Multiple sequence alignment - TraesCS4D01G008600

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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 TraesCS4D01G008600 chr4D 100.000 4861 0 0 1 4861 4245828 4250688 0.000000e+00 8977.0
1 TraesCS4D01G008600 chr4D 86.901 1710 138 27 129 1806 4287940 4286285 0.000000e+00 1838.0
2 TraesCS4D01G008600 chr4D 92.086 973 65 10 2948 3914 4285342 4284376 0.000000e+00 1360.0
3 TraesCS4D01G008600 chr4D 78.587 1415 234 39 2625 3994 4208868 4210258 0.000000e+00 870.0
4 TraesCS4D01G008600 chr4D 79.293 1217 218 26 2867 4061 4273340 4272136 0.000000e+00 821.0
5 TraesCS4D01G008600 chr4D 87.975 632 45 12 992 1614 4333066 4332457 0.000000e+00 717.0
6 TraesCS4D01G008600 chr4D 89.919 496 41 4 1610 2097 4331976 4331482 8.880000e-177 630.0
7 TraesCS4D01G008600 chr4D 88.402 388 42 3 1 386 4333511 4333125 9.530000e-127 464.0
8 TraesCS4D01G008600 chr4D 77.138 538 101 16 1286 1817 4321142 4320621 4.760000e-75 292.0
9 TraesCS4D01G008600 chr4D 90.863 197 16 1 2596 2790 4285583 4285387 3.730000e-66 263.0
10 TraesCS4D01G008600 chr4D 80.403 347 54 9 4514 4854 6385798 6385460 8.080000e-63 252.0
11 TraesCS4D01G008600 chr4D 72.931 894 161 40 1901 2774 4274321 4273489 8.130000e-58 235.0
12 TraesCS4D01G008600 chr4A 93.317 4923 237 30 1 4861 599647364 599642472 0.000000e+00 7184.0
13 TraesCS4D01G008600 chr4A 73.565 1498 273 64 1283 2764 599628296 599629686 4.430000e-125 459.0
14 TraesCS4D01G008600 chr4A 77.939 621 104 21 1 602 600279776 600280382 1.660000e-94 357.0
15 TraesCS4D01G008600 chr4B 93.202 2589 127 13 1 2573 4334281 4331726 0.000000e+00 3760.0
16 TraesCS4D01G008600 chr4B 92.110 2573 133 23 1908 4430 4301749 4299197 0.000000e+00 3563.0
17 TraesCS4D01G008600 chr4B 91.549 1846 102 16 2625 4430 4331715 4329884 0.000000e+00 2495.0
18 TraesCS4D01G008600 chr4B 90.880 932 59 9 1 923 4303229 4302315 0.000000e+00 1227.0
19 TraesCS4D01G008600 chr4B 95.096 571 27 1 1308 1877 4302320 4301750 0.000000e+00 898.0
20 TraesCS4D01G008600 chr4B 88.558 437 40 3 4425 4861 4287631 4287205 5.580000e-144 521.0
21 TraesCS4D01G008600 chr4B 77.108 166 30 7 2601 2762 7501274 7501435 6.700000e-14 89.8
22 TraesCS4D01G008600 chr5A 84.530 724 92 8 1072 1790 555596479 555595771 0.000000e+00 699.0
23 TraesCS4D01G008600 chr5A 77.839 361 62 13 4515 4859 219678491 219678849 1.770000e-49 207.0
