Multiple sequence alignment - TraesCS7D01G140000

Loading Multiple Alignment...

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 TraesCS7D01G140000 chr7D 100.000 3047 0 0 1 3047 89521303 89524349 0.000000e+00 5627.0
1 TraesCS7D01G140000 chr7D 93.201 1515 87 13 579 2085 89791828 89790322 0.000000e+00 2213.0
2 TraesCS7D01G140000 chr7D 89.262 1788 138 28 983 2739 89486419 89488183 0.000000e+00 2189.0
3 TraesCS7D01G140000 chr7D 93.699 1095 59 6 991 2084 89731734 89730649 0.000000e+00 1631.0
4 TraesCS7D01G140000 chr7D 95.551 472 20 1 2577 3047 89488179 89488650 0.000000e+00 754.0
5 TraesCS7D01G140000 chr7D 91.533 437 34 3 21 455 89792258 89791823 1.560000e-167 599.0
6 TraesCS7D01G140000 chr7B 88.664 1879 154 23 983 2848 40346741 40348573 0.000000e+00 2235.0
7 TraesCS7D01G140000 chr7B 88.750 1520 108 32 590 2066 40444169 40442670 0.000000e+00 1801.0
8 TraesCS7D01G140000 chr7B 91.049 1106 73 17 1270 2367 40351704 40352791 0.000000e+00 1471.0
9 TraesCS7D01G140000 chr7B 88.767 454 46 4 7 456 40444625 40444173 4.440000e-153 551.0
10 TraesCS7D01G140000 chr7B 92.958 142 10 0 2884 3025 40348814 40348955 1.110000e-49 207.0
11 TraesCS7D01G140000 chr7B 90.323 93 6 3 451 543 658512596 658512507 5.340000e-23 119.0
12 TraesCS7D01G140000 chr7A 87.092 1991 188 36 789 2739 90586295 90588256 0.000000e+00 2189.0
13 TraesCS7D01G140000 chr7A 89.437 1439 85 27 654 2059 90665372 90663968 0.000000e+00 1753.0
14 TraesCS7D01G140000 chr7A 90.107 1122 90 17 991 2103 91017271 91016162 0.000000e+00 1437.0
15 TraesCS7D01G140000 chr7A 91.741 448 35 2 7 453 90665857 90665411 3.340000e-174 621.0
16 TraesCS7D01G140000 chr7A 90.647 417 34 5 1 415 90585784 90586197 1.600000e-152 549.0
17 TraesCS7D01G140000 chr7A 86.747 498 51 11 789 1282 90615915 90616401 9.610000e-150 540.0
18 TraesCS7D01G140000 chr7A 92.945 326 21 2 2577 2901 90588252 90588576 9.890000e-130 473.0
19 TraesCS7D01G140000 chr7A 97.516 161 4 0 2887 3047 90590101 90590261 2.990000e-70 276.0
20 TraesCS7D01G140000 chr7A 89.756 205 19 2 252 456 90585088 90585290 8.380000e-66 261.0
21 TraesCS7D01G140000 chr7A 84.234 222 17 3 2151 2370 90616474 90616679 1.850000e-47 200.0
22 TraesCS7D01G140000 chr7A 94.059 101 6 0 115 215 90584994 90585094 1.460000e-33 154.0
23 TraesCS7D01G140000 chr7A 94.898 98 5 0 1 98 90613995 90614092 1.460000e-33 154.0
24 TraesCS7D01G140000 chr7A 91.398 93 5 2 449 540 561598608 561598698 1.150000e-24 124.0
25 TraesCS7D01G140000 chrUn 89.843 1083 99 11 975 2052 91490441 91491517 0.000000e+00 1380.0
26 TraesCS7D01G140000 chrUn 90.323 93 6 3 451 543 399203735 399203646 5.340000e-23 119.0
27 TraesCS7D01G140000 chr3A 90.526 95 7 2 449 543 52348383 52348291 1.150000e-24 124.0
28 TraesCS7D01G140000 chr3A 88.421 95 10 1 447 540 365965573 365965667 2.480000e-21 113.0
