Multiple sequence alignment - TraesCS2D01G169400

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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 TraesCS2D01G169400 chr2D 100.000 3305 0 0 1 3305 113090365 113093669 0.000000e+00 6104.0
1 TraesCS2D01G169400 chr2D 92.822 1421 78 4 914 2319 113480423 113481834 0.000000e+00 2037.0
2 TraesCS2D01G169400 chr2B 95.065 2918 77 21 419 3305 163741219 163744100 0.000000e+00 4529.0
3 TraesCS2D01G169400 chr2B 93.211 1414 79 5 914 2320 163977177 163978580 0.000000e+00 2063.0
4 TraesCS2D01G169400 chr2B 89.837 246 17 7 160 401 163740677 163740918 3.200000e-80 309.0
5 TraesCS2D01G169400 chr2B 87.634 186 13 5 612 787 163736832 163737017 1.200000e-49 207.0
6 TraesCS2D01G169400 chr2B 87.786 131 13 2 269 396 144436026 144435896 2.050000e-32 150.0
7 TraesCS2D01G169400 chr2A 92.018 1353 93 3 982 2319 115094741 115096093 0.000000e+00 1886.0
8 TraesCS2D01G169400 chr2A 97.289 996 27 0 1325 2320 114498414 114497419 0.000000e+00 1690.0
9 TraesCS2D01G169400 chr2A 90.395 531 27 11 817 1334 114499421 114498902 0.000000e+00 676.0
10 TraesCS2D01G169400 chr2A 88.797 241 18 6 618 852 115094464 115094701 1.500000e-73 287.0
11 TraesCS2D01G169400 chr2A 85.263 285 20 13 567 831 114503678 114503396 1.170000e-69 274.0
12 TraesCS2D01G169400 chr2A 87.121 132 15 2 273 404 203785804 203785933 7.390000e-32 148.0
13 TraesCS2D01G169400 chr2A 87.121 132 15 2 273 404 203844513 203844642 7.390000e-32 148.0
14 TraesCS2D01G169400 chr3A 83.807 1371 151 25 959 2308 100847761 100849081 0.000000e+00 1236.0
15 TraesCS2D01G169400 chr3A 88.561 271 31 0 1876 2146 100869738 100870008 2.460000e-86 329.0
16 TraesCS2D01G169400 chr3A 89.764 127 13 0 273 399 641865637 641865763 2.640000e-36 163.0
17 TraesCS2D01G169400 chr3B 87.076 1091 132 7 1224 2308 132910201 132911288 0.000000e+00 1225.0
18 TraesCS2D01G169400 chr3B 85.858 997 136 5 1192 2187 132956169 132957161 0.000000e+00 1055.0
19 TraesCS2D01G169400 chr3B 84.726 1041 144 8 1280 2308 132052916 132051879 0.000000e+00 1027.0
20 TraesCS2D01G169400 chr3B 85.322 838 98 18 2486 3304 754757783 754756952 0.000000e+00 843.0
21 TraesCS2D01G169400 chr3D 89.260 959 76 10 2373 3305 484453462 484454419 0.000000e+00 1175.0
22 TraesCS2D01G169400 chr3D 79.970 1328 200 35 1000 2315 1196972 1195699 0.000000e+00 918.0
23 TraesCS2D01G169400 chr3D 90.000 70 4 2 93 159 131490341 131490272 1.630000e-13 87.9
24 TraesCS2D01G169400 chr3D 88.406 69 5 2 91 156 56444962 56445030 2.730000e-11 80.5
25 TraesCS2D01G169400 chrUn 80.230 1305 195 35 1010 2305 34009660 34010910 0.000000e+00 922.0
26 TraesCS2D01G169400 chrUn 81.481 1107 165 27 1210 2305 34465190 34464113 0.000000e+00 872.0
27 TraesCS2D01G169400 chrUn 83.242 913 125 23 2414 3304 101610889 101609983 0.000000e+00 813.0
28 TraesCS2D01G169400 chrUn 87.121 132 15 2 273 404 356074543 356074414 7.390000e-32 148.0
29 TraesCS2D01G169400 chr7A 89.310 739 72 5 2573 3305 732895721 732896458 0.000000e+00 920.0
