Multiple sequence alignment - TraesCS1D01G426400

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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 TraesCS1D01G426400 chr1D 100.000 5304 0 0 1 5304 479596139 479590836 0.000000e+00 9795.0
1 TraesCS1D01G426400 chr1B 95.682 4446 150 18 1 4420 667824135 667819706 0.000000e+00 7108.0
2 TraesCS1D01G426400 chr1B 93.873 816 49 1 4490 5304 667819708 667818893 0.000000e+00 1229.0
3 TraesCS1D01G426400 chr1A 97.505 3727 82 2 648 4371 575871165 575867447 0.000000e+00 6357.0
4 TraesCS1D01G426400 chr1A 95.418 742 31 3 4563 5304 575867393 575866655 0.000000e+00 1179.0
5 TraesCS1D01G426400 chr1A 90.047 643 35 15 1 617 575872379 575871740 0.000000e+00 806.0
6 TraesCS1D01G426400 chr5B 74.423 1474 340 27 2395 3848 695812913 695811457 2.730000e-167 599.0
7 TraesCS1D01G426400 chr6D 92.833 293 19 2 5014 5304 389247540 389247832 1.770000e-114 424.0
8 TraesCS1D01G426400 chr6D 100.000 30 0 0 4986 5015 388158056 388158085 7.420000e-04 56.5
9 TraesCS1D01G426400 chr5D 92.833 293 19 2 5014 5304 503236151 503236443 1.770000e-114 424.0
10 TraesCS1D01G426400 chr5D 92.833 293 19 2 5014 5304 503240400 503240692 1.770000e-114 424.0
11 TraesCS1D01G426400 chr5D 92.491 293 20 2 5014 5304 503225834 503226126 8.220000e-113 418.0
12 TraesCS1D01G426400 chr5D 77.568 584 116 11 3272 3849 555557886 555558460 6.580000e-89 339.0
13 TraesCS1D01G426400 chr6A 92.491 293 20 2 5014 5304 531825993 531826285 8.220000e-113 418.0
14 TraesCS1D01G426400 chr3D 92.759 290 19 2 5017 5304 589268300 589268011 8.220000e-113 418.0
15 TraesCS1D01G426400 chr3B 92.491 293 20 2 5014 5304 201534645 201534937 8.220000e-113 418.0
16 TraesCS1D01G426400 chr7D 90.385 52 4 1 337 388 5355839 5355889 3.430000e-07 67.6
17 TraesCS1D01G426400 chr2B 100.000 28 0 0 4988 5015 597277072 597277099 1.000000e-02 52.8


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 TraesCS1D01G426400 chr1D 479590836 479596139 5303 True 9795.000000 9795 100.000000 1 5304 1 chr1D.!!$R1 5303
1 TraesCS1D01G426400 chr1B 667818893 667824135 5242 True 4168.500000 7108 94.777500 1 5304 2 chr1B.!!$R1 5303
2 TraesCS1D01G426400 chr1A 575866655 575872379 5724 True 2780.666667 6357 94.323333 1 5304 3 chr1A.!!$R1 5303
3 TraesCS1D01G426400 chr5B 695811457 695812913 1456 True 599.000000 599 74.423000 2395 3848 1 chr5B.!!$R1 1453
4 TraesCS1D01G426400 chr5D 503236151 503240692 4541 False 424.000000 424 92.833000 5014 5304 2 chr5D.!!$F3 290
5 TraesCS1D01G426400 chr5D 555557886 555558460 574 False 339.000000 339 77.568000 3272 3849 1 chr5D.!!$F2 577

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
805 1377 0.389948 GCGTGTCACTCAGGTAAGGG 60.390 60.000 0.65 0.0 34.79 3.95 F
1192 1767 0.680061 AAACTGGACCACGGAGAGTC 59.320 55.000 0.00 0.0 34.57 3.36 F
