Multiple sequence alignment - TraesCS1D01G343900

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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 TraesCS1D01G343900 chr1D 100.000 3915 0 0 1 3915 432789120 432785206 0.000000e+00 7230
1 TraesCS1D01G343900 chr1A 94.333 3335 109 27 1 3289 531225404 531222104 0.000000e+00 5038
2 TraesCS1D01G343900 chr1A 86.719 512 42 13 3381 3877 531222103 531221603 2.660000e-151 545
3 TraesCS1D01G343900 chr1B 96.582 2604 73 11 1 2593 584142649 584140051 0.000000e+00 4301
4 TraesCS1D01G343900 chr1B 88.248 1353 85 42 2599 3915 584139714 584138400 0.000000e+00 1550


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 TraesCS1D01G343900 chr1D 432785206 432789120 3914 True 7230.0 7230 100.000 1 3915 1 chr1D.!!$R1 3914
1 TraesCS1D01G343900 chr1A 531221603 531225404 3801 True 2791.5 5038 90.526 1 3877 2 chr1A.!!$R1 3876
2 TraesCS1D01G343900 chr1B 584138400 584142649 4249 True 2925.5 4301 92.415 1 3915 2 chr1B.!!$R1 3914

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
401 402 0.820871 TGCTGTTTTGTTTCGCCCTT 59.179 45.0 0.0 0.0 0.00 3.95 F
874 876 0.832135 AGGAACAGTGAAGCCTCCGA 60.832 55.0 0.0 0.0 0.00 4.55 F
2420 2433 0.323999 TGCAGCTCCTTTGCCATGAT 60.324 50.0 0.0 0.0 40.81 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 1737 0.173708 GCCTCTAAGAGTCCACCACG 59.826 60.0 0.00 0.0 0.00 4.94 R
2808 3176 0.668535 TGGCGAGATCGGATACACAG 59.331 55.0 4.18 0.0 40.23 3.66 R
3406 3804 0.103208 AAAGAGCGGCGAGTGATAGG 59.897 55.0 12.98 0.0 0.00 2.57 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
22 23 3.248024 TCTCTACCTTTCTTTGGGCTGA 58.752 45.455 0.00 0.00 0.00 4.26
110 111 7.362315 CCACATTATGCTTGAACTTTGAGATGA 60.362 37.037 0.00 0.00 0.00 2.92
120 121 7.156876 TGAACTTTGAGATGAACAAACACTT 57.843 32.000 0.00 0.00 34.30 3.16
173 174 2.605837 TTAGTTCCTGCAACGTGTCA 57.394 45.000 0.00 0.00 40.32 3.58
217 218 6.136155 TCAGGACAGTTCATATATCCAGACA 58.864 40.000 0.00 0.00 31.41 3.41
223 224 7.795047 ACAGTTCATATATCCAGACATGACAA 58.205 34.615 0.00 0.00 0.00 3.18
372 373 3.605634 CATGTAAATGTTCCTCACCGGA 58.394 45.455 9.46 0.00 41.06 5.14
401 402 0.820871 TGCTGTTTTGTTTCGCCCTT 59.179 45.000 0.00 0.00 0.00 3.95
427 429 6.764308 TGAATGACCATTGATTCCTTCTTC 57.236 37.500 0.00 0.00 0.00 2.87
678 680 4.985538 TGCATAGACCAAAGAAGAAAGGT 58.014 39.130 0.00 0.00 37.00 3.50
