Multiple sequence alignment - TraesCS1A01G284900

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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 TraesCS1A01G284900 chr1A 100.000 2993 0 0 1 2993 482327595 482330587 0.000000e+00 5528.0
1 TraesCS1A01G284900 chr1A 85.687 517 71 3 1 515 280491031 280490516 2.620000e-150 542.0
2 TraesCS1A01G284900 chr1D 89.413 2078 126 34 280 2322 382218240 382220258 0.000000e+00 2532.0
3 TraesCS1A01G284900 chr1B 92.465 637 45 3 2332 2966 269218258 269218893 0.000000e+00 907.0
4 TraesCS1A01G284900 chr1B 91.616 656 50 5 2314 2966 25227089 25227742 0.000000e+00 902.0
5 TraesCS1A01G284900 chr1B 91.994 637 48 3 2332 2966 636662519 636663154 0.000000e+00 891.0
6 TraesCS1A01G284900 chr1B 91.994 637 48 3 2332 2966 644278845 644278210 0.000000e+00 891.0
7 TraesCS1A01G284900 chr1B 85.687 517 72 2 1 515 668914376 668914892 7.300000e-151 544.0
8 TraesCS1A01G284900 chr1B 85.106 517 75 2 1 515 256208238 256208754 7.350000e-146 527.0
9 TraesCS1A01G284900 chr1B 96.000 50 1 1 2244 2293 587664217 587664265 2.470000e-11 80.5
10 TraesCS1A01G284900 chr3D 92.308 637 46 3 2332 2966 559109486 559108851 0.000000e+00 902.0
11 TraesCS1A01G284900 chr2D 92.296 636 47 2 2332 2966 617082844 617082210 0.000000e+00 902.0
12 TraesCS1A01G284900 chr2D 94.444 54 2 1 2239 2292 5197897 5197845 6.880000e-12 82.4
13 TraesCS1A01G284900 chr4D 92.031 640 44 5 2332 2966 8274418 8275055 0.000000e+00 893.0
14 TraesCS1A01G284900 chr4D 91.244 651 52 5 2319 2966 6226613 6227261 0.000000e+00 881.0
15 TraesCS1A01G284900 chr4B 91.654 647 50 4 2323 2966 629957945 629957300 0.000000e+00 893.0
16 TraesCS1A01G284900 chr4B 85.493 517 72 3 1 515 376257125 376256610 1.220000e-148 536.0
17 TraesCS1A01G284900 chr4B 84.884 516 77 1 1 515 479402135 479402650 1.230000e-143 520.0
18 TraesCS1A01G284900 chr7D 81.612 881 132 18 1027 1895 452140897 452140035 0.000000e+00 702.0
19 TraesCS1A01G284900 chr7D 85.934 519 67 5 1 516 601143754 601144269 1.570000e-152 549.0
20 TraesCS1A01G284900 chr7A 81.038 886 136 21 1023 1895 545519789 545520655 0.000000e+00 676.0
21 TraesCS1A01G284900 chr7B 81.242 773 117 16 1023 1784 468058471 468059226 1.540000e-167 599.0
22 TraesCS1A01G284900 chr7B 82.500 680 99 14 1023 1695 474435284 474434618 2.000000e-161 579.0
23 TraesCS1A01G284900 chr7B 86.214 515 69 2 1 513 27485594 27486108 9.370000e-155 556.0
24 TraesCS1A01G284900 chr7B 96.000 50 1 1 2244 2293 593400995 593401043 2.470000e-11 80.5
25 TraesCS1A01G284900 chr6A 87.500 512 62 2 1 510 416648058 416647547 9.240000e-165 590.0
26 TraesCS1A01G284900 chr6B 85.106 517 72 4 1 515 626885559 626885046 9.510000e-145 523.0
27 TraesCS1A01G284900 chr6B 91.071 56 3 2 2244 2298 699606381 699606435 1.150000e-09 75.0
28 TraesCS1A01G284900 chr3B 89.706 68 6 1 2239 2306 788514258 788514192 5.320000e-13 86.1
29 TraesCS1A01G284900 chr3B 97.959 49 0 1 2245 2293 513807438 513807485 1.910000e-12 84.2
30 TraesCS1A01G284900 chr3B 92.593 54 3 1 2244 2297 55392382 55392330 3.200000e-10 76.8
31 TraesCS1A01G284900 chrUn 92.593 54 3 1 2244 2297 333063166 333063218 3.200000e-10 76.8
32 TraesCS1A01G284900 chr6D 92.593 54 3 1 2244 2297 468143098 468143150 3.200000e-10 76.8


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 TraesCS1A01G284900 chr1A 482327595 482330587 2992 False 5528 5528 100.000 1 2993 1 chr1A.!!$F1 2992
1 TraesCS1A01G284900 chr1A 280490516 280491031 515 True 542 542 85.687 1 515 1 chr1A.!!$R1 514
2 TraesCS1A01G284900 chr1D 382218240 382220258 2018 False 2532 2532 89.413 280 2322 1 chr1D.!!$F1 2042
3 TraesCS1A01G284900 chr1B 269218258 269218893 635 False 907 907 92.465 2332 2966 1 chr1B.!!$F3 634
4 TraesCS1A01G284900 chr1B 25227089 25227742 653 False 902 902 91.616 2314 2966 1 chr1B.!!$F1 652
5 TraesCS1A01G284900 chr1B 636662519 636663154 635 False 891 891 91.994 2332 2966 1 chr1B.!!$F5 634
6 TraesCS1A01G284900 chr1B 644278210 644278845 635 True 891 891 91.994 2332 2966 1 chr1B.!!$R1 634
