Multiple sequence alignment - TraesCS6A01G317000

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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 TraesCS6A01G317000 chr6A 100.000 2499 0 0 1 2499 553187524 553190022 0.000000e+00 4615
1 TraesCS6A01G317000 chr6D 91.725 1994 80 34 505 2471 407828489 407830424 0.000000e+00 2689
2 TraesCS6A01G317000 chr6D 88.803 259 24 2 252 505 407827982 407828240 1.870000e-81 313
3 TraesCS6A01G317000 chr6B 91.437 1308 46 23 1176 2465 612133567 612134826 0.000000e+00 1735
4 TraesCS6A01G317000 chr6B 92.849 909 50 10 228 1122 612132640 612133547 0.000000e+00 1304


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 TraesCS6A01G317000 chr6A 553187524 553190022 2498 False 4615.0 4615 100.000 1 2499 1 chr6A.!!$F1 2498
1 TraesCS6A01G317000 chr6D 407827982 407830424 2442 False 1501.0 2689 90.264 252 2471 2 chr6D.!!$F1 2219
2 TraesCS6A01G317000 chr6B 612132640 612134826 2186 False 1519.5 1735 92.143 228 2465 2 chr6B.!!$F1 2237

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
518 775 0.251922 ACACTAGGAGCCGTGGGTTA 60.252 55.0 0.0 0.0 35.51 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2452 2758 0.038159 CTCTCGGGTCTTGACACACC 60.038 60.0 3.83 0.0 0.0 4.16 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 6.400568 TGAAATCCATTTGAATCAAAGGAGC 58.599 36.000 20.19 15.05 37.32 4.70
26 27 5.349061 AATCCATTTGAATCAAAGGAGCC 57.651 39.130 20.19 0.00 37.32 4.70
27 28 4.051661 TCCATTTGAATCAAAGGAGCCT 57.948 40.909 20.19 0.00 37.32 4.58
28 29 4.419282 TCCATTTGAATCAAAGGAGCCTT 58.581 39.130 20.19 0.00 37.32 4.35
29 30 4.221262 TCCATTTGAATCAAAGGAGCCTTG 59.779 41.667 20.19 8.71 37.32 3.61
30 31 4.221262 CCATTTGAATCAAAGGAGCCTTGA 59.779 41.667 20.19 3.58 37.32 3.02
31 32 5.279607 CCATTTGAATCAAAGGAGCCTTGAA 60.280 40.000 20.19 0.00 37.32 2.69
32 33 5.867903 TTTGAATCAAAGGAGCCTTGAAA 57.132 34.783 4.03 0.00 36.26 2.69
33 34 5.867903 TTGAATCAAAGGAGCCTTGAAAA 57.132 34.783 1.91 0.00 36.26 2.29
34 35 5.867903 TGAATCAAAGGAGCCTTGAAAAA 57.132 34.783 1.91 0.00 36.26 1.94
35 36 6.423776 TGAATCAAAGGAGCCTTGAAAAAT 57.576 33.333 1.91 0.00 36.26 1.82
36 37 6.829849 TGAATCAAAGGAGCCTTGAAAAATT 58.170 32.000 1.91 0.00 36.26 1.82
37 38 7.281841 TGAATCAAAGGAGCCTTGAAAAATTT 58.718 30.769 1.91 0.00 36.26 1.82
38 39 7.227116 TGAATCAAAGGAGCCTTGAAAAATTTG 59.773 33.333 1.91 0.00 36.26 2.32
39 40 5.367302 TCAAAGGAGCCTTGAAAAATTTGG 58.633 37.500 1.91 0.00 36.26 3.28
40 41 4.356405 AAGGAGCCTTGAAAAATTTGGG 57.644 40.909 0.00 0.00 34.60 4.12
41 42 2.639347 AGGAGCCTTGAAAAATTTGGGG 59.361 45.455 0.00 0.00 0.00 4.96
42 43 2.637382 GGAGCCTTGAAAAATTTGGGGA 59.363 45.455 0.00 0.00 0.00 4.81
43 44 3.557054 GGAGCCTTGAAAAATTTGGGGAC 60.557 47.826 0.00 0.00 0.00 4.46
58 59 2.455674 GGGACCAATTTCTTTGCCAC 57.544 50.000 0.00 0.00 33.73 5.01
59 60 1.336795 GGGACCAATTTCTTTGCCACG 60.337 52.381 0.00 0.00 33.73 4.94
60 61 1.339929 GGACCAATTTCTTTGCCACGT 59.660 47.619 0.00 0.00 33.73 4.49
61 62 2.223947 GGACCAATTTCTTTGCCACGTT 60.224 45.455 0.00 0.00 33.73 3.99
62 63 2.794350 GACCAATTTCTTTGCCACGTTG 59.206 45.455 0.00 0.00 33.73 4.10
63 64 2.428890 ACCAATTTCTTTGCCACGTTGA 59.571 40.909 0.00 0.00 33.73 3.18
64 65 3.118956 ACCAATTTCTTTGCCACGTTGAA 60.119 39.130 0.00 0.00 33.73 2.69
65 66 3.868077 CCAATTTCTTTGCCACGTTGAAA 59.132 39.130 0.00 0.00 33.73 2.69
66 67 4.511082 CCAATTTCTTTGCCACGTTGAAAT 59.489 37.500 0.00 0.00 38.49 2.17
67 68 5.007528 CCAATTTCTTTGCCACGTTGAAATT 59.992 36.000 0.00 0.00 43.62 1.82
68 69 5.905480 ATTTCTTTGCCACGTTGAAATTC 57.095 34.783 0.00 0.00 34.83 2.17
69 70 2.993545 TCTTTGCCACGTTGAAATTCG 58.006 42.857 0.00 0.00 0.00 3.34
70 71 2.614520 TCTTTGCCACGTTGAAATTCGA 59.385 40.909 0.00 0.00 0.00 3.71
71 72 2.392933 TTGCCACGTTGAAATTCGAC 57.607 45.000 3.29 3.29 0.00 4.20
72 73 1.588674 TGCCACGTTGAAATTCGACT 58.411 45.000 11.22 0.00 0.00 4.18
73 74 2.756829 TGCCACGTTGAAATTCGACTA 58.243 42.857 11.22 0.00 0.00 2.59
74 75 3.331150 TGCCACGTTGAAATTCGACTAT 58.669 40.909 11.22 0.00 0.00 2.12
75 76 3.124466 TGCCACGTTGAAATTCGACTATG 59.876 43.478 11.22 9.00 0.00 2.23
