Multiple sequence alignment - TraesCS2B01G436000

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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 TraesCS2B01G436000 chr2B 100.000 2379 0 0 4050 6428 626230578 626228200 0.000000e+00 4394
1 TraesCS2B01G436000 chr2B 100.000 2204 0 0 1319 3522 626233309 626231106 0.000000e+00 4071
2 TraesCS2B01G436000 chr2B 100.000 1114 0 0 1 1114 626234627 626233514 0.000000e+00 2058
3 TraesCS2B01G436000 chr2B 95.657 944 37 4 2559 3500 138541028 138541969 0.000000e+00 1513
4 TraesCS2B01G436000 chr2B 94.886 176 9 0 4050 4225 138542824 138542999 6.350000e-70 276
5 TraesCS2B01G436000 chr2A 92.112 2206 123 24 4261 6428 672972628 672970436 0.000000e+00 3062
6 TraesCS2B01G436000 chr2A 92.316 1926 103 23 4512 6428 673071456 673073345 0.000000e+00 2695
7 TraesCS2B01G436000 chr2A 88.434 1245 110 15 1327 2557 673070004 673071228 0.000000e+00 1471
8 TraesCS2B01G436000 chr2A 97.200 857 23 1 240 1096 672975755 672974900 0.000000e+00 1448
9 TraesCS2B01G436000 chr2A 96.561 785 24 2 1338 2119 672974609 672973825 0.000000e+00 1297
10 TraesCS2B01G436000 chr2A 96.272 456 16 1 2105 2560 672973072 672972618 0.000000e+00 747
11 TraesCS2B01G436000 chr2A 87.799 418 34 7 712 1114 673069572 673069987 2.100000e-129 473
12 TraesCS2B01G436000 chr2A 88.811 143 16 0 536 678 673069348 673069490 6.620000e-40 176
13 TraesCS2B01G436000 chr7B 86.275 2113 174 54 4390 6428 430832090 430830020 0.000000e+00 2189
14 TraesCS2B01G436000 chr7B 95.742 963 39 2 2560 3521 589942917 589941956 0.000000e+00 1550
15 TraesCS2B01G436000 chr7B 95.513 936 40 2 2559 3492 718858562 718859497 0.000000e+00 1495
16 TraesCS2B01G436000 chr7B 88.699 1053 91 13 1326 2365 430833740 430832703 0.000000e+00 1260
17 TraesCS2B01G436000 chr7B 96.000 175 6 1 4058 4232 116483527 116483700 3.790000e-72 283
18 TraesCS2B01G436000 chr7B 92.553 94 7 0 424 517 430834446 430834353 1.120000e-27 135
19 TraesCS2B01G436000 chr2D 94.139 1382 47 12 4259 5628 528389896 528388537 0.000000e+00 2073
20 TraesCS2B01G436000 chr2D 96.383 1244 37 6 1319 2560 528391121 528389884 0.000000e+00 2041
21 TraesCS2B01G436000 chr2D 86.738 837 70 19 5631 6428 528386259 528385425 0.000000e+00 893
22 TraesCS2B01G436000 chr2D 98.196 499 8 1 611 1109 528391744 528391247 0.000000e+00 870
23 TraesCS2B01G436000 chr6B 95.155 970 45 2 2552 3520 37237310 37238278 0.000000e+00 1530
24 TraesCS2B01G436000 chr6B 97.093 172 5 0 4053 4224 512313416 512313245 2.270000e-74 291
25 TraesCS2B01G436000 chr6B 96.552 174 6 0 4053 4226 679653602 679653429 8.150000e-74 289
26 TraesCS2B01G436000 chr3B 95.680 949 39 2 2559 3505 51785555 51786503 0.000000e+00 1524
27 TraesCS2B01G436000 chr3B 95.288 955 43 2 2561 3514 29772651 29771698 0.000000e+00 1513
28 TraesCS2B01G436000 chr3B 94.211 190 9 2 4050 4238 51786880 51787068 8.150000e-74 289
29 TraesCS2B01G436000 chr3B 95.455 176 7 1 4055 4230 29770876 29770702 4.910000e-71 279
30 TraesCS2B01G436000 chr5B 94.928 966 46 3 2559 3522 562992853 562993817 0.000000e+00 1509
31 TraesCS2B01G436000 chr4B 94.704 963 46 3 2562 3522 666564007 666563048 0.000000e+00 1491
32 TraesCS2B01G436000 chrUn 94.209 967 52 4 2554 3519 372566745 372567708 0.000000e+00 1472
33 TraesCS2B01G436000 chrUn 96.154 182 7 0 4053 4234 376621752 376621571 1.350000e-76 298
34 TraesCS2B01G436000 chr7A 97.191 178 5 0 4053 4230 630491344 630491167 1.050000e-77 302
35 TraesCS2B01G436000 chr1B 97.191 178 5 0 4050 4227 12639874 12640051 1.050000e-77 302


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 TraesCS2B01G436000 chr2B 626228200 626234627 6427 True 3507.666667 4394 100.000000 1 6428 3 chr2B.!!$R1 6427
1 TraesCS2B01G436000 chr2B 138541028 138542999 1971 False 894.500000 1513 95.271500 2559 4225 2 chr2B.!!$F1 1666
2 TraesCS2B01G436000 chr2A 672970436 672975755 5319 True 1638.500000 3062 95.536250 240 6428 4 chr2A.!!$R1 6188
3 TraesCS2B01G436000 chr2A 673069348 673073345 3997 False 1203.750000 2695 89.340000 536 6428 4 chr2A.!!$F1 5892
4 TraesCS2B01G436000 chr7B 589941956 589942917 961 True 1550.000000 1550 95.742000 2560 3521 1 chr7B.!!$R1 961
5 TraesCS2B01G436000 chr7B 718858562 718859497 935 False 1495.000000 1495 95.513000 2559 3492 1 chr7B.!!$F2 933
6 TraesCS2B01G436000 chr7B 430830020 430834446 4426 True 1194.666667 2189 89.175667 424 6428 3 chr7B.!!$R2 6004
7 TraesCS2B01G436000 chr2D 528385425 528391744 6319 True 1469.250000 2073 93.864000 611 6428 4 chr2D.!!$R1 5817
8 TraesCS2B01G436000 chr6B 37237310 37238278 968 False 1530.000000 1530 95.155000 2552 3520 1 chr6B.!!$F1 968
9 TraesCS2B01G436000 chr3B 51785555 51787068 1513 False 906.500000 1524 94.945500 2559 4238 2 chr3B.!!$F1 1679
