Multiple sequence alignment - TraesCS1A01G047700

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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 TraesCS1A01G047700 chr1A 100.000 3552 0 0 1 3552 29786459 29790010 0.000000e+00 6560.0
1 TraesCS1A01G047700 chr1D 88.942 3545 215 87 70 3552 28563933 28567362 0.000000e+00 4211.0
2 TraesCS1A01G047700 chr1B 88.780 3173 199 64 338 3453 47172389 47175461 0.000000e+00 3742.0
3 TraesCS1A01G047700 chr1B 89.965 289 14 6 242 530 47166895 47167168 3.370000e-95 359.0
4 TraesCS1A01G047700 chr1B 92.073 164 8 1 79 237 47172228 47172391 3.570000e-55 226.0
5 TraesCS1A01G047700 chr1B 94.444 54 3 0 3498 3551 47175461 47175514 2.270000e-12 84.2
6 TraesCS1A01G047700 chr6D 86.154 260 23 9 3301 3552 470858583 470858329 5.840000e-68 268.0
7 TraesCS1A01G047700 chr5A 75.499 551 107 22 1746 2288 589329025 589329555 9.850000e-61 244.0
8 TraesCS1A01G047700 chr5A 86.452 155 21 0 2111 2265 589585149 589585303 1.700000e-38 171.0
9 TraesCS1A01G047700 chr5A 88.971 136 15 0 2111 2246 590527395 590527530 6.100000e-38 169.0
10 TraesCS1A01G047700 chr5A 88.235 136 16 0 2111 2246 590453210 590453345 2.840000e-36 163.0
11 TraesCS1A01G047700 chr5A 81.034 116 16 5 1029 1141 590455513 590455625 1.760000e-13 87.9
12 TraesCS1A01G047700 chr5A 95.556 45 1 1 1092 1135 619359906 619359950 1.770000e-08 71.3
13 TraesCS1A01G047700 chr5B 75.362 552 106 24 1746 2288 576055149 576055679 4.580000e-59 239.0
14 TraesCS1A01G047700 chr5B 75.271 554 101 28 1746 2287 576226130 576226659 7.670000e-57 231.0
15 TraesCS1A01G047700 chr5B 75.368 475 88 20 1862 2326 576260681 576261136 6.010000e-48 202.0
16 TraesCS1A01G047700 chr5B 76.678 283 61 3 1746 2027 576257393 576257671 6.140000e-33 152.0
17 TraesCS1A01G047700 chr5B 95.556 45 1 1 1092 1135 611868621 611868665 1.770000e-08 71.3
18 TraesCS1A01G047700 chr4B 81.567 217 27 5 3301 3509 24551254 24551465 2.190000e-37 167.0
19 TraesCS1A01G047700 chr2D 79.200 125 23 3 1013 1135 337923093 337923216 2.270000e-12 84.2
20 TraesCS1A01G047700 chr2B 79.200 125 23 3 1013 1135 405262351 405262474 2.270000e-12 84.2
21 TraesCS1A01G047700 chr2A 78.906 128 18 6 1013 1135 448153121 448153244 1.060000e-10 78.7
22 TraesCS1A01G047700 chr5D 95.556 45 1 1 1092 1135 495290612 495290656 1.770000e-08 71.3


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 TraesCS1A01G047700 chr1A 29786459 29790010 3551 False 6560.000000 6560 100.000000 1 3552 1 chr1A.!!$F1 3551
1 TraesCS1A01G047700 chr1D 28563933 28567362 3429 False 4211.000000 4211 88.942000 70 3552 1 chr1D.!!$F1 3482
2 TraesCS1A01G047700 chr1B 47172228 47175514 3286 False 1350.733333 3742 91.765667 79 3551 3 chr1B.!!$F2 3472
3 TraesCS1A01G047700 chr5A 589329025 589329555 530 False 244.000000 244 75.499000 1746 2288 1 chr5A.!!$F1 542
4 TraesCS1A01G047700 chr5B 576055149 576055679 530 False 239.000000 239 75.362000 1746 2288 1 chr5B.!!$F1 542
5 TraesCS1A01G047700 chr5B 576226130 576226659 529 False 231.000000 231 75.271000 1746 2287 1 chr5B.!!$F2 541

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
65 66 0.038892 CGCCTGCTTTGCAAGAATGT 60.039 50.0 0.0 0.0 38.41 2.71 F
792 829 0.249280 GCAAACCCCAACAAGAACCG 60.249 55.0 0.0 0.0 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 1404 0.246360 TGTAGTCCGTGACCATGCAG 59.754 55.0 0.0 0.0 32.18 4.41 R
2559 2624 0.713883 CCACACGTACAATCGAGCAC 59.286 55.0 0.0 0.0 34.70 4.40 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
27 28 6.550371 CGTAGTAACGTTTCATAAGTCTGG 57.450 41.667 5.91 0.00 44.21 3.86
28 29 6.317088 CGTAGTAACGTTTCATAAGTCTGGA 58.683 40.000 5.91 0.00 44.21 3.86
29 30 6.468319 CGTAGTAACGTTTCATAAGTCTGGAG 59.532 42.308 5.91 0.00 44.21 3.86
30 31 5.721232 AGTAACGTTTCATAAGTCTGGAGG 58.279 41.667 5.91 0.00 0.00 4.30
31 32 3.611766 ACGTTTCATAAGTCTGGAGGG 57.388 47.619 0.00 0.00 0.00 4.30
32 33 3.170717 ACGTTTCATAAGTCTGGAGGGA 58.829 45.455 0.00 0.00 0.00 4.20
33 34 3.195825 ACGTTTCATAAGTCTGGAGGGAG 59.804 47.826 0.00 0.00 0.00 4.30
34 35 3.536570 GTTTCATAAGTCTGGAGGGAGC 58.463 50.000 0.00 0.00 0.00 4.70
35 36 2.550277 TCATAAGTCTGGAGGGAGCA 57.450 50.000 0.00 0.00 0.00 4.26
36 37 2.832838 TCATAAGTCTGGAGGGAGCAA 58.167 47.619 0.00 0.00 0.00 3.91
37 38 3.181329 TCATAAGTCTGGAGGGAGCAAA 58.819 45.455 0.00 0.00 0.00 3.68