785 787 1.258458 CACGCTGCAACAAAACCATTG 59.742 47.619 0.00 0.00 0.00 2.82
874 876 0.832135 AGGAACAGTGAAGCCTCCGA 60.832 55.000 0.00 0.00 0.00 4.55
911 913 6.867662 ACCTGATGTTCAACTTTCTACAAG 57.132 37.500 0.00 0.00 0.00 3.16
921 923 6.162079 TCAACTTTCTACAAGCAGAGAGATG 58.838 40.000 0.00 0.00 33.45 2.90
985 987 2.308570 TGCTTAGCCTCTTTTCCCATCA 59.691 45.455 0.29 0.00 0.00 3.07
996 998 6.088016 TCTTTTCCCATCATTCAACACTTG 57.912 37.500 0.00 0.00 0.00 3.16
1235 1238 9.533253 AAATATTGAATAAGTTTGCTACCATGC 57.467 29.630 0.00 0.00 0.00 4.06
1250 1253 3.164268 ACCATGCAGTGCTTAAATTCCA 58.836 40.909 17.60 0.00 0.00 3.53
1287 1290 9.933723 ATTTTCAGCAATGCTTTAAGAATACTT 57.066 25.926 4.36 0.00 36.40 2.24
1660 1668 2.683362 GGCAGCTGTTTTAGGTATGTCC 59.317 50.000 16.64 0.00 34.81 4.02
1689 1697 7.665559 ACAGTCAAGTTTGAATATCTTTAGGCA 59.334 33.333 0.00 0.00 39.21 4.75
1729 1737 5.653507 TGCATGCCTATGTGAAAGAAATTC 58.346 37.500 16.68 0.00 36.65 2.17
1807 1815 3.139077 GGTCTTGATTACCTATTGGGCG 58.861 50.000 0.00 0.00 39.10 6.13
2120 2133 4.002982 TGTCCTCAATTCTCGAAACCATG 58.997 43.478 0.00 0.00 0.00 3.66
2219 2232 5.432885 TGTTTTACTTTAAGTGCCTCAGC 57.567 39.130 8.00 0.00 40.48 4.26
2290 2303 6.719365 ACGCAGAGATTTATATTGCTTTCAC 58.281 36.000 0.00 0.00 32.80 3.18
2293 2306 7.521099 CGCAGAGATTTATATTGCTTTCACCAT 60.521 37.037 0.00 0.00 32.80 3.55
2420 2433 0.323999 TGCAGCTCCTTTGCCATGAT 60.324 50.000 0.00 0.00 40.81 2.45
2445 2458 7.823149 ATAAAGAGCTGACATTTTGCATTTC 57.177 32.000 0.00 0.00 0.00 2.17
2662 3008 7.672983 ATATCCAAAGCATACAGGTTAATCG 57.327 36.000 0.00 0.00 36.83 3.34
2799 3145 7.405292 ACTTCCAGGTAATCTTCATGAATCAA 58.595 34.615 8.96 0.00 0.00 2.57
2807 3175 9.064706 GGTAATCTTCATGAATCAATCATCACT 57.935 33.333 8.96 0.00 45.91 3.41
2838 3206 2.535984 CGATCTCGCCATGTGTTCTAAC 59.464 50.000 0.00 0.00 0.00 2.34
2857 3225 0.960286 CAACATGACATGGCCACACA 59.040 50.000 19.39 9.43 33.60 3.72
2952 3327 2.779506 CTTTACAGGGAGGTGAACCAC 58.220 52.381 1.62 0.00 38.89 4.16
2996 3373 2.354604 GCAGAGAAAGAAGACCCAGGAG 60.355 54.545 0.00 0.00 0.00 3.69
3037 3414 1.408822 GCCATGGGTGCTAGCTAGTTT 60.409 52.381 21.62 0.00 0.00 2.66
3144 3527 9.776158 GTTGGATAATAGTCTGATATAGTCGTG 57.224 37.037 0.00 0.00 0.00 4.35
3179 3562 5.343058 TCCGCGCTTATGTACGATAAATAAC 59.657 40.000 5.56 0.00 0.00 1.89
3182 3565 5.999361 GCGCTTATGTACGATAAATAACACG 59.001 40.000 0.00 0.00 0.00 4.49
3278 3676 5.220931 GCTAACTGGAAAGCAATGGTCATAG 60.221 44.000 0.00 0.00 38.63 2.23
