Multiple sequence alignment - TraesCS6B01G318100

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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 TraesCS6B01G318100 chr6B 100.000 3032 0 0 1 3032 566123391 566120360 0.000000e+00 5600.0
1 TraesCS6B01G318100 chr6B 91.600 1119 83 5 948 2064 566039038 566037929 0.000000e+00 1535.0
2 TraesCS6B01G318100 chr6B 94.564 791 32 4 2252 3032 192056477 192055688 0.000000e+00 1212.0
3 TraesCS6B01G318100 chr6B 90.035 853 84 1 1212 2064 566027192 566026341 0.000000e+00 1103.0
4 TraesCS6B01G318100 chr6B 90.695 806 54 10 2244 3032 473733386 473732585 0.000000e+00 1053.0
5 TraesCS6B01G318100 chr6B 82.817 355 39 10 874 1217 566028018 566027675 6.350000e-77 298.0
6 TraesCS6B01G318100 chr6B 97.561 164 4 0 1 164 80241557 80241720 6.400000e-72 281.0
7 TraesCS6B01G318100 chr6B 97.561 164 4 0 1 164 534065872 534066035 6.400000e-72 281.0
8 TraesCS6B01G318100 chr6B 97.561 164 4 0 1 164 566139344 566139181 6.400000e-72 281.0
9 TraesCS6B01G318100 chr6B 97.561 164 4 0 1 164 685193294 685193131 6.400000e-72 281.0
10 TraesCS6B01G318100 chr6D 94.249 1930 73 23 340 2247 380176928 380178841 0.000000e+00 2915.0
11 TraesCS6B01G318100 chr6D 91.273 1123 86 6 945 2064 380254816 380255929 0.000000e+00 1520.0
12 TraesCS6B01G318100 chr6D 90.294 1123 97 6 945 2064 380366528 380367641 0.000000e+00 1459.0
13 TraesCS6B01G318100 chr6A 92.937 1515 55 13 625 2134 520670901 520669434 0.000000e+00 2158.0
14 TraesCS6B01G318100 chr6A 90.089 1120 99 6 948 2064 520650413 520649303 0.000000e+00 1443.0
15 TraesCS6B01G318100 chr6A 88.119 303 33 2 163 462 520671515 520671213 1.030000e-94 357.0
16 TraesCS6B01G318100 chr1B 93.633 801 39 8 2242 3032 24508904 24508106 0.000000e+00 1186.0
17 TraesCS6B01G318100 chr1B 97.561 164 4 0 1 164 93844267 93844104 6.400000e-72 281.0
18 TraesCS6B01G318100 chr1B 97.561 164 4 0 1 164 252342278 252342441 6.400000e-72 281.0
19 TraesCS6B01G318100 chr1B 97.561 164 4 0 1 164 471642563 471642726 6.400000e-72 281.0
20 TraesCS6B01G318100 chr1B 97.561 164 4 0 1 164 473029413 473029576 6.400000e-72 281.0
21 TraesCS6B01G318100 chr5B 92.902 803 37 8 2245 3032 282067180 282066383 0.000000e+00 1149.0
22 TraesCS6B01G318100 chr5B 92.145 802 45 11 2245 3032 657140885 657141682 0.000000e+00 1116.0
23 TraesCS6B01G318100 chr3B 92.597 797 41 6 2252 3032 629590867 629590073 0.000000e+00 1129.0
24 TraesCS6B01G318100 chr3B 82.883 111 16 2 1547 1654 684617249 684617359 2.490000e-16 97.1
25 TraesCS6B01G318100 chr2B 92.346 797 43 10 2252 3032 381545212 381544418 0.000000e+00 1118.0
26 TraesCS6B01G318100 chr2B 93.906 722 29 10 2321 3032 90414056 90414772 0.000000e+00 1075.0
27 TraesCS6B01G318100 chr2B 82.353 68 9 2 1192 1259 41381511 41381575 4.220000e-04 56.5
28 TraesCS6B01G318100 chr7B 91.925 805 44 10 2245 3032 635063599 635062799 0.000000e+00 1107.0
29 TraesCS6B01G318100 chr7B 79.412 136 25 2 463 595 22539583 22539718 3.220000e-15 93.5
30 TraesCS6B01G318100 chr4B 91.003 678 39 11 2258 2917 148216064 148215391 0.000000e+00 894.0
31 TraesCS6B01G318100 chr4B 93.011 186 11 2 1 184 374694648 374694463 1.390000e-68 270.0
