Multiple sequence alignment - TraesCS5B01G054200

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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 TraesCS5B01G054200 chr5B 100.000 6617 0 0 1 6617 59171153 59164537 0.000000e+00 12220.0
1 TraesCS5B01G054200 chr5B 90.110 91 8 1 2861 2950 59168135 59168045 4.190000e-22 117.0
2 TraesCS5B01G054200 chr5B 90.110 91 8 1 3019 3109 59168293 59168204 4.190000e-22 117.0
3 TraesCS5B01G054200 chr5D 93.666 6631 246 67 7 6570 56460787 56454264 0.000000e+00 9758.0
4 TraesCS5B01G054200 chr5D 85.294 238 26 6 2750 2980 37141031 37140796 3.080000e-58 237.0
5 TraesCS5B01G054200 chr5D 81.818 165 22 4 3019 3176 37140915 37140752 1.500000e-26 132.0
6 TraesCS5B01G054200 chr5D 91.954 87 5 2 2865 2950 56457794 56457709 3.240000e-23 121.0
7 TraesCS5B01G054200 chr5A 93.772 2601 118 21 3341 5911 44986241 44983655 0.000000e+00 3866.0
8 TraesCS5B01G054200 chr5A 92.082 1667 72 25 458 2091 44988849 44987210 0.000000e+00 2292.0
9 TraesCS5B01G054200 chr5A 91.292 712 51 9 2128 2831 44987215 44986507 0.000000e+00 961.0
10 TraesCS5B01G054200 chr5A 86.353 425 40 11 1597 2012 26143552 26143137 1.310000e-121 448.0
11 TraesCS5B01G054200 chr5A 84.286 210 24 7 2008 2211 26142332 26142126 5.230000e-46 196.0
12 TraesCS5B01G054200 chr5A 86.207 174 20 3 2800 2972 26138502 26138332 1.130000e-42 185.0
13 TraesCS5B01G054200 chr5A 91.429 105 7 1 2915 3019 44986510 44986408 6.920000e-30 143.0
14 TraesCS5B01G054200 chr5A 85.714 133 13 4 3079 3206 44986396 44986265 1.160000e-27 135.0
15 TraesCS5B01G054200 chr5A 88.235 102 11 1 1 102 44991183 44991083 3.240000e-23 121.0
16 TraesCS5B01G054200 chr5A 100.000 31 0 0 3079 3109 44986505 44986475 2.580000e-04 58.4
17 TraesCS5B01G054200 chr2A 79.781 183 30 7 1017 1195 708058382 708058561 6.970000e-25 126.0
18 TraesCS5B01G054200 chr2A 87.500 72 6 3 1027 1097 54882373 54882442 5.500000e-11 80.5
19 TraesCS5B01G054200 chr2A 90.323 62 3 3 1036 1095 54955478 54955418 1.980000e-10 78.7
20 TraesCS5B01G054200 chr2D 77.660 188 31 7 1017 1195 568801327 568801512 3.260000e-18 104.0
21 TraesCS5B01G054200 chr2D 77.439 164 25 10 1036 1198 54487979 54487827 3.290000e-13 87.9
22 TraesCS5B01G054200 chr2B 77.301 163 25 10 1036 1197 85177910 85177759 1.180000e-12 86.1
23 TraesCS5B01G054200 chr1D 86.667 60 6 2 1035 1093 359666065 359666007 1.540000e-06 65.8


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 TraesCS5B01G054200 chr5B 59164537 59171153 6616 True 4151.333333 12220 93.406667 1 6617 3 chr5B.!!$R1 6616
1 TraesCS5B01G054200 chr5D 56454264 56460787 6523 True 4939.500000 9758 92.810000 7 6570 2 chr5D.!!$R2 6563
2 TraesCS5B01G054200 chr5A 44983655 44991183 7528 True 1082.342857 3866 91.789143 1 5911 7 chr5A.!!$R2 5910
3 TraesCS5B01G054200 chr5A 26138332 26143552 5220 True 276.333333 448 85.615333 1597 2972 3 chr5A.!!$R1 1375

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
735 2624 0.032130 GGTCGTCTCTTGTGCTGACA 59.968 55.000 0.0 0.0 0.00 3.58 F
984 2887 0.243636 TCTCGTCGCATCAGCAAAGA 59.756 50.000 0.0 0.0 42.27 2.52 F
986 2889 0.243636 TCGTCGCATCAGCAAAGAGA 59.756 50.000 0.0 0.0 42.27 3.10 F
