Multiple sequence alignment - TraesCS3D01G459800

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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 TraesCS3D01G459800 chr3D 100.000 3895 0 0 1 3895 564918127 564922021 0.000000e+00 7193.0
1 TraesCS3D01G459800 chr3D 97.189 498 9 2 3399 3895 143398291 143397798 0.000000e+00 837.0
2 TraesCS3D01G459800 chr3D 95.866 508 9 5 3388 3893 143406237 143405740 0.000000e+00 811.0
3 TraesCS3D01G459800 chr3D 92.857 56 2 2 1744 1798 22654805 22654859 3.230000e-11 80.5
4 TraesCS3D01G459800 chr3B 91.635 2379 130 25 988 3361 752439344 752441658 0.000000e+00 3227.0
5 TraesCS3D01G459800 chr3B 91.527 838 54 5 1 836 752437993 752438815 0.000000e+00 1138.0
6 TraesCS3D01G459800 chr3B 84.051 395 52 8 2 392 788208597 788208210 1.710000e-98 370.0
7 TraesCS3D01G459800 chr3B 96.429 84 3 0 852 935 392303362 392303279 5.250000e-29 139.0
8 TraesCS3D01G459800 chr3B 91.667 60 5 0 1758 1817 189114153 189114212 2.490000e-12 84.2
9 TraesCS3D01G459800 chr3B 91.379 58 3 2 1743 1798 622273174 622273231 1.160000e-10 78.7
10 TraesCS3D01G459800 chr4D 97.183 497 11 3 3399 3893 241135665 241135170 0.000000e+00 837.0
11 TraesCS3D01G459800 chr4D 96.787 498 12 3 3399 3893 401035562 401035066 0.000000e+00 828.0
12 TraesCS3D01G459800 chr4D 97.778 45 1 0 1817 1861 256559477 256559521 1.160000e-10 78.7
13 TraesCS3D01G459800 chr4D 94.118 51 2 1 1750 1799 35618783 35618733 4.170000e-10 76.8
14 TraesCS3D01G459800 chr2D 97.006 501 9 2 3399 3893 399420243 399420743 0.000000e+00 837.0
15 TraesCS3D01G459800 chr2D 80.932 923 141 28 2128 3040 11460713 11459816 0.000000e+00 697.0
16 TraesCS3D01G459800 chr2D 83.208 530 62 17 1000 1502 11462480 11461951 9.860000e-126 460.0
17 TraesCS3D01G459800 chr2D 80.000 515 75 19 1003 1500 11824839 11824336 4.790000e-94 355.0
18 TraesCS3D01G459800 chr2D 83.390 295 48 1 2621 2915 11431707 11431414 4.960000e-69 272.0
19 TraesCS3D01G459800 chr7D 96.429 504 8 4 3398 3893 390560179 390560680 0.000000e+00 822.0
20 TraesCS3D01G459800 chr7D 94.466 506 9 9 3399 3893 390568081 390568578 0.000000e+00 761.0
21 TraesCS3D01G459800 chr5D 95.992 499 15 4 3399 3893 345553413 345553910 0.000000e+00 806.0
22 TraesCS3D01G459800 chr5D 90.805 87 5 2 1758 1843 112241317 112241401 3.180000e-21 113.0
23 TraesCS3D01G459800 chr5D 82.667 75 11 1 1758 1830 378618818 378618892 9.030000e-07 65.8
24 TraesCS3D01G459800 chr1D 95.285 509 10 4 3399 3893 24082543 24082035 0.000000e+00 795.0
25 TraesCS3D01G459800 chr2B 81.690 781 128 12 2128 2902 17836556 17835785 1.530000e-178 636.0
26 TraesCS3D01G459800 chr2B 80.228 703 131 7 2196 2898 18176189 18176883 4.460000e-144 521.0
27 TraesCS3D01G459800 chr2B 83.852 514 72 9 1005 1508 17838130 17837618 2.720000e-131 479.0
28 TraesCS3D01G459800 chr2B 80.754 504 82 11 1003 1500 18197882 18197388 2.840000e-101 379.0
29 TraesCS3D01G459800 chr2B 80.154 519 81 8 1007 1505 18175067 18175583 6.150000e-98 368.0
30 TraesCS3D01G459800 chr2B 82.143 420 65 10 1 414 619961188 619961603 6.190000e-93 351.0
31 TraesCS3D01G459800 chr2B 73.472 671 144 20 2235 2899 18040761 18040119 5.070000e-54 222.0
32 TraesCS3D01G459800 chr2B 94.118 68 3 1 1750 1817 738679255 738679189 6.890000e-18 102.0
33 TraesCS3D01G459800 chrUn 79.630 918 160 22 2129 3040 276512198 276511302 5.490000e-178 634.0
34 TraesCS3D01G459800 chrUn 93.878 49 3 0 1811 1859 88050340 88050388 1.500000e-09 75.0
35 TraesCS3D01G459800 chr2A 79.630 918 160 22 2129 3040 12035012 12034116 5.490000e-178 634.0
36 TraesCS3D01G459800 chr2A 76.876 813 151 27 2129 2919 12140626 12139829 3.600000e-115 425.0
37 TraesCS3D01G459800 chr2A 80.078 512 90 6 1010 1509 12291432 12290921 1.710000e-98 370.0
38 TraesCS3D01G459800 chr2A 78.906 512 86 16 1003 1500 12316515 12316012 1.040000e-85 327.0
39 TraesCS3D01G459800 chr2A 80.469 128 8 9 1753 1879 102289436 102289547 8.970000e-12 82.4
40 TraesCS3D01G459800 chr1A 84.180 512 69 8 1004 1506 12355211 12355719 1.630000e-133 486.0
41 TraesCS3D01G459800 chr1A 83.254 418 60 7 2 414 521906534 521906946 3.670000e-100 375.0
42 TraesCS3D01G459800 chr1A 89.474 57 6 0 1817 1873 6561159 6561103 5.400000e-09 73.1
43 TraesCS3D01G459800 chr5B 83.411 428 50 15 2 416 11554206 11554625 1.020000e-100 377.0
44 TraesCS3D01G459800 chr5B 87.500 64 6 2 1804 1867 167283363 167283424 5.400000e-09 73.1
