Multiple sequence alignment - TraesCS6B01G174800

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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 TraesCS6B01G174800 chr6B 100.000 2807 0 0 1 2807 189276024 189278830 0.000000e+00 5184.0
1 TraesCS6B01G174800 chr6B 91.319 599 45 4 2210 2806 321325460 321326053 0.000000e+00 811.0
2 TraesCS6B01G174800 chr6B 95.192 104 5 0 1 104 22426648 22426545 6.220000e-37 165.0
3 TraesCS6B01G174800 chr6B 81.921 177 21 6 343 514 618657586 618657416 3.770000e-29 139.0
4 TraesCS6B01G174800 chr6B 97.619 42 1 0 106 147 714087401 714087360 3.880000e-09 73.1
5 TraesCS6B01G174800 chr6D 91.478 1854 98 20 102 1924 104145411 104147235 0.000000e+00 2494.0
6 TraesCS6B01G174800 chr6D 97.638 127 3 0 2085 2211 104147234 104147360 4.710000e-53 219.0
7 TraesCS6B01G174800 chr6D 95.349 86 3 1 20 104 145356527 145356442 4.880000e-28 135.0
8 TraesCS6B01G174800 chr6D 79.661 177 24 9 342 514 181694031 181693863 1.770000e-22 117.0
9 TraesCS6B01G174800 chr6D 79.839 124 20 3 342 465 379559273 379559391 4.980000e-13 86.1
10 TraesCS6B01G174800 chr6D 77.465 142 23 6 377 514 470930572 470930436 3.000000e-10 76.8
11 TraesCS6B01G174800 chr6D 84.848 66 8 2 343 408 46871611 46871674 6.490000e-07 65.8
12 TraesCS6B01G174800 chr6A 92.227 1621 77 15 303 1901 125540780 125542373 0.000000e+00 2250.0
13 TraesCS6B01G174800 chr6A 85.377 212 22 3 106 316 125540466 125540669 7.880000e-51 211.0
14 TraesCS6B01G174800 chr6A 81.006 179 20 10 342 514 235075156 235075326 2.270000e-26 130.0
15 TraesCS6B01G174800 chr6A 95.714 70 3 0 1 70 162649486 162649417 2.290000e-21 113.0
16 TraesCS6B01G174800 chr6A 86.813 91 12 0 107 197 55266314 55266404 4.950000e-18 102.0
17 TraesCS6B01G174800 chr2B 94.649 598 32 0 2209 2806 135236722 135236125 0.000000e+00 928.0
18 TraesCS6B01G174800 chr2B 90.879 603 47 5 2209 2806 394389971 394389372 0.000000e+00 802.0
19 TraesCS6B01G174800 chr2B 75.879 825 166 18 994 1794 745724457 745723642 9.430000e-105 390.0
20 TraesCS6B01G174800 chr2B 97.605 167 4 0 1920 2086 180617957 180618123 1.270000e-73 287.0
21 TraesCS6B01G174800 chr2B 97.605 167 4 0 1920 2086 254691791 254691625 1.270000e-73 287.0
22 TraesCS6B01G174800 chr2B 97.024 168 5 0 1919 2086 681216914 681217081 1.650000e-72 283.0
23 TraesCS6B01G174800 chr2B 97.041 169 4 1 1918 2086 785225147 785224980 1.650000e-72 283.0
24 TraesCS6B01G174800 chr2B 84.834 211 27 4 1922 2130 656370218 656370011 1.020000e-49 207.0
25 TraesCS6B01G174800 chr2B 86.631 187 17 7 1922 2105 41123268 41123449 1.710000e-47 200.0
26 TraesCS6B01G174800 chr2B 84.343 198 24 7 1916 2109 756556828 756556634 1.330000e-43 187.0
27 TraesCS6B01G174800 chr2B 89.796 98 10 0 105 202 363428344 363428247 2.940000e-25 126.0
28 TraesCS6B01G174800 chr4B 93.000 600 37 4 2212 2807 643500624 643500026 0.000000e+00 870.0
29 TraesCS6B01G174800 chr3B 91.833 600 47 1 2210 2807 727130271 727129672 0.000000e+00 835.0
30 TraesCS6B01G174800 chr3B 91.486 599 45 4 2211 2806 95143614 95143019 0.000000e+00 819.0
31 TraesCS6B01G174800 chr3B 95.192 104 5 0 1 104 201513805 201513702 6.220000e-37 165.0
32 TraesCS6B01G174800 chr3B 84.416 77 6 6 2035 2106 480334800 480334725 1.390000e-08 71.3
33 TraesCS6B01G174800 chr7B 91.290 597 46 4 2213 2806 59339922 59339329 0.000000e+00 809.0
34 TraesCS6B01G174800 chr7B 98.193 166 3 0 1921 2086 710105050 710104885 9.840000e-75 291.0
35 TraesCS6B01G174800 chr7B 98.193 166 3 0 1921 2086 710116659 710116494 9.840000e-75 291.0
36 TraesCS6B01G174800 chr7B 98.193 166 3 0 1921 2086 710127759 710127594 9.840000e-75 291.0
37 TraesCS6B01G174800 chr7B 97.619 168 3 1 1926 2092 483770767 483770600 1.270000e-73 287.0
38 TraesCS6B01G174800 chr7B 97.006 167 5 0 1926 2092 64695619 64695453 5.920000e-72 281.0
39 TraesCS6B01G174800 chr7B 94.231 104 6 0 1 104 45215485 45215588 2.890000e-35 159.0
40 TraesCS6B01G174800 chr1B 91.030 602 48 4 2209 2807 422368928 422369526 0.000000e+00 808.0
41 TraesCS6B01G174800 chr1B 95.192 104 5 0 1 104 184376418 184376315 6.220000e-37 165.0
42 TraesCS6B01G174800 chr1B 80.814 172 26 4 345 514 39989231 39989397 8.160000e-26 128.0
43 TraesCS6B01G174800 chr5B 91.000 600 47 5 2210 2807 470276581 470275987 0.000000e+00 802.0
44 TraesCS6B01G174800 chr5B 81.457 151 20 6 346 494 547412189 547412333 1.770000e-22 117.0
45 TraesCS6B01G174800 chr2D 76.039 818 163 19 1001 1794 610297832 610297024 7.290000e-106 394.0
46 TraesCS6B01G174800 chr2D 79.429 175 28 5 342 514 352792708 352792540 1.770000e-22 117.0
47 TraesCS6B01G174800 chr2A 76.344 744 146 17 1001 1720 743114562 743113825 3.410000e-99 372.0
48 TraesCS6B01G174800 chr3D 89.362 188 16 4 1920 2106 66122674 66122858 1.680000e-57 233.0
49 TraesCS6B01G174800 chr3D 95.192 104 5 0 1 104 21905331 21905228 6.220000e-37 165.0
50 TraesCS6B01G174800 chr3D 95.192 104 5 0 1 104 555743808 555743705 6.220000e-37 165.0
51 TraesCS6B01G174800 chr3D 79.191 173 27 6 344 514 539576000 539576165 8.220000e-21 111.0
