Multiple sequence alignment - TraesCS7D01G170800

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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 TraesCS7D01G170800 chr7D 100.000 2963 0 0 1 2963 123164779 123161817 0.000000e+00 5472.0
1 TraesCS7D01G170800 chr7D 89.048 210 21 2 252 460 16293161 16293369 2.930000e-65 259.0
2 TraesCS7D01G170800 chr7B 94.629 2383 104 11 600 2963 84380553 84378176 0.000000e+00 3670.0
3 TraesCS7D01G170800 chr7B 75.916 191 32 11 2577 2754 566757681 566757870 5.260000e-13 86.1
4 TraesCS7D01G170800 chr7A 93.449 1435 56 10 712 2138 126116793 126115389 0.000000e+00 2095.0
5 TraesCS7D01G170800 chr7A 84.355 799 98 11 2184 2957 126114219 126113423 0.000000e+00 758.0
6 TraesCS7D01G170800 chr4A 95.364 302 9 4 1 299 706429293 706428994 2.670000e-130 475.0
7 TraesCS7D01G170800 chr4A 90.547 201 18 1 261 460 718502214 718502014 6.300000e-67 265.0
8 TraesCS7D01G170800 chr4A 96.970 66 1 1 296 361 706427826 706427762 3.120000e-20 110.0
9 TraesCS7D01G170800 chr4A 92.105 76 5 1 391 466 706427358 706427284 4.040000e-19 106.0
10 TraesCS7D01G170800 chr5B 91.429 210 17 1 252 460 429170173 429170382 1.340000e-73 287.0
11 TraesCS7D01G170800 chr4B 91.787 207 15 2 261 466 602734264 602734059 1.340000e-73 287.0
12 TraesCS7D01G170800 chr2A 90.500 200 18 1 261 459 659281886 659281687 2.260000e-66 263.0
13 TraesCS7D01G170800 chr3D 87.981 208 23 2 261 466 90151541 90151334 8.200000e-61 244.0


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 TraesCS7D01G170800 chr7D 123161817 123164779 2962 True 5472.000000 5472 100.000 1 2963 1 chr7D.!!$R1 2962
1 TraesCS7D01G170800 chr7B 84378176 84380553 2377 True 3670.000000 3670 94.629 600 2963 1 chr7B.!!$R1 2363
2 TraesCS7D01G170800 chr7A 126113423 126116793 3370 True 1426.500000 2095 88.902 712 2957 2 chr7A.!!$R1 2245
3 TraesCS7D01G170800 chr4A 706427284 706429293 2009 True 230.333333 475 94.813 1 466 3 chr4A.!!$R2 465

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
766 2317 0.040157 TCGCAACTTGCAAGCATGAC 60.04 50.0 27.79 19.66 45.36 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 4889 0.037697 TCAGACAATTGGGTCCGACG 60.038 55.0 10.83 0.0 38.59 5.12 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
36 37 7.644986 TCTCACTCTCTTCTTTTTCGAAATC 57.355 36.000 12.12 0.00 0.00 2.17
50 51 9.937175 CTTTTTCGAAATCTTCTTTACAGAACT 57.063 29.630 12.12 0.00 33.80 3.01
71 72 9.462606 AGAACTCCTTTTGAACTCTTCTTTTTA 57.537 29.630 0.00 0.00 0.00 1.52
159 163 1.004277 GGGCCTGTGAAGTGGACAATA 59.996 52.381 0.84 0.00 31.61 1.90
235 239 6.761242 TGAGGTGGATATATCGAGTGTTTTTG 59.239 38.462 6.64 0.00 0.00 2.44
238 242 5.295787 GTGGATATATCGAGTGTTTTTGGCA 59.704 40.000 6.64 0.00 0.00 4.92
248 252 7.598278 TCGAGTGTTTTTGGCAAATATGTATT 58.402 30.769 14.29 0.00 0.00 1.89
275 279 3.889815 TCCCCTTGCAGTTCATCTATTG 58.110 45.455 0.00 0.00 0.00 1.90
309 1484 2.260844 ATCATGTACCGCTCAATGGG 57.739 50.000 0.00 0.00 0.00 4.00
