Multiple sequence alignment - TraesCS7D01G482800

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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 TraesCS7D01G482800 chr7D 100.000 4445 0 0 1 4445 593122519 593118075 0.000000e+00 8209.0
1 TraesCS7D01G482800 chr7D 94.643 56 3 0 3785 3840 78306059 78306004 2.200000e-13 87.9
2 TraesCS7D01G482800 chr7A 93.524 3768 146 37 1 3711 685834188 685830462 0.000000e+00 5517.0
3 TraesCS7D01G482800 chr7A 87.847 288 22 7 3731 4008 685830475 685830191 4.290000e-85 326.0
4 TraesCS7D01G482800 chr7A 91.866 209 9 5 4238 4445 685797013 685796812 7.280000e-73 285.0
5 TraesCS7D01G482800 chr7A 91.866 209 9 5 4238 4445 685829975 685829774 7.280000e-73 285.0
6 TraesCS7D01G482800 chr7A 91.388 209 10 3 4238 4445 685751249 685751048 3.390000e-71 279.0
7 TraesCS7D01G482800 chr7A 91.388 209 10 5 4238 4445 685814050 685813849 3.390000e-71 279.0
8 TraesCS7D01G482800 chr7A 90.909 209 11 5 4238 4445 685734657 685734456 1.580000e-69 274.0
9 TraesCS7D01G482800 chr7A 90.909 209 11 5 4238 4445 685781016 685780815 1.580000e-69 274.0
10 TraesCS7D01G482800 chr7A 85.714 196 18 6 4022 4216 685751424 685751238 9.750000e-47 198.0
11 TraesCS7D01G482800 chr7A 85.714 196 18 6 4022 4216 685781191 685781005 9.750000e-47 198.0
12 TraesCS7D01G482800 chr7A 85.204 196 19 6 4022 4216 685734832 685734646 4.540000e-45 193.0
13 TraesCS7D01G482800 chr7A 85.204 196 19 6 4022 4216 685797188 685797002 4.540000e-45 193.0
14 TraesCS7D01G482800 chr7A 85.204 196 19 6 4022 4216 685814225 685814039 4.540000e-45 193.0
15 TraesCS7D01G482800 chr7A 85.204 196 18 7 4022 4216 685830149 685829964 1.630000e-44 191.0
16 TraesCS7D01G482800 chr7A 91.667 60 5 0 3780 3839 398924513 398924454 2.850000e-12 84.2
17 TraesCS7D01G482800 chr7B 96.582 1726 53 1 993 2718 668029936 668031655 0.000000e+00 2856.0
18 TraesCS7D01G482800 chr7B 95.743 1010 26 5 2715 3709 668031735 668032742 0.000000e+00 1611.0
19 TraesCS7D01G482800 chr7B 86.311 694 29 10 300 969 668029289 668029940 0.000000e+00 695.0
20 TraesCS7D01G482800 chr7B 82.794 587 64 25 3847 4412 668032793 668033363 1.440000e-134 490.0
21 TraesCS7D01G482800 chr7B 91.954 261 18 1 1 258 668029019 668029279 3.270000e-96 363.0
22 TraesCS7D01G482800 chr7B 88.333 60 6 1 3780 3839 25889547 25889605 2.220000e-08 71.3
23 TraesCS7D01G482800 chr5D 93.197 441 10 2 1065 1505 3523869 3523449 8.110000e-177 630.0
24 TraesCS7D01G482800 chr5D 98.344 302 5 0 1529 1830 3523057 3522756 8.470000e-147 531.0
25 TraesCS7D01G482800 chr5B 83.673 196 13 10 1223 1418 426541778 426541602 2.750000e-37 167.0
