Multiple sequence alignment - TraesCS3A01G527800

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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 TraesCS3A01G527800 chr3A 100.000 4674 0 0 1 4674 742244145 742239472 0.000000e+00 8632.0
1 TraesCS3A01G527800 chr3A 82.913 1744 222 40 644 2350 742228967 742227263 0.000000e+00 1500.0
2 TraesCS3A01G527800 chr3A 83.557 1563 219 27 643 2185 742327375 742325831 0.000000e+00 1428.0
3 TraesCS3A01G527800 chr3A 98.908 641 7 0 2 642 235403728 235404368 0.000000e+00 1146.0
4 TraesCS3A01G527800 chr3A 81.287 1010 155 21 3578 4585 742323294 742322317 0.000000e+00 787.0
5 TraesCS3A01G527800 chr3A 78.155 412 74 14 2252 2653 742325816 742325411 1.000000e-61 248.0
6 TraesCS3A01G527800 chr3B 85.138 1487 187 19 644 2115 819635193 819633726 0.000000e+00 1491.0
7 TraesCS3A01G527800 chr3B 80.108 2046 302 63 644 2639 819507811 819505821 0.000000e+00 1426.0
8 TraesCS3A01G527800 chr3B 82.562 1577 215 38 643 2202 819285252 819283719 0.000000e+00 1334.0
9 TraesCS3A01G527800 chr3B 84.003 1394 176 23 798 2176 819192552 819191191 0.000000e+00 1295.0
10 TraesCS3A01G527800 chr3B 85.339 1180 156 10 644 1819 819368582 819367416 0.000000e+00 1205.0
11 TraesCS3A01G527800 chr3B 84.631 976 131 15 3621 4585 819189279 819188312 0.000000e+00 953.0
12 TraesCS3A01G527800 chr3B 82.348 1116 171 18 3478 4585 819366343 819365246 0.000000e+00 946.0
13 TraesCS3A01G527800 chr3B 82.769 975 157 8 3613 4585 819632336 819631371 0.000000e+00 859.0
14 TraesCS3A01G527800 chr3B 81.980 1010 151 18 3578 4585 819281863 819280883 0.000000e+00 828.0
15 TraesCS3A01G527800 chr3B 81.092 989 148 26 3607 4586 819505530 819504572 0.000000e+00 754.0
16 TraesCS3A01G527800 chr3B 88.486 634 57 10 2666 3289 11130212 11130839 0.000000e+00 752.0
17 TraesCS3A01G527800 chr3B 89.268 615 41 12 2704 3298 752045493 752044884 0.000000e+00 747.0
18 TraesCS3A01G527800 chr3B 90.814 479 33 9 2667 3142 820580055 820579585 8.530000e-177 630.0
19 TraesCS3A01G527800 chr3B 90.588 85 8 0 4584 4668 86950819 86950735 3.820000e-21 113.0
20 TraesCS3A01G527800 chr3B 88.710 62 5 2 3704 3764 819507425 819507365 1.800000e-09 75.0
21 TraesCS3A01G527800 chr3D 82.606 1742 225 36 643 2366 608931972 608930291 0.000000e+00 1467.0
22 TraesCS3A01G527800 chr3D 80.312 1026 165 19 3572 4585 608926833 608925833 0.000000e+00 741.0
23 TraesCS3A01G527800 chr3D 85.400 500 59 9 652 1147 608968734 608968245 1.500000e-139 507.0
24 TraesCS3A01G527800 chr3D 98.400 125 2 0 3170 3294 52422953 52423077 2.190000e-53 220.0
25 TraesCS3A01G527800 chr3D 87.302 63 8 0 3702 3764 608968356 608968294 6.490000e-09 73.1
26 TraesCS3A01G527800 chr3D 89.362 47 5 0 4628 4674 377201905 377201859 5.050000e-05 60.2
27 TraesCS3A01G527800 chr1B 98.754 642 8 0 2 643 649037209 649036568 0.000000e+00 1142.0
28 TraesCS3A01G527800 chr1B 90.000 630 46 11 2667 3294 481851641 481851027 0.000000e+00 798.0
29 TraesCS3A01G527800 chr1B 98.400 125 2 0 3170 3294 662907672 662907796 2.190000e-53 220.0
30 TraesCS3A01G527800 chr1B 90.588 85 8 0 4584 4668 186799421 186799337 3.820000e-21 113.0
31 TraesCS3A01G527800 chr5B 98.752 641 8 0 2 642 606716856 606716216 0.000000e+00 1140.0
32 TraesCS3A01G527800 chr5B 98.287 642 11 0 1 642 133415626 133416267 0.000000e+00 1125.0
33 TraesCS3A01G527800 chr5B 97.508 642 16 0 1 642 379343834 379344475 0.000000e+00 1098.0
34 TraesCS3A01G527800 chr5B 96.412 641 22 1 2 642 80207529 80206890 0.000000e+00 1055.0
35 TraesCS3A01G527800 chr5B 83.871 93 8 4 4583 4668 578541503 578541411 1.080000e-11 82.4
36 TraesCS3A01G527800 chr6B 98.442 642 10 0 1 642 60098221 60098862 0.000000e+00 1131.0
37 TraesCS3A01G527800 chr6B 85.106 94 14 0 4577 4670 437483016 437482923 3.850000e-16 97.1
38 TraesCS3A01G527800 chr4B 98.442 642 10 0 1 642 364158816 364159457 0.000000e+00 1131.0
39 TraesCS3A01G527800 chr4B 99.206 126 1 0 3169 3294 54520317 54520192 1.310000e-55 228.0
40 TraesCS3A01G527800 chr4B 99.187 123 1 0 3172 3294 653314251 653314373 6.090000e-54 222.0
41 TraesCS3A01G527800 chr4B 100.000 28 0 0 4645 4672 486092512 486092539 8.000000e-03 52.8
42 TraesCS3A01G527800 chr2B 98.131 642 12 0 1 642 63273556 63274197 0.000000e+00 1120.0
43 TraesCS3A01G527800 chr2B 90.515 485 35 7 2666 3142 581429142 581428661 8.530000e-177 630.0
44 TraesCS3A01G527800 chr2B 95.035 141 6 1 3170 3309 581428572 581428432 2.190000e-53 220.0
45 TraesCS3A01G527800 chr2B 84.783 92 10 4 4579 4668 408725080 408725169 6.440000e-14 89.8
46 TraesCS3A01G527800 chr2B 84.058 69 11 0 1752 1820 775357883 775357951 3.020000e-07 67.6
47 TraesCS3A01G527800 chr2D 91.858 479 33 3 2666 3142 359436896 359437370 0.000000e+00 664.0
48 TraesCS3A01G527800 chr2D 91.209 91 7 1 4580 4669 102881951 102881861 6.350000e-24 122.0
49 TraesCS3A01G527800 chr2D 89.535 86 9 0 4584 4669 612945420 612945335 4.940000e-20 110.0
50 TraesCS3A01G527800 chr2D 90.000 50 4 1 4581 4629 309939683 309939732 3.900000e-06 63.9
51 TraesCS3A01G527800 chr2D 96.970 33 1 0 3735 3767 16765107 16765075 6.530000e-04 56.5
52 TraesCS3A01G527800 chr7B 91.286 482 32 6 2665 3141 673437448 673437924 0.000000e+00 649.0
53 TraesCS3A01G527800 chr7B 98.400 125 2 0 3170 3294 673438013 673438137 2.190000e-53 220.0
54 TraesCS3A01G527800 chr1A 90.204 490 35 8 2661 3142 2102777 2103261 1.100000e-175 627.0
55 TraesCS3A01G527800 chr1A 86.517 89 12 0 4580 4668 23177992 23178080 1.070000e-16 99.0
56 TraesCS3A01G527800 chr1A 96.875 32 1 0 3736 3767 54019049 54019018 2.000000e-03 54.7
