Multiple sequence alignment - TraesCS1B01G135300

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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 TraesCS1B01G135300 chr1B 100.000 2465 0 0 1 2465 172256067 172258531 0.000000e+00 4553
1 TraesCS1B01G135300 chr1B 91.729 798 57 8 1668 2464 142120554 142119765 0.000000e+00 1099
2 TraesCS1B01G135300 chr1A 93.786 1400 59 13 288 1672 119739099 119740485 0.000000e+00 2078
3 TraesCS1B01G135300 chr1A 94.737 114 3 2 150 260 119739008 119739121 9.060000e-40 174
4 TraesCS1B01G135300 chr1D 91.721 1389 61 21 307 1672 112632873 112634230 0.000000e+00 1879
5 TraesCS1B01G135300 chr1D 90.977 133 11 1 129 260 112632738 112632870 7.000000e-41 178
6 TraesCS1B01G135300 chr2B 93.687 792 41 7 1674 2464 465806894 465807677 0.000000e+00 1177
7 TraesCS1B01G135300 chr2B 92.172 792 51 6 1674 2464 69120876 69121657 0.000000e+00 1109
8 TraesCS1B01G135300 chr2B 91.677 793 58 4 1673 2464 200223161 200223946 0.000000e+00 1092
9 TraesCS1B01G135300 chr2B 91.572 795 55 7 1672 2464 275723600 275722816 0.000000e+00 1086
10 TraesCS1B01G135300 chr5B 91.824 795 55 7 1671 2464 540908822 540909607 0.000000e+00 1099
11 TraesCS1B01G135300 chr5B 91.824 795 52 7 1673 2464 596922574 596923358 0.000000e+00 1096
12 TraesCS1B01G135300 chr5B 91.667 792 53 8 1675 2464 533753118 533753898 0.000000e+00 1085
13 TraesCS1B01G135300 chr5B 95.789 95 4 0 152 246 136410543 136410449 1.180000e-33 154
14 TraesCS1B01G135300 chr3B 91.793 792 56 4 1674 2464 39355047 39355830 0.000000e+00 1094
15 TraesCS1B01G135300 chr3B 77.500 360 63 11 1036 1392 140131615 140131271 1.490000e-47 200
16 TraesCS1B01G135300 chr3A 78.212 358 64 8 1036 1392 106835063 106834719 1.480000e-52 217
17 TraesCS1B01G135300 chr3D 77.933 358 65 8 1036 1392 90743045 90742701 6.910000e-51 211
18 TraesCS1B01G135300 chr3D 91.743 109 7 2 155 261 90781706 90781598 1.530000e-32 150
19 TraesCS1B01G135300 chr5D 95.192 104 1 4 152 253 123451914 123451813 7.050000e-36 161
20 TraesCS1B01G135300 chr5A 94.393 107 2 4 152 256 136393719 136393615 7.050000e-36 161
21 TraesCS1B01G135300 chr7A 96.842 95 1 2 154 248 731255826 731255734 9.130000e-35 158
22 TraesCS1B01G135300 chr6A 94.059 101 3 3 153 252 146548511 146548609 1.530000e-32 150
23 TraesCS1B01G135300 chr6B 97.674 86 2 0 153 238 720559461 720559376 5.490000e-32 148


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 TraesCS1B01G135300 chr1B 172256067 172258531 2464 False 4553.0 4553 100.0000 1 2465 1 chr1B.!!$F1 2464
1 TraesCS1B01G135300 chr1B 142119765 142120554 789 True 1099.0 1099 91.7290 1668 2464 1 chr1B.!!$R1 796
2 TraesCS1B01G135300 chr1A 119739008 119740485 1477 False 1126.0 2078 94.2615 150 1672 2 chr1A.!!$F1 1522
3 TraesCS1B01G135300 chr1D 112632738 112634230 1492 False 1028.5 1879 91.3490 129 1672 2 chr1D.!!$F1 1543
4 TraesCS1B01G135300 chr2B 465806894 465807677 783 False 1177.0 1177 93.6870 1674 2464 1 chr2B.!!$F3 790
5 TraesCS1B01G135300 chr2B 69120876 69121657 781 False 1109.0 1109 92.1720 1674 2464 1 chr2B.!!$F1 790
6 TraesCS1B01G135300 chr2B 200223161 200223946 785 False 1092.0 1092 91.6770 1673 2464 1 chr2B.!!$F2 791
7 TraesCS1B01G135300 chr2B 275722816 275723600 784 True 1086.0 1086 91.5720 1672 2464 1 chr2B.!!$R1 792