45 TraesCS3D01G459800 chr1B 83.911 404 55 7 2 400 494067233 494066835 1.020000e-100 377.0
46 TraesCS3D01G459800 chr1B 96.774 62 1 1 1756 1817 67023345 67023405 6.890000e-18 102.0
47 TraesCS3D01G459800 chr1B 94.595 37 2 0 504 540 427675210 427675246 1.510000e-04 58.4
48 TraesCS3D01G459800 chr5A 84.304 395 51 8 2 392 620407927 620407540 3.670000e-100 375.0
49 TraesCS3D01G459800 chr5A 85.345 116 15 2 1746 1859 546393814 546393929 6.840000e-23 119.0
50 TraesCS3D01G459800 chr5A 100.000 28 0 0 3358 3385 159527025 159526998 7.000000e-03 52.8
51 TraesCS3D01G459800 chr7A 82.578 419 62 11 2 414 686924330 686923917 3.700000e-95 359.0
52 TraesCS3D01G459800 chr4B 82.381 420 63 11 2 415 519801170 519800756 4.790000e-94 355.0
53 TraesCS3D01G459800 chr6A 81.739 115 6 4 1755 1869 435249376 435249475 8.970000e-12 82.4


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 TraesCS3D01G459800 chr3D 564918127 564922021 3894 False 7193.0 7193 100.000 1 3895 1 chr3D.!!$F2 3894
1 TraesCS3D01G459800 chr3B 752437993 752441658 3665 False 2182.5 3227 91.581 1 3361 2 chr3B.!!$F3 3360
2 TraesCS3D01G459800 chr2D 399420243 399420743 500 False 837.0 837 97.006 3399 3893 1 chr2D.!!$F1 494
3 TraesCS3D01G459800 chr2D 11459816 11462480 2664 True 578.5 697 82.070 1000 3040 2 chr2D.!!$R3 2040
4 TraesCS3D01G459800 chr2D 11824336 11824839 503 True 355.0 355 80.000 1003 1500 1 chr2D.!!$R2 497
5 TraesCS3D01G459800 chr7D 390560179 390560680 501 False 822.0 822 96.429 3398 3893 1 chr7D.!!$F1 495
6 TraesCS3D01G459800 chr1D 24082035 24082543 508 True 795.0 795 95.285 3399 3893 1 chr1D.!!$R1 494
7 TraesCS3D01G459800 chr2B 17835785 17838130 2345 True 557.5 636 82.771 1005 2902 2 chr2B.!!$R4 1897
8 TraesCS3D01G459800 chr2B 18175067 18176883 1816 False 444.5 521 80.191 1007 2898 2 chr2B.!!$F2 1891
9 TraesCS3D01G459800 chr2B 18040119 18040761 642 True 222.0 222 73.472 2235 2899 1 chr2B.!!$R1 664
10 TraesCS3D01G459800 chrUn 276511302 276512198 896 True 634.0 634 79.630 2129 3040 1 chrUn.!!$R1 911
11 TraesCS3D01G459800 chr2A 12034116 12035012 896 True 634.0 634 79.630 2129 3040 1 chr2A.!!$R1 911
12 TraesCS3D01G459800 chr2A 12139829 12140626 797 True 425.0 425 76.876 2129 2919 1 chr2A.!!$R2 790
13 TraesCS3D01G459800 chr2A 12290921 12291432 511 True 370.0 370 80.078 1010 1509 1 chr2A.!!$R3 499
14 TraesCS3D01G459800 chr2A 12316012 12316515 503 True 327.0 327 78.906 1003 1500 1 chr2A.!!$R4 497
15 TraesCS3D01G459800 chr1A 12355211 12355719 508 False 486.0 486 84.180 1004 1506 1 chr1A.!!$F1 502

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
957 1292 0.106149 AAGGAAAGGCGTCAGTTCGT 59.894 50.0 0.0 0.0 0.0 3.85 F
1649 2172 0.235665 GTGTGTGCTTGATGGTGTCG 59.764 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2705 4089 0.388649 AAAAGCACGCGATCGAGACT 60.389 50.0 25.85 17.9 39.41 3.24 R
3396 4782 0.250793 AATTATCCGGGCGTCACACA 59.749 50.0 0.00 0.0 0.00 3.72 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
47 48 1.202302 CGTCATCACTAGCATCCACGT 60.202 52.381 0.00 0.00 0.00 4.49
48 49 2.464865 GTCATCACTAGCATCCACGTC 58.535 52.381 0.00 0.00 0.00 4.34
57 58 2.994995 ATCCACGTCACTCCCGCA 60.995 61.111 0.00 0.00 0.00 5.69
80 81 1.691434 GACTGCTGGAGGGAATAGAGG 59.309 57.143 0.14 0.00 0.00 3.69
94 95 5.432645 GGAATAGAGGAGAAACAAGGAAGG 58.567 45.833 0.00 0.00 0.00 3.46
101 102 0.961753 GAAACAAGGAAGGCACCAGG 59.038 55.000 3.78 0.00 0.00 4.45
105 106 0.984230 CAAGGAAGGCACCAGGAGTA 59.016 55.000 0.00 0.00 0.00 2.59
124 125 3.760035 ACGCAGTCACCGCCCTAG 61.760 66.667 0.00 0.00 29.74 3.02
125 126 4.514577 CGCAGTCACCGCCCTAGG 62.515 72.222 0.06 0.06 37.30 3.02
127 128 2.056223 GCAGTCACCGCCCTAGGTA 61.056 63.158 8.29 0.00 43.89 3.08
128 129 1.814527 CAGTCACCGCCCTAGGTAC 59.185 63.158 8.29 0.00 43.89 3.34
129 130 1.380920 AGTCACCGCCCTAGGTACC 60.381 63.158 8.29 2.73 43.89 3.34
130 131 2.440796 TCACCGCCCTAGGTACCG 60.441 66.667 8.29 7.35 43.89 4.02
131 132 2.440796 CACCGCCCTAGGTACCGA 60.441 66.667 8.29 0.00 43.89 4.69
132 133 2.440980 ACCGCCCTAGGTACCGAC 60.441 66.667 8.29 0.00 43.89 4.79
178 179 0.868406 GCAACGGAGAAGACAACAGG 59.132 55.000 0.00 0.00 0.00 4.00
187 188 2.435805 AGAAGACAACAGGAGCACAAGA 59.564 45.455 0.00 0.00 0.00 3.02
189 190 0.861837 GACAACAGGAGCACAAGACG 59.138 55.000 0.00 0.00 0.00 4.18