57 TraesCS3A01G527800 chr5D 90.486 473 37 4 2666 3132 144223198 144222728 6.640000e-173 617.0
58 TraesCS3A01G527800 chr5D 98.425 127 1 1 3170 3295 55586406 55586280 6.090000e-54 222.0
59 TraesCS3A01G527800 chr5D 82.759 145 23 2 998 1141 447711932 447712075 1.370000e-25 128.0
60 TraesCS3A01G527800 chr5D 82.734 139 24 0 998 1136 447713370 447713508 1.770000e-24 124.0
61 TraesCS3A01G527800 chr5D 100.000 28 0 0 4642 4669 45484340 45484313 8.000000e-03 52.8
62 TraesCS3A01G527800 chr2A 89.938 487 34 9 2663 3142 142681069 142680591 8.600000e-172 614.0
63 TraesCS3A01G527800 chr2A 85.714 91 8 5 4584 4672 167380693 167380606 1.790000e-14 91.6
64 TraesCS3A01G527800 chr2A 100.000 30 0 0 3735 3764 18544776 18544805 6.530000e-04 56.5
65 TraesCS3A01G527800 chr7D 100.000 125 0 0 3170 3294 49387586 49387710 1.010000e-56 231.0
66 TraesCS3A01G527800 chr7D 90.588 85 8 0 4584 4668 156686585 156686501 3.820000e-21 113.0
67 TraesCS3A01G527800 chr7A 82.796 93 15 1 4580 4671 4000679 4000771 1.080000e-11 82.4
68 TraesCS3A01G527800 chr6D 88.235 68 5 1 1037 1104 27056973 27057037 1.390000e-10 78.7
69 TraesCS3A01G527800 chr6D 84.507 71 11 0 3694 3764 35493943 35493873 2.330000e-08 71.3
70 TraesCS3A01G527800 chr6D 81.395 86 14 2 4584 4668 255445413 255445497 8.390000e-08 69.4
71 TraesCS3A01G527800 chr1D 87.500 64 8 0 3704 3767 55428331 55428268 1.800000e-09 75.0
72 TraesCS3A01G527800 chr1D 96.875 32 1 0 3736 3767 55424623 55424592 2.000000e-03 54.7
73 TraesCS3A01G527800 chr4A 91.304 46 4 0 4623 4668 102613258 102613213 3.900000e-06 63.9
74 TraesCS3A01G527800 chr6A 74.510 153 26 11 1125 1272 74233146 74233002 2.000000e-03 54.7
75 TraesCS3A01G527800 chr4D 100.000 29 0 0 4643 4671 32346543 32346571 2.000000e-03 54.7


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 TraesCS3A01G527800 chr3A 742239472 742244145 4673 True 8632.000000 8632 100.000000 1 4674 1 chr3A.!!$R2 4673
1 TraesCS3A01G527800 chr3A 742227263 742228967 1704 True 1500.000000 1500 82.913000 644 2350 1 chr3A.!!$R1 1706
2 TraesCS3A01G527800 chr3A 235403728 235404368 640 False 1146.000000 1146 98.908000 2 642 1 chr3A.!!$F1 640
3 TraesCS3A01G527800 chr3A 742322317 742327375 5058 True 821.000000 1428 80.999667 643 4585 3 chr3A.!!$R3 3942
4 TraesCS3A01G527800 chr3B 819631371 819635193 3822 True 1175.000000 1491 83.953500 644 4585 2 chr3B.!!$R8 3941
5 TraesCS3A01G527800 chr3B 819188312 819192552 4240 True 1124.000000 1295 84.317000 798 4585 2 chr3B.!!$R4 3787
6 TraesCS3A01G527800 chr3B 819280883 819285252 4369 True 1081.000000 1334 82.271000 643 4585 2 chr3B.!!$R5 3942
7 TraesCS3A01G527800 chr3B 819365246 819368582 3336 True 1075.500000 1205 83.843500 644 4585 2 chr3B.!!$R6 3941
8 TraesCS3A01G527800 chr3B 11130212 11130839 627 False 752.000000 752 88.486000 2666 3289 1 chr3B.!!$F1 623
9 TraesCS3A01G527800 chr3B 819504572 819507811 3239 True 751.666667 1426 83.303333 644 4586 3 chr3B.!!$R7 3942
10 TraesCS3A01G527800 chr3B 752044884 752045493 609 True 747.000000 747 89.268000 2704 3298 1 chr3B.!!$R2 594
11 TraesCS3A01G527800 chr3D 608925833 608931972 6139 True 1104.000000 1467 81.459000 643 4585 2 chr3D.!!$R2 3942
12 TraesCS3A01G527800 chr1B 649036568 649037209 641 True 1142.000000 1142 98.754000 2 643 1 chr1B.!!$R3 641
13 TraesCS3A01G527800 chr1B 481851027 481851641 614 True 798.000000 798 90.000000 2667 3294 1 chr1B.!!$R2 627
14 TraesCS3A01G527800 chr5B 606716216 606716856 640 True 1140.000000 1140 98.752000 2 642 1 chr5B.!!$R3 640
15 TraesCS3A01G527800 chr5B 133415626 133416267 641 False 1125.000000 1125 98.287000 1 642 1 chr5B.!!$F1 641
16 TraesCS3A01G527800 chr5B 379343834 379344475 641 False 1098.000000 1098 97.508000 1 642 1 chr5B.!!$F2 641
17 TraesCS3A01G527800 chr5B 80206890 80207529 639 True 1055.000000 1055 96.412000 2 642 1 chr5B.!!$R1 640
18 TraesCS3A01G527800 chr6B 60098221 60098862 641 False 1131.000000 1131 98.442000 1 642 1 chr6B.!!$F1 641
19 TraesCS3A01G527800 chr4B 364158816 364159457 641 False 1131.000000 1131 98.442000 1 642 1 chr4B.!!$F1 641
20 TraesCS3A01G527800 chr2B 63273556 63274197 641 False 1120.000000 1120 98.131000 1 642 1 chr2B.!!$F1 641
21 TraesCS3A01G527800 chr2B 581428432 581429142 710 True 425.000000 630 92.775000 2666 3309 2 chr2B.!!$R1 643
22 TraesCS3A01G527800 chr7B 673437448 673438137 689 False 434.500000 649 94.843000 2665 3294 2 chr7B.!!$F1 629

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
728 731 0.875059 GCCCTTGGTTCTCACTTTCG 59.125 55.0 0.00 0.0 0.00 3.46 F
1341 1359 0.101579 TCAAGAACAGCGACGTGACA 59.898 50.0 0.00 0.0 0.00 3.58 F
1416 1434 0.461548 CCAGACTCGAAGCAGGCATA 59.538 55.0 0.00 0.0 0.00 3.14 F
2231 2463 0.461339 TAAAGGATCCGCAAGACCGC 60.461 55.0 5.98 0.0 43.02 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2230 2462 0.039165 GTAGTTGGCTGCCTTGTTGC 60.039 55.0 21.03 3.03 0.00 4.17 R
2231 2463 0.598065 GGTAGTTGGCTGCCTTGTTG 59.402 55.0 21.03 0.00 43.14 3.33 R
3383 8044 0.039708 GAGCTTTGCTGCAACAGACC 60.040 55.0 15.72 7.47 39.88 3.85 R
3882 10415 0.034186 ATGACGGCATTGGTGTGGAT 60.034 50.0 0.00 0.00 0.00 3.41 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
473 474 2.202905 CGGCGGTGCGGGTATTAA 60.203 61.111 0.00 0.00 0.00 1.40
726 729 2.108952 AGATGCCCTTGGTTCTCACTTT 59.891 45.455 0.00 0.00 0.00 2.66
727 730 1.981256 TGCCCTTGGTTCTCACTTTC 58.019 50.000 0.00 0.00 0.00 2.62
728 731 0.875059 GCCCTTGGTTCTCACTTTCG 59.125 55.000 0.00 0.00 0.00 3.46
729 732 1.542547 GCCCTTGGTTCTCACTTTCGA 60.543 52.381 0.00 0.00 0.00 3.71
