Multiple sequence alignment - TraesCS3B01G398200

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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 TraesCS3B01G398200 chr3B 100.000 5288 0 0 1 5288 628480701 628475414 0.000000e+00 9766.0
1 TraesCS3B01G398200 chr3D 95.303 3385 107 26 1941 5288 473461928 473458559 0.000000e+00 5323.0
2 TraesCS3B01G398200 chr3D 92.724 1127 64 8 715 1829 473463051 473461931 0.000000e+00 1611.0
3 TraesCS3B01G398200 chr3D 86.547 892 79 16 1 867 473464606 473463731 0.000000e+00 944.0
4 TraesCS3B01G398200 chr3D 91.803 61 0 4 5184 5239 473458722 473458662 4.390000e-11 80.5
5 TraesCS3B01G398200 chr3A 96.323 1958 46 14 1941 3889 615722666 615720726 0.000000e+00 3193.0
6 TraesCS3B01G398200 chr3A 91.009 912 56 12 936 1829 615723572 615722669 0.000000e+00 1206.0
7 TraesCS3B01G398200 chr3A 90.098 919 39 11 3930 4829 615720463 615719578 0.000000e+00 1146.0
8 TraesCS3B01G398200 chr3A 83.469 369 36 9 4834 5187 615719527 615719169 2.380000e-83 320.0
9 TraesCS3B01G398200 chr3A 87.195 164 8 5 801 952 615723753 615723591 1.960000e-39 174.0
10 TraesCS3B01G398200 chr5D 98.864 88 1 0 1858 1945 310742497 310742410 1.970000e-34 158.0
11 TraesCS3B01G398200 chr5D 97.778 90 2 0 1853 1942 301581314 301581403 7.090000e-34 156.0
12 TraesCS3B01G398200 chrUn 96.774 93 3 0 1853 1945 37006452 37006360 7.090000e-34 156.0
13 TraesCS3B01G398200 chrUn 96.774 93 3 0 1853 1945 38258673 38258581 7.090000e-34 156.0
14 TraesCS3B01G398200 chrUn 96.774 93 3 0 1853 1945 196709557 196709649 7.090000e-34 156.0
15 TraesCS3B01G398200 chr1B 96.774 93 3 0 1850 1942 117282835 117282743 7.090000e-34 156.0
16 TraesCS3B01G398200 chr7D 96.739 92 3 0 1858 1949 622185148 622185057 2.550000e-33 154.0
17 TraesCS3B01G398200 chr7D 92.308 104 8 0 1840 1943 351579985 351579882 1.190000e-31 148.0
18 TraesCS3B01G398200 chr7D 97.647 85 2 0 1858 1942 463109044 463109128 4.270000e-31 147.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G398200 chr3B 628475414 628480701 5287 True 9766.000 9766 100.00000 1 5288 1 chr3B.!!$R1 5287
1 TraesCS3B01G398200 chr3D 473458559 473464606 6047 True 1989.625 5323 91.59425 1 5288 4 chr3D.!!$R1 5287
2 TraesCS3B01G398200 chr3A 615719169 615723753 4584 True 1207.800 3193 89.61880 801 5187 5 chr3A.!!$R1 4386

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
631 645 0.035317 AGATTGCGCTCCACACTTGA 59.965 50.0 9.73 0.0 0.00 3.02 F
1838 2754 0.249447 GTTCTTGTTTGCCCACTGCC 60.249 55.0 0.00 0.0 40.16 4.85 F
1839 2755 0.396974 TTCTTGTTTGCCCACTGCCT 60.397 50.0 0.00 0.0 40.16 4.75 F
1872 2788 0.410663 TTTCTACTCCCTCCGTCCCA 59.589 55.0 0.00 0.0 0.00 4.37 F
3901 4828 0.044092 AATTTCATTCCCCCACCCCC 59.956 55.0 0.00 0.0 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 2841 0.253160 ATGTACTCCCTCTGCCCCAA 60.253 55.000 0.00 0.0 0.00 4.12 R
3732 4658 1.135460 GCTGGACTCTTTGCTGCATTC 60.135 52.381 1.84 0.0 39.86 2.67 R
3883 4810 1.158963 TGGGGGTGGGGGAATGAAAT 61.159 55.000 0.00 0.0 0.00 2.17 R
3908 4835 0.034089 GAATTGGGTGTCAGGGGAGG 60.034 60.000 0.00 0.0 0.00 4.30 R
4982 6217 0.179018 GCGCCCCCTCTATTTCACAT 60.179 55.000 0.00 0.0 0.00 3.21 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
29 30 1.353358 TCACTAGGTCTTGGTCCTCGA 59.647 52.381 0.00 0.00 36.60 4.04
39 40 2.998949 GTCCTCGAGGGCCCAAAT 59.001 61.111 30.80 1.91 32.49 2.32
49 50 0.524414 GGGCCCAAATACAACACGAC 59.476 55.000 19.95 0.00 0.00 4.34
50 51 1.530323 GGCCCAAATACAACACGACT 58.470 50.000 0.00 0.00 0.00 4.18
73 74 2.413837 GTGCATTCTAACGGTGAGTGT 58.586 47.619 0.00 0.00 0.00 3.55
77 78 0.956633 TTCTAACGGTGAGTGTCGCT 59.043 50.000 0.00 0.00 0.00 4.93
84 85 2.120232 CGGTGAGTGTCGCTATGAATC 58.880 52.381 0.00 0.00 0.00 2.52
97 98 3.548818 GCTATGAATCAACATTCCCGCAC 60.549 47.826 0.00 0.00 38.14 5.34
100 101 2.824936 TGAATCAACATTCCCGCACAAT 59.175 40.909 0.00 0.00 38.14 2.71
101 102 4.013050 TGAATCAACATTCCCGCACAATA 58.987 39.130 0.00 0.00 38.14 1.90
120 121 6.689178 CAATACACAATTGTTGGTTGTAGC 57.311 37.500 8.77 0.00 40.19 3.58
121 122 3.726291 ACACAATTGTTGGTTGTAGCC 57.274 42.857 8.77 0.00 37.69 3.93
122 123 3.027412 ACACAATTGTTGGTTGTAGCCA 58.973 40.909 8.77 0.00 37.69 4.75
128 129 3.724508 TGTTGGTTGTAGCCATGTTTG 57.275 42.857 0.00 0.00 38.48 2.93
136 137 4.233632 TGTAGCCATGTTTGGATGATGA 57.766 40.909 0.00 0.00 46.92 2.92
138 139 5.015515 TGTAGCCATGTTTGGATGATGAAA 58.984 37.500 0.00 0.00 46.92 2.69
144 145 8.926374 AGCCATGTTTGGATGATGAAATAAATA 58.074 29.630 0.00 0.00 46.92 1.40
149 150 7.866898 TGTTTGGATGATGAAATAAATATGCCG 59.133 33.333 0.00 0.00 0.00 5.69
151 152 7.144722 TGGATGATGAAATAAATATGCCGAC 57.855 36.000 0.00 0.00 0.00 4.79
159 160 5.371115 AATAAATATGCCGACGGAATTGG 57.629 39.130 20.50 0.00 34.40 3.16
