Multiple sequence alignment - TraesCS3A01G063500

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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 TraesCS3A01G063500 chr3A 100.000 3717 0 0 1 3717 38015040 38011324 0.000000e+00 6865.0
1 TraesCS3A01G063500 chr3A 86.727 1439 152 19 1494 2911 37800160 37801580 0.000000e+00 1563.0
2 TraesCS3A01G063500 chr3A 94.939 652 31 2 2932 3582 698714567 698715217 0.000000e+00 1020.0
3 TraesCS3A01G063500 chr3A 96.441 590 19 2 2932 3520 37996914 37996326 0.000000e+00 972.0
4 TraesCS3A01G063500 chr3A 96.108 591 22 1 2932 3521 698719399 698719989 0.000000e+00 963.0
5 TraesCS3A01G063500 chr3A 78.224 1644 251 40 1301 2882 38136803 38135205 0.000000e+00 953.0
6 TraesCS3A01G063500 chr3A 76.389 288 34 19 2605 2882 38157950 38157687 1.400000e-24 124.0
7 TraesCS3A01G063500 chr3A 91.304 46 4 0 1 46 680981718 680981673 3.100000e-06 63.9
8 TraesCS3A01G063500 chr3A 96.774 31 1 0 711 741 38014284 38014254 7.000000e-03 52.8
9 TraesCS3A01G063500 chr3A 96.774 31 1 0 757 787 38014330 38014300 7.000000e-03 52.8
10 TraesCS3A01G063500 chr3D 91.944 1564 97 7 1365 2921 28124559 28123018 0.000000e+00 2163.0
11 TraesCS3A01G063500 chr3D 92.316 898 50 8 1 896 28125763 28124883 0.000000e+00 1258.0
12 TraesCS3A01G063500 chr3D 78.597 1654 255 40 1301 2911 28218133 28216536 0.000000e+00 1002.0
13 TraesCS3A01G063500 chr3D 78.287 1483 219 52 1450 2883 27663138 27664566 0.000000e+00 859.0
14 TraesCS3A01G063500 chr3D 77.901 1258 188 57 1683 2911 28224566 28223370 0.000000e+00 701.0
15 TraesCS3A01G063500 chr3D 75.086 1449 283 50 1512 2909 28275262 28276683 4.110000e-169 604.0
16 TraesCS3A01G063500 chr3D 90.489 368 26 7 44 406 27662189 27662552 9.340000e-131 477.0
17 TraesCS3A01G063500 chr3D 91.949 236 13 4 1032 1265 28124839 28124608 3.580000e-85 326.0
18 TraesCS3A01G063500 chr3D 71.799 695 154 32 1972 2646 4505359 4506031 3.840000e-35 159.0
19 TraesCS3A01G063500 chr3D 74.834 302 63 10 2353 2643 9629028 9628729 1.400000e-24 124.0
20 TraesCS3A01G063500 chr3D 81.513 119 16 2 2534 2646 4908910 4909028 3.950000e-15 93.5
21 TraesCS3A01G063500 chr3D 75.641 156 32 3 2497 2646 4474563 4474408 5.150000e-09 73.1
22 TraesCS3A01G063500 chr3D 94.872 39 1 1 704 741 28125030 28124992 4.010000e-05 60.2
23 TraesCS3A01G063500 chr3D 100.000 29 0 0 676 704 28124990 28124962 2.000000e-03 54.7
24 TraesCS3A01G063500 chr3B 94.090 1083 55 7 1854 2931 46328490 46329568 0.000000e+00 1637.0
25 TraesCS3A01G063500 chr3B 95.686 765 28 2 2168 2931 46305476 46306236 0.000000e+00 1225.0
26 TraesCS3A01G063500 chr3B 88.258 1056 68 12 1125 2173 46303290 46304296 0.000000e+00 1212.0
27 TraesCS3A01G063500 chr3B 79.463 1490 214 56 1450 2911 47222956 47221531 0.000000e+00 972.0
28 TraesCS3A01G063500 chr3B 77.622 1573 254 34 1375 2882 47211232 47209693 0.000000e+00 865.0
29 TraesCS3A01G063500 chr3B 83.288 730 63 24 1055 1771 46327819 46328502 5.270000e-173 617.0
30 TraesCS3A01G063500 chr3B 82.946 516 49 15 178 655 46302546 46303060 2.650000e-116 429.0
31 TraesCS3A01G063500 chr3B 83.738 412 48 12 157 556 46778947 46779351 4.530000e-99 372.0
32 TraesCS3A01G063500 chr3B 97.297 148 4 0 3570 3717 30397430 30397283 6.160000e-63 252.0
33 TraesCS3A01G063500 chr3B 89.256 121 10 3 44 164 46763457 46763574 8.320000e-32 148.0
34 TraesCS3A01G063500 chr3B 97.403 77 2 0 820 896 46303105 46303181 8.380000e-27 132.0
35 TraesCS3A01G063500 chr3B 96.104 77 3 0 820 896 46327718 46327794 3.900000e-25 126.0
36 TraesCS3A01G063500 chr3B 97.619 42 1 0 638 679 46327668 46327709 5.150000e-09 73.1
37 TraesCS3A01G063500 chr1A 95.712 653 27 1 2931 3582 24811979 24811327 0.000000e+00 1050.0
38 TraesCS3A01G063500 chr1A 95.559 653 27 2 2931 3582 77069090 77068439 0.000000e+00 1044.0
39 TraesCS3A01G063500 chr1A 96.610 590 19 1 2932 3520 24798905 24798316 0.000000e+00 977.0
40 TraesCS3A01G063500 chr1A 96.610 590 19 1 2932 3520 77061675 77061086 0.000000e+00 977.0
41 TraesCS3A01G063500 chr1A 80.699 1202 186 28 1452 2646 481628046 481629208 0.000000e+00 893.0
42 TraesCS3A01G063500 chr1A 87.879 66 8 0 1973 2038 367010855 367010920 1.110000e-10 78.7
43 TraesCS3A01G063500 chr7A 95.652 598 24 2 2932 3528 731038706 731039302 0.000000e+00 959.0
44 TraesCS3A01G063500 chr5A 92.308 650 42 6 2932 3578 2764103 2763459 0.000000e+00 917.0
45 TraesCS3A01G063500 chr1B 80.776 1212 182 29 1452 2646 510790811 510791988 0.000000e+00 900.0
46 TraesCS3A01G063500 chr1B 96.667 150 3 2 3569 3717 62213654 62213506 7.970000e-62 248.0
47 TraesCS3A01G063500 chr1B 88.060 67 8 0 1973 2039 395968022 395968088 3.080000e-11 80.5
48 TraesCS3A01G063500 chr1D 77.610 1590 239 65 1360 2883 456280606 456279068 0.000000e+00 856.0
49 TraesCS3A01G063500 chr1D 80.116 1212 188 36 1452 2646 381004968 381006143 0.000000e+00 854.0
50 TraesCS3A01G063500 chr1D 88.462 156 13 1 884 1034 486120749 486120904 2.280000e-42 183.0
51 TraesCS3A01G063500 chr1D 88.060 67 8 0 1973 2039 294219780 294219846 3.080000e-11 80.5
52 TraesCS3A01G063500 chr4B 98.630 146 2 0 3572 3717 551760835 551760690 3.680000e-65 259.0
