Multiple sequence alignment - TraesCS6B01G262500

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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 TraesCS6B01G262500 chr6B 100.000 3218 0 0 1 3218 472707690 472710907 0.000000e+00 5943
1 TraesCS6B01G262500 chr6B 84.326 772 68 29 3 743 57319632 57320381 0.000000e+00 706
2 TraesCS6B01G262500 chr6D 95.238 2352 79 14 874 3201 304693037 304690695 0.000000e+00 3692
3 TraesCS6B01G262500 chr6A 93.208 2400 98 31 827 3201 410835099 410837458 0.000000e+00 3469
4 TraesCS6B01G262500 chr3B 86.684 751 73 16 3 736 493160351 493161091 0.000000e+00 808
5 TraesCS6B01G262500 chrUn 85.252 773 70 24 3 748 41894229 41894984 0.000000e+00 756
6 TraesCS6B01G262500 chr4A 84.073 766 73 21 3 742 688108608 688107866 0.000000e+00 693
7 TraesCS6B01G262500 chr5B 83.533 753 75 19 3 743 593936900 593936185 0.000000e+00 658
8 TraesCS6B01G262500 chr5B 90.119 506 40 8 3 506 432320135 432319638 0.000000e+00 649
9 TraesCS6B01G262500 chr5B 82.124 744 76 32 2 735 369476345 369477041 4.630000e-163 584
10 TraesCS6B01G262500 chr5B 83.626 171 19 3 2241 2411 539928622 539928783 5.560000e-33 152
11 TraesCS6B01G262500 chr1B 85.168 654 74 18 101 742 469167798 469167156 0.000000e+00 649
12 TraesCS6B01G262500 chr1B 83.426 718 86 25 3 711 470293962 470294655 1.260000e-178 636
13 TraesCS6B01G262500 chr4B 89.328 506 44 9 3 506 527963977 527964474 7.580000e-176 627
14 TraesCS6B01G262500 chr4B 80.390 770 69 34 3 741 546657662 546656944 7.960000e-141 510
15 TraesCS6B01G262500 chr2B 89.349 507 43 7 3 506 205481264 205480766 7.580000e-176 627
16 TraesCS6B01G262500 chr2B 81.417 748 60 24 3 742 141720473 141719797 3.650000e-149 538
17 TraesCS6B01G262500 chr7B 81.783 774 70 28 3 742 643163899 643163163 1.660000e-162 582
18 TraesCS6B01G262500 chr7A 82.225 692 97 20 63 742 526615063 526615740 1.000000e-159 573
19 TraesCS6B01G262500 chr5A 83.721 172 18 6 2241 2411 559738621 559738783 1.550000e-33 154


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 TraesCS6B01G262500 chr6B 472707690 472710907 3217 False 5943 5943 100.000 1 3218 1 chr6B.!!$F2 3217
1 TraesCS6B01G262500 chr6B 57319632 57320381 749 False 706 706 84.326 3 743 1 chr6B.!!$F1 740
2 TraesCS6B01G262500 chr6D 304690695 304693037 2342 True 3692 3692 95.238 874 3201 1 chr6D.!!$R1 2327
3 TraesCS6B01G262500 chr6A 410835099 410837458 2359 False 3469 3469 93.208 827 3201 1 chr6A.!!$F1 2374
4 TraesCS6B01G262500 chr3B 493160351 493161091 740 False 808 808 86.684 3 736 1 chr3B.!!$F1 733
5 TraesCS6B01G262500 chrUn 41894229 41894984 755 False 756 756 85.252 3 748 1 chrUn.!!$F1 745
6 TraesCS6B01G262500 chr4A 688107866 688108608 742 True 693 693 84.073 3 742 1 chr4A.!!$R1 739
7 TraesCS6B01G262500 chr5B 593936185 593936900 715 True 658 658 83.533 3 743 1 chr5B.!!$R2 740
8 TraesCS6B01G262500 chr5B 369476345 369477041 696 False 584 584 82.124 2 735 1 chr5B.!!$F1 733
