Multiple sequence alignment - TraesCS6A01G025100

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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 TraesCS6A01G025100 chr6A 100.000 2540 0 0 1 2540 12419997 12422536 0.000000e+00 4691.0
1 TraesCS6A01G025100 chr6A 82.655 2260 297 44 331 2538 7977673 7979889 0.000000e+00 1914.0
2 TraesCS6A01G025100 chr6A 82.533 229 34 6 2251 2476 8210981 8210756 1.990000e-46 196.0
3 TraesCS6A01G025100 chr4A 92.290 2205 133 14 354 2540 667380012 667382197 0.000000e+00 3096.0
4 TraesCS6A01G025100 chr4A 85.273 1229 151 10 354 1555 667425298 667426523 0.000000e+00 1240.0
5 TraesCS6A01G025100 chr4A 79.852 809 105 26 1609 2389 667426540 667427318 2.880000e-149 538.0
6 TraesCS6A01G025100 chr4A 97.222 36 1 0 265 300 667425170 667425205 7.590000e-06 62.1
7 TraesCS6A01G025100 chr6B 84.119 2248 248 47 331 2540 14303231 14305407 0.000000e+00 2073.0
8 TraesCS6A01G025100 chr6B 89.909 1536 131 15 328 1843 54422329 54420798 0.000000e+00 1956.0
9 TraesCS6A01G025100 chr6B 85.901 1603 187 15 336 1914 39326083 39327670 0.000000e+00 1672.0
10 TraesCS6A01G025100 chr6B 85.229 1442 189 18 660 2089 14318227 14319656 0.000000e+00 1461.0
11 TraesCS6A01G025100 chr6B 87.057 1213 136 9 351 1545 14323485 14324694 0.000000e+00 1351.0
12 TraesCS6A01G025100 chr6B 85.938 1216 145 13 354 1548 14311086 14312296 0.000000e+00 1275.0
13 TraesCS6A01G025100 chr6B 85.408 1213 157 9 354 1548 39311039 39312249 0.000000e+00 1242.0
14 TraesCS6A01G025100 chr6B 85.350 1215 147 18 357 1548 13934115 13932909 0.000000e+00 1229.0
15 TraesCS6A01G025100 chr6B 92.006 638 40 7 1906 2540 39327866 39328495 0.000000e+00 885.0
16 TraesCS6A01G025100 chr6B 89.337 694 57 6 1848 2540 54420670 54419993 0.000000e+00 856.0
17 TraesCS6A01G025100 chr6B 82.234 394 49 9 1996 2374 39312419 39312806 1.130000e-83 320.0
18 TraesCS6A01G025100 chr6D 82.710 2221 242 58 353 2540 7678760 7680871 0.000000e+00 1844.0
19 TraesCS6A01G025100 chr6D 89.833 1200 110 7 357 1548 7424100 7422905 0.000000e+00 1530.0
20 TraesCS6A01G025100 chr6D 84.228 1211 162 15 363 1548 7651505 7652711 0.000000e+00 1151.0
21 TraesCS6A01G025100 chr6D 89.722 827 68 5 1096 1914 24252296 24253113 0.000000e+00 1040.0
22 TraesCS6A01G025100 chr6D 88.630 774 69 12 1777 2539 7654186 7654951 0.000000e+00 924.0
23 TraesCS6A01G025100 chr6D 90.588 340 25 5 1906 2242 24253310 24253645 6.450000e-121 444.0
24 TraesCS6A01G025100 chr6D 91.935 310 20 3 2232 2540 24254491 24254796 1.810000e-116 429.0
25 TraesCS6A01G025100 chr6D 83.929 168 23 4 2311 2476 7997560 7997395 9.410000e-35 158.0
26 TraesCS6A01G025100 chr2B 75.800 1219 233 45 364 1548 54044040 54042850 6.140000e-156 560.0
27 TraesCS6A01G025100 chr7B 89.804 255 26 0 2120 2374 639999363 639999617 6.780000e-86 327.0
28 TraesCS6A01G025100 chr7B 90.419 167 14 2 2374 2540 639999774 639999938 4.250000e-53 219.0
29 TraesCS6A01G025100 chr1B 83.125 160 22 5 2230 2385 630651149 630651307 9.470000e-30 141.0


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 TraesCS6A01G025100 chr6A 12419997 12422536 2539 False 4691.000000 4691 100.000000 1 2540 1 chr6A.!!$F2 2539
1 TraesCS6A01G025100 chr6A 7977673 7979889 2216 False 1914.000000 1914 82.655000 331 2538 1 chr6A.!!$F1 2207
2 TraesCS6A01G025100 chr4A 667380012 667382197 2185 False 3096.000000 3096 92.290000 354 2540 1 chr4A.!!$F1 2186