38 39 3.587061 TCATAAGTCTGGAGGGAGCAAAA 59.413 43.478 0.00 0.00 0.00 2.44
39 40 2.575805 AAGTCTGGAGGGAGCAAAAG 57.424 50.000 0.00 0.00 0.00 2.27
40 41 1.734655 AGTCTGGAGGGAGCAAAAGA 58.265 50.000 0.00 0.00 0.00 2.52
41 42 2.057922 AGTCTGGAGGGAGCAAAAGAA 58.942 47.619 0.00 0.00 0.00 2.52
42 43 2.155279 GTCTGGAGGGAGCAAAAGAAC 58.845 52.381 0.00 0.00 0.00 3.01
43 44 1.073923 TCTGGAGGGAGCAAAAGAACC 59.926 52.381 0.00 0.00 0.00 3.62
44 45 0.250727 TGGAGGGAGCAAAAGAACCG 60.251 55.000 0.00 0.00 0.00 4.44
45 46 0.250770 GGAGGGAGCAAAAGAACCGT 60.251 55.000 0.00 0.00 0.00 4.83
46 47 1.157585 GAGGGAGCAAAAGAACCGTC 58.842 55.000 0.00 0.00 0.00 4.79
47 48 0.602905 AGGGAGCAAAAGAACCGTCG 60.603 55.000 0.00 0.00 0.00 5.12
48 49 1.206831 GGAGCAAAAGAACCGTCGC 59.793 57.895 0.00 0.00 0.00 5.19
49 50 1.206831 GAGCAAAAGAACCGTCGCC 59.793 57.895 0.00 0.00 0.00 5.54
50 51 1.227853 AGCAAAAGAACCGTCGCCT 60.228 52.632 0.00 0.00 0.00 5.52
51 52 1.082104 GCAAAAGAACCGTCGCCTG 60.082 57.895 0.00 0.00 0.00 4.85
52 53 1.082104 CAAAAGAACCGTCGCCTGC 60.082 57.895 0.00 0.00 0.00 4.85
53 54 1.227853 AAAAGAACCGTCGCCTGCT 60.228 52.632 0.00 0.00 0.00 4.24
54 55 0.818040 AAAAGAACCGTCGCCTGCTT 60.818 50.000 0.00 0.00 0.00 3.91
55 56 0.818040 AAAGAACCGTCGCCTGCTTT 60.818 50.000 0.00 0.00 0.00 3.51
56 57 1.507141 AAGAACCGTCGCCTGCTTTG 61.507 55.000 0.00 0.00 0.00 2.77
57 58 3.595108 GAACCGTCGCCTGCTTTGC 62.595 63.158 0.00 0.00 0.00 3.68
58 59 4.927782 ACCGTCGCCTGCTTTGCA 62.928 61.111 0.00 0.00 36.92 4.08
59 60 3.659092 CCGTCGCCTGCTTTGCAA 61.659 61.111 0.00 0.00 38.41 4.08
60 61 2.127118 CGTCGCCTGCTTTGCAAG 60.127 61.111 0.00 0.00 38.41 4.01
61 62 2.606961 CGTCGCCTGCTTTGCAAGA 61.607 57.895 0.00 0.00 38.41 3.02
62 63 1.654220 GTCGCCTGCTTTGCAAGAA 59.346 52.632 0.00 0.00 38.41 2.52
63 64 0.242017 GTCGCCTGCTTTGCAAGAAT 59.758 50.000 0.00 0.00 38.41 2.40
64 65 0.241749 TCGCCTGCTTTGCAAGAATG 59.758 50.000 0.00 0.00 38.41 2.67
65 66 0.038892 CGCCTGCTTTGCAAGAATGT 60.039 50.000 0.00 0.00 38.41 2.71
66 67 1.603678 CGCCTGCTTTGCAAGAATGTT 60.604 47.619 0.00 0.00 38.41 2.71
67 68 2.486918 GCCTGCTTTGCAAGAATGTTT 58.513 42.857 0.00 0.00 38.41 2.83
68 69 2.874086 GCCTGCTTTGCAAGAATGTTTT 59.126 40.909 0.00 0.00 38.41 2.43
69 70 3.303526 GCCTGCTTTGCAAGAATGTTTTG 60.304 43.478 0.00 0.00 38.41 2.44
70 71 3.872771 CCTGCTTTGCAAGAATGTTTTGT 59.127 39.130 0.00 0.00 38.41 2.83
71 72 5.049167 CCTGCTTTGCAAGAATGTTTTGTA 58.951 37.500 0.00 0.00 38.41 2.41
72 73 5.697633 CCTGCTTTGCAAGAATGTTTTGTAT 59.302 36.000 0.00 0.00 38.41 2.29
73 74 6.203338 CCTGCTTTGCAAGAATGTTTTGTATT 59.797 34.615 0.00 0.00 38.41 1.89
74 75 7.176285 TGCTTTGCAAGAATGTTTTGTATTC 57.824 32.000 0.00 0.00 34.76 1.75
75 76 6.760298 TGCTTTGCAAGAATGTTTTGTATTCA 59.240 30.769 0.00 0.00 34.76 2.57
193 199 1.696832 GGTCGAATGTTCCGAGCTGC 61.697 60.000 0.00 0.00 46.92 5.25
197 203 1.571919 GAATGTTCCGAGCTGCGTAT 58.428 50.000 0.00 0.00 38.67 3.06
204 210 2.018866 CGAGCTGCGTATGCTAGGC 61.019 63.158 8.69 9.80 41.30 3.93
254 260 2.359107 CCAGACAGCACGCACCAT 60.359 61.111 0.00 0.00 0.00 3.55
267 273 1.406205 CGCACCATGTACATGTACCCA 60.406 52.381 29.25 14.86 37.11 4.51
298 304 2.165167 TGTCGTCGGAGTTCAACCTAT 58.835 47.619 0.00 0.00 0.00 2.57
299 305 3.346315 TGTCGTCGGAGTTCAACCTATA 58.654 45.455 0.00 0.00 0.00 1.31
300 306 3.758023 TGTCGTCGGAGTTCAACCTATAA 59.242 43.478 0.00 0.00 0.00 0.98
302 308 5.105635 TGTCGTCGGAGTTCAACCTATAATT 60.106 40.000 0.00 0.00 0.00 1.40
303 309 5.809051 GTCGTCGGAGTTCAACCTATAATTT 59.191 40.000 0.00 0.00 0.00 1.82
305 311 5.501897 CGTCGGAGTTCAACCTATAATTTGC 60.502 44.000 0.00 0.00 0.00 3.68
306 312 4.569162 TCGGAGTTCAACCTATAATTTGCG 59.431 41.667 0.00 0.00 0.00 4.85
307 313 4.598062 GGAGTTCAACCTATAATTTGCGC 58.402 43.478 0.00 0.00 0.00 6.09
311 317 0.306533 AACCTATAATTTGCGCGGCG 59.693 50.000 19.62 19.62 0.00 6.46
390 396 9.041354 ACAGCTTTAAATGGGGTAAAATTGATA 57.959 29.630 0.00 0.00 0.00 2.15
477 483 0.251916 TTGTTCCATACGCCTCCCAG 59.748 55.000 0.00 0.00 0.00 4.45
478 484 1.146263 GTTCCATACGCCTCCCAGG 59.854 63.158 0.00 0.00 38.80 4.45
593 603 7.226918 GTGAAGACTTGGTAAAAGAACTAGCTT 59.773 37.037 0.00 0.00 0.00 3.74
594 604 7.441458 TGAAGACTTGGTAAAAGAACTAGCTTC 59.559 37.037 0.00 0.00 0.00 3.86
595 605 7.068686 AGACTTGGTAAAAGAACTAGCTTCT 57.931 36.000 0.00 0.00 41.39 2.85
