Multiple sequence alignment - TraesCS3A01G444300

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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 TraesCS3A01G444300 chr3A 100.000 3459 0 0 1 3459 686123994 686120536 0.000000e+00 6388.0
1 TraesCS3A01G444300 chr3A 92.771 166 9 3 3035 3198 1673706 1673542 1.600000e-58 237.0
2 TraesCS3A01G444300 chr3D 94.507 2203 99 9 845 3036 548533674 548531483 0.000000e+00 3378.0
3 TraesCS3A01G444300 chr3D 95.817 263 9 1 3199 3459 548531431 548531169 1.150000e-114 424.0
4 TraesCS3A01G444300 chr3D 89.600 125 12 1 2784 2907 575685937 575685813 1.290000e-34 158.0
5 TraesCS3A01G444300 chr3D 88.525 122 13 1 2787 2907 46395403 46395282 2.780000e-31 147.0
6 TraesCS3A01G444300 chr3D 87.324 71 7 2 2307 2377 548475211 548475143 2.860000e-11 80.5
7 TraesCS3A01G444300 chr3B 93.697 1888 102 13 845 2728 726443008 726441134 0.000000e+00 2811.0
8 TraesCS3A01G444300 chr3B 91.813 171 10 4 3035 3202 754220888 754220719 5.770000e-58 235.0
9 TraesCS3A01G444300 chr6A 95.621 708 15 11 1 698 38765688 38764987 0.000000e+00 1122.0
10 TraesCS3A01G444300 chr6A 88.206 797 68 17 1 787 188418260 188417480 0.000000e+00 928.0
11 TraesCS3A01G444300 chr6A 89.983 589 43 13 1 582 605161591 605161012 0.000000e+00 747.0
12 TraesCS3A01G444300 chr6A 93.452 168 9 2 3035 3201 587974501 587974667 7.410000e-62 248.0
13 TraesCS3A01G444300 chr6A 92.899 169 9 3 3035 3201 145746229 145746062 3.450000e-60 243.0
14 TraesCS3A01G444300 chr6A 95.652 92 4 0 700 791 38764916 38764825 7.730000e-32 148.0
15 TraesCS3A01G444300 chr6A 100.000 29 0 0 758 786 605161008 605160980 2.000000e-03 54.7
16 TraesCS3A01G444300 chr4A 87.186 796 80 15 1 788 164490008 164490789 0.000000e+00 885.0
17 TraesCS3A01G444300 chr1B 89.209 556 44 11 238 787 122951270 122950725 0.000000e+00 680.0
18 TraesCS3A01G444300 chr1B 88.542 480 42 10 1 475 461246769 461246298 1.390000e-158 569.0
19 TraesCS3A01G444300 chr1B 86.455 347 33 9 466 801 461246096 461245753 5.450000e-98 368.0
20 TraesCS3A01G444300 chr5B 87.126 334 31 7 1 331 470202523 470202847 5.450000e-98 368.0
21 TraesCS3A01G444300 chr5B 85.537 242 31 3 312 550 470204422 470204662 2.060000e-62 250.0
22 TraesCS3A01G444300 chr5A 92.899 169 9 3 3035 3201 669909865 669909698 3.450000e-60 243.0
23 TraesCS3A01G444300 chr7A 93.293 164 10 1 3035 3198 123271471 123271309 1.240000e-59 241.0
24 TraesCS3A01G444300 chr7A 92.771 166 9 3 3035 3198 549353678 549353514 1.600000e-58 237.0
25 TraesCS3A01G444300 chr7A 93.548 62 4 0 1 62 146675403 146675342 3.680000e-15 93.5
26 TraesCS3A01G444300 chr2D 92.771 166 9 3 3035 3198 519128168 519128004 1.600000e-58 237.0
27 TraesCS3A01G444300 chr2A 92.727 165 10 2 3035 3198 748780014 748780177 1.600000e-58 237.0
28 TraesCS3A01G444300 chr2A 76.712 219 38 10 2212 2424 2711362 2711151 3.650000e-20 110.0
29 TraesCS3A01G444300 chr4B 83.700 227 24 8 569 787 507256700 507256921 5.850000e-48 202.0
30 TraesCS3A01G444300 chr6B 89.683 126 11 2 2784 2907 26482722 26482597 3.570000e-35 159.0
31 TraesCS3A01G444300 chr1D 89.600 125 12 1 2784 2907 17430316 17430440 1.290000e-34 158.0
32 TraesCS3A01G444300 chr7D 89.344 122 11 2 2788 2907 552332296 552332417 5.980000e-33 152.0


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 TraesCS3A01G444300 chr3A 686120536 686123994 3458 True 6388.00 6388 100.0000 1 3459 1 chr3A.!!$R2 3458
