Multiple sequence alignment - TraesCS5D01G000800

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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 TraesCS5D01G000800 chr5D 100.000 3653 0 0 1 3653 931500 935152 0.000000e+00 6746.0
1 TraesCS5D01G000800 chr5D 84.328 134 20 1 2 134 360174255 360174122 2.960000e-26 130.0
2 TraesCS5D01G000800 chr5D 89.888 89 8 1 273 361 404233723 404233810 2.980000e-21 113.0
3 TraesCS5D01G000800 chr5B 87.092 1929 140 36 916 2777 219453 217567 0.000000e+00 2082.0
4 TraesCS5D01G000800 chr5B 93.905 804 32 6 2860 3653 217392 216596 0.000000e+00 1197.0
5 TraesCS5D01G000800 chr5B 88.600 693 54 14 2 682 220333 219654 0.000000e+00 819.0
6 TraesCS5D01G000800 chr5B 86.139 101 13 1 267 367 15277903 15277804 1.390000e-19 108.0
7 TraesCS5D01G000800 chr5A 93.067 851 29 7 2809 3653 646018 645192 0.000000e+00 1218.0
8 TraesCS5D01G000800 chr5A 92.260 646 34 2 1916 2561 646928 646299 0.000000e+00 902.0
9 TraesCS5D01G000800 chr5A 92.814 167 8 2 2608 2773 646296 646133 4.710000e-59 239.0
10 TraesCS5D01G000800 chr5A 100.000 35 0 0 976 1010 646963 646929 8.470000e-07 65.8
11 TraesCS5D01G000800 chr2A 80.964 809 128 13 2861 3653 763449896 763450694 5.180000e-173 617.0
12 TraesCS5D01G000800 chr2A 83.846 130 20 1 3 131 226574999 226575128 4.950000e-24 122.0
13 TraesCS5D01G000800 chr7A 90.102 394 24 5 3260 3653 728650517 728650139 7.040000e-137 497.0
14 TraesCS5D01G000800 chr7A 82.647 340 52 6 363 700 419932897 419932563 9.920000e-76 294.0
15 TraesCS5D01G000800 chrUn 85.000 420 51 8 347 756 223002276 223001859 2.030000e-112 416.0
16 TraesCS5D01G000800 chrUn 86.139 101 13 1 267 367 344216358 344216259 1.390000e-19 108.0
17 TraesCS5D01G000800 chrUn 87.368 95 11 1 267 361 471140613 471140706 1.390000e-19 108.0
18 TraesCS5D01G000800 chr1B 85.575 409 45 10 362 757 679234344 679233937 2.030000e-112 416.0
19 TraesCS5D01G000800 chr3D 84.561 421 51 10 347 756 29493929 29493512 4.390000e-109 405.0
20 TraesCS5D01G000800 chr3D 84.323 421 52 10 347 756 29528858 29528441 2.040000e-107 399.0
21 TraesCS5D01G000800 chr3D 84.323 421 52 10 347 756 29565798 29565381 2.040000e-107 399.0
22 TraesCS5D01G000800 chr3D 77.660 282 36 12 271 528 590333740 590333462 2.940000e-31 147.0
23 TraesCS5D01G000800 chr3D 83.333 132 19 3 2 131 239164463 239164593 6.410000e-23 119.0
24 TraesCS5D01G000800 chr7D 84.848 363 40 10 339 690 465920642 465920284 5.800000e-93 351.0
25 TraesCS5D01G000800 chr7D 83.459 133 19 3 4 134 313632391 313632260 1.780000e-23 121.0
26 TraesCS5D01G000800 chr6B 82.294 401 52 12 347 735 548538971 548539364 2.720000e-86 329.0
27 TraesCS5D01G000800 chr6B 89.130 92 10 0 273 364 492858075 492857984 8.290000e-22 115.0
28 TraesCS5D01G000800 chr6D 85.185 135 19 1 1 134 223289975 223289841 1.770000e-28 137.0
29 TraesCS5D01G000800 chr3B 88.288 111 13 0 20 130 178760962 178761072 2.290000e-27 134.0
30 TraesCS5D01G000800 chr2B 88.182 110 13 0 20 129 538007013 538006904 8.230000e-27 132.0
31 TraesCS5D01G000800 chr7B 83.206 131 19 3 3 131 232065602 232065731 2.300000e-22 117.0
32 TraesCS5D01G000800 chr1A 88.421 95 11 0 273 367 12126317 12126223 8.290000e-22 115.0
33 TraesCS5D01G000800 chr6A 84.167 120 14 3 273 392 592219933 592220047 1.070000e-20 111.0


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 TraesCS5D01G000800 chr5D 931500 935152 3652 False 6746.0 6746 100.000000 1 3653 1 chr5D.!!$F1 3652
1 TraesCS5D01G000800 chr5B 216596 220333 3737 True 1366.0 2082 89.865667 2 3653 3 chr5B.!!$R2 3651
2 TraesCS5D01G000800 chr5A 645192 646963 1771 True 606.2 1218 94.535250 976 3653 4 chr5A.!!$R1 2677
3 TraesCS5D01G000800 chr2A 763449896 763450694 798 False 617.0 617 80.964000 2861 3653 1 chr2A.!!$F2 792

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
906 945 0.029700 GGTTTTGTTTGGACCGACGG 59.970 55.0 13.61 13.61 0.00 4.79 F
914 953 0.245539 TTGGACCGACGGATCAAGTC 59.754 55.0 23.38 6.10 35.41 3.01 F
1799 1886 0.533755 GATCGGGGGTTCATGAGCTG 60.534 60.0 9.57 0.00 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 1909 0.249238 TTGTTGCGGCCATTGTCAAC 60.249 50.0 2.24 8.99 39.23 3.18 R
1823 1910 0.249238 GTTGTTGCGGCCATTGTCAA 60.249 50.0 2.24 0.00 0.00 3.18 R
3575 3871 0.329596 CCAAGAAGACCCTCCCCAAG 59.670 60.0 0.00 0.00 0.00 3.61 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
44 45 4.851843 AGGCATTCATCTGAAGTCAATGA 58.148 39.130 0.00 3.53 37.48 2.57
63 64 3.596214 TGAAGGGCGAAGACATAGTTTC 58.404 45.455 0.00 0.00 37.00 2.78
