Multiple sequence alignment - TraesCS2B01G302300

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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 TraesCS2B01G302300 chr2B 100.000 6876 0 0 1 6876 425450929 425444054 0.000000e+00 12698.0
1 TraesCS2B01G302300 chr2B 85.546 339 34 6 11 345 198911615 198911288 2.380000e-89 340.0
2 TraesCS2B01G302300 chr2B 94.068 118 3 2 753 869 442803307 442803193 7.090000e-40 176.0
3 TraesCS2B01G302300 chr2B 100.000 34 0 0 721 754 166853776 166853809 5.760000e-06 63.9
4 TraesCS2B01G302300 chr2D 95.163 3349 97 17 882 4211 357987820 357984518 0.000000e+00 5227.0
5 TraesCS2B01G302300 chr2D 97.802 2593 45 6 4217 6806 357984410 357981827 0.000000e+00 4462.0
6 TraesCS2B01G302300 chr2D 90.426 94 8 1 755 847 642014949 642015042 9.370000e-24 122.0
7 TraesCS2B01G302300 chr2D 100.000 35 0 0 6842 6876 357981828 357981794 1.600000e-06 65.8
8 TraesCS2B01G302300 chr2A 96.564 2561 68 12 877 3419 478918856 478916298 0.000000e+00 4224.0
9 TraesCS2B01G302300 chr2A 97.123 2051 41 9 4826 6876 478914602 478912570 0.000000e+00 3445.0
10 TraesCS2B01G302300 chr2A 98.200 1389 17 7 3447 4831 478916227 478914843 0.000000e+00 2420.0
11 TraesCS2B01G302300 chr2A 90.426 94 8 1 755 847 294765459 294765552 9.370000e-24 122.0
12 TraesCS2B01G302300 chr2A 95.745 47 1 1 3413 3458 478916227 478916273 2.660000e-09 75.0
13 TraesCS2B01G302300 chr1B 97.869 704 12 3 1 703 597399077 597399778 0.000000e+00 1214.0
14 TraesCS2B01G302300 chr1B 94.000 50 1 2 3418 3466 334894556 334894508 2.660000e-09 75.0
15 TraesCS2B01G302300 chr1B 95.238 42 1 1 3418 3458 636490649 636490690 1.600000e-06 65.8
16 TraesCS2B01G302300 chr1B 100.000 34 0 0 719 752 656142660 656142693 5.760000e-06 63.9
17 TraesCS2B01G302300 chr1B 97.222 36 1 0 717 752 415724627 415724662 2.070000e-05 62.1
18 TraesCS2B01G302300 chr1B 94.872 39 1 1 721 758 415724248 415724210 7.450000e-05 60.2
19 TraesCS2B01G302300 chr6A 92.798 722 47 4 1 720 506463946 506463228 0.000000e+00 1040.0
20 TraesCS2B01G302300 chr6A 94.595 37 1 1 3460 3496 35644997 35645032 1.000000e-03 56.5
21 TraesCS2B01G302300 chr7B 89.239 381 35 4 346 720 217766342 217765962 8.070000e-129 472.0
22 TraesCS2B01G302300 chr7B 87.240 384 39 6 346 720 682285196 682285578 4.930000e-116 429.0
23 TraesCS2B01G302300 chr7B 88.333 60 3 3 3418 3473 484855143 484855202 1.240000e-07 69.4
24 TraesCS2B01G302300 chr6D 88.947 380 38 4 346 722 408885363 408884985 3.760000e-127 466.0
25 TraesCS2B01G302300 chr6D 88.131 337 33 3 11 344 462314766 462314434 1.800000e-105 394.0
26 TraesCS2B01G302300 chr6D 96.610 118 3 1 753 869 63325872 63325755 1.960000e-45 195.0
27 TraesCS2B01G302300 chr6D 89.831 59 3 3 3418 3474 194248277 194248220 9.570000e-09 73.1
28 TraesCS2B01G302300 chr5A 89.153 378 36 5 346 720 203806426 203806051 3.760000e-127 466.0
29 TraesCS2B01G302300 chr5A 88.564 376 39 4 346 718 203722555 203722181 2.920000e-123 453.0
30 TraesCS2B01G302300 chr3D 91.916 334 22 3 3648 3980 552444620 552444291 4.860000e-126 462.0
31 TraesCS2B01G302300 chr3D 86.427 361 18 13 3649 3981 552446929 552447286 3.920000e-97 366.0
32 TraesCS2B01G302300 chr3D 95.556 45 1 1 3418 3461 595302892 595302936 3.440000e-08 71.3
33 TraesCS2B01G302300 chr5D 87.958 382 37 7 346 723 390367410 390367786 6.330000e-120 442.0
34 TraesCS2B01G302300 chr5D 84.104 346 26 6 11 345 390367032 390367359 2.410000e-79 307.0
35 TraesCS2B01G302300 chr1A 87.173 382 41 7 346 721 121398222 121398601 1.770000e-115 427.0
36 TraesCS2B01G302300 chr1A 87.764 237 25 2 12 246 123547687 123547453 2.440000e-69 274.0
37 TraesCS2B01G302300 chr4D 88.724 337 32 3 11 345 128771582 128771250 2.310000e-109 407.0
38 TraesCS2B01G302300 chr4D 93.750 96 5 1 753 847 259488126 259488031 7.190000e-30 143.0
39 TraesCS2B01G302300 chr4D 97.222 36 1 0 3461 3496 414149559 414149524 2.070000e-05 62.1
40 TraesCS2B01G302300 chr4D 97.059 34 1 0 3461 3494 401422778 401422745 2.680000e-04 58.4
41 TraesCS2B01G302300 chr3A 88.288 333 35 3 14 345 244355588 244355259 5.000000e-106 396.0
42 TraesCS2B01G302300 chr3A 97.059 34 1 0 3460 3493 581869753 581869786 2.680000e-04 58.4
43 TraesCS2B01G302300 chr3A 97.059 34 1 0 3461 3494 623033912 623033879 2.680000e-04 58.4
44 TraesCS2B01G302300 chr7D 87.537 337 38 2 11 345 523431515 523431181 3.010000e-103 387.0