52 TraesCS6B01G174800 chr3D 86.735 98 12 1 106 202 615399396 615399493 1.060000e-19 108.0
53 TraesCS6B01G174800 chrUn 95.192 104 5 0 1 104 445812359 445812462 6.220000e-37 165.0
54 TraesCS6B01G174800 chrUn 79.213 178 27 5 343 514 67440189 67440016 6.350000e-22 115.0
55 TraesCS6B01G174800 chrUn 77.966 177 28 6 344 514 16376045 16375874 1.780000e-17 100.0
56 TraesCS6B01G174800 chr5D 95.192 104 5 0 1 104 560873172 560873069 6.220000e-37 165.0
57 TraesCS6B01G174800 chr5D 94.231 104 6 0 1 104 6200578 6200681 2.890000e-35 159.0
58 TraesCS6B01G174800 chr5D 93.269 104 7 0 1 104 329162881 329162778 1.350000e-33 154.0
59 TraesCS6B01G174800 chr5D 79.661 177 22 9 344 514 9128302 9128470 6.350000e-22 115.0
60 TraesCS6B01G174800 chr3A 95.192 104 5 0 1 104 393235950 393235847 6.220000e-37 165.0
61 TraesCS6B01G174800 chr1A 94.231 104 6 0 1 104 31951068 31950965 2.890000e-35 159.0
62 TraesCS6B01G174800 chr1A 94.231 104 6 0 1 104 168449863 168449966 2.890000e-35 159.0
63 TraesCS6B01G174800 chr1A 81.699 153 21 5 344 494 380321323 380321176 1.370000e-23 121.0
64 TraesCS6B01G174800 chr1A 79.191 173 27 6 345 514 1939156 1939322 8.220000e-21 111.0
65 TraesCS6B01G174800 chr1A 80.392 153 21 6 344 494 459978623 459978768 1.060000e-19 108.0
66 TraesCS6B01G174800 chr1A 78.613 173 28 6 345 514 1990708 1990874 3.820000e-19 106.0
67 TraesCS6B01G174800 chr1D 93.269 104 7 0 1 104 254498702 254498599 1.350000e-33 154.0
68 TraesCS6B01G174800 chr1D 92.308 104 8 0 1 104 244483345 244483448 6.260000e-32 148.0
69 TraesCS6B01G174800 chr1D 78.846 156 25 5 342 494 121307312 121307462 6.400000e-17 99.0
70 TraesCS6B01G174800 chr4D 92.308 104 8 0 1 104 19917199 19917096 6.260000e-32 148.0
71 TraesCS6B01G174800 chr4D 79.710 138 22 4 344 480 12601857 12601989 8.280000e-16 95.3
72 TraesCS6B01G174800 chr4D 94.737 38 2 0 67 104 120444085 120444122 3.020000e-05 60.2
73 TraesCS6B01G174800 chr5A 93.548 93 5 1 106 197 441207232 441207324 1.360000e-28 137.0
74 TraesCS6B01G174800 chr5A 91.667 96 8 0 107 202 692913564 692913469 1.750000e-27 134.0
75 TraesCS6B01G174800 chr7D 81.818 154 20 5 364 514 39552062 39551914 3.800000e-24 122.0
76 TraesCS6B01G174800 chr7D 80.347 173 22 8 344 512 633522552 633522388 1.370000e-23 121.0
77 TraesCS6B01G174800 chr7A 92.683 41 1 2 239 278 197998361 197998400 1.090000e-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 TraesCS6B01G174800 chr6B 189276024 189278830 2806 False 5184.0 5184 100.000 1 2807 1 chr6B.!!$F1 2806
1 TraesCS6B01G174800 chr6B 321325460 321326053 593 False 811.0 811 91.319 2210 2806 1 chr6B.!!$F2 596
2 TraesCS6B01G174800 chr6D 104145411 104147360 1949 False 1356.5 2494 94.558 102 2211 2 chr6D.!!$F3 2109
3 TraesCS6B01G174800 chr6A 125540466 125542373 1907 False 1230.5 2250 88.802 106 1901 2 chr6A.!!$F3 1795
4 TraesCS6B01G174800 chr2B 135236125 135236722 597 True 928.0 928 94.649 2209 2806 1 chr2B.!!$R1 597
5 TraesCS6B01G174800 chr2B 394389372 394389971 599 True 802.0 802 90.879 2209 2806 1 chr2B.!!$R4 597
6 TraesCS6B01G174800 chr2B 745723642 745724457 815 True 390.0 390 75.879 994 1794 1 chr2B.!!$R6 800
7 TraesCS6B01G174800 chr4B 643500026 643500624 598 True 870.0 870 93.000 2212 2807 1 chr4B.!!$R1 595
8 TraesCS6B01G174800 chr3B 727129672 727130271 599 True 835.0 835 91.833 2210 2807 1 chr3B.!!$R4 597
9 TraesCS6B01G174800 chr3B 95143019 95143614 595 True 819.0 819 91.486 2211 2806 1 chr3B.!!$R1 595
10 TraesCS6B01G174800 chr7B 59339329 59339922 593 True 809.0 809 91.290 2213 2806 1 chr7B.!!$R1 593
11 TraesCS6B01G174800 chr1B 422368928 422369526 598 False 808.0 808 91.030 2209 2807 1 chr1B.!!$F2 598
12 TraesCS6B01G174800 chr5B 470275987 470276581 594 True 802.0 802 91.000 2210 2807 1 chr5B.!!$R1 597
13 TraesCS6B01G174800 chr2D 610297024 610297832 808 True 394.0 394 76.039 1001 1794 1 chr2D.!!$R2 793
14 TraesCS6B01G174800 chr2A 743113825 743114562 737 True 372.0 372 76.344 1001 1720 1 chr2A.!!$R1 719

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
595 752 0.24746 CAGATGGACTTGCGACCAGA 59.753 55.0 0.0 0.0 38.33 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2382 2600 0.032017 TCCAGACTAGGGGCTTCCTC 60.032 60.0 2.51 0.0 44.06 3.71 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
24 25 6.522625 TCTCACACTTTTTGGAATGTTTCA 57.477 33.333 0.00 0.00 0.00 2.69
25 26 6.929625 TCTCACACTTTTTGGAATGTTTCAA 58.070 32.000 0.00 0.00 0.00 2.69
26 27 7.382110 TCTCACACTTTTTGGAATGTTTCAAA 58.618 30.769 0.00 0.00 0.00 2.69
27 28 8.040132 TCTCACACTTTTTGGAATGTTTCAAAT 58.960 29.630 0.33 0.00 33.58 2.32
28 29 8.558973 TCACACTTTTTGGAATGTTTCAAATT 57.441 26.923 0.33 0.00 33.58 1.82
29 30 8.663911 TCACACTTTTTGGAATGTTTCAAATTC 58.336 29.630 0.33 0.00 33.58 2.17
38 39 6.457851 GAATGTTTCAAATTCCACTTGAGC 57.542 37.500 0.00 0.00 34.41 4.26
39 40 4.998671 TGTTTCAAATTCCACTTGAGCA 57.001 36.364 0.00 0.00 34.41 4.26
40 41 5.534207 TGTTTCAAATTCCACTTGAGCAT 57.466 34.783 0.00 0.00 34.41 3.79
