Multiple sequence alignment - TraesCS6D01G189700

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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 TraesCS6D01G189700 chr6D 100.000 6323 0 0 1 6323 262518816 262512494 0.000000e+00 11677.0
1 TraesCS6D01G189700 chr6D 83.636 110 9 2 6034 6134 262512685 262512576 1.880000e-15 95.3
2 TraesCS6D01G189700 chr6D 83.636 110 9 2 6132 6241 262512783 262512683 1.880000e-15 95.3
3 TraesCS6D01G189700 chr6A 94.996 3777 135 25 1 3769 322056508 322060238 0.000000e+00 5879.0
4 TraesCS6D01G189700 chr6A 97.245 871 17 2 3941 4804 322060230 322061100 0.000000e+00 1469.0
5 TraesCS6D01G189700 chr6A 91.907 902 38 19 4919 5813 322061096 322061969 0.000000e+00 1229.0
6 TraesCS6D01G189700 chr6A 89.017 173 18 1 3768 3940 64662423 64662252 4.970000e-51 213.0
7 TraesCS6D01G189700 chr6A 88.757 169 11 1 6154 6322 322062432 322062592 3.870000e-47 200.0
8 TraesCS6D01G189700 chr6A 87.079 178 20 2 3767 3941 38404444 38404621 1.390000e-46 198.0
9 TraesCS6D01G189700 chr6B 94.506 2166 89 16 1472 3636 347748712 347750848 0.000000e+00 3314.0
10 TraesCS6D01G189700 chr6B 93.753 2097 68 29 3941 6024 347751170 347753216 0.000000e+00 3088.0
11 TraesCS6D01G189700 chr6B 95.812 1576 54 9 1 1575 347747145 347748709 0.000000e+00 2534.0
12 TraesCS6D01G189700 chr6B 91.176 102 8 1 6222 6322 347753318 347753419 3.070000e-28 137.0
13 TraesCS6D01G189700 chr6B 89.535 86 5 1 4844 4925 487591321 487591406 8.670000e-19 106.0
14 TraesCS6D01G189700 chr6B 86.747 83 7 1 4847 4925 802059 801977 8.730000e-14 89.8
15 TraesCS6D01G189700 chr3D 93.933 956 47 6 2819 3769 534053530 534052581 0.000000e+00 1434.0
16 TraesCS6D01G189700 chr3D 91.781 146 6 1 3941 4080 387323152 387323297 1.390000e-46 198.0
17 TraesCS6D01G189700 chr3D 91.781 146 6 1 3941 4080 534052589 534052444 1.390000e-46 198.0
18 TraesCS6D01G189700 chr3D 89.024 82 7 2 6044 6124 537790414 537790334 4.030000e-17 100.0
19 TraesCS6D01G189700 chr1D 90.466 923 50 7 2852 3769 406702962 406703851 0.000000e+00 1182.0
20 TraesCS6D01G189700 chr1D 92.466 146 5 1 3941 4080 406703843 406703988 2.990000e-48 204.0
21 TraesCS6D01G189700 chr1D 86.066 122 14 3 3836 3957 470555219 470555101 1.850000e-25 128.0
22 TraesCS6D01G189700 chrUn 90.358 923 46 10 2852 3769 31822617 31821733 0.000000e+00 1171.0
23 TraesCS6D01G189700 chrUn 89.604 404 13 3 3371 3769 325215656 325216035 2.650000e-133 486.0
24 TraesCS6D01G189700 chrUn 89.604 404 13 3 3371 3769 344949150 344948771 2.650000e-133 486.0
25 TraesCS6D01G189700 chrUn 91.781 146 6 1 3941 4080 31821741 31821596 1.390000e-46 198.0
26 TraesCS6D01G189700 chrUn 91.781 146 6 1 3941 4080 325216027 325216172 1.390000e-46 198.0
27 TraesCS6D01G189700 chrUn 91.781 146 6 1 3941 4080 344948779 344948634 1.390000e-46 198.0
28 TraesCS6D01G189700 chrUn 88.312 77 7 2 4847 4922 176719693 176719618 2.430000e-14 91.6
29 TraesCS6D01G189700 chrUn 88.158 76 9 0 4847 4922 176753896 176753821 2.430000e-14 91.6
30 TraesCS6D01G189700 chrUn 88.158 76 9 0 4847 4922 355020708 355020633 2.430000e-14 91.6
31 TraesCS6D01G189700 chrUn 88.312 77 7 2 4847 4922 359477377 359477302 2.430000e-14 91.6
32 TraesCS6D01G189700 chrUn 87.500 80 8 2 4844 4922 386553502 386553580 2.430000e-14 91.6
33 TraesCS6D01G189700 chrUn 86.250 80 10 1 4844 4922 238523576 238523655 1.130000e-12 86.1
34 TraesCS6D01G189700 chrUn 86.250 80 10 1 4844 4922 238537685 238537764 1.130000e-12 86.1
35 TraesCS6D01G189700 chrUn 86.250 80 10 1 4844 4922 271022457 271022536 1.130000e-12 86.1
36 TraesCS6D01G189700 chrUn 87.013 77 9 1 4847 4922 278812420 278812344 1.130000e-12 86.1
37 TraesCS6D01G189700 chr2D 89.610 924 47 14 2852 3769 557101663 557102543 0.000000e+00 1129.0
38 TraesCS6D01G189700 chr2D 89.069 924 53 15 2852 3769 607129493 607128612 0.000000e+00 1103.0
39 TraesCS6D01G189700 chr2D 91.120 518 37 6 2852 3369 633372536 633372028 0.000000e+00 693.0
40 TraesCS6D01G189700 chr2D 89.604 404 13 3 3371 3769 633371257 633370878 2.650000e-133 486.0
41 TraesCS6D01G189700 chr2D 93.151 146 4 1 3941 4080 557102535 557102680 6.420000e-50 209.0
42 TraesCS6D01G189700 chr2D 78.646 192 30 5 6132 6322 157865678 157865859 4.010000e-22 117.0
43 TraesCS6D01G189700 chr2D 90.361 83 5 2 4844 4923 461076325 461076407 8.670000e-19 106.0
44 TraesCS6D01G189700 chr2D 79.042 167 22 9 6132 6297 206255414 206255260 1.120000e-17 102.0
45 TraesCS6D01G189700 chr2D 90.789 76 2 1 4847 4922 566655153 566655083 5.220000e-16 97.1
46 TraesCS6D01G189700 chr2D 88.095 84 5 2 4847 4926 461076387 461076305 1.880000e-15 95.3
47 TraesCS6D01G189700 chr4D 89.273 839 51 14 2852 3684 488435476 488434671 0.000000e+00 1014.0
48 TraesCS6D01G189700 chr4D 84.000 200 23 7 3763 3954 59039991 59040189 3.890000e-42 183.0
49 TraesCS6D01G189700 chr4D 89.610 77 8 0 4847 4923 313572397 313572321 1.450000e-16 99.0
50 TraesCS6D01G189700 chr5D 89.525 821 50 6 2954 3769 448503022 448503811 0.000000e+00 1007.0
51 TraesCS6D01G189700 chr5D 87.640 178 21 1 3763 3940 560281000 560280824 8.310000e-49 206.0
52 TraesCS6D01G189700 chr5D 91.096 146 7 1 3941 4080 448503803 448503948 6.470000e-45 193.0
53 TraesCS6D01G189700 chr5B 92.063 378 27 2 3136 3513 521831492 521831118 4.340000e-146 529.0
54 TraesCS6D01G189700 chr5B 90.972 144 7 1 3943 4080 521830914 521830771 8.370000e-44 189.0
55 TraesCS6D01G189700 chr5B 87.000 100 13 0 6035 6134 466614199 466614100 5.180000e-21 113.0
56 TraesCS6D01G189700 chr7A 89.216 408 34 4 2908 3315 610034994 610034597 9.460000e-138 501.0
