Multiple sequence alignment - TraesCS6A01G084700

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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 TraesCS6A01G084700 chr6A 100.000 3970 0 0 1 3970 53115973 53119942 0.000000e+00 7332.0
1 TraesCS6A01G084700 chrUn 89.042 1816 93 49 1 1743 97736790 97738572 0.000000e+00 2154.0
2 TraesCS6A01G084700 chrUn 94.959 853 42 1 2323 3174 97738960 97739812 0.000000e+00 1336.0
3 TraesCS6A01G084700 chrUn 95.293 786 27 5 3191 3970 355949121 355948340 0.000000e+00 1238.0
4 TraesCS6A01G084700 chrUn 89.744 390 25 10 1851 2227 97738574 97738961 5.960000e-133 484.0
5 TraesCS6A01G084700 chr2A 98.467 783 12 0 3188 3970 83926694 83925912 0.000000e+00 1380.0
6 TraesCS6A01G084700 chr2A 97.297 37 1 0 210 246 709700323 709700359 3.310000e-06 63.9
7 TraesCS6A01G084700 chr6B 95.210 856 34 6 2321 3176 106469151 106469999 0.000000e+00 1347.0
8 TraesCS6A01G084700 chr6B 96.178 785 23 1 3186 3970 17950709 17949932 0.000000e+00 1277.0
9 TraesCS6A01G084700 chr6B 93.147 715 36 10 1525 2227 106468438 106469151 0.000000e+00 1037.0
10 TraesCS6A01G084700 chr6B 90.452 597 24 6 822 1406 106467602 106468177 0.000000e+00 756.0
11 TraesCS6A01G084700 chr6B 87.200 125 6 6 1744 1860 106468769 106468647 2.490000e-27 134.0
12 TraesCS6A01G084700 chr6B 98.276 58 1 0 1 58 223663162 223663105 7.020000e-18 102.0
13 TraesCS6A01G084700 chr6B 90.625 64 4 2 1798 1860 534090438 534090500 2.540000e-12 84.2
14 TraesCS6A01G084700 chr4D 95.431 788 26 4 3186 3967 504093260 504094043 0.000000e+00 1247.0
15 TraesCS6A01G084700 chr4D 91.509 106 6 2 2225 2330 323929572 323929674 4.140000e-30 143.0
16 TraesCS6A01G084700 chr4D 90.476 63 3 3 1734 1795 496301753 496301693 3.290000e-11 80.5
17 TraesCS6A01G084700 chr4D 88.235 68 2 6 1730 1796 447746557 447746495 4.250000e-10 76.8
18 TraesCS6A01G084700 chr4D 97.368 38 1 0 208 245 36590516 36590479 9.210000e-07 65.8
19 TraesCS6A01G084700 chr4D 94.872 39 2 0 208 246 36590432 36590470 1.190000e-05 62.1
20 TraesCS6A01G084700 chr4D 92.500 40 3 0 1849 1888 67195685 67195646 1.540000e-04 58.4
21 TraesCS6A01G084700 chr5D 95.208 793 28 3 3184 3970 555471255 555470467 0.000000e+00 1245.0
22 TraesCS6A01G084700 chr5D 95.311 789 27 3 3185 3967 485756754 485757538 0.000000e+00 1243.0
23 TraesCS6A01G084700 chr5D 94.350 708 34 2 3266 3967 525576364 525577071 0.000000e+00 1081.0
24 TraesCS6A01G084700 chr5D 90.741 108 8 1 2218 2325 496587555 496587450 4.140000e-30 143.0
25 TraesCS6A01G084700 chr5D 90.476 63 2 4 1734 1795 556773744 556773803 3.290000e-11 80.5
26 TraesCS6A01G084700 chr5D 92.500 40 3 0 1849 1888 147618987 147619026 1.540000e-04 58.4
27 TraesCS6A01G084700 chr1D 95.076 792 29 3 3185 3970 28586941 28586154 0.000000e+00 1238.0
28 TraesCS6A01G084700 chr1D 91.667 108 7 1 2225 2332 483907679 483907574 8.890000e-32 148.0
29 TraesCS6A01G084700 chr1D 90.826 109 8 1 2218 2326 106959961 106959855 1.150000e-30 145.0
30 TraesCS6A01G084700 chr1D 84.298 121 10 7 1743 1858 33623038 33622922 4.190000e-20 110.0
31 TraesCS6A01G084700 chr1D 86.598 97 7 4 1760 1851 16607951 16608046 7.020000e-18 102.0
32 TraesCS6A01G084700 chr1D 86.598 97 7 5 1744 1835 16608046 16607951 7.020000e-18 102.0
33 TraesCS6A01G084700 chr1D 96.552 58 2 0 1 58 43200516 43200459 3.270000e-16 97.1
34 TraesCS6A01G084700 chr1D 96.552 58 2 0 1 58 287464776 287464719 3.270000e-16 97.1
35 TraesCS6A01G084700 chr1D 96.552 58 2 0 1 58 473536938 473536995 3.270000e-16 97.1
36 TraesCS6A01G084700 chr1D 92.308 39 3 0 208 246 7129729 7129767 5.540000e-04 56.5
37 TraesCS6A01G084700 chr3A 98.694 536 7 0 3185 3720 729869615 729869080 0.000000e+00 952.0
38 TraesCS6A01G084700 chr4B 98.476 525 7 1 3446 3970 16702012 16701489 0.000000e+00 924.0
39 TraesCS6A01G084700 chr4B 92.500 40 3 0 1849 1888 515363736 515363775 1.540000e-04 58.4
40 TraesCS6A01G084700 chr5B 94.872 117 6 0 1631 1747 711784598 711784482 2.440000e-42 183.0
41 TraesCS6A01G084700 chr5B 91.045 67 3 3 1798 1862 472739726 472739661 1.970000e-13 87.9
