Multiple sequence alignment - TraesCS1D01G144600

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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 TraesCS1D01G144600 chr1D 100.000 3336 0 0 1 3336 199844773 199841438 0.000000e+00 6161.0
1 TraesCS1D01G144600 chr1D 91.111 90 4 2 3216 3301 295954302 295954213 5.850000e-23 119.0
2 TraesCS1D01G144600 chr1A 92.120 3236 162 35 137 3336 252325164 252321986 0.000000e+00 4477.0
3 TraesCS1D01G144600 chr1A 96.479 142 5 0 1 142 252325576 252325435 5.560000e-58 235.0
4 TraesCS1D01G144600 chr1B 95.112 2455 95 9 4 2446 286613785 286611344 0.000000e+00 3845.0
5 TraesCS1D01G144600 chr1B 83.613 537 39 24 2431 2941 286611330 286610817 3.030000e-125 459.0
6 TraesCS1D01G144600 chr1B 90.301 299 21 5 2927 3220 286610770 286610475 5.220000e-103 385.0
7 TraesCS1D01G144600 chr1B 96.364 55 2 0 4 58 288976531 288976477 1.270000e-14 91.6
8 TraesCS1D01G144600 chr3D 92.941 85 5 1 3215 3299 61804528 61804611 4.520000e-24 122.0
9 TraesCS1D01G144600 chr2D 89.796 98 6 2 3208 3301 14895370 14895273 4.520000e-24 122.0
10 TraesCS1D01G144600 chr2D 90.323 93 5 2 3212 3300 378043088 378043180 5.850000e-23 119.0
11 TraesCS1D01G144600 chr7B 91.209 91 5 1 3218 3305 517395784 517395874 1.630000e-23 121.0
12 TraesCS1D01G144600 chr4D 87.037 108 10 4 3196 3301 384974263 384974368 5.850000e-23 119.0
13 TraesCS1D01G144600 chr4D 88.542 96 7 2 3210 3301 124628862 124628767 2.720000e-21 113.0
14 TraesCS1D01G144600 chr6B 86.364 110 8 5 3197 3300 717901515 717901623 2.720000e-21 113.0
15 TraesCS1D01G144600 chr6B 87.879 99 6 5 3206 3300 471227569 471227665 9.780000e-21 111.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G144600 chr1D 199841438 199844773 3335 True 6161 6161 100.000000 1 3336 1 chr1D.!!$R1 3335
1 TraesCS1D01G144600 chr1A 252321986 252325576 3590 True 2356 4477 94.299500 1 3336 2 chr1A.!!$R1 3335
2 TraesCS1D01G144600 chr1B 286610475 286613785 3310 True 1563 3845 89.675333 4 3220 3 chr1B.!!$R2 3216

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
927 1221 0.032540 GCCTGCAAAAAGTGACTGGG 59.967 55.0 0.0 0.0 0.00 4.45 F
2194 2497 0.108585 TGGACTTGGTTCTGCTCACC 59.891 55.0 0.0 0.0 34.52 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2327 2630 1.475280 CATGGGTTCAGTTCAGGCATG 59.525 52.381 0.0 0.0 0.0 4.06 R
3298 3724 0.106149 CCATCCCGGCTGTTAGGTAC 59.894 60.000 0.0 0.0 0.0 3.34 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
