Multiple sequence alignment - TraesCS4A01G010900

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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 TraesCS4A01G010900 chr4A 100.000 2111 0 0 1 2111 6034544 6032434 0.000000e+00 3899.0
1 TraesCS4A01G010900 chr4A 85.106 423 44 13 863 1283 11623008 11622603 4.190000e-112 414.0
2 TraesCS4A01G010900 chr4A 83.696 460 48 20 858 1313 21844251 21844687 1.950000e-110 409.0
3 TraesCS4A01G010900 chr4A 90.690 290 27 0 874 1163 684615221 684615510 9.140000e-104 387.0
4 TraesCS4A01G010900 chr4A 96.970 33 0 1 1888 1920 548540172 548540203 1.000000e-03 54.7
5 TraesCS4A01G010900 chr4A 96.970 33 0 1 1888 1920 548540782 548540813 1.000000e-03 54.7
6 TraesCS4A01G010900 chr4D 87.841 1357 98 43 775 2111 463402197 463403506 0.000000e+00 1530.0
7 TraesCS4A01G010900 chr4D 88.067 595 30 19 21 599 463401546 463402115 0.000000e+00 667.0
8 TraesCS4A01G010900 chr4D 88.221 399 33 11 884 1278 477914199 477914587 4.100000e-127 464.0
9 TraesCS4A01G010900 chr4D 84.561 421 45 15 875 1293 456124203 456124605 1.170000e-107 399.0
10 TraesCS4A01G010900 chr4B 85.375 1347 129 33 785 2111 579390457 579391755 0.000000e+00 1334.0
11 TraesCS4A01G010900 chr4B 89.983 579 31 4 21 575 579102463 579103038 0.000000e+00 723.0
12 TraesCS4A01G010900 chr4B 83.845 749 77 32 1364 2103 579103796 579104509 0.000000e+00 673.0
13 TraesCS4A01G010900 chr4B 86.698 639 31 25 21 638 579389783 579390388 0.000000e+00 660.0
14 TraesCS4A01G010900 chr4B 90.741 432 26 7 884 1314 579103373 579103791 3.930000e-157 564.0
15 TraesCS4A01G010900 chr4B 87.346 324 33 7 856 1177 570346607 570346924 4.280000e-97 364.0
16 TraesCS4A01G010900 chr3A 94.872 39 0 2 1885 1921 733517710 733517748 2.260000e-05 60.2
17 TraesCS4A01G010900 chr6D 100.000 31 0 0 1888 1918 332501228 332501198 8.140000e-05 58.4
18 TraesCS4A01G010900 chr6B 100.000 31 0 0 1888 1918 487833391 487833421 8.140000e-05 58.4
19 TraesCS4A01G010900 chr1D 96.875 32 1 0 1888 1919 25233951 25233920 1.000000e-03 54.7
20 TraesCS4A01G010900 chr5B 100.000 28 0 0 1888 1915 665559999 665560026 4.000000e-03 52.8
21 TraesCS4A01G010900 chr2D 94.118 34 2 0 1886 1919 524566853 524566820 4.000000e-03 52.8
22 TraesCS4A01G010900 chr1A 100.000 28 0 0 1885 1912 135522555 135522528 4.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G010900 chr4A 6032434 6034544 2110 True 3899.000000 3899 100.000000 1 2111 1 chr4A.!!$R1 2110
1 TraesCS4A01G010900 chr4D 463401546 463403506 1960 False 1098.500000 1530 87.954000 21 2111 2 chr4D.!!$F3 2090
2 TraesCS4A01G010900 chr4B 579389783 579391755 1972 False 997.000000 1334 86.036500 21 2111 2 chr4B.!!$F3 2090
3 TraesCS4A01G010900 chr4B 579102463 579104509 2046 False 653.333333 723 88.189667 21 2103 3 chr4B.!!$F2 2082

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
709 820 0.108585 ACAGCTTTCGCAAAGAGGGA 59.891 50.0 11.34 0.0 41.02 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1625 1918 0.838608 AGTTTTGTACCACCGACCCA 59.161 50.0 0.0 0.0 0.0 4.51 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
350 381 4.106925 GCTGGTGCTCCTGGAGGG 62.107 72.222 24.43 2.00 36.03 4.30
466 508 2.202810 CCGAGAAGGCGAGGAAGC 60.203 66.667 0.00 0.00 0.00 3.86
467 509 2.580867 CGAGAAGGCGAGGAAGCG 60.581 66.667 0.00 0.00 38.18 4.68
