Multiple sequence alignment - TraesCS1A01G071900

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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 TraesCS1A01G071900 chr1A 100.000 2630 0 0 1 2630 54128426 54125797 0.000000e+00 4857
1 TraesCS1A01G071900 chr1A 92.082 682 50 4 1 681 464845031 464844353 0.000000e+00 957
2 TraesCS1A01G071900 chr3D 96.692 1814 54 2 817 2630 71374673 71372866 0.000000e+00 3013
3 TraesCS1A01G071900 chr3D 92.070 681 51 3 1 680 454751076 454751754 0.000000e+00 955
4 TraesCS1A01G071900 chr3D 91.813 684 52 4 1 683 13635795 13636475 0.000000e+00 950
5 TraesCS1A01G071900 chr7A 93.265 683 43 3 1 682 478140149 478140829 0.000000e+00 1003
6 TraesCS1A01G071900 chr3A 93.013 687 41 5 1 683 667166592 667165909 0.000000e+00 996
7 TraesCS1A01G071900 chr7D 92.962 682 45 3 1 681 236177275 236176596 0.000000e+00 990
8 TraesCS1A01G071900 chr1D 92.826 683 45 3 1 681 403567476 403568156 0.000000e+00 987
9 TraesCS1A01G071900 chr1D 91.608 143 8 1 679 817 55679045 55678903 7.430000e-46 195
10 TraesCS1A01G071900 chr6D 92.353 680 46 5 1 679 256166262 256166936 0.000000e+00 963
11 TraesCS1A01G071900 chr6A 92.059 680 51 3 1 679 94241413 94240736 0.000000e+00 953
12 TraesCS1A01G071900 chr1B 88.966 145 9 4 679 817 91031929 91031786 3.480000e-39 172


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 TraesCS1A01G071900 chr1A 54125797 54128426 2629 True 4857 4857 100.000 1 2630 1 chr1A.!!$R1 2629
1 TraesCS1A01G071900 chr1A 464844353 464845031 678 True 957 957 92.082 1 681 1 chr1A.!!$R2 680
2 TraesCS1A01G071900 chr3D 71372866 71374673 1807 True 3013 3013 96.692 817 2630 1 chr3D.!!$R1 1813
3 TraesCS1A01G071900 chr3D 454751076 454751754 678 False 955 955 92.070 1 680 1 chr3D.!!$F2 679
4 TraesCS1A01G071900 chr3D 13635795 13636475 680 False 950 950 91.813 1 683 1 chr3D.!!$F1 682
5 TraesCS1A01G071900 chr7A 478140149 478140829 680 False 1003 1003 93.265 1 682 1 chr7A.!!$F1 681
6 TraesCS1A01G071900 chr3A 667165909 667166592 683 True 996 996 93.013 1 683 1 chr3A.!!$R1 682
7 TraesCS1A01G071900 chr7D 236176596 236177275 679 True 990 990 92.962 1 681 1 chr7D.!!$R1 680
8 TraesCS1A01G071900 chr1D 403567476 403568156 680 False 987 987 92.826 1 681 1 chr1D.!!$F1 680
9 TraesCS1A01G071900 chr6D 256166262 256166936 674 False 963 963 92.353 1 679 1 chr6D.!!$F1 678
10 TraesCS1A01G071900 chr6A 94240736 94241413 677 True 953 953 92.059 1 679 1 chr6A.!!$R1 678

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
984 990 0.589708 GCTGTACCACGTTGTTTCCC 59.41 55.0 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2589 2595 0.31716 CACTCAACTACAGTGCCGGA 59.683 55.0 5.05 0.0 35.15 5.14 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
138 139 9.281371 CATGATATGGCAAGAAGAGAAATCTTA 57.719 33.333 0.00 0.00 35.43 2.10
159 160 0.976641 AGAGAAGAATGGTGGCGTCA 59.023 50.000 0.00 0.00 0.00 4.35
184 185 2.551504 GGTCCATGTTACAGTTCCGGTT 60.552 50.000 0.00 0.00 0.00 4.44
323 324 4.981674 GGAGTGAAGATCGATCAAGATGAC 59.018 45.833 26.47 13.49 0.00 3.06
363 365 2.247358 CTTTTGCAGGGCCCTCTTTTA 58.753 47.619 25.77 6.81 0.00 1.52
414 416 4.212213 TGCGCGTAAAACTGTTTATGTT 57.788 36.364 8.43 0.00 38.15 2.71
