Multiple sequence alignment - TraesCS1B01G266000

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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 TraesCS1B01G266000 chr1B 100.000 3512 0 0 1 3512 467207894 467204383 0.000000e+00 6486
1 TraesCS1B01G266000 chr1B 94.220 173 10 0 1 173 521655965 521656137 7.470000e-67 265
2 TraesCS1B01G266000 chr1B 95.385 65 2 1 745 808 467207115 467207051 6.200000e-18 102
3 TraesCS1B01G266000 chr1B 95.385 65 2 1 780 844 467207150 467207087 6.200000e-18 102
4 TraesCS1B01G266000 chr1A 94.654 2619 94 10 739 3329 447120337 447117737 0.000000e+00 4019
5 TraesCS1B01G266000 chr1A 91.322 484 32 6 173 654 447122212 447121737 0.000000e+00 652
6 TraesCS1B01G266000 chr1A 90.119 253 14 4 3260 3504 447117363 447117114 5.660000e-83 318
7 TraesCS1B01G266000 chr1D 95.507 2537 57 19 561 3076 346878592 346876092 0.000000e+00 4000
8 TraesCS1B01G266000 chr1D 96.347 438 8 5 3076 3512 346875960 346875530 0.000000e+00 713
9 TraesCS1B01G266000 chr1D 91.315 403 28 4 173 569 346908064 346907663 8.570000e-151 544
10 TraesCS1B01G266000 chr1D 94.767 172 9 0 1 172 445140914 445141085 5.780000e-68 268
11 TraesCS1B01G266000 chr1D 91.979 187 11 4 3 187 200470157 200469973 3.480000e-65 259
12 TraesCS1B01G266000 chr5D 83.080 461 65 7 177 629 212625500 212625045 1.170000e-109 407
13 TraesCS1B01G266000 chr5D 95.732 164 7 0 3 166 223132277 223132440 7.470000e-67 265
14 TraesCS1B01G266000 chr5D 94.706 170 9 0 3 172 385731091 385731260 7.470000e-67 265
15 TraesCS1B01G266000 chr3B 85.101 396 56 3 245 638 764992507 764992113 5.460000e-108 401
16 TraesCS1B01G266000 chr2A 95.294 170 8 0 3 172 431355 431186 1.610000e-68 270
17 TraesCS1B01G266000 chr6D 94.706 170 9 0 3 172 202430199 202430368 7.470000e-67 265
18 TraesCS1B01G266000 chr4A 94.706 170 9 0 3 172 628199437 628199606 7.470000e-67 265
19 TraesCS1B01G266000 chr3D 94.706 170 9 0 3 172 25818431 25818262 7.470000e-67 265


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 TraesCS1B01G266000 chr1B 467204383 467207894 3511 True 2230.0 6486 96.923333 1 3512 3 chr1B.!!$R1 3511
1 TraesCS1B01G266000 chr1A 447117114 447122212 5098 True 1663.0 4019 92.031667 173 3504 3 chr1A.!!$R1 3331
2 TraesCS1B01G266000 chr1D 346875530 346878592 3062 True 2356.5 4000 95.927000 561 3512 2 chr1D.!!$R3 2951

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
792 2128 0.036010 CCCACATCACTGGTCTGACC 60.036 60.0 19.96 19.96 39.22 4.02 F
1847 3203 0.682209 ATGATGGCAGGTGGAGTTGC 60.682 55.0 0.00 0.00 39.56 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 3300 1.000163 ACTATATCAACCTCGCCAGCG 60.000 52.381 5.5 5.5 41.35 5.18 R
2761 4117 1.557099 TGCCTTACGACCTGATCACT 58.443 50.000 0.0 0.0 0.00 3.41 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
19 20 2.937994 CATGATTGGATCGCGAAGAC 57.062 50.000 15.24 7.03 0.00 3.01
20 21 2.204237 CATGATTGGATCGCGAAGACA 58.796 47.619 15.24 10.00 0.00 3.41
21 22 2.602257 TGATTGGATCGCGAAGACAT 57.398 45.000 15.24 3.03 0.00 3.06
22 23 2.905075 TGATTGGATCGCGAAGACATT 58.095 42.857 15.24 8.94 0.00 2.71
23 24 2.866156 TGATTGGATCGCGAAGACATTC 59.134 45.455 15.24 17.20 0.00 2.67
37 38 6.191534 GAAGACATTCGACTACATCAATCG 57.808 41.667 0.00 0.00 37.20 3.34
38 39 4.045104 AGACATTCGACTACATCAATCGC 58.955 43.478 0.00 0.00 35.82 4.58
39 40 2.789339 ACATTCGACTACATCAATCGCG 59.211 45.455 0.00 0.00 35.82 5.87
40 41 2.554806 TTCGACTACATCAATCGCGT 57.445 45.000 5.77 0.00 35.82 6.01