41 42 5.531634 TGTTTCAAATTCCACTTGAGCATC 58.468 37.500 0.00 0.00 34.41 3.91
42 43 4.789012 TTCAAATTCCACTTGAGCATCC 57.211 40.909 0.00 0.00 34.41 3.51
43 44 3.765381 TCAAATTCCACTTGAGCATCCA 58.235 40.909 0.00 0.00 0.00 3.41
44 45 4.151121 TCAAATTCCACTTGAGCATCCAA 58.849 39.130 0.00 0.00 0.00 3.53
45 46 4.588106 TCAAATTCCACTTGAGCATCCAAA 59.412 37.500 0.00 0.00 0.00 3.28
46 47 5.246656 TCAAATTCCACTTGAGCATCCAAAT 59.753 36.000 0.00 0.00 0.00 2.32
47 48 4.996788 ATTCCACTTGAGCATCCAAATC 57.003 40.909 0.00 0.00 0.00 2.17
48 49 3.726557 TCCACTTGAGCATCCAAATCT 57.273 42.857 0.00 0.00 0.00 2.40
49 50 3.349927 TCCACTTGAGCATCCAAATCTG 58.650 45.455 0.00 0.00 0.00 2.90
50 51 2.426024 CCACTTGAGCATCCAAATCTGG 59.574 50.000 0.00 0.00 45.08 3.86
51 52 2.097825 ACTTGAGCATCCAAATCTGGC 58.902 47.619 0.00 0.00 43.17 4.85
52 53 2.291411 ACTTGAGCATCCAAATCTGGCT 60.291 45.455 0.00 0.00 43.17 4.75
55 56 2.519771 AGCATCCAAATCTGGCTCAA 57.480 45.000 0.00 0.00 43.17 3.02
56 57 3.028094 AGCATCCAAATCTGGCTCAAT 57.972 42.857 0.00 0.00 43.17 2.57
57 58 4.174704 AGCATCCAAATCTGGCTCAATA 57.825 40.909 0.00 0.00 43.17 1.90
58 59 3.887716 AGCATCCAAATCTGGCTCAATAC 59.112 43.478 0.00 0.00 43.17 1.89
59 60 3.005155 GCATCCAAATCTGGCTCAATACC 59.995 47.826 0.00 0.00 43.17 2.73
60 61 4.209538 CATCCAAATCTGGCTCAATACCA 58.790 43.478 0.00 0.00 43.17 3.25
68 69 3.658757 TGGCTCAATACCAGCAAAAAC 57.341 42.857 0.00 0.00 38.77 2.43
69 70 2.961741 TGGCTCAATACCAGCAAAAACA 59.038 40.909 0.00 0.00 38.77 2.83
70 71 3.577848 TGGCTCAATACCAGCAAAAACAT 59.422 39.130 0.00 0.00 38.77 2.71
71 72 4.176271 GGCTCAATACCAGCAAAAACATC 58.824 43.478 0.00 0.00 38.77 3.06
72 73 4.082026 GGCTCAATACCAGCAAAAACATCT 60.082 41.667 0.00 0.00 38.77 2.90
73 74 5.098211 GCTCAATACCAGCAAAAACATCTC 58.902 41.667 0.00 0.00 36.82 2.75
74 75 5.335897 GCTCAATACCAGCAAAAACATCTCA 60.336 40.000 0.00 0.00 36.82 3.27
75 76 6.626623 GCTCAATACCAGCAAAAACATCTCAT 60.627 38.462 0.00 0.00 36.82 2.90
76 77 7.415541 GCTCAATACCAGCAAAAACATCTCATA 60.416 37.037 0.00 0.00 36.82 2.15
77 78 8.347004 TCAATACCAGCAAAAACATCTCATAA 57.653 30.769 0.00 0.00 0.00 1.90
78 79 8.243426 TCAATACCAGCAAAAACATCTCATAAC 58.757 33.333 0.00 0.00 0.00 1.89
79 80 7.701539 ATACCAGCAAAAACATCTCATAACA 57.298 32.000 0.00 0.00 0.00 2.41
80 81 6.403866 ACCAGCAAAAACATCTCATAACAA 57.596 33.333 0.00 0.00 0.00 2.83
81 82 6.996509 ACCAGCAAAAACATCTCATAACAAT 58.003 32.000 0.00 0.00 0.00 2.71
82 83 6.869913 ACCAGCAAAAACATCTCATAACAATG 59.130 34.615 0.00 0.00 0.00 2.82
83 84 6.869913 CCAGCAAAAACATCTCATAACAATGT 59.130 34.615 0.00 0.00 35.20 2.71
84 85 7.385752 CCAGCAAAAACATCTCATAACAATGTT 59.614 33.333 3.43 3.43 43.53 2.71
85 86 8.430063 CAGCAAAAACATCTCATAACAATGTTC 58.570 33.333 0.22 0.00 41.47 3.18
86 87 8.362639 AGCAAAAACATCTCATAACAATGTTCT 58.637 29.630 0.22 0.00 41.47 3.01
87 88 9.624697 GCAAAAACATCTCATAACAATGTTCTA 57.375 29.630 0.22 0.00 41.47 2.10
89 90 9.846248 AAAAACATCTCATAACAATGTTCTAGC 57.154 29.630 0.22 0.00 41.47 3.42
90 91 6.834959 ACATCTCATAACAATGTTCTAGCG 57.165 37.500 0.22 0.00 29.51 4.26
91 92 5.235186 ACATCTCATAACAATGTTCTAGCGC 59.765 40.000 0.22 0.00 29.51 5.92
92 93 4.119862 TCTCATAACAATGTTCTAGCGCC 58.880 43.478 2.29 0.00 0.00 6.53
93 94 3.867857 TCATAACAATGTTCTAGCGCCA 58.132 40.909 2.29 0.00 0.00 5.69
94 95 4.450976 TCATAACAATGTTCTAGCGCCAT 58.549 39.130 2.29 0.00 0.00 4.40
95 96 4.273235 TCATAACAATGTTCTAGCGCCATG 59.727 41.667 2.29 0.00 0.00 3.66
96 97 0.734889 ACAATGTTCTAGCGCCATGC 59.265 50.000 2.29 0.00 46.98 4.06
111 112 2.354906 GCCATGCCAAATGTCCAATTGA 60.355 45.455 7.12 0.00 0.00 2.57
144 145 7.810282 CGTGTATTACTATCTCCCTTCAAGATG 59.190 40.741 0.00 0.00 35.20 2.90
197 198 8.690203 TTGATTTCCTATTCTCACAAAAGACA 57.310 30.769 0.00 0.00 0.00 3.41
231 232 8.445275 AGAGTTAAACAACATAACACATGTCA 57.555 30.769 0.00 0.00 36.04 3.58
238 239 7.517614 ACAACATAACACATGTCATGGTTTA 57.482 32.000 17.08 12.79 33.60 2.01
239 240 7.367285 ACAACATAACACATGTCATGGTTTAC 58.633 34.615 17.08 0.00 33.60 2.01
240 241 7.230510 ACAACATAACACATGTCATGGTTTACT 59.769 33.333 17.08 4.91 33.60 2.24
285 289 7.205297 TGGAACAGAAGTAGTACTTAACACAC 58.795 38.462 15.52 2.59 38.80 3.82
417 546 7.617533 GGATACAAACACAATAAACACACAC 57.382 36.000 0.00 0.00 0.00 3.82
422 551 2.614983 ACACAATAAACACACACCCGAC 59.385 45.455 0.00 0.00 0.00 4.79
423 552 2.031508 CACAATAAACACACACCCGACC 60.032 50.000 0.00 0.00 0.00 4.79
465 598 2.159448 ACACACAACCAACATCAACACG 60.159 45.455 0.00 0.00 0.00 4.49
483 617 1.057526 CGCGCACAAATAACACACCG 61.058 55.000 8.75 0.00 0.00 4.94
495 629 1.156736 ACACACCGACAAATAGCAGC 58.843 50.000 0.00 0.00 0.00 5.25
496 630 0.447801 CACACCGACAAATAGCAGCC 59.552 55.000 0.00 0.00 0.00 4.85
552 689 4.439974 GGTGAAAACAGTGATCAACAAGCA 60.440 41.667 0.00 0.00 31.11 3.91
553 690 5.101628 GTGAAAACAGTGATCAACAAGCAA 58.898 37.500 0.00 0.00 0.00 3.91
554 691 5.750067 GTGAAAACAGTGATCAACAAGCAAT 59.250 36.000 0.00 0.00 0.00 3.56
595 752 0.247460 CAGATGGACTTGCGACCAGA 59.753 55.000 0.00 0.00 38.33 3.86