10 TraesCS2B01G436000 chr3B 29770702 29772651 1949 True 896.000000 1513 95.371500 2561 4230 2 chr3B.!!$R1 1669
11 TraesCS2B01G436000 chr5B 562992853 562993817 964 False 1509.000000 1509 94.928000 2559 3522 1 chr5B.!!$F1 963
12 TraesCS2B01G436000 chr4B 666563048 666564007 959 True 1491.000000 1491 94.704000 2562 3522 1 chr4B.!!$R1 960
13 TraesCS2B01G436000 chrUn 372566745 372567708 963 False 1472.000000 1472 94.209000 2554 3519 1 chrUn.!!$F1 965

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
230 231 0.038159 GTTGTCACTCTGGTAGCGCT 60.038 55.000 17.26 17.26 0.00 5.92 F
231 232 0.038251 TTGTCACTCTGGTAGCGCTG 60.038 55.000 22.90 4.03 0.00 5.18 F
240 241 0.321564 TGGTAGCGCTGCTTGTTGAT 60.322 50.000 24.82 0.00 40.44 2.57 F
241 242 0.804989 GGTAGCGCTGCTTGTTGATT 59.195 50.000 24.82 0.00 40.44 2.57 F
242 243 2.006888 GGTAGCGCTGCTTGTTGATTA 58.993 47.619 24.82 0.00 40.44 1.75 F
243 244 2.030946 GGTAGCGCTGCTTGTTGATTAG 59.969 50.000 24.82 0.00 40.44 1.73 F
2780 3702 1.360551 CTCCGATCATCCGAAGCGT 59.639 57.895 0.00 0.00 0.00 5.07 F
3012 3934 0.182537 CCACCAAACAGACCCTCACA 59.817 55.000 0.00 0.00 0.00 3.58 F
4248 5760 0.623723 GGGGGTCCTATGCAAGTTCA 59.376 55.000 0.00 0.00 0.00 3.18 F
4256 5768 0.546122 TATGCAAGTTCATCGCCCCT 59.454 50.000 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 1734 0.035458 GGCGTTCCATAGCTATGCCT 59.965 55.000 25.60 0.00 40.14 4.75 R
2181 3102 2.507407 ACACAACAAAGGTGACAGGT 57.493 45.000 0.00 0.00 39.53 4.00 R
2365 3286 6.320418 ACCTGTAAACCTTCGAAGTTTTTGAT 59.680 34.615 23.24 4.51 38.37 2.57 R
2509 3430 3.340814 AGGAACAACAGCGAATGATCT 57.659 42.857 0.00 0.00 0.00 2.75 R
2780 3702 0.535335 GAGGTGCTGATTGGTACCGA 59.465 55.000 3.71 3.71 44.73 4.69 R
2815 3737 2.810887 GCAGCAGCGTCGTCATCA 60.811 61.111 0.00 0.00 0.00 3.07 R
4254 5766 0.040958 GTGAACTGCAAAGCGTGAGG 60.041 55.000 0.00 0.00 0.00 3.86 R
4255 5767 0.657312 TGTGAACTGCAAAGCGTGAG 59.343 50.000 0.00 0.00 0.00 3.51 R
5374 7359 2.009774 CTTTTCTCCTGCGTACCATGG 58.990 52.381 11.19 11.19 0.00 3.66 R
5815 10084 5.123186 ACACGTTGAAGTTGTGAGAAAATCA 59.877 36.000 0.00 0.00 37.08 2.57 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
22 23 4.573900 CAGAGGTTATGCTAGCCTTATGG 58.426 47.826 13.29 0.00 39.70 2.74
35 36 2.917933 CCTTATGGCCGAGTTCAATGA 58.082 47.619 0.00 0.00 0.00 2.57
36 37 3.278574 CCTTATGGCCGAGTTCAATGAA 58.721 45.455 0.00 0.00 0.00 2.57
37 38 3.065371 CCTTATGGCCGAGTTCAATGAAC 59.935 47.826 17.67 17.67 42.25 3.18
38 39 1.086696 ATGGCCGAGTTCAATGAACG 58.913 50.000 18.99 9.41 45.96 3.95
39 40 1.134694 GGCCGAGTTCAATGAACGC 59.865 57.895 18.99 18.40 45.96 4.84
40 41 1.573829 GGCCGAGTTCAATGAACGCA 61.574 55.000 24.93 0.00 45.96 5.24
41 42 0.452784 GCCGAGTTCAATGAACGCAC 60.453 55.000 24.93 14.92 45.96 5.34
42 43 0.165944 CCGAGTTCAATGAACGCACC 59.834 55.000 24.93 13.25 45.96 5.01
43 44 0.179250 CGAGTTCAATGAACGCACCG 60.179 55.000 24.93 19.20 45.96 4.94
44 45 0.165944 GAGTTCAATGAACGCACCGG 59.834 55.000 21.76 0.00 45.96 5.28
45 46 0.534203 AGTTCAATGAACGCACCGGT 60.534 50.000 18.99 0.00 45.96 5.28
46 47 1.149987 GTTCAATGAACGCACCGGTA 58.850 50.000 6.87 0.00 32.81 4.02
47 48 1.127951 GTTCAATGAACGCACCGGTAG 59.872 52.381 6.87 7.33 32.81 3.18
48 49 0.390603 TCAATGAACGCACCGGTAGG 60.391 55.000 6.87 4.30 45.13 3.18
49 50 0.390603 CAATGAACGCACCGGTAGGA 60.391 55.000 6.87 0.00 41.02 2.94
50 51 0.322322 AATGAACGCACCGGTAGGAA 59.678 50.000 6.87 0.00 41.02 3.36
51 52 0.390735 ATGAACGCACCGGTAGGAAC 60.391 55.000 6.87 0.00 41.02 3.62
52 53 1.005867 GAACGCACCGGTAGGAACA 60.006 57.895 6.87 0.00 41.02 3.18
53 54 0.390735 GAACGCACCGGTAGGAACAT 60.391 55.000 6.87 0.00 41.02 2.71
54 55 0.896923 AACGCACCGGTAGGAACATA 59.103 50.000 6.87 0.00 41.02 2.29
55 56 0.458669 ACGCACCGGTAGGAACATAG 59.541 55.000 6.87 0.00 41.02 2.23
56 57 0.874607 CGCACCGGTAGGAACATAGC 60.875 60.000 6.87 1.44 41.02 2.97
57 58 0.464452 GCACCGGTAGGAACATAGCT 59.536 55.000 6.87 0.00 41.02 3.32
58 59 1.806623 GCACCGGTAGGAACATAGCTG 60.807 57.143 6.87 0.00 41.02 4.24
59 60 1.480954 CACCGGTAGGAACATAGCTGT 59.519 52.381 6.87 0.00 41.02 4.40
61 62 3.131577 CACCGGTAGGAACATAGCTGTTA 59.868 47.826 6.87 0.00 45.57 2.41
62 63 3.770933 ACCGGTAGGAACATAGCTGTTAA 59.229 43.478 4.49 0.00 45.57 2.01
63 64 4.407945 ACCGGTAGGAACATAGCTGTTAAT 59.592 41.667 4.49 0.00 45.57 1.40
64 65 5.599656 ACCGGTAGGAACATAGCTGTTAATA 59.400 40.000 4.49 0.00 45.57 0.98
65 66 6.269307 ACCGGTAGGAACATAGCTGTTAATAT 59.731 38.462 4.49 0.00 45.57 1.28
66 67 6.590292 CCGGTAGGAACATAGCTGTTAATATG 59.410 42.308 0.00 0.00 45.57 1.78
67 68 6.090898 CGGTAGGAACATAGCTGTTAATATGC 59.909 42.308 0.00 0.00 45.57 3.14
68 69 7.162082 GGTAGGAACATAGCTGTTAATATGCT 58.838 38.462 0.00 0.00 45.57 3.79
69 70 7.118390 GGTAGGAACATAGCTGTTAATATGCTG 59.882 40.741 0.00 0.00 45.57 4.41
