Multiple sequence alignment - TraesCS6B01G129000

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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 TraesCS6B01G129000 chr6B 100.000 3382 0 0 1 3382 124634283 124630902 0.000000e+00 6246.0
1 TraesCS6B01G129000 chr6B 90.614 586 38 5 1734 2314 644070546 644071119 0.000000e+00 761.0
2 TraesCS6B01G129000 chr6B 90.179 336 27 3 1405 1737 644050809 644051141 1.860000e-117 433.0
3 TraesCS6B01G129000 chr6B 90.541 74 5 2 858 930 706024848 706024920 2.780000e-16 97.1
4 TraesCS6B01G129000 chr7B 99.258 2559 19 0 824 3382 646038560 646036002 0.000000e+00 4621.0
5 TraesCS6B01G129000 chr3D 92.835 963 48 10 1405 2351 501160005 501159048 0.000000e+00 1376.0
6 TraesCS6B01G129000 chr3D 92.597 824 47 5 2349 3170 501158587 501157776 0.000000e+00 1171.0
7 TraesCS6B01G129000 chr5B 98.691 611 5 2 1 611 564469461 564468854 0.000000e+00 1081.0
8 TraesCS6B01G129000 chr5B 96.854 604 18 1 1 604 687894072 687893470 0.000000e+00 1009.0
9 TraesCS6B01G129000 chr5B 90.306 392 27 6 971 1352 118956756 118957146 1.400000e-138 503.0
10 TraesCS6B01G129000 chr5B 90.833 360 29 3 1656 2012 441650807 441650449 2.360000e-131 479.0
11 TraesCS6B01G129000 chr5B 79.715 281 15 15 605 863 599960038 599960298 7.510000e-37 165.0
12 TraesCS6B01G129000 chr5B 83.333 120 14 3 608 723 706025504 706025621 4.620000e-19 106.0
13 TraesCS6B01G129000 chr2B 99.007 604 5 1 1 604 726761625 726762227 0.000000e+00 1081.0
14 TraesCS6B01G129000 chr2B 93.694 222 14 0 1134 1355 415442643 415442422 1.940000e-87 333.0
15 TraesCS6B01G129000 chr2B 89.057 265 15 2 1405 1655 530107722 530107458 1.960000e-82 316.0
16 TraesCS6B01G129000 chr2B 79.715 281 15 15 605 863 17451685 17451945 7.510000e-37 165.0
17 TraesCS6B01G129000 chr2B 87.407 135 6 3 850 973 415442935 415442801 9.780000e-31 145.0
18 TraesCS6B01G129000 chr2B 83.146 178 9 6 611 767 17450988 17451165 3.520000e-30 143.0
19 TraesCS6B01G129000 chr1B 98.839 603 6 1 1 603 383901263 383900662 0.000000e+00 1074.0
20 TraesCS6B01G129000 chr7A 98.675 604 7 1 1 604 251346217 251345615 0.000000e+00 1070.0
21 TraesCS6B01G129000 chr3A 98.173 602 10 1 1 602 556365127 556365727 0.000000e+00 1050.0
22 TraesCS6B01G129000 chr5A 98.010 603 11 1 1 603 477547360 477547961 0.000000e+00 1046.0
23 TraesCS6B01G129000 chr5A 90.601 383 34 2 971 1352 112094156 112094537 1.080000e-139 507.0
24 TraesCS6B01G129000 chr5A 88.981 363 33 4 1656 2012 474832570 474832209 3.100000e-120 442.0
25 TraesCS6B01G129000 chr5A 89.256 121 9 4 852 968 510159958 510160078 7.560000e-32 148.0
26 TraesCS6B01G129000 chrUn 99.101 556 4 1 49 604 345296421 345296975 0.000000e+00 998.0
27 TraesCS6B01G129000 chrUn 79.715 281 15 15 605 863 458116368 458116628 7.510000e-37 165.0
28 TraesCS6B01G129000 chrUn 83.750 160 23 2 1656 1812 46035657 46035816 7.560000e-32 148.0
29 TraesCS6B01G129000 chr4B 97.442 391 9 1 1 391 124922536 124922147 0.000000e+00 665.0
