Multiple sequence alignment - TraesCS2A01G380400

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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 TraesCS2A01G380400 chr2A 100.000 4271 0 0 1 4271 623936490 623940760 0.000000e+00 7888.0
1 TraesCS2A01G380400 chr2A 90.909 99 3 1 2 100 623936654 623936746 1.250000e-25 128.0
2 TraesCS2A01G380400 chr2D 97.254 3423 85 4 851 4271 481047535 481050950 0.000000e+00 5792.0
3 TraesCS2A01G380400 chr2D 86.736 573 54 14 96 656 192758980 192758418 6.070000e-173 617.0
4 TraesCS2A01G380400 chr2D 86.038 573 65 10 96 656 151899090 151899659 6.110000e-168 601.0
5 TraesCS2A01G380400 chr2D 86.323 563 61 10 96 646 309438821 309439379 2.200000e-167 599.0
6 TraesCS2A01G380400 chr2D 85.839 572 67 8 96 656 186869762 186869194 2.840000e-166 595.0
7 TraesCS2A01G380400 chr2D 85.417 576 65 13 96 657 122749010 122748440 7.960000e-162 580.0
8 TraesCS2A01G380400 chr2B 97.325 3402 86 3 867 4268 564228569 564231965 0.000000e+00 5773.0
9 TraesCS2A01G380400 chr5D 88.333 540 44 9 135 656 391546806 391547344 7.790000e-177 630.0
10 TraesCS2A01G380400 chr5D 85.515 573 69 9 96 657 178735092 178735661 1.710000e-163 586.0
11 TraesCS2A01G380400 chr4D 85.913 575 62 14 96 656 293670199 293669630 2.840000e-166 595.0
12 TraesCS2A01G380400 chr3D 85.839 572 56 14 96 648 260707116 260707681 6.150000e-163 584.0
13 TraesCS2A01G380400 chr4A 93.137 102 3 2 2 100 376580215 376580115 3.440000e-31 147.0
14 TraesCS2A01G380400 chr7D 96.970 33 1 0 68 100 50546884 50546916 5.970000e-04 56.5
15 TraesCS2A01G380400 chr7A 100.000 28 0 0 68 95 571627166 571627139 8.000000e-03 52.8


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 TraesCS2A01G380400 chr2A 623936490 623940760 4270 False 7888 7888 100.000 1 4271 1 chr2A.!!$F1 4270
1 TraesCS2A01G380400 chr2D 481047535 481050950 3415 False 5792 5792 97.254 851 4271 1 chr2D.!!$F3 3420
2 TraesCS2A01G380400 chr2D 192758418 192758980 562 True 617 617 86.736 96 656 1 chr2D.!!$R3 560
3 TraesCS2A01G380400 chr2D 151899090 151899659 569 False 601 601 86.038 96 656 1 chr2D.!!$F1 560
4 TraesCS2A01G380400 chr2D 309438821 309439379 558 False 599 599 86.323 96 646 1 chr2D.!!$F2 550
5 TraesCS2A01G380400 chr2D 186869194 186869762 568 True 595 595 85.839 96 656 1 chr2D.!!$R2 560
6 TraesCS2A01G380400 chr2D 122748440 122749010 570 True 580 580 85.417 96 657 1 chr2D.!!$R1 561
7 TraesCS2A01G380400 chr2B 564228569 564231965 3396 False 5773 5773 97.325 867 4268 1 chr2B.!!$F1 3401
8 TraesCS2A01G380400 chr5D 391546806 391547344 538 False 630 630 88.333 135 656 1 chr5D.!!$F2 521
9 TraesCS2A01G380400 chr5D 178735092 178735661 569 False 586 586 85.515 96 657 1 chr5D.!!$F1 561
10 TraesCS2A01G380400 chr4D 293669630 293670199 569 True 595 595 85.913 96 656 1 chr4D.!!$R1 560
11 TraesCS2A01G380400 chr3D 260707116 260707681 565 False 584 584 85.839 96 648 1 chr3D.!!$F1 552

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
86 87 0.034198 TGAAGATGGCGGTTCGTGAA 59.966 50.0 0.00 0.0 0.00 3.18 F
583 606 0.035176 TGTCCCGTTTAACCCCTTCG 59.965 55.0 0.00 0.0 0.00 3.79 F
784 807 0.250424 CCGGGTTTTTACGGGTCACT 60.250 55.0 0.00 0.0 46.08 3.41 F
911 934 0.323816 TGAGCTCCTGATCGTCACCT 60.324 55.0 12.15 0.0 0.00 4.00 F
2139 2162 0.334676 TGGGTTTGGATGGGGATGTC 59.665 55.0 0.00 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1577 0.461961 AGCCGCTCTTGGAGTACATC 59.538 55.000 0.00 0.00 31.39 3.06 R
1592 1615 0.820226 CCTCATCCTCGTGAAGAGCA 59.180 55.000 4.99 0.00 45.54 4.26 R
2119 2142 1.018031 ACATCCCCATCCAAACCCAT 58.982 50.000 0.00 0.00 0.00 4.00 R
2499 2522 3.122278 CCATCATTTCAAAGTGCTTTGCG 59.878 43.478 17.16 7.85 46.92 4.85 R
3848 3873 3.239449 ACATGTGTCTCTGTTACTCCCA 58.761 45.455 0.00 0.00 0.00 4.37 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
37 38 2.961768 GCTGCTGGCGGCTTAAAA 59.038 55.556 20.66 0.00 44.39 1.52
38 39 1.153958 GCTGCTGGCGGCTTAAAAG 60.154 57.895 20.66 9.07 44.39 2.27
39 40 1.586154 GCTGCTGGCGGCTTAAAAGA 61.586 55.000 20.66 0.00 44.39 2.52
40 41 1.098050 CTGCTGGCGGCTTAAAAGAT 58.902 50.000 20.66 0.00 42.39 2.40
41 42 0.810648 TGCTGGCGGCTTAAAAGATG 59.189 50.000 20.66 0.00 42.39 2.90
42 43 1.094785 GCTGGCGGCTTAAAAGATGA 58.905 50.000 11.99 0.00 38.06 2.92
43 44 1.472480 GCTGGCGGCTTAAAAGATGAA 59.528 47.619 11.99 0.00 38.06 2.57
44 45 2.478539 GCTGGCGGCTTAAAAGATGAAG 60.479 50.000 11.99 0.00 38.06 3.02
45 46 3.009723 CTGGCGGCTTAAAAGATGAAGA 58.990 45.455 11.43 0.00 0.00 2.87
46 47 3.417101 TGGCGGCTTAAAAGATGAAGAA 58.583 40.909 11.43 0.00 0.00 2.52
47 48 3.440173 TGGCGGCTTAAAAGATGAAGAAG 59.560 43.478 11.43 0.00 0.00 2.85
48 49 3.440522 GGCGGCTTAAAAGATGAAGAAGT 59.559 43.478 0.00 0.00 0.00 3.01
49 50 4.437524 GGCGGCTTAAAAGATGAAGAAGTC 60.438 45.833 0.00 0.00 0.00 3.01
50 51 4.437524 GCGGCTTAAAAGATGAAGAAGTCC 60.438 45.833 0.00 0.00 0.00 3.85
51 52 4.201724 CGGCTTAAAAGATGAAGAAGTCCG 60.202 45.833 0.00 0.00 33.69 4.79
52 53 4.935808 GGCTTAAAAGATGAAGAAGTCCGA 59.064 41.667 0.00 0.00 0.00 4.55
53 54 5.163844 GGCTTAAAAGATGAAGAAGTCCGAC 60.164 44.000 0.00 0.00 0.00 4.79
54 55 5.444745 GCTTAAAAGATGAAGAAGTCCGACG 60.445 44.000 0.00 0.00 0.00 5.12