32 TraesCS6B01G318100 chr4B 81.955 133 22 1 466 596 222113106 222112974 8.890000e-21 111.0
33 TraesCS6B01G318100 chrUn 90.950 674 41 11 2252 2917 17895774 17895113 0.000000e+00 889.0
34 TraesCS6B01G318100 chrUn 83.562 73 10 2 1176 1246 24657923 24657851 1.950000e-07 67.6
35 TraesCS6B01G318100 chr7D 82.099 162 25 3 437 595 240911831 240911671 5.270000e-28 135.0
36 TraesCS6B01G318100 chr1D 82.707 133 20 2 466 595 439969326 439969194 6.870000e-22 115.0
37 TraesCS6B01G318100 chr5D 80.882 136 23 2 463 595 233968011 233968146 1.490000e-18 104.0
38 TraesCS6B01G318100 chr4D 77.160 162 25 5 437 595 173181241 173181089 1.940000e-12 84.2


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 TraesCS6B01G318100 chr6B 566120360 566123391 3031 True 5600.0 5600 100.000 1 3032 1 chr6B.!!$R4 3031
1 TraesCS6B01G318100 chr6B 566037929 566039038 1109 True 1535.0 1535 91.600 948 2064 1 chr6B.!!$R3 1116
2 TraesCS6B01G318100 chr6B 192055688 192056477 789 True 1212.0 1212 94.564 2252 3032 1 chr6B.!!$R1 780
3 TraesCS6B01G318100 chr6B 473732585 473733386 801 True 1053.0 1053 90.695 2244 3032 1 chr6B.!!$R2 788
4 TraesCS6B01G318100 chr6B 566026341 566028018 1677 True 700.5 1103 86.426 874 2064 2 chr6B.!!$R7 1190
5 TraesCS6B01G318100 chr6D 380176928 380178841 1913 False 2915.0 2915 94.249 340 2247 1 chr6D.!!$F1 1907
6 TraesCS6B01G318100 chr6D 380254816 380255929 1113 False 1520.0 1520 91.273 945 2064 1 chr6D.!!$F2 1119
7 TraesCS6B01G318100 chr6D 380366528 380367641 1113 False 1459.0 1459 90.294 945 2064 1 chr6D.!!$F3 1119
8 TraesCS6B01G318100 chr6A 520649303 520650413 1110 True 1443.0 1443 90.089 948 2064 1 chr6A.!!$R1 1116
9 TraesCS6B01G318100 chr6A 520669434 520671515 2081 True 1257.5 2158 90.528 163 2134 2 chr6A.!!$R2 1971
10 TraesCS6B01G318100 chr1B 24508106 24508904 798 True 1186.0 1186 93.633 2242 3032 1 chr1B.!!$R1 790
11 TraesCS6B01G318100 chr5B 282066383 282067180 797 True 1149.0 1149 92.902 2245 3032 1 chr5B.!!$R1 787
12 TraesCS6B01G318100 chr5B 657140885 657141682 797 False 1116.0 1116 92.145 2245 3032 1 chr5B.!!$F1 787
13 TraesCS6B01G318100 chr3B 629590073 629590867 794 True 1129.0 1129 92.597 2252 3032 1 chr3B.!!$R1 780
14 TraesCS6B01G318100 chr2B 381544418 381545212 794 True 1118.0 1118 92.346 2252 3032 1 chr2B.!!$R1 780
15 TraesCS6B01G318100 chr2B 90414056 90414772 716 False 1075.0 1075 93.906 2321 3032 1 chr2B.!!$F2 711
16 TraesCS6B01G318100 chr7B 635062799 635063599 800 True 1107.0 1107 91.925 2245 3032 1 chr7B.!!$R1 787
17 TraesCS6B01G318100 chr4B 148215391 148216064 673 True 894.0 894 91.003 2258 2917 1 chr4B.!!$R1 659
18 TraesCS6B01G318100 chrUn 17895113 17895774 661 True 889.0 889 90.950 2252 2917 1 chrUn.!!$R1 665

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
331 332 0.034186 TCATGGCAAGGATGGTGGTC 60.034 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 2926 2.434336 AGTCGTTATTCTATGGCTGGCA 59.566 45.455 6.31 6.31 0.0 4.92 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
21 22 4.922471 GTCAACTAGAGGCTTACTAGGG 57.078 50.000 13.13 6.54 40.86 3.53
22 23 4.534797 GTCAACTAGAGGCTTACTAGGGA 58.465 47.826 13.13 8.30 40.86 4.20