70 71 5.471456 AGGAACATAGCTGTTAATATGCTGC 59.529 40.000 0.00 0.00 45.57 5.25
71 72 5.239306 GGAACATAGCTGTTAATATGCTGCA 59.761 40.000 4.13 4.13 45.57 4.41
72 73 6.072286 GGAACATAGCTGTTAATATGCTGCAT 60.072 38.462 20.18 20.18 45.57 3.96
73 74 6.889301 ACATAGCTGTTAATATGCTGCATT 57.111 33.333 21.56 7.10 37.62 3.56
74 75 6.675026 ACATAGCTGTTAATATGCTGCATTG 58.325 36.000 21.56 10.37 37.62 2.82
75 76 4.579454 AGCTGTTAATATGCTGCATTGG 57.421 40.909 21.56 4.91 35.54 3.16
76 77 4.209538 AGCTGTTAATATGCTGCATTGGA 58.790 39.130 21.56 2.89 35.54 3.53
77 78 4.646040 AGCTGTTAATATGCTGCATTGGAA 59.354 37.500 21.56 9.29 35.54 3.53
78 79 4.741676 GCTGTTAATATGCTGCATTGGAAC 59.258 41.667 21.56 19.61 0.00 3.62
79 80 5.679382 GCTGTTAATATGCTGCATTGGAACA 60.679 40.000 21.56 22.47 0.00 3.18
80 81 9.193127 AGCTGTTAATATGCTGCATTGGAACAA 62.193 37.037 21.56 0.41 38.65 2.83
95 96 5.705609 TGGAACAAGCTCTTGGTAATTTC 57.294 39.130 13.48 7.66 41.20 2.17
96 97 5.136828 TGGAACAAGCTCTTGGTAATTTCA 58.863 37.500 13.48 2.01 41.20 2.69
97 98 5.596361 TGGAACAAGCTCTTGGTAATTTCAA 59.404 36.000 13.48 0.07 41.20 2.69
98 99 6.097554 TGGAACAAGCTCTTGGTAATTTCAAA 59.902 34.615 13.48 0.00 41.20 2.69
99 100 6.983890 GGAACAAGCTCTTGGTAATTTCAAAA 59.016 34.615 13.48 0.00 41.20 2.44
100 101 7.494298 GGAACAAGCTCTTGGTAATTTCAAAAA 59.506 33.333 13.48 0.00 41.20 1.94
101 102 8.962884 AACAAGCTCTTGGTAATTTCAAAAAT 57.037 26.923 13.48 0.00 44.45 1.82
103 104 9.696917 ACAAGCTCTTGGTAATTTCAAAAATAG 57.303 29.630 13.48 0.00 44.45 1.73
104 105 9.912634 CAAGCTCTTGGTAATTTCAAAAATAGA 57.087 29.630 1.79 0.00 36.95 1.98
117 118 8.647143 TTTCAAAAATAGAAACAAGCTCTTGG 57.353 30.769 13.48 0.00 44.45 3.61
118 119 7.346751 TCAAAAATAGAAACAAGCTCTTGGT 57.653 32.000 13.48 4.48 43.33 3.67
119 120 8.458573 TCAAAAATAGAAACAAGCTCTTGGTA 57.541 30.769 13.48 1.49 40.05 3.25
120 121 8.908903 TCAAAAATAGAAACAAGCTCTTGGTAA 58.091 29.630 13.48 0.00 40.05 2.85
121 122 9.696917 CAAAAATAGAAACAAGCTCTTGGTAAT 57.303 29.630 13.48 2.90 40.05 1.89
125 126 9.914131 AATAGAAACAAGCTCTTGGTAATTTTC 57.086 29.630 13.48 12.33 40.05 2.29
126 127 7.346751 AGAAACAAGCTCTTGGTAATTTTCA 57.653 32.000 13.48 0.00 40.05 2.69
127 128 7.781056 AGAAACAAGCTCTTGGTAATTTTCAA 58.219 30.769 13.48 0.00 40.05 2.69
128 129 8.257306 AGAAACAAGCTCTTGGTAATTTTCAAA 58.743 29.630 13.48 0.00 40.05 2.69
129 130 8.785329 AAACAAGCTCTTGGTAATTTTCAAAA 57.215 26.923 13.48 0.00 40.05 2.44
130 131 8.785329 AACAAGCTCTTGGTAATTTTCAAAAA 57.215 26.923 13.48 0.00 44.45 1.94
184 185 9.793259 AAAAAGAACACTATGGAACTAATCTGA 57.207 29.630 0.00 0.00 0.00 3.27
185 186 9.793259 AAAAGAACACTATGGAACTAATCTGAA 57.207 29.630 0.00 0.00 0.00 3.02
186 187 9.793259 AAAGAACACTATGGAACTAATCTGAAA 57.207 29.630 0.00 0.00 0.00 2.69
187 188 8.779354 AGAACACTATGGAACTAATCTGAAAC 57.221 34.615 0.00 0.00 0.00 2.78
188 189 7.824779 AGAACACTATGGAACTAATCTGAAACC 59.175 37.037 0.00 0.00 0.00 3.27
189 190 7.016153 ACACTATGGAACTAATCTGAAACCA 57.984 36.000 0.00 0.00 0.00 3.67
190 191 6.879458 ACACTATGGAACTAATCTGAAACCAC 59.121 38.462 0.00 0.00 0.00 4.16
191 192 6.878923 CACTATGGAACTAATCTGAAACCACA 59.121 38.462 0.00 0.00 0.00 4.17
192 193 6.879458 ACTATGGAACTAATCTGAAACCACAC 59.121 38.462 0.00 0.00 0.00 3.82
193 194 5.042463 TGGAACTAATCTGAAACCACACA 57.958 39.130 0.00 0.00 0.00 3.72
194 195 5.441500 TGGAACTAATCTGAAACCACACAA 58.558 37.500 0.00 0.00 0.00 3.33
195 196 5.530915 TGGAACTAATCTGAAACCACACAAG 59.469 40.000 0.00 0.00 0.00 3.16
196 197 5.048713 GGAACTAATCTGAAACCACACAAGG 60.049 44.000 0.00 0.00 0.00 3.61
197 198 5.304686 ACTAATCTGAAACCACACAAGGA 57.695 39.130 0.00 0.00 0.00 3.36
198 199 5.880901 ACTAATCTGAAACCACACAAGGAT 58.119 37.500 0.00 0.00 0.00 3.24
199 200 7.016153 ACTAATCTGAAACCACACAAGGATA 57.984 36.000 0.00 0.00 0.00 2.59
200 201 7.633789 ACTAATCTGAAACCACACAAGGATAT 58.366 34.615 0.00 0.00 0.00 1.63
201 202 8.109634 ACTAATCTGAAACCACACAAGGATATT 58.890 33.333 0.00 0.00 0.00 1.28
202 203 7.396540 AATCTGAAACCACACAAGGATATTC 57.603 36.000 0.00 0.00 0.00 1.75
203 204 5.875224 TCTGAAACCACACAAGGATATTCA 58.125 37.500 0.00 0.00 32.63 2.57
204 205 6.303054 TCTGAAACCACACAAGGATATTCAA 58.697 36.000 0.00 0.00 32.95 2.69
205 206 6.947733 TCTGAAACCACACAAGGATATTCAAT 59.052 34.615 0.00 0.00 32.95 2.57
206 207 6.923012 TGAAACCACACAAGGATATTCAATG 58.077 36.000 0.00 0.00 31.55 2.82
207 208 6.493115 TGAAACCACACAAGGATATTCAATGT 59.507 34.615 0.00 0.00 31.55 2.71
208 209 5.902613 ACCACACAAGGATATTCAATGTG 57.097 39.130 15.00 15.00 45.18 3.21
209 210 4.158394 ACCACACAAGGATATTCAATGTGC 59.842 41.667 16.03 0.00 43.89 4.57
210 211 4.400251 CCACACAAGGATATTCAATGTGCT 59.600 41.667 16.03 5.19 43.89 4.40
211 212 5.337554 CACACAAGGATATTCAATGTGCTG 58.662 41.667 16.03 11.27 43.89 4.41
