Multiple sequence alignment - TraesCS5D01G073100

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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 TraesCS5D01G073100 chr5D 100.000 3671 0 0 1 3671 72503296 72499626 0.000000e+00 6780.0
1 TraesCS5D01G073100 chr5D 79.624 319 53 10 983 1298 463370466 463370157 6.170000e-53 219.0
2 TraesCS5D01G073100 chr5B 95.533 2149 44 8 882 2994 81482324 81484456 0.000000e+00 3389.0
3 TraesCS5D01G073100 chr5B 96.406 473 14 1 1 470 81481305 81481777 0.000000e+00 776.0
4 TraesCS5D01G073100 chr5B 94.947 376 16 2 471 846 81481857 81482229 1.470000e-163 586.0
5 TraesCS5D01G073100 chr5B 87.365 277 18 7 2995 3266 81484506 81484770 5.960000e-78 302.0
6 TraesCS5D01G073100 chr5B 94.631 149 4 1 1 145 493484916 493484768 1.030000e-55 228.0
7 TraesCS5D01G073100 chr5B 84.579 214 16 7 3371 3580 81484769 81484969 2.890000e-46 196.0
8 TraesCS5D01G073100 chr5B 96.226 53 2 0 819 871 81482329 81482277 1.820000e-13 87.9
9 TraesCS5D01G073100 chr5B 100.000 36 0 0 906 941 81482278 81482243 2.370000e-07 67.6
10 TraesCS5D01G073100 chr5A 93.805 2260 77 15 776 2994 64960952 64958715 0.000000e+00 3339.0
11 TraesCS5D01G073100 chr5A 93.617 282 14 2 146 423 64961599 64961318 5.670000e-113 418.0
12 TraesCS5D01G073100 chr5A 92.213 244 13 3 3428 3671 64958327 64958090 1.260000e-89 340.0
13 TraesCS5D01G073100 chr5A 88.612 281 26 5 471 749 64961223 64960947 1.630000e-88 337.0
14 TraesCS5D01G073100 chr5A 86.765 272 26 6 2995 3266 64958665 64958404 9.970000e-76 294.0
15 TraesCS5D01G073100 chr2D 79.752 805 121 28 983 1779 168148083 168147313 2.490000e-151 545.0
16 TraesCS5D01G073100 chr2D 93.814 97 6 0 3265 3361 633439903 633439807 2.950000e-31 147.0
17 TraesCS5D01G073100 chr6D 79.353 804 129 25 983 1779 441966569 441965796 6.980000e-147 531.0
18 TraesCS5D01G073100 chr6D 78.868 265 43 8 1657 1918 6227410 6227156 2.270000e-37 167.0
19 TraesCS5D01G073100 chr3A 80.205 682 106 20 983 1658 647019122 647019780 5.510000e-133 484.0
20 TraesCS5D01G073100 chr3A 90.991 111 8 2 3265 3374 710276427 710276318 8.210000e-32 148.0
21 TraesCS5D01G073100 chr4A 81.932 559 82 8 1328 1881 669400332 669400876 4.320000e-124 455.0
22 TraesCS5D01G073100 chr4B 78.863 563 96 11 1328 1885 243887975 243887431 3.490000e-95 359.0
23 TraesCS5D01G073100 chr2A 96.644 149 1 1 1 145 764086591 764086739 1.020000e-60 244.0
24 TraesCS5D01G073100 chr3B 95.973 149 2 1 1 145 140994361 140994213 4.740000e-59 239.0
25 TraesCS5D01G073100 chr1D 95.973 149 2 1 1 145 217301551 217301403 4.740000e-59 239.0
26 TraesCS5D01G073100 chr1A 95.918 147 2 1 1 143 126324964 126325110 6.130000e-58 235.0
27 TraesCS5D01G073100 chr1A 95.652 92 4 0 3270 3361 161622753 161622662 8.210000e-32 148.0
28 TraesCS5D01G073100 chr7D 93.960 149 5 1 1 145 587067905 587067757 4.770000e-54 222.0
29 TraesCS5D01G073100 chr7A 93.960 149 5 1 1 145 678576951 678576803 4.770000e-54 222.0
30 TraesCS5D01G073100 chr6A 93.960 149 5 1 1 145 139361927 139361779 4.770000e-54 222.0
31 TraesCS5D01G073100 chr6A 92.632 95 5 2 1516 1609 5291210 5291117 6.390000e-28 135.0
32 TraesCS5D01G073100 chr2B 94.949 99 5 0 3264 3362 695410853 695410951 4.910000e-34 156.0
33 TraesCS5D01G073100 chr7B 93.814 97 6 0 3265 3361 390106800 390106896 2.950000e-31 147.0
34 TraesCS5D01G073100 chr7B 93.814 97 6 0 3265 3361 717178142 717178046 2.950000e-31 147.0
35 TraesCS5D01G073100 chr7B 93.814 97 6 0 3265 3361 717252795 717252699 2.950000e-31 147.0
