Multiple sequence alignment - TraesCS7A01G387000

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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 TraesCS7A01G387000 chr7A 100.000 3533 0 0 1 3533 563247815 563244283 0.000000e+00 6525.0
1 TraesCS7A01G387000 chr7A 87.183 2364 237 31 599 2931 563293760 563291432 0.000000e+00 2627.0
2 TraesCS7A01G387000 chr7A 96.000 50 2 0 1 50 19929099 19929148 8.130000e-12 82.4
3 TraesCS7A01G387000 chr7A 96.000 50 2 0 1 50 130595919 130595870 8.130000e-12 82.4
4 TraesCS7A01G387000 chr7A 96.000 50 2 0 48 97 410827149 410827198 8.130000e-12 82.4
5 TraesCS7A01G387000 chr7B 92.708 2578 148 14 989 3533 525598504 525595934 0.000000e+00 3683.0
6 TraesCS7A01G387000 chr7B 84.412 417 19 20 578 994 525598897 525598527 5.570000e-98 368.0
7 TraesCS7A01G387000 chr7B 93.590 78 4 1 389 465 525599243 525599166 8.010000e-22 115.0
8 TraesCS7A01G387000 chr7B 86.905 84 6 4 492 571 525599105 525599023 4.860000e-14 89.8
9 TraesCS7A01G387000 chr7B 96.000 50 2 0 1 50 586726361 586726312 8.130000e-12 82.4
10 TraesCS7A01G387000 chr7D 94.785 2301 81 18 492 2786 497321216 497318949 0.000000e+00 3548.0
11 TraesCS7A01G387000 chr7D 87.448 1920 226 11 989 2900 28578581 28576669 0.000000e+00 2196.0
12 TraesCS7A01G387000 chr7D 87.086 604 42 14 2877 3448 497318562 497317963 0.000000e+00 651.0
13 TraesCS7A01G387000 chr7D 88.372 344 28 6 94 425 497322067 497321724 1.530000e-108 403.0
14 TraesCS7A01G387000 chr1D 85.370 2201 261 38 589 2778 33595363 33597513 0.000000e+00 2224.0
15 TraesCS7A01G387000 chr1A 87.480 1901 211 14 886 2778 32111033 32112914 0.000000e+00 2167.0
16 TraesCS7A01G387000 chr1A 97.917 48 1 0 48 95 516764566 516764613 2.260000e-12 84.2
17 TraesCS7A01G387000 chr4A 87.493 1887 220 12 996 2873 702298809 702296930 0.000000e+00 2163.0
18 TraesCS7A01G387000 chr4A 96.078 51 2 0 1 51 596742264 596742314 2.260000e-12 84.2
19 TraesCS7A01G387000 chr4A 94.444 54 2 1 48 101 554068752 554068804 8.130000e-12 82.4
20 TraesCS7A01G387000 chr4A 96.000 50 2 0 1 50 589778988 589778939 8.130000e-12 82.4
21 TraesCS7A01G387000 chr4A 92.857 56 3 1 48 103 309082485 309082431 2.920000e-11 80.5
22 TraesCS7A01G387000 chr2D 86.215 2053 195 41 654 2676 608578733 608576739 0.000000e+00 2143.0
23 TraesCS7A01G387000 chr2A 87.513 1874 199 17 988 2851 740143052 740141204 0.000000e+00 2132.0
24 TraesCS7A01G387000 chr2A 96.000 50 2 0 1 50 238404618 238404569 8.130000e-12 82.4
25 TraesCS7A01G387000 chr5A 96.154 52 1 1 48 98 14043374 14043323 2.260000e-12 84.2
26 TraesCS7A01G387000 chr5A 91.667 60 3 2 48 106 492313600 492313542 8.130000e-12 82.4
27 TraesCS7A01G387000 chr5A 96.000 50 2 0 1 50 522073786 522073835 8.130000e-12 82.4
28 TraesCS7A01G387000 chr5A 96.000 50 2 0 1 50 638657683 638657634 8.130000e-12 82.4
29 TraesCS7A01G387000 chr3A 96.078 51 2 0 44 94 571438579 571438529 2.260000e-12 84.2
30 TraesCS7A01G387000 chr5B 96.000 50 2 0 1 50 113452783 113452734 8.130000e-12 82.4
31 TraesCS7A01G387000 chr4D 96.000 50 2 0 48 97 347514761 347514810 8.130000e-12 82.4
32 TraesCS7A01G387000 chr6A 94.340 53 2 1 48 100 85150727 85150676 2.920000e-11 80.5
33 TraesCS7A01G387000 chr3D 87.097 62 6 2 48 109 611242232 611242291 6.330000e-08 69.4