23 24 4.338964 GTCAACTAGAGGCTTACTAGGGAC 59.661 50.000 13.13 14.30 40.86 4.46
24 25 3.211718 ACTAGAGGCTTACTAGGGACG 57.788 52.381 13.13 0.00 40.86 4.79
25 26 2.509131 ACTAGAGGCTTACTAGGGACGT 59.491 50.000 13.13 0.00 40.86 4.34
26 27 3.713764 ACTAGAGGCTTACTAGGGACGTA 59.286 47.826 13.13 0.00 40.86 3.57
27 28 3.880168 AGAGGCTTACTAGGGACGTAT 57.120 47.619 0.00 0.00 0.00 3.06
28 29 4.181799 AGAGGCTTACTAGGGACGTATT 57.818 45.455 0.00 0.00 0.00 1.89
29 30 3.890147 AGAGGCTTACTAGGGACGTATTG 59.110 47.826 0.00 0.00 0.00 1.90
30 31 3.635836 GAGGCTTACTAGGGACGTATTGT 59.364 47.826 0.00 0.00 0.00 2.71
31 32 3.383825 AGGCTTACTAGGGACGTATTGTG 59.616 47.826 0.00 0.00 0.00 3.33
32 33 3.492137 GGCTTACTAGGGACGTATTGTGG 60.492 52.174 0.00 0.00 0.00 4.17
33 34 3.131755 GCTTACTAGGGACGTATTGTGGT 59.868 47.826 0.00 0.00 0.00 4.16
34 35 4.735873 GCTTACTAGGGACGTATTGTGGTC 60.736 50.000 0.00 0.00 0.00 4.02
35 36 3.097342 ACTAGGGACGTATTGTGGTCT 57.903 47.619 0.00 0.00 33.70 3.85
36 37 4.240881 ACTAGGGACGTATTGTGGTCTA 57.759 45.455 0.00 0.00 33.70 2.59
37 38 4.801164 ACTAGGGACGTATTGTGGTCTAT 58.199 43.478 0.00 0.00 33.70 1.98
38 39 4.583489 ACTAGGGACGTATTGTGGTCTATG 59.417 45.833 0.00 0.00 33.70 2.23
39 40 3.371965 AGGGACGTATTGTGGTCTATGT 58.628 45.455 0.00 0.00 33.70 2.29
40 41 4.539726 AGGGACGTATTGTGGTCTATGTA 58.460 43.478 0.00 0.00 33.70 2.29
41 42 5.145564 AGGGACGTATTGTGGTCTATGTAT 58.854 41.667 0.00 0.00 33.70 2.29
42 43 5.601313 AGGGACGTATTGTGGTCTATGTATT 59.399 40.000 0.00 0.00 33.70 1.89
43 44 5.924825 GGGACGTATTGTGGTCTATGTATTC 59.075 44.000 0.00 0.00 33.70 1.75
44 45 6.461927 GGGACGTATTGTGGTCTATGTATTCA 60.462 42.308 0.00 0.00 33.70 2.57
45 46 6.420008 GGACGTATTGTGGTCTATGTATTCAC 59.580 42.308 0.00 0.00 33.70 3.18
46 47 6.869695 ACGTATTGTGGTCTATGTATTCACA 58.130 36.000 0.00 0.00 39.52 3.58
47 48 6.755141 ACGTATTGTGGTCTATGTATTCACAC 59.245 38.462 0.00 0.00 37.96 3.82
48 49 6.075046 CGTATTGTGGTCTATGTATTCACACG 60.075 42.308 0.00 0.00 37.96 4.49
49 50 4.794278 TGTGGTCTATGTATTCACACGT 57.206 40.909 0.00 0.00 37.54 4.49
50 51 4.490743 TGTGGTCTATGTATTCACACGTG 58.509 43.478 15.48 15.48 37.54 4.49
51 52 4.021807 TGTGGTCTATGTATTCACACGTGT 60.022 41.667 17.22 17.22 37.54 4.49
52 53 5.183522 TGTGGTCTATGTATTCACACGTGTA 59.816 40.000 22.90 7.35 37.54 2.90
53 54 6.127563 TGTGGTCTATGTATTCACACGTGTAT 60.128 38.462 22.90 14.96 37.54 2.29
54 55 6.755141 GTGGTCTATGTATTCACACGTGTATT 59.245 38.462 22.90 11.42 37.54 1.89
55 56 7.916977 GTGGTCTATGTATTCACACGTGTATTA 59.083 37.037 22.90 9.93 37.54 0.98
56 57 7.916977 TGGTCTATGTATTCACACGTGTATTAC 59.083 37.037 22.90 20.91 37.54 1.89
73 74 8.746922 GTGTATTACGATTTCCGGATAATACA 57.253 34.615 28.04 28.04 43.07 2.29
74 75 9.195411 GTGTATTACGATTTCCGGATAATACAA 57.805 33.333 30.81 20.23 44.67 2.41
75 76 9.932207 TGTATTACGATTTCCGGATAATACAAT 57.068 29.630 28.86 17.11 42.76 2.71
81 82 9.667107 ACGATTTCCGGATAATACAATTATGAT 57.333 29.630 4.15 0.00 43.93 2.45
161 162 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33
192 193 1.674057 CAGACTCGCTTCCAAGGGT 59.326 57.895 3.55 0.00 39.69 4.34
198 199 2.269241 GCTTCCAAGGGTCGAGGG 59.731 66.667 0.00 0.00 0.00 4.30
201 202 1.915078 CTTCCAAGGGTCGAGGGCAT 61.915 60.000 0.00 0.00 0.00 4.40