1 TraesCS3A01G444300 chr3D 548531169 548533674 2505 True 1901.00 3378 95.1620 845 3459 2 chr3D.!!$R4 2614
2 TraesCS3A01G444300 chr3B 726441134 726443008 1874 True 2811.00 2811 93.6970 845 2728 1 chr3B.!!$R1 1883
3 TraesCS3A01G444300 chr6A 188417480 188418260 780 True 928.00 928 88.2060 1 787 1 chr6A.!!$R2 786
4 TraesCS3A01G444300 chr6A 38764825 38765688 863 True 635.00 1122 95.6365 1 791 2 chr6A.!!$R3 790
5 TraesCS3A01G444300 chr6A 605160980 605161591 611 True 400.85 747 94.9915 1 786 2 chr6A.!!$R4 785
6 TraesCS3A01G444300 chr4A 164490008 164490789 781 False 885.00 885 87.1860 1 788 1 chr4A.!!$F1 787
7 TraesCS3A01G444300 chr1B 122950725 122951270 545 True 680.00 680 89.2090 238 787 1 chr1B.!!$R1 549
8 TraesCS3A01G444300 chr1B 461245753 461246769 1016 True 468.50 569 87.4985 1 801 2 chr1B.!!$R2 800
9 TraesCS3A01G444300 chr5B 470202523 470204662 2139 False 309.00 368 86.3315 1 550 2 chr5B.!!$F1 549

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
740 2648 0.236187 CTCTCGATGATCGGGTCGTC 59.764 60.0 15.05 0.15 41.96 4.2 F
1540 3454 0.329261 TGCCTAATTGCCTGAGCTGT 59.671 50.0 0.00 0.00 40.80 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2256 4176 0.835543 AGACCTGTCAGCAAGCCTCT 60.836 55.0 0.0 0.0 0.00 3.69 R
3089 5015 0.040204 AGCTACTTGCAGGCCCAATT 59.960 50.0 0.0 0.0 45.94 2.32 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
166 170 6.737254 TTTTTCCTCAGGCTAAAGTTATCG 57.263 37.500 0.00 0.00 0.00 2.92
179 183 8.298140 GGCTAAAGTTATCGTGATGATAGTACT 58.702 37.037 0.00 0.00 40.58 2.73
498 2322 5.514204 GCACTAGCAGCATTTGTCAAAATAG 59.486 40.000 1.31 0.00 41.58 1.73
631 2457 5.949735 TGGGAGAAAAATCAATTAGCGAAC 58.050 37.500 0.00 0.00 0.00 3.95
693 2531 5.668558 AATAAAAATCGATACTGCGGGAC 57.331 39.130 0.00 0.00 0.00 4.46
740 2648 0.236187 CTCTCGATGATCGGGTCGTC 59.764 60.000 15.05 0.15 41.96 4.20
801 2709 8.980481 AGAAATTCCCATACATAAATTCGAGT 57.020 30.769 0.00 0.00 0.00 4.18
838 2746 9.846248 ACTAACATAAATTCAAGTTGAAGCATC 57.154 29.630 22.03 0.00 40.05 3.91
905 2813 5.420104 CCCATGGACTCTTATTTGCTCTTTT 59.580 40.000 15.22 0.00 0.00 2.27
906 2814 6.405176 CCCATGGACTCTTATTTGCTCTTTTC 60.405 42.308 15.22 0.00 0.00 2.29
921 2829 4.619160 GCTCTTTTCTGTTGGGCTTAATGG 60.619 45.833 0.00 0.00 0.00 3.16
932 2840 1.106285 GCTTAATGGTCTTGGGGCTG 58.894 55.000 0.00 0.00 0.00 4.85
937 2845 2.034221 GGTCTTGGGGCTGTGGTC 59.966 66.667 0.00 0.00 0.00 4.02
944 2852 4.286447 GGGCTGTGGTCCCAAAAA 57.714 55.556 0.00 0.00 43.37 1.94
997 2911 2.024464 ACAGTACAGCAGAGGGAGAGAT 60.024 50.000 0.00 0.00 0.00 2.75
999 2913 3.568007 CAGTACAGCAGAGGGAGAGATAC 59.432 52.174 0.00 0.00 0.00 2.24
1010 2924 2.903135 GGGAGAGATACATGGGGAAGAG 59.097 54.545 0.00 0.00 0.00 2.85
1212 3126 2.753043 GGCCTCCACGTCGTCCTA 60.753 66.667 0.00 0.00 0.00 2.94
1267 3181 0.896479 GGAGAGTATCCTCCGGGAGC 60.896 65.000 18.91 4.91 45.86 4.70
1411 3325 2.297315 TGCCATGCTCTTCCTCTATACG 59.703 50.000 0.00 0.00 0.00 3.06
1412 3326 2.353208 GCCATGCTCTTCCTCTATACGG 60.353 54.545 0.00 0.00 0.00 4.02
1504 3418 6.813293 TCTCTATCCAATTGAGTGATGGAA 57.187 37.500 7.12 0.00 45.75 3.53
1534 3448 2.017049 GTAGTGGTGCCTAATTGCCTG 58.983 52.381 0.00 0.00 0.00 4.85
1540 3454 0.329261 TGCCTAATTGCCTGAGCTGT 59.671 50.000 0.00 0.00 40.80 4.40
1544 3458 3.004106 GCCTAATTGCCTGAGCTGTATTG 59.996 47.826 0.00 0.00 40.80 1.90