351 1526 3.240302 TCCTTCCTCGGATATTTCTCCC 58.760 50.000 0.00 0.00 31.04 4.30
391 1814 5.172591 GCATCATTTTGTCAATCGTATGCAG 59.827 40.000 14.02 0.00 37.67 4.41
392 1815 6.488817 CATCATTTTGTCAATCGTATGCAGA 58.511 36.000 0.00 0.00 0.00 4.26
393 1816 6.682423 TCATTTTGTCAATCGTATGCAGAT 57.318 33.333 0.00 0.00 0.00 2.90
394 1817 6.718388 TCATTTTGTCAATCGTATGCAGATC 58.282 36.000 0.00 0.00 0.00 2.75
395 1818 6.315891 TCATTTTGTCAATCGTATGCAGATCA 59.684 34.615 0.00 0.00 0.00 2.92
400 1948 4.805719 GTCAATCGTATGCAGATCACTGAA 59.194 41.667 0.00 0.00 46.03 3.02
401 1949 4.805719 TCAATCGTATGCAGATCACTGAAC 59.194 41.667 0.00 0.00 46.03 3.18
466 2014 1.917955 TGAGATAAAAGAGAACGCGCG 59.082 47.619 30.96 30.96 0.00 6.86
467 2015 1.918609 GAGATAAAAGAGAACGCGCGT 59.081 47.619 32.73 32.73 0.00 6.01
468 2016 1.654105 AGATAAAAGAGAACGCGCGTG 59.346 47.619 38.44 19.78 0.00 5.34
469 2017 1.389106 GATAAAAGAGAACGCGCGTGT 59.611 47.619 38.44 27.07 0.00 4.49
470 2018 1.210870 TAAAAGAGAACGCGCGTGTT 58.789 45.000 38.44 35.63 34.02 3.32
471 2019 0.375803 AAAAGAGAACGCGCGTGTTT 59.624 45.000 38.44 27.40 30.75 2.83
472 2020 0.315869 AAAGAGAACGCGCGTGTTTG 60.316 50.000 38.44 6.11 30.75 2.93
473 2021 2.695712 AAGAGAACGCGCGTGTTTGC 62.696 55.000 38.44 28.22 30.75 3.68
474 2022 3.223435 GAGAACGCGCGTGTTTGCT 62.223 57.895 38.44 28.35 30.75 3.91
475 2023 2.351888 GAACGCGCGTGTTTGCTT 60.352 55.556 38.44 19.69 30.75 3.91
476 2024 2.347168 GAACGCGCGTGTTTGCTTC 61.347 57.895 38.44 24.04 30.75 3.86
477 2025 2.695712 GAACGCGCGTGTTTGCTTCT 62.696 55.000 38.44 17.94 30.75 2.85
478 2026 1.492319 AACGCGCGTGTTTGCTTCTA 61.492 50.000 38.44 0.00 0.00 2.10
479 2027 1.225475 CGCGCGTGTTTGCTTCTAG 60.225 57.895 24.19 0.00 0.00 2.43
480 2028 1.860078 GCGCGTGTTTGCTTCTAGT 59.140 52.632 8.43 0.00 0.00 2.57
481 2029 0.179248 GCGCGTGTTTGCTTCTAGTC 60.179 55.000 8.43 0.00 0.00 2.59
482 2030 1.136690 CGCGTGTTTGCTTCTAGTCA 58.863 50.000 0.00 0.00 0.00 3.41
483 2031 1.136611 CGCGTGTTTGCTTCTAGTCAC 60.137 52.381 0.00 0.00 0.00 3.67
484 2032 1.194772 GCGTGTTTGCTTCTAGTCACC 59.805 52.381 0.00 0.00 0.00 4.02
485 2033 2.755650 CGTGTTTGCTTCTAGTCACCT 58.244 47.619 0.00 0.00 0.00 4.00
486 2034 3.131396 CGTGTTTGCTTCTAGTCACCTT 58.869 45.455 0.00 0.00 0.00 3.50
487 2035 3.184581 CGTGTTTGCTTCTAGTCACCTTC 59.815 47.826 0.00 0.00 0.00 3.46
488 2036 4.381411 GTGTTTGCTTCTAGTCACCTTCT 58.619 43.478 0.00 0.00 0.00 2.85
489 2037 5.539048 GTGTTTGCTTCTAGTCACCTTCTA 58.461 41.667 0.00 0.00 0.00 2.10
490 2038 6.166982 GTGTTTGCTTCTAGTCACCTTCTAT 58.833 40.000 0.00 0.00 0.00 1.98
491 2039 7.321153 GTGTTTGCTTCTAGTCACCTTCTATA 58.679 38.462 0.00 0.00 0.00 1.31
492 2040 7.275999 GTGTTTGCTTCTAGTCACCTTCTATAC 59.724 40.741 0.00 0.00 0.00 1.47
493 2041 6.466885 TTGCTTCTAGTCACCTTCTATACC 57.533 41.667 0.00 0.00 0.00 2.73
494 2042 4.894114 TGCTTCTAGTCACCTTCTATACCC 59.106 45.833 0.00 0.00 0.00 3.69
