Multiple sequence alignment - TraesCS1A01G167300

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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 TraesCS1A01G167300 chr1A 100.000 3401 0 0 1 3401 300107916 300104516 0.000000e+00 6281.0
1 TraesCS1A01G167300 chr1B 92.948 2510 129 26 239 2724 330505265 330502780 0.000000e+00 3611.0
2 TraesCS1A01G167300 chr1B 83.529 425 40 17 2993 3398 330502732 330502319 1.490000e-98 370.0
3 TraesCS1A01G167300 chr1B 88.550 131 6 4 104 232 330505438 330505315 2.110000e-32 150.0
4 TraesCS1A01G167300 chr1D 93.233 2202 98 25 239 2403 247303454 247305641 0.000000e+00 3193.0
5 TraesCS1A01G167300 chr1D 84.141 990 86 33 2431 3387 247305632 247306583 0.000000e+00 893.0
6 TraesCS1A01G167300 chr1D 93.985 133 4 1 104 232 247303112 247303244 7.440000e-47 198.0
7 TraesCS1A01G167300 chr1D 96.226 106 4 0 1 106 247302981 247303086 1.250000e-39 174.0
8 TraesCS1A01G167300 chr6D 93.548 62 3 1 2936 2996 460779866 460779805 1.300000e-14 91.6
9 TraesCS1A01G167300 chr3D 91.935 62 3 2 2936 2996 378194759 378194819 6.050000e-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 TraesCS1A01G167300 chr1A 300104516 300107916 3400 True 6281.0 6281 100.000000 1 3401 1 chr1A.!!$R1 3400
1 TraesCS1A01G167300 chr1B 330502319 330505438 3119 True 1377.0 3611 88.342333 104 3398 3 chr1B.!!$R1 3294
2 TraesCS1A01G167300 chr1D 247302981 247306583 3602 False 1114.5 3193 91.896250 1 3387 4 chr1D.!!$F1 3386

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
492 729 0.029300 CGCCCGGATGCAAAACATAG 59.971 55.0 0.73 0.0 39.84 2.23 F
790 1038 0.110486 AAGAGACCAAATGCCACGGT 59.890 50.0 0.00 0.0 35.12 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1987 1.214175 TCCCCAAGAAGTCAGCAAACA 59.786 47.619 0.0 0.0 0.0 2.83 R
2646 2969 1.896220 TCTGCTGCGAAATCAAAGGT 58.104 45.000 0.0 0.0 0.0 3.50 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
40 41 4.218635 TGACTATGGAGTGACAGAGAACAC 59.781 45.833 0.00 0.00 35.45 3.32
45 46 2.891580 GGAGTGACAGAGAACACAGGTA 59.108 50.000 0.00 0.00 39.18 3.08
232 265 2.633481 GAGGCTAACCACGGGATAGAAT 59.367 50.000 10.17 0.25 39.06 2.40
234 267 4.426704 AGGCTAACCACGGGATAGAATAT 58.573 43.478 10.17 0.00 39.06 1.28
235 268 5.586877 AGGCTAACCACGGGATAGAATATA 58.413 41.667 10.17 0.00 39.06 0.86
236 269 6.203072 AGGCTAACCACGGGATAGAATATAT 58.797 40.000 10.17 0.00 39.06 0.86
237 270 6.324254 AGGCTAACCACGGGATAGAATATATC 59.676 42.308 10.17 0.00 39.06 1.63
257 493 2.960384 TCCACTAGACGAACAACCAGAA 59.040 45.455 0.00 0.00 0.00 3.02
264 500 2.285977 ACGAACAACCAGAACTGAACC 58.714 47.619 3.19 0.00 0.00 3.62
266 502 2.680841 CGAACAACCAGAACTGAACCAA 59.319 45.455 3.19 0.00 0.00 3.67
267 503 3.242739 CGAACAACCAGAACTGAACCAAG 60.243 47.826 3.19 0.00 0.00 3.61
274 510 3.306641 CCAGAACTGAACCAAGAGAGAGG 60.307 52.174 3.19 0.00 0.00 3.69
338 574 8.797438 AGATTCAAAAGTTAGACAGGGAAATTC 58.203 33.333 0.00 0.00 0.00 2.17
