Multiple sequence alignment - TraesCS4B01G397700

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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 TraesCS4B01G397700 chr4B 100.000 5889 0 0 2262 8150 671756297 671762185 0.000000e+00 10876.0
1 TraesCS4B01G397700 chr4B 100.000 2001 0 0 1 2001 671754036 671756036 0.000000e+00 3696.0
2 TraesCS4B01G397700 chr4B 98.551 69 1 0 1 69 2350029 2350097 1.110000e-23 122.0
3 TraesCS4B01G397700 chr4B 98.551 69 1 0 1 69 22883465 22883397 1.110000e-23 122.0
4 TraesCS4B01G397700 chr4B 98.551 69 1 0 1 69 404925027 404924959 1.110000e-23 122.0
5 TraesCS4B01G397700 chrUn 91.257 3477 230 40 2407 5844 100257551 100254110 0.000000e+00 4669.0
6 TraesCS4B01G397700 chrUn 84.790 1407 118 43 6186 7530 100254104 100252732 0.000000e+00 1325.0
7 TraesCS4B01G397700 chrUn 81.970 660 53 20 987 1621 100258658 100258040 4.390000e-137 499.0
8 TraesCS4B01G397700 chrUn 83.636 385 50 11 7770 8145 100251506 100251126 4.680000e-92 350.0
9 TraesCS4B01G397700 chrUn 87.293 181 18 2 7540 7719 100252657 100252481 1.390000e-47 202.0
10 TraesCS4B01G397700 chrUn 95.050 101 5 0 2262 2362 100258002 100257902 8.470000e-35 159.0
11 TraesCS4B01G397700 chr5A 90.909 1914 112 20 3884 5771 709759447 709761324 0.000000e+00 2514.0
12 TraesCS4B01G397700 chr5A 91.226 1493 95 13 3947 5416 659163280 659161801 0.000000e+00 1999.0
13 TraesCS4B01G397700 chr5A 91.523 1215 70 15 2407 3593 659166576 659165367 0.000000e+00 1642.0
14 TraesCS4B01G397700 chr5A 91.751 1091 77 10 2798 3882 709758309 709759392 0.000000e+00 1504.0
15 TraesCS4B01G397700 chr5A 86.748 1396 107 36 6186 7530 659161424 659160056 0.000000e+00 1482.0
16 TraesCS4B01G397700 chr5A 91.099 1101 49 16 5658 6745 709761317 709762381 0.000000e+00 1445.0
17 TraesCS4B01G397700 chr5A 87.266 801 46 17 6742 7530 709762484 709763240 0.000000e+00 863.0
18 TraesCS4B01G397700 chr5A 81.250 704 56 33 879 1532 659168427 659167750 4.390000e-137 499.0
19 TraesCS4B01G397700 chr5A 89.751 361 30 5 3595 3952 659163743 659163387 9.640000e-124 455.0
20 TraesCS4B01G397700 chr5A 83.077 390 48 14 7770 8148 709764417 709764799 1.010000e-88 339.0
21 TraesCS4B01G397700 chr5A 92.308 52 4 0 1775 1826 659167512 659167461 3.150000e-09 75.0
22 TraesCS4B01G397700 chr4D 94.861 1479 59 9 2407 3882 490941604 490940140 0.000000e+00 2294.0
23 TraesCS4B01G397700 chr4D 84.830 2406 213 75 5420 7741 490938613 490936276 0.000000e+00 2281.0
24 TraesCS4B01G397700 chr4D 91.782 1448 78 17 3887 5307 490940040 490938607 0.000000e+00 1977.0
25 TraesCS4B01G397700 chr4D 84.335 932 77 26 943 1826 490943235 490942325 0.000000e+00 848.0
26 TraesCS4B01G397700 chr4D 94.133 375 15 4 7783 8150 490936165 490935791 1.540000e-156 564.0
27 TraesCS4B01G397700 chr4D 93.431 137 6 1 1832 1968 490942253 490942120 4.990000e-47 200.0
28 TraesCS4B01G397700 chr4D 96.040 101 4 0 2262 2362 490942055 490941955 1.820000e-36 165.0
29 TraesCS4B01G397700 chr1B 96.135 828 25 7 63 884 45251167 45250341 0.000000e+00 1345.0
30 TraesCS4B01G397700 chr1B 96.215 819 24 7 68 880 622579316 622578499 0.000000e+00 1334.0
31 TraesCS4B01G397700 chr1B 95.859 821 28 5 68 883 553637968 553637149 0.000000e+00 1323.0
32 TraesCS4B01G397700 chr1B 95.849 819 27 6 68 880 51222286 51221469 0.000000e+00 1317.0
33 TraesCS4B01G397700 chr1B 98.551 69 1 0 1 69 45252020 45251952 1.110000e-23 122.0
34 TraesCS4B01G397700 chr1B 98.551 69 1 0 1 69 328145321 328145389 1.110000e-23 122.0
35 TraesCS4B01G397700 chr1B 98.551 69 1 0 1 69 623401857 623401789 1.110000e-23 122.0
36 TraesCS4B01G397700 chr1B 94.444 72 4 0 1155 1226 121025599 121025670 2.400000e-20 111.0
37 TraesCS4B01G397700 chr2B 96.229 822 23 7 68 884 49526417 49527235 0.000000e+00 1339.0
38 TraesCS4B01G397700 chr2B 88.406 69 6 2 2359 2425 47831534 47831466 1.890000e-11 82.4
39 TraesCS4B01G397700 chr3B 96.107 822 25 6 68 884 775441624 775442443 0.000000e+00 1334.0
40 TraesCS4B01G397700 chr3B 95.636 825 30 6 68 886 206230703 206231527 0.000000e+00 1319.0
41 TraesCS4B01G397700 chr3B 96.000 75 2 1 2 76 716707322 716707249 4.000000e-23 121.0
42 TraesCS4B01G397700 chr3B 95.000 60 2 1 2359 2417 729660479 729660420 8.710000e-15 93.5
43 TraesCS4B01G397700 chr3B 94.915 59 2 1 2359 2417 805579343 805579286 3.130000e-14 91.6
44 TraesCS4B01G397700 chr5B 96.093 819 25 6 68 880 590556081 590556898 0.000000e+00 1328.0
45 TraesCS4B01G397700 chr5B 98.551 69 1 0 1 69 247349575 247349643 1.110000e-23 122.0
46 TraesCS4B01G397700 chr5B 98.551 69 1 0 1 69 512495926 512495994 1.110000e-23 122.0
47 TraesCS4B01G397700 chr7B 95.971 819 26 6 68 880 708516360 708517177 0.000000e+00 1323.0
48 TraesCS4B01G397700 chr7B 95.652 46 2 0 1145 1190 703901983 703902028 3.150000e-09 75.0
49 TraesCS4B01G397700 chr4A 96.491 57 1 1 2359 2415 422945155 422945100 8.710000e-15 93.5
50 TraesCS4B01G397700 chr4A 90.141 71 2 5 2359 2424 503221614 503221684 4.050000e-13 87.9
51 TraesCS4B01G397700 chr4A 95.455 44 2 0 1145 1188 653988615 653988572 4.080000e-08 71.3
52 TraesCS4B01G397700 chr7D 96.429 56 1 1 2359 2414 618321403 618321457 3.130000e-14 91.6
53 TraesCS4B01G397700 chr2A 94.915 59 2 1 2359 2417 210311078 210311021 3.130000e-14 91.6
54 TraesCS4B01G397700 chr1D 98.077 52 0 1 2359 2409 197821605 197821656 1.130000e-13 89.8
