Multiple sequence alignment - TraesCS4D01G225100

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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 TraesCS4D01G225100 chr4D 100.000 8084 0 0 1 8084 382321423 382329506 0.000000e+00 14929.0
1 TraesCS4D01G225100 chr4B 94.929 4555 152 24 3594 8084 469507185 469511724 0.000000e+00 7059.0
2 TraesCS4D01G225100 chr4B 95.002 2181 67 18 1316 3477 469504509 469506666 0.000000e+00 3386.0
3 TraesCS4D01G225100 chr4B 91.940 670 39 5 618 1281 469503848 469504508 0.000000e+00 924.0
4 TraesCS4D01G225100 chr4B 91.564 569 42 6 4 570 469502794 469503358 0.000000e+00 780.0
5 TraesCS4D01G225100 chr4B 97.581 124 3 0 3478 3601 469506696 469506819 6.360000e-51 213.0
6 TraesCS4D01G225100 chr4B 86.207 87 7 5 3001 3086 164765106 164765024 1.120000e-13 89.8
7 TraesCS4D01G225100 chr4A 94.614 2692 94 15 821 3475 81280735 81278058 0.000000e+00 4120.0
8 TraesCS4D01G225100 chr4A 95.484 2126 81 9 3478 5591 81278026 81275904 0.000000e+00 3380.0
9 TraesCS4D01G225100 chr4A 96.181 864 27 2 5579 6442 81275051 81274194 0.000000e+00 1408.0
10 TraesCS4D01G225100 chr4A 95.692 882 21 6 7218 8084 81273369 81272490 0.000000e+00 1402.0
11 TraesCS4D01G225100 chr4A 97.333 600 14 2 6576 7174 81273977 81273379 0.000000e+00 1018.0
12 TraesCS4D01G225100 chr4A 89.417 463 40 3 109 570 81281665 81281211 7.040000e-160 575.0
13 TraesCS4D01G225100 chr4A 97.093 172 3 2 6470 6639 81274130 81273959 1.030000e-73 289.0
14 TraesCS4D01G225100 chr4A 89.450 218 18 2 614 826 81281206 81280989 3.720000e-68 270.0
15 TraesCS4D01G225100 chr4A 92.708 96 7 0 4 99 81313513 81313418 1.090000e-28 139.0
16 TraesCS4D01G225100 chr4A 86.777 121 14 2 2207 2327 111905478 111905360 5.090000e-27 134.0
17 TraesCS4D01G225100 chr4A 84.034 119 16 2 2206 2321 616236976 616236858 2.380000e-20 111.0
18 TraesCS4D01G225100 chr7A 85.938 192 23 4 7 196 719594701 719594512 1.380000e-47 202.0
19 TraesCS4D01G225100 chr7A 83.193 119 17 3 1891 2009 48103189 48103074 1.110000e-18 106.0
20 TraesCS4D01G225100 chr3A 80.000 215 41 2 5088 5301 323407184 323406971 3.020000e-34 158.0
21 TraesCS4D01G225100 chr3A 84.685 111 11 6 2214 2321 80090600 80090493 1.110000e-18 106.0
22 TraesCS4D01G225100 chr3D 79.535 215 42 2 5088 5301 236647917 236648130 1.410000e-32 152.0
23 TraesCS4D01G225100 chr3D 92.857 70 5 0 3017 3086 5653682 5653751 1.440000e-17 102.0
24 TraesCS4D01G225100 chr3D 93.056 72 2 3 3016 3087 564316162 564316230 1.440000e-17 102.0
25 TraesCS4D01G225100 chr2B 86.066 122 13 2 1899 2020 216462915 216462798 2.370000e-25 128.0
26 TraesCS4D01G225100 chr2A 88.182 110 10 1 1900 2009 559118516 559118410 2.370000e-25 128.0
27 TraesCS4D01G225100 chr2D 87.273 110 11 1 1900 2009 619562449 619562343 1.100000e-23 122.0
28 TraesCS4D01G225100 chr5D 84.746 118 16 1 2206 2321 552050261 552050144 5.130000e-22 117.0
29 TraesCS4D01G225100 chr5D 94.118 68 3 1 3019 3086 41139969 41140035 1.440000e-17 102.0
30 TraesCS4D01G225100 chr1D 85.981 107 15 0 2215 2321 103682729 103682835 1.840000e-21 115.0
31 TraesCS4D01G225100 chr1D 85.849 106 15 0 2216 2321 283041261 283041366 6.630000e-21 113.0
32 TraesCS4D01G225100 chr1B 85.455 110 13 2 1900 2009 160325324 160325218 2.380000e-20 111.0