8 TraesCS1B01G135300 chr5B 540908822 540909607 785 False 1099.0 1099 91.8240 1671 2464 1 chr5B.!!$F2 793
9 TraesCS1B01G135300 chr5B 596922574 596923358 784 False 1096.0 1096 91.8240 1673 2464 1 chr5B.!!$F3 791
10 TraesCS1B01G135300 chr5B 533753118 533753898 780 False 1085.0 1085 91.6670 1675 2464 1 chr5B.!!$F1 789
11 TraesCS1B01G135300 chr3B 39355047 39355830 783 False 1094.0 1094 91.7930 1674 2464 1 chr3B.!!$F1 790

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
106 107 0.044092 TTGGAGTAGGGGAGGATGCA 59.956 55.0 0.0 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 1797 0.109597 GCCTGCTGGTTTCGTTCATG 60.11 55.0 11.69 0.0 35.27 3.07 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
37 38 7.832503 ATATTGCCAACTTAGCATGAAAAAC 57.167 32.000 0.00 0.00 40.59 2.43
38 39 3.988819 TGCCAACTTAGCATGAAAAACC 58.011 40.909 0.00 0.00 34.69 3.27
39 40 3.386078 TGCCAACTTAGCATGAAAAACCA 59.614 39.130 0.00 0.00 34.69 3.67
40 41 4.141846 TGCCAACTTAGCATGAAAAACCAA 60.142 37.500 0.00 0.00 34.69 3.67
41 42 4.996758 GCCAACTTAGCATGAAAAACCAAT 59.003 37.500 0.00 0.00 0.00 3.16
42 43 5.469760 GCCAACTTAGCATGAAAAACCAATT 59.530 36.000 0.00 0.00 0.00 2.32
43 44 6.347644 GCCAACTTAGCATGAAAAACCAATTC 60.348 38.462 0.00 0.00 0.00 2.17
44 45 6.705381 CCAACTTAGCATGAAAAACCAATTCA 59.295 34.615 0.00 0.00 40.76 2.57
45 46 7.226325 CCAACTTAGCATGAAAAACCAATTCAA 59.774 33.333 0.00 0.00 39.98 2.69
46 47 7.951530 ACTTAGCATGAAAAACCAATTCAAG 57.048 32.000 0.00 0.00 39.98 3.02
47 48 7.725251 ACTTAGCATGAAAAACCAATTCAAGA 58.275 30.769 0.00 0.00 39.98 3.02
48 49 8.203485 ACTTAGCATGAAAAACCAATTCAAGAA 58.797 29.630 0.00 0.00 39.98 2.52
49 50 8.954950 TTAGCATGAAAAACCAATTCAAGAAA 57.045 26.923 0.00 0.00 39.98 2.52
50 51 7.862512 AGCATGAAAAACCAATTCAAGAAAA 57.137 28.000 0.00 0.00 39.98 2.29
51 52 7.922837 AGCATGAAAAACCAATTCAAGAAAAG 58.077 30.769 0.00 0.00 39.98 2.27
52 53 6.634035 GCATGAAAAACCAATTCAAGAAAAGC 59.366 34.615 0.00 0.00 39.98 3.51
53 54 7.679164 GCATGAAAAACCAATTCAAGAAAAGCA 60.679 33.333 0.00 0.00 39.98 3.91
54 55 7.678947 TGAAAAACCAATTCAAGAAAAGCAA 57.321 28.000 0.00 0.00 34.04 3.91
55 56 8.278729 TGAAAAACCAATTCAAGAAAAGCAAT 57.721 26.923 0.00 0.00 34.04 3.56
56 57 9.388506 TGAAAAACCAATTCAAGAAAAGCAATA 57.611 25.926 0.00 0.00 34.04 1.90
57 58 9.868389 GAAAAACCAATTCAAGAAAAGCAATAG 57.132 29.630 0.00 0.00 0.00 1.73
58 59 7.967890 AAACCAATTCAAGAAAAGCAATAGG 57.032 32.000 0.00 0.00 0.00 2.57
59 60 6.916360 ACCAATTCAAGAAAAGCAATAGGA 57.084 33.333 0.00 0.00 0.00 2.94
60 61 7.486407 ACCAATTCAAGAAAAGCAATAGGAT 57.514 32.000 0.00 0.00 0.00 3.24
61 62 7.910584 ACCAATTCAAGAAAAGCAATAGGATT 58.089 30.769 0.00 0.00 0.00 3.01
62 63 7.820872 ACCAATTCAAGAAAAGCAATAGGATTG 59.179 33.333 0.00 0.00 0.00 2.67
63 64 8.036575 CCAATTCAAGAAAAGCAATAGGATTGA 58.963 33.333 3.38 0.00 0.00 2.57
64 65 9.595823 CAATTCAAGAAAAGCAATAGGATTGAT 57.404 29.630 3.38 0.00 0.00 2.57
68 69 8.397906 TCAAGAAAAGCAATAGGATTGATAACG 58.602 33.333 3.38 0.00 0.00 3.18
69 70 7.264373 AGAAAAGCAATAGGATTGATAACGG 57.736 36.000 3.38 0.00 0.00 4.44
70 71 7.054124 AGAAAAGCAATAGGATTGATAACGGA 58.946 34.615 3.38 0.00 0.00 4.69
71 72 6.867662 AAAGCAATAGGATTGATAACGGAG 57.132 37.500 3.38 0.00 0.00 4.63