596 606 8.191534 AGACTTGGTAAAAGAACTAGCTTCTA 57.808 34.615 0.00 0.00 38.37 2.10
597 607 8.308207 AGACTTGGTAAAAGAACTAGCTTCTAG 58.692 37.037 0.00 0.00 38.37 2.43
598 608 7.964624 ACTTGGTAAAAGAACTAGCTTCTAGT 58.035 34.615 0.00 0.94 38.37 2.57
599 609 9.086758 ACTTGGTAAAAGAACTAGCTTCTAGTA 57.913 33.333 6.91 2.69 38.37 1.82
600 610 9.575783 CTTGGTAAAAGAACTAGCTTCTAGTAG 57.424 37.037 6.91 0.00 38.37 2.57
601 611 8.874744 TGGTAAAAGAACTAGCTTCTAGTAGA 57.125 34.615 6.91 0.00 38.37 2.59
602 612 8.958506 TGGTAAAAGAACTAGCTTCTAGTAGAG 58.041 37.037 6.91 0.00 38.37 2.43
603 613 7.916977 GGTAAAAGAACTAGCTTCTAGTAGAGC 59.083 40.741 6.91 11.48 38.37 4.09
604 614 6.459670 AAAGAACTAGCTTCTAGTAGAGCC 57.540 41.667 14.31 5.03 38.37 4.70
607 617 4.513406 ACTAGCTTCTAGTAGAGCCACT 57.487 45.455 14.31 7.77 0.00 4.00
608 618 4.204012 ACTAGCTTCTAGTAGAGCCACTG 58.796 47.826 14.31 7.82 0.00 3.66
609 619 3.374042 AGCTTCTAGTAGAGCCACTGA 57.626 47.619 14.31 0.00 0.00 3.41
610 620 3.702792 AGCTTCTAGTAGAGCCACTGAA 58.297 45.455 14.31 0.00 0.00 3.02
611 621 3.445805 AGCTTCTAGTAGAGCCACTGAAC 59.554 47.826 14.31 0.00 0.00 3.18
613 623 4.676723 GCTTCTAGTAGAGCCACTGAACAG 60.677 50.000 0.00 0.00 0.00 3.16
614 624 2.755655 TCTAGTAGAGCCACTGAACAGC 59.244 50.000 0.00 0.00 0.00 4.40
615 625 1.342074 AGTAGAGCCACTGAACAGCA 58.658 50.000 1.46 0.00 0.00 4.41
616 626 1.001406 AGTAGAGCCACTGAACAGCAC 59.999 52.381 1.46 0.00 0.00 4.40
617 627 0.321671 TAGAGCCACTGAACAGCACC 59.678 55.000 1.46 0.00 0.00 5.01
618 628 1.072159 GAGCCACTGAACAGCACCT 59.928 57.895 1.46 0.00 0.00 4.00
619 629 0.952984 GAGCCACTGAACAGCACCTC 60.953 60.000 1.46 2.01 0.00 3.85
637 647 1.939934 CTCAGTTGTCGAGTTGCCAAA 59.060 47.619 0.00 0.00 0.00 3.28
741 751 6.135290 TGCCTGATCATAAAATACAAGCAC 57.865 37.500 0.00 0.00 0.00 4.40
758 795 1.614317 GCACAATGCCAGACCCTAACT 60.614 52.381 0.00 0.00 37.42 2.24
760 797 3.685550 GCACAATGCCAGACCCTAACTAT 60.686 47.826 0.00 0.00 37.42 2.12
761 798 4.526970 CACAATGCCAGACCCTAACTATT 58.473 43.478 0.00 0.00 0.00 1.73
762 799 4.576463 CACAATGCCAGACCCTAACTATTC 59.424 45.833 0.00 0.00 0.00 1.75
763 800 4.475016 ACAATGCCAGACCCTAACTATTCT 59.525 41.667 0.00 0.00 0.00 2.40
764 801 5.044846 ACAATGCCAGACCCTAACTATTCTT 60.045 40.000 0.00 0.00 0.00 2.52
765 802 4.755266 TGCCAGACCCTAACTATTCTTC 57.245 45.455 0.00 0.00 0.00 2.87
766 803 4.362677 TGCCAGACCCTAACTATTCTTCT 58.637 43.478 0.00 0.00 0.00 2.85
767 804 4.783227 TGCCAGACCCTAACTATTCTTCTT 59.217 41.667 0.00 0.00 0.00 2.52
768 805 5.119694 GCCAGACCCTAACTATTCTTCTTG 58.880 45.833 0.00 0.00 0.00 3.02
769 806 5.119694 CCAGACCCTAACTATTCTTCTTGC 58.880 45.833 0.00 0.00 0.00 4.01
770 807 5.104735 CCAGACCCTAACTATTCTTCTTGCT 60.105 44.000 0.00 0.00 0.00 3.91
771 808 5.814705 CAGACCCTAACTATTCTTCTTGCTG 59.185 44.000 0.00 0.00 0.00 4.41
772 809 5.485708 AGACCCTAACTATTCTTCTTGCTGT 59.514 40.000 0.00 0.00 0.00 4.40
773 810 5.491982 ACCCTAACTATTCTTCTTGCTGTG 58.508 41.667 0.00 0.00 0.00 3.66
774 811 4.333926 CCCTAACTATTCTTCTTGCTGTGC 59.666 45.833 0.00 0.00 0.00 4.57
792 829 0.249280 GCAAACCCCAACAAGAACCG 60.249 55.000 0.00 0.00 0.00 4.44
828 865 6.783708 AGAAGATCCAAGAACGAGATTAGT 57.216 37.500 0.00 0.00 0.00 2.24
909 950 8.428063 ACTTAGCATCTCACTATAAATTCTGCT 58.572 33.333 0.00 0.00 40.29 4.24
915 956 6.341316 TCTCACTATAAATTCTGCTGGTCAC 58.659 40.000 0.00 0.00 0.00 3.67
919 960 6.765036 CACTATAAATTCTGCTGGTCACTCAT 59.235 38.462 0.00 0.00 0.00 2.90
924 965 0.742281 CTGCTGGTCACTCATTCGGG 60.742 60.000 0.00 0.00 0.00 5.14
928 969 1.208052 CTGGTCACTCATTCGGGTGAT 59.792 52.381 0.00 0.00 43.07 3.06
934 975 5.452776 GGTCACTCATTCGGGTGATATAACA 60.453 44.000 0.00 0.00 43.07 2.41
935 976 6.046593 GTCACTCATTCGGGTGATATAACAA 58.953 40.000 0.00 0.00 43.07 2.83
936 977 6.018994 GTCACTCATTCGGGTGATATAACAAC 60.019 42.308 0.00 0.00 43.07 3.32
937 978 5.236478 CACTCATTCGGGTGATATAACAACC 59.764 44.000 7.00 7.00 43.50 3.77
959 1007 2.492088 ACACAGCATCGACAGCTACTAA 59.508 45.455 13.22 0.00 41.14 2.24
960 1008 2.854777 CACAGCATCGACAGCTACTAAC 59.145 50.000 13.22 0.00 41.14 2.34
963 1011 2.099921 AGCATCGACAGCTACTAACCTG 59.900 50.000 12.10 0.00 41.32 4.00
965 1013 2.502142 TCGACAGCTACTAACCTGGA 57.498 50.000 0.00 0.00 33.43 3.86
973 1021 2.483188 GCTACTAACCTGGAATCACCGG 60.483 54.545 0.00 0.00 44.27 5.28