68 69 4.455877 AGGGCGAAGACATAGTTTCTTTTG 59.544 41.667 0.00 0.00 37.00 2.44
113 114 1.523934 GTTGTACGAACCACCGAACTG 59.476 52.381 0.00 0.00 0.00 3.16
118 119 2.476821 ACGAACCACCGAACTGTTAAG 58.523 47.619 0.00 0.00 0.00 1.85
125 126 1.071228 ACCGAACTGTTAAGTGGGGTC 59.929 52.381 0.00 0.00 37.98 4.46
142 143 8.999905 AGTGGGGTCAAAGTAAAAGTAATTTA 57.000 30.769 0.00 0.00 32.27 1.40
265 266 6.466885 TTACCATAAGCAGAGACTAGGTTC 57.533 41.667 0.00 0.00 0.00 3.62
271 272 8.041323 CCATAAGCAGAGACTAGGTTCTTTTTA 58.959 37.037 0.00 0.00 0.00 1.52
272 273 9.606631 CATAAGCAGAGACTAGGTTCTTTTTAT 57.393 33.333 0.00 1.45 0.00 1.40
274 275 8.926092 AAGCAGAGACTAGGTTCTTTTTATTT 57.074 30.769 0.00 0.00 0.00 1.40
275 276 8.554835 AGCAGAGACTAGGTTCTTTTTATTTC 57.445 34.615 0.00 0.00 0.00 2.17
327 328 9.811995 TCATACTCATAACAATTACAGGTACAC 57.188 33.333 0.00 0.00 0.00 2.90
382 383 9.586435 CAAAGAAAATCTCTTGTAAACACCTTT 57.414 29.630 0.00 0.00 44.00 3.11
389 390 2.759538 TGTAAACACCTTTTTCGCGG 57.240 45.000 6.13 0.00 0.00 6.46
399 400 4.557301 CACCTTTTTCGCGGTATCAATTTC 59.443 41.667 6.13 0.00 30.91 2.17
402 403 4.349663 TTTTCGCGGTATCAATTTCTGG 57.650 40.909 6.13 0.00 0.00 3.86
404 405 3.804786 TCGCGGTATCAATTTCTGGTA 57.195 42.857 6.13 0.00 0.00 3.25
408 409 4.209288 CGCGGTATCAATTTCTGGTAGAAG 59.791 45.833 0.00 0.00 35.37 2.85
433 434 9.416284 AGAAATACTTCAAAGACTTGGGTAAAA 57.584 29.630 0.00 0.00 33.64 1.52
443 444 2.972021 ACTTGGGTAAAAAGGCTGCAAT 59.028 40.909 0.50 0.00 0.00 3.56
453 454 5.789643 AAAAGGCTGCAATTAGACTGAAA 57.210 34.783 0.50 0.00 35.81 2.69
458 459 3.908382 GCTGCAATTAGACTGAAACAACG 59.092 43.478 0.00 0.00 0.00 4.10
465 466 7.044706 GCAATTAGACTGAAACAACGATATTGC 60.045 37.037 0.00 0.00 37.08 3.56
476 477 4.943705 ACAACGATATTGCCACTCTTTCAT 59.056 37.500 0.00 0.00 0.00 2.57
513 514 5.343249 ACCAATAATGATTTCTGAAAGCGC 58.657 37.500 13.04 0.00 0.00 5.92
517 518 2.995466 TGATTTCTGAAAGCGCCTTG 57.005 45.000 13.04 0.00 0.00 3.61
538 539 4.470602 TGAGTCGCCCATCTAGAAAGATA 58.529 43.478 0.00 0.00 40.65 1.98
558 559 6.709281 AGATAGGAAGCATTGATCGATGAAT 58.291 36.000 24.63 12.80 0.00 2.57
599 600 1.805945 CGTAGAAGTGCAGGCCGTC 60.806 63.158 0.00 0.00 0.00 4.79
602 603 1.529152 TAGAAGTGCAGGCCGTCGAA 61.529 55.000 0.00 0.00 0.00 3.71
623 624 5.349817 CGAATCACTATATCTTCACCATGGC 59.650 44.000 13.04 0.00 0.00 4.40
626 627 4.100963 TCACTATATCTTCACCATGGCGTT 59.899 41.667 13.04 0.00 0.00 4.84
635 636 2.625314 TCACCATGGCGTTGATGAAAAA 59.375 40.909 13.04 0.00 0.00 1.94
682 694 5.574891 AGCTTGACACAACAACATAAACA 57.425 34.783 0.00 0.00 0.00 2.83
684 696 4.204168 GCTTGACACAACAACATAAACACG 59.796 41.667 0.00 0.00 0.00 4.49
685 697 4.948608 TGACACAACAACATAAACACGT 57.051 36.364 0.00 0.00 0.00 4.49
687 699 4.392138 TGACACAACAACATAAACACGTCA 59.608 37.500 0.00 0.00 0.00 4.35
688 700 4.904116 ACACAACAACATAAACACGTCAG 58.096 39.130 0.00 0.00 0.00 3.51
689 701 4.632251 ACACAACAACATAAACACGTCAGA 59.368 37.500 0.00 0.00 0.00 3.27
690 702 4.961551 CACAACAACATAAACACGTCAGAC 59.038 41.667 0.00 0.00 0.00 3.51
691 703 4.034742 ACAACAACATAAACACGTCAGACC 59.965 41.667 0.00 0.00 0.00 3.85
692 704 3.799366 ACAACATAAACACGTCAGACCA 58.201 40.909 0.00 0.00 0.00 4.02
693 705 4.193090 ACAACATAAACACGTCAGACCAA 58.807 39.130 0.00 0.00 0.00 3.67
694 706 4.636648 ACAACATAAACACGTCAGACCAAA 59.363 37.500 0.00 0.00 0.00 3.28
695 707 5.298276 ACAACATAAACACGTCAGACCAAAT 59.702 36.000 0.00 0.00 0.00 2.32
696 708 6.483974 ACAACATAAACACGTCAGACCAAATA 59.516 34.615 0.00 0.00 0.00 1.40
697 709 7.012515 ACAACATAAACACGTCAGACCAAATAA 59.987 33.333 0.00 0.00 0.00 1.40
698 710 7.681939 ACATAAACACGTCAGACCAAATAAT 57.318 32.000 0.00 0.00 0.00 1.28
699 711 7.748847 ACATAAACACGTCAGACCAAATAATC 58.251 34.615 0.00 0.00 0.00 1.75
700 712 4.921470 AACACGTCAGACCAAATAATCG 57.079 40.909 0.00 0.00 0.00 3.34
701 713 4.182693 ACACGTCAGACCAAATAATCGA 57.817 40.909 0.00 0.00 0.00 3.59
702 714 4.562082 ACACGTCAGACCAAATAATCGAA 58.438 39.130 0.00 0.00 0.00 3.71
703 715 5.175859 ACACGTCAGACCAAATAATCGAAT 58.824 37.500 0.00 0.00 0.00 3.34
704 716 5.291128 ACACGTCAGACCAAATAATCGAATC 59.709 40.000 0.00 0.00 0.00 2.52
705 717 4.809426 ACGTCAGACCAAATAATCGAATCC 59.191 41.667 0.00 0.00 0.00 3.01
706 718 4.085055 CGTCAGACCAAATAATCGAATCCG 60.085 45.833 0.00 0.00 37.07 4.18
707 719 3.807622 TCAGACCAAATAATCGAATCCGC 59.192 43.478 0.00 0.00 35.37 5.54
708 720 2.800544 AGACCAAATAATCGAATCCGCG 59.199 45.455 0.00 0.00 35.37 6.46
709 721 2.798283 GACCAAATAATCGAATCCGCGA 59.202 45.455 8.23 0.00 45.22 5.87