3 TraesCS6A01G025100 chr4A 667425170 667427318 2148 False 613.366667 1240 87.449000 265 2389 3 chr4A.!!$F2 2124
4 TraesCS6A01G025100 chr6B 14303231 14305407 2176 False 2073.000000 2073 84.119000 331 2540 1 chr6B.!!$F1 2209
5 TraesCS6A01G025100 chr6B 14318227 14324694 6467 False 1406.000000 1461 86.143000 351 2089 2 chr6B.!!$F3 1738
6 TraesCS6A01G025100 chr6B 54419993 54422329 2336 True 1406.000000 1956 89.623000 328 2540 2 chr6B.!!$R2 2212
7 TraesCS6A01G025100 chr6B 39326083 39328495 2412 False 1278.500000 1672 88.953500 336 2540 2 chr6B.!!$F5 2204
8 TraesCS6A01G025100 chr6B 14311086 14312296 1210 False 1275.000000 1275 85.938000 354 1548 1 chr6B.!!$F2 1194
9 TraesCS6A01G025100 chr6B 13932909 13934115 1206 True 1229.000000 1229 85.350000 357 1548 1 chr6B.!!$R1 1191
10 TraesCS6A01G025100 chr6B 39311039 39312806 1767 False 781.000000 1242 83.821000 354 2374 2 chr6B.!!$F4 2020
11 TraesCS6A01G025100 chr6D 7678760 7680871 2111 False 1844.000000 1844 82.710000 353 2540 1 chr6D.!!$F1 2187
12 TraesCS6A01G025100 chr6D 7422905 7424100 1195 True 1530.000000 1530 89.833000 357 1548 1 chr6D.!!$R1 1191
13 TraesCS6A01G025100 chr6D 7651505 7654951 3446 False 1037.500000 1151 86.429000 363 2539 2 chr6D.!!$F2 2176
14 TraesCS6A01G025100 chr6D 24252296 24254796 2500 False 637.666667 1040 90.748333 1096 2540 3 chr6D.!!$F3 1444
15 TraesCS6A01G025100 chr2B 54042850 54044040 1190 True 560.000000 560 75.800000 364 1548 1 chr2B.!!$R1 1184
16 TraesCS6A01G025100 chr7B 639999363 639999938 575 False 273.000000 327 90.111500 2120 2540 2 chr7B.!!$F1 420

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
252 253 0.033601 TTTGGGCTCTGGTGTTGTGT 60.034 50.000 0.00 0.0 0.00 3.72 F
318 324 0.035881 TGGAGCTCAGCCAAGTTCAG 59.964 55.000 17.19 0.0 31.13 3.02 F
1054 6005 1.367665 GTTGCGTGCACAGAACGTC 60.368 57.895 18.64 0.0 42.93 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1272 6223 0.466189 CAATGTAGGCCGGCTCCAAT 60.466 55.000 28.56 12.75 0.00 3.16 R
1458 6409 1.008079 GTGTGGTGCAGCTTGCTTC 60.008 57.895 18.08 1.77 45.31 3.86 R
2263 9706 3.391296 ACTAGAGGAAGCAACCAACAGAA 59.609 43.478 0.00 0.00 0.00 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
30 31 3.850508 GGTTTTCCCTGTGCCGTT 58.149 55.556 0.00 0.00 0.00 4.44
31 32 1.362355 GGTTTTCCCTGTGCCGTTG 59.638 57.895 0.00 0.00 0.00 4.10
32 33 1.388837 GGTTTTCCCTGTGCCGTTGT 61.389 55.000 0.00 0.00 0.00 3.32
33 34 1.310904 GTTTTCCCTGTGCCGTTGTA 58.689 50.000 0.00 0.00 0.00 2.41
34 35 1.677052 GTTTTCCCTGTGCCGTTGTAA 59.323 47.619 0.00 0.00 0.00 2.41
39 40 2.280933 TGTGCCGTTGTAACCGGG 60.281 61.111 6.32 0.00 45.57 5.73
41 42 2.030958 GTGCCGTTGTAACCGGGAG 61.031 63.158 6.32 0.00 46.75 4.30
42 43 2.344872 GCCGTTGTAACCGGGAGT 59.655 61.111 6.32 0.00 45.57 3.85
44 45 1.375013 CCGTTGTAACCGGGAGTGG 60.375 63.158 6.32 0.00 41.78 4.00
45 46 1.368579 CGTTGTAACCGGGAGTGGT 59.631 57.895 6.32 0.00 46.67 4.16
51 52 4.468007 ACCGGGAGTGGTTTTTCG 57.532 55.556 6.32 0.00 39.99 3.46
52 53 1.528339 ACCGGGAGTGGTTTTTCGT 59.472 52.632 6.32 0.00 39.99 3.85
53 54 0.533531 ACCGGGAGTGGTTTTTCGTC 60.534 55.000 6.32 0.00 39.99 4.20
54 55 0.533308 CCGGGAGTGGTTTTTCGTCA 60.533 55.000 0.00 0.00 0.00 4.35
55 56 1.301423 CGGGAGTGGTTTTTCGTCAA 58.699 50.000 0.00 0.00 0.00 3.18
57 58 2.018515 GGGAGTGGTTTTTCGTCAACA 58.981 47.619 0.00 0.00 0.00 3.33
58 59 2.621526 GGGAGTGGTTTTTCGTCAACAT 59.378 45.455 0.00 0.00 0.00 2.71
59 60 3.067601 GGGAGTGGTTTTTCGTCAACATT 59.932 43.478 0.00 0.00 0.00 2.71
