Multiple sequence alignment - TraesCS6A01G299400

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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 TraesCS6A01G299400 chr6A 100.000 7249 0 0 1 7249 532645529 532652777 0.000000e+00 13387.0
1 TraesCS6A01G299400 chr6A 90.901 1176 100 5 4315 5489 199999926 199998757 0.000000e+00 1572.0
2 TraesCS6A01G299400 chr6A 88.755 747 78 5 5523 6263 199995473 199994727 0.000000e+00 909.0
3 TraesCS6A01G299400 chr6A 83.938 909 99 27 2382 3257 200003938 200003044 0.000000e+00 826.0
4 TraesCS6A01G299400 chr6A 88.793 580 50 7 3733 4303 200000547 199999974 0.000000e+00 697.0
5 TraesCS6A01G299400 chr6A 86.444 450 56 4 3305 3750 200002968 200002520 8.450000e-134 488.0
6 TraesCS6A01G299400 chr6A 88.561 271 22 5 1279 1541 532646541 532646810 3.260000e-83 320.0
7 TraesCS6A01G299400 chr6A 88.561 271 22 5 1013 1282 532646807 532647069 3.260000e-83 320.0
8 TraesCS6A01G299400 chr6A 95.556 45 2 0 2142 2186 200004189 200004145 1.010000e-08 73.1
9 TraesCS6A01G299400 chr6D 96.401 6530 153 32 13 6512 387638548 387645025 0.000000e+00 10682.0
10 TraesCS6A01G299400 chr6D 90.057 1941 179 8 4315 6248 147665125 147667058 0.000000e+00 2503.0
11 TraesCS6A01G299400 chr6D 87.936 1003 104 10 3305 4294 147664070 147665068 0.000000e+00 1166.0
12 TraesCS6A01G299400 chr6D 84.176 910 97 27 2382 3257 147654438 147655334 0.000000e+00 839.0
13 TraesCS6A01G299400 chr6D 91.353 266 16 4 1279 1541 387639527 387639788 2.490000e-94 357.0
14 TraesCS6A01G299400 chr6D 89.744 273 21 5 1013 1283 387639785 387640052 6.960000e-90 342.0
15 TraesCS6A01G299400 chr6D 76.733 649 118 20 1545 2175 147650364 147650997 1.510000e-86 331.0
16 TraesCS6A01G299400 chr6B 94.971 6502 240 39 45 6512 578511942 578518390 0.000000e+00 10115.0
17 TraesCS6A01G299400 chr6B 90.619 1940 170 9 4315 6248 260109035 260110968 0.000000e+00 2564.0
18 TraesCS6A01G299400 chr6B 88.391 982 98 7 3323 4294 260108003 260108978 0.000000e+00 1168.0
19 TraesCS6A01G299400 chr6B 90.836 622 55 2 2382 3001 260106853 260107474 0.000000e+00 832.0
20 TraesCS6A01G299400 chr6B 91.429 245 11 1 1279 1523 578512923 578513157 1.950000e-85 327.0
21 TraesCS6A01G299400 chr6B 87.500 280 24 5 1007 1284 578513151 578513421 5.460000e-81 313.0
22 TraesCS6A01G299400 chr6B 95.833 48 2 0 2139 2186 260106599 260106646 2.170000e-10 78.7
23 TraesCS6A01G299400 chr4A 89.750 761 52 2 6514 7249 661443208 661443967 0.000000e+00 950.0
24 TraesCS6A01G299400 chr7A 87.209 774 65 6 6509 7249 42448868 42449640 0.000000e+00 850.0
25 TraesCS6A01G299400 chr2A 87.160 771 65 6 6512 7249 451876770 451877539 0.000000e+00 845.0
26 TraesCS6A01G299400 chr1D 84.072 835 99 16 3488 4308 462493972 462493158 0.000000e+00 774.0
27 TraesCS6A01G299400 chr1D 88.673 565 18 9 6710 7249 348020111 348019568 0.000000e+00 647.0