76 77 3.369756 GCCACGTTGAAATTCGACTATGA 59.630 43.478 11.22 0.00 0.00 2.15
77 78 4.142988 GCCACGTTGAAATTCGACTATGAA 60.143 41.667 11.22 0.00 0.00 2.57
78 79 5.313623 CCACGTTGAAATTCGACTATGAAC 58.686 41.667 11.22 0.00 0.00 3.18
79 80 5.313623 CACGTTGAAATTCGACTATGAACC 58.686 41.667 11.22 0.00 0.00 3.62
80 81 4.992319 ACGTTGAAATTCGACTATGAACCA 59.008 37.500 11.22 0.00 0.00 3.67
81 82 5.642063 ACGTTGAAATTCGACTATGAACCAT 59.358 36.000 11.22 0.00 0.00 3.55
82 83 5.959527 CGTTGAAATTCGACTATGAACCATG 59.040 40.000 11.22 0.00 0.00 3.66
83 84 6.402118 CGTTGAAATTCGACTATGAACCATGT 60.402 38.462 11.22 0.00 0.00 3.21
84 85 7.201487 CGTTGAAATTCGACTATGAACCATGTA 60.201 37.037 11.22 0.00 0.00 2.29
85 86 8.612619 GTTGAAATTCGACTATGAACCATGTAT 58.387 33.333 6.13 0.00 0.00 2.29
86 87 8.141835 TGAAATTCGACTATGAACCATGTATG 57.858 34.615 0.00 0.00 0.00 2.39
87 88 6.545504 AATTCGACTATGAACCATGTATGC 57.454 37.500 0.00 0.00 0.00 3.14
88 89 4.937201 TCGACTATGAACCATGTATGCT 57.063 40.909 0.00 0.00 0.00 3.79
89 90 4.871513 TCGACTATGAACCATGTATGCTC 58.128 43.478 0.00 0.00 0.00 4.26
90 91 4.584743 TCGACTATGAACCATGTATGCTCT 59.415 41.667 0.00 0.00 0.00 4.09
91 92 5.768164 TCGACTATGAACCATGTATGCTCTA 59.232 40.000 0.00 0.00 0.00 2.43
92 93 6.264518 TCGACTATGAACCATGTATGCTCTAA 59.735 38.462 0.00 0.00 0.00 2.10
93 94 6.363626 CGACTATGAACCATGTATGCTCTAAC 59.636 42.308 0.00 0.00 0.00 2.34
94 95 7.124573 ACTATGAACCATGTATGCTCTAACA 57.875 36.000 0.00 0.00 0.00 2.41
95 96 6.986817 ACTATGAACCATGTATGCTCTAACAC 59.013 38.462 0.00 0.00 0.00 3.32
96 97 5.420725 TGAACCATGTATGCTCTAACACT 57.579 39.130 0.00 0.00 0.00 3.55
97 98 5.804639 TGAACCATGTATGCTCTAACACTT 58.195 37.500 0.00 0.00 0.00 3.16
98 99 6.237901 TGAACCATGTATGCTCTAACACTTT 58.762 36.000 0.00 0.00 0.00 2.66
99 100 6.149308 TGAACCATGTATGCTCTAACACTTTG 59.851 38.462 0.00 0.00 0.00 2.77
100 101 5.560724 ACCATGTATGCTCTAACACTTTGT 58.439 37.500 0.00 0.00 0.00 2.83
101 102 6.707290 ACCATGTATGCTCTAACACTTTGTA 58.293 36.000 0.00 0.00 0.00 2.41
102 103 6.818644 ACCATGTATGCTCTAACACTTTGTAG 59.181 38.462 0.00 0.00 0.00 2.74
103 104 6.258727 CCATGTATGCTCTAACACTTTGTAGG 59.741 42.308 0.00 0.00 0.00 3.18
104 105 6.599356 TGTATGCTCTAACACTTTGTAGGA 57.401 37.500 0.00 0.00 0.00 2.94
105 106 6.395629 TGTATGCTCTAACACTTTGTAGGAC 58.604 40.000 0.00 0.00 0.00 3.85
106 107 4.267349 TGCTCTAACACTTTGTAGGACC 57.733 45.455 0.00 0.00 0.00 4.46
107 108 3.644265 TGCTCTAACACTTTGTAGGACCA 59.356 43.478 0.00 0.00 0.00 4.02
108 109 3.995048 GCTCTAACACTTTGTAGGACCAC 59.005 47.826 0.00 0.00 0.00 4.16
109 110 4.262506 GCTCTAACACTTTGTAGGACCACT 60.263 45.833 0.00 0.00 0.00 4.00
110 111 5.742255 GCTCTAACACTTTGTAGGACCACTT 60.742 44.000 0.00 0.00 0.00 3.16
111 112 6.243216 TCTAACACTTTGTAGGACCACTTT 57.757 37.500 0.00 0.00 0.00 2.66
112 113 6.053005 TCTAACACTTTGTAGGACCACTTTG 58.947 40.000 0.00 0.00 0.00 2.77
113 114 3.551846 ACACTTTGTAGGACCACTTTGG 58.448 45.455 0.00 0.00 45.02 3.28
114 115 3.201266 ACACTTTGTAGGACCACTTTGGA 59.799 43.478 0.00 0.00 40.96 3.53
115 116 4.141251 ACACTTTGTAGGACCACTTTGGAT 60.141 41.667 0.00 0.00 40.96 3.41
116 117 4.827284 CACTTTGTAGGACCACTTTGGATT 59.173 41.667 0.00 0.00 40.96 3.01
117 118 6.001460 CACTTTGTAGGACCACTTTGGATTA 58.999 40.000 0.00 0.00 40.96 1.75
118 119 6.659242 CACTTTGTAGGACCACTTTGGATTAT 59.341 38.462 0.00 0.00 40.96 1.28
119 120 7.827236 CACTTTGTAGGACCACTTTGGATTATA 59.173 37.037 0.00 0.00 40.96 0.98
120 121 8.047310 ACTTTGTAGGACCACTTTGGATTATAG 58.953 37.037 0.00 0.00 40.96 1.31
121 122 7.504926 TTGTAGGACCACTTTGGATTATAGT 57.495 36.000 0.00 0.00 40.96 2.12
122 123 8.612486 TTGTAGGACCACTTTGGATTATAGTA 57.388 34.615 0.00 0.00 40.96 1.82
123 124 8.792830 TGTAGGACCACTTTGGATTATAGTAT 57.207 34.615 0.00 0.00 40.96 2.12
124 125 9.220906 TGTAGGACCACTTTGGATTATAGTATT 57.779 33.333 0.00 0.00 40.96 1.89
125 126 9.708092 GTAGGACCACTTTGGATTATAGTATTC 57.292 37.037 0.00 0.00 40.96 1.75
126 127 8.568617 AGGACCACTTTGGATTATAGTATTCT 57.431 34.615 0.00 0.00 40.96 2.40
127 128 9.004231 AGGACCACTTTGGATTATAGTATTCTT 57.996 33.333 0.00 0.00 40.96 2.52
128 129 9.628500 GGACCACTTTGGATTATAGTATTCTTT 57.372 33.333 0.00 0.00 40.96 2.52