3280 3678 5.435686 ACTGGAAAGCAATGGTCATAGTA 57.564 39.130 0.00 0.00 0.00 1.82
3284 3682 7.067494 ACTGGAAAGCAATGGTCATAGTATTTC 59.933 37.037 0.00 0.00 0.00 2.17
3286 3684 7.615365 TGGAAAGCAATGGTCATAGTATTTCTT 59.385 33.333 0.00 0.00 0.00 2.52
3287 3685 9.120538 GGAAAGCAATGGTCATAGTATTTCTTA 57.879 33.333 0.00 0.00 0.00 2.10
3307 3705 7.180322 TCTTATATCCTCTCAAGATGCCATC 57.820 40.000 0.00 0.00 0.00 3.51
3308 3706 6.958778 TCTTATATCCTCTCAAGATGCCATCT 59.041 38.462 0.08 0.08 42.61 2.90
3317 3715 7.387397 CCTCTCAAGATGCCATCTAATAAAGTC 59.613 40.741 7.81 0.00 39.08 3.01
3325 3723 6.504398 TGCCATCTAATAAAGTCGACTACAG 58.496 40.000 20.39 11.35 0.00 2.74
3420 3818 0.459585 TGAAACCTATCACTCGCCGC 60.460 55.000 0.00 0.00 0.00 6.53
3491 3890 8.392372 AGAGGTTAGTAAATCTTTTTCGCTTT 57.608 30.769 0.00 0.00 0.00 3.51
3501 3900 4.805219 TCTTTTTCGCTTTGCCTTTATCC 58.195 39.130 0.00 0.00 0.00 2.59
3512 3911 3.637769 TGCCTTTATCCGCCCTTATTTT 58.362 40.909 0.00 0.00 0.00 1.82
3513 3912 3.383185 TGCCTTTATCCGCCCTTATTTTG 59.617 43.478 0.00 0.00 0.00 2.44
3514 3913 3.383505 GCCTTTATCCGCCCTTATTTTGT 59.616 43.478 0.00 0.00 0.00 2.83
3515 3914 4.736464 GCCTTTATCCGCCCTTATTTTGTG 60.736 45.833 0.00 0.00 0.00 3.33
3516 3915 4.401202 CCTTTATCCGCCCTTATTTTGTGT 59.599 41.667 0.00 0.00 0.00 3.72
3517 3916 4.974368 TTATCCGCCCTTATTTTGTGTG 57.026 40.909 0.00 0.00 0.00 3.82
3518 3917 2.570415 TCCGCCCTTATTTTGTGTGA 57.430 45.000 0.00 0.00 0.00 3.58
3519 3918 2.432444 TCCGCCCTTATTTTGTGTGAG 58.568 47.619 0.00 0.00 0.00 3.51
3520 3919 2.039216 TCCGCCCTTATTTTGTGTGAGA 59.961 45.455 0.00 0.00 0.00 3.27
3521 3920 2.161609 CCGCCCTTATTTTGTGTGAGAC 59.838 50.000 0.00 0.00 0.00 3.36
3522 3921 2.159707 CGCCCTTATTTTGTGTGAGACG 60.160 50.000 0.00 0.00 0.00 4.18
3523 3922 2.812011 GCCCTTATTTTGTGTGAGACGT 59.188 45.455 0.00 0.00 0.00 4.34
3524 3923 3.120304 GCCCTTATTTTGTGTGAGACGTC 60.120 47.826 7.70 7.70 0.00 4.34
3544 3943 4.135153 CCAGACTGCGAGGGGTCG 62.135 72.222 0.00 0.00 37.52 4.79
3605 4021 2.350522 CACTGATGTGGTAGGCTGAAC 58.649 52.381 0.00 0.00 40.33 3.18
3690 4106 2.169978 GAGCTAACGGGGGAATAGTTGT 59.830 50.000 0.00 0.00 0.00 3.32
3699 4115 4.207955 GGGGGAATAGTTGTGAAATCTCC 58.792 47.826 0.00 0.00 0.00 3.71
3700 4116 4.207955 GGGGAATAGTTGTGAAATCTCCC 58.792 47.826 0.00 0.00 40.57 4.30
3725 4141 3.046283 TGGGTATGACTGAGCTACCAT 57.954 47.619 2.17 0.00 37.28 3.55