72 73 4.899502 AGCAATAGGATTGATAACGGAGG 58.100 43.478 3.38 0.00 0.00 4.30
73 74 4.593206 AGCAATAGGATTGATAACGGAGGA 59.407 41.667 3.38 0.00 0.00 3.71
74 75 5.249393 AGCAATAGGATTGATAACGGAGGAT 59.751 40.000 3.38 0.00 0.00 3.24
75 76 5.940470 GCAATAGGATTGATAACGGAGGATT 59.060 40.000 3.38 0.00 0.00 3.01
76 77 6.092807 GCAATAGGATTGATAACGGAGGATTC 59.907 42.308 3.38 0.00 0.00 2.52
77 78 6.935240 ATAGGATTGATAACGGAGGATTCA 57.065 37.500 0.00 0.00 0.00 2.57
78 79 5.832539 AGGATTGATAACGGAGGATTCAT 57.167 39.130 0.00 0.00 0.00 2.57
79 80 6.192970 AGGATTGATAACGGAGGATTCATT 57.807 37.500 0.00 0.00 0.00 2.57
80 81 6.234177 AGGATTGATAACGGAGGATTCATTC 58.766 40.000 0.00 0.00 0.00 2.67
81 82 5.997746 GGATTGATAACGGAGGATTCATTCA 59.002 40.000 0.00 0.00 0.00 2.57
82 83 6.073003 GGATTGATAACGGAGGATTCATTCAC 60.073 42.308 0.00 0.00 0.00 3.18
83 84 5.351948 TGATAACGGAGGATTCATTCACA 57.648 39.130 0.00 0.00 0.00 3.58
84 85 5.116180 TGATAACGGAGGATTCATTCACAC 58.884 41.667 0.00 0.00 0.00 3.82
85 86 2.403252 ACGGAGGATTCATTCACACC 57.597 50.000 0.00 0.00 0.00 4.16
86 87 1.065418 ACGGAGGATTCATTCACACCC 60.065 52.381 0.00 0.00 0.00 4.61
87 88 1.210478 CGGAGGATTCATTCACACCCT 59.790 52.381 0.00 0.00 0.00 4.34
88 89 2.356125 CGGAGGATTCATTCACACCCTT 60.356 50.000 0.00 0.00 0.00 3.95
89 90 3.019564 GGAGGATTCATTCACACCCTTG 58.980 50.000 0.00 0.00 0.00 3.61
90 91 3.019564 GAGGATTCATTCACACCCTTGG 58.980 50.000 0.00 0.00 0.00 3.61
91 92 2.649312 AGGATTCATTCACACCCTTGGA 59.351 45.455 0.00 0.00 0.00 3.53
92 93 3.019564 GGATTCATTCACACCCTTGGAG 58.980 50.000 0.00 0.00 0.00 3.86
93 94 3.562176 GGATTCATTCACACCCTTGGAGT 60.562 47.826 0.00 0.00 0.00 3.85
94 95 4.324254 GGATTCATTCACACCCTTGGAGTA 60.324 45.833 0.00 0.00 0.00 2.59
95 96 3.981071 TCATTCACACCCTTGGAGTAG 57.019 47.619 0.00 0.00 0.00 2.57
96 97 2.571653 TCATTCACACCCTTGGAGTAGG 59.428 50.000 0.00 0.00 34.92 3.18
103 104 3.979313 CCTTGGAGTAGGGGAGGAT 57.021 57.895 0.00 0.00 0.00 3.24
104 105 1.428869 CCTTGGAGTAGGGGAGGATG 58.571 60.000 0.00 0.00 0.00 3.51
105 106 0.761802 CTTGGAGTAGGGGAGGATGC 59.238 60.000 0.00 0.00 0.00 3.91
106 107 0.044092 TTGGAGTAGGGGAGGATGCA 59.956 55.000 0.00 0.00 0.00 3.96
107 108 0.268869 TGGAGTAGGGGAGGATGCAT 59.731 55.000 0.00 0.00 0.00 3.96
108 109 1.345422 TGGAGTAGGGGAGGATGCATT 60.345 52.381 0.00 0.00 0.00 3.56
109 110 1.349357 GGAGTAGGGGAGGATGCATTC 59.651 57.143 0.00 0.00 0.00 2.67
110 111 2.050144 GAGTAGGGGAGGATGCATTCA 58.950 52.381 7.96 0.00 0.00 2.57
111 112 2.439507 GAGTAGGGGAGGATGCATTCAA 59.560 50.000 7.96 0.00 0.00 2.69
112 113 3.059097 AGTAGGGGAGGATGCATTCAAT 58.941 45.455 7.96 0.00 0.00 2.57
113 114 4.242811 AGTAGGGGAGGATGCATTCAATA 58.757 43.478 7.96 0.00 0.00 1.90
114 115 4.665009 AGTAGGGGAGGATGCATTCAATAA 59.335 41.667 7.96 0.00 0.00 1.40
115 116 3.837355 AGGGGAGGATGCATTCAATAAC 58.163 45.455 7.96 0.00 0.00 1.89
116 117 2.554032 GGGGAGGATGCATTCAATAACG 59.446 50.000 7.96 0.00 0.00 3.18
117 118 3.214328 GGGAGGATGCATTCAATAACGT 58.786 45.455 7.96 0.00 0.00 3.99
118 119 4.385825 GGGAGGATGCATTCAATAACGTA 58.614 43.478 7.96 0.00 0.00 3.57
119 120 5.003804 GGGAGGATGCATTCAATAACGTAT 58.996 41.667 7.96 0.00 0.00 3.06
120 121 5.473504 GGGAGGATGCATTCAATAACGTATT 59.526 40.000 7.96 0.00 0.00 1.89