2244 2819 1.000396 GGGCATGGGCTTCTTGTCT 60.000 57.895 0.00 0.0 40.87 3.41 F
3315 3896 0.462047 CCTACCATGAACTCGCCCAC 60.462 60.000 0.00 0.0 0.00 4.61 F
3588 4169 1.001406 AGCTTGGAGACACTGCTACAC 59.999 52.381 0.00 0.0 45.06 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 2280 1.028868 GGCACTAGGCTGGAAAGCTG 61.029 60.000 4.33 0.00 44.01 4.24 R
3064 3639 3.619929 GCATTCCCAATGAAAGATTGTGC 59.380 43.478 0.25 0.00 41.46 4.57 R
4090 4671 0.384309 GATGGCTATCCACGACGTGA 59.616 55.000 28.83 15.08 46.92 4.35 R
4216 4797 1.078709 CAACCACATCGCTCATCGTT 58.921 50.000 0.00 0.00 39.67 3.85 R
4817 5398 1.377725 CGATCCAAACCCAGCAGCT 60.378 57.895 0.00 0.00 0.00 4.24 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
52 53 7.151999 TGAGTTCAGCACTAGTTTTTCAAAA 57.848 32.000 0.00 0.00 35.01 2.44
135 136 1.476471 GGGTCGATCTAGGACTTCGGA 60.476 57.143 0.00 0.00 34.82 4.55
142 143 3.870633 TCTAGGACTTCGGAGCTTTTC 57.129 47.619 0.00 0.00 0.00 2.29
143 144 3.432378 TCTAGGACTTCGGAGCTTTTCT 58.568 45.455 0.00 0.00 0.00 2.52
186 187 2.438434 CAAGCCGGTGATGGGGTC 60.438 66.667 1.90 0.00 33.29 4.46
204 205 2.094442 GGTCAAGGAGGAAGAGAGTTCG 60.094 54.545 0.00 0.00 0.00 3.95
227 228 5.419471 CGTTAGGGGGTTTTAATTGGAATGA 59.581 40.000 0.00 0.00 0.00 2.57
228 229 6.097696 CGTTAGGGGGTTTTAATTGGAATGAT 59.902 38.462 0.00 0.00 0.00 2.45
414 415 5.405571 GTGACATGGGTACTAGCATATTTCG 59.594 44.000 0.00 0.00 0.00 3.46
416 417 6.265876 TGACATGGGTACTAGCATATTTCGTA 59.734 38.462 0.00 0.00 0.00 3.43
420 421 8.999431 CATGGGTACTAGCATATTTCGTAAATT 58.001 33.333 0.00 0.00 32.38 1.82
508 514 3.557595 CGTGTGGAAGGAAAGATATGCTC 59.442 47.826 0.00 0.00 0.00 4.26
509 515 4.681781 CGTGTGGAAGGAAAGATATGCTCT 60.682 45.833 0.00 0.00 34.96 4.09
536 542 6.615088 TCATTTCATTAGCAAGACAAAGAGC 58.385 36.000 0.00 0.00 0.00 4.09
593 619 7.275183 CCAAGGAGTCATATTCACTCATACAA 58.725 38.462 11.91 0.00 41.94 2.41
700 1272 6.611613 TTATAAACAACAAATGGCCATGGA 57.388 33.333 21.63 0.00 0.00 3.41
709 1281 2.092598 ATGGCCATGGATTTTCCTCC 57.907 50.000 20.04 4.72 37.46 4.30
718 1290 1.397343 GGATTTTCCTCCGCGTCTTTC 59.603 52.381 4.92 0.00 32.53 2.62
763 1335 7.944554 TGAGATGGAGTCTTTTTCTATTGGTTT 59.055 33.333 0.00 0.00 37.29 3.27
764 1336 8.712228 AGATGGAGTCTTTTTCTATTGGTTTT 57.288 30.769 0.00 0.00 31.47 2.43
765 1337 9.807921 AGATGGAGTCTTTTTCTATTGGTTTTA 57.192 29.630 0.00 0.00 31.47 1.52
805 1377 0.389948 GCGTGTCACTCAGGTAAGGG 60.390 60.000 0.65 0.00 34.79 3.95
845 1417 2.969443 AAGTGCTTATTGTGTCGTGC 57.031 45.000 0.00 0.00 0.00 5.34
1192 1767 0.680061 AAACTGGACCACGGAGAGTC 59.320 55.000 0.00 0.00 34.57 3.36
1255 1830 1.203237 AGAGGGTCACTGGACTGTCAT 60.203 52.381 10.38 0.00 43.77 3.06
1334 1909 5.309543 TCCTTTCTTTCCTAGACATCACCAA 59.690 40.000 0.00 0.00 30.90 3.67
