Multiple sequence alignment - TraesCS3D01G276100

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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 TraesCS3D01G276100 chr3D 100.000 4036 0 0 1 4036 382809164 382805129 0.000000e+00 7454.0
1 TraesCS3D01G276100 chr3D 89.880 1581 82 23 1945 3476 382754356 382752805 0.000000e+00 1962.0
2 TraesCS3D01G276100 chr3D 88.224 1622 137 25 1409 2980 383111962 383110345 0.000000e+00 1888.0
3 TraesCS3D01G276100 chr3D 84.810 474 59 4 1016 1489 382777525 382777065 7.900000e-127 464.0
4 TraesCS3D01G276100 chr3D 89.972 359 33 2 1536 1891 382777064 382776706 1.020000e-125 460.0
5 TraesCS3D01G276100 chr3D 81.845 336 35 15 967 1288 383113423 383113100 4.000000e-65 259.0
6 TraesCS3D01G276100 chr3D 87.288 236 9 5 2315 2549 382796025 382795810 2.410000e-62 250.0
7 TraesCS3D01G276100 chr3D 98.077 52 1 0 2677 2728 515230690 515230639 1.540000e-14 91.6
8 TraesCS3D01G276100 chr3D 81.013 79 15 0 2650 2728 143460095 143460173 3.370000e-06 63.9
9 TraesCS3D01G276100 chr3B 90.848 2513 175 24 1016 3476 498368810 498366301 0.000000e+00 3315.0
10 TraesCS3D01G276100 chr3B 87.002 1631 148 26 1412 2980 498729123 498727495 0.000000e+00 1779.0
11 TraesCS3D01G276100 chr3B 96.752 739 20 4 3005 3740 498432916 498432179 0.000000e+00 1229.0
12 TraesCS3D01G276100 chr3B 85.818 691 89 3 1040 1730 498453552 498452871 0.000000e+00 725.0
13 TraesCS3D01G276100 chr3B 97.712 306 6 1 3731 4036 498409723 498409419 3.570000e-145 525.0
14 TraesCS3D01G276100 chr3B 82.318 509 73 12 1436 1937 498917228 498916730 3.730000e-115 425.0
15 TraesCS3D01G276100 chr3B 93.985 266 16 0 2284 2549 498392903 498392638 1.750000e-108 403.0
16 TraesCS3D01G276100 chr3B 93.722 223 10 1 3254 3476 498666339 498666121 8.360000e-87 331.0
17 TraesCS3D01G276100 chr3B 84.337 332 38 11 967 1288 498730591 498730264 3.030000e-81 313.0
18 TraesCS3D01G276100 chr3B 93.678 174 8 2 183 353 633396634 633396807 1.440000e-64 257.0
19 TraesCS3D01G276100 chr3B 94.366 142 7 1 1 141 734998264 734998123 2.440000e-52 217.0
20 TraesCS3D01G276100 chr3B 83.688 141 20 2 714 851 5463824 5463684 3.270000e-26 130.0
21 TraesCS3D01G276100 chr3B 98.438 64 1 0 3872 3935 498409957 498409894 3.300000e-21 113.0
22 TraesCS3D01G276100 chr3B 98.438 64 1 0 3872 3935 792715818 792715881 3.300000e-21 113.0
23 TraesCS3D01G276100 chr3B 82.203 118 8 6 648 765 464165809 464165913 5.560000e-14 89.8
24 TraesCS3D01G276100 chr3B 82.301 113 6 7 648 760 464332800 464332898 7.190000e-13 86.1
