Multiple sequence alignment - TraesCS4B01G252100

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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 TraesCS4B01G252100 chr4B 100.000 6225 0 0 1 6225 518094269 518100493 0.000000e+00 11496.0
1 TraesCS4B01G252100 chr4B 83.956 1365 197 16 3865 5218 19736659 19738012 0.000000e+00 1288.0
2 TraesCS4B01G252100 chr4B 79.835 1334 239 21 3874 5195 69378936 69380251 0.000000e+00 946.0
3 TraesCS4B01G252100 chr4B 90.660 621 56 2 5604 6223 622626747 622626128 0.000000e+00 824.0
4 TraesCS4B01G252100 chr4B 85.421 535 78 0 3208 3742 19736101 19736635 1.960000e-154 556.0
5 TraesCS4B01G252100 chr4B 84.946 465 67 2 3207 3668 69378047 69378511 9.450000e-128 468.0
6 TraesCS4B01G252100 chr4B 83.284 341 45 9 1079 1416 19735565 19735896 2.820000e-78 303.0
7 TraesCS4B01G252100 chr4B 83.113 302 47 4 1115 1414 69375913 69376212 7.950000e-69 272.0
8 TraesCS4B01G252100 chr4D 95.184 2886 95 18 2749 5607 420941705 420944573 0.000000e+00 4519.0
9 TraesCS4B01G252100 chr4D 93.867 1810 62 15 1 1804 420938985 420940751 0.000000e+00 2682.0
10 TraesCS4B01G252100 chr4D 84.359 1381 192 17 3858 5226 10250851 10252219 0.000000e+00 1332.0
11 TraesCS4B01G252100 chr4D 80.515 1360 231 25 3874 5219 47535711 47534372 0.000000e+00 1013.0
12 TraesCS4B01G252100 chr4D 92.640 394 18 5 2121 2504 420941087 420941479 1.960000e-154 556.0
13 TraesCS4B01G252100 chr4D 84.926 544 77 5 3201 3742 10250294 10250834 4.240000e-151 545.0
14 TraesCS4B01G252100 chr4D 84.731 465 68 2 3207 3668 47536520 47536056 4.400000e-126 462.0
15 TraesCS4B01G252100 chr4D 86.713 286 35 3 1132 1416 10249561 10249844 1.300000e-81 315.0
16 TraesCS4B01G252100 chr4A 93.699 2714 97 29 2749 5413 43234218 43231530 0.000000e+00 3997.0
17 TraesCS4B01G252100 chr4A 89.577 1842 82 33 1 1807 43236832 43235066 0.000000e+00 2237.0
18 TraesCS4B01G252100 chr4A 83.760 1367 202 15 3871 5227 593356264 593354908 0.000000e+00 1277.0
19 TraesCS4B01G252100 chr4A 79.559 1360 244 24 3874 5219 550482508 550481169 0.000000e+00 941.0
20 TraesCS4B01G252100 chr4A 83.865 564 88 3 3201 3763 593356834 593356273 9.190000e-148 534.0
21 TraesCS4B01G252100 chr4A 84.861 469 67 3 3204 3668 550483264 550482796 2.630000e-128 470.0
22 TraesCS4B01G252100 chr4A 88.312 385 31 7 2124 2504 43234789 43234415 3.420000e-122 449.0
23 TraesCS4B01G252100 chr4A 87.629 291 33 3 1136 1425 593357385 593357097 1.000000e-87 335.0
24 TraesCS4B01G252100 chr4A 81.788 302 51 4 1119 1418 550487281 550486982 3.730000e-62 250.0
25 TraesCS4B01G252100 chr4A 90.052 191 9 7 5414 5604 42836827 42837007 8.060000e-59 239.0
26 TraesCS4B01G252100 chr4A 86.486 74 10 0 2042 2115 665959843 665959916 1.440000e-11 82.4
27 TraesCS4B01G252100 chr3B 92.937 623 42 2 5605 6225 632616874 632616252 0.000000e+00 905.0
28 TraesCS4B01G252100 chr3B 81.443 194 28 3 4094 4280 104157461 104157653 1.080000e-32 152.0
29 TraesCS4B01G252100 chr3B 89.655 87 7 2 2643 2729 199529383 199529299 6.600000e-20 110.0
30 TraesCS4B01G252100 chr3B 88.506 87 8 2 2643 2729 741580536 741580452 3.070000e-18 104.0
31 TraesCS4B01G252100 chr5B 92.869 617 38 2 5604 6219 222751883 222751272 0.000000e+00 891.0
32 TraesCS4B01G252100 chr5B 87.342 79 9 1 2041 2118 315833281 315833203 8.600000e-14 89.8
33 TraesCS4B01G252100 chr1D 92.110 621 48 1 5604 6223 452859413 452858793 0.000000e+00 874.0
34 TraesCS4B01G252100 chr1D 87.521 601 73 2 5604 6203 193684239 193683640 0.000000e+00 693.0
35 TraesCS4B01G252100 chr1D 88.421 95 8 3 2635 2729 448689888 448689979 1.830000e-20 111.0
36 TraesCS4B01G252100 chr5A 89.338 619 62 4 5604 6220 480781140 480781756 0.000000e+00 774.0
37 TraesCS4B01G252100 chr7D 87.000 600 78 0 5604 6203 91059037 91058438 0.000000e+00 676.0
38 TraesCS4B01G252100 chr7D 88.506 87 8 2 2643 2729 70056257 70056341 3.070000e-18 104.0
39 TraesCS4B01G252100 chr3D 86.107 619 81 5 5604 6220 121944037 121944652 0.000000e+00 662.0
40 TraesCS4B01G252100 chr6A 85.737 624 83 6 5600 6220 267447461 267448081 0.000000e+00 654.0
41 TraesCS4B01G252100 chr6D 76.054 593 124 16 4630 5216 389370151 389370731 6.100000e-75 292.0
42 TraesCS4B01G252100 chr6D 71.630 779 206 13 3856 4628 389369297 389370066 3.810000e-47 200.0
43 TraesCS4B01G252100 chr6D 89.011 91 8 2 2643 2733 464854695 464854607 1.830000e-20 111.0
44 TraesCS4B01G252100 chr6B 71.483 782 197 19 3859 4628 582400057 582400824 1.070000e-42 185.0
45 TraesCS4B01G252100 chr6B 84.211 76 11 1 2041 2115 34258300 34258375 8.660000e-09 73.1
46 TraesCS4B01G252100 chr2B 84.667 150 18 3 3221 3369 748723219 748723364 1.810000e-30 145.0
47 TraesCS4B01G252100 chr2B 84.314 102 11 5 2639 2740 454012372 454012468 1.850000e-15 95.3
48 TraesCS4B01G252100 chr2B 85.526 76 10 1 2041 2115 4647211 4647286 1.860000e-10 78.7
49 TraesCS4B01G252100 chr1A 88.298 94 8 3 2636 2729 394590634 394590544 6.600000e-20 110.0
50 TraesCS4B01G252100 chr2D 88.636 88 8 2 2642 2729 649753729 649753814 8.530000e-19 106.0
51 TraesCS4B01G252100 chr2D 85.294 102 10 5 2639 2740 383553797 383553893 3.970000e-17 100.0
52 TraesCS4B01G252100 chr7A 91.935 62 5 0 2055 2116 594413654 594413593 3.090000e-13 87.9
53 TraesCS4B01G252100 chr1B 86.842 76 9 1 2041 2115 532713709 532713784 4.000000e-12 84.2