134 135 4.631813 TCAAACAACAAAAATCCAAACCCG 59.368 37.500 0.00 0.00 0.00 5.28
176 453 2.742053 GCTACTGTGCAGATTCCGAAAA 59.258 45.455 6.17 0.00 0.00 2.29
220 497 5.243060 TGGATACATATGACCCAACTACTCG 59.757 44.000 10.38 0.00 46.17 4.18
250 527 1.727062 CACTCCCCATGCTCCTAGAT 58.273 55.000 0.00 0.00 0.00 1.98
315 592 6.732896 ATCCGAACTATCTTCACCAGTTAT 57.267 37.500 0.00 0.00 32.79 1.89
335 612 2.430465 TCTCAAATCTTCAGCAGTGGC 58.570 47.619 0.00 0.00 41.61 5.01
360 637 1.881973 GTGCCAGTGCTCAAAGATCAA 59.118 47.619 0.00 0.00 38.71 2.57
382 659 8.833231 TCAAAAGAGAGGTTAATGTAAGTCAG 57.167 34.615 0.00 0.00 0.00 3.51
397 674 3.529216 AGTCAGCTATACTACCTCCCC 57.471 52.381 0.00 0.00 0.00 4.81
412 689 7.891328 ACTACCTCCCCTTAACTTCTTCTATA 58.109 38.462 0.00 0.00 0.00 1.31
425 712 8.734593 AACTTCTTCTATATTCCTATCCTGCT 57.265 34.615 0.00 0.00 0.00 4.24
426 713 9.830186 AACTTCTTCTATATTCCTATCCTGCTA 57.170 33.333 0.00 0.00 0.00 3.49
440 727 1.981495 CCTGCTATAGGGGGAAAGAGG 59.019 57.143 1.04 0.00 43.33 3.69
448 735 6.271624 GCTATAGGGGGAAAGAGGTTATGTTA 59.728 42.308 1.04 0.00 0.00 2.41
455 742 6.155737 GGGGAAAGAGGTTATGTTACTGTCTA 59.844 42.308 0.00 0.00 0.00 2.59
522 809 6.487689 AGAAAAATCCGTCTGAGATGAAAC 57.512 37.500 2.61 0.00 0.00 2.78
654 948 0.820871 TCGGCAAACCACAAAGCTTT 59.179 45.000 5.69 5.69 34.57 3.51
668 962 5.174943 CACAAAGCTTTCCGAACCAAATTAC 59.825 40.000 9.23 0.00 0.00 1.89
769 1063 7.040478 CCAGCAATATGTTAGCCTATTAAGCAA 60.040 37.037 0.00 0.00 0.00 3.91
782 1076 8.989980 AGCCTATTAAGCAAATAGTTAACGATC 58.010 33.333 14.32 0.00 43.85 3.69
793 1087 3.714391 AGTTAACGATCCGGTAATCTGC 58.286 45.455 0.00 0.00 41.08 4.26
820 1114 4.752101 CCAGTTAGTCATAGCTTGTATGGC 59.248 45.833 0.00 0.00 0.00 4.40
927 1221 0.032540 GCCTGCAAAAAGTGACTGGG 59.967 55.000 0.00 0.00 0.00 4.45
933 1227 3.896888 TGCAAAAAGTGACTGGGAATGAT 59.103 39.130 0.00 0.00 0.00 2.45
978 1279 9.241919 TGTTGTAACATTGATTCATACCTTCAT 57.758 29.630 0.00 0.00 33.17 2.57
993 1294 7.719193 TCATACCTTCATTGTTTCAAGACAGAA 59.281 33.333 0.00 0.00 0.00 3.02
1078 1379 4.072131 GTCAACAGTAGCCATCAAGGAAA 58.928 43.478 0.00 0.00 41.22 3.13
1110 1411 2.425143 TTGAGGATGTGCTTGATCCC 57.575 50.000 0.00 0.00 40.44 3.85
1185 1486 3.378427 CACTTAGGCTTAGGCAAATGGAC 59.622 47.826 8.84 0.00 40.87 4.02
1194 1495 1.574428 GCAAATGGACGTTCGCTGT 59.426 52.632 0.00 0.00 0.00 4.40
1219 1520 7.169476 GTGAGACAAAGACAAAGGTACTCTTAC 59.831 40.741 0.00 0.00 38.49 2.34
1221 1522 7.562135 AGACAAAGACAAAGGTACTCTTACAA 58.438 34.615 0.00 0.00 38.49 2.41