212 213 5.012239 ACACAAGGATATTCAATGTGCTGT 58.988 37.500 16.03 0.00 43.89 4.40
213 214 5.477984 ACACAAGGATATTCAATGTGCTGTT 59.522 36.000 16.03 0.00 43.89 3.16
214 215 5.803461 CACAAGGATATTCAATGTGCTGTTG 59.197 40.000 6.93 0.00 35.50 3.33
215 216 5.477984 ACAAGGATATTCAATGTGCTGTTGT 59.522 36.000 0.00 0.00 0.00 3.32
216 217 5.824904 AGGATATTCAATGTGCTGTTGTC 57.175 39.130 0.00 0.00 0.00 3.18
217 218 5.255687 AGGATATTCAATGTGCTGTTGTCA 58.744 37.500 0.00 0.00 0.00 3.58
218 219 5.124457 AGGATATTCAATGTGCTGTTGTCAC 59.876 40.000 0.00 0.00 35.14 3.67
219 220 5.124457 GGATATTCAATGTGCTGTTGTCACT 59.876 40.000 0.00 0.00 35.58 3.41
220 221 3.969117 TTCAATGTGCTGTTGTCACTC 57.031 42.857 0.00 0.00 35.58 3.51
221 222 3.198409 TCAATGTGCTGTTGTCACTCT 57.802 42.857 0.00 0.00 35.58 3.24
222 223 2.874086 TCAATGTGCTGTTGTCACTCTG 59.126 45.455 0.00 0.00 35.58 3.35
223 224 1.888215 ATGTGCTGTTGTCACTCTGG 58.112 50.000 0.00 0.00 35.58 3.86
224 225 0.541392 TGTGCTGTTGTCACTCTGGT 59.459 50.000 0.00 0.00 35.58 4.00
225 226 1.760029 TGTGCTGTTGTCACTCTGGTA 59.240 47.619 0.00 0.00 35.58 3.25
226 227 2.224042 TGTGCTGTTGTCACTCTGGTAG 60.224 50.000 0.00 0.00 35.58 3.18
227 228 1.270305 TGCTGTTGTCACTCTGGTAGC 60.270 52.381 0.00 0.00 0.00 3.58
228 229 1.702886 CTGTTGTCACTCTGGTAGCG 58.297 55.000 0.00 0.00 0.00 4.26
229 230 0.319555 TGTTGTCACTCTGGTAGCGC 60.320 55.000 0.00 0.00 0.00 5.92
230 231 0.038159 GTTGTCACTCTGGTAGCGCT 60.038 55.000 17.26 17.26 0.00 5.92
231 232 0.038251 TTGTCACTCTGGTAGCGCTG 60.038 55.000 22.90 4.03 0.00 5.18
232 233 1.807573 GTCACTCTGGTAGCGCTGC 60.808 63.158 22.90 20.34 0.00 5.25
233 234 1.979155 TCACTCTGGTAGCGCTGCT 60.979 57.895 24.82 1.48 43.41 4.24
234 235 1.079543 CACTCTGGTAGCGCTGCTT 60.080 57.895 24.82 0.00 40.44 3.91
235 236 1.079543 ACTCTGGTAGCGCTGCTTG 60.080 57.895 24.82 16.91 40.44 4.01
236 237 1.079543 CTCTGGTAGCGCTGCTTGT 60.080 57.895 24.82 0.00 40.44 3.16
237 238 0.671781 CTCTGGTAGCGCTGCTTGTT 60.672 55.000 24.82 0.00 40.44 2.83
238 239 0.950555 TCTGGTAGCGCTGCTTGTTG 60.951 55.000 24.82 10.63 40.44 3.33
239 240 0.950555 CTGGTAGCGCTGCTTGTTGA 60.951 55.000 24.82 0.00 40.44 3.18
240 241 0.321564 TGGTAGCGCTGCTTGTTGAT 60.322 50.000 24.82 0.00 40.44 2.57
241 242 0.804989 GGTAGCGCTGCTTGTTGATT 59.195 50.000 24.82 0.00 40.44 2.57
242 243 2.006888 GGTAGCGCTGCTTGTTGATTA 58.993 47.619 24.82 0.00 40.44 1.75
243 244 2.030946 GGTAGCGCTGCTTGTTGATTAG 59.969 50.000 24.82 0.00 40.44 1.73
244 245 2.099141 AGCGCTGCTTGTTGATTAGA 57.901 45.000 10.39 0.00 33.89 2.10
270 271 6.555360 AGTCATACTAGATCCTTTAAGTGGGG 59.445 42.308 0.00 0.00 0.00 4.96
282 283 6.896307 TCCTTTAAGTGGGGTTTAAACAAAGA 59.104 34.615 19.57 6.81 0.00 2.52
372 373 7.088272 TCCAATTAGATGGACGTATGTAATCG 58.912 38.462 0.00 0.00 44.52 3.34
735 802 4.340666 ACATCAGGTGTAACAATGCAAACA 59.659 37.500 0.00 0.00 39.91 2.83
906 988 4.091509 CGTTCCTGATTAGTTTCTCGGTTG 59.908 45.833 0.00 0.00 0.00 3.77
908 990 4.817517 TCCTGATTAGTTTCTCGGTTGTC 58.182 43.478 0.00 0.00 0.00 3.18
1411 1542 2.061848 TCCTTGGGGACTGTGATCAAA 58.938 47.619 0.00 0.00 36.57 2.69
1504 1635 6.857964 GTGCAATGGTGATTATATGTGCTTAC 59.142 38.462 0.00 0.00 0.00 2.34
1512 1643 9.077674 GGTGATTATATGTGCTTACTATTCTCG 57.922 37.037 0.00 0.00 0.00 4.04
1601 1734 5.877012 GGAGACAGTCTTATTTTCATGCTCA 59.123 40.000 4.05 0.00 0.00 4.26
1710 1843 5.762179 AGACCATGATGACTTGAAGGTTA 57.238 39.130 0.00 0.00 0.00 2.85
1777 1912 5.070001 TGTGTGCTTATTTCTTGCCTTACT 58.930 37.500 0.00 0.00 0.00 2.24
1873 2009 3.038017 CAACTTTGCTGTTGTCGATGTG 58.962 45.455 0.00 0.00 41.50 3.21
2029 2165 4.443598 GGTGATTCAAGGGTATCTGAGGAC 60.444 50.000 0.00 0.00 0.00 3.85
2101 2247 4.056740 TGCGCATTTTATTTATGCATGGG 58.943 39.130 5.66 0.00 46.77 4.00
2117 3038 3.325716 GCATGGGGGCAATAAGAATGATT 59.674 43.478 0.00 0.00 0.00 2.57
2118 3039 4.202388 GCATGGGGGCAATAAGAATGATTT 60.202 41.667 0.00 0.00 0.00 2.17
2119 3040 5.688235 GCATGGGGGCAATAAGAATGATTTT 60.688 40.000 0.00 0.00 0.00 1.82
2120 3041 6.358991 CATGGGGGCAATAAGAATGATTTTT 58.641 36.000 0.00 0.00 0.00 1.94
2505 3426 6.072893 TGCTAGACAACATATGCATGCAATAG 60.073 38.462 26.68 18.62 35.39 1.73
2509 3430 7.219322 AGACAACATATGCATGCAATAGTCTA 58.781 34.615 26.68 11.84 35.39 2.59
2760 3682 3.550431 CCGGAGATCGCCCACCAT 61.550 66.667 10.18 0.00 37.59 3.55
2780 3702 1.360551 CTCCGATCATCCGAAGCGT 59.639 57.895 0.00 0.00 0.00 5.07
3012 3934 0.182537 CCACCAAACAGACCCTCACA 59.817 55.000 0.00 0.00 0.00 3.58
3321 4247 1.846712 GCCTCCCCTCACAGAAAGCT 61.847 60.000 0.00 0.00 0.00 3.74
4247 5759 3.496675 GGGGGTCCTATGCAAGTTC 57.503 57.895 0.00 0.00 0.00 3.01
4248 5760 0.623723 GGGGGTCCTATGCAAGTTCA 59.376 55.000 0.00 0.00 0.00 3.18
4249 5761 1.215423 GGGGGTCCTATGCAAGTTCAT 59.785 52.381 0.00 0.00 0.00 2.57
