Multiple sequence alignment - TraesCS5B01G308600

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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 TraesCS5B01G308600 chr5B 100.000 3145 0 0 1 3145 491271567 491274711 0.000000e+00 5808.0
1 TraesCS5B01G308600 chr5B 92.391 644 49 0 1105 1748 491370163 491370806 0.000000e+00 918.0
2 TraesCS5B01G308600 chr5B 92.562 484 30 2 1139 1622 491280038 491280515 0.000000e+00 689.0
3 TraesCS5B01G308600 chr5B 88.272 162 8 5 812 973 491369888 491370038 1.930000e-42 183.0
4 TraesCS5B01G308600 chr5D 89.345 1436 93 31 762 2180 409522908 409524300 0.000000e+00 1749.0
5 TraesCS5B01G308600 chr5D 86.819 1009 108 17 2146 3136 409524304 409525305 0.000000e+00 1103.0
6 TraesCS5B01G308600 chr5D 89.314 758 59 11 988 1724 409575431 409576187 0.000000e+00 931.0
7 TraesCS5B01G308600 chr5D 85.648 648 70 14 1115 1743 409454496 409455139 0.000000e+00 660.0
8 TraesCS5B01G308600 chr5D 88.571 385 33 7 336 716 409522197 409522574 1.030000e-124 457.0
9 TraesCS5B01G308600 chr5D 88.158 76 9 0 1 76 409521873 409521948 1.200000e-14 91.6
10 TraesCS5B01G308600 chr5A 93.146 890 47 7 1000 1875 520697326 520698215 0.000000e+00 1293.0
11 TraesCS5B01G308600 chr5A 86.889 961 82 13 805 1748 520729215 520730148 0.000000e+00 1037.0
12 TraesCS5B01G308600 chr5A 89.883 682 51 9 83 759 520696429 520697097 0.000000e+00 861.0
13 TraesCS5B01G308600 chr5A 89.247 558 41 6 1078 1622 520705832 520706383 0.000000e+00 680.0
14 TraesCS5B01G308600 chr5A 86.349 630 65 15 1132 1743 520680753 520681379 0.000000e+00 667.0
15 TraesCS5B01G308600 chr5A 80.461 824 97 30 1943 2738 520698244 520699031 3.520000e-159 571.0
16 TraesCS5B01G308600 chr5A 85.938 448 32 11 2728 3145 520699241 520699687 1.720000e-122 449.0
17 TraesCS5B01G308600 chr5A 93.396 212 12 2 743 954 520697111 520697320 2.360000e-81 313.0
18 TraesCS5B01G308600 chr6B 100.000 30 0 0 661 690 528291255 528291226 4.380000e-04 56.5


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 TraesCS5B01G308600 chr5B 491271567 491274711 3144 False 5808.00 5808 100.00000 1 3145 1 chr5B.!!$F1 3144
1 TraesCS5B01G308600 chr5B 491369888 491370806 918 False 550.50 918 90.33150 812 1748 2 chr5B.!!$F3 936
2 TraesCS5B01G308600 chr5D 409575431 409576187 756 False 931.00 931 89.31400 988 1724 1 chr5D.!!$F2 736
3 TraesCS5B01G308600 chr5D 409521873 409525305 3432 False 850.15 1749 88.22325 1 3136 4 chr5D.!!$F3 3135
4 TraesCS5B01G308600 chr5D 409454496 409455139 643 False 660.00 660 85.64800 1115 1743 1 chr5D.!!$F1 628
5 TraesCS5B01G308600 chr5A 520729215 520730148 933 False 1037.00 1037 86.88900 805 1748 1 chr5A.!!$F3 943
6 TraesCS5B01G308600 chr5A 520696429 520699687 3258 False 697.40 1293 88.56480 83 3145 5 chr5A.!!$F4 3062
7 TraesCS5B01G308600 chr5A 520705832 520706383 551 False 680.00 680 89.24700 1078 1622 1 chr5A.!!$F2 544
8 TraesCS5B01G308600 chr5A 520680753 520681379 626 False 667.00 667 86.34900 1132 1743 1 chr5A.!!$F1 611

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