758 766 5.538849 ACTTTTACCTCTAGATAGCTGGC 57.461 43.478 0.00 0.00 0.00 4.85
812 826 2.095853 CCAGTGTGCGCAACCTTATAAG 59.904 50.000 14.00 5.43 0.00 1.73
813 827 1.737793 AGTGTGCGCAACCTTATAAGC 59.262 47.619 14.00 0.00 0.00 3.09
814 828 1.737793 GTGTGCGCAACCTTATAAGCT 59.262 47.619 14.00 0.00 0.00 3.74
815 829 1.737236 TGTGCGCAACCTTATAAGCTG 59.263 47.619 14.00 7.55 0.00 4.24
848 862 1.820519 GGAGAGCAATGCATGGTTCAA 59.179 47.619 18.94 0.00 40.59 2.69
856 870 1.742761 TGCATGGTTCAAGAGCTAGC 58.257 50.000 6.62 6.62 0.00 3.42
857 871 1.280133 TGCATGGTTCAAGAGCTAGCT 59.720 47.619 19.45 19.45 0.00 3.32
858 872 2.501316 TGCATGGTTCAAGAGCTAGCTA 59.499 45.455 19.38 0.00 0.00 3.32
859 873 3.129871 GCATGGTTCAAGAGCTAGCTAG 58.870 50.000 19.38 16.84 0.00 3.42
883 897 1.338579 GCTAGGCAGACAAGCTCAACT 60.339 52.381 0.00 0.00 33.40 3.16
888 902 1.989165 GCAGACAAGCTCAACTACTCG 59.011 52.381 0.00 0.00 0.00 4.18
894 908 1.186200 AGCTCAACTACTCGATGGCA 58.814 50.000 0.00 0.00 0.00 4.92
1053 1067 2.284276 TGTGCCATACCCGTTCGGA 61.284 57.895 13.08 0.00 34.64 4.55
1056 1070 0.253610 TGCCATACCCGTTCGGAATT 59.746 50.000 13.08 0.00 34.64 2.17
1152 1167 2.358737 GACGGCACCCTCCAAGTG 60.359 66.667 0.00 0.00 38.30 3.16
1211 1229 3.803715 GCCATACGCACTGGAGACATAAT 60.804 47.826 2.89 0.00 37.24 1.28
1341 1359 0.101579 TCAAGAACAGCGACGTGACA 59.898 50.000 0.00 0.00 0.00 3.58
1367 1385 2.686235 CAGCTGTTCTTCTCTCTGTGG 58.314 52.381 5.25 0.00 0.00 4.17
1388 1406 2.835431 CGGCGATGGACTCTCCCT 60.835 66.667 0.00 0.00 35.03 4.20
1416 1434 0.461548 CCAGACTCGAAGCAGGCATA 59.538 55.000 0.00 0.00 0.00 3.14
1461 1479 2.254459 CAGTCGGACATTGTCTTCGAG 58.746 52.381 16.02 4.13 29.97 4.04
1465 1483 1.673033 CGGACATTGTCTTCGAGCCTT 60.673 52.381 16.02 0.00 32.47 4.35
1467 1485 2.354203 GGACATTGTCTTCGAGCCTTCT 60.354 50.000 16.02 0.00 32.47 2.85
1468 1486 2.926838 GACATTGTCTTCGAGCCTTCTC 59.073 50.000 9.59 0.00 35.99 2.87
1626 1644 6.043411 GGTCTTTCATGAGCTATTACGAACT 58.957 40.000 0.00 0.00 0.00 3.01
1695 1721 1.228862 GGAGGTTGTTGGCCATGGT 60.229 57.895 14.67 0.00 0.00 3.55
1697 1723 0.827507 GAGGTTGTTGGCCATGGTGT 60.828 55.000 14.67 0.00 0.00 4.16
1783 1809 1.877576 CTCCTGCACAGACGGCTACA 61.878 60.000 0.00 0.00 0.00 2.74
1819 1845 1.072505 ACCGACGGATGCAAAGGTT 59.927 52.632 23.38 0.00 0.00 3.50
1895 1929 9.764363 ATTTTCAGGGTTTCTCTTTGTTTAATC 57.236 29.630 0.00 0.00 0.00 1.75
1903 1937 8.523658 GGTTTCTCTTTGTTTAATCCTAGCATT 58.476 33.333 0.00 0.00 0.00 3.56
1984 2049 5.163519 GGTGATTGTACCAATTTGGATGGAG 60.164 44.000 22.19 0.00 40.96 3.86
2058 2126 0.540923 GCTGCCTCAGTTCCATCTCT 59.459 55.000 0.00 0.00 33.43 3.10
2059 2127 1.743091 GCTGCCTCAGTTCCATCTCTG 60.743 57.143 0.00 0.00 33.43 3.35
2060 2128 1.554160 CTGCCTCAGTTCCATCTCTGT 59.446 52.381 0.00 0.00 33.89 3.41
2061 2129 1.552337 TGCCTCAGTTCCATCTCTGTC 59.448 52.381 0.00 0.00 33.89 3.51
2062 2130 1.830477 GCCTCAGTTCCATCTCTGTCT 59.170 52.381 0.00 0.00 33.89 3.41
2063 2131 2.159114 GCCTCAGTTCCATCTCTGTCTC 60.159 54.545 0.00 0.00 33.89 3.36
2071 2140 3.636679 TCCATCTCTGTCTCAGGTAAGG 58.363 50.000 0.00 0.00 31.51 2.69
2078 2147 7.979786 TCTCTGTCTCAGGTAAGGAATATTT 57.020 36.000 0.00 0.00 31.51 1.40
2080 2154 7.619698 TCTCTGTCTCAGGTAAGGAATATTTCA 59.380 37.037 0.00 0.00 31.51 2.69
2088 2162 6.378280 CAGGTAAGGAATATTTCAGCAACCTT 59.622 38.462 0.00 0.00 39.21 3.50
2089 2163 6.378280 AGGTAAGGAATATTTCAGCAACCTTG 59.622 38.462 10.94 0.00 36.98 3.61
2092 2166 7.775053 AAGGAATATTTCAGCAACCTTGTTA 57.225 32.000 0.00 0.00 35.39 2.41
2105 2179 9.128107 CAGCAACCTTGTTATGTTTTTACTATG 57.872 33.333 0.00 0.00 0.00 2.23
2107 2181 7.544217 GCAACCTTGTTATGTTTTTACTATGGG 59.456 37.037 0.00 0.00 0.00 4.00
2115 2189 9.403583 GTTATGTTTTTACTATGGGGATGAAGA 57.596 33.333 0.00 0.00 0.00 2.87
2138 2317 8.186709 AGACAAATGAAGGATGAACAAGAAAT 57.813 30.769 0.00 0.00 0.00 2.17
2144 2323 7.452880 TGAAGGATGAACAAGAAATAACAGG 57.547 36.000 0.00 0.00 0.00 4.00
2145 2324 5.904362 AGGATGAACAAGAAATAACAGGC 57.096 39.130 0.00 0.00 0.00 4.85
2157 2336 5.074929 AGAAATAACAGGCCATATCCATCCA 59.925 40.000 5.01 0.00 0.00 3.41
2202 2394 6.371809 AAACACGCGGATACATTCAATTAT 57.628 33.333 12.47 0.00 0.00 1.28
2206 2398 4.151070 CGCGGATACATTCAATTATGTGC 58.849 43.478 0.00 0.00 39.06 4.57
2221 2413 1.448985 TGTGCGCAGTTAAAGGATCC 58.551 50.000 12.22 2.48 0.00 3.36
2226 2458 1.062587 CGCAGTTAAAGGATCCGCAAG 59.937 52.381 5.98 0.00 0.00 4.01
2227 2459 2.356135 GCAGTTAAAGGATCCGCAAGA 58.644 47.619 5.98 0.00 43.02 3.02
2228 2460 2.096013 GCAGTTAAAGGATCCGCAAGAC 59.904 50.000 5.98 3.30 43.02 3.01
2229 2461 2.678336 CAGTTAAAGGATCCGCAAGACC 59.322 50.000 5.98 0.00 43.02 3.85
2230 2462 1.664151 GTTAAAGGATCCGCAAGACCG 59.336 52.381 5.98 0.00 43.02 4.79
2231 2463 0.461339 TAAAGGATCCGCAAGACCGC 60.461 55.000 5.98 0.00 43.02 5.68
2232 2464 2.463589 AAAGGATCCGCAAGACCGCA 62.464 55.000 5.98 0.00 43.02 5.69
2233 2465 2.435938 GGATCCGCAAGACCGCAA 60.436 61.111 0.00 0.00 43.02 4.85
2234 2466 2.750888 GGATCCGCAAGACCGCAAC 61.751 63.158 0.00 0.00 43.02 4.17
2235 2467 2.031919 ATCCGCAAGACCGCAACA 59.968 55.556 0.00 0.00 43.02 3.33
2236 2468 1.573829 GATCCGCAAGACCGCAACAA 61.574 55.000 0.00 0.00 43.02 2.83
2237 2469 1.577328 ATCCGCAAGACCGCAACAAG 61.577 55.000 0.00 0.00 43.02 3.16
2238 2470 2.252260 CGCAAGACCGCAACAAGG 59.748 61.111 0.00 0.00 43.02 3.61
2239 2471 2.050077 GCAAGACCGCAACAAGGC 60.050 61.111 0.00 0.00 0.00 4.35
2271 2503 5.949735 ACCGAGTTGCCAATTAGTTATTTG 58.050 37.500 0.00 0.00 0.00 2.32
