Multiple sequence alignment - TraesCS5A01G048000

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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 TraesCS5A01G048000 chr5A 100.000 2216 0 0 1 2216 44091911 44094126 0.000000e+00 4093
1 TraesCS5A01G048000 chr5A 98.512 1075 16 0 458 1532 129595600 129596674 0.000000e+00 1897
2 TraesCS5A01G048000 chr5A 98.482 461 7 0 1 461 129595501 129595961 0.000000e+00 813
3 TraesCS5A01G048000 chr5A 95.445 461 21 0 1 461 33168351 33168811 0.000000e+00 736
4 TraesCS5A01G048000 chr5A 99.724 362 1 0 458 819 44092010 44092371 0.000000e+00 664
5 TraesCS5A01G048000 chr5A 94.363 408 21 1 458 863 33168450 33168857 1.870000e-175 625
6 TraesCS5A01G048000 chr4B 98.699 1076 14 0 458 1533 251997282 251998357 0.000000e+00 1910
7 TraesCS5A01G048000 chr4B 98.420 1076 17 0 458 1533 395243816 395244891 0.000000e+00 1893
8 TraesCS5A01G048000 chr4B 98.915 461 5 0 1 461 251997183 251997643 0.000000e+00 824
9 TraesCS5A01G048000 chr4B 98.698 461 6 0 1 461 395243717 395244177 0.000000e+00 819
10 TraesCS5A01G048000 chr4B 93.284 134 9 0 869 1002 564154017 564154150 4.830000e-47 198
11 TraesCS5A01G048000 chr7A 96.735 1072 35 0 461 1532 16637659 16636588 0.000000e+00 1786
12 TraesCS5A01G048000 chr7A 96.459 593 20 1 941 1532 16636587 16635995 0.000000e+00 977
13 TraesCS5A01G048000 chr7A 98.052 462 8 1 1 461 16637762 16637301 0.000000e+00 802
14 TraesCS5A01G048000 chr2A 98.015 806 16 0 736 1541 442717682 442716877 0.000000e+00 1400
15 TraesCS5A01G048000 chr2A 98.390 559 9 0 975 1533 442716885 442716327 0.000000e+00 983
16 TraesCS5A01G048000 chr2A 98.488 463 5 1 1 461 442718234 442717772 0.000000e+00 815
17 TraesCS5A01G048000 chr2A 99.107 448 4 0 461 908 442718130 442717683 0.000000e+00 806
18 TraesCS5A01G048000 chr2A 94.574 129 7 0 869 997 565266123 565265995 1.340000e-47 200
19 TraesCS5A01G048000 chr5B 90.000 710 45 8 1532 2216 57959220 57959928 0.000000e+00 894
20 TraesCS5A01G048000 chr5B 93.989 549 31 2 996 1542 492815934 492815386 0.000000e+00 830
21 TraesCS5A01G048000 chr5B 88.871 638 43 9 1532 2143 57924077 57924712 0.000000e+00 760
22 TraesCS5A01G048000 chr5D 88.669 706 55 8 1535 2216 55060771 55061475 0.000000e+00 837
23 TraesCS5A01G048000 chr3A 94.424 538 30 0 996 1533 27583464 27584001 0.000000e+00 828
24 TraesCS5A01G048000 chr3A 94.321 405 20 2 461 863 675319130 675318727 3.130000e-173 617
25 TraesCS5A01G048000 chr7B 95.879 461 19 0 1 461 226421160 226421620 0.000000e+00 747
26 TraesCS5A01G048000 chr7B 94.853 408 19 1 458 863 226421259 226421666 8.630000e-179 636
27 TraesCS5A01G048000 chr3B 94.828 464 21 1 1 461 12307959 12308422 0.000000e+00 721
28 TraesCS5A01G048000 chr3B 94.574 129 7 0 869 997 669726872 669726744 1.340000e-47 200
29 TraesCS5A01G048000 chr1A 94.794 461 24 0 1 461 82715802 82715342 0.000000e+00 719
30 TraesCS5A01G048000 chr6B 93.798 129 8 0 869 997 127740601 127740473 6.240000e-46 195