596 753 1.134580 CAGATGGACTTGCGACCAGAT 60.135 52.381 0.00 0.00 38.33 2.90
597 754 2.101415 CAGATGGACTTGCGACCAGATA 59.899 50.000 0.00 0.00 38.33 1.98
598 755 2.968574 AGATGGACTTGCGACCAGATAT 59.031 45.455 0.00 0.00 38.33 1.63
599 756 3.389329 AGATGGACTTGCGACCAGATATT 59.611 43.478 0.00 0.00 38.33 1.28
600 757 3.627395 TGGACTTGCGACCAGATATTT 57.373 42.857 0.00 0.00 31.37 1.40
601 758 3.531538 TGGACTTGCGACCAGATATTTC 58.468 45.455 0.00 0.00 31.37 2.17
602 759 3.055458 TGGACTTGCGACCAGATATTTCA 60.055 43.478 0.00 0.00 31.37 2.69
603 760 4.130118 GGACTTGCGACCAGATATTTCAT 58.870 43.478 0.00 0.00 0.00 2.57
604 761 5.163353 TGGACTTGCGACCAGATATTTCATA 60.163 40.000 0.00 0.00 31.37 2.15
605 762 5.934625 GGACTTGCGACCAGATATTTCATAT 59.065 40.000 0.00 0.00 0.00 1.78
606 763 6.428159 GGACTTGCGACCAGATATTTCATATT 59.572 38.462 0.00 0.00 0.00 1.28
607 764 7.360438 GGACTTGCGACCAGATATTTCATATTC 60.360 40.741 0.00 0.00 0.00 1.75
608 765 6.428159 ACTTGCGACCAGATATTTCATATTCC 59.572 38.462 0.00 0.00 0.00 3.01
609 766 5.245531 TGCGACCAGATATTTCATATTCCC 58.754 41.667 0.00 0.00 0.00 3.97
610 767 5.013079 TGCGACCAGATATTTCATATTCCCT 59.987 40.000 0.00 0.00 0.00 4.20
611 768 5.352569 GCGACCAGATATTTCATATTCCCTG 59.647 44.000 0.00 0.00 0.00 4.45
612 769 5.352569 CGACCAGATATTTCATATTCCCTGC 59.647 44.000 0.00 0.00 0.00 4.85
613 770 6.204852 ACCAGATATTTCATATTCCCTGCA 57.795 37.500 0.00 0.00 0.00 4.41
614 771 6.243900 ACCAGATATTTCATATTCCCTGCAG 58.756 40.000 6.78 6.78 0.00 4.41
717 879 4.106197 GAGAGACTATTTGTGTACCAGCG 58.894 47.826 0.00 0.00 0.00 5.18
746 908 6.272318 TGTTTTCTGGTGATGAACAATTGAC 58.728 36.000 13.59 6.46 30.80 3.18
940 1103 7.424803 CAGATCAAGAAGTATACAGAGTCCTG 58.575 42.308 5.50 0.00 45.76 3.86
953 1118 3.501445 CAGAGTCCTGGCAGAAAGAAAAG 59.499 47.826 17.94 0.00 36.77 2.27
992 1157 0.528684 CAGCACTAGGTAGCTTCCGC 60.529 60.000 0.00 1.37 39.50 5.54
1041 1214 4.955774 AACGTGGTGCCGACGGTC 62.956 66.667 16.73 8.54 41.21 4.79
1629 1823 6.399743 GGAGTTCTTCCGTCTTAAGAAGATT 58.600 40.000 18.57 4.97 45.84 2.40
1674 1868 4.147449 CGCCAGATGGAGTCCGCA 62.147 66.667 4.30 0.00 37.39 5.69
1680 1874 0.392193 AGATGGAGTCCGCAAAGCTG 60.392 55.000 4.30 0.00 0.00 4.24
1764 1958 0.323633 CCACCATGCTGGACAATGGA 60.324 55.000 0.16 0.00 40.96 3.41
1795 1989 4.697352 AGAGGGACGAAGACATCATTTTTG 59.303 41.667 0.00 0.00 0.00 2.44
1916 2124 9.176181 CATTTGAAATTCCTTTGAAATTTGCAG 57.824 29.630 0.00 0.00 36.44 4.41
1922 2130 9.783081 AAATTCCTTTGAAATTTGCAGAATACT 57.217 25.926 0.00 0.00 33.32 2.12
1927 2135 9.305925 CCTTTGAAATTTGCAGAATACTATTCC 57.694 33.333 0.00 0.00 0.00 3.01
1928 2136 9.305925 CTTTGAAATTTGCAGAATACTATTCCC 57.694 33.333 0.00 0.00 0.00 3.97
1929 2137 8.593945 TTGAAATTTGCAGAATACTATTCCCT 57.406 30.769 0.00 0.00 0.00 4.20
1930 2138 8.225603 TGAAATTTGCAGAATACTATTCCCTC 57.774 34.615 0.00 0.00 0.00 4.30
1931 2139 7.285401 TGAAATTTGCAGAATACTATTCCCTCC 59.715 37.037 0.00 0.00 0.00 4.30
1932 2140 5.708736 TTTGCAGAATACTATTCCCTCCA 57.291 39.130 5.32 0.00 0.00 3.86
1933 2141 5.912149 TTGCAGAATACTATTCCCTCCAT 57.088 39.130 5.32 0.00 0.00 3.41
1934 2142 5.912149 TGCAGAATACTATTCCCTCCATT 57.088 39.130 5.32 0.00 0.00 3.16
1935 2143 5.869579 TGCAGAATACTATTCCCTCCATTC 58.130 41.667 5.32 0.00 0.00 2.67
1936 2144 5.221925 TGCAGAATACTATTCCCTCCATTCC 60.222 44.000 5.32 0.00 0.00 3.01
1937 2145 5.013599 GCAGAATACTATTCCCTCCATTCCT 59.986 44.000 5.32 0.00 0.00 3.36
1938 2146 6.213600 GCAGAATACTATTCCCTCCATTCCTA 59.786 42.308 5.32 0.00 0.00 2.94
1939 2147 7.256691 GCAGAATACTATTCCCTCCATTCCTAA 60.257 40.741 5.32 0.00 0.00 2.69
1940 2148 8.660435 CAGAATACTATTCCCTCCATTCCTAAA 58.340 37.037 5.32 0.00 0.00 1.85
1941 2149 9.411848 AGAATACTATTCCCTCCATTCCTAAAT 57.588 33.333 5.32 0.00 0.00 1.40
1946 2154 9.813826 ACTATTCCCTCCATTCCTAAATATTTG 57.186 33.333 11.05 1.40 0.00 2.32
1947 2155 9.813826 CTATTCCCTCCATTCCTAAATATTTGT 57.186 33.333 11.05 0.00 0.00 2.83
1948 2156 8.712228 ATTCCCTCCATTCCTAAATATTTGTC 57.288 34.615 11.05 0.00 0.00 3.18
1949 2157 7.465900 TCCCTCCATTCCTAAATATTTGTCT 57.534 36.000 11.05 0.00 0.00 3.41
1950 2158 7.882755 TCCCTCCATTCCTAAATATTTGTCTT 58.117 34.615 11.05 0.00 0.00 3.01
1951 2159 8.343787 TCCCTCCATTCCTAAATATTTGTCTTT 58.656 33.333 11.05 0.00 0.00 2.52
1952 2160 8.633561 CCCTCCATTCCTAAATATTTGTCTTTC 58.366 37.037 11.05 0.00 0.00 2.62
1953 2161 9.413734 CCTCCATTCCTAAATATTTGTCTTTCT 57.586 33.333 11.05 0.00 0.00 2.52
1969 2177 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
1970 2178 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
1971 2179 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
1972 2180 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
1973 2181 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
1974 2182 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
1975 2183 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
1976 2184 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
1977 2185 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
