Multiple sequence alignment - TraesCS5D01G214600

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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 TraesCS5D01G214600 chr5D 100.000 3594 0 0 1 3594 324358988 324355395 0.000000e+00 6637.0
1 TraesCS5D01G214600 chr5D 86.538 52 6 1 1 51 387617307 387617256 5.010000e-04 56.5
2 TraesCS5D01G214600 chr5B 91.994 1374 60 23 924 2255 375744742 375743377 0.000000e+00 1882.0
3 TraesCS5D01G214600 chr5B 93.309 837 23 14 1 835 375746655 375745850 0.000000e+00 1205.0
4 TraesCS5D01G214600 chr5B 95.768 449 18 1 2719 3167 375742000 375741553 0.000000e+00 723.0
5 TraesCS5D01G214600 chr5B 88.164 414 42 7 2249 2659 375743353 375742944 1.500000e-133 486.0
6 TraesCS5D01G214600 chr5B 93.878 245 12 2 3192 3434 375741605 375741362 2.040000e-97 366.0
7 TraesCS5D01G214600 chr5B 91.573 178 10 2 3421 3594 375741346 375741170 1.290000e-59 241.0
8 TraesCS5D01G214600 chr5A 89.888 1068 62 18 1614 2659 422029709 422028666 0.000000e+00 1332.0
9 TraesCS5D01G214600 chr5A 87.106 349 28 6 2826 3165 422027817 422027477 2.620000e-101 379.0
10 TraesCS5D01G214600 chr5A 91.304 207 13 4 3260 3464 422027370 422027167 9.830000e-71 278.0
11 TraesCS5D01G214600 chr3A 81.034 116 17 5 1 112 668219160 668219046 1.780000e-13 87.9
12 TraesCS5D01G214600 chr3D 88.158 76 3 6 1 74 38912709 38912638 6.390000e-13 86.1


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 TraesCS5D01G214600 chr5D 324355395 324358988 3593 True 6637.000000 6637 100.000000 1 3594 1 chr5D.!!$R1 3593
1 TraesCS5D01G214600 chr5B 375741170 375746655 5485 True 817.166667 1882 92.447667 1 3594 6 chr5B.!!$R1 3593
2 TraesCS5D01G214600 chr5A 422027167 422029709 2542 True 663.000000 1332 89.432667 1614 3464 3 chr5A.!!$R1 1850

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
240 243 1.532505 CCAGCGAAAAATCTGATGCCG 60.533 52.381 0.0 0.0 32.26 5.69 F
1284 2335 0.108615 CCAGCCATCGTCGTCTTCTT 60.109 55.000 0.0 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1375 2426 0.179045 ATTGCGCCTGTGATACTCCC 60.179 55.0 4.18 0.0 0.00 4.3 R
3155 5147 0.260816 ACTTGCCCCATGATGCTCAT 59.739 50.0 0.00 0.0 37.65 2.9 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
76 78 9.072375 TGTTATCATGTAGTTTGGAAATGTGAA 57.928 29.630 0.00 0.00 0.00 3.18
240 243 1.532505 CCAGCGAAAAATCTGATGCCG 60.533 52.381 0.00 0.00 32.26 5.69
247 250 2.768253 AAATCTGATGCCGACACTGA 57.232 45.000 0.00 0.00 0.00 3.41
351 354 3.750130 ACGAAACTAACTCTAGCGACTGA 59.250 43.478 0.00 0.00 0.00 3.41
353 356 4.378149 CGAAACTAACTCTAGCGACTGACA 60.378 45.833 0.00 0.00 0.00 3.58
376 379 2.141011 AATAGCCCTGCTGCACCACA 62.141 55.000 0.00 0.00 40.10 4.17
379 382 2.034532 CCCTGCTGCACCACATGA 59.965 61.111 0.00 0.00 0.00 3.07
521 524 4.539509 TTACAACGGTTGACATGTGAAC 57.460 40.909 26.39 18.60 0.00 3.18
920 1829 6.538742 AGGGAATCATCAACGTAATAAGTGTG 59.461 38.462 0.00 0.00 0.00 3.82
922 1831 7.180079 GGAATCATCAACGTAATAAGTGTGTG 58.820 38.462 0.00 0.00 0.00 3.82
1006 2030 3.736740 GCCCGCATACAAATTCCGAAATT 60.737 43.478 0.00 0.00 36.64 1.82
1015 2050 4.280677 ACAAATTCCGAAATTGCTCTCCAA 59.719 37.500 8.56 0.00 35.27 3.53
1092 2131 3.134127 GGACAATGGAGCCCGTGC 61.134 66.667 0.00 0.00 37.95 5.34
1170 2212 0.602638 GGTCCGGATGATATGCGCAA 60.603 55.000 17.11 4.13 43.11 4.85
1182 2224 3.627218 GCGCAAGATACCGCCGAC 61.627 66.667 0.30 0.00 44.10 4.79
1229 2277 1.300620 CCTGTCGTTGCGTTCTCCA 60.301 57.895 0.00 0.00 0.00 3.86
1232 2280 0.669318 TGTCGTTGCGTTCTCCATCC 60.669 55.000 0.00 0.00 0.00 3.51
