Multiple sequence alignment - TraesCS7D01G503400

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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 TraesCS7D01G503400 chr7D 100.000 2333 0 0 1 2333 608489082 608486750 0.000000e+00 4309.0
1 TraesCS7D01G503400 chr7D 87.821 468 45 10 1869 2328 610236560 610237023 2.640000e-149 538.0
2 TraesCS7D01G503400 chr7D 84.111 579 51 22 992 1535 607562194 607561622 2.660000e-144 521.0
3 TraesCS7D01G503400 chr7D 80.408 735 68 37 851 1545 610235545 610236243 7.490000e-135 490.0
4 TraesCS7D01G503400 chr7D 85.865 474 46 13 1867 2328 607561297 607560833 3.490000e-133 484.0
5 TraesCS7D01G503400 chr7D 78.986 690 87 30 683 1336 610240232 610240899 3.590000e-113 418.0
6 TraesCS7D01G503400 chr7D 76.257 855 106 51 626 1426 607547014 607546203 4.740000e-97 364.0
7 TraesCS7D01G503400 chr7D 81.450 469 57 13 967 1426 608455331 608454884 7.930000e-95 357.0
8 TraesCS7D01G503400 chr7D 79.496 556 47 25 973 1501 608450468 608449953 1.340000e-87 333.0
9 TraesCS7D01G503400 chr7D 80.778 463 55 20 869 1318 514993905 514993464 4.810000e-87 331.0
10 TraesCS7D01G503400 chr7D 85.792 183 10 7 1689 1857 610236331 610236511 1.840000e-41 180.0
11 TraesCS7D01G503400 chr7D 92.562 121 6 3 1870 1987 608445971 608445851 1.110000e-38 171.0
12 TraesCS7D01G503400 chr7D 83.060 183 9 9 80 244 610234760 610234938 1.870000e-31 147.0
13 TraesCS7D01G503400 chr7D 75.281 267 34 20 1272 1518 515030418 515030164 5.310000e-17 99.0
14 TraesCS7D01G503400 chr7D 84.337 83 6 5 770 846 608450671 608450590 8.940000e-10 75.0
15 TraesCS7D01G503400 chr7D 100.000 38 0 0 770 807 607563927 607563890 1.160000e-08 71.3
16 TraesCS7D01G503400 chr7D 87.302 63 6 1 1722 1784 608454719 608454659 1.160000e-08 71.3
17 TraesCS7D01G503400 chrUn 95.547 741 27 4 1592 2328 83367068 83366330 0.000000e+00 1181.0
18 TraesCS7D01G503400 chrUn 87.190 484 47 8 851 1324 83371234 83370756 9.490000e-149 536.0
19 TraesCS7D01G503400 chrUn 85.616 438 49 5 881 1317 77586910 77586486 4.570000e-122 448.0
20 TraesCS7D01G503400 chrUn 95.652 207 9 0 1384 1590 83370739 83370533 1.340000e-87 333.0
21 TraesCS7D01G503400 chr7A 82.213 759 70 29 640 1336 699766847 699766092 5.550000e-166 593.0
22 TraesCS7D01G503400 chr7A 85.825 388 47 3 948 1330 700451362 700450978 2.790000e-109 405.0
23 TraesCS7D01G503400 chr7A 80.068 296 28 9 1566 1847 699765870 699765592 8.510000e-45 191.0
24 TraesCS7D01G503400 chr7A 82.587 201 31 4 1349 1548 699766051 699765854 8.570000e-40 174.0
25 TraesCS7D01G503400 chr7A 85.366 123 15 1 716 838 700451611 700451492 8.750000e-25 124.0
26 TraesCS7D01G503400 chr7B 81.948 698 82 25 876 1548 696595237 696594559 3.390000e-153 551.0