42 TraesCS6A01G084700 chr3B 94.872 117 6 0 1631 1747 727082853 727082969 2.440000e-42 183.0
43 TraesCS6A01G084700 chr3B 88.710 124 10 3 2211 2332 406870569 406870690 8.890000e-32 148.0
44 TraesCS6A01G084700 chr3B 92.233 103 6 1 2224 2326 421903056 421902956 1.150000e-30 145.0
45 TraesCS6A01G084700 chr3B 89.552 67 5 2 1798 1863 693059870 693059935 2.540000e-12 84.2
46 TraesCS6A01G084700 chr7B 92.308 104 6 1 2223 2326 747370731 747370630 3.200000e-31 147.0
47 TraesCS6A01G084700 chr7B 89.076 119 8 5 2218 2335 425252177 425252063 4.140000e-30 143.0
48 TraesCS6A01G084700 chr7B 83.465 127 12 6 1740 1859 419527491 419527367 4.190000e-20 110.0
49 TraesCS6A01G084700 chr7B 95.000 40 2 0 1849 1888 597765196 597765235 3.310000e-06 63.9
50 TraesCS6A01G084700 chr7B 95.000 40 2 0 1849 1888 709577766 709577727 3.310000e-06 63.9
51 TraesCS6A01G084700 chr7D 90.826 109 7 2 2219 2326 491253405 491253299 4.140000e-30 143.0
52 TraesCS6A01G084700 chr7D 84.874 119 6 9 1744 1851 613870636 613870753 4.190000e-20 110.0
53 TraesCS6A01G084700 chr7D 83.871 124 8 9 1744 1856 613870753 613870631 1.510000e-19 108.0
54 TraesCS6A01G084700 chr7D 95.238 63 3 0 1798 1860 634836508 634836446 2.520000e-17 100.0
55 TraesCS6A01G084700 chr7D 94.872 39 2 0 208 246 177996770 177996732 1.190000e-05 62.1
56 TraesCS6A01G084700 chr7D 97.143 35 1 0 208 242 629490846 629490812 4.280000e-05 60.2
57 TraesCS6A01G084700 chr2B 98.276 58 1 0 1 58 12965974 12965917 7.020000e-18 102.0
58 TraesCS6A01G084700 chr2B 90.323 62 4 2 1735 1795 721702710 721702770 3.290000e-11 80.5
59 TraesCS6A01G084700 chr4A 96.610 59 2 0 1 59 717830686 717830628 9.080000e-17 99.0
60 TraesCS6A01G084700 chr4A 97.368 38 1 0 208 245 565723469 565723506 9.210000e-07 65.8
61 TraesCS6A01G084700 chr1A 96.610 59 2 0 1 59 504836791 504836733 9.080000e-17 99.0
62 TraesCS6A01G084700 chr1A 94.595 37 2 0 208 244 8677329 8677365 1.540000e-04 58.4
63 TraesCS6A01G084700 chr1A 92.500 40 3 0 1849 1888 102763293 102763332 1.540000e-04 58.4
64 TraesCS6A01G084700 chr6D 96.552 58 2 0 1 58 259286036 259285979 3.270000e-16 97.1
65 TraesCS6A01G084700 chr3D 85.870 92 7 4 1763 1853 47491191 47491105 4.220000e-15 93.5
66 TraesCS6A01G084700 chr3D 87.692 65 4 4 1734 1796 55189418 55189480 5.500000e-09 73.1
67 TraesCS6A01G084700 chr2D 89.474 76 4 4 1794 1866 515460825 515460899 4.220000e-15 93.5
68 TraesCS6A01G084700 chr2D 88.312 77 5 4 1794 1867 399676907 399676832 5.460000e-14 89.8
69 TraesCS6A01G084700 chr2D 86.047 86 7 5 1784 1866 267844612 267844695 1.970000e-13 87.9
70 TraesCS6A01G084700 chr2D 91.379 58 2 3 1739 1795 483261159 483261104 4.250000e-10 76.8
71 TraesCS6A01G084700 chr2D 90.164 61 2 4 1733 1792 649222789 649222846 4.250000e-10 76.8
72 TraesCS6A01G084700 chr7A 92.683 41 3 0 1849 1889 305582046 305582006 4.280000e-05 60.2


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 TraesCS6A01G084700 chr6A 53115973 53119942 3969 False 7332.000000 7332 100.000000 1 3970 1 chr6A.!!$F1 3969
1 TraesCS6A01G084700 chrUn 97736790 97739812 3022 False 1324.666667 2154 91.248333 1 3174 3 chrUn.!!$F1 3173
2 TraesCS6A01G084700 chrUn 355948340 355949121 781 True 1238.000000 1238 95.293000 3191 3970 1 chrUn.!!$R1 779
3 TraesCS6A01G084700 chr2A 83925912 83926694 782 True 1380.000000 1380 98.467000 3188 3970 1 chr2A.!!$R1 782
4 TraesCS6A01G084700 chr6B 17949932 17950709 777 True 1277.000000 1277 96.178000 3186 3970 1 chr6B.!!$R1 784
5 TraesCS6A01G084700 chr6B 106467602 106469999 2397 False 1046.666667 1347 92.936333 822 3176 3 chr6B.!!$F2 2354
6 TraesCS6A01G084700 chr4D 504093260 504094043 783 False 1247.000000 1247 95.431000 3186 3967 1 chr4D.!!$F3 781
7 TraesCS6A01G084700 chr5D 555470467 555471255 788 True 1245.000000 1245 95.208000 3184 3970 1 chr5D.!!$R2 786
8 TraesCS6A01G084700 chr5D 485756754 485757538 784 False 1243.000000 1243 95.311000 3185 3967 1 chr5D.!!$F2 782
9 TraesCS6A01G084700 chr5D 525576364 525577071 707 False 1081.000000 1081 94.350000 3266 3967 1 chr5D.!!$F3 701
10 TraesCS6A01G084700 chr1D 28586154 28586941 787 True 1238.000000 1238 95.076000 3185 3970 1 chr1D.!!$R2 785