24 TraesCS4D01G008600 chr5D 82.988 723 104 10 1072 1789 439980444 439979736 1.910000e-178 636.0
25 TraesCS4D01G008600 chr5B 82.148 745 102 8 1072 1811 534776171 534775453 1.160000e-170 610.0
26 TraesCS4D01G008600 chr5B 84.320 625 79 7 1192 1811 534487935 534487325 1.160000e-165 593.0
27 TraesCS4D01G008600 chr5B 80.163 736 90 22 1077 1806 534589622 534588937 2.610000e-137 499.0
28 TraesCS4D01G008600 chr5B 81.329 316 46 7 1072 1381 534605461 534605153 1.350000e-60 244.0
29 TraesCS4D01G008600 chrUn 73.565 1498 273 64 1283 2764 47346710 47348100 4.430000e-125 459.0
30 TraesCS4D01G008600 chrUn 77.108 166 30 7 2601 2762 476939207 476939368 6.700000e-14 89.8
31 TraesCS4D01G008600 chrUn 84.270 89 13 1 4514 4602 99119094 99119181 8.670000e-13 86.1
32 TraesCS4D01G008600 chr2D 82.955 352 38 16 4515 4857 190329174 190328836 1.020000e-76 298.0
33 TraesCS4D01G008600 chr2D 82.386 352 52 9 4514 4861 472020066 472020411 1.020000e-76 298.0
34 TraesCS4D01G008600 chr2D 81.768 362 49 12 4514 4860 537450884 537450525 2.210000e-73 287.0
35 TraesCS4D01G008600 chr2B 82.029 345 43 13 4525 4861 247365745 247365412 4.790000e-70 276.0
36 TraesCS4D01G008600 chr1B 81.127 355 49 14 4514 4857 325272393 325272740 8.020000e-68 268.0
37 TraesCS4D01G008600 chr7D 80.398 352 50 15 4516 4858 603802212 603802553 2.900000e-62 250.0
38 TraesCS4D01G008600 chr7D 77.814 311 56 9 1300 1607 629888198 629887898 3.870000e-41 180.0
39 TraesCS4D01G008600 chr6D 78.992 357 61 9 4513 4861 301739402 301739752 1.050000e-56 231.0
40 TraesCS4D01G008600 chr3D 86.826 167 13 4 882 1040 542140147 542140312 1.390000e-40 178.0
41 TraesCS4D01G008600 chr3D 86.624 157 13 3 882 1030 542132283 542132439 3.010000e-37 167.0
42 TraesCS4D01G008600 chr3D 85.030 167 16 4 882 1040 542143788 542143953 1.400000e-35 161.0
43 TraesCS4D01G008600 chr3A 87.421 159 12 3 882 1032 678379032 678379190 5.000000e-40 176.0
44 TraesCS4D01G008600 chr3B 85.629 167 15 4 882 1040 717689044 717689209 3.010000e-37 167.0
45 TraesCS4D01G008600 chr3B 84.431 167 17 5 882 1040 717692789 717692954 6.510000e-34 156.0
46 TraesCS4D01G008600 chr1D 91.045 67 6 0 4514 4580 95931360 95931426 1.860000e-14 91.6


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 TraesCS4D01G008600 chr4D 4245828 4250688 4860 False 8977.000000 8977 100.000000 1 4861 1 chr4D.!!$F2 4860