55 56 3.936372 AAAGATGAAGAAGTCCGACGA 57.064 42.857 0.00 0.00 0.00 4.20
56 57 3.495670 AAGATGAAGAAGTCCGACGAG 57.504 47.619 0.00 0.00 0.00 4.18
57 58 1.746220 AGATGAAGAAGTCCGACGAGG 59.254 52.381 0.00 0.00 42.97 4.63
58 59 0.173708 ATGAAGAAGTCCGACGAGGC 59.826 55.000 0.00 0.00 40.77 4.70
59 60 1.153804 GAAGAAGTCCGACGAGGCC 60.154 63.158 0.00 0.00 40.77 5.19
60 61 2.560051 GAAGAAGTCCGACGAGGCCC 62.560 65.000 0.00 0.00 40.77 5.80
61 62 3.379445 GAAGTCCGACGAGGCCCA 61.379 66.667 0.00 0.00 40.77 5.36
62 63 2.920912 AAGTCCGACGAGGCCCAA 60.921 61.111 0.00 0.00 40.77 4.12
63 64 2.837371 GAAGTCCGACGAGGCCCAAG 62.837 65.000 0.00 0.00 40.77 3.61
64 65 3.379445 GTCCGACGAGGCCCAAGA 61.379 66.667 0.00 0.00 40.77 3.02
65 66 3.379445 TCCGACGAGGCCCAAGAC 61.379 66.667 0.00 0.00 40.77 3.01
66 67 3.691342 CCGACGAGGCCCAAGACA 61.691 66.667 0.00 0.00 0.00 3.41
67 68 2.579201 CGACGAGGCCCAAGACAT 59.421 61.111 0.00 0.00 0.00 3.06
68 69 1.811266 CGACGAGGCCCAAGACATG 60.811 63.158 0.00 0.00 0.00 3.21
69 70 1.596934 GACGAGGCCCAAGACATGA 59.403 57.895 0.00 0.00 0.00 3.07
70 71 0.036388 GACGAGGCCCAAGACATGAA 60.036 55.000 0.00 0.00 0.00 2.57
71 72 0.036010 ACGAGGCCCAAGACATGAAG 60.036 55.000 0.00 0.00 0.00 3.02
72 73 0.250234 CGAGGCCCAAGACATGAAGA 59.750 55.000 0.00 0.00 0.00 2.87
73 74 1.134280 CGAGGCCCAAGACATGAAGAT 60.134 52.381 0.00 0.00 0.00 2.40
74 75 2.295885 GAGGCCCAAGACATGAAGATG 58.704 52.381 0.00 0.00 35.49 2.90
75 76 1.064166 AGGCCCAAGACATGAAGATGG 60.064 52.381 0.00 2.12 33.39 3.51
76 77 0.743097 GCCCAAGACATGAAGATGGC 59.257 55.000 0.00 1.88 37.98 4.40
77 78 1.019673 CCCAAGACATGAAGATGGCG 58.980 55.000 0.00 0.00 43.25 5.69
78 79 1.019673 CCAAGACATGAAGATGGCGG 58.980 55.000 0.00 0.00 43.25 6.13
79 80 1.679944 CCAAGACATGAAGATGGCGGT 60.680 52.381 0.00 0.00 43.25 5.68
80 81 2.086869 CAAGACATGAAGATGGCGGTT 58.913 47.619 0.00 0.00 43.25 4.44
81 82 2.029838 AGACATGAAGATGGCGGTTC 57.970 50.000 0.00 0.00 43.25 3.62
82 83 0.652592 GACATGAAGATGGCGGTTCG 59.347 55.000 0.00 0.00 33.39 3.95
83 84 0.036388 ACATGAAGATGGCGGTTCGT 60.036 50.000 0.00 0.00 33.39 3.85
84 85 0.374758 CATGAAGATGGCGGTTCGTG 59.625 55.000 0.00 2.35 34.30 4.35
85 86 0.249120 ATGAAGATGGCGGTTCGTGA 59.751 50.000 0.00 0.00 0.00 4.35
86 87 0.034198 TGAAGATGGCGGTTCGTGAA 59.966 50.000 0.00 0.00 0.00 3.18
87 88 0.721718 GAAGATGGCGGTTCGTGAAG 59.278 55.000 0.00 0.00 0.00 3.02
88 89 1.298859 AAGATGGCGGTTCGTGAAGC 61.299 55.000 1.79 1.79 35.61 3.86
89 90 2.031919 ATGGCGGTTCGTGAAGCA 59.968 55.556 11.81 0.00 38.62 3.91
90 91 1.970917 GATGGCGGTTCGTGAAGCAG 61.971 60.000 11.81 6.08 38.62 4.24
91 92 3.423154 GGCGGTTCGTGAAGCAGG 61.423 66.667 11.81 0.00 38.62 4.85
92 93 4.090057 GCGGTTCGTGAAGCAGGC 62.090 66.667 11.81 4.62 38.62 4.85
93 94 2.357517 CGGTTCGTGAAGCAGGCT 60.358 61.111 11.81 0.00 38.62 4.58
94 95 1.961277 CGGTTCGTGAAGCAGGCTT 60.961 57.895 6.17 6.17 38.62 4.35
106 107 4.951715 TGAAGCAGGCTTATTGATGTGAAT 59.048 37.500 6.49 0.00 36.26 2.57
107 108 4.913335 AGCAGGCTTATTGATGTGAATG 57.087 40.909 0.00 0.00 0.00 2.67
152 153 7.689299 CCTAATGTTGGGGATATGACTATTGA 58.311 38.462 0.00 0.00 0.00 2.57
201 202 1.153958 GCTGCTGGCGGCTTAAAAG 60.154 57.895 20.66 9.07 44.39 2.27
202 203 1.586154 GCTGCTGGCGGCTTAAAAGA 61.586 55.000 20.66 0.00 44.39 2.52
203 204 1.098050 CTGCTGGCGGCTTAAAAGAT 58.902 50.000 20.66 0.00 42.39 2.40
204 205 0.810648 TGCTGGCGGCTTAAAAGATG 59.189 50.000 20.66 0.00 42.39 2.90
206 207 1.472480 GCTGGCGGCTTAAAAGATGAA 59.528 47.619 11.99 0.00 38.06 2.57
207 208 2.478539 GCTGGCGGCTTAAAAGATGAAG 60.479 50.000 11.99 0.00 38.06 3.02
209 210 3.417101 TGGCGGCTTAAAAGATGAAGAA 58.583 40.909 11.43 0.00 0.00 2.52
210 211 3.440173 TGGCGGCTTAAAAGATGAAGAAG 59.560 43.478 11.43 0.00 0.00 2.85
213 214 4.437524 GCGGCTTAAAAGATGAAGAAGTCC 60.438 45.833 0.00 0.00 0.00 3.85
216 217 4.437524 GCTTAAAAGATGAAGAAGTCCGCC 60.438 45.833 0.00 0.00 0.00 6.13
217 218 2.115343 AAAGATGAAGAAGTCCGCCC 57.885 50.000 0.00 0.00 0.00 6.13
245 254 4.271696 TGAAGATGACGGTTCATGAAGT 57.728 40.909 8.80 4.01 42.95 3.01
308 318 3.007940 CCAAAGGGATGAGACGCCATATA 59.992 47.826 0.00 0.00 35.59 0.86
450 471 6.231211 ACTGAAGTAACAACCAATCGAGAAT 58.769 36.000 0.00 0.00 0.00 2.40
464 485 4.707030 TCGAGAATTAGGTCAAGCGTAA 57.293 40.909 0.00 0.00 32.81 3.18
542 563 1.961180 CTCGTTGAGAGGGGCCGAAT 61.961 60.000 0.00 0.00 43.20 3.34
562 584 2.160205 TCTGGGTAACTCTCTGTGTCG 58.840 52.381 0.00 0.00 0.00 4.35
583 606 0.035176 TGTCCCGTTTAACCCCTTCG 59.965 55.000 0.00 0.00 0.00 3.79
606 629 3.550437 CTAACCTAGCTGTGATGGCTT 57.450 47.619 0.00 0.00 40.74 4.35
648 671 4.307032 AGGGCATCTGTCATGTTAAGTT 57.693 40.909 0.00 0.00 0.00 2.66
660 683 6.299023 TCATGTTAAGTTCATGACACACAC 57.701 37.500 0.00 0.00 44.14 3.82
661 684 4.787381 TGTTAAGTTCATGACACACACG 57.213 40.909 0.00 0.00 0.00 4.49
662 685 3.558006 TGTTAAGTTCATGACACACACGG 59.442 43.478 0.00 0.00 0.00 4.94
663 686 2.325583 AAGTTCATGACACACACGGT 57.674 45.000 0.00 0.00 0.00 4.83
671 694 3.115556 CACACACGGTGGGTTTGG 58.884 61.111 14.49 0.00 44.04 3.28
672 695 1.751162 CACACACGGTGGGTTTGGT 60.751 57.895 14.49 0.00 44.04 3.67
