Multiple sequence alignment - TraesCS1D01G162400

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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 TraesCS1D01G162400 chr1D 100.000 5261 0 0 1 5261 231468241 231462981 0.000000e+00 9716
1 TraesCS1D01G162400 chr1A 94.994 5134 123 39 193 5261 317810378 317815442 0.000000e+00 7934
2 TraesCS1D01G162400 chr1A 91.579 190 9 3 1 186 317810053 317810239 6.760000e-64 255
3 TraesCS1D01G162400 chr1B 95.209 4801 130 32 507 5261 365018801 365023547 0.000000e+00 7500
4 TraesCS1D01G162400 chr1B 90.649 385 7 12 144 516 366295551 366295184 7.920000e-133 484
5 TraesCS1D01G162400 chr5A 87.213 305 32 6 3175 3477 708807355 708807056 1.810000e-89 340
6 TraesCS1D01G162400 chr4B 87.129 303 31 7 3175 3473 671632078 671631780 2.350000e-88 337
7 TraesCS1D01G162400 chrUn 86.262 313 35 7 3175 3483 28396958 28397266 3.040000e-87 333
8 TraesCS1D01G162400 chr2A 88.172 279 33 0 3174 3452 637678932 637678654 3.040000e-87 333
9 TraesCS1D01G162400 chr2A 88.000 150 18 0 2072 2221 637680040 637679891 1.510000e-40 178
10 TraesCS1D01G162400 chr2D 87.455 279 35 0 3174 3452 492509715 492509437 6.570000e-84 322
11 TraesCS1D01G162400 chr2D 85.350 157 23 0 2072 2228 492510808 492510652 4.220000e-36 163
12 TraesCS1D01G162400 chr2B 87.455 279 35 0 3174 3452 578137511 578137233 6.570000e-84 322
13 TraesCS1D01G162400 chr2B 86.624 157 21 0 2072 2228 578138610 578138454 1.950000e-39 174
14 TraesCS1D01G162400 chr6D 86.667 285 33 4 3170 3452 313281969 313281688 1.420000e-80 311
15 TraesCS1D01G162400 chr6D 84.967 153 21 2 2071 2222 313282694 313282543 2.540000e-33 154
16 TraesCS1D01G162400 chr6B 83.333 156 24 2 2068 2222 512872807 512872961 5.490000e-30 143
17 TraesCS1D01G162400 chr6A 83.553 152 25 0 2071 2222 450465984 450465833 5.490000e-30 143


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 TraesCS1D01G162400 chr1D 231462981 231468241 5260 True 9716.0 9716 100.0000 1 5261 1 chr1D.!!$R1 5260
1 TraesCS1D01G162400 chr1A 317810053 317815442 5389 False 4094.5 7934 93.2865 1 5261 2 chr1A.!!$F1 5260
2 TraesCS1D01G162400 chr1B 365018801 365023547 4746 False 7500.0 7500 95.2090 507 5261 1 chr1B.!!$F1 4754
3 TraesCS1D01G162400 chr2A 637678654 637680040 1386 True 255.5 333 88.0860 2072 3452 2 chr2A.!!$R1 1380
4 TraesCS1D01G162400 chr2D 492509437 492510808 1371 True 242.5 322 86.4025 2072 3452 2 chr2D.!!$R1 1380