710 722 2.800544 ACCAAATAATCGAATCCGCGAG 59.199 45.455 8.23 0.00 44.26 5.03
726 738 1.970447 CGAGGACGAAACACTCTCTG 58.030 55.000 0.00 0.00 42.66 3.35
730 742 1.001597 GGACGAAACACTCTCTGACGT 60.002 52.381 0.00 0.00 33.33 4.34
755 767 1.069636 GCACTGCCAAAAGAACGAGAG 60.070 52.381 0.00 0.00 0.00 3.20
756 768 1.532868 CACTGCCAAAAGAACGAGAGG 59.467 52.381 0.00 0.00 0.00 3.69
757 769 1.160137 CTGCCAAAAGAACGAGAGGG 58.840 55.000 0.00 0.00 0.00 4.30
758 770 0.762418 TGCCAAAAGAACGAGAGGGA 59.238 50.000 0.00 0.00 0.00 4.20
759 771 1.270839 TGCCAAAAGAACGAGAGGGAG 60.271 52.381 0.00 0.00 0.00 4.30
761 773 2.810767 GCCAAAAGAACGAGAGGGAGTT 60.811 50.000 0.00 0.00 0.00 3.01
763 775 3.251004 CCAAAAGAACGAGAGGGAGTTTG 59.749 47.826 0.00 0.00 0.00 2.93
764 776 3.840124 AAAGAACGAGAGGGAGTTTGT 57.160 42.857 0.00 0.00 0.00 2.83
766 778 3.840124 AGAACGAGAGGGAGTTTGTTT 57.160 42.857 0.00 0.00 0.00 2.83
767 779 4.152284 AGAACGAGAGGGAGTTTGTTTT 57.848 40.909 0.00 0.00 0.00 2.43
768 780 4.524053 AGAACGAGAGGGAGTTTGTTTTT 58.476 39.130 0.00 0.00 0.00 1.94
819 831 1.017387 AAAAATCAGATCCGGAGCGC 58.983 50.000 15.18 0.00 0.00 5.92
821 833 0.179000 AAATCAGATCCGGAGCGCTT 59.821 50.000 13.26 6.35 0.00 4.68
824 836 3.141488 AGATCCGGAGCGCTTCGT 61.141 61.111 34.36 19.27 0.00 3.85
826 838 3.701604 GATCCGGAGCGCTTCGTGT 62.702 63.158 34.36 23.10 0.00 4.49
827 839 3.701604 ATCCGGAGCGCTTCGTGTC 62.702 63.158 34.36 10.55 0.00 3.67
828 840 4.717629 CCGGAGCGCTTCGTGTCA 62.718 66.667 34.36 0.00 0.00 3.58
829 841 3.470567 CGGAGCGCTTCGTGTCAC 61.471 66.667 29.91 4.78 0.00 3.67
836 875 1.321743 GCGCTTCGTGTCACTTATCAG 59.678 52.381 0.00 0.00 0.00 2.90
845 884 4.561938 CGTGTCACTTATCAGGTGGGTAAA 60.562 45.833 0.65 0.00 35.61 2.01
846 885 5.310451 GTGTCACTTATCAGGTGGGTAAAA 58.690 41.667 0.00 0.00 35.61 1.52
847 886 5.766174 GTGTCACTTATCAGGTGGGTAAAAA 59.234 40.000 0.00 0.00 35.61 1.94
848 887 6.433093 GTGTCACTTATCAGGTGGGTAAAAAT 59.567 38.462 0.00 0.00 35.61 1.82
849 888 7.007723 TGTCACTTATCAGGTGGGTAAAAATT 58.992 34.615 0.00 0.00 35.61 1.82
864 903 8.939932 TGGGTAAAAATTAAAATTGAGGGAAGT 58.060 29.630 0.00 0.00 0.00 3.01
885 924 1.679305 TGAGAGGCTGAGTCGGTCC 60.679 63.158 0.00 2.14 0.00 4.46
886 925 1.679305 GAGAGGCTGAGTCGGTCCA 60.679 63.158 12.98 0.00 0.00 4.02
887 926 1.662438 GAGAGGCTGAGTCGGTCCAG 61.662 65.000 12.98 0.00 0.00 3.86
888 927 2.681778 AGGCTGAGTCGGTCCAGG 60.682 66.667 12.98 0.00 0.00 4.45
889 928 2.997897 GGCTGAGTCGGTCCAGGT 60.998 66.667 0.00 0.00 0.00 4.00
890 929 2.584391 GGCTGAGTCGGTCCAGGTT 61.584 63.158 0.00 0.00 0.00 3.50
891 930 1.371558 GCTGAGTCGGTCCAGGTTT 59.628 57.895 0.00 0.00 0.00 3.27
892 931 0.250338 GCTGAGTCGGTCCAGGTTTT 60.250 55.000 0.00 0.00 0.00 2.43
893 932 1.512926 CTGAGTCGGTCCAGGTTTTG 58.487 55.000 0.00 0.00 0.00 2.44
894 933 0.834612 TGAGTCGGTCCAGGTTTTGT 59.165 50.000 0.00 0.00 0.00 2.83
895 934 1.210967 TGAGTCGGTCCAGGTTTTGTT 59.789 47.619 0.00 0.00 0.00 2.83
896 935 2.294979 GAGTCGGTCCAGGTTTTGTTT 58.705 47.619 0.00 0.00 0.00 2.83
897 936 2.021457 AGTCGGTCCAGGTTTTGTTTG 58.979 47.619 0.00 0.00 0.00 2.93
898 937 1.066454 GTCGGTCCAGGTTTTGTTTGG 59.934 52.381 0.00 0.00 0.00 3.28
899 938 1.064611 TCGGTCCAGGTTTTGTTTGGA 60.065 47.619 0.00 0.00 38.62 3.53
902 941 1.394618 TCCAGGTTTTGTTTGGACCG 58.605 50.000 0.00 0.00 36.13 4.79
903 942 1.064611 TCCAGGTTTTGTTTGGACCGA 60.065 47.619 0.00 0.00 36.13 4.69
904 943 1.066454 CCAGGTTTTGTTTGGACCGAC 59.934 52.381 0.00 0.00 38.48 4.79
905 944 1.018910 AGGTTTTGTTTGGACCGACG 58.981 50.000 0.00 0.00 38.48 5.12
906 945 0.029700 GGTTTTGTTTGGACCGACGG 59.970 55.000 13.61 13.61 0.00 4.79
907 946 1.015868 GTTTTGTTTGGACCGACGGA 58.984 50.000 23.38 0.00 0.00 4.69
908 947 1.605232 GTTTTGTTTGGACCGACGGAT 59.395 47.619 23.38 4.57 0.00 4.18
909 948 1.515081 TTTGTTTGGACCGACGGATC 58.485 50.000 23.38 13.98 0.00 3.36
910 949 0.393448 TTGTTTGGACCGACGGATCA 59.607 50.000 23.38 14.97 0.00 2.92
911 950 0.393448 TGTTTGGACCGACGGATCAA 59.607 50.000 23.38 19.83 0.00 2.57
912 951 1.076332 GTTTGGACCGACGGATCAAG 58.924 55.000 23.38 0.00 0.00 3.02
913 952 0.682852 TTTGGACCGACGGATCAAGT 59.317 50.000 23.38 0.00 0.00 3.16
914 953 0.245539 TTGGACCGACGGATCAAGTC 59.754 55.000 23.38 6.10 35.41 3.01
954 993 6.314784 GTGGTGAGATAAAAATCCGTTCTTG 58.685 40.000 0.00 0.00 0.00 3.02
1010 1058 2.808543 GGAGTTCATCAATGGCGGATAC 59.191 50.000 0.00 0.00 0.00 2.24
1016 1064 2.851263 TCAATGGCGGATACATACCC 57.149 50.000 0.00 0.00 0.00 3.69
1018 1066 2.642311 TCAATGGCGGATACATACCCAT 59.358 45.455 0.00 0.00 37.88 4.00