60 61 4.440940 GGGAGTGGTTTTTCGTCAACATTT 60.441 41.667 0.00 0.00 0.00 2.32
61 62 5.106442 GGAGTGGTTTTTCGTCAACATTTT 58.894 37.500 0.00 0.00 0.00 1.82
62 63 5.231357 GGAGTGGTTTTTCGTCAACATTTTC 59.769 40.000 0.00 0.00 0.00 2.29
64 65 5.105513 AGTGGTTTTTCGTCAACATTTTCCT 60.106 36.000 0.00 0.00 0.00 3.36
66 67 6.752815 GTGGTTTTTCGTCAACATTTTCCTTA 59.247 34.615 0.00 0.00 0.00 2.69
67 68 7.436970 GTGGTTTTTCGTCAACATTTTCCTTAT 59.563 33.333 0.00 0.00 0.00 1.73
68 69 7.982354 TGGTTTTTCGTCAACATTTTCCTTATT 59.018 29.630 0.00 0.00 0.00 1.40
69 70 9.465985 GGTTTTTCGTCAACATTTTCCTTATTA 57.534 29.630 0.00 0.00 0.00 0.98
72 73 8.736751 TTTCGTCAACATTTTCCTTATTAAGC 57.263 30.769 0.00 0.00 0.00 3.09
73 74 7.441890 TCGTCAACATTTTCCTTATTAAGCA 57.558 32.000 0.00 0.00 0.00 3.91
74 75 7.526608 TCGTCAACATTTTCCTTATTAAGCAG 58.473 34.615 0.00 0.00 0.00 4.24
76 77 7.315890 GTCAACATTTTCCTTATTAAGCAGCT 58.684 34.615 0.00 0.00 0.00 4.24
77 78 8.458843 GTCAACATTTTCCTTATTAAGCAGCTA 58.541 33.333 0.00 0.00 0.00 3.32
78 79 9.019656 TCAACATTTTCCTTATTAAGCAGCTAA 57.980 29.630 0.00 0.00 0.00 3.09
79 80 9.076596 CAACATTTTCCTTATTAAGCAGCTAAC 57.923 33.333 0.00 0.00 0.00 2.34
80 81 8.581253 ACATTTTCCTTATTAAGCAGCTAACT 57.419 30.769 0.00 0.00 0.00 2.24
81 82 8.678199 ACATTTTCCTTATTAAGCAGCTAACTC 58.322 33.333 0.00 0.00 0.00 3.01
82 83 8.897752 CATTTTCCTTATTAAGCAGCTAACTCT 58.102 33.333 0.00 0.00 0.00 3.24
83 84 8.494016 TTTTCCTTATTAAGCAGCTAACTCTC 57.506 34.615 0.00 0.00 0.00 3.20
84 85 7.425224 TTCCTTATTAAGCAGCTAACTCTCT 57.575 36.000 0.00 0.00 0.00 3.10
85 86 8.534954 TTCCTTATTAAGCAGCTAACTCTCTA 57.465 34.615 0.00 0.00 0.00 2.43
86 87 7.942990 TCCTTATTAAGCAGCTAACTCTCTAC 58.057 38.462 0.00 0.00 0.00 2.59
87 88 7.780745 TCCTTATTAAGCAGCTAACTCTCTACT 59.219 37.037 0.00 0.00 0.00 2.57
88 89 9.069082 CCTTATTAAGCAGCTAACTCTCTACTA 57.931 37.037 0.00 0.00 0.00 1.82
91 92 5.682943 AAGCAGCTAACTCTCTACTATCG 57.317 43.478 0.00 0.00 0.00 2.92
93 94 3.665848 GCAGCTAACTCTCTACTATCGCG 60.666 52.174 0.00 0.00 0.00 5.87
94 95 3.068560 AGCTAACTCTCTACTATCGCGG 58.931 50.000 6.13 0.00 0.00 6.46
96 97 3.497640 GCTAACTCTCTACTATCGCGGAA 59.502 47.826 6.13 0.00 0.00 4.30
97 98 3.967203 AACTCTCTACTATCGCGGAAC 57.033 47.619 6.13 0.00 0.00 3.62
99 100 3.543665 ACTCTCTACTATCGCGGAACTT 58.456 45.455 6.13 0.00 0.00 2.66
100 101 3.946558 ACTCTCTACTATCGCGGAACTTT 59.053 43.478 6.13 0.00 0.00 2.66
101 102 4.035441 ACTCTCTACTATCGCGGAACTTTC 59.965 45.833 6.13 0.00 0.00 2.62
102 103 3.002042 TCTCTACTATCGCGGAACTTTCG 59.998 47.826 6.13 0.00 0.00 3.46
105 106 1.471684 ACTATCGCGGAACTTTCGTCT 59.528 47.619 6.13 0.00 0.00 4.18
107 108 0.526662 ATCGCGGAACTTTCGTCTCT 59.473 50.000 6.13 0.00 0.00 3.10
108 109 0.313043 TCGCGGAACTTTCGTCTCTT 59.687 50.000 6.13 0.00 0.00 2.85
110 111 1.499049 GCGGAACTTTCGTCTCTTGT 58.501 50.000 0.00 0.00 0.00 3.16
112 113 1.714460 CGGAACTTTCGTCTCTTGTCG 59.286 52.381 0.00 0.00 0.00 4.35
113 114 2.059541 GGAACTTTCGTCTCTTGTCGG 58.940 52.381 0.00 0.00 0.00 4.79
114 115 1.456165 GAACTTTCGTCTCTTGTCGGC 59.544 52.381 0.00 0.00 0.00 5.54
115 116 0.319641 ACTTTCGTCTCTTGTCGGCC 60.320 55.000 0.00 0.00 0.00 6.13
117 118 1.750341 TTTCGTCTCTTGTCGGCCCA 61.750 55.000 0.00 0.00 0.00 5.36
118 119 1.750341 TTCGTCTCTTGTCGGCCCAA 61.750 55.000 0.00 0.00 0.00 4.12
119 120 1.301401 CGTCTCTTGTCGGCCCAAA 60.301 57.895 0.00 0.00 0.00 3.28
120 121 0.882927 CGTCTCTTGTCGGCCCAAAA 60.883 55.000 0.00 0.00 0.00 2.44