54 TraesCS4B01G252100 chr1B 83.544 79 12 1 2041 2118 472167854 472167776 8.660000e-09 73.1
55 TraesCS4B01G252100 chr7B 86.957 69 8 1 2047 2115 220123481 220123548 6.690000e-10 76.8
56 TraesCS4B01G252100 chr7B 83.544 79 12 1 2041 2118 88941935 88941857 8.660000e-09 73.1


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 TraesCS4B01G252100 chr4B 518094269 518100493 6224 False 11496.000000 11496 100.000000 1 6225 1 chr4B.!!$F1 6224
1 TraesCS4B01G252100 chr4B 622626128 622626747 619 True 824.000000 824 90.660000 5604 6223 1 chr4B.!!$R1 619
2 TraesCS4B01G252100 chr4B 19735565 19738012 2447 False 715.666667 1288 84.220333 1079 5218 3 chr4B.!!$F2 4139
3 TraesCS4B01G252100 chr4B 69375913 69380251 4338 False 562.000000 946 82.631333 1115 5195 3 chr4B.!!$F3 4080
4 TraesCS4B01G252100 chr4D 420938985 420944573 5588 False 2585.666667 4519 93.897000 1 5607 3 chr4D.!!$F2 5606
5 TraesCS4B01G252100 chr4D 47534372 47536520 2148 True 737.500000 1013 82.623000 3207 5219 2 chr4D.!!$R1 2012
6 TraesCS4B01G252100 chr4D 10249561 10252219 2658 False 730.666667 1332 85.332667 1132 5226 3 chr4D.!!$F1 4094
7 TraesCS4B01G252100 chr4A 43231530 43236832 5302 True 2227.666667 3997 90.529333 1 5413 3 chr4A.!!$R1 5412
8 TraesCS4B01G252100 chr4A 593354908 593357385 2477 True 715.333333 1277 85.084667 1136 5227 3 chr4A.!!$R3 4091
9 TraesCS4B01G252100 chr4A 550481169 550487281 6112 True 553.666667 941 82.069333 1119 5219 3 chr4A.!!$R2 4100
10 TraesCS4B01G252100 chr3B 632616252 632616874 622 True 905.000000 905 92.937000 5605 6225 1 chr3B.!!$R2 620
11 TraesCS4B01G252100 chr5B 222751272 222751883 611 True 891.000000 891 92.869000 5604 6219 1 chr5B.!!$R1 615
12 TraesCS4B01G252100 chr1D 452858793 452859413 620 True 874.000000 874 92.110000 5604 6223 1 chr1D.!!$R2 619
13 TraesCS4B01G252100 chr1D 193683640 193684239 599 True 693.000000 693 87.521000 5604 6203 1 chr1D.!!$R1 599
14 TraesCS4B01G252100 chr5A 480781140 480781756 616 False 774.000000 774 89.338000 5604 6220 1 chr5A.!!$F1 616
15 TraesCS4B01G252100 chr7D 91058438 91059037 599 True 676.000000 676 87.000000 5604 6203 1 chr7D.!!$R1 599
16 TraesCS4B01G252100 chr3D 121944037 121944652 615 False 662.000000 662 86.107000 5604 6220 1 chr3D.!!$F1 616
17 TraesCS4B01G252100 chr6A 267447461 267448081 620 False 654.000000 654 85.737000 5600 6220 1 chr6A.!!$F1 620
18 TraesCS4B01G252100 chr6D 389369297 389370731 1434 False 246.000000 292 73.842000 3856 5216 2 chr6D.!!$F1 1360

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
597 618 0.031111 TCCGTCCTCTTGATCCCCAT 60.031 55.000 0.00 0.0 0.00 4.00 F
599 620 0.032678 CGTCCTCTTGATCCCCATCG 59.967 60.000 0.00 0.0 0.00 3.84 F
2059 3719 0.031515 TCCCCTGTCCCGTCATGTAT 60.032 55.000 0.00 0.0 0.00 2.29 F
2491 4164 0.323087 GGCCGGCCCCGATATTAATT 60.323 55.000 36.64 0.0 42.83 1.40 F
2730 4403 0.702902 TGGGACGAGAAGGGAGTAGT 59.297 55.000 0.00 0.0 0.00 2.73 F
3121 6544 1.226745 CGCGTGTACCGGAAGCATA 60.227 57.895 9.46 0.0 36.94 3.14 F
4618 8421 0.397816 CCAGGGTCCTCTTCGGAGAT 60.398 60.000 0.00 0.0 44.20 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 2935 0.036306 AGTTGGTCCGGCTTAACCAG 59.964 55.000 12.13 0.0 45.84 4.00 R
2164 3824 0.320374 CTGTCCTGCCACTACGGAAA 59.680 55.000 0.00 0.0 36.56 3.13 R
3532 6983 0.603707 CCTCCACGCAGCTCTTGAAA 60.604 55.000 0.00 0.0 0.00 2.69 R
4201 8004 0.393808 GAGGGCCGAAGTAATTGCCA 60.394 55.000 6.60 0.0 45.83 4.92 R
4337 8140 2.874648 TAGTCCGACGAGGCCGCTAA 62.875 60.000 4.53 0.0 40.77 3.09 R
4829 8715 1.126846 CAGATTCGTGTTCGGTGCTTC 59.873 52.381 0.00 0.0 37.69 3.86 R
5704 9606 1.018148 GACGATCTCGGAGAAGCTGA 58.982 55.000 12.40 0.0 44.95 4.26 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 1.208052 CCACTACCACCACCAGATGAG 59.792 57.143 0.00 0.00 0.00 2.90
114 116 1.079819 CCGACGAGAACACAGGCAT 60.080 57.895 0.00 0.00 0.00 4.40
115 117 0.172578 CCGACGAGAACACAGGCATA 59.827 55.000 0.00 0.00 0.00 3.14
181 187 4.640855 ACGTGGCGTGTGACCTCG 62.641 66.667 3.00 3.00 46.68 4.63
245 251 5.363868 CCATCCTACAAGTCTATCTTCCACA 59.636 44.000 0.00 0.00 33.63 4.17
305 311 0.097674 CTGCATGCTACCGCTCAAAC 59.902 55.000 20.33 0.00 36.97 2.93
330 336 1.820519 TGGCATGATCTCCTTTGTTGC 59.179 47.619 0.00 0.00 0.00 4.17
391 397 0.830648 TCGTTTATCTGCTCAGGGGG 59.169 55.000 0.00 0.00 0.00 5.40
453 459 1.065273 ACGGACGATATGACACCGC 59.935 57.895 0.00 0.00 46.18 5.68
552 569 8.794335 AGCTTAGAAAGAATTAAACCTAGGTG 57.206 34.615 17.14 0.00 0.00 4.00
553 570 8.383947 AGCTTAGAAAGAATTAAACCTAGGTGT 58.616 33.333 17.14 13.50 0.00 4.16
596 617 0.976073 GTCCGTCCTCTTGATCCCCA 60.976 60.000 0.00 0.00 0.00 4.96
597 618 0.031111 TCCGTCCTCTTGATCCCCAT 60.031 55.000 0.00 0.00 0.00 4.00
598 619 0.394565 CCGTCCTCTTGATCCCCATC 59.605 60.000 0.00 0.00 0.00 3.51
599 620 0.032678 CGTCCTCTTGATCCCCATCG 59.967 60.000 0.00 0.00 0.00 3.84
693 714 3.427233 GCAGTCATGTCCAAGAATCTTGC 60.427 47.826 17.03 5.66 0.00 4.01
728 749 4.485024 TCGATCGAACCTAGCTACATTC 57.515 45.455 16.99 0.00 0.00 2.67
753 776 0.179200 CATGGCAACGGAAAGTACGC 60.179 55.000 0.00 0.00 42.51 4.42
888 911 5.841957 AATAGGTTAATGCCAGCTTTCTG 57.158 39.130 0.00 0.00 40.02 3.02
901 924 5.192327 CAGCTTTCTGGTTTCAACAAGAT 57.808 39.130 0.00 0.00 38.70 2.40