4250 5762 2.576615 GGGGTCCTATGCAAGTTCATC 58.423 52.381 0.00 0.00 0.00 2.92
4251 5763 2.213499 GGGTCCTATGCAAGTTCATCG 58.787 52.381 0.00 0.00 0.00 3.84
4252 5764 1.599542 GGTCCTATGCAAGTTCATCGC 59.400 52.381 0.00 0.00 0.00 4.58
4253 5765 1.599542 GTCCTATGCAAGTTCATCGCC 59.400 52.381 0.00 0.00 0.00 5.54
4254 5766 0.947244 CCTATGCAAGTTCATCGCCC 59.053 55.000 0.00 0.00 0.00 6.13
4255 5767 0.947244 CTATGCAAGTTCATCGCCCC 59.053 55.000 0.00 0.00 0.00 5.80
4256 5768 0.546122 TATGCAAGTTCATCGCCCCT 59.454 50.000 0.00 0.00 0.00 4.79
4257 5769 0.749454 ATGCAAGTTCATCGCCCCTC 60.749 55.000 0.00 0.00 0.00 4.30
4258 5770 1.377202 GCAAGTTCATCGCCCCTCA 60.377 57.895 0.00 0.00 0.00 3.86
4259 5771 1.648467 GCAAGTTCATCGCCCCTCAC 61.648 60.000 0.00 0.00 0.00 3.51
4325 5837 3.974719 TGGCCAGCTCAACCAAAATATA 58.025 40.909 0.00 0.00 0.00 0.86
4473 6415 0.906775 TTCATACGACTTGGGGTCCC 59.093 55.000 0.00 0.00 41.64 4.46
4532 6480 1.211457 AGGTTTTGGCACCATTTTGCA 59.789 42.857 0.00 0.00 44.94 4.08
4571 6519 7.928706 CACTGGTTTGGTCCATTTTACATTTTA 59.071 33.333 0.00 0.00 36.84 1.52
4674 6632 0.831711 TGAGCACACAGGCACTCCTA 60.832 55.000 0.00 0.00 41.93 2.94
4756 6723 5.619625 AGAAGCTGCAAATCTAGTGTTTC 57.380 39.130 1.02 0.00 0.00 2.78
4813 6780 7.042389 GCCTTCTCACTTGTACTCTTATATTGC 60.042 40.741 0.00 0.00 0.00 3.56
5145 7128 3.334583 ACAGCAACCATGTACCACTAG 57.665 47.619 0.00 0.00 0.00 2.57
5347 7332 7.912250 GTGCCATTTACTATTTCATCTCTGTTG 59.088 37.037 0.00 0.00 0.00 3.33
5374 7359 7.926555 TGATTACAACTAGCTAATAGCCAGAAC 59.073 37.037 14.31 0.00 43.77 3.01
5788 10057 0.042731 TGGCTACTACTGGGGAGCTT 59.957 55.000 6.98 0.00 35.23 3.74
5815 10084 0.320771 GGACAGGCACACTCGATTGT 60.321 55.000 2.04 2.04 0.00 2.71
6079 10358 4.161189 TGGTCAAAGCTTGAATTTGGACAA 59.839 37.500 0.00 0.00 42.15 3.18
6284 10589 8.472007 TTGGTGGACATTTACAAAATTCTAGT 57.528 30.769 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.573900 CCATAAGGCTAGCATAACCTCTG 58.426 47.826 18.24 5.47 31.86 3.35
1 2 4.899352 CCATAAGGCTAGCATAACCTCT 57.101 45.455 18.24 0.00 31.86 3.69
15 16 2.917933 TCATTGAACTCGGCCATAAGG 58.082 47.619 2.24 0.00 38.23 2.69
16 17 3.242413 CGTTCATTGAACTCGGCCATAAG 60.242 47.826 23.29 0.00 40.05 1.73
17 18 2.675844 CGTTCATTGAACTCGGCCATAA 59.324 45.455 23.29 0.00 40.05 1.90
18 19 2.276201 CGTTCATTGAACTCGGCCATA 58.724 47.619 23.29 0.00 40.05 2.74
19 20 1.086696 CGTTCATTGAACTCGGCCAT 58.913 50.000 23.29 0.00 40.05 4.40
20 21 1.573829 GCGTTCATTGAACTCGGCCA 61.574 55.000 23.29 0.00 40.05 5.36
21 22 1.134694 GCGTTCATTGAACTCGGCC 59.865 57.895 23.29 0.00 40.05 6.13
22 23 0.452784 GTGCGTTCATTGAACTCGGC 60.453 55.000 23.29 19.58 40.05 5.54
23 24 0.165944 GGTGCGTTCATTGAACTCGG 59.834 55.000 23.29 11.84 40.05 4.63
24 25 0.179250 CGGTGCGTTCATTGAACTCG 60.179 55.000 23.29 17.45 40.05 4.18
25 26 0.165944 CCGGTGCGTTCATTGAACTC 59.834 55.000 23.29 17.71 40.05 3.01
26 27 0.534203 ACCGGTGCGTTCATTGAACT 60.534 50.000 23.29 4.08 40.05 3.01
27 28 1.127951 CTACCGGTGCGTTCATTGAAC 59.872 52.381 19.93 17.76 38.97 3.18
28 29 1.434555 CTACCGGTGCGTTCATTGAA 58.565 50.000 19.93 0.00 0.00 2.69
29 30 0.390603 CCTACCGGTGCGTTCATTGA 60.391 55.000 19.93 0.00 0.00 2.57
30 31 0.390603 TCCTACCGGTGCGTTCATTG 60.391 55.000 19.93 0.00 0.00 2.82
31 32 0.322322 TTCCTACCGGTGCGTTCATT 59.678 50.000 19.93 0.00 0.00 2.57
32 33 0.390735 GTTCCTACCGGTGCGTTCAT 60.391 55.000 19.93 0.00 0.00 2.57
33 34 1.005867 GTTCCTACCGGTGCGTTCA 60.006 57.895 19.93 0.00 0.00 3.18
34 35 0.390735 ATGTTCCTACCGGTGCGTTC 60.391 55.000 19.93 5.66 0.00 3.95
35 36 0.896923 TATGTTCCTACCGGTGCGTT 59.103 50.000 19.93 0.00 0.00 4.84
36 37 0.458669 CTATGTTCCTACCGGTGCGT 59.541 55.000 19.93 6.15 0.00 5.24
37 38 0.874607 GCTATGTTCCTACCGGTGCG 60.875 60.000 19.93 8.16 0.00 5.34
38 39 0.464452 AGCTATGTTCCTACCGGTGC 59.536 55.000 19.93 8.68 0.00 5.01
39 40 1.480954 ACAGCTATGTTCCTACCGGTG 59.519 52.381 19.93 7.24 35.63 4.94
40 41 1.861982 ACAGCTATGTTCCTACCGGT 58.138 50.000 13.98 13.98 35.63 5.28
41 42 2.981859 AACAGCTATGTTCCTACCGG 57.018 50.000 0.00 0.00 46.90 5.28
42 43 6.090898 GCATATTAACAGCTATGTTCCTACCG 59.909 42.308 0.00 0.00 46.90 4.02
43 44 7.118390 CAGCATATTAACAGCTATGTTCCTACC 59.882 40.741 0.00 0.00 46.90 3.18
44 45 7.360438 GCAGCATATTAACAGCTATGTTCCTAC 60.360 40.741 0.00 0.00 46.90 3.18
45 46 6.650807 GCAGCATATTAACAGCTATGTTCCTA 59.349 38.462 0.00 0.00 46.90 2.94
46 47 5.471456 GCAGCATATTAACAGCTATGTTCCT 59.529 40.000 0.00 0.00 46.90 3.36
47 48 5.239306 TGCAGCATATTAACAGCTATGTTCC 59.761 40.000 0.00 0.00 46.90 3.62
48 49 6.304356 TGCAGCATATTAACAGCTATGTTC 57.696 37.500 0.00 0.00 46.90 3.18
50 51 6.294342 CCAATGCAGCATATTAACAGCTATGT 60.294 38.462 8.75 0.00 43.15 2.29
51 52 6.072342 TCCAATGCAGCATATTAACAGCTATG 60.072 38.462 8.75 0.00 36.73 2.23