11 TraesCS6A01G084700 chr3A 729869080 729869615 535 True 952.000000 952 98.694000 3185 3720 1 chr3A.!!$R1 535
12 TraesCS6A01G084700 chr4B 16701489 16702012 523 True 924.000000 924 98.476000 3446 3970 1 chr4B.!!$R1 524

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
335 336 0.034198 TCGGCGAAGGTTGTGATTGA 59.966 50.0 7.35 0.0 0.00 2.57 F
855 894 0.252742 GAGGTCTCCTCCTTCCCCAA 60.253 60.0 4.60 0.0 44.36 4.12 F
859 898 0.327576 TCTCCTCCTTCCCCAATCCC 60.328 60.0 0.00 0.0 0.00 3.85 F
2658 2873 0.839946 AGTCTCCACTGGCAACTTGT 59.160 50.0 0.00 0.0 37.61 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2190 1.156736 ATAGACACCAAGCAACACGC 58.843 50.000 0.00 0.00 42.91 5.34 R
2534 2748 1.066908 AGGTGCAATCAACAAACCACG 59.933 47.619 0.00 0.00 33.13 4.94 R
2808 3023 5.678955 AGAGGGAGTTTGTATTACAGGAC 57.321 43.478 0.00 1.26 0.00 3.85 R
3710 3931 2.952245 GAACCTGTGCAGCAGCTG 59.048 61.111 18.93 18.93 43.71 4.24 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
31 32 0.179468 TAAGCATTACACCCGGCCTC 59.821 55.000 0.00 0.00 0.00 4.70
75 76 3.187227 ACCAACGTCACTGTAGTACTACG 59.813 47.826 24.36 20.63 38.85 3.51
76 77 3.159026 CAACGTCACTGTAGTACTACGC 58.841 50.000 24.36 12.68 38.85 4.42
77 78 1.391485 ACGTCACTGTAGTACTACGCG 59.609 52.381 24.36 22.36 38.85 6.01
81 82 2.926200 TCACTGTAGTACTACGCGTCTC 59.074 50.000 24.36 4.79 38.85 3.36
99 100 1.399440 CTCGTGAATGCCTGAATGGTG 59.601 52.381 0.00 0.00 38.35 4.17
106 107 4.581409 TGAATGCCTGAATGGTGATGTATG 59.419 41.667 0.00 0.00 38.35 2.39
110 111 4.158209 TGCCTGAATGGTGATGTATGTTTG 59.842 41.667 0.00 0.00 38.35 2.93
201 202 9.331282 GGTTCATATTTACTGCTGAGTATCTTT 57.669 33.333 0.00 0.00 34.53 2.52
215 216 9.026121 GCTGAGTATCTTTGATATTACTCCCTA 57.974 37.037 7.29 0.00 34.64 3.53
280 281 1.601903 TGTCGCATTGGTGAAGACAAC 59.398 47.619 5.23 0.00 39.68 3.32
305 306 4.759183 GGAGAAAGCATTCTTCTCTTGTGT 59.241 41.667 5.55 0.00 45.91 3.72
335 336 0.034198 TCGGCGAAGGTTGTGATTGA 59.966 50.000 7.35 0.00 0.00 2.57
343 344 2.503331 AGGTTGTGATTGACATTGCGA 58.497 42.857 0.00 0.00 33.40 5.10
372 373 8.910351 ATTGTAGTAATCTCTTTATCTTGCCC 57.090 34.615 0.00 0.00 0.00 5.36
373 374 6.827727 TGTAGTAATCTCTTTATCTTGCCCC 58.172 40.000 0.00 0.00 0.00 5.80
378 379 4.602340 TCTCTTTATCTTGCCCCGTATC 57.398 45.455 0.00 0.00 0.00 2.24
415 416 2.215907 TTGTTTGTTTCGTGCCCATG 57.784 45.000 0.00 0.00 0.00 3.66
486 487 3.660865 GACCGAAGTAGAGCTCCAAAAA 58.339 45.455 10.93 0.00 0.00 1.94
516 517 4.394300 CGATGGCTGAAAGAGAACTTTGAT 59.606 41.667 0.00 0.00 44.97 2.57
699 738 2.747686 GACTGGGAGGGCGAACAA 59.252 61.111 0.00 0.00 0.00 2.83
730 769 2.642154 TAACCCAGGAAAGAAACGCA 57.358 45.000 0.00 0.00 0.00 5.24
796 835 2.807044 CGAGATATGCGGATCCATCTG 58.193 52.381 15.23 6.13 36.26 2.90
799 838 4.497173 CGAGATATGCGGATCCATCTGTAG 60.497 50.000 15.23 5.12 35.60 2.74
801 840 4.774726 AGATATGCGGATCCATCTGTAGTT 59.225 41.667 13.41 0.00 35.60 2.24
802 841 5.952347 AGATATGCGGATCCATCTGTAGTTA 59.048 40.000 13.41 0.00 35.60 2.24
803 842 3.728076 TGCGGATCCATCTGTAGTTAC 57.272 47.619 13.41 0.00 35.60 2.50
804 843 2.034179 TGCGGATCCATCTGTAGTTACG 59.966 50.000 13.41 0.00 35.60 3.18
806 845 3.852572 GCGGATCCATCTGTAGTTACGAC 60.853 52.174 13.41 0.00 35.60 4.34
836 875 2.255252 CCGCAACGCAAAAGGGAG 59.745 61.111 0.00 0.00 0.00 4.30
855 894 0.252742 GAGGTCTCCTCCTTCCCCAA 60.253 60.000 4.60 0.00 44.36 4.12
856 895 0.423544 AGGTCTCCTCCTTCCCCAAT 59.576 55.000 0.00 0.00 33.52 3.16
857 896 0.840617 GGTCTCCTCCTTCCCCAATC 59.159 60.000 0.00 0.00 0.00 2.67
858 897 0.840617 GTCTCCTCCTTCCCCAATCC 59.159 60.000 0.00 0.00 0.00 3.01
859 898 0.327576 TCTCCTCCTTCCCCAATCCC 60.328 60.000 0.00 0.00 0.00 3.85
860 899 1.308746 TCCTCCTTCCCCAATCCCC 60.309 63.158 0.00 0.00 0.00 4.81
861 900 1.622442 CCTCCTTCCCCAATCCCCA 60.622 63.158 0.00 0.00 0.00 4.96
942 981 3.062466 GCAAAACCCTCCGCCCTC 61.062 66.667 0.00 0.00 0.00 4.30
976 1015 3.687102 CCTCGCCGTACACCACCA 61.687 66.667 0.00 0.00 0.00 4.17
1342 1393 4.143333 TGGACGGCGCCTTAGCTC 62.143 66.667 26.68 10.38 36.60 4.09