41 42 2.554806 TCGACTACATCAATCGCGTT 57.445 45.000 5.77 0.00 35.82 4.84
42 43 2.871133 TCGACTACATCAATCGCGTTT 58.129 42.857 5.77 0.00 35.82 3.60
43 44 2.850060 TCGACTACATCAATCGCGTTTC 59.150 45.455 5.77 0.00 35.82 2.78
44 45 2.852413 CGACTACATCAATCGCGTTTCT 59.148 45.455 5.77 0.00 0.00 2.52
45 46 3.303495 CGACTACATCAATCGCGTTTCTT 59.697 43.478 5.77 0.00 0.00 2.52
46 47 4.497966 CGACTACATCAATCGCGTTTCTTA 59.502 41.667 5.77 0.00 0.00 2.10
47 48 5.004061 CGACTACATCAATCGCGTTTCTTAA 59.996 40.000 5.77 0.00 0.00 1.85
48 49 6.091123 ACTACATCAATCGCGTTTCTTAAC 57.909 37.500 5.77 0.00 0.00 2.01
61 62 4.575718 GTTTCTTAACGATTCCGCTTAGC 58.424 43.478 0.00 0.00 39.95 3.09
78 79 5.721232 GCTTAGCGATATACAAGGGTATGT 58.279 41.667 0.00 0.00 40.40 2.29
79 80 6.860080 GCTTAGCGATATACAAGGGTATGTA 58.140 40.000 0.00 0.00 40.40 2.29
80 81 6.973474 GCTTAGCGATATACAAGGGTATGTAG 59.027 42.308 0.00 0.00 40.40 2.74
81 82 7.148120 GCTTAGCGATATACAAGGGTATGTAGA 60.148 40.741 0.00 0.00 40.40 2.59
82 83 8.818622 TTAGCGATATACAAGGGTATGTAGAT 57.181 34.615 0.00 0.00 39.67 1.98
83 84 7.101652 AGCGATATACAAGGGTATGTAGATG 57.898 40.000 0.00 0.00 37.72 2.90
84 85 5.749109 GCGATATACAAGGGTATGTAGATGC 59.251 44.000 0.00 1.72 37.72 3.91
85 86 6.627287 GCGATATACAAGGGTATGTAGATGCA 60.627 42.308 0.00 0.00 37.72 3.96
86 87 7.320399 CGATATACAAGGGTATGTAGATGCAA 58.680 38.462 0.00 0.00 37.72 4.08
87 88 7.981789 CGATATACAAGGGTATGTAGATGCAAT 59.018 37.037 0.00 0.00 37.72 3.56
88 89 9.319143 GATATACAAGGGTATGTAGATGCAATC 57.681 37.037 0.00 0.00 41.18 2.67
89 90 7.321717 ATACAAGGGTATGTAGATGCAATCT 57.678 36.000 0.00 0.00 46.48 2.40
90 91 7.390027 ATACAAGGGTATGTAGATGCAATCTC 58.610 38.462 0.00 0.00 43.78 2.75
91 92 7.236432 ATACAAGGGTATGTAGATGCAATCTCT 59.764 37.037 0.00 0.00 43.78 3.10
101 102 4.159377 GATGCAATCTCTCCTCTCGTAG 57.841 50.000 0.00 0.00 41.17 3.51
102 103 3.283259 TGCAATCTCTCCTCTCGTAGA 57.717 47.619 0.00 0.00 0.00 2.59
103 104 3.826524 TGCAATCTCTCCTCTCGTAGAT 58.173 45.455 0.00 0.00 33.89 1.98
104 105 3.567585 TGCAATCTCTCCTCTCGTAGATG 59.432 47.826 0.00 0.00 33.89 2.90
105 106 3.568007 GCAATCTCTCCTCTCGTAGATGT 59.432 47.826 0.00 0.00 33.89 3.06
106 107 4.037446 GCAATCTCTCCTCTCGTAGATGTT 59.963 45.833 0.00 0.00 33.89 2.71
107 108 5.757886 CAATCTCTCCTCTCGTAGATGTTC 58.242 45.833 0.00 0.00 33.89 3.18
108 109 4.489306 TCTCTCCTCTCGTAGATGTTCA 57.511 45.455 0.00 0.00 33.89 3.18
109 110 5.042463 TCTCTCCTCTCGTAGATGTTCAT 57.958 43.478 0.00 0.00 33.89 2.57
110 111 5.060506 TCTCTCCTCTCGTAGATGTTCATC 58.939 45.833 4.80 4.80 33.89 2.92
111 112 5.042463 TCTCCTCTCGTAGATGTTCATCT 57.958 43.478 17.55 17.55 33.89 2.90
112 113 5.060506 TCTCCTCTCGTAGATGTTCATCTC 58.939 45.833 17.04 9.39 33.89 2.75
113 114 4.138290 TCCTCTCGTAGATGTTCATCTCC 58.862 47.826 17.04 6.90 33.89 3.71
114 115 4.141287 CCTCTCGTAGATGTTCATCTCCT 58.859 47.826 17.04 0.00 33.89 3.69
115 116 5.071923 TCCTCTCGTAGATGTTCATCTCCTA 59.928 44.000 17.04 0.00 33.89 2.94
116 117 5.411361 CCTCTCGTAGATGTTCATCTCCTAG 59.589 48.000 17.04 12.72 33.89 3.02
117 118 6.176014 TCTCGTAGATGTTCATCTCCTAGA 57.824 41.667 17.04 14.36 33.89 2.43
118 119 6.774673 TCTCGTAGATGTTCATCTCCTAGAT 58.225 40.000 17.04 0.00 32.24 1.98
119 120 7.227873 TCTCGTAGATGTTCATCTCCTAGATT 58.772 38.462 17.04 0.00 30.08 2.40
120 121 7.174080 TCTCGTAGATGTTCATCTCCTAGATTG 59.826 40.741 17.04 4.92 30.08 2.67
121 122 6.998673 TCGTAGATGTTCATCTCCTAGATTGA 59.001 38.462 17.04 4.61 31.32 2.57