987 2890 1.134995 TCGTCGCATCAGCAAAGAGAT 60.135 47.619 0.0 0.0 42.27 2.75 F
1201 3104 1.209990 TCCCTGGTACGTCTCTCTCTC 59.790 57.143 0.0 0.0 0.00 3.20 F
2957 8779 1.194547 CACCACGACACCTTTCGATTG 59.805 52.381 0.0 0.0 41.78 2.67 F
3453 9309 0.314302 CGTGGTCTGTTCCGTCTCTT 59.686 55.000 0.0 0.0 0.00 2.85 F
4629 10492 0.606130 ACATGGATGCAGTCACGCAA 60.606 50.000 0.0 0.0 46.87 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 3789 1.071471 CCCGTTTCAGACTGCCACT 59.929 57.895 0.00 0.0 0.00 4.00 R
2034 4778 2.550175 AGGTGGGAAAATGATTTGGGG 58.450 47.619 0.00 0.0 0.00 4.96 R
2798 5842 3.704061 TCCCTTTTTCCCACTGAACTTTG 59.296 43.478 0.00 0.0 31.05 2.77 R
2802 8617 4.343814 TCATTTCCCTTTTTCCCACTGAAC 59.656 41.667 0.00 0.0 31.05 3.18 R
3050 8874 0.173708 ACGCTGAAGATCTCCGGTTC 59.826 55.000 0.00 0.0 0.00 3.62 R
4626 10489 2.095263 TGTTTTAGAGGAGCGCATTTGC 60.095 45.455 11.47 0.0 37.78 3.68 R
5262 11128 1.748122 CATGAGAGGTGGCAGTGGC 60.748 63.158 10.30 10.3 40.13 5.01 R
6176 12060 0.168128 GCAACCACGCAACATAGTCC 59.832 55.000 0.00 0.0 0.00 3.85 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
38 39 8.227119 GGACAAAATTTATTGCATTACAACCAC 58.773 33.333 0.00 0.00 42.27 4.16
120 150 2.684001 TAAGTGCCATTCTGTACCCG 57.316 50.000 0.00 0.00 0.00 5.28
155 185 4.025040 AGTGCTGTCAATTTGGAGATCA 57.975 40.909 0.00 0.00 0.00 2.92
364 562 9.682465 AAAGAAACTTCTACTTTACCAGAAAGT 57.318 29.630 7.74 7.74 42.53 2.66
394 592 7.633193 TCTCCTAGAGAAACAAACTAGCTAG 57.367 40.000 19.44 19.44 35.59 3.42
529 2413 3.189910 CACACATTGACAAGTGGATCCAG 59.810 47.826 16.81 6.28 39.99 3.86
586 2470 5.473504 TCAGCCTTTTTCAGTTCCACTTATC 59.526 40.000 0.00 0.00 0.00 1.75
612 2496 3.774842 TGATATTCCTTTTTGCCCCCT 57.225 42.857 0.00 0.00 0.00 4.79
728 2617 2.915659 TGGCCGGTCGTCTCTTGT 60.916 61.111 0.00 0.00 0.00 3.16
735 2624 0.032130 GGTCGTCTCTTGTGCTGACA 59.968 55.000 0.00 0.00 0.00 3.58
761 2650 2.573462 AGCTGCTCCTCTTATTTGTGGA 59.427 45.455 0.00 0.00 0.00 4.02
905 2797 1.903404 CAAGCACAACTCCACCCCC 60.903 63.158 0.00 0.00 0.00 5.40
930 2822 1.733360 CTCTCTCTCTTGCTTGCTTGC 59.267 52.381 0.00 0.00 0.00 4.01
933 2825 1.593296 CTCTCTTGCTTGCTTGCCCC 61.593 60.000 0.00 0.00 0.00 5.80
936 2828 2.837291 TTGCTTGCTTGCCCCGTT 60.837 55.556 0.00 0.00 0.00 4.44
938 2830 4.056125 GCTTGCTTGCCCCGTTCC 62.056 66.667 0.00 0.00 0.00 3.62
939 2831 3.737172 CTTGCTTGCCCCGTTCCG 61.737 66.667 0.00 0.00 0.00 4.30
969 2864 0.803117 TACTGCGTGTTCCTCTCTCG 59.197 55.000 0.00 0.00 0.00 4.04
984 2887 0.243636 TCTCGTCGCATCAGCAAAGA 59.756 50.000 0.00 0.00 42.27 2.52
985 2888 0.644331 CTCGTCGCATCAGCAAAGAG 59.356 55.000 0.00 0.00 42.27 2.85
986 2889 0.243636 TCGTCGCATCAGCAAAGAGA 59.756 50.000 0.00 0.00 42.27 3.10
987 2890 1.134995 TCGTCGCATCAGCAAAGAGAT 60.135 47.619 0.00 0.00 42.27 2.75
991 2894 3.735240 GTCGCATCAGCAAAGAGATAGAG 59.265 47.826 0.00 0.00 42.27 2.43
1201 3104 1.209990 TCCCTGGTACGTCTCTCTCTC 59.790 57.143 0.00 0.00 0.00 3.20
1202 3105 1.210967 CCCTGGTACGTCTCTCTCTCT 59.789 57.143 0.00 0.00 0.00 3.10
1355 3264 2.996621 CGGTGGAGAGAGAAAATGTGTC 59.003 50.000 0.00 0.00 0.00 3.67
