Multiple sequence alignment - TraesCS6B01G094800

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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 TraesCS6B01G094800 chr6B 100.000 3104 0 0 1 3104 71196932 71200035 0.000000e+00 5733.0
1 TraesCS6B01G094800 chr6B 86.256 1397 118 35 905 2260 71226594 71227957 0.000000e+00 1448.0
2 TraesCS6B01G094800 chr6B 83.110 1267 142 39 895 2117 71262061 71263299 0.000000e+00 1088.0
3 TraesCS6B01G094800 chr6B 93.939 132 5 2 1 132 392364975 392365103 2.440000e-46 196.0
4 TraesCS6B01G094800 chr6B 83.333 108 16 2 2502 2608 71263899 71264005 7.080000e-17 99.0
5 TraesCS6B01G094800 chr6A 92.000 2175 119 25 120 2260 38683715 38685868 0.000000e+00 3001.0
6 TraesCS6B01G094800 chr6A 87.923 1242 111 15 905 2122 38723638 38724864 0.000000e+00 1426.0
7 TraesCS6B01G094800 chr6A 82.578 1412 139 55 895 2256 38741713 38743067 0.000000e+00 1146.0
8 TraesCS6B01G094800 chr6A 95.118 594 24 2 2516 3104 38686462 38687055 0.000000e+00 931.0
9 TraesCS6B01G094800 chr6A 85.542 166 8 5 2353 2518 38686047 38686196 3.200000e-35 159.0
10 TraesCS6B01G094800 chr6A 89.412 85 4 2 2269 2352 38685927 38686007 5.480000e-18 102.0
11 TraesCS6B01G094800 chr6D 90.759 1883 97 23 414 2260 34430151 34431992 0.000000e+00 2442.0
12 TraesCS6B01G094800 chr6D 87.948 1228 107 14 905 2108 34501988 34503198 0.000000e+00 1410.0
13 TraesCS6B01G094800 chr6D 81.171 1264 152 44 895 2108 34508025 34509252 0.000000e+00 937.0
14 TraesCS6B01G094800 chr6D 91.323 461 39 1 2383 2843 34433905 34434364 2.030000e-176 628.0
15 TraesCS6B01G094800 chr6D 90.909 462 40 2 2383 2843 34432804 34433264 1.220000e-173 619.0
16 TraesCS6B01G094800 chr6D 96.154 52 2 0 290 341 34430066 34430117 5.520000e-13 86.1
17 TraesCS6B01G094800 chr7A 80.446 762 109 22 956 1707 634446721 634445990 2.100000e-151 545.0
18 TraesCS6B01G094800 chr5D 94.007 267 11 2 2842 3104 519286446 519286181 1.730000e-107 399.0
19 TraesCS6B01G094800 chr5D 94.553 257 10 1 2852 3104 510549788 510549532 8.070000e-106 394.0
20 TraesCS6B01G094800 chr4A 92.086 278 15 3 2833 3104 490151868 490152144 4.860000e-103 385.0
21 TraesCS6B01G094800 chr4A 99.153 118 1 0 1 118 664326507 664326624 2.420000e-51 213.0
22 TraesCS6B01G094800 chr1A 93.774 257 12 2 2852 3104 592541288 592541032 1.750000e-102 383.0
23 TraesCS6B01G094800 chr3A 93.385 257 13 2 2852 3104 748077349 748077093 8.130000e-101 377.0
24 TraesCS6B01G094800 chr3A 92.996 257 14 2 2852 3104 746840064 746839808 3.780000e-99 372.0
25 TraesCS6B01G094800 chr2D 92.996 257 14 1 2852 3104 280779010 280778754 3.780000e-99 372.0
26 TraesCS6B01G094800 chr1D 92.218 257 16 3 2852 3104 396335030 396334774 8.180000e-96 361.0
27 TraesCS6B01G094800 chr5B 99.167 120 1 0 1 120 308299451 308299332 1.870000e-52 217.0
28 TraesCS6B01G094800 chr5B 96.124 129 4 1 1 128 166273304 166273176 3.140000e-50 209.0
29 TraesCS6B01G094800 chr2B 99.167 120 1 0 1 120 379969817 379969936 1.870000e-52 217.0
30 TraesCS6B01G094800 chr3B 98.361 122 2 0 1 122 60731394 60731515 6.740000e-52 215.0
31 TraesCS6B01G094800 chr7D 96.154 130 3 2 1 129 158121149 158121021 8.720000e-51 211.0
32 TraesCS6B01G094800 chr4B 98.347 121 1 1 1 120 472981277 472981157 8.720000e-51 211.0
33 TraesCS6B01G094800 chr3D 96.774 124 4 0 1 124 33539597 33539474 1.130000e-49 207.0


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 TraesCS6B01G094800 chr6B 71196932 71200035 3103 False 5733.000 5733 100.00000 1 3104 1 chr6B.!!$F1 3103
