Multiple sequence alignment - TraesCS2B01G295000

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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 TraesCS2B01G295000 chr2B 100.000 2336 0 0 1 2336 412057061 412059396 0.000000e+00 4314.0
1 TraesCS2B01G295000 chr2B 88.006 617 58 6 1 616 262528049 262528650 0.000000e+00 715.0
2 TraesCS2B01G295000 chr2B 88.968 562 49 5 1 562 704814370 704813822 0.000000e+00 682.0
3 TraesCS2B01G295000 chr2B 86.190 630 57 10 1 622 675366348 675366955 0.000000e+00 654.0
4 TraesCS2B01G295000 chr2B 85.321 545 68 10 1 536 577245841 577245300 9.430000e-154 553.0
5 TraesCS2B01G295000 chr2D 88.600 1693 118 27 665 2320 346088975 346090629 0.000000e+00 1988.0
6 TraesCS2B01G295000 chr2D 77.500 200 32 12 1681 1872 120441516 120441322 8.830000e-20 108.0
7 TraesCS2B01G295000 chr2A 90.052 965 58 18 719 1680 459799665 459800594 0.000000e+00 1216.0
8 TraesCS2B01G295000 chr2A 81.938 609 59 27 1737 2328 459800597 459801171 3.510000e-128 468.0
9 TraesCS2B01G295000 chr2A 97.222 36 1 0 665 700 459799630 459799665 6.970000e-06 62.1
10 TraesCS2B01G295000 chr7B 89.583 624 45 7 1 622 368143171 368143776 0.000000e+00 774.0
11 TraesCS2B01G295000 chr7B 83.442 308 47 4 2 308 697173721 697174025 1.370000e-72 283.0
12 TraesCS2B01G295000 chr3B 87.302 630 51 9 1 622 605004765 605004157 0.000000e+00 693.0
13 TraesCS2B01G295000 chr1B 81.051 628 103 12 1 618 311244971 311244350 9.700000e-134 486.0
14 TraesCS2B01G295000 chr5B 81.983 605 64 21 1 595 437770618 437771187 2.720000e-129 472.0


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 TraesCS2B01G295000 chr2B 412057061 412059396 2335 False 4314.000000 4314 100.000000 1 2336 1 chr2B.!!$F2 2335
1 TraesCS2B01G295000 chr2B 262528049 262528650 601 False 715.000000 715 88.006000 1 616 1 chr2B.!!$F1 615
2 TraesCS2B01G295000 chr2B 704813822 704814370 548 True 682.000000 682 88.968000 1 562 1 chr2B.!!$R2 561
3 TraesCS2B01G295000 chr2B 675366348 675366955 607 False 654.000000 654 86.190000 1 622 1 chr2B.!!$F3 621
4 TraesCS2B01G295000 chr2B 577245300 577245841 541 True 553.000000 553 85.321000 1 536 1 chr2B.!!$R1 535
5 TraesCS2B01G295000 chr2D 346088975 346090629 1654 False 1988.000000 1988 88.600000 665 2320 1 chr2D.!!$F1 1655
6 TraesCS2B01G295000 chr2A 459799630 459801171 1541 False 582.033333 1216 89.737333 665 2328 3 chr2A.!!$F1 1663
7 TraesCS2B01G295000 chr7B 368143171 368143776 605 False 774.000000 774 89.583000 1 622 1 chr7B.!!$F1 621
8 TraesCS2B01G295000 chr3B 605004157 605004765 608 True 693.000000 693 87.302000 1 622 1 chr3B.!!$R1 621
