Multiple sequence alignment - TraesCS4A01G112400

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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 TraesCS4A01G112400 chr4A 100.000 2708 0 0 1 2708 137018187 137020894 0.000000e+00 5001
1 TraesCS4A01G112400 chr5D 95.220 1883 88 1 826 2708 504972268 504974148 0.000000e+00 2977
2 TraesCS4A01G112400 chr5D 94.636 1883 99 1 826 2708 288114795 288116675 0.000000e+00 2916
3 TraesCS4A01G112400 chr5D 94.701 736 39 0 1 736 504971534 504972269 0.000000e+00 1144
4 TraesCS4A01G112400 chr5D 94.118 663 39 0 1 663 288114083 288114745 0.000000e+00 1009
5 TraesCS4A01G112400 chr5D 79.743 701 136 6 1004 1701 520970012 520970709 1.120000e-138 503
6 TraesCS4A01G112400 chr5D 98.276 58 1 0 679 736 288114739 288114796 4.770000e-18 102
7 TraesCS4A01G112400 chr4D 93.574 1883 103 7 826 2708 245843112 245841248 0.000000e+00 2791
8 TraesCS4A01G112400 chr4D 93.960 745 44 1 1 745 245843845 245843102 0.000000e+00 1125
9 TraesCS4A01G112400 chr3D 79.915 702 133 8 1004 1701 520168916 520169613 2.410000e-140 508
10 TraesCS4A01G112400 chr3D 76.477 948 201 20 1004 1937 584734705 584735644 1.870000e-136 496
11 TraesCS4A01G112400 chr3D 78.632 702 131 10 1004 1701 40534498 40535184 5.320000e-122 448
12 TraesCS4A01G112400 chr1D 80.000 675 127 8 1031 1701 404222657 404221987 2.420000e-135 492
13 TraesCS4A01G112400 chr1D 78.917 702 136 11 1004 1701 33552689 33553382 1.470000e-127 466


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 TraesCS4A01G112400 chr4A 137018187 137020894 2707 False 5001.000000 5001 100.000000 1 2708 1 chr4A.!!$F1 2707
1 TraesCS4A01G112400 chr5D 504971534 504974148 2614 False 2060.500000 2977 94.960500 1 2708 2 chr5D.!!$F3 2707
2 TraesCS4A01G112400 chr5D 288114083 288116675 2592 False 1342.333333 2916 95.676667 1 2708 3 chr5D.!!$F2 2707
3 TraesCS4A01G112400 chr5D 520970012 520970709 697 False 503.000000 503 79.743000 1004 1701 1 chr5D.!!$F1 697
4 TraesCS4A01G112400 chr4D 245841248 245843845 2597 True 1958.000000 2791 93.767000 1 2708 2 chr4D.!!$R1 2707
5 TraesCS4A01G112400 chr3D 520168916 520169613 697 False 508.000000 508 79.915000 1004 1701 1 chr3D.!!$F2 697
6 TraesCS4A01G112400 chr3D 584734705 584735644 939 False 496.000000 496 76.477000 1004 1937 1 chr3D.!!$F3 933
7 TraesCS4A01G112400 chr3D 40534498 40535184 686 False 448.000000 448 78.632000 1004 1701 1 chr3D.!!$F1 697
8 TraesCS4A01G112400 chr1D 404221987 404222657 670 True 492.000000 492 80.000000 1031 1701 1 chr1D.!!$R1 670
9 TraesCS4A01G112400 chr1D 33552689 33553382 693 False 466.000000 466 78.917000 1004 1701 1 chr1D.!!$F1 697

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
384 385 0.460311 CGAACCTTATCTCACCCGCT 59.54 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 2257 0.107508 ACATCCATGAGGTTGGCTCG 60.108 55.0 0.0 0.0 38.65 5.03 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
22 23 3.387699 CCATTCTTTTGGTGGTGGTTCTT 59.612 43.478 0.00 0.00 31.74 2.52
28 29 1.429930 TGGTGGTGGTTCTTCTGCTA 58.570 50.000 0.00 0.00 0.00 3.49
32 33 2.047061 TGGTGGTTCTTCTGCTACTGT 58.953 47.619 0.00 0.00 0.00 3.55
34 35 2.300437 GGTGGTTCTTCTGCTACTGTCT 59.700 50.000 0.00 0.00 0.00 3.41
142 143 2.510928 AGAAGTGGTACGGTAGCTCT 57.489 50.000 17.26 15.68 0.00 4.09
148 149 1.779092 TGGTACGGTAGCTCTAGGGAT 59.221 52.381 17.26 0.00 0.00 3.85
153 154 5.479724 GGTACGGTAGCTCTAGGGATTTAAT 59.520 44.000 9.97 0.00 0.00 1.40