1231 1532 8.713271 CAAAGGTACTCTTACAATTCACTTCTC 58.287 37.037 0.00 0.00 38.49 2.87
1242 1543 7.308782 ACAATTCACTTCTCGAATTATCCAC 57.691 36.000 0.00 0.00 40.29 4.02
1266 1567 0.178938 AACACCCCCATGCATCACAA 60.179 50.000 0.00 0.00 0.00 3.33
1287 1588 8.344831 TCACAAAAACTTGTAGAGATCACATTG 58.655 33.333 0.00 0.00 33.17 2.82
1288 1589 8.344831 CACAAAAACTTGTAGAGATCACATTGA 58.655 33.333 0.00 0.00 33.17 2.57
1324 1625 3.615224 TTCTGCTGACACTATGCATCA 57.385 42.857 0.19 0.00 36.07 3.07
1335 1636 5.605534 ACACTATGCATCATCTTACAGGAC 58.394 41.667 0.19 0.00 0.00 3.85
1338 1639 6.709397 CACTATGCATCATCTTACAGGACAAT 59.291 38.462 0.19 0.00 0.00 2.71
1512 1813 8.109705 TGGAAATTCTCATGAATCGAAGAAAA 57.890 30.769 0.00 0.00 43.58 2.29
1518 1819 8.746922 TTCTCATGAATCGAAGAAAATTTTGG 57.253 30.769 8.47 0.00 43.58 3.28
1546 1847 7.072177 TGTAAATGCTAAAAATCCTCTCACG 57.928 36.000 0.00 0.00 0.00 4.35
1547 1848 6.876789 TGTAAATGCTAAAAATCCTCTCACGA 59.123 34.615 0.00 0.00 0.00 4.35
1633 1935 6.479660 TGGATGATGTTTTTGAGCAAAAGAAC 59.520 34.615 8.23 6.15 40.83 3.01
1773 2075 3.684103 TGAAATTAATGCCGGTAAGCG 57.316 42.857 1.90 0.00 34.65 4.68
1845 2147 2.821969 GCATCAACTCAGGTGTTCCATT 59.178 45.455 0.00 0.00 35.89 3.16
1900 2202 7.849322 TCACATTAGGGTGTTGATATAGCTA 57.151 36.000 0.00 0.00 39.76 3.32
2002 2305 2.082366 GCGTGTTGCGGCAAATGAG 61.082 57.895 18.23 10.25 41.69 2.90
2047 2350 2.909006 TCAAATCAAGAGAGCTGAGGGT 59.091 45.455 0.00 0.00 0.00 4.34
2194 2497 0.108585 TGGACTTGGTTCTGCTCACC 59.891 55.000 0.00 0.00 34.52 4.02
2221 2524 8.517878 CAATACTTTGACACCATGAAAGAGATT 58.482 33.333 9.99 6.78 34.60 2.40
2327 2630 0.037326 TCTTCAGGCGTCCACACATC 60.037 55.000 0.00 0.00 0.00 3.06
2447 2779 6.960992 CGTGATAATATTGTGTGAGTTTGTGG 59.039 38.462 0.00 0.00 0.00 4.17
2456 2788 1.334869 GTGAGTTTGTGGCTTGTGAGG 59.665 52.381 0.00 0.00 0.00 3.86
2463 2795 5.045578 AGTTTGTGGCTTGTGAGGTATCTAT 60.046 40.000 0.00 0.00 0.00 1.98
2493 2825 9.752961 AGCTTGTAAAACGGTTTGTATTTTATT 57.247 25.926 9.15 0.00 32.16 1.40
2494 2826 9.786224 GCTTGTAAAACGGTTTGTATTTTATTG 57.214 29.630 9.15 0.00 32.16 1.90
2497 2829 9.798994 TGTAAAACGGTTTGTATTTTATTGTGT 57.201 25.926 9.15 0.00 32.16 3.72
2513 2845 4.895224 TTGTGTACTATCAGCTAGTCCG 57.105 45.455 0.00 0.00 41.10 4.79
2690 3051 5.037385 TCATCTTAGTCTCGCTGAATTTCG 58.963 41.667 0.00 0.00 0.00 3.46
2702 3063 3.433615 GCTGAATTTCGTCAACTAGCACT 59.566 43.478 0.00 0.00 0.00 4.40
2751 3112 9.784531 TTGAATCAAACTAAGAAACTGAGATCT 57.215 29.630 0.00 0.00 0.00 2.75