45 TraesCS2B01G302300 chr7D 89.474 57 4 2 3418 3473 1545725 1545780 3.440000e-08 71.3
46 TraesCS2B01G302300 chr7D 89.655 58 3 3 3418 3474 46857876 46857821 3.440000e-08 71.3
47 TraesCS2B01G302300 chr7A 87.172 343 33 4 11 345 438023526 438023187 5.030000e-101 379.0
48 TraesCS2B01G302300 chr6B 90.426 94 8 1 755 847 485535764 485535671 9.370000e-24 122.0
49 TraesCS2B01G302300 chr6B 88.333 60 3 3 3418 3473 674364233 674364174 1.240000e-07 69.4
50 TraesCS2B01G302300 chr6B 100.000 34 0 0 721 754 161452649 161452616 5.760000e-06 63.9
51 TraesCS2B01G302300 chr6B 97.297 37 0 1 721 756 82716233 82716197 2.070000e-05 62.1
52 TraesCS2B01G302300 chr5B 90.426 94 8 1 755 847 565831978 565832071 9.370000e-24 122.0
53 TraesCS2B01G302300 chr5B 90.426 94 8 1 755 847 565904582 565904675 9.370000e-24 122.0
54 TraesCS2B01G302300 chrUn 100.000 35 0 0 721 755 34582426 34582460 1.600000e-06 65.8
55 TraesCS2B01G302300 chrUn 97.297 37 1 0 721 757 339126476 339126512 5.760000e-06 63.9
56 TraesCS2B01G302300 chrUn 97.297 37 1 0 721 757 404732330 404732366 5.760000e-06 63.9


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 TraesCS2B01G302300 chr2B 425444054 425450929 6875 True 12698.0 12698 100.000000 1 6876 1 chr2B.!!$R2 6875
1 TraesCS2B01G302300 chr2D 357981794 357987820 6026 True 3251.6 5227 97.655000 882 6876 3 chr2D.!!$R1 5994
2 TraesCS2B01G302300 chr2A 478912570 478918856 6286 True 3363.0 4224 97.295667 877 6876 3 chr2A.!!$R1 5999
3 TraesCS2B01G302300 chr1B 597399077 597399778 701 False 1214.0 1214 97.869000 1 703 1 chr1B.!!$F2 702
4 TraesCS2B01G302300 chr6A 506463228 506463946 718 True 1040.0 1040 92.798000 1 720 1 chr6A.!!$R1 719
5 TraesCS2B01G302300 chr5D 390367032 390367786 754 False 374.5 442 86.031000 11 723 2 chr5D.!!$F1 712

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
728 795 0.036010 CTCCGTTCCTGGTGAAGCAT 60.036 55.0 0.00 0.00 32.37 3.79 F
731 798 0.109597 CGTTCCTGGTGAAGCATTGC 60.110 55.0 0.00 0.00 32.37 3.56 F
733 800 0.178967 TTCCTGGTGAAGCATTGCCA 60.179 50.0 4.70 0.00 0.00 4.92 F
734 801 0.178967 TCCTGGTGAAGCATTGCCAA 60.179 50.0 4.70 0.00 30.83 4.52 F
849 916 0.179000 CAGCTCCGGTCAAAGGCTAT 59.821 55.0 0.00 0.00 0.00 2.97 F
854 921 0.251916 CCGGTCAAAGGCTATCCACA 59.748 55.0 0.00 0.00 33.74 4.17 F
880 947 0.333993 ATTCAACCAGGCTCCTGCAT 59.666 50.0 10.37 0.00 42.35 3.96 F
2369 2449 0.685458 ATGAAGGTGATTGCTGGCCC 60.685 55.0 0.00 0.00 0.00 5.80 F
4442 4676 0.038892 CACATGCCCTGTTCTTGCAC 60.039 55.0 0.00 0.00 37.92 4.57 F
5169 5650 2.356665 TTGTCAAGCAAGTTGCCCTA 57.643 45.0 24.02 6.87 46.52 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 2176 1.604378 CTACACCAGGAGGGCCAAG 59.396 63.158 6.18 0.0 42.05 3.61 R
2269 2349 5.696724 GTCACTAAGCTGAAGTAAAGCAAGA 59.303 40.000 1.86 0.0 43.37 3.02 R
2311 2391 6.248569 ACTCCAAAGTTCTGACTAAGGAAA 57.751 37.500 0.00 0.0 38.04 3.13 R
2726 2812 6.260936 GGTTACATTCATGAAACGATCCTGAT 59.739 38.462 13.09 0.0 33.44 2.90 R
2733 2819 7.065324 GGTTAGATGGTTACATTCATGAAACGA 59.935 37.037 13.09 3.7 37.47 3.85 R
2965 3051 5.190528 ACCTTCTCAGGAAAATGAGCAGATA 59.809 40.000 5.17 0.0 45.25 1.98 R
3299 3385 6.777580 GGTGGAACATTAAGGGTGATGAATAT 59.222 38.462 0.00 0.0 44.52 1.28 R
4782 5017 1.269936 ACACATTGCTGGCAAAGAAGC 60.270 47.619 15.75 0.0 39.55 3.86 R
5323 5804 1.084289 GTGCTCGGACACCATTTACC 58.916 55.000 0.00 0.0 34.35 2.85 R
6268 6750 1.746220 AGCTCGTACTCTCTGCGATTT 59.254 47.619 0.00 0.0 36.32 2.17 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
322 335 3.310193 AGAGAACTACCCTAATCCTGCC 58.690 50.000 0.00 0.00 0.00 4.85
382 445 1.798626 TGCATGACCTCCTCTATGCT 58.201 50.000 0.00 0.00 44.59 3.79
384 447 2.507058 TGCATGACCTCCTCTATGCTTT 59.493 45.455 0.00 0.00 44.59 3.51
417 480 6.371595 ACTCCTCTCATCAACTTCAAATCT 57.628 37.500 0.00 0.00 0.00 2.40
705 772 2.372172 CGCCCTCCCTATACCAAATTCT 59.628 50.000 0.00 0.00 0.00 2.40
721 788 1.415672 TTCTTGGCTCCGTTCCTGGT 61.416 55.000 0.00 0.00 0.00 4.00
722 789 1.672356 CTTGGCTCCGTTCCTGGTG 60.672 63.158 0.00 0.00 0.00 4.17
723 790 2.111999 CTTGGCTCCGTTCCTGGTGA 62.112 60.000 0.00 0.00 0.00 4.02
724 791 1.701031 TTGGCTCCGTTCCTGGTGAA 61.701 55.000 0.00 0.00 0.00 3.18
725 792 1.376037 GGCTCCGTTCCTGGTGAAG 60.376 63.158 0.00 0.00 32.37 3.02
726 793 2.035442 GCTCCGTTCCTGGTGAAGC 61.035 63.158 0.00 0.00 32.37 3.86
727 794 1.371183 CTCCGTTCCTGGTGAAGCA 59.629 57.895 0.00 0.00 32.37 3.91