452 454 7.425606 ACTTGTTTGTGAAATCCTATGTCAAC 58.574 34.615 0.00 0.00 0.00 3.18
486 488 2.070783 GTTTATCTGTTTGCGGGTCGA 58.929 47.619 0.00 0.00 0.00 4.20
619 625 0.595310 GGCACGCAAAAGCGGTTTTA 60.595 50.000 23.52 0.00 33.93 1.52
683 689 4.081917 GGTCTGCTAGAGTTGCTCTTAGTT 60.082 45.833 3.87 0.00 41.50 2.24
684 690 5.474825 GTCTGCTAGAGTTGCTCTTAGTTT 58.525 41.667 3.87 0.00 41.50 2.66
685 691 5.347364 GTCTGCTAGAGTTGCTCTTAGTTTG 59.653 44.000 3.87 0.00 41.50 2.93
686 692 5.011125 TCTGCTAGAGTTGCTCTTAGTTTGT 59.989 40.000 3.87 0.00 41.50 2.83
687 693 5.611374 TGCTAGAGTTGCTCTTAGTTTGTT 58.389 37.500 3.87 0.00 41.50 2.83
688 694 6.755206 TGCTAGAGTTGCTCTTAGTTTGTTA 58.245 36.000 3.87 0.00 41.50 2.41
689 695 7.214381 TGCTAGAGTTGCTCTTAGTTTGTTAA 58.786 34.615 3.87 0.00 41.50 2.01
690 696 7.878127 TGCTAGAGTTGCTCTTAGTTTGTTAAT 59.122 33.333 3.87 0.00 41.50 1.40
691 697 9.367444 GCTAGAGTTGCTCTTAGTTTGTTAATA 57.633 33.333 3.87 0.00 41.50 0.98
693 699 8.779354 AGAGTTGCTCTTAGTTTGTTAATAGG 57.221 34.615 0.00 0.00 37.60 2.57
694 700 8.594550 AGAGTTGCTCTTAGTTTGTTAATAGGA 58.405 33.333 0.00 0.00 37.60 2.94
695 701 9.384764 GAGTTGCTCTTAGTTTGTTAATAGGAT 57.615 33.333 0.00 0.00 0.00 3.24
696 702 9.384764 AGTTGCTCTTAGTTTGTTAATAGGATC 57.615 33.333 0.00 0.00 0.00 3.36
697 703 8.613482 GTTGCTCTTAGTTTGTTAATAGGATCC 58.387 37.037 2.48 2.48 0.00 3.36
698 704 7.857456 TGCTCTTAGTTTGTTAATAGGATCCA 58.143 34.615 15.82 0.00 0.00 3.41
699 705 8.494433 TGCTCTTAGTTTGTTAATAGGATCCAT 58.506 33.333 15.82 2.53 0.00 3.41
700 706 9.343539 GCTCTTAGTTTGTTAATAGGATCCATT 57.656 33.333 15.82 13.60 0.00 3.16
705 711 8.433421 AGTTTGTTAATAGGATCCATTACGTG 57.567 34.615 15.82 0.00 0.00 4.49
706 712 8.044908 AGTTTGTTAATAGGATCCATTACGTGT 58.955 33.333 15.82 0.00 0.00 4.49
707 713 8.333186 GTTTGTTAATAGGATCCATTACGTGTC 58.667 37.037 15.82 4.07 0.00 3.67
708 714 6.518493 TGTTAATAGGATCCATTACGTGTCC 58.482 40.000 15.82 0.00 0.00 4.02
709 715 6.098552 TGTTAATAGGATCCATTACGTGTCCA 59.901 38.462 15.82 3.99 0.00 4.02
710 716 5.623956 AATAGGATCCATTACGTGTCCAA 57.376 39.130 15.82 0.00 0.00 3.53
711 717 3.992943 AGGATCCATTACGTGTCCAAA 57.007 42.857 15.82 0.00 0.00 3.28
712 718 3.873910 AGGATCCATTACGTGTCCAAAG 58.126 45.455 15.82 0.00 0.00 2.77
713 719 2.354821 GGATCCATTACGTGTCCAAAGC 59.645 50.000 6.95 0.00 0.00 3.51
714 720 1.816074 TCCATTACGTGTCCAAAGCC 58.184 50.000 0.00 0.00 0.00 4.35
715 721 1.349688 TCCATTACGTGTCCAAAGCCT 59.650 47.619 0.00 0.00 0.00 4.58
716 722 2.159382 CCATTACGTGTCCAAAGCCTT 58.841 47.619 0.00 0.00 0.00 4.35
717 723 2.556622 CCATTACGTGTCCAAAGCCTTT 59.443 45.455 0.00 0.00 0.00 3.11
718 724 3.005367 CCATTACGTGTCCAAAGCCTTTT 59.995 43.478 0.00 0.00 0.00 2.27
719 725 3.701532 TTACGTGTCCAAAGCCTTTTG 57.298 42.857 0.00 0.00 42.66 2.44
720 726 1.470051 ACGTGTCCAAAGCCTTTTGT 58.530 45.000 0.00 0.00 41.68 2.83
721 727 1.822371 ACGTGTCCAAAGCCTTTTGTT 59.178 42.857 0.00 0.00 41.68 2.83
722 728 2.159296 ACGTGTCCAAAGCCTTTTGTTC 60.159 45.455 0.00 0.00 41.68 3.18
723 729 2.798145 CGTGTCCAAAGCCTTTTGTTCC 60.798 50.000 0.00 0.00 41.68 3.62
724 730 2.430694 GTGTCCAAAGCCTTTTGTTCCT 59.569 45.455 0.00 0.00 41.68 3.36
725 731 2.693074 TGTCCAAAGCCTTTTGTTCCTC 59.307 45.455 0.00 0.00 41.68 3.71