9 TraesCS2B01G295000 chr1B 311244350 311244971 621 True 486.000000 486 81.051000 1 618 1 chr1B.!!$R1 617
10 TraesCS2B01G295000 chr5B 437770618 437771187 569 False 472.000000 472 81.983000 1 595 1 chr5B.!!$F1 594

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
776 818 0.036483 GATTGGCGGCAAAAATGGGT 60.036 50.0 29.04 10.17 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 1864 0.227986 CGACGACGACGATGACGATA 59.772 55.0 15.32 0.0 41.06 2.92 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
138 143 3.837146 TGAAGCAGAGACCAAAGAGATCT 59.163 43.478 0.00 0.00 0.00 2.75
404 415 1.344191 GGCTGGAGCTTGGAGGAGAT 61.344 60.000 0.00 0.00 41.70 2.75
408 419 1.115467 GGAGCTTGGAGGAGATCGAA 58.885 55.000 0.00 0.00 32.97 3.71
611 650 4.514577 GAAGGGCGCGCTAGAGCA 62.515 66.667 32.29 0.00 45.28 4.26
622 661 4.075793 TAGAGCAGGGGAGCGGGT 62.076 66.667 0.00 0.00 40.15 5.28
623 662 2.642183 CTAGAGCAGGGGAGCGGGTA 62.642 65.000 0.00 0.00 40.15 3.69
624 663 2.020100 TAGAGCAGGGGAGCGGGTAT 62.020 60.000 0.00 0.00 40.15 2.73
625 664 2.366972 AGCAGGGGAGCGGGTATT 60.367 61.111 0.00 0.00 40.15 1.89
626 665 2.203209 GCAGGGGAGCGGGTATTG 60.203 66.667 0.00 0.00 0.00 1.90
627 666 2.203209 CAGGGGAGCGGGTATTGC 60.203 66.667 0.00 0.00 0.00 3.56
633 672 3.081409 AGCGGGTATTGCTCGGGT 61.081 61.111 0.00 0.00 42.38 5.28
634 673 2.588034 GCGGGTATTGCTCGGGTC 60.588 66.667 0.00 0.00 42.38 4.46
635 674 2.108362 CGGGTATTGCTCGGGTCC 59.892 66.667 0.00 0.00 37.44 4.46
636 675 2.432300 CGGGTATTGCTCGGGTCCT 61.432 63.158 0.00 0.00 37.44 3.85
637 676 1.912971 GGGTATTGCTCGGGTCCTT 59.087 57.895 0.00 0.00 0.00 3.36
638 677 0.463833 GGGTATTGCTCGGGTCCTTG 60.464 60.000 0.00 0.00 0.00 3.61
639 678 0.463833 GGTATTGCTCGGGTCCTTGG 60.464 60.000 0.00 0.00 0.00 3.61
640 679 0.539986 GTATTGCTCGGGTCCTTGGA 59.460 55.000 0.00 0.00 0.00 3.53
641 680 0.539986 TATTGCTCGGGTCCTTGGAC 59.460 55.000 11.13 11.13 0.00 4.02
642 681 1.201429 ATTGCTCGGGTCCTTGGACT 61.201 55.000 17.99 0.00 0.00 3.85
643 682 2.111999 TTGCTCGGGTCCTTGGACTG 62.112 60.000 17.99 11.69 0.00 3.51
644 683 2.283529 GCTCGGGTCCTTGGACTGA 61.284 63.158 17.99 14.71 0.00 3.41
645 684 1.827399 GCTCGGGTCCTTGGACTGAA 61.827 60.000 17.99 4.56 0.00 3.02
646 685 0.037232 CTCGGGTCCTTGGACTGAAC 60.037 60.000 17.99 3.00 0.00 3.18
647 686 1.374252 CGGGTCCTTGGACTGAACG 60.374 63.158 17.99 13.55 0.00 3.95
648 687 1.752833 GGGTCCTTGGACTGAACGT 59.247 57.895 17.99 0.00 0.00 3.99
649 688 0.108019 GGGTCCTTGGACTGAACGTT 59.892 55.000 17.99 0.00 0.00 3.99
650 689 1.226746 GGTCCTTGGACTGAACGTTG 58.773 55.000 17.99 0.00 0.00 4.10
651 690 1.226746 GTCCTTGGACTGAACGTTGG 58.773 55.000 5.00 0.23 0.00 3.77
