Multiple sequence alignment - TraesCS2A01G081200

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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 TraesCS2A01G081200 chr2A 100.000 2955 0 0 1 2955 36720239 36717285 0.000000e+00 5457.0
1 TraesCS2A01G081200 chr2A 92.637 1005 53 9 1145 2132 36657641 36658641 0.000000e+00 1426.0
2 TraesCS2A01G081200 chr2A 82.033 718 95 18 1223 1940 772663513 772664196 5.490000e-162 580.0
3 TraesCS2A01G081200 chr2A 87.395 357 41 1 1603 1959 36706265 36705913 9.860000e-110 407.0
4 TraesCS2A01G081200 chr2A 90.397 302 15 9 851 1143 36652116 36652412 4.620000e-103 385.0
5 TraesCS2A01G081200 chr2A 81.132 106 8 3 765 859 36636813 36636917 1.140000e-09 75.0
6 TraesCS2A01G081200 chr2D 92.066 1084 60 14 1143 2218 33875154 33874089 0.000000e+00 1502.0
7 TraesCS2A01G081200 chr2D 86.224 784 70 18 1197 1957 33727151 33727919 0.000000e+00 815.0
8 TraesCS2A01G081200 chr2D 85.602 764 91 13 1197 1947 56530804 56531561 0.000000e+00 784.0
9 TraesCS2A01G081200 chr2D 82.483 725 98 11 1220 1940 647814673 647813974 2.520000e-170 608.0
10 TraesCS2A01G081200 chr2D 90.722 388 25 8 767 1146 33875600 33875216 9.450000e-140 507.0
11 TraesCS2A01G081200 chr2D 80.741 675 68 29 2 655 5676199 5675566 1.240000e-128 470.0
12 TraesCS2A01G081200 chr2D 88.669 353 38 2 1199 1550 33850180 33849829 2.100000e-116 429.0
13 TraesCS2A01G081200 chr2D 87.955 357 38 2 1603 1959 33855511 33855160 1.640000e-112 416.0
14 TraesCS2A01G081200 chr2D 87.864 206 17 4 950 1147 33726846 33727051 4.920000e-58 235.0
15 TraesCS2A01G081200 chr2D 86.325 117 6 7 655 766 33875586 33875475 5.170000e-23 119.0
16 TraesCS2A01G081200 chr2B 89.731 1003 67 18 1141 2132 55887833 55888810 0.000000e+00 1249.0
17 TraesCS2A01G081200 chr2B 86.115 749 80 15 1209 1956 55891644 55892369 0.000000e+00 785.0
18 TraesCS2A01G081200 chr2B 84.334 766 106 10 1199 1955 55896210 55896970 0.000000e+00 737.0
19 TraesCS2A01G081200 chr2B 87.532 393 27 7 766 1143 55887353 55887738 4.520000e-118 435.0
20 TraesCS2A01G081200 chr2B 96.552 58 2 0 597 654 762013092 762013149 2.420000e-16 97.1
21 TraesCS2A01G081200 chr2B 95.918 49 2 0 2165 2213 55888811 55888859 2.440000e-11 80.5
22 TraesCS2A01G081200 chr7B 95.405 740 29 2 2217 2952 711156457 711157195 0.000000e+00 1173.0
23 TraesCS2A01G081200 chr6D 91.071 672 30 11 1 654 450701808 450701149 0.000000e+00 881.0
24 TraesCS2A01G081200 chr5D 94.851 369 19 0 2587 2955 554760669 554760301 7.100000e-161 577.0
25 TraesCS2A01G081200 chr7A 82.784 668 77 17 2 654 5878173 5878817 1.990000e-156 562.0
26 TraesCS2A01G081200 chr7A 89.024 82 7 2 574 654 125693707 125693787 1.870000e-17 100.0
27 TraesCS2A01G081200 chr7A 90.385 52 4 1 603 654 12229182 12229132 1.900000e-07 67.6
28 TraesCS2A01G081200 chr5A 82.132 666 80 24 2 656 417248138 417248775 4.340000e-148 534.0