194 195 3.026630 TCATAGGATTTCGATGTCGCC 57.973 47.619 0.00 0.00 39.60 5.54
195 196 2.628178 TCATAGGATTTCGATGTCGCCT 59.372 45.455 0.00 1.44 39.60 5.52
196 197 3.824443 TCATAGGATTTCGATGTCGCCTA 59.176 43.478 8.33 8.33 39.60 3.93
197 198 2.510768 AGGATTTCGATGTCGCCTAC 57.489 50.000 0.00 0.00 39.60 3.18
198 199 1.068741 AGGATTTCGATGTCGCCTACC 59.931 52.381 0.00 0.00 39.60 3.18
199 200 1.202486 GGATTTCGATGTCGCCTACCA 60.202 52.381 0.00 0.00 39.60 3.25
200 201 1.859080 GATTTCGATGTCGCCTACCAC 59.141 52.381 0.00 0.00 39.60 4.16
201 202 0.604073 TTTCGATGTCGCCTACCACA 59.396 50.000 0.00 0.00 39.60 4.17
202 203 0.604073 TTCGATGTCGCCTACCACAA 59.396 50.000 0.00 0.00 39.60 3.33
203 204 0.604073 TCGATGTCGCCTACCACAAA 59.396 50.000 0.00 0.00 39.60 2.83
204 205 1.001068 TCGATGTCGCCTACCACAAAA 59.999 47.619 0.00 0.00 39.60 2.44
205 206 2.006888 CGATGTCGCCTACCACAAAAT 58.993 47.619 0.00 0.00 0.00 1.82
206 207 2.030457 CGATGTCGCCTACCACAAAATC 59.970 50.000 0.00 0.00 0.00 2.17
207 208 1.816074 TGTCGCCTACCACAAAATCC 58.184 50.000 0.00 0.00 0.00 3.01
208 209 1.072489 TGTCGCCTACCACAAAATCCA 59.928 47.619 0.00 0.00 0.00 3.41
209 210 2.156098 GTCGCCTACCACAAAATCCAA 58.844 47.619 0.00 0.00 0.00 3.53
210 211 2.752903 GTCGCCTACCACAAAATCCAAT 59.247 45.455 0.00 0.00 0.00 3.16
211 212 3.942748 GTCGCCTACCACAAAATCCAATA 59.057 43.478 0.00 0.00 0.00 1.90
212 213 4.035208 GTCGCCTACCACAAAATCCAATAG 59.965 45.833 0.00 0.00 0.00 1.73
213 214 3.315191 CGCCTACCACAAAATCCAATAGG 59.685 47.826 0.00 0.00 0.00 2.57
224 225 1.208706 TCCAATAGGATTCACCCGCA 58.791 50.000 0.00 0.00 39.61 5.69
225 226 1.562008 TCCAATAGGATTCACCCGCAA 59.438 47.619 0.00 0.00 39.61 4.85
226 227 2.025793 TCCAATAGGATTCACCCGCAAA 60.026 45.455 0.00 0.00 39.61 3.68
227 228 2.757868 CCAATAGGATTCACCCGCAAAA 59.242 45.455 0.00 0.00 40.05 2.44
228 229 3.194542 CCAATAGGATTCACCCGCAAAAA 59.805 43.478 0.00 0.00 40.05 1.94
321 322 6.263168 ACACAGAAATTTTAGAGTGTTGAGGG 59.737 38.462 10.91 0.00 36.91 4.30
359 362 6.775629 AGAGATAGAGTGTATTGGACTTCTCC 59.224 42.308 0.00 0.00 37.04 3.71
399 402 7.042254 TGAGATTTGAGCTCATGTTCATATTCG 60.042 37.037 19.04 0.00 37.46 3.34
417 420 3.044235 TCGTATGGAATAGGCAGCATG 57.956 47.619 0.00 0.00 34.80 4.06
429 432 2.234414 AGGCAGCATGTAAATTTGGTGG 59.766 45.455 0.00 0.00 39.31 4.61
431 434 2.612471 GCAGCATGTAAATTTGGTGGCA 60.612 45.455 0.00 0.00 39.31 4.92
432 435 3.255725 CAGCATGTAAATTTGGTGGCAG 58.744 45.455 0.00 0.00 0.00 4.85
453 461 5.636543 GCAGCAATCCTATGATTTAAATGGC 59.363 40.000 5.17 0.00 39.20 4.40
505 513 3.603965 ATCTAGGGAGGGTGACACTAG 57.396 52.381 5.39 0.00 34.03 2.57
506 763 1.569548 TCTAGGGAGGGTGACACTAGG 59.430 57.143 5.39 0.00 33.65 3.02
518 775 0.251922 ACACTAGGAGCCGTGGGTTA 60.252 55.000 0.00 0.00 35.51 2.85
798 1059 1.973812 GGCCACCTTGAGCTCCAAC 60.974 63.158 12.15 0.00 0.00 3.77
975 1238 1.084370 GTCACCGGCACATACTCTGC 61.084 60.000 0.00 0.00 0.00 4.26
1047 1310 4.802051 TTCCTGGCGGCCATGCTC 62.802 66.667 24.10 0.00 30.82 4.26
1070 1333 2.355193 GCTTCCTCCTCGGAGCTGT 61.355 63.158 7.46 0.00 44.28 4.40
1123 1386 1.068474 CTCCGCTTTTCAGGTACGTG 58.932 55.000 9.30 9.30 0.00 4.49
1125 1388 1.612950 TCCGCTTTTCAGGTACGTGTA 59.387 47.619 14.78 3.11 0.00 2.90
1131 1394 4.619863 GCTTTTCAGGTACGTGTATCCTCA 60.620 45.833 14.78 0.00 0.00 3.86
1144 1407 5.125257 CGTGTATCCTCAGAGCATAGATGAT 59.875 44.000 0.00 0.00 0.00 2.45
1157 1420 5.245526 AGCATAGATGATAGAGCATCACACA 59.754 40.000 10.19 0.00 46.41 3.72
1164 1427 0.901124 AGAGCATCACACACTCTCCC 59.099 55.000 0.00 0.00 35.96 4.30
1170 1433 0.251832 TCACACACTCTCCCTCTCCC 60.252 60.000 0.00 0.00 0.00 4.30
1171 1434 0.252012 CACACACTCTCCCTCTCCCT 60.252 60.000 0.00 0.00 0.00 4.20
1172 1435 0.040499 ACACACTCTCCCTCTCCCTC 59.960 60.000 0.00 0.00 0.00 4.30
1173 1436 1.034838 CACACTCTCCCTCTCCCTCG 61.035 65.000 0.00 0.00 0.00 4.63
1174 1437 2.124693 CACTCTCCCTCTCCCTCGC 61.125 68.421 0.00 0.00 0.00 5.03
1196 1459 6.765989 TCGCACTTGTAGCTCCATTAATTTAT 59.234 34.615 0.00 0.00 0.00 1.40
1204 1467 4.516698 AGCTCCATTAATTTATGTGGCTCG 59.483 41.667 12.45 0.00 30.89 5.03