726 732 2.959030 GTCCAAAGCCTTTTGTTCCTCT 59.041 45.455 0.00 0.00 41.68 3.69
727 733 3.384789 GTCCAAAGCCTTTTGTTCCTCTT 59.615 43.478 0.00 0.00 41.68 2.85
728 734 3.636764 TCCAAAGCCTTTTGTTCCTCTTC 59.363 43.478 0.00 0.00 41.68 2.87
729 735 3.550842 CCAAAGCCTTTTGTTCCTCTTCG 60.551 47.826 0.00 0.00 41.68 3.79
730 736 1.239347 AGCCTTTTGTTCCTCTTCGC 58.761 50.000 0.00 0.00 0.00 4.70
731 737 0.951558 GCCTTTTGTTCCTCTTCGCA 59.048 50.000 0.00 0.00 0.00 5.10
732 738 1.541588 GCCTTTTGTTCCTCTTCGCAT 59.458 47.619 0.00 0.00 0.00 4.73
733 739 2.747446 GCCTTTTGTTCCTCTTCGCATA 59.253 45.455 0.00 0.00 0.00 3.14
734 740 3.378427 GCCTTTTGTTCCTCTTCGCATAT 59.622 43.478 0.00 0.00 0.00 1.78
735 741 4.731773 GCCTTTTGTTCCTCTTCGCATATG 60.732 45.833 0.00 0.00 0.00 1.78
736 742 4.396166 CCTTTTGTTCCTCTTCGCATATGT 59.604 41.667 4.29 0.00 0.00 2.29
737 743 5.106157 CCTTTTGTTCCTCTTCGCATATGTT 60.106 40.000 4.29 0.00 0.00 2.71
738 744 6.093495 CCTTTTGTTCCTCTTCGCATATGTTA 59.907 38.462 4.29 0.00 0.00 2.41
739 745 7.201732 CCTTTTGTTCCTCTTCGCATATGTTAT 60.202 37.037 4.29 0.00 0.00 1.89
740 746 7.624360 TTTGTTCCTCTTCGCATATGTTATT 57.376 32.000 4.29 0.00 0.00 1.40
741 747 7.624360 TTGTTCCTCTTCGCATATGTTATTT 57.376 32.000 4.29 0.00 0.00 1.40
742 748 7.624360 TGTTCCTCTTCGCATATGTTATTTT 57.376 32.000 4.29 0.00 0.00 1.82
743 749 7.471721 TGTTCCTCTTCGCATATGTTATTTTG 58.528 34.615 4.29 0.00 0.00 2.44
744 750 6.618287 TCCTCTTCGCATATGTTATTTTGG 57.382 37.500 4.29 0.19 0.00 3.28
745 751 5.008613 TCCTCTTCGCATATGTTATTTTGGC 59.991 40.000 4.29 0.00 0.00 4.52
746 752 5.221028 CCTCTTCGCATATGTTATTTTGGCA 60.221 40.000 4.29 0.00 0.00 4.92
747 753 5.577835 TCTTCGCATATGTTATTTTGGCAC 58.422 37.500 4.29 0.00 0.00 5.01
748 754 4.972514 TCGCATATGTTATTTTGGCACA 57.027 36.364 4.29 0.00 0.00 4.57
763 769 4.935352 TGGCACAAGTTTTTGCTATTCT 57.065 36.364 6.25 0.00 38.85 2.40
765 771 6.398234 TGGCACAAGTTTTTGCTATTCTAA 57.602 33.333 6.25 0.00 38.85 2.10
766 772 6.446318 TGGCACAAGTTTTTGCTATTCTAAG 58.554 36.000 6.25 0.00 38.85 2.18
767 773 6.264292 TGGCACAAGTTTTTGCTATTCTAAGA 59.736 34.615 6.25 0.00 38.85 2.10
768 774 7.145323 GGCACAAGTTTTTGCTATTCTAAGAA 58.855 34.615 6.25 0.00 38.85 2.52
769 775 7.651704 GGCACAAGTTTTTGCTATTCTAAGAAA 59.348 33.333 6.25 0.00 38.85 2.52
770 776 9.030301 GCACAAGTTTTTGCTATTCTAAGAAAA 57.970 29.630 0.00 0.00 37.85 2.29
801 807 8.188139 TGAAAAGTTTCAATTGTAAGTCAGACC 58.812 33.333 5.13 0.00 43.62 3.85
802 808 5.924475 AGTTTCAATTGTAAGTCAGACCG 57.076 39.130 5.13 0.00 0.00 4.79
803 809 5.365619 AGTTTCAATTGTAAGTCAGACCGT 58.634 37.500 5.13 0.00 0.00 4.83
804 810 5.820947 AGTTTCAATTGTAAGTCAGACCGTT 59.179 36.000 5.13 0.00 0.00 4.44
805 811 6.317893 AGTTTCAATTGTAAGTCAGACCGTTT 59.682 34.615 5.13 0.00 0.00 3.60
806 812 5.666969 TCAATTGTAAGTCAGACCGTTTG 57.333 39.130 5.13 0.00 0.00 2.93
807 813 4.024387 TCAATTGTAAGTCAGACCGTTTGC 60.024 41.667 5.13 0.00 0.00 3.68
808 814 2.902705 TGTAAGTCAGACCGTTTGCT 57.097 45.000 0.00 0.00 0.00 3.91
809 815 2.479837 TGTAAGTCAGACCGTTTGCTG 58.520 47.619 0.00 0.00 0.00 4.41
810 816 2.101750 TGTAAGTCAGACCGTTTGCTGA 59.898 45.455 0.00 0.00 38.72 4.26
811 817 1.871080 AAGTCAGACCGTTTGCTGAG 58.129 50.000 0.00 0.00 41.42 3.35
