Multiple sequence alignment - TraesCS1D01G276300

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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 TraesCS1D01G276300 chr1D 100.000 4958 0 0 1 4958 372833862 372838819 0.000000e+00 9156.0
1 TraesCS1D01G276300 chr1D 92.632 760 50 1 4204 4957 427594122 427593363 0.000000e+00 1088.0
2 TraesCS1D01G276300 chr1D 91.459 761 57 3 4204 4957 468101569 468102328 0.000000e+00 1038.0
3 TraesCS1D01G276300 chr1D 78.997 957 156 26 2209 3141 372861236 372862171 3.280000e-171 612.0
4 TraesCS1D01G276300 chr1D 79.504 605 82 21 1286 1884 372874871 372875439 4.650000e-105 392.0
5 TraesCS1D01G276300 chr1D 82.025 484 59 19 3624 4103 372862396 372862855 2.160000e-103 387.0
6 TraesCS1D01G276300 chr1D 78.595 598 88 26 1291 1882 372860456 372861019 4.720000e-95 359.0
7 TraesCS1D01G276300 chr1D 84.951 206 24 5 3268 3466 372862186 372862391 8.420000e-48 202.0
8 TraesCS1D01G276300 chr1D 90.066 151 12 3 3479 3628 7349848 7349700 5.060000e-45 193.0
9 TraesCS1D01G276300 chr1D 93.617 94 6 0 1889 1982 372835843 372835750 1.860000e-29 141.0
10 TraesCS1D01G276300 chr1D 94.382 89 4 1 1891 1979 249030405 249030318 8.660000e-28 135.0
11 TraesCS1D01G276300 chr1D 90.196 102 8 2 1890 1990 484242464 484242364 1.120000e-26 132.0
12 TraesCS1D01G276300 chr1D 94.186 86 4 1 1893 1978 249030319 249030403 4.030000e-26 130.0
13 TraesCS1D01G276300 chr1D 89.899 99 9 1 1880 1978 484242364 484242461 5.210000e-25 126.0
14 TraesCS1D01G276300 chr1D 89.773 88 9 0 3163 3250 313214477 313214564 4.060000e-21 113.0
15 TraesCS1D01G276300 chr1A 92.094 1872 103 18 2253 4104 472080959 472082805 0.000000e+00 2595.0
16 TraesCS1D01G276300 chr1A 85.574 1941 179 42 51 1937 472078843 472080736 0.000000e+00 1940.0
17 TraesCS1D01G276300 chr1A 79.162 955 155 27 2206 3141 472141847 472142776 5.450000e-174 621.0
18 TraesCS1D01G276300 chr1A 83.565 432 51 14 3624 4049 472143008 472143425 2.160000e-103 387.0
19 TraesCS1D01G276300 chr1A 78.798 599 81 28 1288 1884 472164788 472165342 1.310000e-95 361.0
20 TraesCS1D01G276300 chr1A 80.822 438 67 15 2184 2614 472167469 472167896 1.330000e-85 327.0
21 TraesCS1D01G276300 chr1A 88.186 237 27 1 1646 1882 472141420 472141655 1.050000e-71 281.0
22 TraesCS1D01G276300 chr1A 79.726 365 62 5 3629 3986 472168658 472169017 2.290000e-63 254.0
23 TraesCS1D01G276300 chr1A 86.538 208 20 5 3268 3468 472142792 472142998 6.460000e-54 222.0
24 TraesCS1D01G276300 chr1A 93.043 115 6 2 4091 4204 472082825 472082938 3.070000e-37 167.0
25 TraesCS1D01G276300 chr1A 94.382 89 4 1 1891 1979 298603603 298603690 8.660000e-28 135.0
26 TraesCS1D01G276300 chr1A 88.298 94 9 2 2093 2185 415638040 415638132 1.460000e-20 111.0
27 TraesCS1D01G276300 chr1B 89.425 1201 67 27 773 1937 497470475 497471651 0.000000e+00 1459.0
28 TraesCS1D01G276300 chr1B 89.187 1156 65 22 3083 4194 497472786 497473925 0.000000e+00 1387.0
29 TraesCS1D01G276300 chr1B 92.071 845 44 11 2253 3086 497471874 497472706 0.000000e+00 1168.0
30 TraesCS1D01G276300 chr1B 79.476 955 157 24 2206 3141 497780283 497781217 4.180000e-180 641.0
31 TraesCS1D01G276300 chr1B 82.970 734 93 16 19 730 497469738 497470461 7.000000e-178 634.0
32 TraesCS1D01G276300 chr1B 80.102 588 76 24 1288 1872 497799601 497800150 2.780000e-107 399.0
33 TraesCS1D01G276300 chr1B 80.785 484 65 17 3624 4103 497781444 497781903 2.200000e-93 353.0
34 TraesCS1D01G276300 chr1B 80.525 457 67 15 2184 2626 497820503 497820951 1.030000e-86 331.0
35 TraesCS1D01G276300 chr1B 88.608 237 26 1 1646 1882 497779639 497779874 2.260000e-73 287.0
36 TraesCS1D01G276300 chr1B 77.855 429 58 17 2753 3168 497821035 497821439 1.070000e-56 231.0
37 TraesCS1D01G276300 chr1B 86.010 193 20 5 3268 3453 497781233 497781425 3.030000e-47 200.0
38 TraesCS1D01G276300 chr1B 91.045 67 6 0 1687 1753 67503003 67502937 1.900000e-14 91.6
39 TraesCS1D01G276300 chr1B 93.750 48 3 0 1835 1882 497780053 497780100 6.880000e-09 73.1
40 TraesCS1D01G276300 chr5D 93.026 760 47 1 4204 4957 334015547 334014788 0.000000e+00 1105.0
41 TraesCS1D01G276300 chr5D 92.368 760 52 1 4204 4957 40706908 40706149 0.000000e+00 1077.0
42 TraesCS1D01G276300 chr5D 88.387 155 13 3 3479 3632 204323241 204323391 1.100000e-41 182.0
43 TraesCS1D01G276300 chr7A 92.277 764 49 1 4204 4957 567516215 567515452 0.000000e+00 1075.0
44 TraesCS1D01G276300 chr6D 92.105 760 53 2 4204 4957 413053351 413052593 0.000000e+00 1064.0
45 TraesCS1D01G276300 chr2B 91.974 760 53 3 4204 4957 283183845 283184602 0.000000e+00 1059.0
46 TraesCS1D01G276300 chr2B 82.727 110 16 3 2086 2192 65314857 65314966 1.470000e-15 95.3
47 TraesCS1D01G276300 chr3A 91.546 757 56 7 4204 4953 41173716 41174471 0.000000e+00 1037.0
48 TraesCS1D01G276300 chr3A 86.458 96 11 2 2093 2186 510299770 510299865 2.440000e-18 104.0
49 TraesCS1D01G276300 chr3D 91.327 761 59 2 4204 4957 397385993 397386753 0.000000e+00 1033.0
50 TraesCS1D01G276300 chr3D 87.500 96 10 2 2093 2186 389633121 389633216 5.250000e-20 110.0
51 TraesCS1D01G276300 chr3D 87.912 91 9 2 2096 2185 131489257 131489168 6.790000e-19 106.0