1205 1468 4.515191 GCTCCATTAATTTATGTGGCTCGA 59.485 41.667 3.92 0.00 0.00 4.04
1206 1469 5.008613 GCTCCATTAATTTATGTGGCTCGAA 59.991 40.000 3.92 0.00 0.00 3.71
1207 1470 6.371809 TCCATTAATTTATGTGGCTCGAAC 57.628 37.500 3.92 0.00 0.00 3.95
1208 1471 6.119536 TCCATTAATTTATGTGGCTCGAACT 58.880 36.000 3.92 0.00 0.00 3.01
1209 1472 6.260050 TCCATTAATTTATGTGGCTCGAACTC 59.740 38.462 3.92 0.00 0.00 3.01
1210 1473 5.712217 TTAATTTATGTGGCTCGAACTCG 57.288 39.130 0.00 0.00 41.45 4.18
1247 1510 0.324614 TGACGCTGATGTTCATGGGT 59.675 50.000 0.00 0.00 0.00 4.51
1253 1516 2.945668 GCTGATGTTCATGGGTAGAACC 59.054 50.000 0.00 0.00 43.57 3.62
1276 1539 2.507324 GAGGACAAGTCGCGGCTC 60.507 66.667 16.36 0.53 0.00 4.70
1506 1769 1.001597 CTACAACCCCTAGATCGTCGC 60.002 57.143 0.00 0.00 0.00 5.19
1705 1973 2.223782 GGCTTGCATTGTCTTGTGTTCA 60.224 45.455 0.00 0.00 0.00 3.18
1736 2005 2.924880 GCTGGTTCCAACATTTTACGGC 60.925 50.000 0.00 0.00 0.00 5.68
1794 2079 6.462073 AGCGGTAAATTATGTATTGTAGCG 57.538 37.500 0.00 0.00 35.84 4.26
1795 2080 5.987347 AGCGGTAAATTATGTATTGTAGCGT 59.013 36.000 0.00 0.00 35.55 5.07
1796 2081 7.147312 AGCGGTAAATTATGTATTGTAGCGTA 58.853 34.615 0.00 0.00 35.55 4.42
2034 2325 2.349438 CGAAGTAATTGCGCTTGTGTGT 60.349 45.455 9.73 0.00 0.00 3.72
2036 2327 1.946768 AGTAATTGCGCTTGTGTGTGT 59.053 42.857 9.73 0.00 0.00 3.72
2037 2328 3.135225 AGTAATTGCGCTTGTGTGTGTA 58.865 40.909 9.73 0.00 0.00 2.90
2038 2329 2.399396 AATTGCGCTTGTGTGTGTAC 57.601 45.000 9.73 0.00 0.00 2.90
2039 2330 1.593196 ATTGCGCTTGTGTGTGTACT 58.407 45.000 9.73 0.00 0.00 2.73
2040 2331 0.934496 TTGCGCTTGTGTGTGTACTC 59.066 50.000 9.73 0.00 0.00 2.59
2041 2332 0.878523 TGCGCTTGTGTGTGTACTCC 60.879 55.000 9.73 0.00 0.00 3.85
2098 2389 2.663188 GAATGGAGGCTAGCGCGG 60.663 66.667 8.83 0.00 36.88 6.46
2198 2494 3.214250 CTGGGGCTCGGCTCGTATC 62.214 68.421 0.00 0.00 0.00 2.24
2200 2496 3.593794 GGGCTCGGCTCGTATCGT 61.594 66.667 0.00 0.00 0.00 3.73
2201 2497 2.256591 GGGCTCGGCTCGTATCGTA 61.257 63.158 0.00 0.00 0.00 3.43
2204 2507 0.454620 GCTCGGCTCGTATCGTATGG 60.455 60.000 0.00 0.00 0.00 2.74
2272 2575 4.475135 GCTTGTCGGGCCTCCCTC 62.475 72.222 0.84 0.00 42.67 4.30
2273 2576 3.787001 CTTGTCGGGCCTCCCTCC 61.787 72.222 0.84 0.00 42.67 4.30
2285 2588 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
2426 2732 0.329261 TTGATGAAGTGAGGCAGGGG 59.671 55.000 0.00 0.00 0.00 4.79
2427 2733 0.842030 TGATGAAGTGAGGCAGGGGT 60.842 55.000 0.00 0.00 0.00 4.95
2428 2734 1.204146 GATGAAGTGAGGCAGGGGTA 58.796 55.000 0.00 0.00 0.00 3.69
2429 2735 1.139853 GATGAAGTGAGGCAGGGGTAG 59.860 57.143 0.00 0.00 0.00 3.18
2450 2756 6.035758 GGTAGGTAGTTTTCGTCTGCAAATAG 59.964 42.308 0.00 0.00 0.00 1.73
2452 2758 4.094442 GGTAGTTTTCGTCTGCAAATAGGG 59.906 45.833 0.00 0.00 0.00 3.53
2465 2771 3.081804 CAAATAGGGGTGTGTCAAGACC 58.918 50.000 0.00 0.00 39.06 3.85
2471 2777 0.038159 GGTGTGTCAAGACCCGAGAG 60.038 60.000 0.00 0.00 33.50 3.20
2472 2778 0.959553 GTGTGTCAAGACCCGAGAGA 59.040 55.000 0.00 0.00 0.00 3.10
2473 2779 1.068194 GTGTGTCAAGACCCGAGAGAG 60.068 57.143 0.00 0.00 0.00 3.20
2474 2780 0.528470 GTGTCAAGACCCGAGAGAGG 59.472 60.000 0.00 0.00 0.00 3.69
2475 2781 1.251527 TGTCAAGACCCGAGAGAGGC 61.252 60.000 0.00 0.00 0.00 4.70
2476 2782 1.076727 TCAAGACCCGAGAGAGGCA 59.923 57.895 0.00 0.00 0.00 4.75
2477 2783 0.324738 TCAAGACCCGAGAGAGGCAT 60.325 55.000 0.00 0.00 0.00 4.40
2478 2784 0.103937 CAAGACCCGAGAGAGGCATC 59.896 60.000 0.00 0.00 0.00 3.91
2479 2785 0.324738 AAGACCCGAGAGAGGCATCA 60.325 55.000 0.00 0.00 0.00 3.07
2480 2786 0.324738 AGACCCGAGAGAGGCATCAA 60.325 55.000 0.00 0.00 0.00 2.57
2481 2787 0.537188 GACCCGAGAGAGGCATCAAA 59.463 55.000 0.00 0.00 0.00 2.69
2482 2788 0.539051 ACCCGAGAGAGGCATCAAAG 59.461 55.000 0.00 0.00 0.00 2.77
2483 2789 0.813210 CCCGAGAGAGGCATCAAAGC 60.813 60.000 0.00 0.00 0.00 3.51
2484 2790 0.177604 CCGAGAGAGGCATCAAAGCT 59.822 55.000 0.00 0.00 34.17 3.74
2485 2791 1.410517 CCGAGAGAGGCATCAAAGCTA 59.589 52.381 0.00 0.00 34.17 3.32
2486 2792 2.545532 CCGAGAGAGGCATCAAAGCTAG 60.546 54.545 0.00 0.00 34.17 3.42
2487 2793 2.360483 CGAGAGAGGCATCAAAGCTAGA 59.640 50.000 0.00 0.00 34.17 2.43