1019 1067 3.841255 TCAATGGCGGATACATACCCATA 59.159 43.478 0.00 0.00 35.34 2.74
1020 1068 3.906720 ATGGCGGATACATACCCATAC 57.093 47.619 0.00 0.00 34.68 2.39
1021 1069 1.903860 TGGCGGATACATACCCATACC 59.096 52.381 0.00 0.00 0.00 2.73
1044 1098 1.385206 AGGGGAGGGGAAGCAGATC 60.385 63.158 0.00 0.00 0.00 2.75
1046 1100 2.812619 GGGAGGGGAAGCAGATCGG 61.813 68.421 0.00 0.00 0.00 4.18
1047 1101 2.812619 GGAGGGGAAGCAGATCGGG 61.813 68.421 0.00 0.00 0.00 5.14
1048 1102 1.762460 GAGGGGAAGCAGATCGGGA 60.762 63.158 0.00 0.00 0.00 5.14
1049 1103 2.034048 GAGGGGAAGCAGATCGGGAC 62.034 65.000 0.00 0.00 0.00 4.46
1050 1104 2.506472 GGGAAGCAGATCGGGACC 59.494 66.667 0.00 0.00 0.00 4.46
1051 1105 2.107141 GGAAGCAGATCGGGACCG 59.893 66.667 3.96 3.96 41.35 4.79
1052 1106 2.107141 GAAGCAGATCGGGACCGG 59.893 66.667 11.27 0.00 40.25 5.28
1053 1107 3.447025 GAAGCAGATCGGGACCGGG 62.447 68.421 6.32 0.00 40.25 5.73
1054 1108 3.976490 AAGCAGATCGGGACCGGGA 62.976 63.158 6.32 0.00 40.25 5.14
1055 1109 3.234730 GCAGATCGGGACCGGGAT 61.235 66.667 6.32 0.00 40.25 3.85
1056 1110 2.737180 CAGATCGGGACCGGGATG 59.263 66.667 6.32 3.52 40.25 3.51
1057 1111 3.234730 AGATCGGGACCGGGATGC 61.235 66.667 6.32 0.00 40.25 3.91
1058 1112 3.234730 GATCGGGACCGGGATGCT 61.235 66.667 6.32 0.00 40.25 3.79
1075 1129 2.285368 TGGATCGGGCCAAGAGGT 60.285 61.111 4.39 0.00 34.31 3.85
1078 1132 4.162690 ATCGGGCCAAGAGGTCGC 62.163 66.667 4.39 0.00 41.80 5.19
1307 1379 1.478137 CACGAAACTCCGATCCGATC 58.522 55.000 0.00 0.00 0.00 3.69
1317 1389 0.598562 CGATCCGATCCCGATCAGTT 59.401 55.000 14.61 0.00 37.69 3.16
1326 1398 3.918220 CGATCAGTTGCCGCGCTC 61.918 66.667 5.56 0.00 0.00 5.03
1327 1399 3.918220 GATCAGTTGCCGCGCTCG 61.918 66.667 5.56 0.00 0.00 5.03
1389 1467 4.734134 CTGGAGATCAGCTGCGAG 57.266 61.111 9.47 0.00 37.86 5.03
1398 1476 4.104417 AGCTGCGAGACGACGGAC 62.104 66.667 0.00 0.00 0.00 4.79
1399 1477 4.400109 GCTGCGAGACGACGGACA 62.400 66.667 0.00 0.00 0.00 4.02
1400 1478 2.485582 CTGCGAGACGACGGACAT 59.514 61.111 0.00 0.00 0.00 3.06
1401 1479 1.869574 CTGCGAGACGACGGACATG 60.870 63.158 0.00 0.00 0.00 3.21
1402 1480 2.579787 GCGAGACGACGGACATGG 60.580 66.667 0.00 0.00 0.00 3.66
1405 1492 1.226717 GAGACGACGGACATGGAGC 60.227 63.158 0.00 0.00 0.00 4.70
1411 1498 2.202987 CGGACATGGAGCAGGAGC 60.203 66.667 0.00 0.00 42.56 4.70
1413 1500 1.153208 GGACATGGAGCAGGAGCAG 60.153 63.158 0.00 0.00 45.49 4.24
1622 1709 4.601794 CAGCCCCCACCTGCACAA 62.602 66.667 0.00 0.00 0.00 3.33
1626 1713 2.669569 CCCCACCTGCACAAGACG 60.670 66.667 0.00 0.00 0.00 4.18
1630 1717 1.564622 CACCTGCACAAGACGTTCG 59.435 57.895 0.00 0.00 0.00 3.95
1674 1761 4.821589 GGCGGCAGGGTCTTCTCG 62.822 72.222 3.07 0.00 0.00 4.04
1703 1790 2.753701 CGGGTGGGTCATGGTCAA 59.246 61.111 0.00 0.00 0.00 3.18
1704 1791 1.377202 CGGGTGGGTCATGGTCAAG 60.377 63.158 0.00 0.00 0.00 3.02
1710 1797 2.100631 GGTCATGGTCAAGACGCCG 61.101 63.158 0.00 0.00 35.63 6.46
1711 1798 2.100631 GTCATGGTCAAGACGCCGG 61.101 63.158 0.00 0.00 0.00 6.13
1795 1882 1.820581 GACGATCGGGGGTTCATGA 59.179 57.895 20.98 0.00 0.00 3.07
1799 1886 0.533755 GATCGGGGGTTCATGAGCTG 60.534 60.000 9.57 0.00 0.00 4.24
1847 1934 0.529555 AATGGCCGCAACAACAACAC 60.530 50.000 0.00 0.00 0.00 3.32
1849 1936 2.653766 GCCGCAACAACAACACCG 60.654 61.111 0.00 0.00 0.00 4.94
1850 1937 2.025441 CCGCAACAACAACACCGG 59.975 61.111 0.00 0.00 0.00 5.28
1855 1942 0.804156 CAACAACAACACCGGCAACC 60.804 55.000 0.00 0.00 0.00 3.77
1856 1943 1.950973 AACAACAACACCGGCAACCC 61.951 55.000 0.00 0.00 0.00 4.11
1857 1944 2.124693 CAACAACACCGGCAACCCT 61.125 57.895 0.00 0.00 0.00 4.34
1858 1945 1.826487 AACAACACCGGCAACCCTC 60.826 57.895 0.00 0.00 0.00 4.30
1859 1946 2.983592 CAACACCGGCAACCCTCC 60.984 66.667 0.00 0.00 0.00 4.30
1863 1953 4.280019 ACCGGCAACCCTCCCAAC 62.280 66.667 0.00 0.00 0.00 3.77
1865 1955 4.323477 CGGCAACCCTCCCAACGA 62.323 66.667 0.00 0.00 0.00 3.85
1875 1965 1.294659 CTCCCAACGACTGCTGCTTC 61.295 60.000 0.00 0.00 0.00 3.86
1894 1984 2.726274 ACGTGTTCGCCGTCTTCT 59.274 55.556 0.00 0.00 41.18 2.85
1897 1987 2.087009 GTGTTCGCCGTCTTCTCCG 61.087 63.158 0.00 0.00 0.00 4.63
1904 1994 2.501492 CCGTCTTCTCCGGTATGGT 58.499 57.895 0.00 0.00 40.59 3.55
1905 1995 0.822164 CCGTCTTCTCCGGTATGGTT 59.178 55.000 0.00 0.00 40.59 3.67
1929 2019 3.673597 AGGGTCGAGAGCTGGGGA 61.674 66.667 0.00 0.00 0.00 4.81
1970 2060 3.443925 CGTGGAGGAGCAGAGCGA 61.444 66.667 0.00 0.00 0.00 4.93
2277 2367 0.841289 AGTCCCTTTTCACCGGAACA 59.159 50.000 9.46 0.00 31.35 3.18