177 178 1.949257 GTTGTTGAGCCAACCTCCG 59.051 57.895 13.35 0.00 42.96 4.63
181 182 3.591073 TGTTGAGCCAACCTCCGAAGG 62.591 57.143 13.35 0.00 46.67 3.46
205 206 5.924475 ATATTCTAATTTTCGAGGGCACG 57.076 39.130 0.00 0.00 0.00 5.34
209 210 0.591170 AATTTTCGAGGGCACGTGTG 59.409 50.000 18.38 2.62 34.70 3.82
234 235 4.525912 TCCATAGATGACACCATGATCG 57.474 45.455 0.00 0.00 32.09 3.69
240 241 4.375272 AGATGACACCATGATCGATGTTC 58.625 43.478 0.54 0.00 32.09 3.18
263 264 0.316204 TTCGGAGTTTGACGAGTCCC 59.684 55.000 0.34 0.00 40.51 4.46
300 301 2.338577 ATGACAAGCATCTGGTAGGC 57.661 50.000 0.00 0.00 28.85 3.93
305 306 3.041211 ACAAGCATCTGGTAGGCTGATA 58.959 45.455 0.00 0.00 46.58 2.15
330 331 1.560146 GGAGAAGGTCCCCTTTCGATT 59.440 52.381 0.00 0.00 44.82 3.34
361 362 3.261897 ACGACCAGAAATCCTCAATCTGT 59.738 43.478 0.00 0.00 39.10 3.41
364 365 5.163509 CGACCAGAAATCCTCAATCTGTCTA 60.164 44.000 0.00 0.00 39.10 2.59
419 420 5.697633 ACATCAAAAGCCATGAATGTGTTTC 59.302 36.000 0.00 0.00 34.72 2.78
444 445 0.260523 AGCTCCCTGTCCTAGTCTCC 59.739 60.000 0.00 0.00 0.00 3.71
445 446 0.757561 GCTCCCTGTCCTAGTCTCCC 60.758 65.000 0.00 0.00 0.00 4.30
446 447 0.466555 CTCCCTGTCCTAGTCTCCCG 60.467 65.000 0.00 0.00 0.00 5.14
448 449 0.549950 CCCTGTCCTAGTCTCCCGTA 59.450 60.000 0.00 0.00 0.00 4.02
457 463 0.603569 AGTCTCCCGTACTGTGCAAG 59.396 55.000 0.00 0.00 0.00 4.01
465 471 2.668457 CCGTACTGTGCAAGATGAGTTC 59.332 50.000 0.00 0.00 0.00 3.01
513 519 2.543848 TCAAACTTGTGATGTGTCTCGC 59.456 45.455 0.00 0.00 0.00 5.03
522 528 4.143200 TGTGATGTGTCTCGCGTTAAAATC 60.143 41.667 5.77 4.85 0.00 2.17
535 542 4.853743 GCGTTAAAATCTTGAGGAAGCAAG 59.146 41.667 0.00 0.00 45.10 4.01
539 546 3.930634 AATCTTGAGGAAGCAAGTTGC 57.069 42.857 20.44 20.44 44.30 4.17
548 555 0.311790 AAGCAAGTTGCCACGTCATG 59.688 50.000 24.02 0.00 46.52 3.07
554 561 3.052455 AGTTGCCACGTCATGTATGAA 57.948 42.857 0.00 0.00 38.75 2.57
568 575 5.819901 TCATGTATGAATCGTTGCACCATTA 59.180 36.000 0.00 0.00 33.08 1.90
569 576 6.486320 TCATGTATGAATCGTTGCACCATTAT 59.514 34.615 0.00 0.00 33.08 1.28
570 577 7.659390 TCATGTATGAATCGTTGCACCATTATA 59.341 33.333 0.00 0.00 33.08 0.98
576 583 7.995289 TGAATCGTTGCACCATTATAAATTCT 58.005 30.769 0.00 0.00 0.00 2.40
577 584 9.114952 TGAATCGTTGCACCATTATAAATTCTA 57.885 29.630 0.00 0.00 0.00 2.10
578 585 9.382244 GAATCGTTGCACCATTATAAATTCTAC 57.618 33.333 0.00 0.00 0.00 2.59
579 586 6.939627 TCGTTGCACCATTATAAATTCTACG 58.060 36.000 0.00 0.00 0.00 3.51
616 630 3.638160 TGAGCAAGTTGCCTTCAAAGATT 59.362 39.130 24.02 1.14 46.52 2.40
630 644 0.877071 AAGATTGCGCTCCACACTTG 59.123 50.000 9.73 0.00 0.00 3.16
631 645 0.035317 AGATTGCGCTCCACACTTGA 59.965 50.000 9.73 0.00 0.00 3.02
633 647 1.470098 GATTGCGCTCCACACTTGAAT 59.530 47.619 9.73 0.00 0.00 2.57
634 648 0.592637 TTGCGCTCCACACTTGAATG 59.407 50.000 9.73 0.00 0.00 2.67
660 675 2.636830 CTACCCAACTCTGATTGCAGG 58.363 52.381 0.00 0.00 42.53 4.85
675 690 2.449464 TGCAGGAATTCAGATTGTGGG 58.551 47.619 7.93 0.00 0.00 4.61
677 692 3.091545 GCAGGAATTCAGATTGTGGGAA 58.908 45.455 7.93 0.00 0.00 3.97
678 693 3.511146 GCAGGAATTCAGATTGTGGGAAA 59.489 43.478 7.93 0.00 0.00 3.13
679 694 4.161001 GCAGGAATTCAGATTGTGGGAAAT 59.839 41.667 7.93 0.00 0.00 2.17
680 695 5.360714 GCAGGAATTCAGATTGTGGGAAATA 59.639 40.000 7.93 0.00 0.00 1.40
681 696 6.041296 GCAGGAATTCAGATTGTGGGAAATAT 59.959 38.462 7.93 0.00 0.00 1.28
682 697 7.231317 GCAGGAATTCAGATTGTGGGAAATATA 59.769 37.037 7.93 0.00 0.00 0.86
683 698 8.571336 CAGGAATTCAGATTGTGGGAAATATAC 58.429 37.037 7.93 0.00 0.00 1.47
689 704 8.893563 TCAGATTGTGGGAAATATACCTTTTT 57.106 30.769 0.00 0.00 0.00 1.94
717 732 7.593875 TTTTTGTTTTCTGAGACAATTGTGG 57.406 32.000 17.58 3.62 35.85 4.17
723 738 3.743521 TCTGAGACAATTGTGGGAAGTG 58.256 45.455 17.58 0.00 0.00 3.16
747 763 2.156917 TGCCTGAGAATTCTTGCACAG 58.843 47.619 18.63 15.77 0.00 3.66
750 766 2.161808 CCTGAGAATTCTTGCACAGCAG 59.838 50.000 9.87 9.87 40.61 4.24
751 767 1.538512 TGAGAATTCTTGCACAGCAGC 59.461 47.619 9.87 0.00 40.61 5.25
752 768 1.538512 GAGAATTCTTGCACAGCAGCA 59.461 47.619 9.87 0.00 40.61 4.41
763 779 1.447489 CAGCAGCAGACCGGAGAAG 60.447 63.158 9.46 0.00 0.00 2.85
844 1697 2.157834 ATTGCGAGTTGTACCGTCAA 57.842 45.000 0.00 0.00 0.00 3.18
905 1762 3.058501 CGTGAACAAAGAAGCCCGTAAAT 60.059 43.478 0.00 0.00 0.00 1.40
1006 1908 1.336795 GGAGAAAACAAACCATGGCCG 60.337 52.381 13.04 2.47 0.00 6.13
1041 1949 4.394712 CCCTTGACCCGCTCGCTT 62.395 66.667 0.00 0.00 0.00 4.68
1158 2066 2.344203 CCTCGCGTGTCCTTCTCCT 61.344 63.158 5.77 0.00 0.00 3.69
1161 2069 0.894184 TCGCGTGTCCTTCTCCTCTT 60.894 55.000 5.77 0.00 0.00 2.85
1469 2377 2.557056 TCTGCACTACACTACACCACTC 59.443 50.000 0.00 0.00 0.00 3.51
1491 2399 1.069978 TCCATCAGTGACTGAACGCAA 59.930 47.619 20.26 1.11 44.04 4.85