25 TraesCS3D01G276100 chr3B 81.356 118 9 6 648 765 464090219 464090323 2.580000e-12 84.2
26 TraesCS3D01G276100 chr3A 91.477 1584 110 12 968 2544 505737891 505736326 0.000000e+00 2154.0
27 TraesCS3D01G276100 chr3A 87.706 1635 138 27 1406 2980 506229640 506228009 0.000000e+00 1847.0
28 TraesCS3D01G276100 chr3A 92.621 515 25 8 2542 3045 505723525 505723013 0.000000e+00 728.0
29 TraesCS3D01G276100 chr3A 94.981 259 7 2 3220 3476 505722851 505722597 6.280000e-108 401.0
30 TraesCS3D01G276100 chr3A 98.077 52 1 0 2677 2728 649772531 649772480 1.540000e-14 91.6
31 TraesCS3D01G276100 chr7D 97.268 915 14 2 1 904 280660 279746 0.000000e+00 1541.0
32 TraesCS3D01G276100 chr7D 96.090 665 22 2 1 663 124502495 124503157 0.000000e+00 1081.0
33 TraesCS3D01G276100 chr4D 97.262 913 15 6 1 903 484193541 484192629 0.000000e+00 1539.0
34 TraesCS3D01G276100 chr4D 89.109 101 8 2 806 903 39238845 39238745 5.480000e-24 122.0
35 TraesCS3D01G276100 chr6D 95.524 916 15 6 1 905 108244590 108243690 0.000000e+00 1441.0
36 TraesCS3D01G276100 chr4B 86.869 693 63 22 200 884 128948506 128949178 0.000000e+00 750.0
37 TraesCS3D01G276100 chr1A 88.095 588 61 5 323 903 492887625 492888210 0.000000e+00 689.0
38 TraesCS3D01G276100 chr1A 93.617 188 10 2 1 188 17870706 17870521 3.070000e-71 279.0
39 TraesCS3D01G276100 chr1A 87.000 100 11 2 806 903 436448122 436448221 1.190000e-20 111.0
40 TraesCS3D01G276100 chr4A 95.508 423 15 2 310 728 616659028 616659450 0.000000e+00 673.0
41 TraesCS3D01G276100 chr2A 86.265 597 62 7 310 903 278542051 278541472 7.360000e-177 630.0
42 TraesCS3D01G276100 chr2B 93.043 345 18 3 183 522 717363054 717362711 2.170000e-137 499.0
43 TraesCS3D01G276100 chr2B 80.537 149 17 10 786 926 82485855 82485711 1.980000e-18 104.0
44 TraesCS3D01G276100 chr5D 94.709 189 7 2 1 188 539737961 539737775 1.420000e-74 291.0
45 TraesCS3D01G276100 chr7B 93.642 173 8 2 183 353 226614691 226614862 5.180000e-64 255.0
46 TraesCS3D01G276100 chr5A 89.385 179 13 4 1 173 701072712 701072534 1.890000e-53 220.0
47 TraesCS3D01G276100 chrUn 88.827 179 15 4 1 175 110795406 110795229 8.790000e-52 215.0
48 TraesCS3D01G276100 chrUn 83.688 141 20 2 714 851 36271597 36271457 3.270000e-26 130.0
49 TraesCS3D01G276100 chrUn 83.688 141 20 2 714 851 320087798 320087938 3.270000e-26 130.0
50 TraesCS3D01G276100 chr7A 85.915 142 16 3 714 851 625072283 625072142 9.040000e-32 148.0
51 TraesCS3D01G276100 chr7A 88.119 101 9 3 806 904 688024562 688024661 2.550000e-22 117.0