1979 2187 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
1980 2188 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
1981 2189 7.375834 AGATTTCAACAAGTGACTACATACGA 58.624 34.615 0.00 0.00 35.39 3.43
1982 2190 7.870954 AGATTTCAACAAGTGACTACATACGAA 59.129 33.333 0.00 0.00 35.39 3.85
1983 2191 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
1984 2192 6.509656 TTCAACAAGTGACTACATACGAAGT 58.490 36.000 0.00 0.00 39.84 3.01
1985 2193 7.650890 TTCAACAAGTGACTACATACGAAGTA 58.349 34.615 0.00 0.00 41.66 2.24
1986 2194 8.136800 TTCAACAAGTGACTACATACGAAGTAA 58.863 33.333 0.00 0.00 41.03 2.24
2004 2212 9.436957 ACGAAGTAAAATGAGTGAATCTACATT 57.563 29.630 0.00 0.00 41.94 2.71
2005 2213 9.907576 CGAAGTAAAATGAGTGAATCTACATTC 57.092 33.333 0.00 0.00 39.24 2.67
2039 2247 9.511272 TGTCTACATACATCCGTATATTGTAGT 57.489 33.333 0.00 0.00 38.60 2.73
2040 2248 9.985318 GTCTACATACATCCGTATATTGTAGTC 57.015 37.037 0.00 0.00 38.60 2.59
2041 2249 9.170734 TCTACATACATCCGTATATTGTAGTCC 57.829 37.037 0.00 0.00 38.60 3.85
2042 2250 7.770366 ACATACATCCGTATATTGTAGTCCA 57.230 36.000 0.00 0.00 36.11 4.02
2043 2251 8.362464 ACATACATCCGTATATTGTAGTCCAT 57.638 34.615 0.00 0.00 36.11 3.41
2044 2252 8.812972 ACATACATCCGTATATTGTAGTCCATT 58.187 33.333 0.00 0.00 36.11 3.16
2045 2253 9.653287 CATACATCCGTATATTGTAGTCCATTT 57.347 33.333 0.00 0.00 36.11 2.32
2046 2254 7.962964 ACATCCGTATATTGTAGTCCATTTG 57.037 36.000 0.00 0.00 0.00 2.32
2047 2255 7.732025 ACATCCGTATATTGTAGTCCATTTGA 58.268 34.615 0.00 0.00 0.00 2.69
2048 2256 8.208224 ACATCCGTATATTGTAGTCCATTTGAA 58.792 33.333 0.00 0.00 0.00 2.69
2049 2257 9.219603 CATCCGTATATTGTAGTCCATTTGAAT 57.780 33.333 0.00 0.00 0.00 2.57
2050 2258 8.601845 TCCGTATATTGTAGTCCATTTGAATG 57.398 34.615 0.00 0.00 36.17 2.67
2051 2259 8.208224 TCCGTATATTGTAGTCCATTTGAATGT 58.792 33.333 3.30 0.00 34.60 2.71
2052 2260 8.495949 CCGTATATTGTAGTCCATTTGAATGTC 58.504 37.037 3.30 0.00 34.60 3.06
2053 2261 9.261180 CGTATATTGTAGTCCATTTGAATGTCT 57.739 33.333 3.30 4.19 34.60 3.41
2058 2266 9.739276 ATTGTAGTCCATTTGAATGTCTAGAAA 57.261 29.630 0.00 0.00 33.18 2.52
2059 2267 8.777865 TGTAGTCCATTTGAATGTCTAGAAAG 57.222 34.615 0.00 0.00 34.60 2.62
2060 2268 8.593679 TGTAGTCCATTTGAATGTCTAGAAAGA 58.406 33.333 0.00 0.00 34.60 2.52
2077 2285 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2078 2286 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2079 2287 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2080 2288 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2081 2289 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2082 2290 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2083 2291 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2172 2380 4.629115 GGCCACACTGCACGCAAC 62.629 66.667 0.00 0.00 0.00 4.17
2212 2420 7.328493 GGTCATAATCAAAGCCACAAAGTTTAC 59.672 37.037 0.00 0.00 0.00 2.01
2214 2422 4.600692 ATCAAAGCCACAAAGTTTACCC 57.399 40.909 0.00 0.00 0.00 3.69
2281 2491 5.873712 CAGAGCATACAATCAGAGTCAAGTT 59.126 40.000 0.00 0.00 0.00 2.66
2325 2539 4.242475 CGACAAAGTACATAGGTTCTGCA 58.758 43.478 0.00 0.00 0.00 4.41
2354 2568 2.140065 GCTCAACAAGCCCAGAAAAC 57.860 50.000 0.00 0.00 45.92 2.43
2617 2837 2.681778 CAGAGGGTCCAGGCGAGT 60.682 66.667 0.00 0.00 0.00 4.18
2653 2873 2.795329 CACCTAATGTGGCAAGAGGTT 58.205 47.619 7.85 0.00 41.52 3.50
2734 2954 0.319555 CGACCACCTCTCGAAAGCAA 60.320 55.000 0.00 0.00 32.65 3.91
2796 3016 1.000496 GTTCGAGTCTTCGGGAACACT 60.000 52.381 3.75 0.00 46.67 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.111247 TGAAACATTCCAAAAAGTGTGAGAT 57.889 32.000 0.00 0.00 0.00 2.75
3 4 8.558973 AATTTGAAACATTCCAAAAAGTGTGA 57.441 26.923 0.00 0.00 36.10 3.58
5 6 7.984391 GGAATTTGAAACATTCCAAAAAGTGT 58.016 30.769 5.63 0.00 46.40 3.55
14 15 5.406477 GCTCAAGTGGAATTTGAAACATTCC 59.594 40.000 3.86 3.86 42.20 3.01
15 16 5.984926 TGCTCAAGTGGAATTTGAAACATTC 59.015 36.000 0.00 0.00 42.20 2.67
16 17 5.916318 TGCTCAAGTGGAATTTGAAACATT 58.084 33.333 0.00 0.00 42.20 2.71
17 18 5.534207 TGCTCAAGTGGAATTTGAAACAT 57.466 34.783 0.00 0.00 42.20 2.71
18 19 4.998671 TGCTCAAGTGGAATTTGAAACA 57.001 36.364 0.00 0.00 42.20 2.83
19 20 4.925646 GGATGCTCAAGTGGAATTTGAAAC 59.074 41.667 0.00 0.00 42.20 2.78
20 21 4.588106 TGGATGCTCAAGTGGAATTTGAAA 59.412 37.500 0.00 0.00 42.20 2.69
21 22 4.151121 TGGATGCTCAAGTGGAATTTGAA 58.849 39.130 0.00 0.00 42.20 2.69
22 23 3.765381 TGGATGCTCAAGTGGAATTTGA 58.235 40.909 0.00 0.00 40.46 2.69
23 24 4.524316 TTGGATGCTCAAGTGGAATTTG 57.476 40.909 0.00 0.00 34.49 2.32
24 25 5.482878 AGATTTGGATGCTCAAGTGGAATTT 59.517 36.000 0.00 0.00 0.00 1.82
25 26 5.021458 AGATTTGGATGCTCAAGTGGAATT 58.979 37.500 0.00 0.00 0.00 2.17
26 27 4.401519 CAGATTTGGATGCTCAAGTGGAAT 59.598 41.667 0.00 0.00 0.00 3.01
27 28 3.760151 CAGATTTGGATGCTCAAGTGGAA 59.240 43.478 0.00 0.00 0.00 3.53
28 29 3.349927 CAGATTTGGATGCTCAAGTGGA 58.650 45.455 0.00 0.00 0.00 4.02
29 30 3.777465 CAGATTTGGATGCTCAAGTGG 57.223 47.619 0.00 0.00 0.00 4.00