53 TraesCS3A01G063500 chr2A 100.000 138 0 0 3580 3717 613703827 613703964 4.760000e-64 255.0
54 TraesCS3A01G063500 chr6B 98.601 143 2 0 3575 3717 674038527 674038669 1.710000e-63 254.0
55 TraesCS3A01G063500 chr6B 100.000 29 0 0 1 29 96889366 96889338 2.000000e-03 54.7
56 TraesCS3A01G063500 chrUn 98.592 142 2 0 3576 3717 263855572 263855431 6.160000e-63 252.0
57 TraesCS3A01G063500 chr7B 97.945 146 1 2 3572 3717 668925008 668924865 6.160000e-63 252.0
58 TraesCS3A01G063500 chr5B 98.601 143 0 2 3577 3717 587768228 587768370 6.160000e-63 252.0
59 TraesCS3A01G063500 chr5B 100.000 30 0 0 1 30 27490320 27490349 5.190000e-04 56.5
60 TraesCS3A01G063500 chr4A 98.561 139 2 0 3579 3717 620448281 620448143 2.870000e-61 246.0
61 TraesCS3A01G063500 chr6A 89.655 145 10 2 893 1032 147477357 147477501 2.950000e-41 180.0
62 TraesCS3A01G063500 chr6A 83.478 115 14 1 922 1031 603296966 603297080 6.570000e-18 102.0
63 TraesCS3A01G063500 chr6A 95.238 42 2 0 1 42 457357705 457357746 2.400000e-07 67.6
64 TraesCS3A01G063500 chr2B 87.755 147 13 1 893 1034 415996301 415996155 2.300000e-37 167.0
65 TraesCS3A01G063500 chr5D 87.500 120 10 3 910 1024 339715080 339715199 2.330000e-27 134.0
66 TraesCS3A01G063500 chr6D 83.846 130 16 2 910 1034 291387008 291387137 6.520000e-23 119.0
67 TraesCS3A01G063500 chr4D 83.721 129 16 1 910 1033 499775632 499775760 2.350000e-22 117.0


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 TraesCS3A01G063500 chr3A 38011324 38015040 3716 True 2323.533333 6865 97.849333 1 3717 3 chr3A.!!$R5 3716
1 TraesCS3A01G063500 chr3A 37800160 37801580 1420 False 1563.000000 1563 86.727000 1494 2911 1 chr3A.!!$F1 1417
2 TraesCS3A01G063500 chr3A 698714567 698715217 650 False 1020.000000 1020 94.939000 2932 3582 1 chr3A.!!$F2 650
3 TraesCS3A01G063500 chr3A 37996326 37996914 588 True 972.000000 972 96.441000 2932 3520 1 chr3A.!!$R1 588
4 TraesCS3A01G063500 chr3A 698719399 698719989 590 False 963.000000 963 96.108000 2932 3521 1 chr3A.!!$F3 589
5 TraesCS3A01G063500 chr3A 38135205 38136803 1598 True 953.000000 953 78.224000 1301 2882 1 chr3A.!!$R2 1581
6 TraesCS3A01G063500 chr3D 28216536 28218133 1597 True 1002.000000 1002 78.597000 1301 2911 1 chr3D.!!$R3 1610
7 TraesCS3A01G063500 chr3D 28123018 28125763 2745 True 772.380000 2163 94.216200 1 2921 5 chr3D.!!$R5 2920
8 TraesCS3A01G063500 chr3D 28223370 28224566 1196 True 701.000000 701 77.901000 1683 2911 1 chr3D.!!$R4 1228
9 TraesCS3A01G063500 chr3D 27662189 27664566 2377 False 668.000000 859 84.388000 44 2883 2 chr3D.!!$F4 2839
10 TraesCS3A01G063500 chr3D 28275262 28276683 1421 False 604.000000 604 75.086000 1512 2909 1 chr3D.!!$F3 1397
11 TraesCS3A01G063500 chr3B 47221531 47222956 1425 True 972.000000 972 79.463000 1450 2911 1 chr3B.!!$R3 1461
12 TraesCS3A01G063500 chr3B 47209693 47211232 1539 True 865.000000 865 77.622000 1375 2882 1 chr3B.!!$R2 1507
13 TraesCS3A01G063500 chr3B 46302546 46306236 3690 False 749.500000 1225 91.073250 178 2931 4 chr3B.!!$F3 2753
14 TraesCS3A01G063500 chr3B 46327668 46329568 1900 False 613.275000 1637 92.775250 638 2931 4 chr3B.!!$F4 2293
15 TraesCS3A01G063500 chr1A 24811327 24811979 652 True 1050.000000 1050 95.712000 2931 3582 1 chr1A.!!$R2 651
16 TraesCS3A01G063500 chr1A 77068439 77069090 651 True 1044.000000 1044 95.559000 2931 3582 1 chr1A.!!$R4 651
17 TraesCS3A01G063500 chr1A 24798316 24798905 589 True 977.000000 977 96.610000 2932 3520 1 chr1A.!!$R1 588
18 TraesCS3A01G063500 chr1A 77061086 77061675 589 True 977.000000 977 96.610000 2932 3520 1 chr1A.!!$R3 588
19 TraesCS3A01G063500 chr1A 481628046 481629208 1162 False 893.000000 893 80.699000 1452 2646 1 chr1A.!!$F2 1194
20 TraesCS3A01G063500 chr7A 731038706 731039302 596 False 959.000000 959 95.652000 2932 3528 1 chr7A.!!$F1 596
21 TraesCS3A01G063500 chr5A 2763459 2764103 644 True 917.000000 917 92.308000 2932 3578 1 chr5A.!!$R1 646
22 TraesCS3A01G063500 chr1B 510790811 510791988 1177 False 900.000000 900 80.776000 1452 2646 1 chr1B.!!$F2 1194
23 TraesCS3A01G063500 chr1D 456279068 456280606 1538 True 856.000000 856 77.610000 1360 2883 1 chr1D.!!$R1 1523
24 TraesCS3A01G063500 chr1D 381004968 381006143 1175 False 854.000000 854 80.116000 1452 2646 1 chr1D.!!$F2 1194

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
921 991 0.319555 TTCGGTTTCTCTCCACTGCG 60.320 55.0 0.0 0.0 0.00 5.18 F
1019 1089 0.317479 ACGGGAGTGGAGAGAAAACG 59.683 55.0 0.0 0.0 44.82 3.60 F
1658 1814 0.392998 CGACCCCAAGTTCCTCCATG 60.393 60.0 0.0 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1888 2074 1.078497 GGGGTCGCACATGATGACA 60.078 57.895 0.0 0.0 34.32 3.58 R
2166 3540 2.224161 GCATTACCAACAAGCAACCCAA 60.224 45.455 0.0 0.0 0.00 4.12 R
3609 5071 0.096976 CTAATGGCAGTTGCGAACCG 59.903 55.000 0.0 0.0 43.26 4.44 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
23 24 2.821366 CACGGGTGCAGATGAGCC 60.821 66.667 0.00 0.00 0.00 4.70
42 43 1.180029 CTGGGCTTGGAAGTGGATTG 58.820 55.000 0.00 0.00 0.00 2.67
67 68 3.504134 GGTTTCTTTCTTTCTCCTCTGCC 59.496 47.826 0.00 0.00 0.00 4.85
