Multiple sequence alignment - TraesCS3A01G109400

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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 TraesCS3A01G109400 chr3A 100.000 4453 0 0 1 4453 75414769 75410317 0.000000e+00 8224.0
1 TraesCS3A01G109400 chr3A 80.861 836 86 28 3 793 75441514 75440708 1.380000e-164 590.0
2 TraesCS3A01G109400 chr3A 81.690 142 20 6 3 142 175363196 175363333 3.640000e-21 113.0
3 TraesCS3A01G109400 chr3D 94.886 1975 88 9 1668 3636 64648589 64646622 0.000000e+00 3075.0
4 TraesCS3A01G109400 chr3D 92.776 526 28 6 823 1344 64649494 64648975 0.000000e+00 752.0
5 TraesCS3A01G109400 chr3D 85.575 617 60 17 29 620 64650811 64650199 1.760000e-173 619.0
6 TraesCS3A01G109400 chr3D 91.899 395 18 7 3629 4012 64646579 64646188 1.410000e-149 540.0
7 TraesCS3A01G109400 chr3D 75.895 531 113 11 2536 3062 508203876 508203357 1.590000e-64 257.0
8 TraesCS3A01G109400 chr3D 90.909 143 6 3 1413 1548 64648835 64648693 7.610000e-43 185.0
9 TraesCS3A01G109400 chr3D 96.154 78 3 0 1337 1414 64648943 64648866 1.300000e-25 128.0
10 TraesCS3A01G109400 chr3D 90.000 60 5 1 4 62 5861055 5861114 4.780000e-10 76.8
11 TraesCS3A01G109400 chr3B 95.791 1378 50 4 2117 3489 107670019 107668645 0.000000e+00 2217.0
12 TraesCS3A01G109400 chr3B 90.951 652 35 10 3806 4453 107668145 107667514 0.000000e+00 856.0
13 TraesCS3A01G109400 chr3B 91.205 614 30 12 1537 2139 107670711 107670111 0.000000e+00 813.0
14 TraesCS3A01G109400 chr3B 84.080 848 90 20 3 812 107772089 107771249 0.000000e+00 776.0
15 TraesCS3A01G109400 chr3B 91.361 463 28 4 882 1344 107671502 107671052 1.360000e-174 623.0
16 TraesCS3A01G109400 chr3B 76.770 551 115 10 2536 3083 670533825 670533285 3.370000e-76 296.0
17 TraesCS3A01G109400 chr3B 93.431 137 8 1 1413 1548 107670920 107670784 7.550000e-48 202.0
18 TraesCS3A01G109400 chr3B 90.071 141 10 4 3488 3626 107668484 107668346 3.540000e-41 180.0
19 TraesCS3A01G109400 chr3B 100.000 36 0 0 823 858 107671538 107671503 2.870000e-07 67.6
20 TraesCS3A01G109400 chr5A 85.333 150 15 7 4 149 145682084 145681938 9.980000e-32 148.0
21 TraesCS3A01G109400 chr2D 83.696 92 10 5 54 142 32767077 32766988 1.030000e-11 82.4
22 TraesCS3A01G109400 chr2B 77.444 133 20 9 20 142 710050080 710050212 2.220000e-08 71.3
23 TraesCS3A01G109400 chr1B 87.302 63 7 1 88 149 86954113 86954175 2.220000e-08 71.3