198 199 2.411547 GGAGCACAAGACGTCAAATTCG 60.412 50.000 19.50 1.86 0.00 3.34
204 205 1.418755 GACGTCAAATTCGGGCGTC 59.581 57.895 17.61 17.61 43.53 5.19
238 239 3.888093 CCCGCTACGATTAAGAGGG 57.112 57.895 0.00 0.00 45.94 4.30
239 240 0.317479 CCCGCTACGATTAAGAGGGG 59.683 60.000 4.16 0.00 46.99 4.79
284 285 9.357161 GGTTTGAGTTAGAGATTAGGAGATAGA 57.643 37.037 0.00 0.00 0.00 1.98
328 329 4.035675 GCAATGCCTTATCTTGTACTCCAC 59.964 45.833 0.00 0.00 0.00 4.02
340 341 0.994247 TACTCCACGTCTCTACCCCA 59.006 55.000 0.00 0.00 0.00 4.96
341 342 0.335361 ACTCCACGTCTCTACCCCAT 59.665 55.000 0.00 0.00 0.00 4.00
345 346 1.069204 CCACGTCTCTACCCCATCATG 59.931 57.143 0.00 0.00 0.00 3.07
351 352 4.215908 GTCTCTACCCCATCATGTACTCA 58.784 47.826 0.00 0.00 0.00 3.41
378 379 6.786967 ATATACCCCATACGAGGAACATAC 57.213 41.667 0.00 0.00 0.00 2.39
402 403 8.696410 ACCAATAAAACAACAAATATTAGCCG 57.304 30.769 0.00 0.00 0.00 5.52
446 448 5.222027 TGTCCAACCCTCTCACATAATTCAA 60.222 40.000 0.00 0.00 0.00 2.69
489 491 5.353938 TGGAGCATGAATTTAGTACGGTAC 58.646 41.667 10.29 10.29 0.00 3.34
507 509 4.342359 GGTACCAGAGTGAAGAGGTCTTA 58.658 47.826 7.15 0.00 36.11 2.10
561 563 2.543777 TCTGCGGCCTACATAAATCC 57.456 50.000 0.00 0.00 0.00 3.01
574 576 7.689313 GCCTACATAAATCCCATGTCTAAGTCA 60.689 40.741 0.00 0.00 37.74 3.41
596 598 8.103305 AGTCATAAGTTTCAAAGGAGCATAGAA 58.897 33.333 0.00 0.00 0.00 2.10
597 599 8.178313 GTCATAAGTTTCAAAGGAGCATAGAAC 58.822 37.037 0.00 0.00 0.00 3.01
603 605 2.932614 CAAAGGAGCATAGAACGTGAGG 59.067 50.000 0.00 0.00 0.00 3.86
609 611 2.826128 AGCATAGAACGTGAGGAGAACA 59.174 45.455 0.00 0.00 0.00 3.18
662 664 1.767681 TCTACTCCCTCGTACTCTCCC 59.232 57.143 0.00 0.00 0.00 4.30
671 673 2.807392 CTCGTACTCTCCCGATCCTAAC 59.193 54.545 0.00 0.00 31.90 2.34
689 691 2.272471 CCCCTTTTCTCCGCCTCC 59.728 66.667 0.00 0.00 0.00 4.30
707 709 2.484264 CTCCGACGGCTTCAAATTCTTT 59.516 45.455 9.66 0.00 0.00 2.52
721 723 1.408969 TTCTTTTGCAACCCCTCCAC 58.591 50.000 0.00 0.00 0.00 4.02
752 754 2.351726 GCTAACCTAACCACATGCGAAG 59.648 50.000 0.00 0.00 0.00 3.79
775 778 7.321745 AGCAAAGCTAGGAAATGTGTATTAC 57.678 36.000 0.00 0.00 36.99 1.89
792 795 3.760035 CGGTCGTGTGCCCTAGCT 61.760 66.667 0.00 0.00 40.80 3.32
794 797 1.437986 GGTCGTGTGCCCTAGCTAG 59.562 63.158 14.20 14.20 40.80 3.42
795 798 1.227002 GTCGTGTGCCCTAGCTAGC 60.227 63.158 15.74 6.62 40.80 3.42
816 819 2.103153 ACACACAAGAGGGAAGAGGA 57.897 50.000 0.00 0.00 0.00 3.71
824 827 2.406559 AGAGGGAAGAGGATGATGGTG 58.593 52.381 0.00 0.00 0.00 4.17
828 831 2.444766 GGGAAGAGGATGATGGTGGAAT 59.555 50.000 0.00 0.00 0.00 3.01
836 839 3.181436 GGATGATGGTGGAATGTCTGGAT 60.181 47.826 0.00 0.00 0.00 3.41
838 841 2.092267 TGATGGTGGAATGTCTGGATGG 60.092 50.000 0.00 0.00 0.00 3.51
839 842 1.667595 TGGTGGAATGTCTGGATGGA 58.332 50.000 0.00 0.00 0.00 3.41
840 843 2.207988 TGGTGGAATGTCTGGATGGAT 58.792 47.619 0.00 0.00 0.00 3.41
841 844 2.092267 TGGTGGAATGTCTGGATGGATG 60.092 50.000 0.00 0.00 0.00 3.51
842 845 1.952296 GTGGAATGTCTGGATGGATGC 59.048 52.381 0.00 0.00 0.00 3.91
843 846 1.233019 GGAATGTCTGGATGGATGCG 58.767 55.000 0.00 0.00 0.00 4.73
846 849 0.249615 ATGTCTGGATGGATGCGTCG 60.250 55.000 0.00 0.00 0.00 5.12
847 850 2.106938 TCTGGATGGATGCGTCGC 59.893 61.111 11.10 11.10 0.00 5.19
848 851 3.333189 CTGGATGGATGCGTCGCG 61.333 66.667 13.38 0.00 0.00 5.87
849 852 4.141965 TGGATGGATGCGTCGCGT 62.142 61.111 12.68 12.68 0.00 6.01
851 854 3.682315 GATGGATGCGTCGCGTCG 61.682 66.667 28.02 21.06 44.61 5.12
875 878 4.624364 CGTCTGCCAGTGCCACCA 62.624 66.667 0.00 0.00 36.33 4.17
876 879 2.034687 GTCTGCCAGTGCCACCAT 59.965 61.111 0.00 0.00 36.33 3.55
878 881 3.755628 CTGCCAGTGCCACCATGC 61.756 66.667 0.00 0.00 36.33 4.06
902 1237 3.640000 GCAATCCGGCGATGGTCG 61.640 66.667 9.30 0.00 43.89 4.79
907 1242 2.147315 ATCCGGCGATGGTCGATCTG 62.147 60.000 9.30 0.00 46.20 2.90
912 1247 2.663188 GATGGTCGATCTGGCGGC 60.663 66.667 0.00 0.00 34.63 6.53
913 1248 3.157217 GATGGTCGATCTGGCGGCT 62.157 63.158 11.43 0.00 35.93 5.52
915 1250 2.892425 GGTCGATCTGGCGGCTTG 60.892 66.667 11.43 3.13 35.93 4.01
916 1251 3.567797 GTCGATCTGGCGGCTTGC 61.568 66.667 11.43 0.00 45.38 4.01
926 1261 3.737172 CGGCTTGCGACCTTTGGG 61.737 66.667 0.00 0.00 38.88 4.12
927 1262 2.282180 GGCTTGCGACCTTTGGGA 60.282 61.111 0.00 0.00 36.25 4.37
