Multiple sequence alignment - TraesCS1B01G114100

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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 TraesCS1B01G114100 chr1B 100.000 5561 0 0 1 5561 133129733 133124173 0.000000e+00 10270.0
1 TraesCS1B01G114100 chr1B 80.942 1317 206 34 2686 3990 426499555 426498272 0.000000e+00 1000.0
2 TraesCS1B01G114100 chr1B 81.240 1274 195 27 2732 3990 133113911 133112667 0.000000e+00 989.0
3 TraesCS1B01G114100 chr1B 90.167 478 44 2 695 1169 426502603 426502126 2.200000e-173 619.0
4 TraesCS1B01G114100 chr7B 93.146 3487 131 39 533 3990 588883081 588879674 0.000000e+00 5016.0
5 TraesCS1B01G114100 chr7B 95.009 1062 45 3 4206 5262 588879553 588878495 0.000000e+00 1661.0
6 TraesCS1B01G114100 chr7B 83.057 844 102 24 4206 5027 537826568 537825744 0.000000e+00 728.0
7 TraesCS1B01G114100 chr7B 90.303 495 46 2 686 1179 588869416 588868923 0.000000e+00 647.0
8 TraesCS1B01G114100 chr7B 90.531 433 10 4 5130 5561 589919489 589919891 1.360000e-150 544.0
9 TraesCS1B01G114100 chr7B 97.175 177 4 1 5386 5561 588878456 588878280 1.170000e-76 298.0
10 TraesCS1B01G114100 chr7B 89.308 159 6 2 5399 5557 498300240 498300093 7.350000e-44 189.0
11 TraesCS1B01G114100 chr7B 100.000 39 0 0 5523 5561 589735140 589735178 7.730000e-09 73.1
12 TraesCS1B01G114100 chr7B 100.000 28 0 0 5130 5157 589934822 589934849 1.000000e-02 52.8
13 TraesCS1B01G114100 chr5D 93.322 2456 115 19 548 2963 289501317 289498871 0.000000e+00 3581.0
14 TraesCS1B01G114100 chr5D 93.092 1491 79 14 3308 4778 289498308 289496822 0.000000e+00 2161.0
15 TraesCS1B01G114100 chr5D 92.210 1104 61 9 4171 5262 289356723 289355633 0.000000e+00 1539.0
16 TraesCS1B01G114100 chr5D 80.389 1336 212 33 2667 3990 289423452 289422155 0.000000e+00 970.0
17 TraesCS1B01G114100 chr5D 89.557 699 61 7 3310 3999 289357504 289356809 0.000000e+00 876.0
18 TraesCS1B01G114100 chr5D 92.070 517 41 0 5 521 482528413 482527897 0.000000e+00 728.0
19 TraesCS1B01G114100 chr5D 97.324 299 8 0 2991 3289 289498874 289498576 4.970000e-140 508.0
20 TraesCS1B01G114100 chr5D 89.172 157 8 2 5406 5561 289355493 289355345 2.650000e-43 187.0
21 TraesCS1B01G114100 chr5D 90.722 97 4 2 5264 5355 289355587 289355491 2.100000e-24 124.0
22 TraesCS1B01G114100 chr5D 97.619 42 1 0 5232 5273 29906376 29906417 7.730000e-09 73.1
23 TraesCS1B01G114100 chr5D 100.000 29 0 0 5532 5560 289727238 289727210 3.000000e-03 54.7
24 TraesCS1B01G114100 chr7A 91.734 2589 152 34 2392 4959 627236816 627234269 0.000000e+00 3539.0
25 TraesCS1B01G114100 chr7A 92.183 1484 70 13 926 2395 627238395 627236944 0.000000e+00 2056.0
26 TraesCS1B01G114100 chr7A 90.449 869 69 10 3687 4549 627015210 627014350 0.000000e+00 1133.0
