Multiple sequence alignment - TraesCS3A01G301300

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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 TraesCS3A01G301300 chr3A 100.000 3464 0 0 645 4108 535169841 535166378 0.000000e+00 6397
1 TraesCS3A01G301300 chr3A 97.193 3491 68 7 645 4108 733321670 733325157 0.000000e+00 5877
2 TraesCS3A01G301300 chr3A 100.000 499 0 0 3610 4108 535181384 535180886 0.000000e+00 922
3 TraesCS3A01G301300 chr3A 100.000 199 0 0 1 199 535170485 535170287 6.490000e-98 368
4 TraesCS3A01G301300 chr2B 95.621 3494 103 15 646 4108 477604191 477600717 0.000000e+00 5559
5 TraesCS3A01G301300 chr2B 95.560 3491 107 11 645 4108 424379644 424383113 0.000000e+00 5544
6 TraesCS3A01G301300 chr2B 83.531 1178 115 42 1957 3086 142595256 142594110 0.000000e+00 1027
7 TraesCS3A01G301300 chr2B 85.114 833 86 17 2221 3041 728625999 728626805 0.000000e+00 817
8 TraesCS3A01G301300 chr2D 94.892 3485 118 15 651 4108 629447970 629444519 0.000000e+00 5395
9 TraesCS3A01G301300 chr2D 86.768 461 50 7 1088 1537 118223545 118224005 1.700000e-138 503
10 TraesCS3A01G301300 chrUn 94.307 3478 134 19 658 4108 178180886 178184326 0.000000e+00 5267
11 TraesCS3A01G301300 chr7A 92.892 2279 122 23 645 2909 713723232 713725484 0.000000e+00 3275
12 TraesCS3A01G301300 chr7A 93.031 574 29 6 3543 4108 713730157 713730727 0.000000e+00 828
13 TraesCS3A01G301300 chr7A 84.944 445 54 11 2907 3345 713729703 713730140 4.880000e-119 438
14 TraesCS3A01G301300 chr5D 90.685 1782 117 9 1345 3080 456631233 456633011 0.000000e+00 2326
15 TraesCS3A01G301300 chr5D 83.841 1609 170 44 1539 3086 250404888 250403309 0.000000e+00 1448
16 TraesCS3A01G301300 chr5D 89.915 823 75 6 3106 3923 456633692 456634511 0.000000e+00 1053
17 TraesCS3A01G301300 chr5D 85.298 721 68 12 651 1347 456630209 456630915 0.000000e+00 710
18 TraesCS3A01G301300 chr3B 82.957 1637 163 46 1539 3086 718698738 718697129 0.000000e+00 1371
19 TraesCS3A01G301300 chr3B 95.327 107 2 2 55 160 541217505 541217609 2.540000e-37 167
20 TraesCS3A01G301300 chr7D 88.998 1118 85 16 1732 2818 90192097 90190987 0.000000e+00 1349
21 TraesCS3A01G301300 chr7D 86.745 1109 93 28 651 1736 90240198 90239121 0.000000e+00 1184
22 TraesCS3A01G301300 chr7D 89.621 713 63 8 3106 3815 90183427 90182723 0.000000e+00 896
23 TraesCS3A01G301300 chr7D 91.544 272 23 0 3811 4082 90139526 90139255 3.880000e-100 375
24 TraesCS3A01G301300 chr7D 89.558 249 24 2 2814 3062 90184368 90184122 8.570000e-82 315
25 TraesCS3A01G301300 chr5B 89.812 1011 79 13 3107 4108 558554925 558555920 0.000000e+00 1275
26 TraesCS3A01G301300 chr5B 89.567 1016 59 17 1419 2389 558449529 558450542 0.000000e+00 1245
27 TraesCS3A01G301300 chr5B 90.537 782 64 8 3165 3940 558546974 558547751 0.000000e+00 1026
28 TraesCS3A01G301300 chr5B 90.377 717 49 10 1377 2074 558448807 558449522 0.000000e+00 924
29 TraesCS3A01G301300 chr5B 88.051 703 68 5 2384 3086 558452115 558452801 0.000000e+00 819
30 TraesCS3A01G301300 chr3D 84.653 202 14 8 1 199 415174937 415175124 7.010000e-43 185


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 TraesCS3A01G301300 chr3A 535166378 535170485 4107 True 3382.5 6397 100.000000 1 4108 2 chr3A.!!$R2 4107
1 TraesCS3A01G301300 chr3A 733321670 733325157 3487 False 5877.0 5877 97.193000 645 4108 1 chr3A.!!$F1 3463
