Multiple sequence alignment - TraesCS6A01G002600

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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 TraesCS6A01G002600 chr6A 100.000 2677 0 0 262 2938 969536 966860 0.000000e+00 4944.0
1 TraesCS6A01G002600 chr6A 85.946 1231 146 16 998 2222 932261 933470 0.000000e+00 1290.0
2 TraesCS6A01G002600 chr6A 80.959 772 98 19 2205 2938 977016 976256 1.530000e-157 566.0
3 TraesCS6A01G002600 chr6A 80.064 622 78 20 2223 2804 933426 934041 1.260000e-113 420.0
4 TraesCS6A01G002600 chr6A 100.000 134 0 0 1 134 969797 969664 6.290000e-62 248.0
5 TraesCS6A01G002600 chr6A 90.323 62 5 1 834 894 932139 932200 2.430000e-11 80.5
6 TraesCS6A01G002600 chr6D 93.959 2599 121 11 271 2851 1800711 1798131 0.000000e+00 3897.0
7 TraesCS6A01G002600 chr6D 94.696 1923 74 12 1016 2938 1635755 1637649 0.000000e+00 2961.0
8 TraesCS6A01G002600 chr6D 84.262 1544 200 28 987 2520 1850016 1848506 0.000000e+00 1465.0
9 TraesCS6A01G002600 chr6D 85.714 1302 157 17 987 2281 1903423 1902144 0.000000e+00 1347.0
10 TraesCS6A01G002600 chr6D 85.425 1235 154 18 993 2222 1760629 1761842 0.000000e+00 1260.0
11 TraesCS6A01G002600 chr6D 86.280 1035 101 16 1253 2278 1809413 1808411 0.000000e+00 1086.0
12 TraesCS6A01G002600 chr6D 82.069 290 45 4 2520 2804 1901918 1901631 1.050000e-59 241.0
13 TraesCS6A01G002600 chr6D 77.027 444 73 18 2520 2938 1848471 1848032 8.190000e-56 228.0
14 TraesCS6A01G002600 chr6D 78.591 369 53 17 2588 2938 1762106 1762466 1.370000e-53 220.0
15 TraesCS6A01G002600 chr6D 91.525 59 4 1 837 894 1903508 1903450 2.430000e-11 80.5
16 TraesCS6A01G002600 chr6D 87.755 49 5 1 2223 2270 1798806 1798758 4.090000e-04 56.5
17 TraesCS6A01G002600 chr6B 84.552 1463 192 21 919 2379 4885362 4883932 0.000000e+00 1419.0
18 TraesCS6A01G002600 chr6B 84.094 1402 188 24 919 2317 4856434 4857803 0.000000e+00 1321.0
19 TraesCS6A01G002600 chr6B 93.617 47 3 0 837 883 4885404 4885358 1.460000e-08 71.3
20 TraesCS6A01G002600 chr6B 90.000 50 5 0 834 883 4856389 4856438 6.800000e-07 65.8
21 TraesCS6A01G002600 chr3D 79.440 1143 169 41 818 1952 582909772 582908688 0.000000e+00 749.0
22 TraesCS6A01G002600 chr3D 79.850 1067 153 37 818 1879 582922194 582921185 0.000000e+00 723.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G002600 chr6A 966860 969797 2937 True 2596.000000 4944 100.000000 1 2938 2 chr6A.!!$R2 2937
1 TraesCS6A01G002600 chr6A 932139 934041 1902 False 596.833333 1290 85.444333 834 2804 3 chr6A.!!$F1 1970
2 TraesCS6A01G002600 chr6A 976256 977016 760 True 566.000000 566 80.959000 2205 2938 1 chr6A.!!$R1 733
3 TraesCS6A01G002600 chr6D 1635755 1637649 1894 False 2961.000000 2961 94.696000 1016 2938 1 chr6D.!!$F1 1922
4 TraesCS6A01G002600 chr6D 1798131 1800711 2580 True 1976.750000 3897 90.857000 271 2851 2 chr6D.!!$R2 2580
5 TraesCS6A01G002600 chr6D 1808411 1809413 1002 True 1086.000000 1086 86.280000 1253 2278 1 chr6D.!!$R1 1025
6 TraesCS6A01G002600 chr6D 1848032 1850016 1984 True 846.500000 1465 80.644500 987 2938 2 chr6D.!!$R3 1951
7 TraesCS6A01G002600 chr6D 1760629 1762466 1837 False 740.000000 1260 82.008000 993 2938 2 chr6D.!!$F2 1945
8 TraesCS6A01G002600 chr6D 1901631 1903508 1877 True 556.166667 1347 86.436000 837 2804 3 chr6D.!!$R4 1967