29 TraesCS7D01G140000 chr2D 90.323 93 7 2 447 538 513090499 513090408 1.480000e-23 121.0
30 TraesCS7D01G140000 chr6D 88.542 96 9 2 447 541 462439588 462439494 6.900000e-22 115.0
31 TraesCS7D01G140000 chr3D 87.879 99 9 3 443 540 450878880 450878784 2.480000e-21 113.0
32 TraesCS7D01G140000 chr3B 85.455 110 11 4 430 539 674419853 674419749 3.210000e-20 110.0
33 TraesCS7D01G140000 chr3B 85.965 57 8 0 545 601 481651989 481652045 9.120000e-06 62.1
34 TraesCS7D01G140000 chr2B 92.308 52 3 1 541 591 154193463 154193412 4.210000e-09 73.1
35 TraesCS7D01G140000 chr2B 91.489 47 4 0 545 591 286515317 286515363 7.050000e-07 65.8
36 TraesCS7D01G140000 chr2B 85.455 55 7 1 537 591 797731346 797731399 4.240000e-04 56.5
37 TraesCS7D01G140000 chr6B 91.489 47 4 0 545 591 605587260 605587306 7.050000e-07 65.8
38 TraesCS7D01G140000 chr5B 93.023 43 3 0 545 587 54346666 54346624 2.540000e-06 63.9
39 TraesCS7D01G140000 chr5B 93.023 43 3 0 545 587 360464286 360464244 2.540000e-06 63.9
40 TraesCS7D01G140000 chr6A 89.583 48 5 0 540 587 93885309 93885262 9.120000e-06 62.1
41 TraesCS7D01G140000 chr1B 84.483 58 7 2 538 594 552854144 552854200 4.240000e-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 TraesCS7D01G140000 chr7D 89521303 89524349 3046 False 5627.000000 5627 100.000000 1 3047 1 chr7D.!!$F1 3046
1 TraesCS7D01G140000 chr7D 89730649 89731734 1085 True 1631.000000 1631 93.699000 991 2084 1 chr7D.!!$R1 1093
2 TraesCS7D01G140000 chr7D 89486419 89488650 2231 False 1471.500000 2189 92.406500 983 3047 2 chr7D.!!$F2 2064
3 TraesCS7D01G140000 chr7D 89790322 89792258 1936 True 1406.000000 2213 92.367000 21 2085 2 chr7D.!!$R2 2064
4 TraesCS7D01G140000 chr7B 40346741 40352791 6050 False 1304.333333 2235 90.890333 983 3025 3 chr7B.!!$F1 2042
5 TraesCS7D01G140000 chr7B 40442670 40444625 1955 True 1176.000000 1801 88.758500 7 2066 2 chr7B.!!$R2 2059
6 TraesCS7D01G140000 chr7A 91016162 91017271 1109 True 1437.000000 1437 90.107000 991 2103 1 chr7A.!!$R1 1112
7 TraesCS7D01G140000 chr7A 90663968 90665857 1889 True 1187.000000 1753 90.589000 7 2059 2 chr7A.!!$R2 2052
8 TraesCS7D01G140000 chr7A 90584994 90590261 5267 False 650.333333 2189 92.002500 1 3047 6 chr7A.!!$F2 3046
9 TraesCS7D01G140000 chr7A 90613995 90616679 2684 False 298.000000 540 88.626333 1 2370 3 chr7A.!!$F3 2369
10 TraesCS7D01G140000 chrUn 91490441 91491517 1076 False 1380.000000 1380 89.843000 975 2052 1 chrUn.!!$F1 1077

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
565 1886 0.179468 CTCCCTCCGCCCGAAAATAA 59.821 55.0 0.0 0.0 0.0 1.4 F
566 1887 0.619505 TCCCTCCGCCCGAAAATAAA 59.380 50.0 0.0 0.0 0.0 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 8126 2.092429 GGGCCTCACATTGTCTGGATAA 60.092 50.000 0.84 0.0 0.0 1.75 R
2215 8607 2.158726 TCCTACAGAAAAACCCGTTGCT 60.159 45.455 0.00 0.0 0.0 3.91 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