673 696 1.751162 ACACACGGTGGGTTTGGTG 60.751 57.895 10.90 0.45 37.94 4.17
674 697 2.831284 ACACGGTGGGTTTGGTGC 60.831 61.111 13.48 0.00 33.81 5.01
675 698 3.601685 CACGGTGGGTTTGGTGCC 61.602 66.667 0.00 0.00 0.00 5.01
678 701 4.589675 GGTGGGTTTGGTGCCGGA 62.590 66.667 5.05 0.00 0.00 5.14
679 702 2.983592 GTGGGTTTGGTGCCGGAG 60.984 66.667 5.05 0.00 0.00 4.63
680 703 3.172106 TGGGTTTGGTGCCGGAGA 61.172 61.111 5.05 0.00 0.00 3.71
681 704 2.359975 GGGTTTGGTGCCGGAGAG 60.360 66.667 5.05 0.00 0.00 3.20
682 705 2.747686 GGTTTGGTGCCGGAGAGA 59.252 61.111 5.05 0.00 0.00 3.10
683 706 1.376037 GGTTTGGTGCCGGAGAGAG 60.376 63.158 5.05 0.00 0.00 3.20
684 707 1.671742 GTTTGGTGCCGGAGAGAGA 59.328 57.895 5.05 0.00 0.00 3.10
685 708 0.390472 GTTTGGTGCCGGAGAGAGAG 60.390 60.000 5.05 0.00 0.00 3.20
686 709 1.544825 TTTGGTGCCGGAGAGAGAGG 61.545 60.000 5.05 0.00 0.00 3.69
687 710 2.043852 GGTGCCGGAGAGAGAGGA 60.044 66.667 5.05 0.00 0.00 3.71
688 711 1.682684 GGTGCCGGAGAGAGAGGAA 60.683 63.158 5.05 0.00 0.00 3.36
689 712 1.045911 GGTGCCGGAGAGAGAGGAAT 61.046 60.000 5.05 0.00 0.00 3.01
690 713 0.827368 GTGCCGGAGAGAGAGGAATT 59.173 55.000 5.05 0.00 0.00 2.17
691 714 0.826715 TGCCGGAGAGAGAGGAATTG 59.173 55.000 5.05 0.00 0.00 2.32
692 715 0.827368 GCCGGAGAGAGAGGAATTGT 59.173 55.000 5.05 0.00 0.00 2.71
693 716 2.032620 GCCGGAGAGAGAGGAATTGTA 58.967 52.381 5.05 0.00 0.00 2.41
694 717 2.431057 GCCGGAGAGAGAGGAATTGTAA 59.569 50.000 5.05 0.00 0.00 2.41
695 718 3.738590 GCCGGAGAGAGAGGAATTGTAAC 60.739 52.174 5.05 0.00 0.00 2.50
696 719 3.489398 CCGGAGAGAGAGGAATTGTAACG 60.489 52.174 0.00 0.00 0.00 3.18
697 720 3.489398 CGGAGAGAGAGGAATTGTAACGG 60.489 52.174 0.00 0.00 0.00 4.44
698 721 3.700038 GGAGAGAGAGGAATTGTAACGGA 59.300 47.826 0.00 0.00 0.00 4.69
699 722 4.202070 GGAGAGAGAGGAATTGTAACGGAG 60.202 50.000 0.00 0.00 0.00 4.63
700 723 3.702045 AGAGAGAGGAATTGTAACGGAGG 59.298 47.826 0.00 0.00 0.00 4.30
701 724 3.700038 GAGAGAGGAATTGTAACGGAGGA 59.300 47.826 0.00 0.00 0.00 3.71
702 725 4.094476 AGAGAGGAATTGTAACGGAGGAA 58.906 43.478 0.00 0.00 0.00 3.36
703 726 4.160626 AGAGAGGAATTGTAACGGAGGAAG 59.839 45.833 0.00 0.00 0.00 3.46
704 727 2.937149 GAGGAATTGTAACGGAGGAAGC 59.063 50.000 0.00 0.00 0.00 3.86
705 728 2.572104 AGGAATTGTAACGGAGGAAGCT 59.428 45.455 0.00 0.00 0.00 3.74
706 729 2.678336 GGAATTGTAACGGAGGAAGCTG 59.322 50.000 0.00 0.00 0.00 4.24
707 730 2.403252 ATTGTAACGGAGGAAGCTGG 57.597 50.000 0.00 0.00 0.00 4.85
708 731 0.323629 TTGTAACGGAGGAAGCTGGG 59.676 55.000 0.00 0.00 0.00 4.45
709 732 1.221021 GTAACGGAGGAAGCTGGGG 59.779 63.158 0.00 0.00 0.00 4.96
710 733 1.993391 TAACGGAGGAAGCTGGGGG 60.993 63.158 0.00 0.00 0.00 5.40
711 734 2.465010 TAACGGAGGAAGCTGGGGGA 62.465 60.000 0.00 0.00 0.00 4.81
712 735 2.770048 CGGAGGAAGCTGGGGGAT 60.770 66.667 0.00 0.00 0.00 3.85
713 736 2.378634 CGGAGGAAGCTGGGGGATT 61.379 63.158 0.00 0.00 0.00 3.01
714 737 1.926426 CGGAGGAAGCTGGGGGATTT 61.926 60.000 0.00 0.00 0.00 2.17
715 738 0.396278 GGAGGAAGCTGGGGGATTTG 60.396 60.000 0.00 0.00 0.00 2.32
716 739 0.625849 GAGGAAGCTGGGGGATTTGA 59.374 55.000 0.00 0.00 0.00 2.69
717 740 0.332972 AGGAAGCTGGGGGATTTGAC 59.667 55.000 0.00 0.00 0.00 3.18
718 741 1.032114 GGAAGCTGGGGGATTTGACG 61.032 60.000 0.00 0.00 0.00 4.35
719 742 1.000896 AAGCTGGGGGATTTGACGG 60.001 57.895 0.00 0.00 0.00 4.79
720 743 1.497309 AAGCTGGGGGATTTGACGGA 61.497 55.000 0.00 0.00 0.00 4.69
721 744 1.227383 GCTGGGGGATTTGACGGAT 59.773 57.895 0.00 0.00 0.00 4.18
722 745 0.472471 GCTGGGGGATTTGACGGATA 59.528 55.000 0.00 0.00 0.00 2.59
723 746 1.543429 GCTGGGGGATTTGACGGATAG 60.543 57.143 0.00 0.00 0.00 2.08
724 747 2.047061 CTGGGGGATTTGACGGATAGA 58.953 52.381 0.00 0.00 0.00 1.98
725 748 2.438021 CTGGGGGATTTGACGGATAGAA 59.562 50.000 0.00 0.00 0.00 2.10
726 749 2.847449 TGGGGGATTTGACGGATAGAAA 59.153 45.455 0.00 0.00 0.00 2.52
727 750 3.211865 GGGGGATTTGACGGATAGAAAC 58.788 50.000 0.00 0.00 0.00 2.78
728 751 3.211865 GGGGATTTGACGGATAGAAACC 58.788 50.000 0.00 0.00 0.00 3.27
729 752 3.211865 GGGATTTGACGGATAGAAACCC 58.788 50.000 0.00 0.00 0.00 4.11
730 753 3.118000 GGGATTTGACGGATAGAAACCCT 60.118 47.826 0.00 0.00 0.00 4.34
731 754 4.102054 GGGATTTGACGGATAGAAACCCTA 59.898 45.833 0.00 0.00 0.00 3.53
732 755 5.397109 GGGATTTGACGGATAGAAACCCTAA 60.397 44.000 0.00 0.00 0.00 2.69
733 756 6.117488 GGATTTGACGGATAGAAACCCTAAA 58.883 40.000 0.00 0.00 0.00 1.85
734 757 6.600427 GGATTTGACGGATAGAAACCCTAAAA 59.400 38.462 0.00 0.00 0.00 1.52
735 758 6.806388 TTTGACGGATAGAAACCCTAAAAC 57.194 37.500 0.00 0.00 0.00 2.43
736 759 5.486735 TGACGGATAGAAACCCTAAAACA 57.513 39.130 0.00 0.00 0.00 2.83
737 760 6.057321 TGACGGATAGAAACCCTAAAACAT 57.943 37.500 0.00 0.00 0.00 2.71
738 761 5.878116 TGACGGATAGAAACCCTAAAACATG 59.122 40.000 0.00 0.00 0.00 3.21
739 762 4.638865 ACGGATAGAAACCCTAAAACATGC 59.361 41.667 0.00 0.00 0.00 4.06
740 763 4.036380 CGGATAGAAACCCTAAAACATGCC 59.964 45.833 0.00 0.00 0.00 4.40
741 764 4.036380 GGATAGAAACCCTAAAACATGCCG 59.964 45.833 0.00 0.00 0.00 5.69
742 765 2.167662 AGAAACCCTAAAACATGCCGG 58.832 47.619 0.00 0.00 0.00 6.13
743 766 2.164338 GAAACCCTAAAACATGCCGGA 58.836 47.619 5.05 0.00 0.00 5.14
