Multiple sequence alignment - TraesCS6D01G196200

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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 TraesCS6D01G196200 chr6D 100.000 4517 0 0 1 4517 272108842 272113358 0.000000e+00 8342.0
1 TraesCS6D01G196200 chr6D 74.648 284 61 11 3806 4083 368767784 368768062 1.030000e-21 115.0
2 TraesCS6D01G196200 chr6D 85.000 100 12 2 3710 3806 11700023 11700122 1.030000e-16 99.0
3 TraesCS6D01G196200 chr6D 84.211 95 15 0 3712 3806 393942333 393942239 4.810000e-15 93.5
4 TraesCS6D01G196200 chr6D 92.857 42 3 0 4237 4278 187314349 187314390 1.360000e-05 62.1
5 TraesCS6D01G196200 chr6B 97.416 2593 44 7 1 2585 433272071 433274648 0.000000e+00 4396.0
6 TraesCS6D01G196200 chr6B 95.463 1102 32 6 2618 3709 433274642 433275735 0.000000e+00 1742.0
7 TraesCS6D01G196200 chr6B 87.500 320 32 2 4196 4507 433281537 433281856 3.320000e-96 363.0
8 TraesCS6D01G196200 chr6B 84.967 153 23 0 3885 4037 433277878 433278030 6.050000e-34 156.0
9 TraesCS6D01G196200 chr6B 86.957 92 12 0 3713 3804 154179494 154179403 2.220000e-18 104.0
10 TraesCS6D01G196200 chr6B 75.936 187 41 4 3895 4080 554809250 554809433 4.810000e-15 93.5
11 TraesCS6D01G196200 chr7B 97.253 2475 41 13 123 2585 438420703 438423162 0.000000e+00 4169.0
12 TraesCS6D01G196200 chr7B 94.742 1065 36 6 2618 3670 438423156 438424212 0.000000e+00 1639.0
13 TraesCS6D01G196200 chr7B 86.061 330 36 4 4196 4517 438436825 438437152 3.340000e-91 346.0
14 TraesCS6D01G196200 chr7B 84.387 269 40 2 3885 4152 438436446 438436713 3.470000e-66 263.0
15 TraesCS6D01G196200 chr7B 97.727 132 3 0 1 132 438399633 438399764 1.260000e-55 228.0
16 TraesCS6D01G196200 chr7B 97.619 42 1 0 3668 3709 438424270 438424311 6.270000e-09 73.1
17 TraesCS6D01G196200 chr6A 96.365 1293 35 2 1300 2585 388211451 388212738 0.000000e+00 2117.0
18 TraesCS6D01G196200 chr6A 95.889 1265 40 7 1 1263 388210219 388211473 0.000000e+00 2037.0
19 TraesCS6D01G196200 chr6A 95.640 1101 34 5 2618 3709 388212732 388213827 0.000000e+00 1755.0
20 TraesCS6D01G196200 chr6A 86.189 391 44 4 4135 4517 388214191 388214579 9.040000e-112 414.0
21 TraesCS6D01G196200 chr3A 74.375 480 89 26 3807 4266 352450193 352450658 1.670000e-39 174.0
22 TraesCS6D01G196200 chr3A 88.679 53 2 3 4245 4294 350307785 350307734 1.360000e-05 62.1
23 TraesCS6D01G196200 chr3D 78.571 238 44 6 3870 4103 437396031 437396265 2.810000e-32 150.0
24 TraesCS6D01G196200 chr3D 76.655 287 49 16 3813 4091 193537990 193538266 4.710000e-30 143.0
25 TraesCS6D01G196200 chr3D 74.667 300 53 18 3834 4125 271480642 271480926 1.330000e-20 111.0
26 TraesCS6D01G196200 chr3D 86.316 95 13 0 3713 3807 584340470 584340376 2.220000e-18 104.0
27 TraesCS6D01G196200 chr3D 85.714 91 13 0 3715 3805 557653945 557653855 3.720000e-16 97.1
28 TraesCS6D01G196200 chr2B 79.213 178 31 6 3818 3991 233745823 233745648 7.940000e-23 119.0
29 TraesCS6D01G196200 chr1A 71.670 533 114 31 3812 4322 272616250 272616767 3.690000e-21 113.0
30 TraesCS6D01G196200 chrUn 86.957 92 12 0 3713 3804 234099685 234099594 2.220000e-18 104.0
31 TraesCS6D01G196200 chr4D 87.640 89 11 0 3715 3803 52774010 52773922 2.220000e-18 104.0
32 TraesCS6D01G196200 chr4D 83.495 103 13 4 3817 3917 398055683 398055583 4.810000e-15 93.5
33 TraesCS6D01G196200 chr4B 87.640 89 11 0 3710 3798 534792035 534791947 2.220000e-18 104.0
34 TraesCS6D01G196200 chr3B 86.316 95 13 0 3712 3806 669289523 669289617 2.220000e-18 104.0
35 TraesCS6D01G196200 chr3B 95.349 43 2 0 4237 4279 36092192 36092234 8.110000e-08 69.4