29 TraesCS2A01G081200 chr3D 82.310 554 47 19 70 609 96638377 96638893 1.630000e-117 433.0
30 TraesCS2A01G081200 chrUn 88.630 343 37 2 1209 1550 12882685 12882344 1.640000e-112 416.0
31 TraesCS2A01G081200 chrUn 87.395 357 41 1 1603 1959 12891430 12891782 9.860000e-110 407.0
32 TraesCS2A01G081200 chr4B 89.527 296 7 1 2684 2955 608488971 608489266 1.300000e-93 353.0
33 TraesCS2A01G081200 chr3B 82.990 194 25 8 464 654 22795938 22795750 5.070000e-38 169.0
34 TraesCS2A01G081200 chr3B 96.970 99 3 0 2857 2955 725027588 725027686 1.820000e-37 167.0
35 TraesCS2A01G081200 chr3B 96.875 64 2 0 2771 2834 725027528 725027591 1.120000e-19 108.0
36 TraesCS2A01G081200 chr1B 93.182 44 2 1 607 650 161579446 161579404 2.460000e-06 63.9


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 TraesCS2A01G081200 chr2A 36717285 36720239 2954 True 5457.000000 5457 100.000000 1 2955 1 chr2A.!!$R2 2954
1 TraesCS2A01G081200 chr2A 36657641 36658641 1000 False 1426.000000 1426 92.637000 1145 2132 1 chr2A.!!$F3 987
2 TraesCS2A01G081200 chr2A 772663513 772664196 683 False 580.000000 580 82.033000 1223 1940 1 chr2A.!!$F4 717
3 TraesCS2A01G081200 chr2D 56530804 56531561 757 False 784.000000 784 85.602000 1197 1947 1 chr2D.!!$F1 750
4 TraesCS2A01G081200 chr2D 33874089 33875600 1511 True 709.333333 1502 89.704333 655 2218 3 chr2D.!!$R5 1563
5 TraesCS2A01G081200 chr2D 647813974 647814673 699 True 608.000000 608 82.483000 1220 1940 1 chr2D.!!$R4 720
6 TraesCS2A01G081200 chr2D 33726846 33727919 1073 False 525.000000 815 87.044000 950 1957 2 chr2D.!!$F2 1007
7 TraesCS2A01G081200 chr2D 5675566 5676199 633 True 470.000000 470 80.741000 2 655 1 chr2D.!!$R1 653
8 TraesCS2A01G081200 chr2B 55887353 55896970 9617 False 657.300000 1249 88.726000 766 2213 5 chr2B.!!$F2 1447
9 TraesCS2A01G081200 chr7B 711156457 711157195 738 False 1173.000000 1173 95.405000 2217 2952 1 chr7B.!!$F1 735
10 TraesCS2A01G081200 chr6D 450701149 450701808 659 True 881.000000 881 91.071000 1 654 1 chr6D.!!$R1 653
11 TraesCS2A01G081200 chr7A 5878173 5878817 644 False 562.000000 562 82.784000 2 654 1 chr7A.!!$F1 652
12 TraesCS2A01G081200 chr5A 417248138 417248775 637 False 534.000000 534 82.132000 2 656 1 chr5A.!!$F1 654
13 TraesCS2A01G081200 chr3D 96638377 96638893 516 False 433.000000 433 82.310000 70 609 1 chr3D.!!$F1 539

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
972 1023 0.242825 CCTTCCTCTCACGTACGCAA 59.757 55.0 16.72 2.21 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2794 10357 0.181587 TCGACAACAAGGGGAAGCAA 59.818 50.0 0.0 0.0 0.0 3.91 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
334 349 1.984990 CAAACAAGCACACACACACAC 59.015 47.619 0.00 0.00 0.00 3.82
338 353 0.521291 AAGCACACACACACACACAC 59.479 50.000 0.00 0.00 0.00 3.82
339 354 0.605050 AGCACACACACACACACACA 60.605 50.000 0.00 0.00 0.00 3.72
340 355 0.454285 GCACACACACACACACACAC 60.454 55.000 0.00 0.00 0.00 3.82