1381 1432 1.429423 GGCCTCAACTGTATTGCGC 59.571 57.895 0.00 0.00 0.00 6.09
1398 1450 4.657824 CTGTGTTCGTCGGGCGGT 62.658 66.667 0.71 0.00 41.72 5.68
1406 1458 4.419921 GTCGGGCGGTGGGGATTT 62.420 66.667 0.00 0.00 0.00 2.17
1416 1468 3.845178 CGGTGGGGATTTTTAAAGAAGC 58.155 45.455 0.00 0.00 0.00 3.86
1451 1503 7.548196 TTGGTCGATTTGGTTATAGATTGTC 57.452 36.000 0.00 0.00 0.00 3.18
1487 1539 2.170607 AGTAGCGATTGTATTGCCTGGT 59.829 45.455 0.00 0.00 40.67 4.00
1491 1543 2.163412 GCGATTGTATTGCCTGGTTTGA 59.837 45.455 0.00 0.00 33.42 2.69
1492 1544 3.181487 GCGATTGTATTGCCTGGTTTGAT 60.181 43.478 0.00 0.00 33.42 2.57
1493 1545 4.353737 CGATTGTATTGCCTGGTTTGATG 58.646 43.478 0.00 0.00 0.00 3.07
1495 1547 5.622007 CGATTGTATTGCCTGGTTTGATGTT 60.622 40.000 0.00 0.00 0.00 2.71
1500 1692 1.203162 TGCCTGGTTTGATGTTGGGAT 60.203 47.619 0.00 0.00 0.00 3.85
1503 1695 2.234414 CCTGGTTTGATGTTGGGATTGG 59.766 50.000 0.00 0.00 0.00 3.16
1504 1696 2.234414 CTGGTTTGATGTTGGGATTGGG 59.766 50.000 0.00 0.00 0.00 4.12
1548 1742 5.648092 GGGATTTACTGCTGTATTGTTGTCT 59.352 40.000 4.12 0.00 0.00 3.41
1615 1809 9.167311 GTTTCATCCAAGTGAGTCTAAATATGT 57.833 33.333 0.00 0.00 0.00 2.29
1620 1814 7.907389 TCCAAGTGAGTCTAAATATGTGTTCT 58.093 34.615 0.00 0.00 0.00 3.01
1625 1819 7.542477 AGTGAGTCTAAATATGTGTTCTGTTCG 59.458 37.037 0.00 0.00 0.00 3.95
1750 1944 7.023171 TCCCTGTCTTAGATAGATACTCCTC 57.977 44.000 7.58 0.00 34.79 3.71
1757 1951 7.118680 GTCTTAGATAGATACTCCTCCTGTTCG 59.881 44.444 0.00 0.00 34.79 3.95
1764 1958 9.756571 ATAGATACTCCTCCTGTTCGTAAATAT 57.243 33.333 0.00 0.00 0.00 1.28
1985 2190 4.645535 TCAGTCTTGGTTCTTTCTGGATG 58.354 43.478 0.00 0.00 0.00 3.51
1986 2191 3.190118 CAGTCTTGGTTCTTTCTGGATGC 59.810 47.826 0.00 0.00 0.00 3.91
2005 2210 1.535462 GCGTGTTGCTTGGTGTCTATT 59.465 47.619 0.00 0.00 41.73 1.73
2006 2211 2.412847 GCGTGTTGCTTGGTGTCTATTC 60.413 50.000 0.00 0.00 41.73 1.75
2016 2221 3.599343 TGGTGTCTATTCAGCACATCAC 58.401 45.455 0.00 0.00 40.20 3.06
2030 2235 5.181056 CAGCACATCACCAACAATACTTGTA 59.819 40.000 0.00 0.00 44.59 2.41
2064 2272 3.691609 GGCCCTAATCTTTCTGTTCACTG 59.308 47.826 0.00 0.00 0.00 3.66
2066 2274 4.154918 GCCCTAATCTTTCTGTTCACTGTG 59.845 45.833 0.17 0.17 0.00 3.66
2067 2275 5.308825 CCCTAATCTTTCTGTTCACTGTGT 58.691 41.667 7.79 0.00 0.00 3.72
2101 2311 3.245990 GGCAAGAATTTCTGTGTGTTTGC 59.754 43.478 0.00 4.26 39.02 3.68
2109 2319 3.988379 TCTGTGTGTTTGCAGGAATTC 57.012 42.857 0.00 0.00 33.81 2.17
2202 2413 7.770897 CCCATGGTTAAACCTATATGATCTAGC 59.229 40.741 11.73 0.00 39.58 3.42
2235 2446 8.904099 ATCAAAATTAGTTAATACTCCCTCCG 57.096 34.615 0.00 0.00 35.78 4.63
2236 2447 7.854337 TCAAAATTAGTTAATACTCCCTCCGT 58.146 34.615 0.00 0.00 35.78 4.69
2237 2448 8.323567 TCAAAATTAGTTAATACTCCCTCCGTT 58.676 33.333 0.00 0.00 35.78 4.44
2238 2449 8.953313 CAAAATTAGTTAATACTCCCTCCGTTT 58.047 33.333 0.00 0.00 35.78 3.60
2239 2450 8.728337 AAATTAGTTAATACTCCCTCCGTTTC 57.272 34.615 0.00 0.00 35.78 2.78
2240 2451 6.855763 TTAGTTAATACTCCCTCCGTTTCA 57.144 37.500 0.00 0.00 35.78 2.69
2241 2452 5.750352 AGTTAATACTCCCTCCGTTTCAA 57.250 39.130 0.00 0.00 0.00 2.69
2242 2453 6.117975 AGTTAATACTCCCTCCGTTTCAAA 57.882 37.500 0.00 0.00 0.00 2.69
2243 2454 6.536447 AGTTAATACTCCCTCCGTTTCAAAA 58.464 36.000 0.00 0.00 0.00 2.44
2244 2455 7.173032 AGTTAATACTCCCTCCGTTTCAAAAT 58.827 34.615 0.00 0.00 0.00 1.82
2245 2456 8.323567 AGTTAATACTCCCTCCGTTTCAAAATA 58.676 33.333 0.00 0.00 0.00 1.40
2246 2457 8.949177 GTTAATACTCCCTCCGTTTCAAAATAA 58.051 33.333 0.00 0.00 0.00 1.40
2247 2458 7.625828 AATACTCCCTCCGTTTCAAAATAAG 57.374 36.000 0.00 0.00 0.00 1.73
2248 2459 4.981812 ACTCCCTCCGTTTCAAAATAAGT 58.018 39.130 0.00 0.00 0.00 2.24
2249 2460 4.760204 ACTCCCTCCGTTTCAAAATAAGTG 59.240 41.667 0.00 0.00 0.00 3.16
2250 2461 4.721132 TCCCTCCGTTTCAAAATAAGTGT 58.279 39.130 0.00 0.00 0.00 3.55
2251 2462 4.758165 TCCCTCCGTTTCAAAATAAGTGTC 59.242 41.667 0.00 0.00 0.00 3.67
2252 2463 4.760204 CCCTCCGTTTCAAAATAAGTGTCT 59.240 41.667 0.00 0.00 0.00 3.41
2253 2464 5.106673 CCCTCCGTTTCAAAATAAGTGTCTC 60.107 44.000 0.00 0.00 0.00 3.36
