Multiple sequence alignment - TraesCS7D01G075000

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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 TraesCS7D01G075000 chr7D 100.000 5286 0 0 1 5286 44526896 44521611 0.000000e+00 9762.0
1 TraesCS7D01G075000 chr7D 85.515 1933 223 34 1699 3619 567659145 567657258 0.000000e+00 1965.0
2 TraesCS7D01G075000 chr7D 86.462 650 42 28 972 1598 567659831 567659205 0.000000e+00 671.0
3 TraesCS7D01G075000 chr7D 86.059 373 46 2 3948 4314 567657077 567656705 3.840000e-106 396.0
4 TraesCS7D01G075000 chr7D 100.000 36 0 0 4443 4478 44522336 44522301 3.420000e-07 67.6
5 TraesCS7D01G075000 chr7D 100.000 36 0 0 4561 4596 44522454 44522419 3.420000e-07 67.6
6 TraesCS7D01G075000 chr4A 92.901 4691 193 66 573 5170 655627733 655623090 0.000000e+00 6689.0
7 TraesCS7D01G075000 chr4A 85.217 115 17 0 1 115 724319897 724320011 9.300000e-23 119.0
8 TraesCS7D01G075000 chr4A 85.217 115 17 0 1 115 724331013 724331127 9.300000e-23 119.0
9 TraesCS7D01G075000 chr4A 97.222 36 1 0 4443 4478 655623728 655623693 1.590000e-05 62.1
10 TraesCS7D01G075000 chr4A 97.222 36 1 0 4561 4596 655623842 655623807 1.590000e-05 62.1
11 TraesCS7D01G075000 chr7A 94.402 3519 135 27 1684 5167 46969122 46965631 0.000000e+00 5350.0
12 TraesCS7D01G075000 chr7A 90.248 1692 101 35 3 1671 46970917 46969267 0.000000e+00 2152.0
13 TraesCS7D01G075000 chr7A 86.253 1884 214 30 1745 3619 654206384 654204537 0.000000e+00 2002.0
14 TraesCS7D01G075000 chr7A 84.322 708 52 41 971 1649 654207160 654206483 5.770000e-179 638.0
15 TraesCS7D01G075000 chr7A 91.667 120 6 1 5167 5286 46965456 46965341 4.240000e-36 163.0
16 TraesCS7D01G075000 chr7A 100.000 36 0 0 4561 4596 46966374 46966339 3.420000e-07 67.6
17 TraesCS7D01G075000 chr7B 85.916 1839 218 22 1789 3619 621475005 621473200 0.000000e+00 1923.0
18 TraesCS7D01G075000 chr7B 83.520 716 61 31 959 1649 621475820 621475137 2.710000e-172 616.0
19 TraesCS7D01G075000 chr7B 86.179 369 44 4 3950 4314 621473001 621472636 4.960000e-105 392.0
20 TraesCS7D01G075000 chr3A 95.726 117 5 0 4212 4328 80369 80485 6.990000e-44 189.0
21 TraesCS7D01G075000 chr3A 92.913 127 8 1 4212 4337 514598 514724 3.250000e-42 183.0
22 TraesCS7D01G075000 chr3A 73.840 237 51 11 199 430 28130420 28130190 3.390000e-12 84.2
23 TraesCS7D01G075000 chrUn 90.698 129 11 1 4212 4339 43317359 43317487 2.530000e-38 171.0
24 TraesCS7D01G075000 chrUn 81.034 174 28 5 4990 5160 15528868 15529039 3.320000e-27 134.0
25 TraesCS7D01G075000 chrUn 81.034 174 28 5 4990 5160 212997438 212997609 3.320000e-27 134.0
26 TraesCS7D01G075000 chrUn 81.034 174 28 5 4990 5160 224609612 224609783 3.320000e-27 134.0
27 TraesCS7D01G075000 chrUn 81.034 174 28 5 4990 5160 255474769 255474940 3.320000e-27 134.0