1619 3534 6.893583 TCTTTCTCCCTCATAGAAATCCAAG 58.106 40.000 0.00 0.00 41.00 3.61
1676 3595 6.366604 GGAAACCGTCTTTGAAGTTTGAAAAA 59.633 34.615 0.00 0.00 32.80 1.94
1721 3641 4.688413 GGAGTACTCTTTGAAGCTTCACAG 59.312 45.833 28.97 28.97 36.83 3.66
2034 4778 2.783135 TGTCCTTCACAATTCCAGCTC 58.217 47.619 0.00 0.00 29.30 4.09
2126 4875 3.066369 TGATCTCTAAGCTTACGTGCG 57.934 47.619 0.86 0.00 38.13 5.34
2141 4890 8.534778 AGCTTACGTGCGTATATTTTTAGTAAC 58.465 33.333 0.00 0.00 38.13 2.50
2255 5004 7.134815 GCTGAGCACCATGTTATACTTTTATG 58.865 38.462 0.00 0.00 0.00 1.90
2256 5005 7.026631 TGAGCACCATGTTATACTTTTATGC 57.973 36.000 0.00 0.00 0.00 3.14
2293 5042 3.209152 ACCTTTGATCTAGCTAGGGGGTA 59.791 47.826 20.58 0.96 0.00 3.69
2294 5043 4.232091 CCTTTGATCTAGCTAGGGGGTAA 58.768 47.826 20.58 8.13 0.00 2.85
2551 5592 5.460646 ACAAGACAAATAATGCTTGTTCCG 58.539 37.500 0.00 0.00 45.57 4.30
2553 5594 4.331968 AGACAAATAATGCTTGTTCCGGA 58.668 39.130 0.00 0.00 37.14 5.14
2592 5634 8.289618 TGAGACGATGTGAGGAAAATTTTAAAG 58.710 33.333 2.75 0.00 0.00 1.85
2627 5669 4.278170 TCACATGTGGTTCAACATTCCTTC 59.722 41.667 25.16 0.00 38.75 3.46
2717 5760 9.688091 TTTAAATGTATGCACTACTTTATGGGA 57.312 29.630 0.00 0.00 29.98 4.37
2789 5833 4.949856 CCATTACCAAGTTCAGTAGGCAAT 59.050 41.667 0.00 0.00 0.00 3.56
2817 8632 7.665561 TTTTTCAAAGTTCAGTGGGAAAAAG 57.334 32.000 0.00 0.00 38.53 2.27
2835 8650 7.771361 GGGAAAAAGGGAAATGAAAAACAGTAA 59.229 33.333 0.00 0.00 0.00 2.24
2957 8779 1.194547 CACCACGACACCTTTCGATTG 59.805 52.381 0.00 0.00 41.78 2.67
3003 8825 5.304357 TGGTATGACGTCATCATCACCTATT 59.696 40.000 32.75 14.77 45.52 1.73
3008 8832 5.362717 TGACGTCATCATCACCTATTTAGGT 59.637 40.000 15.76 3.34 44.68 3.08
3050 8874 4.444838 TGGCATCGTCCGGGTTCG 62.445 66.667 0.00 4.85 0.00 3.95
3075 8899 2.854777 CGGAGATCTTCAGCGTGTAAAG 59.145 50.000 0.96 0.00 0.00 1.85
3077 8901 2.605366 GAGATCTTCAGCGTGTAAAGCC 59.395 50.000 0.00 0.00 44.61 4.35
3117 8941 1.483415 ACCACGACACCTGTACAGTTT 59.517 47.619 21.18 5.29 0.00 2.66
3125 8949 5.061311 CGACACCTGTACAGTTTATTAACGG 59.939 44.000 21.18 5.58 39.31 4.44
3129 8953 6.020121 CACCTGTACAGTTTATTAACGGATCG 60.020 42.308 21.18 2.96 39.31 3.69
3132 8956 7.166473 CCTGTACAGTTTATTAACGGATCGTAC 59.834 40.741 21.18 5.10 39.99 3.67
3183 9010 0.899720 TTATGACGTCACCCTGGGAC 59.100 55.000 22.71 7.17 0.00 4.46
3220 9072 2.415512 GTCTAATCCCGACAAACTGCAC 59.584 50.000 0.00 0.00 0.00 4.57
3311 9163 2.636893 ACATCTAGGATGGCATGTCTCC 59.363 50.000 3.81 0.00 0.00 3.71
3325 9177 4.798882 CATGTCTCCCTCTAACCTCTAGT 58.201 47.826 0.00 0.00 0.00 2.57
3378 9231 5.818857 GTGGTAAATAAGCCGACTTCCATTA 59.181 40.000 0.00 0.00 37.33 1.90
3389 9242 2.760650 GACTTCCATTAAAAGGGGCCAG 59.239 50.000 4.39 0.00 0.00 4.85
3453 9309 0.314302 CGTGGTCTGTTCCGTCTCTT 59.686 55.000 0.00 0.00 0.00 2.85
3454 9310 1.784525 GTGGTCTGTTCCGTCTCTTG 58.215 55.000 0.00 0.00 0.00 3.02
3497 9353 3.617669 GTGTCAATGTCACCGTCAAAAG 58.382 45.455 0.00 0.00 0.00 2.27
3524 9381 1.005924 ACACATGATGGAGAAACCCCC 59.994 52.381 0.00 0.00 38.00 5.40
3601 9458 4.583489 AGTTTGATAGCTTAGCGGCTACTA 59.417 41.667 9.68 9.32 45.82 1.82
