Multiple sequence alignment - TraesCS2D01G224700

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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 TraesCS2D01G224700 chr2D 100.000 2723 0 0 1 2723 192187457 192184735 0.000000e+00 5029.0
1 TraesCS2D01G224700 chr2D 88.825 698 50 10 88 759 142021229 142020534 0.000000e+00 832.0
2 TraesCS2D01G224700 chr2D 89.453 512 28 9 275 761 448510445 448509935 8.280000e-175 623.0
3 TraesCS2D01G224700 chr2D 89.301 458 30 10 1 457 391337582 391338021 8.520000e-155 556.0
4 TraesCS2D01G224700 chr2B 95.031 966 17 10 763 1724 248136860 248137798 0.000000e+00 1489.0
5 TraesCS2D01G224700 chr2B 85.517 725 66 20 68 759 134248566 134247848 0.000000e+00 721.0
6 TraesCS2D01G224700 chr2B 88.124 421 26 9 2326 2723 248138502 248138921 1.900000e-131 479.0
7 TraesCS2D01G224700 chr2B 81.534 639 35 22 1749 2333 248137795 248138404 1.490000e-122 449.0
8 TraesCS2D01G224700 chr2B 77.538 325 55 12 1003 1319 728398394 728398080 2.150000e-41 180.0
9 TraesCS2D01G224700 chr2A 96.875 832 16 4 903 1734 205910830 205911651 0.000000e+00 1384.0
10 TraesCS2D01G224700 chr2A 94.581 609 25 4 2121 2723 205913954 205914560 0.000000e+00 935.0
11 TraesCS2D01G224700 chr2A 89.700 534 28 3 253 759 68539839 68540372 0.000000e+00 656.0
12 TraesCS2D01G224700 chr2A 91.756 279 14 5 1849 2122 205913596 205913870 1.980000e-101 379.0
13 TraesCS2D01G224700 chr2A 94.286 105 5 1 1733 1836 205913305 205913409 2.810000e-35 159.0
14 TraesCS2D01G224700 chr2A 97.561 41 0 1 795 835 205910709 205910748 4.870000e-08 69.4
15 TraesCS2D01G224700 chr1D 89.313 786 47 11 1 759 40864289 40863514 0.000000e+00 952.0
16 TraesCS2D01G224700 chr1D 88.604 781 52 16 5 759 410251368 410250599 0.000000e+00 915.0
17 TraesCS2D01G224700 chr1D 91.941 546 38 5 65 608 62438383 62437842 0.000000e+00 760.0
18 TraesCS2D01G224700 chr1D 83.004 253 37 3 1067 1319 262341552 262341798 9.810000e-55 224.0
19 TraesCS2D01G224700 chr4A 90.669 718 43 9 56 759 95193263 95193970 0.000000e+00 933.0
20 TraesCS2D01G224700 chr4A 87.006 785 66 12 1 759 507919028 507918254 0.000000e+00 852.0
21 TraesCS2D01G224700 chr4A 87.258 722 54 18 1 695 123254390 123253680 0.000000e+00 789.0
22 TraesCS2D01G224700 chr4A 82.592 787 61 26 1 759 712564496 712565234 2.300000e-175 625.0
23 TraesCS2D01G224700 chr4A 82.500 440 55 6 1 427 685796407 685796837 1.540000e-97 366.0
24 TraesCS2D01G224700 chr4A 74.102 668 134 29 1003 1651 5115255 5114608 3.500000e-59 239.0
