Multiple sequence alignment - TraesCS1B01G048100

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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 TraesCS1B01G048100 chr1B 100.000 4286 0 0 1 4286 28309512 28305227 0.000000e+00 7915.0
1 TraesCS1B01G048100 chr1B 91.649 3257 181 30 434 3682 28325232 28322059 0.000000e+00 4423.0
2 TraesCS1B01G048100 chr1B 91.828 2582 188 14 988 3566 28375818 28373257 0.000000e+00 3578.0
3 TraesCS1B01G048100 chr1B 83.855 3450 390 86 463 3828 28483183 28486549 0.000000e+00 3131.0
4 TraesCS1B01G048100 chr1B 95.255 569 19 4 3726 4286 28322063 28321495 0.000000e+00 894.0
5 TraesCS1B01G048100 chr1B 85.843 332 35 8 2 327 28325661 28325336 4.100000e-90 342.0
6 TraesCS1B01G048100 chr1B 80.731 301 29 13 48 325 28376691 28376397 1.560000e-49 207.0
7 TraesCS1B01G048100 chr1B 84.906 212 20 7 3783 3982 28373140 28372929 2.020000e-48 204.0
8 TraesCS1B01G048100 chr1B 81.557 244 28 13 4035 4277 28441273 28441046 7.320000e-43 185.0
9 TraesCS1B01G048100 chr1B 79.741 232 29 6 3590 3807 28443119 28442892 7.420000e-33 152.0
10 TraesCS1B01G048100 chr1B 86.813 91 5 2 313 403 28325318 28325235 1.270000e-15 95.3
11 TraesCS1B01G048100 chr1D 92.175 3131 178 37 466 3552 19003042 18999935 0.000000e+00 4362.0
12 TraesCS1B01G048100 chr1D 89.377 2777 234 29 802 3551 19021005 19018263 0.000000e+00 3437.0
13 TraesCS1B01G048100 chr1D 85.771 3015 318 63 463 3432 19021964 19024912 0.000000e+00 3088.0
14 TraesCS1B01G048100 chr1D 87.803 1648 134 35 2352 3982 19013249 19011652 0.000000e+00 1868.0
15 TraesCS1B01G048100 chr1D 83.529 425 42 12 3635 4032 19018218 19017795 5.230000e-99 372.0
16 TraesCS1B01G048100 chr1D 82.007 289 32 11 48 324 19015411 19015131 1.200000e-55 228.0
17 TraesCS1B01G048100 chr1D 89.844 128 8 2 178 302 19003307 19003182 4.440000e-35 159.0
18 TraesCS1B01G048100 chr1D 95.062 81 2 1 3676 3756 18999930 18999852 4.500000e-25 126.0
19 TraesCS1B01G048100 chr1D 78.924 223 19 13 400 601 19015096 19014881 4.500000e-25 126.0
20 TraesCS1B01G048100 chr1D 81.148 122 16 5 3707 3828 19034732 19034846 1.640000e-14 91.6
21 TraesCS1B01G048100 chr1A 92.158 2665 169 15 982 3624 20927402 20924756 0.000000e+00 3727.0
22 TraesCS1B01G048100 chr1A 88.436 2750 249 32 802 3518 20932688 20929975 0.000000e+00 3253.0
23 TraesCS1B01G048100 chr1A 86.441 2832 285 50 648 3424 20935182 20937969 0.000000e+00 3011.0
24 TraesCS1B01G048100 chr1A 93.593 437 26 2 3852 4286 20924743 20924307 0.000000e+00 651.0
25 TraesCS1B01G048100 chr1A 88.710 124 14 0 4163 4286 20929207 20929084 7.420000e-33 152.0
26 TraesCS1B01G048100 chr1A 88.991 109 9 1 359 467 20927970 20927865 9.670000e-27 132.0
27 TraesCS1B01G048100 chr4A 92.595 2593 155 18 982 3552 675285704 675283127 0.000000e+00 3690.0
28 TraesCS1B01G048100 chr4A 93.008 615 26 7 3676 4276 675283122 675282511 0.000000e+00 881.0
29 TraesCS1B01G048100 chr4A 95.750 400 17 0 3887 4286 675282509 675282110 0.000000e+00 645.0
30 TraesCS1B01G048100 chr4A 83.636 110 10 4 358 467 675286414 675286313 3.530000e-16 97.1