33 TraesCS4D01G225100 chr1A 85.455 110 13 2 1900 2009 106228181 106228075 2.380000e-20 111.0
34 TraesCS4D01G225100 chr1A 93.151 73 5 0 3016 3088 60284310 60284382 3.090000e-19 108.0
35 TraesCS4D01G225100 chr6B 85.185 108 13 3 2207 2313 343027025 343027130 3.090000e-19 108.0
36 TraesCS4D01G225100 chr6A 84.685 111 14 2 1899 2009 18460719 18460826 3.090000e-19 108.0
37 TraesCS4D01G225100 chr6A 87.805 82 8 2 3008 3087 460643354 460643435 2.400000e-15 95.3
38 TraesCS4D01G225100 chr7D 89.873 79 8 0 108 186 627428201 627428123 1.440000e-17 102.0
39 TraesCS4D01G225100 chr7D 92.857 70 3 2 3019 3088 89726677 89726744 5.160000e-17 100.0


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 TraesCS4D01G225100 chr4D 382321423 382329506 8083 False 14929.00 14929 100.0000 1 8084 1 chr4D.!!$F1 8083
1 TraesCS4D01G225100 chr4B 469502794 469511724 8930 False 2472.40 7059 94.2032 4 8084 5 chr4B.!!$F1 8080
2 TraesCS4D01G225100 chr4A 81272490 81281665 9175 True 1557.75 4120 94.4080 109 8084 8 chr4A.!!$R4 7975

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
657 1101 0.178955 GACCCTCCTAGCCCCTAGAC 60.179 65.0 0.00 0.00 36.26 2.59 F
666 1110 0.553819 AGCCCCTAGACTCGTCATCT 59.446 55.0 0.00 0.00 0.00 2.90 F
669 1113 1.231221 CCCTAGACTCGTCATCTCCG 58.769 60.0 0.00 0.00 0.00 4.63 F
2292 3018 0.318784 GCGTCGCTTAGGTATCAGGG 60.319 60.0 10.68 0.00 0.00 4.45 F
3453 4215 0.107654 GCCATTCCTACCAACGCTCT 60.108 55.0 0.00 0.00 0.00 4.09 F
4914 6097 0.108804 ACGTAGGACACATCGCCTTG 60.109 55.0 0.00 0.00 35.73 3.61 F
5122 6305 0.320771 CACTGGCCGCTAGAACAAGT 60.321 55.0 11.19 0.00 0.00 3.16 F
6280 8328 0.328592 GAAGGGGTTGGAGGTCCTTC 59.671 60.0 5.38 5.38 45.42 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 2263 0.250234 CTCATCTTCCGTGCCTCCAA 59.750 55.000 0.00 0.00 0.00 3.53 R
2272 2998 0.318784 CCTGATACCTAAGCGACGCC 60.319 60.000 17.79 0.00 0.00 5.68 R
2324 3050 0.800683 TAGCATGTGTAGTGCGTCGC 60.801 55.000 11.10 11.10 46.86 5.19 R
3746 4910 0.321122 CAGGAGCCCAGTGTCAAGAC 60.321 60.000 0.00 0.00 0.00 3.01 R
5020 6203 1.072852 TGCATGTAGCTGGTGCACA 59.927 52.632 20.43 3.92 43.30 4.57 R
6658 8791 0.329261 TCAGCAATCAGGGTTCAGGG 59.671 55.000 0.00 0.00 0.00 4.45 R
6999 9132 3.521126 ACAATGAGCCCTGTGAAGTATCT 59.479 43.478 0.00 0.00 0.00 1.98 R
7178 9320 0.254747 AATGTGGGTCCATGGTACCG 59.745 55.000 20.46 0.00 37.93 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
29 30 2.483491 CTCTCTTCTCTGCAAGGCAAAC 59.517 50.000 0.00 0.00 38.41 2.93
33 34 3.005050 TCTTCTCTGCAAGGCAAACATTG 59.995 43.478 0.00 0.00 38.41 2.82
79 80 7.197017 TCTCGTTAGAATGTAGCATTCTTCTC 58.803 38.462 23.74 15.19 39.01 2.87
85 86 7.043961 AGAATGTAGCATTCTTCTCGATACA 57.956 36.000 16.04 0.00 34.99 2.29
86 87 7.665690 AGAATGTAGCATTCTTCTCGATACAT 58.334 34.615 16.04 0.00 34.99 2.29
95 96 7.652727 CATTCTTCTCGATACATCAGGAACTA 58.347 38.462 0.00 0.00 36.02 2.24
99 100 8.353684 TCTTCTCGATACATCAGGAACTATTTC 58.646 37.037 0.00 0.00 36.02 2.17
101 102 7.877003 TCTCGATACATCAGGAACTATTTCTC 58.123 38.462 0.00 0.00 36.02 2.87
102 103 7.721842 TCTCGATACATCAGGAACTATTTCTCT 59.278 37.037 0.00 0.00 36.02 3.10
103 104 8.919777 TCGATACATCAGGAACTATTTCTCTA 57.080 34.615 0.00 0.00 36.02 2.43
105 106 9.566530 CGATACATCAGGAACTATTTCTCTATG 57.433 37.037 0.00 0.00 36.02 2.23