1247 2295 4.042062 TCTCCATCCATGTTTGAGTTCAGT 59.958 41.667 0.00 0.00 0.00 3.41
1279 2330 0.460284 AATCACCAGCCATCGTCGTC 60.460 55.000 0.00 0.00 0.00 4.20
1284 2335 0.108615 CCAGCCATCGTCGTCTTCTT 60.109 55.000 0.00 0.00 0.00 2.52
1285 2336 1.272781 CAGCCATCGTCGTCTTCTTC 58.727 55.000 0.00 0.00 0.00 2.87
1289 2340 1.260206 CATCGTCGTCTTCTTCGTGG 58.740 55.000 0.00 0.00 0.00 4.94
1301 2352 5.992217 GTCTTCTTCGTGGCCAGATATATTT 59.008 40.000 5.11 0.00 0.00 1.40
1345 2396 1.151668 CTGCTGCCACAAGACTACAC 58.848 55.000 0.00 0.00 0.00 2.90
1375 2426 4.363999 CGCCTCTATTTTGACTACCTCAG 58.636 47.826 0.00 0.00 0.00 3.35
1386 2437 3.268595 TGACTACCTCAGGGAGTATCACA 59.731 47.826 9.28 0.00 45.06 3.58
1442 2493 2.045536 GGCAAGCCTGAGGAGTGG 60.046 66.667 0.65 0.00 0.00 4.00
1474 2525 2.120909 GGCCACCGGTTGATGATGG 61.121 63.158 10.41 5.15 0.00 3.51
1532 2583 2.034687 ACTGCTGCCGCCAGATTT 59.965 55.556 0.00 0.00 41.77 2.17
1536 2587 0.607762 TGCTGCCGCCAGATTTGTAA 60.608 50.000 0.00 0.00 41.77 2.41
1537 2588 0.179163 GCTGCCGCCAGATTTGTAAC 60.179 55.000 0.00 0.00 41.77 2.50
1541 2592 0.725117 CCGCCAGATTTGTAACGTCC 59.275 55.000 0.00 0.00 0.00 4.79
1542 2593 1.674817 CCGCCAGATTTGTAACGTCCT 60.675 52.381 0.00 0.00 0.00 3.85
1543 2594 1.393539 CGCCAGATTTGTAACGTCCTG 59.606 52.381 0.00 0.00 0.00 3.86
1544 2595 1.130561 GCCAGATTTGTAACGTCCTGC 59.869 52.381 0.00 0.00 0.00 4.85
1597 2656 3.988379 TCCGTACTAACTTGTTCGTGT 57.012 42.857 1.67 0.00 0.00 4.49
1652 2711 2.069273 GTTCATGTCGGTGTGGAAGAG 58.931 52.381 0.00 0.00 0.00 2.85
1659 2718 2.047179 GTGTGGAAGAGCCGACCC 60.047 66.667 0.00 0.00 40.66 4.46
1678 2737 2.970324 TGCGCAACGTGGAACTCC 60.970 61.111 8.16 0.00 31.75 3.85
1775 2834 2.360600 GGTGGTATGTGCGGGCAA 60.361 61.111 0.00 0.00 0.00 4.52
1809 2868 1.200020 CCCAAACGATCACCTTTCAGC 59.800 52.381 0.00 0.00 0.00 4.26
1820 2879 1.701847 ACCTTTCAGCCTGTGATCTGT 59.298 47.619 0.00 0.00 34.17 3.41
1821 2880 2.107204 ACCTTTCAGCCTGTGATCTGTT 59.893 45.455 0.00 0.00 34.17 3.16
1822 2881 2.486982 CCTTTCAGCCTGTGATCTGTTG 59.513 50.000 0.00 0.00 34.17 3.33
1823 2882 2.936919 TTCAGCCTGTGATCTGTTGT 57.063 45.000 0.00 0.00 34.17 3.32
1824 2883 4.318332 CTTTCAGCCTGTGATCTGTTGTA 58.682 43.478 0.00 0.00 34.17 2.41
1825 2884 3.319137 TCAGCCTGTGATCTGTTGTAC 57.681 47.619 0.00 0.00 0.00 2.90
1853 2912 5.365619 TCTTGTCTAAACTTTGAGGTGGAC 58.634 41.667 0.00 0.00 0.00 4.02
2002 3064 4.514577 CCGCGTTCCGATGCCTCT 62.515 66.667 4.92 0.00 40.02 3.69
2047 3109 1.753470 CCCTGCCAATTTGCCAACA 59.247 52.632 0.00 0.00 0.00 3.33
2087 3149 9.899226 AAACTTGTACTAGCATTCAATCTTTTC 57.101 29.630 4.10 0.00 0.00 2.29
2119 3184 0.820871 TGTTGGTTGCAAGGGTGTTC 59.179 50.000 0.00 0.00 0.00 3.18
2136 3201 0.475632 TTCCCAAGGAGGCCAGAAGA 60.476 55.000 5.01 0.00 35.39 2.87
2240 3305 0.180406 ATCCGGATTCCCACCTTTCG 59.820 55.000 12.38 0.00 0.00 3.46
2248 3313 1.873698 TCCCACCTTTCGTCTTTTCG 58.126 50.000 0.00 0.00 0.00 3.46
2322 3420 4.095483 GCAATTCATGTTCTTCGATGGTCT 59.905 41.667 0.00 0.00 0.00 3.85
2376 3475 8.413229 CAATGTTTTGTAATATACCCAGGGAAG 58.587 37.037 14.54 0.00 0.00 3.46
2411 3510 7.060383 TGTGCTTATGGATTTTGGAAAGAAA 57.940 32.000 0.00 0.00 0.00 2.52
2417 3516 5.806654 TGGATTTTGGAAAGAAAAGGGAG 57.193 39.130 0.00 0.00 0.00 4.30
2428 3527 4.779993 AGAAAAGGGAGAAGACACAAGT 57.220 40.909 0.00 0.00 0.00 3.16
2436 3535 3.991121 GGAGAAGACACAAGTGTAAGAGC 59.009 47.826 5.74 0.00 45.05 4.09
2489 3588 8.673711 TCACAGGTAACATAACTCAATTATTGC 58.326 33.333 0.00 0.00 41.41 3.56
2498 3597 8.462016 ACATAACTCAATTATTGCTGTTTCTCC 58.538 33.333 16.30 0.00 30.54 3.71