7 TraesCS1A01G284900 chr1B 668914376 668914892 516 False 544 544 85.687 1 515 1 chr1B.!!$F6 514
8 TraesCS1A01G284900 chr1B 256208238 256208754 516 False 527 527 85.106 1 515 1 chr1B.!!$F2 514
9 TraesCS1A01G284900 chr3D 559108851 559109486 635 True 902 902 92.308 2332 2966 1 chr3D.!!$R1 634
10 TraesCS1A01G284900 chr2D 617082210 617082844 634 True 902 902 92.296 2332 2966 1 chr2D.!!$R2 634
11 TraesCS1A01G284900 chr4D 8274418 8275055 637 False 893 893 92.031 2332 2966 1 chr4D.!!$F2 634
12 TraesCS1A01G284900 chr4D 6226613 6227261 648 False 881 881 91.244 2319 2966 1 chr4D.!!$F1 647
13 TraesCS1A01G284900 chr4B 629957300 629957945 645 True 893 893 91.654 2323 2966 1 chr4B.!!$R2 643
14 TraesCS1A01G284900 chr4B 376256610 376257125 515 True 536 536 85.493 1 515 1 chr4B.!!$R1 514
15 TraesCS1A01G284900 chr4B 479402135 479402650 515 False 520 520 84.884 1 515 1 chr4B.!!$F1 514
16 TraesCS1A01G284900 chr7D 452140035 452140897 862 True 702 702 81.612 1027 1895 1 chr7D.!!$R1 868
17 TraesCS1A01G284900 chr7D 601143754 601144269 515 False 549 549 85.934 1 516 1 chr7D.!!$F1 515
18 TraesCS1A01G284900 chr7A 545519789 545520655 866 False 676 676 81.038 1023 1895 1 chr7A.!!$F1 872
19 TraesCS1A01G284900 chr7B 468058471 468059226 755 False 599 599 81.242 1023 1784 1 chr7B.!!$F2 761
20 TraesCS1A01G284900 chr7B 474434618 474435284 666 True 579 579 82.500 1023 1695 1 chr7B.!!$R1 672
21 TraesCS1A01G284900 chr7B 27485594 27486108 514 False 556 556 86.214 1 513 1 chr7B.!!$F1 512
22 TraesCS1A01G284900 chr6A 416647547 416648058 511 True 590 590 87.500 1 510 1 chr6A.!!$R1 509
23 TraesCS1A01G284900 chr6B 626885046 626885559 513 True 523 523 85.106 1 515 1 chr6B.!!$R1 514

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
646 650 0.107945 GTCTGCCCATGTGGAGACTC 60.108 60.0 19.89 0.0 37.85 3.36 F
1020 1047 0.032815 GCCTCCTCCAGCTCGATTAC 59.967 60.0 0.00 0.0 0.00 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 1953 0.027979 TGTAGTGTATACCGCGCGTC 59.972 55.0 29.95 13.37 0.00 5.19 R
2492 2545 0.174617 CAACAAGTTGTGCCCGGTTT 59.825 50.0 9.79 0.00 35.92 3.27 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
61 63 0.981183 ACATAGTTCCACCAAGCGGA 59.019 50.000 0.00 0.00 35.59 5.54
63 65 2.224670 ACATAGTTCCACCAAGCGGAAA 60.225 45.455 0.00 0.00 44.02 3.13
98 100 2.469826 TCGCGGCATTACATTACTCAG 58.530 47.619 6.13 0.00 0.00 3.35
135 137 3.896479 GCCCAAAGAGAGGCTTCG 58.104 61.111 0.00 0.00 46.14 3.79
155 157 6.483640 GCTTCGTCCTTAATCTTGGTAATGAT 59.516 38.462 0.00 0.00 0.00 2.45
164 166 8.621532 TTAATCTTGGTAATGATGATGGTAGC 57.378 34.615 0.00 0.00 0.00 3.58
167 169 5.130975 TCTTGGTAATGATGATGGTAGCAGT 59.869 40.000 0.00 0.00 0.00 4.40
179 181 0.876342 GTAGCAGTGGCGGCTATGTC 60.876 60.000 11.43 5.57 44.86 3.06
199 201 0.389948 GCGGAAGATCCTCGTGTTGT 60.390 55.000 0.00 0.00 33.30 3.32
254 256 2.584835 AAGGTGTTATGAGCCTTGCA 57.415 45.000 0.00 0.00 40.71 4.08
278 280 1.679153 GTCGCCCCTTTTGTGAGAAAA 59.321 47.619 0.00 0.00 0.00 2.29
318 320 1.515952 CGAGAGCGCAAGTCTCCAG 60.516 63.158 11.47 0.00 39.64 3.86
322 324 2.159819 GAGCGCAAGTCTCCAGTCCA 62.160 60.000 11.47 0.00 41.68 4.02
418 420 4.500116 GGTGAGCCGCCGTCTCTC 62.500 72.222 0.00 0.00 0.00 3.20
453 455 0.961753 GAGGGGAAAGGTTGCAGTTG 59.038 55.000 0.00 0.00 0.00 3.16
499 502 0.179081 GCGGTCCACACCCTATTCTC 60.179 60.000 0.00 0.00 40.01 2.87
516 519 6.652481 CCTATTCTCGATAATCAACCAAGCAT 59.348 38.462 0.00 0.00 0.00 3.79
517 520 6.949352 ATTCTCGATAATCAACCAAGCATT 57.051 33.333 0.00 0.00 0.00 3.56
518 521 6.757897 TTCTCGATAATCAACCAAGCATTT 57.242 33.333 0.00 0.00 0.00 2.32
519 522 6.757897 TCTCGATAATCAACCAAGCATTTT 57.242 33.333 0.00 0.00 0.00 1.82
520 523 7.156876 TCTCGATAATCAACCAAGCATTTTT 57.843 32.000 0.00 0.00 0.00 1.94
574 577 3.238108 CACTACAAGGGTGCTCTACAG 57.762 52.381 0.00 0.00 0.00 2.74
588 591 2.009051 TCTACAGGATTTGCATGTGCG 58.991 47.619 0.12 0.00 42.28 5.34
589 592 0.451383 TACAGGATTTGCATGTGCGC 59.549 50.000 0.00 0.00 42.28 6.09
636 640 0.538057 CACCAACAGTGTCTGCCCAT 60.538 55.000 0.00 0.00 41.93 4.00