31 TraesCS1B01G048100 chr4A 94.545 55 3 0 243 297 675286472 675286418 7.640000e-13 86.1
32 TraesCS1B01G048100 chr5B 88.727 3025 270 28 976 3982 641833321 641836292 0.000000e+00 3631.0
33 TraesCS1B01G048100 chr5B 88.600 3035 252 38 1034 4032 641822232 641825208 0.000000e+00 3602.0
34 TraesCS1B01G048100 chr5B 79.135 393 25 26 497 837 641818049 641817662 7.220000e-53 219.0
35 TraesCS1B01G048100 chr5B 87.302 126 14 1 4163 4286 641825449 641825574 4.470000e-30 143.0
36 TraesCS1B01G048100 chrUn 93.008 615 26 10 3676 4276 305780630 305780019 0.000000e+00 881.0
37 TraesCS1B01G048100 chrUn 92.383 512 18 14 3061 3552 305781145 305780635 0.000000e+00 710.0
38 TraesCS1B01G048100 chrUn 96.000 400 16 0 3887 4286 305780017 305779618 0.000000e+00 651.0


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 TraesCS1B01G048100 chr1B 28305227 28309512 4285 True 7915.000000 7915 100.000000 1 4286 1 chr1B.!!$R1 4285
1 TraesCS1B01G048100 chr1B 28483183 28486549 3366 False 3131.000000 3131 83.855000 463 3828 1 chr1B.!!$F1 3365
2 TraesCS1B01G048100 chr1B 28321495 28325661 4166 True 1438.575000 4423 89.890000 2 4286 4 chr1B.!!$R2 4284
3 TraesCS1B01G048100 chr1B 28372929 28376691 3762 True 1329.666667 3578 85.821667 48 3982 3 chr1B.!!$R3 3934
4 TraesCS1B01G048100 chr1D 19021964 19024912 2948 False 3088.000000 3088 85.771000 463 3432 1 chr1D.!!$F1 2969
5 TraesCS1B01G048100 chr1D 18999852 19003307 3455 True 1549.000000 4362 92.360333 178 3756 3 chr1D.!!$R1 3578
6 TraesCS1B01G048100 chr1D 19011652 19021005 9353 True 1206.200000 3437 84.328000 48 4032 5 chr1D.!!$R2 3984
7 TraesCS1B01G048100 chr1A 20935182 20937969 2787 False 3011.000000 3011 86.441000 648 3424 1 chr1A.!!$F1 2776
8 TraesCS1B01G048100 chr1A 20924307 20932688 8381 True 1583.000000 3727 90.377600 359 4286 5 chr1A.!!$R1 3927
9 TraesCS1B01G048100 chr4A 675282110 675286472 4362 True 1079.840000 3690 91.906800 243 4286 5 chr4A.!!$R1 4043
10 TraesCS1B01G048100 chr5B 641833321 641836292 2971 False 3631.000000 3631 88.727000 976 3982 1 chr5B.!!$F1 3006
11 TraesCS1B01G048100 chr5B 641822232 641825574 3342 False 1872.500000 3602 87.951000 1034 4286 2 chr5B.!!$F2 3252
12 TraesCS1B01G048100 chrUn 305779618 305781145 1527 True 747.333333 881 93.797000 3061 4286 3 chrUn.!!$R1 1225

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
113 114 0.104855 TGTGGCTCATATCTGGTCGC 59.895 55.0 0.0 0.0 0.00 5.19 F
907 1225 0.108472 TTCATCTGCGACCTGAGCTG 60.108 55.0 0.0 0.0 35.28 4.24 F
916 1235 0.534873 GACCTGAGCTGTCTCCCTTC 59.465 60.0 0.0 0.0 38.58 3.46 F
1020 1381 0.539669 TGGAGTGCGAGAACAGAGGA 60.540 55.0 0.0 0.0 0.00 3.71 F
1024 1385 0.667792 GTGCGAGAACAGAGGACACC 60.668 60.0 0.0 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 8753 0.599060 TGTTGACACGGACGAGCATA 59.401 50.000 0.00 0.0 0.00 3.14 R
2072 9230 1.177256 GGATGTGCTCCATGATGGCC 61.177 60.000 6.59 0.0 44.26 5.36 R
2474 9632 1.915489 TCAGCTCCCTTGAAGCCATAA 59.085 47.619 0.00 0.0 0.00 1.90 R