492 729 0.029300 CGCCCGGATGCAAAACATAG 59.971 55.000 0.73 0.00 39.84 2.23
496 733 1.531677 CCGGATGCAAAACATAGCACG 60.532 52.381 0.00 0.00 44.49 5.34
499 736 0.887247 ATGCAAAACATAGCACGCCA 59.113 45.000 0.00 0.00 44.49 5.69
604 841 1.375326 GCGAAACCAAGGAGAGGGT 59.625 57.895 0.00 0.00 39.65 4.34
672 909 3.219928 TCTCGGATCCAGCGAGGC 61.220 66.667 13.41 0.00 37.29 4.70
790 1038 0.110486 AAGAGACCAAATGCCACGGT 59.890 50.000 0.00 0.00 35.12 4.83
791 1039 0.606401 AGAGACCAAATGCCACGGTG 60.606 55.000 0.00 0.00 31.63 4.94
795 1043 3.669344 CAAATGCCACGGTGCGGT 61.669 61.111 1.68 0.00 0.00 5.68
860 1108 2.504244 GCCAGAACGGACGACTCG 60.504 66.667 0.00 0.00 36.56 4.18
989 1237 4.527583 CCTGGAGCAGAGGAGCGC 62.528 72.222 0.00 0.00 40.15 5.92
1510 1758 2.184322 GGCTCGCCGATGAGTTCA 59.816 61.111 0.00 0.00 38.28 3.18
1572 1820 1.248785 CCGAGGACGACAAGGAGGAA 61.249 60.000 0.00 0.00 42.66 3.36
1614 1862 2.887454 TCCACCCCAATGAGGAGATA 57.113 50.000 0.00 0.00 41.22 1.98
1665 1913 1.349688 GTGGATGGTGGTGGTGAAGTA 59.650 52.381 0.00 0.00 0.00 2.24
1682 1930 0.741927 GTATTGTTACCGCCACCGCT 60.742 55.000 0.00 0.00 0.00 5.52
1725 1985 1.480498 GGTGACCAATTGGAGGGTTGT 60.480 52.381 31.22 6.33 37.57 3.32
1726 1986 2.316108 GTGACCAATTGGAGGGTTGTT 58.684 47.619 31.22 5.50 37.57 2.83
1727 1987 2.698274 GTGACCAATTGGAGGGTTGTTT 59.302 45.455 31.22 4.68 37.57 2.83
1741 2001 3.119137 GGGTTGTTTGTTTGCTGACTTCT 60.119 43.478 0.00 0.00 0.00 2.85
2012 2274 9.508567 GAGTTTCTAATGCTGTTTGATAAATCC 57.491 33.333 0.00 0.00 0.00 3.01
2032 2294 8.786826 AAATCCTGACTGTAAATATCGACAAA 57.213 30.769 0.00 0.00 0.00 2.83
2089 2370 5.021033 AGTCCACTGAAGATGATAAGCAG 57.979 43.478 0.00 0.00 0.00 4.24
2096 2377 7.066645 CCACTGAAGATGATAAGCAGAATTCAA 59.933 37.037 8.44 0.00 30.57 2.69
2110 2391 8.218338 AGCAGAATTCAAAAGTACATAGGATG 57.782 34.615 8.44 0.00 0.00 3.51
2111 2392 7.831193 AGCAGAATTCAAAAGTACATAGGATGT 59.169 33.333 8.44 0.00 46.92 3.06
2112 2393 9.109393 GCAGAATTCAAAAGTACATAGGATGTA 57.891 33.333 8.44 0.00 44.38 2.29
2129 2410 9.775854 ATAGGATGTATTCATATTGCTATGAGC 57.224 33.333 0.00 0.00 43.48 4.26
2145 2426 5.064707 GCTATGAGCGAAACCTGTTTATTCA 59.935 40.000 0.00 1.48 32.11 2.57
2174 2456 6.891908 ACACAAGTAGAGGAATATTTGCCAAT 59.108 34.615 0.00 0.00 0.00 3.16
2195 2477 7.575720 GCCAATAAGAGCTGTAAATCTTGTGTT 60.576 37.037 0.00 0.00 36.47 3.32
2196 2478 7.752239 CCAATAAGAGCTGTAAATCTTGTGTTG 59.248 37.037 0.00 0.00 36.47 3.33
2400 2686 9.337396 AGTCAATTACTGAAACAACTTATGTGA 57.663 29.630 0.00 0.00 38.72 3.58
2401 2687 9.599322 GTCAATTACTGAAACAACTTATGTGAG 57.401 33.333 0.00 0.00 42.99 3.51
2402 2688 8.289618 TCAATTACTGAAACAACTTATGTGAGC 58.710 33.333 0.00 0.00 42.99 4.26
2403 2689 6.554334 TTACTGAAACAACTTATGTGAGCC 57.446 37.500 0.00 0.00 42.99 4.70
2404 2690 4.718961 ACTGAAACAACTTATGTGAGCCT 58.281 39.130 0.00 0.00 42.99 4.58
2405 2691 5.133221 ACTGAAACAACTTATGTGAGCCTT 58.867 37.500 0.00 0.00 42.99 4.35
2406 2692 5.239525 ACTGAAACAACTTATGTGAGCCTTC 59.760 40.000 0.00 0.00 42.99 3.46
