Multiple sequence alignment - TraesCS5B01G478600

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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 TraesCS5B01G478600 chr5B 100.000 2518 0 0 1 2518 650165877 650163360 0.000000e+00 4650
1 TraesCS5B01G478600 chr5B 88.235 340 31 8 209 544 643976823 643976489 5.050000e-107 398
2 TraesCS5B01G478600 chr5B 92.308 182 14 0 831 1012 650174107 650173926 2.480000e-65 259
3 TraesCS5B01G478600 chr5D 93.029 1248 55 14 1296 2518 517670739 517669499 0.000000e+00 1794
4 TraesCS5B01G478600 chr5D 93.187 455 23 4 39 493 517672423 517671977 0.000000e+00 662
5 TraesCS5B01G478600 chr5D 87.190 484 32 15 831 1294 517671253 517670780 7.980000e-145 523
6 TraesCS5B01G478600 chr5D 85.586 444 40 15 67 506 513466455 513466032 6.390000e-121 444
7 TraesCS5B01G478600 chr5D 89.286 336 32 4 203 536 512894502 512894169 3.870000e-113 418
8 TraesCS5B01G478600 chr5D 91.246 297 23 2 200 495 499619429 499619135 3.900000e-108 401
9 TraesCS5B01G478600 chr5D 89.308 318 28 6 180 495 425984800 425984487 6.530000e-106 394
10 TraesCS5B01G478600 chr5A 87.097 1116 79 30 831 1906 645125129 645124039 0.000000e+00 1203
11 TraesCS5B01G478600 chr5A 90.909 616 28 10 1903 2518 645124008 645123421 0.000000e+00 802
12 TraesCS5B01G478600 chr5A 92.100 481 25 8 59 532 645126491 645126017 0.000000e+00 665
13 TraesCS5B01G478600 chr5A 83.830 470 49 18 66 530 641117499 641117052 2.990000e-114 422
14 TraesCS5B01G478600 chr5A 89.308 318 28 6 180 495 540263030 540262717 6.530000e-106 394
15 TraesCS5B01G478600 chr4A 86.141 368 36 9 1471 1837 17268836 17269189 1.410000e-102 383
16 TraesCS5B01G478600 chr4D 86.226 363 35 9 1476 1837 446988095 446988443 1.830000e-101 379
17 TraesCS5B01G478600 chr7A 85.598 368 38 9 1471 1837 643995721 643996074 3.060000e-99 372
18 TraesCS5B01G478600 chr2A 85.753 365 37 10 1474 1837 654734806 654734456 3.060000e-99 372
19 TraesCS5B01G478600 chr3A 85.366 369 37 10 1471 1837 157989524 157989877 1.420000e-97 366
20 TraesCS5B01G478600 chr3B 84.511 368 42 9 1471 1837 755564997 755565350 1.430000e-92 350
21 TraesCS5B01G478600 chr2B 84.615 364 43 8 1475 1837 225356707 225356356 1.430000e-92 350


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 TraesCS5B01G478600 chr5B 650163360 650165877 2517 True 4650 4650 100.000000 1 2518 1 chr5B.!!$R2 2517
1 TraesCS5B01G478600 chr5D 517669499 517672423 2924 True 993 1794 91.135333 39 2518 3 chr5D.!!$R5 2479
2 TraesCS5B01G478600 chr5A 645123421 645126491 3070 True 890 1203 90.035333 59 2518 3 chr5A.!!$R3 2459

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
510 578 0.036732 TTGGTCTGGCCTGCTTAGTG 59.963 55.0 3.32 0.0 38.35 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 2695 0.253044 ATCTGTAGCGGTGGCATGTT 59.747 50.0 0.0 0.0 43.41 2.71 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
25 26 8.976986 AAGAGCAATAGTGAATGAACATTTTC 57.023 30.769 0.00 0.00 0.00 2.29
26 27 8.345724 AGAGCAATAGTGAATGAACATTTTCT 57.654 30.769 0.00 6.21 32.36 2.52
