Multiple sequence alignment - TraesCS2A01G326700

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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 TraesCS2A01G326700 chr2A 100.000 3575 0 0 1 3575 558465177 558468751 0.000000e+00 6602.0
1 TraesCS2A01G326700 chr2D 96.150 2000 75 2 818 2817 429380004 429378007 0.000000e+00 3265.0
2 TraesCS2A01G326700 chr2D 93.987 765 25 10 2818 3575 429377977 429377227 0.000000e+00 1138.0
3 TraesCS2A01G326700 chr2B 96.685 1840 61 0 978 2817 506357926 506356087 0.000000e+00 3061.0
4 TraesCS2A01G326700 chr2B 90.638 705 52 6 2818 3519 506356057 506355364 0.000000e+00 924.0
5 TraesCS2A01G326700 chr2B 82.022 178 18 9 652 818 551400847 551400673 4.810000e-29 139.0
6 TraesCS2A01G326700 chr2B 83.654 104 15 1 717 818 789415350 789415453 2.940000e-16 97.1
7 TraesCS2A01G326700 chr6B 95.579 656 27 1 1 654 705856230 705855575 0.000000e+00 1050.0
8 TraesCS2A01G326700 chr6B 88.953 172 10 4 652 814 527934499 527934670 1.680000e-48 204.0
9 TraesCS2A01G326700 chr3D 95.427 656 27 2 1 654 584687154 584687808 0.000000e+00 1042.0
10 TraesCS2A01G326700 chr3D 94.946 653 29 3 4 654 74319705 74319055 0.000000e+00 1020.0
11 TraesCS2A01G326700 chr3D 80.791 177 24 9 652 819 518131373 518131198 2.900000e-26 130.0
12 TraesCS2A01G326700 chr6D 95.274 656 29 1 1 654 83435164 83435819 0.000000e+00 1038.0
13 TraesCS2A01G326700 chr6D 84.153 183 12 7 652 818 83435957 83436138 1.030000e-35 161.0
14 TraesCS2A01G326700 chr6D 85.294 102 12 3 720 818 413326742 413326843 6.310000e-18 102.0
15 TraesCS2A01G326700 chr5D 95.122 656 30 1 1 654 310556475 310557130 0.000000e+00 1033.0
16 TraesCS2A01G326700 chr4D 94.502 673 32 3 1 671 297380687 297381356 0.000000e+00 1033.0
17 TraesCS2A01G326700 chr7B 94.785 652 32 1 5 654 484632946 484632295 0.000000e+00 1014.0
18 TraesCS2A01G326700 chr7B 85.799 169 13 6 652 809 336660051 336660219 6.140000e-38 169.0
19 TraesCS2A01G326700 chr7B 100.000 29 0 0 3389 3417 172336134 172336106 2.000000e-03 54.7
20 TraesCS2A01G326700 chr7D 94.665 656 30 3 1 654 16201285 16200633 0.000000e+00 1013.0
21 TraesCS2A01G326700 chr7D 82.222 180 19 8 652 818 566560929 566561108 3.720000e-30 143.0
22 TraesCS2A01G326700 chr1B 94.632 652 32 2 5 654 194779616 194780266 0.000000e+00 1007.0
23 TraesCS2A01G326700 chr1B 88.136 177 10 6 652 818 114464120 114464295 2.180000e-47 200.0
24 TraesCS2A01G326700 chr3A 86.932 176 14 6 652 818 602872412 602872587 4.710000e-44 189.0
25 TraesCS2A01G326700 chr4A 86.441 177 14 6 652 818 594255808 594255984 6.090000e-43 185.0
26 TraesCS2A01G326700 chr6A 85.795 176 16 5 652 818 1447260 1447435 1.020000e-40 178.0