25 TraesCS2D01G224700 chr6D 88.662 785 44 19 1 762 300294186 300294948 0.000000e+00 915.0
26 TraesCS2D01G224700 chr6D 89.124 708 37 9 1 695 414103764 414104444 0.000000e+00 845.0
27 TraesCS2D01G224700 chr6D 89.029 556 48 5 1 543 141140942 141141497 0.000000e+00 676.0
28 TraesCS2D01G224700 chr6D 95.652 69 3 0 693 761 33214604 33214672 7.970000e-21 111.0
29 TraesCS2D01G224700 chr7B 91.266 561 32 6 1 547 162112742 162112185 0.000000e+00 749.0
30 TraesCS2D01G224700 chr7B 86.027 730 62 14 64 761 440217043 440217764 0.000000e+00 747.0
31 TraesCS2D01G224700 chr7B 82.881 590 40 29 199 762 439255195 439255749 8.820000e-130 473.0
32 TraesCS2D01G224700 chr7B 95.714 70 3 0 693 762 72981989 72982058 2.220000e-21 113.0
33 TraesCS2D01G224700 chr5B 83.611 781 66 21 10 761 454692513 454691766 0.000000e+00 676.0
34 TraesCS2D01G224700 chr5B 75.371 337 65 13 994 1321 17952349 17952676 2.180000e-31 147.0
35 TraesCS2D01G224700 chr3D 83.919 740 62 25 64 762 355894578 355895301 0.000000e+00 654.0
36 TraesCS2D01G224700 chr3D 88.934 244 26 1 2480 2723 570840246 570840004 1.580000e-77 300.0
37 TraesCS2D01G224700 chr5D 84.202 652 65 17 64 695 50861091 50861724 1.400000e-167 599.0
38 TraesCS2D01G224700 chr5D 76.398 322 62 10 1003 1319 25042321 25042633 7.800000e-36 161.0
39 TraesCS2D01G224700 chr5D 93.671 79 3 2 693 771 375200331 375200255 1.710000e-22 117.0
40 TraesCS2D01G224700 chr3B 82.166 757 67 27 32 761 460110443 460111158 3.020000e-164 588.0
41 TraesCS2D01G224700 chr3A 78.771 716 115 22 990 1687 107047935 107048631 1.920000e-121 446.0
42 TraesCS2D01G224700 chr3A 88.800 250 27 1 2474 2723 703844009 703844257 3.410000e-79 305.0
43 TraesCS2D01G224700 chr1A 75.079 634 128 25 1003 1623 337658533 337657917 4.470000e-68 268.0
44 TraesCS2D01G224700 chr1A 81.176 255 38 6 1067 1319 337629745 337629499 2.140000e-46 196.0
45 TraesCS2D01G224700 chr1B 75.000 632 129 24 1003 1623 349547301 349546688 5.780000e-67 265.0
46 TraesCS2D01G224700 chr4D 74.595 618 120 26 1003 1605 465357896 465358491 1.260000e-58 237.0
47 TraesCS2D01G224700 chr6B 84.000 150 10 5 625 761 663708546 663708694 6.120000e-27 132.0


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 TraesCS2D01G224700 chr2D 192184735 192187457 2722 True 5029.000000 5029 100.000000 1 2723 1 chr2D.!!$R2 2722
1 TraesCS2D01G224700 chr2D 142020534 142021229 695 True 832.000000 832 88.825000 88 759 1 chr2D.!!$R1 671