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 TraesCS3D01G276100 chr3D 382805129 382809164 4035 True 7454.0 7454 100.0000 1 4036 1 chr3D.!!$R3 4035
1 TraesCS3D01G276100 chr3D 382752805 382754356 1551 True 1962.0 1962 89.8800 1945 3476 1 chr3D.!!$R1 1531
2 TraesCS3D01G276100 chr3D 383110345 383113423 3078 True 1073.5 1888 85.0345 967 2980 2 chr3D.!!$R6 2013
3 TraesCS3D01G276100 chr3D 382776706 382777525 819 True 462.0 464 87.3910 1016 1891 2 chr3D.!!$R5 875
4 TraesCS3D01G276100 chr3B 498366301 498368810 2509 True 3315.0 3315 90.8480 1016 3476 1 chr3B.!!$R2 2460
5 TraesCS3D01G276100 chr3B 498432179 498432916 737 True 1229.0 1229 96.7520 3005 3740 1 chr3B.!!$R4 735
6 TraesCS3D01G276100 chr3B 498727495 498730591 3096 True 1046.0 1779 85.6695 967 2980 2 chr3B.!!$R10 2013
7 TraesCS3D01G276100 chr3B 498452871 498453552 681 True 725.0 725 85.8180 1040 1730 1 chr3B.!!$R5 690
8 TraesCS3D01G276100 chr3B 498409419 498409957 538 True 319.0 525 98.0750 3731 4036 2 chr3B.!!$R9 305
9 TraesCS3D01G276100 chr3A 505736326 505737891 1565 True 2154.0 2154 91.4770 968 2544 1 chr3A.!!$R1 1576
10 TraesCS3D01G276100 chr3A 506228009 506229640 1631 True 1847.0 1847 87.7060 1406 2980 1 chr3A.!!$R2 1574
11 TraesCS3D01G276100 chr3A 505722597 505723525 928 True 564.5 728 93.8010 2542 3476 2 chr3A.!!$R4 934
12 TraesCS3D01G276100 chr7D 279746 280660 914 True 1541.0 1541 97.2680 1 904 1 chr7D.!!$R1 903
13 TraesCS3D01G276100 chr7D 124502495 124503157 662 False 1081.0 1081 96.0900 1 663 1 chr7D.!!$F1 662
14 TraesCS3D01G276100 chr4D 484192629 484193541 912 True 1539.0 1539 97.2620 1 903 1 chr4D.!!$R2 902
15 TraesCS3D01G276100 chr6D 108243690 108244590 900 True 1441.0 1441 95.5240 1 905 1 chr6D.!!$R1 904
16 TraesCS3D01G276100 chr4B 128948506 128949178 672 False 750.0 750 86.8690 200 884 1 chr4B.!!$F1 684
17 TraesCS3D01G276100 chr1A 492887625 492888210 585 False 689.0 689 88.0950 323 903 1 chr1A.!!$F2 580
18 TraesCS3D01G276100 chr2A 278541472 278542051 579 True 630.0 630 86.2650 310 903 1 chr2A.!!$R1 593

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
781 799 0.165295 CGTGCGAGAGAACTACGTGA 59.835 55.000 0.0 0.0 37.57 4.35 F
1021 1057 1.146263 GCCACCTTACCATCCCTCG 59.854 63.158 0.0 0.0 0.00 4.63 F
1806 2933 1.065926 TGCGAGATCACAAGCCATCTT 60.066 47.619 0.0 0.0 29.01 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 2906 0.033920 TTGTGATCTCGCAGCACAGT 59.966 50.000 5.59 0.0 42.7 3.55 R