928 1263 1.901464 GGCTTGCGACCTTTGGGAA 60.901 57.895 0.00 0.00 36.25 3.97
940 1275 2.911484 CTTTGGGAAGGATCTCGGAAG 58.089 52.381 0.00 0.00 0.00 3.46
941 1276 1.204146 TTGGGAAGGATCTCGGAAGG 58.796 55.000 0.00 0.00 0.00 3.46
943 1278 1.273609 TGGGAAGGATCTCGGAAGGAA 60.274 52.381 0.00 0.00 0.00 3.36
946 1281 2.158885 GGAAGGATCTCGGAAGGAAAGG 60.159 54.545 0.00 0.00 0.00 3.11
949 1284 0.175989 GATCTCGGAAGGAAAGGCGT 59.824 55.000 0.00 0.00 0.00 5.68
950 1285 0.175989 ATCTCGGAAGGAAAGGCGTC 59.824 55.000 0.00 0.00 0.00 5.19
951 1286 1.183030 TCTCGGAAGGAAAGGCGTCA 61.183 55.000 0.00 0.00 0.00 4.35
952 1287 0.737715 CTCGGAAGGAAAGGCGTCAG 60.738 60.000 0.00 0.00 0.00 3.51
953 1288 1.004918 CGGAAGGAAAGGCGTCAGT 60.005 57.895 0.00 0.00 0.00 3.41
956 1291 0.790814 GAAGGAAAGGCGTCAGTTCG 59.209 55.000 0.00 0.00 0.00 3.95
957 1292 0.106149 AAGGAAAGGCGTCAGTTCGT 59.894 50.000 0.00 0.00 0.00 3.85
958 1293 0.319641 AGGAAAGGCGTCAGTTCGTC 60.320 55.000 0.00 0.00 35.56 4.20
960 1295 1.061485 GAAAGGCGTCAGTTCGTCTC 58.939 55.000 0.00 0.00 45.09 3.36
963 1298 1.444553 GGCGTCAGTTCGTCTCCTG 60.445 63.158 0.00 0.00 32.43 3.86
974 1344 1.005340 CGTCTCCTGCTGCAGAAATC 58.995 55.000 30.10 15.77 32.44 2.17
978 1348 2.402388 CTGCTGCAGAAATCCGCG 59.598 61.111 24.88 0.00 32.44 6.46
1517 1948 3.200593 GTGAGCGCTCCTGCCATG 61.201 66.667 33.23 0.00 35.36 3.66
1518 1949 3.709633 TGAGCGCTCCTGCCATGT 61.710 61.111 33.23 0.00 35.36 3.21
1519 1950 2.358372 TGAGCGCTCCTGCCATGTA 61.358 57.895 33.23 9.65 35.36 2.29
1563 2053 2.440539 AACTGTCTGGCTGTAGAACG 57.559 50.000 0.00 0.00 0.00 3.95
1580 2070 3.555428 GTTGTCACGAGCTGGAGC 58.445 61.111 1.44 0.00 42.49 4.70
1591 2081 1.807573 GCTGGAGCTACGCTGTGTC 60.808 63.158 0.00 0.00 39.88 3.67
1592 2082 1.515088 CTGGAGCTACGCTGTGTCG 60.515 63.158 0.00 0.00 39.88 4.35
1604 2094 2.460918 GCTGTGTCGCGTTAGTATCAT 58.539 47.619 5.77 0.00 0.00 2.45
1646 2169 3.374220 AATTGTGTGTGCTTGATGGTG 57.626 42.857 0.00 0.00 0.00 4.17
1649 2172 0.235665 GTGTGTGCTTGATGGTGTCG 59.764 55.000 0.00 0.00 0.00 4.35
1661 2184 1.675641 GGTGTCGGCAGCAAATCCT 60.676 57.895 15.44 0.00 42.26 3.24
1666 2189 2.817423 CGGCAGCAAATCCTCGAGC 61.817 63.158 6.99 0.00 0.00 5.03
1688 2284 8.715088 CGAGCATCACATCATTTCTATTTGATA 58.285 33.333 0.00 0.00 30.51 2.15
1801 2603 5.391060 AAAAGCGTTTAGATCACTATCGC 57.609 39.130 11.99 11.99 44.16 4.58
1802 2604 3.992260 AGCGTTTAGATCACTATCGCT 57.008 42.857 15.15 15.15 46.27 4.93
1804 2606 3.891324 GCGTTTAGATCACTATCGCTCT 58.109 45.455 12.42 0.00 42.55 4.09
1805 2607 4.291783 GCGTTTAGATCACTATCGCTCTT 58.708 43.478 12.42 0.00 42.55 2.85
1806 2608 5.450171 GCGTTTAGATCACTATCGCTCTTA 58.550 41.667 12.42 0.00 42.55 2.10
1809 2611 7.911205 GCGTTTAGATCACTATCGCTCTTATAT 59.089 37.037 12.42 0.00 42.55 0.86
1810 2612 9.776158 CGTTTAGATCACTATCGCTCTTATATT 57.224 33.333 0.00 0.00 37.19 1.28
1970 3181 3.299340 TGTTCTTCTCTTACGGTCAGC 57.701 47.619 0.00 0.00 0.00 4.26
2010 3222 4.792068 TCCTGAAAACTGAACCAATCTGT 58.208 39.130 0.00 0.00 41.47 3.41
2030 3242 7.934855 TCTGTAGTTAGTAGTAAAGGTCTGG 57.065 40.000 0.00 0.00 0.00 3.86
2118 3346 7.118825 TGACAAGAGCTAAATGAAATCACTCTG 59.881 37.037 0.00 0.00 33.51 3.35
2230 3590 2.091432 CGACACGATGTTTGAATACGCA 59.909 45.455 0.00 0.00 0.00 5.24
2314 3674 5.588246 TGATCCGAGCTATCTGACAGATATC 59.412 44.000 22.48 18.86 36.67 1.63
2377 3737 0.323178 CATGCCCTCAGCCTGAACTT 60.323 55.000 0.00 0.00 39.28 2.66
2383 3743 1.542492 CTCAGCCTGAACTTGCCATT 58.458 50.000 0.00 0.00 0.00 3.16
2494 3854 3.167945 GACGTTACGCCGACACCG 61.168 66.667 4.09 0.00 0.00 4.94
2562 3931 5.974156 TTGAGACCATCCAATCCTGAATA 57.026 39.130 0.00 0.00 0.00 1.75
2563 3932 6.520021 TTGAGACCATCCAATCCTGAATAT 57.480 37.500 0.00 0.00 0.00 1.28
2600 3979 4.614284 CGAGCATTGTGTTTGTTCATTCTC 59.386 41.667 0.00 0.00 0.00 2.87
2705 4089 2.143122 GTGAAGAACATTGCACCGAGA 58.857 47.619 0.00 0.00 0.00 4.04
2786 4170 0.994995 CGATCAAGGAGCTGTTGTCG 59.005 55.000 0.00 3.75 0.00 4.35
2890 4274 6.551385 AAATGCTATGTCTGATTTCCGATC 57.449 37.500 0.00 0.00 0.00 3.69
2997 4382 4.723248 GCAGTGTGTAATGCTAAGGAAAC 58.277 43.478 0.00 0.00 44.06 2.78
2998 4383 4.215399 GCAGTGTGTAATGCTAAGGAAACA 59.785 41.667 0.00 0.00 44.06 2.83
3003 4388 6.017440 GTGTGTAATGCTAAGGAAACAACTGA 60.017 38.462 0.00 0.00 0.00 3.41