2 TraesCS2D01G224700 chr2D 448509935 448510445 510 True 623.000000 623 89.453000 275 761 1 chr2D.!!$R3 486
3 TraesCS2D01G224700 chr2B 248136860 248138921 2061 False 805.666667 1489 88.229667 763 2723 3 chr2B.!!$F1 1960
4 TraesCS2D01G224700 chr2B 134247848 134248566 718 True 721.000000 721 85.517000 68 759 1 chr2B.!!$R1 691
5 TraesCS2D01G224700 chr2A 68539839 68540372 533 False 656.000000 656 89.700000 253 759 1 chr2A.!!$F1 506
6 TraesCS2D01G224700 chr2A 205910709 205914560 3851 False 585.280000 1384 95.011800 795 2723 5 chr2A.!!$F2 1928
7 TraesCS2D01G224700 chr1D 40863514 40864289 775 True 952.000000 952 89.313000 1 759 1 chr1D.!!$R1 758
8 TraesCS2D01G224700 chr1D 410250599 410251368 769 True 915.000000 915 88.604000 5 759 1 chr1D.!!$R3 754
9 TraesCS2D01G224700 chr1D 62437842 62438383 541 True 760.000000 760 91.941000 65 608 1 chr1D.!!$R2 543
10 TraesCS2D01G224700 chr4A 95193263 95193970 707 False 933.000000 933 90.669000 56 759 1 chr4A.!!$F1 703
11 TraesCS2D01G224700 chr4A 507918254 507919028 774 True 852.000000 852 87.006000 1 759 1 chr4A.!!$R3 758
12 TraesCS2D01G224700 chr4A 123253680 123254390 710 True 789.000000 789 87.258000 1 695 1 chr4A.!!$R2 694
13 TraesCS2D01G224700 chr4A 712564496 712565234 738 False 625.000000 625 82.592000 1 759 1 chr4A.!!$F3 758
14 TraesCS2D01G224700 chr4A 5114608 5115255 647 True 239.000000 239 74.102000 1003 1651 1 chr4A.!!$R1 648
15 TraesCS2D01G224700 chr6D 300294186 300294948 762 False 915.000000 915 88.662000 1 762 1 chr6D.!!$F3 761
16 TraesCS2D01G224700 chr6D 414103764 414104444 680 False 845.000000 845 89.124000 1 695 1 chr6D.!!$F4 694
17 TraesCS2D01G224700 chr6D 141140942 141141497 555 False 676.000000 676 89.029000 1 543 1 chr6D.!!$F2 542
18 TraesCS2D01G224700 chr7B 162112185 162112742 557 True 749.000000 749 91.266000 1 547 1 chr7B.!!$R1 546
19 TraesCS2D01G224700 chr7B 440217043 440217764 721 False 747.000000 747 86.027000 64 761 1 chr7B.!!$F3 697
20 TraesCS2D01G224700 chr7B 439255195 439255749 554 False 473.000000 473 82.881000 199 762 1 chr7B.!!$F2 563
21 TraesCS2D01G224700 chr5B 454691766 454692513 747 True 676.000000 676 83.611000 10 761 1 chr5B.!!$R1 751
22 TraesCS2D01G224700 chr3D 355894578 355895301 723 False 654.000000 654 83.919000 64 762 1 chr3D.!!$F1 698
23 TraesCS2D01G224700 chr5D 50861091 50861724 633 False 599.000000 599 84.202000 64 695 1 chr5D.!!$F2 631
24 TraesCS2D01G224700 chr3B 460110443 460111158 715 False 588.000000 588 82.166000 32 761 1 chr3B.!!$F1 729