109 110 6.715347 ATTATGGGATCAGTAAGTTTTGCC 57.285 37.500 0.00 0.00 0.00 4.52
114 115 4.156739 GGGATCAGTAAGTTTTGCCTTGAG 59.843 45.833 0.00 0.00 0.00 3.02
159 163 4.170256 ACAAGCAAACAACCGTACTTTTG 58.830 39.130 2.61 2.61 33.03 2.44
171 175 4.822896 ACCGTACTTTTGAAATTGGCTGTA 59.177 37.500 0.00 0.00 0.00 2.74
212 216 2.263077 CGAGTCATGTACCTGTTGAGC 58.737 52.381 0.00 0.00 0.00 4.26
219 223 1.411246 TGTACCTGTTGAGCGTCTGTT 59.589 47.619 0.00 0.00 0.00 3.16
223 227 2.870411 ACCTGTTGAGCGTCTGTTTTAC 59.130 45.455 0.00 0.00 0.00 2.01
239 247 4.271533 TGTTTTACTGTAGCCACGTTTCTG 59.728 41.667 0.00 0.00 0.00 3.02
287 295 2.777832 AGTCTGGTGGATTTGAGCTC 57.222 50.000 6.82 6.82 0.00 4.09
289 297 1.003580 GTCTGGTGGATTTGAGCTCCA 59.996 52.381 12.15 0.00 40.49 3.86
310 318 7.122204 GCTCCACCAAGTAATATTACAGGTTTT 59.878 37.037 27.14 12.99 40.21 2.43
352 360 4.901197 TGTTACATGTCTGGGCTTCTTA 57.099 40.909 0.00 0.00 0.00 2.10
426 443 8.758633 AAAAAGAAAGAGAGAATGCAATCATG 57.241 30.769 4.25 0.00 32.23 3.07
443 460 7.598189 CAATCATGCATGGTTCAAATTAACA 57.402 32.000 22.34 0.03 0.00 2.41
501 543 8.617290 TCAGTTGGAACTAAAGGAAGAATAAC 57.383 34.615 0.00 0.00 37.08 1.89
508 550 8.613482 GGAACTAAAGGAAGAATAACTGTATGC 58.387 37.037 0.00 0.00 0.00 3.14
521 563 7.928307 ATAACTGTATGCCATGGTGATAATC 57.072 36.000 14.67 0.00 0.00 1.75
692 762 3.406764 GAGAGTGAAACAGCACCAATCT 58.593 45.455 0.00 0.00 41.43 2.40
693 763 3.144506 AGAGTGAAACAGCACCAATCTG 58.855 45.455 0.00 0.00 41.43 2.90
694 764 2.880890 GAGTGAAACAGCACCAATCTGT 59.119 45.455 0.00 0.00 45.83 3.41
749 819 7.851228 TGGTTCATCAGTTCTGTATAGTTCAT 58.149 34.615 0.00 0.00 0.00 2.57
755 825 6.867550 TCAGTTCTGTATAGTTCATCACTGG 58.132 40.000 0.00 0.00 35.97 4.00
788 858 3.141398 TCTTGGTTCATCAGTTCAGTGC 58.859 45.455 0.00 0.00 0.00 4.40
865 935 5.251601 ACAGCGGTAGAATAGAAGAAGAC 57.748 43.478 0.00 0.00 0.00 3.01
896 966 6.877611 AACAACACCAATCTGTTAGTTAGG 57.122 37.500 0.00 0.00 32.90 2.69
897 967 4.760204 ACAACACCAATCTGTTAGTTAGGC 59.240 41.667 0.00 0.00 32.90 3.93
898 968 4.634012 ACACCAATCTGTTAGTTAGGCA 57.366 40.909 0.00 0.00 0.00 4.75
899 969 4.324267 ACACCAATCTGTTAGTTAGGCAC 58.676 43.478 0.00 0.00 0.00 5.01
904 974 3.975168 TCTGTTAGTTAGGCACCCTTC 57.025 47.619 0.00 0.00 34.61 3.46
905 975 2.232941 TCTGTTAGTTAGGCACCCTTCG 59.767 50.000 0.00 0.00 34.61 3.79
908 978 1.648116 TAGTTAGGCACCCTTCGGTT 58.352 50.000 0.00 0.00 42.04 4.44
910 980 1.162698 GTTAGGCACCCTTCGGTTTC 58.837 55.000 0.00 0.00 42.04 2.78
911 981 1.061546 TTAGGCACCCTTCGGTTTCT 58.938 50.000 0.00 0.00 42.04 2.52
913 983 1.128188 AGGCACCCTTCGGTTTCTCT 61.128 55.000 0.00 0.00 42.04 3.10
914 984 0.673956 GGCACCCTTCGGTTTCTCTC 60.674 60.000 0.00 0.00 42.04 3.20
915 985 0.673956 GCACCCTTCGGTTTCTCTCC 60.674 60.000 0.00 0.00 42.04 3.71
917 987 0.685660 ACCCTTCGGTTTCTCTCCAC 59.314 55.000 0.00 0.00 40.58 4.02
919 989 1.338200 CCCTTCGGTTTCTCTCCACTG 60.338 57.143 0.00 0.00 0.00 3.66
920 990 1.433534 CTTCGGTTTCTCTCCACTGC 58.566 55.000 0.00 0.00 0.00 4.40
921 991 0.319555 TTCGGTTTCTCTCCACTGCG 60.320 55.000 0.00 0.00 0.00 5.18
922 992 2.383527 CGGTTTCTCTCCACTGCGC 61.384 63.158 0.00 0.00 0.00 6.09
923 993 1.004440 GGTTTCTCTCCACTGCGCT 60.004 57.895 9.73 0.00 0.00 5.92
924 994 1.016653 GGTTTCTCTCCACTGCGCTC 61.017 60.000 9.73 0.00 0.00 5.03
925 995 0.319900 GTTTCTCTCCACTGCGCTCA 60.320 55.000 9.73 0.00 0.00 4.26
927 997 0.319900 TTCTCTCCACTGCGCTCAAC 60.320 55.000 9.73 0.00 0.00 3.18
929 999 0.735632 CTCTCCACTGCGCTCAACTC 60.736 60.000 9.73 0.00 0.00 3.01
930 1000 1.739562 CTCCACTGCGCTCAACTCC 60.740 63.158 9.73 0.00 0.00 3.85
932 1002 1.376424 CCACTGCGCTCAACTCCAT 60.376 57.895 9.73 0.00 0.00 3.41
940 1010 2.777969 CTCAACTCCATGGAGCTGC 58.222 57.895 36.78 0.00 45.54 5.25
941 1011 1.078918 TCAACTCCATGGAGCTGCG 60.079 57.895 36.78 23.42 45.54 5.18
942 1012 2.110967 CAACTCCATGGAGCTGCGG 61.111 63.158 36.78 19.85 45.54 5.69
943 1013 2.293318 AACTCCATGGAGCTGCGGA 61.293 57.895 36.78 3.35 45.54 5.54
944 1014 2.108566 CTCCATGGAGCTGCGGAG 59.891 66.667 28.45 13.35 39.20 4.63
963 1033 2.918571 CTCGGTTTGAGCAGCTTCA 58.081 52.632 0.00 0.00 38.03 3.02
964 1034 1.446907 CTCGGTTTGAGCAGCTTCAT 58.553 50.000 0.00 0.00 38.03 2.57
965 1035 2.621338 CTCGGTTTGAGCAGCTTCATA 58.379 47.619 0.00 0.00 38.03 2.15
966 1036 3.002791 CTCGGTTTGAGCAGCTTCATAA 58.997 45.455 0.00 0.00 38.03 1.90
967 1037 3.407698 TCGGTTTGAGCAGCTTCATAAA 58.592 40.909 0.00 0.00 0.00 1.40
968 1038 3.818210 TCGGTTTGAGCAGCTTCATAAAA 59.182 39.130 0.00 0.00 0.00 1.52
969 1039 4.277174 TCGGTTTGAGCAGCTTCATAAAAA 59.723 37.500 0.00 0.00 0.00 1.94
970 1040 4.618489 CGGTTTGAGCAGCTTCATAAAAAG 59.382 41.667 0.00 0.00 0.00 2.27
978 1048 2.950433 GCTTCATAAAAAGCTGCAGCA 58.050 42.857 38.24 19.65 46.51 4.41
979 1049 3.319755 GCTTCATAAAAAGCTGCAGCAA 58.680 40.909 38.24 20.61 46.51 3.91
980 1050 3.122445 GCTTCATAAAAAGCTGCAGCAAC 59.878 43.478 38.24 11.74 46.51 4.17
981 1051 4.553323 CTTCATAAAAAGCTGCAGCAACT 58.447 39.130 38.24 20.64 45.16 3.16
982 1052 4.589216 TCATAAAAAGCTGCAGCAACTT 57.411 36.364 38.24 27.39 45.16 2.66