1380 1955 4.095483 CCAACTGATCTTGGCAATCTACAC 59.905 45.833 0.00 0.00 34.50 2.90
1397 1972 2.222886 ACACCGTCTCAGATATCTCCG 58.777 52.381 1.03 3.23 0.00 4.63
1423 1998 7.232941 GTCTAGGTGAAAATAGCCTATCAGGTA 59.767 40.741 0.00 0.00 37.80 3.08
1459 2034 1.043022 AGGAAACTTGGCAAGGCTTG 58.957 50.000 29.26 22.75 37.44 4.01
1476 2051 4.000988 GGCTTGAGGTCTTTGATTTACGA 58.999 43.478 0.00 0.00 0.00 3.43
1535 2110 5.700832 TGTTACTGCATCTGAACAACCTTAG 59.299 40.000 0.00 0.00 0.00 2.18
1552 2127 8.487028 ACAACCTTAGGGAGATTTATCTACAAG 58.513 37.037 2.32 0.86 39.61 3.16
1632 2207 6.213677 GAGGTACCTCAAATTTGGAAACAAC 58.786 40.000 32.91 3.39 45.46 3.32
1705 2280 7.205992 TGAGATCTTAGACATGCAGTACAATC 58.794 38.462 0.00 0.00 0.00 2.67
1726 2301 1.308783 GCTTTCCAGCCTAGTGCCAC 61.309 60.000 0.00 0.00 40.61 5.01
1737 2312 3.495100 GCCTAGTGCCACAAGCTATGTAT 60.495 47.826 0.00 0.00 41.46 2.29
1746 2321 6.878923 TGCCACAAGCTATGTATAATATGTCC 59.121 38.462 0.00 0.00 41.46 4.02
2163 2738 1.344438 CAACTGTCTGGCTCAGTACCA 59.656 52.381 9.90 0.00 44.03 3.25
2244 2819 1.000396 GGGCATGGGCTTCTTGTCT 60.000 57.895 0.00 0.00 40.87 3.41
3064 3639 4.324267 AGGTATTTTCTCAAACCTCACGG 58.676 43.478 0.00 0.00 37.87 4.94
3140 3715 2.760650 CTCCTTGCCATAAAAAGTCCCC 59.239 50.000 0.00 0.00 0.00 4.81
3306 3887 6.688922 GCCATCAATTAGTCTCCTACCATGAA 60.689 42.308 0.00 0.00 0.00 2.57
3315 3896 0.462047 CCTACCATGAACTCGCCCAC 60.462 60.000 0.00 0.00 0.00 4.61
3408 3989 3.744238 AGTAATGGTTTGGTTGTTGCC 57.256 42.857 0.00 0.00 0.00 4.52
3477 4058 1.807165 CGAGTGTCATGTGCTCCGG 60.807 63.158 0.00 0.00 0.00 5.14
3588 4169 1.001406 AGCTTGGAGACACTGCTACAC 59.999 52.381 0.00 0.00 45.06 2.90
3927 4508 8.499403 AGAGTCTTTACATATTTTTCTCCTGC 57.501 34.615 0.00 0.00 0.00 4.85
3976 4557 6.510879 TCACGTAAGAGTGATGTATTCAGT 57.489 37.500 0.00 0.00 45.18 3.41
4165 4746 8.697507 ACTTGAATGAAGATTTTCTTGTACCT 57.302 30.769 0.00 0.00 36.73 3.08
4207 4788 1.312815 GCTCTAGCCATTCGCCAAAT 58.687 50.000 0.00 0.00 38.78 2.32
4216 4797 3.278574 CCATTCGCCAAATGAGAGGTTA 58.721 45.455 7.80 0.00 46.54 2.85
4264 4845 5.378230 TGAAGAAGATCAAGGTGGCATAT 57.622 39.130 0.00 0.00 0.00 1.78
4341 4922 7.173032 TGTGTATCTGTCTTGTTCCTACTCTA 58.827 38.462 0.00 0.00 0.00 2.43
4425 5006 8.506168 AATTTGTCTTGGTTATATGTCATCGT 57.494 30.769 0.00 0.00 0.00 3.73
4426 5007 7.534085 TTTGTCTTGGTTATATGTCATCGTC 57.466 36.000 0.00 0.00 0.00 4.20
4427 5008 6.215495 TGTCTTGGTTATATGTCATCGTCA 57.785 37.500 0.00 0.00 0.00 4.35
4428 5009 6.816136 TGTCTTGGTTATATGTCATCGTCAT 58.184 36.000 0.00 0.00 0.00 3.06
4429 5010 6.923508 TGTCTTGGTTATATGTCATCGTCATC 59.076 38.462 0.00 0.00 0.00 2.92
4430 5011 6.088217 GTCTTGGTTATATGTCATCGTCATCG 59.912 42.308 0.00 0.00 38.55 3.84
4431 5012 5.447624 TGGTTATATGTCATCGTCATCGT 57.552 39.130 0.00 0.00 38.33 3.73