903 926 4.023707 AGCTTTCTGGTTTCAACAAGATCG 60.024 41.667 0.00 0.00 38.70 3.69
904 927 3.896648 TTCTGGTTTCAACAAGATCGC 57.103 42.857 0.00 0.00 38.70 4.58
910 933 0.250684 TTCAACAAGATCGCTGGCCA 60.251 50.000 4.71 4.71 0.00 5.36
961 984 1.271652 TGAGCTTCTCTCACGTCCTCT 60.272 52.381 0.00 0.00 46.34 3.69
1281 1304 3.637273 AAGTGGTGGTCGGAGGGC 61.637 66.667 0.00 0.00 0.00 5.19
1445 1468 3.760035 CACCTCCACTCGACGGGG 61.760 72.222 0.00 0.00 0.00 5.73
1456 1479 3.407967 GACGGGGAGATGGGCCAA 61.408 66.667 11.89 0.00 0.00 4.52
1457 1480 3.406595 GACGGGGAGATGGGCCAAG 62.407 68.421 11.89 0.00 0.00 3.61
1459 1482 3.825623 GGGGAGATGGGCCAAGGG 61.826 72.222 11.89 0.00 0.00 3.95
1460 1483 3.825623 GGGAGATGGGCCAAGGGG 61.826 72.222 11.89 0.00 37.18 4.79
1520 1648 3.006728 GATGGGGTGTGGGACGGA 61.007 66.667 0.00 0.00 0.00 4.69
1522 1650 2.814913 GATGGGGTGTGGGACGGAAC 62.815 65.000 0.00 0.00 0.00 3.62
1579 2195 2.335011 CACACCAGTCGTCGAGCA 59.665 61.111 0.00 0.00 0.00 4.26
1592 2208 1.065701 GTCGAGCATACATCGTGGTCT 59.934 52.381 0.00 0.00 40.84 3.85
1670 2286 2.503356 GGAAGGACACTCTGATGGTGAT 59.497 50.000 4.29 0.00 38.01 3.06
1671 2287 3.529533 GAAGGACACTCTGATGGTGATG 58.470 50.000 4.29 0.00 38.01 3.07
1709 2935 2.262915 CAGGTGCACCTCCTCGTC 59.737 66.667 35.79 6.38 46.65 4.20
1807 3226 0.108329 ATTTGATCGGTTCGGACGCT 60.108 50.000 0.00 0.00 0.00 5.07
1808 3227 0.320073 TTTGATCGGTTCGGACGCTT 60.320 50.000 0.00 0.00 0.00 4.68
1809 3228 0.320073 TTGATCGGTTCGGACGCTTT 60.320 50.000 0.00 0.00 0.00 3.51
1811 3230 1.135527 TGATCGGTTCGGACGCTTTAT 59.864 47.619 0.00 0.00 0.00 1.40
1812 3231 2.199236 GATCGGTTCGGACGCTTTATT 58.801 47.619 0.00 0.00 0.00 1.40
1813 3232 2.083167 TCGGTTCGGACGCTTTATTT 57.917 45.000 0.00 0.00 0.00 1.40
1814 3233 2.415776 TCGGTTCGGACGCTTTATTTT 58.584 42.857 0.00 0.00 0.00 1.82
1821 3314 7.441864 GGTTCGGACGCTTTATTTTTAAAATG 58.558 34.615 12.62 0.00 0.00 2.32
1881 3379 9.730420 TGCTAAATTAAAGTGAAAGTTTGTCTC 57.270 29.630 0.00 0.00 40.30 3.36
1882 3380 9.181805 GCTAAATTAAAGTGAAAGTTTGTCTCC 57.818 33.333 0.00 0.00 40.30 3.71
1884 3382 5.744666 TTAAAGTGAAAGTTTGTCTCCCG 57.255 39.130 0.00 0.00 40.30 5.14
1885 3383 1.594331 AGTGAAAGTTTGTCTCCCGC 58.406 50.000 0.00 0.00 0.00 6.13
1886 3384 1.141053 AGTGAAAGTTTGTCTCCCGCT 59.859 47.619 0.00 0.00 0.00 5.52
1887 3385 1.947456 GTGAAAGTTTGTCTCCCGCTT 59.053 47.619 0.00 0.00 0.00 4.68
1888 3386 2.357952 GTGAAAGTTTGTCTCCCGCTTT 59.642 45.455 0.00 0.00 32.81 3.51
1889 3387 3.020984 TGAAAGTTTGTCTCCCGCTTTT 58.979 40.909 0.00 0.00 30.64 2.27
1890 3388 3.445805 TGAAAGTTTGTCTCCCGCTTTTT 59.554 39.130 0.00 0.00 30.64 1.94
1930 3428 7.120726 ACCTGCTTTGAAAGTTTATAAGCGTAT 59.879 33.333 20.49 0.00 43.04 3.06
1958 3456 7.976135 AAATTGGCAAAGCATGTGTAAAATA 57.024 28.000 3.01 0.00 0.00 1.40
2051 3711 4.410400 GCAAGGTCCCCTGTCCCG 62.410 72.222 0.00 0.00 32.13 5.14
2056 3716 2.584608 GTCCCCTGTCCCGTCATG 59.415 66.667 0.00 0.00 0.00 3.07
2059 3719 0.031515 TCCCCTGTCCCGTCATGTAT 60.032 55.000 0.00 0.00 0.00 2.29
2114 3774 8.425577 AAAACGTCTTACATTATGAGATGGAG 57.574 34.615 0.00 0.00 34.85 3.86
2115 3775 6.961360 ACGTCTTACATTATGAGATGGAGA 57.039 37.500 0.00 0.00 34.85 3.71
2116 3776 6.976088 ACGTCTTACATTATGAGATGGAGAG 58.024 40.000 0.00 0.00 34.85 3.20
2117 3777 6.773200 ACGTCTTACATTATGAGATGGAGAGA 59.227 38.462 0.00 0.00 34.85 3.10
2119 3779 7.593273 CGTCTTACATTATGAGATGGAGAGAAC 59.407 40.741 0.00 0.00 29.72 3.01
2141 3801 4.081586 ACAGTTAGCTACTTAAGGCTCCAC 60.082 45.833 9.21 8.16 39.65 4.02
2160 3820 4.141344 TCCACCAATTAACCCATACTAGCC 60.141 45.833 0.00 0.00 0.00 3.93
2164 3824 5.103686 ACCAATTAACCCATACTAGCCACAT 60.104 40.000 0.00 0.00 0.00 3.21
2249 3909 4.517285 AGTAACATGATTGCACTACAGGG 58.483 43.478 0.00 0.00 0.00 4.45
2280 3940 4.305769 GTGTGCAGCAAATTGGTTCATTA 58.694 39.130 0.00 0.00 0.00 1.90
2333 3993 1.131126 GCGAGCAAACATGCATGTAGT 59.869 47.619 31.55 19.88 40.80 2.73
2338 3998 4.588899 AGCAAACATGCATGTAGTCCTAA 58.411 39.130 31.55 0.00 40.80 2.69
2346 4006 3.196901 TGCATGTAGTCCTAAACGTCCAT 59.803 43.478 0.00 0.00 0.00 3.41
2400 4065 0.817654 GTTTATTCCTGTGCTGGCCC 59.182 55.000 0.00 0.00 0.00 5.80
2424 4089 2.467880 CTAGAGTGTACCCACCACCAT 58.532 52.381 0.00 0.00 42.88 3.55
2454 4123 0.464452 GCGTCCTTGGTGGTAGCTAT 59.536 55.000 0.00 0.00 36.76 2.97
2466 4139 0.880718 GTAGCTATGGGGCGTTGCTC 60.881 60.000 0.00 0.00 33.93 4.26
2467 4140 1.334384 TAGCTATGGGGCGTTGCTCA 61.334 55.000 0.00 0.00 33.93 4.26
2491 4164 0.323087 GGCCGGCCCCGATATTAATT 60.323 55.000 36.64 0.00 42.83 1.40
2500 4173 6.257193 CGGCCCCGATATTAATTAGTGATAAC 59.743 42.308 0.00 0.00 42.83 1.89
2504 4177 8.248945 CCCCGATATTAATTAGTGATAACGTCT 58.751 37.037 0.00 0.00 0.00 4.18
2505 4178 9.635520 CCCGATATTAATTAGTGATAACGTCTT 57.364 33.333 0.00 0.00 0.00 3.01
2518 4191 9.684448 AGTGATAACGTCTTATCTTATGTGATG 57.316 33.333 8.36 0.00 39.34 3.07
2519 4192 8.916654 GTGATAACGTCTTATCTTATGTGATGG 58.083 37.037 8.36 0.00 39.34 3.51
2520 4193 8.088365 TGATAACGTCTTATCTTATGTGATGGG 58.912 37.037 8.36 0.00 39.34 4.00
2521 4194 5.215252 ACGTCTTATCTTATGTGATGGGG 57.785 43.478 0.00 0.00 0.00 4.96
2534 4207 8.792830 TTATGTGATGGGGTACTACTTAATCT 57.207 34.615 0.00 0.00 0.00 2.40