1514 2422 5.906113 TTGTGTAACTGTGTTTGGTGATT 57.094 34.783 0.00 0.00 38.04 2.57
1545 2453 5.466058 TCAACTGCGACGATTAAGGTTTAAA 59.534 36.000 0.00 0.00 0.00 1.52
1575 2483 4.081406 TCCAGTGCTCAATTGCAATTACT 58.919 39.130 23.69 19.46 45.12 2.24
1599 2515 6.844254 TGTTTAATACTTTAACGGTGGCATC 58.156 36.000 0.00 0.00 0.00 3.91
1616 2532 0.529337 ATCGCTCGGATGACAAGCTG 60.529 55.000 0.00 0.00 32.92 4.24
1715 2631 5.387113 ACATTATGCATAGTTTCCTCCCA 57.613 39.130 6.50 0.00 0.00 4.37
1743 2659 6.747280 GCAGCCATAAAGTAATGTACAAACTG 59.253 38.462 13.30 4.17 0.00 3.16
1795 2711 4.850680 TGTCTGTTCACCTTAACCAAACT 58.149 39.130 0.00 0.00 0.00 2.66
1824 2740 2.092914 GCCCACTGCCTATACTGTTCTT 60.093 50.000 0.00 0.00 0.00 2.52
1829 2745 5.106555 CCACTGCCTATACTGTTCTTGTTTG 60.107 44.000 0.00 0.00 0.00 2.93
1831 2747 3.756434 TGCCTATACTGTTCTTGTTTGCC 59.244 43.478 0.00 0.00 0.00 4.52
1832 2748 3.128764 GCCTATACTGTTCTTGTTTGCCC 59.871 47.826 0.00 0.00 0.00 5.36
1833 2749 4.331968 CCTATACTGTTCTTGTTTGCCCA 58.668 43.478 0.00 0.00 0.00 5.36
1834 2750 4.156008 CCTATACTGTTCTTGTTTGCCCAC 59.844 45.833 0.00 0.00 0.00 4.61
1835 2751 2.143876 ACTGTTCTTGTTTGCCCACT 57.856 45.000 0.00 0.00 0.00 4.00
1836 2752 1.750778 ACTGTTCTTGTTTGCCCACTG 59.249 47.619 0.00 0.00 0.00 3.66
1837 2753 0.459489 TGTTCTTGTTTGCCCACTGC 59.541 50.000 0.00 0.00 41.77 4.40
1838 2754 0.249447 GTTCTTGTTTGCCCACTGCC 60.249 55.000 0.00 0.00 40.16 4.85
1839 2755 0.396974 TTCTTGTTTGCCCACTGCCT 60.397 50.000 0.00 0.00 40.16 4.75
1840 2756 0.476338 TCTTGTTTGCCCACTGCCTA 59.524 50.000 0.00 0.00 40.16 3.93
1841 2757 1.075374 TCTTGTTTGCCCACTGCCTAT 59.925 47.619 0.00 0.00 40.16 2.57
1842 2758 2.307392 TCTTGTTTGCCCACTGCCTATA 59.693 45.455 0.00 0.00 40.16 1.31
1843 2759 2.122783 TGTTTGCCCACTGCCTATAC 57.877 50.000 0.00 0.00 40.16 1.47
1844 2760 1.633432 TGTTTGCCCACTGCCTATACT 59.367 47.619 0.00 0.00 40.16 2.12
1845 2761 2.017049 GTTTGCCCACTGCCTATACTG 58.983 52.381 0.00 0.00 40.16 2.74
1846 2762 1.285280 TTGCCCACTGCCTATACTGT 58.715 50.000 0.00 0.00 40.16 3.55
1847 2763 1.285280 TGCCCACTGCCTATACTGTT 58.715 50.000 0.00 0.00 40.16 3.16
1848 2764 1.209504 TGCCCACTGCCTATACTGTTC 59.790 52.381 0.00 0.00 40.16 3.18
1849 2765 1.486726 GCCCACTGCCTATACTGTTCT 59.513 52.381 0.00 0.00 0.00 3.01
1850 2766 2.092914 GCCCACTGCCTATACTGTTCTT 60.093 50.000 0.00 0.00 0.00 2.52
1851 2767 3.535561 CCCACTGCCTATACTGTTCTTG 58.464 50.000 0.00 0.00 0.00 3.02
1852 2768 3.055094 CCCACTGCCTATACTGTTCTTGT 60.055 47.826 0.00 0.00 0.00 3.16
1853 2769 4.565652 CCCACTGCCTATACTGTTCTTGTT 60.566 45.833 0.00 0.00 0.00 2.83
1854 2770 5.003804 CCACTGCCTATACTGTTCTTGTTT 58.996 41.667 0.00 0.00 0.00 2.83
1855 2771 5.473504 CCACTGCCTATACTGTTCTTGTTTT 59.526 40.000 0.00 0.00 0.00 2.43
1856 2772 6.348540 CCACTGCCTATACTGTTCTTGTTTTC 60.349 42.308 0.00 0.00 0.00 2.29
1857 2773 6.428159 CACTGCCTATACTGTTCTTGTTTTCT 59.572 38.462 0.00 0.00 0.00 2.52
1858 2774 7.602644 CACTGCCTATACTGTTCTTGTTTTCTA 59.397 37.037 0.00 0.00 0.00 2.10
1859 2775 7.603024 ACTGCCTATACTGTTCTTGTTTTCTAC 59.397 37.037 0.00 0.00 0.00 2.59
1860 2776 7.676947 TGCCTATACTGTTCTTGTTTTCTACT 58.323 34.615 0.00 0.00 0.00 2.57
1861 2777 7.817962 TGCCTATACTGTTCTTGTTTTCTACTC 59.182 37.037 0.00 0.00 0.00 2.59
1862 2778 7.278203 GCCTATACTGTTCTTGTTTTCTACTCC 59.722 40.741 0.00 0.00 0.00 3.85
1863 2779 7.764901 CCTATACTGTTCTTGTTTTCTACTCCC 59.235 40.741 0.00 0.00 0.00 4.30
1864 2780 5.632034 ACTGTTCTTGTTTTCTACTCCCT 57.368 39.130 0.00 0.00 0.00 4.20
1865 2781 5.612351 ACTGTTCTTGTTTTCTACTCCCTC 58.388 41.667 0.00 0.00 0.00 4.30
1866 2782 4.969484 TGTTCTTGTTTTCTACTCCCTCC 58.031 43.478 0.00 0.00 0.00 4.30
1867 2783 3.955650 TCTTGTTTTCTACTCCCTCCG 57.044 47.619 0.00 0.00 0.00 4.63
1868 2784 3.236896 TCTTGTTTTCTACTCCCTCCGT 58.763 45.455 0.00 0.00 0.00 4.69
1869 2785 3.257624 TCTTGTTTTCTACTCCCTCCGTC 59.742 47.826 0.00 0.00 0.00 4.79
1870 2786 1.897802 TGTTTTCTACTCCCTCCGTCC 59.102 52.381 0.00 0.00 0.00 4.79
1871 2787 1.206610 GTTTTCTACTCCCTCCGTCCC 59.793 57.143 0.00 0.00 0.00 4.46
1872 2788 0.410663 TTTCTACTCCCTCCGTCCCA 59.589 55.000 0.00 0.00 0.00 4.37
1873 2789 0.635009 TTCTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
1874 2790 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
1875 2791 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
1876 2792 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
1877 2793 3.659195 TCTACTCCCTCCGTCCCATAATA 59.341 47.826 0.00 0.00 0.00 0.98
1878 2794 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
1879 2795 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
1880 2796 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
1881 2797 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