164 165 5.891551 TCTAGGGATTTAATTTTGTGAGGGC 59.108 40.000 0.00 0.00 0.00 5.19
251 252 9.994432 GATCAATCATTGTTCTACTTAACCAAG 57.006 33.333 0.00 0.00 37.81 3.61
327 328 2.413112 GACACGCGTAGTAGTAGACACA 59.587 50.000 13.44 0.00 0.00 3.72
364 365 2.320681 TTGTACCTACCAGCTCCAGT 57.679 50.000 0.00 0.00 0.00 4.00
384 385 0.460311 CGAACCTTATCTCACCCGCT 59.540 55.000 0.00 0.00 0.00 5.52
419 420 1.825191 CACCAGCCGATCCCCATTG 60.825 63.158 0.00 0.00 0.00 2.82
434 435 3.558746 CCCCATTGCAGCCATTTGTTTTA 60.559 43.478 0.00 0.00 0.00 1.52
457 458 3.374402 CCCGCAGTCAGGTCGTCT 61.374 66.667 0.00 0.00 0.00 4.18
463 464 1.153061 AGTCAGGTCGTCTCCCACA 59.847 57.895 0.00 0.00 0.00 4.17
480 481 2.047655 AAGCAATCGCCGGTTCGA 60.048 55.556 1.90 4.68 43.09 3.71
518 519 2.332654 CCGGCAGCACAACCTTACC 61.333 63.158 0.00 0.00 0.00 2.85
663 686 7.244192 GCACAATGTTAGACTAGTTTGGATTC 58.756 38.462 0.00 0.00 0.00 2.52
664 687 7.456253 CACAATGTTAGACTAGTTTGGATTCG 58.544 38.462 0.00 0.00 0.00 3.34
665 688 7.117812 CACAATGTTAGACTAGTTTGGATTCGT 59.882 37.037 0.00 0.00 0.00 3.85
666 689 8.308931 ACAATGTTAGACTAGTTTGGATTCGTA 58.691 33.333 0.00 0.00 0.00 3.43
667 690 8.592998 CAATGTTAGACTAGTTTGGATTCGTAC 58.407 37.037 0.00 0.00 0.00 3.67
668 691 7.218228 TGTTAGACTAGTTTGGATTCGTACA 57.782 36.000 0.00 0.00 0.00 2.90
669 692 7.660112 TGTTAGACTAGTTTGGATTCGTACAA 58.340 34.615 0.00 0.00 0.00 2.41
670 693 7.596248 TGTTAGACTAGTTTGGATTCGTACAAC 59.404 37.037 0.00 0.00 0.00 3.32
671 694 6.092955 AGACTAGTTTGGATTCGTACAACA 57.907 37.500 0.00 0.00 0.00 3.33
672 695 6.698380 AGACTAGTTTGGATTCGTACAACAT 58.302 36.000 0.00 0.00 0.00 2.71
673 696 7.159372 AGACTAGTTTGGATTCGTACAACATT 58.841 34.615 0.00 0.00 0.00 2.71
674 697 7.660208 AGACTAGTTTGGATTCGTACAACATTT 59.340 33.333 0.00 0.00 0.00 2.32
675 698 7.581476 ACTAGTTTGGATTCGTACAACATTTG 58.419 34.615 0.00 0.00 0.00 2.32
676 699 6.627395 AGTTTGGATTCGTACAACATTTGA 57.373 33.333 0.00 0.00 0.00 2.69
677 700 6.435428 AGTTTGGATTCGTACAACATTTGAC 58.565 36.000 0.00 0.00 0.00 3.18
678 701 6.262273 AGTTTGGATTCGTACAACATTTGACT 59.738 34.615 0.00 0.00 0.00 3.41
679 702 6.627395 TTGGATTCGTACAACATTTGACTT 57.373 33.333 0.00 0.00 0.00 3.01
680 703 5.996219 TGGATTCGTACAACATTTGACTTG 58.004 37.500 0.00 0.00 0.00 3.16
681 704 5.049060 TGGATTCGTACAACATTTGACTTGG 60.049 40.000 0.00 0.00 0.00 3.61
682 705 5.180492 GGATTCGTACAACATTTGACTTGGA 59.820 40.000 0.00 0.00 0.00 3.53
683 706 6.128007 GGATTCGTACAACATTTGACTTGGAT 60.128 38.462 0.00 0.00 0.00 3.41
684 707 6.627395 TTCGTACAACATTTGACTTGGATT 57.373 33.333 0.00 0.00 0.00 3.01
746 791 1.202114 CCATGTGTGGTTGGATTTCCG 59.798 52.381 0.00 0.00 40.83 4.30
747 792 1.885887 CATGTGTGGTTGGATTTCCGT 59.114 47.619 0.00 0.00 39.43 4.69
748 793 2.932855 TGTGTGGTTGGATTTCCGTA 57.067 45.000 0.00 0.00 39.43 4.02
749 794 2.773487 TGTGTGGTTGGATTTCCGTAG 58.227 47.619 0.00 0.00 39.43 3.51
750 795 2.105134 TGTGTGGTTGGATTTCCGTAGT 59.895 45.455 0.00 0.00 39.43 2.73
751 796 3.324268 TGTGTGGTTGGATTTCCGTAGTA 59.676 43.478 0.00 0.00 39.43 1.82
752 797 3.681417 GTGTGGTTGGATTTCCGTAGTAC 59.319 47.826 0.00 0.00 39.43 2.73
753 798 2.925563 GTGGTTGGATTTCCGTAGTACG 59.074 50.000 15.86 15.86 42.11 3.67
762 807 3.818787 CGTAGTACGGGCACGGCT 61.819 66.667 15.46 13.46 46.48 5.52
763 808 2.202703 GTAGTACGGGCACGGCTG 60.203 66.667 15.46 0.00 46.48 4.85
764 809 2.361483 TAGTACGGGCACGGCTGA 60.361 61.111 15.46 0.00 46.48 4.26