30 TraesCS6B01G129000 chr4B 86.207 116 11 2 611 723 361750702 361750589 1.650000e-23 121.0
31 TraesCS6B01G129000 chr4B 96.774 31 1 0 932 962 645634686 645634656 6.000000e-03 52.8
32 TraesCS6B01G129000 chr4B 96.774 31 1 0 932 962 645713939 645713909 6.000000e-03 52.8
33 TraesCS6B01G129000 chr4B 96.774 31 1 0 932 962 645806068 645806038 6.000000e-03 52.8
34 TraesCS6B01G129000 chr5D 91.906 383 28 3 971 1352 108367446 108367826 1.790000e-147 532.0
35 TraesCS6B01G129000 chr5D 90.582 361 30 3 1656 2012 371801251 371800891 3.050000e-130 475.0
36 TraesCS6B01G129000 chr5D 84.000 275 14 13 611 863 220783503 220783237 1.570000e-58 237.0
37 TraesCS6B01G129000 chr2A 99.543 219 1 0 388 606 639699141 639698923 1.890000e-107 399.0
38 TraesCS6B01G129000 chr2A 89.434 265 14 2 1405 1655 593303042 593303306 4.210000e-84 322.0
39 TraesCS6B01G129000 chr2D 90.038 261 14 4 1405 1655 449712534 449712276 9.050000e-86 327.0
40 TraesCS6B01G129000 chr2D 83.750 160 23 2 1656 1812 136177997 136178156 7.560000e-32 148.0
41 TraesCS6B01G129000 chr2D 86.735 98 5 1 873 962 180529865 180529768 5.970000e-18 102.0
42 TraesCS6B01G129000 chr6D 87.739 261 11 8 608 848 423459816 423460075 5.520000e-73 285.0
43 TraesCS6B01G129000 chr6D 83.125 160 24 2 1656 1812 129168516 129168357 3.520000e-30 143.0
44 TraesCS6B01G129000 chr6D 88.542 96 11 0 611 706 27427280 27427375 2.130000e-22 117.0
45 TraesCS6B01G129000 chr4A 91.765 85 7 0 618 702 90390883 90390799 5.930000e-23 119.0
46 TraesCS6B01G129000 chr4A 96.875 32 1 0 932 963 722432880 722432849 2.000000e-03 54.7
47 TraesCS6B01G129000 chr4D 88.000 75 7 2 604 678 443719645 443719573 1.670000e-13 87.9
48 TraesCS6B01G129000 chr3B 86.667 75 8 2 604 678 75332261 75332333 7.780000e-12 82.4


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 TraesCS6B01G129000 chr6B 124630902 124634283 3381 True 6246.0 6246 100.0000 1 3382 1 chr6B.!!$R1 3381
1 TraesCS6B01G129000 chr6B 644070546 644071119 573 False 761.0 761 90.6140 1734 2314 1 chr6B.!!$F2 580
2 TraesCS6B01G129000 chr7B 646036002 646038560 2558 True 4621.0 4621 99.2580 824 3382 1 chr7B.!!$R1 2558
3 TraesCS6B01G129000 chr3D 501157776 501160005 2229 True 1273.5 1376 92.7160 1405 3170 2 chr3D.!!$R1 1765
4 TraesCS6B01G129000 chr5B 564468854 564469461 607 True 1081.0 1081 98.6910 1 611 1 chr5B.!!$R2 610
5 TraesCS6B01G129000 chr5B 687893470 687894072 602 True 1009.0 1009 96.8540 1 604 1 chr5B.!!$R3 603
6 TraesCS6B01G129000 chr2B 726761625 726762227 602 False 1081.0 1081 99.0070 1 604 1 chr2B.!!$F1 603
7 TraesCS6B01G129000 chr2B 415442422 415442935 513 True 239.0 333 90.5505 850 1355 2 chr2B.!!$R2 505
8 TraesCS6B01G129000 chr1B 383900662 383901263 601 True 1074.0 1074 98.8390 1 603 1 chr1B.!!$R1 602
9 TraesCS6B01G129000 chr7A 251345615 251346217 602 True 1070.0 1070 98.6750 1 604 1 chr7A.!!$R1 603
10 TraesCS6B01G129000 chr3A 556365127 556365727 600 False 1050.0 1050 98.1730 1 602 1 chr3A.!!$F1 601