203 204 2.669133 CCAAGGGTCGAGGGCATGA 61.669 63.158 0.00 0.00 0.00 3.07
222 223 2.738521 CAGAGGGTTGCGGTCACG 60.739 66.667 0.00 0.00 44.63 4.35
232 233 4.742201 CGGTCACGGACAGGCCAG 62.742 72.222 5.01 0.00 35.94 4.85
243 244 2.527624 AGGCCAGGCTGACAGTCA 60.528 61.111 17.94 2.48 0.00 3.41
260 261 2.158900 AGTCAGAGTTGTTGGTGTCAGG 60.159 50.000 0.00 0.00 0.00 3.86
266 267 0.106268 TTGTTGGTGTCAGGCCACAT 60.106 50.000 5.01 0.00 37.06 3.21
267 268 0.822944 TGTTGGTGTCAGGCCACATG 60.823 55.000 5.01 0.00 37.06 3.21
270 271 1.377725 GGTGTCAGGCCACATGGAG 60.378 63.158 5.01 0.00 37.06 3.86
287 288 0.250901 GAGTTGGTGTGCAGGATGGT 60.251 55.000 0.00 0.00 35.86 3.55
290 291 1.763546 TTGGTGTGCAGGATGGTCGA 61.764 55.000 0.00 0.00 35.86 4.20
319 320 2.905996 AAGGGCGAAGGTCATGGCA 61.906 57.895 0.00 0.00 0.00 4.92
330 331 0.323725 GTCATGGCAAGGATGGTGGT 60.324 55.000 0.00 0.00 0.00 4.16
331 332 0.034186 TCATGGCAAGGATGGTGGTC 60.034 55.000 0.00 0.00 0.00 4.02
369 370 2.281484 GTTGGAGGCAGGCAACGA 60.281 61.111 0.00 0.00 46.39 3.85
392 393 0.249657 GCTCATCGGAGATGGTGGAC 60.250 60.000 9.77 0.00 44.26 4.02
394 395 1.068083 CATCGGAGATGGTGGACGG 59.932 63.158 2.29 0.00 45.12 4.79
424 425 1.153269 TCACTGCAGTTGGTTCGCA 60.153 52.632 18.94 0.00 0.00 5.10
439 440 0.803117 TCGCACGAGAAGAACGAGAT 59.197 50.000 0.00 0.00 34.70 2.75
442 443 2.716504 CGCACGAGAAGAACGAGATATG 59.283 50.000 0.00 0.00 34.70 1.78
443 444 3.046390 GCACGAGAAGAACGAGATATGG 58.954 50.000 0.00 0.00 34.70 2.74
444 445 3.243101 GCACGAGAAGAACGAGATATGGA 60.243 47.826 0.00 0.00 34.70 3.41
445 446 4.733815 GCACGAGAAGAACGAGATATGGAA 60.734 45.833 0.00 0.00 34.70 3.53
474 485 0.532115 GCCTCGGTGAATTTGGCATT 59.468 50.000 0.00 0.00 42.79 3.56
475 486 1.736696 GCCTCGGTGAATTTGGCATTG 60.737 52.381 0.00 0.00 42.79 2.82
512 523 2.399448 CGGTTCCCGGAATTTTTGTTG 58.601 47.619 0.73 0.00 44.15 3.33
532 740 4.335214 CCACCGATTGGGCAATGA 57.665 55.556 3.39 0.00 42.54 2.57
569 777 9.823647 TGCCAAATGAAGTAAAAGTCAATTTAA 57.176 25.926 0.00 0.00 0.00 1.52
586 794 2.883122 TAACACCGGTTTTGGCCTAT 57.117 45.000 16.26 0.00 38.45 2.57
588 796 2.413310 ACACCGGTTTTGGCCTATAG 57.587 50.000 2.97 0.00 0.00 1.31
589 797 1.631898 ACACCGGTTTTGGCCTATAGT 59.368 47.619 2.97 0.00 0.00 2.12
591 799 1.910671 ACCGGTTTTGGCCTATAGTGA 59.089 47.619 0.00 0.00 0.00 3.41
592 800 2.306512 ACCGGTTTTGGCCTATAGTGAA 59.693 45.455 0.00 0.00 0.00 3.18
594 802 2.943033 CGGTTTTGGCCTATAGTGAAGG 59.057 50.000 3.32 0.00 37.17 3.46
595 803 3.288092 GGTTTTGGCCTATAGTGAAGGG 58.712 50.000 3.32 0.00 34.46 3.95
597 805 4.341487 GTTTTGGCCTATAGTGAAGGGTT 58.659 43.478 3.32 0.00 34.46 4.11
598 806 5.503002 GTTTTGGCCTATAGTGAAGGGTTA 58.497 41.667 3.32 0.00 34.46 2.85
599 807 5.367945 TTTGGCCTATAGTGAAGGGTTAG 57.632 43.478 3.32 0.00 34.46 2.34
600 808 2.704065 TGGCCTATAGTGAAGGGTTAGC 59.296 50.000 3.32 0.00 34.46 3.09
601 809 2.038689 GGCCTATAGTGAAGGGTTAGCC 59.961 54.545 0.00 0.00 34.46 3.93
602 810 2.704065 GCCTATAGTGAAGGGTTAGCCA 59.296 50.000 2.44 0.00 34.46 4.75
603 811 3.135895 GCCTATAGTGAAGGGTTAGCCAA 59.864 47.826 2.44 0.00 34.46 4.52
604 812 4.384868 GCCTATAGTGAAGGGTTAGCCAAA 60.385 45.833 2.44 0.00 34.46 3.28