219 1011 7.417612 GCATCGGTTATGAAAGTTATTCATGT 58.582 34.615 12.62 0.00 39.30 3.21
223 1015 9.051679 TCGGTTATGAAAGTTATTCATGTATGG 57.948 33.333 12.62 1.23 39.30 2.74
244 1036 9.120538 GTATGGGAAGTACAATATTCATGTGTT 57.879 33.333 0.00 0.00 32.27 3.32
260 1052 6.629128 TCATGTGTTTTCAACAGTTGTTCAT 58.371 32.000 13.14 7.27 43.10 2.57
460 1781 8.196378 ACAAGAACTTGATATATACTCCCTCC 57.804 38.462 19.35 0.00 42.93 4.30
461 1782 7.039644 ACAAGAACTTGATATATACTCCCTCCG 60.040 40.741 19.35 0.00 42.93 4.63
462 1783 6.553857 AGAACTTGATATATACTCCCTCCGT 58.446 40.000 0.00 0.00 0.00 4.69
463 1784 7.696981 AGAACTTGATATATACTCCCTCCGTA 58.303 38.462 0.00 0.00 0.00 4.02
464 1785 8.168725 AGAACTTGATATATACTCCCTCCGTAA 58.831 37.037 0.00 0.00 0.00 3.18
465 1786 8.716674 AACTTGATATATACTCCCTCCGTAAA 57.283 34.615 0.00 0.00 0.00 2.01
466 1787 8.350852 ACTTGATATATACTCCCTCCGTAAAG 57.649 38.462 0.00 0.00 0.00 1.85
467 1788 8.168725 ACTTGATATATACTCCCTCCGTAAAGA 58.831 37.037 0.00 0.00 0.00 2.52
468 1789 8.945195 TTGATATATACTCCCTCCGTAAAGAA 57.055 34.615 0.00 0.00 0.00 2.52
469 1790 8.945195 TGATATATACTCCCTCCGTAAAGAAA 57.055 34.615 0.00 0.00 0.00 2.52
470 1791 9.543231 TGATATATACTCCCTCCGTAAAGAAAT 57.457 33.333 0.00 0.00 0.00 2.17
477 1798 8.959705 ACTCCCTCCGTAAAGAAATATAAAAG 57.040 34.615 0.00 0.00 0.00 2.27
478 1799 7.498239 ACTCCCTCCGTAAAGAAATATAAAAGC 59.502 37.037 0.00 0.00 0.00 3.51
479 1800 7.340256 TCCCTCCGTAAAGAAATATAAAAGCA 58.660 34.615 0.00 0.00 0.00 3.91
480 1801 7.996644 TCCCTCCGTAAAGAAATATAAAAGCAT 59.003 33.333 0.00 0.00 0.00 3.79
481 1802 8.630037 CCCTCCGTAAAGAAATATAAAAGCATT 58.370 33.333 0.00 0.00 0.00 3.56
548 1869 8.977267 TTTACAGAGGGAGTACTATTCTACTC 57.023 38.462 0.00 0.00 41.37 2.59
555 1876 3.752747 GAGTACTATTCTACTCCCTCCGC 59.247 52.174 0.00 0.00 37.67 5.54
556 1877 1.998222 ACTATTCTACTCCCTCCGCC 58.002 55.000 0.00 0.00 0.00 6.13
557 1878 1.258676 CTATTCTACTCCCTCCGCCC 58.741 60.000 0.00 0.00 0.00 6.13
558 1879 0.538977 TATTCTACTCCCTCCGCCCG 60.539 60.000 0.00 0.00 0.00 6.13
559 1880 2.294170 ATTCTACTCCCTCCGCCCGA 62.294 60.000 0.00 0.00 0.00 5.14
560 1881 2.441532 CTACTCCCTCCGCCCGAA 60.442 66.667 0.00 0.00 0.00 4.30
561 1882 2.037687 TACTCCCTCCGCCCGAAA 59.962 61.111 0.00 0.00 0.00 3.46
562 1883 1.610086 TACTCCCTCCGCCCGAAAA 60.610 57.895 0.00 0.00 0.00 2.29
563 1884 0.979187 TACTCCCTCCGCCCGAAAAT 60.979 55.000 0.00 0.00 0.00 1.82
564 1885 0.979187 ACTCCCTCCGCCCGAAAATA 60.979 55.000 0.00 0.00 0.00 1.40
565 1886 0.179468 CTCCCTCCGCCCGAAAATAA 59.821 55.000 0.00 0.00 0.00 1.40
566 1887 0.619505 TCCCTCCGCCCGAAAATAAA 59.380 50.000 0.00 0.00 0.00 1.40
567 1888 1.213430 TCCCTCCGCCCGAAAATAAAT 59.787 47.619 0.00 0.00 0.00 1.40
568 1889 1.336755 CCCTCCGCCCGAAAATAAATG 59.663 52.381 0.00 0.00 0.00 2.32
569 1890 2.021457 CCTCCGCCCGAAAATAAATGT 58.979 47.619 0.00 0.00 0.00 2.71