495 2043 5.141910 GCTTCTAGTCACCTTCTATACCCT 58.858 45.833 0.00 0.00 0.00 4.34
496 2044 6.126273 TGCTTCTAGTCACCTTCTATACCCTA 60.126 42.308 0.00 0.00 0.00 3.53
497 2045 6.431852 GCTTCTAGTCACCTTCTATACCCTAG 59.568 46.154 0.00 0.00 0.00 3.02
498 2046 7.463054 TTCTAGTCACCTTCTATACCCTAGT 57.537 40.000 0.00 0.00 0.00 2.57
499 2047 6.839454 TCTAGTCACCTTCTATACCCTAGTG 58.161 44.000 0.00 0.00 0.00 2.74
500 2048 5.469210 AGTCACCTTCTATACCCTAGTGT 57.531 43.478 0.00 0.00 0.00 3.55
501 2049 5.840081 AGTCACCTTCTATACCCTAGTGTT 58.160 41.667 0.00 0.00 0.00 3.32
502 2050 6.262207 AGTCACCTTCTATACCCTAGTGTTT 58.738 40.000 0.00 0.00 0.00 2.83
503 2051 6.729569 AGTCACCTTCTATACCCTAGTGTTTT 59.270 38.462 0.00 0.00 0.00 2.43
504 2052 6.817140 GTCACCTTCTATACCCTAGTGTTTTG 59.183 42.308 0.00 0.00 0.00 2.44
505 2053 6.499350 TCACCTTCTATACCCTAGTGTTTTGT 59.501 38.462 0.00 0.00 0.00 2.83
506 2054 7.016858 TCACCTTCTATACCCTAGTGTTTTGTT 59.983 37.037 0.00 0.00 0.00 2.83
507 2055 7.664318 CACCTTCTATACCCTAGTGTTTTGTTT 59.336 37.037 0.00 0.00 0.00 2.83
508 2056 7.881751 ACCTTCTATACCCTAGTGTTTTGTTTC 59.118 37.037 0.00 0.00 0.00 2.78
509 2057 7.064253 CCTTCTATACCCTAGTGTTTTGTTTCG 59.936 40.741 0.00 0.00 0.00 3.46
510 2058 7.230849 TCTATACCCTAGTGTTTTGTTTCGA 57.769 36.000 0.00 0.00 0.00 3.71
511 2059 7.092716 TCTATACCCTAGTGTTTTGTTTCGAC 58.907 38.462 0.00 0.00 0.00 4.20
512 2060 2.867975 ACCCTAGTGTTTTGTTTCGACG 59.132 45.455 0.00 0.00 0.00 5.12
513 2061 2.222445 CCCTAGTGTTTTGTTTCGACGG 59.778 50.000 0.00 0.00 0.00 4.79
514 2062 2.867975 CCTAGTGTTTTGTTTCGACGGT 59.132 45.455 0.00 0.00 0.00 4.83
515 2063 2.817538 AGTGTTTTGTTTCGACGGTG 57.182 45.000 0.00 0.00 0.00 4.94
516 2064 2.078392 AGTGTTTTGTTTCGACGGTGT 58.922 42.857 0.00 0.00 0.00 4.16
517 2065 2.094734 AGTGTTTTGTTTCGACGGTGTC 59.905 45.455 0.00 0.00 0.00 3.67
518 2066 2.074576 TGTTTTGTTTCGACGGTGTCA 58.925 42.857 0.00 0.00 32.09 3.58
519 2067 2.483106 TGTTTTGTTTCGACGGTGTCAA 59.517 40.909 0.00 0.00 32.09 3.18
520 2068 3.095738 GTTTTGTTTCGACGGTGTCAAG 58.904 45.455 0.00 0.00 32.09 3.02
521 2069 2.296831 TTGTTTCGACGGTGTCAAGA 57.703 45.000 0.00 0.00 32.09 3.02
522 2070 1.847818 TGTTTCGACGGTGTCAAGAG 58.152 50.000 0.00 0.00 32.09 2.85
523 2071 1.406180 TGTTTCGACGGTGTCAAGAGA 59.594 47.619 0.00 0.00 32.09 3.10
524 2072 2.035449 TGTTTCGACGGTGTCAAGAGAT 59.965 45.455 0.00 0.00 32.09 2.75
525 2073 3.253921 TGTTTCGACGGTGTCAAGAGATA 59.746 43.478 0.00 0.00 32.09 1.98
526 2074 3.759527 TTCGACGGTGTCAAGAGATAG 57.240 47.619 0.00 0.00 32.09 2.08
527 2075 1.400846 TCGACGGTGTCAAGAGATAGC 59.599 52.381 0.00 0.00 32.09 2.97
528 2076 1.402259 CGACGGTGTCAAGAGATAGCT 59.598 52.381 0.00 0.00 32.03 3.32
529 2077 2.792890 CGACGGTGTCAAGAGATAGCTG 60.793 54.545 0.00 0.00 32.03 4.24
530 2078 2.423892 GACGGTGTCAAGAGATAGCTGA 59.576 50.000 0.00 0.00 32.03 4.26
531 2079 2.164624 ACGGTGTCAAGAGATAGCTGAC 59.835 50.000 0.00 0.00 32.03 3.51
532 2080 2.164422 CGGTGTCAAGAGATAGCTGACA 59.836 50.000 0.00 0.00 37.20 3.58