122 123 7.667635 TCGTAGATGTTCATCTCCTAGATTGAT 59.332 37.037 17.04 0.00 31.32 2.57
123 124 7.967854 CGTAGATGTTCATCTCCTAGATTGATC 59.032 40.741 17.04 0.00 31.32 2.92
124 125 9.023962 GTAGATGTTCATCTCCTAGATTGATCT 57.976 37.037 17.04 0.00 31.32 2.75
125 126 8.495160 AGATGTTCATCTCCTAGATTGATCTT 57.505 34.615 9.22 0.00 38.32 2.40
126 127 8.369424 AGATGTTCATCTCCTAGATTGATCTTG 58.631 37.037 9.22 0.00 38.32 3.02
127 128 6.824553 TGTTCATCTCCTAGATTGATCTTGG 58.175 40.000 13.24 13.24 46.71 3.61
128 129 5.480642 TCATCTCCTAGATTGATCTTGGC 57.519 43.478 14.24 0.00 45.52 4.52
129 130 4.021632 TCATCTCCTAGATTGATCTTGGCG 60.022 45.833 14.24 9.87 45.52 5.69
130 131 3.566351 TCTCCTAGATTGATCTTGGCGA 58.434 45.455 14.24 11.68 45.52 5.54
131 132 3.571828 TCTCCTAGATTGATCTTGGCGAG 59.428 47.826 14.24 9.19 45.52 5.03
132 133 2.036475 TCCTAGATTGATCTTGGCGAGC 59.964 50.000 14.24 0.00 45.52 5.03
133 134 2.057316 CTAGATTGATCTTGGCGAGCG 58.943 52.381 0.00 0.00 38.32 5.03
134 135 0.176680 AGATTGATCTTGGCGAGCGT 59.823 50.000 0.00 0.00 31.97 5.07
135 136 1.409064 AGATTGATCTTGGCGAGCGTA 59.591 47.619 0.00 0.00 31.97 4.42
136 137 1.789464 GATTGATCTTGGCGAGCGTAG 59.211 52.381 0.00 0.00 0.00 3.51
137 138 0.179111 TTGATCTTGGCGAGCGTAGG 60.179 55.000 0.00 0.00 0.00 3.18
138 139 1.035385 TGATCTTGGCGAGCGTAGGA 61.035 55.000 0.00 0.00 0.00 2.94
139 140 0.102481 GATCTTGGCGAGCGTAGGAA 59.898 55.000 0.00 0.00 0.00 3.36
140 141 0.535335 ATCTTGGCGAGCGTAGGAAA 59.465 50.000 0.00 0.00 0.00 3.13
141 142 0.535335 TCTTGGCGAGCGTAGGAAAT 59.465 50.000 0.00 0.00 0.00 2.17
142 143 1.066430 TCTTGGCGAGCGTAGGAAATT 60.066 47.619 0.00 0.00 0.00 1.82
143 144 1.737793 CTTGGCGAGCGTAGGAAATTT 59.262 47.619 0.00 0.00 0.00 1.82
144 145 1.816074 TGGCGAGCGTAGGAAATTTT 58.184 45.000 0.00 0.00 0.00 1.82
145 146 2.156098 TGGCGAGCGTAGGAAATTTTT 58.844 42.857 0.00 0.00 0.00 1.94
162 163 2.969628 TTTTGTTTCCCATGCAACGT 57.030 40.000 0.00 0.00 0.00 3.99
163 164 2.969628 TTTGTTTCCCATGCAACGTT 57.030 40.000 0.00 0.00 0.00 3.99
164 165 2.500509 TTGTTTCCCATGCAACGTTC 57.499 45.000 0.00 0.00 0.00 3.95
165 166 0.671251 TGTTTCCCATGCAACGTTCC 59.329 50.000 0.00 0.00 0.00 3.62
166 167 0.038618 GTTTCCCATGCAACGTTCCC 60.039 55.000 0.00 0.00 0.00 3.97
167 168 1.182385 TTTCCCATGCAACGTTCCCC 61.182 55.000 0.00 0.00 0.00 4.81
168 169 3.439540 CCCATGCAACGTTCCCCG 61.440 66.667 0.00 0.00 44.03 5.73
169 170 2.359354 CCATGCAACGTTCCCCGA 60.359 61.111 0.00 0.00 40.70 5.14
170 171 2.686816 CCATGCAACGTTCCCCGAC 61.687 63.158 0.00 0.00 40.70 4.79
171 172 1.963855 CATGCAACGTTCCCCGACA 60.964 57.895 0.00 0.00 40.70 4.35
196 197 2.930826 TGTTGTCCTCCAAGTCCTTC 57.069 50.000 0.00 0.00 32.51 3.46
197 198 2.408565 TGTTGTCCTCCAAGTCCTTCT 58.591 47.619 0.00 0.00 32.51 2.85
198 199 2.777692 TGTTGTCCTCCAAGTCCTTCTT 59.222 45.455 0.00 0.00 36.75 2.52
212 213 3.128242 GTCCTTCTTGAGCCATCAACATG 59.872 47.826 0.00 0.00 40.54 3.21
215 216 2.715046 TCTTGAGCCATCAACATGACC 58.285 47.619 0.00 0.00 40.54 4.02
217 218 0.612744 TGAGCCATCAACATGACCGA 59.387 50.000 0.00 0.00 30.61 4.69
221 222 1.372582 CCATCAACATGACCGACTGG 58.627 55.000 0.00 0.00 42.84 4.00
325 326 0.940126 GCTGACTGGGCATAACATCG 59.060 55.000 0.00 0.00 0.00 3.84
340 341 1.414181 ACATCGGCCTGATAGAACCTG 59.586 52.381 0.00 0.00 34.83 4.00
379 380 1.068127 CATACCGGGTAGAACCTTCCG 59.932 57.143 13.15 0.00 38.64 4.30
383 384 0.172803 CGGGTAGAACCTTCCGACTG 59.827 60.000 0.00 0.00 44.69 3.51
384 385 1.553706 GGGTAGAACCTTCCGACTGA 58.446 55.000 0.00 0.00 38.64 3.41