2500 3599 4.396166 ACTCAATTATTGCTGTTTCTCCCG 59.604 41.667 0.00 0.00 0.00 5.14
2509 3608 2.674462 GCTGTTTCTCCCGTAGAACTCC 60.674 54.545 0.00 0.00 44.02 3.85
2534 3633 4.023878 CAGTCCTCGCTGAGTACCTATTAC 60.024 50.000 5.15 0.00 38.70 1.89
2543 3642 8.133627 TCGCTGAGTACCTATTACTGTTTATTC 58.866 37.037 0.00 0.00 41.48 1.75
2556 3655 5.607477 ACTGTTTATTCAACTCGAACCTGA 58.393 37.500 0.00 0.00 36.12 3.86
2560 3659 3.594603 ATTCAACTCGAACCTGACGAT 57.405 42.857 0.00 0.00 39.02 3.73
2564 3663 0.603569 ACTCGAACCTGACGATTGCT 59.396 50.000 0.00 0.00 39.02 3.91
2567 3666 2.854777 CTCGAACCTGACGATTGCTAAG 59.145 50.000 0.00 0.00 39.02 2.18
2576 3675 5.352569 CCTGACGATTGCTAAGTTGAGAAAT 59.647 40.000 0.00 0.00 0.00 2.17
2605 3704 4.003648 CCCAAGTCCATTGTAGTCAAGAC 58.996 47.826 0.00 0.00 37.17 3.01
2636 3735 2.672098 GTAGCTGGGAGGATCAAGAGA 58.328 52.381 0.00 0.00 36.25 3.10
2673 4090 1.062044 GGAACTACTCCCTCCTCCCAT 60.062 57.143 0.00 0.00 38.44 4.00
2674 4091 2.179424 GGAACTACTCCCTCCTCCCATA 59.821 54.545 0.00 0.00 38.44 2.74
2675 4092 3.374984 GGAACTACTCCCTCCTCCCATAA 60.375 52.174 0.00 0.00 38.44 1.90
2676 4093 4.494591 GAACTACTCCCTCCTCCCATAAT 58.505 47.826 0.00 0.00 0.00 1.28
2677 4094 5.460720 GGAACTACTCCCTCCTCCCATAATA 60.461 48.000 0.00 0.00 38.44 0.98
2678 4095 5.905633 ACTACTCCCTCCTCCCATAATAT 57.094 43.478 0.00 0.00 0.00 1.28
2679 4096 7.372060 AACTACTCCCTCCTCCCATAATATA 57.628 40.000 0.00 0.00 0.00 0.86
2680 4097 7.372060 ACTACTCCCTCCTCCCATAATATAA 57.628 40.000 0.00 0.00 0.00 0.98
2682 4099 6.500490 ACTCCCTCCTCCCATAATATAAGA 57.500 41.667 0.00 0.00 0.00 2.10
2683 4100 6.507568 ACTCCCTCCTCCCATAATATAAGAG 58.492 44.000 0.00 0.00 0.00 2.85
2684 4101 5.281314 TCCCTCCTCCCATAATATAAGAGC 58.719 45.833 0.00 0.00 0.00 4.09
2685 4102 5.032846 CCCTCCTCCCATAATATAAGAGCA 58.967 45.833 0.00 0.00 0.00 4.26
2686 4103 5.669447 CCCTCCTCCCATAATATAAGAGCAT 59.331 44.000 0.00 0.00 0.00 3.79
2687 4104 6.159398 CCCTCCTCCCATAATATAAGAGCATT 59.841 42.308 0.00 0.00 0.00 3.56
2688 4105 7.312183 CCCTCCTCCCATAATATAAGAGCATTT 60.312 40.741 0.00 0.00 0.00 2.32
2691 4108 9.959721 TCCTCCCATAATATAAGAGCATTTTAC 57.040 33.333 0.00 0.00 0.00 2.01
2692 4109 9.739276 CCTCCCATAATATAAGAGCATTTTACA 57.261 33.333 0.00 0.00 0.00 2.41
2705 4122 9.545105 AAGAGCATTTTACAAACATGATTTTGA 57.455 25.926 13.93 0.00 38.54 2.69
2706 4123 9.199982 AGAGCATTTTACAAACATGATTTTGAG 57.800 29.630 13.93 0.00 38.54 3.02
2708 4125 8.981647 AGCATTTTACAAACATGATTTTGAGTC 58.018 29.630 13.93 0.00 38.54 3.36
2709 4126 8.223100 GCATTTTACAAACATGATTTTGAGTCC 58.777 33.333 13.93 0.00 38.54 3.85
2711 4128 9.829507 ATTTTACAAACATGATTTTGAGTCCAA 57.170 25.926 13.93 2.69 38.54 3.53
2713 4130 6.469782 ACAAACATGATTTTGAGTCCAAGT 57.530 33.333 13.93 0.00 38.54 3.16
2714 4131 7.581213 ACAAACATGATTTTGAGTCCAAGTA 57.419 32.000 13.93 0.00 38.54 2.24
2763 4752 3.180507 AGAGAAGAAGATGAAGCCCACT 58.819 45.455 0.00 0.00 0.00 4.00
2777 4766 0.029300 CCCACTGTCACAAAAGCACG 59.971 55.000 0.00 0.00 0.00 5.34
2794 4783 0.815213 ACGCAACAAGCAGCAGAGAA 60.815 50.000 0.00 0.00 46.13 2.87
2819 4808 4.858965 AGAGCAGGAGAATGGAAGAAAT 57.141 40.909 0.00 0.00 0.00 2.17
2880 4872 7.833285 AATGGTTGTACAAACCTCTACAAAT 57.167 32.000 20.69 2.24 40.88 2.32
3055 5047 8.717821 CAGTGAGACAACTCGGAAATTTTATAA 58.282 33.333 0.00 0.00 45.25 0.98
3148 5140 8.879260 AAAATTCAAAAAGAAAAGCGAAAGTG 57.121 26.923 0.00 0.00 40.22 3.16
3149 5141 7.826260 AATTCAAAAAGAAAAGCGAAAGTGA 57.174 28.000 0.00 0.00 40.22 3.41