728 795 0.036010 CTCCGTTCCTGGTGAAGCAT 60.036 55.000 0.00 0.00 32.37 3.79
729 796 0.400213 TCCGTTCCTGGTGAAGCATT 59.600 50.000 0.00 0.00 32.37 3.56
730 797 0.523072 CCGTTCCTGGTGAAGCATTG 59.477 55.000 0.00 0.00 32.37 2.82
731 798 0.109597 CGTTCCTGGTGAAGCATTGC 60.110 55.000 0.00 0.00 32.37 3.56
732 799 0.244721 GTTCCTGGTGAAGCATTGCC 59.755 55.000 4.70 0.00 32.37 4.52
733 800 0.178967 TTCCTGGTGAAGCATTGCCA 60.179 50.000 4.70 0.00 0.00 4.92
734 801 0.178967 TCCTGGTGAAGCATTGCCAA 60.179 50.000 4.70 0.00 30.83 4.52
735 802 0.680618 CCTGGTGAAGCATTGCCAAA 59.319 50.000 4.70 0.00 30.83 3.28
736 803 1.070445 CCTGGTGAAGCATTGCCAAAA 59.930 47.619 4.70 0.00 30.83 2.44
737 804 2.137523 CTGGTGAAGCATTGCCAAAAC 58.862 47.619 4.70 0.00 30.83 2.43
738 805 1.483827 TGGTGAAGCATTGCCAAAACA 59.516 42.857 4.70 0.00 28.56 2.83
739 806 2.093288 TGGTGAAGCATTGCCAAAACAA 60.093 40.909 4.70 0.00 28.56 2.83
740 807 3.140623 GGTGAAGCATTGCCAAAACAAT 58.859 40.909 4.70 0.00 40.90 2.71
741 808 3.187022 GGTGAAGCATTGCCAAAACAATC 59.813 43.478 4.70 0.00 38.19 2.67
742 809 3.058450 TGAAGCATTGCCAAAACAATCG 58.942 40.909 4.70 0.00 38.19 3.34
743 810 2.818130 AGCATTGCCAAAACAATCGT 57.182 40.000 4.70 0.00 38.19 3.73
744 811 3.110447 AGCATTGCCAAAACAATCGTT 57.890 38.095 4.70 0.00 38.19 3.85
746 813 3.494251 AGCATTGCCAAAACAATCGTTTC 59.506 39.130 4.70 0.00 44.65 2.78
747 814 3.363871 GCATTGCCAAAACAATCGTTTCC 60.364 43.478 0.00 0.00 44.65 3.13
748 815 3.526931 TTGCCAAAACAATCGTTTCCA 57.473 38.095 0.00 0.00 44.65 3.53
749 816 3.526931 TGCCAAAACAATCGTTTCCAA 57.473 38.095 0.00 0.00 44.65 3.53
750 817 3.190874 TGCCAAAACAATCGTTTCCAAC 58.809 40.909 0.00 0.00 44.65 3.77
751 818 3.190874 GCCAAAACAATCGTTTCCAACA 58.809 40.909 0.00 0.00 44.65 3.33
752 819 3.619038 GCCAAAACAATCGTTTCCAACAA 59.381 39.130 0.00 0.00 44.65 2.83
753 820 4.272261 GCCAAAACAATCGTTTCCAACAAT 59.728 37.500 0.00 0.00 44.65 2.71
754 821 5.463724 GCCAAAACAATCGTTTCCAACAATA 59.536 36.000 0.00 0.00 44.65 1.90
755 822 6.147000 GCCAAAACAATCGTTTCCAACAATAT 59.853 34.615 0.00 0.00 44.65 1.28
756 823 7.508965 CCAAAACAATCGTTTCCAACAATATG 58.491 34.615 0.00 0.00 44.65 1.78
757 824 7.170658 CCAAAACAATCGTTTCCAACAATATGT 59.829 33.333 0.00 0.00 44.65 2.29
758 825 9.186323 CAAAACAATCGTTTCCAACAATATGTA 57.814 29.630 0.00 0.00 44.65 2.29
759 826 8.736751 AAACAATCGTTTCCAACAATATGTAC 57.263 30.769 0.00 0.00 41.60 2.90
760 827 7.681939 ACAATCGTTTCCAACAATATGTACT 57.318 32.000 0.00 0.00 0.00 2.73
761 828 7.526608 ACAATCGTTTCCAACAATATGTACTG 58.473 34.615 0.00 0.00 0.00 2.74
762 829 7.389330 ACAATCGTTTCCAACAATATGTACTGA 59.611 33.333 0.00 0.00 0.00 3.41
763 830 8.397906 CAATCGTTTCCAACAATATGTACTGAT 58.602 33.333 0.00 0.00 0.00 2.90
764 831 7.302350 TCGTTTCCAACAATATGTACTGATG 57.698 36.000 0.00 0.00 0.00 3.07
765 832 6.876789 TCGTTTCCAACAATATGTACTGATGT 59.123 34.615 0.00 0.00 0.00 3.06
766 833 6.960992 CGTTTCCAACAATATGTACTGATGTG 59.039 38.462 0.00 0.00 0.00 3.21
767 834 7.360861 CGTTTCCAACAATATGTACTGATGTGT 60.361 37.037 0.00 0.00 0.00 3.72
768 835 6.983474 TCCAACAATATGTACTGATGTGTG 57.017 37.500 0.00 0.00 0.00 3.82
769 836 5.353956 TCCAACAATATGTACTGATGTGTGC 59.646 40.000 0.00 0.00 0.00 4.57
770 837 5.355071 CCAACAATATGTACTGATGTGTGCT 59.645 40.000 0.00 0.00 0.00 4.40
771 838 6.127925 CCAACAATATGTACTGATGTGTGCTT 60.128 38.462 0.00 0.00 0.00 3.91
772 839 7.307694 CAACAATATGTACTGATGTGTGCTTT 58.692 34.615 0.00 0.00 0.00 3.51
773 840 7.076842 ACAATATGTACTGATGTGTGCTTTC 57.923 36.000 0.00 0.00 0.00 2.62
774 841 6.881065 ACAATATGTACTGATGTGTGCTTTCT 59.119 34.615 0.00 0.00 0.00 2.52
775 842 7.065085 ACAATATGTACTGATGTGTGCTTTCTC 59.935 37.037 0.00 0.00 0.00 2.87
776 843 3.664107 TGTACTGATGTGTGCTTTCTCC 58.336 45.455 0.00 0.00 0.00 3.71
777 844 2.936919 ACTGATGTGTGCTTTCTCCA 57.063 45.000 0.00 0.00 0.00 3.86
778 845 3.430042 ACTGATGTGTGCTTTCTCCAT 57.570 42.857 0.00 0.00 0.00 3.41
779 846 3.759581 ACTGATGTGTGCTTTCTCCATT 58.240 40.909 0.00 0.00 0.00 3.16
780 847 3.504906 ACTGATGTGTGCTTTCTCCATTG 59.495 43.478 0.00 0.00 0.00 2.82
781 848 3.753815 TGATGTGTGCTTTCTCCATTGA 58.246 40.909 0.00 0.00 0.00 2.57
782 849 4.338012 TGATGTGTGCTTTCTCCATTGAT 58.662 39.130 0.00 0.00 0.00 2.57
783 850 4.768448 TGATGTGTGCTTTCTCCATTGATT 59.232 37.500 0.00 0.00 0.00 2.57
784 851 5.244402 TGATGTGTGCTTTCTCCATTGATTT 59.756 36.000 0.00 0.00 0.00 2.17