341 356 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
342 357 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
343 358 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
382 397 3.235200 AGTGCTTCTTGGTACAGAGACT 58.765 45.455 0.00 0.00 42.39 3.24
385 400 5.482175 AGTGCTTCTTGGTACAGAGACTAAT 59.518 40.000 0.00 0.00 42.39 1.73
386 401 6.014156 AGTGCTTCTTGGTACAGAGACTAATT 60.014 38.462 0.00 0.00 42.39 1.40
387 402 7.178628 AGTGCTTCTTGGTACAGAGACTAATTA 59.821 37.037 0.00 0.00 42.39 1.40
388 403 7.817962 GTGCTTCTTGGTACAGAGACTAATTAA 59.182 37.037 0.00 0.00 42.39 1.40
431 463 3.315191 TCTGTTGAGTACCTTTTTGCTGC 59.685 43.478 0.00 0.00 0.00 5.25
548 584 1.748591 GCCCAGAACCTAAGCCAGATG 60.749 57.143 0.00 0.00 0.00 2.90
595 631 5.339282 GGAAACAGGCCTAATCTTCCTTAGT 60.339 44.000 19.76 3.28 31.53 2.24
661 697 5.216614 GTCTTAGACAGACCCTTGTTTCT 57.783 43.478 7.59 0.00 45.84 2.52
662 698 5.231702 GTCTTAGACAGACCCTTGTTTCTC 58.768 45.833 7.59 0.00 45.84 2.87
663 699 4.899457 TCTTAGACAGACCCTTGTTTCTCA 59.101 41.667 0.00 0.00 0.00 3.27
664 700 3.760580 AGACAGACCCTTGTTTCTCAG 57.239 47.619 0.00 0.00 0.00 3.35
665 701 3.309296 AGACAGACCCTTGTTTCTCAGA 58.691 45.455 0.00 0.00 0.00 3.27
666 702 3.711704 AGACAGACCCTTGTTTCTCAGAA 59.288 43.478 0.00 0.00 0.00 3.02
667 703 4.164221 AGACAGACCCTTGTTTCTCAGAAA 59.836 41.667 0.00 0.00 0.00 2.52
668 704 5.053978 ACAGACCCTTGTTTCTCAGAAAT 57.946 39.130 2.39 0.00 0.00 2.17
669 705 6.043243 AGACAGACCCTTGTTTCTCAGAAATA 59.957 38.462 2.39 0.00 0.00 1.40
670 706 5.998363 ACAGACCCTTGTTTCTCAGAAATAC 59.002 40.000 2.39 0.00 0.00 1.89
671 707 5.412904 CAGACCCTTGTTTCTCAGAAATACC 59.587 44.000 2.39 0.00 0.00 2.73
672 708 5.073144 AGACCCTTGTTTCTCAGAAATACCA 59.927 40.000 2.39 0.00 0.00 3.25
673 709 5.701224 ACCCTTGTTTCTCAGAAATACCAA 58.299 37.500 2.39 2.53 0.00 3.67
674 710 6.133356 ACCCTTGTTTCTCAGAAATACCAAA 58.867 36.000 2.39 0.00 0.00 3.28
675 711 6.782494 ACCCTTGTTTCTCAGAAATACCAAAT 59.218 34.615 2.39 0.00 0.00 2.32
676 712 7.039714 ACCCTTGTTTCTCAGAAATACCAAATC 60.040 37.037 2.39 0.00 0.00 2.17
677 713 7.315890 CCTTGTTTCTCAGAAATACCAAATCC 58.684 38.462 2.39 0.00 0.00 3.01
678 714 6.494893 TGTTTCTCAGAAATACCAAATCCG 57.505 37.500 2.39 0.00 0.00 4.18
679 715 6.234920 TGTTTCTCAGAAATACCAAATCCGA 58.765 36.000 2.39 0.00 0.00 4.55
680 716 6.884295 TGTTTCTCAGAAATACCAAATCCGAT 59.116 34.615 2.39 0.00 0.00 4.18
721 757 9.598517 AAGATGCTTTGTTTTCATGAAGTTAAA 57.401 25.926 8.41 9.79 0.00 1.52
722 758 9.598517 AGATGCTTTGTTTTCATGAAGTTAAAA 57.401 25.926 8.41 7.63 0.00 1.52
738 774 9.554724 TGAAGTTAAAAATCTTTGATGATACGC 57.445 29.630 0.00 0.00 0.00 4.42
739 775 9.774742 GAAGTTAAAAATCTTTGATGATACGCT 57.225 29.630 0.00 0.00 0.00 5.07
754 790 9.663904 TGATGATACGCTAATTGAATAAAAAGC 57.336 29.630 0.00 0.00 0.00 3.51
755 791 9.884465 GATGATACGCTAATTGAATAAAAAGCT 57.116 29.630 0.00 0.00 0.00 3.74