2787 3148 8.894409 TTTAAAACATGTAATCAGAAGCATCG 57.106 30.769 0.00 0.00 0.00 3.84
2804 3165 3.605461 GCATCGATGTTCGTGGATCATTG 60.605 47.826 25.47 0.00 41.35 2.82
2814 3175 3.701542 TCGTGGATCATTGACTTAGCTCT 59.298 43.478 0.00 0.00 0.00 4.09
2815 3176 3.801050 CGTGGATCATTGACTTAGCTCTG 59.199 47.826 0.00 0.00 0.00 3.35
2816 3177 3.559242 GTGGATCATTGACTTAGCTCTGC 59.441 47.826 0.00 0.00 0.00 4.26
2817 3178 3.453717 TGGATCATTGACTTAGCTCTGCT 59.546 43.478 0.00 0.00 43.41 4.24
2818 3179 4.651045 TGGATCATTGACTTAGCTCTGCTA 59.349 41.667 0.00 0.00 40.44 3.49
2819 3180 5.129320 TGGATCATTGACTTAGCTCTGCTAA 59.871 40.000 10.93 10.93 46.97 3.09
2832 3193 6.615264 AGCTCTGCTAAATGATGTAACATG 57.385 37.500 0.00 0.00 36.99 3.21
2833 3194 6.351711 AGCTCTGCTAAATGATGTAACATGA 58.648 36.000 0.00 0.00 36.99 3.07
2834 3195 6.482641 AGCTCTGCTAAATGATGTAACATGAG 59.517 38.462 0.00 0.00 36.99 2.90
2835 3196 6.259608 GCTCTGCTAAATGATGTAACATGAGT 59.740 38.462 0.00 0.00 0.00 3.41
2841 3202 9.529325 GCTAAATGATGTAACATGAGTAGTACA 57.471 33.333 0.00 0.31 0.00 2.90
2856 3218 7.552459 TGAGTAGTACATGCACAGCTTAAATA 58.448 34.615 2.52 0.00 0.00 1.40
2893 3255 2.882761 GGGTGGGAAAGTGAACAGTTAC 59.117 50.000 0.00 0.00 0.00 2.50
2909 3271 9.431887 TGAACAGTTACCAGTTAAGATATGAAC 57.568 33.333 0.00 0.00 0.00 3.18
2954 3377 7.615757 ACCAAAAAGAGTTAGCAAGGCTATAAT 59.384 33.333 0.00 0.00 41.01 1.28
2994 3420 4.516698 GGTAAGACATGATCCATTTCGCAT 59.483 41.667 0.00 0.00 0.00 4.73
3020 3446 2.455674 TCATTTCAGACACCGAGTGG 57.544 50.000 8.57 0.00 37.94 4.00
3033 3459 2.163815 ACCGAGTGGAGATAAACTCACG 59.836 50.000 3.94 0.00 46.54 4.35
3041 3467 3.119101 GGAGATAAACTCACGCTGAAGGA 60.119 47.826 0.00 0.00 46.54 3.36
3054 3480 3.003068 CGCTGAAGGAATCATTGGATCAC 59.997 47.826 0.00 0.00 37.44 3.06
3055 3481 3.949754 GCTGAAGGAATCATTGGATCACA 59.050 43.478 0.00 0.00 37.44 3.58
3056 3482 4.583489 GCTGAAGGAATCATTGGATCACAT 59.417 41.667 0.00 0.00 37.44 3.21
3058 3484 6.459670 TGAAGGAATCATTGGATCACATTG 57.540 37.500 0.00 0.00 31.50 2.82
3059 3485 5.953548 TGAAGGAATCATTGGATCACATTGT 59.046 36.000 0.00 0.00 33.34 2.71
3060 3486 5.847111 AGGAATCATTGGATCACATTGTG 57.153 39.130 10.64 10.64 33.34 3.33
3116 3542 0.940126 GCACAGGATAGTCATTGGCG 59.060 55.000 0.00 0.00 0.00 5.69
3162 3588 4.892934 AGATGATCAACTCCTAGACTGGAC 59.107 45.833 0.00 0.00 31.94 4.02
3167 3593 2.761208 CAACTCCTAGACTGGACCGATT 59.239 50.000 0.00 0.00 31.94 3.34
3173 3599 1.049289 AGACTGGACCGATTAGGGGC 61.049 60.000 0.00 0.00 46.96 5.80