3040 4426 6.605849 CAATACCAGCATCTTGTATACATGC 58.394 40.000 18.19 18.19 38.43 4.06
3042 4428 4.384056 ACCAGCATCTTGTATACATGCTC 58.616 43.478 23.35 11.08 45.59 4.26
3045 4431 5.297527 CCAGCATCTTGTATACATGCTCAAA 59.702 40.000 23.35 4.93 45.59 2.69
3049 4435 5.756195 TCTTGTATACATGCTCAAATGGC 57.244 39.130 6.36 0.00 31.46 4.40
3053 4439 1.473258 TACATGCTCAAATGGCCCAC 58.527 50.000 0.00 0.00 31.46 4.61
3057 4443 2.713967 GCTCAAATGGCCCACGCAT 61.714 57.895 0.00 0.00 36.38 4.73
3070 4456 3.736100 CGCATTGAGCCGGCAACA 61.736 61.111 31.54 24.72 41.38 3.33
3074 4460 1.135141 GCATTGAGCCGGCAACATTTA 60.135 47.619 31.54 13.57 37.23 1.40
3078 4464 3.951775 TGAGCCGGCAACATTTATTTT 57.048 38.095 31.54 1.71 0.00 1.82
3079 4465 4.264460 TGAGCCGGCAACATTTATTTTT 57.736 36.364 31.54 1.45 0.00 1.94
3119 4505 5.457140 TCGAAATTTGTGTGAACAATAGCC 58.543 37.500 0.00 0.00 0.00 3.93
3219 4605 4.671831 TGTCAAGAATAAAATGGCCAGGA 58.328 39.130 13.05 0.00 0.00 3.86
3222 4608 6.213195 TGTCAAGAATAAAATGGCCAGGAAAT 59.787 34.615 13.05 0.00 0.00 2.17
3223 4609 7.105588 GTCAAGAATAAAATGGCCAGGAAATT 58.894 34.615 13.05 8.73 0.00 1.82
3225 4611 8.162746 TCAAGAATAAAATGGCCAGGAAATTTT 58.837 29.630 13.05 14.99 37.32 1.82
3240 4626 9.294030 CCAGGAAATTTTTCGAGATTATTCTTG 57.706 33.333 0.00 7.18 38.06 3.02
3242 4628 9.025041 AGGAAATTTTTCGAGATTATTCTTGGT 57.975 29.630 0.00 0.00 38.06 3.67
3254 4640 0.179043 TTCTTGGTGCACCGCTTACA 60.179 50.000 30.07 9.47 39.43 2.41
3258 4644 2.485122 GTGCACCGCTTACATGGC 59.515 61.111 5.22 0.00 0.00 4.40
3259 4645 2.033294 TGCACCGCTTACATGGCA 59.967 55.556 0.00 0.00 0.00 4.92
3297 4683 1.599071 CTGCAAGTTCTCGTCAGCAAA 59.401 47.619 0.00 0.00 0.00 3.68
3304 4690 2.612212 GTTCTCGTCAGCAAAGGTTTGA 59.388 45.455 6.63 0.00 40.55 2.69
3308 4694 1.069636 CGTCAGCAAAGGTTTGAGAGC 60.070 52.381 6.63 0.00 40.55 4.09
3327 4713 2.892425 CCATGCCGAGCCGAAGTC 60.892 66.667 0.00 0.00 0.00 3.01
3329 4715 4.514577 ATGCCGAGCCGAAGTCCG 62.515 66.667 0.00 0.00 38.18 4.79
3361 4747 1.134401 TGGCTCCTGCTACACAATAGC 60.134 52.381 0.00 0.00 40.76 2.97
3362 4748 1.134401 GGCTCCTGCTACACAATAGCA 60.134 52.381 8.27 8.27 47.00 3.49
3368 4754 2.897436 TGCTACACAATAGCAGAGCTG 58.103 47.619 4.53 0.00 44.65 4.24
3369 4755 2.208431 GCTACACAATAGCAGAGCTGG 58.792 52.381 0.00 0.00 40.10 4.85
3370 4756 2.208431 CTACACAATAGCAGAGCTGGC 58.792 52.381 0.00 0.00 40.10 4.85
3371 4757 0.393537 ACACAATAGCAGAGCTGGCC 60.394 55.000 0.00 0.00 40.10 5.36
3372 4758 0.393402 CACAATAGCAGAGCTGGCCA 60.393 55.000 4.71 4.71 40.10 5.36
3373 4759 0.329261 ACAATAGCAGAGCTGGCCAA 59.671 50.000 7.01 0.00 40.10 4.52
3374 4760 1.272092 ACAATAGCAGAGCTGGCCAAA 60.272 47.619 7.01 0.00 40.10 3.28
3375 4761 1.133790 CAATAGCAGAGCTGGCCAAAC 59.866 52.381 7.01 1.16 40.10 2.93
3376 4762 0.745845 ATAGCAGAGCTGGCCAAACG 60.746 55.000 7.01 0.00 40.10 3.60
3377 4763 2.803155 TAGCAGAGCTGGCCAAACGG 62.803 60.000 7.01 3.03 40.10 4.44
3378 4764 3.058160 CAGAGCTGGCCAAACGGG 61.058 66.667 7.01 0.00 40.85 5.28
3392 4778 4.841861 CGGGCCGGCCGATTGTAA 62.842 66.667 38.22 0.00 36.85 2.41
3393 4779 2.203294 GGGCCGGCCGATTGTAAT 60.203 61.111 38.22 0.00 36.85 1.89
3394 4780 2.258726 GGGCCGGCCGATTGTAATC 61.259 63.158 38.22 18.05 36.85 1.75
3435 4821 5.609533 ATTAAGCTACAGTAATCCCACGT 57.390 39.130 0.00 0.00 0.00 4.49
3476 4862 3.181476 ACGGTTACTGTTGTTAACCTCGT 60.181 43.478 2.48 0.00 40.66 4.18
3599 4986 7.761409 TGCACTGATAATTATTGTGGAGAAAC 58.239 34.615 22.56 12.31 0.00 2.78
3800 5202 4.467107 GGTCGCCTCCCTCCTCCT 62.467 72.222 0.00 0.00 0.00 3.69
3852 5254 4.309950 GCCACCGAACCCTGTCGT 62.310 66.667 0.00 0.00 39.43 4.34
3893 5295 3.234730 GGGCGACATCCCCTCGAT 61.235 66.667 0.00 0.00 40.51 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.134965 GCGGATGCTGTTGACTAGAGT 60.135 52.381 0.00 0.00 38.39 3.24
57 58 2.114616 CTATTCCCTCCAGCAGTCACT 58.885 52.381 0.00 0.00 0.00 3.41
66 67 4.074799 TGTTTCTCCTCTATTCCCTCCA 57.925 45.455 0.00 0.00 0.00 3.86
80 81 1.882623 CTGGTGCCTTCCTTGTTTCTC 59.117 52.381 0.00 0.00 0.00 2.87
94 95 1.153745 CTGCGTCTACTCCTGGTGC 60.154 63.158 0.00 0.00 0.00 5.01
101 102 1.514443 GCGGTGACTGCGTCTACTC 60.514 63.158 0.00 0.00 33.15 2.59
121 122 2.158652 TCTCTGATGGGTCGGTACCTAG 60.159 54.545 10.90 0.00 45.95 3.02
122 123 1.848388 TCTCTGATGGGTCGGTACCTA 59.152 52.381 10.90 0.00 45.95 3.08