36 TraesCS6D01G196200 chr3B 88.679 53 4 2 4245 4295 332955163 332955111 3.770000e-06 63.9
37 TraesCS6D01G196200 chr2D 82.692 104 14 4 3816 3917 363878667 363878566 6.220000e-14 89.8
38 TraesCS6D01G196200 chr1D 89.474 57 4 2 4232 4287 157134919 157134974 2.250000e-08 71.3


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 TraesCS6D01G196200 chr6D 272108842 272113358 4516 False 8342.000000 8342 100.00000 1 4517 1 chr6D.!!$F3 4516
1 TraesCS6D01G196200 chr6B 433272071 433281856 9785 False 1664.250000 4396 91.33650 1 4507 4 chr6B.!!$F2 4506
2 TraesCS6D01G196200 chr7B 438420703 438424311 3608 False 1960.366667 4169 96.53800 123 3709 3 chr7B.!!$F2 3586
3 TraesCS6D01G196200 chr7B 438436446 438437152 706 False 304.500000 346 85.22400 3885 4517 2 chr7B.!!$F3 632
4 TraesCS6D01G196200 chr6A 388210219 388214579 4360 False 1580.750000 2117 93.52075 1 4517 4 chr6A.!!$F1 4516

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
398 404 1.227999 ACAGAAATGGTGGTGACGCG 61.228 55.000 3.53 3.53 43.5 6.01 F
1470 1478 1.338973 GCCTTACGATGGTACCGATCA 59.661 52.381 18.49 0.00 0.0 2.92 F
2611 2626 0.326927 TTGAAACGGAGGACATCCCC 59.673 55.000 0.00 0.00 46.5 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 1989 0.776810 TCCCCATCCTGCAAAGTCAA 59.223 50.0 0.0 0.0 0.0 3.18 R
2971 2986 0.161446 GCGTTGCCAAAAATTGCTCG 59.839 50.0 0.0 0.0 0.0 5.03 R
3868 3972 0.110295 TGTCCCCATGTGTCCTGTTG 59.890 55.0 0.0 0.0 0.0 3.33 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
42 43 9.628746 TGTCATACAGAATGAAAATGTTTGATG 57.371 29.630 0.00 0.00 46.17 3.07
155 156 8.632906 ATCTCTGAATTTGACTTGAATTCTGT 57.367 30.769 7.05 5.73 41.70 3.41
156 157 8.455903 TCTCTGAATTTGACTTGAATTCTGTT 57.544 30.769 7.05 0.00 41.70 3.16
157 158 9.559732 TCTCTGAATTTGACTTGAATTCTGTTA 57.440 29.630 7.05 0.23 41.70 2.41
311 312 4.083003 GGACGCCAAAACAAGAATCATGTA 60.083 41.667 0.00 0.00 0.00 2.29
312 313 5.046910 ACGCCAAAACAAGAATCATGTAG 57.953 39.130 0.00 0.00 0.00 2.74
313 314 4.518970 ACGCCAAAACAAGAATCATGTAGT 59.481 37.500 0.00 0.00 0.00 2.73
314 315 5.703592 ACGCCAAAACAAGAATCATGTAGTA 59.296 36.000 0.00 0.00 0.00 1.82
315 316 6.128282 ACGCCAAAACAAGAATCATGTAGTAG 60.128 38.462 0.00 0.00 0.00 2.57
316 317 6.128282 CGCCAAAACAAGAATCATGTAGTAGT 60.128 38.462 0.00 0.00 0.00 2.73
398 404 1.227999 ACAGAAATGGTGGTGACGCG 61.228 55.000 3.53 3.53 43.50 6.01
604 610 2.049433 CGGCCTTCTCGAACACGT 60.049 61.111 0.00 0.00 0.00 4.49
1266 1274 2.496871 TGGTGCCATGAACCATGATTTC 59.503 45.455 14.28 0.00 43.81 2.17
1470 1478 1.338973 GCCTTACGATGGTACCGATCA 59.661 52.381 18.49 0.00 0.00 2.92
1974 1989 6.484364 AAAGAAATGATGGTTGTTTCCTGT 57.516 33.333 0.00 0.00 33.46 4.00
2077 2092 8.952278 ACGATAAATTAAGCACATTTTGAGGTA 58.048 29.630 0.00 0.00 0.00 3.08
2214 2229 7.410174 TGATTACTTCCAAGTTCCAACCATAT 58.590 34.615 0.00 0.00 40.37 1.78
2260 2275 7.956328 ACTTGTCTGATGTAATAGGTCACTA 57.044 36.000 0.00 0.00 0.00 2.74
2338 2353 6.349300 GCAATTGGAGAGAGAATAAGGTGTA 58.651 40.000 7.72 0.00 0.00 2.90
2423 2438 9.224058 CCAATCAGTTGCTTTTTGTTTAAATTG 57.776 29.630 0.00 0.00 33.90 2.32
2580 2595 4.885413 TCACGAGGATTTCCGTTTCTTAA 58.115 39.130 0.00 0.00 42.08 1.85
2581 2596 5.299148 TCACGAGGATTTCCGTTTCTTAAA 58.701 37.500 0.00 0.00 42.08 1.52
2582 2597 5.178067 TCACGAGGATTTCCGTTTCTTAAAC 59.822 40.000 0.00 0.00 42.08 2.01
2583 2598 5.049954 CACGAGGATTTCCGTTTCTTAAACA 60.050 40.000 0.00 0.00 41.44 2.83
2584 2599 5.704053 ACGAGGATTTCCGTTTCTTAAACAT 59.296 36.000 0.00 0.00 41.44 2.71
2585 2600 6.206048 ACGAGGATTTCCGTTTCTTAAACATT 59.794 34.615 0.00 0.00 41.44 2.71
2586 2601 7.081976 CGAGGATTTCCGTTTCTTAAACATTT 58.918 34.615 3.68 0.00 41.44 2.32