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 TraesCS3A01G109400 chr3A 75410317 75414769 4452 True 8224.000000 8224 100.000000 1 4453 1 chr3A.!!$R1 4452
1 TraesCS3A01G109400 chr3A 75440708 75441514 806 True 590.000000 590 80.861000 3 793 1 chr3A.!!$R2 790
2 TraesCS3A01G109400 chr3D 64646188 64650811 4623 True 883.166667 3075 92.033167 29 4012 6 chr3D.!!$R2 3983
3 TraesCS3A01G109400 chr3D 508203357 508203876 519 True 257.000000 257 75.895000 2536 3062 1 chr3D.!!$R1 526
4 TraesCS3A01G109400 chr3B 107771249 107772089 840 True 776.000000 776 84.080000 3 812 1 chr3B.!!$R1 809
5 TraesCS3A01G109400 chr3B 107667514 107671538 4024 True 708.371429 2217 93.258571 823 4453 7 chr3B.!!$R3 3630
6 TraesCS3A01G109400 chr3B 670533285 670533825 540 True 296.000000 296 76.770000 2536 3083 1 chr3B.!!$R2 547

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
460 468 0.175760 GCCCATCTAGCGTTCAGTGA 59.824 55.000 0.0 0.0 0.0 3.41 F
1368 1961 1.228429 TTGGCTCCCGGTTTCCTTG 60.228 57.895 0.0 0.0 0.0 3.61 F
2804 3649 0.106708 TGGAGCATGACGGCCTTATC 59.893 55.000 0.0 0.0 0.0 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 2577 1.693627 ACTTCGATCGATAGGTGGCT 58.306 50.0 20.18 0.8 0.0 4.75 R
2806 3651 0.106894 CCTCTTAGGGCCGGACATTC 59.893 60.0 11.00 0.0 0.0 2.67 R
4282 5358 0.391661 GTGCCATGTCGTCCACTCAT 60.392 55.0 0.00 0.0 0.0 2.90 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
45 46 7.624344 GCATATGCTTCCGGATGAATAGTAAAC 60.624 40.741 20.64 5.97 38.21 2.01
164 167 6.617879 GGTGTAACATTTGGAGGTAACATTC 58.382 40.000 0.00 0.00 39.98 2.67
168 171 6.834168 AACATTTGGAGGTAACATTCGAAT 57.166 33.333 4.39 4.39 41.41 3.34
238 242 9.750125 CTAAAAATTTAGGGATAGCATTTGGAC 57.250 33.333 5.23 0.00 37.16 4.02
260 264 6.959311 GGACGTGACAATAAACACATGTATTC 59.041 38.462 0.00 0.00 36.91 1.75
333 341 5.694995 CTCCCTAGAGCCAAATTGGATTTA 58.305 41.667 17.47 8.34 35.51 1.40
345 353 4.589216 ATTGGATTTACGCATTCCATGG 57.411 40.909 4.97 4.97 39.22 3.66
423 431 6.535508 GCTTTATGAGCGAATAACCCCTATAG 59.464 42.308 0.00 0.00 42.46 1.31
428 436 2.334838 CGAATAACCCCTATAGTGCGC 58.665 52.381 0.00 0.00 0.00 6.09
434 442 1.399744 CCCCTATAGTGCGCTGTGGA 61.400 60.000 10.80 0.00 0.00 4.02
453 461 2.503061 CAGCAGCCCATCTAGCGT 59.497 61.111 0.00 0.00 34.64 5.07
455 463 1.144936 AGCAGCCCATCTAGCGTTC 59.855 57.895 0.00 0.00 34.64 3.95