534 2082 3.876274 TGTCAAGAGATAGCTGACACC 57.124 47.619 0.00 0.00 35.00 4.16
535 2083 3.165071 TGTCAAGAGATAGCTGACACCA 58.835 45.455 0.00 0.00 35.00 4.17
536 2084 3.578282 TGTCAAGAGATAGCTGACACCAA 59.422 43.478 0.00 0.00 35.00 3.67
537 2085 4.180057 GTCAAGAGATAGCTGACACCAAG 58.820 47.826 0.00 0.00 0.00 3.61
538 2086 4.081972 GTCAAGAGATAGCTGACACCAAGA 60.082 45.833 0.00 0.00 0.00 3.02
539 2087 4.528206 TCAAGAGATAGCTGACACCAAGAA 59.472 41.667 0.00 0.00 0.00 2.52
540 2088 5.012046 TCAAGAGATAGCTGACACCAAGAAA 59.988 40.000 0.00 0.00 0.00 2.52
541 2089 5.690464 AGAGATAGCTGACACCAAGAAAT 57.310 39.130 0.00 0.00 0.00 2.17
542 2090 5.426504 AGAGATAGCTGACACCAAGAAATG 58.573 41.667 0.00 0.00 0.00 2.32
543 2091 3.944015 AGATAGCTGACACCAAGAAATGC 59.056 43.478 0.00 0.00 0.00 3.56
544 2092 1.985473 AGCTGACACCAAGAAATGCA 58.015 45.000 0.00 0.00 0.00 3.96
545 2093 2.309613 AGCTGACACCAAGAAATGCAA 58.690 42.857 0.00 0.00 0.00 4.08
546 2094 2.694628 AGCTGACACCAAGAAATGCAAA 59.305 40.909 0.00 0.00 0.00 3.68
547 2095 3.322828 AGCTGACACCAAGAAATGCAAAT 59.677 39.130 0.00 0.00 0.00 2.32
548 2096 4.060205 GCTGACACCAAGAAATGCAAATT 58.940 39.130 0.00 0.00 0.00 1.82
549 2097 4.084223 GCTGACACCAAGAAATGCAAATTG 60.084 41.667 0.00 0.00 0.00 2.32
550 2098 5.021033 TGACACCAAGAAATGCAAATTGT 57.979 34.783 0.00 0.00 0.00 2.71
551 2099 5.049167 TGACACCAAGAAATGCAAATTGTC 58.951 37.500 0.00 0.00 33.09 3.18
552 2100 5.163426 TGACACCAAGAAATGCAAATTGTCT 60.163 36.000 0.00 0.00 33.54 3.41
553 2101 5.051816 ACACCAAGAAATGCAAATTGTCTG 58.948 37.500 0.00 0.00 0.00 3.51
554 2102 5.163426 ACACCAAGAAATGCAAATTGTCTGA 60.163 36.000 0.00 0.00 0.00 3.27
555 2103 5.754406 CACCAAGAAATGCAAATTGTCTGAA 59.246 36.000 0.00 0.00 0.00 3.02
556 2104 6.258287 CACCAAGAAATGCAAATTGTCTGAAA 59.742 34.615 0.00 0.00 0.00 2.69
557 2105 6.993902 ACCAAGAAATGCAAATTGTCTGAAAT 59.006 30.769 0.00 0.00 0.00 2.17
558 2106 7.499895 ACCAAGAAATGCAAATTGTCTGAAATT 59.500 29.630 0.00 0.00 0.00 1.82
559 2107 8.347035 CCAAGAAATGCAAATTGTCTGAAATTT 58.653 29.630 0.00 0.00 39.71 1.82
560 2108 9.724839 CAAGAAATGCAAATTGTCTGAAATTTT 57.275 25.926 0.00 0.00 37.59 1.82
630 2178 5.756195 TTTGATTCCTGCATTAATCGGAG 57.244 39.130 13.49 0.00 35.32 4.63
766 2317 0.040157 TCGCAACTTGCAAGCATGAC 60.040 50.000 27.79 19.66 45.36 3.06
820 2371 0.179018 ACCACCTCACAAGCCAGAAC 60.179 55.000 0.00 0.00 0.00 3.01
842 2396 4.283722 ACCGTATTCTGTATCCATCTTCCC 59.716 45.833 0.00 0.00 0.00 3.97
900 2454 1.837439 TCCACCATCACCCTACATGAC 59.163 52.381 0.00 0.00 0.00 3.06
931 2485 0.536724 TCACATCACATCCTCGTGGG 59.463 55.000 3.23 0.00 37.50 4.61
958 2512 4.007644 CCTCTGTCGGCAGGCACA 62.008 66.667 18.55 0.00 42.78 4.57
1158 2715 0.456221 GCTTCCTCCACGAGATCGAA 59.544 55.000 9.58 0.00 43.02 3.71
1440 2997 1.589993 CCTGAACGCGCTCATCGAT 60.590 57.895 13.30 0.00 41.67 3.59
1837 3400 1.380302 GGCGGCTGGGATAATGGAT 59.620 57.895 0.00 0.00 0.00 3.41