570 1891 2.032924 CCTCCGCCCGAAAATAAATGTC 59.967 50.000 0.00 0.00 0.00 3.06
571 1892 2.943033 CTCCGCCCGAAAATAAATGTCT 59.057 45.455 0.00 0.00 0.00 3.41
572 1893 2.940410 TCCGCCCGAAAATAAATGTCTC 59.060 45.455 0.00 0.00 0.00 3.36
573 1894 2.680841 CCGCCCGAAAATAAATGTCTCA 59.319 45.455 0.00 0.00 0.00 3.27
574 1895 3.127895 CCGCCCGAAAATAAATGTCTCAA 59.872 43.478 0.00 0.00 0.00 3.02
575 1896 4.095610 CGCCCGAAAATAAATGTCTCAAC 58.904 43.478 0.00 0.00 0.00 3.18
576 1897 4.142687 CGCCCGAAAATAAATGTCTCAACT 60.143 41.667 0.00 0.00 0.00 3.16
577 1898 5.619086 CGCCCGAAAATAAATGTCTCAACTT 60.619 40.000 0.00 0.00 0.00 2.66
578 1899 6.156519 GCCCGAAAATAAATGTCTCAACTTT 58.843 36.000 0.00 0.00 0.00 2.66
579 1900 7.309920 GCCCGAAAATAAATGTCTCAACTTTA 58.690 34.615 0.00 0.00 0.00 1.85
580 1901 7.973944 GCCCGAAAATAAATGTCTCAACTTTAT 59.026 33.333 0.00 0.00 0.00 1.40
595 1916 9.092338 TCTCAACTTTATACTAACCTTACCACA 57.908 33.333 0.00 0.00 0.00 4.17
638 1960 4.055360 TGTGTTTAGATGAGTGTTCACGG 58.945 43.478 0.00 0.00 35.83 4.94
726 2057 8.833231 TTCAACATGGAACTTTGTGTTAAAAA 57.167 26.923 0.00 0.00 39.30 1.94
1041 2424 3.967335 GCCGCGGCGACTATCTCT 61.967 66.667 37.24 0.00 0.00 3.10
1072 2455 4.013050 ACTGCTCCTAATCTTTTGCTTCC 58.987 43.478 0.00 0.00 0.00 3.46
1678 3331 0.625849 CACTTACCCCAATGGCCTCT 59.374 55.000 3.32 0.00 37.83 3.69
1911 8240 2.402305 CTGCTAGCATTGAGGATCGAC 58.598 52.381 19.72 0.00 38.61 4.20
2149 8531 9.528018 GTTTTGACTGATTTTATTTGGAAGACA 57.472 29.630 0.00 0.00 0.00 3.41
2223 8615 8.779303 TGTATTCAATATAATGTAAGCAACGGG 58.221 33.333 0.00 0.00 0.00 5.28
2257 8649 7.461182 AGGACTAGATAATAGCAGATGTGTC 57.539 40.000 0.00 0.00 0.00 3.67
2259 8651 7.507277 AGGACTAGATAATAGCAGATGTGTCAA 59.493 37.037 0.00 0.00 0.00 3.18
2262 8654 9.703892 ACTAGATAATAGCAGATGTGTCAATTC 57.296 33.333 0.00 0.00 0.00 2.17
2299 8691 3.213506 AGCACTAGCATTGTTGTGAACA 58.786 40.909 0.00 0.00 45.49 3.18
2302 8694 4.083110 GCACTAGCATTGTTGTGAACATCT 60.083 41.667 0.00 0.00 40.13 2.90
2303 8695 5.625251 CACTAGCATTGTTGTGAACATCTC 58.375 41.667 0.00 0.00 41.79 2.75
2304 8696 3.818961 AGCATTGTTGTGAACATCTCG 57.181 42.857 0.00 0.00 41.79 4.04
2330 8743 6.963083 AGTTAGCATAGGAGTACAGGTTAG 57.037 41.667 0.00 0.00 0.00 2.34
2333 8746 8.226112 AGTTAGCATAGGAGTACAGGTTAGTAT 58.774 37.037 0.00 0.00 0.00 2.12
2376 8789 3.521524 ATCGTGCAAAAAGAGAACGAC 57.478 42.857 0.00 0.00 44.98 4.34
2396 8809 9.107367 GAACGACTTTGTAAGAGAAATCAATTG 57.893 33.333 0.00 0.00 0.00 2.32
2397 8810 8.154649 ACGACTTTGTAAGAGAAATCAATTGT 57.845 30.769 5.13 0.00 0.00 2.71
2399 8812 8.895845 CGACTTTGTAAGAGAAATCAATTGTTG 58.104 33.333 5.13 0.00 0.00 3.33
2400 8813 9.950680 GACTTTGTAAGAGAAATCAATTGTTGA 57.049 29.630 5.13 0.00 45.01 3.18
2401 8814 9.736023 ACTTTGTAAGAGAAATCAATTGTTGAC 57.264 29.630 5.13 0.00 43.48 3.18
2407 8820 8.822652 AAGAGAAATCAATTGTTGACCAAATC 57.177 30.769 5.13 0.00 43.48 2.17
