Multiple sequence alignment - TraesCS5A01G002600

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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 TraesCS5A01G002600 chr5A 100.000 4838 0 0 1 4838 2109603 2114440 0.000000e+00 8935.0
1 TraesCS5A01G002600 chr5D 95.504 3247 120 17 346 3578 2671888 2668654 0.000000e+00 5164.0
2 TraesCS5A01G002600 chr5D 91.508 577 31 7 3572 4130 2668525 2667949 0.000000e+00 778.0
3 TraesCS5A01G002600 chr5D 89.591 269 14 4 43 306 2672119 2671860 3.610000e-86 329.0
4 TraesCS5A01G002600 chr5B 93.182 1760 80 16 210 1929 2563407 2561648 0.000000e+00 2549.0
5 TraesCS5A01G002600 chr5B 90.468 1794 107 21 2527 4270 2560677 2558898 0.000000e+00 2307.0
6 TraesCS5A01G002600 chr5B 87.067 982 108 5 951 1929 686469917 686470882 0.000000e+00 1092.0
7 TraesCS5A01G002600 chr5B 90.106 566 37 6 4286 4838 4541504 4542063 0.000000e+00 717.0
8 TraesCS5A01G002600 chr5B 81.236 453 53 23 4407 4838 2558553 2558112 2.160000e-88 337.0
9 TraesCS5A01G002600 chr3B 92.431 1057 67 7 882 1928 720834180 720833127 0.000000e+00 1496.0
10 TraesCS5A01G002600 chr3B 92.836 335 23 1 364 697 720853945 720853611 7.280000e-133 484.0
11 TraesCS5A01G002600 chr3B 87.603 242 13 8 57 291 720857768 720857537 1.030000e-66 265.0
12 TraesCS5A01G002600 chr3B 82.143 84 13 2 152 235 720858114 720858033 2.420000e-08 71.3
13 TraesCS5A01G002600 chr4A 86.165 983 111 9 950 1929 624121222 624122182 0.000000e+00 1038.0
14 TraesCS5A01G002600 chr4A 82.088 910 161 2 1001 1909 584272892 584273800 0.000000e+00 776.0
15 TraesCS5A01G002600 chr4A 79.673 733 135 13 2571 3300 584274104 584274825 2.580000e-142 516.0
16 TraesCS5A01G002600 chr4D 79.048 735 140 13 2571 3300 16233810 16233085 4.350000e-135 492.0
17 TraesCS5A01G002600 chr4B 78.940 736 139 15 2571 3300 28071523 28070798 2.020000e-133 486.0
18 TraesCS5A01G002600 chr7D 87.500 48 5 1 1638 1685 78172513 78172467 2.000000e-03 54.7
19 TraesCS5A01G002600 chr7B 100.000 28 0 0 144 171 741338006 741338033 9.000000e-03 52.8


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 TraesCS5A01G002600 chr5A 2109603 2114440 4837 False 8935.000000 8935 100.000000 1 4838 1 chr5A.!!$F1 4837
1 TraesCS5A01G002600 chr5D 2667949 2672119 4170 True 2090.333333 5164 92.201000 43 4130 3 chr5D.!!$R1 4087
2 TraesCS5A01G002600 chr5B 2558112 2563407 5295 True 1731.000000 2549 88.295333 210 4838 3 chr5B.!!$R1 4628
3 TraesCS5A01G002600 chr5B 686469917 686470882 965 False 1092.000000 1092 87.067000 951 1929 1 chr5B.!!$F2 978
4 TraesCS5A01G002600 chr5B 4541504 4542063 559 False 717.000000 717 90.106000 4286 4838 1 chr5B.!!$F1 552
5 TraesCS5A01G002600 chr3B 720833127 720834180 1053 True 1496.000000 1496 92.431000 882 1928 1 chr3B.!!$R1 1046
6 TraesCS5A01G002600 chr3B 720853611 720858114 4503 True 273.433333 484 87.527333 57 697 3 chr3B.!!$R2 640
7 TraesCS5A01G002600 chr4A 624121222 624122182 960 False 1038.000000 1038 86.165000 950 1929 1 chr4A.!!$F1 979
8 TraesCS5A01G002600 chr4A 584272892 584274825 1933 False 646.000000 776 80.880500 1001 3300 2 chr4A.!!$F2 2299
9 TraesCS5A01G002600 chr4D 16233085 16233810 725 True 492.000000 492 79.048000 2571 3300 1 chr4D.!!$R1 729
10 TraesCS5A01G002600 chr4B 28070798 28071523 725 True 486.000000 486 78.940000 2571 3300 1 chr4B.!!$R1 729

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
784 4638 0.451783 GGATGACACGTGCCCAAATC 59.548 55.0 17.22 11.15 0.00 2.17 F
1674 5548 0.814010 GTAGCAACCGGGCGATCATT 60.814 55.0 6.32 0.00 39.27 2.57 F