27 TraesCS7D01G503400 chr7B 80.457 788 83 31 623 1352 696383291 696382517 9.490000e-149 536.0
28 TraesCS7D01G503400 chr7B 83.306 605 66 21 973 1548 693821441 693820843 2.050000e-145 525.0
29 TraesCS7D01G503400 chr7B 77.500 1000 83 68 627 1546 693200717 693199780 9.760000e-129 470.0
30 TraesCS7D01G503400 chr7B 85.201 473 39 11 1867 2328 693199474 693199022 7.600000e-125 457.0
31 TraesCS7D01G503400 chr7B 80.236 339 36 19 1 326 693201341 693201021 2.330000e-55 226.0
32 TraesCS7D01G503400 chr7B 85.641 195 24 2 1868 2060 698860772 698860580 3.930000e-48 202.0
33 TraesCS7D01G503400 chr7B 86.857 175 15 6 1689 1857 693199693 693199521 3.060000e-44 189.0
34 TraesCS7D01G503400 chr7B 86.391 169 13 5 1689 1847 694798030 694797862 2.380000e-40 176.0
35 TraesCS7D01G503400 chr7B 90.164 122 10 2 1867 1986 694797808 694797687 8.630000e-35 158.0
36 TraesCS7D01G503400 chr7B 83.200 125 15 3 1708 1826 698856890 698856766 2.450000e-20 110.0
37 TraesCS7D01G503400 chr7B 83.077 130 12 2 682 802 698857915 698857787 2.450000e-20 110.0
38 TraesCS7D01G503400 chr7B 86.316 95 5 6 717 807 693793144 693793054 1.910000e-16 97.1
39 TraesCS7D01G503400 chr7B 78.472 144 7 17 684 807 696595497 696595358 3.220000e-09 73.1
40 TraesCS7D01G503400 chr7B 91.837 49 3 1 1709 1756 696362386 696362338 1.500000e-07 67.6
41 TraesCS7D01G503400 chr4A 82.629 639 69 15 950 1548 661969487 661970123 5.710000e-146 527.0
42 TraesCS7D01G503400 chr4A 85.787 394 48 5 948 1336 661973667 661974057 6.000000e-111 411.0
43 TraesCS7D01G503400 chr4A 82.171 129 15 5 680 802 661973371 661973497 1.140000e-18 104.0
44 TraesCS7D01G503400 chr4A 97.917 48 1 0 1705 1752 661974405 661974452 1.490000e-12 84.2
45 TraesCS7D01G503400 chr3D 96.875 32 0 1 2287 2317 14080106 14080137 4.000000e-03 52.8


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 TraesCS7D01G503400 chr7D 608486750 608489082 2332 True 4309.000000 4309 100.000000 1 2333 1 chr7D.!!$R4 2332
1 TraesCS7D01G503400 chr7D 607546203 607547014 811 True 364.000000 364 76.257000 626 1426 1 chr7D.!!$R3 800
2 TraesCS7D01G503400 chr7D 607560833 607563927 3094 True 358.766667 521 89.992000 770 2328 3 chr7D.!!$R5 1558
3 TraesCS7D01G503400 chr7D 610234760 610240899 6139 False 354.600000 538 83.213400 80 2328 5 chr7D.!!$F1 2248
4 TraesCS7D01G503400 chr7D 608445851 608455331 9480 True 201.460000 357 85.029400 770 1987 5 chr7D.!!$R6 1217
5 TraesCS7D01G503400 chrUn 83366330 83371234 4904 True 683.333333 1181 92.796333 851 2328 3 chrUn.!!$R2 1477
6 TraesCS7D01G503400 chr7A 699765592 699766847 1255 True 319.333333 593 81.622667 640 1847 3 chr7A.!!$R1 1207