983 1053 4.300803 TCATAAAAAGCTGCAGCAACTTG 58.699 39.130 38.24 25.39 45.16 3.16
984 1054 1.292992 AAAAAGCTGCAGCAACTTGC 58.707 45.000 38.24 12.83 45.46 4.01
1001 1071 2.888863 CTCCGGGAGCTGAGTCAC 59.111 66.667 11.83 0.00 0.00 3.67
1002 1072 3.057547 CTCCGGGAGCTGAGTCACG 62.058 68.421 11.83 0.00 43.30 4.35
1004 1074 4.135153 CGGGAGCTGAGTCACGGG 62.135 72.222 0.00 0.00 39.81 5.28
1005 1075 2.680352 GGGAGCTGAGTCACGGGA 60.680 66.667 0.00 0.00 0.00 5.14
1006 1076 2.716017 GGGAGCTGAGTCACGGGAG 61.716 68.421 0.00 0.00 0.00 4.30
1019 1089 0.317479 ACGGGAGTGGAGAGAAAACG 59.683 55.000 0.00 0.00 44.82 3.60
1020 1090 0.601558 CGGGAGTGGAGAGAAAACGA 59.398 55.000 0.00 0.00 0.00 3.85
1021 1091 1.000506 CGGGAGTGGAGAGAAAACGAA 59.999 52.381 0.00 0.00 0.00 3.85
1022 1092 2.414806 GGGAGTGGAGAGAAAACGAAC 58.585 52.381 0.00 0.00 0.00 3.95
1023 1093 2.224209 GGGAGTGGAGAGAAAACGAACA 60.224 50.000 0.00 0.00 0.00 3.18
1024 1094 3.060602 GGAGTGGAGAGAAAACGAACAG 58.939 50.000 0.00 0.00 0.00 3.16
1025 1095 3.060602 GAGTGGAGAGAAAACGAACAGG 58.939 50.000 0.00 0.00 0.00 4.00
1026 1096 1.531578 GTGGAGAGAAAACGAACAGGC 59.468 52.381 0.00 0.00 0.00 4.85
1027 1097 1.157585 GGAGAGAAAACGAACAGGCC 58.842 55.000 0.00 0.00 0.00 5.19
1028 1098 1.157585 GAGAGAAAACGAACAGGCCC 58.842 55.000 0.00 0.00 0.00 5.80
1029 1099 0.765510 AGAGAAAACGAACAGGCCCT 59.234 50.000 0.00 0.00 0.00 5.19
1030 1100 1.143073 AGAGAAAACGAACAGGCCCTT 59.857 47.619 0.00 0.00 0.00 3.95
1099 1174 4.927422 AGTCTCGAAATGCTTCTAGCTAC 58.073 43.478 0.00 0.00 42.97 3.58
1101 1176 5.823570 AGTCTCGAAATGCTTCTAGCTACTA 59.176 40.000 0.00 0.00 42.97 1.82
1102 1177 6.017440 AGTCTCGAAATGCTTCTAGCTACTAG 60.017 42.308 0.00 0.00 42.97 2.57
1103 1178 4.861210 TCGAAATGCTTCTAGCTACTAGC 58.139 43.478 13.12 13.12 42.97 3.42
1218 1316 3.129287 CCCAACACCATCACTTTATCAGC 59.871 47.826 0.00 0.00 0.00 4.26
1270 1380 2.143925 GGTGAACTCACTGGTTACTGC 58.856 52.381 9.60 0.00 45.73 4.40
1271 1381 2.224305 GGTGAACTCACTGGTTACTGCT 60.224 50.000 9.60 0.00 45.73 4.24
1272 1382 3.006537 GGTGAACTCACTGGTTACTGCTA 59.993 47.826 9.60 0.00 45.73 3.49
1273 1383 3.988517 GTGAACTCACTGGTTACTGCTAC 59.011 47.826 2.51 0.00 43.25 3.58
1274 1384 3.243336 GAACTCACTGGTTACTGCTACG 58.757 50.000 0.00 0.00 0.00 3.51
1275 1385 1.067776 ACTCACTGGTTACTGCTACGC 60.068 52.381 0.00 0.00 0.00 4.42
1288 1398 3.711541 CTACGCCTACGCCCACCAC 62.712 68.421 0.00 0.00 45.53 4.16
1409 1525 3.432051 GATGAGGCCGTCGGAGTGG 62.432 68.421 17.49 0.00 0.00 4.00
1469 1612 2.511600 GTTCCCAGATCCACGCGG 60.512 66.667 12.47 0.00 0.00 6.46
1658 1814 0.392998 CGACCCCAAGTTCCTCCATG 60.393 60.000 0.00 0.00 0.00 3.66
1693 1849 4.048470 GGAAAGCCGCCCCTCCTT 62.048 66.667 0.00 0.00 0.00 3.36
1762 1921 2.588877 GACCATCCCGACCGCATG 60.589 66.667 0.00 0.00 0.00 4.06
1839 2022 2.350522 AGTCTTACTGCTTGATTGCCG 58.649 47.619 0.00 0.00 0.00 5.69
1840 2023 2.076863 GTCTTACTGCTTGATTGCCGT 58.923 47.619 0.00 0.00 34.86 5.68
1841 2024 2.094417 GTCTTACTGCTTGATTGCCGTC 59.906 50.000 0.00 0.00 32.85 4.79
1842 2025 2.076100 CTTACTGCTTGATTGCCGTCA 58.924 47.619 0.00 0.00 32.85 4.35
1843 2026 1.438651 TACTGCTTGATTGCCGTCAC 58.561 50.000 0.00 0.00 32.85 3.67
1844 2027 1.133253 CTGCTTGATTGCCGTCACG 59.867 57.895 0.00 0.00 0.00 4.35
2118 2307 1.871408 CGAGACTGGCATATGGAGCAC 60.871 57.143 4.56 0.00 0.00 4.40
2135 2324 1.067846 GCACTATCATCGTATCGGCCA 60.068 52.381 2.24 0.00 0.00 5.36
2334 3720 0.600518 CATGCTGAGGATGGAGCTCG 60.601 60.000 7.83 0.00 36.11 5.03
3158 4618 7.621006 TTTATATTGGAAAGACTATCCGGGA 57.379 36.000 0.00 0.00 39.98 5.14
3164 4624 3.703052 GGAAAGACTATCCGGGAACACTA 59.297 47.826 0.00 0.00 0.00 2.74
3252 4712 8.915036 AGAGGAATTTACACTCTATTATGACGT 58.085 33.333 0.00 0.00 39.65 4.34
3307 4767 3.429822 CGGGTAGAATCCGTTAAGCAGAA 60.430 47.826 0.00 0.00 42.33 3.02
3337 4797 7.689446 TGATCGTGGTTGGTAATTTGATTTA 57.311 32.000 0.00 0.00 0.00 1.40
3360 4820 4.079901 AGACTCTATCCCGGAAACTAGTGA 60.080 45.833 0.73 0.00 0.00 3.41
3531 4993 8.352942 CCTAAATTTCTAACATTGGTATCCTGC 58.647 37.037 0.00 0.00 0.00 4.85
3582 5044 4.767255 CCGCTGTGCACTCTCCCC 62.767 72.222 19.41 0.00 0.00 4.81
3583 5045 4.007644 CGCTGTGCACTCTCCCCA 62.008 66.667 19.41 0.00 0.00 4.96
3584 5046 2.359230 GCTGTGCACTCTCCCCAC 60.359 66.667 19.41 0.00 0.00 4.61
3585 5047 2.888447 GCTGTGCACTCTCCCCACT 61.888 63.158 19.41 0.00 0.00 4.00
3586 5048 1.004080 CTGTGCACTCTCCCCACTG 60.004 63.158 19.41 0.00 0.00 3.66
3587 5049 2.348998 GTGCACTCTCCCCACTGG 59.651 66.667 10.32 0.00 0.00 4.00
3588 5050 2.122413 TGCACTCTCCCCACTGGT 60.122 61.111 0.00 0.00 34.77 4.00
3589 5051 2.348998 GCACTCTCCCCACTGGTG 59.651 66.667 0.00 0.00 34.77 4.17
3600 5062 2.049435 CACTGGTGGAAAAAGGGCC 58.951 57.895 0.00 0.00 0.00 5.80
3601 5063 0.469892 CACTGGTGGAAAAAGGGCCT 60.470 55.000 0.00 0.00 0.00 5.19
3602 5064 0.264657 ACTGGTGGAAAAAGGGCCTT 59.735 50.000 14.48 14.48 0.00 4.35
3603 5065 1.343985 ACTGGTGGAAAAAGGGCCTTT 60.344 47.619 25.68 25.68 34.94 3.11
3604 5066 1.070601 CTGGTGGAAAAAGGGCCTTTG 59.929 52.381 31.06 12.80 33.64 2.77
3605 5067 0.396435 GGTGGAAAAAGGGCCTTTGG 59.604 55.000 31.06 0.00 33.64 3.28