2368 7061 0.250901 CTGTTACCTGCAGTTGGCCT 60.251 55.0 13.81 0.00 43.89 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 6840 4.155063 TGCTAGTTCACCATGCATATGT 57.845 40.909 0.0 0.0 32.21 2.29 R
3304 8004 0.027194 CATGGAGTTTCTGCGATGCG 59.973 55.000 0.0 0.0 0.00 4.73 R
4153 9015 0.108585 GGTCTTCACTGGCTTGGACA 59.891 55.000 0.0 0.0 0.00 4.02 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
20 21 2.627515 ATTGCGCACTATGGATCTGT 57.372 45.000 11.12 0.00 0.00 3.41
22 23 2.401583 TGCGCACTATGGATCTGTTT 57.598 45.000 5.66 0.00 0.00 2.83
24 25 2.009774 GCGCACTATGGATCTGTTTGT 58.990 47.619 0.30 0.00 0.00 2.83
25 26 3.194861 GCGCACTATGGATCTGTTTGTA 58.805 45.455 0.30 0.00 0.00 2.41
26 27 3.621268 GCGCACTATGGATCTGTTTGTAA 59.379 43.478 0.30 0.00 0.00 2.41
27 28 4.273480 GCGCACTATGGATCTGTTTGTAAT 59.727 41.667 0.30 0.00 0.00 1.89
28 29 5.741425 CGCACTATGGATCTGTTTGTAATG 58.259 41.667 0.00 0.00 0.00 1.90
29 30 5.514279 GCACTATGGATCTGTTTGTAATGC 58.486 41.667 0.00 0.00 0.00 3.56
30 31 5.297776 GCACTATGGATCTGTTTGTAATGCT 59.702 40.000 0.00 0.00 0.00 3.79
32 33 7.012327 GCACTATGGATCTGTTTGTAATGCTTA 59.988 37.037 0.00 0.00 0.00 3.09
33 34 8.554528 CACTATGGATCTGTTTGTAATGCTTAG 58.445 37.037 0.00 0.00 0.00 2.18
35 36 6.985188 TGGATCTGTTTGTAATGCTTAGAC 57.015 37.500 0.00 0.00 0.00 2.59
36 37 6.472016 TGGATCTGTTTGTAATGCTTAGACA 58.528 36.000 0.00 0.00 0.00 3.41
37 38 6.595326 TGGATCTGTTTGTAATGCTTAGACAG 59.405 38.462 0.00 0.00 35.55 3.51
38 39 6.595716 GGATCTGTTTGTAATGCTTAGACAGT 59.404 38.462 0.00 0.00 35.68 3.55
39 40 7.764443 GGATCTGTTTGTAATGCTTAGACAGTA 59.236 37.037 0.00 0.00 35.68 2.74
41 42 7.892609 TCTGTTTGTAATGCTTAGACAGTAGA 58.107 34.615 0.00 0.00 35.68 2.59
77 369 2.653726 TCACATACAATGGATGCACCC 58.346 47.619 5.16 0.00 38.00 4.61
78 370 1.334556 CACATACAATGGATGCACCCG 59.665 52.381 5.16 0.00 38.00 5.28
90 382 4.137543 GGATGCACCCGAATTTATCTTCT 58.862 43.478 0.00 0.00 0.00 2.85
92 384 4.487714 TGCACCCGAATTTATCTTCTCT 57.512 40.909 0.00 0.00 0.00 3.10
118 411 7.045416 TGTTGTTTTTCTCTGCTAGTTCAGTA 58.955 34.615 0.00 0.00 35.63 2.74
145 438 9.899226 GTTCTGCATTTTCTTACAATATATCCC 57.101 33.333 0.00 0.00 0.00 3.85
146 439 8.635765 TCTGCATTTTCTTACAATATATCCCC 57.364 34.615 0.00 0.00 0.00 4.81
147 440 8.448008 TCTGCATTTTCTTACAATATATCCCCT 58.552 33.333 0.00 0.00 0.00 4.79
148 441 8.408043 TGCATTTTCTTACAATATATCCCCTG 57.592 34.615 0.00 0.00 0.00 4.45
149 442 7.039784 TGCATTTTCTTACAATATATCCCCTGC 60.040 37.037 0.00 0.00 0.00 4.85
150 443 7.177392 GCATTTTCTTACAATATATCCCCTGCT 59.823 37.037 0.00 0.00 0.00 4.24
199 496 1.555075 TGGTTTAGGTCTGGCAGCTAG 59.445 52.381 10.34 0.00 36.44 3.42
202 505 0.691078 TTAGGTCTGGCAGCTAGGGG 60.691 60.000 10.34 0.00 36.44 4.79
275 582 2.672195 GCTGCGCTTTTGCCTAAGATTT 60.672 45.455 9.73 0.00 43.93 2.17
330 1859 8.848474 TTGTTAATTAGGAATAGCATAGCTCC 57.152 34.615 0.00 0.00 40.44 4.70
336 1865 3.173965 GGAATAGCATAGCTCCACCCTA 58.826 50.000 0.00 0.00 40.44 3.53
632 4485 9.725019 TCATGACATAATTAGTTTGAGAACAGT 57.275 29.630 0.00 0.00 38.26 3.55
723 4577 8.807118 AGATAATTAGATTTCTACATCTCCGCA 58.193 33.333 0.00 0.00 35.08 5.69
759 4613 7.735326 ACAATACAGATACCTATCCCATACC 57.265 40.000 0.00 0.00 33.17 2.73
784 4638 0.451783 GGATGACACGTGCCCAAATC 59.548 55.000 17.22 11.15 0.00 2.17
862 4716 6.322931 TCATCACATACTATGGATGTACCCT 58.677 40.000 17.93 0.00 38.25 4.34
903 4760 4.035558 TGTTGTTCTGACACTTCATCAAGC 59.964 41.667 0.00 0.00 34.98 4.01
918 4777 6.889301 TCATCAAGCTGTTTCTCTGATTTT 57.111 33.333 0.00 0.00 0.00 1.82
1266 5137 2.230940 CGCCATCGTCATGACCGTC 61.231 63.158 20.03 4.51 30.57 4.79
1314 5185 4.221422 GCGACCGCCCTCATGCTA 62.221 66.667 2.55 0.00 34.56 3.49