123 124 0.629596 TCTCTGATGGGTCGGTACCT 59.370 55.000 10.90 0.00 45.95 3.08
124 125 0.745468 GTCTCTGATGGGTCGGTACC 59.255 60.000 0.16 0.16 45.97 3.34
125 126 0.381089 CGTCTCTGATGGGTCGGTAC 59.619 60.000 0.00 0.00 32.33 3.34
126 127 1.381928 GCGTCTCTGATGGGTCGGTA 61.382 60.000 0.00 0.00 32.33 4.02
127 128 2.711922 GCGTCTCTGATGGGTCGGT 61.712 63.158 0.00 0.00 32.33 4.69
128 129 2.105128 GCGTCTCTGATGGGTCGG 59.895 66.667 0.00 0.00 0.00 4.79
129 130 2.278206 CGCGTCTCTGATGGGTCG 60.278 66.667 0.00 0.00 0.00 4.79
130 131 2.105128 CCGCGTCTCTGATGGGTC 59.895 66.667 4.92 0.00 30.95 4.46
131 132 2.283529 AACCGCGTCTCTGATGGGT 61.284 57.895 4.92 0.00 30.95 4.51
132 133 1.811266 CAACCGCGTCTCTGATGGG 60.811 63.158 4.92 0.00 0.00 4.00
133 134 0.179100 ATCAACCGCGTCTCTGATGG 60.179 55.000 4.92 0.00 0.00 3.51
178 179 2.411547 CCGAATTTGACGTCTTGTGCTC 60.412 50.000 17.92 5.17 0.00 4.26
187 188 0.672401 ATGACGCCCGAATTTGACGT 60.672 50.000 11.96 11.96 40.11 4.34
189 190 0.026285 CGATGACGCCCGAATTTGAC 59.974 55.000 0.00 0.00 0.00 3.18
204 205 1.519455 GGGAGTGAAGCGGACGATG 60.519 63.158 0.00 0.00 0.00 3.84
257 258 9.362151 CTATCTCCTAATCTCTAACTCAAACCT 57.638 37.037 0.00 0.00 0.00 3.50
306 307 4.271049 CGTGGAGTACAAGATAAGGCATTG 59.729 45.833 0.00 0.00 0.00 2.82
307 308 4.081087 ACGTGGAGTACAAGATAAGGCATT 60.081 41.667 0.00 0.00 32.54 3.56
328 329 3.223435 AGTACATGATGGGGTAGAGACG 58.777 50.000 0.00 0.00 0.00 4.18
345 346 9.228949 CCTCGTATGGGGTATATATATGAGTAC 57.771 40.741 5.44 0.00 38.14 2.73
378 379 7.254286 GGCGGCTAATATTTGTTGTTTTATTGG 60.254 37.037 0.00 0.00 0.00 3.16
418 420 2.862541 TGTGAGAGGGTTGGACATTTG 58.137 47.619 0.00 0.00 0.00 2.32
446 448 6.151817 GCTCCATCCAACTTATTCAAAAGTCT 59.848 38.462 0.00 0.00 38.76 3.24
463 465 4.452455 CCGTACTAAATTCATGCTCCATCC 59.548 45.833 0.00 0.00 0.00 3.51
489 491 5.011125 TGAACTTAAGACCTCTTCACTCTGG 59.989 44.000 10.09 0.00 37.40 3.86
507 509 3.565307 TCATTGGCAAGGTCTTGAACTT 58.435 40.909 12.03 0.00 42.93 2.66
539 541 4.384208 GGGATTTATGTAGGCCGCAGATAT 60.384 45.833 8.88 5.22 0.00 1.63
540 542 3.055385 GGGATTTATGTAGGCCGCAGATA 60.055 47.826 8.88 1.77 0.00 1.98
543 545 1.202758 TGGGATTTATGTAGGCCGCAG 60.203 52.381 8.88 0.00 0.00 5.18
561 563 8.454106 CCTTTGAAACTTATGACTTAGACATGG 58.546 37.037 7.39 3.46 0.00 3.66
574 576 6.879458 ACGTTCTATGCTCCTTTGAAACTTAT 59.121 34.615 0.00 0.00 0.00 1.73
596 598 1.971357 ACTCCAATGTTCTCCTCACGT 59.029 47.619 0.00 0.00 0.00 4.49
597 599 2.751166 ACTCCAATGTTCTCCTCACG 57.249 50.000 0.00 0.00 0.00 4.35
603 605 7.552687 TGTTGGACATTATACTCCAATGTTCTC 59.447 37.037 7.73 3.14 46.03 2.87
609 611 4.574828 GCGTGTTGGACATTATACTCCAAT 59.425 41.667 8.34 0.00 46.03 3.16
662 664 2.158798 GGAGAAAAGGGGGTTAGGATCG 60.159 54.545 0.00 0.00 0.00 3.69
671 673 2.272471 GAGGCGGAGAAAAGGGGG 59.728 66.667 0.00 0.00 0.00 5.40
707 709 0.555769 AGAAAGTGGAGGGGTTGCAA 59.444 50.000 0.00 0.00 0.00 4.08
721 723 4.636206 GTGGTTAGGTTAGCATGGAGAAAG 59.364 45.833 0.00 0.00 0.00 2.62
752 754 6.192360 CGTAATACACATTTCCTAGCTTTGC 58.808 40.000 0.00 0.00 0.00 3.68
792 795 2.703536 TCTTCCCTCTTGTGTGTTGCTA 59.296 45.455 0.00 0.00 0.00 3.49
794 797 1.876156 CTCTTCCCTCTTGTGTGTTGC 59.124 52.381 0.00 0.00 0.00 4.17
795 798 2.104792 TCCTCTTCCCTCTTGTGTGTTG 59.895 50.000 0.00 0.00 0.00 3.33
816 819 3.436035 CCATCCAGACATTCCACCATCAT 60.436 47.826 0.00 0.00 0.00 2.45
824 827 1.233019 CGCATCCATCCAGACATTCC 58.767 55.000 0.00 0.00 0.00 3.01
828 831 1.141665 CGACGCATCCATCCAGACA 59.858 57.895 0.00 0.00 0.00 3.41
858 861 3.907260 ATGGTGGCACTGGCAGACG 62.907 63.158 23.66 12.82 43.71 4.18
859 862 2.034687 ATGGTGGCACTGGCAGAC 59.965 61.111 23.66 12.58 43.71 3.51
860 863 2.034532 CATGGTGGCACTGGCAGA 59.965 61.111 23.66 0.00 43.71 4.26
861 864 3.755628 GCATGGTGGCACTGGCAG 61.756 66.667 18.45 14.16 43.71 4.85
881 884 4.596180 CATCGCCGGATTGCACGC 62.596 66.667 5.05 0.00 0.00 5.34
882 885 3.940640 CCATCGCCGGATTGCACG 61.941 66.667 5.05 0.00 0.00 5.34
884 887 2.513666 GACCATCGCCGGATTGCA 60.514 61.111 5.05 0.00 0.00 4.08
886 889 1.284982 GATCGACCATCGCCGGATTG 61.285 60.000 5.05 0.00 40.21 2.67
888 891 1.903890 AGATCGACCATCGCCGGAT 60.904 57.895 5.05 0.00 40.21 4.18
889 892 2.518587 AGATCGACCATCGCCGGA 60.519 61.111 5.05 0.00 40.21 5.14
890 893 2.355126 CAGATCGACCATCGCCGG 60.355 66.667 0.00 0.00 40.21 6.13