36 TraesCS5D01G073100 chr7B 92.233 103 7 1 3265 3367 38968307 38968408 1.060000e-30 145.0
37 TraesCS5D01G073100 chr1B 89.474 114 10 1 3260 3371 429278902 429279015 3.820000e-30 143.0


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 TraesCS5D01G073100 chr5D 72499626 72503296 3670 True 6780.0 6780 100.0000 1 3671 1 chr5D.!!$R1 3670
1 TraesCS5D01G073100 chr5B 81481305 81484969 3664 False 1049.8 3389 91.7660 1 3580 5 chr5B.!!$F1 3579
2 TraesCS5D01G073100 chr5A 64958090 64961599 3509 True 945.6 3339 91.0024 146 3671 5 chr5A.!!$R1 3525
3 TraesCS5D01G073100 chr2D 168147313 168148083 770 True 545.0 545 79.7520 983 1779 1 chr2D.!!$R1 796
4 TraesCS5D01G073100 chr6D 441965796 441966569 773 True 531.0 531 79.3530 983 1779 1 chr6D.!!$R2 796
5 TraesCS5D01G073100 chr3A 647019122 647019780 658 False 484.0 484 80.2050 983 1658 1 chr3A.!!$F1 675
6 TraesCS5D01G073100 chr4A 669400332 669400876 544 False 455.0 455 81.9320 1328 1881 1 chr4A.!!$F1 553
7 TraesCS5D01G073100 chr4B 243887431 243887975 544 True 359.0 359 78.8630 1328 1885 1 chr4B.!!$R1 557

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
864 951 0.251073 GCTGCATCATTTGGGCCTTT 59.749 50.000 4.53 0.0 0.0 3.11 F
1837 2003 3.630312 TGTGTTTTCTTCTTGCAGGGTAC 59.370 43.478 0.00 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2481 2663 0.674581 TCTGAAGGATGTGCTTGGCG 60.675 55.0 0.00 0.00 0.00 5.69 R
2936 3143 0.106167 ATGGAGCAGCTCAATGGCAT 60.106 50.0 24.09 14.06 31.08 4.40 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
92 93 2.159071 TGCATATTGCCCATCAACAAGC 60.159 45.455 0.00 0.00 44.23 4.01
106 107 3.826157 TCAACAAGCCTTCCTTAACCATG 59.174 43.478 0.00 0.00 31.00 3.66
207 208 4.609018 CCGCCCCTGCATCCTACG 62.609 72.222 0.00 0.00 37.32 3.51
277 279 1.081092 AAGAGCAGGCCCCTACTGA 59.919 57.895 0.00 0.00 38.20 3.41
296 298 5.045215 ACTGACGTAATTTCGTGTTCTTCA 58.955 37.500 15.13 4.77 44.21 3.02
301 303 7.383029 TGACGTAATTTCGTGTTCTTCACTAAT 59.617 33.333 15.13 0.00 44.21 1.73
406 411 4.216257 TCAACAGCTTAGCATCTTTGGTTC 59.784 41.667 7.07 0.00 34.79 3.62
477 561 2.544486 CCTGAGGTTTGTCTTGCTTTGC 60.544 50.000 0.00 0.00 0.00 3.68
516 600 4.421948 ACTAGTAGAATCGCCGAGTTTTG 58.578 43.478 3.59 0.00 0.00 2.44
583 667 5.005394 CGTTGCGCAGTGTAATCTATTTAGT 59.995 40.000 11.31 0.00 0.00 2.24
656 741 7.466590 GCTCAGAGAAGATGCATTTAACTAACC 60.467 40.741 0.00 0.00 0.00 2.85
664 749 8.276252 AGATGCATTTAACTAACCGTTACATT 57.724 30.769 0.00 0.00 37.80 2.71
665 750 8.181573 AGATGCATTTAACTAACCGTTACATTG 58.818 33.333 0.00 0.00 37.80 2.82
703 788 8.960591 AGTAACTAAGTGCATTATGAAAGCAAT 58.039 29.630 0.00 0.00 40.35 3.56
733 820 4.229096 CCAAAACAAAGTGGATGATGTCG 58.771 43.478 0.00 0.00 37.03 4.35
759 846 6.017605 CCAAATTGATAGAGGTGATGTAGTGC 60.018 42.308 0.00 0.00 0.00 4.40
763 850 0.539051 AGAGGTGATGTAGTGCCAGC 59.461 55.000 0.00 0.00 0.00 4.85
808 895 4.023291 TGGAAAACCAAGCTCAAAAGTCT 58.977 39.130 0.00 0.00 0.00 3.24
864 951 0.251073 GCTGCATCATTTGGGCCTTT 59.749 50.000 4.53 0.00 0.00 3.11
873 960 6.642430 CATCATTTGGGCCTTTTATTTCTCA 58.358 36.000 4.53 0.00 0.00 3.27
959 1116 6.917477 TGTTGTTATTGTTGAAGTGAGCATTC 59.083 34.615 0.00 0.00 0.00 2.67
1091 1248 4.871933 TCTGTCATGCAGTTAGTCAAGA 57.128 40.909 14.21 0.00 45.23 3.02
1837 2003 3.630312 TGTGTTTTCTTCTTGCAGGGTAC 59.370 43.478 0.00 0.00 0.00 3.34
1892 2061 5.301551 TGCAGACAAGAACACATTACCAATT 59.698 36.000 0.00 0.00 0.00 2.32
1893 2062 6.488344 TGCAGACAAGAACACATTACCAATTA 59.512 34.615 0.00 0.00 0.00 1.40
