Multiple sequence alignment - TraesCS2A01G538500

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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 TraesCS2A01G538500 chr2A 100.000 4729 0 0 1 4729 751384827 751380099 0.000000e+00 8733.0
1 TraesCS2A01G538500 chr2A 79.150 1482 178 76 794 2202 719720748 719722171 0.000000e+00 904.0
2 TraesCS2A01G538500 chr2A 80.876 434 38 20 3118 3541 719723105 719723503 2.770000e-77 300.0
3 TraesCS2A01G538500 chr2A 86.875 160 13 7 2575 2730 719722518 719722673 6.290000e-39 172.0
4 TraesCS2A01G538500 chr2A 75.556 405 46 37 3646 4026 719723576 719723951 2.950000e-32 150.0
5 TraesCS2A01G538500 chr2B 90.428 4555 235 79 1 4410 759451756 759447258 0.000000e+00 5810.0
6 TraesCS2A01G538500 chr2B 79.310 1711 199 104 814 2431 706724162 706725810 0.000000e+00 1055.0
7 TraesCS2A01G538500 chr2B 95.732 328 10 3 4406 4729 759447179 759446852 4.190000e-145 525.0
8 TraesCS2A01G538500 chr2B 74.714 1309 155 111 3064 4303 706726536 706727737 5.660000e-114 422.0
9 TraesCS2A01G538500 chr2B 84.940 166 13 9 2576 2734 706725991 706726151 1.760000e-34 158.0
10 TraesCS2A01G538500 chr2B 91.346 104 8 1 2900 3002 706726406 706726509 1.770000e-29 141.0
11 TraesCS2A01G538500 chr2D 93.081 3917 145 67 599 4442 619712148 619708285 0.000000e+00 5616.0
12 TraesCS2A01G538500 chr2D 80.341 763 65 41 794 1496 585679364 585680101 2.540000e-137 499.0
13 TraesCS2A01G538500 chr2D 81.683 606 70 21 1627 2202 585680254 585680848 2.580000e-127 466.0
14 TraesCS2A01G538500 chr2D 75.715 1223 136 92 3118 4275 585681926 585683052 9.270000e-127 464.0
15 TraesCS2A01G538500 chr2D 96.610 236 2 4 4498 4729 619708289 619708056 2.060000e-103 387.0
16 TraesCS2A01G538500 chr2D 83.152 368 31 14 1 363 619712644 619712303 1.650000e-79 307.0
17 TraesCS2A01G538500 chr2D 76.524 443 61 35 2312 2730 585681076 585681499 8.020000e-48 202.0
18 TraesCS2A01G538500 chr2D 92.929 99 6 1 2905 3002 585681751 585681849 4.930000e-30 143.0
19 TraesCS2A01G538500 chr5B 90.667 75 3 1 112 182 372654349 372654423 3.900000e-16 97.1
20 TraesCS2A01G538500 chr4A 88.158 76 4 2 112 182 424369508 424369433 8.430000e-13 86.1
21 TraesCS2A01G538500 chr7A 89.552 67 3 2 112 174 232532163 232532097 1.090000e-11 82.4
22 TraesCS2A01G538500 chr3A 87.500 72 5 2 112 179 708218732 708218803 3.920000e-11 80.5
23 TraesCS2A01G538500 chr4D 85.714 77 6 3 112 183 506898102 506898026 5.070000e-10 76.8
24 TraesCS2A01G538500 chr4D 84.932 73 7 3 515 585 102139711 102139781 2.360000e-08 71.3