397 398 0.179127 CGACTGAGACATGACGGCAT 60.179 55.000 0.00 0.00 34.29 4.40
411 412 3.334078 GGCATTGCCGACTCAAATG 57.666 52.632 12.82 0.00 39.62 2.32
424 425 3.659786 ACTCAAATGTCGAACCGAATCA 58.340 40.909 0.00 0.00 37.72 2.57
428 429 3.313012 AATGTCGAACCGAATCAGTGA 57.687 42.857 0.00 0.00 37.72 3.41
451 452 0.379669 GCTTGCCGATTGAGTCATGG 59.620 55.000 0.00 0.00 0.00 3.66
452 453 0.379669 CTTGCCGATTGAGTCATGGC 59.620 55.000 19.40 19.40 45.91 4.40
454 455 2.020131 GCCGATTGAGTCATGGCAG 58.980 57.895 20.64 1.23 45.06 4.85
493 494 4.093011 AGAGCTAGAATTGGTCACTGTCT 58.907 43.478 0.00 0.00 34.73 3.41
504 506 1.956170 CACTGTCTGACCCGTGTGC 60.956 63.158 15.17 0.00 0.00 4.57
518 520 2.511600 GTGCGCCTTGCTACCGAT 60.512 61.111 4.18 0.00 46.63 4.18
541 544 7.094805 CGATTTTTCCTCCATGTCTCTTGTTTA 60.095 37.037 0.00 0.00 0.00 2.01
575 578 0.530744 AGTACCTTCTCGAATGCGCA 59.469 50.000 14.96 14.96 37.46 6.09
579 582 1.224075 CCTTCTCGAATGCGCATCAT 58.776 50.000 25.53 9.22 37.46 2.45
638 641 1.947456 GAGGTTTGCCAGAAACGAGTT 59.053 47.619 0.00 0.00 37.19 3.01
641 644 0.941542 TTTGCCAGAAACGAGTTCGG 59.058 50.000 6.48 0.17 44.95 4.30
648 651 2.864343 CAGAAACGAGTTCGGACACTTT 59.136 45.455 6.48 0.00 44.95 2.66
704 707 4.204168 GTGCAAACACATACAAACGTCAAG 59.796 41.667 0.00 0.00 46.61 3.02
709 712 1.600013 ACATACAAACGTCAAGCGCAA 59.400 42.857 11.47 0.00 46.11 4.85
731 2040 2.159382 TCGAAAACCCTGGATTTGAGC 58.841 47.619 0.00 0.00 0.00 4.26
784 2120 1.300971 CCGTCAAGCCCACATCACTG 61.301 60.000 0.00 0.00 0.00 3.66
785 2121 1.300971 CGTCAAGCCCACATCACTGG 61.301 60.000 0.00 0.00 0.00 4.00
786 2122 0.250901 GTCAAGCCCACATCACTGGT 60.251 55.000 0.00 0.00 0.00 4.00
787 2123 0.036732 TCAAGCCCACATCACTGGTC 59.963 55.000 0.00 0.00 0.00 4.02
788 2124 0.037303 CAAGCCCACATCACTGGTCT 59.963 55.000 0.00 0.00 0.00 3.85
789 2125 0.037303 AAGCCCACATCACTGGTCTG 59.963 55.000 0.00 0.00 0.00 3.51
790 2126 0.837691 AGCCCACATCACTGGTCTGA 60.838 55.000 0.00 0.00 0.00 3.27
791 2127 0.674895 GCCCACATCACTGGTCTGAC 60.675 60.000 0.00 0.00 0.00 3.51
792 2128 0.036010 CCCACATCACTGGTCTGACC 60.036 60.000 19.96 19.96 39.22 4.02
804 2140 4.767255 CTGACCAGCAGGCCCGTC 62.767 72.222 0.00 0.00 41.07 4.79
816 2152 2.819595 CCCGTCAAGCCCACATCG 60.820 66.667 0.00 0.00 0.00 3.84
824 2160 2.045926 GCCCACATCGCTGGTCTT 60.046 61.111 0.00 0.00 0.00 3.01
1354 2710 4.116585 TCGCCTCCCTCGAGCTCT 62.117 66.667 12.85 0.00 34.49 4.09
1356 2712 1.824329 CGCCTCCCTCGAGCTCTTA 60.824 63.158 12.85 0.00 34.49 2.10
1558 2914 1.473965 CGCTCTACAATGCCCTCATGT 60.474 52.381 0.00 0.00 32.23 3.21
1655 3011 2.908015 GCCCAATGCGGACTCCTA 59.092 61.111 0.00 0.00 36.56 2.94
1847 3203 0.682209 ATGATGGCAGGTGGAGTTGC 60.682 55.000 0.00 0.00 39.56 4.17
2115 3471 1.562475 GTGTATGCCAAGGAGGGGTTA 59.438 52.381 0.00 0.00 38.09 2.85
2235 3591 0.317938 GTGACGCTGTCGACAGACTT 60.318 55.000 42.03 27.72 46.59 3.01
2589 3945 5.466058 TGTTCTTTTTGCATAAGTTGGCATG 59.534 36.000 5.08 0.00 40.17 4.06
2593 3949 2.945447 TGCATAAGTTGGCATGCTTC 57.055 45.000 18.92 8.32 46.19 3.86
2973 4330 7.148407 CCGAGCAGACTTTTACTGTGAATAAAT 60.148 37.037 0.00 0.00 37.64 1.40
3163 4652 1.656587 TCACACTGGCTGGGAGTTAT 58.343 50.000 0.00 0.00 0.00 1.89
3164 4653 1.985159 TCACACTGGCTGGGAGTTATT 59.015 47.619 0.00 0.00 0.00 1.40
3166 4655 2.749621 CACACTGGCTGGGAGTTATTTC 59.250 50.000 0.00 0.00 0.00 2.17
3167 4656 2.375174 ACACTGGCTGGGAGTTATTTCA 59.625 45.455 0.00 0.00 0.00 2.69
3168 4657 3.012518 CACTGGCTGGGAGTTATTTCAG 58.987 50.000 0.00 0.00 0.00 3.02