1 TraesCS4D01G008600 chr4D 4284376 4287940 3564 True 1153.666667 1838 89.950000 129 3914 3 chr4D.!!$R4 3785
2 TraesCS4D01G008600 chr4D 4208868 4210258 1390 False 870.000000 870 78.587000 2625 3994 1 chr4D.!!$F1 1369
3 TraesCS4D01G008600 chr4D 4331482 4333511 2029 True 603.666667 717 88.765333 1 2097 3 chr4D.!!$R5 2096
4 TraesCS4D01G008600 chr4D 4272136 4274321 2185 True 528.000000 821 76.112000 1901 4061 2 chr4D.!!$R3 2160
5 TraesCS4D01G008600 chr4D 4320621 4321142 521 True 292.000000 292 77.138000 1286 1817 1 chr4D.!!$R1 531
6 TraesCS4D01G008600 chr4A 599642472 599647364 4892 True 7184.000000 7184 93.317000 1 4861 1 chr4A.!!$R1 4860
7 TraesCS4D01G008600 chr4A 599628296 599629686 1390 False 459.000000 459 73.565000 1283 2764 1 chr4A.!!$F1 1481
8 TraesCS4D01G008600 chr4A 600279776 600280382 606 False 357.000000 357 77.939000 1 602 1 chr4A.!!$F2 601
9 TraesCS4D01G008600 chr4B 4329884 4334281 4397 True 3127.500000 3760 92.375500 1 4430 2 chr4B.!!$R3 4429
10 TraesCS4D01G008600 chr4B 4299197 4303229 4032 True 1896.000000 3563 92.695333 1 4430 3 chr4B.!!$R2 4429
11 TraesCS4D01G008600 chr5A 555595771 555596479 708 True 699.000000 699 84.530000 1072 1790 1 chr5A.!!$R1 718
12 TraesCS4D01G008600 chr5D 439979736 439980444 708 True 636.000000 636 82.988000 1072 1789 1 chr5D.!!$R1 717
13 TraesCS4D01G008600 chr5B 534775453 534776171 718 True 610.000000 610 82.148000 1072 1811 1 chr5B.!!$R4 739
14 TraesCS4D01G008600 chr5B 534487325 534487935 610 True 593.000000 593 84.320000 1192 1811 1 chr5B.!!$R1 619
15 TraesCS4D01G008600 chr5B 534588937 534589622 685 True 499.000000 499 80.163000 1077 1806 1 chr5B.!!$R2 729
16 TraesCS4D01G008600 chrUn 47346710 47348100 1390 False 459.000000 459 73.565000 1283 2764 1 chrUn.!!$F1 1481

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
179 198 0.096628 GCAGCACTTCAATGAGCTCG 59.903 55.000 9.64 0.0 34.61 5.03 F
335 364 0.393944 ACATCCTCTACCGCTCGACA 60.394 55.000 0.00 0.0 0.00 4.35 F
532 577 0.596600 GTTATCGATTCTGCGCCGGA 60.597 55.000 5.05 0.0 0.00 5.14 F
1846 2448 1.070758 AGTTATGGCTTGCCGATCGAT 59.929 47.619 18.66 0.0 0.00 3.59 F
2595 3257 2.778299 TGGCACAATAGCGTTTTCTCT 58.222 42.857 0.00 0.0 31.92 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1502 1597 0.037790 GATGGATGAGTAGCCGAGCC 60.038 60.000 0.00 0.00 34.20 4.70 R
1820 2422 1.543802 CGGCAAGCCATAACTTTTCCA 59.456 47.619 12.19 0.00 35.37 3.53 R