30 TraesCS2D01G169400 chr7A 83.352 913 122 23 2417 3304 7841210 7840303 0.000000e+00 817.0
31 TraesCS2D01G169400 chr7A 88.571 70 5 2 93 159 149597713 149597782 7.600000e-12 82.4
32 TraesCS2D01G169400 chr6D 84.029 958 121 23 2372 3301 179933 180886 0.000000e+00 893.0
33 TraesCS2D01G169400 chr6D 83.574 968 113 21 2370 3304 3079760 3080714 0.000000e+00 865.0
34 TraesCS2D01G169400 chr6D 86.765 136 15 3 269 403 147691147 147691280 7.390000e-32 148.0
35 TraesCS2D01G169400 chr1D 84.136 914 114 27 2414 3304 428689357 428688452 0.000000e+00 856.0
36 TraesCS2D01G169400 chr1D 83.025 919 106 30 2414 3304 454849961 454849065 0.000000e+00 787.0
37 TraesCS2D01G169400 chr1D 86.667 75 6 3 86 156 229310823 229310897 2.730000e-11 80.5
38 TraesCS2D01G169400 chr7D 83.969 917 115 25 2414 3304 18060100 18059190 0.000000e+00 850.0
39 TraesCS2D01G169400 chr7D 82.462 918 113 31 2414 3304 6851965 6852861 0.000000e+00 760.0
40 TraesCS2D01G169400 chr7D 87.500 136 14 3 269 403 55416982 55417115 1.590000e-33 154.0
41 TraesCS2D01G169400 chr4D 83.025 919 106 30 2414 3304 440446214 440445318 0.000000e+00 787.0
42 TraesCS2D01G169400 chr7B 87.373 689 78 6 2623 3304 665539200 665538514 0.000000e+00 782.0
43 TraesCS2D01G169400 chr7B 86.765 136 15 3 269 403 7270500 7270633 7.390000e-32 148.0
44 TraesCS2D01G169400 chr7B 94.444 36 2 0 528 563 666146437 666146402 4.610000e-04 56.5
45 TraesCS2D01G169400 chr5D 82.353 918 112 31 2414 3304 81157770 81158664 0.000000e+00 752.0
46 TraesCS2D01G169400 chr5D 82.692 520 66 12 2362 2866 378615373 378615883 1.090000e-119 440.0
47 TraesCS2D01G169400 chr5A 90.141 71 4 2 92 159 660186835 660186765 4.540000e-14 89.8
48 TraesCS2D01G169400 chr6A 91.045 67 3 2 93 156 36704443 36704509 1.630000e-13 87.9
49 TraesCS2D01G169400 chr6A 88.406 69 5 2 94 159 76098199 76098131 2.730000e-11 80.5
50 TraesCS2D01G169400 chr1B 89.706 68 4 2 95 159 545641269 545641202 2.110000e-12 84.2
51 TraesCS2D01G169400 chr1A 88.732 71 5 2 92 159 320154358 320154288 2.110000e-12 84.2
52 TraesCS2D01G169400 chr1A 92.308 39 3 0 525 563 489400871 489400833 4.610000e-04 56.5
53 TraesCS2D01G169400 chr6B 92.308 39 3 0 525 563 279095757 279095795 4.610000e-04 56.5


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 TraesCS2D01G169400 chr2D 113090365 113093669 3304 False 6104.000000 6104 100.000000 1 3305 1 chr2D.!!$F1 3304
1 TraesCS2D01G169400 chr2D 113480423 113481834 1411 False 2037.000000 2037 92.822000 914 2319 1 chr2D.!!$F2 1405
2 TraesCS2D01G169400 chr2B 163977177 163978580 1403 False 2063.000000 2063 93.211000 914 2320 1 chr2B.!!$F1 1406
3 TraesCS2D01G169400 chr2B 163736832 163744100 7268 False 1681.666667 4529 90.845333 160 3305 3 chr2B.!!$F2 3145
4 TraesCS2D01G169400 chr2A 115094464 115096093 1629 False 1086.500000 1886 90.407500 618 2319 2 chr2A.!!$F3 1701
5 TraesCS2D01G169400 chr2A 114497419 114503678 6259 True 880.000000 1690 90.982333 567 2320 3 chr2A.!!$R1 1753