3169 4658 2.644798 ACTGGCTGGGAGTTATTTCAGT 59.355 45.455 0.00 0.00 0.00 3.41
3172 4661 3.181434 TGGCTGGGAGTTATTTCAGTGTT 60.181 43.478 0.00 0.00 0.00 3.32
3174 4663 5.007682 GGCTGGGAGTTATTTCAGTGTTTA 58.992 41.667 0.00 0.00 0.00 2.01
3175 4664 5.652452 GGCTGGGAGTTATTTCAGTGTTTAT 59.348 40.000 0.00 0.00 0.00 1.40
3176 4665 6.826741 GGCTGGGAGTTATTTCAGTGTTTATA 59.173 38.462 0.00 0.00 0.00 0.98
3177 4666 7.012421 GGCTGGGAGTTATTTCAGTGTTTATAG 59.988 40.741 0.00 0.00 0.00 1.31
3178 4667 7.769044 GCTGGGAGTTATTTCAGTGTTTATAGA 59.231 37.037 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.204237 TGTCTTCGCGATCCAATCATG 58.796 47.619 10.88 0.00 0.00 3.07
1 2 2.602257 TGTCTTCGCGATCCAATCAT 57.398 45.000 10.88 0.00 0.00 2.45
2 3 2.602257 ATGTCTTCGCGATCCAATCA 57.398 45.000 10.88 4.54 0.00 2.57
3 4 2.097202 CGAATGTCTTCGCGATCCAATC 60.097 50.000 10.88 8.76 46.76 2.67
4 5 1.860950 CGAATGTCTTCGCGATCCAAT 59.139 47.619 10.88 0.00 46.76 3.16
5 6 1.277326 CGAATGTCTTCGCGATCCAA 58.723 50.000 10.88 0.00 46.76 3.53
6 7 2.957871 CGAATGTCTTCGCGATCCA 58.042 52.632 10.88 7.55 46.76 3.41
14 15 5.331905 GCGATTGATGTAGTCGAATGTCTTC 60.332 44.000 0.00 0.00 40.55 2.87
15 16 4.504461 GCGATTGATGTAGTCGAATGTCTT 59.496 41.667 0.00 0.00 40.55 3.01
16 17 4.045104 GCGATTGATGTAGTCGAATGTCT 58.955 43.478 0.00 0.00 40.55 3.41
17 18 3.121663 CGCGATTGATGTAGTCGAATGTC 60.122 47.826 0.00 0.00 40.55 3.06
18 19 2.789339 CGCGATTGATGTAGTCGAATGT 59.211 45.455 0.00 0.00 40.55 2.71
19 20 2.789339 ACGCGATTGATGTAGTCGAATG 59.211 45.455 15.93 0.00 40.55 2.67
20 21 3.079960 ACGCGATTGATGTAGTCGAAT 57.920 42.857 15.93 0.00 40.55 3.34
21 22 2.554806 ACGCGATTGATGTAGTCGAA 57.445 45.000 15.93 0.00 40.55 3.71
22 23 2.554806 AACGCGATTGATGTAGTCGA 57.445 45.000 15.93 0.00 40.55 4.20
23 24 2.852413 AGAAACGCGATTGATGTAGTCG 59.148 45.455 15.93 0.00 40.99 4.18
24 25 4.842139 AAGAAACGCGATTGATGTAGTC 57.158 40.909 15.93 0.00 0.00 2.59
25 26 6.091123 GTTAAGAAACGCGATTGATGTAGT 57.909 37.500 15.93 0.00 0.00 2.73
39 40 4.575718 GCTAAGCGGAATCGTTAAGAAAC 58.424 43.478 0.00 0.00 38.89 2.78
40 41 4.852609 GCTAAGCGGAATCGTTAAGAAA 57.147 40.909 0.00 0.00 38.89 2.52
50 51 8.986294 ATACCCTTGTATATCGCTAAGCGGAAT 61.986 40.741 0.00 0.00 42.99 3.01
51 52 7.750934 ATACCCTTGTATATCGCTAAGCGGAA 61.751 42.308 0.00 0.00 42.99 4.30
52 53 6.327781 ATACCCTTGTATATCGCTAAGCGGA 61.328 44.000 0.00 0.00 42.99 5.54
53 54 4.142227 ATACCCTTGTATATCGCTAAGCGG 60.142 45.833 0.00 0.00 42.99 5.52
54 55 4.798907 CATACCCTTGTATATCGCTAAGCG 59.201 45.833 0.00 0.00 43.58 4.68
55 56 5.721232 ACATACCCTTGTATATCGCTAAGC 58.279 41.667 0.00 0.00 35.89 3.09
56 57 8.277490 TCTACATACCCTTGTATATCGCTAAG 57.723 38.462 0.00 0.00 35.89 2.18
57 58 8.683615 CATCTACATACCCTTGTATATCGCTAA 58.316 37.037 0.00 0.00 35.89 3.09
58 59 7.201794 GCATCTACATACCCTTGTATATCGCTA 60.202 40.741 0.00 0.00 35.89 4.26
59 60 6.405953 GCATCTACATACCCTTGTATATCGCT 60.406 42.308 0.00 0.00 35.89 4.93
60 61 5.749109 GCATCTACATACCCTTGTATATCGC 59.251 44.000 0.00 0.00 35.89 4.58
61 62 6.863275 TGCATCTACATACCCTTGTATATCG 58.137 40.000 0.00 0.00 35.89 2.92
62 63 9.319143 GATTGCATCTACATACCCTTGTATATC 57.681 37.037 0.00 0.00 35.89 1.63
63 64 9.051259 AGATTGCATCTACATACCCTTGTATAT 57.949 33.333 0.00 0.00 38.00 0.86
64 65 8.435931 AGATTGCATCTACATACCCTTGTATA 57.564 34.615 0.00 0.00 38.00 1.47
65 66 7.236432 AGAGATTGCATCTACATACCCTTGTAT 59.764 37.037 0.00 0.00 40.38 2.29