1894 2063 7.023575 GCAGACAAGAACACATTACCAATTAG 58.976 38.462 0.00 0.00 0.00 1.73
2016 2188 4.017591 TCCCATTCATGGCCTCTTTTTAGA 60.018 41.667 3.32 0.00 46.70 2.10
2123 2295 5.627499 TTCTGCCAATGTTAGTGATTGAC 57.373 39.130 0.00 0.00 33.36 3.18
2339 2518 7.341256 AGCATCAAGAAATTGTCAATGGACTAT 59.659 33.333 1.02 0.00 44.61 2.12
2481 2663 3.550842 GCCAAACTGTTGATGTGGAAGAC 60.551 47.826 12.06 0.00 36.83 3.01
2565 2747 0.849417 GGGATGCCCAGAAGGAAGAT 59.151 55.000 0.00 0.00 44.65 2.40
2734 2940 2.167693 CCTGCTCATGCCATTTTGTCAT 59.832 45.455 0.00 0.00 38.71 3.06
2762 2968 1.198713 ATCGACATTGGGCTGACTCT 58.801 50.000 0.00 0.00 0.00 3.24
2786 2992 6.236409 TGCATGCCCAAAATATTCTTGAAAA 58.764 32.000 16.68 0.00 0.00 2.29
2932 3139 4.435425 GCATTTTTGCATGCTTCTATCCA 58.565 39.130 20.33 0.00 45.35 3.41
2933 3140 4.269363 GCATTTTTGCATGCTTCTATCCAC 59.731 41.667 20.33 0.00 45.35 4.02
2934 3141 5.412640 CATTTTTGCATGCTTCTATCCACA 58.587 37.500 20.33 0.00 0.00 4.17
2935 3142 5.664294 TTTTTGCATGCTTCTATCCACAT 57.336 34.783 20.33 0.00 0.00 3.21
2936 3143 6.772360 TTTTTGCATGCTTCTATCCACATA 57.228 33.333 20.33 0.00 0.00 2.29
2937 3144 6.964807 TTTTGCATGCTTCTATCCACATAT 57.035 33.333 20.33 0.00 0.00 1.78
2938 3145 5.952526 TTGCATGCTTCTATCCACATATG 57.047 39.130 20.33 0.00 0.00 1.78
2939 3146 3.754850 TGCATGCTTCTATCCACATATGC 59.245 43.478 20.33 0.00 39.89 3.14
2940 3147 3.128242 GCATGCTTCTATCCACATATGCC 59.872 47.826 11.37 0.00 35.03 4.40
2941 3148 4.329392 CATGCTTCTATCCACATATGCCA 58.671 43.478 1.58 0.00 0.00 4.92
2960 3167 1.945394 CATTGAGCTGCTCCATGTACC 59.055 52.381 26.87 4.92 31.58 3.34
2972 3179 4.717877 CTCCATGTACCCATTAAGCATCA 58.282 43.478 0.00 0.00 0.00 3.07
2973 3180 5.319453 CTCCATGTACCCATTAAGCATCAT 58.681 41.667 0.00 0.00 0.00 2.45
2978 3185 7.558807 CCATGTACCCATTAAGCATCATCATAT 59.441 37.037 0.00 0.00 0.00 1.78
3018 3276 6.349280 CGATGTGTTCACCCTTTGTTGATATT 60.349 38.462 0.37 0.00 0.00 1.28
3019 3277 6.723298 TGTGTTCACCCTTTGTTGATATTT 57.277 33.333 0.37 0.00 0.00 1.40
3045 3303 5.934781 ACCAAGGGCATAAACAATGAAAAA 58.065 33.333 0.00 0.00 37.86 1.94
3051 3309 5.412286 GGGCATAAACAATGAAAAAGCACAT 59.588 36.000 0.00 0.00 37.86 3.21
3105 3363 1.039068 TGCAAAATATGGGGATGGCG 58.961 50.000 0.00 0.00 0.00 5.69
3108 3366 0.188342 AAAATATGGGGATGGCGCCT 59.812 50.000 29.70 13.55 46.68 5.52
3175 3437 4.341502 GGCAAAAGAGCGCCGCAA 62.342 61.111 13.36 0.00 38.82 4.85
3176 3438 2.354539 GCAAAAGAGCGCCGCAAA 60.355 55.556 13.36 0.00 0.00 3.68
3177 3439 1.948635 GCAAAAGAGCGCCGCAAAA 60.949 52.632 13.36 0.00 0.00 2.44
3178 3440 1.486644 GCAAAAGAGCGCCGCAAAAA 61.487 50.000 13.36 0.00 0.00 1.94
3179 3441 0.503961 CAAAAGAGCGCCGCAAAAAG 59.496 50.000 13.36 0.00 0.00 2.27
3180 3442 0.383949 AAAAGAGCGCCGCAAAAAGA 59.616 45.000 13.36 0.00 0.00 2.52
3181 3443 0.383949 AAAGAGCGCCGCAAAAAGAA 59.616 45.000 13.36 0.00 0.00 2.52
3237 3502 4.058817 GGTGAAAGCCAGATATCCTAACG 58.941 47.826 0.00 0.00 0.00 3.18
3258 3523 2.009774 GGACTGGACAACGATGGATTG 58.990 52.381 0.00 0.00 0.00 2.67
3266 3531 5.180492 TGGACAACGATGGATTGTTTTCTAC 59.820 40.000 0.00 0.00 40.36 2.59
3268 3533 6.402226 GGACAACGATGGATTGTTTTCTACTC 60.402 42.308 0.00 0.00 40.36 2.59
3269 3534 5.411669 ACAACGATGGATTGTTTTCTACTCC 59.588 40.000 0.00 0.00 36.93 3.85
3270 3535 4.514401 ACGATGGATTGTTTTCTACTCCC 58.486 43.478 0.00 0.00 0.00 4.30
3271 3536 4.225267 ACGATGGATTGTTTTCTACTCCCT 59.775 41.667 0.00 0.00 0.00 4.20
3273 3538 4.569719 TGGATTGTTTTCTACTCCCTCC 57.430 45.455 0.00 0.00 0.00 4.30