756 792 9.884465 ATGATACGCTAATTGAATAAAAAGCTC 57.116 29.630 0.00 0.00 0.00 4.09
757 793 9.109393 TGATACGCTAATTGAATAAAAAGCTCT 57.891 29.630 0.00 0.00 0.00 4.09
758 794 9.587461 GATACGCTAATTGAATAAAAAGCTCTC 57.413 33.333 0.00 0.00 0.00 3.20
759 795 6.786207 ACGCTAATTGAATAAAAAGCTCTCC 58.214 36.000 0.00 0.00 0.00 3.71
760 796 6.599638 ACGCTAATTGAATAAAAAGCTCTCCT 59.400 34.615 0.00 0.00 0.00 3.69
761 797 7.128976 CGCTAATTGAATAAAAAGCTCTCCTC 58.871 38.462 0.00 0.00 0.00 3.71
762 798 7.421599 GCTAATTGAATAAAAAGCTCTCCTCC 58.578 38.462 0.00 0.00 0.00 4.30
763 799 7.067494 GCTAATTGAATAAAAAGCTCTCCTCCA 59.933 37.037 0.00 0.00 0.00 3.86
764 800 7.781324 AATTGAATAAAAAGCTCTCCTCCAA 57.219 32.000 0.00 0.00 0.00 3.53
807 843 3.934068 TCTCAGAAATACCAAACCCGAC 58.066 45.455 0.00 0.00 0.00 4.79
808 844 2.671396 CTCAGAAATACCAAACCCGACG 59.329 50.000 0.00 0.00 0.00 5.12
809 845 1.129811 CAGAAATACCAAACCCGACGC 59.870 52.381 0.00 0.00 0.00 5.19
835 886 6.861065 AGATGCTTCGTTTTCAAGAAGTTA 57.139 33.333 6.99 0.00 44.07 2.24
864 915 7.482654 TCTTTGAGGATACGCTAATTGAATG 57.517 36.000 0.00 0.00 46.39 2.67
867 918 8.450578 TTTGAGGATACGCTAATTGAATGAAT 57.549 30.769 0.00 0.00 46.39 2.57
872 923 7.667219 AGGATACGCTAATTGAATGAATGGAAT 59.333 33.333 0.00 0.00 46.39 3.01
895 946 1.688735 TCTCCTCCAATCGGCATGTAG 59.311 52.381 0.00 0.00 0.00 2.74
924 975 1.306825 ATCCCTCTGGCTGTCTGCT 60.307 57.895 1.44 0.00 42.39 4.24
969 1020 1.666700 CTCTCCTTCCTCTCACGTACG 59.333 57.143 15.01 15.01 0.00 3.67
971 1022 0.607217 TCCTTCCTCTCACGTACGCA 60.607 55.000 16.72 0.58 0.00 5.24
972 1023 0.242825 CCTTCCTCTCACGTACGCAA 59.757 55.000 16.72 2.21 0.00 4.85
978 1029 2.660236 CCTCTCACGTACGCAAAGTAAC 59.340 50.000 16.72 0.00 37.02 2.50
982 1033 1.130955 ACGTACGCAAAGTAACCGTG 58.869 50.000 16.72 0.00 36.89 4.94
1179 1340 8.285776 ACATAGTAGTTGTTGTTTACGTGTAC 57.714 34.615 0.00 0.00 0.00 2.90
1180 1341 5.871531 AGTAGTTGTTGTTTACGTGTACG 57.128 39.130 0.00 2.43 46.33 3.67
1212 1373 3.231260 CGAGTAGTGACGCGTGCG 61.231 66.667 20.70 13.39 43.05 5.34
1347 1508 3.306088 GGCGCTTGCTATCAGGTTAGATA 60.306 47.826 7.64 0.00 39.13 1.98
1358 1519 5.290493 TCAGGTTAGATACATCGGCAATT 57.710 39.130 0.00 0.00 0.00 2.32
1563 1765 0.652592 GCTAGCGCACACACTTATGG 59.347 55.000 11.47 0.00 35.78 2.74
1590 1800 1.803922 CGCCTACGTGCATGTTCGA 60.804 57.895 18.34 0.00 33.53 3.71
1628 1860 3.067106 TCTTTGATTTCTTCGCTCGCTT 58.933 40.909 0.00 0.00 0.00 4.68
1714 1946 0.324943 ACTACCTTGCGGTGCTCATT 59.675 50.000 0.00 0.00 45.18 2.57
1831 2063 2.918802 TACAACGCCGGGTCCACT 60.919 61.111 2.18 0.00 0.00 4.00
1904 2136 1.526917 GCCAGGAATGTCATCCCCG 60.527 63.158 0.00 0.00 40.59 5.73
1977 2209 0.837272 ATCCGTCCGTGGGATCAATT 59.163 50.000 0.00 0.00 40.22 2.32
1982 2214 2.009774 GTCCGTGGGATCAATTGAGTG 58.990 52.381 14.54 0.07 32.73 3.51
1991 2224 3.065233 GGATCAATTGAGTGCGCATGTTA 59.935 43.478 15.91 0.00 0.00 2.41