9 TraesCS6A01G002600 chr6B 4883932 4885404 1472 True 745.150000 1419 89.084500 837 2379 2 chr6B.!!$R1 1542
10 TraesCS6A01G002600 chr6B 4856389 4857803 1414 False 693.400000 1321 87.047000 834 2317 2 chr6B.!!$F1 1483
11 TraesCS6A01G002600 chr3D 582908688 582909772 1084 True 749.000000 749 79.440000 818 1952 1 chr3D.!!$R1 1134
12 TraesCS6A01G002600 chr3D 582921185 582922194 1009 True 723.000000 723 79.850000 818 1879 1 chr3D.!!$R2 1061

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
32 33 0.036388 ATGATCGGCAAGGTGAACGT 60.036 50.0 0.00 0.00 0.00 3.99 F
558 565 0.040514 TGGAAATTGTTGCGTGCTCG 60.041 50.0 3.31 3.31 40.37 5.03 F
1293 1317 0.103755 TCATCTCCACGCTCTGCATC 59.896 55.0 0.00 0.00 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 1413 0.387929 TCAAGCGGTCGTTGAAGACT 59.612 50.0 0.0 0.0 40.76 3.24 R
1928 1960 0.687757 TGGATTAGGCTCAGGCGTCT 60.688 55.0 0.0 0.0 39.81 4.18 R
2902 3137 0.738975 CCATCTCGTAGTCCGCTCAA 59.261 55.0 0.0 0.0 36.19 3.02 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
20 21 2.042686 ACACAACCCATCATGATCGG 57.957 50.000 16.94 16.94 0.00 4.18
21 22 0.664761 CACAACCCATCATGATCGGC 59.335 55.000 18.27 0.00 0.00 5.54
22 23 0.255604 ACAACCCATCATGATCGGCA 59.744 50.000 18.27 0.00 0.00 5.69
23 24 1.340893 ACAACCCATCATGATCGGCAA 60.341 47.619 18.27 0.00 0.00 4.52
24 25 1.335810 CAACCCATCATGATCGGCAAG 59.664 52.381 18.27 5.71 0.00 4.01
25 26 0.179009 ACCCATCATGATCGGCAAGG 60.179 55.000 18.27 9.53 0.00 3.61
26 27 0.179009 CCCATCATGATCGGCAAGGT 60.179 55.000 6.40 0.00 0.00 3.50
27 28 0.949397 CCATCATGATCGGCAAGGTG 59.051 55.000 4.86 0.00 0.00 4.00
28 29 1.475571 CCATCATGATCGGCAAGGTGA 60.476 52.381 4.86 0.00 27.78 4.02
29 30 2.291365 CATCATGATCGGCAAGGTGAA 58.709 47.619 4.86 0.00 27.78 3.18
30 31 1.737838 TCATGATCGGCAAGGTGAAC 58.262 50.000 0.00 0.00 0.00 3.18
31 32 0.374758 CATGATCGGCAAGGTGAACG 59.625 55.000 0.00 0.00 0.00 3.95
32 33 0.036388 ATGATCGGCAAGGTGAACGT 60.036 50.000 0.00 0.00 0.00 3.99
33 34 0.250124 TGATCGGCAAGGTGAACGTT 60.250 50.000 0.00 0.00 0.00 3.99
34 35 0.165944 GATCGGCAAGGTGAACGTTG 59.834 55.000 5.00 10.70 42.65 4.10
35 36 0.534203 ATCGGCAAGGTGAACGTTGT 60.534 50.000 5.00 0.00 42.02 3.32
36 37 1.010125 CGGCAAGGTGAACGTTGTG 60.010 57.895 5.00 6.75 42.02 3.33
37 38 1.358759 GGCAAGGTGAACGTTGTGG 59.641 57.895 5.00 0.00 42.02 4.17
38 39 1.098712 GGCAAGGTGAACGTTGTGGA 61.099 55.000 5.00 0.00 42.02 4.02
39 40 0.307760 GCAAGGTGAACGTTGTGGAG 59.692 55.000 5.00 0.00 42.02 3.86
40 41 0.944386 CAAGGTGAACGTTGTGGAGG 59.056 55.000 5.00 0.00 37.07 4.30
41 42 0.818040 AAGGTGAACGTTGTGGAGGC 60.818 55.000 5.00 0.00 0.00 4.70
42 43 2.604174 GGTGAACGTTGTGGAGGCG 61.604 63.158 5.00 0.00 0.00 5.52
43 44 2.280524 TGAACGTTGTGGAGGCGG 60.281 61.111 5.00 0.00 0.00 6.13
44 45 2.280592 GAACGTTGTGGAGGCGGT 60.281 61.111 5.00 0.00 0.00 5.68
45 46 2.590575 AACGTTGTGGAGGCGGTG 60.591 61.111 0.00 0.00 0.00 4.94
47 48 4.988598 CGTTGTGGAGGCGGTGCT 62.989 66.667 0.00 0.00 0.00 4.40
48 49 2.345991 GTTGTGGAGGCGGTGCTA 59.654 61.111 0.00 0.00 0.00 3.49
49 50 1.302192 GTTGTGGAGGCGGTGCTAA 60.302 57.895 0.00 0.00 0.00 3.09
50 51 1.003839 TTGTGGAGGCGGTGCTAAG 60.004 57.895 0.00 0.00 0.00 2.18
51 52 2.125106 GTGGAGGCGGTGCTAAGG 60.125 66.667 0.00 0.00 0.00 2.69
52 53 2.606519 TGGAGGCGGTGCTAAGGT 60.607 61.111 0.00 0.00 0.00 3.50
53 54 2.221299 TGGAGGCGGTGCTAAGGTT 61.221 57.895 0.00 0.00 0.00 3.50