644 648 0.674895 GTGTCTGCCCATGTGGAGAC 60.675 60.000 20.26 20.26 39.65 3.36
645 649 0.837691 TGTCTGCCCATGTGGAGACT 60.838 55.000 25.39 0.00 39.78 3.24
646 650 0.107945 GTCTGCCCATGTGGAGACTC 60.108 60.000 19.89 0.00 37.85 3.36
647 651 1.153489 CTGCCCATGTGGAGACTCG 60.153 63.158 0.00 0.00 37.39 4.18
648 652 2.512515 GCCCATGTGGAGACTCGC 60.513 66.667 0.00 0.00 37.39 5.03
649 653 2.187946 CCCATGTGGAGACTCGCC 59.812 66.667 0.00 0.00 37.39 5.54
650 654 2.659063 CCCATGTGGAGACTCGCCA 61.659 63.158 0.00 0.00 37.39 5.69
651 655 1.524002 CCATGTGGAGACTCGCCAT 59.476 57.895 4.65 0.00 35.49 4.40
652 656 0.531532 CCATGTGGAGACTCGCCATC 60.532 60.000 4.65 0.43 35.49 3.51
653 657 0.176449 CATGTGGAGACTCGCCATCA 59.824 55.000 4.65 5.81 35.49 3.07
667 671 3.316029 TCGCCATCATGGACAATTCAATC 59.684 43.478 8.30 0.00 40.96 2.67
669 673 4.556104 CGCCATCATGGACAATTCAATCTC 60.556 45.833 8.30 0.00 40.96 2.75
672 676 5.826208 CCATCATGGACAATTCAATCTCTCA 59.174 40.000 0.00 0.00 40.96 3.27
674 678 6.058553 TCATGGACAATTCAATCTCTCACT 57.941 37.500 0.00 0.00 0.00 3.41
675 679 5.878669 TCATGGACAATTCAATCTCTCACTG 59.121 40.000 0.00 0.00 0.00 3.66
676 680 5.233083 TGGACAATTCAATCTCTCACTGT 57.767 39.130 0.00 0.00 0.00 3.55
677 681 6.358974 TGGACAATTCAATCTCTCACTGTA 57.641 37.500 0.00 0.00 0.00 2.74
679 683 6.820152 TGGACAATTCAATCTCTCACTGTATG 59.180 38.462 0.00 0.00 0.00 2.39
680 684 6.259608 GGACAATTCAATCTCTCACTGTATGG 59.740 42.308 0.00 0.00 0.00 2.74
722 728 3.221771 ACTAGTCATGGAGAGCTAGCTG 58.778 50.000 24.99 7.59 34.27 4.24
778 784 0.962855 GAGCCTTCTTCCTTGCCCAC 60.963 60.000 0.00 0.00 0.00 4.61
793 799 1.227234 CCACATCGCTCATACGCCA 60.227 57.895 0.00 0.00 0.00 5.69
805 811 0.740737 ATACGCCATTGAAAGCTGCC 59.259 50.000 0.00 0.00 0.00 4.85
825 831 3.854666 CCGCTATCCACCATATCTTGAG 58.145 50.000 0.00 0.00 0.00 3.02
830 836 6.754209 CGCTATCCACCATATCTTGAGATTAC 59.246 42.308 0.00 0.00 36.05 1.89
839 845 3.355626 TCTTGAGATTACGCTCATCCG 57.644 47.619 0.00 0.00 43.84 4.18
840 846 2.949644 TCTTGAGATTACGCTCATCCGA 59.050 45.455 0.00 0.00 43.84 4.55
852 858 0.750546 TCATCCGAGTCGACCCGATT 60.751 55.000 21.79 4.65 38.42 3.34
870 876 0.442310 TTAGCTGCAACGTCGCATTC 59.558 50.000 0.00 0.00 42.06 2.67
872 878 2.480555 CTGCAACGTCGCATTCCC 59.519 61.111 0.00 0.00 42.06 3.97
891 897 0.517132 CAGCTGCGAATTCGTCAACG 60.517 55.000 27.24 15.45 42.22 4.10
897 903 2.532723 TGCGAATTCGTCAACGTATAGC 59.467 45.455 27.24 8.00 42.22 2.97
975 981 3.772619 GCCACTGCGTATTTAGGGA 57.227 52.632 0.00 0.00 0.00 4.20
1008 1035 4.173924 GCCAGCTCCAGCCTCCTC 62.174 72.222 0.00 0.00 43.38 3.71
1009 1036 3.478274 CCAGCTCCAGCCTCCTCC 61.478 72.222 0.00 0.00 43.38 4.30
1018 1045 1.382420 AGCCTCCTCCAGCTCGATT 60.382 57.895 0.00 0.00 32.71 3.34
1019 1046 0.105964 AGCCTCCTCCAGCTCGATTA 60.106 55.000 0.00 0.00 32.71 1.75
1020 1047 0.032815 GCCTCCTCCAGCTCGATTAC 59.967 60.000 0.00 0.00 0.00 1.89
1025 1052 2.658593 CCAGCTCGATTACCGCCG 60.659 66.667 0.00 0.00 38.37 6.46
1254 1281 3.950794 GACGTGGCCGCCATCAAGA 62.951 63.158 16.96 0.00 35.28 3.02
1696 1735 4.530857 CTTCTACCCCGGCGCCAG 62.531 72.222 28.98 16.49 0.00 4.85
1730 1769 2.738521 CAGACCGGCAAGACCACG 60.739 66.667 0.00 0.00 39.03 4.94
1787 1826 4.473520 GCCGCCAAGGAGCTGCTA 62.474 66.667 8.68 0.00 45.00 3.49
1788 1827 2.268920 CCGCCAAGGAGCTGCTAA 59.731 61.111 8.68 0.00 45.00 3.09
1826 1865 1.092345 GCTTCTTCATCTGGTCGGCC 61.092 60.000 0.00 0.00 0.00 6.13
1899 1938 1.083489 GATCGTCGCCAACCATTGAA 58.917 50.000 0.00 0.00 0.00 2.69
1900 1939 1.670811 GATCGTCGCCAACCATTGAAT 59.329 47.619 0.00 0.00 0.00 2.57
1902 1941 1.198867 TCGTCGCCAACCATTGAATTG 59.801 47.619 0.00 0.00 0.00 2.32
1903 1942 1.198867 CGTCGCCAACCATTGAATTGA 59.801 47.619 3.08 0.00 0.00 2.57
1904 1943 2.159393 CGTCGCCAACCATTGAATTGAT 60.159 45.455 3.08 0.00 0.00 2.57
1905 1944 3.438360 GTCGCCAACCATTGAATTGATC 58.562 45.455 3.08 0.00 0.00 2.92
1906 1945 3.129287 GTCGCCAACCATTGAATTGATCT 59.871 43.478 0.00 0.00 0.00 2.75
1907 1946 3.378112 TCGCCAACCATTGAATTGATCTC 59.622 43.478 0.00 0.00 0.00 2.75