3178 3604 0.544697 GGACCGATTAGGGGCAAAGA 59.455 55.000 0.00 0.00 46.96 2.52
3179 3605 1.664873 GACCGATTAGGGGCAAAGAC 58.335 55.000 0.00 0.00 46.96 3.01
3192 3618 1.823250 GCAAAGACCCCCAACACTGAT 60.823 52.381 0.00 0.00 0.00 2.90
3194 3620 1.149101 AAGACCCCCAACACTGATGT 58.851 50.000 0.00 0.00 42.46 3.06
3230 3656 6.895756 TGCAATATATATTACTCCCTCCGTCT 59.104 38.462 7.65 0.00 0.00 4.18
3232 3658 7.640852 CAATATATATTACTCCCTCCGTCTCG 58.359 42.308 7.65 0.00 0.00 4.04
3245 3671 4.696402 CCTCCGTCTCGTAATATAAGAGCT 59.304 45.833 0.00 0.00 34.82 4.09
3246 3672 5.181622 CCTCCGTCTCGTAATATAAGAGCTT 59.818 44.000 0.00 0.00 34.82 3.74
3247 3673 6.294065 CCTCCGTCTCGTAATATAAGAGCTTT 60.294 42.308 0.00 0.00 34.82 3.51
3248 3674 7.035840 TCCGTCTCGTAATATAAGAGCTTTT 57.964 36.000 0.00 0.00 34.82 2.27
3249 3675 7.486647 TCCGTCTCGTAATATAAGAGCTTTTT 58.513 34.615 0.00 0.00 34.82 1.94
3298 3724 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
3312 3739 1.680207 GGAGTAGTACCTAACAGCCGG 59.320 57.143 0.00 0.00 0.00 6.13
3333 3760 1.480954 GATGGGCTTCAGTAAGGTCGA 59.519 52.381 0.00 0.00 32.98 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 2.356227 CCTGGGAGAAACTTCTTAGGGC 60.356 54.545 9.05 0.00 37.73 5.19
176 453 0.598065 GGTCAACGCCAGCATTTCTT 59.402 50.000 0.00 0.00 0.00 2.52
220 497 3.066760 GCATGGGGAGTGCTTTTATACAC 59.933 47.826 0.00 0.00 39.45 2.90
250 527 8.966868 GGGATAACTGGATTTTGTCTTGAATTA 58.033 33.333 0.00 0.00 0.00 1.40
315 592 2.430465 GCCACTGCTGAAGATTTGAGA 58.570 47.619 0.00 0.00 33.53 3.27
335 612 1.102809 TTTGAGCACTGGCACCACAG 61.103 55.000 0.00 0.00 44.61 3.66
360 637 7.010339 AGCTGACTTACATTAACCTCTCTTT 57.990 36.000 0.00 0.00 0.00 2.52
382 659 6.076653 AGAAGTTAAGGGGAGGTAGTATAGC 58.923 44.000 0.00 0.00 39.93 2.97
420 707 1.981495 CCTCTTTCCCCCTATAGCAGG 59.019 57.143 0.00 0.00 45.07 4.85
421 708 2.695585 ACCTCTTTCCCCCTATAGCAG 58.304 52.381 0.00 0.00 0.00 4.24
422 709 2.889522 ACCTCTTTCCCCCTATAGCA 57.110 50.000 0.00 0.00 0.00 3.49
423 710 4.597940 ACATAACCTCTTTCCCCCTATAGC 59.402 45.833 0.00 0.00 0.00 2.97
424 711 6.765355 AACATAACCTCTTTCCCCCTATAG 57.235 41.667 0.00 0.00 0.00 1.31
425 712 7.291651 CAGTAACATAACCTCTTTCCCCCTATA 59.708 40.741 0.00 0.00 0.00 1.31
426 713 6.101296 CAGTAACATAACCTCTTTCCCCCTAT 59.899 42.308 0.00 0.00 0.00 2.57
427 714 5.427481 CAGTAACATAACCTCTTTCCCCCTA 59.573 44.000 0.00 0.00 0.00 3.53
428 715 4.227527 CAGTAACATAACCTCTTTCCCCCT 59.772 45.833 0.00 0.00 0.00 4.79