106 107 9.364989 GATACATCAGGAACTATTTCTCTATGC 57.635 37.037 0.00 0.00 36.02 3.14
226 227 6.317140 TCAGCAGCTTCATAATCGATTTCTTT 59.683 34.615 17.19 0.00 0.00 2.52
268 269 0.247736 GCAGACCATGTCCGAGTCTT 59.752 55.000 0.00 0.00 38.80 3.01
269 270 1.476891 GCAGACCATGTCCGAGTCTTA 59.523 52.381 0.00 0.00 38.80 2.10
313 314 6.509418 TTACTATCCAAATGCCACTTTGTC 57.491 37.500 0.00 0.00 34.90 3.18
346 347 5.829986 TCCCATGAAAAATCTCTCCATGAA 58.170 37.500 0.00 0.00 37.41 2.57
347 348 5.889853 TCCCATGAAAAATCTCTCCATGAAG 59.110 40.000 0.00 0.00 37.41 3.02
370 371 5.186215 AGAATCATGCATGTGAACAAATCCA 59.814 36.000 25.43 2.66 0.00 3.41
371 372 5.607939 ATCATGCATGTGAACAAATCCAT 57.392 34.783 25.43 5.02 0.00 3.41
390 391 8.985315 AATCCATGTTCTCAGCTAATTCATTA 57.015 30.769 0.00 0.00 0.00 1.90
496 498 4.236935 CAATGCTAGCAACAAATCCGTTT 58.763 39.130 23.54 4.14 0.00 3.60
559 561 0.999406 GATCACGTGCTGTATTGCGT 59.001 50.000 11.67 0.00 38.14 5.24
586 588 4.489771 CCTTCCTGGCGGCGGATT 62.490 66.667 21.09 0.00 0.00 3.01
588 590 2.749839 TTCCTGGCGGCGGATTTG 60.750 61.111 21.09 1.96 0.00 2.32
589 591 4.794648 TCCTGGCGGCGGATTTGG 62.795 66.667 21.09 6.97 0.00 3.28
609 611 3.257561 CGTTGGCGGCGATCTGAG 61.258 66.667 12.98 0.00 0.00 3.35
610 612 2.184322 GTTGGCGGCGATCTGAGA 59.816 61.111 12.98 0.00 0.00 3.27
612 614 3.723235 TTGGCGGCGATCTGAGAGC 62.723 63.158 12.98 0.00 0.00 4.09
621 1065 1.743321 GATCTGAGAGCCGACCCCTG 61.743 65.000 0.00 0.00 0.00 4.45
657 1101 0.178955 GACCCTCCTAGCCCCTAGAC 60.179 65.000 0.00 0.00 36.26 2.59
666 1110 0.553819 AGCCCCTAGACTCGTCATCT 59.446 55.000 0.00 0.00 0.00 2.90
669 1113 1.231221 CCCTAGACTCGTCATCTCCG 58.769 60.000 0.00 0.00 0.00 4.63
701 1146 3.774959 CTCGCCGGTCGCTATGCTT 62.775 63.158 12.56 0.00 38.27 3.91
709 1154 4.495422 CCGGTCGCTATGCTTATAGAAAT 58.505 43.478 0.00 0.00 0.00 2.17
714 1159 5.856986 GTCGCTATGCTTATAGAAATCACGA 59.143 40.000 0.00 0.00 0.00 4.35
720 1165 4.649674 TGCTTATAGAAATCACGAGAGGGT 59.350 41.667 0.00 0.00 34.73 4.34
738 1183 3.947834 AGGGTCTAAATGCAAAATCTCCG 59.052 43.478 0.00 0.00 0.00 4.63
743 1188 1.821216 AATGCAAAATCTCCGACCGT 58.179 45.000 0.00 0.00 0.00 4.83
758 1207 2.202570 CGTTCGGGTCTGCCTACG 60.203 66.667 0.00 0.00 34.45 3.51
860 1568 3.831715 GCGTTTTGCAAGTAGGAAGAT 57.168 42.857 0.00 0.00 45.45 2.40
913 1621 6.042208 GGGCTGATACTGTATTTAACTCCTCT 59.958 42.308 1.22 0.00 0.00 3.69
921 1629 5.651530 TGTATTTAACTCCTCTTCTCGCTG 58.348 41.667 0.00 0.00 0.00 5.18
966 1674 3.078837 CTCGCTCTATCTCTTCCCCTAC 58.921 54.545 0.00 0.00 0.00 3.18
987 1697 1.699730 CCCAGAAACCCGAAAACCTT 58.300 50.000 0.00 0.00 0.00 3.50
1161 1872 1.705997 AAACCCTCACCTTCCGCTGT 61.706 55.000 0.00 0.00 0.00 4.40
1283 1994 5.057149 TGAACTTGAGCTGTTTTCTCCTAC 58.943 41.667 0.00 0.00 0.00 3.18
1305 2016 9.492973 CCTACATCTTGAAACATTTGGAATTTT 57.507 29.630 0.00 0.00 0.00 1.82
1430 2145 2.420129 GCTAGCGGGGAGAAGAAAATCA 60.420 50.000 0.00 0.00 0.00 2.57
1548 2263 2.544277 CGATCATTTGCAATGGCGGAAT 60.544 45.455 0.00 0.00 45.35 3.01
1655 2370 3.297134 TGGATCTTACATTTCTGCCCC 57.703 47.619 0.00 0.00 0.00 5.80
1826 2541 7.923414 AGAATAATTGAGGCGTTAGAACTTT 57.077 32.000 0.00 0.00 0.00 2.66
1990 2705 2.060326 TCCGTTTGAGCGTCAACTAG 57.940 50.000 0.76 0.00 35.89 2.57
2292 3018 0.318784 GCGTCGCTTAGGTATCAGGG 60.319 60.000 10.68 0.00 0.00 4.45