27 28 8.800332 AGAGCAATAGTGAATGAACATTTTCTT 58.200 29.630 0.00 0.00 32.36 2.52
28 29 9.415544 GAGCAATAGTGAATGAACATTTTCTTT 57.584 29.630 0.00 0.00 33.04 2.52
29 30 9.768662 AGCAATAGTGAATGAACATTTTCTTTT 57.231 25.926 0.00 3.41 31.07 2.27
164 165 1.385368 ACGTAGTACCTCCCAGCCA 59.615 57.895 0.00 0.00 41.94 4.75
483 488 7.828717 CCCCTGCCAATTCTGTAAAATTAAATT 59.171 33.333 0.00 0.00 0.00 1.82
496 564 9.549078 TGTAAAATTAAATTTTGGTCCTTGGTC 57.451 29.630 0.00 0.00 42.08 4.02
501 569 0.469144 TTTTGGTCCTTGGTCTGGCC 60.469 55.000 0.00 0.00 37.90 5.36
502 570 1.360393 TTTGGTCCTTGGTCTGGCCT 61.360 55.000 3.32 0.00 38.35 5.19
508 576 0.393537 CCTTGGTCTGGCCTGCTTAG 60.394 60.000 3.32 0.00 38.35 2.18
509 577 0.326264 CTTGGTCTGGCCTGCTTAGT 59.674 55.000 3.32 0.00 38.35 2.24
510 578 0.036732 TTGGTCTGGCCTGCTTAGTG 59.963 55.000 3.32 0.00 38.35 2.74
511 579 1.746991 GGTCTGGCCTGCTTAGTGC 60.747 63.158 3.32 0.00 43.25 4.40
526 596 4.441087 GCTTAGTGCAGCTGTTTTTACAAC 59.559 41.667 16.64 1.74 42.31 3.32
532 602 3.316868 GCAGCTGTTTTTACAACCCAGTA 59.683 43.478 16.64 0.00 0.00 2.74
535 605 4.820173 AGCTGTTTTTACAACCCAGTACTC 59.180 41.667 0.00 0.00 0.00 2.59
540 610 2.291209 TACAACCCAGTACTCGGTCA 57.709 50.000 12.97 0.00 0.00 4.02
544 614 0.700564 ACCCAGTACTCGGTCAGGTA 59.299 55.000 6.32 0.00 0.00 3.08
559 636 2.602676 GGTACTGGGAGGCAGCCAA 61.603 63.158 15.80 0.00 0.00 4.52
560 637 1.377333 GTACTGGGAGGCAGCCAAC 60.377 63.158 15.80 7.18 0.00 3.77
561 638 1.845664 TACTGGGAGGCAGCCAACA 60.846 57.895 15.80 8.39 0.00 3.33
562 639 1.841302 TACTGGGAGGCAGCCAACAG 61.841 60.000 21.82 21.82 0.00 3.16
563 640 4.666253 TGGGAGGCAGCCAACAGC 62.666 66.667 15.80 0.00 44.25 4.40
588 665 7.996002 CAAATCTCATTTGTTTTACACCTTCG 58.004 34.615 1.46 0.00 43.47 3.79
589 666 7.504924 AATCTCATTTGTTTTACACCTTCGA 57.495 32.000 0.00 0.00 0.00 3.71
590 667 7.687941 ATCTCATTTGTTTTACACCTTCGAT 57.312 32.000 0.00 0.00 0.00 3.59
591 668 7.129109 TCTCATTTGTTTTACACCTTCGATC 57.871 36.000 0.00 0.00 0.00 3.69
592 669 6.708502 TCTCATTTGTTTTACACCTTCGATCA 59.291 34.615 0.00 0.00 0.00 2.92
593 670 6.664515 TCATTTGTTTTACACCTTCGATCAC 58.335 36.000 0.00 0.00 0.00 3.06
594 671 6.261158 TCATTTGTTTTACACCTTCGATCACA 59.739 34.615 0.00 0.00 0.00 3.58
595 672 5.412526 TTGTTTTACACCTTCGATCACAC 57.587 39.130 0.00 0.00 0.00 3.82
596 673 4.443621 TGTTTTACACCTTCGATCACACA 58.556 39.130 0.00 0.00 0.00 3.72
597 674 5.060506 TGTTTTACACCTTCGATCACACAT 58.939 37.500 0.00 0.00 0.00 3.21
598 675 5.049749 TGTTTTACACCTTCGATCACACATG 60.050 40.000 0.00 0.00 0.00 3.21
599 676 4.529109 TTACACCTTCGATCACACATGA 57.471 40.909 0.00 0.00 39.83 3.07
600 677 3.401033 ACACCTTCGATCACACATGAA 57.599 42.857 0.00 0.00 38.69 2.57
601 678 3.067106 ACACCTTCGATCACACATGAAC 58.933 45.455 0.00 0.00 38.69 3.18
610 687 1.067565 TCACACATGAACGAGAGAGGC 60.068 52.381 0.00 0.00 0.00 4.70
611 688 0.969149 ACACATGAACGAGAGAGGCA 59.031 50.000 0.00 0.00 0.00 4.75
614 691 2.414481 CACATGAACGAGAGAGGCAAAG 59.586 50.000 0.00 0.00 0.00 2.77