2 TraesCS3A01G301300 chr2B 477600717 477604191 3474 True 5559.0 5559 95.621000 646 4108 1 chr2B.!!$R2 3462
3 TraesCS3A01G301300 chr2B 424379644 424383113 3469 False 5544.0 5544 95.560000 645 4108 1 chr2B.!!$F1 3463
4 TraesCS3A01G301300 chr2B 142594110 142595256 1146 True 1027.0 1027 83.531000 1957 3086 1 chr2B.!!$R1 1129
5 TraesCS3A01G301300 chr2B 728625999 728626805 806 False 817.0 817 85.114000 2221 3041 1 chr2B.!!$F2 820
6 TraesCS3A01G301300 chr2D 629444519 629447970 3451 True 5395.0 5395 94.892000 651 4108 1 chr2D.!!$R1 3457
7 TraesCS3A01G301300 chrUn 178180886 178184326 3440 False 5267.0 5267 94.307000 658 4108 1 chrUn.!!$F1 3450
8 TraesCS3A01G301300 chr7A 713723232 713725484 2252 False 3275.0 3275 92.892000 645 2909 1 chr7A.!!$F1 2264
9 TraesCS3A01G301300 chr7A 713729703 713730727 1024 False 633.0 828 88.987500 2907 4108 2 chr7A.!!$F2 1201
10 TraesCS3A01G301300 chr5D 250403309 250404888 1579 True 1448.0 1448 83.841000 1539 3086 1 chr5D.!!$R1 1547
11 TraesCS3A01G301300 chr5D 456630209 456634511 4302 False 1363.0 2326 88.632667 651 3923 3 chr5D.!!$F1 3272
12 TraesCS3A01G301300 chr3B 718697129 718698738 1609 True 1371.0 1371 82.957000 1539 3086 1 chr3B.!!$R1 1547
13 TraesCS3A01G301300 chr7D 90190987 90192097 1110 True 1349.0 1349 88.998000 1732 2818 1 chr7D.!!$R2 1086
14 TraesCS3A01G301300 chr7D 90239121 90240198 1077 True 1184.0 1184 86.745000 651 1736 1 chr7D.!!$R3 1085
15 TraesCS3A01G301300 chr7D 90182723 90184368 1645 True 605.5 896 89.589500 2814 3815 2 chr7D.!!$R4 1001
16 TraesCS3A01G301300 chr5B 558554925 558555920 995 False 1275.0 1275 89.812000 3107 4108 1 chr5B.!!$F2 1001
17 TraesCS3A01G301300 chr5B 558546974 558547751 777 False 1026.0 1026 90.537000 3165 3940 1 chr5B.!!$F1 775
18 TraesCS3A01G301300 chr5B 558448807 558452801 3994 False 996.0 1245 89.331667 1377 3086 3 chr5B.!!$F3 1709

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
19 20 0.169230 CGTCTCCTTCGTCAGTCCTG 59.831 60.000 0.00 0.00 0.00 3.86 F
80 81 0.250858 TCATTGGCCAGTCAGGTGTG 60.251 55.000 5.11 0.00 40.61 3.82 F
976 992 0.761802 CTGCTCTCTATCCCCAACCC 59.238 60.000 0.00 0.00 0.00 4.11 F
1176 1230 2.917363 GAAAGTTTCCACTAGCGCAAC 58.083 47.619 11.47 2.84 30.68 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1176 1230 7.176340 ACAAAATTGAGAGAGAAAAGAGGATGG 59.824 37.037 0.00 0.00 0.00 3.51 R
1940 3038 8.814038 ATCAGGCTGAAGTTTCATAAGTTATT 57.186 30.769 22.84 0.00 36.46 1.40 R
2557 5294 0.894184 AAGGTTGAGCGACTCGGAGA 60.894 55.000 12.86 0.00 32.35 3.71 R
3540 7462 0.737715 CCCTCCTTGCTCGAAGTTCG 60.738 60.000 19.23 19.23 42.10 3.95 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
18 19 2.557451 CGTCTCCTTCGTCAGTCCT 58.443 57.895 0.00 0.00 0.00 3.85
19 20 0.169230 CGTCTCCTTCGTCAGTCCTG 59.831 60.000 0.00 0.00 0.00 3.86
20 21 0.528470 GTCTCCTTCGTCAGTCCTGG 59.472 60.000 0.00 0.00 0.00 4.45
21 22 0.404426 TCTCCTTCGTCAGTCCTGGA 59.596 55.000 0.00 0.00 0.00 3.86
22 23 1.006043 TCTCCTTCGTCAGTCCTGGAT 59.994 52.381 0.00 0.00 0.00 3.41
23 24 2.241430 TCTCCTTCGTCAGTCCTGGATA 59.759 50.000 0.00 0.00 0.00 2.59
24 25 3.024547 CTCCTTCGTCAGTCCTGGATAA 58.975 50.000 0.00 0.00 0.00 1.75
25 26 3.437213 TCCTTCGTCAGTCCTGGATAAA 58.563 45.455 0.00 0.00 0.00 1.40
26 27 3.194968 TCCTTCGTCAGTCCTGGATAAAC 59.805 47.826 0.00 0.00 0.00 2.01
27 28 3.195825 CCTTCGTCAGTCCTGGATAAACT 59.804 47.826 0.00 0.00 0.00 2.66