27 TraesCS2A01G326700 chr6A 79.769 173 21 10 661 822 228628033 228627864 2.920000e-21 113.0
28 TraesCS2A01G326700 chr4B 85.393 178 15 7 652 818 74338324 74338501 1.320000e-39 174.0
29 TraesCS2A01G326700 chr3B 84.571 175 19 5 652 818 369101695 369101521 2.210000e-37 167.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G326700 chr2A 558465177 558468751 3574 False 6602.0 6602 100.0000 1 3575 1 chr2A.!!$F1 3574
1 TraesCS2A01G326700 chr2D 429377227 429380004 2777 True 2201.5 3265 95.0685 818 3575 2 chr2D.!!$R1 2757
2 TraesCS2A01G326700 chr2B 506355364 506357926 2562 True 1992.5 3061 93.6615 978 3519 2 chr2B.!!$R2 2541
3 TraesCS2A01G326700 chr6B 705855575 705856230 655 True 1050.0 1050 95.5790 1 654 1 chr6B.!!$R1 653
4 TraesCS2A01G326700 chr3D 584687154 584687808 654 False 1042.0 1042 95.4270 1 654 1 chr3D.!!$F1 653
5 TraesCS2A01G326700 chr3D 74319055 74319705 650 True 1020.0 1020 94.9460 4 654 1 chr3D.!!$R1 650
6 TraesCS2A01G326700 chr6D 83435164 83436138 974 False 599.5 1038 89.7135 1 818 2 chr6D.!!$F2 817
7 TraesCS2A01G326700 chr5D 310556475 310557130 655 False 1033.0 1033 95.1220 1 654 1 chr5D.!!$F1 653
8 TraesCS2A01G326700 chr4D 297380687 297381356 669 False 1033.0 1033 94.5020 1 671 1 chr4D.!!$F1 670
9 TraesCS2A01G326700 chr7B 484632295 484632946 651 True 1014.0 1014 94.7850 5 654 1 chr7B.!!$R2 649
10 TraesCS2A01G326700 chr7D 16200633 16201285 652 True 1013.0 1013 94.6650 1 654 1 chr7D.!!$R1 653
11 TraesCS2A01G326700 chr1B 194779616 194780266 650 False 1007.0 1007 94.6320 5 654 1 chr1B.!!$F2 649

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
753 757 0.103208 CTATGCAGAGACCGGGTGTC 59.897 60.0 16.08 16.08 44.82 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2727 2731 0.098376 CGCTCCTGCAAGAATTCAGC 59.902 55.0 8.44 11.72 39.64 4.26 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
67 68 4.704103 TGCTCAGCTCCTCCCCGT 62.704 66.667 0.00 0.00 0.00 5.28
175 176 2.597455 CACAAGGGAGGGATGTGTTTT 58.403 47.619 0.00 0.00 39.60 2.43
245 248 2.610727 GCACTCTCGCACTAAGAGGTTT 60.611 50.000 5.25 0.00 43.75 3.27
319 323 9.613428 AATAAGATTTTCATGTGGTATCTTCGA 57.387 29.630 14.00 0.00 36.98 3.71
405 409 5.078411 AGCTTTTGTACTCATGACGAGAT 57.922 39.130 0.00 0.00 45.45 2.75
468 472 8.727100 TCTATATGGTCAGTCATCCAAATAGT 57.273 34.615 0.00 0.00 37.27 2.12
557 561 9.236691 CAAATACTTTTAGTACGCTAATACGGA 57.763 33.333 0.00 0.00 37.09 4.69
566 570 1.336887 CGCTAATACGGATGGGAGTGG 60.337 57.143 0.00 0.00 0.00 4.00
589 593 2.357637 TGCCTTATTATGGTCGCTTTGC 59.642 45.455 0.00 0.00 0.00 3.68
633 637 7.826744 TGTTTTTAATGGCAAAACCTCTTCTTT 59.173 29.630 9.37 0.00 41.53 2.52
670 674 2.550978 CGTTTCGGACTCATATGGCTT 58.449 47.619 2.13 0.00 0.00 4.35