2416 8829 5.521906 TTGTTGACCAAATCGGAAATCAA 57.478 34.783 0.00 0.00 38.63 2.57
2417 8830 5.720371 TGTTGACCAAATCGGAAATCAAT 57.280 34.783 0.00 0.00 38.63 2.57
2425 8838 5.801947 CCAAATCGGAAATCAATCAAGTGAC 59.198 40.000 0.00 0.00 36.56 3.67
2426 8839 6.349611 CCAAATCGGAAATCAATCAAGTGACT 60.350 38.462 0.00 0.00 36.56 3.41
2435 8848 3.748048 TCAATCAAGTGACTGTTAGCAGC 59.252 43.478 6.48 0.56 46.30 5.25
2436 8849 3.692257 ATCAAGTGACTGTTAGCAGCT 57.308 42.857 6.48 0.00 46.30 4.24
2444 8857 6.511416 AGTGACTGTTAGCAGCTTATATCTG 58.489 40.000 0.00 0.00 46.30 2.90
2445 8858 5.694006 GTGACTGTTAGCAGCTTATATCTGG 59.306 44.000 0.00 0.00 46.30 3.86
2451 8864 3.041211 AGCAGCTTATATCTGGGTCACA 58.959 45.455 0.00 0.00 32.41 3.58
2453 8866 3.432186 GCAGCTTATATCTGGGTCACACA 60.432 47.826 0.00 0.00 32.41 3.72
2464 8877 2.706723 TGGGTCACACAGCTTAGGTAAA 59.293 45.455 0.00 0.00 0.00 2.01
2465 8878 3.136809 TGGGTCACACAGCTTAGGTAAAA 59.863 43.478 0.00 0.00 0.00 1.52
2473 8886 5.473504 ACACAGCTTAGGTAAAAGAACCATG 59.526 40.000 0.00 0.00 42.40 3.66
2484 8897 7.119262 AGGTAAAAGAACCATGTTATCACGAAG 59.881 37.037 0.00 0.00 42.40 3.79
2487 8900 4.517285 AGAACCATGTTATCACGAAGCAT 58.483 39.130 0.00 0.00 0.00 3.79
2488 8901 4.572389 AGAACCATGTTATCACGAAGCATC 59.428 41.667 0.00 0.00 0.00 3.91
2490 8903 4.122776 ACCATGTTATCACGAAGCATCTC 58.877 43.478 0.00 0.00 0.00 2.75
2493 8906 3.521560 TGTTATCACGAAGCATCTCCAC 58.478 45.455 0.00 0.00 0.00 4.02
2510 8923 7.309438 GCATCTCCACTGGTTTTCTTTATTTCT 60.309 37.037 0.00 0.00 0.00 2.52
2563 8976 6.535963 AATCAAGGAAAAGATTGGCCTAAG 57.464 37.500 3.32 0.00 33.47 2.18
2566 8979 3.969553 AGGAAAAGATTGGCCTAAGACC 58.030 45.455 3.32 0.00 0.00 3.85
2569 8982 4.399618 GGAAAAGATTGGCCTAAGACCTTC 59.600 45.833 3.32 0.00 0.00 3.46
2637 9206 8.445275 TTTGAAACTTAATAGCAGAGTCACAA 57.555 30.769 0.00 0.00 0.00 3.33
2642 9211 7.426929 ACTTAATAGCAGAGTCACAACTTTG 57.573 36.000 0.00 0.00 39.90 2.77
2649 9218 4.747810 CAGAGTCACAACTTTGCCTTTTT 58.252 39.130 0.00 0.00 35.28 1.94
2652 9221 4.747810 AGTCACAACTTTGCCTTTTTCAG 58.252 39.130 0.00 0.00 28.74 3.02
2686 9255 9.790389 GATCTATCTGTTCTAATACATAACGGG 57.210 37.037 0.00 0.00 31.71 5.28
2703 9273 1.135517 CGGGGGCGTTTAAATGAACAG 60.136 52.381 11.68 0.00 0.00 3.16
2817 9387 2.358898 AGTTGGACAATGTTCTGTGTGC 59.641 45.455 0.00 0.00 36.69 4.57
2823 9393 2.031769 ACAATGTTCTGTGTGCGTCATG 60.032 45.455 0.00 0.00 0.00 3.07
2832 9402 0.795698 TGTGCGTCATGTTTGGATCG 59.204 50.000 0.00 0.00 0.00 3.69
2869 9439 2.403252 ATGGACAAACTAGCTTCCCG 57.597 50.000 0.00 0.00 0.00 5.14
2875 9445 1.940613 CAAACTAGCTTCCCGCCATAC 59.059 52.381 0.00 0.00 40.39 2.39
2920 11028 4.196971 GGTGGCCTTATGTCGTTTTAGAT 58.803 43.478 3.32 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
219 1011 9.693739 AAACACATGAATATTGTACTTCCCATA 57.306 29.630 0.00 0.00 0.00 2.74