28 29 4.401519 CCTTCGTCAGTCCTGGATAAACTA 59.598 45.833 0.00 0.00 0.00 2.24
29 30 5.069251 CCTTCGTCAGTCCTGGATAAACTAT 59.931 44.000 0.00 0.00 0.00 2.12
30 31 6.264744 CCTTCGTCAGTCCTGGATAAACTATA 59.735 42.308 0.00 0.00 0.00 1.31
31 32 7.039644 CCTTCGTCAGTCCTGGATAAACTATAT 60.040 40.741 0.00 0.00 0.00 0.86
32 33 8.929260 TTCGTCAGTCCTGGATAAACTATATA 57.071 34.615 0.00 0.00 0.00 0.86
33 34 8.332996 TCGTCAGTCCTGGATAAACTATATAC 57.667 38.462 0.00 0.00 0.00 1.47
34 35 7.118825 TCGTCAGTCCTGGATAAACTATATACG 59.881 40.741 0.00 2.29 0.00 3.06
35 36 7.094890 CGTCAGTCCTGGATAAACTATATACGT 60.095 40.741 0.00 0.00 0.00 3.57
36 37 8.574737 GTCAGTCCTGGATAAACTATATACGTT 58.425 37.037 0.00 0.00 0.00 3.99
37 38 9.139734 TCAGTCCTGGATAAACTATATACGTTT 57.860 33.333 0.00 12.12 38.13 3.60
38 39 9.193133 CAGTCCTGGATAAACTATATACGTTTG 57.807 37.037 0.00 4.33 36.18 2.93
39 40 8.921205 AGTCCTGGATAAACTATATACGTTTGT 58.079 33.333 0.00 11.01 36.18 2.83
40 41 8.975439 GTCCTGGATAAACTATATACGTTTGTG 58.025 37.037 0.00 0.00 36.18 3.33
41 42 8.916062 TCCTGGATAAACTATATACGTTTGTGA 58.084 33.333 15.06 5.31 36.18 3.58
42 43 9.193133 CCTGGATAAACTATATACGTTTGTGAG 57.807 37.037 15.06 9.47 36.18 3.51
43 44 9.961265 CTGGATAAACTATATACGTTTGTGAGA 57.039 33.333 15.06 2.49 36.18 3.27
71 72 6.906157 AAATAGGTTATCATCATTGGCCAG 57.094 37.500 5.11 0.00 0.00 4.85
72 73 3.959495 AGGTTATCATCATTGGCCAGT 57.041 42.857 5.11 0.00 0.00 4.00
73 74 3.825328 AGGTTATCATCATTGGCCAGTC 58.175 45.455 5.11 0.00 0.00 3.51
74 75 3.202818 AGGTTATCATCATTGGCCAGTCA 59.797 43.478 5.11 0.00 0.00 3.41
75 76 3.567164 GGTTATCATCATTGGCCAGTCAG 59.433 47.826 5.11 0.00 0.00 3.51
76 77 2.359981 ATCATCATTGGCCAGTCAGG 57.640 50.000 5.11 0.00 41.84 3.86
77 78 0.994247 TCATCATTGGCCAGTCAGGT 59.006 50.000 5.11 0.00 40.61 4.00
78 79 1.100510 CATCATTGGCCAGTCAGGTG 58.899 55.000 5.11 0.00 40.61 4.00
79 80 0.700564 ATCATTGGCCAGTCAGGTGT 59.299 50.000 5.11 0.00 40.61 4.16
80 81 0.250858 TCATTGGCCAGTCAGGTGTG 60.251 55.000 5.11 0.00 40.61 3.82
81 82 1.604593 ATTGGCCAGTCAGGTGTGC 60.605 57.895 5.11 0.00 40.61 4.57
82 83 4.624364 TGGCCAGTCAGGTGTGCG 62.624 66.667 0.00 0.00 40.61 5.34
83 84 4.626081 GGCCAGTCAGGTGTGCGT 62.626 66.667 0.00 0.00 40.61 5.24
84 85 2.591715 GCCAGTCAGGTGTGCGTT 60.592 61.111 0.00 0.00 40.61 4.84
85 86 2.186826 GCCAGTCAGGTGTGCGTTT 61.187 57.895 0.00 0.00 40.61 3.60
86 87 0.882927 GCCAGTCAGGTGTGCGTTTA 60.883 55.000 0.00 0.00 40.61 2.01
87 88 1.808411 CCAGTCAGGTGTGCGTTTAT 58.192 50.000 0.00 0.00 0.00 1.40
88 89 2.933492 GCCAGTCAGGTGTGCGTTTATA 60.933 50.000 0.00 0.00 40.61 0.98
89 90 3.531538 CCAGTCAGGTGTGCGTTTATAT 58.468 45.455 0.00 0.00 0.00 0.86
90 91 3.938963 CCAGTCAGGTGTGCGTTTATATT 59.061 43.478 0.00 0.00 0.00 1.28
91 92 4.034048 CCAGTCAGGTGTGCGTTTATATTC 59.966 45.833 0.00 0.00 0.00 1.75
92 93 4.870426 CAGTCAGGTGTGCGTTTATATTCT 59.130 41.667 0.00 0.00 0.00 2.40
93 94 4.870426 AGTCAGGTGTGCGTTTATATTCTG 59.130 41.667 0.00 0.00 0.00 3.02
94 95 4.034048 GTCAGGTGTGCGTTTATATTCTGG 59.966 45.833 0.00 0.00 0.00 3.86
95 96 3.312421 CAGGTGTGCGTTTATATTCTGGG 59.688 47.826 0.00 0.00 0.00 4.45
96 97 2.616842 GGTGTGCGTTTATATTCTGGGG 59.383 50.000 0.00 0.00 0.00 4.96
97 98 3.275999 GTGTGCGTTTATATTCTGGGGT 58.724 45.455 0.00 0.00 0.00 4.95
98 99 3.311596 GTGTGCGTTTATATTCTGGGGTC 59.688 47.826 0.00 0.00 0.00 4.46