2254 2465 5.468746 CCTCCGTTTCAAAATAAGTGTCTCA 59.531 40.000 0.00 0.00 0.00 3.27
2255 2466 6.017440 CCTCCGTTTCAAAATAAGTGTCTCAA 60.017 38.462 0.00 0.00 0.00 3.02
2256 2467 6.954944 TCCGTTTCAAAATAAGTGTCTCAAG 58.045 36.000 0.00 0.00 0.00 3.02
2257 2468 5.625311 CCGTTTCAAAATAAGTGTCTCAAGC 59.375 40.000 0.00 0.00 0.00 4.01
2258 2469 6.430451 CGTTTCAAAATAAGTGTCTCAAGCT 58.570 36.000 0.00 0.00 0.00 3.74
2259 2470 6.912591 CGTTTCAAAATAAGTGTCTCAAGCTT 59.087 34.615 0.00 0.00 0.00 3.74
2260 2471 8.067784 CGTTTCAAAATAAGTGTCTCAAGCTTA 58.932 33.333 0.00 0.00 0.00 3.09
2261 2472 9.387123 GTTTCAAAATAAGTGTCTCAAGCTTAG 57.613 33.333 0.00 0.00 0.00 2.18
2262 2473 8.677148 TTCAAAATAAGTGTCTCAAGCTTAGT 57.323 30.769 0.00 0.00 0.00 2.24
2263 2474 9.772973 TTCAAAATAAGTGTCTCAAGCTTAGTA 57.227 29.630 0.00 0.00 0.00 1.82
2264 2475 9.204570 TCAAAATAAGTGTCTCAAGCTTAGTAC 57.795 33.333 0.00 0.00 0.00 2.73
2265 2476 8.988934 CAAAATAAGTGTCTCAAGCTTAGTACA 58.011 33.333 0.00 0.36 0.00 2.90
2266 2477 8.764524 AAATAAGTGTCTCAAGCTTAGTACAG 57.235 34.615 0.00 0.00 0.00 2.74
2267 2478 5.793030 AAGTGTCTCAAGCTTAGTACAGT 57.207 39.130 0.00 3.76 0.00 3.55
2268 2479 5.793030 AGTGTCTCAAGCTTAGTACAGTT 57.207 39.130 0.00 0.00 0.00 3.16
2269 2480 6.163135 AGTGTCTCAAGCTTAGTACAGTTT 57.837 37.500 0.00 0.00 0.00 2.66
2270 2481 6.583562 AGTGTCTCAAGCTTAGTACAGTTTT 58.416 36.000 0.00 0.00 0.00 2.43
2271 2482 7.048512 AGTGTCTCAAGCTTAGTACAGTTTTT 58.951 34.615 0.00 0.00 0.00 1.94
2299 2510 9.857957 ATACTAAAGCTAGTACAAAGTTGAGAC 57.142 33.333 0.00 0.00 42.19 3.36
2300 2511 7.723324 ACTAAAGCTAGTACAAAGTTGAGACA 58.277 34.615 0.00 0.00 36.56 3.41
2301 2512 6.846325 AAAGCTAGTACAAAGTTGAGACAC 57.154 37.500 0.00 0.00 0.00 3.67
2302 2513 5.793030 AGCTAGTACAAAGTTGAGACACT 57.207 39.130 0.00 0.00 0.00 3.55
2303 2514 6.163135 AGCTAGTACAAAGTTGAGACACTT 57.837 37.500 0.00 0.00 38.74 3.16
2304 2515 7.286215 AGCTAGTACAAAGTTGAGACACTTA 57.714 36.000 0.00 0.00 35.87 2.24
2305 2516 7.897864 AGCTAGTACAAAGTTGAGACACTTAT 58.102 34.615 0.00 0.00 35.87 1.73
2306 2517 8.368668 AGCTAGTACAAAGTTGAGACACTTATT 58.631 33.333 0.00 0.00 35.87 1.40
2307 2518 8.989980 GCTAGTACAAAGTTGAGACACTTATTT 58.010 33.333 0.00 0.00 35.87 1.40
2310 2521 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
2311 2522 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
2312 2523 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
2313 2524 7.287696 ACAAAGTTGAGACACTTATTTTGGGAT 59.712 33.333 0.00 0.00 35.87 3.85
2314 2525 6.824305 AGTTGAGACACTTATTTTGGGATG 57.176 37.500 0.00 0.00 0.00 3.51
2315 2526 5.711976 AGTTGAGACACTTATTTTGGGATGG 59.288 40.000 0.00 0.00 0.00 3.51
2316 2527 5.512942 TGAGACACTTATTTTGGGATGGA 57.487 39.130 0.00 0.00 0.00 3.41
2317 2528 5.500234 TGAGACACTTATTTTGGGATGGAG 58.500 41.667 0.00 0.00 0.00 3.86
2318 2529 4.860022 AGACACTTATTTTGGGATGGAGG 58.140 43.478 0.00 0.00 0.00 4.30
2319 2530 3.954258 GACACTTATTTTGGGATGGAGGG 59.046 47.826 0.00 0.00 0.00 4.30
2320 2531 3.596046 ACACTTATTTTGGGATGGAGGGA 59.404 43.478 0.00 0.00 0.00 4.20
2321 2532 4.210331 CACTTATTTTGGGATGGAGGGAG 58.790 47.826 0.00 0.00 0.00 4.30
2322 2533 3.858638 ACTTATTTTGGGATGGAGGGAGT 59.141 43.478 0.00 0.00 0.00 3.85
2323 2534 5.043762 ACTTATTTTGGGATGGAGGGAGTA 58.956 41.667 0.00 0.00 0.00 2.59
2370 2584 8.702163 GCACTTGCAATTTTATAAACCATAGT 57.298 30.769 0.00 0.00 41.59 2.12
2573 2788 5.348451 GCACCTTTTTAATTGCATCGTTGAT 59.652 36.000 0.00 0.00 34.97 2.57
2658 2873 0.839946 AGTCTCCACTGGCAACTTGT 59.160 50.000 0.00 0.00 37.61 3.16
2662 2877 1.605710 CTCCACTGGCAACTTGTGAAG 59.394 52.381 6.20 0.00 41.79 3.02
2732 2947 7.554118 TGAGTGCTTTTAATAGCTAGCTCAATT 59.446 33.333 23.26 18.44 41.76 2.32
2873 3088 4.099633 TGAACAAGAGGGAGATCATCTGT 58.900 43.478 0.00 0.00 0.00 3.41
3059 3274 0.179000 GCGATCCCTGTCCAAGTCAT 59.821 55.000 0.00 0.00 0.00 3.06
3131 3346 0.252513 GCCATTTAAGGGTTGGGGGT 60.253 55.000 0.00 0.00 0.00 4.95
3176 3391 1.474879 CCCTGTGTTTTGTGGTTCGTT 59.525 47.619 0.00 0.00 0.00 3.85
3177 3392 2.478879 CCCTGTGTTTTGTGGTTCGTTC 60.479 50.000 0.00 0.00 0.00 3.95