1 TraesCS6B01G094800 chr6B 71226594 71227957 1363 False 1448.000 1448 86.25600 905 2260 1 chr6B.!!$F2 1355
2 TraesCS6B01G094800 chr6B 71262061 71264005 1944 False 593.500 1088 83.22150 895 2608 2 chr6B.!!$F4 1713
3 TraesCS6B01G094800 chr6A 38723638 38724864 1226 False 1426.000 1426 87.92300 905 2122 1 chr6A.!!$F1 1217
4 TraesCS6B01G094800 chr6A 38741713 38743067 1354 False 1146.000 1146 82.57800 895 2256 1 chr6A.!!$F2 1361
5 TraesCS6B01G094800 chr6A 38683715 38687055 3340 False 1048.250 3001 90.51800 120 3104 4 chr6A.!!$F3 2984
6 TraesCS6B01G094800 chr6D 34501988 34503198 1210 False 1410.000 1410 87.94800 905 2108 1 chr6D.!!$F1 1203
7 TraesCS6B01G094800 chr6D 34430066 34434364 4298 False 943.775 2442 92.28625 290 2843 4 chr6D.!!$F3 2553
8 TraesCS6B01G094800 chr6D 34508025 34509252 1227 False 937.000 937 81.17100 895 2108 1 chr6D.!!$F2 1213
9 TraesCS6B01G094800 chr7A 634445990 634446721 731 True 545.000 545 80.44600 956 1707 1 chr7A.!!$R1 751

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
95 96 0.261991 TCGCCTATTCACCCTCCTCT 59.738 55.0 0.0 0.0 0.0 3.69 F
722 731 0.394352 GCTGCTTAGCTTTGCCCCTA 60.394 55.0 5.6 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 1809 1.375523 GCAGGTCGTCGTGGGAATT 60.376 57.895 4.63 0.0 0.0 2.17 R
2180 2335 2.169352 AGACAGTTCAGTTCAGTGTGCT 59.831 45.455 0.00 0.0 0.0 4.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.934515 ACTTATTCCGCTGCTAGTAGTTC 58.065 43.478 9.73 0.00 0.00 3.01
23 24 4.645588 ACTTATTCCGCTGCTAGTAGTTCT 59.354 41.667 9.73 0.00 0.00 3.01
24 25 5.127356 ACTTATTCCGCTGCTAGTAGTTCTT 59.873 40.000 9.73 0.00 0.00 2.52
25 26 3.505464 TTCCGCTGCTAGTAGTTCTTC 57.495 47.619 9.73 0.00 0.00 2.87
26 27 2.443416 TCCGCTGCTAGTAGTTCTTCA 58.557 47.619 9.73 0.00 0.00 3.02
27 28 3.024547 TCCGCTGCTAGTAGTTCTTCAT 58.975 45.455 9.73 0.00 0.00 2.57
28 29 3.447586 TCCGCTGCTAGTAGTTCTTCATT 59.552 43.478 9.73 0.00 0.00 2.57
29 30 4.081642 TCCGCTGCTAGTAGTTCTTCATTT 60.082 41.667 9.73 0.00 0.00 2.32
30 31 5.126545 TCCGCTGCTAGTAGTTCTTCATTTA 59.873 40.000 9.73 0.00 0.00 1.40
31 32 5.460419 CCGCTGCTAGTAGTTCTTCATTTAG 59.540 44.000 9.73 0.00 0.00 1.85
32 33 5.460419 CGCTGCTAGTAGTTCTTCATTTAGG 59.540 44.000 9.73 0.00 0.00 2.69
33 34 6.574350 GCTGCTAGTAGTTCTTCATTTAGGA 58.426 40.000 9.73 0.00 0.00 2.94
34 35 7.042335 GCTGCTAGTAGTTCTTCATTTAGGAA 58.958 38.462 9.73 0.00 0.00 3.36
35 36 7.713073 GCTGCTAGTAGTTCTTCATTTAGGAAT 59.287 37.037 9.73 0.00 0.00 3.01
36 37 9.606631 CTGCTAGTAGTTCTTCATTTAGGAATT 57.393 33.333 0.00 0.00 0.00 2.17
37 38 9.959721 TGCTAGTAGTTCTTCATTTAGGAATTT 57.040 29.630 0.00 0.00 0.00 1.82
41 42 9.674068 AGTAGTTCTTCATTTAGGAATTTCCTC 57.326 33.333 21.20 3.54 45.66 3.71
42 43 9.449719 GTAGTTCTTCATTTAGGAATTTCCTCA 57.550 33.333 21.20 8.27 45.66 3.86
43 44 8.341892 AGTTCTTCATTTAGGAATTTCCTCAC 57.658 34.615 21.20 6.05 45.66 3.51
44 45 7.394641 AGTTCTTCATTTAGGAATTTCCTCACC 59.605 37.037 21.20 0.00 45.66 4.02
45 46 6.789268 TCTTCATTTAGGAATTTCCTCACCA 58.211 36.000 21.20 1.21 45.66 4.17
46 47 6.886459 TCTTCATTTAGGAATTTCCTCACCAG 59.114 38.462 21.20 10.97 45.66 4.00
47 48 4.949856 TCATTTAGGAATTTCCTCACCAGC 59.050 41.667 21.20 0.00 45.66 4.85
48 49 4.380843 TTTAGGAATTTCCTCACCAGCA 57.619 40.909 21.20 0.00 45.66 4.41
49 50 2.978156 AGGAATTTCCTCACCAGCAA 57.022 45.000 12.37 0.00 45.66 3.91
50 51 3.243359 AGGAATTTCCTCACCAGCAAA 57.757 42.857 12.37 0.00 45.66 3.68