456 464 1.153369 GCAGCCCATCTAGCGTTCA 60.153 57.895 0.00 0.00 34.64 3.18
460 468 0.175760 GCCCATCTAGCGTTCAGTGA 59.824 55.000 0.00 0.00 0.00 3.41
864 1415 4.966168 ACCCTAACCAAACAAATCCAAACT 59.034 37.500 0.00 0.00 0.00 2.66
866 1417 6.266786 ACCCTAACCAAACAAATCCAAACTAG 59.733 38.462 0.00 0.00 0.00 2.57
939 1490 2.004733 GCCTGCGGAGTAAAAACGTAT 58.995 47.619 2.36 0.00 0.00 3.06
978 1529 1.600663 CGAGGACAATCCGATCGAAGG 60.601 57.143 18.66 5.59 42.75 3.46
979 1530 1.681793 GAGGACAATCCGATCGAAGGA 59.318 52.381 18.66 14.22 42.75 3.36
980 1531 2.100916 GAGGACAATCCGATCGAAGGAA 59.899 50.000 18.66 0.00 42.75 3.36
981 1532 2.101582 AGGACAATCCGATCGAAGGAAG 59.898 50.000 18.66 13.36 42.75 3.46
1045 1596 4.831307 CGCCGTCGAAGTCCTCCG 62.831 72.222 0.00 0.00 38.10 4.63
1263 1814 2.161609 CAGAAGCAACGGTTATTGGACC 59.838 50.000 0.00 0.00 36.31 4.46
1339 1891 2.447408 ATGATTGCTGAATGGCTCCA 57.553 45.000 0.00 0.00 0.00 3.86
1359 1952 1.338136 ATGTAGGAGGTTGGCTCCCG 61.338 60.000 0.00 0.00 41.76 5.14
1368 1961 1.228429 TTGGCTCCCGGTTTCCTTG 60.228 57.895 0.00 0.00 0.00 3.61
1477 2105 6.982852 TGTTTCAGTAAAAACCAAAGACACA 58.017 32.000 0.00 0.00 38.16 3.72
1478 2106 6.864165 TGTTTCAGTAAAAACCAAAGACACAC 59.136 34.615 0.00 0.00 38.16 3.82
1555 2270 5.948758 TGTGGCCAAAATCATAAGATGTGTA 59.051 36.000 7.24 0.00 33.90 2.90
1731 2451 7.458397 TCTATAAACTTGGTCACTTGGTCAAT 58.542 34.615 0.00 0.00 0.00 2.57
1778 2498 7.818642 TGAAAATTAACGAACGGATGGTATTT 58.181 30.769 0.00 0.00 0.00 1.40
1847 2567 6.064846 ACAAGCACTGTTTCTGTTGATTAG 57.935 37.500 0.00 0.00 32.99 1.73
1857 2577 6.378564 TGTTTCTGTTGATTAGAAAACCCACA 59.621 34.615 0.00 0.00 43.48 4.17
1859 2579 4.518970 TCTGTTGATTAGAAAACCCACAGC 59.481 41.667 0.00 0.00 0.00 4.40
1867 2587 2.092323 GAAAACCCACAGCCACCTATC 58.908 52.381 0.00 0.00 0.00 2.08
2049 2770 5.966935 TCTTTTTGGATGAGTAGGAGGATCT 59.033 40.000 0.00 0.00 33.73 2.75
2101 2825 9.212687 CACTGTTTTCAAATTTTGTATTGCTTG 57.787 29.630 8.89 0.00 0.00 4.01
2112 2836 6.817765 TTTGTATTGCTTGTCCTAAAGAGG 57.182 37.500 0.00 0.00 45.35 3.69
2125 2967 1.523758 AAAGAGGCCACGTGATTCAC 58.476 50.000 19.30 6.73 0.00 3.18
2155 2997 6.936900 TCTAGATTAAAAAGACTGTGCAGCTT 59.063 34.615 0.00 1.76 0.00 3.74
2226 3068 8.455903 AACTTTCTCATTCTCATGAAAGACAA 57.544 30.769 17.53 0.00 44.58 3.18
2227 3069 8.455903 ACTTTCTCATTCTCATGAAAGACAAA 57.544 30.769 17.53 0.00 44.58 2.83