25 TraesCS2D01G224700 chr3A 107047935 107048631 696 False 446.000000 446 78.771000 990 1687 1 chr3A.!!$F1 697
26 TraesCS2D01G224700 chr1A 337657917 337658533 616 True 268.000000 268 75.079000 1003 1623 1 chr1A.!!$R2 620
27 TraesCS2D01G224700 chr1B 349546688 349547301 613 True 265.000000 265 75.000000 1003 1623 1 chr1B.!!$R1 620
28 TraesCS2D01G224700 chr4D 465357896 465358491 595 False 237.000000 237 74.595000 1003 1605 1 chr4D.!!$F1 602


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
798 926 0.032678 CCGATGCCGCACTAAGAGAT 59.967 55.0 0.0 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 3875 0.402504 AGGGGCAAACGGTATTCACA 59.597 50.0 0.0 0.0 0.0 3.58 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
34 35 0.738762 CGAGACGGAGGAGTACGACA 60.739 60.000 0.00 0.00 0.00 4.35
187 218 0.525668 CTTCGAGTTCGTCCCCATCG 60.526 60.000 1.07 0.00 40.80 3.84
529 627 6.005198 CCACCCCTCTAGTACTAGTATTGAG 58.995 48.000 25.58 16.58 34.84 3.02
767 895 7.174946 GTCTGCTAGAGTTGCTCTAATAGAGAT 59.825 40.741 20.58 3.32 45.07 2.75
769 897 8.926092 TGCTAGAGTTGCTCTAATAGAGATAA 57.074 34.615 20.58 11.44 45.07 1.75
793 921 1.066716 AGTAAACCGATGCCGCACTAA 60.067 47.619 0.00 0.00 0.00 2.24
794 922 1.326548 GTAAACCGATGCCGCACTAAG 59.673 52.381 0.00 0.00 0.00 2.18
795 923 0.036765 AAACCGATGCCGCACTAAGA 60.037 50.000 0.00 0.00 0.00 2.10
796 924 0.460284 AACCGATGCCGCACTAAGAG 60.460 55.000 0.00 0.00 0.00 2.85
798 926 0.032678 CCGATGCCGCACTAAGAGAT 59.967 55.000 0.00 0.00 0.00 2.75
799 927 1.269723 CCGATGCCGCACTAAGAGATA 59.730 52.381 0.00 0.00 0.00 1.98
858 989 5.698741 TGGAGTATTGAGGAATCACATGT 57.301 39.130 0.00 0.00 0.00 3.21
859 990 5.674525 TGGAGTATTGAGGAATCACATGTC 58.325 41.667 0.00 0.00 0.00 3.06
860 991 5.189539 TGGAGTATTGAGGAATCACATGTCA 59.810 40.000 0.00 0.00 0.00 3.58
861 992 5.525378 GGAGTATTGAGGAATCACATGTCAC 59.475 44.000 0.00 0.00 0.00 3.67
862 993 6.053632 AGTATTGAGGAATCACATGTCACA 57.946 37.500 0.00 0.00 0.00 3.58
863 994 6.656902 AGTATTGAGGAATCACATGTCACAT 58.343 36.000 0.00 0.00 0.00 3.21
864 995 5.830000 ATTGAGGAATCACATGTCACATG 57.170 39.130 16.68 16.68 0.00 3.21
895 1069 3.423123 GCACGTGATCGAAAACCAACTAG 60.423 47.826 22.23 0.00 40.62 2.57
896 1070 3.122948 CACGTGATCGAAAACCAACTAGG 59.877 47.826 10.90 0.00 41.25 3.02
897 1071 3.006110 ACGTGATCGAAAACCAACTAGGA 59.994 43.478 0.00 0.00 39.72 2.94
898 1072 3.612860 CGTGATCGAAAACCAACTAGGAG 59.387 47.826 0.00 0.00 39.16 3.69