3030 10188 2.273179 CGTTCTCCACGGAGGTCCA 61.273 63.158 13.13 0.0 45.89 4.02 R
3366 10554 6.344572 TCCATCTTACAAAACATCGATTCG 57.655 37.500 0.00 0.0 0.00 3.34 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
27 28 3.454082 ACCCAAACTGAAAAATCAGGCAA 59.546 39.130 10.32 0.00 41.76 4.52
43 44 3.214696 GGCAACTCACCTATAGCCATT 57.785 47.619 0.00 0.00 41.63 3.16
60 61 4.389992 AGCCATTGCGATGAAATATAGACG 59.610 41.667 15.98 0.00 44.33 4.18
65 66 4.910746 GCGATGAAATATAGACGCACAT 57.089 40.909 0.00 0.00 44.29 3.21
70 71 6.183359 CGATGAAATATAGACGCACATGACTC 60.183 42.308 0.00 0.00 0.00 3.36
73 74 0.249073 ATAGACGCACATGACTCGGC 60.249 55.000 0.00 1.32 0.00 5.54
95 96 1.217882 GACCAACGACTTGACCACTG 58.782 55.000 0.00 0.00 0.00 3.66
96 97 0.539986 ACCAACGACTTGACCACTGT 59.460 50.000 0.00 0.00 0.00 3.55
97 98 0.937304 CCAACGACTTGACCACTGTG 59.063 55.000 0.00 0.00 0.00 3.66
99 100 0.814010 AACGACTTGACCACTGTGGC 60.814 55.000 26.20 18.47 42.67 5.01
100 101 1.069765 CGACTTGACCACTGTGGCT 59.930 57.895 26.20 13.59 42.67 4.75
112 113 1.410517 ACTGTGGCTCATATCTGGTCG 59.589 52.381 0.00 0.00 0.00 4.79
113 114 0.104855 TGTGGCTCATATCTGGTCGC 59.895 55.000 0.00 0.00 0.00 5.19
133 134 2.472816 CAATTTTCTGTGGCGTGCTTT 58.527 42.857 0.00 0.00 0.00 3.51
158 159 2.630872 CGTTCACATGTGCGCACA 59.369 55.556 41.97 41.97 46.44 4.57
176 177 2.088423 ACAGATGACTGACGAGAGGAC 58.912 52.381 0.00 0.00 46.03 3.85
185 186 0.524862 GACGAGAGGACGGCAGTTTA 59.475 55.000 0.00 0.00 41.34 2.01
192 195 3.515901 AGAGGACGGCAGTTTATTCTTCT 59.484 43.478 0.00 0.00 0.00 2.85
193 196 4.710375 AGAGGACGGCAGTTTATTCTTCTA 59.290 41.667 0.00 0.00 0.00 2.10
302 327 1.121407 TACATGCAGCCCGCTAGGAT 61.121 55.000 0.00 0.00 43.06 3.24
306 331 2.030262 CAGCCCGCTAGGATCAGC 59.970 66.667 0.00 0.00 41.02 4.26
307 332 2.444706 AGCCCGCTAGGATCAGCA 60.445 61.111 5.93 0.00 41.88 4.41
308 333 2.066393 AGCCCGCTAGGATCAGCAA 61.066 57.895 5.93 0.00 41.88 3.91
310 335 1.162800 GCCCGCTAGGATCAGCAAAG 61.163 60.000 5.93 0.00 41.88 2.77
311 336 1.162800 CCCGCTAGGATCAGCAAAGC 61.163 60.000 5.93 0.94 41.88 3.51
318 377 3.498774 AGGATCAGCAAAGCGGAATAT 57.501 42.857 0.00 0.00 36.25 1.28
319 378 3.406764 AGGATCAGCAAAGCGGAATATC 58.593 45.455 0.00 0.00 36.25 1.63
327 386 1.410004 AAGCGGAATATCCCTCGTCA 58.590 50.000 0.00 0.00 31.13 4.35
345 404 2.813754 GTCATTTAGCTCACTTGCACCA 59.186 45.455 0.00 0.00 34.99 4.17
349 408 0.250727 TAGCTCACTTGCACCAACCC 60.251 55.000 0.00 0.00 34.99 4.11
350 409 1.827789 GCTCACTTGCACCAACCCA 60.828 57.895 0.00 0.00 0.00 4.51
351 410 1.181098 GCTCACTTGCACCAACCCAT 61.181 55.000 0.00 0.00 0.00 4.00
352 411 0.599558 CTCACTTGCACCAACCCATG 59.400 55.000 0.00 0.00 0.00 3.66
386 445 3.664025 GCACGTGCAAGCTTAAGTTTAAG 59.336 43.478 34.52 7.17 40.82 1.85
387 446 4.553938 GCACGTGCAAGCTTAAGTTTAAGA 60.554 41.667 34.52 0.00 40.59 2.10
388 447 5.507077 CACGTGCAAGCTTAAGTTTAAGAA 58.493 37.500 14.21 0.00 42.05 2.52
389 448 5.968848 CACGTGCAAGCTTAAGTTTAAGAAA 59.031 36.000 14.21 0.00 42.05 2.52