7 TraesCS7D01G503400 chr7A 700450978 700451611 633 True 264.500000 405 85.595500 716 1330 2 chr7A.!!$R2 614
8 TraesCS7D01G503400 chr7B 696382517 696383291 774 True 536.000000 536 80.457000 623 1352 1 chr7B.!!$R4 729
9 TraesCS7D01G503400 chr7B 693820843 693821441 598 True 525.000000 525 83.306000 973 1548 1 chr7B.!!$R2 575
10 TraesCS7D01G503400 chr7B 693199022 693201341 2319 True 335.500000 470 82.448500 1 2328 4 chr7B.!!$R5 2327
11 TraesCS7D01G503400 chr7B 696594559 696595497 938 True 312.050000 551 80.210000 684 1548 2 chr7B.!!$R7 864
12 TraesCS7D01G503400 chr4A 661969487 661974452 4965 False 281.550000 527 87.126000 680 1752 4 chr4A.!!$F1 1072

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
478 630 0.4546 ATCGTACATCCGCGTGAGTT 59.545 50.0 4.92 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1757 14517 0.966179 GGCAACACCCTTTTACCCAG 59.034 55.0 0.0 0.0 0.0 4.45 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
119 125 4.175489 CGTCTGCATGCAGGCTGC 62.175 66.667 40.34 31.91 45.63 5.25
210 230 2.430244 CGAGGTGCACGTACGCTT 60.430 61.111 16.72 0.00 0.00 4.68
214 234 1.203313 GGTGCACGTACGCTTTGAC 59.797 57.895 16.72 5.12 0.00 3.18
270 320 4.513692 CACGGGAATTAAAATGCCTCGATA 59.486 41.667 14.04 0.00 34.24 2.92
300 358 1.030457 GTCAGATCGGACCGTACCAT 58.970 55.000 14.79 0.00 0.00 3.55
321 379 1.529713 GAAACCTTTCACCCGGCCA 60.530 57.895 2.24 0.00 37.15 5.36
322 380 1.524008 GAAACCTTTCACCCGGCCAG 61.524 60.000 2.24 0.00 37.15 4.85
365 462 1.498865 GGCGTTCGCATCCATCGATT 61.499 55.000 18.46 0.00 35.75 3.34
366 463 1.136690 GCGTTCGCATCCATCGATTA 58.863 50.000 12.33 0.00 35.75 1.75
406 510 2.618053 CATACAGAAACACGGAGTCCC 58.382 52.381 2.80 0.00 41.61 4.46
412 516 2.949644 AGAAACACGGAGTCCCTTTTTG 59.050 45.455 2.80 0.00 41.61 2.44
413 517 1.029681 AACACGGAGTCCCTTTTTGC 58.970 50.000 2.80 0.00 41.61 3.68
466 618 4.783055 AGCCTCTTCTCTTCTATCGTACA 58.217 43.478 0.00 0.00 0.00 2.90
478 630 0.454600 ATCGTACATCCGCGTGAGTT 59.545 50.000 4.92 0.00 0.00 3.01
489 641 2.282555 CCGCGTGAGTTATCAGATGTTG 59.717 50.000 4.92 0.00 35.66 3.33
492 644 4.085363 CGCGTGAGTTATCAGATGTTGATC 60.085 45.833 0.00 0.00 43.03 2.92
523 675 4.859629 AAAAAGAGTATCGGATTGACGC 57.140 40.909 0.00 0.00 42.67 5.19
526 678 3.357166 AGAGTATCGGATTGACGCTTC 57.643 47.619 0.00 0.00 42.67 3.86
527 679 2.688446 AGAGTATCGGATTGACGCTTCA 59.312 45.455 0.00 0.00 42.67 3.02
529 681 2.165641 AGTATCGGATTGACGCTTCACA 59.834 45.455 0.00 0.00 0.00 3.58
530 682 2.315925 ATCGGATTGACGCTTCACAT 57.684 45.000 0.00 0.00 0.00 3.21
532 684 1.067213 TCGGATTGACGCTTCACATGA 60.067 47.619 0.00 0.00 0.00 3.07
533 685 1.061131 CGGATTGACGCTTCACATGAC 59.939 52.381 0.00 0.00 0.00 3.06