3610 9469 4.215827 GCTTAGCGGCTACTACTTCTGATA 59.784 45.833 9.68 0.00 0.00 2.15
3722 9581 8.064336 TCTATAGCCTAAAGGATCGGAAATAC 57.936 38.462 0.00 0.00 37.39 1.89
4013 9872 2.942376 CAGTGAGTAGTGGTGTGCAAAA 59.058 45.455 0.00 0.00 0.00 2.44
4132 9991 6.320418 TCGTATAGGAGATTTCTTGCAGTGTA 59.680 38.462 0.00 0.00 0.00 2.90
4210 10069 5.221461 GGACTTCTTGACCTGTCACTTTCTA 60.221 44.000 0.00 0.00 39.66 2.10
4391 10254 1.856629 AGGAAAATGGTGGGCTGATG 58.143 50.000 0.00 0.00 0.00 3.07
4406 10269 7.883311 GGTGGGCTGATGTTAACATATAGTATT 59.117 37.037 20.83 0.00 36.57 1.89
4466 10329 9.628500 AACTACTTGAAGTACCATTTTCTTTCT 57.372 29.630 0.00 0.00 0.00 2.52
4518 10381 9.681692 TGTTCAAATAGTTCAATGAAGTTCATG 57.318 29.630 18.94 12.70 37.15 3.07
4624 10487 3.252979 CACCACATGGATGCAGTCA 57.747 52.632 4.53 0.00 38.94 3.41
4626 10489 0.674581 ACCACATGGATGCAGTCACG 60.675 55.000 4.53 0.00 38.94 4.35
4629 10492 0.606130 ACATGGATGCAGTCACGCAA 60.606 50.000 0.00 0.00 46.87 4.85
4648 10511 3.428045 GCAAATGCGCTCCTCTAAAACAT 60.428 43.478 9.73 0.00 0.00 2.71
4669 10532 7.956328 ACATACTTACAACTGATAGAGACCA 57.044 36.000 0.00 0.00 0.00 4.02
4750 10613 3.584834 ACTTTGCAAACAAGTTGGTCAC 58.415 40.909 8.05 0.00 37.04 3.67
4806 10669 1.352352 TCTTAGCCAGCTTTCTTGCCT 59.648 47.619 0.00 0.00 31.81 4.75
4882 10748 7.425224 TCCAAATAAAAAGAGGTGACCAAAA 57.575 32.000 3.63 0.00 0.00 2.44
4924 10790 8.909423 AAAAGGTAAATCTTATCAATTCCCCA 57.091 30.769 0.00 0.00 0.00 4.96
4928 10794 8.981659 AGGTAAATCTTATCAATTCCCCAAAAG 58.018 33.333 0.00 0.00 0.00 2.27
4929 10795 8.977412 GGTAAATCTTATCAATTCCCCAAAAGA 58.023 33.333 0.00 0.00 0.00 2.52
4947 10813 7.148103 CCCAAAAGAAAAAGGAAAAATGCTTGA 60.148 33.333 0.00 0.00 0.00 3.02
5021 10887 1.597742 ACTGTGACAAGTGATGCACC 58.402 50.000 0.00 0.00 36.11 5.01
5262 11128 1.290324 CACAGACACCTCCTCACCG 59.710 63.158 0.00 0.00 0.00 4.94
5323 11189 1.380302 GCCACCATGAACACCTCCT 59.620 57.895 0.00 0.00 0.00 3.69
5324 11190 0.678048 GCCACCATGAACACCTCCTC 60.678 60.000 0.00 0.00 0.00 3.71
5325 11191 0.692476 CCACCATGAACACCTCCTCA 59.308 55.000 0.00 0.00 0.00 3.86
5619 11485 1.002087 ACTTGGAACCACTTCTAGGCG 59.998 52.381 0.00 0.00 0.00 5.52
5626 11492 2.084546 ACCACTTCTAGGCGAATTTGC 58.915 47.619 9.36 9.36 0.00 3.68
5640 11506 6.321181 AGGCGAATTTGCTTATTTATCCAGAA 59.679 34.615 17.19 0.00 34.52 3.02
5765 11649 6.262944 TGCAATGTTTCTTGAGTGTGAGTATT 59.737 34.615 0.00 0.00 0.00 1.89
5900 11784 3.580458 AGAAGTACAGGTTGCAGTGATCT 59.420 43.478 0.00 0.00 0.00 2.75
5973 11857 6.379417 GGAATTCTGAATGTTCTTCCCTCAAT 59.621 38.462 3.22 0.00 0.00 2.57
6039 11923 3.193267 GGCATGCTTATCACAGTTCCAAA 59.807 43.478 18.92 0.00 0.00 3.28
6092 11976 9.326413 ACTAATTCCACATAAATAGTACTGTGC 57.674 33.333 5.39 0.00 38.10 4.57
6095 11979 5.670485 TCCACATAAATAGTACTGTGCCAG 58.330 41.667 5.39 1.16 38.10 4.85
6138 12022 3.102204 TCAGAATCAGTCCAGATGCAGA 58.898 45.455 0.00 0.00 0.00 4.26
6148 12032 1.376424 AGATGCAGAACAGGTGCCG 60.376 57.895 0.00 0.00 40.43 5.69
6162 12046 2.632512 AGGTGCCGGTGAAATTCATTTT 59.367 40.909 1.90 0.00 0.00 1.82
6196 12086 0.871722 GACTATGTTGCGTGGTTGCA 59.128 50.000 0.00 0.00 44.61 4.08