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 TraesCS5A01G048000 chr5A 44091911 44094126 2215 False 2378.500000 4093 99.862 1 2216 2 chr5A.!!$F2 2215
1 TraesCS5A01G048000 chr5A 129595501 129596674 1173 False 1355.000000 1897 98.497 1 1532 2 chr5A.!!$F3 1531
2 TraesCS5A01G048000 chr5A 33168351 33168857 506 False 680.500000 736 94.904 1 863 2 chr5A.!!$F1 862
3 TraesCS5A01G048000 chr4B 251997183 251998357 1174 False 1367.000000 1910 98.807 1 1533 2 chr4B.!!$F2 1532
4 TraesCS5A01G048000 chr4B 395243717 395244891 1174 False 1356.000000 1893 98.559 1 1533 2 chr4B.!!$F3 1532
5 TraesCS5A01G048000 chr7A 16635995 16637762 1767 True 1188.333333 1786 97.082 1 1532 3 chr7A.!!$R1 1531
6 TraesCS5A01G048000 chr2A 442716327 442718234 1907 True 1001.000000 1400 98.500 1 1541 4 chr2A.!!$R2 1540
7 TraesCS5A01G048000 chr5B 57959220 57959928 708 False 894.000000 894 90.000 1532 2216 1 chr5B.!!$F2 684
8 TraesCS5A01G048000 chr5B 492815386 492815934 548 True 830.000000 830 93.989 996 1542 1 chr5B.!!$R1 546
9 TraesCS5A01G048000 chr5B 57924077 57924712 635 False 760.000000 760 88.871 1532 2143 1 chr5B.!!$F1 611
10 TraesCS5A01G048000 chr5D 55060771 55061475 704 False 837.000000 837 88.669 1535 2216 1 chr5D.!!$F1 681
11 TraesCS5A01G048000 chr3A 27583464 27584001 537 False 828.000000 828 94.424 996 1533 1 chr3A.!!$F1 537
12 TraesCS5A01G048000 chr7B 226421160 226421666 506 False 691.500000 747 95.366 1 863 2 chr7B.!!$F1 862

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
491 494 1.116308 TGCCTTACGGTGCAGCTATA 58.884 50.0 14.92 3.47 32.77 1.31 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1352 2122 1.228215 TGACCGTACTCCACCGTGA 60.228 57.895 0.0 0.0 0.0 4.35 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
445 448 3.761897 TGCTTTGGCAACCATACTAACT 58.238 40.909 0.00 0.00 46.36 2.24
446 449 4.148838 TGCTTTGGCAACCATACTAACTT 58.851 39.130 0.00 0.00 46.36 2.66
447 450 5.317808 TGCTTTGGCAACCATACTAACTTA 58.682 37.500 0.00 0.00 46.36 2.24
448 451 5.182380 TGCTTTGGCAACCATACTAACTTAC 59.818 40.000 0.00 0.00 46.36 2.34
449 452 5.182380 GCTTTGGCAACCATACTAACTTACA 59.818 40.000 0.00 0.00 38.54 2.41
450 453 6.294286 GCTTTGGCAACCATACTAACTTACAA 60.294 38.462 0.00 0.00 38.54 2.41
451 454 7.576856 GCTTTGGCAACCATACTAACTTACAAT 60.577 37.037 0.00 0.00 38.54 2.71
452 455 6.751514 TGGCAACCATACTAACTTACAATG 57.248 37.500 0.00 0.00 0.00 2.82
453 456 5.124776 TGGCAACCATACTAACTTACAATGC 59.875 40.000 0.00 0.00 0.00 3.56
454 457 5.357032 GGCAACCATACTAACTTACAATGCT 59.643 40.000 0.00 0.00 0.00 3.79
455 458 6.258160 GCAACCATACTAACTTACAATGCTG 58.742 40.000 0.00 0.00 0.00 4.41
456 459 6.128007 GCAACCATACTAACTTACAATGCTGT 60.128 38.462 0.00 0.00 39.75 4.40
457 460 7.065324 GCAACCATACTAACTTACAATGCTGTA 59.935 37.037 0.00 0.00 36.96 2.74
458 461 8.941977 CAACCATACTAACTTACAATGCTGTAA 58.058 33.333 0.00 0.00 44.10 2.41
474 477 9.065871 CAATGCTGTAAGAAAAGTATAAACTGC 57.934 33.333 0.00 0.00 32.87 4.40