652 691 0.107831 TCCTTGGACTGAACGTTGGG 59.892 55.000 5.00 0.00 0.00 4.12
653 692 0.179029 CCTTGGACTGAACGTTGGGT 60.179 55.000 5.00 3.68 0.00 4.51
654 693 0.944386 CTTGGACTGAACGTTGGGTG 59.056 55.000 5.00 0.00 0.00 4.61
655 694 0.253610 TTGGACTGAACGTTGGGTGT 59.746 50.000 5.00 0.00 0.00 4.16
656 695 0.253610 TGGACTGAACGTTGGGTGTT 59.746 50.000 5.00 0.00 0.00 3.32
657 696 0.661020 GGACTGAACGTTGGGTGTTG 59.339 55.000 5.00 0.00 0.00 3.33
658 697 0.661020 GACTGAACGTTGGGTGTTGG 59.339 55.000 5.00 0.00 0.00 3.77
659 698 0.253610 ACTGAACGTTGGGTGTTGGA 59.746 50.000 5.00 0.00 0.00 3.53
660 699 1.340211 ACTGAACGTTGGGTGTTGGAA 60.340 47.619 5.00 0.00 0.00 3.53
661 700 1.064952 CTGAACGTTGGGTGTTGGAAC 59.935 52.381 5.00 0.00 0.00 3.62
662 701 1.340211 TGAACGTTGGGTGTTGGAACT 60.340 47.619 5.00 0.00 0.00 3.01
663 702 1.064952 GAACGTTGGGTGTTGGAACTG 59.935 52.381 5.00 0.00 0.00 3.16
664 703 0.253610 ACGTTGGGTGTTGGAACTGA 59.746 50.000 0.00 0.00 0.00 3.41
665 704 1.133915 ACGTTGGGTGTTGGAACTGAT 60.134 47.619 0.00 0.00 0.00 2.90
666 705 2.105134 ACGTTGGGTGTTGGAACTGATA 59.895 45.455 0.00 0.00 0.00 2.15
705 744 4.521256 TGTAAGCCAAAAGATGTTGTACCC 59.479 41.667 0.00 0.00 0.00 3.69
706 745 3.525800 AGCCAAAAGATGTTGTACCCT 57.474 42.857 0.00 0.00 0.00 4.34
735 774 7.332182 CGCCTCTAGTAGAAAAGAAAAAGACAT 59.668 37.037 0.64 0.00 0.00 3.06
745 787 6.463995 AAAGAAAAAGACATTGTACCAGCA 57.536 33.333 0.00 0.00 0.00 4.41
749 791 5.438761 AAAAGACATTGTACCAGCACTTC 57.561 39.130 0.00 0.00 0.00 3.01
776 818 0.036483 GATTGGCGGCAAAAATGGGT 60.036 50.000 29.04 10.17 0.00 4.51
827 869 6.317893 ACTCTACATTTAAATACGGCCAAAGG 59.682 38.462 2.24 0.00 0.00 3.11
828 870 4.729227 ACATTTAAATACGGCCAAAGGG 57.271 40.909 2.24 0.00 37.18 3.95
853 895 3.690460 AGGGGAGTAAAGCAAAGACATG 58.310 45.455 0.00 0.00 0.00 3.21
872 914 2.046285 GTGGGGCCACGAGAATTGG 61.046 63.158 4.39 0.00 37.19 3.16
894 936 2.492881 CCAATACCAAACCCCCGTTTAC 59.507 50.000 0.00 0.00 40.28 2.01
903 945 0.824182 CCCCCGTTTACAAGTTGCCA 60.824 55.000 1.81 0.00 0.00 4.92
922 964 1.239968 ACCCGAGTCTACCGTGACAC 61.240 60.000 0.00 0.00 39.27 3.67
923 965 1.134075 CCGAGTCTACCGTGACACG 59.866 63.158 21.02 21.02 45.62 4.49
924 966 1.511464 CGAGTCTACCGTGACACGC 60.511 63.158 22.46 8.39 42.01 5.34
925 967 1.511464 GAGTCTACCGTGACACGCG 60.511 63.158 22.46 17.02 40.91 6.01
926 968 1.904852 GAGTCTACCGTGACACGCGA 61.905 60.000 22.46 14.34 40.91 5.87
927 969 1.795177 GTCTACCGTGACACGCGAC 60.795 63.158 22.46 20.86 40.91 5.19
928 970 2.868331 CTACCGTGACACGCGACG 60.868 66.667 22.46 12.75 40.91 5.12
985 1038 3.012518 CAAAAGCATCTACAGGTCCAGG 58.987 50.000 0.00 0.00 0.00 4.45