52 TraesCS1D01G276300 chr4B 90.411 146 12 2 3479 3623 483581995 483582139 1.820000e-44 191.0
53 TraesCS1D01G276300 chr4B 89.333 150 14 2 3479 3627 613321830 613321978 2.360000e-43 187.0
54 TraesCS1D01G276300 chr4B 87.209 86 10 1 2101 2185 492223457 492223542 4.090000e-16 97.1
55 TraesCS1D01G276300 chr7B 89.796 147 15 0 3479 3625 211374052 211374198 6.550000e-44 189.0
56 TraesCS1D01G276300 chr2D 89.865 148 14 1 3477 3623 122864258 122864111 6.550000e-44 189.0
57 TraesCS1D01G276300 chr5B 88.387 155 13 3 3479 3632 208523308 208523458 1.100000e-41 182.0
58 TraesCS1D01G276300 chr5B 87.234 94 10 2 2100 2192 391148408 391148500 6.790000e-19 106.0
59 TraesCS1D01G276300 chr7D 92.473 93 7 0 1886 1978 4027529 4027621 3.110000e-27 134.0
60 TraesCS1D01G276300 chr7D 89.130 92 8 1 3167 3256 413234104 413234013 4.060000e-21 113.0
61 TraesCS1D01G276300 chr7D 90.698 86 6 2 3167 3250 413234019 413234104 4.060000e-21 113.0
62 TraesCS1D01G276300 chr6A 91.209 91 5 3 3162 3249 609314445 609314535 2.420000e-23 121.0
63 TraesCS1D01G276300 chr6A 88.421 95 5 5 3167 3257 563741862 563741770 5.250000e-20 110.0
64 TraesCS1D01G276300 chr6A 86.869 99 11 2 2093 2189 604890656 604890754 5.250000e-20 110.0
65 TraesCS1D01G276300 chr4D 88.421 95 9 2 2092 2185 107696617 107696524 4.060000e-21 113.0
66 TraesCS1D01G276300 chr4D 86.275 102 10 3 3166 3264 34660036 34659936 1.890000e-19 108.0
67 TraesCS1D01G276300 chr6B 88.889 90 8 2 3170 3257 705317448 705317537 5.250000e-20 110.0


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 TraesCS1D01G276300 chr1D 372833862 372838819 4957 False 9156.000000 9156 100.00000 1 4958 1 chr1D.!!$F3 4957
1 TraesCS1D01G276300 chr1D 427593363 427594122 759 True 1088.000000 1088 92.63200 4204 4957 1 chr1D.!!$R4 753
2 TraesCS1D01G276300 chr1D 468101569 468102328 759 False 1038.000000 1038 91.45900 4204 4957 1 chr1D.!!$F5 753
3 TraesCS1D01G276300 chr1D 372874871 372875439 568 False 392.000000 392 79.50400 1286 1884 1 chr1D.!!$F4 598
4 TraesCS1D01G276300 chr1D 372860456 372862855 2399 False 390.000000 612 81.14200 1291 4103 4 chr1D.!!$F7 2812
5 TraesCS1D01G276300 chr1A 472078843 472082938 4095 False 1567.333333 2595 90.23700 51 4204 3 chr1A.!!$F3 4153
6 TraesCS1D01G276300 chr1A 472141420 472143425 2005 False 377.750000 621 84.36275 1646 4049 4 chr1A.!!$F4 2403
7 TraesCS1D01G276300 chr1A 472164788 472169017 4229 False 314.000000 361 79.78200 1288 3986 3 chr1A.!!$F5 2698
8 TraesCS1D01G276300 chr1B 497469738 497473925 4187 False 1162.000000 1459 88.41325 19 4194 4 chr1B.!!$F2 4175
9 TraesCS1D01G276300 chr1B 497799601 497800150 549 False 399.000000 399 80.10200 1288 1872 1 chr1B.!!$F1 584
10 TraesCS1D01G276300 chr1B 497779639 497781903 2264 False 310.820000 641 85.72580 1646 4103 5 chr1B.!!$F3 2457
11 TraesCS1D01G276300 chr1B 497820503 497821439 936 False 281.000000 331 79.19000 2184 3168 2 chr1B.!!$F4 984
12 TraesCS1D01G276300 chr5D 334014788 334015547 759 True 1105.000000 1105 93.02600 4204 4957 1 chr5D.!!$R2 753
13 TraesCS1D01G276300 chr5D 40706149 40706908 759 True 1077.000000 1077 92.36800 4204 4957 1 chr5D.!!$R1 753
14 TraesCS1D01G276300 chr7A 567515452 567516215 763 True 1075.000000 1075 92.27700 4204 4957 1 chr7A.!!$R1 753
15 TraesCS1D01G276300 chr6D 413052593 413053351 758 True 1064.000000 1064 92.10500 4204 4957 1 chr6D.!!$R1 753
16 TraesCS1D01G276300 chr2B 283183845 283184602 757 False 1059.000000 1059 91.97400 4204 4957 1 chr2B.!!$F2 753
17 TraesCS1D01G276300 chr3A 41173716 41174471 755 False 1037.000000 1037 91.54600 4204 4953 1 chr3A.!!$F1 749
18 TraesCS1D01G276300 chr3D 397385993 397386753 760 False 1033.000000 1033 91.32700 4204 4957 1 chr3D.!!$F2 753

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
989 1022 0.108207 CTCTCCTGTGCATCCCCATC 59.892 60.000 0.00 0.0 0.00 3.51 F
996 1029 0.179034 GTGCATCCCCATCTGAGGTC 60.179 60.000 0.00 0.0 0.00 3.85 F
1001 1050 0.326904 TCCCCATCTGAGGTCAGCAT 60.327 55.000 1.81 0.0 43.46 3.79 F
1446 1495 0.907704 ACCGGTCATGGAGCTTACCA 60.908 55.000 0.00 0.0 44.41 3.25 F
1448 1497 1.134098 CCGGTCATGGAGCTTACCATT 60.134 52.381 4.20 0.0 47.00 3.16 F
3454 5997 0.976641 TTCTGACCGATCCTTGCACT 59.023 50.000 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2239 4558 1.206610 AGCACATCTGTACCTGCTCTG 59.793 52.381 0.00 0.00 0.00 3.35 R
2826 5197 1.341383 ACCAGGCAATTGCTTCTAGGG 60.341 52.381 28.42 20.16 41.70 3.53 R
3052 5436 6.856895 AGCTTAATTTCTGCCTAACATGTTC 58.143 36.000 15.85 1.15 0.00 3.18 R
3423 5965 1.001974 CGGTCAGAAATGGTCACCTGA 59.998 52.381 0.00 0.00 33.72 3.86 R
3477 6027 6.643770 GGAACATCTTATAATAGCGAACGGAA 59.356 38.462 0.00 0.00 0.00 4.30 R
4296 6918 0.318441 GCTCAGCGCCTATGTATCCA 59.682 55.000 2.29 0.00 0.00 3.41 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
49 50 4.537433 GCCCCTCACCTAGCGCTG 62.537 72.222 22.90 6.70 0.00 5.18
111 112 2.177594 GAGGACCACCACCAGCTCTG 62.178 65.000 0.00 0.00 38.94 3.35
159 161 4.796231 GCCATCACCGCGTCGTCT 62.796 66.667 4.92 0.00 0.00 4.18
276 284 4.161295 CTTCCTCCGGCGATGGCA 62.161 66.667 9.30 0.00 42.47 4.92