9 TraesCS6B01G262500 chr1B 469167156 469167798 642 True 649 649 85.168 101 742 1 chr1B.!!$R1 641
10 TraesCS6B01G262500 chr1B 470293962 470294655 693 False 636 636 83.426 3 711 1 chr1B.!!$F1 708
11 TraesCS6B01G262500 chr4B 546656944 546657662 718 True 510 510 80.390 3 741 1 chr4B.!!$R1 738
12 TraesCS6B01G262500 chr2B 141719797 141720473 676 True 538 538 81.417 3 742 1 chr2B.!!$R1 739
13 TraesCS6B01G262500 chr7B 643163163 643163899 736 True 582 582 81.783 3 742 1 chr7B.!!$R1 739
14 TraesCS6B01G262500 chr7A 526615063 526615740 677 False 573 573 82.225 63 742 1 chr7A.!!$F1 679

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
781 917 0.034380 AGGTAGGTGCTCTCGCTGTA 60.034 55.0 0.0 0.0 36.97 2.74 F
818 954 0.035056 CTCGGCTCACCCCTCAAATT 60.035 55.0 0.0 0.0 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1892 1.472662 ATCCTTACCCTCCGCATCCG 61.473 60.000 0.0 0.0 0.0 4.18 R
2283 2448 1.946768 CAGTACCAACACCAACACCAG 59.053 52.381 0.0 0.0 0.0 4.00 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
238 254 0.951040 CTTTCCGAAAGAGGCACGCT 60.951 55.000 14.72 0.00 43.09 5.07
420 449 1.399855 GCCTCTCGCGAAAGGAAAAAC 60.400 52.381 32.19 10.01 34.35 2.43
550 677 1.738350 GAAAAGCTAGGAAAGACCGGC 59.262 52.381 0.00 0.00 44.74 6.13
571 698 4.492247 GGCGGAAAACCAAAACGTAAAAAC 60.492 41.667 0.00 0.00 0.00 2.43
681 817 1.153745 GGCGAATGACTGAGAGCGT 60.154 57.895 0.00 0.00 0.00 5.07
705 841 3.120385 TGGCGCTGATCGTTGCAG 61.120 61.111 7.64 0.00 41.07 4.41
711 847 2.125552 TGATCGTTGCAGGGCTCG 60.126 61.111 0.00 0.00 0.00 5.03
712 848 2.125512 GATCGTTGCAGGGCTCGT 60.126 61.111 0.00 0.00 0.00 4.18
743 879 3.869065 CTCGTTAATTAGTTGCTCCCCA 58.131 45.455 0.00 0.00 0.00 4.96
744 880 3.602483 TCGTTAATTAGTTGCTCCCCAC 58.398 45.455 0.00 0.00 0.00 4.61
745 881 2.350498 CGTTAATTAGTTGCTCCCCACG 59.650 50.000 0.00 0.00 0.00 4.94
747 883 2.871096 AATTAGTTGCTCCCCACGAA 57.129 45.000 0.00 0.00 0.00 3.85
748 884 2.871096 ATTAGTTGCTCCCCACGAAA 57.129 45.000 0.00 0.00 0.00 3.46
749 885 2.642154 TTAGTTGCTCCCCACGAAAA 57.358 45.000 0.00 0.00 0.00 2.29
750 886 1.886886 TAGTTGCTCCCCACGAAAAC 58.113 50.000 0.00 0.00 0.00 2.43
751 887 0.106918 AGTTGCTCCCCACGAAAACA 60.107 50.000 0.00 0.00 0.00 2.83
752 888 0.958822 GTTGCTCCCCACGAAAACAT 59.041 50.000 0.00 0.00 0.00 2.71
753 889 1.339929 GTTGCTCCCCACGAAAACATT 59.660 47.619 0.00 0.00 0.00 2.71
754 890 1.243902 TGCTCCCCACGAAAACATTC 58.756 50.000 0.00 0.00 0.00 2.67
755 891 1.243902 GCTCCCCACGAAAACATTCA 58.756 50.000 0.00 0.00 0.00 2.57
756 892 1.200020 GCTCCCCACGAAAACATTCAG 59.800 52.381 0.00 0.00 0.00 3.02
757 893 1.812571 CTCCCCACGAAAACATTCAGG 59.187 52.381 0.00 0.00 0.00 3.86
758 894 1.144093 TCCCCACGAAAACATTCAGGT 59.856 47.619 0.00 0.00 0.00 4.00
759 895 1.269448 CCCCACGAAAACATTCAGGTG 59.731 52.381 0.00 0.00 0.00 4.00
