Multiple sequence alignment - TraesCS1D01G003100

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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 TraesCS1D01G003100 chr1D 100.000 2862 0 0 1 2862 828734 831595 0.000000e+00 5286
1 TraesCS1D01G003100 chr1D 86.817 2215 161 54 206 2337 335412171 335414337 0.000000e+00 2351
2 TraesCS1D01G003100 chr1D 99.238 525 4 0 2338 2862 468544018 468543494 0.000000e+00 948
3 TraesCS1D01G003100 chr1D 98.866 529 6 0 2334 2862 372573393 372573921 0.000000e+00 944
4 TraesCS1D01G003100 chr1D 84.564 907 79 27 206 1079 444898365 444899243 0.000000e+00 843
5 TraesCS1D01G003100 chr1D 92.667 150 11 0 206 355 848646 848497 1.730000e-52 217
6 TraesCS1D01G003100 chr5B 92.564 2165 113 21 206 2340 708182153 708180007 0.000000e+00 3062
7 TraesCS1D01G003100 chr5B 88.330 2168 120 53 206 2336 498513971 498516042 0.000000e+00 2479
8 TraesCS1D01G003100 chr5D 92.220 1928 97 16 199 2089 274114120 274116031 0.000000e+00 2680
9 TraesCS1D01G003100 chr5D 87.398 2079 127 47 209 2176 459925475 459923421 0.000000e+00 2263
10 TraesCS1D01G003100 chr5D 86.463 1869 137 49 206 1978 408555343 408553495 0.000000e+00 1943
11 TraesCS1D01G003100 chr5D 99.429 525 3 0 2338 2862 472423697 472423173 0.000000e+00 953
12 TraesCS1D01G003100 chr3D 91.021 1949 92 26 207 2089 502048028 502046097 0.000000e+00 2553
13 TraesCS1D01G003100 chr3D 99.240 526 4 0 2337 2862 57195825 57196350 0.000000e+00 950
14 TraesCS1D01G003100 chr3D 99.240 526 4 0 2337 2862 569853801 569854326 0.000000e+00 950
15 TraesCS1D01G003100 chr3D 98.868 530 6 0 2333 2862 614960652 614960123 0.000000e+00 946
16 TraesCS1D01G003100 chr3D 91.447 152 13 0 204 355 45053013 45053164 2.890000e-50 209
17 TraesCS1D01G003100 chr3B 89.468 1918 138 41 206 2089 638378127 638380014 0.000000e+00 2364
18 TraesCS1D01G003100 chr3B 92.667 150 11 0 206 355 610168921 610168772 1.730000e-52 217
19 TraesCS1D01G003100 chr6B 87.116 2181 160 62 227 2324 12465849 12467991 0.000000e+00 2359
20 TraesCS1D01G003100 chr2B 85.233 2228 157 80 227 2324 748926910 748924725 0.000000e+00 2134
21 TraesCS1D01G003100 chr2B 90.455 1100 57 23 1242 2337 80094009 80092954 0.000000e+00 1406
22 TraesCS1D01G003100 chr2B 87.552 964 72 30 294 1245 80103468 80102541 0.000000e+00 1072
23 TraesCS1D01G003100 chr6D 87.357 1922 144 41 204 2089 63805763 63807621 0.000000e+00 2111
24 TraesCS1D01G003100 chr6D 99.238 525 4 0 2338 2862 456365320 456364796 0.000000e+00 948
25 TraesCS1D01G003100 chr6D 91.275 149 13 0 206 354 24260311 24260163 1.340000e-48 204
26 TraesCS1D01G003100 chr7B 86.459 1861 159 41 548 2340 53112094 53110259 0.000000e+00 1954
27 TraesCS1D01G003100 chr7B 86.966 1757 144 36 564 2254 648430036 648428299 0.000000e+00 1897
28 TraesCS1D01G003100 chrUn 93.385 907 43 9 1192 2089 97175473 97176371 0.000000e+00 1327
29 TraesCS1D01G003100 chrUn 90.373 966 46 8 205 1130 97254874 97255832 0.000000e+00 1225
30 TraesCS1D01G003100 chrUn 90.062 966 48 10 205 1130 97174531 97175488 0.000000e+00 1208
31 TraesCS1D01G003100 chrUn 91.333 150 13 0 206 355 70151421 70151570 3.740000e-49 206
32 TraesCS1D01G003100 chr4B 88.191 940 70 31 206 1119 37138129 37139053 0.000000e+00 1083
33 TraesCS1D01G003100 chr1B 86.727 1002 81 17 206 1180 572992371 572991395 0.000000e+00 1066
34 TraesCS1D01G003100 chr1B 89.262 596 33 13 1755 2324 168421677 168422267 0.000000e+00 717
35 TraesCS1D01G003100 chr1B 91.489 188 7 3 4 184 4836792 4836607 1.700000e-62 250
36 TraesCS1D01G003100 chr4A 90.617 778 41 11 208 957 708367214 708366441 0.000000e+00 1003
37 TraesCS1D01G003100 chr4A 85.106 235 12 7 205 416 702241039 702241273 4.800000e-53 219
38 TraesCS1D01G003100 chr2D 99.049 526 5 0 2337 2862 6798929 6799454 0.000000e+00 944
39 TraesCS1D01G003100 chr2D 98.859 526 6 0 2337 2862 609280859 609280334 0.000000e+00 939
40 TraesCS1D01G003100 chr7D 84.666 913 81 19 206 1079 393113868 393112976 0.000000e+00 856
41 TraesCS1D01G003100 chr4D 91.166 283 14 4 2060 2340 97479359 97479086 9.680000e-100 374


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 TraesCS1D01G003100 chr1D 828734 831595 2861 False 5286.0 5286 100.0000 1 2862 1 chr1D.!!$F1 2861
1 TraesCS1D01G003100 chr1D 335412171 335414337 2166 False 2351.0 2351 86.8170 206 2337 1 chr1D.!!$F2 2131