57 TraesCS6D01G189700 chr7A 87.709 179 18 2 3767 3941 543447850 543447672 8.310000e-49 206.0
58 TraesCS6D01G189700 chr7A 91.096 146 7 1 3941 4080 610034486 610034341 6.470000e-45 193.0
59 TraesCS6D01G189700 chr7A 81.553 206 23 5 3768 3959 130378379 130378175 8.490000e-34 156.0
60 TraesCS6D01G189700 chr7B 90.393 229 17 4 2691 2919 709771514 709771291 4.790000e-76 296.0
61 TraesCS6D01G189700 chr7B 95.918 49 2 0 6273 6321 595449027 595448979 5.250000e-11 80.5
62 TraesCS6D01G189700 chr3A 92.935 184 12 1 2691 2874 722426957 722426775 3.760000e-67 267.0
63 TraesCS6D01G189700 chr3A 86.592 179 20 3 3767 3941 561038729 561038551 1.800000e-45 195.0
64 TraesCS6D01G189700 chr3A 85.714 189 18 4 3769 3951 674733992 674734177 2.330000e-44 191.0
65 TraesCS6D01G189700 chr3A 82.915 199 18 11 3767 3952 716806716 716806521 1.410000e-36 165.0
66 TraesCS6D01G189700 chr3A 81.667 180 23 5 3784 3953 562100667 562100846 2.380000e-29 141.0
67 TraesCS6D01G189700 chr1B 89.655 174 16 2 3769 3940 662547638 662547465 2.970000e-53 220.0
68 TraesCS6D01G189700 chr1B 87.429 175 19 3 3767 3941 569524021 569523850 1.390000e-46 198.0
69 TraesCS6D01G189700 chr2A 87.861 173 19 2 3768 3940 715471731 715471561 1.070000e-47 202.0
70 TraesCS6D01G189700 chr2A 84.422 199 26 5 3763 3958 15940227 15940423 2.330000e-44 191.0
71 TraesCS6D01G189700 chr2A 80.928 194 27 4 3764 3952 602489283 602489095 1.840000e-30 145.0
72 TraesCS6D01G189700 chr2A 88.235 85 7 3 6033 6116 277069839 277069921 1.450000e-16 99.0
73 TraesCS6D01G189700 chr1A 83.636 165 21 5 3790 3951 362406235 362406074 3.950000e-32 150.0
74 TraesCS6D01G189700 chr1A 80.928 194 23 6 6132 6322 456655364 456655182 2.380000e-29 141.0
75 TraesCS6D01G189700 chr1A 86.567 67 7 1 6198 6264 374930747 374930683 8.790000e-09 73.1
76 TraesCS6D01G189700 chr3B 92.308 78 5 1 4849 4925 191257512 191257589 6.700000e-20 110.0
77 TraesCS6D01G189700 chr4B 82.857 105 15 3 6199 6300 624872763 624872659 2.430000e-14 91.6
78 TraesCS6D01G189700 chr2B 76.829 164 25 9 6132 6294 261050413 261050564 5.250000e-11 80.5
79 TraesCS6D01G189700 chr5A 84.722 72 11 0 6251 6322 586728584 586728655 8.790000e-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 TraesCS6D01G189700 chr6D 262512494 262518816 6322 True 11677.00 11677 100.00000 1 6323 1 chr6D.!!$R1 6322
1 TraesCS6D01G189700 chr6A 322056508 322062592 6084 False 2194.25 5879 93.22625 1 6322 4 chr6A.!!$F2 6321
2 TraesCS6D01G189700 chr6B 347747145 347753419 6274 False 2268.25 3314 93.81175 1 6322 4 chr6B.!!$F2 6321
3 TraesCS6D01G189700 chr3D 534052444 534053530 1086 True 816.00 1434 92.85700 2819 4080 2 chr3D.!!$R2 1261
4 TraesCS6D01G189700 chr1D 406702962 406703988 1026 False 693.00 1182 91.46600 2852 4080 2 chr1D.!!$F1 1228
5 TraesCS6D01G189700 chrUn 31821596 31822617 1021 True 684.50 1171 91.06950 2852 4080 2 chrUn.!!$R6 1228
6 TraesCS6D01G189700 chrUn 325215656 325216172 516 False 342.00 486 90.69250 3371 4080 2 chrUn.!!$F5 709
7 TraesCS6D01G189700 chrUn 344948634 344949150 516 True 342.00 486 90.69250 3371 4080 2 chrUn.!!$R7 709
8 TraesCS6D01G189700 chr2D 607128612 607129493 881 True 1103.00 1103 89.06900 2852 3769 1 chr2D.!!$R4 917
9 TraesCS6D01G189700 chr2D 557101663 557102680 1017 False 669.00 1129 91.38050 2852 4080 2 chr2D.!!$F3 1228
10 TraesCS6D01G189700 chr2D 633370878 633372536 1658 True 589.50 693 90.36200 2852 3769 2 chr2D.!!$R5 917
11 TraesCS6D01G189700 chr4D 488434671 488435476 805 True 1014.00 1014 89.27300 2852 3684 1 chr4D.!!$R2 832
12 TraesCS6D01G189700 chr5D 448503022 448503948 926 False 600.00 1007 90.31050 2954 4080 2 chr5D.!!$F1 1126
13 TraesCS6D01G189700 chr5B 521830771 521831492 721 True 359.00 529 91.51750 3136 4080 2 chr5B.!!$R2 944
14 TraesCS6D01G189700 chr7A 610034341 610034994 653 True 347.00 501 90.15600 2908 4080 2 chr7A.!!$R3 1172

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
377 384 1.892209 CGTTGGCTTTTGAGGTAGGT 58.108 50.0 0.00 0.00 0.00 3.08 F
1272 1287 0.179059 ATGTCGTCACACTGGTTGCA 60.179 50.0 0.00 0.00 34.48 4.08 F
1744 1865 0.390340 TTGTAGCTTGGCTCTCTGCG 60.390 55.0 0.00 0.00 44.05 5.18 F
2419 2541 0.602562 CCACATGTTCGCACCCAAAT 59.397 50.0 0.00 0.00 0.00 2.32 F
3788 4884 0.107654 GGGTGTGTCTAGGGCACATC 60.108 60.0 18.92 18.25 46.66 3.06 F
3789 4885 0.905357 GGTGTGTCTAGGGCACATCT 59.095 55.0 18.92 0.00 46.66 2.90 F
5101 6208 0.037303 CCCTGAGGCAAAAGCTCAGA 59.963 55.0 15.91 0.00 45.22 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1410 1425 0.524392 CAAAAACCGCGTTGCAGACA 60.524 50.000 4.92 0.0 0.00 3.41 R
3234 3357 0.371989 TGGCGCGTCAAATACAATCG 59.628 50.000 12.88 0.0 0.00 3.34 R
3435 4329 2.869192 GAGGATGCGAAATGAGGACTTC 59.131 50.000 0.00 0.0 0.00 3.01 R
3886 4982 1.831736 AGTATTGCACTTCTACGCCCT 59.168 47.619 0.00 0.0 31.59 5.19 R
4804 5909 0.108585 CACATTATGGGACGGAGGGG 59.891 60.000 0.00 0.0 0.00 4.79 R
5115 6222 0.113972 TCCCATTGGTTGCATGGTCA 59.886 50.000 1.20 0.0 39.86 4.02 R
6040 7157 0.878961 GTGTTGTCCGGTCACTGTCC 60.879 60.000 0.00 0.0 0.00 4.02 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
156 157 2.252714 GACCAACTTCTCCTCTCCACT 58.747 52.381 0.00 0.00 0.00 4.00
254 255 4.341783 GCTGCTGTCCCACTGCCT 62.342 66.667 3.42 0.00 41.58 4.75
281 288 2.027751 CGTAGCTTAGCGCCTCCC 59.972 66.667 2.29 0.00 40.39 4.30
310 317 2.601367 CACCCCAAACCCCTGCAG 60.601 66.667 6.78 6.78 0.00 4.41
317 324 3.133365 AAACCCCTGCAGCCTTCGT 62.133 57.895 8.66 0.00 0.00 3.85