760 896 2.226330 CCCACGAAAACATTCAGGTGA 58.774 47.619 0.00 0.00 0.00 4.02
761 897 2.226437 CCCACGAAAACATTCAGGTGAG 59.774 50.000 0.00 0.00 0.00 3.51
762 898 3.138304 CCACGAAAACATTCAGGTGAGA 58.862 45.455 0.00 0.00 0.00 3.27
763 899 3.187227 CCACGAAAACATTCAGGTGAGAG 59.813 47.826 0.00 0.00 0.00 3.20
764 900 3.187227 CACGAAAACATTCAGGTGAGAGG 59.813 47.826 0.00 0.00 0.00 3.69
765 901 3.181454 ACGAAAACATTCAGGTGAGAGGT 60.181 43.478 0.00 0.00 0.00 3.85
766 902 4.039973 ACGAAAACATTCAGGTGAGAGGTA 59.960 41.667 0.00 0.00 0.00 3.08
767 903 4.627467 CGAAAACATTCAGGTGAGAGGTAG 59.373 45.833 0.00 0.00 0.00 3.18
768 904 4.559862 AAACATTCAGGTGAGAGGTAGG 57.440 45.455 0.00 0.00 0.00 3.18
769 905 3.191888 ACATTCAGGTGAGAGGTAGGT 57.808 47.619 0.00 0.00 0.00 3.08
770 906 2.834549 ACATTCAGGTGAGAGGTAGGTG 59.165 50.000 0.00 0.00 0.00 4.00
771 907 1.267121 TTCAGGTGAGAGGTAGGTGC 58.733 55.000 0.00 0.00 0.00 5.01
772 908 0.409876 TCAGGTGAGAGGTAGGTGCT 59.590 55.000 0.00 0.00 0.00 4.40
773 909 0.820871 CAGGTGAGAGGTAGGTGCTC 59.179 60.000 0.00 0.00 0.00 4.26
774 910 0.707616 AGGTGAGAGGTAGGTGCTCT 59.292 55.000 0.00 0.00 0.00 4.09
775 911 1.107945 GGTGAGAGGTAGGTGCTCTC 58.892 60.000 0.00 0.00 42.69 3.20
776 912 0.736053 GTGAGAGGTAGGTGCTCTCG 59.264 60.000 0.00 0.00 44.62 4.04
777 913 1.032657 TGAGAGGTAGGTGCTCTCGC 61.033 60.000 0.00 0.00 44.62 5.03
778 914 0.750182 GAGAGGTAGGTGCTCTCGCT 60.750 60.000 0.00 0.00 35.02 4.93
779 915 1.034838 AGAGGTAGGTGCTCTCGCTG 61.035 60.000 0.00 0.00 36.97 5.18
780 916 1.304547 AGGTAGGTGCTCTCGCTGT 60.305 57.895 0.00 0.00 36.97 4.40
781 917 0.034380 AGGTAGGTGCTCTCGCTGTA 60.034 55.000 0.00 0.00 36.97 2.74
782 918 0.815734 GGTAGGTGCTCTCGCTGTAA 59.184 55.000 0.00 0.00 36.97 2.41
783 919 1.202313 GGTAGGTGCTCTCGCTGTAAG 60.202 57.143 0.00 0.00 36.97 2.34
801 937 7.820044 CTGTAAGCGAGATATAATTTCCCTC 57.180 40.000 0.00 0.00 0.00 4.30
802 938 6.387465 TGTAAGCGAGATATAATTTCCCTCG 58.613 40.000 0.00 0.00 46.48 4.63
803 939 4.457834 AGCGAGATATAATTTCCCTCGG 57.542 45.455 0.00 0.00 44.63 4.63
804 940 2.930682 GCGAGATATAATTTCCCTCGGC 59.069 50.000 0.00 0.00 44.63 5.54
805 941 3.368531 GCGAGATATAATTTCCCTCGGCT 60.369 47.826 0.00 0.00 44.63 5.52
806 942 4.425520 CGAGATATAATTTCCCTCGGCTC 58.574 47.826 0.00 0.00 41.88 4.70
807 943 4.082190 CGAGATATAATTTCCCTCGGCTCA 60.082 45.833 0.00 0.00 41.88 4.26
808 944 5.153950 AGATATAATTTCCCTCGGCTCAC 57.846 43.478 0.00 0.00 0.00 3.51
809 945 2.640316 ATAATTTCCCTCGGCTCACC 57.360 50.000 0.00 0.00 0.00 4.02
810 946 0.544697 TAATTTCCCTCGGCTCACCC 59.455 55.000 0.00 0.00 0.00 4.61
811 947 2.211468 AATTTCCCTCGGCTCACCCC 62.211 60.000 0.00 0.00 0.00 4.95
812 948 3.864983 TTTCCCTCGGCTCACCCCT 62.865 63.158 0.00 0.00 0.00 4.79
813 949 4.779733 TCCCTCGGCTCACCCCTC 62.780 72.222 0.00 0.00 0.00 4.30
815 951 3.003173 CCTCGGCTCACCCCTCAA 61.003 66.667 0.00 0.00 0.00 3.02