4451 5032 4.207224 TCGTTGTTGTTGTTGTTGTTGTTG 59.793 37.500 0.00 0.00 0.00 3.33
4457 5038 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
4463 5044 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
4471 5052 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
4472 5053 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
4473 5054 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
4474 5055 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
4475 5056 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
4476 5057 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
4477 5058 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
4478 5059 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
4479 5060 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
4480 5061 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
4481 5062 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
4482 5063 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
4483 5064 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
4484 5065 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
4485 5066 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
4486 5067 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
4487 5068 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
4488 5069 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
4499 5080 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
4674 5255 7.115414 ACTTCCCTTATTCATCTCCTTCTTTG 58.885 38.462 0.00 0.00 0.00 2.77
4817 5398 2.552315 GGTTTCAAGAAATCAGGCGTCA 59.448 45.455 1.09 0.00 31.92 4.35
4917 5498 3.432782 GCGTTGCATTACTAGTACGAGT 58.567 45.455 15.80 13.41 0.00 4.18
4963 5544 6.696148 AGATCGTTGACCGTAATGATTCTTAC 59.304 38.462 0.00 0.00 36.65 2.34
4976 5557 3.756434 TGATTCTTACTCTTTTTGCGGGG 59.244 43.478 0.00 0.00 0.00 5.73
5185 10018 5.047590 ACCATACACGTCACATGTTTCTAGA 60.048 40.000 0.00 0.00 0.00 2.43
5239 10072 2.469826 TGCATAAGAATCTACACCGCG 58.530 47.619 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.886563 GCTGAACTCATGCTTTGCCT 59.113 50.000 0.00 0.00 0.00 4.75
135 136 3.430042 TGCTCATCCTTCAGAAAAGCT 57.570 42.857 0.00 0.00 37.14 3.74
142 143 3.001414 CTCACACTTGCTCATCCTTCAG 58.999 50.000 0.00 0.00 0.00 3.02
143 144 2.634453 TCTCACACTTGCTCATCCTTCA 59.366 45.455 0.00 0.00 0.00 3.02
186 187 3.669251 AACGAACTCTCTTCCTCCTTG 57.331 47.619 0.00 0.00 0.00 3.61
204 205 6.860790 TCATTCCAATTAAAACCCCCTAAC 57.139 37.500 0.00 0.00 0.00 2.34
227 228 8.820831 TCTGAAGGAGAGTAAGAAAGATTCAAT 58.179 33.333 0.00 0.00 0.00 2.57
228 229 8.195165 TCTGAAGGAGAGTAAGAAAGATTCAA 57.805 34.615 0.00 0.00 0.00 2.69
339 340 3.264964 TCCACCATAAGGAACCTAACCAC 59.735 47.826 0.00 0.00 38.69 4.16
461 467 3.770666 CTCATTTCTTCAGGCATGCTTG 58.229 45.455 22.93 22.93 0.00 4.01