25 TraesCS2A01G538500 chr7B 86.957 69 5 2 115 179 684400338 684400270 1.830000e-09 75.0
26 TraesCS2A01G538500 chr6B 86.111 72 6 1 112 179 648196262 648196333 1.830000e-09 75.0
27 TraesCS2A01G538500 chr3B 86.111 72 6 2 112 179 763058170 763058241 1.830000e-09 75.0


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 TraesCS2A01G538500 chr2A 751380099 751384827 4728 True 8733.000000 8733 100.000000 1 4729 1 chr2A.!!$R1 4728
1 TraesCS2A01G538500 chr2A 719720748 719723951 3203 False 381.500000 904 80.614250 794 4026 4 chr2A.!!$F1 3232
2 TraesCS2A01G538500 chr2B 759446852 759451756 4904 True 3167.500000 5810 93.080000 1 4729 2 chr2B.!!$R1 4728
3 TraesCS2A01G538500 chr2B 706724162 706727737 3575 False 444.000000 1055 82.577500 814 4303 4 chr2B.!!$F1 3489
4 TraesCS2A01G538500 chr2D 619708056 619712644 4588 True 2103.333333 5616 90.947667 1 4729 3 chr2D.!!$R1 4728
5 TraesCS2A01G538500 chr2D 585679364 585683052 3688 False 354.800000 499 81.438400 794 4275 5 chr2D.!!$F1 3481

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
230 256 0.107214 TGGTTGGGCATGTAGCTAGC 60.107 55.0 6.62 6.62 44.79 3.42 F
250 280 0.109458 CATGCAGGCATGTGTGTGAC 60.109 55.0 22.73 0.00 46.20 3.67 F
1135 1261 0.179062 GGAGCGGTGATCAGCAGATT 60.179 55.0 23.68 6.45 37.23 2.40 F
2567 3023 0.174845 TAGACGCAAACCCAGATCGG 59.825 55.0 0.00 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1935 1.011463 GCGTTCATCATGCTCTGCG 60.011 57.895 0.0 0.0 34.13 5.18 R
1904 2119 1.154150 CGACGACTGGAACCCGTAC 60.154 63.158 0.0 0.0 36.60 3.67 R
3036 3672 0.098728 GCCATGATTAAAGCGTGCGT 59.901 50.000 0.0 0.0 0.00 5.24 R
4134 4867 1.431488 AAGACACACAGCACGCACAG 61.431 55.000 0.0 0.0 0.00 3.66 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
26 27 0.609957 TTTGGCATGGCAGAGAGTGG 60.610 55.000 22.17 0.00 0.00 4.00
102 104 1.699730 GGTTGGTTTGGCTGGTACTT 58.300 50.000 0.00 0.00 0.00 2.24
104 106 1.265905 GTTGGTTTGGCTGGTACTTCG 59.734 52.381 0.00 0.00 0.00 3.79
109 111 0.948678 TTGGCTGGTACTTCGTTTGC 59.051 50.000 0.00 0.00 0.00 3.68
110 112 1.225376 TGGCTGGTACTTCGTTTGCG 61.225 55.000 0.00 0.00 39.92 4.85
189 215 1.482593 AGAGGAAGTACATTGGAGCGG 59.517 52.381 0.00 0.00 0.00 5.52
214 240 2.031120 CCTGAATGTTGGTGTGTTGGT 58.969 47.619 0.00 0.00 0.00 3.67
230 256 0.107214 TGGTTGGGCATGTAGCTAGC 60.107 55.000 6.62 6.62 44.79 3.42
250 280 0.109458 CATGCAGGCATGTGTGTGAC 60.109 55.000 22.73 0.00 46.20 3.67
276 306 3.437049 GTGGTGTATTTGGAAGTGAGAGC 59.563 47.826 0.00 0.00 0.00 4.09
286 316 2.744768 AAGTGAGAGCAGCAGCCCAC 62.745 60.000 0.00 4.19 43.56 4.61