11 TraesCS6B01G129000 chr5A 477547360 477547961 601 False 1046.0 1046 98.0100 1 603 1 chr5A.!!$F2 602
12 TraesCS6B01G129000 chrUn 345296421 345296975 554 False 998.0 998 99.1010 49 604 1 chrUn.!!$F2 555

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
709 710 0.232303 GACCACACGAGCGAAAAGTG 59.768 55.0 0.0 0.0 41.28 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 3062 0.397187 AAAATGTGGCTTGCCATGCA 59.603 45.0 17.86 12.06 36.47 3.96 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
147 148 4.091549 ACCGATATGTACGATACCCCATT 58.908 43.478 0.00 0.00 0.00 3.16
604 605 2.443394 CCGAATGCCCAGCCCTAGA 61.443 63.158 0.00 0.00 0.00 2.43
605 606 1.526887 CGAATGCCCAGCCCTAGAA 59.473 57.895 0.00 0.00 0.00 2.10
606 607 0.533755 CGAATGCCCAGCCCTAGAAG 60.534 60.000 0.00 0.00 0.00 2.85
608 609 0.624500 AATGCCCAGCCCTAGAAGGA 60.625 55.000 0.00 0.00 37.67 3.36
609 610 1.059006 ATGCCCAGCCCTAGAAGGAG 61.059 60.000 0.00 0.00 37.67 3.69
610 611 2.447714 GCCCAGCCCTAGAAGGAGG 61.448 68.421 0.00 0.00 37.67 4.30
611 612 1.003573 CCCAGCCCTAGAAGGAGGT 59.996 63.158 0.00 0.00 37.67 3.85
612 613 1.341156 CCCAGCCCTAGAAGGAGGTG 61.341 65.000 0.00 1.26 37.67 4.00
613 614 1.524482 CAGCCCTAGAAGGAGGTGC 59.476 63.158 0.00 0.00 37.67 5.01
614 615 0.980231 CAGCCCTAGAAGGAGGTGCT 60.980 60.000 0.00 0.00 41.23 4.40
615 616 0.637195 AGCCCTAGAAGGAGGTGCTA 59.363 55.000 0.00 0.00 39.75 3.49
616 617 1.044611 GCCCTAGAAGGAGGTGCTAG 58.955 60.000 0.00 0.00 37.67 3.42
617 618 1.710816 CCCTAGAAGGAGGTGCTAGG 58.289 60.000 0.00 0.00 46.96 3.02
618 619 1.044611 CCTAGAAGGAGGTGCTAGGC 58.955 60.000 0.00 0.00 43.26 3.93
619 620 1.689575 CCTAGAAGGAGGTGCTAGGCA 60.690 57.143 0.00 0.00 43.26 4.75
628 629 4.615901 TGCTAGGCACAACCATCG 57.384 55.556 0.00 0.00 43.14 3.84
629 630 1.745115 TGCTAGGCACAACCATCGC 60.745 57.895 0.00 0.00 43.14 4.58
630 631 1.450312 GCTAGGCACAACCATCGCT 60.450 57.895 0.00 0.00 43.14 4.93
631 632 1.432270 GCTAGGCACAACCATCGCTC 61.432 60.000 0.00 0.00 43.14 5.03
632 633 1.148157 CTAGGCACAACCATCGCTCG 61.148 60.000 0.00 0.00 43.14 5.03
633 634 1.600511 TAGGCACAACCATCGCTCGA 61.601 55.000 0.00 0.00 43.14 4.04
634 635 2.456119 GGCACAACCATCGCTCGAG 61.456 63.158 8.45 8.45 38.86 4.04
635 636 3.084579 CACAACCATCGCTCGAGC 58.915 61.111 27.64 27.64 37.78 5.03
663 664 1.871077 CACGCGAGGGGTAAAAACC 59.129 57.895 15.93 0.00 0.00 3.27
664 665 0.885596 CACGCGAGGGGTAAAAACCA 60.886 55.000 15.93 0.00 0.00 3.67
665 666 0.886043 ACGCGAGGGGTAAAAACCAC 60.886 55.000 15.93 0.00 0.00 4.16
666 667 1.579964 CGCGAGGGGTAAAAACCACC 61.580 60.000 0.00 0.00 32.34 4.61
667 668 1.579964 GCGAGGGGTAAAAACCACCG 61.580 60.000 0.00 0.00 36.89 4.94
668 669 1.579964 CGAGGGGTAAAAACCACCGC 61.580 60.000 0.63 0.63 46.52 5.68
669 670 4.177673 GGGGTAAAAACCACCGCA 57.822 55.556 3.92 0.00 45.70 5.69
670 671 2.661054 GGGGTAAAAACCACCGCAT 58.339 52.632 3.92 0.00 45.70 4.73