510 564 4.504916 CAGGCAGAGTCGGCGGAG 62.505 72.222 7.21 0.00 36.37 4.63
594 682 0.508641 CCAACGAGTGCTGAACGAAG 59.491 55.000 0.00 0.00 0.00 3.79
595 683 1.487482 CAACGAGTGCTGAACGAAGA 58.513 50.000 0.00 0.00 0.00 2.87
596 684 2.061773 CAACGAGTGCTGAACGAAGAT 58.938 47.619 0.00 0.00 0.00 2.40
597 685 1.702886 ACGAGTGCTGAACGAAGATG 58.297 50.000 0.00 0.00 0.00 2.90
598 686 1.000163 ACGAGTGCTGAACGAAGATGT 60.000 47.619 0.00 0.00 0.00 3.06
600 688 3.242518 CGAGTGCTGAACGAAGATGTAA 58.757 45.455 0.00 0.00 0.00 2.41
601 689 3.673338 CGAGTGCTGAACGAAGATGTAAA 59.327 43.478 0.00 0.00 0.00 2.01
602 690 4.433022 CGAGTGCTGAACGAAGATGTAAAC 60.433 45.833 0.00 0.00 0.00 2.01
603 691 3.746492 AGTGCTGAACGAAGATGTAAACC 59.254 43.478 0.00 0.00 0.00 3.27
640 732 3.119531 CCATGATGTGCCGTGTGTTTAAT 60.120 43.478 0.00 0.00 0.00 1.40
641 733 3.822594 TGATGTGCCGTGTGTTTAATC 57.177 42.857 0.00 0.00 0.00 1.75
644 736 3.889196 TGTGCCGTGTGTTTAATCTTC 57.111 42.857 0.00 0.00 0.00 2.87
653 745 5.406780 CGTGTGTTTAATCTTCAGAGCTCTT 59.593 40.000 15.27 0.20 0.00 2.85
656 748 4.697352 TGTTTAATCTTCAGAGCTCTTGGC 59.303 41.667 15.27 0.00 42.19 4.52
660 752 0.676151 CTTCAGAGCTCTTGGCCACC 60.676 60.000 15.27 0.00 43.05 4.61
664 756 1.003580 CAGAGCTCTTGGCCACCTTTA 59.996 52.381 15.27 0.00 43.05 1.85
665 757 1.003696 AGAGCTCTTGGCCACCTTTAC 59.996 52.381 11.45 0.00 43.05 2.01
667 759 1.425448 AGCTCTTGGCCACCTTTACTT 59.575 47.619 3.88 0.00 43.05 2.24
668 760 2.642807 AGCTCTTGGCCACCTTTACTTA 59.357 45.455 3.88 0.00 43.05 2.24
669 761 3.010420 GCTCTTGGCCACCTTTACTTAG 58.990 50.000 3.88 0.00 34.27 2.18
670 762 3.010420 CTCTTGGCCACCTTTACTTAGC 58.990 50.000 3.88 0.00 0.00 3.09
671 763 2.642807 TCTTGGCCACCTTTACTTAGCT 59.357 45.455 3.88 0.00 0.00 3.32
672 764 3.073946 TCTTGGCCACCTTTACTTAGCTT 59.926 43.478 3.88 0.00 0.00 3.74
673 765 3.518992 TGGCCACCTTTACTTAGCTTT 57.481 42.857 0.00 0.00 0.00 3.51
674 766 3.839778 TGGCCACCTTTACTTAGCTTTT 58.160 40.909 0.00 0.00 0.00 2.27
675 767 3.824443 TGGCCACCTTTACTTAGCTTTTC 59.176 43.478 0.00 0.00 0.00 2.29
676 768 4.079970 GGCCACCTTTACTTAGCTTTTCT 58.920 43.478 0.00 0.00 0.00 2.52
677 769 4.156190 GGCCACCTTTACTTAGCTTTTCTC 59.844 45.833 0.00 0.00 0.00 2.87
704 815 2.032054 TGTCTGAACAGCTTTCGCAAAG 59.968 45.455 0.00 4.78 41.46 2.77
706 817 2.545526 TCTGAACAGCTTTCGCAAAGAG 59.454 45.455 11.34 6.46 41.02 2.85
707 818 1.603802 TGAACAGCTTTCGCAAAGAGG 59.396 47.619 11.34 5.93 41.02 3.69
709 820 0.108585 ACAGCTTTCGCAAAGAGGGA 59.891 50.000 11.34 0.00 41.02 4.20
712 823 2.229784 CAGCTTTCGCAAAGAGGGATTT 59.770 45.455 11.34 0.00 41.02 2.17
714 825 2.672195 GCTTTCGCAAAGAGGGATTTGG 60.672 50.000 11.34 0.00 41.02 3.28
720 831 4.283212 TCGCAAAGAGGGATTTGGATTTTT 59.717 37.500 1.80 0.00 39.94 1.94
745 856 6.947644 TTTTAAGAGGACAAGTAAACCCAC 57.052 37.500 0.00 0.00 0.00 4.61
746 857 5.899631 TTAAGAGGACAAGTAAACCCACT 57.100 39.130 0.00 0.00 0.00 4.00
747 858 4.790718 AAGAGGACAAGTAAACCCACTT 57.209 40.909 0.00 0.00 39.34 3.16
748 859 5.899631 AAGAGGACAAGTAAACCCACTTA 57.100 39.130 0.00 0.00 36.61 2.24
749 860 5.899631 AGAGGACAAGTAAACCCACTTAA 57.100 39.130 0.00 0.00 36.61 1.85
750 861 6.256643 AGAGGACAAGTAAACCCACTTAAA 57.743 37.500 0.00 0.00 36.61 1.52
751 862 6.060136 AGAGGACAAGTAAACCCACTTAAAC 58.940 40.000 0.00 0.00 36.61 2.01
752 863 5.757988 AGGACAAGTAAACCCACTTAAACA 58.242 37.500 0.00 0.00 36.61 2.83