99 100 2.542595 GTGCGTTTATATTCTGGGGTCG 59.457 50.000 0.00 0.00 0.00 4.79
100 101 2.168936 TGCGTTTATATTCTGGGGTCGT 59.831 45.455 0.00 0.00 0.00 4.34
101 102 2.798847 GCGTTTATATTCTGGGGTCGTC 59.201 50.000 0.00 0.00 0.00 4.20
102 103 3.047796 CGTTTATATTCTGGGGTCGTCG 58.952 50.000 0.00 0.00 0.00 5.12
103 104 3.489738 CGTTTATATTCTGGGGTCGTCGT 60.490 47.826 0.00 0.00 0.00 4.34
104 105 4.261155 CGTTTATATTCTGGGGTCGTCGTA 60.261 45.833 0.00 0.00 0.00 3.43
105 106 5.591099 GTTTATATTCTGGGGTCGTCGTAA 58.409 41.667 0.00 0.00 0.00 3.18
106 107 6.218746 GTTTATATTCTGGGGTCGTCGTAAT 58.781 40.000 0.00 0.00 0.00 1.89
107 108 4.950205 ATATTCTGGGGTCGTCGTAATT 57.050 40.909 0.00 0.00 0.00 1.40
108 109 7.523293 TTATATTCTGGGGTCGTCGTAATTA 57.477 36.000 0.00 0.00 0.00 1.40
109 110 4.741321 ATTCTGGGGTCGTCGTAATTAA 57.259 40.909 0.00 0.00 0.00 1.40
110 111 3.788333 TCTGGGGTCGTCGTAATTAAG 57.212 47.619 0.00 0.00 0.00 1.85
111 112 2.159198 TCTGGGGTCGTCGTAATTAAGC 60.159 50.000 0.00 0.00 0.00 3.09
112 113 1.134729 TGGGGTCGTCGTAATTAAGCC 60.135 52.381 0.00 0.00 0.00 4.35
113 114 1.203065 GGGTCGTCGTAATTAAGCCG 58.797 55.000 0.00 0.00 0.00 5.52
114 115 1.469767 GGGTCGTCGTAATTAAGCCGT 60.470 52.381 2.05 0.00 0.00 5.68
115 116 2.262211 GGTCGTCGTAATTAAGCCGTT 58.738 47.619 2.05 0.00 0.00 4.44
116 117 2.028404 GGTCGTCGTAATTAAGCCGTTG 59.972 50.000 2.05 0.00 0.00 4.10
117 118 2.663119 GTCGTCGTAATTAAGCCGTTGT 59.337 45.455 2.05 0.00 0.00 3.32
118 119 3.121778 GTCGTCGTAATTAAGCCGTTGTT 59.878 43.478 2.05 0.00 0.00 2.83
119 120 3.740321 TCGTCGTAATTAAGCCGTTGTTT 59.260 39.130 2.05 0.00 0.00 2.83
120 121 3.836348 CGTCGTAATTAAGCCGTTGTTTG 59.164 43.478 0.00 0.00 0.00 2.93
121 122 4.376210 CGTCGTAATTAAGCCGTTGTTTGA 60.376 41.667 0.00 0.00 0.00 2.69
122 123 5.624292 GTCGTAATTAAGCCGTTGTTTGAT 58.376 37.500 0.00 0.00 0.00 2.57
123 124 6.081693 GTCGTAATTAAGCCGTTGTTTGATT 58.918 36.000 0.00 0.00 0.00 2.57
124 125 6.579666 GTCGTAATTAAGCCGTTGTTTGATTT 59.420 34.615 0.00 0.00 0.00 2.17
125 126 6.797995 TCGTAATTAAGCCGTTGTTTGATTTC 59.202 34.615 0.00 0.00 0.00 2.17
126 127 6.799925 CGTAATTAAGCCGTTGTTTGATTTCT 59.200 34.615 0.00 0.00 0.00 2.52
127 128 7.201232 CGTAATTAAGCCGTTGTTTGATTTCTG 60.201 37.037 0.00 0.00 0.00 3.02
128 129 3.369546 AAGCCGTTGTTTGATTTCTGG 57.630 42.857 0.00 0.00 0.00 3.86
129 130 1.613437 AGCCGTTGTTTGATTTCTGGG 59.387 47.619 0.00 0.00 0.00 4.45
130 131 1.611491 GCCGTTGTTTGATTTCTGGGA 59.389 47.619 0.00 0.00 0.00 4.37
131 132 2.607038 GCCGTTGTTTGATTTCTGGGAC 60.607 50.000 0.00 0.00 0.00 4.46
132 133 2.621055 CCGTTGTTTGATTTCTGGGACA 59.379 45.455 0.00 0.00 0.00 4.02
133 134 3.067461 CCGTTGTTTGATTTCTGGGACAA 59.933 43.478 0.00 0.00 38.70 3.18
134 135 4.440802 CCGTTGTTTGATTTCTGGGACAAA 60.441 41.667 0.00 0.00 38.70 2.83
135 136 5.288804 CGTTGTTTGATTTCTGGGACAAAT 58.711 37.500 0.00 0.00 38.70 2.32
136 137 5.175491 CGTTGTTTGATTTCTGGGACAAATG 59.825 40.000 0.00 0.00 38.70 2.32
137 138 5.867903 TGTTTGATTTCTGGGACAAATGT 57.132 34.783 0.00 0.00 38.70 2.71
138 139 5.599732 TGTTTGATTTCTGGGACAAATGTG 58.400 37.500 0.00 0.00 38.70 3.21
139 140 5.128499 TGTTTGATTTCTGGGACAAATGTGT 59.872 36.000 0.00 0.00 42.10 3.72
140 141 5.867903 TTGATTTCTGGGACAAATGTGTT 57.132 34.783 0.00 0.00 38.41 3.32
141 142 5.452078 TGATTTCTGGGACAAATGTGTTC 57.548 39.130 0.00 0.00 38.41 3.18