292 322 0.598419 GAGCAGCAGCCCACAAAAAC 60.598 55.000 0.00 0.00 43.56 2.43
376 406 5.546621 TTAACTAATCCCTCCGATCCAAG 57.453 43.478 0.00 0.00 0.00 3.61
377 407 3.330126 ACTAATCCCTCCGATCCAAGA 57.670 47.619 0.00 0.00 0.00 3.02
378 408 3.863086 ACTAATCCCTCCGATCCAAGAT 58.137 45.455 0.00 0.00 0.00 2.40
385 415 3.895656 CCCTCCGATCCAAGATAAGTGTA 59.104 47.826 0.00 0.00 0.00 2.90
386 416 4.021894 CCCTCCGATCCAAGATAAGTGTAG 60.022 50.000 0.00 0.00 0.00 2.74
389 419 4.341235 TCCGATCCAAGATAAGTGTAGTGG 59.659 45.833 0.00 0.00 0.00 4.00
435 470 7.436536 AATCATGAAACATATTTTCGAACGC 57.563 32.000 0.00 0.00 0.00 4.84
452 496 0.323629 CGCAGGGAGTAGGGTTTTCA 59.676 55.000 0.00 0.00 0.00 2.69
456 500 0.392595 GGGAGTAGGGTTTTCAGCCG 60.393 60.000 0.00 0.00 46.26 5.52
467 511 3.372060 GTTTTCAGCCGACTTTTCCTTG 58.628 45.455 0.00 0.00 0.00 3.61
483 527 6.479972 TTTCCTTGTAAACAGAGTCTCTCA 57.520 37.500 0.00 0.00 32.06 3.27
485 529 4.281182 TCCTTGTAAACAGAGTCTCTCACC 59.719 45.833 0.00 0.00 32.06 4.02
491 535 5.888982 AAACAGAGTCTCTCACCCTTTTA 57.111 39.130 0.00 0.00 32.06 1.52
509 561 8.939932 ACCCTTTTATCCATTCAAGGTTTAAAA 58.060 29.630 0.00 0.00 34.97 1.52
550 602 3.520290 ATTAGATGACGCTCAAACGGA 57.480 42.857 0.00 0.00 37.37 4.69
556 608 2.267426 TGACGCTCAAACGGATGTATG 58.733 47.619 0.00 0.00 37.37 2.39
557 609 2.268298 GACGCTCAAACGGATGTATGT 58.732 47.619 0.00 0.00 37.37 2.29
561 613 4.980434 ACGCTCAAACGGATGTATGTATAC 59.020 41.667 0.00 0.00 37.37 1.47
562 614 4.979815 CGCTCAAACGGATGTATGTATACA 59.020 41.667 8.27 8.27 46.21 2.29
584 636 6.398918 ACATATTTCGGTGCTAGATACATCC 58.601 40.000 0.00 0.00 0.00 3.51
585 637 6.211584 ACATATTTCGGTGCTAGATACATCCT 59.788 38.462 0.00 0.00 0.00 3.24
587 639 4.322080 TTCGGTGCTAGATACATCCTTG 57.678 45.455 0.00 0.00 0.00 3.61
588 640 3.562182 TCGGTGCTAGATACATCCTTGA 58.438 45.455 0.00 0.00 0.00 3.02
590 642 3.305676 CGGTGCTAGATACATCCTTGAGG 60.306 52.174 0.00 0.00 0.00 3.86
601 675 1.192146 TCCTTGAGGACGGAGGTTGG 61.192 60.000 0.00 0.00 39.78 3.77
605 679 1.946984 TGAGGACGGAGGTTGGTTAT 58.053 50.000 0.00 0.00 0.00 1.89
617 691 8.323567 ACGGAGGTTGGTTATTCTTTAAGATTA 58.676 33.333 0.00 0.00 0.00 1.75
747 824 9.826574 TTACTGTTACAACTACAAGACAAGATT 57.173 29.630 0.00 0.00 0.00 2.40
775 852 6.006449 AGTTAAAAGAGACTACTACCGGTGA 58.994 40.000 19.93 0.76 0.00 4.02
1135 1261 0.179062 GGAGCGGTGATCAGCAGATT 60.179 55.000 23.68 6.45 37.23 2.40
1138 1264 1.065926 AGCGGTGATCAGCAGATTGAA 60.066 47.619 23.68 0.00 37.23 2.69
1213 1349 4.148825 GCCGGAGCCGTGTCTCAT 62.149 66.667 5.05 0.00 37.81 2.90
1290 1426 3.423154 GCTCGCCGGGTTCAACAG 61.423 66.667 2.18 0.00 0.00 3.16