28 TraesCS6A01G299400 chr1D 96.098 205 6 2 6514 6717 348029027 348028824 4.190000e-87 333.0
29 TraesCS6A01G299400 chr1D 89.865 148 14 1 4316 4462 462493101 462492954 9.600000e-44 189.0
30 TraesCS6A01G299400 chr1D 83.495 206 27 3 4532 4737 462492950 462492752 1.240000e-42 185.0
31 TraesCS6A01G299400 chr1D 87.582 153 11 5 6265 6413 473742321 473742173 3.480000e-38 171.0
32 TraesCS6A01G299400 chr1B 81.401 828 89 24 4744 5568 637635838 637635073 3.720000e-172 616.0
33 TraesCS6A01G299400 chr1B 83.482 224 26 6 4532 4753 637636163 637635949 1.600000e-46 198.0
34 TraesCS6A01G299400 chr1B 81.579 228 35 7 6503 6726 53084607 53084383 1.610000e-41 182.0
35 TraesCS6A01G299400 chr1B 92.157 102 8 0 4361 4462 637636268 637636167 2.110000e-30 145.0
36 TraesCS6A01G299400 chr5A 87.218 399 44 4 6509 6900 194870492 194870890 1.430000e-121 448.0
37 TraesCS6A01G299400 chr5A 85.549 346 24 2 6898 7217 194877987 194878332 9.010000e-89 339.0
38 TraesCS6A01G299400 chr4D 76.709 790 111 36 6509 7249 381507770 381508535 8.880000e-99 372.0
39 TraesCS6A01G299400 chrUn 90.638 235 17 2 1552 1786 96732136 96732365 2.540000e-79 307.0
40 TraesCS6A01G299400 chr7B 77.302 467 96 10 5821 6283 490686286 490685826 4.310000e-67 267.0
41 TraesCS6A01G299400 chr7B 85.526 152 22 0 3340 3491 490686627 490686476 7.530000e-35 159.0
42 TraesCS6A01G299400 chr7D 96.970 33 1 0 1285 1317 467438535 467438503 1.000000e-03 56.5


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 TraesCS6A01G299400 chr6A 532645529 532652777 7248 False 13387.000000 13387 100.000000 1 7249 1 chr6A.!!$F1 7248
1 TraesCS6A01G299400 chr6A 199994727 200004189 9462 True 760.850000 1572 89.064500 2142 6263 6 chr6A.!!$R1 4121
2 TraesCS6A01G299400 chr6A 532646541 532647069 528 False 320.000000 320 88.561000 1013 1541 2 chr6A.!!$F2 528
3 TraesCS6A01G299400 chr6D 387638548 387645025 6477 False 10682.000000 10682 96.401000 13 6512 1 chr6D.!!$F1 6499
4 TraesCS6A01G299400 chr6D 147664070 147667058 2988 False 1834.500000 2503 88.996500 3305 6248 2 chr6D.!!$F3 2943
5 TraesCS6A01G299400 chr6D 147650364 147655334 4970 False 585.000000 839 80.454500 1545 3257 2 chr6D.!!$F2 1712
6 TraesCS6A01G299400 chr6D 387639527 387640052 525 False 349.500000 357 90.548500 1013 1541 2 chr6D.!!$F4 528
7 TraesCS6A01G299400 chr6B 578511942 578518390 6448 False 10115.000000 10115 94.971000 45 6512 1 chr6B.!!$F1 6467
8 TraesCS6A01G299400 chr6B 260106599 260110968 4369 False 1160.675000 2564 91.419750 2139 6248 4 chr6B.!!$F2 4109
9 TraesCS6A01G299400 chr4A 661443208 661443967 759 False 950.000000 950 89.750000 6514 7249 1 chr4A.!!$F1 735
10 TraesCS6A01G299400 chr7A 42448868 42449640 772 False 850.000000 850 87.209000 6509 7249 1 chr7A.!!$F1 740
11 TraesCS6A01G299400 chr2A 451876770 451877539 769 False 845.000000 845 87.160000 6512 7249 1 chr2A.!!$F1 737