26 TraesCS7D01G482800 chr3A 90.000 60 6 0 3780 3839 700747707 700747648 1.330000e-10 78.7
27 TraesCS7D01G482800 chr4B 87.500 64 8 0 3776 3839 623325067 623325130 1.710000e-09 75.0
28 TraesCS7D01G482800 chr3D 88.525 61 6 1 3780 3839 28509407 28509347 6.170000e-09 73.1
29 TraesCS7D01G482800 chr1B 95.238 42 2 0 3786 3827 509149788 509149829 2.870000e-07 67.6
30 TraesCS7D01G482800 chr4A 91.304 46 4 0 3774 3819 686881688 686881733 3.710000e-06 63.9


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 TraesCS7D01G482800 chr7D 593118075 593122519 4444 True 8209.00 8209 100.00000 1 4445 1 chr7D.!!$R2 4444
1 TraesCS7D01G482800 chr7A 685829774 685834188 4414 True 1579.75 5517 89.61025 1 4445 4 chr7A.!!$R7 4444
2 TraesCS7D01G482800 chr7B 668029019 668033363 4344 False 1203.00 2856 90.67680 1 4412 5 chr7B.!!$F2 4411
3 TraesCS7D01G482800 chr5D 3522756 3523869 1113 True 580.50 630 95.77050 1065 1830 2 chr5D.!!$R1 765

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
590 608 0.110509 CATCTTGCGTGACACTGCAC 60.111 55.0 19.76 2.17 41.57 4.57 F
592 610 1.153597 TCTTGCGTGACACTGCACTG 61.154 55.0 19.76 16.08 41.57 3.66 F
2277 2699 0.319383 CGGCGATGCTAGAGATGCTT 60.319 55.0 0.00 0.00 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2277 2699 1.758514 GCTCCTCGACATCTCCCCA 60.759 63.158 0.0 0.0 0.0 4.96 R
2434 2856 2.158682 ACCGGCCATAAGCACATATCAA 60.159 45.455 0.0 0.0 46.5 2.57 R
4186 4757 0.107848 AAAGATTACGCACGGAGGGG 60.108 55.000 0.0 0.0 33.8 4.79 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
103 107 0.525668 AGAGCAAACGACGCCGATAG 60.526 55.000 0.00 0.00 39.50 2.08
260 264 0.172578 TACCGTTGATCCTGACTGCG 59.827 55.000 0.00 0.00 0.00 5.18
261 265 2.456119 CCGTTGATCCTGACTGCGC 61.456 63.158 0.00 0.00 0.00 6.09
272 276 2.196749 CTGACTGCGCATATTTCTCGT 58.803 47.619 12.24 1.45 0.00 4.18
274 278 3.776340 TGACTGCGCATATTTCTCGTTA 58.224 40.909 12.24 0.00 0.00 3.18
283 287 5.333339 CGCATATTTCTCGTTACCATTCAGG 60.333 44.000 0.00 0.00 45.67 3.86
286 290 2.961526 TCTCGTTACCATTCAGGCTC 57.038 50.000 0.00 0.00 43.14 4.70
288 292 0.892755 TCGTTACCATTCAGGCTCGT 59.107 50.000 0.00 0.00 43.14 4.18
324 335 3.445096 GGTGGCAAGAAATCTGCAGTATT 59.555 43.478 14.67 9.98 0.00 1.89
372 383 1.135721 GGACTGCCATGGAATTTCAGC 59.864 52.381 18.40 8.72 29.12 4.26
381 392 1.623311 TGGAATTTCAGCGAGGACTGA 59.377 47.619 0.00 0.00 44.84 3.41
393 404 3.304659 GCGAGGACTGATCTGAATCTCTC 60.305 52.174 6.60 4.97 32.75 3.20
428 441 2.169769 CCTGCTGGACGGGTTATTTAGA 59.830 50.000 2.92 0.00 40.35 2.10
578 596 8.937634 ATTCAGTTCCATTTTATTCATCTTGC 57.062 30.769 0.00 0.00 0.00 4.01