816 952 2.592993 CCTCGGCTCACCCCTCAAA 61.593 63.158 0.00 0.00 0.00 2.69
817 953 1.604378 CTCGGCTCACCCCTCAAAT 59.396 57.895 0.00 0.00 0.00 2.32
818 954 0.035056 CTCGGCTCACCCCTCAAATT 60.035 55.000 0.00 0.00 0.00 1.82
819 955 0.322456 TCGGCTCACCCCTCAAATTG 60.322 55.000 0.00 0.00 0.00 2.32
820 956 0.609131 CGGCTCACCCCTCAAATTGT 60.609 55.000 0.00 0.00 0.00 2.71
821 957 1.632589 GGCTCACCCCTCAAATTGTT 58.367 50.000 0.00 0.00 0.00 2.83
822 958 1.970640 GGCTCACCCCTCAAATTGTTT 59.029 47.619 0.00 0.00 0.00 2.83
823 959 2.368548 GGCTCACCCCTCAAATTGTTTT 59.631 45.455 0.00 0.00 0.00 2.43
824 960 3.181455 GGCTCACCCCTCAAATTGTTTTT 60.181 43.478 0.00 0.00 0.00 1.94
825 961 4.058124 GCTCACCCCTCAAATTGTTTTTC 58.942 43.478 0.00 0.00 0.00 2.29
851 988 1.078848 CAGACGGAAGAAGGGCCAG 60.079 63.158 6.18 0.00 0.00 4.85
866 1003 2.461110 CCAGCGCCCACGACATTAC 61.461 63.158 2.29 0.00 43.93 1.89
874 1017 2.544277 GCCCACGACATTACGCTGTATA 60.544 50.000 0.00 0.00 36.70 1.47
920 1063 3.554129 GGCCCATCAAACTAAAACCACAC 60.554 47.826 0.00 0.00 0.00 3.82
1203 1356 1.658717 CTCCGCCGACGATGATGTC 60.659 63.158 0.00 0.00 43.93 3.06
1459 1612 2.579787 GCGACGATGACCAGGACG 60.580 66.667 0.00 0.00 0.00 4.79
1461 1614 1.062685 CGACGATGACCAGGACGAG 59.937 63.158 0.00 0.00 0.00 4.18
1483 1636 1.047801 GGAGGGAGATGAAGAGGAGC 58.952 60.000 0.00 0.00 0.00 4.70
1497 1662 0.619832 AGGAGCAGGCAGAGGATGAA 60.620 55.000 0.00 0.00 0.00 2.57
1608 1773 1.568504 TTACAGAGCTCCGTGGGAAT 58.431 50.000 12.99 0.00 0.00 3.01
1641 1806 2.092699 GCCAGAGTTCCTGAATAAGCCT 60.093 50.000 0.00 0.00 45.78 4.58
1807 1972 5.392703 CCAGATATCATGTATGGCAATGTGC 60.393 44.000 5.32 0.00 44.08 4.57
2264 2429 7.976734 GTGACTGAGTACTGTATCTGCTTTATT 59.023 37.037 0.00 0.00 0.00 1.40
2386 2551 4.381292 GGCAGGTCATCTGGAAAAGATTTG 60.381 45.833 0.00 0.00 43.52 2.32
2391 2556 5.124617 GGTCATCTGGAAAAGATTTGGAGAC 59.875 44.000 0.00 0.00 43.52 3.36
2412 2577 5.352569 AGACATTCCTTCTGCTGTATTTTCG 59.647 40.000 0.00 0.00 0.00 3.46
2433 2598 9.959749 TTTTCGTTGAGCTTAGATAAATTTGTT 57.040 25.926 0.00 0.00 0.00 2.83
2552 2717 7.064847 TGTTAATGATGCTTCAATGGATTTTGC 59.935 33.333 6.36 0.00 34.96 3.68
2580 2745 5.499004 TCTTTGTTATTCCTAGCAGTGGT 57.501 39.130 0.00 0.00 0.00 4.16
2625 2790 6.630444 ATTATGCATCAGTGAAGATGTTCC 57.370 37.500 0.19 0.00 45.58 3.62
2691 2856 2.575735 TCCACAATGCCCACTTCTCATA 59.424 45.455 0.00 0.00 0.00 2.15
2692 2857 3.202818 TCCACAATGCCCACTTCTCATAT 59.797 43.478 0.00 0.00 0.00 1.78
2693 2858 3.317149 CCACAATGCCCACTTCTCATATG 59.683 47.826 0.00 0.00 0.00 1.78
2694 2859 3.949754 CACAATGCCCACTTCTCATATGT 59.050 43.478 1.90 0.00 0.00 2.29
2695 2860 4.036027 CACAATGCCCACTTCTCATATGTC 59.964 45.833 1.90 0.00 0.00 3.06
2696 2861 4.201657 CAATGCCCACTTCTCATATGTCA 58.798 43.478 1.90 0.00 0.00 3.58
2697 2862 4.719026 ATGCCCACTTCTCATATGTCAT 57.281 40.909 1.90 0.00 0.00 3.06
2706 2872 4.456280 TCTCATATGTCATGGATACGCC 57.544 45.455 1.90 0.00 42.51 5.68