534 686 1.398390 GGATTGACGCTTCACATGACC 59.602 52.381 0.00 0.00 0.00 4.02
538 690 2.227968 GACGCTTCACATGACCGTGC 62.228 60.000 0.00 0.00 36.80 5.34
540 692 1.568612 CGCTTCACATGACCGTGCTT 61.569 55.000 0.00 0.00 36.80 3.91
543 695 2.412847 GCTTCACATGACCGTGCTTAAC 60.413 50.000 0.00 0.00 36.80 2.01
545 697 3.052455 TCACATGACCGTGCTTAACAT 57.948 42.857 0.00 0.00 36.80 2.71
547 699 3.818210 TCACATGACCGTGCTTAACATTT 59.182 39.130 0.00 0.00 36.80 2.32
548 700 4.083537 TCACATGACCGTGCTTAACATTTC 60.084 41.667 0.00 0.00 36.80 2.17
550 702 4.083324 ACATGACCGTGCTTAACATTTCAG 60.083 41.667 0.00 0.00 0.00 3.02
551 703 2.225491 TGACCGTGCTTAACATTTCAGC 59.775 45.455 0.00 0.00 0.00 4.26
552 704 2.484264 GACCGTGCTTAACATTTCAGCT 59.516 45.455 0.00 0.00 34.42 4.24
553 705 2.484264 ACCGTGCTTAACATTTCAGCTC 59.516 45.455 0.00 0.00 34.42 4.09
555 707 2.159517 CGTGCTTAACATTTCAGCTCCC 60.160 50.000 0.00 0.00 34.42 4.30
556 708 2.164422 GTGCTTAACATTTCAGCTCCCC 59.836 50.000 0.00 0.00 34.42 4.81
557 709 1.401905 GCTTAACATTTCAGCTCCCCG 59.598 52.381 0.00 0.00 0.00 5.73
558 710 1.401905 CTTAACATTTCAGCTCCCCGC 59.598 52.381 0.00 0.00 39.57 6.13
561 713 0.539438 ACATTTCAGCTCCCCGCAAA 60.539 50.000 0.00 0.00 42.61 3.68
563 715 1.000731 CATTTCAGCTCCCCGCAAAAA 59.999 47.619 0.00 0.00 42.61 1.94
564 716 1.337118 TTTCAGCTCCCCGCAAAAAT 58.663 45.000 0.00 0.00 42.61 1.82
569 721 0.530288 GCTCCCCGCAAAAATGCTTA 59.470 50.000 0.00 0.00 38.92 3.09
571 723 2.606108 CTCCCCGCAAAAATGCTTAAC 58.394 47.619 0.00 0.00 0.00 2.01
572 724 1.964223 TCCCCGCAAAAATGCTTAACA 59.036 42.857 0.00 0.00 0.00 2.41
573 725 2.564947 TCCCCGCAAAAATGCTTAACAT 59.435 40.909 0.00 0.00 42.30 2.71
588 740 4.484236 CTTAACATTTCAGCATCCGCAAA 58.516 39.130 0.00 0.00 42.27 3.68
590 742 3.383620 ACATTTCAGCATCCGCAAAAA 57.616 38.095 0.00 0.00 42.27 1.94
591 743 3.929094 ACATTTCAGCATCCGCAAAAAT 58.071 36.364 0.00 0.00 42.27 1.82
592 744 5.070770 ACATTTCAGCATCCGCAAAAATA 57.929 34.783 0.00 0.00 42.27 1.40
593 745 5.477510 ACATTTCAGCATCCGCAAAAATAA 58.522 33.333 0.00 0.00 42.27 1.40
596 748 6.851222 TTTCAGCATCCGCAAAAATAAAAA 57.149 29.167 0.00 0.00 42.27 1.94
598 750 5.777802 TCAGCATCCGCAAAAATAAAAAGA 58.222 33.333 0.00 0.00 42.27 2.52
599 751 6.219473 TCAGCATCCGCAAAAATAAAAAGAA 58.781 32.000 0.00 0.00 42.27 2.52
600 752 6.703607 TCAGCATCCGCAAAAATAAAAAGAAA 59.296 30.769 0.00 0.00 42.27 2.52
601 753 7.225538 TCAGCATCCGCAAAAATAAAAAGAAAA 59.774 29.630 0.00 0.00 42.27 2.29
602 754 7.854916 CAGCATCCGCAAAAATAAAAAGAAAAA 59.145 29.630 0.00 0.00 42.27 1.94
821 4744 3.441290 CTTCCCCGCGTCTCTCGT 61.441 66.667 4.92 0.00 42.13 4.18
838 4761 4.063967 TCATTCACGCCGTCGCCT 62.064 61.111 0.00 0.00 39.84 5.52