2536 4209 5.163343 TGTGATGGGGTACTACTTAATCTGC 60.163 44.000 0.00 0.00 0.00 4.26
2537 4210 5.070580 GTGATGGGGTACTACTTAATCTGCT 59.929 44.000 0.00 0.00 0.00 4.24
2538 4211 6.267014 GTGATGGGGTACTACTTAATCTGCTA 59.733 42.308 0.00 0.00 0.00 3.49
2539 4212 7.016914 TGATGGGGTACTACTTAATCTGCTAT 58.983 38.462 0.00 0.00 0.00 2.97
2541 4214 9.203163 GATGGGGTACTACTTAATCTGCTATAT 57.797 37.037 0.00 0.00 0.00 0.86
2555 4228 8.864069 AATCTGCTATATATGTTGTAGATCGC 57.136 34.615 12.70 0.00 32.32 4.58
2556 4229 7.631717 TCTGCTATATATGTTGTAGATCGCT 57.368 36.000 0.00 0.00 0.00 4.93
2557 4230 7.698628 TCTGCTATATATGTTGTAGATCGCTC 58.301 38.462 0.00 0.00 0.00 5.03
2560 4233 5.899120 ATATATGTTGTAGATCGCTCCGT 57.101 39.130 0.00 0.00 0.00 4.69
2561 4234 2.961526 ATGTTGTAGATCGCTCCGTT 57.038 45.000 0.00 0.00 0.00 4.44
2562 4235 1.990799 TGTTGTAGATCGCTCCGTTG 58.009 50.000 0.00 0.00 0.00 4.10
2563 4236 1.278238 GTTGTAGATCGCTCCGTTGG 58.722 55.000 0.00 0.00 0.00 3.77
2565 4238 1.399714 TGTAGATCGCTCCGTTGGAT 58.600 50.000 0.00 0.00 0.00 3.41
2566 4239 1.337071 TGTAGATCGCTCCGTTGGATC 59.663 52.381 0.00 0.00 37.44 3.36
2568 4241 1.982660 AGATCGCTCCGTTGGATCTA 58.017 50.000 1.19 0.00 43.69 1.98
2571 4244 1.982660 TCGCTCCGTTGGATCTAGAT 58.017 50.000 4.47 4.47 0.00 1.98
2576 4249 4.192317 GCTCCGTTGGATCTAGATTGTTT 58.808 43.478 6.70 0.00 0.00 2.83
2577 4250 4.034510 GCTCCGTTGGATCTAGATTGTTTG 59.965 45.833 6.70 0.00 0.00 2.93
2578 4251 4.513442 TCCGTTGGATCTAGATTGTTTGG 58.487 43.478 6.70 7.23 0.00 3.28
2581 4254 4.032900 CGTTGGATCTAGATTGTTTGGTCG 59.967 45.833 6.70 1.59 0.00 4.79
2582 4255 4.137116 TGGATCTAGATTGTTTGGTCGG 57.863 45.455 6.70 0.00 0.00 4.79
2584 4257 4.120589 GGATCTAGATTGTTTGGTCGGTC 58.879 47.826 6.70 0.00 0.00 4.79
2587 4260 2.631160 AGATTGTTTGGTCGGTCACA 57.369 45.000 0.00 0.00 0.00 3.58
2588 4261 3.140325 AGATTGTTTGGTCGGTCACAT 57.860 42.857 0.00 0.00 0.00 3.21
2589 4262 2.813754 AGATTGTTTGGTCGGTCACATG 59.186 45.455 0.00 0.00 0.00 3.21
2593 4266 1.673920 GTTTGGTCGGTCACATGTTGT 59.326 47.619 0.00 0.00 0.00 3.32
2607 4280 6.888747 CACATGTTGTGTACGATGTTTTAC 57.111 37.500 0.00 0.00 43.08 2.01
2610 4283 8.440059 CACATGTTGTGTACGATGTTTTACTAT 58.560 33.333 0.00 0.00 43.08 2.12
2611 4284 9.642327 ACATGTTGTGTACGATGTTTTACTATA 57.358 29.630 0.00 0.00 39.91 1.31
2657 4330 9.765295 GTTTAACTATATACTCCCTCCATCCTA 57.235 37.037 0.00 0.00 0.00 2.94
2658 4331 9.765295 TTTAACTATATACTCCCTCCATCCTAC 57.235 37.037 0.00 0.00 0.00 3.18
2659 4332 6.989709 ACTATATACTCCCTCCATCCTACA 57.010 41.667 0.00 0.00 0.00 2.74
2660 4333 7.358255 ACTATATACTCCCTCCATCCTACAA 57.642 40.000 0.00 0.00 0.00 2.41
2661 4334 7.956357 ACTATATACTCCCTCCATCCTACAAT 58.044 38.462 0.00 0.00 0.00 2.71
2662 4335 9.081508 ACTATATACTCCCTCCATCCTACAATA 57.918 37.037 0.00 0.00 0.00 1.90
2667 4340 7.947782 ACTCCCTCCATCCTACAATATTAAA 57.052 36.000 0.00 0.00 0.00 1.52
2669 4342 8.218488 ACTCCCTCCATCCTACAATATTAAAAC 58.782 37.037 0.00 0.00 0.00 2.43
2670 4343 7.221450 TCCCTCCATCCTACAATATTAAAACG 58.779 38.462 0.00 0.00 0.00 3.60
2671 4344 6.996282 CCCTCCATCCTACAATATTAAAACGT 59.004 38.462 0.00 0.00 0.00 3.99
2672 4345 7.501225 CCCTCCATCCTACAATATTAAAACGTT 59.499 37.037 0.00 0.00 0.00 3.99
2673 4346 8.899771 CCTCCATCCTACAATATTAAAACGTTT 58.100 33.333 7.96 7.96 0.00 3.60
2714 4387 9.750125 GCTTGAAAAAGGTTCTTATATTATGGG 57.250 33.333 0.00 0.00 0.00 4.00
2719 4392 8.904099 AAAAGGTTCTTATATTATGGGACGAG 57.096 34.615 0.00 0.00 0.00 4.18
2720 4393 7.850935 AAGGTTCTTATATTATGGGACGAGA 57.149 36.000 0.00 0.00 0.00 4.04
2721 4394 7.850935 AGGTTCTTATATTATGGGACGAGAA 57.149 36.000 0.00 0.00 0.00 2.87
2724 4397 6.852420 TCTTATATTATGGGACGAGAAGGG 57.148 41.667 0.00 0.00 0.00 3.95
2725 4398 6.558498 TCTTATATTATGGGACGAGAAGGGA 58.442 40.000 0.00 0.00 0.00 4.20
2726 4399 6.663953 TCTTATATTATGGGACGAGAAGGGAG 59.336 42.308 0.00 0.00 0.00 4.30
2727 4400 2.544844 TTATGGGACGAGAAGGGAGT 57.455 50.000 0.00 0.00 0.00 3.85
2728 4401 3.675348 TTATGGGACGAGAAGGGAGTA 57.325 47.619 0.00 0.00 0.00 2.59
2729 4402 2.074729 ATGGGACGAGAAGGGAGTAG 57.925 55.000 0.00 0.00 0.00 2.57
2730 4403 0.702902 TGGGACGAGAAGGGAGTAGT 59.297 55.000 0.00 0.00 0.00 2.73
2732 4405 1.477295 GGGACGAGAAGGGAGTAGTTG 59.523 57.143 0.00 0.00 0.00 3.16
2733 4406 2.169330 GGACGAGAAGGGAGTAGTTGT 58.831 52.381 0.00 0.00 0.00 3.32
2734 4407 2.164017 GGACGAGAAGGGAGTAGTTGTC 59.836 54.545 0.00 0.00 0.00 3.18
2735 4408 2.818432 GACGAGAAGGGAGTAGTTGTCA 59.182 50.000 0.00 0.00 0.00 3.58
2737 4410 3.833070 ACGAGAAGGGAGTAGTTGTCATT 59.167 43.478 0.00 0.00 0.00 2.57
2738 4411 4.177026 CGAGAAGGGAGTAGTTGTCATTG 58.823 47.826 0.00 0.00 0.00 2.82
2739 4412 4.322049 CGAGAAGGGAGTAGTTGTCATTGT 60.322 45.833 0.00 0.00 0.00 2.71
2741 4414 5.308825 AGAAGGGAGTAGTTGTCATTGTTG 58.691 41.667 0.00 0.00 0.00 3.33
2742 4415 4.706842 AGGGAGTAGTTGTCATTGTTGT 57.293 40.909 0.00 0.00 0.00 3.32
2743 4416 5.048846 AGGGAGTAGTTGTCATTGTTGTT 57.951 39.130 0.00 0.00 0.00 2.83
2744 4417 5.445964 AGGGAGTAGTTGTCATTGTTGTTT 58.554 37.500 0.00 0.00 0.00 2.83
2746 4419 7.057894 AGGGAGTAGTTGTCATTGTTGTTTTA 58.942 34.615 0.00 0.00 0.00 1.52
2747 4420 7.012989 AGGGAGTAGTTGTCATTGTTGTTTTAC 59.987 37.037 0.00 0.00 0.00 2.01
2761 4486 7.023197 TGTTGTTTTACTTTCTCCTTGTAGC 57.977 36.000 0.00 0.00 0.00 3.58