2488 2794 3.181482 CGAGAGAGGCATCAAAGCTAGAA 60.181 47.826 0.00 0.00 34.17 2.10
2489 2795 4.501229 CGAGAGAGGCATCAAAGCTAGAAT 60.501 45.833 0.00 0.00 34.17 2.40
2490 2796 4.706035 AGAGAGGCATCAAAGCTAGAATG 58.294 43.478 0.00 0.00 34.17 2.67
2491 2797 3.814283 GAGAGGCATCAAAGCTAGAATGG 59.186 47.826 0.00 0.00 34.17 3.16
2492 2798 2.883386 GAGGCATCAAAGCTAGAATGGG 59.117 50.000 0.00 0.00 34.17 4.00
2493 2799 1.339291 GGCATCAAAGCTAGAATGGGC 59.661 52.381 0.00 0.00 34.17 5.36
2494 2800 2.026641 GCATCAAAGCTAGAATGGGCA 58.973 47.619 0.00 0.00 0.00 5.36
2495 2801 2.034305 GCATCAAAGCTAGAATGGGCAG 59.966 50.000 0.00 0.00 0.00 4.85
2496 2802 3.548770 CATCAAAGCTAGAATGGGCAGA 58.451 45.455 0.00 0.00 0.00 4.26
2497 2803 3.719268 TCAAAGCTAGAATGGGCAGAA 57.281 42.857 0.00 0.00 0.00 3.02
2498 2804 4.032960 TCAAAGCTAGAATGGGCAGAAA 57.967 40.909 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.400568 GCTCCTTTGATTCAAATGGATTTCA 58.599 36.000 20.77 7.62 33.64 2.69
2 3 5.814188 GGCTCCTTTGATTCAAATGGATTTC 59.186 40.000 20.77 15.48 33.64 2.17
4 5 5.028131 AGGCTCCTTTGATTCAAATGGATT 58.972 37.500 20.77 12.48 33.64 3.01
5 6 4.617593 AGGCTCCTTTGATTCAAATGGAT 58.382 39.130 20.77 10.80 33.64 3.41
6 7 4.051661 AGGCTCCTTTGATTCAAATGGA 57.948 40.909 19.96 19.96 32.70 3.41
7 8 4.221262 TCAAGGCTCCTTTGATTCAAATGG 59.779 41.667 12.04 14.27 32.70 3.16
8 9 5.395682 TCAAGGCTCCTTTGATTCAAATG 57.604 39.130 12.04 9.74 32.70 2.32
9 10 6.423776 TTTCAAGGCTCCTTTGATTCAAAT 57.576 33.333 12.04 0.00 32.70 2.32
10 11 5.867903 TTTCAAGGCTCCTTTGATTCAAA 57.132 34.783 11.19 11.19 33.42 2.69
11 12 5.867903 TTTTCAAGGCTCCTTTGATTCAA 57.132 34.783 0.00 0.00 33.42 2.69
12 13 5.867903 TTTTTCAAGGCTCCTTTGATTCA 57.132 34.783 0.00 0.00 33.42 2.57
13 14 7.308169 CCAAATTTTTCAAGGCTCCTTTGATTC 60.308 37.037 0.00 0.00 33.42 2.52
14 15 6.487668 CCAAATTTTTCAAGGCTCCTTTGATT 59.512 34.615 0.00 0.00 33.42 2.57
15 16 5.999600 CCAAATTTTTCAAGGCTCCTTTGAT 59.000 36.000 0.00 0.00 33.42 2.57
16 17 5.367302 CCAAATTTTTCAAGGCTCCTTTGA 58.633 37.500 0.00 0.00 33.42 2.69
17 18 4.516321 CCCAAATTTTTCAAGGCTCCTTTG 59.484 41.667 0.00 0.00 33.42 2.77
18 19 4.446167 CCCCAAATTTTTCAAGGCTCCTTT 60.446 41.667 0.00 0.00 33.42 3.11
19 20 3.072915 CCCCAAATTTTTCAAGGCTCCTT 59.927 43.478 0.00 0.00 36.60 3.36
20 21 2.639347 CCCCAAATTTTTCAAGGCTCCT 59.361 45.455 0.00 0.00 0.00 3.69
21 22 2.637382 TCCCCAAATTTTTCAAGGCTCC 59.363 45.455 0.00 0.00 0.00 4.70
22 23 3.557054 GGTCCCCAAATTTTTCAAGGCTC 60.557 47.826 0.00 0.00 0.00 4.70
23 24 2.371841 GGTCCCCAAATTTTTCAAGGCT 59.628 45.455 0.00 0.00 0.00 4.58
24 25 2.105649 TGGTCCCCAAATTTTTCAAGGC 59.894 45.455 0.00 0.00 0.00 4.35
25 26 4.429854 TTGGTCCCCAAATTTTTCAAGG 57.570 40.909 0.00 0.00 40.92 3.61
37 38 1.347062 GGCAAAGAAATTGGTCCCCA 58.653 50.000 0.00 0.00 39.54 4.96
38 39 1.001974 GTGGCAAAGAAATTGGTCCCC 59.998 52.381 0.00 0.00 39.54 4.81
39 40 1.336795 CGTGGCAAAGAAATTGGTCCC 60.337 52.381 0.00 0.00 39.54 4.46
40 41 1.339929 ACGTGGCAAAGAAATTGGTCC 59.660 47.619 0.00 0.00 39.54 4.46
41 42 2.793278 ACGTGGCAAAGAAATTGGTC 57.207 45.000 0.00 0.00 39.54 4.02
42 43 2.428890 TCAACGTGGCAAAGAAATTGGT 59.571 40.909 0.00 0.00 39.54 3.67
43 44 3.090952 TCAACGTGGCAAAGAAATTGG 57.909 42.857 0.00 0.00 39.54 3.16
44 45 5.655893 ATTTCAACGTGGCAAAGAAATTG 57.344 34.783 10.16 1.44 42.21 2.32
45 46 5.051106 CGAATTTCAACGTGGCAAAGAAATT 60.051 36.000 20.53 20.53 45.97 1.82
46 47 4.444056 CGAATTTCAACGTGGCAAAGAAAT 59.556 37.500 10.16 10.16 39.74 2.17
47 48 3.794028 CGAATTTCAACGTGGCAAAGAAA 59.206 39.130 0.00 0.00 33.33 2.52
48 49 3.065510 TCGAATTTCAACGTGGCAAAGAA 59.934 39.130 0.00 0.00 0.00 2.52
49 50 2.614520 TCGAATTTCAACGTGGCAAAGA 59.385 40.909 0.00 0.00 0.00 2.52
50 51 2.719046 GTCGAATTTCAACGTGGCAAAG 59.281 45.455 0.00 0.00 0.00 2.77
51 52 2.356382 AGTCGAATTTCAACGTGGCAAA 59.644 40.909 0.00 0.00 0.00 3.68
52 53 1.944024 AGTCGAATTTCAACGTGGCAA 59.056 42.857 0.00 0.00 0.00 4.52
53 54 1.588674 AGTCGAATTTCAACGTGGCA 58.411 45.000 0.00 0.00 0.00 4.92
54 55 3.369756 TCATAGTCGAATTTCAACGTGGC 59.630 43.478 0.00 0.00 0.00 5.01