1558 3472 8.654230 TGAGCTGTATTGAGTTCTGAATATTC 57.346 34.615 8.60 8.60 0.00 1.75
1665 3579 9.317936 TGATATTCAGTTTCATACATGTGAGAC 57.682 33.333 9.11 3.76 34.43 3.36
1934 3848 1.414919 GGTGGCCGGATAGTGAATGTA 59.585 52.381 5.05 0.00 0.00 2.29
2023 3937 3.834231 CCCAAGTGACCCATTCTGAATTT 59.166 43.478 0.00 0.00 0.00 1.82
2032 3946 4.528206 ACCCATTCTGAATTTTCCTTGACC 59.472 41.667 0.00 0.00 0.00 4.02
2042 3961 4.893424 TTTTCCTTGACCTGTCTTTTCG 57.107 40.909 0.00 0.00 0.00 3.46
2212 4132 4.580995 CCTCAGATGTACACGGACTATTCT 59.419 45.833 0.00 0.00 0.00 2.40
2213 4133 5.763698 CCTCAGATGTACACGGACTATTCTA 59.236 44.000 0.00 0.00 0.00 2.10
2254 4174 5.620738 ATGTGTATACAAGACTCATGGCT 57.379 39.130 7.25 0.00 40.84 4.75
2256 4176 6.538945 TGTGTATACAAGACTCATGGCTAA 57.461 37.500 7.25 0.00 32.88 3.09
2261 4181 2.093235 ACAAGACTCATGGCTAAGAGGC 60.093 50.000 7.26 3.44 40.28 4.70
2263 4183 2.998316 GACTCATGGCTAAGAGGCTT 57.002 50.000 7.26 0.00 41.96 4.35
2264 4184 2.559440 GACTCATGGCTAAGAGGCTTG 58.441 52.381 7.26 8.97 44.03 4.01
2406 4326 0.678048 CTTGCTCTGTTACCCCAGGC 60.678 60.000 0.00 0.00 33.14 4.85
2484 4404 6.369065 GGTGACTAGTCTTGTCCATACTTTTG 59.631 42.308 23.01 0.00 33.83 2.44
2495 4415 3.774766 TCCATACTTTTGCTCCAGCTAGA 59.225 43.478 0.00 0.00 42.66 2.43
2604 4525 5.446143 TTTGTGTTACTTGCACCTATTGG 57.554 39.130 0.00 0.00 36.11 3.16
2619 4540 6.524734 CACCTATTGGCATAGAAGTGATACA 58.475 40.000 0.00 0.00 35.20 2.29
2745 4666 7.602644 TCTGATATTTAATGCAGTAACGGATCC 59.397 37.037 6.03 0.00 0.00 3.36
2746 4667 7.220740 TGATATTTAATGCAGTAACGGATCCA 58.779 34.615 13.41 0.00 0.00 3.41
2753 4674 3.055458 TGCAGTAACGGATCCATCTTTCA 60.055 43.478 13.41 0.00 0.00 2.69
2850 4771 6.424812 GCATAGCAAAGAAACCAAATTGTCTT 59.575 34.615 0.00 0.00 31.69 3.01
2854 4775 7.327214 AGCAAAGAAACCAAATTGTCTTACAA 58.673 30.769 0.00 0.00 42.95 2.41
2868 4789 4.642437 TGTCTTACAAACACCAATTCAGCA 59.358 37.500 0.00 0.00 0.00 4.41
2984 4910 0.102120 GCGACTCTAGCAGCACAGAT 59.898 55.000 0.00 0.00 34.19 2.90
3036 4962 5.694458 CACACATATTACATAACCGCAGCTA 59.306 40.000 0.00 0.00 0.00 3.32
3037 4963 5.926542 ACACATATTACATAACCGCAGCTAG 59.073 40.000 0.00 0.00 0.00 3.42
3039 4965 6.645003 CACATATTACATAACCGCAGCTAGAA 59.355 38.462 0.00 0.00 0.00 2.10
3040 4966 7.170828 CACATATTACATAACCGCAGCTAGAAA 59.829 37.037 0.00 0.00 0.00 2.52
3041 4967 7.713507 ACATATTACATAACCGCAGCTAGAAAA 59.286 33.333 0.00 0.00 0.00 2.29
3074 5000 3.736224 CTGGGCTGCCTGGGTCAT 61.736 66.667 19.68 0.00 0.00 3.06
3078 5004 2.677524 GCTGCCTGGGTCATGCAA 60.678 61.111 0.00 0.00 34.90 4.08
3079 5005 2.277591 GCTGCCTGGGTCATGCAAA 61.278 57.895 0.00 0.00 34.90 3.68
3080 5006 1.610554 GCTGCCTGGGTCATGCAAAT 61.611 55.000 0.00 0.00 34.90 2.32
3081 5007 1.766494 CTGCCTGGGTCATGCAAATA 58.234 50.000 0.00 0.00 34.90 1.40
3082 5008 2.313317 CTGCCTGGGTCATGCAAATAT 58.687 47.619 0.00 0.00 34.90 1.28
3084 5010 2.034124 GCCTGGGTCATGCAAATATGT 58.966 47.619 0.00 0.00 0.00 2.29
3085 5011 2.223876 GCCTGGGTCATGCAAATATGTG 60.224 50.000 0.00 0.00 0.00 3.21
3089 5015 4.085009 TGGGTCATGCAAATATGTGTTGA 58.915 39.130 0.00 0.00 0.00 3.18
3090 5016 4.525874 TGGGTCATGCAAATATGTGTTGAA 59.474 37.500 0.00 0.00 0.00 2.69
3091 5017 5.187381 TGGGTCATGCAAATATGTGTTGAAT 59.813 36.000 0.00 0.00 0.00 2.57
3092 5018 6.108015 GGGTCATGCAAATATGTGTTGAATT 58.892 36.000 0.00 0.00 0.00 2.17
3093 5019 6.036300 GGGTCATGCAAATATGTGTTGAATTG 59.964 38.462 0.00 0.00 0.00 2.32