54 55 1.002502 GGAGGCGGTGCTAAGGTTT 60.003 57.895 0.00 0.00 0.00 3.27
55 56 1.305930 GGAGGCGGTGCTAAGGTTTG 61.306 60.000 0.00 0.00 0.00 2.93
56 57 1.303317 AGGCGGTGCTAAGGTTTGG 60.303 57.895 0.00 0.00 0.00 3.28
57 58 1.602605 GGCGGTGCTAAGGTTTGGT 60.603 57.895 0.00 0.00 0.00 3.67
58 59 1.176619 GGCGGTGCTAAGGTTTGGTT 61.177 55.000 0.00 0.00 0.00 3.67
59 60 1.525941 GCGGTGCTAAGGTTTGGTTA 58.474 50.000 0.00 0.00 0.00 2.85
60 61 1.467342 GCGGTGCTAAGGTTTGGTTAG 59.533 52.381 0.00 0.00 0.00 2.34
61 62 2.081462 CGGTGCTAAGGTTTGGTTAGG 58.919 52.381 0.00 0.00 0.00 2.69
62 63 2.551504 CGGTGCTAAGGTTTGGTTAGGT 60.552 50.000 0.00 0.00 0.00 3.08
63 64 3.493334 GGTGCTAAGGTTTGGTTAGGTT 58.507 45.455 0.00 0.00 0.00 3.50
64 65 3.893200 GGTGCTAAGGTTTGGTTAGGTTT 59.107 43.478 0.00 0.00 0.00 3.27
65 66 4.342951 GGTGCTAAGGTTTGGTTAGGTTTT 59.657 41.667 0.00 0.00 0.00 2.43
66 67 5.286438 GTGCTAAGGTTTGGTTAGGTTTTG 58.714 41.667 0.00 0.00 0.00 2.44
67 68 5.068067 GTGCTAAGGTTTGGTTAGGTTTTGA 59.932 40.000 0.00 0.00 0.00 2.69
68 69 5.657302 TGCTAAGGTTTGGTTAGGTTTTGAA 59.343 36.000 0.00 0.00 0.00 2.69
69 70 6.154706 TGCTAAGGTTTGGTTAGGTTTTGAAA 59.845 34.615 0.00 0.00 0.00 2.69
70 71 6.700081 GCTAAGGTTTGGTTAGGTTTTGAAAG 59.300 38.462 0.00 0.00 0.00 2.62
71 72 6.614694 AAGGTTTGGTTAGGTTTTGAAAGT 57.385 33.333 0.00 0.00 0.00 2.66
72 73 5.972935 AGGTTTGGTTAGGTTTTGAAAGTG 58.027 37.500 0.00 0.00 0.00 3.16
73 74 5.105106 AGGTTTGGTTAGGTTTTGAAAGTGG 60.105 40.000 0.00 0.00 0.00 4.00
74 75 5.105269 GGTTTGGTTAGGTTTTGAAAGTGGA 60.105 40.000 0.00 0.00 0.00 4.02
75 76 6.407639 GGTTTGGTTAGGTTTTGAAAGTGGAT 60.408 38.462 0.00 0.00 0.00 3.41
76 77 6.800072 TTGGTTAGGTTTTGAAAGTGGATT 57.200 33.333 0.00 0.00 0.00 3.01
77 78 6.155475 TGGTTAGGTTTTGAAAGTGGATTG 57.845 37.500 0.00 0.00 0.00 2.67
78 79 5.069781 TGGTTAGGTTTTGAAAGTGGATTGG 59.930 40.000 0.00 0.00 0.00 3.16
79 80 5.510690 GGTTAGGTTTTGAAAGTGGATTGGG 60.511 44.000 0.00 0.00 0.00 4.12
80 81 2.972021 AGGTTTTGAAAGTGGATTGGGG 59.028 45.455 0.00 0.00 0.00 4.96
81 82 2.038426 GGTTTTGAAAGTGGATTGGGGG 59.962 50.000 0.00 0.00 0.00 5.40
82 83 2.969262 GTTTTGAAAGTGGATTGGGGGA 59.031 45.455 0.00 0.00 0.00 4.81
83 84 2.603075 TTGAAAGTGGATTGGGGGAG 57.397 50.000 0.00 0.00 0.00 4.30
84 85 1.753903 TGAAAGTGGATTGGGGGAGA 58.246 50.000 0.00 0.00 0.00 3.71
85 86 1.635487 TGAAAGTGGATTGGGGGAGAG 59.365 52.381 0.00 0.00 0.00 3.20
86 87 1.916181 GAAAGTGGATTGGGGGAGAGA 59.084 52.381 0.00 0.00 0.00 3.10
87 88 2.059756 AAGTGGATTGGGGGAGAGAA 57.940 50.000 0.00 0.00 0.00 2.87
88 89 1.589414 AGTGGATTGGGGGAGAGAAG 58.411 55.000 0.00 0.00 0.00 2.85
89 90 1.081174 AGTGGATTGGGGGAGAGAAGA 59.919 52.381 0.00 0.00 0.00 2.87
90 91 1.916181 GTGGATTGGGGGAGAGAAGAA 59.084 52.381 0.00 0.00 0.00 2.52
91 92 2.308866 GTGGATTGGGGGAGAGAAGAAA 59.691 50.000 0.00 0.00 0.00 2.52
92 93 3.053320 GTGGATTGGGGGAGAGAAGAAAT 60.053 47.826 0.00 0.00 0.00 2.17
93 94 3.053395 TGGATTGGGGGAGAGAAGAAATG 60.053 47.826 0.00 0.00 0.00 2.32
94 95 3.560105 GATTGGGGGAGAGAAGAAATGG 58.440 50.000 0.00 0.00 0.00 3.16
95 96 2.359376 TGGGGGAGAGAAGAAATGGA 57.641 50.000 0.00 0.00 0.00 3.41
96 97 1.916181 TGGGGGAGAGAAGAAATGGAC 59.084 52.381 0.00 0.00 0.00 4.02
97 98 1.134371 GGGGGAGAGAAGAAATGGACG 60.134 57.143 0.00 0.00 0.00 4.79
98 99 1.134371 GGGGAGAGAAGAAATGGACGG 60.134 57.143 0.00 0.00 0.00 4.79