785 852 5.534207 TGTGTGCTTTCTCCATTGATTTT 57.466 34.783 0.00 0.00 0.00 1.82
786 853 5.531634 TGTGTGCTTTCTCCATTGATTTTC 58.468 37.500 0.00 0.00 0.00 2.29
787 854 5.302568 TGTGTGCTTTCTCCATTGATTTTCT 59.697 36.000 0.00 0.00 0.00 2.52
788 855 6.489700 TGTGTGCTTTCTCCATTGATTTTCTA 59.510 34.615 0.00 0.00 0.00 2.10
789 856 7.177216 TGTGTGCTTTCTCCATTGATTTTCTAT 59.823 33.333 0.00 0.00 0.00 1.98
790 857 7.699812 GTGTGCTTTCTCCATTGATTTTCTATC 59.300 37.037 0.00 0.00 0.00 2.08
791 858 7.148018 TGTGCTTTCTCCATTGATTTTCTATCC 60.148 37.037 0.00 0.00 0.00 2.59
792 859 6.891361 TGCTTTCTCCATTGATTTTCTATCCA 59.109 34.615 0.00 0.00 0.00 3.41
793 860 7.148018 TGCTTTCTCCATTGATTTTCTATCCAC 60.148 37.037 0.00 0.00 0.00 4.02
794 861 7.645058 TTTCTCCATTGATTTTCTATCCACC 57.355 36.000 0.00 0.00 0.00 4.61
795 862 6.581388 TCTCCATTGATTTTCTATCCACCT 57.419 37.500 0.00 0.00 0.00 4.00
796 863 6.359804 TCTCCATTGATTTTCTATCCACCTG 58.640 40.000 0.00 0.00 0.00 4.00
797 864 4.889409 TCCATTGATTTTCTATCCACCTGC 59.111 41.667 0.00 0.00 0.00 4.85
798 865 4.891756 CCATTGATTTTCTATCCACCTGCT 59.108 41.667 0.00 0.00 0.00 4.24
799 866 6.064060 CCATTGATTTTCTATCCACCTGCTA 58.936 40.000 0.00 0.00 0.00 3.49
800 867 6.547141 CCATTGATTTTCTATCCACCTGCTAA 59.453 38.462 0.00 0.00 0.00 3.09
801 868 7.232127 CCATTGATTTTCTATCCACCTGCTAAT 59.768 37.037 0.00 0.00 0.00 1.73
802 869 8.636213 CATTGATTTTCTATCCACCTGCTAATT 58.364 33.333 0.00 0.00 0.00 1.40
803 870 9.866655 ATTGATTTTCTATCCACCTGCTAATTA 57.133 29.630 0.00 0.00 0.00 1.40
804 871 9.866655 TTGATTTTCTATCCACCTGCTAATTAT 57.133 29.630 0.00 0.00 0.00 1.28
805 872 9.866655 TGATTTTCTATCCACCTGCTAATTATT 57.133 29.630 0.00 0.00 0.00 1.40
841 908 4.383861 CTGCAGCAGCTCCGGTCA 62.384 66.667 10.14 0.00 42.74 4.02
842 909 3.889134 CTGCAGCAGCTCCGGTCAA 62.889 63.158 10.14 0.00 42.74 3.18
843 910 2.669569 GCAGCAGCTCCGGTCAAA 60.670 61.111 0.00 0.00 37.91 2.69
844 911 2.684843 GCAGCAGCTCCGGTCAAAG 61.685 63.158 0.00 0.00 37.91 2.77
845 912 2.037136 CAGCAGCTCCGGTCAAAGG 61.037 63.158 0.00 0.00 0.00 3.11
846 913 3.435186 GCAGCTCCGGTCAAAGGC 61.435 66.667 0.00 0.00 0.00 4.35
847 914 2.348998 CAGCTCCGGTCAAAGGCT 59.651 61.111 0.00 0.13 0.00 4.58
848 915 1.596934 CAGCTCCGGTCAAAGGCTA 59.403 57.895 0.00 0.00 0.00 3.93
849 916 0.179000 CAGCTCCGGTCAAAGGCTAT 59.821 55.000 0.00 0.00 0.00 2.97
850 917 0.466124 AGCTCCGGTCAAAGGCTATC 59.534 55.000 0.00 0.00 0.00 2.08
851 918 0.533085 GCTCCGGTCAAAGGCTATCC 60.533 60.000 0.00 0.00 0.00 2.59
852 919 0.830648 CTCCGGTCAAAGGCTATCCA 59.169 55.000 0.00 0.00 33.74 3.41
853 920 0.539986 TCCGGTCAAAGGCTATCCAC 59.460 55.000 0.00 0.00 33.74 4.02
854 921 0.251916 CCGGTCAAAGGCTATCCACA 59.748 55.000 0.00 0.00 33.74 4.17
855 922 1.134098 CCGGTCAAAGGCTATCCACAT 60.134 52.381 0.00 0.00 33.74 3.21
856 923 2.213499 CGGTCAAAGGCTATCCACATC 58.787 52.381 0.00 0.00 33.74 3.06
857 924 2.576615 GGTCAAAGGCTATCCACATCC 58.423 52.381 0.00 0.00 33.74 3.51
858 925 2.092429 GGTCAAAGGCTATCCACATCCA 60.092 50.000 0.00 0.00 33.74 3.41
859 926 3.620488 GTCAAAGGCTATCCACATCCAA 58.380 45.455 0.00 0.00 33.74 3.53
860 927 3.629398 GTCAAAGGCTATCCACATCCAAG 59.371 47.826 0.00 0.00 33.74 3.61
861 928 3.523157 TCAAAGGCTATCCACATCCAAGA 59.477 43.478 0.00 0.00 33.74 3.02
862 929 4.166725 TCAAAGGCTATCCACATCCAAGAT 59.833 41.667 0.00 0.00 33.74 2.40
863 930 4.803329 AAGGCTATCCACATCCAAGATT 57.197 40.909 0.00 0.00 33.74 2.40
864 931 4.363991 AGGCTATCCACATCCAAGATTC 57.636 45.455 0.00 0.00 33.74 2.52
865 932 3.718434 AGGCTATCCACATCCAAGATTCA 59.282 43.478 0.00 0.00 33.74 2.57
866 933 4.166725 AGGCTATCCACATCCAAGATTCAA 59.833 41.667 0.00 0.00 33.74 2.69
867 934 4.276926 GGCTATCCACATCCAAGATTCAAC 59.723 45.833 0.00 0.00 0.00 3.18
868 935 4.276926 GCTATCCACATCCAAGATTCAACC 59.723 45.833 0.00 0.00 0.00 3.77
869 936 3.805066 TCCACATCCAAGATTCAACCA 57.195 42.857 0.00 0.00 0.00 3.67
870 937 3.689347 TCCACATCCAAGATTCAACCAG 58.311 45.455 0.00 0.00 0.00 4.00
871 938 2.756760 CCACATCCAAGATTCAACCAGG 59.243 50.000 0.00 0.00 0.00 4.45
872 939 2.165030 CACATCCAAGATTCAACCAGGC 59.835 50.000 0.00 0.00 0.00 4.85
873 940 2.042162 ACATCCAAGATTCAACCAGGCT 59.958 45.455 0.00 0.00 0.00 4.58
874 941 2.496899 TCCAAGATTCAACCAGGCTC 57.503 50.000 0.00 0.00 0.00 4.70
875 942 1.004745 TCCAAGATTCAACCAGGCTCC 59.995 52.381 0.00 0.00 0.00 4.70
880 947 0.333993 ATTCAACCAGGCTCCTGCAT 59.666 50.000 10.37 0.00 42.35 3.96