3150 5142 6.869421 TTCAAAAAGAAAAGCGAAAGTGAG 57.131 33.333 0.00 0.00 32.05 3.51
3151 5143 6.189677 TCAAAAAGAAAAGCGAAAGTGAGA 57.810 33.333 0.00 0.00 0.00 3.27
3152 5144 6.616947 TCAAAAAGAAAAGCGAAAGTGAGAA 58.383 32.000 0.00 0.00 0.00 2.87
3153 5145 7.087639 TCAAAAAGAAAAGCGAAAGTGAGAAA 58.912 30.769 0.00 0.00 0.00 2.52
3154 5146 7.273381 TCAAAAAGAAAAGCGAAAGTGAGAAAG 59.727 33.333 0.00 0.00 0.00 2.62
3155 5147 6.436843 AAAGAAAAGCGAAAGTGAGAAAGA 57.563 33.333 0.00 0.00 0.00 2.52
3156 5148 6.625873 AAGAAAAGCGAAAGTGAGAAAGAT 57.374 33.333 0.00 0.00 0.00 2.40
3157 5149 5.995055 AGAAAAGCGAAAGTGAGAAAGATG 58.005 37.500 0.00 0.00 0.00 2.90
3158 5150 5.760253 AGAAAAGCGAAAGTGAGAAAGATGA 59.240 36.000 0.00 0.00 0.00 2.92
3159 5151 5.604010 AAAGCGAAAGTGAGAAAGATGAG 57.396 39.130 0.00 0.00 0.00 2.90
3160 5152 2.999355 AGCGAAAGTGAGAAAGATGAGC 59.001 45.455 0.00 0.00 0.00 4.26
3161 5153 2.738846 GCGAAAGTGAGAAAGATGAGCA 59.261 45.455 0.00 0.00 0.00 4.26
3162 5154 3.373439 GCGAAAGTGAGAAAGATGAGCAT 59.627 43.478 0.00 0.00 0.00 3.79
3163 5155 4.493872 GCGAAAGTGAGAAAGATGAGCATC 60.494 45.833 2.27 2.27 38.09 3.91
3173 5165 4.670199 TGAGCATCATGGGGCAAG 57.330 55.556 11.25 0.00 42.56 4.01
3174 5166 1.693034 TGAGCATCATGGGGCAAGT 59.307 52.632 11.25 0.00 42.56 3.16
3175 5167 0.918258 TGAGCATCATGGGGCAAGTA 59.082 50.000 11.25 0.00 42.56 2.24
3176 5168 1.496001 TGAGCATCATGGGGCAAGTAT 59.504 47.619 11.25 0.00 42.56 2.12
3177 5169 2.157738 GAGCATCATGGGGCAAGTATC 58.842 52.381 11.25 0.00 33.17 2.24
3178 5170 1.202976 AGCATCATGGGGCAAGTATCC 60.203 52.381 11.25 0.00 0.00 2.59
3179 5171 1.202976 GCATCATGGGGCAAGTATCCT 60.203 52.381 4.87 0.00 0.00 3.24
3180 5172 2.787994 CATCATGGGGCAAGTATCCTC 58.212 52.381 0.00 0.00 0.00 3.71
3181 5173 1.140312 TCATGGGGCAAGTATCCTCC 58.860 55.000 0.00 0.00 0.00 4.30
3182 5174 0.111253 CATGGGGCAAGTATCCTCCC 59.889 60.000 0.00 0.00 38.03 4.30
3183 5175 0.028642 ATGGGGCAAGTATCCTCCCT 60.029 55.000 0.00 0.00 38.78 4.20
3184 5176 0.988145 TGGGGCAAGTATCCTCCCTG 60.988 60.000 0.00 0.00 38.78 4.45
3185 5177 0.694444 GGGGCAAGTATCCTCCCTGA 60.694 60.000 0.00 0.00 38.78 3.86
3186 5178 0.470341 GGGCAAGTATCCTCCCTGAC 59.530 60.000 0.00 0.00 35.87 3.51
3187 5179 1.501582 GGCAAGTATCCTCCCTGACT 58.498 55.000 0.00 0.00 0.00 3.41
3188 5180 2.679082 GGCAAGTATCCTCCCTGACTA 58.321 52.381 0.00 0.00 0.00 2.59
3189 5181 2.365941 GGCAAGTATCCTCCCTGACTAC 59.634 54.545 0.00 0.00 0.00 2.73
3190 5182 3.301274 GCAAGTATCCTCCCTGACTACT 58.699 50.000 0.00 0.00 0.00 2.57
3191 5183 3.068873 GCAAGTATCCTCCCTGACTACTG 59.931 52.174 0.00 0.00 0.00 2.74
3192 5184 3.603965 AGTATCCTCCCTGACTACTGG 57.396 52.381 0.00 0.00 35.34 4.00
3193 5185 3.132056 AGTATCCTCCCTGACTACTGGA 58.868 50.000 0.00 0.00 37.31 3.86
3194 5186 3.532232 AGTATCCTCCCTGACTACTGGAA 59.468 47.826 0.00 0.00 37.31 3.53
3195 5187 2.233305 TCCTCCCTGACTACTGGAAC 57.767 55.000 0.00 0.00 37.31 3.62
3196 5188 1.196012 CCTCCCTGACTACTGGAACC 58.804 60.000 0.00 0.00 37.31 3.62
3197 5189 1.273324 CCTCCCTGACTACTGGAACCT 60.273 57.143 0.00 0.00 37.31 3.50
3198 5190 2.024273 CCTCCCTGACTACTGGAACCTA 60.024 54.545 0.00 0.00 37.31 3.08
3199 5191 3.565890 CCTCCCTGACTACTGGAACCTAA 60.566 52.174 0.00 0.00 37.31 2.69
3200 5192 4.094476 CTCCCTGACTACTGGAACCTAAA 58.906 47.826 0.00 0.00 37.31 1.85
3201 5193 4.495565 TCCCTGACTACTGGAACCTAAAA 58.504 43.478 0.00 0.00 37.31 1.52
3202 5194 4.909088 TCCCTGACTACTGGAACCTAAAAA 59.091 41.667 0.00 0.00 37.31 1.94
3404 5491 5.277297 CGCATCATTTTTCTACGATTGCCTA 60.277 40.000 0.00 0.00 0.00 3.93