765 810 1.755395 TAGTACGGGCACGGCTGAT 60.755 57.895 15.46 0.00 46.48 2.90
766 811 0.466007 TAGTACGGGCACGGCTGATA 60.466 55.000 15.46 0.00 46.48 2.15
767 812 1.590792 GTACGGGCACGGCTGATAC 60.591 63.158 15.46 0.95 46.48 2.24
768 813 2.053277 TACGGGCACGGCTGATACA 61.053 57.895 15.46 0.00 46.48 2.29
769 814 2.287457 TACGGGCACGGCTGATACAC 62.287 60.000 15.46 0.00 46.48 2.90
770 815 2.267642 GGGCACGGCTGATACACA 59.732 61.111 0.00 0.00 0.00 3.72
771 816 1.376683 GGGCACGGCTGATACACAA 60.377 57.895 0.00 0.00 0.00 3.33
772 817 0.958382 GGGCACGGCTGATACACAAA 60.958 55.000 0.00 0.00 0.00 2.83
773 818 1.094785 GGCACGGCTGATACACAAAT 58.905 50.000 0.00 0.00 0.00 2.32
774 819 1.472480 GGCACGGCTGATACACAAATT 59.528 47.619 0.00 0.00 0.00 1.82
775 820 2.680841 GGCACGGCTGATACACAAATTA 59.319 45.455 0.00 0.00 0.00 1.40
776 821 3.486875 GGCACGGCTGATACACAAATTAC 60.487 47.826 0.00 0.00 0.00 1.89
777 822 3.486875 GCACGGCTGATACACAAATTACC 60.487 47.826 0.00 0.00 0.00 2.85
778 823 3.938963 CACGGCTGATACACAAATTACCT 59.061 43.478 0.00 0.00 0.00 3.08
779 824 3.938963 ACGGCTGATACACAAATTACCTG 59.061 43.478 0.00 0.00 0.00 4.00
780 825 3.938963 CGGCTGATACACAAATTACCTGT 59.061 43.478 0.00 0.00 0.00 4.00
781 826 5.113383 CGGCTGATACACAAATTACCTGTA 58.887 41.667 0.00 0.00 0.00 2.74
782 827 5.583061 CGGCTGATACACAAATTACCTGTAA 59.417 40.000 0.00 0.00 0.00 2.41
783 828 6.092944 CGGCTGATACACAAATTACCTGTAAA 59.907 38.462 0.00 0.00 0.00 2.01
784 829 7.201696 CGGCTGATACACAAATTACCTGTAAAT 60.202 37.037 0.00 0.00 0.00 1.40
785 830 9.116067 GGCTGATACACAAATTACCTGTAAATA 57.884 33.333 0.00 0.00 0.00 1.40
809 854 9.893305 ATATTGCTTAAATTTACGTTAGATGCC 57.107 29.630 0.00 0.00 0.00 4.40
810 855 6.745159 TGCTTAAATTTACGTTAGATGCCA 57.255 33.333 0.00 0.00 0.00 4.92
811 856 6.781138 TGCTTAAATTTACGTTAGATGCCAG 58.219 36.000 0.00 0.00 0.00 4.85
812 857 6.183360 TGCTTAAATTTACGTTAGATGCCAGG 60.183 38.462 0.00 0.00 0.00 4.45
813 858 6.183360 GCTTAAATTTACGTTAGATGCCAGGT 60.183 38.462 0.00 0.00 0.00 4.00
814 859 5.813080 AAATTTACGTTAGATGCCAGGTC 57.187 39.130 0.00 0.00 0.00 3.85
815 860 4.755266 ATTTACGTTAGATGCCAGGTCT 57.245 40.909 0.00 0.00 0.00 3.85
816 861 4.546829 TTTACGTTAGATGCCAGGTCTT 57.453 40.909 0.00 0.00 0.00 3.01
817 862 4.546829 TTACGTTAGATGCCAGGTCTTT 57.453 40.909 0.00 0.00 0.00 2.52
818 863 2.699954 ACGTTAGATGCCAGGTCTTTG 58.300 47.619 0.00 0.00 0.00 2.77
819 864 1.398390 CGTTAGATGCCAGGTCTTTGC 59.602 52.381 0.00 0.00 0.00 3.68
820 865 2.436417 GTTAGATGCCAGGTCTTTGCA 58.564 47.619 0.00 0.00 39.68 4.08
821 866 2.113860 TAGATGCCAGGTCTTTGCAC 57.886 50.000 0.00 0.00 37.92 4.57
822 867 0.957395 AGATGCCAGGTCTTTGCACG 60.957 55.000 0.00 0.00 37.92 5.34
823 868 1.926511 GATGCCAGGTCTTTGCACGG 61.927 60.000 0.00 0.00 37.92 4.94
824 869 2.281484 GCCAGGTCTTTGCACGGA 60.281 61.111 0.00 0.00 0.00 4.69
825 870 2.328099 GCCAGGTCTTTGCACGGAG 61.328 63.158 0.00 0.00 0.00 4.63
826 871 1.672356 CCAGGTCTTTGCACGGAGG 60.672 63.158 0.00 0.00 0.00 4.30
901 946 9.472361 ACGTAAATGCTAAGTATGATTCGTATT 57.528 29.630 0.00 0.00 0.00 1.89
902 947 9.727403 CGTAAATGCTAAGTATGATTCGTATTG 57.273 33.333 0.00 0.00 0.00 1.90
907 952 6.420903 TGCTAAGTATGATTCGTATTGCAGTC 59.579 38.462 0.00 0.00 0.00 3.51
911 956 5.980116 AGTATGATTCGTATTGCAGTCAGTC 59.020 40.000 0.00 0.00 0.00 3.51
948 993 8.066000 CCATGAAGCTCAATTTTTGTTTTCTTC 58.934 33.333 0.00 0.00 0.00 2.87