318 325 3.553095 AACCCCTGCAGCCTTCGTC 62.553 63.158 8.66 0.00 0.00 4.20
377 384 1.892209 CGTTGGCTTTTGAGGTAGGT 58.108 50.000 0.00 0.00 0.00 3.08
387 394 4.755266 TTTGAGGTAGGTATGAGCTTCC 57.245 45.455 0.00 0.00 33.95 3.46
499 506 9.265901 CCTCGTTCATATTTGAGTTAGATCATT 57.734 33.333 0.00 0.00 32.27 2.57
585 593 7.911651 TCTAACTGATGGAGAACTCTGAAATT 58.088 34.615 1.86 0.00 0.00 1.82
586 594 8.037758 TCTAACTGATGGAGAACTCTGAAATTC 58.962 37.037 1.86 0.00 0.00 2.17
587 595 6.371595 ACTGATGGAGAACTCTGAAATTCT 57.628 37.500 4.06 4.06 37.88 2.40
588 596 6.405538 ACTGATGGAGAACTCTGAAATTCTC 58.594 40.000 17.17 17.17 46.76 2.87
602 617 5.994250 TGAAATTCTCAGGGTCTCTTATGG 58.006 41.667 0.00 0.00 0.00 2.74
684 699 3.609853 TCTGATGGTTATGCTTGTGGTC 58.390 45.455 0.00 0.00 0.00 4.02
707 722 3.167485 AGCATTGCCTCATGGAGAAAAA 58.833 40.909 4.70 0.00 34.57 1.94
845 860 4.021368 GTGGGCTTCTTAGACTGTTAGACA 60.021 45.833 0.00 0.00 0.00 3.41
889 904 9.418045 TCTTAAAGTAAATATTTGGCTTTGTGC 57.582 29.630 25.92 2.61 41.94 4.57
895 910 6.940831 AAATATTTGGCTTTGTGCTTGTTT 57.059 29.167 0.00 0.00 42.39 2.83
916 931 3.634568 TGCACGTCGGAATTTTCATTT 57.365 38.095 0.00 0.00 0.00 2.32
1042 1057 2.197465 GGGGGAAAGTACAGACTGGAT 58.803 52.381 7.51 0.00 35.52 3.41
1080 1095 8.274322 ACCATTGATGTAAGGAATGTGAAGATA 58.726 33.333 0.00 0.00 0.00 1.98
1149 1164 1.594021 ATGTGACGCGTTGCACTCA 60.594 52.632 25.48 15.38 36.05 3.41
1200 1215 0.579156 GCAATGACTCGGAATCGCTC 59.421 55.000 0.00 0.00 36.13 5.03
1272 1287 0.179059 ATGTCGTCACACTGGTTGCA 60.179 50.000 0.00 0.00 34.48 4.08
1329 1344 2.798976 TGCTTGTGATGGAGTTTTGC 57.201 45.000 0.00 0.00 0.00 3.68
1383 1398 5.892119 CAGAGGTACTGGTTACTATGAGGAA 59.108 44.000 0.00 0.00 41.55 3.36
1410 1425 4.712476 AGGCGCTTTTGATATTCAGAGAT 58.288 39.130 7.64 0.00 0.00 2.75
1475 1490 2.766313 TGCGCATAGGTACATGGAATC 58.234 47.619 5.66 0.00 0.00 2.52
1659 1780 4.925054 GTGATGGTACGTTAGTAAACTGCA 59.075 41.667 0.00 0.00 34.16 4.41
1689 1810 5.777850 ATTTGTTTGCCCGTACTACTTTT 57.222 34.783 0.00 0.00 0.00 2.27
1708 1829 5.534654 ACTTTTTATTCTTGCCTGCAGTACA 59.465 36.000 13.81 7.82 0.00 2.90
1738 1859 1.897560 ACCTTGTTGTAGCTTGGCTC 58.102 50.000 0.00 0.00 40.44 4.70
1744 1865 0.390340 TTGTAGCTTGGCTCTCTGCG 60.390 55.000 0.00 0.00 44.05 5.18
1751 1872 1.748329 TTGGCTCTCTGCGTGTGAGT 61.748 55.000 9.32 0.00 44.05 3.41
1768 1889 5.181245 GTGTGAGTAAATACCATGTGCAAGT 59.819 40.000 0.00 0.00 0.00 3.16
1841 1962 6.092092 GCTTTGAAGTTTTGCAAACCATTTT 58.908 32.000 12.39 2.14 31.37 1.82
1842 1963 6.033725 GCTTTGAAGTTTTGCAAACCATTTTG 59.966 34.615 12.39 0.77 44.42 2.44
1919 2041 5.751586 AGGGATCTTAAAGCCGAAAATGTA 58.248 37.500 0.00 0.00 0.00 2.29
2072 2194 3.902881 AGAGCACCTGAGGTTAATGAG 57.097 47.619 0.00 0.00 31.02 2.90
2229 2351 8.806429 AAGTCCATAACATATGAACATGTGAA 57.194 30.769 10.38 6.29 39.10 3.18
2230 2352 8.806429 AGTCCATAACATATGAACATGTGAAA 57.194 30.769 10.38 6.01 39.10 2.69
2261 2383 6.925610 TTCATACTCAAATGGAATTCTCCG 57.074 37.500 5.23 0.00 45.85 4.63
2263 2385 6.830912 TCATACTCAAATGGAATTCTCCGAT 58.169 36.000 5.23 0.00 45.85 4.18
2264 2386 7.282585 TCATACTCAAATGGAATTCTCCGATT 58.717 34.615 5.23 0.00 45.85 3.34
2265 2387 7.775093 TCATACTCAAATGGAATTCTCCGATTT 59.225 33.333 5.23 3.06 45.85 2.17
2267 2389 7.938140 ACTCAAATGGAATTCTCCGATTTAA 57.062 32.000 5.23 0.00 45.85 1.52
2268 2390 8.525290 ACTCAAATGGAATTCTCCGATTTAAT 57.475 30.769 5.23 0.00 45.85 1.40
2269 2391 8.971073 ACTCAAATGGAATTCTCCGATTTAATT 58.029 29.630 5.23 0.00 45.85 1.40
2380 2502 5.163713 GGATCACAACTAAATCCTCAACTGC 60.164 44.000 0.00 0.00 36.76 4.40
2413 2535 2.704725 ATCAAACCACATGTTCGCAC 57.295 45.000 0.00 0.00 35.67 5.34
2419 2541 0.602562 CCACATGTTCGCACCCAAAT 59.397 50.000 0.00 0.00 0.00 2.32
2527 2649 1.656095 CGTTTGATGGAGAGTCGAAGC 59.344 52.381 0.00 0.00 0.00 3.86
2532 2654 0.610174 ATGGAGAGTCGAAGCTGCAA 59.390 50.000 12.68 0.00 36.08 4.08
2832 2954 1.971505 TACCTGATGGGGCTTCAGCG 61.972 60.000 7.00 4.42 39.42 5.18
2885 3007 7.336931 TGGTGAGGTTTTCTTTAGATGCTATTC 59.663 37.037 0.00 0.00 0.00 1.75
2886 3008 7.336931 GGTGAGGTTTTCTTTAGATGCTATTCA 59.663 37.037 0.00 0.00 0.00 2.57
2956 3078 4.923893 TGCAATGGCTAGAATTTGAATCG 58.076 39.130 0.00 0.00 41.91 3.34
3134 3257 3.980646 TTTGGAAACCAGATTGACACG 57.019 42.857 0.00 0.00 33.81 4.49
3165 3288 4.404640 TCCTAGAGAGTTTGGACTTTCGA 58.595 43.478 0.00 0.00 40.83 3.71
3247 3370 7.407337 GGATAACTCCAACGATTGTATTTGAC 58.593 38.462 0.00 0.00 41.64 3.18
3317 3442 8.810427 GTTTGCATCACTCCATATTTTTGTATG 58.190 33.333 0.00 0.00 32.95 2.39
3463 4357 5.471116 TCCTCATTTCGCATCCTCATAATTG 59.529 40.000 0.00 0.00 0.00 2.32
3474 4368 6.514048 GCATCCTCATAATTGTAGAAACTGCC 60.514 42.308 0.00 0.00 0.00 4.85
3487 4381 7.224297 TGTAGAAACTGCCATTTATAGATCCC 58.776 38.462 0.00 0.00 0.00 3.85
3675 4771 2.492088 TCTGACTGGGTCAATCACTACG 59.508 50.000 2.04 0.00 42.26 3.51
3769 4865 3.679980 ACTGCGTGCTAGAACAAAGTATG 59.320 43.478 0.74 0.00 0.00 2.39
3770 4866 3.000041 TGCGTGCTAGAACAAAGTATGG 59.000 45.455 0.74 0.00 0.00 2.74
3771 4867 2.351726 GCGTGCTAGAACAAAGTATGGG 59.648 50.000 0.74 0.00 0.00 4.00
3772 4868 3.596214 CGTGCTAGAACAAAGTATGGGT 58.404 45.455 0.74 0.00 0.00 4.51
3773 4869 3.370978 CGTGCTAGAACAAAGTATGGGTG 59.629 47.826 0.74 0.00 0.00 4.61
3774 4870 4.324267 GTGCTAGAACAAAGTATGGGTGT 58.676 43.478 0.00 0.00 0.00 4.16
3775 4871 4.154195 GTGCTAGAACAAAGTATGGGTGTG 59.846 45.833 0.00 0.00 0.00 3.82
3776 4872 4.202419 TGCTAGAACAAAGTATGGGTGTGT 60.202 41.667 0.00 0.00 0.00 3.72