2587 2602 7.593644 CGAGGATTTCCGTTTCTTAAACATTTT 59.406 33.333 3.68 0.00 41.44 1.82
2588 2603 9.256477 GAGGATTTCCGTTTCTTAAACATTTTT 57.744 29.630 3.68 0.00 41.44 1.94
2610 2625 2.194201 TTTGAAACGGAGGACATCCC 57.806 50.000 0.00 0.00 46.50 3.85
2611 2626 0.326927 TTGAAACGGAGGACATCCCC 59.673 55.000 0.00 0.00 46.50 4.81
2612 2627 1.223763 GAAACGGAGGACATCCCCC 59.776 63.158 0.00 0.00 46.50 5.40
2613 2628 2.588856 GAAACGGAGGACATCCCCCG 62.589 65.000 18.44 18.44 46.50 5.73
2618 2633 3.768833 GAGGACATCCCCCGGCCTA 62.769 68.421 0.00 0.00 36.42 3.93
2638 2653 5.532406 GCCTAAACATATGCATCCTCAGAAA 59.468 40.000 0.19 0.00 0.00 2.52
2730 2745 4.083164 TGTCTCGACGCTGTTTATCACTTA 60.083 41.667 0.00 0.00 0.00 2.24
2814 2829 7.595819 TTTTGTACTTCCAATGGATTTCAGT 57.404 32.000 1.39 6.18 0.00 3.41
2842 2857 1.341852 TGAACAAGTACGGCTACAGCA 59.658 47.619 3.24 0.00 44.36 4.41
2924 2939 4.251268 CACACCTGTAAGTAACCTTAGCC 58.749 47.826 0.00 0.00 33.87 3.93
2974 2989 2.126914 GCTAGATAGCCACACACGAG 57.873 55.000 0.09 0.00 43.39 4.18
2975 2990 1.866063 GCTAGATAGCCACACACGAGC 60.866 57.143 0.09 0.00 43.39 5.03
2976 2991 1.405463 CTAGATAGCCACACACGAGCA 59.595 52.381 0.00 0.00 0.00 4.26
2977 2992 0.608130 AGATAGCCACACACGAGCAA 59.392 50.000 0.00 0.00 0.00 3.91
3137 3162 4.256920 ACAATATGTGCAGACTTGTCTCC 58.743 43.478 7.57 0.00 0.00 3.71
3138 3163 4.256110 CAATATGTGCAGACTTGTCTCCA 58.744 43.478 0.00 0.00 0.00 3.86
3148 3173 3.567164 AGACTTGTCTCCACTGCAAAATG 59.433 43.478 0.00 0.00 0.00 2.32
3149 3174 3.554934 ACTTGTCTCCACTGCAAAATGA 58.445 40.909 0.00 0.00 0.00 2.57
3156 3181 2.102252 TCCACTGCAAAATGACCCAAAC 59.898 45.455 0.00 0.00 0.00 2.93
3164 3189 0.033366 AATGACCCAAACGCAAAGCC 59.967 50.000 0.00 0.00 0.00 4.35
3219 3244 5.470098 TCAGCAAACTCTTAGGATGAAACAC 59.530 40.000 0.00 0.00 0.00 3.32
3268 3301 7.429633 GTGTAGCTGTAACTGAGATATGTCAT 58.570 38.462 2.58 0.00 0.00 3.06
3307 3340 3.302092 CGTCTGCTTTTCGTGATAGATGC 60.302 47.826 0.00 0.00 0.00 3.91
3489 3531 3.243128 GGTGCTGGTTACCGTCAAT 57.757 52.632 0.00 0.00 0.00 2.57
3555 3597 0.386352 CGTCAGCGTACCGTTTGAGA 60.386 55.000 0.00 0.00 0.00 3.27
3588 3631 0.389817 CGAGTTCAGCCCATTGACGA 60.390 55.000 0.00 0.00 0.00 4.20
3589 3632 1.808411 GAGTTCAGCCCATTGACGAA 58.192 50.000 0.00 0.00 0.00 3.85
3590 3633 1.734465 GAGTTCAGCCCATTGACGAAG 59.266 52.381 0.00 0.00 0.00 3.79
3705 3808 6.227522 TCAAAACATGAGGACGTCAAGATAA 58.772 36.000 18.91 0.00 39.19 1.75
3709 3812 6.137794 ACATGAGGACGTCAAGATAAGTAG 57.862 41.667 18.91 0.00 39.19 2.57
3710 3813 4.634184 TGAGGACGTCAAGATAAGTAGC 57.366 45.455 18.91 0.00 29.64 3.58
3711 3814 4.014406 TGAGGACGTCAAGATAAGTAGCA 58.986 43.478 18.91 0.00 29.64 3.49
3712 3815 4.645136 TGAGGACGTCAAGATAAGTAGCAT 59.355 41.667 18.91 0.00 29.64 3.79
3713 3816 5.826208 TGAGGACGTCAAGATAAGTAGCATA 59.174 40.000 18.91 0.00 29.64 3.14
3714 3817 6.320418 TGAGGACGTCAAGATAAGTAGCATAA 59.680 38.462 18.91 0.00 29.64 1.90
3715 3818 6.740110 AGGACGTCAAGATAAGTAGCATAAG 58.260 40.000 18.91 0.00 0.00 1.73
3716 3819 6.546403 AGGACGTCAAGATAAGTAGCATAAGA 59.454 38.462 18.91 0.00 0.00 2.10
3717 3820 6.858993 GGACGTCAAGATAAGTAGCATAAGAG 59.141 42.308 18.91 0.00 0.00 2.85
3718 3821 6.210078 ACGTCAAGATAAGTAGCATAAGAGC 58.790 40.000 0.00 0.00 0.00 4.09
3719 3822 6.183360 ACGTCAAGATAAGTAGCATAAGAGCA 60.183 38.462 0.00 0.00 36.85 4.26
3720 3823 6.865726 CGTCAAGATAAGTAGCATAAGAGCAT 59.134 38.462 0.00 0.00 36.85 3.79
3721 3824 7.148836 CGTCAAGATAAGTAGCATAAGAGCATG 60.149 40.741 0.00 0.00 36.85 4.06
3722 3825 7.117523 GTCAAGATAAGTAGCATAAGAGCATGG 59.882 40.741 0.00 0.00 36.85 3.66