978 1026 4.096003 CTGGAATCACCGGGGCGT 62.096 66.667 6.32 0.00 41.14 5.68
979 1027 4.402528 TGGAATCACCGGGGCGTG 62.403 66.667 6.32 0.00 42.61 5.34
980 1028 4.090588 GGAATCACCGGGGCGTGA 62.091 66.667 6.32 0.00 46.36 4.35
992 1044 2.741878 CGGGGCGTGAATCTCAGTTATT 60.742 50.000 0.00 0.00 0.00 1.40
993 1045 3.279434 GGGGCGTGAATCTCAGTTATTT 58.721 45.455 0.00 0.00 0.00 1.40
994 1046 4.448210 GGGGCGTGAATCTCAGTTATTTA 58.552 43.478 0.00 0.00 0.00 1.40
995 1047 4.511826 GGGGCGTGAATCTCAGTTATTTAG 59.488 45.833 0.00 0.00 0.00 1.85
1041 1095 2.766651 GTCATCCCCTACCCGGCA 60.767 66.667 0.00 0.00 0.00 5.69
1398 1452 2.786512 ATTGGGCGGTGGACATTGCT 62.787 55.000 0.00 0.00 0.00 3.91
1473 1527 0.767375 TCACCTTGCTGAGCTTTCCT 59.233 50.000 5.83 0.00 0.00 3.36
1514 1568 2.562738 TCATCGATGCGGAAGATGGTAT 59.437 45.455 20.81 0.00 41.35 2.73
1516 1570 3.850122 TCGATGCGGAAGATGGTATAG 57.150 47.619 0.00 0.00 0.00 1.31
1569 1628 9.577110 CTTACATTATTTACTGACCAGTTCGTA 57.423 33.333 8.06 0.00 42.54 3.43
1597 1656 1.348064 CAGGGTCTACAGTGGGTGAA 58.652 55.000 0.00 0.00 0.00 3.18
1948 2007 0.537143 TCGGCAGCTTCACCATGTTT 60.537 50.000 0.00 0.00 0.00 2.83
1949 2008 1.164411 CGGCAGCTTCACCATGTTTA 58.836 50.000 0.00 0.00 0.00 2.01
2116 2175 1.153939 CAAGCTCGTCTCCTGGTCG 60.154 63.158 0.00 0.00 0.00 4.79
2197 2256 2.933287 TCCACCATGGAGGGCGTT 60.933 61.111 25.96 0.00 42.67 4.84
2269 2328 2.160721 ACCAGGTGTACATCTCCGAT 57.839 50.000 5.41 0.00 35.13 4.18
2425 2484 1.066573 CACGAGAGCATTCAGGAAGGT 60.067 52.381 0.00 0.00 0.00 3.50
2476 2535 0.749091 CGGAGGCCATGAAGAATGCA 60.749 55.000 5.01 0.00 34.67 3.96
2488 2553 1.449246 GAATGCAGCGCCTGAGAGT 60.449 57.895 2.29 0.00 32.44 3.24
2536 2601 0.605589 ACTTCCACTCTCTTGCGGAG 59.394 55.000 0.70 0.70 43.12 4.63
2559 2624 4.008330 GGTATGAAGGCATGATCATCTGG 58.992 47.826 4.86 0.00 37.46 3.86
2567 2632 2.870835 GCATGATCATCTGGTGCTCGAT 60.871 50.000 4.86 0.00 33.25 3.59
2627 2694 8.293867 CCAAACAGAATAAAAAGTTCGACCATA 58.706 33.333 0.00 0.00 0.00 2.74
2639 2706 3.746045 TCGACCATAACCATTAGCCTC 57.254 47.619 0.00 0.00 0.00 4.70
2649 2716 7.831193 CCATAACCATTAGCCTCTATATTTGCT 59.169 37.037 0.00 0.00 37.84 3.91
2677 2780 3.007182 TCTGTTCCGTCCCGAATTACTTT 59.993 43.478 0.00 0.00 0.00 2.66
2678 2781 3.068560 TGTTCCGTCCCGAATTACTTTG 58.931 45.455 0.00 0.00 0.00 2.77
2679 2782 3.069289 GTTCCGTCCCGAATTACTTTGT 58.931 45.455 0.00 0.00 0.00 2.83
2680 2783 2.963432 TCCGTCCCGAATTACTTTGTC 58.037 47.619 0.00 0.00 0.00 3.18
2681 2784 1.657094 CCGTCCCGAATTACTTTGTCG 59.343 52.381 0.00 0.00 34.58 4.35
2682 2785 1.060122 CGTCCCGAATTACTTTGTCGC 59.940 52.381 0.00 0.00 33.46 5.19
2689 2792 4.788100 CCGAATTACTTTGTCGCAGAAATG 59.212 41.667 0.00 0.00 39.69 2.32
2693 2796 5.545658 TTACTTTGTCGCAGAAATGGATC 57.454 39.130 0.00 0.00 39.69 3.36
2696 2799 2.028420 TGTCGCAGAAATGGATCTGG 57.972 50.000 6.46 0.00 45.60 3.86
2697 2800 1.554617 TGTCGCAGAAATGGATCTGGA 59.445 47.619 6.46 0.24 45.60 3.86
2699 2802 2.547211 GTCGCAGAAATGGATCTGGATG 59.453 50.000 6.46 0.00 45.60 3.51
2702 2805 3.764218 GCAGAAATGGATCTGGATGGAT 58.236 45.455 6.46 0.00 45.60 3.41
2703 2806 3.506455 GCAGAAATGGATCTGGATGGATG 59.494 47.826 6.46 0.00 45.60 3.51
2704 2807 4.079970 CAGAAATGGATCTGGATGGATGG 58.920 47.826 0.00 0.00 42.52 3.51
2706 2809 4.417854 AGAAATGGATCTGGATGGATGGAA 59.582 41.667 0.00 0.00 0.00 3.53
2707 2810 5.076039 AGAAATGGATCTGGATGGATGGAAT 59.924 40.000 0.00 0.00 0.00 3.01
2716 2819 5.780282 TCTGGATGGATGGAATATAAGACGT 59.220 40.000 0.00 0.00 0.00 4.34
2721 2824 8.290325 GGATGGATGGAATATAAGACGTTTTTC 58.710 37.037 0.00 0.00 0.00 2.29
2731 2834 2.883574 AGACGTTTTTCGACACTGTCA 58.116 42.857 9.84 0.00 42.86 3.58
2750 2853 7.540400 CACTGTCAGACTCTAAACACATCTTAG 59.460 40.741 6.91 0.00 0.00 2.18
2809 2912 3.914966 GCGTCCGTAGATAACATGATGAG 59.085 47.826 0.00 0.00 0.00 2.90
2846 2974 2.911926 AAGGCCAAGACAGGGAGGC 61.912 63.158 5.01 0.00 46.28 4.70
2848 2976 4.785453 GCCAAGACAGGGAGGCCG 62.785 72.222 0.00 0.00 41.25 6.13
2849 2977 4.785453 CCAAGACAGGGAGGCCGC 62.785 72.222 0.00 0.00 0.00 6.53
2864 2992 4.717629 CGCGACGAGGCCTTGTCA 62.718 66.667 39.92 0.00 42.71 3.58
2865 2993 2.811317 GCGACGAGGCCTTGTCAG 60.811 66.667 39.92 33.15 42.71 3.51
2866 2994 2.125912 CGACGAGGCCTTGTCAGG 60.126 66.667 39.92 26.85 42.71 3.86
2947 3085 3.653009 CAGCGCACACACCACCTG 61.653 66.667 11.47 0.00 0.00 4.00