121 122 1.314730 GTCTCTTGTCGGCCCAAAAA 58.685 50.000 0.00 0.00 0.00 1.94
146 147 7.953305 AATCGTCATGAATTATGTTTGTTCG 57.047 32.000 0.00 0.00 38.01 3.95
147 148 6.713792 TCGTCATGAATTATGTTTGTTCGA 57.286 33.333 0.00 0.00 38.01 3.71
148 149 7.302350 TCGTCATGAATTATGTTTGTTCGAT 57.698 32.000 0.00 0.00 38.01 3.59
149 150 8.413899 TCGTCATGAATTATGTTTGTTCGATA 57.586 30.769 0.00 0.00 38.01 2.92
150 151 9.040939 TCGTCATGAATTATGTTTGTTCGATAT 57.959 29.630 0.00 0.00 38.01 1.63
162 163 7.156000 TGTTTGTTCGATATTCTAGTTGTGGA 58.844 34.615 0.00 0.00 0.00 4.02
163 164 7.658167 TGTTTGTTCGATATTCTAGTTGTGGAA 59.342 33.333 0.00 0.00 0.00 3.53
164 165 7.591006 TTGTTCGATATTCTAGTTGTGGAAC 57.409 36.000 10.48 10.48 33.69 3.62
194 195 8.535690 TTTTTAACTGTCGTGGAACAATTTTT 57.464 26.923 0.00 0.00 44.16 1.94
199 200 4.667262 TGTCGTGGAACAATTTTTGTCAG 58.333 39.130 0.00 0.00 44.59 3.51
200 201 4.156922 TGTCGTGGAACAATTTTTGTCAGT 59.843 37.500 0.00 0.00 44.59 3.41
202 203 5.229260 GTCGTGGAACAATTTTTGTCAGTTC 59.771 40.000 0.00 0.00 44.59 3.01
222 223 7.823745 AGTTCCATACTGTGAAAACAATCTT 57.176 32.000 0.00 0.00 35.19 2.40
224 225 6.573664 TCCATACTGTGAAAACAATCTTGG 57.426 37.500 0.00 0.00 0.00 3.61
225 226 5.476599 TCCATACTGTGAAAACAATCTTGGG 59.523 40.000 0.00 0.00 0.00 4.12
226 227 5.476599 CCATACTGTGAAAACAATCTTGGGA 59.523 40.000 0.00 0.00 0.00 4.37
227 228 6.015519 CCATACTGTGAAAACAATCTTGGGAA 60.016 38.462 0.00 0.00 0.00 3.97
229 230 4.956075 ACTGTGAAAACAATCTTGGGAAGT 59.044 37.500 0.00 0.00 0.00 3.01
230 231 5.422012 ACTGTGAAAACAATCTTGGGAAGTT 59.578 36.000 0.00 0.00 0.00 2.66
231 232 6.605594 ACTGTGAAAACAATCTTGGGAAGTTA 59.394 34.615 0.00 0.00 0.00 2.24
233 234 8.017418 TGTGAAAACAATCTTGGGAAGTTATT 57.983 30.769 0.00 0.00 0.00 1.40
234 235 8.482128 TGTGAAAACAATCTTGGGAAGTTATTT 58.518 29.630 0.00 0.00 0.00 1.40
236 237 9.323985 TGAAAACAATCTTGGGAAGTTATTTTG 57.676 29.630 0.00 0.00 0.00 2.44
238 239 6.358974 ACAATCTTGGGAAGTTATTTTGGG 57.641 37.500 0.00 0.00 0.00 4.12
244 245 2.760650 GGGAAGTTATTTTGGGCTCTGG 59.239 50.000 0.00 0.00 0.00 3.86
245 246 3.431415 GGAAGTTATTTTGGGCTCTGGT 58.569 45.455 0.00 0.00 0.00 4.00
246 247 3.193479 GGAAGTTATTTTGGGCTCTGGTG 59.807 47.826 0.00 0.00 0.00 4.17
248 249 3.844640 AGTTATTTTGGGCTCTGGTGTT 58.155 40.909 0.00 0.00 0.00 3.32
250 251 2.086610 ATTTTGGGCTCTGGTGTTGT 57.913 45.000 0.00 0.00 0.00 3.32
252 253 0.033601 TTTGGGCTCTGGTGTTGTGT 60.034 50.000 0.00 0.00 0.00 3.72
253 254 0.751277 TTGGGCTCTGGTGTTGTGTG 60.751 55.000 0.00 0.00 0.00 3.82
255 256 1.152963 GGCTCTGGTGTTGTGTGGT 60.153 57.895 0.00 0.00 0.00 4.16
257 258 0.381801 GCTCTGGTGTTGTGTGGTTG 59.618 55.000 0.00 0.00 0.00 3.77
259 260 0.621082 TCTGGTGTTGTGTGGTTGGA 59.379 50.000 0.00 0.00 0.00 3.53
260 261 1.004862 TCTGGTGTTGTGTGGTTGGAA 59.995 47.619 0.00 0.00 0.00 3.53
262 263 2.430332 CTGGTGTTGTGTGGTTGGAAAT 59.570 45.455 0.00 0.00 0.00 2.17
263 264 3.632333 TGGTGTTGTGTGGTTGGAAATA 58.368 40.909 0.00 0.00 0.00 1.40
302 303 1.002069 AGTGGCAGGGATTGAATGGA 58.998 50.000 0.00 0.00 0.00 3.41
303 304 1.064166 AGTGGCAGGGATTGAATGGAG 60.064 52.381 0.00 0.00 0.00 3.86
304 305 0.396139 TGGCAGGGATTGAATGGAGC 60.396 55.000 0.00 0.00 0.00 4.70
306 307 1.316651 GCAGGGATTGAATGGAGCTC 58.683 55.000 4.71 4.71 0.00 4.09
309 310 1.133853 AGGGATTGAATGGAGCTCAGC 60.134 52.381 17.19 0.00 0.00 4.26
311 312 1.409241 GGATTGAATGGAGCTCAGCCA 60.409 52.381 17.19 5.44 40.24 4.75