2280 2370 1.064611 TCCCTTTTCACCGGAACAACA 60.065 47.619 9.46 0.00 31.35 3.33
2322 2412 2.237751 GGTCGTCGAATCCATGGCG 61.238 63.158 6.96 5.26 0.00 5.69
2440 2536 1.376553 GAGCAGGAGCAACAGGGAC 60.377 63.158 0.00 0.00 45.49 4.46
2447 2543 0.252197 GAGCAACAGGGACCGGTTAT 59.748 55.000 9.42 0.00 33.36 1.89
2453 2549 2.269883 GGGACCGGTTATGGCGTT 59.730 61.111 9.42 0.00 0.00 4.84
2530 2626 1.325476 GCAATTCCTGGGCTCCAAGG 61.325 60.000 2.74 2.74 30.80 3.61
2607 2703 1.288439 CTCGCCGGATGAGGATGAG 59.712 63.158 5.05 0.00 0.00 2.90
2613 2709 1.549620 CCGGATGAGGATGAGGATGAG 59.450 57.143 0.00 0.00 0.00 2.90
2619 2715 3.508426 TGAGGATGAGGATGAGGATGAG 58.492 50.000 0.00 0.00 0.00 2.90
2625 2721 3.508426 TGAGGATGAGGATGAGGATGAG 58.492 50.000 0.00 0.00 0.00 2.90
2631 2727 4.143406 TGAGGATGAGGATGAGGATGAT 57.857 45.455 0.00 0.00 0.00 2.45
2661 2775 2.364324 GGTTATAGACTGACCGGCATCA 59.636 50.000 0.00 0.00 0.00 3.07
2675 2789 2.684374 CGGCATCAATCCATGAAACTGA 59.316 45.455 0.00 0.00 42.54 3.41
2807 2999 9.646427 TTCTTCTAAGAACTAATCTTTGCTCTC 57.354 33.333 1.00 0.00 46.39 3.20
2808 3000 9.030452 TCTTCTAAGAACTAATCTTTGCTCTCT 57.970 33.333 0.00 0.00 46.39 3.10
2810 3002 8.588290 TCTAAGAACTAATCTTTGCTCTCTCT 57.412 34.615 0.00 0.00 46.39 3.10
2811 3003 8.682710 TCTAAGAACTAATCTTTGCTCTCTCTC 58.317 37.037 0.00 0.00 46.39 3.20
2812 3004 7.480760 AAGAACTAATCTTTGCTCTCTCTCT 57.519 36.000 0.00 0.00 46.39 3.10
2813 3005 7.100458 AGAACTAATCTTTGCTCTCTCTCTC 57.900 40.000 0.00 0.00 33.39 3.20
2814 3006 6.891908 AGAACTAATCTTTGCTCTCTCTCTCT 59.108 38.462 0.00 0.00 33.39 3.10
2815 3007 6.455360 ACTAATCTTTGCTCTCTCTCTCTG 57.545 41.667 0.00 0.00 0.00 3.35
2816 3008 3.806625 ATCTTTGCTCTCTCTCTCTGC 57.193 47.619 0.00 0.00 0.00 4.26
2817 3009 1.824230 TCTTTGCTCTCTCTCTCTGCC 59.176 52.381 0.00 0.00 0.00 4.85
2818 3010 1.826720 CTTTGCTCTCTCTCTCTGCCT 59.173 52.381 0.00 0.00 0.00 4.75
2820 3012 1.184431 TGCTCTCTCTCTCTGCCTTG 58.816 55.000 0.00 0.00 0.00 3.61
2822 3014 1.550072 GCTCTCTCTCTCTGCCTTGTT 59.450 52.381 0.00 0.00 0.00 2.83
3494 3775 3.311110 GTGAGGGTGCGGAGGTGA 61.311 66.667 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.865385 TGCCTTCAAGTGTATTATTTTCAACAC 59.135 33.333 0.00 0.00 41.97 3.32
1 2 7.946207 TGCCTTCAAGTGTATTATTTTCAACA 58.054 30.769 0.00 0.00 0.00 3.33
2 3 8.986477 ATGCCTTCAAGTGTATTATTTTCAAC 57.014 30.769 0.00 0.00 0.00 3.18
3 4 9.638239 GAATGCCTTCAAGTGTATTATTTTCAA 57.362 29.630 0.00 0.00 0.00 2.69
4 5 8.801299 TGAATGCCTTCAAGTGTATTATTTTCA 58.199 29.630 1.53 0.00 38.43 2.69
5 6 9.807649 ATGAATGCCTTCAAGTGTATTATTTTC 57.192 29.630 8.55 0.00 44.29 2.29
7 8 9.193806 AGATGAATGCCTTCAAGTGTATTATTT 57.806 29.630 8.55 0.00 44.29 1.40
9 10 7.994911 TCAGATGAATGCCTTCAAGTGTATTAT 59.005 33.333 8.55 0.00 44.29 1.28
10 11 7.337938 TCAGATGAATGCCTTCAAGTGTATTA 58.662 34.615 8.55 0.00 44.29 0.98
12 13 5.748402 TCAGATGAATGCCTTCAAGTGTAT 58.252 37.500 8.55 0.00 44.29 2.29
13 14 5.164620 TCAGATGAATGCCTTCAAGTGTA 57.835 39.130 8.55 0.00 44.29 2.90
18 19 4.654915 TGACTTCAGATGAATGCCTTCAA 58.345 39.130 8.55 0.00 44.29 2.69
24 25 5.450137 CCCTTCATTGACTTCAGATGAATGC 60.450 44.000 12.90 0.00 38.63 3.56
44 45 3.983044 AGAAACTATGTCTTCGCCCTT 57.017 42.857 0.00 0.00 0.00 3.95
68 69 9.803315 ACTTGGAAAAGAAGAAAATGAAACTAC 57.197 29.630 0.00 0.00 0.00 2.73
88 89 1.538634 CGGTGGTTCGTACAACTTGGA 60.539 52.381 0.00 0.00 0.00 3.53
90 91 1.855513 TCGGTGGTTCGTACAACTTG 58.144 50.000 0.00 0.00 0.00 3.16
91 92 2.159057 AGTTCGGTGGTTCGTACAACTT 60.159 45.455 0.00 0.00 33.82 2.66
113 114 6.704289 ACTTTTACTTTGACCCCACTTAAC 57.296 37.500 0.00 0.00 0.00 2.01
196 197 2.253452 GCCAAGCTTGCGTCACTG 59.747 61.111 21.43 6.59 0.00 3.66
221 222 0.318275 CCGGAGATTGAGCTCGTAGC 60.318 60.000 9.64 2.30 42.84 3.58
229 230 4.932200 GCTTATGGTAATCCGGAGATTGAG 59.068 45.833 11.34 1.52 42.78 3.02
306 307 8.948631 ATCAGTGTACCTGTAATTGTTATGAG 57.051 34.615 10.08 0.00 42.19 2.90
316 317 9.653287 CTTAGATTCAAATCAGTGTACCTGTAA 57.347 33.333 5.59 0.00 42.19 2.41
382 383 3.340034 ACCAGAAATTGATACCGCGAAA 58.660 40.909 8.23 0.00 0.00 3.46
416 417 4.340950 CAGCCTTTTTACCCAAGTCTTTGA 59.659 41.667 0.00 0.00 36.36 2.69
426 427 4.462834 AGTCTAATTGCAGCCTTTTTACCC 59.537 41.667 0.00 0.00 0.00 3.69
428 429 6.254281 TCAGTCTAATTGCAGCCTTTTTAC 57.746 37.500 0.00 0.00 0.00 2.01
433 434 4.144297 TGTTTCAGTCTAATTGCAGCCTT 58.856 39.130 0.00 0.00 0.00 4.35
443 444 5.935206 TGGCAATATCGTTGTTTCAGTCTAA 59.065 36.000 0.00 0.00 0.00 2.10