2762 4487 5.917541 TGTTTTACTTTCTCCTTGTAGCG 57.082 39.130 0.00 0.00 0.00 4.26
2787 4512 6.320164 GTGACACAGTCTAGAGACCATAGAAT 59.680 42.308 6.05 0.00 45.85 2.40
2856 4581 3.365472 AGAACCACTTTTGACTTTGCCT 58.635 40.909 0.00 0.00 0.00 4.75
3068 6356 2.641321 GGGTTGGTACTTTGTACTCCCT 59.359 50.000 18.47 0.00 0.00 4.20
3069 6357 3.307269 GGGTTGGTACTTTGTACTCCCTC 60.307 52.174 18.47 3.34 0.00 4.30
3121 6544 1.226745 CGCGTGTACCGGAAGCATA 60.227 57.895 9.46 0.00 36.94 3.14
3250 6698 3.431725 GCGCTGTACAACCTGGGC 61.432 66.667 0.00 6.20 35.68 5.36
3532 6983 2.430367 GACACCTTCAACCCGCCT 59.570 61.111 0.00 0.00 0.00 5.52
3718 7314 2.158959 GCACGACGCGCAGTTCTAT 61.159 57.895 5.73 0.00 0.00 1.98
3789 7388 2.299867 GCACCAAAACCACCATGAGAAT 59.700 45.455 0.00 0.00 0.00 2.40
4000 7803 2.178521 CTCGGACACTTCGACGGG 59.821 66.667 0.00 0.00 32.86 5.28
4138 7941 3.849951 GGCATCCTCCCGCTTCGA 61.850 66.667 0.00 0.00 0.00 3.71
4190 7993 1.341080 CCATAATGCCAATGACCCCC 58.659 55.000 0.00 0.00 0.00 5.40
4207 8010 4.541482 CGCGCGCTCAATGGCAAT 62.541 61.111 30.48 0.00 0.00 3.56
4618 8421 0.397816 CCAGGGTCCTCTTCGGAGAT 60.398 60.000 0.00 0.00 44.20 2.75
5252 9153 2.110967 CCATTCTGGCTCTGGCACG 61.111 63.158 0.00 0.00 40.87 5.34
5264 9165 2.183555 GGCACGGGTAGAAGACGG 59.816 66.667 0.00 0.00 0.00 4.79
5267 9168 1.870055 GCACGGGTAGAAGACGGACA 61.870 60.000 0.00 0.00 0.00 4.02
5276 9177 0.667792 GAAGACGGACAGCAGTGACC 60.668 60.000 0.00 0.00 35.37 4.02
5345 9246 9.905713 TTATAATTCAGTTGCCTCAGAAATACT 57.094 29.630 0.00 0.00 0.00 2.12
5488 9389 5.799827 AAAGGTATGTCTAGCTCTCATCC 57.200 43.478 0.00 0.00 34.63 3.51
5490 9391 5.009436 AGGTATGTCTAGCTCTCATCCAT 57.991 43.478 0.00 0.00 29.71 3.41
5497 9398 2.729383 AGCTCTCATCCATATCCCCA 57.271 50.000 0.00 0.00 0.00 4.96
5547 9448 8.445275 AGAAGAAAGAAGAAAGAAAAGGAGAC 57.555 34.615 0.00 0.00 0.00 3.36
5572 9473 5.369685 TCAGCATGAATCTTTGCGTAAAA 57.630 34.783 0.00 0.00 45.97 1.52
5573 9474 5.953183 TCAGCATGAATCTTTGCGTAAAAT 58.047 33.333 0.00 0.00 45.97 1.82
5574 9475 6.029607 TCAGCATGAATCTTTGCGTAAAATC 58.970 36.000 0.00 0.29 45.97 2.17
5575 9476 5.801444 CAGCATGAATCTTTGCGTAAAATCA 59.199 36.000 0.00 5.80 43.61 2.57
5576 9477 6.308524 CAGCATGAATCTTTGCGTAAAATCAA 59.691 34.615 0.00 0.00 43.61 2.57
5577 9478 6.867816 AGCATGAATCTTTGCGTAAAATCAAA 59.132 30.769 0.00 0.00 43.61 2.69
5578 9479 7.546667 AGCATGAATCTTTGCGTAAAATCAAAT 59.453 29.630 0.00 0.00 43.61 2.32
5579 9480 7.633281 GCATGAATCTTTGCGTAAAATCAAATG 59.367 33.333 0.00 8.60 32.51 2.32
5659 9561 1.068741 GTTCTACAGTGGCTATCCCCG 59.931 57.143 0.00 0.00 0.00 5.73
5664 9566 0.035439 CAGTGGCTATCCCCGTTGTT 60.035 55.000 0.00 0.00 0.00 2.83
5704 9606 8.082242 CCCTTGAAGATTAAGATTTTCGTTTGT 58.918 33.333 0.00 0.00 30.94 2.83
5919 9821 0.704076 TTTCTGCAGGTTAGGGCCAT 59.296 50.000 15.13 0.00 0.00 4.40
5925 9827 0.918983 CAGGTTAGGGCCATTCAGGA 59.081 55.000 6.18 0.00 41.22 3.86
5978 9885 0.530650 CGCGGCTATGATGTGGACTT 60.531 55.000 0.00 0.00 0.00 3.01
6091 9998 3.916544 CATCCGCTCGCTAGGCCA 61.917 66.667 5.01 0.00 0.00 5.36
6190 10097 2.531685 TAGCTTGCCCCTGGTGGT 60.532 61.111 0.00 0.00 0.00 4.16
6219 10127 4.142038 TGTTTCCTCTTAGTTCTTTGGGC 58.858 43.478 0.00 0.00 0.00 5.36
6220 10128 4.142038 GTTTCCTCTTAGTTCTTTGGGCA 58.858 43.478 0.00 0.00 0.00 5.36
6221 10129 4.657814 TTCCTCTTAGTTCTTTGGGCAT 57.342 40.909 0.00 0.00 0.00 4.40
6222 10130 4.222124 TCCTCTTAGTTCTTTGGGCATC 57.778 45.455 0.00 0.00 0.00 3.91
6223 10131 3.587061 TCCTCTTAGTTCTTTGGGCATCA 59.413 43.478 0.00 0.00 0.00 3.07
6224 10132 4.228210 TCCTCTTAGTTCTTTGGGCATCAT 59.772 41.667 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.503363 GCTCCATGGCGTCTGTGC 61.503 66.667 6.96 0.00 0.00 4.57
76 78 2.686816 GGTGGTGTCCGCGATTTGG 61.687 63.158 8.23 0.00 34.37 3.28
114 116 9.062524 GTGTTTACATAGAATGGCATATTGGTA 57.937 33.333 0.00 0.00 33.60 3.25
115 117 7.559533 TGTGTTTACATAGAATGGCATATTGGT 59.440 33.333 0.00 0.00 33.60 3.67
124 126 6.252967 TGCAGTTGTGTTTACATAGAATGG 57.747 37.500 0.00 0.00 36.53 3.16
153 155 2.380410 CGCCACGTGTCCTGCTTAC 61.380 63.158 15.65 0.00 0.00 2.34
181 187 1.475213 GGCTGGCTATACAGGTGGAAC 60.475 57.143 0.00 0.00 38.90 3.62
245 251 6.099341 GCCATCAGTTTTATCGTTTTTCCAT 58.901 36.000 0.00 0.00 0.00 3.41
305 311 2.806818 CAAAGGAGATCATGCCATCGAG 59.193 50.000 0.00 0.00 0.00 4.04
382 388 2.680370 CCCTAACCACCCCCTGAGC 61.680 68.421 0.00 0.00 0.00 4.26
391 397 3.383505 GCCATTAAATCCACCCTAACCAC 59.616 47.826 0.00 0.00 0.00 4.16
453 459 1.664016 GCAAGACGACAGCAACATTGG 60.664 52.381 0.00 0.00 0.00 3.16
596 617 4.985538 ACTCCAGTAAAGAACGATCGAT 57.014 40.909 24.34 10.66 0.00 3.59
597 618 4.940046 AGTACTCCAGTAAAGAACGATCGA 59.060 41.667 24.34 0.00 31.52 3.59
598 619 5.232610 AGTACTCCAGTAAAGAACGATCG 57.767 43.478 14.88 14.88 31.52 3.69
599 620 6.727215 CCTAGTACTCCAGTAAAGAACGATC 58.273 44.000 0.00 0.00 31.52 3.69
693 714 0.996229 GATCGATCGTGCAGCTCTCG 60.996 60.000 15.94 0.00 0.00 4.04
715 736 1.553248 TGCCGTTGAATGTAGCTAGGT 59.447 47.619 0.00 0.00 0.00 3.08
720 741 0.248621 GCCATGCCGTTGAATGTAGC 60.249 55.000 0.00 0.00 0.00 3.58
728 749 2.413437 TTTCCGTTGCCATGCCGTTG 62.413 55.000 0.00 0.00 0.00 4.10
888 911 1.401539 GCCAGCGATCTTGTTGAAACC 60.402 52.381 0.00 0.00 0.00 3.27