1882 2798 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
1883 2799 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
1884 2800 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
1885 2801 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
1886 2802 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
1887 2803 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
1888 2804 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
1889 2805 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
1890 2806 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
1891 2807 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
1892 2808 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
1893 2809 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
1894 2810 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
1895 2811 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
1902 2818 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
1903 2819 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
1904 2820 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
1933 2849 8.791327 AAAAATGTTCTTATATTTTGGGGCAG 57.209 30.769 0.00 0.00 35.87 4.85
1934 2850 7.732222 AAATGTTCTTATATTTTGGGGCAGA 57.268 32.000 0.00 0.00 0.00 4.26
1935 2851 6.966534 ATGTTCTTATATTTTGGGGCAGAG 57.033 37.500 0.00 0.00 0.00 3.35
1936 2852 5.200483 TGTTCTTATATTTTGGGGCAGAGG 58.800 41.667 0.00 0.00 0.00 3.69
1937 2853 4.453480 TCTTATATTTTGGGGCAGAGGG 57.547 45.455 0.00 0.00 0.00 4.30
1938 2854 4.051478 TCTTATATTTTGGGGCAGAGGGA 58.949 43.478 0.00 0.00 0.00 4.20
1939 2855 4.104738 TCTTATATTTTGGGGCAGAGGGAG 59.895 45.833 0.00 0.00 0.00 4.30
1949 2865 1.137872 GGCAGAGGGAGTACATGACTG 59.862 57.143 0.00 0.00 39.06 3.51
1955 2871 1.001974 GGGAGTACATGACTGTGTGCA 59.998 52.381 0.00 0.00 39.06 4.57
1958 2874 3.588955 GAGTACATGACTGTGTGCATCA 58.411 45.455 0.00 0.00 39.06 3.07
2024 2940 0.473117 AGTCGTCCTTCCTTTGGGGA 60.473 55.000 0.00 0.00 43.41 4.81
2069 2985 2.260481 GGAGCGCTTGTTGACTACTAC 58.740 52.381 13.26 0.00 0.00 2.73
2171 3087 5.192927 TCACTTTGGTTGTTCATCTCAACT 58.807 37.500 8.34 0.00 42.97 3.16
2878 3797 4.216902 AGTGTATTTCAAAACCGTAAGCCC 59.783 41.667 0.00 0.00 0.00 5.19
2931 3850 4.993705 ACTGATTCTCCCTGTGGTTTAA 57.006 40.909 0.00 0.00 0.00 1.52
3061 3980 2.034179 TGTATCAGACGCACTTATCCGG 59.966 50.000 0.00 0.00 0.00 5.14
3237 4157 7.140705 ACCATAATTTTGTGATATGATGTGCG 58.859 34.615 0.00 0.00 30.32 5.34
3240 4160 8.684655 CATAATTTTGTGATATGATGTGCGTTC 58.315 33.333 0.00 0.00 30.32 3.95
3342 4262 4.340381 GGCATGGATATTCTCAAAGCAACT 59.660 41.667 0.00 0.00 0.00 3.16
3501 4421 7.124573 TGGCTAAATTATAGTCAGAGCTGAA 57.875 36.000 1.08 0.00 41.85 3.02
3526 4446 7.688478 TTGTATATCCGTAACACAATTCTCG 57.312 36.000 0.00 0.00 0.00 4.04
3538 4458 5.401550 ACACAATTCTCGCAATGGTAAATG 58.598 37.500 0.00 0.00 0.00 2.32
3546 4466 5.079689 TCGCAATGGTAAATGACAGTAGA 57.920 39.130 0.00 0.00 0.00 2.59
3597 4518 2.610833 GCTACCACCTGCCGTTTATTAC 59.389 50.000 0.00 0.00 0.00 1.89
3674 4600 7.790782 ATTAAATCCAAGCTTTGACCCTTTA 57.209 32.000 1.73 2.11 0.00 1.85
3732 4658 5.652014 TCCTGGTATTGCTCTTATTGGTTTG 59.348 40.000 0.00 0.00 0.00 2.93
3901 4828 0.044092 AATTTCATTCCCCCACCCCC 59.956 55.000 0.00 0.00 0.00 5.40
3927 4854 0.034089 CCTCCCCTGACACCCAATTC 60.034 60.000 0.00 0.00 0.00 2.17
3941 5090 3.267031 ACCCAATTCGGATTCTCTTTCCT 59.733 43.478 0.00 0.00 36.56 3.36
3953 5102 7.512992 GGATTCTCTTTCCTATCTGATGGAAA 58.487 38.462 21.89 21.89 46.37 3.13
4043 5192 1.756538 CCTTGTGCTCCCTGTGTTTTT 59.243 47.619 0.00 0.00 0.00 1.94
4051 5200 5.240844 GTGCTCCCTGTGTTTTTGTTATAGT 59.759 40.000 0.00 0.00 0.00 2.12
4119 5268 0.029300 CAGGAATGGCAAATACGGCG 59.971 55.000 4.80 4.80 0.00 6.46
4280 5429 1.987770 GCGTGTTGATTTTGATGGCAG 59.012 47.619 0.00 0.00 0.00 4.85
4290 5439 0.104855 TTGATGGCAGTAGCTAGCGG 59.895 55.000 9.55 1.66 40.87 5.52
4291 5440 1.043116 TGATGGCAGTAGCTAGCGGT 61.043 55.000 9.55 0.00 40.87 5.68
4297 5446 2.544069 GGCAGTAGCTAGCGGTAAAGAG 60.544 54.545 9.55 0.00 41.70 2.85
4298 5447 2.358267 GCAGTAGCTAGCGGTAAAGAGA 59.642 50.000 9.55 0.00 37.91 3.10
4366 5515 6.223852 GCATTATCATATGGGATAGTACCGG 58.776 44.000 0.00 0.00 31.77 5.28
4402 5552 3.986572 CGAGAGATGAGCATTACACATCC 59.013 47.826 0.00 0.00 44.72 3.51
4404 5554 3.062763 GAGATGAGCATTACACATCCGG 58.937 50.000 0.00 0.00 44.72 5.14
4425 5575 2.058798 ACTACAACATCGTGTGCTTCG 58.941 47.619 0.00 0.00 32.75 3.79
4442 5592 4.159693 TGCTTCGATGTAGTGGAAGTATGT 59.840 41.667 0.00 0.00 42.63 2.29
4469 5619 5.183713 TGAATTGTCTTATTGTGGAAGCAGG 59.816 40.000 0.00 0.00 0.00 4.85
4623 5791 0.528684 GCGATGGCAGTGGTAGAGAC 60.529 60.000 0.00 0.00 39.62 3.36