1336 1478 4.731729 TACGACGTGGCGGGGGTA 62.732 66.667 11.56 0.00 35.12 3.69
1406 1548 2.429930 CCGGGAACAACAGCTCCA 59.570 61.111 0.00 0.00 32.95 3.86
1423 1565 3.127030 GCTCCATAACCTTCCAAGAAACG 59.873 47.826 0.00 0.00 0.00 3.60
1502 1644 3.493503 GTGAGTTGTTCGTTCCCACTTAG 59.506 47.826 0.00 0.00 0.00 2.18
1562 1704 2.467838 TCGTCCGTGATCTCGTACTAG 58.532 52.381 15.34 0.87 0.00 2.57
1625 1811 0.238289 CCCGTGACATGCACTGAAAC 59.762 55.000 15.20 0.00 45.49 2.78
1741 1935 1.668101 ATGAGCTCGAGAACGGACCC 61.668 60.000 18.75 0.00 40.21 4.46
1816 2028 2.435663 CCACCACCACCATCAGCA 59.564 61.111 0.00 0.00 0.00 4.41
1817 2029 1.676635 CCACCACCACCATCAGCAG 60.677 63.158 0.00 0.00 0.00 4.24
1818 2030 2.034687 ACCACCACCATCAGCAGC 59.965 61.111 0.00 0.00 0.00 5.25
1819 2031 2.034532 CCACCACCATCAGCAGCA 59.965 61.111 0.00 0.00 0.00 4.41
1820 2032 2.044555 CCACCACCATCAGCAGCAG 61.045 63.158 0.00 0.00 0.00 4.24
1821 2033 2.360852 ACCACCATCAGCAGCAGC 60.361 61.111 0.00 0.00 42.56 5.25
1841 2053 1.812922 GCAGCAGGACGATCACCAG 60.813 63.158 8.36 2.17 0.00 4.00
1946 2164 2.841988 AGGAGCCTCATCGAGCCC 60.842 66.667 0.00 0.00 0.00 5.19
1949 2167 3.453070 GAGCCTCATCGAGCCCACC 62.453 68.421 0.00 0.00 0.00 4.61
2128 2349 0.580104 GACAACACTAGCGTGCGTTT 59.420 50.000 0.00 0.00 45.10 3.60
2142 2363 1.655959 CGTTTGGCGAAACAACCGG 60.656 57.895 21.90 0.00 41.48 5.28
2247 2568 8.400947 ACTCTATACAAGCAGTTGCAAATATTG 58.599 33.333 17.49 17.49 45.16 1.90
2320 2666 5.749109 GGTTGTCTGTATGTATAGACTGTGC 59.251 44.000 15.08 5.74 42.66 4.57
2328 2674 7.061054 TGTATGTATAGACTGTGCTAGAAGGT 58.939 38.462 0.00 0.00 0.00 3.50
2337 2683 1.834263 GTGCTAGAAGGTGTGGGAGAT 59.166 52.381 0.00 0.00 0.00 2.75
2352 2698 3.319405 TGGGAGATTCTAGCTCAATCGTC 59.681 47.826 11.03 9.37 35.69 4.20
2364 2710 1.071542 TCAATCGTCACCAAGAAGGCA 59.928 47.619 0.00 0.00 43.14 4.75
2446 2854 4.109766 CAAGGTAAACATGCATGCTCATG 58.890 43.478 26.53 17.09 46.86 3.07
2458 2866 4.670227 CATGCTCATGCTCATACTCATG 57.330 45.455 0.00 0.00 40.92 3.07
2460 2868 2.158871 TGCTCATGCTCATACTCATGCA 60.159 45.455 0.00 0.00 39.76 3.96
2464 2872 3.503800 ATGCTCATACTCATGCATGGT 57.496 42.857 25.97 22.52 43.41 3.55
2465 2873 3.286329 TGCTCATACTCATGCATGGTT 57.714 42.857 25.97 15.35 31.73 3.67
2466 2874 4.420522 TGCTCATACTCATGCATGGTTA 57.579 40.909 25.97 16.94 31.73 2.85
2467 2875 4.383173 TGCTCATACTCATGCATGGTTAG 58.617 43.478 25.97 18.08 31.73 2.34
2468 2876 3.750130 GCTCATACTCATGCATGGTTAGG 59.250 47.826 25.97 17.67 31.73 2.69