12 TraesCS6A01G299400 chr1D 348019568 348020111 543 True 647.000000 647 88.673000 6710 7249 1 chr1D.!!$R1 539
13 TraesCS6A01G299400 chr1D 462492752 462493972 1220 True 382.666667 774 85.810667 3488 4737 3 chr1D.!!$R4 1249
14 TraesCS6A01G299400 chr1B 637635073 637636268 1195 True 319.666667 616 85.680000 4361 5568 3 chr1B.!!$R2 1207
15 TraesCS6A01G299400 chr4D 381507770 381508535 765 False 372.000000 372 76.709000 6509 7249 1 chr4D.!!$F1 740
16 TraesCS6A01G299400 chr7B 490685826 490686627 801 True 213.000000 267 81.414000 3340 6283 2 chr7B.!!$R1 2943

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
980 1041 0.605319 TCCGCGGTTTCTGATGCTTT 60.605 50.000 27.15 0.00 0.0 3.51 F
1802 1884 0.322187 ATTGGTCAAGTACGGTGGCC 60.322 55.000 14.37 14.37 41.4 5.36 F
2056 2138 0.389426 TAGTTCAGGCCGCGAAACTC 60.389 55.000 8.23 4.33 0.0 3.01 F
2132 2214 1.031235 TGGTGTTGGTGTGAGCATTG 58.969 50.000 0.00 0.00 0.0 2.82 F
2201 2283 3.189287 ACATCAGAGCATTCCGAAACAAC 59.811 43.478 0.00 0.00 0.0 3.32 F
3949 9499 3.623203 GCCTGAAATGGTTGGAGATGAGA 60.623 47.826 0.00 0.00 0.0 3.27 F
4605 10214 0.034896 CTGGGCACTGTTACCGTCTT 59.965 55.000 0.00 0.00 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 2106 1.002087 CTGAACTAACTTCACCGGGCT 59.998 52.381 6.32 0.0 33.65 5.19 R
3290 6661 4.082571 ACACAGCTTCCATTAAAGTGATGC 60.083 41.667 0.00 0.0 0.00 3.91 R
3294 6665 4.516698 ACAGACACAGCTTCCATTAAAGTG 59.483 41.667 0.00 0.0 0.00 3.16 R
4116 9666 2.894731 TCCTCCTCATCACTGTCAGTT 58.105 47.619 1.67 0.0 0.00 3.16 R
4218 9768 6.936900 GTCCTGATATAGCTTTAAAGGATGCA 59.063 38.462 16.78 0.0 34.98 3.96 R
5281 11017 0.319900 TCTGCAGAACTCAACTCGGC 60.320 55.000 15.67 0.0 34.96 5.54 R
6595 15588 1.705337 CCAAATGCGGCGGTAGACTG 61.705 60.000 9.78 0.0 0.00 3.51 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
23 24 4.639078 TCATGACCTTCAATTCAGACCA 57.361 40.909 0.00 0.00 0.00 4.02
29 30 5.656416 TGACCTTCAATTCAGACCAAAACTT 59.344 36.000 0.00 0.00 0.00 2.66
34 35 7.167468 CCTTCAATTCAGACCAAAACTTAAACG 59.833 37.037 0.00 0.00 0.00 3.60
37 38 8.030106 TCAATTCAGACCAAAACTTAAACGTTT 58.970 29.630 18.90 18.90 38.66 3.60
39 40 5.096849 TCAGACCAAAACTTAAACGTTTGC 58.903 37.500 23.46 1.36 37.20 3.68
50 51 5.124297 ACTTAAACGTTTGCAGTTGTAAGGT 59.876 36.000 23.46 3.83 32.75 3.50
52 53 5.761165 AAACGTTTGCAGTTGTAAGGTAT 57.239 34.783 13.81 0.00 31.43 2.73
55 56 4.212636 ACGTTTGCAGTTGTAAGGTATCAC 59.787 41.667 0.00 0.00 0.00 3.06
64 65 5.523916 AGTTGTAAGGTATCACGATGCATTC 59.476 40.000 0.00 0.00 30.66 2.67
65 66 4.377021 TGTAAGGTATCACGATGCATTCC 58.623 43.478 0.00 0.00 30.66 3.01
66 67 2.550830 AGGTATCACGATGCATTCCC 57.449 50.000 0.00 0.00 0.00 3.97
85 94 1.272212 CCCTTACAAATGTGGTGTGGC 59.728 52.381 0.00 0.00 0.00 5.01
92 101 3.326588 ACAAATGTGGTGTGGCTCTAGTA 59.673 43.478 0.00 0.00 0.00 1.82