590 608 0.110509 CATCTTGCGTGACACTGCAC 60.111 55.000 19.76 2.17 41.57 4.57
592 610 1.153597 TCTTGCGTGACACTGCACTG 61.154 55.000 19.76 16.08 41.57 3.66
597 615 1.821241 CGTGACACTGCACTGGTTCG 61.821 60.000 3.68 0.00 36.65 3.95
600 618 2.591429 CACTGCACTGGTTCGGCA 60.591 61.111 0.00 0.00 35.96 5.69
618 636 3.350833 GGCATTGAACTTCTCTCATGGT 58.649 45.455 0.00 0.00 0.00 3.55
682 701 1.354040 AGCTTCGATTTGCTCTGTCG 58.646 50.000 2.82 0.00 33.90 4.35
728 764 2.292802 GATCTTTTGACGCGCCGGTC 62.293 60.000 5.73 4.97 37.45 4.79
752 788 5.518128 CGTAGTTCAGATTCAGATCAAGTGG 59.482 44.000 0.00 0.00 34.60 4.00
905 958 1.687563 GTATCCCCAAAACCCCATCG 58.312 55.000 0.00 0.00 0.00 3.84
2079 2501 2.315925 AATGCCTCGACACGATGATT 57.684 45.000 0.00 0.00 34.61 2.57
2121 2543 4.072131 ACACATTCACCTACAACACCATC 58.928 43.478 0.00 0.00 0.00 3.51
2163 2585 3.991536 GAAGGTGGACGAGGCGCTC 62.992 68.421 7.64 1.63 0.00 5.03
2277 2699 0.319383 CGGCGATGCTAGAGATGCTT 60.319 55.000 0.00 0.00 0.00 3.91
2434 2856 1.337823 GCCGAGACACCTACAACACAT 60.338 52.381 0.00 0.00 0.00 3.21
2469 2891 2.113139 CGGTGTGGTTCAAGGGCT 59.887 61.111 0.00 0.00 0.00 5.19
2709 3131 2.630580 GGCCATCGAGAAGGAAGTCTAT 59.369 50.000 0.00 0.00 0.00 1.98
2906 3411 2.025981 ACAGCAAGGCAATGGAGATGTA 60.026 45.455 0.00 0.00 0.00 2.29
3219 3730 2.125106 GCGAGCCGGGAGATGTTT 60.125 61.111 2.18 0.00 0.00 2.83
3222 3733 2.044946 AGCCGGGAGATGTTTGCC 60.045 61.111 2.18 0.00 0.00 4.52
3356 3867 4.047059 GTTCCTCGCCGTGGTCGA 62.047 66.667 4.98 5.55 39.71 4.20
3390 3901 0.107945 AATCCGACCAGAAGCTGCTC 60.108 55.000 1.00 0.00 0.00 4.26
3453 3967 1.046472 TGAGACGGTGACCAAGGTGT 61.046 55.000 1.11 0.00 0.00 4.16
3483 3997 0.525761 AGCTGTGTTGTTGCGTGTTT 59.474 45.000 0.00 0.00 0.00 2.83
3551 4071 6.253727 CGTAGCATACTTACTTGTGAAGAAGG 59.746 42.308 0.00 0.00 40.12 3.46
3557 4077 9.141400 CATACTTACTTGTGAAGAAGGTAAGAC 57.859 37.037 15.12 0.00 0.00 3.01
3558 4078 6.214399 ACTTACTTGTGAAGAAGGTAAGACG 58.786 40.000 15.12 0.00 0.00 4.18
3627 4150 8.377681 TCTTACAAAGTTATTATGAAAGTCGCG 58.622 33.333 0.00 0.00 0.00 5.87
3702 4225 3.365465 CGGATGTATCGTTTGGTTTTGCA 60.365 43.478 0.00 0.00 0.00 4.08
3709 4232 8.270080 TGTATCGTTTGGTTTTGCAGAATATA 57.730 30.769 0.00 0.00 0.00 0.86
3710 4233 8.178964 TGTATCGTTTGGTTTTGCAGAATATAC 58.821 33.333 0.00 0.00 0.00 1.47
3711 4234 6.811253 TCGTTTGGTTTTGCAGAATATACT 57.189 33.333 0.00 0.00 0.00 2.12
3712 4235 7.209471 TCGTTTGGTTTTGCAGAATATACTT 57.791 32.000 0.00 0.00 0.00 2.24
3713 4236 7.653647 TCGTTTGGTTTTGCAGAATATACTTT 58.346 30.769 0.00 0.00 0.00 2.66
3715 4238 8.760569 CGTTTGGTTTTGCAGAATATACTTTTT 58.239 29.630 0.00 0.00 0.00 1.94