522 809 8.485976 ACATCTTCTTTTTCCTCTCGATTTAG 57.514 34.615 0.00 0.00 0.00 1.85
757 1051 8.228464 GGATCGTTAACTATTTGCTTAATAGGC 58.772 37.037 17.65 0.00 46.67 3.93
769 1063 5.924825 GCAGATTACCGGATCGTTAACTATT 59.075 40.000 9.46 0.00 0.00 1.73
778 1072 0.946221 GCCAGCAGATTACCGGATCG 60.946 60.000 9.46 0.00 0.00 3.69
782 1076 1.524621 CTGGCCAGCAGATTACCGG 60.525 63.158 22.33 0.00 0.00 5.28
793 1087 3.201290 CAAGCTATGACTAACTGGCCAG 58.799 50.000 31.60 31.60 0.00 4.85
820 1114 8.970859 AATCCTCCTGTATGAAATAGTGAAAG 57.029 34.615 0.00 0.00 0.00 2.62
867 1161 5.163723 GCAGCAGCACTATACAAGAAAATGA 60.164 40.000 0.00 0.00 41.58 2.57
978 1279 8.359642 CCCATTCTTATTTCTGTCTTGAAACAA 58.640 33.333 0.00 0.00 38.54 2.83
1078 1379 5.337813 GCACATCCTCAAATTTCCCAAATCT 60.338 40.000 0.00 0.00 0.00 2.40
1110 1411 2.972505 GGCACACAGTGACACCCG 60.973 66.667 7.81 0.00 41.94 5.28
1185 1486 1.190323 GTCTTTGTCTCACAGCGAACG 59.810 52.381 0.00 0.00 0.00 3.95
1194 1495 5.871396 AGAGTACCTTTGTCTTTGTCTCA 57.129 39.130 0.00 0.00 0.00 3.27
1219 1520 7.278646 TGAGTGGATAATTCGAGAAGTGAATTG 59.721 37.037 10.34 0.00 43.77 2.32
1221 1522 6.878317 TGAGTGGATAATTCGAGAAGTGAAT 58.122 36.000 0.00 0.00 37.65 2.57
1231 1532 4.142469 GGGGTGTTTTGAGTGGATAATTCG 60.142 45.833 0.00 0.00 0.00 3.34
1242 1543 1.205417 GATGCATGGGGGTGTTTTGAG 59.795 52.381 2.46 0.00 0.00 3.02
1287 1588 7.743838 GTCAGCAGAAAATAGATCGCATAAATC 59.256 37.037 0.00 0.00 0.00 2.17
1288 1589 7.227314 TGTCAGCAGAAAATAGATCGCATAAAT 59.773 33.333 0.00 0.00 0.00 1.40
1324 1625 8.908903 TGTAACAAAAACATTGTCCTGTAAGAT 58.091 29.630 0.00 0.00 34.07 2.40
1335 1636 8.838452 ATGCAACAATTGTAACAAAAACATTG 57.162 26.923 12.39 2.87 0.00 2.82
1338 1639 6.595326 TGGATGCAACAATTGTAACAAAAACA 59.405 30.769 12.39 8.27 0.00 2.83
1404 1705 5.591877 AGATTTTGGGTTGCTCAGCTTATAG 59.408 40.000 0.00 0.00 0.00 1.31
1544 1845 8.246430 TCATATACCCTTGTTAAGAATCTCGT 57.754 34.615 0.00 0.00 0.00 4.18
1545 1846 9.360093 GATCATATACCCTTGTTAAGAATCTCG 57.640 37.037 0.00 0.00 0.00 4.04
1633 1935 3.242543 GCTCCACAGATTTTGCTATGTCG 60.243 47.826 0.00 0.00 0.00 4.35
1773 2075 4.195225 AGCTCTACTCAAGTAGGCAAAC 57.805 45.455 21.86 9.06 46.01 2.93
1845 2147 9.391006 CTCCTAAGGTTTGTTAGCAATACATAA 57.609 33.333 0.00 0.00 34.18 1.90
1925 2228 9.791801 ATGGTTATACATATACATCAAACTGCA 57.208 29.630 0.00 0.00 0.00 4.41
2002 2305 2.191128 TCTTTTCTGCCTCTGCCTTC 57.809 50.000 0.00 0.00 36.33 3.46
2047 2350 4.541705 AGAGATACTTAGCTTCAGCCTCA 58.458 43.478 0.00 0.00 43.38 3.86