95 104 5.950544 AATGTGGTGTGGCTCTAGTATAA 57.049 39.130 0.00 0.00 0.00 0.98
102 111 5.712917 GGTGTGGCTCTAGTATAATCTAGCT 59.287 44.000 0.00 0.00 37.78 3.32
103 112 6.127842 GGTGTGGCTCTAGTATAATCTAGCTC 60.128 46.154 0.00 2.89 37.78 4.09
104 113 6.431543 GTGTGGCTCTAGTATAATCTAGCTCA 59.568 42.308 0.00 4.76 37.78 4.26
105 114 7.004691 TGTGGCTCTAGTATAATCTAGCTCAA 58.995 38.462 0.00 0.00 37.78 3.02
110 119 8.085296 GCTCTAGTATAATCTAGCTCAAAGCAA 58.915 37.037 0.00 0.00 45.56 3.91
111 120 9.405587 CTCTAGTATAATCTAGCTCAAAGCAAC 57.594 37.037 0.00 0.00 45.56 4.17
129 138 6.842437 AGCAACACTTCTAGAACTGAGATA 57.158 37.500 16.25 0.00 0.00 1.98
130 139 6.862209 AGCAACACTTCTAGAACTGAGATAG 58.138 40.000 16.25 1.39 0.00 2.08
131 140 5.518487 GCAACACTTCTAGAACTGAGATAGC 59.482 44.000 16.25 9.60 0.00 2.97
174 183 3.270027 TCGAAGCAACTACCAATCCATG 58.730 45.455 0.00 0.00 0.00 3.66
175 184 2.223340 CGAAGCAACTACCAATCCATGC 60.223 50.000 0.00 0.00 0.00 4.06
227 241 5.811100 CCAAAGCTTACAACTACTAGTAGCC 59.189 44.000 26.54 8.90 36.66 3.93
235 249 4.591924 ACAACTACTAGTAGCCAACAAGGT 59.408 41.667 26.54 11.95 40.61 3.50
255 269 3.518303 GGTCCACTACTTGGTTCACCTAT 59.482 47.826 0.00 0.00 46.97 2.57
338 353 2.747855 GGCTCCAAGGAAGCGTGG 60.748 66.667 0.00 0.00 36.13 4.94
364 379 2.737039 GCCTCGACTGGACTCAATTCTC 60.737 54.545 0.00 0.00 0.00 2.87
436 451 2.370519 TGAGAACGAGGGTTTTGGATGA 59.629 45.455 0.00 0.00 36.24 2.92
497 512 3.063084 GAGGAGCACGAGGACGGT 61.063 66.667 0.00 0.00 44.46 4.83
622 637 2.751913 CGTCTCGTCTCTGACCGGG 61.752 68.421 6.32 0.00 0.00 5.73
699 723 3.509967 CCCTTATGGCCGTTTTCTTCTTT 59.490 43.478 0.77 0.00 0.00 2.52
788 817 4.891037 GCCATCCCCCTGCTGCTC 62.891 72.222 0.00 0.00 0.00 4.26
789 818 3.095163 CCATCCCCCTGCTGCTCT 61.095 66.667 0.00 0.00 0.00 4.09
790 819 2.509916 CATCCCCCTGCTGCTCTC 59.490 66.667 0.00 0.00 0.00 3.20
791 820 2.771762 ATCCCCCTGCTGCTCTCC 60.772 66.667 0.00 0.00 0.00 3.71
792 821 3.344511 ATCCCCCTGCTGCTCTCCT 62.345 63.158 0.00 0.00 0.00 3.69
793 822 3.478274 CCCCCTGCTGCTCTCCTC 61.478 72.222 0.00 0.00 0.00 3.71
794 823 3.478274 CCCCTGCTGCTCTCCTCC 61.478 72.222 0.00 0.00 0.00 4.30
795 824 3.847602 CCCTGCTGCTCTCCTCCG 61.848 72.222 0.00 0.00 0.00 4.63
796 825 3.073735 CCTGCTGCTCTCCTCCGT 61.074 66.667 0.00 0.00 0.00 4.69
797 826 2.654079 CCTGCTGCTCTCCTCCGTT 61.654 63.158 0.00 0.00 0.00 4.44
798 827 1.447489 CTGCTGCTCTCCTCCGTTG 60.447 63.158 0.00 0.00 0.00 4.10
799 828 2.125350 GCTGCTCTCCTCCGTTGG 60.125 66.667 0.00 0.00 0.00 3.77
800 829 2.125350 CTGCTCTCCTCCGTTGGC 60.125 66.667 0.00 0.00 0.00 4.52
801 830 3.997064 CTGCTCTCCTCCGTTGGCG 62.997 68.421 0.00 0.00 37.95 5.69
803 832 4.821589 CTCTCCTCCGTTGGCGCC 62.822 72.222 22.73 22.73 36.67 6.53
838 892 4.220163 TCGCCCCTCTCGGCCTAT 62.220 66.667 0.00 0.00 46.98 2.57