3723 3826 6.678568 AGATAAGTAGCATAAGAGCATGGT 57.321 37.500 0.00 0.00 39.78 3.55
3724 3827 7.072263 AGATAAGTAGCATAAGAGCATGGTT 57.928 36.000 0.00 0.00 37.74 3.67
3725 3828 8.195165 AGATAAGTAGCATAAGAGCATGGTTA 57.805 34.615 0.00 0.00 37.74 2.85
3726 3829 8.651389 AGATAAGTAGCATAAGAGCATGGTTAA 58.349 33.333 0.00 0.00 37.74 2.01
3727 3830 9.442047 GATAAGTAGCATAAGAGCATGGTTAAT 57.558 33.333 0.00 0.00 37.74 1.40
3730 3833 9.799106 AAGTAGCATAAGAGCATGGTTAATAAT 57.201 29.630 0.00 0.00 37.74 1.28
3738 3841 8.798859 AAGAGCATGGTTAATAATATAGCCAG 57.201 34.615 0.00 0.00 39.18 4.85
3739 3842 7.922382 AGAGCATGGTTAATAATATAGCCAGT 58.078 34.615 0.00 0.00 39.18 4.00
3740 3843 8.386264 AGAGCATGGTTAATAATATAGCCAGTT 58.614 33.333 0.00 0.00 39.18 3.16
3741 3844 8.340618 AGCATGGTTAATAATATAGCCAGTTG 57.659 34.615 0.00 0.00 39.18 3.16
3742 3845 7.029563 GCATGGTTAATAATATAGCCAGTTGC 58.970 38.462 0.00 0.00 39.18 4.17
3753 3856 2.315925 GCCAGTTGCTAGCTACATCA 57.684 50.000 27.17 0.00 36.87 3.07
3754 3857 2.843701 GCCAGTTGCTAGCTACATCAT 58.156 47.619 27.17 7.43 36.87 2.45
3755 3858 3.995199 GCCAGTTGCTAGCTACATCATA 58.005 45.455 27.17 0.00 36.87 2.15
3756 3859 4.573900 GCCAGTTGCTAGCTACATCATAT 58.426 43.478 27.17 6.40 36.87 1.78
3757 3860 4.999950 GCCAGTTGCTAGCTACATCATATT 59.000 41.667 27.17 5.72 36.87 1.28
3758 3861 5.106791 GCCAGTTGCTAGCTACATCATATTG 60.107 44.000 27.17 15.95 36.87 1.90
3759 3862 5.994054 CCAGTTGCTAGCTACATCATATTGT 59.006 40.000 27.17 4.37 0.00 2.71
3760 3863 6.146837 CCAGTTGCTAGCTACATCATATTGTC 59.853 42.308 27.17 0.16 0.00 3.18
3761 3864 6.927936 CAGTTGCTAGCTACATCATATTGTCT 59.072 38.462 27.17 3.21 0.00 3.41
3762 3865 7.440556 CAGTTGCTAGCTACATCATATTGTCTT 59.559 37.037 27.17 3.03 0.00 3.01
3763 3866 7.440556 AGTTGCTAGCTACATCATATTGTCTTG 59.559 37.037 27.17 0.00 0.00 3.02
3764 3867 6.820335 TGCTAGCTACATCATATTGTCTTGT 58.180 36.000 17.23 0.00 0.00 3.16
3765 3868 6.925718 TGCTAGCTACATCATATTGTCTTGTC 59.074 38.462 17.23 0.00 0.00 3.18
3766 3869 6.925718 GCTAGCTACATCATATTGTCTTGTCA 59.074 38.462 7.70 0.00 0.00 3.58
3767 3870 7.601886 GCTAGCTACATCATATTGTCTTGTCAT 59.398 37.037 7.70 0.00 0.00 3.06
3768 3871 9.486497 CTAGCTACATCATATTGTCTTGTCATT 57.514 33.333 0.00 0.00 0.00 2.57
3769 3872 8.743085 AGCTACATCATATTGTCTTGTCATTT 57.257 30.769 0.00 0.00 0.00 2.32
3770 3873 9.836864 AGCTACATCATATTGTCTTGTCATTTA 57.163 29.630 0.00 0.00 0.00 1.40
3829 3932 1.802069 GGAGCTAAATCCGGCAGATC 58.198 55.000 0.00 0.00 32.47 2.75
3833 3936 2.435805 AGCTAAATCCGGCAGATCTTGA 59.564 45.455 0.00 0.00 32.47 3.02
3843 3946 2.679082 GCAGATCTTGAGTAGGGGGTA 58.321 52.381 0.00 0.00 0.00 3.69
3868 3972 1.303561 TGGTGTCTTGCTGGATGGC 60.304 57.895 0.00 0.00 0.00 4.40
3871 3975 0.242017 GTGTCTTGCTGGATGGCAAC 59.758 55.000 0.00 0.00 45.64 4.17
3900 6059 1.272037 TGGGGACACCGATTTTTACCC 60.272 52.381 0.00 0.00 44.64 3.69
3906 6065 3.568443 ACACCGATTTTTACCCAGGTTT 58.432 40.909 0.00 0.00 0.00 3.27
3907 6066 3.319689 ACACCGATTTTTACCCAGGTTTG 59.680 43.478 0.00 0.00 0.00 2.93
3920 6079 0.560688 AGGTTTGGGCCCTCTCAAAA 59.439 50.000 25.70 12.08 35.08 2.44
3922 6081 1.344438 GGTTTGGGCCCTCTCAAAAAG 59.656 52.381 25.70 0.00 35.08 2.27
3930 6089 4.322725 GGGCCCTCTCAAAAAGGTAAAATG 60.323 45.833 17.04 0.00 31.51 2.32
3931 6090 4.322725 GGCCCTCTCAAAAAGGTAAAATGG 60.323 45.833 0.00 0.00 31.51 3.16
3933 6092 5.783111 CCCTCTCAAAAAGGTAAAATGGTG 58.217 41.667 0.00 0.00 31.51 4.17
3940 6099 3.706600 AAGGTAAAATGGTGCGTCCTA 57.293 42.857 0.00 0.00 37.07 2.94
3941 6100 2.981898 AGGTAAAATGGTGCGTCCTAC 58.018 47.619 0.00 0.00 37.07 3.18