897 920 1.451028 GCTCTTGGCCAGCGATCTT 60.451 57.895 5.11 0.00 34.27 2.40
898 921 2.188994 GCTCTTGGCCAGCGATCT 59.811 61.111 5.11 0.00 34.27 2.75
961 984 0.613292 GGTGAGAGCAGACAGGAGGA 60.613 60.000 0.00 0.00 0.00 3.71
1281 1304 2.685380 AAGGAGAGCCCGTGGAGG 60.685 66.667 0.00 0.00 40.87 4.30
1454 1477 2.115291 GCTTTCTAGCGGCCCCTTG 61.115 63.158 0.00 0.00 37.71 3.61
1455 1478 2.272471 GCTTTCTAGCGGCCCCTT 59.728 61.111 0.00 0.00 37.71 3.95
1520 1648 0.105039 GGATTCGATCGGAGCCTGTT 59.895 55.000 23.54 0.00 0.00 3.16
1522 1650 0.319383 CTGGATTCGATCGGAGCCTG 60.319 60.000 29.69 25.36 0.00 4.85
1579 2195 2.101582 GGAGAGCAAGACCACGATGTAT 59.898 50.000 0.00 0.00 0.00 2.29
1592 2208 1.004560 CCACGAAGCAGGAGAGCAA 60.005 57.895 0.00 0.00 36.85 3.91
1670 2286 2.281414 CACGTCATGGCCACCACA 60.281 61.111 8.16 0.00 35.80 4.17
1671 2287 3.055719 CCACGTCATGGCCACCAC 61.056 66.667 8.16 6.72 43.24 4.16
1709 2935 0.036306 AGTTGGTCCGGCTTAACCAG 59.964 55.000 12.13 0.00 45.84 4.00
1863 3361 3.562557 GCGGGAGACAAACTTTCACTTTA 59.437 43.478 0.00 0.00 0.00 1.85
1864 3362 2.357952 GCGGGAGACAAACTTTCACTTT 59.642 45.455 0.00 0.00 0.00 2.66
1865 3363 1.947456 GCGGGAGACAAACTTTCACTT 59.053 47.619 0.00 0.00 0.00 3.16
1867 3365 1.594331 AGCGGGAGACAAACTTTCAC 58.406 50.000 0.00 0.00 0.00 3.18
1868 3366 2.341846 AAGCGGGAGACAAACTTTCA 57.658 45.000 0.00 0.00 0.00 2.69
1869 3367 3.710326 AAAAGCGGGAGACAAACTTTC 57.290 42.857 0.00 0.00 30.80 2.62
1887 3385 7.852971 AAGCAGGTGTATAAGCGTATAAAAA 57.147 32.000 0.65 0.00 0.00 1.94
1888 3386 7.549842 TCAAAGCAGGTGTATAAGCGTATAAAA 59.450 33.333 0.65 0.00 0.00 1.52
1889 3387 7.042950 TCAAAGCAGGTGTATAAGCGTATAAA 58.957 34.615 0.65 0.00 0.00 1.40
1890 3388 6.575267 TCAAAGCAGGTGTATAAGCGTATAA 58.425 36.000 0.65 0.00 0.00 0.98
1891 3389 6.151663 TCAAAGCAGGTGTATAAGCGTATA 57.848 37.500 0.00 0.00 0.00 1.47
1892 3390 5.018539 TCAAAGCAGGTGTATAAGCGTAT 57.981 39.130 0.00 0.00 0.00 3.06
1893 3391 4.459390 TCAAAGCAGGTGTATAAGCGTA 57.541 40.909 0.00 0.00 0.00 4.42
1894 3392 3.328382 TCAAAGCAGGTGTATAAGCGT 57.672 42.857 0.00 0.00 0.00 5.07
1895 3393 4.154195 ACTTTCAAAGCAGGTGTATAAGCG 59.846 41.667 0.00 0.00 0.00 4.68
1896 3394 5.629079 ACTTTCAAAGCAGGTGTATAAGC 57.371 39.130 0.00 0.00 0.00 3.09
1900 3398 8.244113 GCTTATAAACTTTCAAAGCAGGTGTAT 58.756 33.333 12.61 0.00 41.65 2.29
1901 3399 7.572353 CGCTTATAAACTTTCAAAGCAGGTGTA 60.572 37.037 15.69 0.00 42.03 2.90
1902 3400 6.447162 GCTTATAAACTTTCAAAGCAGGTGT 58.553 36.000 12.61 0.00 41.65 4.16
1903 3401 5.569059 CGCTTATAAACTTTCAAAGCAGGTG 59.431 40.000 15.69 2.58 42.03 4.00
1904 3402 5.240844 ACGCTTATAAACTTTCAAAGCAGGT 59.759 36.000 15.69 7.77 42.03 4.00
1905 3403 5.699839 ACGCTTATAAACTTTCAAAGCAGG 58.300 37.500 15.69 7.35 42.03 4.85
1906 3404 9.982291 TTATACGCTTATAAACTTTCAAAGCAG 57.018 29.630 15.69 12.08 42.03 4.24
1935 3433 7.823310 TCATATTTTACACATGCTTTGCCAATT 59.177 29.630 0.00 0.00 0.00 2.32
1936 3434 7.329499 TCATATTTTACACATGCTTTGCCAAT 58.671 30.769 0.00 0.00 0.00 3.16
1937 3435 6.695429 TCATATTTTACACATGCTTTGCCAA 58.305 32.000 0.00 0.00 0.00 4.52
2088 3748 8.786826 TCCATCTCATAATGTAAGACGTTTTT 57.213 30.769 0.00 0.00 0.00 1.94
2089 3749 8.258007 TCTCCATCTCATAATGTAAGACGTTTT 58.742 33.333 0.00 0.00 0.00 2.43
2090 3750 7.782049 TCTCCATCTCATAATGTAAGACGTTT 58.218 34.615 0.00 0.00 0.00 3.60
2091 3751 7.285629 TCTCTCCATCTCATAATGTAAGACGTT 59.714 37.037 0.00 0.00 0.00 3.99
2092 3752 6.773200 TCTCTCCATCTCATAATGTAAGACGT 59.227 38.462 0.00 0.00 0.00 4.34
2093 3753 7.208225 TCTCTCCATCTCATAATGTAAGACG 57.792 40.000 0.00 0.00 0.00 4.18
2094 3754 8.417106 TGTTCTCTCCATCTCATAATGTAAGAC 58.583 37.037 0.00 0.00 0.00 3.01
2095 3755 8.539117 TGTTCTCTCCATCTCATAATGTAAGA 57.461 34.615 0.00 0.00 0.00 2.10
2096 3756 8.420222 ACTGTTCTCTCCATCTCATAATGTAAG 58.580 37.037 0.00 0.00 0.00 2.34
2097 3757 8.311395 ACTGTTCTCTCCATCTCATAATGTAA 57.689 34.615 0.00 0.00 0.00 2.41
2098 3758 7.904558 ACTGTTCTCTCCATCTCATAATGTA 57.095 36.000 0.00 0.00 0.00 2.29
2099 3759 6.805016 ACTGTTCTCTCCATCTCATAATGT 57.195 37.500 0.00 0.00 0.00 2.71
2100 3760 7.384660 GCTAACTGTTCTCTCCATCTCATAATG 59.615 40.741 0.00 0.00 0.00 1.90
2101 3761 7.289782 AGCTAACTGTTCTCTCCATCTCATAAT 59.710 37.037 0.00 0.00 0.00 1.28
2102 3762 6.609212 AGCTAACTGTTCTCTCCATCTCATAA 59.391 38.462 0.00 0.00 0.00 1.90
2103 3763 6.132658 AGCTAACTGTTCTCTCCATCTCATA 58.867 40.000 0.00 0.00 0.00 2.15
2104 3764 4.961730 AGCTAACTGTTCTCTCCATCTCAT 59.038 41.667 0.00 0.00 0.00 2.90
2105 3765 4.348486 AGCTAACTGTTCTCTCCATCTCA 58.652 43.478 0.00 0.00 0.00 3.27
2107 3767 5.515106 AGTAGCTAACTGTTCTCTCCATCT 58.485 41.667 0.00 0.00 36.93 2.90
2109 3769 7.147811 CCTTAAGTAGCTAACTGTTCTCTCCAT 60.148 40.741 0.00 0.00 38.88 3.41
2110 3770 6.153000 CCTTAAGTAGCTAACTGTTCTCTCCA 59.847 42.308 0.00 0.00 38.88 3.86
2112 3772 6.037726 GCCTTAAGTAGCTAACTGTTCTCTC 58.962 44.000 0.00 0.00 38.88 3.20
2114 3774 5.968254 AGCCTTAAGTAGCTAACTGTTCTC 58.032 41.667 4.60 0.00 38.88 2.87
2115 3775 5.105269 GGAGCCTTAAGTAGCTAACTGTTCT 60.105 44.000 6.26 0.00 40.11 3.01
2116 3776 5.110598 GGAGCCTTAAGTAGCTAACTGTTC 58.889 45.833 6.26 0.00 40.11 3.18
2117 3777 4.530946 TGGAGCCTTAAGTAGCTAACTGTT 59.469 41.667 6.26 0.00 40.11 3.16