3094 5020 6.036300 GGTCATGCAAATATGTGTTGAATTGG 59.964 38.462 0.00 0.00 0.00 3.16
3095 5021 6.036300 GTCATGCAAATATGTGTTGAATTGGG 59.964 38.462 0.00 0.00 0.00 4.12
3096 5022 4.252073 TGCAAATATGTGTTGAATTGGGC 58.748 39.130 0.00 0.00 0.00 5.36
3097 5023 3.622612 GCAAATATGTGTTGAATTGGGCC 59.377 43.478 0.00 0.00 0.00 5.80
3098 5024 4.623647 GCAAATATGTGTTGAATTGGGCCT 60.624 41.667 4.53 0.00 0.00 5.19
3099 5025 4.741321 AATATGTGTTGAATTGGGCCTG 57.259 40.909 4.53 0.00 0.00 4.85
3100 5026 0.609662 ATGTGTTGAATTGGGCCTGC 59.390 50.000 4.53 0.00 0.00 4.85
3101 5027 0.758310 TGTGTTGAATTGGGCCTGCA 60.758 50.000 4.53 0.00 0.00 4.41
3102 5028 0.392336 GTGTTGAATTGGGCCTGCAA 59.608 50.000 4.53 0.00 0.00 4.08
3103 5029 0.680618 TGTTGAATTGGGCCTGCAAG 59.319 50.000 4.53 0.00 0.00 4.01
3104 5030 0.681175 GTTGAATTGGGCCTGCAAGT 59.319 50.000 4.53 0.00 0.00 3.16
3105 5031 1.892474 GTTGAATTGGGCCTGCAAGTA 59.108 47.619 4.53 0.00 0.00 2.24
3106 5032 1.838112 TGAATTGGGCCTGCAAGTAG 58.162 50.000 4.53 0.00 0.00 2.57
3107 5033 0.457443 GAATTGGGCCTGCAAGTAGC 59.543 55.000 4.53 0.00 45.96 3.58
3108 5034 0.040204 AATTGGGCCTGCAAGTAGCT 59.960 50.000 4.53 0.00 45.94 3.32
3109 5035 0.682209 ATTGGGCCTGCAAGTAGCTG 60.682 55.000 4.53 0.00 45.94 4.24
3114 5040 3.900855 CTGCAAGTAGCTGGGCTG 58.099 61.111 0.00 0.00 45.94 4.85
3115 5041 1.748122 CTGCAAGTAGCTGGGCTGG 60.748 63.158 0.00 0.00 45.94 4.85
3116 5042 2.439156 GCAAGTAGCTGGGCTGGG 60.439 66.667 0.00 0.00 40.10 4.45
3117 5043 2.439156 CAAGTAGCTGGGCTGGGC 60.439 66.667 0.00 0.00 40.10 5.36
3132 5058 4.533815 GGCTGGGCCTTAAAATTAGTAGT 58.466 43.478 4.53 0.00 46.69 2.73
3133 5059 5.687780 GGCTGGGCCTTAAAATTAGTAGTA 58.312 41.667 4.53 0.00 46.69 1.82
3134 5060 5.763698 GGCTGGGCCTTAAAATTAGTAGTAG 59.236 44.000 4.53 0.00 46.69 2.57
3135 5061 6.408891 GGCTGGGCCTTAAAATTAGTAGTAGA 60.409 42.308 4.53 0.00 46.69 2.59
3136 5062 7.225011 GCTGGGCCTTAAAATTAGTAGTAGAT 58.775 38.462 4.53 0.00 0.00 1.98
3137 5063 8.373220 GCTGGGCCTTAAAATTAGTAGTAGATA 58.627 37.037 4.53 0.00 0.00 1.98
3138 5064 9.708092 CTGGGCCTTAAAATTAGTAGTAGATAC 57.292 37.037 4.53 0.00 34.30 2.24
3139 5065 9.216148 TGGGCCTTAAAATTAGTAGTAGATACA 57.784 33.333 4.53 0.00 36.79 2.29
3155 5081 8.268850 AGTAGATACAAATTTTACAGTGCTGG 57.731 34.615 4.11 0.00 34.19 4.85
3156 5082 8.100791 AGTAGATACAAATTTTACAGTGCTGGA 58.899 33.333 4.11 0.00 34.19 3.86
3157 5083 7.383102 AGATACAAATTTTACAGTGCTGGAG 57.617 36.000 4.11 0.00 34.19 3.86
3158 5084 4.853924 ACAAATTTTACAGTGCTGGAGG 57.146 40.909 4.11 0.00 34.19 4.30
3159 5085 3.573967 ACAAATTTTACAGTGCTGGAGGG 59.426 43.478 4.11 0.00 34.19 4.30
3160 5086 2.514458 ATTTTACAGTGCTGGAGGGG 57.486 50.000 4.11 0.00 34.19 4.79
3161 5087 0.404040 TTTTACAGTGCTGGAGGGGG 59.596 55.000 4.11 0.00 34.19 5.40
3162 5088 0.474854 TTTACAGTGCTGGAGGGGGA 60.475 55.000 4.11 0.00 34.19 4.81
3163 5089 1.198759 TTACAGTGCTGGAGGGGGAC 61.199 60.000 4.11 0.00 34.19 4.46
3164 5090 2.106923 TACAGTGCTGGAGGGGGACT 62.107 60.000 4.11 0.00 35.82 3.85
3165 5091 2.208349 AGTGCTGGAGGGGGACTT 59.792 61.111 0.00 0.00 31.52 3.01
3166 5092 2.227036 AGTGCTGGAGGGGGACTTG 61.227 63.158 0.00 0.00 31.52 3.16
3167 5093 2.206900 TGCTGGAGGGGGACTTGA 59.793 61.111 0.00 0.00 0.00 3.02
3168 5094 1.920325 TGCTGGAGGGGGACTTGAG 60.920 63.158 0.00 0.00 0.00 3.02
3169 5095 2.993853 CTGGAGGGGGACTTGAGC 59.006 66.667 0.00 0.00 0.00 4.26