121 122 6.653320 GGGAGGATGCATTCAATAACGTATTA 59.347 38.462 7.96 0.00 0.00 0.98
122 123 7.336931 GGGAGGATGCATTCAATAACGTATTAT 59.663 37.037 7.96 0.00 32.01 1.28
123 124 8.177663 GGAGGATGCATTCAATAACGTATTATG 58.822 37.037 7.96 0.00 31.07 1.90
124 125 8.621532 AGGATGCATTCAATAACGTATTATGT 57.378 30.769 7.96 0.00 31.07 2.29
125 126 9.066892 AGGATGCATTCAATAACGTATTATGTT 57.933 29.630 7.96 6.53 31.07 2.71
126 127 9.329913 GGATGCATTCAATAACGTATTATGTTC 57.670 33.333 0.00 0.00 31.07 3.18
233 235 1.824230 CAATTCTCGGAATGCCCCAAA 59.176 47.619 0.70 0.00 0.00 3.28
267 269 5.878406 TTTTGTTTCCTCTCTGACTCTCT 57.122 39.130 0.00 0.00 0.00 3.10
268 270 5.461032 TTTGTTTCCTCTCTGACTCTCTC 57.539 43.478 0.00 0.00 0.00 3.20
269 271 4.380843 TGTTTCCTCTCTGACTCTCTCT 57.619 45.455 0.00 0.00 0.00 3.10
270 272 4.331968 TGTTTCCTCTCTGACTCTCTCTC 58.668 47.826 0.00 0.00 0.00 3.20
271 273 4.042809 TGTTTCCTCTCTGACTCTCTCTCT 59.957 45.833 0.00 0.00 0.00 3.10
272 274 4.487714 TTCCTCTCTGACTCTCTCTCTC 57.512 50.000 0.00 0.00 0.00 3.20
273 275 3.724478 TCCTCTCTGACTCTCTCTCTCT 58.276 50.000 0.00 0.00 0.00 3.10
274 276 3.706594 TCCTCTCTGACTCTCTCTCTCTC 59.293 52.174 0.00 0.00 0.00 3.20
275 277 3.708631 CCTCTCTGACTCTCTCTCTCTCT 59.291 52.174 0.00 0.00 0.00 3.10
276 278 4.202202 CCTCTCTGACTCTCTCTCTCTCTC 60.202 54.167 0.00 0.00 0.00 3.20
277 279 4.614475 TCTCTGACTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
278 280 4.646945 TCTCTGACTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
279 281 4.614475 TCTGACTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
280 282 4.646945 TCTGACTCTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
281 283 4.614475 TGACTCTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
282 284 4.646945 TGACTCTCTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
283 285 4.877773 ACTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
284 286 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
285 287 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
286 288 2.959030 TCTCTCTCTCTCTCTCTCTCCG 59.041 54.545 0.00 0.00 0.00 4.63
324 326 6.765989 TGAACTTCTTTCTCTCCGATTTGAAA 59.234 34.615 0.00 0.00 34.97 2.69
383 391 4.755266 TTTGAGAACCATCTACCTAGCC 57.245 45.455 0.00 0.00 35.54 3.93
394 402 5.540337 CCATCTACCTAGCCTCTGTTTCATA 59.460 44.000 0.00 0.00 0.00 2.15
513 529 0.591659 CTGACTTCTGTCCGTCGACA 59.408 55.000 17.16 0.00 46.91 4.35
557 575 2.804931 CGAGCATGACGACACGCA 60.805 61.111 8.81 0.00 37.70 5.24
677 695 0.390860 CTCATCCCCATCTCGACACC 59.609 60.000 0.00 0.00 0.00 4.16
689 707 3.036084 GACACCGTGACACGCCAG 61.036 66.667 22.46 15.26 40.91 4.85
690 708 4.602259 ACACCGTGACACGCCAGG 62.602 66.667 22.46 11.15 40.91 4.45
742 760 2.321060 CGGCGCAATCACATCGAC 59.679 61.111 10.83 0.00 0.00 4.20
768 786 3.231736 CCGTCCCCCGTCCCATAG 61.232 72.222 0.00 0.00 33.66 2.23
914 937 4.446051 CACCGTGAGTTCTTCTTCTTCTTC 59.554 45.833 0.00 0.00 0.00 2.87
915 938 4.342665 ACCGTGAGTTCTTCTTCTTCTTCT 59.657 41.667 0.00 0.00 0.00 2.85
925 948 4.060038 TCTTCTTCTTCTTCTTGCACGT 57.940 40.909 0.00 0.00 0.00 4.49
929 952 0.529773 TCTTCTTCTTGCACGTGCGT 60.530 50.000 33.22 0.00 45.83 5.24
983 1018 2.125188 GACTGCTCTGCTCTGCCC 60.125 66.667 0.00 0.00 0.00 5.36