1840 3403 1.677217 GCGGCTGGGATAATGGATCTC 60.677 57.143 0.00 0.00 35.32 2.75
1844 3407 1.625315 CTGGGATAATGGATCTCGGCA 59.375 52.381 0.00 0.00 37.96 5.69
1932 3495 1.154836 GTTTGTTCTCGTCGCTGCG 60.155 57.895 17.25 17.25 0.00 5.18
2002 3565 4.002982 ACTGTCACGTGTGCATATCATTT 58.997 39.130 16.51 0.00 0.00 2.32
2007 3570 5.840781 GTCACGTGTGCATATCATTTATTCG 59.159 40.000 16.51 0.00 0.00 3.34
2022 3585 7.375053 TCATTTATTCGGAAAAGAAAACCCAG 58.625 34.615 0.00 0.00 33.43 4.45
2029 3592 4.439057 GGAAAAGAAAACCCAGGTTTCAC 58.561 43.478 14.95 11.94 46.22 3.18
2035 3598 1.381165 AACCCAGGTTTCACGTGCAC 61.381 55.000 11.67 6.82 34.22 4.57
2038 3601 1.355210 CAGGTTTCACGTGCACCAC 59.645 57.895 28.42 15.33 32.43 4.16
2141 3733 5.317808 TCATTATTCGGAACAGAAAACCCA 58.682 37.500 0.00 0.00 33.43 4.51
2144 3736 1.975660 TCGGAACAGAAAACCCAAGG 58.024 50.000 0.00 0.00 0.00 3.61
2170 3762 2.732412 AGTAATCCATCTCCGATGCG 57.268 50.000 0.00 0.00 0.00 4.73
2174 3766 1.466851 ATCCATCTCCGATGCGAGCA 61.467 55.000 0.00 0.00 0.00 4.26
2180 3772 1.202973 CTCCGATGCGAGCACTTACG 61.203 60.000 0.00 4.59 0.00 3.18
2181 4869 2.230940 CCGATGCGAGCACTTACGG 61.231 63.158 15.57 15.57 0.00 4.02
2182 4870 2.230940 CGATGCGAGCACTTACGGG 61.231 63.158 0.00 0.00 0.00 5.28
2186 4874 2.264794 CGAGCACTTACGGGCCTT 59.735 61.111 0.84 0.00 0.00 4.35
2201 4889 1.333791 GGCCTTAAATCGCACGCATAC 60.334 52.381 0.00 0.00 0.00 2.39
2260 4948 5.420725 ACTAGGTCATGTATTTGTCTGCA 57.579 39.130 0.00 0.00 0.00 4.41
2302 4992 4.571372 TTTTCGCAAACCGGAAGTAAAT 57.429 36.364 9.46 0.00 35.49 1.40
2396 5092 2.554344 GGAGCCCACATTTTGACTGGTA 60.554 50.000 0.00 0.00 0.00 3.25
2520 5216 1.444119 GACCCGCACAAAGAGTTGCA 61.444 55.000 0.00 0.00 38.39 4.08
2521 5217 1.008538 CCCGCACAAAGAGTTGCAC 60.009 57.895 0.00 0.00 38.39 4.57
2639 5344 1.266989 CAAAAAGAAGGGTGACGGAGC 59.733 52.381 0.00 0.00 0.00 4.70
2763 5474 0.244994 CTTCTACGCCACTGAGCAGT 59.755 55.000 0.00 0.00 43.61 4.40
2774 5485 1.153066 TGAGCAGTTTGGGCGACAA 60.153 52.632 0.00 0.00 37.28 3.18
2822 5534 4.436852 GGGTAGTGCAATATTGTGTCAACG 60.437 45.833 16.61 0.00 0.00 4.10
2823 5535 3.201726 AGTGCAATATTGTGTCAACGC 57.798 42.857 16.61 5.76 0.00 4.84
2826 5538 2.095314 TGCAATATTGTGTCAACGCCAG 60.095 45.455 16.61 0.00 0.00 4.85
2846 5558 4.413928 TGGACCCGCTCCATTTTG 57.586 55.556 0.00 0.00 44.99 2.44
2958 5673 2.126463 CGAGCCGTCGTGTGACAT 60.126 61.111 0.00 0.00 45.80 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 8.214721 AGTTCAAAAGGAGTTCTGTAAAGAAG 57.785 34.615 0.00 0.00 0.00 2.85
50 51 9.730420 CGATTTAAAAAGAAGAGTTCAAAAGGA 57.270 29.630 0.00 0.00 0.00 3.36
71 72 2.505819 AGCATACTTCCCAGTCCGATTT 59.494 45.455 0.00 0.00 34.06 2.17
159 163 3.123804 GTCTCGTTGACACTTGTGTCAT 58.876 45.455 29.44 0.08 46.61 3.06
235 239 7.961326 AGGGGATCAATAATACATATTTGCC 57.039 36.000 0.00 0.00 31.69 4.52
238 242 8.954834 TGCAAGGGGATCAATAATACATATTT 57.045 30.769 0.00 0.00 31.69 1.40
248 252 4.166725 AGATGAACTGCAAGGGGATCAATA 59.833 41.667 0.00 0.00 39.30 1.90