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 TraesCS7A01G387000 chr7A 563244283 563247815 3532 True 6525.00 6525 100.00000 1 3533 1 chr7A.!!$R2 3532
1 TraesCS7A01G387000 chr7A 563291432 563293760 2328 True 2627.00 2627 87.18300 599 2931 1 chr7A.!!$R3 2332
2 TraesCS7A01G387000 chr7B 525595934 525599243 3309 True 1063.95 3683 89.40375 389 3533 4 chr7B.!!$R2 3144
3 TraesCS7A01G387000 chr7D 28576669 28578581 1912 True 2196.00 2196 87.44800 989 2900 1 chr7D.!!$R1 1911
4 TraesCS7A01G387000 chr7D 497317963 497322067 4104 True 1534.00 3548 90.08100 94 3448 3 chr7D.!!$R2 3354
5 TraesCS7A01G387000 chr1D 33595363 33597513 2150 False 2224.00 2224 85.37000 589 2778 1 chr1D.!!$F1 2189
6 TraesCS7A01G387000 chr1A 32111033 32112914 1881 False 2167.00 2167 87.48000 886 2778 1 chr1A.!!$F1 1892
7 TraesCS7A01G387000 chr4A 702296930 702298809 1879 True 2163.00 2163 87.49300 996 2873 1 chr4A.!!$R3 1877
8 TraesCS7A01G387000 chr2D 608576739 608578733 1994 True 2143.00 2143 86.21500 654 2676 1 chr2D.!!$R1 2022
9 TraesCS7A01G387000 chr2A 740141204 740143052 1848 True 2132.00 2132 87.51300 988 2851 1 chr2A.!!$R2 1863

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
64 65 0.246635 CCGCACGGGGATATAGGAAG 59.753 60.000 0.00 0.00 0.00 3.46 F
65 66 0.389948 CGCACGGGGATATAGGAAGC 60.390 60.000 0.00 0.00 0.00 3.86 F
364 375 0.669318 TCACGACCGAAGAATGGTGC 60.669 55.000 0.00 0.00 40.63 5.01 F
958 1611 0.813210 GGCAGCAAATCGAGCTAGCT 60.813 55.000 19.45 19.45 41.14 3.32 F
1023 1704 1.151450 CAGCTTGGACACCAACCCT 59.849 57.895 0.00 0.00 38.75 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 2365 0.036732 GGATGGAGCGGATATTGGCA 59.963 55.000 2.36 0.00 0.00 4.92 R
1731 2416 1.003355 CTCAAGAAGCTTGGCCGGA 60.003 57.895 5.05 0.00 0.00 5.14 R
2094 2779 1.739338 GATCAGTGACCTCGCCGGAT 61.739 60.000 5.05 0.00 36.31 4.18 R
2505 3190 4.645136 TCCATGATACTGCTCGTAGTCTTT 59.355 41.667 0.00 0.00 32.19 2.52 R
3016 4019 0.744414 TCCTGAGTTAATGCTGCGGC 60.744 55.000 11.65 11.65 39.26 6.53 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
35 36 8.771920 TGAATACGAATTCACTGACATAACTT 57.228 30.769 6.22 0.00 45.17 2.66
36 37 9.214957 TGAATACGAATTCACTGACATAACTTT 57.785 29.630 6.22 0.00 45.17 2.66
38 39 9.825972 AATACGAATTCACTGACATAACTTTTG 57.174 29.630 6.22 0.00 0.00 2.44
39 40 6.142817 ACGAATTCACTGACATAACTTTTGC 58.857 36.000 6.22 0.00 0.00 3.68
40 41 6.017109 ACGAATTCACTGACATAACTTTTGCT 60.017 34.615 6.22 0.00 0.00 3.91
41 42 6.521133 CGAATTCACTGACATAACTTTTGCTC 59.479 38.462 6.22 0.00 0.00 4.26
42 43 5.689383 TTCACTGACATAACTTTTGCTCC 57.311 39.130 0.00 0.00 0.00 4.70
43 44 4.973168 TCACTGACATAACTTTTGCTCCT 58.027 39.130 0.00 0.00 0.00 3.69
44 45 4.756642 TCACTGACATAACTTTTGCTCCTG 59.243 41.667 0.00 0.00 0.00 3.86
45 46 3.503748 ACTGACATAACTTTTGCTCCTGC 59.496 43.478 0.00 0.00 40.20 4.85
46 47 2.819608 TGACATAACTTTTGCTCCTGCC 59.180 45.455 0.00 0.00 38.71 4.85
47 48 1.812571 ACATAACTTTTGCTCCTGCCG 59.187 47.619 0.00 0.00 38.71 5.69
48 49 0.811281 ATAACTTTTGCTCCTGCCGC 59.189 50.000 0.00 0.00 38.71 6.53
49 50 0.536233 TAACTTTTGCTCCTGCCGCA 60.536 50.000 0.00 0.00 38.71 5.69
50 51 2.075426 AACTTTTGCTCCTGCCGCAC 62.075 55.000 0.00 0.00 37.07 5.34
51 52 3.599792 CTTTTGCTCCTGCCGCACG 62.600 63.158 0.00 0.00 37.07 5.34
58 59 3.941188 CCTGCCGCACGGGGATAT 61.941 66.667 11.65 0.00 41.71 1.63