3274 3539 3.055385 TGGATTGTTTTCTACTCCCTCCG 60.055 47.826 0.00 0.00 0.00 4.63
3275 3540 3.055312 GGATTGTTTTCTACTCCCTCCGT 60.055 47.826 0.00 0.00 0.00 4.69
3276 3541 3.672767 TTGTTTTCTACTCCCTCCGTC 57.327 47.619 0.00 0.00 0.00 4.79
3277 3542 1.897802 TGTTTTCTACTCCCTCCGTCC 59.102 52.381 0.00 0.00 0.00 4.79
3278 3543 1.206610 GTTTTCTACTCCCTCCGTCCC 59.793 57.143 0.00 0.00 0.00 4.46
3279 3544 0.410663 TTTCTACTCCCTCCGTCCCA 59.589 55.000 0.00 0.00 0.00 4.37
3280 3545 0.410663 TTCTACTCCCTCCGTCCCAA 59.589 55.000 0.00 0.00 0.00 4.12
3281 3546 0.410663 TCTACTCCCTCCGTCCCAAA 59.589 55.000 0.00 0.00 0.00 3.28
3282 3547 1.203212 TCTACTCCCTCCGTCCCAAAA 60.203 52.381 0.00 0.00 0.00 2.44
3283 3548 0.978907 TACTCCCTCCGTCCCAAAAC 59.021 55.000 0.00 0.00 0.00 2.43
3284 3549 1.057851 ACTCCCTCCGTCCCAAAACA 61.058 55.000 0.00 0.00 0.00 2.83
3285 3550 0.109723 CTCCCTCCGTCCCAAAACAA 59.890 55.000 0.00 0.00 0.00 2.83
3286 3551 0.109723 TCCCTCCGTCCCAAAACAAG 59.890 55.000 0.00 0.00 0.00 3.16
3287 3552 0.179001 CCCTCCGTCCCAAAACAAGT 60.179 55.000 0.00 0.00 0.00 3.16
3288 3553 0.951558 CCTCCGTCCCAAAACAAGTG 59.048 55.000 0.00 0.00 0.00 3.16
3289 3554 1.675552 CTCCGTCCCAAAACAAGTGT 58.324 50.000 0.00 0.00 0.00 3.55
3290 3555 1.602377 CTCCGTCCCAAAACAAGTGTC 59.398 52.381 0.00 0.00 0.00 3.67
3291 3556 1.210967 TCCGTCCCAAAACAAGTGTCT 59.789 47.619 0.00 0.00 0.00 3.41
3292 3557 1.602377 CCGTCCCAAAACAAGTGTCTC 59.398 52.381 0.00 0.00 0.00 3.36
3293 3558 2.285083 CGTCCCAAAACAAGTGTCTCA 58.715 47.619 0.00 0.00 0.00 3.27
3294 3559 2.680841 CGTCCCAAAACAAGTGTCTCAA 59.319 45.455 0.00 0.00 0.00 3.02
3295 3560 3.486875 CGTCCCAAAACAAGTGTCTCAAC 60.487 47.826 0.00 0.00 0.00 3.18
3296 3561 3.694566 GTCCCAAAACAAGTGTCTCAACT 59.305 43.478 0.00 0.00 0.00 3.16
3297 3562 4.157840 GTCCCAAAACAAGTGTCTCAACTT 59.842 41.667 0.00 0.00 41.08 2.66
3298 3563 4.770010 TCCCAAAACAAGTGTCTCAACTTT 59.230 37.500 0.00 0.00 38.34 2.66
3299 3564 4.864247 CCCAAAACAAGTGTCTCAACTTTG 59.136 41.667 0.00 0.00 38.34 2.77
3300 3565 5.469479 CCAAAACAAGTGTCTCAACTTTGT 58.531 37.500 4.31 0.00 38.34 2.83
3301 3566 6.349777 CCCAAAACAAGTGTCTCAACTTTGTA 60.350 38.462 4.31 0.00 38.34 2.41
3302 3567 6.526674 CCAAAACAAGTGTCTCAACTTTGTAC 59.473 38.462 0.00 0.00 38.34 2.90
3303 3568 7.305474 CAAAACAAGTGTCTCAACTTTGTACT 58.695 34.615 0.00 0.00 38.34 2.73
3304 3569 8.447833 CAAAACAAGTGTCTCAACTTTGTACTA 58.552 33.333 0.00 0.00 38.34 1.82
3305 3570 7.772332 AACAAGTGTCTCAACTTTGTACTAG 57.228 36.000 0.00 0.00 38.34 2.57
3306 3571 5.753921 ACAAGTGTCTCAACTTTGTACTAGC 59.246 40.000 0.00 0.00 38.34 3.42
3307 3572 5.793030 AGTGTCTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
3308 3573 6.163135 AGTGTCTCAACTTTGTACTAGCTT 57.837 37.500 0.00 0.00 0.00 3.74
3309 3574 6.583562 AGTGTCTCAACTTTGTACTAGCTTT 58.416 36.000 0.00 0.00 0.00 3.51
3310 3575 7.723324 AGTGTCTCAACTTTGTACTAGCTTTA 58.277 34.615 0.00 0.00 0.00 1.85
3311 3576 7.868415 AGTGTCTCAACTTTGTACTAGCTTTAG 59.132 37.037 0.00 0.00 0.00 1.85
3312 3577 7.652507 GTGTCTCAACTTTGTACTAGCTTTAGT 59.347 37.037 0.00 0.00 0.00 2.24
3313 3578 8.853126 TGTCTCAACTTTGTACTAGCTTTAGTA 58.147 33.333 0.00 0.00 0.00 1.82
3314 3579 9.857957 GTCTCAACTTTGTACTAGCTTTAGTAT 57.142 33.333 0.00 0.00 35.30 2.12
3330 3595 9.620259 AGCTTTAGTATAAATTTCTGCTAAGCT 57.380 29.630 19.43 19.43 0.00 3.74
3331 3596 9.871299 GCTTTAGTATAAATTTCTGCTAAGCTC 57.129 33.333 17.47 9.10 0.00 4.09
3336 3601 9.103861 AGTATAAATTTCTGCTAAGCTCAAGAC 57.896 33.333 0.00 0.00 0.00 3.01