1908 1947 3.489738 CGCCAACCATTGAATTGATCTCC 60.490 47.826 0.00 0.00 0.00 3.71
1909 1948 3.448301 GCCAACCATTGAATTGATCTCCA 59.552 43.478 0.00 0.00 0.00 3.86
1910 1949 4.081531 GCCAACCATTGAATTGATCTCCAA 60.082 41.667 0.00 0.00 39.41 3.53
1911 1950 5.569227 GCCAACCATTGAATTGATCTCCAAA 60.569 40.000 0.00 0.00 38.43 3.28
1914 1953 4.158394 ACCATTGAATTGATCTCCAAACGG 59.842 41.667 0.00 0.00 38.43 4.44
1918 1957 1.369625 ATTGATCTCCAAACGGACGC 58.630 50.000 0.00 0.00 38.43 5.19
1919 1958 1.011968 TTGATCTCCAAACGGACGCG 61.012 55.000 3.53 3.53 0.00 6.01
1930 1969 2.410469 GGACGCGCGGTATACACT 59.590 61.111 35.22 10.37 0.00 3.55
1931 1970 1.648720 GGACGCGCGGTATACACTA 59.351 57.895 35.22 0.00 0.00 2.74
1932 1971 0.658536 GGACGCGCGGTATACACTAC 60.659 60.000 35.22 7.05 0.00 2.73
1934 1973 0.028505 ACGCGCGGTATACACTACAG 59.971 55.000 35.22 0.47 0.00 2.74
1983 2022 3.178539 GCTTGCCAAGAGCCGTAC 58.821 61.111 9.04 0.00 42.71 3.67
1984 2023 1.376037 GCTTGCCAAGAGCCGTACT 60.376 57.895 9.04 0.00 42.71 2.73
1986 2025 1.927895 CTTGCCAAGAGCCGTACTAG 58.072 55.000 0.00 0.00 42.71 2.57
1987 2026 1.476891 CTTGCCAAGAGCCGTACTAGA 59.523 52.381 0.00 0.00 42.71 2.43
1988 2027 1.552578 TGCCAAGAGCCGTACTAGAA 58.447 50.000 0.00 0.00 42.71 2.10
1989 2028 2.108168 TGCCAAGAGCCGTACTAGAAT 58.892 47.619 0.00 0.00 42.71 2.40
1990 2029 3.293337 TGCCAAGAGCCGTACTAGAATA 58.707 45.455 0.00 0.00 42.71 1.75
1991 2030 3.702548 TGCCAAGAGCCGTACTAGAATAA 59.297 43.478 0.00 0.00 42.71 1.40
1992 2031 4.202121 TGCCAAGAGCCGTACTAGAATAAG 60.202 45.833 0.00 0.00 42.71 1.73
1993 2032 4.202131 GCCAAGAGCCGTACTAGAATAAGT 60.202 45.833 0.00 0.00 34.35 2.24
1994 2033 5.282510 CCAAGAGCCGTACTAGAATAAGTG 58.717 45.833 0.00 0.00 0.00 3.16
1995 2034 4.571372 AGAGCCGTACTAGAATAAGTGC 57.429 45.455 0.00 0.00 0.00 4.40
1996 2035 3.952323 AGAGCCGTACTAGAATAAGTGCA 59.048 43.478 0.00 0.00 32.22 4.57
1997 2036 4.043037 AGCCGTACTAGAATAAGTGCAC 57.957 45.455 9.40 9.40 32.22 4.57
1998 2037 3.700038 AGCCGTACTAGAATAAGTGCACT 59.300 43.478 15.25 15.25 32.22 4.40
1999 2038 4.159879 AGCCGTACTAGAATAAGTGCACTT 59.840 41.667 32.97 32.97 39.85 3.16
2000 2039 4.267928 GCCGTACTAGAATAAGTGCACTTG 59.732 45.833 36.50 22.99 37.40 3.16
2001 2040 4.267928 CCGTACTAGAATAAGTGCACTTGC 59.732 45.833 36.50 25.55 42.50 4.01
2041 2092 9.891828 CAATCATACTTGTTTGCAAAACTACTA 57.108 29.630 14.67 0.00 33.73 1.82
2042 2093 9.893305 AATCATACTTGTTTGCAAAACTACTAC 57.107 29.630 14.67 0.29 33.73 2.73
2043 2094 8.671384 TCATACTTGTTTGCAAAACTACTACT 57.329 30.769 14.67 0.00 33.73 2.57
2044 2095 8.556194 TCATACTTGTTTGCAAAACTACTACTG 58.444 33.333 14.67 5.63 33.73 2.74
2045 2096 6.753107 ACTTGTTTGCAAAACTACTACTGT 57.247 33.333 14.67 1.60 33.73 3.55
2046 2097 7.852971 ACTTGTTTGCAAAACTACTACTGTA 57.147 32.000 14.67 0.00 33.73 2.74
2047 2098 8.446599 ACTTGTTTGCAAAACTACTACTGTAT 57.553 30.769 14.67 0.00 33.73 2.29
2048 2099 8.342634 ACTTGTTTGCAAAACTACTACTGTATG 58.657 33.333 14.67 0.00 33.73 2.39
2049 2100 8.439993 TTGTTTGCAAAACTACTACTGTATGA 57.560 30.769 14.67 0.00 0.00 2.15
2050 2101 7.857569 TGTTTGCAAAACTACTACTGTATGAC 58.142 34.615 14.67 0.00 0.00 3.06
2051 2102 7.496263 TGTTTGCAAAACTACTACTGTATGACA 59.504 33.333 14.67 0.00 0.00 3.58
2069 2120 4.089361 TGACAGTATGAGAGTGGTGTGAT 58.911 43.478 0.00 0.00 39.69 3.06
2084 2135 5.291128 GTGGTGTGATGACCGTAAGAATAAG 59.709 44.000 0.00 0.00 39.07 1.73
2086 2137 4.270325 GTGTGATGACCGTAAGAATAAGGC 59.730 45.833 0.00 0.00 43.02 4.35
2096 2147 3.644966 AAGAATAAGGCGGATGGTTCA 57.355 42.857 0.00 0.00 0.00 3.18
2099 2150 0.474184 ATAAGGCGGATGGTTCAGGG 59.526 55.000 0.00 0.00 0.00 4.45
2102 2153 0.399949 AGGCGGATGGTTCAGGGATA 60.400 55.000 0.00 0.00 0.00 2.59
2113 2164 4.273318 GGTTCAGGGATAAAGTGAAGCAT 58.727 43.478 8.25 0.00 44.42 3.79
2118 2169 3.941483 AGGGATAAAGTGAAGCATCGTTG 59.059 43.478 0.00 0.00 0.00 4.10
2119 2170 3.938963 GGGATAAAGTGAAGCATCGTTGA 59.061 43.478 0.00 0.00 0.00 3.18
2126 2177 2.033407 GTGAAGCATCGTTGATCCATCG 60.033 50.000 0.00 0.00 0.00 3.84