28 TraesCS7D01G075000 chrUn 81.287 171 27 5 4993 5160 265176452 265176284 3.320000e-27 134.0
29 TraesCS7D01G075000 chrUn 81.287 171 27 5 4993 5160 268968567 268968399 3.320000e-27 134.0
30 TraesCS7D01G075000 chr2B 81.034 174 28 5 4990 5160 8363145 8363316 3.320000e-27 134.0
31 TraesCS7D01G075000 chr1A 73.840 237 51 11 199 430 61380890 61380660 3.390000e-12 84.2
32 TraesCS7D01G075000 chr2D 83.516 91 10 2 5194 5283 2352048 2352134 4.390000e-11 80.5
33 TraesCS7D01G075000 chr5A 73.251 243 54 11 193 430 632774066 632774302 1.580000e-10 78.7


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 TraesCS7D01G075000 chr7D 44521611 44526896 5285 True 9762.000000 9762 100.00000 1 5286 1 chr7D.!!$R1 5285
1 TraesCS7D01G075000 chr7D 567656705 567659831 3126 True 1010.666667 1965 86.01200 972 4314 3 chr7D.!!$R3 3342
2 TraesCS7D01G075000 chr4A 655623090 655627733 4643 True 6689.000000 6689 92.90100 573 5170 1 chr4A.!!$R1 4597
3 TraesCS7D01G075000 chr7A 46965341 46970917 5576 True 1933.150000 5350 94.07925 3 5286 4 chr7A.!!$R1 5283
4 TraesCS7D01G075000 chr7A 654204537 654207160 2623 True 1320.000000 2002 85.28750 971 3619 2 chr7A.!!$R2 2648
5 TraesCS7D01G075000 chr7B 621472636 621475820 3184 True 977.000000 1923 85.20500 959 4314 3 chr7B.!!$R1 3355

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
758 768 0.025128 GCTTTCTTCGACGATTCGGC 59.975 55.000 11.29 6.4 45.90 5.54 F
813 836 0.178992 TGCAACTCCCAAGGTCCAAG 60.179 55.000 0.00 0.0 0.00 3.61 F
1606 1697 0.270699 TATGCCCCTGTCCCCTGTAT 59.729 55.000 0.00 0.0 0.00 2.29 F
1872 2141 1.102222 AGGCTAGGTTCTACGGCTCG 61.102 60.000 0.00 0.0 0.00 5.03 F
2135 2406 1.831389 CGTCGGGCACTTTGTCTGTG 61.831 60.000 0.00 0.0 38.36 3.66 F
2276 2550 2.208431 GAAGATGATGCGTTGGAGGAG 58.792 52.381 0.00 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 2231 1.900016 TTCTGCTGCAACCTGCCAG 60.900 57.895 3.02 0.0 44.23 4.85 R
2135 2406 3.059982 GCCTTTTGGGGGACTTGC 58.940 61.111 0.00 0.0 40.82 4.01 R
3529 3814 0.888736 TGGTCAAGTGGTTCATGCGG 60.889 55.000 0.00 0.0 0.00 5.69 R
3640 3926 3.279434 GCTTTCCCAAGGTACATACAGG 58.721 50.000 0.00 0.0 0.00 4.00 R
3903 4198 3.518590 CACCTTACAGTAAAGTAGGCCG 58.481 50.000 0.00 0.0 0.00 6.13 R
4403 4717 2.125147 TACACGCCCAGCATCAGC 60.125 61.111 0.00 0.0 42.56 4.26 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
120 121 3.317150 TGTAGCTTGAAGTCATGTGTCG 58.683 45.455 0.00 0.00 0.00 4.35
155 156 5.357032 ACTTGTGTCTTGTCCCAACTAAAAG 59.643 40.000 0.00 0.00 0.00 2.27
170 171 4.682787 ACTAAAAGAAACTTGTGGCTTGC 58.317 39.130 0.00 0.00 0.00 4.01
174 175 0.746659 GAAACTTGTGGCTTGCCTGT 59.253 50.000 13.18 4.17 0.00 4.00
211 212 7.661437 TCATAGGTCCAAGTATGCATTTATGAC 59.339 37.037 3.54 6.05 0.00 3.06
232 233 7.159322 TGACCAGAGAGATCAAAACTAGTAC 57.841 40.000 0.00 0.00 0.00 2.73