99 100 1.831736 GGGAGAGAAGAAATGGACGGA 59.168 52.381 0.00 0.00 0.00 4.69
100 101 2.236395 GGGAGAGAAGAAATGGACGGAA 59.764 50.000 0.00 0.00 0.00 4.30
101 102 3.307480 GGGAGAGAAGAAATGGACGGAAA 60.307 47.826 0.00 0.00 0.00 3.13
102 103 4.324267 GGAGAGAAGAAATGGACGGAAAA 58.676 43.478 0.00 0.00 0.00 2.29
103 104 4.944317 GGAGAGAAGAAATGGACGGAAAAT 59.056 41.667 0.00 0.00 0.00 1.82
104 105 5.163713 GGAGAGAAGAAATGGACGGAAAATG 60.164 44.000 0.00 0.00 0.00 2.32
105 106 5.560724 AGAGAAGAAATGGACGGAAAATGA 58.439 37.500 0.00 0.00 0.00 2.57
106 107 6.003950 AGAGAAGAAATGGACGGAAAATGAA 58.996 36.000 0.00 0.00 0.00 2.57
107 108 6.150140 AGAGAAGAAATGGACGGAAAATGAAG 59.850 38.462 0.00 0.00 0.00 3.02
108 109 4.440839 AGAAATGGACGGAAAATGAAGC 57.559 40.909 0.00 0.00 0.00 3.86
109 110 4.082125 AGAAATGGACGGAAAATGAAGCT 58.918 39.130 0.00 0.00 0.00 3.74
110 111 3.855689 AATGGACGGAAAATGAAGCTG 57.144 42.857 0.00 0.00 0.00 4.24
111 112 2.270352 TGGACGGAAAATGAAGCTGT 57.730 45.000 0.00 0.00 0.00 4.40
112 113 1.879380 TGGACGGAAAATGAAGCTGTG 59.121 47.619 0.00 0.00 0.00 3.66
113 114 1.200020 GGACGGAAAATGAAGCTGTGG 59.800 52.381 0.00 0.00 0.00 4.17
114 115 1.880027 GACGGAAAATGAAGCTGTGGT 59.120 47.619 0.00 0.00 0.00 4.16
115 116 1.608590 ACGGAAAATGAAGCTGTGGTG 59.391 47.619 0.00 0.00 0.00 4.17
116 117 1.666888 CGGAAAATGAAGCTGTGGTGC 60.667 52.381 0.00 0.00 0.00 5.01
117 118 1.615392 GGAAAATGAAGCTGTGGTGCT 59.385 47.619 0.00 0.00 46.40 4.40
124 125 3.614399 AGCTGTGGTGCTTGAGTAC 57.386 52.632 0.00 0.00 40.93 2.73
130 131 3.735181 GGTGCTTGAGTACCCGTAG 57.265 57.895 6.98 0.00 43.79 3.51
131 132 1.180029 GGTGCTTGAGTACCCGTAGA 58.820 55.000 6.98 0.00 43.79 2.59
132 133 1.134560 GGTGCTTGAGTACCCGTAGAG 59.865 57.143 6.98 0.00 43.79 2.43
133 134 2.089980 GTGCTTGAGTACCCGTAGAGA 58.910 52.381 0.00 0.00 0.00 3.10
329 336 2.094234 ACCAACCGCCTGCAATATTTTC 60.094 45.455 0.00 0.00 0.00 2.29
331 338 3.438360 CAACCGCCTGCAATATTTTCTC 58.562 45.455 0.00 0.00 0.00 2.87
361 368 1.216710 GGAGTTCTGACAGCCTCCG 59.783 63.158 19.22 0.00 34.62 4.63
395 402 3.244078 ACAGACGCCTACATTCTGTTTGA 60.244 43.478 0.00 0.00 46.23 2.69
429 436 2.123982 GGGCTGCTGCTAATGCCT 60.124 61.111 15.64 0.00 44.36 4.75
452 459 7.771826 GCCTGTTTTTATACTAGTGTGGGAATA 59.228 37.037 5.39 0.00 0.00 1.75
558 565 0.040514 TGGAAATTGTTGCGTGCTCG 60.041 50.000 3.31 3.31 40.37 5.03
668 675 6.042552 AGCTGGAGCATGGATATATGGTATAC 59.957 42.308 0.65 0.00 45.16 1.47
756 763 6.359883 GGATAAGAACAGCGTTTGAAAAGAAC 59.640 38.462 0.00 0.00 0.00 3.01
761 768 6.691388 AGAACAGCGTTTGAAAAGAACAATAC 59.309 34.615 0.00 0.00 0.00 1.89
764 771 4.976116 AGCGTTTGAAAAGAACAATACTGC 59.024 37.500 0.00 0.00 0.00 4.40
934 948 0.184211 TGCCATCCATCCATCACCTG 59.816 55.000 0.00 0.00 0.00 4.00
943 957 2.405618 TCCATCACCTGGCTAGCTAT 57.594 50.000 15.72 0.00 45.52 2.97
982 1004 0.243636 GGCGCTTGGTGCAATAAACT 59.756 50.000 7.64 0.00 41.25 2.66
983 1005 1.339711 GCGCTTGGTGCAATAAACTG 58.660 50.000 0.00 0.00 43.06 3.16
1008 1032 1.823041 GAGAGCAAGCATGGAGGGC 60.823 63.158 0.00 0.00 0.00 5.19
1293 1317 0.103755 TCATCTCCACGCTCTGCATC 59.896 55.000 0.00 0.00 0.00 3.91
1327 1351 0.177604 CATCGAGCCAGGCTTCTTCT 59.822 55.000 17.46 0.00 39.88 2.85
1389 1413 1.153784 CGAAGGCGCCGGTAAGTTA 60.154 57.895 23.20 0.00 0.00 2.24