3606 5068 1.128200 GTGGAAAAAGGGCCTTTGGT 58.872 50.000 31.06 21.81 33.64 3.67
3607 5069 1.070134 GTGGAAAAAGGGCCTTTGGTC 59.930 52.381 31.06 27.31 33.64 4.02
3608 5070 0.317160 GGAAAAAGGGCCTTTGGTCG 59.683 55.000 31.06 0.00 33.64 4.79
3609 5071 0.319555 GAAAAAGGGCCTTTGGTCGC 60.320 55.000 31.06 14.98 33.64 5.19
3610 5072 2.082629 AAAAAGGGCCTTTGGTCGCG 62.083 55.000 31.06 0.00 33.64 5.87
3614 5076 3.733960 GGCCTTTGGTCGCGGTTC 61.734 66.667 6.13 0.00 0.00 3.62
3615 5077 4.084888 GCCTTTGGTCGCGGTTCG 62.085 66.667 6.13 0.00 40.15 3.95
3626 5088 2.953821 CGGTTCGCAACTGCCATT 59.046 55.556 0.00 0.00 37.91 3.16
3627 5089 2.167161 CGGTTCGCAACTGCCATTA 58.833 52.632 0.00 0.00 37.91 1.90
3628 5090 0.096976 CGGTTCGCAACTGCCATTAG 59.903 55.000 0.00 0.00 37.91 1.73
3629 5091 1.165270 GGTTCGCAACTGCCATTAGT 58.835 50.000 0.00 0.00 37.91 2.24
3630 5092 1.130561 GGTTCGCAACTGCCATTAGTC 59.869 52.381 0.00 0.00 37.91 2.59
3631 5093 1.075542 TTCGCAACTGCCATTAGTCG 58.924 50.000 0.00 0.00 37.91 4.18
3632 5094 1.060937 CGCAACTGCCATTAGTCGC 59.939 57.895 0.00 0.00 37.91 5.19
3633 5095 1.060937 GCAACTGCCATTAGTCGCG 59.939 57.895 0.00 0.00 34.31 5.87
3634 5096 1.715585 CAACTGCCATTAGTCGCGG 59.284 57.895 6.13 0.00 37.39 6.46
3635 5097 1.019278 CAACTGCCATTAGTCGCGGT 61.019 55.000 6.13 0.00 46.47 5.68
3636 5098 1.295423 ACTGCCATTAGTCGCGGTT 59.705 52.632 6.13 0.00 41.86 4.44
3637 5099 1.019278 ACTGCCATTAGTCGCGGTTG 61.019 55.000 6.13 0.00 41.86 3.77
3638 5100 2.309764 CTGCCATTAGTCGCGGTTGC 62.310 60.000 6.13 0.28 37.91 4.17
3666 5128 4.781959 CCGAACGGGCGCGACTAA 62.782 66.667 30.98 0.00 0.00 2.24
3667 5129 2.806198 CGAACGGGCGCGACTAAA 60.806 61.111 30.98 0.00 0.00 1.85
3668 5130 2.785105 CGAACGGGCGCGACTAAAG 61.785 63.158 30.98 10.35 0.00 1.85
3669 5131 2.433664 AACGGGCGCGACTAAAGG 60.434 61.111 30.98 0.00 0.00 3.11
3674 5136 4.770874 GCGCGACTAAAGGCCCCA 62.771 66.667 12.10 0.00 0.00 4.96
3675 5137 2.818274 CGCGACTAAAGGCCCCAC 60.818 66.667 0.00 0.00 0.00 4.61
3676 5138 2.437895 GCGACTAAAGGCCCCACC 60.438 66.667 0.00 0.00 39.61 4.61
3677 5139 2.271173 CGACTAAAGGCCCCACCC 59.729 66.667 0.00 0.00 40.58 4.61
3678 5140 2.298661 CGACTAAAGGCCCCACCCT 61.299 63.158 0.00 0.00 40.58 4.34
3679 5141 1.848886 CGACTAAAGGCCCCACCCTT 61.849 60.000 0.00 0.00 46.97 3.95
3683 5145 4.369496 AAGGCCCCACCCTTTAGT 57.631 55.556 0.00 0.00 42.48 2.24
3684 5146 2.084596 AAGGCCCCACCCTTTAGTC 58.915 57.895 0.00 0.00 42.48 2.59
3685 5147 1.848886 AAGGCCCCACCCTTTAGTCG 61.849 60.000 0.00 0.00 42.48 4.18
3686 5148 2.437895 GCCCCACCCTTTAGTCGC 60.438 66.667 0.00 0.00 0.00 5.19
3687 5149 2.125269 CCCCACCCTTTAGTCGCG 60.125 66.667 0.00 0.00 0.00 5.87
3688 5150 2.125269 CCCACCCTTTAGTCGCGG 60.125 66.667 6.13 0.00 0.00 6.46
3689 5151 2.660802 CCACCCTTTAGTCGCGGT 59.339 61.111 6.13 0.00 0.00 5.68
3690 5152 1.004200 CCACCCTTTAGTCGCGGTT 60.004 57.895 6.13 0.00 0.00 4.44
3691 5153 1.296056 CCACCCTTTAGTCGCGGTTG 61.296 60.000 6.13 0.00 0.00 3.77
3692 5154 1.670083 ACCCTTTAGTCGCGGTTGC 60.670 57.895 6.13 0.00 37.91 4.17
3693 5155 1.375523 CCCTTTAGTCGCGGTTGCT 60.376 57.895 6.13 2.31 39.65 3.91
3694 5156 0.953960 CCCTTTAGTCGCGGTTGCTT 60.954 55.000 6.13 0.00 39.65 3.91
3695 5157 1.673626 CCCTTTAGTCGCGGTTGCTTA 60.674 52.381 6.13 0.00 39.65 3.09
3696 5158 2.070783 CCTTTAGTCGCGGTTGCTTAA 58.929 47.619 6.13 0.00 39.65 1.85
3697 5159 2.093783 CCTTTAGTCGCGGTTGCTTAAG 59.906 50.000 6.13 9.06 39.65 1.85
3698 5160 2.728690 TTAGTCGCGGTTGCTTAAGA 57.271 45.000 6.13 0.00 39.65 2.10
3699 5161 2.728690 TAGTCGCGGTTGCTTAAGAA 57.271 45.000 6.13 0.00 39.65 2.52
3700 5162 1.145803 AGTCGCGGTTGCTTAAGAAC 58.854 50.000 6.13 7.82 39.65 3.01
3701 5163 0.165295 GTCGCGGTTGCTTAAGAACC 59.835 55.000 19.09 19.09 39.71 3.62
3705 5167 2.535588 GGTTGCTTAAGAACCGCGA 58.464 52.632 8.23 0.00 33.85 5.87
3706 5168 0.165295 GGTTGCTTAAGAACCGCGAC 59.835 55.000 8.23 0.93 37.34 5.19
3707 5169 1.145803 GTTGCTTAAGAACCGCGACT 58.854 50.000 8.23 0.30 35.64 4.18
3708 5170 2.331194 GTTGCTTAAGAACCGCGACTA 58.669 47.619 8.23 0.00 35.64 2.59
3709 5171 2.728690 TGCTTAAGAACCGCGACTAA 57.271 45.000 8.23 0.00 0.00 2.24
3710 5172 3.029320 TGCTTAAGAACCGCGACTAAA 57.971 42.857 8.23 0.00 0.00 1.85
3711 5173 2.991190 TGCTTAAGAACCGCGACTAAAG 59.009 45.455 8.23 4.60 0.00 1.85
3712 5174 2.347755 GCTTAAGAACCGCGACTAAAGG 59.652 50.000 8.23 0.00 0.00 3.11
3713 5175 2.000429 TAAGAACCGCGACTAAAGGC 58.000 50.000 8.23 0.00 0.00 4.35
3714 5176 0.672711 AAGAACCGCGACTAAAGGCC 60.673 55.000 8.23 0.00 0.00 5.19
3715 5177 2.046604 AACCGCGACTAAAGGCCC 60.047 61.111 8.23 0.00 0.00 5.80
3716 5178 3.945304 AACCGCGACTAAAGGCCCG 62.945 63.158 8.23 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.821366 GGCTCATCTGCACCCGTG 60.821 66.667 0.00 0.00 34.04 4.94
7 8 3.005539 AGGCTCATCTGCACCCGT 61.006 61.111 0.00 0.00 34.04 5.28
23 24 1.180029 CAATCCACTTCCAAGCCCAG 58.820 55.000 0.00 0.00 0.00 4.45
42 43 4.449405 CAGAGGAGAAAGAAAGAAACCGAC 59.551 45.833 0.00 0.00 0.00 4.79
67 68 7.598493 CCCATAATACACAACCAAACAGAAAAG 59.402 37.037 0.00 0.00 0.00 2.27