986 1039 1.207791 AAGCATCTACAGGTCCAGGG 58.792 55.000 0.00 0.00 0.00 4.45
987 1040 1.147153 GCATCTACAGGTCCAGGGC 59.853 63.158 0.00 0.00 0.00 5.19
988 1041 1.626356 GCATCTACAGGTCCAGGGCA 61.626 60.000 0.00 0.00 0.00 5.36
1182 1235 4.021925 GGCGTGGACCCTGAGCTT 62.022 66.667 0.00 0.00 0.00 3.74
1393 1446 2.736995 CATGCACGTTCGACCGGT 60.737 61.111 6.92 6.92 0.00 5.28
1489 1542 5.867174 TGTGACGTGATATCGATTGTTCTTT 59.133 36.000 1.71 0.00 34.70 2.52
1491 1544 7.542824 TGTGACGTGATATCGATTGTTCTTTTA 59.457 33.333 1.71 0.00 34.70 1.52
1493 1546 6.919188 ACGTGATATCGATTGTTCTTTTACG 58.081 36.000 1.71 7.34 34.70 3.18
1547 1603 0.445436 CATCTTCAACGCTCACCTGC 59.555 55.000 0.00 0.00 0.00 4.85
1551 1607 1.267806 CTTCAACGCTCACCTGCAAAT 59.732 47.619 0.00 0.00 0.00 2.32
1553 1609 0.592637 CAACGCTCACCTGCAAATCA 59.407 50.000 0.00 0.00 0.00 2.57
1554 1610 0.593128 AACGCTCACCTGCAAATCAC 59.407 50.000 0.00 0.00 0.00 3.06
1558 1614 1.335324 GCTCACCTGCAAATCACACAC 60.335 52.381 0.00 0.00 0.00 3.82
1563 1619 0.386352 CTGCAAATCACACACCGCAG 60.386 55.000 0.00 0.00 40.68 5.18
1568 1624 4.961511 TCACACACCGCAGCCGTC 62.962 66.667 0.00 0.00 0.00 4.79
1593 1649 3.548770 TGATACGGATGTAGAAGTCGGT 58.451 45.455 0.00 0.00 33.17 4.69
1601 1657 4.950050 GATGTAGAAGTCGGTCATCCAAT 58.050 43.478 0.00 0.00 31.74 3.16
1604 1660 0.652592 GAAGTCGGTCATCCAATGCG 59.347 55.000 0.00 0.00 0.00 4.73
1608 1664 2.180204 CGGTCATCCAATGCGACCC 61.180 63.158 8.48 0.00 45.34 4.46
1802 1864 2.048877 ATCGCCGTTCGTTCCGTT 60.049 55.556 0.00 0.00 39.67 4.44
1803 1865 1.072116 CATCGCCGTTCGTTCCGTTA 61.072 55.000 0.00 0.00 39.67 3.18
1804 1866 0.179129 ATCGCCGTTCGTTCCGTTAT 60.179 50.000 0.00 0.00 39.67 1.89
1805 1867 0.798009 TCGCCGTTCGTTCCGTTATC 60.798 55.000 0.00 0.00 39.67 1.75
1806 1868 1.627424 GCCGTTCGTTCCGTTATCG 59.373 57.895 0.00 0.00 0.00 2.92
1807 1869 1.072666 GCCGTTCGTTCCGTTATCGT 61.073 55.000 0.00 0.00 35.01 3.73
1808 1870 0.909843 CCGTTCGTTCCGTTATCGTC 59.090 55.000 0.00 0.00 35.01 4.20
1809 1871 1.605500 CGTTCGTTCCGTTATCGTCA 58.394 50.000 0.00 0.00 35.01 4.35
1810 1872 2.179589 CGTTCGTTCCGTTATCGTCAT 58.820 47.619 0.00 0.00 35.01 3.06
1811 1873 2.212687 CGTTCGTTCCGTTATCGTCATC 59.787 50.000 0.00 0.00 35.01 2.92
1812 1874 2.095384 TCGTTCCGTTATCGTCATCG 57.905 50.000 0.00 0.00 38.55 3.84
1813 1875 1.398041 TCGTTCCGTTATCGTCATCGT 59.602 47.619 0.00 0.00 38.33 3.73
1880 1942 1.290955 CTTGTCCGGCGGTTGTCTA 59.709 57.895 27.32 1.27 0.00 2.59
1901 1963 3.688235 ACTACTCGTGAAGGAGCTACTT 58.312 45.455 12.17 12.17 39.94 2.24
1951 2013 2.409055 GCGGCCAATGCAGATGACA 61.409 57.895 2.24 0.00 40.13 3.58
1995 2057 3.065306 CCCCTGCAGACGTTGGTA 58.935 61.111 17.39 0.00 0.00 3.25