605 813 5.751586 CCTATAGTGAAGGGTTAGCCAAAA 58.248 41.667 2.44 0.00 36.17 2.44
607 815 7.514721 CCTATAGTGAAGGGTTAGCCAAAATA 58.485 38.462 2.44 0.00 36.17 1.40
609 817 9.574516 CTATAGTGAAGGGTTAGCCAAAATATT 57.425 33.333 2.44 0.00 36.17 1.28
610 818 6.530019 AGTGAAGGGTTAGCCAAAATATTG 57.470 37.500 2.44 0.00 36.17 1.90
611 819 6.252995 AGTGAAGGGTTAGCCAAAATATTGA 58.747 36.000 2.44 0.00 38.94 2.57
612 820 6.378280 AGTGAAGGGTTAGCCAAAATATTGAG 59.622 38.462 2.44 0.00 38.94 3.02
613 821 6.377146 GTGAAGGGTTAGCCAAAATATTGAGA 59.623 38.462 2.44 0.00 38.94 3.27
614 822 6.377146 TGAAGGGTTAGCCAAAATATTGAGAC 59.623 38.462 2.44 0.00 38.94 3.36
615 823 5.201243 AGGGTTAGCCAAAATATTGAGACC 58.799 41.667 2.44 0.00 38.94 3.85
616 824 5.044105 AGGGTTAGCCAAAATATTGAGACCT 60.044 40.000 2.44 0.00 38.94 3.85
639 849 0.246910 GTTGAGACTTCCGGTCCCTC 59.753 60.000 0.00 5.20 45.54 4.30
645 855 1.306226 CTTCCGGTCCCTCCCTCTT 60.306 63.158 0.00 0.00 0.00 2.85
647 857 0.414629 TTCCGGTCCCTCCCTCTTTA 59.585 55.000 0.00 0.00 0.00 1.85
746 959 2.094675 CAAGTAGCCACCATCCAAAGG 58.905 52.381 0.00 0.00 0.00 3.11
749 962 2.378547 AGTAGCCACCATCCAAAGGAAA 59.621 45.455 0.00 0.00 34.34 3.13
765 982 6.246163 CAAAGGAAAATAGAACCTACCACCT 58.754 40.000 0.00 0.00 33.34 4.00
772 989 6.793505 AATAGAACCTACCACCTAGAACAG 57.206 41.667 0.00 0.00 0.00 3.16
818 1035 2.756760 CCCACAATTGCATCAAGCTAGT 59.243 45.455 5.05 0.00 45.94 2.57
1698 2415 1.875813 GATGCTGCTCCACGACGAG 60.876 63.158 0.00 0.00 0.00 4.18
1704 2421 4.180946 CTCCACGACGAGGGCGAG 62.181 72.222 11.55 0.00 41.64 5.03
2059 2776 5.600908 TGTCGGCTTAATTTTCTGTACAC 57.399 39.130 0.00 0.00 0.00 2.90
2209 2926 2.159382 CATTGGGTTCTACCGCAGTTT 58.841 47.619 0.00 0.00 39.83 2.66
2210 2927 1.600023 TTGGGTTCTACCGCAGTTTG 58.400 50.000 0.00 0.00 39.83 2.93
2211 2928 0.887387 TGGGTTCTACCGCAGTTTGC 60.887 55.000 0.00 0.00 39.83 3.68
2212 2929 1.583495 GGGTTCTACCGCAGTTTGCC 61.583 60.000 0.00 0.00 41.12 4.52
2213 2930 0.887387 GGTTCTACCGCAGTTTGCCA 60.887 55.000 0.00 0.00 41.12 4.92
2222 2939 1.176527 GCAGTTTGCCAGCCATAGAA 58.823 50.000 0.00 0.00 37.42 2.10
2248 2965 5.498393 ACGACTAGGTCTCAACATCTTAGA 58.502 41.667 0.00 0.00 0.00 2.10
2250 2967 5.587043 CGACTAGGTCTCAACATCTTAGACT 59.413 44.000 0.00 0.00 39.65 3.24
2304 3022 2.074547 TTGTCCGGATTCTGTCGTTC 57.925 50.000 7.81 0.00 0.00 3.95
2335 3053 2.361610 GGGTCGTGTCCGGGTCTA 60.362 66.667 0.00 0.00 33.95 2.59
2390 3110 0.537371 CGCATCCTTTACCCCATCCC 60.537 60.000 0.00 0.00 0.00 3.85
2564 3300 1.000731 CAGCCGGCCTTCAAAATGAAA 59.999 47.619 26.15 0.00 35.73 2.69
2857 3602 4.722700 GAGCTGCCTTTGCCGGGA 62.723 66.667 2.18 0.00 36.33 5.14
2905 3650 4.247380 GGCCGCCTCCTCCATCTG 62.247 72.222 0.71 0.00 0.00 2.90
2923 3668 2.975489 TCTGAAGCTTCCTTCTCTTGGT 59.025 45.455 23.42 0.00 46.13 3.67
2941 3686 0.537188 GTCGCCTCCTCCATCTCAAA 59.463 55.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.338964 GTCCCTAGTAAGCCTCTAGTTGAC 59.661 50.000 0.00 8.18 34.72 3.18
1 2 4.534797 GTCCCTAGTAAGCCTCTAGTTGA 58.465 47.826 0.00 1.98 34.72 3.18
2 3 3.315749 CGTCCCTAGTAAGCCTCTAGTTG 59.684 52.174 0.00 0.00 34.72 3.16