2421 3052 1.724582 GGCAAAGTGTCACTTGCCGT 61.725 55.000 28.06 11.14 40.11 5.68 R
2682 3344 0.099436 GACGGAATTGCATGCAGGAC 59.901 55.000 21.50 14.82 0.00 3.85 R
3910 4686 0.526211 GGCATTCCAAAAGACGGGAC 59.474 55.000 0.00 0.00 31.59 4.46 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
124 143 3.354678 GTGCAGGCACGAAACCAT 58.645 55.556 8.84 0.00 37.19 3.55
179 198 0.096628 GCAGCACTTCAATGAGCTCG 59.903 55.000 9.64 0.00 34.61 5.03
236 257 2.587194 GAGATCGCGCACCATGCT 60.587 61.111 8.75 0.00 42.25 3.79
319 348 2.005960 GACCACGAGCTCGCCTACAT 62.006 60.000 34.83 12.67 44.43 2.29
333 362 1.542767 CCTACATCCTCTACCGCTCGA 60.543 57.143 0.00 0.00 0.00 4.04
335 364 0.393944 ACATCCTCTACCGCTCGACA 60.394 55.000 0.00 0.00 0.00 4.35
452 497 3.619242 CGGCGAGGTCTGGACTATCTATA 60.619 52.174 0.00 0.00 0.00 1.31
453 498 4.528920 GGCGAGGTCTGGACTATCTATAT 58.471 47.826 0.67 0.00 0.00 0.86
454 499 5.682659 GGCGAGGTCTGGACTATCTATATA 58.317 45.833 0.67 0.00 0.00 0.86
455 500 5.761234 GGCGAGGTCTGGACTATCTATATAG 59.239 48.000 3.10 3.10 40.90 1.31
456 501 5.237779 GCGAGGTCTGGACTATCTATATAGC 59.762 48.000 4.75 0.00 39.01 2.97
457 502 6.350103 CGAGGTCTGGACTATCTATATAGCA 58.650 44.000 4.75 0.00 39.01 3.49
458 503 6.481976 CGAGGTCTGGACTATCTATATAGCAG 59.518 46.154 4.75 7.17 39.01 4.24
459 504 7.517898 AGGTCTGGACTATCTATATAGCAGA 57.482 40.000 14.62 12.29 39.01 4.26
481 526 8.405531 GCAGATATAGCAGGAACATGTTTTAAA 58.594 33.333 13.36 0.00 0.00 1.52
532 577 0.596600 GTTATCGATTCTGCGCCGGA 60.597 55.000 5.05 0.00 0.00 5.14
564 609 1.629013 GCAAAATTGTCTTAGGGCGC 58.371 50.000 0.00 0.00 0.00 6.53
805 869 2.315925 ACCAGACAGTTCACACACAG 57.684 50.000 0.00 0.00 0.00 3.66
818 882 5.794687 TCACACACAGAAAAGTACAACAG 57.205 39.130 0.00 0.00 0.00 3.16
1502 1597 1.203928 CGCTTCTGTTATCTCGGCTG 58.796 55.000 0.00 0.00 0.00 4.85
1780 2382 7.284489 AGCCATAAGTAGAATTGCCGAATTTAA 59.716 33.333 0.00 0.00 31.58 1.52
1820 2422 3.569194 TGTACCGTTATCCATGCCAAT 57.431 42.857 0.00 0.00 0.00 3.16
1846 2448 1.070758 AGTTATGGCTTGCCGATCGAT 59.929 47.619 18.66 0.00 0.00 3.59
1861 2463 3.485743 CGATCGATGAATACTTTGTCGCA 59.514 43.478 10.26 0.00 32.74 5.10
2084 2688 3.243501 GCTCTGCAAGGAACAATTTGTCA 60.244 43.478 1.83 0.00 0.00 3.58
2107 2716 4.995124 TCTTGCGGACATTTCTAGTAGTC 58.005 43.478 0.00 0.00 0.00 2.59
2292 2913 5.760743 TGTTGTTTCTATTCCGATGTGTTGA 59.239 36.000 0.00 0.00 0.00 3.18