6 TraesCS2D01G169400 chr3A 100847761 100849081 1320 False 1236.000000 1236 83.807000 959 2308 1 chr3A.!!$F1 1349
7 TraesCS2D01G169400 chr3B 132910201 132911288 1087 False 1225.000000 1225 87.076000 1224 2308 1 chr3B.!!$F1 1084
8 TraesCS2D01G169400 chr3B 132956169 132957161 992 False 1055.000000 1055 85.858000 1192 2187 1 chr3B.!!$F2 995
9 TraesCS2D01G169400 chr3B 132051879 132052916 1037 True 1027.000000 1027 84.726000 1280 2308 1 chr3B.!!$R1 1028
10 TraesCS2D01G169400 chr3B 754756952 754757783 831 True 843.000000 843 85.322000 2486 3304 1 chr3B.!!$R2 818
11 TraesCS2D01G169400 chr3D 484453462 484454419 957 False 1175.000000 1175 89.260000 2373 3305 1 chr3D.!!$F2 932
12 TraesCS2D01G169400 chr3D 1195699 1196972 1273 True 918.000000 918 79.970000 1000 2315 1 chr3D.!!$R1 1315
13 TraesCS2D01G169400 chrUn 34009660 34010910 1250 False 922.000000 922 80.230000 1010 2305 1 chrUn.!!$F1 1295
14 TraesCS2D01G169400 chrUn 34464113 34465190 1077 True 872.000000 872 81.481000 1210 2305 1 chrUn.!!$R1 1095
15 TraesCS2D01G169400 chrUn 101609983 101610889 906 True 813.000000 813 83.242000 2414 3304 1 chrUn.!!$R2 890
16 TraesCS2D01G169400 chr7A 732895721 732896458 737 False 920.000000 920 89.310000 2573 3305 1 chr7A.!!$F2 732
17 TraesCS2D01G169400 chr7A 7840303 7841210 907 True 817.000000 817 83.352000 2417 3304 1 chr7A.!!$R1 887
18 TraesCS2D01G169400 chr6D 179933 180886 953 False 893.000000 893 84.029000 2372 3301 1 chr6D.!!$F1 929
19 TraesCS2D01G169400 chr6D 3079760 3080714 954 False 865.000000 865 83.574000 2370 3304 1 chr6D.!!$F2 934
20 TraesCS2D01G169400 chr1D 428688452 428689357 905 True 856.000000 856 84.136000 2414 3304 1 chr1D.!!$R1 890
21 TraesCS2D01G169400 chr1D 454849065 454849961 896 True 787.000000 787 83.025000 2414 3304 1 chr1D.!!$R2 890
22 TraesCS2D01G169400 chr7D 18059190 18060100 910 True 850.000000 850 83.969000 2414 3304 1 chr7D.!!$R1 890
23 TraesCS2D01G169400 chr7D 6851965 6852861 896 False 760.000000 760 82.462000 2414 3304 1 chr7D.!!$F1 890
24 TraesCS2D01G169400 chr4D 440445318 440446214 896 True 787.000000 787 83.025000 2414 3304 1 chr4D.!!$R1 890
25 TraesCS2D01G169400 chr7B 665538514 665539200 686 True 782.000000 782 87.373000 2623 3304 1 chr7B.!!$R1 681
26 TraesCS2D01G169400 chr5D 81157770 81158664 894 False 752.000000 752 82.353000 2414 3304 1 chr5D.!!$F1 890
27 TraesCS2D01G169400 chr5D 378615373 378615883 510 False 440.000000 440 82.692000 2362 2866 1 chr5D.!!$F2 504

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
537 4509 0.043334 AGCTAGCTCCCTCCTTTCCA 59.957 55.0 12.68 0.0 0.00 3.53 F
663 4652 0.251165 GGCACAAGGTTTAGAGGCCA 60.251 55.0 5.01 0.0 39.66 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 10415 1.207339 CTGCAGCGCGAATGTTTGA 59.793 52.632 12.1 0.0 0.0 2.69 R
2543 11098 0.828022 TTGGATTCGGCAGGTCGTAT 59.172 50.000 0.0 0.0 0.0 3.06 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