2407 2693 5.376625 TGAAACAACTTATGTGAGCCTTCT 58.623 37.500 0.00 0.00 42.99 2.85
2408 2694 5.827797 TGAAACAACTTATGTGAGCCTTCTT 59.172 36.000 0.00 0.00 42.99 2.52
2409 2695 6.995686 TGAAACAACTTATGTGAGCCTTCTTA 59.004 34.615 0.00 0.00 42.99 2.10
2410 2696 7.665559 TGAAACAACTTATGTGAGCCTTCTTAT 59.334 33.333 0.00 0.00 42.99 1.73
2411 2697 9.162764 GAAACAACTTATGTGAGCCTTCTTATA 57.837 33.333 0.00 0.00 42.99 0.98
2412 2698 8.494016 AACAACTTATGTGAGCCTTCTTATAC 57.506 34.615 0.00 0.00 42.99 1.47
2413 2699 7.620880 ACAACTTATGTGAGCCTTCTTATACA 58.379 34.615 0.00 0.00 41.93 2.29
2414 2700 8.100791 ACAACTTATGTGAGCCTTCTTATACAA 58.899 33.333 0.00 0.00 41.93 2.41
2415 2701 8.391106 CAACTTATGTGAGCCTTCTTATACAAC 58.609 37.037 0.00 0.00 0.00 3.32
2416 2702 7.852263 ACTTATGTGAGCCTTCTTATACAACT 58.148 34.615 0.00 0.00 0.00 3.16
2417 2703 8.322091 ACTTATGTGAGCCTTCTTATACAACTT 58.678 33.333 0.00 0.00 0.00 2.66
2418 2704 9.167311 CTTATGTGAGCCTTCTTATACAACTTT 57.833 33.333 0.00 0.00 0.00 2.66
2419 2705 6.801539 TGTGAGCCTTCTTATACAACTTTG 57.198 37.500 0.00 0.00 0.00 2.77
2420 2706 6.296026 TGTGAGCCTTCTTATACAACTTTGT 58.704 36.000 0.00 0.00 44.86 2.83
2421 2707 6.770785 TGTGAGCCTTCTTATACAACTTTGTT 59.229 34.615 0.00 0.00 42.35 2.83
2422 2708 7.284489 TGTGAGCCTTCTTATACAACTTTGTTT 59.716 33.333 0.00 0.00 42.35 2.83
2423 2709 7.803659 GTGAGCCTTCTTATACAACTTTGTTTC 59.196 37.037 0.00 0.00 42.35 2.78
2424 2710 7.719633 TGAGCCTTCTTATACAACTTTGTTTCT 59.280 33.333 0.00 0.00 42.35 2.52
2425 2711 9.216117 GAGCCTTCTTATACAACTTTGTTTCTA 57.784 33.333 0.00 0.00 42.35 2.10
2426 2712 9.740710 AGCCTTCTTATACAACTTTGTTTCTAT 57.259 29.630 0.00 0.00 42.35 1.98
2427 2713 9.774742 GCCTTCTTATACAACTTTGTTTCTATG 57.225 33.333 0.00 0.00 42.35 2.23
2435 2721 6.656003 ACAACTTTGTTTCTATGAGTTACGC 58.344 36.000 0.00 0.00 38.47 4.42
2436 2722 6.259167 ACAACTTTGTTTCTATGAGTTACGCA 59.741 34.615 0.00 0.00 38.47 5.24
2445 2768 7.786178 TTCTATGAGTTACGCAAGCATAAAT 57.214 32.000 0.00 0.00 45.62 1.40
2446 2769 7.786178 TCTATGAGTTACGCAAGCATAAATT 57.214 32.000 0.00 0.00 45.62 1.82
2545 2868 5.324409 TGCCTTTATCTGGTCAAGTTCATT 58.676 37.500 0.00 0.00 0.00 2.57
2550 2873 8.244113 CCTTTATCTGGTCAAGTTCATTTAACC 58.756 37.037 0.00 0.00 39.03 2.85
2574 2897 2.787473 ACATTTGCGATCAGAGGGAA 57.213 45.000 0.00 0.00 0.00 3.97
2589 2912 9.868277 GATCAGAGGGAATATTAGATAACACTG 57.132 37.037 0.00 0.00 0.00 3.66
2593 2916 8.317679 AGAGGGAATATTAGATAACACTGATGC 58.682 37.037 0.00 0.00 0.00 3.91
2602 2925 5.625150 AGATAACACTGATGCCCCTTTATC 58.375 41.667 0.00 0.00 0.00 1.75
2616 2939 7.963532 TGCCCCTTTATCTGTCTAGTATAAAG 58.036 38.462 15.20 15.20 40.48 1.85
2646 2969 5.692115 TTCAGTTGTGATTCCATAGCCTA 57.308 39.130 0.00 0.00 30.85 3.93
2653 2976 4.473196 TGTGATTCCATAGCCTACCTTTGA 59.527 41.667 0.00 0.00 0.00 2.69
2657 2980 6.772716 TGATTCCATAGCCTACCTTTGATTTC 59.227 38.462 0.00 0.00 0.00 2.17