3777 4873 4.392138 GCTAGAACAAAGTATGGGTGTGTC 59.608 45.833 0.00 0.00 0.00 3.67
3778 4874 4.706842 AGAACAAAGTATGGGTGTGTCT 57.293 40.909 0.00 0.00 0.00 3.41
3779 4875 5.818678 AGAACAAAGTATGGGTGTGTCTA 57.181 39.130 0.00 0.00 0.00 2.59
3780 4876 5.794894 AGAACAAAGTATGGGTGTGTCTAG 58.205 41.667 0.00 0.00 0.00 2.43
3781 4877 4.553330 ACAAAGTATGGGTGTGTCTAGG 57.447 45.455 0.00 0.00 0.00 3.02
3782 4878 3.263425 ACAAAGTATGGGTGTGTCTAGGG 59.737 47.826 0.00 0.00 0.00 3.53
3783 4879 1.497161 AGTATGGGTGTGTCTAGGGC 58.503 55.000 0.00 0.00 0.00 5.19
3784 4880 1.200519 GTATGGGTGTGTCTAGGGCA 58.799 55.000 0.00 0.00 0.00 5.36
3785 4881 1.134491 GTATGGGTGTGTCTAGGGCAC 60.134 57.143 10.20 10.20 37.37 5.01
3786 4882 0.840288 ATGGGTGTGTCTAGGGCACA 60.840 55.000 14.22 14.22 43.60 4.57
3787 4883 0.840288 TGGGTGTGTCTAGGGCACAT 60.840 55.000 18.92 0.00 46.66 3.21
3788 4884 0.107654 GGGTGTGTCTAGGGCACATC 60.108 60.000 18.92 18.25 46.66 3.06
3789 4885 0.905357 GGTGTGTCTAGGGCACATCT 59.095 55.000 18.92 0.00 46.66 2.90
3790 4886 2.108168 GGTGTGTCTAGGGCACATCTA 58.892 52.381 18.92 0.21 46.66 1.98
3791 4887 2.101582 GGTGTGTCTAGGGCACATCTAG 59.898 54.545 18.92 0.00 46.66 2.43
3792 4888 3.024547 GTGTGTCTAGGGCACATCTAGA 58.975 50.000 18.92 0.00 46.66 2.43
3793 4889 3.639094 GTGTGTCTAGGGCACATCTAGAT 59.361 47.826 18.92 0.00 46.66 1.98
3794 4890 3.638627 TGTGTCTAGGGCACATCTAGATG 59.361 47.826 27.63 27.63 43.25 2.90
3809 4905 7.069852 CATCTAGATGTGCCATAGTTATTGC 57.930 40.000 22.42 0.00 34.23 3.56
3810 4906 6.173427 TCTAGATGTGCCATAGTTATTGCA 57.827 37.500 0.00 0.00 32.69 4.08
3818 4914 6.866010 TGCCATAGTTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
3819 4915 6.356556 TGCCATAGTTATTGCACATCTAAGT 58.643 36.000 0.00 0.00 30.49 2.24
3820 4916 7.505258 TGCCATAGTTATTGCACATCTAAGTA 58.495 34.615 0.00 0.00 30.49 2.24
3821 4917 8.156820 TGCCATAGTTATTGCACATCTAAGTAT 58.843 33.333 0.00 0.00 30.49 2.12
3822 4918 8.660373 GCCATAGTTATTGCACATCTAAGTATC 58.340 37.037 0.00 0.00 0.00 2.24
3823 4919 9.935241 CCATAGTTATTGCACATCTAAGTATCT 57.065 33.333 0.00 0.00 0.00 1.98
3833 4929 9.830975 TGCACATCTAAGTATCTTAATTAAGCA 57.169 29.630 18.68 9.42 33.40 3.91
3860 4956 8.628882 AAAAAGGAAAAGAAAATACTCACACG 57.371 30.769 0.00 0.00 0.00 4.49
3861 4957 7.562454 AAAGGAAAAGAAAATACTCACACGA 57.438 32.000 0.00 0.00 0.00 4.35
3862 4958 7.562454 AAGGAAAAGAAAATACTCACACGAA 57.438 32.000 0.00 0.00 0.00 3.85
3863 4959 7.745620 AGGAAAAGAAAATACTCACACGAAT 57.254 32.000 0.00 0.00 0.00 3.34
3864 4960 7.807680 AGGAAAAGAAAATACTCACACGAATC 58.192 34.615 0.00 0.00 0.00 2.52
3865 4961 7.661847 AGGAAAAGAAAATACTCACACGAATCT 59.338 33.333 0.00 0.00 0.00 2.40
3866 4962 8.290325 GGAAAAGAAAATACTCACACGAATCTT 58.710 33.333 0.00 0.00 0.00 2.40
3890 4986 5.306532 TCGTAAGATCAACGATATAGGGC 57.693 43.478 16.52 0.00 43.90 5.19
3891 4987 4.096311 CGTAAGATCAACGATATAGGGCG 58.904 47.826 13.59 0.00 42.90 6.13
3892 4988 4.379186 CGTAAGATCAACGATATAGGGCGT 60.379 45.833 13.59 0.00 42.90 5.68
3893 4989 5.163824 CGTAAGATCAACGATATAGGGCGTA 60.164 44.000 13.59 0.00 42.90 4.42
3894 4990 4.966965 AGATCAACGATATAGGGCGTAG 57.033 45.455 0.00 0.00 40.23 3.51
3895 4991 4.586884 AGATCAACGATATAGGGCGTAGA 58.413 43.478 0.00 0.00 40.23 2.59
3896 4992 5.008331 AGATCAACGATATAGGGCGTAGAA 58.992 41.667 0.00 0.00 40.23 2.10
3897 4993 4.761235 TCAACGATATAGGGCGTAGAAG 57.239 45.455 0.00 0.00 40.23 2.85
3898 4994 4.139786 TCAACGATATAGGGCGTAGAAGT 58.860 43.478 0.00 0.00 40.23 3.01
3899 4995 4.023450 TCAACGATATAGGGCGTAGAAGTG 60.023 45.833 0.00 0.00 40.23 3.16
3900 4996 2.228343 ACGATATAGGGCGTAGAAGTGC 59.772 50.000 0.00 0.00 39.21 4.40
3901 4997 2.228103 CGATATAGGGCGTAGAAGTGCA 59.772 50.000 0.00 0.00 0.00 4.57
3902 4998 3.305131 CGATATAGGGCGTAGAAGTGCAA 60.305 47.826 0.00 0.00 0.00 4.08
3903 4999 4.618460 CGATATAGGGCGTAGAAGTGCAAT 60.618 45.833 0.00 0.00 0.00 3.56
3904 5000 5.392703 CGATATAGGGCGTAGAAGTGCAATA 60.393 44.000 0.00 0.00 0.00 1.90
3905 5001 2.311124 AGGGCGTAGAAGTGCAATAC 57.689 50.000 0.00 0.00 0.00 1.89
3906 5002 1.831736 AGGGCGTAGAAGTGCAATACT 59.168 47.619 0.00 0.00 42.89 2.12
4066 5168 7.394359 AGGTGCTTATAAAAGAACACATGTGAT 59.606 33.333 31.94 21.14 42.43 3.06
4463 5565 4.038162 AGCAAGACTATATCTGGGAACGAC 59.962 45.833 0.00 0.00 37.88 4.34
4482 5584 3.020984 GACCCCTTCAACAGTTTTGTCA 58.979 45.455 0.00 0.00 36.23 3.58
4538 5640 5.511363 ACTACTGCTACTGGTAAGACATCT 58.489 41.667 0.00 0.00 0.00 2.90
4668 5770 2.227388 CAGCGCCAAGAAATTCAAGAGT 59.773 45.455 2.29 0.00 0.00 3.24
4727 5829 5.240891 TCAAGTAAAGTCAGCTCAAGGATG 58.759 41.667 0.00 0.00 0.00 3.51
4804 5909 8.185505 GTGCTTGCTCTATGTATATCTAGTACC 58.814 40.741 0.00 0.00 0.00 3.34
4821 5926 1.060163 ACCCCCTCCGTCCCATAATG 61.060 60.000 0.00 0.00 0.00 1.90
4822 5927 1.060163 CCCCCTCCGTCCCATAATGT 61.060 60.000 0.00 0.00 0.00 2.71
4823 5928 0.108585 CCCCTCCGTCCCATAATGTG 59.891 60.000 0.00 0.00 0.00 3.21
4824 5929 1.128200 CCCTCCGTCCCATAATGTGA 58.872 55.000 0.00 0.00 0.00 3.58
4825 5930 1.070758 CCCTCCGTCCCATAATGTGAG 59.929 57.143 0.00 0.00 0.00 3.51
4826 5931 1.541233 CCTCCGTCCCATAATGTGAGC 60.541 57.143 0.00 0.00 0.00 4.26
4827 5932 0.104120 TCCGTCCCATAATGTGAGCG 59.896 55.000 0.00 0.00 0.00 5.03
4828 5933 0.179084 CCGTCCCATAATGTGAGCGT 60.179 55.000 0.00 0.00 0.00 5.07
4829 5934 1.651987 CGTCCCATAATGTGAGCGTT 58.348 50.000 0.00 0.00 0.00 4.84
4830 5935 2.006888 CGTCCCATAATGTGAGCGTTT 58.993 47.619 0.00 0.00 0.00 3.60
4831 5936 2.418628 CGTCCCATAATGTGAGCGTTTT 59.581 45.455 0.00 0.00 0.00 2.43