6307 12197 2.747396 TGGTAGTACGTGCGGAAAAT 57.253 45.000 0.00 0.00 0.00 1.82
6383 12273 3.443329 CCATCCGATCCACAAAACATTGA 59.557 43.478 0.00 0.00 0.00 2.57
6388 12278 3.906008 CGATCCACAAAACATTGACGTTC 59.094 43.478 0.00 0.00 0.00 3.95
6392 12282 5.361427 TCCACAAAACATTGACGTTCTAGA 58.639 37.500 0.00 0.00 0.00 2.43
6406 12296 6.765036 TGACGTTCTAGATATAGTTTCGGTCT 59.235 38.462 0.00 0.00 0.00 3.85
6481 12371 4.285260 TGTGGATCTATGCATAGATGTGCT 59.715 41.667 40.73 25.16 46.98 4.40
6491 12381 4.951715 TGCATAGATGTGCTCCTCAAAATT 59.048 37.500 3.20 0.00 45.27 1.82
6567 12459 3.751698 GGCTAACTCAAAGTTACACCTGG 59.248 47.826 0.00 0.00 39.51 4.45
6570 12462 3.771577 ACTCAAAGTTACACCTGGGAG 57.228 47.619 0.00 0.00 0.00 4.30
6571 12463 3.314693 ACTCAAAGTTACACCTGGGAGA 58.685 45.455 0.00 0.00 0.00 3.71
6572 12464 3.071167 ACTCAAAGTTACACCTGGGAGAC 59.929 47.826 0.00 0.00 0.00 3.36
6573 12465 3.314693 TCAAAGTTACACCTGGGAGACT 58.685 45.455 0.00 0.00 0.00 3.24
6574 12466 3.714798 TCAAAGTTACACCTGGGAGACTT 59.285 43.478 0.00 0.08 0.00 3.01
6575 12467 4.165372 TCAAAGTTACACCTGGGAGACTTT 59.835 41.667 11.44 11.44 37.70 2.66
6576 12468 3.771577 AGTTACACCTGGGAGACTTTG 57.228 47.619 0.00 0.00 0.00 2.77
6577 12469 3.046374 AGTTACACCTGGGAGACTTTGT 58.954 45.455 0.00 0.00 0.00 2.83
6578 12470 3.071167 AGTTACACCTGGGAGACTTTGTC 59.929 47.826 0.00 0.00 0.00 3.18
6579 12471 1.507140 ACACCTGGGAGACTTTGTCA 58.493 50.000 0.00 0.00 34.60 3.58
6580 12472 2.057922 ACACCTGGGAGACTTTGTCAT 58.942 47.619 0.00 0.00 34.60 3.06
6581 12473 2.443255 ACACCTGGGAGACTTTGTCATT 59.557 45.455 0.00 0.00 34.60 2.57
6582 12474 2.816087 CACCTGGGAGACTTTGTCATTG 59.184 50.000 0.00 0.00 34.60 2.82
6583 12475 2.443255 ACCTGGGAGACTTTGTCATTGT 59.557 45.455 0.00 0.00 34.60 2.71
6584 12476 3.077359 CCTGGGAGACTTTGTCATTGTC 58.923 50.000 0.46 0.00 34.60 3.18
6585 12477 2.738846 CTGGGAGACTTTGTCATTGTCG 59.261 50.000 0.46 0.00 34.60 4.35
6586 12478 2.367241 TGGGAGACTTTGTCATTGTCGA 59.633 45.455 0.46 0.00 34.60 4.20
6587 12479 3.181459 TGGGAGACTTTGTCATTGTCGAA 60.181 43.478 0.00 0.00 34.60 3.71
6588 12480 3.813166 GGGAGACTTTGTCATTGTCGAAA 59.187 43.478 0.00 0.00 34.60 3.46
6589 12481 4.274950 GGGAGACTTTGTCATTGTCGAAAA 59.725 41.667 0.00 0.00 34.60 2.29
6590 12482 5.220970 GGGAGACTTTGTCATTGTCGAAAAA 60.221 40.000 0.00 0.00 34.60 1.94
6610 12502 6.937436 AAAAATAGTAACTAGATTGGCGGG 57.063 37.500 0.00 0.00 0.00 6.13
6611 12503 5.881923 AAATAGTAACTAGATTGGCGGGA 57.118 39.130 0.00 0.00 0.00 5.14
6612 12504 5.470047 AATAGTAACTAGATTGGCGGGAG 57.530 43.478 0.00 0.00 0.00 4.30
6613 12505 2.748388 AGTAACTAGATTGGCGGGAGT 58.252 47.619 0.00 0.00 0.00 3.85
6614 12506 3.907221 AGTAACTAGATTGGCGGGAGTA 58.093 45.455 0.00 0.00 0.00 2.59
6615 12507 4.481072 AGTAACTAGATTGGCGGGAGTAT 58.519 43.478 0.00 0.00 0.00 2.12
6616 12508 5.638133 AGTAACTAGATTGGCGGGAGTATA 58.362 41.667 0.00 0.00 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 137 0.179073 CCAGAGCGGGTACAGAATGG 60.179 60.000 0.00 0.00 43.62 3.16
120 150 1.131883 CAGCACTTGCATTACCAGAGC 59.868 52.381 3.62 0.00 45.16 4.09