2693 3016 4.307432 TCGGTAGTTTCTTTCTGCTTCTG 58.693 43.478 0.00 0.00 0.00 3.02
2724 3047 9.044150 TGCAGTCATTTTTCCTTCTTATTTTTG 57.956 29.630 0.00 0.00 0.00 2.44
2744 3067 3.892284 TGAAGGGAAAACTTGTAGTGCA 58.108 40.909 0.00 0.00 0.00 4.57
2747 3070 3.477530 AGGGAAAACTTGTAGTGCAGAC 58.522 45.455 0.00 0.00 0.00 3.51
2754 3077 4.881019 ACTTGTAGTGCAGACTTGATCT 57.119 40.909 0.00 0.00 38.66 2.75
2770 3093 6.058183 ACTTGATCTAGACACTTTGCAAGTT 58.942 36.000 11.29 0.00 41.07 2.66
2783 3106 5.880332 ACTTTGCAAGTTTGACAGAACTAGA 59.120 36.000 0.00 0.00 39.04 2.43
2811 3135 7.622893 AAAAAGTGAGAGAGAGATATTTGCC 57.377 36.000 0.00 0.00 0.00 4.52
2812 3136 5.946942 AAGTGAGAGAGAGATATTTGCCA 57.053 39.130 0.00 0.00 0.00 4.92
2813 3137 6.497624 AAGTGAGAGAGAGATATTTGCCAT 57.502 37.500 0.00 0.00 0.00 4.40
2814 3138 6.100404 AGTGAGAGAGAGATATTTGCCATC 57.900 41.667 0.00 0.00 0.00 3.51
2815 3139 5.601729 AGTGAGAGAGAGATATTTGCCATCA 59.398 40.000 0.00 0.00 0.00 3.07
2819 3143 7.134362 AGAGAGAGATATTTGCCATCAGAAA 57.866 36.000 0.00 0.00 0.00 2.52
2830 3154 4.415596 TGCCATCAGAAAATAAAGGGTGT 58.584 39.130 0.00 0.00 0.00 4.16
2852 3176 7.807907 GGTGTTTCCATGTATACAGAAAGTTTG 59.192 37.037 16.46 6.89 35.97 2.93
2915 3239 8.437742 CAGTTTCATGACCAATTCATTTTTAGC 58.562 33.333 0.00 0.00 42.87 3.09
2919 3243 7.322664 TCATGACCAATTCATTTTTAGCCTTC 58.677 34.615 0.00 0.00 42.87 3.46
2920 3244 5.708948 TGACCAATTCATTTTTAGCCTTCG 58.291 37.500 0.00 0.00 0.00 3.79
2931 3255 4.546829 TTTAGCCTTCGGTCTGTTACAT 57.453 40.909 0.00 0.00 0.00 2.29
2940 3264 4.890088 TCGGTCTGTTACATTTGCTTAGT 58.110 39.130 0.00 0.00 0.00 2.24
2948 3272 5.106197 TGTTACATTTGCTTAGTGATGCTGG 60.106 40.000 0.00 0.00 0.00 4.85
3004 3352 4.946160 AAGGGGATCTATTTTGGTGTCA 57.054 40.909 0.00 0.00 0.00 3.58
3012 3360 6.374333 GGATCTATTTTGGTGTCAACAAGCTA 59.626 38.462 3.03 0.00 31.78 3.32
3024 3372 4.750098 GTCAACAAGCTAGCTTCTTACACA 59.250 41.667 27.08 5.06 33.42 3.72
3043 3391 4.201910 ACACAGTTTTCTTGGTTGATGACG 60.202 41.667 0.00 0.00 0.00 4.35
3045 3393 4.821805 ACAGTTTTCTTGGTTGATGACGAT 59.178 37.500 0.00 0.00 0.00 3.73
3053 3401 1.818674 GGTTGATGACGATGCCCTTTT 59.181 47.619 0.00 0.00 0.00 2.27
3102 3452 7.445707 TGTGTCACTATATGTAAGCTAGAGAGG 59.554 40.741 4.27 0.00 0.00 3.69
3132 3482 7.756395 ATTGGGAGATAAATAGCATTGTGAG 57.244 36.000 0.00 0.00 0.00 3.51
3140 3490 3.735237 ATAGCATTGTGAGACCCTACG 57.265 47.619 0.00 0.00 0.00 3.51
3143 3493 1.732259 GCATTGTGAGACCCTACGTTG 59.268 52.381 0.00 0.00 0.00 4.10
3148 3498 0.601558 TGAGACCCTACGTTGTCAGC 59.398 55.000 12.99 6.82 33.89 4.26
3149 3499 0.601558 GAGACCCTACGTTGTCAGCA 59.398 55.000 12.99 0.00 33.89 4.41
3150 3500 0.317479 AGACCCTACGTTGTCAGCAC 59.683 55.000 12.99 0.00 33.89 4.40
3156 3506 2.097954 CCTACGTTGTCAGCACGGTATA 59.902 50.000 0.00 0.00 0.00 1.47
3157 3507 1.986698 ACGTTGTCAGCACGGTATAC 58.013 50.000 2.39 0.00 0.00 1.47
3189 3539 4.849518 TCCATTTCAATCCCGTCATTGTA 58.150 39.130 4.09 0.00 35.56 2.41