66 67 6.554982 AGAGATTGCATCTACATACCCTTGTA 59.445 38.462 0.00 0.00 40.38 2.41
67 68 5.367937 AGAGATTGCATCTACATACCCTTGT 59.632 40.000 0.00 0.00 40.38 3.16
68 69 5.862845 AGAGATTGCATCTACATACCCTTG 58.137 41.667 0.00 0.00 40.38 3.61
69 70 5.012561 GGAGAGATTGCATCTACATACCCTT 59.987 44.000 0.00 0.00 40.38 3.95
70 71 4.530161 GGAGAGATTGCATCTACATACCCT 59.470 45.833 0.00 0.00 40.38 4.34
71 72 4.530161 AGGAGAGATTGCATCTACATACCC 59.470 45.833 0.96 0.00 40.38 3.69
72 73 5.480073 AGAGGAGAGATTGCATCTACATACC 59.520 44.000 0.96 0.00 40.38 2.73
73 74 6.588719 AGAGGAGAGATTGCATCTACATAC 57.411 41.667 0.96 0.00 40.38 2.39
74 75 5.414144 CGAGAGGAGAGATTGCATCTACATA 59.586 44.000 0.96 0.00 40.38 2.29
75 76 4.218200 CGAGAGGAGAGATTGCATCTACAT 59.782 45.833 0.96 0.00 40.38 2.29
76 77 3.567585 CGAGAGGAGAGATTGCATCTACA 59.432 47.826 0.96 0.00 40.38 2.74
77 78 3.568007 ACGAGAGGAGAGATTGCATCTAC 59.432 47.826 0.00 0.00 40.38 2.59
78 79 3.826524 ACGAGAGGAGAGATTGCATCTA 58.173 45.455 0.00 0.00 40.38 1.98
79 80 2.665165 ACGAGAGGAGAGATTGCATCT 58.335 47.619 0.00 0.00 43.70 2.90
98 99 9.023962 AGATCAATCTAGGAGATGAACATCTAC 57.976 37.037 16.61 16.61 46.80 2.59
99 100 9.599056 AAGATCAATCTAGGAGATGAACATCTA 57.401 33.333 15.86 2.61 41.21 1.98
100 101 8.369424 CAAGATCAATCTAGGAGATGAACATCT 58.631 37.037 15.83 15.83 42.63 2.90
101 102 7.603404 CCAAGATCAATCTAGGAGATGAACATC 59.397 40.741 6.68 6.68 34.65 3.06
102 103 7.451732 CCAAGATCAATCTAGGAGATGAACAT 58.548 38.462 0.00 0.00 34.65 2.71
103 104 6.687393 GCCAAGATCAATCTAGGAGATGAACA 60.687 42.308 0.00 0.00 34.65 3.18
104 105 5.700373 GCCAAGATCAATCTAGGAGATGAAC 59.300 44.000 0.00 0.00 34.65 3.18
105 106 5.510349 CGCCAAGATCAATCTAGGAGATGAA 60.510 44.000 0.00 0.00 34.65 2.57
106 107 4.021632 CGCCAAGATCAATCTAGGAGATGA 60.022 45.833 0.00 0.00 34.65 2.92
107 108 4.021632 TCGCCAAGATCAATCTAGGAGATG 60.022 45.833 0.00 0.00 34.65 2.90
108 109 4.155709 TCGCCAAGATCAATCTAGGAGAT 58.844 43.478 0.00 0.00 36.28 2.75
109 110 3.566351 TCGCCAAGATCAATCTAGGAGA 58.434 45.455 0.00 0.00 35.76 3.71
110 111 3.860378 GCTCGCCAAGATCAATCTAGGAG 60.860 52.174 0.00 0.46 35.76 3.69
111 112 2.036475 GCTCGCCAAGATCAATCTAGGA 59.964 50.000 0.00 0.00 35.76 2.94
112 113 2.411904 GCTCGCCAAGATCAATCTAGG 58.588 52.381 0.00 0.00 35.76 3.02
113 114 2.057316 CGCTCGCCAAGATCAATCTAG 58.943 52.381 0.00 0.00 35.76 2.43
114 115 1.409064 ACGCTCGCCAAGATCAATCTA 59.591 47.619 0.00 0.00 35.76 1.98
115 116 0.176680 ACGCTCGCCAAGATCAATCT 59.823 50.000 0.00 0.00 39.22 2.40
116 117 1.789464 CTACGCTCGCCAAGATCAATC 59.211 52.381 0.00 0.00 0.00 2.67
117 118 1.539065 CCTACGCTCGCCAAGATCAAT 60.539 52.381 0.00 0.00 0.00 2.57
118 119 0.179111 CCTACGCTCGCCAAGATCAA 60.179 55.000 0.00 0.00 0.00 2.57
119 120 1.035385 TCCTACGCTCGCCAAGATCA 61.035 55.000 0.00 0.00 0.00 2.92
120 121 0.102481 TTCCTACGCTCGCCAAGATC 59.898 55.000 0.00 0.00 0.00 2.75
121 122 0.535335 TTTCCTACGCTCGCCAAGAT 59.465 50.000 0.00 0.00 0.00 2.40
122 123 0.535335 ATTTCCTACGCTCGCCAAGA 59.465 50.000 0.00 0.00 0.00 3.02
123 124 1.369625 AATTTCCTACGCTCGCCAAG 58.630 50.000 0.00 0.00 0.00 3.61
124 125 1.816074 AAATTTCCTACGCTCGCCAA 58.184 45.000 0.00 0.00 0.00 4.52
125 126 1.816074 AAAATTTCCTACGCTCGCCA 58.184 45.000 0.00 0.00 0.00 5.69
126 127 2.913777 AAAAATTTCCTACGCTCGCC 57.086 45.000 0.00 0.00 0.00 5.54
142 143 3.252974 ACGTTGCATGGGAAACAAAAA 57.747 38.095 0.00 0.00 31.43 1.94
143 144 2.969628 ACGTTGCATGGGAAACAAAA 57.030 40.000 0.00 0.00 31.43 2.44
144 145 2.482142 GGAACGTTGCATGGGAAACAAA 60.482 45.455 15.52 0.00 31.43 2.83