51 52 3.782992 AGGAATTTCCTCACCAGCAAAT 58.217 40.909 12.37 0.00 45.66 2.32
52 53 4.162651 AGGAATTTCCTCACCAGCAAATT 58.837 39.130 12.37 0.00 45.66 1.82
53 54 4.221482 AGGAATTTCCTCACCAGCAAATTC 59.779 41.667 12.37 7.23 45.66 2.17
54 55 4.498241 GAATTTCCTCACCAGCAAATTCC 58.502 43.478 0.00 0.00 38.48 3.01
55 56 2.978156 TTCCTCACCAGCAAATTCCT 57.022 45.000 0.00 0.00 0.00 3.36
56 57 2.496899 TCCTCACCAGCAAATTCCTC 57.503 50.000 0.00 0.00 0.00 3.71
57 58 1.704628 TCCTCACCAGCAAATTCCTCA 59.295 47.619 0.00 0.00 0.00 3.86
58 59 2.089980 CCTCACCAGCAAATTCCTCAG 58.910 52.381 0.00 0.00 0.00 3.35
59 60 2.553904 CCTCACCAGCAAATTCCTCAGT 60.554 50.000 0.00 0.00 0.00 3.41
60 61 2.486982 CTCACCAGCAAATTCCTCAGTG 59.513 50.000 0.00 0.00 0.00 3.66
61 62 2.106338 TCACCAGCAAATTCCTCAGTGA 59.894 45.455 0.00 0.00 0.00 3.41
62 63 2.886523 CACCAGCAAATTCCTCAGTGAA 59.113 45.455 0.00 0.00 0.00 3.18
63 64 3.057736 CACCAGCAAATTCCTCAGTGAAG 60.058 47.826 0.00 0.00 0.00 3.02
64 65 3.181440 ACCAGCAAATTCCTCAGTGAAGA 60.181 43.478 0.00 0.00 0.00 2.87
65 66 3.822735 CCAGCAAATTCCTCAGTGAAGAA 59.177 43.478 6.64 6.64 0.00 2.52
66 67 4.461781 CCAGCAAATTCCTCAGTGAAGAAT 59.538 41.667 10.62 10.62 0.00 2.40
67 68 5.047519 CCAGCAAATTCCTCAGTGAAGAATT 60.048 40.000 19.64 19.64 40.92 2.17
86 87 9.950680 GAAGAATTCATAAAAATCGCCTATTCA 57.049 29.630 8.44 0.00 46.62 2.57
87 88 9.736023 AAGAATTCATAAAAATCGCCTATTCAC 57.264 29.630 8.44 0.00 0.00 3.18
88 89 8.352942 AGAATTCATAAAAATCGCCTATTCACC 58.647 33.333 8.44 0.00 0.00 4.02
89 90 6.385649 TTCATAAAAATCGCCTATTCACCC 57.614 37.500 0.00 0.00 0.00 4.61
90 91 5.690865 TCATAAAAATCGCCTATTCACCCT 58.309 37.500 0.00 0.00 0.00 4.34
91 92 5.763204 TCATAAAAATCGCCTATTCACCCTC 59.237 40.000 0.00 0.00 0.00 4.30
92 93 2.640316 AAATCGCCTATTCACCCTCC 57.360 50.000 0.00 0.00 0.00 4.30
93 94 1.807814 AATCGCCTATTCACCCTCCT 58.192 50.000 0.00 0.00 0.00 3.69
94 95 1.343069 ATCGCCTATTCACCCTCCTC 58.657 55.000 0.00 0.00 0.00 3.71
95 96 0.261991 TCGCCTATTCACCCTCCTCT 59.738 55.000 0.00 0.00 0.00 3.69
96 97 1.497716 TCGCCTATTCACCCTCCTCTA 59.502 52.381 0.00 0.00 0.00 2.43
97 98 1.889829 CGCCTATTCACCCTCCTCTAG 59.110 57.143 0.00 0.00 0.00 2.43
98 99 2.753507 CGCCTATTCACCCTCCTCTAGT 60.754 54.545 0.00 0.00 0.00 2.57
99 100 2.894765 GCCTATTCACCCTCCTCTAGTC 59.105 54.545 0.00 0.00 0.00 2.59
100 101 3.150767 CCTATTCACCCTCCTCTAGTCG 58.849 54.545 0.00 0.00 0.00 4.18
101 102 3.181442 CCTATTCACCCTCCTCTAGTCGA 60.181 52.174 0.00 0.00 0.00 4.20
102 103 3.603965 ATTCACCCTCCTCTAGTCGAT 57.396 47.619 0.00 0.00 0.00 3.59
103 104 4.726035 ATTCACCCTCCTCTAGTCGATA 57.274 45.455 0.00 0.00 0.00 2.92
104 105 4.726035 TTCACCCTCCTCTAGTCGATAT 57.274 45.455 0.00 0.00 0.00 1.63
105 106 5.837770 TTCACCCTCCTCTAGTCGATATA 57.162 43.478 0.00 0.00 0.00 0.86
106 107 5.837770 TCACCCTCCTCTAGTCGATATAA 57.162 43.478 0.00 0.00 0.00 0.98
107 108 5.558818 TCACCCTCCTCTAGTCGATATAAC 58.441 45.833 0.00 0.00 0.00 1.89
108 109 4.392445 CACCCTCCTCTAGTCGATATAACG 59.608 50.000 0.00 0.00 0.00 3.18
109 110 3.374678 CCCTCCTCTAGTCGATATAACGC 59.625 52.174 0.00 0.00 0.00 4.84
110 111 4.001652 CCTCCTCTAGTCGATATAACGCA 58.998 47.826 0.00 0.00 0.00 5.24
111 112 4.142859 CCTCCTCTAGTCGATATAACGCAC 60.143 50.000 0.00 0.00 0.00 5.34
112 113 4.639334 TCCTCTAGTCGATATAACGCACT 58.361 43.478 0.00 5.39 0.00 4.40
113 114 5.061853 TCCTCTAGTCGATATAACGCACTT 58.938 41.667 10.84 0.00 0.00 3.16
114 115 5.530171 TCCTCTAGTCGATATAACGCACTTT 59.470 40.000 10.84 0.00 0.00 2.66