744 767 2.525105 AACCCTAAAACATGCCGGAT 57.475 45.000 5.05 0.00 0.00 4.18
745 768 3.655615 AACCCTAAAACATGCCGGATA 57.344 42.857 5.05 0.00 0.00 2.59
746 769 2.927028 ACCCTAAAACATGCCGGATAC 58.073 47.619 5.05 0.00 0.00 2.24
765 788 1.630148 CGGTAATATAGCGGCTGAGC 58.370 55.000 13.86 0.00 45.08 4.26
766 789 1.736032 CGGTAATATAGCGGCTGAGCC 60.736 57.143 14.89 14.89 46.75 4.70
775 798 4.408378 GGCTGAGCCGGGTTTTTA 57.592 55.556 8.16 0.00 39.62 1.52
776 799 1.880894 GGCTGAGCCGGGTTTTTAC 59.119 57.895 8.16 0.00 39.62 2.01
777 800 1.500396 GCTGAGCCGGGTTTTTACG 59.500 57.895 8.00 0.00 0.00 3.18
782 805 4.796314 CCGGGTTTTTACGGGTCA 57.204 55.556 0.00 0.00 46.08 4.02
783 806 2.246841 CCGGGTTTTTACGGGTCAC 58.753 57.895 0.00 0.00 46.08 3.67
784 807 0.250424 CCGGGTTTTTACGGGTCACT 60.250 55.000 0.00 0.00 46.08 3.41
785 808 1.596603 CGGGTTTTTACGGGTCACTT 58.403 50.000 0.00 0.00 0.00 3.16
786 809 1.948834 CGGGTTTTTACGGGTCACTTT 59.051 47.619 0.00 0.00 0.00 2.66
787 810 2.358582 CGGGTTTTTACGGGTCACTTTT 59.641 45.455 0.00 0.00 0.00 2.27
788 811 3.181488 CGGGTTTTTACGGGTCACTTTTT 60.181 43.478 0.00 0.00 0.00 1.94
832 855 9.353999 ACAAAATCGATAAAAATTGTAAGAGCC 57.646 29.630 0.00 0.00 29.89 4.70
833 856 8.523464 CAAAATCGATAAAAATTGTAAGAGCCG 58.477 33.333 0.00 0.00 0.00 5.52
834 857 7.548196 AATCGATAAAAATTGTAAGAGCCGA 57.452 32.000 0.00 0.00 0.00 5.54
835 858 6.340537 TCGATAAAAATTGTAAGAGCCGAC 57.659 37.500 0.00 0.00 0.00 4.79
836 859 5.005012 TCGATAAAAATTGTAAGAGCCGACG 59.995 40.000 0.00 0.00 0.00 5.12
837 860 5.005012 CGATAAAAATTGTAAGAGCCGACGA 59.995 40.000 0.00 0.00 0.00 4.20
838 861 4.663636 AAAAATTGTAAGAGCCGACGAG 57.336 40.909 0.00 0.00 0.00 4.18
839 862 2.295253 AATTGTAAGAGCCGACGAGG 57.705 50.000 0.00 0.00 44.97 4.63
840 863 1.183549 ATTGTAAGAGCCGACGAGGT 58.816 50.000 0.00 0.00 43.70 3.85
841 864 0.963962 TTGTAAGAGCCGACGAGGTT 59.036 50.000 0.00 0.00 43.70 3.50
842 865 1.825090 TGTAAGAGCCGACGAGGTTA 58.175 50.000 0.00 0.00 43.70 2.85
843 866 2.372264 TGTAAGAGCCGACGAGGTTAT 58.628 47.619 0.00 0.00 43.70 1.89
844 867 3.544684 TGTAAGAGCCGACGAGGTTATA 58.455 45.455 0.00 0.00 43.70 0.98
845 868 3.313526 TGTAAGAGCCGACGAGGTTATAC 59.686 47.826 0.00 0.00 43.70 1.47
846 869 2.345124 AGAGCCGACGAGGTTATACT 57.655 50.000 0.00 0.00 43.70 2.12
847 870 1.948145 AGAGCCGACGAGGTTATACTG 59.052 52.381 0.00 0.00 43.70 2.74
848 871 1.001597 GAGCCGACGAGGTTATACTGG 60.002 57.143 0.00 0.00 43.70 4.00
849 872 1.027357 GCCGACGAGGTTATACTGGA 58.973 55.000 0.00 0.00 43.70 3.86
865 888 2.629137 ACTGGATCTGCTAGAGATGCTG 59.371 50.000 18.80 18.80 46.99 4.41
883 906 3.134442 TGCTGTGATGATACTGGCACATA 59.866 43.478 0.00 0.00 40.12 2.29
911 934 0.323816 TGAGCTCCTGATCGTCACCT 60.324 55.000 12.15 0.00 0.00 4.00
912 935 1.064685 TGAGCTCCTGATCGTCACCTA 60.065 52.381 12.15 0.00 0.00 3.08
1219 1242 2.825836 CTGATGCCGGACTTGCCC 60.826 66.667 5.05 0.00 0.00 5.36
1347 1370 2.607892 GGCATCTGTTATCGCGGCC 61.608 63.158 6.13 3.45 0.00 6.13
1352 1375 4.071875 TGTTATCGCGGCCCACGT 62.072 61.111 6.13 3.56 46.52 4.49
1394 1417 3.735237 TGCTCTCGTTCTGTTCTCTTT 57.265 42.857 0.00 0.00 0.00 2.52
1437 1460 2.665185 GACCAGTTTGCGCTCGGT 60.665 61.111 9.73 7.76 0.00 4.69
1479 1502 2.908073 GCTTGGGGACGCTGTTGTG 61.908 63.158 0.00 0.00 0.00 3.33
1482 1505 3.948719 GGGGACGCTGTTGTGGGA 61.949 66.667 0.00 0.00 0.00 4.37
1523 1546 4.081420 GGCTATGAAGTCTGAGACTGGAAA 60.081 45.833 16.95 2.66 42.59 3.13
1542 1565 4.095483 GGAAATGACTTGATCGTGCAGAAT 59.905 41.667 0.00 0.00 0.00 2.40
1589 1612 1.605453 GCTTCGTTGGGGATGGGTA 59.395 57.895 0.00 0.00 0.00 3.69
1592 1615 1.280998 CTTCGTTGGGGATGGGTACTT 59.719 52.381 0.00 0.00 0.00 2.24
1725 1748 1.695239 TGAGGGGCTGCATCATCCT 60.695 57.895 0.50 1.97 0.00 3.24
1836 1859 4.868268 AGTATAGGCTGGACTGTAACTCA 58.132 43.478 0.00 0.00 0.00 3.41
1854 1877 7.826744 TGTAACTCATATGCAGGTTGTTCATTA 59.173 33.333 14.37 0.00 0.00 1.90
1974 1997 1.943507 GCTTGCTCTGTTGAGGGTCTC 60.944 57.143 0.00 0.00 40.53 3.36
2085 2108 1.164411 CGGGCTGTGATGCTTTACAA 58.836 50.000 0.00 0.00 0.00 2.41
2087 2110 1.885887 GGGCTGTGATGCTTTACAACA 59.114 47.619 0.00 0.00 0.00 3.33
2091 2114 3.191162 GCTGTGATGCTTTACAACATGGA 59.809 43.478 0.00 0.00 33.17 3.41
2119 2142 5.935945 TGATCCACTCTTACTTGGTCAAAA 58.064 37.500 0.00 0.00 34.19 2.44
2139 2162 0.334676 TGGGTTTGGATGGGGATGTC 59.665 55.000 0.00 0.00 0.00 3.06
2211 2234 3.379372 CCTCTGCGATGGATGTTTTTCAT 59.621 43.478 0.00 0.00 39.77 2.57
2219 2242 6.380995 CGATGGATGTTTTTCATGAGACAAA 58.619 36.000 11.17 0.74 36.83 2.83
2499 2522 5.841957 AATGTGGAAGTTTAGATGATGCC 57.158 39.130 0.00 0.00 0.00 4.40
2633 2656 4.853007 AGGATGAGAAACTTGGGAATCAG 58.147 43.478 0.00 0.00 0.00 2.90
3073 3096 1.630878 CAGGGAAGAGCTGGGTTAAGT 59.369 52.381 0.00 0.00 0.00 2.24
3253 3276 7.154435 AGTGATTTGTCAGATGAAGAAATGG 57.846 36.000 6.03 0.00 0.00 3.16
3254 3277 6.718454 AGTGATTTGTCAGATGAAGAAATGGT 59.282 34.615 6.03 0.00 0.00 3.55
3720 3745 2.615447 CACTGCACTGAGAAGCTTTTCA 59.385 45.455 17.86 17.86 0.00 2.69
3758 3783 1.324383 TGTCAGCACGAGTTCTACCA 58.676 50.000 0.00 0.00 0.00 3.25
3759 3784 1.000607 TGTCAGCACGAGTTCTACCAC 60.001 52.381 0.00 0.00 0.00 4.16