2024 2086 1.806623 GCTATGCGACCATTCCTCGTT 60.807 52.381 0.00 0.00 33.51 3.85
2059 2121 1.961277 CTGTCAAGGTGGTGGCGAC 60.961 63.158 0.00 0.00 0.00 5.19
2078 2140 3.733960 CGTGGCGGTCGTCTCTGA 61.734 66.667 0.00 0.00 0.00 3.27
2131 2193 1.002430 TGGTGAGGTCTGAGTCATTGC 59.998 52.381 0.00 0.00 0.00 3.56
2221 2308 1.533033 TCGGAGACAACAGCCCTCA 60.533 57.895 0.00 0.00 0.00 3.86
2324 2411 3.282157 CTTGATGGGGCGGCGATG 61.282 66.667 12.98 0.00 0.00 3.84
2325 2412 4.108299 TTGATGGGGCGGCGATGT 62.108 61.111 12.98 0.00 0.00 3.06
2326 2413 2.658679 CTTGATGGGGCGGCGATGTA 62.659 60.000 12.98 0.00 0.00 2.29
2327 2414 2.357517 GATGGGGCGGCGATGTAG 60.358 66.667 12.98 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
320 331 0.970937 CCTCTCCACTAGTGCCGGAA 60.971 60.000 17.86 0.00 0.00 4.30
329 340 1.656092 ATCCGAGGGCCTCTCCACTA 61.656 60.000 29.81 9.93 39.30 2.74
408 419 4.496336 GGATCTGCAAGCCCGGCT 62.496 66.667 5.94 5.94 42.56 5.52
611 650 2.366972 AGCAATACCCGCTCCCCT 60.367 61.111 0.00 0.00 33.35 4.79
622 661 0.539986 GTCCAAGGACCCGAGCAATA 59.460 55.000 8.06 0.00 39.08 1.90
623 662 1.201429 AGTCCAAGGACCCGAGCAAT 61.201 55.000 15.36 0.00 45.59 3.56
624 663 1.841556 AGTCCAAGGACCCGAGCAA 60.842 57.895 15.36 0.00 45.59 3.91
625 664 2.203788 AGTCCAAGGACCCGAGCA 60.204 61.111 15.36 0.00 45.59 4.26
626 665 1.827399 TTCAGTCCAAGGACCCGAGC 61.827 60.000 15.36 0.00 45.59 5.03
627 666 0.037232 GTTCAGTCCAAGGACCCGAG 60.037 60.000 15.36 4.28 45.59 4.63
628 667 1.812686 CGTTCAGTCCAAGGACCCGA 61.813 60.000 15.36 9.84 45.59 5.14
629 668 1.374252 CGTTCAGTCCAAGGACCCG 60.374 63.158 15.36 7.67 45.59 5.28
630 669 0.108019 AACGTTCAGTCCAAGGACCC 59.892 55.000 15.36 1.40 45.59 4.46
631 670 1.226746 CAACGTTCAGTCCAAGGACC 58.773 55.000 15.36 0.00 45.59 4.46
632 671 1.226746 CCAACGTTCAGTCCAAGGAC 58.773 55.000 11.29 11.29 44.86 3.85
633 672 0.107831 CCCAACGTTCAGTCCAAGGA 59.892 55.000 0.00 0.00 0.00 3.36
634 673 0.179029 ACCCAACGTTCAGTCCAAGG 60.179 55.000 0.00 0.00 0.00 3.61
635 674 0.944386 CACCCAACGTTCAGTCCAAG 59.056 55.000 0.00 0.00 0.00 3.61
636 675 0.253610 ACACCCAACGTTCAGTCCAA 59.746 50.000 0.00 0.00 0.00 3.53
637 676 0.253610 AACACCCAACGTTCAGTCCA 59.746 50.000 0.00 0.00 0.00 4.02
638 677 0.661020 CAACACCCAACGTTCAGTCC 59.339 55.000 0.00 0.00 0.00 3.85
639 678 0.661020 CCAACACCCAACGTTCAGTC 59.339 55.000 0.00 0.00 0.00 3.51
640 679 0.253610 TCCAACACCCAACGTTCAGT 59.746 50.000 0.00 0.00 0.00 3.41
641 680 1.064952 GTTCCAACACCCAACGTTCAG 59.935 52.381 0.00 0.00 0.00 3.02
642 681 1.096416 GTTCCAACACCCAACGTTCA 58.904 50.000 0.00 0.00 0.00 3.18