223 1015 9.906660 TTGAAAACACATGAATATTGTACTTCC 57.093 29.630 0.00 0.00 0.00 3.46
244 1036 9.645059 TTGAATTTACATGAACAACTGTTGAAA 57.355 25.926 26.00 14.07 38.56 2.69
276 1069 7.934665 TGCCTAAACACTTTATCTACTGAAACA 59.065 33.333 0.00 0.00 0.00 2.83
298 1091 6.058183 GGTAGAACACATTTATCTCATGCCT 58.942 40.000 0.00 0.00 0.00 4.75
522 1843 9.577222 GAGTAGAATAGTACTCCCTCTGTAAAT 57.423 37.037 0.00 0.00 42.16 1.40
523 1844 8.977267 GAGTAGAATAGTACTCCCTCTGTAAA 57.023 38.462 0.00 0.00 42.16 2.01
533 1854 3.752747 GCGGAGGGAGTAGAATAGTACTC 59.247 52.174 0.00 2.93 45.70 2.59
534 1855 3.498301 GGCGGAGGGAGTAGAATAGTACT 60.498 52.174 0.00 0.00 35.88 2.73
535 1856 2.819019 GGCGGAGGGAGTAGAATAGTAC 59.181 54.545 0.00 0.00 0.00 2.73
536 1857 2.224967 GGGCGGAGGGAGTAGAATAGTA 60.225 54.545 0.00 0.00 0.00 1.82
537 1858 1.480869 GGGCGGAGGGAGTAGAATAGT 60.481 57.143 0.00 0.00 0.00 2.12
538 1859 1.258676 GGGCGGAGGGAGTAGAATAG 58.741 60.000 0.00 0.00 0.00 1.73
539 1860 0.538977 CGGGCGGAGGGAGTAGAATA 60.539 60.000 0.00 0.00 0.00 1.75
540 1861 1.833049 CGGGCGGAGGGAGTAGAAT 60.833 63.158 0.00 0.00 0.00 2.40
541 1862 2.441532 CGGGCGGAGGGAGTAGAA 60.442 66.667 0.00 0.00 0.00 2.10
542 1863 2.503846 TTTCGGGCGGAGGGAGTAGA 62.504 60.000 0.00 0.00 0.00 2.59
543 1864 1.610554 TTTTCGGGCGGAGGGAGTAG 61.611 60.000 0.00 0.00 0.00 2.57
544 1865 0.979187 ATTTTCGGGCGGAGGGAGTA 60.979 55.000 0.00 0.00 0.00 2.59
545 1866 0.979187 TATTTTCGGGCGGAGGGAGT 60.979 55.000 0.00 0.00 0.00 3.85
546 1867 0.179468 TTATTTTCGGGCGGAGGGAG 59.821 55.000 0.00 0.00 0.00 4.30
547 1868 0.619505 TTTATTTTCGGGCGGAGGGA 59.380 50.000 0.00 0.00 0.00 4.20
548 1869 1.336755 CATTTATTTTCGGGCGGAGGG 59.663 52.381 0.00 0.00 0.00 4.30
549 1870 2.021457 ACATTTATTTTCGGGCGGAGG 58.979 47.619 0.00 0.00 0.00 4.30
550 1871 2.943033 AGACATTTATTTTCGGGCGGAG 59.057 45.455 0.00 0.00 0.00 4.63
551 1872 2.940410 GAGACATTTATTTTCGGGCGGA 59.060 45.455 0.00 0.00 0.00 5.54
552 1873 2.680841 TGAGACATTTATTTTCGGGCGG 59.319 45.455 0.00 0.00 0.00 6.13
553 1874 4.095610 GTTGAGACATTTATTTTCGGGCG 58.904 43.478 0.00 0.00 0.00 6.13
554 1875 5.310720 AGTTGAGACATTTATTTTCGGGC 57.689 39.130 0.00 0.00 0.00 6.13
567 1888 9.092338 TGGTAAGGTTAGTATAAAGTTGAGACA 57.908 33.333 0.00 0.00 0.00 3.41
568 1889 9.363763 GTGGTAAGGTTAGTATAAAGTTGAGAC 57.636 37.037 0.00 0.00 0.00 3.36
569 1890 9.092338 TGTGGTAAGGTTAGTATAAAGTTGAGA 57.908 33.333 0.00 0.00 0.00 3.27
570 1891 9.148104 GTGTGGTAAGGTTAGTATAAAGTTGAG 57.852 37.037 0.00 0.00 0.00 3.02
571 1892 8.649591 TGTGTGGTAAGGTTAGTATAAAGTTGA 58.350 33.333 0.00 0.00 0.00 3.18
572 1893 8.836268 TGTGTGGTAAGGTTAGTATAAAGTTG 57.164 34.615 0.00 0.00 0.00 3.16
573 1894 8.654094 ACTGTGTGGTAAGGTTAGTATAAAGTT 58.346 33.333 0.00 0.00 0.00 2.66
574 1895 8.198807 ACTGTGTGGTAAGGTTAGTATAAAGT 57.801 34.615 0.00 0.00 0.00 2.66
575 1896 7.763071 GGACTGTGTGGTAAGGTTAGTATAAAG 59.237 40.741 0.00 0.00 0.00 1.85