910 977 2.852075 TGGAAGCCCGGAACCTGT 60.852 61.111 0.73 0.00 34.29 4.00
934 1001 4.814967 TCCAAAATTTCTCCAGGGAAACT 58.185 39.130 0.00 0.00 37.91 2.66
955 1023 1.857348 CCCCAAAACCCTCTCCCCT 60.857 63.158 0.00 0.00 0.00 4.79
960 1028 1.146452 AAAACCCTCTCCCCTCGTTT 58.854 50.000 0.00 0.00 0.00 3.60
971 1039 1.542187 CCCTCGTTTCCTTCCTCCGT 61.542 60.000 0.00 0.00 0.00 4.69
989 1057 1.834822 TCCAAACCGCCCCCAAAAG 60.835 57.895 0.00 0.00 0.00 2.27
1083 1151 4.083862 GCCTCCGCCTCCGTTTCT 62.084 66.667 0.00 0.00 0.00 2.52
1239 1307 3.450115 CAGGACCCCGACGAGGAC 61.450 72.222 0.95 0.00 45.00 3.85
1645 1719 2.906458 CCGCATCAGCTCCTCCTT 59.094 61.111 0.00 0.00 39.10 3.36
1953 2027 1.518325 TTGCCGACATGAACGAATGT 58.482 45.000 15.70 0.00 43.47 2.71
2101 2176 4.141937 TGAGTTGTGGATATCAGTACTGCC 60.142 45.833 18.45 13.49 0.00 4.85
2117 2195 3.260100 CCTTGGCCCTCCTGGTGT 61.260 66.667 0.00 0.00 36.04 4.16
2269 2349 5.894964 TGCTGGAACCTAAACCTTTAGTTTT 59.105 36.000 4.50 0.00 46.79 2.43
2284 2364 8.406297 ACCTTTAGTTTTCTTGCTTTACTTCAG 58.594 33.333 0.00 0.00 0.00 3.02
2369 2449 0.685458 ATGAAGGTGATTGCTGGCCC 60.685 55.000 0.00 0.00 0.00 5.80
2566 2646 6.770785 ACTGTAGTAGGACTGATGATCTCTTC 59.229 42.308 0.00 0.00 0.00 2.87
2726 2812 4.455533 GGTGTAGATTTGTCATGTGCAGAA 59.544 41.667 0.00 0.00 0.00 3.02
2733 2819 3.639672 TGTCATGTGCAGAATCAGGAT 57.360 42.857 0.00 0.00 0.00 3.24
3012 3098 5.229921 TGTCTTGCCTTACGATTTTATGC 57.770 39.130 0.00 0.00 0.00 3.14
3131 3217 4.576053 TGTGTTCATGGCAATAGTATCAGC 59.424 41.667 0.00 0.16 0.00 4.26
3423 3548 6.201044 GGATTGTAACATGAATGTCTAGTCCG 59.799 42.308 0.00 0.00 40.80 4.79
3425 3550 6.762702 TGTAACATGAATGTCTAGTCCGTA 57.237 37.500 0.00 0.00 40.80 4.02
3427 3552 7.778083 TGTAACATGAATGTCTAGTCCGTATT 58.222 34.615 0.00 0.00 40.80 1.89
3430 3555 6.873997 ACATGAATGTCTAGTCCGTATTGAA 58.126 36.000 0.00 0.00 35.87 2.69
3433 3558 8.491152 CATGAATGTCTAGTCCGTATTGAAATC 58.509 37.037 0.00 0.00 0.00 2.17
3436 3561 7.589958 ATGTCTAGTCCGTATTGAAATCTCT 57.410 36.000 0.00 0.00 0.00 3.10
3438 3563 8.515695 TGTCTAGTCCGTATTGAAATCTCTAA 57.484 34.615 0.00 0.00 0.00 2.10
3440 3565 9.798994 GTCTAGTCCGTATTGAAATCTCTAAAA 57.201 33.333 0.00 0.00 0.00 1.52
3446 3571 8.319146 TCCGTATTGAAATCTCTAAAAGGACTT 58.681 33.333 0.00 0.00 0.00 3.01
3447 3572 9.595823 CCGTATTGAAATCTCTAAAAGGACTTA 57.404 33.333 0.00 0.00 0.00 2.24
3459 3584 9.694137 CTCTAAAAGGACTTATATTAGGAACGG 57.306 37.037 0.00 0.00 0.00 4.44
3480 3610 9.387257 GAACGGAAAGGACTTATATTTAGGAAA 57.613 33.333 0.00 0.00 0.00 3.13
3693 3823 3.626670 CCTGGCATTCTCTGAAACTCATC 59.373 47.826 0.00 0.00 0.00 2.92
4038 4169 4.044065 TGGGGTAGTTGATGAATTGGAAGT 59.956 41.667 0.00 0.00 0.00 3.01
4189 4320 8.232913 TCACCTTGTATTTTAAGCAAGAACTT 57.767 30.769 5.24 0.00 41.31 2.66
4442 4676 0.038892 CACATGCCCTGTTCTTGCAC 60.039 55.000 0.00 0.00 37.92 4.57
4782 5017 8.725148 GGCAACTGAATTACTATGGATGATTAG 58.275 37.037 0.00 0.00 0.00 1.73
4873 5354 8.741603 TTTACCTGCAATTAATTACTCCTACC 57.258 34.615 0.00 0.00 0.00 3.18
4874 5355 6.576778 ACCTGCAATTAATTACTCCTACCT 57.423 37.500 0.00 0.00 0.00 3.08
4875 5356 6.357367 ACCTGCAATTAATTACTCCTACCTG 58.643 40.000 0.00 0.00 0.00 4.00
4876 5357 6.069615 ACCTGCAATTAATTACTCCTACCTGT 60.070 38.462 0.00 0.00 0.00 4.00
4877 5358 6.260936 CCTGCAATTAATTACTCCTACCTGTG 59.739 42.308 0.00 0.00 0.00 3.66
4878 5359 6.953101 TGCAATTAATTACTCCTACCTGTGA 58.047 36.000 0.00 0.00 0.00 3.58
4903 5384 4.248859 GTGAGTCTATGCTGCTGAAAGAA 58.751 43.478 0.00 0.00 34.07 2.52
5134 5615 5.182001 GTCATTCTTGTGGCTCAATACTGTT 59.818 40.000 2.04 0.00 35.35 3.16
5169 5650 2.356665 TTGTCAAGCAAGTTGCCCTA 57.643 45.000 24.02 6.87 46.52 3.53
5302 5783 7.721399 AGAACTACACAAACAATGGAAGAAGAT 59.279 33.333 0.00 0.00 0.00 2.40
5323 5804 3.135225 TCGTGTTAACCATCCTGTTGTG 58.865 45.455 2.48 0.00 0.00 3.33
5366 5847 6.090223 ACAACGTCAACATTTTCAAGAAAACC 59.910 34.615 9.90 0.00 42.32 3.27
5394 5875 4.521256 GCAGGACCGATCTACTTCTCTTAT 59.479 45.833 0.00 0.00 0.00 1.73
5424 5905 1.374190 CAGAGGCTTCTGCACCTGT 59.626 57.895 13.41 0.00 43.98 4.00
5489 5970 5.745294 GCACGAACTTTGGTAGACGAATATA 59.255 40.000 0.00 0.00 33.89 0.86
5841 6322 9.341899 CTACATTCAAGGAAAAATTAAGGTTCG 57.658 33.333 0.00 0.00 0.00 3.95
5962 6444 7.862512 TTTCCTGTTTGATCAAAATGCTTTT 57.137 28.000 22.07 0.00 31.33 2.27