949 994 7.538303 TGAAGCTCAATTTTTGTTTTCTTCC 57.462 32.000 0.00 0.00 0.00 3.46
960 1005 8.744568 TTTTTGTTTTCTTCCATTTAGGCATT 57.255 26.923 0.00 0.00 37.29 3.56
972 1017 2.526304 TAGGCATTATGTCTGACGCC 57.474 50.000 9.85 13.65 39.90 5.68
981 1026 2.675423 TCTGACGCCGGTAGCTGT 60.675 61.111 1.90 0.00 40.39 4.40
1033 1078 1.490490 AGCAACCACTTGAGGAACAGA 59.510 47.619 0.00 0.00 0.00 3.41
1146 1194 4.440127 GGGTTTGGCGGCATGCTG 62.440 66.667 22.66 22.66 45.43 4.41
1180 1228 6.109359 GCTATTCAGAAGCTTAACCTGAAGA 58.891 40.000 24.74 21.25 46.17 2.87
1184 1232 6.114187 TCAGAAGCTTAACCTGAAGATCAA 57.886 37.500 12.57 0.00 34.38 2.57
1261 1309 8.668353 CCGAATCAAAGATCATAAAGTTCTTCA 58.332 33.333 0.00 0.00 35.69 3.02
1287 1335 1.408702 GATGTGCACAAGGTGTTTGGT 59.591 47.619 25.72 2.19 41.25 3.67
1304 1352 2.131023 TGGTATACCATGTGGCCATCA 58.869 47.619 21.05 9.85 42.01 3.07
1308 1356 2.566833 TACCATGTGGCCATCATAGC 57.433 50.000 9.72 0.00 39.32 2.97
1319 1367 2.571212 CCATCATAGCGTTAAAGGGCA 58.429 47.619 0.00 0.00 0.00 5.36
1404 1452 2.472909 GGTTCATAGCCTGCGTGCC 61.473 63.158 0.00 0.00 0.00 5.01
1443 1491 2.546368 GCGTGAGATATCTGAGTCGTCT 59.454 50.000 10.74 0.00 0.00 4.18
1540 1588 7.496591 GGACAAAACACGATTATGGGACTATAA 59.503 37.037 0.00 0.00 0.00 0.98
1578 1626 5.700832 ACTTGCGAACACAAAGAATATCTCA 59.299 36.000 0.00 0.00 0.00 3.27
1653 1701 6.017605 GTCGTTTGAAGAATGATATGATGGCT 60.018 38.462 0.00 0.00 0.00 4.75
1695 1743 7.921786 CCTTGTTGGTTGTCATCTATTTCTA 57.078 36.000 0.00 0.00 0.00 2.10
1707 1755 9.072375 TGTCATCTATTTCTACAGGTCAGATAG 57.928 37.037 0.00 0.00 0.00 2.08
1841 1895 8.713971 TCAATAAGAAGCATAATGTCCTTCCTA 58.286 33.333 0.00 0.00 36.50 2.94
1863 1917 2.616510 GGATCAGTGAGTTTGACCAGGG 60.617 54.545 0.00 0.00 0.00 4.45
1870 1924 2.107378 TGAGTTTGACCAGGGCACAATA 59.893 45.455 0.00 0.00 0.00 1.90
1910 1964 1.068352 AACTGACTTGGGGAAGGGCT 61.068 55.000 0.00 0.00 0.00 5.19
1944 1998 1.953559 AAATGCATGGTAGCGACGAT 58.046 45.000 0.00 0.00 37.31 3.73
1966 2020 7.962918 ACGATACTGATTAATTGAAAGCACAAC 59.037 33.333 0.00 0.00 32.50 3.32
2004 2058 5.457140 TGTTTAGTTATTCGCTTGCCTTTG 58.543 37.500 0.00 0.00 0.00 2.77
2032 2086 7.902387 ATCATATGTTTTCCATCTCAGATCG 57.098 36.000 1.90 0.00 34.86 3.69
2060 2114 4.191544 GGTAGTGATTTGTGCTATGCTCA 58.808 43.478 0.00 0.00 0.00 4.26
2087 2141 3.478857 TTTATGTGGAGGTGTTGACGT 57.521 42.857 0.00 0.00 0.00 4.34
2094 2148 2.279918 GGTGTTGACGTCGCCACT 60.280 61.111 26.53 0.00 35.75 4.00
2124 2178 4.312443 CAGCAGAAGTTGGCAATTTTCAT 58.688 39.130 21.62 10.13 0.00 2.57
2139 2193 2.957402 TTCATCAGCCAACCAGTCTT 57.043 45.000 0.00 0.00 0.00 3.01
2169 2223 6.155565 AGGAGCATGGAAATCAAATGAATGAA 59.844 34.615 0.00 0.00 32.06 2.57
2203 2257 6.684555 GTCGTTTCATGATTCTTATTCAGCAC 59.315 38.462 0.00 0.00 0.00 4.40
2204 2258 5.674148 CGTTTCATGATTCTTATTCAGCACG 59.326 40.000 0.00 0.00 0.00 5.34
2251 2305 1.053424 ACTACGTGTGTTGGGTCCAT 58.947 50.000 0.00 0.00 0.00 3.41
2263 2317 4.202440 TGTTGGGTCCATTTGATTTTGCAT 60.202 37.500 0.00 0.00 0.00 3.96
2277 2331 2.411628 TTGCATACCACCTACGCAAT 57.588 45.000 0.00 0.00 37.64 3.56
2306 2360 4.130118 CCAAGTCTGGTAGGTGCATAATC 58.870 47.826 0.00 0.00 38.00 1.75
2333 2387 3.947196 TCCCATGTGTATTTGCATCACTC 59.053 43.478 11.16 2.26 33.82 3.51
2342 2396 7.557358 TGTGTATTTGCATCACTCCTGAATATT 59.443 33.333 11.16 0.00 33.82 1.28
2358 2412 9.225682 TCCTGAATATTTCTACTGGGAGTATTT 57.774 33.333 0.00 0.00 29.08 1.40