3170 5096 2.610859 TGGAGGGGGACTTGAGCC 60.611 66.667 0.00 0.00 0.00 4.70
3171 5097 2.285743 GGAGGGGGACTTGAGCCT 60.286 66.667 0.00 0.00 0.00 4.58
3172 5098 2.674220 GGAGGGGGACTTGAGCCTG 61.674 68.421 0.00 0.00 0.00 4.85
3173 5099 1.920835 GAGGGGGACTTGAGCCTGT 60.921 63.158 0.00 0.00 0.00 4.00
3174 5100 1.464198 AGGGGGACTTGAGCCTGTT 60.464 57.895 0.00 0.00 0.00 3.16
3175 5101 0.178873 AGGGGGACTTGAGCCTGTTA 60.179 55.000 0.00 0.00 0.00 2.41
3176 5102 0.696501 GGGGGACTTGAGCCTGTTAA 59.303 55.000 0.00 0.00 0.00 2.01
3177 5103 1.074889 GGGGGACTTGAGCCTGTTAAA 59.925 52.381 0.00 0.00 0.00 1.52
3178 5104 2.437413 GGGGACTTGAGCCTGTTAAAG 58.563 52.381 0.00 0.00 0.00 1.85
3179 5105 1.813178 GGGACTTGAGCCTGTTAAAGC 59.187 52.381 0.00 0.00 0.00 3.51
3180 5106 1.813178 GGACTTGAGCCTGTTAAAGCC 59.187 52.381 0.00 0.00 0.00 4.35
3181 5107 1.813178 GACTTGAGCCTGTTAAAGCCC 59.187 52.381 0.00 0.00 0.00 5.19
3182 5108 1.177401 CTTGAGCCTGTTAAAGCCCC 58.823 55.000 0.00 0.00 0.00 5.80
3183 5109 0.251608 TTGAGCCTGTTAAAGCCCCC 60.252 55.000 0.00 0.00 0.00 5.40
3198 5124 3.579496 CCCCCAGTAGATTAGCCCT 57.421 57.895 0.00 0.00 0.00 5.19
3199 5125 1.059913 CCCCCAGTAGATTAGCCCTG 58.940 60.000 0.00 0.00 0.00 4.45
3200 5126 0.398318 CCCCAGTAGATTAGCCCTGC 59.602 60.000 0.00 0.00 0.00 4.85
3201 5127 0.398318 CCCAGTAGATTAGCCCTGCC 59.602 60.000 0.00 0.00 0.00 4.85
3202 5128 0.398318 CCAGTAGATTAGCCCTGCCC 59.602 60.000 0.00 0.00 0.00 5.36
3203 5129 0.398318 CAGTAGATTAGCCCTGCCCC 59.602 60.000 0.00 0.00 0.00 5.80
3204 5130 0.768609 AGTAGATTAGCCCTGCCCCC 60.769 60.000 0.00 0.00 0.00 5.40
3271 5197 5.301805 CCCTTGTCTTCTTTTCCAGCTTTTA 59.698 40.000 0.00 0.00 0.00 1.52
3346 5272 1.578206 GAAAGACTTGCTGCCGTCCC 61.578 60.000 13.38 3.17 0.00 4.46
3376 5302 2.570386 ACCTATAGACCAGGCCAAGT 57.430 50.000 5.01 0.00 36.57 3.16
3378 5304 4.214993 ACCTATAGACCAGGCCAAGTAT 57.785 45.455 5.01 0.67 36.57 2.12
3424 5350 9.768215 ATTCCTTAAATTCCAGATAGTCCAAAA 57.232 29.630 0.00 0.00 0.00 2.44
3437 5363 0.033781 TCCAAAAACCAGCTGCATGC 59.966 50.000 11.82 11.82 43.29 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 112 5.827797 ACTCGGTAACCTTAACGTGGATATA 59.172 40.000 8.85 0.00 43.87 0.86
110 113 4.646492 ACTCGGTAACCTTAACGTGGATAT 59.354 41.667 8.85 0.00 43.87 1.63
121 124 7.395190 AAAAAGTTTACAACTCGGTAACCTT 57.605 32.000 0.00 0.00 41.91 3.50
498 2322 9.425577 GTGGTTAGATACAGATTAGGCTATTTC 57.574 37.037 0.00 0.00 0.00 2.17
610 2434 7.867445 TTTGTTCGCTAATTGATTTTTCTCC 57.133 32.000 0.00 0.00 0.00 3.71
693 2531 2.165301 GCACGTTCCCTCGATTCGG 61.165 63.158 6.18 0.00 34.70 4.30
740 2648 5.874895 TCGTAATATGACAGTAGATCCGG 57.125 43.478 0.00 0.00 0.00 5.14
749 2657 6.397831 TTCCAAACGTTCGTAATATGACAG 57.602 37.500 0.00 0.00 0.00 3.51
812 2720 9.846248 GATGCTTCAACTTGAATTTATGTTAGT 57.154 29.630 4.65 0.00 35.59 2.24
847 2755 1.956629 GCCGTTAGCCTGGTCAGCTA 61.957 60.000 0.00 0.00 41.83 3.32
872 2780 3.806949 AGAGTCCATGGGCTTGTTTAA 57.193 42.857 22.38 0.00 0.00 1.52
905 2813 3.420893 CAAGACCATTAAGCCCAACAGA 58.579 45.455 0.00 0.00 0.00 3.41
906 2814 2.493278 CCAAGACCATTAAGCCCAACAG 59.507 50.000 0.00 0.00 0.00 3.16
921 2829 2.034221 GGACCACAGCCCCAAGAC 59.966 66.667 0.00 0.00 0.00 3.01
942 2850 3.581332 TCGAACTCAGATAGGGGTGTTTT 59.419 43.478 0.00 0.00 0.00 2.43
943 2851 3.170717 TCGAACTCAGATAGGGGTGTTT 58.829 45.455 0.00 0.00 0.00 2.83