747 932 0.527565 ACGGGTACGACGTATGCTTT 59.472 50.0 11.46 0.0 43.6 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2684 3321 0.107017 CTGGTGGGGATTTGCTCGAT 60.107 55.0 0.0 0.0 0.0 3.59 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
53 54 6.995091 GGATGGCTTCTAACATCTTTCATACT 59.005 38.462 0.00 0.00 42.34 2.12
138 221 4.637977 TCCTTTTTGGTGCAAATTTTCCAC 59.362 37.500 9.28 9.28 33.19 4.02
147 230 3.133542 TGCAAATTTTCCACATCACCACA 59.866 39.130 0.00 0.00 0.00 4.17
154 237 2.296792 TCCACATCACCACAGTGTTTG 58.703 47.619 0.00 0.00 44.83 2.93
162 245 5.554822 TCACCACAGTGTTTGTAGTTTTC 57.445 39.130 0.00 0.00 44.83 2.29
170 253 7.330700 CACAGTGTTTGTAGTTTTCCATTTGTT 59.669 33.333 0.00 0.00 38.16 2.83
194 277 9.437045 GTTTTCAAAATTGCACTTTCCTAATTG 57.563 29.630 2.17 0.00 0.00 2.32
281 460 8.716646 ATATATAAAAGTGCCCAAAGTTTTGC 57.283 30.769 0.00 0.84 35.05 3.68
282 461 2.777832 AAAGTGCCCAAAGTTTTGCA 57.222 40.000 5.65 5.65 36.86 4.08
283 462 3.280197 AAAGTGCCCAAAGTTTTGCAT 57.720 38.095 11.57 0.00 36.86 3.96
284 463 3.280197 AAGTGCCCAAAGTTTTGCATT 57.720 38.095 11.57 6.09 36.86 3.56
285 464 3.280197 AGTGCCCAAAGTTTTGCATTT 57.720 38.095 11.57 3.14 36.86 2.32
286 465 4.414337 AGTGCCCAAAGTTTTGCATTTA 57.586 36.364 11.57 0.00 36.86 1.40
287 466 4.971939 AGTGCCCAAAGTTTTGCATTTAT 58.028 34.783 11.57 0.00 36.86 1.40
288 467 5.375773 AGTGCCCAAAGTTTTGCATTTATT 58.624 33.333 11.57 0.00 36.86 1.40
289 468 5.827267 AGTGCCCAAAGTTTTGCATTTATTT 59.173 32.000 11.57 0.00 36.86 1.40
290 469 5.914074 GTGCCCAAAGTTTTGCATTTATTTG 59.086 36.000 11.57 0.00 36.86 2.32
291 470 5.824624 TGCCCAAAGTTTTGCATTTATTTGA 59.175 32.000 13.46 0.00 36.86 2.69
292 471 6.017275 TGCCCAAAGTTTTGCATTTATTTGAG 60.017 34.615 13.46 4.96 36.86 3.02
293 472 6.372981 CCCAAAGTTTTGCATTTATTTGAGC 58.627 36.000 13.46 0.00 36.86 4.26
294 473 6.372981 CCAAAGTTTTGCATTTATTTGAGCC 58.627 36.000 13.46 0.00 36.86 4.70
295 474 6.017275 CCAAAGTTTTGCATTTATTTGAGCCA 60.017 34.615 13.46 0.00 36.86 4.75
296 475 7.308710 CCAAAGTTTTGCATTTATTTGAGCCAT 60.309 33.333 13.46 0.00 36.86 4.40
297 476 8.719648 CAAAGTTTTGCATTTATTTGAGCCATA 58.280 29.630 8.48 0.00 31.01 2.74
298 477 9.452287 AAAGTTTTGCATTTATTTGAGCCATAT 57.548 25.926 0.00 0.00 0.00 1.78
326 505 7.907841 TGGCCTTGTTAGTACTATTCATAGA 57.092 36.000 3.32 0.00 34.50 1.98
327 506 8.492415 TGGCCTTGTTAGTACTATTCATAGAT 57.508 34.615 3.32 0.00 34.50 1.98
328 507 9.596308 TGGCCTTGTTAGTACTATTCATAGATA 57.404 33.333 3.32 0.00 34.50 1.98
375 555 9.736023 GTGCTAGTTTAGAATTTCCCATTATTG 57.264 33.333 0.00 0.00 0.00 1.90
400 580 9.204337 TGACATTGAAATGAATTATTGGGATCT 57.796 29.630 9.94 0.00 39.67 2.75
407 587 5.857471 TGAATTATTGGGATCTGCTTTGG 57.143 39.130 0.00 0.00 0.00 3.28
421 601 2.960384 TGCTTTGGCATATCTTCATGGG 59.040 45.455 0.00 0.00 44.28 4.00
431 611 5.239525 GCATATCTTCATGGGGTTTGTAGTC 59.760 44.000 0.00 0.00 0.00 2.59
437 617 3.392947 TCATGGGGTTTGTAGTCTCACAA 59.607 43.478 0.00 0.00 36.65 3.33
440 620 5.570205 TGGGGTTTGTAGTCTCACAATTA 57.430 39.130 0.00 0.00 38.18 1.40
447 627 9.391006 GGTTTGTAGTCTCACAATTATATGGAA 57.609 33.333 0.00 0.00 38.18 3.53
481 664 9.912634 CCTAATATAAAATGGCTATTTGTGTGG 57.087 33.333 8.97 2.58 36.65 4.17
539 722 8.154649 TCTCAAGCTTTTAAAACTGAACTAGG 57.845 34.615 0.00 0.00 0.00 3.02