2497 2551 2.336341 GTGAAATCAACACGGCCCA 58.664 52.632 0.00 0.00 0.00 5.36
2515 2569 2.086869 CCAAGTCAACATACAGGCAGG 58.913 52.381 0.00 0.00 0.00 4.85
2559 2613 6.432607 AACTCATGACATCACTTAGCAATG 57.567 37.500 0.00 0.00 0.00 2.82
2575 2629 2.070783 CAATGGGTGCATTTGCTGTTC 58.929 47.619 3.94 0.00 42.66 3.18
2643 2697 1.887854 CATCACCAGGTGCATGAACAA 59.112 47.619 15.64 0.00 32.98 2.83
2650 2704 1.949525 AGGTGCATGAACAACACAGTC 59.050 47.619 6.08 0.00 36.00 3.51
2666 2720 7.122055 ACAACACAGTCCAATGAAGAAACTAAA 59.878 33.333 0.00 0.00 0.00 1.85
2667 2721 7.639113 ACACAGTCCAATGAAGAAACTAAAA 57.361 32.000 0.00 0.00 0.00 1.52
2675 2729 9.528018 TCCAATGAAGAAACTAAAACACATTTC 57.472 29.630 0.00 0.00 32.27 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.281941 ACTTTCATCACAGACAGTAGCAGA 59.718 41.667 0.00 0.00 27.37 4.26
28 29 7.179338 AGGAATACTACTTTCATCACAGACAGT 59.821 37.037 0.00 0.00 33.47 3.55
69 70 5.201243 ACTAGTACATCATCAGTGCCTACA 58.799 41.667 0.00 0.00 0.00 2.74
113 114 6.045072 ACCGTACCACTTCTTCATTGATAA 57.955 37.500 0.00 0.00 0.00 1.75
142 143 5.837829 AGCCCTCACAAAATTAAATCCCTA 58.162 37.500 0.00 0.00 0.00 3.53
148 149 6.667414 ACATGGATAGCCCTCACAAAATTAAA 59.333 34.615 0.00 0.00 35.38 1.52
153 154 3.737559 ACATGGATAGCCCTCACAAAA 57.262 42.857 0.00 0.00 35.38 2.44
164 165 7.757173 CCGAATACATGAGTCTTACATGGATAG 59.243 40.741 0.00 0.00 45.16 2.08
290 291 0.033796 TGTCCCTCCTGGTAGGTACG 60.034 60.000 10.14 0.00 36.53 3.67
298 299 3.064987 CTACGCGTGTCCCTCCTGG 62.065 68.421 24.59 0.00 0.00 4.45
327 328 3.799281 CAATTTATTGTGACCGGCCAT 57.201 42.857 0.00 0.00 33.22 4.40
364 365 0.458669 GCGGGTGAGATAAGGTTCGA 59.541 55.000 0.00 0.00 0.00 3.71
400 401 2.000701 AATGGGGATCGGCTGGTGA 61.001 57.895 0.00 0.00 0.00 4.02
406 407 3.599704 GCTGCAATGGGGATCGGC 61.600 66.667 0.00 0.00 0.00 5.54
419 420 1.000394 ACGGGTAAAACAAATGGCTGC 60.000 47.619 0.00 0.00 0.00 5.25
457 458 2.745884 CGGCGATTGCTTGTGGGA 60.746 61.111 0.00 0.00 42.25 4.37
463 464 2.047655 TCGAACCGGCGATTGCTT 60.048 55.556 9.30 0.00 42.25 3.91
497 498 0.037590 TAAGGTTGTGCTGCCGGATT 59.962 50.000 5.05 0.00 0.00 3.01
505 506 2.552373 GCTTACCAGGTAAGGTTGTGCT 60.552 50.000 32.21 0.00 43.81 4.40
518 519 6.198591 GCTTAAATACAGTACGAGCTTACCAG 59.801 42.308 0.00 0.00 0.00 4.00
595 596 1.184970 CCGGTGCCCCTTTTGAATGT 61.185 55.000 0.00 0.00 0.00 2.71
663 686 6.142161 CACAAATCCAAGTCAAATGTTGTACG 59.858 38.462 0.00 0.00 0.00 3.67
664 687 7.167468 GTCACAAATCCAAGTCAAATGTTGTAC 59.833 37.037 0.00 0.00 0.00 2.90
665 688 7.068103 AGTCACAAATCCAAGTCAAATGTTGTA 59.932 33.333 0.00 0.00 0.00 2.41
666 689 6.042143 GTCACAAATCCAAGTCAAATGTTGT 58.958 36.000 0.00 0.00 0.00 3.32
667 690 6.275335 AGTCACAAATCCAAGTCAAATGTTG 58.725 36.000 0.00 0.00 0.00 3.33
668 691 6.322201 AGAGTCACAAATCCAAGTCAAATGTT 59.678 34.615 0.00 0.00 0.00 2.71
669 692 5.829924 AGAGTCACAAATCCAAGTCAAATGT 59.170 36.000 0.00 0.00 0.00 2.71
670 693 6.147581 CAGAGTCACAAATCCAAGTCAAATG 58.852 40.000 0.00 0.00 0.00 2.32
671 694 5.242393 CCAGAGTCACAAATCCAAGTCAAAT 59.758 40.000 0.00 0.00 0.00 2.32
672 695 4.580167 CCAGAGTCACAAATCCAAGTCAAA 59.420 41.667 0.00 0.00 0.00 2.69
673 696 4.136796 CCAGAGTCACAAATCCAAGTCAA 58.863 43.478 0.00 0.00 0.00 3.18
674 697 3.390967 TCCAGAGTCACAAATCCAAGTCA 59.609 43.478 0.00 0.00 0.00 3.41
675 698 4.008074 TCCAGAGTCACAAATCCAAGTC 57.992 45.455 0.00 0.00 0.00 3.01