3406 5493 6.430451 CATCATTTTTCTACGATTGCCTACC 58.570 40.000 0.00 0.00 0.00 3.18
3424 5511 0.462375 CCGGATTGGTGTCGGTGATA 59.538 55.000 0.00 0.00 39.04 2.15
3439 5555 9.477484 GTGTCGGTGATAAAATGATAGATAACT 57.523 33.333 0.00 0.00 0.00 2.24
3472 5588 7.865706 TTCTTGAATACAATCTAAAGAGGGC 57.134 36.000 0.00 0.00 35.37 5.19
3473 5589 6.357367 TCTTGAATACAATCTAAAGAGGGCC 58.643 40.000 0.00 0.00 35.37 5.80
3474 5590 5.048846 TGAATACAATCTAAAGAGGGCCC 57.951 43.478 16.46 16.46 0.00 5.80
3475 5591 4.476846 TGAATACAATCTAAAGAGGGCCCA 59.523 41.667 27.56 0.00 0.00 5.36
3477 5593 3.372440 ACAATCTAAAGAGGGCCCAAG 57.628 47.619 27.56 12.95 0.00 3.61
3488 5608 5.248380 AGAGGGCCCAAGATTATGATAAC 57.752 43.478 27.56 0.00 0.00 1.89
3490 5610 5.373854 AGAGGGCCCAAGATTATGATAACTT 59.626 40.000 27.56 0.00 0.00 2.66
3516 5636 8.485392 TGTCTCAATCTTACCATCATTATGTGA 58.515 33.333 0.00 0.00 42.06 3.58
3552 5672 1.065126 AGATGGCTAGGTTCCTTGTGC 60.065 52.381 0.00 0.29 0.00 4.57
3560 5680 1.425066 AGGTTCCTTGTGCTGGAATCA 59.575 47.619 8.26 0.00 44.77 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 155 8.726988 TCTGTTTCTTATTCATTTTTCTACGGG 58.273 33.333 0.00 0.00 0.00 5.28
376 379 3.017581 GGTGCCCTGGACCCTCAT 61.018 66.667 0.00 0.00 0.00 2.90
379 382 2.706341 TAACTGGTGCCCTGGACCCT 62.706 60.000 2.17 0.00 31.84 4.34
521 524 1.002366 CATGCTTTTCGGAGTCCTCG 58.998 55.000 7.77 0.00 0.00 4.63
554 557 6.575162 AAGCTGTTCACGAAAATTCCTATT 57.425 33.333 0.00 0.00 0.00 1.73
557 560 4.918810 AAAGCTGTTCACGAAAATTCCT 57.081 36.364 0.00 0.00 0.00 3.36
558 561 8.911247 ATATAAAAGCTGTTCACGAAAATTCC 57.089 30.769 0.00 0.00 0.00 3.01
781 784 5.067283 GCTGGCCCTTCTCGAAATAAAAATA 59.933 40.000 0.00 0.00 0.00 1.40
853 1762 9.923143 CGTTTTTCTTTCCTTTTTAGGGATAAT 57.077 29.630 0.00 0.00 32.41 1.28
855 1764 8.467963 ACGTTTTTCTTTCCTTTTTAGGGATA 57.532 30.769 0.00 0.00 32.41 2.59
856 1765 7.356089 ACGTTTTTCTTTCCTTTTTAGGGAT 57.644 32.000 0.00 0.00 32.41 3.85
857 1766 6.778834 ACGTTTTTCTTTCCTTTTTAGGGA 57.221 33.333 0.00 0.00 0.00 4.20
893 1802 7.610305 ACACTTATTACGTTGATGATTCCCTTT 59.390 33.333 0.00 0.00 0.00 3.11
906 1815 8.609176 CCATAAATAGCACACACTTATTACGTT 58.391 33.333 0.00 0.00 0.00 3.99
920 1829 0.961753 GGCCAGCCCATAAATAGCAC 59.038 55.000 0.00 0.00 0.00 4.40
942 1966 1.302366 GCCGCTTGATGTCATCATGA 58.698 50.000 25.35 9.36 39.39 3.07
986 2010 3.242712 GCAATTTCGGAATTTGTATGCGG 59.757 43.478 20.29 0.00 33.25 5.69
1006 2030 2.048222 CGCGGAAGTTGGAGAGCA 60.048 61.111 0.00 0.00 0.00 4.26
1111 2150 2.794910 CGTTTCCATGTACAGCCTATCG 59.205 50.000 0.33 0.00 0.00 2.92
1182 2224 1.069204 CTGGGTACATGAGGATCCGTG 59.931 57.143 5.98 9.53 0.00 4.94
1261 2309 1.141881 GACGACGATGGCTGGTGAT 59.858 57.895 0.00 0.00 0.00 3.06
1263 2311 1.078759 GAAGACGACGATGGCTGGTG 61.079 60.000 0.00 0.00 0.00 4.17
1279 2330 5.991606 TCAAATATATCTGGCCACGAAGAAG 59.008 40.000 0.00 0.00 0.00 2.85
1284 2335 4.832823 TCTCTCAAATATATCTGGCCACGA 59.167 41.667 0.00 4.02 0.00 4.35
1285 2336 5.139435 TCTCTCAAATATATCTGGCCACG 57.861 43.478 0.00 0.00 0.00 4.94
1289 2340 4.624882 CACGCTCTCTCAAATATATCTGGC 59.375 45.833 0.00 0.00 0.00 4.85
1301 2352 2.583441 CCAACCCCACGCTCTCTCA 61.583 63.158 0.00 0.00 0.00 3.27
1345 2396 0.527817 AAAATAGAGGCGCGAGGACG 60.528 55.000 12.10 0.00 42.93 4.79
1375 2426 0.179045 ATTGCGCCTGTGATACTCCC 60.179 55.000 4.18 0.00 0.00 4.30
1423 2474 3.710722 ACTCCTCAGGCTTGCCGG 61.711 66.667 5.95 0.00 0.00 6.13
1457 2508 1.378514 ACCATCATCAACCGGTGGC 60.379 57.895 8.52 0.00 33.24 5.01
1474 2525 1.940613 GGAAGCATCCGGTGATAACAC 59.059 52.381 0.00 0.00 39.95 3.32