899 1073 4.566987 GTGATCGAAAACCAACTAGGAGT 58.433 43.478 0.00 0.00 41.22 3.85
900 1074 5.620654 CGTGATCGAAAACCAACTAGGAGTA 60.621 44.000 0.00 0.00 39.16 2.59
901 1075 5.805994 GTGATCGAAAACCAACTAGGAGTAG 59.194 44.000 0.00 0.00 41.22 2.57
902 1076 5.479375 TGATCGAAAACCAACTAGGAGTAGT 59.521 40.000 0.00 0.00 41.61 2.73
903 1077 6.660521 TGATCGAAAACCAACTAGGAGTAGTA 59.339 38.462 0.00 0.00 38.66 1.82
991 1165 2.125773 AGGAGTACTACACCAGTCGG 57.874 55.000 8.10 0.00 38.80 4.79
992 1166 0.455005 GGAGTACTACACCAGTCGGC 59.545 60.000 0.00 0.00 38.80 5.54
993 1167 0.098376 GAGTACTACACCAGTCGGCG 59.902 60.000 0.00 0.00 38.80 6.46
1810 3661 6.203530 CCTGTACCAATAACTGAGCATGTATG 59.796 42.308 0.00 0.00 0.00 2.39
1842 3754 8.035394 ACTGTGTATGTATTTCTACCTTCTGTG 58.965 37.037 0.00 0.00 0.00 3.66
1844 3756 8.590204 TGTGTATGTATTTCTACCTTCTGTGAA 58.410 33.333 0.00 0.00 0.00 3.18
1845 3757 9.601217 GTGTATGTATTTCTACCTTCTGTGAAT 57.399 33.333 0.00 0.00 0.00 2.57
1878 3903 0.525761 CGTTTGCCCCTAATGGTGTG 59.474 55.000 0.00 0.00 0.00 3.82
1879 3904 1.627864 GTTTGCCCCTAATGGTGTGT 58.372 50.000 0.00 0.00 0.00 3.72
1880 3905 2.797786 GTTTGCCCCTAATGGTGTGTA 58.202 47.619 0.00 0.00 0.00 2.90
1881 3906 2.490509 GTTTGCCCCTAATGGTGTGTAC 59.509 50.000 0.00 0.00 0.00 2.90
1882 3907 1.363246 TGCCCCTAATGGTGTGTACA 58.637 50.000 0.00 0.00 0.00 2.90
1890 3916 6.183361 CCCCTAATGGTGTGTACATGAGATTA 60.183 42.308 0.00 0.15 29.70 1.75
1945 3972 7.493645 TCATGTTAGCAACTCTTCATCATGTAG 59.506 37.037 0.00 0.00 34.02 2.74
2032 4088 6.620678 TGGTTTTGCTGAATAATACTCAAGC 58.379 36.000 0.00 0.00 0.00 4.01
2062 4118 1.858458 GGCAAAAGAAAACGAAGTGCC 59.142 47.619 0.00 0.00 45.00 5.01
2128 4271 6.821388 AGAAGATGCCTTATACAGTACAAGG 58.179 40.000 12.77 12.77 41.53 3.61
2161 4304 2.376695 TGGAGAATAGGGTCCCTACG 57.623 55.000 20.58 0.00 39.10 3.51
2230 4376 7.516481 CACTAATCAGTCATTTGTCAAGTCAG 58.484 38.462 0.00 0.00 29.03 3.51
2231 4377 5.368256 AATCAGTCATTTGTCAAGTCAGC 57.632 39.130 0.00 0.00 0.00 4.26
2232 4378 3.807553 TCAGTCATTTGTCAAGTCAGCA 58.192 40.909 0.00 0.00 0.00 4.41
2233 4379 4.392047 TCAGTCATTTGTCAAGTCAGCAT 58.608 39.130 0.00 0.00 0.00 3.79
2234 4380 5.550290 TCAGTCATTTGTCAAGTCAGCATA 58.450 37.500 0.00 0.00 0.00 3.14
2235 4381 6.175471 TCAGTCATTTGTCAAGTCAGCATAT 58.825 36.000 0.00 0.00 0.00 1.78
2236 4382 7.330262 TCAGTCATTTGTCAAGTCAGCATATA 58.670 34.615 0.00 0.00 0.00 0.86
2237 4383 7.493645 TCAGTCATTTGTCAAGTCAGCATATAG 59.506 37.037 0.00 0.00 0.00 1.31