2 TraesCS1D01G003100 chr1D 468543494 468544018 524 True 948.0 948 99.2380 2338 2862 1 chr1D.!!$R2 524
3 TraesCS1D01G003100 chr1D 372573393 372573921 528 False 944.0 944 98.8660 2334 2862 1 chr1D.!!$F3 528
4 TraesCS1D01G003100 chr1D 444898365 444899243 878 False 843.0 843 84.5640 206 1079 1 chr1D.!!$F4 873
5 TraesCS1D01G003100 chr5B 708180007 708182153 2146 True 3062.0 3062 92.5640 206 2340 1 chr5B.!!$R1 2134
6 TraesCS1D01G003100 chr5B 498513971 498516042 2071 False 2479.0 2479 88.3300 206 2336 1 chr5B.!!$F1 2130
7 TraesCS1D01G003100 chr5D 274114120 274116031 1911 False 2680.0 2680 92.2200 199 2089 1 chr5D.!!$F1 1890
8 TraesCS1D01G003100 chr5D 459923421 459925475 2054 True 2263.0 2263 87.3980 209 2176 1 chr5D.!!$R2 1967
9 TraesCS1D01G003100 chr5D 408553495 408555343 1848 True 1943.0 1943 86.4630 206 1978 1 chr5D.!!$R1 1772
10 TraesCS1D01G003100 chr5D 472423173 472423697 524 True 953.0 953 99.4290 2338 2862 1 chr5D.!!$R3 524
11 TraesCS1D01G003100 chr3D 502046097 502048028 1931 True 2553.0 2553 91.0210 207 2089 1 chr3D.!!$R1 1882
12 TraesCS1D01G003100 chr3D 57195825 57196350 525 False 950.0 950 99.2400 2337 2862 1 chr3D.!!$F2 525
13 TraesCS1D01G003100 chr3D 569853801 569854326 525 False 950.0 950 99.2400 2337 2862 1 chr3D.!!$F3 525
14 TraesCS1D01G003100 chr3D 614960123 614960652 529 True 946.0 946 98.8680 2333 2862 1 chr3D.!!$R2 529
15 TraesCS1D01G003100 chr3B 638378127 638380014 1887 False 2364.0 2364 89.4680 206 2089 1 chr3B.!!$F1 1883
16 TraesCS1D01G003100 chr6B 12465849 12467991 2142 False 2359.0 2359 87.1160 227 2324 1 chr6B.!!$F1 2097
17 TraesCS1D01G003100 chr2B 748924725 748926910 2185 True 2134.0 2134 85.2330 227 2324 1 chr2B.!!$R3 2097
18 TraesCS1D01G003100 chr2B 80092954 80094009 1055 True 1406.0 1406 90.4550 1242 2337 1 chr2B.!!$R1 1095
19 TraesCS1D01G003100 chr2B 80102541 80103468 927 True 1072.0 1072 87.5520 294 1245 1 chr2B.!!$R2 951
20 TraesCS1D01G003100 chr6D 63805763 63807621 1858 False 2111.0 2111 87.3570 204 2089 1 chr6D.!!$F1 1885
21 TraesCS1D01G003100 chr6D 456364796 456365320 524 True 948.0 948 99.2380 2338 2862 1 chr6D.!!$R2 524
22 TraesCS1D01G003100 chr7B 53110259 53112094 1835 True 1954.0 1954 86.4590 548 2340 1 chr7B.!!$R1 1792
23 TraesCS1D01G003100 chr7B 648428299 648430036 1737 True 1897.0 1897 86.9660 564 2254 1 chr7B.!!$R2 1690
24 TraesCS1D01G003100 chrUn 97174531 97176371 1840 False 1267.5 1327 91.7235 205 2089 2 chrUn.!!$F3 1884
25 TraesCS1D01G003100 chrUn 97254874 97255832 958 False 1225.0 1225 90.3730 205 1130 1 chrUn.!!$F2 925
26 TraesCS1D01G003100 chr4B 37138129 37139053 924 False 1083.0 1083 88.1910 206 1119 1 chr4B.!!$F1 913
27 TraesCS1D01G003100 chr1B 572991395 572992371 976 True 1066.0 1066 86.7270 206 1180 1 chr1B.!!$R2 974
28 TraesCS1D01G003100 chr1B 168421677 168422267 590 False 717.0 717 89.2620 1755 2324 1 chr1B.!!$F1 569
29 TraesCS1D01G003100 chr4A 708366441 708367214 773 True 1003.0 1003 90.6170 208 957 1 chr4A.!!$R1 749
30 TraesCS1D01G003100 chr2D 6798929 6799454 525 False 944.0 944 99.0490 2337 2862 1 chr2D.!!$F1 525
31 TraesCS1D01G003100 chr2D 609280334 609280859 525 True 939.0 939 98.8590 2337 2862 1 chr2D.!!$R1 525
32 TraesCS1D01G003100 chr7D 393112976 393113868 892 True 856.0 856 84.6660 206 1079 1 chr7D.!!$R1 873

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
185 186 0.249120 TGTTATCTGGACCACTGCGG 59.751 55.000 0.00 0.0 42.50 5.69 F
603 706 1.004918 ACAAGGAAACGAGCTCCGG 60.005 57.895 8.47 0.0 43.93 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1048 1244 0.995024 ACTGGGCAGCCATAGAAACT 59.005 50.000 15.19 0.0 0.0 2.66 R
2219 2643 1.002134 GACAGTGGTGGATGGGGTG 60.002 63.158 0.00 0.0 0.0 4.61 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
25 26 7.849496 CAGTCTCTTATGCATCATTAGTTGAC 58.151 38.462 0.19 9.66 37.11 3.18
26 27 7.493645 CAGTCTCTTATGCATCATTAGTTGACA 59.506 37.037 0.19 0.00 37.11 3.58
27 28 8.209584 AGTCTCTTATGCATCATTAGTTGACAT 58.790 33.333 0.19 0.00 37.11 3.06
28 29 8.281194 GTCTCTTATGCATCATTAGTTGACATG 58.719 37.037 0.19 0.00 37.11 3.21
29 30 7.989170 TCTCTTATGCATCATTAGTTGACATGT 59.011 33.333 0.19 0.00 37.11 3.21
30 31 8.146479 TCTTATGCATCATTAGTTGACATGTC 57.854 34.615 19.27 19.27 37.11 3.06
31 32 7.989170 TCTTATGCATCATTAGTTGACATGTCT 59.011 33.333 25.55 9.24 37.11 3.41
32 33 6.615264 ATGCATCATTAGTTGACATGTCTC 57.385 37.500 25.55 17.86 37.11 3.36