1566 5440 2.579201 CCATCACGGAGCGGTTCT 59.421 61.111 0.00 0.00 36.56 3.01
1674 5548 0.814010 GTAGCAACCGGGCGATCATT 60.814 55.000 6.32 0.00 39.27 2.57
1869 5743 1.353103 CGCGAGGAAATGGCATGTC 59.647 57.895 9.27 9.27 31.94 3.06
1948 6558 8.080417 CCCTGATGCTATATTGTTCATTTCTTG 58.920 37.037 0.00 0.00 0.00 3.02
1949 6559 8.627403 CCTGATGCTATATTGTTCATTTCTTGT 58.373 33.333 0.00 0.00 0.00 3.16
2001 6615 6.757897 TGTTCTGATGGACATAAATCAACC 57.242 37.500 0.00 0.00 32.60 3.77
2005 6619 6.962182 TCTGATGGACATAAATCAACCTTCT 58.038 36.000 0.00 0.00 32.60 2.85
2010 6624 5.939883 TGGACATAAATCAACCTTCTCTGTG 59.060 40.000 0.00 0.00 0.00 3.66
2087 6774 4.744570 CAGAAATTTCTCATGTGCTGCAT 58.255 39.130 17.91 0.00 34.97 3.96
2096 6783 2.425668 TCATGTGCTGCATTCCATTCTG 59.574 45.455 5.27 0.00 35.19 3.02
2182 6869 4.034510 GCATGGTGAACTAGCATTCTACAC 59.965 45.833 0.00 0.00 44.75 2.90
2284 6973 9.462606 TCTCTGTAGTTTTCTTTTCTTTCCTTT 57.537 29.630 0.00 0.00 0.00 3.11
2368 7061 0.250901 CTGTTACCTGCAGTTGGCCT 60.251 55.000 13.81 0.00 43.89 5.19
2390 7083 5.455056 TTTAAATGAAGCTGGGCGTTAAA 57.545 34.783 0.00 0.00 0.00 1.52
2818 7512 1.024579 AGCGCCTAATGGTGGAAACG 61.025 55.000 2.29 0.00 43.74 3.60
2822 7516 0.808755 CCTAATGGTGGAAACGGTGC 59.191 55.000 0.00 0.00 0.00 5.01
2827 7521 0.817634 TGGTGGAAACGGTGCTGAAG 60.818 55.000 0.00 0.00 0.00 3.02
2962 7656 9.783256 AAAGAGGTTTGTACAAAAATATATCGC 57.217 29.630 22.14 6.90 31.33 4.58
2963 7657 7.927048 AGAGGTTTGTACAAAAATATATCGCC 58.073 34.615 22.14 14.99 31.33 5.54
2967 7661 6.870971 TTGTACAAAAATATATCGCCCTCC 57.129 37.500 5.64 0.00 0.00 4.30
2981 7676 1.137697 CCCTCCCCACCTAATACCAC 58.862 60.000 0.00 0.00 0.00 4.16
3013 7709 7.047891 TGCATATTACTCTAACCTGAACTTGG 58.952 38.462 0.00 0.00 0.00 3.61
3103 7803 1.668826 TGTTATCCCCTGACTTGCCT 58.331 50.000 0.00 0.00 0.00 4.75
3200 7900 2.364842 AGGGCCACATCTCGCTCT 60.365 61.111 6.18 0.00 0.00 4.09
3308 8008 6.653320 TGTAAAAGTTCAGGTAAAGATCGCAT 59.347 34.615 0.00 0.00 0.00 4.73
3343 8043 8.327941 TCCATGCTCTAATCAATGTATTAAGC 57.672 34.615 0.00 0.00 32.31 3.09
3358 8062 1.358725 TAAGCGAGAATGGCACGTGC 61.359 55.000 32.15 32.15 44.88 5.34
3545 8249 3.206150 CCAATGTCCTAACAGATTCCCG 58.794 50.000 0.00 0.00 39.20 5.14
3548 8252 0.831307 GTCCTAACAGATTCCCGGCT 59.169 55.000 0.00 0.00 0.00 5.52
3599 8438 6.929606 ACATAGTGACTTAGAAACACCTGAAC 59.070 38.462 0.00 0.00 35.47 3.18
3654 8493 4.247380 CTGGAGAGCGATGGGGCC 62.247 72.222 0.00 0.00 0.00 5.80
3699 8538 3.971702 GTGAAGCTGGGGGCCTGT 61.972 66.667 0.84 0.00 43.05 4.00
3846 8685 8.907829 ACCAGAGGAGTATATGACATGATAAT 57.092 34.615 0.00 0.00 0.00 1.28
3848 8687 8.975295 CCAGAGGAGTATATGACATGATAATCA 58.025 37.037 0.00 0.00 0.00 2.57
3859 8698 6.118852 TGACATGATAATCAAAACCGATGGA 58.881 36.000 0.00 0.00 0.00 3.41
3864 8703 7.822161 TGATAATCAAAACCGATGGATCATT 57.178 32.000 0.00 0.00 29.82 2.57
3902 8747 2.113777 GGGGGAGGTAGGAGATGGAATA 59.886 54.545 0.00 0.00 0.00 1.75
4010 8867 0.541392 CATGGCAGCAGTAGGGTACA 59.459 55.000 0.00 0.00 0.00 2.90
4020 8877 3.674997 CAGTAGGGTACAGTTGTTGCAT 58.325 45.455 0.00 0.00 0.00 3.96
4046 8903 1.092348 GATGATTCTGCTGCAGTGCA 58.908 50.000 27.24 18.58 41.05 4.57
4112 8974 1.143620 GCAAAGCACCAGCAACCAA 59.856 52.632 0.00 0.00 45.49 3.67
4120 8982 2.161609 GCACCAGCAACCAATGTAGTAC 59.838 50.000 0.00 0.00 41.58 2.73
4124 8986 5.645929 CACCAGCAACCAATGTAGTACATTA 59.354 40.000 24.54 0.00 46.22 1.90
4130 8992 6.038161 GCAACCAATGTAGTACATTATGCAGA 59.962 38.462 31.19 5.19 46.22 4.26
4131 8993 7.633621 CAACCAATGTAGTACATTATGCAGAG 58.366 38.462 24.54 12.55 46.22 3.35
4132 8994 6.889198 ACCAATGTAGTACATTATGCAGAGT 58.111 36.000 24.54 12.36 46.22 3.24