142 143 5.139727 TGATTTCTGGGACAAATGTGTTCT 58.860 37.500 0.00 0.00 38.41 3.01
143 144 6.303054 TGATTTCTGGGACAAATGTGTTCTA 58.697 36.000 0.00 0.00 38.41 2.10
144 145 6.430925 TGATTTCTGGGACAAATGTGTTCTAG 59.569 38.462 1.06 1.06 42.03 2.43
145 146 5.560722 TTCTGGGACAAATGTGTTCTAGA 57.439 39.130 6.28 6.28 46.26 2.43
146 147 5.152623 TCTGGGACAAATGTGTTCTAGAG 57.847 43.478 6.28 0.00 43.86 2.43
147 148 4.020218 TCTGGGACAAATGTGTTCTAGAGG 60.020 45.833 6.28 0.00 43.86 3.69
148 149 3.907474 TGGGACAAATGTGTTCTAGAGGA 59.093 43.478 0.00 0.00 38.41 3.71
149 150 4.254492 GGGACAAATGTGTTCTAGAGGAC 58.746 47.826 0.00 0.00 38.41 3.85
150 151 4.262894 GGGACAAATGTGTTCTAGAGGACA 60.263 45.833 8.02 8.02 38.41 4.02
151 152 5.305585 GGACAAATGTGTTCTAGAGGACAA 58.694 41.667 9.31 0.00 38.41 3.18
152 153 5.409826 GGACAAATGTGTTCTAGAGGACAAG 59.590 44.000 9.31 6.24 38.41 3.16
153 154 5.930135 ACAAATGTGTTCTAGAGGACAAGT 58.070 37.500 9.31 6.70 32.58 3.16
154 155 5.992217 ACAAATGTGTTCTAGAGGACAAGTC 59.008 40.000 9.31 0.00 32.58 3.01
155 156 6.183361 ACAAATGTGTTCTAGAGGACAAGTCT 60.183 38.462 9.31 0.00 32.58 3.24
156 157 6.426646 AATGTGTTCTAGAGGACAAGTCTT 57.573 37.500 9.31 0.00 0.00 3.01
157 158 5.201713 TGTGTTCTAGAGGACAAGTCTTG 57.798 43.478 11.17 11.17 0.00 3.02
159 160 5.831525 TGTGTTCTAGAGGACAAGTCTTGTA 59.168 40.000 18.17 1.72 45.52 2.41
160 161 6.016192 TGTGTTCTAGAGGACAAGTCTTGTAG 60.016 42.308 18.17 11.48 45.52 2.74
161 162 6.207025 GTGTTCTAGAGGACAAGTCTTGTAGA 59.793 42.308 18.17 13.51 45.52 2.59
162 163 6.948886 TGTTCTAGAGGACAAGTCTTGTAGAT 59.051 38.462 18.17 7.29 45.52 1.98
163 164 7.451877 TGTTCTAGAGGACAAGTCTTGTAGATT 59.548 37.037 18.17 7.66 45.52 2.40
164 165 8.308207 GTTCTAGAGGACAAGTCTTGTAGATTT 58.692 37.037 18.17 5.59 45.52 2.17
165 166 8.423906 TCTAGAGGACAAGTCTTGTAGATTTT 57.576 34.615 18.17 5.43 45.52 1.82
166 167 8.871125 TCTAGAGGACAAGTCTTGTAGATTTTT 58.129 33.333 18.17 4.02 45.52 1.94
196 197 8.551682 AAGAAGAGAGATCCAATAACTCATCT 57.448 34.615 0.00 0.00 37.29 2.90
197 198 8.551682 AGAAGAGAGATCCAATAACTCATCTT 57.448 34.615 0.00 0.00 33.81 2.40
198 199 8.991275 AGAAGAGAGATCCAATAACTCATCTTT 58.009 33.333 0.00 0.00 33.81 2.52
737 745 2.738000 CGATCTGCACAGGAGAAGAAGG 60.738 54.545 0.00 0.00 0.00 3.46
738 746 2.015456 TCTGCACAGGAGAAGAAGGA 57.985 50.000 0.00 0.00 0.00 3.36
739 747 2.329267 TCTGCACAGGAGAAGAAGGAA 58.671 47.619 0.00 0.00 0.00 3.36
740 748 2.705658 TCTGCACAGGAGAAGAAGGAAA 59.294 45.455 0.00 0.00 0.00 3.13
741 749 3.136443 TCTGCACAGGAGAAGAAGGAAAA 59.864 43.478 0.00 0.00 0.00 2.29
742 750 3.214328 TGCACAGGAGAAGAAGGAAAAC 58.786 45.455 0.00 0.00 0.00 2.43
743 751 2.224314 GCACAGGAGAAGAAGGAAAACG 59.776 50.000 0.00 0.00 0.00 3.60
748 756 4.762251 CAGGAGAAGAAGGAAAACGGAAAT 59.238 41.667 0.00 0.00 0.00 2.17
976 992 0.761802 CTGCTCTCTATCCCCAACCC 59.238 60.000 0.00 0.00 0.00 4.11
1176 1230 2.917363 GAAAGTTTCCACTAGCGCAAC 58.083 47.619 11.47 2.84 30.68 4.17
1236 1290 9.896645 ATATAGCATTGAATCAGTTACTATGGG 57.103 33.333 7.76 0.00 0.00 4.00
1906 3001 3.311596 GTGCCAACAGTTTAACTCGAACT 59.688 43.478 0.00 0.00 37.82 3.01
2253 3407 6.560711 ACTTTCAACCCGATAATTATGCAAC 58.439 36.000 1.78 0.00 0.00 4.17
2557 5294 1.066858 CATGCTCGTTGTAGTCACCCT 60.067 52.381 0.00 0.00 0.00 4.34
3540 7462 5.108630 CGATAAGTACGTATAAACACCGTGC 60.109 44.000 0.00 0.00 37.45 5.34
3745 7675 8.453320 CACGATAATATACGAACCACATACCTA 58.547 37.037 0.00 0.00 0.00 3.08