812 818 0.753262 AGTCAGACCGTTTGCTGAGT 59.247 50.000 0.00 0.00 41.42 3.41
813 819 1.139058 AGTCAGACCGTTTGCTGAGTT 59.861 47.619 0.00 0.00 40.85 3.01
814 820 1.940613 GTCAGACCGTTTGCTGAGTTT 59.059 47.619 0.00 0.00 41.42 2.66
815 821 2.354821 GTCAGACCGTTTGCTGAGTTTT 59.645 45.455 0.00 0.00 41.42 2.43
918 924 4.606457 AAAAATCAATCTCCTTCGCTCG 57.394 40.909 0.00 0.00 0.00 5.03
965 971 1.135315 CGGCAGCAGGATTTGTTCG 59.865 57.895 0.00 0.00 0.00 3.95
984 990 0.589708 GCTGTACCACGTTGTTTCCC 59.410 55.000 0.00 0.00 0.00 3.97
985 991 1.812708 GCTGTACCACGTTGTTTCCCT 60.813 52.381 0.00 0.00 0.00 4.20
988 994 2.171027 TGTACCACGTTGTTTCCCTTCT 59.829 45.455 0.00 0.00 0.00 2.85
995 1001 3.006644 ACGTTGTTTCCCTTCTAGAGGTC 59.993 47.826 0.71 0.00 44.71 3.85
998 1004 3.858135 TGTTTCCCTTCTAGAGGTCAGT 58.142 45.455 0.71 0.00 44.71 3.41
1003 1009 2.102252 CCCTTCTAGAGGTCAGTGATGC 59.898 54.545 0.00 0.00 44.71 3.91
1086 1092 1.818785 GCTGCAGCTCCATGAGGAC 60.819 63.158 31.33 0.00 39.61 3.85
1227 1233 1.521457 GCGATCTGCGTGGAATCCA 60.521 57.895 0.00 0.00 43.41 3.41
1235 1241 1.299648 CGTGGAATCCAGCAAGGGA 59.700 57.895 0.27 0.00 42.21 4.20
1273 1279 1.483004 TGGAAGACAACCTGTTCACGA 59.517 47.619 0.00 0.00 0.00 4.35
1284 1290 3.138304 CCTGTTCACGATTCAGTTTGGA 58.862 45.455 0.00 0.00 0.00 3.53
1290 1296 4.245660 TCACGATTCAGTTTGGATGTCTC 58.754 43.478 0.00 0.00 0.00 3.36
1302 1308 2.280628 GGATGTCTCGGTGATTGGAAC 58.719 52.381 0.00 0.00 0.00 3.62
1306 1312 0.963225 TCTCGGTGATTGGAACACGA 59.037 50.000 0.00 0.00 39.29 4.35
1334 1340 2.283821 GGGGCCATGGCTGTTCAA 60.284 61.111 34.70 0.00 41.60 2.69
1382 1388 7.721399 GGAGTATGATGGTTTCACAAATCCTAT 59.279 37.037 0.00 0.00 36.02 2.57
1426 1432 1.071385 CAGTGTGGGCAAGAGTTCTCT 59.929 52.381 0.00 0.00 0.00 3.10
1464 1470 2.620251 TGATCCCCGTAGCAATCAAG 57.380 50.000 0.00 0.00 0.00 3.02
1492 1498 1.562672 CCGGAAGATGGGGAAGGTGT 61.563 60.000 0.00 0.00 0.00 4.16
1521 1527 0.615850 AAACTACTCTCCCTGCAGGC 59.384 55.000 28.39 0.00 34.51 4.85
1542 1548 3.250744 CTTCGCTGGAGAATTTGTACGA 58.749 45.455 0.00 0.00 0.00 3.43
1589 1595 7.992754 ACAAGAAGCTTATCAGATTTGTCTT 57.007 32.000 0.00 0.00 0.00 3.01
1591 1597 7.663081 ACAAGAAGCTTATCAGATTTGTCTTGA 59.337 33.333 18.38 0.00 34.07 3.02
1627 1633 6.440647 TGAGGAAACTGAGTATTATCAGGTGT 59.559 38.462 8.46 0.00 46.58 4.16
1632 1638 9.733219 GAAACTGAGTATTATCAGGTGTAGTAC 57.267 37.037 8.46 0.00 46.58 2.73
1639 1645 8.619546 AGTATTATCAGGTGTAGTACGAGAAAC 58.380 37.037 0.00 0.00 0.00 2.78
1647 1653 6.886459 AGGTGTAGTACGAGAAACTACCAATA 59.114 38.462 10.08 0.00 45.72 1.90
1755 1761 0.107897 TTATGCTCGTTGATGGCGGT 60.108 50.000 0.00 0.00 0.00 5.68
1965 1971 2.621998 GCAAGTGGAGCATGATAGCAAT 59.378 45.455 0.00 0.00 36.85 3.56
1966 1972 3.304525 GCAAGTGGAGCATGATAGCAATC 60.305 47.826 0.00 0.00 36.85 2.67
2053 2059 4.228210 AGAGCATACTGGGAAAAAGATCCA 59.772 41.667 0.00 0.00 41.55 3.41
2107 2113 2.030274 GCACCGGTTCAAGCAATAGTTT 60.030 45.455 2.97 0.00 0.00 2.66
2171 2177 1.591619 GCCGCAGATAGTTAACCGTTC 59.408 52.381 0.88 0.00 0.00 3.95
2176 2182 4.804139 CGCAGATAGTTAACCGTTCTGAAT 59.196 41.667 23.71 0.25 36.72 2.57
2183 2189 6.038997 AGTTAACCGTTCTGAATTAGAGCT 57.961 37.500 0.88 0.00 36.61 4.09