30 31 6.219381 GAGCCAGATTTGGATGCTCAAGTG 62.219 50.000 6.43 0.00 44.86 3.16
31 32 4.184909 GAGCCAGATTTGGATGCTCAAGT 61.185 47.826 6.43 0.00 44.86 3.16
32 33 2.358267 GAGCCAGATTTGGATGCTCAAG 59.642 50.000 6.43 0.00 44.86 3.02
33 34 2.372264 GAGCCAGATTTGGATGCTCAA 58.628 47.619 6.43 0.00 44.86 3.02
34 35 2.048444 GAGCCAGATTTGGATGCTCA 57.952 50.000 6.43 0.00 44.86 4.26
35 36 2.048444 TGAGCCAGATTTGGATGCTC 57.952 50.000 6.43 6.27 44.86 4.26
36 37 2.519771 TTGAGCCAGATTTGGATGCT 57.480 45.000 6.43 0.00 44.86 3.79
37 38 3.005155 GGTATTGAGCCAGATTTGGATGC 59.995 47.826 6.43 0.00 44.86 3.91
38 39 4.209538 TGGTATTGAGCCAGATTTGGATG 58.790 43.478 6.43 0.00 44.86 3.51
48 49 2.961741 TGTTTTTGCTGGTATTGAGCCA 59.038 40.909 0.00 0.00 35.43 4.75
49 50 3.658757 TGTTTTTGCTGGTATTGAGCC 57.341 42.857 0.00 0.00 35.43 4.70
50 51 5.064441 AGATGTTTTTGCTGGTATTGAGC 57.936 39.130 0.00 0.00 36.95 4.26
51 52 6.258230 TGAGATGTTTTTGCTGGTATTGAG 57.742 37.500 0.00 0.00 0.00 3.02
52 53 6.839124 ATGAGATGTTTTTGCTGGTATTGA 57.161 33.333 0.00 0.00 0.00 2.57
53 54 8.028354 TGTTATGAGATGTTTTTGCTGGTATTG 58.972 33.333 0.00 0.00 0.00 1.90
54 55 8.121305 TGTTATGAGATGTTTTTGCTGGTATT 57.879 30.769 0.00 0.00 0.00 1.89
55 56 7.701539 TGTTATGAGATGTTTTTGCTGGTAT 57.298 32.000 0.00 0.00 0.00 2.73
56 57 7.517614 TTGTTATGAGATGTTTTTGCTGGTA 57.482 32.000 0.00 0.00 0.00 3.25
57 58 6.403866 TTGTTATGAGATGTTTTTGCTGGT 57.596 33.333 0.00 0.00 0.00 4.00
58 59 6.869913 ACATTGTTATGAGATGTTTTTGCTGG 59.130 34.615 0.00 0.00 35.65 4.85
59 60 7.878477 ACATTGTTATGAGATGTTTTTGCTG 57.122 32.000 0.00 0.00 35.65 4.41
60 61 8.362639 AGAACATTGTTATGAGATGTTTTTGCT 58.637 29.630 1.15 0.00 42.31 3.91
61 62 8.524870 AGAACATTGTTATGAGATGTTTTTGC 57.475 30.769 1.15 0.00 42.31 3.68
63 64 9.846248 GCTAGAACATTGTTATGAGATGTTTTT 57.154 29.630 6.92 0.00 42.31 1.94
64 65 8.177663 CGCTAGAACATTGTTATGAGATGTTTT 58.822 33.333 6.92 0.72 42.31 2.43
65 66 7.677276 GCGCTAGAACATTGTTATGAGATGTTT 60.677 37.037 6.92 0.00 42.31 2.83
66 67 6.238211 GCGCTAGAACATTGTTATGAGATGTT 60.238 38.462 6.92 1.00 44.25 2.71
67 68 5.235186 GCGCTAGAACATTGTTATGAGATGT 59.765 40.000 6.92 0.00 35.65 3.06
68 69 5.333645 GGCGCTAGAACATTGTTATGAGATG 60.334 44.000 7.64 1.65 35.65 2.90
69 70 4.752101 GGCGCTAGAACATTGTTATGAGAT 59.248 41.667 7.64 0.00 35.65 2.75
70 71 4.119862 GGCGCTAGAACATTGTTATGAGA 58.880 43.478 7.64 0.00 35.65 3.27
71 72 3.871006 TGGCGCTAGAACATTGTTATGAG 59.129 43.478 7.64 4.16 35.65 2.90
72 73 3.867857 TGGCGCTAGAACATTGTTATGA 58.132 40.909 7.64 0.00 35.65 2.15
73 74 4.530388 CATGGCGCTAGAACATTGTTATG 58.470 43.478 7.64 0.00 37.79 1.90
74 75 3.003689 GCATGGCGCTAGAACATTGTTAT 59.996 43.478 7.64 1.53 37.77 1.89
75 76 2.354510 GCATGGCGCTAGAACATTGTTA 59.645 45.455 7.64 0.00 37.77 2.41
76 77 1.133025 GCATGGCGCTAGAACATTGTT 59.867 47.619 7.64 0.63 37.77 2.83
77 78 0.734889 GCATGGCGCTAGAACATTGT 59.265 50.000 7.64 0.00 37.77 2.71
78 79 0.029834 GGCATGGCGCTAGAACATTG 59.970 55.000 7.64 0.00 41.91 2.82
79 80 0.394216 TGGCATGGCGCTAGAACATT 60.394 50.000 15.27 0.00 41.91 2.71
80 81 0.394216 TTGGCATGGCGCTAGAACAT 60.394 50.000 15.27 0.00 41.91 2.71
81 82 0.607762 TTTGGCATGGCGCTAGAACA 60.608 50.000 15.27 0.00 41.91 3.18
82 83 0.740737 ATTTGGCATGGCGCTAGAAC 59.259 50.000 15.27 0.00 41.91 3.01
83 84 0.740149 CATTTGGCATGGCGCTAGAA 59.260 50.000 15.27 0.00 41.91 2.10
84 85 0.394216 ACATTTGGCATGGCGCTAGA 60.394 50.000 15.27 0.00 41.91 2.43
85 86 0.029834 GACATTTGGCATGGCGCTAG 59.970 55.000 15.27 7.36 41.91 3.42
86 87 1.383456 GGACATTTGGCATGGCGCTA 61.383 55.000 15.27 0.00 41.91 4.26
87 88 2.713967 GGACATTTGGCATGGCGCT 61.714 57.895 15.27 0.00 41.91 5.92
88 89 2.202783 GGACATTTGGCATGGCGC 60.203 61.111 15.27 0.00 41.28 6.53
89 90 0.176219 ATTGGACATTTGGCATGGCG 59.824 50.000 15.27 2.39 0.00 5.69
90 91 2.011222 CAATTGGACATTTGGCATGGC 58.989 47.619 13.29 13.29 0.00 4.40
91 92 3.613494 TCAATTGGACATTTGGCATGG 57.387 42.857 5.42 0.00 0.00 3.66
92 93 4.998672 ACTTTCAATTGGACATTTGGCATG 59.001 37.500 5.42 0.00 0.00 4.06
93 94 5.231702 ACTTTCAATTGGACATTTGGCAT 57.768 34.783 5.42 0.00 0.00 4.40
94 95 4.686191 ACTTTCAATTGGACATTTGGCA 57.314 36.364 5.42 0.00 0.00 4.92
95 96 5.516339 CGATACTTTCAATTGGACATTTGGC 59.484 40.000 5.42 0.00 0.00 4.52
96 97 6.527722 CACGATACTTTCAATTGGACATTTGG 59.472 38.462 5.42 0.00 0.00 3.28
97 98 7.083858 ACACGATACTTTCAATTGGACATTTG 58.916 34.615 5.42 1.59 0.00 2.32
98 99 7.214467 ACACGATACTTTCAATTGGACATTT 57.786 32.000 5.42 0.00 0.00 2.32
99 100 6.817765 ACACGATACTTTCAATTGGACATT 57.182 33.333 5.42 0.00 0.00 2.71
100 101 8.506168 AATACACGATACTTTCAATTGGACAT 57.494 30.769 5.42 0.00 0.00 3.06
101 102 7.915293 AATACACGATACTTTCAATTGGACA 57.085 32.000 5.42 0.00 0.00 4.02
102 103 9.095065 AGTAATACACGATACTTTCAATTGGAC 57.905 33.333 5.42 0.00 0.00 4.02
111 112 8.937207 AGGGAGATAGTAATACACGATACTTT 57.063 34.615 0.00 0.00 34.37 2.66
182 183 8.043113 TCTATACTGCATGTCTTTTGTGAGAAT 58.957 33.333 0.00 0.00 0.00 2.40
188 189 9.502091 TTTAACTCTATACTGCATGTCTTTTGT 57.498 29.630 0.00 0.00 0.00 2.83