59 60 2.579657 CCTGCCGCACGGGGATATA 61.580 63.158 11.65 0.00 41.71 0.86
60 61 1.079819 CTGCCGCACGGGGATATAG 60.080 63.158 11.65 0.00 34.56 1.31
61 62 2.264794 GCCGCACGGGGATATAGG 59.735 66.667 11.65 0.00 35.78 2.57
62 63 2.280552 GCCGCACGGGGATATAGGA 61.281 63.158 11.65 0.00 35.78 2.94
63 64 1.823169 GCCGCACGGGGATATAGGAA 61.823 60.000 11.65 0.00 35.78 3.36
64 65 0.246635 CCGCACGGGGATATAGGAAG 59.753 60.000 0.00 0.00 0.00 3.46
65 66 0.389948 CGCACGGGGATATAGGAAGC 60.390 60.000 0.00 0.00 0.00 3.86
66 67 0.685097 GCACGGGGATATAGGAAGCA 59.315 55.000 0.00 0.00 0.00 3.91
67 68 1.608283 GCACGGGGATATAGGAAGCAC 60.608 57.143 0.00 0.00 0.00 4.40
68 69 1.971357 CACGGGGATATAGGAAGCACT 59.029 52.381 0.00 0.00 0.00 4.40
69 70 3.162666 CACGGGGATATAGGAAGCACTA 58.837 50.000 0.00 0.00 0.00 2.74
70 71 3.056749 CACGGGGATATAGGAAGCACTAC 60.057 52.174 0.00 0.00 0.00 2.73
71 72 3.162666 CGGGGATATAGGAAGCACTACA 58.837 50.000 0.00 0.00 0.00 2.74
72 73 3.769844 CGGGGATATAGGAAGCACTACAT 59.230 47.826 0.00 0.00 0.00 2.29
73 74 4.223032 CGGGGATATAGGAAGCACTACATT 59.777 45.833 0.00 0.00 0.00 2.71
74 75 5.491982 GGGGATATAGGAAGCACTACATTG 58.508 45.833 0.00 0.00 0.00 2.82
75 76 5.013183 GGGGATATAGGAAGCACTACATTGT 59.987 44.000 0.00 0.00 0.00 2.71
76 77 5.934625 GGGATATAGGAAGCACTACATTGTG 59.065 44.000 0.00 0.00 40.62 3.33
77 78 5.934625 GGATATAGGAAGCACTACATTGTGG 59.065 44.000 0.00 0.00 38.31 4.17
78 79 6.239600 GGATATAGGAAGCACTACATTGTGGA 60.240 42.308 7.20 0.00 38.31 4.02
79 80 3.788227 AGGAAGCACTACATTGTGGAA 57.212 42.857 7.20 0.00 38.31 3.53
80 81 4.307032 AGGAAGCACTACATTGTGGAAT 57.693 40.909 7.20 0.00 38.31 3.01
81 82 4.012374 AGGAAGCACTACATTGTGGAATG 58.988 43.478 7.20 0.00 44.11 2.67
82 83 3.129287 GGAAGCACTACATTGTGGAATGG 59.871 47.826 7.20 0.00 43.00 3.16
83 84 3.719268 AGCACTACATTGTGGAATGGA 57.281 42.857 7.20 0.00 43.00 3.41
87 88 3.931907 CTACATTGTGGAATGGAGGGA 57.068 47.619 0.00 0.00 44.23 4.20
88 89 2.814805 ACATTGTGGAATGGAGGGAG 57.185 50.000 0.00 0.00 43.00 4.30
89 90 1.995542 ACATTGTGGAATGGAGGGAGT 59.004 47.619 0.00 0.00 43.00 3.85
90 91 3.189606 ACATTGTGGAATGGAGGGAGTA 58.810 45.455 0.00 0.00 43.00 2.59
91 92 3.788142 ACATTGTGGAATGGAGGGAGTAT 59.212 43.478 0.00 0.00 43.00 2.12
92 93 4.230502 ACATTGTGGAATGGAGGGAGTATT 59.769 41.667 0.00 0.00 43.00 1.89
100 101 8.532819 GTGGAATGGAGGGAGTATTACTATAAG 58.467 40.741 0.00 0.00 0.00 1.73
152 153 5.480642 TTTTCCATGCAATACACAATGGT 57.519 34.783 0.00 0.00 0.00 3.55
159 160 5.981088 TGCAATACACAATGGTCAAGAAT 57.019 34.783 0.00 0.00 0.00 2.40
160 161 5.712004 TGCAATACACAATGGTCAAGAATG 58.288 37.500 0.00 0.00 0.00 2.67
182 183 4.395231 TGTGACCTCAGTTATACAGAGACG 59.605 45.833 1.36 0.00 34.12 4.18
229 230 9.906660 TTTATGGATTTTTGTCCGCATATATTC 57.093 29.630 0.00 0.00 41.35 1.75
283 284 7.915508 TCGGCAATACTGTTGTAAGATAATTG 58.084 34.615 0.00 0.00 31.80 2.32
289 300 6.165659 ACTGTTGTAAGATAATTGACGCAC 57.834 37.500 0.00 0.00 0.00 5.34
305 316 4.681978 ACAGCGAGCCAACCGACC 62.682 66.667 0.00 0.00 0.00 4.79
339 350 8.862074 ACCGTGTACAAAATAAACAAAGAAAAC 58.138 29.630 0.00 0.00 0.00 2.43
340 351 8.045557 CCGTGTACAAAATAAACAAAGAAAACG 58.954 33.333 0.00 0.00 0.00 3.60
361 372 2.080286 AACTCACGACCGAAGAATGG 57.920 50.000 0.00 0.00 0.00 3.16
362 373 0.966920 ACTCACGACCGAAGAATGGT 59.033 50.000 0.00 0.00 44.10 3.55