622 699 2.548920 CGAGAGAGGCAAAGGTGTTCTT 60.549 50.000 0.00 0.00 37.28 2.52
671 768 4.855340 TGAACTTCTGGTCCAAGTTTTCT 58.145 39.130 9.80 0.00 42.84 2.52
672 769 5.261216 TGAACTTCTGGTCCAAGTTTTCTT 58.739 37.500 9.80 0.00 42.84 2.52
674 771 6.210584 TGAACTTCTGGTCCAAGTTTTCTTTT 59.789 34.615 9.80 0.00 42.84 2.27
689 788 6.691388 AGTTTTCTTTTAGCAACATGAACGAC 59.309 34.615 0.00 0.00 0.00 4.34
690 789 4.742438 TCTTTTAGCAACATGAACGACC 57.258 40.909 0.00 0.00 0.00 4.79
697 796 4.827692 AGCAACATGAACGACCTAACATA 58.172 39.130 0.00 0.00 0.00 2.29
699 798 6.578944 AGCAACATGAACGACCTAACATATA 58.421 36.000 0.00 0.00 0.00 0.86
705 804 9.261180 ACATGAACGACCTAACATATAAATCTG 57.739 33.333 0.00 0.00 0.00 2.90
725 826 3.872696 TGGTGCTGTCAGGTTGTATATG 58.127 45.455 1.14 0.00 0.00 1.78
726 827 3.263170 TGGTGCTGTCAGGTTGTATATGT 59.737 43.478 1.14 0.00 0.00 2.29
739 840 6.655003 AGGTTGTATATGTTGGTGTTCTTCAG 59.345 38.462 0.00 0.00 0.00 3.02
742 843 6.237901 TGTATATGTTGGTGTTCTTCAGCTT 58.762 36.000 0.00 0.00 43.97 3.74
744 845 3.281727 TGTTGGTGTTCTTCAGCTTCT 57.718 42.857 0.00 0.00 43.97 2.85
759 860 3.273919 GCTTCTGCTTACAACCAAGTG 57.726 47.619 0.00 0.00 36.03 3.16
782 883 7.553760 AGTGAAATTTGGCAAGAAATTCACTTT 59.446 29.630 27.52 17.19 38.62 2.66
784 885 8.397148 TGAAATTTGGCAAGAAATTCACTTTTC 58.603 29.630 0.00 0.00 35.01 2.29
785 886 7.862512 AATTTGGCAAGAAATTCACTTTTCA 57.137 28.000 0.00 0.00 37.93 2.69
786 887 6.660887 TTTGGCAAGAAATTCACTTTTCAC 57.339 33.333 0.00 0.00 37.93 3.18
787 888 5.336150 TGGCAAGAAATTCACTTTTCACA 57.664 34.783 0.00 0.00 37.93 3.58
788 889 5.108517 TGGCAAGAAATTCACTTTTCACAC 58.891 37.500 0.00 0.00 37.93 3.82
789 890 4.207019 GGCAAGAAATTCACTTTTCACACG 59.793 41.667 0.00 0.00 37.93 4.49
791 892 4.630894 AGAAATTCACTTTTCACACGCA 57.369 36.364 0.00 0.00 37.93 5.24
792 893 4.601019 AGAAATTCACTTTTCACACGCAG 58.399 39.130 0.00 0.00 37.93 5.18
793 894 4.335315 AGAAATTCACTTTTCACACGCAGA 59.665 37.500 0.00 0.00 37.93 4.26
795 896 4.630894 ATTCACTTTTCACACGCAGAAA 57.369 36.364 0.00 0.00 33.48 2.52
798 899 2.845967 CACTTTTCACACGCAGAAACAC 59.154 45.455 0.00 0.00 34.94 3.32
799 900 2.159435 ACTTTTCACACGCAGAAACACC 60.159 45.455 0.00 0.00 34.94 4.16
800 901 0.736053 TTTCACACGCAGAAACACCC 59.264 50.000 0.00 0.00 30.56 4.61
802 903 0.813610 TCACACGCAGAAACACCCAG 60.814 55.000 0.00 0.00 0.00 4.45
804 905 0.108585 ACACGCAGAAACACCCAGAT 59.891 50.000 0.00 0.00 0.00 2.90
806 907 2.224426 ACACGCAGAAACACCCAGATAA 60.224 45.455 0.00 0.00 0.00 1.75
807 908 2.811431 CACGCAGAAACACCCAGATAAA 59.189 45.455 0.00 0.00 0.00 1.40
808 909 3.440173 CACGCAGAAACACCCAGATAAAT 59.560 43.478 0.00 0.00 0.00 1.40
809 910 4.079253 ACGCAGAAACACCCAGATAAATT 58.921 39.130 0.00 0.00 0.00 1.82
810 911 4.156008 ACGCAGAAACACCCAGATAAATTC 59.844 41.667 0.00 0.00 0.00 2.17
811 912 4.662145 GCAGAAACACCCAGATAAATTCG 58.338 43.478 0.00 0.00 0.00 3.34
812 913 4.394920 GCAGAAACACCCAGATAAATTCGA 59.605 41.667 0.00 0.00 0.00 3.71
813 914 5.447818 GCAGAAACACCCAGATAAATTCGAG 60.448 44.000 0.00 0.00 0.00 4.04