3954 6113 5.144359 GTGCGTCCTACTTTTGTTGTATTG 58.856 41.667 0.00 0.00 0.00 1.90
3961 6120 8.564574 GTCCTACTTTTGTTGTATTGATTGTGA 58.435 33.333 0.00 0.00 0.00 3.58
3991 6150 6.369615 GGTACAAAATACATGTGAACTACCGT 59.630 38.462 9.11 0.00 32.27 4.83
3997 6156 4.111375 ACATGTGAACTACCGTGAGATC 57.889 45.455 0.00 0.00 0.00 2.75
3998 6157 3.509967 ACATGTGAACTACCGTGAGATCA 59.490 43.478 0.00 0.00 0.00 2.92
4013 6172 6.091849 CCGTGAGATCATGTATGAATGAATCC 59.908 42.308 0.00 0.00 39.90 3.01
4037 9478 0.402887 TCTACGGTCCTGACACCTCA 59.597 55.000 0.00 0.00 33.77 3.86
4042 9483 1.873903 CGGTCCTGACACCTCAGTTTG 60.874 57.143 0.00 0.00 42.36 2.93
4056 9498 4.831155 CCTCAGTTTGTATAGGTATCGGGA 59.169 45.833 0.00 0.00 0.00 5.14
4084 9526 3.583966 AGGGTTACAAATAGGTCGGTTGA 59.416 43.478 0.00 0.00 0.00 3.18
4104 9546 0.108329 ATCTAGGGTCAAACGTGCCG 60.108 55.000 0.00 0.00 0.00 5.69
4122 9564 1.686355 CGGAGTCTGTCTCTATGCCT 58.314 55.000 2.14 0.00 42.40 4.75
4127 9569 4.081420 GGAGTCTGTCTCTATGCCTTGAAA 60.081 45.833 2.14 0.00 42.40 2.69
4129 9571 5.426504 AGTCTGTCTCTATGCCTTGAAATG 58.573 41.667 0.00 0.00 0.00 2.32
4132 9574 4.910195 TGTCTCTATGCCTTGAAATGTGT 58.090 39.130 0.00 0.00 0.00 3.72
4145 9616 3.698539 TGAAATGTGTGCCAAGTCTTTGA 59.301 39.130 0.00 0.00 36.36 2.69
4159 9630 6.072230 CCAAGTCTTTGAATCTTTCCTTCCTC 60.072 42.308 0.00 0.00 36.36 3.71
4177 9648 3.321111 TCCTCATGTAGACGAATTAGGCC 59.679 47.826 0.00 0.00 0.00 5.19
4178 9649 3.555168 CCTCATGTAGACGAATTAGGCCC 60.555 52.174 0.00 0.00 0.00 5.80
4200 9671 1.696314 GGTGATGGGCTTAGGGGGA 60.696 63.158 0.00 0.00 0.00 4.81
4201 9672 1.068352 GGTGATGGGCTTAGGGGGAT 61.068 60.000 0.00 0.00 0.00 3.85
4237 9748 0.756903 AGACTGGTAACCAACACGCT 59.243 50.000 0.00 0.00 30.80 5.07
4243 9754 1.156736 GTAACCAACACGCTGAGCAT 58.843 50.000 4.88 0.00 0.00 3.79
4253 9764 1.202698 ACGCTGAGCATCCCTTAATCC 60.203 52.381 4.88 0.00 0.00 3.01
4262 9773 1.789523 TCCCTTAATCCAGGACTCCG 58.210 55.000 0.00 0.00 35.71 4.63
4273 9784 2.424733 GGACTCCGTCAGTAGCCCC 61.425 68.421 0.00 0.00 34.41 5.80
4287 9799 1.302907 AGCCCCTGAATGGTCTTCAT 58.697 50.000 0.00 0.00 37.79 2.57
4291 9803 1.341285 CCCTGAATGGTCTTCATGCCA 60.341 52.381 0.00 0.00 39.33 4.92
4363 9882 0.478072 TGGTTCAACTCCCATGCAGT 59.522 50.000 0.00 0.00 0.00 4.40
4368 9887 1.003580 TCAACTCCCATGCAGTCTTCC 59.996 52.381 0.00 0.00 0.00 3.46
4395 9914 4.381932 GCAATTTCATTTTGGGTCGAGGAT 60.382 41.667 0.00 0.00 0.00 3.24
4404 9923 0.387929 GGGTCGAGGATTCGCATACA 59.612 55.000 0.00 0.00 46.28 2.29
4427 9946 3.531059 TGGATATCCAGGGTATTCCAGG 58.469 50.000 20.98 0.00 42.01 4.45
4463 9982 7.816945 ATTTAATCAAAAGATTCCTGCAACG 57.183 32.000 0.00 0.00 0.00 4.10
4495 10014 0.949105 CTTGGGTTCGAGGACCAACG 60.949 60.000 8.50 0.00 41.65 4.10
4503 10022 1.988406 GAGGACCAACGCCCTAGGT 60.988 63.158 8.29 0.00 38.63 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
311 312 2.522185 TGCTTCCACGGACTTACTACT 58.478 47.619 0.00 0.00 0.00 2.57
312 313 3.308438 TTGCTTCCACGGACTTACTAC 57.692 47.619 0.00 0.00 0.00 2.73
313 314 4.250464 CAATTGCTTCCACGGACTTACTA 58.750 43.478 0.00 0.00 0.00 1.82
314 315 3.074412 CAATTGCTTCCACGGACTTACT 58.926 45.455 0.00 0.00 0.00 2.24
315 316 2.414161 GCAATTGCTTCCACGGACTTAC 60.414 50.000 23.21 0.00 38.21 2.34
316 317 1.810151 GCAATTGCTTCCACGGACTTA 59.190 47.619 23.21 0.00 38.21 2.24
398 404 2.222976 CGCATGTCTCAGCAATCTGTTC 60.223 50.000 0.00 0.00 41.10 3.18
1470 1478 2.705658 TCGGGATTTACATCTGGCAGAT 59.294 45.455 24.01 24.01 34.74 2.90
1945 1960 5.473066 ACAACCATCATTTCTTTTCAGGG 57.527 39.130 0.00 0.00 0.00 4.45