1942 3070 0.326264 AAAGGCGTGATCTTCCAGCT 59.674 50.000 0.00 0.0 0.0 4.24 R
3385 4655 1.540363 GCGAACCAAACAGAGGAGACA 60.540 52.381 0.00 0.0 0.0 3.41 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
43 44 2.746904 TCACATACAGCACCGAAAATGG 59.253 45.455 0.00 0.00 0.00 3.16
227 228 4.100084 CTCCGATGGTGCCTGGCA 62.100 66.667 19.30 19.30 35.60 4.92
371 378 2.526873 AGCGTGTGGGAGGGAAGT 60.527 61.111 0.00 0.00 0.00 3.01
781 799 0.165295 CGTGCGAGAGAACTACGTGA 59.835 55.000 0.00 0.00 37.57 4.35
801 819 3.508793 TGAACGTGGTTTTGGTTGGTTTA 59.491 39.130 0.00 0.00 0.00 2.01
861 882 6.350949 CCATGAAAGGTGGGACGAAATTAAAT 60.351 38.462 0.00 0.00 32.98 1.40
869 890 5.005094 TGGGACGAAATTAAATCCGAAACT 58.995 37.500 0.00 0.00 31.48 2.66
905 926 8.685838 ACTGAGACATTAGGAGTAGAGATAAC 57.314 38.462 0.00 0.00 0.00 1.89
906 927 8.275758 ACTGAGACATTAGGAGTAGAGATAACA 58.724 37.037 0.00 0.00 0.00 2.41
907 928 8.684386 TGAGACATTAGGAGTAGAGATAACAG 57.316 38.462 0.00 0.00 0.00 3.16
908 929 8.275758 TGAGACATTAGGAGTAGAGATAACAGT 58.724 37.037 0.00 0.00 0.00 3.55
909 930 9.781633 GAGACATTAGGAGTAGAGATAACAGTA 57.218 37.037 0.00 0.00 0.00 2.74
917 938 8.605065 AGGAGTAGAGATAACAGTATAGGTACC 58.395 40.741 2.73 2.73 0.00 3.34
918 939 8.381636 GGAGTAGAGATAACAGTATAGGTACCA 58.618 40.741 15.94 0.00 0.00 3.25
919 940 9.962809 GAGTAGAGATAACAGTATAGGTACCAT 57.037 37.037 15.94 8.29 0.00 3.55
929 950 8.904099 ACAGTATAGGTACCATAAAAATGCTC 57.096 34.615 15.94 0.00 0.00 4.26
930 951 8.714906 ACAGTATAGGTACCATAAAAATGCTCT 58.285 33.333 15.94 0.00 0.00 4.09
931 952 9.561069 CAGTATAGGTACCATAAAAATGCTCTT 57.439 33.333 15.94 0.00 0.00 2.85
935 956 7.158099 AGGTACCATAAAAATGCTCTTTCAC 57.842 36.000 15.94 0.00 0.00 3.18
936 957 6.027749 GGTACCATAAAAATGCTCTTTCACG 58.972 40.000 7.15 0.00 0.00 4.35
937 958 5.957842 ACCATAAAAATGCTCTTTCACGA 57.042 34.783 0.00 0.00 0.00 4.35
938 959 5.942872 ACCATAAAAATGCTCTTTCACGAG 58.057 37.500 0.00 0.00 0.00 4.18
939 960 5.705441 ACCATAAAAATGCTCTTTCACGAGA 59.295 36.000 0.00 0.00 32.74 4.04
940 961 6.024049 CCATAAAAATGCTCTTTCACGAGAC 58.976 40.000 0.00 0.00 32.74 3.36
941 962 3.795561 AAAATGCTCTTTCACGAGACG 57.204 42.857 0.00 0.00 32.74 4.18
942 963 2.440539 AATGCTCTTTCACGAGACGT 57.559 45.000 0.00 0.00 42.36 4.34
993 1014 2.750350 CCCAGCCCAGAAACGACT 59.250 61.111 0.00 0.00 0.00 4.18
1005 1029 2.166664 AGAAACGACTCTAGTCATGGCC 59.833 50.000 10.55 0.00 44.99 5.36
1021 1057 1.146263 GCCACCTTACCATCCCTCG 59.854 63.158 0.00 0.00 0.00 4.63