671 672 0.528924 GGGGTAAAAACCACCGCATC 59.471 55.000 3.92 0.00 45.70 3.91
672 673 1.249407 GGGTAAAAACCACCGCATCA 58.751 50.000 0.00 0.00 36.89 3.07
673 674 1.068125 GGGTAAAAACCACCGCATCAC 60.068 52.381 0.00 0.00 36.89 3.06
674 675 1.400500 GGTAAAAACCACCGCATCACG 60.400 52.381 0.00 0.00 43.15 4.35
675 676 0.238817 TAAAAACCACCGCATCACGC 59.761 50.000 0.00 0.00 41.76 5.34
704 705 4.351938 CCGGACCACACGAGCGAA 62.352 66.667 0.00 0.00 0.00 4.70
705 706 2.355363 CGGACCACACGAGCGAAA 60.355 61.111 0.00 0.00 0.00 3.46
706 707 1.952133 CGGACCACACGAGCGAAAA 60.952 57.895 0.00 0.00 0.00 2.29
707 708 1.860078 GGACCACACGAGCGAAAAG 59.140 57.895 0.00 0.00 0.00 2.27
708 709 0.878961 GGACCACACGAGCGAAAAGT 60.879 55.000 0.00 0.00 0.00 2.66
709 710 0.232303 GACCACACGAGCGAAAAGTG 59.768 55.000 0.00 0.00 41.28 3.16
710 711 1.082756 CCACACGAGCGAAAAGTGC 60.083 57.895 0.00 0.00 39.31 4.40
711 712 1.437089 CACACGAGCGAAAAGTGCG 60.437 57.895 0.00 0.00 39.31 5.34
712 713 1.590525 ACACGAGCGAAAAGTGCGA 60.591 52.632 0.00 0.00 39.31 5.10
713 714 1.128611 CACGAGCGAAAAGTGCGAG 59.871 57.895 0.00 0.00 37.44 5.03
714 715 2.094724 CGAGCGAAAAGTGCGAGC 59.905 61.111 0.00 0.00 37.44 5.03
715 716 2.094724 GAGCGAAAAGTGCGAGCG 59.905 61.111 0.00 0.00 37.44 5.03
716 717 2.355837 AGCGAAAAGTGCGAGCGA 60.356 55.556 0.00 0.00 37.44 4.93
717 718 2.094724 GCGAAAAGTGCGAGCGAG 59.905 61.111 0.00 0.00 0.00 5.03
718 719 2.094724 CGAAAAGTGCGAGCGAGC 59.905 61.111 0.00 0.00 37.71 5.03
719 720 2.094724 GAAAAGTGCGAGCGAGCG 59.905 61.111 0.00 0.00 40.67 5.03
720 721 2.355837 AAAAGTGCGAGCGAGCGA 60.356 55.556 1.41 0.00 40.67 4.93
721 722 2.272293 GAAAAGTGCGAGCGAGCGAG 62.272 60.000 1.41 0.00 40.67 5.03
736 737 4.925861 GAGCCGGCCTGCATCTCC 62.926 72.222 26.15 1.17 0.00 3.71
741 742 3.424105 GGCCTGCATCTCCCCCTT 61.424 66.667 0.00 0.00 0.00 3.95
742 743 2.685999 GCCTGCATCTCCCCCTTT 59.314 61.111 0.00 0.00 0.00 3.11
743 744 1.454663 GCCTGCATCTCCCCCTTTC 60.455 63.158 0.00 0.00 0.00 2.62
744 745 1.153086 CCTGCATCTCCCCCTTTCG 60.153 63.158 0.00 0.00 0.00 3.46
745 746 1.821332 CTGCATCTCCCCCTTTCGC 60.821 63.158 0.00 0.00 0.00 4.70
746 747 2.262774 CTGCATCTCCCCCTTTCGCT 62.263 60.000 0.00 0.00 0.00 4.93
747 748 1.524849 GCATCTCCCCCTTTCGCTC 60.525 63.158 0.00 0.00 0.00 5.03
748 749 1.227380 CATCTCCCCCTTTCGCTCG 60.227 63.158 0.00 0.00 0.00 5.03
749 750 1.381327 ATCTCCCCCTTTCGCTCGA 60.381 57.895 0.00 0.00 0.00 4.04
750 751 1.395826 ATCTCCCCCTTTCGCTCGAG 61.396 60.000 8.45 8.45 0.00 4.04
751 752 3.724914 CTCCCCCTTTCGCTCGAGC 62.725 68.421 27.64 27.64 37.78 5.03
752 753 4.840005 CCCCCTTTCGCTCGAGCC 62.840 72.222 30.66 13.79 37.91 4.70
754 755 4.436998 CCCTTTCGCTCGAGCCGT 62.437 66.667 30.66 0.00 37.91 5.68
755 756 2.881352 CCTTTCGCTCGAGCCGTC 60.881 66.667 30.66 4.69 37.91 4.79
757 758 3.948086 CTTTCGCTCGAGCCGTCGT 62.948 63.158 30.66 0.00 46.85 4.34
758 759 3.940975 TTTCGCTCGAGCCGTCGTC 62.941 63.158 30.66 2.72 46.85 4.20