33 34 5.490159 TGCATCATTAGTTGACATGTCTCA 58.510 37.500 25.55 10.52 37.11 3.27
34 35 6.117488 TGCATCATTAGTTGACATGTCTCAT 58.883 36.000 25.55 13.61 37.11 2.90
35 36 7.274447 TGCATCATTAGTTGACATGTCTCATA 58.726 34.615 25.55 12.68 37.11 2.15
36 37 7.769970 TGCATCATTAGTTGACATGTCTCATAA 59.230 33.333 25.55 19.36 37.11 1.90
37 38 8.781196 GCATCATTAGTTGACATGTCTCATAAT 58.219 33.333 25.55 20.46 37.11 1.28
40 41 9.889128 TCATTAGTTGACATGTCTCATAATCAA 57.111 29.630 25.55 7.74 0.00 2.57
45 46 9.107177 AGTTGACATGTCTCATAATCAAATCTC 57.893 33.333 25.55 0.00 0.00 2.75
46 47 8.341173 GTTGACATGTCTCATAATCAAATCTCC 58.659 37.037 25.55 0.00 0.00 3.71
47 48 6.703165 TGACATGTCTCATAATCAAATCTCCG 59.297 38.462 25.55 0.00 0.00 4.63
48 49 5.994054 ACATGTCTCATAATCAAATCTCCGG 59.006 40.000 0.00 0.00 0.00 5.14
49 50 4.960938 TGTCTCATAATCAAATCTCCGGG 58.039 43.478 0.00 0.00 0.00 5.73
50 51 4.653801 TGTCTCATAATCAAATCTCCGGGA 59.346 41.667 0.00 0.00 0.00 5.14
51 52 5.130311 TGTCTCATAATCAAATCTCCGGGAA 59.870 40.000 0.00 0.00 0.00 3.97
52 53 5.467063 GTCTCATAATCAAATCTCCGGGAAC 59.533 44.000 0.00 0.00 0.00 3.62
53 54 5.366768 TCTCATAATCAAATCTCCGGGAACT 59.633 40.000 0.00 0.00 0.00 3.01
54 55 6.001449 TCATAATCAAATCTCCGGGAACTT 57.999 37.500 0.00 0.00 0.00 2.66
55 56 5.822519 TCATAATCAAATCTCCGGGAACTTG 59.177 40.000 0.00 6.69 0.00 3.16
56 57 1.821216 TCAAATCTCCGGGAACTTGC 58.179 50.000 0.00 0.00 0.00 4.01
57 58 0.811281 CAAATCTCCGGGAACTTGCC 59.189 55.000 0.00 0.00 0.00 4.52
58 59 0.404040 AAATCTCCGGGAACTTGCCA 59.596 50.000 0.00 0.00 0.00 4.92
59 60 0.404040 AATCTCCGGGAACTTGCCAA 59.596 50.000 0.00 0.00 0.00 4.52
60 61 0.322546 ATCTCCGGGAACTTGCCAAC 60.323 55.000 0.00 0.00 0.00 3.77
61 62 1.228124 CTCCGGGAACTTGCCAACA 60.228 57.895 0.00 0.00 0.00 3.33
62 63 0.821711 CTCCGGGAACTTGCCAACAA 60.822 55.000 0.00 0.00 0.00 2.83
63 64 0.395862 TCCGGGAACTTGCCAACAAA 60.396 50.000 0.00 0.00 34.74 2.83
64 65 0.461961 CCGGGAACTTGCCAACAAAA 59.538 50.000 0.00 0.00 34.74 2.44
65 66 1.134670 CCGGGAACTTGCCAACAAAAA 60.135 47.619 0.00 0.00 34.74 1.94
66 67 2.484594 CCGGGAACTTGCCAACAAAAAT 60.485 45.455 0.00 0.00 34.74 1.82
67 68 3.202097 CGGGAACTTGCCAACAAAAATT 58.798 40.909 0.00 0.00 34.74 1.82
68 69 3.002144 CGGGAACTTGCCAACAAAAATTG 59.998 43.478 0.00 0.00 34.74 2.32
69 70 4.195416 GGGAACTTGCCAACAAAAATTGA 58.805 39.130 0.00 0.00 34.74 2.57
70 71 4.637977 GGGAACTTGCCAACAAAAATTGAA 59.362 37.500 0.00 0.00 34.74 2.69
71 72 5.220835 GGGAACTTGCCAACAAAAATTGAAG 60.221 40.000 0.00 0.00 34.74 3.02
72 73 4.880886 ACTTGCCAACAAAAATTGAAGC 57.119 36.364 0.00 0.00 34.74 3.86
73 74 4.260170 ACTTGCCAACAAAAATTGAAGCA 58.740 34.783 0.00 0.59 34.74 3.91
74 75 4.699257 ACTTGCCAACAAAAATTGAAGCAA 59.301 33.333 13.82 13.82 39.31 3.91
75 76 5.357596 ACTTGCCAACAAAAATTGAAGCAAT 59.642 32.000 14.45 0.00 40.08 3.56
76 77 5.171147 TGCCAACAAAAATTGAAGCAATG 57.829 34.783 0.00 0.00 34.04 2.82
77 78 4.880120 TGCCAACAAAAATTGAAGCAATGA 59.120 33.333 0.00 0.00 34.04 2.57
78 79 5.207033 GCCAACAAAAATTGAAGCAATGAC 58.793 37.500 0.00 0.00 34.04 3.06
79 80 5.220815 GCCAACAAAAATTGAAGCAATGACA 60.221 36.000 0.00 0.00 34.04 3.58
80 81 6.513720 GCCAACAAAAATTGAAGCAATGACAT 60.514 34.615 0.00 0.00 34.04 3.06
81 82 6.853872 CCAACAAAAATTGAAGCAATGACATG 59.146 34.615 0.00 0.00 34.04 3.21
82 83 6.548441 ACAAAAATTGAAGCAATGACATGG 57.452 33.333 0.00 0.00 34.04 3.66
83 84 6.289834 ACAAAAATTGAAGCAATGACATGGA 58.710 32.000 0.00 0.00 34.04 3.41
84 85 6.766944 ACAAAAATTGAAGCAATGACATGGAA 59.233 30.769 0.00 0.00 34.04 3.53
85 86 7.282675 ACAAAAATTGAAGCAATGACATGGAAA 59.717 29.630 0.00 0.00 34.04 3.13
86 87 7.429636 AAAATTGAAGCAATGACATGGAAAG 57.570 32.000 0.00 0.00 34.04 2.62
87 88 5.988310 ATTGAAGCAATGACATGGAAAGA 57.012 34.783 0.00 0.00 32.39 2.52
88 89 5.787953 TTGAAGCAATGACATGGAAAGAA 57.212 34.783 0.00 0.00 0.00 2.52
89 90 5.125100 TGAAGCAATGACATGGAAAGAAC 57.875 39.130 0.00 0.00 0.00 3.01
90 91 4.828939 TGAAGCAATGACATGGAAAGAACT 59.171 37.500 0.00 0.00 0.00 3.01
91 92 4.778534 AGCAATGACATGGAAAGAACTG 57.221 40.909 0.00 0.00 0.00 3.16
92 93 3.057033 AGCAATGACATGGAAAGAACTGC 60.057 43.478 0.00 0.00 0.00 4.40
93 94 3.305539 GCAATGACATGGAAAGAACTGCA 60.306 43.478 0.00 0.00 0.00 4.41
94 95 4.232221 CAATGACATGGAAAGAACTGCAC 58.768 43.478 0.00 0.00 0.00 4.57
95 96 3.213206 TGACATGGAAAGAACTGCACT 57.787 42.857 0.00 0.00 0.00 4.40