390 449 6.636850 CACGTGCAAGCTTAAGTTTAAGAAAT 59.363 34.615 14.21 0.00 42.05 2.17
391 450 6.636850 ACGTGCAAGCTTAAGTTTAAGAAATG 59.363 34.615 14.21 10.08 42.05 2.32
392 451 6.855914 CGTGCAAGCTTAAGTTTAAGAAATGA 59.144 34.615 14.21 0.00 42.05 2.57
393 452 7.378461 CGTGCAAGCTTAAGTTTAAGAAATGAA 59.622 33.333 14.21 3.18 42.05 2.57
416 478 7.654116 TGAAATAATATATGTTGGCTTCGTCGA 59.346 33.333 0.00 0.00 0.00 4.20
420 482 0.250124 ATGTTGGCTTCGTCGAACCA 60.250 50.000 19.05 19.05 0.00 3.67
464 528 3.205784 AGCTCTTGTGGATCATTAGCC 57.794 47.619 0.00 0.00 35.87 3.93
468 532 3.797039 TCTTGTGGATCATTAGCCGAAG 58.203 45.455 0.00 0.00 32.07 3.79
602 821 1.741145 ACGCTTGTTTGAAACGTTCCT 59.259 42.857 0.00 0.00 32.09 3.36
610 829 7.968405 GCTTGTTTGAAACGTTCCTATATCATT 59.032 33.333 0.00 0.00 0.00 2.57
630 849 6.598525 TCATTGACAATACGACACATGTTTC 58.401 36.000 0.00 0.00 0.00 2.78
665 941 4.135306 AGCACATGATTAGCAGAGGAATG 58.865 43.478 0.00 0.00 0.00 2.67
674 950 2.409948 GCAGAGGAATGCACCTAGTT 57.590 50.000 0.00 0.00 45.77 2.24
675 951 2.012673 GCAGAGGAATGCACCTAGTTG 58.987 52.381 0.00 0.00 45.77 3.16
676 952 2.355108 GCAGAGGAATGCACCTAGTTGA 60.355 50.000 0.00 0.00 45.77 3.18
732 1032 3.562973 ACTGAACACTTGCATGTGAGAAG 59.437 43.478 32.41 25.51 40.12 2.85
776 1077 3.057548 CCATCTTGCGCACCTGCA 61.058 61.111 11.12 0.00 44.61 4.41
897 1215 0.179089 CTCCCTCACCTTCATCTGCG 60.179 60.000 0.00 0.00 0.00 5.18
907 1225 0.108472 TTCATCTGCGACCTGAGCTG 60.108 55.000 0.00 0.00 35.28 4.24
913 1232 2.888863 CGACCTGAGCTGTCTCCC 59.111 66.667 0.00 0.00 38.58 4.30
914 1233 1.680651 CGACCTGAGCTGTCTCCCT 60.681 63.158 0.00 0.00 38.58 4.20
916 1235 0.534873 GACCTGAGCTGTCTCCCTTC 59.465 60.000 0.00 0.00 38.58 3.46
918 1237 0.617249 CCTGAGCTGTCTCCCTTCCT 60.617 60.000 0.00 0.00 38.58 3.36
970 1326 1.003696 ACCTGCCCAGTTTCTAGCTTC 59.996 52.381 0.00 0.00 0.00 3.86
976 1332 3.339141 CCCAGTTTCTAGCTTCCTTGTC 58.661 50.000 0.00 0.00 0.00 3.18
1020 1381 0.539669 TGGAGTGCGAGAACAGAGGA 60.540 55.000 0.00 0.00 0.00 3.71
1024 1385 0.667792 GTGCGAGAACAGAGGACACC 60.668 60.000 0.00 0.00 0.00 4.16
1146 1507 1.349259 CGGTGAAACGGATGGTCGAC 61.349 60.000 7.13 7.13 39.89 4.20
1311 8442 1.973281 CAGCATGGCCAACGGAACT 60.973 57.895 10.96 0.00 0.00 3.01
1314 8445 1.315257 GCATGGCCAACGGAACTGAT 61.315 55.000 10.96 0.00 0.00 2.90
1386 8517 4.074526 GGCGGTGCTCTGCAGAGA 62.075 66.667 41.20 25.34 46.81 3.10
1471 8620 5.970317 TGTTGATCGTCTGTACTCCTTAA 57.030 39.130 0.00 0.00 0.00 1.85
1479 8629 9.362539 GATCGTCTGTACTCCTTAATTTTTGTA 57.637 33.333 0.00 0.00 0.00 2.41
1556 8714 3.361977 GCGTTCGGCAATGGTGGT 61.362 61.111 0.00 0.00 42.87 4.16
1559 8717 1.305219 CGTTCGGCAATGGTGGTCAT 61.305 55.000 0.00 0.00 37.79 3.06
1579 8737 2.046023 CCATGTTCTGCCTGCCGA 60.046 61.111 0.00 0.00 0.00 5.54
1595 8753 2.359230 GAAGCGACAAGGGCAGCT 60.359 61.111 0.00 0.00 42.35 4.24
1619 8777 1.534163 CTCGTCCGTGTCAACACTCTA 59.466 52.381 11.23 0.00 44.34 2.43
1698 8856 2.260869 GCCAACGTGACACCATGCT 61.261 57.895 0.00 0.00 32.58 3.79