5973 6455 6.959671 TCAAAATGCTTTTTCAACGAGTTT 57.040 29.167 7.31 0.00 32.72 2.66
6080 6562 8.073467 TCCTTTCAAACCTTTTGTCTACAAAT 57.927 30.769 8.96 0.00 44.30 2.32
6268 6750 7.444183 ACCTCTGTCAAACGATTTCAATTTAGA 59.556 33.333 0.00 0.00 0.00 2.10
6297 6779 4.154375 CAGAGAGTACGAGCTTCTTGTGTA 59.846 45.833 0.00 0.00 29.93 2.90
6340 6822 1.202806 TCAGAGGCCTTTGTTGACTGG 60.203 52.381 21.87 1.70 0.00 4.00
6441 6923 7.604927 ACACAGATTGTACGTAACATAATTGGT 59.395 33.333 0.00 0.00 38.10 3.67
6471 6953 0.250338 AGGAGGTTTCAACTGCCGTC 60.250 55.000 0.00 0.00 0.00 4.79
6576 7058 1.767681 CCTCCCTCTTTCCCTCTCATG 59.232 57.143 0.00 0.00 0.00 3.07
6580 7062 3.264450 TCCCTCTTTCCCTCTCATGAAAC 59.736 47.826 0.00 0.00 0.00 2.78
6632 7114 4.324254 CCTTATGGTCCTTTCTTACTGGCA 60.324 45.833 0.00 0.00 0.00 4.92
6637 7119 3.307762 GGTCCTTTCTTACTGGCATGACT 60.308 47.826 0.00 0.00 0.00 3.41
6638 7120 3.686726 GTCCTTTCTTACTGGCATGACTG 59.313 47.826 3.49 3.49 0.00 3.51
6727 7215 6.986817 CCCTCCCGATTAATATAAGTATGCTG 59.013 42.308 0.00 0.00 0.00 4.41
6819 7307 3.205056 TCAAGGGGATGGCAATGTCTTAT 59.795 43.478 0.00 0.00 0.00 1.73
6840 7328 7.705325 TCTTATACGCACAAGAGATTTTAGGTC 59.295 37.037 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.169696 CCGGCCGGAATGTGCCTA 62.170 66.667 41.82 0.00 45.71 3.93
382 445 3.427573 TGAGAGGAGTCGTACCATGAAA 58.572 45.455 0.00 0.00 0.00 2.69
384 447 2.801077 TGAGAGGAGTCGTACCATGA 57.199 50.000 0.00 0.00 0.00 3.07
645 711 5.631512 GCTCTTACATACTAATGAGCTTCGG 59.368 44.000 0.00 0.00 42.28 4.30
705 772 1.701031 TTCACCAGGAACGGAGCCAA 61.701 55.000 0.00 0.00 0.00 4.52
715 782 0.178967 TTGGCAATGCTTCACCAGGA 60.179 50.000 4.82 0.00 32.79 3.86
721 788 3.058450 CGATTGTTTTGGCAATGCTTCA 58.942 40.909 4.82 0.00 38.98 3.02
722 789 3.059166 ACGATTGTTTTGGCAATGCTTC 58.941 40.909 4.82 0.00 38.98 3.86
723 790 3.110447 ACGATTGTTTTGGCAATGCTT 57.890 38.095 4.82 0.00 38.98 3.91
724 791 2.818130 ACGATTGTTTTGGCAATGCT 57.182 40.000 4.82 0.00 38.98 3.79
725 792 3.876242 AAACGATTGTTTTGGCAATGC 57.124 38.095 5.16 0.00 45.89 3.56
743 810 7.574779 GCACACATCAGTACATATTGTTGGAAA 60.575 37.037 0.00 0.00 0.00 3.13
744 811 6.128035 GCACACATCAGTACATATTGTTGGAA 60.128 38.462 0.00 0.00 0.00 3.53
745 812 5.353956 GCACACATCAGTACATATTGTTGGA 59.646 40.000 0.00 0.00 0.00 3.53
746 813 5.355071 AGCACACATCAGTACATATTGTTGG 59.645 40.000 0.00 0.00 0.00 3.77
747 814 6.426980 AGCACACATCAGTACATATTGTTG 57.573 37.500 0.00 0.00 0.00 3.33
748 815 7.391554 AGAAAGCACACATCAGTACATATTGTT 59.608 33.333 0.00 0.00 0.00 2.83
749 816 6.881065 AGAAAGCACACATCAGTACATATTGT 59.119 34.615 0.00 0.00 0.00 2.71
750 817 7.312657 AGAAAGCACACATCAGTACATATTG 57.687 36.000 0.00 0.00 0.00 1.90
751 818 6.540189 GGAGAAAGCACACATCAGTACATATT 59.460 38.462 0.00 0.00 0.00 1.28
752 819 6.051717 GGAGAAAGCACACATCAGTACATAT 58.948 40.000 0.00 0.00 0.00 1.78
753 820 5.046663 TGGAGAAAGCACACATCAGTACATA 60.047 40.000 0.00 0.00 0.00 2.29
754 821 4.256920 GGAGAAAGCACACATCAGTACAT 58.743 43.478 0.00 0.00 0.00 2.29
755 822 3.070878 TGGAGAAAGCACACATCAGTACA 59.929 43.478 0.00 0.00 0.00 2.90
756 823 3.664107 TGGAGAAAGCACACATCAGTAC 58.336 45.455 0.00 0.00 0.00 2.73
757 824 4.558226 ATGGAGAAAGCACACATCAGTA 57.442 40.909 0.00 0.00 0.00 2.74
758 825 2.936919 TGGAGAAAGCACACATCAGT 57.063 45.000 0.00 0.00 0.00 3.41
759 826 3.754850 TCAATGGAGAAAGCACACATCAG 59.245 43.478 0.00 0.00 0.00 2.90
760 827 3.753815 TCAATGGAGAAAGCACACATCA 58.246 40.909 0.00 0.00 0.00 3.07
761 828 4.978083 ATCAATGGAGAAAGCACACATC 57.022 40.909 0.00 0.00 0.00 3.06
762 829 5.733620 AAATCAATGGAGAAAGCACACAT 57.266 34.783 0.00 0.00 0.00 3.21
763 830 5.302568 AGAAAATCAATGGAGAAAGCACACA 59.697 36.000 0.00 0.00 0.00 3.72
764 831 5.776744 AGAAAATCAATGGAGAAAGCACAC 58.223 37.500 0.00 0.00 0.00 3.82
765 832 7.148018 GGATAGAAAATCAATGGAGAAAGCACA 60.148 37.037 0.00 0.00 0.00 4.57
766 833 7.148018 TGGATAGAAAATCAATGGAGAAAGCAC 60.148 37.037 0.00 0.00 0.00 4.40
767 834 6.891361 TGGATAGAAAATCAATGGAGAAAGCA 59.109 34.615 0.00 0.00 0.00 3.91
768 835 7.199078 GTGGATAGAAAATCAATGGAGAAAGC 58.801 38.462 0.00 0.00 0.00 3.51
769 836 7.559170 AGGTGGATAGAAAATCAATGGAGAAAG 59.441 37.037 0.00 0.00 0.00 2.62
770 837 7.340232 CAGGTGGATAGAAAATCAATGGAGAAA 59.660 37.037 0.00 0.00 0.00 2.52
771 838 6.830324 CAGGTGGATAGAAAATCAATGGAGAA 59.170 38.462 0.00 0.00 0.00 2.87
772 839 6.359804 CAGGTGGATAGAAAATCAATGGAGA 58.640 40.000 0.00 0.00 0.00 3.71