944 2852 2.816411 TCGAACTCAGATAGGGGTGTT 58.184 47.619 0.00 0.00 0.00 3.32
945 2853 2.526888 TCGAACTCAGATAGGGGTGT 57.473 50.000 0.00 0.00 0.00 4.16
946 2854 3.243907 GGAATCGAACTCAGATAGGGGTG 60.244 52.174 0.00 0.00 0.00 4.61
947 2855 2.966516 GGAATCGAACTCAGATAGGGGT 59.033 50.000 0.00 0.00 0.00 4.95
948 2856 2.029828 CGGAATCGAACTCAGATAGGGG 60.030 54.545 0.00 0.00 39.00 4.79
949 2857 2.029828 CCGGAATCGAACTCAGATAGGG 60.030 54.545 0.00 0.00 39.00 3.53
950 2858 2.608261 GCCGGAATCGAACTCAGATAGG 60.608 54.545 5.05 0.00 39.00 2.57
951 2859 2.667137 GCCGGAATCGAACTCAGATAG 58.333 52.381 5.05 0.00 39.00 2.08
952 2860 1.001706 CGCCGGAATCGAACTCAGATA 60.002 52.381 5.05 0.00 39.00 1.98
954 2862 1.138883 CGCCGGAATCGAACTCAGA 59.861 57.895 5.05 0.00 39.00 3.27
955 2863 0.457853 TTCGCCGGAATCGAACTCAG 60.458 55.000 5.05 0.00 40.49 3.35
956 2864 1.587568 TTCGCCGGAATCGAACTCA 59.412 52.632 5.05 0.00 40.49 3.41
957 2865 4.489249 TTCGCCGGAATCGAACTC 57.511 55.556 5.05 0.00 40.49 3.01
997 2911 0.551377 TTGCCCCTCTTCCCCATGTA 60.551 55.000 0.00 0.00 0.00 2.29
999 2913 1.076485 CTTGCCCCTCTTCCCCATG 60.076 63.158 0.00 0.00 0.00 3.66
1411 3325 1.066430 TGAAGCGTTCCATGGTACTCC 60.066 52.381 18.18 9.74 0.00 3.85
1412 3326 2.380084 TGAAGCGTTCCATGGTACTC 57.620 50.000 18.18 11.26 0.00 2.59
1418 3332 3.302365 ACCAAATTGAAGCGTTCCATG 57.698 42.857 0.00 0.00 0.00 3.66
1504 3418 1.878656 GCACCACTACTCTCAGCCGT 61.879 60.000 0.00 0.00 0.00 5.68
1534 3448 8.654230 TGAATATTCAGAACTCAATACAGCTC 57.346 34.615 14.23 0.00 32.50 4.09
1653 3567 9.760926 ACCTATGTATCATAGTCTCACATGTAT 57.239 33.333 0.00 0.00 32.39 2.29
1665 3579 7.307632 GCTTTGTGCAGAACCTATGTATCATAG 60.308 40.741 0.00 9.11 42.31 2.23
1964 3878 2.697431 TGGTGAAACTTACATTGCGC 57.303 45.000 0.00 0.00 36.74 6.09
2023 3937 2.158813 AGCGAAAAGACAGGTCAAGGAA 60.159 45.455 1.84 0.00 0.00 3.36
2212 4132 6.430925 ACACATTAACAGCAAGCTTTGAGATA 59.569 34.615 5.15 0.00 0.00 1.98
2213 4133 5.242393 ACACATTAACAGCAAGCTTTGAGAT 59.758 36.000 5.15 0.00 0.00 2.75
2254 4174 1.276421 GACCTGTCAGCAAGCCTCTTA 59.724 52.381 0.00 0.00 0.00 2.10
2256 4176 0.835543 AGACCTGTCAGCAAGCCTCT 60.836 55.000 0.00 0.00 0.00 3.69
2261 4181 1.805869 CCTTCAGACCTGTCAGCAAG 58.194 55.000 0.00 0.00 0.00 4.01
2263 4183 1.372683 GCCTTCAGACCTGTCAGCA 59.627 57.895 0.00 0.00 0.00 4.41
2264 4184 1.376553 GGCCTTCAGACCTGTCAGC 60.377 63.158 0.00 0.00 0.00 4.26
2406 4326 5.111293 AGAACTTTCCAATTGTTGCTTGTG 58.889 37.500 4.43 0.00 0.00 3.33
2495 4415 6.463995 TGGAAAATTTCAACTTGTAGCTGT 57.536 33.333 8.09 0.00 0.00 4.40
2507 4427 5.513962 GGGGGCAAAACTATGGAAAATTTCA 60.514 40.000 8.09 0.00 0.00 2.69
2604 4525 7.721286 AAGTAAGCATGTATCACTTCTATGC 57.279 36.000 0.00 0.00 43.23 3.14
2640 4561 3.552890 GCAAACCACAAGCCCTTTAAGAG 60.553 47.826 0.00 0.00 0.00 2.85
2711 4632 8.174733 ACTGCATTAAATATCAGAGGAAATGG 57.825 34.615 0.00 0.00 0.00 3.16
2850 4771 2.287308 GCGTGCTGAATTGGTGTTTGTA 60.287 45.455 0.00 0.00 0.00 2.41
2854 4775 1.282570 CGCGTGCTGAATTGGTGTT 59.717 52.632 0.00 0.00 0.00 3.32
3057 4983 3.736224 ATGACCCAGGCAGCCCAG 61.736 66.667 8.22 0.21 0.00 4.45
3058 4984 4.051167 CATGACCCAGGCAGCCCA 62.051 66.667 8.22 0.00 0.00 5.36
3060 4986 4.746309 TGCATGACCCAGGCAGCC 62.746 66.667 1.84 1.84 46.09 4.85
3064 4990 2.034124 ACATATTTGCATGACCCAGGC 58.966 47.619 0.00 0.00 41.79 4.85
3066 4992 4.158209 TCAACACATATTTGCATGACCCAG 59.842 41.667 0.00 0.00 0.00 4.45