285 293 2.725312 GGCGATGGCAGAGGAGACA 61.725 63.158 1.01 0.00 42.47 3.41
435 454 2.836372 ACTTCTGATCCAGAGATGCACA 59.164 45.455 0.00 0.00 41.75 4.57
436 455 2.975732 TCTGATCCAGAGATGCACAC 57.024 50.000 0.00 0.00 35.39 3.82
455 474 6.754209 TGCACACGAATGAACAGTAAAATTTT 59.246 30.769 8.75 8.75 0.00 1.82
499 519 3.128242 AGCGAATCTGATCTTTTTGGCAG 59.872 43.478 0.00 0.00 0.00 4.85
508 528 6.814644 TCTGATCTTTTTGGCAGCAAATATTG 59.185 34.615 0.00 0.00 0.00 1.90
509 529 5.875910 TGATCTTTTTGGCAGCAAATATTGG 59.124 36.000 0.00 0.00 0.00 3.16
518 538 6.105333 TGGCAGCAAATATTGGTAAATTGTC 58.895 36.000 0.00 0.00 39.79 3.18
523 543 6.212388 AGCAAATATTGGTAAATTGTCCACCA 59.788 34.615 1.93 0.39 40.04 4.17
592 618 2.222640 CGACGCTACAAAATAACCACGG 60.223 50.000 0.00 0.00 0.00 4.94
607 633 1.942657 CCACGGATGTCATTCCATCAC 59.057 52.381 3.83 0.00 42.47 3.06
709 736 7.513190 TTGTTTTTGGATTTTACAGTTCACG 57.487 32.000 0.00 0.00 0.00 4.35
710 737 5.517054 TGTTTTTGGATTTTACAGTTCACGC 59.483 36.000 0.00 0.00 0.00 5.34
723 750 3.353029 CACGCGGGTGCATGTGAA 61.353 61.111 20.24 0.00 42.97 3.18
738 765 4.569966 GCATGTGAACTCGAGATCAGAAAT 59.430 41.667 23.94 15.28 0.00 2.17
739 766 5.502058 GCATGTGAACTCGAGATCAGAAATG 60.502 44.000 23.94 24.08 0.00 2.32
741 768 4.180057 GTGAACTCGAGATCAGAAATGCT 58.820 43.478 23.94 0.00 0.00 3.79
744 771 3.519579 ACTCGAGATCAGAAATGCTGTG 58.480 45.455 21.68 0.00 45.14 3.66
745 772 3.056250 ACTCGAGATCAGAAATGCTGTGT 60.056 43.478 21.68 0.00 45.14 3.72
746 773 3.515630 TCGAGATCAGAAATGCTGTGTC 58.484 45.455 0.00 0.00 45.14 3.67
747 774 2.606725 CGAGATCAGAAATGCTGTGTCC 59.393 50.000 0.00 0.00 45.14 4.02
748 775 3.678252 CGAGATCAGAAATGCTGTGTCCT 60.678 47.826 0.00 0.00 45.14 3.85
749 776 3.870419 GAGATCAGAAATGCTGTGTCCTC 59.130 47.826 0.00 0.00 45.14 3.71
750 777 3.262660 AGATCAGAAATGCTGTGTCCTCA 59.737 43.478 0.00 0.00 45.14 3.86
763 790 2.681778 CCTCAGTCCTCACCCGCT 60.682 66.667 0.00 0.00 0.00 5.52
769 796 2.076863 CAGTCCTCACCCGCTAAAAAG 58.923 52.381 0.00 0.00 0.00 2.27
770 797 1.003233 AGTCCTCACCCGCTAAAAAGG 59.997 52.381 0.00 0.00 0.00 3.11
777 804 1.623163 CCCGCTAAAAAGGGGAAACA 58.377 50.000 9.85 0.00 44.10 2.83
778 805 1.271379 CCCGCTAAAAAGGGGAAACAC 59.729 52.381 9.85 0.00 44.10 3.32
779 806 1.271379 CCGCTAAAAAGGGGAAACACC 59.729 52.381 2.48 0.00 43.67 4.16
780 807 1.068816 CGCTAAAAAGGGGAAACACCG 60.069 52.381 0.00 0.00 40.11 4.94
803 830 4.399303 GTGTCCTGATTTGGTAATCTTGGG 59.601 45.833 0.00 0.00 40.68 4.12
827 854 1.208052 ACCCTCAATGAGATGGTCACG 59.792 52.381 12.53 0.00 40.79 4.35
844 871 2.476499 GCGTTGCTCTCGGCTTTC 59.524 61.111 0.00 0.00 42.39 2.62
867 894 3.402628 TTTCTTGAAAGGGACTCTCCG 57.597 47.619 0.00 0.00 38.49 4.63
890 923 5.190677 GTCTCTCTCTCAGCTAACCTTAGT 58.809 45.833 0.00 0.00 33.32 2.24
892 925 6.152154 GTCTCTCTCTCAGCTAACCTTAGTTT 59.848 42.308 0.00 0.00 37.42 2.66
893 926 7.337436 GTCTCTCTCTCAGCTAACCTTAGTTTA 59.663 40.741 0.00 0.00 37.42 2.01
894 927 7.337436 TCTCTCTCTCAGCTAACCTTAGTTTAC 59.663 40.741 0.00 0.00 37.42 2.01
895 928 6.093771 TCTCTCTCAGCTAACCTTAGTTTACG 59.906 42.308 0.00 0.00 37.42 3.18
932 965 2.093921 GCCAGTCTACCTTCCACTCTTC 60.094 54.545 0.00 0.00 0.00 2.87
959 992 1.271926 GGCTTTTCCCCTCAGTAAGCA 60.272 52.381 0.00 0.00 42.17 3.91
989 1022 0.108207 CTCTCCTGTGCATCCCCATC 59.892 60.000 0.00 0.00 0.00 3.51
995 1028 0.915872 TGTGCATCCCCATCTGAGGT 60.916 55.000 0.00 0.00 0.00 3.85
996 1029 0.179034 GTGCATCCCCATCTGAGGTC 60.179 60.000 0.00 0.00 0.00 3.85
997 1030 0.621280 TGCATCCCCATCTGAGGTCA 60.621 55.000 0.00 0.00 0.00 4.02
1001 1050 0.326904 TCCCCATCTGAGGTCAGCAT 60.327 55.000 1.81 0.00 43.46 3.79
1020 1069 3.876320 GCATGGAGATCAAGAAGAAGGAC 59.124 47.826 0.00 0.00 0.00 3.85
1026 1075 1.244816 TCAAGAAGAAGGACGCGAGA 58.755 50.000 15.93 0.00 0.00 4.04
1029 1078 1.517475 GAAGAAGGACGCGAGAGGC 60.517 63.158 15.93 0.00 38.69 4.70
1072 1121 1.449246 CAGCTCTTGGCCTTCTCCG 60.449 63.158 3.32 0.00 43.05 4.63
1125 1174 0.999712 CCAATCTTGGTACCCACCCT 59.000 55.000 10.07 0.00 45.11 4.34
1132 1181 1.202769 TGGTACCCACCCTGCCTAAC 61.203 60.000 10.07 0.00 45.11 2.34
1134 1183 1.617233 TACCCACCCTGCCTAACCC 60.617 63.158 0.00 0.00 0.00 4.11
1135 1184 2.418963 TACCCACCCTGCCTAACCCA 62.419 60.000 0.00 0.00 0.00 4.51
1139 1188 1.507140 CACCCTGCCTAACCCATAGA 58.493 55.000 0.00 0.00 33.04 1.98
1143 1192 2.711009 CCCTGCCTAACCCATAGATTCA 59.289 50.000 0.00 0.00 33.04 2.57
1144 1193 3.244700 CCCTGCCTAACCCATAGATTCAG 60.245 52.174 0.00 0.00 33.04 3.02
1150 1199 7.224297 TGCCTAACCCATAGATTCAGAATTAC 58.776 38.462 0.00 0.00 33.04 1.89
1163 1212 8.844244 AGATTCAGAATTACCATTTCATACAGC 58.156 33.333 0.00 0.00 0.00 4.40
1164 1213 8.757982 ATTCAGAATTACCATTTCATACAGCT 57.242 30.769 0.00 0.00 0.00 4.24
1182 1231 6.399639 ACAGCTAGCTCTTACTAATCTTCC 57.600 41.667 16.15 0.00 0.00 3.46
1209 1258 8.840200 TCTCAGTTACTAAGAATTACCCATCT 57.160 34.615 0.00 0.00 0.00 2.90
1234 1283 2.291741 GCATGCATTGGCCTAGTTAGTC 59.708 50.000 14.21 0.00 40.13 2.59
1242 1291 1.763545 GGCCTAGTTAGTCCAAGAGGG 59.236 57.143 0.00 0.00 34.83 4.30
1348 1397 3.735237 TCATTCTTCGCATACCTCCTC 57.265 47.619 0.00 0.00 0.00 3.71