2754 2922 8.391075 TCTTATTTTGCAAGCTTACTGTAGTT 57.609 30.769 0.00 0.00 0.00 2.24
2915 3083 0.179018 ACTGTTGTCAAGGGTGAGGC 60.179 55.000 0.00 0.00 33.27 4.70
2934 3102 2.029020 GGCACTTGTTCCCTTCCATTTC 60.029 50.000 0.00 0.00 0.00 2.17
2935 3103 2.893489 GCACTTGTTCCCTTCCATTTCT 59.107 45.455 0.00 0.00 0.00 2.52
2937 3105 4.797275 GCACTTGTTCCCTTCCATTTCTTG 60.797 45.833 0.00 0.00 0.00 3.02
2938 3106 3.321968 ACTTGTTCCCTTCCATTTCTTGC 59.678 43.478 0.00 0.00 0.00 4.01
2940 3108 2.247358 GTTCCCTTCCATTTCTTGCCA 58.753 47.619 0.00 0.00 0.00 4.92
2941 3109 2.220653 TCCCTTCCATTTCTTGCCAG 57.779 50.000 0.00 0.00 0.00 4.85
2942 3110 0.533951 CCCTTCCATTTCTTGCCAGC 59.466 55.000 0.00 0.00 0.00 4.85
2943 3111 1.259609 CCTTCCATTTCTTGCCAGCA 58.740 50.000 0.00 0.00 0.00 4.41
3037 3206 8.630054 TCTGTTGTTACATATTTTACCTGCTT 57.370 30.769 0.00 0.00 32.86 3.91
3098 3268 3.421844 ACTTGGAATGCAAGGTTAGGAC 58.578 45.455 18.39 0.00 34.20 3.85
3115 3285 1.407258 GGACCATCTCTCTCGACAAGG 59.593 57.143 0.00 0.00 0.00 3.61
3133 3303 3.695830 AGGTATTCTTTCTGTTCGGCA 57.304 42.857 0.00 0.00 0.00 5.69
3144 3314 2.948979 TCTGTTCGGCAACAAGTTTGAT 59.051 40.909 0.00 0.00 42.13 2.57
3201 3371 1.953559 TGGAATGTAGATGCGCCTTC 58.046 50.000 4.18 1.35 0.00 3.46
3202 3372 1.230324 GGAATGTAGATGCGCCTTCC 58.770 55.000 4.18 2.31 0.00 3.46
3203 3373 1.202698 GGAATGTAGATGCGCCTTCCT 60.203 52.381 4.18 0.00 31.53 3.36
3204 3374 2.565841 GAATGTAGATGCGCCTTCCTT 58.434 47.619 4.18 0.00 0.00 3.36
3205 3375 3.494398 GGAATGTAGATGCGCCTTCCTTA 60.494 47.826 4.18 0.00 31.53 2.69
3206 3376 2.890808 TGTAGATGCGCCTTCCTTAG 57.109 50.000 4.18 0.00 0.00 2.18
3207 3377 1.202533 TGTAGATGCGCCTTCCTTAGC 60.203 52.381 4.18 0.00 0.00 3.09
3208 3378 1.119684 TAGATGCGCCTTCCTTAGCA 58.880 50.000 4.18 0.00 44.13 3.49
3209 3379 0.253044 AGATGCGCCTTCCTTAGCAA 59.747 50.000 4.18 0.00 43.19 3.91
3210 3380 0.659957 GATGCGCCTTCCTTAGCAAG 59.340 55.000 4.18 0.00 43.19 4.01
3211 3381 1.379642 ATGCGCCTTCCTTAGCAAGC 61.380 55.000 4.18 0.00 43.19 4.01
3212 3382 2.040544 GCGCCTTCCTTAGCAAGCA 61.041 57.895 0.00 0.00 0.00 3.91
3213 3383 1.796796 CGCCTTCCTTAGCAAGCAC 59.203 57.895 0.00 0.00 0.00 4.40
3214 3384 0.674895 CGCCTTCCTTAGCAAGCACT 60.675 55.000 0.00 0.00 0.00 4.40
3215 3385 1.539157 GCCTTCCTTAGCAAGCACTT 58.461 50.000 0.00 0.00 0.00 3.16
3216 3386 1.470494 GCCTTCCTTAGCAAGCACTTC 59.530 52.381 0.00 0.00 0.00 3.01
3217 3387 2.087646 CCTTCCTTAGCAAGCACTTCC 58.912 52.381 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
175 183 2.126463 CTTTCGCGAGAGGCACGA 60.126 61.111 18.35 0.00 43.84 4.35
238 254 2.126463 CTTTCGCGAGAGGCACGA 60.126 61.111 18.35 0.00 43.84 4.35
274 290 2.331265 GAGGCACGGTTTTGCTTCT 58.669 52.632 1.28 0.00 43.46 2.85
354 376 0.111089 GTTGTGCTTTCGCGAGAGTG 60.111 55.000 25.34 11.13 43.69 3.51
386 408 1.947456 GAGAGGCACGGTTTTGTTTCT 59.053 47.619 0.00 0.00 0.00 2.52