1814 8972 1.971505 CTCCGGATGGCAGCAAGGTA 61.972 60.000 3.57 3.42 34.14 3.08
2072 9230 2.892425 GGACAGATTGAGGCCGCG 60.892 66.667 0.00 0.00 0.00 6.46
2131 9289 1.284982 GCACTCGCAAAGAAGCTCGA 61.285 55.000 0.00 0.00 38.36 4.04
2168 9326 4.847198 TGATGAAGCCAAAGCAAGATAGA 58.153 39.130 0.00 0.00 43.56 1.98
2282 9440 0.895530 ACGACAACCCACTCATCGAT 59.104 50.000 0.00 0.00 36.64 3.59
2885 10043 1.741770 CAGCGCCAACTACCCACTC 60.742 63.158 2.29 0.00 0.00 3.51
3030 10188 3.914551 AAGGAGGTCGAGGCTGCCT 62.915 63.158 23.64 23.64 36.03 4.75
3339 10524 8.625651 TCTGTATCTTCTTAGCTGATAAGTGAC 58.374 37.037 11.96 0.71 41.52 3.67
3442 10647 6.017192 GCCAAAAATTGCAACCTCATAACTTT 60.017 34.615 0.00 0.00 0.00 2.66
3475 10694 7.765307 TCTATGTTGTAAGTTAGAAGGGTACG 58.235 38.462 0.00 0.00 0.00 3.67
3552 10776 0.531974 TGGAGACAACACCGAACAGC 60.532 55.000 0.00 0.00 37.44 4.40
3567 10791 3.722082 CGAACAGCGCAAAACATCTACTC 60.722 47.826 11.47 0.00 0.00 2.59
3579 10803 4.970860 ACATCTACTCTTAGCATGCCAT 57.029 40.909 15.66 0.00 0.00 4.40
3580 10804 5.301835 ACATCTACTCTTAGCATGCCATT 57.698 39.130 15.66 0.00 0.00 3.16
3581 10805 5.061853 ACATCTACTCTTAGCATGCCATTG 58.938 41.667 15.66 3.90 0.00 2.82
3582 10806 3.470709 TCTACTCTTAGCATGCCATTGC 58.529 45.455 15.66 0.00 43.09 3.56
3583 10807 1.396653 ACTCTTAGCATGCCATTGCC 58.603 50.000 15.66 0.00 43.83 4.52
3584 10808 1.341285 ACTCTTAGCATGCCATTGCCA 60.341 47.619 15.66 0.00 43.83 4.92
3585 10809 1.752498 CTCTTAGCATGCCATTGCCAA 59.248 47.619 15.66 0.00 43.83 4.52
3586 10810 2.364324 CTCTTAGCATGCCATTGCCAAT 59.636 45.455 15.66 0.00 43.83 3.16
3624 10871 2.036992 GGACAGAGGACATGATGCCTAG 59.963 54.545 0.00 7.14 33.84 3.02
3625 10872 2.697751 GACAGAGGACATGATGCCTAGT 59.302 50.000 0.00 9.62 33.84 2.57
3626 10873 3.110705 ACAGAGGACATGATGCCTAGTT 58.889 45.455 0.00 0.00 33.84 2.24
3627 10874 3.118482 ACAGAGGACATGATGCCTAGTTG 60.118 47.826 0.00 9.36 33.84 3.16
3628 10875 2.158842 AGAGGACATGATGCCTAGTTGC 60.159 50.000 0.00 0.00 33.84 4.17
3629 10876 1.133976 AGGACATGATGCCTAGTTGCC 60.134 52.381 0.00 0.00 31.31 4.52
3630 10877 1.133976 GGACATGATGCCTAGTTGCCT 60.134 52.381 0.00 0.00 0.00 4.75
3631 10878 2.104792 GGACATGATGCCTAGTTGCCTA 59.895 50.000 0.00 0.00 0.00 3.93
3638 10889 3.502123 TGCCTAGTTGCCTACAAAGTT 57.498 42.857 0.00 0.00 37.58 2.66
3825 11101 6.667848 TCTCTGTTCCTGAATGGTCATAAGTA 59.332 38.462 0.00 0.00 37.07 2.24
3826 11102 7.180229 TCTCTGTTCCTGAATGGTCATAAGTAA 59.820 37.037 0.00 0.00 37.07 2.24
3827 11103 7.331026 TCTGTTCCTGAATGGTCATAAGTAAG 58.669 38.462 0.00 0.00 37.07 2.34
3828 11104 7.016153 TGTTCCTGAATGGTCATAAGTAAGT 57.984 36.000 0.00 0.00 37.07 2.24
3829 11105 7.103641 TGTTCCTGAATGGTCATAAGTAAGTC 58.896 38.462 0.00 0.00 37.07 3.01
3830 11106 7.038302 TGTTCCTGAATGGTCATAAGTAAGTCT 60.038 37.037 0.00 0.00 37.07 3.24
3831 11107 8.475639 GTTCCTGAATGGTCATAAGTAAGTCTA 58.524 37.037 0.00 0.00 37.07 2.59
3832 11108 8.603898 TCCTGAATGGTCATAAGTAAGTCTAA 57.396 34.615 0.00 0.00 37.07 2.10