475 478 7.141100 TGCTGTAAGAAAAGTATAAACTGCC 57.859 36.000 0.00 0.00 32.87 4.85
476 479 6.940298 TGCTGTAAGAAAAGTATAAACTGCCT 59.060 34.615 0.00 0.00 32.87 4.75
477 480 7.447238 TGCTGTAAGAAAAGTATAAACTGCCTT 59.553 33.333 0.00 0.00 32.87 4.35
478 481 8.943002 GCTGTAAGAAAAGTATAAACTGCCTTA 58.057 33.333 0.00 0.00 32.87 2.69
480 483 8.928733 TGTAAGAAAAGTATAAACTGCCTTACG 58.071 33.333 0.00 0.00 40.70 3.18
481 484 6.980051 AGAAAAGTATAAACTGCCTTACGG 57.020 37.500 0.00 0.00 35.62 4.02
482 485 6.470278 AGAAAAGTATAAACTGCCTTACGGT 58.530 36.000 0.00 0.00 40.66 4.83
483 486 6.370718 AGAAAAGTATAAACTGCCTTACGGTG 59.629 38.462 0.00 0.00 38.15 4.94
484 487 3.528532 AGTATAAACTGCCTTACGGTGC 58.471 45.455 0.00 0.00 38.15 5.01
485 488 2.483014 ATAAACTGCCTTACGGTGCA 57.517 45.000 0.00 0.00 38.15 4.57
489 492 3.383229 TGCCTTACGGTGCAGCTA 58.617 55.556 14.92 2.76 32.77 3.32
490 493 1.904771 TGCCTTACGGTGCAGCTAT 59.095 52.632 14.92 4.52 32.77 2.97
491 494 1.116308 TGCCTTACGGTGCAGCTATA 58.884 50.000 14.92 3.47 32.77 1.31
492 495 1.691976 TGCCTTACGGTGCAGCTATAT 59.308 47.619 14.92 0.00 32.77 0.86
493 496 2.104111 TGCCTTACGGTGCAGCTATATT 59.896 45.455 14.92 0.00 32.77 1.28
494 497 2.480419 GCCTTACGGTGCAGCTATATTG 59.520 50.000 14.92 0.00 0.00 1.90
495 498 3.728845 CCTTACGGTGCAGCTATATTGT 58.271 45.455 14.92 5.73 0.00 2.71
496 499 4.127171 CCTTACGGTGCAGCTATATTGTT 58.873 43.478 14.92 0.00 0.00 2.83
497 500 4.211374 CCTTACGGTGCAGCTATATTGTTC 59.789 45.833 14.92 0.00 0.00 3.18
498 501 3.260475 ACGGTGCAGCTATATTGTTCA 57.740 42.857 14.92 0.00 0.00 3.18
499 502 3.605634 ACGGTGCAGCTATATTGTTCAA 58.394 40.909 14.92 0.00 0.00 2.69
500 503 3.623060 ACGGTGCAGCTATATTGTTCAAG 59.377 43.478 14.92 0.00 0.00 3.02
501 504 3.871006 CGGTGCAGCTATATTGTTCAAGA 59.129 43.478 14.92 0.00 0.00 3.02
502 505 4.512944 CGGTGCAGCTATATTGTTCAAGAT 59.487 41.667 14.92 0.00 0.00 2.40
503 506 5.559608 CGGTGCAGCTATATTGTTCAAGATG 60.560 44.000 14.92 0.00 0.00 2.90
505 508 5.686159 GCAGCTATATTGTTCAAGATGCT 57.314 39.130 4.33 6.96 45.38 3.79
506 509 6.069684 GCAGCTATATTGTTCAAGATGCTT 57.930 37.500 4.33 0.00 45.38 3.91
507 510 7.194607 GCAGCTATATTGTTCAAGATGCTTA 57.805 36.000 4.33 0.00 45.38 3.09
508 511 7.642669 GCAGCTATATTGTTCAAGATGCTTAA 58.357 34.615 4.33 0.00 45.38 1.85
509 512 8.295288 GCAGCTATATTGTTCAAGATGCTTAAT 58.705 33.333 4.33 0.00 45.38 1.40
515 518 7.615582 ATTGTTCAAGATGCTTAATTCTCGA 57.384 32.000 0.00 0.00 0.00 4.04
516 519 7.433708 TTGTTCAAGATGCTTAATTCTCGAA 57.566 32.000 0.00 0.00 0.00 3.71
517 520 7.615582 TGTTCAAGATGCTTAATTCTCGAAT 57.384 32.000 0.00 0.00 0.00 3.34
518 521 7.688372 TGTTCAAGATGCTTAATTCTCGAATC 58.312 34.615 0.00 0.00 0.00 2.52
519 522 7.550551 TGTTCAAGATGCTTAATTCTCGAATCT 59.449 33.333 0.00 0.00 0.00 2.40
520 523 8.394121 GTTCAAGATGCTTAATTCTCGAATCTT 58.606 33.333 0.00 0.00 34.17 2.40
521 524 9.599866 TTCAAGATGCTTAATTCTCGAATCTTA 57.400 29.630 3.58 0.00 32.97 2.10