4133 8995 7.338710 ACCAATGTAGTACATTATGCAGAGTT 58.661 34.615 24.54 0.94 46.22 3.01
4135 8997 7.712639 CCAATGTAGTACATTATGCAGAGTTCT 59.287 37.037 24.54 0.00 46.22 3.01
4136 8998 9.102757 CAATGTAGTACATTATGCAGAGTTCTT 57.897 33.333 24.54 0.00 46.22 2.52
4137 8999 9.672673 AATGTAGTACATTATGCAGAGTTCTTT 57.327 29.630 23.95 0.00 46.11 2.52
4138 9000 8.703604 TGTAGTACATTATGCAGAGTTCTTTC 57.296 34.615 0.00 0.00 0.00 2.62
4139 9001 7.764443 TGTAGTACATTATGCAGAGTTCTTTCC 59.236 37.037 0.00 0.00 0.00 3.13
4140 9002 6.711277 AGTACATTATGCAGAGTTCTTTCCA 58.289 36.000 0.00 0.00 0.00 3.53
4141 9003 6.820656 AGTACATTATGCAGAGTTCTTTCCAG 59.179 38.462 0.00 0.00 0.00 3.86
4142 9004 4.946157 ACATTATGCAGAGTTCTTTCCAGG 59.054 41.667 0.00 0.00 0.00 4.45
4144 9006 5.441718 TTATGCAGAGTTCTTTCCAGGAT 57.558 39.130 0.00 0.00 0.00 3.24
4145 9007 3.795688 TGCAGAGTTCTTTCCAGGATT 57.204 42.857 0.00 0.00 0.00 3.01
4146 9008 4.104383 TGCAGAGTTCTTTCCAGGATTT 57.896 40.909 0.00 0.00 0.00 2.17
4148 9010 3.823304 GCAGAGTTCTTTCCAGGATTTGT 59.177 43.478 0.00 0.00 0.00 2.83
4149 9011 4.320788 GCAGAGTTCTTTCCAGGATTTGTG 60.321 45.833 0.00 0.00 0.00 3.33
4151 9013 5.532406 CAGAGTTCTTTCCAGGATTTGTGAA 59.468 40.000 0.00 0.00 0.00 3.18
4152 9014 6.208204 CAGAGTTCTTTCCAGGATTTGTGAAT 59.792 38.462 0.00 0.00 0.00 2.57
4153 9015 6.779539 AGAGTTCTTTCCAGGATTTGTGAATT 59.220 34.615 0.00 0.00 0.00 2.17
4154 9016 6.752168 AGTTCTTTCCAGGATTTGTGAATTG 58.248 36.000 0.00 0.00 0.00 2.32
4155 9017 6.324770 AGTTCTTTCCAGGATTTGTGAATTGT 59.675 34.615 0.00 0.00 0.00 2.71
4156 9018 6.331369 TCTTTCCAGGATTTGTGAATTGTC 57.669 37.500 0.00 0.00 0.00 3.18
4157 9019 5.243730 TCTTTCCAGGATTTGTGAATTGTCC 59.756 40.000 0.00 0.00 0.00 4.02
4160 9022 4.523943 TCCAGGATTTGTGAATTGTCCAAG 59.476 41.667 0.00 0.00 0.00 3.61
4161 9023 4.240096 CAGGATTTGTGAATTGTCCAAGC 58.760 43.478 0.00 0.00 0.00 4.01
4164 9045 3.731652 TTTGTGAATTGTCCAAGCCAG 57.268 42.857 0.00 0.00 0.00 4.85
4171 9052 1.967319 TTGTCCAAGCCAGTGAAGAC 58.033 50.000 0.00 0.00 0.00 3.01
4180 9061 1.815408 GCCAGTGAAGACCTCTTGCAA 60.815 52.381 0.00 0.00 36.11 4.08
4186 9067 3.569701 GTGAAGACCTCTTGCAATTTGGA 59.430 43.478 16.19 3.24 36.11 3.53
4189 9070 3.359950 AGACCTCTTGCAATTTGGATCC 58.640 45.455 16.19 4.20 0.00 3.36
4201 9082 2.781681 TTGGATCCCTCGGTTTCTTC 57.218 50.000 9.90 0.00 0.00 2.87
4202 9083 0.909623 TGGATCCCTCGGTTTCTTCC 59.090 55.000 9.90 0.00 0.00 3.46
4203 9084 0.909623 GGATCCCTCGGTTTCTTCCA 59.090 55.000 0.00 0.00 0.00 3.53
4208 9089 4.644163 TCCCTCGGTTTCTTCCATTTTA 57.356 40.909 0.00 0.00 0.00 1.52
4213 9094 6.811665 CCCTCGGTTTCTTCCATTTTATTTTC 59.188 38.462 0.00 0.00 0.00 2.29
4215 9096 6.383415 TCGGTTTCTTCCATTTTATTTTCCG 58.617 36.000 0.00 0.00 0.00 4.30
4216 9097 6.207025 TCGGTTTCTTCCATTTTATTTTCCGA 59.793 34.615 0.00 0.00 38.55 4.55
4217 9098 7.033185 CGGTTTCTTCCATTTTATTTTCCGAT 58.967 34.615 0.00 0.00 34.76 4.18
4218 9099 8.185505 CGGTTTCTTCCATTTTATTTTCCGATA 58.814 33.333 0.00 0.00 34.76 2.92
4251 9133 8.341173 GGACTATTTTCTTGATGCATAACTCTG 58.659 37.037 0.00 0.00 0.00 3.35
4265 9147 2.514205 ACTCTGGCATTTGCAACAAC 57.486 45.000 0.00 0.00 44.36 3.32
4270 9152 2.477375 CTGGCATTTGCAACAACACATC 59.523 45.455 0.00 0.00 44.36 3.06
4271 9153 2.159000 TGGCATTTGCAACAACACATCA 60.159 40.909 0.00 0.00 44.36 3.07
4272 9154 2.477375 GGCATTTGCAACAACACATCAG 59.523 45.455 0.00 0.00 44.36 2.90
4273 9155 2.096614 GCATTTGCAACAACACATCAGC 60.097 45.455 0.00 0.00 41.59 4.26
4274 9156 3.386486 CATTTGCAACAACACATCAGCT 58.614 40.909 0.00 0.00 0.00 4.24