115 116 5.852229 CCTCTAGTCGATATAACGCACTTTC 59.148 44.000 10.84 0.00 0.00 2.62
116 117 6.367686 TCTAGTCGATATAACGCACTTTCA 57.632 37.500 10.84 0.00 0.00 2.69
117 118 6.427974 TCTAGTCGATATAACGCACTTTCAG 58.572 40.000 10.84 5.51 0.00 3.02
118 119 4.995124 AGTCGATATAACGCACTTTCAGT 58.005 39.130 0.00 0.00 0.00 3.41
141 142 5.878669 GTCCGTCACCAATAATAAACTTCCT 59.121 40.000 0.00 0.00 0.00 3.36
172 173 2.777832 AAGCAACCTCAGTCCTCATC 57.222 50.000 0.00 0.00 0.00 2.92
204 205 1.755179 AAGGGTGAATCATTCGGCTG 58.245 50.000 0.00 0.00 0.00 4.85
206 207 1.134280 AGGGTGAATCATTCGGCTGAG 60.134 52.381 0.00 0.00 0.00 3.35
237 238 8.635765 ACTTGAAATAAGGTCTTAGAATGCAA 57.364 30.769 0.00 0.00 0.00 4.08
248 249 8.947115 AGGTCTTAGAATGCAAATACTTGTTAC 58.053 33.333 0.00 0.00 34.79 2.50
254 255 7.757526 AGAATGCAAATACTTGTTACGCAATA 58.242 30.769 0.00 0.00 36.36 1.90
259 260 7.110511 GCAAATACTTGTTACGCAATAAATGC 58.889 34.615 0.00 0.00 42.10 3.56
274 275 2.283145 AATGCATGCATACTCCCTCC 57.717 50.000 32.36 0.00 35.31 4.30
277 278 1.141657 TGCATGCATACTCCCTCCTTC 59.858 52.381 18.46 0.00 0.00 3.46
282 283 2.292521 TGCATACTCCCTCCTTCTCAGT 60.293 50.000 0.00 0.00 0.00 3.41
387 388 7.381789 TTTGCCTACACATAATATCCCACTA 57.618 36.000 0.00 0.00 0.00 2.74
390 399 8.673456 TGCCTACACATAATATCCCACTATAA 57.327 34.615 0.00 0.00 0.00 0.98
419 428 5.177511 TGTTTTATTCTCGTTGCTCTGTCAG 59.822 40.000 0.00 0.00 0.00 3.51
433 442 4.212214 GCTCTGTCAGAAAAACAACGATCT 59.788 41.667 3.67 0.00 0.00 2.75
434 443 5.405571 GCTCTGTCAGAAAAACAACGATCTA 59.594 40.000 3.67 0.00 0.00 1.98
435 444 6.091441 GCTCTGTCAGAAAAACAACGATCTAT 59.909 38.462 3.67 0.00 0.00 1.98
436 445 7.275779 GCTCTGTCAGAAAAACAACGATCTATA 59.724 37.037 3.67 0.00 0.00 1.31
489 498 9.952188 GCTACAGTTATTTTGAAGAAAGAAAGT 57.048 29.630 0.00 0.00 0.00 2.66
505 514 8.270744 AGAAAGAAAGTATGAACATAGGCAGAT 58.729 33.333 0.00 0.00 0.00 2.90
542 551 1.508256 ACAAGTATCAGCCTACCCCC 58.492 55.000 0.00 0.00 0.00 5.40
544 553 2.057922 CAAGTATCAGCCTACCCCCAT 58.942 52.381 0.00 0.00 0.00 4.00
545 554 2.031495 AGTATCAGCCTACCCCCATC 57.969 55.000 0.00 0.00 0.00 3.51
722 731 0.394352 GCTGCTTAGCTTTGCCCCTA 60.394 55.000 5.60 0.00 0.00 3.53
766 776 4.530857 GGCCCCTCGTGTGGATCG 62.531 72.222 0.00 0.00 0.00 3.69
802 823 8.081517 AGAAATTGCAAAGGATGATCCATTTA 57.918 30.769 14.90 0.00 39.61 1.40
803 824 7.983484 AGAAATTGCAAAGGATGATCCATTTAC 59.017 33.333 14.90 6.90 39.61 2.01
806 827 6.602410 TGCAAAGGATGATCCATTTACAAA 57.398 33.333 14.90 0.00 39.61 2.83
807 828 6.632909 TGCAAAGGATGATCCATTTACAAAG 58.367 36.000 14.90 0.00 39.61 2.77
809 830 5.859205 AAGGATGATCCATTTACAAAGCC 57.141 39.130 14.90 0.00 39.61 4.35
810 831 4.870636 AGGATGATCCATTTACAAAGCCA 58.129 39.130 14.90 0.00 39.61 4.75
812 833 4.202151 GGATGATCCATTTACAAAGCCACC 60.202 45.833 6.60 0.00 36.28 4.61
813 834 2.752354 TGATCCATTTACAAAGCCACCG 59.248 45.455 0.00 0.00 0.00 4.94
814 835 2.570415 TCCATTTACAAAGCCACCGA 57.430 45.000 0.00 0.00 0.00 4.69
815 836 3.080300 TCCATTTACAAAGCCACCGAT 57.920 42.857 0.00 0.00 0.00 4.18
835 860 4.268644 CGATGCTACCATACAAGACAACAG 59.731 45.833 0.00 0.00 0.00 3.16
1084 1128 1.043116 CCTGGGTCGCCTAGTGATCA 61.043 60.000 8.09 0.00 29.60 2.92
1119 1163 2.452813 CCTCGACGCGGGTTTCATG 61.453 63.158 12.47 0.00 0.00 3.07
1259 1309 4.735132 CGACATGGACACCGCCGT 62.735 66.667 0.00 0.00 0.00 5.68
1321 1377 2.424474 CAGATCTCCTCTGTCCGGG 58.576 63.158 0.00 0.00 45.42 5.73
1618 1695 2.919856 AGAGCACCTGCACCGAGT 60.920 61.111 0.00 0.00 45.16 4.18