1428 1477 1.277495 GCACACAGCGGCATGAAAAC 61.277 55.000 10.76 0.00 0.00 2.43
1446 1495 0.907704 ACCGGTCATGGAGCTTACCA 60.908 55.000 0.00 0.00 44.41 3.25
1448 1497 1.134098 CCGGTCATGGAGCTTACCATT 60.134 52.381 4.20 0.00 47.00 3.16
1453 1502 5.049405 CGGTCATGGAGCTTACCATTATTTC 60.049 44.000 4.20 0.00 47.00 2.17
1454 1503 5.049405 GGTCATGGAGCTTACCATTATTTCG 60.049 44.000 4.20 0.00 47.00 3.46
1456 1505 5.527214 TCATGGAGCTTACCATTATTTCGTG 59.473 40.000 4.20 0.00 47.00 4.35
1457 1506 3.625764 TGGAGCTTACCATTATTTCGTGC 59.374 43.478 0.00 0.00 34.77 5.34
1458 1507 3.877508 GGAGCTTACCATTATTTCGTGCT 59.122 43.478 0.00 0.00 0.00 4.40
1459 1508 4.335594 GGAGCTTACCATTATTTCGTGCTT 59.664 41.667 0.00 0.00 0.00 3.91
1460 1509 5.163652 GGAGCTTACCATTATTTCGTGCTTT 60.164 40.000 0.00 0.00 0.00 3.51
1463 1512 5.739161 GCTTACCATTATTTCGTGCTTTCAG 59.261 40.000 0.00 0.00 0.00 3.02
1464 1513 6.622896 GCTTACCATTATTTCGTGCTTTCAGT 60.623 38.462 0.00 0.00 0.00 3.41
1465 1514 5.296813 ACCATTATTTCGTGCTTTCAGTC 57.703 39.130 0.00 0.00 0.00 3.51
1608 1697 6.010294 ACTTCAGTGAGATGCAAAGAAATG 57.990 37.500 0.00 0.00 0.00 2.32
1609 1698 5.533903 ACTTCAGTGAGATGCAAAGAAATGT 59.466 36.000 0.00 0.00 0.00 2.71
1610 1699 6.040166 ACTTCAGTGAGATGCAAAGAAATGTT 59.960 34.615 0.00 0.00 0.00 2.71
1611 1700 7.229306 ACTTCAGTGAGATGCAAAGAAATGTTA 59.771 33.333 0.00 0.00 0.00 2.41
1613 1702 8.791327 TCAGTGAGATGCAAAGAAATGTTATA 57.209 30.769 0.00 0.00 0.00 0.98
1614 1703 9.230122 TCAGTGAGATGCAAAGAAATGTTATAA 57.770 29.630 0.00 0.00 0.00 0.98
1617 1706 9.455847 GTGAGATGCAAAGAAATGTTATAATCC 57.544 33.333 0.00 0.00 0.00 3.01
1618 1707 9.412460 TGAGATGCAAAGAAATGTTATAATCCT 57.588 29.630 0.00 0.00 0.00 3.24
1758 1860 1.339151 GGACTGTTGTCTGGGTCATCC 60.339 57.143 0.00 0.00 42.54 3.51
1937 3068 9.495572 TTCTTGTTGTGGTTTTAGTTCAAATTT 57.504 25.926 0.00 0.00 0.00 1.82
1968 3099 5.371115 ACCACAACAAGAATTATGGAACG 57.629 39.130 0.00 0.00 0.00 3.95
1981 4006 3.611766 ATGGAACGGAAGGAGTACTTG 57.388 47.619 0.00 0.00 40.21 3.16
2000 4025 6.743575 ACTTGAGAGTTACAATACCAATGC 57.256 37.500 0.00 0.00 29.87 3.56
2063 4340 4.560128 TCTTGACAGAGTTGACAGTATGC 58.440 43.478 0.00 0.00 42.53 3.14
2077 4354 4.161102 ACAGTATGCCTCTCCCCTATTAC 58.839 47.826 0.00 0.00 42.53 1.89
2083 4360 4.371681 TGCCTCTCCCCTATTACTTTTCT 58.628 43.478 0.00 0.00 0.00 2.52
2124 4417 6.704056 AGTCCCTCCGATCCATATTAATTT 57.296 37.500 0.00 0.00 0.00 1.82
2128 4421 5.938125 CCCTCCGATCCATATTAATTTTCGT 59.062 40.000 0.00 0.00 0.00 3.85
2160 4453 8.950403 ATTAAACTTTGAACTAAATCAGCGAC 57.050 30.769 0.00 0.00 0.00 5.19
2161 4454 6.371809 AAACTTTGAACTAAATCAGCGACA 57.628 33.333 0.00 0.00 0.00 4.35
2162 4455 6.371809 AACTTTGAACTAAATCAGCGACAA 57.628 33.333 0.00 0.00 0.00 3.18
2163 4456 6.560253 ACTTTGAACTAAATCAGCGACAAT 57.440 33.333 0.00 0.00 0.00 2.71
2164 4457 6.970484 ACTTTGAACTAAATCAGCGACAATT 58.030 32.000 0.00 0.00 0.00 2.32
2165 4458 8.094798 ACTTTGAACTAAATCAGCGACAATTA 57.905 30.769 0.00 0.00 0.00 1.40
2166 4459 8.564574 ACTTTGAACTAAATCAGCGACAATTAA 58.435 29.630 0.00 0.00 0.00 1.40
2167 4460 9.559958 CTTTGAACTAAATCAGCGACAATTAAT 57.440 29.630 0.00 0.00 0.00 1.40
2171 4464 9.599322 GAACTAAATCAGCGACAATTAATATGG 57.401 33.333 0.00 0.00 0.00 2.74
2188 4481 5.735733 ATATGGATCGGAGGGAGTAGTAT 57.264 43.478 0.00 0.00 0.00 2.12
2189 4482 3.156288 TGGATCGGAGGGAGTAGTATG 57.844 52.381 0.00 0.00 0.00 2.39
2194 4487 3.952931 TCGGAGGGAGTAGTATGATAGC 58.047 50.000 0.00 0.00 0.00 2.97
2196 4489 3.561528 CGGAGGGAGTAGTATGATAGCCA 60.562 52.174 0.00 0.00 0.00 4.75
2198 4491 5.026790 GGAGGGAGTAGTATGATAGCCAAT 58.973 45.833 0.00 0.00 0.00 3.16
2239 4558 9.807649 AGATGAATAAGATGTAAAATTGGCAAC 57.192 29.630 0.00 0.00 0.00 4.17
2320 4642 6.839124 ATGGTTTCATCAATTTCTACAGCA 57.161 33.333 0.00 0.00 0.00 4.41
2516 4861 9.862371 TCTAGTAAGTAGAGCAATTTCTTTGAG 57.138 33.333 0.00 0.00 33.39 3.02
2595 4940 4.378874 GGACTATTTCAGTTGCTTGTCAGC 60.379 45.833 0.00 0.00 41.62 4.26
2617 4963 8.435187 TCAGCATAATTCAGATGTATCCTTTCT 58.565 33.333 0.00 0.00 0.00 2.52
2668 5018 5.799213 AGAGAAAACTGAGATGATCCGTTT 58.201 37.500 0.00 0.00 44.36 3.60
2679 5029 4.889409 AGATGATCCGTTTATGTTGCCATT 59.111 37.500 0.00 0.00 32.29 3.16
2784 5155 5.586243 TCTGAAGCAAATACTCATGTTAGCC 59.414 40.000 0.00 0.00 0.00 3.93
2896 5267 9.529325 AGTTTTGGTTTAACTCTTTTTATCTGC 57.471 29.630 0.00 0.00 30.20 4.26
2897 5268 9.308318 GTTTTGGTTTAACTCTTTTTATCTGCA 57.692 29.630 0.00 0.00 0.00 4.41
2956 5340 7.233348 TGACTTCTGCTTTGAATATTTTTCCCT 59.767 33.333 0.00 0.00 0.00 4.20
3052 5436 4.020839 TGTCCTTAAGGTTAAGTTCCCTCG 60.021 45.833 21.04 0.00 38.73 4.63
3192 5725 5.617252 TCTCTCCGTTCCAAAATAAGTGTT 58.383 37.500 0.00 0.00 0.00 3.32
3193 5726 5.468746 TCTCTCCGTTCCAAAATAAGTGTTG 59.531 40.000 0.00 0.00 0.00 3.33
3233 5766 9.720667 AATTTAAACTAAAACCACGACACTTAC 57.279 29.630 0.00 0.00 0.00 2.34
3276 5812 6.051717 TCATTAGGAACTATCAGCAAGAAGC 58.948 40.000 0.00 0.00 42.38 3.86
3418 5960 7.115520 CAGTAGCCATTCGACTATTGTTCTATG 59.884 40.741 0.00 0.00 0.00 2.23
3423 5965 7.041780 GCCATTCGACTATTGTTCTATGAACAT 60.042 37.037 12.95 7.11 0.00 2.71