3848 3873 9.630098 GACAACAATTACAGAATGAATTCACAT 57.370 29.630 11.07 2.44 39.69 3.21
3976 4001 7.177568 CACCAGCAGTCTATCAGGTATTACTAT 59.822 40.741 0.00 0.00 0.00 2.12
4009 4034 7.770433 ACAGTTGCAACATAAAGCTGATCTATA 59.230 33.333 30.11 0.00 0.00 1.31
4018 4043 3.244033 AGCTGATCTATAGGAATGCGC 57.756 47.619 0.00 0.00 0.00 6.09
4019 4044 2.564504 AGCTGATCTATAGGAATGCGCA 59.435 45.455 14.96 14.96 0.00 6.09
4196 4221 6.192044 GGATTTTAATAAAGGACTGTGGGGA 58.808 40.000 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.094785 TCATCTTTTAAGCCGCCAGC 58.905 50.000 0.00 0.00 44.25 4.85
24 25 3.009723 TCTTCATCTTTTAAGCCGCCAG 58.990 45.455 0.00 0.00 0.00 4.85
25 26 3.066291 TCTTCATCTTTTAAGCCGCCA 57.934 42.857 0.00 0.00 0.00 5.69
26 27 3.440522 ACTTCTTCATCTTTTAAGCCGCC 59.559 43.478 0.00 0.00 0.00 6.13
27 28 4.437524 GGACTTCTTCATCTTTTAAGCCGC 60.438 45.833 0.00 0.00 0.00 6.53
28 29 4.201724 CGGACTTCTTCATCTTTTAAGCCG 60.202 45.833 0.00 0.00 33.75 5.52
29 30 4.935808 TCGGACTTCTTCATCTTTTAAGCC 59.064 41.667 0.00 0.00 0.00 4.35
30 31 5.444745 CGTCGGACTTCTTCATCTTTTAAGC 60.445 44.000 6.57 0.00 0.00 3.09
31 32 5.862323 TCGTCGGACTTCTTCATCTTTTAAG 59.138 40.000 6.57 0.00 0.00 1.85
32 33 5.775686 TCGTCGGACTTCTTCATCTTTTAA 58.224 37.500 6.57 0.00 0.00 1.52
33 34 5.381174 TCGTCGGACTTCTTCATCTTTTA 57.619 39.130 6.57 0.00 0.00 1.52
34 35 4.238514 CTCGTCGGACTTCTTCATCTTTT 58.761 43.478 6.57 0.00 0.00 2.27
35 36 3.367498 CCTCGTCGGACTTCTTCATCTTT 60.367 47.826 6.57 0.00 33.16 2.52
36 37 2.164624 CCTCGTCGGACTTCTTCATCTT 59.835 50.000 6.57 0.00 33.16 2.40
37 38 1.746220 CCTCGTCGGACTTCTTCATCT 59.254 52.381 6.57 0.00 33.16 2.90
38 39 1.799548 GCCTCGTCGGACTTCTTCATC 60.800 57.143 6.57 0.00 33.16 2.92
39 40 0.173708 GCCTCGTCGGACTTCTTCAT 59.826 55.000 6.57 0.00 33.16 2.57
40 41 1.585006 GCCTCGTCGGACTTCTTCA 59.415 57.895 6.57 0.00 33.16 3.02
41 42 1.153804 GGCCTCGTCGGACTTCTTC 60.154 63.158 6.57 0.00 38.04 2.87
42 43 2.647158 GGGCCTCGTCGGACTTCTT 61.647 63.158 0.84 0.00 42.26 2.52
43 44 3.069318 GGGCCTCGTCGGACTTCT 61.069 66.667 0.84 0.00 42.26 2.85
44 45 2.837371 CTTGGGCCTCGTCGGACTTC 62.837 65.000 4.53 0.00 42.26 3.01
45 46 2.920912 TTGGGCCTCGTCGGACTT 60.921 61.111 4.53 0.00 42.26 3.01
46 47 3.382832 CTTGGGCCTCGTCGGACT 61.383 66.667 4.53 0.00 42.26 3.85
47 48 3.379445 TCTTGGGCCTCGTCGGAC 61.379 66.667 4.53 0.00 41.67 4.79
48 49 3.379445 GTCTTGGGCCTCGTCGGA 61.379 66.667 4.53 0.00 33.16 4.55
49 50 3.019003 ATGTCTTGGGCCTCGTCGG 62.019 63.158 4.53 0.00 0.00 4.79
50 51 1.811266 CATGTCTTGGGCCTCGTCG 60.811 63.158 4.53 0.00 0.00 5.12
51 52 0.036388 TTCATGTCTTGGGCCTCGTC 60.036 55.000 4.53 0.00 0.00 4.20
52 53 0.036010 CTTCATGTCTTGGGCCTCGT 60.036 55.000 4.53 0.00 0.00 4.18
53 54 0.250234 TCTTCATGTCTTGGGCCTCG 59.750 55.000 4.53 0.00 0.00 4.63
54 55 2.295885 CATCTTCATGTCTTGGGCCTC 58.704 52.381 4.53 0.00 0.00 4.70
55 56 1.064166 CCATCTTCATGTCTTGGGCCT 60.064 52.381 4.53 0.00 0.00 5.19
56 57 1.396653 CCATCTTCATGTCTTGGGCC 58.603 55.000 0.00 0.00 0.00 5.80
57 58 0.743097 GCCATCTTCATGTCTTGGGC 59.257 55.000 0.00 0.00 0.00 5.36
58 59 1.019673 CGCCATCTTCATGTCTTGGG 58.980 55.000 0.00 0.00 0.00 4.12
59 60 1.019673 CCGCCATCTTCATGTCTTGG 58.980 55.000 0.00 0.00 0.00 3.61
60 61 1.742761 ACCGCCATCTTCATGTCTTG 58.257 50.000 0.00 0.00 0.00 3.02
61 62 2.359900 GAACCGCCATCTTCATGTCTT 58.640 47.619 0.00 0.00 0.00 3.01
62 63 1.740380 CGAACCGCCATCTTCATGTCT 60.740 52.381 0.00 0.00 0.00 3.41
63 64 0.652592 CGAACCGCCATCTTCATGTC 59.347 55.000 0.00 0.00 0.00 3.06
64 65 0.036388 ACGAACCGCCATCTTCATGT 60.036 50.000 0.00 0.00 0.00 3.21
65 66 0.374758 CACGAACCGCCATCTTCATG 59.625 55.000 0.00 0.00 0.00 3.07
66 67 0.249120 TCACGAACCGCCATCTTCAT 59.751 50.000 0.00 0.00 0.00 2.57
67 68 0.034198 TTCACGAACCGCCATCTTCA 59.966 50.000 0.00 0.00 0.00 3.02
68 69 0.721718 CTTCACGAACCGCCATCTTC 59.278 55.000 0.00 0.00 0.00 2.87
69 70 1.298859 GCTTCACGAACCGCCATCTT 61.299 55.000 0.00 0.00 0.00 2.40
70 71 1.741770 GCTTCACGAACCGCCATCT 60.742 57.895 0.00 0.00 0.00 2.90
71 72 1.970917 CTGCTTCACGAACCGCCATC 61.971 60.000 0.00 0.00 0.00 3.51
72 73 2.031919 TGCTTCACGAACCGCCAT 59.968 55.556 0.00 0.00 0.00 4.40
73 74 2.664851 CTGCTTCACGAACCGCCA 60.665 61.111 0.00 0.00 0.00 5.69
74 75 3.423154 CCTGCTTCACGAACCGCC 61.423 66.667 0.00 0.00 0.00 6.13
75 76 4.090057 GCCTGCTTCACGAACCGC 62.090 66.667 0.00 0.00 0.00 5.68
76 77 0.669318 TAAGCCTGCTTCACGAACCG 60.669 55.000 7.81 0.00 37.47 4.44
77 78 1.739067 ATAAGCCTGCTTCACGAACC 58.261 50.000 7.81 0.00 37.47 3.62
78 79 2.742053 TCAATAAGCCTGCTTCACGAAC 59.258 45.455 7.81 0.00 37.47 3.95
79 80 3.052455 TCAATAAGCCTGCTTCACGAA 57.948 42.857 7.81 0.00 37.47 3.85
80 81 2.760634 TCAATAAGCCTGCTTCACGA 57.239 45.000 7.81 0.67 37.47 4.35
81 82 2.679837 ACATCAATAAGCCTGCTTCACG 59.320 45.455 7.81 0.00 37.47 4.35
82 83 3.691118 TCACATCAATAAGCCTGCTTCAC 59.309 43.478 7.81 0.00 37.47 3.18
83 84 3.954200 TCACATCAATAAGCCTGCTTCA 58.046 40.909 7.81 0.00 37.47 3.02
84 85 4.970662 TTCACATCAATAAGCCTGCTTC 57.029 40.909 7.81 0.00 37.47 3.86
85 86 4.951715 TCATTCACATCAATAAGCCTGCTT 59.048 37.500 9.63 9.63 39.83 3.91