2129 2180 1.159713 GCATCGTTGATCCATCGCCA 61.160 55.000 0.00 0.00 0.00 5.69
2135 2186 0.397941 TTGATCCATCGCCATCCTCC 59.602 55.000 0.00 0.00 0.00 4.30
2158 2209 2.355986 CCGTCCCCTCCATGTTCGA 61.356 63.158 0.00 0.00 0.00 3.71
2159 2210 1.686325 CCGTCCCCTCCATGTTCGAT 61.686 60.000 0.00 0.00 0.00 3.59
2162 2213 0.107214 TCCCCTCCATGTTCGATTGC 60.107 55.000 0.00 0.00 0.00 3.56
2176 2227 4.776322 TTGCCGACCATCCTGCCG 62.776 66.667 0.00 0.00 0.00 5.69
2198 2249 0.618458 CCCCAATCACCTCTTCGGAA 59.382 55.000 0.00 0.00 36.31 4.30
2199 2250 1.407437 CCCCAATCACCTCTTCGGAAG 60.407 57.143 11.54 11.54 36.31 3.46
2200 2251 1.279271 CCCAATCACCTCTTCGGAAGT 59.721 52.381 16.78 0.00 36.31 3.01
2201 2252 2.290323 CCCAATCACCTCTTCGGAAGTT 60.290 50.000 16.78 0.84 36.31 2.66
2202 2253 3.003480 CCAATCACCTCTTCGGAAGTTC 58.997 50.000 16.78 0.00 36.31 3.01
2203 2254 2.656560 ATCACCTCTTCGGAAGTTCG 57.343 50.000 16.78 8.38 36.31 3.95
2204 2255 0.601558 TCACCTCTTCGGAAGTTCGG 59.398 55.000 16.78 16.47 36.31 4.30
2205 2256 0.601558 CACCTCTTCGGAAGTTCGGA 59.398 55.000 16.78 8.92 36.31 4.55
2220 2271 6.238814 GGAAGTTCGGATGGTTTTAACTTTCA 60.239 38.462 0.00 0.00 39.72 2.69
2221 2272 6.894339 AGTTCGGATGGTTTTAACTTTCAT 57.106 33.333 0.00 0.00 0.00 2.57
2225 2276 7.278461 TCGGATGGTTTTAACTTTCATTGAA 57.722 32.000 0.00 0.00 0.00 2.69
2226 2277 7.717568 TCGGATGGTTTTAACTTTCATTGAAA 58.282 30.769 11.19 11.19 0.00 2.69
2227 2278 8.364142 TCGGATGGTTTTAACTTTCATTGAAAT 58.636 29.630 12.04 1.81 30.85 2.17
2228 2279 8.987890 CGGATGGTTTTAACTTTCATTGAAATT 58.012 29.630 12.04 4.34 30.85 1.82
2258 2309 9.893634 ATGAAATTCATCCAAAATATTTCAGCA 57.106 25.926 2.07 0.00 43.99 4.41
2259 2310 9.722184 TGAAATTCATCCAAAATATTTCAGCAA 57.278 25.926 0.10 0.00 39.16 3.91
2264 2315 9.722184 TTCATCCAAAATATTTCAGCAATTTCA 57.278 25.926 0.10 0.00 0.00 2.69
2265 2316 9.373603 TCATCCAAAATATTTCAGCAATTTCAG 57.626 29.630 0.10 0.00 0.00 3.02
2266 2317 9.158233 CATCCAAAATATTTCAGCAATTTCAGT 57.842 29.630 0.10 0.00 0.00 3.41
2268 2319 9.859427 TCCAAAATATTTCAGCAATTTCAGTAG 57.141 29.630 0.10 0.00 0.00 2.57
2269 2320 9.643693 CCAAAATATTTCAGCAATTTCAGTAGT 57.356 29.630 0.10 0.00 0.00 2.73
2274 2325 7.744087 ATTTCAGCAATTTCAGTAGTACACA 57.256 32.000 2.52 0.00 0.00 3.72
2275 2326 7.744087 TTTCAGCAATTTCAGTAGTACACAT 57.256 32.000 2.52 0.00 0.00 3.21
2276 2327 6.726258 TCAGCAATTTCAGTAGTACACATG 57.274 37.500 2.52 0.00 0.00 3.21
2277 2328 6.463360 TCAGCAATTTCAGTAGTACACATGA 58.537 36.000 0.00 0.00 0.00 3.07
2278 2329 6.934083 TCAGCAATTTCAGTAGTACACATGAA 59.066 34.615 0.00 1.39 0.00 2.57
2279 2330 7.607607 TCAGCAATTTCAGTAGTACACATGAAT 59.392 33.333 0.00 0.00 32.13 2.57
2280 2331 8.239314 CAGCAATTTCAGTAGTACACATGAATT 58.761 33.333 0.00 0.00 32.13 2.17
2281 2332 8.454106 AGCAATTTCAGTAGTACACATGAATTC 58.546 33.333 0.00 0.00 32.13 2.17
2282 2333 8.236586 GCAATTTCAGTAGTACACATGAATTCA 58.763 33.333 11.26 11.26 32.13 2.57
2430 2483 3.394940 TCCAGATCCGTAGACCATCTAGT 59.605 47.826 0.00 0.00 28.01 2.57
2492 2545 4.770362 TCACCCCTCCATCGCCGA 62.770 66.667 0.00 0.00 0.00 5.54
2494 2547 3.006728 ACCCCTCCATCGCCGAAA 61.007 61.111 0.00 0.00 0.00 3.46
2522 2575 4.318831 GCACAACTTGTTGTAGTAGACAGC 60.319 45.833 17.26 10.96 39.88 4.40
2526 2579 1.913778 TGTTGTAGTAGACAGCCGGA 58.086 50.000 5.05 0.00 39.88 5.14
2552 2605 0.397957 TCGTGCTAAGGCCCCATAGA 60.398 55.000 0.00 0.00 37.74 1.98
2555 2608 0.468226 TGCTAAGGCCCCATAGAACG 59.532 55.000 0.00 0.00 37.74 3.95
2558 2611 2.040178 CTAAGGCCCCATAGAACGAGT 58.960 52.381 0.00 0.00 0.00 4.18
2560 2613 2.400467 AGGCCCCATAGAACGAGTAT 57.600 50.000 0.00 0.00 0.00 2.12
2627 2680 2.489971 GATCCAAACCGAAGACACACA 58.510 47.619 0.00 0.00 0.00 3.72
2631 2684 2.162608 CCAAACCGAAGACACACAAACA 59.837 45.455 0.00 0.00 0.00 2.83
2656 2709 3.432782 ACGAATAACGACGAGATCCAAC 58.567 45.455 0.00 0.00 45.77 3.77
2824 2878 7.176589 ACACAAACCCTAACAAGATTGAAAA 57.823 32.000 0.00 0.00 0.00 2.29
2904 2961 2.122813 CCTAGGGCCACCGGAGAT 60.123 66.667 9.46 0.00 43.47 2.75
2966 3023 5.124617 CCATAACTTTCTTTCTTGGAGGAGC 59.875 44.000 0.00 0.00 0.00 4.70