545 728 6.262496 GCTTTTAAAACTGAACTAGGTGACCT 59.738 38.462 10.00 10.00 37.71 3.85
546 729 7.443272 GCTTTTAAAACTGAACTAGGTGACCTA 59.557 37.037 11.47 11.47 34.61 3.08
547 730 9.503399 CTTTTAAAACTGAACTAGGTGACCTAT 57.497 33.333 12.49 0.00 35.36 2.57
674 859 3.793797 TCACAGAAAACTGACGTCAGA 57.206 42.857 43.55 21.09 46.59 3.27
720 905 8.992349 TCTATTGATATCTCCCAAGAACAGAAA 58.008 33.333 3.98 0.00 34.49 2.52
729 914 4.887655 TCCCAAGAACAGAAAAGAAAGGAC 59.112 41.667 0.00 0.00 0.00 3.85
747 932 0.527565 ACGGGTACGACGTATGCTTT 59.472 50.000 11.46 0.00 43.60 3.51
773 1246 1.536940 TTTTTAACCGGCAGTAGGGC 58.463 50.000 0.00 0.00 39.06 5.19
900 1373 2.059541 GACGTGAGCTTTCACTACCAC 58.940 52.381 0.00 0.00 38.40 4.16
901 1374 1.270147 ACGTGAGCTTTCACTACCACC 60.270 52.381 4.76 0.00 38.40 4.61
902 1375 1.270094 CGTGAGCTTTCACTACCACCA 60.270 52.381 4.76 0.00 38.40 4.17
903 1376 2.417719 GTGAGCTTTCACTACCACCAG 58.582 52.381 0.00 0.00 37.62 4.00
963 1437 2.032894 CCAACAAACTACACTCGCACAG 60.033 50.000 0.00 0.00 0.00 3.66
982 1456 2.192175 GGCACCCCCGGAATAGTG 59.808 66.667 0.73 5.85 0.00 2.74
983 1457 2.192175 GCACCCCCGGAATAGTGG 59.808 66.667 0.73 0.00 0.00 4.00
984 1458 2.676265 GCACCCCCGGAATAGTGGT 61.676 63.158 0.73 0.00 0.00 4.16
985 1459 1.223487 CACCCCCGGAATAGTGGTG 59.777 63.158 0.73 5.93 40.39 4.17
986 1460 1.999002 ACCCCCGGAATAGTGGTGG 60.999 63.158 0.73 0.00 0.00 4.61
989 1463 2.675242 CCCGGAATAGTGGTGGGCA 61.675 63.158 0.73 0.00 32.09 5.36
1036 1513 0.600557 ACAGAGCAGAGAACGACAGG 59.399 55.000 0.00 0.00 0.00 4.00
1082 1565 7.620880 ACAACAACCATAACTTCATCTAGCTA 58.379 34.615 0.00 0.00 0.00 3.32
1258 1797 1.566018 CCTTTCGAGACCAACGTGGC 61.566 60.000 0.00 0.00 42.67 5.01
1484 2035 4.400109 ATCGACGACGTGTGCGCT 62.400 61.111 4.58 0.00 42.83 5.92
1733 2294 3.266686 TACAGCACAGCCCCGCATT 62.267 57.895 0.00 0.00 0.00 3.56
1748 2309 0.108945 GCATTCCCAAGCTCTTGTGC 60.109 55.000 8.60 7.74 38.85 4.57
1749 2310 0.169672 CATTCCCAAGCTCTTGTGCG 59.830 55.000 8.60 0.00 38.85 5.34
1774 2335 3.352648 GGAAGTTTCCGGGAATGATTGA 58.647 45.455 10.86 0.00 37.65 2.57
1782 2343 1.958579 CGGGAATGATTGATGCCATGT 59.041 47.619 0.00 0.00 29.38 3.21
1838 2404 4.934075 TGATCGAAGAGCTCAATTGTTG 57.066 40.909 17.77 1.26 46.78 3.33
1854 2420 7.531716 TCAATTGTTGGTGTAAATATTCGACC 58.468 34.615 5.13 0.00 0.00 4.79
1875 2441 1.197721 GCGCAAAATGCTGTACTGACT 59.802 47.619 0.30 0.00 42.25 3.41
1877 2443 3.853307 GCGCAAAATGCTGTACTGACTTT 60.853 43.478 0.30 0.00 42.25 2.66
1878 2444 3.665409 CGCAAAATGCTGTACTGACTTTG 59.335 43.478 3.61 9.70 42.25 2.77
1879 2445 3.426525 GCAAAATGCTGTACTGACTTTGC 59.573 43.478 20.17 20.17 40.96 3.68
1880 2446 4.794003 GCAAAATGCTGTACTGACTTTGCT 60.794 41.667 23.71 4.11 42.28 3.91
1882 2448 2.908688 TGCTGTACTGACTTTGCTCA 57.091 45.000 3.61 0.00 0.00 4.26
1883 2449 3.407424 TGCTGTACTGACTTTGCTCAT 57.593 42.857 3.61 0.00 0.00 2.90
1884 2450 3.069289 TGCTGTACTGACTTTGCTCATG 58.931 45.455 3.61 0.00 0.00 3.07
1885 2451 3.070018 GCTGTACTGACTTTGCTCATGT 58.930 45.455 3.61 0.00 0.00 3.21
1886 2452 3.120408 GCTGTACTGACTTTGCTCATGTG 60.120 47.826 3.61 0.00 0.00 3.21