3192 3542 5.220854 CCATTTCAATCCCGTCATTGTACTC 60.221 44.000 0.00 0.00 35.56 2.59
3194 3544 4.386867 TCAATCCCGTCATTGTACTCTC 57.613 45.455 0.00 0.00 35.56 3.20
3200 3550 4.579340 TCCCGTCATTGTACTCTCATACTC 59.421 45.833 0.00 0.00 0.00 2.59
3226 3576 5.171476 AGAAGGATATGTTCAGTGTGTTCG 58.829 41.667 0.00 0.00 0.00 3.95
3227 3577 4.537135 AGGATATGTTCAGTGTGTTCGT 57.463 40.909 0.00 0.00 0.00 3.85
3237 3587 4.951254 TCAGTGTGTTCGTCCTTTTATCA 58.049 39.130 0.00 0.00 0.00 2.15
3243 3593 4.748102 GTGTTCGTCCTTTTATCACACTGA 59.252 41.667 0.00 0.00 32.14 3.41
3260 3618 4.202398 ACACTGATGGTCATTTCACTCTGT 60.202 41.667 0.00 0.00 0.00 3.41
3265 3623 5.705441 TGATGGTCATTTCACTCTGTTTACC 59.295 40.000 0.00 0.00 0.00 2.85
3266 3624 5.042463 TGGTCATTTCACTCTGTTTACCA 57.958 39.130 0.00 0.00 32.30 3.25
3269 3627 6.206634 TGGTCATTTCACTCTGTTTACCATTC 59.793 38.462 0.00 0.00 29.85 2.67
3305 3664 4.807643 GCCTTGGTTGGTATTCTTGTCTCT 60.808 45.833 0.00 0.00 0.00 3.10
3319 3678 5.189928 TCTTGTCTCTTTGTTGGCTTGTTA 58.810 37.500 0.00 0.00 0.00 2.41
3324 3683 7.648142 TGTCTCTTTGTTGGCTTGTTAATTAG 58.352 34.615 0.00 0.00 0.00 1.73
3340 3700 9.502091 TTGTTAATTAGCTAAGCTTTCTCTTGA 57.498 29.630 12.54 0.00 40.44 3.02
3343 3703 9.890629 TTAATTAGCTAAGCTTTCTCTTGATCA 57.109 29.630 12.54 0.00 40.44 2.92
3361 3724 4.037089 TGATCACACAAATATGCAGCCATC 59.963 41.667 0.00 0.00 32.85 3.51
3370 3738 8.905850 CACAAATATGCAGCCATCCATATAATA 58.094 33.333 0.00 0.00 34.47 0.98
3398 3766 8.255905 TGCTAAACTAGGAAACTATAGTTGTCC 58.744 37.037 24.64 24.64 43.39 4.02
3399 3767 7.434602 GCTAAACTAGGAAACTATAGTTGTCCG 59.565 40.741 25.11 19.30 43.39 4.79
3400 3768 6.847421 AACTAGGAAACTATAGTTGTCCGT 57.153 37.500 25.11 19.69 43.39 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.604156 TCTGTCACTCCATAGTCACATCT 58.396 43.478 0.00 0.00 36.03 2.90
14 15 4.604156 TCTCTGTCACTCCATAGTCACAT 58.396 43.478 0.00 0.00 36.03 3.21
40 41 1.915614 CTTTGCACAGCCGCTACCTG 61.916 60.000 0.00 0.00 36.41 4.00
45 46 1.533625 TATTTCTTTGCACAGCCGCT 58.466 45.000 0.00 0.00 0.00 5.52
215 248 7.342284 AGTGGATATATTCTATCCCGTGGTTAG 59.658 40.741 8.43 3.06 42.10 2.34
223 256 8.623030 GTTCGTCTAGTGGATATATTCTATCCC 58.377 40.741 8.43 1.73 42.10 3.85
232 265 6.124340 TCTGGTTGTTCGTCTAGTGGATATA 58.876 40.000 0.00 0.00 0.00 0.86
234 267 4.338012 TCTGGTTGTTCGTCTAGTGGATA 58.662 43.478 0.00 0.00 0.00 2.59
235 268 3.162666 TCTGGTTGTTCGTCTAGTGGAT 58.837 45.455 0.00 0.00 0.00 3.41
236 269 2.589720 TCTGGTTGTTCGTCTAGTGGA 58.410 47.619 0.00 0.00 0.00 4.02
237 270 3.057734 GTTCTGGTTGTTCGTCTAGTGG 58.942 50.000 0.00 0.00 0.00 4.00
257 493 2.704190 TCCCTCTCTCTTGGTTCAGT 57.296 50.000 0.00 0.00 0.00 3.41
264 500 7.609532 AGTTGTTGATATTTTCCCTCTCTCTTG 59.390 37.037 0.00 0.00 0.00 3.02
266 502 7.264294 AGTTGTTGATATTTTCCCTCTCTCT 57.736 36.000 0.00 0.00 0.00 3.10
267 503 7.496263 GGTAGTTGTTGATATTTTCCCTCTCTC 59.504 40.741 0.00 0.00 0.00 3.20
338 574 5.003402 CGTTTAAAATTGGAATGCTACGCTG 59.997 40.000 0.00 0.00 0.00 5.18