676 699 4.566488 GGATCCAGAGTCACAAATCCAAGT 60.566 45.833 6.95 0.00 34.20 3.16
677 700 3.944015 GGATCCAGAGTCACAAATCCAAG 59.056 47.826 6.95 0.00 34.20 3.61
678 701 3.619733 CGGATCCAGAGTCACAAATCCAA 60.620 47.826 13.41 0.00 33.75 3.53
679 702 2.093500 CGGATCCAGAGTCACAAATCCA 60.093 50.000 13.41 0.00 33.75 3.41
680 703 2.555199 CGGATCCAGAGTCACAAATCC 58.445 52.381 13.41 0.00 0.00 3.01
681 704 1.936547 GCGGATCCAGAGTCACAAATC 59.063 52.381 13.41 0.00 0.00 2.17
682 705 1.556911 AGCGGATCCAGAGTCACAAAT 59.443 47.619 13.41 0.00 0.00 2.32
683 706 0.976641 AGCGGATCCAGAGTCACAAA 59.023 50.000 13.41 0.00 0.00 2.83
684 707 0.532573 GAGCGGATCCAGAGTCACAA 59.467 55.000 13.41 0.00 0.00 3.33
731 776 3.614630 CGTACTACGGAAATCCAACCACA 60.615 47.826 0.26 0.00 38.08 4.17
745 790 3.818787 AGCCGTGCCCGTACTACG 61.819 66.667 1.32 1.32 42.11 3.51
746 791 2.012902 ATCAGCCGTGCCCGTACTAC 62.013 60.000 0.00 0.00 0.00 2.73
747 792 0.466007 TATCAGCCGTGCCCGTACTA 60.466 55.000 0.00 0.00 0.00 1.82
748 793 1.755395 TATCAGCCGTGCCCGTACT 60.755 57.895 0.00 0.00 0.00 2.73
749 794 1.590792 GTATCAGCCGTGCCCGTAC 60.591 63.158 0.00 0.00 0.00 3.67
750 795 2.053277 TGTATCAGCCGTGCCCGTA 61.053 57.895 0.00 0.00 0.00 4.02
751 796 3.387091 TGTATCAGCCGTGCCCGT 61.387 61.111 0.00 0.00 0.00 5.28
752 797 2.890474 GTGTATCAGCCGTGCCCG 60.890 66.667 0.00 0.00 0.00 6.13
753 798 0.958382 TTTGTGTATCAGCCGTGCCC 60.958 55.000 0.00 0.00 0.00 5.36
754 799 1.094785 ATTTGTGTATCAGCCGTGCC 58.905 50.000 0.00 0.00 0.00 5.01
755 800 2.919666 AATTTGTGTATCAGCCGTGC 57.080 45.000 0.00 0.00 0.00 5.34
756 801 3.938963 AGGTAATTTGTGTATCAGCCGTG 59.061 43.478 0.00 0.00 0.00 4.94
757 802 3.938963 CAGGTAATTTGTGTATCAGCCGT 59.061 43.478 0.00 0.00 0.00 5.68
758 803 3.938963 ACAGGTAATTTGTGTATCAGCCG 59.061 43.478 0.00 0.00 0.00 5.52
759 804 6.995511 TTACAGGTAATTTGTGTATCAGCC 57.004 37.500 0.00 0.00 0.00 4.85
783 828 9.893305 GGCATCTAACGTAAATTTAAGCAATAT 57.107 29.630 10.57 0.00 0.00 1.28
784 829 8.894731 TGGCATCTAACGTAAATTTAAGCAATA 58.105 29.630 10.57 2.57 0.00 1.90
785 830 7.767261 TGGCATCTAACGTAAATTTAAGCAAT 58.233 30.769 10.57 1.63 0.00 3.56
786 831 7.147143 TGGCATCTAACGTAAATTTAAGCAA 57.853 32.000 10.57 0.00 0.00 3.91
787 832 6.183360 CCTGGCATCTAACGTAAATTTAAGCA 60.183 38.462 10.57 0.00 0.00 3.91
788 833 6.183360 ACCTGGCATCTAACGTAAATTTAAGC 60.183 38.462 10.57 0.00 0.00 3.09
789 834 7.280205 AGACCTGGCATCTAACGTAAATTTAAG 59.720 37.037 9.27 9.27 0.00 1.85
790 835 7.107542 AGACCTGGCATCTAACGTAAATTTAA 58.892 34.615 0.00 0.00 0.00 1.52
791 836 6.646267 AGACCTGGCATCTAACGTAAATTTA 58.354 36.000 0.00 0.00 0.00 1.40
792 837 5.497474 AGACCTGGCATCTAACGTAAATTT 58.503 37.500 0.00 0.00 0.00 1.82
793 838 5.099042 AGACCTGGCATCTAACGTAAATT 57.901 39.130 0.00 0.00 0.00 1.82
794 839 4.755266 AGACCTGGCATCTAACGTAAAT 57.245 40.909 0.00 0.00 0.00 1.40
795 840 4.546829 AAGACCTGGCATCTAACGTAAA 57.453 40.909 0.00 0.00 0.00 2.01
796 841 4.250464 CAAAGACCTGGCATCTAACGTAA 58.750 43.478 0.00 0.00 0.00 3.18
797 842 3.857052 CAAAGACCTGGCATCTAACGTA 58.143 45.455 0.00 0.00 0.00 3.57
798 843 2.699954 CAAAGACCTGGCATCTAACGT 58.300 47.619 0.00 0.00 0.00 3.99
799 844 1.398390 GCAAAGACCTGGCATCTAACG 59.602 52.381 0.00 0.00 0.00 3.18
800 845 2.162408 GTGCAAAGACCTGGCATCTAAC 59.838 50.000 0.00 0.00 40.05 2.34
801 846 2.436417 GTGCAAAGACCTGGCATCTAA 58.564 47.619 0.00 0.00 40.05 2.10
802 847 1.675714 CGTGCAAAGACCTGGCATCTA 60.676 52.381 0.00 0.00 40.05 1.98