3337 3602 7.928307 ATAAATTTCTGCTAAGCTCAAGACA 57.072 32.000 0.00 0.00 0.00 3.41
3338 3603 5.619625 AATTTCTGCTAAGCTCAAGACAC 57.380 39.130 0.32 0.00 0.00 3.67
3339 3604 4.342862 TTTCTGCTAAGCTCAAGACACT 57.657 40.909 0.32 0.00 0.00 3.55
3340 3605 4.342862 TTCTGCTAAGCTCAAGACACTT 57.657 40.909 0.32 0.00 0.00 3.16
3341 3606 5.468540 TTCTGCTAAGCTCAAGACACTTA 57.531 39.130 0.32 0.00 0.00 2.24
3342 3607 5.667539 TCTGCTAAGCTCAAGACACTTAT 57.332 39.130 0.32 0.00 0.00 1.73
3343 3608 6.042638 TCTGCTAAGCTCAAGACACTTATT 57.957 37.500 0.32 0.00 0.00 1.40
3344 3609 6.467677 TCTGCTAAGCTCAAGACACTTATTT 58.532 36.000 0.32 0.00 0.00 1.40
3345 3610 6.936900 TCTGCTAAGCTCAAGACACTTATTTT 59.063 34.615 0.32 0.00 0.00 1.82
3346 3611 6.902341 TGCTAAGCTCAAGACACTTATTTTG 58.098 36.000 0.32 0.00 0.00 2.44
3347 3612 6.072508 TGCTAAGCTCAAGACACTTATTTTGG 60.073 38.462 0.32 0.00 0.00 3.28
3348 3613 6.149474 GCTAAGCTCAAGACACTTATTTTGGA 59.851 38.462 0.32 0.00 0.00 3.53
3349 3614 6.959639 AAGCTCAAGACACTTATTTTGGAA 57.040 33.333 0.00 0.00 0.00 3.53
3350 3615 6.319141 AGCTCAAGACACTTATTTTGGAAC 57.681 37.500 0.00 0.00 0.00 3.62
3351 3616 5.049405 AGCTCAAGACACTTATTTTGGAACG 60.049 40.000 0.00 0.00 0.00 3.95
3352 3617 5.682943 TCAAGACACTTATTTTGGAACGG 57.317 39.130 0.00 0.00 0.00 4.44
3353 3618 5.369833 TCAAGACACTTATTTTGGAACGGA 58.630 37.500 0.00 0.00 0.00 4.69
3354 3619 5.468746 TCAAGACACTTATTTTGGAACGGAG 59.531 40.000 0.00 0.00 0.00 4.63
3355 3620 4.324267 AGACACTTATTTTGGAACGGAGG 58.676 43.478 0.00 0.00 0.00 4.30
3356 3621 3.418047 ACACTTATTTTGGAACGGAGGG 58.582 45.455 0.00 0.00 0.00 4.30
3357 3622 3.073356 ACACTTATTTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 0.00 4.20
3358 3623 3.689649 CACTTATTTTGGAACGGAGGGAG 59.310 47.826 0.00 0.00 0.00 4.30
3359 3624 3.329814 ACTTATTTTGGAACGGAGGGAGT 59.670 43.478 0.00 0.00 0.00 3.85
3360 3625 4.533311 ACTTATTTTGGAACGGAGGGAGTA 59.467 41.667 0.00 0.00 0.00 2.59
3361 3626 5.191124 ACTTATTTTGGAACGGAGGGAGTAT 59.809 40.000 0.00 0.00 0.00 2.12
3362 3627 3.343941 TTTTGGAACGGAGGGAGTATG 57.656 47.619 0.00 0.00 0.00 2.39
3363 3628 1.946984 TTGGAACGGAGGGAGTATGT 58.053 50.000 0.00 0.00 0.00 2.29
3364 3629 2.832643 TGGAACGGAGGGAGTATGTA 57.167 50.000 0.00 0.00 0.00 2.29
3365 3630 3.323774 TGGAACGGAGGGAGTATGTAT 57.676 47.619 0.00 0.00 0.00 2.29
3366 3631 3.649843 TGGAACGGAGGGAGTATGTATT 58.350 45.455 0.00 0.00 0.00 1.89
3367 3632 4.806892 TGGAACGGAGGGAGTATGTATTA 58.193 43.478 0.00 0.00 0.00 0.98
3368 3633 5.210430 TGGAACGGAGGGAGTATGTATTAA 58.790 41.667 0.00 0.00 0.00 1.40
3369 3634 5.662208 TGGAACGGAGGGAGTATGTATTAAA 59.338 40.000 0.00 0.00 0.00 1.52
3370 3635 6.328148 TGGAACGGAGGGAGTATGTATTAAAT 59.672 38.462 0.00 0.00 0.00 1.40
3371 3636 7.510001 TGGAACGGAGGGAGTATGTATTAAATA 59.490 37.037 0.00 0.00 0.00 1.40
3372 3637 8.537858 GGAACGGAGGGAGTATGTATTAAATAT 58.462 37.037 0.00 0.00 0.00 1.28
3403 3668 6.941436 AGAAATAGGTATATCGGAGTTCGTCT 59.059 38.462 0.00 0.00 40.32 4.18
3421 3689 6.302535 TCGTCTTCCCATCCTTACAAAATA 57.697 37.500 0.00 0.00 0.00 1.40
3476 3764 6.701145 TTTGTGCCTAACTGTGATAAAACA 57.299 33.333 0.00 0.00 0.00 2.83
3505 3793 1.705256 TTAACTTGAGTAGCCACGCG 58.295 50.000 3.53 3.53 0.00 6.01
3565 3853 8.250332 GGAGTTGAAGCATTAATCACCAATAAA 58.750 33.333 0.00 0.00 0.00 1.40
3630 3918 8.950210 CACAAAGACATAGGAGTAATTCATTGT 58.050 33.333 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 8.578308 TGCAACATTTGAAGAAGAATACAAAG 57.422 30.769 0.00 0.00 36.07 2.77
79 80 0.613012 AGGAAGGCTTGTTGATGGGC 60.613 55.000 3.46 0.00 0.00 5.36