390 412 2.251642 GCGAGAGGCACGGTTTTGT 61.252 57.895 0.00 0.00 42.87 2.83
523 628 6.455246 CGGTCTTTCCTAGCTTTTCGATAAAC 60.455 42.308 0.00 0.00 0.00 2.01
550 677 5.758570 TGTTTTTACGTTTTGGTTTTCCG 57.241 34.783 0.00 0.00 44.36 4.30
681 817 1.737735 CGATCAGCGCCACTTGACA 60.738 57.895 2.29 0.00 0.00 3.58
711 847 1.641577 ATTAACGAGCGCTCCTTCAC 58.358 50.000 30.66 6.65 0.00 3.18
712 848 2.380084 AATTAACGAGCGCTCCTTCA 57.620 45.000 30.66 17.41 0.00 3.02
743 879 3.181454 ACCTCTCACCTGAATGTTTTCGT 60.181 43.478 0.00 0.00 34.39 3.85
744 880 3.403038 ACCTCTCACCTGAATGTTTTCG 58.597 45.455 0.00 0.00 34.39 3.46
745 881 4.938226 CCTACCTCTCACCTGAATGTTTTC 59.062 45.833 0.00 0.00 0.00 2.29
747 883 3.910627 ACCTACCTCTCACCTGAATGTTT 59.089 43.478 0.00 0.00 0.00 2.83
748 884 3.261897 CACCTACCTCTCACCTGAATGTT 59.738 47.826 0.00 0.00 0.00 2.71
749 885 2.834549 CACCTACCTCTCACCTGAATGT 59.165 50.000 0.00 0.00 0.00 2.71
750 886 2.419297 GCACCTACCTCTCACCTGAATG 60.419 54.545 0.00 0.00 0.00 2.67
751 887 1.834263 GCACCTACCTCTCACCTGAAT 59.166 52.381 0.00 0.00 0.00 2.57
752 888 1.203187 AGCACCTACCTCTCACCTGAA 60.203 52.381 0.00 0.00 0.00 3.02
753 889 0.409876 AGCACCTACCTCTCACCTGA 59.590 55.000 0.00 0.00 0.00 3.86
754 890 0.820871 GAGCACCTACCTCTCACCTG 59.179 60.000 0.00 0.00 0.00 4.00
755 891 0.707616 AGAGCACCTACCTCTCACCT 59.292 55.000 0.00 0.00 34.71 4.00
756 892 3.291497 AGAGCACCTACCTCTCACC 57.709 57.895 0.00 0.00 34.71 4.02
776 912 6.166982 AGGGAAATTATATCTCGCTTACAGC 58.833 40.000 0.00 0.00 38.02 4.40
777 913 6.528423 CGAGGGAAATTATATCTCGCTTACAG 59.472 42.308 0.00 0.00 40.29 2.74
778 914 6.387465 CGAGGGAAATTATATCTCGCTTACA 58.613 40.000 0.00 0.00 40.29 2.41
779 915 5.805994 CCGAGGGAAATTATATCTCGCTTAC 59.194 44.000 12.10 0.00 43.87 2.34
780 916 5.623824 GCCGAGGGAAATTATATCTCGCTTA 60.624 44.000 12.10 0.00 43.87 3.09
781 917 4.822026 CCGAGGGAAATTATATCTCGCTT 58.178 43.478 12.10 0.00 43.87 4.68
782 918 3.368531 GCCGAGGGAAATTATATCTCGCT 60.369 47.826 12.10 4.66 43.87 4.93
783 919 2.930682 GCCGAGGGAAATTATATCTCGC 59.069 50.000 12.10 0.48 43.87 5.03
784 920 4.082190 TGAGCCGAGGGAAATTATATCTCG 60.082 45.833 0.00 0.00 44.54 4.04
785 921 5.172205 GTGAGCCGAGGGAAATTATATCTC 58.828 45.833 0.00 0.00 0.00 2.75
786 922 4.020128 GGTGAGCCGAGGGAAATTATATCT 60.020 45.833 0.00 0.00 0.00 1.98
787 923 4.254492 GGTGAGCCGAGGGAAATTATATC 58.746 47.826 0.00 0.00 0.00 1.63
788 924 3.009143 GGGTGAGCCGAGGGAAATTATAT 59.991 47.826 0.00 0.00 34.97 0.86
789 925 2.370849 GGGTGAGCCGAGGGAAATTATA 59.629 50.000 0.00 0.00 34.97 0.98
790 926 1.143073 GGGTGAGCCGAGGGAAATTAT 59.857 52.381 0.00 0.00 34.97 1.28
791 927 0.544697 GGGTGAGCCGAGGGAAATTA 59.455 55.000 0.00 0.00 34.97 1.40
792 928 1.303282 GGGTGAGCCGAGGGAAATT 59.697 57.895 0.00 0.00 34.97 1.82
793 929 2.680370 GGGGTGAGCCGAGGGAAAT 61.680 63.158 0.00 0.00 34.97 2.17