1477 1528 2.240500 GGCTAGCGCGACCTGATTG 61.241 63.158 12.10 0.00 36.88 2.67
1478 1529 1.226974 GCTAGCGCGACCTGATTGA 60.227 57.895 12.10 0.00 0.00 2.57
1479 1530 0.598680 GCTAGCGCGACCTGATTGAT 60.599 55.000 12.10 0.00 0.00 2.57
1480 1531 1.858091 CTAGCGCGACCTGATTGATT 58.142 50.000 12.10 0.00 0.00 2.57
1490 1541 3.034635 ACCTGATTGATTCGGCTCTACT 58.965 45.455 0.00 0.00 0.00 2.57
1606 1657 2.859165 TCCGAAATATGATGAGGCCC 57.141 50.000 0.00 0.00 0.00 5.80
1736 1787 2.734591 GACAGCGTCACAGACCCA 59.265 61.111 4.20 0.00 32.09 4.51
1746 1797 2.293399 GTCACAGACCCAAACATGAACC 59.707 50.000 0.00 0.00 0.00 3.62
1747 1798 2.092158 TCACAGACCCAAACATGAACCA 60.092 45.455 0.00 0.00 0.00 3.67
1748 1799 2.892852 CACAGACCCAAACATGAACCAT 59.107 45.455 0.00 0.00 0.00 3.55
1749 1800 2.892852 ACAGACCCAAACATGAACCATG 59.107 45.455 0.00 5.48 46.18 3.66
1750 1801 3.156293 CAGACCCAAACATGAACCATGA 58.844 45.455 13.22 0.00 43.81 3.07
1751 1802 3.573538 CAGACCCAAACATGAACCATGAA 59.426 43.478 13.22 0.00 43.81 2.57
1752 1803 3.573967 AGACCCAAACATGAACCATGAAC 59.426 43.478 13.22 0.00 43.81 3.18
1760 1811 3.253188 ACATGAACCATGAACGAAACCAG 59.747 43.478 13.22 0.00 43.81 4.00
1773 1824 1.000274 GAAACCAGCAGGCGAAACATT 60.000 47.619 0.00 0.00 39.06 2.71
1788 1839 3.634568 AACATTGCGAATTCACCGAAA 57.365 38.095 6.22 0.00 0.00 3.46
1894 1946 4.119442 ACCAAACTACGATAACAGCGAT 57.881 40.909 0.00 0.00 0.00 4.58
1939 1991 1.225704 CCAGAGATGTGGGAAGCCC 59.774 63.158 0.00 0.00 45.71 5.19
1978 2030 2.202236 GAGCAAGTCCAGGGCATCCA 62.202 60.000 0.00 0.00 34.83 3.41
2218 2270 3.025322 TCCAAGAAACCTGAAGCCAAA 57.975 42.857 0.00 0.00 0.00 3.28
2345 2401 1.800805 CGCTTGTGAATCTGGTCAGT 58.199 50.000 0.00 0.00 0.00 3.41
2394 2450 7.804600 GCTTGCCAAAGGAAAATTTTAATCTTG 59.195 33.333 2.75 5.66 33.68 3.02
2443 2499 3.456277 AGAAAATCTGCTCGAAGGGGTAT 59.544 43.478 0.00 0.00 0.00 2.73
2447 2503 0.249073 CTGCTCGAAGGGGTATCACG 60.249 60.000 0.00 0.00 0.00 4.35
2452 2508 2.488545 CTCGAAGGGGTATCACGGATAG 59.511 54.545 0.00 0.00 0.00 2.08
2464 2520 2.161030 CACGGATAGGCCTAGAGTACC 58.839 57.143 19.33 14.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.964303 TGCTAAGTTGGCAATATTATTATTGTG 57.036 29.630 11.96 0.00 44.37 3.33
11 12 9.364989 GTTTTTCATGCTAAGTTGGCAATATTA 57.635 29.630 18.38 5.50 43.14 0.98
12 13 7.334171 GGTTTTTCATGCTAAGTTGGCAATATT 59.666 33.333 18.38 4.51 43.14 1.28
13 14 6.818142 GGTTTTTCATGCTAAGTTGGCAATAT 59.182 34.615 18.38 0.00 43.14 1.28
14 15 6.162777 GGTTTTTCATGCTAAGTTGGCAATA 58.837 36.000 18.38 6.39 43.14 1.90
15 16 4.996758 GGTTTTTCATGCTAAGTTGGCAAT 59.003 37.500 18.38 4.33 43.14 3.56
16 17 4.141846 TGGTTTTTCATGCTAAGTTGGCAA 60.142 37.500 18.38 0.00 43.14 4.52
17 18 3.386078 TGGTTTTTCATGCTAAGTTGGCA 59.614 39.130 16.79 16.79 44.05 4.92
18 19 3.988819 TGGTTTTTCATGCTAAGTTGGC 58.011 40.909 3.92 3.92 0.00 4.52
19 20 6.705381 TGAATTGGTTTTTCATGCTAAGTTGG 59.295 34.615 0.00 0.00 0.00 3.77
20 21 7.712264 TGAATTGGTTTTTCATGCTAAGTTG 57.288 32.000 0.00 0.00 0.00 3.16
21 22 8.203485 TCTTGAATTGGTTTTTCATGCTAAGTT 58.797 29.630 0.00 0.00 33.37 2.66
22 23 7.725251 TCTTGAATTGGTTTTTCATGCTAAGT 58.275 30.769 0.00 0.00 33.37 2.24
23 24 8.592105 TTCTTGAATTGGTTTTTCATGCTAAG 57.408 30.769 0.00 0.00 33.37 2.18