5 TraesCS1D01G162400 chr2B 578137233 578138610 1377 True 248.0 322 87.0395 2072 3452 2 chr2B.!!$R1 1380
6 TraesCS1D01G162400 chr6D 313281688 313282694 1006 True 232.5 311 85.8170 2071 3452 2 chr6D.!!$R1 1381

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
645 800 0.465460 CTCGTCCCCTCTCTCTCCTG 60.465 65.000 0.00 0.0 0.00 3.86 F
1732 1944 0.110104 GGGGCATCAATCCCAGAGAG 59.890 60.000 0.06 0.0 45.73 3.20 F
1736 1948 1.696336 GCATCAATCCCAGAGAGGCTA 59.304 52.381 0.00 0.0 36.28 3.93 F
3012 3399 2.596046 AACAATGCCGCCCGTGAA 60.596 55.556 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2395 2725 0.473755 TTGAGAAGCTCAGGTTGCCA 59.526 50.000 0.00 0.00 41.75 4.92 R
2810 3167 2.203209 GATGGACGGCATGGGGAC 60.203 66.667 0.00 0.00 0.00 4.46 R
3039 3426 2.266376 CTGTAGCTGTGGCGTCGCTA 62.266 60.000 18.11 8.52 44.37 4.26 R
4897 5400 0.606096 TGCAGCACGTACAGTACCAT 59.394 50.000 5.07 0.00 0.00 3.55 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
35 36 2.481276 GCGATTAATTGTTTCCCTGCCC 60.481 50.000 4.60 0.00 0.00 5.36
37 38 3.066760 CGATTAATTGTTTCCCTGCCCTC 59.933 47.826 0.00 0.00 0.00 4.30
55 56 4.688413 GCCCTCTAAATTAGCTTCATCGAG 59.312 45.833 0.00 0.00 0.00 4.04
68 69 4.095483 GCTTCATCGAGATGTTTTGATGGT 59.905 41.667 12.22 0.00 38.81 3.55
80 82 9.334947 AGATGTTTTGATGGTGATCAATACTAG 57.665 33.333 15.02 0.00 45.91 2.57
111 113 3.053395 TGGAAAAGGATGCCAGAAGCTAT 60.053 43.478 0.00 0.00 44.23 2.97
112 114 4.165950 TGGAAAAGGATGCCAGAAGCTATA 59.834 41.667 0.00 0.00 44.23 1.31
113 115 4.759183 GGAAAAGGATGCCAGAAGCTATAG 59.241 45.833 0.00 0.00 44.23 1.31
136 138 7.973048 AGTAGTACTTGGAGGAAATGATACA 57.027 36.000 0.00 0.00 0.00 2.29
138 140 8.478877 AGTAGTACTTGGAGGAAATGATACAAG 58.521 37.037 0.00 0.00 40.66 3.16
139 141 6.653989 AGTACTTGGAGGAAATGATACAAGG 58.346 40.000 0.00 0.00 39.53 3.61
140 142 5.520748 ACTTGGAGGAAATGATACAAGGT 57.479 39.130 0.00 0.00 39.53 3.50
141 143 5.892348 ACTTGGAGGAAATGATACAAGGTT 58.108 37.500 0.00 0.00 39.53 3.50
186 191 4.553330 ATCCGGTGGATAACATATGACC 57.447 45.455 10.38 4.31 41.16 4.02
187 192 3.583228 TCCGGTGGATAACATATGACCT 58.417 45.455 10.38 0.00 0.00 3.85
189 194 5.338632 TCCGGTGGATAACATATGACCTAT 58.661 41.667 10.38 3.30 0.00 2.57
190 195 5.783360 TCCGGTGGATAACATATGACCTATT 59.217 40.000 10.38 0.00 0.00 1.73
191 196 6.955267 TCCGGTGGATAACATATGACCTATTA 59.045 38.462 10.38 0.00 0.00 0.98