2380 3011 6.303839 AGAAGAGCCCAATTTACTTGTGTTA 58.696 36.000 0.00 0.00 32.61 2.41
2595 3257 2.778299 TGGCACAATAGCGTTTTCTCT 58.222 42.857 0.00 0.00 31.92 3.10
2596 3258 3.932822 TGGCACAATAGCGTTTTCTCTA 58.067 40.909 0.00 0.00 31.92 2.43
2597 3259 3.932710 TGGCACAATAGCGTTTTCTCTAG 59.067 43.478 0.00 0.00 31.92 2.43
2682 3344 3.476552 TGGTGCTAAGAAAGTGAACCTG 58.523 45.455 0.00 0.00 0.00 4.00
2721 3383 1.470098 CGGTTCAATGAGCCAAGAAGG 59.530 52.381 16.22 0.00 41.84 3.46
2803 3513 9.277565 CACACTCTGTATTGTTTACATTATTGC 57.722 33.333 0.00 0.00 0.00 3.56
2883 3608 2.031769 TGCTCGTTCACTTCATTTGCAG 60.032 45.455 0.00 0.00 0.00 4.41
3001 3727 7.124901 TGACTAAATCTGAGATGGCTAGAGTTT 59.875 37.037 0.00 0.00 32.01 2.66
3401 4137 5.938710 TCAGTAGCTATATGAGGTAGTTCGG 59.061 44.000 0.00 0.00 39.34 4.30
3754 4504 3.134574 TCTTGCGTAGGAACACCATTT 57.865 42.857 0.00 0.00 31.87 2.32
3910 4686 7.151999 TGGTTTTGTTATATGTTGTAGGCTG 57.848 36.000 0.00 0.00 0.00 4.85
3937 4724 1.535462 CTTTTGGAATGCCGACGTCTT 59.465 47.619 14.70 0.01 36.79 3.01
3961 4748 4.322080 CTTGAACAAGGGGAAAGGTTTC 57.678 45.455 6.66 0.00 34.87 2.78
3987 4774 9.893305 CTTGGTTATCAAAAACTACACTAAAGG 57.107 33.333 0.00 0.00 34.56 3.11
4063 4850 2.055689 TTGCTGACCTCCACCACCTG 62.056 60.000 0.00 0.00 0.00 4.00
4097 4907 2.357034 TCTGCGGGCGAACAAGAC 60.357 61.111 0.00 0.00 0.00 3.01
4098 4908 2.357517 CTGCGGGCGAACAAGACT 60.358 61.111 0.00 0.00 0.00 3.24
4121 4931 2.587053 ACTAGGAGGAGGAGGTAAGGT 58.413 52.381 0.00 0.00 0.00 3.50
4248 5058 4.985538 TGAGTGTCTTCAAGGCCTTTATT 58.014 39.130 17.61 0.00 0.00 1.40
4281 5091 2.650116 CCAGGGACTCGGTCACCTG 61.650 68.421 21.22 21.22 43.74 4.00
4341 5151 0.855349 GCCATCTACGCGATCAAGTG 59.145 55.000 15.93 3.47 0.00 3.16
4417 5227 1.272816 TGACCCCCTCGATGTTCTACA 60.273 52.381 0.00 0.00 0.00 2.74
4470 5280 2.252676 TCTCCCCCTCCCAGAAATATCA 59.747 50.000 0.00 0.00 0.00 2.15
4471 5281 3.115803 TCTCCCCCTCCCAGAAATATCAT 60.116 47.826 0.00 0.00 0.00 2.45
4478 5288 4.596643 CCTCCCAGAAATATCATGTCCTCT 59.403 45.833 0.00 0.00 0.00 3.69
4484 5294 4.526262 AGAAATATCATGTCCTCTCCTCCG 59.474 45.833 0.00 0.00 0.00 4.63
4499 5309 4.077184 CCGCCCGCAGAGTTGGTA 62.077 66.667 0.00 0.00 0.00 3.25
4504 5314 1.369625 CCCGCAGAGTTGGTACATTC 58.630 55.000 0.00 0.00 39.30 2.67
4508 5318 3.325870 CGCAGAGTTGGTACATTCTTCA 58.674 45.455 0.00 0.00 39.30 3.02