55 TraesCS4B01G397700 chr1A 87.179 78 6 4 2359 2433 518662808 518662732 1.460000e-12 86.1
56 TraesCS4B01G397700 chr1A 91.489 47 4 0 1145 1191 11791921 11791875 1.900000e-06 65.8
57 TraesCS4B01G397700 chr2D 91.489 47 4 0 1145 1191 83637278 83637232 1.900000e-06 65.8
58 TraesCS4B01G397700 chr6B 100.000 31 0 0 1155 1185 706263407 706263377 3.180000e-04 58.4


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 TraesCS4B01G397700 chr4B 671754036 671762185 8149 False 7286.000000 10876 100.000000 1 8150 2 chr4B.!!$F2 8149
1 TraesCS4B01G397700 chrUn 100251126 100258658 7532 True 1200.666667 4669 87.332667 987 8145 6 chrUn.!!$R1 7158
2 TraesCS4B01G397700 chr5A 709758309 709764799 6490 False 1333.000000 2514 88.820400 2798 8148 5 chr5A.!!$F1 5350
3 TraesCS4B01G397700 chr5A 659160056 659168427 8371 True 1025.333333 1999 88.801000 879 7530 6 chr5A.!!$R1 6651
4 TraesCS4B01G397700 chr4D 490935791 490943235 7444 True 1189.857143 2294 91.344571 943 8150 7 chr4D.!!$R1 7207
5 TraesCS4B01G397700 chr1B 622578499 622579316 817 True 1334.000000 1334 96.215000 68 880 1 chr1B.!!$R3 812
6 TraesCS4B01G397700 chr1B 553637149 553637968 819 True 1323.000000 1323 95.859000 68 883 1 chr1B.!!$R2 815
7 TraesCS4B01G397700 chr1B 51221469 51222286 817 True 1317.000000 1317 95.849000 68 880 1 chr1B.!!$R1 812
8 TraesCS4B01G397700 chr1B 45250341 45252020 1679 True 733.500000 1345 97.343000 1 884 2 chr1B.!!$R5 883
9 TraesCS4B01G397700 chr2B 49526417 49527235 818 False 1339.000000 1339 96.229000 68 884 1 chr2B.!!$F1 816
10 TraesCS4B01G397700 chr3B 775441624 775442443 819 False 1334.000000 1334 96.107000 68 884 1 chr3B.!!$F2 816
11 TraesCS4B01G397700 chr3B 206230703 206231527 824 False 1319.000000 1319 95.636000 68 886 1 chr3B.!!$F1 818
12 TraesCS4B01G397700 chr5B 590556081 590556898 817 False 1328.000000 1328 96.093000 68 880 1 chr5B.!!$F3 812
13 TraesCS4B01G397700 chr7B 708516360 708517177 817 False 1323.000000 1323 95.971000 68 880 1 chr7B.!!$F2 812

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
849 1645 0.034186 CAGAGGGGGCTTTGTATGCA 60.034 55.000 0.00 0.00 0.00 3.96 F
1587 2495 0.396060 GATGTCTCAGGCTGGATCCC 59.604 60.000 15.73 0.00 0.00 3.85 F
1973 3011 0.388659 CATCGGAGCTGGAGGAGAAG 59.611 60.000 0.00 0.00 0.00 2.85 F
3289 4654 0.106519 ATAGTGCCTTGGCATGGACC 60.107 55.000 22.50 11.33 0.00 4.46 F
3800 6804 0.107831 TGCAACTCCCAGCGTTAAGT 59.892 50.000 0.00 0.00 0.00 2.24 F
3882 6886 1.523758 AAGGGCGTGCTTCTTAACTG 58.476 50.000 0.00 0.00 0.00 3.16 F
5359 8619 1.604278 GTTCTTTCTGGAAGCTTGCGT 59.396 47.619 13.65 0.00 35.24 5.24 F
6079 9491 0.533308 TCAAAACTCGACCAACCGGG 60.533 55.000 6.32 0.00 44.81 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 2875 0.324943 TCAGGGCACTCCTTACTTGC 59.675 55.000 0.00 0.00 45.47 4.01 R
2620 3977 1.887956 GCTGTCCTGGCTGAAATGGAA 60.888 52.381 0.00 0.00 0.00 3.53 R
3781 6785 0.107831 ACTTAACGCTGGGAGTTGCA 59.892 50.000 0.00 0.00 33.42 4.08 R
5195 8454 0.722676 TATCAGGACCCCCAGACCTT 59.277 55.000 0.00 0.00 30.30 3.50 R
5337 8597 1.068954 GCAAGCTTCCAGAAAGAACCG 60.069 52.381 0.00 0.00 37.12 4.44 R
5644 8924 2.295349 GGCCCACAATCTTGCATATGAG 59.705 50.000 6.97 0.00 0.00 2.90 R
6534 10018 0.035915 TATGGCAACGGTAGCTGCAA 60.036 50.000 3.61 0.00 40.98 4.08 R
7174 10764 0.881796 TGTCCAGACACAGCTAGTCG 59.118 55.000 11.51 7.66 40.84 4.18 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
72 863 0.750911 GCTGGAGGAGGAAGCCAATG 60.751 60.000 0.00 0.00 0.00 2.82
184 975 1.028905 CCTGGTTTGCGAAGGTTCAA 58.971 50.000 0.00 0.00 0.00 2.69
455 1246 1.337071 GTATGCGTCAGGAGATCCGAA 59.663 52.381 0.00 0.00 42.08 4.30
691 1485 1.282817 CGAAACCACGCCGATTATGA 58.717 50.000 0.00 0.00 0.00 2.15
699 1493 3.067106 CACGCCGATTATGAGCCTATTT 58.933 45.455 0.00 0.00 0.00 1.40
743 1537 1.015607 CCGAAATTGGGCTGCAAAGC 61.016 55.000 0.50 0.00 0.00 3.51
754 1548 0.603439 CTGCAAAGCGGGCCAATTTT 60.603 50.000 4.39 0.00 0.00 1.82
849 1645 0.034186 CAGAGGGGGCTTTGTATGCA 60.034 55.000 0.00 0.00 0.00 3.96
888 1685 0.689080 GGAGATGCCCTGAGGAGTGA 60.689 60.000 0.00 0.00 33.47 3.41
910 1708 0.886490 CCAAGACGTGGCAAGAAGCT 60.886 55.000 7.60 0.00 41.72 3.74
919 1717 1.067283 TGGCAAGAAGCTTCTCTCTCG 60.067 52.381 28.58 15.40 44.79 4.04
928 1726 1.201181 GCTTCTCTCTCGTGCTCTCAA 59.799 52.381 0.00 0.00 0.00 3.02
930 1728 1.169577 TCTCTCTCGTGCTCTCAACC 58.830 55.000 0.00 0.00 0.00 3.77
932 1730 1.216710 CTCTCGTGCTCTCAACCCC 59.783 63.158 0.00 0.00 0.00 4.95
937 1745 1.302832 GTGCTCTCAACCCCCACAG 60.303 63.158 0.00 0.00 0.00 3.66
980 1790 2.031012 CCGCACTTGACAGCCAGA 59.969 61.111 0.00 0.00 0.00 3.86
981 1791 2.031516 CCGCACTTGACAGCCAGAG 61.032 63.158 0.00 0.00 0.00 3.35
982 1792 1.301244 CGCACTTGACAGCCAGAGT 60.301 57.895 0.00 0.00 0.00 3.24
1029 1839 4.803426 GAGGAGTCCACGCAGCCG 62.803 72.222 12.86 0.00 41.14 5.52
1335 2202 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
1336 2203 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
1337 2204 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1338 2205 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
1377 2244 1.983119 GATCTCCATCGCCCCAACCA 61.983 60.000 0.00 0.00 0.00 3.67
1378 2245 1.570857 ATCTCCATCGCCCCAACCAA 61.571 55.000 0.00 0.00 0.00 3.67