2196 2202 4.744795 ATTAGAGCTCGTTGGTGATCTT 57.255 40.909 8.37 0.00 34.56 2.40
2363 2369 2.086869 CTCTCAACCACGGCAATTCAT 58.913 47.619 0.00 0.00 0.00 2.57
2372 2378 2.938451 CACGGCAATTCATGAGCTTCTA 59.062 45.455 5.52 0.00 0.00 2.10
2379 2385 5.759273 GCAATTCATGAGCTTCTAGAGATGT 59.241 40.000 0.00 0.00 0.00 3.06
2396 2402 0.253327 TGTAGGAGCGAGAGAGAGCA 59.747 55.000 0.00 0.00 35.48 4.26
2445 2451 3.207265 TGAACAAAGCTAAGGCAGACA 57.793 42.857 0.00 0.00 41.70 3.41
2504 2510 1.628846 ACTAAAAGTGATGGTCGGGCT 59.371 47.619 0.00 0.00 0.00 5.19
2593 2599 6.794374 TCATTGATGTTTTATTCATGTCCGG 58.206 36.000 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.389687 GCAACATGGACATGGATTTGTTTC 59.610 41.667 15.94 0.00 42.91 2.78
138 139 2.224523 TGACGCCACCATTCTTCTCTTT 60.225 45.455 0.00 0.00 0.00 2.52
159 160 0.690762 AACTGTAACATGGACCGGCT 59.309 50.000 0.00 0.00 0.00 5.52
168 169 6.713450 AGAAAACATAACCGGAACTGTAACAT 59.287 34.615 9.46 0.00 0.00 2.71
414 416 7.953158 TCACAAACAAGTTCAAATTCAAACA 57.047 28.000 5.89 0.00 0.00 2.83
486 488 4.796231 GCTCGGACACCATCGCGT 62.796 66.667 5.77 0.00 0.00 6.01
491 493 1.690219 GGGATCTGCTCGGACACCAT 61.690 60.000 0.00 0.00 0.00 3.55
619 625 1.973137 AACACGTTTGCAGTTCGCGT 61.973 50.000 5.77 3.04 46.97 6.01
683 689 6.987992 GGACACGTAATGGATCCTATTAACAA 59.012 38.462 14.23 0.00 0.00 2.83
684 690 6.098552 TGGACACGTAATGGATCCTATTAACA 59.901 38.462 14.23 6.14 0.00 2.41
685 691 6.518493 TGGACACGTAATGGATCCTATTAAC 58.482 40.000 14.23 3.51 0.00 2.01
686 692 6.734502 TGGACACGTAATGGATCCTATTAA 57.265 37.500 14.23 0.00 0.00 1.40
687 693 6.734502 TTGGACACGTAATGGATCCTATTA 57.265 37.500 14.23 12.05 0.00 0.98
688 694 5.623956 TTGGACACGTAATGGATCCTATT 57.376 39.130 14.23 13.01 0.00 1.73
689 695 5.611374 CTTTGGACACGTAATGGATCCTAT 58.389 41.667 14.23 4.12 0.00 2.57
690 696 4.682320 GCTTTGGACACGTAATGGATCCTA 60.682 45.833 14.23 0.00 0.00 2.94
691 697 3.873910 CTTTGGACACGTAATGGATCCT 58.126 45.455 14.23 0.00 0.00 3.24
692 698 2.354821 GCTTTGGACACGTAATGGATCC 59.645 50.000 4.20 4.20 0.00 3.36
693 699 2.354821 GGCTTTGGACACGTAATGGATC 59.645 50.000 0.00 0.00 0.00 3.36
694 700 2.026262 AGGCTTTGGACACGTAATGGAT 60.026 45.455 0.00 0.00 0.00 3.41
695 701 1.349688 AGGCTTTGGACACGTAATGGA 59.650 47.619 0.00 0.00 0.00 3.41
696 702 1.821216 AGGCTTTGGACACGTAATGG 58.179 50.000 0.00 0.00 0.00 3.16
697 703 3.915437 AAAGGCTTTGGACACGTAATG 57.085 42.857 12.53 0.00 0.00 1.90
698 704 3.634910 ACAAAAGGCTTTGGACACGTAAT 59.365 39.130 21.00 0.00 45.30 1.89
699 705 3.018149 ACAAAAGGCTTTGGACACGTAA 58.982 40.909 21.00 0.00 45.30 3.18
700 706 2.645802 ACAAAAGGCTTTGGACACGTA 58.354 42.857 21.00 0.00 45.30 3.57
701 707 1.470051 ACAAAAGGCTTTGGACACGT 58.530 45.000 21.00 5.64 45.30 4.49
702 708 2.459934 GAACAAAAGGCTTTGGACACG 58.540 47.619 21.00 5.05 45.30 4.49
703 709 2.430694 AGGAACAAAAGGCTTTGGACAC 59.569 45.455 21.00 9.55 45.30 3.67
704 710 2.693074 GAGGAACAAAAGGCTTTGGACA 59.307 45.455 21.00 0.00 45.30 4.02
705 711 2.959030 AGAGGAACAAAAGGCTTTGGAC 59.041 45.455 21.00 13.11 45.30 4.02
706 712 3.312736 AGAGGAACAAAAGGCTTTGGA 57.687 42.857 21.00 0.00 45.30 3.53
707 713 3.550842 CGAAGAGGAACAAAAGGCTTTGG 60.551 47.826 14.19 13.49 45.30 3.28
708 714 3.632189 CGAAGAGGAACAAAAGGCTTTG 58.368 45.455 14.19 10.18 46.26 2.77