4275 9157 2.495409 TTGCAACAACACATCAGCTG 57.505 45.000 7.63 7.63 0.00 4.24
4276 9158 1.391577 TGCAACAACACATCAGCTGT 58.608 45.000 14.67 0.00 39.20 4.40
4294 9176 3.462021 CTGTGAGGCTAGGCAGAATAAC 58.538 50.000 19.70 7.45 0.00 1.89
4321 9462 1.274728 TGAAATGGGTCCAAATTGGCG 59.725 47.619 7.24 0.00 37.47 5.69
4326 9467 1.069358 TGGGTCCAAATTGGCGAAAAC 59.931 47.619 7.24 0.00 37.47 2.43
4365 9506 4.223320 TCCTTGAAAGTGAAAATCGCAC 57.777 40.909 0.00 0.00 36.53 5.34
4371 9512 2.693797 AGTGAAAATCGCACAAGCAG 57.306 45.000 0.00 0.00 42.27 4.24
4372 9513 1.267806 AGTGAAAATCGCACAAGCAGG 59.732 47.619 0.00 0.00 42.27 4.85
4375 9516 1.000274 GAAAATCGCACAAGCAGGGTT 60.000 47.619 0.00 0.00 42.27 4.11
4376 9517 1.039856 AAATCGCACAAGCAGGGTTT 58.960 45.000 0.00 0.00 42.27 3.27
4402 9543 6.266103 GGAAATATGAAGAATGCATTCTCCCA 59.734 38.462 35.67 32.47 45.83 4.37
4404 9545 4.996788 ATGAAGAATGCATTCTCCCAAC 57.003 40.909 35.67 24.27 45.83 3.77
4415 9556 7.243604 TGCATTCTCCCAACAAAAAGATAAT 57.756 32.000 0.00 0.00 0.00 1.28
4550 9702 1.613836 CAATGCCCTTATCTCTGGCC 58.386 55.000 0.00 0.00 44.72 5.36
4583 9735 5.861251 TCATTCACGCCAAATAAACAACATC 59.139 36.000 0.00 0.00 0.00 3.06
4584 9736 4.837896 TCACGCCAAATAAACAACATCA 57.162 36.364 0.00 0.00 0.00 3.07
4607 9759 1.696063 AGCAGCCATGAACTGTTGTT 58.304 45.000 14.70 0.00 37.47 2.83
4640 9805 7.089770 TGAAGCACATGTACAAAGTAACAAA 57.910 32.000 0.00 0.00 0.00 2.83
4645 9810 6.196353 GCACATGTACAAAGTAACAAACACAG 59.804 38.462 0.00 0.00 0.00 3.66
4656 9821 1.768870 ACAAACACAGTGGTAGCTCCT 59.231 47.619 5.31 0.00 37.07 3.69
4751 9916 4.520492 GGCTTCTTCAGATTTCAAAGGTGA 59.480 41.667 0.00 0.00 0.00 4.02
4800 9966 9.484806 AGAAAGACAAAATAATCCAATCCATCT 57.515 29.630 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.751479 ACAGATCCATAGTGCGCAATA 57.249 42.857 20.84 20.84 0.00 1.90
1 2 2.627515 ACAGATCCATAGTGCGCAAT 57.372 45.000 17.03 17.03 0.00 3.56
2 3 2.401583 AACAGATCCATAGTGCGCAA 57.598 45.000 14.00 0.00 0.00 4.85
4 5 2.009774 ACAAACAGATCCATAGTGCGC 58.990 47.619 0.00 0.00 0.00 6.09
6 7 5.297776 AGCATTACAAACAGATCCATAGTGC 59.702 40.000 0.00 0.00 0.00 4.40
7 8 6.932356 AGCATTACAAACAGATCCATAGTG 57.068 37.500 0.00 0.00 0.00 2.74
8 9 8.486210 TCTAAGCATTACAAACAGATCCATAGT 58.514 33.333 0.00 0.00 0.00 2.12
11 12 7.112122 TGTCTAAGCATTACAAACAGATCCAT 58.888 34.615 0.00 0.00 0.00 3.41
12 13 6.472016 TGTCTAAGCATTACAAACAGATCCA 58.528 36.000 0.00 0.00 0.00 3.41
13 14 6.595716 ACTGTCTAAGCATTACAAACAGATCC 59.404 38.462 6.61 0.00 0.00 3.36
15 16 8.531982 TCTACTGTCTAAGCATTACAAACAGAT 58.468 33.333 6.61 0.00 0.00 2.90
16 17 7.813148 GTCTACTGTCTAAGCATTACAAACAGA 59.187 37.037 6.61 0.00 0.00 3.41
17 18 7.598869 TGTCTACTGTCTAAGCATTACAAACAG 59.401 37.037 0.00 0.00 0.00 3.16
18 19 7.384115 GTGTCTACTGTCTAAGCATTACAAACA 59.616 37.037 0.00 0.00 0.00 2.83
19 20 7.148623 GGTGTCTACTGTCTAAGCATTACAAAC 60.149 40.741 0.00 0.00 0.00 2.93
20 21 6.872020 GGTGTCTACTGTCTAAGCATTACAAA 59.128 38.462 0.00 0.00 0.00 2.83
22 23 5.105473 GGGTGTCTACTGTCTAAGCATTACA 60.105 44.000 0.00 0.00 0.00 2.41
24 25 5.020795 TGGGTGTCTACTGTCTAAGCATTA 58.979 41.667 0.00 0.00 0.00 1.90
25 26 3.838317 TGGGTGTCTACTGTCTAAGCATT 59.162 43.478 0.00 0.00 0.00 3.56
26 27 3.441101 TGGGTGTCTACTGTCTAAGCAT 58.559 45.455 0.00 0.00 0.00 3.79
27 28 2.884320 TGGGTGTCTACTGTCTAAGCA 58.116 47.619 0.00 0.00 0.00 3.91
28 29 3.851098 CTTGGGTGTCTACTGTCTAAGC 58.149 50.000 0.00 0.00 0.00 3.09
29 30 3.258372 TGCTTGGGTGTCTACTGTCTAAG 59.742 47.826 0.00 0.00 0.00 2.18
30 31 3.236047 TGCTTGGGTGTCTACTGTCTAA 58.764 45.455 0.00 0.00 0.00 2.10
32 33 1.717032 TGCTTGGGTGTCTACTGTCT 58.283 50.000 0.00 0.00 0.00 3.41