814 915 5.874810 CAGAAACACCCAGATAAATTCGAGA 59.125 40.000 0.00 0.00 0.00 4.04
815 916 6.371548 CAGAAACACCCAGATAAATTCGAGAA 59.628 38.462 0.00 0.00 0.00 2.87
816 917 6.371825 AGAAACACCCAGATAAATTCGAGAAC 59.628 38.462 0.00 0.00 0.00 3.01
817 918 5.422214 ACACCCAGATAAATTCGAGAACT 57.578 39.130 0.00 0.00 0.00 3.01
818 919 5.805728 ACACCCAGATAAATTCGAGAACTT 58.194 37.500 0.00 0.00 0.00 2.66
819 920 6.238648 ACACCCAGATAAATTCGAGAACTTT 58.761 36.000 0.00 0.00 0.00 2.66
869 1641 1.376037 CTGCCACGGAAGGGAAGAC 60.376 63.158 0.00 0.00 35.60 3.01
894 1666 1.825622 GCTGGCTGGTGGATAAGGC 60.826 63.158 0.00 0.00 39.33 4.35
988 1764 0.250467 CTCCACACAGACCAACCCAG 60.250 60.000 0.00 0.00 0.00 4.45
994 1770 0.466189 ACAGACCAACCCAGCAACAG 60.466 55.000 0.00 0.00 0.00 3.16
1077 1865 3.464494 ACTACCCCGCTTACGCCC 61.464 66.667 0.00 0.00 38.22 6.13
1079 1867 3.001994 TACCCCGCTTACGCCCAA 61.002 61.111 0.00 0.00 38.22 4.12
1131 1919 4.292178 CGCTCCAGGATCTCCGCC 62.292 72.222 0.00 0.00 42.08 6.13
1190 1978 3.443037 TGTTGCATTTTGTTTGAGTCCG 58.557 40.909 0.00 0.00 0.00 4.79
1199 1989 3.241067 TGTTTGAGTCCGTATGCTACC 57.759 47.619 0.00 0.00 0.00 3.18
1201 1991 1.855295 TTGAGTCCGTATGCTACCCA 58.145 50.000 0.00 0.00 0.00 4.51
1220 2013 2.106338 CCATGTATATGCAGGTGGTGGA 59.894 50.000 4.77 0.00 32.79 4.02
1229 2025 3.175710 GGTGGTGGAGGTGGTGGT 61.176 66.667 0.00 0.00 0.00 4.16
1294 2090 1.625818 ACAGGAACCAGAGCAGTAAGG 59.374 52.381 0.00 0.00 0.00 2.69
1302 2138 3.055530 ACCAGAGCAGTAAGGATGAGTTG 60.056 47.826 0.00 0.00 0.00 3.16
1316 2152 4.937620 GGATGAGTTGATGTATGTGTGTGT 59.062 41.667 0.00 0.00 0.00 3.72
1317 2153 5.163824 GGATGAGTTGATGTATGTGTGTGTG 60.164 44.000 0.00 0.00 0.00 3.82
1323 2160 1.304254 TGTATGTGTGTGTGTGTGGC 58.696 50.000 0.00 0.00 0.00 5.01
1433 2271 4.096003 ACGCCGCTGCCCTACATT 62.096 61.111 0.00 0.00 0.00 2.71
1524 2362 2.113767 CTCATCCGCTGAGCTCTCA 58.886 57.895 16.19 0.00 44.73 3.27
1535 2373 2.128853 GAGCTCTCATCGGGCTCTCG 62.129 65.000 6.43 0.00 46.04 4.04
1575 2413 3.134442 AGAGAGATGATGACTTGCTTCCC 59.866 47.826 0.00 0.00 0.00 3.97
1620 2462 8.492673 AAGCTGTATGTAATTCATTTCTTCGA 57.507 30.769 0.00 0.00 37.91 3.71
1669 2515 1.202154 GCTCTGCATTCATGACTGCAC 60.202 52.381 30.35 19.89 43.11 4.57
1675 2521 1.741706 CATTCATGACTGCACCTGGTC 59.258 52.381 0.00 0.00 0.00 4.02
1676 2522 1.059098 TTCATGACTGCACCTGGTCT 58.941 50.000 0.00 0.00 34.01 3.85
1762 2608 3.165058 TCGATCGATCAAGAAACTGGG 57.835 47.619 24.40 4.90 0.00 4.45
1849 2695 9.830975 AATCTACACATAAGCACATACAATACA 57.169 29.630 0.00 0.00 0.00 2.29
1877 2723 3.119291 CACCGCTACAGATTCATCTCAC 58.881 50.000 0.00 0.00 34.22 3.51
1890 2754 5.385509 TTCATCTCACGTCAGACATACAA 57.614 39.130 0.00 0.00 0.00 2.41
1891 2755 4.733850 TCATCTCACGTCAGACATACAAC 58.266 43.478 0.00 0.00 0.00 3.32
1892 2756 4.217550 TCATCTCACGTCAGACATACAACA 59.782 41.667 0.00 0.00 0.00 3.33
1893 2757 4.577834 TCTCACGTCAGACATACAACAA 57.422 40.909 0.41 0.00 0.00 2.83
1895 2759 4.743151 TCTCACGTCAGACATACAACAAAC 59.257 41.667 0.41 0.00 0.00 2.93