86 87 4.529897 TCATTCACATCAATAAGCCTGCT 58.470 39.130 0.00 0.00 0.00 4.24
87 88 4.337555 ACTCATTCACATCAATAAGCCTGC 59.662 41.667 0.00 0.00 0.00 4.85
88 89 6.094464 TGAACTCATTCACATCAATAAGCCTG 59.906 38.462 0.00 0.00 40.01 4.85
89 90 6.182627 TGAACTCATTCACATCAATAAGCCT 58.817 36.000 0.00 0.00 40.01 4.58
90 91 6.441093 TGAACTCATTCACATCAATAAGCC 57.559 37.500 0.00 0.00 40.01 4.35
91 92 8.922058 ATTTGAACTCATTCACATCAATAAGC 57.078 30.769 0.00 0.00 44.66 3.09
106 107 2.875296 CCCCAGGTTGATTTGAACTCA 58.125 47.619 0.00 0.00 0.00 3.41
107 108 1.546029 GCCCCAGGTTGATTTGAACTC 59.454 52.381 0.00 0.00 0.00 3.01
152 153 1.418908 CCTCCTGGGCGGGTCATATT 61.419 60.000 0.00 0.00 0.00 1.28
201 202 1.066143 TCTTGGGCGGACTTCTTCATC 60.066 52.381 0.00 0.00 0.00 2.92
202 203 0.984230 TCTTGGGCGGACTTCTTCAT 59.016 50.000 0.00 0.00 0.00 2.57
203 204 0.034896 GTCTTGGGCGGACTTCTTCA 59.965 55.000 0.00 0.00 0.00 3.02
204 205 0.034896 TGTCTTGGGCGGACTTCTTC 59.965 55.000 0.00 0.00 35.04 2.87
206 207 0.036010 CATGTCTTGGGCGGACTTCT 60.036 55.000 0.00 0.00 35.04 2.85
207 208 0.036388 TCATGTCTTGGGCGGACTTC 60.036 55.000 0.00 0.00 35.04 3.01
209 210 0.036010 CTTCATGTCTTGGGCGGACT 60.036 55.000 0.00 0.00 35.04 3.85
210 211 0.036388 TCTTCATGTCTTGGGCGGAC 60.036 55.000 0.00 0.00 0.00 4.79
213 214 1.667724 GTCATCTTCATGTCTTGGGCG 59.332 52.381 0.00 0.00 0.00 6.13
216 217 2.977914 ACCGTCATCTTCATGTCTTGG 58.022 47.619 0.00 0.00 0.00 3.61
217 218 3.996363 TGAACCGTCATCTTCATGTCTTG 59.004 43.478 0.00 0.00 0.00 3.02
245 254 2.849943 TCTTGGGCCTTCAATAAGCCTA 59.150 45.455 4.53 0.00 32.59 3.93
429 450 7.333672 ACCTAATTCTCGATTGGTTGTTACTTC 59.666 37.037 0.00 0.00 30.10 3.01
464 485 5.009110 TGAGTTTCGATTATCAGAGAGCGAT 59.991 40.000 0.00 0.00 0.00 4.58
471 492 7.763985 TGTATTGCTTGAGTTTCGATTATCAGA 59.236 33.333 0.00 0.00 0.00 3.27
475 496 7.336931 AGGTTGTATTGCTTGAGTTTCGATTAT 59.663 33.333 0.00 0.00 0.00 1.28
542 563 2.160205 CGACACAGAGAGTTACCCAGA 58.840 52.381 0.00 0.00 0.00 3.86
562 584 1.881973 GAAGGGGTTAAACGGGACAAC 59.118 52.381 0.00 0.00 0.00 3.32
606 629 3.857157 AGCAAAAGGACTTAGGTGTGA 57.143 42.857 0.00 0.00 0.00 3.58
639 662 4.213270 CCGTGTGTGTCATGAACTTAACAT 59.787 41.667 0.00 0.00 35.23 2.71
648 671 1.070615 CCCACCGTGTGTGTCATGA 59.929 57.895 0.00 0.00 43.85 3.07
657 680 2.831284 GCACCAAACCCACCGTGT 60.831 61.111 0.00 0.00 0.00 4.49
658 681 3.601685 GGCACCAAACCCACCGTG 61.602 66.667 0.00 0.00 0.00 4.94
661 684 4.589675 TCCGGCACCAAACCCACC 62.590 66.667 0.00 0.00 0.00 4.61
662 685 2.983592 CTCCGGCACCAAACCCAC 60.984 66.667 0.00 0.00 0.00 4.61
663 686 3.172106 TCTCCGGCACCAAACCCA 61.172 61.111 0.00 0.00 0.00 4.51
664 687 2.359975 CTCTCCGGCACCAAACCC 60.360 66.667 0.00 0.00 0.00 4.11
665 688 1.376037 CTCTCTCCGGCACCAAACC 60.376 63.158 0.00 0.00 0.00 3.27
666 689 0.390472 CTCTCTCTCCGGCACCAAAC 60.390 60.000 0.00 0.00 0.00 2.93
667 690 1.544825 CCTCTCTCTCCGGCACCAAA 61.545 60.000 0.00 0.00 0.00 3.28
668 691 1.984570 CCTCTCTCTCCGGCACCAA 60.985 63.158 0.00 0.00 0.00 3.67
669 692 2.363018 CCTCTCTCTCCGGCACCA 60.363 66.667 0.00 0.00 0.00 4.17
670 693 1.045911 ATTCCTCTCTCTCCGGCACC 61.046 60.000 0.00 0.00 0.00 5.01
671 694 0.827368 AATTCCTCTCTCTCCGGCAC 59.173 55.000 0.00 0.00 0.00 5.01
672 695 0.826715 CAATTCCTCTCTCTCCGGCA 59.173 55.000 0.00 0.00 0.00 5.69
673 696 0.827368 ACAATTCCTCTCTCTCCGGC 59.173 55.000 0.00 0.00 0.00 6.13
674 697 3.489398 CGTTACAATTCCTCTCTCTCCGG 60.489 52.174 0.00 0.00 0.00 5.14
675 698 3.489398 CCGTTACAATTCCTCTCTCTCCG 60.489 52.174 0.00 0.00 0.00 4.63
676 699 3.700038 TCCGTTACAATTCCTCTCTCTCC 59.300 47.826 0.00 0.00 0.00 3.71
677 700 4.202070 CCTCCGTTACAATTCCTCTCTCTC 60.202 50.000 0.00 0.00 0.00 3.20
678 701 3.702045 CCTCCGTTACAATTCCTCTCTCT 59.298 47.826 0.00 0.00 0.00 3.10
679 702 3.700038 TCCTCCGTTACAATTCCTCTCTC 59.300 47.826 0.00 0.00 0.00 3.20
680 703 3.709587 TCCTCCGTTACAATTCCTCTCT 58.290 45.455 0.00 0.00 0.00 3.10
681 704 4.434520 CTTCCTCCGTTACAATTCCTCTC 58.565 47.826 0.00 0.00 0.00 3.20
682 705 3.369576 GCTTCCTCCGTTACAATTCCTCT 60.370 47.826 0.00 0.00 0.00 3.69
683 706 2.937149 GCTTCCTCCGTTACAATTCCTC 59.063 50.000 0.00 0.00 0.00 3.71
684 707 2.572104 AGCTTCCTCCGTTACAATTCCT 59.428 45.455 0.00 0.00 0.00 3.36
685 708 2.678336 CAGCTTCCTCCGTTACAATTCC 59.322 50.000 0.00 0.00 0.00 3.01
686 709 2.678336 CCAGCTTCCTCCGTTACAATTC 59.322 50.000 0.00 0.00 0.00 2.17
687 710 2.618045 CCCAGCTTCCTCCGTTACAATT 60.618 50.000 0.00 0.00 0.00 2.32
688 711 1.065418 CCCAGCTTCCTCCGTTACAAT 60.065 52.381 0.00 0.00 0.00 2.71
689 712 0.323629 CCCAGCTTCCTCCGTTACAA 59.676 55.000 0.00 0.00 0.00 2.41
690 713 1.550130 CCCCAGCTTCCTCCGTTACA 61.550 60.000 0.00 0.00 0.00 2.41
691 714 1.221021 CCCCAGCTTCCTCCGTTAC 59.779 63.158 0.00 0.00 0.00 2.50
692 715 1.993391 CCCCCAGCTTCCTCCGTTA 60.993 63.158 0.00 0.00 0.00 3.18
693 716 3.330720 CCCCCAGCTTCCTCCGTT 61.331 66.667 0.00 0.00 0.00 4.44
694 717 3.642741 ATCCCCCAGCTTCCTCCGT 62.643 63.158 0.00 0.00 0.00 4.69
695 718 1.926426 AAATCCCCCAGCTTCCTCCG 61.926 60.000 0.00 0.00 0.00 4.63
696 719 0.396278 CAAATCCCCCAGCTTCCTCC 60.396 60.000 0.00 0.00 0.00 4.30
697 720 0.625849 TCAAATCCCCCAGCTTCCTC 59.374 55.000 0.00 0.00 0.00 3.71