1434 2327 1.592081 GCGCTTAGTTGCAGATCTCTG 59.408 52.381 0.00 2.75 46.40 3.35
1444 2337 5.873712 AGTTGCAGATCTCTGATGTAGTTTG 59.126 40.000 11.34 0.00 46.59 2.93
1447 2340 3.244814 CAGATCTCTGATGTAGTTTGCGC 59.755 47.826 0.00 0.00 46.59 6.09
1479 2372 2.363680 TGCTCCTGCTTAGCTCTGTATC 59.636 50.000 5.60 0.00 40.73 2.24
1484 2378 4.580995 TCCTGCTTAGCTCTGTATCTGTAC 59.419 45.833 5.60 0.00 0.00 2.90
1489 2383 1.841450 GCTCTGTATCTGTACGGTGC 58.159 55.000 0.64 5.92 44.56 5.01
1539 2433 1.080705 GCTTGCTTGCTGCTTCCAG 60.081 57.895 0.00 0.00 43.37 3.86
1573 2481 4.083271 GGGTTGCTTGACTTGTTAGATGTC 60.083 45.833 0.00 0.00 0.00 3.06
1587 2495 0.396060 GATGTCTCAGGCTGGATCCC 59.604 60.000 15.73 0.00 0.00 3.85
1604 2512 1.820519 TCCCTCATGTCATTTTGCAGC 59.179 47.619 0.00 0.00 0.00 5.25
1609 2517 0.961019 ATGTCATTTTGCAGCACGGT 59.039 45.000 0.00 0.00 0.00 4.83
1629 2594 7.015289 CACGGTTTAATTGACTAGATGTGTTG 58.985 38.462 0.00 0.00 0.00 3.33
1647 2612 1.737838 TGATTCATGTCCCGTGAAGC 58.262 50.000 7.33 7.33 43.42 3.86
1704 2673 0.883814 GCTGCTGCTAGTAGGCATGG 60.884 60.000 10.06 0.00 41.63 3.66
1706 2675 1.139654 CTGCTGCTAGTAGGCATGGAA 59.860 52.381 10.06 0.00 41.63 3.53
1707 2676 1.770658 TGCTGCTAGTAGGCATGGAAT 59.229 47.619 10.06 0.00 41.63 3.01
1708 2677 2.972021 TGCTGCTAGTAGGCATGGAATA 59.028 45.455 10.06 0.00 41.63 1.75
1709 2678 3.244215 TGCTGCTAGTAGGCATGGAATAC 60.244 47.826 10.06 0.00 41.63 1.89
1710 2679 3.244215 GCTGCTAGTAGGCATGGAATACA 60.244 47.826 10.06 0.00 41.63 2.29
1719 2688 4.234550 AGGCATGGAATACAGGTCTATGA 58.765 43.478 0.00 0.00 45.15 2.15
1780 2752 3.795101 CGCTTAAGTATGTCAAGTACCGG 59.205 47.826 0.00 0.00 0.00 5.28
1813 2785 1.656441 GCTGTTTGAGCTGTGTGGG 59.344 57.895 0.00 0.00 45.21 4.61
1819 2791 1.920734 TTGAGCTGTGTGGGTGTGGT 61.921 55.000 0.00 0.00 0.00 4.16
1828 2800 3.717294 GGGTGTGGTGGAGGCGAT 61.717 66.667 0.00 0.00 0.00 4.58
1829 2801 2.436646 GGTGTGGTGGAGGCGATG 60.437 66.667 0.00 0.00 0.00 3.84
1845 2883 1.920574 CGATGACGTCTGGCAAGTAAG 59.079 52.381 17.92 0.00 34.56 2.34
1918 2956 1.344953 ACTTGACACCACTGGAGGCA 61.345 55.000 0.71 0.00 27.13 4.75
1968 3006 3.160047 AGGCATCGGAGCTGGAGG 61.160 66.667 0.00 0.00 34.17 4.30
1969 3007 3.157252 GGCATCGGAGCTGGAGGA 61.157 66.667 0.00 0.00 34.17 3.71
1970 3008 2.420890 GCATCGGAGCTGGAGGAG 59.579 66.667 0.00 0.00 0.00 3.69
1971 3009 2.130426 GCATCGGAGCTGGAGGAGA 61.130 63.158 0.00 0.00 0.00 3.71
1972 3010 1.680522 GCATCGGAGCTGGAGGAGAA 61.681 60.000 0.00 0.00 0.00 2.87
1973 3011 0.388659 CATCGGAGCTGGAGGAGAAG 59.611 60.000 0.00 0.00 0.00 2.85
1974 3012 0.758685 ATCGGAGCTGGAGGAGAAGG 60.759 60.000 0.00 0.00 0.00 3.46
1975 3013 1.684049 CGGAGCTGGAGGAGAAGGT 60.684 63.158 0.00 0.00 0.00 3.50
1976 3014 1.904032 GGAGCTGGAGGAGAAGGTG 59.096 63.158 0.00 0.00 0.00 4.00
1977 3015 1.220477 GAGCTGGAGGAGAAGGTGC 59.780 63.158 0.00 0.00 0.00 5.01
1978 3016 2.250741 GAGCTGGAGGAGAAGGTGCC 62.251 65.000 0.00 0.00 0.00 5.01
1979 3017 2.596851 GCTGGAGGAGAAGGTGCCA 61.597 63.158 0.00 0.00 0.00 4.92
1980 3018 1.601171 CTGGAGGAGAAGGTGCCAG 59.399 63.158 0.00 0.00 40.03 4.85
1981 3019 1.152030 TGGAGGAGAAGGTGCCAGT 60.152 57.895 0.00 0.00 0.00 4.00
1982 3020 1.298014 GGAGGAGAAGGTGCCAGTG 59.702 63.158 0.00 0.00 0.00 3.66
1983 3021 1.484444 GGAGGAGAAGGTGCCAGTGT 61.484 60.000 0.00 0.00 0.00 3.55
2347 3385 7.143340 TGTAGTAGCGCCAACTTAATATACTG 58.857 38.462 17.12 0.00 0.00 2.74
2362 3400 9.764363 CTTAATATACTGTGGATGCTTGACTAA 57.236 33.333 0.00 0.00 0.00 2.24
2364 3402 8.668510 AATATACTGTGGATGCTTGACTAAAG 57.331 34.615 0.00 0.00 39.07 1.85
2365 3403 4.357918 ACTGTGGATGCTTGACTAAAGT 57.642 40.909 0.00 0.00 38.25 2.66
2367 3405 5.482908 ACTGTGGATGCTTGACTAAAGTAG 58.517 41.667 0.00 0.00 38.25 2.57
2368 3406 5.012148 ACTGTGGATGCTTGACTAAAGTAGT 59.988 40.000 0.00 0.00 42.86 2.73
2369 3407 5.237815 TGTGGATGCTTGACTAAAGTAGTG 58.762 41.667 0.00 0.00 39.59 2.74
2371 3409 6.109359 GTGGATGCTTGACTAAAGTAGTGAT 58.891 40.000 0.00 0.00 39.59 3.06
2373 3411 6.155221 TGGATGCTTGACTAAAGTAGTGATCT 59.845 38.462 0.00 0.00 39.59 2.75
2374 3412 7.342026 TGGATGCTTGACTAAAGTAGTGATCTA 59.658 37.037 0.00 0.00 39.59 1.98
2375 3413 8.198109 GGATGCTTGACTAAAGTAGTGATCTAA 58.802 37.037 0.00 0.00 39.59 2.10
2376 3414 9.587772 GATGCTTGACTAAAGTAGTGATCTAAA 57.412 33.333 0.00 0.00 39.59 1.85
2377 3415 8.758633 TGCTTGACTAAAGTAGTGATCTAAAC 57.241 34.615 0.00 0.00 39.59 2.01
2379 3417 7.462988 GCTTGACTAAAGTAGTGATCTAAACGC 60.463 40.741 0.00 0.00 39.59 4.84
2381 3419 7.249147 TGACTAAAGTAGTGATCTAAACGCTC 58.751 38.462 0.00 0.00 39.59 5.03
2382 3420 7.120873 TGACTAAAGTAGTGATCTAAACGCTCT 59.879 37.037 0.00 0.00 39.59 4.09
2383 3421 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
2384 3422 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
2385 3423 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
2401 3439 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2402 3440 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2404 3442 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2497 3847 5.758296 TGACTACAAGTTGCCTTCTTAACAG 59.242 40.000 1.81 0.00 0.00 3.16
2620 3977 9.574516 ACACAAGTTATAGAACTCTTCCATTTT 57.425 29.630 2.67 0.00 45.50 1.82
2832 4191 6.569179 ACTTTGCATGTTTTCTAACGGTAT 57.431 33.333 0.00 0.00 37.06 2.73