286 290 4.761739 CCCATTGAGCGGTACATGATTTAT 59.238 41.667 0.00 0.00 0.00 1.40
309 1484 8.451908 AAGGAGCACAATAGTTTATATTCCAC 57.548 34.615 0.00 0.00 0.00 4.02
377 1800 4.363138 TCAGTGATCTGCATACGATTGAC 58.637 43.478 0.00 0.00 41.10 3.18
384 1807 6.045318 ACTGTATGTTCAGTGATCTGCATAC 58.955 40.000 19.58 19.58 45.40 2.39
400 1948 2.658285 CATGGGCCATGAACTGTATGT 58.342 47.619 37.69 0.54 43.81 2.29
401 1949 1.958579 CCATGGGCCATGAACTGTATG 59.041 52.381 41.10 21.59 43.81 2.39
412 1960 0.409092 AACTGAATCACCATGGGCCA 59.591 50.000 18.09 9.61 0.00 5.36
451 1999 1.210870 AACACGCGCGTTCTCTTTTA 58.789 45.000 35.90 0.00 0.00 1.52
461 2009 1.225475 CTAGAAGCAAACACGCGCG 60.225 57.895 30.96 30.96 36.85 6.86
466 2014 4.381411 AGAAGGTGACTAGAAGCAAACAC 58.619 43.478 0.00 0.00 42.68 3.32
467 2015 4.689612 AGAAGGTGACTAGAAGCAAACA 57.310 40.909 0.00 0.00 42.68 2.83
468 2016 6.757478 GGTATAGAAGGTGACTAGAAGCAAAC 59.243 42.308 0.00 0.00 42.68 2.93
469 2017 6.127140 GGGTATAGAAGGTGACTAGAAGCAAA 60.127 42.308 0.00 0.00 42.68 3.68
470 2018 5.363005 GGGTATAGAAGGTGACTAGAAGCAA 59.637 44.000 0.00 0.00 42.68 3.91
471 2019 4.894114 GGGTATAGAAGGTGACTAGAAGCA 59.106 45.833 0.00 0.00 42.68 3.91
472 2020 5.141910 AGGGTATAGAAGGTGACTAGAAGC 58.858 45.833 0.00 0.00 42.68 3.86
473 2021 7.446013 CACTAGGGTATAGAAGGTGACTAGAAG 59.554 44.444 0.00 0.00 42.68 2.85
474 2022 7.092083 ACACTAGGGTATAGAAGGTGACTAGAA 60.092 40.741 0.00 0.00 42.68 2.10
475 2023 6.389278 ACACTAGGGTATAGAAGGTGACTAGA 59.611 42.308 0.00 0.00 42.68 2.43
476 2024 6.603224 ACACTAGGGTATAGAAGGTGACTAG 58.397 44.000 0.00 0.00 42.68 2.57
477 2025 6.587560 ACACTAGGGTATAGAAGGTGACTA 57.412 41.667 0.00 0.00 42.68 2.59
479 2027 6.541934 AAACACTAGGGTATAGAAGGTGAC 57.458 41.667 0.00 0.00 0.00 3.67
480 2028 6.499350 ACAAAACACTAGGGTATAGAAGGTGA 59.501 38.462 0.00 0.00 0.00 4.02
481 2029 6.708285 ACAAAACACTAGGGTATAGAAGGTG 58.292 40.000 0.00 0.00 0.00 4.00
482 2030 6.947376 ACAAAACACTAGGGTATAGAAGGT 57.053 37.500 0.00 0.00 0.00 3.50
483 2031 7.064253 CGAAACAAAACACTAGGGTATAGAAGG 59.936 40.741 0.00 0.00 0.00 3.46
484 2032 7.816031 TCGAAACAAAACACTAGGGTATAGAAG 59.184 37.037 0.00 0.00 0.00 2.85
485 2033 7.599998 GTCGAAACAAAACACTAGGGTATAGAA 59.400 37.037 0.00 0.00 0.00 2.10
486 2034 7.092716 GTCGAAACAAAACACTAGGGTATAGA 58.907 38.462 0.00 0.00 0.00 1.98
487 2035 6.034256 CGTCGAAACAAAACACTAGGGTATAG 59.966 42.308 0.00 0.00 0.00 1.31
488 2036 5.863397 CGTCGAAACAAAACACTAGGGTATA 59.137 40.000 0.00 0.00 0.00 1.47
489 2037 4.687483 CGTCGAAACAAAACACTAGGGTAT 59.313 41.667 0.00 0.00 0.00 2.73
490 2038 4.050553 CGTCGAAACAAAACACTAGGGTA 58.949 43.478 0.00 0.00 0.00 3.69
491 2039 2.867975 CGTCGAAACAAAACACTAGGGT 59.132 45.455 0.00 0.00 0.00 4.34
492 2040 2.222445 CCGTCGAAACAAAACACTAGGG 59.778 50.000 0.00 0.00 0.00 3.53
493 2041 2.867975 ACCGTCGAAACAAAACACTAGG 59.132 45.455 0.00 0.00 0.00 3.02