219 356 4.898014 ATTGTATGGGGAAGGGAAATGA 57.102 40.909 0.00 0.00 0.00 2.57
220 357 3.951563 TGTATGGGGAAGGGAAATGAG 57.048 47.619 0.00 0.00 0.00 2.90
228 365 4.381411 GGGAAGGGAAATGAGTAAGATCG 58.619 47.826 0.00 0.00 0.00 3.69
250 387 3.003689 GCCACAGAATCCAACATATTCCG 59.996 47.826 0.00 0.00 34.50 4.30
261 398 1.428912 ACATATTCCGCCATGGGGATT 59.571 47.619 29.29 21.41 44.01 3.01
344 481 2.843113 CCCAACCCATCTCTTTCTCTCT 59.157 50.000 0.00 0.00 0.00 3.10
345 482 3.118445 CCCAACCCATCTCTTTCTCTCTC 60.118 52.174 0.00 0.00 0.00 3.20
346 483 3.118445 CCAACCCATCTCTTTCTCTCTCC 60.118 52.174 0.00 0.00 0.00 3.71
347 484 3.774216 CAACCCATCTCTTTCTCTCTCCT 59.226 47.826 0.00 0.00 0.00 3.69
348 485 3.642141 ACCCATCTCTTTCTCTCTCCTC 58.358 50.000 0.00 0.00 0.00 3.71
349 486 3.272020 ACCCATCTCTTTCTCTCTCCTCT 59.728 47.826 0.00 0.00 0.00 3.69
350 487 4.480537 ACCCATCTCTTTCTCTCTCCTCTA 59.519 45.833 0.00 0.00 0.00 2.43
384 531 5.064452 CACATGTTTCTCTCTCTACCATTGC 59.936 44.000 0.00 0.00 0.00 3.56
414 561 1.309688 GCACTCCTCTCCCTCTCCT 59.690 63.158 0.00 0.00 0.00 3.69
438 585 4.320714 CCGTCCTTTGGGTTTTTAACTAGC 60.321 45.833 0.00 0.00 0.00 3.42
439 586 4.276431 CGTCCTTTGGGTTTTTAACTAGCA 59.724 41.667 0.00 0.00 0.00 3.49
440 587 5.562113 CGTCCTTTGGGTTTTTAACTAGCAG 60.562 44.000 0.00 0.00 0.00 4.24
441 588 4.830600 TCCTTTGGGTTTTTAACTAGCAGG 59.169 41.667 0.00 0.00 0.00 4.85
442 589 4.830600 CCTTTGGGTTTTTAACTAGCAGGA 59.169 41.667 0.00 0.00 0.00 3.86
443 590 5.048013 CCTTTGGGTTTTTAACTAGCAGGAG 60.048 44.000 0.00 0.00 0.00 3.69
444 591 3.418047 TGGGTTTTTAACTAGCAGGAGC 58.582 45.455 0.00 0.00 42.56 4.70
445 592 3.181438 TGGGTTTTTAACTAGCAGGAGCA 60.181 43.478 0.00 0.00 45.49 4.26
446 593 4.017126 GGGTTTTTAACTAGCAGGAGCAT 58.983 43.478 0.00 0.00 45.49 3.79
447 594 4.462834 GGGTTTTTAACTAGCAGGAGCATT 59.537 41.667 0.00 0.00 45.49 3.56
448 595 5.650703 GGGTTTTTAACTAGCAGGAGCATTA 59.349 40.000 0.00 0.00 45.49 1.90
449 596 6.183360 GGGTTTTTAACTAGCAGGAGCATTAG 60.183 42.308 0.00 0.00 45.49 1.73
450 597 6.183360 GGTTTTTAACTAGCAGGAGCATTAGG 60.183 42.308 0.00 0.00 45.49 2.69
543 690 1.807142 TCGTCTGCACACAACAAACAA 59.193 42.857 0.00 0.00 0.00 2.83
564 711 1.202879 CCCTCTCTCCTCTCGCTGTAT 60.203 57.143 0.00 0.00 0.00 2.29
645 800 0.465460 CTCGTCCCCTCTCTCTCCTG 60.465 65.000 0.00 0.00 0.00 3.86
658 813 1.139853 CTCTCCTGCAATCCACCCTAC 59.860 57.143 0.00 0.00 0.00 3.18