3217 4582 7.458397 AGTTTATTGGTTCATGTTCTGGACTA 58.542 34.615 0.00 0.00 33.40 2.59
3289 4654 0.106519 ATAGTGCCTTGGCATGGACC 60.107 55.000 22.50 11.33 0.00 4.46
3302 4667 4.461081 TGGCATGGACCACTAATTTTGTAC 59.539 41.667 0.00 0.00 33.75 2.90
3303 4668 4.142249 GGCATGGACCACTAATTTTGTACC 60.142 45.833 0.00 0.00 0.00 3.34
3304 4669 4.461081 GCATGGACCACTAATTTTGTACCA 59.539 41.667 0.00 0.00 0.00 3.25
3305 4670 5.047660 GCATGGACCACTAATTTTGTACCAA 60.048 40.000 0.00 0.00 0.00 3.67
3306 4671 6.517529 GCATGGACCACTAATTTTGTACCAAA 60.518 38.462 0.00 0.00 0.00 3.28
3307 4672 6.642707 TGGACCACTAATTTTGTACCAAAG 57.357 37.500 0.00 0.00 0.00 2.77
3308 4673 6.366340 TGGACCACTAATTTTGTACCAAAGA 58.634 36.000 0.00 0.00 0.00 2.52
3377 4745 3.006859 TGCTAACTTGCTACTCTGCTGAA 59.993 43.478 0.00 0.00 0.00 3.02
3384 4752 5.997746 ACTTGCTACTCTGCTGAAAAACATA 59.002 36.000 0.00 0.00 0.00 2.29
3521 4891 2.426738 TGGCAGCAGGTAATAACAATGC 59.573 45.455 0.00 0.00 39.12 3.56
3543 4913 5.868801 TGCTAATAAAGTTTGCTTGCATTCC 59.131 36.000 0.00 0.00 34.71 3.01
3590 4966 0.750249 ACCAAAGGGCAAAAGGTTCG 59.250 50.000 0.00 0.00 37.90 3.95
3617 6618 6.423182 TCCCCTGTTCTGTTATATTTCAAGG 58.577 40.000 0.00 0.00 0.00 3.61
3620 6621 6.884295 CCCTGTTCTGTTATATTTCAAGGTCA 59.116 38.462 0.00 0.00 0.00 4.02
3633 6634 2.154462 CAAGGTCACATCCACTGTTCC 58.846 52.381 0.00 0.00 35.29 3.62
3682 6683 4.743057 AGAAAAGGGGCAATGCTATTTC 57.257 40.909 4.82 10.53 0.00 2.17
3685 6686 3.971468 AAGGGGCAATGCTATTTCCTA 57.029 42.857 4.82 0.00 0.00 2.94
3686 6687 3.515602 AGGGGCAATGCTATTTCCTAG 57.484 47.619 4.82 0.00 0.00 3.02
3687 6688 2.785857 AGGGGCAATGCTATTTCCTAGT 59.214 45.455 4.82 0.00 0.00 2.57
3708 6709 3.976942 GTGTCGCTAACTGAACTTACGAA 59.023 43.478 0.00 0.00 0.00 3.85
3794 6798 0.318107 CAAGTTTGCAACTCCCAGCG 60.318 55.000 0.00 0.00 41.91 5.18
3800 6804 0.107831 TGCAACTCCCAGCGTTAAGT 59.892 50.000 0.00 0.00 0.00 2.24
3882 6886 1.523758 AAGGGCGTGCTTCTTAACTG 58.476 50.000 0.00 0.00 0.00 3.16
3885 6984 2.084546 GGGCGTGCTTCTTAACTGATT 58.915 47.619 0.00 0.00 0.00 2.57
3912 7013 5.744666 ACATTCCCGATTTTACCATTACG 57.255 39.130 0.00 0.00 0.00 3.18
3916 7017 4.829968 TCCCGATTTTACCATTACGTTGA 58.170 39.130 0.00 0.00 0.00 3.18
4103 7318 6.438741 ACTGACTCTCTTGACTGATTTATGGA 59.561 38.462 0.00 0.00 0.00 3.41
4153 7372 9.719279 TTTGAAGTGTTTTAAATAACGTGGTAG 57.281 29.630 0.00 0.00 0.00 3.18
4188 7407 5.343307 AGGAAACAATTGGAATATGGTGC 57.657 39.130 10.83 0.00 0.00 5.01
4191 7410 5.398603 AAACAATTGGAATATGGTGCGAA 57.601 34.783 10.83 0.00 0.00 4.70
4197 7416 6.899393 ATTGGAATATGGTGCGAACAATAT 57.101 33.333 0.00 0.00 0.00 1.28
4256 7475 8.623030 CATCACCAAACATATGATATCACACAA 58.377 33.333 10.38 0.00 31.83 3.33
4287 7511 4.380841 TTGCTATTACTCCACACTACCG 57.619 45.455 0.00 0.00 0.00 4.02
4363 7588 6.915544 TTGAGCAGTCAATCTGTATGATTC 57.084 37.500 0.00 0.00 43.00 2.52
4375 7600 9.376075 CAATCTGTATGATTCTGTATACATCCC 57.624 37.037 5.91 0.00 43.00 3.85
4412 7637 3.795623 TGGCTTACATCTCCGTTAGAC 57.204 47.619 0.00 0.00 36.93 2.59
4445 7670 8.099364 TCTGAGAACACTGTTTAAATGATTCC 57.901 34.615 0.00 0.00 0.00 3.01
4454 7679 9.439500 CACTGTTTAAATGATTCCATCCATTTT 57.561 29.630 0.00 0.00 41.54 1.82
4616 7845 8.960591 TCTTGTTTTCCATCAATCCTCTAAATC 58.039 33.333 0.00 0.00 0.00 2.17
4718 7947 4.360563 CTTGGACTACAGGTACATTAGCG 58.639 47.826 0.00 0.00 38.76 4.26
4734 7963 7.962964 ACATTAGCGTATGCACTGTAATATT 57.037 32.000 10.11 0.00 46.23 1.28
4891 8120 5.070685 GGTAGTTCCACTTTCCATCTTTGT 58.929 41.667 0.00 0.00 35.97 2.83
4957 8214 7.316544 TCAAGGAAGTGTTGAAACTAAGTTC 57.683 36.000 0.00 0.00 30.89 3.01
5106 8363 5.335897 GGACAGCACTGCTTCAATTTGAATA 60.336 40.000 12.04 4.57 36.40 1.75
5109 8366 5.344128 CAGCACTGCTTCAATTTGAATACAC 59.656 40.000 12.04 4.06 36.40 2.90
5111 8368 4.321745 CACTGCTTCAATTTGAATACACGC 59.678 41.667 12.04 11.66 35.59 5.34
5337 8597 2.816672 GCTGCCTGCTAATTTCCCTATC 59.183 50.000 0.00 0.00 38.95 2.08
5359 8619 1.604278 GTTCTTTCTGGAAGCTTGCGT 59.396 47.619 13.65 0.00 35.24 5.24
5371 8631 4.148174 GGAAGCTTGCGTTTTTACATTGTC 59.852 41.667 2.10 0.00 0.00 3.18
5389 8649 6.039717 ACATTGTCACTGTAAGCAATTCAGTT 59.960 34.615 0.00 0.00 39.89 3.16
5396 8656 5.292101 ACTGTAAGCAATTCAGTTATCTCGC 59.708 40.000 0.00 0.00 39.00 5.03
5397 8657 5.175127 TGTAAGCAATTCAGTTATCTCGCA 58.825 37.500 0.00 0.00 0.00 5.10
5400 8660 2.939103 GCAATTCAGTTATCTCGCACCT 59.061 45.455 0.00 0.00 0.00 4.00
5452 8712 6.693315 TTTCCCTAAGTTGTGAAAGTCTTG 57.307 37.500 0.00 0.00 0.00 3.02
5476 8736 6.162777 GCTGTTTGCCCTTGATTGTAATAAA 58.837 36.000 0.00 0.00 35.15 1.40
5527 8788 4.338964 TGTAGAACTGTTTACTCGTCACCA 59.661 41.667 0.00 0.00 0.00 4.17
5576 8843 7.400599 ACTTGTATGTCAGTCTACCGATTTA 57.599 36.000 0.00 0.00 0.00 1.40
5598 8865 7.681939 TTAATCGCTTCCAGTTTTCAATAGT 57.318 32.000 0.00 0.00 0.00 2.12
5599 8866 5.551760 ATCGCTTCCAGTTTTCAATAGTG 57.448 39.130 0.00 0.00 0.00 2.74
5644 8924 6.822170 CACCTTATAGTTTTCAGGGGTACTTC 59.178 42.308 0.00 0.00 0.00 3.01
5759 9144 5.529800 ACAGTTGTCAACGCCTACTTAAATT 59.470 36.000 10.02 0.00 36.23 1.82
5771 9158 6.447162 GCCTACTTAAATTCTGTTGTTTGCT 58.553 36.000 0.00 0.00 0.00 3.91
5845 9234 5.994250 TGGCAGCTCTAAGATTTCAGTTAT 58.006 37.500 0.00 0.00 0.00 1.89