52 53 6.005823 TCCAATGCAGCATATTAACAGCTAT 58.994 36.000 8.75 0.00 36.73 2.97
53 54 5.375773 TCCAATGCAGCATATTAACAGCTA 58.624 37.500 8.75 0.00 36.73 3.32
54 55 4.209538 TCCAATGCAGCATATTAACAGCT 58.790 39.130 8.75 0.00 39.63 4.24
55 56 4.572985 TCCAATGCAGCATATTAACAGC 57.427 40.909 8.75 0.00 0.00 4.40
56 57 5.893687 TGTTCCAATGCAGCATATTAACAG 58.106 37.500 18.51 2.56 0.00 3.16
57 58 5.911378 TGTTCCAATGCAGCATATTAACA 57.089 34.783 18.51 18.51 0.00 2.41
58 59 5.232838 GCTTGTTCCAATGCAGCATATTAAC 59.767 40.000 8.75 12.93 0.00 2.01
59 60 5.127519 AGCTTGTTCCAATGCAGCATATTAA 59.872 36.000 8.75 0.12 0.00 1.40
60 61 4.646040 AGCTTGTTCCAATGCAGCATATTA 59.354 37.500 8.75 0.00 0.00 0.98
61 62 3.449737 AGCTTGTTCCAATGCAGCATATT 59.550 39.130 8.75 0.00 0.00 1.28
62 63 3.028850 AGCTTGTTCCAATGCAGCATAT 58.971 40.909 8.75 0.00 0.00 1.78
63 64 2.424601 GAGCTTGTTCCAATGCAGCATA 59.575 45.455 8.75 0.00 0.00 3.14
64 65 1.203994 GAGCTTGTTCCAATGCAGCAT 59.796 47.619 0.52 0.52 0.00 3.79
65 66 0.599558 GAGCTTGTTCCAATGCAGCA 59.400 50.000 0.00 0.00 0.00 4.41
66 67 0.886563 AGAGCTTGTTCCAATGCAGC 59.113 50.000 0.00 0.00 0.00 5.25
67 68 2.352421 CCAAGAGCTTGTTCCAATGCAG 60.352 50.000 9.18 0.00 38.85 4.41
68 69 1.614903 CCAAGAGCTTGTTCCAATGCA 59.385 47.619 9.18 0.00 38.85 3.96
69 70 1.615392 ACCAAGAGCTTGTTCCAATGC 59.385 47.619 9.18 0.00 38.85 3.56
70 71 5.649782 ATTACCAAGAGCTTGTTCCAATG 57.350 39.130 9.18 0.00 38.85 2.82
71 72 6.267471 TGAAATTACCAAGAGCTTGTTCCAAT 59.733 34.615 9.18 1.30 38.85 3.16
72 73 5.596361 TGAAATTACCAAGAGCTTGTTCCAA 59.404 36.000 9.18 0.00 38.85 3.53
73 74 5.136828 TGAAATTACCAAGAGCTTGTTCCA 58.863 37.500 9.18 0.00 38.85 3.53
74 75 5.705609 TGAAATTACCAAGAGCTTGTTCC 57.294 39.130 9.18 0.00 38.85 3.62
75 76 8.419076 TTTTTGAAATTACCAAGAGCTTGTTC 57.581 30.769 9.18 6.54 38.85 3.18
76 77 8.962884 ATTTTTGAAATTACCAAGAGCTTGTT 57.037 26.923 9.18 0.00 38.85 2.83
77 78 9.696917 CTATTTTTGAAATTACCAAGAGCTTGT 57.303 29.630 9.18 1.18 38.85 3.16
78 79 9.912634 TCTATTTTTGAAATTACCAAGAGCTTG 57.087 29.630 3.27 3.27 40.13 4.01
91 92 9.264719 CCAAGAGCTTGTTTCTATTTTTGAAAT 57.735 29.630 9.18 0.00 38.85 2.17
92 93 8.257306 ACCAAGAGCTTGTTTCTATTTTTGAAA 58.743 29.630 9.18 0.00 38.85 2.69
93 94 7.781056 ACCAAGAGCTTGTTTCTATTTTTGAA 58.219 30.769 9.18 0.00 38.85 2.69
94 95 7.346751 ACCAAGAGCTTGTTTCTATTTTTGA 57.653 32.000 9.18 0.00 38.85 2.69
95 96 9.696917 ATTACCAAGAGCTTGTTTCTATTTTTG 57.303 29.630 9.18 0.00 38.85 2.44
99 100 9.914131 GAAAATTACCAAGAGCTTGTTTCTATT 57.086 29.630 9.18 0.00 38.85 1.73
100 101 9.077885 TGAAAATTACCAAGAGCTTGTTTCTAT 57.922 29.630 16.94 2.16 38.85 1.98
101 102 8.458573 TGAAAATTACCAAGAGCTTGTTTCTA 57.541 30.769 16.94 7.43 38.85 2.10
102 103 7.346751 TGAAAATTACCAAGAGCTTGTTTCT 57.653 32.000 16.94 0.00 38.85 2.52
103 104 8.419076 TTTGAAAATTACCAAGAGCTTGTTTC 57.581 30.769 9.18 11.18 38.85 2.78
104 105 8.785329 TTTTGAAAATTACCAAGAGCTTGTTT 57.215 26.923 9.18 3.15 38.85 2.83
105 106 8.785329 TTTTTGAAAATTACCAAGAGCTTGTT 57.215 26.923 9.18 0.00 38.85 2.83
158 159 9.793259 TCAGATTAGTTCCATAGTGTTCTTTTT 57.207 29.630 0.00 0.00 0.00 1.94
159 160 9.793259 TTCAGATTAGTTCCATAGTGTTCTTTT 57.207 29.630 0.00 0.00 0.00 2.27
160 161 9.793259 TTTCAGATTAGTTCCATAGTGTTCTTT 57.207 29.630 0.00 0.00 0.00 2.52
161 162 9.220767 GTTTCAGATTAGTTCCATAGTGTTCTT 57.779 33.333 0.00 0.00 0.00 2.52
162 163 7.824779 GGTTTCAGATTAGTTCCATAGTGTTCT 59.175 37.037 0.00 0.00 0.00 3.01
163 164 7.606456 TGGTTTCAGATTAGTTCCATAGTGTTC 59.394 37.037 0.00 0.00 0.00 3.18
164 165 7.390718 GTGGTTTCAGATTAGTTCCATAGTGTT 59.609 37.037 0.00 0.00 0.00 3.32
165 166 6.879458 GTGGTTTCAGATTAGTTCCATAGTGT 59.121 38.462 0.00 0.00 0.00 3.55
166 167 6.878923 TGTGGTTTCAGATTAGTTCCATAGTG 59.121 38.462 0.00 0.00 0.00 2.74
167 168 6.879458 GTGTGGTTTCAGATTAGTTCCATAGT 59.121 38.462 0.00 0.00 0.00 2.12
168 169 6.878923 TGTGTGGTTTCAGATTAGTTCCATAG 59.121 38.462 0.00 0.00 0.00 2.23
169 170 6.774673 TGTGTGGTTTCAGATTAGTTCCATA 58.225 36.000 0.00 0.00 0.00 2.74
170 171 5.630121 TGTGTGGTTTCAGATTAGTTCCAT 58.370 37.500 0.00 0.00 0.00 3.41
171 172 5.042463 TGTGTGGTTTCAGATTAGTTCCA 57.958 39.130 0.00 0.00 0.00 3.53
172 173 5.048713 CCTTGTGTGGTTTCAGATTAGTTCC 60.049 44.000 0.00 0.00 0.00 3.62
173 174 5.763204 TCCTTGTGTGGTTTCAGATTAGTTC 59.237 40.000 0.00 0.00 0.00 3.01
174 175 5.690865 TCCTTGTGTGGTTTCAGATTAGTT 58.309 37.500 0.00 0.00 0.00 2.24
175 176 5.304686 TCCTTGTGTGGTTTCAGATTAGT 57.695 39.130 0.00 0.00 0.00 2.24
176 177 8.511604 AATATCCTTGTGTGGTTTCAGATTAG 57.488 34.615 0.00 0.00 0.00 1.73
177 178 8.106462 TGAATATCCTTGTGTGGTTTCAGATTA 58.894 33.333 0.00 0.00 0.00 1.75
178 179 6.947733 TGAATATCCTTGTGTGGTTTCAGATT 59.052 34.615 0.00 0.00 0.00 2.40
179 180 6.484288 TGAATATCCTTGTGTGGTTTCAGAT 58.516 36.000 0.00 0.00 0.00 2.90