3980 7918 4.497291 AAATGATGGAACTAGGGCGTAA 57.503 40.909 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.528470 CCAGGACTGACGAAGGAGAC 59.472 60.000 0.00 0.00 0.00 3.36
6 7 4.457834 AGTTTATCCAGGACTGACGAAG 57.542 45.455 0.00 0.00 0.00 3.79
7 8 7.834881 ATATAGTTTATCCAGGACTGACGAA 57.165 36.000 0.00 0.00 0.00 3.85
8 9 7.118825 CGTATATAGTTTATCCAGGACTGACGA 59.881 40.741 0.00 0.00 0.00 4.20
9 10 7.094890 ACGTATATAGTTTATCCAGGACTGACG 60.095 40.741 0.00 0.92 0.00 4.35
10 11 8.108551 ACGTATATAGTTTATCCAGGACTGAC 57.891 38.462 0.00 0.00 0.00 3.51
11 12 8.701908 AACGTATATAGTTTATCCAGGACTGA 57.298 34.615 0.00 0.00 0.00 3.41
12 13 9.193133 CAAACGTATATAGTTTATCCAGGACTG 57.807 37.037 0.00 0.00 39.50 3.51
13 14 8.921205 ACAAACGTATATAGTTTATCCAGGACT 58.079 33.333 0.00 0.00 39.50 3.85
14 15 8.975439 CACAAACGTATATAGTTTATCCAGGAC 58.025 37.037 0.00 0.00 39.50 3.85
15 16 8.916062 TCACAAACGTATATAGTTTATCCAGGA 58.084 33.333 0.00 0.00 39.50 3.86
16 17 9.193133 CTCACAAACGTATATAGTTTATCCAGG 57.807 37.037 8.37 0.00 39.50 4.45
17 18 9.961265 TCTCACAAACGTATATAGTTTATCCAG 57.039 33.333 8.37 4.59 39.50 3.86
45 46 9.685276 CTGGCCAATGATGATAACCTATTTATA 57.315 33.333 7.01 0.00 29.85 0.98
46 47 8.172741 ACTGGCCAATGATGATAACCTATTTAT 58.827 33.333 7.01 0.00 32.64 1.40
47 48 7.526041 ACTGGCCAATGATGATAACCTATTTA 58.474 34.615 7.01 0.00 0.00 1.40
48 49 6.376248 ACTGGCCAATGATGATAACCTATTT 58.624 36.000 7.01 0.00 0.00 1.40
49 50 5.957132 ACTGGCCAATGATGATAACCTATT 58.043 37.500 7.01 0.00 0.00 1.73
50 51 5.073554 TGACTGGCCAATGATGATAACCTAT 59.926 40.000 7.01 0.00 0.00 2.57
51 52 4.411869 TGACTGGCCAATGATGATAACCTA 59.588 41.667 7.01 0.00 0.00 3.08
52 53 3.202818 TGACTGGCCAATGATGATAACCT 59.797 43.478 7.01 0.00 0.00 3.50
53 54 3.554934 TGACTGGCCAATGATGATAACC 58.445 45.455 7.01 0.00 0.00 2.85
54 55 3.567164 CCTGACTGGCCAATGATGATAAC 59.433 47.826 7.01 0.00 0.00 1.89
55 56 3.202818 ACCTGACTGGCCAATGATGATAA 59.797 43.478 7.01 0.00 40.22 1.75
56 57 2.779430 ACCTGACTGGCCAATGATGATA 59.221 45.455 7.01 0.00 40.22 2.15
57 58 1.567649 ACCTGACTGGCCAATGATGAT 59.432 47.619 7.01 0.00 40.22 2.45
58 59 0.994247 ACCTGACTGGCCAATGATGA 59.006 50.000 7.01 0.00 40.22 2.92
59 60 1.100510 CACCTGACTGGCCAATGATG 58.899 55.000 7.01 0.00 40.22 3.07
60 61 0.700564 ACACCTGACTGGCCAATGAT 59.299 50.000 7.01 0.00 40.22 2.45
61 62 0.250858 CACACCTGACTGGCCAATGA 60.251 55.000 7.01 0.00 40.22 2.57
62 63 1.870055 GCACACCTGACTGGCCAATG 61.870 60.000 7.01 0.00 40.22 2.82
63 64 1.604593 GCACACCTGACTGGCCAAT 60.605 57.895 7.01 0.00 40.22 3.16
64 65 2.203337 GCACACCTGACTGGCCAA 60.203 61.111 7.01 0.00 40.22 4.52
65 66 4.624364 CGCACACCTGACTGGCCA 62.624 66.667 4.71 4.71 40.22 5.36
66 67 4.626081 ACGCACACCTGACTGGCC 62.626 66.667 0.00 0.00 40.22 5.36
67 68 0.882927 TAAACGCACACCTGACTGGC 60.883 55.000 0.00 0.00 40.22 4.85
68 69 1.808411 ATAAACGCACACCTGACTGG 58.192 50.000 0.00 0.00 42.93 4.00
69 70 4.870426 AGAATATAAACGCACACCTGACTG 59.130 41.667 0.00 0.00 0.00 3.51
70 71 4.870426 CAGAATATAAACGCACACCTGACT 59.130 41.667 0.00 0.00 0.00 3.41
71 72 4.034048 CCAGAATATAAACGCACACCTGAC 59.966 45.833 0.00 0.00 0.00 3.51
72 73 4.188462 CCAGAATATAAACGCACACCTGA 58.812 43.478 0.00 0.00 0.00 3.86
73 74 3.312421 CCCAGAATATAAACGCACACCTG 59.688 47.826 0.00 0.00 0.00 4.00
74 75 3.541632 CCCAGAATATAAACGCACACCT 58.458 45.455 0.00 0.00 0.00 4.00