1896 2760 4.434520 TCACGTCAGACATACAACAAACA 58.565 39.130 0.41 0.00 0.00 2.83
1898 2762 4.961551 CACGTCAGACATACAACAAACAAC 59.038 41.667 0.41 0.00 0.00 3.32
1899 2763 4.873827 ACGTCAGACATACAACAAACAACT 59.126 37.500 0.41 0.00 0.00 3.16
1901 2765 6.535865 ACGTCAGACATACAACAAACAACTAA 59.464 34.615 0.41 0.00 0.00 2.24
2003 2883 3.301835 CGCAGCAGTATACAGTTAAAGCG 60.302 47.826 5.50 7.50 0.00 4.68
2065 2945 2.618053 CGCGGTTTCCTATCAAACTCT 58.382 47.619 0.00 0.00 36.62 3.24
2101 2981 4.717629 TCAAGCCAGTCGCGACGG 62.718 66.667 31.92 31.92 44.76 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.800332 AGAAAATGTTCATTCACTATTGCTCTT 58.200 29.630 0.00 0.00 36.09 2.85
1 2 8.345724 AGAAAATGTTCATTCACTATTGCTCT 57.654 30.769 0.00 0.00 36.09 4.09
2 3 8.976986 AAGAAAATGTTCATTCACTATTGCTC 57.023 30.769 0.00 0.00 36.09 4.26
3 4 9.768662 AAAAGAAAATGTTCATTCACTATTGCT 57.231 25.926 0.00 0.00 36.09 3.91
45 46 8.478066 AGCTTTTTCCTAGTTTTCTGTTCATTT 58.522 29.630 0.00 0.00 0.00 2.32
48 49 6.680378 GCAGCTTTTTCCTAGTTTTCTGTTCA 60.680 38.462 0.00 0.00 0.00 3.18
51 52 4.889995 AGCAGCTTTTTCCTAGTTTTCTGT 59.110 37.500 0.00 0.00 0.00 3.41
57 58 3.335579 CCGTAGCAGCTTTTTCCTAGTT 58.664 45.455 0.00 0.00 0.00 2.24
61 62 0.036875 AGCCGTAGCAGCTTTTTCCT 59.963 50.000 0.00 0.00 43.56 3.36
211 216 1.264826 GGACTAAAAACCGAAGCGCAA 59.735 47.619 11.47 0.00 0.00 4.85
357 362 1.005867 CAAGTGCAATGTGGGCCAC 60.006 57.895 29.75 29.75 34.56 5.01
471 476 9.772973 AGACCAAGGACCAAAATTTAATTTTAC 57.227 29.630 14.28 9.44 40.27 2.01
473 478 7.719193 CCAGACCAAGGACCAAAATTTAATTTT 59.281 33.333 9.58 9.58 42.81 1.82
483 488 1.152830 GGCCAGACCAAGGACCAAA 59.847 57.895 0.00 0.00 38.86 3.28
493 561 1.746991 GCACTAAGCAGGCCAGACC 60.747 63.158 5.01 0.00 44.79 3.85
508 576 2.159170 TGGGTTGTAAAAACAGCTGCAC 60.159 45.455 15.27 4.89 0.00 4.57
509 577 2.100584 CTGGGTTGTAAAAACAGCTGCA 59.899 45.455 15.27 0.00 0.00 4.41
510 578 2.100749 ACTGGGTTGTAAAAACAGCTGC 59.899 45.455 15.27 0.00 35.85 5.25
511 579 4.578928 AGTACTGGGTTGTAAAAACAGCTG 59.421 41.667 13.48 13.48 35.85 4.24
512 580 4.788679 AGTACTGGGTTGTAAAAACAGCT 58.211 39.130 0.00 0.00 35.85 4.24
515 583 4.128643 CCGAGTACTGGGTTGTAAAAACA 58.871 43.478 15.41 0.00 0.00 2.83
516 584 4.129380 ACCGAGTACTGGGTTGTAAAAAC 58.871 43.478 22.69 0.00 38.61 2.43
517 585 4.141756 TGACCGAGTACTGGGTTGTAAAAA 60.142 41.667 27.86 7.95 41.92 1.94
526 596 1.101331 GTACCTGACCGAGTACTGGG 58.899 60.000 21.30 21.30 36.69 4.45
532 602 0.323542 CTCCCAGTACCTGACCGAGT 60.324 60.000 0.00 0.00 32.44 4.18
535 605 2.722201 GCCTCCCAGTACCTGACCG 61.722 68.421 0.00 0.00 32.44 4.79
540 610 2.689034 GGCTGCCTCCCAGTACCT 60.689 66.667 12.43 0.00 43.71 3.08
544 614 3.177884 TGTTGGCTGCCTCCCAGT 61.178 61.111 21.03 0.00 43.71 4.00
547 617 4.666253 TGCTGTTGGCTGCCTCCC 62.666 66.667 21.03 7.98 42.39 4.30
549 626 0.108945 GATTTGCTGTTGGCTGCCTC 60.109 55.000 21.03 13.25 42.39 4.70
551 628 0.108945 GAGATTTGCTGTTGGCTGCC 60.109 55.000 12.87 12.87 42.39 4.85
552 629 0.599558 TGAGATTTGCTGTTGGCTGC 59.400 50.000 0.00 0.00 42.39 5.25