672 676 4.116961 CGTTTCGGACTCATATGGCTTTA 58.883 43.478 2.13 0.00 0.00 1.85
673 677 4.025979 CGTTTCGGACTCATATGGCTTTAC 60.026 45.833 2.13 0.00 0.00 2.01
674 678 5.116882 GTTTCGGACTCATATGGCTTTACT 58.883 41.667 2.13 0.00 0.00 2.24
675 679 4.322080 TCGGACTCATATGGCTTTACTG 57.678 45.455 2.13 0.00 0.00 2.74
676 680 3.704566 TCGGACTCATATGGCTTTACTGT 59.295 43.478 2.13 0.00 0.00 3.55
677 681 4.161565 TCGGACTCATATGGCTTTACTGTT 59.838 41.667 2.13 0.00 0.00 3.16
678 682 4.271049 CGGACTCATATGGCTTTACTGTTG 59.729 45.833 2.13 0.00 0.00 3.33
679 683 4.035675 GGACTCATATGGCTTTACTGTTGC 59.964 45.833 2.13 0.00 0.00 4.17
680 684 3.947834 ACTCATATGGCTTTACTGTTGCC 59.052 43.478 2.13 10.75 46.26 4.52
686 690 2.742774 GGCTTTACTGTTGCCAACTTG 58.257 47.619 9.30 4.54 45.46 3.16
687 691 2.100749 GGCTTTACTGTTGCCAACTTGT 59.899 45.455 9.30 10.03 45.46 3.16
688 692 3.372060 GCTTTACTGTTGCCAACTTGTC 58.628 45.455 9.30 0.00 0.00 3.18
689 693 3.617669 CTTTACTGTTGCCAACTTGTCG 58.382 45.455 9.30 0.00 0.00 4.35
690 694 2.319136 TACTGTTGCCAACTTGTCGT 57.681 45.000 9.30 1.53 0.00 4.34
691 695 1.459450 ACTGTTGCCAACTTGTCGTT 58.541 45.000 9.30 0.00 35.88 3.85
692 696 1.816224 ACTGTTGCCAACTTGTCGTTT 59.184 42.857 9.30 0.00 32.27 3.60
693 697 2.230266 ACTGTTGCCAACTTGTCGTTTT 59.770 40.909 9.30 0.00 32.27 2.43
694 698 3.249917 CTGTTGCCAACTTGTCGTTTTT 58.750 40.909 9.30 0.00 32.27 1.94
726 730 6.322491 ACTTCTTTTTGTTAAGACTGTGTGC 58.678 36.000 0.00 0.00 34.04 4.57
727 731 5.888691 TCTTTTTGTTAAGACTGTGTGCA 57.111 34.783 0.00 0.00 0.00 4.57
728 732 6.449635 TCTTTTTGTTAAGACTGTGTGCAT 57.550 33.333 0.00 0.00 0.00 3.96
729 733 6.494842 TCTTTTTGTTAAGACTGTGTGCATC 58.505 36.000 0.00 0.00 0.00 3.91
730 734 6.318648 TCTTTTTGTTAAGACTGTGTGCATCT 59.681 34.615 0.00 0.00 0.00 2.90
731 735 6.449635 TTTTGTTAAGACTGTGTGCATCTT 57.550 33.333 4.97 4.97 36.64 2.40
732 736 7.561021 TTTTGTTAAGACTGTGTGCATCTTA 57.439 32.000 3.17 3.17 34.55 2.10
733 737 6.785488 TTGTTAAGACTGTGTGCATCTTAG 57.215 37.500 6.77 0.00 36.54 2.18
734 738 4.690748 TGTTAAGACTGTGTGCATCTTAGC 59.309 41.667 11.70 11.70 36.54 3.09
735 739 3.692257 AAGACTGTGTGCATCTTAGCT 57.308 42.857 0.00 0.00 30.88 3.32
736 740 4.808414 AAGACTGTGTGCATCTTAGCTA 57.192 40.909 0.00 0.00 30.88 3.32
737 741 5.350504 AAGACTGTGTGCATCTTAGCTAT 57.649 39.130 0.00 0.00 30.88 2.97
738 742 4.691175 AGACTGTGTGCATCTTAGCTATG 58.309 43.478 0.00 0.00 34.99 2.23
747 751 3.573598 CATCTTAGCTATGCAGAGACCG 58.426 50.000 13.69 0.00 0.00 4.79
748 752 1.957177 TCTTAGCTATGCAGAGACCGG 59.043 52.381 13.69 0.00 0.00 5.28
749 753 1.000283 CTTAGCTATGCAGAGACCGGG 60.000 57.143 13.69 0.00 0.00 5.73