234 235 5.944599 ACCAGAGAGATCAAAACTAGTACGA 59.055 40.000 0.00 0.00 0.00 3.43
268 270 8.568041 CGATTCTTGTATTACTCATATTCGTCG 58.432 37.037 0.00 0.00 0.00 5.12
271 273 7.582352 TCTTGTATTACTCATATTCGTCGGAG 58.418 38.462 0.00 0.00 0.00 4.63
284 286 1.792949 CGTCGGAGCTGTAATAATGCC 59.207 52.381 0.00 0.00 0.00 4.40
285 287 1.792949 GTCGGAGCTGTAATAATGCCG 59.207 52.381 0.00 0.00 38.68 5.69
297 299 4.589216 AATAATGCCGGTCATTTCATGG 57.411 40.909 23.09 0.00 42.48 3.66
300 302 0.254462 TGCCGGTCATTTCATGGCTA 59.746 50.000 1.90 0.00 45.90 3.93
301 303 1.340502 TGCCGGTCATTTCATGGCTAA 60.341 47.619 1.90 0.00 45.90 3.09
302 304 1.065551 GCCGGTCATTTCATGGCTAAC 59.934 52.381 1.90 0.00 42.44 2.34
305 307 3.443681 CCGGTCATTTCATGGCTAACTTT 59.556 43.478 0.00 0.00 34.67 2.66
323 325 4.906618 ACTTTGATAGGTTGAATGACCGT 58.093 39.130 0.00 0.00 44.62 4.83
331 333 1.324736 GTTGAATGACCGTCTGCGATC 59.675 52.381 0.00 0.00 41.33 3.69
334 336 0.179100 AATGACCGTCTGCGATCTGG 60.179 55.000 0.00 0.00 41.33 3.86
359 361 1.138069 GCTCTGGCCTAGAAGAAGTCC 59.862 57.143 3.32 0.00 34.32 3.85
371 373 7.386851 CCTAGAAGAAGTCCTGAACATTGTTA 58.613 38.462 1.15 0.00 0.00 2.41
374 376 7.684529 AGAAGAAGTCCTGAACATTGTTAGAT 58.315 34.615 1.15 0.00 0.00 1.98
379 381 7.192852 AGTCCTGAACATTGTTAGATGAGAT 57.807 36.000 1.15 0.00 0.00 2.75
382 384 7.335422 GTCCTGAACATTGTTAGATGAGATTGT 59.665 37.037 1.15 0.00 0.00 2.71
384 386 9.334947 CCTGAACATTGTTAGATGAGATTGTAT 57.665 33.333 1.15 0.00 0.00 2.29
411 413 9.362539 TCCTTAATCGTTGAGTAATACAAGAAC 57.637 33.333 0.00 0.00 0.00 3.01
419 421 9.671521 CGTTGAGTAATACAAGAACTATTTTCG 57.328 33.333 0.00 0.00 0.00 3.46
533 535 3.130516 TGTCTGACGGTATGAGATGGTTC 59.869 47.826 2.98 0.00 0.00 3.62
534 536 3.130516 GTCTGACGGTATGAGATGGTTCA 59.869 47.826 0.00 0.00 0.00 3.18
555 557 8.545749 GTTCAAAACCAAGCAAACATTTAATG 57.454 30.769 3.07 3.07 0.00 1.90
560 562 9.786105 AAAACCAAGCAAACATTTAATGAAAAG 57.214 25.926 12.28 0.28 0.00 2.27
561 563 8.729805 AACCAAGCAAACATTTAATGAAAAGA 57.270 26.923 12.28 0.00 0.00 2.52
563 565 9.341078 ACCAAGCAAACATTTAATGAAAAGAAT 57.659 25.926 12.28 0.00 0.00 2.40
676 686 7.595311 AAAAAGACTCCACAATGTTTGTTTC 57.405 32.000 0.00 0.00 43.23 2.78
678 688 7.639113 AAAGACTCCACAATGTTTGTTTCTA 57.361 32.000 0.00 0.00 43.23 2.10
681 691 7.875971 AGACTCCACAATGTTTGTTTCTAATC 58.124 34.615 0.00 0.00 43.23 1.75
682 692 7.502226 AGACTCCACAATGTTTGTTTCTAATCA 59.498 33.333 0.00 0.00 43.23 2.57
684 694 8.084073 ACTCCACAATGTTTGTTTCTAATCATG 58.916 33.333 0.00 0.00 43.23 3.07
686 696 8.420222 TCCACAATGTTTGTTTCTAATCATGTT 58.580 29.630 0.00 0.00 43.23 2.71
687 697 9.044150 CCACAATGTTTGTTTCTAATCATGTTT 57.956 29.630 0.00 0.00 43.23 2.83
749 759 0.108585 ACCAGGCTTGCTTTCTTCGA 59.891 50.000 0.00 0.00 0.00 3.71