318 324 0.035881 TGGAGCTCAGCCAAGTTCAG 59.964 55.000 17.19 0.00 31.13 3.02
402 5332 2.121538 CGTCATGCTCCTCCTCCGA 61.122 63.158 0.00 0.00 0.00 4.55
487 5417 4.316823 ACCGCCTCCTCTCCACCA 62.317 66.667 0.00 0.00 0.00 4.17
962 5913 2.681778 AGAGTGCGGGCTAGCTGT 60.682 61.111 15.72 0.00 38.13 4.40
1047 5998 4.024143 GCGATGGTTGCGTGCACA 62.024 61.111 18.64 0.00 0.00 4.57
1054 6005 1.367665 GTTGCGTGCACAGAACGTC 60.368 57.895 18.64 0.00 42.93 4.34
1229 6180 4.687483 GGTTTTGCTGACAAGATCAAATGG 59.313 41.667 0.00 0.00 36.69 3.16
1272 6223 3.012959 ACTTCCTAATCTCTGAGGTGGGA 59.987 47.826 4.59 6.80 34.20 4.37
1420 6371 5.068636 ACTACTATAGTATGGTGGTGGTCG 58.931 45.833 13.69 0.22 34.36 4.79
1437 6388 1.925185 GTCGGCGAGAAGGTATTTGTC 59.075 52.381 11.20 0.00 0.00 3.18
1458 6409 3.068732 TCGAGAAGTTCATATGCCCTCAG 59.931 47.826 5.50 0.00 0.00 3.35
1483 6434 1.600636 GCTGCACCACACCTTGCTA 60.601 57.895 0.00 0.00 39.62 3.49
1529 6488 1.089920 CAGGTGCCTGCTACATTCAC 58.910 55.000 5.19 0.00 37.24 3.18
1580 6543 2.025441 GCTAGAGCGCGAGTGGAG 59.975 66.667 12.10 0.00 0.00 3.86
1753 7978 5.560148 CCATGAGAATTTGTAACTGCGTAC 58.440 41.667 0.00 0.00 0.00 3.67
1756 7981 3.656559 AGAATTTGTAACTGCGTACGGT 58.343 40.909 18.39 4.18 36.79 4.83
1844 8083 5.891551 TGGTTGTCTGCTATAGTATGTCAGA 59.108 40.000 0.84 10.38 0.00 3.27
1873 8240 3.630101 GCTAATTTAGCGTCGCTAGTCT 58.370 45.455 24.76 15.71 42.34 3.24
1884 8251 3.673338 CGTCGCTAGTCTTGAATGAAACA 59.327 43.478 0.00 0.00 0.00 2.83
1886 8253 4.092091 GTCGCTAGTCTTGAATGAAACAGG 59.908 45.833 0.00 0.00 0.00 4.00
1907 8479 6.817140 ACAGGTAATTTTATCGTGAGTCCTTC 59.183 38.462 0.00 0.00 0.00 3.46
2109 8682 2.843401 TGCCATTGCAGCTTTCAATT 57.157 40.000 7.94 0.00 44.23 2.32
2110 8683 3.128852 TGCCATTGCAGCTTTCAATTT 57.871 38.095 7.94 0.00 44.23 1.82
2176 8751 9.320352 CATTTTTGCCATGAAGATGATATGAAA 57.680 29.630 0.00 0.00 0.00 2.69
2263 9706 4.397417 GCTGAGGTTGCAGTTTTGATCTAT 59.603 41.667 0.00 0.00 38.17 1.98
2362 9812 2.017049 ACTGTTGTGAAAGCAGGTCAC 58.983 47.619 7.32 7.32 44.67 3.67
2375 9982 6.415206 AAGCAGGTCACTGTTTACTACTAA 57.585 37.500 0.00 0.00 44.84 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.478507 CACAGGGAAAACCCAGACCT 59.521 55.000 8.05 0.00 41.63 3.85
9 10 1.152830 GGCACAGGGAAAACCCAGA 59.847 57.895 8.05 0.00 41.63 3.86
10 11 2.268076 CGGCACAGGGAAAACCCAG 61.268 63.158 8.05 2.15 41.63 4.45
11 12 2.203422 CGGCACAGGGAAAACCCA 60.203 61.111 8.05 0.00 41.63 4.51
12 13 1.830847 AACGGCACAGGGAAAACCC 60.831 57.895 0.00 0.00 41.63 4.11
13 14 1.362355 CAACGGCACAGGGAAAACC 59.638 57.895 0.00 0.00 40.67 3.27
14 15 1.310904 TACAACGGCACAGGGAAAAC 58.689 50.000 0.00 0.00 0.00 2.43
15 16 1.677052 GTTACAACGGCACAGGGAAAA 59.323 47.619 0.00 0.00 0.00 2.29
16 17 1.310904 GTTACAACGGCACAGGGAAA 58.689 50.000 0.00 0.00 0.00 3.13
17 18 0.535553 GGTTACAACGGCACAGGGAA 60.536 55.000 0.00 0.00 0.00 3.97
18 19 1.071814 GGTTACAACGGCACAGGGA 59.928 57.895 0.00 0.00 0.00 4.20
21 22 3.249999 CCGGTTACAACGGCACAG 58.750 61.111 0.00 0.00 45.34 3.66
34 35 0.533531 GACGAAAAACCACTCCCGGT 60.534 55.000 0.00 0.00 42.71 5.28
39 40 5.231357 GGAAAATGTTGACGAAAAACCACTC 59.769 40.000 0.00 0.00 0.00 3.51
41 42 5.106442 AGGAAAATGTTGACGAAAAACCAC 58.894 37.500 0.00 0.00 0.00 4.16
42 43 5.331876 AGGAAAATGTTGACGAAAAACCA 57.668 34.783 0.00 0.00 0.00 3.67
46 47 9.187455 GCTTAATAAGGAAAATGTTGACGAAAA 57.813 29.630 1.88 0.00 0.00 2.29