471 477 1.872952 CACACGTGGCTCATTTCTTCA 59.127 47.619 21.57 0.00 0.00 3.02
473 479 1.238439 CCACACGTGGCTCATTTCTT 58.762 50.000 21.57 0.00 44.73 2.52
508 514 8.509690 TCTTTGTCTTGCTAATGAAATGAGAAG 58.490 33.333 0.00 0.00 0.00 2.85
509 515 8.394971 TCTTTGTCTTGCTAATGAAATGAGAA 57.605 30.769 0.00 0.00 0.00 2.87
567 592 4.142609 TGAGTGAATATGACTCCTTGGC 57.857 45.455 11.03 0.00 39.36 4.52
593 619 6.659242 AGGTAGCTTATATGCACAACACTTTT 59.341 34.615 12.65 0.00 34.99 2.27
678 1250 6.805016 ATCCATGGCCATTTGTTGTTTATA 57.195 33.333 17.92 0.00 0.00 0.98
700 1272 2.028020 AGAGAAAGACGCGGAGGAAAAT 60.028 45.455 12.47 0.00 0.00 1.82
709 1281 5.957910 AAAGATCATTAGAGAAAGACGCG 57.042 39.130 3.53 3.53 0.00 6.01
763 1335 9.005777 ACGCTTCTGGTCATATTAAAAGTTTAA 57.994 29.630 0.00 0.00 37.08 1.52
764 1336 8.447833 CACGCTTCTGGTCATATTAAAAGTTTA 58.552 33.333 0.00 0.00 0.00 2.01
765 1337 7.040686 ACACGCTTCTGGTCATATTAAAAGTTT 60.041 33.333 0.00 0.00 0.00 2.66
766 1338 6.430000 ACACGCTTCTGGTCATATTAAAAGTT 59.570 34.615 0.00 0.00 0.00 2.66
767 1339 5.938125 ACACGCTTCTGGTCATATTAAAAGT 59.062 36.000 0.00 0.00 0.00 2.66
768 1340 6.092122 TGACACGCTTCTGGTCATATTAAAAG 59.908 38.462 0.00 0.00 36.69 2.27
769 1341 5.935206 TGACACGCTTCTGGTCATATTAAAA 59.065 36.000 0.00 0.00 36.69 1.52
770 1342 5.350365 GTGACACGCTTCTGGTCATATTAAA 59.650 40.000 0.00 0.00 42.81 1.52
805 1377 9.187455 GCACTTTTAACTCTAGAGCTATCATAC 57.813 37.037 19.97 0.00 0.00 2.39
845 1417 0.098200 TAGTCGTCTTGCGGTCATCG 59.902 55.000 0.00 0.00 41.72 3.84
1140 1715 2.632512 GCCAAAGGGGTCAGAAAATTGA 59.367 45.455 0.00 0.00 39.65 2.57
1192 1767 4.085876 CACCCAGTGGCAGAAAGG 57.914 61.111 2.61 0.00 33.59 3.11
1233 1808 1.294780 CAGTCCAGTGACCCTCTGC 59.705 63.158 0.00 0.00 42.81 4.26
1255 1830 1.891933 TGGAGGGATCTGTATGGCAA 58.108 50.000 0.00 0.00 0.00 4.52
1334 1909 1.451936 GAGCCAGTGAGGTTGGTGT 59.548 57.895 0.00 0.00 40.61 4.16
1380 1955 2.773487 AGACGGAGATATCTGAGACGG 58.227 52.381 10.74 2.73 0.00 4.79
1397 1972 6.042208 ACCTGATAGGCTATTTTCACCTAGAC 59.958 42.308 8.71 0.00 39.63 2.59
1447 2022 0.185901 AAGACCTCAAGCCTTGCCAA 59.814 50.000 0.00 0.00 0.00 4.52
1453 2028 4.003648 CGTAAATCAAAGACCTCAAGCCT 58.996 43.478 0.00 0.00 0.00 4.58
1459 2034 5.333875 GGTTGTGTCGTAAATCAAAGACCTC 60.334 44.000 0.00 0.00 33.04 3.85
1476 2051 1.227853 GCCCGAGAGTTGGTTGTGT 60.228 57.895 0.00 0.00 0.00 3.72
1515 2090 3.560025 CCCTAAGGTTGTTCAGATGCAGT 60.560 47.826 0.00 0.00 0.00 4.40
1535 2110 9.579932 AATGATTTCCTTGTAGATAAATCTCCC 57.420 33.333 0.00 0.00 38.54 4.30
1552 2127 3.959535 TTGCCCACTCAAATGATTTCC 57.040 42.857 0.00 0.00 0.00 3.13
1585 2160 3.963129 AGGAAGGAGTGTTGTTGAACAA 58.037 40.909 6.66 6.66 43.77 2.83
1657 2232 3.971702 GGGCAGGGAGGCAACACT 61.972 66.667 0.00 0.00 46.44 3.55
1705 2280 1.028868 GGCACTAGGCTGGAAAGCTG 61.029 60.000 4.33 0.00 44.01 4.24