33 34 2.770164 ATGCTTGGGTGTCTACTGTC 57.230 50.000 0.00 0.00 0.00 3.51
35 36 2.236146 TGGTATGCTTGGGTGTCTACTG 59.764 50.000 0.00 0.00 0.00 2.74
36 37 2.546899 TGGTATGCTTGGGTGTCTACT 58.453 47.619 0.00 0.00 0.00 2.57
37 38 3.118408 TGATGGTATGCTTGGGTGTCTAC 60.118 47.826 0.00 0.00 0.00 2.59
38 39 3.111484 TGATGGTATGCTTGGGTGTCTA 58.889 45.455 0.00 0.00 0.00 2.59
39 40 1.915489 TGATGGTATGCTTGGGTGTCT 59.085 47.619 0.00 0.00 0.00 3.41
41 42 1.354031 TGTGATGGTATGCTTGGGTGT 59.646 47.619 0.00 0.00 0.00 4.16
90 382 6.597672 TGAACTAGCAGAGAAAAACAACAAGA 59.402 34.615 0.00 0.00 0.00 3.02
92 384 6.374333 ACTGAACTAGCAGAGAAAAACAACAA 59.626 34.615 4.57 0.00 39.20 2.83
164 457 1.920734 AACCATGGCCGATGCAGGTA 61.921 55.000 13.04 0.00 37.59 3.08
199 496 1.282447 GGAAAGGAAAGGAGAGACCCC 59.718 57.143 0.00 0.00 40.05 4.95
202 505 2.640332 ACAGGGAAAGGAAAGGAGAGAC 59.360 50.000 0.00 0.00 0.00 3.36
264 571 1.283029 AGAGCAGGCAAATCTTAGGCA 59.717 47.619 0.00 0.00 0.00 4.75
275 582 0.675837 CAAGCTTAGCAGAGCAGGCA 60.676 55.000 7.07 0.00 45.12 4.75
330 1859 1.383248 CAGGGAGGGAGGTAGGGTG 60.383 68.421 0.00 0.00 0.00 4.61
459 4305 8.572884 TCCACTTATCTAAGTAGTCTAGGGTA 57.427 38.462 2.43 0.00 44.19 3.69
723 4577 8.540388 AGGTATCTGTATTGTTACACATTGAGT 58.460 33.333 0.00 0.00 34.62 3.41
759 4613 1.290203 GGCACGTGTCATCCATAGTG 58.710 55.000 16.80 0.00 37.51 2.74
889 4746 4.754114 AGAGAAACAGCTTGATGAAGTGTC 59.246 41.667 0.00 0.00 0.00 3.67
903 4760 6.420008 CCTGCAAAGAAAAATCAGAGAAACAG 59.580 38.462 0.00 0.00 0.00 3.16
918 4777 2.224257 GGCATTTGTTCCCTGCAAAGAA 60.224 45.455 0.00 0.00 38.91 2.52
1314 5185 3.006967 GCAGGTCGGGTATGATATGAACT 59.993 47.826 0.00 0.00 0.00 3.01
2058 6745 5.742453 GCACATGAGAAATTTCTGCATACAG 59.258 40.000 25.12 17.54 45.95 2.74
2087 6774 9.454859 AAAAATTAAACCACAAACAGAATGGAA 57.545 25.926 0.00 0.00 43.62 3.53
2151 6838 5.056480 TGCTAGTTCACCATGCATATGTAC 58.944 41.667 0.00 5.37 32.21 2.90
2152 6839 5.289083 TGCTAGTTCACCATGCATATGTA 57.711 39.130 0.00 0.00 32.21 2.29
2153 6840 4.155063 TGCTAGTTCACCATGCATATGT 57.845 40.909 0.00 0.00 32.21 2.29
2154 6841 5.472478 AGAATGCTAGTTCACCATGCATATG 59.528 40.000 0.00 0.70 42.57 1.78
2182 6869 4.262377 CCATACAGGACCTCATTAGAGCAG 60.262 50.000 0.00 0.00 39.19 4.24
2284 6973 8.782144 GGCATTTCCACTGAAAATGAAAAATTA 58.218 29.630 4.98 0.00 43.37 1.40
2368 7061 5.224135 GTTTAACGCCCAGCTTCATTTAAA 58.776 37.500 0.00 0.00 0.00 1.52
2822 7516 3.365767 GCTAAAAGGTTGCTGCTCTTCAG 60.366 47.826 0.00 5.12 45.62 3.02
2827 7521 1.135944 GTCGCTAAAAGGTTGCTGCTC 60.136 52.381 0.00 0.00 0.00 4.26
2890 7584 4.980434 GCGCTTATATCCAGTTCGAAACTA 59.020 41.667 0.00 0.00 40.46 2.24
2958 7652 0.192566 TATTAGGTGGGGAGGGCGAT 59.807 55.000 0.00 0.00 0.00 4.58
2961 7655 0.696485 TGGTATTAGGTGGGGAGGGC 60.696 60.000 0.00 0.00 0.00 5.19
2962 7656 1.137697 GTGGTATTAGGTGGGGAGGG 58.862 60.000 0.00 0.00 0.00 4.30
2963 7657 1.768870 CAGTGGTATTAGGTGGGGAGG 59.231 57.143 0.00 0.00 0.00 4.30
2967 7661 2.710096 CACCAGTGGTATTAGGTGGG 57.290 55.000 16.22 0.00 45.96 4.61
2981 7676 6.648310 CAGGTTAGAGTAATATGCATCACCAG 59.352 42.308 0.19 0.00 0.00 4.00
3013 7709 4.074259 TCATCACCTGCAATGCCATATAC 58.926 43.478 1.53 0.00 0.00 1.47
3103 7803 2.560105 CTCATCACCGATGGCAGATAGA 59.440 50.000 4.24 0.00 40.15 1.98
3200 7900 0.947180 GGCTTCACAACCGACGCTAA 60.947 55.000 0.00 0.00 31.24 3.09
3268 7968 8.664798 TGAACTTTTACATAGAAATGTCCATCG 58.335 33.333 0.00 0.00 42.92 3.84
3304 8004 0.027194 CATGGAGTTTCTGCGATGCG 59.973 55.000 0.00 0.00 0.00 4.73
3308 8008 0.610174 AGAGCATGGAGTTTCTGCGA 59.390 50.000 0.00 0.00 40.78 5.10