96 97 3.554934 TGACATGGAAAGAACTGCACTT 58.445 40.909 0.00 0.00 0.00 3.16
97 98 3.565482 TGACATGGAAAGAACTGCACTTC 59.435 43.478 0.00 0.00 0.00 3.01
98 99 3.554934 ACATGGAAAGAACTGCACTTCA 58.445 40.909 8.53 0.00 0.00 3.02
99 100 3.953612 ACATGGAAAGAACTGCACTTCAA 59.046 39.130 8.53 0.00 0.00 2.69
100 101 4.586001 ACATGGAAAGAACTGCACTTCAAT 59.414 37.500 8.53 0.00 0.00 2.57
101 102 5.069516 ACATGGAAAGAACTGCACTTCAATT 59.930 36.000 8.53 3.64 0.00 2.32
102 103 5.186996 TGGAAAGAACTGCACTTCAATTC 57.813 39.130 8.53 10.71 31.48 2.17
103 104 4.222114 GGAAAGAACTGCACTTCAATTCG 58.778 43.478 8.53 0.00 36.15 3.34
104 105 4.024048 GGAAAGAACTGCACTTCAATTCGA 60.024 41.667 8.53 0.00 36.15 3.71
105 106 5.499139 AAAGAACTGCACTTCAATTCGAA 57.501 34.783 0.00 0.00 36.15 3.71
106 107 4.474226 AGAACTGCACTTCAATTCGAAC 57.526 40.909 0.00 0.00 36.15 3.95
107 108 3.251004 AGAACTGCACTTCAATTCGAACC 59.749 43.478 0.00 0.00 36.15 3.62
108 109 2.571212 ACTGCACTTCAATTCGAACCA 58.429 42.857 0.00 0.00 0.00 3.67
109 110 2.549754 ACTGCACTTCAATTCGAACCAG 59.450 45.455 0.00 0.00 0.00 4.00
110 111 1.879380 TGCACTTCAATTCGAACCAGG 59.121 47.619 0.00 0.00 0.00 4.45
111 112 1.200020 GCACTTCAATTCGAACCAGGG 59.800 52.381 0.00 0.00 0.00 4.45
112 113 2.504367 CACTTCAATTCGAACCAGGGT 58.496 47.619 0.00 0.00 0.00 4.34
113 114 2.484264 CACTTCAATTCGAACCAGGGTC 59.516 50.000 0.00 0.00 0.00 4.46
114 115 2.105821 ACTTCAATTCGAACCAGGGTCA 59.894 45.455 5.03 0.00 0.00 4.02
115 116 2.940994 TCAATTCGAACCAGGGTCAA 57.059 45.000 5.03 0.00 0.00 3.18
116 117 3.433306 TCAATTCGAACCAGGGTCAAT 57.567 42.857 5.03 0.90 0.00 2.57
117 118 3.761897 TCAATTCGAACCAGGGTCAATT 58.238 40.909 5.03 7.14 0.00 2.32
118 119 3.756434 TCAATTCGAACCAGGGTCAATTC 59.244 43.478 5.03 0.00 0.00 2.17
119 120 2.194201 TTCGAACCAGGGTCAATTCC 57.806 50.000 5.03 0.00 0.00 3.01
120 121 1.060729 TCGAACCAGGGTCAATTCCA 58.939 50.000 5.03 0.00 0.00 3.53
121 122 1.422024 TCGAACCAGGGTCAATTCCAA 59.578 47.619 5.03 0.00 0.00 3.53
122 123 2.158593 TCGAACCAGGGTCAATTCCAAA 60.159 45.455 5.03 0.00 0.00 3.28
123 124 2.625790 CGAACCAGGGTCAATTCCAAAA 59.374 45.455 5.03 0.00 0.00 2.44
124 125 3.258123 CGAACCAGGGTCAATTCCAAAAT 59.742 43.478 5.03 0.00 0.00 1.82
125 126 4.262420 CGAACCAGGGTCAATTCCAAAATT 60.262 41.667 5.03 0.00 35.43 1.82
133 134 2.686235 CAATTCCAAAATTGCTCGGCA 58.314 42.857 0.00 0.00 43.78 5.69
141 142 3.667087 TTGCTCGGCAATGTCACC 58.333 55.556 7.15 0.00 43.99 4.02
142 143 1.228094 TTGCTCGGCAATGTCACCA 60.228 52.632 7.15 0.00 43.99 4.17
143 144 0.821301 TTGCTCGGCAATGTCACCAA 60.821 50.000 7.15 0.00 43.99 3.67
144 145 1.236616 TGCTCGGCAATGTCACCAAG 61.237 55.000 0.00 0.00 34.76 3.61
145 146 1.503542 CTCGGCAATGTCACCAAGC 59.496 57.895 0.00 0.00 0.00 4.01
146 147 0.957395 CTCGGCAATGTCACCAAGCT 60.957 55.000 0.00 0.00 0.00 3.74
147 148 0.537143 TCGGCAATGTCACCAAGCTT 60.537 50.000 0.00 0.00 0.00 3.74
148 149 0.387622 CGGCAATGTCACCAAGCTTG 60.388 55.000 19.93 19.93 0.00 4.01
149 150 0.961019 GGCAATGTCACCAAGCTTGA 59.039 50.000 28.05 7.69 0.00 3.02
150 151 1.336240 GGCAATGTCACCAAGCTTGAC 60.336 52.381 28.05 18.22 43.22 3.18
156 157 4.734398 TGTCACCAAGCTTGACATTTTT 57.266 36.364 28.05 0.00 46.64 1.94
157 158 4.681744 TGTCACCAAGCTTGACATTTTTC 58.318 39.130 28.05 9.59 46.64 2.29
158 159 4.402155 TGTCACCAAGCTTGACATTTTTCT 59.598 37.500 28.05 0.00 46.64 2.52
159 160 5.592282 TGTCACCAAGCTTGACATTTTTCTA 59.408 36.000 28.05 0.00 46.64 2.10
160 161 6.145535 GTCACCAAGCTTGACATTTTTCTAG 58.854 40.000 28.05 8.58 42.58 2.43
161 162 5.241506 TCACCAAGCTTGACATTTTTCTAGG 59.758 40.000 28.05 8.50 0.00 3.02
162 163 5.241506 CACCAAGCTTGACATTTTTCTAGGA 59.758 40.000 28.05 0.00 0.00 2.94
163 164 5.833131 ACCAAGCTTGACATTTTTCTAGGAA 59.167 36.000 28.05 0.00 0.00 3.36
164 165 6.152379 CCAAGCTTGACATTTTTCTAGGAAC 58.848 40.000 28.05 0.00 0.00 3.62
165 166 6.015940 CCAAGCTTGACATTTTTCTAGGAACT 60.016 38.462 28.05 0.00 46.37 3.01
166 167 7.428826 CAAGCTTGACATTTTTCTAGGAACTT 58.571 34.615 22.31 0.00 41.75 2.66
167 168 6.974965 AGCTTGACATTTTTCTAGGAACTTG 58.025 36.000 0.00 0.00 41.75 3.16
168 169 6.547510 AGCTTGACATTTTTCTAGGAACTTGT 59.452 34.615 0.00 0.00 41.75 3.16
169 170 7.068716 AGCTTGACATTTTTCTAGGAACTTGTT 59.931 33.333 0.46 0.00 41.75 2.83
170 171 8.349983 GCTTGACATTTTTCTAGGAACTTGTTA 58.650 33.333 0.46 0.00 41.75 2.41