3758 4281 6.348050 GCAGAATATACATAAGCAGCAAGGTC 60.348 42.308 0.00 0.00 0.00 3.85
3829 4355 3.883830 AGAGTCTATGGCAGTGTCAAG 57.116 47.619 0.00 0.91 0.00 3.02
3833 4359 5.046014 AGAGTCTATGGCAGTGTCAAGAAAT 60.046 40.000 0.00 0.00 0.00 2.17
3835 4361 4.697352 GTCTATGGCAGTGTCAAGAAATGT 59.303 41.667 0.00 0.00 0.00 2.71
3860 4386 3.008375 TGCCTTAGTTCTCAGTTGCTGAT 59.992 43.478 0.00 0.00 39.92 2.90
3875 4401 1.926511 CTGATGCCTGAACGCAACCC 61.927 60.000 0.00 0.00 43.24 4.11
3919 4449 1.068948 TCCGTGGAATCTTTGGGGAA 58.931 50.000 0.00 0.00 0.00 3.97
3942 4472 3.642705 TCAAACTCTGTCATGTCACTCG 58.357 45.455 0.00 0.00 0.00 4.18
3945 4475 1.615883 ACTCTGTCATGTCACTCGCTT 59.384 47.619 0.00 0.00 0.00 4.68
3958 4496 1.202533 ACTCGCTTGCTACACACTTGT 60.203 47.619 0.00 0.00 40.02 3.16
3978 4516 1.109920 ACGCTGTCAGGTCAGTCACT 61.110 55.000 1.14 0.00 37.70 3.41
4018 4558 5.398603 CAGATAGTTCTGTCACTCCAAGT 57.601 43.478 0.01 0.00 43.73 3.16
4019 4559 5.788450 CAGATAGTTCTGTCACTCCAAGTT 58.212 41.667 0.01 0.00 43.73 2.66
4020 4560 6.226787 CAGATAGTTCTGTCACTCCAAGTTT 58.773 40.000 0.01 0.00 43.73 2.66
4025 4593 4.214986 TCTGTCACTCCAAGTTTTGTGA 57.785 40.909 0.00 0.00 37.14 3.58
4064 4632 2.995283 TGTCTGAATTGCTCCAGATGG 58.005 47.619 0.00 0.00 40.95 3.51
4078 4649 4.283337 TCCAGATGGTGCATCATTTGATT 58.717 39.130 27.35 0.00 42.72 2.57
4082 4653 3.613494 TGGTGCATCATTTGATTTGGG 57.387 42.857 0.00 0.00 31.21 4.12
4083 4654 2.905085 TGGTGCATCATTTGATTTGGGT 59.095 40.909 0.00 0.00 31.21 4.51
4084 4655 3.327172 TGGTGCATCATTTGATTTGGGTT 59.673 39.130 0.00 0.00 31.21 4.11
4085 4656 4.529769 TGGTGCATCATTTGATTTGGGTTA 59.470 37.500 0.00 0.00 31.21 2.85
4086 4657 5.012458 TGGTGCATCATTTGATTTGGGTTAA 59.988 36.000 0.00 0.00 31.21 2.01
4087 4658 6.114767 GGTGCATCATTTGATTTGGGTTAAT 58.885 36.000 0.00 0.00 31.21 1.40
4088 4659 6.037391 GGTGCATCATTTGATTTGGGTTAATG 59.963 38.462 0.00 0.00 31.21 1.90
4089 4660 6.037391 GTGCATCATTTGATTTGGGTTAATGG 59.963 38.462 0.00 0.00 31.21 3.16
4090 4661 5.528320 GCATCATTTGATTTGGGTTAATGGG 59.472 40.000 0.00 0.00 31.21 4.00
4100 4671 1.191535 GGTTAATGGGGCTGGTTTCC 58.808 55.000 0.00 0.00 0.00 3.13
4101 4672 1.551329 GGTTAATGGGGCTGGTTTCCA 60.551 52.381 0.00 0.00 34.79 3.53
4122 4693 2.836636 AGTCCAGAGCATCCTCAGTA 57.163 50.000 0.00 0.00 40.68 2.74
4136 4707 2.615869 CTCAGTAGCTGAAGCCTGAAC 58.384 52.381 10.99 1.25 40.18 3.18
4177 4748 1.004277 AGCCAATCCTGCTTTCCGTTA 59.996 47.619 0.00 0.00 34.87 3.18
4178 4749 1.132453 GCCAATCCTGCTTTCCGTTAC 59.868 52.381 0.00 0.00 0.00 2.50
4179 4750 1.396996 CCAATCCTGCTTTCCGTTACG 59.603 52.381 0.00 0.00 0.00 3.18