753 864 6.370453 AGGACAAGTAAACCCACTTAAACAT 58.630 36.000 0.00 0.00 36.61 2.71
754 865 6.264518 AGGACAAGTAAACCCACTTAAACATG 59.735 38.462 0.00 0.00 36.61 3.21
755 866 6.399639 ACAAGTAAACCCACTTAAACATGG 57.600 37.500 0.00 0.00 36.61 3.66
756 867 5.221362 ACAAGTAAACCCACTTAAACATGGC 60.221 40.000 0.00 0.00 36.61 4.40
757 868 4.475345 AGTAAACCCACTTAAACATGGCA 58.525 39.130 0.00 0.00 34.37 4.92
758 869 4.522789 AGTAAACCCACTTAAACATGGCAG 59.477 41.667 0.00 0.00 34.37 4.85
759 870 2.675658 ACCCACTTAAACATGGCAGT 57.324 45.000 0.00 0.00 34.37 4.40
760 871 3.799432 ACCCACTTAAACATGGCAGTA 57.201 42.857 0.00 0.00 34.37 2.74
761 872 4.107127 ACCCACTTAAACATGGCAGTAA 57.893 40.909 0.00 0.00 34.37 2.24
762 873 4.475345 ACCCACTTAAACATGGCAGTAAA 58.525 39.130 0.00 0.00 34.37 2.01
763 874 4.896482 ACCCACTTAAACATGGCAGTAAAA 59.104 37.500 0.00 0.00 34.37 1.52
764 875 5.221362 ACCCACTTAAACATGGCAGTAAAAC 60.221 40.000 0.00 0.00 34.37 2.43
765 876 5.010617 CCCACTTAAACATGGCAGTAAAACT 59.989 40.000 0.00 0.00 34.37 2.66
766 877 6.207810 CCCACTTAAACATGGCAGTAAAACTA 59.792 38.462 0.00 0.00 34.37 2.24
767 878 7.305474 CCACTTAAACATGGCAGTAAAACTAG 58.695 38.462 0.00 0.00 0.00 2.57
768 879 7.040686 CCACTTAAACATGGCAGTAAAACTAGT 60.041 37.037 0.00 0.00 0.00 2.57
769 880 7.803189 CACTTAAACATGGCAGTAAAACTAGTG 59.197 37.037 0.00 0.00 0.00 2.74
770 881 7.501225 ACTTAAACATGGCAGTAAAACTAGTGT 59.499 33.333 0.00 0.00 0.00 3.55
771 882 8.905660 TTAAACATGGCAGTAAAACTAGTGTA 57.094 30.769 0.00 0.00 0.00 2.90
772 883 6.796705 AACATGGCAGTAAAACTAGTGTAC 57.203 37.500 0.00 2.39 0.00 2.90
773 884 5.860611 ACATGGCAGTAAAACTAGTGTACA 58.139 37.500 15.72 0.00 0.00 2.90
774 885 5.932303 ACATGGCAGTAAAACTAGTGTACAG 59.068 40.000 15.72 10.65 0.00 2.74
775 886 5.540400 TGGCAGTAAAACTAGTGTACAGT 57.460 39.130 8.55 8.55 0.00 3.55
776 887 5.920903 TGGCAGTAAAACTAGTGTACAGTT 58.079 37.500 8.85 0.47 37.85 3.16
777 888 7.053316 TGGCAGTAAAACTAGTGTACAGTTA 57.947 36.000 8.85 0.00 35.19 2.24
778 889 7.499292 TGGCAGTAAAACTAGTGTACAGTTAA 58.501 34.615 8.85 0.00 35.19 2.01
779 890 7.986320 TGGCAGTAAAACTAGTGTACAGTTAAA 59.014 33.333 8.85 0.00 35.19 1.52
780 891 8.493547 GGCAGTAAAACTAGTGTACAGTTAAAG 58.506 37.037 8.85 2.94 35.19 1.85
781 892 9.038803 GCAGTAAAACTAGTGTACAGTTAAAGT 57.961 33.333 8.85 3.62 35.19 2.66
783 894 9.038803 AGTAAAACTAGTGTACAGTTAAAGTGC 57.961 33.333 8.85 0.00 35.19 4.40
793 904 7.224167 GTGTACAGTTAAAGTGCTCTACTGTTT 59.776 37.037 21.50 6.77 45.05 2.83
855 1093 4.586001 AGAAGAAAGCCAAAGCAAATCAGA 59.414 37.500 0.00 0.00 43.56 3.27
873 1111 7.587037 AATCAGACAGAAGAAATTTTCCACA 57.413 32.000 5.52 0.00 0.00 4.17
876 1114 5.632347 CAGACAGAAGAAATTTTCCACATGC 59.368 40.000 5.52 0.00 0.00 4.06
882 1120 4.410099 AGAAATTTTCCACATGCTCTGGA 58.590 39.130 5.52 0.00 35.91 3.86
1089 1328 0.831307 AAGGTATGCTTCTCCCCGTC 59.169 55.000 0.00 0.00 0.00 4.79
1170 1409 0.516524 GACTAAACGAAAGCGCTGCG 60.517 55.000 25.43 25.43 42.48 5.18
1248 1487 4.341502 CGGTTTGCTTGGGCCGTG 62.342 66.667 0.00 0.00 39.41 4.94
1254 1493 2.909965 GCTTGGGCCGTGGTTGAA 60.910 61.111 0.00 0.00 0.00 2.69
1255 1494 2.275380 GCTTGGGCCGTGGTTGAAT 61.275 57.895 0.00 0.00 0.00 2.57
1267 1506 3.740141 CGTGGTTGAATATAAGGCCGAGT 60.740 47.826 0.00 0.00 0.00 4.18
1293 1532 0.179018 GGGCTGCTGATTCCCGTAAT 60.179 55.000 0.00 0.00 0.00 1.89