3731 4147 4.881019 ATGACTGAGCTACCATGGATAC 57.119 45.455 21.47 6.65 0.00 2.24
3826 4248 1.299541 CTGTGAAGTCGCAACCACTT 58.700 50.000 0.00 0.00 36.77 3.16
3878 4300 3.084786 GGAAACCAAGATGAACTCCCAG 58.915 50.000 0.00 0.00 0.00 4.45
3879 4301 3.498661 GGAAACCAAGATGAACTCCCAGT 60.499 47.826 0.00 0.00 0.00 4.00
3883 4305 1.815003 CAAGATGAACTCCCAGTTGCC 59.185 52.381 0.00 0.00 38.80 4.52
3890 4312 0.250338 ACTCCCAGTTGCCGAAGAAC 60.250 55.000 0.00 0.00 0.00 3.01
3891 4313 0.250295 CTCCCAGTTGCCGAAGAACA 60.250 55.000 0.00 0.00 0.00 3.18
3894 4316 1.151668 CCAGTTGCCGAAGAACAGAG 58.848 55.000 0.00 0.00 0.00 3.35
3899 4321 2.291043 GCCGAAGAACAGAGGGGGA 61.291 63.158 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.600057 GTGCTCAGCCCAAAGAAAGG 59.400 55.000 0.00 0.00 0.00 3.11
22 23 6.284459 GTCTAAGATATGCCTACTTTGTGCT 58.716 40.000 0.00 0.00 0.00 4.40
120 121 7.896496 ACATAAGGGGAATGGTATAACAAAACA 59.104 33.333 0.00 0.00 0.00 2.83
217 218 8.408043 TCTTACAGGAAATGAACATTTGTCAT 57.592 30.769 15.92 0.04 40.77 3.06
223 224 7.363268 GGCTCATTCTTACAGGAAATGAACATT 60.363 37.037 0.00 0.00 0.00 2.71
291 292 5.738909 AGTCCGAGAATCAAGACAATGAAT 58.261 37.500 0.00 0.00 39.70 2.57
372 373 6.455513 GCGAAACAAAACAGCATTCTCTTTTT 60.456 34.615 0.00 0.00 0.00 1.94
401 402 6.429151 AGAAGGAATCAATGGTCATTCATCA 58.571 36.000 12.26 0.00 37.09 3.07
427 429 7.420800 GCTTGACATTATCAGACTAAATTGGG 58.579 38.462 0.00 0.00 38.99 4.12
545 547 8.225416 ACTCCAGAAGAAGGTAAAAAGGTAAAT 58.775 33.333 0.00 0.00 0.00 1.40
546 548 7.580007 ACTCCAGAAGAAGGTAAAAAGGTAAA 58.420 34.615 0.00 0.00 0.00 2.01
547 549 7.145474 ACTCCAGAAGAAGGTAAAAAGGTAA 57.855 36.000 0.00 0.00 0.00 2.85
548 550 6.758806 ACTCCAGAAGAAGGTAAAAAGGTA 57.241 37.500 0.00 0.00 0.00 3.08
678 680 2.054232 TTGGCGTGTAGAAACCCAAA 57.946 45.000 0.00 0.00 31.53 3.28
785 787 7.533426 CAAAGCCTTATCATCTTACATATGCC 58.467 38.462 1.58 0.00 0.00 4.40
874 876 9.461312 TTGAACATCAGGTTGTTTATATAGCTT 57.539 29.630 0.00 0.00 40.63 3.74
911 913 1.406614 CCAACTGGTCCATCTCTCTGC 60.407 57.143 0.00 0.00 0.00 4.26
921 923 4.160252 ACAAAATGCATATCCAACTGGTCC 59.840 41.667 0.00 0.00 36.34 4.46
985 987 7.394359 AGCATACTCCATTTACAAGTGTTGAAT 59.606 33.333 0.00 0.00 0.00 2.57
996 998 8.212495 CGTCGTAAATTAGCATACTCCATTTAC 58.788 37.037 9.06 9.06 38.00 2.01
1235 1238 8.424274 AAAGAAAAAGTGGAATTTAAGCACTG 57.576 30.769 0.00 0.00 0.00 3.66