3178 3393 2.436670 CTGTGTTTTGTGGTTCGTTCG 58.563 47.619 0.00 0.00 0.00 3.95
3179 3394 1.130749 TGTGTTTTGTGGTTCGTTCGG 59.869 47.619 0.00 0.00 0.00 4.30
3180 3395 1.130938 GTGTTTTGTGGTTCGTTCGGT 59.869 47.619 0.00 0.00 0.00 4.69
3181 3396 1.130749 TGTTTTGTGGTTCGTTCGGTG 59.869 47.619 0.00 0.00 0.00 4.94
3182 3397 1.130938 GTTTTGTGGTTCGTTCGGTGT 59.869 47.619 0.00 0.00 0.00 4.16
3546 3767 0.183492 TTGTGCCTCCTTGAGCTTGT 59.817 50.000 0.00 0.00 0.00 3.16
3879 4100 2.888414 TCCCAGAAATTCACGGTTTTCC 59.112 45.455 0.00 0.00 33.30 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.531532 CTCAGTTATGCAGAGGCCGG 60.532 60.000 0.00 0.00 40.13 6.13
75 76 1.014044 TTCAGGCATTCACGAGACGC 61.014 55.000 0.00 0.00 0.00 5.19
76 77 1.325640 CATTCAGGCATTCACGAGACG 59.674 52.381 0.00 0.00 0.00 4.18
77 78 1.667724 CCATTCAGGCATTCACGAGAC 59.332 52.381 0.00 0.00 0.00 3.36
81 82 1.452110 TCACCATTCAGGCATTCACG 58.548 50.000 0.00 0.00 43.14 4.35
280 281 5.002516 ACAAGAGAAGAATGCTTTCTCCAG 58.997 41.667 14.62 10.32 41.42 3.86
305 306 2.167693 ACCTTCGCCGACAAGATAATGA 59.832 45.455 0.00 0.00 0.00 2.57
335 336 7.712639 AGAGATTACTACAATTCATCGCAATGT 59.287 33.333 0.00 0.00 34.32 2.71
443 444 3.723764 CGTTGTCGAATTTTGTGGTTCTG 59.276 43.478 0.00 0.00 39.71 3.02
486 487 0.877071 CTTTCAGCCATCGTGCACTT 59.123 50.000 16.19 0.00 0.00 3.16
494 495 5.893897 ATCAAAGTTCTCTTTCAGCCATC 57.106 39.130 0.00 0.00 41.31 3.51
655 692 9.416794 CTACTGCTGATTCATATTTCGAAGTAT 57.583 33.333 7.32 7.32 0.00 2.12
661 698 6.145209 CAGTCCTACTGCTGATTCATATTTCG 59.855 42.308 0.00 0.00 39.62 3.46
699 738 1.338389 CCTGGGTTAATCGTGACGGTT 60.338 52.381 9.03 9.03 33.65 4.44
730 769 2.033550 TCGTGCACTTTACGGCAAATTT 59.966 40.909 16.19 0.00 42.45 1.82
744 783 1.053811 GTCTTCGACTCTTCGTGCAC 58.946 55.000 6.82 6.82 46.01 4.57
758 797 0.040067 CGCCTTTGCCAAGTGTCTTC 60.040 55.000 0.00 0.00 0.00 2.87
801 840 1.464608 CGGTCCTTACGACTTGTCGTA 59.535 52.381 25.77 25.77 45.19 3.43
803 842 1.069378 GCGGTCCTTACGACTTGTCG 61.069 60.000 19.74 19.74 41.64 4.35
804 843 0.038892 TGCGGTCCTTACGACTTGTC 60.039 55.000 0.00 0.00 41.64 3.18
806 845 0.788391 GTTGCGGTCCTTACGACTTG 59.212 55.000 0.00 0.00 41.64 3.16
814 853 1.358759 CTTTTGCGTTGCGGTCCTT 59.641 52.632 0.00 0.00 0.00 3.36
855 894 3.728373 GGACTTGGCCGTGGGGAT 61.728 66.667 0.00 0.00 34.06 3.85
857 896 4.278513 TTGGACTTGGCCGTGGGG 62.279 66.667 0.00 0.00 0.00 4.96
858 897 2.672996 CTTGGACTTGGCCGTGGG 60.673 66.667 0.00 0.00 0.00 4.61
859 898 2.672996 CCTTGGACTTGGCCGTGG 60.673 66.667 0.00 0.00 0.00 4.94
860 899 3.365265 GCCTTGGACTTGGCCGTG 61.365 66.667 0.00 0.00 43.11 4.94
1163 1214 1.299976 GGATCCACCGGCTTCTTGT 59.700 57.895 6.95 0.00 0.00 3.16
1332 1383 1.855360 GATCAACGAAGAGCTAAGGCG 59.145 52.381 0.00 0.00 44.37 5.52
1336 1387 6.535150 CACAAATAGGATCAACGAAGAGCTAA 59.465 38.462 0.00 0.00 0.00 3.09
1342 1393 3.242413 CCGCACAAATAGGATCAACGAAG 60.242 47.826 0.00 0.00 0.00 3.79
1395 1447 3.672241 CGCTTCTTTAAAAATCCCCACCG 60.672 47.826 0.00 0.00 0.00 4.94
1398 1450 4.585162 TGTTCGCTTCTTTAAAAATCCCCA 59.415 37.500 0.00 0.00 0.00 4.96
1400 1452 6.386654 TGATGTTCGCTTCTTTAAAAATCCC 58.613 36.000 0.00 0.00 0.00 3.85
1401 1453 8.466086 AATGATGTTCGCTTCTTTAAAAATCC 57.534 30.769 0.00 0.00 0.00 3.01
1404 1456 8.547069 CCAAAATGATGTTCGCTTCTTTAAAAA 58.453 29.630 0.00 0.00 0.00 1.94
1405 1457 7.708752 ACCAAAATGATGTTCGCTTCTTTAAAA 59.291 29.630 0.00 0.00 0.00 1.52
1406 1458 7.206687 ACCAAAATGATGTTCGCTTCTTTAAA 58.793 30.769 0.00 0.00 0.00 1.52
1416 1468 4.558470 CCAAATCGACCAAAATGATGTTCG 59.442 41.667 0.00 0.00 0.00 3.95
1451 1503 1.202313 GCTACTGGCTGGTAAGTCGAG 60.202 57.143 0.00 0.00 38.06 4.04
1473 1525 5.481105 CAACATCAAACCAGGCAATACAAT 58.519 37.500 0.00 0.00 0.00 2.71
1487 1539 2.711895 ACCCCAATCCCAACATCAAA 57.288 45.000 0.00 0.00 0.00 2.69
1522 1714 3.898482 ACAATACAGCAGTAAATCCCCC 58.102 45.455 0.00 0.00 33.13 5.40
1523 1715 4.705023 ACAACAATACAGCAGTAAATCCCC 59.295 41.667 0.00 0.00 33.13 4.81
1548 1742 8.354711 TGTGCCAATTACTGTTATATCCAAAA 57.645 30.769 0.00 0.00 0.00 2.44