145 146 1.067821 GGAACGTTGCATGGGAAACAA 59.932 47.619 15.52 0.00 31.43 2.83
146 147 0.671251 GGAACGTTGCATGGGAAACA 59.329 50.000 15.52 0.00 31.43 2.83
147 148 0.038618 GGGAACGTTGCATGGGAAAC 60.039 55.000 21.74 0.00 0.00 2.78
148 149 1.182385 GGGGAACGTTGCATGGGAAA 61.182 55.000 21.74 0.00 0.00 3.13
149 150 1.605165 GGGGAACGTTGCATGGGAA 60.605 57.895 21.74 0.00 0.00 3.97
150 151 2.034999 GGGGAACGTTGCATGGGA 59.965 61.111 21.74 0.00 0.00 4.37
151 152 3.439540 CGGGGAACGTTGCATGGG 61.440 66.667 21.74 3.38 37.93 4.00
152 153 2.359354 TCGGGGAACGTTGCATGG 60.359 61.111 21.74 9.59 44.69 3.66
153 154 1.305219 ATGTCGGGGAACGTTGCATG 61.305 55.000 21.74 12.63 44.69 4.06
154 155 1.002624 ATGTCGGGGAACGTTGCAT 60.003 52.632 21.74 2.90 44.69 3.96
155 156 1.669760 GATGTCGGGGAACGTTGCA 60.670 57.895 21.74 0.25 44.69 4.08
156 157 1.024579 ATGATGTCGGGGAACGTTGC 61.025 55.000 11.85 11.85 44.69 4.17
157 158 2.303163 TATGATGTCGGGGAACGTTG 57.697 50.000 5.00 0.00 44.69 4.10
158 159 2.169769 ACATATGATGTCGGGGAACGTT 59.830 45.455 10.38 0.00 39.92 3.99
159 160 1.760613 ACATATGATGTCGGGGAACGT 59.239 47.619 10.38 0.00 39.92 3.99
160 161 2.526304 ACATATGATGTCGGGGAACG 57.474 50.000 10.38 0.00 39.92 3.95
161 162 3.541632 ACAACATATGATGTCGGGGAAC 58.458 45.455 12.47 0.00 44.07 3.62
162 163 3.433031 GGACAACATATGATGTCGGGGAA 60.433 47.826 29.06 0.00 45.27 3.97
163 164 2.104111 GGACAACATATGATGTCGGGGA 59.896 50.000 29.06 0.00 45.27 4.81
164 165 2.104792 AGGACAACATATGATGTCGGGG 59.895 50.000 29.06 2.86 45.27 5.73
165 166 3.393800 GAGGACAACATATGATGTCGGG 58.606 50.000 29.06 3.48 45.27 5.14
166 167 3.181466 TGGAGGACAACATATGATGTCGG 60.181 47.826 29.06 8.56 45.27 4.79
167 168 4.058721 TGGAGGACAACATATGATGTCG 57.941 45.455 29.06 9.17 45.27 4.35
168 169 5.431765 ACTTGGAGGACAACATATGATGTC 58.568 41.667 28.71 28.71 44.07 3.06
170 171 4.818546 GGACTTGGAGGACAACATATGATG 59.181 45.833 10.38 10.81 34.76 3.07
171 172 4.723789 AGGACTTGGAGGACAACATATGAT 59.276 41.667 10.38 0.00 34.76 2.45
196 197 1.399440 CGGTCATGTTGATGGCTCAAG 59.601 52.381 0.00 0.00 41.96 3.02
197 198 1.003003 TCGGTCATGTTGATGGCTCAA 59.997 47.619 0.00 0.00 39.07 3.02
198 199 0.612744 TCGGTCATGTTGATGGCTCA 59.387 50.000 0.00 0.00 34.34 4.26
212 213 3.814005 ACCACAATATACCAGTCGGTC 57.186 47.619 0.00 0.00 44.71 4.79
215 216 6.085555 AGTCATACCACAATATACCAGTCG 57.914 41.667 0.00 0.00 0.00 4.18
217 218 6.014499 GCCTAGTCATACCACAATATACCAGT 60.014 42.308 0.00 0.00 0.00 4.00
221 222 6.994221 AGTGCCTAGTCATACCACAATATAC 58.006 40.000 0.00 0.00 0.00 1.47
256 257 7.148239 GCTTGTTGTTATACCTATTCAGCAAGT 60.148 37.037 16.50 0.00 43.68 3.16
325 326 1.227674 CGGCAGGTTCTATCAGGCC 60.228 63.158 0.00 0.00 38.04 5.19
340 341 2.887568 CGTCATGTCTCAGCCGGC 60.888 66.667 21.89 21.89 0.00 6.13
379 380 1.662629 CAATGCCGTCATGTCTCAGTC 59.337 52.381 0.00 0.00 32.23 3.51
383 384 1.723870 GGCAATGCCGTCATGTCTC 59.276 57.895 9.14 0.00 39.62 3.36
384 385 3.909662 GGCAATGCCGTCATGTCT 58.090 55.556 9.14 0.00 39.62 3.41
411 412 2.251893 GACTCACTGATTCGGTTCGAC 58.748 52.381 0.00 0.00 34.89 4.20
414 415 0.992802 GCGACTCACTGATTCGGTTC 59.007 55.000 17.54 1.34 35.73 3.62
424 425 1.016130 CAATCGGCAAGCGACTCACT 61.016 55.000 0.00 0.00 0.00 3.41
428 429 0.737715 GACTCAATCGGCAAGCGACT 60.738 55.000 0.00 0.00 0.00 4.18
451 452 0.174162 CCCAAGGTAATGCAAGCTGC 59.826 55.000 0.00 0.00 45.29 5.25
452 453 1.747355 CTCCCAAGGTAATGCAAGCTG 59.253 52.381 0.00 0.00 0.00 4.24