27 TraesCS1B01G114100 chr7A 90.449 869 69 10 3687 4549 627052886 627052026 0.000000e+00 1133.0
28 TraesCS1B01G114100 chr7A 80.209 1339 222 35 2667 3990 627047828 627046518 0.000000e+00 965.0
29 TraesCS1B01G114100 chr7A 91.626 609 41 5 4250 4848 628386923 628386315 0.000000e+00 833.0
30 TraesCS1B01G114100 chr7A 88.276 580 54 11 4208 4778 627046394 627045820 0.000000e+00 682.0
31 TraesCS1B01G114100 chr7A 90.554 487 46 0 683 1169 628363812 628363326 0.000000e+00 645.0
32 TraesCS1B01G114100 chr7A 89.918 486 47 2 686 1170 627165853 627165369 4.730000e-175 625.0
33 TraesCS1B01G114100 chr7A 89.583 144 8 5 4887 5030 628386313 628386177 5.730000e-40 176.0
34 TraesCS1B01G114100 chr7A 96.970 99 2 1 5119 5217 627234228 627234131 1.240000e-36 165.0
35 TraesCS1B01G114100 chr7A 98.667 75 1 0 5487 5561 628386020 628385946 3.500000e-27 134.0
36 TraesCS1B01G114100 chr7A 82.550 149 16 6 4889 5027 580504815 580504667 7.570000e-24 122.0
37 TraesCS1B01G114100 chr7A 85.897 78 2 1 5365 5433 628386099 628386022 2.150000e-09 75.0
38 TraesCS1B01G114100 chr7A 100.000 33 0 0 5456 5488 627232648 627232616 1.670000e-05 62.1
39 TraesCS1B01G114100 chr7A 100.000 30 0 0 5532 5561 627008772 627008743 7.780000e-04 56.5
40 TraesCS1B01G114100 chr2B 94.110 1596 83 8 3113 4699 127792235 127790642 0.000000e+00 2416.0
41 TraesCS1B01G114100 chr2B 93.474 1088 61 9 3731 4813 135511153 135512235 0.000000e+00 1607.0
42 TraesCS1B01G114100 chr2B 96.785 591 18 1 3215 3804 135510220 135510810 0.000000e+00 985.0
43 TraesCS1B01G114100 chr2B 93.135 539 37 0 610 1148 182147906 182147368 0.000000e+00 791.0
44 TraesCS1B01G114100 chr2B 81.509 530 85 8 2740 3267 182141045 182140527 1.850000e-114 424.0
45 TraesCS1B01G114100 chr2B 88.535 157 13 4 5061 5217 135512325 135512476 9.510000e-43 185.0
46 TraesCS1B01G114100 chr2B 98.361 61 1 0 3113 3173 135509415 135509475 2.120000e-19 108.0
47 TraesCS1B01G114100 chr2B 100.000 45 0 0 5516 5560 135512529 135512573 3.570000e-12 84.2
48 TraesCS1B01G114100 chr2B 90.909 55 5 0 5436 5490 135512479 135512533 2.150000e-09 75.0
49 TraesCS1B01G114100 chr7D 92.812 640 32 6 533 1169 545270722 545270094 0.000000e+00 915.0
50 TraesCS1B01G114100 chr7D 82.500 520 88 3 7 523 568247061 568247580 2.360000e-123 453.0
51 TraesCS1B01G114100 chr7D 84.783 184 19 5 4849 5023 509580053 509579870 5.730000e-40 176.0
52 TraesCS1B01G114100 chr7D 100.000 32 0 0 5063 5094 509599036 509599005 6.020000e-05 60.2
53 TraesCS1B01G114100 chr7D 96.875 32 0 1 4910 4940 545254722 545254753 1.000000e-02 52.8
54 TraesCS1B01G114100 chr6A 90.248 564 49 3 4208 4771 107263265 107263822 0.000000e+00 732.0
55 TraesCS1B01G114100 chr6A 94.521 73 4 0 5475 5547 107264255 107264327 4.550000e-21 113.0
56 TraesCS1B01G114100 chr6A 100.000 32 0 0 5120 5151 107264075 107264106 6.020000e-05 60.2