1250 1253 8.667076 AGCATTGCTGAAAATAAAGAAAAAGT 57.333 26.923 11.09 0.00 37.57 2.66
1263 1266 9.762933 AAAAGTATTCTTAAAGCATTGCTGAAA 57.237 25.926 12.82 8.66 34.34 2.69
1284 1287 7.344612 AGGAGAGTTCCAAAATGGTTAAAAAGT 59.655 33.333 0.00 0.00 46.64 2.66
1285 1288 7.726216 AGGAGAGTTCCAAAATGGTTAAAAAG 58.274 34.615 0.00 0.00 46.64 2.27
1286 1289 7.669089 AGGAGAGTTCCAAAATGGTTAAAAA 57.331 32.000 0.00 0.00 46.64 1.94
1287 1290 7.669089 AAGGAGAGTTCCAAAATGGTTAAAA 57.331 32.000 0.00 0.00 46.64 1.52
1331 1339 7.458677 CACATATCCATATCAACGCACATTAG 58.541 38.462 0.00 0.00 0.00 1.73
1596 1604 6.921857 GTGCATCCCATCTATTGAAATCTTTG 59.078 38.462 0.00 0.00 0.00 2.77
1689 1697 6.492429 AGGCATGCAACATGTAATCATCTATT 59.508 34.615 21.36 0.00 31.15 1.73
1701 1709 3.786516 TTCACATAGGCATGCAACATG 57.213 42.857 21.36 19.59 35.39 3.21
1729 1737 0.173708 GCCTCTAAGAGTCCACCACG 59.826 60.000 0.00 0.00 0.00 4.94
1786 1794 3.139077 CGCCCAATAGGTAATCAAGACC 58.861 50.000 0.00 0.00 38.26 3.85
1807 1815 2.997315 GGCAAAAGCAGGGGTCCC 60.997 66.667 0.00 0.00 0.00 4.46
1871 1879 2.232696 TGAGTTTAGCCATGCACGTCTA 59.767 45.455 0.00 0.00 0.00 2.59
1877 1885 2.483877 CGAAACTGAGTTTAGCCATGCA 59.516 45.455 11.01 0.00 35.77 3.96
1878 1886 2.484264 ACGAAACTGAGTTTAGCCATGC 59.516 45.455 16.40 0.12 35.77 4.06
1951 1964 8.092687 TGGTAGTAGTCAAAGGTTCAGATTAAC 58.907 37.037 0.00 0.00 0.00 2.01
2057 2070 6.980593 AGACACATCTGATATCTAGAAGCAC 58.019 40.000 3.98 0.00 32.29 4.40
2219 2232 5.236478 AGAAAAACTCTGGTGTACACATTCG 59.764 40.000 26.51 14.17 31.12 3.34
2290 2303 3.059393 CGCACATGATTAGTACTGCATGG 60.059 47.826 25.59 19.12 41.71 3.66
2293 2306 3.186909 GACGCACATGATTAGTACTGCA 58.813 45.455 5.39 1.37 0.00 4.41
2420 2433 8.742777 AGAAATGCAAAATGTCAGCTCTTTATA 58.257 29.630 0.00 0.00 0.00 0.98
2637 2983 7.308589 GCGATTAACCTGTATGCTTTGGATATT 60.309 37.037 0.00 0.00 0.00 1.28
2638 2984 6.149474 GCGATTAACCTGTATGCTTTGGATAT 59.851 38.462 0.00 0.00 0.00 1.63
2662 3008 0.731855 AAAGAAGACGCGTCGGTAGC 60.732 55.000 31.56 19.69 34.09 3.58
2799 3145 5.076182 AGATCGGATACACAGAGTGATGAT 58.924 41.667 3.88 0.29 36.96 2.45
2807 3175 0.952280 GGCGAGATCGGATACACAGA 59.048 55.000 4.18 0.00 40.23 3.41
2808 3176 0.668535 TGGCGAGATCGGATACACAG 59.331 55.000 4.18 0.00 40.23 3.66
2838 3206 0.960286 TGTGTGGCCATGTCATGTTG 59.040 50.000 9.72 0.00 0.00 3.33
2857 3225 3.352222 GCTTGTCGCAGCAGCTGT 61.352 61.111 23.60 0.00 39.83 4.40