1633 1710 1.598130 GAGTTGAGGCGCTTGGTGT 60.598 57.895 7.64 0.00 0.00 4.16
2180 2335 3.079578 CAGAAGCATCTGCCTTTGAAGA 58.920 45.455 5.94 0.00 46.11 2.87
2215 2570 4.527509 AACTGTCTGTTCATCGATCACT 57.472 40.909 0.00 0.00 32.63 3.41
2216 2571 4.103365 ACTGTCTGTTCATCGATCACTC 57.897 45.455 0.00 0.00 0.00 3.51
2217 2572 3.507622 ACTGTCTGTTCATCGATCACTCA 59.492 43.478 0.00 0.00 0.00 3.41
2218 2573 3.838120 TGTCTGTTCATCGATCACTCAC 58.162 45.455 0.00 0.00 0.00 3.51
2263 2621 4.883585 TCTTCTCATTTGCACTTCACAGTT 59.116 37.500 0.00 0.00 0.00 3.16
2264 2622 6.054941 TCTTCTCATTTGCACTTCACAGTTA 58.945 36.000 0.00 0.00 0.00 2.24
2265 2623 5.929697 TCTCATTTGCACTTCACAGTTAG 57.070 39.130 0.00 0.00 0.00 2.34
2267 2625 5.698089 TCTCATTTGCACTTCACAGTTAGAG 59.302 40.000 0.00 0.00 0.00 2.43
2303 2977 9.713713 TGTATTTGTGCATAACAGTTAGAGTAA 57.286 29.630 0.00 0.00 40.74 2.24
2343 3017 6.681729 TTTGTAACCTGTACTCATCTTCCT 57.318 37.500 0.00 0.00 0.00 3.36
2344 3018 7.786046 TTTGTAACCTGTACTCATCTTCCTA 57.214 36.000 0.00 0.00 0.00 2.94
2346 3020 7.406031 TGTAACCTGTACTCATCTTCCTAAG 57.594 40.000 0.00 0.00 0.00 2.18
2347 3021 7.179966 TGTAACCTGTACTCATCTTCCTAAGA 58.820 38.462 0.00 0.00 42.69 2.10
2349 3023 6.969993 ACCTGTACTCATCTTCCTAAGATC 57.030 41.667 0.00 0.00 46.20 2.75
2351 3025 6.074648 CCTGTACTCATCTTCCTAAGATCCT 58.925 44.000 0.00 0.00 46.20 3.24
2357 3071 5.280499 TCATCTTCCTAAGATCCTTCACCA 58.720 41.667 0.00 0.00 46.20 4.17
2368 3102 5.178797 AGATCCTTCACCAAGTATGTTTCG 58.821 41.667 0.00 0.00 0.00 3.46
2389 3440 9.590088 GTTTCGTACTCGACTTCATTTAATTTT 57.410 29.630 0.00 0.00 46.03 1.82
2448 3499 6.813152 CCCACCTGAACTTAATTGCTTAATTG 59.187 38.462 0.00 0.00 0.00 2.32
2467 4619 2.101783 TGTCATGCACAATCAATCCCC 58.898 47.619 0.00 0.00 29.30 4.81
2627 5047 7.406916 TGAAGTTAGGCCAATAATCCTAAACA 58.593 34.615 5.01 2.45 44.03 2.83
2634 5054 5.411669 GGCCAATAATCCTAAACATACGGAG 59.588 44.000 0.00 0.00 0.00 4.63
2714 5134 2.346803 TGACTTTCGCTATGGTTCTGC 58.653 47.619 0.00 0.00 0.00 4.26
2726 5146 2.270858 TGGTTCTGCCACTAACCCATA 58.729 47.619 0.00 0.00 43.78 2.74
2774 5194 6.749923 AATCTCCTCTGCAACTAAAATGTC 57.250 37.500 0.00 0.00 0.00 3.06
2806 5227 6.758416 TGTAGCATTACTCTTTCTGCAGTATG 59.242 38.462 14.67 6.75 37.09 2.39
2984 5409 1.264020 GTGAGCAGCAACATTCAACGA 59.736 47.619 0.00 0.00 0.00 3.85
2998 5423 2.325082 AACGACCGCTTGACATGGC 61.325 57.895 0.00 0.00 0.00 4.40
3063 5488 3.568443 TGACACTACTACACCCACTTCA 58.432 45.455 0.00 0.00 0.00 3.02
3079 5504 4.895889 CCACTTCAGACCTGTCTATGGATA 59.104 45.833 0.00 0.00 37.98 2.59
3091 5516 7.147811 ACCTGTCTATGGATAAAGAGTTCACTC 60.148 40.741 0.00 0.00 43.17 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.126545 TGAAGAACTACTAGCAGCGGAATAA 59.873 40.000 0.00 0.00 0.00 1.40
3 4 4.643334 TGAAGAACTACTAGCAGCGGAATA 59.357 41.667 0.00 0.00 0.00 1.75
4 5 3.447586 TGAAGAACTACTAGCAGCGGAAT 59.552 43.478 0.00 0.00 0.00 3.01
5 6 2.823747 TGAAGAACTACTAGCAGCGGAA 59.176 45.455 0.00 0.00 0.00 4.30
6 7 2.443416 TGAAGAACTACTAGCAGCGGA 58.557 47.619 0.00 0.00 0.00 5.54
7 8 2.941453 TGAAGAACTACTAGCAGCGG 57.059 50.000 0.00 0.00 0.00 5.52
8 9 5.460419 CCTAAATGAAGAACTACTAGCAGCG 59.540 44.000 0.00 0.00 0.00 5.18
9 10 6.574350 TCCTAAATGAAGAACTACTAGCAGC 58.426 40.000 0.00 0.00 0.00 5.25
10 11 9.606631 AATTCCTAAATGAAGAACTACTAGCAG 57.393 33.333 0.00 0.00 0.00 4.24
11 12 9.959721 AAATTCCTAAATGAAGAACTACTAGCA 57.040 29.630 0.00 0.00 0.00 3.49