476 713 1.531677 CGTGCTATGTTTTGCATCCGG 60.532 52.381 0.00 0.00 41.45 5.14
492 729 4.666532 GTGCGTTCTGTGGCGTGC 62.667 66.667 0.00 0.00 0.00 5.34
496 733 1.368850 GTTTCGTGCGTTCTGTGGC 60.369 57.895 0.00 0.00 0.00 5.01
499 736 1.647346 TTCTGTTTCGTGCGTTCTGT 58.353 45.000 0.00 0.00 0.00 3.41
531 768 1.194896 CTTCGTCTCGTCGATTCGGC 61.195 60.000 6.18 2.87 39.57 5.54
790 1038 0.676736 GGGGTCATTTTGAAACCGCA 59.323 50.000 3.27 0.00 43.44 5.69
791 1039 0.676736 TGGGGTCATTTTGAAACCGC 59.323 50.000 0.00 0.00 44.03 5.68
795 1043 1.347062 GGGCTGGGGTCATTTTGAAA 58.653 50.000 0.00 0.00 0.00 2.69
962 1210 1.908340 CTGCTCCAGGAACCAGGAGG 61.908 65.000 25.98 12.21 46.96 4.30
989 1237 4.834892 CGGCCATTTTCGCTGCGG 62.835 66.667 23.03 5.75 0.00 5.69
1152 1400 3.052181 GCTACTCGAGGCAAGGAAC 57.948 57.895 18.41 0.00 0.00 3.62
1350 1598 2.439245 GGGACCCACTGGAAACCC 59.561 66.667 5.33 2.73 36.50 4.11
1353 1601 4.323477 CGCGGGACCCACTGGAAA 62.323 66.667 12.15 0.00 34.81 3.13
1552 1800 2.182030 CTCCTTGTCGTCCTCGGC 59.818 66.667 0.00 0.00 42.45 5.54
1665 1913 1.743995 GAGCGGTGGCGGTAACAAT 60.744 57.895 0.00 0.00 46.35 2.71
1682 1930 4.075793 CCTCCTCCACCTCCCGGA 62.076 72.222 0.73 0.00 0.00 5.14
1725 1985 2.430332 CCCCAAGAAGTCAGCAAACAAA 59.570 45.455 0.00 0.00 0.00 2.83
1726 1986 2.031120 CCCCAAGAAGTCAGCAAACAA 58.969 47.619 0.00 0.00 0.00 2.83
1727 1987 1.214175 TCCCCAAGAAGTCAGCAAACA 59.786 47.619 0.00 0.00 0.00 2.83
1741 2001 3.192944 AGTTCATCCTCATCTTCCCCAA 58.807 45.455 0.00 0.00 0.00 4.12
2053 2334 9.421399 TCTTCAGTGGACTATAGAAACATATGA 57.579 33.333 10.38 7.90 0.00 2.15
2074 2355 9.017509 ACTTTTGAATTCTGCTTATCATCTTCA 57.982 29.630 7.05 0.00 0.00 3.02
2104 2385 7.922811 CGCTCATAGCAATATGAATACATCCTA 59.077 37.037 0.00 0.00 42.58 2.94
2105 2386 6.760298 CGCTCATAGCAATATGAATACATCCT 59.240 38.462 0.00 0.00 42.58 3.24
2106 2387 6.758416 TCGCTCATAGCAATATGAATACATCC 59.242 38.462 0.00 0.00 42.58 3.51
2107 2388 7.761651 TCGCTCATAGCAATATGAATACATC 57.238 36.000 0.00 0.00 42.58 3.06
2110 2391 7.118390 AGGTTTCGCTCATAGCAATATGAATAC 59.882 37.037 0.00 0.00 42.58 1.89
2111 2392 7.118245 CAGGTTTCGCTCATAGCAATATGAATA 59.882 37.037 0.00 0.00 42.58 1.75
2112 2393 6.000219 AGGTTTCGCTCATAGCAATATGAAT 59.000 36.000 0.00 0.00 42.58 2.57
2113 2394 5.237127 CAGGTTTCGCTCATAGCAATATGAA 59.763 40.000 0.00 0.00 42.58 2.57
2114 2395 4.751600 CAGGTTTCGCTCATAGCAATATGA 59.248 41.667 0.00 0.00 42.58 2.15
2115 2396 4.512944 ACAGGTTTCGCTCATAGCAATATG 59.487 41.667 0.00 0.00 42.58 1.78
2116 2397 4.708177 ACAGGTTTCGCTCATAGCAATAT 58.292 39.130 0.00 0.00 42.58 1.28
2123 2404 7.441890 TTTGAATAAACAGGTTTCGCTCATA 57.558 32.000 0.00 0.00 34.23 2.15
2129 2410 7.513190 TGTGTTTTTGAATAAACAGGTTTCG 57.487 32.000 0.00 0.00 45.67 3.46
2145 2426 8.088365 GGCAAATATTCCTCTACTTGTGTTTTT 58.912 33.333 0.00 0.00 0.00 1.94
2163 2444 9.359653 AGATTTACAGCTCTTATTGGCAAATAT 57.640 29.630 3.01 0.00 0.00 1.28