755 765 2.474691 GGCTTGCTTTCTTCGACGATTC 60.475 50.000 0.00 0.00 0.00 2.52
757 767 1.346365 TGCTTTCTTCGACGATTCGG 58.654 50.000 11.29 0.00 45.90 4.30
758 768 0.025128 GCTTTCTTCGACGATTCGGC 59.975 55.000 11.29 6.40 45.90 5.54
759 769 0.645868 CTTTCTTCGACGATTCGGCC 59.354 55.000 11.29 0.00 45.90 6.13
813 836 0.178992 TGCAACTCCCAAGGTCCAAG 60.179 55.000 0.00 0.00 0.00 3.61
818 841 1.778383 TCCCAAGGTCCAAGCCCTT 60.778 57.895 0.00 0.00 43.11 3.95
1393 1454 4.393778 GGTCCGTCCCTCCCTCCA 62.394 72.222 0.00 0.00 0.00 3.86
1483 1571 1.091771 CAATGCAGGTCGAGGCGAAT 61.092 55.000 0.00 0.00 37.72 3.34
1603 1694 2.757124 GGTATGCCCCTGTCCCCTG 61.757 68.421 0.00 0.00 0.00 4.45
1604 1695 2.001269 GTATGCCCCTGTCCCCTGT 61.001 63.158 0.00 0.00 0.00 4.00
1605 1696 0.693092 GTATGCCCCTGTCCCCTGTA 60.693 60.000 0.00 0.00 0.00 2.74
1606 1697 0.270699 TATGCCCCTGTCCCCTGTAT 59.729 55.000 0.00 0.00 0.00 2.29
1621 1712 8.560039 TGTCCCCTGTATAGTAGAAACTAGTAA 58.440 37.037 0.00 0.00 41.46 2.24
1673 1775 2.216881 TGGAATGAGACCCATGGGATT 58.783 47.619 38.07 24.94 38.96 3.01
1675 1777 2.961062 GGAATGAGACCCATGGGATTTG 59.039 50.000 38.07 10.87 38.96 2.32
1678 1780 1.710244 TGAGACCCATGGGATTTGTGT 59.290 47.619 38.07 13.23 38.96 3.72
1729 1957 8.602328 TGAAATAAACTGCAGAACAAAATGTTG 58.398 29.630 23.35 0.00 41.28 3.33
1761 2030 1.202758 TGCTTGAACCTACACCACAGG 60.203 52.381 0.00 0.00 39.25 4.00
1872 2141 1.102222 AGGCTAGGTTCTACGGCTCG 61.102 60.000 0.00 0.00 0.00 5.03
1899 2169 2.027625 GTTCGTCTTGTCGCAGGGG 61.028 63.158 0.00 0.00 0.00 4.79
1960 2231 2.489329 CCATGACCAGTGTTGTTGGATC 59.511 50.000 0.00 0.00 39.08 3.36
2135 2406 1.831389 CGTCGGGCACTTTGTCTGTG 61.831 60.000 0.00 0.00 38.36 3.66
2276 2550 2.208431 GAAGATGATGCGTTGGAGGAG 58.792 52.381 0.00 0.00 0.00 3.69
2427 2701 9.857656 AGCTAGAGATCCATGAAAAATTATTCA 57.142 29.630 0.00 0.00 43.03 2.57
2891 3171 3.260740 CAGAGTCTGCAGGTGAAGATTC 58.739 50.000 15.13 2.83 36.88 2.52
2993 3274 9.449896 TGTGGTATAACTACTATTATTTCCCCA 57.550 33.333 0.00 0.00 30.28 4.96
3035 3320 3.460825 ACCATGGGTGTAGTAGATTGGT 58.539 45.455 18.09 0.00 32.98 3.67
3230 3515 3.926616 AGTACAAATCTTCCAGGACACG 58.073 45.455 0.00 0.00 0.00 4.49
3273 3558 3.516300 TGAAGGACGGCCAGATAAGTTTA 59.484 43.478 11.69 0.00 36.29 2.01
3279 3564 3.053917 ACGGCCAGATAAGTTTATTGGGT 60.054 43.478 2.24 0.00 0.00 4.51
3288 3573 3.451402 AGTTTATTGGGTGAGGGTTCC 57.549 47.619 0.00 0.00 0.00 3.62
3336 3621 2.750141 AGCCCTCTGACGGTTATCTA 57.250 50.000 0.00 0.00 0.00 1.98
3451 3736 2.749280 TATCGCTGATATGCACTGGG 57.251 50.000 0.00 0.00 0.00 4.45
3553 3838 4.142403 CGCATGAACCACTTGACCATATTT 60.142 41.667 0.00 0.00 0.00 1.40
3554 3839 5.622007 CGCATGAACCACTTGACCATATTTT 60.622 40.000 0.00 0.00 0.00 1.82
3624 3910 3.139077 GGTCGTTGTTCAGTCCTTTCAT 58.861 45.455 0.00 0.00 0.00 2.57