135 139 5.564048 AAAGTACGGTTGTTTGCTTGTAA 57.436 34.783 0.00 0.00 0.00 2.41
138 142 4.416620 TCAAAAGTACGGTTGTTTGCTTG 58.583 39.130 10.25 0.00 32.27 4.01
151 155 8.028938 ACATGATACAGCCAATTTCAAAAGTAC 58.971 33.333 0.00 0.00 0.00 2.73
171 175 9.424319 GACTCGGTCAATTAATATGTACATGAT 57.576 33.333 18.81 9.27 32.09 2.45
212 216 2.407361 CGTGGCTACAGTAAAACAGACG 59.593 50.000 0.00 0.00 0.00 4.18
219 223 4.325028 TCAGAAACGTGGCTACAGTAAA 57.675 40.909 0.00 0.00 0.00 2.01
223 227 2.688507 ACATCAGAAACGTGGCTACAG 58.311 47.619 0.00 0.00 0.00 2.74
320 328 6.878923 CCCAGACATGTAACAAGAAAGTATGA 59.121 38.462 0.00 0.00 0.00 2.15
327 335 3.788227 AGCCCAGACATGTAACAAGAA 57.212 42.857 0.00 0.00 0.00 2.52
329 337 3.679389 AGAAGCCCAGACATGTAACAAG 58.321 45.455 0.00 0.00 0.00 3.16
330 338 3.788227 AGAAGCCCAGACATGTAACAA 57.212 42.857 0.00 0.00 0.00 2.83
352 360 6.774656 CAGTTCAAAATATATCCTCCTGGCTT 59.225 38.462 0.00 0.00 0.00 4.35
423 440 5.927689 AGTGTGTTAATTTGAACCATGCATG 59.072 36.000 20.19 20.19 0.00 4.06
424 441 5.927689 CAGTGTGTTAATTTGAACCATGCAT 59.072 36.000 0.00 0.00 0.00 3.96
425 442 5.163468 ACAGTGTGTTAATTTGAACCATGCA 60.163 36.000 0.00 0.00 0.00 3.96
426 443 5.288804 ACAGTGTGTTAATTTGAACCATGC 58.711 37.500 0.00 0.00 0.00 4.06
501 543 4.698780 CCAGATTATCACCATGGCATACAG 59.301 45.833 13.04 0.00 0.00 2.74
508 550 4.022589 GCATCAACCAGATTATCACCATGG 60.023 45.833 11.19 11.19 33.72 3.66
521 563 3.005050 ACAATGTGAACTGCATCAACCAG 59.995 43.478 0.00 0.00 36.41 4.00
611 655 3.258372 ACTGCTTCTCCGTGTCTCATTTA 59.742 43.478 0.00 0.00 0.00 1.40
722 792 7.819415 TGAACTATACAGAACTGATGAACCAAG 59.181 37.037 8.87 0.00 0.00 3.61
749 819 1.064758 AGAAACAGCACCAACCAGTGA 60.065 47.619 0.00 0.00 40.34 3.41
755 825 2.165437 TGAACCAAGAAACAGCACCAAC 59.835 45.455 0.00 0.00 0.00 3.77
788 858 8.542132 CAAATTAACAGATTGGTGTTGTTTCAG 58.458 33.333 0.00 0.00 40.89 3.02
865 935 4.142182 ACAGATTGGTGTTGTTTCTTGGTG 60.142 41.667 0.00 0.00 0.00 4.17
904 974 2.383527 GCGCAGTGGAGAGAAACCG 61.384 63.158 0.30 0.00 0.00 4.44
905 975 1.004440 AGCGCAGTGGAGAGAAACC 60.004 57.895 11.47 0.00 0.00 3.27
908 978 0.319900 GTTGAGCGCAGTGGAGAGAA 60.320 55.000 11.47 0.00 0.00 2.87
910 980 0.735632 GAGTTGAGCGCAGTGGAGAG 60.736 60.000 11.47 0.00 0.00 3.20
911 981 1.290324 GAGTTGAGCGCAGTGGAGA 59.710 57.895 11.47 0.00 0.00 3.71
913 983 1.830587 ATGGAGTTGAGCGCAGTGGA 61.831 55.000 11.47 0.00 0.00 4.02
914 984 1.376424 ATGGAGTTGAGCGCAGTGG 60.376 57.895 11.47 0.00 0.00 4.00
915 985 1.642037 CCATGGAGTTGAGCGCAGTG 61.642 60.000 11.47 0.00 0.00 3.66
917 987 1.078918 TCCATGGAGTTGAGCGCAG 60.079 57.895 11.44 0.00 0.00 5.18
919 989 2.467826 GCTCCATGGAGTTGAGCGC 61.468 63.158 36.32 21.37 41.74 5.92
920 990 3.805267 GCTCCATGGAGTTGAGCG 58.195 61.111 36.32 15.94 41.74 5.03
925 995 2.249413 CTCCGCAGCTCCATGGAGTT 62.249 60.000 36.32 30.76 42.45 3.01
927 997 2.108566 CTCCGCAGCTCCATGGAG 59.891 66.667 33.73 33.73 44.56 3.86
937 1007 2.048222 TCAAACCGAGCTCCGCAG 60.048 61.111 8.47 0.00 36.84 5.18
938 1008 2.048222 CTCAAACCGAGCTCCGCA 60.048 61.111 8.47 0.00 34.18 5.69
945 1015 1.446907 ATGAAGCTGCTCAAACCGAG 58.553 50.000 1.00 0.00 45.37 4.63
946 1016 2.760634 TATGAAGCTGCTCAAACCGA 57.239 45.000 1.00 0.00 0.00 4.69
947 1017 3.829886 TTTATGAAGCTGCTCAAACCG 57.170 42.857 1.00 0.00 0.00 4.44
948 1018 4.386954 GCTTTTTATGAAGCTGCTCAAACC 59.613 41.667 1.00 0.00 46.55 3.27
949 1019 5.506644 GCTTTTTATGAAGCTGCTCAAAC 57.493 39.130 1.00 0.00 46.55 2.93
959 1029 4.553323 AGTTGCTGCAGCTTTTTATGAAG 58.447 39.130 36.61 0.00 42.66 3.02
960 1030 4.589216 AGTTGCTGCAGCTTTTTATGAA 57.411 36.364 36.61 18.85 42.66 2.57
961 1031 4.300803 CAAGTTGCTGCAGCTTTTTATGA 58.699 39.130 36.61 13.65 42.66 2.15
962 1032 3.120786 GCAAGTTGCTGCAGCTTTTTATG 60.121 43.478 36.61 26.18 42.17 1.90
963 1033 3.062042 GCAAGTTGCTGCAGCTTTTTAT 58.938 40.909 36.61 16.80 42.17 1.40
964 1034 2.472816 GCAAGTTGCTGCAGCTTTTTA 58.527 42.857 36.61 16.02 42.17 1.52
965 1035 1.292992 GCAAGTTGCTGCAGCTTTTT 58.707 45.000 36.61 24.11 42.17 1.94
966 1036 2.981997 GCAAGTTGCTGCAGCTTTT 58.018 47.368 36.61 24.44 42.17 2.27
967 1037 4.744316 GCAAGTTGCTGCAGCTTT 57.256 50.000 36.61 24.77 42.17 3.51
984 1054 2.888863 GTGACTCAGCTCCCGGAG 59.111 66.667 10.41 10.41 38.94 4.63
985 1055 3.062466 CGTGACTCAGCTCCCGGA 61.062 66.667 0.73 0.00 0.00 5.14
986 1056 4.135153 CCGTGACTCAGCTCCCGG 62.135 72.222 0.00 0.00 0.00 5.73
987 1057 4.135153 CCCGTGACTCAGCTCCCG 62.135 72.222 0.00 0.00 0.00 5.14
988 1058 2.680352 TCCCGTGACTCAGCTCCC 60.680 66.667 0.00 0.00 0.00 4.30
989 1059 1.979693 ACTCCCGTGACTCAGCTCC 60.980 63.158 0.00 0.00 0.00 4.70
990 1060 1.214062 CACTCCCGTGACTCAGCTC 59.786 63.158 0.00 0.00 43.97 4.09
991 1061 2.279069 CCACTCCCGTGACTCAGCT 61.279 63.158 0.00 0.00 43.97 4.24
992 1062 2.219325 CTCCACTCCCGTGACTCAGC 62.219 65.000 0.00 0.00 43.97 4.26
993 1063 0.609406 TCTCCACTCCCGTGACTCAG 60.609 60.000 0.00 0.00 43.97 3.35
994 1064 0.609406 CTCTCCACTCCCGTGACTCA 60.609 60.000 0.00 0.00 43.97 3.41
995 1065 0.322636 TCTCTCCACTCCCGTGACTC 60.323 60.000 0.00 0.00 43.97 3.36