3454 5997 0.976641 TTCTGACCGATCCTTGCACT 59.023 50.000 0.00 0.00 0.00 4.40
3502 6052 6.154445 TCCGTTCGCTATTATAAGATGTTCC 58.846 40.000 0.00 0.00 0.00 3.62
3505 6055 7.281484 CGTTCGCTATTATAAGATGTTCCAAC 58.719 38.462 0.00 0.00 0.00 3.77
3571 6123 5.409520 TGTTCACTCATTTCAGTCTGTATGC 59.590 40.000 0.00 0.00 0.00 3.14
3622 6175 7.451877 GTCTTATATCTGTGAATGGAGGGAGTA 59.548 40.741 0.00 0.00 0.00 2.59
3718 6281 6.280643 CCATTGGATTAATCGTCTACTCACA 58.719 40.000 9.32 0.00 0.00 3.58
3782 6351 5.106277 ACATGTCAGTCATTGCAGAAATCTG 60.106 40.000 6.05 6.05 39.67 2.90
3794 6363 6.048732 TGCAGAAATCTGACACACCTAATA 57.951 37.500 14.43 0.00 46.59 0.98
3795 6364 6.472016 TGCAGAAATCTGACACACCTAATAA 58.528 36.000 14.43 0.00 46.59 1.40
3796 6365 7.112122 TGCAGAAATCTGACACACCTAATAAT 58.888 34.615 14.43 0.00 46.59 1.28
3889 6458 4.792068 TCAACAACTTCCAAGTGAGGATT 58.208 39.130 0.00 0.00 39.66 3.01
3914 6486 5.772521 CTCAACAAGTGGTTCTAATTTGGG 58.227 41.667 0.00 0.00 37.72 4.12
4004 6583 1.608590 CATGATTTCGGGTATGGCCAC 59.391 52.381 8.16 0.00 39.65 5.01
4071 6650 4.158949 TGCAATTCATGTAAATGCAGAGCT 59.841 37.500 13.27 0.00 0.00 4.09
4182 6794 7.455058 ACCTACAACTACACACCATAATGAAA 58.545 34.615 0.00 0.00 0.00 2.69
4197 6809 8.955794 ACCATAATGAAACCTATATTGTACCCT 58.044 33.333 0.00 0.00 0.00 4.34
4198 6810 9.449719 CCATAATGAAACCTATATTGTACCCTC 57.550 37.037 0.00 0.00 0.00 4.30
4201 6813 7.691993 ATGAAACCTATATTGTACCCTCACT 57.308 36.000 0.00 0.00 0.00 3.41
4202 6814 6.884832 TGAAACCTATATTGTACCCTCACTG 58.115 40.000 0.00 0.00 0.00 3.66
4214 6826 2.436911 ACCCTCACTGTACCGAAAAAGT 59.563 45.455 0.00 0.00 0.00 2.66
4257 6869 0.322816 AGCACCGACCATCAAGCATT 60.323 50.000 0.00 0.00 0.00 3.56
4291 6913 2.515991 CACCGCAACACACACCCT 60.516 61.111 0.00 0.00 0.00 4.34
4296 6918 1.073199 GCAACACACACCCTAGGCT 59.927 57.895 2.05 0.00 0.00 4.58
4389 7011 0.610232 GAACCATGTGCTCCAAGGCT 60.610 55.000 0.00 0.00 35.23 4.58
4518 7140 1.187087 AGAAGGGAACGATCTTCGCT 58.813 50.000 14.46 14.46 45.12 4.93
4571 7193 0.104120 CACCTCGTCCAACACTCACA 59.896 55.000 0.00 0.00 0.00 3.58
4578 7201 1.152984 CCAACACTCACAGCCACCA 60.153 57.895 0.00 0.00 0.00 4.17
4681 7304 2.153401 TGCTACCACCACCAAGGCT 61.153 57.895 0.00 0.00 43.14 4.58
4717 7340 1.734655 AGACCTTGACACCACCTCAT 58.265 50.000 0.00 0.00 0.00 2.90
4836 7461 2.185310 GAACTGGCATCCACCGACCT 62.185 60.000 0.00 0.00 0.00 3.85
4957 7582 3.440415 ACCGTGCGCGAGATGAGA 61.440 61.111 23.45 0.00 41.33 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.162690 CTAGGTGAGGGGCGTGGC 62.163 72.222 0.00 0.00 0.00 5.01
28 29 4.162690 GCTAGGTGAGGGGCGTGG 62.163 72.222 0.00 0.00 0.00 4.94
29 30 4.514577 CGCTAGGTGAGGGGCGTG 62.515 72.222 0.00 0.00 42.23 5.34
115 116 1.610086 TTGGGAGCCAAGGCAATGG 60.610 57.895 14.40 5.07 44.88 3.16
124 126 3.797353 GGCGGAGATTGGGAGCCA 61.797 66.667 0.00 0.00 46.48 4.75
127 129 4.918201 GGCGGCGGAGATTGGGAG 62.918 72.222 9.78 0.00 0.00 4.30
173 175 1.289380 GGAGCTCTCCGTTCGTGTT 59.711 57.895 14.64 0.00 40.36 3.32
200 202 0.947180 TACTTGCGTGGCGGTTTCTC 60.947 55.000 0.00 0.00 0.00 2.87
268 276 0.809241 CTTGTCTCCTCTGCCATCGC 60.809 60.000 0.00 0.00 0.00 4.58
271 279 0.252881 TCCCTTGTCTCCTCTGCCAT 60.253 55.000 0.00 0.00 0.00 4.40
273 281 0.616111 TCTCCCTTGTCTCCTCTGCC 60.616 60.000 0.00 0.00 0.00 4.85
276 284 3.244735 GCTTTTTCTCCCTTGTCTCCTCT 60.245 47.826 0.00 0.00 0.00 3.69
285 293 0.115152 CCCCCAGCTTTTTCTCCCTT 59.885 55.000 0.00 0.00 0.00 3.95
410 428 6.496218 TGTGCATCTCTGGATCAGAAGTATAT 59.504 38.462 0.00 0.00 40.18 0.86
413 431 4.026052 TGTGCATCTCTGGATCAGAAGTA 58.974 43.478 0.00 0.00 40.18 2.24
478 497 3.432782 CTGCCAAAAAGATCAGATTCGC 58.567 45.455 0.00 0.00 0.00 4.70
479 498 3.119743 TGCTGCCAAAAAGATCAGATTCG 60.120 43.478 0.00 0.00 0.00 3.34
489 509 7.432350 TTTACCAATATTTGCTGCCAAAAAG 57.568 32.000 0.00 0.00 43.58 2.27
499 519 6.402222 TGGTGGACAATTTACCAATATTTGC 58.598 36.000 0.00 0.00 41.25 3.68
508 528 0.170339 GCGCTGGTGGACAATTTACC 59.830 55.000 0.00 0.00 35.05 2.85
509 529 1.130561 GAGCGCTGGTGGACAATTTAC 59.869 52.381 18.48 0.00 0.00 2.01
518 538 4.988598 ACGTTGGAGCGCTGGTGG 62.989 66.667 18.48 2.05 34.88 4.61
523 543 2.434884 CCATCACGTTGGAGCGCT 60.435 61.111 11.27 11.27 39.25 5.92
574 599 3.372822 ACATCCGTGGTTATTTTGTAGCG 59.627 43.478 0.00 0.00 0.00 4.26
585 611 2.026356 TGATGGAATGACATCCGTGGTT 60.026 45.455 7.26 0.00 45.16 3.67
623 650 9.844790 GTGATAAACATTGATGAATCTTTCACA 57.155 29.630 0.00 0.00 43.48 3.58
683 710 9.239002 CGTGAACTGTAAAATCCAAAAACAATA 57.761 29.630 0.00 0.00 0.00 1.90
697 724 1.500512 GCACCCGCGTGAACTGTAAA 61.501 55.000 4.92 0.00 43.14 2.01
698 725 1.957186 GCACCCGCGTGAACTGTAA 60.957 57.895 4.92 0.00 43.14 2.41
699 726 2.356553 GCACCCGCGTGAACTGTA 60.357 61.111 4.92 0.00 43.14 2.74
709 736 2.870372 GAGTTCACATGCACCCGC 59.130 61.111 0.00 0.00 39.24 6.13
710 737 1.354337 CTCGAGTTCACATGCACCCG 61.354 60.000 3.62 0.00 0.00 5.28
723 750 3.056250 ACACAGCATTTCTGATCTCGAGT 60.056 43.478 13.13 0.00 45.72 4.18
738 765 0.469892 TGAGGACTGAGGACACAGCA 60.470 55.000 0.00 0.00 41.06 4.41
739 766 0.037790 GTGAGGACTGAGGACACAGC 60.038 60.000 0.00 0.00 41.06 4.40