1611 1637 9.316730 GGTTACCGAGATATACTACTAGATCTG 57.683 40.741 5.18 0.00 32.12 2.90
1702 1734 9.881649 TTGGATCTTCATATAATAGATGTCTGC 57.118 33.333 0.00 0.00 0.00 4.26
1722 1754 2.933906 GCTGATTGGCAATTTGTCATGG 59.066 45.455 14.93 0.00 29.04 3.66
1723 1755 3.368635 GCTGATTGGCAATTTGTCATGGA 60.369 43.478 14.93 0.00 29.04 3.41
1724 1756 4.682320 GCTGATTGGCAATTTGTCATGGAT 60.682 41.667 14.93 0.00 29.04 3.41
1922 1954 4.634004 CGCAAATACATTCCCAGAGTAACA 59.366 41.667 0.00 0.00 0.00 2.41
1926 1958 7.312899 CAAATACATTCCCAGAGTAACAAACC 58.687 38.462 0.00 0.00 0.00 3.27
1928 1960 5.836024 ACATTCCCAGAGTAACAAACCTA 57.164 39.130 0.00 0.00 0.00 3.08
1978 2010 2.282407 CATCATCGTCTTGTCCATGCA 58.718 47.619 0.00 0.00 0.00 3.96
1981 2013 1.019673 ATCGTCTTGTCCATGCATGC 58.980 50.000 21.69 11.82 0.00 4.06
1987 2019 0.609681 TTGTCCATGCATGCTGCTCA 60.610 50.000 21.69 11.36 45.31 4.26
1992 2024 1.032794 CATGCATGCTGCTCATCCTT 58.967 50.000 20.33 0.00 45.31 3.36
2118 2154 2.910688 AGAAGTTTGTTGCTCCTCGA 57.089 45.000 0.00 0.00 0.00 4.04
2123 2159 2.030805 AGTTTGTTGCTCCTCGATTTGC 60.031 45.455 0.00 0.00 0.00 3.68
2218 2262 2.281498 GCGCACAAAAGTTCTTGGTTTC 59.719 45.455 0.30 0.00 0.00 2.78
2322 2456 2.217620 CGCGCAAAGGTTTTTGGTTTAG 59.782 45.455 8.75 0.00 43.12 1.85
2405 2546 6.902408 TCCCCACTACGTTATTTGGATATTT 58.098 36.000 0.00 0.00 0.00 1.40
2585 2781 3.580458 AGAAACTATGTGTCAGTGCCTCT 59.420 43.478 0.00 0.00 0.00 3.69
2859 3093 3.541632 CGAACACCCTTAGGCACATTAT 58.458 45.455 0.00 0.00 36.11 1.28
2866 3101 4.905456 ACCCTTAGGCACATTATACTAGCA 59.095 41.667 0.00 0.00 36.11 3.49
2926 3161 1.068250 GGACTACGAGATGGCAGCC 59.932 63.158 3.66 3.66 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.744823 GCCGATCATGATGGGTTGTGTA 60.745 50.000 30.39 0.00 38.72 2.90
1 2 2.018644 GCCGATCATGATGGGTTGTGT 61.019 52.381 30.39 0.00 38.72 3.72
2 3 0.664761 GCCGATCATGATGGGTTGTG 59.335 55.000 30.39 11.38 38.72 3.33
3 4 0.255604 TGCCGATCATGATGGGTTGT 59.744 50.000 30.39 0.36 38.72 3.32
4 5 1.335810 CTTGCCGATCATGATGGGTTG 59.664 52.381 30.39 19.45 38.72 3.77
5 6 1.683943 CTTGCCGATCATGATGGGTT 58.316 50.000 30.39 1.89 38.72 4.11
6 7 0.179009 CCTTGCCGATCATGATGGGT 60.179 55.000 30.39 2.29 38.72 4.51
7 8 0.179009 ACCTTGCCGATCATGATGGG 60.179 55.000 27.48 27.48 39.38 4.00
8 9 0.949397 CACCTTGCCGATCATGATGG 59.051 55.000 14.30 12.19 0.00 3.51
9 10 1.957668 TCACCTTGCCGATCATGATG 58.042 50.000 14.30 5.58 0.00 3.07
10 11 2.292267 GTTCACCTTGCCGATCATGAT 58.708 47.619 8.25 8.25 0.00 2.45
11 12 1.737838 GTTCACCTTGCCGATCATGA 58.262 50.000 0.00 0.00 0.00 3.07
12 13 0.374758 CGTTCACCTTGCCGATCATG 59.625 55.000 0.00 0.00 0.00 3.07
13 14 0.036388 ACGTTCACCTTGCCGATCAT 60.036 50.000 0.00 0.00 0.00 2.45
14 15 0.250124 AACGTTCACCTTGCCGATCA 60.250 50.000 0.00 0.00 0.00 2.92
15 16 0.165944 CAACGTTCACCTTGCCGATC 59.834 55.000 0.00 0.00 0.00 3.69
16 17 0.534203 ACAACGTTCACCTTGCCGAT 60.534 50.000 0.00 0.00 0.00 4.18
17 18 1.153329 ACAACGTTCACCTTGCCGA 60.153 52.632 0.00 0.00 0.00 5.54
18 19 1.010125 CACAACGTTCACCTTGCCG 60.010 57.895 0.00 0.00 0.00 5.69
19 20 1.098712 TCCACAACGTTCACCTTGCC 61.099 55.000 0.00 0.00 0.00 4.52
20 21 0.307760 CTCCACAACGTTCACCTTGC 59.692 55.000 0.00 0.00 0.00 4.01
21 22 0.944386 CCTCCACAACGTTCACCTTG 59.056 55.000 0.00 0.00 0.00 3.61
22 23 0.818040 GCCTCCACAACGTTCACCTT 60.818 55.000 0.00 0.00 0.00 3.50