659 814 1.207791 CTCCTGCAATCCACCCTACT 58.792 55.000 0.00 0.00 0.00 2.57
660 815 1.139853 CTCCTGCAATCCACCCTACTC 59.860 57.143 0.00 0.00 0.00 2.59
834 1016 0.755686 CTGCCTACCACCTCATCTCC 59.244 60.000 0.00 0.00 0.00 3.71
869 1054 3.531821 CCCCCTCTCCTTCTCTCTC 57.468 63.158 0.00 0.00 0.00 3.20
1427 1618 1.218047 CGAATTGACCTCCGCCAGA 59.782 57.895 0.00 0.00 0.00 3.86
1511 1717 3.799755 GGCGGCGTGGTGTGATTC 61.800 66.667 9.37 0.00 0.00 2.52
1637 1843 0.261991 TATCGCTCTCCTTCCCCACT 59.738 55.000 0.00 0.00 0.00 4.00
1647 1853 1.272147 CCTTCCCCACTTTTCCCTGAG 60.272 57.143 0.00 0.00 0.00 3.35
1684 1892 3.280295 TCTCTTCGACATGAGAGGTACC 58.720 50.000 2.73 2.73 34.77 3.34
1685 1893 3.017442 CTCTTCGACATGAGAGGTACCA 58.983 50.000 15.94 0.00 32.44 3.25
1686 1894 3.017442 TCTTCGACATGAGAGGTACCAG 58.983 50.000 15.94 0.00 0.00 4.00
1732 1944 0.110104 GGGGCATCAATCCCAGAGAG 59.890 60.000 0.06 0.00 45.73 3.20
1736 1948 1.696336 GCATCAATCCCAGAGAGGCTA 59.304 52.381 0.00 0.00 36.28 3.93
1738 1950 3.517100 GCATCAATCCCAGAGAGGCTATA 59.483 47.826 0.00 0.00 36.28 1.31
1740 1952 5.684552 GCATCAATCCCAGAGAGGCTATATC 60.685 48.000 0.00 0.00 36.28 1.63
1744 1956 7.425834 TCAATCCCAGAGAGGCTATATCTTAT 58.574 38.462 0.00 0.00 35.39 1.73
1745 1957 8.569596 TCAATCCCAGAGAGGCTATATCTTATA 58.430 37.037 0.00 0.00 35.39 0.98
1950 2162 2.713863 TGTGTGAGGGTTACGGTTTT 57.286 45.000 0.00 0.00 0.00 2.43
1978 2190 4.493057 GCATGATGTGTGAGTTCGTATGTG 60.493 45.833 0.00 0.00 0.00 3.21
2890 3271 3.499737 CCTCACGCCACGCCAATC 61.500 66.667 0.00 0.00 0.00 2.67
3012 3399 2.596046 AACAATGCCGCCCGTGAA 60.596 55.556 0.00 0.00 0.00 3.18
3620 4121 1.522806 AAGAACGACGCCAGCAACA 60.523 52.632 0.00 0.00 0.00 3.33
3789 4290 0.112995 ATGTGCATTCTGGGTGTGGT 59.887 50.000 0.00 0.00 0.00 4.16
3883 4384 2.295909 ACTGCGCATTTAAAGCCAGAAA 59.704 40.909 12.24 0.00 35.58 2.52
3921 4422 4.172512 ATGGAGCAGAGGCAGCCG 62.173 66.667 5.55 0.00 44.61 5.52
4395 4896 2.974698 CGCATCTTCCATCCCCGC 60.975 66.667 0.00 0.00 0.00 6.13
4551 5052 3.553765 TGCATGCGCATCGTCGTC 61.554 61.111 22.51 6.44 45.36 4.20
4552 5053 4.617454 GCATGCGCATCGTCGTCG 62.617 66.667 22.51 8.71 38.36 5.12
4553 5054 3.247455 CATGCGCATCGTCGTCGT 61.247 61.111 22.51 0.00 38.33 4.34
4554 5055 2.949678 ATGCGCATCGTCGTCGTC 60.950 61.111 19.28 0.00 38.33 4.20
4719 5222 6.750039 GGTTATTTATTGATTTGTCGTGGTGG 59.250 38.462 0.00 0.00 0.00 4.61