364 375 0.669318 TCACGACCGAAGAATGGTGC 60.669 55.000 0.00 0.00 40.63 5.01
374 385 4.722855 AATGGTGCGGCAAAGCGC 62.723 61.111 3.23 0.00 46.01 5.92
417 430 1.835531 GTTCCCCCTGATTTCTCCGTA 59.164 52.381 0.00 0.00 0.00 4.02
422 435 2.035632 CCCTGATTTCTCCGTAGCTCT 58.964 52.381 0.00 0.00 0.00 4.09
425 438 3.305064 CCTGATTTCTCCGTAGCTCTAGC 60.305 52.174 0.00 0.00 42.49 3.42
426 439 3.288092 TGATTTCTCCGTAGCTCTAGCA 58.712 45.455 4.54 0.00 45.16 3.49
431 614 3.288092 TCTCCGTAGCTCTAGCATTTCA 58.712 45.455 4.54 0.00 45.16 2.69
443 626 6.554334 TCTAGCATTTCACTGTAACAAACC 57.446 37.500 0.00 0.00 0.00 3.27
465 928 4.502259 CCATCCCTGAGTAAGTGTAGCATC 60.502 50.000 0.00 0.00 0.00 3.91
467 930 2.688446 CCCTGAGTAAGTGTAGCATCGA 59.312 50.000 0.00 0.00 0.00 3.59
468 931 3.243234 CCCTGAGTAAGTGTAGCATCGAG 60.243 52.174 0.00 0.00 0.00 4.04
469 932 3.628032 CCTGAGTAAGTGTAGCATCGAGA 59.372 47.826 0.00 0.00 0.00 4.04
471 934 5.470437 CCTGAGTAAGTGTAGCATCGAGATA 59.530 44.000 0.00 0.00 0.00 1.98
472 935 6.348132 CCTGAGTAAGTGTAGCATCGAGATAG 60.348 46.154 0.00 0.00 0.00 2.08
474 937 6.937465 TGAGTAAGTGTAGCATCGAGATAGAT 59.063 38.462 0.00 0.00 0.00 1.98
476 939 7.165485 AGTAAGTGTAGCATCGAGATAGATCT 58.835 38.462 0.00 0.00 40.50 2.75
540 1037 2.083774 ACGAAAACGATCCATGCATGT 58.916 42.857 24.58 7.78 0.00 3.21
560 1062 4.131596 TGTATAGCCCTCCGCAAAAATAC 58.868 43.478 0.00 0.00 41.38 1.89
565 1067 3.070302 AGCCCTCCGCAAAAATACAAAAA 59.930 39.130 0.00 0.00 41.38 1.94
748 1378 2.771943 CCTACCCATGCACTTTCCTAGA 59.228 50.000 0.00 0.00 0.00 2.43
752 1382 1.667724 CCATGCACTTTCCTAGAAGCG 59.332 52.381 0.00 0.00 33.29 4.68
753 1383 2.350522 CATGCACTTTCCTAGAAGCGT 58.649 47.619 0.00 0.00 33.29 5.07
790 1425 0.891373 ACCAGGACTCACGACTCATG 59.109 55.000 0.00 0.00 0.00 3.07
854 1503 3.132289 CACCTATATATACCCCGCACCAG 59.868 52.174 0.00 0.00 0.00 4.00
866 1515 1.891919 GCACCAGCAACGAACTCCA 60.892 57.895 0.00 0.00 41.58 3.86
955 1608 1.521457 CCGGCAGCAAATCGAGCTA 60.521 57.895 0.00 0.00 41.14 3.32
956 1609 1.493950 CCGGCAGCAAATCGAGCTAG 61.494 60.000 0.00 0.00 41.14 3.42
957 1610 1.645997 GGCAGCAAATCGAGCTAGC 59.354 57.895 6.62 6.62 41.14 3.42
958 1611 0.813210 GGCAGCAAATCGAGCTAGCT 60.813 55.000 19.45 19.45 41.14 3.32
1023 1704 1.151450 CAGCTTGGACACCAACCCT 59.849 57.895 0.00 0.00 38.75 4.34
1680 2365 3.764466 CTCGCAGGCTTCGACCCT 61.764 66.667 4.84 0.00 32.08 4.34
1731 2416 2.100418 GGAAACTAACTACGGGCTCGAT 59.900 50.000 15.95 0.00 40.11 3.59
1746 2431 1.450312 CGATCCGGCCAAGCTTCTT 60.450 57.895 2.24 0.00 0.00 2.52
2091 2776 1.245732 ACCTCAAGAACGACGCTACT 58.754 50.000 0.00 0.00 0.00 2.57
2094 2779 2.351447 CCTCAAGAACGACGCTACTGAA 60.351 50.000 0.00 0.00 0.00 3.02
2127 2812 4.937620 GTCACTGATCTTAAGGACATGCAA 59.062 41.667 1.85 0.00 0.00 4.08
2505 3190 0.038166 GTGCCTGGGACCTCATCAAA 59.962 55.000 7.16 0.00 0.00 2.69
2891 3886 4.321974 GGTTTTAGGTTTCAAGATGCCAGG 60.322 45.833 0.00 0.00 0.00 4.45
2932 3930 4.342665 TGTGTTCCCAACTTCCCATTAAAC 59.657 41.667 0.00 0.00 0.00 2.01
2936 3934 2.233676 CCCAACTTCCCATTAAACTGGC 59.766 50.000 0.00 0.00 34.77 4.85
2969 3972 4.209538 TGCCATACAATTCCATCTTCAGG 58.790 43.478 0.00 0.00 0.00 3.86
2977 3980 1.225704 CCATCTTCAGGGTCCAGGC 59.774 63.158 0.00 0.00 0.00 4.85
3016 4019 3.763097 TCTGAATTAATGGTGCTTGCG 57.237 42.857 0.00 0.00 0.00 4.85