21 22 3.872696 TCTTAGCAATCAATCAAGCGGA 58.127 40.909 0.00 0.00 0.00 5.54
22 23 4.454678 TCTTAGCAATCAATCAAGCGGAT 58.545 39.130 0.00 0.00 38.05 4.18
23 24 4.512944 TCTTAGCAATCAATCAAGCGGATC 59.487 41.667 0.00 0.00 34.28 3.36
24 25 1.600957 AGCAATCAATCAAGCGGATCG 59.399 47.619 0.00 0.00 34.28 3.69
36 37 2.106938 GGATCGCACATCGCCTGA 59.893 61.111 0.00 0.00 37.30 3.86
37 38 1.953138 GGATCGCACATCGCCTGAG 60.953 63.158 0.00 0.00 37.30 3.35
39 40 0.528466 GATCGCACATCGCCTGAGAA 60.528 55.000 0.00 0.00 37.30 2.87
40 41 0.105593 ATCGCACATCGCCTGAGAAT 59.894 50.000 0.00 0.00 37.30 2.40
41 42 0.528466 TCGCACATCGCCTGAGAATC 60.528 55.000 0.00 0.00 37.30 2.52
42 43 0.807275 CGCACATCGCCTGAGAATCA 60.807 55.000 0.00 0.00 39.84 2.57
43 44 2.334472 CGCACATCGCCTGAGAATCAA 61.334 52.381 0.00 0.00 39.27 2.57
44 45 4.422165 CGCACATCGCCTGAGAATCAAC 62.422 54.545 0.00 0.00 39.27 3.18
56 57 5.679734 TGAGAATCAACAAAACTCTCAGC 57.320 39.130 0.00 0.00 45.97 4.26
58 59 4.380531 AGAATCAACAAAACTCTCAGCGA 58.619 39.130 0.00 0.00 0.00 4.93
59 60 4.212214 AGAATCAACAAAACTCTCAGCGAC 59.788 41.667 0.00 0.00 0.00 5.19
60 61 3.179443 TCAACAAAACTCTCAGCGACT 57.821 42.857 0.00 0.00 0.00 4.18
61 62 2.866156 TCAACAAAACTCTCAGCGACTG 59.134 45.455 0.00 0.00 0.00 3.51
85 86 5.810587 GCGAATTAGCAATTCCGATATAGGA 59.189 40.000 5.59 0.00 43.39 2.94
88 89 9.529325 CGAATTAGCAATTCCGATATAGGATAA 57.471 33.333 5.30 1.88 43.39 1.75
94 95 9.220767 AGCAATTCCGATATAGGATAAGAAAAC 57.779 33.333 5.30 0.00 40.48 2.43
95 96 8.999431 GCAATTCCGATATAGGATAAGAAAACA 58.001 33.333 5.30 0.00 40.48 2.83
102 103 9.651718 CGATATAGGATAAGAAAACAGTTTTGC 57.348 33.333 16.21 7.83 31.94 3.68
143 144 9.929180 TGTCATAAGTATTGCATATCTAAGTCC 57.071 33.333 0.00 0.00 0.00 3.85
175 176 9.815936 CATTGATTTTTAAGAAAATGGCTTGTC 57.184 29.630 2.17 0.00 43.61 3.18
183 3871 3.269381 AGAAAATGGCTTGTCTATCCCCA 59.731 43.478 0.00 0.00 0.00 4.96
187 3875 1.345422 TGGCTTGTCTATCCCCATCCT 60.345 52.381 0.00 0.00 0.00 3.24
189 3877 1.349357 GCTTGTCTATCCCCATCCTCC 59.651 57.143 0.00 0.00 0.00 4.30
191 3879 1.255033 TGTCTATCCCCATCCTCCCT 58.745 55.000 0.00 0.00 0.00 4.20
193 3881 1.981495 GTCTATCCCCATCCTCCCTTG 59.019 57.143 0.00 0.00 0.00 3.61
231 3919 0.693622 GGGCCCCTAAATCCTAGAGC 59.306 60.000 12.23 0.00 0.00 4.09
431 4144 8.216423 TCAACTCTAGTATAACGGAGGAAGTAT 58.784 37.037 0.00 0.00 31.05 2.12
433 4146 8.993404 ACTCTAGTATAACGGAGGAAGTATTT 57.007 34.615 0.00 0.00 31.05 1.40
436 4149 9.512588 TCTAGTATAACGGAGGAAGTATTTAGG 57.487 37.037 0.00 0.00 0.00 2.69
437 4150 9.512588 CTAGTATAACGGAGGAAGTATTTAGGA 57.487 37.037 0.00 0.00 0.00 2.94
438 4151 8.773033 AGTATAACGGAGGAAGTATTTAGGAA 57.227 34.615 0.00 0.00 0.00 3.36
439 4152 9.377238 AGTATAACGGAGGAAGTATTTAGGAAT 57.623 33.333 0.00 0.00 0.00 3.01
442 4155 7.909485 AACGGAGGAAGTATTTAGGAATAGA 57.091 36.000 0.00 0.00 0.00 1.98
443 4156 7.527568 ACGGAGGAAGTATTTAGGAATAGAG 57.472 40.000 0.00 0.00 0.00 2.43
444 4157 6.015265 ACGGAGGAAGTATTTAGGAATAGAGC 60.015 42.308 0.00 0.00 0.00 4.09