709 715 2.034685 GCGAAGAGGAACAAAAGGCTTT 59.965 45.455 6.68 6.68 0.00 3.51
710 716 1.609072 GCGAAGAGGAACAAAAGGCTT 59.391 47.619 0.00 0.00 0.00 4.35
711 717 1.239347 GCGAAGAGGAACAAAAGGCT 58.761 50.000 0.00 0.00 0.00 4.58
712 718 0.951558 TGCGAAGAGGAACAAAAGGC 59.048 50.000 0.00 0.00 0.00 4.35
713 719 4.396166 ACATATGCGAAGAGGAACAAAAGG 59.604 41.667 1.58 0.00 0.00 3.11
714 720 5.551760 ACATATGCGAAGAGGAACAAAAG 57.448 39.130 1.58 0.00 0.00 2.27
715 721 5.957842 AACATATGCGAAGAGGAACAAAA 57.042 34.783 1.58 0.00 0.00 2.44
716 722 7.624360 AATAACATATGCGAAGAGGAACAAA 57.376 32.000 1.58 0.00 0.00 2.83
717 723 7.624360 AAATAACATATGCGAAGAGGAACAA 57.376 32.000 1.58 0.00 0.00 2.83
718 724 7.415095 CCAAAATAACATATGCGAAGAGGAACA 60.415 37.037 1.58 0.00 0.00 3.18
719 725 6.912591 CCAAAATAACATATGCGAAGAGGAAC 59.087 38.462 1.58 0.00 0.00 3.62
720 726 6.459573 GCCAAAATAACATATGCGAAGAGGAA 60.460 38.462 1.58 0.00 0.00 3.36
721 727 5.008613 GCCAAAATAACATATGCGAAGAGGA 59.991 40.000 1.58 0.00 0.00 3.71
722 728 5.215160 GCCAAAATAACATATGCGAAGAGG 58.785 41.667 1.58 0.00 0.00 3.69
723 729 5.682862 GTGCCAAAATAACATATGCGAAGAG 59.317 40.000 1.58 0.00 0.00 2.85
724 730 5.124617 TGTGCCAAAATAACATATGCGAAGA 59.875 36.000 1.58 0.00 0.00 2.87
725 731 5.339177 TGTGCCAAAATAACATATGCGAAG 58.661 37.500 1.58 0.00 0.00 3.79
726 732 5.316327 TGTGCCAAAATAACATATGCGAA 57.684 34.783 1.58 0.00 0.00 4.70
727 733 4.972514 TGTGCCAAAATAACATATGCGA 57.027 36.364 1.58 0.00 0.00 5.10
728 734 5.101628 ACTTGTGCCAAAATAACATATGCG 58.898 37.500 1.58 0.00 0.00 4.73
729 735 6.966435 AACTTGTGCCAAAATAACATATGC 57.034 33.333 1.58 0.00 0.00 3.14
730 736 9.596677 CAAAAACTTGTGCCAAAATAACATATG 57.403 29.630 0.00 0.00 0.00 1.78
731 737 8.288913 GCAAAAACTTGTGCCAAAATAACATAT 58.711 29.630 0.00 0.00 34.58 1.78
732 738 7.497249 AGCAAAAACTTGTGCCAAAATAACATA 59.503 29.630 0.85 0.00 41.88 2.29
733 739 6.318396 AGCAAAAACTTGTGCCAAAATAACAT 59.682 30.769 0.85 0.00 41.88 2.71
734 740 5.645497 AGCAAAAACTTGTGCCAAAATAACA 59.355 32.000 0.85 0.00 41.88 2.41
735 741 6.117911 AGCAAAAACTTGTGCCAAAATAAC 57.882 33.333 0.85 0.00 41.88 1.89
736 742 8.443953 AATAGCAAAAACTTGTGCCAAAATAA 57.556 26.923 0.85 0.00 41.88 1.40
737 743 7.930865 AGAATAGCAAAAACTTGTGCCAAAATA 59.069 29.630 0.85 0.00 41.88 1.40
738 744 6.767423 AGAATAGCAAAAACTTGTGCCAAAAT 59.233 30.769 0.85 0.00 41.88 1.82
739 745 6.112058 AGAATAGCAAAAACTTGTGCCAAAA 58.888 32.000 0.85 0.00 41.88 2.44
740 746 5.669477 AGAATAGCAAAAACTTGTGCCAAA 58.331 33.333 0.85 0.00 41.88 3.28
741 747 5.275067 AGAATAGCAAAAACTTGTGCCAA 57.725 34.783 0.85 0.00 41.88 4.52
742 748 4.935352 AGAATAGCAAAAACTTGTGCCA 57.065 36.364 0.85 0.00 41.88 4.92
743 749 6.677913 TCTTAGAATAGCAAAAACTTGTGCC 58.322 36.000 0.85 0.00 41.88 5.01
744 750 8.574196 TTTCTTAGAATAGCAAAAACTTGTGC 57.426 30.769 0.00 0.00 41.22 4.57
775 781 8.188139 GGTCTGACTTACAATTGAAACTTTTCA 58.812 33.333 13.59 0.07 44.78 2.69
776 782 7.376072 CGGTCTGACTTACAATTGAAACTTTTC 59.624 37.037 13.59 0.00 37.69 2.29
777 783 7.148137 ACGGTCTGACTTACAATTGAAACTTTT 60.148 33.333 13.59 0.00 0.00 2.27
778 784 6.317893 ACGGTCTGACTTACAATTGAAACTTT 59.682 34.615 13.59 0.00 0.00 2.66