4217 4793 2.095768 CGTAATCTTTGGCCACACACTG 60.096 50.000 3.88 0.00 0.00 3.66
4219 4795 0.185901 ATCTTTGGCCACACACTGGT 59.814 50.000 3.88 0.00 42.99 4.00
4221 4797 1.423541 TCTTTGGCCACACACTGGTAT 59.576 47.619 3.88 0.00 42.99 2.73
4224 4800 2.483014 TGGCCACACACTGGTATAAC 57.517 50.000 0.00 0.00 42.99 1.89
4235 4811 5.179368 CACACTGGTATAACCTGTCAACTTG 59.821 44.000 5.72 0.00 45.70 3.16
4243 4819 0.313043 CCTGTCAACTTGCTTGGCTG 59.687 55.000 0.00 0.00 35.30 4.85
4310 4886 1.546476 CAGTTCCTCGGTACTCTTGCT 59.454 52.381 0.00 0.00 0.00 3.91
4311 4887 2.028930 CAGTTCCTCGGTACTCTTGCTT 60.029 50.000 0.00 0.00 0.00 3.91
4312 4888 2.028930 AGTTCCTCGGTACTCTTGCTTG 60.029 50.000 0.00 0.00 0.00 4.01
4313 4889 0.246635 TCCTCGGTACTCTTGCTTGC 59.753 55.000 0.00 0.00 0.00 4.01
4320 4896 0.602638 TACTCTTGCTTGCCCACACG 60.603 55.000 0.00 0.00 0.00 4.49
4415 4992 2.486966 CGTCCGTTCTACCCGTCC 59.513 66.667 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.190578 GAATCTGTGGCCCTCGGG 59.809 66.667 0.00 0.00 38.57 5.14
16 17 2.514592 CATGGCGGGCGAATCTGT 60.515 61.111 0.00 0.00 0.00 3.41
71 72 3.796178 CGTTTGCTCTAGCTTGATCTCTC 59.204 47.826 0.00 0.00 42.66 3.20
103 107 0.659957 GGATCTTGCTTGTCCATCGC 59.340 55.000 0.00 0.00 32.23 4.58
173 177 2.711009 TGAACAGGATCCAGGACAAGTT 59.289 45.455 15.82 6.57 0.00 2.66
260 264 5.560953 GCCTGAATGGTAACGAGAAATATGC 60.561 44.000 0.00 0.00 42.51 3.14
261 265 5.760253 AGCCTGAATGGTAACGAGAAATATG 59.240 40.000 0.00 0.00 42.51 1.78
272 276 0.892755 ACGACGAGCCTGAATGGTAA 59.107 50.000 0.00 0.00 38.35 2.85
274 278 1.215647 GACGACGAGCCTGAATGGT 59.784 57.895 0.00 0.00 38.35 3.55
283 287 3.324099 TTCAGAGGCGACGACGAGC 62.324 63.158 12.29 6.69 42.66 5.03
286 290 2.202492 CCTTCAGAGGCGACGACG 60.202 66.667 2.12 2.12 42.93 5.12
324 335 2.502947 CCTGTCAGTTCATCATCCTCCA 59.497 50.000 0.00 0.00 0.00 3.86
372 383 3.058983 CGAGAGATTCAGATCAGTCCTCG 60.059 52.174 0.00 0.00 35.80 4.63
428 441 4.228438 CCTTTCCCTTCTCCCTCTAAACAT 59.772 45.833 0.00 0.00 0.00 2.71
565 583 4.378356 GCAGTGTCACGCAAGATGAATAAA 60.378 41.667 12.81 0.00 43.62 1.40
578 596 1.821241 CGAACCAGTGCAGTGTCACG 61.821 60.000 19.93 16.36 41.61 4.35
590 608 2.154462 AGAAGTTCAATGCCGAACCAG 58.846 47.619 5.50 0.00 45.27 4.00
592 610 2.416893 GAGAGAAGTTCAATGCCGAACC 59.583 50.000 5.50 0.00 45.27 3.62
597 615 3.350833 ACCATGAGAGAAGTTCAATGCC 58.649 45.455 5.50 0.00 0.00 4.40
600 618 4.401022 TGCAACCATGAGAGAAGTTCAAT 58.599 39.130 5.50 0.00 0.00 2.57
618 636 1.063912 CGTGTCAGAAAACAGCTGCAA 59.936 47.619 15.27 0.00 33.45 4.08
682 701 3.322828 TGCCCGGTTATTCTATCAGTACC 59.677 47.826 0.00 0.00 0.00 3.34