3030 4033 2.745884 TGCGCCGCAGCATTAACT 60.746 55.556 8.16 0.00 42.92 2.24
3038 4041 2.159517 CCGCAGCATTAACTCAGGAAAC 60.160 50.000 0.00 0.00 0.00 2.78
3119 4122 3.627732 ACGATCGACAGGTGATATCAC 57.372 47.619 24.95 24.95 45.72 3.06
3234 4240 4.744137 TGATTCAATCAAAGCAAAACACGG 59.256 37.500 0.00 0.00 36.11 4.94
3235 4241 2.468831 TCAATCAAAGCAAAACACGGC 58.531 42.857 0.00 0.00 0.00 5.68
3243 4249 1.226030 GCAAAACACGGCGGAGTACT 61.226 55.000 13.24 0.00 0.00 2.73
3244 4250 1.223187 CAAAACACGGCGGAGTACTT 58.777 50.000 13.24 4.19 0.00 2.24
3245 4251 1.193874 CAAAACACGGCGGAGTACTTC 59.806 52.381 13.24 0.00 0.00 3.01
3281 4289 5.011125 ACTGCAGTTAAGTGACTGTACTGAT 59.989 40.000 23.39 10.50 46.81 2.90
3297 4305 6.873997 TGTACTGATTGATTTGATCCGTACT 58.126 36.000 15.08 0.00 41.16 2.73
3339 4358 4.599041 CCACCCAACTGAAAAGATCCATA 58.401 43.478 0.00 0.00 0.00 2.74
3362 4384 6.308015 AGAGGAGCTATCTATCAGTACGAT 57.692 41.667 0.00 5.71 38.21 3.73
3368 4390 7.308649 GGAGCTATCTATCAGTACGATTTGTGA 60.309 40.741 5.71 0.00 35.39 3.58
3373 4395 7.818997 TCTATCAGTACGATTTGTGACCTAT 57.181 36.000 5.71 0.00 35.39 2.57
3380 4402 2.951642 CGATTTGTGACCTATGGGCATT 59.048 45.455 0.00 0.00 35.63 3.56
3388 4410 1.005450 ACCTATGGGCATTTCCAACGT 59.995 47.619 0.00 0.00 40.62 3.99
3389 4411 1.676006 CCTATGGGCATTTCCAACGTC 59.324 52.381 0.00 0.00 40.62 4.34
3396 4418 0.947180 CATTTCCAACGTCGACCCGT 60.947 55.000 10.58 2.01 44.23 5.28
3400 4422 1.016627 TCCAACGTCGACCCGTATAG 58.983 55.000 10.58 0.00 40.85 1.31
3418 4451 6.641314 CCGTATAGATGTCTGTTTGTATGTCC 59.359 42.308 0.00 0.00 0.00 4.02
3422 4455 3.973206 TGTCTGTTTGTATGTCCGGAT 57.027 42.857 7.81 0.00 0.00 4.18
3441 4474 1.220703 TGTGGTCCATGGGCATGATA 58.779 50.000 20.13 0.00 41.20 2.15
3454 4487 4.164796 TGGGCATGATATCAAAGTGAGTCT 59.835 41.667 9.99 0.00 0.00 3.24
3456 4489 5.591877 GGGCATGATATCAAAGTGAGTCTTT 59.408 40.000 9.99 0.00 45.96 2.52
3469 4502 7.934855 AAGTGAGTCTTTCAATGCTAATCAT 57.065 32.000 0.00 0.00 37.61 2.45
3484 4517 9.950680 AATGCTAATCATAAAGTATTCGGTTTG 57.049 29.630 0.00 0.00 34.33 2.93
3485 4518 7.925993 TGCTAATCATAAAGTATTCGGTTTGG 58.074 34.615 0.00 0.00 0.00 3.28
3486 4519 7.771361 TGCTAATCATAAAGTATTCGGTTTGGA 59.229 33.333 0.00 0.00 0.00 3.53
3493 4526 9.855021 CATAAAGTATTCGGTTTGGAAAGAAAT 57.145 29.630 0.00 0.00 0.00 2.17
3520 4554 4.886163 TGTAGGGACTTATATGTGGTGGA 58.114 43.478 0.00 0.00 41.75 4.02
3526 4560 7.461749 AGGGACTTATATGTGGTGGAATATTG 58.538 38.462 0.00 0.00 27.25 1.90
3529 4563 7.174946 GGACTTATATGTGGTGGAATATTGTGG 59.825 40.741 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.771920 AAGTTATGTCAGTGAATTCGTATTCA 57.228 30.769 12.80 12.80 45.99 2.57
12 13 9.825972 CAAAAGTTATGTCAGTGAATTCGTATT 57.174 29.630 0.00 0.00 0.00 1.89
13 14 7.962918 GCAAAAGTTATGTCAGTGAATTCGTAT 59.037 33.333 0.00 0.00 0.00 3.06
14 15 7.172532 AGCAAAAGTTATGTCAGTGAATTCGTA 59.827 33.333 0.00 0.00 0.00 3.43
15 16 6.017109 AGCAAAAGTTATGTCAGTGAATTCGT 60.017 34.615 0.00 0.00 0.00 3.85
16 17 6.373779 AGCAAAAGTTATGTCAGTGAATTCG 58.626 36.000 0.00 0.00 0.00 3.34
17 18 6.803807 GGAGCAAAAGTTATGTCAGTGAATTC 59.196 38.462 0.00 0.00 0.00 2.17
18 19 6.491403 AGGAGCAAAAGTTATGTCAGTGAATT 59.509 34.615 0.00 0.00 0.00 2.17
19 20 6.006449 AGGAGCAAAAGTTATGTCAGTGAAT 58.994 36.000 0.00 0.00 0.00 2.57