448 4420 6.778559 AGGAAGTATTTAGGAATAGAGCGAGT 59.221 38.462 0.00 0.00 0.00 4.18
499 4471 4.219725 TGTGAGATGAACAAGACGGTCATA 59.780 41.667 11.27 0.00 0.00 2.15
532 4504 4.943373 GCTAGCTAGCTCCCTCCT 57.057 61.111 33.71 0.00 45.62 3.69
534 4506 1.419381 GCTAGCTAGCTCCCTCCTTT 58.581 55.000 33.71 0.00 45.62 3.11
535 4507 1.343142 GCTAGCTAGCTCCCTCCTTTC 59.657 57.143 33.71 4.79 45.62 2.62
536 4508 1.967779 CTAGCTAGCTCCCTCCTTTCC 59.032 57.143 23.26 0.00 0.00 3.13
537 4509 0.043334 AGCTAGCTCCCTCCTTTCCA 59.957 55.000 12.68 0.00 0.00 3.53
540 4512 2.706190 GCTAGCTCCCTCCTTTCCATAA 59.294 50.000 7.70 0.00 0.00 1.90
542 4514 3.872459 AGCTCCCTCCTTTCCATAATG 57.128 47.619 0.00 0.00 0.00 1.90
543 4515 3.126453 AGCTCCCTCCTTTCCATAATGT 58.874 45.455 0.00 0.00 0.00 2.71
545 4517 4.726825 AGCTCCCTCCTTTCCATAATGTAA 59.273 41.667 0.00 0.00 0.00 2.41
546 4518 5.066593 GCTCCCTCCTTTCCATAATGTAAG 58.933 45.833 0.00 0.00 0.00 2.34
547 4519 5.163195 GCTCCCTCCTTTCCATAATGTAAGA 60.163 44.000 0.00 0.00 0.00 2.10
548 4520 6.466470 GCTCCCTCCTTTCCATAATGTAAGAT 60.466 42.308 0.00 0.00 0.00 2.40
549 4521 7.256691 GCTCCCTCCTTTCCATAATGTAAGATA 60.257 40.741 0.00 0.00 0.00 1.98
550 4522 8.757307 TCCCTCCTTTCCATAATGTAAGATAT 57.243 34.615 0.00 0.00 0.00 1.63
551 4523 9.182642 TCCCTCCTTTCCATAATGTAAGATATT 57.817 33.333 0.00 0.00 0.00 1.28
552 4524 9.813826 CCCTCCTTTCCATAATGTAAGATATTT 57.186 33.333 0.00 0.00 0.00 1.40
623 4611 1.549170 GGGTCGTTTCTTCCTAGCTCA 59.451 52.381 0.00 0.00 0.00 4.26
663 4652 0.251165 GGCACAAGGTTTAGAGGCCA 60.251 55.000 5.01 0.00 39.66 5.36
720 4712 1.408127 CCAACAATATGGGCAGACGGA 60.408 52.381 0.00 0.00 36.79 4.69
845 8835 9.639601 CTACTACTTACTGTTGTCATTCATTCA 57.360 33.333 0.00 0.00 36.20 2.57
878 8868 1.202651 CGTTGTCAGAAGGTTCAGGGT 60.203 52.381 0.00 0.00 0.00 4.34
884 8874 0.977395 AGAAGGTTCAGGGTCTTCCG 59.023 55.000 0.00 0.00 41.52 4.30
926 8924 4.976540 AGCCGCTAAAACCTTCCTATAT 57.023 40.909 0.00 0.00 0.00 0.86
945 8943 9.733556 TCCTATATAAAGACTTGCAAGTTTCAA 57.266 29.630 31.58 17.93 39.88 2.69
957 8955 6.804534 TGCAAGTTTCAACAAATTTACTCG 57.195 33.333 0.00 0.00 0.00 4.18
974 8972 2.277969 CTCGAGCTTTGCACTGATCAT 58.722 47.619 0.00 0.00 0.00 2.45
975 8973 2.274437 TCGAGCTTTGCACTGATCATC 58.726 47.619 0.00 0.00 0.00 2.92
976 8974 1.329906 CGAGCTTTGCACTGATCATCC 59.670 52.381 0.00 0.00 0.00 3.51
978 8976 2.355132 GAGCTTTGCACTGATCATCCAG 59.645 50.000 0.00 0.00 39.93 3.86
1884 10415 1.457643 TCTCCTGCCGATCCCGAAT 60.458 57.895 0.00 0.00 38.22 3.34
2400 10938 0.984230 TTCAGTGCTCCCCCTAACTG 59.016 55.000 0.00 0.00 41.11 3.16
2471 11015 1.142688 ACCCAGATCCAAGCCCTGTT 61.143 55.000 0.00 0.00 0.00 3.16
2543 11098 2.204461 ACACGACCCCACGATCACA 61.204 57.895 0.00 0.00 37.03 3.58
2688 11280 1.519455 GCCGTCGTGAATCTCCAGG 60.519 63.158 0.00 0.00 0.00 4.45
2695 11287 1.687146 TGAATCTCCAGGGCTCGCT 60.687 57.895 0.00 0.00 0.00 4.93
3090 11732 5.512921 CCTCGGTTGGGGTAGTTTACTTAAA 60.513 44.000 0.00 0.00 0.00 1.52