2469 2877 4.744867 GCTCATACTCATGCATGGTTAGGT 60.745 45.833 25.97 17.52 31.73 3.08
2471 2879 5.853936 TCATACTCATGCATGGTTAGGTAC 58.146 41.667 25.97 0.00 31.73 3.34
2567 3023 0.174845 TAGACGCAAACCCAGATCGG 59.825 55.000 0.00 0.00 0.00 4.18
2757 3221 6.410243 CATGCATGCATCACATAAACAAAA 57.590 33.333 30.07 0.00 36.64 2.44
2829 3432 1.460743 TCTCTGCAAAAGCGTTCATCG 59.539 47.619 0.00 0.00 43.12 3.84
2895 3510 3.442625 TGTGGAGGAGTATCTAACACACG 59.557 47.826 0.00 0.00 37.02 4.49
2912 3542 2.778679 GATCTCGTTGTGCGTGCC 59.221 61.111 0.00 0.00 42.13 5.01
3032 3668 4.818863 TCCATGCCCCCATGCACG 62.819 66.667 0.00 0.00 45.97 5.34
3547 4226 7.092846 CCCAATTTAGGTAGAGGAAGAAGAAGA 60.093 40.741 0.00 0.00 0.00 2.87
3696 4387 4.530710 TTGTAACAGGTAGTAGCACCAG 57.469 45.455 1.58 0.00 41.40 4.00
3697 4388 3.503365 TGTAACAGGTAGTAGCACCAGT 58.497 45.455 1.58 0.00 39.77 4.00
3704 4395 2.094130 GGTAGTAGCACCAGTGAGGAAC 60.094 54.545 0.99 0.00 41.22 3.62
3897 4610 2.787129 TCGATTGTCGTCGTATGATTGC 59.213 45.455 0.00 0.00 41.35 3.56
3944 4657 3.951775 TGTGGAACAGCTTGTTGTTTT 57.048 38.095 6.31 0.00 45.67 2.43
3980 4697 8.894768 ACTAGTACTTTAATTCAGCCATGATC 57.105 34.615 0.00 0.00 34.73 2.92
4021 4738 7.044798 GTCTGTAGCAGGTTTCATTTCTCTAT 58.955 38.462 0.00 0.00 31.51 1.98
4134 4867 5.944007 TGTTTTAAGTAGGGCTTCCAGAATC 59.056 40.000 0.00 0.00 38.57 2.52
4187 4922 2.291153 TGCCTTCCAGAATCTTTCAGGG 60.291 50.000 0.00 0.00 37.00 4.45
4260 5008 8.887717 AGCATATTCTTCTGTGTGTTTCTTATC 58.112 33.333 0.00 0.00 0.00 1.75
4298 5046 0.251653 TCCTCTCAGCGGTACCAACT 60.252 55.000 13.54 5.59 0.00 3.16
4447 5283 4.084328 CGATGAAACTCACCTGAAAGTGAC 60.084 45.833 0.00 0.00 41.78 3.67
4456 5292 1.891060 CTGAAAGTGACTCGCGGCAC 61.891 60.000 2.29 2.29 35.30 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.055819 TCACCCTTCTAGCACAAGATCAC 60.056 47.826 0.00 0.00 0.00 3.06
61 62 3.756434 CCCGTTTGATTGTGTACTTGGAT 59.244 43.478 0.00 0.00 0.00 3.41
168 194 2.693591 CCGCTCCAATGTACTTCCTCTA 59.306 50.000 0.00 0.00 0.00 2.43
186 212 1.517694 CAACATTCAGGCATGCCGC 60.518 57.895 30.50 8.59 41.95 6.53
189 215 0.604578 ACACCAACATTCAGGCATGC 59.395 50.000 9.90 9.90 0.00 4.06
196 222 2.167281 CCAACCAACACACCAACATTCA 59.833 45.455 0.00 0.00 0.00 2.57
214 240 0.846015 ATGGCTAGCTACATGCCCAA 59.154 50.000 15.72 3.13 45.56 4.12
237 263 1.301716 ACTCGGTCACACACATGCC 60.302 57.895 0.00 0.00 0.00 4.40
239 265 0.249868 ACCACTCGGTCACACACATG 60.250 55.000 0.00 0.00 44.71 3.21
250 280 2.742053 CACTTCCAAATACACCACTCGG 59.258 50.000 0.00 0.00 38.77 4.63
276 306 0.314935 ATCGTTTTTGTGGGCTGCTG 59.685 50.000 0.00 0.00 0.00 4.41