741 768 0.832135 GGGTGAGGACTGAGGACACA 60.832 60.000 0.00 0.00 33.82 3.72
744 771 3.007973 GCGGGTGAGGACTGAGGAC 62.008 68.421 0.00 0.00 0.00 3.85
745 772 1.859841 TAGCGGGTGAGGACTGAGGA 61.860 60.000 0.00 0.00 0.00 3.71
746 773 0.970937 TTAGCGGGTGAGGACTGAGG 60.971 60.000 0.00 0.00 0.00 3.86
747 774 0.895530 TTTAGCGGGTGAGGACTGAG 59.104 55.000 0.00 0.00 0.00 3.35
748 775 1.344065 TTTTAGCGGGTGAGGACTGA 58.656 50.000 0.00 0.00 0.00 3.41
749 776 2.076863 CTTTTTAGCGGGTGAGGACTG 58.923 52.381 0.00 0.00 0.00 3.51
750 777 1.003233 CCTTTTTAGCGGGTGAGGACT 59.997 52.381 0.00 0.00 0.00 3.85
763 790 2.950975 GACACGGTGTTTCCCCTTTTTA 59.049 45.455 15.94 0.00 0.00 1.52
769 796 1.599797 CAGGACACGGTGTTTCCCC 60.600 63.158 15.94 11.63 33.28 4.81
770 797 0.036306 ATCAGGACACGGTGTTTCCC 59.964 55.000 15.94 12.00 33.28 3.97
772 799 2.031157 CCAAATCAGGACACGGTGTTTC 60.031 50.000 15.94 10.86 0.00 2.78
775 802 0.472471 ACCAAATCAGGACACGGTGT 59.528 50.000 14.66 14.66 0.00 4.16
776 803 2.465860 TACCAAATCAGGACACGGTG 57.534 50.000 6.58 6.58 0.00 4.94
777 804 3.263425 AGATTACCAAATCAGGACACGGT 59.737 43.478 1.35 0.00 43.44 4.83
778 805 3.873910 AGATTACCAAATCAGGACACGG 58.126 45.455 1.35 0.00 43.44 4.94
779 806 4.094887 CCAAGATTACCAAATCAGGACACG 59.905 45.833 1.35 0.00 43.44 4.49
780 807 4.399303 CCCAAGATTACCAAATCAGGACAC 59.601 45.833 9.74 0.00 43.44 3.67
844 871 4.214332 CGGAGAGTCCCTTTCAAGAAAAAG 59.786 45.833 0.00 0.00 36.26 2.27
867 894 5.190677 ACTAAGGTTAGCTGAGAGAGAGAC 58.809 45.833 2.35 0.00 34.09 3.36
890 923 1.080093 CTGAGCCTCGTGCCGTAAA 60.080 57.895 0.00 0.00 42.71 2.01
892 925 4.129737 GCTGAGCCTCGTGCCGTA 62.130 66.667 0.00 0.00 42.71 4.02
932 965 2.751837 GGGGAAAAGCCGGAGCAG 60.752 66.667 5.05 0.00 43.56 4.24
959 992 8.709308 GGGATGCACAGGAGAGTTTATATATAT 58.291 37.037 0.00 0.00 0.00 0.86
989 1022 1.761198 TGATCTCCATGCTGACCTCAG 59.239 52.381 0.00 0.00 46.40 3.35
995 1028 4.383880 CCTTCTTCTTGATCTCCATGCTGA 60.384 45.833 0.00 0.00 0.00 4.26
996 1029 3.878103 CCTTCTTCTTGATCTCCATGCTG 59.122 47.826 0.00 0.00 0.00 4.41
997 1030 3.779183 TCCTTCTTCTTGATCTCCATGCT 59.221 43.478 0.00 0.00 0.00 3.79
1001 1050 2.093973 GCGTCCTTCTTCTTGATCTCCA 60.094 50.000 0.00 0.00 0.00 3.86
1029 1078 1.673665 GAAGAGCACCAGCACCAGG 60.674 63.158 0.00 0.00 45.49 4.45
1033 1082 1.739562 CGAGGAAGAGCACCAGCAC 60.740 63.158 0.00 0.00 45.49 4.40
1038 1087 3.672295 CTGGCCGAGGAAGAGCACC 62.672 68.421 0.00 0.00 0.00 5.01
1089 1138 2.606587 GGCAAGGAAGGAGGAGGCA 61.607 63.158 0.00 0.00 0.00 4.75
1095 1144 2.097825 CCAAGATTGGCAAGGAAGGAG 58.902 52.381 5.96 0.00 42.21 3.69
1120 1169 1.507140 TCTATGGGTTAGGCAGGGTG 58.493 55.000 0.00 0.00 0.00 4.61
1121 1170 2.514726 ATCTATGGGTTAGGCAGGGT 57.485 50.000 0.00 0.00 0.00 4.34
1122 1171 2.711009 TGAATCTATGGGTTAGGCAGGG 59.289 50.000 0.00 0.00 0.00 4.45
1123 1172 3.648067 TCTGAATCTATGGGTTAGGCAGG 59.352 47.826 0.00 0.00 0.00 4.85
1125 1174 5.912149 ATTCTGAATCTATGGGTTAGGCA 57.088 39.130 0.00 0.00 0.00 4.75
1132 1181 8.696043 TGAAATGGTAATTCTGAATCTATGGG 57.304 34.615 2.92 0.00 0.00 4.00
1139 1188 8.757982 AGCTGTATGAAATGGTAATTCTGAAT 57.242 30.769 0.00 0.00 0.00 2.57
1143 1192 7.512992 AGCTAGCTGTATGAAATGGTAATTCT 58.487 34.615 18.57 0.00 0.00 2.40
1144 1193 7.659390 AGAGCTAGCTGTATGAAATGGTAATTC 59.341 37.037 24.99 0.48 0.00 2.17
1150 1199 6.520272 AGTAAGAGCTAGCTGTATGAAATGG 58.480 40.000 24.99 0.00 0.00 3.16
1161 1210 7.066781 AGAAGGAAGATTAGTAAGAGCTAGCT 58.933 38.462 19.45 19.45 0.00 3.32
1162 1211 7.013846 TGAGAAGGAAGATTAGTAAGAGCTAGC 59.986 40.741 6.62 6.62 0.00 3.42
1163 1212 8.458573 TGAGAAGGAAGATTAGTAAGAGCTAG 57.541 38.462 0.00 0.00 0.00 3.42
1164 1213 8.056400 ACTGAGAAGGAAGATTAGTAAGAGCTA 58.944 37.037 0.00 0.00 0.00 3.32
1182 1231 9.535878 GATGGGTAATTCTTAGTAACTGAGAAG 57.464 37.037 0.00 0.00 38.98 2.85
1209 1258 1.341285 ACTAGGCCAATGCATGCAGAA 60.341 47.619 26.69 1.91 40.13 3.02
1234 1283 6.208204 GGTTATCAAATGATGATCCCTCTTGG 59.792 42.308 6.17 0.00 45.91 3.61
1242 1291 6.537355 TCTCCTGGGTTATCAAATGATGATC 58.463 40.000 6.17 0.00 45.91 2.92
1348 1397 8.047310 AGGATTGGTACATAAACTAAGGTCAAG 58.953 37.037 0.00 0.00 39.30 3.02
1418 1467 0.173255 CCATGACCGGTTTTCATGCC 59.827 55.000 23.01 4.23 46.16 4.40
1428 1477 0.469917 ATGGTAAGCTCCATGACCGG 59.530 55.000 6.15 0.00 45.26 5.28
1446 1495 7.078228 GTGAAAGACTGAAAGCACGAAATAAT 58.922 34.615 0.00 0.00 37.60 1.28
1448 1497 5.525745 TGTGAAAGACTGAAAGCACGAAATA 59.474 36.000 0.00 0.00 37.60 1.40
1453 1502 2.351418 TGTGTGAAAGACTGAAAGCACG 59.649 45.455 0.00 0.00 37.60 5.34
1454 1503 3.487544 GGTGTGTGAAAGACTGAAAGCAC 60.488 47.826 0.00 0.00 37.60 4.40
1456 1505 2.945668 AGGTGTGTGAAAGACTGAAAGC 59.054 45.455 0.00 0.00 37.60 3.51
1457 1506 4.034510 GTGAGGTGTGTGAAAGACTGAAAG 59.965 45.833 0.00 0.00 42.29 2.62
1458 1507 3.938963 GTGAGGTGTGTGAAAGACTGAAA 59.061 43.478 0.00 0.00 0.00 2.69
1459 1508 3.055458 TGTGAGGTGTGTGAAAGACTGAA 60.055 43.478 0.00 0.00 0.00 3.02
1460 1509 2.499693 TGTGAGGTGTGTGAAAGACTGA 59.500 45.455 0.00 0.00 0.00 3.41
1463 1512 2.866762 GAGTGTGAGGTGTGTGAAAGAC 59.133 50.000 0.00 0.00 0.00 3.01
1464 1513 2.766263 AGAGTGTGAGGTGTGTGAAAGA 59.234 45.455 0.00 0.00 0.00 2.52