4832 5937 3.119990 CGTCCCATAATGTGAGCGTTTTT 60.120 43.478 0.00 0.00 0.00 1.94
4833 5938 4.165779 GTCCCATAATGTGAGCGTTTTTG 58.834 43.478 0.00 0.00 0.00 2.44
4834 5939 4.075682 TCCCATAATGTGAGCGTTTTTGA 58.924 39.130 0.00 0.00 0.00 2.69
4835 5940 4.083003 TCCCATAATGTGAGCGTTTTTGAC 60.083 41.667 0.00 0.00 0.00 3.18
4836 5941 4.082787 CCCATAATGTGAGCGTTTTTGACT 60.083 41.667 0.00 0.00 0.00 3.41
4837 5942 5.088739 CCATAATGTGAGCGTTTTTGACTC 58.911 41.667 0.00 0.00 0.00 3.36
4838 5943 5.106555 CCATAATGTGAGCGTTTTTGACTCT 60.107 40.000 0.00 0.00 0.00 3.24
4839 5944 6.092122 CCATAATGTGAGCGTTTTTGACTCTA 59.908 38.462 0.00 0.00 0.00 2.43
4840 5945 5.597813 AATGTGAGCGTTTTTGACTCTAG 57.402 39.130 0.00 0.00 0.00 2.43
4841 5946 4.054780 TGTGAGCGTTTTTGACTCTAGT 57.945 40.909 0.00 0.00 0.00 2.57
4842 5947 3.802139 TGTGAGCGTTTTTGACTCTAGTG 59.198 43.478 0.00 0.00 0.00 2.74
4843 5948 3.802685 GTGAGCGTTTTTGACTCTAGTGT 59.197 43.478 0.00 0.00 0.00 3.55
4844 5949 4.980434 GTGAGCGTTTTTGACTCTAGTGTA 59.020 41.667 0.00 0.00 0.00 2.90
4845 5950 5.117287 GTGAGCGTTTTTGACTCTAGTGTAG 59.883 44.000 0.00 0.00 0.00 2.74
4846 5951 5.197682 AGCGTTTTTGACTCTAGTGTAGT 57.802 39.130 0.00 0.00 0.00 2.73
4847 5952 6.016860 TGAGCGTTTTTGACTCTAGTGTAGTA 60.017 38.462 0.00 0.00 0.00 1.82
4893 6000 5.459762 TGTACACTACACTAGCGTCAAAAAC 59.540 40.000 0.00 0.00 32.89 2.43
4894 6001 4.435425 ACACTACACTAGCGTCAAAAACA 58.565 39.130 0.00 0.00 0.00 2.83
4912 6019 9.104965 TCAAAAACACTCTTATATTATGGGACG 57.895 33.333 0.00 0.00 0.00 4.79
5101 6208 0.037303 CCCTGAGGCAAAAGCTCAGA 59.963 55.000 15.91 0.00 45.22 3.27
5115 6222 0.111253 CTCAGACCAGGCCAAAGGTT 59.889 55.000 14.74 4.11 38.50 3.50
5210 6317 0.463654 GGCACATCATCGGGTAGCAA 60.464 55.000 0.00 0.00 0.00 3.91
5214 6321 0.514255 CATCATCGGGTAGCAATGCG 59.486 55.000 0.00 0.00 0.00 4.73
5215 6322 0.392706 ATCATCGGGTAGCAATGCGA 59.607 50.000 0.00 0.00 0.00 5.10
5273 6380 2.172293 GTTCCTCCCAGAGATTGAGCAT 59.828 50.000 0.00 0.00 0.00 3.79
5404 6511 5.143376 AGTTGCAAAAGGATGAGATTTGG 57.857 39.130 0.00 0.00 35.21 3.28
5475 6582 3.063084 GAGCCGACCTGGACGTCT 61.063 66.667 16.46 9.83 42.00 4.18
5567 6677 1.812571 CCTTGTACCATGTGGAACTGC 59.187 52.381 5.96 0.00 38.04 4.40
5575 6685 0.527565 ATGTGGAACTGCGGAAATGC 59.472 50.000 0.00 0.00 38.04 3.56
5595 6705 2.545742 GCCCCTTTTAACTTGTGCTGTG 60.546 50.000 0.00 0.00 0.00 3.66
5643 6753 4.887748 TGTTTCCTTGAGCTTACTCTCAG 58.112 43.478 0.00 0.00 43.23 3.35
5644 6754 4.345257 TGTTTCCTTGAGCTTACTCTCAGT 59.655 41.667 0.00 0.00 43.23 3.41
5648 6758 3.583806 CTTGAGCTTACTCTCAGTGTGG 58.416 50.000 0.00 0.00 43.23 4.17
5649 6759 1.895798 TGAGCTTACTCTCAGTGTGGG 59.104 52.381 0.00 0.00 43.85 4.61
5762 6876 4.935808 AGCACTGCTACAATGTTTAGTACC 59.064 41.667 0.21 0.00 36.99 3.34
5767 6881 4.117685 GCTACAATGTTTAGTACCGAGGG 58.882 47.826 0.00 0.00 0.00 4.30
5790 6904 2.434331 CACCGGGAGCCCTCAAAA 59.566 61.111 6.32 0.00 0.00 2.44
5791 6905 1.971695 CACCGGGAGCCCTCAAAAC 60.972 63.158 6.32 0.00 0.00 2.43
5793 6907 1.074951 CCGGGAGCCCTCAAAACTT 59.925 57.895 3.70 0.00 0.00 2.66
5813 6927 1.027792 ACGCGTGGAACAGTTTGGTT 61.028 50.000 12.93 0.00 41.80 3.67
5815 6929 0.736053 GCGTGGAACAGTTTGGTTGA 59.264 50.000 0.00 0.00 41.80 3.18
5854 6968 7.441157 TGTTCAAACTCATAGTAACTTGACAGG 59.559 37.037 0.00 0.00 26.31 4.00
5897 7011 4.431131 CCCACAGGGCGATTGGCT 62.431 66.667 6.45 0.00 42.94 4.75
5983 7100 4.939052 TCCCCGCAAAATAAAGTTCAAA 57.061 36.364 0.00 0.00 0.00 2.69
5985 7102 5.474825 TCCCCGCAAAATAAAGTTCAAATC 58.525 37.500 0.00 0.00 0.00 2.17
6024 7141 2.225650 ACTAGGGAAGTCATCACACCCT 60.226 50.000 9.21 9.21 46.68 4.34
6025 7142 1.280457 AGGGAAGTCATCACACCCTC 58.720 55.000 0.00 0.00 43.80 4.30
6026 7143 0.984230 GGGAAGTCATCACACCCTCA 59.016 55.000 0.00 0.00 37.98 3.86
6027 7144 1.065854 GGGAAGTCATCACACCCTCAG 60.066 57.143 0.00 0.00 37.98 3.35
6028 7145 1.677217 GGAAGTCATCACACCCTCAGC 60.677 57.143 0.00 0.00 0.00 4.26
6030 7147 0.612229 AGTCATCACACCCTCAGCAG 59.388 55.000 0.00 0.00 0.00 4.24
6031 7148 0.322975 GTCATCACACCCTCAGCAGT 59.677 55.000 0.00 0.00 0.00 4.40
6034 7151 2.793160 ATCACACCCTCAGCAGTGCG 62.793 60.000 10.00 5.01 37.51 5.34
6039 7156 2.740055 CCTCAGCAGTGCGTCCAC 60.740 66.667 10.00 0.00 42.39 4.02
6040 7157 3.108289 CTCAGCAGTGCGTCCACG 61.108 66.667 10.00 0.00 46.62 4.94
6059 7176 0.878961 GGACAGTGACCGGACAACAC 60.879 60.000 9.46 12.74 35.15 3.32
6060 7177 0.179094 GACAGTGACCGGACAACACA 60.179 55.000 9.46 0.00 37.05 3.72
6061 7178 0.468226 ACAGTGACCGGACAACACAT 59.532 50.000 9.46 2.99 37.05 3.21
6062 7179 1.689813 ACAGTGACCGGACAACACATA 59.310 47.619 9.46 0.00 37.05 2.29
6064 7181 3.135225 CAGTGACCGGACAACACATAAA 58.865 45.455 9.46 0.00 37.05 1.40
6065 7182 3.751175 CAGTGACCGGACAACACATAAAT 59.249 43.478 9.46 0.00 37.05 1.40
6066 7183 4.215399 CAGTGACCGGACAACACATAAATT 59.785 41.667 9.46 0.00 37.05 1.82
6067 7184 4.825085 AGTGACCGGACAACACATAAATTT 59.175 37.500 9.46 0.00 37.05 1.82
6069 7186 3.908213 ACCGGACAACACATAAATTTGC 58.092 40.909 9.46 0.00 0.00 3.68
6070 7187 3.572255 ACCGGACAACACATAAATTTGCT 59.428 39.130 9.46 0.00 0.00 3.91
6071 7188 4.165779 CCGGACAACACATAAATTTGCTC 58.834 43.478 0.00 0.00 0.00 4.26
6072 7189 4.165779 CGGACAACACATAAATTTGCTCC 58.834 43.478 0.00 0.00 0.00 4.70
6073 7190 4.082787 CGGACAACACATAAATTTGCTCCT 60.083 41.667 0.00 0.00 0.00 3.69
6074 7191 5.402398 GGACAACACATAAATTTGCTCCTC 58.598 41.667 0.00 0.00 0.00 3.71
6075 7192 5.391312 ACAACACATAAATTTGCTCCTCC 57.609 39.130 0.00 0.00 0.00 4.30
6076 7193 4.832266 ACAACACATAAATTTGCTCCTCCA 59.168 37.500 0.00 0.00 0.00 3.86