75 76 2.616842 CCCCAGAATATAAACGCACACC 59.383 50.000 0.00 0.00 0.00 4.16
76 77 3.275999 ACCCCAGAATATAAACGCACAC 58.724 45.455 0.00 0.00 0.00 3.82
77 78 3.537580 GACCCCAGAATATAAACGCACA 58.462 45.455 0.00 0.00 0.00 4.57
78 79 2.542595 CGACCCCAGAATATAAACGCAC 59.457 50.000 0.00 0.00 0.00 5.34
79 80 2.168936 ACGACCCCAGAATATAAACGCA 59.831 45.455 0.00 0.00 0.00 5.24
80 81 2.798847 GACGACCCCAGAATATAAACGC 59.201 50.000 0.00 0.00 0.00 4.84
81 82 3.047796 CGACGACCCCAGAATATAAACG 58.952 50.000 0.00 0.00 0.00 3.60
82 83 4.050852 ACGACGACCCCAGAATATAAAC 57.949 45.455 0.00 0.00 0.00 2.01
83 84 5.850557 TTACGACGACCCCAGAATATAAA 57.149 39.130 0.00 0.00 0.00 1.40
84 85 6.409524 AATTACGACGACCCCAGAATATAA 57.590 37.500 0.00 0.00 0.00 0.98
85 86 7.523293 TTAATTACGACGACCCCAGAATATA 57.477 36.000 0.00 0.00 0.00 0.86
86 87 4.950205 AATTACGACGACCCCAGAATAT 57.050 40.909 0.00 0.00 0.00 1.28
87 88 5.737063 GCTTAATTACGACGACCCCAGAATA 60.737 44.000 0.00 0.00 0.00 1.75
88 89 4.690122 CTTAATTACGACGACCCCAGAAT 58.310 43.478 0.00 0.00 0.00 2.40
89 90 3.676873 GCTTAATTACGACGACCCCAGAA 60.677 47.826 0.00 0.00 0.00 3.02
90 91 2.159198 GCTTAATTACGACGACCCCAGA 60.159 50.000 0.00 0.00 0.00 3.86
91 92 2.199236 GCTTAATTACGACGACCCCAG 58.801 52.381 0.00 0.00 0.00 4.45
92 93 1.134729 GGCTTAATTACGACGACCCCA 60.135 52.381 0.00 0.00 0.00 4.96
93 94 1.575244 GGCTTAATTACGACGACCCC 58.425 55.000 0.00 0.00 0.00 4.95
94 95 1.203065 CGGCTTAATTACGACGACCC 58.797 55.000 11.57 0.00 0.00 4.46
95 96 1.913317 ACGGCTTAATTACGACGACC 58.087 50.000 22.57 0.00 0.00 4.79
96 97 2.663119 ACAACGGCTTAATTACGACGAC 59.337 45.455 22.57 0.00 0.00 4.34
97 98 2.945278 ACAACGGCTTAATTACGACGA 58.055 42.857 22.57 0.00 0.00 4.20
98 99 3.710437 AACAACGGCTTAATTACGACG 57.290 42.857 15.07 15.07 0.00 5.12
99 100 5.021120 TCAAACAACGGCTTAATTACGAC 57.979 39.130 0.00 0.00 0.00 4.34
100 101 5.866335 ATCAAACAACGGCTTAATTACGA 57.134 34.783 0.00 0.00 0.00 3.43
101 102 6.799925 AGAAATCAAACAACGGCTTAATTACG 59.200 34.615 0.00 0.00 0.00 3.18
102 103 7.061789 CCAGAAATCAAACAACGGCTTAATTAC 59.938 37.037 0.00 0.00 0.00 1.89
103 104 7.087639 CCAGAAATCAAACAACGGCTTAATTA 58.912 34.615 0.00 0.00 0.00 1.40
104 105 5.925969 CCAGAAATCAAACAACGGCTTAATT 59.074 36.000 0.00 0.00 0.00 1.40
105 106 5.469479 CCAGAAATCAAACAACGGCTTAAT 58.531 37.500 0.00 0.00 0.00 1.40
106 107 4.261825 CCCAGAAATCAAACAACGGCTTAA 60.262 41.667 0.00 0.00 0.00 1.85
107 108 3.254657 CCCAGAAATCAAACAACGGCTTA 59.745 43.478 0.00 0.00 0.00 3.09
108 109 2.035832 CCCAGAAATCAAACAACGGCTT 59.964 45.455 0.00 0.00 0.00 4.35
109 110 1.613437 CCCAGAAATCAAACAACGGCT 59.387 47.619 0.00 0.00 0.00 5.52
110 111 1.611491 TCCCAGAAATCAAACAACGGC 59.389 47.619 0.00 0.00 0.00 5.68
111 112 2.621055 TGTCCCAGAAATCAAACAACGG 59.379 45.455 0.00 0.00 0.00 4.44
112 113 3.980646 TGTCCCAGAAATCAAACAACG 57.019 42.857 0.00 0.00 0.00 4.10
113 114 6.018832 CACATTTGTCCCAGAAATCAAACAAC 60.019 38.462 0.00 0.00 33.63 3.32
114 115 6.047870 CACATTTGTCCCAGAAATCAAACAA 58.952 36.000 0.00 0.00 33.63 2.83
115 116 5.128499 ACACATTTGTCCCAGAAATCAAACA 59.872 36.000 0.00 0.00 33.63 2.83
116 117 5.600696 ACACATTTGTCCCAGAAATCAAAC 58.399 37.500 0.00 0.00 33.63 2.93
117 118 5.867903 ACACATTTGTCCCAGAAATCAAA 57.132 34.783 0.00 0.00 34.95 2.69
118 119 5.598005 AGAACACATTTGTCCCAGAAATCAA 59.402 36.000 0.00 0.00 33.55 2.57