1737 2312 7.686859 GCCATGACTTGTAGTCTGGACATATTA 60.687 40.741 20.04 0.00 45.27 0.98
1746 2321 3.257393 GAGTGCCATGACTTGTAGTCTG 58.743 50.000 8.18 4.50 45.27 3.51
1755 2330 2.267006 CCAGCGAGTGCCATGACT 59.733 61.111 0.00 0.00 44.31 3.41
2176 2751 7.854534 ACAAGCTTTTTCAAAGCAACAATATC 58.145 30.769 20.42 0.00 45.30 1.63
2244 2819 4.284490 AGTTGTCTACATCCAGAAAGAGCA 59.716 41.667 0.00 0.00 0.00 4.26
3064 3639 3.619929 GCATTCCCAATGAAAGATTGTGC 59.380 43.478 0.25 0.00 41.46 4.57
3140 3715 7.841282 TTGAGAAGATGACTACTATAAGGGG 57.159 40.000 0.00 0.00 0.00 4.79
3243 3818 1.606668 TCGCCGTGAGCTTTGAAAATT 59.393 42.857 0.00 0.00 40.39 1.82
3245 3820 1.069296 CATCGCCGTGAGCTTTGAAAA 60.069 47.619 0.00 0.00 40.39 2.29
3315 3896 2.416747 TCACTGAAATTCTGAGTGGCG 58.583 47.619 11.83 0.00 38.12 5.69
3408 3989 6.506500 AGCTTCATGTCAAGAACCTTTATG 57.493 37.500 0.00 0.00 0.00 1.90
3477 4058 1.641677 GTTACGATGCCGCACCATC 59.358 57.895 0.00 4.03 39.95 3.51
3588 4169 0.662619 ACATTGCGCCATCATAACGG 59.337 50.000 4.18 0.00 0.00 4.44
3924 4505 3.584406 TCCCATAGACCCATATTCTGCAG 59.416 47.826 7.63 7.63 0.00 4.41
3927 4508 5.474876 GCTTTTCCCATAGACCCATATTCTG 59.525 44.000 0.00 0.00 0.00 3.02
3976 4557 5.245531 ACTTCAAGAAGCATGATTCCGTAA 58.754 37.500 19.65 10.33 41.99 3.18
4090 4671 0.384309 GATGGCTATCCACGACGTGA 59.616 55.000 28.83 15.08 46.92 4.35
4165 4746 5.125417 GCAGAGCAAACCCAACTCAAATATA 59.875 40.000 0.00 0.00 32.71 0.86
4207 4788 2.089201 TCGCTCATCGTTAACCTCTCA 58.911 47.619 0.00 0.00 39.67 3.27
4216 4797 1.078709 CAACCACATCGCTCATCGTT 58.921 50.000 0.00 0.00 39.67 3.85
4264 4845 3.410631 TTCGCTGACATCCTTTTGGTA 57.589 42.857 0.00 0.00 41.38 3.25
4341 4922 1.812571 GTGCCGTTGATGGATGTTCTT 59.187 47.619 0.00 0.00 0.00 2.52
4402 4983 7.100409 TGACGATGACATATAACCAAGACAAA 58.900 34.615 0.00 0.00 0.00 2.83
4403 4984 6.635755 TGACGATGACATATAACCAAGACAA 58.364 36.000 0.00 0.00 0.00 3.18
4417 4998 2.749776 ACAACAACGATGACGATGACA 58.250 42.857 0.00 0.00 43.20 3.58
4418 4999 3.059868 ACAACAACAACGATGACGATGAC 60.060 43.478 0.00 0.00 43.20 3.06
4419 5000 3.127589 ACAACAACAACGATGACGATGA 58.872 40.909 0.00 0.00 43.20 2.92
4420 5001 3.519908 ACAACAACAACGATGACGATG 57.480 42.857 0.00 0.00 45.33 3.84
4421 5002 3.311322 ACAACAACAACAACGATGACGAT 59.689 39.130 0.00 0.00 42.66 3.73
4422 5003 2.673862 ACAACAACAACAACGATGACGA 59.326 40.909 0.00 0.00 42.66 4.20
4423 5004 3.046285 ACAACAACAACAACGATGACG 57.954 42.857 0.00 0.00 45.75 4.35
4424 5005 4.162812 ACAACAACAACAACAACGATGAC 58.837 39.130 0.00 0.00 0.00 3.06
4425 5006 4.427096 ACAACAACAACAACAACGATGA 57.573 36.364 0.00 0.00 0.00 2.92
4426 5007 4.384247 ACAACAACAACAACAACAACGATG 59.616 37.500 0.00 0.00 0.00 3.84
4427 5008 4.551388 ACAACAACAACAACAACAACGAT 58.449 34.783 0.00 0.00 0.00 3.73