3625 3911 3.186613 GGTCGTTGTTCAGTCCTTTCATC 59.813 47.826 0.00 0.00 0.00 2.92
3627 3913 3.071023 TCGTTGTTCAGTCCTTTCATCCT 59.929 43.478 0.00 0.00 0.00 3.24
3628 3914 3.815401 CGTTGTTCAGTCCTTTCATCCTT 59.185 43.478 0.00 0.00 0.00 3.36
3636 3922 3.823304 AGTCCTTTCATCCTTTGCACTTC 59.177 43.478 0.00 0.00 0.00 3.01
3640 3926 5.010012 TCCTTTCATCCTTTGCACTTCTTTC 59.990 40.000 0.00 0.00 0.00 2.62
3760 4055 6.719829 TGACTTCAGTTCAGAGAATAGGTACA 59.280 38.462 0.00 0.00 0.00 2.90
3903 4198 0.043822 CTTTACGCGCATCTCTTCGC 60.044 55.000 5.73 0.00 46.98 4.70
3915 4210 1.133790 TCTCTTCGCGGCCTACTTTAC 59.866 52.381 6.13 0.00 0.00 2.01
4403 4717 2.690778 GGTGCCTTGCTTAGGTGCG 61.691 63.158 7.20 0.00 46.61 5.34
4510 4824 9.787435 TTTAATTCGGATAAGCCATGTATTACT 57.213 29.630 0.00 0.00 35.94 2.24
4552 4866 8.299570 GTGATTTCTGGTATCTGACATGTTTTT 58.700 33.333 0.00 0.00 0.00 1.94
4553 4867 9.513906 TGATTTCTGGTATCTGACATGTTTTTA 57.486 29.630 0.00 0.00 0.00 1.52
4662 4977 1.125633 GGGCTTGATCCATGGCATTT 58.874 50.000 6.96 0.00 36.17 2.32
4693 5008 1.546476 CCGTTCTCTAGAAGCACCACT 59.454 52.381 0.00 0.00 34.27 4.00
4738 5073 3.127589 GTTTTTATTTTGGCTGTGGCGT 58.872 40.909 0.00 0.00 39.81 5.68
4871 5206 8.864087 TCATATCATGCTTACTCTACTGTCAAT 58.136 33.333 0.00 0.00 0.00 2.57
4872 5207 8.923683 CATATCATGCTTACTCTACTGTCAATG 58.076 37.037 0.00 0.00 0.00 2.82
4874 5209 3.861840 TGCTTACTCTACTGTCAATGGC 58.138 45.455 0.00 0.00 0.00 4.40
4889 5226 8.368668 ACTGTCAATGGCTACTAACTTATATCC 58.631 37.037 0.00 0.00 0.00 2.59
4893 5230 6.912951 ATGGCTACTAACTTATATCCGTGT 57.087 37.500 0.00 0.00 0.00 4.49
4924 5261 8.894768 AGAGGTGAAGTGAAATATACTATTGC 57.105 34.615 0.00 0.00 0.00 3.56
4925 5262 8.709308 AGAGGTGAAGTGAAATATACTATTGCT 58.291 33.333 0.00 0.00 0.00 3.91
4926 5263 8.668510 AGGTGAAGTGAAATATACTATTGCTG 57.331 34.615 0.00 0.00 0.00 4.41
4928 5265 7.499232 GGTGAAGTGAAATATACTATTGCTGGT 59.501 37.037 0.00 0.00 0.00 4.00
4940 5286 4.773149 ACTATTGCTGGTCCTACTATAGGC 59.227 45.833 4.43 0.00 45.82 3.93
4952 5298 7.452189 GGTCCTACTATAGGCAAGACTTCTTAT 59.548 40.741 4.43 0.00 45.82 1.73
5031 5378 6.840780 ATTTAACTGAGGTGCTTAATGCTT 57.159 33.333 0.00 0.00 43.37 3.91
5038 5385 6.261826 ACTGAGGTGCTTAATGCTTCATTATC 59.738 38.462 0.73 0.00 43.37 1.75
5189 5713 6.157994 TCCTCTACTGTTAATTGCTTATGGGT 59.842 38.462 0.00 0.00 0.00 4.51
5210 5734 7.134162 TGGGTATATAGGGTCTTTGTAGTGAA 58.866 38.462 0.00 0.00 0.00 3.18
5211 5735 7.624478 TGGGTATATAGGGTCTTTGTAGTGAAA 59.376 37.037 0.00 0.00 0.00 2.69
5212 5736 8.657712 GGGTATATAGGGTCTTTGTAGTGAAAT 58.342 37.037 0.00 0.00 0.00 2.17
5213 5737 9.708092 GGTATATAGGGTCTTTGTAGTGAAATC 57.292 37.037 0.00 0.00 0.00 2.17
5263 5787 6.049790 CCTGTACATAAGGCTTCTTACCTTC 58.950 44.000 1.30 0.00 44.35 3.46