996 1066 0.112606 TTCTCTCCACTCCCGTGACT 59.887 55.000 0.00 0.00 43.97 3.41
997 1067 0.966920 TTTCTCTCCACTCCCGTGAC 59.033 55.000 0.00 0.00 43.97 3.67
998 1068 1.343465 GTTTTCTCTCCACTCCCGTGA 59.657 52.381 0.00 0.00 43.97 4.35
999 1069 1.797025 GTTTTCTCTCCACTCCCGTG 58.203 55.000 0.00 0.00 40.89 4.94
1000 1070 0.317479 CGTTTTCTCTCCACTCCCGT 59.683 55.000 0.00 0.00 0.00 5.28
1001 1071 0.601558 TCGTTTTCTCTCCACTCCCG 59.398 55.000 0.00 0.00 0.00 5.14
1002 1072 2.224209 TGTTCGTTTTCTCTCCACTCCC 60.224 50.000 0.00 0.00 0.00 4.30
1003 1073 3.060602 CTGTTCGTTTTCTCTCCACTCC 58.939 50.000 0.00 0.00 0.00 3.85
1004 1074 3.060602 CCTGTTCGTTTTCTCTCCACTC 58.939 50.000 0.00 0.00 0.00 3.51
1005 1075 2.807108 GCCTGTTCGTTTTCTCTCCACT 60.807 50.000 0.00 0.00 0.00 4.00
1006 1076 1.531578 GCCTGTTCGTTTTCTCTCCAC 59.468 52.381 0.00 0.00 0.00 4.02
1007 1077 1.542547 GGCCTGTTCGTTTTCTCTCCA 60.543 52.381 0.00 0.00 0.00 3.86
1008 1078 1.157585 GGCCTGTTCGTTTTCTCTCC 58.842 55.000 0.00 0.00 0.00 3.71
1009 1079 1.157585 GGGCCTGTTCGTTTTCTCTC 58.842 55.000 0.84 0.00 0.00 3.20
1010 1080 0.765510 AGGGCCTGTTCGTTTTCTCT 59.234 50.000 4.50 0.00 0.00 3.10
1011 1081 1.605753 AAGGGCCTGTTCGTTTTCTC 58.394 50.000 6.92 0.00 0.00 2.87
1012 1082 2.105993 ACTAAGGGCCTGTTCGTTTTCT 59.894 45.455 6.92 0.00 0.00 2.52
1013 1083 2.501261 ACTAAGGGCCTGTTCGTTTTC 58.499 47.619 6.92 0.00 0.00 2.29
1014 1084 2.651382 ACTAAGGGCCTGTTCGTTTT 57.349 45.000 6.92 0.00 0.00 2.43
1015 1085 2.636403 AGTACTAAGGGCCTGTTCGTTT 59.364 45.455 6.92 0.00 0.00 3.60
1016 1086 2.254508 AGTACTAAGGGCCTGTTCGTT 58.745 47.619 6.92 0.00 0.00 3.85
1017 1087 1.934410 AGTACTAAGGGCCTGTTCGT 58.066 50.000 6.92 4.58 0.00 3.85
1018 1088 3.022406 ACTAGTACTAAGGGCCTGTTCG 58.978 50.000 6.92 0.00 0.00 3.95
1019 1089 5.199723 AGTACTAGTACTAAGGGCCTGTTC 58.800 45.833 29.96 0.00 43.98 3.18
1020 1090 5.204131 AGTACTAGTACTAAGGGCCTGTT 57.796 43.478 29.96 5.58 43.98 3.16
1021 1091 4.877436 AGTACTAGTACTAAGGGCCTGT 57.123 45.455 29.96 3.82 43.98 4.00
1022 1092 5.764192 CAGTAGTACTAGTACTAAGGGCCTG 59.236 48.000 33.96 29.85 46.55 4.85
1023 1093 5.669447 TCAGTAGTACTAGTACTAAGGGCCT 59.331 44.000 33.96 25.45 46.55 5.19
1024 1094 5.934781 TCAGTAGTACTAGTACTAAGGGCC 58.065 45.833 33.96 24.06 46.55 5.80
1025 1095 7.452562 AGATCAGTAGTACTAGTACTAAGGGC 58.547 42.308 33.96 24.34 46.55 5.19
1107 1182 2.939756 TCTCTCTCTGTTGTAGCGCTAG 59.060 50.000 19.48 7.71 0.00 3.42
1108 1183 2.987232 TCTCTCTCTGTTGTAGCGCTA 58.013 47.619 14.45 14.45 0.00 4.26
1109 1184 1.827681 TCTCTCTCTGTTGTAGCGCT 58.172 50.000 17.26 17.26 0.00 5.92
1218 1316 0.252197 GTAGTACCACTGGGCCTTGG 59.748 60.000 19.74 19.74 37.90 3.61
1275 1385 4.143333 CGGAGTGGTGGGCGTAGG 62.143 72.222 0.00 0.00 0.00 3.18
1317 1427 4.194720 CGTCCTCGCTCCCTTCCG 62.195 72.222 0.00 0.00 0.00 4.30
1361 1471 4.794648 TTGGGAATGGAGGCGCGG 62.795 66.667 8.83 0.00 0.00 6.46
1362 1472 2.749839 TTTGGGAATGGAGGCGCG 60.750 61.111 0.00 0.00 0.00 6.86
1363 1473 2.710902 GGTTTGGGAATGGAGGCGC 61.711 63.158 0.00 0.00 0.00 6.53
1415 1531 4.284550 GTGAAGCTGGGGGTGGCA 62.285 66.667 0.00 0.00 0.00 4.92
1611 1767 2.749044 ATCGCCACTGCTTGCAGG 60.749 61.111 23.98 11.32 34.43 4.85
1676 1832 4.048470 AAGGAGGGGCGGCTTTCC 62.048 66.667 19.56 19.56 0.00 3.13
1693 1849 4.020617 CGCTGGTGGAAGAGGCCA 62.021 66.667 5.01 0.00 35.02 5.36
1888 2074 1.078497 GGGGTCGCACATGATGACA 60.078 57.895 0.00 0.00 34.32 3.58
2118 2307 3.448686 GGAATGGCCGATACGATGATAG 58.551 50.000 0.00 0.00 0.00 2.08
2166 3540 2.224161 GCATTACCAACAAGCAACCCAA 60.224 45.455 0.00 0.00 0.00 4.12
2458 3845 5.565509 ACCTTTCTTCCTTCCTTCAATCTC 58.434 41.667 0.00 0.00 0.00 2.75
2783 4223 7.118971 AGAGAGAAGACAACTACATTTGAATGC 59.881 37.037 3.71 0.00 40.04 3.56
2846 4300 4.401022 TGAATGATGACAACAAGAAGGCT 58.599 39.130 0.00 0.00 0.00 4.58
2847 4301 4.771590 TGAATGATGACAACAAGAAGGC 57.228 40.909 0.00 0.00 0.00 4.35
2848 4302 6.684686 ACATTGAATGATGACAACAAGAAGG 58.315 36.000 12.80 0.00 33.17 3.46
2849 4303 8.509690 ACTACATTGAATGATGACAACAAGAAG 58.490 33.333 12.80 0.00 33.17 2.85
2925 4383 7.223971 GCAGGACACATAATTCTAACACGAATA 59.776 37.037 0.00 0.00 33.47 1.75
3158 4618 5.184892 AGCTCCTTCCAATCATTAGTGTT 57.815 39.130 0.00 0.00 0.00 3.32
3164 4624 4.346418 ACGATCTAGCTCCTTCCAATCATT 59.654 41.667 0.00 0.00 0.00 2.57
3302 4762 5.036737 CCAACCACGATCATATTTTTCTGC 58.963 41.667 0.00 0.00 0.00 4.26
3307 4767 8.744652 TCAAATTACCAACCACGATCATATTTT 58.255 29.630 0.00 0.00 0.00 1.82
3337 4797 4.079901 TCACTAGTTTCCGGGATAGAGTCT 60.080 45.833 0.00 0.00 0.00 3.24
3433 4893 8.193953 TCACAATTCACATATATGAGGCTAGA 57.806 34.615 19.63 4.92 0.00 2.43
3468 4928 2.814336 CCTAATTCCTTGCGCTTATCCC 59.186 50.000 9.73 0.00 0.00 3.85
3582 5044 0.469892 AGGCCCTTTTTCCACCAGTG 60.470 55.000 0.00 0.00 0.00 3.66
3583 5045 0.264657 AAGGCCCTTTTTCCACCAGT 59.735 50.000 0.00 0.00 0.00 4.00
3584 5046 1.070601 CAAAGGCCCTTTTTCCACCAG 59.929 52.381 5.84 0.00 30.60 4.00
3585 5047 1.127343 CAAAGGCCCTTTTTCCACCA 58.873 50.000 5.84 0.00 30.60 4.17
3586 5048 0.396435 CCAAAGGCCCTTTTTCCACC 59.604 55.000 5.84 0.00 30.60 4.61