1465 1514 3.185246 AGAGTGTGAGGTGTGTGAAAG 57.815 47.619 0.00 0.00 0.00 2.62
1607 1696 7.237679 AGCAAAGATAGCCCTAGGATTATAACA 59.762 37.037 11.48 0.00 0.00 2.41
1608 1697 7.625469 AGCAAAGATAGCCCTAGGATTATAAC 58.375 38.462 11.48 0.00 0.00 1.89
1609 1698 7.092846 GGAGCAAAGATAGCCCTAGGATTATAA 60.093 40.741 11.48 0.00 0.00 0.98
1610 1699 6.384305 GGAGCAAAGATAGCCCTAGGATTATA 59.616 42.308 11.48 0.00 0.00 0.98
1611 1700 5.190726 GGAGCAAAGATAGCCCTAGGATTAT 59.809 44.000 11.48 7.52 0.00 1.28
1613 1702 3.329225 GGAGCAAAGATAGCCCTAGGATT 59.671 47.826 11.48 0.00 0.00 3.01
1614 1703 2.909662 GGAGCAAAGATAGCCCTAGGAT 59.090 50.000 11.48 0.31 0.00 3.24
1615 1704 2.090494 AGGAGCAAAGATAGCCCTAGGA 60.090 50.000 11.48 0.00 33.01 2.94
1616 1705 2.038295 CAGGAGCAAAGATAGCCCTAGG 59.962 54.545 0.06 0.06 33.32 3.02
1617 1706 2.968574 TCAGGAGCAAAGATAGCCCTAG 59.031 50.000 0.00 0.00 33.32 3.02
1618 1707 2.700897 GTCAGGAGCAAAGATAGCCCTA 59.299 50.000 0.00 0.00 33.32 3.53
1619 1708 1.488393 GTCAGGAGCAAAGATAGCCCT 59.512 52.381 0.00 0.00 34.40 5.19
1620 1709 1.808133 CGTCAGGAGCAAAGATAGCCC 60.808 57.143 0.00 0.00 0.00 5.19
1621 1710 1.137086 TCGTCAGGAGCAAAGATAGCC 59.863 52.381 0.00 0.00 0.00 3.93
1671 1773 4.229876 GCCTTGACAACTGAAATACAAGC 58.770 43.478 0.00 0.00 35.09 4.01
1758 1860 2.941453 AGTGCGTACCATGTGAGTAG 57.059 50.000 0.00 0.00 0.00 2.57
1939 3070 8.919145 TCCATAATTCTTGTTGTGGTTTTAGTT 58.081 29.630 2.99 0.00 40.20 2.24
1940 3071 8.472007 TCCATAATTCTTGTTGTGGTTTTAGT 57.528 30.769 2.99 0.00 40.20 2.24
1944 3075 6.212955 CGTTCCATAATTCTTGTTGTGGTTT 58.787 36.000 2.99 0.00 40.20 3.27
1945 3076 5.278758 CCGTTCCATAATTCTTGTTGTGGTT 60.279 40.000 2.99 0.00 40.20 3.67
1946 3077 4.217550 CCGTTCCATAATTCTTGTTGTGGT 59.782 41.667 2.99 0.00 40.20 4.16
1947 3078 4.457603 TCCGTTCCATAATTCTTGTTGTGG 59.542 41.667 0.00 0.00 40.52 4.17
1948 3079 5.621197 TCCGTTCCATAATTCTTGTTGTG 57.379 39.130 0.00 0.00 0.00 3.33
1949 3080 5.183140 CCTTCCGTTCCATAATTCTTGTTGT 59.817 40.000 0.00 0.00 0.00 3.32
1950 3081 5.414454 TCCTTCCGTTCCATAATTCTTGTTG 59.586 40.000 0.00 0.00 0.00 3.33
1952 3083 5.174037 TCCTTCCGTTCCATAATTCTTGT 57.826 39.130 0.00 0.00 0.00 3.16
1953 3084 5.186198 ACTCCTTCCGTTCCATAATTCTTG 58.814 41.667 0.00 0.00 0.00 3.02
1954 3085 5.437191 ACTCCTTCCGTTCCATAATTCTT 57.563 39.130 0.00 0.00 0.00 2.52
1955 3086 5.661759 AGTACTCCTTCCGTTCCATAATTCT 59.338 40.000 0.00 0.00 0.00 2.40
1956 3087 5.915175 AGTACTCCTTCCGTTCCATAATTC 58.085 41.667 0.00 0.00 0.00 2.17
1968 3099 5.979288 TGTAACTCTCAAGTACTCCTTCC 57.021 43.478 0.00 0.00 33.48 3.46
1981 4006 6.985188 TTCTGCATTGGTATTGTAACTCTC 57.015 37.500 0.00 0.00 0.00 3.20
2027 4060 3.872696 TGTCAAGAACTTGTTGCTGAGA 58.127 40.909 13.15 0.00 41.16 3.27
2029 4306 3.872696 TCTGTCAAGAACTTGTTGCTGA 58.127 40.909 13.15 10.97 41.16 4.26
2035 4312 4.832248 TGTCAACTCTGTCAAGAACTTGT 58.168 39.130 13.15 0.00 41.16 3.16
2036 4313 4.872691 ACTGTCAACTCTGTCAAGAACTTG 59.127 41.667 8.09 8.09 41.71 3.16
2063 4340 8.769359 TCTAAAAGAAAAGTAATAGGGGAGAGG 58.231 37.037 0.00 0.00 0.00 3.69
2083 4360 9.847224 GGAGGGACTACATATTTTGATCTAAAA 57.153 33.333 6.42 6.07 40.63 1.52
2090 4382 5.011738 GGATCGGAGGGACTACATATTTTGA 59.988 44.000 0.00 0.00 41.36 2.69
2096 4388 3.827817 ATGGATCGGAGGGACTACATA 57.172 47.619 0.00 0.00 41.36 2.29
2134 4427 9.394477 GTCGCTGATTTAGTTCAAAGTTTAATT 57.606 29.630 0.00 0.00 0.00 1.40
2136 4429 7.921787 TGTCGCTGATTTAGTTCAAAGTTTAA 58.078 30.769 0.00 0.00 0.00 1.52
2139 4432 6.371809 TTGTCGCTGATTTAGTTCAAAGTT 57.628 33.333 0.00 0.00 0.00 2.66
2141 4434 8.948853 TTAATTGTCGCTGATTTAGTTCAAAG 57.051 30.769 0.00 0.00 0.00 2.77
2145 4438 9.599322 CCATATTAATTGTCGCTGATTTAGTTC 57.401 33.333 0.00 0.00 0.00 3.01
2146 4439 9.337396 TCCATATTAATTGTCGCTGATTTAGTT 57.663 29.630 0.00 0.00 0.00 2.24
2147 4440 8.902540 TCCATATTAATTGTCGCTGATTTAGT 57.097 30.769 0.00 0.00 0.00 2.24
2148 4441 9.979270 GATCCATATTAATTGTCGCTGATTTAG 57.021 33.333 0.00 0.00 0.00 1.85
2149 4442 8.655970 CGATCCATATTAATTGTCGCTGATTTA 58.344 33.333 0.00 0.00 0.00 1.40
2150 4443 7.361201 CCGATCCATATTAATTGTCGCTGATTT 60.361 37.037 0.00 0.00 0.00 2.17
2151 4444 6.092670 CCGATCCATATTAATTGTCGCTGATT 59.907 38.462 0.00 0.00 0.00 2.57
2152 4445 5.582269 CCGATCCATATTAATTGTCGCTGAT 59.418 40.000 0.00 0.00 0.00 2.90
2153 4446 4.929211 CCGATCCATATTAATTGTCGCTGA 59.071 41.667 0.00 0.00 0.00 4.26
2154 4447 4.929211 TCCGATCCATATTAATTGTCGCTG 59.071 41.667 0.00 0.00 0.00 5.18
2155 4448 5.147330 TCCGATCCATATTAATTGTCGCT 57.853 39.130 0.00 0.00 0.00 4.93
2156 4449 4.330074 CCTCCGATCCATATTAATTGTCGC 59.670 45.833 0.00 0.00 0.00 5.19
2157 4450 4.870426 CCCTCCGATCCATATTAATTGTCG 59.130 45.833 0.00 0.00 0.00 4.35
2158 4451 6.049955 TCCCTCCGATCCATATTAATTGTC 57.950 41.667 0.00 0.00 0.00 3.18
2159 4452 5.548056 ACTCCCTCCGATCCATATTAATTGT 59.452 40.000 0.00 0.00 0.00 2.71
2160 4453 6.054860 ACTCCCTCCGATCCATATTAATTG 57.945 41.667 0.00 0.00 0.00 2.32
2161 4454 6.960542 ACTACTCCCTCCGATCCATATTAATT 59.039 38.462 0.00 0.00 0.00 1.40
2162 4455 6.503944 ACTACTCCCTCCGATCCATATTAAT 58.496 40.000 0.00 0.00 0.00 1.40