773 840 5.009410 GCAGGTGGATAGAAAATCAATGGAG 59.991 44.000 0.00 0.00 0.00 3.86
774 841 4.889409 GCAGGTGGATAGAAAATCAATGGA 59.111 41.667 0.00 0.00 0.00 3.41
775 842 4.891756 AGCAGGTGGATAGAAAATCAATGG 59.108 41.667 0.00 0.00 0.00 3.16
776 843 7.572523 TTAGCAGGTGGATAGAAAATCAATG 57.427 36.000 0.00 0.00 0.00 2.82
777 844 8.773033 AATTAGCAGGTGGATAGAAAATCAAT 57.227 30.769 0.00 0.00 0.00 2.57
778 845 9.866655 ATAATTAGCAGGTGGATAGAAAATCAA 57.133 29.630 0.00 0.00 0.00 2.57
779 846 9.866655 AATAATTAGCAGGTGGATAGAAAATCA 57.133 29.630 0.00 0.00 0.00 2.57
824 891 3.889134 TTGACCGGAGCTGCTGCAG 62.889 63.158 24.80 24.80 42.74 4.41
825 892 3.474486 TTTGACCGGAGCTGCTGCA 62.474 57.895 21.11 0.88 42.74 4.41
826 893 2.669569 TTTGACCGGAGCTGCTGC 60.670 61.111 9.46 9.56 40.05 5.25
827 894 2.037136 CCTTTGACCGGAGCTGCTG 61.037 63.158 9.46 0.00 0.00 4.41
828 895 2.348998 CCTTTGACCGGAGCTGCT 59.651 61.111 9.46 0.00 0.00 4.24
829 896 2.521958 TAGCCTTTGACCGGAGCTGC 62.522 60.000 9.46 2.55 35.03 5.25
830 897 0.179000 ATAGCCTTTGACCGGAGCTG 59.821 55.000 9.46 0.00 35.03 4.24
831 898 0.466124 GATAGCCTTTGACCGGAGCT 59.534 55.000 9.46 8.74 37.58 4.09
832 899 0.533085 GGATAGCCTTTGACCGGAGC 60.533 60.000 9.46 0.00 0.00 4.70
833 900 0.830648 TGGATAGCCTTTGACCGGAG 59.169 55.000 9.46 0.00 34.31 4.63
834 901 0.539986 GTGGATAGCCTTTGACCGGA 59.460 55.000 9.46 0.00 34.31 5.14
835 902 0.251916 TGTGGATAGCCTTTGACCGG 59.748 55.000 0.00 0.00 34.31 5.28
836 903 2.213499 GATGTGGATAGCCTTTGACCG 58.787 52.381 0.00 0.00 34.31 4.79
837 904 2.092429 TGGATGTGGATAGCCTTTGACC 60.092 50.000 0.00 0.00 34.31 4.02
838 905 3.281727 TGGATGTGGATAGCCTTTGAC 57.718 47.619 0.00 0.00 34.31 3.18
839 906 3.523157 TCTTGGATGTGGATAGCCTTTGA 59.477 43.478 0.00 0.00 34.31 2.69
840 907 3.889815 TCTTGGATGTGGATAGCCTTTG 58.110 45.455 0.00 0.00 34.31 2.77
841 908 4.803329 ATCTTGGATGTGGATAGCCTTT 57.197 40.909 0.00 0.00 34.31 3.11
842 909 4.166725 TGAATCTTGGATGTGGATAGCCTT 59.833 41.667 0.00 0.00 34.31 4.35
843 910 3.718434 TGAATCTTGGATGTGGATAGCCT 59.282 43.478 0.00 0.00 34.31 4.58
844 911 4.090761 TGAATCTTGGATGTGGATAGCC 57.909 45.455 0.00 0.00 0.00 3.93
845 912 4.276926 GGTTGAATCTTGGATGTGGATAGC 59.723 45.833 0.00 0.00 0.00 2.97
846 913 5.439721 TGGTTGAATCTTGGATGTGGATAG 58.560 41.667 0.00 0.00 0.00 2.08
847 914 5.439721 CTGGTTGAATCTTGGATGTGGATA 58.560 41.667 0.00 0.00 0.00 2.59
848 915 4.275810 CTGGTTGAATCTTGGATGTGGAT 58.724 43.478 0.00 0.00 0.00 3.41
849 916 3.561960 CCTGGTTGAATCTTGGATGTGGA 60.562 47.826 0.00 0.00 0.00 4.02
850 917 2.756760 CCTGGTTGAATCTTGGATGTGG 59.243 50.000 0.00 0.00 0.00 4.17
851 918 2.165030 GCCTGGTTGAATCTTGGATGTG 59.835 50.000 0.00 0.00 0.00 3.21
852 919 2.042162 AGCCTGGTTGAATCTTGGATGT 59.958 45.455 0.00 0.00 0.00 3.06
853 920 2.686915 GAGCCTGGTTGAATCTTGGATG 59.313 50.000 0.00 0.00 0.00 3.51
854 921 2.357569 GGAGCCTGGTTGAATCTTGGAT 60.358 50.000 0.00 0.00 0.00 3.41
855 922 1.004745 GGAGCCTGGTTGAATCTTGGA 59.995 52.381 0.00 0.00 0.00 3.53
856 923 1.005215 AGGAGCCTGGTTGAATCTTGG 59.995 52.381 0.00 0.00 0.00 3.61
857 924 2.089980 CAGGAGCCTGGTTGAATCTTG 58.910 52.381 8.69 0.00 40.17 3.02
858 925 1.615384 GCAGGAGCCTGGTTGAATCTT 60.615 52.381 17.64 0.00 43.77 2.40
859 926 0.034670 GCAGGAGCCTGGTTGAATCT 60.035 55.000 17.64 0.00 43.77 2.40
860 927 0.322816 TGCAGGAGCCTGGTTGAATC 60.323 55.000 17.64 0.48 43.77 2.52
861 928 0.333993 ATGCAGGAGCCTGGTTGAAT 59.666 50.000 17.64 0.00 43.77 2.57
862 929 0.991146 TATGCAGGAGCCTGGTTGAA 59.009 50.000 17.64 0.00 43.77 2.69
863 930 1.141657 GATATGCAGGAGCCTGGTTGA 59.858 52.381 17.64 0.00 43.77 3.18
864 931 1.602311 GATATGCAGGAGCCTGGTTG 58.398 55.000 17.64 0.00 43.77 3.77
865 932 0.475906 GGATATGCAGGAGCCTGGTT 59.524 55.000 17.64 0.00 43.77 3.67
866 933 0.401105 AGGATATGCAGGAGCCTGGT 60.401 55.000 17.64 0.00 43.77 4.00
867 934 0.324285 GAGGATATGCAGGAGCCTGG 59.676 60.000 17.64 0.00 43.77 4.45
868 935 0.324285 GGAGGATATGCAGGAGCCTG 59.676 60.000 12.63 12.17 46.15 4.85
869 936 0.839853 GGGAGGATATGCAGGAGCCT 60.840 60.000 7.89 7.89 41.13 4.58
870 937 1.682257 GGGAGGATATGCAGGAGCC 59.318 63.158 0.00 0.00 41.13 4.70
871 938 1.294780 CGGGAGGATATGCAGGAGC 59.705 63.158 0.00 0.00 42.57 4.70
872 939 1.294780 GCGGGAGGATATGCAGGAG 59.705 63.158 0.00 0.00 0.00 3.69
873 940 2.574018 CGCGGGAGGATATGCAGGA 61.574 63.158 0.00 0.00 0.00 3.86