522 525 9.770097 TCAAGATGCTTAATTCTCGAATCTTAT 57.230 29.630 3.58 0.00 32.97 1.73
608 611 4.412796 TTTTTGATTGTGTGGATTGCCA 57.587 36.364 0.00 0.00 43.47 4.92
668 671 9.684448 AATAGAAGATGATATGTGACTACAACG 57.316 33.333 0.00 0.00 40.84 4.10
669 672 7.334844 AGAAGATGATATGTGACTACAACGA 57.665 36.000 0.00 0.00 40.84 3.85
670 673 7.197017 AGAAGATGATATGTGACTACAACGAC 58.803 38.462 0.00 0.00 40.84 4.34
671 674 6.701145 AGATGATATGTGACTACAACGACT 57.299 37.500 0.00 0.00 40.84 4.18
672 675 7.101652 AGATGATATGTGACTACAACGACTT 57.898 36.000 0.00 0.00 40.84 3.01
673 676 7.197017 AGATGATATGTGACTACAACGACTTC 58.803 38.462 0.00 0.00 40.84 3.01
674 677 6.510879 TGATATGTGACTACAACGACTTCT 57.489 37.500 0.00 0.00 40.84 2.85
675 678 7.619964 TGATATGTGACTACAACGACTTCTA 57.380 36.000 0.00 0.00 40.84 2.10
676 679 8.221965 TGATATGTGACTACAACGACTTCTAT 57.778 34.615 0.00 0.00 40.84 1.98
677 680 9.333724 TGATATGTGACTACAACGACTTCTATA 57.666 33.333 0.00 0.00 40.84 1.31
721 724 9.981114 ACAAGAACTAATTGAAATGTAAAAGGG 57.019 29.630 0.00 0.00 0.00 3.95
722 725 8.925700 CAAGAACTAATTGAAATGTAAAAGGGC 58.074 33.333 0.00 0.00 0.00 5.19
723 726 8.422577 AGAACTAATTGAAATGTAAAAGGGCT 57.577 30.769 0.00 0.00 0.00 5.19
724 727 9.528489 AGAACTAATTGAAATGTAAAAGGGCTA 57.472 29.630 0.00 0.00 0.00 3.93
733 736 9.705290 TGAAATGTAAAAGGGCTAAAAGAAATC 57.295 29.630 0.00 0.00 0.00 2.17
734 737 9.151471 GAAATGTAAAAGGGCTAAAAGAAATCC 57.849 33.333 0.00 0.00 0.00 3.01
735 738 7.790782 ATGTAAAAGGGCTAAAAGAAATCCA 57.209 32.000 0.00 0.00 0.00 3.41
736 739 7.604657 TGTAAAAGGGCTAAAAGAAATCCAA 57.395 32.000 0.00 0.00 0.00 3.53
737 740 8.201242 TGTAAAAGGGCTAAAAGAAATCCAAT 57.799 30.769 0.00 0.00 0.00 3.16
738 741 9.315363 TGTAAAAGGGCTAAAAGAAATCCAATA 57.685 29.630 0.00 0.00 0.00 1.90
765 768 8.763049 TTATCATGATAGAAAGTATTCAGCCG 57.237 34.615 14.86 0.00 38.06 5.52
766 769 5.541845 TCATGATAGAAAGTATTCAGCCGG 58.458 41.667 0.00 0.00 38.06 6.13
767 770 5.070446 TCATGATAGAAAGTATTCAGCCGGT 59.930 40.000 1.90 0.00 38.06 5.28
768 771 5.353394 TGATAGAAAGTATTCAGCCGGTT 57.647 39.130 1.90 0.00 38.06 4.44
769 772 5.741011 TGATAGAAAGTATTCAGCCGGTTT 58.259 37.500 1.90 0.00 38.06 3.27
770 773 6.177610 TGATAGAAAGTATTCAGCCGGTTTT 58.822 36.000 1.90 0.00 38.06 2.43
771 774 4.766404 AGAAAGTATTCAGCCGGTTTTG 57.234 40.909 1.90 0.00 38.06 2.44
772 775 4.142038 AGAAAGTATTCAGCCGGTTTTGT 58.858 39.130 1.90 0.00 38.06 2.83
773 776 5.310451 AGAAAGTATTCAGCCGGTTTTGTA 58.690 37.500 1.90 0.00 38.06 2.41
774 777 5.944007 AGAAAGTATTCAGCCGGTTTTGTAT 59.056 36.000 1.90 1.89 38.06 2.29
775 778 5.560966 AAGTATTCAGCCGGTTTTGTATG 57.439 39.130 1.90 0.00 0.00 2.39
776 779 4.585879 AGTATTCAGCCGGTTTTGTATGT 58.414 39.130 1.90 0.00 0.00 2.29
777 780 3.848272 ATTCAGCCGGTTTTGTATGTG 57.152 42.857 1.90 0.00 0.00 3.21
778 781 2.264005 TCAGCCGGTTTTGTATGTGT 57.736 45.000 1.90 0.00 0.00 3.72
779 782 2.577700 TCAGCCGGTTTTGTATGTGTT 58.422 42.857 1.90 0.00 0.00 3.32