92 93 7.557719 AGACAATGAATACATGGTTAAGGAAGG 59.442 37.037 0.00 0.00 40.37 3.46
106 107 9.862371 CATATACTACCTGGAGACAATGAATAC 57.138 37.037 0.00 0.00 42.06 1.89
296 298 1.826385 GTTGCTGAGGTGGCATTAGT 58.174 50.000 0.00 0.00 39.54 2.24
301 303 2.591429 CACGTTGCTGAGGTGGCA 60.591 61.111 0.00 0.00 39.78 4.92
477 561 8.211116 TCTACTAGTTCCGAAAAGAGTGATAG 57.789 38.462 0.00 0.00 0.00 2.08
516 600 6.348704 GGCCGTCAGTCTAGAATAATCTCTAC 60.349 46.154 0.00 0.00 37.10 2.59
583 667 5.070001 ACTAGTAAGCAAGCATTCACCAAA 58.930 37.500 0.00 0.00 0.00 3.28
664 749 9.767228 TGCACTTAGTTACTTTTAACTATCACA 57.233 29.630 5.36 1.21 45.93 3.58
733 820 6.017605 CACTACATCACCTCTATCAATTTGGC 60.018 42.308 0.00 0.00 0.00 4.52
759 846 3.833070 ACCTTATATTCTCTACGGGCTGG 59.167 47.826 0.00 0.00 0.00 4.85
763 850 5.047943 CAGTCCACCTTATATTCTCTACGGG 60.048 48.000 0.00 0.00 0.00 5.28
808 895 3.011566 TGCTTGTTCTCCCTTTTGTGA 57.988 42.857 0.00 0.00 0.00 3.58
846 933 2.773993 AAAAGGCCCAAATGATGCAG 57.226 45.000 0.00 0.00 0.00 4.41
857 944 2.163613 CACGGTGAGAAATAAAAGGCCC 59.836 50.000 0.74 0.00 0.00 5.80
864 951 4.527038 AGAGAACTCCACGGTGAGAAATAA 59.473 41.667 10.28 0.00 36.22 1.40
873 960 3.367646 TCTATCAGAGAACTCCACGGT 57.632 47.619 0.00 0.00 0.00 4.83
959 1116 2.157668 CGTGAACCTGAATCCAGAAACG 59.842 50.000 0.00 0.00 43.02 3.60
1140 1297 1.863267 TGCAATTTTCCTGCCAAACG 58.137 45.000 0.00 0.00 39.13 3.60
1837 2003 6.931840 AGAATATAGCGAAGGGAAAAGCTTAG 59.068 38.462 0.00 0.00 40.73 2.18
2123 2295 2.159282 ACTGGAATCGTTACAGGCTACG 60.159 50.000 12.60 1.94 36.57 3.51
2163 2335 2.414481 CAGCACTACACAGCTTAGCAAG 59.586 50.000 7.07 0.55 39.50 4.01
2243 2422 7.170658 GCAACAGAAGAGAATATGAGTACCATC 59.829 40.741 0.76 0.00 36.71 3.51
2255 2434 4.077300 TGTGTCAGCAACAGAAGAGAAT 57.923 40.909 0.00 0.00 38.97 2.40
2339 2518 2.493278 GGCTGATTCTTTGGCTTTAGCA 59.507 45.455 3.88 0.00 44.36 3.49
2481 2663 0.674581 TCTGAAGGATGTGCTTGGCG 60.675 55.000 0.00 0.00 0.00 5.69
2643 2825 1.800805 GCAGCAGCTGTTCTAGTTCA 58.199 50.000 23.60 0.00 37.91 3.18
2734 2940 1.391577 CCAATGTCGATTCCATGCCA 58.608 50.000 0.00 0.00 0.00 4.92
2762 2968 5.417754 TTCAAGAATATTTTGGGCATGCA 57.582 34.783 21.36 0.00 0.00 3.96
2929 3136 2.578786 CAGCTCAATGGCATATGTGGA 58.421 47.619 0.00 0.00 34.17 4.02
2930 3137 1.000607 GCAGCTCAATGGCATATGTGG 60.001 52.381 0.00 1.77 34.17 4.17
2931 3138 1.954382 AGCAGCTCAATGGCATATGTG 59.046 47.619 0.00 4.14 34.17 3.21
2932 3139 2.228059 GAGCAGCTCAATGGCATATGT 58.772 47.619 18.17 0.00 34.17 2.29
2933 3140 1.540267 GGAGCAGCTCAATGGCATATG 59.460 52.381 24.09 0.00 31.08 1.78
2934 3141 1.144298 TGGAGCAGCTCAATGGCATAT 59.856 47.619 24.09 0.00 31.08 1.78
2935 3142 0.547553 TGGAGCAGCTCAATGGCATA 59.452 50.000 24.09 0.00 31.08 3.14
2936 3143 0.106167 ATGGAGCAGCTCAATGGCAT 60.106 50.000 24.09 14.06 31.08 4.40
2937 3144 1.035385 CATGGAGCAGCTCAATGGCA 61.035 55.000 27.00 14.90 38.04 4.92
2938 3145 1.035932 ACATGGAGCAGCTCAATGGC 61.036 55.000 34.15 15.01 43.99 4.40
2939 3146 1.945394 GTACATGGAGCAGCTCAATGG 59.055 52.381 34.15 20.69 43.99 3.16
2940 3147 1.945394 GGTACATGGAGCAGCTCAATG 59.055 52.381 31.14 31.14 44.91 2.82
2941 3148 1.133976 GGGTACATGGAGCAGCTCAAT 60.134 52.381 24.09 15.96 31.08 2.57
2972 3179 5.554070 TCGAGATGTTCAATGGCATATGAT 58.446 37.500 6.97 0.00 0.00 2.45
2973 3180 4.959723 TCGAGATGTTCAATGGCATATGA 58.040 39.130 6.97 4.35 0.00 2.15
3018 3276 6.672266 TCATTGTTTATGCCCTTGGTAAAA 57.328 33.333 0.00 0.00 34.06 1.52