453 454 4.323417 TGAAAGAGTGGCAATATCGTTGT 58.677 39.130 0.00 0.00 0.00 3.32
458 459 3.058639 GCGGATGAAAGAGTGGCAATATC 60.059 47.826 0.00 0.00 0.00 1.63
465 466 0.389817 TCGTGCGGATGAAAGAGTGG 60.390 55.000 0.00 0.00 0.00 4.00
476 477 2.102070 ATTGGTAATGTTCGTGCGGA 57.898 45.000 0.00 0.00 0.00 5.54
513 514 1.403814 TCTAGATGGGCGACTCAAGG 58.596 55.000 0.00 0.00 0.00 3.61
517 518 5.054390 CTATCTTTCTAGATGGGCGACTC 57.946 47.826 0.00 0.00 41.25 3.36
538 539 4.458397 ACATTCATCGATCAATGCTTCCT 58.542 39.130 20.39 0.00 33.92 3.36
558 559 2.285818 ATCCCCGGCCCAAGTACA 60.286 61.111 0.00 0.00 0.00 2.90
599 600 5.349817 GCCATGGTGAAGATATAGTGATTCG 59.650 44.000 14.67 0.00 0.00 3.34
602 603 4.284490 ACGCCATGGTGAAGATATAGTGAT 59.716 41.667 31.66 1.02 0.00 3.06
658 670 6.310224 GTGTTTATGTTGTTGTGTCAAGCTTT 59.690 34.615 0.00 0.00 0.00 3.51
662 674 5.328691 ACGTGTTTATGTTGTTGTGTCAAG 58.671 37.500 0.00 0.00 0.00 3.02
671 683 3.799366 TGGTCTGACGTGTTTATGTTGT 58.201 40.909 0.00 0.00 0.00 3.32
682 694 4.809426 GGATTCGATTATTTGGTCTGACGT 59.191 41.667 1.07 0.00 0.00 4.34
684 696 4.318831 GCGGATTCGATTATTTGGTCTGAC 60.319 45.833 0.00 0.00 39.00 3.51
685 697 3.807622 GCGGATTCGATTATTTGGTCTGA 59.192 43.478 0.00 0.00 39.00 3.27
687 699 2.800544 CGCGGATTCGATTATTTGGTCT 59.199 45.455 0.00 0.00 39.00 3.85
688 700 2.798283 TCGCGGATTCGATTATTTGGTC 59.202 45.455 6.13 0.00 39.00 4.02
689 701 2.800544 CTCGCGGATTCGATTATTTGGT 59.199 45.455 6.13 0.00 37.87 3.67
690 702 2.157668 CCTCGCGGATTCGATTATTTGG 59.842 50.000 6.13 0.00 37.87 3.28
691 703 3.057019 TCCTCGCGGATTCGATTATTTG 58.943 45.455 6.13 0.00 37.87 2.32
692 704 3.057734 GTCCTCGCGGATTCGATTATTT 58.942 45.455 6.13 0.00 42.43 1.40
693 705 2.673833 GTCCTCGCGGATTCGATTATT 58.326 47.619 6.13 0.00 42.43 1.40
694 706 1.401148 CGTCCTCGCGGATTCGATTAT 60.401 52.381 6.13 0.00 42.43 1.28
695 707 0.040692 CGTCCTCGCGGATTCGATTA 60.041 55.000 6.13 0.00 42.43 1.75
696 708 1.299165 CGTCCTCGCGGATTCGATT 60.299 57.895 6.13 0.00 42.43 3.34
697 709 1.721664 TTCGTCCTCGCGGATTCGAT 61.722 55.000 6.13 0.00 42.43 3.59
698 710 1.925415 TTTCGTCCTCGCGGATTCGA 61.925 55.000 6.13 9.70 42.43 3.71
699 711 1.515519 TTTCGTCCTCGCGGATTCG 60.516 57.895 6.13 7.30 42.43 3.34
700 712 0.734942 TGTTTCGTCCTCGCGGATTC 60.735 55.000 6.13 0.00 42.43 2.52
701 713 1.012486 GTGTTTCGTCCTCGCGGATT 61.012 55.000 6.13 0.00 42.43 3.01
702 714 1.445582 GTGTTTCGTCCTCGCGGAT 60.446 57.895 6.13 0.00 42.43 4.18
703 715 2.049802 GTGTTTCGTCCTCGCGGA 60.050 61.111 6.13 0.00 36.83 5.54
704 716 2.049433 AGTGTTTCGTCCTCGCGG 60.049 61.111 6.13 0.00 36.96 6.46
705 717 1.066114 GAGAGTGTTTCGTCCTCGCG 61.066 60.000 0.00 0.00 36.96 5.87
706 718 0.241481 AGAGAGTGTTTCGTCCTCGC 59.759 55.000 0.00 0.00 36.96 5.03
707 719 1.535896 TCAGAGAGTGTTTCGTCCTCG 59.464 52.381 0.00 0.00 38.55 4.63
708 720 2.666069 CGTCAGAGAGTGTTTCGTCCTC 60.666 54.545 0.00 0.00 0.00 3.71
709 721 1.267261 CGTCAGAGAGTGTTTCGTCCT 59.733 52.381 0.00 0.00 0.00 3.85
710 722 1.001597 ACGTCAGAGAGTGTTTCGTCC 60.002 52.381 0.00 0.00 0.00 4.79
711 723 2.286831 TGACGTCAGAGAGTGTTTCGTC 60.287 50.000 15.76 0.00 41.37 4.20
712 724 1.674441 TGACGTCAGAGAGTGTTTCGT 59.326 47.619 15.76 0.00 34.10 3.85
713 725 2.401017 TGACGTCAGAGAGTGTTTCG 57.599 50.000 15.76 0.00 0.00 3.46
714 726 2.989840 CCATGACGTCAGAGAGTGTTTC 59.010 50.000 24.41 0.00 0.00 2.78
718 730 0.244721 TGCCATGACGTCAGAGAGTG 59.755 55.000 24.41 15.98 0.00 3.51
800 812 1.017387 GCGCTCCGGATCTGATTTTT 58.983 50.000 3.57 0.00 0.00 1.94
803 815 0.249657 GAAGCGCTCCGGATCTGATT 60.250 55.000 12.06 2.24 0.00 2.57
806 818 2.656651 CGAAGCGCTCCGGATCTG 60.657 66.667 12.06 0.00 0.00 2.90
808 820 2.956964 CACGAAGCGCTCCGGATC 60.957 66.667 22.93 8.64 0.00 3.36
809 821 3.701604 GACACGAAGCGCTCCGGAT 62.702 63.158 22.93 7.66 0.00 4.18
810 822 4.415332 GACACGAAGCGCTCCGGA 62.415 66.667 22.93 2.93 0.00 5.14
811 823 4.717629 TGACACGAAGCGCTCCGG 62.718 66.667 22.93 12.12 0.00 5.14
814 826 1.584308 GATAAGTGACACGAAGCGCTC 59.416 52.381 12.06 3.22 0.00 5.03
817 829 1.920574 CCTGATAAGTGACACGAAGCG 59.079 52.381 0.00 0.00 0.00 4.68
819 831 3.254060 CCACCTGATAAGTGACACGAAG 58.746 50.000 0.00 0.00 37.42 3.79
821 833 1.548719 CCCACCTGATAAGTGACACGA 59.451 52.381 0.00 0.00 37.42 4.35
824 836 5.570205 TTTTACCCACCTGATAAGTGACA 57.430 39.130 0.00 0.00 37.42 3.58
826 838 9.589461 TTTAATTTTTACCCACCTGATAAGTGA 57.411 29.630 0.00 0.00 37.42 3.41
836 875 7.681679 TCCCTCAATTTTAATTTTTACCCACC 58.318 34.615 0.00 0.00 0.00 4.61
845 884 8.923270 TCTCACAACTTCCCTCAATTTTAATTT 58.077 29.630 0.00 0.00 0.00 1.82