494 2042 3.307782 ACACCGTCGAAACAAAACACTAG 59.692 43.478 0.00 0.00 0.00 2.57
495 2043 3.260740 ACACCGTCGAAACAAAACACTA 58.739 40.909 0.00 0.00 0.00 2.74
496 2044 2.078392 ACACCGTCGAAACAAAACACT 58.922 42.857 0.00 0.00 0.00 3.55
497 2045 2.159680 TGACACCGTCGAAACAAAACAC 60.160 45.455 0.00 0.00 34.95 3.32
498 2046 2.074576 TGACACCGTCGAAACAAAACA 58.925 42.857 0.00 0.00 34.95 2.83
499 2047 2.810028 TGACACCGTCGAAACAAAAC 57.190 45.000 0.00 0.00 34.95 2.43
500 2048 3.001414 TCTTGACACCGTCGAAACAAAA 58.999 40.909 0.00 0.00 34.95 2.44
501 2049 2.605818 CTCTTGACACCGTCGAAACAAA 59.394 45.455 0.00 0.00 34.95 2.83
502 2050 2.159212 TCTCTTGACACCGTCGAAACAA 60.159 45.455 0.00 0.00 34.95 2.83
503 2051 1.406180 TCTCTTGACACCGTCGAAACA 59.594 47.619 0.00 0.00 34.95 2.83
504 2052 2.129823 TCTCTTGACACCGTCGAAAC 57.870 50.000 0.00 0.00 34.95 2.78
505 2053 3.672511 GCTATCTCTTGACACCGTCGAAA 60.673 47.826 0.00 0.00 34.95 3.46
506 2054 2.159421 GCTATCTCTTGACACCGTCGAA 60.159 50.000 0.00 0.00 34.95 3.71
507 2055 1.400846 GCTATCTCTTGACACCGTCGA 59.599 52.381 0.00 0.00 34.95 4.20
508 2056 1.402259 AGCTATCTCTTGACACCGTCG 59.598 52.381 0.00 0.00 34.95 5.12
509 2057 2.423892 TCAGCTATCTCTTGACACCGTC 59.576 50.000 0.00 0.00 0.00 4.79
510 2058 2.164624 GTCAGCTATCTCTTGACACCGT 59.835 50.000 0.00 0.00 0.00 4.83
511 2059 2.164422 TGTCAGCTATCTCTTGACACCG 59.836 50.000 2.68 0.00 35.00 4.94
512 2060 3.876274 TGTCAGCTATCTCTTGACACC 57.124 47.619 2.68 0.00 35.00 4.16
514 2062 3.165071 TGGTGTCAGCTATCTCTTGACA 58.835 45.455 3.30 2.68 37.20 3.58
515 2063 3.876274 TGGTGTCAGCTATCTCTTGAC 57.124 47.619 3.30 0.00 0.00 3.18
516 2064 4.089361 TCTTGGTGTCAGCTATCTCTTGA 58.911 43.478 3.30 0.00 0.00 3.02
517 2065 4.462508 TCTTGGTGTCAGCTATCTCTTG 57.537 45.455 3.30 0.00 0.00 3.02
518 2066 5.489792 TTTCTTGGTGTCAGCTATCTCTT 57.510 39.130 3.30 0.00 0.00 2.85
519 2067 5.426504 CATTTCTTGGTGTCAGCTATCTCT 58.573 41.667 3.30 0.00 0.00 3.10
520 2068 4.034975 GCATTTCTTGGTGTCAGCTATCTC 59.965 45.833 3.30 0.00 0.00 2.75
521 2069 3.944015 GCATTTCTTGGTGTCAGCTATCT 59.056 43.478 3.30 0.00 0.00 1.98
522 2070 3.691118 TGCATTTCTTGGTGTCAGCTATC 59.309 43.478 3.30 0.00 0.00 2.08
523 2071 3.689347 TGCATTTCTTGGTGTCAGCTAT 58.311 40.909 3.30 0.00 0.00 2.97
524 2072 3.138884 TGCATTTCTTGGTGTCAGCTA 57.861 42.857 3.30 0.00 0.00 3.32
525 2073 1.985473 TGCATTTCTTGGTGTCAGCT 58.015 45.000 3.30 0.00 0.00 4.24
526 2074 2.798976 TTGCATTTCTTGGTGTCAGC 57.201 45.000 0.00 0.00 0.00 4.26
527 2075 5.051816 ACAATTTGCATTTCTTGGTGTCAG 58.948 37.500 0.00 0.00 0.00 3.51
528 2076 5.021033 ACAATTTGCATTTCTTGGTGTCA 57.979 34.783 0.00 0.00 0.00 3.58
529 2077 5.176223 CAGACAATTTGCATTTCTTGGTGTC 59.824 40.000 0.00 0.00 34.46 3.67
530 2078 5.051816 CAGACAATTTGCATTTCTTGGTGT 58.948 37.500 0.00 0.00 0.00 4.16
531 2079 5.291178 TCAGACAATTTGCATTTCTTGGTG 58.709 37.500 0.00 0.00 0.00 4.17
532 2080 5.534207 TCAGACAATTTGCATTTCTTGGT 57.466 34.783 0.00 0.00 0.00 3.67