553 630 3.587797 AATGAGATTTGCTGTTGGCTG 57.412 42.857 0.00 0.00 42.39 4.85
554 631 3.921677 CAAATGAGATTTGCTGTTGGCT 58.078 40.909 0.00 0.00 42.57 4.75
564 641 7.936584 TCGAAGGTGTAAAACAAATGAGATTT 58.063 30.769 0.00 0.00 0.00 2.17
565 642 7.504924 TCGAAGGTGTAAAACAAATGAGATT 57.495 32.000 0.00 0.00 0.00 2.40
566 643 7.390440 TGATCGAAGGTGTAAAACAAATGAGAT 59.610 33.333 0.00 0.00 0.00 2.75
567 644 6.708502 TGATCGAAGGTGTAAAACAAATGAGA 59.291 34.615 0.00 0.00 0.00 3.27
568 645 6.797033 GTGATCGAAGGTGTAAAACAAATGAG 59.203 38.462 0.00 0.00 0.00 2.90
569 646 6.261158 TGTGATCGAAGGTGTAAAACAAATGA 59.739 34.615 0.00 0.00 0.00 2.57
570 647 6.359617 GTGTGATCGAAGGTGTAAAACAAATG 59.640 38.462 0.00 0.00 0.00 2.32
571 648 6.038825 TGTGTGATCGAAGGTGTAAAACAAAT 59.961 34.615 0.00 0.00 0.00 2.32
572 649 5.354513 TGTGTGATCGAAGGTGTAAAACAAA 59.645 36.000 0.00 0.00 0.00 2.83
573 650 4.876679 TGTGTGATCGAAGGTGTAAAACAA 59.123 37.500 0.00 0.00 0.00 2.83
574 651 4.443621 TGTGTGATCGAAGGTGTAAAACA 58.556 39.130 0.00 0.00 0.00 2.83
575 652 5.178623 TCATGTGTGATCGAAGGTGTAAAAC 59.821 40.000 0.00 0.00 0.00 2.43
576 653 5.301555 TCATGTGTGATCGAAGGTGTAAAA 58.698 37.500 0.00 0.00 0.00 1.52
577 654 4.888917 TCATGTGTGATCGAAGGTGTAAA 58.111 39.130 0.00 0.00 0.00 2.01
578 655 4.529109 TCATGTGTGATCGAAGGTGTAA 57.471 40.909 0.00 0.00 0.00 2.41
579 656 4.242475 GTTCATGTGTGATCGAAGGTGTA 58.758 43.478 0.00 0.00 33.56 2.90
580 657 3.067106 GTTCATGTGTGATCGAAGGTGT 58.933 45.455 0.00 0.00 33.56 4.16
581 658 2.092681 CGTTCATGTGTGATCGAAGGTG 59.907 50.000 0.00 0.00 45.72 4.00
582 659 2.337583 CGTTCATGTGTGATCGAAGGT 58.662 47.619 0.00 0.00 45.72 3.50
587 664 3.104470 CTCTCTCGTTCATGTGTGATCG 58.896 50.000 0.00 3.27 44.76 3.69
588 665 3.443037 CCTCTCTCGTTCATGTGTGATC 58.557 50.000 0.00 0.00 33.56 2.92
589 666 2.417924 GCCTCTCTCGTTCATGTGTGAT 60.418 50.000 0.00 0.00 33.56 3.06
590 667 1.067565 GCCTCTCTCGTTCATGTGTGA 60.068 52.381 0.00 0.00 0.00 3.58
591 668 1.337167 TGCCTCTCTCGTTCATGTGTG 60.337 52.381 0.00 0.00 0.00 3.82
592 669 0.969149 TGCCTCTCTCGTTCATGTGT 59.031 50.000 0.00 0.00 0.00 3.72
593 670 2.084610 TTGCCTCTCTCGTTCATGTG 57.915 50.000 0.00 0.00 0.00 3.21
594 671 2.613977 CCTTTGCCTCTCTCGTTCATGT 60.614 50.000 0.00 0.00 0.00 3.21
595 672 2.005451 CCTTTGCCTCTCTCGTTCATG 58.995 52.381 0.00 0.00 0.00 3.07
596 673 1.625818 ACCTTTGCCTCTCTCGTTCAT 59.374 47.619 0.00 0.00 0.00 2.57
597 674 1.048601 ACCTTTGCCTCTCTCGTTCA 58.951 50.000 0.00 0.00 0.00 3.18
598 675 1.270358 ACACCTTTGCCTCTCTCGTTC 60.270 52.381 0.00 0.00 0.00 3.95
599 676 0.759346 ACACCTTTGCCTCTCTCGTT 59.241 50.000 0.00 0.00 0.00 3.85
600 677 0.759346 AACACCTTTGCCTCTCTCGT 59.241 50.000 0.00 0.00 0.00 4.18
601 678 1.001406 AGAACACCTTTGCCTCTCTCG 59.999 52.381 0.00 0.00 0.00 4.04
602 679 2.849294 AGAACACCTTTGCCTCTCTC 57.151 50.000 0.00 0.00 0.00 3.20
603 680 3.584733 AAAGAACACCTTTGCCTCTCT 57.415 42.857 0.00 0.00 43.10 3.10
611 688 4.799564 TGTTTGCTCAAAGAACACCTTT 57.200 36.364 0.00 0.00 45.48 3.11