4789 5292 4.531732 ACTACTACATCGGGGTGGTAAAAA 59.468 41.667 5.45 0.00 34.85 1.94
4844 5347 4.638963 CGCGGTTAAAATGAAGAGAAGAC 58.361 43.478 0.00 0.00 0.00 3.01
4888 5391 0.107897 TTGGTGCATACGGCTACTGG 60.108 55.000 0.00 0.00 45.15 4.00
4928 5431 2.267351 TGCTGCAATGGAACGGTGG 61.267 57.895 0.00 0.00 0.00 4.61
4980 5484 1.839994 CAGGCCATGAGGAAGAAGGTA 59.160 52.381 5.01 0.00 36.89 3.08
5000 5504 6.743774 AGGTACTGGAGCATATGCGGATTTA 61.744 44.000 21.57 9.26 42.35 1.40
5011 5515 8.351495 GCATATGCGGATTTATTTTCTTTTGA 57.649 30.769 12.82 0.00 0.00 2.69
5012 5516 8.981647 GCATATGCGGATTTATTTTCTTTTGAT 58.018 29.630 12.82 0.00 0.00 2.57
5100 5607 9.233649 TCTTCTTACCAACTGTTTTTACTGAAA 57.766 29.630 0.00 0.00 0.00 2.69
5200 5709 1.773052 ACTCCATCACTGCATGCCTAT 59.227 47.619 16.68 0.02 0.00 2.57
5208 5717 3.191162 TCACTGCATGCCTATTGTGTTTC 59.809 43.478 16.68 0.00 0.00 2.78
5220 5729 8.861086 TGCCTATTGTGTTTCCTGTATTTTAAA 58.139 29.630 0.00 0.00 0.00 1.52
5247 5756 3.969976 AGAGGCAGATGCAGGATAAAGTA 59.030 43.478 7.19 0.00 44.36 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 8.586570 AACATCTCGATGAAGCTAATTTAGAG 57.413 34.615 13.45 0.00 41.20 2.43
37 38 9.430838 CAAAACATCTCGATGAAGCTAATTTAG 57.569 33.333 13.45 0.00 41.20 1.85
68 69 5.046663 TCCAACACTGCACTAGTATTGATCA 60.047 40.000 0.00 0.00 44.70 2.92
80 82 2.863704 GCATCCTTTTCCAACACTGCAC 60.864 50.000 0.00 0.00 0.00 4.57
111 113 9.483489 TTGTATCATTTCCTCCAAGTACTACTA 57.517 33.333 0.00 0.00 0.00 1.82
112 114 7.973048 TGTATCATTTCCTCCAAGTACTACT 57.027 36.000 0.00 0.00 0.00 2.57
113 115 7.711339 CCTTGTATCATTTCCTCCAAGTACTAC 59.289 40.741 0.00 0.00 0.00 2.73
189 194 8.998957 TCCCTTCCCCATACAATATATCTTAA 57.001 34.615 0.00 0.00 0.00 1.85
190 195 8.998957 TTCCCTTCCCCATACAATATATCTTA 57.001 34.615 0.00 0.00 0.00 2.10
191 196 7.905144 TTCCCTTCCCCATACAATATATCTT 57.095 36.000 0.00 0.00 0.00 2.40
219 356 2.766263 TGGATTCTGTGGCGATCTTACT 59.234 45.455 0.00 0.00 0.00 2.24
220 357 3.179443 TGGATTCTGTGGCGATCTTAC 57.821 47.619 0.00 0.00 0.00 2.34
228 365 3.003689 CGGAATATGTTGGATTCTGTGGC 59.996 47.826 0.00 0.00 35.70 5.01
250 387 0.111253 CCTACCTCAATCCCCATGGC 59.889 60.000 6.09 0.00 0.00 4.40
261 398 4.094476 CTCTACAAAACTCCCCTACCTCA 58.906 47.826 0.00 0.00 0.00 3.86
327 464 3.272020 AGAGGAGAGAGAAAGAGATGGGT 59.728 47.826 0.00 0.00 0.00 4.51
337 474 2.692557 GCAGCATGTAGAGGAGAGAGAA 59.307 50.000 0.00 0.00 39.31 2.87