180 181 5.875224 TGAATATCCTTGTGTGGTTTCAGA 58.125 37.500 0.00 0.00 0.00 3.27
181 182 6.573664 TTGAATATCCTTGTGTGGTTTCAG 57.426 37.500 0.00 0.00 0.00 3.02
182 183 6.493115 ACATTGAATATCCTTGTGTGGTTTCA 59.507 34.615 0.00 0.00 0.00 2.69
183 184 6.808212 CACATTGAATATCCTTGTGTGGTTTC 59.192 38.462 0.00 0.00 34.43 2.78
184 185 6.690530 CACATTGAATATCCTTGTGTGGTTT 58.309 36.000 0.00 0.00 34.43 3.27
185 186 5.336690 GCACATTGAATATCCTTGTGTGGTT 60.337 40.000 0.00 0.00 39.79 3.67
186 187 4.158394 GCACATTGAATATCCTTGTGTGGT 59.842 41.667 0.00 0.00 39.79 4.16
187 188 4.400251 AGCACATTGAATATCCTTGTGTGG 59.600 41.667 0.00 0.00 39.79 4.17
188 189 5.106038 ACAGCACATTGAATATCCTTGTGTG 60.106 40.000 0.00 0.00 39.79 3.82
189 190 5.012239 ACAGCACATTGAATATCCTTGTGT 58.988 37.500 0.00 0.00 39.79 3.72
190 191 5.571784 ACAGCACATTGAATATCCTTGTG 57.428 39.130 0.00 0.00 40.42 3.33
191 192 5.477984 ACAACAGCACATTGAATATCCTTGT 59.522 36.000 2.06 0.00 0.00 3.16
192 193 5.957798 ACAACAGCACATTGAATATCCTTG 58.042 37.500 2.06 0.00 0.00 3.61
193 194 5.711506 TGACAACAGCACATTGAATATCCTT 59.288 36.000 2.06 0.00 0.00 3.36
194 195 5.124457 GTGACAACAGCACATTGAATATCCT 59.876 40.000 2.06 0.00 36.31 3.24
195 196 5.124457 AGTGACAACAGCACATTGAATATCC 59.876 40.000 0.00 0.00 38.70 2.59
196 197 6.093219 AGAGTGACAACAGCACATTGAATATC 59.907 38.462 0.00 0.00 38.70 1.63
197 198 5.942236 AGAGTGACAACAGCACATTGAATAT 59.058 36.000 0.00 0.00 38.70 1.28
198 199 5.179929 CAGAGTGACAACAGCACATTGAATA 59.820 40.000 0.00 0.00 38.70 1.75
199 200 4.023450 CAGAGTGACAACAGCACATTGAAT 60.023 41.667 0.00 0.00 38.70 2.57
200 201 3.313249 CAGAGTGACAACAGCACATTGAA 59.687 43.478 0.00 0.00 38.70 2.69
201 202 2.874086 CAGAGTGACAACAGCACATTGA 59.126 45.455 0.00 0.00 38.70 2.57
202 203 2.031420 CCAGAGTGACAACAGCACATTG 60.031 50.000 0.00 0.00 38.70 2.82
203 204 2.224606 CCAGAGTGACAACAGCACATT 58.775 47.619 0.00 0.00 38.70 2.71
204 205 1.141657 ACCAGAGTGACAACAGCACAT 59.858 47.619 0.00 0.00 38.70 3.21
205 206 0.541392 ACCAGAGTGACAACAGCACA 59.459 50.000 0.00 0.00 38.70 4.57
206 207 2.408050 CTACCAGAGTGACAACAGCAC 58.592 52.381 0.00 0.00 36.53 4.40
207 208 1.270305 GCTACCAGAGTGACAACAGCA 60.270 52.381 0.00 0.00 0.00 4.41
208 209 1.433534 GCTACCAGAGTGACAACAGC 58.566 55.000 0.00 0.00 0.00 4.40
209 210 1.702886 CGCTACCAGAGTGACAACAG 58.297 55.000 0.00 0.00 37.96 3.16
210 211 0.319555 GCGCTACCAGAGTGACAACA 60.320 55.000 0.00 0.00 37.96 3.33
211 212 0.038159 AGCGCTACCAGAGTGACAAC 60.038 55.000 8.99 0.00 37.96 3.32
212 213 0.038251 CAGCGCTACCAGAGTGACAA 60.038 55.000 10.99 0.00 37.96 3.18
213 214 1.586541 CAGCGCTACCAGAGTGACA 59.413 57.895 10.99 0.00 37.96 3.58
214 215 1.807573 GCAGCGCTACCAGAGTGAC 60.808 63.158 10.99 0.00 37.96 3.67
215 216 1.536073 AAGCAGCGCTACCAGAGTGA 61.536 55.000 10.99 0.00 38.25 3.41
216 217 1.079543 AAGCAGCGCTACCAGAGTG 60.080 57.895 10.99 0.00 38.25 3.51
217 218 1.079543 CAAGCAGCGCTACCAGAGT 60.080 57.895 10.99 0.00 38.25 3.24
218 219 0.671781 AACAAGCAGCGCTACCAGAG 60.672 55.000 10.99 0.00 38.25 3.35
219 220 0.950555 CAACAAGCAGCGCTACCAGA 60.951 55.000 10.99 0.00 38.25 3.86
220 221 0.950555 TCAACAAGCAGCGCTACCAG 60.951 55.000 10.99 1.86 38.25 4.00
221 222 0.321564 ATCAACAAGCAGCGCTACCA 60.322 50.000 10.99 0.00 38.25 3.25
222 223 0.804989 AATCAACAAGCAGCGCTACC 59.195 50.000 10.99 3.97 38.25 3.18
223 224 2.930040 TCTAATCAACAAGCAGCGCTAC 59.070 45.455 10.99 3.74 38.25 3.58
224 225 3.245518 TCTAATCAACAAGCAGCGCTA 57.754 42.857 10.99 0.00 38.25 4.26
225 226 2.099141 TCTAATCAACAAGCAGCGCT 57.901 45.000 2.64 2.64 42.56 5.92
226 227 2.160417 ACTTCTAATCAACAAGCAGCGC 59.840 45.455 0.00 0.00 0.00 5.92
227 228 3.433274 TGACTTCTAATCAACAAGCAGCG 59.567 43.478 0.00 0.00 0.00 5.18
228 229 5.557891 ATGACTTCTAATCAACAAGCAGC 57.442 39.130 0.00 0.00 0.00 5.25
229 230 7.840342 AGTATGACTTCTAATCAACAAGCAG 57.160 36.000 0.00 0.00 0.00 4.24
230 231 8.749354 TCTAGTATGACTTCTAATCAACAAGCA 58.251 33.333 0.00 0.00 0.00 3.91
231 232 9.757227 ATCTAGTATGACTTCTAATCAACAAGC 57.243 33.333 0.00 0.00 0.00 4.01
234 235 9.647918 AGGATCTAGTATGACTTCTAATCAACA 57.352 33.333 0.00 0.00 0.00 3.33
242 243 8.919145 CCACTTAAAGGATCTAGTATGACTTCT 58.081 37.037 0.00 0.00 0.00 2.85
243 244 8.145122 CCCACTTAAAGGATCTAGTATGACTTC 58.855 40.741 0.00 0.00 0.00 3.01
244 245 7.071321 CCCCACTTAAAGGATCTAGTATGACTT 59.929 40.741 0.00 0.00 0.00 3.01
265 266 8.799367 AGTATACAATCTTTGTTTAAACCCCAC 58.201 33.333 15.59 0.00 42.22 4.61
266 267 8.943594 AGTATACAATCTTTGTTTAAACCCCA 57.056 30.769 15.59 0.00 42.22 4.96
296 297 6.976088 TGATTAGGTGTGTACAATTTTGGTG 58.024 36.000 0.00 0.00 0.00 4.17
360 361 3.390135 CAATGGAGCCGATTACATACGT 58.610 45.455 0.00 0.00 0.00 3.57
363 364 2.778299 GGCAATGGAGCCGATTACATA 58.222 47.619 0.00 0.00 46.12 2.29