980 1041 0.605319 TCCGCGGTTTCTGATGCTTT 60.605 50.000 27.15 0.00 0.00 3.51
985 1047 3.578688 GCGGTTTCTGATGCTTTTTCAT 58.421 40.909 0.00 0.00 0.00 2.57
1005 1067 1.446099 TCGCAGTTCGAGCATGGAC 60.446 57.895 1.01 0.00 43.16 4.02
1541 1607 5.728741 AGGTTGGGACTTCTTCTCTTGATAT 59.271 40.000 0.00 0.00 0.00 1.63
1652 1718 2.863739 TCGAGACTTTGCAGTATGTCG 58.136 47.619 6.43 6.43 39.31 4.35
1654 1720 3.437741 TCGAGACTTTGCAGTATGTCGTA 59.562 43.478 10.89 0.00 39.31 3.43
1660 1726 7.149973 AGACTTTGCAGTATGTCGTAAACTTA 58.850 34.615 0.00 0.00 39.31 2.24
1706 1788 6.643770 GGTTTGTATTTCTTCTGACGACTGTA 59.356 38.462 0.00 0.00 0.00 2.74
1802 1884 0.322187 ATTGGTCAAGTACGGTGGCC 60.322 55.000 14.37 14.37 41.40 5.36
1804 1886 2.046604 GTCAAGTACGGTGGCCCC 60.047 66.667 0.00 0.00 0.00 5.80
1809 1891 1.205460 AAGTACGGTGGCCCCATCTT 61.205 55.000 0.00 3.38 0.00 2.40
1812 1894 0.834612 TACGGTGGCCCCATCTTTAG 59.165 55.000 0.00 0.00 0.00 1.85
1915 1997 3.124270 CGTAGGCGTGCCATGCAA 61.124 61.111 14.29 0.00 41.47 4.08
1980 2062 8.174422 GCTATTCAAGAAAAACTCTGATCAGAC 58.826 37.037 21.67 10.70 33.37 3.51
2056 2138 0.389426 TAGTTCAGGCCGCGAAACTC 60.389 55.000 8.23 4.33 0.00 3.01
2077 2159 4.533815 TCTATCATCCTGGTAGTGAACGT 58.466 43.478 0.00 0.00 32.96 3.99
2112 2194 3.698250 ACGCAGTGAAGCCTAACAA 57.302 47.368 0.00 0.00 42.51 2.83
2117 2199 2.095059 GCAGTGAAGCCTAACAATGGTG 60.095 50.000 0.00 0.00 33.62 4.17
2132 2214 1.031235 TGGTGTTGGTGTGAGCATTG 58.969 50.000 0.00 0.00 0.00 2.82
2201 2283 3.189287 ACATCAGAGCATTCCGAAACAAC 59.811 43.478 0.00 0.00 0.00 3.32
2325 5570 5.863965 TGGTCCGCATCTGAAATATATTCA 58.136 37.500 0.00 0.00 0.00 2.57
2341 5666 8.845413 AATATATTCATCTCAGAAAGCTGGTC 57.155 34.615 0.00 0.00 42.53 4.02
3286 6657 9.932207 AAACAAATTCTGAAATTCATATGCTGA 57.068 25.926 0.00 0.00 33.93 4.26
3291 6662 9.856488 AATTCTGAAATTCATATGCTGATATGC 57.144 29.630 0.00 0.00 40.92 3.14
3539 7096 8.588290 ATGAAAGGTAAAACATACAGGCATTA 57.412 30.769 0.00 0.00 0.00 1.90
3949 9499 3.623203 GCCTGAAATGGTTGGAGATGAGA 60.623 47.826 0.00 0.00 0.00 3.27
4116 9666 4.562347 GCTGAAACAGAGAGTGAGATGGAA 60.562 45.833 2.81 0.00 32.44 3.53
4218 9768 5.186603 TGCTGAGAGTTCATCTGTACTGAAT 59.813 40.000 6.54 0.00 38.84 2.57
4605 10214 0.034896 CTGGGCACTGTTACCGTCTT 59.965 55.000 0.00 0.00 0.00 3.01
4635 10244 4.034510 GGTGCAGCATACAGTAAAGATGAC 59.965 45.833 11.86 2.59 0.00 3.06
5171 10906 2.869192 GGATCGACATGAAAGGAAGAGC 59.131 50.000 0.00 0.00 0.00 4.09
5281 11017 6.300354 ACGGTCATTTGAGTGTTCTAAAAG 57.700 37.500 0.00 0.00 28.68 2.27
5537 14523 5.126067 GCTGATAGGGTTGCAAAGAAGATA 58.874 41.667 0.00 0.00 0.00 1.98
5615 14601 5.178809 TCAATCTTGCGCTCTCAATGATATG 59.821 40.000 9.73 3.45 0.00 1.78
5894 14880 4.211125 TGCACAGTTTACCCATCAAAGAA 58.789 39.130 0.00 0.00 0.00 2.52
6417 15410 8.565896 AGCATTCAATGTAATGAACAGTAAGA 57.434 30.769 0.00 0.00 42.70 2.10