4624 5792 3.816064 GCGATGGCAGTGGTAGAGACC 62.816 61.905 0.00 0.00 42.12 3.85
4710 5878 4.220602 CCCTTGTTTAAAATGGCTAGCAGT 59.779 41.667 18.24 0.46 0.00 4.40
4899 6121 9.817365 CGAAGGAGAATTATAGTTATTGCAATG 57.183 33.333 22.27 0.00 0.00 2.82
4922 6154 5.121611 TGTCTTACTGTTCATAAATGTGCGG 59.878 40.000 0.00 0.00 0.00 5.69
4930 6162 8.898761 ACTGTTCATAAATGTGCGGAAAATATA 58.101 29.630 0.00 0.00 0.00 0.86
4959 6194 6.610020 TGGTACTTGTAACTATCAGCATACCT 59.390 38.462 0.00 0.00 31.56 3.08
4979 6214 6.848562 ACCTAGTCCCCTCAAATATTGATT 57.151 37.500 0.00 0.00 39.30 2.57
4998 6233 5.448654 TGATTTGATGTGAAATAGAGGGGG 58.551 41.667 0.00 0.00 0.00 5.40
5061 6301 1.804601 GAAACAGGGTTAGGGTGTCG 58.195 55.000 0.00 0.00 0.00 4.35
5070 6310 0.034863 TTAGGGTGTCGAAATGCCCC 60.035 55.000 10.16 1.95 41.99 5.80
5078 6318 3.066203 GTGTCGAAATGCCCCGAATAAAT 59.934 43.478 0.00 0.00 36.50 1.40
5086 6326 4.464069 TGCCCCGAATAAATGAAAAAGG 57.536 40.909 0.00 0.00 0.00 3.11
5135 6376 3.243434 GGACGTGTACATCCTGGTCATAG 60.243 52.174 8.07 0.00 31.75 2.23
5142 6383 3.034635 ACATCCTGGTCATAGTGACTCC 58.965 50.000 9.66 0.00 46.19 3.85
5222 6463 8.062065 TCTTACTGAAAGAACAAACACCAAAT 57.938 30.769 0.00 0.00 41.35 2.32
5243 6486 0.770499 TGAATCAACTGCTGGGGTGA 59.230 50.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.094649 CGAGGACCAAGACCTAGTGAAC 60.095 54.545 0.00 0.00 37.93 3.18
13 14 0.033405 CCCTCGAGGACCAAGACCTA 60.033 60.000 33.39 0.00 37.93 3.08
16 17 2.579738 GCCCTCGAGGACCAAGAC 59.420 66.667 33.39 8.81 38.24 3.01
29 30 0.402504 TCGTGTTGTATTTGGGCCCT 59.597 50.000 25.70 5.02 0.00 5.19
39 40 2.248280 ATGCACCAAGTCGTGTTGTA 57.752 45.000 0.00 0.00 36.08 2.41
49 50 2.416547 CTCACCGTTAGAATGCACCAAG 59.583 50.000 0.00 0.00 0.00 3.61
50 51 2.224426 ACTCACCGTTAGAATGCACCAA 60.224 45.455 0.00 0.00 0.00 3.67
73 74 3.130633 CGGGAATGTTGATTCATAGCGA 58.869 45.455 0.00 0.00 39.98 4.93
77 78 3.615155 TGTGCGGGAATGTTGATTCATA 58.385 40.909 0.00 0.00 39.98 2.15
84 85 2.227626 TGTGTATTGTGCGGGAATGTTG 59.772 45.455 0.00 0.00 0.00 3.33
97 98 6.737070 TGGCTACAACCAACAATTGTGTATTG 60.737 38.462 12.82 17.27 41.22 1.90
100 101 4.207955 TGGCTACAACCAACAATTGTGTA 58.792 39.130 12.82 8.60 40.47 2.90
101 102 3.027412 TGGCTACAACCAACAATTGTGT 58.973 40.909 12.82 7.84 40.47 3.72
122 123 9.715121 GGCATATTTATTTCATCATCCAAACAT 57.285 29.630 0.00 0.00 0.00 2.71
128 129 6.250819 CGTCGGCATATTTATTTCATCATCC 58.749 40.000 0.00 0.00 0.00 3.51
136 137 5.300792 ACCAATTCCGTCGGCATATTTATTT 59.699 36.000 6.34 0.00 0.00 1.40
138 139 4.394729 ACCAATTCCGTCGGCATATTTAT 58.605 39.130 6.34 0.00 0.00 1.40
144 145 0.608035 ACAACCAATTCCGTCGGCAT 60.608 50.000 6.34 0.00 0.00 4.40
149 150 1.068541 GGCTCAACAACCAATTCCGTC 60.069 52.381 0.00 0.00 0.00 4.79
151 152 0.958091 TGGCTCAACAACCAATTCCG 59.042 50.000 0.00 0.00 31.46 4.30
159 160 0.534203 TCGGAGGTTGGCTCAACAAC 60.534 55.000 16.55 7.51 45.11 3.32
177 178 7.228706 TGCCCTCGAAAATTAGAATATTCCTTC 59.771 37.037 11.92 6.76 0.00 3.46
181 182 6.018180 ACGTGCCCTCGAAAATTAGAATATTC 60.018 38.462 7.41 7.41 34.70 1.75
205 206 3.375299 GGTGTCATCTATGGAAAGCACAC 59.625 47.826 10.59 7.97 33.61 3.82
209 210 4.454678 TCATGGTGTCATCTATGGAAAGC 58.545 43.478 0.00 0.00 0.00 3.51
214 215 4.525912 TCGATCATGGTGTCATCTATGG 57.474 45.455 0.00 0.00 0.00 2.74
215 216 5.476614 ACATCGATCATGGTGTCATCTATG 58.523 41.667 0.00 0.00 36.72 2.23
234 235 1.128692 CAAACTCCGAAGCCGAACATC 59.871 52.381 0.00 0.00 38.22 3.06
240 241 1.344942 CTCGTCAAACTCCGAAGCCG 61.345 60.000 0.00 0.00 31.92 5.52
270 271 1.337703 TGCTTGTCATCACAAAGCACC 59.662 47.619 5.27 0.00 42.13 5.01
271 272 2.780065 TGCTTGTCATCACAAAGCAC 57.220 45.000 5.27 0.00 42.13 4.40
281 282 1.842562 AGCCTACCAGATGCTTGTCAT 59.157 47.619 0.00 0.00 38.32 3.06
293 294 5.544176 CCTTCTCCTTTATATCAGCCTACCA 59.456 44.000 0.00 0.00 0.00 3.25
294 295 5.544562 ACCTTCTCCTTTATATCAGCCTACC 59.455 44.000 0.00 0.00 0.00 3.18
325 326 0.242825 GGTCGTGGAGTCACAATCGA 59.757 55.000 0.00 0.00 43.79 3.59
330 331 1.116308 TTTCTGGTCGTGGAGTCACA 58.884 50.000 0.00 0.00 43.79 3.58
364 365 8.454106 GCGATTATTTCTATTCCATTATGCACT 58.546 33.333 0.00 0.00 0.00 4.40
419 420 0.984230 TAGGACAGGGAGCTGGTTTG 59.016 55.000 0.00 0.00 0.00 2.93
444 445 2.370281 ACTCATCTTGCACAGTACGG 57.630 50.000 0.00 0.00 0.00 4.02
445 446 2.342651 CGAACTCATCTTGCACAGTACG 59.657 50.000 0.00 0.00 0.00 3.67
446 447 2.092838 GCGAACTCATCTTGCACAGTAC 59.907 50.000 0.00 0.00 0.00 2.73
448 449 1.151668 GCGAACTCATCTTGCACAGT 58.848 50.000 0.00 0.00 0.00 3.55
457 463 1.728971 CAGTTGGTCAGCGAACTCATC 59.271 52.381 0.00 0.00 40.82 2.92
513 519 6.002062 ACTTGCTTCCTCAAGATTTTAACG 57.998 37.500 10.10 0.00 44.61 3.18
522 528 1.000938 GTGGCAACTTGCTTCCTCAAG 60.001 52.381 13.43 2.33 46.57 3.02