750 754 0.106167 TAGCTATGCAGAGACCGGGT 60.106 55.000 13.69 0.00 0.00 5.28
751 755 1.227380 GCTATGCAGAGACCGGGTG 60.227 63.158 13.69 0.00 0.00 4.61
752 756 1.961180 GCTATGCAGAGACCGGGTGT 61.961 60.000 13.69 0.00 0.00 4.16
753 757 0.103208 CTATGCAGAGACCGGGTGTC 59.897 60.000 16.08 16.08 44.82 3.67
764 768 4.133013 GACCGGGTGTCACTTATTATGT 57.867 45.455 3.30 0.00 43.85 2.29
765 769 4.510571 GACCGGGTGTCACTTATTATGTT 58.489 43.478 3.30 0.00 43.85 2.71
766 770 4.258543 ACCGGGTGTCACTTATTATGTTG 58.741 43.478 6.32 0.00 0.00 3.33
767 771 4.258543 CCGGGTGTCACTTATTATGTTGT 58.741 43.478 2.35 0.00 0.00 3.32
768 772 5.046448 ACCGGGTGTCACTTATTATGTTGTA 60.046 40.000 6.32 0.00 0.00 2.41
769 773 6.053005 CCGGGTGTCACTTATTATGTTGTAT 58.947 40.000 2.35 0.00 0.00 2.29
770 774 6.202188 CCGGGTGTCACTTATTATGTTGTATC 59.798 42.308 2.35 0.00 0.00 2.24
771 775 6.202188 CGGGTGTCACTTATTATGTTGTATCC 59.798 42.308 2.35 0.00 0.00 2.59
772 776 7.051623 GGGTGTCACTTATTATGTTGTATCCA 58.948 38.462 2.35 0.00 0.00 3.41
773 777 7.012044 GGGTGTCACTTATTATGTTGTATCCAC 59.988 40.741 2.35 0.00 0.00 4.02
774 778 7.769044 GGTGTCACTTATTATGTTGTATCCACT 59.231 37.037 2.35 0.00 0.00 4.00
775 779 9.162764 GTGTCACTTATTATGTTGTATCCACTT 57.837 33.333 0.00 0.00 0.00 3.16
776 780 9.161629 TGTCACTTATTATGTTGTATCCACTTG 57.838 33.333 0.00 0.00 0.00 3.16
777 781 9.378551 GTCACTTATTATGTTGTATCCACTTGA 57.621 33.333 0.00 0.00 0.00 3.02
805 809 9.893305 ACTACATAATGAATTAATAAAAGCGCC 57.107 29.630 2.29 0.00 0.00 6.53
808 812 9.816354 ACATAATGAATTAATAAAAGCGCCTTT 57.184 25.926 9.28 9.28 34.94 3.11
847 851 4.437390 CCGTTCTGAATTTTATCGCAGCTT 60.437 41.667 0.00 0.00 0.00 3.74
885 889 3.192541 TCAGAGTGCTGCTGTTTTGTA 57.807 42.857 0.00 0.00 42.01 2.41
895 899 4.466828 CTGCTGTTTTGTATTCTGAACGG 58.533 43.478 0.00 0.00 0.00 4.44
900 904 2.396590 TTGTATTCTGAACGGGCTCC 57.603 50.000 0.00 0.00 0.00 4.70
932 936 2.361230 GCAAACCCGCCTAGGCTT 60.361 61.111 30.55 16.19 39.21 4.35
938 942 0.756070 ACCCGCCTAGGCTTCTAGTC 60.756 60.000 30.55 0.15 38.99 2.59
941 945 1.689273 CCGCCTAGGCTTCTAGTCATT 59.311 52.381 30.55 0.00 38.99 2.57
942 946 2.891580 CCGCCTAGGCTTCTAGTCATTA 59.108 50.000 30.55 0.00 38.99 1.90
943 947 3.305471 CCGCCTAGGCTTCTAGTCATTAC 60.305 52.174 30.55 0.00 38.99 1.89
944 948 3.570550 CGCCTAGGCTTCTAGTCATTACT 59.429 47.826 30.55 0.00 38.99 2.24
945 949 4.557695 CGCCTAGGCTTCTAGTCATTACTG 60.558 50.000 30.55 5.99 38.99 2.74
1317 1321 1.433879 CTTCGTCCTCTTCGCCGAT 59.566 57.895 0.00 0.00 0.00 4.18
1429 1433 3.144120 CTCCTCCGACAGATGCCCG 62.144 68.421 0.00 0.00 0.00 6.13
1456 1460 1.070105 GCCGTCACCTACAACACCA 59.930 57.895 0.00 0.00 0.00 4.17
1672 1676 1.143373 TCCGATGATGTACAACGCGC 61.143 55.000 5.73 0.00 42.07 6.86