698 721 0.332972 GTCAAATCCCCCAGCTTCCT 59.667 55.000 0.00 0.00 0.00 3.36
699 722 1.032114 CGTCAAATCCCCCAGCTTCC 61.032 60.000 0.00 0.00 0.00 3.46
700 723 1.032114 CCGTCAAATCCCCCAGCTTC 61.032 60.000 0.00 0.00 0.00 3.86
701 724 1.000896 CCGTCAAATCCCCCAGCTT 60.001 57.895 0.00 0.00 0.00 3.74
702 725 1.281925 ATCCGTCAAATCCCCCAGCT 61.282 55.000 0.00 0.00 0.00 4.24
703 726 0.472471 TATCCGTCAAATCCCCCAGC 59.528 55.000 0.00 0.00 0.00 4.85
704 727 2.047061 TCTATCCGTCAAATCCCCCAG 58.953 52.381 0.00 0.00 0.00 4.45
705 728 2.184088 TCTATCCGTCAAATCCCCCA 57.816 50.000 0.00 0.00 0.00 4.96
706 729 3.211865 GTTTCTATCCGTCAAATCCCCC 58.788 50.000 0.00 0.00 0.00 5.40
707 730 3.211865 GGTTTCTATCCGTCAAATCCCC 58.788 50.000 0.00 0.00 0.00 4.81
708 731 3.118000 AGGGTTTCTATCCGTCAAATCCC 60.118 47.826 0.00 0.00 31.48 3.85
709 732 4.152284 AGGGTTTCTATCCGTCAAATCC 57.848 45.455 0.00 0.00 31.30 3.01
710 733 7.120138 TGTTTTAGGGTTTCTATCCGTCAAATC 59.880 37.037 0.00 0.00 0.00 2.17
711 734 6.943718 TGTTTTAGGGTTTCTATCCGTCAAAT 59.056 34.615 0.00 0.00 0.00 2.32
712 735 6.297582 TGTTTTAGGGTTTCTATCCGTCAAA 58.702 36.000 0.00 0.00 0.00 2.69
713 736 5.867330 TGTTTTAGGGTTTCTATCCGTCAA 58.133 37.500 0.00 0.00 0.00 3.18
714 737 5.486735 TGTTTTAGGGTTTCTATCCGTCA 57.513 39.130 0.00 0.00 0.00 4.35
715 738 5.220796 GCATGTTTTAGGGTTTCTATCCGTC 60.221 44.000 0.00 0.00 0.00 4.79
716 739 4.638865 GCATGTTTTAGGGTTTCTATCCGT 59.361 41.667 0.00 0.00 0.00 4.69
717 740 4.036380 GGCATGTTTTAGGGTTTCTATCCG 59.964 45.833 0.00 0.00 0.00 4.18
718 741 4.036380 CGGCATGTTTTAGGGTTTCTATCC 59.964 45.833 0.00 0.00 0.00 2.59
719 742 4.036380 CCGGCATGTTTTAGGGTTTCTATC 59.964 45.833 0.00 0.00 0.00 2.08
720 743 3.951680 CCGGCATGTTTTAGGGTTTCTAT 59.048 43.478 0.00 0.00 0.00 1.98
721 744 3.009253 TCCGGCATGTTTTAGGGTTTCTA 59.991 43.478 0.00 0.00 0.00 2.10
722 745 2.167662 CCGGCATGTTTTAGGGTTTCT 58.832 47.619 0.00 0.00 0.00 2.52
723 746 2.164338 TCCGGCATGTTTTAGGGTTTC 58.836 47.619 0.00 0.00 0.00 2.78
724 747 2.296073 TCCGGCATGTTTTAGGGTTT 57.704 45.000 0.00 0.00 0.00 3.27
725 748 2.525105 ATCCGGCATGTTTTAGGGTT 57.475 45.000 0.00 0.00 0.00 4.11
726 749 2.743838 CGTATCCGGCATGTTTTAGGGT 60.744 50.000 0.00 0.00 0.00 4.34
727 750 1.871039 CGTATCCGGCATGTTTTAGGG 59.129 52.381 0.00 0.00 0.00 3.53
740 763 2.357009 AGCCGCTATATTACCGTATCCG 59.643 50.000 0.00 0.00 0.00 4.18
741 764 3.379372 TCAGCCGCTATATTACCGTATCC 59.621 47.826 0.00 0.00 0.00 2.59
742 765 4.599047 CTCAGCCGCTATATTACCGTATC 58.401 47.826 0.00 0.00 0.00 2.24
743 766 3.181489 GCTCAGCCGCTATATTACCGTAT 60.181 47.826 0.00 0.00 0.00 3.06
744 767 2.163010 GCTCAGCCGCTATATTACCGTA 59.837 50.000 0.00 0.00 0.00 4.02
745 768 1.067776 GCTCAGCCGCTATATTACCGT 60.068 52.381 0.00 0.00 0.00 4.83
746 769 1.630148 GCTCAGCCGCTATATTACCG 58.370 55.000 0.00 0.00 0.00 4.02
747 770 2.011540 GGCTCAGCCGCTATATTACC 57.988 55.000 0.00 0.00 39.62 2.85
758 781 1.880894 GTAAAAACCCGGCTCAGCC 59.119 57.895 5.22 5.22 46.75 4.85
759 782 1.500396 CGTAAAAACCCGGCTCAGC 59.500 57.895 0.00 0.00 0.00 4.26
760 783 1.303091 CCCGTAAAAACCCGGCTCAG 61.303 60.000 0.00 0.00 0.00 3.35
761 784 1.302671 CCCGTAAAAACCCGGCTCA 60.303 57.895 0.00 0.00 0.00 4.26
762 785 1.300971 GACCCGTAAAAACCCGGCTC 61.301 60.000 0.00 0.00 0.00 4.70
763 786 1.302752 GACCCGTAAAAACCCGGCT 60.303 57.895 0.00 0.00 0.00 5.52
764 787 1.600356 TGACCCGTAAAAACCCGGC 60.600 57.895 0.00 0.00 0.00 6.13
765 788 0.250424 AGTGACCCGTAAAAACCCGG 60.250 55.000 0.00 0.00 0.00 5.73
766 789 1.596603 AAGTGACCCGTAAAAACCCG 58.403 50.000 0.00 0.00 0.00 5.28
767 790 4.389890 AAAAAGTGACCCGTAAAAACCC 57.610 40.909 0.00 0.00 0.00 4.11
806 829 9.353999 GGCTCTTACAATTTTTATCGATTTTGT 57.646 29.630 1.71 9.00 0.00 2.83
807 830 8.523464 CGGCTCTTACAATTTTTATCGATTTTG 58.477 33.333 1.71 3.49 0.00 2.44
808 831 8.455682 TCGGCTCTTACAATTTTTATCGATTTT 58.544 29.630 1.71 0.00 0.00 1.82
809 832 7.908601 GTCGGCTCTTACAATTTTTATCGATTT 59.091 33.333 1.71 0.00 0.00 2.17
810 833 7.407337 GTCGGCTCTTACAATTTTTATCGATT 58.593 34.615 1.71 0.00 0.00 3.34
811 834 6.292168 CGTCGGCTCTTACAATTTTTATCGAT 60.292 38.462 2.16 2.16 0.00 3.59
812 835 5.005012 CGTCGGCTCTTACAATTTTTATCGA 59.995 40.000 0.00 0.00 0.00 3.59
813 836 5.005012 TCGTCGGCTCTTACAATTTTTATCG 59.995 40.000 0.00 0.00 0.00 2.92
814 837 6.340537 TCGTCGGCTCTTACAATTTTTATC 57.659 37.500 0.00 0.00 0.00 1.75
815 838 5.293569 CCTCGTCGGCTCTTACAATTTTTAT 59.706 40.000 0.00 0.00 0.00 1.40
816 839 4.628333 CCTCGTCGGCTCTTACAATTTTTA 59.372 41.667 0.00 0.00 0.00 1.52
817 840 3.435671 CCTCGTCGGCTCTTACAATTTTT 59.564 43.478 0.00 0.00 0.00 1.94
818 841 3.000727 CCTCGTCGGCTCTTACAATTTT 58.999 45.455 0.00 0.00 0.00 1.82
819 842 2.028385 ACCTCGTCGGCTCTTACAATTT 60.028 45.455 0.00 0.00 35.61 1.82
820 843 1.549170 ACCTCGTCGGCTCTTACAATT 59.451 47.619 0.00 0.00 35.61 2.32
821 844 1.183549 ACCTCGTCGGCTCTTACAAT 58.816 50.000 0.00 0.00 35.61 2.71
822 845 0.963962 AACCTCGTCGGCTCTTACAA 59.036 50.000 0.00 0.00 35.61 2.41
823 846 1.825090 TAACCTCGTCGGCTCTTACA 58.175 50.000 0.00 0.00 35.61 2.41
824 847 3.563390 AGTATAACCTCGTCGGCTCTTAC 59.437 47.826 0.00 0.00 35.61 2.34