2174 2456 7.715249 AGTTCAACACAAGATTTACAGCTCTTA 59.285 33.333 0.00 0.00 30.70 2.10
2208 2490 4.752101 GCCTGCGAGAAAGTATGAATACAT 59.248 41.667 3.43 0.00 40.16 2.29
2400 2686 9.740710 ATAGAAACAAAGTTGTATAAGAAGGCT 57.259 29.630 0.00 0.00 41.31 4.58
2401 2687 9.774742 CATAGAAACAAAGTTGTATAAGAAGGC 57.225 33.333 0.00 0.00 41.31 4.35
2409 2695 8.440833 GCGTAACTCATAGAAACAAAGTTGTAT 58.559 33.333 0.00 0.00 41.31 2.29
2410 2696 7.438757 TGCGTAACTCATAGAAACAAAGTTGTA 59.561 33.333 0.00 0.00 41.31 2.41
2411 2697 6.259167 TGCGTAACTCATAGAAACAAAGTTGT 59.741 34.615 0.00 0.00 44.72 3.32
2412 2698 6.655062 TGCGTAACTCATAGAAACAAAGTTG 58.345 36.000 0.00 0.00 32.71 3.16
2413 2699 6.854496 TGCGTAACTCATAGAAACAAAGTT 57.146 33.333 0.00 0.00 34.70 2.66
2414 2700 6.565999 GCTTGCGTAACTCATAGAAACAAAGT 60.566 38.462 0.00 0.00 0.00 2.66
2415 2701 5.790495 GCTTGCGTAACTCATAGAAACAAAG 59.210 40.000 0.00 0.00 0.00 2.77
2416 2702 5.237561 TGCTTGCGTAACTCATAGAAACAAA 59.762 36.000 0.00 0.00 0.00 2.83
2417 2703 4.752604 TGCTTGCGTAACTCATAGAAACAA 59.247 37.500 0.00 0.00 0.00 2.83
2418 2704 4.311606 TGCTTGCGTAACTCATAGAAACA 58.688 39.130 0.00 0.00 0.00 2.83
2419 2705 4.921470 TGCTTGCGTAACTCATAGAAAC 57.079 40.909 0.00 0.00 0.00 2.78
2420 2706 7.603963 TTTATGCTTGCGTAACTCATAGAAA 57.396 32.000 6.76 0.00 0.00 2.52
2421 2707 7.786178 ATTTATGCTTGCGTAACTCATAGAA 57.214 32.000 6.76 0.00 0.00 2.10
2422 2708 7.710907 AGAATTTATGCTTGCGTAACTCATAGA 59.289 33.333 6.76 2.05 0.00 1.98
2423 2709 7.855545 AGAATTTATGCTTGCGTAACTCATAG 58.144 34.615 6.76 0.00 0.00 2.23
2424 2710 7.786178 AGAATTTATGCTTGCGTAACTCATA 57.214 32.000 6.76 1.19 0.00 2.15
2425 2711 6.683974 AGAATTTATGCTTGCGTAACTCAT 57.316 33.333 6.76 2.72 0.00 2.90
2426 2712 6.494893 AAGAATTTATGCTTGCGTAACTCA 57.505 33.333 6.76 0.00 0.00 3.41
2545 2868 4.580868 TGATCGCAAATGTAGGTGGTTAA 58.419 39.130 0.00 0.00 0.00 2.01
2550 2873 2.868583 CCTCTGATCGCAAATGTAGGTG 59.131 50.000 0.00 0.00 0.00 4.00
2574 2897 6.959606 AGGGGCATCAGTGTTATCTAATAT 57.040 37.500 0.00 0.00 0.00 1.28
2589 2912 4.965200 ACTAGACAGATAAAGGGGCATC 57.035 45.455 0.00 0.00 0.00 3.91
2593 2916 9.369672 AGACTTTATACTAGACAGATAAAGGGG 57.630 37.037 21.38 9.36 43.10 4.79
2616 2939 6.861065 TGGAATCACAACTGAAAACTAGAC 57.139 37.500 0.00 0.00 0.00 2.59
2631 2954 5.036117 TCAAAGGTAGGCTATGGAATCAC 57.964 43.478 0.00 0.00 0.00 3.06
2646 2969 1.896220 TCTGCTGCGAAATCAAAGGT 58.104 45.000 0.00 0.00 0.00 3.50
2653 2976 2.609459 CCGAGTAAATCTGCTGCGAAAT 59.391 45.455 0.00 0.00 0.00 2.17
2657 2980 2.120232 CTACCGAGTAAATCTGCTGCG 58.880 52.381 0.00 0.00 0.00 5.18
2693 3016 7.719778 AAGAAGGAAAAATGACTGCAAAATC 57.280 32.000 0.00 0.00 0.00 2.17
2724 3047 4.023963 GTCTGCACTACAAGTTTTCCCTTC 60.024 45.833 0.00 0.00 0.00 3.46
2734 3057 6.033341 GTCTAGATCAAGTCTGCACTACAAG 58.967 44.000 0.00 0.00 37.83 3.16
2735 3058 5.476945 TGTCTAGATCAAGTCTGCACTACAA 59.523 40.000 0.00 0.00 37.83 2.41
2744 3067 5.474578 TGCAAAGTGTCTAGATCAAGTCT 57.525 39.130 0.00 0.00 41.11 3.24
