2380 8.638629 AAGATCAAACTAGTCAGTACTACAGT 57.361 34.615 0.00 0.00 37.15 3.55
2043 2381 8.185505 GGAAGATCAAACTAGTCAGTACTACAG 58.814 40.741 0.00 0.00 37.15 2.74
2044 2382 7.668469 TGGAAGATCAAACTAGTCAGTACTACA 59.332 37.037 0.00 0.00 37.15 2.74
2146 2484 9.226345 CTGAACAGAAACTTGTCTAAAAATGTC 57.774 33.333 0.00 0.00 0.00 3.06
2152 2490 6.112734 TGAGCTGAACAGAAACTTGTCTAAA 58.887 36.000 5.97 0.00 0.00 1.85
2206 2544 0.770499 TGAGGTGCCCACATTTCTCA 59.230 50.000 0.40 1.55 31.98 3.27
2344 2682 0.463295 CAGAGGGTGCCATAGTGCAG 60.463 60.000 0.00 0.00 43.02 4.41
2539 2877 0.250901 AAGAAGCCACCGCACTGAAT 60.251 50.000 0.00 0.00 37.52 2.57
2710 3048 0.172352 GAGGAAGAGCAGGAGTGACG 59.828 60.000 0.00 0.00 0.00 4.35
2862 3632 5.734855 ATACCGCAGCTAAATAACACTTG 57.265 39.130 0.00 0.00 0.00 3.16
2894 3664 1.755179 ATCCTCACAAGCCAAATCGG 58.245 50.000 0.00 0.00 38.11 4.18
2915 3686 4.018960 ACACTGATAAGGGAATTGAGCAGT 60.019 41.667 0.00 0.00 35.92 4.40
2986 3757 1.869574 CGTCACAGCCAGATCGACG 60.870 63.158 0.00 0.00 42.79 5.12
2997 3768 3.811722 TTAAGCAGCAAATCGTCACAG 57.188 42.857 0.00 0.00 0.00 3.66
3039 3811 9.109393 GTAGATTAATTTACATGAGCAGGTTCA 57.891 33.333 10.47 0.00 0.00 3.18
3084 3857 5.401531 TTCCATACAAGCGAAGTAGAAGT 57.598 39.130 0.00 0.00 0.00 3.01
3089 3862 7.269316 TCATAACATTCCATACAAGCGAAGTA 58.731 34.615 0.00 0.00 0.00 2.24
3147 3920 6.610741 TGGTTTAATTCAAATTTGTGCCAC 57.389 33.333 17.47 8.30 0.00 5.01
3206 3979 4.293415 GGAAGAGCACACAAAACAATGAG 58.707 43.478 0.00 0.00 0.00 2.90
3207 3980 3.068024 GGGAAGAGCACACAAAACAATGA 59.932 43.478 0.00 0.00 0.00 2.57
3239 4012 4.016444 GCACCAGAAACTCCATTGGATAA 58.984 43.478 5.70 0.00 34.76 1.75
3287 4060 4.985409 CAGAACAGAGGTGAAACTAGACAC 59.015 45.833 0.00 3.93 36.74 3.67
3296 4069 7.099764 GTCTTATGATTCAGAACAGAGGTGAA 58.900 38.462 0.00 0.00 34.79 3.18
3371 4144 6.959311 CGTATTTAGATGTGTTTTAGTGTGCC 59.041 38.462 0.00 0.00 0.00 5.01
3433 4233 2.903375 AGAGTTACTCCCTCCGTTCT 57.097 50.000 8.96 0.00 0.00 3.01
3467 4267 5.826208 GGGGTAAGGAATTCGTGAATTGTAT 59.174 40.000 12.27 1.66 40.77 2.29
3471 4271 4.310022 TGGGGTAAGGAATTCGTGAATT 57.690 40.909 7.52 7.52 43.14 2.17
3477 4277 3.418047 ACAAGTTGGGGTAAGGAATTCG 58.582 45.455 7.96 0.00 0.00 3.34
3487 4287 1.339727 GCCTATTCGACAAGTTGGGGT 60.340 52.381 7.96 0.00 0.00 4.95
3491 4291 3.521560 TGCTAGCCTATTCGACAAGTTG 58.478 45.455 13.29 0.00 0.00 3.16
3505 4305 2.093235 ACTGAGAAAGGACATGCTAGCC 60.093 50.000 13.29 0.00 0.00 3.93
3589 4389 4.361783 TCCTCTCCATAACATTCCTGTGA 58.638 43.478 0.00 0.00 35.22 3.58
3656 4456 5.302313 AGTTCTGGAGTTATTACCGAGGATC 59.698 44.000 0.00 0.00 0.00 3.36
3683 4483 6.040054 TCGATCGGATATTGGAGAAACTTACA 59.960 38.462 16.41 0.00 0.00 2.41
3701 4501 6.448006 ACTCTATCCTAATTTTGTCGATCGG 58.552 40.000 16.41 0.00 0.00 4.18
3845 4655 7.437748 AGCTGACATAGTTATATCACTTGGAC 58.562 38.462 0.00 0.00 0.00 4.02
3884 4694 9.959749 GATTTCACAATTTAAGTGGTTAACTCA 57.040 29.630 5.42 0.00 38.56 3.41
3918 4729 5.760253 ACTTCGTGATGAACAAGTGATTTCT 59.240 36.000 0.00 0.00 32.44 2.52
4053 4864 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
4054 4865 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
4055 4866 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