24 25 8.954950 TTTCTTGAATTGGTTTTTCATGCTAA 57.045 26.923 0.00 0.00 33.37 3.09
25 26 8.954950 TTTTCTTGAATTGGTTTTTCATGCTA 57.045 26.923 0.00 0.00 33.37 3.49
26 27 7.467675 GCTTTTCTTGAATTGGTTTTTCATGCT 60.468 33.333 0.00 0.00 33.37 3.79
27 28 6.634035 GCTTTTCTTGAATTGGTTTTTCATGC 59.366 34.615 0.00 0.00 33.37 4.06
28 29 7.695820 TGCTTTTCTTGAATTGGTTTTTCATG 58.304 30.769 0.00 0.00 33.37 3.07
29 30 7.862512 TGCTTTTCTTGAATTGGTTTTTCAT 57.137 28.000 0.00 0.00 33.37 2.57
30 31 7.678947 TTGCTTTTCTTGAATTGGTTTTTCA 57.321 28.000 0.00 0.00 0.00 2.69
31 32 9.868389 CTATTGCTTTTCTTGAATTGGTTTTTC 57.132 29.630 0.00 0.00 0.00 2.29
32 33 8.839343 CCTATTGCTTTTCTTGAATTGGTTTTT 58.161 29.630 0.00 0.00 0.00 1.94
33 34 8.210265 TCCTATTGCTTTTCTTGAATTGGTTTT 58.790 29.630 0.00 0.00 0.00 2.43
34 35 7.734942 TCCTATTGCTTTTCTTGAATTGGTTT 58.265 30.769 0.00 0.00 0.00 3.27
35 36 7.301868 TCCTATTGCTTTTCTTGAATTGGTT 57.698 32.000 0.00 0.00 0.00 3.67
36 37 6.916360 TCCTATTGCTTTTCTTGAATTGGT 57.084 33.333 0.00 0.00 0.00 3.67
37 38 8.036575 TCAATCCTATTGCTTTTCTTGAATTGG 58.963 33.333 0.00 0.00 0.00 3.16
38 39 8.991243 TCAATCCTATTGCTTTTCTTGAATTG 57.009 30.769 0.00 0.00 0.00 2.32
42 43 8.397906 CGTTATCAATCCTATTGCTTTTCTTGA 58.602 33.333 0.00 0.00 0.00 3.02
43 44 7.645340 CCGTTATCAATCCTATTGCTTTTCTTG 59.355 37.037 0.00 0.00 0.00 3.02
44 45 7.556275 TCCGTTATCAATCCTATTGCTTTTCTT 59.444 33.333 0.00 0.00 0.00 2.52
45 46 7.054124 TCCGTTATCAATCCTATTGCTTTTCT 58.946 34.615 0.00 0.00 0.00 2.52
46 47 7.259290 TCCGTTATCAATCCTATTGCTTTTC 57.741 36.000 0.00 0.00 0.00 2.29
47 48 6.263168 CCTCCGTTATCAATCCTATTGCTTTT 59.737 38.462 0.00 0.00 0.00 2.27
48 49 5.765182 CCTCCGTTATCAATCCTATTGCTTT 59.235 40.000 0.00 0.00 0.00 3.51
49 50 5.071788 TCCTCCGTTATCAATCCTATTGCTT 59.928 40.000 0.00 0.00 0.00 3.91
50 51 4.593206 TCCTCCGTTATCAATCCTATTGCT 59.407 41.667 0.00 0.00 0.00 3.91
51 52 4.894784 TCCTCCGTTATCAATCCTATTGC 58.105 43.478 0.00 0.00 0.00 3.56
52 53 7.161404 TGAATCCTCCGTTATCAATCCTATTG 58.839 38.462 0.00 0.00 0.00 1.90
53 54 7.316393 TGAATCCTCCGTTATCAATCCTATT 57.684 36.000 0.00 0.00 0.00 1.73
54 55 6.935240 TGAATCCTCCGTTATCAATCCTAT 57.065 37.500 0.00 0.00 0.00 2.57
55 56 6.935240 ATGAATCCTCCGTTATCAATCCTA 57.065 37.500 0.00 0.00 0.00 2.94
56 57 5.832539 ATGAATCCTCCGTTATCAATCCT 57.167 39.130 0.00 0.00 0.00 3.24
57 58 5.997746 TGAATGAATCCTCCGTTATCAATCC 59.002 40.000 0.00 0.00 0.00 3.01
58 59 6.483307 TGTGAATGAATCCTCCGTTATCAATC 59.517 38.462 0.00 0.00 0.00 2.67
59 60 6.260936 GTGTGAATGAATCCTCCGTTATCAAT 59.739 38.462 0.00 0.00 0.00 2.57
60 61 5.584649 GTGTGAATGAATCCTCCGTTATCAA 59.415 40.000 0.00 0.00 0.00 2.57
61 62 5.116180 GTGTGAATGAATCCTCCGTTATCA 58.884 41.667 0.00 0.00 0.00 2.15
62 63 4.511826 GGTGTGAATGAATCCTCCGTTATC 59.488 45.833 0.00 0.00 0.00 1.75
63 64 4.451900 GGTGTGAATGAATCCTCCGTTAT 58.548 43.478 0.00 0.00 0.00 1.89
64 65 3.370103 GGGTGTGAATGAATCCTCCGTTA 60.370 47.826 0.00 0.00 0.00 3.18
65 66 2.618045 GGGTGTGAATGAATCCTCCGTT 60.618 50.000 0.00 0.00 0.00 4.44
66 67 1.065418 GGGTGTGAATGAATCCTCCGT 60.065 52.381 0.00 0.00 0.00 4.69
67 68 1.210478 AGGGTGTGAATGAATCCTCCG 59.790 52.381 0.00 0.00 0.00 4.63
68 69 3.019564 CAAGGGTGTGAATGAATCCTCC 58.980 50.000 0.00 0.00 0.00 4.30