576 1897 7.235193 TGGACTGTGTGGTAAGGTTAGTATAAA 59.765 37.037 0.00 0.00 0.00 1.40
577 1898 6.725369 TGGACTGTGTGGTAAGGTTAGTATAA 59.275 38.462 0.00 0.00 0.00 0.98
578 1899 6.255287 TGGACTGTGTGGTAAGGTTAGTATA 58.745 40.000 0.00 0.00 0.00 1.47
579 1900 5.088730 TGGACTGTGTGGTAAGGTTAGTAT 58.911 41.667 0.00 0.00 0.00 2.12
580 1901 4.482030 TGGACTGTGTGGTAAGGTTAGTA 58.518 43.478 0.00 0.00 0.00 1.82
581 1902 3.311091 TGGACTGTGTGGTAAGGTTAGT 58.689 45.455 0.00 0.00 0.00 2.24
582 1903 4.020573 TCATGGACTGTGTGGTAAGGTTAG 60.021 45.833 0.00 0.00 0.00 2.34
583 1904 3.904965 TCATGGACTGTGTGGTAAGGTTA 59.095 43.478 0.00 0.00 0.00 2.85
584 1905 2.708861 TCATGGACTGTGTGGTAAGGTT 59.291 45.455 0.00 0.00 0.00 3.50
585 1906 2.334977 TCATGGACTGTGTGGTAAGGT 58.665 47.619 0.00 0.00 0.00 3.50
586 1907 3.417069 TTCATGGACTGTGTGGTAAGG 57.583 47.619 0.00 0.00 0.00 2.69
587 1908 4.133820 TGTTTCATGGACTGTGTGGTAAG 58.866 43.478 0.00 0.00 0.00 2.34
588 1909 4.157849 TGTTTCATGGACTGTGTGGTAA 57.842 40.909 0.00 0.00 0.00 2.85
592 1913 6.638063 CACTAAAATGTTTCATGGACTGTGTG 59.362 38.462 0.00 0.00 0.00 3.82
595 1916 6.321181 ACACACTAAAATGTTTCATGGACTGT 59.679 34.615 0.00 0.00 0.00 3.55
1041 2424 0.393402 TTAGGAGCAGTACGGCGAGA 60.393 55.000 16.62 0.00 39.27 4.04
1797 8126 2.092429 GGGCCTCACATTGTCTGGATAA 60.092 50.000 0.84 0.00 0.00 1.75
1911 8240 3.363970 CCTCGATTATTTTTCCATCGGCG 60.364 47.826 0.00 0.00 40.21 6.46
2215 8607 2.158726 TCCTACAGAAAAACCCGTTGCT 60.159 45.455 0.00 0.00 0.00 3.91
2257 8649 7.869429 AGTGCTTTATTTCTGTCTTTGGAATTG 59.131 33.333 0.00 0.00 0.00 2.32
2259 8651 7.530426 AGTGCTTTATTTCTGTCTTTGGAAT 57.470 32.000 0.00 0.00 0.00 3.01
2262 8654 6.072508 TGCTAGTGCTTTATTTCTGTCTTTGG 60.073 38.462 0.00 0.00 40.48 3.28
2299 8691 7.395617 TGTACTCCTATGCTAACTATCGAGAT 58.604 38.462 0.00 0.00 0.00 2.75
2302 8694 5.938710 CCTGTACTCCTATGCTAACTATCGA 59.061 44.000 0.00 0.00 0.00 3.59
2303 8695 5.706369 ACCTGTACTCCTATGCTAACTATCG 59.294 44.000 0.00 0.00 0.00 2.92
2304 8696 7.527568 AACCTGTACTCCTATGCTAACTATC 57.472 40.000 0.00 0.00 0.00 2.08
2343 8756 3.548745 TGCACGATTGGATTCTCTCAT 57.451 42.857 0.00 0.00 0.00 2.90
2349 8762 5.046910 TCTCTTTTTGCACGATTGGATTC 57.953 39.130 0.00 0.00 0.00 2.52
2359 8772 4.412207 ACAAAGTCGTTCTCTTTTTGCAC 58.588 39.130 0.00 0.00 33.58 4.57
2376 8789 9.185192 GGTCAACAATTGATTTCTCTTACAAAG 57.815 33.333 13.59 0.00 42.47 2.77
2396 8809 5.708948 TGATTGATTTCCGATTTGGTCAAC 58.291 37.500 0.00 0.00 34.24 3.18
2397 8810 5.973899 TGATTGATTTCCGATTTGGTCAA 57.026 34.783 0.00 0.00 39.52 3.18
2399 8812 5.801947 CACTTGATTGATTTCCGATTTGGTC 59.198 40.000 0.00 0.00 39.52 4.02
2400 8813 5.476599 TCACTTGATTGATTTCCGATTTGGT 59.523 36.000 0.00 0.00 39.52 3.67
2401 8814 5.801947 GTCACTTGATTGATTTCCGATTTGG 59.198 40.000 0.00 0.00 40.09 3.28
2407 8820 5.362556 AACAGTCACTTGATTGATTTCCG 57.637 39.130 8.58 0.00 35.63 4.30