892 895 2.663188 GCCAGATCGACCATCGCC 60.663 66.667 0.00 0.00 40.21 5.54
896 1231 2.735772 AAGCCGCCAGATCGACCAT 61.736 57.895 0.00 0.00 0.00 3.55
902 1237 3.567797 GTCGCAAGCCGCCAGATC 61.568 66.667 0.00 0.00 37.30 2.75
907 1242 4.404654 CAAAGGTCGCAAGCCGCC 62.405 66.667 0.00 0.00 38.35 6.13
912 1247 2.257353 CCTTCCCAAAGGTCGCAAG 58.743 57.895 0.00 0.00 46.10 4.01
913 1248 4.492604 CCTTCCCAAAGGTCGCAA 57.507 55.556 0.00 0.00 46.10 4.85
921 1256 1.559682 CCTTCCGAGATCCTTCCCAAA 59.440 52.381 0.00 0.00 0.00 3.28
923 1258 0.338467 TCCTTCCGAGATCCTTCCCA 59.662 55.000 0.00 0.00 0.00 4.37
924 1259 1.497161 TTCCTTCCGAGATCCTTCCC 58.503 55.000 0.00 0.00 0.00 3.97
926 1261 2.743510 GCCTTTCCTTCCGAGATCCTTC 60.744 54.545 0.00 0.00 0.00 3.46
927 1262 1.210722 GCCTTTCCTTCCGAGATCCTT 59.789 52.381 0.00 0.00 0.00 3.36
928 1263 0.833949 GCCTTTCCTTCCGAGATCCT 59.166 55.000 0.00 0.00 0.00 3.24
930 1265 0.175989 ACGCCTTTCCTTCCGAGATC 59.824 55.000 0.00 0.00 0.00 2.75
931 1266 0.175989 GACGCCTTTCCTTCCGAGAT 59.824 55.000 0.00 0.00 0.00 2.75
932 1267 1.183030 TGACGCCTTTCCTTCCGAGA 61.183 55.000 0.00 0.00 0.00 4.04
933 1268 0.737715 CTGACGCCTTTCCTTCCGAG 60.738 60.000 0.00 0.00 0.00 4.63
935 1270 0.602905 AACTGACGCCTTTCCTTCCG 60.603 55.000 0.00 0.00 0.00 4.30
937 1272 0.790814 CGAACTGACGCCTTTCCTTC 59.209 55.000 0.00 0.00 0.00 3.46
938 1273 0.106149 ACGAACTGACGCCTTTCCTT 59.894 50.000 0.00 0.00 36.70 3.36
939 1274 0.319641 GACGAACTGACGCCTTTCCT 60.320 55.000 0.00 0.00 36.70 3.36
940 1275 0.319641 AGACGAACTGACGCCTTTCC 60.320 55.000 0.00 0.00 36.70 3.13
941 1276 1.061485 GAGACGAACTGACGCCTTTC 58.939 55.000 0.00 0.00 36.70 2.62
943 1278 1.179814 AGGAGACGAACTGACGCCTT 61.180 55.000 0.00 0.00 39.26 4.35
946 1281 2.089349 GCAGGAGACGAACTGACGC 61.089 63.158 0.00 0.00 36.86 5.19
949 1284 1.290324 GCAGCAGGAGACGAACTGA 59.710 57.895 0.00 0.00 36.86 3.41
950 1285 1.005748 TGCAGCAGGAGACGAACTG 60.006 57.895 0.00 0.00 37.76 3.16
951 1286 1.181741 TCTGCAGCAGGAGACGAACT 61.182 55.000 22.62 0.00 37.29 3.01
952 1287 0.319900 TTCTGCAGCAGGAGACGAAC 60.320 55.000 22.62 0.00 42.31 3.95
953 1288 0.392706 TTTCTGCAGCAGGAGACGAA 59.607 50.000 22.62 5.49 42.31 3.85
956 1291 1.377536 GGATTTCTGCAGCAGGAGAC 58.622 55.000 22.62 11.10 42.31 3.36
957 1292 0.107993 CGGATTTCTGCAGCAGGAGA 60.108 55.000 22.62 8.97 40.77 3.71
958 1293 2.391469 CGGATTTCTGCAGCAGGAG 58.609 57.895 22.62 0.00 31.51 3.69
959 1294 4.623814 CGGATTTCTGCAGCAGGA 57.376 55.556 22.62 11.66 31.51 3.86
1511 1942 1.993956 AAACTTGCAGGTACATGGCA 58.006 45.000 9.91 5.46 35.41 4.92
1514 1945 4.023279 TGCAGTAAAACTTGCAGGTACATG 60.023 41.667 0.22 2.43 31.85 3.21
1517 1948 4.766404 ATGCAGTAAAACTTGCAGGTAC 57.234 40.909 0.22 0.00 36.34 3.34
1518 1949 5.782893 AAATGCAGTAAAACTTGCAGGTA 57.217 34.783 0.22 0.00 36.34 3.08
1519 1950 4.670896 AAATGCAGTAAAACTTGCAGGT 57.329 36.364 0.00 0.00 36.34 4.00
1563 2053 3.555428 GCTCCAGCTCGTGACAAC 58.445 61.111 0.00 0.00 38.21 3.32
1585 2075 4.352039 AGAATGATACTAACGCGACACAG 58.648 43.478 15.93 6.28 0.00 3.66
1587 2077 4.910456 CCTAGAATGATACTAACGCGACAC 59.090 45.833 15.93 0.00 0.00 3.67
1588 2078 4.556104 GCCTAGAATGATACTAACGCGACA 60.556 45.833 15.93 0.00 0.00 4.35
1589 2079 3.913163 GCCTAGAATGATACTAACGCGAC 59.087 47.826 15.93 0.00 0.00 5.19
1591 2081 3.243336 GGCCTAGAATGATACTAACGCG 58.757 50.000 3.53 3.53 0.00 6.01
1592 2082 3.243336 CGGCCTAGAATGATACTAACGC 58.757 50.000 0.00 0.00 0.00 4.84
1595 2085 3.576982 CACCCGGCCTAGAATGATACTAA 59.423 47.826 0.00 0.00 0.00 2.24
1597 2087 1.971357 CACCCGGCCTAGAATGATACT 59.029 52.381 0.00 0.00 0.00 2.12
1598 2088 1.002087 CCACCCGGCCTAGAATGATAC 59.998 57.143 0.00 0.00 0.00 2.24
1600 2090 1.418908 CCCACCCGGCCTAGAATGAT 61.419 60.000 0.00 0.00 0.00 2.45
1601 2091 2.070039 CCCACCCGGCCTAGAATGA 61.070 63.158 0.00 0.00 0.00 2.57
1602 2092 1.921869 AACCCACCCGGCCTAGAATG 61.922 60.000 0.00 0.00 33.26 2.67
1604 2094 0.979187 CTAACCCACCCGGCCTAGAA 60.979 60.000 0.00 0.00 33.26 2.10
1646 2169 1.424493 CTCGAGGATTTGCTGCCGAC 61.424 60.000 3.91 0.00 0.00 4.79
1649 2172 1.099879 ATGCTCGAGGATTTGCTGCC 61.100 55.000 14.37 0.00 0.00 4.85
1661 2184 6.762661 TCAAATAGAAATGATGTGATGCTCGA 59.237 34.615 0.00 0.00 0.00 4.04
1761 2563 9.880157 AACGCTTTTATATTAGTTTACAGAGGA 57.120 29.630 0.00 0.00 0.00 3.71
1784 2586 9.776158 AATATAAGAGCGATAGTGATCTAAACG 57.224 33.333 0.00 0.00 39.35 3.60