5887 9277 8.608844 TGTACAATTGTATCATGTGTTGTGTA 57.391 30.769 20.72 0.00 32.64 2.90
5917 9308 3.048600 AGGCAGCCCATCTCTGTATTTA 58.951 45.455 8.22 0.00 34.21 1.40
5998 9391 1.813513 CTGGTGTCAGGGCTAACTTG 58.186 55.000 0.00 0.00 37.36 3.16
6078 9490 1.196808 CATCAAAACTCGACCAACCGG 59.803 52.381 0.00 0.00 38.77 5.28
6079 9491 0.533308 TCAAAACTCGACCAACCGGG 60.533 55.000 6.32 0.00 44.81 5.73
6080 9492 1.228033 AAAACTCGACCAACCGGGG 60.228 57.895 6.32 0.00 42.91 5.73
6081 9493 1.698067 AAAACTCGACCAACCGGGGA 61.698 55.000 6.32 0.00 42.91 4.81
6082 9494 2.387476 AAACTCGACCAACCGGGGAC 62.387 60.000 6.32 0.00 42.91 4.46
6083 9495 2.995574 CTCGACCAACCGGGGACT 60.996 66.667 6.32 0.00 42.91 3.85
6084 9496 1.679977 CTCGACCAACCGGGGACTA 60.680 63.158 6.32 0.00 42.91 2.59
6085 9497 1.664321 CTCGACCAACCGGGGACTAG 61.664 65.000 6.32 0.00 42.91 2.57
6086 9498 2.582978 GACCAACCGGGGACTAGC 59.417 66.667 6.32 0.00 42.91 3.42
6087 9499 3.007323 ACCAACCGGGGACTAGCC 61.007 66.667 6.32 0.00 42.91 3.93
6239 9653 8.947055 AAAAGTTGAGCACAGTTATTGAAATT 57.053 26.923 0.00 0.00 0.00 1.82
6290 9707 8.073768 GCACAAAGCAGAACATAAAAACTAGTA 58.926 33.333 0.00 0.00 44.79 1.82
6291 9708 9.382244 CACAAAGCAGAACATAAAAACTAGTAC 57.618 33.333 0.00 0.00 0.00 2.73
6292 9709 8.280497 ACAAAGCAGAACATAAAAACTAGTACG 58.720 33.333 0.00 0.00 0.00 3.67
6293 9710 7.958053 AAGCAGAACATAAAAACTAGTACGT 57.042 32.000 0.00 0.00 0.00 3.57
6294 9711 9.480053 AAAGCAGAACATAAAAACTAGTACGTA 57.520 29.630 0.00 0.00 0.00 3.57
6295 9712 8.684973 AGCAGAACATAAAAACTAGTACGTAG 57.315 34.615 0.00 0.00 34.52 3.51
6330 9750 6.090358 CACACAAATCATGAAATGCCTTCTTC 59.910 38.462 0.00 0.00 46.21 2.87
6389 9826 4.187694 CCTCTCCAGTAAGATTTGTGAGC 58.812 47.826 0.00 0.00 0.00 4.26
6390 9827 4.323028 CCTCTCCAGTAAGATTTGTGAGCA 60.323 45.833 0.00 0.00 0.00 4.26
6532 10016 2.205022 TCCTTGCTGCTATGCTTTGT 57.795 45.000 0.00 0.00 0.00 2.83
6533 10017 2.517959 TCCTTGCTGCTATGCTTTGTT 58.482 42.857 0.00 0.00 0.00 2.83
6534 10018 2.892852 TCCTTGCTGCTATGCTTTGTTT 59.107 40.909 0.00 0.00 0.00 2.83
6535 10019 3.321682 TCCTTGCTGCTATGCTTTGTTTT 59.678 39.130 0.00 0.00 0.00 2.43
6536 10020 3.430895 CCTTGCTGCTATGCTTTGTTTTG 59.569 43.478 0.00 0.00 0.00 2.44
6677 10161 5.337250 CCAGCAGGTAGTTGTGTTACTGATA 60.337 44.000 0.00 0.00 0.00 2.15
6690 10174 6.981559 TGTGTTACTGATAATAACGCATAGCA 59.018 34.615 6.97 0.00 44.18 3.49
6717 10201 7.044181 ACTTGTGTGTCTATTCATATCACTGG 58.956 38.462 0.00 0.00 0.00 4.00
6763 10353 7.829725 TGCTACTGAGTTTGCAATCATAAATT 58.170 30.769 10.05 0.00 32.12 1.82
7002 10592 3.859411 AGAAAGCGTTGTTGGTTTTCA 57.141 38.095 0.00 0.00 39.47 2.69
7021 10611 7.229907 GGTTTTCAAACTAATTGTCCACCTCTA 59.770 37.037 2.55 0.00 40.11 2.43
7031 10621 2.301870 TGTCCACCTCTATGTTTTCGCT 59.698 45.455 0.00 0.00 0.00 4.93
7163 10753 2.057316 CGGCTGATCGATGATGTCTTC 58.943 52.381 0.54 0.00 0.00 2.87
7174 10764 4.548916 CGATGATGTCTTCGTTGTATGTGC 60.549 45.833 9.38 0.00 38.30 4.57
7199 10789 1.080230 CTGTGTCTGGACAGAGCGG 60.080 63.158 13.48 0.81 45.39 5.52
7223 10813 7.423199 GGCATGTATATCAATATGCATTCTGG 58.577 38.462 3.54 0.00 45.73 3.86
7237 10827 5.055812 TGCATTCTGGGTCAATTCAAAAAC 58.944 37.500 0.00 0.00 0.00 2.43
7256 10847 3.603965 ACCCCACCACAGTTGATTTTA 57.396 42.857 0.00 0.00 0.00 1.52
7257 10848 4.126520 ACCCCACCACAGTTGATTTTAT 57.873 40.909 0.00 0.00 0.00 1.40
7258 10849 3.831911 ACCCCACCACAGTTGATTTTATG 59.168 43.478 0.00 0.00 0.00 1.90
7259 10850 3.368323 CCCCACCACAGTTGATTTTATGC 60.368 47.826 0.00 0.00 0.00 3.14
7260 10851 3.500982 CCACCACAGTTGATTTTATGCG 58.499 45.455 0.00 0.00 0.00 4.73
7302 10897 6.241207 TCCGATGTGAATTTTCAGAGTTTC 57.759 37.500 0.00 0.00 37.98 2.78
7343 10938 3.414700 CCGAATCATAGGCGCGCC 61.415 66.667 42.34 42.34 0.00 6.53
7344 10939 3.767230 CGAATCATAGGCGCGCCG 61.767 66.667 41.70 28.95 41.95 6.46
7367 10962 2.550606 TCACGGCATTGTTTTGTACCTC 59.449 45.455 0.00 0.00 0.00 3.85
7442 11037 6.503524 GGATGAGAAGATGAGTCTGTACTTC 58.496 44.000 0.00 0.00 35.56 3.01
7450 11055 6.905736 AGATGAGTCTGTACTTCCATCTAGA 58.094 40.000 0.00 0.00 41.77 2.43
7501 11107 9.103861 GTATTTTTGACTTCCAAATTCAAACCA 57.896 29.630 5.13 0.00 43.59 3.67
7502 11108 7.986085 TTTTTGACTTCCAAATTCAAACCAA 57.014 28.000 5.13 0.00 43.59 3.67
7536 11150 3.262405 GGTCAATGTCCAAGTGGTACCTA 59.738 47.826 14.36 0.00 36.34 3.08
7538 11152 5.116882 GTCAATGTCCAAGTGGTACCTATC 58.883 45.833 14.36 3.90 36.34 2.08
7551 11222 6.773685 AGTGGTACCTATCACTTGTCTCTATC 59.226 42.308 14.36 0.00 44.85 2.08
7552 11223 6.016108 GTGGTACCTATCACTTGTCTCTATCC 60.016 46.154 14.36 0.00 34.54 2.59
7569 11240 7.704472 GTCTCTATCCATCTACTCAGTTTGTTG 59.296 40.741 0.00 0.00 0.00 3.33
7669 11341 5.594926 AGTCCAAGAAAAAGAAACTGCATG 58.405 37.500 0.00 0.00 0.00 4.06
7818 12479 8.253810 TCAAATCTAAAATCAAAACACACACCA 58.746 29.630 0.00 0.00 0.00 4.17
7829 12490 3.866883 ACACACACCAGGAAACAAAAG 57.133 42.857 0.00 0.00 0.00 2.27
7940 12602 7.325821 GTGCATTTCGAATTTGAACATGAACTA 59.674 33.333 22.01 5.26 30.50 2.24
8142 12811 6.133356 CCCTTGAGAATCTCCTAGTTCTACT 58.867 44.000 7.91 0.00 34.97 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 1.426251 TTGGCTTCCTCCTCCAGCAA 61.426 55.000 0.00 0.00 35.05 3.91
72 863 3.388350 AGCTAGATAGTACCCCTTGTTGC 59.612 47.826 0.00 0.00 0.00 4.17