4550 5360 1.450848 CATCACACGGCCTCTGCAT 60.451 57.895 0.00 0.00 40.13 3.96
4556 5366 0.463295 CACGGCCTCTGCATCAGAAT 60.463 55.000 0.00 0.00 40.18 2.40
4557 5367 0.463295 ACGGCCTCTGCATCAGAATG 60.463 55.000 0.00 0.00 40.18 2.67
4569 5379 1.029681 TCAGAATGATGCATGCAGCC 58.970 50.000 31.30 22.02 42.56 4.85
4572 5382 1.613925 AGAATGATGCATGCAGCCATC 59.386 47.619 31.30 26.60 44.83 3.51
4602 5412 3.188254 ACAGTGCCAAAACAAAACAAAGC 59.812 39.130 0.00 0.00 0.00 3.51
4604 5414 2.746904 GTGCCAAAACAAAACAAAGCCT 59.253 40.909 0.00 0.00 0.00 4.58
4623 5433 3.064545 GCCTGCAATTCAGTACATCTCAC 59.935 47.826 0.00 0.00 41.25 3.51
4633 5443 1.476891 GTACATCTCACGGAAGGAGCA 59.523 52.381 0.00 0.00 32.38 4.26
4638 5448 4.141620 ACATCTCACGGAAGGAGCATAAAT 60.142 41.667 0.00 0.00 32.38 1.40
4676 5486 2.893671 GCCACAAACGGCGAAAAAT 58.106 47.368 16.62 0.00 43.52 1.82
4679 5489 2.350964 GCCACAAACGGCGAAAAATAGA 60.351 45.455 16.62 0.00 43.52 1.98
4736 5546 3.306433 GCCATCCAAACCGGTTGTAAATT 60.306 43.478 23.08 0.00 35.23 1.82
4741 5551 3.310246 CAAACCGGTTGTAAATTTCCCG 58.690 45.455 23.08 2.88 38.39 5.14
4748 5558 3.119743 GGTTGTAAATTTCCCGTGCTACC 60.120 47.826 0.00 0.00 0.00 3.18
4749 5559 2.348660 TGTAAATTTCCCGTGCTACCG 58.651 47.619 0.00 0.00 0.00 4.02
4753 5563 0.611714 ATTTCCCGTGCTACCGTCTT 59.388 50.000 0.00 0.00 0.00 3.01
4815 5625 4.566759 CCATATGAGTGAGTAACAACCACG 59.433 45.833 3.65 0.00 36.06 4.94
4827 5637 1.337447 ACAACCACGTACGGATCCAAG 60.337 52.381 21.06 5.61 0.00 3.61
4828 5638 0.390735 AACCACGTACGGATCCAAGC 60.391 55.000 21.06 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 127 1.305219 GCTATGGTTTCGTGCCTGCA 61.305 55.000 0.00 0.00 0.00 4.41
179 198 4.459089 GCCGTCCAGAGTGGCTCC 62.459 72.222 4.06 0.00 45.40 4.70
319 348 1.725557 GCATGTCGAGCGGTAGAGGA 61.726 60.000 0.00 0.00 0.00 3.71
452 497 6.617782 ACATGTTCCTGCTATATCTGCTAT 57.382 37.500 0.00 0.00 0.00 2.97
453 498 6.425210 AACATGTTCCTGCTATATCTGCTA 57.575 37.500 4.92 0.00 0.00 3.49
454 499 4.970860 ACATGTTCCTGCTATATCTGCT 57.029 40.909 0.00 0.00 0.00 4.24
455 500 6.382869 AAAACATGTTCCTGCTATATCTGC 57.617 37.500 12.39 0.00 0.00 4.26
512 557 0.874175 CCGGCGCAGAATCGATAACA 60.874 55.000 10.83 0.00 0.00 2.41
514 559 0.318699 CTCCGGCGCAGAATCGATAA 60.319 55.000 10.83 0.00 0.00 1.75
532 577 1.549203 ATTTTGCGGGCAGTTCATCT 58.451 45.000 0.00 0.00 0.00 2.90