173 174 9.793259 TGACATTTTTCTAGGAACTTGTTATCT 57.207 29.630 0.46 0.00 41.75 1.98
175 176 9.014297 ACATTTTTCTAGGAACTTGTTATCTGG 57.986 33.333 0.00 0.00 41.75 3.86
176 177 9.231297 CATTTTTCTAGGAACTTGTTATCTGGA 57.769 33.333 0.00 0.00 41.75 3.86
177 178 8.617290 TTTTTCTAGGAACTTGTTATCTGGAC 57.383 34.615 0.00 0.00 41.75 4.02
178 179 5.934402 TCTAGGAACTTGTTATCTGGACC 57.066 43.478 0.00 0.00 41.75 4.46
179 180 5.338632 TCTAGGAACTTGTTATCTGGACCA 58.661 41.667 0.00 0.00 41.75 4.02
180 181 4.287766 AGGAACTTGTTATCTGGACCAC 57.712 45.455 0.00 0.00 27.25 4.16
181 182 3.910627 AGGAACTTGTTATCTGGACCACT 59.089 43.478 0.00 0.00 27.25 4.00
182 183 4.003648 GGAACTTGTTATCTGGACCACTG 58.996 47.826 0.00 0.00 0.00 3.66
183 184 3.059352 ACTTGTTATCTGGACCACTGC 57.941 47.619 0.00 0.00 0.00 4.40
184 185 2.002586 CTTGTTATCTGGACCACTGCG 58.997 52.381 0.00 0.00 0.00 5.18
185 186 0.249120 TGTTATCTGGACCACTGCGG 59.751 55.000 0.00 0.00 42.50 5.69
186 187 1.090052 GTTATCTGGACCACTGCGGC 61.090 60.000 0.00 0.00 39.03 6.53
187 188 1.549243 TTATCTGGACCACTGCGGCA 61.549 55.000 1.29 1.29 39.03 5.69
188 189 2.238847 TATCTGGACCACTGCGGCAC 62.239 60.000 0.00 0.00 39.03 5.01
189 190 4.320456 CTGGACCACTGCGGCACT 62.320 66.667 0.00 0.00 39.03 4.40
190 191 4.624364 TGGACCACTGCGGCACTG 62.624 66.667 0.00 0.00 39.03 3.66
248 249 3.190439 AGTTTACAGGCTAGGGTTCCAT 58.810 45.455 0.00 0.00 0.00 3.41
298 302 2.716244 CTATCAGTCGCGCGGTCT 59.284 61.111 31.69 24.37 0.00 3.85
299 303 1.504647 CCTATCAGTCGCGCGGTCTA 61.505 60.000 31.69 14.10 0.00 2.59
487 570 2.441901 CCAGCTCGCTCTCTCCCT 60.442 66.667 0.00 0.00 0.00 4.20
603 706 1.004918 ACAAGGAAACGAGCTCCGG 60.005 57.895 8.47 0.00 43.93 5.14
622 725 2.104859 CGAGGACTGCGAGGTCGTA 61.105 63.158 0.69 0.00 42.22 3.43
623 726 1.437772 CGAGGACTGCGAGGTCGTAT 61.438 60.000 0.69 0.00 42.22 3.06
701 818 4.591924 GGGTTAAATGCTAGTAGGCCTAGA 59.408 45.833 14.38 3.13 45.21 2.43
746 888 6.663944 AGTTTAGTGTTGTTGTTGTCTCTC 57.336 37.500 0.00 0.00 0.00 3.20
1048 1244 4.101114 TGAAGGCACTATAACAGGAAGGA 58.899 43.478 0.00 0.00 38.49 3.36
1108 1327 0.257905 ACTGGCCTCACATGATGCAT 59.742 50.000 3.32 0.00 37.41 3.96
1240 1538 8.571336 GTTAATCATGGCACTGAAATTAGCTAT 58.429 33.333 0.00 0.00 0.00 2.97
1249 1547 6.017852 GCACTGAAATTAGCTATTACTCCACC 60.018 42.308 0.00 0.00 0.00 4.61
1267 1565 3.684788 CCACCTGCACTAACTTATCACAC 59.315 47.826 0.00 0.00 0.00 3.82
1286 1584 4.751098 CACACTTACAAATGCAGGCAAATT 59.249 37.500 0.00 0.00 0.00 1.82
1547 1866 4.646040 CCAAGATGTTTGATTGGCAGGATA 59.354 41.667 0.00 0.00 37.28 2.59
1573 1892 2.490991 GTGGACAAGAAGGTGTACCAC 58.509 52.381 3.56 0.00 39.86 4.16
1645 1979 3.041211 AGCTATGTTGGAGGTGCAGATA 58.959 45.455 0.00 0.00 0.00 1.98
1833 2167 1.003580 TGGCAGCAAGGAGAAGTTAGG 59.996 52.381 0.00 0.00 0.00 2.69
2048 2397 8.251750 TGCTATGTTCTTAAGTATGTTGTGAC 57.748 34.615 1.63 0.00 0.00 3.67
2050 2399 5.585500 TGTTCTTAAGTATGTTGTGACGC 57.415 39.130 1.63 0.00 0.00 5.19
2110 2477 1.548081 TACGCTGTTGGCCAGTAGTA 58.452 50.000 5.11 5.07 43.55 1.82
2216 2640 4.169666 TGACTTAGGCCTACTAAAACCCA 58.830 43.478 13.46 0.00 40.97 4.51
2217 2641 4.019950 TGACTTAGGCCTACTAAAACCCAC 60.020 45.833 13.46 0.00 40.97 4.61
2218 2642 3.265221 ACTTAGGCCTACTAAAACCCACC 59.735 47.826 13.46 0.00 40.97 4.61
2219 2643 0.997363 AGGCCTACTAAAACCCACCC 59.003 55.000 1.29 0.00 0.00 4.61
2225 2660 1.000041 ACTAAAACCCACCCACCCCA 61.000 55.000 0.00 0.00 0.00 4.96
2257 2692 3.462205 GTCAATATAAACCCCTCCCCACT 59.538 47.826 0.00 0.00 0.00 4.00
2294 2739 4.488136 CAGCAGCCGCCACCCATA 62.488 66.667 0.00 0.00 39.83 2.74
2295 2740 3.727258 AGCAGCCGCCACCCATAA 61.727 61.111 0.00 0.00 39.83 1.90
2319 2767 4.286813 AACCCTAGAGATGGATCCTGAA 57.713 45.455 14.23 0.00 0.00 3.02
2355 2803 5.780793 AGATGTCACTAGTAGAAAACAGGGT 59.219 40.000 3.59 0.00 0.00 4.34
2737 3185 1.000827 CTAGCTCACCTCCTATGCACG 60.001 57.143 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.493645 TGTCAACTAATGATGCATAAGAGACTG 59.506 37.037 0.00 0.00 40.97 3.51
4 5 8.151141 ACATGTCAACTAATGATGCATAAGAG 57.849 34.615 0.00 0.00 40.97 2.85
5 6 7.989170 AGACATGTCAACTAATGATGCATAAGA 59.011 33.333 27.02 0.00 40.97 2.10
6 7 8.151141 AGACATGTCAACTAATGATGCATAAG 57.849 34.615 27.02 0.00 40.97 1.73
7 8 7.769970 TGAGACATGTCAACTAATGATGCATAA 59.230 33.333 27.02 0.00 40.97 1.90
8 9 7.274447 TGAGACATGTCAACTAATGATGCATA 58.726 34.615 27.02 0.00 40.97 3.14