1827 2688 8.985805 CCTCCGTAAAATAATATAAGAGCGTTT 58.014 33.333 0.00 0.00 0.00 3.60
1970 3181 4.644234 TCAGGATACAGAGAAAGAGAGCAG 59.356 45.833 0.00 0.00 41.41 4.24
2050 3262 8.574251 TGGCTCACAATAACAATAAGTACATT 57.426 30.769 0.00 0.00 0.00 2.71
2066 3278 2.036217 CCAAGCAAGAAATGGCTCACAA 59.964 45.455 0.00 0.00 40.01 3.33
2118 3346 8.593492 AAAATTCACAGAAAAGGTTTCTATGC 57.407 30.769 4.49 0.00 0.00 3.14
2179 3504 7.944729 AATCAACATGTTAGCTCCAAGTTAT 57.055 32.000 11.53 1.27 0.00 1.89
2230 3590 5.033589 TGCCCAAATTCATCACTTGTTTT 57.966 34.783 0.00 0.00 0.00 2.43
2314 3674 2.791383 TTTGTCCTTGGTTGCAATCG 57.209 45.000 0.59 0.00 0.00 3.34
2494 3854 1.737838 TGTTGACGATGAATGCTCCC 58.262 50.000 0.00 0.00 0.00 4.30
2562 3931 2.028130 TGCTCGGGTGTTGAACAAAAT 58.972 42.857 0.00 0.00 0.00 1.82
2563 3932 1.464734 TGCTCGGGTGTTGAACAAAA 58.535 45.000 0.00 0.00 0.00 2.44
2634 4014 3.400255 CGTCATTGGAGATCATCTGCAT 58.600 45.455 10.03 0.00 44.28 3.96
2669 4049 1.153369 CACCACCACCCTATGCTCG 60.153 63.158 0.00 0.00 0.00 5.03
2705 4089 0.388649 AAAAGCACGCGATCGAGACT 60.389 50.000 25.85 17.90 39.41 3.24
2890 4274 4.458295 ACAAGCTCTCCTTCACAATTCATG 59.542 41.667 0.00 0.00 0.00 3.07
2996 4381 7.171337 GGTATTGCATTGTCATTTTTCAGTTGT 59.829 33.333 0.00 0.00 0.00 3.32
2997 4382 7.171167 TGGTATTGCATTGTCATTTTTCAGTTG 59.829 33.333 0.00 0.00 0.00 3.16
2998 4383 7.215789 TGGTATTGCATTGTCATTTTTCAGTT 58.784 30.769 0.00 0.00 0.00 3.16
3003 4388 5.549347 TGCTGGTATTGCATTGTCATTTTT 58.451 33.333 0.00 0.00 35.31 1.94
3040 4426 0.458889 CAATGCGTGGGCCATTTGAG 60.459 55.000 10.70 0.14 38.85 3.02
3042 4428 0.458889 CTCAATGCGTGGGCCATTTG 60.459 55.000 10.70 11.91 38.85 2.32
3053 4439 2.546645 AATGTTGCCGGCTCAATGCG 62.547 55.000 29.70 0.00 44.05 4.73
3057 4443 3.951775 AAATAAATGTTGCCGGCTCAA 57.048 38.095 29.70 12.19 0.00 3.02
3081 4467 9.808808 CACAAATTTCGAAATGATTTATTGCAA 57.191 25.926 23.38 0.00 0.00 4.08
3082 4468 8.986847 ACACAAATTTCGAAATGATTTATTGCA 58.013 25.926 23.38 0.00 0.00 4.08
3083 4469 9.253275 CACACAAATTTCGAAATGATTTATTGC 57.747 29.630 23.38 0.00 0.00 3.56
3112 4498 5.091261 AGAGAGTACAAGGTTGGCTATTG 57.909 43.478 0.00 0.00 0.00 1.90
3119 4505 5.237815 TGTATGCAAGAGAGTACAAGGTTG 58.762 41.667 0.00 0.00 0.00 3.77
3206 4592 6.015010 TCTCGAAAAATTTCCTGGCCATTTTA 60.015 34.615 5.51 0.00 31.35 1.52
3219 4605 8.087750 TGCACCAAGAATAATCTCGAAAAATTT 58.912 29.630 0.00 0.00 33.77 1.82
3222 4608 6.378582 GTGCACCAAGAATAATCTCGAAAAA 58.621 36.000 5.22 0.00 33.77 1.94
3223 4609 5.106317 GGTGCACCAAGAATAATCTCGAAAA 60.106 40.000 31.23 0.00 33.77 2.29
3225 4611 3.938963 GGTGCACCAAGAATAATCTCGAA 59.061 43.478 31.23 0.00 33.77 3.71
3240 4626 3.051392 GCCATGTAAGCGGTGCACC 62.051 63.158 26.78 26.78 0.00 5.01
3242 4628 2.033294 TGCCATGTAAGCGGTGCA 59.967 55.556 0.00 0.00 0.00 4.57
3254 4640 1.560505 GACCCCAAGAATTGTGCCAT 58.439 50.000 0.00 0.00 46.99 4.40
3258 4644 3.763931 TGGGACCCCAAGAATTGTG 57.236 52.632 8.45 0.00 46.99 3.33
3291 4677 0.600057 GGGCTCTCAAACCTTTGCTG 59.400 55.000 0.00 0.00 38.05 4.41
3293 4679 0.827507 TGGGGCTCTCAAACCTTTGC 60.828 55.000 0.00 0.00 38.05 3.68
3297 4683 1.000396 GCATGGGGCTCTCAAACCT 60.000 57.895 0.00 0.00 40.25 3.50
3323 4709 3.392616 AGCCATGAGAATAATCCGGACTT 59.607 43.478 6.12 5.26 0.00 3.01
3327 4713 2.304180 AGGAGCCATGAGAATAATCCGG 59.696 50.000 0.00 0.00 0.00 5.14
3329 4715 3.080319 GCAGGAGCCATGAGAATAATCC 58.920 50.000 0.00 0.00 33.58 3.01
3334 4720 2.121948 TGTAGCAGGAGCCATGAGAAT 58.878 47.619 0.00 0.00 43.56 2.40
3337 4723 0.538584 TGTGTAGCAGGAGCCATGAG 59.461 55.000 0.00 0.00 43.56 2.90
3361 4747 3.058160 CCCGTTTGGCCAGCTCTG 61.058 66.667 5.11 0.00 0.00 3.35
3376 4762 2.203294 ATTACAATCGGCCGGCCC 60.203 61.111 39.24 21.72 0.00 5.80
3377 4763 3.340789 GATTACAATCGGCCGGCC 58.659 61.111 36.69 36.69 0.00 6.13
3395 4781 0.461339 ATTATCCGGGCGTCACACAC 60.461 55.000 0.00 0.00 0.00 3.82
3396 4782 0.250793 AATTATCCGGGCGTCACACA 59.749 50.000 0.00 0.00 0.00 3.72
3435 4821 2.080693 GTGGTGACGTGGCATCATTAA 58.919 47.619 0.00 0.00 30.53 1.40
3476 4862 5.425577 TTTGAAACGGTTTCGAATCATCA 57.574 34.783 25.26 8.79 42.55 3.07
3540 4926 6.258947 CACCCACCGAACATTTTTGTTTAAAT 59.741 34.615 0.00 0.00 31.35 1.40
3800 5202 3.961414 GCTGGGTCGGGGGAACAA 61.961 66.667 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.