3114 11757 2.159240 TCGTGATCCTGTGCTATGTGTC 60.159 50.000 0.00 0.00 0.00 3.67
3243 11886 2.027377 AGAACTGCTGAAGGACTGGATG 60.027 50.000 0.00 0.00 0.00 3.51
3274 11917 7.186570 TGGTCAGATGATGAAAGTTCAGATA 57.813 36.000 0.00 0.00 40.43 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.600957 CGATCCGCTTGATTGATTGCT 59.399 47.619 0.00 0.00 37.06 3.91
5 6 2.028287 CGATCCGCTTGATTGATTGC 57.972 50.000 0.00 0.00 37.06 3.56
24 25 1.063174 GTTGATTCTCAGGCGATGTGC 59.937 52.381 0.00 0.00 45.38 4.57
25 26 2.349590 TGTTGATTCTCAGGCGATGTG 58.650 47.619 0.00 0.00 0.00 3.21
26 27 2.768253 TGTTGATTCTCAGGCGATGT 57.232 45.000 0.00 0.00 0.00 3.06
29 30 3.476552 AGTTTTGTTGATTCTCAGGCGA 58.523 40.909 0.00 0.00 0.00 5.54
30 31 3.499918 AGAGTTTTGTTGATTCTCAGGCG 59.500 43.478 0.00 0.00 0.00 5.52
31 32 4.516698 TGAGAGTTTTGTTGATTCTCAGGC 59.483 41.667 0.00 0.00 39.31 4.85
34 35 4.212004 CGCTGAGAGTTTTGTTGATTCTCA 59.788 41.667 2.91 2.91 41.25 3.27
36 37 4.212214 GTCGCTGAGAGTTTTGTTGATTCT 59.788 41.667 0.00 0.00 0.00 2.40
37 38 4.212214 AGTCGCTGAGAGTTTTGTTGATTC 59.788 41.667 0.00 0.00 0.00 2.52
39 40 3.496130 CAGTCGCTGAGAGTTTTGTTGAT 59.504 43.478 1.18 0.00 32.44 2.57
40 41 2.866156 CAGTCGCTGAGAGTTTTGTTGA 59.134 45.455 1.18 0.00 32.44 3.18
41 42 2.600792 GCAGTCGCTGAGAGTTTTGTTG 60.601 50.000 10.46 0.00 32.44 3.33
42 43 1.599542 GCAGTCGCTGAGAGTTTTGTT 59.400 47.619 10.46 0.00 32.44 2.83
43 44 1.221414 GCAGTCGCTGAGAGTTTTGT 58.779 50.000 10.46 0.00 32.44 2.83
44 45 0.162507 CGCAGTCGCTGAGAGTTTTG 59.837 55.000 10.46 0.00 33.20 2.44
45 46 0.032130 TCGCAGTCGCTGAGAGTTTT 59.968 50.000 10.46 0.00 35.54 2.43
46 47 0.032130 TTCGCAGTCGCTGAGAGTTT 59.968 50.000 10.46 0.00 40.91 2.66
48 49 0.244994 AATTCGCAGTCGCTGAGAGT 59.755 50.000 10.46 6.85 40.91 3.24
49 50 2.115595 CTAATTCGCAGTCGCTGAGAG 58.884 52.381 10.46 2.31 40.91 3.20
50 51 1.799181 GCTAATTCGCAGTCGCTGAGA 60.799 52.381 10.46 9.52 38.43 3.27
51 52 0.574454 GCTAATTCGCAGTCGCTGAG 59.426 55.000 10.46 7.48 32.44 3.35
52 53 0.108851 TGCTAATTCGCAGTCGCTGA 60.109 50.000 10.46 0.00 34.44 4.26
54 55 1.656652 ATTGCTAATTCGCAGTCGCT 58.343 45.000 4.71 0.00 41.55 4.93
56 57 2.597505 CGGAATTGCTAATTCGCAGTCG 60.598 50.000 4.71 4.78 46.45 4.18
58 59 2.627945 TCGGAATTGCTAATTCGCAGT 58.372 42.857 4.71 0.00 46.45 4.40
59 60 3.885484 ATCGGAATTGCTAATTCGCAG 57.115 42.857 4.71 0.00 46.45 5.18
60 61 5.580691 CCTATATCGGAATTGCTAATTCGCA 59.419 40.000 0.00 0.00 46.45 5.10
61 62 5.810587 TCCTATATCGGAATTGCTAATTCGC 59.189 40.000 12.43 0.00 46.45 4.70
68 69 9.220767 GTTTTCTTATCCTATATCGGAATTGCT 57.779 33.333 0.00 0.00 36.49 3.91
69 70 8.999431 TGTTTTCTTATCCTATATCGGAATTGC 58.001 33.333 0.00 0.00 36.49 3.56
76 77 9.651718 GCAAAACTGTTTTCTTATCCTATATCG 57.348 33.333 15.17 1.52 0.00 2.92
82 83 8.914011 ACTTTAGCAAAACTGTTTTCTTATCCT 58.086 29.630 15.17 7.86 0.00 3.24
117 118 9.929180 GGACTTAGATATGCAATACTTATGACA 57.071 33.333 0.00 0.00 0.00 3.58
148 149 9.558396 ACAAGCCATTTTCTTAAAAATCAATGA 57.442 25.926 0.00 0.00 41.96 2.57