2119 3779 4.434520 GTGGAGCCTTAAGTAGCTAACTG 58.565 47.826 6.26 0.00 40.11 3.16
2141 3801 4.787551 TGTGGCTAGTATGGGTTAATTGG 58.212 43.478 0.00 0.00 0.00 3.16
2160 3820 1.086696 CCTGCCACTACGGAAATGTG 58.913 55.000 0.00 0.00 36.56 3.21
2164 3824 0.320374 CTGTCCTGCCACTACGGAAA 59.680 55.000 0.00 0.00 36.56 3.13
2249 3909 1.444119 TTGCTGCACACCGACCTTTC 61.444 55.000 0.00 0.00 0.00 2.62
2333 3993 3.568853 GCTAGCTAGATGGACGTTTAGGA 59.431 47.826 25.15 0.00 0.00 2.94
2338 3998 2.074729 AGGCTAGCTAGATGGACGTT 57.925 50.000 25.15 0.00 0.00 3.99
2346 4006 1.275291 ACGCACAAAAGGCTAGCTAGA 59.725 47.619 25.15 0.00 0.00 2.43
2400 4065 0.824759 GGTGGGTACACTCTAGCCAG 59.175 60.000 0.00 0.00 46.85 4.85
2424 4089 2.829720 ACCAAGGACGCTGTACAAGATA 59.170 45.455 0.00 0.00 0.00 1.98
2454 4123 2.274645 CCAAATGAGCAACGCCCCA 61.275 57.895 0.00 0.00 0.00 4.96
2479 4152 9.635520 AAGACGTTATCACTAATTAATATCGGG 57.364 33.333 0.00 0.00 0.00 5.14
2500 4173 5.215252 ACCCCATCACATAAGATAAGACG 57.785 43.478 0.00 0.00 0.00 4.18
2504 4177 8.792830 AAGTAGTACCCCATCACATAAGATAA 57.207 34.615 0.00 0.00 0.00 1.75
2505 4178 9.886337 TTAAGTAGTACCCCATCACATAAGATA 57.114 33.333 0.00 0.00 0.00 1.98
2506 4179 8.792830 TTAAGTAGTACCCCATCACATAAGAT 57.207 34.615 0.00 0.00 0.00 2.40
2507 4180 8.792830 ATTAAGTAGTACCCCATCACATAAGA 57.207 34.615 0.00 0.00 0.00 2.10
2508 4181 8.871125 AGATTAAGTAGTACCCCATCACATAAG 58.129 37.037 0.00 0.00 0.00 1.73
2509 4182 8.647796 CAGATTAAGTAGTACCCCATCACATAA 58.352 37.037 0.00 0.00 0.00 1.90
2510 4183 7.256190 GCAGATTAAGTAGTACCCCATCACATA 60.256 40.741 0.00 0.00 0.00 2.29
2511 4184 6.464465 GCAGATTAAGTAGTACCCCATCACAT 60.464 42.308 0.00 0.00 0.00 3.21
2512 4185 5.163343 GCAGATTAAGTAGTACCCCATCACA 60.163 44.000 0.00 0.00 0.00 3.58
2513 4186 5.070580 AGCAGATTAAGTAGTACCCCATCAC 59.929 44.000 0.00 0.00 0.00 3.06
2514 4187 5.216622 AGCAGATTAAGTAGTACCCCATCA 58.783 41.667 0.00 0.00 0.00 3.07
2515 4188 5.810080 AGCAGATTAAGTAGTACCCCATC 57.190 43.478 0.00 0.00 0.00 3.51
2534 4207 6.458342 CGGAGCGATCTACAACATATATAGCA 60.458 42.308 0.00 0.00 0.00 3.49
2536 4209 7.017498 ACGGAGCGATCTACAACATATATAG 57.983 40.000 0.00 0.00 0.00 1.31
2537 4210 6.997239 ACGGAGCGATCTACAACATATATA 57.003 37.500 0.00 0.00 0.00 0.86
2538 4211 5.899120 ACGGAGCGATCTACAACATATAT 57.101 39.130 0.00 0.00 0.00 0.86
2539 4212 5.458015 CAACGGAGCGATCTACAACATATA 58.542 41.667 0.00 0.00 0.00 0.86
2541 4214 3.490249 CCAACGGAGCGATCTACAACATA 60.490 47.826 0.00 0.00 0.00 2.29
2544 4217 1.135199 TCCAACGGAGCGATCTACAAC 60.135 52.381 0.00 0.00 0.00 3.32
2545 4218 1.179152 TCCAACGGAGCGATCTACAA 58.821 50.000 0.00 0.00 0.00 2.41
2546 4219 1.337071 GATCCAACGGAGCGATCTACA 59.663 52.381 0.00 0.00 34.05 2.74
2547 4220 1.609555 AGATCCAACGGAGCGATCTAC 59.390 52.381 0.00 0.00 43.66 2.59
2548 4221 1.982660 AGATCCAACGGAGCGATCTA 58.017 50.000 0.00 0.00 43.66 1.98
2550 4223 1.880675 TCTAGATCCAACGGAGCGATC 59.119 52.381 0.00 0.00 43.66 3.69
2551 4224 1.982660 TCTAGATCCAACGGAGCGAT 58.017 50.000 0.00 0.00 43.66 4.58
2552 4225 1.982660 ATCTAGATCCAACGGAGCGA 58.017 50.000 0.00 0.00 43.66 4.93
2553 4226 2.223829 ACAATCTAGATCCAACGGAGCG 60.224 50.000 5.51 0.00 43.66 5.03
2554 4227 3.460857 ACAATCTAGATCCAACGGAGC 57.539 47.619 5.51 0.00 38.56 4.70
2555 4228 4.572389 CCAAACAATCTAGATCCAACGGAG 59.428 45.833 5.51 0.00 34.05 4.63
2556 4229 4.019681 ACCAAACAATCTAGATCCAACGGA 60.020 41.667 5.51 0.00 35.55 4.69
2557 4230 4.261801 ACCAAACAATCTAGATCCAACGG 58.738 43.478 5.51 7.23 0.00 4.44
2560 4233 4.019681 ACCGACCAAACAATCTAGATCCAA 60.020 41.667 5.51 0.00 0.00 3.53
2561 4234 3.517901 ACCGACCAAACAATCTAGATCCA 59.482 43.478 5.51 0.00 0.00 3.41
2562 4235 4.120589 GACCGACCAAACAATCTAGATCC 58.879 47.826 5.51 0.00 0.00 3.36
2563 4236 4.567159 GTGACCGACCAAACAATCTAGATC 59.433 45.833 5.51 0.00 0.00 2.75
2565 4238 3.322541 TGTGACCGACCAAACAATCTAGA 59.677 43.478 0.00 0.00 0.00 2.43
2566 4239 3.659786 TGTGACCGACCAAACAATCTAG 58.340 45.455 0.00 0.00 0.00 2.43
2568 4241 2.631160 TGTGACCGACCAAACAATCT 57.369 45.000 0.00 0.00 0.00 2.40
2571 4244 2.045561 ACATGTGACCGACCAAACAA 57.954 45.000 0.00 0.00 0.00 2.83
2629 4302 9.047947 GGATGGAGGGAGTATATAGTTAAACAT 57.952 37.037 0.00 0.00 0.00 2.71
2631 4304 8.667592 AGGATGGAGGGAGTATATAGTTAAAC 57.332 38.462 0.00 0.00 0.00 2.01
2632 4305 9.765295 GTAGGATGGAGGGAGTATATAGTTAAA 57.235 37.037 0.00 0.00 0.00 1.52
2641 4314 9.629649 TTTAATATTGTAGGATGGAGGGAGTAT 57.370 33.333 0.00 0.00 0.00 2.12
2644 4317 7.387948 CGTTTTAATATTGTAGGATGGAGGGAG 59.612 40.741 0.00 0.00 0.00 4.30
2646 4319 6.996282 ACGTTTTAATATTGTAGGATGGAGGG 59.004 38.462 0.00 0.00 0.00 4.30
2647 4320 8.446599 AACGTTTTAATATTGTAGGATGGAGG 57.553 34.615 0.00 0.00 0.00 4.30
2688 4361 9.750125 CCCATAATATAAGAACCTTTTTCAAGC 57.250 33.333 0.00 0.00 0.00 4.01
2691 4364 9.116067 CGTCCCATAATATAAGAACCTTTTTCA 57.884 33.333 0.00 0.00 0.00 2.69
2692 4365 9.333724 TCGTCCCATAATATAAGAACCTTTTTC 57.666 33.333 0.00 0.00 0.00 2.29
2693 4366 9.338622 CTCGTCCCATAATATAAGAACCTTTTT 57.661 33.333 0.00 0.00 0.00 1.94
2694 4367 8.711170 TCTCGTCCCATAATATAAGAACCTTTT 58.289 33.333 0.00 0.00 0.00 2.27
2695 4368 8.258850 TCTCGTCCCATAATATAAGAACCTTT 57.741 34.615 0.00 0.00 0.00 3.11
2696 4369 7.850935 TCTCGTCCCATAATATAAGAACCTT 57.149 36.000 0.00 0.00 0.00 3.50