3019 3277 6.672266 TTCATTGTTTATGCCCTTGGTAAA 57.328 33.333 0.00 0.00 34.06 2.01
3045 3303 8.798859 ATGAGTTTACTTTTCTATGATGTGCT 57.201 30.769 0.00 0.00 0.00 4.40
3085 3343 1.619827 CGCCATCCCCATATTTTGCAT 59.380 47.619 0.00 0.00 0.00 3.96
3087 3345 0.319813 GCGCCATCCCCATATTTTGC 60.320 55.000 0.00 0.00 0.00 3.68
3165 3427 0.984829 GAATTCTTTTTGCGGCGCTC 59.015 50.000 33.26 14.74 0.00 5.03
3175 3437 1.102978 CCCGGCGATGGAATTCTTTT 58.897 50.000 9.30 0.00 0.00 2.27
3176 3438 0.254747 TCCCGGCGATGGAATTCTTT 59.745 50.000 9.30 0.00 0.00 2.52
3177 3439 0.474184 ATCCCGGCGATGGAATTCTT 59.526 50.000 9.30 0.00 35.03 2.52
3178 3440 0.474184 AATCCCGGCGATGGAATTCT 59.526 50.000 9.30 0.00 35.03 2.40
3179 3441 1.001378 CAAATCCCGGCGATGGAATTC 60.001 52.381 9.30 0.00 35.03 2.17
3180 3442 1.032014 CAAATCCCGGCGATGGAATT 58.968 50.000 9.30 3.80 35.03 2.17
3181 3443 0.182537 TCAAATCCCGGCGATGGAAT 59.817 50.000 9.30 0.00 35.03 3.01
3237 3502 0.541863 ATCCATCGTTGTCCAGTCCC 59.458 55.000 0.00 0.00 0.00 4.46
3243 3508 4.766404 AGAAAACAATCCATCGTTGTCC 57.234 40.909 0.00 0.00 38.76 4.02
3247 3512 4.941873 GGGAGTAGAAAACAATCCATCGTT 59.058 41.667 0.00 0.00 0.00 3.85
3258 3523 1.206610 GGGACGGAGGGAGTAGAAAAC 59.793 57.143 0.00 0.00 0.00 2.43
3266 3531 0.109723 TTGTTTTGGGACGGAGGGAG 59.890 55.000 0.00 0.00 0.00 4.30
3268 3533 0.179001 ACTTGTTTTGGGACGGAGGG 60.179 55.000 0.00 0.00 0.00 4.30
3269 3534 0.951558 CACTTGTTTTGGGACGGAGG 59.048 55.000 0.00 0.00 0.00 4.30
3270 3535 1.602377 GACACTTGTTTTGGGACGGAG 59.398 52.381 0.00 0.00 0.00 4.63
3271 3536 1.210967 AGACACTTGTTTTGGGACGGA 59.789 47.619 0.00 0.00 0.00 4.69
3273 3538 2.285083 TGAGACACTTGTTTTGGGACG 58.715 47.619 0.00 0.00 0.00 4.79
3274 3539 3.694566 AGTTGAGACACTTGTTTTGGGAC 59.305 43.478 0.00 0.00 0.00 4.46
3275 3540 3.963129 AGTTGAGACACTTGTTTTGGGA 58.037 40.909 0.00 0.00 0.00 4.37
3276 3541 4.718940 AAGTTGAGACACTTGTTTTGGG 57.281 40.909 0.00 0.00 35.57 4.12
3277 3542 5.469479 ACAAAGTTGAGACACTTGTTTTGG 58.531 37.500 0.00 0.00 37.07 3.28
3278 3543 7.305474 AGTACAAAGTTGAGACACTTGTTTTG 58.695 34.615 0.00 2.02 37.07 2.44
3279 3544 7.448748 AGTACAAAGTTGAGACACTTGTTTT 57.551 32.000 0.00 0.00 37.07 2.43
3280 3545 7.201617 GCTAGTACAAAGTTGAGACACTTGTTT 60.202 37.037 0.00 0.00 37.07 2.83
3281 3546 6.258068 GCTAGTACAAAGTTGAGACACTTGTT 59.742 38.462 0.00 0.00 37.07 2.83
3282 3547 5.753921 GCTAGTACAAAGTTGAGACACTTGT 59.246 40.000 0.00 0.00 37.07 3.16
3283 3548 5.986135 AGCTAGTACAAAGTTGAGACACTTG 59.014 40.000 0.00 0.00 37.07 3.16
3284 3549 6.163135 AGCTAGTACAAAGTTGAGACACTT 57.837 37.500 0.00 0.00 38.74 3.16
3285 3550 5.793030 AGCTAGTACAAAGTTGAGACACT 57.207 39.130 0.00 0.00 0.00 3.55
3286 3551 6.846325 AAAGCTAGTACAAAGTTGAGACAC 57.154 37.500 0.00 0.00 0.00 3.67
3287 3552 7.723324 ACTAAAGCTAGTACAAAGTTGAGACA 58.277 34.615 0.00 0.00 36.56 3.41
3288 3553 9.857957 ATACTAAAGCTAGTACAAAGTTGAGAC 57.142 33.333 0.00 0.00 42.19 3.36
3304 3569 9.620259 AGCTTAGCAGAAATTTATACTAAAGCT 57.380 29.630 7.07 16.04 0.00 3.74
3305 3570 9.871299 GAGCTTAGCAGAAATTTATACTAAAGC 57.129 33.333 7.07 10.81 0.00 3.51
3310 3575 9.103861 GTCTTGAGCTTAGCAGAAATTTATACT 57.896 33.333 7.07 0.00 0.00 2.12
3311 3576 8.883731 TGTCTTGAGCTTAGCAGAAATTTATAC 58.116 33.333 7.07 0.00 0.00 1.47
3312 3577 8.883731 GTGTCTTGAGCTTAGCAGAAATTTATA 58.116 33.333 7.07 0.00 0.00 0.98
3313 3578 7.609532 AGTGTCTTGAGCTTAGCAGAAATTTAT 59.390 33.333 7.07 0.00 0.00 1.40
3314 3579 6.936900 AGTGTCTTGAGCTTAGCAGAAATTTA 59.063 34.615 7.07 0.00 0.00 1.40