2034 2038 0.339859 TGGTCCAGGAGGCTGATAGT 59.660 55.000 0.00 0.00 33.74 2.12
2112 2116 1.945394 CTGATCAATAGCCACTGCACC 59.055 52.381 0.00 0.00 41.13 5.01
2256 2260 1.851021 CGCGTGGGCTCATTGACAAA 61.851 55.000 0.00 0.00 36.88 2.83
2448 2452 1.284111 ATGGCCAAGGAGAGGATGCA 61.284 55.000 10.96 0.00 0.00 3.96
2621 2625 2.638480 TTTGTAGCAAGCAGAGGTGT 57.362 45.000 0.00 0.00 0.00 4.16
2695 2699 1.544724 ACCTGTATTGGCGTGCAATT 58.455 45.000 0.00 0.00 0.00 2.32
2705 2709 1.202114 GGCGTGCAATTCCATTCTGAA 59.798 47.619 0.00 0.00 0.00 3.02
2712 2716 6.237279 CGTGCAATTCCATTCTGAATTTTACG 60.237 38.462 0.00 13.20 41.74 3.18
2716 2720 5.539582 TTCCATTCTGAATTTTACGTCGG 57.460 39.130 0.00 0.00 0.00 4.79
2727 2731 2.350899 TTACGTCGGTGTACCATGTG 57.649 50.000 0.00 0.00 35.14 3.21
2817 2821 1.635487 TCAGCTTACTCCTTGGCCAAT 59.365 47.619 20.85 6.59 0.00 3.16
2818 2822 2.019984 CAGCTTACTCCTTGGCCAATC 58.980 52.381 20.85 1.21 0.00 2.67
2819 2823 1.635487 AGCTTACTCCTTGGCCAATCA 59.365 47.619 20.85 7.52 0.00 2.57
2820 2824 1.745653 GCTTACTCCTTGGCCAATCAC 59.254 52.381 20.85 0.00 0.00 3.06
2821 2825 2.619074 GCTTACTCCTTGGCCAATCACT 60.619 50.000 20.85 4.87 0.00 3.41
2822 2826 3.370527 GCTTACTCCTTGGCCAATCACTA 60.371 47.826 20.85 3.83 0.00 2.74
2823 2827 4.687219 GCTTACTCCTTGGCCAATCACTAT 60.687 45.833 20.85 5.51 0.00 2.12
2824 2828 5.454755 GCTTACTCCTTGGCCAATCACTATA 60.455 44.000 20.85 4.49 0.00 1.31
2825 2829 6.569127 TTACTCCTTGGCCAATCACTATAA 57.431 37.500 20.85 10.32 0.00 0.98
2826 2830 5.450818 ACTCCTTGGCCAATCACTATAAA 57.549 39.130 20.85 0.00 0.00 1.40
2831 2863 5.163622 CCTTGGCCAATCACTATAAACACAG 60.164 44.000 20.85 0.18 0.00 3.66
2874 2909 5.244626 AGACCAAAATTTTCACTGAGATGGG 59.755 40.000 0.00 0.00 0.00 4.00
2920 2955 8.603898 TGAAGATCACCAGGTACTTAGAATAA 57.396 34.615 0.00 0.00 34.60 1.40
2922 2957 7.604657 AGATCACCAGGTACTTAGAATAAGG 57.395 40.000 0.00 0.00 34.60 2.69
2945 2980 3.261897 GGAGACTGGATCTTTCAACCTGA 59.738 47.826 0.00 0.00 38.00 3.86
3087 3122 2.975851 GTGCTTTCAGAATGCAAGTTCG 59.024 45.455 21.88 0.00 41.53 3.95
3091 3126 5.048782 TGCTTTCAGAATGCAAGTTCGTATT 60.049 36.000 18.86 0.00 41.53 1.89
3124 3159 5.860941 ACTCAGATGATACTCGGATTGTT 57.139 39.130 0.00 0.00 0.00 2.83
3125 3160 6.961360 ACTCAGATGATACTCGGATTGTTA 57.039 37.500 0.00 0.00 0.00 2.41
3251 3287 3.909430 TGTTCAGGTAGCACTAACTTCG 58.091 45.455 0.00 0.00 28.94 3.79
3334 3370 3.604582 AGCTAGCTTTCCTGTCATTGAC 58.395 45.455 12.68 9.93 0.00 3.18
3373 3409 1.544246 GTTTGTGGGGGATGCAAGTAC 59.456 52.381 0.00 0.00 0.00 2.73
3472 3513 6.925718 TCTTATATGCCTGAATCTTCTTCACG 59.074 38.462 0.00 0.00 0.00 4.35