865 4809 6.440354 CCCATTTTCCCTTCTCCCTATTTAA 58.560 40.000 0.00 0.00 0.00 1.52
886 4864 1.341156 CCCGCCTTCCTTCTCCATCT 61.341 60.000 0.00 0.00 0.00 2.90
925 4911 1.274728 CCTCCACTTCCTCACTCACAG 59.725 57.143 0.00 0.00 0.00 3.66
958 4965 1.951209 TGTTCCCACATCTCCAGCTA 58.049 50.000 0.00 0.00 0.00 3.32
997 6479 1.127567 AGTACCAAGGCAGGCAGTCA 61.128 55.000 0.00 0.00 0.00 3.41
1029 6517 1.154221 GGAGTCCTCCTCGCCCTAT 59.846 63.158 0.41 0.00 46.16 2.57
1126 6614 2.348998 CAGAGAGGCCACACACCC 59.651 66.667 5.01 0.00 0.00 4.61
1214 6702 3.827784 CGCGCTCAACTTCGACGG 61.828 66.667 5.56 0.00 0.00 4.79
1342 6836 2.523015 CAATCGCCTGAAGTGAATTGC 58.477 47.619 0.00 0.00 38.82 3.56
1377 6917 6.234177 TCTGTCCCTCTGATTTTTCTTCTTC 58.766 40.000 0.00 0.00 0.00 2.87
1378 6918 6.043706 TCTGTCCCTCTGATTTTTCTTCTTCT 59.956 38.462 0.00 0.00 0.00 2.85
1379 6919 6.234177 TGTCCCTCTGATTTTTCTTCTTCTC 58.766 40.000 0.00 0.00 0.00 2.87
1380 6920 6.043706 TGTCCCTCTGATTTTTCTTCTTCTCT 59.956 38.462 0.00 0.00 0.00 3.10
1381 6921 7.235606 TGTCCCTCTGATTTTTCTTCTTCTCTA 59.764 37.037 0.00 0.00 0.00 2.43
1382 6922 8.097662 GTCCCTCTGATTTTTCTTCTTCTCTAA 58.902 37.037 0.00 0.00 0.00 2.10
1416 6972 7.430793 CGAGACTGAATCACTACATCTGTAAAG 59.569 40.741 0.00 0.00 0.00 1.85
1453 7014 1.153842 CGGGGAAACGTACGTACCC 60.154 63.158 35.38 35.38 41.08 3.69
1521 7107 9.657419 ATCAATCACTTCATTTTTAATGTTCCC 57.343 29.630 0.00 0.00 0.00 3.97
1561 7147 5.105392 AGGCAACAGATTTCTCAACAACAAA 60.105 36.000 0.00 0.00 41.41 2.83
1564 7150 7.175410 GCAACAGATTTCTCAACAACAAAAAG 58.825 34.615 0.00 0.00 0.00 2.27
1573 7159 5.811613 TCTCAACAACAAAAAGAATGCAAGG 59.188 36.000 0.00 0.00 0.00 3.61
1584 7170 2.679837 AGAATGCAAGGCAACAGATACG 59.320 45.455 0.00 0.00 43.62 3.06
1590 7176 4.116961 GCAAGGCAACAGATACGTGTATA 58.883 43.478 0.00 0.00 41.41 1.47
1627 10714 4.142859 CGAATTCGTTTGGTCGGGAATTTA 60.143 41.667 19.67 0.00 38.74 1.40
1629 10716 4.688511 TTCGTTTGGTCGGGAATTTATG 57.311 40.909 0.00 0.00 0.00 1.90
1682 10769 3.148412 CTGTGATGATGAACCAACCACA 58.852 45.455 0.00 0.00 0.00 4.17
1684 10771 2.095768 GTGATGATGAACCAACCACACG 60.096 50.000 0.00 0.00 0.00 4.49
1686 10773 0.464554 TGATGAACCAACCACACGCA 60.465 50.000 0.00 0.00 0.00 5.24
1757 14517 2.024176 ATCCAACGATGTACAGCACC 57.976 50.000 12.28 0.00 0.00 5.01
1776 14544 0.966179 CTGGGTAAAAGGGTGTTGCC 59.034 55.000 0.00 0.00 0.00 4.52
2126 14954 0.235926 GTCTCCAACTGCGAACAAGC 59.764 55.000 0.00 0.00 37.71 4.01
2155 14983 1.250840 AACGAAGGAAATGGGCTGGC 61.251 55.000 0.00 0.00 0.00 4.85
2243 15072 3.600388 CCGTAGAGAGGAAAACTTGCAT 58.400 45.455 0.00 0.00 0.00 3.96
2328 15158 3.955471 TCCTCTGAAATGCAAACCCTAG 58.045 45.455 0.00 0.00 0.00 3.02