3 4 3.053768 ACGTCCCTAGTAAGCCTCTAGTT 60.054 47.826 0.00 0.00 34.72 2.24
4 5 2.509131 ACGTCCCTAGTAAGCCTCTAGT 59.491 50.000 0.00 0.00 34.72 2.57
5 6 3.211718 ACGTCCCTAGTAAGCCTCTAG 57.788 52.381 0.00 0.00 35.86 2.43
6 7 4.989875 ATACGTCCCTAGTAAGCCTCTA 57.010 45.455 0.00 0.00 0.00 2.43
7 8 3.880168 ATACGTCCCTAGTAAGCCTCT 57.120 47.619 0.00 0.00 0.00 3.69
8 9 3.635836 ACAATACGTCCCTAGTAAGCCTC 59.364 47.826 0.00 0.00 0.00 4.70
9 10 3.383825 CACAATACGTCCCTAGTAAGCCT 59.616 47.826 0.00 0.00 0.00 4.58
10 11 3.492137 CCACAATACGTCCCTAGTAAGCC 60.492 52.174 0.00 0.00 0.00 4.35
11 12 3.131755 ACCACAATACGTCCCTAGTAAGC 59.868 47.826 0.00 0.00 0.00 3.09
12 13 4.643784 AGACCACAATACGTCCCTAGTAAG 59.356 45.833 0.00 0.00 0.00 2.34
13 14 4.603131 AGACCACAATACGTCCCTAGTAA 58.397 43.478 0.00 0.00 0.00 2.24
14 15 4.240881 AGACCACAATACGTCCCTAGTA 57.759 45.455 0.00 0.00 0.00 1.82
15 16 3.097342 AGACCACAATACGTCCCTAGT 57.903 47.619 0.00 0.00 0.00 2.57
16 17 4.583489 ACATAGACCACAATACGTCCCTAG 59.417 45.833 0.00 0.00 0.00 3.02
17 18 4.539726 ACATAGACCACAATACGTCCCTA 58.460 43.478 0.00 0.00 0.00 3.53
18 19 3.371965 ACATAGACCACAATACGTCCCT 58.628 45.455 0.00 0.00 0.00 4.20
19 20 3.814005 ACATAGACCACAATACGTCCC 57.186 47.619 0.00 0.00 0.00 4.46
20 21 6.420008 GTGAATACATAGACCACAATACGTCC 59.580 42.308 0.00 0.00 0.00 4.79
21 22 6.976349 TGTGAATACATAGACCACAATACGTC 59.024 38.462 0.00 0.00 35.16 4.34
22 23 6.755141 GTGTGAATACATAGACCACAATACGT 59.245 38.462 0.00 0.00 39.13 3.57
23 24 6.075046 CGTGTGAATACATAGACCACAATACG 60.075 42.308 0.00 0.00 39.13 3.06
24 25 6.755141 ACGTGTGAATACATAGACCACAATAC 59.245 38.462 0.00 0.00 39.13 1.89
25 26 6.754675 CACGTGTGAATACATAGACCACAATA 59.245 38.462 7.58 0.00 39.13 1.90
26 27 5.580691 CACGTGTGAATACATAGACCACAAT 59.419 40.000 7.58 0.00 39.13 2.71
27 28 4.926832 CACGTGTGAATACATAGACCACAA 59.073 41.667 7.58 0.00 39.13 3.33
28 29 4.021807 ACACGTGTGAATACATAGACCACA 60.022 41.667 22.71 0.00 39.39 4.17
29 30 4.491676 ACACGTGTGAATACATAGACCAC 58.508 43.478 22.71 0.00 39.39 4.16
30 31 4.794278 ACACGTGTGAATACATAGACCA 57.206 40.909 22.71 0.00 39.39 4.02
31 32 7.112565 CGTAATACACGTGTGAATACATAGACC 59.887 40.741 30.83 6.57 45.82 3.85
32 33 7.979037 CGTAATACACGTGTGAATACATAGAC 58.021 38.462 30.83 14.41 45.82 2.59
48 49 8.746922 TGTATTATCCGGAAATCGTAATACAC 57.253 34.615 28.04 16.29 42.13 2.90
49 50 9.932207 ATTGTATTATCCGGAAATCGTAATACA 57.068 29.630 28.04 28.04 43.49 2.29
55 56 9.667107 ATCATAATTGTATTATCCGGAAATCGT 57.333 29.630 9.01 0.00 37.11 3.73
140 141 4.141390 ACTGTTGGAAATATGCCCTAGAGG 60.141 45.833 0.00 0.00 39.47 3.69
141 142 4.818546 CACTGTTGGAAATATGCCCTAGAG 59.181 45.833 0.00 0.00 0.00 2.43
142 143 4.780815 CACTGTTGGAAATATGCCCTAGA 58.219 43.478 0.00 0.00 0.00 2.43
143 144 3.316308 GCACTGTTGGAAATATGCCCTAG 59.684 47.826 0.00 0.00 0.00 3.02
144 145 3.287222 GCACTGTTGGAAATATGCCCTA 58.713 45.455 0.00 0.00 0.00 3.53
145 146 2.102578 GCACTGTTGGAAATATGCCCT 58.897 47.619 0.00 0.00 0.00 5.19
146 147 1.202290 CGCACTGTTGGAAATATGCCC 60.202 52.381 0.00 0.00 0.00 5.36
147 148 1.202290 CCGCACTGTTGGAAATATGCC 60.202 52.381 0.00 0.00 0.00 4.40
148 149 1.202290 CCCGCACTGTTGGAAATATGC 60.202 52.381 0.00 0.00 0.00 3.14