3502 3543 3.515901 AGGCTCTTTGTACTAGGGTCTTG 59.484 47.826 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 6.935240 ATCCCTCCTAAATGATACATTCGA 57.065 37.500 0.00 0.00 0.00 3.71
175 176 3.133542 CCAGATGTAGTGAGATTCCAGCA 59.866 47.826 0.00 0.00 0.00 4.41
319 323 7.224297 TGTCTTTTGTTAGCATAACTCCTCTT 58.776 34.615 1.76 0.00 0.00 2.85
329 333 3.058224 GCGAGGTTGTCTTTTGTTAGCAT 60.058 43.478 0.00 0.00 0.00 3.79
405 409 7.500892 TGCACTGAAAGAAGAGGTGTTTAATTA 59.499 33.333 0.00 0.00 37.43 1.40
468 472 2.490115 GTTGGCGGATACAAATTGGACA 59.510 45.455 0.00 0.00 0.00 4.02
557 561 0.929244 AATAAGGCAGCCACTCCCAT 59.071 50.000 15.80 0.00 0.00 4.00
566 570 1.884235 AGCGACCATAATAAGGCAGC 58.116 50.000 0.00 0.00 33.68 5.25
654 658 3.704566 ACAGTAAAGCCATATGAGTCCGA 59.295 43.478 3.65 0.00 0.00 4.55
655 659 4.060038 ACAGTAAAGCCATATGAGTCCG 57.940 45.455 3.65 0.00 0.00 4.79
656 660 4.035675 GCAACAGTAAAGCCATATGAGTCC 59.964 45.833 3.65 0.00 0.00 3.85
657 661 5.162000 GCAACAGTAAAGCCATATGAGTC 57.838 43.478 3.65 0.00 0.00 3.36
700 704 8.129211 GCACACAGTCTTAACAAAAAGAAGTAT 58.871 33.333 0.00 0.00 37.24 2.12
701 705 7.119992 TGCACACAGTCTTAACAAAAAGAAGTA 59.880 33.333 0.00 0.00 37.24 2.24
702 706 6.072175 TGCACACAGTCTTAACAAAAAGAAGT 60.072 34.615 0.00 0.00 37.24 3.01
703 707 6.321717 TGCACACAGTCTTAACAAAAAGAAG 58.678 36.000 0.00 0.00 37.24 2.85
704 708 6.260870 TGCACACAGTCTTAACAAAAAGAA 57.739 33.333 0.00 0.00 37.24 2.52
705 709 5.888691 TGCACACAGTCTTAACAAAAAGA 57.111 34.783 0.00 0.00 33.10 2.52
706 710 6.498304 AGATGCACACAGTCTTAACAAAAAG 58.502 36.000 0.00 0.00 0.00 2.27
707 711 6.449635 AGATGCACACAGTCTTAACAAAAA 57.550 33.333 0.00 0.00 0.00 1.94
708 712 6.449635 AAGATGCACACAGTCTTAACAAAA 57.550 33.333 0.00 0.00 30.85 2.44
709 713 6.293407 GCTAAGATGCACACAGTCTTAACAAA 60.293 38.462 7.83 0.00 34.93 2.83
710 714 5.179368 GCTAAGATGCACACAGTCTTAACAA 59.821 40.000 7.83 0.00 34.93 2.83
711 715 4.690748 GCTAAGATGCACACAGTCTTAACA 59.309 41.667 7.83 0.00 34.93 2.41
712 716 4.932200 AGCTAAGATGCACACAGTCTTAAC 59.068 41.667 7.83 4.39 34.93 2.01
713 717 5.152623 AGCTAAGATGCACACAGTCTTAA 57.847 39.130 7.83 0.00 34.93 1.85
714 718 4.808414 AGCTAAGATGCACACAGTCTTA 57.192 40.909 6.56 6.56 34.33 2.10
715 719 3.692257 AGCTAAGATGCACACAGTCTT 57.308 42.857 4.97 4.97 36.30 3.01
716 720 4.691175 CATAGCTAAGATGCACACAGTCT 58.309 43.478 0.00 0.00 34.99 3.24
726 730 3.573598 CGGTCTCTGCATAGCTAAGATG 58.426 50.000 0.00 0.00 0.00 2.90
727 731 2.560542 CCGGTCTCTGCATAGCTAAGAT 59.439 50.000 0.00 0.00 0.00 2.40
728 732 1.957177 CCGGTCTCTGCATAGCTAAGA 59.043 52.381 0.00 0.00 0.00 2.10
729 733 1.000283 CCCGGTCTCTGCATAGCTAAG 60.000 57.143 0.00 0.00 0.00 2.18
730 734 1.040646 CCCGGTCTCTGCATAGCTAA 58.959 55.000 0.00 0.00 0.00 3.09