1615 1809 4.819105 ATTATCAGGGTCGAACAGAACA 57.181 40.909 1.31 0.00 38.65 3.18
1620 1814 4.006989 CCACAAATTATCAGGGTCGAACA 58.993 43.478 1.31 0.00 0.00 3.18
1878 2078 8.559536 TCAGCACATAATTAAAATGCTAGTAGC 58.440 33.333 15.56 15.56 44.62 3.58
1985 2190 1.156736 ATAGACACCAAGCAACACGC 58.843 50.000 0.00 0.00 42.91 5.34
1986 2191 2.805671 TGAATAGACACCAAGCAACACG 59.194 45.455 0.00 0.00 0.00 4.49
2005 2210 4.019792 AGTATTGTTGGTGATGTGCTGA 57.980 40.909 0.00 0.00 0.00 4.26
2006 2211 4.478699 CAAGTATTGTTGGTGATGTGCTG 58.521 43.478 0.00 0.00 42.34 4.41
2030 2235 3.591977 AGATTAGGGCCTAACACCAGTTT 59.408 43.478 27.61 9.77 39.15 2.66
2101 2311 7.273320 ACTCTCAATTATGCATGAATTCCTG 57.727 36.000 10.16 4.58 0.00 3.86
2109 2319 9.229784 GTATCAAACAACTCTCAATTATGCATG 57.770 33.333 10.16 0.00 0.00 4.06
2163 2373 8.595421 GGTTTAACCATGGGAATAAAAAGGTAA 58.405 33.333 18.09 0.00 38.42 2.85
2164 2374 7.956881 AGGTTTAACCATGGGAATAAAAAGGTA 59.043 33.333 18.09 0.00 41.95 3.08
2227 2438 4.760204 ACACTTATTTTGAAACGGAGGGAG 59.240 41.667 0.00 0.00 0.00 4.30
2228 2439 4.721132 ACACTTATTTTGAAACGGAGGGA 58.279 39.130 0.00 0.00 0.00 4.20
2229 2440 4.760204 AGACACTTATTTTGAAACGGAGGG 59.240 41.667 0.00 0.00 0.00 4.30
2230 2441 5.468746 TGAGACACTTATTTTGAAACGGAGG 59.531 40.000 0.00 0.00 0.00 4.30
2231 2442 6.539649 TGAGACACTTATTTTGAAACGGAG 57.460 37.500 0.00 0.00 0.00 4.63
2232 2443 6.512741 GCTTGAGACACTTATTTTGAAACGGA 60.513 38.462 0.00 0.00 0.00 4.69
2233 2444 5.625311 GCTTGAGACACTTATTTTGAAACGG 59.375 40.000 0.00 0.00 0.00 4.44
2234 2445 6.430451 AGCTTGAGACACTTATTTTGAAACG 58.570 36.000 0.00 0.00 0.00 3.60
2235 2446 9.387123 CTAAGCTTGAGACACTTATTTTGAAAC 57.613 33.333 9.86 0.00 0.00 2.78
2236 2447 9.120538 ACTAAGCTTGAGACACTTATTTTGAAA 57.879 29.630 9.86 0.00 0.00 2.69
2237 2448 8.677148 ACTAAGCTTGAGACACTTATTTTGAA 57.323 30.769 9.86 0.00 0.00 2.69
2238 2449 9.204570 GTACTAAGCTTGAGACACTTATTTTGA 57.795 33.333 9.86 0.00 0.00 2.69
2239 2450 8.988934 TGTACTAAGCTTGAGACACTTATTTTG 58.011 33.333 9.86 0.00 0.00 2.44
2240 2451 9.209175 CTGTACTAAGCTTGAGACACTTATTTT 57.791 33.333 9.86 0.00 0.00 1.82
2241 2452 8.368668 ACTGTACTAAGCTTGAGACACTTATTT 58.631 33.333 9.86 0.00 0.00 1.40
2242 2453 7.897864 ACTGTACTAAGCTTGAGACACTTATT 58.102 34.615 9.86 0.00 0.00 1.40
2243 2454 7.469537 ACTGTACTAAGCTTGAGACACTTAT 57.530 36.000 9.86 0.00 0.00 1.73
2244 2455 6.896021 ACTGTACTAAGCTTGAGACACTTA 57.104 37.500 9.86 0.00 0.00 2.24
2245 2456 5.793030 ACTGTACTAAGCTTGAGACACTT 57.207 39.130 9.86 0.00 0.00 3.16
2246 2457 5.793030 AACTGTACTAAGCTTGAGACACT 57.207 39.130 9.86 0.00 0.00 3.55
2247 2458 6.846325 AAAACTGTACTAAGCTTGAGACAC 57.154 37.500 9.86 7.18 0.00 3.67
2273 2484 9.857957 GTCTCAACTTTGTACTAGCTTTAGTAT 57.142 33.333 0.00 0.00 35.30 2.12
2274 2485 8.853126 TGTCTCAACTTTGTACTAGCTTTAGTA 58.147 33.333 0.00 0.00 0.00 1.82
2275 2486 7.652507 GTGTCTCAACTTTGTACTAGCTTTAGT 59.347 37.037 0.00 0.00 0.00 2.24
2276 2487 7.868415 AGTGTCTCAACTTTGTACTAGCTTTAG 59.132 37.037 0.00 0.00 0.00 1.85
2277 2488 7.723324 AGTGTCTCAACTTTGTACTAGCTTTA 58.277 34.615 0.00 0.00 0.00 1.85
2278 2489 6.583562 AGTGTCTCAACTTTGTACTAGCTTT 58.416 36.000 0.00 0.00 0.00 3.51
2279 2490 6.163135 AGTGTCTCAACTTTGTACTAGCTT 57.837 37.500 0.00 0.00 0.00 3.74
2280 2491 5.793030 AGTGTCTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
2281 2492 8.535690 AATAAGTGTCTCAACTTTGTACTAGC 57.464 34.615 0.00 0.00 40.77 3.42
2284 2495 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
2285 2496 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
2286 2497 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
2287 2498 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
2288 2499 7.038154 TCCCAAAATAAGTGTCTCAACTTTG 57.962 36.000 0.00 0.00 40.77 2.77
2289 2500 7.255942 CCATCCCAAAATAAGTGTCTCAACTTT 60.256 37.037 0.00 0.00 40.77 2.66
2290 2501 6.209391 CCATCCCAAAATAAGTGTCTCAACTT 59.791 38.462 0.00 0.00 42.89 2.66
2291 2502 5.711976 CCATCCCAAAATAAGTGTCTCAACT 59.288 40.000 0.00 0.00 0.00 3.16
2292 2503 5.710099 TCCATCCCAAAATAAGTGTCTCAAC 59.290 40.000 0.00 0.00 0.00 3.18