643 682 1.064952 CAGTTCCAACACCCAACGTTC 59.935 52.381 0.00 0.00 0.00 3.95
644 683 1.099689 CAGTTCCAACACCCAACGTT 58.900 50.000 0.00 0.00 0.00 3.99
645 684 0.253610 TCAGTTCCAACACCCAACGT 59.746 50.000 0.00 0.00 0.00 3.99
646 685 1.604604 ATCAGTTCCAACACCCAACG 58.395 50.000 0.00 0.00 0.00 4.10
647 686 2.488153 GCTATCAGTTCCAACACCCAAC 59.512 50.000 0.00 0.00 0.00 3.77
648 687 2.790433 GCTATCAGTTCCAACACCCAA 58.210 47.619 0.00 0.00 0.00 4.12
649 688 1.338674 CGCTATCAGTTCCAACACCCA 60.339 52.381 0.00 0.00 0.00 4.51
650 689 1.369625 CGCTATCAGTTCCAACACCC 58.630 55.000 0.00 0.00 0.00 4.61
651 690 0.727398 GCGCTATCAGTTCCAACACC 59.273 55.000 0.00 0.00 0.00 4.16
652 691 1.438651 TGCGCTATCAGTTCCAACAC 58.561 50.000 9.73 0.00 0.00 3.32
653 692 2.009051 CATGCGCTATCAGTTCCAACA 58.991 47.619 9.73 0.00 0.00 3.33
654 693 2.279741 TCATGCGCTATCAGTTCCAAC 58.720 47.619 9.73 0.00 0.00 3.77
655 694 2.689553 TCATGCGCTATCAGTTCCAA 57.310 45.000 9.73 0.00 0.00 3.53
656 695 2.916702 ATCATGCGCTATCAGTTCCA 57.083 45.000 9.73 0.00 0.00 3.53
657 696 4.032217 CGATAATCATGCGCTATCAGTTCC 59.968 45.833 9.73 0.00 0.00 3.62
658 697 4.623167 ACGATAATCATGCGCTATCAGTTC 59.377 41.667 9.73 0.00 0.00 3.01
659 698 4.560128 ACGATAATCATGCGCTATCAGTT 58.440 39.130 9.73 0.00 0.00 3.16
660 699 4.179926 ACGATAATCATGCGCTATCAGT 57.820 40.909 9.73 7.04 0.00 3.41
661 700 4.386954 ACAACGATAATCATGCGCTATCAG 59.613 41.667 9.73 6.46 0.00 2.90
662 701 4.306600 ACAACGATAATCATGCGCTATCA 58.693 39.130 9.73 0.00 0.00 2.15
663 702 4.910746 ACAACGATAATCATGCGCTATC 57.089 40.909 9.73 6.24 0.00 2.08
664 703 5.163953 GCTTACAACGATAATCATGCGCTAT 60.164 40.000 9.73 0.00 0.00 2.97
665 704 4.149922 GCTTACAACGATAATCATGCGCTA 59.850 41.667 9.73 0.00 0.00 4.26
666 705 3.059597 GCTTACAACGATAATCATGCGCT 60.060 43.478 9.73 0.00 0.00 5.92
705 744 5.821516 TTCTTTTCTACTAGAGGCGAGAG 57.178 43.478 0.00 0.00 0.00 3.20
706 745 6.585695 TTTTCTTTTCTACTAGAGGCGAGA 57.414 37.500 0.00 0.00 0.00 4.04
735 774 2.331166 TGGGTAGAAGTGCTGGTACAA 58.669 47.619 0.00 0.00 38.70 2.41
776 818 1.887242 GTGCGCACAGAACTGACCA 60.887 57.895 34.52 0.00 0.00 4.02
801 843 7.148137 CCTTTGGCCGTATTTAAATGTAGAGTT 60.148 37.037 11.05 0.00 0.00 3.01
827 869 1.627864 TTGCTTTACTCCCCTTTGCC 58.372 50.000 0.00 0.00 0.00 4.52
828 870 2.890945 TCTTTGCTTTACTCCCCTTTGC 59.109 45.455 0.00 0.00 0.00 3.68
829 871 3.888930 TGTCTTTGCTTTACTCCCCTTTG 59.111 43.478 0.00 0.00 0.00 2.77
830 872 4.178956 TGTCTTTGCTTTACTCCCCTTT 57.821 40.909 0.00 0.00 0.00 3.11
831 873 3.876309 TGTCTTTGCTTTACTCCCCTT 57.124 42.857 0.00 0.00 0.00 3.95
832 874 3.562176 CCATGTCTTTGCTTTACTCCCCT 60.562 47.826 0.00 0.00 0.00 4.79