5264 5788 5.657474 TGTACATAAGGCTTCTTACCTTCG 58.343 41.667 1.30 0.00 44.35 3.79
5282 5806 7.816945 ACCTTCGAATTAGCATTTGAAATTG 57.183 32.000 0.00 0.00 40.77 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 3.243737 ACGACACATGACTTCAAGCTACA 60.244 43.478 0.00 0.00 0.00 2.74
155 156 0.746659 ACAGGCAAGCCACAAGTTTC 59.253 50.000 14.40 0.00 38.92 2.78
170 171 6.096705 TGGACCTATGAATTTATTGCAACAGG 59.903 38.462 0.00 0.18 0.00 4.00
174 175 7.716799 ACTTGGACCTATGAATTTATTGCAA 57.283 32.000 0.00 0.00 0.00 4.08
211 212 6.438259 TCGTACTAGTTTTGATCTCTCTGG 57.562 41.667 0.00 0.00 0.00 3.86
232 233 2.080286 ACAAGAATCGTGTTCCCTCG 57.920 50.000 0.00 0.00 0.00 4.63
234 235 6.070995 TGAGTAATACAAGAATCGTGTTCCCT 60.071 38.462 7.19 0.00 0.00 4.20
243 245 8.851416 CCGACGAATATGAGTAATACAAGAATC 58.149 37.037 0.00 0.00 0.00 2.52
268 270 2.143925 GACCGGCATTATTACAGCTCC 58.856 52.381 0.00 0.00 0.00 4.70
271 273 4.036262 TGAAATGACCGGCATTATTACAGC 59.964 41.667 19.82 8.21 46.25 4.40
297 299 6.456988 CGGTCATTCAACCTATCAAAGTTAGC 60.457 42.308 0.00 0.00 37.15 3.09
300 302 5.313712 ACGGTCATTCAACCTATCAAAGTT 58.686 37.500 0.00 0.00 37.15 2.66
301 303 4.906618 ACGGTCATTCAACCTATCAAAGT 58.093 39.130 0.00 0.00 37.15 2.66
302 304 5.063944 CAGACGGTCATTCAACCTATCAAAG 59.936 44.000 11.27 0.00 37.15 2.77
305 307 3.678806 GCAGACGGTCATTCAACCTATCA 60.679 47.826 11.27 0.00 37.15 2.15
323 325 0.747255 GAGCCTAACCAGATCGCAGA 59.253 55.000 0.00 0.00 45.75 4.26
348 350 8.190326 TCTAACAATGTTCAGGACTTCTTCTA 57.810 34.615 0.22 0.00 0.00 2.10
371 373 9.265901 CAACGATTAAGGAATACAATCTCATCT 57.734 33.333 0.00 0.00 0.00 2.90
374 376 8.258007 ACTCAACGATTAAGGAATACAATCTCA 58.742 33.333 0.00 0.00 0.00 3.27
384 386 9.932207 TTCTTGTATTACTCAACGATTAAGGAA 57.068 29.630 0.00 0.00 0.00 3.36
394 396 9.474249 GCGAAAATAGTTCTTGTATTACTCAAC 57.526 33.333 0.00 0.00 0.00 3.18
495 497 6.422701 CCGTCAGACATAACAGTTTCAAACTA 59.577 38.462 1.43 0.00 40.46 2.24
496 498 5.236478 CCGTCAGACATAACAGTTTCAAACT 59.764 40.000 0.00 0.00 44.06 2.66
497 499 5.007332 ACCGTCAGACATAACAGTTTCAAAC 59.993 40.000 0.41 0.00 0.00 2.93
533 535 9.565213 TTTTCATTAAATGTTTGCTTGGTTTTG 57.435 25.926 0.00 0.00 0.00 2.44
534 536 9.786105 CTTTTCATTAAATGTTTGCTTGGTTTT 57.214 25.926 0.00 0.00 0.00 2.43
608 613 9.689976 CAGTCTCATGAAATTATATCGTCTTCT 57.310 33.333 0.00 0.00 0.00 2.85
625 630 4.845387 GCAGAATATTGTGCAGTCTCATG 58.155 43.478 27.51 0.00 45.72 3.07
731 741 0.519077 GTCGAAGAAAGCAAGCCTGG 59.481 55.000 0.00 0.00 39.69 4.45
813 836 2.835049 GGGGAGATAGGGCAAGGGC 61.835 68.421 0.00 0.00 40.13 5.19
818 841 2.448542 GGCAGGGGAGATAGGGCA 60.449 66.667 0.00 0.00 0.00 5.36
938 961 0.319728 CGAGATCGATTGGCCTGGAT 59.680 55.000 3.32 0.78 43.02 3.41
1393 1454 4.194720 GCGTCGGGCTCGAGATGT 62.195 66.667 18.75 0.00 46.91 3.06