1887 2453 4.060900 CTGTACTGACTTTGCTCATGTGT 58.939 43.478 0.00 0.00 0.00 3.72
1888 2454 5.208463 TGTACTGACTTTGCTCATGTGTA 57.792 39.130 0.00 0.00 0.00 2.90
1891 2457 5.679734 ACTGACTTTGCTCATGTGTAAAG 57.320 39.130 26.53 26.53 42.55 1.85
1896 2462 6.005583 ACTTTGCTCATGTGTAAAGTCATG 57.994 37.500 27.54 12.84 45.10 3.07
1897 2463 4.424061 TTGCTCATGTGTAAAGTCATGC 57.576 40.909 0.00 0.00 40.54 4.06
1901 2467 4.670992 GCTCATGTGTAAAGTCATGCTGTG 60.671 45.833 0.00 0.00 40.54 3.66
1902 2468 3.189080 TCATGTGTAAAGTCATGCTGTGC 59.811 43.478 0.00 0.00 40.54 4.57
1911 2484 2.227388 AGTCATGCTGTGCTTACTTTGC 59.773 45.455 0.00 0.00 0.00 3.68
1914 2487 1.965935 TGCTGTGCTTACTTTGCTCA 58.034 45.000 0.00 0.00 33.71 4.26
1960 2533 2.814336 GACAAGTAGGGTTGCCTTTGAG 59.186 50.000 0.00 0.00 0.00 3.02
1970 2543 0.318441 TGCCTTTGAGTCTCCGTCTG 59.682 55.000 0.00 0.00 0.00 3.51
1971 2544 0.318762 GCCTTTGAGTCTCCGTCTGT 59.681 55.000 0.00 0.00 0.00 3.41
2017 2591 1.611491 CTGCTGCCCTTTTAAACGGAA 59.389 47.619 12.15 0.00 0.00 4.30
2058 2632 1.272769 GTCTAGGACAAAGGTGACGCT 59.727 52.381 0.00 0.00 32.09 5.07
2071 2645 1.269998 GTGACGCTGTCTCACCTTACT 59.730 52.381 9.49 0.00 33.23 2.24
2075 2649 5.875108 TGACGCTGTCTCACCTTACTTAGG 61.875 50.000 9.49 0.00 40.61 2.69
2097 2671 4.686554 GGGAATGTACAACGATGCTATCTC 59.313 45.833 0.00 0.00 0.00 2.75
2108 2682 4.236147 CGATGCTATCTCAGGATTGTCAG 58.764 47.826 0.00 0.00 35.06 3.51
2109 2683 4.022503 CGATGCTATCTCAGGATTGTCAGA 60.023 45.833 0.00 0.00 35.06 3.27
2140 2717 7.511959 AAATCTTAAGGTGAAGGACAGAAAC 57.488 36.000 1.85 0.00 0.00 2.78
2146 2756 5.319043 AGGTGAAGGACAGAAACCATAAA 57.681 39.130 0.00 0.00 33.13 1.40
2288 2908 2.634940 TGCCTCCTCTAGATTATGTGGC 59.365 50.000 13.53 13.53 38.42 5.01
2289 2909 2.634940 GCCTCCTCTAGATTATGTGGCA 59.365 50.000 14.70 0.00 37.91 4.92
2296 2933 6.558775 TCCTCTAGATTATGTGGCAGGTTATT 59.441 38.462 0.00 0.00 0.00 1.40
2309 2946 6.150474 GTGGCAGGTTATTAACTGTTGTACAT 59.850 38.462 2.69 0.00 37.07 2.29
2310 2947 7.334921 GTGGCAGGTTATTAACTGTTGTACATA 59.665 37.037 2.69 0.00 37.07 2.29
2499 3136 8.664798 GCAAATTTAACCAGAACAAACTTCTTT 58.335 29.630 0.00 0.00 0.00 2.52
2524 3161 4.008933 GGTCACCACCGCAGCTCT 62.009 66.667 0.00 0.00 31.06 4.09
2525 3162 2.646175 GGTCACCACCGCAGCTCTA 61.646 63.158 0.00 0.00 31.06 2.43
2534 3171 0.598680 CCGCAGCTCTACACCATAGC 60.599 60.000 0.00 0.00 36.48 2.97
2575 3212 0.107508 AGCCATCCATTCAGACCACG 60.108 55.000 0.00 0.00 0.00 4.94
2582 3219 0.677731 CATTCAGACCACGGGCACAT 60.678 55.000 0.00 0.00 0.00 3.21
2654 3291 0.541392 ACTAGCGATGAACATGGCCA 59.459 50.000 8.56 8.56 42.49 5.36
2676 3313 1.194781 ACGGTCATCTTCCTGGCACT 61.195 55.000 0.00 0.00 0.00 4.40
2677 3314 0.460987 CGGTCATCTTCCTGGCACTC 60.461 60.000 0.00 0.00 0.00 3.51
2678 3315 0.460987 GGTCATCTTCCTGGCACTCG 60.461 60.000 0.00 0.00 0.00 4.18
2679 3316 0.532573 GTCATCTTCCTGGCACTCGA 59.467 55.000 0.00 0.00 0.00 4.04
2681 3318 1.410517 TCATCTTCCTGGCACTCGATC 59.589 52.381 0.00 0.00 0.00 3.69
2682 3319 1.411977 CATCTTCCTGGCACTCGATCT 59.588 52.381 0.00 0.00 0.00 2.75
2683 3320 0.820226 TCTTCCTGGCACTCGATCTG 59.180 55.000 0.00 0.00 0.00 2.90
2684 3321 0.820226 CTTCCTGGCACTCGATCTGA 59.180 55.000 0.00 0.00 0.00 3.27