1327 1566 5.577860 GTGCAACTAGTCAACTACACTTC 57.422 43.478 0.00 0.00 0.00 3.01
1328 1567 5.290386 GTGCAACTAGTCAACTACACTTCT 58.710 41.667 0.00 0.00 0.00 2.85
1329 1568 5.402867 GTGCAACTAGTCAACTACACTTCTC 59.597 44.000 0.00 0.00 0.00 2.87
1330 1569 5.302059 TGCAACTAGTCAACTACACTTCTCT 59.698 40.000 0.00 0.00 0.00 3.10
1333 1573 5.774630 ACTAGTCAACTACACTTCTCTTGC 58.225 41.667 0.00 0.00 0.00 4.01
1341 1581 3.951979 ACACTTCTCTTGCGTTTTCAG 57.048 42.857 0.00 0.00 0.00 3.02
1387 1627 4.580868 TCTTGGGTTTTCACGCATACATA 58.419 39.130 0.00 0.00 44.76 2.29
1394 1634 7.329717 TGGGTTTTCACGCATACATAATTTTTC 59.670 33.333 0.00 0.00 40.78 2.29
1397 1637 9.937577 GTTTTCACGCATACATAATTTTTCTTC 57.062 29.630 0.00 0.00 0.00 2.87
1398 1638 7.946918 TTCACGCATACATAATTTTTCTTCG 57.053 32.000 0.00 0.00 0.00 3.79
1399 1639 6.482835 TCACGCATACATAATTTTTCTTCGG 58.517 36.000 0.00 0.00 0.00 4.30
1583 1876 2.170397 TCATATCAGGGACGCATGTGTT 59.830 45.455 14.16 0.00 0.00 3.32
1624 1917 2.034507 GCAAGAATCGACTCGTATGTGC 60.035 50.000 0.00 0.56 0.00 4.57
1625 1918 3.439293 CAAGAATCGACTCGTATGTGCT 58.561 45.455 0.00 0.00 0.00 4.40
1637 1930 0.615261 TATGTGCTGGGTCGGTGGTA 60.615 55.000 0.00 0.00 0.00 3.25
1638 1931 2.047560 GTGCTGGGTCGGTGGTAC 60.048 66.667 0.00 0.00 0.00 3.34
1647 1940 2.613725 GGGTCGGTGGTACAAAACTAGG 60.614 54.545 0.00 0.00 44.16 3.02
1710 2005 2.670905 TGTGTCTCGGCAAATAATCGTG 59.329 45.455 0.00 0.00 0.00 4.35
1735 2030 9.742144 TGTCTACCCTATAATATCTGAGACTTC 57.258 37.037 0.00 0.00 33.55 3.01
1886 2183 3.203716 CATCACCAGATGTCACCAGATG 58.796 50.000 0.00 0.00 45.28 2.90
1887 2184 2.259917 TCACCAGATGTCACCAGATGT 58.740 47.619 0.00 0.00 0.00 3.06
1888 2185 2.639347 TCACCAGATGTCACCAGATGTT 59.361 45.455 0.00 0.00 0.00 2.71
1890 2187 3.935203 CACCAGATGTCACCAGATGTTAC 59.065 47.826 0.00 0.00 0.00 2.50
1891 2188 3.582647 ACCAGATGTCACCAGATGTTACA 59.417 43.478 0.00 0.00 35.64 2.41
1893 2190 5.188434 CCAGATGTCACCAGATGTTACATT 58.812 41.667 0.00 0.00 40.90 2.71
1894 2191 6.070251 ACCAGATGTCACCAGATGTTACATTA 60.070 38.462 0.00 0.00 40.90 1.90
1896 2193 7.041576 CCAGATGTCACCAGATGTTACATTATG 60.042 40.741 0.00 2.12 40.90 1.90
1897 2194 6.994496 AGATGTCACCAGATGTTACATTATGG 59.006 38.462 21.37 21.37 40.90 2.74
1898 2195 5.436175 TGTCACCAGATGTTACATTATGGG 58.564 41.667 24.53 17.02 31.95 4.00
1899 2196 5.190726 TGTCACCAGATGTTACATTATGGGA 59.809 40.000 24.53 18.34 31.95 4.37
1900 2197 5.527582 GTCACCAGATGTTACATTATGGGAC 59.472 44.000 24.53 22.66 31.95 4.46
1901 2198 4.511454 CACCAGATGTTACATTATGGGACG 59.489 45.833 24.53 14.23 31.95 4.79
1902 2199 4.065088 CCAGATGTTACATTATGGGACGG 58.935 47.826 17.54 0.00 0.00 4.79
1903 2200 4.202315 CCAGATGTTACATTATGGGACGGA 60.202 45.833 17.54 0.00 0.00 4.69
1904 2201 4.991056 CAGATGTTACATTATGGGACGGAG 59.009 45.833 0.00 0.00 0.00 4.63
1905 2202 3.830744 TGTTACATTATGGGACGGAGG 57.169 47.619 0.00 0.00 0.00 4.30
1906 2203 2.436542 TGTTACATTATGGGACGGAGGG 59.563 50.000 0.00 0.00 0.00 4.30
1907 2204 2.701951 GTTACATTATGGGACGGAGGGA 59.298 50.000 0.00 0.00 0.00 4.20
1908 2205 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
1909 2206 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
1910 2207 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
1937 2234 3.572682 ACAAATGTGACTGAGGAGACGTA 59.427 43.478 0.00 0.00 0.00 3.57