2329 15159 3.330701 TCCTCTGAAATGCAAACCCTAGT 59.669 43.478 0.00 0.00 0.00 2.57
2330 15160 3.441572 CCTCTGAAATGCAAACCCTAGTG 59.558 47.826 0.00 0.00 0.00 2.74
2332 15162 5.235850 TCTGAAATGCAAACCCTAGTGTA 57.764 39.130 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.103803 CTAGGACAGCGCTACCTTCA 58.896 55.000 30.68 18.13 35.52 3.02
10 11 0.526662 ACACACTAGGACAGCGCTAC 59.473 55.000 10.99 7.50 0.00 3.58
47 49 3.243128 CGCACAACGCACATCTCA 58.757 55.556 0.00 0.00 42.60 3.27
117 123 1.911269 TTACCCTGCTCTCCACGCA 60.911 57.895 0.00 0.00 35.80 5.24
119 125 1.218316 GGTTACCCTGCTCTCCACG 59.782 63.158 0.00 0.00 0.00 4.94
120 126 0.690762 TTGGTTACCCTGCTCTCCAC 59.309 55.000 0.00 0.00 0.00 4.02
123 129 1.073284 TGGTTTGGTTACCCTGCTCTC 59.927 52.381 0.00 0.00 37.39 3.20
124 130 1.145571 TGGTTTGGTTACCCTGCTCT 58.854 50.000 0.00 0.00 37.39 4.09
133 149 1.102222 AAGCGCCGTTGGTTTGGTTA 61.102 50.000 2.29 0.00 0.00 2.85
205 225 0.038251 TGCTCGATCAGTCAAAGCGT 60.038 50.000 0.00 0.00 36.23 5.07
206 226 0.644331 CTGCTCGATCAGTCAAAGCG 59.356 55.000 8.12 0.00 36.23 4.68
207 227 1.925847 CTCTGCTCGATCAGTCAAAGC 59.074 52.381 15.40 0.00 35.63 3.51
209 229 2.414691 CGACTCTGCTCGATCAGTCAAA 60.415 50.000 15.40 0.00 35.91 2.69
210 230 1.131315 CGACTCTGCTCGATCAGTCAA 59.869 52.381 15.40 0.00 35.91 3.18
214 234 1.299014 GGCGACTCTGCTCGATCAG 60.299 63.158 10.02 10.02 35.58 2.90
270 320 1.645704 CGATCTGACGGACGGACAGT 61.646 60.000 16.03 7.83 36.66 3.55
296 354 2.786777 GGGTGAAAGGTTTCGTATGGT 58.213 47.619 0.00 0.00 40.01 3.55
300 358 0.603439 GCCGGGTGAAAGGTTTCGTA 60.603 55.000 2.18 0.00 40.01 3.43
321 379 0.257039 AATCGGATGCCAAGCCTTCT 59.743 50.000 0.00 0.00 0.00 2.85
322 380 0.665298 GAATCGGATGCCAAGCCTTC 59.335 55.000 0.00 0.00 0.00 3.46
365 462 4.343231 TGGGCAGAAATGCAGAAGAAATA 58.657 39.130 2.29 0.00 36.33 1.40
366 463 3.167485 TGGGCAGAAATGCAGAAGAAAT 58.833 40.909 2.29 0.00 36.33 2.17
392 489 2.543031 GCAAAAAGGGACTCCGTGTTTC 60.543 50.000 3.30 0.00 38.49 2.78
440 544 5.305585 ACGATAGAAGAGAAGAGGCTAGAG 58.694 45.833 0.00 0.00 41.38 2.43
449 553 4.468643 GCGGATGTACGATAGAAGAGAAG 58.531 47.826 0.00 0.00 41.38 2.85
466 618 2.362397 ACATCTGATAACTCACGCGGAT 59.638 45.455 12.47 0.00 0.00 4.18
478 630 6.325993 TCTTTTGGGGATCAACATCTGATA 57.674 37.500 0.00 0.00 45.23 2.15
511 663 1.935873 CATGTGAAGCGTCAATCCGAT 59.064 47.619 3.20 0.00 34.87 4.18
512 664 1.067213 TCATGTGAAGCGTCAATCCGA 60.067 47.619 3.20 0.00 34.87 4.55
514 666 1.398390 GGTCATGTGAAGCGTCAATCC 59.602 52.381 3.20 0.00 34.87 3.01
515 667 1.061131 CGGTCATGTGAAGCGTCAATC 59.939 52.381 3.20 0.00 34.87 2.67