23 24 1.227853 GCCTCCACAACGTTCACCT 60.228 57.895 0.00 0.00 0.00 4.00
24 25 2.604174 CGCCTCCACAACGTTCACC 61.604 63.158 0.00 0.00 0.00 4.02
25 26 2.604174 CCGCCTCCACAACGTTCAC 61.604 63.158 0.00 0.00 0.00 3.18
26 27 2.280524 CCGCCTCCACAACGTTCA 60.281 61.111 0.00 0.00 0.00 3.18
27 28 2.280592 ACCGCCTCCACAACGTTC 60.281 61.111 0.00 0.00 0.00 3.95
28 29 2.590575 CACCGCCTCCACAACGTT 60.591 61.111 0.00 0.00 0.00 3.99
30 31 3.583276 TAGCACCGCCTCCACAACG 62.583 63.158 0.00 0.00 0.00 4.10
31 32 1.298859 CTTAGCACCGCCTCCACAAC 61.299 60.000 0.00 0.00 0.00 3.32
32 33 1.003839 CTTAGCACCGCCTCCACAA 60.004 57.895 0.00 0.00 0.00 3.33
33 34 2.662596 CTTAGCACCGCCTCCACA 59.337 61.111 0.00 0.00 0.00 4.17
34 35 2.125106 CCTTAGCACCGCCTCCAC 60.125 66.667 0.00 0.00 0.00 4.02
35 36 1.774894 AAACCTTAGCACCGCCTCCA 61.775 55.000 0.00 0.00 0.00 3.86
36 37 1.002502 AAACCTTAGCACCGCCTCC 60.003 57.895 0.00 0.00 0.00 4.30
37 38 1.305930 CCAAACCTTAGCACCGCCTC 61.306 60.000 0.00 0.00 0.00 4.70
38 39 1.303317 CCAAACCTTAGCACCGCCT 60.303 57.895 0.00 0.00 0.00 5.52
39 40 1.176619 AACCAAACCTTAGCACCGCC 61.177 55.000 0.00 0.00 0.00 6.13
40 41 1.467342 CTAACCAAACCTTAGCACCGC 59.533 52.381 0.00 0.00 0.00 5.68
41 42 2.081462 CCTAACCAAACCTTAGCACCG 58.919 52.381 0.00 0.00 0.00 4.94
42 43 3.150458 ACCTAACCAAACCTTAGCACC 57.850 47.619 0.00 0.00 0.00 5.01
43 44 5.068067 TCAAAACCTAACCAAACCTTAGCAC 59.932 40.000 0.00 0.00 0.00 4.40
44 45 5.202004 TCAAAACCTAACCAAACCTTAGCA 58.798 37.500 0.00 0.00 0.00 3.49
45 46 5.777850 TCAAAACCTAACCAAACCTTAGC 57.222 39.130 0.00 0.00 0.00 3.09
46 47 7.704899 CACTTTCAAAACCTAACCAAACCTTAG 59.295 37.037 0.00 0.00 0.00 2.18
47 48 7.363968 CCACTTTCAAAACCTAACCAAACCTTA 60.364 37.037 0.00 0.00 0.00 2.69
48 49 6.403049 CACTTTCAAAACCTAACCAAACCTT 58.597 36.000 0.00 0.00 0.00 3.50
49 50 5.105106 CCACTTTCAAAACCTAACCAAACCT 60.105 40.000 0.00 0.00 0.00 3.50
50 51 5.105269 TCCACTTTCAAAACCTAACCAAACC 60.105 40.000 0.00 0.00 0.00 3.27
51 52 5.968254 TCCACTTTCAAAACCTAACCAAAC 58.032 37.500 0.00 0.00 0.00 2.93
52 53 6.800072 ATCCACTTTCAAAACCTAACCAAA 57.200 33.333 0.00 0.00 0.00 3.28
53 54 6.407525 CCAATCCACTTTCAAAACCTAACCAA 60.408 38.462 0.00 0.00 0.00 3.67
54 55 5.069781 CCAATCCACTTTCAAAACCTAACCA 59.930 40.000 0.00 0.00 0.00 3.67
55 56 5.510690 CCCAATCCACTTTCAAAACCTAACC 60.511 44.000 0.00 0.00 0.00 2.85
56 57 5.510690 CCCCAATCCACTTTCAAAACCTAAC 60.511 44.000 0.00 0.00 0.00 2.34
57 58 4.591072 CCCCAATCCACTTTCAAAACCTAA 59.409 41.667 0.00 0.00 0.00 2.69
58 59 4.156477 CCCCAATCCACTTTCAAAACCTA 58.844 43.478 0.00 0.00 0.00 3.08
59 60 2.972021 CCCCAATCCACTTTCAAAACCT 59.028 45.455 0.00 0.00 0.00 3.50
60 61 2.038426 CCCCCAATCCACTTTCAAAACC 59.962 50.000 0.00 0.00 0.00 3.27
61 62 2.969262 TCCCCCAATCCACTTTCAAAAC 59.031 45.455 0.00 0.00 0.00 2.43
62 63 3.116939 TCTCCCCCAATCCACTTTCAAAA 60.117 43.478 0.00 0.00 0.00 2.44
63 64 2.448961 TCTCCCCCAATCCACTTTCAAA 59.551 45.455 0.00 0.00 0.00 2.69
64 65 2.041620 CTCTCCCCCAATCCACTTTCAA 59.958 50.000 0.00 0.00 0.00 2.69
65 66 1.635487 CTCTCCCCCAATCCACTTTCA 59.365 52.381 0.00 0.00 0.00 2.69
66 67 1.916181 TCTCTCCCCCAATCCACTTTC 59.084 52.381 0.00 0.00 0.00 2.62
67 68 2.059756 TCTCTCCCCCAATCCACTTT 57.940 50.000 0.00 0.00 0.00 2.66
68 69 1.918957 CTTCTCTCCCCCAATCCACTT 59.081 52.381 0.00 0.00 0.00 3.16
69 70 1.081174 TCTTCTCTCCCCCAATCCACT 59.919 52.381 0.00 0.00 0.00 4.00