2046 2279 1.741327 TAGTAATCGAGCCCGTGCCC 61.741 60.000 0.00 0.00 38.69 5.36
2062 2295 2.290641 GTGCCCGGAATAATACTTGCTG 59.709 50.000 0.73 0.00 0.00 4.41
2089 2322 8.283992 TCATGCTTTGAAAAATTGCAAACATAG 58.716 29.630 1.71 5.37 37.20 2.23
2152 2386 7.601886 GCTGATCTGCTCTTTATCTGCTTAATA 59.398 37.037 16.60 0.00 39.85 0.98
2153 2387 9.486497 CTGATCTGCTCTTTATCTGCTTAATAA 57.514 33.333 0.00 0.00 0.00 1.40
2195 2429 4.376413 CGATGGATATTGCTAAACGCTCAC 60.376 45.833 0.00 0.00 40.11 3.51
2219 4787 3.438216 TGATGCCAACTGATCTTTCCA 57.562 42.857 0.00 0.00 0.00 3.53
2225 4793 2.507484 CAACTGATCTTTCCACTGGCA 58.493 47.619 0.00 0.00 0.00 4.92
2337 6843 3.232279 GGAGCCACTCCCTGATACT 57.768 57.895 1.98 0.00 44.36 2.12
2341 6847 0.466124 GCCACTCCCTGATACTGTCC 59.534 60.000 0.00 0.00 0.00 4.02
2525 9961 2.029380 GGGAAATGGTGTTGCACTTACC 60.029 50.000 6.31 6.31 34.40 2.85
2535 9971 1.899534 GCACTTACCGGCCACCAAA 60.900 57.895 0.00 0.00 0.00 3.28
2625 10188 0.179018 GGGCCAAGCTGAATACGGAT 60.179 55.000 4.39 0.00 0.00 4.18
2635 10198 3.001330 GCTGAATACGGATGGAAGTTTCG 59.999 47.826 0.00 0.00 0.00 3.46
2685 10248 1.371558 GGTCCTGCGGGATGATACC 59.628 63.158 19.55 10.84 44.33 2.73
2694 10257 0.110486 GGGATGATACCGGCACCATT 59.890 55.000 0.00 0.00 0.00 3.16
2700 10263 4.530710 TGATACCGGCACCATTATCTAC 57.469 45.455 0.00 0.00 0.00 2.59
2719 10282 1.098050 CACAGCCTGCAGGGAAATAC 58.902 55.000 33.46 15.92 37.23 1.89
2760 10323 0.255890 AGGCGGAACTATTGGCATGT 59.744 50.000 0.00 0.00 0.00 3.21
2762 10325 2.092646 AGGCGGAACTATTGGCATGTAA 60.093 45.455 0.00 0.00 0.00 2.41
2794 10357 3.362399 CTCGCGATGCACAGGACCT 62.362 63.158 10.36 0.00 0.00 3.85
2871 10434 1.560004 CCACGCGGGATCGATCAATG 61.560 60.000 25.93 15.50 40.01 2.82
2882 10445 1.078709 CGATCAATGTTCACGGCACT 58.921 50.000 0.00 0.00 0.00 4.40
2952 10519 7.639162 AGTTTTTACTCATATTAGCCGATCG 57.361 36.000 8.51 8.51 0.00 3.69
2953 10520 6.145696 AGTTTTTACTCATATTAGCCGATCGC 59.854 38.462 10.32 5.46 37.98 4.58
2954 10521 4.776795 TTACTCATATTAGCCGATCGCA 57.223 40.909 10.32 0.00 41.38 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 8.339714 ACAGATGCACATTTCAAAAATCAAAAG 58.660 29.630 0.00 0.00 0.00 2.27
185 191 4.941263 CCCAGCAGCTATAAACAAGTGTTA 59.059 41.667 0.00 0.00 37.25 2.41
238 248 3.322211 TCGCTGGAAAATTTCGGTAGA 57.678 42.857 0.00 0.00 0.00 2.59
312 327 0.108898 TGTGTGTGTGCTTGTTTGGC 60.109 50.000 0.00 0.00 0.00 4.52
334 349 0.026674 CAGCTCGTTGTGTGTGTGTG 59.973 55.000 0.00 0.00 0.00 3.82
338 353 0.578683 CTGTCAGCTCGTTGTGTGTG 59.421 55.000 0.00 0.00 0.00 3.82
339 354 1.154205 GCTGTCAGCTCGTTGTGTGT 61.154 55.000 17.89 0.00 38.45 3.72
340 355 1.566563 GCTGTCAGCTCGTTGTGTG 59.433 57.895 17.89 0.00 38.45 3.82
341 356 4.033894 GCTGTCAGCTCGTTGTGT 57.966 55.556 17.89 0.00 38.45 3.72
385 400 9.910267 AGAAAAGGAACAGGTTTAAGTACTTAA 57.090 29.630 21.52 21.52 33.63 1.85