184 975 0.255318 CATCCTTCCTGCAAGCCTCT 59.745 55.000 0.00 0.00 0.00 3.69
455 1246 2.825532 GTTAATGATGCACCTGTGGGTT 59.174 45.455 0.00 0.00 44.73 4.11
473 1264 7.065085 GTGCTCAATTAGATCTTTCTGCAGTTA 59.935 37.037 14.67 0.00 33.17 2.24
743 1537 2.126110 GGCGTCAAAATTGGCCCG 60.126 61.111 0.00 0.00 39.67 6.13
837 1633 1.035139 CCCAGGATGCATACAAAGCC 58.965 55.000 12.53 1.23 31.97 4.35
839 1635 1.696063 CCCCCAGGATGCATACAAAG 58.304 55.000 12.53 0.04 33.47 2.77
907 1705 1.094785 GAGAGCACGAGAGAGAAGCT 58.905 55.000 0.00 0.00 38.43 3.74
910 1708 1.542030 GGTTGAGAGCACGAGAGAGAA 59.458 52.381 0.00 0.00 0.00 2.87
919 1717 1.302832 CTGTGGGGGTTGAGAGCAC 60.303 63.158 0.00 0.00 0.00 4.40
928 1726 4.204028 GTGGTGTGCTGTGGGGGT 62.204 66.667 0.00 0.00 0.00 4.95
930 1728 2.595463 CTGTGGTGTGCTGTGGGG 60.595 66.667 0.00 0.00 0.00 4.96
932 1730 1.727511 CCAACTGTGGTGTGCTGTGG 61.728 60.000 0.00 0.00 40.42 4.17
937 1745 1.160137 GATCTCCAACTGTGGTGTGC 58.840 55.000 0.00 0.00 46.11 4.57
980 1790 1.826054 CGGCGAGAGATCTGGGACT 60.826 63.158 0.00 0.00 0.00 3.85
981 1791 2.725008 CGGCGAGAGATCTGGGAC 59.275 66.667 0.00 0.00 0.00 4.46
982 1792 2.359015 ATCCGGCGAGAGATCTGGGA 62.359 60.000 9.30 0.00 0.00 4.37
1354 2221 4.008933 GGGCGATGGAGATCCGGG 62.009 72.222 0.00 0.00 39.43 5.73
1364 2231 2.359354 TCGTTGGTTGGGGCGATG 60.359 61.111 0.00 0.00 0.00 3.84
1377 2244 4.080687 AGACTGCTAAAGTAGAGGTCGTT 58.919 43.478 1.86 0.00 40.07 3.85
1378 2245 3.688235 AGACTGCTAAAGTAGAGGTCGT 58.312 45.455 1.86 0.00 40.07 4.34
1434 2327 1.578915 CAATTGCGCGCAAACTACATC 59.421 47.619 45.24 8.44 39.55 3.06
1462 2355 4.555708 CGTACAGATACAGAGCTAAGCAGG 60.556 50.000 0.00 0.00 0.00 4.85
1539 2433 4.400410 GCAACCCATATGCGCAAC 57.600 55.556 17.11 0.00 33.57 4.17
1573 2481 0.397187 CATGAGGGATCCAGCCTGAG 59.603 60.000 15.23 0.00 0.00 3.35
1587 2495 2.247637 CGTGCTGCAAAATGACATGAG 58.752 47.619 2.77 0.00 0.00 2.90
1604 2512 6.721571 ACACATCTAGTCAATTAAACCGTG 57.278 37.500 0.00 0.00 0.00 4.94
1629 2594 2.029838 AGCTTCACGGGACATGAATC 57.970 50.000 0.00 0.00 40.64 2.52
1647 2612 3.985279 CACACAGCACATTTCATTCCAAG 59.015 43.478 0.00 0.00 0.00 3.61
1709 2678 9.209175 GCTACCTACAATAAAATCATAGACCTG 57.791 37.037 0.00 0.00 0.00 4.00
1710 2679 8.934697 TGCTACCTACAATAAAATCATAGACCT 58.065 33.333 0.00 0.00 0.00 3.85
1715 2684 8.275758 TGGGTTGCTACCTACAATAAAATCATA 58.724 33.333 17.03 0.00 44.38 2.15
1719 2688 7.398904 ACATTGGGTTGCTACCTACAATAAAAT 59.601 33.333 17.03 0.00 44.38 1.82
1727 2699 2.026636 TGGACATTGGGTTGCTACCTAC 60.027 50.000 17.03 2.04 44.38 3.18
1728 2700 2.238646 CTGGACATTGGGTTGCTACCTA 59.761 50.000 17.03 8.42 44.38 3.08
1729 2701 1.004745 CTGGACATTGGGTTGCTACCT 59.995 52.381 17.03 0.00 44.38 3.08
1730 2702 1.463674 CTGGACATTGGGTTGCTACC 58.536 55.000 9.03 9.03 44.22 3.18
1765 2737 0.457035 TCGGCCGGTACTTGACATAC 59.543 55.000 27.83 0.00 0.00 2.39
1780 2752 1.010797 CAGCGCAATGTATGTCGGC 60.011 57.895 11.47 0.00 0.00 5.54
1813 2785 1.741770 GTCATCGCCTCCACCACAC 60.742 63.158 0.00 0.00 0.00 3.82
1819 2791 2.710902 CCAGACGTCATCGCCTCCA 61.711 63.158 19.50 0.00 41.18 3.86
1826 2798 2.094182 TCCTTACTTGCCAGACGTCATC 60.094 50.000 19.50 6.55 0.00 2.92
1827 2799 1.899814 TCCTTACTTGCCAGACGTCAT 59.100 47.619 19.50 0.00 0.00 3.06
1828 2800 1.272490 CTCCTTACTTGCCAGACGTCA 59.728 52.381 19.50 0.00 0.00 4.35
1829 2801 1.272769 ACTCCTTACTTGCCAGACGTC 59.727 52.381 7.70 7.70 0.00 4.34
1837 2875 0.324943 TCAGGGCACTCCTTACTTGC 59.675 55.000 0.00 0.00 45.47 4.01
1839 2877 1.561542 CCATCAGGGCACTCCTTACTT 59.438 52.381 0.00 0.00 45.47 2.24
1866 2904 1.078848 CCCCCGAACAAGCTCTCAG 60.079 63.158 0.00 0.00 0.00 3.35
1968 3006 0.890996 CCCAACACTGGCACCTTCTC 60.891 60.000 0.00 0.00 41.99 2.87
1969 3007 1.151450 CCCAACACTGGCACCTTCT 59.849 57.895 0.00 0.00 41.99 2.85
1970 3008 0.890996 CTCCCAACACTGGCACCTTC 60.891 60.000 0.00 0.00 41.99 3.46
1971 3009 1.151450 CTCCCAACACTGGCACCTT 59.849 57.895 0.00 0.00 41.99 3.50
1972 3010 1.770110 TCTCCCAACACTGGCACCT 60.770 57.895 0.00 0.00 41.99 4.00
1973 3011 1.302832 CTCTCCCAACACTGGCACC 60.303 63.158 0.00 0.00 41.99 5.01
1974 3012 1.302832 CCTCTCCCAACACTGGCAC 60.303 63.158 0.00 0.00 41.99 5.01
1975 3013 1.461268 TCCTCTCCCAACACTGGCA 60.461 57.895 0.00 0.00 41.99 4.92
1976 3014 1.298014 CTCCTCTCCCAACACTGGC 59.702 63.158 0.00 0.00 41.99 4.85
1977 3015 1.557269 CCCTCCTCTCCCAACACTGG 61.557 65.000 0.00 0.00 43.10 4.00
1978 3016 1.557269 CCCCTCCTCTCCCAACACTG 61.557 65.000 0.00 0.00 0.00 3.66
1979 3017 1.229658 CCCCTCCTCTCCCAACACT 60.230 63.158 0.00 0.00 0.00 3.55
1980 3018 1.539124 ACCCCTCCTCTCCCAACAC 60.539 63.158 0.00 0.00 0.00 3.32
1981 3019 1.538876 CACCCCTCCTCTCCCAACA 60.539 63.158 0.00 0.00 0.00 3.33
1982 3020 2.301738 CCACCCCTCCTCTCCCAAC 61.302 68.421 0.00 0.00 0.00 3.77
1983 3021 2.124996 CCACCCCTCCTCTCCCAA 59.875 66.667 0.00 0.00 0.00 4.12
2327 3365 5.069383 TCCACAGTATATTAAGTTGGCGCTA 59.931 40.000 7.64 0.00 0.00 4.26
2347 3385 5.479306 TCACTACTTTAGTCAAGCATCCAC 58.521 41.667 0.00 0.00 36.76 4.02
2374 3412 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2375 3413 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2376 3414 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2377 3415 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2385 3423 9.765295 ACTAAAGACTCCCTCTGTAAACTAATA 57.235 33.333 0.00 0.00 0.00 0.98