728 764 5.518128 CCACTTGATCTGAATCTGAACTACG 59.482 44.000 0.00 0.00 32.75 3.51
818 871 2.586914 CGAGCGCCATCTGATGCA 60.587 61.111 12.17 0.00 0.00 3.96
820 873 1.485838 GACACGAGCGCCATCTGATG 61.486 60.000 10.71 10.71 0.00 3.07
905 958 1.004440 GAGTGTGTCAGTCAGGGGC 60.004 63.158 0.44 0.00 34.29 5.80
940 993 2.202756 GGAAGCAGCCGTACGGAG 60.203 66.667 37.62 27.44 37.50 4.63
1752 2174 4.593864 GCGGCCCTCATCTCGTCC 62.594 72.222 0.00 0.00 0.00 4.79
1956 2378 2.103941 GTCCTCCATCTCCTTGATCACC 59.896 54.545 0.00 0.00 32.05 4.02
2103 2525 4.943705 GTCATGATGGTGTTGTAGGTGAAT 59.056 41.667 0.00 0.00 0.00 2.57
2121 2543 2.162754 GTTCCCGTACGCCGTCATG 61.163 63.158 10.49 0.00 33.66 3.07
2163 2585 4.143333 ATCCGGTCGAACAGGGCG 62.143 66.667 0.00 0.00 34.05 6.13
2277 2699 1.758514 GCTCCTCGACATCTCCCCA 60.759 63.158 0.00 0.00 0.00 4.96
2434 2856 2.158682 ACCGGCCATAAGCACATATCAA 60.159 45.455 0.00 0.00 46.50 2.57
2469 2891 7.784633 TTCATCATACATCTTGAATGCGTTA 57.215 32.000 0.00 0.00 0.00 3.18
2682 3104 2.242926 TCCTTCTCGATGGCCTCTATG 58.757 52.381 3.32 0.00 0.00 2.23
2685 3107 1.118838 CTTCCTTCTCGATGGCCTCT 58.881 55.000 3.32 0.00 0.00 3.69
2709 3131 2.108168 CTCGGGAAGATGGTACCTTGA 58.892 52.381 14.36 0.00 0.00 3.02
2832 3337 1.819288 GAGTTGAGGATGACGAGGTCA 59.181 52.381 0.38 0.38 46.90 4.02
3026 3531 4.792804 GCTGCTGGGACTGGGAGC 62.793 72.222 0.00 0.00 38.52 4.70
3339 3850 4.047059 TCGACCACGGCGAGGAAC 62.047 66.667 29.75 19.79 40.21 3.62
3356 3867 1.328430 GGATTTCGGGTCGGTCTCCT 61.328 60.000 0.00 0.00 0.00 3.69
3430 3941 1.134965 CCTTGGTCACCGTCTCATCTC 60.135 57.143 0.00 0.00 0.00 2.75
3453 3967 5.733091 GCAACAACACAGCTCTATGAACAAA 60.733 40.000 0.00 0.00 0.00 2.83
3483 3997 2.040947 TCACCCAACATATCTGCCACAA 59.959 45.455 0.00 0.00 0.00 3.33
3535 4055 5.634020 CCGTCTTACCTTCTTCACAAGTAAG 59.366 44.000 0.00 0.00 0.00 2.34
3551 4071 2.584791 CATTTTGCAGCACCGTCTTAC 58.415 47.619 0.00 0.00 0.00 2.34
3557 4077 2.339348 TGCCATTTTGCAGCACCG 59.661 55.556 0.00 0.00 36.04 4.94
3587 4107 4.759516 TTGTAAGAATGCGAGGAAAACC 57.240 40.909 0.00 0.00 0.00 3.27
3627 4150 2.157085 GCTAACAACTGTACAGCCGAAC 59.843 50.000 22.90 3.19 32.94 3.95
3660 4183 3.441572 CCGAAGCACCTCAAAATTCAGAT 59.558 43.478 0.00 0.00 0.00 2.90
3719 4242 0.537188 TTCTGCAAACCCCGCAAAAA 59.463 45.000 0.00 0.00 39.30 1.94
3720 4243 0.755686 ATTCTGCAAACCCCGCAAAA 59.244 45.000 0.00 0.00 39.30 2.44
3721 4244 1.621992 TATTCTGCAAACCCCGCAAA 58.378 45.000 0.00 0.00 39.30 3.68
3722 4245 1.846007 ATATTCTGCAAACCCCGCAA 58.154 45.000 0.00 0.00 39.30 4.85