454 455 2.019984 CTCTCCCAAGGTAATGCAAGC 58.980 52.381 0.00 0.00 0.00 4.01
499 501 3.788766 CGGTAGCAAGGCGCACAC 61.789 66.667 10.83 0.00 46.13 3.82
504 506 1.202143 GGAAAAATCGGTAGCAAGGCG 60.202 52.381 0.00 0.00 0.00 5.52
518 520 8.477419 AATAAACAAGAGACATGGAGGAAAAA 57.523 30.769 0.00 0.00 0.00 1.94
547 550 6.312918 GCATTCGAGAAGGTACTCAAAACATA 59.687 38.462 0.00 0.00 38.49 2.29
554 557 1.469251 GCGCATTCGAGAAGGTACTCA 60.469 52.381 0.30 0.00 35.66 3.41
555 558 1.201343 GCGCATTCGAGAAGGTACTC 58.799 55.000 0.30 0.00 35.66 2.59
556 559 0.530744 TGCGCATTCGAGAAGGTACT 59.469 50.000 5.66 0.00 38.22 2.73
557 560 1.523095 GATGCGCATTCGAGAAGGTAC 59.477 52.381 26.12 2.67 38.10 3.34
575 578 1.037579 TGACAGGCGACTCGGATGAT 61.038 55.000 0.00 0.00 40.21 2.45
579 582 2.710902 CCATGACAGGCGACTCGGA 61.711 63.158 0.00 0.00 40.21 4.55
678 681 2.964123 CGTTTGTATGTGTTTGCACTCG 59.036 45.455 0.00 0.00 45.44 4.18
685 688 3.613563 CGCTTGACGTTTGTATGTGTTT 58.386 40.909 0.00 0.00 36.87 2.83
704 707 1.082104 CAGGGTTTTCGAGTTGCGC 60.082 57.895 0.00 0.00 40.61 6.09
709 712 3.412386 CTCAAATCCAGGGTTTTCGAGT 58.588 45.455 0.00 0.00 0.00 4.18
731 2040 0.108898 CCAGTGAGAGAGGAGCAACG 60.109 60.000 0.00 0.00 0.00 4.10
739 2048 1.916506 TGGTCAGACCAGTGAGAGAG 58.083 55.000 19.21 0.00 44.79 3.20
784 2120 4.416738 GGGCCTGCTGGTCAGACC 62.417 72.222 16.72 13.35 45.72 3.85
785 2121 4.767255 CGGGCCTGCTGGTCAGAC 62.767 72.222 16.72 0.00 45.72 3.51
787 2123 4.767255 GACGGGCCTGCTGGTCAG 62.767 72.222 16.72 14.62 40.42 3.51
789 2125 4.329545 TTGACGGGCCTGCTGGTC 62.330 66.667 12.89 8.80 37.19 4.02
790 2126 4.335647 CTTGACGGGCCTGCTGGT 62.336 66.667 12.89 0.00 35.27 4.00
804 2140 2.360350 ACCAGCGATGTGGGCTTG 60.360 61.111 0.00 0.00 42.54 4.01
1302 2658 0.926293 GGAGGGTGGGGAATGAATGA 59.074 55.000 0.00 0.00 0.00 2.57
1354 2710 2.122547 GGGGCGGAGGAGGGATAA 60.123 66.667 0.00 0.00 0.00 1.75
1356 2712 4.431524 TTGGGGCGGAGGAGGGAT 62.432 66.667 0.00 0.00 0.00 3.85
1558 2914 1.079197 CACTGTGCATGTAGGCGGA 60.079 57.895 0.00 0.00 36.28 5.54
1655 3011 2.106566 AGAGAGCGATGAGGATGTTGT 58.893 47.619 0.00 0.00 0.00 3.32
1825 3181 2.564062 CAACTCCACCTGCCATCATTTT 59.436 45.455 0.00 0.00 0.00 1.82
1847 3203 3.685139 AATGTGTAGTGGTGTCTGGAG 57.315 47.619 0.00 0.00 0.00 3.86
1944 3300 1.000163 ACTATATCAACCTCGCCAGCG 60.000 52.381 5.50 5.50 41.35 5.18
2115 3471 2.310052 CCTTCTTTCCATCCCCTCAACT 59.690 50.000 0.00 0.00 0.00 3.16
2235 3591 2.124529 TGCCGGACAAAGTGTGCA 60.125 55.556 5.05 0.00 38.73 4.57
2265 3621 2.825836 CGGCACAGCTTCCATCCC 60.826 66.667 0.00 0.00 0.00 3.85
2681 4037 6.785488 TCTTCTACACAACAATTGCACTAG 57.215 37.500 5.05 0.00 0.00 2.57
2759 4115 2.301870 TGCCTTACGACCTGATCACTTT 59.698 45.455 0.00 0.00 0.00 2.66
2761 4117 1.557099 TGCCTTACGACCTGATCACT 58.443 50.000 0.00 0.00 0.00 3.41
3070 4427 5.959618 ATGCTAAACACTGAAACCTAACC 57.040 39.130 0.00 0.00 0.00 2.85
3172 4661 9.672673 GCAAAGGGAAGCATCTATAATCTATAA 57.327 33.333 0.00 0.00 0.00 0.98
3174 4663 7.609532 GTGCAAAGGGAAGCATCTATAATCTAT 59.390 37.037 0.00 0.00 43.44 1.98
3175 4664 6.936900 GTGCAAAGGGAAGCATCTATAATCTA 59.063 38.462 0.00 0.00 43.44 1.98
3176 4665 5.767168 GTGCAAAGGGAAGCATCTATAATCT 59.233 40.000 0.00 0.00 43.44 2.40
3177 4666 5.767168 AGTGCAAAGGGAAGCATCTATAATC 59.233 40.000 0.00 0.00 43.44 1.75
3178 4667 5.699143 AGTGCAAAGGGAAGCATCTATAAT 58.301 37.500 0.00 0.00 43.44 1.28


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

AutoCloner maintained by Alex Coulton.