3834 11110 9.099454 CCTGAATGGTCATAAGTAAGTCTAAAC 57.901 37.037 0.00 0.00 31.85 2.01
3835 11111 9.877178 CTGAATGGTCATAAGTAAGTCTAAACT 57.123 33.333 0.00 0.00 32.61 2.66
3880 11166 2.808543 GTGAACCTTGTGAGAAATCGCT 59.191 45.455 0.00 0.00 0.00 4.93
4145 12213 7.168219 TGTAATTCTTACCTCAAGTTGCTGAT 58.832 34.615 0.00 0.00 35.25 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.507985 CCTGATTTTTCAGTTTGGGTCAGTC 60.508 44.000 2.61 0.00 36.06 3.51
20 21 1.762957 GGCTATAGGTGAGTTGCCTGA 59.237 52.381 1.04 0.00 37.54 3.86
27 28 2.039418 TCGCAATGGCTATAGGTGAGT 58.961 47.619 1.04 0.00 38.10 3.41
60 61 2.432456 TCACGCCGAGTCATGTGC 60.432 61.111 0.00 0.00 32.48 4.57
65 66 2.028484 GTTGGTCACGCCGAGTCA 59.972 61.111 0.00 0.00 41.21 3.41
95 96 0.104855 TGCGACCAGATATGAGCCAC 59.895 55.000 0.00 0.00 0.00 5.01
96 97 0.829990 TTGCGACCAGATATGAGCCA 59.170 50.000 0.00 0.00 0.00 4.75
97 98 2.175878 ATTGCGACCAGATATGAGCC 57.824 50.000 0.00 0.00 0.00 4.70
99 100 5.295292 ACAGAAAATTGCGACCAGATATGAG 59.705 40.000 0.00 0.00 0.00 2.90
100 101 5.065090 CACAGAAAATTGCGACCAGATATGA 59.935 40.000 0.00 0.00 0.00 2.15
112 113 0.318955 AGCACGCCACAGAAAATTGC 60.319 50.000 0.00 0.00 0.00 3.56
113 114 2.138596 AAGCACGCCACAGAAAATTG 57.861 45.000 0.00 0.00 0.00 2.32
127 128 1.299089 GAACGCCACCACAAAGCAC 60.299 57.895 0.00 0.00 0.00 4.40
133 134 1.153066 ACATGTGAACGCCACCACA 60.153 52.632 0.00 0.00 45.09 4.17
156 157 2.088423 GTCCTCTCGTCAGTCATCTGT 58.912 52.381 0.00 0.00 41.91 3.41
158 159 1.374560 CGTCCTCTCGTCAGTCATCT 58.625 55.000 0.00 0.00 0.00 2.90
192 195 6.403049 TGCTCAGTGGAAACGATTTCTTATA 58.597 36.000 0.00 0.00 39.59 0.98
193 196 5.245531 TGCTCAGTGGAAACGATTTCTTAT 58.754 37.500 0.00 0.00 39.59 1.73
302 327 1.490490 AGGGATATTCCGCTTTGCTGA 59.510 47.619 0.00 0.00 37.43 4.26
306 331 2.135933 GACGAGGGATATTCCGCTTTG 58.864 52.381 1.93 0.00 37.43 2.77
307 332 1.760613 TGACGAGGGATATTCCGCTTT 59.239 47.619 1.93 0.00 37.43 3.51
308 333 1.410004 TGACGAGGGATATTCCGCTT 58.590 50.000 1.93 0.00 37.43 4.68
310 335 2.457366 AATGACGAGGGATATTCCGC 57.543 50.000 0.00 0.00 37.43 5.54
311 336 3.927142 GCTAAATGACGAGGGATATTCCG 59.073 47.826 0.00 0.00 37.43 4.30
318 377 2.457598 AGTGAGCTAAATGACGAGGGA 58.542 47.619 0.00 0.00 0.00 4.20
319 378 2.932614 CAAGTGAGCTAAATGACGAGGG 59.067 50.000 0.00 0.00 0.00 4.30
327 386 2.558359 GGTTGGTGCAAGTGAGCTAAAT 59.442 45.455 0.00 0.00 34.99 1.40
345 404 1.815408 GCTCGGTCATATGCATGGGTT 60.815 52.381 10.16 0.00 32.61 4.11
349 408 0.509929 CGTGCTCGGTCATATGCATG 59.490 55.000 10.16 0.00 37.76 4.06
350 409 0.104855 ACGTGCTCGGTCATATGCAT 59.895 50.000 13.32 3.79 41.85 3.96
351 410 0.805711 CACGTGCTCGGTCATATGCA 60.806 55.000 13.32 0.00 41.85 3.96
352 411 1.927210 CACGTGCTCGGTCATATGC 59.073 57.895 13.32 0.00 41.85 3.14
389 448 8.443160 CGACGAAGCCAACATATATTATTTCAT 58.557 33.333 0.00 0.00 0.00 2.57
390 449 7.654116 TCGACGAAGCCAACATATATTATTTCA 59.346 33.333 0.00 0.00 0.00 2.69
391 450 8.014322 TCGACGAAGCCAACATATATTATTTC 57.986 34.615 0.00 0.00 0.00 2.17