2324 3050 2.295349 TCGCCTTAGGTCGCCTTATAAG 59.705 50.000 5.43 5.43 34.61 1.73
2343 3069 0.800683 GCGACGCACTACACATGCTA 60.801 55.000 16.42 0.00 41.10 3.49
2344 3070 1.191944 CGACGCACTACACATGCTAG 58.808 55.000 0.00 0.00 41.10 3.42
2345 3071 1.202143 CGACGCACTACACATGCTAGA 60.202 52.381 0.00 0.00 41.10 2.43
2471 3198 6.092955 ACATTGCTATGCCTATTTTGATGG 57.907 37.500 8.11 0.00 35.03 3.51
2551 3279 4.337555 GCTAATGGAATCACATTGCTCACT 59.662 41.667 0.00 0.00 40.97 3.41
2785 3515 2.698855 AACAGTATCTGATTGCGCCT 57.301 45.000 4.18 0.00 35.18 5.52
2971 3701 4.942483 TCGTCTTGGGTTTAACACAAAGAA 59.058 37.500 13.99 0.31 41.55 2.52
2974 3704 6.854381 CGTCTTGGGTTTAACACAAAGAATAC 59.146 38.462 13.99 6.66 41.55 1.89
3152 3891 7.094162 ACGATGACTATATGTTACCATCTCCTG 60.094 40.741 0.00 0.00 30.04 3.86
3167 3906 1.698532 CTCCTGCAATCTGGATAGCCT 59.301 52.381 0.00 0.00 39.23 4.58
3453 4215 0.107654 GCCATTCCTACCAACGCTCT 60.108 55.000 0.00 0.00 0.00 4.09
3668 4832 5.632347 GCAGTGTCTTTGATTTCATTTCTGG 59.368 40.000 0.00 0.00 0.00 3.86
3736 4900 2.370189 GGGGGAGAACATACTGATGAGG 59.630 54.545 0.00 0.00 36.48 3.86
3746 4910 7.440556 AGAACATACTGATGAGGATCGAAATTG 59.559 37.037 0.00 0.00 38.61 2.32
3766 4930 1.673665 CTTGACACTGGGCTCCTGC 60.674 63.158 0.00 0.00 38.76 4.85
3867 5031 5.684704 TCTCAGATGTTTGAAAAGTGAGGT 58.315 37.500 0.00 0.00 32.52 3.85
3907 5071 6.151049 ACCCTGAGAACCCATAACTATACAT 58.849 40.000 0.00 0.00 0.00 2.29
4016 5180 1.903860 TGCCGTAAGTCTATTGTGGGT 59.096 47.619 0.00 0.00 0.00 4.51
4076 5242 3.316308 CAGCCTATGCCCACTTTATGTTC 59.684 47.826 0.00 0.00 38.69 3.18
4107 5273 2.818432 CCCAAATGGAGAGAGCATATGC 59.182 50.000 20.36 20.36 38.33 3.14
4241 5411 1.318785 CAGTTCGCTCTTCACGATTCG 59.681 52.381 4.14 4.14 39.65 3.34
4254 5424 1.553248 ACGATTCGGGTTCAGGATTCA 59.447 47.619 11.29 0.00 0.00 2.57
4388 5558 3.775202 CGATGACTCGGATTCTGAACTT 58.225 45.455 0.00 0.00 41.27 2.66
4395 5565 8.155821 TGACTCGGATTCTGAACTTAGTATAG 57.844 38.462 0.00 0.00 0.00 1.31
4398 5568 6.069331 TCGGATTCTGAACTTAGTATAGGCT 58.931 40.000 0.00 0.00 0.00 4.58
4624 5805 5.347620 TGACCCTTTGTGCGTATATAAGT 57.652 39.130 0.00 0.00 0.00 2.24
4727 5908 0.187117 TTCACTTTGGGGCCACATGA 59.813 50.000 9.55 7.22 0.00 3.07
4832 6014 2.505819 TCAGGCCTTCCTAATTCCAGAC 59.494 50.000 0.00 0.00 41.93 3.51
4836 6018 1.571919 CTTCCTAATTCCAGACCGCG 58.428 55.000 0.00 0.00 0.00 6.46
4849 6031 1.870055 GACCGCGAACTGGTGGACTA 61.870 60.000 8.23 0.00 40.63 2.59
4914 6097 0.108804 ACGTAGGACACATCGCCTTG 60.109 55.000 0.00 0.00 35.73 3.61
4917 6100 1.264749 TAGGACACATCGCCTTGCCT 61.265 55.000 0.00 0.00 35.73 4.75
5068 6251 2.608988 AGTAGCTGCTGCCCACCT 60.609 61.111 13.43 0.24 40.80 4.00
5122 6305 0.320771 CACTGGCCGCTAGAACAAGT 60.321 55.000 11.19 0.00 0.00 3.16
5201 6384 1.533731 TGTTTTGAGTTCGGCGAATCC 59.466 47.619 26.42 19.43 0.00 3.01
5259 6442 4.960469 ACCCCGTTCTAGATAAATCTGTCA 59.040 41.667 2.66 0.00 37.76 3.58
5319 6502 7.198390 GCAACTATGATTCACATTAGCATGTT 58.802 34.615 0.00 0.00 41.16 2.71
5366 6549 2.943033 CCGAAGTGGACAAGTTTTGACT 59.057 45.455 0.00 0.00 42.00 3.41
5367 6550 3.242739 CCGAAGTGGACAAGTTTTGACTG 60.243 47.826 0.00 0.00 42.00 3.51
5373 6556 4.157840 GTGGACAAGTTTTGACTGGACTTT 59.842 41.667 0.00 0.00 31.63 2.66
5424 6607 2.195567 GCAAGCAGCCAAGGACACA 61.196 57.895 0.00 0.00 37.23 3.72