286 316 0.974836 GCCGCGAGAAATCGTTTTTG 59.025 50.000 8.23 0.00 35.26 2.44
292 322 0.596083 AGATCTGCCGCGAGAAATCG 60.596 55.000 8.23 0.00 0.00 3.34
363 393 2.700897 ACACTTATCTTGGATCGGAGGG 59.299 50.000 0.00 0.00 0.00 4.30
367 397 4.099573 ACCACTACACTTATCTTGGATCGG 59.900 45.833 0.00 0.00 0.00 4.18
368 398 5.263968 ACCACTACACTTATCTTGGATCG 57.736 43.478 0.00 0.00 0.00 3.69
419 454 3.340034 TCCCTGCGTTCGAAAATATGTT 58.660 40.909 0.00 0.00 0.00 2.71
422 457 3.261981 ACTCCCTGCGTTCGAAAATAT 57.738 42.857 0.00 0.00 0.00 1.28
429 464 1.885163 AACCCTACTCCCTGCGTTCG 61.885 60.000 0.00 0.00 0.00 3.95
432 467 0.323957 GAAAACCCTACTCCCTGCGT 59.676 55.000 0.00 0.00 0.00 5.24
435 470 1.340114 GGCTGAAAACCCTACTCCCTG 60.340 57.143 0.00 0.00 0.00 4.45
452 496 3.547746 TGTTTACAAGGAAAAGTCGGCT 58.452 40.909 0.00 0.00 0.00 5.52
456 500 6.987404 AGAGACTCTGTTTACAAGGAAAAGTC 59.013 38.462 3.56 1.55 0.00 3.01
467 511 4.875561 AAGGGTGAGAGACTCTGTTTAC 57.124 45.455 10.44 3.71 34.61 2.01
483 527 8.499288 TTTAAACCTTGAATGGATAAAAGGGT 57.501 30.769 5.37 0.00 41.55 4.34
513 565 5.130292 TCTAATTTCGAACGGAGTGAGTT 57.870 39.130 0.00 0.00 45.00 3.01
523 575 5.450376 TTGAGCGTCATCTAATTTCGAAC 57.550 39.130 0.00 0.00 0.00 3.95
525 577 4.031314 CGTTTGAGCGTCATCTAATTTCGA 59.969 41.667 0.00 0.00 0.00 3.71
561 613 6.634805 AGGATGTATCTAGCACCGAAATATG 58.365 40.000 0.00 0.00 0.00 1.78
562 614 6.859112 AGGATGTATCTAGCACCGAAATAT 57.141 37.500 0.00 0.00 0.00 1.28
569 621 3.898123 TCCTCAAGGATGTATCTAGCACC 59.102 47.826 0.00 0.00 39.78 5.01
584 636 0.396811 AACCAACCTCCGTCCTCAAG 59.603 55.000 0.00 0.00 0.00 3.02
585 637 1.719529 TAACCAACCTCCGTCCTCAA 58.280 50.000 0.00 0.00 0.00 3.02
587 639 2.500504 AGAATAACCAACCTCCGTCCTC 59.499 50.000 0.00 0.00 0.00 3.71
588 640 2.547990 AGAATAACCAACCTCCGTCCT 58.452 47.619 0.00 0.00 0.00 3.85
590 642 6.168389 TCTTAAAGAATAACCAACCTCCGTC 58.832 40.000 0.00 0.00 0.00 4.79
595 647 9.239551 GGTGTAATCTTAAAGAATAACCAACCT 57.760 33.333 0.00 0.00 0.00 3.50
596 648 9.239551 AGGTGTAATCTTAAAGAATAACCAACC 57.760 33.333 0.00 0.00 0.00 3.77
605 679 9.653287 CATCACACTAGGTGTAATCTTAAAGAA 57.347 33.333 2.92 0.00 45.65 2.52
653 727 4.936411 TGACTACCAACAACGAAAAAGACA 59.064 37.500 0.00 0.00 0.00 3.41
747 824 6.373774 CCGGTAGTAGTCTCTTTTAACTCTCA 59.626 42.308 0.00 0.00 0.00 3.27
775 852 1.681793 ACTACACAACACTCTCGTGCT 59.318 47.619 0.00 0.00 45.10 4.40
887 977 2.741211 GTCGTTGGCGGTCTTCCC 60.741 66.667 0.00 0.00 38.89 3.97
957 1051 7.732025 TGTGTGGTCTGGGTATATATAAACTG 58.268 38.462 0.00 0.00 0.00 3.16