2967 3024 4.445557 AACTTTCTTTCTTGGAGGAGCT 57.554 40.909 0.00 0.00 0.00 4.09
2968 3025 5.568620 AACTTTCTTTCTTGGAGGAGCTA 57.431 39.130 0.00 0.00 0.00 3.32
2969 3026 5.568620 ACTTTCTTTCTTGGAGGAGCTAA 57.431 39.130 0.00 0.00 0.00 3.09
2970 3027 6.133253 ACTTTCTTTCTTGGAGGAGCTAAT 57.867 37.500 0.00 0.00 0.00 1.73
2971 3028 6.547402 ACTTTCTTTCTTGGAGGAGCTAATT 58.453 36.000 0.00 0.00 0.00 1.40
2972 3029 6.432472 ACTTTCTTTCTTGGAGGAGCTAATTG 59.568 38.462 0.00 0.00 0.00 2.32
2973 3030 5.762179 TCTTTCTTGGAGGAGCTAATTGA 57.238 39.130 0.00 0.00 0.00 2.57
2974 3031 6.126863 TCTTTCTTGGAGGAGCTAATTGAA 57.873 37.500 0.00 0.00 0.00 2.69
2975 3032 6.725364 TCTTTCTTGGAGGAGCTAATTGAAT 58.275 36.000 0.00 0.00 0.00 2.57
2976 3033 7.177878 TCTTTCTTGGAGGAGCTAATTGAATT 58.822 34.615 0.00 0.00 0.00 2.17
2977 3034 7.337942 TCTTTCTTGGAGGAGCTAATTGAATTC 59.662 37.037 0.00 0.00 0.00 2.17
2978 3035 6.065976 TCTTGGAGGAGCTAATTGAATTCA 57.934 37.500 3.38 3.38 0.00 2.57
2979 3036 6.484288 TCTTGGAGGAGCTAATTGAATTCAA 58.516 36.000 22.52 22.52 40.51 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 63 4.270325 GCCGCGAGAGTGATTTATACTTTT 59.730 41.667 8.23 0.00 46.66 2.27
63 65 3.181479 TGCCGCGAGAGTGATTTATACTT 60.181 43.478 8.23 0.00 46.66 2.24
98 100 0.108992 TCGTGTGGGTGCGAAGTATC 60.109 55.000 0.00 0.00 33.96 2.24
135 137 7.721399 ACCATCATCATTACCAAGATTAAGGAC 59.279 37.037 0.00 0.00 0.00 3.85
155 157 2.584064 CCGCCACTGCTACCATCA 59.416 61.111 0.00 0.00 34.43 3.07
164 166 3.264897 GCGACATAGCCGCCACTG 61.265 66.667 0.00 0.00 46.22 3.66
199 201 1.611491 GTGGGAAATTTGGAACGAGCA 59.389 47.619 0.00 0.00 0.00 4.26
254 256 0.400213 TCACAAAAGGGGCGACTCAT 59.600 50.000 0.00 0.00 0.00 2.90
278 280 0.108019 GGAAGTTTGGTGGGACGAGT 59.892 55.000 0.00 0.00 0.00 4.18
418 420 1.001378 CCCTCTTTGCAAACAGGTTCG 60.001 52.381 25.99 11.81 0.00 3.95
439 441 1.367471 GGCCCAACTGCAACCTTTC 59.633 57.895 0.00 0.00 0.00 2.62
538 541 4.553687 TGCAAAGCTTGGCCCCCA 62.554 61.111 23.11 0.93 0.00 4.96
570 573 0.451383 GCGCACATGCAAATCCTGTA 59.549 50.000 0.30 0.00 42.21 2.74
574 577 1.517694 CCAGCGCACATGCAAATCC 60.518 57.895 11.47 0.00 42.21 3.01
609 613 4.771127 ACTGTTGGTGACGCGAAT 57.229 50.000 15.93 0.00 0.00 3.34
636 640 0.176449 CATGATGGCGAGTCTCCACA 59.824 55.000 3.39 5.53 36.26 4.17
644 648 2.291365 TGAATTGTCCATGATGGCGAG 58.709 47.619 6.59 0.00 37.47 5.03
645 649 2.416680 TGAATTGTCCATGATGGCGA 57.583 45.000 6.59 2.43 37.47 5.54
646 650 3.317149 AGATTGAATTGTCCATGATGGCG 59.683 43.478 6.59 0.00 37.47 5.69
647 651 4.583489 AGAGATTGAATTGTCCATGATGGC 59.417 41.667 6.59 2.68 37.47 4.40
648 652 5.826208 TGAGAGATTGAATTGTCCATGATGG 59.174 40.000 4.74 4.74 39.43 3.51
649 653 6.542735 AGTGAGAGATTGAATTGTCCATGATG 59.457 38.462 0.00 0.00 0.00 3.07
650 654 6.542735 CAGTGAGAGATTGAATTGTCCATGAT 59.457 38.462 0.00 0.00 0.00 2.45
651 655 5.878669 CAGTGAGAGATTGAATTGTCCATGA 59.121 40.000 0.00 0.00 0.00 3.07
652 656 5.646793 ACAGTGAGAGATTGAATTGTCCATG 59.353 40.000 0.00 0.00 0.00 3.66
653 657 5.813383 ACAGTGAGAGATTGAATTGTCCAT 58.187 37.500 0.00 0.00 0.00 3.41
667 671 2.094494 AGCGTCAACCATACAGTGAGAG 60.094 50.000 0.00 0.00 0.00 3.20
669 673 2.370281 AGCGTCAACCATACAGTGAG 57.630 50.000 0.00 0.00 0.00 3.51
672 676 3.000727 GCTTAAGCGTCAACCATACAGT 58.999 45.455 12.53 0.00 0.00 3.55
674 678 2.289756 TGGCTTAAGCGTCAACCATACA 60.290 45.455 20.80 6.51 43.26 2.29
675 679 2.352388 TGGCTTAAGCGTCAACCATAC 58.648 47.619 20.80 3.92 43.26 2.39
676 680 2.772077 TGGCTTAAGCGTCAACCATA 57.228 45.000 20.80 0.00 43.26 2.74
677 681 1.812571 CTTGGCTTAAGCGTCAACCAT 59.187 47.619 20.80 0.00 43.26 3.55
722 728 2.980233 AAGTCCTGGCGTGCAAGC 60.980 61.111 16.86 16.86 0.00 4.01
778 784 1.501169 TCAATGGCGTATGAGCGATG 58.499 50.000 0.00 0.00 35.75 3.84
805 811 4.790765 TCTCAAGATATGGTGGATAGCG 57.209 45.455 0.00 0.00 0.00 4.26
825 831 1.263484 TCGACTCGGATGAGCGTAATC 59.737 52.381 0.00 0.00 46.69 1.75
830 836 2.024871 GGTCGACTCGGATGAGCG 59.975 66.667 16.46 0.00 46.69 5.03