5431 6614 2.875672 GCAGCCAAGGACACATTCACTA 60.876 50.000 0.00 0.00 0.00 2.74
5480 6663 3.748048 CCAAGCATAGGACCATACATTCG 59.252 47.826 0.00 0.00 0.00 3.34
5491 6674 3.386078 ACCATACATTCGAGCATCAGACT 59.614 43.478 0.00 0.00 33.17 3.24
5649 7696 8.028938 ACATCTGCAACACCAAATTAATAGAAC 58.971 33.333 0.00 0.00 0.00 3.01
5824 7871 6.594159 CGACTTGATAAAGGACTTACCAACAT 59.406 38.462 0.00 0.00 42.04 2.71
5934 7982 2.067365 TGAAGCCTAGATCTACCGCA 57.933 50.000 15.95 5.50 0.00 5.69
6030 8078 2.360801 TGAGTTTAAAAGCACACTGGGC 59.639 45.455 0.00 0.00 0.00 5.36
6276 8324 2.041755 AGAATTGAAGGGGTTGGAGGTC 59.958 50.000 0.00 0.00 0.00 3.85
6280 8328 0.328592 GAAGGGGTTGGAGGTCCTTC 59.671 60.000 5.38 5.38 45.42 3.46
6587 8673 1.726853 CCACTCCCTTCTTAAGTGCG 58.273 55.000 1.63 0.00 39.23 5.34
6618 8704 7.492994 GCTTAGAGTCCTGTTGGTTTTATCTAG 59.507 40.741 0.00 0.00 34.23 2.43
6629 8715 6.417191 TGGTTTTATCTAGCGCTTGTTAAG 57.583 37.500 18.68 6.50 0.00 1.85
6658 8791 5.371115 TGCACTATTCTTAACTTTGTGCC 57.629 39.130 11.73 0.00 45.72 5.01
6723 8856 3.447586 GGTAGCACTGTTCCTGATCTGTA 59.552 47.826 0.00 0.00 0.00 2.74
6724 8857 4.081642 GGTAGCACTGTTCCTGATCTGTAA 60.082 45.833 0.00 0.00 0.00 2.41
6999 9132 4.264253 TGGTCTAATTCTTCGTCGAGGTA 58.736 43.478 4.85 0.00 0.00 3.08
7019 9161 4.101741 GGTAGATACTTCACAGGGCTCATT 59.898 45.833 0.00 0.00 0.00 2.57
7257 9399 3.626217 GGTTTTAAGATCGGTTAGGCAGG 59.374 47.826 0.00 0.00 0.00 4.85
7449 9598 5.936372 TCTGTTCAATCTGAATCCTGACAAG 59.064 40.000 0.00 0.00 38.79 3.16
7513 9663 2.383298 AAGTTTGACGCGTGACATTG 57.617 45.000 20.70 0.00 0.00 2.82
7540 9690 4.332543 TCATTTGCGCCTAAGAAGTGTATG 59.667 41.667 4.18 0.00 0.00 2.39
7776 9926 5.302568 TCGGGAGGTTATACATTGTATTCGT 59.697 40.000 14.23 9.68 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.040936 TGCAGAGAAGAGAGAGTTACCT 57.959 45.455 0.00 0.00 0.00 3.08
1 2 4.381505 CCTTGCAGAGAAGAGAGAGTTACC 60.382 50.000 0.00 0.00 0.00 2.85
2 3 4.743493 CCTTGCAGAGAAGAGAGAGTTAC 58.257 47.826 0.00 0.00 0.00 2.50
3 4 3.194542 GCCTTGCAGAGAAGAGAGAGTTA 59.805 47.826 0.00 0.00 0.00 2.24
4 5 2.028203 GCCTTGCAGAGAAGAGAGAGTT 60.028 50.000 0.00 0.00 0.00 3.01
5 6 1.550072 GCCTTGCAGAGAAGAGAGAGT 59.450 52.381 0.00 0.00 0.00 3.24
6 7 1.549620 TGCCTTGCAGAGAAGAGAGAG 59.450 52.381 0.00 0.00 33.32 3.20
79 80 9.566530 CATAGAGAAATAGTTCCTGATGTATCG 57.433 37.037 0.00 0.00 33.92 2.92
85 86 6.219473 CACGCATAGAGAAATAGTTCCTGAT 58.781 40.000 0.00 0.00 33.92 2.90
86 87 5.592054 CACGCATAGAGAAATAGTTCCTGA 58.408 41.667 0.00 0.00 33.92 3.86
95 96 3.126831 GCTAGTGCACGCATAGAGAAAT 58.873 45.455 12.01 0.00 39.41 2.17
99 100 3.648528 TGCTAGTGCACGCATAGAG 57.351 52.632 14.43 6.47 45.31 2.43
120 121 9.967451 TGTCATAAACAATAAGGGACTGATTTA 57.033 29.630 0.00 0.00 35.62 1.40
141 142 6.295462 CCTTGGATTTTGGAGATTGTTGTCAT 60.295 38.462 0.00 0.00 0.00 3.06
182 183 0.179056 ACGGAGTGAGGTTGTGTTGG 60.179 55.000 0.00 0.00 42.51 3.77
226 227 4.865925 CGGAAGTAACCAACGACATTATCA 59.134 41.667 0.00 0.00 0.00 2.15
294 295 3.509575 GTGGACAAAGTGGCATTTGGATA 59.490 43.478 19.37 8.07 43.10 2.59
295 296 2.299867 GTGGACAAAGTGGCATTTGGAT 59.700 45.455 19.37 6.39 43.10 3.41
346 347 5.186215 TGGATTTGTTCACATGCATGATTCT 59.814 36.000 32.75 7.78 0.00 2.40