2238 4384 6.259608 AGTCATTTGTCAAGTCAGCATATAGC 59.740 38.462 0.00 0.00 46.19 2.97
2269 4442 4.899352 ACTCACTGCTTAGAGTGGAAAT 57.101 40.909 10.33 0.00 43.09 2.17
2293 4466 1.228459 AAACCGAGGGGAAACTGCC 60.228 57.895 0.00 0.00 36.97 4.85
2422 4700 4.147321 ACATGACTGCAAAAATCCTCTGT 58.853 39.130 0.00 0.00 0.00 3.41
2425 4726 5.689383 TGACTGCAAAAATCCTCTGTTAC 57.311 39.130 0.00 0.00 0.00 2.50
2449 4750 6.551227 ACATACATCTAGATACAGTGCTCCAA 59.449 38.462 4.54 0.00 0.00 3.53
2541 4843 7.495934 AGGAAACTCTATTGACACCAAATATCG 59.504 37.037 0.00 0.00 32.90 2.92
2566 4868 6.202226 GTTTCAAAGTGGTGACTGAGATTTC 58.798 40.000 0.00 0.00 30.61 2.17
2596 4898 4.335594 CACAAGGGACCTTTCGATAATTCC 59.664 45.833 0.00 0.00 33.42 3.01
2717 5019 3.582208 AGTCTTATCTCCCTCATCATGCC 59.418 47.826 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 2.507324 GAGAAGGACGCGGCAGAC 60.507 66.667 17.00 3.41 0.00 3.51
187 218 2.520741 CTCCTCGGGCTCCTCCTC 60.521 72.222 0.00 0.00 34.39 3.71
235 284 2.494918 CGACGAAATCTCCGGCCT 59.505 61.111 0.00 0.00 0.00 5.19
614 726 1.135402 GTTTCGCGGGAGAAATTGCAT 60.135 47.619 6.13 0.00 41.46 3.96
767 895 2.883574 CGGCATCGGTTTACTCTGTTA 58.116 47.619 0.00 0.00 0.00 2.41
769 897 0.739813 GCGGCATCGGTTTACTCTGT 60.740 55.000 0.00 0.00 36.79 3.41
793 921 5.221422 GCCAGACTTTGCTATCAGTATCTCT 60.221 44.000 0.00 0.00 0.00 3.10
794 922 4.987912 GCCAGACTTTGCTATCAGTATCTC 59.012 45.833 0.00 0.00 0.00 2.75
795 923 4.653341 AGCCAGACTTTGCTATCAGTATCT 59.347 41.667 0.00 0.00 35.69 1.98
796 924 4.954875 AGCCAGACTTTGCTATCAGTATC 58.045 43.478 0.00 0.00 35.69 2.24
798 926 3.769300 TGAGCCAGACTTTGCTATCAGTA 59.231 43.478 0.00 0.00 38.11 2.74
799 927 2.568956 TGAGCCAGACTTTGCTATCAGT 59.431 45.455 0.00 0.00 38.11 3.41
859 990 5.004156 CGATCACGTGCTATATGATCATGTG 59.996 44.000 18.72 14.69 46.01 3.21
860 991 5.098211 CGATCACGTGCTATATGATCATGT 58.902 41.667 18.72 14.26 46.01 3.21
861 992 5.335127 TCGATCACGTGCTATATGATCATG 58.665 41.667 18.72 2.74 46.01 3.07
862 993 5.567138 TCGATCACGTGCTATATGATCAT 57.433 39.130 13.81 13.81 46.01 2.45
863 994 5.371115 TTCGATCACGTGCTATATGATCA 57.629 39.130 11.67 0.00 46.01 2.92
864 995 6.400091 GGTTTTCGATCACGTGCTATATGATC 60.400 42.308 11.67 5.88 43.48 2.92
895 1069 8.156822 ACTACTGGGGTACTATATACTACTCC 57.843 42.308 10.18 10.18 34.43 3.85
897 1071 9.851267 AGTACTACTGGGGTACTATATACTACT 57.149 37.037 11.35 0.00 45.22 2.57