1974 1989 0.776810 TCCCCATCCTGCAAAGTCAA 59.223 50.000 0.00 0.00 0.00 3.18
2015 2030 7.932683 AGGGCCTACTACATTTAAGTAGATT 57.067 36.000 2.82 0.00 46.20 2.40
2016 2031 9.617053 AATAGGGCCTACTACATTTAAGTAGAT 57.383 33.333 17.19 0.00 46.20 1.98
2260 2275 1.957113 GCCCCTTAGCATGCACTCTTT 60.957 52.381 21.98 0.00 0.00 2.52
2338 2353 7.684529 ACTATTGTCCAAAATCTGAGAGAACT 58.315 34.615 0.00 0.00 0.00 3.01
2434 2449 4.692625 GTGCTGGCATCTGGTAATAGTATG 59.307 45.833 0.00 0.00 0.00 2.39
2438 2453 3.198409 TGTGCTGGCATCTGGTAATAG 57.802 47.619 0.00 0.00 0.00 1.73
2589 2604 2.888414 GGGATGTCCTCCGTTTCAAAAA 59.112 45.455 0.00 0.00 46.01 1.94
2590 2605 2.510613 GGGATGTCCTCCGTTTCAAAA 58.489 47.619 0.00 0.00 46.01 2.44
2591 2606 1.271707 GGGGATGTCCTCCGTTTCAAA 60.272 52.381 0.00 0.00 46.01 2.69
2592 2607 0.326927 GGGGATGTCCTCCGTTTCAA 59.673 55.000 0.00 0.00 46.01 2.69
2593 2608 1.988015 GGGGATGTCCTCCGTTTCA 59.012 57.895 0.00 0.00 46.01 2.69
2594 2609 4.957164 GGGGATGTCCTCCGTTTC 57.043 61.111 0.00 0.00 46.01 2.78
2600 2615 3.768833 TAGGCCGGGGGATGTCCTC 62.769 68.421 2.18 0.00 35.95 3.71
2601 2616 2.850851 TTTAGGCCGGGGGATGTCCT 62.851 60.000 2.18 0.90 35.95 3.85
2602 2617 2.380285 TTTAGGCCGGGGGATGTCC 61.380 63.158 2.18 0.00 0.00 4.02
2603 2618 1.153025 GTTTAGGCCGGGGGATGTC 60.153 63.158 2.18 0.00 0.00 3.06
2604 2619 1.286305 ATGTTTAGGCCGGGGGATGT 61.286 55.000 2.18 0.00 0.00 3.06
2605 2620 0.768622 TATGTTTAGGCCGGGGGATG 59.231 55.000 2.18 0.00 0.00 3.51
2606 2621 1.354368 CATATGTTTAGGCCGGGGGAT 59.646 52.381 2.18 0.00 0.00 3.85
2607 2622 0.768622 CATATGTTTAGGCCGGGGGA 59.231 55.000 2.18 0.00 0.00 4.81
2608 2623 0.893727 GCATATGTTTAGGCCGGGGG 60.894 60.000 2.18 0.00 0.00 5.40
2609 2624 0.179004 TGCATATGTTTAGGCCGGGG 60.179 55.000 2.18 0.00 34.24 5.73
2610 2625 1.812571 GATGCATATGTTTAGGCCGGG 59.187 52.381 2.18 0.00 34.24 5.73
2611 2626 1.812571 GGATGCATATGTTTAGGCCGG 59.187 52.381 0.00 0.00 34.24 6.13
2612 2627 2.744202 GAGGATGCATATGTTTAGGCCG 59.256 50.000 0.00 0.00 34.24 6.13
2613 2628 3.754965 TGAGGATGCATATGTTTAGGCC 58.245 45.455 0.00 0.00 34.24 5.19
2614 2629 4.645535 TCTGAGGATGCATATGTTTAGGC 58.354 43.478 0.00 0.00 35.70 3.93
2615 2630 7.572523 TTTTCTGAGGATGCATATGTTTAGG 57.427 36.000 0.00 0.00 0.00 2.69
2616 2631 7.594015 GCATTTTCTGAGGATGCATATGTTTAG 59.406 37.037 17.19 0.00 44.18 1.85
2617 2632 7.428020 GCATTTTCTGAGGATGCATATGTTTA 58.572 34.615 17.19 0.00 44.18 2.01
2618 2633 6.278363 GCATTTTCTGAGGATGCATATGTTT 58.722 36.000 17.19 0.00 44.18 2.83
2638 2653 4.708421 ACTGATAAACTGCATCAAGGCATT 59.292 37.500 0.00 0.00 43.97 3.56
2682 2697 6.839124 TTTCTGAGGATGCATATGTTTTGT 57.161 33.333 0.00 0.00 0.00 2.83
2683 2698 7.762615 ACATTTTCTGAGGATGCATATGTTTTG 59.237 33.333 0.00 0.00 0.00 2.44
2748 2763 8.464770 ACACAACAATTACATGCATTGATAAC 57.535 30.769 20.05 0.00 35.51 1.89
2814 2829 2.546368 GCCGTACTTGTTCACATGTTCA 59.454 45.455 0.00 0.00 36.02 3.18
2969 2984 1.189884 CGTTGCCAAAAATTGCTCGTG 59.810 47.619 0.00 0.00 0.00 4.35
2970 2985 1.486439 CGTTGCCAAAAATTGCTCGT 58.514 45.000 0.00 0.00 0.00 4.18
2971 2986 0.161446 GCGTTGCCAAAAATTGCTCG 59.839 50.000 0.00 0.00 0.00 5.03
2973 2988 1.069049 AGAGCGTTGCCAAAAATTGCT 59.931 42.857 0.00 0.00 0.00 3.91
2974 2989 1.192980 CAGAGCGTTGCCAAAAATTGC 59.807 47.619 0.00 0.00 0.00 3.56
2975 2990 1.794116 CCAGAGCGTTGCCAAAAATTG 59.206 47.619 0.00 0.00 0.00 2.32
2976 2991 1.412343 ACCAGAGCGTTGCCAAAAATT 59.588 42.857 0.00 0.00 0.00 1.82
2977 2992 1.000274 GACCAGAGCGTTGCCAAAAAT 60.000 47.619 0.00 0.00 0.00 1.82
3099 3115 9.713740 GCACATATTGTTATCTTGAAGAAGAAG 57.286 33.333 0.00 0.00 41.64 2.85