2685 3322 1.411977 CTTCCTGGCACTCGATCTGAT 59.588 52.381 0.00 0.00 0.00 2.90
2734 3593 0.188342 AGTTTCCACATGGGTTGCCT 59.812 50.000 0.00 0.00 38.11 4.75
2747 3606 0.610232 GTTGCCTCTGCCACCAGATT 60.610 55.000 0.00 0.00 46.44 2.40
2770 3629 2.352960 GGTGAAGAAGGCGCAATAAGAG 59.647 50.000 10.83 0.00 0.00 2.85
2780 3639 2.843701 CGCAATAAGAGGCTGGATCTT 58.156 47.619 0.00 0.00 40.13 2.40
2827 3686 2.498167 GACCATAGCACCATCCACATC 58.502 52.381 0.00 0.00 0.00 3.06
2832 3691 1.524621 GCACCATCCACATCCTCCG 60.525 63.158 0.00 0.00 0.00 4.63
2842 3724 0.108585 ACATCCTCCGCACAACAAGT 59.891 50.000 0.00 0.00 0.00 3.16
2854 3736 2.869801 CACAACAAGTAGCAACTTCCGA 59.130 45.455 0.00 0.00 44.28 4.55
2867 3749 3.771577 ACTTCCGAAGATTGTTGTCCT 57.228 42.857 15.23 0.00 0.00 3.85
2880 3762 3.391965 TGTTGTCCTGATGCAAAAATGC 58.608 40.909 0.00 0.00 0.00 3.56
2916 3798 0.667993 ATGGTGACCGCACAACTTTG 59.332 50.000 0.00 0.00 46.96 2.77
2990 3873 0.676782 GGCACGGCAAGGTATCAACT 60.677 55.000 0.00 0.00 0.00 3.16
3118 4007 5.705609 TTAGCGACTGATACATGCATAGA 57.294 39.130 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.896021 AAGCCATCCTTCTCATAATTGATG 57.104 37.500 0.00 0.00 36.82 3.07
131 214 3.011566 ACACTGTGGTGATGTGGAAAA 57.988 42.857 13.09 0.00 45.61 2.29
147 230 8.840833 AAAACAAATGGAAAACTACAAACACT 57.159 26.923 0.00 0.00 0.00 3.55
162 245 7.220491 GGAAAGTGCAATTTTGAAAACAAATGG 59.780 33.333 14.04 0.00 0.00 3.16
170 253 8.729805 ACAATTAGGAAAGTGCAATTTTGAAA 57.270 26.923 14.04 8.47 34.03 2.69
210 293 8.918961 ACATCGAAACAAAACAAATGTTAGAA 57.081 26.923 0.00 0.00 39.98 2.10
255 434 9.810545 GCAAAACTTTGGGCACTTTTATATATA 57.189 29.630 4.45 0.00 38.57 0.86
256 435 8.317679 TGCAAAACTTTGGGCACTTTTATATAT 58.682 29.630 4.45 0.00 38.57 0.86
257 436 7.671302 TGCAAAACTTTGGGCACTTTTATATA 58.329 30.769 4.45 0.00 38.57 0.86
258 437 6.529220 TGCAAAACTTTGGGCACTTTTATAT 58.471 32.000 4.45 0.00 38.57 0.86
259 438 5.918608 TGCAAAACTTTGGGCACTTTTATA 58.081 33.333 4.45 0.00 38.57 0.98
260 439 4.775236 TGCAAAACTTTGGGCACTTTTAT 58.225 34.783 4.45 0.00 38.57 1.40
261 440 4.207891 TGCAAAACTTTGGGCACTTTTA 57.792 36.364 4.45 0.00 38.57 1.52
262 441 3.064900 TGCAAAACTTTGGGCACTTTT 57.935 38.095 4.45 0.00 38.57 2.27
263 442 2.777832 TGCAAAACTTTGGGCACTTT 57.222 40.000 4.45 0.00 38.57 2.66
264 443 3.280197 AATGCAAAACTTTGGGCACTT 57.720 38.095 4.45 0.00 39.34 3.16
265 444 3.280197 AAATGCAAAACTTTGGGCACT 57.720 38.095 4.45 0.00 39.34 4.40
266 445 5.687770 AATAAATGCAAAACTTTGGGCAC 57.312 34.783 4.45 0.00 39.34 5.01
267 446 5.824624 TCAAATAAATGCAAAACTTTGGGCA 59.175 32.000 12.38 4.19 41.00 5.36
268 447 6.311055 TCAAATAAATGCAAAACTTTGGGC 57.689 33.333 12.38 0.00 38.57 5.36
269 448 6.372981 GCTCAAATAAATGCAAAACTTTGGG 58.627 36.000 12.38 10.97 38.57 4.12
270 449 6.017275 TGGCTCAAATAAATGCAAAACTTTGG 60.017 34.615 12.38 7.04 38.57 3.28
271 450 6.957150 TGGCTCAAATAAATGCAAAACTTTG 58.043 32.000 0.00 0.00 41.03 2.77
272 451 7.748691 ATGGCTCAAATAAATGCAAAACTTT 57.251 28.000 0.00 0.00 0.00 2.66
300 479 9.596308 TCTATGAATAGTACTAACAAGGCCATA 57.404 33.333 5.01 6.42 0.00 2.74