794 930 3.327404 GGGGTGAGCCGAGGGAAA 61.327 66.667 0.00 0.00 34.97 3.13
795 931 4.332543 AGGGGTGAGCCGAGGGAA 62.333 66.667 0.00 0.00 34.97 3.97
796 932 4.779733 GAGGGGTGAGCCGAGGGA 62.780 72.222 0.00 0.00 34.97 4.20
798 934 1.915078 ATTTGAGGGGTGAGCCGAGG 61.915 60.000 0.00 0.00 34.97 4.63
799 935 0.035056 AATTTGAGGGGTGAGCCGAG 60.035 55.000 0.00 0.00 34.97 4.63
800 936 0.322456 CAATTTGAGGGGTGAGCCGA 60.322 55.000 0.00 0.00 34.97 5.54
801 937 0.609131 ACAATTTGAGGGGTGAGCCG 60.609 55.000 2.79 0.00 34.97 5.52
802 938 1.632589 AACAATTTGAGGGGTGAGCC 58.367 50.000 2.79 0.00 0.00 4.70
803 939 3.751479 AAAACAATTTGAGGGGTGAGC 57.249 42.857 2.79 0.00 0.00 4.26
804 940 4.344968 AGGAAAAACAATTTGAGGGGTGAG 59.655 41.667 2.79 0.00 0.00 3.51
805 941 4.294347 AGGAAAAACAATTTGAGGGGTGA 58.706 39.130 2.79 0.00 0.00 4.02
806 942 4.631131 GAGGAAAAACAATTTGAGGGGTG 58.369 43.478 2.79 0.00 0.00 4.61
807 943 3.320826 CGAGGAAAAACAATTTGAGGGGT 59.679 43.478 2.79 0.00 0.00 4.95
808 944 3.306019 CCGAGGAAAAACAATTTGAGGGG 60.306 47.826 2.79 0.00 0.00 4.79
809 945 3.860754 GCCGAGGAAAAACAATTTGAGGG 60.861 47.826 2.79 0.00 0.00 4.30
810 946 3.005791 AGCCGAGGAAAAACAATTTGAGG 59.994 43.478 2.79 0.00 0.00 3.86
811 947 4.229876 GAGCCGAGGAAAAACAATTTGAG 58.770 43.478 2.79 0.00 0.00 3.02
812 948 3.634448 TGAGCCGAGGAAAAACAATTTGA 59.366 39.130 2.79 0.00 0.00 2.69
813 949 3.976169 TGAGCCGAGGAAAAACAATTTG 58.024 40.909 0.00 0.00 0.00 2.32
814 950 3.888930 TCTGAGCCGAGGAAAAACAATTT 59.111 39.130 0.00 0.00 0.00 1.82
815 951 3.253432 GTCTGAGCCGAGGAAAAACAATT 59.747 43.478 0.00 0.00 0.00 2.32
816 952 2.814336 GTCTGAGCCGAGGAAAAACAAT 59.186 45.455 0.00 0.00 0.00 2.71
817 953 2.218603 GTCTGAGCCGAGGAAAAACAA 58.781 47.619 0.00 0.00 0.00 2.83
818 954 1.872237 CGTCTGAGCCGAGGAAAAACA 60.872 52.381 0.00 0.00 0.00 2.83
819 955 0.790814 CGTCTGAGCCGAGGAAAAAC 59.209 55.000 0.00 0.00 0.00 2.43
820 956 0.320421 CCGTCTGAGCCGAGGAAAAA 60.320 55.000 0.00 0.00 0.00 1.94
821 957 1.183030 TCCGTCTGAGCCGAGGAAAA 61.183 55.000 0.00 0.00 0.00 2.29
822 958 1.183030 TTCCGTCTGAGCCGAGGAAA 61.183 55.000 0.00 0.00 37.96 3.13
823 959 1.595993 CTTCCGTCTGAGCCGAGGAA 61.596 60.000 0.00 0.00 38.51 3.36
824 960 2.035155 TTCCGTCTGAGCCGAGGA 59.965 61.111 0.00 0.00 0.00 3.71
825 961 1.595993 TTCTTCCGTCTGAGCCGAGG 61.596 60.000 0.00 0.00 0.00 4.63
851 988 4.218478 GCGTAATGTCGTGGGCGC 62.218 66.667 0.00 0.00 38.14 6.53
864 1001 8.242053 GCTTCTAATGGATAACTATACAGCGTA 58.758 37.037 0.00 0.00 28.33 4.42
866 1003 6.531948 GGCTTCTAATGGATAACTATACAGCG 59.468 42.308 0.00 0.00 28.33 5.18
874 1017 6.240002 CCATACTGGGCTTCTAATGGATAACT 60.240 42.308 0.00 0.00 36.76 2.24
906 1049 2.100749 GGCTGCAGTGTGGTTTTAGTTT 59.899 45.455 16.64 0.00 0.00 2.66
910 1053 1.993956 ATGGCTGCAGTGTGGTTTTA 58.006 45.000 16.64 0.00 0.00 1.52
941 1085 0.250467 TGCTGTCTCTGGCCTTCAAC 60.250 55.000 3.32 0.00 0.00 3.18