47 48 8.353684 TGCTTAATAAGGAAAATGTTGACGAAA 58.646 29.630 1.88 0.00 0.00 3.46
48 49 7.877003 TGCTTAATAAGGAAAATGTTGACGAA 58.123 30.769 1.88 0.00 0.00 3.85
49 50 7.441890 TGCTTAATAAGGAAAATGTTGACGA 57.558 32.000 1.88 0.00 0.00 4.20
51 52 7.315890 AGCTGCTTAATAAGGAAAATGTTGAC 58.684 34.615 0.00 0.00 0.00 3.18
52 53 7.466746 AGCTGCTTAATAAGGAAAATGTTGA 57.533 32.000 0.00 0.00 0.00 3.18
53 54 9.076596 GTTAGCTGCTTAATAAGGAAAATGTTG 57.923 33.333 7.79 0.00 0.00 3.33
54 55 9.025041 AGTTAGCTGCTTAATAAGGAAAATGTT 57.975 29.630 7.79 0.00 0.00 2.71
55 56 8.581253 AGTTAGCTGCTTAATAAGGAAAATGT 57.419 30.769 7.79 0.00 0.00 2.71
57 58 9.114952 GAGAGTTAGCTGCTTAATAAGGAAAAT 57.885 33.333 7.79 0.00 0.00 1.82
58 59 8.322091 AGAGAGTTAGCTGCTTAATAAGGAAAA 58.678 33.333 7.79 0.00 0.00 2.29
59 60 7.852263 AGAGAGTTAGCTGCTTAATAAGGAAA 58.148 34.615 7.79 0.00 0.00 3.13
60 61 7.425224 AGAGAGTTAGCTGCTTAATAAGGAA 57.575 36.000 7.79 0.00 0.00 3.36
61 62 7.780745 AGTAGAGAGTTAGCTGCTTAATAAGGA 59.219 37.037 7.79 0.00 0.00 3.36
62 63 7.947282 AGTAGAGAGTTAGCTGCTTAATAAGG 58.053 38.462 7.79 0.00 0.00 2.69
66 67 7.574217 GCGATAGTAGAGAGTTAGCTGCTTAAT 60.574 40.741 7.79 0.00 39.35 1.40
67 68 6.293516 GCGATAGTAGAGAGTTAGCTGCTTAA 60.294 42.308 7.79 0.00 39.35 1.85
68 69 5.179742 GCGATAGTAGAGAGTTAGCTGCTTA 59.820 44.000 7.79 0.00 39.35 3.09
69 70 4.023536 GCGATAGTAGAGAGTTAGCTGCTT 60.024 45.833 7.79 0.00 39.35 3.91
70 71 3.500680 GCGATAGTAGAGAGTTAGCTGCT 59.499 47.826 7.57 7.57 39.35 4.24
72 73 3.120477 CCGCGATAGTAGAGAGTTAGCTG 60.120 52.174 8.23 0.00 39.35 4.24
73 74 3.068560 CCGCGATAGTAGAGAGTTAGCT 58.931 50.000 8.23 0.00 39.35 3.32
74 75 3.065655 TCCGCGATAGTAGAGAGTTAGC 58.934 50.000 8.23 0.00 39.35 3.09
76 77 4.701765 AGTTCCGCGATAGTAGAGAGTTA 58.298 43.478 8.23 0.00 39.35 2.24
77 78 3.543665 AGTTCCGCGATAGTAGAGAGTT 58.456 45.455 8.23 0.00 39.35 3.01
78 79 3.196939 AGTTCCGCGATAGTAGAGAGT 57.803 47.619 8.23 0.00 39.35 3.24
79 80 4.529446 GAAAGTTCCGCGATAGTAGAGAG 58.471 47.826 8.23 0.00 39.35 3.20
80 81 3.002042 CGAAAGTTCCGCGATAGTAGAGA 59.998 47.826 8.23 0.00 39.35 3.10
81 82 3.242673 ACGAAAGTTCCGCGATAGTAGAG 60.243 47.826 8.23 0.00 46.40 2.43
82 83 2.679837 ACGAAAGTTCCGCGATAGTAGA 59.320 45.455 8.23 0.00 46.40 2.59
83 84 3.062323 ACGAAAGTTCCGCGATAGTAG 57.938 47.619 8.23 0.00 46.40 2.57
97 98 1.014564 GGGCCGACAAGAGACGAAAG 61.015 60.000 0.00 0.00 34.91 2.62
99 100 1.750341 TTGGGCCGACAAGAGACGAA 61.750 55.000 0.00 0.00 34.91 3.85
100 101 1.750341 TTTGGGCCGACAAGAGACGA 61.750 55.000 0.00 0.00 34.91 4.20
101 102 0.882927 TTTTGGGCCGACAAGAGACG 60.883 55.000 0.00 0.00 0.00 4.18
102 103 1.314730 TTTTTGGGCCGACAAGAGAC 58.685 50.000 0.00 0.00 0.00 3.36
120 121 8.849490 CGAACAAACATAATTCATGACGATTTT 58.151 29.630 0.00 0.00 38.10 1.82
121 122 8.233868 TCGAACAAACATAATTCATGACGATTT 58.766 29.630 0.00 0.00 38.10 2.17
122 123 7.747888 TCGAACAAACATAATTCATGACGATT 58.252 30.769 0.00 0.00 38.10 3.34
123 124 7.302350 TCGAACAAACATAATTCATGACGAT 57.698 32.000 0.00 0.00 38.10 3.73
124 125 6.713792 TCGAACAAACATAATTCATGACGA 57.286 33.333 0.00 0.00 38.10 4.20
136 137 7.822334 TCCACAACTAGAATATCGAACAAACAT 59.178 33.333 0.00 0.00 0.00 2.71
137 138 7.156000 TCCACAACTAGAATATCGAACAAACA 58.844 34.615 0.00 0.00 0.00 2.83
138 139 7.591006 TCCACAACTAGAATATCGAACAAAC 57.409 36.000 0.00 0.00 0.00 2.93
139 140 7.658167 TGTTCCACAACTAGAATATCGAACAAA 59.342 33.333 0.00 0.00 35.44 2.83
140 141 7.156000 TGTTCCACAACTAGAATATCGAACAA 58.844 34.615 0.00 0.00 35.44 2.83