70 71 1.584724 TCTTCTCTCCCCCAATCCAC 58.415 55.000 0.00 0.00 0.00 4.02
71 72 2.359376 TTCTTCTCTCCCCCAATCCA 57.641 50.000 0.00 0.00 0.00 3.41
72 73 3.560105 CATTTCTTCTCTCCCCCAATCC 58.440 50.000 0.00 0.00 0.00 3.01
73 74 3.203040 TCCATTTCTTCTCTCCCCCAATC 59.797 47.826 0.00 0.00 0.00 2.67
74 75 3.053320 GTCCATTTCTTCTCTCCCCCAAT 60.053 47.826 0.00 0.00 0.00 3.16
75 76 2.308866 GTCCATTTCTTCTCTCCCCCAA 59.691 50.000 0.00 0.00 0.00 4.12
76 77 1.916181 GTCCATTTCTTCTCTCCCCCA 59.084 52.381 0.00 0.00 0.00 4.96
77 78 1.134371 CGTCCATTTCTTCTCTCCCCC 60.134 57.143 0.00 0.00 0.00 5.40
78 79 1.134371 CCGTCCATTTCTTCTCTCCCC 60.134 57.143 0.00 0.00 0.00 4.81
79 80 1.831736 TCCGTCCATTTCTTCTCTCCC 59.168 52.381 0.00 0.00 0.00 4.30
80 81 3.611766 TTCCGTCCATTTCTTCTCTCC 57.388 47.619 0.00 0.00 0.00 3.71
81 82 5.643777 TCATTTTCCGTCCATTTCTTCTCTC 59.356 40.000 0.00 0.00 0.00 3.20
82 83 5.560724 TCATTTTCCGTCCATTTCTTCTCT 58.439 37.500 0.00 0.00 0.00 3.10
83 84 5.880054 TCATTTTCCGTCCATTTCTTCTC 57.120 39.130 0.00 0.00 0.00 2.87
84 85 5.335976 GCTTCATTTTCCGTCCATTTCTTCT 60.336 40.000 0.00 0.00 0.00 2.85
85 86 4.859245 GCTTCATTTTCCGTCCATTTCTTC 59.141 41.667 0.00 0.00 0.00 2.87
86 87 4.524328 AGCTTCATTTTCCGTCCATTTCTT 59.476 37.500 0.00 0.00 0.00 2.52
87 88 4.082125 AGCTTCATTTTCCGTCCATTTCT 58.918 39.130 0.00 0.00 0.00 2.52
88 89 4.168760 CAGCTTCATTTTCCGTCCATTTC 58.831 43.478 0.00 0.00 0.00 2.17
89 90 3.573967 ACAGCTTCATTTTCCGTCCATTT 59.426 39.130 0.00 0.00 0.00 2.32
90 91 3.057315 CACAGCTTCATTTTCCGTCCATT 60.057 43.478 0.00 0.00 0.00 3.16
91 92 2.489329 CACAGCTTCATTTTCCGTCCAT 59.511 45.455 0.00 0.00 0.00 3.41
92 93 1.879380 CACAGCTTCATTTTCCGTCCA 59.121 47.619 0.00 0.00 0.00 4.02
93 94 1.200020 CCACAGCTTCATTTTCCGTCC 59.800 52.381 0.00 0.00 0.00 4.79
94 95 1.880027 ACCACAGCTTCATTTTCCGTC 59.120 47.619 0.00 0.00 0.00 4.79
95 96 1.608590 CACCACAGCTTCATTTTCCGT 59.391 47.619 0.00 0.00 0.00 4.69
96 97 1.666888 GCACCACAGCTTCATTTTCCG 60.667 52.381 0.00 0.00 0.00 4.30
97 98 1.615392 AGCACCACAGCTTCATTTTCC 59.385 47.619 0.00 0.00 43.70 3.13
107 108 0.955919 GGGTACTCAAGCACCACAGC 60.956 60.000 1.95 0.00 36.48 4.40
108 109 0.670546 CGGGTACTCAAGCACCACAG 60.671 60.000 1.95 0.00 36.48 3.66
109 110 1.369692 CGGGTACTCAAGCACCACA 59.630 57.895 1.95 0.00 36.48 4.17
110 111 0.604578 TACGGGTACTCAAGCACCAC 59.395 55.000 1.95 0.00 36.48 4.16
111 112 0.892755 CTACGGGTACTCAAGCACCA 59.107 55.000 1.95 0.00 36.48 4.17
112 113 1.134560 CTCTACGGGTACTCAAGCACC 59.865 57.143 0.00 0.00 0.00 5.01
113 114 2.089980 TCTCTACGGGTACTCAAGCAC 58.910 52.381 0.00 0.00 0.00 4.40
114 115 2.502142 TCTCTACGGGTACTCAAGCA 57.498 50.000 0.00 0.00 0.00 3.91
261 262 2.806244 GCAAACGGCTTCACTCTAGAAA 59.194 45.455 0.00 0.00 40.25 2.52
262 263 2.224185 TGCAAACGGCTTCACTCTAGAA 60.224 45.455 0.00 0.00 45.15 2.10
263 264 1.343142 TGCAAACGGCTTCACTCTAGA 59.657 47.619 0.00 0.00 45.15 2.43
264 265 1.461127 GTGCAAACGGCTTCACTCTAG 59.539 52.381 0.00 0.00 45.15 2.43
265 266 1.070134 AGTGCAAACGGCTTCACTCTA 59.930 47.619 0.00 0.00 45.15 2.43
266 267 0.179045 AGTGCAAACGGCTTCACTCT 60.179 50.000 0.00 0.00 45.15 3.24
267 268 0.235926 GAGTGCAAACGGCTTCACTC 59.764 55.000 12.12 12.12 45.50 3.51
268 269 1.498865 CGAGTGCAAACGGCTTCACT 61.499 55.000 5.98 2.99 45.15 3.41