3067 4993 4.085009 TCAACACATATTTGCATGACCCA 58.915 39.130 0.00 0.00 0.00 4.51
3070 4996 6.036300 CCCAATTCAACACATATTTGCATGAC 59.964 38.462 0.00 0.00 0.00 3.06
3071 4997 6.107343 CCCAATTCAACACATATTTGCATGA 58.893 36.000 0.00 0.00 0.00 3.07
3072 4998 5.220700 GCCCAATTCAACACATATTTGCATG 60.221 40.000 0.00 0.00 0.00 4.06
3073 4999 4.877251 GCCCAATTCAACACATATTTGCAT 59.123 37.500 0.00 0.00 0.00 3.96
3074 5000 4.252073 GCCCAATTCAACACATATTTGCA 58.748 39.130 0.00 0.00 0.00 4.08
3078 5004 3.118665 GCAGGCCCAATTCAACACATATT 60.119 43.478 0.00 0.00 0.00 1.28
3079 5005 2.431782 GCAGGCCCAATTCAACACATAT 59.568 45.455 0.00 0.00 0.00 1.78
3080 5006 1.824230 GCAGGCCCAATTCAACACATA 59.176 47.619 0.00 0.00 0.00 2.29
3081 5007 0.609662 GCAGGCCCAATTCAACACAT 59.390 50.000 0.00 0.00 0.00 3.21
3082 5008 0.758310 TGCAGGCCCAATTCAACACA 60.758 50.000 0.00 0.00 0.00 3.72
3084 5010 0.680618 CTTGCAGGCCCAATTCAACA 59.319 50.000 0.00 0.00 0.00 3.33
3085 5011 0.681175 ACTTGCAGGCCCAATTCAAC 59.319 50.000 0.00 0.00 0.00 3.18
3089 5015 0.040204 AGCTACTTGCAGGCCCAATT 59.960 50.000 0.00 0.00 45.94 2.32
3090 5016 0.682209 CAGCTACTTGCAGGCCCAAT 60.682 55.000 0.00 0.00 45.94 3.16
3091 5017 1.303561 CAGCTACTTGCAGGCCCAA 60.304 57.895 0.00 0.00 45.94 4.12
3092 5018 2.352422 CAGCTACTTGCAGGCCCA 59.648 61.111 0.00 0.00 45.94 5.36
3093 5019 2.439156 CCAGCTACTTGCAGGCCC 60.439 66.667 0.00 0.00 45.94 5.80
3094 5020 2.439156 CCCAGCTACTTGCAGGCC 60.439 66.667 0.00 0.00 45.69 5.19
3096 5022 1.748122 CAGCCCAGCTACTTGCAGG 60.748 63.158 0.00 0.00 46.48 4.85
3097 5023 1.748122 CCAGCCCAGCTACTTGCAG 60.748 63.158 0.00 0.00 45.94 4.41
3098 5024 2.352422 CCAGCCCAGCTACTTGCA 59.648 61.111 0.00 0.00 45.94 4.08
3099 5025 2.439156 CCCAGCCCAGCTACTTGC 60.439 66.667 0.00 0.00 36.40 4.01
3100 5026 2.439156 GCCCAGCCCAGCTACTTG 60.439 66.667 0.00 0.00 36.40 3.16
3101 5027 3.732849 GGCCCAGCCCAGCTACTT 61.733 66.667 0.00 0.00 44.06 2.24
3111 5037 6.589135 TCTACTACTAATTTTAAGGCCCAGC 58.411 40.000 0.00 0.00 0.00 4.85
3112 5038 9.708092 GTATCTACTACTAATTTTAAGGCCCAG 57.292 37.037 0.00 0.00 0.00 4.45
3113 5039 9.216148 TGTATCTACTACTAATTTTAAGGCCCA 57.784 33.333 0.00 0.00 0.00 5.36
3129 5055 9.378551 CCAGCACTGTAAAATTTGTATCTACTA 57.621 33.333 0.00 0.00 0.00 1.82
3130 5056 8.100791 TCCAGCACTGTAAAATTTGTATCTACT 58.899 33.333 0.00 0.00 0.00 2.57
3131 5057 8.263940 TCCAGCACTGTAAAATTTGTATCTAC 57.736 34.615 0.00 0.00 0.00 2.59
3132 5058 7.552687 CCTCCAGCACTGTAAAATTTGTATCTA 59.447 37.037 0.00 0.00 0.00 1.98
3133 5059 6.375455 CCTCCAGCACTGTAAAATTTGTATCT 59.625 38.462 0.00 0.00 0.00 1.98
3134 5060 6.404734 CCCTCCAGCACTGTAAAATTTGTATC 60.405 42.308 0.00 0.00 0.00 2.24
3135 5061 5.418840 CCCTCCAGCACTGTAAAATTTGTAT 59.581 40.000 0.00 0.00 0.00 2.29
3136 5062 4.764823 CCCTCCAGCACTGTAAAATTTGTA 59.235 41.667 0.00 0.00 0.00 2.41
3137 5063 3.573967 CCCTCCAGCACTGTAAAATTTGT 59.426 43.478 0.00 0.00 0.00 2.83
3138 5064 3.056607 CCCCTCCAGCACTGTAAAATTTG 60.057 47.826 0.00 0.00 0.00 2.32
3139 5065 3.165071 CCCCTCCAGCACTGTAAAATTT 58.835 45.455 0.00 0.00 0.00 1.82
3140 5066 2.557452 CCCCCTCCAGCACTGTAAAATT 60.557 50.000 0.00 0.00 0.00 1.82
3141 5067 1.005924 CCCCCTCCAGCACTGTAAAAT 59.994 52.381 0.00 0.00 0.00 1.82
3142 5068 0.404040 CCCCCTCCAGCACTGTAAAA 59.596 55.000 0.00 0.00 0.00 1.52
3143 5069 0.474854 TCCCCCTCCAGCACTGTAAA 60.475 55.000 0.00 0.00 0.00 2.01