2386 3424 8.667592 ACTAAAGACTCCCTCTGTAAACTAAT 57.332 34.615 0.00 0.00 0.00 1.73
2387 3425 8.488308 AACTAAAGACTCCCTCTGTAAACTAA 57.512 34.615 0.00 0.00 0.00 2.24
2388 3426 8.488308 AAACTAAAGACTCCCTCTGTAAACTA 57.512 34.615 0.00 0.00 0.00 2.24
2389 3427 6.997942 AACTAAAGACTCCCTCTGTAAACT 57.002 37.500 0.00 0.00 0.00 2.66
2390 3428 6.649973 GGAAACTAAAGACTCCCTCTGTAAAC 59.350 42.308 0.00 0.00 0.00 2.01
2392 3430 5.842328 TGGAAACTAAAGACTCCCTCTGTAA 59.158 40.000 0.00 0.00 0.00 2.41
2393 3431 5.399991 TGGAAACTAAAGACTCCCTCTGTA 58.600 41.667 0.00 0.00 0.00 2.74
2394 3432 4.232091 TGGAAACTAAAGACTCCCTCTGT 58.768 43.478 0.00 0.00 0.00 3.41
2395 3433 4.891992 TGGAAACTAAAGACTCCCTCTG 57.108 45.455 0.00 0.00 0.00 3.35
2396 3434 6.455690 AATTGGAAACTAAAGACTCCCTCT 57.544 37.500 0.00 0.00 0.00 3.69
2397 3435 7.309255 GGAAAATTGGAAACTAAAGACTCCCTC 60.309 40.741 0.00 0.00 0.00 4.30
2398 3436 6.493802 GGAAAATTGGAAACTAAAGACTCCCT 59.506 38.462 0.00 0.00 0.00 4.20
2433 3778 5.640189 ATATATACACGTACTGGACTGGC 57.360 43.478 0.00 0.00 0.00 4.85
2606 3962 6.367149 GCTGAAATGGAAAAATGGAAGAGTTC 59.633 38.462 0.00 0.00 0.00 3.01
2620 3977 1.887956 GCTGTCCTGGCTGAAATGGAA 60.888 52.381 0.00 0.00 0.00 3.53
2646 4003 2.928334 ACATCATGATGGGTTGAGAGC 58.072 47.619 33.31 0.00 42.91 4.09
2832 4191 4.819088 TGGCGCTAATATATCTGCAAAACA 59.181 37.500 7.64 0.00 0.00 2.83
3217 4582 8.949177 GGCAAAAATCTGAACAATTTCCAATAT 58.051 29.630 0.00 0.00 0.00 1.28
3238 4603 7.775053 ATTCTCTTTGGTATAACAAGGCAAA 57.225 32.000 7.73 5.16 0.00 3.68
3302 4667 4.618489 GTGCGTCTCATTGATTTTCTTTGG 59.382 41.667 0.00 0.00 0.00 3.28
3303 4668 5.214417 TGTGCGTCTCATTGATTTTCTTTG 58.786 37.500 0.00 0.00 0.00 2.77
3304 4669 5.437289 TGTGCGTCTCATTGATTTTCTTT 57.563 34.783 0.00 0.00 0.00 2.52
3305 4670 5.181811 TCATGTGCGTCTCATTGATTTTCTT 59.818 36.000 0.00 0.00 0.00 2.52
3306 4671 4.696877 TCATGTGCGTCTCATTGATTTTCT 59.303 37.500 0.00 0.00 0.00 2.52
3307 4672 4.973396 TCATGTGCGTCTCATTGATTTTC 58.027 39.130 0.00 0.00 0.00 2.29
3308 4673 5.375417 TTCATGTGCGTCTCATTGATTTT 57.625 34.783 0.00 0.00 0.00 1.82
3377 4745 8.506168 TGAGAAGTTGAGAACTGTTATGTTTT 57.494 30.769 0.00 0.00 41.91 2.43
3384 4752 3.817647 GGCATGAGAAGTTGAGAACTGTT 59.182 43.478 0.00 0.00 41.91 3.16
3521 4891 6.033831 CACGGAATGCAAGCAAACTTTATTAG 59.966 38.462 0.00 0.00 32.29 1.73
3543 4913 6.021596 GCATAGTAAAAACAGAACCATCACG 58.978 40.000 0.00 0.00 0.00 4.35
3590 4966 8.519799 TTGAAATATAACAGAACAGGGGATTC 57.480 34.615 0.00 0.00 0.00 2.52
3633 6634 5.410067 ACAATCTGAACAACACCAAAACTG 58.590 37.500 0.00 0.00 0.00 3.16
3682 6683 3.851976 AGTTCAGTTAGCGACACTAGG 57.148 47.619 0.00 0.00 30.79 3.02
3685 6686 3.251729 TCGTAAGTTCAGTTAGCGACACT 59.748 43.478 0.00 0.00 39.48 3.55
3686 6687 3.558505 TCGTAAGTTCAGTTAGCGACAC 58.441 45.455 0.00 0.00 39.48 3.67
3687 6688 3.902261 TCGTAAGTTCAGTTAGCGACA 57.098 42.857 0.00 0.00 39.48 4.35
3758 6762 8.585881 TGCAAACTTGATTTCTAGACTACTACT 58.414 33.333 0.00 0.00 0.00 2.57
3781 6785 0.107831 ACTTAACGCTGGGAGTTGCA 59.892 50.000 0.00 0.00 33.42 4.08
3868 6872 7.060600 TGTTATCAATCAGTTAAGAAGCACG 57.939 36.000 0.00 0.00 0.00 5.34
3882 6886 7.936584 TGGTAAAATCGGGAATGTTATCAATC 58.063 34.615 0.00 0.00 27.16 2.67
3885 6984 7.889873 AATGGTAAAATCGGGAATGTTATCA 57.110 32.000 0.00 0.00 33.57 2.15
4077 7292 7.038729 TCCATAAATCAGTCAAGAGAGTCAGTT 60.039 37.037 0.00 0.00 0.00 3.16
4153 7372 5.684550 ATTGTTTCCTACGGTGAACTTTC 57.315 39.130 0.00 0.00 0.00 2.62
4173 7392 5.596836 ATTGTTCGCACCATATTCCAATT 57.403 34.783 0.00 0.00 0.00 2.32
4197 7416 3.669536 TGTTGCTGGTATTCGTGATGAA 58.330 40.909 0.00 0.00 41.81 2.57
4266 7485 3.429822 GCGGTAGTGTGGAGTAATAGCAA 60.430 47.826 0.00 0.00 0.00 3.91
4267 7486 2.100252 GCGGTAGTGTGGAGTAATAGCA 59.900 50.000 0.00 0.00 0.00 3.49
4287 7511 3.343617 TCCAGTGCAACCTTATAACTGC 58.656 45.455 0.00 3.52 37.80 4.40
4363 7588 6.837312 TGTTTTATCCAGGGGATGTATACAG 58.163 40.000 11.91 0.00 43.06 2.74
4375 7600 5.603170 AAGCCATTGATGTTTTATCCAGG 57.397 39.130 0.00 0.00 0.00 4.45
4412 7637 2.294791 ACAGTGTTCTCAGAAGAGGTCG 59.705 50.000 0.00 0.00 42.34 4.79
4445 7670 4.892433 TGTAACTTGGGCAAAAATGGATG 58.108 39.130 0.00 0.00 0.00 3.51
4454 7679 6.065374 TGAGAACTTTATGTAACTTGGGCAA 58.935 36.000 0.00 0.00 0.00 4.52
4512 7737 6.448207 TCAGAGAACTGATCTGACATACAG 57.552 41.667 6.60 0.00 46.30 2.74
4545 7770 9.153721 GCAAGATCATGGAATTTGAATGTAAAA 57.846 29.630 0.00 0.00 0.00 1.52
4616 7845 9.850628 CATGAAGATTAATGGCCAATTACATAG 57.149 33.333 10.96 0.67 30.21 2.23
4891 8120 5.012239 AGCAATGCTCAGAAGTAATTTCCA 58.988 37.500 0.00 0.00 32.55 3.53
4957 8214 2.874849 ACTGTGCGACAAAACAAAAGG 58.125 42.857 0.00 0.00 0.00 3.11
5106 8363 4.177026 CAGAGTTCAATAAGCTAGCGTGT 58.823 43.478 13.82 3.40 0.00 4.49
5109 8366 3.786635 ACCAGAGTTCAATAAGCTAGCG 58.213 45.455 9.55 0.00 0.00 4.26
5111 8368 8.723942 ATTGTTACCAGAGTTCAATAAGCTAG 57.276 34.615 0.00 0.00 31.89 3.42
5195 8454 0.722676 TATCAGGACCCCCAGACCTT 59.277 55.000 0.00 0.00 30.30 3.50
5337 8597 1.068954 GCAAGCTTCCAGAAAGAACCG 60.069 52.381 0.00 0.00 37.12 4.44
5359 8619 9.243637 GAATTGCTTACAGTGACAATGTAAAAA 57.756 29.630 24.02 20.85 41.31 1.94
5371 8631 6.700020 CGAGATAACTGAATTGCTTACAGTG 58.300 40.000 0.00 0.00 42.81 3.66