3100 3116 9.230122 TGCACATATTGTTATCTTGAAGAAGAA 57.770 29.630 0.00 0.00 41.64 2.52
3101 3117 8.791327 TGCACATATTGTTATCTTGAAGAAGA 57.209 30.769 0.00 0.00 42.53 2.87
3137 3162 2.126467 CGTTTGGGTCATTTTGCAGTG 58.874 47.619 0.00 0.00 0.00 3.66
3138 3163 1.537990 GCGTTTGGGTCATTTTGCAGT 60.538 47.619 0.00 0.00 0.00 4.40
3148 3173 1.172812 AGAGGCTTTGCGTTTGGGTC 61.173 55.000 0.00 0.00 0.00 4.46
3149 3174 1.152756 AGAGGCTTTGCGTTTGGGT 60.153 52.632 0.00 0.00 0.00 4.51
3156 3181 0.886490 AACCAGACAGAGGCTTTGCG 60.886 55.000 4.73 0.00 0.00 4.85
3164 3189 2.836981 AGAAGGGATCAACCAGACAGAG 59.163 50.000 0.00 0.00 41.20 3.35
3307 3340 6.028368 CACATACTCAGTCCTACGTTACTTG 58.972 44.000 0.00 0.00 0.00 3.16
3432 3474 2.687200 AGGCTGCCATCCACCGTA 60.687 61.111 22.65 0.00 0.00 4.02
3489 3531 0.321346 TTGTGAGAATCTCTGCGCCA 59.679 50.000 11.92 0.00 34.92 5.69
3555 3597 3.990092 TGAACTCGCTTGTGAACATACT 58.010 40.909 0.00 0.00 0.00 2.12
3588 3631 0.984230 TCTTCAATGAGACGGGCCTT 59.016 50.000 0.84 0.00 0.00 4.35
3589 3632 0.984230 TTCTTCAATGAGACGGGCCT 59.016 50.000 0.84 0.00 0.00 5.19
3590 3633 1.821216 TTTCTTCAATGAGACGGGCC 58.179 50.000 0.00 0.00 0.00 5.80
3629 3672 9.581099 GACCTGAAACATAACTTTTTCTTCAAA 57.419 29.630 0.00 0.00 33.61 2.69
3650 3693 2.257207 TGTAGGTTCCAAGGAGACCTG 58.743 52.381 22.40 0.00 43.38 4.00
3712 3815 9.890629 CTGGCTATATTATTAACCATGCTCTTA 57.109 33.333 0.00 0.00 0.00 2.10
3713 3816 8.386264 ACTGGCTATATTATTAACCATGCTCTT 58.614 33.333 0.00 0.00 0.00 2.85
3714 3817 7.922382 ACTGGCTATATTATTAACCATGCTCT 58.078 34.615 0.00 0.00 0.00 4.09
3715 3818 8.454106 CAACTGGCTATATTATTAACCATGCTC 58.546 37.037 0.00 0.00 0.00 4.26
3716 3819 7.094205 GCAACTGGCTATATTATTAACCATGCT 60.094 37.037 0.00 0.00 40.25 3.79
3717 3820 7.029563 GCAACTGGCTATATTATTAACCATGC 58.970 38.462 0.00 0.00 40.25 4.06
3734 3837 2.315925 TGATGTAGCTAGCAACTGGC 57.684 50.000 18.83 2.05 45.30 4.85
3735 3838 5.994054 ACAATATGATGTAGCTAGCAACTGG 59.006 40.000 18.83 0.00 0.00 4.00
3736 3839 6.927936 AGACAATATGATGTAGCTAGCAACTG 59.072 38.462 18.83 1.95 32.57 3.16
3737 3840 7.060383 AGACAATATGATGTAGCTAGCAACT 57.940 36.000 18.83 0.00 32.57 3.16
3738 3841 7.225538 ACAAGACAATATGATGTAGCTAGCAAC 59.774 37.037 18.83 3.75 32.57 4.17
3739 3842 7.275183 ACAAGACAATATGATGTAGCTAGCAA 58.725 34.615 18.83 1.95 32.57 3.91
3740 3843 6.820335 ACAAGACAATATGATGTAGCTAGCA 58.180 36.000 18.83 0.00 32.57 3.49
3741 3844 6.925718 TGACAAGACAATATGATGTAGCTAGC 59.074 38.462 6.62 6.62 32.57 3.42
3742 3845 9.486497 AATGACAAGACAATATGATGTAGCTAG 57.514 33.333 0.00 0.00 32.57 3.42
3743 3846 9.836864 AAATGACAAGACAATATGATGTAGCTA 57.163 29.630 0.00 0.00 32.57 3.32
3744 3847 8.743085 AAATGACAAGACAATATGATGTAGCT 57.257 30.769 0.00 0.00 32.57 3.32
3784 3887 9.856488 CGTCACTAACTATTATATATGTTGGCT 57.144 33.333 0.00 0.00 0.00 4.75
3785 3888 9.084164 CCGTCACTAACTATTATATATGTTGGC 57.916 37.037 0.00 0.00 0.00 4.52
3789 3892 9.463902 AGCTCCGTCACTAACTATTATATATGT 57.536 33.333 0.00 0.00 0.00 2.29
3795 3898 8.305317 GGATTTAGCTCCGTCACTAACTATTAT 58.695 37.037 0.00 0.00 0.00 1.28
3796 3899 7.655490 GGATTTAGCTCCGTCACTAACTATTA 58.345 38.462 0.00 0.00 0.00 0.98
3797 3900 6.514063 GGATTTAGCTCCGTCACTAACTATT 58.486 40.000 0.00 0.00 0.00 1.73
3829 3932 3.134804 CAGATTGGTACCCCCTACTCAAG 59.865 52.174 10.07 0.00 0.00 3.02
3833 3936 2.191981 CCAGATTGGTACCCCCTACT 57.808 55.000 10.07 0.00 31.35 2.57
3860 3964 0.250858 TGTGTCCTGTTGCCATCCAG 60.251 55.000 0.00 0.00 0.00 3.86
3868 3972 0.110295 TGTCCCCATGTGTCCTGTTG 59.890 55.000 0.00 0.00 0.00 3.33
3871 3975 1.002134 GGTGTCCCCATGTGTCCTG 60.002 63.158 0.00 0.00 0.00 3.86