533 2081 6.847956 TTTCAGACAATTTGCATTTCTTGG 57.152 33.333 0.00 0.00 0.00 3.61
534 2082 9.724839 AAAATTTCAGACAATTTGCATTTCTTG 57.275 25.926 0.00 0.00 36.63 3.02
576 2124 9.685276 TGATATGGAGTAGTTTTGAATTCATGT 57.315 29.630 9.40 0.00 0.00 3.21
614 2162 2.708216 TTGCTCCGATTAATGCAGGA 57.292 45.000 0.00 0.00 36.75 3.86
630 2178 0.937304 TGTGCGAGAGTGTTCTTTGC 59.063 50.000 0.00 0.00 36.32 3.68
665 2214 2.226437 CAGTTGCAATCGGTAGCACTTT 59.774 45.455 0.59 0.00 41.05 2.66
766 2317 3.303791 GCACGTTTACCTTCACTTCCTTG 60.304 47.826 0.00 0.00 0.00 3.61
842 2396 2.399611 GAAGGAATGGCGTTCGCG 59.600 61.111 13.00 0.00 44.73 5.87
900 2454 1.070445 GATGTGATCGAGGCAGGGG 59.930 63.158 0.00 0.00 0.00 4.79
931 2485 3.418068 GACAGAGGCTGCGTGCAC 61.418 66.667 6.82 6.82 45.15 4.57
993 2547 1.530771 GGGCTCTGACATGGCAGAT 59.469 57.895 31.18 0.00 43.43 2.90
1440 2997 1.007734 GTCGTTCTGCGTCAGACCA 60.008 57.895 8.73 0.00 40.46 4.02
1829 3392 0.681733 ACGCTGCCGAGATCCATTAT 59.318 50.000 0.00 0.00 38.29 1.28
1932 3495 5.895928 AGAAAGGAGACAAAGAAAAAGCAC 58.104 37.500 0.00 0.00 0.00 4.40
2002 3565 4.732065 ACCTGGGTTTTCTTTTCCGAATA 58.268 39.130 0.00 0.00 0.00 1.75
2007 3570 4.439057 GTGAAACCTGGGTTTTCTTTTCC 58.561 43.478 17.37 5.35 46.80 3.13
2018 3581 2.551912 GGTGCACGTGAAACCTGGG 61.552 63.158 25.48 0.00 0.00 4.45
2035 3598 3.557577 TTTTTGTCTGATCATGCGTGG 57.442 42.857 5.98 0.00 0.00 4.94
2074 3638 6.864685 TGTTCATGAAATTGAATCACTGAAGC 59.135 34.615 10.35 0.00 37.88 3.86
2141 3733 4.413851 GGAGATGGATTACTTTCTCCCCTT 59.586 45.833 6.56 0.00 38.17 3.95
2144 3736 3.641906 TCGGAGATGGATTACTTTCTCCC 59.358 47.826 11.21 0.00 40.27 4.30
2170 3762 2.103537 TTTAAGGCCCGTAAGTGCTC 57.896 50.000 0.00 0.00 0.00 4.26
2174 3766 1.065998 TGCGATTTAAGGCCCGTAAGT 60.066 47.619 0.00 0.00 0.00 2.24
2180 3772 1.724582 ATGCGTGCGATTTAAGGCCC 61.725 55.000 0.00 0.00 0.00 5.80
2181 4869 0.941542 TATGCGTGCGATTTAAGGCC 59.058 50.000 0.00 0.00 0.00 5.19
2182 4870 1.656429 CGTATGCGTGCGATTTAAGGC 60.656 52.381 11.25 0.00 35.29 4.35
2201 4889 0.037697 TCAGACAATTGGGTCCGACG 60.038 55.000 10.83 0.00 38.59 5.12
2298 4988 2.491693 CTCCCGCAAAGCCTTTGATTTA 59.508 45.455 21.00 2.45 43.26 1.40
2302 4992 2.268076 GCTCCCGCAAAGCCTTTGA 61.268 57.895 21.00 0.00 43.26 2.69
2391 5087 0.940126 GCGGAGACAATGCATACCAG 59.060 55.000 0.00 0.00 0.00 4.00
2396 5092 0.673333 TTGACGCGGAGACAATGCAT 60.673 50.000 12.47 0.00 30.10 3.96
2520 5216 4.954118 TGGGTCCTCCACCTGCGT 62.954 66.667 0.00 0.00 45.95 5.24
2521 5217 4.087892 CTGGGTCCTCCACCTGCG 62.088 72.222 0.00 0.00 45.95 5.18
2652 5363 2.589157 CCTGGCAACTACACCCCGA 61.589 63.158 0.00 0.00 37.61 5.14
2698 5409 1.227674 TGTGGCGTGTGCATGTACA 60.228 52.632 13.02 13.02 45.35 2.90
2701 5412 2.203195 AGTGTGGCGTGTGCATGT 60.203 55.556 0.00 0.00 45.35 3.21
2763 5474 1.003118 AGACTGCTATTGTCGCCCAAA 59.997 47.619 0.00 0.00 39.24 3.28


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

AutoCloner maintained by Alex Coulton.