958 1052 7.924358 TGTGTGGTCTGGGTATATATAAACT 57.076 36.000 0.00 0.00 0.00 2.66
1108 1231 1.148759 GATCACCGCTCCGCTTCTTC 61.149 60.000 0.00 0.00 0.00 2.87
1114 1237 4.819761 TGCTGATCACCGCTCCGC 62.820 66.667 8.27 1.64 0.00 5.54
1128 1254 3.382278 TCTCCCATCTCTTCAATCTGCT 58.618 45.455 0.00 0.00 0.00 4.24
1135 1261 3.324268 GCTGATGATCTCCCATCTCTTCA 59.676 47.826 0.00 0.00 42.49 3.02
1138 1264 2.901192 CAGCTGATGATCTCCCATCTCT 59.099 50.000 8.42 0.00 42.49 3.10
1213 1349 1.902918 GCTGTTCCACCACATGCCA 60.903 57.895 0.00 0.00 0.00 4.92
1309 1448 4.065281 ACGTCGTAGCCACCAGCC 62.065 66.667 0.00 0.00 45.47 4.85
1332 1474 4.525949 GCTTCCCGCCGTCTACCC 62.526 72.222 0.00 0.00 0.00 3.69
1335 1477 3.458163 CCTGCTTCCCGCCGTCTA 61.458 66.667 0.00 0.00 38.05 2.59
1406 1548 2.224917 TGGCCGTTTCTTGGAAGGTTAT 60.225 45.455 0.00 0.00 0.00 1.89
1423 1565 3.134127 GGGTCGTTGATGCTGGCC 61.134 66.667 0.00 0.00 0.00 5.36
1502 1644 2.215942 ATTAAGGGCAGGTGTGGAAC 57.784 50.000 0.00 0.00 37.35 3.62
1582 1728 6.233430 AGTATGTACGTATGTGTATCGACC 57.767 41.667 0.00 0.00 0.00 4.79
1583 1729 6.302615 GGAGTATGTACGTATGTGTATCGAC 58.697 44.000 0.00 0.00 0.00 4.20
1653 1839 4.021981 GCTGCTCCTGTTGGAAGTTAAAAT 60.022 41.667 0.00 0.00 42.66 1.82
1655 1841 2.884639 GCTGCTCCTGTTGGAAGTTAAA 59.115 45.455 0.00 0.00 42.66 1.52
1741 1935 1.011463 GCGTTCATCATGCTCTGCG 60.011 57.895 0.00 0.00 34.13 5.18
1818 2030 2.125229 ATCGTCCTGCTGCTGCTG 60.125 61.111 17.00 15.58 40.48 4.41
1819 2031 2.186384 GATCGTCCTGCTGCTGCT 59.814 61.111 17.00 0.00 40.48 4.24
1820 2032 2.125391 TGATCGTCCTGCTGCTGC 60.125 61.111 8.89 8.89 40.20 5.25
1821 2033 1.812922 GGTGATCGTCCTGCTGCTG 60.813 63.158 0.00 0.00 0.00 4.41
1904 2119 1.154150 CGACGACTGGAACCCGTAC 60.154 63.158 0.00 0.00 36.60 3.67
1946 2164 2.746277 GGTGCTGGCTTACCGGTG 60.746 66.667 19.93 1.47 45.10 4.94
2024 2245 2.343758 GTGAACTGGAGCGGCTCA 59.656 61.111 29.33 15.42 31.08 4.26
2247 2568 1.328680 CATCTGTACGTGCTTCCATGC 59.671 52.381 4.97 0.00 0.00 4.06
2320 2666 4.038642 GCTAGAATCTCCCACACCTTCTAG 59.961 50.000 11.45 11.45 44.08 2.43
2328 2674 3.068732 CGATTGAGCTAGAATCTCCCACA 59.931 47.826 13.47 0.00 0.00 4.17
2337 2683 3.509967 TCTTGGTGACGATTGAGCTAGAA 59.490 43.478 0.00 0.00 0.00 2.10
2352 2698 2.956987 CCGCTTGCCTTCTTGGTG 59.043 61.111 0.00 0.00 38.35 4.17
2446 2854 3.750130 CCTAACCATGCATGAGTATGAGC 59.250 47.826 28.31 0.00 39.88 4.26
2447 2855 4.965814 ACCTAACCATGCATGAGTATGAG 58.034 43.478 28.31 18.19 39.88 2.90
2458 2866 5.129980 ACCTAACCTAAGTACCTAACCATGC 59.870 44.000 0.00 0.00 0.00 4.06