301 480 8.492415 TCTATGAATAGTACTAACAAGGCCAT 57.508 34.615 5.01 0.00 0.00 4.40
302 481 7.907841 TCTATGAATAGTACTAACAAGGCCA 57.092 36.000 5.01 0.00 0.00 5.36
324 503 9.817809 ACGAATGATTACAACACTAACATATCT 57.182 29.630 0.00 0.00 0.00 1.98
325 504 9.849607 CACGAATGATTACAACACTAACATATC 57.150 33.333 0.00 0.00 0.00 1.63
326 505 8.335356 GCACGAATGATTACAACACTAACATAT 58.665 33.333 0.00 0.00 0.00 1.78
327 506 7.547722 AGCACGAATGATTACAACACTAACATA 59.452 33.333 0.00 0.00 0.00 2.29
328 507 6.371548 AGCACGAATGATTACAACACTAACAT 59.628 34.615 0.00 0.00 0.00 2.71
329 508 5.699001 AGCACGAATGATTACAACACTAACA 59.301 36.000 0.00 0.00 0.00 2.41
330 509 6.165659 AGCACGAATGATTACAACACTAAC 57.834 37.500 0.00 0.00 0.00 2.34
331 510 7.094631 ACTAGCACGAATGATTACAACACTAA 58.905 34.615 0.00 0.00 0.00 2.24
332 511 6.627243 ACTAGCACGAATGATTACAACACTA 58.373 36.000 0.00 0.00 0.00 2.74
333 512 5.479306 ACTAGCACGAATGATTACAACACT 58.521 37.500 0.00 0.00 0.00 3.55
334 513 5.779806 ACTAGCACGAATGATTACAACAC 57.220 39.130 0.00 0.00 0.00 3.32
335 514 6.795098 AAACTAGCACGAATGATTACAACA 57.205 33.333 0.00 0.00 0.00 3.33
336 515 8.181487 TCTAAACTAGCACGAATGATTACAAC 57.819 34.615 0.00 0.00 0.00 3.32
337 516 8.766000 TTCTAAACTAGCACGAATGATTACAA 57.234 30.769 0.00 0.00 0.00 2.41
348 527 6.436843 AATGGGAAATTCTAAACTAGCACG 57.563 37.500 0.00 0.00 0.00 5.34
375 555 9.472361 CAGATCCCAATAATTCATTTCAATGTC 57.528 33.333 0.00 0.00 37.65 3.06
407 587 5.133221 ACTACAAACCCCATGAAGATATGC 58.867 41.667 0.00 0.00 0.00 3.14
421 601 8.958119 TCCATATAATTGTGAGACTACAAACC 57.042 34.615 0.00 0.00 43.13 3.27
467 647 0.398696 ACGACCCACACAAATAGCCA 59.601 50.000 0.00 0.00 0.00 4.75
481 664 3.126343 AGTCACACAAAAGAACAACGACC 59.874 43.478 0.00 0.00 0.00 4.79
565 748 2.375146 TCGAGCTGCAGTTGGTCTATA 58.625 47.619 16.64 0.00 0.00 1.31
625 809 2.166459 TCATCTTTACGCAGTAGCAGCT 59.834 45.455 0.00 0.00 46.93 4.24
720 905 0.242017 CGTCGTACCCGTCCTTTCTT 59.758 55.000 0.00 0.00 35.01 2.52
729 914 0.918619 CAAAGCATACGTCGTACCCG 59.081 55.000 7.36 0.69 0.00 5.28
773 1246 4.853924 ATAGGTATTACGTTGTACCCGG 57.146 45.455 19.57 0.00 41.01 5.73
900 1373 9.482627 GTAAAGTTCATGAATCCTATCTACTGG 57.517 37.037 12.12 0.00 0.00 4.00
901 1374 9.482627 GGTAAAGTTCATGAATCCTATCTACTG 57.517 37.037 12.12 0.00 0.00 2.74
902 1375 8.652290 GGGTAAAGTTCATGAATCCTATCTACT 58.348 37.037 12.12 0.00 0.00 2.57
903 1376 8.429641 TGGGTAAAGTTCATGAATCCTATCTAC 58.570 37.037 12.12 7.58 0.00 2.59
963 1437 4.929707 CTATTCCGGGGGTGCCGC 62.930 72.222 0.00 0.00 0.00 6.53
966 1440 2.192175 CCACTATTCCGGGGGTGC 59.808 66.667 0.00 0.00 0.00 5.01
968 1442 1.999002 CCACCACTATTCCGGGGGT 60.999 63.158 0.00 0.00 41.40 4.95
969 1443 2.752807 CCCACCACTATTCCGGGGG 61.753 68.421 0.00 0.00 46.45 5.40
971 1445 2.192175 GCCCACCACTATTCCGGG 59.808 66.667 0.00 0.00 40.11 5.73
974 1448 1.032114 GCTGTGCCCACCACTATTCC 61.032 60.000 0.00 0.00 44.92 3.01
975 1449 1.369091 CGCTGTGCCCACCACTATTC 61.369 60.000 0.00 0.00 44.92 1.75
976 1450 1.377202 CGCTGTGCCCACCACTATT 60.377 57.895 0.00 0.00 44.92 1.73
977 1451 2.268920 CGCTGTGCCCACCACTAT 59.731 61.111 0.00 0.00 44.92 2.12
978 1452 4.015406 CCGCTGTGCCCACCACTA 62.015 66.667 0.00 0.00 44.92 2.74