839 845 0.595310 GCAGCTAATCGGGTCGACTC 60.595 60.000 16.46 11.18 39.18 3.36
840 846 1.320344 TGCAGCTAATCGGGTCGACT 61.320 55.000 16.46 0.00 39.18 4.18
870 876 1.298157 TTGACGAATTCGCAGCTGGG 61.298 55.000 27.03 23.98 44.43 4.45
872 878 0.517132 CGTTGACGAATTCGCAGCTG 60.517 55.000 27.03 10.11 44.43 4.24
891 897 1.274447 GATGGGGTACGTGGGCTATAC 59.726 57.143 0.00 0.00 0.00 1.47
897 903 1.692173 AATCCGATGGGGTACGTGGG 61.692 60.000 0.00 0.00 37.00 4.61
961 967 3.574396 TCAGGATCTCCCTAAATACGCAG 59.426 47.826 0.00 0.00 45.60 5.18
965 971 4.262079 CGGTGTCAGGATCTCCCTAAATAC 60.262 50.000 0.00 0.00 45.60 1.89
975 981 2.060980 GGCCTCGGTGTCAGGATCT 61.061 63.158 0.00 0.00 31.91 2.75
982 1009 4.459089 GGAGCTGGCCTCGGTGTC 62.459 72.222 3.32 0.00 41.71 3.67
1007 1034 2.812499 GGCGGTAATCGAGCTGGA 59.188 61.111 0.00 0.00 42.43 3.86
1008 1035 2.658593 CGGCGGTAATCGAGCTGG 60.659 66.667 0.00 0.00 42.43 4.85
1009 1036 2.658593 CCGGCGGTAATCGAGCTG 60.659 66.667 19.97 0.00 42.43 4.24
1025 1052 1.812507 GTACCCGTTCGTCATGGCC 60.813 63.158 0.00 0.00 0.00 5.36
1100 1127 4.308458 CTGACGCCGGGGTTGACA 62.308 66.667 26.42 17.53 0.00 3.58
1184 1211 2.631428 CTGAACACGCCGTTGGTG 59.369 61.111 0.00 0.00 38.19 4.17
1196 1223 2.357034 TCCCAGAACGCGCTGAAC 60.357 61.111 14.33 0.00 38.14 3.18
1335 1365 4.477975 CCACGAGTCGACGGAGGC 62.478 72.222 21.50 0.00 37.61 4.70
1579 1609 2.025727 CGATGACGCCGGAGTACC 59.974 66.667 12.06 0.00 0.00 3.34
1826 1865 4.182132 CTCTGCTTGGAGCTGTCG 57.818 61.111 0.00 0.00 42.97 4.35
1908 1947 1.873125 TATACCGCGCGTCCGTTTG 60.873 57.895 29.95 13.89 36.67 2.93
1909 1948 1.873572 GTATACCGCGCGTCCGTTT 60.874 57.895 29.95 16.42 36.67 3.60
1910 1949 2.278142 GTATACCGCGCGTCCGTT 60.278 61.111 29.95 10.93 36.67 4.44
1911 1950 3.507924 TGTATACCGCGCGTCCGT 61.508 61.111 29.95 21.48 36.67 4.69
1914 1953 0.027979 TGTAGTGTATACCGCGCGTC 59.972 55.000 29.95 13.37 0.00 5.19
1918 1957 4.747108 AGTAGTACTGTAGTGTATACCGCG 59.253 45.833 5.39 0.00 0.00 6.46
1919 1958 7.600375 TGATAGTAGTACTGTAGTGTATACCGC 59.400 40.741 13.29 0.00 0.00 5.68
1949 1988 6.817184 TGGCAAGCCTAATAGTAACTCTTAG 58.183 40.000 12.96 0.00 36.94 2.18
1950 1989 6.801718 TGGCAAGCCTAATAGTAACTCTTA 57.198 37.500 12.96 0.00 36.94 2.10
1952 1991 5.425539 TCTTGGCAAGCCTAATAGTAACTCT 59.574 40.000 22.31 0.00 36.94 3.24
1953 1992 5.671493 TCTTGGCAAGCCTAATAGTAACTC 58.329 41.667 22.31 0.00 36.94 3.01
1954 1993 5.675538 CTCTTGGCAAGCCTAATAGTAACT 58.324 41.667 22.31 0.00 36.94 2.24
1955 1994 4.273724 GCTCTTGGCAAGCCTAATAGTAAC 59.726 45.833 22.31 0.00 41.35 2.50
1956 1995 4.451900 GCTCTTGGCAAGCCTAATAGTAA 58.548 43.478 22.31 0.10 41.35 2.24
1957 1996 4.073293 GCTCTTGGCAAGCCTAATAGTA 57.927 45.455 22.31 0.85 41.35 1.82
1958 1997 2.924421 GCTCTTGGCAAGCCTAATAGT 58.076 47.619 22.31 0.00 41.35 2.12
1967 2006 1.476891 TCTAGTACGGCTCTTGGCAAG 59.523 52.381 21.17 21.17 44.01 4.01
2043 2094 5.016831 ACACCACTCTCATACTGTCATACA 58.983 41.667 0.00 0.00 0.00 2.29
2044 2095 5.125578 TCACACCACTCTCATACTGTCATAC 59.874 44.000 0.00 0.00 0.00 2.39
2045 2096 5.261216 TCACACCACTCTCATACTGTCATA 58.739 41.667 0.00 0.00 0.00 2.15
2046 2097 4.089361 TCACACCACTCTCATACTGTCAT 58.911 43.478 0.00 0.00 0.00 3.06
2047 2098 3.496331 TCACACCACTCTCATACTGTCA 58.504 45.455 0.00 0.00 0.00 3.58
2048 2099 4.158579 TCATCACACCACTCTCATACTGTC 59.841 45.833 0.00 0.00 0.00 3.51
2049 2100 4.081972 GTCATCACACCACTCTCATACTGT 60.082 45.833 0.00 0.00 0.00 3.55
2050 2101 4.428209 GTCATCACACCACTCTCATACTG 58.572 47.826 0.00 0.00 0.00 2.74
2051 2102 3.449018 GGTCATCACACCACTCTCATACT 59.551 47.826 0.00 0.00 36.32 2.12
2069 2120 2.101783 TCCGCCTTATTCTTACGGTCA 58.898 47.619 0.00 0.00 44.17 4.02
2084 2135 0.472471 TTATCCCTGAACCATCCGCC 59.528 55.000 0.00 0.00 0.00 6.13
2086 2137 3.118408 TCACTTTATCCCTGAACCATCCG 60.118 47.826 0.00 0.00 0.00 4.18
2096 2147 3.914426 ACGATGCTTCACTTTATCCCT 57.086 42.857 0.08 0.00 0.00 4.20
2099 2150 5.294306 TGGATCAACGATGCTTCACTTTATC 59.706 40.000 0.00 0.00 31.64 1.75
2102 2153 3.411446 TGGATCAACGATGCTTCACTTT 58.589 40.909 0.00 0.00 31.64 2.66