2795 3119 6.744175 TTCTGATGGCAAATATCTCTCTCT 57.256 37.500 0.00 0.00 0.00 3.10
2797 3121 9.857656 TTATTTTCTGATGGCAAATATCTCTCT 57.142 29.630 0.00 0.00 0.00 3.10
2811 3135 6.991938 TGGAAACACCCTTTATTTTCTGATG 58.008 36.000 0.00 0.00 38.00 3.07
2830 3154 9.739276 AGATCAAACTTTCTGTATACATGGAAA 57.261 29.630 15.58 15.58 0.00 3.13
2884 3208 4.022068 TGAATTGGTCATGAAACTGGAAGC 60.022 41.667 0.00 0.00 37.60 3.86
2919 3243 4.688879 TCACTAAGCAAATGTAACAGACCG 59.311 41.667 0.00 0.00 0.00 4.79
2920 3244 6.546395 CATCACTAAGCAAATGTAACAGACC 58.454 40.000 0.00 0.00 0.00 3.85
2931 3255 5.068987 ACTTTTTCCAGCATCACTAAGCAAA 59.931 36.000 0.00 0.00 0.00 3.68
2940 3264 6.096141 TGAAGTTAACACTTTTTCCAGCATCA 59.904 34.615 8.61 0.00 43.79 3.07
3004 3352 4.962155 ACTGTGTAAGAAGCTAGCTTGTT 58.038 39.130 34.02 34.02 41.44 2.83
3012 3360 5.193679 ACCAAGAAAACTGTGTAAGAAGCT 58.806 37.500 0.00 0.00 0.00 3.74
3024 3372 4.320494 GCATCGTCATCAACCAAGAAAACT 60.320 41.667 0.00 0.00 0.00 2.66
3053 3401 8.410141 CACAGAAATACAAAAAGGTAGGACAAA 58.590 33.333 0.00 0.00 0.00 2.83
3056 3404 7.227910 TGACACAGAAATACAAAAAGGTAGGAC 59.772 37.037 0.00 0.00 0.00 3.85
3132 3482 1.007336 CGTGCTGACAACGTAGGGTC 61.007 60.000 7.71 7.71 36.66 4.46
3150 3500 3.720949 TGGAGAATGGAACGTATACCG 57.279 47.619 0.00 0.00 44.03 4.02
3156 3506 4.399303 GGATTGAAATGGAGAATGGAACGT 59.601 41.667 0.00 0.00 0.00 3.99
3157 3507 4.202050 GGGATTGAAATGGAGAATGGAACG 60.202 45.833 0.00 0.00 0.00 3.95
3158 3508 4.202050 CGGGATTGAAATGGAGAATGGAAC 60.202 45.833 0.00 0.00 0.00 3.62
3189 3539 7.001674 ACATATCCTTCTTCGAGTATGAGAGT 58.998 38.462 0.00 0.00 0.00 3.24
3192 3542 7.652727 TGAACATATCCTTCTTCGAGTATGAG 58.347 38.462 0.00 0.00 0.00 2.90
3194 3544 7.380870 CACTGAACATATCCTTCTTCGAGTATG 59.619 40.741 0.00 0.00 0.00 2.39
3200 3550 5.171476 ACACACTGAACATATCCTTCTTCG 58.829 41.667 0.00 0.00 0.00 3.79
3226 3576 5.245531 TGACCATCAGTGTGATAAAAGGAC 58.754 41.667 0.00 0.00 34.28 3.85
3227 3577 5.497464 TGACCATCAGTGTGATAAAAGGA 57.503 39.130 0.00 0.00 34.28 3.36
3237 3587 4.202398 ACAGAGTGAAATGACCATCAGTGT 60.202 41.667 0.00 0.00 29.56 3.55
3243 3593 5.630121 TGGTAAACAGAGTGAAATGACCAT 58.370 37.500 0.00 0.00 29.67 3.55
3260 3618 7.573710 AGGCTACATGAATACTGAATGGTAAA 58.426 34.615 0.00 0.00 0.00 2.01
3265 3623 5.824624 ACCAAGGCTACATGAATACTGAATG 59.175 40.000 0.00 0.00 0.00 2.67
3266 3624 6.006275 ACCAAGGCTACATGAATACTGAAT 57.994 37.500 0.00 0.00 0.00 2.57
3269 3627 4.336433 CCAACCAAGGCTACATGAATACTG 59.664 45.833 0.00 0.00 0.00 2.74
3305 3664 6.866248 GCTTAGCTAATTAACAAGCCAACAAA 59.134 34.615 6.64 0.00 39.64 2.83
3319 3678 7.826252 TGTGATCAAGAGAAAGCTTAGCTAATT 59.174 33.333 7.32 0.00 38.25 1.40
3324 3683 4.692625 TGTGTGATCAAGAGAAAGCTTAGC 59.307 41.667 0.00 0.00 0.00 3.09
3340 3700 3.319972 GGATGGCTGCATATTTGTGTGAT 59.680 43.478 0.50 0.00 0.00 3.06
3343 3703 2.737544 TGGATGGCTGCATATTTGTGT 58.262 42.857 0.50 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.