2005 2304 0.744414 AGGGTGTCATGGCGAAATCG 60.744 55.000 0.00 0.00 43.27 3.34
2008 2307 1.670811 GGTGTCATGGCGAAATCGAAT 59.329 47.619 7.06 0.00 43.02 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.388703 GAGCAGGCTGGAGCTGGAG 62.389 68.421 17.64 0.00 42.04 3.86
9 10 3.397439 GAGCAGGCTGGAGCTGGA 61.397 66.667 17.64 0.00 42.04 3.86
10 11 4.486503 GGAGCAGGCTGGAGCTGG 62.487 72.222 17.64 0.00 42.04 4.85
11 12 2.872931 GAAGGAGCAGGCTGGAGCTG 62.873 65.000 17.64 0.00 42.04 4.24
12 13 2.610233 AAGGAGCAGGCTGGAGCT 60.610 61.111 17.64 7.14 45.25 4.09
13 14 2.124778 GAAGGAGCAGGCTGGAGC 60.125 66.667 17.64 1.20 41.14 4.70
14 15 2.588989 GGAAGGAGCAGGCTGGAG 59.411 66.667 17.64 0.00 0.00 3.86
15 16 3.011517 GGGAAGGAGCAGGCTGGA 61.012 66.667 17.64 0.00 0.00 3.86
16 17 4.120755 GGGGAAGGAGCAGGCTGG 62.121 72.222 17.64 0.00 0.00 4.85
17 18 2.910737 TTGGGGAAGGAGCAGGCTG 61.911 63.158 10.94 10.94 0.00 4.85
18 19 2.532715 TTGGGGAAGGAGCAGGCT 60.533 61.111 0.00 0.00 0.00 4.58
19 20 2.361737 GTTGGGGAAGGAGCAGGC 60.362 66.667 0.00 0.00 0.00 4.85
459 501 3.724914 CTTCCTCCCGCGCTTCCTC 62.725 68.421 5.56 0.00 0.00 3.71
460 502 3.775654 CTTCCTCCCGCGCTTCCT 61.776 66.667 5.56 0.00 0.00 3.36
461 503 3.095347 ATCTTCCTCCCGCGCTTCC 62.095 63.158 5.56 0.00 0.00 3.46
462 504 1.884926 CATCTTCCTCCCGCGCTTC 60.885 63.158 5.56 0.00 0.00 3.86
463 505 2.187946 CATCTTCCTCCCGCGCTT 59.812 61.111 5.56 0.00 0.00 4.68
464 506 3.854669 CCATCTTCCTCCCGCGCT 61.855 66.667 5.56 0.00 0.00 5.92
493 547 4.504916 CTCCGCCGACTCTGCCTG 62.505 72.222 0.00 0.00 0.00 4.85
517 571 3.721706 CTCCTCCACTGCCCCCAC 61.722 72.222 0.00 0.00 0.00 4.61
519 573 4.741239 TCCTCCTCCACTGCCCCC 62.741 72.222 0.00 0.00 0.00 5.40
523 577 1.621672 CCCTTCTCCTCCTCCACTGC 61.622 65.000 0.00 0.00 0.00 4.40
577 665 2.061773 CATCTTCGTTCAGCACTCGTT 58.938 47.619 0.00 0.00 0.00 3.85
594 682 3.202151 TGATCCTTCCCCTGGTTTACATC 59.798 47.826 0.00 0.00 0.00 3.06
595 683 3.197983 TGATCCTTCCCCTGGTTTACAT 58.802 45.455 0.00 0.00 0.00 2.29
596 684 2.576191 CTGATCCTTCCCCTGGTTTACA 59.424 50.000 0.00 0.00 0.00 2.41
597 685 2.684038 GCTGATCCTTCCCCTGGTTTAC 60.684 54.545 0.00 0.00 0.00 2.01
598 686 1.564348 GCTGATCCTTCCCCTGGTTTA 59.436 52.381 0.00 0.00 0.00 2.01
600 688 1.575447 GGCTGATCCTTCCCCTGGTT 61.575 60.000 0.00 0.00 0.00 3.67
601 689 2.003548 GGCTGATCCTTCCCCTGGT 61.004 63.158 0.00 0.00 0.00 4.00
602 690 1.358830 ATGGCTGATCCTTCCCCTGG 61.359 60.000 0.00 0.00 35.26 4.45
603 691 0.178998 CATGGCTGATCCTTCCCCTG 60.179 60.000 0.00 0.00 35.26 4.45
640 732 0.322975 GTGGCCAAGAGCTCTGAAGA 59.677 55.000 19.06 0.00 43.05 2.87
641 733 0.676151 GGTGGCCAAGAGCTCTGAAG 60.676 60.000 19.06 10.24 43.05 3.02
644 736 0.251077 AAAGGTGGCCAAGAGCTCTG 60.251 55.000 19.06 11.38 43.05 3.35
653 745 3.518992 AAAGCTAAGTAAAGGTGGCCA 57.481 42.857 0.00 0.00 0.00 5.36
656 748 5.313712 TGGAGAAAAGCTAAGTAAAGGTGG 58.686 41.667 0.00 0.00 0.00 4.61
664 756 7.624549 TCAGACAATATGGAGAAAAGCTAAGT 58.375 34.615 0.00 0.00 0.00 2.24
665 757 8.394121 GTTCAGACAATATGGAGAAAAGCTAAG 58.606 37.037 0.00 0.00 0.00 2.18
667 759 7.394016 TGTTCAGACAATATGGAGAAAAGCTA 58.606 34.615 0.00 0.00 31.49 3.32
668 760 6.240894 TGTTCAGACAATATGGAGAAAAGCT 58.759 36.000 0.00 0.00 31.49 3.74
669 761 6.500684 TGTTCAGACAATATGGAGAAAAGC 57.499 37.500 0.00 0.00 31.49 3.51
670 762 6.373774 AGCTGTTCAGACAATATGGAGAAAAG 59.626 38.462 3.84 0.00 34.85 2.27