141 142 6.693466 TGTTCCACAACTAGAATATCGAACA 58.307 36.000 0.00 4.55 35.87 3.18
143 144 8.786826 AATTGTTCCACAACTAGAATATCGAA 57.213 30.769 0.00 0.00 41.40 3.71
144 145 8.786826 AAATTGTTCCACAACTAGAATATCGA 57.213 30.769 0.00 0.00 41.40 3.59
145 146 9.840427 AAAAATTGTTCCACAACTAGAATATCG 57.160 29.630 0.00 0.00 41.40 2.92
169 170 8.436200 CAAAAATTGTTCCACGACAGTTAAAAA 58.564 29.630 0.00 0.00 30.51 1.94
170 171 7.599245 ACAAAAATTGTTCCACGACAGTTAAAA 59.401 29.630 0.00 0.00 42.22 1.52
172 173 6.622549 ACAAAAATTGTTCCACGACAGTTAA 58.377 32.000 0.00 0.00 42.22 2.01
173 174 6.127980 TGACAAAAATTGTTCCACGACAGTTA 60.128 34.615 0.00 0.00 45.52 2.24
174 175 5.066968 ACAAAAATTGTTCCACGACAGTT 57.933 34.783 0.00 0.00 42.22 3.16
175 176 4.156922 TGACAAAAATTGTTCCACGACAGT 59.843 37.500 0.00 0.00 45.52 3.55
176 177 4.667262 TGACAAAAATTGTTCCACGACAG 58.333 39.130 0.00 0.00 45.52 3.51
177 178 4.156922 ACTGACAAAAATTGTTCCACGACA 59.843 37.500 0.00 0.00 45.52 4.35
178 179 4.668289 ACTGACAAAAATTGTTCCACGAC 58.332 39.130 0.00 0.00 45.52 4.34
179 180 4.974368 ACTGACAAAAATTGTTCCACGA 57.026 36.364 0.00 0.00 45.52 4.35
180 181 5.620098 GAACTGACAAAAATTGTTCCACG 57.380 39.130 0.00 0.00 45.52 4.94
199 200 6.863126 CCAAGATTGTTTTCACAGTATGGAAC 59.137 38.462 0.00 0.00 43.62 3.62
200 201 6.015519 CCCAAGATTGTTTTCACAGTATGGAA 60.016 38.462 0.00 0.00 43.62 3.53
202 203 5.476599 TCCCAAGATTGTTTTCACAGTATGG 59.523 40.000 0.00 0.00 43.62 2.74
203 204 6.573664 TCCCAAGATTGTTTTCACAGTATG 57.426 37.500 0.00 0.00 46.00 2.39
204 205 6.777580 ACTTCCCAAGATTGTTTTCACAGTAT 59.222 34.615 0.00 0.00 33.22 2.12
206 207 4.956075 ACTTCCCAAGATTGTTTTCACAGT 59.044 37.500 0.00 0.00 33.22 3.55
208 209 5.930837 AACTTCCCAAGATTGTTTTCACA 57.069 34.783 0.00 0.00 0.00 3.58
210 211 9.323985 CAAAATAACTTCCCAAGATTGTTTTCA 57.676 29.630 0.00 0.00 29.69 2.69
211 212 8.773645 CCAAAATAACTTCCCAAGATTGTTTTC 58.226 33.333 0.00 0.00 29.69 2.29
212 213 7.719193 CCCAAAATAACTTCCCAAGATTGTTTT 59.281 33.333 0.00 0.00 30.85 2.43
213 214 7.223584 CCCAAAATAACTTCCCAAGATTGTTT 58.776 34.615 0.00 0.00 0.00 2.83
214 215 6.744056 GCCCAAAATAACTTCCCAAGATTGTT 60.744 38.462 0.00 0.00 0.00 2.83
215 216 5.279960 GCCCAAAATAACTTCCCAAGATTGT 60.280 40.000 0.00 0.00 0.00 2.71
216 217 5.046376 AGCCCAAAATAACTTCCCAAGATTG 60.046 40.000 0.00 0.00 0.00 2.67
219 220 4.086457 GAGCCCAAAATAACTTCCCAAGA 58.914 43.478 0.00 0.00 0.00 3.02
220 221 4.082026 CAGAGCCCAAAATAACTTCCCAAG 60.082 45.833 0.00 0.00 0.00 3.61
221 222 3.831911 CAGAGCCCAAAATAACTTCCCAA 59.168 43.478 0.00 0.00 0.00 4.12
222 223 3.430453 CAGAGCCCAAAATAACTTCCCA 58.570 45.455 0.00 0.00 0.00 4.37
224 225 3.193479 CACCAGAGCCCAAAATAACTTCC 59.807 47.826 0.00 0.00 0.00 3.46
225 226 3.826729 ACACCAGAGCCCAAAATAACTTC 59.173 43.478 0.00 0.00 0.00 3.01
226 227 3.844640 ACACCAGAGCCCAAAATAACTT 58.155 40.909 0.00 0.00 0.00 2.66
227 228 3.525800 ACACCAGAGCCCAAAATAACT 57.474 42.857 0.00 0.00 0.00 2.24
229 230 3.320541 CACAACACCAGAGCCCAAAATAA 59.679 43.478 0.00 0.00 0.00 1.40
230 231 2.890311 CACAACACCAGAGCCCAAAATA 59.110 45.455 0.00 0.00 0.00 1.40
231 232 1.688197 CACAACACCAGAGCCCAAAAT 59.312 47.619 0.00 0.00 0.00 1.82
233 234 0.033601 ACACAACACCAGAGCCCAAA 60.034 50.000 0.00 0.00 0.00 3.28
234 235 0.751277 CACACAACACCAGAGCCCAA 60.751 55.000 0.00 0.00 0.00 4.12
236 237 1.898574 CCACACAACACCAGAGCCC 60.899 63.158 0.00 0.00 0.00 5.19