853 895 2.046285 CAATTCTCGTGGCCCCACC 61.046 63.158 11.62 0.00 43.49 4.61
872 914 0.901114 AACGGGGGTTTGGTATTGGC 60.901 55.000 0.00 0.00 0.00 4.52
886 928 0.312729 GGTGGCAACTTGTAAACGGG 59.687 55.000 0.00 0.00 37.61 5.28
894 936 0.320374 TAGACTCGGGTGGCAACTTG 59.680 55.000 0.97 0.00 37.61 3.16
903 945 1.073722 TGTCACGGTAGACTCGGGT 59.926 57.895 0.00 0.00 39.27 5.28
922 964 3.163110 GAGGAGAGAGAGCGTCGCG 62.163 68.421 12.30 0.00 0.00 5.87
923 965 2.713154 GAGGAGAGAGAGCGTCGC 59.287 66.667 9.80 9.80 0.00 5.19
924 966 1.436195 CTGGAGGAGAGAGAGCGTCG 61.436 65.000 0.00 0.00 0.00 5.12
925 967 1.724582 GCTGGAGGAGAGAGAGCGTC 61.725 65.000 0.00 0.00 0.00 5.19
926 968 1.752694 GCTGGAGGAGAGAGAGCGT 60.753 63.158 0.00 0.00 0.00 5.07
927 969 1.453745 AGCTGGAGGAGAGAGAGCG 60.454 63.158 0.00 0.00 34.75 5.03
928 970 2.019897 GCAGCTGGAGGAGAGAGAGC 62.020 65.000 17.12 0.00 0.00 4.09
929 971 0.683828 TGCAGCTGGAGGAGAGAGAG 60.684 60.000 17.12 0.00 0.00 3.20
930 972 0.251967 TTGCAGCTGGAGGAGAGAGA 60.252 55.000 17.12 0.00 0.00 3.10
931 973 0.612229 TTTGCAGCTGGAGGAGAGAG 59.388 55.000 17.12 0.00 0.00 3.20
932 974 0.612229 CTTTGCAGCTGGAGGAGAGA 59.388 55.000 17.12 0.00 0.00 3.10
985 1038 1.457346 CCCATTCTCTGTCACTTGCC 58.543 55.000 0.00 0.00 0.00 4.52
986 1039 0.807496 GCCCATTCTCTGTCACTTGC 59.193 55.000 0.00 0.00 0.00 4.01
987 1040 2.082231 CTGCCCATTCTCTGTCACTTG 58.918 52.381 0.00 0.00 0.00 3.16
988 1041 1.980765 TCTGCCCATTCTCTGTCACTT 59.019 47.619 0.00 0.00 0.00 3.16
1143 1196 0.387202 CCTCCAGCTTCATCGACGAT 59.613 55.000 4.05 4.05 0.00 3.73
1281 1334 1.192428 GGTTGGTGTACGATCCTCCT 58.808 55.000 0.00 0.00 0.00 3.69
1421 1474 5.527214 CACATTATTCCAAGATAGCGGAACA 59.473 40.000 0.00 0.00 43.88 3.18
1489 1542 3.485110 CGCCATGCTTCTGCGTAA 58.515 55.556 5.29 0.00 43.12 3.18
1493 1546 0.875908 TATCGACGCCATGCTTCTGC 60.876 55.000 0.00 0.00 40.20 4.26
1547 1603 1.081242 GGCTGCGGTGTGTGATTTG 60.081 57.895 0.00 0.00 0.00 2.32
1551 1607 4.961511 GACGGCTGCGGTGTGTGA 62.962 66.667 17.89 0.00 0.00 3.58
1558 1614 3.709880 TATCAACGGACGGCTGCGG 62.710 63.158 0.00 5.60 35.09 5.69
1572 1628 3.548770 ACCGACTTCTACATCCGTATCA 58.451 45.455 0.00 0.00 0.00 2.15
1586 1642 0.249120 TCGCATTGGATGACCGACTT 59.751 50.000 0.00 0.00 39.42 3.01
1593 1649 0.255604 ATGTGGGTCGCATTGGATGA 59.744 50.000 0.00 0.00 29.65 2.92
1601 1657 5.906113 ATTTTTAATGTATGTGGGTCGCA 57.094 34.783 0.00 0.00 0.00 5.10
1689 1749 9.840427 AAACGATCAAAATGTCGATCTTTTTAT 57.160 25.926 1.49 4.28 37.00 1.40
1727 1787 7.201758 CCGGTATAAGGATTAGGTTGTTTTTCC 60.202 40.741 0.00 0.00 31.76 3.13
1732 1792 4.445305 GCCCGGTATAAGGATTAGGTTGTT 60.445 45.833 0.00 0.00 31.76 2.83