5452 8712 3.658757 TTACAATCAAGGGCAAACAGC 57.341 42.857 0.00 0.00 44.65 4.40
5476 8736 9.834628 CAACAAATATAACGTTGTGGTAAGATT 57.165 29.630 11.99 0.00 37.99 2.40
5576 8843 5.705441 TCACTATTGAAAACTGGAAGCGATT 59.295 36.000 0.00 0.00 37.60 3.34
5644 8924 2.295349 GGCCCACAATCTTGCATATGAG 59.705 50.000 6.97 0.00 0.00 2.90
5771 9158 2.486203 CACTGCGGTAAACCTGCATTAA 59.514 45.455 15.53 0.00 41.79 1.40
5851 9240 8.575649 TGATACAATTGTACAGACTGTAGAGA 57.424 34.615 20.26 5.41 32.84 3.10
5887 9277 2.785857 AGATGGGCTGCCTAAAGGTAAT 59.214 45.455 19.68 0.00 37.57 1.89
5891 9282 0.842635 AGAGATGGGCTGCCTAAAGG 59.157 55.000 19.68 0.00 38.53 3.11
5897 9288 2.355010 AAATACAGAGATGGGCTGCC 57.645 50.000 11.05 11.05 36.86 4.85
5917 9308 1.412453 TACCGGAGCACCAACCAGTT 61.412 55.000 9.46 0.00 35.59 3.16
6025 9418 6.276091 GCAAAATCAAGAATCCAGTATTCCC 58.724 40.000 0.00 0.00 44.44 3.97
6221 9633 8.746922 TCAATTGAATTTCAATAACTGTGCTC 57.253 30.769 21.68 0.00 45.57 4.26
6222 9634 9.715121 AATCAATTGAATTTCAATAACTGTGCT 57.285 25.926 21.68 7.81 45.57 4.40
6239 9653 7.331440 GCACAACCATGTAATCAAATCAATTGA 59.669 33.333 11.26 11.26 44.51 2.57
6290 9707 7.094631 TGATTTGTGTGCTTCTATTACTACGT 58.905 34.615 0.00 0.00 0.00 3.57
6291 9708 7.520119 TGATTTGTGTGCTTCTATTACTACG 57.480 36.000 0.00 0.00 0.00 3.51
6292 9709 9.098355 TCATGATTTGTGTGCTTCTATTACTAC 57.902 33.333 0.00 0.00 0.00 2.73
6293 9710 9.665719 TTCATGATTTGTGTGCTTCTATTACTA 57.334 29.630 0.00 0.00 0.00 1.82
6294 9711 8.565896 TTCATGATTTGTGTGCTTCTATTACT 57.434 30.769 0.00 0.00 0.00 2.24
6295 9712 9.793252 ATTTCATGATTTGTGTGCTTCTATTAC 57.207 29.630 0.00 0.00 0.00 1.89
6358 9795 3.764434 TCTTACTGGAGAGGCACACTTAG 59.236 47.826 0.00 0.00 0.00 2.18
6389 9826 1.303799 GCTCACACACTGAGGGCATG 61.304 60.000 0.00 0.00 46.08 4.06
6390 9827 1.002868 GCTCACACACTGAGGGCAT 60.003 57.895 0.00 0.00 46.08 4.40
6473 9913 2.205074 GAGACTGACCCAACATATGCG 58.795 52.381 1.58 0.00 0.00 4.73
6486 9928 5.185056 TCACAAACTCCATAATCGAGACTGA 59.815 40.000 0.00 0.00 0.00 3.41
6532 10016 1.103987 TGGCAACGGTAGCTGCAAAA 61.104 50.000 3.61 0.00 40.98 2.44
6533 10017 0.893270 ATGGCAACGGTAGCTGCAAA 60.893 50.000 3.61 0.00 40.98 3.68
6534 10018 0.035915 TATGGCAACGGTAGCTGCAA 60.036 50.000 3.61 0.00 40.98 4.08
6535 10019 0.180171 ATATGGCAACGGTAGCTGCA 59.820 50.000 3.61 0.00 40.98 4.41
6536 10020 1.308998 AATATGGCAACGGTAGCTGC 58.691 50.000 0.00 0.00 38.65 5.25
6597 10081 1.932511 CCAATGTTTGTGTGGTGCAAC 59.067 47.619 0.00 0.00 0.00 4.17
6677 10161 5.584649 ACACACAAGTATGCTATGCGTTATT 59.415 36.000 0.00 0.00 0.00 1.40
6690 10174 9.755804 CAGTGATATGAATAGACACACAAGTAT 57.244 33.333 0.00 0.00 34.47 2.12
6717 10201 7.573968 AGCATAAAACAAAGATGGATCCTAC 57.426 36.000 14.23 6.97 0.00 3.18
6763 10353 4.094294 CGCTTTCGGAATCATTGACCTTAA 59.906 41.667 0.00 0.00 0.00 1.85
7002 10592 8.706322 AAAACATAGAGGTGGACAATTAGTTT 57.294 30.769 0.00 0.00 0.00 2.66
7021 10611 1.967319 ACCTGACACAGCGAAAACAT 58.033 45.000 0.00 0.00 0.00 2.71
7163 10753 1.583856 CAGCTAGTCGCACATACAACG 59.416 52.381 0.00 0.00 42.61 4.10
7174 10764 0.881796 TGTCCAGACACAGCTAGTCG 59.118 55.000 11.51 7.66 40.84 4.18
7199 10789 7.067859 ACCCAGAATGCATATTGATATACATGC 59.932 37.037 0.00 0.00 34.00 4.06
7223 10813 2.436173 TGGTGGGGTTTTTGAATTGACC 59.564 45.455 0.00 0.00 0.00 4.02
7237 10827 3.368323 GCATAAAATCAACTGTGGTGGGG 60.368 47.826 0.00 0.00 0.00 4.96
7256 10847 3.411517 CAAGGGGAGGGGACGCAT 61.412 66.667 0.00 0.00 0.00 4.73
7257 10848 4.649705 TCAAGGGGAGGGGACGCA 62.650 66.667 0.00 0.00 0.00 5.24
7258 10849 4.097361 GTCAAGGGGAGGGGACGC 62.097 72.222 0.00 0.00 0.00 5.19
7259 10850 2.284699 AGTCAAGGGGAGGGGACG 60.285 66.667 0.00 0.00 35.49 4.79
7260 10851 2.972819 GCAGTCAAGGGGAGGGGAC 61.973 68.421 0.00 0.00 0.00 4.46
7302 10897 5.147330 TGGGTAAACACATCACTCTACAG 57.853 43.478 0.00 0.00 0.00 2.74
7344 10939 2.315901 GTACAAAACAATGCCGTGAGC 58.684 47.619 0.00 0.00 44.14 4.26
7345 10940 2.552315 AGGTACAAAACAATGCCGTGAG 59.448 45.455 0.00 0.00 0.00 3.51
7346 10941 2.550606 GAGGTACAAAACAATGCCGTGA 59.449 45.455 0.00 0.00 0.00 4.35
7347 10942 2.552315 AGAGGTACAAAACAATGCCGTG 59.448 45.455 0.00 0.00 0.00 4.94
7348 10943 2.858745 AGAGGTACAAAACAATGCCGT 58.141 42.857 0.00 0.00 0.00 5.68
7349 10944 4.214545 TGTTAGAGGTACAAAACAATGCCG 59.785 41.667 0.00 0.00 0.00 5.69
7350 10945 5.009210 TGTGTTAGAGGTACAAAACAATGCC 59.991 40.000 0.00 0.00 33.92 4.40
7442 11037 9.941664 GAACATACAAACATTTGATCTAGATGG 57.058 33.333 10.74 0.00 40.55 3.51
7450 11055 7.231317 ACAGGACAGAACATACAAACATTTGAT 59.769 33.333 11.24 0.00 40.55 2.57
7501 11107 6.489603 TGGACATTGACCCTAATACAACATT 58.510 36.000 2.69 0.00 0.00 2.71
7502 11108 6.073447 TGGACATTGACCCTAATACAACAT 57.927 37.500 2.69 0.00 0.00 2.71
7536 11150 7.293828 TGAGTAGATGGATAGAGACAAGTGAT 58.706 38.462 0.00 0.00 0.00 3.06
7538 11152 6.545666 ACTGAGTAGATGGATAGAGACAAGTG 59.454 42.308 0.00 0.00 0.00 3.16
7579 11250 8.597662 TTGACTTACGATAAAGCTACAACTTT 57.402 30.769 0.00 0.00 42.41 2.66
7669 11341 1.286257 AGGAGAAGGAAAATGAGGCCC 59.714 52.381 0.00 0.00 0.00 5.80
7814 12475 4.981806 TGTCTTCTTTTGTTTCCTGGTG 57.018 40.909 0.00 0.00 0.00 4.17
7816 12477 6.809869 AGATTTGTCTTCTTTTGTTTCCTGG 58.190 36.000 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.