517 669 0.249699 ACGGTCATGTGAAGCGTCAA 60.250 50.000 3.20 0.00 46.80 3.18
519 671 1.781555 CACGGTCATGTGAAGCGTC 59.218 57.895 7.10 0.00 46.80 5.19
521 673 1.568612 AAGCACGGTCATGTGAAGCG 61.569 55.000 3.26 3.26 42.55 4.68
523 675 2.805671 TGTTAAGCACGGTCATGTGAAG 59.194 45.455 0.00 0.00 42.55 3.02
526 678 3.829886 AATGTTAAGCACGGTCATGTG 57.170 42.857 0.00 0.00 42.81 3.21
527 679 3.818210 TGAAATGTTAAGCACGGTCATGT 59.182 39.130 0.00 0.00 0.00 3.21
529 681 3.119849 GCTGAAATGTTAAGCACGGTCAT 60.120 43.478 0.00 0.00 36.91 3.06
530 682 2.225491 GCTGAAATGTTAAGCACGGTCA 59.775 45.455 0.00 0.00 36.91 4.02
532 684 2.484264 GAGCTGAAATGTTAAGCACGGT 59.516 45.455 0.00 0.00 39.47 4.83
533 685 2.159517 GGAGCTGAAATGTTAAGCACGG 60.160 50.000 0.00 0.00 39.47 4.94
534 686 2.159517 GGGAGCTGAAATGTTAAGCACG 60.160 50.000 0.00 0.00 39.47 5.34
538 690 1.401905 GCGGGGAGCTGAAATGTTAAG 59.598 52.381 0.00 0.00 44.04 1.85
540 692 3.168773 GCGGGGAGCTGAAATGTTA 57.831 52.632 0.00 0.00 44.04 2.41
550 702 6.938776 ATGTTAAGCATTTTTGCGGGGAGC 62.939 45.833 0.00 0.00 39.78 4.70
551 703 2.029470 TGTTAAGCATTTTTGCGGGGAG 60.029 45.455 0.00 0.00 40.27 4.30
552 704 1.964223 TGTTAAGCATTTTTGCGGGGA 59.036 42.857 0.00 0.00 40.27 4.81
553 705 2.447244 TGTTAAGCATTTTTGCGGGG 57.553 45.000 0.00 0.00 40.27 5.73
569 721 3.383620 TTTTGCGGATGCTGAAATGTT 57.616 38.095 0.00 0.00 43.34 2.71
571 723 6.406093 TTTATTTTTGCGGATGCTGAAATG 57.594 33.333 9.83 0.00 43.34 2.32
572 724 7.387397 TCTTTTTATTTTTGCGGATGCTGAAAT 59.613 29.630 0.00 6.63 43.34 2.17
573 725 6.703607 TCTTTTTATTTTTGCGGATGCTGAAA 59.296 30.769 0.00 0.00 43.34 2.69
575 727 5.777802 TCTTTTTATTTTTGCGGATGCTGA 58.222 33.333 0.00 0.00 43.34 4.26
576 728 6.464895 TTCTTTTTATTTTTGCGGATGCTG 57.535 33.333 0.00 0.00 43.34 4.41
577 729 7.489574 TTTTCTTTTTATTTTTGCGGATGCT 57.510 28.000 0.00 0.00 43.34 3.79
602 754 6.286758 TGGCACACACATCATTACAATTTTT 58.713 32.000 0.00 0.00 0.00 1.94
603 755 5.851720 TGGCACACACATCATTACAATTTT 58.148 33.333 0.00 0.00 0.00 1.82
604 756 5.465532 TGGCACACACATCATTACAATTT 57.534 34.783 0.00 0.00 0.00 1.82
607 759 2.228582 GCTGGCACACACATCATTACAA 59.771 45.455 0.00 0.00 0.00 2.41
618 770 1.667830 GTCGCTTAGCTGGCACACA 60.668 57.895 1.76 0.00 0.00 3.72
694 3900 4.953868 TGGCAACGGTCGGTCGTG 62.954 66.667 4.88 2.04 43.07 4.35
737 3986 0.605319 TGGGATTTCGCAGGTGTCAC 60.605 55.000 0.00 0.00 34.59 3.67
738 3987 0.109532 TTGGGATTTCGCAGGTGTCA 59.890 50.000 0.00 0.00 39.98 3.58
741 3990 1.200020 GTTCTTGGGATTTCGCAGGTG 59.800 52.381 6.63 0.00 39.98 4.00
821 4744 3.982372 GAGGCGACGGCGTGAATGA 62.982 63.158 21.19 0.00 41.24 2.57
838 4761 0.034477 GGAGAAGGGAAAATGGGCGA 60.034 55.000 0.00 0.00 0.00 5.54