57 TraesCS1B01G114100 chr3D 88.910 523 55 1 1 520 492112007 492112529 4.700000e-180 641.0
58 TraesCS1B01G114100 chrUn 90.377 478 43 2 695 1169 383291375 383291852 4.730000e-175 625.0
59 TraesCS1B01G114100 chr6D 86.460 517 66 3 7 521 239053089 239053603 1.050000e-156 564.0
60 TraesCS1B01G114100 chr6B 85.992 514 59 6 10 521 645346238 645346740 6.340000e-149 538.0
61 TraesCS1B01G114100 chr1D 84.848 528 70 3 3 520 455778417 455777890 1.770000e-144 523.0
62 TraesCS1B01G114100 chr1D 82.659 519 85 3 7 520 57127416 57126898 6.570000e-124 455.0
63 TraesCS1B01G114100 chr4D 82.979 517 85 3 7 520 425221673 425222189 1.090000e-126 464.0
64 TraesCS1B01G114100 chr1A 85.333 450 64 2 3 451 549411935 549411487 1.090000e-126 464.0


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 TraesCS1B01G114100 chr1B 133124173 133129733 5560 True 10270.000000 10270 100.000000 1 5561 1 chr1B.!!$R2 5560
1 TraesCS1B01G114100 chr1B 133112667 133113911 1244 True 989.000000 989 81.240000 2732 3990 1 chr1B.!!$R1 1258
2 TraesCS1B01G114100 chr1B 426498272 426502603 4331 True 809.500000 1000 85.554500 695 3990 2 chr1B.!!$R3 3295
3 TraesCS1B01G114100 chr7B 588878280 588883081 4801 True 2325.000000 5016 95.110000 533 5561 3 chr7B.!!$R4 5028
4 TraesCS1B01G114100 chr7B 537825744 537826568 824 True 728.000000 728 83.057000 4206 5027 1 chr7B.!!$R2 821
5 TraesCS1B01G114100 chr5D 289496822 289501317 4495 True 2083.333333 3581 94.579333 548 4778 3 chr5D.!!$R5 4230
6 TraesCS1B01G114100 chr5D 289422155 289423452 1297 True 970.000000 970 80.389000 2667 3990 1 chr5D.!!$R1 1323
7 TraesCS1B01G114100 chr5D 482527897 482528413 516 True 728.000000 728 92.070000 5 521 1 chr5D.!!$R3 516
8 TraesCS1B01G114100 chr5D 289355345 289357504 2159 True 681.500000 1539 90.415250 3310 5561 4 chr5D.!!$R4 2251
9 TraesCS1B01G114100 chr7A 627232616 627238395 5779 True 1455.525000 3539 95.221750 926 5488 4 chr7A.!!$R8 4562
10 TraesCS1B01G114100 chr7A 627014350 627015210 860 True 1133.000000 1133 90.449000 3687 4549 1 chr7A.!!$R3 862
11 TraesCS1B01G114100 chr7A 627052026 627052886 860 True 1133.000000 1133 90.449000 3687 4549 1 chr7A.!!$R4 862
12 TraesCS1B01G114100 chr7A 627045820 627047828 2008 True 823.500000 965 84.242500 2667 4778 2 chr7A.!!$R7 2111
13 TraesCS1B01G114100 chr7A 628385946 628386923 977 True 304.500000 833 91.443250 4250 5561 4 chr7A.!!$R9 1311
14 TraesCS1B01G114100 chr2B 127790642 127792235 1593 True 2416.000000 2416 94.110000 3113 4699 1 chr2B.!!$R1 1586
15 TraesCS1B01G114100 chr2B 182147368 182147906 538 True 791.000000 791 93.135000 610 1148 1 chr2B.!!$R3 538
16 TraesCS1B01G114100 chr2B 135509415 135512573 3158 False 507.366667 1607 94.677333 3113 5560 6 chr2B.!!$F1 2447