2293 2504 5.886609 TCCATCCCAAAATAAGTGTCTCAA 58.113 37.500 0.00 0.00 0.00 3.02
2294 2505 5.500234 CTCCATCCCAAAATAAGTGTCTCA 58.500 41.667 0.00 0.00 0.00 3.27
2295 2506 4.884164 CCTCCATCCCAAAATAAGTGTCTC 59.116 45.833 0.00 0.00 0.00 3.36
2296 2507 4.325344 CCCTCCATCCCAAAATAAGTGTCT 60.325 45.833 0.00 0.00 0.00 3.41
2297 2508 3.954258 CCCTCCATCCCAAAATAAGTGTC 59.046 47.826 0.00 0.00 0.00 3.67
2298 2509 3.596046 TCCCTCCATCCCAAAATAAGTGT 59.404 43.478 0.00 0.00 0.00 3.55
2299 2510 4.210331 CTCCCTCCATCCCAAAATAAGTG 58.790 47.826 0.00 0.00 0.00 3.16
2300 2511 3.858638 ACTCCCTCCATCCCAAAATAAGT 59.141 43.478 0.00 0.00 0.00 2.24
2301 2512 4.526438 ACTCCCTCCATCCCAAAATAAG 57.474 45.455 0.00 0.00 0.00 1.73
2302 2513 5.043762 ACTACTCCCTCCATCCCAAAATAA 58.956 41.667 0.00 0.00 0.00 1.40
2303 2514 4.641868 ACTACTCCCTCCATCCCAAAATA 58.358 43.478 0.00 0.00 0.00 1.40
2304 2515 3.474920 ACTACTCCCTCCATCCCAAAAT 58.525 45.455 0.00 0.00 0.00 1.82
2305 2516 2.929301 ACTACTCCCTCCATCCCAAAA 58.071 47.619 0.00 0.00 0.00 2.44
2306 2517 2.661176 ACTACTCCCTCCATCCCAAA 57.339 50.000 0.00 0.00 0.00 3.28
2307 2518 2.661176 AACTACTCCCTCCATCCCAA 57.339 50.000 0.00 0.00 0.00 4.12
2308 2519 2.225779 TGAAACTACTCCCTCCATCCCA 60.226 50.000 0.00 0.00 0.00 4.37
2309 2520 2.478292 TGAAACTACTCCCTCCATCCC 58.522 52.381 0.00 0.00 0.00 3.85
2310 2521 4.779993 ATTGAAACTACTCCCTCCATCC 57.220 45.455 0.00 0.00 0.00 3.51
2311 2522 5.745227 TCAATTGAAACTACTCCCTCCATC 58.255 41.667 5.45 0.00 0.00 3.51
2312 2523 5.779241 TCAATTGAAACTACTCCCTCCAT 57.221 39.130 5.45 0.00 0.00 3.41
2313 2524 5.073144 ACTTCAATTGAAACTACTCCCTCCA 59.927 40.000 20.82 0.00 33.07 3.86
2314 2525 5.561679 ACTTCAATTGAAACTACTCCCTCC 58.438 41.667 20.82 0.00 33.07 4.30
2315 2526 5.644206 GGACTTCAATTGAAACTACTCCCTC 59.356 44.000 20.82 5.51 33.07 4.30
2316 2527 5.073144 TGGACTTCAATTGAAACTACTCCCT 59.927 40.000 20.82 0.00 33.07 4.20
2317 2528 5.181433 GTGGACTTCAATTGAAACTACTCCC 59.819 44.000 20.82 13.56 33.07 4.30
2318 2529 5.998363 AGTGGACTTCAATTGAAACTACTCC 59.002 40.000 24.37 19.89 31.99 3.85
2319 2530 6.931840 AGAGTGGACTTCAATTGAAACTACTC 59.068 38.462 33.46 33.46 42.16 2.59
2320 2531 6.708054 CAGAGTGGACTTCAATTGAAACTACT 59.292 38.462 27.32 27.32 36.15 2.57
2321 2532 6.566753 GCAGAGTGGACTTCAATTGAAACTAC 60.567 42.308 20.82 21.56 33.07 2.73
2322 2533 5.470098 GCAGAGTGGACTTCAATTGAAACTA 59.530 40.000 20.82 13.04 33.07 2.24
2323 2534 4.276926 GCAGAGTGGACTTCAATTGAAACT 59.723 41.667 20.82 19.63 33.07 2.66
2455 2669 7.201548 GCTAGTAAAATGGTCAATTGCATTTGG 60.202 37.037 18.75 11.17 0.00 3.28
2534 2748 1.066908 AGGTGCAATCAACAAACCACG 59.933 47.619 0.00 0.00 33.13 4.94
2658 2873 9.739276 AATTACAACCTCATCTTTATGACTTCA 57.261 29.630 0.00 0.00 37.20 3.02
2700 2915 9.046296 GCTAGCTATTAAAAGCACTCAGAATAA 57.954 33.333 7.70 0.00 45.30 1.40
2705 2920 6.045318 TGAGCTAGCTATTAAAAGCACTCAG 58.955 40.000 19.38 0.00 45.30 3.35
2732 2947 9.625747 TCCATAGATTGTGCAAAATCAGTAATA 57.374 29.630 27.48 13.54 38.74 0.98
2742 2957 6.543465 CCTAATCAGTCCATAGATTGTGCAAA 59.457 38.462 0.00 0.00 36.07 3.68
2808 3023 5.678955 AGAGGGAGTTTGTATTACAGGAC 57.321 43.478 0.00 1.26 0.00 3.85
2873 3088 2.613026 TGGTTTTGAGCTTCTCGTCA 57.387 45.000 0.00 0.00 32.35 4.35
3131 3346 3.055458 TCCTTCTTACATGCATCACCGAA 60.055 43.478 0.00 0.00 0.00 4.30
3176 3391 2.235016 CTCAAATTCCCCAAACACCGA 58.765 47.619 0.00 0.00 0.00 4.69
3177 3392 1.272212 CCTCAAATTCCCCAAACACCG 59.728 52.381 0.00 0.00 0.00 4.94
3178 3393 2.604139 TCCTCAAATTCCCCAAACACC 58.396 47.619 0.00 0.00 0.00 4.16
3179 3394 4.890158 AATCCTCAAATTCCCCAAACAC 57.110 40.909 0.00 0.00 0.00 3.32
3180 3395 4.504689 GCAAATCCTCAAATTCCCCAAACA 60.505 41.667 0.00 0.00 0.00 2.83
3181 3396 4.002982 GCAAATCCTCAAATTCCCCAAAC 58.997 43.478 0.00 0.00 0.00 2.93
3182 3397 3.008923 GGCAAATCCTCAAATTCCCCAAA 59.991 43.478 0.00 0.00 0.00 3.28
3710 3931 2.952245 GAACCTGTGCAGCAGCTG 59.048 61.111 18.93 18.93 43.71 4.24
3879 4100 5.689514 TGCAGGAAACATTGAAACAATTACG 59.310 36.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.