731 735 0.106167 ACCCGGTCTCTGCATAGCTA 60.106 55.000 0.00 0.00 0.00 3.32
732 736 1.381872 ACCCGGTCTCTGCATAGCT 60.382 57.895 0.00 0.00 0.00 3.32
733 737 1.227380 CACCCGGTCTCTGCATAGC 60.227 63.158 0.00 0.00 0.00 2.97
734 738 0.103208 GACACCCGGTCTCTGCATAG 59.897 60.000 0.00 0.00 43.46 2.23
735 739 2.199117 GACACCCGGTCTCTGCATA 58.801 57.895 0.00 0.00 43.46 3.14
736 740 2.982130 GACACCCGGTCTCTGCAT 59.018 61.111 0.00 0.00 43.46 3.96
738 742 2.100879 AAGTGACACCCGGTCTCTGC 62.101 60.000 0.00 0.00 46.65 4.26
739 743 1.254026 TAAGTGACACCCGGTCTCTG 58.746 55.000 0.00 0.00 46.65 3.35
744 748 4.258543 CAACATAATAAGTGACACCCGGT 58.741 43.478 0.00 0.00 0.00 5.28
745 749 4.258543 ACAACATAATAAGTGACACCCGG 58.741 43.478 0.84 0.00 0.00 5.73
746 750 6.202188 GGATACAACATAATAAGTGACACCCG 59.798 42.308 0.84 0.00 0.00 5.28
747 751 7.492352 GGATACAACATAATAAGTGACACCC 57.508 40.000 0.84 0.00 0.00 4.61
779 783 9.893305 GGCGCTTTTATTAATTCATTATGTAGT 57.107 29.630 7.64 0.00 0.00 2.73
782 786 9.816354 AAAGGCGCTTTTATTAATTCATTATGT 57.184 25.926 16.62 0.00 28.27 2.29
796 800 6.383415 ACATTTTCGATAAAAGGCGCTTTTA 58.617 32.000 18.45 19.24 45.77 1.52
797 801 5.227152 ACATTTTCGATAAAAGGCGCTTTT 58.773 33.333 12.22 12.22 44.46 2.27
798 802 4.805219 ACATTTTCGATAAAAGGCGCTTT 58.195 34.783 7.64 1.79 39.41 3.51
799 803 4.412207 GACATTTTCGATAAAAGGCGCTT 58.588 39.130 7.64 0.00 39.41 4.68
800 804 4.016113 GACATTTTCGATAAAAGGCGCT 57.984 40.909 7.64 0.00 39.41 5.92
813 817 1.153353 TCAGAACGGGCGACATTTTC 58.847 50.000 0.00 0.00 0.00 2.29
814 818 1.600023 TTCAGAACGGGCGACATTTT 58.400 45.000 0.00 0.00 0.00 1.82
815 819 1.821216 ATTCAGAACGGGCGACATTT 58.179 45.000 0.00 0.00 0.00 2.32
816 820 1.821216 AATTCAGAACGGGCGACATT 58.179 45.000 0.00 0.00 0.00 2.71
847 851 2.731691 GAACTCTGAAGGGCACGCCA 62.732 60.000 10.83 0.00 37.98 5.69
854 858 1.622811 AGCACTCTGAACTCTGAAGGG 59.377 52.381 0.00 0.00 0.00 3.95
900 904 1.006494 GTTTGCGAGGTTTTGTTTGCG 60.006 47.619 0.00 0.00 0.00 4.85
904 908 0.101579 CGGGTTTGCGAGGTTTTGTT 59.898 50.000 0.00 0.00 0.00 2.83
932 936 5.914898 TGCTGCTAACAGTAATGACTAGA 57.085 39.130 0.00 0.00 46.30 2.43
941 945 7.737972 TTTGATTTAGTTGCTGCTAACAGTA 57.262 32.000 14.29 0.00 46.30 2.74
942 946 6.633500 TTTGATTTAGTTGCTGCTAACAGT 57.367 33.333 14.29 1.79 46.30 3.55
1233 1237 2.851588 GGGATGGGGAGGGAGAGC 60.852 72.222 0.00 0.00 0.00 4.09
1345 1349 1.203052 CATGATGTTGAAGGTGGTGGC 59.797 52.381 0.00 0.00 0.00 5.01
1456 1460 2.203070 GCAGAACCCGGCGATGAT 60.203 61.111 9.30 0.00 0.00 2.45
1537 1541 1.597797 TAGGTGTACTTGTCGGGCGG 61.598 60.000 0.00 0.00 0.00 6.13
1575 1579 1.973281 CTTGCCGACCTTGCACCAT 60.973 57.895 0.00 0.00 38.72 3.55