898 1072 9.883142 CAGTACTACTGGGGTACTATATACTAC 57.117 40.741 8.19 0.00 45.27 2.73
991 1165 4.899239 CTCCTCCATGCCGACCGC 62.899 72.222 0.00 0.00 38.31 5.68
992 1166 4.227134 CCTCCTCCATGCCGACCG 62.227 72.222 0.00 0.00 0.00 4.79
993 1167 2.764128 TCCTCCTCCATGCCGACC 60.764 66.667 0.00 0.00 0.00 4.79
1734 1929 9.678260 AGCCCTGATTCTAGCATTATTTTATAG 57.322 33.333 0.00 0.00 0.00 1.31
1735 1930 9.453572 CAGCCCTGATTCTAGCATTATTTTATA 57.546 33.333 0.00 0.00 0.00 0.98
1736 1931 7.395489 CCAGCCCTGATTCTAGCATTATTTTAT 59.605 37.037 0.00 0.00 0.00 1.40
1738 1933 5.537674 CCAGCCCTGATTCTAGCATTATTTT 59.462 40.000 0.00 0.00 0.00 1.82
1810 3661 7.980099 AGGTAGAAATACATACACAGTGTAAGC 59.020 37.037 17.43 7.31 36.31 3.09
1812 3663 9.865321 GAAGGTAGAAATACATACACAGTGTAA 57.135 33.333 17.43 1.71 36.31 2.41
1816 3667 8.035394 CACAGAAGGTAGAAATACATACACAGT 58.965 37.037 0.00 0.00 0.00 3.55
1846 3758 3.492829 GGGGCAAACGGTATTCACAAAAA 60.493 43.478 0.00 0.00 0.00 1.94
1850 3875 0.402504 AGGGGCAAACGGTATTCACA 59.597 50.000 0.00 0.00 0.00 3.58
1878 3903 8.543774 GTTGTTACAGCAGATAATCTCATGTAC 58.456 37.037 0.00 0.00 29.34 2.90
1879 3904 8.257306 TGTTGTTACAGCAGATAATCTCATGTA 58.743 33.333 0.00 0.00 0.00 2.29
1880 3905 7.105588 TGTTGTTACAGCAGATAATCTCATGT 58.894 34.615 0.00 0.00 0.00 3.21
1881 3906 7.543947 TGTTGTTACAGCAGATAATCTCATG 57.456 36.000 0.00 0.00 0.00 3.07
1882 3907 9.836864 TTATGTTGTTACAGCAGATAATCTCAT 57.163 29.630 8.04 0.00 37.77 2.90
1890 3916 7.315142 CCAATTGTTATGTTGTTACAGCAGAT 58.685 34.615 8.04 0.00 37.77 2.90
1945 3972 4.005650 TGCTGGATTGAGATCAAACTCAC 58.994 43.478 0.00 0.00 44.94 3.51
2032 4088 4.085619 CGTTTTCTTTTGCCGTCATTCAAG 60.086 41.667 0.00 0.00 0.00 3.02
2062 4118 5.408604 GGGCTATTTATAACATGACTCACCG 59.591 44.000 0.00 0.00 0.00 4.94
2099 4155 9.197306 TGTACTGTATAAGGCATCTTCTAAGAA 57.803 33.333 0.00 0.00 38.77 2.52
2119 4262 3.693085 AGCTGATTTCATGCCTTGTACTG 59.307 43.478 0.00 0.00 0.00 2.74
2120 4263 3.960571 AGCTGATTTCATGCCTTGTACT 58.039 40.909 0.00 0.00 0.00 2.73
2128 4271 4.650754 ATTCTCCAAGCTGATTTCATGC 57.349 40.909 0.00 0.00 0.00 4.06
2161 4304 3.629398 CAGCATATTGTCCAACCCTCTTC 59.371 47.826 0.00 0.00 0.00 2.87
2230 4376 7.360438 GCAGTGAGTAATTTAGGTGCTATATGC 60.360 40.741 0.00 0.00 43.25 3.14
2231 4377 7.875041 AGCAGTGAGTAATTTAGGTGCTATATG 59.125 37.037 0.00 0.00 38.23 1.78
2232 4378 7.967908 AGCAGTGAGTAATTTAGGTGCTATAT 58.032 34.615 0.00 0.00 38.23 0.86
2233 4379 7.361457 AGCAGTGAGTAATTTAGGTGCTATA 57.639 36.000 0.00 0.00 38.23 1.31