35 36 3.157087 GAGGAATTTGCTGGTGAGGAAA 58.843 45.455 0.00 0.00 42.94 3.13
36 37 2.108075 TGAGGAATTTGCTGGTGAGGAA 59.892 45.455 0.00 0.00 0.00 3.36
37 38 1.704628 TGAGGAATTTGCTGGTGAGGA 59.295 47.619 0.00 0.00 0.00 3.71
38 39 2.089980 CTGAGGAATTTGCTGGTGAGG 58.910 52.381 0.00 0.00 0.00 3.86
39 40 2.486982 CACTGAGGAATTTGCTGGTGAG 59.513 50.000 12.18 0.35 0.00 3.51
40 41 2.106338 TCACTGAGGAATTTGCTGGTGA 59.894 45.455 14.65 14.65 29.87 4.02
41 42 2.507484 TCACTGAGGAATTTGCTGGTG 58.493 47.619 11.64 11.64 0.00 4.17
42 43 2.957402 TCACTGAGGAATTTGCTGGT 57.043 45.000 0.00 0.00 0.00 4.00
43 44 3.415212 TCTTCACTGAGGAATTTGCTGG 58.585 45.455 0.00 0.00 0.00 4.85
44 45 5.640189 ATTCTTCACTGAGGAATTTGCTG 57.360 39.130 9.96 0.00 35.36 4.41
45 46 5.771666 TGAATTCTTCACTGAGGAATTTGCT 59.228 36.000 23.03 7.70 44.41 3.91
46 47 6.017400 TGAATTCTTCACTGAGGAATTTGC 57.983 37.500 23.03 15.08 44.41 3.68
52 53 8.668353 CGATTTTTATGAATTCTTCACTGAGGA 58.332 33.333 7.05 0.00 43.48 3.71
53 54 7.430502 GCGATTTTTATGAATTCTTCACTGAGG 59.569 37.037 7.05 0.00 43.48 3.86
54 55 7.430502 GGCGATTTTTATGAATTCTTCACTGAG 59.569 37.037 7.05 0.00 43.48 3.35
55 56 7.121168 AGGCGATTTTTATGAATTCTTCACTGA 59.879 33.333 7.05 0.00 43.48 3.41
56 57 7.253422 AGGCGATTTTTATGAATTCTTCACTG 58.747 34.615 7.05 0.00 43.48 3.66
57 58 7.396540 AGGCGATTTTTATGAATTCTTCACT 57.603 32.000 7.05 0.00 43.48 3.41
58 59 9.736023 AATAGGCGATTTTTATGAATTCTTCAC 57.264 29.630 7.05 0.00 43.48 3.18
59 60 9.950680 GAATAGGCGATTTTTATGAATTCTTCA 57.049 29.630 7.05 0.00 45.01 3.02
60 61 9.950680 TGAATAGGCGATTTTTATGAATTCTTC 57.049 29.630 7.05 0.00 0.00 2.87
61 62 9.736023 GTGAATAGGCGATTTTTATGAATTCTT 57.264 29.630 7.05 2.84 0.00 2.52
62 63 8.352942 GGTGAATAGGCGATTTTTATGAATTCT 58.647 33.333 7.05 0.00 0.00 2.40
63 64 7.595130 GGGTGAATAGGCGATTTTTATGAATTC 59.405 37.037 0.00 0.00 0.00 2.17
64 65 7.287696 AGGGTGAATAGGCGATTTTTATGAATT 59.712 33.333 0.00 0.00 0.00 2.17
65 66 6.777580 AGGGTGAATAGGCGATTTTTATGAAT 59.222 34.615 0.00 0.00 0.00 2.57
66 67 6.126409 AGGGTGAATAGGCGATTTTTATGAA 58.874 36.000 0.00 0.00 0.00 2.57
67 68 5.690865 AGGGTGAATAGGCGATTTTTATGA 58.309 37.500 0.00 0.00 0.00 2.15
68 69 5.048713 GGAGGGTGAATAGGCGATTTTTATG 60.049 44.000 0.00 0.00 0.00 1.90
69 70 5.070685 GGAGGGTGAATAGGCGATTTTTAT 58.929 41.667 0.00 0.00 0.00 1.40
70 71 4.165372 AGGAGGGTGAATAGGCGATTTTTA 59.835 41.667 0.00 0.00 0.00 1.52
71 72 3.053619 AGGAGGGTGAATAGGCGATTTTT 60.054 43.478 0.00 0.00 0.00 1.94
72 73 2.509964 AGGAGGGTGAATAGGCGATTTT 59.490 45.455 0.00 0.00 0.00 1.82
73 74 2.104963 GAGGAGGGTGAATAGGCGATTT 59.895 50.000 0.00 0.00 0.00 2.17
74 75 1.694696 GAGGAGGGTGAATAGGCGATT 59.305 52.381 0.00 0.00 0.00 3.34
75 76 1.133009 AGAGGAGGGTGAATAGGCGAT 60.133 52.381 0.00 0.00 0.00 4.58
76 77 0.261991 AGAGGAGGGTGAATAGGCGA 59.738 55.000 0.00 0.00 0.00 5.54
77 78 1.889829 CTAGAGGAGGGTGAATAGGCG 59.110 57.143 0.00 0.00 0.00 5.52
78 79 2.894765 GACTAGAGGAGGGTGAATAGGC 59.105 54.545 0.00 0.00 0.00 3.93
79 80 3.150767 CGACTAGAGGAGGGTGAATAGG 58.849 54.545 0.00 0.00 0.00 2.57
80 81 4.088056 TCGACTAGAGGAGGGTGAATAG 57.912 50.000 0.00 0.00 0.00 1.73
81 82 4.726035 ATCGACTAGAGGAGGGTGAATA 57.274 45.455 0.00 0.00 0.00 1.75
82 83 3.603965 ATCGACTAGAGGAGGGTGAAT 57.396 47.619 0.00 0.00 0.00 2.57
83 84 4.726035 ATATCGACTAGAGGAGGGTGAA 57.274 45.455 0.00 0.00 0.00 3.18
84 85 5.558818 GTTATATCGACTAGAGGAGGGTGA 58.441 45.833 0.00 0.00 0.00 4.02
85 86 4.392445 CGTTATATCGACTAGAGGAGGGTG 59.608 50.000 0.00 0.00 0.00 4.61