238 239 8.927675 TCCATAATAAGTGTTGTGGTTTTAGT 57.072 30.769 4.02 0.00 40.20 2.24
239 240 9.620660 GTTCCATAATAAGTGTTGTGGTTTTAG 57.379 33.333 4.02 0.00 40.20 1.85
240 241 9.132923 TGTTCCATAATAAGTGTTGTGGTTTTA 57.867 29.630 4.02 0.00 40.20 1.52
276 280 3.009723 CCATGGCCTGTAGTGTGTTAAG 58.990 50.000 3.32 0.00 0.00 1.85
285 289 1.065199 TCTTTGAGCCATGGCCTGTAG 60.065 52.381 33.14 23.38 43.17 2.74
373 502 8.801299 TGTATCCACTTGATGCTTCATTTTAAA 58.199 29.630 2.75 0.00 37.04 1.52
408 537 1.091197 GTTCGGTCGGGTGTGTGTTT 61.091 55.000 0.00 0.00 0.00 2.83
417 546 1.935300 GCTATGCATAGTTCGGTCGGG 60.935 57.143 29.62 6.73 32.96 5.14
422 551 4.727507 ATCCTAGCTATGCATAGTTCGG 57.272 45.455 29.62 27.71 30.83 4.30
423 552 6.030849 GTGTATCCTAGCTATGCATAGTTCG 58.969 44.000 29.62 21.32 32.96 3.95
465 598 0.236187 TCGGTGTGTTATTTGTGCGC 59.764 50.000 0.00 0.00 0.00 6.09
483 617 2.100916 TCTCCTACGGCTGCTATTTGTC 59.899 50.000 0.00 0.00 0.00 3.18
495 629 3.604875 TTTAGCTTTGGTCTCCTACGG 57.395 47.619 0.00 0.00 0.00 4.02
552 689 9.566432 CTGATCCCTAGCTTTCAAACTATTATT 57.434 33.333 0.00 0.00 0.00 1.40
553 690 8.938883 TCTGATCCCTAGCTTTCAAACTATTAT 58.061 33.333 0.00 0.00 0.00 1.28
554 691 8.319057 TCTGATCCCTAGCTTTCAAACTATTA 57.681 34.615 0.00 0.00 0.00 0.98
634 791 1.296056 AACGAACCCGAATTGAGCCG 61.296 55.000 0.00 0.00 39.50 5.52
717 879 1.881973 TCATCACCAGAAAACAGCTGC 59.118 47.619 15.27 0.00 32.06 5.25
746 908 7.101652 TCTTAAGACTTGTGTAGCTATCTGG 57.898 40.000 0.00 0.00 0.00 3.86
873 1036 2.874019 CATACGCAGGCGCCAAAA 59.126 55.556 31.54 9.48 44.19 2.44
893 1056 2.996621 GCTAGCTCGCACCAATTATAGG 59.003 50.000 7.70 0.00 0.00 2.57
940 1103 4.134563 TCTGTGTACCTTTTCTTTCTGCC 58.865 43.478 0.00 0.00 0.00 4.85
953 1118 1.566018 GCGTGTTGGCTCTGTGTACC 61.566 60.000 0.00 0.00 0.00 3.34
1021 1194 2.962786 CGTCGGCACCACGTTCAA 60.963 61.111 0.00 0.00 34.94 2.69
1041 1214 0.464193 TGATCATGCCCATCACCGTG 60.464 55.000 0.00 0.00 0.00 4.94
1126 1299 1.153086 GGATGGCTCGGAACTGCAT 60.153 57.895 0.00 0.00 0.00 3.96
1248 1421 1.184970 TGACGGACTGCTGGATGACA 61.185 55.000 0.00 0.00 0.00 3.58
1602 1796 4.664392 TCTTAAGACGGAAGAACTCCTCT 58.336 43.478 0.00 0.00 42.85 3.69
1680 1874 3.073101 ACCTTCTCCCCGGCGTAC 61.073 66.667 6.01 0.00 0.00 3.67
1764 1958 3.881019 TTCGTCCCTCTGGCCGTCT 62.881 63.158 0.00 0.00 0.00 4.18
1795 1989 1.270358 GCTTCCGGATCAGGTGTATCC 60.270 57.143 4.15 0.00 39.71 2.59
1922 2130 9.807921 GACAAATATTTAGGAATGGAGGGAATA 57.192 33.333 0.00 0.00 0.00 1.75
1923 2131 8.514504 AGACAAATATTTAGGAATGGAGGGAAT 58.485 33.333 0.00 0.00 0.00 3.01
1924 2132 7.882755 AGACAAATATTTAGGAATGGAGGGAA 58.117 34.615 0.00 0.00 0.00 3.97
1925 2133 7.465900 AGACAAATATTTAGGAATGGAGGGA 57.534 36.000 0.00 0.00 0.00 4.20
1926 2134 8.539117 AAAGACAAATATTTAGGAATGGAGGG 57.461 34.615 0.00 0.00 0.00 4.30
1927 2135 9.413734 AGAAAGACAAATATTTAGGAATGGAGG 57.586 33.333 0.00 0.00 0.00 4.30
1943 2151 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
1944 2152 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
1945 2153 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
1946 2154 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
1947 2155 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
1948 2156 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
1949 2157 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
1950 2158 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
1951 2159 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
1952 2160 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
1953 2161 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
1954 2162 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
1955 2163 7.541091 TCGTATGTAGTCACTTGTTGAAATCTC 59.459 37.037 0.00 0.00 35.39 2.75
1956 2164 7.375834 TCGTATGTAGTCACTTGTTGAAATCT 58.624 34.615 0.00 0.00 35.39 2.40
1957 2165 7.576750 TCGTATGTAGTCACTTGTTGAAATC 57.423 36.000 0.00 0.00 35.39 2.17
1958 2166 7.656137 ACTTCGTATGTAGTCACTTGTTGAAAT 59.344 33.333 0.00 0.00 35.39 2.17
1959 2167 6.982141 ACTTCGTATGTAGTCACTTGTTGAAA 59.018 34.615 0.00 0.00 35.39 2.69
1960 2168 6.509656 ACTTCGTATGTAGTCACTTGTTGAA 58.490 36.000 0.00 0.00 35.39 2.69
1961 2169 6.080648 ACTTCGTATGTAGTCACTTGTTGA 57.919 37.500 0.00 0.00 0.00 3.18
1962 2170 7.862741 TTACTTCGTATGTAGTCACTTGTTG 57.137 36.000 0.00 0.00 0.00 3.33
1963 2171 8.876275 TTTTACTTCGTATGTAGTCACTTGTT 57.124 30.769 0.00 0.00 0.00 2.83
1964 2172 8.922676 CATTTTACTTCGTATGTAGTCACTTGT 58.077 33.333 0.00 0.00 0.00 3.16
1965 2173 9.135843 TCATTTTACTTCGTATGTAGTCACTTG 57.864 33.333 0.00 0.00 0.00 3.16
1966 2174 9.355215 CTCATTTTACTTCGTATGTAGTCACTT 57.645 33.333 0.00 0.00 0.00 3.16
1967 2175 8.521176 ACTCATTTTACTTCGTATGTAGTCACT 58.479 33.333 0.00 0.00 0.00 3.41
1968 2176 8.584600 CACTCATTTTACTTCGTATGTAGTCAC 58.415 37.037 0.00 0.00 0.00 3.67
1969 2177 8.517056 TCACTCATTTTACTTCGTATGTAGTCA 58.483 33.333 0.00 0.00 0.00 3.41