3144 5070 1.159905 TCCCCCTCCAGCACTGTAA 59.840 57.895 0.00 0.00 0.00 2.41
3145 5071 1.612442 GTCCCCCTCCAGCACTGTA 60.612 63.158 0.00 0.00 0.00 2.74
3146 5072 2.930562 GTCCCCCTCCAGCACTGT 60.931 66.667 0.00 0.00 0.00 3.55
3147 5073 2.227036 AAGTCCCCCTCCAGCACTG 61.227 63.158 0.00 0.00 0.00 3.66
3148 5074 2.208349 AAGTCCCCCTCCAGCACT 59.792 61.111 0.00 0.00 0.00 4.40
3149 5075 2.190488 CTCAAGTCCCCCTCCAGCAC 62.190 65.000 0.00 0.00 0.00 4.40
3150 5076 1.920325 CTCAAGTCCCCCTCCAGCA 60.920 63.158 0.00 0.00 0.00 4.41
3151 5077 2.993853 CTCAAGTCCCCCTCCAGC 59.006 66.667 0.00 0.00 0.00 4.85
3152 5078 2.674220 GGCTCAAGTCCCCCTCCAG 61.674 68.421 0.00 0.00 0.00 3.86
3153 5079 2.610859 GGCTCAAGTCCCCCTCCA 60.611 66.667 0.00 0.00 0.00 3.86
3154 5080 2.285743 AGGCTCAAGTCCCCCTCC 60.286 66.667 0.00 0.00 0.00 4.30
3155 5081 1.492993 AACAGGCTCAAGTCCCCCTC 61.493 60.000 0.00 0.00 0.00 4.30
3156 5082 0.178873 TAACAGGCTCAAGTCCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
3157 5083 0.696501 TTAACAGGCTCAAGTCCCCC 59.303 55.000 0.00 0.00 0.00 5.40
3158 5084 2.437413 CTTTAACAGGCTCAAGTCCCC 58.563 52.381 0.00 0.00 0.00 4.81
3159 5085 1.813178 GCTTTAACAGGCTCAAGTCCC 59.187 52.381 0.00 0.00 0.00 4.46
3160 5086 1.813178 GGCTTTAACAGGCTCAAGTCC 59.187 52.381 0.00 0.00 45.03 3.85
3180 5106 1.059913 CAGGGCTAATCTACTGGGGG 58.940 60.000 0.00 0.00 0.00 5.40
3181 5107 0.398318 GCAGGGCTAATCTACTGGGG 59.602 60.000 0.00 0.00 0.00 4.96
3182 5108 0.398318 GGCAGGGCTAATCTACTGGG 59.602 60.000 0.00 0.00 0.00 4.45
3183 5109 0.398318 GGGCAGGGCTAATCTACTGG 59.602 60.000 0.00 0.00 0.00 4.00
3184 5110 0.398318 GGGGCAGGGCTAATCTACTG 59.602 60.000 0.00 0.00 0.00 2.74
3185 5111 0.768609 GGGGGCAGGGCTAATCTACT 60.769 60.000 0.00 0.00 0.00 2.57
3186 5112 1.761822 GGGGGCAGGGCTAATCTAC 59.238 63.158 0.00 0.00 0.00 2.59
3187 5113 1.841556 CGGGGGCAGGGCTAATCTA 60.842 63.158 0.00 0.00 0.00 1.98
3188 5114 3.171388 CGGGGGCAGGGCTAATCT 61.171 66.667 0.00 0.00 0.00 2.40
3189 5115 3.168528 TCGGGGGCAGGGCTAATC 61.169 66.667 0.00 0.00 0.00 1.75
3190 5116 3.489513 GTCGGGGGCAGGGCTAAT 61.490 66.667 0.00 0.00 0.00 1.73
3191 5117 4.733725 AGTCGGGGGCAGGGCTAA 62.734 66.667 0.00 0.00 0.00 3.09
3195 5121 3.406595 GATTGAGTCGGGGGCAGGG 62.407 68.421 0.00 0.00 0.00 4.45
3196 5122 2.190578 GATTGAGTCGGGGGCAGG 59.809 66.667 0.00 0.00 0.00 4.85
3197 5123 1.153289 CTGATTGAGTCGGGGGCAG 60.153 63.158 0.00 0.00 0.00 4.85
3198 5124 2.989639 CTGATTGAGTCGGGGGCA 59.010 61.111 0.00 0.00 0.00 5.36
3199 5125 2.514824 GCTGATTGAGTCGGGGGC 60.515 66.667 0.00 0.00 33.56 5.80
3200 5126 2.190578 GGCTGATTGAGTCGGGGG 59.809 66.667 0.00 0.00 33.56 5.40
3201 5127 1.153289 CAGGCTGATTGAGTCGGGG 60.153 63.158 9.42 0.00 33.56 5.73
3202 5128 1.153289 CCAGGCTGATTGAGTCGGG 60.153 63.158 17.94 0.00 35.12 5.14
3203 5129 1.153289 CCCAGGCTGATTGAGTCGG 60.153 63.158 17.94 1.45 36.23 4.79
3204 5130 0.460987 GACCCAGGCTGATTGAGTCG 60.461 60.000 17.94 0.00 0.00 4.18
3271 5197 0.249405 CCAACTGCAAAACATGGCGT 60.249 50.000 0.00 0.00 0.00 5.68
3356 5282 2.846950 ACTTGGCCTGGTCTATAGGTT 58.153 47.619 3.32 0.00 37.64 3.50
3361 5287 3.117888 CCACAATACTTGGCCTGGTCTAT 60.118 47.826 3.32 0.00 34.12 1.98
3424 5350 6.653526 TTAATATTATGCATGCAGCTGGTT 57.346 33.333 26.69 18.47 45.94 3.67


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

AutoCloner maintained by Alex Coulton.