9 10 6.117488 TGAGACATGTCAACTAATGATGCAT 58.883 36.000 27.02 0.00 40.97 3.96
10 11 5.490159 TGAGACATGTCAACTAATGATGCA 58.510 37.500 27.02 0.00 40.97 3.96
11 12 6.615264 ATGAGACATGTCAACTAATGATGC 57.385 37.500 27.02 0.00 40.97 3.91
14 15 9.889128 TTGATTATGAGACATGTCAACTAATGA 57.111 29.630 27.02 15.97 35.05 2.57
19 20 9.107177 GAGATTTGATTATGAGACATGTCAACT 57.893 33.333 27.02 12.96 0.00 3.16
20 21 8.341173 GGAGATTTGATTATGAGACATGTCAAC 58.659 37.037 27.02 19.57 0.00 3.18
21 22 7.225341 CGGAGATTTGATTATGAGACATGTCAA 59.775 37.037 27.02 15.38 0.00 3.18
22 23 6.703165 CGGAGATTTGATTATGAGACATGTCA 59.297 38.462 27.02 9.20 0.00 3.58
23 24 6.146837 CCGGAGATTTGATTATGAGACATGTC 59.853 42.308 18.47 18.47 0.00 3.06
24 25 5.994054 CCGGAGATTTGATTATGAGACATGT 59.006 40.000 0.00 0.00 0.00 3.21
25 26 5.410746 CCCGGAGATTTGATTATGAGACATG 59.589 44.000 0.73 0.00 0.00 3.21
26 27 5.307976 TCCCGGAGATTTGATTATGAGACAT 59.692 40.000 0.73 0.00 0.00 3.06
27 28 4.653801 TCCCGGAGATTTGATTATGAGACA 59.346 41.667 0.73 0.00 0.00 3.41
28 29 5.215252 TCCCGGAGATTTGATTATGAGAC 57.785 43.478 0.73 0.00 0.00 3.36
29 30 5.366768 AGTTCCCGGAGATTTGATTATGAGA 59.633 40.000 0.73 0.00 0.00 3.27
30 31 5.615289 AGTTCCCGGAGATTTGATTATGAG 58.385 41.667 0.73 0.00 0.00 2.90
31 32 5.630415 AGTTCCCGGAGATTTGATTATGA 57.370 39.130 0.73 0.00 0.00 2.15
32 33 5.506317 GCAAGTTCCCGGAGATTTGATTATG 60.506 44.000 0.73 0.00 0.00 1.90
33 34 4.580580 GCAAGTTCCCGGAGATTTGATTAT 59.419 41.667 0.73 0.00 0.00 1.28
34 35 3.945285 GCAAGTTCCCGGAGATTTGATTA 59.055 43.478 0.73 0.00 0.00 1.75
35 36 2.755103 GCAAGTTCCCGGAGATTTGATT 59.245 45.455 0.73 0.00 0.00 2.57
36 37 2.369394 GCAAGTTCCCGGAGATTTGAT 58.631 47.619 0.73 0.00 0.00 2.57
37 38 1.613255 GGCAAGTTCCCGGAGATTTGA 60.613 52.381 0.73 0.00 0.00 2.69
38 39 0.811281 GGCAAGTTCCCGGAGATTTG 59.189 55.000 0.73 5.44 0.00 2.32
39 40 0.404040 TGGCAAGTTCCCGGAGATTT 59.596 50.000 0.73 0.00 0.00 2.17
40 41 0.404040 TTGGCAAGTTCCCGGAGATT 59.596 50.000 0.73 0.00 0.00 2.40
41 42 0.322546 GTTGGCAAGTTCCCGGAGAT 60.323 55.000 0.73 0.00 0.00 2.75
42 43 1.072505 GTTGGCAAGTTCCCGGAGA 59.927 57.895 0.73 0.00 0.00 3.71
43 44 0.821711 TTGTTGGCAAGTTCCCGGAG 60.822 55.000 0.73 0.00 0.00 4.63
44 45 0.395862 TTTGTTGGCAAGTTCCCGGA 60.396 50.000 0.73 0.00 35.82 5.14
45 46 0.461961 TTTTGTTGGCAAGTTCCCGG 59.538 50.000 0.00 0.00 35.82 5.73
46 47 2.301577 TTTTTGTTGGCAAGTTCCCG 57.698 45.000 0.00 0.00 35.82 5.14
47 48 4.195416 TCAATTTTTGTTGGCAAGTTCCC 58.805 39.130 0.00 0.00 35.82 3.97
48 49 5.730289 GCTTCAATTTTTGTTGGCAAGTTCC 60.730 40.000 0.00 0.00 35.82 3.62
49 50 5.163774 TGCTTCAATTTTTGTTGGCAAGTTC 60.164 36.000 0.00 0.00 35.82 3.01
50 51 4.699257 TGCTTCAATTTTTGTTGGCAAGTT 59.301 33.333 0.00 0.00 35.82 2.66
51 52 4.260170 TGCTTCAATTTTTGTTGGCAAGT 58.740 34.783 0.00 0.00 35.82 3.16
52 53 4.879104 TGCTTCAATTTTTGTTGGCAAG 57.121 36.364 0.00 0.00 35.82 4.01
53 54 5.356190 TCATTGCTTCAATTTTTGTTGGCAA 59.644 32.000 0.00 0.00 40.83 4.52
54 55 4.880120 TCATTGCTTCAATTTTTGTTGGCA 59.120 33.333 0.00 0.00 31.05 4.92
55 56 5.207033 GTCATTGCTTCAATTTTTGTTGGC 58.793 37.500 0.00 0.00 31.05 4.52
56 57 6.360844 TGTCATTGCTTCAATTTTTGTTGG 57.639 33.333 0.00 0.00 31.05 3.77
57 58 6.853872 CCATGTCATTGCTTCAATTTTTGTTG 59.146 34.615 0.00 0.00 31.05 3.33
58 59 6.766944 TCCATGTCATTGCTTCAATTTTTGTT 59.233 30.769 0.00 0.00 31.05 2.83
59 60 6.289834 TCCATGTCATTGCTTCAATTTTTGT 58.710 32.000 0.00 0.00 31.05 2.83
60 61 6.788684 TCCATGTCATTGCTTCAATTTTTG 57.211 33.333 0.00 0.00 31.05 2.44
61 62 7.716123 TCTTTCCATGTCATTGCTTCAATTTTT 59.284 29.630 0.00 0.00 31.05 1.94
62 63 7.218614 TCTTTCCATGTCATTGCTTCAATTTT 58.781 30.769 0.00 0.00 31.05 1.82
63 64 6.761312 TCTTTCCATGTCATTGCTTCAATTT 58.239 32.000 0.00 0.00 31.05 1.82
64 65 6.349243 TCTTTCCATGTCATTGCTTCAATT 57.651 33.333 0.00 0.00 31.05 2.32
65 66 5.988310 TCTTTCCATGTCATTGCTTCAAT 57.012 34.783 0.00 0.00 34.04 2.57
66 67 5.302568 AGTTCTTTCCATGTCATTGCTTCAA 59.697 36.000 0.00 0.00 0.00 2.69
67 68 4.828939 AGTTCTTTCCATGTCATTGCTTCA 59.171 37.500 0.00 0.00 0.00 3.02
68 69 5.159209 CAGTTCTTTCCATGTCATTGCTTC 58.841 41.667 0.00 0.00 0.00 3.86
69 70 4.560108 GCAGTTCTTTCCATGTCATTGCTT 60.560 41.667 0.00 0.00 0.00 3.91
70 71 3.057033 GCAGTTCTTTCCATGTCATTGCT 60.057 43.478 0.00 0.00 0.00 3.91
71 72 3.248266 GCAGTTCTTTCCATGTCATTGC 58.752 45.455 0.00 0.00 0.00 3.56