6077 7194 5.163513 CAACACATAAATTTGCTCCTCCAC 58.836 41.667 0.00 0.00 0.00 4.02
6078 7195 4.406456 ACACATAAATTTGCTCCTCCACA 58.594 39.130 0.00 0.00 0.00 4.17
6081 7198 5.047802 CACATAAATTTGCTCCTCCACAACT 60.048 40.000 0.00 0.00 0.00 3.16
6086 7223 0.325933 TGCTCCTCCACAACTGGATG 59.674 55.000 0.00 0.00 46.18 3.51
6097 7234 3.009723 ACAACTGGATGCATCTAAACCG 58.990 45.455 25.28 10.67 0.00 4.44
6109 7246 7.624360 TGCATCTAAACCGAATACTCAAATT 57.376 32.000 0.00 0.00 0.00 1.82
6149 7400 4.451150 GTCCGCGGGCAGTGATCA 62.451 66.667 27.96 0.00 0.00 2.92
6158 7409 0.792640 GGCAGTGATCAGACAACACG 59.207 55.000 0.00 0.00 39.19 4.49
6179 7481 2.154462 CAAATTTGCTCCTCCACGACT 58.846 47.619 5.01 0.00 0.00 4.18
6243 7545 1.624487 CTCATGCAACGTAGCGTACA 58.376 50.000 0.00 0.00 39.99 2.90
6261 7564 5.220340 GCGTACATACCTAAACACATGTCAC 60.220 44.000 0.00 0.00 33.78 3.67
6264 7567 2.922740 ACCTAAACACATGTCACCGT 57.077 45.000 0.00 0.00 0.00 4.83
6266 7569 4.546829 ACCTAAACACATGTCACCGTAT 57.453 40.909 0.00 0.00 0.00 3.06
6322 7625 3.421826 CGAAACGATGACCGAAGAAGTTG 60.422 47.826 0.00 0.00 41.76 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 127 4.006319 GGAGAAGTTGGTCAGATTCCAAG 58.994 47.826 0.00 0.00 44.21 3.61
156 157 1.120530 GAGAGGAAAGGTGCGGGATA 58.879 55.000 0.00 0.00 0.00 2.59
410 417 2.158726 TGGAGGTTAGTGTGGGTTCAAC 60.159 50.000 0.00 0.00 0.00 3.18
499 506 1.904287 AATAACCGCTTGTCTTGGCA 58.096 45.000 0.00 0.00 0.00 4.92
540 547 0.108329 AGTTAATCACTCGCACCCCG 60.108 55.000 0.00 0.00 38.61 5.73
585 593 3.033659 GGTCCATAAGAGACCCTGAGA 57.966 52.381 0.00 0.00 46.85 3.27
592 600 2.176247 TCCCTGGGTCCATAAGAGAC 57.824 55.000 13.56 0.00 0.00 3.36
602 617 1.134491 CGTGTTTCCTATCCCTGGGTC 60.134 57.143 13.56 0.00 0.00 4.46
684 699 0.179065 TCTCCATGAGGCAATGCTCG 60.179 55.000 4.82 0.00 33.74 5.03
707 722 3.907221 AGGCTGATGTTTGGCATTCTAT 58.093 40.909 0.00 0.00 38.06 1.98
889 904 2.399396 ATTCCGACGTGCAAAACAAG 57.601 45.000 0.00 0.00 0.00 3.16
895 910 3.634568 AATGAAAATTCCGACGTGCAA 57.365 38.095 0.00 0.00 0.00 4.08
1042 1057 2.117206 AATGGTGCGGCCTTCCAA 59.883 55.556 12.99 0.24 38.35 3.53
1080 1095 2.634982 CAATGGCATTGCGTACTGTT 57.365 45.000 25.69 0.00 32.92 3.16
1200 1215 4.202192 TGGATCTCCTTCATGACAAGATCG 60.202 45.833 22.56 4.32 42.02 3.69
1272 1287 3.306919 GGCCCATGTCAAAAACATCATGT 60.307 43.478 0.00 0.00 45.78 3.21
1329 1344 1.937108 GCACTCACCAAGGACTTCTCG 60.937 57.143 0.00 0.00 0.00 4.04
1383 1398 5.415701 TCTGAATATCAAAAGCGCCTTCTTT 59.584 36.000 2.29 0.00 37.86 2.52
1410 1425 0.524392 CAAAAACCGCGTTGCAGACA 60.524 50.000 4.92 0.00 0.00 3.41
1554 1675 9.903682 CATAATTGTGAAGAAATCTGACTTGTT 57.096 29.630 0.00 0.00 0.00 2.83
1630 1751 3.693807 ACTAACGTACCATCACTCCAGA 58.306 45.455 0.00 0.00 0.00 3.86
1659 1780 1.269448 CGGGCAAACAAATAGCAGTGT 59.731 47.619 0.00 0.00 0.00 3.55
1689 1810 4.551702 TCTGTACTGCAGGCAAGAATAA 57.448 40.909 19.93 0.00 45.08 1.40
1708 1829 7.380423 AGCTACAACAAGGTATATGGATTCT 57.620 36.000 0.00 0.00 0.00 2.40
1738 1859 3.845178 TGGTATTTACTCACACGCAGAG 58.155 45.455 0.00 0.00 39.04 3.35
1744 1865 5.181245 ACTTGCACATGGTATTTACTCACAC 59.819 40.000 0.00 0.00 0.00 3.82
1751 1872 9.158233 GTAAGAGTTACTTGCACATGGTATTTA 57.842 33.333 0.00 0.00 40.16 1.40
1768 1889 6.939730 TGAAACATTCATGCAGGTAAGAGTTA 59.060 34.615 0.00 0.00 34.08 2.24
1919 2041 4.574674 TGCACCATCTAATCCAAGAAGT 57.425 40.909 0.00 0.00 0.00 3.01
2072 2194 5.964758 TGTATCCATCATGCCAAAAAGTTC 58.035 37.500 0.00 0.00 0.00 3.01
2107 2229 1.200760 AGACCACTGCAGGCCATACA 61.201 55.000 19.93 0.00 0.00 2.29
2259 2381 9.811655 CACATGCTAGTGTAATAATTAAATCGG 57.188 33.333 0.00 0.00 34.83 4.18
2271 2393 8.244113 CGGAGAATATATCACATGCTAGTGTAA 58.756 37.037 8.57 0.55 40.37 2.41
2272 2394 7.610305 TCGGAGAATATATCACATGCTAGTGTA 59.390 37.037 8.57 2.81 40.37 2.90
2273 2395 6.434340 TCGGAGAATATATCACATGCTAGTGT 59.566 38.462 8.57 0.00 40.37 3.55
2274 2396 6.856895 TCGGAGAATATATCACATGCTAGTG 58.143 40.000 0.00 3.14 40.85 2.74
2275 2397 7.652524 ATCGGAGAATATATCACATGCTAGT 57.347 36.000 0.00 0.00 43.58 2.57
2276 2398 8.939201 AAATCGGAGAATATATCACATGCTAG 57.061 34.615 0.00 0.00 43.58 3.42
2380 2502 8.967218 CATGTGGTTTGATAAACAGTAACTTTG 58.033 33.333 6.74 0.00 43.15 2.77
2413 2535 6.649973 TGCAAATCACTTCAACATAATTTGGG 59.350 34.615 0.00 0.00 35.61 4.12
2419 2541 6.804677 AGTGTTGCAAATCACTTCAACATAA 58.195 32.000 15.03 0.00 46.71 1.90
2527 2649 4.460948 AATTGCCATTAAGGACTTGCAG 57.539 40.909 0.00 0.00 41.22 4.41
2532 2654 4.460263 TGCGATAATTGCCATTAAGGACT 58.540 39.130 0.00 0.00 41.22 3.85
2832 2954 1.481772 TGCAAGCCCATAGAAATTGCC 59.518 47.619 5.83 0.00 44.30 4.52
2885 3007 5.163468 ACAGAACATGTACTCTGCTCCTATG 60.163 44.000 22.06 4.15 42.39 2.23
2886 3008 4.959210 ACAGAACATGTACTCTGCTCCTAT 59.041 41.667 22.06 4.44 42.39 2.57
2956 3078 4.394610 ACCAACAAAAGAAACAAACATGCC 59.605 37.500 0.00 0.00 0.00 4.40
3039 3162 8.495949 CACGAGGGTATTTTAGTTAGCATAATG 58.504 37.037 0.00 0.00 0.00 1.90
3041 3164 7.558604 ACACGAGGGTATTTTAGTTAGCATAA 58.441 34.615 0.00 0.00 0.00 1.90
3134 3257 4.991687 CCAAACTCTCTAGGAAACACTGTC 59.008 45.833 0.00 0.00 0.00 3.51
3234 3357 0.371989 TGGCGCGTCAAATACAATCG 59.628 50.000 12.88 0.00 0.00 3.34
3435 4329 2.869192 GAGGATGCGAAATGAGGACTTC 59.131 50.000 0.00 0.00 0.00 3.01
3463 4357 7.173390 GTGGGATCTATAAATGGCAGTTTCTAC 59.827 40.741 5.17 0.00 0.00 2.59
3474 4368 9.745018 AATTAGGTGATGTGGGATCTATAAATG 57.255 33.333 0.00 0.00 0.00 2.32
3675 4771 4.935205 TCACAATACCTAACACATGACAGC 59.065 41.667 0.00 0.00 0.00 4.40