1501 1589 1.891722 GCCTGGGCTTGGAAATGGTG 61.892 60.000 4.12 0.00 38.26 4.17
1598 1689 9.287373 CTCTTACTAGTTTCTACTATACAGGGG 57.713 40.741 0.00 0.00 36.32 4.79
1600 1691 9.339850 TGCTCTTACTAGTTTCTACTATACAGG 57.660 37.037 0.00 0.00 36.32 4.00
1605 1696 8.573035 GCAGATGCTCTTACTAGTTTCTACTAT 58.427 37.037 0.00 0.00 35.81 2.12
1606 1697 7.556635 TGCAGATGCTCTTACTAGTTTCTACTA 59.443 37.037 0.00 0.00 42.66 1.82
1621 1712 2.092538 ACTAATTGGCTGCAGATGCTCT 60.093 45.455 20.43 0.00 42.66 4.09
1673 1775 6.014840 CCTCCTCTTACTGGTAAGTTACACAA 60.015 42.308 14.81 2.41 42.29 3.33
1675 1777 5.105432 CCCTCCTCTTACTGGTAAGTTACAC 60.105 48.000 14.81 5.18 42.29 2.90
1678 1780 4.295775 TCCCCTCCTCTTACTGGTAAGTTA 59.704 45.833 16.82 6.33 42.29 2.24
1761 2030 5.066505 CGGAATGGAGCATAATAATTAGGGC 59.933 44.000 0.00 0.00 0.00 5.19
1872 2141 2.408704 CGACAAGACGAACCTGATCAAC 59.591 50.000 0.00 0.00 35.09 3.18
1899 2169 2.325583 TGATACCTGGAATCCGCAAC 57.674 50.000 0.00 0.00 0.00 4.17
1905 2175 8.410673 TCACTACTTAGATGATACCTGGAATC 57.589 38.462 0.00 0.00 0.00 2.52
1960 2231 1.900016 TTCTGCTGCAACCTGCCAG 60.900 57.895 3.02 0.00 44.23 4.85
2135 2406 3.059982 GCCTTTTGGGGGACTTGC 58.940 61.111 0.00 0.00 40.82 4.01
2276 2550 7.119699 TGTTTGACAGACTTATTGACATCATCC 59.880 37.037 0.00 0.00 0.00 3.51
2427 2701 5.503927 AGGAGACAGCATATTTTGTCACAT 58.496 37.500 15.25 6.98 44.72 3.21
2481 2758 4.696479 AGGCATACACTAAGCTAAGCAT 57.304 40.909 0.00 0.00 0.00 3.79
2891 3171 3.427233 GCAGAAATGACTTAGCAAGCCAG 60.427 47.826 0.00 0.00 0.00 4.85
3035 3320 7.067615 TGCATTAGTGAAAAGGAAGTTACAACA 59.932 33.333 0.00 0.00 0.00 3.33
3230 3515 4.272504 TCAAGACAATCTTCGTGTTGAACC 59.727 41.667 0.92 0.00 41.89 3.62
3288 3573 4.899239 GACCCAGCGATGCTCGGG 62.899 72.222 18.61 18.61 41.18 5.14
3336 3621 8.908903 TCCAAGTCACAATTGTAACTGTTTATT 58.091 29.630 15.23 0.00 0.00 1.40
3412 3697 9.832445 AGCGATAAAGGATAATGACTTAAAAGA 57.168 29.630 0.00 0.00 0.00 2.52
3472 3757 5.515797 TCATAAATACTCCCGACAGACAG 57.484 43.478 0.00 0.00 0.00 3.51
3473 3758 6.097696 TGAATCATAAATACTCCCGACAGACA 59.902 38.462 0.00 0.00 0.00 3.41
3474 3759 6.513180 TGAATCATAAATACTCCCGACAGAC 58.487 40.000 0.00 0.00 0.00 3.51
3475 3760 6.549736 TCTGAATCATAAATACTCCCGACAGA 59.450 38.462 0.00 0.00 0.00 3.41
3480 3765 6.525629 ACCTTCTGAATCATAAATACTCCCG 58.474 40.000 0.00 0.00 0.00 5.14
3522 3807 2.394632 AGTGGTTCATGCGGTATCCTA 58.605 47.619 0.00 0.00 0.00 2.94
3529 3814 0.888736 TGGTCAAGTGGTTCATGCGG 60.889 55.000 0.00 0.00 0.00 5.69
3569 3854 9.123902 TCAATCATAGGACAACAATGGATTTAG 57.876 33.333 0.00 0.00 0.00 1.85
3578 3863 4.650734 TGCAGTCAATCATAGGACAACAA 58.349 39.130 0.00 0.00 36.50 2.83
3579 3864 4.284829 TGCAGTCAATCATAGGACAACA 57.715 40.909 0.00 0.00 36.50 3.33