17 TraesCS1B01G114100 chr2B 182140527 182141045 518 True 424.000000 424 81.509000 2740 3267 1 chr2B.!!$R2 527
18 TraesCS1B01G114100 chr7D 545270094 545270722 628 True 915.000000 915 92.812000 533 1169 1 chr7D.!!$R3 636
19 TraesCS1B01G114100 chr7D 568247061 568247580 519 False 453.000000 453 82.500000 7 523 1 chr7D.!!$F2 516
20 TraesCS1B01G114100 chr6A 107263265 107264327 1062 False 301.733333 732 94.923000 4208 5547 3 chr6A.!!$F1 1339
21 TraesCS1B01G114100 chr3D 492112007 492112529 522 False 641.000000 641 88.910000 1 520 1 chr3D.!!$F1 519
22 TraesCS1B01G114100 chr6D 239053089 239053603 514 False 564.000000 564 86.460000 7 521 1 chr6D.!!$F1 514
23 TraesCS1B01G114100 chr6B 645346238 645346740 502 False 538.000000 538 85.992000 10 521 1 chr6B.!!$F1 511
24 TraesCS1B01G114100 chr1D 455777890 455778417 527 True 523.000000 523 84.848000 3 520 1 chr1D.!!$R2 517
25 TraesCS1B01G114100 chr1D 57126898 57127416 518 True 455.000000 455 82.659000 7 520 1 chr1D.!!$R1 513
26 TraesCS1B01G114100 chr4D 425221673 425222189 516 False 464.000000 464 82.979000 7 520 1 chr4D.!!$F1 513

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
123 124 0.107703 TTGCAGGGATGACGATGGAC 60.108 55.000 0.0 0.0 0.00 4.02 F
431 434 1.613255 GCTTTTGGTCTGGATTCGGGA 60.613 52.381 0.0 0.0 0.00 5.14 F
1664 1766 0.736053 TGTGGCGTCTTTGACCAAAC 59.264 50.000 0.0 0.0 34.63 2.93 F
2337 3974 0.950116 GCAATACCCTGCTGCTCATC 59.050 55.000 0.0 0.0 39.34 2.92 F
3715 6536 1.448013 GAAGGGCACACGAGTAGGC 60.448 63.158 0.0 0.0 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1514 1582 1.202627 GCCTGCTAGACAAGGATCAGG 60.203 57.143 9.98 7.39 42.83 3.86 R
2135 3749 2.701107 GTTCAGTAGCTCCTTGAACCC 58.299 52.381 19.44 4.20 42.91 4.11 R
3117 4973 5.108518 CGAAATCAAATATCGTTGCATGCTG 60.109 40.000 20.33 9.00 0.00 4.41 R
3881 7125 0.248458 AAACGCCAAAGCTGAACACG 60.248 50.000 0.00 0.00 36.60 4.49 R
5370 8777 3.347958 TTTTGGCACGAATGTCTGAAC 57.652 42.857 0.00 0.00 0.00 3.18 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
25 26 3.736094 TCAGGAAACCTAGGTGGATCAT 58.264 45.455 17.14 9.50 39.71 2.45
123 124 0.107703 TTGCAGGGATGACGATGGAC 60.108 55.000 0.00 0.00 0.00 4.02
227 230 3.820557 TGCACTAGCCCAAGATTTATCC 58.179 45.455 0.00 0.00 41.13 2.59
237 240 8.454859 AGCCCAAGATTTATCCTTATCTCATA 57.545 34.615 0.00 0.00 30.95 2.15
256 259 5.432645 TCATATAATTGTTGCCTCGGACAA 58.567 37.500 0.00 0.00 39.78 3.18
307 310 2.895404 GCATTGGAGGGATGTATGCAAT 59.105 45.455 0.00 0.00 40.86 3.56
314 317 5.163109 TGGAGGGATGTATGCAATCATTGTA 60.163 40.000 0.00 0.00 34.22 2.41
431 434 1.613255 GCTTTTGGTCTGGATTCGGGA 60.613 52.381 0.00 0.00 0.00 5.14
456 464 3.627237 CCATGTGTGGCTTATAAACCCCT 60.627 47.826 2.45 0.00 39.01 4.79
458 466 2.285977 GTGTGGCTTATAAACCCCTCG 58.714 52.381 2.45 0.00 0.00 4.63