1505 2556 2.045634 GCAGCAGTGAGGGCATCA 60.046 61.111 0.00 0.00 34.79 3.07
1526 2577 2.416547 CAGGCAGGACGTTACAAATCTG 59.583 50.000 0.00 0.00 0.00 2.90
1532 2583 0.899019 TATGCAGGCAGGACGTTACA 59.101 50.000 0.00 0.00 0.00 2.41
1536 2587 2.462456 CATATATGCAGGCAGGACGT 57.538 50.000 0.00 0.00 0.00 4.34
1570 2629 4.877378 ACAAGTTAGTACGGATGAACCA 57.123 40.909 0.00 0.00 38.90 3.67
1575 2634 4.232221 ACACGAACAAGTTAGTACGGATG 58.768 43.478 0.00 0.00 0.00 3.51
1597 2656 2.364970 CCAGGCACTTCAAATTGGTGAA 59.635 45.455 6.57 0.19 34.60 3.18
1678 2737 1.413445 CTCCTGGATCTTCTGGCTCAG 59.587 57.143 0.00 0.00 0.00 3.35
1775 2834 1.967779 GTTTGGGTTATGCAACTGGGT 59.032 47.619 0.00 0.00 34.88 4.51
1809 2868 7.604164 ACAAGAAATAGTACAACAGATCACAGG 59.396 37.037 0.00 0.00 0.00 4.00
1824 2883 9.057089 CACCTCAAAGTTTAGACAAGAAATAGT 57.943 33.333 0.00 0.00 0.00 2.12
1825 2884 8.507249 CCACCTCAAAGTTTAGACAAGAAATAG 58.493 37.037 0.00 0.00 0.00 1.73
1853 2912 1.133253 CGTTGGCGATGCACTGAAG 59.867 57.895 0.00 0.00 41.33 3.02
2002 3064 0.839277 ATACCACCATAGCAGCAGCA 59.161 50.000 3.17 0.00 45.49 4.41
2108 3173 0.895559 CTCCTTGGGAACACCCTTGC 60.896 60.000 6.85 0.00 43.80 4.01
2119 3184 0.627986 ATTCTTCTGGCCTCCTTGGG 59.372 55.000 3.32 0.00 36.00 4.12
2136 3201 4.263639 ACATTCCTCATCCACTCACACATT 60.264 41.667 0.00 0.00 0.00 2.71
2248 3313 8.281212 ACCCAACAAGAAAATGATGTATACTC 57.719 34.615 4.17 0.36 0.00 2.59
2315 3413 6.166279 TCACTTCACTATGTTTGAGACCATC 58.834 40.000 0.00 0.00 0.00 3.51
2352 3450 7.878495 TCTTCCCTGGGTATATTACAAAACAT 58.122 34.615 13.56 0.00 0.00 2.71
2356 3454 7.758820 TCTTCTTCCCTGGGTATATTACAAA 57.241 36.000 13.56 0.00 0.00 2.83
2366 3465 0.767060 ACGGTTCTTCTTCCCTGGGT 60.767 55.000 13.56 0.00 0.00 4.51
2376 3475 3.500680 TCCATAAGCACAAACGGTTCTTC 59.499 43.478 0.00 0.00 34.69 2.87
2411 3510 4.654262 TCTTACACTTGTGTCTTCTCCCTT 59.346 41.667 9.85 0.00 0.00 3.95
2417 3516 3.743396 CAGGCTCTTACACTTGTGTCTTC 59.257 47.826 9.85 0.00 0.00 2.87
2428 3527 1.352083 AGTTCCTGCAGGCTCTTACA 58.648 50.000 28.91 5.83 34.44 2.41
2436 3535 4.213564 ACTTATCTGAAGTTCCTGCAGG 57.786 45.455 27.87 27.87 37.71 4.85
2477 3576 4.396166 CGGGAGAAACAGCAATAATTGAGT 59.604 41.667 0.00 0.00 0.00 3.41
2489 3588 2.826725 AGGAGTTCTACGGGAGAAACAG 59.173 50.000 3.76 0.00 45.90 3.16
2498 3597 2.018515 GAGGACTGAGGAGTTCTACGG 58.981 57.143 0.00 0.00 38.28 4.02
2500 3599 1.402613 GCGAGGACTGAGGAGTTCTAC 59.597 57.143 0.00 0.00 38.28 2.59
2534 3633 5.388475 CGTCAGGTTCGAGTTGAATAAACAG 60.388 44.000 0.00 0.00 41.61 3.16
2543 3642 1.126846 GCAATCGTCAGGTTCGAGTTG 59.873 52.381 0.00 0.00 40.57 3.16
2556 3655 6.650807 TCTTCATTTCTCAACTTAGCAATCGT 59.349 34.615 0.00 0.00 0.00 3.73
2560 3659 5.473504 GGGTCTTCATTTCTCAACTTAGCAA 59.526 40.000 0.00 0.00 0.00 3.91
2564 3663 5.576563 TGGGGTCTTCATTTCTCAACTTA 57.423 39.130 0.00 0.00 0.00 2.24
2567 3666 4.145052 ACTTGGGGTCTTCATTTCTCAAC 58.855 43.478 0.00 0.00 0.00 3.18
2576 3675 1.780309 ACAATGGACTTGGGGTCTTCA 59.220 47.619 0.00 0.00 43.97 3.02
2605 3704 2.151202 TCCCAGCTACGCTTTTGAAAG 58.849 47.619 0.00 0.00 36.40 2.62
2659 3758 6.500490 TCTTATATTATGGGAGGAGGGAGT 57.500 41.667 0.00 0.00 0.00 3.85
2660 3759 5.365314 GCTCTTATATTATGGGAGGAGGGAG 59.635 48.000 8.67 0.00 0.00 4.30
2662 3761 5.032846 TGCTCTTATATTATGGGAGGAGGG 58.967 45.833 8.67 0.00 0.00 4.30
2679 4096 9.545105 TCAAAATCATGTTTGTAAAATGCTCTT 57.455 25.926 8.23 0.00 39.16 2.85
2680 4097 9.199982 CTCAAAATCATGTTTGTAAAATGCTCT 57.800 29.630 8.23 0.00 39.16 4.09