72 73 4.022589 AGTGCAGTTCTTTCCATGTCATTG 60.023 41.667 0.00 0.00 0.00 2.82
73 74 4.147321 AGTGCAGTTCTTTCCATGTCATT 58.853 39.130 0.00 0.00 0.00 2.57
74 75 3.759581 AGTGCAGTTCTTTCCATGTCAT 58.240 40.909 0.00 0.00 0.00 3.06
75 76 3.213206 AGTGCAGTTCTTTCCATGTCA 57.787 42.857 0.00 0.00 0.00 3.58
76 77 3.565482 TGAAGTGCAGTTCTTTCCATGTC 59.435 43.478 29.45 5.81 0.00 3.06
77 78 3.554934 TGAAGTGCAGTTCTTTCCATGT 58.445 40.909 29.45 0.00 0.00 3.21
78 79 4.572985 TTGAAGTGCAGTTCTTTCCATG 57.427 40.909 29.45 0.00 0.00 3.66
79 80 5.563475 CGAATTGAAGTGCAGTTCTTTCCAT 60.563 40.000 29.45 13.99 40.08 3.41
80 81 4.261155 CGAATTGAAGTGCAGTTCTTTCCA 60.261 41.667 29.45 11.45 40.08 3.53
81 82 4.024048 TCGAATTGAAGTGCAGTTCTTTCC 60.024 41.667 29.45 17.22 40.08 3.13
82 83 5.095691 TCGAATTGAAGTGCAGTTCTTTC 57.904 39.130 29.45 26.94 40.08 2.62
83 84 5.273944 GTTCGAATTGAAGTGCAGTTCTTT 58.726 37.500 29.45 23.02 40.08 2.52
84 85 4.261197 GGTTCGAATTGAAGTGCAGTTCTT 60.261 41.667 29.45 19.09 40.08 2.52
85 86 3.251004 GGTTCGAATTGAAGTGCAGTTCT 59.749 43.478 29.45 13.92 40.08 3.01
86 87 3.003275 TGGTTCGAATTGAAGTGCAGTTC 59.997 43.478 24.59 24.59 39.19 3.01
87 88 2.948979 TGGTTCGAATTGAAGTGCAGTT 59.051 40.909 6.46 6.46 37.23 3.16
88 89 2.549754 CTGGTTCGAATTGAAGTGCAGT 59.450 45.455 0.00 0.00 37.23 4.40
89 90 2.095567 CCTGGTTCGAATTGAAGTGCAG 60.096 50.000 0.00 0.00 37.23 4.41
90 91 1.879380 CCTGGTTCGAATTGAAGTGCA 59.121 47.619 0.00 0.00 37.23 4.57
91 92 1.200020 CCCTGGTTCGAATTGAAGTGC 59.800 52.381 0.00 0.00 37.23 4.40
92 93 2.484264 GACCCTGGTTCGAATTGAAGTG 59.516 50.000 0.00 0.00 37.23 3.16
93 94 2.105821 TGACCCTGGTTCGAATTGAAGT 59.894 45.455 0.00 0.00 37.23 3.01
94 95 2.778299 TGACCCTGGTTCGAATTGAAG 58.222 47.619 0.00 0.00 37.23 3.02
95 96 2.940994 TGACCCTGGTTCGAATTGAA 57.059 45.000 0.00 0.00 0.00 2.69
96 97 2.940994 TTGACCCTGGTTCGAATTGA 57.059 45.000 0.00 0.00 0.00 2.57
97 98 3.119495 GGAATTGACCCTGGTTCGAATTG 60.119 47.826 0.00 0.00 0.00 2.32
98 99 3.089284 GGAATTGACCCTGGTTCGAATT 58.911 45.455 0.00 0.00 0.00 2.17
99 100 2.041081 TGGAATTGACCCTGGTTCGAAT 59.959 45.455 0.00 0.00 0.00 3.34
100 101 1.422024 TGGAATTGACCCTGGTTCGAA 59.578 47.619 0.00 0.00 0.00 3.71
101 102 1.060729 TGGAATTGACCCTGGTTCGA 58.939 50.000 0.00 0.00 0.00 3.71
102 103 1.904287 TTGGAATTGACCCTGGTTCG 58.096 50.000 0.00 0.00 0.00 3.95
103 104 4.890158 ATTTTGGAATTGACCCTGGTTC 57.110 40.909 0.00 0.00 0.00 3.62
114 115 3.399440 TTGCCGAGCAATTTTGGAATT 57.601 38.095 7.15 0.00 43.99 2.17
125 126 1.228094 TTGGTGACATTGCCGAGCA 60.228 52.632 0.00 0.00 42.32 4.26
126 127 1.503542 CTTGGTGACATTGCCGAGC 59.496 57.895 0.00 0.00 42.32 5.03
127 128 0.957395 AGCTTGGTGACATTGCCGAG 60.957 55.000 0.00 0.00 42.32 4.63
128 129 0.537143 AAGCTTGGTGACATTGCCGA 60.537 50.000 0.00 0.00 42.32 5.54
129 130 0.387622 CAAGCTTGGTGACATTGCCG 60.388 55.000 19.14 0.00 42.32 5.69
130 131 0.961019 TCAAGCTTGGTGACATTGCC 59.039 50.000 25.73 0.00 42.32 4.52
131 132 2.056094 GTCAAGCTTGGTGACATTGC 57.944 50.000 25.73 2.64 44.00 3.56
136 137 4.936891 AGAAAAATGTCAAGCTTGGTGAC 58.063 39.130 25.73 17.32 44.67 3.67
137 138 5.241506 CCTAGAAAAATGTCAAGCTTGGTGA 59.758 40.000 25.73 10.64 0.00 4.02
138 139 5.241506 TCCTAGAAAAATGTCAAGCTTGGTG 59.758 40.000 25.73 1.51 0.00 4.17
139 140 5.385198 TCCTAGAAAAATGTCAAGCTTGGT 58.615 37.500 25.73 10.04 0.00 3.67
140 141 5.964958 TCCTAGAAAAATGTCAAGCTTGG 57.035 39.130 25.73 8.01 0.00 3.61
141 142 6.974965 AGTTCCTAGAAAAATGTCAAGCTTG 58.025 36.000 20.81 20.81 0.00 4.01
142 143 7.068716 ACAAGTTCCTAGAAAAATGTCAAGCTT 59.931 33.333 0.00 0.00 0.00 3.74
143 144 6.547510 ACAAGTTCCTAGAAAAATGTCAAGCT 59.452 34.615 0.00 0.00 0.00 3.74
144 145 6.739112 ACAAGTTCCTAGAAAAATGTCAAGC 58.261 36.000 0.00 0.00 0.00 4.01
147 148 9.793259 AGATAACAAGTTCCTAGAAAAATGTCA 57.207 29.630 0.00 0.00 0.00 3.58
149 150 9.014297 CCAGATAACAAGTTCCTAGAAAAATGT 57.986 33.333 0.00 0.00 0.00 2.71
150 151 9.231297 TCCAGATAACAAGTTCCTAGAAAAATG 57.769 33.333 0.00 0.00 0.00 2.32
151 152 9.232473 GTCCAGATAACAAGTTCCTAGAAAAAT 57.768 33.333 0.00 0.00 0.00 1.82
152 153 7.664318 GGTCCAGATAACAAGTTCCTAGAAAAA 59.336 37.037 0.00 0.00 0.00 1.94
153 154 7.166167 GGTCCAGATAACAAGTTCCTAGAAAA 58.834 38.462 0.00 0.00 0.00 2.29
154 155 6.271391 TGGTCCAGATAACAAGTTCCTAGAAA 59.729 38.462 0.00 0.00 0.00 2.52
155 156 5.783360 TGGTCCAGATAACAAGTTCCTAGAA 59.217 40.000 0.00 0.00 0.00 2.10