3343 8043 2.792290 CTCGCACGTGCCATTCTCG 61.792 63.158 33.23 18.04 37.91 4.04
3358 8062 3.854666 ACAGAGTTTCATGTGATCCTCG 58.145 45.455 0.00 0.00 0.00 4.63
3417 8121 2.568546 ACACATGGGATAGGTCCTGA 57.431 50.000 0.00 0.00 44.44 3.86
3531 8235 1.209504 TCAAGCCGGGAATCTGTTAGG 59.790 52.381 2.18 0.00 0.00 2.69
3548 8252 2.046700 GACCCATCGGCCGTTCAA 60.047 61.111 27.15 5.72 0.00 2.69
3567 8271 7.008447 GTGTTTCTAAGTCACTATGTCATCGAC 59.992 40.741 0.00 0.00 0.00 4.20
3570 8409 7.276658 CAGGTGTTTCTAAGTCACTATGTCATC 59.723 40.741 0.00 0.00 33.30 2.92
3599 8438 1.893808 AGGCTCACAAACCTGCACG 60.894 57.895 0.00 0.00 34.07 5.34
3624 8463 1.598962 CTCCAGCCATATGTGCCCG 60.599 63.158 11.22 4.99 0.00 6.13
3681 8520 3.655211 CAGGCCCCCAGCTTCACT 61.655 66.667 0.00 0.00 43.05 3.41
3699 8538 4.735132 GGCTGCTGGTACGCGTCA 62.735 66.667 18.63 7.95 0.00 4.35
3777 8616 2.015227 CTCTCTCTTCCCAGCGAGCC 62.015 65.000 0.00 0.00 32.59 4.70
3846 8685 4.588899 AGACAATGATCCATCGGTTTTGA 58.411 39.130 0.00 0.00 0.00 2.69
3848 8687 7.645058 AATTAGACAATGATCCATCGGTTTT 57.355 32.000 0.00 0.00 0.00 2.43
3859 8698 5.125417 CCCGACCACAAAATTAGACAATGAT 59.875 40.000 0.00 0.00 0.00 2.45
3864 8703 2.553466 CCCCCGACCACAAAATTAGACA 60.553 50.000 0.00 0.00 0.00 3.41
3902 8747 5.650266 TCATGTGTACAAACAAACACCTTCT 59.350 36.000 0.00 0.00 44.29 2.85
4020 8877 2.235402 TGCAGCAGAATCATCAGTCAGA 59.765 45.455 0.00 0.00 0.00 3.27
4046 8903 2.629656 GCAACATTCGGCCAGCACT 61.630 57.895 2.24 0.00 0.00 4.40
4056 8918 3.737774 GCTTCCAACTCTTTGCAACATTC 59.262 43.478 0.00 0.00 0.00 2.67
4112 8974 9.319143 GAAAGAACTCTGCATAATGTACTACAT 57.681 33.333 0.00 0.00 41.31 2.29
4120 8982 5.188434 TCCTGGAAAGAACTCTGCATAATG 58.812 41.667 0.00 0.00 0.00 1.90
4124 8986 4.313020 AATCCTGGAAAGAACTCTGCAT 57.687 40.909 0.00 0.00 0.00 3.96
4130 8992 6.324770 ACAATTCACAAATCCTGGAAAGAACT 59.675 34.615 0.00 0.00 0.00 3.01
4131 8993 6.515832 ACAATTCACAAATCCTGGAAAGAAC 58.484 36.000 0.00 0.00 0.00 3.01
4132 8994 6.239289 GGACAATTCACAAATCCTGGAAAGAA 60.239 38.462 0.00 1.51 0.00 2.52
4133 8995 5.243730 GGACAATTCACAAATCCTGGAAAGA 59.756 40.000 0.00 0.00 0.00 2.52
4135 8997 4.898265 TGGACAATTCACAAATCCTGGAAA 59.102 37.500 0.00 0.00 0.00 3.13
4136 8998 4.478203 TGGACAATTCACAAATCCTGGAA 58.522 39.130 0.00 0.00 0.00 3.53
4137 8999 4.111255 TGGACAATTCACAAATCCTGGA 57.889 40.909 0.00 0.00 0.00 3.86
4138 9000 4.813027 CTTGGACAATTCACAAATCCTGG 58.187 43.478 0.00 0.00 0.00 4.45
4139 9001 4.240096 GCTTGGACAATTCACAAATCCTG 58.760 43.478 0.00 0.00 0.00 3.86
4140 9002 3.259123 GGCTTGGACAATTCACAAATCCT 59.741 43.478 0.00 0.00 0.00 3.24
4141 9003 3.006752 TGGCTTGGACAATTCACAAATCC 59.993 43.478 0.00 0.00 0.00 3.01
4142 9004 4.240096 CTGGCTTGGACAATTCACAAATC 58.760 43.478 0.00 0.00 0.00 2.17
4144 9006 3.030291 ACTGGCTTGGACAATTCACAAA 58.970 40.909 0.00 0.00 0.00 2.83
4145 9007 2.361757 CACTGGCTTGGACAATTCACAA 59.638 45.455 0.00 0.00 0.00 3.33
4146 9008 1.955778 CACTGGCTTGGACAATTCACA 59.044 47.619 0.00 0.00 0.00 3.58
4148 9010 2.655090 TCACTGGCTTGGACAATTCA 57.345 45.000 0.00 0.00 0.00 2.57
4149 9011 3.057946 GTCTTCACTGGCTTGGACAATTC 60.058 47.826 0.00 0.00 0.00 2.17
4151 9013 2.508526 GTCTTCACTGGCTTGGACAAT 58.491 47.619 0.00 0.00 0.00 2.71
4152 9014 1.476833 GGTCTTCACTGGCTTGGACAA 60.477 52.381 0.00 0.00 0.00 3.18
4153 9015 0.108585 GGTCTTCACTGGCTTGGACA 59.891 55.000 0.00 0.00 0.00 4.02
4154 9016 0.398318 AGGTCTTCACTGGCTTGGAC 59.602 55.000 0.00 0.00 0.00 4.02
4155 9017 0.687354 GAGGTCTTCACTGGCTTGGA 59.313 55.000 0.00 0.00 0.00 3.53
4156 9018 0.689623 AGAGGTCTTCACTGGCTTGG 59.310 55.000 0.00 0.00 0.00 3.61