3587 5049 1.070134 GACCAAAGGCCCTTTTTCCAC 59.930 52.381 5.84 0.00 30.60 4.02
3588 5050 1.419381 GACCAAAGGCCCTTTTTCCA 58.581 50.000 5.84 0.00 30.60 3.53
3589 5051 0.317160 CGACCAAAGGCCCTTTTTCC 59.683 55.000 5.84 0.00 30.60 3.13
3590 5052 0.319555 GCGACCAAAGGCCCTTTTTC 60.320 55.000 5.84 5.31 30.60 2.29
3591 5053 1.745890 GCGACCAAAGGCCCTTTTT 59.254 52.632 5.84 0.00 30.60 1.94
3592 5054 2.561037 CGCGACCAAAGGCCCTTTT 61.561 57.895 5.84 0.00 30.60 2.27
3593 5055 2.983592 CGCGACCAAAGGCCCTTT 60.984 61.111 1.93 1.93 33.58 3.11
3597 5059 3.733960 GAACCGCGACCAAAGGCC 61.734 66.667 8.23 0.00 0.00 5.19
3598 5060 4.084888 CGAACCGCGACCAAAGGC 62.085 66.667 8.23 0.00 44.57 4.35
3599 5061 4.084888 GCGAACCGCGACCAAAGG 62.085 66.667 8.23 0.00 44.55 3.11
3609 5071 0.096976 CTAATGGCAGTTGCGAACCG 59.903 55.000 0.00 0.00 43.26 4.44
3610 5072 1.130561 GACTAATGGCAGTTGCGAACC 59.869 52.381 0.00 0.00 43.26 3.62
3611 5073 1.201921 CGACTAATGGCAGTTGCGAAC 60.202 52.381 0.00 0.00 43.26 3.95
3612 5074 1.075542 CGACTAATGGCAGTTGCGAA 58.924 50.000 0.00 0.00 43.26 4.70
3613 5075 1.358725 GCGACTAATGGCAGTTGCGA 61.359 55.000 14.22 0.00 44.02 5.10
3614 5076 1.060937 GCGACTAATGGCAGTTGCG 59.939 57.895 0.00 0.70 44.02 4.85
3616 5078 1.019278 ACCGCGACTAATGGCAGTTG 61.019 55.000 8.23 0.00 33.66 3.16
3617 5079 0.321298 AACCGCGACTAATGGCAGTT 60.321 50.000 8.23 0.00 0.00 3.16
3618 5080 1.019278 CAACCGCGACTAATGGCAGT 61.019 55.000 8.23 0.00 0.00 4.40
3619 5081 1.715585 CAACCGCGACTAATGGCAG 59.284 57.895 8.23 0.00 0.00 4.85
3620 5082 2.395360 GCAACCGCGACTAATGGCA 61.395 57.895 8.23 0.00 0.00 4.92
3621 5083 2.403586 GCAACCGCGACTAATGGC 59.596 61.111 8.23 0.00 0.00 4.40
3649 5111 4.781959 TTAGTCGCGCCCGTTCGG 62.782 66.667 0.00 4.08 35.54 4.30
3650 5112 2.785105 CTTTAGTCGCGCCCGTTCG 61.785 63.158 0.00 0.00 35.54 3.95
3651 5113 2.450345 CCTTTAGTCGCGCCCGTTC 61.450 63.158 0.00 0.00 35.54 3.95
3652 5114 2.433664 CCTTTAGTCGCGCCCGTT 60.434 61.111 0.00 0.00 35.54 4.44
3657 5119 4.770874 TGGGGCCTTTAGTCGCGC 62.771 66.667 0.84 0.00 37.22 6.86
3658 5120 2.818274 GTGGGGCCTTTAGTCGCG 60.818 66.667 0.84 0.00 0.00 5.87
3659 5121 2.437895 GGTGGGGCCTTTAGTCGC 60.438 66.667 0.84 0.00 0.00 5.19
3660 5122 1.848886 AAGGGTGGGGCCTTTAGTCG 61.849 60.000 0.84 0.00 34.49 4.18
3661 5123 0.408309 AAAGGGTGGGGCCTTTAGTC 59.592 55.000 0.84 0.00 35.27 2.59
3662 5124 1.639108 CTAAAGGGTGGGGCCTTTAGT 59.361 52.381 9.25 0.00 44.74 2.24
3663 5125 2.437085 CTAAAGGGTGGGGCCTTTAG 57.563 55.000 5.72 5.72 44.57 1.85
3664 5126 1.637035 GACTAAAGGGTGGGGCCTTTA 59.363 52.381 0.84 0.00 35.27 1.85
3665 5127 0.408309 GACTAAAGGGTGGGGCCTTT 59.592 55.000 0.84 0.00 38.29 3.11
3666 5128 1.848886 CGACTAAAGGGTGGGGCCTT 61.849 60.000 0.84 0.00 37.43 4.35
3667 5129 2.298661 CGACTAAAGGGTGGGGCCT 61.299 63.158 0.84 0.00 37.43 5.19
3668 5130 2.271173 CGACTAAAGGGTGGGGCC 59.729 66.667 0.00 0.00 0.00 5.80
3669 5131 2.437895 GCGACTAAAGGGTGGGGC 60.438 66.667 0.00 0.00 0.00 5.80
3670 5132 2.125269 CGCGACTAAAGGGTGGGG 60.125 66.667 0.00 0.00 0.00 4.96
3671 5133 2.125269 CCGCGACTAAAGGGTGGG 60.125 66.667 8.23 0.00 0.00 4.61
3672 5134 1.004200 AACCGCGACTAAAGGGTGG 60.004 57.895 8.23 2.48 37.36 4.61
3673 5135 1.908066 GCAACCGCGACTAAAGGGTG 61.908 60.000 8.23 0.00 45.13 4.61
3674 5136 1.670083 GCAACCGCGACTAAAGGGT 60.670 57.895 8.23 0.00 0.00 4.34
3675 5137 0.953960 AAGCAACCGCGACTAAAGGG 60.954 55.000 8.23 0.00 45.49 3.95
3676 5138 1.717194 TAAGCAACCGCGACTAAAGG 58.283 50.000 8.23 0.00 45.49 3.11
3677 5139 2.991190 TCTTAAGCAACCGCGACTAAAG 59.009 45.455 8.23 1.88 45.49 1.85
3678 5140 3.029320 TCTTAAGCAACCGCGACTAAA 57.971 42.857 8.23 0.00 45.49 1.85
3679 5141 2.728690 TCTTAAGCAACCGCGACTAA 57.271 45.000 8.23 0.00 45.49 2.24
3680 5142 2.331194 GTTCTTAAGCAACCGCGACTA 58.669 47.619 8.23 0.00 45.49 2.59
3681 5143 1.145803 GTTCTTAAGCAACCGCGACT 58.854 50.000 8.23 0.00 45.49 4.18
3682 5144 0.165295 GGTTCTTAAGCAACCGCGAC 59.835 55.000 8.23 0.00 45.49 5.19
3683 5145 2.535588 GGTTCTTAAGCAACCGCGA 58.464 52.632 8.23 0.00 45.49 5.87
3687 5149 0.165295 GTCGCGGTTCTTAAGCAACC 59.835 55.000 19.09 19.09 40.12 3.77
3688 5150 1.145803 AGTCGCGGTTCTTAAGCAAC 58.854 50.000 6.13 3.71 0.00 4.17
3689 5151 2.728690 TAGTCGCGGTTCTTAAGCAA 57.271 45.000 6.13 0.00 0.00 3.91
3690 5152 2.728690 TTAGTCGCGGTTCTTAAGCA 57.271 45.000 6.13 0.00 0.00 3.91
3691 5153 2.347755 CCTTTAGTCGCGGTTCTTAAGC 59.652 50.000 6.13 0.00 0.00 3.09
3692 5154 2.347755 GCCTTTAGTCGCGGTTCTTAAG 59.652 50.000 6.13 11.57 0.00 1.85
3693 5155 2.340337 GCCTTTAGTCGCGGTTCTTAA 58.660 47.619 6.13 2.46 0.00 1.85
3694 5156 1.404583 GGCCTTTAGTCGCGGTTCTTA 60.405 52.381 6.13 0.00 0.00 2.10
3695 5157 0.672711 GGCCTTTAGTCGCGGTTCTT 60.673 55.000 6.13 0.00 0.00 2.52
3696 5158 1.079336 GGCCTTTAGTCGCGGTTCT 60.079 57.895 6.13 5.42 0.00 3.01
3697 5159 2.104859 GGGCCTTTAGTCGCGGTTC 61.105 63.158 6.13 0.00 0.00 3.62
3698 5160 2.046604 GGGCCTTTAGTCGCGGTT 60.047 61.111 6.13 0.00 0.00 4.44
3699 5161 4.446413 CGGGCCTTTAGTCGCGGT 62.446 66.667 6.13 0.00 35.43 5.68


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

AutoCloner maintained by Alex Coulton.