1970 2178 8.906636 TCACTCATTTTACTTCGTATGTAGTC 57.093 34.615 0.00 0.00 0.00 2.59
1971 2179 9.871238 ATTCACTCATTTTACTTCGTATGTAGT 57.129 29.630 0.00 0.00 0.00 2.73
1978 2186 9.436957 AATGTAGATTCACTCATTTTACTTCGT 57.563 29.630 0.00 0.00 0.00 3.85
1979 2187 9.907576 GAATGTAGATTCACTCATTTTACTTCG 57.092 33.333 7.69 0.00 38.33 3.79
2013 2221 9.511272 ACTACAATATACGGATGTATGTAGACA 57.489 33.333 24.44 0.00 40.69 3.41
2014 2222 9.985318 GACTACAATATACGGATGTATGTAGAC 57.015 37.037 24.44 18.37 40.69 2.59
2015 2223 9.170734 GGACTACAATATACGGATGTATGTAGA 57.829 37.037 24.44 2.20 40.69 2.59
2016 2224 8.953313 TGGACTACAATATACGGATGTATGTAG 58.047 37.037 19.56 19.56 42.27 2.74
2017 2225 8.866970 TGGACTACAATATACGGATGTATGTA 57.133 34.615 0.00 0.00 41.37 2.29
2018 2226 7.770366 TGGACTACAATATACGGATGTATGT 57.230 36.000 0.00 0.00 41.37 2.29
2019 2227 9.653287 AAATGGACTACAATATACGGATGTATG 57.347 33.333 0.00 0.00 41.37 2.39
2020 2228 9.653287 CAAATGGACTACAATATACGGATGTAT 57.347 33.333 0.00 0.00 43.62 2.29
2021 2229 8.862085 TCAAATGGACTACAATATACGGATGTA 58.138 33.333 0.00 0.00 34.45 2.29
2022 2230 7.732025 TCAAATGGACTACAATATACGGATGT 58.268 34.615 0.00 0.00 0.00 3.06
2023 2231 8.601845 TTCAAATGGACTACAATATACGGATG 57.398 34.615 0.00 0.00 0.00 3.51
2024 2232 9.219603 CATTCAAATGGACTACAATATACGGAT 57.780 33.333 0.00 0.00 32.78 4.18
2025 2233 8.208224 ACATTCAAATGGACTACAATATACGGA 58.792 33.333 7.58 0.00 40.70 4.69
2026 2234 8.378172 ACATTCAAATGGACTACAATATACGG 57.622 34.615 7.58 0.00 40.70 4.02
2027 2235 9.261180 AGACATTCAAATGGACTACAATATACG 57.739 33.333 7.58 0.00 40.70 3.06
2032 2240 9.739276 TTTCTAGACATTCAAATGGACTACAAT 57.261 29.630 7.58 0.00 40.70 2.71
2033 2241 9.219603 CTTTCTAGACATTCAAATGGACTACAA 57.780 33.333 7.58 3.08 40.70 2.41
2034 2242 8.593679 TCTTTCTAGACATTCAAATGGACTACA 58.406 33.333 7.58 0.00 40.70 2.74
2051 2259 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2052 2260 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2053 2261 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2054 2262 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2055 2263 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2056 2264 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2057 2265 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2058 2266 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2059 2267 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2060 2268 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2061 2269 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2062 2270 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2063 2271 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
2064 2272 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
2065 2273 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
2066 2274 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
2067 2275 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
2068 2276 3.011032 ACTTCTACTCCCTCCGTTCCTAA 59.989 47.826 0.00 0.00 0.00 2.69
2069 2277 2.579860 ACTTCTACTCCCTCCGTTCCTA 59.420 50.000 0.00 0.00 0.00 2.94
2070 2278 1.358445 ACTTCTACTCCCTCCGTTCCT 59.642 52.381 0.00 0.00 0.00 3.36
2071 2279 1.849977 ACTTCTACTCCCTCCGTTCC 58.150 55.000 0.00 0.00 0.00 3.62
2072 2280 2.674462 GCAACTTCTACTCCCTCCGTTC 60.674 54.545 0.00 0.00 0.00 3.95
2073 2281 1.275573 GCAACTTCTACTCCCTCCGTT 59.724 52.381 0.00 0.00 0.00 4.44
2074 2282 0.896226 GCAACTTCTACTCCCTCCGT 59.104 55.000 0.00 0.00 0.00 4.69
2075 2283 0.179134 CGCAACTTCTACTCCCTCCG 60.179 60.000 0.00 0.00 0.00 4.63
2076 2284 0.460459 GCGCAACTTCTACTCCCTCC 60.460 60.000 0.30 0.00 0.00 4.30
2077 2285 0.802607 CGCGCAACTTCTACTCCCTC 60.803 60.000 8.75 0.00 0.00 4.30
2078 2286 1.215647 CGCGCAACTTCTACTCCCT 59.784 57.895 8.75 0.00 0.00 4.20
2079 2287 1.810030 CCGCGCAACTTCTACTCCC 60.810 63.158 8.75 0.00 0.00 4.30
2080 2288 0.669625 AACCGCGCAACTTCTACTCC 60.670 55.000 8.75 0.00 0.00 3.85
2081 2289 0.714439 GAACCGCGCAACTTCTACTC 59.286 55.000 8.75 0.00 0.00 2.59
2082 2290 0.032952 TGAACCGCGCAACTTCTACT 59.967 50.000 8.75 0.00 0.00 2.57
2083 2291 1.076332 ATGAACCGCGCAACTTCTAC 58.924 50.000 8.75 0.00 0.00 2.59
2155 2363 4.629115 GTTGCGTGCAGTGTGGCC 62.629 66.667 0.00 0.00 0.00 5.36
2157 2365 3.208383 TGGTTGCGTGCAGTGTGG 61.208 61.111 0.00 0.00 0.00 4.17
2281 2491 0.986019 AGACTTGGGTGGGTGTGTGA 60.986 55.000 0.00 0.00 0.00 3.58
2325 2539 0.250640 CTTGTTGAGCTGTGCCCTCT 60.251 55.000 0.00 0.00 0.00 3.69
2382 2600 0.032017 TCCAGACTAGGGGCTTCCTC 60.032 60.000 2.51 0.00 44.06 3.71
2391 2609 2.565645 CCGCCGGATCCAGACTAGG 61.566 68.421 13.41 4.55 0.00 3.02
2437 2655 4.514577 CTCCGCTCGATGGCCGTT 62.515 66.667 0.00 0.00 39.75 4.44
2617 2837 1.765074 GTGGCTTGAGGTTGGGGTA 59.235 57.895 0.00 0.00 0.00 3.69
2653 2873 3.636231 CTCCAGTTGTCCCCCGCA 61.636 66.667 0.00 0.00 0.00 5.69
2734 2954 0.111253 CTGCCCAGTTCCTTTGGAGT 59.889 55.000 0.00 0.00 37.96 3.85


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

AutoCloner maintained by Alex Coulton.