55 56 5.313623 GTTCATAGTCGAATTTCAACGTGG 58.686 41.667 0.00 0.00 0.00 4.94
56 57 5.107259 TGGTTCATAGTCGAATTTCAACGTG 60.107 40.000 0.00 0.00 0.00 4.49
57 58 4.992319 TGGTTCATAGTCGAATTTCAACGT 59.008 37.500 0.00 0.00 0.00 3.99
58 59 5.524511 TGGTTCATAGTCGAATTTCAACG 57.475 39.130 0.00 0.00 0.00 4.10
59 60 6.842163 ACATGGTTCATAGTCGAATTTCAAC 58.158 36.000 0.00 0.00 0.00 3.18
60 61 8.611757 CATACATGGTTCATAGTCGAATTTCAA 58.388 33.333 0.00 0.00 0.00 2.69
61 62 7.254761 GCATACATGGTTCATAGTCGAATTTCA 60.255 37.037 0.00 0.00 0.00 2.69
62 63 7.041780 AGCATACATGGTTCATAGTCGAATTTC 60.042 37.037 0.00 0.00 34.35 2.17
63 64 6.767902 AGCATACATGGTTCATAGTCGAATTT 59.232 34.615 0.00 0.00 34.35 1.82
64 65 6.291377 AGCATACATGGTTCATAGTCGAATT 58.709 36.000 0.00 0.00 34.35 2.17
65 66 5.858381 AGCATACATGGTTCATAGTCGAAT 58.142 37.500 0.00 0.00 34.35 3.34
66 67 5.069119 AGAGCATACATGGTTCATAGTCGAA 59.931 40.000 0.00 0.00 38.85 3.71
67 68 4.584743 AGAGCATACATGGTTCATAGTCGA 59.415 41.667 0.00 0.00 38.85 4.20
68 69 4.876125 AGAGCATACATGGTTCATAGTCG 58.124 43.478 0.00 0.00 38.85 4.18
69 70 7.169982 GTGTTAGAGCATACATGGTTCATAGTC 59.830 40.741 0.00 0.00 38.85 2.59
70 71 6.986817 GTGTTAGAGCATACATGGTTCATAGT 59.013 38.462 0.00 0.00 38.85 2.12
71 72 7.212976 AGTGTTAGAGCATACATGGTTCATAG 58.787 38.462 0.00 0.00 38.85 2.23
72 73 7.124573 AGTGTTAGAGCATACATGGTTCATA 57.875 36.000 0.00 0.00 38.85 2.15
73 74 5.994250 AGTGTTAGAGCATACATGGTTCAT 58.006 37.500 0.00 0.00 38.85 2.57
74 75 5.420725 AGTGTTAGAGCATACATGGTTCA 57.579 39.130 0.00 0.00 38.85 3.18
75 76 6.149474 ACAAAGTGTTAGAGCATACATGGTTC 59.851 38.462 0.00 0.00 38.85 3.62
76 77 6.003950 ACAAAGTGTTAGAGCATACATGGTT 58.996 36.000 0.00 0.00 38.85 3.67
77 78 5.560724 ACAAAGTGTTAGAGCATACATGGT 58.439 37.500 0.00 0.00 41.89 3.55
78 79 6.258727 CCTACAAAGTGTTAGAGCATACATGG 59.741 42.308 0.00 0.00 0.00 3.66
79 80 7.010552 GTCCTACAAAGTGTTAGAGCATACATG 59.989 40.741 0.00 0.00 0.00 3.21
80 81 7.042335 GTCCTACAAAGTGTTAGAGCATACAT 58.958 38.462 0.00 0.00 0.00 2.29
81 82 6.395629 GTCCTACAAAGTGTTAGAGCATACA 58.604 40.000 0.00 0.00 0.00 2.29
82 83 5.811100 GGTCCTACAAAGTGTTAGAGCATAC 59.189 44.000 0.00 0.00 32.48 2.39
83 84 5.482526 TGGTCCTACAAAGTGTTAGAGCATA 59.517 40.000 7.66 0.00 35.35 3.14
84 85 4.286032 TGGTCCTACAAAGTGTTAGAGCAT 59.714 41.667 7.66 0.00 35.35 3.79
85 86 3.644265 TGGTCCTACAAAGTGTTAGAGCA 59.356 43.478 7.66 7.66 36.79 4.26
86 87 3.995048 GTGGTCCTACAAAGTGTTAGAGC 59.005 47.826 0.00 0.00 32.69 4.09
87 88 5.470047 AGTGGTCCTACAAAGTGTTAGAG 57.530 43.478 0.00 0.00 0.00 2.43
88 89 5.881923 AAGTGGTCCTACAAAGTGTTAGA 57.118 39.130 0.00 0.00 0.00 2.10
89 90 5.238650 CCAAAGTGGTCCTACAAAGTGTTAG 59.761 44.000 0.00 0.00 31.35 2.34
90 91 5.104444 TCCAAAGTGGTCCTACAAAGTGTTA 60.104 40.000 0.00 0.00 39.03 2.41
91 92 3.951680 CCAAAGTGGTCCTACAAAGTGTT 59.048 43.478 0.00 0.00 31.35 3.32
92 93 3.201266 TCCAAAGTGGTCCTACAAAGTGT 59.799 43.478 0.00 0.00 39.03 3.55
93 94 3.815809 TCCAAAGTGGTCCTACAAAGTG 58.184 45.455 0.00 0.00 39.03 3.16
94 95 4.724279 ATCCAAAGTGGTCCTACAAAGT 57.276 40.909 0.00 0.00 39.03 2.66
95 96 8.047310 ACTATAATCCAAAGTGGTCCTACAAAG 58.953 37.037 0.00 0.00 39.03 2.77
96 97 7.924541 ACTATAATCCAAAGTGGTCCTACAAA 58.075 34.615 0.00 0.00 39.03 2.83
97 98 7.504926 ACTATAATCCAAAGTGGTCCTACAA 57.495 36.000 0.00 0.00 39.03 2.41
98 99 8.792830 ATACTATAATCCAAAGTGGTCCTACA 57.207 34.615 0.00 0.00 39.03 2.74
99 100 9.708092 GAATACTATAATCCAAAGTGGTCCTAC 57.292 37.037 0.00 0.00 39.03 3.18
100 101 9.670442 AGAATACTATAATCCAAAGTGGTCCTA 57.330 33.333 0.00 0.00 39.03 2.94
101 102 8.568617 AGAATACTATAATCCAAAGTGGTCCT 57.431 34.615 0.00 0.00 39.03 3.85
102 103 9.628500 AAAGAATACTATAATCCAAAGTGGTCC 57.372 33.333 0.00 0.00 39.03 4.46
172 173 3.997021 GGCGACATCGAAATCCTATGATT 59.003 43.478 5.26 0.00 43.02 2.57
173 174 3.259374 AGGCGACATCGAAATCCTATGAT 59.741 43.478 5.26 0.00 43.02 2.45
174 175 2.628178 AGGCGACATCGAAATCCTATGA 59.372 45.455 5.26 0.00 43.02 2.15
175 176 3.032017 AGGCGACATCGAAATCCTATG 57.968 47.619 5.26 0.00 43.02 2.23
176 177 3.056749 GGTAGGCGACATCGAAATCCTAT 60.057 47.826 5.26 0.00 43.02 2.57