2949 3087 3.649986 GCGCACACACCACCTGAC 61.650 66.667 0.30 0.00 0.00 3.51
2981 3122 3.219198 GCCGGCCCATGTGGAATC 61.219 66.667 18.11 0.00 37.39 2.52
3228 3375 9.709495 TCCTTTCCAAATCTGTGAATATTTTTG 57.291 29.630 0.00 0.00 0.00 2.44
3273 3421 9.243637 TCAAAATGAATGAACTTTTTAAGTCCG 57.756 29.630 0.00 0.00 41.91 4.79
3352 3500 3.478857 ACGACAAACTACCCATGTTGA 57.521 42.857 0.00 0.00 33.56 3.18
3369 3518 5.850557 TGTTGAAATCAATGTGAAGTGGT 57.149 34.783 0.00 0.00 38.24 4.16
3470 3629 1.682087 GGGCATACCTTGGACCTTGTC 60.682 57.143 0.00 0.00 35.85 3.18
3473 3632 3.054655 GGCATACCTTGGACCTTGTCTAA 60.055 47.826 0.00 0.00 32.45 2.10
3486 3645 0.528017 TGTCTAAGACCTGCAGCTCG 59.472 55.000 8.66 0.00 0.00 5.03
3494 3653 4.928398 CTGCAGCTCGTCAGGAAT 57.072 55.556 0.00 0.00 0.00 3.01
3496 3655 0.108472 CTGCAGCTCGTCAGGAATGA 60.108 55.000 0.00 0.00 0.00 2.57
3500 3659 0.453793 AGCTCGTCAGGAATGAGTCG 59.546 55.000 0.00 0.00 42.20 4.18
3538 3697 1.078759 CTACTGCAAGCTTCCGGTCG 61.079 60.000 4.77 0.00 37.60 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.750963 CCTCCAGACTTATGAAACGTTACTAC 59.249 42.308 0.00 0.00 0.00 2.73
6 7 6.127535 CCCTCCAGACTTATGAAACGTTACTA 60.128 42.308 0.00 0.00 0.00 1.82
7 8 5.337330 CCCTCCAGACTTATGAAACGTTACT 60.337 44.000 0.00 0.00 0.00 2.24
8 9 4.868734 CCCTCCAGACTTATGAAACGTTAC 59.131 45.833 0.00 0.00 0.00 2.50
9 10 4.773674 TCCCTCCAGACTTATGAAACGTTA 59.226 41.667 0.00 0.00 0.00 3.18
10 11 3.581332 TCCCTCCAGACTTATGAAACGTT 59.419 43.478 0.00 0.00 0.00 3.99
11 12 3.170717 TCCCTCCAGACTTATGAAACGT 58.829 45.455 0.00 0.00 0.00 3.99
12 13 3.786635 CTCCCTCCAGACTTATGAAACG 58.213 50.000 0.00 0.00 0.00 3.60
13 14 3.055094 TGCTCCCTCCAGACTTATGAAAC 60.055 47.826 0.00 0.00 0.00 2.78
14 15 3.181329 TGCTCCCTCCAGACTTATGAAA 58.819 45.455 0.00 0.00 0.00 2.69
15 16 2.832838 TGCTCCCTCCAGACTTATGAA 58.167 47.619 0.00 0.00 0.00 2.57
16 17 2.550277 TGCTCCCTCCAGACTTATGA 57.450 50.000 0.00 0.00 0.00 2.15
17 18 3.634397 TTTGCTCCCTCCAGACTTATG 57.366 47.619 0.00 0.00 0.00 1.90
18 19 3.846588 TCTTTTGCTCCCTCCAGACTTAT 59.153 43.478 0.00 0.00 0.00 1.73
19 20 3.248024 TCTTTTGCTCCCTCCAGACTTA 58.752 45.455 0.00 0.00 0.00 2.24
20 21 2.057922 TCTTTTGCTCCCTCCAGACTT 58.942 47.619 0.00 0.00 0.00 3.01
21 22 1.734655 TCTTTTGCTCCCTCCAGACT 58.265 50.000 0.00 0.00 0.00 3.24
22 23 2.155279 GTTCTTTTGCTCCCTCCAGAC 58.845 52.381 0.00 0.00 0.00 3.51
23 24 1.073923 GGTTCTTTTGCTCCCTCCAGA 59.926 52.381 0.00 0.00 0.00 3.86
24 25 1.539157 GGTTCTTTTGCTCCCTCCAG 58.461 55.000 0.00 0.00 0.00 3.86
25 26 0.250727 CGGTTCTTTTGCTCCCTCCA 60.251 55.000 0.00 0.00 0.00 3.86
26 27 0.250770 ACGGTTCTTTTGCTCCCTCC 60.251 55.000 0.00 0.00 0.00 4.30
27 28 1.157585 GACGGTTCTTTTGCTCCCTC 58.842 55.000 0.00 0.00 0.00 4.30
28 29 0.602905 CGACGGTTCTTTTGCTCCCT 60.603 55.000 0.00 0.00 0.00 4.20
29 30 1.866925 CGACGGTTCTTTTGCTCCC 59.133 57.895 0.00 0.00 0.00 4.30
30 31 1.206831 GCGACGGTTCTTTTGCTCC 59.793 57.895 0.00 0.00 0.00 4.70
31 32 1.206831 GGCGACGGTTCTTTTGCTC 59.793 57.895 0.00 0.00 0.00 4.26
32 33 1.227853 AGGCGACGGTTCTTTTGCT 60.228 52.632 0.00 0.00 0.00 3.91
33 34 1.082104 CAGGCGACGGTTCTTTTGC 60.082 57.895 0.00 0.00 0.00 3.68
34 35 1.082104 GCAGGCGACGGTTCTTTTG 60.082 57.895 0.00 0.00 0.00 2.44
35 36 0.818040 AAGCAGGCGACGGTTCTTTT 60.818 50.000 0.00 0.00 0.00 2.27
36 37 0.818040 AAAGCAGGCGACGGTTCTTT 60.818 50.000 0.00 0.00 0.00 2.52
37 38 1.227853 AAAGCAGGCGACGGTTCTT 60.228 52.632 0.00 0.00 0.00 2.52
38 39 1.961277 CAAAGCAGGCGACGGTTCT 60.961 57.895 0.00 0.00 0.00 3.01
39 40 2.556287 CAAAGCAGGCGACGGTTC 59.444 61.111 0.00 0.00 0.00 3.62
40 41 3.660111 GCAAAGCAGGCGACGGTT 61.660 61.111 0.00 0.00 0.00 4.44
41 42 4.927782 TGCAAAGCAGGCGACGGT 62.928 61.111 0.00 0.00 33.32 4.83
42 43 3.599792 CTTGCAAAGCAGGCGACGG 62.600 63.158 0.00 0.00 40.61 4.79
43 44 2.116736 TTCTTGCAAAGCAGGCGACG 62.117 55.000 0.00 0.00 45.70 5.12
44 45 0.242017 ATTCTTGCAAAGCAGGCGAC 59.758 50.000 0.00 0.00 45.70 5.19
45 46 0.241749 CATTCTTGCAAAGCAGGCGA 59.758 50.000 0.00 0.00 45.70 5.54
46 47 0.038892 ACATTCTTGCAAAGCAGGCG 60.039 50.000 0.00 0.00 45.70 5.52
47 48 2.159327 AACATTCTTGCAAAGCAGGC 57.841 45.000 0.00 0.00 45.70 4.85
48 49 3.872771 ACAAAACATTCTTGCAAAGCAGG 59.127 39.130 0.00 0.00 45.70 4.85