149 150 1.202290 GCCCGCACTGTTGGAAATATG 60.202 52.381 0.00 0.00 0.00 1.78
150 151 1.102978 GCCCGCACTGTTGGAAATAT 58.897 50.000 0.00 0.00 0.00 1.28
151 152 0.037590 AGCCCGCACTGTTGGAAATA 59.962 50.000 0.00 0.00 0.00 1.40
152 153 1.228552 AGCCCGCACTGTTGGAAAT 60.229 52.632 0.00 0.00 0.00 2.17
153 154 2.192861 CAGCCCGCACTGTTGGAAA 61.193 57.895 0.00 0.00 32.78 3.13
154 155 2.594303 CAGCCCGCACTGTTGGAA 60.594 61.111 0.00 0.00 32.78 3.53
155 156 4.641645 CCAGCCCGCACTGTTGGA 62.642 66.667 2.74 0.00 35.83 3.53
180 181 2.125512 CCTCGACCCTTGGAAGCG 60.126 66.667 0.00 0.00 0.00 4.68
183 184 1.923395 ATGCCCTCGACCCTTGGAA 60.923 57.895 0.00 0.00 0.00 3.53
192 193 2.060383 CCTCTGGTCATGCCCTCGA 61.060 63.158 0.00 0.00 36.04 4.04
222 223 3.618780 CTGTCAGCCTGGCCTGTCC 62.619 68.421 16.57 8.79 34.47 4.02
231 232 1.418334 ACAACTCTGACTGTCAGCCT 58.582 50.000 28.56 15.17 43.95 4.58
232 233 1.869767 CAACAACTCTGACTGTCAGCC 59.130 52.381 28.56 0.00 43.95 4.85
236 237 2.866762 GACACCAACAACTCTGACTGTC 59.133 50.000 0.00 0.00 0.00 3.51
237 238 2.236146 TGACACCAACAACTCTGACTGT 59.764 45.455 0.00 0.00 0.00 3.55
243 244 0.179018 GGCCTGACACCAACAACTCT 60.179 55.000 0.00 0.00 0.00 3.24
246 247 1.034838 TGTGGCCTGACACCAACAAC 61.035 55.000 3.32 0.00 39.39 3.32
260 261 1.959085 CACACCAACTCCATGTGGC 59.041 57.895 0.10 0.00 40.05 5.01
266 267 0.250858 CATCCTGCACACCAACTCCA 60.251 55.000 0.00 0.00 0.00 3.86
267 268 0.962356 CCATCCTGCACACCAACTCC 60.962 60.000 0.00 0.00 0.00 3.85
270 271 1.577328 CGACCATCCTGCACACCAAC 61.577 60.000 0.00 0.00 0.00 3.77
287 288 2.049156 CCTTGCACACGAGCTCGA 60.049 61.111 40.58 17.00 43.02 4.04
319 320 2.670148 GCCCTCGACCACCATCCTT 61.670 63.158 0.00 0.00 0.00 3.36
330 331 3.379445 GACTCCAACGGCCCTCGA 61.379 66.667 0.00 0.00 42.43 4.04
331 332 3.234630 TTGACTCCAACGGCCCTCG 62.235 63.158 0.00 0.00 45.88 4.63
369 370 1.411977 CACCATCTCCGATGAGCTCTT 59.588 52.381 16.19 8.82 38.58 2.85
392 393 1.749638 AGTGACTACCTCCGCTCCG 60.750 63.158 0.00 0.00 0.00 4.63
394 395 1.139947 GCAGTGACTACCTCCGCTC 59.860 63.158 0.00 0.00 0.00 5.03
424 425 5.776173 ATTCCATATCTCGTTCTTCTCGT 57.224 39.130 0.00 0.00 0.00 4.18
454 465 2.485122 GCCAAATTCACCGAGGCG 59.515 61.111 0.00 0.00 35.42 5.52
569 777 1.631898 ACTATAGGCCAAAACCGGTGT 59.368 47.619 8.52 0.00 33.69 4.16
586 794 7.406916 TCAATATTTTGGCTAACCCTTCACTA 58.593 34.615 0.00 0.00 33.44 2.74
588 796 6.377146 TCTCAATATTTTGGCTAACCCTTCAC 59.623 38.462 0.00 0.00 33.44 3.18
589 797 6.377146 GTCTCAATATTTTGGCTAACCCTTCA 59.623 38.462 0.00 0.00 33.44 3.02
591 799 5.656859 GGTCTCAATATTTTGGCTAACCCTT 59.343 40.000 0.00 0.00 33.44 3.95
592 800 5.044105 AGGTCTCAATATTTTGGCTAACCCT 60.044 40.000 0.00 0.00 33.44 4.34
594 802 6.603599 AGAAGGTCTCAATATTTTGGCTAACC 59.396 38.462 0.00 0.50 33.44 2.85
595 803 7.121315 ACAGAAGGTCTCAATATTTTGGCTAAC 59.879 37.037 0.00 0.00 33.44 2.34
597 805 6.721318 ACAGAAGGTCTCAATATTTTGGCTA 58.279 36.000 0.00 0.00 33.44 3.93
598 806 5.574188 ACAGAAGGTCTCAATATTTTGGCT 58.426 37.500 0.00 0.00 33.44 4.75
599 807 5.904362 ACAGAAGGTCTCAATATTTTGGC 57.096 39.130 0.00 0.00 33.44 4.52
600 808 7.391554 TCTCAACAGAAGGTCTCAATATTTTGG 59.608 37.037 0.00 0.00 33.44 3.28