2416 8829 3.692257 AGCTGCTAACAGTCACTTGAT 57.308 42.857 0.00 0.00 46.30 2.57
2417 8830 3.475566 AAGCTGCTAACAGTCACTTGA 57.524 42.857 0.90 0.00 46.30 3.02
2426 8839 4.653801 TGACCCAGATATAAGCTGCTAACA 59.346 41.667 0.90 0.00 32.06 2.41
2434 8847 3.134458 GCTGTGTGACCCAGATATAAGC 58.866 50.000 0.00 0.00 31.38 3.09
2435 8848 4.679373 AGCTGTGTGACCCAGATATAAG 57.321 45.455 0.00 0.00 31.38 1.73
2436 8849 5.070446 CCTAAGCTGTGTGACCCAGATATAA 59.930 44.000 0.00 0.00 31.38 0.98
2444 8857 3.412237 TTTACCTAAGCTGTGTGACCC 57.588 47.619 0.00 0.00 0.00 4.46
2445 8858 4.638304 TCTTTTACCTAAGCTGTGTGACC 58.362 43.478 0.00 0.00 0.00 4.02
2451 8864 5.631119 ACATGGTTCTTTTACCTAAGCTGT 58.369 37.500 0.00 0.00 39.04 4.40
2453 8866 8.107095 TGATAACATGGTTCTTTTACCTAAGCT 58.893 33.333 0.00 0.00 39.04 3.74
2464 8877 4.323417 TGCTTCGTGATAACATGGTTCTT 58.677 39.130 0.00 0.00 34.18 2.52
2465 8878 3.937814 TGCTTCGTGATAACATGGTTCT 58.062 40.909 0.00 0.00 34.18 3.01
2473 8886 3.553511 CAGTGGAGATGCTTCGTGATAAC 59.446 47.826 0.00 0.00 0.00 1.89
2484 8897 5.904362 ATAAAGAAAACCAGTGGAGATGC 57.096 39.130 18.40 0.00 0.00 3.91
2487 8900 9.063615 GTTAGAAATAAAGAAAACCAGTGGAGA 57.936 33.333 18.40 0.00 0.00 3.71
2488 8901 8.297426 GGTTAGAAATAAAGAAAACCAGTGGAG 58.703 37.037 18.40 0.00 37.05 3.86
2490 8903 7.947282 TGGTTAGAAATAAAGAAAACCAGTGG 58.053 34.615 7.91 7.91 40.94 4.00
2535 8948 7.921304 AGGCCAATCTTTTCCTTGATTTATTT 58.079 30.769 5.01 0.00 31.35 1.40
2536 8949 7.500629 AGGCCAATCTTTTCCTTGATTTATT 57.499 32.000 5.01 0.00 31.35 1.40
2552 8965 2.168728 ACTCGAAGGTCTTAGGCCAATC 59.831 50.000 5.39 1.95 0.00 2.67
2553 8966 2.188817 ACTCGAAGGTCTTAGGCCAAT 58.811 47.619 5.39 0.00 0.00 3.16
2637 9206 6.872920 TCATACAAACTGAAAAAGGCAAAGT 58.127 32.000 0.00 0.00 0.00 2.66
2642 9211 8.897752 AGATAGATCATACAAACTGAAAAAGGC 58.102 33.333 0.00 0.00 0.00 4.35
2684 9253 1.890489 ACTGTTCATTTAAACGCCCCC 59.110 47.619 0.00 0.00 31.58 5.40
2686 9255 2.287909 TGCACTGTTCATTTAAACGCCC 60.288 45.455 0.00 0.00 31.58 6.13
2771 9341 4.584327 AGGTTGAATGTTGTTTAGCCAC 57.416 40.909 0.00 0.00 0.00 5.01
2772 9342 4.404073 ACAAGGTTGAATGTTGTTTAGCCA 59.596 37.500 0.00 0.00 30.07 4.75
2780 9350 5.067153 TGTCCAACTACAAGGTTGAATGTTG 59.933 40.000 8.64 14.23 46.55 3.33
2817 9387 0.247814 GCTGCGATCCAAACATGACG 60.248 55.000 0.00 0.00 0.00 4.35
2823 9393 2.159393 TGCTAATTGCTGCGATCCAAAC 60.159 45.455 2.20 0.00 43.37 2.93
2832 9402 3.120792 CCATTGTGATGCTAATTGCTGC 58.879 45.455 0.00 0.00 43.37 5.25
2869 9439 5.443185 ACATGTATGATTGCAAGTATGGC 57.557 39.130 4.94 1.13 33.57 4.40
2875 9445 5.751509 CCATCCAAACATGTATGATTGCAAG 59.248 40.000 4.94 0.00 38.68 4.01
2920 11028 9.896645 AACTTCAGAAGAATTATCAGCTAATCA 57.103 29.630 17.56 0.00 32.31 2.57


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

AutoCloner maintained by Alex Coulton.