347 348 5.412640 TGGATTTGTTCACATGCATGATTC 58.587 37.500 32.75 18.29 0.00 2.52
416 417 5.765576 TGGCTAGGGTTTGTGAAGTTATA 57.234 39.130 0.00 0.00 0.00 0.98
480 482 6.757010 TGCTTTTTAAAACGGATTTGTTGCTA 59.243 30.769 0.00 0.00 32.27 3.49
496 498 5.255710 TGCTGCAAAGTAGTGCTTTTTAA 57.744 34.783 3.16 0.00 44.41 1.52
548 550 2.025359 GAGTCGCCACGCAATACAGC 62.025 60.000 0.00 0.00 0.00 4.40
570 572 2.438434 AAATCCGCCGCCAGGAAG 60.438 61.111 0.00 0.00 41.69 3.46
571 573 2.749839 CAAATCCGCCGCCAGGAA 60.750 61.111 0.00 0.00 41.69 3.36
572 574 4.794648 CCAAATCCGCCGCCAGGA 62.795 66.667 0.00 0.00 42.69 3.86
592 594 3.257561 CTCAGATCGCCGCCAACG 61.258 66.667 0.00 0.00 39.67 4.10
593 595 1.880340 CTCTCAGATCGCCGCCAAC 60.880 63.158 0.00 0.00 0.00 3.77
594 596 2.496341 CTCTCAGATCGCCGCCAA 59.504 61.111 0.00 0.00 0.00 4.52
595 597 4.212913 GCTCTCAGATCGCCGCCA 62.213 66.667 0.00 0.00 0.00 5.69
599 601 2.026879 GTCGGCTCTCAGATCGCC 59.973 66.667 0.00 0.00 40.40 5.54
600 602 2.026879 GGTCGGCTCTCAGATCGC 59.973 66.667 0.00 0.00 0.00 4.58
601 603 2.725008 GGGTCGGCTCTCAGATCG 59.275 66.667 0.00 0.00 0.00 3.69
602 604 1.456705 AGGGGTCGGCTCTCAGATC 60.457 63.158 0.00 0.00 0.00 2.75
603 605 1.760086 CAGGGGTCGGCTCTCAGAT 60.760 63.158 0.00 0.00 0.00 2.90
605 607 4.154347 GCAGGGGTCGGCTCTCAG 62.154 72.222 0.00 0.00 0.00 3.35
607 609 4.154347 CTGCAGGGGTCGGCTCTC 62.154 72.222 5.57 0.00 35.13 3.20
639 1083 0.631085 AGTCTAGGGGCTAGGAGGGT 60.631 60.000 0.00 0.00 35.03 4.34
647 1091 0.553819 AGATGACGAGTCTAGGGGCT 59.446 55.000 4.78 0.00 0.00 5.19
657 1101 0.523546 CGGTTGACGGAGATGACGAG 60.524 60.000 0.00 0.00 39.42 4.18
666 1110 0.815734 GAGGAAGATCGGTTGACGGA 59.184 55.000 0.00 0.00 44.45 4.69
669 1113 0.806492 GGCGAGGAAGATCGGTTGAC 60.806 60.000 0.00 0.00 42.94 3.18
701 1146 8.577296 CATTTAGACCCTCTCGTGATTTCTATA 58.423 37.037 0.00 0.00 0.00 1.31
709 1154 2.176045 TGCATTTAGACCCTCTCGTGA 58.824 47.619 0.00 0.00 0.00 4.35
714 1159 5.196695 GGAGATTTTGCATTTAGACCCTCT 58.803 41.667 0.00 0.00 0.00 3.69
720 1165 3.621268 CGGTCGGAGATTTTGCATTTAGA 59.379 43.478 0.00 0.00 40.67 2.10
743 1188 2.642254 CCACGTAGGCAGACCCGAA 61.642 63.158 0.00 0.00 39.21 4.30
816 1265 2.037251 ACTTTGCACACTGTACTCGGAT 59.963 45.455 0.00 0.00 0.00 4.18
852 1560 7.099764 CACTGAAGCTCACTTAAATCTTCCTA 58.900 38.462 0.00 0.00 35.82 2.94
857 1565 4.006319 GCCACTGAAGCTCACTTAAATCT 58.994 43.478 0.00 0.00 35.82 2.40
860 1568 3.207265 TGCCACTGAAGCTCACTTAAA 57.793 42.857 0.00 0.00 35.82 1.52
913 1621 1.829222 CTTTAGGGGGTACAGCGAGAA 59.171 52.381 0.00 0.00 0.00 2.87
921 1629 6.386342 AGAGGATAGTTTTCTTTAGGGGGTAC 59.614 42.308 0.00 0.00 0.00 3.34
966 1674 1.183030 GGTTTTCGGGTTTCTGGGGG 61.183 60.000 0.00 0.00 0.00 5.40
1283 1994 7.588488 GTGCAAAATTCCAAATGTTTCAAGATG 59.412 33.333 0.00 0.00 0.00 2.90
1305 2016 7.229228 CGCAAAAGTAGTTATACTATGTGCA 57.771 36.000 13.62 0.00 41.54 4.57
1390 2101 1.459539 TAGCTCCGGAATCCTGGGG 60.460 63.158 5.23 7.77 42.53 4.96
1402 2117 2.203509 TCCCCGCTAGCTAGCTCC 60.204 66.667 36.02 12.79 46.85 4.70
1430 2145 4.087907 GTCGAGGGGATTATAGCTTACCT 58.912 47.826 0.00 0.00 0.00 3.08
1548 2263 0.250234 CTCATCTTCCGTGCCTCCAA 59.750 55.000 0.00 0.00 0.00 3.53
1636 2351 3.297134 TGGGGCAGAAATGTAAGATCC 57.703 47.619 0.00 0.00 0.00 3.36
1655 2370 7.650504 ACAAGCATAGCAAATAAGCATATGTTG 59.349 33.333 4.29 1.78 36.85 3.33