1181 1217 3.031417 GCACCTGGCCCTACGTGAT 62.031 63.158 0.00 0.00 36.11 3.06
1309 1345 1.270839 ACCTCTCCAACAACCACATCG 60.271 52.381 0.00 0.00 0.00 3.84
1677 2802 3.706373 AACCAGCTCGACGGCCAT 61.706 61.111 2.24 0.00 0.00 4.40
1803 2930 1.094073 GCTGCGAGATCACAAGCCAT 61.094 55.000 0.00 0.00 0.00 4.40
1806 2933 1.065926 TGCGAGATCACAAGCCATCTT 60.066 47.619 0.00 0.00 29.01 2.40
1875 3003 2.032681 GGCGTGCTCCTTGTCCTT 59.967 61.111 0.00 0.00 0.00 3.36
1879 3007 1.405526 GCGTGCTCCTTGTCCTTATCA 60.406 52.381 0.00 0.00 0.00 2.15
1962 3090 1.168714 GCTGGAAGATCACGCCTTTT 58.831 50.000 0.00 0.00 34.07 2.27
1973 3104 1.374947 CGCCTTTTCAGACCCTGGA 59.625 57.895 0.00 0.00 31.51 3.86
1974 3105 0.035056 CGCCTTTTCAGACCCTGGAT 60.035 55.000 0.00 0.00 31.51 3.41
2016 3147 2.095252 GGCGCTGACCGAAGAGAAC 61.095 63.158 7.64 0.00 40.02 3.01
2843 4037 2.813474 CGCATCAGAAACGCGGGA 60.813 61.111 12.47 0.00 45.08 5.14
2849 4043 0.108329 TCAGAAACGCGGGATTCTCC 60.108 55.000 19.87 0.00 33.50 3.71
2896 4090 1.374631 GCCTGATGTGCACGACAGA 60.375 57.895 30.86 9.98 38.23 3.41
3003 4201 2.126149 CGCTCTTGCAGACGCTCT 60.126 61.111 0.00 0.00 39.64 4.09
3146 4352 7.497773 AGAGTTATAAGTCCAAACCTAGCTT 57.502 36.000 15.34 0.00 0.00 3.74
3385 4655 4.912317 ATAGAAGATCAGATGCAGGCAT 57.088 40.909 6.44 6.44 39.69 4.40
3494 4766 4.908601 TTCACATAAGAGCAGGAAAGGA 57.091 40.909 0.00 0.00 0.00 3.36
3508 4780 5.337491 GCAGGAAAGGAAAATAATTGCAGGA 60.337 40.000 0.00 0.00 0.00 3.86
3539 4811 8.768397 AGGTATTGAGTGGACATTACATAAAGA 58.232 33.333 0.00 0.00 32.04 2.52
3595 4867 3.942829 TGAACAGGAGGAAGCAGTATTG 58.057 45.455 0.00 0.00 0.00 1.90
3602 4874 3.010420 GAGGAAGCAGTATTGGAACCAC 58.990 50.000 0.00 0.00 0.00 4.16
3671 4943 3.555527 AAATTAGCGAAGGGGTAGGAC 57.444 47.619 0.00 0.00 0.00 3.85
3727 4999 5.828328 GGGAAGTAAATGGACATAGGGAAAG 59.172 44.000 0.00 0.00 0.00 2.62
3736 5008 9.432982 AAATGGACATAGGGAAAGCAAATATAA 57.567 29.630 0.00 0.00 0.00 0.98
3857 5129 7.763172 AGAGTATGTAATCTCTCGCAAAAAG 57.237 36.000 0.00 0.00 36.45 2.27
3937 5209 0.328258 AGGGCTCGCCAAAGTATTGT 59.672 50.000 10.51 0.00 37.98 2.71
3984 5256 7.103641 TCTCGTATTCAGGCAGTTAAAGAATT 58.896 34.615 0.00 0.00 31.89 2.17
4023 5295 3.243704 CCAATTTCCGTGGAAACATGTGT 60.244 43.478 15.89 0.00 45.34 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.470709 TCGGAATCTCCAGCATTTGATC 58.529 45.455 0.00 0.00 35.91 2.92
227 228 2.194056 CTGGCCGCCATGGATCTT 59.806 61.111 18.40 0.00 42.00 2.40
781 799 4.739587 ATAAACCAACCAAAACCACGTT 57.260 36.364 0.00 0.00 0.00 3.99