780 783 2.952978 TCAGCCGGTTTTGTATGTGTTT 59.047 40.909 1.90 0.00 0.00 2.83
781 784 4.135306 TCAGCCGGTTTTGTATGTGTTTA 58.865 39.130 1.90 0.00 0.00 2.01
782 785 4.762765 TCAGCCGGTTTTGTATGTGTTTAT 59.237 37.500 1.90 0.00 0.00 1.40
783 786 4.856487 CAGCCGGTTTTGTATGTGTTTATG 59.144 41.667 1.90 0.00 0.00 1.90
784 787 3.610677 GCCGGTTTTGTATGTGTTTATGC 59.389 43.478 1.90 0.00 0.00 3.14
785 788 4.617298 GCCGGTTTTGTATGTGTTTATGCT 60.617 41.667 1.90 0.00 0.00 3.79
786 789 5.465935 CCGGTTTTGTATGTGTTTATGCTT 58.534 37.500 0.00 0.00 0.00 3.91
787 790 5.923684 CCGGTTTTGTATGTGTTTATGCTTT 59.076 36.000 0.00 0.00 0.00 3.51
788 791 6.128956 CCGGTTTTGTATGTGTTTATGCTTTG 60.129 38.462 0.00 0.00 0.00 2.77
789 792 6.128956 CGGTTTTGTATGTGTTTATGCTTTGG 60.129 38.462 0.00 0.00 0.00 3.28
790 793 6.347321 GGTTTTGTATGTGTTTATGCTTTGGC 60.347 38.462 0.00 0.00 39.26 4.52
897 1075 6.860790 TGTAACAGTGTAATACCTGATCCA 57.139 37.500 13.29 5.88 0.00 3.41
1352 2122 6.314917 AGGTGTGGAGTTTCATATTTTCCTT 58.685 36.000 0.00 0.00 0.00 3.36
1451 2222 9.693739 TTAGATTGATTTTACTTGGCCTAATCA 57.306 29.630 3.32 7.03 34.44 2.57
1455 2226 5.655974 TGATTTTACTTGGCCTAATCATGCA 59.344 36.000 3.32 0.00 32.10 3.96
1646 2418 4.010349 GTGAGTGGGAAGAATTTGTAGGG 58.990 47.826 0.00 0.00 0.00 3.53
1648 2420 4.847512 TGAGTGGGAAGAATTTGTAGGGTA 59.152 41.667 0.00 0.00 0.00 3.69
1660 2432 4.669206 TTGTAGGGTACACAAAACTCGA 57.331 40.909 0.00 0.00 38.63 4.04
1752 2537 7.664318 ACTCCATTTGTTCCGTATTAGTTTTCT 59.336 33.333 0.00 0.00 0.00 2.52
1819 2607 8.586570 AAAATCTCTCTCTCTAATTGTATGCG 57.413 34.615 0.00 0.00 0.00 4.73
1850 2638 0.563173 CCCTCTCTCCTATCCCACCA 59.437 60.000 0.00 0.00 0.00 4.17
1860 2648 6.502138 TCTCCTATCCCACCAATTGATTTTT 58.498 36.000 7.12 0.00 0.00 1.94
1886 2674 4.219944 TCTGGTGTAGCGAGATTTAGTTGT 59.780 41.667 0.00 0.00 0.00 3.32
1909 2698 8.398491 TGTCTTTTATTAGGTCGTTCGTTATC 57.602 34.615 0.00 0.00 0.00 1.75
1918 2707 3.428589 GGTCGTTCGTTATCTAGTTGCCT 60.429 47.826 0.00 0.00 0.00 4.75
1969 2759 6.885376 TGCTTAGGGTATTTTCGTCCAAAATA 59.115 34.615 0.00 0.00 42.02 1.40
1997 2787 3.713826 ATTATGTTCCTTGGTCACCGT 57.286 42.857 0.00 0.00 0.00 4.83
2086 2884 5.931724 CAGGATCGTGTACCATATGCAAATA 59.068 40.000 7.25 0.00 0.00 1.40
2122 2920 6.780457 ACAAACTTTATCAGATGGGGAATG 57.220 37.500 0.00 0.00 0.00 2.67
2143 2945 2.487762 GCAAGTTCATTCGATCCAACCA 59.512 45.455 0.00 0.00 0.00 3.67
2169 2975 6.475727 AGGAACACACGATACTATCAAATTCG 59.524 38.462 0.00 0.00 35.99 3.34
2202 3008 7.759489 TCAACAAGACCTAGCACATTTATTT 57.241 32.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 5.106475 CGAAGAGAAGACTACACTACAAGCT 60.106 44.000 0.00 0.00 0.00 3.74
235 238 9.985730 CTATATAATTTTGGCAATCCACACAAT 57.014 29.630 0.00 0.00 43.33 2.71
448 451 9.065871 GCAGTTTATACTTTTCTTACAGCATTG 57.934 33.333 0.00 0.00 30.26 2.82
449 452 8.244113 GGCAGTTTATACTTTTCTTACAGCATT 58.756 33.333 0.00 0.00 30.26 3.56