2272 2504 5.708230 ACCGAGTTGCCAATTAGTTATTTGA 59.292 36.000 0.00 0.00 0.00 2.69
2312 2544 8.106247 AGAATAAATGCAGAACTAAAACGGAA 57.894 30.769 0.00 0.00 0.00 4.30
2334 2570 7.906010 CGGAAATTAACGTAATAGATTGCACAA 59.094 33.333 0.00 0.00 0.00 3.33
2389 3653 9.384764 GATTTAGTTAGCAAGAGTATGAAACCT 57.615 33.333 0.00 0.00 0.00 3.50
2393 3657 6.819146 AGTTAGCAAGAGTATGAAACCTTAGC 59.181 38.462 0.00 0.00 0.00 3.09
2398 3662 5.606348 AGAGTATGAAACCTTAGCTGGAG 57.394 43.478 0.00 0.00 0.00 3.86
2444 3710 4.600062 AGGGATTAACATTGTTCACTCCC 58.400 43.478 23.67 23.67 41.20 4.30
2461 3729 3.941483 ACTCCCATTTCGCAAATCTACTG 59.059 43.478 0.00 0.00 0.00 2.74
2464 3732 5.192927 TCCCATTTCGCAAATCTACTGATT 58.807 37.500 0.00 0.00 44.08 2.57
2466 3734 6.260050 TCCCATTTCGCAAATCTACTGATTAC 59.740 38.462 0.00 0.00 41.62 1.89
2486 3760 4.640789 ACCAGCGTCATTTTGTTACAAA 57.359 36.364 6.41 6.41 0.00 2.83
2512 3793 3.777522 CAGTTTAGACCTCCCTCCAGAAT 59.222 47.826 0.00 0.00 0.00 2.40
2520 3801 2.763448 CCTCCCTCCAGAATATCGATCC 59.237 54.545 0.00 0.00 0.00 3.36
2538 3819 4.595116 GATCCAAAGTGAAGATTCGCATG 58.405 43.478 8.69 6.86 40.06 4.06
2545 3826 3.055530 AGTGAAGATTCGCATGAGAGGTT 60.056 43.478 8.69 0.00 40.06 3.50
2555 4288 4.083324 TCGCATGAGAGGTTGAAAATGAAC 60.083 41.667 0.00 0.00 0.00 3.18
2559 4292 6.309737 GCATGAGAGGTTGAAAATGAACATTC 59.690 38.462 0.00 0.00 0.00 2.67
2608 4346 4.183865 GAGGGCAAATGATTTTAACAGCC 58.816 43.478 7.46 7.46 40.08 4.85
2648 4386 5.167845 CCAATTGACCATAAAAACCTTCGG 58.832 41.667 7.12 0.00 0.00 4.30
2653 4391 1.818674 CCATAAAAACCTTCGGCAGCT 59.181 47.619 0.00 0.00 0.00 4.24
2656 4394 0.881796 AAAAACCTTCGGCAGCTAGC 59.118 50.000 6.62 6.62 44.65 3.42
2686 4424 8.623903 TCTGTCACTAGTAGAAAAACGACTTTA 58.376 33.333 3.59 0.00 36.06 1.85
2740 4479 2.044555 GGAACCGGCACTAAAGGGC 61.045 63.158 0.00 0.00 0.00 5.19
2882 4635 2.124983 CGCCTACTGTGCCAGCAT 60.125 61.111 0.00 0.00 34.37 3.79
2909 4662 4.720046 TGCATACAACTAGAAACCCAACA 58.280 39.130 0.00 0.00 0.00 3.33
3003 4756 2.172293 CAAAGGCCTGCTTAGAGAGGAT 59.828 50.000 5.69 0.00 0.00 3.24
3019 4772 1.381928 GGATCTCGACACGGTAGCCA 61.382 60.000 0.00 0.00 0.00 4.75
3142 4896 2.633967 TGGCTTCAACCGGTACTAAAGA 59.366 45.455 8.00 0.00 0.00 2.52
3143 4897 2.998670 GGCTTCAACCGGTACTAAAGAC 59.001 50.000 8.00 7.94 0.00 3.01
3144 4898 2.998670 GCTTCAACCGGTACTAAAGACC 59.001 50.000 8.00 0.00 0.00 3.85
3145 4899 3.593096 CTTCAACCGGTACTAAAGACCC 58.407 50.000 8.00 0.00 32.95 4.46
3146 4900 2.893424 TCAACCGGTACTAAAGACCCT 58.107 47.619 8.00 0.00 32.95 4.34
3161 4964 2.658489 AGACCCTCCTTTAGTACCAGGA 59.342 50.000 0.00 6.03 36.80 3.86
3162 4965 2.765135 GACCCTCCTTTAGTACCAGGAC 59.235 54.545 0.00 0.00 33.99 3.85
3163 4966 2.386113 ACCCTCCTTTAGTACCAGGACT 59.614 50.000 0.00 0.00 33.99 3.85
3165 4968 4.046360 ACCCTCCTTTAGTACCAGGACTAA 59.954 45.833 0.00 0.00 39.58 2.24
3166 4969 5.217400 CCCTCCTTTAGTACCAGGACTAAT 58.783 45.833 3.34 0.00 40.66 1.73
3167 4970 5.070580 CCCTCCTTTAGTACCAGGACTAATG 59.929 48.000 3.34 6.10 40.66 1.90
3168 4971 5.453480 CCTCCTTTAGTACCAGGACTAATGC 60.453 48.000 3.34 0.00 40.66 3.56
3358 8019 9.899226 AAGTTAGCAACAAGAAATATTCAAGAC 57.101 29.630 0.00 0.00 0.00 3.01
3374 8035 9.793259 ATATTCAAGACTACAAAAGAACTCCAA 57.207 29.630 0.00 0.00 0.00 3.53
3376 8037 6.650120 TCAAGACTACAAAAGAACTCCAACT 58.350 36.000 0.00 0.00 0.00 3.16
3377 8038 6.761714 TCAAGACTACAAAAGAACTCCAACTC 59.238 38.462 0.00 0.00 0.00 3.01
3379 8040 6.650120 AGACTACAAAAGAACTCCAACTCAA 58.350 36.000 0.00 0.00 0.00 3.02
3381 8042 6.415573 ACTACAAAAGAACTCCAACTCAACT 58.584 36.000 0.00 0.00 0.00 3.16
3382 8043 5.567138 ACAAAAGAACTCCAACTCAACTG 57.433 39.130 0.00 0.00 0.00 3.16
3383 8044 4.399303 ACAAAAGAACTCCAACTCAACTGG 59.601 41.667 0.00 0.00 35.05 4.00
3384 8045 2.938956 AGAACTCCAACTCAACTGGG 57.061 50.000 0.00 0.00 34.46 4.45
3385 8046 2.127708 AGAACTCCAACTCAACTGGGT 58.872 47.619 0.00 0.00 34.46 4.51
3386 8047 2.104963 AGAACTCCAACTCAACTGGGTC 59.895 50.000 0.00 0.00 34.46 4.46
3387 8048 1.807814 ACTCCAACTCAACTGGGTCT 58.192 50.000 0.00 0.00 34.46 3.85
3388 8049 1.417890 ACTCCAACTCAACTGGGTCTG 59.582 52.381 0.00 0.00 34.46 3.51
3389 8050 1.417890 CTCCAACTCAACTGGGTCTGT 59.582 52.381 0.00 0.00 34.46 3.41
3422 8154 1.606224 CCATTTGGGAACAGCAACAGC 60.606 52.381 0.00 0.00 44.54 4.40
3446 8178 3.972950 ACGAGAACATGAGATCTACCG 57.027 47.619 0.00 3.95 0.00 4.02
3470 8253 4.136796 TCTGGCCATATACAACAATGAGC 58.863 43.478 5.51 0.00 0.00 4.26
3478 8261 6.145209 CCATATACAACAATGAGCGAGAGAAG 59.855 42.308 0.00 0.00 0.00 2.85
3542 8818 8.658499 TCAATCTGTATCATGATCACTTTGAG 57.342 34.615 12.53 3.48 0.00 3.02
3543 8819 7.226128 TCAATCTGTATCATGATCACTTTGAGC 59.774 37.037 12.53 0.00 32.56 4.26
3544 8820 5.045872 TCTGTATCATGATCACTTTGAGCG 58.954 41.667 12.53 0.00 35.14 5.03
3547 8823 6.337356 TGTATCATGATCACTTTGAGCGTAA 58.663 36.000 12.53 0.00 35.14 3.18
3548 8824 6.986231 TGTATCATGATCACTTTGAGCGTAAT 59.014 34.615 12.53 0.00 35.14 1.89
3563 8839 5.129815 TGAGCGTAATTAATTACACCTCCCT 59.870 40.000 29.90 19.82 42.02 4.20
3567 8843 5.763204 CGTAATTAATTACACCTCCCTGCAT 59.237 40.000 28.93 0.00 42.02 3.96
3616 8892 0.998145 AGAAGAGGCAGCCCAAATCT 59.002 50.000 8.22 0.57 0.00 2.40
3632 10152 6.976925 GCCCAAATCTATCAGAAATTGAAGTG 59.023 38.462 6.63 0.00 39.77 3.16
3647 10171 9.559958 GAAATTGAAGTGAATGAATAATGACGT 57.440 29.630 0.00 0.00 0.00 4.34
3652 10176 9.377312 TGAAGTGAATGAATAATGACGTTATCA 57.623 29.630 0.37 2.28 43.13 2.15
3689 10216 0.600255 GTAACTGCAGCACGTCCTGT 60.600 55.000 15.27 0.00 35.28 4.00