6489 15482 4.515191 TGAACCTGCACATTTTGTCTCTAC 59.485 41.667 0.00 0.00 0.00 2.59
6591 15584 2.279784 CCGAGCAGAATCGAGCCC 60.280 66.667 0.00 0.00 45.56 5.19
6601 15594 3.733507 ATCGAGCCCGGGCAGTCTA 62.734 63.158 45.13 27.57 44.88 2.59
6638 15631 2.647949 AACGAGGGGGAGGGATCCT 61.648 63.158 12.58 0.00 36.03 3.24
6639 15632 2.525381 CGAGGGGGAGGGATCCTG 60.525 72.222 12.58 0.00 31.76 3.86
6649 15642 2.603580 GGATCCTGGCCCTTTCCC 59.396 66.667 3.84 0.00 0.00 3.97
6650 15643 2.009302 GGATCCTGGCCCTTTCCCT 61.009 63.158 3.84 0.00 0.00 4.20
6738 15731 2.951745 CGACTGAGATGCGACGGC 60.952 66.667 0.00 0.00 40.52 5.68
6769 15788 3.822192 CGACCGGGAGCGATGTGA 61.822 66.667 6.32 0.00 0.00 3.58
6889 15915 2.039480 AGAAGATCCACTCTTTGCTGCA 59.961 45.455 0.00 0.00 44.42 4.41
6892 15918 0.877071 ATCCACTCTTTGCTGCAACG 59.123 50.000 15.72 13.77 0.00 4.10
6921 15949 2.422519 CCATGAAGCTAAGTGATGCCCT 60.423 50.000 0.00 0.00 0.00 5.19
6942 15970 2.205342 CCACCAAAGGATCTTCCCCTA 58.795 52.381 0.00 0.00 37.19 3.53
7205 16279 0.241749 TGGAAATTTCGCTGCTGCAG 59.758 50.000 24.80 24.80 39.64 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.573219 TGGTCTGAATTGAAGGTCATGATT 58.427 37.500 0.00 0.00 0.00 2.57
1 2 5.183530 TGGTCTGAATTGAAGGTCATGAT 57.816 39.130 0.00 0.00 0.00 2.45
3 4 5.710513 TTTGGTCTGAATTGAAGGTCATG 57.289 39.130 0.00 0.00 0.00 3.07
4 5 5.835280 AGTTTTGGTCTGAATTGAAGGTCAT 59.165 36.000 0.00 0.00 0.00 3.06
5 6 5.200483 AGTTTTGGTCTGAATTGAAGGTCA 58.800 37.500 0.00 0.00 0.00 4.02
6 7 5.774498 AGTTTTGGTCTGAATTGAAGGTC 57.226 39.130 0.00 0.00 0.00 3.85
7 8 7.654022 TTAAGTTTTGGTCTGAATTGAAGGT 57.346 32.000 0.00 0.00 0.00 3.50
8 9 7.167468 CGTTTAAGTTTTGGTCTGAATTGAAGG 59.833 37.037 0.00 0.00 0.00 3.46
9 10 7.700656 ACGTTTAAGTTTTGGTCTGAATTGAAG 59.299 33.333 0.00 0.00 0.00 3.02
10 11 7.540299 ACGTTTAAGTTTTGGTCTGAATTGAA 58.460 30.769 0.00 0.00 0.00 2.69
11 12 7.090953 ACGTTTAAGTTTTGGTCTGAATTGA 57.909 32.000 0.00 0.00 0.00 2.57
19 20 4.860352 ACTGCAAACGTTTAAGTTTTGGTC 59.140 37.500 14.20 0.00 41.84 4.02
20 21 4.811908 ACTGCAAACGTTTAAGTTTTGGT 58.188 34.783 14.20 2.10 41.84 3.67
21 22 5.119434 ACAACTGCAAACGTTTAAGTTTTGG 59.881 36.000 26.53 20.71 41.84 3.28
23 24 7.062488 CCTTACAACTGCAAACGTTTAAGTTTT 59.938 33.333 26.53 23.85 41.84 2.43
29 30 6.482641 TGATACCTTACAACTGCAAACGTTTA 59.517 34.615 14.20 0.00 0.00 2.01
34 35 4.449743 TCGTGATACCTTACAACTGCAAAC 59.550 41.667 0.00 0.00 0.00 2.93
37 38 3.945981 TCGTGATACCTTACAACTGCA 57.054 42.857 0.00 0.00 0.00 4.41
39 40 4.180817 TGCATCGTGATACCTTACAACTG 58.819 43.478 0.00 0.00 0.00 3.16
50 51 3.389656 TGTAAGGGGAATGCATCGTGATA 59.610 43.478 0.00 0.00 0.00 2.15
52 53 1.557371 TGTAAGGGGAATGCATCGTGA 59.443 47.619 0.00 0.00 0.00 4.35
55 56 3.381272 ACATTTGTAAGGGGAATGCATCG 59.619 43.478 0.00 0.00 34.86 3.84
64 65 1.892474 CCACACCACATTTGTAAGGGG 59.108 52.381 0.00 0.00 0.00 4.79