386 401 9.333724 CAGAAAAGGAACAGGTTTAAGTACTTA 57.666 33.333 11.38 11.38 0.00 2.24
387 402 7.832685 ACAGAAAAGGAACAGGTTTAAGTACTT 59.167 33.333 13.68 13.68 0.00 2.24
388 403 7.344134 ACAGAAAAGGAACAGGTTTAAGTACT 58.656 34.615 0.00 0.00 0.00 2.73
431 463 6.034898 AGCTTGTTCATTTGTTTTCTTTGACG 59.965 34.615 0.00 0.00 0.00 4.35
548 584 1.004080 TTGCTCTCTGCTGGACTGC 60.004 57.895 0.00 0.00 43.37 4.40
561 597 1.454201 GCCTGTTTCCTAGGTTGCTC 58.546 55.000 9.08 0.00 37.64 4.26
656 692 6.737254 TCGGATTTGGTATTTCTGAGAAAC 57.263 37.500 10.18 0.00 0.00 2.78
658 694 9.929180 CTATATCGGATTTGGTATTTCTGAGAA 57.071 33.333 0.00 0.00 0.00 2.87
659 695 9.309224 TCTATATCGGATTTGGTATTTCTGAGA 57.691 33.333 0.00 0.00 0.00 3.27
660 696 9.929180 TTCTATATCGGATTTGGTATTTCTGAG 57.071 33.333 0.00 0.00 0.00 3.35
663 699 9.892130 GGATTCTATATCGGATTTGGTATTTCT 57.108 33.333 0.00 0.00 0.00 2.52
664 700 9.110502 GGGATTCTATATCGGATTTGGTATTTC 57.889 37.037 0.00 0.00 0.00 2.17
665 701 8.836735 AGGGATTCTATATCGGATTTGGTATTT 58.163 33.333 0.00 0.00 0.00 1.40
666 702 8.267894 CAGGGATTCTATATCGGATTTGGTATT 58.732 37.037 0.00 0.00 0.00 1.89
667 703 7.635971 GCAGGGATTCTATATCGGATTTGGTAT 60.636 40.741 0.00 0.00 0.00 2.73
668 704 6.351881 GCAGGGATTCTATATCGGATTTGGTA 60.352 42.308 0.00 0.00 0.00 3.25
669 705 5.571658 GCAGGGATTCTATATCGGATTTGGT 60.572 44.000 0.00 0.00 0.00 3.67
670 706 4.878397 GCAGGGATTCTATATCGGATTTGG 59.122 45.833 0.00 0.00 0.00 3.28
671 707 5.491070 TGCAGGGATTCTATATCGGATTTG 58.509 41.667 0.00 0.00 0.00 2.32
672 708 5.762179 TGCAGGGATTCTATATCGGATTT 57.238 39.130 0.00 0.00 0.00 2.17
673 709 5.762179 TTGCAGGGATTCTATATCGGATT 57.238 39.130 0.00 0.00 0.00 3.01
674 710 5.485353 TCTTTGCAGGGATTCTATATCGGAT 59.515 40.000 0.00 0.00 0.00 4.18
675 711 4.838423 TCTTTGCAGGGATTCTATATCGGA 59.162 41.667 0.00 0.00 0.00 4.55
676 712 5.152623 TCTTTGCAGGGATTCTATATCGG 57.847 43.478 0.00 0.00 0.00 4.18
677 713 6.659361 CATCTTTGCAGGGATTCTATATCG 57.341 41.667 1.48 0.00 0.00 2.92
712 748 9.554724 GCGTATCATCAAAGATTTTTAACTTCA 57.445 29.630 0.00 0.00 0.00 3.02
728 764 9.663904 GCTTTTTATTCAATTAGCGTATCATCA 57.336 29.630 0.00 0.00 0.00 3.07
729 765 9.884465 AGCTTTTTATTCAATTAGCGTATCATC 57.116 29.630 0.00 0.00 34.01 2.92
730 766 9.884465 GAGCTTTTTATTCAATTAGCGTATCAT 57.116 29.630 0.00 0.00 34.01 2.45
731 767 9.109393 AGAGCTTTTTATTCAATTAGCGTATCA 57.891 29.630 0.00 0.00 34.01 2.15
732 768 9.587461 GAGAGCTTTTTATTCAATTAGCGTATC 57.413 33.333 0.00 0.00 34.01 2.24
733 769 8.560374 GGAGAGCTTTTTATTCAATTAGCGTAT 58.440 33.333 0.00 0.00 34.01 3.06
734 770 7.769044 AGGAGAGCTTTTTATTCAATTAGCGTA 59.231 33.333 0.00 0.00 34.01 4.42
735 771 6.599638 AGGAGAGCTTTTTATTCAATTAGCGT 59.400 34.615 0.00 0.00 34.01 5.07
736 772 7.020914 AGGAGAGCTTTTTATTCAATTAGCG 57.979 36.000 0.00 0.00 34.01 4.26
737 773 7.067494 TGGAGGAGAGCTTTTTATTCAATTAGC 59.933 37.037 0.00 0.00 0.00 3.09