760 761 4.872485 CGCTCGAGCCGTCGTCTC 62.872 72.222 30.66 1.17 46.85 3.36
761 762 4.539881 GCTCGAGCCGTCGTCTCC 62.540 72.222 27.22 0.00 46.85 3.71
762 763 3.878519 CTCGAGCCGTCGTCTCCC 61.879 72.222 0.00 0.00 46.85 4.30
791 792 4.927782 GAGCCACACGCACACCCA 62.928 66.667 0.00 0.00 41.38 4.51
792 793 4.497984 AGCCACACGCACACCCAA 62.498 61.111 0.00 0.00 41.38 4.12
793 794 3.294493 GCCACACGCACACCCAAT 61.294 61.111 0.00 0.00 37.47 3.16
794 795 2.953821 CCACACGCACACCCAATC 59.046 61.111 0.00 0.00 0.00 2.67
795 796 2.625823 CCACACGCACACCCAATCC 61.626 63.158 0.00 0.00 0.00 3.01
796 797 2.282180 ACACGCACACCCAATCCC 60.282 61.111 0.00 0.00 0.00 3.85
797 798 3.061848 CACGCACACCCAATCCCC 61.062 66.667 0.00 0.00 0.00 4.81
798 799 3.256960 ACGCACACCCAATCCCCT 61.257 61.111 0.00 0.00 0.00 4.79
799 800 2.438434 CGCACACCCAATCCCCTC 60.438 66.667 0.00 0.00 0.00 4.30
800 801 2.043953 GCACACCCAATCCCCTCC 60.044 66.667 0.00 0.00 0.00 4.30
801 802 2.683475 CACACCCAATCCCCTCCC 59.317 66.667 0.00 0.00 0.00 4.30
802 803 2.617215 ACACCCAATCCCCTCCCC 60.617 66.667 0.00 0.00 0.00 4.81
803 804 2.287194 CACCCAATCCCCTCCCCT 60.287 66.667 0.00 0.00 0.00 4.79
804 805 2.044620 ACCCAATCCCCTCCCCTC 59.955 66.667 0.00 0.00 0.00 4.30
805 806 2.778717 CCCAATCCCCTCCCCTCC 60.779 72.222 0.00 0.00 0.00 4.30
806 807 2.044450 CCAATCCCCTCCCCTCCA 59.956 66.667 0.00 0.00 0.00 3.86
807 808 1.622442 CCAATCCCCTCCCCTCCAA 60.622 63.158 0.00 0.00 0.00 3.53
808 809 1.615262 CAATCCCCTCCCCTCCAAC 59.385 63.158 0.00 0.00 0.00 3.77
809 810 1.622752 AATCCCCTCCCCTCCAACC 60.623 63.158 0.00 0.00 0.00 3.77
810 811 3.677689 ATCCCCTCCCCTCCAACCC 62.678 68.421 0.00 0.00 0.00 4.11
811 812 4.371231 CCCCTCCCCTCCAACCCT 62.371 72.222 0.00 0.00 0.00 4.34
812 813 2.792222 CCCTCCCCTCCAACCCTA 59.208 66.667 0.00 0.00 0.00 3.53
813 814 1.384643 CCCTCCCCTCCAACCCTAG 60.385 68.421 0.00 0.00 0.00 3.02
814 815 2.073101 CCTCCCCTCCAACCCTAGC 61.073 68.421 0.00 0.00 0.00 3.42
815 816 2.042261 TCCCCTCCAACCCTAGCC 59.958 66.667 0.00 0.00 0.00 3.93
816 817 3.480133 CCCCTCCAACCCTAGCCG 61.480 72.222 0.00 0.00 0.00 5.52
817 818 4.176752 CCCTCCAACCCTAGCCGC 62.177 72.222 0.00 0.00 0.00 6.53
818 819 4.176752 CCTCCAACCCTAGCCGCC 62.177 72.222 0.00 0.00 0.00 6.13
819 820 3.083997 CTCCAACCCTAGCCGCCT 61.084 66.667 0.00 0.00 0.00 5.52
820 821 3.391665 CTCCAACCCTAGCCGCCTG 62.392 68.421 0.00 0.00 0.00 4.85
821 822 4.489771 CCAACCCTAGCCGCCTGG 62.490 72.222 0.00 0.00 38.77 4.45
1276 1405 4.765273 TGTTTTTCTTTTCCTTTCTGCCC 58.235 39.130 0.00 0.00 0.00 5.36
1800 1930 0.682209 GGGCACAAGACCTGCATCAT 60.682 55.000 0.00 0.00 41.07 2.45
1835 1965 2.494445 TCGCATTCGACATCGGCT 59.506 55.556 0.73 0.00 40.21 5.52
1944 2074 2.030981 GGTTCGTCTCGTCTCTGTTCTT 60.031 50.000 0.00 0.00 0.00 2.52
2176 2324 6.992063 AGATAGGATGTGTAGTTGCTTTTG 57.008 37.500 0.00 0.00 0.00 2.44
2336 2491 1.105167 CAGATTGTCCCCATGCGCAT 61.105 55.000 19.28 19.28 0.00 4.73