535 542 3.544048 CGATTCATACATGACGTGGCAAC 60.544 47.826 0.00 0.00 36.36 4.17
539 546 3.544048 GCAACGATTCATACATGACGTGG 60.544 47.826 0.00 6.90 38.80 4.94
548 555 9.677567 AATTTATAATGGTGCAACGATTCATAC 57.322 29.630 0.00 0.00 41.66 2.39
554 561 7.225931 ACGTAGAATTTATAATGGTGCAACGAT 59.774 33.333 0.00 0.00 36.59 3.73
568 575 7.655490 AGGCTTGATACGTACGTAGAATTTAT 58.345 34.615 29.65 14.87 33.77 1.40
569 576 7.031226 AGGCTTGATACGTACGTAGAATTTA 57.969 36.000 29.65 10.57 33.77 1.40
570 577 5.899299 AGGCTTGATACGTACGTAGAATTT 58.101 37.500 29.65 15.28 33.77 1.82
576 583 3.488047 GCTCAAGGCTTGATACGTACGTA 60.488 47.826 28.67 28.62 39.30 3.57
577 584 2.734492 GCTCAAGGCTTGATACGTACGT 60.734 50.000 28.67 25.98 39.30 3.57
578 585 1.852895 GCTCAAGGCTTGATACGTACG 59.147 52.381 28.67 15.01 39.30 3.67
579 586 2.888594 TGCTCAAGGCTTGATACGTAC 58.111 47.619 28.67 14.70 39.30 3.67
616 630 1.236616 CCATTCAAGTGTGGAGCGCA 61.237 55.000 11.47 0.00 37.72 6.09
660 675 8.697507 AGGTATATTTCCCACAATCTGAATTC 57.302 34.615 0.00 0.00 0.00 2.17
693 708 6.593382 CCCACAATTGTCTCAGAAAACAAAAA 59.407 34.615 8.48 0.00 38.74 1.94
694 709 6.071108 TCCCACAATTGTCTCAGAAAACAAAA 60.071 34.615 8.48 0.00 38.74 2.44
697 712 4.531854 TCCCACAATTGTCTCAGAAAACA 58.468 39.130 8.48 0.00 0.00 2.83
698 713 5.067805 ACTTCCCACAATTGTCTCAGAAAAC 59.932 40.000 8.48 0.00 0.00 2.43
699 714 5.067674 CACTTCCCACAATTGTCTCAGAAAA 59.932 40.000 8.48 0.00 0.00 2.29
700 715 4.580167 CACTTCCCACAATTGTCTCAGAAA 59.420 41.667 8.48 0.00 0.00 2.52
702 717 3.743521 CACTTCCCACAATTGTCTCAGA 58.256 45.455 8.48 0.19 0.00 3.27
703 718 2.227388 GCACTTCCCACAATTGTCTCAG 59.773 50.000 8.48 5.19 0.00 3.35
704 719 2.229792 GCACTTCCCACAATTGTCTCA 58.770 47.619 8.48 0.00 0.00 3.27
705 720 1.541588 GGCACTTCCCACAATTGTCTC 59.458 52.381 8.48 0.00 0.00 3.36
723 738 1.135170 GCAAGAATTCTCAGGCAAGGC 60.135 52.381 8.78 0.00 0.00 4.35
731 746 1.538512 GCTGCTGTGCAAGAATTCTCA 59.461 47.619 8.78 0.08 38.41 3.27
732 747 1.538512 TGCTGCTGTGCAAGAATTCTC 59.461 47.619 8.78 0.00 40.29 2.87
747 763 1.446966 GTCTTCTCCGGTCTGCTGC 60.447 63.158 0.00 0.00 0.00 5.25
750 766 2.182030 CCGTCTTCTCCGGTCTGC 59.818 66.667 0.00 0.00 40.59 4.26
751 767 1.803943 CTCCGTCTTCTCCGGTCTG 59.196 63.158 0.00 0.00 45.63 3.51
752 768 2.047443 GCTCCGTCTTCTCCGGTCT 61.047 63.158 0.00 0.00 45.63 3.85
844 1697 2.597510 GTTTGTTCTGGCCCGGCT 60.598 61.111 9.86 0.00 0.00 5.52
905 1762 0.747852 TGGTGCAGTGACGTGTAAGA 59.252 50.000 0.00 0.00 0.00 2.10
979 1881 1.527380 TTTGTTTTCTCCGCCGCCT 60.527 52.632 0.00 0.00 0.00 5.52
981 1883 1.371267 GGTTTGTTTTCTCCGCCGC 60.371 57.895 0.00 0.00 0.00 6.53
1144 2052 0.603569 TGAAGAGGAGAAGGACACGC 59.396 55.000 0.00 0.00 0.00 5.34
1145 2053 1.403514 GCTGAAGAGGAGAAGGACACG 60.404 57.143 0.00 0.00 0.00 4.49
1152 2060 1.608717 GGAGCGGCTGAAGAGGAGAA 61.609 60.000 7.50 0.00 0.00 2.87
1153 2061 2.055042 GGAGCGGCTGAAGAGGAGA 61.055 63.158 7.50 0.00 0.00 3.71
1251 2159 3.390521 ATGAACTCCGCCGCCAGA 61.391 61.111 0.00 0.00 0.00 3.86
1469 2377 1.728971 GCGTTCAGTCACTGATGGAAG 59.271 52.381 8.74 0.00 40.39 3.46
1491 2399 6.096141 TCAATCACCAAACACAGTTACACAAT 59.904 34.615 0.00 0.00 0.00 2.71
1514 2422 0.319469 TCGTCGCAGTTGAGCATTCA 60.319 50.000 0.00 0.00 0.00 2.57
1545 2453 1.344953 TTGAGCACTGGACCACCTGT 61.345 55.000 0.00 0.00 46.65 4.00
1575 2483 6.402334 CGATGCCACCGTTAAAGTATTAAACA 60.402 38.462 0.00 0.00 32.98 2.83
1649 2565 8.784043 ACTGAAAGAATTAACATGTGAGTAACC 58.216 33.333 0.00 0.00 37.43 2.85
1697 2613 3.498481 GCCATGGGAGGAAACTATGCATA 60.498 47.826 15.13 6.20 44.43 3.14
1715 2631 5.445069 TGTACATTACTTTATGGCTGCCAT 58.555 37.500 34.21 34.21 46.99 4.40
1743 2659 4.116747 TCCATGGTTTGTCAAACACAAC 57.883 40.909 25.72 11.81 45.12 3.32
1804 2720 3.055094 ACAAGAACAGTATAGGCAGTGGG 60.055 47.826 0.00 0.00 0.00 4.61
1829 2745 1.486726 AGAACAGTATAGGCAGTGGGC 59.513 52.381 0.00 0.00 43.74 5.36
1831 2747 4.207891 ACAAGAACAGTATAGGCAGTGG 57.792 45.455 0.00 0.00 0.00 4.00
1832 2748 6.428159 AGAAAACAAGAACAGTATAGGCAGTG 59.572 38.462 0.00 0.00 0.00 3.66
1833 2749 6.534634 AGAAAACAAGAACAGTATAGGCAGT 58.465 36.000 0.00 0.00 0.00 4.40
1834 2750 7.819900 AGTAGAAAACAAGAACAGTATAGGCAG 59.180 37.037 0.00 0.00 0.00 4.85
1835 2751 7.676947 AGTAGAAAACAAGAACAGTATAGGCA 58.323 34.615 0.00 0.00 0.00 4.75
1836 2752 7.278203 GGAGTAGAAAACAAGAACAGTATAGGC 59.722 40.741 0.00 0.00 0.00 3.93
1837 2753 7.764901 GGGAGTAGAAAACAAGAACAGTATAGG 59.235 40.741 0.00 0.00 0.00 2.57
1838 2754 8.532819 AGGGAGTAGAAAACAAGAACAGTATAG 58.467 37.037 0.00 0.00 0.00 1.31
1839 2755 8.431910 AGGGAGTAGAAAACAAGAACAGTATA 57.568 34.615 0.00 0.00 0.00 1.47
1840 2756 7.317722 AGGGAGTAGAAAACAAGAACAGTAT 57.682 36.000 0.00 0.00 0.00 2.12
1841 2757 6.239515 GGAGGGAGTAGAAAACAAGAACAGTA 60.240 42.308 0.00 0.00 0.00 2.74