119 120 5.139727 AGAACACATTTGTCCCAGAAATCA 58.860 37.500 0.00 0.00 33.55 2.57
120 121 5.712152 AGAACACATTTGTCCCAGAAATC 57.288 39.130 0.00 0.00 33.55 2.17
121 122 6.542821 TCTAGAACACATTTGTCCCAGAAAT 58.457 36.000 0.00 0.00 33.55 2.17
122 123 5.935945 TCTAGAACACATTTGTCCCAGAAA 58.064 37.500 0.00 0.00 33.55 2.52
123 124 5.513094 CCTCTAGAACACATTTGTCCCAGAA 60.513 44.000 0.00 0.00 33.55 3.02
124 125 4.020218 CCTCTAGAACACATTTGTCCCAGA 60.020 45.833 0.00 0.00 33.55 3.86
125 126 4.020218 TCCTCTAGAACACATTTGTCCCAG 60.020 45.833 0.00 0.00 33.55 4.45
126 127 3.907474 TCCTCTAGAACACATTTGTCCCA 59.093 43.478 0.00 0.00 33.55 4.37
127 128 4.254492 GTCCTCTAGAACACATTTGTCCC 58.746 47.826 0.00 0.00 33.55 4.46
128 129 4.894784 TGTCCTCTAGAACACATTTGTCC 58.105 43.478 0.00 0.00 33.55 4.02
129 130 5.992217 ACTTGTCCTCTAGAACACATTTGTC 59.008 40.000 4.62 0.00 33.55 3.18
130 131 5.930135 ACTTGTCCTCTAGAACACATTTGT 58.070 37.500 4.62 2.99 37.67 2.83
131 132 6.226787 AGACTTGTCCTCTAGAACACATTTG 58.773 40.000 4.62 2.52 0.00 2.32
132 133 6.426646 AGACTTGTCCTCTAGAACACATTT 57.573 37.500 4.62 0.00 0.00 2.32
133 134 6.183361 ACAAGACTTGTCCTCTAGAACACATT 60.183 38.462 15.23 0.00 40.56 2.71
134 135 5.305644 ACAAGACTTGTCCTCTAGAACACAT 59.694 40.000 15.23 0.00 40.56 3.21
135 136 4.649674 ACAAGACTTGTCCTCTAGAACACA 59.350 41.667 15.23 0.00 40.56 3.72
136 137 5.203060 ACAAGACTTGTCCTCTAGAACAC 57.797 43.478 15.23 0.00 40.56 3.32
137 138 6.304624 TCTACAAGACTTGTCCTCTAGAACA 58.695 40.000 23.79 2.26 44.12 3.18
138 139 6.821031 TCTACAAGACTTGTCCTCTAGAAC 57.179 41.667 23.79 0.00 44.12 3.01
139 140 8.423906 AAATCTACAAGACTTGTCCTCTAGAA 57.576 34.615 23.79 3.70 44.12 2.10
140 141 8.423906 AAAATCTACAAGACTTGTCCTCTAGA 57.576 34.615 23.79 19.49 44.12 2.43
170 171 8.991275 AGATGAGTTATTGGATCTCTCTTCTTT 58.009 33.333 0.00 0.00 36.77 2.52
171 172 8.551682 AGATGAGTTATTGGATCTCTCTTCTT 57.448 34.615 0.00 0.00 36.77 2.52
172 173 8.551682 AAGATGAGTTATTGGATCTCTCTTCT 57.448 34.615 0.00 0.00 39.54 2.85
737 745 3.120165 GCTCCTGTCAGATTTCCGTTTTC 60.120 47.826 0.00 0.00 0.00 2.29
738 746 2.814336 GCTCCTGTCAGATTTCCGTTTT 59.186 45.455 0.00 0.00 0.00 2.43
739 747 2.427506 GCTCCTGTCAGATTTCCGTTT 58.572 47.619 0.00 0.00 0.00 3.60
740 748 1.339151 GGCTCCTGTCAGATTTCCGTT 60.339 52.381 0.00 0.00 0.00 4.44
741 749 0.250513 GGCTCCTGTCAGATTTCCGT 59.749 55.000 0.00 0.00 0.00 4.69
742 750 0.539051 AGGCTCCTGTCAGATTTCCG 59.461 55.000 0.00 0.00 0.00 4.30
743 751 2.797177 AAGGCTCCTGTCAGATTTCC 57.203 50.000 0.00 0.00 0.00 3.13
771 779 0.250513 GAGAGGAAATGGGTGCGAGT 59.749 55.000 0.00 0.00 0.00 4.18
976 992 1.381872 AGTCGAGGAGATGGTGGGG 60.382 63.158 0.00 0.00 0.00 4.96
1176 1230 7.176340 ACAAAATTGAGAGAGAAAAGAGGATGG 59.824 37.037 0.00 0.00 0.00 3.51
1236 1290 9.404348 GACTTCAGAGAAGGAATTTTTCAATTC 57.596 33.333 11.08 0.00 45.42 2.17
1940 3038 8.814038 ATCAGGCTGAAGTTTCATAAGTTATT 57.186 30.769 22.84 0.00 36.46 1.40
2253 3407 6.348295 GCTGACATATTGTTATCATGCTCAGG 60.348 42.308 0.00 0.00 33.39 3.86
2557 5294 0.894184 AAGGTTGAGCGACTCGGAGA 60.894 55.000 12.86 0.00 32.35 3.71
3540 7462 0.737715 CCCTCCTTGCTCGAAGTTCG 60.738 60.000 19.23 19.23 42.10 3.95
3745 7675 9.709495 TTAACACGGTGTCTTATGTAAGTTATT 57.291 29.630 15.09 0.00 34.93 1.40


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

AutoCloner maintained by Alex Coulton.