1116 1269 3.824425 TGCCCATGGATGCCCTCC 61.824 66.667 15.22 0.00 45.19 4.30
1158 1311 3.134879 CGCGGGGGTATAAGCTGA 58.865 61.111 0.00 0.00 0.00 4.26
1396 1549 0.108567 GACTCCTGGCTTCCGTCTTC 60.109 60.000 0.00 0.00 0.00 2.87
1459 1612 2.597455 CTCTTCATCTCCCTCCTCCTC 58.403 57.143 0.00 0.00 0.00 3.71
1461 1614 1.219213 TCCTCTTCATCTCCCTCCTCC 59.781 57.143 0.00 0.00 0.00 4.30
1483 1636 2.641305 CTCCTTTTCATCCTCTGCCTG 58.359 52.381 0.00 0.00 0.00 4.85
1497 1662 1.133853 GCCATCTGCATCTCCTCCTTT 60.134 52.381 0.00 0.00 40.77 3.11
1581 1746 1.226974 GAGCTCTGTAATGCGGCGA 60.227 57.895 12.98 0.00 0.00 5.54
1641 1806 4.097418 CCTTCTTACCCTTCTCCTTCTGA 58.903 47.826 0.00 0.00 0.00 3.27
1727 1892 1.472662 ATCCTTACCCTCCGCATCCG 61.473 60.000 0.00 0.00 0.00 4.18
1956 2121 2.530151 TGCACCTTCTCCCCAGCT 60.530 61.111 0.00 0.00 0.00 4.24
2219 2384 5.053145 GTCACCATCATCTCCAATGTAGAC 58.947 45.833 0.00 0.00 0.00 2.59
2229 2394 4.400884 ACAGTACTCAGTCACCATCATCTC 59.599 45.833 0.00 0.00 0.00 2.75
2283 2448 1.946768 CAGTACCAACACCAACACCAG 59.053 52.381 0.00 0.00 0.00 4.00
2386 2551 2.777832 ACAGCAGAAGGAATGTCTCC 57.222 50.000 0.00 0.00 45.81 3.71
2391 2556 5.551760 ACGAAAATACAGCAGAAGGAATG 57.448 39.130 0.00 0.00 0.00 2.67
2433 2598 5.580297 GCCAGACATGAAAGTTTGTTTTTCA 59.420 36.000 0.00 3.25 45.49 2.69
2552 2717 8.233190 CACTGCTAGGAATAACAAAGAAAAGAG 58.767 37.037 0.00 0.00 0.00 2.85
2625 2790 3.753294 ATTCAGATAAGCCTGTACCCG 57.247 47.619 0.00 0.00 35.71 5.28
2697 2862 2.708216 ATTGACATGTGGCGTATCCA 57.292 45.000 1.15 0.00 44.18 3.41
2754 2922 8.973182 TCAACACCATAATACAGACTGTACATA 58.027 33.333 17.46 13.50 35.42 2.29
2775 2943 3.845178 CGTCCTGCAGTATAACTCAACA 58.155 45.455 13.81 0.00 0.00 3.33
2915 3083 4.797275 GCAAGAAATGGAAGGGAACAAGTG 60.797 45.833 0.00 0.00 0.00 3.16
2934 3102 1.530013 CTGTCCCCTTTGCTGGCAAG 61.530 60.000 8.04 3.61 37.24 4.01
2935 3103 1.531365 CTGTCCCCTTTGCTGGCAA 60.531 57.895 3.72 3.72 0.00 4.52
2937 3105 1.973812 GTCTGTCCCCTTTGCTGGC 60.974 63.158 0.00 0.00 0.00 4.85
2938 3106 0.178992 TTGTCTGTCCCCTTTGCTGG 60.179 55.000 0.00 0.00 0.00 4.85
2940 3108 0.550914 TGTTGTCTGTCCCCTTTGCT 59.449 50.000 0.00 0.00 0.00 3.91
2941 3109 0.668535 GTGTTGTCTGTCCCCTTTGC 59.331 55.000 0.00 0.00 0.00 3.68
2942 3110 1.133792 AGGTGTTGTCTGTCCCCTTTG 60.134 52.381 0.00 0.00 0.00 2.77
2943 3111 1.133792 CAGGTGTTGTCTGTCCCCTTT 60.134 52.381 0.00 0.00 0.00 3.11
2981 3149 1.156736 ACAAGACAGGCCGAAAATCG 58.843 50.000 0.00 0.00 40.07 3.34
2989 3157 0.804989 GTGCACATACAAGACAGGCC 59.195 55.000 13.17 0.00 0.00 5.19
3109 3279 4.142881 GCCGAACAGAAAGAATACCTTGTC 60.143 45.833 0.00 0.00 34.79 3.18
3115 3285 4.742438 TGTTGCCGAACAGAAAGAATAC 57.258 40.909 0.00 0.00 37.15 1.89
3144 3314 6.275494 TCCGCCACGATTCATATAAATCTA 57.725 37.500 0.00 0.00 34.19 1.98
3160 3330 1.700042 AATCCTCCCTCATCCGCCAC 61.700 60.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.