601 809 8.233190 GTCTCAACAGAAGGTCTCAATATTTTG 58.767 37.037 0.00 0.00 0.00 2.44
602 810 8.160106 AGTCTCAACAGAAGGTCTCAATATTTT 58.840 33.333 0.00 0.00 0.00 1.82
603 811 7.684529 AGTCTCAACAGAAGGTCTCAATATTT 58.315 34.615 0.00 0.00 0.00 1.40
604 812 7.251321 AGTCTCAACAGAAGGTCTCAATATT 57.749 36.000 0.00 0.00 0.00 1.28
605 813 6.865834 AGTCTCAACAGAAGGTCTCAATAT 57.134 37.500 0.00 0.00 0.00 1.28
607 815 5.512232 GGAAGTCTCAACAGAAGGTCTCAAT 60.512 44.000 0.00 0.00 0.00 2.57
609 817 3.322254 GGAAGTCTCAACAGAAGGTCTCA 59.678 47.826 0.00 0.00 0.00 3.27
610 818 3.612955 CGGAAGTCTCAACAGAAGGTCTC 60.613 52.174 0.00 0.00 0.00 3.36
611 819 2.297597 CGGAAGTCTCAACAGAAGGTCT 59.702 50.000 0.00 0.00 0.00 3.85
612 820 2.610727 CCGGAAGTCTCAACAGAAGGTC 60.611 54.545 0.00 0.00 0.00 3.85
613 821 1.344763 CCGGAAGTCTCAACAGAAGGT 59.655 52.381 0.00 0.00 0.00 3.50
614 822 1.344763 ACCGGAAGTCTCAACAGAAGG 59.655 52.381 9.46 0.00 0.00 3.46
615 823 2.610727 GGACCGGAAGTCTCAACAGAAG 60.611 54.545 9.46 0.00 45.54 2.85
616 824 1.343465 GGACCGGAAGTCTCAACAGAA 59.657 52.381 9.46 0.00 45.54 3.02
729 942 2.507407 TTCCTTTGGATGGTGGCTAC 57.493 50.000 0.00 0.00 0.00 3.58
746 959 7.618137 TGTTCTAGGTGGTAGGTTCTATTTTC 58.382 38.462 0.00 0.00 0.00 2.29
749 962 6.262207 ACTGTTCTAGGTGGTAGGTTCTATT 58.738 40.000 0.00 0.00 0.00 1.73
765 982 5.722021 TTGTGAGCATGAGTACTGTTCTA 57.278 39.130 0.00 0.00 0.00 2.10
772 989 6.470235 GCAAACAATATTGTGAGCATGAGTAC 59.530 38.462 27.46 7.33 41.31 2.73
818 1035 5.353111 GCTTTTAAATAATTGGCCGGCTAA 58.647 37.500 28.35 28.35 0.00 3.09
867 1085 3.652274 ACTTTTGATTGGAACCAATGCG 58.348 40.909 21.56 8.88 45.50 4.73
957 1181 3.282021 ACTTGCATATGCCGATCAGTTT 58.718 40.909 24.54 0.00 41.18 2.66
1143 1372 4.492160 GCGATCCTGCCGTCGTCA 62.492 66.667 0.00 0.00 39.87 4.35
2079 2796 9.478019 CTTTGCGTAATACAAGAAGAATTACAG 57.522 33.333 0.00 0.00 36.37 2.74
2080 2797 9.210329 TCTTTGCGTAATACAAGAAGAATTACA 57.790 29.630 0.00 0.00 36.37 2.41
2209 2926 2.434336 AGTCGTTATTCTATGGCTGGCA 59.566 45.455 6.31 6.31 0.00 4.92
2210 2927 3.113260 AGTCGTTATTCTATGGCTGGC 57.887 47.619 0.00 0.00 0.00 4.85
2211 2928 4.281182 ACCTAGTCGTTATTCTATGGCTGG 59.719 45.833 0.00 0.00 0.00 4.85
2212 2929 5.241949 AGACCTAGTCGTTATTCTATGGCTG 59.758 44.000 0.00 0.00 37.67 4.85
2213 2930 5.386924 AGACCTAGTCGTTATTCTATGGCT 58.613 41.667 0.00 0.00 37.67 4.75
2222 2939 6.777213 AAGATGTTGAGACCTAGTCGTTAT 57.223 37.500 0.00 0.00 37.67 1.89
2248 2965 3.367743 TCGCGCGGTGGAGTTAGT 61.368 61.111 31.69 0.00 0.00 2.24
2250 2967 4.424566 GGTCGCGCGGTGGAGTTA 62.425 66.667 31.69 4.34 0.00 2.24
2564 3300 1.169661 TGTGCCGGCGAGAAAAACAT 61.170 50.000 23.90 0.00 0.00 2.71
2703 3448 0.681564 ATGAGCGAGAAGACGAGGGT 60.682 55.000 0.00 0.00 35.09 4.34
2857 3602 2.362503 TCGACATGGAGGAGGCGT 60.363 61.111 0.00 0.00 0.00 5.68
2905 3650 2.342179 CGACCAAGAGAAGGAAGCTTC 58.658 52.381 18.54 18.54 0.00 3.86
2923 3668 0.537188 GTTTGAGATGGAGGAGGCGA 59.463 55.000 0.00 0.00 0.00 5.54
2941 3686 4.039366 ACCTAGAGCTTCAAACGAAGAAGT 59.961 41.667 6.39 5.28 42.19 3.01


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

AutoCloner maintained by Alex Coulton.