3876 3980 1.544724 AAAATCGGTGTCCCCATGTG 58.455 50.000 0.00 0.00 0.00 3.21
3879 3983 2.622190 GGGTAAAAATCGGTGTCCCCAT 60.622 50.000 0.00 0.00 0.00 4.00
3880 3984 1.272037 GGGTAAAAATCGGTGTCCCCA 60.272 52.381 0.00 0.00 0.00 4.96
3900 6059 0.178964 TTTGAGAGGGCCCAAACCTG 60.179 55.000 27.56 0.00 38.79 4.00
3906 6065 1.451449 TACCTTTTTGAGAGGGCCCA 58.549 50.000 27.56 0.00 38.65 5.36
3907 6066 2.597578 TTACCTTTTTGAGAGGGCCC 57.402 50.000 16.46 16.46 38.65 5.80
3920 6079 2.579410 AGGACGCACCATTTTACCTT 57.421 45.000 2.21 0.00 42.04 3.50
3922 6081 2.981898 AGTAGGACGCACCATTTTACC 58.018 47.619 2.21 0.00 42.04 2.85
3930 6089 1.944709 ACAACAAAAGTAGGACGCACC 59.055 47.619 0.00 0.00 39.35 5.01
3931 6090 5.049954 TCAATACAACAAAAGTAGGACGCAC 60.050 40.000 0.00 0.00 0.00 5.34
3933 6092 5.600908 TCAATACAACAAAAGTAGGACGC 57.399 39.130 0.00 0.00 0.00 5.19
3940 6099 7.656948 CCCATTCACAATCAATACAACAAAAGT 59.343 33.333 0.00 0.00 0.00 2.66
3941 6100 7.118101 CCCCATTCACAATCAATACAACAAAAG 59.882 37.037 0.00 0.00 0.00 2.27
3954 6113 7.164230 TGTATTTTGTACCCCATTCACAATC 57.836 36.000 0.00 0.00 32.57 2.67
3961 6120 6.723977 AGTTCACATGTATTTTGTACCCCATT 59.276 34.615 0.00 0.00 0.00 3.16
3991 6150 6.762333 ACGGATTCATTCATACATGATCTCA 58.238 36.000 0.00 0.00 36.56 3.27
3997 6156 5.545588 AGAGGACGGATTCATTCATACATG 58.454 41.667 0.00 0.00 0.00 3.21
3998 6157 5.815233 AGAGGACGGATTCATTCATACAT 57.185 39.130 0.00 0.00 0.00 2.29
4030 6189 5.068723 CCGATACCTATACAAACTGAGGTGT 59.931 44.000 2.66 0.00 42.36 4.16
4037 9478 4.020485 GGCATCCCGATACCTATACAAACT 60.020 45.833 0.00 0.00 0.00 2.66
4042 9483 3.890147 CCTAGGCATCCCGATACCTATAC 59.110 52.174 0.00 0.00 36.50 1.47
4056 9498 4.202326 CGACCTATTTGTAACCCTAGGCAT 60.202 45.833 2.05 0.00 35.20 4.40
4084 9526 2.109425 GGCACGTTTGACCCTAGATT 57.891 50.000 0.00 0.00 0.00 2.40
4104 9546 3.027412 TCAAGGCATAGAGACAGACTCC 58.973 50.000 0.00 0.00 45.96 3.85
4122 9564 4.159321 TCAAAGACTTGGCACACATTTCAA 59.841 37.500 0.00 0.00 39.29 2.69
4127 9569 4.147321 AGATTCAAAGACTTGGCACACAT 58.853 39.130 0.00 0.00 39.29 3.21
4129 9571 4.574599 AAGATTCAAAGACTTGGCACAC 57.425 40.909 0.00 0.00 39.29 3.82
4132 9574 4.473444 AGGAAAGATTCAAAGACTTGGCA 58.527 39.130 0.00 0.00 33.01 4.92
4145 9616 5.422331 TCGTCTACATGAGGAAGGAAAGATT 59.578 40.000 0.00 0.00 36.74 2.40
4159 9630 3.469008 TGGGCCTAATTCGTCTACATG 57.531 47.619 4.53 0.00 0.00 3.21
4178 9649 0.250467 CCCTAAGCCCATCACCGATG 60.250 60.000 0.00 0.00 39.52 3.84
4200 9671 1.384502 TCTTGGATGGGCCGAGGAT 60.385 57.895 0.00 0.00 46.73 3.24
4201 9672 2.040442 TCTTGGATGGGCCGAGGA 59.960 61.111 0.00 0.00 46.73 3.71
4237 9748 2.439507 GTCCTGGATTAAGGGATGCTCA 59.560 50.000 0.00 0.00 37.96 4.26
4243 9754 1.007963 ACGGAGTCCTGGATTAAGGGA 59.992 52.381 7.77 0.00 29.74 4.20
4262 9773 0.912486 ACCATTCAGGGGCTACTGAC 59.088 55.000 11.05 0.00 46.44 3.51
4273 9784 2.426024 CCTTGGCATGAAGACCATTCAG 59.574 50.000 0.00 0.00 35.42 3.02
4363 9882 5.229423 CCAAAATGAAATTGCTTCGGAAGA 58.771 37.500 21.45 1.63 36.10 2.87
4368 9887 3.364621 CGACCCAAAATGAAATTGCTTCG 59.635 43.478 0.00 0.00 36.10 3.79
4395 9914 4.565444 CCCTGGATATCCAATGTATGCGAA 60.565 45.833 24.54 0.00 46.97 4.70
4404 9923 5.786121 CTGGAATACCCTGGATATCCAAT 57.214 43.478 24.54 12.79 46.97 3.16
4445 9964 1.269448 GGCGTTGCAGGAATCTTTTGA 59.731 47.619 0.00 0.00 0.00 2.69
4474 9993 1.003233 GTTGGTCCTCGAACCCAAGAT 59.997 52.381 9.63 0.00 38.84 2.40
4481 10000 2.741211 GGGCGTTGGTCCTCGAAC 60.741 66.667 10.34 0.00 34.09 3.95


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

AutoCloner maintained by Alex Coulton.