599 622 4.099881 AGAATGCAACAAAACTCCACACAT 59.900 37.500 0.00 0.00 0.00 3.21
655 681 2.421131 CACGCCGATAGATACGTGC 58.579 57.895 0.00 0.00 45.32 5.34
1140 1166 1.644372 CTCATCTCCCTCGTCGACG 59.356 63.158 31.30 31.30 41.45 5.12
1259 1288 5.652014 TCAAAATTGAAGCCCATGGTAGTAG 59.348 40.000 11.73 0.00 33.55 2.57
1260 1289 3.864789 ATTGAAGCCCATGGTAGTAGG 57.135 47.619 11.73 0.00 0.00 3.18
1261 1290 2.561209 TGAAGCCCATGGTAGTAGGA 57.439 50.000 11.73 0.00 0.00 2.94
1262 1291 2.398588 TGAAGCCCATGGTAGTAGGAG 58.601 52.381 11.73 0.00 0.00 3.69
1263 1292 2.292918 TGAAGCCCATGGTAGTAGGAGT 60.293 50.000 11.73 0.00 0.00 3.85
1264 1293 3.052414 TGAAGCCCATGGTAGTAGGAGTA 60.052 47.826 11.73 0.00 0.00 2.59
1586 1654 5.536538 AGACAGTTCAAGTAGTCACATCAGA 59.463 40.000 0.00 0.00 33.56 3.27
1664 1766 0.736053 TGTGGCGTCTTTGACCAAAC 59.264 50.000 0.00 0.00 34.63 2.93
1702 1804 7.724061 AGGTTAACCACTTGTTATCTGACAAAT 59.276 33.333 26.26 0.00 39.14 2.32
1709 1811 7.379529 CCACTTGTTATCTGACAAATTGACAAC 59.620 37.037 0.00 0.00 38.90 3.32
1968 2078 9.746457 ATTAAGCATCCTTCTTATATCCCTTTC 57.254 33.333 0.00 0.00 32.47 2.62
2035 2159 6.292923 AGTTATGTAGCCGTGCCATAATTTA 58.707 36.000 9.18 0.00 34.58 1.40
2036 2160 6.768861 AGTTATGTAGCCGTGCCATAATTTAA 59.231 34.615 9.18 0.00 34.58 1.52
2037 2161 7.447238 AGTTATGTAGCCGTGCCATAATTTAAT 59.553 33.333 9.18 0.00 34.58 1.40
2038 2162 6.648879 ATGTAGCCGTGCCATAATTTAATT 57.351 33.333 0.00 0.00 0.00 1.40
2039 2163 6.067263 TGTAGCCGTGCCATAATTTAATTC 57.933 37.500 0.00 0.00 0.00 2.17
2135 3749 4.332819 AGCTTTGGAATTCTCCGAAATACG 59.667 41.667 5.23 0.00 43.43 3.06
2184 3811 4.916983 TGTTGGAGAAAAACCATCTGTG 57.083 40.909 0.00 0.00 37.26 3.66
2267 3904 6.711277 AGTAGAGTGAAGTTTCATGCCAATA 58.289 36.000 0.00 0.00 39.73 1.90
2337 3974 0.950116 GCAATACCCTGCTGCTCATC 59.050 55.000 0.00 0.00 39.34 2.92
2433 4200 6.306356 GTGCATACTTGTTCATGACAAACATC 59.694 38.462 0.00 0.00 46.99 3.06
2463 4230 5.010617 ACCACTCACCACATCAAATTTTACC 59.989 40.000 0.00 0.00 0.00 2.85
2562 4413 9.184062 CCAAATGAAATATATGACGTTGAATGG 57.816 33.333 0.00 0.00 0.00 3.16
2828 4681 3.601443 AGAACTCGCTGAGCTTTGTAT 57.399 42.857 1.78 0.00 32.04 2.29
3018 4871 5.015178 TGTCCTCCTTGTCTTCCCAATAAAT 59.985 40.000 0.00 0.00 0.00 1.40
3117 4973 5.957798 TGATTGCCATCAAAAGACTTGATC 58.042 37.500 0.00 0.00 36.41 2.92
3213 5772 2.059786 GGGTGGTGCATTCATGGGG 61.060 63.158 0.00 0.00 0.00 4.96
3289 5848 9.701098 TTACATATCTGGTACATTTTCCGTATC 57.299 33.333 0.00 0.00 38.20 2.24
3715 6536 1.448013 GAAGGGCACACGAGTAGGC 60.448 63.158 0.00 0.00 0.00 3.93
3796 7038 7.672983 TTGTTTTCAGATGTCCTAATCTCAC 57.327 36.000 0.00 0.00 34.60 3.51
3797 7039 6.768483 TGTTTTCAGATGTCCTAATCTCACA 58.232 36.000 0.00 0.00 34.60 3.58