779 785 5.820947 ACGGTCTGACTTACAATTGAAACTT 59.179 36.000 13.59 0.00 0.00 2.66
780 786 5.365619 ACGGTCTGACTTACAATTGAAACT 58.634 37.500 13.59 0.00 0.00 2.66
781 787 5.668558 ACGGTCTGACTTACAATTGAAAC 57.331 39.130 13.59 0.00 0.00 2.78
782 788 6.491394 CAAACGGTCTGACTTACAATTGAAA 58.509 36.000 13.59 0.00 0.00 2.69
783 789 5.504994 GCAAACGGTCTGACTTACAATTGAA 60.505 40.000 13.59 1.41 0.00 2.69
784 790 4.024387 GCAAACGGTCTGACTTACAATTGA 60.024 41.667 13.59 0.00 0.00 2.57
785 791 4.024048 AGCAAACGGTCTGACTTACAATTG 60.024 41.667 7.85 3.24 0.00 2.32
786 792 4.024048 CAGCAAACGGTCTGACTTACAATT 60.024 41.667 7.85 0.00 32.26 2.32
787 793 3.498397 CAGCAAACGGTCTGACTTACAAT 59.502 43.478 7.85 0.00 32.26 2.71
788 794 2.869801 CAGCAAACGGTCTGACTTACAA 59.130 45.455 7.85 0.00 32.26 2.41
789 795 2.101750 TCAGCAAACGGTCTGACTTACA 59.898 45.455 7.85 0.00 34.69 2.41
790 796 2.731976 CTCAGCAAACGGTCTGACTTAC 59.268 50.000 7.85 0.00 35.66 2.34
791 797 2.364324 ACTCAGCAAACGGTCTGACTTA 59.636 45.455 7.85 0.00 35.66 2.24
792 798 1.139058 ACTCAGCAAACGGTCTGACTT 59.861 47.619 7.85 0.00 35.66 3.01
793 799 0.753262 ACTCAGCAAACGGTCTGACT 59.247 50.000 7.85 0.00 35.66 3.41
794 800 1.583054 AACTCAGCAAACGGTCTGAC 58.417 50.000 0.00 0.00 35.66 3.51
795 801 2.325583 AAACTCAGCAAACGGTCTGA 57.674 45.000 0.00 0.00 37.70 3.27
796 802 3.363178 GAAAAACTCAGCAAACGGTCTG 58.637 45.455 0.00 0.00 0.00 3.51
797 803 2.357952 GGAAAAACTCAGCAAACGGTCT 59.642 45.455 0.00 0.00 0.00 3.85
798 804 2.543031 GGGAAAAACTCAGCAAACGGTC 60.543 50.000 0.00 0.00 0.00 4.79
799 805 1.407618 GGGAAAAACTCAGCAAACGGT 59.592 47.619 0.00 0.00 0.00 4.83
800 806 1.269569 GGGGAAAAACTCAGCAAACGG 60.270 52.381 0.00 0.00 0.00 4.44
801 807 1.681264 AGGGGAAAAACTCAGCAAACG 59.319 47.619 0.00 0.00 0.00 3.60
802 808 3.304458 CGTAGGGGAAAAACTCAGCAAAC 60.304 47.826 0.00 0.00 0.00 2.93
803 809 2.882137 CGTAGGGGAAAAACTCAGCAAA 59.118 45.455 0.00 0.00 0.00 3.68
804 810 2.158726 ACGTAGGGGAAAAACTCAGCAA 60.159 45.455 0.00 0.00 0.00 3.91
805 811 1.418637 ACGTAGGGGAAAAACTCAGCA 59.581 47.619 0.00 0.00 0.00 4.41
806 812 2.074576 GACGTAGGGGAAAAACTCAGC 58.925 52.381 0.00 0.00 0.00 4.26
807 813 3.586892 GAGACGTAGGGGAAAAACTCAG 58.413 50.000 0.00 0.00 0.00 3.35
808 814 2.029649 CGAGACGTAGGGGAAAAACTCA 60.030 50.000 0.00 0.00 0.00 3.41
809 815 2.603953 CGAGACGTAGGGGAAAAACTC 58.396 52.381 0.00 0.00 0.00 3.01
810 816 1.274447 CCGAGACGTAGGGGAAAAACT 59.726 52.381 0.00 0.00 0.00 2.66
811 817 1.718396 CCGAGACGTAGGGGAAAAAC 58.282 55.000 0.00 0.00 0.00 2.43
812 818 0.037046 GCCGAGACGTAGGGGAAAAA 60.037 55.000 6.37 0.00 0.00 1.94
813 819 1.593265 GCCGAGACGTAGGGGAAAA 59.407 57.895 6.37 0.00 0.00 2.29
814 820 2.703798 CGCCGAGACGTAGGGGAAA 61.704 63.158 13.60 0.00 42.30 3.13
815 821 3.136123 CGCCGAGACGTAGGGGAA 61.136 66.667 13.60 0.00 42.30 3.97
897 903 4.253685 TCGAGCGAAGGAGATTGATTTTT 58.746 39.130 0.00 0.00 0.00 1.94
898 904 3.861840 TCGAGCGAAGGAGATTGATTTT 58.138 40.909 0.00 0.00 0.00 1.82
899 905 3.526931 TCGAGCGAAGGAGATTGATTT 57.473 42.857 0.00 0.00 0.00 2.17
900 906 3.648009 GATCGAGCGAAGGAGATTGATT 58.352 45.455 0.00 0.00 31.41 2.57
965 971 0.589708 GGGAAACAACGTGGTACAGC 59.410 55.000 0.00 0.00 41.80 4.40
998 1004 2.231964 GCTTCATTTGGGTTCAGCATCA 59.768 45.455 0.00 0.00 0.00 3.07