2228 3070 9.075678 ACTTTCTCATTCTCATGAAAGACAAAT 57.924 29.630 17.53 0.00 44.58 2.32
2269 3111 7.546250 AGTTTCCTCTGATTTTCTCTAGTCA 57.454 36.000 0.00 0.00 0.00 3.41
2287 3129 9.994432 CTCTAGTCATCAATTTATTTTGTGACC 57.006 33.333 12.18 0.00 37.81 4.02
2289 3131 6.620678 AGTCATCAATTTATTTTGTGACCGG 58.379 36.000 0.00 0.00 37.81 5.28
2292 3134 5.379732 TCAATTTATTTTGTGACCGGACC 57.620 39.130 9.46 0.00 0.00 4.46
2293 3135 4.827835 TCAATTTATTTTGTGACCGGACCA 59.172 37.500 9.46 2.07 0.00 4.02
2336 3178 7.755591 AGTTAGTGCAAACTGTGATTGATATG 58.244 34.615 2.97 0.00 38.28 1.78
2604 3449 2.672908 CCTCCTGCATGCCTGACA 59.327 61.111 16.68 0.00 0.00 3.58
2693 3538 1.086696 CTTCACATGTTACTGGCCCG 58.913 55.000 0.00 0.00 0.00 6.13
2804 3649 0.106708 TGGAGCATGACGGCCTTATC 59.893 55.000 0.00 0.00 0.00 1.75
3006 3851 4.910585 GCGGGGCGGTGGACATAG 62.911 72.222 0.00 0.00 0.00 2.23
3014 3859 0.667487 CGGTGGACATAGCCTATGCG 60.667 60.000 11.65 3.26 44.33 4.73
3176 4021 4.443266 GCCGAGGCGACTGAGCTT 62.443 66.667 0.00 0.00 44.43 3.74
3177 4022 2.262915 CCGAGGCGACTGAGCTTT 59.737 61.111 0.00 0.00 44.43 3.51
3366 4211 1.891150 TGAAGGTAACCTGGTCGACTC 59.109 52.381 16.46 6.30 32.13 3.36
3469 4314 5.928839 GTGACTGAATAGCACTTTCTCTTGA 59.071 40.000 0.00 0.00 32.10 3.02
3493 4500 2.759535 GGGTGTCCTCACTCCTAACTAC 59.240 54.545 0.00 0.00 43.41 2.73
3594 4601 0.250727 TGGTTTGCTGGTACCTCTGC 60.251 55.000 14.36 14.75 35.41 4.26
3621 4628 9.698309 TCAAGTTTGTTTGTGTTTGATTTTCTA 57.302 25.926 0.00 0.00 0.00 2.10
3626 4633 8.715191 TTGTTTGTGTTTGATTTTCTAATGCT 57.285 26.923 0.00 0.00 0.00 3.79
3652 4714 7.279615 CAAGTATTGTCATTATACTGGGGACA 58.720 38.462 0.00 0.00 42.34 4.02
3653 4715 7.633018 AGTATTGTCATTATACTGGGGACAT 57.367 36.000 0.00 0.00 41.51 3.06
3654 4716 7.453393 AGTATTGTCATTATACTGGGGACATG 58.547 38.462 0.00 0.00 41.51 3.21
3663 4725 2.057922 ACTGGGGACATGTTCAGACTT 58.942 47.619 22.78 6.32 41.51 3.01
3698 4760 8.299570 CAAATATAATTCCCCTGTAAGTGCATC 58.700 37.037 0.00 0.00 0.00 3.91
3738 4800 9.897744 ACATCTGGATTATTATTTTTGTATGCG 57.102 29.630 0.00 0.00 0.00 4.73
3768 4830 4.008330 ACTCTGTCCTGATGCAATTCTTG 58.992 43.478 0.00 0.00 0.00 3.02
3795 4868 1.303561 TTGGCTTGCCACTAGCTGG 60.304 57.895 14.52 0.00 44.23 4.85
3818 4891 2.151202 CAGCCTGATTTACCGTTGTGT 58.849 47.619 0.00 0.00 0.00 3.72
3910 4983 9.744468 ACAACAAAAATCTGAGTAAATTGTACC 57.256 29.630 4.91 0.00 0.00 3.34