450 453 7.611855 AGGCAGTTTATACTTTTCTTACAGCAT 59.388 33.333 0.00 0.00 30.26 3.79
451 454 6.940298 AGGCAGTTTATACTTTTCTTACAGCA 59.060 34.615 0.00 0.00 30.26 4.41
452 455 7.379098 AGGCAGTTTATACTTTTCTTACAGC 57.621 36.000 0.00 0.00 30.26 4.40
454 457 8.928733 CGTAAGGCAGTTTATACTTTTCTTACA 58.071 33.333 18.66 0.00 37.79 2.41
475 478 4.808895 TGAACAATATAGCTGCACCGTAAG 59.191 41.667 1.02 0.00 0.00 2.34
476 479 4.760878 TGAACAATATAGCTGCACCGTAA 58.239 39.130 1.02 0.00 0.00 3.18
477 480 4.394439 TGAACAATATAGCTGCACCGTA 57.606 40.909 1.02 0.00 0.00 4.02
478 481 3.260475 TGAACAATATAGCTGCACCGT 57.740 42.857 1.02 0.00 0.00 4.83
479 482 3.871006 TCTTGAACAATATAGCTGCACCG 59.129 43.478 1.02 0.00 0.00 4.94
480 483 5.755813 CATCTTGAACAATATAGCTGCACC 58.244 41.667 1.02 0.00 0.00 5.01
481 484 5.008415 AGCATCTTGAACAATATAGCTGCAC 59.992 40.000 1.02 0.00 0.00 4.57
482 485 5.128205 AGCATCTTGAACAATATAGCTGCA 58.872 37.500 1.02 0.00 0.00 4.41
483 486 5.686159 AGCATCTTGAACAATATAGCTGC 57.314 39.130 0.00 0.00 0.00 5.25
489 492 9.330063 TCGAGAATTAAGCATCTTGAACAATAT 57.670 29.630 4.11 0.00 34.02 1.28
490 493 8.716646 TCGAGAATTAAGCATCTTGAACAATA 57.283 30.769 4.11 0.00 34.02 1.90
491 494 7.615582 TCGAGAATTAAGCATCTTGAACAAT 57.384 32.000 4.11 0.00 34.02 2.71
492 495 7.433708 TTCGAGAATTAAGCATCTTGAACAA 57.566 32.000 11.54 0.00 39.84 2.83
493 496 7.550551 AGATTCGAGAATTAAGCATCTTGAACA 59.449 33.333 15.37 2.29 44.67 3.18
494 497 7.914465 AGATTCGAGAATTAAGCATCTTGAAC 58.086 34.615 15.37 11.47 44.67 3.18
495 498 8.498054 AAGATTCGAGAATTAAGCATCTTGAA 57.502 30.769 15.39 15.39 45.47 2.69
496 499 9.770097 ATAAGATTCGAGAATTAAGCATCTTGA 57.230 29.630 11.57 2.90 34.91 3.02
587 590 4.412796 TGGCAATCCACACAATCAAAAA 57.587 36.364 0.00 0.00 37.47 1.94
588 591 4.412796 TTGGCAATCCACACAATCAAAA 57.587 36.364 0.00 0.00 43.33 2.44
589 592 4.412796 TTTGGCAATCCACACAATCAAA 57.587 36.364 0.00 0.00 43.33 2.69
590 593 4.412796 TTTTGGCAATCCACACAATCAA 57.587 36.364 0.00 0.00 43.33 2.57
591 594 4.620589 ATTTTGGCAATCCACACAATCA 57.379 36.364 0.00 0.00 43.33 2.57
592 595 8.891671 ATATAATTTTGGCAATCCACACAATC 57.108 30.769 0.00 0.00 43.33 2.67
593 596 9.985730 CTATATAATTTTGGCAATCCACACAAT 57.014 29.630 0.00 0.00 43.33 2.71
594 597 8.976353 ACTATATAATTTTGGCAATCCACACAA 58.024 29.630 0.00 0.00 43.33 3.33
595 598 8.532186 ACTATATAATTTTGGCAATCCACACA 57.468 30.769 0.00 0.00 43.33 3.72
642 645 9.684448 CGTTGTAGTCACATATCATCTTCTATT 57.316 33.333 0.00 0.00 33.76 1.73
643 646 9.067986 TCGTTGTAGTCACATATCATCTTCTAT 57.932 33.333 0.00 0.00 33.76 1.98
644 647 8.343366 GTCGTTGTAGTCACATATCATCTTCTA 58.657 37.037 0.00 0.00 33.76 2.10
645 648 7.067615 AGTCGTTGTAGTCACATATCATCTTCT 59.932 37.037 0.00 0.00 33.76 2.85
646 649 7.197017 AGTCGTTGTAGTCACATATCATCTTC 58.803 38.462 0.00 0.00 33.76 2.87
647 650 7.101652 AGTCGTTGTAGTCACATATCATCTT 57.898 36.000 0.00 0.00 33.76 2.40
648 651 6.701145 AGTCGTTGTAGTCACATATCATCT 57.299 37.500 0.00 0.00 33.76 2.90