155 185 2.891112 TCGTGTTTACAAGACCGTGTT 58.109 42.857 0.00 0.00 32.75 3.32
310 508 7.925483 TGGTTTTGAACATGGATAAAGTCAAAG 59.075 33.333 0.00 0.00 0.00 2.77
364 562 5.305644 AGTTTGTTTCTCTAGGAGAGCAAGA 59.694 40.000 0.00 0.00 42.04 3.02
394 592 2.610873 ACTATGAAGTAGCCTAGGCCC 58.389 52.381 30.42 20.61 43.17 5.80
525 2409 4.447138 ACACCAAAGATAACCAACTGGA 57.553 40.909 1.86 0.00 38.94 3.86
529 2413 5.722021 ATCCAACACCAAAGATAACCAAC 57.278 39.130 0.00 0.00 0.00 3.77
586 2470 5.453762 GGGGCAAAAAGGAATATCATCTTGG 60.454 44.000 0.00 0.00 0.00 3.61
686 2575 2.675032 GCTAGCTCCACGCATATGCATA 60.675 50.000 26.52 9.27 42.61 3.14
687 2576 1.943046 GCTAGCTCCACGCATATGCAT 60.943 52.381 26.52 9.89 42.61 3.96
688 2577 0.601046 GCTAGCTCCACGCATATGCA 60.601 55.000 26.52 6.89 42.61 3.96
689 2578 0.320247 AGCTAGCTCCACGCATATGC 60.320 55.000 18.08 18.08 42.61 3.14
690 2579 1.797046 CAAGCTAGCTCCACGCATATG 59.203 52.381 19.65 5.22 42.61 1.78
691 2580 1.414181 ACAAGCTAGCTCCACGCATAT 59.586 47.619 19.65 0.00 42.61 1.78
728 2617 0.675837 GAGCAGCTTCCATGTCAGCA 60.676 55.000 14.14 0.00 38.61 4.41
735 2624 4.205587 CAAATAAGAGGAGCAGCTTCCAT 58.794 43.478 7.20 0.00 39.84 3.41
761 2650 8.147704 TCTTTATTTCCATTTCGCCTTTTCTTT 58.852 29.630 0.00 0.00 0.00 2.52
905 2797 2.159198 GCAAGCAAGAGAGAGAGAGAGG 60.159 54.545 0.00 0.00 0.00 3.69
909 2801 2.612471 GCAAGCAAGCAAGAGAGAGAGA 60.612 50.000 0.00 0.00 0.00 3.10
936 2828 1.738350 CGCAGTAGAGAGAGAAACGGA 59.262 52.381 0.00 0.00 0.00 4.69
938 2830 2.095668 ACACGCAGTAGAGAGAGAAACG 60.096 50.000 0.00 0.00 41.61 3.60
939 2831 3.562567 ACACGCAGTAGAGAGAGAAAC 57.437 47.619 0.00 0.00 41.61 2.78
969 2864 3.711086 TCTATCTCTTTGCTGATGCGAC 58.289 45.455 0.00 0.00 43.34 5.19
984 2887 6.211384 TCATCGACATCTCTCTCTCTCTATCT 59.789 42.308 0.00 0.00 0.00 1.98
985 2888 6.398095 TCATCGACATCTCTCTCTCTCTATC 58.602 44.000 0.00 0.00 0.00 2.08
986 2889 6.358974 TCATCGACATCTCTCTCTCTCTAT 57.641 41.667 0.00 0.00 0.00 1.98
987 2890 5.783111 CTCATCGACATCTCTCTCTCTCTA 58.217 45.833 0.00 0.00 0.00 2.43
991 2894 3.141398 AGCTCATCGACATCTCTCTCTC 58.859 50.000 0.00 0.00 0.00 3.20
1185 3088 3.101437 AGAGAGAGAGAGAGACGTACCA 58.899 50.000 0.00 0.00 0.00 3.25
1201 3104 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1202 3105 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1355 3264 0.039256 CCAAGAACGTTGCATGTGGG 60.039 55.000 5.00 0.00 0.00 4.61
1407 3316 7.379059 AAAAGGAGAACAAAATCAAAGGGAT 57.621 32.000 0.00 0.00 38.05 3.85
1556 3468 4.918810 AACGCTGGAGTTTCTTTTTCAT 57.081 36.364 0.00 0.00 0.00 2.57
1721 3641 6.516718 TGCATGCCTACTAGAACTATTCTTC 58.483 40.000 16.68 0.00 41.14 2.87
1862 3789 1.071471 CCCGTTTCAGACTGCCACT 59.929 57.895 0.00 0.00 0.00 4.00
2034 4778 2.550175 AGGTGGGAAAATGATTTGGGG 58.450 47.619 0.00 0.00 0.00 4.96
2344 5094 8.554835 TGAATTCTTATTGGAACACAACGATA 57.445 30.769 7.05 0.00 42.94 2.92
2385 5419 5.219739 AGTAAATGGAAGATCCCTGCTCTA 58.780 41.667 0.00 0.00 35.03 2.43
2391 5426 4.166919 CCTTGGAGTAAATGGAAGATCCCT 59.833 45.833 0.00 0.00 35.03 4.20
2592 5634 7.097192 TGAACCACATGTGAACTAAGTAGATC 58.903 38.462 27.46 11.05 0.00 2.75