874 941 2.047844 CGCGGGAGGATATGCAGG 60.048 66.667 0.00 0.00 0.00 4.85
875 942 2.740055 GCGCGGGAGGATATGCAG 60.740 66.667 8.83 0.00 0.00 4.41
880 947 2.443203 TTCCAGCGCGGGAGGATA 60.443 61.111 27.90 11.98 38.42 2.59
910 977 4.740154 TTCCCTGGAGAAATTTTGGAGA 57.260 40.909 0.00 0.00 0.00 3.71
934 1001 2.851045 GAGAGGGTTTTGGGGGCA 59.149 61.111 0.00 0.00 0.00 5.36
955 1023 0.828762 TGGACGGAGGAAGGAAACGA 60.829 55.000 0.00 0.00 0.00 3.85
960 1028 1.823169 CGGTTTGGACGGAGGAAGGA 61.823 60.000 0.00 0.00 0.00 3.36
971 1039 1.834822 CTTTTGGGGGCGGTTTGGA 60.835 57.895 0.00 0.00 0.00 3.53
989 1057 1.706287 GCGCCCCATTCTCGAAGAAC 61.706 60.000 0.00 0.00 37.00 3.01
1072 1140 1.810030 CGCCAGTAGAAACGGAGGC 60.810 63.158 0.00 0.00 38.64 4.70
1392 1466 0.956633 GGGTTCGGAACAAAGGAACC 59.043 55.000 21.36 12.51 0.00 3.62
1506 1580 2.203351 GGCGATGGGATTGGGGTC 60.203 66.667 0.00 0.00 0.00 4.46
1684 1758 3.938637 TTCGAGGCCGAGGAGCAGA 62.939 63.158 0.00 0.00 46.39 4.26
2078 2153 4.141937 GGCAGTACTGATATCCACAACTCA 60.142 45.833 27.08 0.00 0.00 3.41
2101 2176 1.604378 CTACACCAGGAGGGCCAAG 59.396 63.158 6.18 0.00 42.05 3.61
2269 2349 5.696724 GTCACTAAGCTGAAGTAAAGCAAGA 59.303 40.000 1.86 0.00 43.37 3.02
2311 2391 6.248569 ACTCCAAAGTTCTGACTAAGGAAA 57.751 37.500 0.00 0.00 38.04 3.13
2726 2812 6.260936 GGTTACATTCATGAAACGATCCTGAT 59.739 38.462 13.09 0.00 33.44 2.90
2733 2819 7.065324 GGTTAGATGGTTACATTCATGAAACGA 59.935 37.037 13.09 3.70 37.47 3.85
2965 3051 5.190528 ACCTTCTCAGGAAAATGAGCAGATA 59.809 40.000 5.17 0.00 45.25 1.98
3299 3385 6.777580 GGTGGAACATTAAGGGTGATGAATAT 59.222 38.462 0.00 0.00 44.52 1.28
3300 3386 6.126409 GGTGGAACATTAAGGGTGATGAATA 58.874 40.000 0.00 0.00 44.52 1.75
3433 3558 9.694137 CCGTTCCTAATATAAGTCCTTTTAGAG 57.306 37.037 0.00 0.00 0.00 2.43
3438 3563 7.991460 CCTTTCCGTTCCTAATATAAGTCCTTT 59.009 37.037 0.00 0.00 0.00 3.11
3440 3565 6.842807 TCCTTTCCGTTCCTAATATAAGTCCT 59.157 38.462 0.00 0.00 0.00 3.85
3453 3578 7.503549 TCCTAAATATAAGTCCTTTCCGTTCC 58.496 38.462 0.00 0.00 0.00 3.62
3454 3579 8.953368 TTCCTAAATATAAGTCCTTTCCGTTC 57.047 34.615 0.00 0.00 0.00 3.95
3455 3580 9.392259 CTTTCCTAAATATAAGTCCTTTCCGTT 57.608 33.333 0.00 0.00 0.00 4.44
3457 3582 8.208903 TCCTTTCCTAAATATAAGTCCTTTCCG 58.791 37.037 0.00 0.00 0.00 4.30
3459 3584 9.562408 CCTCCTTTCCTAAATATAAGTCCTTTC 57.438 37.037 0.00 0.00 0.00 2.62
3480 3610 4.338795 TCTTTCACATCTACTCCCTCCT 57.661 45.455 0.00 0.00 0.00 3.69
3693 3823 2.022764 TGCAGACAATGGTATGACCG 57.977 50.000 0.00 0.00 42.58 4.79
3722 3852 7.426929 AAAAACGCTATATAAGAGGATGCTG 57.573 36.000 0.00 0.00 0.00 4.41
4038 4169 2.882927 AACAAGTCTGACACGTGCTA 57.117 45.000 17.22 3.55 37.98 3.49
4189 4320 5.872617 CGGACACTTCCATAAATAACTGTCA 59.127 40.000 0.00 0.00 43.00 3.58
4442 4676 7.149080 CGAACAGAACACATTGAATAGCAAAAG 60.149 37.037 0.00 0.00 40.48 2.27
4782 5017 1.269936 ACACATTGCTGGCAAAGAAGC 60.270 47.619 15.75 0.00 39.55 3.86
4877 5358 2.165234 TCAGCAGCATAGACTCACAGTC 59.835 50.000 0.00 0.00 45.38 3.51
4878 5359 2.174360 TCAGCAGCATAGACTCACAGT 58.826 47.619 0.00 0.00 0.00 3.55
4928 5409 1.557099 TTCAGTCACCTGTATCGCCT 58.443 50.000 0.00 0.00 39.82 5.52
5134 5615 5.971202 GCTTGACAAATCGACTTTCTTTGAA 59.029 36.000 13.78 1.43 34.69 2.69
5302 5783 3.135225 CACAACAGGATGGTTAACACGA 58.865 45.455 8.10 0.00 43.62 4.35
5323 5804 1.084289 GTGCTCGGACACCATTTACC 58.916 55.000 0.00 0.00 34.35 2.85
5366 5847 2.520069 AGTAGATCGGTCCTGCATAGG 58.480 52.381 0.00 0.00 46.06 2.57
5394 5875 1.896660 GCCTCTGCGTTGTTCCCAA 60.897 57.895 0.00 0.00 0.00 4.12
5424 5905 5.727279 TGTTGGGGTTCATGTCTATAGGTAA 59.273 40.000 0.00 0.00 0.00 2.85
5489 5970 2.172505 TCGCCACAATAGGATGGTCAAT 59.827 45.455 0.00 0.00 38.34 2.57
5962 6444 4.124238 CCACCAGTCTTAAACTCGTTGAA 58.876 43.478 0.00 0.00 35.45 2.69
5973 6455 6.727231 TGTAGGAAAATCTACCACCAGTCTTA 59.273 38.462 0.00 0.00 38.97 2.10
6268 6750 1.746220 AGCTCGTACTCTCTGCGATTT 59.254 47.619 0.00 0.00 36.32 2.17
6297 6779 8.812513 TGAAATTTGACTTCCATCATCTATGT 57.187 30.769 0.00 0.00 33.34 2.29
6598 7080 4.536765 AGGACCATAAGGCAAAGGTATTG 58.463 43.478 0.00 0.00 39.06 1.90
6819 7307 4.082625 TCGACCTAAAATCTCTTGTGCGTA 60.083 41.667 0.00 0.00 0.00 4.42
6840 7328 8.516234 ACTAGGAGCATACTTATAAGACATTCG 58.484 37.037 19.38 2.79 0.00 3.34


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

AutoCloner maintained by Alex Coulton.