986 1460 2.397413 ATATAGGGTGCCGCTGTGCC 62.397 60.000 0.00 0.00 0.00 5.01
989 1463 2.764572 GGTATATATAGGGTGCCGCTGT 59.235 50.000 0.00 0.00 0.00 4.40
1036 1513 0.880278 TCGAACTGGTTGCTGTCTGC 60.880 55.000 0.00 0.00 43.25 4.26
1082 1565 1.070289 GTTCACCCGACCTCTGTTTCT 59.930 52.381 0.00 0.00 0.00 2.52
1239 1778 1.566018 GCCACGTTGGTCTCGAAAGG 61.566 60.000 6.02 0.00 40.46 3.11
1484 2035 1.954382 ACGAACTCGCTCAGGCATATA 59.046 47.619 0.00 0.00 44.43 0.86
1544 2095 4.680237 CAGCGGACGTGGAAGCCA 62.680 66.667 0.00 0.00 0.00 4.75
1633 2184 2.867855 TTCGTGTCTGCCGCCTTCT 61.868 57.895 0.00 0.00 0.00 2.85
1733 2294 1.597854 CACGCACAAGAGCTTGGGA 60.598 57.895 16.20 0.00 46.48 4.37
1735 2296 1.280746 CACACGCACAAGAGCTTGG 59.719 57.895 14.14 5.09 44.45 3.61
1765 2326 5.412640 TGACAAACATGGCATCAATCATTC 58.587 37.500 0.00 0.00 0.00 2.67
1774 2335 1.885157 CGGCTGACAAACATGGCAT 59.115 52.632 0.00 0.00 0.00 4.40
1798 2359 8.753497 TCGATCATATATACATTCCACTAGCT 57.247 34.615 0.00 0.00 0.00 3.32
1838 2404 1.071041 GCGCGGTCGAATATTTACACC 60.071 52.381 8.83 0.00 38.10 4.16
1875 2441 4.520111 AGCATGACTTTACACATGAGCAAA 59.480 37.500 0.00 0.00 44.28 3.68
1877 2443 3.437741 CAGCATGACTTTACACATGAGCA 59.562 43.478 0.00 0.00 44.28 4.26
1878 2444 3.438087 ACAGCATGACTTTACACATGAGC 59.562 43.478 0.00 0.00 44.28 4.26
1879 2445 4.670992 GCACAGCATGACTTTACACATGAG 60.671 45.833 0.00 0.00 44.28 2.90
1880 2446 3.189080 GCACAGCATGACTTTACACATGA 59.811 43.478 0.00 0.00 44.28 3.07
1882 2448 3.415212 AGCACAGCATGACTTTACACAT 58.585 40.909 0.00 0.00 39.69 3.21
1883 2449 2.849942 AGCACAGCATGACTTTACACA 58.150 42.857 0.00 0.00 39.69 3.72
1884 2450 3.904136 AAGCACAGCATGACTTTACAC 57.096 42.857 0.00 0.00 39.69 2.90
1885 2451 4.641396 AGTAAGCACAGCATGACTTTACA 58.359 39.130 0.00 0.00 39.69 2.41
1886 2452 5.613358 AAGTAAGCACAGCATGACTTTAC 57.387 39.130 0.00 0.00 39.69 2.01
1887 2453 5.562696 GCAAAGTAAGCACAGCATGACTTTA 60.563 40.000 0.00 0.00 39.69 1.85
1888 2454 4.794003 GCAAAGTAAGCACAGCATGACTTT 60.794 41.667 0.00 0.00 39.69 2.66
1891 2457 2.227388 AGCAAAGTAAGCACAGCATGAC 59.773 45.455 0.00 0.00 39.69 3.06
1892 2458 2.485426 GAGCAAAGTAAGCACAGCATGA 59.515 45.455 0.00 0.00 39.69 3.07
1893 2459 2.227149 TGAGCAAAGTAAGCACAGCATG 59.773 45.455 0.00 0.00 46.00 4.06
1894 2460 2.507484 TGAGCAAAGTAAGCACAGCAT 58.493 42.857 0.00 0.00 0.00 3.79
1896 2462 2.227388 ACATGAGCAAAGTAAGCACAGC 59.773 45.455 0.00 0.00 36.10 4.40
1897 2463 3.251729 ACACATGAGCAAAGTAAGCACAG 59.748 43.478 0.00 0.00 36.10 3.66
1901 2467 2.162408 GGGACACATGAGCAAAGTAAGC 59.838 50.000 0.00 0.00 0.00 3.09
1902 2468 3.411446 TGGGACACATGAGCAAAGTAAG 58.589 45.455 0.00 0.00 0.00 2.34
1960 2533 0.108615 CCCATGACACAGACGGAGAC 60.109 60.000 0.00 0.00 0.00 3.36
1970 2543 1.734707 CGGTCGTTAGTCCCATGACAC 60.735 57.143 0.00 0.00 44.33 3.67
1971 2544 0.528924 CGGTCGTTAGTCCCATGACA 59.471 55.000 0.00 0.00 44.33 3.58
2003 2576 8.878769 CAATTTATGGAATTCCGTTTAAAAGGG 58.121 33.333 24.06 10.81 35.79 3.95
2042 2616 0.249911 GACAGCGTCACCTTTGTCCT 60.250 55.000 4.20 0.00 35.15 3.85
2047 2621 3.290776 GTGAGACAGCGTCACCTTT 57.709 52.632 10.52 0.00 38.75 3.11