2444 3062 2.747177 TCGTCTAAGATGACCATGGGT 58.253 47.619 18.09 0.99 39.44 4.51
2939 3558 2.044758 AGGCCCTTATAACCTACACCG 58.955 52.381 0.00 0.00 29.98 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 148 5.176590 GCATTTTCGAAAACAAGGTATTGCA 59.823 36.000 24.68 0.00 40.27 4.08
190 191 3.492482 GCCACAACCAACAAGTATTTGCT 60.492 43.478 0.00 0.00 37.85 3.91
611 612 1.745115 GCGATGGTTGTGCCTAGCA 60.745 57.895 0.00 0.00 38.35 3.49
612 613 1.432270 GAGCGATGGTTGTGCCTAGC 61.432 60.000 0.00 0.00 38.35 3.42
613 614 1.148157 CGAGCGATGGTTGTGCCTAG 61.148 60.000 0.00 0.00 38.35 3.02
614 615 1.153647 CGAGCGATGGTTGTGCCTA 60.154 57.895 0.00 0.00 38.35 3.93
615 616 2.434884 CGAGCGATGGTTGTGCCT 60.435 61.111 0.00 0.00 38.35 4.75
616 617 2.434185 TCGAGCGATGGTTGTGCC 60.434 61.111 0.00 0.00 37.90 5.01
617 618 3.084579 CTCGAGCGATGGTTGTGC 58.915 61.111 0.00 0.00 0.00 4.57
618 619 3.084579 GCTCGAGCGATGGTTGTG 58.915 61.111 23.61 0.00 0.00 3.33
641 642 3.887335 TTTACCCCTCGCGTGGTGC 62.887 63.158 24.30 0.00 41.47 5.01
642 643 0.885596 TTTTTACCCCTCGCGTGGTG 60.886 55.000 24.30 16.78 36.04 4.17
643 644 0.886043 GTTTTTACCCCTCGCGTGGT 60.886 55.000 24.30 21.15 38.69 4.16
644 645 1.579964 GGTTTTTACCCCTCGCGTGG 61.580 60.000 20.08 20.08 0.00 4.94
645 646 0.885596 TGGTTTTTACCCCTCGCGTG 60.886 55.000 5.77 2.75 0.00 5.34
646 647 0.886043 GTGGTTTTTACCCCTCGCGT 60.886 55.000 5.77 0.00 0.00 6.01
647 648 1.579964 GGTGGTTTTTACCCCTCGCG 61.580 60.000 0.00 0.00 31.89 5.87
648 649 1.579964 CGGTGGTTTTTACCCCTCGC 61.580 60.000 0.00 0.00 34.66 5.03
649 650 1.579964 GCGGTGGTTTTTACCCCTCG 61.580 60.000 0.00 0.00 34.66 4.63
650 651 0.537828 TGCGGTGGTTTTTACCCCTC 60.538 55.000 0.00 0.00 34.66 4.30
651 652 0.113580 ATGCGGTGGTTTTTACCCCT 59.886 50.000 0.00 0.00 34.66 4.79
652 653 0.528924 GATGCGGTGGTTTTTACCCC 59.471 55.000 0.00 0.00 34.66 4.95
653 654 1.068125 GTGATGCGGTGGTTTTTACCC 60.068 52.381 0.00 0.00 34.66 3.69
654 655 1.400500 CGTGATGCGGTGGTTTTTACC 60.400 52.381 0.00 0.00 36.85 2.85
655 656 1.958417 CGTGATGCGGTGGTTTTTAC 58.042 50.000 0.00 0.00 36.85 2.01
656 657 0.238817 GCGTGATGCGGTGGTTTTTA 59.761 50.000 0.00 0.00 41.69 1.52
657 658 1.007849 GCGTGATGCGGTGGTTTTT 60.008 52.632 0.00 0.00 41.69 1.94
658 659 2.642700 GCGTGATGCGGTGGTTTT 59.357 55.556 0.00 0.00 41.69 2.43
687 688 3.851845 TTTCGCTCGTGTGGTCCGG 62.852 63.158 0.00 0.00 0.00 5.14
688 689 1.886861 CTTTTCGCTCGTGTGGTCCG 61.887 60.000 0.00 0.00 0.00 4.79
689 690 0.878961 ACTTTTCGCTCGTGTGGTCC 60.879 55.000 0.00 0.00 0.00 4.46
690 691 0.232303 CACTTTTCGCTCGTGTGGTC 59.768 55.000 0.00 0.00 0.00 4.02
691 692 1.772063 GCACTTTTCGCTCGTGTGGT 61.772 55.000 0.00 0.00 0.00 4.16
692 693 1.082756 GCACTTTTCGCTCGTGTGG 60.083 57.895 0.00 0.00 0.00 4.17
693 694 1.437089 CGCACTTTTCGCTCGTGTG 60.437 57.895 0.00 0.00 33.56 3.82
694 695 1.548973 CTCGCACTTTTCGCTCGTGT 61.549 55.000 0.00 0.00 0.00 4.49
695 696 1.128611 CTCGCACTTTTCGCTCGTG 59.871 57.895 0.00 0.00 0.00 4.35