3624 3910 3.297134 ACAGGAAAGAAGTGCAAAGGA 57.703 42.857 0.00 0.00 0.00 3.36
3625 3911 4.520492 ACATACAGGAAAGAAGTGCAAAGG 59.480 41.667 0.00 0.00 0.00 3.11
3627 3913 5.472137 GGTACATACAGGAAAGAAGTGCAAA 59.528 40.000 0.00 0.00 0.00 3.68
3628 3914 5.001232 GGTACATACAGGAAAGAAGTGCAA 58.999 41.667 0.00 0.00 0.00 4.08
3636 3922 4.837093 TCCCAAGGTACATACAGGAAAG 57.163 45.455 0.00 0.00 0.00 2.62
3640 3926 3.279434 GCTTTCCCAAGGTACATACAGG 58.721 50.000 0.00 0.00 0.00 4.00
3760 4055 5.934625 GGCAATGATCCTAAGACGTATCATT 59.065 40.000 13.63 13.63 45.39 2.57
3828 4123 8.208718 TGGACTTTTCTTATATGCATGTGTAC 57.791 34.615 10.16 0.00 0.00 2.90
3903 4198 3.518590 CACCTTACAGTAAAGTAGGCCG 58.481 50.000 0.00 0.00 0.00 6.13
4403 4717 2.125147 TACACGCCCAGCATCAGC 60.125 61.111 0.00 0.00 42.56 4.26
4509 4823 3.663464 TCACGTCGTCTTCCGTAATAG 57.337 47.619 0.00 0.00 35.16 1.73
4510 4824 4.621068 AATCACGTCGTCTTCCGTAATA 57.379 40.909 0.00 0.00 35.16 0.98
4511 4825 3.498927 AATCACGTCGTCTTCCGTAAT 57.501 42.857 0.00 0.00 35.16 1.89
4523 4837 4.744570 TGTCAGATACCAGAAATCACGTC 58.255 43.478 0.00 0.00 0.00 4.34
4552 4866 5.534654 CCAAGGATCCGAATTAAAGCCAATA 59.465 40.000 5.98 0.00 0.00 1.90
4553 4867 4.342092 CCAAGGATCCGAATTAAAGCCAAT 59.658 41.667 5.98 0.00 0.00 3.16
4645 4960 3.492137 GGAGAAAATGCCATGGATCAAGC 60.492 47.826 18.40 0.00 0.00 4.01
4662 4977 0.251832 AGAGAACGGAGCCAGGAGAA 60.252 55.000 0.00 0.00 0.00 2.87
4693 5008 3.936203 AGCTTTCGTCCCGGTGCA 61.936 61.111 0.00 0.00 0.00 4.57
4871 5206 6.720112 AACACGGATATAAGTTAGTAGCCA 57.280 37.500 0.00 0.00 0.00 4.75
4872 5207 9.136952 CATAAACACGGATATAAGTTAGTAGCC 57.863 37.037 0.00 0.00 0.00 3.93
4889 5226 4.556233 TCACTTCACCTCTCATAAACACG 58.444 43.478 0.00 0.00 0.00 4.49
4925 5262 7.586779 TAAGAAGTCTTGCCTATAGTAGGACCA 60.587 40.741 7.20 0.00 41.57 4.02
4926 5263 6.776603 TAAGAAGTCTTGCCTATAGTAGGACC 59.223 42.308 7.20 0.00 41.57 4.46
4928 5265 8.449625 AGATAAGAAGTCTTGCCTATAGTAGGA 58.550 37.037 7.20 0.00 41.57 2.94
5031 5378 3.296854 ACAGGTAGCAGGACGATAATGA 58.703 45.455 0.00 0.00 0.00 2.57
5038 5385 1.132643 GTACAGACAGGTAGCAGGACG 59.867 57.143 0.00 0.00 0.00 4.79
5129 5478 9.549078 TTGTAAATTCCATTTAACTTGGGAAAC 57.451 29.630 0.00 0.00 42.26 2.78
5185 5709 6.685541 TCACTACAAAGACCCTATATACCCA 58.314 40.000 0.00 0.00 0.00 4.51
5210 5734 7.173907 CAGCGGTCTCCAATAAATAGATTGATT 59.826 37.037 0.00 0.00 38.83 2.57
5211 5735 6.652481 CAGCGGTCTCCAATAAATAGATTGAT 59.348 38.462 0.00 0.00 38.83 2.57
5212 5736 5.991606 CAGCGGTCTCCAATAAATAGATTGA 59.008 40.000 0.00 0.00 38.83 2.57
5213 5737 5.180117 CCAGCGGTCTCCAATAAATAGATTG 59.820 44.000 0.00 0.00 36.70 2.67
5232 5756 1.806623 GCCTTATGTACAGGACCAGCG 60.807 57.143 0.33 0.00 32.41 5.18


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

AutoCloner maintained by Alex Coulton.