156 157 5.187186 GTGGTCCAGATAACAAGTTCCTAGA 59.813 44.000 0.00 0.00 0.00 2.43
157 158 5.187967 AGTGGTCCAGATAACAAGTTCCTAG 59.812 44.000 0.00 0.00 0.00 3.02
158 159 5.046591 CAGTGGTCCAGATAACAAGTTCCTA 60.047 44.000 0.00 0.00 0.00 2.94
159 160 3.910627 AGTGGTCCAGATAACAAGTTCCT 59.089 43.478 0.00 0.00 0.00 3.36
160 161 4.003648 CAGTGGTCCAGATAACAAGTTCC 58.996 47.826 0.00 0.00 0.00 3.62
161 162 3.437049 GCAGTGGTCCAGATAACAAGTTC 59.563 47.826 0.00 0.00 0.00 3.01
162 163 3.412386 GCAGTGGTCCAGATAACAAGTT 58.588 45.455 0.00 0.00 0.00 2.66
163 164 2.612972 CGCAGTGGTCCAGATAACAAGT 60.613 50.000 0.00 0.00 0.00 3.16
164 165 2.002586 CGCAGTGGTCCAGATAACAAG 58.997 52.381 0.00 0.00 0.00 3.16
165 166 1.338674 CCGCAGTGGTCCAGATAACAA 60.339 52.381 0.00 0.00 0.00 2.83
166 167 0.249120 CCGCAGTGGTCCAGATAACA 59.751 55.000 0.00 0.00 0.00 2.41
167 168 1.090052 GCCGCAGTGGTCCAGATAAC 61.090 60.000 0.89 0.00 41.21 1.89
168 169 1.220749 GCCGCAGTGGTCCAGATAA 59.779 57.895 0.89 0.00 41.21 1.75
169 170 1.987306 TGCCGCAGTGGTCCAGATA 60.987 57.895 0.89 0.00 41.21 1.98
170 171 3.321648 TGCCGCAGTGGTCCAGAT 61.322 61.111 0.89 0.00 41.21 2.90
171 172 4.314440 GTGCCGCAGTGGTCCAGA 62.314 66.667 0.89 0.00 41.21 3.86
172 173 4.320456 AGTGCCGCAGTGGTCCAG 62.320 66.667 0.00 0.00 41.21 3.86
173 174 4.624364 CAGTGCCGCAGTGGTCCA 62.624 66.667 18.93 0.00 41.21 4.02
185 186 2.297033 TCTGAAAATCCAAAGGCAGTGC 59.703 45.455 6.55 6.55 0.00 4.40
186 187 3.571401 ACTCTGAAAATCCAAAGGCAGTG 59.429 43.478 0.00 0.00 0.00 3.66
187 188 3.837355 ACTCTGAAAATCCAAAGGCAGT 58.163 40.909 0.00 0.00 0.00 4.40
188 189 5.964958 TTACTCTGAAAATCCAAAGGCAG 57.035 39.130 0.00 0.00 0.00 4.85
189 190 6.916360 ATTTACTCTGAAAATCCAAAGGCA 57.084 33.333 0.00 0.00 0.00 4.75
190 191 6.975197 GCTATTTACTCTGAAAATCCAAAGGC 59.025 38.462 0.00 0.00 0.00 4.35
191 192 8.055279 TGCTATTTACTCTGAAAATCCAAAGG 57.945 34.615 0.00 0.00 0.00 3.11
223 224 5.252164 TGGAACCCTAGCCTGTAAACTAATT 59.748 40.000 0.00 0.00 0.00 1.40
487 570 3.650950 GCAGGGGAGTGGGAGCAA 61.651 66.667 0.00 0.00 0.00 3.91
559 662 2.751436 GAAGGCATGGCGGCAAGA 60.751 61.111 18.31 0.00 44.47 3.02
603 706 4.838486 CGACCTCGCAGTCCTCGC 62.838 72.222 0.00 0.00 32.91 5.03
622 725 3.493334 CATAAGTCCCATGTCCATGCAT 58.507 45.455 0.00 0.00 37.49 3.96
623 726 2.423231 CCATAAGTCCCATGTCCATGCA 60.423 50.000 1.64 0.00 37.49 3.96
701 818 1.842562 AGCAAGATCCATGGCTGTAGT 59.157 47.619 6.96 0.00 34.83 2.73
746 888 7.989741 ACCCTCACTAATCAAGAAACATATCAG 59.010 37.037 0.00 0.00 0.00 2.90
1048 1244 0.995024 ACTGGGCAGCCATAGAAACT 59.005 50.000 15.19 0.00 0.00 2.66
1240 1538 5.482526 TGATAAGTTAGTGCAGGTGGAGTAA 59.517 40.000 0.00 0.00 0.00 2.24
1249 1547 7.652300 TTGTAAGTGTGATAAGTTAGTGCAG 57.348 36.000 0.00 0.00 0.00 4.41
1267 1565 4.751098 ACACAATTTGCCTGCATTTGTAAG 59.249 37.500 15.98 10.29 33.71 2.34
1286 1584 4.518249 TCTACAACACCACAATTCACACA 58.482 39.130 0.00 0.00 0.00 3.72
1547 1866 1.978580 CACCTTCTTGTCCACCCTACT 59.021 52.381 0.00 0.00 0.00 2.57
1573 1892 3.492102 TCTTCCTCCTCCACTTGTTTG 57.508 47.619 0.00 0.00 0.00 2.93
1645 1979 6.256539 GCTCTTTTGCAAGTTTAAGCTTTTCT 59.743 34.615 3.20 0.00 0.00 2.52
1833 2167 2.906268 AGGATGGCCTTGATTTGCC 58.094 52.632 3.32 0.00 43.90 4.52
2048 2397 2.149134 TGCCATAGCATTGGAGATGCG 61.149 52.381 8.99 0.00 46.52 4.73
2216 2640 3.264845 GTGGTGGATGGGGTGGGT 61.265 66.667 0.00 0.00 0.00 4.51
2217 2641 2.941025 AGTGGTGGATGGGGTGGG 60.941 66.667 0.00 0.00 0.00 4.61
2218 2642 2.356278 CAGTGGTGGATGGGGTGG 59.644 66.667 0.00 0.00 0.00 4.61
2219 2643 1.002134 GACAGTGGTGGATGGGGTG 60.002 63.158 0.00 0.00 0.00 4.61
2225 2660 5.445964 GGGTTTATATTGACAGTGGTGGAT 58.554 41.667 0.00 0.00 0.00 3.41
2257 2692 1.774217 AGTGGCTGGGAAAGGGTGA 60.774 57.895 0.00 0.00 0.00 4.02
2293 2738 5.366768 CAGGATCCATCTCTAGGGTTTGTTA 59.633 44.000 15.82 0.00 0.00 2.41
2294 2739 4.164988 CAGGATCCATCTCTAGGGTTTGTT 59.835 45.833 15.82 0.00 0.00 2.83
2295 2740 3.713764 CAGGATCCATCTCTAGGGTTTGT 59.286 47.826 15.82 0.00 0.00 2.83
2319 2767 2.848694 AGTGACATCTCCCATGTCCATT 59.151 45.455 11.31 0.00 45.70 3.16
2355 2803 3.585289 TGAAAACTGCCCTGTGACCTATA 59.415 43.478 0.00 0.00 0.00 1.31
2464 2912 1.546589 TACGAACCGGGACCAATGCT 61.547 55.000 6.32 0.00 0.00 3.79
2737 3185 2.159517 GGCATTTCATCGAACACCTCAC 60.160 50.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.