20 21 5.239306 CAGGAGCAAAAGTTATGTCAGTGAA 59.761 40.000 0.00 0.00 0.00 3.18
21 22 4.756642 CAGGAGCAAAAGTTATGTCAGTGA 59.243 41.667 0.00 0.00 0.00 3.41
22 23 4.614535 GCAGGAGCAAAAGTTATGTCAGTG 60.615 45.833 0.00 0.00 41.58 3.66
23 24 3.503748 GCAGGAGCAAAAGTTATGTCAGT 59.496 43.478 0.00 0.00 41.58 3.41
24 25 3.119708 GGCAGGAGCAAAAGTTATGTCAG 60.120 47.826 0.00 0.00 44.61 3.51
25 26 2.819608 GGCAGGAGCAAAAGTTATGTCA 59.180 45.455 0.00 0.00 44.61 3.58
26 27 2.159517 CGGCAGGAGCAAAAGTTATGTC 60.160 50.000 0.00 0.00 44.61 3.06
27 28 1.812571 CGGCAGGAGCAAAAGTTATGT 59.187 47.619 0.00 0.00 44.61 2.29
28 29 1.468054 GCGGCAGGAGCAAAAGTTATG 60.468 52.381 0.00 0.00 44.61 1.90
29 30 0.811281 GCGGCAGGAGCAAAAGTTAT 59.189 50.000 0.00 0.00 44.61 1.89
30 31 0.536233 TGCGGCAGGAGCAAAAGTTA 60.536 50.000 0.00 0.00 44.61 2.24
31 32 1.827789 TGCGGCAGGAGCAAAAGTT 60.828 52.632 0.00 0.00 44.61 2.66
32 33 2.203337 TGCGGCAGGAGCAAAAGT 60.203 55.556 0.00 0.00 44.61 2.66
33 34 2.256461 GTGCGGCAGGAGCAAAAG 59.744 61.111 1.18 0.00 46.97 2.27
34 35 3.659092 CGTGCGGCAGGAGCAAAA 61.659 61.111 17.16 0.00 46.97 2.44
41 42 2.507110 CTATATCCCCGTGCGGCAGG 62.507 65.000 15.33 15.33 0.00 4.85
42 43 1.079819 CTATATCCCCGTGCGGCAG 60.080 63.158 1.18 0.00 0.00 4.85
43 44 2.579657 CCTATATCCCCGTGCGGCA 61.580 63.158 0.00 0.00 0.00 5.69
44 45 1.823169 TTCCTATATCCCCGTGCGGC 61.823 60.000 4.91 0.00 0.00 6.53
45 46 0.246635 CTTCCTATATCCCCGTGCGG 59.753 60.000 3.25 3.25 0.00 5.69
46 47 0.389948 GCTTCCTATATCCCCGTGCG 60.390 60.000 0.00 0.00 0.00 5.34
47 48 0.685097 TGCTTCCTATATCCCCGTGC 59.315 55.000 0.00 0.00 0.00 5.34
48 49 1.971357 AGTGCTTCCTATATCCCCGTG 59.029 52.381 0.00 0.00 0.00 4.94
49 50 2.400467 AGTGCTTCCTATATCCCCGT 57.600 50.000 0.00 0.00 0.00 5.28
50 51 3.162666 TGTAGTGCTTCCTATATCCCCG 58.837 50.000 0.00 0.00 0.00 5.73
51 52 5.013183 ACAATGTAGTGCTTCCTATATCCCC 59.987 44.000 0.00 0.00 0.00 4.81
52 53 5.934625 CACAATGTAGTGCTTCCTATATCCC 59.065 44.000 0.00 0.00 32.04 3.85
53 54 5.934625 CCACAATGTAGTGCTTCCTATATCC 59.065 44.000 0.00 0.00 38.18 2.59
54 55 6.759272 TCCACAATGTAGTGCTTCCTATATC 58.241 40.000 0.00 0.00 38.18 1.63
55 56 6.747414 TCCACAATGTAGTGCTTCCTATAT 57.253 37.500 0.00 0.00 38.18 0.86
56 57 6.553953 TTCCACAATGTAGTGCTTCCTATA 57.446 37.500 0.00 0.00 38.18 1.31
57 58 5.435686 TTCCACAATGTAGTGCTTCCTAT 57.564 39.130 0.00 0.00 38.18 2.57
58 59 4.901197 TTCCACAATGTAGTGCTTCCTA 57.099 40.909 0.00 0.00 38.18 2.94
59 60 3.788227 TTCCACAATGTAGTGCTTCCT 57.212 42.857 0.00 0.00 38.18 3.36
60 61 3.129287 CCATTCCACAATGTAGTGCTTCC 59.871 47.826 0.00 0.00 38.22 3.46
61 62 4.009675 TCCATTCCACAATGTAGTGCTTC 58.990 43.478 0.00 0.00 38.22 3.86
62 63 4.012374 CTCCATTCCACAATGTAGTGCTT 58.988 43.478 0.00 0.00 38.22 3.91
63 64 3.614092 CTCCATTCCACAATGTAGTGCT 58.386 45.455 0.00 0.00 38.22 4.40
64 65 2.684881 CCTCCATTCCACAATGTAGTGC 59.315 50.000 0.00 0.00 38.22 4.40
65 66 3.054434 TCCCTCCATTCCACAATGTAGTG 60.054 47.826 0.00 0.00 38.22 2.74
66 67 3.189606 TCCCTCCATTCCACAATGTAGT 58.810 45.455 0.00 0.00 38.22 2.73
67 68 3.200825 ACTCCCTCCATTCCACAATGTAG 59.799 47.826 0.00 0.00 38.22 2.74
68 69 3.189606 ACTCCCTCCATTCCACAATGTA 58.810 45.455 0.00 0.00 38.22 2.29
69 70 1.995542 ACTCCCTCCATTCCACAATGT 59.004 47.619 0.00 0.00 38.22 2.71
70 71 2.814805 ACTCCCTCCATTCCACAATG 57.185 50.000 0.00 0.00 39.45 2.82