150 151 9.783081 AGACAAGCCATTTTCTTAAAAATCAAT 57.217 25.926 0.00 0.00 41.96 2.57
154 155 9.875691 GGATAGACAAGCCATTTTCTTAAAAAT 57.124 29.630 0.00 0.00 44.12 1.82
155 156 8.311109 GGGATAGACAAGCCATTTTCTTAAAAA 58.689 33.333 0.00 0.00 38.66 1.94
156 157 7.093509 GGGGATAGACAAGCCATTTTCTTAAAA 60.094 37.037 0.00 0.00 34.41 1.52
157 158 6.379988 GGGGATAGACAAGCCATTTTCTTAAA 59.620 38.462 0.00 0.00 0.00 1.52
158 159 5.891551 GGGGATAGACAAGCCATTTTCTTAA 59.108 40.000 0.00 0.00 0.00 1.85
159 160 5.044476 TGGGGATAGACAAGCCATTTTCTTA 60.044 40.000 0.00 0.00 0.00 2.10
160 161 4.264352 TGGGGATAGACAAGCCATTTTCTT 60.264 41.667 0.00 0.00 0.00 2.52
162 163 3.631250 TGGGGATAGACAAGCCATTTTC 58.369 45.455 0.00 0.00 0.00 2.29
164 165 3.437052 GGATGGGGATAGACAAGCCATTT 60.437 47.826 0.00 0.00 0.00 2.32
165 166 2.108952 GGATGGGGATAGACAAGCCATT 59.891 50.000 0.00 0.00 0.00 3.16
166 167 1.707427 GGATGGGGATAGACAAGCCAT 59.293 52.381 0.00 0.00 0.00 4.40
167 168 1.140312 GGATGGGGATAGACAAGCCA 58.860 55.000 0.00 0.00 0.00 4.75
168 169 1.349357 GAGGATGGGGATAGACAAGCC 59.651 57.143 0.00 0.00 0.00 4.35
169 170 1.349357 GGAGGATGGGGATAGACAAGC 59.651 57.143 0.00 0.00 0.00 4.01
171 172 1.585592 AGGGAGGATGGGGATAGACAA 59.414 52.381 0.00 0.00 0.00 3.18
175 176 2.422939 TCAAGGGAGGATGGGGATAG 57.577 55.000 0.00 0.00 0.00 2.08
177 178 2.000290 TTTCAAGGGAGGATGGGGAT 58.000 50.000 0.00 0.00 0.00 3.85
178 179 1.766951 TTTTCAAGGGAGGATGGGGA 58.233 50.000 0.00 0.00 0.00 4.81
206 3894 2.707554 AGGATTTAGGGGCCCTAAGAG 58.292 52.381 36.64 0.00 45.40 2.85
209 3897 3.870559 CTCTAGGATTTAGGGGCCCTAA 58.129 50.000 36.01 36.01 43.47 2.69
214 3902 2.301583 CTCTGCTCTAGGATTTAGGGGC 59.698 54.545 0.00 0.00 0.00 5.80
231 3919 0.583438 CTTTGTCACACGCCACTCTG 59.417 55.000 0.00 0.00 0.00 3.35
397 4086 9.584008 TCCGTTATACTAGAGTTGAGGAAATAT 57.416 33.333 0.00 0.00 0.00 1.28
401 4090 5.826737 CCTCCGTTATACTAGAGTTGAGGAA 59.173 44.000 0.00 0.00 39.33 3.36
403 4092 5.374921 TCCTCCGTTATACTAGAGTTGAGG 58.625 45.833 0.00 0.00 38.53 3.86
431 4144 5.302059 ACATGCTACTCGCTCTATTCCTAAA 59.698 40.000 0.00 0.00 40.11 1.85
433 4146 4.399219 ACATGCTACTCGCTCTATTCCTA 58.601 43.478 0.00 0.00 40.11 2.94
434 4147 3.226777 ACATGCTACTCGCTCTATTCCT 58.773 45.455 0.00 0.00 40.11 3.36
435 4148 3.651803 ACATGCTACTCGCTCTATTCC 57.348 47.619 0.00 0.00 40.11 3.01
436 4149 5.157781 CCTTACATGCTACTCGCTCTATTC 58.842 45.833 0.00 0.00 40.11 1.75
437 4150 4.559704 GCCTTACATGCTACTCGCTCTATT 60.560 45.833 0.00 0.00 40.11 1.73
438 4151 3.057174 GCCTTACATGCTACTCGCTCTAT 60.057 47.826 0.00 0.00 40.11 1.98
439 4152 2.293677 GCCTTACATGCTACTCGCTCTA 59.706 50.000 0.00 0.00 40.11 2.43
440 4153 1.067821 GCCTTACATGCTACTCGCTCT 59.932 52.381 0.00 0.00 40.11 4.09
441 4154 1.202417 TGCCTTACATGCTACTCGCTC 60.202 52.381 0.00 0.00 40.11 5.03
442 4155 0.824109 TGCCTTACATGCTACTCGCT 59.176 50.000 0.00 0.00 40.11 4.93
443 4156 1.795286 GATGCCTTACATGCTACTCGC 59.205 52.381 0.00 0.00 39.84 5.03