1861 2576 7.984617 AGAAATCATTAGCTCAGACTTACTTCC 59.015 37.037 0.00 0.00 0.00 3.46
1990 2705 8.884424 AGTTTCTTACTTCTTCCGTCCGGAAC 62.884 46.154 16.71 0.00 40.77 3.62
2034 2749 7.174946 AGTTTCTTTTAAGCCAAATCTCATCGA 59.825 33.333 0.00 0.00 0.00 3.59
2035 2750 7.308435 AGTTTCTTTTAAGCCAAATCTCATCG 58.692 34.615 0.00 0.00 0.00 3.84
2222 2937 4.711949 CTGCCAGGGCGACTTGCT 62.712 66.667 5.74 0.00 45.51 3.91
2272 2998 0.318784 CCTGATACCTAAGCGACGCC 60.319 60.000 17.79 0.00 0.00 5.68
2273 2999 0.318784 CCCTGATACCTAAGCGACGC 60.319 60.000 13.03 13.03 0.00 5.19
2274 3000 1.030457 ACCCTGATACCTAAGCGACG 58.970 55.000 0.00 0.00 0.00 5.12
2275 3001 1.068741 CCACCCTGATACCTAAGCGAC 59.931 57.143 0.00 0.00 0.00 5.19
2276 3002 1.342674 ACCACCCTGATACCTAAGCGA 60.343 52.381 0.00 0.00 0.00 4.93
2277 3003 1.120530 ACCACCCTGATACCTAAGCG 58.879 55.000 0.00 0.00 0.00 4.68
2278 3004 2.421529 CCAACCACCCTGATACCTAAGC 60.422 54.545 0.00 0.00 0.00 3.09
2279 3005 2.844348 ACCAACCACCCTGATACCTAAG 59.156 50.000 0.00 0.00 0.00 2.18
2280 3006 2.574369 CACCAACCACCCTGATACCTAA 59.426 50.000 0.00 0.00 0.00 2.69
2281 3007 2.193127 CACCAACCACCCTGATACCTA 58.807 52.381 0.00 0.00 0.00 3.08
2282 3008 0.991920 CACCAACCACCCTGATACCT 59.008 55.000 0.00 0.00 0.00 3.08
2292 3018 1.298859 CTAAGGCGAGCACCAACCAC 61.299 60.000 0.00 0.00 0.00 4.16
2324 3050 0.800683 TAGCATGTGTAGTGCGTCGC 60.801 55.000 11.10 11.10 46.86 5.19
2328 3054 1.524355 GCATCTAGCATGTGTAGTGCG 59.476 52.381 0.00 0.00 46.86 5.34
2349 3076 5.536161 AGATGTCCACTAAAACAGCAATTGT 59.464 36.000 7.40 0.00 43.45 2.71
2471 3198 9.296400 TGAAAGCAACAAATTTGTAGTTTAGTC 57.704 29.630 23.53 14.68 41.31 2.59
2785 3515 5.647658 CCCATAACAGTAAGAACAAGCATGA 59.352 40.000 0.00 0.00 0.00 3.07
2971 3701 4.017808 CCTCTATGCCTAGGTAAGCGTAT 58.982 47.826 11.31 0.00 30.45 3.06
2974 3704 2.490115 CTCCTCTATGCCTAGGTAAGCG 59.510 54.545 11.31 1.86 34.30 4.68
3040 3770 6.701145 AAGAGCGTTTAGATCACTGATCTA 57.299 37.500 20.57 20.57 46.15 1.98
3044 3774 9.464714 GAAATATAAGAGCGTTTAGATCACTGA 57.535 33.333 0.00 0.00 37.82 3.41
3045 3775 9.469807 AGAAATATAAGAGCGTTTAGATCACTG 57.530 33.333 0.00 0.00 37.82 3.66
3152 3891 9.454859 AATTTAAGTATAGGCTATCCAGATTGC 57.545 33.333 10.96 5.63 38.52 3.56
3334 4074 6.169800 TGTCCTACATGAATCATCGTTTTCA 58.830 36.000 0.00 0.00 36.38 2.69
3369 4130 3.319122 AGGAAATTGCAGTGGAACAGAAC 59.681 43.478 0.00 0.00 41.80 3.01
3370 4131 3.565307 AGGAAATTGCAGTGGAACAGAA 58.435 40.909 0.00 0.00 41.80 3.02
3372 4133 2.095567 CGAGGAAATTGCAGTGGAACAG 60.096 50.000 0.00 0.00 41.80 3.16
3453 4215 6.488344 TGTTGTATGCACTTCTATTTTGGACA 59.512 34.615 0.00 0.00 0.00 4.02
3668 4832 7.550551 TCACATATCAACAATTTCAGAGACTCC 59.449 37.037 0.00 0.00 0.00 3.85
3736 4900 4.142816 CCCAGTGTCAAGACAATTTCGATC 60.143 45.833 4.20 0.00 43.77 3.69
3746 4910 0.321122 CAGGAGCCCAGTGTCAAGAC 60.321 60.000 0.00 0.00 0.00 3.01
3766 4930 8.655970 CGATATCTAGATATTAGCTCATCGAGG 58.344 40.741 23.14 0.00 34.36 4.63
3828 4992 6.257411 ACATCTGAGAGAAGCGTAATTGATTG 59.743 38.462 0.00 0.00 0.00 2.67
3867 5031 5.046878 TCTCAGGGTCGCTGTAAGAAAATAA 60.047 40.000 15.83 0.00 34.07 1.40
3907 5071 6.850752 TCCTATTCATCGCATACTCCATAA 57.149 37.500 0.00 0.00 0.00 1.90
3920 5084 8.360390 GGTCCAACCATAAAAATCCTATTCATC 58.640 37.037 0.00 0.00 38.42 2.92