614 691 5.854431 TTTTTGTTTGCTCAAAGAACACC 57.146 34.783 4.69 0.00 38.32 4.16
637 714 6.040504 GGACCAGAAGTTCAAACCATTACTTT 59.959 38.462 5.50 0.00 31.41 2.66
641 718 5.055265 TGGACCAGAAGTTCAAACCATTA 57.945 39.130 5.50 0.00 27.78 1.90
642 719 3.909732 TGGACCAGAAGTTCAAACCATT 58.090 40.909 5.50 0.00 27.78 3.16
643 720 3.593442 TGGACCAGAAGTTCAAACCAT 57.407 42.857 5.50 0.00 27.78 3.55
645 722 3.288092 ACTTGGACCAGAAGTTCAAACC 58.712 45.455 5.50 3.87 43.63 3.27
646 723 4.983671 AACTTGGACCAGAAGTTCAAAC 57.016 40.909 5.50 0.00 43.63 2.93
659 756 6.978080 TCATGTTGCTAAAAGAAAACTTGGAC 59.022 34.615 0.00 0.00 31.90 4.02
671 768 5.527951 TGTTAGGTCGTTCATGTTGCTAAAA 59.472 36.000 0.00 0.00 0.00 1.52
672 769 5.057819 TGTTAGGTCGTTCATGTTGCTAAA 58.942 37.500 0.00 0.00 0.00 1.85
674 771 4.260139 TGTTAGGTCGTTCATGTTGCTA 57.740 40.909 0.00 0.00 0.00 3.49
689 788 6.992123 TGACAGCACCAGATTTATATGTTAGG 59.008 38.462 0.00 0.00 0.00 2.69
690 789 7.172190 CCTGACAGCACCAGATTTATATGTTAG 59.828 40.741 0.00 0.00 33.65 2.34
697 796 4.012374 CAACCTGACAGCACCAGATTTAT 58.988 43.478 0.00 0.00 33.65 1.40
699 798 2.233271 CAACCTGACAGCACCAGATTT 58.767 47.619 0.00 0.00 33.65 2.17
705 804 3.873910 ACATATACAACCTGACAGCACC 58.126 45.455 0.00 0.00 0.00 5.01
725 826 2.287248 GCAGAAGCTGAAGAACACCAAC 60.287 50.000 0.00 0.00 37.91 3.77
726 827 1.949525 GCAGAAGCTGAAGAACACCAA 59.050 47.619 0.00 0.00 37.91 3.67
739 840 2.878406 TCACTTGGTTGTAAGCAGAAGC 59.122 45.455 0.00 0.00 37.74 3.86
742 843 6.272318 CAAATTTCACTTGGTTGTAAGCAGA 58.728 36.000 0.00 0.00 37.74 4.26
744 845 5.355596 CCAAATTTCACTTGGTTGTAAGCA 58.644 37.500 0.00 0.00 38.85 3.91
754 855 7.011669 AGTGAATTTCTTGCCAAATTTCACTTG 59.988 33.333 17.95 0.00 38.82 3.16
759 860 8.397148 TGAAAAGTGAATTTCTTGCCAAATTTC 58.603 29.630 0.00 0.00 39.51 2.17
771 872 4.597079 TCTGCGTGTGAAAAGTGAATTTC 58.403 39.130 0.00 0.00 39.28 2.17
782 883 0.393132 TGGGTGTTTCTGCGTGTGAA 60.393 50.000 0.00 0.00 0.00 3.18
784 885 0.813610 TCTGGGTGTTTCTGCGTGTG 60.814 55.000 0.00 0.00 0.00 3.82
785 886 0.108585 ATCTGGGTGTTTCTGCGTGT 59.891 50.000 0.00 0.00 0.00 4.49
786 887 2.093306 TATCTGGGTGTTTCTGCGTG 57.907 50.000 0.00 0.00 0.00 5.34
787 888 2.851263 TTATCTGGGTGTTTCTGCGT 57.149 45.000 0.00 0.00 0.00 5.24
788 889 4.662145 GAATTTATCTGGGTGTTTCTGCG 58.338 43.478 0.00 0.00 0.00 5.18
789 890 4.394920 TCGAATTTATCTGGGTGTTTCTGC 59.605 41.667 0.00 0.00 0.00 4.26
791 892 6.049955 TCTCGAATTTATCTGGGTGTTTCT 57.950 37.500 0.00 0.00 0.00 2.52
792 893 6.371825 AGTTCTCGAATTTATCTGGGTGTTTC 59.628 38.462 0.00 0.00 0.00 2.78
793 894 6.238648 AGTTCTCGAATTTATCTGGGTGTTT 58.761 36.000 0.00 0.00 0.00 2.83
795 896 5.422214 AGTTCTCGAATTTATCTGGGTGT 57.578 39.130 0.00 0.00 0.00 4.16
823 924 9.862371 TTTAAGTTCTTGAATTTACAGTTGCAA 57.138 25.926 0.00 0.00 0.00 4.08
829 1601 9.346725 GGCAGATTTAAGTTCTTGAATTTACAG 57.653 33.333 4.53 0.00 0.00 2.74
869 1641 3.663176 CACCAGCCAGCCGTGTTG 61.663 66.667 0.47 0.00 0.00 3.33
1077 1865 2.510238 CCGGCGCCTCTCTTCTTG 60.510 66.667 26.68 4.88 0.00 3.02