801 819 1.786441 TCCCACCTCCCACTTTCAAAT 59.214 47.619 0.00 0.00 0.00 2.32
861 882 3.005472 CAGTTGGTAGTCTGAGTTTCGGA 59.995 47.826 0.00 0.00 34.02 4.55
869 890 5.419155 CCTAATGTCTCAGTTGGTAGTCTGA 59.581 44.000 0.00 0.00 38.20 3.27
905 926 9.561069 AAGAGCATTTTTATGGTACCTATACTG 57.439 33.333 14.36 3.58 31.72 2.74
909 930 8.903820 GTGAAAGAGCATTTTTATGGTACCTAT 58.096 33.333 14.36 7.70 31.72 2.57
910 931 7.065324 CGTGAAAGAGCATTTTTATGGTACCTA 59.935 37.037 14.36 0.00 31.72 3.08
911 932 6.128007 CGTGAAAGAGCATTTTTATGGTACCT 60.128 38.462 14.36 1.08 31.72 3.08
912 933 6.027749 CGTGAAAGAGCATTTTTATGGTACC 58.972 40.000 4.43 4.43 31.72 3.34
913 934 6.837992 TCGTGAAAGAGCATTTTTATGGTAC 58.162 36.000 0.00 0.00 31.72 3.34
914 935 6.876789 TCTCGTGAAAGAGCATTTTTATGGTA 59.123 34.615 0.00 0.00 38.12 3.25
915 936 5.705441 TCTCGTGAAAGAGCATTTTTATGGT 59.295 36.000 0.00 0.00 38.12 3.55
916 937 6.024049 GTCTCGTGAAAGAGCATTTTTATGG 58.976 40.000 0.00 0.00 38.12 2.74
917 938 5.729883 CGTCTCGTGAAAGAGCATTTTTATG 59.270 40.000 0.00 0.00 38.12 1.90
918 939 5.408604 ACGTCTCGTGAAAGAGCATTTTTAT 59.591 36.000 0.00 0.00 39.18 1.40
919 940 4.748102 ACGTCTCGTGAAAGAGCATTTTTA 59.252 37.500 0.00 0.00 39.18 1.52
920 941 3.560068 ACGTCTCGTGAAAGAGCATTTTT 59.440 39.130 0.00 0.00 39.18 1.94
921 942 3.131396 ACGTCTCGTGAAAGAGCATTTT 58.869 40.909 0.00 0.00 39.18 1.82
922 943 2.755650 ACGTCTCGTGAAAGAGCATTT 58.244 42.857 0.00 0.00 39.18 2.32
923 944 2.440539 ACGTCTCGTGAAAGAGCATT 57.559 45.000 0.00 0.00 39.18 3.56
951 972 7.858879 GGCTTCTTCGTGAGTATTTAACAAAAA 59.141 33.333 0.00 0.00 0.00 1.94
952 973 7.357303 GGCTTCTTCGTGAGTATTTAACAAAA 58.643 34.615 0.00 0.00 0.00 2.44
953 974 6.072893 GGGCTTCTTCGTGAGTATTTAACAAA 60.073 38.462 0.00 0.00 0.00 2.83
954 975 5.410439 GGGCTTCTTCGTGAGTATTTAACAA 59.590 40.000 0.00 0.00 0.00 2.83
955 976 4.933400 GGGCTTCTTCGTGAGTATTTAACA 59.067 41.667 0.00 0.00 0.00 2.41
956 977 4.933400 TGGGCTTCTTCGTGAGTATTTAAC 59.067 41.667 0.00 0.00 0.00 2.01
957 978 5.155278 TGGGCTTCTTCGTGAGTATTTAA 57.845 39.130 0.00 0.00 0.00 1.52
958 979 4.755411 CTGGGCTTCTTCGTGAGTATTTA 58.245 43.478 0.00 0.00 0.00 1.40
959 980 3.600388 CTGGGCTTCTTCGTGAGTATTT 58.400 45.455 0.00 0.00 0.00 1.40
960 981 2.678190 GCTGGGCTTCTTCGTGAGTATT 60.678 50.000 0.00 0.00 0.00 1.89
961 982 1.134670 GCTGGGCTTCTTCGTGAGTAT 60.135 52.381 0.00 0.00 0.00 2.12
962 983 0.246635 GCTGGGCTTCTTCGTGAGTA 59.753 55.000 0.00 0.00 0.00 2.59