1734 1794 3.671716 GCCCGGTATAAGGATTAGGTTG 58.328 50.000 0.00 0.00 31.76 3.77
1742 1804 1.076118 TGGTCGCCCGGTATAAGGA 60.076 57.895 0.00 0.00 0.00 3.36
1745 1807 0.977108 AAGGTGGTCGCCCGGTATAA 60.977 55.000 0.00 0.00 0.00 0.98
1797 1859 1.004610 GACGACGATGACGATAACGGA 60.005 52.381 0.00 0.00 44.46 4.69
1802 1864 0.227986 CGACGACGACGATGACGATA 59.772 55.000 15.32 0.00 41.06 2.92
1803 1865 1.012562 CGACGACGACGATGACGAT 60.013 57.895 15.32 0.00 41.06 3.73
1804 1866 2.271024 GACGACGACGACGATGACGA 62.271 60.000 25.15 0.00 41.06 4.20
1805 1867 1.922220 GACGACGACGACGATGACG 60.922 63.158 25.15 14.84 42.66 4.35
1806 1868 1.579626 GGACGACGACGACGATGAC 60.580 63.158 25.15 12.72 42.66 3.06
1807 1869 2.743752 GGGACGACGACGACGATGA 61.744 63.158 25.15 0.00 42.66 2.92
1808 1870 2.277120 GGGACGACGACGACGATG 60.277 66.667 25.15 8.06 42.66 3.84
1809 1871 2.435586 AGGGACGACGACGACGAT 60.436 61.111 25.15 10.17 42.66 3.73
1810 1872 3.114616 GAGGGACGACGACGACGA 61.115 66.667 25.15 0.00 42.66 4.20
1811 1873 4.157958 GGAGGGACGACGACGACG 62.158 72.222 17.60 17.60 42.66 5.12
1812 1874 3.052082 TGGAGGGACGACGACGAC 61.052 66.667 15.32 7.84 42.66 4.34
1813 1875 3.052082 GTGGAGGGACGACGACGA 61.052 66.667 15.32 0.00 42.66 4.20
1874 1936 3.439476 GCTCCTTCACGAGTAGTAGACAA 59.561 47.826 0.00 0.00 32.11 3.18
1880 1942 3.353370 AGTAGCTCCTTCACGAGTAGT 57.647 47.619 0.00 0.00 32.11 2.73
1930 1992 4.802051 ATCTGCATTGGCCGCGGT 62.802 61.111 28.70 2.82 40.13 5.68
1936 1998 0.376152 CGAGTGTCATCTGCATTGGC 59.624 55.000 0.00 0.00 41.68 4.52
1951 2013 1.007734 TCGTCAAAGCTTCGCGAGT 60.008 52.632 9.59 0.00 0.00 4.18
1985 2047 1.336609 GCGACTCCTTTACCAACGTCT 60.337 52.381 0.00 0.00 0.00 4.18
1989 2051 2.608090 GCATAGCGACTCCTTTACCAAC 59.392 50.000 0.00 0.00 0.00 3.77
2024 2086 2.124983 GCGAGCTTGCCAGGATCA 60.125 61.111 15.66 0.00 0.00 2.92
2062 2124 1.517257 CATCAGAGACGACCGCCAC 60.517 63.158 0.00 0.00 0.00 5.01
2078 2140 0.740868 CGACCGCTTCATCACCACAT 60.741 55.000 0.00 0.00 0.00 3.21
2110 2172 2.355513 GCAATGACTCAGACCTCACCAT 60.356 50.000 0.00 0.00 0.00 3.55
2114 2176 0.247460 CCGCAATGACTCAGACCTCA 59.753 55.000 0.00 0.00 0.00 3.86
2140 2213 4.514577 CCGCTCGCCAAGTCCGAT 62.515 66.667 0.00 0.00 33.83 4.18
2190 2277 4.426313 TCCGAGGAGGAGCGCAGA 62.426 66.667 11.47 0.00 45.98 4.26
2245 2332 0.394488 CTCCACTACCTCAGAGGCGA 60.394 60.000 17.31 3.84 39.63 5.54
2294 2381 2.053244 CCATCAAGGAGGAGCTACCAT 58.947 52.381 0.00 0.00 41.22 3.55
2298 2385 1.056700 GCCCCATCAAGGAGGAGCTA 61.057 60.000 0.00 0.00 41.22 3.32


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

AutoCloner maintained by Alex Coulton.