3928 5001 2.011222 ACCGAACGACAACAATTGTGT 58.989 42.857 12.82 12.18 45.52 3.72
4013 5086 4.371786 CTGAAGTCAAGTCACTAACTGCA 58.628 43.478 1.80 1.80 38.58 4.41
4038 5111 0.179108 AATAGCGGAACTGACGAGGC 60.179 55.000 0.00 0.00 0.00 4.70
4042 5115 1.289066 CGGAACTGACGAGGCTGAA 59.711 57.895 0.00 0.00 0.00 3.02
4046 5119 0.468226 AACTGACGAGGCTGAACCAA 59.532 50.000 0.00 0.00 43.14 3.67
4070 5143 6.692849 ATATCAGTGCCAATCCATCTAGAA 57.307 37.500 0.00 0.00 0.00 2.10
4081 5154 2.171237 TCCATCTAGAACCTGGCATGTG 59.829 50.000 6.05 0.00 0.00 3.21
4282 5358 0.736053 AACGTTCTTGCTTTTCGGCA 59.264 45.000 0.00 0.00 40.74 5.69
4284 5360 1.330306 CGTTCTTGCTTTTCGGCATG 58.670 50.000 0.00 0.00 42.09 4.06
4351 5427 2.262915 AGCCACTCGTAGCTGCAC 59.737 61.111 1.02 0.00 38.11 4.57
4354 5430 3.181967 CACTCGTAGCTGCACGCC 61.182 66.667 16.13 0.00 41.67 5.68
4362 5438 2.507110 TAGCTGCACGCCTCTGTTCC 62.507 60.000 1.02 0.00 40.39 3.62
4373 5449 2.898705 CCTCTGTTCCATGTACTCAGC 58.101 52.381 0.00 0.00 0.00 4.26
4374 5450 2.419297 CCTCTGTTCCATGTACTCAGCC 60.419 54.545 0.00 0.00 0.00 4.85
4379 5455 1.815421 CCATGTACTCAGCCGTGCC 60.815 63.158 0.00 0.00 0.00 5.01
4384 5460 3.931190 TACTCAGCCGTGCCCTCGA 62.931 63.158 0.00 0.00 0.00 4.04
4392 5468 2.677003 CGTGCCCTCGATTGCGTTT 61.677 57.895 2.38 0.00 38.98 3.60
4415 5491 3.738282 GCATGAGCACCTTCTATACTTCG 59.262 47.826 0.00 0.00 41.58 3.79
4426 5502 5.050972 CCTTCTATACTTCGTTCGATTTGGC 60.051 44.000 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.961753 CTCCCCAGAGCCAAAACAAC 59.038 55.000 0.00 0.00 32.13 3.32
28 29 9.504708 TTTGTTTAAGTTTACTATTCATCCGGA 57.495 29.630 6.61 6.61 0.00 5.14
177 180 9.458374 CTTAAACGTATTGACCTGTGAATTTTT 57.542 29.630 0.00 0.00 0.00 1.94
178 181 7.593644 GCTTAAACGTATTGACCTGTGAATTTT 59.406 33.333 0.00 0.00 0.00 1.82
179 182 7.040686 AGCTTAAACGTATTGACCTGTGAATTT 60.041 33.333 0.00 0.00 0.00 1.82
180 183 6.430000 AGCTTAAACGTATTGACCTGTGAATT 59.570 34.615 0.00 0.00 0.00 2.17
181 184 5.938125 AGCTTAAACGTATTGACCTGTGAAT 59.062 36.000 0.00 0.00 0.00 2.57
237 241 7.667043 AGAATACATGTGTTTATTGTCACGT 57.333 32.000 9.11 0.00 37.38 4.49
333 341 2.198827 TGAAGAACCATGGAATGCGT 57.801 45.000 21.47 2.34 44.97 5.24
345 353 5.406477 GCCCAATTCATGAACTTTGAAGAAC 59.594 40.000 19.00 4.49 36.60 3.01
428 436 3.957586 TGGGCTGCTGGTCCACAG 61.958 66.667 13.95 13.95 45.98 3.66