3769 4865 3.478780 TGTGCCCTAGACACACCC 58.521 61.111 12.81 0.00 42.88 4.61
3773 4869 4.250116 CATCTAGATGTGCCCTAGACAC 57.750 50.000 22.42 8.47 43.57 3.67
3795 4891 6.356556 ACTTAGATGTGCAATAACTATGGCA 58.643 36.000 0.00 0.00 40.19 4.92
3796 4892 6.867662 ACTTAGATGTGCAATAACTATGGC 57.132 37.500 0.00 0.00 33.16 4.40
3797 4893 9.935241 AGATACTTAGATGTGCAATAACTATGG 57.065 33.333 0.00 0.00 0.00 2.74
3807 4903 9.830975 TGCTTAATTAAGATACTTAGATGTGCA 57.169 29.630 26.00 11.15 35.33 4.57
3834 4930 9.724839 CGTGTGAGTATTTTCTTTTCCTTTTTA 57.275 29.630 0.00 0.00 0.00 1.52
3835 4931 8.463607 TCGTGTGAGTATTTTCTTTTCCTTTTT 58.536 29.630 0.00 0.00 0.00 1.94
3836 4932 7.992008 TCGTGTGAGTATTTTCTTTTCCTTTT 58.008 30.769 0.00 0.00 0.00 2.27
3837 4933 7.562454 TCGTGTGAGTATTTTCTTTTCCTTT 57.438 32.000 0.00 0.00 0.00 3.11
3838 4934 7.562454 TTCGTGTGAGTATTTTCTTTTCCTT 57.438 32.000 0.00 0.00 0.00 3.36
3839 4935 7.661847 AGATTCGTGTGAGTATTTTCTTTTCCT 59.338 33.333 0.00 0.00 0.00 3.36
3840 4936 7.807680 AGATTCGTGTGAGTATTTTCTTTTCC 58.192 34.615 0.00 0.00 0.00 3.13
3844 4940 8.808529 CGATAAGATTCGTGTGAGTATTTTCTT 58.191 33.333 0.00 0.00 34.46 2.52
3845 4941 8.341477 CGATAAGATTCGTGTGAGTATTTTCT 57.659 34.615 0.00 0.00 34.46 2.52
3869 4965 4.096311 CGCCCTATATCGTTGATCTTACG 58.904 47.826 12.74 12.74 40.23 3.18
3870 4966 5.056894 ACGCCCTATATCGTTGATCTTAC 57.943 43.478 0.00 0.00 35.09 2.34
3871 4967 6.175471 TCTACGCCCTATATCGTTGATCTTA 58.825 40.000 0.00 0.00 39.79 2.10
3872 4968 5.008331 TCTACGCCCTATATCGTTGATCTT 58.992 41.667 0.00 0.00 39.79 2.40
3873 4969 4.586884 TCTACGCCCTATATCGTTGATCT 58.413 43.478 0.00 0.00 39.79 2.75
3874 4970 4.959596 TCTACGCCCTATATCGTTGATC 57.040 45.455 0.00 0.00 39.79 2.92
3875 4971 4.765856 ACTTCTACGCCCTATATCGTTGAT 59.234 41.667 0.00 0.00 39.34 2.57
3876 4972 4.023450 CACTTCTACGCCCTATATCGTTGA 60.023 45.833 0.00 0.00 39.79 3.18
3877 4973 4.227538 CACTTCTACGCCCTATATCGTTG 58.772 47.826 0.00 0.00 39.79 4.10
3878 4974 3.305199 GCACTTCTACGCCCTATATCGTT 60.305 47.826 0.00 0.00 39.79 3.85
3879 4975 2.228343 GCACTTCTACGCCCTATATCGT 59.772 50.000 0.00 0.00 42.09 3.73
3880 4976 2.228103 TGCACTTCTACGCCCTATATCG 59.772 50.000 0.00 0.00 0.00 2.92
3881 4977 3.936372 TGCACTTCTACGCCCTATATC 57.064 47.619 0.00 0.00 0.00 1.63
3882 4978 4.891992 ATTGCACTTCTACGCCCTATAT 57.108 40.909 0.00 0.00 0.00 0.86
3883 4979 4.831155 AGTATTGCACTTCTACGCCCTATA 59.169 41.667 0.00 0.00 31.59 1.31
3884 4980 3.641906 AGTATTGCACTTCTACGCCCTAT 59.358 43.478 0.00 0.00 31.59 2.57
3885 4981 3.028850 AGTATTGCACTTCTACGCCCTA 58.971 45.455 0.00 0.00 31.59 3.53
3886 4982 1.831736 AGTATTGCACTTCTACGCCCT 59.168 47.619 0.00 0.00 31.59 5.19
3887 4983 2.311124 AGTATTGCACTTCTACGCCC 57.689 50.000 0.00 0.00 31.59 6.13
3888 4984 4.211374 CCATAAGTATTGCACTTCTACGCC 59.789 45.833 0.00 0.00 44.48 5.68
3889 4985 4.318831 GCCATAAGTATTGCACTTCTACGC 60.319 45.833 0.00 0.00 44.48 4.42
3890 4986 4.808895 TGCCATAAGTATTGCACTTCTACG 59.191 41.667 0.00 0.00 44.48 3.51
3891 4987 6.049263 GTGCCATAAGTATTGCACTTCTAC 57.951 41.667 16.35 0.00 44.48 2.59
3898 4994 6.173427 TCTAGATGTGCCATAAGTATTGCA 57.827 37.500 0.00 0.00 32.69 4.08
3899 4995 7.069852 CATCTAGATGTGCCATAAGTATTGC 57.930 40.000 22.42 0.00 34.23 3.56
3920 5016 8.366366 ACTTTGTCAGTTTTGCTAAAGCACATC 61.366 37.037 3.66 0.00 41.64 3.06
3921 5017 6.627953 ACTTTGTCAGTTTTGCTAAAGCACAT 60.628 34.615 3.66 0.00 41.64 3.21
3922 5018 5.336372 ACTTTGTCAGTTTTGCTAAAGCACA 60.336 36.000 3.66 0.00 41.64 4.57
3923 5019 5.102313 ACTTTGTCAGTTTTGCTAAAGCAC 58.898 37.500 3.66 0.00 41.64 4.40
3924 5020 5.323371 ACTTTGTCAGTTTTGCTAAAGCA 57.677 34.783 0.00 0.00 40.61 3.91
3925 5021 7.930513 AATACTTTGTCAGTTTTGCTAAAGC 57.069 32.000 0.00 0.00 36.88 3.51
4463 5565 2.757868 TGTGACAAAACTGTTGAAGGGG 59.242 45.455 0.00 0.00 0.00 4.79
4482 5584 5.407387 GCAGATTGTTTGCATCAAAATCTGT 59.593 36.000 25.95 7.07 43.38 3.41
4727 5829 0.394899 CCTGGGATCCAAGTTCTGGC 60.395 60.000 15.41 0.00 45.98 4.85
4784 5889 6.913545 AGGGGGTACTAGATATACATAGAGC 58.086 44.000 0.00 0.00 0.00 4.09
4804 5909 0.108585 CACATTATGGGACGGAGGGG 59.891 60.000 0.00 0.00 0.00 4.79
4821 5926 3.802685 ACACTAGAGTCAAAAACGCTCAC 59.197 43.478 0.00 0.00 39.01 3.51
4822 5927 4.054780 ACACTAGAGTCAAAAACGCTCA 57.945 40.909 0.00 0.00 39.01 4.26
4823 5928 5.221130 ACTACACTAGAGTCAAAAACGCTC 58.779 41.667 0.00 0.00 39.01 5.03
4824 5929 5.197682 ACTACACTAGAGTCAAAAACGCT 57.802 39.130 0.00 0.00 41.33 5.07
4825 5930 8.679288 TTATACTACACTAGAGTCAAAAACGC 57.321 34.615 0.00 0.00 0.00 4.84
4829 5934 8.396390 CGCTCTTATACTACACTAGAGTCAAAA 58.604 37.037 0.00 0.00 35.81 2.44
4830 5935 7.551974 ACGCTCTTATACTACACTAGAGTCAAA 59.448 37.037 0.00 0.00 35.81 2.69
4831 5936 7.046652 ACGCTCTTATACTACACTAGAGTCAA 58.953 38.462 0.00 0.00 35.81 3.18
4832 5937 6.580788 ACGCTCTTATACTACACTAGAGTCA 58.419 40.000 0.00 0.00 35.81 3.41
4833 5938 7.481275 AACGCTCTTATACTACACTAGAGTC 57.519 40.000 0.00 0.00 35.81 3.36
4834 5939 7.862512 AAACGCTCTTATACTACACTAGAGT 57.137 36.000 0.00 0.00 35.81 3.24
4835 5940 9.011407 CAAAAACGCTCTTATACTACACTAGAG 57.989 37.037 0.00 0.00 36.33 2.43
4836 5941 8.733458 TCAAAAACGCTCTTATACTACACTAGA 58.267 33.333 0.00 0.00 0.00 2.43
4837 5942 8.796278 GTCAAAAACGCTCTTATACTACACTAG 58.204 37.037 0.00 0.00 0.00 2.57
4838 5943 8.298854 TGTCAAAAACGCTCTTATACTACACTA 58.701 33.333 0.00 0.00 0.00 2.74
4839 5944 7.115947 GTGTCAAAAACGCTCTTATACTACACT 59.884 37.037 0.00 0.00 35.42 3.55