2682 4099 8.891671 ACTCAAAATCATGTTTGTAAAATGCT 57.108 26.923 8.23 0.00 39.16 3.79
2683 4100 8.223100 GGACTCAAAATCATGTTTGTAAAATGC 58.777 33.333 8.23 0.00 39.16 3.56
2684 4101 9.258826 TGGACTCAAAATCATGTTTGTAAAATG 57.741 29.630 8.23 0.00 39.16 2.32
2685 4102 9.829507 TTGGACTCAAAATCATGTTTGTAAAAT 57.170 25.926 8.23 0.00 39.16 1.82
2686 4103 9.311916 CTTGGACTCAAAATCATGTTTGTAAAA 57.688 29.630 8.23 0.05 39.16 1.52
2687 4104 8.474025 ACTTGGACTCAAAATCATGTTTGTAAA 58.526 29.630 8.23 0.00 39.16 2.01
2688 4105 8.006298 ACTTGGACTCAAAATCATGTTTGTAA 57.994 30.769 8.23 0.00 39.16 2.41
2690 4107 6.469782 ACTTGGACTCAAAATCATGTTTGT 57.530 33.333 8.23 0.00 39.16 2.83
2691 4108 8.352201 TCTTACTTGGACTCAAAATCATGTTTG 58.648 33.333 3.05 3.05 39.41 2.93
2692 4109 8.463930 TCTTACTTGGACTCAAAATCATGTTT 57.536 30.769 0.00 0.00 31.77 2.83
2694 4111 8.517878 CATTCTTACTTGGACTCAAAATCATGT 58.482 33.333 0.00 0.00 31.77 3.21
2695 4112 8.733458 TCATTCTTACTTGGACTCAAAATCATG 58.267 33.333 0.00 0.00 31.77 3.07
2696 4113 8.868522 TCATTCTTACTTGGACTCAAAATCAT 57.131 30.769 0.00 0.00 31.77 2.45
2697 4114 8.690203 TTCATTCTTACTTGGACTCAAAATCA 57.310 30.769 0.00 0.00 31.77 2.57
2703 4120 5.415701 GCCATTTCATTCTTACTTGGACTCA 59.584 40.000 0.00 0.00 0.00 3.41
2705 4122 4.706962 GGCCATTTCATTCTTACTTGGACT 59.293 41.667 0.00 0.00 0.00 3.85
2706 4123 4.438744 CGGCCATTTCATTCTTACTTGGAC 60.439 45.833 2.24 0.00 0.00 4.02
2708 4125 3.734902 GCGGCCATTTCATTCTTACTTGG 60.735 47.826 2.24 0.00 0.00 3.61
2709 4126 3.438360 GCGGCCATTTCATTCTTACTTG 58.562 45.455 2.24 0.00 0.00 3.16
2711 4128 2.024414 GGCGGCCATTTCATTCTTACT 58.976 47.619 15.62 0.00 0.00 2.24
2713 4130 1.398692 GGGCGGCCATTTCATTCTTA 58.601 50.000 25.33 0.00 0.00 2.10
2714 4131 1.666209 CGGGCGGCCATTTCATTCTT 61.666 55.000 29.19 0.00 0.00 2.52
2763 4752 0.523519 TGTTGCGTGCTTTTGTGACA 59.476 45.000 0.00 0.00 0.00 3.58
2777 4766 1.233019 TCTTCTCTGCTGCTTGTTGC 58.767 50.000 0.00 0.00 43.25 4.17
2794 4783 3.843027 TCTTCCATTCTCCTGCTCTTTCT 59.157 43.478 0.00 0.00 0.00 2.52
2819 4808 3.327626 TCTGCGCGGTAGAACAATTTTA 58.672 40.909 17.37 0.00 0.00 1.52
3029 5021 5.424121 AAAATTTCCGAGTTGTCTCACTG 57.576 39.130 0.00 0.00 40.44 3.66
3055 5047 8.522830 TGAAGACACACAAAAGAAGAAAAAGAT 58.477 29.630 0.00 0.00 0.00 2.40
3136 5128 5.561725 GCTCATCTTTCTCACTTTCGCTTTT 60.562 40.000 0.00 0.00 0.00 2.27
3137 5129 4.083590 GCTCATCTTTCTCACTTTCGCTTT 60.084 41.667 0.00 0.00 0.00 3.51
3138 5130 3.434984 GCTCATCTTTCTCACTTTCGCTT 59.565 43.478 0.00 0.00 0.00 4.68
3139 5131 2.999355 GCTCATCTTTCTCACTTTCGCT 59.001 45.455 0.00 0.00 0.00 4.93
3140 5132 2.738846 TGCTCATCTTTCTCACTTTCGC 59.261 45.455 0.00 0.00 0.00 4.70
3141 5133 4.628766 TGATGCTCATCTTTCTCACTTTCG 59.371 41.667 10.76 0.00 38.60 3.46
3142 5134 6.458478 CCATGATGCTCATCTTTCTCACTTTC 60.458 42.308 10.76 0.00 34.28 2.62
3143 5135 5.357314 CCATGATGCTCATCTTTCTCACTTT 59.643 40.000 10.76 0.00 34.28 2.66
3144 5136 4.882427 CCATGATGCTCATCTTTCTCACTT 59.118 41.667 10.76 0.00 34.28 3.16
3145 5137 4.452825 CCATGATGCTCATCTTTCTCACT 58.547 43.478 10.76 0.00 34.28 3.41
3146 5138 3.564644 CCCATGATGCTCATCTTTCTCAC 59.435 47.826 10.76 0.00 34.28 3.51
3147 5139 3.434596 CCCCATGATGCTCATCTTTCTCA 60.435 47.826 10.76 0.00 34.28 3.27
3148 5140 3.147629 CCCCATGATGCTCATCTTTCTC 58.852 50.000 10.76 0.00 34.28 2.87
3149 5141 2.752154 GCCCCATGATGCTCATCTTTCT 60.752 50.000 10.76 0.00 34.28 2.52
3150 5142 1.612463 GCCCCATGATGCTCATCTTTC 59.388 52.381 10.76 0.00 34.28 2.62
3151 5143 1.063492 TGCCCCATGATGCTCATCTTT 60.063 47.619 10.76 0.00 34.28 2.52