825 848 3.562973 CAGTATAACCTCGTCGGCTCTTA 59.437 47.826 0.00 0.00 35.61 2.10
826 849 2.358267 CAGTATAACCTCGTCGGCTCTT 59.642 50.000 0.00 0.00 35.61 2.85
827 850 1.948145 CAGTATAACCTCGTCGGCTCT 59.052 52.381 0.00 0.00 35.61 4.09
828 851 1.001597 CCAGTATAACCTCGTCGGCTC 60.002 57.143 0.00 0.00 35.61 4.70
829 852 1.030457 CCAGTATAACCTCGTCGGCT 58.970 55.000 0.00 0.00 35.61 5.52
830 853 1.027357 TCCAGTATAACCTCGTCGGC 58.973 55.000 0.00 0.00 35.61 5.54
831 854 3.058155 CAGATCCAGTATAACCTCGTCGG 60.058 52.174 0.00 0.00 39.35 4.79
832 855 3.609644 GCAGATCCAGTATAACCTCGTCG 60.610 52.174 0.00 0.00 0.00 5.12
833 856 3.570550 AGCAGATCCAGTATAACCTCGTC 59.429 47.826 0.00 0.00 0.00 4.20
834 857 3.567397 AGCAGATCCAGTATAACCTCGT 58.433 45.455 0.00 0.00 0.00 4.18
835 858 5.004448 TCTAGCAGATCCAGTATAACCTCG 58.996 45.833 0.00 0.00 0.00 4.63
836 859 6.242396 TCTCTAGCAGATCCAGTATAACCTC 58.758 44.000 0.00 0.00 0.00 3.85
837 860 6.207509 TCTCTAGCAGATCCAGTATAACCT 57.792 41.667 0.00 0.00 0.00 3.50
838 861 6.627065 GCATCTCTAGCAGATCCAGTATAACC 60.627 46.154 0.00 0.00 40.20 2.85
839 862 6.152661 AGCATCTCTAGCAGATCCAGTATAAC 59.847 42.308 0.00 0.00 40.20 1.89
840 863 6.152492 CAGCATCTCTAGCAGATCCAGTATAA 59.848 42.308 0.00 0.00 40.20 0.98
841 864 5.651576 CAGCATCTCTAGCAGATCCAGTATA 59.348 44.000 0.00 0.00 40.20 1.47
842 865 4.463539 CAGCATCTCTAGCAGATCCAGTAT 59.536 45.833 0.00 0.00 40.20 2.12
843 866 3.825585 CAGCATCTCTAGCAGATCCAGTA 59.174 47.826 0.00 0.00 40.20 2.74
844 867 2.629137 CAGCATCTCTAGCAGATCCAGT 59.371 50.000 0.00 0.00 40.20 4.00
845 868 2.629137 ACAGCATCTCTAGCAGATCCAG 59.371 50.000 0.00 0.00 40.20 3.86
846 869 2.364647 CACAGCATCTCTAGCAGATCCA 59.635 50.000 0.00 0.00 40.20 3.41
847 870 2.627221 TCACAGCATCTCTAGCAGATCC 59.373 50.000 0.00 0.00 40.20 3.36
848 871 4.022155 TCATCACAGCATCTCTAGCAGATC 60.022 45.833 2.74 0.00 40.20 2.75
849 872 3.896272 TCATCACAGCATCTCTAGCAGAT 59.104 43.478 0.00 0.44 43.33 2.90
865 888 4.675190 GCATATGTGCCAGTATCATCAC 57.325 45.455 2.47 0.00 45.76 3.06
883 906 1.210538 TCAGGAGCTCAGGAATGCAT 58.789 50.000 17.19 0.00 0.00 3.96
1219 1242 4.062293 TGGTTGTTGAGGACAGTATTTCG 58.938 43.478 0.00 0.00 39.94 3.46
1347 1370 2.943345 GCGTCTGTTCTGCACGTGG 61.943 63.158 18.88 0.92 35.91 4.94
1352 1375 1.300931 GTGGAGCGTCTGTTCTGCA 60.301 57.895 0.00 0.00 0.00 4.41
1394 1417 2.444329 TCCCCGCCCGTAGCATTA 60.444 61.111 0.00 0.00 44.04 1.90
1437 1460 3.035503 CACGCACGCACAGCACTA 61.036 61.111 0.00 0.00 0.00 2.74
1472 1495 1.151450 ACCTGCCTTCCCACAACAG 59.849 57.895 0.00 0.00 0.00 3.16
1479 1502 3.455469 GCATGCACCTGCCTTCCC 61.455 66.667 14.21 0.00 41.18 3.97
1482 1505 2.203523 TGTGCATGCACCTGCCTT 60.204 55.556 40.01 0.00 45.63 4.35
1523 1546 2.353889 GCATTCTGCACGATCAAGTCAT 59.646 45.455 0.00 0.00 44.26 3.06
1542 1565 2.094700 GGAGTACATCGTGACAAGAGCA 60.095 50.000 0.00 0.00 0.00 4.26
1545 1568 3.824443 TCTTGGAGTACATCGTGACAAGA 59.176 43.478 0.00 0.00 40.09 3.02
1554 1577 0.461961 AGCCGCTCTTGGAGTACATC 59.538 55.000 0.00 0.00 31.39 3.06
1589 1612 1.895798 TCATCCTCGTGAAGAGCAAGT 59.104 47.619 0.00 0.00 45.54 3.16
1592 1615 0.820226 CCTCATCCTCGTGAAGAGCA 59.180 55.000 4.99 0.00 45.54 4.26
1836 1859 4.881273 TCGCTTAATGAACAACCTGCATAT 59.119 37.500 0.00 0.00 0.00 1.78
1854 1877 1.523711 CCGGGCATACATGTCGCTT 60.524 57.895 17.04 0.00 31.93 4.68
1881 1904 3.152341 CACTTTCCTTGCAGACTCCAAT 58.848 45.455 0.00 0.00 0.00 3.16
2085 2108 5.447778 AAGAGTGGATCAATCTTCCATGT 57.552 39.130 5.00 0.00 43.78 3.21
2087 2110 6.821616 AGTAAGAGTGGATCAATCTTCCAT 57.178 37.500 12.81 0.47 43.78 3.41
2106 2129 4.962995 TCCAAACCCATTTTGACCAAGTAA 59.037 37.500 0.00 0.00 46.76 2.24
2119 2142 1.018031 ACATCCCCATCCAAACCCAT 58.982 50.000 0.00 0.00 0.00 4.00
2139 2162 6.314648 TGCTGAGTAAAGAATTGCATACTGAG 59.685 38.462 5.36 5.36 34.17 3.35
2211 2234 5.056480 ACAACATCACGATCTTTTGTCTCA 58.944 37.500 0.00 0.00 0.00 3.27
2499 2522 3.122278 CCATCATTTCAAAGTGCTTTGCG 59.878 43.478 17.16 7.85 46.92 4.85
2633 2656 5.122082 CCAACAAATGTTACATGATTTGGCC 59.878 40.000 17.21 0.00 41.78 5.36
3073 3096 5.594199 AAGACTTTTAGCTCCCCCTTTAA 57.406 39.130 0.00 0.00 0.00 1.52
3253 3276 6.357367 ACCTGACTCAACCATATTCCATAAC 58.643 40.000 0.00 0.00 0.00 1.89
3254 3277 6.386927 AGACCTGACTCAACCATATTCCATAA 59.613 38.462 0.00 0.00 0.00 1.90
3720 3745 6.127619 GCTGACAAGCTGATACCCTTAAAAAT 60.128 38.462 0.00 0.00 46.60 1.82
3758 3783 8.140112 AGATATGTTACTCTGAACTTCCTTGT 57.860 34.615 0.00 0.00 0.00 3.16
3759 3784 8.253810 TGAGATATGTTACTCTGAACTTCCTTG 58.746 37.037 0.00 0.00 34.65 3.61
3848 3873 3.239449 ACATGTGTCTCTGTTACTCCCA 58.761 45.455 0.00 0.00 0.00 4.37
3976 4001 8.236586 CAGCTTTATGTTGCAACTGTAAATCTA 58.763 33.333 28.61 7.02 0.00 1.98
4009 4034 4.456911 CCTATGATGTAAATGCGCATTCCT 59.543 41.667 33.93 22.45 0.00 3.36
4018 4043 8.721478 CGAATCCTTAACCCTATGATGTAAATG 58.279 37.037 0.00 0.00 0.00 2.32
4019 4044 7.883311 CCGAATCCTTAACCCTATGATGTAAAT 59.117 37.037 0.00 0.00 0.00 1.40
4196 4221 7.475137 TTTTACTATTTACTGCAGGGCAAAT 57.525 32.000 19.93 20.09 38.41 2.32


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

AutoCloner maintained by Alex Coulton.