3803 7045 6.096141 TCAGATGTCCTAATCTCACAGTCTTC 59.904 42.308 0.00 0.00 34.60 2.87
3840 7084 5.036737 CACTTTTCAGTGGTTACAAAGCTG 58.963 41.667 0.00 0.00 46.10 4.24
3881 7125 4.144534 AGTTTACTCGACGAAGACAGAC 57.855 45.455 0.00 0.00 0.00 3.51
4229 7489 0.111832 CAGGCCTGGCATATGTGGAT 59.888 55.000 26.14 0.00 0.00 3.41
4259 7519 2.089980 GTTGCATGAGCTTGTGGATCT 58.910 47.619 0.00 0.00 42.74 2.75
4344 7604 1.202557 GCTCAGGAAGATCCAGCAGAG 60.203 57.143 0.00 2.32 39.61 3.35
4348 7608 1.519719 GAAGATCCAGCAGAGCGGT 59.480 57.895 0.00 0.00 35.47 5.68
4368 7630 0.448990 CCACCATGACAGATGTTGCG 59.551 55.000 0.00 0.00 0.00 4.85
4677 7953 5.436175 TCAAAGATCAGTTTTGTGGAGTGA 58.564 37.500 0.00 0.00 36.97 3.41
4744 8043 5.850557 TTCCATGGGCTACATTGTAATTG 57.149 39.130 13.02 0.00 37.84 2.32
4841 8184 7.916552 ACAGTTATTCGCATGTCCTTTTATAC 58.083 34.615 0.00 0.00 0.00 1.47
4856 8199 7.280205 GTCCTTTTATACGGACATGAGAACAAT 59.720 37.037 0.00 0.00 46.98 2.71
5359 8766 4.708177 TCTGAGGAATTAGTTATGCCTGC 58.292 43.478 0.00 0.00 42.99 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.183492 AGCAAAGTTCTCTGGTGGCA 59.817 50.000 0.00 0.00 0.00 4.92
65 66 5.504173 GCCTTCATCGTTTGCTCTATTAACC 60.504 44.000 0.00 0.00 0.00 2.85
68 69 5.023533 AGCCTTCATCGTTTGCTCTATTA 57.976 39.130 0.00 0.00 0.00 0.98
123 124 3.670625 TCACCGAAGAACCCAAGTAATG 58.329 45.455 0.00 0.00 0.00 1.90
227 230 7.819415 TCCGAGGCAACAATTATATGAGATAAG 59.181 37.037 0.00 0.00 41.41 1.73
256 259 1.719063 ATCCTGCACCACACCCTTGT 61.719 55.000 0.00 0.00 35.84 3.16
307 310 7.121315 TCGTCTCTCTGATCTCTTTTACAATGA 59.879 37.037 0.00 0.00 0.00 2.57
314 317 4.952957 TCCATCGTCTCTCTGATCTCTTTT 59.047 41.667 0.00 0.00 0.00 2.27
456 464 7.073457 TCATAGGGATACAATTCAAATCCGA 57.927 36.000 4.82 0.00 40.15 4.55
527 539 2.908688 AAAGACACAAATGGCCAACC 57.091 45.000 10.96 0.00 32.13 3.77
528 540 7.954788 TTTTATAAAGACACAAATGGCCAAC 57.045 32.000 10.96 0.00 32.13 3.77
555 567 8.776470 CATTCTAATGCCACATTTCTTGTTTTT 58.224 29.630 0.00 0.00 36.00 1.94
590 602 2.890808 AGCGTGGTATATGTGTGGAG 57.109 50.000 0.00 0.00 0.00 3.86
599 622 4.665212 CGACTTTCACTAAGCGTGGTATA 58.335 43.478 0.00 0.00 43.94 1.47
655 681 3.039202 GACTCGTTGCCGCCATTGG 62.039 63.158 0.00 0.00 0.00 3.16
1259 1288 3.644966 TTGTCCCCAATCACATACTCC 57.355 47.619 0.00 0.00 0.00 3.85
1260 1289 4.156008 GTGTTTGTCCCCAATCACATACTC 59.844 45.833 10.28 0.00 44.86 2.59
1261 1290 4.079253 GTGTTTGTCCCCAATCACATACT 58.921 43.478 10.28 0.00 44.86 2.12
1262 1291 4.079253 AGTGTTTGTCCCCAATCACATAC 58.921 43.478 15.20 0.00 46.58 2.39
1263 1292 4.078537 CAGTGTTTGTCCCCAATCACATA 58.921 43.478 15.20 0.00 46.58 2.29
1264 1293 2.892852 CAGTGTTTGTCCCCAATCACAT 59.107 45.455 15.20 2.92 46.58 3.21
1370 1399 6.737254 AATTTGTAGTTACACTCCCATTCG 57.263 37.500 0.00 0.00 35.64 3.34