846 885 8.477419 TCTCACAACTTCCCTCAATTTTAATT 57.523 30.769 0.00 0.00 0.00 1.40
847 886 7.177392 CCTCTCACAACTTCCCTCAATTTTAAT 59.823 37.037 0.00 0.00 0.00 1.40
848 887 6.490040 CCTCTCACAACTTCCCTCAATTTTAA 59.510 38.462 0.00 0.00 0.00 1.52
849 888 6.003950 CCTCTCACAACTTCCCTCAATTTTA 58.996 40.000 0.00 0.00 0.00 1.52
864 903 0.827925 ACCGACTCAGCCTCTCACAA 60.828 55.000 0.00 0.00 0.00 3.33
885 924 1.268335 CGTCGGTCCAAACAAAACCTG 60.268 52.381 0.00 0.00 0.00 4.00
886 925 1.018910 CGTCGGTCCAAACAAAACCT 58.981 50.000 0.00 0.00 0.00 3.50
887 926 0.029700 CCGTCGGTCCAAACAAAACC 59.970 55.000 2.08 0.00 0.00 3.27
888 927 1.015868 TCCGTCGGTCCAAACAAAAC 58.984 50.000 11.88 0.00 0.00 2.43
889 928 1.874872 GATCCGTCGGTCCAAACAAAA 59.125 47.619 11.88 0.00 0.00 2.44
890 929 1.202663 TGATCCGTCGGTCCAAACAAA 60.203 47.619 11.88 0.00 0.00 2.83
891 930 0.393448 TGATCCGTCGGTCCAAACAA 59.607 50.000 11.88 0.00 0.00 2.83
892 931 0.393448 TTGATCCGTCGGTCCAAACA 59.607 50.000 11.88 0.00 0.00 2.83
893 932 1.076332 CTTGATCCGTCGGTCCAAAC 58.924 55.000 11.88 0.00 0.00 2.93
894 933 0.682852 ACTTGATCCGTCGGTCCAAA 59.317 50.000 11.88 1.57 0.00 3.28
895 934 0.245539 GACTTGATCCGTCGGTCCAA 59.754 55.000 11.88 14.57 0.00 3.53
896 935 1.601419 GGACTTGATCCGTCGGTCCA 61.601 60.000 11.88 7.68 43.36 4.02
897 936 1.141234 GGACTTGATCCGTCGGTCC 59.859 63.158 11.88 5.86 40.23 4.46
898 937 4.808649 GGACTTGATCCGTCGGTC 57.191 61.111 11.88 8.88 37.88 4.79
906 945 4.578105 CAGATTTAAGGCCAGGACTTGATC 59.422 45.833 19.11 19.10 31.11 2.92
907 946 4.530875 CAGATTTAAGGCCAGGACTTGAT 58.469 43.478 19.11 11.49 31.11 2.57
908 947 3.308402 CCAGATTTAAGGCCAGGACTTGA 60.308 47.826 19.11 6.62 31.11 3.02
909 948 3.019564 CCAGATTTAAGGCCAGGACTTG 58.980 50.000 19.11 0.00 31.11 3.16
910 949 2.649816 ACCAGATTTAAGGCCAGGACTT 59.350 45.455 13.75 13.75 34.14 3.01
911 950 2.025887 CACCAGATTTAAGGCCAGGACT 60.026 50.000 5.01 0.00 0.00 3.85
912 951 2.369394 CACCAGATTTAAGGCCAGGAC 58.631 52.381 5.01 0.00 0.00 3.85
913 952 1.284785 CCACCAGATTTAAGGCCAGGA 59.715 52.381 5.01 0.00 0.00 3.86
914 953 1.005924 ACCACCAGATTTAAGGCCAGG 59.994 52.381 5.01 0.00 0.00 4.45
1010 1058 0.321671 CCCTGCTCGGTATGGGTATG 59.678 60.000 0.00 0.00 35.13 2.39
1016 1064 2.511452 CCCTCCCCTGCTCGGTATG 61.511 68.421 0.00 0.00 0.00 2.39
1018 1066 4.475444 CCCCTCCCCTGCTCGGTA 62.475 72.222 0.00 0.00 0.00 4.02
1021 1069 3.474570 CTTCCCCTCCCCTGCTCG 61.475 72.222 0.00 0.00 0.00 5.03
1046 1100 2.427753 GATCCAGCATCCCGGTCC 59.572 66.667 0.00 0.00 0.00 4.46
1047 1101 2.029666 CGATCCAGCATCCCGGTC 59.970 66.667 0.00 0.00 0.00 4.79
1048 1102 3.550431 CCGATCCAGCATCCCGGT 61.550 66.667 0.00 0.00 35.83 5.28
1049 1103 4.320456 CCCGATCCAGCATCCCGG 62.320 72.222 0.00 0.00 39.85 5.73
1050 1104 4.996434 GCCCGATCCAGCATCCCG 62.996 72.222 0.00 0.00 0.00 5.14
1051 1105 4.650377 GGCCCGATCCAGCATCCC 62.650 72.222 0.00 0.00 0.00 3.85
1052 1106 3.420206 TTGGCCCGATCCAGCATCC 62.420 63.158 0.00 0.00 37.44 3.51
1053 1107 1.895707 CTTGGCCCGATCCAGCATC 60.896 63.158 0.00 0.00 37.44 3.91
1054 1108 2.194056 CTTGGCCCGATCCAGCAT 59.806 61.111 0.00 0.00 37.44 3.79
1055 1109 3.008517 TCTTGGCCCGATCCAGCA 61.009 61.111 0.00 0.00 37.44 4.41
1056 1110 2.203126 CTCTTGGCCCGATCCAGC 60.203 66.667 0.00 0.00 37.44 4.85
1057 1111 2.317149 GACCTCTTGGCCCGATCCAG 62.317 65.000 0.00 0.00 37.44 3.86
1058 1112 2.285368 ACCTCTTGGCCCGATCCA 60.285 61.111 0.00 0.00 36.63 3.41
1228 1297 2.670592 GTAACGGGGCCGCTTGTT 60.671 61.111 18.79 16.90 44.19 2.83
1296 1368 0.960861 CTGATCGGGATCGGATCGGA 60.961 60.000 21.18 11.42 44.92 4.55
1330 1402 3.009115 ATGGGGTGGTGACGGGAG 61.009 66.667 0.00 0.00 0.00 4.30
1331 1403 3.326578 CATGGGGTGGTGACGGGA 61.327 66.667 0.00 0.00 0.00 5.14
1332 1404 4.424711 CCATGGGGTGGTGACGGG 62.425 72.222 2.85 0.00 43.44 5.28
1389 1467 1.517257 CTGCTCCATGTCCGTCGTC 60.517 63.158 0.00 0.00 0.00 4.20
1398 1476 2.192443 CCCTGCTCCTGCTCCATG 59.808 66.667 0.00 0.00 40.48 3.66
1399 1477 3.095163 CCCCTGCTCCTGCTCCAT 61.095 66.667 0.00 0.00 40.48 3.41
1622 1709 4.099170 CGGCGAGGACGAACGTCT 62.099 66.667 22.98 11.73 44.04 4.18
1654 1741 4.475135 GAAGACCCTGCCGCCCTC 62.475 72.222 0.00 0.00 0.00 4.30
1656 1743 4.475135 GAGAAGACCCTGCCGCCC 62.475 72.222 0.00 0.00 0.00 6.13
1710 1797 4.309950 AACACGACGGTCCTGCCC 62.310 66.667 1.91 0.00 0.00 5.36
1711 1798 2.737376 GAACACGACGGTCCTGCC 60.737 66.667 1.91 0.00 0.00 4.85
1715 1802 4.651008 TGGCGAACACGACGGTCC 62.651 66.667 1.91 0.00 37.94 4.46