3723 4246 2.294074 GTATATTCTGCAAACCCCGCA 58.706 47.619 0.00 0.00 37.88 5.69
3724 4247 2.294074 TGTATATTCTGCAAACCCCGC 58.706 47.619 0.00 0.00 0.00 6.13
3725 4248 5.334879 GCTTATGTATATTCTGCAAACCCCG 60.335 44.000 0.00 0.00 0.00 5.73
3726 4249 5.534654 TGCTTATGTATATTCTGCAAACCCC 59.465 40.000 0.00 0.00 0.00 4.95
3727 4250 6.633500 TGCTTATGTATATTCTGCAAACCC 57.367 37.500 0.00 0.00 0.00 4.11
3728 4251 6.145535 GCTGCTTATGTATATTCTGCAAACC 58.854 40.000 0.00 0.00 0.00 3.27
3729 4252 6.728200 TGCTGCTTATGTATATTCTGCAAAC 58.272 36.000 0.00 0.00 0.00 2.93
3758 4281 2.315925 TAGAATTTGGGAGCAGCTCG 57.684 50.000 16.47 0.00 0.00 5.03
3802 4325 4.929808 ACACTGCCATAGACTCTAAAAACG 59.070 41.667 0.00 0.00 0.00 3.60
3803 4326 5.932303 TGACACTGCCATAGACTCTAAAAAC 59.068 40.000 0.00 0.00 0.00 2.43
3804 4327 6.109156 TGACACTGCCATAGACTCTAAAAA 57.891 37.500 0.00 0.00 0.00 1.94
3808 4331 4.600062 TCTTGACACTGCCATAGACTCTA 58.400 43.478 0.00 0.00 0.00 2.43
3809 4332 3.435275 TCTTGACACTGCCATAGACTCT 58.565 45.455 0.00 0.00 0.00 3.24
3810 4333 3.876274 TCTTGACACTGCCATAGACTC 57.124 47.619 0.00 0.00 0.00 3.36
3811 4334 4.623932 TTTCTTGACACTGCCATAGACT 57.376 40.909 0.00 0.00 0.00 3.24
3812 4335 4.697352 ACATTTCTTGACACTGCCATAGAC 59.303 41.667 0.00 0.00 0.00 2.59
3813 4336 4.910195 ACATTTCTTGACACTGCCATAGA 58.090 39.130 0.00 0.00 0.00 1.98
3814 4337 4.940046 AGACATTTCTTGACACTGCCATAG 59.060 41.667 0.00 0.00 0.00 2.23
3829 4355 5.703130 ACTGAGAACTAAGGCAAGACATTTC 59.297 40.000 0.00 0.00 0.00 2.17
3833 4359 4.380531 CAACTGAGAACTAAGGCAAGACA 58.619 43.478 0.00 0.00 0.00 3.41
3835 4361 3.071602 AGCAACTGAGAACTAAGGCAAGA 59.928 43.478 0.00 0.00 0.00 3.02
3839 4365 3.045601 TCAGCAACTGAGAACTAAGGC 57.954 47.619 0.00 0.00 35.39 4.35
3845 4371 1.467734 CAGGCATCAGCAACTGAGAAC 59.532 52.381 3.42 0.00 44.08 3.01
3860 4386 0.676466 CATAGGGTTGCGTTCAGGCA 60.676 55.000 0.00 0.00 42.12 4.75
3875 4401 3.443037 GTCAGACACAGCTACTGCATAG 58.557 50.000 0.00 0.00 42.74 2.23
3919 4449 4.626042 GAGTGACATGACAGAGTTTGAGT 58.374 43.478 0.00 0.00 0.00 3.41
3942 4472 1.136336 GCGTACAAGTGTGTAGCAAGC 60.136 52.381 0.00 0.00 40.94 4.01
3945 4475 1.067974 ACAGCGTACAAGTGTGTAGCA 59.932 47.619 0.00 0.00 40.94 3.49
3958 4496 0.596577 GTGACTGACCTGACAGCGTA 59.403 55.000 0.00 0.00 41.06 4.42
4008 4548 2.687935 GCCTTCACAAAACTTGGAGTGA 59.312 45.455 0.00 0.00 39.06 3.41
4009 4549 2.426738 TGCCTTCACAAAACTTGGAGTG 59.573 45.455 0.00 0.00 34.12 3.51
4010 4550 2.689983 CTGCCTTCACAAAACTTGGAGT 59.310 45.455 0.00 0.00 34.12 3.85
4011 4551 2.689983 ACTGCCTTCACAAAACTTGGAG 59.310 45.455 0.00 0.00 34.12 3.86
4012 4552 2.426738 CACTGCCTTCACAAAACTTGGA 59.573 45.455 0.00 0.00 34.12 3.53