2234 4380 6.240549 AGCAGTGAGTAATTTAGGTGCTAT 57.759 37.500 0.00 0.00 38.23 2.97
2235 4381 5.677319 AGCAGTGAGTAATTTAGGTGCTA 57.323 39.130 0.00 0.00 38.23 3.49
2236 4382 4.559862 AGCAGTGAGTAATTTAGGTGCT 57.440 40.909 0.00 0.00 35.22 4.40
2237 4383 6.106673 TCTAAGCAGTGAGTAATTTAGGTGC 58.893 40.000 0.00 0.00 0.00 5.01
2238 4384 7.276658 CACTCTAAGCAGTGAGTAATTTAGGTG 59.723 40.741 0.00 0.00 45.92 4.00
2239 4385 7.324178 CACTCTAAGCAGTGAGTAATTTAGGT 58.676 38.462 0.00 0.00 45.92 3.08
2240 4386 6.758886 CCACTCTAAGCAGTGAGTAATTTAGG 59.241 42.308 3.59 0.00 45.92 2.69
2241 4387 7.548097 TCCACTCTAAGCAGTGAGTAATTTAG 58.452 38.462 3.59 0.00 45.92 1.85
2242 4388 7.476540 TCCACTCTAAGCAGTGAGTAATTTA 57.523 36.000 3.59 0.00 45.92 1.40
2243 4389 6.360370 TCCACTCTAAGCAGTGAGTAATTT 57.640 37.500 3.59 0.00 45.92 1.82
2244 4390 6.360370 TTCCACTCTAAGCAGTGAGTAATT 57.640 37.500 3.59 0.00 45.92 1.40
2245 4391 6.360370 TTTCCACTCTAAGCAGTGAGTAAT 57.640 37.500 3.59 0.00 45.92 1.89
2246 4392 5.801531 TTTCCACTCTAAGCAGTGAGTAA 57.198 39.130 3.59 0.00 45.92 2.24
2247 4393 6.360370 AATTTCCACTCTAAGCAGTGAGTA 57.640 37.500 3.59 0.00 45.92 2.59
2248 4394 4.899352 ATTTCCACTCTAAGCAGTGAGT 57.101 40.909 3.59 2.03 45.92 3.41
2249 4395 7.981789 TGTATAATTTCCACTCTAAGCAGTGAG 59.018 37.037 3.59 1.42 45.92 3.51
2250 4396 7.847096 TGTATAATTTCCACTCTAAGCAGTGA 58.153 34.615 3.59 0.00 45.92 3.41
2251 4397 8.492673 TTGTATAATTTCCACTCTAAGCAGTG 57.507 34.615 0.00 0.00 43.13 3.66
2252 4398 8.947115 GTTTGTATAATTTCCACTCTAAGCAGT 58.053 33.333 0.00 0.00 0.00 4.40
2253 4399 8.398665 GGTTTGTATAATTTCCACTCTAAGCAG 58.601 37.037 0.00 0.00 0.00 4.24
2254 4400 7.065324 CGGTTTGTATAATTTCCACTCTAAGCA 59.935 37.037 0.00 0.00 0.00 3.91
2269 4442 4.581868 CAGTTTCCCCTCGGTTTGTATAA 58.418 43.478 0.00 0.00 0.00 0.98
2293 4466 2.736721 CCGGTCGCATATATTTCCACTG 59.263 50.000 0.00 0.00 0.00 3.66
2422 4700 7.724061 TGGAGCACTGTATCTAGATGTATGTAA 59.276 37.037 15.79 0.00 0.00 2.41
2425 4726 6.581171 TGGAGCACTGTATCTAGATGTATG 57.419 41.667 15.79 9.14 0.00 2.39
2449 4750 3.583086 CCACTGGGATAACGGAGGATATT 59.417 47.826 0.00 0.00 35.59 1.28
2541 4843 3.541632 TCTCAGTCACCACTTTGAAACC 58.458 45.455 0.00 0.00 0.00 3.27
2587 4889 8.230486 GGATATGTAGCTTGTTTGGAATTATCG 58.770 37.037 0.00 0.00 0.00 2.92
2596 4898 5.755375 ACATCGAGGATATGTAGCTTGTTTG 59.245 40.000 3.06 0.00 35.82 2.93



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

AutoCloner maintained by Alex Coulton.