2194 2497 6.430925 TCTCTTTCATGGTGTCAAAGTATTGG 59.569 38.462 0.00 0.00 37.15 3.16
2221 2524 3.760151 CAGAAGATTTGGATGAAGCACCA 59.240 43.478 0.00 0.00 0.00 4.17
2327 2630 1.475280 CATGGGTTCAGTTCAGGCATG 59.525 52.381 0.00 0.00 0.00 4.06
2447 2779 7.281100 ACAAGCTTTTATAGATACCTCACAAGC 59.719 37.037 0.00 0.00 35.41 4.01
2463 2795 9.583765 AAATACAAACCGTTTTACAAGCTTTTA 57.416 25.926 0.00 0.00 0.00 1.52
2493 2825 3.882444 ACGGACTAGCTGATAGTACACA 58.118 45.455 15.05 0.00 44.65 3.72
2494 2826 5.295950 TCTACGGACTAGCTGATAGTACAC 58.704 45.833 15.05 4.41 44.65 2.90
2497 2829 9.163899 CATTTATCTACGGACTAGCTGATAGTA 57.836 37.037 5.45 0.00 45.06 1.82
2499 2831 7.337184 TCCATTTATCTACGGACTAGCTGATAG 59.663 40.741 0.00 0.00 37.53 2.08
2513 2845 4.042187 AGTCCCCATGCTCCATTTATCTAC 59.958 45.833 0.00 0.00 0.00 2.59
2560 2921 5.545723 AGAAGCCTAAGTATAGCCACATGAT 59.454 40.000 0.00 0.00 0.00 2.45
2562 2923 4.993584 CAGAAGCCTAAGTATAGCCACATG 59.006 45.833 0.00 0.00 0.00 3.21
2563 2924 4.901849 TCAGAAGCCTAAGTATAGCCACAT 59.098 41.667 0.00 0.00 0.00 3.21
2577 2938 9.914131 GTAAAAACATTATTTTCTCAGAAGCCT 57.086 29.630 0.00 0.00 34.51 4.58
2625 2986 6.074088 CGCTGAAATATATGAAACGAGAGCTT 60.074 38.462 0.00 0.00 0.00 3.74
2680 3041 3.433615 AGTGCTAGTTGACGAAATTCAGC 59.566 43.478 0.00 0.00 0.00 4.26
2690 3051 5.470368 TGATTGTGAGTAGTGCTAGTTGAC 58.530 41.667 0.00 0.00 0.00 3.18
2702 3063 6.389830 AACTGCATGTTTTGATTGTGAGTA 57.610 33.333 0.00 0.00 34.84 2.59
2787 3148 5.277058 GCTAAGTCAATGATCCACGAACATC 60.277 44.000 0.00 0.00 0.00 3.06
2814 3175 9.529325 GTACTACTCATGTTACATCATTTAGCA 57.471 33.333 0.00 0.00 0.00 3.49
2815 3176 9.529325 TGTACTACTCATGTTACATCATTTAGC 57.471 33.333 0.00 0.00 0.00 3.09
2818 3179 8.830580 GCATGTACTACTCATGTTACATCATTT 58.169 33.333 0.00 0.00 42.94 2.32
2819 3180 7.986889 TGCATGTACTACTCATGTTACATCATT 59.013 33.333 0.00 0.00 42.94 2.57
2820 3181 7.439356 GTGCATGTACTACTCATGTTACATCAT 59.561 37.037 6.69 0.00 42.94 2.45
2821 3182 6.756542 GTGCATGTACTACTCATGTTACATCA 59.243 38.462 6.69 0.00 42.94 3.07
2822 3183 6.756542 TGTGCATGTACTACTCATGTTACATC 59.243 38.462 15.25 0.00 42.94 3.06
2823 3184 6.639563 TGTGCATGTACTACTCATGTTACAT 58.360 36.000 15.25 0.00 42.94 2.29
2824 3185 6.031751 TGTGCATGTACTACTCATGTTACA 57.968 37.500 15.25 9.56 42.94 2.41
2825 3186 5.005779 GCTGTGCATGTACTACTCATGTTAC 59.994 44.000 15.25 7.66 42.94 2.50
2826 3187 5.105351 AGCTGTGCATGTACTACTCATGTTA 60.105 40.000 15.25 0.00 42.94 2.41