1672 1676 2.398498 GTCACAGTATGCGCCTATCAG 58.602 52.381 4.18 0.00 42.53 2.90
2034 2038 2.289882 CCTCACAGCCTCATTGAACAGA 60.290 50.000 0.00 0.00 0.00 3.41
2256 2260 5.189180 GGCTTGATACCTCTCTTTGTCATT 58.811 41.667 0.00 0.00 0.00 2.57
2448 2452 3.560882 CCATTTCTTTCACCAGCTCCTCT 60.561 47.826 0.00 0.00 0.00 3.69
2583 2587 2.262423 AAACTCTTGCTTCCGCTTCT 57.738 45.000 0.00 0.00 36.97 2.85
2589 2593 4.568152 TGCTACAAAAACTCTTGCTTCC 57.432 40.909 0.00 0.00 0.00 3.46
2695 2699 4.390603 CACCGACGTAAAATTCAGAATGGA 59.609 41.667 0.00 0.00 36.16 3.41
2716 2720 7.278737 TGCAAGAATTCAGCACATGGTACAC 62.279 44.000 18.16 0.00 35.11 2.90
2727 2731 0.098376 CGCTCCTGCAAGAATTCAGC 59.902 55.000 8.44 11.72 39.64 4.26
2817 2821 4.780554 TCATCACCCCTGTGTTTATAGTGA 59.219 41.667 0.00 0.00 43.26 3.41
2818 2822 5.097742 TCATCACCCCTGTGTTTATAGTG 57.902 43.478 0.00 0.00 43.26 2.74
2819 2823 5.772393 TTCATCACCCCTGTGTTTATAGT 57.228 39.130 0.00 0.00 43.26 2.12
2820 2824 8.786898 CATATTTCATCACCCCTGTGTTTATAG 58.213 37.037 0.00 0.00 43.26 1.31
2821 2825 8.278639 ACATATTTCATCACCCCTGTGTTTATA 58.721 33.333 0.00 0.00 43.26 0.98
2822 2826 7.068593 CACATATTTCATCACCCCTGTGTTTAT 59.931 37.037 0.00 0.00 43.26 1.40
2823 2827 6.376864 CACATATTTCATCACCCCTGTGTTTA 59.623 38.462 0.00 0.00 43.26 2.01
2824 2828 5.185635 CACATATTTCATCACCCCTGTGTTT 59.814 40.000 0.00 0.00 43.26 2.83
2825 2829 4.706476 CACATATTTCATCACCCCTGTGTT 59.294 41.667 0.00 0.00 43.26 3.32
2826 2830 4.018506 TCACATATTTCATCACCCCTGTGT 60.019 41.667 0.00 0.00 43.26 3.72
2831 2863 4.580580 GGTCTTCACATATTTCATCACCCC 59.419 45.833 0.00 0.00 0.00 4.95
2865 2900 0.617413 ACCAGTGCTTCCCATCTCAG 59.383 55.000 0.00 0.00 0.00 3.35
2866 2901 0.615331 GACCAGTGCTTCCCATCTCA 59.385 55.000 0.00 0.00 0.00 3.27
2907 2942 5.304871 CCAGTCTCCCCTTATTCTAAGTACC 59.695 48.000 0.00 0.00 0.00 3.34
2914 2949 4.567987 AGATCCAGTCTCCCCTTATTCT 57.432 45.455 0.00 0.00 28.45 2.40
2920 2955 2.573915 GTTGAAAGATCCAGTCTCCCCT 59.426 50.000 0.00 0.00 35.67 4.79
2922 2957 2.573915 AGGTTGAAAGATCCAGTCTCCC 59.426 50.000 0.00 0.00 35.67 4.30
2972 3007 3.251004 GCAGGGTAGCATAGCATACAAAC 59.749 47.826 0.00 0.00 41.82 2.93
3087 3122 5.582269 TCATCTGAGTAGCAGCAACAAATAC 59.418 40.000 0.00 0.00 44.52 1.89
3091 3126 3.683365 TCATCTGAGTAGCAGCAACAA 57.317 42.857 0.00 0.00 44.52 2.83
3199 3234 2.158608 AGCTCAACCCAGTTAGTGCTTT 60.159 45.455 0.00 0.00 0.00 3.51
3453 3491 3.616956 TCGTGAAGAAGATTCAGGCAT 57.383 42.857 5.63 0.00 35.13 4.40
3472 3513 6.100668 CCTAGTACAAAGAGCCTAACTGTTC 58.899 44.000 0.00 0.00 28.68 3.18


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

AutoCloner maintained by Alex Coulton.