65 66 1.272212 GCCACACCACATTTGTAAGGG 59.728 52.381 0.00 0.00 0.00 3.95
66 67 2.228822 GAGCCACACCACATTTGTAAGG 59.771 50.000 0.00 0.00 0.00 2.69
85 94 9.405587 GTTGCTTTGAGCTAGATTATACTAGAG 57.594 37.037 0.00 0.00 42.97 2.43
92 101 7.108847 AGAAGTGTTGCTTTGAGCTAGATTAT 58.891 34.615 0.00 0.00 42.97 1.28
95 104 4.904241 AGAAGTGTTGCTTTGAGCTAGAT 58.096 39.130 0.00 0.00 42.97 1.98
102 111 5.670485 TCAGTTCTAGAAGTGTTGCTTTGA 58.330 37.500 30.44 13.10 41.32 2.69
103 112 5.755375 TCTCAGTTCTAGAAGTGTTGCTTTG 59.245 40.000 30.44 16.87 41.32 2.77
104 113 5.918608 TCTCAGTTCTAGAAGTGTTGCTTT 58.081 37.500 30.44 0.00 41.32 3.51
105 114 5.537300 TCTCAGTTCTAGAAGTGTTGCTT 57.463 39.130 30.44 0.09 41.32 3.91
110 119 5.163561 GCTGCTATCTCAGTTCTAGAAGTGT 60.164 44.000 30.44 18.98 41.32 3.55
111 120 5.163571 TGCTGCTATCTCAGTTCTAGAAGTG 60.164 44.000 27.68 27.68 41.79 3.16
190 199 1.663702 CTTTGGCAAGCTGCTGTGC 60.664 57.895 20.90 20.90 44.28 4.57
191 200 4.647654 CTTTGGCAAGCTGCTGTG 57.352 55.556 1.35 5.22 44.28 3.66
216 230 3.767673 TGGACCTTGTTGGCTACTAGTAG 59.232 47.826 23.25 23.25 40.22 2.57
217 231 3.512724 GTGGACCTTGTTGGCTACTAGTA 59.487 47.826 1.89 1.89 40.22 1.82
218 232 2.302157 GTGGACCTTGTTGGCTACTAGT 59.698 50.000 0.00 0.00 40.22 2.57
255 269 0.037303 AGGTCGTCCGTCTCAACCTA 59.963 55.000 0.00 0.00 38.56 3.08
338 353 2.065906 GAGTCCAGTCGAGGCGATCC 62.066 65.000 0.00 0.00 38.42 3.36
364 379 3.666883 TCGCCGTGCTTATTTTATGTG 57.333 42.857 0.00 0.00 0.00 3.21
780 809 1.447489 CAACGGAGGAGAGCAGCAG 60.447 63.158 0.00 0.00 0.00 4.24
781 810 2.659016 CAACGGAGGAGAGCAGCA 59.341 61.111 0.00 0.00 0.00 4.41
782 811 2.125350 CCAACGGAGGAGAGCAGC 60.125 66.667 0.00 0.00 0.00 5.25
783 812 2.125350 GCCAACGGAGGAGAGCAG 60.125 66.667 0.00 0.00 0.00 4.24
784 813 4.069232 CGCCAACGGAGGAGAGCA 62.069 66.667 0.00 0.00 34.97 4.26
786 815 4.821589 GGCGCCAACGGAGGAGAG 62.822 72.222 24.80 0.00 40.57 3.20
805 834 4.862823 GACGGAGGAGGGAGGGGG 62.863 77.778 0.00 0.00 0.00 5.40
980 1041 0.790207 GCTCGAACTGCGACATGAAA 59.210 50.000 0.00 0.00 45.59 2.69
985 1047 1.737735 CCATGCTCGAACTGCGACA 60.738 57.895 0.00 0.00 45.59 4.35
1005 1067 1.658717 CGCGTTGCTATCCTCCTCG 60.659 63.158 0.00 0.00 0.00 4.63
1541 1607 3.820467 CTGATACAAACACCAAAGCTGGA 59.180 43.478 0.00 0.00 46.92 3.86
1654 1720 8.157476 ACCACAGAAAGTAGACATCATAAGTTT 58.843 33.333 0.00 0.00 0.00 2.66
1660 1726 4.287067 ACCACCACAGAAAGTAGACATCAT 59.713 41.667 0.00 0.00 0.00 2.45
1706 1788 1.134128 TGTGCAGGGCGATTGTCATAT 60.134 47.619 0.00 0.00 0.00 1.78
1761 1843 2.623915 CCCTGAAGTGTGCAGCAGC 61.624 63.158 0.00 0.00 42.57 5.25
1802 1884 3.303351 AATCCAGGTGCTAAAGATGGG 57.697 47.619 0.00 0.00 0.00 4.00
1804 1886 6.610741 GAACTAATCCAGGTGCTAAAGATG 57.389 41.667 0.00 0.00 0.00 2.90
2024 2106 1.002087 CTGAACTAACTTCACCGGGCT 59.998 52.381 6.32 0.00 33.65 5.19