86 87 4.577875 CGTTATATCGACTAGAGGAGGGT 58.422 47.826 0.00 0.00 0.00 4.34
87 88 3.374678 GCGTTATATCGACTAGAGGAGGG 59.625 52.174 7.38 0.00 0.00 4.30
88 89 4.001652 TGCGTTATATCGACTAGAGGAGG 58.998 47.826 7.38 0.00 0.00 4.30
89 90 4.691685 AGTGCGTTATATCGACTAGAGGAG 59.308 45.833 7.38 0.00 0.00 3.69
90 91 4.639334 AGTGCGTTATATCGACTAGAGGA 58.361 43.478 7.38 0.00 0.00 3.71
91 92 5.359716 AAGTGCGTTATATCGACTAGAGG 57.640 43.478 7.38 0.00 0.00 3.69
92 93 6.427974 TGAAAGTGCGTTATATCGACTAGAG 58.572 40.000 7.38 0.00 0.00 2.43
93 94 6.367686 TGAAAGTGCGTTATATCGACTAGA 57.632 37.500 7.38 0.00 0.00 2.43
94 95 6.661982 CTGAAAGTGCGTTATATCGACTAG 57.338 41.667 7.38 0.00 0.00 2.57
111 112 6.978343 TTATTATTGGTGACGGACTGAAAG 57.022 37.500 0.00 0.00 42.29 2.62
112 113 6.938030 AGTTTATTATTGGTGACGGACTGAAA 59.062 34.615 0.00 0.00 0.00 2.69
113 114 6.469410 AGTTTATTATTGGTGACGGACTGAA 58.531 36.000 0.00 0.00 0.00 3.02
114 115 6.045072 AGTTTATTATTGGTGACGGACTGA 57.955 37.500 0.00 0.00 0.00 3.41
115 116 6.183360 GGAAGTTTATTATTGGTGACGGACTG 60.183 42.308 0.00 0.00 0.00 3.51
116 117 5.878669 GGAAGTTTATTATTGGTGACGGACT 59.121 40.000 0.00 0.00 0.00 3.85
117 118 5.878669 AGGAAGTTTATTATTGGTGACGGAC 59.121 40.000 0.00 0.00 0.00 4.79
118 119 6.057321 AGGAAGTTTATTATTGGTGACGGA 57.943 37.500 0.00 0.00 0.00 4.69
141 142 6.299141 ACTGAGGTTGCTTTCTTCAATAGAA 58.701 36.000 0.00 0.00 41.11 2.10
162 163 1.484240 GGAAGGGTCTGATGAGGACTG 59.516 57.143 0.00 0.00 34.47 3.51
188 189 0.659957 GCTCAGCCGAATGATTCACC 59.340 55.000 5.95 0.00 0.00 4.02
204 205 7.631717 AAGACCTTATTTCAAGTAATGGCTC 57.368 36.000 0.00 0.00 0.00 4.70
206 207 8.732746 TCTAAGACCTTATTTCAAGTAATGGC 57.267 34.615 0.00 0.00 0.00 4.40
254 255 2.176364 AGGAGGGAGTATGCATGCATTT 59.824 45.455 36.23 24.75 37.82 2.32
259 260 2.702478 TGAGAAGGAGGGAGTATGCATG 59.298 50.000 10.16 0.00 0.00 4.06
265 266 2.000803 TCCACTGAGAAGGAGGGAGTA 58.999 52.381 0.00 0.00 0.00 2.59
274 275 8.316946 TGGCTATATCAATTATCCACTGAGAAG 58.683 37.037 0.00 0.00 0.00 2.85
277 278 9.458727 AAATGGCTATATCAATTATCCACTGAG 57.541 33.333 0.00 0.00 0.00 3.35
330 331 4.403734 GGGTTTGGGTATTGAGAACTTGA 58.596 43.478 0.00 0.00 0.00 3.02
360 361 6.770785 GTGGGATATTATGTGTAGGCAAAAGA 59.229 38.462 0.00 0.00 0.00 2.52
365 366 8.673456 TTATAGTGGGATATTATGTGTAGGCA 57.327 34.615 0.00 0.00 0.00 4.75
390 399 7.920682 ACAGAGCAACGAGAATAAAACAAAATT 59.079 29.630 0.00 0.00 0.00 1.82
407 416 3.786048 CGTTGTTTTTCTGACAGAGCAAC 59.214 43.478 21.32 21.32 33.74 4.17
462 471 9.107367 CTTTCTTTCTTCAAAATAACTGTAGCG 57.893 33.333 0.00 0.00 0.00 4.26
489 498 7.012327 GTGCTTACAAATCTGCCTATGTTCATA 59.988 37.037 0.00 0.00 0.00 2.15
505 514 6.995511 ACTTGTAAACTCAGTGCTTACAAA 57.004 33.333 13.44 2.23 42.79 2.83
610 619 8.825745 TCATCACCAAAAATTAAAGAACAAAGC 58.174 29.630 0.00 0.00 0.00 3.51
722 731 2.175715 AGGCTGAAGAAGTCAAACCCTT 59.824 45.455 0.00 0.00 35.22 3.95
766 776 2.014594 CAATTTCTAGCCGCCGTCC 58.985 57.895 0.00 0.00 0.00 4.79
802 823 0.676782 GGTAGCATCGGTGGCTTTGT 60.677 55.000 0.00 0.00 42.62 2.83
803 824 0.676466 TGGTAGCATCGGTGGCTTTG 60.676 55.000 0.00 0.00 42.62 2.77
806 827 0.393077 GTATGGTAGCATCGGTGGCT 59.607 55.000 11.40 0.00 45.18 4.75
807 828 0.105964 TGTATGGTAGCATCGGTGGC 59.894 55.000 11.40 0.00 0.00 5.01
809 830 3.123804 GTCTTGTATGGTAGCATCGGTG 58.876 50.000 11.40 0.00 0.00 4.94
810 831 2.764010 TGTCTTGTATGGTAGCATCGGT 59.236 45.455 11.40 0.00 0.00 4.69