1842 2758 5.454897 GGAGGGAGTAGAAAACAAGAACAGT 60.455 44.000 0.00 0.00 0.00 3.55
1843 2759 4.998033 GGAGGGAGTAGAAAACAAGAACAG 59.002 45.833 0.00 0.00 0.00 3.16
1844 2760 4.502604 CGGAGGGAGTAGAAAACAAGAACA 60.503 45.833 0.00 0.00 0.00 3.18
1845 2761 3.995048 CGGAGGGAGTAGAAAACAAGAAC 59.005 47.826 0.00 0.00 0.00 3.01
1846 2762 3.644738 ACGGAGGGAGTAGAAAACAAGAA 59.355 43.478 0.00 0.00 0.00 2.52
1847 2763 3.236896 ACGGAGGGAGTAGAAAACAAGA 58.763 45.455 0.00 0.00 0.00 3.02
1848 2764 3.586892 GACGGAGGGAGTAGAAAACAAG 58.413 50.000 0.00 0.00 0.00 3.16
1849 2765 2.301009 GGACGGAGGGAGTAGAAAACAA 59.699 50.000 0.00 0.00 0.00 2.83
1850 2766 1.897802 GGACGGAGGGAGTAGAAAACA 59.102 52.381 0.00 0.00 0.00 2.83
1851 2767 1.206610 GGGACGGAGGGAGTAGAAAAC 59.793 57.143 0.00 0.00 0.00 2.43
1852 2768 1.203212 TGGGACGGAGGGAGTAGAAAA 60.203 52.381 0.00 0.00 0.00 2.29
1853 2769 0.410663 TGGGACGGAGGGAGTAGAAA 59.589 55.000 0.00 0.00 0.00 2.52
1854 2770 0.635009 ATGGGACGGAGGGAGTAGAA 59.365 55.000 0.00 0.00 0.00 2.10
1855 2771 1.526315 TATGGGACGGAGGGAGTAGA 58.474 55.000 0.00 0.00 0.00 2.59
1856 2772 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
1857 2773 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
1858 2774 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
1859 2775 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
1860 2776 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
1861 2777 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
1862 2778 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
1863 2779 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
1864 2780 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
1865 2781 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
1866 2782 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
1867 2783 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
1868 2784 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
1869 2785 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
1875 2791 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
1876 2792 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
1877 2793 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
1878 2794 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
1879 2795 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
1880 2796 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
1881 2797 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
1907 2823 9.883142 CTGCCCCAAAATATAAGAACATTTTTA 57.117 29.630 0.00 0.00 33.23 1.52
1908 2824 8.601546 TCTGCCCCAAAATATAAGAACATTTTT 58.398 29.630 0.00 0.00 33.23 1.94
1909 2825 8.144862 TCTGCCCCAAAATATAAGAACATTTT 57.855 30.769 0.00 0.00 35.30 1.82
1910 2826 7.147672 CCTCTGCCCCAAAATATAAGAACATTT 60.148 37.037 0.00 0.00 0.00 2.32
1911 2827 6.324770 CCTCTGCCCCAAAATATAAGAACATT 59.675 38.462 0.00 0.00 0.00 2.71
1912 2828 5.835280 CCTCTGCCCCAAAATATAAGAACAT 59.165 40.000 0.00 0.00 0.00 2.71
1913 2829 5.200483 CCTCTGCCCCAAAATATAAGAACA 58.800 41.667 0.00 0.00 0.00 3.18
1914 2830 4.584743 CCCTCTGCCCCAAAATATAAGAAC 59.415 45.833 0.00 0.00 0.00 3.01
1915 2831 4.480537 TCCCTCTGCCCCAAAATATAAGAA 59.519 41.667 0.00 0.00 0.00 2.52
1916 2832 4.051478 TCCCTCTGCCCCAAAATATAAGA 58.949 43.478 0.00 0.00 0.00 2.10
1917 2833 4.141158 ACTCCCTCTGCCCCAAAATATAAG 60.141 45.833 0.00 0.00 0.00 1.73
1918 2834 3.791545 ACTCCCTCTGCCCCAAAATATAA 59.208 43.478 0.00 0.00 0.00 0.98
1919 2835 3.403322 ACTCCCTCTGCCCCAAAATATA 58.597 45.455 0.00 0.00 0.00 0.86
1920 2836 2.217776 ACTCCCTCTGCCCCAAAATAT 58.782 47.619 0.00 0.00 0.00 1.28
1921 2837 1.681229 ACTCCCTCTGCCCCAAAATA 58.319 50.000 0.00 0.00 0.00 1.40
1922 2838 1.285078 GTACTCCCTCTGCCCCAAAAT 59.715 52.381 0.00 0.00 0.00 1.82
1923 2839 0.696501 GTACTCCCTCTGCCCCAAAA 59.303 55.000 0.00 0.00 0.00 2.44
1924 2840 0.474854 TGTACTCCCTCTGCCCCAAA 60.475 55.000 0.00 0.00 0.00 3.28
1925 2841 0.253160 ATGTACTCCCTCTGCCCCAA 60.253 55.000 0.00 0.00 0.00 4.12
1926 2842 0.982852 CATGTACTCCCTCTGCCCCA 60.983 60.000 0.00 0.00 0.00 4.96
1927 2843 0.691078 TCATGTACTCCCTCTGCCCC 60.691 60.000 0.00 0.00 0.00 5.80
1928 2844 0.466124 GTCATGTACTCCCTCTGCCC 59.534 60.000 0.00 0.00 0.00 5.36
1929 2845 1.137872 CAGTCATGTACTCCCTCTGCC 59.862 57.143 0.00 0.00 35.76 4.85
1930 2846 1.827969 ACAGTCATGTACTCCCTCTGC 59.172 52.381 0.00 0.00 38.09 4.26
1931 2847 2.828520 ACACAGTCATGTACTCCCTCTG 59.171 50.000 0.00 0.00 37.65 3.35
1932 2848 2.828520 CACACAGTCATGTACTCCCTCT 59.171 50.000 0.00 0.00 37.65 3.69
1933 2849 2.675317 GCACACAGTCATGTACTCCCTC 60.675 54.545 0.00 0.00 37.65 4.30
1934 2850 1.276421 GCACACAGTCATGTACTCCCT 59.724 52.381 0.00 0.00 37.65 4.20
1935 2851 1.001974 TGCACACAGTCATGTACTCCC 59.998 52.381 0.00 0.00 37.65 4.30