671 763 6.240894 AGCTGTTCAGACAATATGGAGAAAA 58.759 36.000 3.84 0.00 34.85 2.29
672 764 5.809001 AGCTGTTCAGACAATATGGAGAAA 58.191 37.500 3.84 0.00 34.85 2.52
673 765 5.426689 AGCTGTTCAGACAATATGGAGAA 57.573 39.130 3.84 0.00 34.85 2.87
674 766 5.426689 AAGCTGTTCAGACAATATGGAGA 57.573 39.130 3.84 0.00 34.85 3.71
675 767 5.220548 CGAAAGCTGTTCAGACAATATGGAG 60.221 44.000 3.84 0.00 34.85 3.86
676 768 4.631377 CGAAAGCTGTTCAGACAATATGGA 59.369 41.667 3.84 0.00 34.85 3.41
677 769 4.901814 CGAAAGCTGTTCAGACAATATGG 58.098 43.478 3.84 0.00 34.85 2.74
721 832 7.120716 AGTGGGTTTACTTGTCCTCTTAAAAA 58.879 34.615 0.00 0.00 0.00 1.94
724 835 5.899631 AGTGGGTTTACTTGTCCTCTTAA 57.100 39.130 0.00 0.00 0.00 1.85
725 836 5.899631 AAGTGGGTTTACTTGTCCTCTTA 57.100 39.130 0.00 0.00 39.33 2.10
728 839 5.824097 TGTTTAAGTGGGTTTACTTGTCCTC 59.176 40.000 0.00 0.00 40.85 3.71
729 840 5.757988 TGTTTAAGTGGGTTTACTTGTCCT 58.242 37.500 0.00 0.00 40.85 3.85
730 841 6.443792 CATGTTTAAGTGGGTTTACTTGTCC 58.556 40.000 0.00 0.00 40.85 4.02
731 842 6.443792 CCATGTTTAAGTGGGTTTACTTGTC 58.556 40.000 0.00 0.00 40.85 3.18
732 843 5.221362 GCCATGTTTAAGTGGGTTTACTTGT 60.221 40.000 0.00 0.00 40.85 3.16
733 844 5.221342 TGCCATGTTTAAGTGGGTTTACTTG 60.221 40.000 0.00 0.00 40.85 3.16
734 845 4.896482 TGCCATGTTTAAGTGGGTTTACTT 59.104 37.500 0.00 0.00 43.03 2.24
735 846 4.475345 TGCCATGTTTAAGTGGGTTTACT 58.525 39.130 0.00 0.00 36.00 2.24
736 847 4.279922 ACTGCCATGTTTAAGTGGGTTTAC 59.720 41.667 0.00 0.00 36.00 2.01
737 848 4.475345 ACTGCCATGTTTAAGTGGGTTTA 58.525 39.130 0.00 0.00 36.00 2.01
738 849 3.304829 ACTGCCATGTTTAAGTGGGTTT 58.695 40.909 0.00 0.00 36.00 3.27
739 850 2.957474 ACTGCCATGTTTAAGTGGGTT 58.043 42.857 0.00 0.00 36.00 4.11
740 851 2.675658 ACTGCCATGTTTAAGTGGGT 57.324 45.000 0.00 0.00 36.00 4.51
741 852 5.010617 AGTTTTACTGCCATGTTTAAGTGGG 59.989 40.000 0.00 0.00 36.00 4.61
742 853 6.084326 AGTTTTACTGCCATGTTTAAGTGG 57.916 37.500 0.00 0.00 38.55 4.00
743 854 7.803189 CACTAGTTTTACTGCCATGTTTAAGTG 59.197 37.037 0.00 0.00 0.00 3.16
744 855 7.501225 ACACTAGTTTTACTGCCATGTTTAAGT 59.499 33.333 0.00 0.00 0.00 2.24
745 856 7.871853 ACACTAGTTTTACTGCCATGTTTAAG 58.128 34.615 0.00 0.00 0.00 1.85
746 857 7.811117 ACACTAGTTTTACTGCCATGTTTAA 57.189 32.000 0.00 0.00 0.00 1.52
747 858 7.932491 TGTACACTAGTTTTACTGCCATGTTTA 59.068 33.333 11.15 0.00 0.00 2.01
748 859 6.768861 TGTACACTAGTTTTACTGCCATGTTT 59.231 34.615 11.15 0.00 0.00 2.83
749 860 6.292923 TGTACACTAGTTTTACTGCCATGTT 58.707 36.000 11.15 0.00 0.00 2.71
750 861 5.860611 TGTACACTAGTTTTACTGCCATGT 58.139 37.500 11.15 0.00 0.00 3.21
751 862 5.932303 ACTGTACACTAGTTTTACTGCCATG 59.068 40.000 13.97 0.00 0.00 3.66
752 863 6.110411 ACTGTACACTAGTTTTACTGCCAT 57.890 37.500 13.97 0.00 0.00 4.40
753 864 5.540400 ACTGTACACTAGTTTTACTGCCA 57.460 39.130 13.97 0.00 0.00 4.92
754 865 7.951530 TTAACTGTACACTAGTTTTACTGCC 57.048 36.000 13.97 0.00 39.06 4.85
755 866 9.038803 ACTTTAACTGTACACTAGTTTTACTGC 57.961 33.333 13.97 0.00 39.06 4.40
757 868 9.038803 GCACTTTAACTGTACACTAGTTTTACT 57.961 33.333 4.52 0.00 39.06 2.24
758 869 9.038803 AGCACTTTAACTGTACACTAGTTTTAC 57.961 33.333 4.52 0.00 39.06 2.01
759 870 9.252962 GAGCACTTTAACTGTACACTAGTTTTA 57.747 33.333 4.52 0.00 39.06 1.52
760 871 7.985752 AGAGCACTTTAACTGTACACTAGTTTT 59.014 33.333 4.52 0.00 39.06 2.43