71 72 5.672194 AGTAATACTCCCTCCATTCCACAAT 59.328 40.000 0.00 0.00 0.00 2.71
72 73 5.036916 AGTAATACTCCCTCCATTCCACAA 58.963 41.667 0.00 0.00 0.00 3.33
73 74 4.631234 AGTAATACTCCCTCCATTCCACA 58.369 43.478 0.00 0.00 0.00 4.17
74 75 6.936968 ATAGTAATACTCCCTCCATTCCAC 57.063 41.667 0.00 0.00 0.00 4.02
75 76 8.239478 ACTTATAGTAATACTCCCTCCATTCCA 58.761 37.037 0.00 0.00 0.00 3.53
76 77 8.667592 ACTTATAGTAATACTCCCTCCATTCC 57.332 38.462 0.00 0.00 0.00 3.01
152 153 7.178451 TCTGTATAACTGAGGTCACATTCTTGA 59.822 37.037 0.00 0.00 0.00 3.02
159 160 4.395231 CGTCTCTGTATAACTGAGGTCACA 59.605 45.833 12.26 0.00 42.31 3.58
160 161 4.634883 TCGTCTCTGTATAACTGAGGTCAC 59.365 45.833 12.26 4.85 42.31 3.67
182 183 2.405892 AATTGTTGCGTGTGAGCTTC 57.594 45.000 0.00 0.00 38.13 3.86
259 260 7.850982 GTCAATTATCTTACAACAGTATTGCCG 59.149 37.037 0.00 0.00 0.00 5.69
267 268 6.164408 TGTGCGTCAATTATCTTACAACAG 57.836 37.500 0.00 0.00 0.00 3.16
269 270 5.022021 GCTGTGCGTCAATTATCTTACAAC 58.978 41.667 0.00 0.00 0.00 3.32
299 310 0.734889 CACGGTCTATTACGGTCGGT 59.265 55.000 0.00 0.00 39.44 4.69
305 316 8.646356 TGTTTATTTTGTACACGGTCTATTACG 58.354 33.333 0.00 0.00 0.00 3.18
340 351 2.921754 CCATTCTTCGGTCGTGAGTTAC 59.078 50.000 0.00 0.00 0.00 2.50
342 353 1.343465 ACCATTCTTCGGTCGTGAGTT 59.657 47.619 0.00 0.00 27.30 3.01
383 394 2.661718 GGGGAACAGTTTGAACCAGAA 58.338 47.619 0.00 0.00 0.00 3.02
384 395 1.133606 GGGGGAACAGTTTGAACCAGA 60.134 52.381 0.00 0.00 0.00 3.86
387 398 1.133606 TCAGGGGGAACAGTTTGAACC 60.134 52.381 0.00 0.00 0.00 3.62
417 430 5.152623 TGTTACAGTGAAATGCTAGAGCT 57.847 39.130 0.00 0.00 42.66 4.09
422 435 6.072175 GGATGGTTTGTTACAGTGAAATGCTA 60.072 38.462 0.00 0.00 0.00 3.49
425 438 5.243730 AGGGATGGTTTGTTACAGTGAAATG 59.756 40.000 0.00 0.00 0.00 2.32
426 439 5.243730 CAGGGATGGTTTGTTACAGTGAAAT 59.756 40.000 0.00 0.00 0.00 2.17
431 614 3.394606 ACTCAGGGATGGTTTGTTACAGT 59.605 43.478 0.00 0.00 0.00 3.55
443 626 4.626042 GATGCTACACTTACTCAGGGATG 58.374 47.826 0.00 0.00 0.00 3.51
540 1037 4.425180 TGTATTTTTGCGGAGGGCTATA 57.575 40.909 0.00 0.00 44.05 1.31
595 1216 1.102978 GCGTTAATTGGCCACCATCT 58.897 50.000 3.88 0.00 31.53 2.90
724 1350 2.238898 AGGAAAGTGCATGGGTAGGTAC 59.761 50.000 0.00 0.00 0.00 3.34
752 1382 4.532903 GCGCGCGCTTACGTACAC 62.533 66.667 44.38 14.45 42.83 2.90
854 1503 4.742438 TTAGTGAATTGGAGTTCGTTGC 57.258 40.909 0.00 0.00 0.00 4.17
866 1515 4.935352 TTGCTGCTTGGTTTAGTGAATT 57.065 36.364 0.00 0.00 0.00 2.17
914 1564 3.451902 AGAGCAAGAAGAATCAGAGGAGG 59.548 47.826 0.00 0.00 0.00 4.30
955 1608 3.432890 GGCTTAATGAAGTGGAGCTAGCT 60.433 47.826 19.45 19.45 34.90 3.32
956 1609 2.875317 GGCTTAATGAAGTGGAGCTAGC 59.125 50.000 6.62 6.62 34.90 3.42
957 1610 4.142609 TGGCTTAATGAAGTGGAGCTAG 57.857 45.455 0.00 0.00 34.90 3.42
958 1611 4.517285 CTTGGCTTAATGAAGTGGAGCTA 58.483 43.478 0.00 0.00 34.90 3.32
1023 1704 0.178068 GCAAGGCGGAGAAGGACATA 59.822 55.000 0.00 0.00 0.00 2.29
1680 2365 0.036732 GGATGGAGCGGATATTGGCA 59.963 55.000 2.36 0.00 0.00 4.92
1731 2416 1.003355 CTCAAGAAGCTTGGCCGGA 60.003 57.895 5.05 0.00 0.00 5.14
1746 2431 2.019249 GCATCAGCTTGCATTACCTCA 58.981 47.619 5.50 0.00 42.31 3.86
2091 2776 1.982395 AGTGACCTCGCCGGATTCA 60.982 57.895 5.05 0.00 36.31 2.57
2094 2779 1.739338 GATCAGTGACCTCGCCGGAT 61.739 60.000 5.05 0.00 36.31 4.18