803 848 0.957395 CGTGCAAAGACCTGGCATCT 60.957 55.000 0.00 0.00 40.05 2.90
804 849 1.503542 CGTGCAAAGACCTGGCATC 59.496 57.895 0.00 0.00 40.05 3.91
805 850 1.973281 CCGTGCAAAGACCTGGCAT 60.973 57.895 0.00 0.00 40.05 4.40
806 851 2.594303 CCGTGCAAAGACCTGGCA 60.594 61.111 0.00 0.00 34.70 4.92
807 852 2.281484 TCCGTGCAAAGACCTGGC 60.281 61.111 0.00 0.00 0.00 4.85
808 853 1.672356 CCTCCGTGCAAAGACCTGG 60.672 63.158 0.00 0.00 0.00 4.45
809 854 0.250295 TTCCTCCGTGCAAAGACCTG 60.250 55.000 0.00 0.00 0.00 4.00
810 855 0.035458 CTTCCTCCGTGCAAAGACCT 59.965 55.000 0.00 0.00 0.00 3.85
811 856 0.034896 TCTTCCTCCGTGCAAAGACC 59.965 55.000 0.00 0.00 0.00 3.85
812 857 1.878953 TTCTTCCTCCGTGCAAAGAC 58.121 50.000 0.00 0.00 0.00 3.01
813 858 2.859165 ATTCTTCCTCCGTGCAAAGA 57.141 45.000 0.00 0.00 0.00 2.52
814 859 3.503748 AGAAATTCTTCCTCCGTGCAAAG 59.496 43.478 0.00 0.00 31.28 2.77
815 860 3.486383 AGAAATTCTTCCTCCGTGCAAA 58.514 40.909 0.00 0.00 31.28 3.68
816 861 3.140325 AGAAATTCTTCCTCCGTGCAA 57.860 42.857 0.00 0.00 31.28 4.08
817 862 2.813754 CAAGAAATTCTTCCTCCGTGCA 59.186 45.455 5.09 0.00 33.78 4.57
818 863 2.814336 ACAAGAAATTCTTCCTCCGTGC 59.186 45.455 5.09 0.00 33.78 5.34
819 864 4.787598 CAACAAGAAATTCTTCCTCCGTG 58.212 43.478 5.09 0.00 33.78 4.94
820 865 3.253432 GCAACAAGAAATTCTTCCTCCGT 59.747 43.478 5.09 0.00 33.78 4.69
821 866 3.253188 TGCAACAAGAAATTCTTCCTCCG 59.747 43.478 5.09 0.00 33.78 4.63
822 867 4.279420 ACTGCAACAAGAAATTCTTCCTCC 59.721 41.667 5.09 0.00 33.78 4.30
823 868 5.444663 ACTGCAACAAGAAATTCTTCCTC 57.555 39.130 5.09 0.00 33.78 3.71
824 869 5.127682 ACAACTGCAACAAGAAATTCTTCCT 59.872 36.000 5.09 0.00 33.78 3.36
825 870 5.351458 ACAACTGCAACAAGAAATTCTTCC 58.649 37.500 5.09 0.00 33.78 3.46
826 871 6.311200 ACAACAACTGCAACAAGAAATTCTTC 59.689 34.615 5.09 0.00 33.78 2.87
877 922 9.530129 GCAATACGAATCATACTTAGCATTTAC 57.470 33.333 0.00 0.00 0.00 2.01
879 924 8.153479 TGCAATACGAATCATACTTAGCATTT 57.847 30.769 0.00 0.00 0.00 2.32
880 925 7.442364 ACTGCAATACGAATCATACTTAGCATT 59.558 33.333 0.00 0.00 0.00 3.56
887 932 5.907207 ACTGACTGCAATACGAATCATACT 58.093 37.500 0.00 0.00 0.00 2.12
901 946 0.396435 AAATGTCGGGACTGACTGCA 59.604 50.000 12.11 0.00 39.64 4.41
902 947 1.464997 GAAAATGTCGGGACTGACTGC 59.535 52.381 12.11 0.00 39.64 4.40
907 952 2.710377 TCATGGAAAATGTCGGGACTG 58.290 47.619 0.00 0.00 0.00 3.51
911 956 2.094675 AGCTTCATGGAAAATGTCGGG 58.905 47.619 0.00 0.00 0.00 5.14
948 993 4.319766 GCGTCAGACATAATGCCTAAATGG 60.320 45.833 0.41 0.00 39.35 3.16
949 994 4.319766 GGCGTCAGACATAATGCCTAAATG 60.320 45.833 8.71 0.00 43.03 2.32
960 1005 1.731700 GCTACCGGCGTCAGACATA 59.268 57.895 6.01 0.00 0.00 2.29
972 1017 2.496817 GCTCCCTCACAGCTACCG 59.503 66.667 0.00 0.00 33.75 4.02
1033 1078 3.586225 ATGAGGGGGCTGGAGGTGT 62.586 63.158 0.00 0.00 0.00 4.16
1146 1194 4.940654 AGCTTCTGAATAGCAGGAAGTTTC 59.059 41.667 4.33 0.00 44.98 2.78
1180 1228 2.091720 TGCTCATAACCCAGGCATTGAT 60.092 45.455 0.00 0.00 0.00 2.57
1184 1232 1.410648 CCTTGCTCATAACCCAGGCAT 60.411 52.381 0.00 0.00 32.87 4.40
1261 1309 1.003355 CCTTGTGCACATCCTCCGT 60.003 57.895 22.39 0.00 0.00 4.69
1287 1335 3.369366 CGCTATGATGGCCACATGGTATA 60.369 47.826 23.16 10.17 37.47 1.47
1304 1352 3.149196 CCATCATGCCCTTTAACGCTAT 58.851 45.455 0.00 0.00 0.00 2.97
1308 1356 3.192422 TGAAACCATCATGCCCTTTAACG 59.808 43.478 0.00 0.00 31.50 3.18
1443 1491 1.474478 CAGTCCTTCTCGAGCTTGCTA 59.526 52.381 7.81 0.00 0.00 3.49