49 50 6.774354 ATACAAAACATTCTTGCAAAGCAG 57.226 33.333 0.00 0.00 45.70 4.24
50 51 6.760298 TGAATACAAAACATTCTTGCAAAGCA 59.240 30.769 0.00 0.00 45.70 3.91
51 52 7.176285 TGAATACAAAACATTCTTGCAAAGC 57.824 32.000 0.00 0.00 45.70 3.51
63 64 9.958180 TCTCAAGGAGATAATGAATACAAAACA 57.042 29.630 0.00 0.00 33.35 2.83
65 66 9.958180 TGTCTCAAGGAGATAATGAATACAAAA 57.042 29.630 0.00 0.00 40.98 2.44
66 67 9.958180 TTGTCTCAAGGAGATAATGAATACAAA 57.042 29.630 0.00 0.00 40.98 2.83
193 199 2.470821 GGTAACACTGCCTAGCATACG 58.529 52.381 0.00 0.00 38.13 3.06
197 203 1.003118 CTTGGGTAACACTGCCTAGCA 59.997 52.381 0.00 0.00 35.75 3.49
204 210 4.021102 AGTTGATCCTTGGGTAACACTG 57.979 45.455 0.00 0.00 39.74 3.66
254 260 3.440872 GCCGATTTTTGGGTACATGTACA 59.559 43.478 31.52 14.13 37.78 2.90
267 273 0.446222 CCGACGACATGCCGATTTTT 59.554 50.000 8.88 0.00 0.00 1.94
298 304 0.179116 TACCTACGCCGCGCAAATTA 60.179 50.000 13.88 0.00 0.00 1.40
299 305 1.426041 CTACCTACGCCGCGCAAATT 61.426 55.000 13.88 0.00 0.00 1.82
300 306 1.881252 CTACCTACGCCGCGCAAAT 60.881 57.895 13.88 0.00 0.00 2.32
302 308 2.877360 CTTCTACCTACGCCGCGCAA 62.877 60.000 13.88 0.00 0.00 4.85
303 309 3.405592 CTTCTACCTACGCCGCGCA 62.406 63.158 13.88 0.00 0.00 6.09
305 311 0.316524 GTACTTCTACCTACGCCGCG 60.317 60.000 12.14 12.14 0.00 6.46
306 312 0.029967 GGTACTTCTACCTACGCCGC 59.970 60.000 0.00 0.00 39.70 6.53
460 466 1.146263 CCTGGGAGGCGTATGGAAC 59.854 63.158 0.00 0.00 0.00 3.62
593 603 2.755655 GCTGTTCAGTGGCTCTACTAGA 59.244 50.000 0.00 0.00 0.00 2.43
594 604 2.493675 TGCTGTTCAGTGGCTCTACTAG 59.506 50.000 1.78 0.00 0.00 2.57
595 605 2.231478 GTGCTGTTCAGTGGCTCTACTA 59.769 50.000 1.78 0.00 0.00 1.82
596 606 1.001406 GTGCTGTTCAGTGGCTCTACT 59.999 52.381 1.78 0.00 0.00 2.57
597 607 1.433534 GTGCTGTTCAGTGGCTCTAC 58.566 55.000 1.78 0.00 0.00 2.59
598 608 0.321671 GGTGCTGTTCAGTGGCTCTA 59.678 55.000 1.78 0.00 0.00 2.43
599 609 1.072159 GGTGCTGTTCAGTGGCTCT 59.928 57.895 1.78 0.00 0.00 4.09
600 610 0.952984 GAGGTGCTGTTCAGTGGCTC 60.953 60.000 1.78 0.00 0.00 4.70
601 611 1.072159 GAGGTGCTGTTCAGTGGCT 59.928 57.895 1.78 0.00 0.00 4.75
602 612 1.227943 TGAGGTGCTGTTCAGTGGC 60.228 57.895 1.78 0.00 0.00 5.01
603 613 2.924185 CTGAGGTGCTGTTCAGTGG 58.076 57.895 1.78 0.00 36.82 4.00
607 617 1.806247 CGACAACTGAGGTGCTGTTCA 60.806 52.381 0.00 0.00 36.64 3.18
608 618 0.861837 CGACAACTGAGGTGCTGTTC 59.138 55.000 0.00 0.00 36.64 3.18
609 619 0.464036 TCGACAACTGAGGTGCTGTT 59.536 50.000 0.00 0.00 38.96 3.16
610 620 0.032678 CTCGACAACTGAGGTGCTGT 59.967 55.000 0.00 0.00 0.00 4.40
611 621 0.032678 ACTCGACAACTGAGGTGCTG 59.967 55.000 0.00 0.00 37.79 4.41
613 623 0.861837 CAACTCGACAACTGAGGTGC 59.138 55.000 0.00 0.00 43.56 5.01
615 625 0.249911 GGCAACTCGACAACTGAGGT 60.250 55.000 0.00 0.00 37.79 3.85
616 626 0.249868 TGGCAACTCGACAACTGAGG 60.250 55.000 0.00 0.00 37.79 3.86
617 627 1.581934 TTGGCAACTCGACAACTGAG 58.418 50.000 0.00 0.00 37.87 3.35
618 628 2.031258 TTTGGCAACTCGACAACTGA 57.969 45.000 0.00 0.00 44.50 3.41
619 629 2.033299 ACATTTGGCAACTCGACAACTG 59.967 45.455 0.00 0.00 44.50 3.16
637 647 9.905713 TTTTAGAAGCATAGGAGATAAACACAT 57.094 29.630 0.00 0.00 0.00 3.21
741 751 5.041191 AGAATAGTTAGGGTCTGGCATTG 57.959 43.478 0.00 0.00 0.00 2.82
767 804 1.260538 TTGTTGGGGTTTGCACAGCA 61.261 50.000 4.22 0.00 36.47 4.41
768 805 0.530431 CTTGTTGGGGTTTGCACAGC 60.530 55.000 0.00 0.00 0.00 4.40
769 806 1.110442 TCTTGTTGGGGTTTGCACAG 58.890 50.000 0.00 0.00 0.00 3.66
770 807 1.205893 GTTCTTGTTGGGGTTTGCACA 59.794 47.619 0.00 0.00 0.00 4.57
771 808 1.472552 GGTTCTTGTTGGGGTTTGCAC 60.473 52.381 0.00 0.00 0.00 4.57
772 809 0.827368 GGTTCTTGTTGGGGTTTGCA 59.173 50.000 0.00 0.00 0.00 4.08
773 810 0.249280 CGGTTCTTGTTGGGGTTTGC 60.249 55.000 0.00 0.00 0.00 3.68
774 811 0.387565 CCGGTTCTTGTTGGGGTTTG 59.612 55.000 0.00 0.00 0.00 2.93
828 865 1.896220 AATTCTTGTTGCTCCAGCGA 58.104 45.000 0.00 0.00 45.83 4.93
887 924 5.996513 CCAGCAGAATTTATAGTGAGATGCT 59.003 40.000 0.00 0.00 41.86 3.79
888 925 5.762218 ACCAGCAGAATTTATAGTGAGATGC 59.238 40.000 0.00 0.00 0.00 3.91
889 926 6.988580 TGACCAGCAGAATTTATAGTGAGATG 59.011 38.462 0.00 0.00 0.00 2.90
890 927 6.989169 GTGACCAGCAGAATTTATAGTGAGAT 59.011 38.462 0.00 0.00 0.00 2.75
909 950 1.275666 ATCACCCGAATGAGTGACCA 58.724 50.000 0.00 0.00 45.24 4.02