344 481 1.560505 TGTGAGCAGCATGTAGAGGA 58.439 50.000 0.00 0.00 39.31 3.71
345 482 2.210961 CATGTGAGCAGCATGTAGAGG 58.789 52.381 0.00 0.00 38.96 3.69
395 542 1.760480 GGAGAGGGAGAGGAGTGCC 60.760 68.421 0.00 0.00 0.00 5.01
396 543 0.755327 GAGGAGAGGGAGAGGAGTGC 60.755 65.000 0.00 0.00 0.00 4.40
397 544 0.106217 GGAGGAGAGGGAGAGGAGTG 60.106 65.000 0.00 0.00 0.00 3.51
414 561 3.900971 AGTTAAAAACCCAAAGGACGGA 58.099 40.909 0.00 0.00 36.73 4.69
438 585 0.108207 CCCTCTGCCTAATGCTCCTG 59.892 60.000 0.00 0.00 42.00 3.86
439 586 0.030705 TCCCTCTGCCTAATGCTCCT 60.031 55.000 0.00 0.00 42.00 3.69
440 587 0.396060 CTCCCTCTGCCTAATGCTCC 59.604 60.000 0.00 0.00 42.00 4.70
441 588 0.396060 CCTCCCTCTGCCTAATGCTC 59.604 60.000 0.00 0.00 42.00 4.26
442 589 0.327000 ACCTCCCTCTGCCTAATGCT 60.327 55.000 0.00 0.00 42.00 3.79
443 590 1.424638 TACCTCCCTCTGCCTAATGC 58.575 55.000 0.00 0.00 41.77 3.56
444 591 3.745797 GCTTTACCTCCCTCTGCCTAATG 60.746 52.174 0.00 0.00 0.00 1.90
445 592 2.439880 GCTTTACCTCCCTCTGCCTAAT 59.560 50.000 0.00 0.00 0.00 1.73
446 593 1.838077 GCTTTACCTCCCTCTGCCTAA 59.162 52.381 0.00 0.00 0.00 2.69
447 594 1.497161 GCTTTACCTCCCTCTGCCTA 58.503 55.000 0.00 0.00 0.00 3.93
448 595 1.275421 GGCTTTACCTCCCTCTGCCT 61.275 60.000 0.00 0.00 36.32 4.75
449 596 1.224870 GGCTTTACCTCCCTCTGCC 59.775 63.158 0.00 0.00 34.51 4.85
450 597 0.393132 GTGGCTTTACCTCCCTCTGC 60.393 60.000 0.00 0.00 40.22 4.26
458 605 0.693049 CTGTCAGGGTGGCTTTACCT 59.307 55.000 0.00 0.00 40.66 3.08
543 690 1.077068 CAGCGAGAGGAGAGAGGGT 60.077 63.158 0.00 0.00 0.00 4.34
564 711 6.260936 GGTTGAGAGAGAAGTGAAATGTTGAA 59.739 38.462 0.00 0.00 0.00 2.69
645 800 7.522236 GCAATAAATAAGAGTAGGGTGGATTGC 60.522 40.741 0.00 0.00 37.99 3.56
658 813 7.792374 TCAGTAAGCCTGCAATAAATAAGAG 57.208 36.000 0.00 0.00 41.25 2.85
659 814 7.283127 CCTTCAGTAAGCCTGCAATAAATAAGA 59.717 37.037 0.00 0.00 41.25 2.10
660 815 7.067494 ACCTTCAGTAAGCCTGCAATAAATAAG 59.933 37.037 0.00 0.00 41.25 1.73
834 1016 1.616865 GGGGGAAAAGGGAAAGAAACG 59.383 52.381 0.00 0.00 0.00 3.60
855 1037 3.287867 AGAGCAGAGAGAGAAGGAGAG 57.712 52.381 0.00 0.00 0.00 3.20
856 1038 3.737559 AAGAGCAGAGAGAGAAGGAGA 57.262 47.619 0.00 0.00 0.00 3.71
857 1039 4.019174 AGAAAGAGCAGAGAGAGAAGGAG 58.981 47.826 0.00 0.00 0.00 3.69
858 1040 3.763360 CAGAAAGAGCAGAGAGAGAAGGA 59.237 47.826 0.00 0.00 0.00 3.36
859 1041 3.119029 CCAGAAAGAGCAGAGAGAGAAGG 60.119 52.174 0.00 0.00 0.00 3.46