2058 2632 5.091552 ACATTCCCTAAGTAAGGTGAGACA 58.908 41.667 0.00 0.00 44.90 3.41
2071 2645 4.481368 AGCATCGTTGTACATTCCCTAA 57.519 40.909 0.00 0.00 0.00 2.69
2075 2649 5.289595 TGAGATAGCATCGTTGTACATTCC 58.710 41.667 0.00 0.00 0.00 3.01
2086 2660 4.022503 TCTGACAATCCTGAGATAGCATCG 60.023 45.833 0.00 0.00 30.42 3.84
2108 2682 9.713713 GTCCTTCACCTTAAGATTTATCCTATC 57.286 37.037 3.36 0.00 0.00 2.08
2109 2683 9.225682 TGTCCTTCACCTTAAGATTTATCCTAT 57.774 33.333 3.36 0.00 0.00 2.57
2228 2840 8.097038 TGTACAATTCCATAGCATTATCTCTCC 58.903 37.037 0.00 0.00 0.00 3.71
2264 2884 5.046304 GCCACATAATCTAGAGGAGGCAATA 60.046 44.000 15.19 0.00 39.35 1.90
2310 2947 9.592196 AAACATTGCTATGATGAATAAGGGTAT 57.408 29.630 15.23 0.00 35.65 2.73
2332 2969 5.855740 AACCCCGACAAGAAATAAAAACA 57.144 34.783 0.00 0.00 0.00 2.83
2345 2982 1.152922 GTCACCCAAAACCCCGACA 60.153 57.895 0.00 0.00 0.00 4.35
2389 3026 4.831107 ACAATTGCAAAGTTTCTGGTGTT 58.169 34.783 1.71 0.00 0.00 3.32
2524 3161 1.341913 ATGGTGCCGGCTATGGTGTA 61.342 55.000 29.70 0.07 0.00 2.90
2525 3162 2.210144 AATGGTGCCGGCTATGGTGT 62.210 55.000 29.70 3.74 0.00 4.16
2551 3188 2.295885 GTCTGAATGGATGGCTTCAGG 58.704 52.381 11.95 0.00 45.41 3.86
2590 3227 0.173708 GAGTCGTCTGGCCGAATCTT 59.826 55.000 0.00 0.00 45.48 2.40
2601 3238 1.228894 TTGCCTCCAGGAGTCGTCT 60.229 57.895 15.86 0.00 37.39 4.18
2649 3286 0.605319 GAAGATGACCGTTGTGGCCA 60.605 55.000 0.00 0.00 43.94 5.36
2654 3291 0.321653 GCCAGGAAGATGACCGTTGT 60.322 55.000 0.00 0.00 0.00 3.32
2678 3315 2.224378 TGGGGATTTGCTCGATCAGATC 60.224 50.000 10.44 10.44 0.00 2.75
2679 3316 1.770658 TGGGGATTTGCTCGATCAGAT 59.229 47.619 0.00 0.00 0.00 2.90
2681 3318 1.303309 GTGGGGATTTGCTCGATCAG 58.697 55.000 0.00 0.00 0.00 2.90
2682 3319 0.107214 GGTGGGGATTTGCTCGATCA 60.107 55.000 0.00 0.00 0.00 2.92
2683 3320 0.107214 TGGTGGGGATTTGCTCGATC 60.107 55.000 0.00 0.00 0.00 3.69
2684 3321 0.107017 CTGGTGGGGATTTGCTCGAT 60.107 55.000 0.00 0.00 0.00 3.59
2685 3322 1.198094 TCTGGTGGGGATTTGCTCGA 61.198 55.000 0.00 0.00 0.00 4.04
2747 3606 2.192664 TATTGCGCCTTCTTCACCAA 57.807 45.000 4.18 0.00 0.00 3.67
2770 3629 3.207669 CGCCAGCAAGATCCAGCC 61.208 66.667 3.57 0.00 0.00 4.85
2795 3654 3.040477 TGCTATGGTCCACTGATGATGA 58.960 45.455 0.00 0.00 0.00 2.92
2827 3686 0.602638 TGCTACTTGTTGTGCGGAGG 60.603 55.000 0.00 0.00 0.00 4.30
2832 3691 2.602217 CGGAAGTTGCTACTTGTTGTGC 60.602 50.000 18.34 2.71 44.51 4.57
2842 3724 4.385825 ACAACAATCTTCGGAAGTTGCTA 58.614 39.130 21.91 5.97 42.47 3.49
2854 3736 5.534207 TTTTGCATCAGGACAACAATCTT 57.466 34.783 0.00 0.00 0.00 2.40
2867 3749 1.079266 GCGGGGCATTTTTGCATCA 60.079 52.632 0.00 0.00 36.33 3.07
2897 3779 0.667993 CAAAGTTGTGCGGTCACCAT 59.332 50.000 0.00 0.00 42.46 3.55
2930 3812 1.987855 CCCTCCTCGCCACCTACAA 60.988 63.158 0.00 0.00 0.00 2.41
2931 3813 2.363795 CCCTCCTCGCCACCTACA 60.364 66.667 0.00 0.00 0.00 2.74
2933 3815 2.711899 ATCCCCTCCTCGCCACCTA 61.712 63.158 0.00 0.00 0.00 3.08
3018 3901 9.046296 CCAGCAAATATCTTTCTCTAAACGTAT 57.954 33.333 0.00 0.00 0.00 3.06
3118 4007 4.558697 GCGATTTAGAGCAGGGTTGTTTTT 60.559 41.667 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.