915 956 5.236478 GTGGTTGTTATATCACCCGAATGAG 59.764 44.000 0.00 0.00 30.46 2.90
919 960 4.255301 GTGTGGTTGTTATATCACCCGAA 58.745 43.478 0.00 0.00 0.00 4.30
924 965 5.502382 CGATGCTGTGTGGTTGTTATATCAC 60.502 44.000 0.00 0.00 0.00 3.06
928 969 3.930229 GTCGATGCTGTGTGGTTGTTATA 59.070 43.478 0.00 0.00 0.00 0.98
934 975 1.230635 GCTGTCGATGCTGTGTGGTT 61.231 55.000 6.18 0.00 0.00 3.67
935 976 1.669115 GCTGTCGATGCTGTGTGGT 60.669 57.895 6.18 0.00 0.00 4.16
936 977 0.108662 TAGCTGTCGATGCTGTGTGG 60.109 55.000 21.07 0.00 41.32 4.17
937 978 0.994995 GTAGCTGTCGATGCTGTGTG 59.005 55.000 21.07 0.00 41.32 3.82
959 1007 3.728373 GCCCCGGTGATTCCAGGT 61.728 66.667 0.00 0.00 31.94 4.00
960 1008 4.856801 CGCCCCGGTGATTCCAGG 62.857 72.222 0.00 0.00 35.57 4.45
963 1011 2.886730 ATTCACGCCCCGGTGATTCC 62.887 60.000 0.00 0.00 45.62 3.01
965 1013 1.451387 GATTCACGCCCCGGTGATT 60.451 57.895 0.00 0.00 45.62 2.57
973 1021 4.511826 CCTAAATAACTGAGATTCACGCCC 59.488 45.833 0.00 0.00 0.00 6.13
974 1022 5.116882 ACCTAAATAACTGAGATTCACGCC 58.883 41.667 0.00 0.00 0.00 5.68
977 1025 8.616076 CCATTGACCTAAATAACTGAGATTCAC 58.384 37.037 0.00 0.00 0.00 3.18
978 1026 7.283127 GCCATTGACCTAAATAACTGAGATTCA 59.717 37.037 0.00 0.00 0.00 2.57
979 1027 7.519008 CGCCATTGACCTAAATAACTGAGATTC 60.519 40.741 0.00 0.00 0.00 2.52
980 1028 6.260936 CGCCATTGACCTAAATAACTGAGATT 59.739 38.462 0.00 0.00 0.00 2.40
992 1044 0.687920 TGGACACGCCATTGACCTAA 59.312 50.000 0.00 0.00 43.33 2.69
993 1045 2.367529 TGGACACGCCATTGACCTA 58.632 52.632 0.00 0.00 43.33 3.08
994 1046 3.156714 TGGACACGCCATTGACCT 58.843 55.556 0.00 0.00 43.33 3.85
1041 1095 3.717294 GGGATGACGTGGCCCTGT 61.717 66.667 0.00 0.00 38.85 4.00
1350 1404 0.246360 TGTAGTCCGTGACCATGCAG 59.754 55.000 0.00 0.00 32.18 4.41
1359 1413 1.443194 CCCGACGTTGTAGTCCGTG 60.443 63.158 1.30 0.00 37.44 4.94
1440 1494 4.760047 GTGACCATGACGGCGGCT 62.760 66.667 16.45 0.00 39.03 5.52
1473 1527 5.164620 TGATGTTGTCCTCAATCAGCTTA 57.835 39.130 0.00 0.00 35.92 3.09
1482 1536 2.554142 GCATCGATGATGTTGTCCTCA 58.446 47.619 29.20 0.00 41.60 3.86
1569 1628 2.291153 ACTGTAGACCCTGCATGCAAAT 60.291 45.455 22.88 9.85 0.00 2.32
1774 1833 3.821033 CGTTGGGGAAGAGTTTGAAAGAT 59.179 43.478 0.00 0.00 0.00 2.40
1948 2007 3.636313 CTCGAACTGGCGCCGGTTA 62.636 63.158 44.99 32.26 44.62 2.85
2041 2100 1.874345 CTTCCGGGTAGTCGTGCACT 61.874 60.000 16.19 0.00 39.41 4.40
2248 2307 3.090210 TCGGAGATGTACACCTGGTTA 57.910 47.619 0.00 0.00 0.00 2.85
2300 2359 1.475682 GGTTATGACTCCCGACTCGTT 59.524 52.381 0.00 0.00 0.00 3.85
2363 2422 3.554342 CCTCTCCCTCATGCCGGG 61.554 72.222 2.18 12.36 43.38 5.73
2425 2484 1.067295 AGTTTCCATGTGAGGAGCCA 58.933 50.000 0.00 0.00 39.25 4.75
2434 2493 4.549458 CAAAAGCATCGAAGTTTCCATGT 58.451 39.130 0.00 0.00 29.93 3.21
2476 2535 1.291588 CTGAACACTCTCAGGCGCT 59.708 57.895 7.64 0.00 39.39 5.92
2488 2553 3.319198 GAGCCCCCGTCCTGAACA 61.319 66.667 0.00 0.00 0.00 3.18
2524 2589 1.403814 TCATACCCTCCGCAAGAGAG 58.596 55.000 2.33 0.00 46.50 3.20
2525 2590 1.757118 CTTCATACCCTCCGCAAGAGA 59.243 52.381 2.33 0.00 46.50 3.10
2536 2601 4.008330 CAGATGATCATGCCTTCATACCC 58.992 47.826 14.30 0.00 32.84 3.69
2539 2604 4.648651 CACCAGATGATCATGCCTTCATA 58.351 43.478 14.30 0.00 32.84 2.15
2559 2624 0.713883 CCACACGTACAATCGAGCAC 59.286 55.000 0.00 0.00 34.70 4.40
2567 2632 2.811855 CACACACTACCACACGTACAA 58.188 47.619 0.00 0.00 0.00 2.41
2604 2669 8.294577 GGTTATGGTCGAACTTTTTATTCTGTT 58.705 33.333 0.33 0.00 0.00 3.16
2627 2694 5.474876 GCAGCAAATATAGAGGCTAATGGTT 59.525 40.000 0.00 0.00 34.25 3.67
2634 2701 5.298777 CAGAAAAGCAGCAAATATAGAGGCT 59.701 40.000 0.00 0.00 36.99 4.58
2639 2706 5.967674 CGGAACAGAAAAGCAGCAAATATAG 59.032 40.000 0.00 0.00 0.00 1.31
2649 2716 3.015516 GGGACGGAACAGAAAAGCA 57.984 52.632 0.00 0.00 0.00 3.91
2677 2780 1.554617 TCCAGATCCATTTCTGCGACA 59.445 47.619 0.00 0.00 41.50 4.35
2678 2781 2.315925 TCCAGATCCATTTCTGCGAC 57.684 50.000 0.00 0.00 41.50 5.19
2679 2782 2.486013 CCATCCAGATCCATTTCTGCGA 60.486 50.000 0.00 0.00 41.50 5.10
2680 2783 1.878088 CCATCCAGATCCATTTCTGCG 59.122 52.381 0.00 0.00 41.50 5.18
2681 2784 3.219176 TCCATCCAGATCCATTTCTGC 57.781 47.619 0.00 0.00 41.50 4.26
2682 2785 4.079970 CCATCCATCCAGATCCATTTCTG 58.920 47.826 0.00 0.00 42.31 3.02
2689 2792 7.278875 GTCTTATATTCCATCCATCCAGATCC 58.721 42.308 0.00 0.00 0.00 3.36