69 70 3.019564 CCAAGGGTGTGAATGAATCCTC 58.980 50.000 0.00 0.00 0.00 3.71
70 71 2.649312 TCCAAGGGTGTGAATGAATCCT 59.351 45.455 0.00 0.00 0.00 3.24
71 72 3.019564 CTCCAAGGGTGTGAATGAATCC 58.980 50.000 0.00 0.00 0.00 3.01
72 73 3.690460 ACTCCAAGGGTGTGAATGAATC 58.310 45.455 0.00 0.00 0.00 2.52
73 74 3.814504 ACTCCAAGGGTGTGAATGAAT 57.185 42.857 0.00 0.00 0.00 2.57
74 75 3.009033 CCTACTCCAAGGGTGTGAATGAA 59.991 47.826 0.50 0.00 32.55 2.57
75 76 2.571653 CCTACTCCAAGGGTGTGAATGA 59.428 50.000 0.50 0.00 32.55 2.57
76 77 2.991250 CCTACTCCAAGGGTGTGAATG 58.009 52.381 0.50 0.00 32.55 2.67
85 86 1.428869 CATCCTCCCCTACTCCAAGG 58.571 60.000 0.00 0.00 36.30 3.61
86 87 0.761802 GCATCCTCCCCTACTCCAAG 59.238 60.000 0.00 0.00 0.00 3.61
87 88 0.044092 TGCATCCTCCCCTACTCCAA 59.956 55.000 0.00 0.00 0.00 3.53
88 89 0.268869 ATGCATCCTCCCCTACTCCA 59.731 55.000 0.00 0.00 0.00 3.86
89 90 1.349357 GAATGCATCCTCCCCTACTCC 59.651 57.143 0.00 0.00 0.00 3.85
90 91 2.050144 TGAATGCATCCTCCCCTACTC 58.950 52.381 0.00 0.00 0.00 2.59
91 92 2.196742 TGAATGCATCCTCCCCTACT 57.803 50.000 0.00 0.00 0.00 2.57
92 93 3.515602 ATTGAATGCATCCTCCCCTAC 57.484 47.619 0.00 0.00 0.00 3.18
93 94 4.504864 CGTTATTGAATGCATCCTCCCCTA 60.505 45.833 0.00 0.00 0.00 3.53
94 95 3.748668 CGTTATTGAATGCATCCTCCCCT 60.749 47.826 0.00 0.00 0.00 4.79
95 96 2.554032 CGTTATTGAATGCATCCTCCCC 59.446 50.000 0.00 0.00 0.00 4.81
96 97 3.214328 ACGTTATTGAATGCATCCTCCC 58.786 45.455 0.00 0.00 0.00 4.30
97 98 6.560253 AATACGTTATTGAATGCATCCTCC 57.440 37.500 0.00 0.00 0.00 4.30
98 99 8.721478 ACATAATACGTTATTGAATGCATCCTC 58.279 33.333 0.00 0.00 0.00 3.71
99 100 8.621532 ACATAATACGTTATTGAATGCATCCT 57.378 30.769 0.00 0.00 0.00 3.24
100 101 9.329913 GAACATAATACGTTATTGAATGCATCC 57.670 33.333 0.00 0.00 0.00 3.51
133 134 9.214957 CTTTGTTGAACATATTACACCTACAGA 57.785 33.333 0.00 0.00 0.00 3.41
135 136 7.392113 CCCTTTGTTGAACATATTACACCTACA 59.608 37.037 0.00 0.00 0.00 2.74
136 137 7.627726 GCCCTTTGTTGAACATATTACACCTAC 60.628 40.741 0.00 0.00 0.00 3.18
140 141 6.019779 TGCCCTTTGTTGAACATATTACAC 57.980 37.500 0.00 0.00 0.00 2.90
143 144 7.102346 CCAAATGCCCTTTGTTGAACATATTA 58.898 34.615 0.00 0.00 42.29 0.98
148 149 2.503356 ACCAAATGCCCTTTGTTGAACA 59.497 40.909 0.00 0.00 42.29 3.18
149 150 3.130633 GACCAAATGCCCTTTGTTGAAC 58.869 45.455 7.75 0.00 42.29 3.18
150 151 3.037549 AGACCAAATGCCCTTTGTTGAA 58.962 40.909 7.75 0.00 42.29 2.69
254 256 4.648762 AGAGAGAGAGAGAGAGTCAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
260 262 4.892934 AGAGAGAGAGAGAGAGAGAGAGTC 59.107 50.000 0.00 0.00 0.00 3.36
261 263 4.877773 AGAGAGAGAGAGAGAGAGAGAGT 58.122 47.826 0.00 0.00 0.00 3.24
262 264 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
263 265 4.219115 GGAGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
264 266 3.005261 CGGAGAGAGAGAGAGAGAGAGAG 59.995 56.522 0.00 0.00 0.00 3.20
265 267 2.959030 CGGAGAGAGAGAGAGAGAGAGA 59.041 54.545 0.00 0.00 0.00 3.10
266 268 2.959030 TCGGAGAGAGAGAGAGAGAGAG 59.041 54.545 0.00 0.00 0.00 3.20
267 269 3.026707 TCGGAGAGAGAGAGAGAGAGA 57.973 52.381 0.00 0.00 0.00 3.10
268 270 4.342862 AATCGGAGAGAGAGAGAGAGAG 57.657 50.000 0.00 0.00 43.63 3.20
269 271 4.771114 AAATCGGAGAGAGAGAGAGAGA 57.229 45.455 0.00 0.00 43.63 3.10