2925 3300 2.046314 TCCCTGTAAAGCGCCAGC 60.046 61.111 2.29 0.00 45.58 4.85
2926 3301 1.450312 CCTCCCTGTAAAGCGCCAG 60.450 63.158 2.29 3.73 0.00 4.85
2927 3302 2.221299 ACCTCCCTGTAAAGCGCCA 61.221 57.895 2.29 0.00 0.00 5.69
2928 3303 1.745489 CACCTCCCTGTAAAGCGCC 60.745 63.158 2.29 0.00 0.00 6.53
2929 3304 0.321298 TTCACCTCCCTGTAAAGCGC 60.321 55.000 0.00 0.00 0.00 5.92
2930 3305 1.439679 GTTCACCTCCCTGTAAAGCG 58.560 55.000 0.00 0.00 0.00 4.68
3077 3458 7.435488 GCGCCCTTATGATTATAGTACAGTATG 59.565 40.741 0.00 0.00 46.00 2.39
3078 3459 7.417570 GGCGCCCTTATGATTATAGTACAGTAT 60.418 40.741 18.11 0.00 0.00 2.12
3080 3461 5.337330 GGCGCCCTTATGATTATAGTACAGT 60.337 44.000 18.11 0.00 0.00 3.55
3081 3462 5.109903 GGCGCCCTTATGATTATAGTACAG 58.890 45.833 18.11 0.00 0.00 2.74
3082 3463 4.528987 TGGCGCCCTTATGATTATAGTACA 59.471 41.667 26.77 0.00 0.00 2.90
3083 3464 5.080969 TGGCGCCCTTATGATTATAGTAC 57.919 43.478 26.77 0.00 0.00 2.73
3144 3527 1.361668 AAGCGCGGACATGACATGAC 61.362 55.000 22.19 15.38 0.00 3.06
3179 3562 1.205064 CTTGCAAGCTCGGTTCGTG 59.795 57.895 14.65 0.00 0.00 4.35
3182 3565 0.235926 GACACTTGCAAGCTCGGTTC 59.764 55.000 26.27 9.63 0.00 3.62
3221 3616 7.168972 GCAAACATTCACAAAGCTTGTTGTATA 59.831 33.333 0.00 0.00 43.23 1.47
3222 3617 6.018832 GCAAACATTCACAAAGCTTGTTGTAT 60.019 34.615 0.00 0.00 43.23 2.29
3223 3618 5.290643 GCAAACATTCACAAAGCTTGTTGTA 59.709 36.000 0.00 0.00 43.23 2.41
3235 3630 2.166050 AGCTGTTGTGCAAACATTCACA 59.834 40.909 12.68 0.00 40.98 3.58
3236 3631 2.813061 AGCTGTTGTGCAAACATTCAC 58.187 42.857 12.68 5.90 34.99 3.18
3278 3676 9.377312 GGCATCTTGAGAGGATATAAGAAATAC 57.623 37.037 0.00 0.00 33.39 1.89
3280 3678 7.982252 TGGCATCTTGAGAGGATATAAGAAAT 58.018 34.615 0.00 0.00 33.39 2.17
3284 3682 7.185318 AGATGGCATCTTGAGAGGATATAAG 57.815 40.000 24.01 0.00 35.76 1.73
3286 3684 8.851106 ATTAGATGGCATCTTGAGAGGATATA 57.149 34.615 32.93 9.54 40.76 0.86
3287 3685 7.752518 ATTAGATGGCATCTTGAGAGGATAT 57.247 36.000 32.93 8.83 40.76 1.63
3300 3698 7.014326 TCTGTAGTCGACTTTATTAGATGGCAT 59.986 37.037 25.44 0.00 0.00 4.40
3301 3699 6.320418 TCTGTAGTCGACTTTATTAGATGGCA 59.680 38.462 25.44 0.00 0.00 4.92
3308 3706 9.745880 GGATCAAATCTGTAGTCGACTTTATTA 57.254 33.333 25.44 1.28 0.00 0.98
3317 3715 3.384789 TGAGGGGATCAAATCTGTAGTCG 59.615 47.826 0.00 0.00 34.02 4.18
3325 3723 3.282885 GGTCAAGTGAGGGGATCAAATC 58.717 50.000 0.00 0.00 40.43 2.17