177 178 2.295349 GGTAGGCGACATCGAAATCCTA 59.705 50.000 5.26 3.55 43.02 2.94
178 179 1.068741 GGTAGGCGACATCGAAATCCT 59.931 52.381 5.26 4.54 43.02 3.24
179 180 1.202486 TGGTAGGCGACATCGAAATCC 60.202 52.381 5.26 2.72 43.02 3.01
180 181 1.859080 GTGGTAGGCGACATCGAAATC 59.141 52.381 5.26 0.00 43.02 2.17
181 182 1.206132 TGTGGTAGGCGACATCGAAAT 59.794 47.619 5.26 0.00 43.02 2.17
182 183 0.604073 TGTGGTAGGCGACATCGAAA 59.396 50.000 5.26 0.00 43.02 3.46
183 184 0.604073 TTGTGGTAGGCGACATCGAA 59.396 50.000 5.26 0.00 43.02 3.71
184 185 0.604073 TTTGTGGTAGGCGACATCGA 59.396 50.000 5.26 0.00 43.02 3.59
185 186 1.434555 TTTTGTGGTAGGCGACATCG 58.565 50.000 0.00 0.00 43.27 3.84
186 187 2.354821 GGATTTTGTGGTAGGCGACATC 59.645 50.000 0.00 0.00 33.46 3.06
187 188 2.290641 TGGATTTTGTGGTAGGCGACAT 60.291 45.455 0.00 0.00 33.46 3.06
188 189 1.072489 TGGATTTTGTGGTAGGCGACA 59.928 47.619 0.00 0.00 0.00 4.35
189 190 1.816074 TGGATTTTGTGGTAGGCGAC 58.184 50.000 0.00 0.00 0.00 5.19
190 191 2.570415 TTGGATTTTGTGGTAGGCGA 57.430 45.000 0.00 0.00 0.00 5.54
191 192 3.315191 CCTATTGGATTTTGTGGTAGGCG 59.685 47.826 0.00 0.00 34.57 5.52
192 193 4.532834 TCCTATTGGATTTTGTGGTAGGC 58.467 43.478 0.00 0.00 37.46 3.93
206 207 2.051334 TTGCGGGTGAATCCTATTGG 57.949 50.000 0.00 0.00 36.25 3.16
207 208 4.448537 TTTTTGCGGGTGAATCCTATTG 57.551 40.909 0.00 0.00 36.25 1.90
246 247 3.119884 CGCATTGCAGAATTCCTGTGTTA 60.120 43.478 9.69 0.00 44.71 2.41
313 314 2.920271 TCTCTACTCTCTCCCCTCAACA 59.080 50.000 0.00 0.00 0.00 3.33
314 315 3.201266 TCTCTCTACTCTCTCCCCTCAAC 59.799 52.174 0.00 0.00 0.00 3.18
321 322 6.267928 ACACTCTATCTCTCTCTACTCTCTCC 59.732 46.154 0.00 0.00 0.00 3.71
368 371 8.339344 TGAACATGAGCTCAAATCTCATTTTA 57.661 30.769 22.50 0.00 45.99 1.52
399 402 6.824305 ATTTACATGCTGCCTATTCCATAC 57.176 37.500 0.00 0.00 0.00 2.39
410 413 2.001872 GCCACCAAATTTACATGCTGC 58.998 47.619 0.00 0.00 0.00 5.25
417 420 3.055891 AGGATTGCTGCCACCAAATTTAC 60.056 43.478 0.00 0.00 0.00 2.01
429 432 5.636543 GCCATTTAAATCATAGGATTGCTGC 59.363 40.000 2.91 0.00 42.87 5.25
431 434 7.607615 AAGCCATTTAAATCATAGGATTGCT 57.392 32.000 2.91 4.13 42.87 3.91
432 435 8.146412 AGAAAGCCATTTAAATCATAGGATTGC 58.854 33.333 2.91 5.24 42.87 3.56
470 478 6.387192 TCCCTAGATTGAAGGAATTTCACA 57.613 37.500 0.00 0.00 45.22 3.58
473 481 5.103898 ACCCTCCCTAGATTGAAGGAATTTC 60.104 44.000 0.00 0.00 36.08 2.17
505 513 2.436115 GTGCTAACCCACGGCTCC 60.436 66.667 0.00 0.00 0.00 4.70
506 763 2.436115 GGTGCTAACCCACGGCTC 60.436 66.667 0.00 0.00 41.04 4.70
518 775 1.228769 TACCACTCCACTCGGTGCT 60.229 57.895 0.00 0.00 34.12 4.40
630 890 3.383825 GGCGTATATGTATGGTAGGGAGG 59.616 52.174 0.00 0.00 0.00 4.30
637 897 2.490903 GAGACGGGCGTATATGTATGGT 59.509 50.000 0.00 0.00 0.00 3.55
970 1233 1.805945 GGTCGTTACAGCCGCAGAG 60.806 63.158 0.00 0.00 0.00 3.35
975 1238 0.866061 CATCTCGGTCGTTACAGCCG 60.866 60.000 8.00 8.00 46.12 5.52
1047 1310 3.215245 CCGAGGAGGAAGCTGAGG 58.785 66.667 0.00 0.00 45.00 3.86
1070 1333 2.027073 GTGCGGCTGAATGTCGTCA 61.027 57.895 0.00 0.00 46.81 4.35
1123 1386 7.255242 GCTCTATCATCTATGCTCTGAGGATAC 60.255 44.444 14.00 0.00 35.68 2.24
1125 1388 5.595542 GCTCTATCATCTATGCTCTGAGGAT 59.404 44.000 16.06 16.06 37.46 3.24
1131 1394 5.715753 TGTGATGCTCTATCATCTATGCTCT 59.284 40.000 5.50 0.00 46.85 4.09
1144 1407 2.103373 GGGAGAGTGTGTGATGCTCTA 58.897 52.381 0.00 0.00 39.43 2.43
1157 1420 2.277404 GCGAGGGAGAGGGAGAGT 59.723 66.667 0.00 0.00 0.00 3.24
1164 1427 0.179124 GCTACAAGTGCGAGGGAGAG 60.179 60.000 0.00 0.00 0.00 3.20
1170 1433 2.015736 AATGGAGCTACAAGTGCGAG 57.984 50.000 0.66 0.00 35.28 5.03
1171 1434 3.603158 TTAATGGAGCTACAAGTGCGA 57.397 42.857 0.66 0.00 35.28 5.10
1172 1435 4.882671 AATTAATGGAGCTACAAGTGCG 57.117 40.909 0.66 0.00 35.28 5.34
1173 1436 7.645340 CACATAAATTAATGGAGCTACAAGTGC 59.355 37.037 0.66 0.00 0.00 4.40
1174 1437 8.131100 CCACATAAATTAATGGAGCTACAAGTG 58.869 37.037 0.66 1.21 33.80 3.16
1204 1467 5.638234 AGTGCCATTTAGTTAGTTCGAGTTC 59.362 40.000 0.00 0.00 0.00 3.01
1205 1468 5.408604 CAGTGCCATTTAGTTAGTTCGAGTT 59.591 40.000 0.00 0.00 0.00 3.01