2798 5842 3.704061 TCCCTTTTTCCCACTGAACTTTG 59.296 43.478 0.00 0.00 31.05 2.77
2802 8617 4.343814 TCATTTCCCTTTTTCCCACTGAAC 59.656 41.667 0.00 0.00 31.05 3.18
2838 8653 8.276252 TGCTGGGTTGTTTATTCTAGAATTAC 57.724 34.615 22.60 19.37 32.50 1.89
2843 8658 7.589958 TTTTTGCTGGGTTGTTTATTCTAGA 57.410 32.000 0.00 0.00 0.00 2.43
2981 8803 7.542477 CCTAAATAGGTGATGATGACGTCATAC 59.458 40.741 30.04 22.85 41.81 2.39
3050 8874 0.173708 ACGCTGAAGATCTCCGGTTC 59.826 55.000 0.00 0.00 0.00 3.62
3075 8899 2.092882 GTTGGTCTAGCACGTCGGC 61.093 63.158 0.00 0.00 0.00 5.54
3077 8901 1.198408 TGTAGTTGGTCTAGCACGTCG 59.802 52.381 0.00 0.00 0.00 5.12
3186 9014 1.414550 GATTAGACAGGGAGAGGGCAC 59.585 57.143 0.00 0.00 0.00 5.01
3193 9021 1.776662 TGTCGGGATTAGACAGGGAG 58.223 55.000 0.00 0.00 42.91 4.30
3220 9072 1.001706 CGAGCATGCAAGATGGGATTG 60.002 52.381 21.98 0.00 0.00 2.67
3311 9163 5.757988 AGTGGTAGAACTAGAGGTTAGAGG 58.242 45.833 0.00 0.00 38.41 3.69
3325 9177 4.471904 AATCGATGAGCAAGTGGTAGAA 57.528 40.909 0.00 0.00 0.00 2.10
3378 9231 0.032615 TGTCACAACTGGCCCCTTTT 60.033 50.000 0.00 0.00 0.00 2.27
3453 9309 0.460459 TCGATAAAACCGCGCATCCA 60.460 50.000 8.75 0.00 0.00 3.41
3454 9310 0.653636 TTCGATAAAACCGCGCATCC 59.346 50.000 8.75 0.00 0.00 3.51
3497 9353 5.529060 GGTTTCTCCATCATGTGTTCTATCC 59.471 44.000 0.00 0.00 35.97 2.59
3524 9381 1.878953 AAGCTTGAGGTACCACAACG 58.121 50.000 19.42 15.84 0.00 4.10
3559 9416 3.143728 ACTGGTCCCACAAATAAACGAC 58.856 45.455 0.00 0.00 0.00 4.34
3643 9502 8.802856 CAGTCACTGATAAGAAACGAAAGATAG 58.197 37.037 0.00 0.00 32.44 2.08
3652 9511 4.033358 CCGATGCAGTCACTGATAAGAAAC 59.967 45.833 9.70 0.00 32.44 2.78
4013 9872 9.677567 CGGAAAATAAATAAATCAATCGATGGT 57.322 29.630 0.00 0.00 30.13 3.55
4240 10099 6.808321 AGTAGCAACCAATAAGTAGATGGA 57.192 37.500 0.00 0.00 37.66 3.41
4406 10269 6.894682 TGTCATTATCCATAACAGCTAACCA 58.105 36.000 0.00 0.00 0.00 3.67
4577 10440 7.636359 GTGTCTACTTTTATGCTTAATCGCAAG 59.364 37.037 0.00 0.00 44.06 4.01
4626 10489 2.095263 TGTTTTAGAGGAGCGCATTTGC 60.095 45.455 11.47 0.00 37.78 3.68
4629 10492 4.770795 AGTATGTTTTAGAGGAGCGCATT 58.229 39.130 11.47 0.00 0.00 3.56
4648 10511 6.728411 TCCTGGTCTCTATCAGTTGTAAGTA 58.272 40.000 0.00 0.00 31.30 2.24
4719 10582 4.044336 TGTTTGCAAAGTCATCACAAGG 57.956 40.909 13.26 0.00 0.00 3.61
4726 10589 4.081752 TGACCAACTTGTTTGCAAAGTCAT 60.082 37.500 18.69 2.91 33.73 3.06
4750 10613 6.726299 TCCACTTCACTATCCTGGATTATAGG 59.274 42.308 15.55 6.88 36.63 2.57
4848 10713 8.478066 ACCTCTTTTTATTTGGATTGGATAAGC 58.522 33.333 0.00 0.00 0.00 3.09
4916 10782 8.694540 CATTTTTCCTTTTTCTTTTGGGGAATT 58.305 29.630 0.00 0.00 33.65 2.17
4918 10784 6.096141 GCATTTTTCCTTTTTCTTTTGGGGAA 59.904 34.615 0.00 0.00 0.00 3.97
4920 10786 5.593909 AGCATTTTTCCTTTTTCTTTTGGGG 59.406 36.000 0.00 0.00 0.00 4.96
4922 10788 7.760437 TCAAGCATTTTTCCTTTTTCTTTTGG 58.240 30.769 0.00 0.00 0.00 3.28
4924 10790 9.791820 CAATCAAGCATTTTTCCTTTTTCTTTT 57.208 25.926 0.00 0.00 0.00 2.27
4928 10794 7.495135 TCCAATCAAGCATTTTTCCTTTTTC 57.505 32.000 0.00 0.00 0.00 2.29
4929 10795 7.522562 GCATCCAATCAAGCATTTTTCCTTTTT 60.523 33.333 0.00 0.00 0.00 1.94