963 984 1.004440 GCTGGGCTTCTTCGTGAGT 60.004 57.895 0.00 0.00 0.00 3.41
964 985 1.743252 GGCTGGGCTTCTTCGTGAG 60.743 63.158 0.00 0.00 0.00 3.51
965 986 2.347490 GGCTGGGCTTCTTCGTGA 59.653 61.111 0.00 0.00 0.00 4.35
993 1014 2.116238 GGTAAGGTGGCCATGACTAGA 58.884 52.381 9.72 0.00 0.00 2.43
1005 1029 0.462047 GCACGAGGGATGGTAAGGTG 60.462 60.000 0.00 0.00 0.00 4.00
1021 1057 1.760480 GGAGGAGGAGGAGGAGCAC 60.760 68.421 0.00 0.00 0.00 4.40
1078 1114 2.125350 GAGAAGCTGCCCCTCACG 60.125 66.667 12.24 0.00 0.00 4.35
1079 1115 0.463474 GATGAGAAGCTGCCCCTCAC 60.463 60.000 19.32 11.97 39.43 3.51
1280 1316 0.035915 GTTGGAGAGGTTGAGGCTCC 60.036 60.000 12.86 0.00 46.60 4.70
1330 1366 2.104331 CGAAGCGCACCGGTAGAT 59.896 61.111 6.87 0.00 36.27 1.98
1575 2700 3.854784 GCTTGTTTGATGACAGGTCAAGC 60.855 47.826 6.17 10.35 43.58 4.01
1677 2802 3.755628 GCGAGTCCTGCCGGTACA 61.756 66.667 1.90 0.00 0.00 2.90
1779 2906 0.033920 TTGTGATCTCGCAGCACAGT 59.966 50.000 5.59 0.00 42.70 3.55
1790 2917 3.113824 AGGAGAAGATGGCTTGTGATCT 58.886 45.455 0.00 0.00 33.61 2.75
1937 3065 0.872021 CGTGATCTTCCAGCTACCGC 60.872 60.000 0.00 0.00 0.00 5.68
1942 3070 0.326264 AAAGGCGTGATCTTCCAGCT 59.674 50.000 0.00 0.00 0.00 4.24
1962 3090 1.271840 CCCCGAAATCCAGGGTCTGA 61.272 60.000 0.00 0.00 46.17 3.27
2557 3721 1.216977 CCATGTAGCCGAACGACCA 59.783 57.895 0.00 0.00 0.00 4.02
2592 3756 0.391263 GTGACGACCAGGGATGGTTC 60.391 60.000 0.72 0.00 43.24 3.62
2843 4037 5.522361 ACGAATTCGATCTCCTCGGAGAAT 61.522 45.833 33.05 5.98 46.83 2.40
3146 4352 5.066375 CGGGCTAATCAATCAAAGAATGTGA 59.934 40.000 0.00 0.00 36.30 3.58
3185 4392 7.339466 GGGGTTTGACTAATGTATCATCAAAGT 59.661 37.037 0.00 0.00 39.31 2.66
3385 4655 1.540363 GCGAACCAAACAGAGGAGACA 60.540 52.381 0.00 0.00 0.00 3.41
3494 4766 5.198602 ACCTCCTCTCCTGCAATTATTTT 57.801 39.130 0.00 0.00 0.00 1.82
3508 4780 3.474798 TGTCCACTCAATACCTCCTCT 57.525 47.619 0.00 0.00 0.00 3.69
3595 4867 1.783071 TCCCCAACTTTTGTGGTTCC 58.217 50.000 0.00 0.00 29.55 3.62
3602 4874 8.620116 AATTGATACATTTTCCCCAACTTTTG 57.380 30.769 0.00 0.00 0.00 2.44
3642 4914 4.466828 CCCTTCGCTAATTTAATGCATCG 58.533 43.478 0.00 0.00 0.00 3.84
3671 4943 2.293677 TCATTCATCCGTTCGTCCTG 57.706 50.000 0.00 0.00 0.00 3.86
3736 5008 8.585018 TCAAGTTTTGTTTCCTTCTCTTTCTTT 58.415 29.630 0.00 0.00 0.00 2.52
3857 5129 6.110707 TCCCATTCCGTTACATACTCTTTTC 58.889 40.000 0.00 0.00 0.00 2.29
3959 5231 5.654603 TCTTTAACTGCCTGAATACGAGA 57.345 39.130 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.