Multiple sequence alignment - TraesCS1B01G134600

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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 TraesCS1B01G134600 chr1B 100.000 4904 0 0 1 4904 171128454 171133357 0.000000e+00 9057
1 TraesCS1B01G134600 chr1B 83.936 249 23 13 4188 4431 684198165 684198401 6.390000e-54 222
2 TraesCS1B01G134600 chr1B 76.991 226 42 8 4430 4649 592854414 592854635 2.400000e-23 121
3 TraesCS1B01G134600 chr1D 94.866 4928 196 25 1 4877 111834500 111839421 0.000000e+00 7646
4 TraesCS1B01G134600 chr1D 92.000 775 42 7 4135 4901 111850980 111851742 0.000000e+00 1070
5 TraesCS1B01G134600 chr1A 93.930 4942 257 15 1 4904 118846547 118851483 0.000000e+00 7424
6 TraesCS1B01G134600 chr1A 80.365 219 35 6 4432 4646 92617149 92617363 5.080000e-35 159
7 TraesCS1B01G134600 chr7D 88.750 240 17 5 4192 4431 204871003 204870774 8.030000e-73 285
8 TraesCS1B01G134600 chr7D 86.831 243 20 7 4189 4431 436499200 436498970 1.350000e-65 261
9 TraesCS1B01G134600 chr4D 87.225 227 20 3 4429 4646 7471768 7471994 2.930000e-62 250
10 TraesCS1B01G134600 chr4D 84.426 244 28 7 4189 4431 502418018 502417784 1.060000e-56 231
11 TraesCS1B01G134600 chr6A 85.841 226 20 7 4188 4411 491921631 491921846 3.820000e-56 230
12 TraesCS1B01G134600 chr3A 82.996 247 28 8 4183 4425 745059713 745059949 1.380000e-50 211
13 TraesCS1B01G134600 chr2D 80.932 236 31 9 4424 4649 80777846 80778077 1.810000e-39 174
14 TraesCS1B01G134600 chr2D 80.952 231 34 5 4429 4649 80816978 80817208 1.810000e-39 174
15 TraesCS1B01G134600 chr3D 80.995 221 35 5 4432 4647 85010830 85011048 8.440000e-38 169


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 TraesCS1B01G134600 chr1B 171128454 171133357 4903 False 9057 9057 100.000 1 4904 1 chr1B.!!$F1 4903
1 TraesCS1B01G134600 chr1D 111834500 111839421 4921 False 7646 7646 94.866 1 4877 1 chr1D.!!$F1 4876
2 TraesCS1B01G134600 chr1D 111850980 111851742 762 False 1070 1070 92.000 4135 4901 1 chr1D.!!$F2 766
3 TraesCS1B01G134600 chr1A 118846547 118851483 4936 False 7424 7424 93.930 1 4904 1 chr1A.!!$F2 4903