1003 1009 3.119245 CCTGATGCTTCATTTGGGTTCAG 60.119 47.826 2.33 0.00 0.00 3.02
1012 1018 3.173953 TCCCAAACCTGATGCTTCATT 57.826 42.857 2.33 0.00 0.00 2.57
1086 1092 4.051922 CCCAGACGAATTTATCTTCCTCG 58.948 47.826 0.00 0.00 35.68 4.63
1227 1233 1.677552 CCAACGTACCTCCCTTGCT 59.322 57.895 0.00 0.00 0.00 3.91
1235 1241 2.358247 CCTTGCGCCAACGTACCT 60.358 61.111 4.18 0.00 42.83 3.08
1273 1279 3.007940 TCACCGAGACATCCAAACTGAAT 59.992 43.478 0.00 0.00 0.00 2.57
1284 1290 2.699954 GTGTTCCAATCACCGAGACAT 58.300 47.619 0.00 0.00 0.00 3.06
1290 1296 0.665068 TCGTCGTGTTCCAATCACCG 60.665 55.000 0.00 0.00 32.86 4.94
1302 1308 1.705337 GCCCCATGTTCATCGTCGTG 61.705 60.000 0.00 0.00 0.00 4.35
1306 1312 0.752743 CATGGCCCCATGTTCATCGT 60.753 55.000 17.23 0.00 46.20 3.73
1334 1340 2.025605 TCAATGAGCAAGCCCTGATTCT 60.026 45.455 0.00 0.00 0.00 2.40
1382 1388 6.154877 TGTTATTTTGTCTAGGACCACCGATA 59.845 38.462 0.00 0.00 41.83 2.92
1454 1460 2.378038 GGCACATTCCCTTGATTGCTA 58.622 47.619 0.00 0.00 0.00 3.49
1464 1470 1.103398 CCATCTTCCGGCACATTCCC 61.103 60.000 0.00 0.00 0.00 3.97
1492 1498 3.514309 GGGAGAGTAGTTTGCACCTCTAA 59.486 47.826 0.00 0.00 34.54 2.10
1521 1527 3.250744 TCGTACAAATTCTCCAGCGAAG 58.749 45.455 0.00 0.00 0.00 3.79
1542 1548 7.161404 TGTTAACATTCATCTGCACTCTAACT 58.839 34.615 3.59 0.00 0.00 2.24
1589 1595 7.038729 ACTCAGTTTCCTCATTCTTAGTCATCA 60.039 37.037 0.00 0.00 0.00 3.07
1591 1597 7.251321 ACTCAGTTTCCTCATTCTTAGTCAT 57.749 36.000 0.00 0.00 0.00 3.06
1632 1638 7.094975 TGACCACAAAATATTGGTAGTTTCTCG 60.095 37.037 0.00 0.00 46.56 4.04
1639 1645 7.035004 CCACAATGACCACAAAATATTGGTAG 58.965 38.462 0.00 0.00 46.56 3.18
1647 1653 3.666274 CATGCCACAATGACCACAAAAT 58.334 40.909 0.00 0.00 0.00 1.82
1755 1761 2.775741 CCCTCTACCTCGGCCCCTA 61.776 68.421 0.00 0.00 0.00 3.53
1965 1971 8.287350 AGGTCTGTACTATTACCTCCAATTAGA 58.713 37.037 0.00 0.00 37.87 2.10
1966 1972 8.361139 CAGGTCTGTACTATTACCTCCAATTAG 58.639 40.741 6.18 0.00 40.39 1.73
2039 2045 2.925653 TCCTCCATGGATCTTTTTCCCA 59.074 45.455 16.63 0.00 40.56 4.37
2171 2177 3.849911 TCACCAACGAGCTCTAATTCAG 58.150 45.455 12.85 0.00 0.00 3.02
2176 2182 5.654603 TTAAGATCACCAACGAGCTCTAA 57.345 39.130 12.85 0.00 28.12 2.10
2183 2189 5.186992 TCCTTCTCATTAAGATCACCAACGA 59.813 40.000 0.00 0.00 32.82 3.85
2302 2308 5.125900 CAGATTATGTGTTTCATTGCTCCCA 59.874 40.000 0.00 0.00 37.91 4.37
2363 2369 4.141287 GCTCCTACATCTCTAGAAGCTCA 58.859 47.826 0.00 0.00 0.00 4.26
2372 2378 2.703536 TCTCTCTCGCTCCTACATCTCT 59.296 50.000 0.00 0.00 0.00 3.10
2379 2385 1.065053 ACTTGCTCTCTCTCGCTCCTA 60.065 52.381 0.00 0.00 0.00 2.94
2396 2402 3.644966 TCAGACAGGAAAACCACACTT 57.355 42.857 0.00 0.00 0.00 3.16
2487 2493 0.609131 CCAGCCCGACCATCACTTTT 60.609 55.000 0.00 0.00 0.00 2.27
2556 2562 7.961325 AAACATCAATGAAATTAGCCGTTTT 57.039 28.000 0.00 0.00 32.46 2.43
2589 2595 0.317160 CACTCAACTACAGTGCCGGA 59.683 55.000 5.05 0.00 35.15 5.14
2591 2597 0.317160 TCCACTCAACTACAGTGCCG 59.683 55.000 0.00 0.00 40.10 5.69
2593 2599 3.601443 ATCTCCACTCAACTACAGTGC 57.399 47.619 0.00 0.00 40.10 4.40


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

AutoCloner maintained by Alex Coulton.