1936 2852 2.455674 TGCACACAGTCATGTACTCC 57.544 50.000 0.00 0.00 37.65 3.85
1937 2853 3.588955 TGATGCACACAGTCATGTACTC 58.411 45.455 0.00 0.00 37.65 2.59
1938 2854 3.683365 TGATGCACACAGTCATGTACT 57.317 42.857 0.00 0.00 37.65 2.73
1939 2855 3.310774 GGATGATGCACACAGTCATGTAC 59.689 47.826 4.51 0.00 37.65 2.90
1949 2865 4.913335 ATCATTCAAGGATGATGCACAC 57.087 40.909 3.05 0.00 43.32 3.82
1955 2871 5.120054 TCACCACATCATTCAAGGATGAT 57.880 39.130 18.71 3.33 45.25 2.45
1958 2874 3.635373 GCATCACCACATCATTCAAGGAT 59.365 43.478 0.00 0.00 0.00 3.24
2069 2985 4.514577 ATGACTCGCTTCCCGCCG 62.515 66.667 0.00 0.00 36.73 6.46
2171 3087 2.289382 TGCAACACCGAGCAGAATTCTA 60.289 45.455 7.86 0.00 35.51 2.10
2260 3177 3.120854 GCGTGAAGACTGATCAAGTGAAC 60.121 47.826 0.00 0.00 40.07 3.18
2604 3521 5.055265 TCACCAATTTCTGACCCTTTGTA 57.945 39.130 0.00 0.00 0.00 2.41
2641 3558 6.943146 GGAGGGATCTTTCTTAGTTTTTCACT 59.057 38.462 0.00 0.00 39.87 3.41
2878 3797 1.741706 AGAAACATGCAGCGGAATCAG 59.258 47.619 0.00 0.00 0.00 2.90
3061 3980 6.389906 AGTTAAAGTAATGCTTGTGCCATTC 58.610 36.000 0.00 0.00 37.52 2.67
3237 4157 4.037446 TGAAACCAACTGCCAATAGTGAAC 59.963 41.667 0.00 0.00 0.00 3.18
3240 4160 3.317711 TGTGAAACCAACTGCCAATAGTG 59.682 43.478 0.00 0.00 34.36 2.74
3288 4208 9.855021 ATTCCAAACATACAATAGCTTACAAAC 57.145 29.630 0.00 0.00 0.00 2.93
3501 4421 7.095774 GCGAGAATTGTGTTACGGATATACAAT 60.096 37.037 0.00 0.00 42.03 2.71
3526 4446 8.438676 AGTATTCTACTGTCATTTACCATTGC 57.561 34.615 0.00 0.00 37.69 3.56
3538 4458 7.201565 GCATTTTCACCAGAGTATTCTACTGTC 60.202 40.741 0.00 0.00 39.59 3.51
3546 4466 5.079643 ACTTGGCATTTTCACCAGAGTATT 58.920 37.500 0.00 0.00 37.24 1.89
3674 4600 5.863397 CCAATTGTCTGCACGAAACAATATT 59.137 36.000 4.43 0.00 41.47 1.28
3732 4658 1.135460 GCTGGACTCTTTGCTGCATTC 60.135 52.381 1.84 0.00 39.86 2.67
3883 4810 1.158963 TGGGGGTGGGGGAATGAAAT 61.159 55.000 0.00 0.00 0.00 2.17
3885 4812 2.120807 TGGGGGTGGGGGAATGAA 60.121 61.111 0.00 0.00 0.00 2.57
3908 4835 0.034089 GAATTGGGTGTCAGGGGAGG 60.034 60.000 0.00 0.00 0.00 4.30
3909 4836 0.392998 CGAATTGGGTGTCAGGGGAG 60.393 60.000 0.00 0.00 0.00 4.30
3927 4854 5.244851 TCCATCAGATAGGAAAGAGAATCCG 59.755 44.000 0.44 0.00 42.03 4.18
4119 5268 2.477845 AAATGGCAGCAAATGTTCCC 57.522 45.000 0.00 0.00 0.00 3.97
4280 5429 9.857957 ATATATTTTCTCTTTACCGCTAGCTAC 57.142 33.333 13.93 0.00 0.00 3.58
4314 5463 7.616935 ACAATACTCCCAGTGAATCATCAAATT 59.383 33.333 0.00 0.00 37.30 1.82
4366 5515 4.625742 TCATCTCTCGTTCACGGAAATTTC 59.374 41.667 9.83 9.83 40.29 2.17
4375 5524 4.266502 GTGTAATGCTCATCTCTCGTTCAC 59.733 45.833 0.00 0.00 0.00 3.18
4402 5552 0.713883 GCACACGATGTTGTAGTCCG 59.286 55.000 0.00 0.00 0.00 4.79
4404 5554 2.090658 CGAAGCACACGATGTTGTAGTC 59.909 50.000 0.00 0.00 0.00 2.59
4425 5575 5.339008 TCACCACATACTTCCACTACATC 57.661 43.478 0.00 0.00 0.00 3.06
4442 5592 5.048083 GCTTCCACAATAAGACAATTCACCA 60.048 40.000 0.00 0.00 0.00 4.17
4469 5619 6.173339 TCACATGATCTAAACCTCTGAAACC 58.827 40.000 0.00 0.00 0.00 3.27
4623 5791 6.317642 TCAACCATACTGTCCATTATTTTCGG 59.682 38.462 0.00 0.00 0.00 4.30
4624 5792 7.315247 TCAACCATACTGTCCATTATTTTCG 57.685 36.000 0.00 0.00 0.00 3.46
4636 5804 4.032960 TCAAGCCATTCAACCATACTGT 57.967 40.909 0.00 0.00 0.00 3.55
4710 5878 6.714810 ACCTTTTCACTAATCATGCAGTACAA 59.285 34.615 0.00 0.00 0.00 2.41
4799 5975 3.517296 TGAGTTTAAATGCCCTCCACA 57.483 42.857 0.00 0.00 0.00 4.17
4829 6005 0.811281 GCCGGCTCAAGCTAAAATGT 59.189 50.000 22.15 0.00 41.70 2.71
4832 6054 0.887387 AACGCCGGCTCAAGCTAAAA 60.887 50.000 26.68 0.00 41.70 1.52
4899 6121 5.350365 TCCGCACATTTATGAACAGTAAGAC 59.650 40.000 0.00 0.00 0.00 3.01
4930 6162 7.655521 TGCTGATAGTTACAAGTACCATACT 57.344 36.000 0.00 0.00 41.73 2.12
4979 6214 2.421388 CGCCCCCTCTATTTCACATCAA 60.421 50.000 0.00 0.00 0.00 2.57
4982 6217 0.179018 GCGCCCCCTCTATTTCACAT 60.179 55.000 0.00 0.00 0.00 3.21
4990 6225 1.271840 AACTCAATGCGCCCCCTCTA 61.272 55.000 4.18 0.00 0.00 2.43
4998 6233 1.905049 GCGTTTTAGAACTCAATGCGC 59.095 47.619 0.00 0.00 33.51 6.09
5061 6301 6.037062 CCTTTTTCATTTATTCGGGGCATTTC 59.963 38.462 0.00 0.00 0.00 2.17
5070 6310 8.216453 CAGCTGTTTTCCTTTTTCATTTATTCG 58.784 33.333 5.25 0.00 0.00 3.34
5078 6318 3.195396 ACAGCAGCTGTTTTCCTTTTTCA 59.805 39.130 23.11 0.00 42.59 2.69
5086 6326 2.056577 GATTGCACAGCAGCTGTTTTC 58.943 47.619 26.16 17.09 42.59 2.29
5114 6355 2.961526 ATGACCAGGATGTACACGTC 57.038 50.000 0.00 0.00 0.00 4.34
5135 6376 5.815740 TGTTTGTTCTTTCAGTAGGAGTCAC 59.184 40.000 0.00 0.00 0.00 3.67
5142 6383 6.852664 AGTTTGGTGTTTGTTCTTTCAGTAG 58.147 36.000 0.00 0.00 0.00 2.57
5222 6463 1.067295 ACCCCAGCAGTTGATTCAGA 58.933 50.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.