2163 4456 5.900437 ACTACTCCCTCCGATCCATATTAA 58.100 41.667 0.00 0.00 0.00 1.40
2164 4457 5.531753 ACTACTCCCTCCGATCCATATTA 57.468 43.478 0.00 0.00 0.00 0.98
2165 4458 4.405756 ACTACTCCCTCCGATCCATATT 57.594 45.455 0.00 0.00 0.00 1.28
2166 4459 5.193930 TCATACTACTCCCTCCGATCCATAT 59.806 44.000 0.00 0.00 0.00 1.78
2167 4460 4.538891 TCATACTACTCCCTCCGATCCATA 59.461 45.833 0.00 0.00 0.00 2.74
2168 4461 3.333980 TCATACTACTCCCTCCGATCCAT 59.666 47.826 0.00 0.00 0.00 3.41
2169 4462 2.714793 TCATACTACTCCCTCCGATCCA 59.285 50.000 0.00 0.00 0.00 3.41
2170 4463 3.436577 TCATACTACTCCCTCCGATCC 57.563 52.381 0.00 0.00 0.00 3.36
2171 4464 4.577283 GCTATCATACTACTCCCTCCGATC 59.423 50.000 0.00 0.00 0.00 3.69
2213 4506 9.807649 GTTGCCAATTTTACATCTTATTCATCT 57.192 29.630 0.00 0.00 0.00 2.90
2215 4508 9.590451 CTGTTGCCAATTTTACATCTTATTCAT 57.410 29.630 0.00 0.00 0.00 2.57
2227 4546 3.230134 ACCTGCTCTGTTGCCAATTTTA 58.770 40.909 0.00 0.00 0.00 1.52
2228 4547 2.041701 ACCTGCTCTGTTGCCAATTTT 58.958 42.857 0.00 0.00 0.00 1.82
2239 4558 1.206610 AGCACATCTGTACCTGCTCTG 59.793 52.381 0.00 0.00 0.00 3.35
2243 4562 2.099141 TTGAGCACATCTGTACCTGC 57.901 50.000 0.00 0.00 0.00 4.85
2244 4563 4.256110 TGATTTGAGCACATCTGTACCTG 58.744 43.478 0.00 0.00 0.00 4.00
2250 4569 8.752766 ATTAAGTTTTGATTTGAGCACATCTG 57.247 30.769 0.00 0.00 0.00 2.90
2501 4845 5.124457 TCCTGCATACTCAAAGAAATTGCTC 59.876 40.000 0.00 0.00 38.98 4.26
2511 4856 5.804639 ACACAGTATTCCTGCATACTCAAA 58.195 37.500 0.00 0.00 45.68 2.69
2516 4861 5.419542 TCTTGACACAGTATTCCTGCATAC 58.580 41.667 0.00 0.00 45.68 2.39
2679 5029 4.083110 GCAAGAACAAGAGCAAAGCTATGA 60.083 41.667 10.17 0.00 39.88 2.15
2764 5134 4.860022 AGGGCTAACATGAGTATTTGCTT 58.140 39.130 0.00 0.00 0.00 3.91
2826 5197 1.341383 ACCAGGCAATTGCTTCTAGGG 60.341 52.381 28.42 20.16 41.70 3.53
3052 5436 6.856895 AGCTTAATTTCTGCCTAACATGTTC 58.143 36.000 15.85 1.15 0.00 3.18
3232 5765 4.154942 TGAAGTACTCCCTCCGTTAAAGT 58.845 43.478 0.00 0.00 0.00 2.66
3233 5766 4.796038 TGAAGTACTCCCTCCGTTAAAG 57.204 45.455 0.00 0.00 0.00 1.85
3276 5812 7.592938 TGCACTGTAATAAGAAATGAAACAGG 58.407 34.615 0.00 0.00 37.71 4.00
3418 5960 4.154918 GTCAGAAATGGTCACCTGATGTTC 59.845 45.833 0.00 0.00 37.88 3.18
3423 5965 1.001974 CGGTCAGAAATGGTCACCTGA 59.998 52.381 0.00 0.00 33.72 3.86
3470 6020 9.970395 TCTTATAATAGCGAACGGAAGAAAATA 57.030 29.630 0.00 0.00 0.00 1.40
3471 6021 8.882415 TCTTATAATAGCGAACGGAAGAAAAT 57.118 30.769 0.00 0.00 0.00 1.82
3472 6022 8.761497 CATCTTATAATAGCGAACGGAAGAAAA 58.239 33.333 0.00 0.00 0.00 2.29
3473 6023 7.924412 ACATCTTATAATAGCGAACGGAAGAAA 59.076 33.333 0.00 0.00 0.00 2.52
3474 6024 7.431249 ACATCTTATAATAGCGAACGGAAGAA 58.569 34.615 0.00 0.00 0.00 2.52
3475 6025 6.978338 ACATCTTATAATAGCGAACGGAAGA 58.022 36.000 0.00 0.00 0.00 2.87
3476 6026 7.148787 GGAACATCTTATAATAGCGAACGGAAG 60.149 40.741 0.00 0.00 0.00 3.46
3477 6027 6.643770 GGAACATCTTATAATAGCGAACGGAA 59.356 38.462 0.00 0.00 0.00 4.30
3529 6081 7.711846 AGTGAACAAACACACTAAAATGCATA 58.288 30.769 0.00 0.00 44.06 3.14
3531 6083 5.960113 AGTGAACAAACACACTAAAATGCA 58.040 33.333 0.00 0.00 44.06 3.96
3571 6123 8.405531 ACGTTTTGGATATTTCAATATGGACTG 58.594 33.333 0.00 0.00 31.96 3.51
3605 6158 1.833630 TGCTACTCCCTCCATTCACAG 59.166 52.381 0.00 0.00 0.00 3.66
3718 6281 7.876896 GAATGTCTCGAAAGAACTTACTTCT 57.123 36.000 0.00 0.00 41.39 2.85
3794 6363 9.950496 AACTCTCACTTCATACATTACAAGATT 57.050 29.630 0.00 0.00 0.00 2.40
3795 6364 9.593134 GAACTCTCACTTCATACATTACAAGAT 57.407 33.333 0.00 0.00 0.00 2.40
3796 6365 8.807118 AGAACTCTCACTTCATACATTACAAGA 58.193 33.333 0.00 0.00 0.00 3.02
3889 6458 5.221224 CCAAATTAGAACCACTTGTTGAGCA 60.221 40.000 0.00 0.00 37.29 4.26
3914 6486 1.594397 GTTGCTTGTTTTCTTGGCTGC 59.406 47.619 0.00 0.00 0.00 5.25
4004 6583 2.920227 GCTCTTCTGCCGTATCTGATCG 60.920 54.545 0.00 0.00 0.00 3.69
4109 6721 7.484975 TGGCCGTATTTATTTTATTGGACTTG 58.515 34.615 0.00 0.00 0.00 3.16
4182 6794 5.837438 GGTACAGTGAGGGTACAATATAGGT 59.163 44.000 0.00 0.00 42.21 3.08
4197 6809 4.505191 CGAAAGACTTTTTCGGTACAGTGA 59.495 41.667 12.72 0.00 45.17 3.41
4198 6810 4.758561 CGAAAGACTTTTTCGGTACAGTG 58.241 43.478 12.72 0.00 45.17 3.66
4214 6826 2.922740 ATATAAAGCGGGGCGAAAGA 57.077 45.000 0.00 0.00 0.00 2.52
4257 6869 1.292061 GTGGCGTGTGTTTGTACTGA 58.708 50.000 0.00 0.00 0.00 3.41
4291 6913 0.895530 GCGCCTATGTATCCAGCCTA 59.104 55.000 0.00 0.00 0.00 3.93
4296 6918 0.318441 GCTCAGCGCCTATGTATCCA 59.682 55.000 2.29 0.00 0.00 3.41
4389 7011 2.889606 TACCCTTGCTGAAGGCGCA 61.890 57.895 10.83 0.00 46.89 6.09
4453 7075 4.147449 CGTCATGCGGCTCCAGGA 62.147 66.667 0.00 0.00 36.85 3.86
4559 7181 1.148273 GGTGGCTGTGAGTGTTGGA 59.852 57.895 0.00 0.00 0.00 3.53
4571 7193 2.203480 ATGTGGCGTTTGGTGGCT 60.203 55.556 0.00 0.00 0.00 4.75
4615 7238 4.155733 CGCTGCCCGGTCACCATA 62.156 66.667 0.00 0.00 0.00 2.74
4717 7340 2.753043 GTGGAGGCGGGTCTCGTA 60.753 66.667 0.00 0.00 41.72 3.43
4806 7430 4.351054 CCAGTTCTGGCCGGCCTT 62.351 66.667 43.34 22.00 36.94 4.35


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

AutoCloner maintained by Alex Coulton.