564 609 3.289911 TCCGCAAAATCGTTTTACGTTG 58.710 40.909 0.00 0.00 43.14 4.10
805 869 4.927425 TGCGATACTCCTGTTGTACTTTTC 59.073 41.667 0.00 0.00 0.00 2.29
1502 1597 0.037790 GATGGATGAGTAGCCGAGCC 60.038 60.000 0.00 0.00 34.20 4.70
1780 2382 4.134563 ACATCCGTTAAAAGAAGCACAGT 58.865 39.130 0.00 0.00 0.00 3.55
1820 2422 1.543802 CGGCAAGCCATAACTTTTCCA 59.456 47.619 12.19 0.00 35.37 3.53
1846 2448 7.428282 TCTTTACAATGCGACAAAGTATTCA 57.572 32.000 0.00 0.00 31.44 2.57
1968 2570 5.543714 TGAGTGTATACGACAACCACAAAT 58.456 37.500 0.00 0.00 40.66 2.32
2084 2688 5.127194 TGACTACTAGAAATGTCCGCAAGAT 59.873 40.000 0.00 0.00 43.02 2.40
2380 3011 9.653287 ACGAATATCGACAATTCCATTATACAT 57.347 29.630 13.82 0.00 43.74 2.29
2421 3052 1.724582 GGCAAAGTGTCACTTGCCGT 61.725 55.000 28.06 11.14 40.11 5.68
2432 3063 7.305474 AGAGATTTTTACAATACGGCAAAGTG 58.695 34.615 0.00 0.00 0.00 3.16
2586 3248 9.214953 CAAGCTTATTAAATGCTAGAGAAAACG 57.785 33.333 0.00 0.00 35.85 3.60
2595 3257 9.816354 GGGAATTTTCAAGCTTATTAAATGCTA 57.184 29.630 0.00 0.00 35.85 3.49
2596 3258 8.542926 AGGGAATTTTCAAGCTTATTAAATGCT 58.457 29.630 0.00 0.00 38.87 3.79
2597 3259 8.606602 CAGGGAATTTTCAAGCTTATTAAATGC 58.393 33.333 0.00 4.29 0.00 3.56
2682 3344 0.099436 GACGGAATTGCATGCAGGAC 59.901 55.000 21.50 14.82 0.00 3.85
2721 3383 7.894708 AGGTACTAAGTACTGACCTTTCTTTC 58.105 38.462 11.42 0.00 37.20 2.62
2766 3434 8.908786 ACAATACAGAGTGTGGATAATAATGG 57.091 34.615 0.00 0.00 31.31 3.16
2803 3513 6.396829 AAAGGAAATCAGTCTTCAGGTTTG 57.603 37.500 0.00 0.00 0.00 2.93
2857 3567 2.325583 TGAAGTGAACGAGCAGGTTT 57.674 45.000 0.00 0.00 0.00 3.27
3401 4137 9.766277 CTGAGAAACAAAGAAATTATACTGCTC 57.234 33.333 0.00 0.00 0.00 4.26
3465 4201 4.735369 TCATCCATGTTACAAGGTGGTTT 58.265 39.130 6.51 0.00 33.47 3.27
3548 4289 6.064060 TCCAGCTTCATCAAAAGAAGAAAGA 58.936 36.000 7.08 0.00 44.00 2.52
3550 4291 5.242393 CCTCCAGCTTCATCAAAAGAAGAAA 59.758 40.000 7.08 0.00 44.00 2.52
3754 4504 4.799678 TGTTTTGTTTGAAGACTTGCGAA 58.200 34.783 0.00 0.00 0.00 4.70
3910 4686 0.526211 GGCATTCCAAAAGACGGGAC 59.474 55.000 0.00 0.00 31.59 4.46
3937 4724 2.246327 ACCTTTCCCCTTGTTCAAGGAA 59.754 45.455 27.06 15.02 42.62 3.36
3961 4748 9.893305 CCTTTAGTGTAGTTTTTGATAACCAAG 57.107 33.333 0.00 0.00 35.94 3.61
3987 4774 1.760192 AAGATCAAGCCATGCACTCC 58.240 50.000 0.00 0.00 0.00 3.85
4021 4808 2.154963 CGACACTCACAATGTACCAACG 59.845 50.000 0.00 0.00 0.00 4.10