3330 3728 2.820197 GTTTTGGTCAAGTGAGGGGATC 59.180 50.000 0.00 0.00 0.00 3.36
3363 3761 8.593945 AATCAATGGGTTCATAGTGTATTGTT 57.406 30.769 0.00 0.00 32.44 2.83
3364 3762 8.055181 AGAATCAATGGGTTCATAGTGTATTGT 58.945 33.333 0.00 0.00 32.44 2.71
3365 3763 8.455903 AGAATCAATGGGTTCATAGTGTATTG 57.544 34.615 0.00 0.00 32.44 1.90
3366 3764 9.125026 GAAGAATCAATGGGTTCATAGTGTATT 57.875 33.333 0.00 0.00 32.44 1.89
3367 3765 8.497745 AGAAGAATCAATGGGTTCATAGTGTAT 58.502 33.333 0.00 0.00 32.44 2.29
3406 3804 0.103208 AAAGAGCGGCGAGTGATAGG 59.897 55.000 12.98 0.00 0.00 2.57
3411 3809 3.120338 TCAAATAAAAAGAGCGGCGAGTG 60.120 43.478 12.98 0.00 0.00 3.51
3491 3890 3.306472 AAATAAGGGCGGATAAAGGCA 57.694 42.857 0.00 0.00 35.71 4.75
3501 3900 2.159707 CGTCTCACACAAAATAAGGGCG 60.160 50.000 0.00 0.00 0.00 6.13
3512 3911 0.816421 TCTGGACGACGTCTCACACA 60.816 55.000 25.87 14.48 32.47 3.72
3513 3912 0.385723 GTCTGGACGACGTCTCACAC 60.386 60.000 25.87 15.86 32.04 3.82
3514 3913 1.947013 GTCTGGACGACGTCTCACA 59.053 57.895 25.87 15.16 32.04 3.58
3515 3914 4.843101 GTCTGGACGACGTCTCAC 57.157 61.111 25.87 16.06 32.04 3.51
3522 3921 2.179517 CCTCGCAGTCTGGACGAC 59.820 66.667 1.14 0.00 43.17 4.34
3523 3922 3.062466 CCCTCGCAGTCTGGACGA 61.062 66.667 1.14 2.28 36.20 4.20
3524 3923 4.135153 CCCCTCGCAGTCTGGACG 62.135 72.222 1.14 0.00 36.20 4.79
3544 3943 0.242017 AAATTTCAGCTCCGCACAGC 59.758 50.000 0.00 0.00 39.99 4.40
3545 3944 3.829886 TTAAATTTCAGCTCCGCACAG 57.170 42.857 0.00 0.00 0.00 3.66
3555 3962 5.674148 CGACGCACATGAGATTAAATTTCAG 59.326 40.000 0.00 0.00 0.00 3.02
3605 4021 0.391263 GGCGGTCCTAACACTCCAAG 60.391 60.000 0.00 0.00 0.00 3.61
3699 4115 1.539065 GCTCAGTCATACCCATCACGG 60.539 57.143 0.00 0.00 0.00 4.94
3700 4116 1.410517 AGCTCAGTCATACCCATCACG 59.589 52.381 0.00 0.00 0.00 4.35
3709 4125 5.393866 TGTATCCATGGTAGCTCAGTCATA 58.606 41.667 12.58 0.00 0.00 2.15
3725 4141 5.130975 AGTTTGGCATAGTGAGATGTATCCA 59.869 40.000 0.00 0.00 0.00 3.41
3731 4147 5.396484 CAACAAGTTTGGCATAGTGAGATG 58.604 41.667 0.00 0.00 0.00 2.90
3732 4148 4.082571 GCAACAAGTTTGGCATAGTGAGAT 60.083 41.667 0.00 0.00 0.00 2.75
3878 4300 0.955919 CCCCTCTGTTCTTCGGCAAC 60.956 60.000 0.00 0.00 0.00 4.17
3879 4301 1.374947 CCCCTCTGTTCTTCGGCAA 59.625 57.895 0.00 0.00 0.00 4.52
3883 4305 2.561478 TTTTCCCCCTCTGTTCTTCG 57.439 50.000 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.