3702 10229 0.956633 GTCCTGTGGTGACGTAGACA 59.043 55.000 0.00 0.00 0.00 3.41
3798 10325 1.352083 ACCAGCAAAGCTACTCCTCA 58.648 50.000 0.00 0.00 36.40 3.86
3799 10326 1.002544 ACCAGCAAAGCTACTCCTCAC 59.997 52.381 0.00 0.00 36.40 3.51
3816 10343 1.078528 ACCCTCCGTGACCTCATCA 59.921 57.895 0.00 0.00 33.79 3.07
3820 10347 0.458543 CTCCGTGACCTCATCAACGG 60.459 60.000 6.75 6.75 45.60 4.44
3837 10370 0.737219 CGGTAAGGTGGACTACTCCG 59.263 60.000 0.00 0.00 39.88 4.63
3861 10394 0.626382 TGTCACGGAGATCTCCCTCT 59.374 55.000 31.77 14.62 46.96 3.69
3897 10430 1.802636 GTCATCCACACCAATGCCG 59.197 57.895 0.00 0.00 0.00 5.69
3909 10442 1.544093 CCAATGCCGTCATGCCTATCT 60.544 52.381 0.00 0.00 32.23 1.98
3956 10492 7.759489 TTTAATGTTTGGCAACTACTCAGAT 57.241 32.000 0.00 0.00 33.58 2.90
3958 10494 4.085357 TGTTTGGCAACTACTCAGATGT 57.915 40.909 0.00 0.00 33.58 3.06
3997 10533 4.666512 ACCAGCAACTTGTTCATCCTATT 58.333 39.130 0.00 0.00 0.00 1.73
4024 10560 2.742372 CCTTCAGGCAACGGTCCG 60.742 66.667 10.48 10.48 46.39 4.79
4026 10562 4.323477 TTCAGGCAACGGTCCGGG 62.323 66.667 17.28 8.57 46.39 5.73
4062 10598 4.728772 TGAGGATTTCATCAGTGGTTGTT 58.271 39.130 0.00 0.00 32.46 2.83
4069 10605 2.303022 TCATCAGTGGTTGTTCCTCCTC 59.697 50.000 0.00 0.00 37.07 3.71
4076 10612 1.151810 TTGTTCCTCCTCCTGCCCT 60.152 57.895 0.00 0.00 0.00 5.19
4116 10652 1.216444 GTCGAGATGGCACTGCAGA 59.784 57.895 23.35 0.00 0.00 4.26
4165 10707 1.000171 CTGCTGTCAGGCGCATATCTA 60.000 52.381 10.83 0.00 36.68 1.98
4166 10708 1.620323 TGCTGTCAGGCGCATATCTAT 59.380 47.619 10.83 0.00 34.52 1.98
4247 10789 2.355837 GAGTTGACGTCGCAGCCA 60.356 61.111 11.62 0.00 0.00 4.75
4284 10826 2.196595 CAGAGGAGGGGTGGTTTGATA 58.803 52.381 0.00 0.00 0.00 2.15
4290 10832 1.564348 AGGGGTGGTTTGATAAGCGAT 59.436 47.619 0.00 0.00 34.50 4.58
4334 10876 4.462483 GTGCAGGAGGAATCCAAAATAACA 59.538 41.667 0.61 0.00 0.00 2.41
4462 11004 3.769228 GCAAGAGCAAGAACAGCAG 57.231 52.632 0.00 0.00 41.58 4.24
4478 11020 1.893808 CAGCTGCAAACGTGGGAGT 60.894 57.895 0.00 0.00 0.00 3.85
4541 11083 1.604378 CAGCAACCCCTACCTCCAG 59.396 63.158 0.00 0.00 0.00 3.86
4565 11107 4.839121 ACGGATGCAAAGGTTAGAACATA 58.161 39.130 0.00 0.00 0.00 2.29
4596 11138 8.522542 ACGATTATAATATACTCCCTCTGTCC 57.477 38.462 0.00 0.00 0.00 4.02
4597 11139 8.337739 ACGATTATAATATACTCCCTCTGTCCT 58.662 37.037 0.00 0.00 0.00 3.85
4598 11140 8.625651 CGATTATAATATACTCCCTCTGTCCTG 58.374 40.741 0.00 0.00 0.00 3.86
4599 11141 9.702253 GATTATAATATACTCCCTCTGTCCTGA 57.298 37.037 0.00 0.00 0.00 3.86
4601 11143 9.892444 TTATAATATACTCCCTCTGTCCTGAAA 57.108 33.333 0.00 0.00 0.00 2.69
4602 11144 8.980832 ATAATATACTCCCTCTGTCCTGAAAT 57.019 34.615 0.00 0.00 0.00 2.17
4603 11145 6.678568 ATATACTCCCTCTGTCCTGAAATG 57.321 41.667 0.00 0.00 0.00 2.32
4604 11146 2.625639 ACTCCCTCTGTCCTGAAATGT 58.374 47.619 0.00 0.00 0.00 2.71
4605 11147 3.791320 ACTCCCTCTGTCCTGAAATGTA 58.209 45.455 0.00 0.00 0.00 2.29
4606 11148 4.168101 ACTCCCTCTGTCCTGAAATGTAA 58.832 43.478 0.00 0.00 0.00 2.41
4607 11149 4.223923 ACTCCCTCTGTCCTGAAATGTAAG 59.776 45.833 0.00 0.00 0.00 2.34
4608 11150 4.425772 TCCCTCTGTCCTGAAATGTAAGA 58.574 43.478 0.00 0.00 0.00 2.10
4609 11151 4.223032 TCCCTCTGTCCTGAAATGTAAGAC 59.777 45.833 0.00 0.00 0.00 3.01
4610 11152 4.177026 CCTCTGTCCTGAAATGTAAGACG 58.823 47.826 0.00 0.00 0.00 4.18
4611 11153 4.322049 CCTCTGTCCTGAAATGTAAGACGT 60.322 45.833 0.00 0.00 0.00 4.34
4612 11154 5.209818 TCTGTCCTGAAATGTAAGACGTT 57.790 39.130 0.00 0.00 0.00 3.99
4613 11155 5.607477 TCTGTCCTGAAATGTAAGACGTTT 58.393 37.500 0.00 0.00 39.79 3.60
4614 11156 6.053005 TCTGTCCTGAAATGTAAGACGTTTT 58.947 36.000 0.00 0.00 37.43 2.43
4615 11157 6.540914 TCTGTCCTGAAATGTAAGACGTTTTT 59.459 34.615 0.00 0.00 37.43 1.94
4648 11190 7.977789 TGATAGTGTTGAAAAGCATCTTACA 57.022 32.000 0.00 0.00 0.00 2.41
4649 11191 8.565896 TGATAGTGTTGAAAAGCATCTTACAT 57.434 30.769 0.00 0.00 0.00 2.29
4650 11192 9.013229 TGATAGTGTTGAAAAGCATCTTACATT 57.987 29.630 0.00 0.00 0.00 2.71
4651 11193 9.846248 GATAGTGTTGAAAAGCATCTTACATTT 57.154 29.630 0.00 0.00 0.00 2.32
4653 11195 8.356533 AGTGTTGAAAAGCATCTTACATTTTG 57.643 30.769 0.00 0.00 0.00 2.44
4654 11196 7.439056 AGTGTTGAAAAGCATCTTACATTTTGG 59.561 33.333 0.00 0.00 0.00 3.28
4655 11197 6.705381 TGTTGAAAAGCATCTTACATTTTGGG 59.295 34.615 0.00 0.00 0.00 4.12
4656 11198 6.662865 TGAAAAGCATCTTACATTTTGGGA 57.337 33.333 0.00 0.00 0.00 4.37
4657 11199 6.454795 TGAAAAGCATCTTACATTTTGGGAC 58.545 36.000 0.00 0.00 0.00 4.46
4658 11200 4.701956 AAGCATCTTACATTTTGGGACG 57.298 40.909 0.00 0.00 0.00 4.79
4659 11201 3.016736 AGCATCTTACATTTTGGGACGG 58.983 45.455 0.00 0.00 0.00 4.79
4660 11202 3.013921 GCATCTTACATTTTGGGACGGA 58.986 45.455 0.00 0.00 0.00 4.69
4661 11203 3.065371 GCATCTTACATTTTGGGACGGAG 59.935 47.826 0.00 0.00 0.00 4.63
4662 11204 3.343941 TCTTACATTTTGGGACGGAGG 57.656 47.619 0.00 0.00 0.00 4.30
4663 11205 2.026636 TCTTACATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
4664 11206 1.659022 TACATTTTGGGACGGAGGGA 58.341 50.000 0.00 0.00 0.00 4.20
4665 11207 0.328258 ACATTTTGGGACGGAGGGAG 59.672 55.000 0.00 0.00 0.00 4.30
4666 11208 0.328258 CATTTTGGGACGGAGGGAGT 59.672 55.000 0.00 0.00 0.00 3.85
4667 11209 1.557832 CATTTTGGGACGGAGGGAGTA 59.442 52.381 0.00 0.00 0.00 2.59
4668 11210 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
4669 11211 1.200519 TTTGGGACGGAGGGAGTATG 58.799 55.000 0.00 0.00 0.00 2.39
4670 11212 0.042131 TTGGGACGGAGGGAGTATGT 59.958 55.000 0.00 0.00 0.00 2.29