270 272 5.835113 AAAAATCGGAGAGAGAGAGAGAG 57.165 43.478 0.00 0.00 43.63 3.20
297 299 6.765989 TCAAATCGGAGAGAAAGAAGTTCAAA 59.234 34.615 5.50 0.00 43.63 2.69
300 302 6.787085 TTCAAATCGGAGAGAAAGAAGTTC 57.213 37.500 0.00 0.00 43.63 3.01
301 303 6.292919 CGTTTCAAATCGGAGAGAAAGAAGTT 60.293 38.462 0.00 0.00 43.63 2.66
302 304 5.177696 CGTTTCAAATCGGAGAGAAAGAAGT 59.822 40.000 0.00 0.00 43.63 3.01
304 306 5.050363 CACGTTTCAAATCGGAGAGAAAGAA 60.050 40.000 0.00 0.00 43.63 2.52
324 326 2.166664 GAGAAAGGTCTCTATGGCACGT 59.833 50.000 0.00 0.00 45.99 4.49
364 366 3.205507 AGAGGCTAGGTAGATGGTTCTCA 59.794 47.826 0.00 0.00 33.17 3.27
394 402 2.103373 ACGATGGTGCATAGTCTCAGT 58.897 47.619 0.00 0.00 0.00 3.41
439 447 7.775561 AGGGAGTTTGATGGTTTATAATCTCAC 59.224 37.037 0.00 0.00 0.00 3.51
536 554 1.080772 GTGTCGTCATGCTCGGTGA 60.081 57.895 9.47 0.00 0.00 4.02
557 575 2.178521 CTAGCGGACACGAGCGTT 59.821 61.111 0.00 0.00 44.60 4.84
768 786 4.144703 GCGAGGACGGGAAGGGAC 62.145 72.222 0.00 0.00 40.15 4.46
914 937 2.243957 TGGACGCACGTGCAAGAAG 61.244 57.895 37.03 23.67 43.23 2.85
915 938 2.202946 TGGACGCACGTGCAAGAA 60.203 55.556 37.03 18.77 43.23 2.52
929 952 0.038251 GTGACACTGCGAGATGTGGA 60.038 55.000 0.00 0.00 38.39 4.02
983 1018 1.516161 CATGGGTCACACACTCACAG 58.484 55.000 0.00 0.00 38.78 3.66
1237 1276 2.201708 GGCGGAGGTAGAGGTAGCC 61.202 68.421 0.00 0.00 36.08 3.93
1552 1603 9.213799 CTCTAATTACTTATTCTGAATCTGGGC 57.786 37.037 6.10 0.00 0.00 5.36
1584 1635 3.691609 GGGCCTCATCATATTTCGGAATC 59.308 47.826 0.84 0.00 0.00 2.52
1586 1637 2.711009 AGGGCCTCATCATATTTCGGAA 59.289 45.455 0.00 0.00 0.00 4.30
1606 1657 0.397941 TGTGAAGAAGGTGCCCTCAG 59.602 55.000 0.00 0.00 30.89 3.35
1736 1787 4.098654 TGGTTTCGTTCATGGTTCATGTTT 59.901 37.500 7.63 0.00 41.98 2.83
1746 1797 0.109597 GCCTGCTGGTTTCGTTCATG 60.110 55.000 11.69 0.00 35.27 3.07
1747 1798 1.577328 CGCCTGCTGGTTTCGTTCAT 61.577 55.000 11.69 0.00 35.27 2.57
1748 1799 2.250939 CGCCTGCTGGTTTCGTTCA 61.251 57.895 11.69 0.00 35.27 3.18
1749 1800 1.503818 TTCGCCTGCTGGTTTCGTTC 61.504 55.000 11.69 0.00 35.27 3.95
1750 1801 1.098712 TTTCGCCTGCTGGTTTCGTT 61.099 50.000 11.69 0.00 35.27 3.85
1751 1802 1.525077 TTTCGCCTGCTGGTTTCGT 60.525 52.632 11.69 0.00 35.27 3.85
1752 1803 1.082104 GTTTCGCCTGCTGGTTTCG 60.082 57.895 11.69 6.64 35.27 3.46
1760 1811 0.456653 ATTCGCAATGTTTCGCCTGC 60.457 50.000 0.00 0.00 0.00 4.85
1773 1824 3.314080 ACTTTCTTTTCGGTGAATTCGCA 59.686 39.130 20.06 0.00 0.00 5.10
1788 1839 2.452600 TGCTGGTCCCAAACTTTCTT 57.547 45.000 0.00 0.00 0.00 2.52
1851 1902 2.687566 TCTTCTCCCTTCCGGCCC 60.688 66.667 0.00 0.00 0.00 5.80
1935 1987 1.543944 CCAAAATTCGGGCTTGGGCT 61.544 55.000 0.00 0.00 36.70 5.19
1978 2030 8.495160 AGATCATTGACTAAGGATGAAGATCT 57.505 34.615 0.00 0.00 37.43 2.75
2039 2091 0.543277 CCCATCTAAGCCTGCTGACA 59.457 55.000 0.00 0.00 0.00 3.58
2218 2270 3.897239 TGGTTTGGAGTTGTGTCAGATT 58.103 40.909 0.00 0.00 0.00 2.40
2394 2450 1.357761 TGGAAATCCAAAGTCCCTCCC 59.642 52.381 0.00 0.00 44.35 4.30
2443 2499 2.224719 GGTACTCTAGGCCTATCCGTGA 60.225 54.545 14.30 5.68 40.77 4.35


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

AutoCloner maintained by Alex Coulton.