649 652 7.197017 AGAAGTCGTTGTAGTCACATATCATC 58.803 38.462 0.00 0.00 33.76 2.92
650 653 7.101652 AGAAGTCGTTGTAGTCACATATCAT 57.898 36.000 0.00 0.00 33.76 2.45
651 654 6.510879 AGAAGTCGTTGTAGTCACATATCA 57.489 37.500 0.00 0.00 33.76 2.15
695 698 9.981114 CCCTTTTACATTTCAATTAGTTCTTGT 57.019 29.630 0.00 0.00 0.00 3.16
696 699 8.925700 GCCCTTTTACATTTCAATTAGTTCTTG 58.074 33.333 0.00 0.00 0.00 3.02
697 700 8.870116 AGCCCTTTTACATTTCAATTAGTTCTT 58.130 29.630 0.00 0.00 0.00 2.52
698 701 8.422577 AGCCCTTTTACATTTCAATTAGTTCT 57.577 30.769 0.00 0.00 0.00 3.01
707 710 9.705290 GATTTCTTTTAGCCCTTTTACATTTCA 57.295 29.630 0.00 0.00 0.00 2.69
708 711 9.151471 GGATTTCTTTTAGCCCTTTTACATTTC 57.849 33.333 0.00 0.00 0.00 2.17
709 712 8.655901 TGGATTTCTTTTAGCCCTTTTACATTT 58.344 29.630 0.00 0.00 0.00 2.32
710 713 8.201242 TGGATTTCTTTTAGCCCTTTTACATT 57.799 30.769 0.00 0.00 0.00 2.71
711 714 7.790782 TGGATTTCTTTTAGCCCTTTTACAT 57.209 32.000 0.00 0.00 0.00 2.29
712 715 7.604657 TTGGATTTCTTTTAGCCCTTTTACA 57.395 32.000 0.00 0.00 0.00 2.41
739 742 9.376075 CGGCTGAATACTTTCTATCATGATAAT 57.624 33.333 16.08 3.52 32.78 1.28
740 743 7.819415 CCGGCTGAATACTTTCTATCATGATAA 59.181 37.037 16.08 1.90 32.78 1.75
741 744 7.039011 ACCGGCTGAATACTTTCTATCATGATA 60.039 37.037 14.64 14.64 32.78 2.15
742 745 6.169094 CCGGCTGAATACTTTCTATCATGAT 58.831 40.000 13.81 13.81 32.78 2.45
743 746 5.070446 ACCGGCTGAATACTTTCTATCATGA 59.930 40.000 0.00 0.00 32.78 3.07
744 747 5.300752 ACCGGCTGAATACTTTCTATCATG 58.699 41.667 0.00 0.00 32.78 3.07
745 748 5.552870 ACCGGCTGAATACTTTCTATCAT 57.447 39.130 0.00 0.00 32.78 2.45
746 749 5.353394 AACCGGCTGAATACTTTCTATCA 57.647 39.130 0.00 0.00 32.78 2.15
747 750 6.093633 ACAAAACCGGCTGAATACTTTCTATC 59.906 38.462 0.00 0.00 32.78 2.08
748 751 5.944007 ACAAAACCGGCTGAATACTTTCTAT 59.056 36.000 0.00 0.00 32.78 1.98
749 752 5.310451 ACAAAACCGGCTGAATACTTTCTA 58.690 37.500 0.00 0.00 32.78 2.10
750 753 4.142038 ACAAAACCGGCTGAATACTTTCT 58.858 39.130 0.00 0.00 32.78 2.52
751 754 4.499037 ACAAAACCGGCTGAATACTTTC 57.501 40.909 0.00 0.00 0.00 2.62
752 755 5.475564 ACATACAAAACCGGCTGAATACTTT 59.524 36.000 0.00 0.00 0.00 2.66
753 756 5.007682 ACATACAAAACCGGCTGAATACTT 58.992 37.500 0.00 0.00 0.00 2.24
754 757 4.394920 CACATACAAAACCGGCTGAATACT 59.605 41.667 0.00 0.00 0.00 2.12
755 758 4.155280 ACACATACAAAACCGGCTGAATAC 59.845 41.667 0.00 0.00 0.00 1.89
756 759 4.328536 ACACATACAAAACCGGCTGAATA 58.671 39.130 0.00 0.00 0.00 1.75
757 760 3.153919 ACACATACAAAACCGGCTGAAT 58.846 40.909 0.00 0.00 0.00 2.57
758 761 2.577700 ACACATACAAAACCGGCTGAA 58.422 42.857 0.00 0.00 0.00 3.02
759 762 2.264005 ACACATACAAAACCGGCTGA 57.736 45.000 0.00 0.00 0.00 4.26
760 763 3.363341 AAACACATACAAAACCGGCTG 57.637 42.857 0.00 0.00 0.00 4.85
761 764 4.617298 GCATAAACACATACAAAACCGGCT 60.617 41.667 0.00 0.00 0.00 5.52
762 765 3.610677 GCATAAACACATACAAAACCGGC 59.389 43.478 0.00 0.00 0.00 6.13
763 766 5.054390 AGCATAAACACATACAAAACCGG 57.946 39.130 0.00 0.00 0.00 5.28