861 1043 2.233431 GCCAGAAAGAGCAGAGAGAGAA 59.767 50.000 0.00 0.00 0.00 2.87
869 1054 0.324285 AGGACAGCCAGAAAGAGCAG 59.676 55.000 0.00 0.00 36.29 4.24
1427 1618 4.383602 GACGGCGTGCGCAATTGT 62.384 61.111 21.19 8.83 44.11 2.71
1732 1944 5.212745 AGGGCCAGAGTATAAGATATAGCC 58.787 45.833 6.18 0.00 35.92 3.93
1736 1948 6.159172 TCAGAGGGCCAGAGTATAAGATAT 57.841 41.667 6.18 0.00 0.00 1.63
1738 1950 4.477536 TCAGAGGGCCAGAGTATAAGAT 57.522 45.455 6.18 0.00 0.00 2.40
1740 1952 5.559148 AATTCAGAGGGCCAGAGTATAAG 57.441 43.478 6.18 0.00 0.00 1.73
1744 1956 3.198635 CAGAAATTCAGAGGGCCAGAGTA 59.801 47.826 6.18 0.00 0.00 2.59
1745 1957 2.026449 CAGAAATTCAGAGGGCCAGAGT 60.026 50.000 6.18 0.00 0.00 3.24
1950 2162 3.679502 CGAACTCACACATCATGCAAGTA 59.320 43.478 0.00 0.00 0.00 2.24
1978 2190 1.001815 ACGCTACAACCACAATTGCAC 60.002 47.619 5.05 0.00 32.47 4.57
2395 2725 0.473755 TTGAGAAGCTCAGGTTGCCA 59.526 50.000 0.00 0.00 41.75 4.92
2810 3167 2.203209 GATGGACGGCATGGGGAC 60.203 66.667 0.00 0.00 0.00 4.46
3039 3426 2.266376 CTGTAGCTGTGGCGTCGCTA 62.266 60.000 18.11 8.52 44.37 4.26
3127 3514 2.665000 TCGTACCCCGACGAGTCT 59.335 61.111 0.00 0.00 46.43 3.24
3883 4384 2.688446 TCGTCGTCTCCTTCATAATGCT 59.312 45.455 0.00 0.00 0.00 3.79
3952 4453 1.000506 ACGGTTGTAGCTGTTGATCGT 59.999 47.619 0.00 0.00 0.00 3.73
4395 4896 1.482593 GGAGGTGCCGAGATATATGGG 59.517 57.143 0.00 0.00 0.00 4.00
4544 5045 2.168621 GACGAACGACGACGACGA 59.831 61.111 25.15 0.00 45.77 4.20
4789 5292 6.126594 TGGATCGATCTTATTACCTGGGTTTT 60.127 38.462 23.96 0.00 0.00 2.43
4790 5293 5.368523 TGGATCGATCTTATTACCTGGGTTT 59.631 40.000 23.96 0.00 0.00 3.27
4796 5299 4.156922 CGAGCTGGATCGATCTTATTACCT 59.843 45.833 23.96 11.05 45.56 3.08
4844 5347 1.595794 ACGAAAGTAACAAGCACACGG 59.404 47.619 0.00 0.00 46.88 4.94
4897 5400 0.606096 TGCAGCACGTACAGTACCAT 59.394 50.000 5.07 0.00 0.00 3.55
4928 5431 5.043189 ACCGTCGATCCTTTTTCATTTTC 57.957 39.130 0.00 0.00 0.00 2.29
4980 5484 2.645838 AAATCCGCATATGCTCCAGT 57.354 45.000 24.56 5.42 39.32 4.00
5200 5709 7.354751 AGCCTTTAAAATACAGGAAACACAA 57.645 32.000 0.00 0.00 0.00 3.33
5208 5717 5.437060 TGCCTCTAGCCTTTAAAATACAGG 58.563 41.667 0.00 0.00 42.71 4.00
5220 5729 1.409251 CCTGCATCTGCCTCTAGCCT 61.409 60.000 0.00 0.00 42.71 4.58


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

AutoCloner maintained by Alex Coulton.