434 442 2.914289 GCTAGATGGGCTGCTGGT 59.086 61.111 0.00 0.00 0.00 4.00
468 497 4.620982 GGTGGATGAAAAACCAACTGAAG 58.379 43.478 0.00 0.00 40.35 3.02
499 528 7.841956 TCCTAAGAAAATGTCAACCAAAACAA 58.158 30.769 0.00 0.00 0.00 2.83
500 529 7.411486 TCCTAAGAAAATGTCAACCAAAACA 57.589 32.000 0.00 0.00 0.00 2.83
939 1490 1.760613 CGCCCCAGGTCATTCTAGTAA 59.239 52.381 0.00 0.00 0.00 2.24
952 1503 2.190578 GGATTGTCCTCGCCCCAG 59.809 66.667 0.00 0.00 32.53 4.45
978 1529 2.351455 CCGGCCTCTTCTCTTTTCTTC 58.649 52.381 0.00 0.00 0.00 2.87
979 1530 1.003696 CCCGGCCTCTTCTCTTTTCTT 59.996 52.381 0.00 0.00 0.00 2.52
980 1531 0.615850 CCCGGCCTCTTCTCTTTTCT 59.384 55.000 0.00 0.00 0.00 2.52
981 1532 0.613777 TCCCGGCCTCTTCTCTTTTC 59.386 55.000 0.00 0.00 0.00 2.29
1030 1581 1.707239 CTCTCGGAGGACTTCGACGG 61.707 65.000 4.96 0.00 0.00 4.79
1227 1778 2.856720 GCTTCTGAAGATAGAGCCGTCG 60.857 54.545 21.06 0.00 0.00 5.12
1263 1814 6.816640 TGGTATCTTGGAGACGATAAACTTTG 59.183 38.462 0.00 0.00 0.00 2.77
1359 1952 6.635030 ACATACAGAAAGTTCAAGGAAACC 57.365 37.500 0.00 0.00 0.00 3.27
1368 1961 7.122353 TGGTCTCCTAGTACATACAGAAAGTTC 59.878 40.741 0.00 0.00 0.00 3.01
1502 2131 4.790765 AGAGGTGCTTTTAGGATTTTGC 57.209 40.909 0.00 0.00 0.00 3.68
1529 2195 4.403432 ACATCTTATGATTTTGGCCACAGG 59.597 41.667 3.88 0.00 0.00 4.00
1763 2483 6.420008 CCTCTACTTTAAATACCATCCGTTCG 59.580 42.308 0.00 0.00 0.00 3.95
1827 2547 6.942532 TTTCTAATCAACAGAAACAGTGCT 57.057 33.333 0.00 0.00 37.15 4.40
1847 2567 2.092323 GATAGGTGGCTGTGGGTTTTC 58.908 52.381 0.00 0.00 0.00 2.29
1857 2577 1.693627 ACTTCGATCGATAGGTGGCT 58.306 50.000 20.18 0.80 0.00 4.75
1859 2579 2.488545 CCCTACTTCGATCGATAGGTGG 59.511 54.545 29.72 24.47 33.60 4.61
1867 2587 5.297029 TCATATAGCATCCCTACTTCGATCG 59.703 44.000 9.36 9.36 0.00 3.69
1999 2720 9.971922 ACAATCTTGATTTAATAATAGGCAAGC 57.028 29.630 0.00 0.00 33.28 4.01
2049 2770 6.544564 GGTCGAGATTGATTAAAATGGGGTTA 59.455 38.462 0.00 0.00 0.00 2.85
2112 2836 1.873591 AGAAACTGTGAATCACGTGGC 59.126 47.619 17.00 6.38 37.14 5.01
2125 2967 8.559536 TGCACAGTCTTTTTAATCTAGAAACTG 58.440 33.333 0.00 3.91 0.00 3.16
2228 3070 9.920946 AGAGGAAACTAAATATTTGGAGCATTA 57.079 29.630 17.45 0.00 44.43 1.90
2269 3111 5.478679 TGGTCCGGTCACAAAATAAATTGAT 59.521 36.000 0.00 0.00 34.38 2.57
2287 3129 5.931724 TGTGCATATATATTTCTGTGGTCCG 59.068 40.000 0.00 0.00 0.00 4.79