4076 5242 3.048600 TCTCCATTTGGGACCTATGAGG 58.951 50.000 0.00 0.00 42.15 3.86
4241 5411 4.082125 AGTGAATTGTGAATCCTGAACCC 58.918 43.478 0.00 0.00 0.00 4.11
4624 5805 5.645067 CACTGATTCAGGTGCTCATTAAGAA 59.355 40.000 17.66 0.00 35.51 2.52
4727 5908 1.751924 GGATGAGACTAAGCACTCCGT 59.248 52.381 0.00 0.00 32.84 4.69
4832 6014 1.445582 GTAGTCCACCAGTTCGCGG 60.446 63.158 6.13 0.00 0.00 6.46
4836 6018 1.618837 TGCAGAGTAGTCCACCAGTTC 59.381 52.381 0.00 0.00 0.00 3.01
4849 6031 2.353958 CCCTGGTGCATGCAGAGT 59.646 61.111 23.41 0.00 0.00 3.24
4875 6058 1.080995 GGTACTCGCTGCAGCTTCTG 61.081 60.000 34.22 22.38 39.32 3.02
4917 6100 4.159901 TGCATCGCCTCCATCGCA 62.160 61.111 0.00 0.00 0.00 5.10
5020 6203 1.072852 TGCATGTAGCTGGTGCACA 59.927 52.632 20.43 3.92 43.30 4.57
5068 6251 1.359117 GCTCGGCGCAGACATAGTA 59.641 57.895 10.83 0.00 38.92 1.82
5259 6442 1.201429 AGCCACTGAACCCCGATTCT 61.201 55.000 0.00 0.00 0.00 2.40
5329 6512 5.277825 CACTTCGGTTTGCTCAATTTTGTA 58.722 37.500 0.00 0.00 0.00 2.41
5335 6518 1.880027 GTCCACTTCGGTTTGCTCAAT 59.120 47.619 0.00 0.00 35.57 2.57
5366 6549 6.767524 ATTAACAAGTTGTGTCAAAGTCCA 57.232 33.333 9.79 0.00 40.60 4.02
5367 6550 7.254852 TGAATTAACAAGTTGTGTCAAAGTCC 58.745 34.615 9.79 0.00 40.60 3.85
5373 6556 7.766283 TGACATTGAATTAACAAGTTGTGTCA 58.234 30.769 9.79 11.93 40.60 3.58
5424 6607 8.584157 TGGCATGTTTTCAGTTATTTAGTGAAT 58.416 29.630 0.00 0.00 43.80 2.57
5480 6663 2.871022 CACATGCCTTAGTCTGATGCTC 59.129 50.000 0.00 0.00 0.00 4.26
5491 6674 6.264292 ACAACAAATGAGTAACACATGCCTTA 59.736 34.615 0.00 0.00 0.00 2.69
5649 7696 9.442047 GGAAAGTATATTTCATGATGGACCTAG 57.558 37.037 0.00 0.00 0.00 3.02
5824 7871 0.963225 TCAATCCAGTGGACGAACGA 59.037 50.000 15.86 3.87 32.98 3.85
6030 8078 1.344458 CAGACAGAGTTGCTAGCACG 58.656 55.000 19.17 6.33 0.00 5.34
6034 8082 2.759191 TGTTGCAGACAGAGTTGCTAG 58.241 47.619 0.00 0.00 40.87 3.42
6280 8328 8.195436 TGGAGAGGTACATAATCTTAACGAAAG 58.805 37.037 0.00 0.00 36.45 2.62
6587 8673 3.118592 ACCAACAGGACTCTAAGCATAGC 60.119 47.826 0.00 0.00 0.00 2.97
6618 8704 2.415168 TGCATAGTCACTTAACAAGCGC 59.585 45.455 0.00 0.00 0.00 5.92
6629 8715 8.936864 ACAAAGTTAAGAATAGTGCATAGTCAC 58.063 33.333 0.00 0.00 37.24 3.67
6658 8791 0.329261 TCAGCAATCAGGGTTCAGGG 59.671 55.000 0.00 0.00 0.00 4.45
6999 9132 3.521126 ACAATGAGCCCTGTGAAGTATCT 59.479 43.478 0.00 0.00 0.00 1.98
7019 9161 4.885325 GGTTGGTAGAAGGTTTGAGAAACA 59.115 41.667 0.00 0.00 43.15 2.83
7178 9320 0.254747 AATGTGGGTCCATGGTACCG 59.745 55.000 20.46 0.00 37.93 4.02
7190 9332 7.979444 TCTCTTCAAGTTAACTTAATGTGGG 57.021 36.000 20.15 6.87 34.28 4.61
7257 9399 4.589908 AGTGGGAGTACACATTTTGGATC 58.410 43.478 0.00 0.00 43.72 3.36
7306 9448 8.166706 GTGTTCGTCTGAAAATACATCGTAAAT 58.833 33.333 0.00 0.00 35.46 1.40
7307 9449 7.503991 GTGTTCGTCTGAAAATACATCGTAAA 58.496 34.615 0.00 0.00 35.46 2.01
7513 9663 3.375299 ACTTCTTAGGCGCAAATGATGAC 59.625 43.478 10.83 0.00 0.00 3.06
7540 9690 5.067023 CCCTGCTTAGAATGATGAGAAAACC 59.933 44.000 0.00 0.00 0.00 3.27
7730 9880 0.308993 GTCACTGTCAGCTTGGTTGC 59.691 55.000 0.00 0.00 0.00 4.17
7776 9926 1.200760 CCATGACACCTCCCTGTCCA 61.201 60.000 0.00 0.00 40.02 4.02


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

AutoCloner maintained by Alex Coulton.