4671 11213 0.042131 TGGGACGGAGGGAGTATGTT 59.958 55.000 0.00 0.00 0.00 2.71
4672 11214 0.464452 GGGACGGAGGGAGTATGTTG 59.536 60.000 0.00 0.00 0.00 3.33
4673 11215 1.192428 GGACGGAGGGAGTATGTTGT 58.808 55.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
473 474 0.606604 TCGCTTCCGCTTCTAAACCT 59.393 50.000 0.00 0.00 0.00 3.50
748 756 1.467678 CGTGCTAGGGCCAGCTATCT 61.468 60.000 22.57 0.00 42.30 1.98
769 778 4.778143 CCGGTACCAGCACCTGCC 62.778 72.222 13.54 0.00 43.38 4.85
790 803 1.586154 ATAAGGTTGCGCACACTGGC 61.586 55.000 11.12 0.00 0.00 4.85
827 841 0.379669 GAACCATGCATTGCTCTCCG 59.620 55.000 10.49 0.00 0.00 4.63
856 870 2.288152 GCTTGTCTGCCTAGCTAGCTAG 60.288 54.545 35.39 35.39 44.07 3.42
857 871 1.683917 GCTTGTCTGCCTAGCTAGCTA 59.316 52.381 22.85 22.85 31.63 3.32
858 872 0.463620 GCTTGTCTGCCTAGCTAGCT 59.536 55.000 23.12 23.12 31.63 3.32
859 873 0.463620 AGCTTGTCTGCCTAGCTAGC 59.536 55.000 15.74 6.62 43.08 3.42
883 897 5.908341 TGTTGTTATATGTGCCATCGAGTA 58.092 37.500 0.00 0.00 0.00 2.59
888 902 6.919662 CCAAGATTGTTGTTATATGTGCCATC 59.080 38.462 0.00 0.00 0.00 3.51
894 908 5.837829 ACCCCCAAGATTGTTGTTATATGT 58.162 37.500 0.00 0.00 0.00 2.29
897 911 6.215841 TCACTACCCCCAAGATTGTTGTTATA 59.784 38.462 0.00 0.00 0.00 0.98
906 920 1.215423 GCCATCACTACCCCCAAGATT 59.785 52.381 0.00 0.00 0.00 2.40
943 957 1.141019 GGAGCGGCGATGTCAGTAA 59.859 57.895 12.98 0.00 0.00 2.24
945 959 3.069980 GAGGAGCGGCGATGTCAGT 62.070 63.158 12.98 0.00 0.00 3.41
1152 1167 3.209410 CATGGTAATGGAGAGGTCTTGC 58.791 50.000 0.00 0.00 0.00 4.01
1200 1218 2.292569 GCCGTCGACTATTATGTCTCCA 59.707 50.000 14.70 0.00 35.00 3.86
1203 1221 4.299155 CATTGCCGTCGACTATTATGTCT 58.701 43.478 14.70 0.00 35.00 3.41
1211 1229 0.604073 TTCACCATTGCCGTCGACTA 59.396 50.000 14.70 0.00 0.00 2.59
1266 1284 3.627577 GCTGGTTGGATGAAATCGTGTAT 59.372 43.478 0.00 0.00 46.86 2.29
1367 1385 0.806492 GGAGAGTCCATCGCCGTTTC 60.806 60.000 0.00 0.00 38.19 2.78
1388 1406 1.035385 TTCGAGTCTGGATAGCGCCA 61.035 55.000 2.29 0.00 36.30 5.69
1400 1418 2.010145 TTGTATGCCTGCTTCGAGTC 57.990 50.000 0.00 0.00 0.00 3.36
1465 1483 0.041833 AGCCTTCCTGCTACCTGAGA 59.958 55.000 0.00 0.00 40.56 3.27
1467 1485 0.615331 CAAGCCTTCCTGCTACCTGA 59.385 55.000 0.00 0.00 41.80 3.86
1468 1486 0.326264 ACAAGCCTTCCTGCTACCTG 59.674 55.000 0.00 0.00 41.80 4.00
1608 1626 4.497507 CCGTCAGTTCGTAATAGCTCATGA 60.498 45.833 0.00 0.00 0.00 3.07
1643 1661 3.463048 AGGGAACTTTCATTGCATCCT 57.537 42.857 0.00 0.00 37.44 3.24
1695 1721 2.930887 GCAGACGTTGGAGCATTCTACA 60.931 50.000 0.00 0.00 0.00 2.74
1697 1723 1.275010 TGCAGACGTTGGAGCATTCTA 59.725 47.619 0.00 0.00 31.05 2.10
1772 1798 2.280628 GATTCCCTTTGTAGCCGTCTG 58.719 52.381 0.00 0.00 0.00 3.51
1819 1845 6.006449 AGAAGGTACTACTAACAAAGACCGA 58.994 40.000 0.00 0.00 38.49 4.69
1832 1858 8.095169 TCTCAAATCAGGAAAAGAAGGTACTAC 58.905 37.037 0.00 0.00 38.49 2.73
1875 1909 6.659668 GCTAGGATTAAACAAAGAGAAACCCT 59.340 38.462 0.00 0.00 0.00 4.34
1895 1929 2.228822 AGCCGAACAAACAAATGCTAGG 59.771 45.455 0.00 0.00 0.00 3.02
1903 1937 4.633175 TCTACACATAGCCGAACAAACAA 58.367 39.130 0.00 0.00 0.00 2.83
1984 2049 0.593128 GGACACCGGCAATCATATGC 59.407 55.000 0.00 0.00 45.67 3.14
2005 2070 2.124151 ATCGCCATGGGTTCCTGC 60.124 61.111 15.13 0.00 0.00 4.85
2058 2126 6.070251 TGCTGAAATATTCCTTACCTGAGACA 60.070 38.462 0.00 0.00 0.00 3.41
2059 2127 6.349300 TGCTGAAATATTCCTTACCTGAGAC 58.651 40.000 0.00 0.00 0.00 3.36
2060 2128 6.560003 TGCTGAAATATTCCTTACCTGAGA 57.440 37.500 0.00 0.00 0.00 3.27
2061 2129 6.038714 GGTTGCTGAAATATTCCTTACCTGAG 59.961 42.308 0.00 0.00 0.00 3.35
2062 2130 5.885912 GGTTGCTGAAATATTCCTTACCTGA 59.114 40.000 0.00 0.00 0.00 3.86
2063 2131 5.888161 AGGTTGCTGAAATATTCCTTACCTG 59.112 40.000 0.00 0.00 0.00 4.00
2071 2140 8.986477 AACATAACAAGGTTGCTGAAATATTC 57.014 30.769 0.00 0.00 0.00 1.75
2078 2147 7.341445 AGTAAAAACATAACAAGGTTGCTGA 57.659 32.000 0.00 0.00 0.00 4.26
2080 2154 8.303876 CCATAGTAAAAACATAACAAGGTTGCT 58.696 33.333 0.00 0.00 0.00 3.91
2088 2162 9.184523 CTTCATCCCCATAGTAAAAACATAACA 57.815 33.333 0.00 0.00 0.00 2.41
2089 2163 9.403583 TCTTCATCCCCATAGTAAAAACATAAC 57.596 33.333 0.00 0.00 0.00 1.89
2092 2166 7.410174 TGTCTTCATCCCCATAGTAAAAACAT 58.590 34.615 0.00 0.00 0.00 2.71
2105 2179 3.968265 TCCTTCATTTGTCTTCATCCCC 58.032 45.455 0.00 0.00 0.00 4.81
2107 2181 6.151648 TGTTCATCCTTCATTTGTCTTCATCC 59.848 38.462 0.00 0.00 0.00 3.51
2115 2189 9.696917 GTTATTTCTTGTTCATCCTTCATTTGT 57.303 29.630 0.00 0.00 0.00 2.83
2138 2317 3.915711 TGATGGATGGATATGGCCTGTTA 59.084 43.478 3.32 0.00 0.00 2.41
2144 2323 4.147321 ACTTGTTGATGGATGGATATGGC 58.853 43.478 0.00 0.00 0.00 4.40
2145 2324 6.298361 TGTACTTGTTGATGGATGGATATGG 58.702 40.000 0.00 0.00 0.00 2.74
2178 2357 4.695217 ATTGAATGTATCCGCGTGTTTT 57.305 36.364 4.92 0.00 0.00 2.43
2179 2358 4.695217 AATTGAATGTATCCGCGTGTTT 57.305 36.364 4.92 0.00 0.00 2.83
2185 2364 4.151070 CGCACATAATTGAATGTATCCGC 58.849 43.478 0.00 0.00 38.01 5.54
2202 2394 1.448985 GGATCCTTTAACTGCGCACA 58.551 50.000 5.66 0.00 0.00 4.57
2206 2398 1.062587 CTTGCGGATCCTTTAACTGCG 59.937 52.381 10.75 0.00 38.56 5.18
2221 2413 2.252260 CCTTGTTGCGGTCTTGCG 59.748 61.111 0.00 0.00 37.81 4.85
2226 2458 4.043200 GGCTGCCTTGTTGCGGTC 62.043 66.667 12.43 0.00 39.88 4.79
2227 2459 4.892965 TGGCTGCCTTGTTGCGGT 62.893 61.111 21.03 0.00 39.88 5.68
2228 2460 3.604667 TTGGCTGCCTTGTTGCGG 61.605 61.111 21.03 0.00 40.70 5.69
2229 2461 1.514678 TAGTTGGCTGCCTTGTTGCG 61.515 55.000 21.03 0.00 0.00 4.85