761 872 7.498443 AGAGCACTTTAACTGTACACTAGTTT 58.502 34.615 4.52 0.00 39.06 2.66
762 873 7.052142 AGAGCACTTTAACTGTACACTAGTT 57.948 36.000 0.00 4.60 41.06 2.24
763 874 6.651975 AGAGCACTTTAACTGTACACTAGT 57.348 37.500 0.00 0.00 0.00 2.57
764 875 7.751348 CAGTAGAGCACTTTAACTGTACACTAG 59.249 40.741 4.84 0.00 35.65 2.57
765 876 7.230108 ACAGTAGAGCACTTTAACTGTACACTA 59.770 37.037 14.23 0.00 46.58 2.74
766 877 6.040616 ACAGTAGAGCACTTTAACTGTACACT 59.959 38.462 14.23 0.00 46.58 3.55
767 878 6.214399 ACAGTAGAGCACTTTAACTGTACAC 58.786 40.000 14.23 0.00 46.58 2.90
768 879 6.401047 ACAGTAGAGCACTTTAACTGTACA 57.599 37.500 14.23 0.00 46.58 2.90
777 888 9.026121 TCTCTCTATTAAACAGTAGAGCACTTT 57.974 33.333 6.11 0.00 42.25 2.66
778 889 8.582657 TCTCTCTATTAAACAGTAGAGCACTT 57.417 34.615 6.11 0.00 42.25 3.16
779 890 8.582657 TTCTCTCTATTAAACAGTAGAGCACT 57.417 34.615 6.11 0.00 42.25 4.40
780 891 9.078753 GTTTCTCTCTATTAAACAGTAGAGCAC 57.921 37.037 6.11 0.00 42.25 4.40
781 892 9.026121 AGTTTCTCTCTATTAAACAGTAGAGCA 57.974 33.333 6.11 0.00 42.25 4.26
782 893 9.511144 GAGTTTCTCTCTATTAAACAGTAGAGC 57.489 37.037 6.11 0.00 42.25 4.09
793 904 7.710676 AACTGAGCTGAGTTTCTCTCTATTA 57.289 36.000 13.24 0.00 43.13 0.98
798 909 5.053145 TGAAAACTGAGCTGAGTTTCTCTC 58.947 41.667 27.95 21.97 43.83 3.20
799 910 5.028549 TGAAAACTGAGCTGAGTTTCTCT 57.971 39.130 27.95 15.24 43.83 3.10
800 911 5.938438 ATGAAAACTGAGCTGAGTTTCTC 57.062 39.130 27.95 24.31 43.83 2.87
855 1093 5.537674 AGAGCATGTGGAAAATTTCTTCTGT 59.462 36.000 5.65 0.00 0.00 3.41
873 1111 3.790437 CGCACCCCTCCAGAGCAT 61.790 66.667 0.00 0.00 0.00 3.79
1089 1328 0.687354 ATATAAGCAGACCCAGGGCG 59.313 55.000 4.91 0.00 0.00 6.13
1170 1409 1.518056 TTTGCTGTGCCTGTGCTAGC 61.518 55.000 8.10 8.10 43.80 3.42
1172 1411 1.518056 GCTTTGCTGTGCCTGTGCTA 61.518 55.000 0.00 0.00 38.71 3.49
1228 1467 4.038080 GGCCCAAGCAAACCGACG 62.038 66.667 0.00 0.00 42.56 5.12
1248 1487 3.805207 ACACTCGGCCTTATATTCAACC 58.195 45.455 0.00 0.00 0.00 3.77
1254 1493 3.769844 CCCATCTACACTCGGCCTTATAT 59.230 47.826 0.00 0.00 0.00 0.86
1255 1494 3.162666 CCCATCTACACTCGGCCTTATA 58.837 50.000 0.00 0.00 0.00 0.98
1267 1506 1.141657 GGAATCAGCAGCCCATCTACA 59.858 52.381 0.00 0.00 0.00 2.74
1293 1532 0.692476 AGTTGCACTGTCAGGCCATA 59.308 50.000 5.01 0.00 0.00 2.74
1314 1553 3.381949 ACGCAAGAGAAGTGTAGTTGAC 58.618 45.455 0.00 0.00 43.62 3.18
1318 1557 4.439057 TGAAAACGCAAGAGAAGTGTAGT 58.561 39.130 0.00 0.00 43.62 2.73
1321 1560 3.270877 ACTGAAAACGCAAGAGAAGTGT 58.729 40.909 0.00 0.00 43.62 3.55
1322 1561 3.951979 ACTGAAAACGCAAGAGAAGTG 57.048 42.857 0.00 0.00 43.62 3.16
1323 1562 4.192317 AGAACTGAAAACGCAAGAGAAGT 58.808 39.130 0.00 0.00 43.62 3.01
1324 1563 4.271049 TGAGAACTGAAAACGCAAGAGAAG 59.729 41.667 0.00 0.00 43.62 2.85
1325 1564 4.188462 TGAGAACTGAAAACGCAAGAGAA 58.812 39.130 0.00 0.00 43.62 2.87
1326 1565 3.792401 TGAGAACTGAAAACGCAAGAGA 58.208 40.909 0.00 0.00 43.62 3.10
1327 1566 4.536364 TTGAGAACTGAAAACGCAAGAG 57.464 40.909 0.00 0.00 43.62 2.85
1328 1567 4.955925 TTTGAGAACTGAAAACGCAAGA 57.044 36.364 0.00 0.00 43.62 3.02
1357 1597 4.676986 GCGTGAAAACCCAAGAGAAGTTTT 60.677 41.667 0.07 0.07 44.18 2.43
1358 1598 3.181490 GCGTGAAAACCCAAGAGAAGTTT 60.181 43.478 0.00 0.00 35.29 2.66
1359 1599 2.357952 GCGTGAAAACCCAAGAGAAGTT 59.642 45.455 0.00 0.00 0.00 2.66