2827 3188 3.935203 GCTGTGCATGTACTACTCATGTT 59.065 43.478 15.25 0.00 42.94 2.71
2828 3189 3.196469 AGCTGTGCATGTACTACTCATGT 59.804 43.478 15.25 0.00 42.94 3.21
2829 3190 3.790091 AGCTGTGCATGTACTACTCATG 58.210 45.455 15.25 0.00 43.58 3.07
2830 3191 4.478206 AAGCTGTGCATGTACTACTCAT 57.522 40.909 15.25 0.00 0.00 2.90
2831 3192 3.961480 AAGCTGTGCATGTACTACTCA 57.039 42.857 15.25 0.00 0.00 3.41
2832 3193 6.910536 ATTTAAGCTGTGCATGTACTACTC 57.089 37.500 15.25 2.02 0.00 2.59
2833 3194 8.786826 TTTATTTAAGCTGTGCATGTACTACT 57.213 30.769 15.25 9.16 0.00 2.57
2834 3195 9.274065 GTTTTATTTAAGCTGTGCATGTACTAC 57.726 33.333 15.25 7.03 0.00 2.73
2835 3196 8.172484 CGTTTTATTTAAGCTGTGCATGTACTA 58.828 33.333 15.25 1.16 0.00 1.82
2841 3202 4.173256 GCCGTTTTATTTAAGCTGTGCAT 58.827 39.130 0.00 0.00 0.00 3.96
2856 3218 2.036604 CCACCCAAAATAGTGCCGTTTT 59.963 45.455 0.00 0.00 32.48 2.43
2909 3271 9.859427 TTTTTGGTTGATGAGATTAAGCTAATG 57.141 29.630 0.00 0.00 0.00 1.90
2920 3282 6.061441 TGCTAACTCTTTTTGGTTGATGAGA 58.939 36.000 0.00 0.00 0.00 3.27
2973 3396 5.929697 GATGCGAAATGGATCATGTCTTA 57.070 39.130 0.00 0.00 44.27 2.10
2994 3420 5.105351 ACTCGGTGTCTGAAATGATATGTGA 60.105 40.000 0.00 0.00 0.00 3.58
3020 3446 4.111375 TCCTTCAGCGTGAGTTTATCTC 57.889 45.455 0.00 0.00 43.03 2.75
3033 3459 3.949754 TGTGATCCAATGATTCCTTCAGC 59.050 43.478 0.00 0.00 37.89 4.26
3054 3480 5.941733 TGCTTAAGATTACTGCACACAATG 58.058 37.500 6.67 0.00 0.00 2.82
3116 3542 4.000988 CCCGTGCCACTAATTATCATACC 58.999 47.826 0.00 0.00 0.00 2.73
3154 3580 1.049289 GCCCCTAATCGGTCCAGTCT 61.049 60.000 0.00 0.00 0.00 3.24
3162 3588 0.465642 GGGTCTTTGCCCCTAATCGG 60.466 60.000 0.00 0.00 42.89 4.18
3173 3599 1.888512 CATCAGTGTTGGGGGTCTTTG 59.111 52.381 0.00 0.00 0.00 2.77
3214 3640 4.422073 TTACGAGACGGAGGGAGTAATA 57.578 45.455 0.00 0.00 0.00 0.98
3215 3641 3.287867 TTACGAGACGGAGGGAGTAAT 57.712 47.619 0.00 0.00 0.00 1.89
3216 3642 2.787473 TTACGAGACGGAGGGAGTAA 57.213 50.000 0.00 0.00 0.00 2.24
3264 3690 7.002276 CCGTCCCATAATATAAGAGGGTTTTT 58.998 38.462 0.00 0.00 40.48 1.94
3265 3691 6.330778 TCCGTCCCATAATATAAGAGGGTTTT 59.669 38.462 0.00 0.00 40.48 2.43
3266 3692 5.847817 TCCGTCCCATAATATAAGAGGGTTT 59.152 40.000 0.00 0.00 40.48 3.27
3270 3696 4.406003 CCCTCCGTCCCATAATATAAGAGG 59.594 50.000 0.00 0.00 38.47 3.69
3298 3724 0.106149 CCATCCCGGCTGTTAGGTAC 59.894 60.000 0.00 0.00 0.00 3.34
3312 3739 1.473434 CGACCTTACTGAAGCCCATCC 60.473 57.143 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.