4840 5945 7.115947 AGTGTCAAAAACGCTCTTATACTACAC 59.884 37.037 0.00 0.00 45.69 2.90
4841 5946 7.149973 AGTGTCAAAAACGCTCTTATACTACA 58.850 34.615 0.00 0.00 45.69 2.74
4842 5947 7.578169 AGTGTCAAAAACGCTCTTATACTAC 57.422 36.000 0.00 0.00 45.69 2.73
4843 5948 8.517878 ACTAGTGTCAAAAACGCTCTTATACTA 58.482 33.333 0.00 0.00 45.69 1.82
4844 5949 7.328737 CACTAGTGTCAAAAACGCTCTTATACT 59.671 37.037 15.06 0.00 45.69 2.12
4845 5950 7.115947 ACACTAGTGTCAAAAACGCTCTTATAC 59.884 37.037 22.95 0.00 45.69 1.47
4846 5951 7.149973 ACACTAGTGTCAAAAACGCTCTTATA 58.850 34.615 22.95 0.00 45.69 0.98
4847 5952 5.989777 ACACTAGTGTCAAAAACGCTCTTAT 59.010 36.000 22.95 0.00 45.69 1.73
4884 5991 9.104965 TCCCATAATATAAGAGTGTTTTTGACG 57.895 33.333 0.00 0.00 0.00 4.35
4887 5994 8.342634 CCGTCCCATAATATAAGAGTGTTTTTG 58.657 37.037 0.00 0.00 0.00 2.44
4893 6000 5.105310 CCCTCCGTCCCATAATATAAGAGTG 60.105 48.000 0.00 0.00 0.00 3.51
4894 6001 5.024118 CCCTCCGTCCCATAATATAAGAGT 58.976 45.833 0.00 0.00 0.00 3.24
4912 6019 3.751518 ACAAATGTGTTGTACTCCCTCC 58.248 45.455 0.00 0.00 32.58 4.30
5048 6155 2.816601 CTTGGCCTCAGAGCTGGGTG 62.817 65.000 3.32 0.00 0.00 4.61
5077 6184 1.549203 GCTTTTGCCTCAGGGAATGA 58.451 50.000 0.00 0.00 40.15 2.57
5101 6208 4.599036 GTCAACCTTTGGCCTGGT 57.401 55.556 3.32 7.10 38.35 4.00
5115 6222 0.113972 TCCCATTGGTTGCATGGTCA 59.886 50.000 1.20 0.00 39.86 4.02
5214 6321 3.133691 TCTGTTCATCTGTGTTGCTGTC 58.866 45.455 0.00 0.00 0.00 3.51
5215 6322 3.198409 TCTGTTCATCTGTGTTGCTGT 57.802 42.857 0.00 0.00 0.00 4.40
5273 6380 1.485294 TACTTTCTTCGCTGCCCCCA 61.485 55.000 0.00 0.00 0.00 4.96
5404 6511 1.290009 GGGCAGGCAACAATCACAC 59.710 57.895 0.00 0.00 41.41 3.82
5475 6582 0.378962 CAAACGACCGCAGAAAACCA 59.621 50.000 0.00 0.00 0.00 3.67
5567 6677 3.006430 ACAAGTTAAAAGGGGCATTTCCG 59.994 43.478 0.00 0.00 34.94 4.30
5575 6685 2.955660 TCACAGCACAAGTTAAAAGGGG 59.044 45.455 0.00 0.00 0.00 4.79
5595 6705 4.965119 AAATCAGCATACGGTCCTTTTC 57.035 40.909 0.00 0.00 0.00 2.29
5661 6775 2.993899 CTCTGAAACACCGGTGTACATC 59.006 50.000 38.93 32.37 44.13 3.06
5662 6776 2.870435 GCTCTGAAACACCGGTGTACAT 60.870 50.000 38.93 27.31 44.13 2.29
5663 6777 1.539496 GCTCTGAAACACCGGTGTACA 60.539 52.381 38.93 34.24 44.13 2.90
5664 6778 1.145803 GCTCTGAAACACCGGTGTAC 58.854 55.000 38.93 31.99 44.13 2.90
5665 6779 0.753867 TGCTCTGAAACACCGGTGTA 59.246 50.000 38.93 23.43 44.13 2.90
5669 6783 1.532868 CTCTTTGCTCTGAAACACCGG 59.467 52.381 0.00 0.00 0.00 5.28
5714 6828 5.240623 TGCCCTTACAATAATTATCAAGCCG 59.759 40.000 0.00 0.00 0.00 5.52
5715 6829 6.648879 TGCCCTTACAATAATTATCAAGCC 57.351 37.500 0.00 0.00 0.00 4.35
5716 6830 6.642540 GCTTGCCCTTACAATAATTATCAAGC 59.357 38.462 19.74 19.74 43.43 4.01
5717 6831 7.649306 GTGCTTGCCCTTACAATAATTATCAAG 59.351 37.037 11.88 11.88 0.00 3.02
5718 6832 7.341769 AGTGCTTGCCCTTACAATAATTATCAA 59.658 33.333 0.00 0.00 0.00 2.57
5719 6833 6.833416 AGTGCTTGCCCTTACAATAATTATCA 59.167 34.615 0.00 0.00 0.00 2.15
5720 6834 7.141363 CAGTGCTTGCCCTTACAATAATTATC 58.859 38.462 0.00 0.00 0.00 1.75
5749 6863 4.630069 CAGTTCCCTCGGTACTAAACATTG 59.370 45.833 0.00 0.00 31.63 2.82
5750 6864 4.828829 CAGTTCCCTCGGTACTAAACATT 58.171 43.478 0.00 0.00 31.63 2.71
5762 6876 4.760047 CCCGGTGCAGTTCCCTCG 62.760 72.222 0.00 0.00 0.00 4.63
5790 6904 1.595794 CAAACTGTTCCACGCGTAAGT 59.404 47.619 13.44 8.16 41.68 2.24
5791 6905 1.070175 CCAAACTGTTCCACGCGTAAG 60.070 52.381 13.44 6.80 43.44 2.34
5793 6907 0.179078 ACCAAACTGTTCCACGCGTA 60.179 50.000 13.44 0.00 0.00 4.42
5854 6968 0.105913 TGGACCAGAAACAAACCCCC 60.106 55.000 0.00 0.00 0.00 5.40
6024 7141 4.662961 CCGTGGACGCACTGCTGA 62.663 66.667 0.00 0.00 38.18 4.26
6025 7142 4.662961 TCCGTGGACGCACTGCTG 62.663 66.667 0.00 0.00 38.18 4.41
6026 7143 4.664677 GTCCGTGGACGCACTGCT 62.665 66.667 2.78 0.00 38.18 4.24
6034 7151 2.049433 CGGTCACTGTCCGTGGAC 60.049 66.667 12.17 12.17 43.94 4.02
6039 7156 1.663702 GTTGTCCGGTCACTGTCCG 60.664 63.158 0.00 7.65 46.49 4.79
6040 7157 0.878961 GTGTTGTCCGGTCACTGTCC 60.879 60.000 0.00 0.00 0.00 4.02
6059 7176 5.404946 CAGTTGTGGAGGAGCAAATTTATG 58.595 41.667 0.00 0.00 0.00 1.90
6060 7177 5.649782 CAGTTGTGGAGGAGCAAATTTAT 57.350 39.130 0.00 0.00 0.00 1.40
6074 7191 3.129287 GGTTTAGATGCATCCAGTTGTGG 59.871 47.826 23.06 0.00 46.63 4.17
6075 7192 3.181507 CGGTTTAGATGCATCCAGTTGTG 60.182 47.826 23.06 4.64 0.00 3.33
6076 7193 3.009723 CGGTTTAGATGCATCCAGTTGT 58.990 45.455 23.06 6.10 0.00 3.32
6077 7194 3.270027 TCGGTTTAGATGCATCCAGTTG 58.730 45.455 23.06 9.29 0.00 3.16
6078 7195 3.627395 TCGGTTTAGATGCATCCAGTT 57.373 42.857 23.06 7.24 0.00 3.16
6081 7198 5.163353 TGAGTATTCGGTTTAGATGCATCCA 60.163 40.000 23.06 6.95 0.00 3.41
6086 7223 7.693952 TGAATTTGAGTATTCGGTTTAGATGC 58.306 34.615 0.00 0.00 37.34 3.91
6109 7246 6.500910 ACGTACGTTTCATGAGCTAATATGA 58.499 36.000 16.72 4.23 0.00 2.15
6199 7501 9.561069 AGCTAATATGAATTTGAGTATTCGGTT 57.439 29.630 0.00 0.00 37.34 4.44
6200 7502 9.209175 GAGCTAATATGAATTTGAGTATTCGGT 57.791 33.333 0.00 0.00 37.34 4.69
6201 7503 9.208022 TGAGCTAATATGAATTTGAGTATTCGG 57.792 33.333 0.00 0.00 37.34 4.30
6215 7517 4.686091 GCTACGTTGCATGAGCTAATATGA 59.314 41.667 17.16 0.00 42.74 2.15
6243 7545 4.546829 ACGGTGACATGTGTTTAGGTAT 57.453 40.909 1.15 0.00 0.00 2.73
6261 7564 6.329496 AGCATGTCAATTTTTGGTAATACGG 58.671 36.000 0.00 0.00 0.00 4.02
6264 7567 9.461312 AGTAGAGCATGTCAATTTTTGGTAATA 57.539 29.630 0.00 0.00 0.00 0.98
6266 7569 7.759489 AGTAGAGCATGTCAATTTTTGGTAA 57.241 32.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.