1190 1978 5.118990 CCTGCATATACATGGGTAGCATAC 58.881 45.833 0.00 0.00 35.11 2.39
1199 1989 2.106338 TCCACCACCTGCATATACATGG 59.894 50.000 0.00 0.00 32.36 3.66
1201 1991 2.373169 CCTCCACCACCTGCATATACAT 59.627 50.000 0.00 0.00 0.00 2.29
1220 2013 0.117140 TCTCTCCATCACCACCACCT 59.883 55.000 0.00 0.00 0.00 4.00
1229 2025 0.907486 CAGGCTTGGTCTCTCCATCA 59.093 55.000 0.00 0.00 46.60 3.07
1294 2090 5.409520 ACACACACACATACATCAACTCATC 59.590 40.000 0.00 0.00 0.00 2.92
1302 2138 2.095768 GCCACACACACACACATACATC 60.096 50.000 0.00 0.00 0.00 3.06
1323 2160 1.347050 TCCACACCATTTGGCAATTGG 59.653 47.619 29.99 29.99 39.32 3.16
1385 2223 4.089757 TCCCCCTTCCTCTCCCCG 62.090 72.222 0.00 0.00 0.00 5.73
1433 2271 1.066858 GTGGAGAAGCCGAAGATGACA 60.067 52.381 0.00 0.00 40.66 3.58
1522 2360 1.379977 AAGGACGAGAGCCCGATGA 60.380 57.895 0.00 0.00 39.40 2.92
1523 2361 1.066587 GAAGGACGAGAGCCCGATG 59.933 63.158 0.00 0.00 39.40 3.84
1524 2362 2.128507 GGAAGGACGAGAGCCCGAT 61.129 63.158 0.00 0.00 39.40 4.18
1528 2366 1.962321 GAAGGGGAAGGACGAGAGCC 61.962 65.000 0.00 0.00 0.00 4.70
1619 2461 8.861086 TGGTGACTCCACTATATAAAGATCTTC 58.139 37.037 8.78 0.00 41.93 2.87
1620 2462 8.783660 TGGTGACTCCACTATATAAAGATCTT 57.216 34.615 0.88 0.88 41.93 2.40
1645 2487 1.065345 AGTCATGAATGCAGAGCAGCT 60.065 47.619 0.00 0.00 43.65 4.24
1669 2515 4.944619 TCACTCTATATGCAAGACCAGG 57.055 45.455 0.00 0.00 0.00 4.45
1675 2521 5.008415 CAGGGCTTTTCACTCTATATGCAAG 59.992 44.000 0.00 0.00 0.00 4.01
1676 2522 4.883585 CAGGGCTTTTCACTCTATATGCAA 59.116 41.667 0.00 0.00 0.00 4.08
1789 2635 4.688413 TGGTTGAAATTTTTAATCGCTGGC 59.312 37.500 0.00 0.00 0.00 4.85
1795 2641 6.934083 TGCCTCCTTGGTTGAAATTTTTAATC 59.066 34.615 0.00 0.00 38.35 1.75
1797 2643 6.240549 TGCCTCCTTGGTTGAAATTTTTAA 57.759 33.333 0.00 0.00 38.35 1.52
1800 2646 4.408596 TCTTGCCTCCTTGGTTGAAATTTT 59.591 37.500 0.00 0.00 38.35 1.82
1849 2695 0.253044 ATCTGTAGCGGTGGCATGTT 59.747 50.000 0.00 0.00 43.41 2.71
1877 2723 5.403897 AGTTGTTTGTTGTATGTCTGACG 57.596 39.130 2.98 0.00 0.00 4.35
1890 2754 8.927675 TGGTATTCTATGGTTTAGTTGTTTGT 57.072 30.769 0.00 0.00 0.00 2.83
1893 2757 8.966868 CCAATGGTATTCTATGGTTTAGTTGTT 58.033 33.333 0.00 0.00 0.00 2.83
1895 2759 7.285401 AGCCAATGGTATTCTATGGTTTAGTTG 59.715 37.037 0.00 0.00 0.00 3.16
1896 2760 7.354312 AGCCAATGGTATTCTATGGTTTAGTT 58.646 34.615 0.00 0.00 0.00 2.24
1898 2762 9.520515 AATAGCCAATGGTATTCTATGGTTTAG 57.479 33.333 0.00 0.00 40.25 1.85
1899 2763 9.875708 AAATAGCCAATGGTATTCTATGGTTTA 57.124 29.630 0.00 0.00 42.71 2.01
1901 2765 8.227507 AGAAATAGCCAATGGTATTCTATGGTT 58.772 33.333 0.00 0.00 42.71 3.67
1975 2855 1.273606 CTGTATACTGCTGCGGGCTAT 59.726 52.381 13.87 5.22 42.39 2.97
1982 2862 3.617263 ACGCTTTAACTGTATACTGCTGC 59.383 43.478 9.48 0.00 0.00 5.25
2003 2883 0.593773 ATGTGTCCGTTTGCGCAAAC 60.594 50.000 42.11 42.11 45.25 2.93
2065 2945 1.040893 ACCCACACTGTCGTGAGTCA 61.041 55.000 10.56 0.00 43.97 3.41
2101 2981 2.115291 GGGCATGGCGAAGAGTTCC 61.115 63.158 13.76 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.