3315 3580 5.767168 AGTGTCTTGAGCTTAGCAGAAATTT 59.233 36.000 7.07 0.00 0.00 1.82
3316 3581 5.312079 AGTGTCTTGAGCTTAGCAGAAATT 58.688 37.500 7.07 0.00 0.00 1.82
3317 3582 4.904241 AGTGTCTTGAGCTTAGCAGAAAT 58.096 39.130 7.07 0.00 0.00 2.17
3318 3583 4.342862 AGTGTCTTGAGCTTAGCAGAAA 57.657 40.909 7.07 0.00 0.00 2.52
3319 3584 4.342862 AAGTGTCTTGAGCTTAGCAGAA 57.657 40.909 7.07 0.00 0.00 3.02
3320 3585 5.667539 ATAAGTGTCTTGAGCTTAGCAGA 57.332 39.130 7.07 0.00 0.00 4.26
3321 3586 6.734104 AAATAAGTGTCTTGAGCTTAGCAG 57.266 37.500 7.07 0.00 0.00 4.24
3322 3587 6.072508 CCAAAATAAGTGTCTTGAGCTTAGCA 60.073 38.462 7.07 0.00 0.00 3.49
3323 3588 6.149474 TCCAAAATAAGTGTCTTGAGCTTAGC 59.851 38.462 0.00 0.00 0.00 3.09
3324 3589 7.672983 TCCAAAATAAGTGTCTTGAGCTTAG 57.327 36.000 0.00 0.00 0.00 2.18
3325 3590 7.307751 CGTTCCAAAATAAGTGTCTTGAGCTTA 60.308 37.037 0.00 0.00 0.00 3.09
3326 3591 6.513393 CGTTCCAAAATAAGTGTCTTGAGCTT 60.513 38.462 0.00 0.00 0.00 3.74
3327 3592 5.049405 CGTTCCAAAATAAGTGTCTTGAGCT 60.049 40.000 0.00 0.00 0.00 4.09
3328 3593 5.147162 CGTTCCAAAATAAGTGTCTTGAGC 58.853 41.667 0.00 0.00 0.00 4.26
3329 3594 5.468746 TCCGTTCCAAAATAAGTGTCTTGAG 59.531 40.000 0.00 0.00 0.00 3.02
3330 3595 5.369833 TCCGTTCCAAAATAAGTGTCTTGA 58.630 37.500 0.00 0.00 0.00 3.02
3331 3596 5.334879 CCTCCGTTCCAAAATAAGTGTCTTG 60.335 44.000 0.00 0.00 0.00 3.02
3332 3597 4.760204 CCTCCGTTCCAAAATAAGTGTCTT 59.240 41.667 0.00 0.00 0.00 3.01
3333 3598 4.324267 CCTCCGTTCCAAAATAAGTGTCT 58.676 43.478 0.00 0.00 0.00 3.41
3334 3599 3.439129 CCCTCCGTTCCAAAATAAGTGTC 59.561 47.826 0.00 0.00 0.00 3.67
3335 3600 3.073356 TCCCTCCGTTCCAAAATAAGTGT 59.927 43.478 0.00 0.00 0.00 3.55
3336 3601 3.681593 TCCCTCCGTTCCAAAATAAGTG 58.318 45.455 0.00 0.00 0.00 3.16
3337 3602 3.329814 ACTCCCTCCGTTCCAAAATAAGT 59.670 43.478 0.00 0.00 0.00 2.24
3338 3603 3.951663 ACTCCCTCCGTTCCAAAATAAG 58.048 45.455 0.00 0.00 0.00 1.73
3339 3604 5.045432 ACATACTCCCTCCGTTCCAAAATAA 60.045 40.000 0.00 0.00 0.00 1.40
3340 3605 4.472108 ACATACTCCCTCCGTTCCAAAATA 59.528 41.667 0.00 0.00 0.00 1.40
3341 3606 3.265995 ACATACTCCCTCCGTTCCAAAAT 59.734 43.478 0.00 0.00 0.00 1.82
3342 3607 2.640826 ACATACTCCCTCCGTTCCAAAA 59.359 45.455 0.00 0.00 0.00 2.44
3343 3608 2.262637 ACATACTCCCTCCGTTCCAAA 58.737 47.619 0.00 0.00 0.00 3.28
3344 3609 1.946984 ACATACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
3345 3610 2.832643 TACATACTCCCTCCGTTCCA 57.167 50.000 0.00 0.00 0.00 3.53
3346 3611 5.796424 TTAATACATACTCCCTCCGTTCC 57.204 43.478 0.00 0.00 0.00 3.62
3375 3640 9.240734 ACGAACTCCGATATACCTATTTCTTAT 57.759 33.333 0.00 0.00 41.76 1.73
3376 3641 8.627208 ACGAACTCCGATATACCTATTTCTTA 57.373 34.615 0.00 0.00 41.76 2.10
3380 3645 7.309073 GGAAGACGAACTCCGATATACCTATTT 60.309 40.741 0.00 0.00 41.76 1.40
3385 3650 3.057666 GGGAAGACGAACTCCGATATACC 60.058 52.174 0.00 0.00 41.76 2.73
3386 3651 3.567164 TGGGAAGACGAACTCCGATATAC 59.433 47.826 0.00 0.00 41.76 1.47
3392 3657 0.179108 GGATGGGAAGACGAACTCCG 60.179 60.000 0.00 0.00 45.44 4.63
3434 3702 8.893727 GGCACAAATAAATATCTGTGAGTAAGT 58.106 33.333 10.33 0.00 41.35 2.24
3457 3745 5.565509 TCCATGTTTTATCACAGTTAGGCA 58.434 37.500 0.00 0.00 0.00 4.75
3476 3764 6.116126 GGCTACTCAAGTTAAACAGATCCAT 58.884 40.000 0.00 0.00 0.00 3.41
3505 3793 0.670546 ATGCACGGTCAGTAGCACAC 60.671 55.000 0.00 0.00 38.79 3.82
3570 3858 8.709386 AATAATTAATGGTTGTATGCGCAAAA 57.291 26.923 17.11 6.83 0.00 2.44


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

AutoCloner maintained by Alex Coulton.