1716 1803 2.659244 TTGGCGAACACGACGGTC 60.659 61.111 0.00 0.00 37.94 4.79
1726 1813 2.747686 GTCCAGGAGGTTGGCGAA 59.252 61.111 0.00 0.00 38.16 4.70
1775 1862 3.441011 ATGAACCCCCGATCGTCGC 62.441 63.158 15.09 0.00 38.82 5.19
1778 1865 1.823295 CTCATGAACCCCCGATCGT 59.177 57.895 15.09 0.00 0.00 3.73
1782 1869 2.989639 CAGCTCATGAACCCCCGA 59.010 61.111 0.00 0.00 0.00 5.14
1784 1871 2.825836 CGCAGCTCATGAACCCCC 60.826 66.667 0.00 0.00 0.00 5.40
1817 1904 3.361977 GGCCATTGTCAACGCCGT 61.362 61.111 9.21 0.00 0.00 5.68
1819 1906 4.776647 GCGGCCATTGTCAACGCC 62.777 66.667 13.36 13.36 44.01 5.68
1822 1909 0.249238 TTGTTGCGGCCATTGTCAAC 60.249 50.000 2.24 8.99 39.23 3.18
1823 1910 0.249238 GTTGTTGCGGCCATTGTCAA 60.249 50.000 2.24 0.00 0.00 3.18
1824 1911 1.361993 GTTGTTGCGGCCATTGTCA 59.638 52.632 2.24 0.00 0.00 3.58
1849 1936 2.671963 GTCGTTGGGAGGGTTGCC 60.672 66.667 0.00 0.00 34.91 4.52
1850 1937 1.966451 CAGTCGTTGGGAGGGTTGC 60.966 63.158 0.00 0.00 0.00 4.17
1855 1942 2.738213 AAGCAGCAGTCGTTGGGAGG 62.738 60.000 0.00 0.00 0.00 4.30
1856 1943 1.294659 GAAGCAGCAGTCGTTGGGAG 61.295 60.000 0.00 0.00 0.00 4.30
1857 1944 1.301716 GAAGCAGCAGTCGTTGGGA 60.302 57.895 0.00 0.00 0.00 4.37
1858 1945 2.671177 CGAAGCAGCAGTCGTTGGG 61.671 63.158 9.73 0.00 32.61 4.12
1859 1946 1.664649 TCGAAGCAGCAGTCGTTGG 60.665 57.895 15.75 0.00 38.41 3.77
1863 1953 2.429236 ACGTCGAAGCAGCAGTCG 60.429 61.111 11.32 11.32 38.62 4.18
1865 1955 1.215655 GAACACGTCGAAGCAGCAGT 61.216 55.000 0.00 0.00 0.00 4.40
1897 1987 1.197812 ACCCTGACGGTAACCATACC 58.802 55.000 0.00 0.00 45.97 2.73
1909 1999 2.716017 CCCAGCTCTCGACCCTGAC 61.716 68.421 4.31 0.00 0.00 3.51
1970 2060 1.350351 AGCAGCAGGACATTCTGAACT 59.650 47.619 0.00 0.00 36.93 3.01
2189 2279 1.227380 CTCAGCACGTAGATGGGCC 60.227 63.158 0.00 0.00 0.00 5.80
2277 2367 3.998672 ACCGCCACCGACGATGTT 61.999 61.111 0.00 0.00 36.29 2.71
2391 2481 4.436998 ACGAAGAAGAGGCGGCCG 62.437 66.667 24.05 24.05 0.00 6.13
2440 2536 3.514362 GCCCAACGCCATAACCGG 61.514 66.667 0.00 0.00 0.00 5.28
2530 2626 1.905354 AAAAGGACTGCAGCAGGGC 60.905 57.895 26.38 16.92 35.51 5.19
2607 2703 2.899975 TCCTCATCCTCATCCTCATCC 58.100 52.381 0.00 0.00 0.00 3.51
2613 2709 4.384318 CCATCATCATCCTCATCCTCATCC 60.384 50.000 0.00 0.00 0.00 3.51
2619 2715 4.263816 ACCATTCCATCATCATCCTCATCC 60.264 45.833 0.00 0.00 0.00 3.51
2625 2721 7.551974 CAGTCTATAACCATTCCATCATCATCC 59.448 40.741 0.00 0.00 0.00 3.51
2631 2727 5.221441 CGGTCAGTCTATAACCATTCCATCA 60.221 44.000 0.00 0.00 32.35 3.07
2661 2775 4.346730 TGGCAAGATCAGTTTCATGGATT 58.653 39.130 0.00 0.00 0.00 3.01
2675 2789 6.986817 GTGTATTCTACTGTACATGGCAAGAT 59.013 38.462 0.00 0.00 33.78 2.40
2793 2985 5.284079 GCAGAGAGAGAGAGCAAAGATTAG 58.716 45.833 0.00 0.00 0.00 1.73
2802 2994 1.185315 ACAAGGCAGAGAGAGAGAGC 58.815 55.000 0.00 0.00 0.00 4.09
2803 2995 3.959535 AAACAAGGCAGAGAGAGAGAG 57.040 47.619 0.00 0.00 0.00 3.20
2804 2996 3.389329 ACAAAACAAGGCAGAGAGAGAGA 59.611 43.478 0.00 0.00 0.00 3.10
2806 2998 3.845781 ACAAAACAAGGCAGAGAGAGA 57.154 42.857 0.00 0.00 0.00 3.10
2807 2999 3.549625 GCAACAAAACAAGGCAGAGAGAG 60.550 47.826 0.00 0.00 0.00 3.20
2808 3000 2.358898 GCAACAAAACAAGGCAGAGAGA 59.641 45.455 0.00 0.00 0.00 3.10
2810 3002 2.098614 TGCAACAAAACAAGGCAGAGA 58.901 42.857 0.00 0.00 0.00 3.10
2811 3003 2.582728 TGCAACAAAACAAGGCAGAG 57.417 45.000 0.00 0.00 0.00 3.35
2812 3004 3.540314 ATTGCAACAAAACAAGGCAGA 57.460 38.095 0.00 0.00 35.68 4.26
2813 3005 4.989797 TCATATTGCAACAAAACAAGGCAG 59.010 37.500 0.00 0.00 35.68 4.85
2814 3006 4.953667 TCATATTGCAACAAAACAAGGCA 58.046 34.783 0.00 0.00 0.00 4.75
2815 3007 5.921004 TTCATATTGCAACAAAACAAGGC 57.079 34.783 0.00 0.00 0.00 4.35
2816 3008 6.649973 TCCATTCATATTGCAACAAAACAAGG 59.350 34.615 0.00 0.00 0.00 3.61
2817 3009 7.599621 TCTCCATTCATATTGCAACAAAACAAG 59.400 33.333 0.00 0.00 0.00 3.16
2818 3010 7.440198 TCTCCATTCATATTGCAACAAAACAA 58.560 30.769 0.00 0.00 0.00 2.83
2820 3012 7.887996 TTCTCCATTCATATTGCAACAAAAC 57.112 32.000 0.00 0.00 0.00 2.43
2822 3014 7.042950 CCATTCTCCATTCATATTGCAACAAA 58.957 34.615 0.00 0.00 0.00 2.83
2858 3061 6.721571 TCAACATCATCATCATCATCATCG 57.278 37.500 0.00 0.00 0.00 3.84
3494 3775 2.597805 AGCCTCGACGACCACTGT 60.598 61.111 0.00 0.00 0.00 3.55
3565 3861 2.365105 TCCCCAAGTCCCGGCTAG 60.365 66.667 0.00 0.00 0.00 3.42
3570 3866 3.400054 GACCCTCCCCAAGTCCCG 61.400 72.222 0.00 0.00 0.00 5.14
3575 3871 0.329596 CCAAGAAGACCCTCCCCAAG 59.670 60.000 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.