1375 1404 6.938596 AGTACCAAATTTGTAGTTACACTCCC 59.061 38.462 16.73 0.00 35.64 4.30
1514 1582 1.202627 GCCTGCTAGACAAGGATCAGG 60.203 57.143 9.98 7.39 42.83 3.86
1664 1766 3.437741 GTGGTTAACCTCCCACGTTATTG 59.562 47.826 24.78 0.00 41.55 1.90
1702 1804 3.066621 GTCATCTGGTTTGCAGTTGTCAA 59.933 43.478 0.00 0.00 0.00 3.18
1709 1811 2.880268 TCAACAGTCATCTGGTTTGCAG 59.120 45.455 0.00 0.00 45.14 4.41
2135 3749 2.701107 GTTCAGTAGCTCCTTGAACCC 58.299 52.381 19.44 4.20 42.91 4.11
2232 3860 9.871238 GAAACTTCACTCTACTAATTCCATACA 57.129 33.333 0.00 0.00 0.00 2.29
2463 4230 1.728425 CTCACCATGACATGTGACACG 59.272 52.381 14.26 0.55 0.00 4.49
2562 4413 9.177304 CATGCAAGATATTGATGATGTTGTTAC 57.823 33.333 3.77 0.00 31.83 2.50
2828 4681 5.475719 CCACACAAGTTTCTTCTATACGGA 58.524 41.667 0.00 0.00 0.00 4.69
3117 4973 5.108518 CGAAATCAAATATCGTTGCATGCTG 60.109 40.000 20.33 9.00 0.00 4.41
3213 5772 8.785329 AACTCATAGACAAGAATCCTTTCTTC 57.215 34.615 0.00 0.00 46.88 2.87
3289 5848 6.971184 GGTGTGCTTGAAAAATATCTCTGATG 59.029 38.462 0.00 0.00 0.00 3.07
3715 6536 1.137086 CTGATACCTGGTTCCCACGAG 59.863 57.143 3.84 0.00 0.00 4.18
3796 7038 6.789262 AGTGAAACAAAAGATGTGAAGACTG 58.211 36.000 0.00 0.00 42.99 3.51
3797 7039 7.396540 AAGTGAAACAAAAGATGTGAAGACT 57.603 32.000 0.00 0.00 42.99 3.24
3803 7045 7.201461 CCACTGAAAAGTGAAACAAAAGATGTG 60.201 37.037 7.43 0.00 40.87 3.21
3840 7084 4.859326 ACTCCTCGAGATGCATACTCTGC 61.859 52.174 15.71 0.00 41.17 4.26
3881 7125 0.248458 AAACGCCAAAGCTGAACACG 60.248 50.000 0.00 0.00 36.60 4.49
4109 7362 5.957842 TGCTTTTACACACCCTATTTGAG 57.042 39.130 0.00 0.00 0.00 3.02
4229 7489 1.619654 CTCATGCAACCTTTGGTCCA 58.380 50.000 0.00 0.00 33.12 4.02
4259 7519 3.376636 TCATATCCGTCCCCTAACAACA 58.623 45.455 0.00 0.00 0.00 3.33
4344 7604 1.091771 CATCTGTCATGGTGGACCGC 61.092 60.000 0.00 0.00 39.43 5.68
4348 7608 1.825090 GCAACATCTGTCATGGTGGA 58.175 50.000 1.96 0.00 37.22 4.02
4368 7630 2.670509 GCTTTCAGAGTTCAGCATTGCC 60.671 50.000 4.70 0.00 32.17 4.52
4391 7653 1.549203 AGGCACCATTGGTAAGCTTG 58.451 50.000 9.86 0.00 32.11 4.01
4458 7720 0.823356 ATTGGCCCATGTATGTCGGC 60.823 55.000 0.00 0.15 40.85 5.54
4459 7721 1.238439 GATTGGCCCATGTATGTCGG 58.762 55.000 0.00 0.00 0.00 4.79
4677 7953 5.814705 CCAACCACACACACATGTTTATTTT 59.185 36.000 0.00 0.00 36.72 1.82
4841 8184 3.670055 GCAAACAATTGTTCTCATGTCCG 59.330 43.478 23.47 5.96 38.85 4.79
4856 8199 6.402222 AGTATCAGTTTTGGTTTGCAAACAA 58.598 32.000 35.95 27.24 40.63 2.83
5106 8464 6.724694 GCATGGTGCATTCAGATTTAAAAA 57.275 33.333 0.00 0.00 44.26 1.94
5359 8766 3.744719 TCTGAACCCGAGTCGGCG 61.745 66.667 26.60 20.44 46.86 6.46
5370 8777 3.347958 TTTTGGCACGAATGTCTGAAC 57.652 42.857 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.