2693 2796 6.042638 ACGTCTTATATTCCATCCATCCAG 57.957 41.667 0.00 0.00 0.00 3.86
2695 2798 7.745620 AAAACGTCTTATATTCCATCCATCC 57.254 36.000 0.00 0.00 0.00 3.51
2696 2799 8.009974 CGAAAAACGTCTTATATTCCATCCATC 58.990 37.037 0.00 0.00 37.22 3.51
2697 2800 7.713507 TCGAAAAACGTCTTATATTCCATCCAT 59.286 33.333 0.00 0.00 43.13 3.41
2699 2802 7.010738 TGTCGAAAAACGTCTTATATTCCATCC 59.989 37.037 0.00 0.00 43.13 3.51
2702 2805 6.869913 AGTGTCGAAAAACGTCTTATATTCCA 59.130 34.615 0.00 0.00 43.13 3.53
2703 2806 7.148689 ACAGTGTCGAAAAACGTCTTATATTCC 60.149 37.037 0.00 0.00 43.13 3.01
2704 2807 7.727017 ACAGTGTCGAAAAACGTCTTATATTC 58.273 34.615 0.00 0.00 43.13 1.75
2706 2809 6.864685 TGACAGTGTCGAAAAACGTCTTATAT 59.135 34.615 18.17 0.00 43.13 0.86
2707 2810 6.207928 TGACAGTGTCGAAAAACGTCTTATA 58.792 36.000 18.17 0.00 43.13 0.98
2716 2819 4.386867 AGAGTCTGACAGTGTCGAAAAA 57.613 40.909 18.17 0.00 34.95 1.94
2721 2824 3.975670 GTGTTTAGAGTCTGACAGTGTCG 59.024 47.826 18.17 12.74 34.95 4.35
2768 2871 4.526970 ACGCATCCAAAATTCTCAGGTAT 58.473 39.130 0.00 0.00 0.00 2.73
2809 2912 2.124942 GGGCTACACTGCTGCTCC 60.125 66.667 0.00 0.00 0.00 4.70
2847 2975 4.717629 TGACAAGGCCTCGTCGCG 62.718 66.667 18.88 0.00 34.78 5.87
2848 2976 2.811317 CTGACAAGGCCTCGTCGC 60.811 66.667 18.88 0.00 34.78 5.19
2849 2977 2.125912 CCTGACAAGGCCTCGTCG 60.126 66.667 18.88 12.99 36.56 5.12
2850 2978 0.670854 GTTCCTGACAAGGCCTCGTC 60.671 60.000 17.42 17.42 44.11 4.20
2851 2979 1.122019 AGTTCCTGACAAGGCCTCGT 61.122 55.000 5.23 0.00 44.11 4.18
2852 2980 0.895530 TAGTTCCTGACAAGGCCTCG 59.104 55.000 5.23 0.00 44.11 4.63
2853 2981 3.075148 GTTTAGTTCCTGACAAGGCCTC 58.925 50.000 5.23 0.00 44.11 4.70
2854 2982 2.550208 CGTTTAGTTCCTGACAAGGCCT 60.550 50.000 0.00 0.00 44.11 5.19
2855 2983 1.804748 CGTTTAGTTCCTGACAAGGCC 59.195 52.381 0.00 0.00 44.11 5.19
2856 2984 1.804748 CCGTTTAGTTCCTGACAAGGC 59.195 52.381 0.00 0.00 44.11 4.35
2857 2985 3.326747 CTCCGTTTAGTTCCTGACAAGG 58.673 50.000 0.00 0.00 46.06 3.61
2858 2986 3.326747 CCTCCGTTTAGTTCCTGACAAG 58.673 50.000 0.00 0.00 0.00 3.16
2859 2987 2.549349 GCCTCCGTTTAGTTCCTGACAA 60.549 50.000 0.00 0.00 0.00 3.18
2860 2988 1.001633 GCCTCCGTTTAGTTCCTGACA 59.998 52.381 0.00 0.00 0.00 3.58
2861 2989 1.001633 TGCCTCCGTTTAGTTCCTGAC 59.998 52.381 0.00 0.00 0.00 3.51
2862 2990 1.275291 CTGCCTCCGTTTAGTTCCTGA 59.725 52.381 0.00 0.00 0.00 3.86
2863 2991 1.676014 CCTGCCTCCGTTTAGTTCCTG 60.676 57.143 0.00 0.00 0.00 3.86
2864 2992 0.613777 CCTGCCTCCGTTTAGTTCCT 59.386 55.000 0.00 0.00 0.00 3.36
2865 2993 0.611714 TCCTGCCTCCGTTTAGTTCC 59.388 55.000 0.00 0.00 0.00 3.62
2866 2994 2.280628 CATCCTGCCTCCGTTTAGTTC 58.719 52.381 0.00 0.00 0.00 3.01
2947 3085 2.445438 GCTCACTACGCAAGCGGTC 61.445 63.158 19.30 0.00 44.69 4.79
2949 3087 3.188786 GGCTCACTACGCAAGCGG 61.189 66.667 19.30 4.29 44.69 5.52
2981 3122 3.172229 TCCAAAAACCAGCGGAAAAAG 57.828 42.857 1.50 0.00 0.00 2.27
3190 3337 9.492973 CAGATTTGGAAAGGATTTGTGTATTTT 57.507 29.630 0.00 0.00 39.27 1.82
3195 3342 5.598005 TCACAGATTTGGAAAGGATTTGTGT 59.402 36.000 0.00 0.00 39.27 3.72
3247 3394 9.243637 CGGACTTAAAAAGTTCATTCATTTTGA 57.756 29.630 0.00 0.00 43.03 2.69
3248 3395 8.003784 GCGGACTTAAAAAGTTCATTCATTTTG 58.996 33.333 0.00 0.00 43.03 2.44
3269 3416 3.565516 GATTTGGAAAAGAGTTGCGGAC 58.434 45.455 0.00 0.00 0.00 4.79
3273 3421 3.308530 CACGGATTTGGAAAAGAGTTGC 58.691 45.455 0.00 0.00 0.00 4.17
3343 3491 5.636121 CACTTCACATTGATTTCAACATGGG 59.364 40.000 0.00 0.00 38.86 4.00
3352 3500 7.765695 AATGACTACCACTTCACATTGATTT 57.234 32.000 0.00 0.00 0.00 2.17
3394 3544 5.287170 TGTGAAAAGCAATCTTGATCGAG 57.713 39.130 3.24 3.24 31.78 4.04
3460 3614 1.623811 GCAGGTCTTAGACAAGGTCCA 59.376 52.381 14.72 0.00 33.68 4.02
3470 3629 0.528017 TGACGAGCTGCAGGTCTTAG 59.472 55.000 35.49 25.26 40.17 2.18
3473 3632 2.644212 CCTGACGAGCTGCAGGTCT 61.644 63.158 35.49 25.10 45.21 3.85
3486 3645 2.801342 GCATCTCCGACTCATTCCTGAC 60.801 54.545 0.00 0.00 0.00 3.51
3494 3653 1.514553 CAGCAGCATCTCCGACTCA 59.485 57.895 0.00 0.00 0.00 3.41
3496 3655 2.186384 GCAGCAGCATCTCCGACT 59.814 61.111 0.00 0.00 41.58 4.18
3500 3659 1.524165 CAGGAGCAGCAGCATCTCC 60.524 63.158 19.89 19.89 45.11 3.71


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

AutoCloner maintained by Alex Coulton.