696 697 2.658707 GCTCGCACTTTTCGCTCGT 61.659 57.895 0.00 0.00 0.00 4.18
697 698 2.094724 GCTCGCACTTTTCGCTCG 59.905 61.111 0.00 0.00 0.00 5.03
698 699 2.094724 CGCTCGCACTTTTCGCTC 59.905 61.111 0.00 0.00 0.00 5.03
699 700 2.355837 TCGCTCGCACTTTTCGCT 60.356 55.556 0.00 0.00 0.00 4.93
700 701 2.094724 CTCGCTCGCACTTTTCGC 59.905 61.111 0.00 0.00 0.00 4.70
701 702 2.094724 GCTCGCTCGCACTTTTCG 59.905 61.111 0.00 0.00 0.00 3.46
702 703 2.094724 CGCTCGCTCGCACTTTTC 59.905 61.111 0.00 0.00 0.00 2.29
703 704 2.355837 TCGCTCGCTCGCACTTTT 60.356 55.556 0.00 0.00 0.00 2.27
704 705 2.807045 CTCGCTCGCTCGCACTTT 60.807 61.111 0.00 0.00 0.00 2.66
719 720 4.925861 GGAGATGCAGGCCGGCTC 62.926 72.222 28.31 21.19 34.04 4.70
724 725 2.918300 GAAAGGGGGAGATGCAGGCC 62.918 65.000 0.00 0.00 0.00 5.19
725 726 1.454663 GAAAGGGGGAGATGCAGGC 60.455 63.158 0.00 0.00 0.00 4.85
726 727 1.153086 CGAAAGGGGGAGATGCAGG 60.153 63.158 0.00 0.00 0.00 4.85
727 728 1.821332 GCGAAAGGGGGAGATGCAG 60.821 63.158 0.00 0.00 0.00 4.41
728 729 2.257409 GAGCGAAAGGGGGAGATGCA 62.257 60.000 0.00 0.00 0.00 3.96
729 730 1.524849 GAGCGAAAGGGGGAGATGC 60.525 63.158 0.00 0.00 0.00 3.91
730 731 1.227380 CGAGCGAAAGGGGGAGATG 60.227 63.158 0.00 0.00 0.00 2.90
731 732 1.381327 TCGAGCGAAAGGGGGAGAT 60.381 57.895 0.00 0.00 0.00 2.75
732 733 2.036731 TCGAGCGAAAGGGGGAGA 59.963 61.111 0.00 0.00 0.00 3.71
733 734 2.496817 CTCGAGCGAAAGGGGGAG 59.503 66.667 0.00 0.00 0.00 4.30
734 735 3.771160 GCTCGAGCGAAAGGGGGA 61.771 66.667 23.61 0.00 0.00 4.81
735 736 4.840005 GGCTCGAGCGAAAGGGGG 62.840 72.222 29.81 0.00 43.26 5.40
737 738 4.436998 ACGGCTCGAGCGAAAGGG 62.437 66.667 29.81 16.40 43.26 3.95
738 739 2.881352 GACGGCTCGAGCGAAAGG 60.881 66.667 29.81 18.04 43.26 3.11
739 740 3.241059 CGACGGCTCGAGCGAAAG 61.241 66.667 29.81 21.89 43.06 2.62
740 741 3.940975 GACGACGGCTCGAGCGAAA 62.941 63.158 29.81 0.00 43.06 3.46
741 742 4.456253 GACGACGGCTCGAGCGAA 62.456 66.667 29.81 0.00 43.06 4.70
743 744 4.872485 GAGACGACGGCTCGAGCG 62.872 72.222 29.81 25.38 43.06 5.03
744 745 4.539881 GGAGACGACGGCTCGAGC 62.540 72.222 29.38 29.38 43.06 5.03
745 746 3.878519 GGGAGACGACGGCTCGAG 61.879 72.222 23.86 8.45 43.06 4.04
774 775 4.927782 TGGGTGTGCGTGTGGCTC 62.928 66.667 0.00 0.00 44.05 4.70
775 776 3.790416 ATTGGGTGTGCGTGTGGCT 62.790 57.895 0.00 0.00 44.05 4.75
776 777 3.267597 GATTGGGTGTGCGTGTGGC 62.268 63.158 0.00 0.00 43.96 5.01
777 778 2.625823 GGATTGGGTGTGCGTGTGG 61.626 63.158 0.00 0.00 0.00 4.17
778 779 2.625823 GGGATTGGGTGTGCGTGTG 61.626 63.158 0.00 0.00 0.00 3.82
779 780 2.282180 GGGATTGGGTGTGCGTGT 60.282 61.111 0.00 0.00 0.00 4.49
780 781 3.061848 GGGGATTGGGTGTGCGTG 61.062 66.667 0.00 0.00 0.00 5.34
781 782 3.256960 AGGGGATTGGGTGTGCGT 61.257 61.111 0.00 0.00 0.00 5.24
782 783 2.438434 GAGGGGATTGGGTGTGCG 60.438 66.667 0.00 0.00 0.00 5.34
783 784 2.043953 GGAGGGGATTGGGTGTGC 60.044 66.667 0.00 0.00 0.00 4.57
784 785 2.683475 GGGAGGGGATTGGGTGTG 59.317 66.667 0.00 0.00 0.00 3.82