2029 2111 1.439679 CGGCCTGAACTAACTTCACC 58.560 55.000 0.00 0.00 33.65 4.02
2056 2138 4.920640 ACGTTCACTACCAGGATGATAG 57.079 45.455 0.00 0.00 38.53 2.08
2077 2159 4.158579 ACTGCGTCACTCTCATGATTCTTA 59.841 41.667 0.00 0.00 0.00 2.10
2112 2194 1.614903 CAATGCTCACACCAACACCAT 59.385 47.619 0.00 0.00 0.00 3.55
2117 2199 3.004629 TGATTCACAATGCTCACACCAAC 59.995 43.478 0.00 0.00 0.00 3.77
2325 5570 1.661463 TGGGACCAGCTTTCTGAGAT 58.339 50.000 0.00 0.00 42.95 2.75
2341 5666 6.824305 AATTCAGTTAAGTCAGAACATGGG 57.176 37.500 0.00 0.00 0.00 4.00
3266 6627 9.020731 TGCATATCAGCATATGAATTTCAGAAT 57.979 29.630 6.97 0.00 43.37 2.40
3285 6656 7.082602 CAGCTTCCATTAAAGTGATGCATATC 58.917 38.462 0.00 0.00 33.13 1.63
3286 6657 6.548622 ACAGCTTCCATTAAAGTGATGCATAT 59.451 34.615 0.00 0.00 33.13 1.78
3288 6659 4.708421 ACAGCTTCCATTAAAGTGATGCAT 59.292 37.500 0.00 0.00 33.13 3.96
3290 6661 4.082571 ACACAGCTTCCATTAAAGTGATGC 60.083 41.667 0.00 0.00 0.00 3.91
3291 6662 5.413833 AGACACAGCTTCCATTAAAGTGATG 59.586 40.000 0.00 0.00 0.00 3.07
3292 6663 5.413833 CAGACACAGCTTCCATTAAAGTGAT 59.586 40.000 0.00 0.00 0.00 3.06
3294 6665 4.516698 ACAGACACAGCTTCCATTAAAGTG 59.483 41.667 0.00 0.00 0.00 3.16
3303 6692 7.334421 TCAATCTTTATTACAGACACAGCTTCC 59.666 37.037 0.00 0.00 0.00 3.46
3539 7096 7.986085 AACTTTCATATGCACAGAAGTTAGT 57.014 32.000 11.47 4.91 0.00 2.24
4116 9666 2.894731 TCCTCCTCATCACTGTCAGTT 58.105 47.619 1.67 0.00 0.00 3.16
4218 9768 6.936900 GTCCTGATATAGCTTTAAAGGATGCA 59.063 38.462 16.78 0.00 34.98 3.96
4605 10214 2.567169 ACTGTATGCTGCACCTGAGTAA 59.433 45.455 3.57 0.00 0.00 2.24
4635 10244 5.220739 CGGCTCAGTGAATTCAGGAAATAAG 60.221 44.000 8.80 1.51 0.00 1.73
5171 10906 1.901591 TGGCTTTGAGCTTCTTCTGG 58.098 50.000 0.00 0.00 41.99 3.86
5281 11017 0.319900 TCTGCAGAACTCAACTCGGC 60.320 55.000 15.67 0.00 34.96 5.54
5537 14523 6.773976 TTTGACAATCCAGAGAAAGTGTTT 57.226 33.333 0.00 0.00 0.00 2.83
6377 15370 5.342806 TGAATGCTTCACTGTTACTTTCG 57.657 39.130 0.00 0.00 34.08 3.46
6417 15410 6.923508 TCGTTTTCATCACGAGCTATATCAAT 59.076 34.615 0.00 0.00 41.66 2.57
6489 15482 2.775890 AGAGACAAACATCTGCACAGG 58.224 47.619 0.00 0.00 0.00 4.00
6595 15588 1.705337 CCAAATGCGGCGGTAGACTG 61.705 60.000 9.78 0.00 0.00 3.51
6601 15594 3.370231 GGAACCAAATGCGGCGGT 61.370 61.111 9.78 0.00 33.32 5.68
6738 15731 0.179225 CGGTCGGCTTTCATCAAACG 60.179 55.000 0.00 0.00 0.00 3.60
6889 15915 1.291877 GCTTCATGGCTGACGTCGTT 61.292 55.000 11.62 0.00 0.00 3.85
6892 15918 1.929836 CTTAGCTTCATGGCTGACGTC 59.070 52.381 9.11 9.11 43.01 4.34
6921 15949 0.999712 GGGGAAGATCCTTTGGTGGA 59.000 55.000 0.00 0.00 40.82 4.02
7205 16279 1.548719 GGCCATACCAGGGAAACAAAC 59.451 52.381 0.00 0.00 38.86 2.93


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

AutoCloner maintained by Alex Coulton.