2230 2462 0.039165 GTAGTTGGCTGCCTTGTTGC 60.039 55.000 21.03 3.03 0.00 4.17
2231 2463 0.598065 GGTAGTTGGCTGCCTTGTTG 59.402 55.000 21.03 0.00 43.14 3.33
2232 2464 0.889186 CGGTAGTTGGCTGCCTTGTT 60.889 55.000 21.03 5.57 44.10 2.83
2233 2465 1.302511 CGGTAGTTGGCTGCCTTGT 60.303 57.895 21.03 6.36 44.10 3.16
2234 2466 1.003839 TCGGTAGTTGGCTGCCTTG 60.004 57.895 21.03 1.94 44.10 3.61
2235 2467 1.296715 CTCGGTAGTTGGCTGCCTT 59.703 57.895 21.03 8.12 44.10 4.35
2236 2468 1.481056 AACTCGGTAGTTGGCTGCCT 61.481 55.000 21.03 1.67 44.40 4.75
2237 2469 1.003718 AACTCGGTAGTTGGCTGCC 60.004 57.895 12.87 12.87 44.40 4.85
2238 2470 4.695560 AACTCGGTAGTTGGCTGC 57.304 55.556 0.00 0.00 44.40 5.25
2309 2541 9.562583 TTTGTGCAATCTATTACGTTAATTTCC 57.437 29.630 0.00 0.00 0.00 3.13
2389 3653 8.911918 TTATGTTCTTGTTTTACTCCAGCTAA 57.088 30.769 0.00 0.00 0.00 3.09
2444 3710 7.015226 TGGTAATCAGTAGATTTGCGAAATG 57.985 36.000 0.00 0.00 41.64 2.32
2461 3729 5.933790 TGTAACAAAATGACGCTGGTAATC 58.066 37.500 0.00 0.00 0.00 1.75
2464 3732 5.752892 TTTGTAACAAAATGACGCTGGTA 57.247 34.783 0.00 0.00 0.00 3.25
2466 3734 7.026562 TGATATTTGTAACAAAATGACGCTGG 58.973 34.615 0.00 0.00 32.16 4.85
2486 3760 5.103043 TCTGGAGGGAGGTCTAAACTGATAT 60.103 44.000 0.00 0.00 0.00 1.63
2500 3781 3.435275 TGGATCGATATTCTGGAGGGAG 58.565 50.000 0.00 0.00 0.00 4.30
2512 3793 4.745125 GCGAATCTTCACTTTGGATCGATA 59.255 41.667 0.00 0.00 0.00 2.92
2520 3801 4.201792 CCTCTCATGCGAATCTTCACTTTG 60.202 45.833 0.00 0.00 0.00 2.77
2538 3819 8.706035 CATTTGAATGTTCATTTTCAACCTCTC 58.294 33.333 0.00 0.00 40.51 3.20
2555 4288 5.846203 AGTTGGGTCAAGAACATTTGAATG 58.154 37.500 2.29 2.29 38.69 2.67
2559 4292 8.485976 TTTTTAAGTTGGGTCAAGAACATTTG 57.514 30.769 0.00 0.00 0.00 2.32
2571 4306 3.582164 TGCCCTCATTTTTAAGTTGGGT 58.418 40.909 0.00 0.00 35.79 4.51
2608 4346 3.601443 TTGGTTTGTCAAAAGTGGTGG 57.399 42.857 0.00 0.00 0.00 4.61
2648 4386 2.354259 AGTGACAGATTTGCTAGCTGC 58.646 47.619 17.23 0.00 43.25 5.25
2653 4391 9.204570 GTTTTTCTACTAGTGACAGATTTGCTA 57.795 33.333 5.39 0.00 0.00 3.49
2656 4394 8.215132 GTCGTTTTTCTACTAGTGACAGATTTG 58.785 37.037 5.39 0.00 0.00 2.32
2658 4396 7.659186 AGTCGTTTTTCTACTAGTGACAGATT 58.341 34.615 5.39 0.00 0.00 2.40
2659 4397 7.216973 AGTCGTTTTTCTACTAGTGACAGAT 57.783 36.000 5.39 0.00 0.00 2.90
2660 4398 6.630444 AGTCGTTTTTCTACTAGTGACAGA 57.370 37.500 5.39 0.00 0.00 3.41
2661 4399 7.695869 AAAGTCGTTTTTCTACTAGTGACAG 57.304 36.000 5.39 0.00 0.00 3.51
2662 4400 9.241317 CTTAAAGTCGTTTTTCTACTAGTGACA 57.759 33.333 5.39 0.00 0.00 3.58
2663 4401 9.242477 ACTTAAAGTCGTTTTTCTACTAGTGAC 57.758 33.333 5.39 1.55 0.00 3.67
2686 4424 1.546029 GGTCCTTACGAACCGGTACTT 59.454 52.381 8.00 0.00 0.00 2.24
2763 4502 1.000060 TCGTGTTGAACCGGGACTAAG 60.000 52.381 6.32 0.00 0.00 2.18
2882 4635 3.343617 GTTTCTAGTTGTATGCAGGCCA 58.656 45.455 5.01 0.00 0.00 5.36
2909 4662 1.565759 TGCATCTTGGCCCAACTAGAT 59.434 47.619 0.00 0.00 0.00 1.98
2923 4676 2.831770 CCGTATGGGCCTGCATCT 59.168 61.111 4.53 0.00 0.00 2.90
3003 4756 2.683859 CGTGGCTACCGTGTCGAGA 61.684 63.158 0.00 0.00 0.00 4.04
3019 4772 1.153107 GGTTTATAAGCCCCGCCGT 60.153 57.895 7.10 0.00 0.00 5.68
3142 4896 2.386113 AGTCCTGGTACTAAAGGAGGGT 59.614 50.000 11.31 0.40 43.27 4.34
3143 4897 3.117552 AGTCCTGGTACTAAAGGAGGG 57.882 52.381 11.31 0.00 43.27 4.30
3144 4898 5.453480 GCATTAGTCCTGGTACTAAAGGAGG 60.453 48.000 16.98 0.00 43.27 4.30
3145 4899 5.128827 TGCATTAGTCCTGGTACTAAAGGAG 59.871 44.000 16.98 11.26 43.27 3.69
3146 4900 5.027460 TGCATTAGTCCTGGTACTAAAGGA 58.973 41.667 16.98 13.19 43.30 3.36
3158 4961 5.435686 TTTGTGACCTATGCATTAGTCCT 57.564 39.130 20.13 0.00 0.00 3.85
3161 4964 6.095440 GGTTCATTTGTGACCTATGCATTAGT 59.905 38.462 3.54 2.14 0.00 2.24
3162 4965 6.498304 GGTTCATTTGTGACCTATGCATTAG 58.502 40.000 3.54 0.00 0.00 1.73
3163 4966 5.065859 CGGTTCATTTGTGACCTATGCATTA 59.934 40.000 3.54 0.00 0.00 1.90
3165 4968 3.378112 CGGTTCATTTGTGACCTATGCAT 59.622 43.478 3.79 3.79 0.00 3.96
3166 4969 2.746904 CGGTTCATTTGTGACCTATGCA 59.253 45.455 0.00 0.00 0.00 3.96
3167 4970 2.097466 CCGGTTCATTTGTGACCTATGC 59.903 50.000 0.00 0.00 0.00 3.14
3168 4971 2.682856 CCCGGTTCATTTGTGACCTATG 59.317 50.000 0.00 0.00 0.00 2.23
3348 5166 9.793259 TTGGAGTTCTTTTGTAGTCTTGAATAT 57.207 29.630 0.00 0.00 0.00 1.28
3349 5167 9.052759 GTTGGAGTTCTTTTGTAGTCTTGAATA 57.947 33.333 0.00 0.00 0.00 1.75
3350 5168 7.775561 AGTTGGAGTTCTTTTGTAGTCTTGAAT 59.224 33.333 0.00 0.00 0.00 2.57
3353 5171 6.538742 TGAGTTGGAGTTCTTTTGTAGTCTTG 59.461 38.462 0.00 0.00 0.00 3.02
3356 8017 6.539103 AGTTGAGTTGGAGTTCTTTTGTAGTC 59.461 38.462 0.00 0.00 0.00 2.59
3358 8019 6.238484 CCAGTTGAGTTGGAGTTCTTTTGTAG 60.238 42.308 0.00 0.00 37.96 2.74
3365 8026 2.104963 GACCCAGTTGAGTTGGAGTTCT 59.895 50.000 0.00 0.00 37.96 3.01
3377 8038 1.102809 TGCTGCAACAGACCCAGTTG 61.103 55.000 0.00 0.00 46.86 3.16
3379 8040 0.395586 TTTGCTGCAACAGACCCAGT 60.396 50.000 15.72 0.00 32.44 4.00
3381 8042 1.737355 GCTTTGCTGCAACAGACCCA 61.737 55.000 15.72 0.00 32.44 4.51
3382 8043 1.006922 GCTTTGCTGCAACAGACCC 60.007 57.895 15.72 0.81 32.44 4.46
3383 8044 0.039708 GAGCTTTGCTGCAACAGACC 60.040 55.000 15.72 7.47 39.88 3.85
3384 8045 0.039708 GGAGCTTTGCTGCAACAGAC 60.040 55.000 15.72 12.05 46.16 3.51
3385 8046 2.334307 GGAGCTTTGCTGCAACAGA 58.666 52.632 15.72 0.00 46.16 3.41
3386 8047 4.959446 GGAGCTTTGCTGCAACAG 57.041 55.556 15.72 15.60 46.16 3.16
3418 8150 4.456280 TCTCATGTTCTCGTATTGCTGT 57.544 40.909 0.00 0.00 0.00 4.40