2289 3131 7.969536 ACTGTGCATATATATTTCTGTGGTC 57.030 36.000 0.00 0.00 0.00 4.02
2336 3178 9.983804 CGATATCCTGAAGTTTAGGTTAAAAAC 57.016 33.333 13.06 3.74 36.67 2.43
2404 3249 6.239036 GCTAGAAAGTGGAACCAAAACAGAAT 60.239 38.462 0.00 0.00 37.80 2.40
2415 3260 2.784347 AGCAAGGCTAGAAAGTGGAAC 58.216 47.619 0.00 0.00 36.99 3.62
2604 3449 2.365293 GTTGCCTTTCACAAACCATCCT 59.635 45.455 0.00 0.00 0.00 3.24
2693 3538 2.199291 CGTATCCGTACAACTGGACC 57.801 55.000 0.00 0.00 37.02 4.46
2806 3651 0.106894 CCTCTTAGGGCCGGACATTC 59.893 60.000 11.00 0.00 0.00 2.67
3006 3851 1.596477 CCCTCAGAAGCGCATAGGC 60.596 63.158 11.47 0.00 0.00 3.93
3168 4013 0.471617 ACAGTCCTGCAAAGCTCAGT 59.528 50.000 0.00 0.00 0.00 3.41
3176 4021 2.195567 GGCAAGCACAGTCCTGCAA 61.196 57.895 0.00 0.00 39.86 4.08
3177 4022 2.595463 GGCAAGCACAGTCCTGCA 60.595 61.111 0.00 0.00 39.86 4.41
3335 4180 0.606604 TTACCTTCACCTCGACAGCC 59.393 55.000 0.00 0.00 0.00 4.85
3336 4181 1.672145 GGTTACCTTCACCTCGACAGC 60.672 57.143 0.00 0.00 0.00 4.40
3339 4184 1.067071 CCAGGTTACCTTCACCTCGAC 60.067 57.143 0.00 0.00 43.30 4.20
3366 4211 2.190578 GCTTCCGGGGATGTCCAG 59.809 66.667 0.00 0.00 37.91 3.86
3469 4314 0.716591 TAGGAGTGAGGACACCCCAT 59.283 55.000 0.00 0.00 45.49 4.00
3507 4514 9.764363 GACATAGACATCCAGATAACAAACATA 57.236 33.333 0.00 0.00 0.00 2.29
3594 4601 8.711457 AGAAAATCAAACACAAACAAACTTGAG 58.289 29.630 0.00 0.00 0.00 3.02
3621 4628 9.060347 CCAGTATAATGACAATACTTGAGCATT 57.940 33.333 0.79 13.08 37.93 3.56
3626 4633 7.126573 TGTCCCCAGTATAATGACAATACTTGA 59.873 37.037 0.79 0.00 37.93 3.02
3652 4714 5.483685 TTGCTACTACCAAGTCTGAACAT 57.516 39.130 0.00 0.00 37.15 2.71
3653 4715 4.948341 TTGCTACTACCAAGTCTGAACA 57.052 40.909 0.00 0.00 37.15 3.18
3654 4716 9.595823 TTATATTTGCTACTACCAAGTCTGAAC 57.404 33.333 0.00 0.00 37.15 3.18
3663 4725 7.073215 ACAGGGGAATTATATTTGCTACTACCA 59.927 37.037 0.00 0.00 0.00 3.25
3698 4760 5.027293 TCCAGATGTCATGTGTCTTATGG 57.973 43.478 8.98 1.41 0.00 2.74
3732 4794 2.325761 ACAGAGTGTCGAAACGCATAC 58.674 47.619 12.26 0.00 38.41 2.39
3795 4868 0.679960 AACGGTAAATCAGGCTGCCC 60.680 55.000 16.57 3.46 0.00 5.36
3803 4876 4.699637 AGAACTCACACAACGGTAAATCA 58.300 39.130 0.00 0.00 0.00 2.57
3818 4891 1.896220 GTGATGCCCACAAGAACTCA 58.104 50.000 1.94 0.00 45.03 3.41
3910 4983 3.026349 GTGACACAATTGTTGTCGTTCG 58.974 45.455 23.74 10.24 43.23 3.95