738 774 8.511604 TGGAGGAGAGCTTTTTATTCAATTAG 57.488 34.615 0.00 0.00 0.00 1.73
739 775 8.877864 TTGGAGGAGAGCTTTTTATTCAATTA 57.122 30.769 0.00 0.00 0.00 1.40
740 776 7.781324 TTGGAGGAGAGCTTTTTATTCAATT 57.219 32.000 0.00 0.00 0.00 2.32
741 777 7.968014 ATTGGAGGAGAGCTTTTTATTCAAT 57.032 32.000 0.00 0.00 0.00 2.57
742 778 7.451255 TCAATTGGAGGAGAGCTTTTTATTCAA 59.549 33.333 5.42 0.00 0.00 2.69
743 779 6.947733 TCAATTGGAGGAGAGCTTTTTATTCA 59.052 34.615 5.42 0.00 0.00 2.57
744 780 7.396540 TCAATTGGAGGAGAGCTTTTTATTC 57.603 36.000 5.42 0.00 0.00 1.75
745 781 7.968014 ATCAATTGGAGGAGAGCTTTTTATT 57.032 32.000 5.42 0.00 0.00 1.40
746 782 7.616935 TCAATCAATTGGAGGAGAGCTTTTTAT 59.383 33.333 5.42 0.00 38.30 1.40
747 783 6.947733 TCAATCAATTGGAGGAGAGCTTTTTA 59.052 34.615 5.42 0.00 38.30 1.52
748 784 5.776716 TCAATCAATTGGAGGAGAGCTTTTT 59.223 36.000 5.42 0.00 38.30 1.94
749 785 5.327732 TCAATCAATTGGAGGAGAGCTTTT 58.672 37.500 5.42 0.00 38.30 2.27
750 786 4.927049 TCAATCAATTGGAGGAGAGCTTT 58.073 39.130 5.42 0.00 38.30 3.51
751 787 4.525024 CTCAATCAATTGGAGGAGAGCTT 58.475 43.478 5.42 0.00 38.30 3.74
752 788 3.684981 GCTCAATCAATTGGAGGAGAGCT 60.685 47.826 21.11 0.00 41.03 4.09
753 789 2.617774 GCTCAATCAATTGGAGGAGAGC 59.382 50.000 18.86 17.91 39.09 4.09
754 790 4.153673 AGCTCAATCAATTGGAGGAGAG 57.846 45.455 18.86 13.81 38.30 3.20
755 791 4.471025 TGTAGCTCAATCAATTGGAGGAGA 59.529 41.667 18.86 6.23 38.30 3.71
756 792 4.774124 TGTAGCTCAATCAATTGGAGGAG 58.226 43.478 5.42 10.53 38.30 3.69
757 793 4.842531 TGTAGCTCAATCAATTGGAGGA 57.157 40.909 5.42 0.00 38.30 3.71
758 794 6.461110 AATTGTAGCTCAATCAATTGGAGG 57.539 37.500 5.42 0.00 44.85 4.30
759 795 7.318141 ACAAATTGTAGCTCAATCAATTGGAG 58.682 34.615 18.86 5.76 44.85 3.86
760 796 7.230849 ACAAATTGTAGCTCAATCAATTGGA 57.769 32.000 18.86 0.00 44.85 3.53
761 797 7.894376 AACAAATTGTAGCTCAATCAATTGG 57.106 32.000 5.42 14.49 44.85 3.16
762 798 9.199982 AGAAACAAATTGTAGCTCAATCAATTG 57.800 29.630 14.92 14.41 44.85 2.32
763 799 9.415544 GAGAAACAAATTGTAGCTCAATCAATT 57.584 29.630 17.56 10.73 44.85 2.32
764 800 8.579006 TGAGAAACAAATTGTAGCTCAATCAAT 58.421 29.630 20.83 6.30 44.85 2.57
780 816 6.460399 CGGGTTTGGTATTTCTGAGAAACAAA 60.460 38.462 10.18 12.81 0.00 2.83
809 845 5.973565 ACTTCTTGAAAACGAAGCATCTTTG 59.026 36.000 0.00 0.00 40.12 2.77
828 879 8.451748 GCGTATCCTCAAAGATTTTTAACTTCT 58.548 33.333 0.00 0.00 0.00 2.85
835 886 8.956426 TCAATTAGCGTATCCTCAAAGATTTTT 58.044 29.630 0.00 0.00 0.00 1.94
864 915 5.233988 CGATTGGAGGAGAGTATTCCATTC 58.766 45.833 5.13 5.13 40.48 2.67
867 918 2.965831 CCGATTGGAGGAGAGTATTCCA 59.034 50.000 0.00 0.00 39.84 3.53
872 923 1.688735 CATGCCGATTGGAGGAGAGTA 59.311 52.381 1.98 0.00 37.49 2.59
924 975 5.011635 TCTCTCGCCATGTATTTATAGGCAA 59.988 40.000 0.00 0.00 45.47 4.52
969 1020 5.098218 TGAACAATACACGGTTACTTTGC 57.902 39.130 0.00 0.00 0.00 3.68
971 1022 4.084223 CGCTGAACAATACACGGTTACTTT 60.084 41.667 0.00 0.00 0.00 2.66