3152 5144 0.554305 TGCCCCATGATGCTCATCTT 59.446 50.000 10.76 2.44 34.28 2.40
3153 5145 0.554305 TTGCCCCATGATGCTCATCT 59.446 50.000 10.76 0.00 34.28 2.90
3154 5146 0.959553 CTTGCCCCATGATGCTCATC 59.040 55.000 0.00 3.03 34.28 2.92
3155 5147 0.260816 ACTTGCCCCATGATGCTCAT 59.739 50.000 0.00 0.00 37.65 2.90
3156 5148 0.918258 TACTTGCCCCATGATGCTCA 59.082 50.000 0.00 0.00 0.00 4.26
3157 5149 2.157738 GATACTTGCCCCATGATGCTC 58.842 52.381 0.00 0.00 0.00 4.26
3158 5150 1.202976 GGATACTTGCCCCATGATGCT 60.203 52.381 0.00 0.00 0.00 3.79
3159 5151 1.251251 GGATACTTGCCCCATGATGC 58.749 55.000 0.00 0.00 0.00 3.91
3173 5165 3.596940 TCCAGTAGTCAGGGAGGATAC 57.403 52.381 0.00 0.00 0.00 2.24
3174 5166 3.373877 GGTTCCAGTAGTCAGGGAGGATA 60.374 52.174 0.00 0.00 31.19 2.59
3175 5167 2.627217 GGTTCCAGTAGTCAGGGAGGAT 60.627 54.545 0.00 0.00 31.19 3.24
3176 5168 1.273098 GGTTCCAGTAGTCAGGGAGGA 60.273 57.143 0.00 0.00 31.19 3.71
3177 5169 1.196012 GGTTCCAGTAGTCAGGGAGG 58.804 60.000 0.00 0.00 31.19 4.30
3178 5170 2.239681 AGGTTCCAGTAGTCAGGGAG 57.760 55.000 0.00 0.00 31.19 4.30
3179 5171 3.839323 TTAGGTTCCAGTAGTCAGGGA 57.161 47.619 0.00 0.00 0.00 4.20
3180 5172 4.903045 TTTTAGGTTCCAGTAGTCAGGG 57.097 45.455 0.00 0.00 0.00 4.45
3200 5192 9.328721 CACTTTCGCTTTTCTTTTTGAATTTTT 57.671 25.926 0.00 0.00 34.24 1.94
3201 5193 8.716909 TCACTTTCGCTTTTCTTTTTGAATTTT 58.283 25.926 0.00 0.00 34.24 1.82
3202 5194 8.250538 TCACTTTCGCTTTTCTTTTTGAATTT 57.749 26.923 0.00 0.00 34.24 1.82
3203 5195 7.759433 TCTCACTTTCGCTTTTCTTTTTGAATT 59.241 29.630 0.00 0.00 34.24 2.17
3204 5196 7.257722 TCTCACTTTCGCTTTTCTTTTTGAAT 58.742 30.769 0.00 0.00 34.24 2.57
3205 5197 6.616947 TCTCACTTTCGCTTTTCTTTTTGAA 58.383 32.000 0.00 0.00 0.00 2.69
3206 5198 6.189677 TCTCACTTTCGCTTTTCTTTTTGA 57.810 33.333 0.00 0.00 0.00 2.69
3207 5199 6.869421 TTCTCACTTTCGCTTTTCTTTTTG 57.131 33.333 0.00 0.00 0.00 2.44
3208 5200 7.312899 TCTTTCTCACTTTCGCTTTTCTTTTT 58.687 30.769 0.00 0.00 0.00 1.94
3209 5201 6.852664 TCTTTCTCACTTTCGCTTTTCTTTT 58.147 32.000 0.00 0.00 0.00 2.27
3210 5202 6.436843 TCTTTCTCACTTTCGCTTTTCTTT 57.563 33.333 0.00 0.00 0.00 2.52
3211 5203 6.260936 TCATCTTTCTCACTTTCGCTTTTCTT 59.739 34.615 0.00 0.00 0.00 2.52
3212 5204 5.760253 TCATCTTTCTCACTTTCGCTTTTCT 59.240 36.000 0.00 0.00 0.00 2.52
3213 5205 5.990408 TCATCTTTCTCACTTTCGCTTTTC 58.010 37.500 0.00 0.00 0.00 2.29
3381 5468 4.925068 AGGCAATCGTAGAAAAATGATGC 58.075 39.130 0.00 0.00 43.58 3.91
3406 5493 2.303163 TTATCACCGACACCAATCCG 57.697 50.000 0.00 0.00 0.00 4.18
3466 5582 4.916424 AGTTATCATAATCTTGGGCCCTCT 59.084 41.667 25.70 5.08 0.00 3.69
3467 5583 5.248380 AGTTATCATAATCTTGGGCCCTC 57.752 43.478 25.70 0.00 0.00 4.30
3469 5585 5.140454 ACAAGTTATCATAATCTTGGGCCC 58.860 41.667 17.59 17.59 40.74 5.80
3470 5586 6.064717 AGACAAGTTATCATAATCTTGGGCC 58.935 40.000 17.12 0.00 40.74 5.80
3472 5588 8.737168 TTGAGACAAGTTATCATAATCTTGGG 57.263 34.615 17.12 2.51 40.74 4.12
3488 5608 9.334947 ACATAATGATGGTAAGATTGAGACAAG 57.665 33.333 0.00 0.00 37.39 3.16
3490 5610 8.485392 TCACATAATGATGGTAAGATTGAGACA 58.515 33.333 0.00 0.00 37.39 3.41
3516 5636 9.091220 CCTAGCCATCTAACCTATACTTAGTTT 57.909 37.037 0.00 0.00 0.00 2.66
3529 5649 4.192317 CACAAGGAACCTAGCCATCTAAC 58.808 47.826 0.00 0.00 0.00 2.34
3552 5672 0.907486 TCCAGGTGAGCTGATTCCAG 59.093 55.000 14.03 0.00 43.22 3.86
3560 5680 2.264455 AGACTTGAATCCAGGTGAGCT 58.736 47.619 0.00 0.00 32.35 4.09


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

AutoCloner maintained by Alex Coulton.