4157 9019 2.149578 CAAGAGGTCTTCACTGGCTTG 58.850 52.381 0.00 0.00 33.11 4.01
4160 9022 0.250467 TGCAAGAGGTCTTCACTGGC 60.250 55.000 0.00 0.00 33.11 4.85
4161 9023 2.260844 TTGCAAGAGGTCTTCACTGG 57.739 50.000 0.00 0.00 33.11 4.00
4164 9045 3.569701 TCCAAATTGCAAGAGGTCTTCAC 59.430 43.478 4.94 0.00 33.11 3.18
4171 9052 2.692041 GAGGGATCCAAATTGCAAGAGG 59.308 50.000 15.23 6.77 0.00 3.69
4180 9061 3.621558 GAAGAAACCGAGGGATCCAAAT 58.378 45.455 15.23 0.00 0.00 2.32
4186 9067 3.739401 AAATGGAAGAAACCGAGGGAT 57.261 42.857 0.00 0.00 0.00 3.85
4189 9070 6.811665 GGAAAATAAAATGGAAGAAACCGAGG 59.188 38.462 0.00 0.00 0.00 4.63
4213 9094 9.929180 TCAAGAAAATAGTCCATTATCTATCGG 57.071 33.333 0.00 0.00 0.00 4.18
4218 9099 8.985315 TGCATCAAGAAAATAGTCCATTATCT 57.015 30.769 0.00 0.00 0.00 1.98
4235 9116 4.913335 AATGCCAGAGTTATGCATCAAG 57.087 40.909 0.19 0.00 44.49 3.02
4247 9129 2.129607 GTGTTGTTGCAAATGCCAGAG 58.870 47.619 0.00 0.00 41.18 3.35
4251 9133 2.477375 CTGATGTGTTGTTGCAAATGCC 59.523 45.455 0.00 0.00 41.18 4.40
4256 9138 1.750206 ACAGCTGATGTGTTGTTGCAA 59.250 42.857 23.35 0.00 41.91 4.08
4270 9152 1.153409 CTGCCTAGCCTCACAGCTG 60.153 63.158 13.48 13.48 44.67 4.24
4272 9154 0.179936 ATTCTGCCTAGCCTCACAGC 59.820 55.000 0.00 0.00 0.00 4.40
4273 9155 3.133721 AGTTATTCTGCCTAGCCTCACAG 59.866 47.826 0.00 0.00 0.00 3.66
4274 9156 3.107601 AGTTATTCTGCCTAGCCTCACA 58.892 45.455 0.00 0.00 0.00 3.58
4275 9157 3.133003 TCAGTTATTCTGCCTAGCCTCAC 59.867 47.826 0.00 0.00 43.32 3.51
4276 9158 3.133003 GTCAGTTATTCTGCCTAGCCTCA 59.867 47.826 0.00 0.00 43.32 3.86
4277 9159 3.493524 GGTCAGTTATTCTGCCTAGCCTC 60.494 52.174 0.00 0.00 43.32 4.70
4278 9160 2.436173 GGTCAGTTATTCTGCCTAGCCT 59.564 50.000 0.00 0.00 43.32 4.58
4279 9161 2.170607 TGGTCAGTTATTCTGCCTAGCC 59.829 50.000 0.00 0.00 43.32 3.93
4280 9162 3.543680 TGGTCAGTTATTCTGCCTAGC 57.456 47.619 0.00 0.00 43.32 3.42
4281 9163 5.282055 TCATGGTCAGTTATTCTGCCTAG 57.718 43.478 0.00 0.00 43.32 3.02
4283 9165 4.574674 TTCATGGTCAGTTATTCTGCCT 57.425 40.909 0.00 0.00 43.32 4.75
4294 9176 8.744465 CCAATTTGGACCCATTTCATGGTCAG 62.744 46.154 10.03 0.00 44.28 3.51
4321 9462 3.721466 CGGTACACGTGCTGTTTTC 57.279 52.632 17.22 0.00 37.93 2.29
4365 9506 5.185635 TCTTCATATTTCCAAACCCTGCTTG 59.814 40.000 0.00 0.00 0.00 4.01
4371 9512 5.976458 TGCATTCTTCATATTTCCAAACCC 58.024 37.500 0.00 0.00 0.00 4.11
4372 9513 7.983484 AGAATGCATTCTTCATATTTCCAAACC 59.017 33.333 31.78 5.19 44.28 3.27
4375 9516 7.201938 GGGAGAATGCATTCTTCATATTTCCAA 60.202 37.037 37.09 0.00 46.47 3.53
4376 9517 6.266103 GGGAGAATGCATTCTTCATATTTCCA 59.734 38.462 37.09 0.00 46.47 3.53
4503 9644 8.806177 TTTGCAAATATCATGCTTGCTATTAG 57.194 30.769 8.05 0.00 44.57 1.73
4504 9645 9.033481 GTTTTGCAAATATCATGCTTGCTATTA 57.967 29.630 13.65 0.00 44.57 0.98
4550 9702 3.389741 GCGTGAATGAAGCCAGTTG 57.610 52.632 0.00 0.00 0.00 3.16
4583 9735 4.577693 ACAACAGTTCATGGCTGCTATATG 59.422 41.667 15.04 2.28 37.47 1.78
4584 9736 4.785301 ACAACAGTTCATGGCTGCTATAT 58.215 39.130 15.04 0.00 37.47 0.86
4640 9805 0.178932 TCCAGGAGCTACCACTGTGT 60.179 55.000 7.08 0.00 42.04 3.72
4645 9810 2.736347 TCTAGTTCCAGGAGCTACCAC 58.264 52.381 8.94 0.00 42.04 4.16
4656 9821 4.081087 GCTGGTCTTATGGTTCTAGTTCCA 60.081 45.833 10.09 10.09 38.14 3.53
4704 9869 2.814336 GGTGGCATCTTCTCGTTCTTTT 59.186 45.455 0.00 0.00 0.00 2.27
4751 9916 1.995542 TCCCTTGATCTTGAGGCCTTT 59.004 47.619 6.77 0.00 0.00 3.11
4800 9966 3.250744 CGATTAGCTCGGTGACAGAAAA 58.749 45.455 0.00 0.00 43.82 2.29


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

AutoCloner maintained by Alex Coulton.