4059 4870 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
4062 4873 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
4063 4874 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
4064 4875 6.016192 GTCTAGATACATCCATTTCCGAGACA 60.016 42.308 0.00 0.00 0.00 3.41
4066 4877 5.181433 CGTCTAGATACATCCATTTCCGAGA 59.819 44.000 0.00 0.00 0.00 4.04
4068 4879 4.825634 ACGTCTAGATACATCCATTTCCGA 59.174 41.667 0.00 0.00 0.00 4.55
4069 4880 5.122512 ACGTCTAGATACATCCATTTCCG 57.877 43.478 0.00 0.00 0.00 4.30
4070 4881 9.490379 AAAATACGTCTAGATACATCCATTTCC 57.510 33.333 0.00 0.00 0.00 3.13
4094 4905 9.542462 CGGAAATGGATGTATCTAGAACTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
4095 4906 8.920174 TCGGAAATGGATGTATCTAGAACTAAA 58.080 33.333 0.00 0.00 0.00 1.85
4096 4907 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
4097 4908 7.942894 TCTCGGAAATGGATGTATCTAGAACTA 59.057 37.037 0.00 0.00 0.00 2.24
4099 4910 6.982852 TCTCGGAAATGGATGTATCTAGAAC 58.017 40.000 0.00 0.00 0.00 3.01
4100 4911 7.451566 TCATCTCGGAAATGGATGTATCTAGAA 59.548 37.037 0.00 0.00 38.28 2.10
4101 4912 6.948309 TCATCTCGGAAATGGATGTATCTAGA 59.052 38.462 0.00 0.00 38.28 2.43
4102 4913 7.093988 ACTCATCTCGGAAATGGATGTATCTAG 60.094 40.741 0.00 0.00 38.28 2.43
4106 4917 5.815233 ACTCATCTCGGAAATGGATGTAT 57.185 39.130 0.00 0.00 38.28 2.29
4107 4918 6.724893 TTACTCATCTCGGAAATGGATGTA 57.275 37.500 0.00 0.00 38.28 2.29
4111 4922 5.611374 GGAATTACTCATCTCGGAAATGGA 58.389 41.667 0.00 0.00 0.00 3.41
4112 4923 4.449068 CGGAATTACTCATCTCGGAAATGG 59.551 45.833 0.00 0.00 0.00 3.16
4113 4924 5.289595 TCGGAATTACTCATCTCGGAAATG 58.710 41.667 0.00 0.00 0.00 2.32
4117 4928 3.242969 CGTTCGGAATTACTCATCTCGGA 60.243 47.826 0.00 0.00 0.00 4.55
4119 4930 3.043586 CCGTTCGGAATTACTCATCTCG 58.956 50.000 5.19 0.00 0.00 4.04
4123 4934 2.102588 CCCTCCGTTCGGAATTACTCAT 59.897 50.000 14.79 0.00 33.41 2.90
4124 4935 1.479323 CCCTCCGTTCGGAATTACTCA 59.521 52.381 14.79 0.00 33.41 3.41
4125 4936 1.753073 TCCCTCCGTTCGGAATTACTC 59.247 52.381 14.79 0.00 33.41 2.59
4127 4938 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
4129 4940 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
4130 4941 1.687123 CATACTCCCTCCGTTCGGAAT 59.313 52.381 14.79 2.14 33.41 3.01
4131 4942 1.108776 CATACTCCCTCCGTTCGGAA 58.891 55.000 14.79 0.00 33.41 4.30
4132 4943 0.256752 TCATACTCCCTCCGTTCGGA 59.743 55.000 13.34 13.34 0.00 4.55
4133 4944 1.108776 TTCATACTCCCTCCGTTCGG 58.891 55.000 4.74 4.74 0.00 4.30
4134 4945 3.454371 AATTCATACTCCCTCCGTTCG 57.546 47.619 0.00 0.00 0.00 3.95
4135 4946 5.915175 AGTTAATTCATACTCCCTCCGTTC 58.085 41.667 0.00 0.00 0.00 3.95
4139 5178 7.368198 AGAGAAGTTAATTCATACTCCCTCC 57.632 40.000 0.00 0.00 40.67 4.30
4157 5196 3.308323 GCGCCTCACAGAAATAAGAGAAG 59.692 47.826 0.00 0.00 0.00 2.85
4191 5231 8.587952 AAAACTAATGGAATAGTTGCAACAAC 57.412 30.769 30.11 17.05 43.52 3.32
4350 5390 7.994425 TCTGGTCAATCTATCTACATCTCTC 57.006 40.000 0.00 0.00 0.00 3.20
4351 5391 8.954834 ATTCTGGTCAATCTATCTACATCTCT 57.045 34.615 0.00 0.00 0.00 3.10
4405 5445 4.229876 GCTCATTTTACAAGTTCTGGTGC 58.770 43.478 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.