269 270 1.082756 CGAGTGCAAACGGCTTCAC 60.083 57.895 5.98 0.00 45.15 3.18
329 336 3.999663 CAGAACTCCAAAACTGCCTAGAG 59.000 47.826 0.00 0.00 0.00 2.43
331 338 3.748568 GTCAGAACTCCAAAACTGCCTAG 59.251 47.826 0.00 0.00 0.00 3.02
361 368 2.697229 AGGCGTCTGTAATAACCCTACC 59.303 50.000 0.00 0.00 0.00 3.18
395 402 4.019174 CAGCCCTTGGAAATAGTTGTGAT 58.981 43.478 0.00 0.00 0.00 3.06
452 459 5.163311 TGTGGAATGATGTGATCGGACTAAT 60.163 40.000 0.00 0.00 0.00 1.73
456 463 2.905075 TGTGGAATGATGTGATCGGAC 58.095 47.619 0.00 0.00 0.00 4.79
558 565 1.003233 ACCTCCTTTCCACGGTCAATC 59.997 52.381 0.00 0.00 0.00 2.67
668 675 9.626045 GTATCTTTTCTTGGAACTGTTTAATGG 57.374 33.333 0.00 0.00 0.00 3.16
792 799 0.179200 GACGGTGGTTTAATGCTGCG 60.179 55.000 0.00 0.00 0.00 5.18
934 948 1.337354 GCCGGAGAAAGATAGCTAGCC 60.337 57.143 12.13 0.00 0.00 3.93
977 991 3.744426 GCTTGCTCTCGTTAACCAGTTTA 59.256 43.478 0.00 0.00 0.00 2.01
982 1004 2.076100 CATGCTTGCTCTCGTTAACCA 58.924 47.619 0.00 0.00 0.00 3.67
983 1005 1.398390 CCATGCTTGCTCTCGTTAACC 59.602 52.381 0.00 0.00 0.00 2.85
1008 1032 4.910585 GTCATAGTGGCGGCCGGG 62.911 72.222 29.38 0.00 0.00 5.73
1225 1249 4.521062 GCGCAGGCACTCGAGGAT 62.521 66.667 18.41 0.00 34.60 3.24
1244 1268 3.512516 GAAGCACAGGCATCGGGC 61.513 66.667 0.00 0.00 44.61 6.13
1293 1317 1.480545 TCGATGTAGACACCACCATGG 59.519 52.381 11.19 11.19 45.02 3.66
1327 1351 0.401395 ACAAGGTCCTGGTGGAAGGA 60.401 55.000 0.00 0.00 45.18 3.36
1389 1413 0.387929 TCAAGCGGTCGTTGAAGACT 59.612 50.000 0.00 0.00 40.76 3.24
1702 1734 4.459390 TCCATGACAAATTGCCAATCAG 57.541 40.909 0.00 0.00 0.00 2.90
1722 1754 2.561419 CCCATTTCCTGCATCCATCATC 59.439 50.000 0.00 0.00 0.00 2.92
1723 1755 2.605257 CCCATTTCCTGCATCCATCAT 58.395 47.619 0.00 0.00 0.00 2.45
1724 1756 1.411930 CCCCATTTCCTGCATCCATCA 60.412 52.381 0.00 0.00 0.00 3.07
1922 1954 0.905337 AGGCTCAGGCGTCTAGGTTT 60.905 55.000 0.00 0.00 39.81 3.27
1926 1958 1.271102 GGATTAGGCTCAGGCGTCTAG 59.729 57.143 0.00 0.00 39.81 2.43
1928 1960 0.687757 TGGATTAGGCTCAGGCGTCT 60.688 55.000 0.00 0.00 39.81 4.18
1978 2010 2.803030 ACAAGAAGGATGAGCAGCAT 57.197 45.000 0.00 0.00 40.77 3.79
1981 2013 2.941720 GGCTAACAAGAAGGATGAGCAG 59.058 50.000 0.00 0.00 0.00 4.24
1987 2019 6.122964 GGTAGATTTGGCTAACAAGAAGGAT 58.877 40.000 0.00 0.00 40.82 3.24
1992 2024 3.516300 TCCGGTAGATTTGGCTAACAAGA 59.484 43.478 0.00 0.00 40.82 3.02
2100 2134 4.222114 CAAATCGAGGAGCAACAAACTTC 58.778 43.478 0.00 0.00 0.00 3.01
2140 2176 8.278408 CCGAAGTATGAAATGACATTATCACAG 58.722 37.037 0.00 0.00 41.24 3.66
2141 2177 7.768582 ACCGAAGTATGAAATGACATTATCACA 59.231 33.333 0.00 1.11 41.24 3.58
2142 2178 8.142994 ACCGAAGTATGAAATGACATTATCAC 57.857 34.615 0.00 0.00 41.24 3.06
2162 2198 2.563039 AGGAAGGGAAGGATACCGAA 57.437 50.000 0.00 0.00 37.17 4.30
2201 2245 6.094881 TGAAGATCGAAACCAAGAACTTTTGT 59.905 34.615 0.00 0.00 31.17 2.83
2218 2262 5.163513 CAAGGTTTGGGAAAATGAAGATCG 58.836 41.667 0.00 0.00 0.00 3.69
2365 2500 1.411651 GGGAGAGGGGTGGCTATGTC 61.412 65.000 0.00 0.00 0.00 3.06
2859 3093 3.857052 CTTTGGGATTCGTGTGCTAGTA 58.143 45.455 0.00 0.00 0.00 1.82
2866 3101 0.872388 GAACGCTTTGGGATTCGTGT 59.128 50.000 0.00 0.00 35.19 4.49
2902 3137 0.738975 CCATCTCGTAGTCCGCTCAA 59.261 55.000 0.00 0.00 36.19 3.02


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

AutoCloner maintained by Alex Coulton.