2505 3190 4.645136 TCCATGATACTGCTCGTAGTCTTT 59.355 41.667 0.00 0.00 32.19 2.52
2734 3424 8.621532 AAGCACTTTTACAGTCTATCATCAAA 57.378 30.769 0.00 0.00 30.92 2.69
2764 3457 7.360101 GCAAATACAGTAACTCGTGTTCATTCT 60.360 37.037 6.07 0.00 37.59 2.40
2936 3934 6.070021 TGGAATTGTATGGCAGATAGATAGGG 60.070 42.308 0.00 0.00 0.00 3.53
2977 3980 1.665679 GATGTGCAAGTGTATGGTCGG 59.334 52.381 0.00 0.00 0.00 4.79
3016 4019 0.744414 TCCTGAGTTAATGCTGCGGC 60.744 55.000 11.65 11.65 39.26 6.53
3030 4033 2.833227 CCCCCGTGTGTTTCCTGA 59.167 61.111 0.00 0.00 0.00 3.86
3038 4041 1.528309 AAAACTCTGCCCCCGTGTG 60.528 57.895 0.00 0.00 0.00 3.82
3119 4122 3.555917 AACTTCGTTCCTACTCAGACG 57.444 47.619 0.00 0.00 36.89 4.18
3141 4144 3.921677 TGGTTGAGTCAGAACCGTAATC 58.078 45.455 9.04 0.00 45.15 1.75
3214 4220 2.863137 GCCGTGTTTTGCTTTGATTGAA 59.137 40.909 0.00 0.00 0.00 2.69
3234 4240 4.136051 ACTATCCTACTGAAGTACTCCGC 58.864 47.826 0.00 0.00 0.00 5.54
3235 4241 6.783892 GTACTATCCTACTGAAGTACTCCG 57.216 45.833 0.00 0.00 40.61 4.63
3243 4249 7.614583 ACTTAACTGCAGTACTATCCTACTGAA 59.385 37.037 22.01 0.00 44.49 3.02
3244 4250 7.067129 CACTTAACTGCAGTACTATCCTACTGA 59.933 40.741 22.01 0.00 44.49 3.41
3245 4251 7.067129 TCACTTAACTGCAGTACTATCCTACTG 59.933 40.741 22.01 5.12 44.52 2.74
3281 4289 3.270027 CTGCCAGTACGGATCAAATCAA 58.730 45.455 7.77 0.00 36.56 2.57
3297 4305 2.679342 GGATGGGTACTGGCTGCCA 61.679 63.158 21.96 21.96 0.00 4.92
3308 4316 4.360405 GTTGGGTGGCGGATGGGT 62.360 66.667 0.00 0.00 0.00 4.51
3339 4358 5.748670 TCGTACTGATAGATAGCTCCTCT 57.251 43.478 0.00 0.00 0.00 3.69
3355 4377 3.431766 GCCCATAGGTCACAAATCGTACT 60.432 47.826 0.00 0.00 34.57 2.73
3362 4384 3.096092 GGAAATGCCCATAGGTCACAAA 58.904 45.455 0.00 0.00 34.57 2.83
3368 4390 1.005450 ACGTTGGAAATGCCCATAGGT 59.995 47.619 0.00 0.00 35.88 3.08
3373 4395 1.071642 TCGACGTTGGAAATGCCCA 59.928 52.632 2.20 0.00 35.88 5.36
3380 4402 1.401552 CTATACGGGTCGACGTTGGAA 59.598 52.381 9.92 0.00 46.25 3.53
3388 4410 3.204306 ACAGACATCTATACGGGTCGA 57.796 47.619 0.00 0.00 35.49 4.20
3389 4411 3.984508 AACAGACATCTATACGGGTCG 57.015 47.619 0.00 0.00 35.49 4.79
3396 4418 6.548251 TCCGGACATACAAACAGACATCTATA 59.452 38.462 0.00 0.00 0.00 1.31
3400 4422 3.857052 TCCGGACATACAAACAGACATC 58.143 45.455 0.00 0.00 0.00 3.06
3422 4455 1.220703 TATCATGCCCATGGACCACA 58.779 50.000 15.22 6.24 39.24 4.17
3430 4463 5.057843 ACTCACTTTGATATCATGCCCAT 57.942 39.130 6.17 0.00 0.00 4.00
3456 4489 8.902540 ACCGAATACTTTATGATTAGCATTGA 57.097 30.769 0.00 0.00 38.44 2.57
3477 4510 9.116067 CCTACATATTATTTCTTTCCAAACCGA 57.884 33.333 0.00 0.00 0.00 4.69
3479 4512 9.416284 TCCCTACATATTATTTCTTTCCAAACC 57.584 33.333 0.00 0.00 0.00 3.27
3493 4526 9.042450 CCACCACATATAAGTCCCTACATATTA 57.958 37.037 0.00 0.00 0.00 0.98
3496 4529 6.626238 TCCACCACATATAAGTCCCTACATA 58.374 40.000 0.00 0.00 0.00 2.29
3498 4531 4.886163 TCCACCACATATAAGTCCCTACA 58.114 43.478 0.00 0.00 0.00 2.74
3507 4540 7.350382 ACACCACAATATTCCACCACATATAA 58.650 34.615 0.00 0.00 0.00 0.98
3508 4541 6.905736 ACACCACAATATTCCACCACATATA 58.094 36.000 0.00 0.00 0.00 0.86
3509 4542 5.765510 ACACCACAATATTCCACCACATAT 58.234 37.500 0.00 0.00 0.00 1.78
3510 4543 5.186256 ACACCACAATATTCCACCACATA 57.814 39.130 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.