3928 5001 7.936847 ACAAGTCATGGTTCTGTAAAATAGTGA 59.063 33.333 0.00 0.00 0.00 3.41
4013 5086 2.733227 CGTCAGTTCCGCTATTAACCGT 60.733 50.000 0.00 0.00 0.00 4.83
4029 5102 1.813513 ATTTGGTTCAGCCTCGTCAG 58.186 50.000 0.00 0.00 38.35 3.51
4038 5111 5.450965 GGATTGGCACTGATATTTGGTTCAG 60.451 44.000 0.00 0.00 43.97 3.02
4042 5115 3.979911 TGGATTGGCACTGATATTTGGT 58.020 40.909 0.00 0.00 0.00 3.67
4046 5119 6.692849 TCTAGATGGATTGGCACTGATATT 57.307 37.500 0.00 0.00 0.00 1.28
4081 5154 2.675032 GCTAATTTGACAAAGCTGGCCC 60.675 50.000 6.77 0.00 32.18 5.80
4089 5162 3.230134 ACCAGGCAGCTAATTTGACAAA 58.770 40.909 2.48 2.48 0.00 2.83
4165 5238 4.950475 TCACCAGTTTCACATTACCACAAA 59.050 37.500 0.00 0.00 0.00 2.83
4282 5358 0.391661 GTGCCATGTCGTCCACTCAT 60.392 55.000 0.00 0.00 0.00 2.90
4284 5360 0.602638 TTGTGCCATGTCGTCCACTC 60.603 55.000 0.00 0.00 0.00 3.51
4327 5403 1.009829 GCTACGAGTGGCTGAAATGG 58.990 55.000 4.29 0.00 34.00 3.16
4362 5438 1.815421 GGGCACGGCTGAGTACATG 60.815 63.158 0.00 0.00 0.00 3.21
4374 5450 2.677003 AAACGCAATCGAGGGCACG 61.677 57.895 11.10 3.68 39.41 5.34
4379 5455 0.447406 TCATGCAAACGCAATCGAGG 59.553 50.000 0.00 0.00 44.09 4.63
4392 5468 7.130288 ACGAAGTATAGAAGGTGCTCATGCA 62.130 44.000 0.00 0.00 44.34 3.96
4395 5471 5.593010 GAACGAAGTATAGAAGGTGCTCAT 58.407 41.667 0.00 0.00 45.00 2.90
4396 5472 4.438336 CGAACGAAGTATAGAAGGTGCTCA 60.438 45.833 0.00 0.00 45.00 4.26
4400 5476 6.019801 CCAAATCGAACGAAGTATAGAAGGTG 60.020 42.308 0.12 0.00 45.00 4.00
4401 5477 6.040878 CCAAATCGAACGAAGTATAGAAGGT 58.959 40.000 0.12 0.00 45.00 3.50
4402 5478 5.050972 GCCAAATCGAACGAAGTATAGAAGG 60.051 44.000 0.12 0.00 45.00 3.46
4403 5479 5.518847 TGCCAAATCGAACGAAGTATAGAAG 59.481 40.000 0.12 0.00 45.00 2.85
4404 5480 5.290158 GTGCCAAATCGAACGAAGTATAGAA 59.710 40.000 0.12 0.00 45.00 2.10
4405 5481 4.802039 GTGCCAAATCGAACGAAGTATAGA 59.198 41.667 0.12 0.00 45.00 1.98
4406 5482 4.565166 TGTGCCAAATCGAACGAAGTATAG 59.435 41.667 0.12 0.00 45.00 1.31
4407 5483 4.496360 TGTGCCAAATCGAACGAAGTATA 58.504 39.130 0.12 0.00 45.00 1.47
4408 5484 3.331150 TGTGCCAAATCGAACGAAGTAT 58.669 40.909 0.12 0.00 45.00 2.12
4415 5491 4.376311 GCAAGAATTTGTGCCAAATCGAAC 60.376 41.667 11.87 6.41 36.65 3.95
4426 5502 3.986277 AGCAAGAAGGCAAGAATTTGTG 58.014 40.909 0.00 0.00 36.65 3.33


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

AutoCloner maintained by Alex Coulton.