1540 1588 1.750778 CGCAAGTGCTCCCCAATAATT 59.249 47.619 1.21 0.00 39.32 1.40
1567 1615 9.028284 ACACCAATTGAATTGTGAGATATTCTT 57.972 29.630 15.93 0.00 38.59 2.52
1578 1626 5.976458 ACAAACTCACACCAATTGAATTGT 58.024 33.333 15.93 4.30 38.59 2.71
1629 1677 6.057533 AGCCATCATATCATTCTTCAAACGA 58.942 36.000 0.00 0.00 0.00 3.85
1653 1701 7.437748 CAACAAGGTTGGTGTTTGGATTATTA 58.562 34.615 0.00 0.00 40.92 0.98
1695 1743 5.780793 ACAAGTAAGAACCTATCTGACCTGT 59.219 40.000 0.00 0.00 40.08 4.00
1735 1783 1.571955 TAGGCATGAGAGCTGGTTCA 58.428 50.000 0.00 0.00 34.17 3.18
1778 1832 4.994852 CACATTGTCGAGGAAAAAGACCTA 59.005 41.667 0.00 0.00 37.93 3.08
1841 1895 2.304180 CCTGGTCAAACTCACTGATCCT 59.696 50.000 0.00 0.00 0.00 3.24
1863 1917 8.320295 CCATTGTAATCATCGTTTTTATTGTGC 58.680 33.333 0.00 0.00 0.00 4.57
1870 1924 6.365789 CAGTTGCCATTGTAATCATCGTTTTT 59.634 34.615 0.00 0.00 0.00 1.94
1910 1964 3.398406 TGCATTTTGAGTACGAAGCAGA 58.602 40.909 0.00 0.00 0.00 4.26
1944 1998 7.517614 TGGTTGTGCTTTCAATTAATCAGTA 57.482 32.000 0.00 0.00 0.00 2.74
1987 2041 3.552604 TGTCAAAGGCAAGCGAATAAC 57.447 42.857 0.00 0.00 0.00 1.89
1994 2048 5.002464 ACATATGATTGTCAAAGGCAAGC 57.998 39.130 10.38 0.00 33.40 4.01
2004 2058 8.442632 TCTGAGATGGAAAACATATGATTGTC 57.557 34.615 10.38 4.88 40.72 3.18
2032 2086 2.084546 GCACAAATCACTACCCTGACC 58.915 52.381 0.00 0.00 0.00 4.02
2060 2114 5.245751 TCAACACCTCCACATAAATTGCAAT 59.754 36.000 5.99 5.99 0.00 3.56
2094 2148 2.715046 CCAACTTCTGCTGCCTGATTA 58.285 47.619 0.00 0.00 0.00 1.75
2124 2178 3.307691 CCTCATTAAGACTGGTTGGCTGA 60.308 47.826 0.00 0.00 31.76 4.26
2139 2193 6.834969 TCATTTGATTTCCATGCTCCTCATTA 59.165 34.615 0.00 0.00 31.79 1.90
2169 2223 1.347707 TCATGAAACGACCCTGCTCTT 59.652 47.619 0.00 0.00 0.00 2.85
2203 2257 0.107508 ACATCCATGAGGTTGGCTCG 60.108 55.000 0.00 0.00 38.65 5.03
2204 2258 1.386533 CACATCCATGAGGTTGGCTC 58.613 55.000 0.00 0.00 38.65 4.70
2251 2305 4.380023 GCGTAGGTGGTATGCAAAATCAAA 60.380 41.667 0.00 0.00 42.52 2.69
2263 2317 2.294233 GGTATCGATTGCGTAGGTGGTA 59.706 50.000 1.71 0.00 38.98 3.25
2306 2360 3.289836 TGCAAATACACATGGGAGATGG 58.710 45.455 0.00 0.00 0.00 3.51
2333 2387 9.277783 CAAATACTCCCAGTAGAAATATTCAGG 57.722 37.037 0.00 0.00 33.66 3.86
2342 2396 6.713450 GGAAACAACAAATACTCCCAGTAGAA 59.287 38.462 0.00 0.00 33.66 2.10
2380 2434 6.862209 ACAACAGCTTCAGAACACAATTTAA 58.138 32.000 0.00 0.00 0.00 1.52
2382 2436 5.329035 ACAACAGCTTCAGAACACAATTT 57.671 34.783 0.00 0.00 0.00 1.82
2383 2437 4.202050 GGACAACAGCTTCAGAACACAATT 60.202 41.667 0.00 0.00 0.00 2.32
2384 2438 3.316308 GGACAACAGCTTCAGAACACAAT 59.684 43.478 0.00 0.00 0.00 2.71
2497 2551 1.073763 TGCCTGCCTGTATGTTGACTT 59.926 47.619 0.00 0.00 0.00 3.01
2559 2613 0.668401 GCAGAACAGCAAATGCACCC 60.668 55.000 8.28 0.00 45.16 4.61
2575 2629 0.872388 GTCAGTAAAACCACGGGCAG 59.128 55.000 0.00 0.00 0.00 4.85
2643 2697 7.122055 TGTTTTAGTTTCTTCATTGGACTGTGT 59.878 33.333 0.00 0.00 0.00 3.72
2650 2704 8.479280 CGAAATGTGTTTTAGTTTCTTCATTGG 58.521 33.333 0.00 0.00 0.00 3.16
2666 2720 3.001127 GTGCATGCAAAACGAAATGTGTT 59.999 39.130 24.58 0.00 0.00 3.32
2667 2721 2.539274 GTGCATGCAAAACGAAATGTGT 59.461 40.909 24.58 0.00 0.00 3.72
2675 2729 1.125384 GCTGAATGTGCATGCAAAACG 59.875 47.619 24.58 10.05 0.00 3.60


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

AutoCloner maintained by Alex Coulton.