1362 1602 2.045561 TGCGTGAAAACCCAAGAGAA 57.954 45.000 0.00 0.00 0.00 2.87
1496 1784 3.685214 CTCGCCACCTTCTCGTCCG 62.685 68.421 0.00 0.00 0.00 4.79
1510 1798 2.410469 GTCCATGCATTGCCTCGC 59.590 61.111 6.12 0.00 0.00 5.03
1624 1917 1.202722 AGTTTTGTACCACCGACCCAG 60.203 52.381 0.00 0.00 0.00 4.45
1625 1918 0.838608 AGTTTTGTACCACCGACCCA 59.161 50.000 0.00 0.00 0.00 4.51
1637 1930 4.381411 GACTGAACTGCTCCTAGTTTTGT 58.619 43.478 0.00 0.00 40.78 2.83
1638 1931 3.430218 CGACTGAACTGCTCCTAGTTTTG 59.570 47.826 0.00 0.00 40.78 2.44
1647 1940 1.011451 GTGCCTCGACTGAACTGCTC 61.011 60.000 0.00 0.00 0.00 4.26
1710 2005 8.885722 CGAAGTCTCAGATATTATAGGGTAGAC 58.114 40.741 0.00 0.00 0.00 2.59
1729 2024 5.104119 GACCTGAAGTCTAGACCGAAGTCT 61.104 50.000 19.38 0.84 45.13 3.24
1735 2030 2.359531 GGATGACCTGAAGTCTAGACCG 59.640 54.545 19.38 5.77 46.46 4.79
1878 2175 4.511454 CGTCCCATAATGTAACATCTGGTG 59.489 45.833 0.00 0.00 0.00 4.17
1881 2178 4.956085 TCCGTCCCATAATGTAACATCTG 58.044 43.478 0.00 0.00 0.00 2.90
1882 2179 4.040461 CCTCCGTCCCATAATGTAACATCT 59.960 45.833 0.00 0.00 0.00 2.90
1883 2180 4.315803 CCTCCGTCCCATAATGTAACATC 58.684 47.826 0.00 0.00 0.00 3.06
1886 2183 2.701951 TCCCTCCGTCCCATAATGTAAC 59.298 50.000 0.00 0.00 0.00 2.50
1887 2184 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
1888 2185 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
1890 2187 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
1891 2188 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
1893 2190 4.687262 ATAATACTCCCTCCGTCCCATA 57.313 45.455 0.00 0.00 0.00 2.74
1894 2191 3.562108 ATAATACTCCCTCCGTCCCAT 57.438 47.619 0.00 0.00 0.00 4.00
1896 2193 3.771216 TGTATAATACTCCCTCCGTCCC 58.229 50.000 0.00 0.00 0.00 4.46
1897 2194 5.796424 TTTGTATAATACTCCCTCCGTCC 57.204 43.478 0.00 0.00 0.00 4.79
1898 2195 6.645415 CACATTTGTATAATACTCCCTCCGTC 59.355 42.308 0.00 0.00 0.00 4.79
1899 2196 6.325545 TCACATTTGTATAATACTCCCTCCGT 59.674 38.462 0.00 0.00 0.00 4.69
1900 2197 6.645415 GTCACATTTGTATAATACTCCCTCCG 59.355 42.308 0.00 0.00 0.00 4.63
1901 2198 7.657761 CAGTCACATTTGTATAATACTCCCTCC 59.342 40.741 0.00 0.00 0.00 4.30
1902 2199 8.421784 TCAGTCACATTTGTATAATACTCCCTC 58.578 37.037 0.00 0.00 0.00 4.30
1903 2200 8.319057 TCAGTCACATTTGTATAATACTCCCT 57.681 34.615 0.00 0.00 0.00 4.20
1904 2201 7.657761 CCTCAGTCACATTTGTATAATACTCCC 59.342 40.741 0.00 0.00 0.00 4.30
1905 2202 8.421784 TCCTCAGTCACATTTGTATAATACTCC 58.578 37.037 0.00 0.00 0.00 3.85
1906 2203 9.469807 CTCCTCAGTCACATTTGTATAATACTC 57.530 37.037 0.00 0.00 0.00 2.59
1907 2204 9.201989 TCTCCTCAGTCACATTTGTATAATACT 57.798 33.333 0.00 0.00 0.00 2.12
1908 2205 9.250624 GTCTCCTCAGTCACATTTGTATAATAC 57.749 37.037 0.00 0.00 0.00 1.89
1909 2206 8.135529 CGTCTCCTCAGTCACATTTGTATAATA 58.864 37.037 0.00 0.00 0.00 0.98
1910 2207 6.980978 CGTCTCCTCAGTCACATTTGTATAAT 59.019 38.462 0.00 0.00 0.00 1.28
1937 2234 2.765699 AGACAGTTGCCATGGTTGTTTT 59.234 40.909 14.67 3.90 0.00 2.43
2005 2304 0.933796 GAGCGCTACTGCCTCAATTC 59.066 55.000 11.50 0.00 36.87 2.17
2008 2307 2.230994 CTGGAGCGCTACTGCCTCAA 62.231 60.000 22.67 0.00 37.86 3.02
2083 2382 2.243602 AAGCAACCATGGCAAAAGTG 57.756 45.000 13.04 1.74 0.00 3.16
2089 2388 2.161855 CTGTCTAAAGCAACCATGGCA 58.838 47.619 13.04 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.