2697 4370 7.038941 CCTTCTCGTCCCATAATATAAGAACCT 60.039 40.741 0.00 0.00 0.00 3.50
2698 4371 7.097834 CCTTCTCGTCCCATAATATAAGAACC 58.902 42.308 0.00 0.00 0.00 3.62
2699 4372 7.039223 TCCCTTCTCGTCCCATAATATAAGAAC 60.039 40.741 0.00 0.00 0.00 3.01
2702 4375 6.437793 ACTCCCTTCTCGTCCCATAATATAAG 59.562 42.308 0.00 0.00 0.00 1.73
2713 4386 2.164017 GACAACTACTCCCTTCTCGTCC 59.836 54.545 0.00 0.00 0.00 4.79
2714 4387 2.818432 TGACAACTACTCCCTTCTCGTC 59.182 50.000 0.00 0.00 0.00 4.20
2719 4392 5.063880 ACAACAATGACAACTACTCCCTTC 58.936 41.667 0.00 0.00 0.00 3.46
2720 4393 5.048846 ACAACAATGACAACTACTCCCTT 57.951 39.130 0.00 0.00 0.00 3.95
2721 4394 4.706842 ACAACAATGACAACTACTCCCT 57.293 40.909 0.00 0.00 0.00 4.20
2724 4397 9.783256 AAAGTAAAACAACAATGACAACTACTC 57.217 29.630 0.00 0.00 0.00 2.59
2725 4398 9.783256 GAAAGTAAAACAACAATGACAACTACT 57.217 29.630 0.00 0.00 0.00 2.57
2726 4399 9.783256 AGAAAGTAAAACAACAATGACAACTAC 57.217 29.630 0.00 0.00 0.00 2.73
2727 4400 9.997482 GAGAAAGTAAAACAACAATGACAACTA 57.003 29.630 0.00 0.00 0.00 2.24
2728 4401 7.973944 GGAGAAAGTAAAACAACAATGACAACT 59.026 33.333 0.00 0.00 0.00 3.16
2729 4402 7.973944 AGGAGAAAGTAAAACAACAATGACAAC 59.026 33.333 0.00 0.00 0.00 3.32
2730 4403 8.062065 AGGAGAAAGTAAAACAACAATGACAA 57.938 30.769 0.00 0.00 0.00 3.18
2732 4405 7.973944 ACAAGGAGAAAGTAAAACAACAATGAC 59.026 33.333 0.00 0.00 0.00 3.06
2733 4406 8.062065 ACAAGGAGAAAGTAAAACAACAATGA 57.938 30.769 0.00 0.00 0.00 2.57
2734 4407 9.450807 CTACAAGGAGAAAGTAAAACAACAATG 57.549 33.333 0.00 0.00 0.00 2.82
2735 4408 8.135529 GCTACAAGGAGAAAGTAAAACAACAAT 58.864 33.333 0.00 0.00 0.00 2.71
2737 4410 6.238266 CGCTACAAGGAGAAAGTAAAACAACA 60.238 38.462 0.00 0.00 0.00 3.33
2738 4411 6.134061 CGCTACAAGGAGAAAGTAAAACAAC 58.866 40.000 0.00 0.00 0.00 3.32
2739 4412 5.818857 ACGCTACAAGGAGAAAGTAAAACAA 59.181 36.000 0.00 0.00 0.00 2.83
2741 4414 5.464389 TCACGCTACAAGGAGAAAGTAAAAC 59.536 40.000 0.00 0.00 0.00 2.43
2742 4415 5.464389 GTCACGCTACAAGGAGAAAGTAAAA 59.536 40.000 0.00 0.00 0.00 1.52
2743 4416 4.986659 GTCACGCTACAAGGAGAAAGTAAA 59.013 41.667 0.00 0.00 0.00 2.01
2744 4417 4.038282 TGTCACGCTACAAGGAGAAAGTAA 59.962 41.667 0.00 0.00 0.00 2.24
2746 4419 2.364324 TGTCACGCTACAAGGAGAAAGT 59.636 45.455 0.00 0.00 0.00 2.66
2747 4420 2.731976 GTGTCACGCTACAAGGAGAAAG 59.268 50.000 0.00 0.00 0.00 2.62
2761 4486 2.152016 TGGTCTCTAGACTGTGTCACG 58.848 52.381 9.84 0.00 44.20 4.35
2762 4487 5.186942 TCTATGGTCTCTAGACTGTGTCAC 58.813 45.833 9.84 0.00 44.20 3.67
2787 4512 4.501071 GAACCTTGCGAATTACTCCTACA 58.499 43.478 0.00 0.00 0.00 2.74
3121 6544 3.776969 TGGACTCTAGATTTGCAGGACAT 59.223 43.478 0.00 0.00 0.00 3.06
3532 6983 0.603707 CCTCCACGCAGCTCTTGAAA 60.604 55.000 0.00 0.00 0.00 2.69
3922 7725 1.901085 GTCCTGCTCCGTCATCCTT 59.099 57.895 0.00 0.00 0.00 3.36
3988 7791 3.308705 GGGTCCCCGTCGAAGTGT 61.309 66.667 0.00 0.00 0.00 3.55
4190 7993 2.645281 TAATTGCCATTGAGCGCGCG 62.645 55.000 28.44 28.44 34.65 6.86
4201 8004 0.393808 GAGGGCCGAAGTAATTGCCA 60.394 55.000 6.60 0.00 45.83 4.92
4337 8140 2.874648 TAGTCCGACGAGGCCGCTAA 62.875 60.000 4.53 0.00 40.77 3.09
4618 8421 4.641645 CTGCCGCTGGGGTTGTGA 62.642 66.667 12.70 0.00 38.44 3.58
4829 8715 1.126846 CAGATTCGTGTTCGGTGCTTC 59.873 52.381 0.00 0.00 37.69 3.86
5068 8966 3.074369 TCGCCGGCCTTGAGATGA 61.074 61.111 23.46 6.57 0.00 2.92
5252 9153 0.173708 CTGCTGTCCGTCTTCTACCC 59.826 60.000 0.00 0.00 0.00 3.69
5264 9165 6.109359 ACTGATAAATAAGGTCACTGCTGTC 58.891 40.000 0.00 0.00 0.00 3.51
5267 9168 7.425224 ACTACTGATAAATAAGGTCACTGCT 57.575 36.000 0.00 0.00 0.00 4.24
5542 9443 5.579718 CAAAGATTCATGCTGATTGTCTCC 58.420 41.667 0.00 0.00 0.00 3.71
5547 9448 3.766151 ACGCAAAGATTCATGCTGATTG 58.234 40.909 11.22 0.00 40.39 2.67
5572 9473 6.182627 TCATCTAACTCTTGTGCCATTTGAT 58.817 36.000 0.00 0.00 0.00 2.57
5573 9474 5.559770 TCATCTAACTCTTGTGCCATTTGA 58.440 37.500 0.00 0.00 0.00 2.69
5574 9475 5.645067 TCTCATCTAACTCTTGTGCCATTTG 59.355 40.000 0.00 0.00 0.00 2.32
5575 9476 5.645497 GTCTCATCTAACTCTTGTGCCATTT 59.355 40.000 0.00 0.00 0.00 2.32
5576 9477 5.046014 AGTCTCATCTAACTCTTGTGCCATT 60.046 40.000 0.00 0.00 0.00 3.16
5577 9478 4.469227 AGTCTCATCTAACTCTTGTGCCAT 59.531 41.667 0.00 0.00 0.00 4.40
5578 9479 3.834813 AGTCTCATCTAACTCTTGTGCCA 59.165 43.478 0.00 0.00 0.00 4.92
5579 9480 4.464069 AGTCTCATCTAACTCTTGTGCC 57.536 45.455 0.00 0.00 0.00 5.01
5589 9490 5.651530 CCGAGCTAACAAAGTCTCATCTAA 58.348 41.667 0.00 0.00 32.10 2.10
5636 9537 2.029623 GGATAGCCACTGTAGAACCGA 58.970 52.381 0.00 0.00 0.00 4.69
5659 9561 1.154225 CATCGGCGCCTTCAACAAC 60.154 57.895 26.68 0.00 0.00 3.32
5704 9606 1.018148 GACGATCTCGGAGAAGCTGA 58.982 55.000 12.40 0.00 44.95 4.26
5885 9787 1.021968 AGAAACCGTGCAAGGTCAAC 58.978 50.000 24.98 17.41 45.21 3.18
5919 9821 1.153449 CGCTTACGGCCATCCTGAA 60.153 57.895 2.24 0.00 37.74 3.02
5978 9885 5.584649 CCATCTTATTGCGAGTAGTCCAAAA 59.415 40.000 5.82 3.01 0.00 2.44
6091 9998 2.169352 CTGAAGATGGTCACGATCCCTT 59.831 50.000 0.00 0.00 0.00 3.95
6127 10034 4.415332 CGCGCGGTAGACACCAGT 62.415 66.667 24.84 0.00 46.14 4.00
6153 10060 3.228085 GAGTCTGTCGAGCGATCAC 57.772 57.895 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.