392 451 7.956420 TCGACGAAGCCAACATATATTATTT 57.044 32.000 0.00 0.00 0.00 1.40
393 452 7.095355 GGTTCGACGAAGCCAACATATATTATT 60.095 37.037 25.34 0.00 34.45 1.40
397 456 4.056050 GGTTCGACGAAGCCAACATATAT 58.944 43.478 25.34 0.00 34.45 0.86
398 457 3.119065 TGGTTCGACGAAGCCAACATATA 60.119 43.478 30.49 11.71 39.02 0.86
416 478 7.554835 TCACTTTCACTAGTATTTTGTGTGGTT 59.445 33.333 0.00 0.00 33.82 3.67
420 482 8.129211 GCTTTCACTTTCACTAGTATTTTGTGT 58.871 33.333 0.00 0.00 33.82 3.72
468 532 2.032681 AGTCCAAAGCGAGTGGGC 59.967 61.111 0.20 0.20 41.34 5.36
548 757 7.607991 GCCTCCACAATGCATAAACTACTATAT 59.392 37.037 0.00 0.00 0.00 0.86
602 821 9.541143 AACATGTGTCGTATTGTCAATGATATA 57.459 29.630 8.39 0.00 0.00 0.86
610 829 4.381411 TGGAAACATGTGTCGTATTGTCA 58.619 39.130 9.95 0.00 33.40 3.58
630 849 6.932356 AATCATGTGCTTGTCTACTAATGG 57.068 37.500 0.00 0.00 0.00 3.16
665 941 2.287009 GCTTGTGTGTTCAACTAGGTGC 60.287 50.000 1.76 0.00 0.00 5.01
670 946 4.195416 TCATGTGCTTGTGTGTTCAACTA 58.805 39.130 0.00 0.00 0.00 2.24
672 948 3.419264 TCATGTGCTTGTGTGTTCAAC 57.581 42.857 0.00 0.00 0.00 3.18
673 949 3.243468 CCATCATGTGCTTGTGTGTTCAA 60.243 43.478 0.00 0.00 0.00 2.69
674 950 2.293955 CCATCATGTGCTTGTGTGTTCA 59.706 45.455 0.00 0.00 0.00 3.18
675 951 2.553602 TCCATCATGTGCTTGTGTGTTC 59.446 45.455 0.00 0.00 0.00 3.18
676 952 2.585330 TCCATCATGTGCTTGTGTGTT 58.415 42.857 0.00 0.00 0.00 3.32
732 1032 1.153804 GGGAAGAAGAGACGCCGAC 60.154 63.158 0.00 0.00 0.00 4.79
897 1215 0.534873 GAAGGGAGACAGCTCAGGTC 59.465 60.000 0.00 0.00 43.14 3.85
907 1225 0.325203 AGGCAGAGAGGAAGGGAGAC 60.325 60.000 0.00 0.00 0.00 3.36
913 1232 2.151502 TCTGGTAGGCAGAGAGGAAG 57.848 55.000 0.00 0.00 0.00 3.46
914 1233 2.623418 TTCTGGTAGGCAGAGAGGAA 57.377 50.000 0.00 0.00 0.00 3.36
916 1235 2.768527 TGAATTCTGGTAGGCAGAGAGG 59.231 50.000 7.05 0.00 0.00 3.69
918 1237 3.389329 GGATGAATTCTGGTAGGCAGAGA 59.611 47.826 7.05 0.00 0.00 3.10
970 1326 3.807622 TGCAAAGAAGTACGAAGACAAGG 59.192 43.478 0.00 0.00 0.00 3.61
976 1332 4.201532 CGAGATGTGCAAAGAAGTACGAAG 60.202 45.833 0.00 0.00 0.00 3.79
1020 1381 4.988598 CCGTTGGCTGCGAGGTGT 62.989 66.667 0.00 0.00 0.00 4.16
1146 1507 2.825836 ACGGGCCTACGGTACTCG 60.826 66.667 0.84 0.00 45.88 4.18
1311 8442 1.033202 TGGTGACGCCGTAGCTATCA 61.033 55.000 0.00 0.00 41.21 2.15
1314 8445 2.879907 GTGGTGACGCCGTAGCTA 59.120 61.111 0.00 0.00 41.21 3.32
1362 8493 2.930562 AGAGCACCGCCCTCCTTT 60.931 61.111 0.00 0.00 0.00 3.11
1386 8517 3.291584 TGATTCGTACCTGATGAGCTCT 58.708 45.455 16.19 0.00 0.00 4.09
1434 8565 8.470805 AGACGATCAACAACTGAAATATCTACT 58.529 33.333 0.00 0.00 37.67 2.57
1502 8653 4.077300 TCTGAACAGACAAGAAGTGCAT 57.923 40.909 0.00 0.00 31.41 3.96
1556 8714 1.951895 GCAGGCAGAACATGGTCATGA 60.952 52.381 14.46 0.00 41.20 3.07
1559 8717 1.303561 GGCAGGCAGAACATGGTCA 60.304 57.895 14.46 0.00 0.00 4.02
1579 8737 0.745845 CATAGCTGCCCTTGTCGCTT 60.746 55.000 0.00 0.00 34.14 4.68
1592 8750 1.313091 TGACACGGACGAGCATAGCT 61.313 55.000 0.00 0.00 43.88 3.32