972 1023 3.430895 CGCTGAACAATACACGGTTACTT 59.569 43.478 0.00 0.00 0.00 2.24
978 1029 1.390123 CTCACGCTGAACAATACACGG 59.610 52.381 0.00 0.00 0.00 4.94
982 1033 2.223112 CCATGCTCACGCTGAACAATAC 60.223 50.000 0.00 0.00 36.97 1.89
1180 1341 6.845280 GTCACTACTCGATCACTACGAAATAC 59.155 42.308 0.00 0.00 39.23 1.89
1181 1342 6.292008 CGTCACTACTCGATCACTACGAAATA 60.292 42.308 0.00 0.00 39.23 1.40
1182 1343 5.502058 CGTCACTACTCGATCACTACGAAAT 60.502 44.000 0.00 0.00 39.23 2.17
1246 1407 4.070552 GGCTTCTCCACGTCGCCT 62.071 66.667 0.00 0.00 37.76 5.52
1303 1464 2.724273 GCCCTTGCCGCCATTGAAT 61.724 57.895 0.00 0.00 0.00 2.57
1358 1519 3.706373 GGACCCAGAGCAAGCGGA 61.706 66.667 0.00 0.00 0.00 5.54
1628 1860 2.904866 GTTGCACGGAACCCTGCA 60.905 61.111 12.07 12.07 41.68 4.41
1831 2063 1.337384 ACGATATGGGTGCCTGCAGA 61.337 55.000 17.39 0.00 0.00 4.26
1977 2209 5.049060 ACAACTAATTTAACATGCGCACTCA 60.049 36.000 14.90 0.00 0.00 3.41
1982 2214 3.917380 TGCACAACTAATTTAACATGCGC 59.083 39.130 0.00 0.00 34.56 6.09
1991 2224 2.878406 ACTCGTGCTGCACAACTAATTT 59.122 40.909 29.86 4.48 33.40 1.82
2046 2279 4.512944 AGCATGACAGCAAGTATTATTCCG 59.487 41.667 0.00 0.00 36.85 4.30
2062 2295 6.256686 TGTTTGCAATTTTTCAAAGCATGAC 58.743 32.000 0.00 0.00 37.92 3.06
2163 2397 9.601217 GTTTAGCAATATCCATCGTATCCTTAT 57.399 33.333 0.00 0.00 0.00 1.73
2195 2429 4.497006 GGAAAGATCAGTTGGCATCAATCG 60.497 45.833 0.00 0.00 35.10 3.34
2231 4799 1.669115 GCCATCGCACGCCATAGAT 60.669 57.895 0.00 0.00 34.03 1.98
2263 4831 1.268899 GATATTGTCGACGTCCGGGAT 59.731 52.381 10.58 2.36 39.14 3.85
2272 6035 5.408356 ACCAGTGTTACAGATATTGTCGAC 58.592 41.667 9.11 9.11 41.29 4.20
2274 6037 4.804139 GGACCAGTGTTACAGATATTGTCG 59.196 45.833 0.00 0.00 41.29 4.35
2329 6835 2.681706 GATCATGCGGACAGTATCAGG 58.318 52.381 0.00 0.00 0.00 3.86
2337 6843 2.951457 TTAAGACGATCATGCGGACA 57.049 45.000 0.00 0.00 35.12 4.02
2525 9961 1.079888 GCCTCAAATTTGGTGGCCG 60.080 57.895 29.37 11.39 40.04 6.13
2625 10188 2.030540 CGTCTCCTGTACGAAACTTCCA 60.031 50.000 0.00 0.00 42.90 3.53
2635 10198 1.215647 CTGCACCCGTCTCCTGTAC 59.784 63.158 0.00 0.00 0.00 2.90
2685 10248 1.867233 GCTGTGTAGATAATGGTGCCG 59.133 52.381 0.00 0.00 0.00 5.69
2694 10257 1.123077 CCCTGCAGGCTGTGTAGATA 58.877 55.000 28.39 0.00 41.25 1.98
2700 10263 1.098050 GTATTTCCCTGCAGGCTGTG 58.902 55.000 28.39 13.92 34.51 3.66
2719 10282 1.858458 CAGGGCGTTATCACATGTACG 59.142 52.381 13.27 13.27 37.09 3.67
2760 10323 1.807886 GAGCTCGACGCCCTCTTTA 59.192 57.895 0.00 0.00 40.39 1.85
2762 10325 3.816524 CGAGCTCGACGCCCTCTT 61.817 66.667 32.06 0.00 43.02 2.85
2782 10345 0.610232 GGAAGCAAGGTCCTGTGCAT 60.610 55.000 20.96 13.30 43.42 3.96
2794 10357 0.181587 TCGACAACAAGGGGAAGCAA 59.818 50.000 0.00 0.00 0.00 3.91
2882 10445 3.213206 ACACTTGAATCTCTTGCACCA 57.787 42.857 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.