764 767 6.128956 CCAAAGCATAAACACATACAAAACCG 60.129 38.462 0.00 0.00 0.00 4.44
765 768 6.347321 GCCAAAGCATAAACACATACAAAACC 60.347 38.462 0.00 0.00 39.53 3.27
766 769 6.201806 TGCCAAAGCATAAACACATACAAAAC 59.798 34.615 0.00 0.00 46.52 2.43
767 770 6.283694 TGCCAAAGCATAAACACATACAAAA 58.716 32.000 0.00 0.00 46.52 2.44
768 771 5.847304 TGCCAAAGCATAAACACATACAAA 58.153 33.333 0.00 0.00 46.52 2.83
769 772 5.459536 TGCCAAAGCATAAACACATACAA 57.540 34.783 0.00 0.00 46.52 2.41
783 786 4.783764 AAGTTAGTATGGTTGCCAAAGC 57.216 40.909 0.00 0.00 36.95 3.51
784 787 6.811253 TGTAAGTTAGTATGGTTGCCAAAG 57.189 37.500 0.00 0.00 36.95 2.77
785 788 7.598278 CATTGTAAGTTAGTATGGTTGCCAAA 58.402 34.615 0.00 0.00 36.95 3.28
786 789 6.349777 GCATTGTAAGTTAGTATGGTTGCCAA 60.350 38.462 0.00 0.00 36.95 4.52
787 790 5.124776 GCATTGTAAGTTAGTATGGTTGCCA 59.875 40.000 6.39 0.00 38.19 4.92
788 791 5.357032 AGCATTGTAAGTTAGTATGGTTGCC 59.643 40.000 4.02 0.00 0.00 4.52
789 792 6.128007 ACAGCATTGTAAGTTAGTATGGTTGC 60.128 38.462 6.26 0.00 35.25 4.17
790 793 7.377766 ACAGCATTGTAAGTTAGTATGGTTG 57.622 36.000 6.26 5.74 35.25 3.77
910 1088 9.667107 CGCCTCTTTCCTCCAATAATATTAATA 57.333 33.333 0.00 0.00 0.00 0.98
1352 2122 1.228215 TGACCGTACTCCACCGTGA 60.228 57.895 0.00 0.00 0.00 4.35
1451 2222 4.592942 ACACAGATCCAATACAACTGCAT 58.407 39.130 0.00 0.00 32.67 3.96
1455 2226 4.081642 AGCGTACACAGATCCAATACAACT 60.082 41.667 0.00 0.00 0.00 3.16
1602 2374 5.568677 CACATTGTATCACATCAAAACACCG 59.431 40.000 0.00 0.00 0.00 4.94
1646 2418 7.541437 ACTTATAGAAGCTCGAGTTTTGTGTAC 59.459 37.037 16.03 2.20 35.97 2.90
1648 2420 6.456501 ACTTATAGAAGCTCGAGTTTTGTGT 58.543 36.000 16.03 9.16 35.97 3.72
1709 2482 9.853555 CAAATGGAGTATTTGCTAAACAACATA 57.146 29.630 0.00 0.00 46.41 2.29
1731 2504 7.081976 GCACAGAAAACTAATACGGAACAAAT 58.918 34.615 0.00 0.00 0.00 2.32
1752 2537 1.485294 ATGGTGGAAGGGTACGCACA 61.485 55.000 12.95 5.38 0.00 4.57
1806 2594 5.817296 AGAAATGTGAGCGCATACAATTAGA 59.183 36.000 18.46 0.00 0.00 2.10
1819 2607 2.158971 GGAGAGAGGGAGAAATGTGAGC 60.159 54.545 0.00 0.00 0.00 4.26
1860 2648 5.790593 ACTAAATCTCGCTACACCAGAAAA 58.209 37.500 0.00 0.00 0.00 2.29
1861 2649 5.401531 ACTAAATCTCGCTACACCAGAAA 57.598 39.130 0.00 0.00 0.00 2.52
1886 2674 9.941664 CTAGATAACGAACGACCTAATAAAAGA 57.058 33.333 0.14 0.00 0.00 2.52
1969 2759 6.431234 GTGACCAAGGAACATAATTGAGAAGT 59.569 38.462 0.00 0.00 0.00 3.01
2042 2838 4.442893 CCTGACCCGTGTGATACATGTAAT 60.443 45.833 10.14 0.00 33.37 1.89
2086 2884 3.712016 AAGTTTGTTTTTGTTGGCCCT 57.288 38.095 0.00 0.00 0.00 5.19
2122 2920 2.487762 TGGTTGGATCGAATGAACTTGC 59.512 45.455 0.00 0.00 0.00 4.01
2143 2945 7.010183 CGAATTTGATAGTATCGTGTGTTCCTT 59.990 37.037 5.68 0.00 0.00 3.36
2169 2975 5.932303 TGCTAGGTCTTGTTGAACTTGTATC 59.068 40.000 0.00 0.00 40.40 2.24


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

AutoCloner maintained by Alex Coulton.