444 4157 3.377346 AGATGCCTTACATGCTACTCG 57.623 47.619 0.00 0.00 39.84 4.18
499 4471 3.515901 AGCTAGCTAACACTAGTGCCTTT 59.484 43.478 22.90 12.13 41.49 3.11
525 4497 8.757307 ATATCTTACATTATGGAAAGGAGGGA 57.243 34.615 8.86 0.00 0.00 4.20
526 4498 9.813826 AAATATCTTACATTATGGAAAGGAGGG 57.186 33.333 8.86 0.00 0.00 4.30
561 4533 9.338622 GGCCTTCAGCTTTAGACTTAAATATTA 57.661 33.333 0.00 0.00 43.05 0.98
562 4534 7.285629 GGGCCTTCAGCTTTAGACTTAAATATT 59.714 37.037 0.84 0.00 43.05 1.28
563 4535 6.773200 GGGCCTTCAGCTTTAGACTTAAATAT 59.227 38.462 0.84 0.00 43.05 1.28
564 4536 6.120220 GGGCCTTCAGCTTTAGACTTAAATA 58.880 40.000 0.84 0.00 43.05 1.40
565 4537 4.950475 GGGCCTTCAGCTTTAGACTTAAAT 59.050 41.667 0.84 0.00 43.05 1.40
566 4538 4.332828 GGGCCTTCAGCTTTAGACTTAAA 58.667 43.478 0.84 0.00 43.05 1.52
567 4539 3.308188 GGGGCCTTCAGCTTTAGACTTAA 60.308 47.826 0.84 0.00 43.05 1.85
568 4540 2.238898 GGGGCCTTCAGCTTTAGACTTA 59.761 50.000 0.84 0.00 43.05 2.24
569 4541 1.004862 GGGGCCTTCAGCTTTAGACTT 59.995 52.381 0.84 0.00 43.05 3.01
570 4542 0.621082 GGGGCCTTCAGCTTTAGACT 59.379 55.000 0.84 0.00 43.05 3.24
571 4543 0.621082 AGGGGCCTTCAGCTTTAGAC 59.379 55.000 0.84 0.00 43.05 2.59
623 4611 1.597797 CCATTTGCCACGGATGTGCT 61.598 55.000 0.00 0.00 45.04 4.40
663 4652 2.757917 GCTGCCTCGGACTCCTCT 60.758 66.667 0.00 0.00 0.00 3.69
720 4712 2.577700 CTATGGAGCAGAGTAGGACGT 58.422 52.381 0.00 0.00 0.00 4.34
845 8835 1.140052 TGACAACGTCAAGGTCACCAT 59.860 47.619 0.00 0.00 39.78 3.55
884 8874 6.457528 CGGCTAAATTTTGATGTCTTCCTCTC 60.458 42.308 3.69 0.00 0.00 3.20
894 8884 6.099341 AGGTTTTAGCGGCTAAATTTTGATG 58.901 36.000 29.65 0.00 36.10 3.07
896 8886 5.715434 AGGTTTTAGCGGCTAAATTTTGA 57.285 34.783 29.65 15.70 36.10 2.69
926 8924 8.770438 AATTTGTTGAAACTTGCAAGTCTTTA 57.230 26.923 31.20 19.71 38.57 1.85
945 8943 4.275936 AGTGCAAAGCTCGAGTAAATTTGT 59.724 37.500 23.04 10.62 34.22 2.83
957 8955 2.355132 CTGGATGATCAGTGCAAAGCTC 59.645 50.000 0.09 0.00 0.00 4.09
974 8972 0.752658 CAGCGTATGGATGGACTGGA 59.247 55.000 0.00 0.00 0.00 3.86
975 8973 3.295734 CAGCGTATGGATGGACTGG 57.704 57.895 0.00 0.00 0.00 4.00
1884 10415 1.207339 CTGCAGCGCGAATGTTTGA 59.793 52.632 12.10 0.00 0.00 2.69
2335 10872 9.369904 GGTAACTCGTATGGTCATAACTTAAAA 57.630 33.333 0.00 0.00 0.00 1.52
2400 10938 3.268330 GAGGGACAAGGGTACGAAATTC 58.732 50.000 0.00 0.00 0.00 2.17
2471 11015 3.448934 TGGTCTGGGTTATACGGGTTAA 58.551 45.455 0.00 0.00 0.00 2.01
2543 11098 0.828022 TTGGATTCGGCAGGTCGTAT 59.172 50.000 0.00 0.00 0.00 3.06
2688 11280 4.530857 ATGCGGTACCAGCGAGCC 62.531 66.667 13.54 0.00 42.41 4.70
2738 11331 1.284297 GGCGGCAGTTTGTTTGATGC 61.284 55.000 3.07 0.00 37.95 3.91
3090 11732 2.497675 ACATAGCACAGGATCACGAACT 59.502 45.455 0.00 0.00 0.00 3.01
3243 11886 5.826737 ACTTTCATCATCTGACCAATCATCC 59.173 40.000 0.00 0.00 33.22 3.51
3274 11917 3.508793 CCATTTTCTGACCAATCTGCACT 59.491 43.478 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.