785 786 2.617215 GGGGAGGGGATTGGGTGT 60.617 66.667 0.00 0.00 0.00 4.16
786 787 2.287194 AGGGGAGGGGATTGGGTG 60.287 66.667 0.00 0.00 0.00 4.61
787 788 2.044620 GAGGGGAGGGGATTGGGT 59.955 66.667 0.00 0.00 0.00 4.51
788 789 2.778717 GGAGGGGAGGGGATTGGG 60.779 72.222 0.00 0.00 0.00 4.12
789 790 1.622442 TTGGAGGGGAGGGGATTGG 60.622 63.158 0.00 0.00 0.00 3.16
790 791 1.615262 GTTGGAGGGGAGGGGATTG 59.385 63.158 0.00 0.00 0.00 2.67
791 792 1.622752 GGTTGGAGGGGAGGGGATT 60.623 63.158 0.00 0.00 0.00 3.01
792 793 2.044620 GGTTGGAGGGGAGGGGAT 59.955 66.667 0.00 0.00 0.00 3.85
793 794 4.364686 GGGTTGGAGGGGAGGGGA 62.365 72.222 0.00 0.00 0.00 4.81
794 795 2.916553 CTAGGGTTGGAGGGGAGGGG 62.917 70.000 0.00 0.00 0.00 4.79
795 796 1.384643 CTAGGGTTGGAGGGGAGGG 60.385 68.421 0.00 0.00 0.00 4.30
796 797 2.073101 GCTAGGGTTGGAGGGGAGG 61.073 68.421 0.00 0.00 0.00 4.30
797 798 2.073101 GGCTAGGGTTGGAGGGGAG 61.073 68.421 0.00 0.00 0.00 4.30
798 799 2.042261 GGCTAGGGTTGGAGGGGA 59.958 66.667 0.00 0.00 0.00 4.81
799 800 3.480133 CGGCTAGGGTTGGAGGGG 61.480 72.222 0.00 0.00 0.00 4.79
800 801 4.176752 GCGGCTAGGGTTGGAGGG 62.177 72.222 0.00 0.00 0.00 4.30
801 802 4.176752 GGCGGCTAGGGTTGGAGG 62.177 72.222 0.00 0.00 0.00 4.30
802 803 3.083997 AGGCGGCTAGGGTTGGAG 61.084 66.667 11.03 0.00 0.00 3.86
803 804 3.399181 CAGGCGGCTAGGGTTGGA 61.399 66.667 12.74 0.00 0.00 3.53
804 805 4.489771 CCAGGCGGCTAGGGTTGG 62.490 72.222 12.74 4.43 0.00 3.77
816 817 4.847444 GGAGGAAGCGAGCCAGGC 62.847 72.222 1.84 1.84 0.00 4.85
817 818 3.080121 AGGAGGAAGCGAGCCAGG 61.080 66.667 0.00 0.00 0.00 4.45
818 819 2.498726 GAGGAGGAAGCGAGCCAG 59.501 66.667 0.00 0.00 0.00 4.85
819 820 3.077556 GGAGGAGGAAGCGAGCCA 61.078 66.667 0.00 0.00 0.00 4.75
820 821 2.376228 GATGGAGGAGGAAGCGAGCC 62.376 65.000 0.00 0.00 0.00 4.70
821 822 1.068921 GATGGAGGAGGAAGCGAGC 59.931 63.158 0.00 0.00 0.00 5.03
822 823 0.758685 AGGATGGAGGAGGAAGCGAG 60.759 60.000 0.00 0.00 0.00 5.03
1276 1405 2.482142 GCAACCTCCCAGACTAAGATCG 60.482 54.545 0.00 0.00 0.00 3.69
1739 1869 2.446036 GTACCCCTCCGCCTCCAT 60.446 66.667 0.00 0.00 0.00 3.41
1800 1930 1.904865 ACGTTGAGGGACGGCACTA 60.905 57.895 0.00 0.00 46.77 2.74
1835 1965 4.329545 GGCGAAGAGTGGGCCACA 62.330 66.667 36.28 0.00 46.13 4.17
1944 2074 5.449862 GCATATGCAAACCGATTAACCAAGA 60.450 40.000 22.84 0.00 41.59 3.02
2176 2324 2.362077 AGAACAAACACAGGGCAACATC 59.638 45.455 0.00 0.00 39.74 3.06
2336 2491 2.211806 GCATGAACCTGCAAAGCAAAA 58.788 42.857 0.00 0.00 41.87 2.44
2444 3062 0.397187 AAAATGTGGCTTGCCATGCA 59.603 45.000 17.86 12.06 36.47 3.96
2713 3331 7.862372 TCAGCTAACAAAAAGACAAATGTGATC 59.138 33.333 0.00 0.00 0.00 2.92
2957 3576 1.372997 GAAGACAACTGCGGCGAGA 60.373 57.895 12.98 0.00 0.00 4.04
3195 3815 2.009774 GATCAGGTAACGCAGTGCAAT 58.990 47.619 16.83 5.35 45.00 3.56


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

AutoCloner maintained by Alex Coulton.