2113 2164 0.249868 GGATGGCGATGGATCAACGA 60.250 55.000 9.02 0.00 31.46 3.85
2118 2169 0.248843 GAGGAGGATGGCGATGGATC 59.751 60.000 0.00 0.00 0.00 3.36
2119 2170 0.178909 AGAGGAGGATGGCGATGGAT 60.179 55.000 0.00 0.00 0.00 3.41
2126 2177 2.444895 ACGGGAGAGGAGGATGGC 60.445 66.667 0.00 0.00 0.00 4.40
2129 2180 2.609920 GGGACGGGAGAGGAGGAT 59.390 66.667 0.00 0.00 0.00 3.24
2135 2186 2.136878 CATGGAGGGGACGGGAGAG 61.137 68.421 0.00 0.00 0.00 3.20
2158 2209 2.124151 GGCAGGATGGTCGGCAAT 60.124 61.111 0.00 0.00 35.86 3.56
2159 2210 4.776322 CGGCAGGATGGTCGGCAA 62.776 66.667 0.00 0.00 35.86 4.52
2176 2227 2.044946 AAGAGGTGATTGGGGCGC 60.045 61.111 0.00 0.00 0.00 6.53
2198 2249 6.894339 ATGAAAGTTAAAACCATCCGAACT 57.106 33.333 0.00 0.00 31.79 3.01
2199 2250 7.142680 TCAATGAAAGTTAAAACCATCCGAAC 58.857 34.615 0.00 0.00 0.00 3.95
2200 2251 7.278461 TCAATGAAAGTTAAAACCATCCGAA 57.722 32.000 0.00 0.00 0.00 4.30
2201 2252 6.885952 TCAATGAAAGTTAAAACCATCCGA 57.114 33.333 0.00 0.00 0.00 4.55
2202 2253 7.938563 TTTCAATGAAAGTTAAAACCATCCG 57.061 32.000 4.03 0.00 0.00 4.18
2232 2283 9.893634 TGCTGAAATATTTTGGATGAATTTCAT 57.106 25.926 11.64 11.64 42.48 2.57
2233 2284 9.722184 TTGCTGAAATATTTTGGATGAATTTCA 57.278 25.926 1.43 0.75 41.68 2.69
2238 2289 9.722184 TGAAATTGCTGAAATATTTTGGATGAA 57.278 25.926 1.43 0.00 0.00 2.57
2239 2290 9.373603 CTGAAATTGCTGAAATATTTTGGATGA 57.626 29.630 1.43 0.00 0.00 2.92
2240 2291 9.158233 ACTGAAATTGCTGAAATATTTTGGATG 57.842 29.630 1.43 0.00 0.00 3.51
2242 2293 9.859427 CTACTGAAATTGCTGAAATATTTTGGA 57.141 29.630 1.43 0.00 0.00 3.53
2243 2294 9.643693 ACTACTGAAATTGCTGAAATATTTTGG 57.356 29.630 1.43 0.09 0.00 3.28
2248 2299 9.448438 TGTGTACTACTGAAATTGCTGAAATAT 57.552 29.630 0.00 0.00 0.00 1.28
2249 2300 8.840833 TGTGTACTACTGAAATTGCTGAAATA 57.159 30.769 0.00 0.00 0.00 1.40
2250 2301 7.744087 TGTGTACTACTGAAATTGCTGAAAT 57.256 32.000 0.00 0.00 0.00 2.17
2251 2302 7.443879 TCATGTGTACTACTGAAATTGCTGAAA 59.556 33.333 0.00 0.00 0.00 2.69
2252 2303 6.934083 TCATGTGTACTACTGAAATTGCTGAA 59.066 34.615 0.00 0.00 0.00 3.02
2253 2304 6.463360 TCATGTGTACTACTGAAATTGCTGA 58.537 36.000 0.00 0.00 0.00 4.26
2254 2305 6.726258 TCATGTGTACTACTGAAATTGCTG 57.274 37.500 0.00 0.00 0.00 4.41
2255 2306 7.928307 ATTCATGTGTACTACTGAAATTGCT 57.072 32.000 8.08 0.00 33.39 3.91
2256 2307 8.236586 TGAATTCATGTGTACTACTGAAATTGC 58.763 33.333 3.38 0.00 33.39 3.56
2361 2413 7.712797 TCGTTGTACTGCTATGATTGAAGATA 58.287 34.615 0.00 0.00 0.00 1.98
2374 2426 1.411246 TCTGGTGTTCGTTGTACTGCT 59.589 47.619 0.00 0.00 0.00 4.24
2430 2483 0.669619 TTCGGTGCTTGTAGTCGTCA 59.330 50.000 0.00 0.00 0.00 4.35
2492 2545 0.174617 CAACAAGTTGTGCCCGGTTT 59.825 50.000 9.79 0.00 35.92 3.27
2494 2547 3.520402 CAACAAGTTGTGCCCGGT 58.480 55.556 9.79 0.00 35.92 5.28
2522 2575 0.387622 TTAGCACGACGACTTTCCGG 60.388 55.000 0.00 0.00 0.00 5.14
2526 2579 0.669625 GGCCTTAGCACGACGACTTT 60.670 55.000 0.00 0.00 42.56 2.66
2552 2605 1.899814 TGCTGTTCTGGGATACTCGTT 59.100 47.619 0.00 0.00 0.00 3.85
2555 2608 2.633488 GGTTGCTGTTCTGGGATACTC 58.367 52.381 0.00 0.00 0.00 2.59
2558 2611 0.392461 GCGGTTGCTGTTCTGGGATA 60.392 55.000 0.00 0.00 38.39 2.59
2560 2613 2.281484 GCGGTTGCTGTTCTGGGA 60.281 61.111 0.00 0.00 38.39 4.37
2627 2680 5.872635 TCTCGTCGTTATTCGTCTATGTTT 58.127 37.500 0.00 0.00 40.80 2.83
2631 2684 4.753610 TGGATCTCGTCGTTATTCGTCTAT 59.246 41.667 0.00 0.00 40.80 1.98
2656 2709 6.712547 GGTAGATCTATCTTTGGTGGATTTGG 59.287 42.308 5.57 0.00 38.32 3.28
2725 2778 2.363406 CCTAGTCCCCGTTCCGGT 60.363 66.667 0.00 0.00 46.80 5.28
2783 2837 1.666189 GTGTCCTATTCAGAAAGGCGC 59.334 52.381 0.00 0.00 32.55 6.53
2824 2878 4.643334 AGGGCTCTGTTTTTAGTCGTTTTT 59.357 37.500 0.00 0.00 0.00 1.94
2854 2908 1.566298 GGTGGATCCTGACAAGGGCT 61.566 60.000 14.23 0.00 44.62 5.19
2938 2995 6.490040 CCTCCAAGAAAGAAAGTTATGGTTCA 59.510 38.462 0.00 0.00 0.00 3.18
2944 3001 6.133253 AGCTCCTCCAAGAAAGAAAGTTAT 57.867 37.500 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.