735 802 2.158623 TGGAGTGCTGACATGAAAAGGT 60.159 45.455 0.00 0.00 0.00 3.50
906 988 6.304683 GTGGTGAAGCAACAATATAAAACGAC 59.695 38.462 0.00 0.00 30.77 4.34
908 990 6.378582 AGTGGTGAAGCAACAATATAAAACG 58.621 36.000 0.00 0.00 30.77 3.60
1318 1400 7.648908 TCAATTAAAGCTCTGAAAATGTGTGTG 59.351 33.333 0.00 0.00 0.00 3.82
1319 1401 7.715657 TCAATTAAAGCTCTGAAAATGTGTGT 58.284 30.769 0.00 0.00 0.00 3.72
1320 1402 8.752766 ATCAATTAAAGCTCTGAAAATGTGTG 57.247 30.769 0.00 0.00 0.00 3.82
1411 1542 0.608640 CTAAGCCTGGACCGAACACT 59.391 55.000 0.00 0.00 0.00 3.55
1601 1734 0.035458 GGCGTTCCATAGCTATGCCT 59.965 55.000 25.60 0.00 40.14 4.75
1710 1843 4.572389 CAGTAAAGGATGATTGTTAGCGCT 59.428 41.667 17.26 17.26 0.00 5.92
1873 2009 2.676076 ACATTTTCAAGGAACGCATGC 58.324 42.857 7.91 7.91 0.00 4.06
2029 2165 9.861138 GAGATTTTACAATCAAGATCTTCATCG 57.139 33.333 4.57 0.00 41.37 3.84
2181 3102 2.507407 ACACAACAAAGGTGACAGGT 57.493 45.000 0.00 0.00 39.53 4.00
2365 3286 6.320418 ACCTGTAAACCTTCGAAGTTTTTGAT 59.680 34.615 23.24 4.51 38.37 2.57
2505 3426 4.268884 GGAACAACAGCGAATGATCTAGAC 59.731 45.833 0.00 0.00 0.00 2.59
2509 3430 3.340814 AGGAACAACAGCGAATGATCT 57.659 42.857 0.00 0.00 0.00 2.75
2780 3702 0.535335 GAGGTGCTGATTGGTACCGA 59.465 55.000 3.71 3.71 44.73 4.69
2815 3737 2.810887 GCAGCAGCGTCGTCATCA 60.811 61.111 0.00 0.00 0.00 3.07
3027 3949 1.016130 CGGCGTGAGAAGCTTCATGT 61.016 55.000 27.57 7.87 36.64 3.21
3030 3952 1.372997 GACGGCGTGAGAAGCTTCA 60.373 57.895 27.57 6.62 34.52 3.02
3137 4060 3.363351 GTCGAGACGGTGGAGGTT 58.637 61.111 0.00 0.00 0.00 3.50
3310 4235 1.544093 CCTCTTGGCAGCTTTCTGTGA 60.544 52.381 0.00 0.00 42.29 3.58
3321 4247 1.228245 GTGGTGCTTCCTCTTGGCA 60.228 57.895 0.00 0.00 37.07 4.92
3416 4343 2.874664 CGTTGGTTCCCCTCCGTCA 61.875 63.158 0.00 0.00 0.00 4.35
4235 5747 0.947244 GGGCGATGAACTTGCATAGG 59.053 55.000 0.00 0.00 35.78 2.57
4237 5749 0.546122 AGGGGCGATGAACTTGCATA 59.454 50.000 0.00 0.00 35.78 3.14
4238 5750 0.749454 GAGGGGCGATGAACTTGCAT 60.749 55.000 0.00 0.00 35.78 3.96
4239 5751 1.377202 GAGGGGCGATGAACTTGCA 60.377 57.895 0.00 0.00 35.78 4.08
4240 5752 1.377202 TGAGGGGCGATGAACTTGC 60.377 57.895 0.00 0.00 0.00 4.01
4241 5753 1.361668 CGTGAGGGGCGATGAACTTG 61.362 60.000 0.00 0.00 0.00 3.16
4242 5754 1.079127 CGTGAGGGGCGATGAACTT 60.079 57.895 0.00 0.00 0.00 2.66
4243 5755 2.579201 CGTGAGGGGCGATGAACT 59.421 61.111 0.00 0.00 0.00 3.01
4244 5756 3.195698 GCGTGAGGGGCGATGAAC 61.196 66.667 0.00 0.00 0.00 3.18
4245 5757 2.463589 AAAGCGTGAGGGGCGATGAA 62.464 55.000 0.00 0.00 35.00 2.57
4246 5758 2.954684 AAAGCGTGAGGGGCGATGA 61.955 57.895 0.00 0.00 35.00 2.92
4247 5759 2.436646 AAAGCGTGAGGGGCGATG 60.437 61.111 0.00 0.00 35.00 3.84
4248 5760 2.436646 CAAAGCGTGAGGGGCGAT 60.437 61.111 0.00 0.00 35.00 4.58
4251 5763 3.741476 CTGCAAAGCGTGAGGGGC 61.741 66.667 0.00 0.00 0.00 5.80
4252 5764 1.856265 GAACTGCAAAGCGTGAGGGG 61.856 60.000 0.00 0.00 0.00 4.79
4253 5765 1.165907 TGAACTGCAAAGCGTGAGGG 61.166 55.000 0.00 0.00 0.00 4.30
4254 5766 0.040958 GTGAACTGCAAAGCGTGAGG 60.041 55.000 0.00 0.00 0.00 3.86
4255 5767 0.657312 TGTGAACTGCAAAGCGTGAG 59.343 50.000 0.00 0.00 0.00 3.51
4256 5768 1.090728 TTGTGAACTGCAAAGCGTGA 58.909 45.000 0.00 0.00 0.00 4.35
4257 5769 1.782569 CATTGTGAACTGCAAAGCGTG 59.217 47.619 0.00 0.00 0.00 5.34
4258 5770 1.405105 ACATTGTGAACTGCAAAGCGT 59.595 42.857 0.00 0.00 0.00 5.07
4259 5771 2.124011 ACATTGTGAACTGCAAAGCG 57.876 45.000 0.00 0.00 0.00 4.68
4473 6415 9.206690 TCATAGGCAAGGAATAAGATAGATAGG 57.793 37.037 0.00 0.00 0.00 2.57
4532 6480 5.951747 ACCAAACCAGTGAGTGCATTAATAT 59.048 36.000 0.00 0.00 0.00 1.28
4545 6493 4.927978 TGTAAAATGGACCAAACCAGTG 57.072 40.909 0.00 0.00 43.49 3.66
4546 6494 6.493189 AAATGTAAAATGGACCAAACCAGT 57.507 33.333 0.00 0.00 43.49 4.00
4547 6495 8.147704 ACTAAAATGTAAAATGGACCAAACCAG 58.852 33.333 0.00 0.00 43.49 4.00
4548 6496 8.024145 ACTAAAATGTAAAATGGACCAAACCA 57.976 30.769 0.00 0.00 44.41 3.67
4615 6564 4.074970 AGATTTCACACATGTGGGTCTTC 58.925 43.478 26.79 19.75 45.65 2.87
4674 6632 2.105477 ACCACAATGTTGAGCAGTCTCT 59.895 45.455 0.00 0.00 40.03 3.10
4841 6808 5.239525 GGATGAACATACCCAAGAATGTAGC 59.760 44.000 0.00 0.00 35.30 3.58
5347 7332 7.644986 CTGGCTATTAGCTAGTTGTAATCAC 57.355 40.000 18.16 0.00 43.76 3.06
5374 7359 2.009774 CTTTTCTCCTGCGTACCATGG 58.990 52.381 11.19 11.19 0.00 3.66
5815 10084 5.123186 ACACGTTGAAGTTGTGAGAAAATCA 59.877 36.000 0.00 0.00 37.08 2.57
5825 10094 6.431198 AGTGATTTTACACGTTGAAGTTGT 57.569 33.333 0.00 0.00 44.35 3.32
6050 10328 7.039152 TCCAAATTCAAGCTTTGACCATTGATA 60.039 33.333 0.00 0.00 39.87 2.15
6284 10589 8.610248 TGAATACCTTTTTGTCTCAAACGATA 57.390 30.769 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.