4428 5009 3.966154 ACAACAACAACAACAACAACGA 58.034 36.364 0.00 0.00 0.00 3.85
4429 5010 4.026475 ACAACAACAACAACAACAACAACG 60.026 37.500 0.00 0.00 0.00 4.10
4430 5011 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
4431 5012 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
4451 5032 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
4457 5038 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
4463 5044 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
4471 5052 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
4472 5053 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
4473 5054 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
4474 5055 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
4475 5056 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
4476 5057 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
4477 5058 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
4478 5059 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
4479 5060 7.534085 TTAACAACAACAACAACAACAACAA 57.466 28.000 0.00 0.00 0.00 2.83
4480 5061 7.534085 TTTAACAACAACAACAACAACAACA 57.466 28.000 0.00 0.00 0.00 3.33
4481 5062 8.117370 AGTTTTAACAACAACAACAACAACAAC 58.883 29.630 0.00 0.00 0.00 3.32
4482 5063 8.197988 AGTTTTAACAACAACAACAACAACAA 57.802 26.923 0.00 0.00 0.00 2.83
4483 5064 7.772332 AGTTTTAACAACAACAACAACAACA 57.228 28.000 0.00 0.00 0.00 3.33
4484 5065 9.734269 CATAGTTTTAACAACAACAACAACAAC 57.266 29.630 0.00 0.00 0.00 3.32
4485 5066 9.477484 ACATAGTTTTAACAACAACAACAACAA 57.523 25.926 0.00 0.00 0.00 2.83
4486 5067 9.477484 AACATAGTTTTAACAACAACAACAACA 57.523 25.926 0.00 0.00 0.00 3.33
4487 5068 9.946418 GAACATAGTTTTAACAACAACAACAAC 57.054 29.630 0.00 0.00 0.00 3.32
4488 5069 9.141400 GGAACATAGTTTTAACAACAACAACAA 57.859 29.630 0.00 0.00 0.00 2.83
4499 5080 5.702209 TGGAACCGAGGAACATAGTTTTAAC 59.298 40.000 0.00 0.00 0.00 2.01
4535 5116 4.411927 ACAACTAATGCACCCCATTACAA 58.588 39.130 0.00 0.00 42.24 2.41
4817 5398 1.377725 CGATCCAAACCCAGCAGCT 60.378 57.895 0.00 0.00 0.00 4.24
4917 5498 6.488769 TCTAGAAAAACCACTGACCAACTA 57.511 37.500 0.00 0.00 0.00 2.24
4963 5544 3.443681 ACAATGATACCCCGCAAAAAGAG 59.556 43.478 0.00 0.00 0.00 2.85
4976 5557 4.973168 TGGAGATGCCCTTACAATGATAC 58.027 43.478 0.00 0.00 34.97 2.24
5118 9948 2.671070 GGGCTGGAGCAAGCTACA 59.329 61.111 6.82 6.82 43.06 2.74
5170 10003 5.773575 TGTGAGTCTCTAGAAACATGTGAC 58.226 41.667 0.00 0.07 0.00 3.67
5185 10018 3.639672 TTGATGATGCCATGTGAGTCT 57.360 42.857 0.00 0.00 32.09 3.24
5221 10054 2.743938 AGCGCGGTGTAGATTCTTATG 58.256 47.619 11.39 0.00 0.00 1.90
5239 10072 1.923227 GCCAACAAGGGCGTTCTAGC 61.923 60.000 0.00 0.00 45.40 3.42


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

AutoCloner maintained by Alex Coulton.