4947 10813 7.548083 AACCCTAATTGGTTCATGCATCCAAT 61.548 38.462 20.18 20.18 45.51 3.16
5021 10887 3.062763 CTGTCACTGTACTTGCTCTTGG 58.937 50.000 0.00 0.00 0.00 3.61
5262 11128 1.748122 CATGAGAGGTGGCAGTGGC 60.748 63.158 10.30 10.30 40.13 5.01
5640 11506 3.490348 AGCCAGTTGTCTGCTTATGTTT 58.510 40.909 0.00 0.00 40.09 2.83
5765 11649 2.048444 ATCACCGCGTCCTCTACTAA 57.952 50.000 4.92 0.00 0.00 2.24
5842 11726 6.593382 ACTTCAGCAATCATTAGAGTGTTCTC 59.407 38.462 0.00 0.00 41.66 2.87
5900 11784 6.464892 GGGGACATAAATGATCTGATCTGTCA 60.465 42.308 25.44 9.37 33.58 3.58
5973 11857 5.106594 CGTTCTCAATCAACCATGATGTTCA 60.107 40.000 0.00 0.00 45.60 3.18
6039 11923 9.829507 TGTGGAATCAGTTGAATTAATTTGTTT 57.170 25.926 1.43 0.00 0.00 2.83
6091 11975 0.453390 GCACAAGCTCCAATACTGGC 59.547 55.000 0.00 0.00 43.17 4.85
6092 11976 1.825090 TGCACAAGCTCCAATACTGG 58.175 50.000 0.00 0.00 42.74 4.00
6138 12022 0.958822 GAATTTCACCGGCACCTGTT 59.041 50.000 0.00 0.00 0.00 3.16
6162 12046 6.318648 GCAACATAGTCCCATGATACTTTTCA 59.681 38.462 0.00 0.00 0.00 2.69
6174 12058 0.398696 AACCACGCAACATAGTCCCA 59.601 50.000 0.00 0.00 0.00 4.37
6176 12060 0.168128 GCAACCACGCAACATAGTCC 59.832 55.000 0.00 0.00 0.00 3.85
6228 12118 9.886132 TTATATCATGATGAAGACTCATGGATG 57.114 33.333 18.72 3.39 46.46 3.51
6260 12150 7.450903 AGAGGTGCAGTTTTTATTGTAGTACT 58.549 34.615 0.00 0.00 0.00 2.73
6261 12151 7.668525 AGAGGTGCAGTTTTTATTGTAGTAC 57.331 36.000 0.00 0.00 0.00 2.73
6262 12152 8.685838 AAAGAGGTGCAGTTTTTATTGTAGTA 57.314 30.769 0.00 0.00 0.00 1.82
6263 12153 7.582667 AAAGAGGTGCAGTTTTTATTGTAGT 57.417 32.000 0.00 0.00 0.00 2.73
6264 12154 7.382218 CCAAAAGAGGTGCAGTTTTTATTGTAG 59.618 37.037 0.00 0.00 0.00 2.74
6265 12155 7.147811 ACCAAAAGAGGTGCAGTTTTTATTGTA 60.148 33.333 0.00 0.00 41.30 2.41
6280 12170 2.608752 CGCACGTACTACCAAAAGAGGT 60.609 50.000 0.00 0.00 45.72 3.85
6307 12197 6.045955 TGCGTGCACAATACATATTCTCTTA 58.954 36.000 18.64 0.00 0.00 2.10
6383 12273 8.668510 TTAGACCGAAACTATATCTAGAACGT 57.331 34.615 0.00 0.00 0.00 3.99
6449 12339 8.605065 TCTATGCATAGATCCACATATCCAAAA 58.395 33.333 28.69 4.27 34.63 2.44
6450 12340 8.149631 TCTATGCATAGATCCACATATCCAAA 57.850 34.615 28.69 4.63 34.63 3.28
6546 12438 3.751698 CCCAGGTGTAACTTTGAGTTAGC 59.248 47.826 1.02 0.00 40.95 3.09
6567 12459 5.418310 TTTTCGACAATGACAAAGTCTCC 57.582 39.130 8.45 0.00 33.15 3.71
6587 12479 6.655930 TCCCGCCAATCTAGTTACTATTTTT 58.344 36.000 0.00 0.00 0.00 1.94
6588 12480 6.126854 ACTCCCGCCAATCTAGTTACTATTTT 60.127 38.462 0.00 0.00 0.00 1.82
6589 12481 5.365895 ACTCCCGCCAATCTAGTTACTATTT 59.634 40.000 0.00 0.00 0.00 1.40
6590 12482 4.900054 ACTCCCGCCAATCTAGTTACTATT 59.100 41.667 0.00 0.00 0.00 1.73
6591 12483 4.481072 ACTCCCGCCAATCTAGTTACTAT 58.519 43.478 0.00 0.00 0.00 2.12
6592 12484 3.907221 ACTCCCGCCAATCTAGTTACTA 58.093 45.455 0.00 0.00 0.00 1.82
6593 12485 2.748388 ACTCCCGCCAATCTAGTTACT 58.252 47.619 0.00 0.00 0.00 2.24
6594 12486 4.868314 ATACTCCCGCCAATCTAGTTAC 57.132 45.455 0.00 0.00 0.00 2.50


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

AutoCloner maintained by Alex Coulton.