1206 1469 4.929808 CAGTGCCATTTAGTTAGTTCGAGT 59.070 41.667 0.00 0.00 0.00 4.18
1207 1470 5.062308 GTCAGTGCCATTTAGTTAGTTCGAG 59.938 44.000 0.00 0.00 0.00 4.04
1208 1471 4.927425 GTCAGTGCCATTTAGTTAGTTCGA 59.073 41.667 0.00 0.00 0.00 3.71
1209 1472 4.201589 CGTCAGTGCCATTTAGTTAGTTCG 60.202 45.833 0.00 0.00 0.00 3.95
1210 1473 4.435651 GCGTCAGTGCCATTTAGTTAGTTC 60.436 45.833 0.00 0.00 0.00 3.01
1222 1485 0.950555 GAACATCAGCGTCAGTGCCA 60.951 55.000 0.00 0.00 34.65 4.92
1223 1486 0.950555 TGAACATCAGCGTCAGTGCC 60.951 55.000 0.00 0.00 34.65 5.01
1247 1510 0.543410 TTGTCCTCCGCCAGGTTCTA 60.543 55.000 0.00 0.00 43.95 2.10
1253 1516 2.125912 CGACTTGTCCTCCGCCAG 60.126 66.667 0.00 0.00 0.00 4.85
1506 1769 3.258372 TGGTAATCAGCGGCTTATCTAGG 59.742 47.826 0.00 0.00 0.00 3.02
1550 1813 1.229359 CCGGAGCCTCTAGGGTACA 59.771 63.158 10.93 0.00 46.79 2.90
1736 2005 3.242944 CCAATCACTCTTACATGCGTACG 59.757 47.826 11.84 11.84 0.00 3.67
1796 2081 9.032624 ACCAGTACTGTTATTACTGTTACATCT 57.967 33.333 21.18 0.00 43.38 2.90
1804 2095 5.348724 CACAGCACCAGTACTGTTATTACTG 59.651 44.000 21.18 18.68 44.59 2.74
2012 2303 1.196808 ACACAAGCGCAATTACTTCGG 59.803 47.619 11.47 0.00 0.00 4.30
2034 2325 4.083643 CGAGAGTTTTCACGTAGGAGTACA 60.084 45.833 0.00 0.00 33.52 2.90
2036 2327 3.438087 CCGAGAGTTTTCACGTAGGAGTA 59.562 47.826 0.00 0.00 35.94 2.59
2037 2328 2.228343 CCGAGAGTTTTCACGTAGGAGT 59.772 50.000 0.00 0.00 35.94 3.85
2038 2329 2.228343 ACCGAGAGTTTTCACGTAGGAG 59.772 50.000 0.00 0.00 35.94 3.69
2039 2330 2.227388 GACCGAGAGTTTTCACGTAGGA 59.773 50.000 0.00 0.00 35.94 2.94
2040 2331 2.030540 TGACCGAGAGTTTTCACGTAGG 60.031 50.000 0.00 0.00 35.94 3.18
2041 2332 3.278367 TGACCGAGAGTTTTCACGTAG 57.722 47.619 0.00 0.00 35.94 3.51
2198 2494 1.448893 CGAACCCCACACCCATACG 60.449 63.158 0.00 0.00 0.00 3.06
2200 2496 2.672295 GCGAACCCCACACCCATA 59.328 61.111 0.00 0.00 0.00 2.74
2201 2497 4.360405 GGCGAACCCCACACCCAT 62.360 66.667 0.00 0.00 0.00 4.00
2269 2572 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
2270 2573 4.548513 CGGGAGGGAGGGAGGGAG 62.549 77.778 0.00 0.00 0.00 4.30
2274 2577 4.150454 AGAGCGGGAGGGAGGGAG 62.150 72.222 0.00 0.00 0.00 4.30
2275 2578 4.465446 CAGAGCGGGAGGGAGGGA 62.465 72.222 0.00 0.00 0.00 4.20
2276 2579 3.375443 TACAGAGCGGGAGGGAGGG 62.375 68.421 0.00 0.00 0.00 4.30
2277 2580 1.830408 CTACAGAGCGGGAGGGAGG 60.830 68.421 0.00 0.00 0.00 4.30
2307 2610 3.058160 ACTGCGCATCTGCCCAAC 61.058 61.111 12.24 0.00 37.91 3.77
2311 2614 3.807538 CCACACTGCGCATCTGCC 61.808 66.667 12.24 0.00 37.91 4.85
2402 2708 3.760151 CCTGCCTCACTTCATCAATTTGA 59.240 43.478 0.75 0.75 0.00 2.69
2403 2709 3.119245 CCCTGCCTCACTTCATCAATTTG 60.119 47.826 0.00 0.00 0.00 2.32
2406 2712 1.064166 CCCCTGCCTCACTTCATCAAT 60.064 52.381 0.00 0.00 0.00 2.57
2407 2713 0.329261 CCCCTGCCTCACTTCATCAA 59.671 55.000 0.00 0.00 0.00 2.57
2408 2714 0.842030 ACCCCTGCCTCACTTCATCA 60.842 55.000 0.00 0.00 0.00 3.07
2409 2715 1.139853 CTACCCCTGCCTCACTTCATC 59.860 57.143 0.00 0.00 0.00 2.92
2410 2716 1.207791 CTACCCCTGCCTCACTTCAT 58.792 55.000 0.00 0.00 0.00 2.57
2426 2732 5.857822 ATTTGCAGACGAAAACTACCTAC 57.142 39.130 0.00 0.00 0.00 3.18
2427 2733 6.103997 CCTATTTGCAGACGAAAACTACCTA 58.896 40.000 0.00 0.00 0.00 3.08
2428 2734 4.935808 CCTATTTGCAGACGAAAACTACCT 59.064 41.667 0.00 0.00 0.00 3.08
2429 2735 4.094442 CCCTATTTGCAGACGAAAACTACC 59.906 45.833 0.00 0.00 0.00 3.18
2452 2758 0.038159 CTCTCGGGTCTTGACACACC 60.038 60.000 3.83 0.00 0.00 4.16
2465 2771 0.177604 AGCTTTGATGCCTCTCTCGG 59.822 55.000 0.00 0.00 0.00 4.63
2471 2777 2.883386 CCCATTCTAGCTTTGATGCCTC 59.117 50.000 0.00 0.00 0.00 4.70
2472 2778 2.941480 CCCATTCTAGCTTTGATGCCT 58.059 47.619 0.00 0.00 0.00 4.75
2473 2779 1.339291 GCCCATTCTAGCTTTGATGCC 59.661 52.381 0.00 0.00 0.00 4.40
2474 2780 2.026641 TGCCCATTCTAGCTTTGATGC 58.973 47.619 0.00 0.00 0.00 3.91
2475 2781 3.548770 TCTGCCCATTCTAGCTTTGATG 58.451 45.455 0.00 0.00 0.00 3.07
2476 2782 3.939740 TCTGCCCATTCTAGCTTTGAT 57.060 42.857 0.00 0.00 0.00 2.57
2477 2783 3.719268 TTCTGCCCATTCTAGCTTTGA 57.281 42.857 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.