844 4769 7.306013 GGGATTAAATAGGGAGAAGGGAAAAT 58.694 38.462 0.00 0.00 0.00 1.82
865 4809 0.695803 ATGGAGAAGGAAGGCGGGAT 60.696 55.000 0.00 0.00 0.00 3.85
886 4864 0.396974 GTGGGGATTGGCAATGGCTA 60.397 55.000 19.07 0.00 40.87 3.93
925 4911 4.249661 GTGGGAACAAGAGATGTCTTCTC 58.750 47.826 1.33 7.51 46.06 2.87
940 4929 1.834263 AGTAGCTGGAGATGTGGGAAC 59.166 52.381 0.00 0.00 0.00 3.62
958 4965 1.488812 TGGTGTGGTTGAGCTTGTAGT 59.511 47.619 0.00 0.00 0.00 2.73
997 6479 2.172483 GACTCCACAGCGTCCATGGT 62.172 60.000 12.58 0.00 34.89 3.55
1161 6649 4.760047 CTGAACTCCCCCGTGGCG 62.760 72.222 0.00 0.00 0.00 5.69
1342 6836 2.092103 AGAGGGACAGAGGCTACTAGTG 60.092 54.545 5.39 0.00 0.00 2.74
1352 6892 5.803552 AGAAGAAAAATCAGAGGGACAGAG 58.196 41.667 0.00 0.00 0.00 3.35
1377 6917 3.266636 TCAGTCTCGCTCAGAGTTAGAG 58.733 50.000 11.27 11.27 46.86 2.43
1378 6918 3.336138 TCAGTCTCGCTCAGAGTTAGA 57.664 47.619 0.00 0.00 46.86 2.10
1379 6919 4.095632 TGATTCAGTCTCGCTCAGAGTTAG 59.904 45.833 0.00 0.00 46.86 2.34
1380 6920 4.010349 TGATTCAGTCTCGCTCAGAGTTA 58.990 43.478 0.00 0.00 46.86 2.24
1381 6921 2.822561 TGATTCAGTCTCGCTCAGAGTT 59.177 45.455 0.00 0.00 46.86 3.01
1382 6922 2.163412 GTGATTCAGTCTCGCTCAGAGT 59.837 50.000 0.00 0.00 46.86 3.24
1416 6972 3.996363 CCCGGCCGTATAAATAAACTACC 59.004 47.826 26.12 0.00 0.00 3.18
1453 7014 3.069300 ACATGATGCTACTGCTACTCCTG 59.931 47.826 0.00 0.00 40.48 3.86
1521 7107 2.097036 TGCCTTGCATTGAGAATGGAG 58.903 47.619 0.00 0.00 40.41 3.86
1561 7147 4.379813 CGTATCTGTTGCCTTGCATTCTTT 60.380 41.667 0.00 0.00 38.76 2.52
1564 7150 2.420022 ACGTATCTGTTGCCTTGCATTC 59.580 45.455 0.00 0.00 38.76 2.67
1590 7176 3.629058 CGAATTCGTCATCTCCGTGTAT 58.371 45.455 19.67 0.00 34.11 2.29
1627 10714 5.072055 TGTTCACAGTTCATCATCCAACAT 58.928 37.500 0.00 0.00 0.00 2.71
1629 10716 5.437289 TTGTTCACAGTTCATCATCCAAC 57.563 39.130 0.00 0.00 0.00 3.77
1682 10769 1.475751 GGGAGATGATTCCACATGCGT 60.476 52.381 0.00 0.00 39.09 5.24
1684 10771 1.233019 CGGGAGATGATTCCACATGC 58.767 55.000 0.00 0.00 39.09 4.06
1686 10773 1.069204 CGACGGGAGATGATTCCACAT 59.931 52.381 0.00 0.00 39.09 3.21
1757 14517 0.966179 GGCAACACCCTTTTACCCAG 59.034 55.000 0.00 0.00 0.00 4.45
1772 14540 2.764010 TCTACTCGCTAATCCTTGGCAA 59.236 45.455 0.00 0.00 36.91 4.52
1776 14544 5.163602 ACTGTTCTCTACTCGCTAATCCTTG 60.164 44.000 0.00 0.00 0.00 3.61
2126 14954 5.634859 CCCATTTCCTTCGTTTGAATTCTTG 59.365 40.000 7.05 0.00 32.61 3.02
2130 14958 3.578282 AGCCCATTTCCTTCGTTTGAATT 59.422 39.130 0.00 0.00 32.61 2.17
2243 15072 3.831911 CCAACCAAATGGCCTTTCTTCTA 59.168 43.478 3.32 0.00 39.32 2.10


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

AutoCloner maintained by Alex Coulton.