4013 4553 2.813061 CACTGCCTTCACAAAACTTGG 58.187 47.619 0.00 0.00 34.12 3.61
4014 4554 2.159198 AGCACTGCCTTCACAAAACTTG 60.159 45.455 0.00 0.00 0.00 3.16
4015 4555 2.102578 AGCACTGCCTTCACAAAACTT 58.897 42.857 0.00 0.00 0.00 2.66
4016 4556 1.406539 CAGCACTGCCTTCACAAAACT 59.593 47.619 0.00 0.00 0.00 2.66
4017 4557 1.843992 CAGCACTGCCTTCACAAAAC 58.156 50.000 0.00 0.00 0.00 2.43
4064 4632 6.037391 CCATTAACCCAAATCAAATGATGCAC 59.963 38.462 0.00 0.00 34.49 4.57
4067 4635 6.056884 CCCCATTAACCCAAATCAAATGATG 58.943 40.000 0.00 0.00 34.49 3.07
4078 4649 0.489567 AACCAGCCCCATTAACCCAA 59.510 50.000 0.00 0.00 0.00 4.12
4082 4653 1.931635 TGGAAACCAGCCCCATTAAC 58.068 50.000 0.00 0.00 0.00 2.01
4083 4654 2.704190 TTGGAAACCAGCCCCATTAA 57.296 45.000 0.00 0.00 33.81 1.40
4084 4655 2.158234 ACTTTGGAAACCAGCCCCATTA 60.158 45.455 0.00 0.00 33.81 1.90
4085 4656 1.351076 CTTTGGAAACCAGCCCCATT 58.649 50.000 0.00 0.00 33.81 3.16
4086 4657 0.190815 ACTTTGGAAACCAGCCCCAT 59.809 50.000 0.00 0.00 33.81 4.00
4087 4658 0.469144 GACTTTGGAAACCAGCCCCA 60.469 55.000 0.00 0.00 33.81 4.96
4088 4659 1.185618 GGACTTTGGAAACCAGCCCC 61.186 60.000 0.00 0.00 33.81 5.80
4089 4660 0.469144 TGGACTTTGGAAACCAGCCC 60.469 55.000 0.00 0.00 33.81 5.19
4090 4661 0.961753 CTGGACTTTGGAAACCAGCC 59.038 55.000 0.00 0.00 42.30 4.85
4100 4671 2.027377 ACTGAGGATGCTCTGGACTTTG 60.027 50.000 21.98 3.73 0.00 2.77
4101 4672 2.264455 ACTGAGGATGCTCTGGACTTT 58.736 47.619 21.98 1.42 0.00 2.66
4122 4693 2.645838 TTTGAGTTCAGGCTTCAGCT 57.354 45.000 0.00 0.00 41.70 4.24
4136 4707 0.169672 CTCCTGCCGCACATTTTGAG 59.830 55.000 0.00 0.00 0.00 3.02
4185 4756 2.588034 GATTACGCACGGAGGGGC 60.588 66.667 0.00 0.00 33.80 5.80
4186 4757 0.107848 AAAGATTACGCACGGAGGGG 60.108 55.000 0.00 0.00 33.80 4.79
4217 4793 4.156008 CCAAGCAAGTTGACAGGTTATACC 59.844 45.833 7.16 0.00 38.60 2.73
4219 4795 3.756434 GCCAAGCAAGTTGACAGGTTATA 59.244 43.478 7.16 0.00 38.60 0.98
4221 4797 1.953686 GCCAAGCAAGTTGACAGGTTA 59.046 47.619 7.16 0.00 38.60 2.85
4224 4800 0.313043 CAGCCAAGCAAGTTGACAGG 59.687 55.000 7.16 5.33 38.60 4.00
4235 4811 1.443194 CGAATGTGTGCAGCCAAGC 60.443 57.895 0.00 0.00 0.00 4.01
4310 4886 0.391130 GAGTAGCATCGTGTGGGCAA 60.391 55.000 0.00 0.00 0.00 4.52
4311 4887 1.218047 GAGTAGCATCGTGTGGGCA 59.782 57.895 0.00 0.00 0.00 5.36
4312 4888 0.744874 TAGAGTAGCATCGTGTGGGC 59.255 55.000 0.00 0.00 0.00 5.36
4313 4889 2.025155 AGTAGAGTAGCATCGTGTGGG 58.975 52.381 0.00 0.00 0.00 4.61
4320 4896 4.023193 GGCAGAGAAGAGTAGAGTAGCATC 60.023 50.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.