812 833 4.180817 TGTTGTCTTGTATGGTAGCATCG 58.819 43.478 11.40 0.00 0.00 3.84
813 834 4.572389 CCTGTTGTCTTGTATGGTAGCATC 59.428 45.833 11.40 4.21 0.00 3.91
814 835 4.225042 TCCTGTTGTCTTGTATGGTAGCAT 59.775 41.667 12.78 12.78 0.00 3.79
815 836 3.580895 TCCTGTTGTCTTGTATGGTAGCA 59.419 43.478 0.00 0.00 0.00 3.49
835 860 1.379776 ACCCCCTTTTCCTAGGTTCC 58.620 55.000 9.08 0.00 33.17 3.62
980 1024 2.506217 CTGGCTACGAGCGCGAAA 60.506 61.111 19.05 2.92 43.62 3.46
1074 1118 1.539065 GCGTGGACCATGATCACTAGG 60.539 57.143 18.32 3.08 0.00 3.02
1084 1128 4.778143 GAAGGCGGCGTGGACCAT 62.778 66.667 9.37 0.00 0.00 3.55
1113 1157 2.745884 CGGCGAGGCACCATGAAA 60.746 61.111 0.00 0.00 0.00 2.69
1321 1377 3.357079 CACCAAGTGCGGGCTGAC 61.357 66.667 0.00 0.00 0.00 3.51
1371 1433 2.202932 CCGTTCAGATGGCCCGAG 60.203 66.667 0.00 0.00 0.00 4.63
1618 1695 2.281484 GGACACCAAGCGCCTCAA 60.281 61.111 2.29 0.00 0.00 3.02
1732 1809 1.375523 GCAGGTCGTCGTGGGAATT 60.376 57.895 4.63 0.00 0.00 2.17
1812 1895 6.052405 ACGAGGATAGGAGTAGAACGATAT 57.948 41.667 0.00 0.00 0.00 1.63
1813 1896 5.011431 TGACGAGGATAGGAGTAGAACGATA 59.989 44.000 0.00 0.00 0.00 2.92
1819 1905 4.322574 CCGTATGACGAGGATAGGAGTAGA 60.323 50.000 0.00 0.00 46.05 2.59
1985 2104 2.638330 TATCGCCAGCGCCTTACCAC 62.638 60.000 2.29 0.00 39.59 4.16
2180 2335 2.169352 AGACAGTTCAGTTCAGTGTGCT 59.831 45.455 0.00 0.00 0.00 4.40
2263 2621 5.390461 GCACAAATACATTGCACGAACTCTA 60.390 40.000 0.00 0.00 43.13 2.43
2264 2622 4.613622 GCACAAATACATTGCACGAACTCT 60.614 41.667 0.00 0.00 43.13 3.24
2265 2623 3.603770 GCACAAATACATTGCACGAACTC 59.396 43.478 0.00 0.00 43.13 3.01
2267 2625 3.304257 TGCACAAATACATTGCACGAAC 58.696 40.909 0.00 0.00 41.29 3.95
2343 3017 6.816640 CGAAACATACTTGGTGAAGGATCTTA 59.183 38.462 0.00 0.00 29.23 2.10
2344 3018 5.643777 CGAAACATACTTGGTGAAGGATCTT 59.356 40.000 0.00 0.00 29.23 2.40
2346 3020 4.935808 ACGAAACATACTTGGTGAAGGATC 59.064 41.667 0.00 0.00 29.23 3.36
2347 3021 4.906618 ACGAAACATACTTGGTGAAGGAT 58.093 39.130 0.00 0.00 32.30 3.24
2348 3022 4.345859 ACGAAACATACTTGGTGAAGGA 57.654 40.909 0.00 0.00 32.95 3.36
2349 3023 5.235516 AGTACGAAACATACTTGGTGAAGG 58.764 41.667 0.00 0.00 32.95 3.46
2351 3025 4.919168 CGAGTACGAAACATACTTGGTGAA 59.081 41.667 0.00 0.00 42.66 3.18
2368 3102 8.718734 ACAGGAAAATTAAATGAAGTCGAGTAC 58.281 33.333 0.00 0.00 0.00 2.73
2389 3440 3.211045 GTTGCCTTTTCACACTACAGGA 58.789 45.455 0.00 0.00 0.00 3.86
2448 3499 2.381911 AGGGGATTGATTGTGCATGAC 58.618 47.619 0.00 0.00 0.00 3.06
2627 5047 6.105397 TGTCTTTAACCACTTTCTCCGTAT 57.895 37.500 0.00 0.00 0.00 3.06
2634 5054 6.713450 TCATAACCCTGTCTTTAACCACTTTC 59.287 38.462 0.00 0.00 0.00 2.62
2726 5146 3.320879 CTGGTGTGGCGCCATCTCT 62.321 63.158 35.23 0.00 43.46 3.10
2774 5194 6.638873 CAGAAAGAGTAATGCTACAGATACGG 59.361 42.308 0.00 0.00 0.00 4.02
2806 5227 9.869844 GTCAAGTACTATTCACATTAATCATGC 57.130 33.333 0.00 0.00 36.14 4.06
2814 5235 8.157476 AGGAAAGTGTCAAGTACTATTCACATT 58.843 33.333 19.16 15.42 0.00 2.71
2922 5347 6.251376 GTGAGTTTGCTAGTTCAAAAGTTGTG 59.749 38.462 0.00 0.00 37.65 3.33
2984 5409 0.957395 CTTCTGCCATGTCAAGCGGT 60.957 55.000 6.87 0.00 36.71 5.68
2998 5423 6.254373 GCTTGTTTTTCTTCAGTTTCCTTCTG 59.746 38.462 0.00 0.00 0.00 3.02
3063 5488 6.897966 TGAACTCTTTATCCATAGACAGGTCT 59.102 38.462 7.18 7.18 43.40 3.85
3079 5504 6.214399 CCTTAGTACAACGAGTGAACTCTTT 58.786 40.000 8.73 2.86 40.75 2.52


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

AutoCloner maintained by Alex Coulton.