1595 8753 0.599060 TGTTGACACGGACGAGCATA 59.401 50.000 0.00 0.00 0.00 3.14
2072 9230 1.177256 GGATGTGCTCCATGATGGCC 61.177 60.000 6.59 0.00 44.26 5.36
2131 9289 3.657398 TCATCAATGGGTCAAGCTCAT 57.343 42.857 0.00 0.00 40.76 2.90
2282 9440 2.343758 GCCTTGCCACGAGAGACA 59.656 61.111 0.00 0.00 0.00 3.41
2474 9632 1.915489 TCAGCTCCCTTGAAGCCATAA 59.085 47.619 0.00 0.00 0.00 1.90
3030 10188 2.273179 CGTTCTCCACGGAGGTCCA 61.273 63.158 13.13 0.00 45.89 4.02
3366 10554 6.344572 TCCATCTTACAAAACATCGATTCG 57.655 37.500 0.00 0.00 0.00 3.34
3552 10776 5.496387 CATGCTAAGAGTAGATGTTTTGCG 58.504 41.667 0.00 0.00 0.00 4.85
3581 10805 2.230992 TCACACTGTATGGCAAATTGGC 59.769 45.455 12.92 12.92 44.03 4.52
3582 10806 3.119388 CCTCACACTGTATGGCAAATTGG 60.119 47.826 0.00 0.00 0.00 3.16
3583 10807 3.758023 TCCTCACACTGTATGGCAAATTG 59.242 43.478 0.00 0.00 0.00 2.32
3584 10808 3.758554 GTCCTCACACTGTATGGCAAATT 59.241 43.478 0.00 0.00 0.00 1.82
3585 10809 3.244875 TGTCCTCACACTGTATGGCAAAT 60.245 43.478 0.00 0.00 0.00 2.32
3586 10810 2.105649 TGTCCTCACACTGTATGGCAAA 59.894 45.455 0.00 0.00 0.00 3.68
3624 10871 5.048713 ACAGAGCAATAACTTTGTAGGCAAC 60.049 40.000 0.00 0.00 33.56 4.17
3625 10872 5.048782 CACAGAGCAATAACTTTGTAGGCAA 60.049 40.000 0.00 0.00 33.56 4.52
3626 10873 4.455533 CACAGAGCAATAACTTTGTAGGCA 59.544 41.667 0.00 0.00 33.56 4.75
3627 10874 4.455877 ACACAGAGCAATAACTTTGTAGGC 59.544 41.667 0.00 0.00 33.56 3.93
3628 10875 5.470098 ACACACAGAGCAATAACTTTGTAGG 59.530 40.000 0.00 0.00 33.56 3.18
3629 10876 6.425114 AGACACACAGAGCAATAACTTTGTAG 59.575 38.462 0.00 0.00 33.56 2.74
3630 10877 6.288294 AGACACACAGAGCAATAACTTTGTA 58.712 36.000 0.00 0.00 33.56 2.41
3631 10878 5.126067 AGACACACAGAGCAATAACTTTGT 58.874 37.500 0.00 0.00 35.53 2.83
3638 10889 4.767409 ACTACAGAGACACACAGAGCAATA 59.233 41.667 0.00 0.00 0.00 1.90
3722 10991 6.326323 TCCTGCTTCCATTACATGTCATACTA 59.674 38.462 0.00 0.00 0.00 1.82
3825 11101 5.208890 AGAAAAAGGGGCAAGTTTAGACTT 58.791 37.500 0.00 0.00 46.85 3.01
3826 11102 4.804597 AGAAAAAGGGGCAAGTTTAGACT 58.195 39.130 0.00 0.00 37.87 3.24
3827 11103 5.531122 AAGAAAAAGGGGCAAGTTTAGAC 57.469 39.130 0.00 0.00 0.00 2.59
3828 11104 6.407639 GGAAAAGAAAAAGGGGCAAGTTTAGA 60.408 38.462 0.00 0.00 0.00 2.10
3829 11105 5.758296 GGAAAAGAAAAAGGGGCAAGTTTAG 59.242 40.000 0.00 0.00 0.00 1.85
3830 11106 5.676552 GGAAAAGAAAAAGGGGCAAGTTTA 58.323 37.500 0.00 0.00 0.00 2.01
3831 11107 4.523083 GGAAAAGAAAAAGGGGCAAGTTT 58.477 39.130 0.00 0.00 0.00 2.66
3832 11108 3.431626 CGGAAAAGAAAAAGGGGCAAGTT 60.432 43.478 0.00 0.00 0.00 2.66
3834 11110 2.102420 ACGGAAAAGAAAAAGGGGCAAG 59.898 45.455 0.00 0.00 0.00 4.01
3835 11111 2.112190 ACGGAAAAGAAAAAGGGGCAA 58.888 42.857 0.00 0.00 0.00 4.52
4005 11682 6.183361 TGCATGGAGTATGTGATAATCTTGGA 60.183 38.462 0.00 0.00 39.08 3.53
4137 12205 4.214119 ACATTACCGCATATCATCAGCAAC 59.786 41.667 0.00 0.00 0.00 4.17
4145 12213 7.222031 GCTATATTTCGACATTACCGCATATCA 59.778 37.037 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.