3422 8154 5.853810 CGGTAGATCTCATGTTCTCGTATTG 59.146 44.000 0.00 0.00 0.00 1.90
3446 8178 4.136796 TCATTGTTGTATATGGCCAGAGC 58.863 43.478 13.05 4.53 38.76 4.09
3543 8819 5.120399 TGCAGGGAGGTGTAATTAATTACG 58.880 41.667 25.76 14.23 44.21 3.18
3544 8820 6.770785 TGATGCAGGGAGGTGTAATTAATTAC 59.229 38.462 25.18 25.18 42.21 1.89
3547 8823 5.380043 CTGATGCAGGGAGGTGTAATTAAT 58.620 41.667 0.00 0.00 0.00 1.40
3548 8824 4.780815 CTGATGCAGGGAGGTGTAATTAA 58.219 43.478 0.00 0.00 0.00 1.40
3689 10216 1.214325 CGGCATGTCTACGTCACCA 59.786 57.895 0.00 0.00 0.00 4.17
3734 10261 1.377333 GAACCCTGGCCAGTAGCAC 60.377 63.158 30.63 14.10 46.50 4.40
3798 10325 0.544357 TTGATGAGGTCACGGAGGGT 60.544 55.000 0.00 0.00 36.32 4.34
3799 10326 0.108138 GTTGATGAGGTCACGGAGGG 60.108 60.000 0.00 0.00 36.32 4.30
3816 10343 2.174360 GGAGTAGTCCACCTTACCGTT 58.826 52.381 12.02 0.00 43.31 4.44
3837 10370 1.067821 GGAGATCTCCGTGACATGGAC 59.932 57.143 25.78 3.59 40.36 4.02
3861 10394 3.578272 GCGCACCGTGTTGTTCCA 61.578 61.111 0.30 0.00 0.00 3.53
3882 10415 0.034186 ATGACGGCATTGGTGTGGAT 60.034 50.000 0.00 0.00 0.00 3.41
3897 10430 1.002544 GCTGGGGTAGATAGGCATGAC 59.997 57.143 0.00 0.00 0.00 3.06
3909 10442 1.534476 TGGTTGAGTCGCTGGGGTA 60.534 57.895 0.00 0.00 0.00 3.69
3956 10492 0.464916 TCGATAGCGAGTAGGGCACA 60.465 55.000 0.00 0.00 42.51 4.57
3958 10494 4.892002 TCGATAGCGAGTAGGGCA 57.108 55.556 0.00 0.00 42.51 5.36
3997 10533 2.115910 CCTGAAGGTTGCAGCCCA 59.884 61.111 16.95 7.17 32.06 5.36
4032 10568 3.055328 TGATGAAATCCTCAGGGCCATA 58.945 45.455 6.18 0.00 44.73 2.74
4062 10598 2.041265 GGAAGGGCAGGAGGAGGA 59.959 66.667 0.00 0.00 0.00 3.71
4069 10605 1.672356 CTGACGTTGGAAGGGCAGG 60.672 63.158 6.99 0.00 44.17 4.85
4076 10612 0.828022 AGGTGTCACTGACGTTGGAA 59.172 50.000 2.35 0.00 34.95 3.53
4165 10707 1.747206 GCAAGCCGTTGGAGGACATAT 60.747 52.381 0.00 0.00 33.87 1.78
4166 10708 0.392461 GCAAGCCGTTGGAGGACATA 60.392 55.000 0.00 0.00 33.87 2.29
4284 10826 0.400213 TCCTTGGACAACCATCGCTT 59.600 50.000 0.00 0.00 46.34 4.68
4290 10832 0.038166 GCCATCTCCTTGGACAACCA 59.962 55.000 0.00 0.00 45.34 3.67
4430 10972 1.900016 CTTGCAGAGCTTGTGGGCA 60.900 57.895 0.00 0.00 34.17 5.36
4462 11004 0.320421 TCTACTCCCACGTTTGCAGC 60.320 55.000 0.00 0.00 0.00 5.25
4541 11083 2.396590 TCTAACCTTTGCATCCGTCC 57.603 50.000 0.00 0.00 0.00 4.79
4577 11119 8.820831 CATTTCAGGACAGAGGGAGTATATTAT 58.179 37.037 0.00 0.00 0.00 1.28
4586 11128 4.223032 GTCTTACATTTCAGGACAGAGGGA 59.777 45.833 0.00 0.00 0.00 4.20
4587 11129 4.508662 GTCTTACATTTCAGGACAGAGGG 58.491 47.826 0.00 0.00 0.00 4.30
4588 11130 4.177026 CGTCTTACATTTCAGGACAGAGG 58.823 47.826 0.00 0.00 0.00 3.69
4589 11131 4.810790 ACGTCTTACATTTCAGGACAGAG 58.189 43.478 0.00 0.00 0.00 3.35
4590 11132 4.866508 ACGTCTTACATTTCAGGACAGA 57.133 40.909 0.00 0.00 0.00 3.41
4591 11133 5.924475 AAACGTCTTACATTTCAGGACAG 57.076 39.130 0.00 0.00 0.00 3.51
4592 11134 6.687081 AAAAACGTCTTACATTTCAGGACA 57.313 33.333 0.00 0.00 0.00 4.02
4622 11164 9.665719 TGTAAGATGCTTTTCAACACTATCATA 57.334 29.630 0.00 0.00 0.00 2.15
4623 11165 8.565896 TGTAAGATGCTTTTCAACACTATCAT 57.434 30.769 0.00 0.00 0.00 2.45
4624 11166 7.977789 TGTAAGATGCTTTTCAACACTATCA 57.022 32.000 0.00 0.00 0.00 2.15
4625 11167 9.846248 AAATGTAAGATGCTTTTCAACACTATC 57.154 29.630 0.00 0.00 0.00 2.08
4627 11169 9.462174 CAAAATGTAAGATGCTTTTCAACACTA 57.538 29.630 0.00 0.00 0.00 2.74
4628 11170 7.439056 CCAAAATGTAAGATGCTTTTCAACACT 59.561 33.333 0.00 0.00 0.00 3.55
4629 11171 7.307337 CCCAAAATGTAAGATGCTTTTCAACAC 60.307 37.037 0.00 0.00 0.00 3.32
4630 11172 6.705381 CCCAAAATGTAAGATGCTTTTCAACA 59.295 34.615 0.00 0.00 0.00 3.33
4631 11173 6.928492 TCCCAAAATGTAAGATGCTTTTCAAC 59.072 34.615 0.00 0.00 0.00 3.18
4632 11174 6.928492 GTCCCAAAATGTAAGATGCTTTTCAA 59.072 34.615 0.00 0.00 0.00 2.69
4633 11175 6.454795 GTCCCAAAATGTAAGATGCTTTTCA 58.545 36.000 0.00 0.00 0.00 2.69
4634 11176 5.572896 CGTCCCAAAATGTAAGATGCTTTTC 59.427 40.000 0.00 0.00 0.00 2.29
4635 11177 5.469479 CGTCCCAAAATGTAAGATGCTTTT 58.531 37.500 0.00 0.00 0.00 2.27
4636 11178 4.082245 CCGTCCCAAAATGTAAGATGCTTT 60.082 41.667 0.00 0.00 0.00 3.51
4637 11179 3.443681 CCGTCCCAAAATGTAAGATGCTT 59.556 43.478 0.00 0.00 0.00 3.91
4638 11180 3.016736 CCGTCCCAAAATGTAAGATGCT 58.983 45.455 0.00 0.00 0.00 3.79
4639 11181 3.013921 TCCGTCCCAAAATGTAAGATGC 58.986 45.455 0.00 0.00 0.00 3.91
4640 11182 3.627577 CCTCCGTCCCAAAATGTAAGATG 59.372 47.826 0.00 0.00 0.00 2.90
4641 11183 3.371595 CCCTCCGTCCCAAAATGTAAGAT 60.372 47.826 0.00 0.00 0.00 2.40
4642 11184 2.026636 CCCTCCGTCCCAAAATGTAAGA 60.027 50.000 0.00 0.00 0.00 2.10
4643 11185 2.026636 TCCCTCCGTCCCAAAATGTAAG 60.027 50.000 0.00 0.00 0.00 2.34
4644 11186 1.986631 TCCCTCCGTCCCAAAATGTAA 59.013 47.619 0.00 0.00 0.00 2.41
4645 11187 1.557832 CTCCCTCCGTCCCAAAATGTA 59.442 52.381 0.00 0.00 0.00 2.29
4646 11188 0.328258 CTCCCTCCGTCCCAAAATGT 59.672 55.000 0.00 0.00 0.00 2.71
4647 11189 0.328258 ACTCCCTCCGTCCCAAAATG 59.672 55.000 0.00 0.00 0.00 2.32
4648 11190 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4649 11191 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
4650 11192 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
4651 11193 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
4652 11194 0.042131 AACATACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
4653 11195 0.464452 CAACATACTCCCTCCGTCCC 59.536 60.000 0.00 0.00 0.00 4.46
4654 11196 1.192428 ACAACATACTCCCTCCGTCC 58.808 55.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.