238 239 0.381801 CAACCACACAACACCAGAGC 59.618 55.000 0.00 0.00 0.00 4.09
244 245 3.552068 GCCTATTTCCAACCACACAACAC 60.552 47.826 0.00 0.00 0.00 3.32
245 246 2.625790 GCCTATTTCCAACCACACAACA 59.374 45.455 0.00 0.00 0.00 3.33
246 247 2.029380 GGCCTATTTCCAACCACACAAC 60.029 50.000 0.00 0.00 0.00 3.32
248 249 1.884497 CGGCCTATTTCCAACCACACA 60.884 52.381 0.00 0.00 0.00 3.72
250 251 0.402504 ACGGCCTATTTCCAACCACA 59.597 50.000 0.00 0.00 0.00 4.17
252 253 1.540267 CAACGGCCTATTTCCAACCA 58.460 50.000 0.00 0.00 0.00 3.67
253 254 0.815095 CCAACGGCCTATTTCCAACC 59.185 55.000 0.00 0.00 0.00 3.77
255 256 2.291282 ACATCCAACGGCCTATTTCCAA 60.291 45.455 0.00 0.00 0.00 3.53
257 258 2.052782 ACATCCAACGGCCTATTTCC 57.947 50.000 0.00 0.00 0.00 3.13
259 260 5.654650 TCAAATAACATCCAACGGCCTATTT 59.345 36.000 0.00 0.00 0.00 1.40
260 261 5.197451 TCAAATAACATCCAACGGCCTATT 58.803 37.500 0.00 0.00 0.00 1.73
262 263 4.196193 CTCAAATAACATCCAACGGCCTA 58.804 43.478 0.00 0.00 0.00 3.93
263 264 3.016736 CTCAAATAACATCCAACGGCCT 58.983 45.455 0.00 0.00 0.00 5.19
302 303 1.141657 TGAACTGAACTTGGCTGAGCT 59.858 47.619 3.72 0.00 0.00 4.09
303 304 1.597742 TGAACTGAACTTGGCTGAGC 58.402 50.000 0.00 0.00 0.00 4.26
304 305 4.276678 TGAAATGAACTGAACTTGGCTGAG 59.723 41.667 0.00 0.00 0.00 3.35
306 307 4.276678 TCTGAAATGAACTGAACTTGGCTG 59.723 41.667 0.00 0.00 0.00 4.85
309 310 6.135290 TGTTCTGAAATGAACTGAACTTGG 57.865 37.500 0.82 0.00 44.63 3.61
311 312 6.547141 TGGATGTTCTGAAATGAACTGAACTT 59.453 34.615 0.82 0.00 44.63 2.66
318 324 3.914364 GCGTTGGATGTTCTGAAATGAAC 59.086 43.478 0.00 0.00 44.60 3.18
634 5564 4.761058 AGCGCCGGAGAGGAAGGA 62.761 66.667 10.31 0.00 45.00 3.36
959 5910 4.171005 CAGCTTGGCAATATCACAAACAG 58.829 43.478 0.00 0.00 0.00 3.16
962 5913 4.280425 TGAACAGCTTGGCAATATCACAAA 59.720 37.500 0.00 0.00 0.00 2.83
1045 5996 0.317479 GGCACACCTAGACGTTCTGT 59.683 55.000 0.00 0.00 0.00 3.41
1047 5998 1.542187 GGGGCACACCTAGACGTTCT 61.542 60.000 0.00 0.00 40.03 3.01
1229 6180 3.425938 GACATACGCTGCAGCACGC 62.426 63.158 36.03 15.95 42.21 5.34
1272 6223 0.466189 CAATGTAGGCCGGCTCCAAT 60.466 55.000 28.56 12.75 0.00 3.16
1420 6371 2.159282 TCTCGACAAATACCTTCTCGCC 60.159 50.000 0.00 0.00 0.00 5.54
1437 6388 3.068732 TCTGAGGGCATATGAACTTCTCG 59.931 47.826 6.97 1.32 0.00 4.04
1458 6409 1.008079 GTGTGGTGCAGCTTGCTTC 60.008 57.895 18.08 1.77 45.31 3.86
1483 6434 1.471684 GCAAGCAGCTGCATAGTCTTT 59.528 47.619 38.24 20.26 45.16 2.52
1529 6488 7.921786 TCCTACTTCTTGGTTCATGTAAATG 57.078 36.000 0.00 0.00 0.00 2.32
1580 6543 3.868077 CACCAAGACTGCTGAATAGTAGC 59.132 47.826 0.00 0.00 39.94 3.58
1605 7016 8.197439 ACGAACTTTTCCATGAAAATCTTCTTT 58.803 29.630 0.00 0.00 40.14 2.52
1606 7017 7.716612 ACGAACTTTTCCATGAAAATCTTCTT 58.283 30.769 0.00 0.06 40.14 2.52
1774 7999 4.158764 AGAGATTACCAGCTCACTACACAC 59.841 45.833 0.00 0.00 33.62 3.82
1873 8240 9.619316 CACGATAAAATTACCTGTTTCATTCAA 57.381 29.630 0.00 0.00 0.00 2.69
1884 8251 7.184067 AGAAGGACTCACGATAAAATTACCT 57.816 36.000 0.00 0.00 0.00 3.08
1886 8253 9.530633 ACATAGAAGGACTCACGATAAAATTAC 57.469 33.333 0.00 0.00 0.00 1.89
2109 8682 7.128728 TGGAAAGATAGATTGACCCAGGATTAA 59.871 37.037 0.00 0.00 0.00 1.40
2110 8683 6.619437 TGGAAAGATAGATTGACCCAGGATTA 59.381 38.462 0.00 0.00 0.00 1.75
2176 8751 7.486407 AAAGACATTCAGCTAATTTTGGGAT 57.514 32.000 0.00 0.00 0.00 3.85
2263 9706 3.391296 ACTAGAGGAAGCAACCAACAGAA 59.609 43.478 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.