2460 2868 8.915813 TTAACCTAACCTAAGTACCTAACCAT 57.084 34.615 0.00 0.00 0.00 3.55
2462 2870 9.823647 GATTTAACCTAACCTAAGTACCTAACC 57.176 37.037 0.00 0.00 0.00 2.85
2466 2874 7.991460 GCATGATTTAACCTAACCTAAGTACCT 59.009 37.037 0.00 0.00 0.00 3.08
2467 2875 7.228108 GGCATGATTTAACCTAACCTAAGTACC 59.772 40.741 0.00 0.00 0.00 3.34
2468 2876 7.771826 TGGCATGATTTAACCTAACCTAAGTAC 59.228 37.037 0.00 0.00 0.00 2.73
2469 2877 7.771826 GTGGCATGATTTAACCTAACCTAAGTA 59.228 37.037 0.00 0.00 0.00 2.24
2471 2879 6.828785 AGTGGCATGATTTAACCTAACCTAAG 59.171 38.462 0.00 0.00 0.00 2.18
2588 3044 5.669122 GTTGCATGCACAACTTTAATCAAC 58.331 37.500 22.58 7.24 45.20 3.18
2757 3221 9.314133 TCAAGGTCATGTGTAATATATCTAGCT 57.686 33.333 0.00 0.00 0.00 3.32
2786 3250 5.563876 AGAGATGCACATTGGATGATACT 57.436 39.130 0.00 0.00 0.00 2.12
2787 3251 5.996513 AGAAGAGATGCACATTGGATGATAC 59.003 40.000 0.00 0.00 0.00 2.24
2788 3252 6.042897 AGAGAAGAGATGCACATTGGATGATA 59.957 38.462 0.00 0.00 0.00 2.15
2829 3432 0.981943 TCGAAAGGAGGGGAGGAAAC 59.018 55.000 0.00 0.00 0.00 2.78
2912 3542 4.547905 ACGCCGTATCCGTCTGCG 62.548 66.667 0.00 0.00 44.26 5.18
3032 3668 0.110419 TGATTAAAGCGTGCGTGTGC 60.110 50.000 0.00 0.00 43.20 4.57
3033 3669 2.168384 CATGATTAAAGCGTGCGTGTG 58.832 47.619 0.00 0.00 0.00 3.82
3034 3670 1.130373 CCATGATTAAAGCGTGCGTGT 59.870 47.619 0.00 0.00 0.00 4.49
3035 3671 1.813896 CCATGATTAAAGCGTGCGTG 58.186 50.000 0.00 0.00 0.00 5.34
3036 3672 0.098728 GCCATGATTAAAGCGTGCGT 59.901 50.000 0.00 0.00 0.00 5.24
3037 3673 0.925267 CGCCATGATTAAAGCGTGCG 60.925 55.000 0.00 0.00 43.45 5.34
3072 3708 0.393448 GGGAGGAAACCGATAGAGCC 59.607 60.000 0.00 0.00 39.76 4.70
3697 4388 8.726988 GCCATATAATTAATTAAGCGTTCCTCA 58.273 33.333 11.80 0.00 0.00 3.86
3897 4610 4.497300 CCCAATGATGCAAACCTAACAAG 58.503 43.478 0.00 0.00 0.00 3.16
4021 4738 9.802039 ACTTCTTTATTTGGTAGTACAAATCCA 57.198 29.630 7.36 0.00 45.24 3.41
4134 4867 1.431488 AAGACACACAGCACGCACAG 61.431 55.000 0.00 0.00 0.00 3.66
4187 4922 5.163301 TGGCTCAGAAATGGGATAGTCTAAC 60.163 44.000 0.00 0.00 0.00 2.34
4260 5008 2.410730 GGAATGAAACGTAGACCACACG 59.589 50.000 0.00 0.00 44.80 4.49
4298 5046 2.313317 CTATACACGGGTCCTGGCTTA 58.687 52.381 0.00 0.00 0.00 3.09
4390 5142 8.849543 ACCCCTATACTTGTTATGAAAGAGTA 57.150 34.615 0.00 0.00 0.00 2.59
4456 5292 5.472822 CGTGTCGAACTTATCTGAATTTCG 58.527 41.667 0.00 4.09 40.28 3.46
4495 5331 4.348863 ACACTTCAGTTGAGATTCAGCT 57.651 40.909 0.00 0.00 38.51 4.24


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

AutoCloner maintained by Alex Coulton.