4063 4850 3.799420 CGCAGAGCTAGTTTATTCTCCAC 59.201 47.826 0.00 0.00 0.00 4.02
4097 4907 4.042435 CCTTACCTCCTCCTCCTAGTAGAG 59.958 54.167 0.00 0.00 0.00 2.43
4098 4908 3.982052 CCTTACCTCCTCCTCCTAGTAGA 59.018 52.174 0.00 0.00 0.00 2.59
4121 4931 3.501828 CCATTTCACACATCGTCCTTCAA 59.498 43.478 0.00 0.00 0.00 2.69
4212 5022 4.803426 CTCAGTGTCTCCGGCGCC 62.803 72.222 19.07 19.07 0.00 6.53
4224 5034 1.428869 AGGCCTTGAAGACACTCAGT 58.571 50.000 0.00 0.00 0.00 3.41
4228 5038 4.082125 CCAATAAAGGCCTTGAAGACACT 58.918 43.478 21.33 2.55 0.00 3.55
4248 5058 1.369692 CTGGCGGACAACACTACCA 59.630 57.895 0.00 0.00 0.00 3.25
4417 5227 3.960102 AGGGTGTGTCAAATGTTGTCATT 59.040 39.130 0.00 0.00 44.94 2.57
4470 5280 2.444895 GGGCGGAGGAGAGGACAT 60.445 66.667 0.00 0.00 0.00 3.06
4484 5294 0.676782 AATGTACCAACTCTGCGGGC 60.677 55.000 0.00 0.00 0.00 6.13
4488 5298 4.153117 CACTGAAGAATGTACCAACTCTGC 59.847 45.833 0.00 0.00 0.00 4.26
4521 5331 1.134965 CCGTGTGATGTCCTCCTTCTC 60.135 57.143 0.00 0.00 0.00 2.87
4536 5346 1.830587 TTCTGATGCAGAGGCCGTGT 61.831 55.000 9.61 0.00 41.75 4.49
4550 5360 1.029681 GGCTGCATGCATCATTCTGA 58.970 50.000 22.97 0.00 45.15 3.27
4556 5366 2.351706 TAAGATGGCTGCATGCATCA 57.648 45.000 22.97 21.78 45.15 3.07
4557 5367 3.936372 AATAAGATGGCTGCATGCATC 57.064 42.857 22.97 17.75 45.15 3.91
4561 5371 5.975344 CACTGTTTAATAAGATGGCTGCATG 59.025 40.000 0.50 0.00 0.00 4.06
4569 5379 8.586570 TTGTTTTGGCACTGTTTAATAAGATG 57.413 30.769 0.00 0.00 0.00 2.90
4572 5382 8.660373 TGTTTTGTTTTGGCACTGTTTAATAAG 58.340 29.630 0.00 0.00 0.00 1.73
4604 5414 3.056179 TCCGTGAGATGTACTGAATTGCA 60.056 43.478 0.00 0.00 0.00 4.08
4666 5476 5.216566 TCATCTTGTTCTATTTTTCGCCG 57.783 39.130 0.00 0.00 0.00 6.46
4667 5477 9.010366 GTTTATCATCTTGTTCTATTTTTCGCC 57.990 33.333 0.00 0.00 0.00 5.54
4696 5506 3.578978 TGGCGGTCCAGTAATAGGATAA 58.421 45.455 0.00 0.00 37.47 1.75
4736 5546 1.588082 GAAGACGGTAGCACGGGAA 59.412 57.895 0.00 0.00 38.39 3.97
4741 5551 1.445582 CGGTGGAAGACGGTAGCAC 60.446 63.158 0.00 0.00 0.00 4.40
4748 5558 2.280524 TGCAACCGGTGGAAGACG 60.281 61.111 15.02 0.00 0.00 4.18
4749 5559 3.340789 GTGCAACCGGTGGAAGAC 58.659 61.111 15.02 1.39 0.00 3.01
4815 5625 1.854227 GCTACTGCTTGGATCCGTAC 58.146 55.000 7.39 0.00 36.03 3.67


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

AutoCloner maintained by Alex Coulton.