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
863 900 0.250338 AGGCGTTTGACAACTCCTCC 60.250 55.0 0.0 0.0 43.53 4.30 F
1664 1708 0.179134 AATCTGCGTACTCTGTCGGC 60.179 55.0 0.0 0.0 0.00 5.54 F
2061 2105 0.261991 TAGAAGGAGGCATCGAGGGT 59.738 55.0 0.0 0.0 0.00 4.34 F
2584 2628 0.603569 GTTCAGGCTTCTCACCGAGA 59.396 55.0 0.0 0.0 36.86 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 1804 0.036164 CCCAATATCCGCCGGAATCA 59.964 55.0 11.19 0.00 34.34 2.57 R
2935 2979 0.035725 TTCAGATGGGTGAGCTGCAG 60.036 55.0 10.11 10.11 38.04 4.41 R
3771 3815 1.263356 CGACCTTCCAGTACTTCCCA 58.737 55.0 0.00 0.00 0.00 4.37 R
3979 4025 1.429148 GCTTAATGGTGGCGACCGAG 61.429 60.0 13.67 9.29 46.62 4.63 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
22 23 1.216678 TGGGGATGGACACAACTGTTT 59.783 47.619 0.00 0.00 0.00 2.83
145 149 9.990868 ACTTTCCCACTACCTTATAATTGAAAT 57.009 29.630 0.00 0.00 0.00 2.17
223 230 5.971792 GCATGTCAGAGATTGTTTCATCATG 59.028 40.000 0.00 0.00 34.19 3.07
283 291 2.555325 AGAAGTATGTCGTCGTGGTTCA 59.445 45.455 0.00 0.00 0.00 3.18
285 293 2.876091 AGTATGTCGTCGTGGTTCATG 58.124 47.619 0.00 0.00 0.00 3.07
321 329 1.510480 GCCACACACTGAACCTGCTC 61.510 60.000 0.00 0.00 0.00 4.26
350 358 3.080300 TGTTTTCGGTTAGATGGCCAT 57.920 42.857 20.96 20.96 0.00 4.40
358 366 3.617531 CGGTTAGATGGCCATCAGTATCC 60.618 52.174 40.05 29.53 40.22 2.59
384 392 3.659183 AGTTGATAGCCTGCCAAGAAT 57.341 42.857 0.00 0.00 0.00 2.40
392 400 2.498885 AGCCTGCCAAGAATGAATTTCC 59.501 45.455 0.00 0.00 34.67 3.13
395 403 3.056607 CCTGCCAAGAATGAATTTCCGTT 60.057 43.478 0.00 0.00 34.67 4.44
396 404 3.911868 TGCCAAGAATGAATTTCCGTTG 58.088 40.909 0.00 0.00 34.67 4.10
397 405 3.571828 TGCCAAGAATGAATTTCCGTTGA 59.428 39.130 0.00 0.00 34.67 3.18
400 408 5.639082 GCCAAGAATGAATTTCCGTTGAATT 59.361 36.000 0.00 0.00 34.67 2.17
401 409 6.401367 GCCAAGAATGAATTTCCGTTGAATTG 60.401 38.462 0.00 0.00 34.67 2.32
402 410 6.646240 CCAAGAATGAATTTCCGTTGAATTGT 59.354 34.615 0.00 0.00 34.67 2.71
404 412 6.980593 AGAATGAATTTCCGTTGAATTGTCA 58.019 32.000 0.00 0.00 34.67 3.58
405 413 7.086376 AGAATGAATTTCCGTTGAATTGTCAG 58.914 34.615 0.00 0.00 33.05 3.51
406 414 6.573664 ATGAATTTCCGTTGAATTGTCAGA 57.426 33.333 0.00 0.00 34.49 3.27
407 415 6.384258 TGAATTTCCGTTGAATTGTCAGAA 57.616 33.333 0.00 0.00 34.49 3.02
408 416 6.800543 TGAATTTCCGTTGAATTGTCAGAAA 58.199 32.000 0.00 0.00 34.49 2.52
409 417 7.261325 TGAATTTCCGTTGAATTGTCAGAAAA 58.739 30.769 0.00 0.00 32.40 2.29
448 476 7.389884 CCTATAGGAGACAATGTAAGTACGCTA 59.610 40.741 14.11 0.00 37.39 4.26
450 478 6.466885 AGGAGACAATGTAAGTACGCTATT 57.533 37.500 0.00 0.00 0.00 1.73
452 480 8.004087 AGGAGACAATGTAAGTACGCTATTTA 57.996 34.615 0.00 0.00 0.00 1.40
453 481 8.136165 AGGAGACAATGTAAGTACGCTATTTAG 58.864 37.037 0.00 0.00 0.00 1.85
454 482 7.919621 GGAGACAATGTAAGTACGCTATTTAGT 59.080 37.037 0.00 0.00 0.00 2.24
467 496 7.492352 ACGCTATTTAGTTTTTCTTGTCACT 57.508 32.000 0.00 0.00 0.00 3.41
496 525 7.065563 AGCTGAGCAAGAACACTATTTAATCAG 59.934 37.037 7.39 0.00 33.99 2.90
497 526 7.615582 TGAGCAAGAACACTATTTAATCAGG 57.384 36.000 0.00 0.00 0.00 3.86
508 537 4.660789 ATTTAATCAGGCATGGAAGCAC 57.339 40.909 0.00 0.00 35.83 4.40
603 632 3.623510 GCACCAGTTTACTAATCTCCAGC 59.376 47.826 0.00 0.00 0.00 4.85
615 644 0.677731 TCTCCAGCGCCCTTTTCATG 60.678 55.000 2.29 0.00 0.00 3.07
649 678 2.847327 TCACCCAGAAGAAGCTGAAG 57.153 50.000 0.00 0.00 38.14 3.02
759 796 5.640189 ATATCTGTAACCGGGATTCTACG 57.360 43.478 6.32 0.00 0.00 3.51
858 895 1.878953 CAGGTAGGCGTTTGACAACT 58.121 50.000 0.00 0.00 0.00 3.16
862 899 2.067013 GTAGGCGTTTGACAACTCCTC 58.933 52.381 0.00 0.00 43.53 3.71
863 900 0.250338 AGGCGTTTGACAACTCCTCC 60.250 55.000 0.00 0.00 43.53 4.30
864 901 0.250338 GGCGTTTGACAACTCCTCCT 60.250 55.000 0.00 0.00 35.21 3.69
865 902 1.594331 GCGTTTGACAACTCCTCCTT 58.406 50.000 0.00 0.00 0.00 3.36
938 982 6.177610 GTTTATACACATCTTCCCAACTCCA 58.822 40.000 0.00 0.00 0.00 3.86
1002 1046 7.700505 AGTTTACACAGTTGCATCATATCATG 58.299 34.615 0.00 0.00 0.00 3.07
1004 1048 3.317149 ACACAGTTGCATCATATCATGGC 59.683 43.478 0.00 0.00 0.00 4.40
1045 1089 2.649516 CGCTTCTTCTATCTCTGCTCG 58.350 52.381 0.00 0.00 0.00 5.03
1374 1418 0.320247 AGAACCTGAAGACGCTGCTG 60.320 55.000 0.00 0.00 0.00 4.41
1552 1596 1.032114 GCTAAGTGGCGCCATTCCTT 61.032 55.000 35.23 30.60 0.00 3.36
1590 1634 0.397941 AGAACTTGCAGCAGCTGGTA 59.602 50.000 24.13 0.12 42.74 3.25
1662 1706 1.321743 GCAAATCTGCGTACTCTGTCG 59.678 52.381 0.00 0.00 39.20 4.35
1664 1708 0.179134 AATCTGCGTACTCTGTCGGC 60.179 55.000 0.00 0.00 0.00 5.54
1713 1757 1.372087 CCTCGTTCATTGGCAGCCTC 61.372 60.000 14.15 0.00 0.00 4.70
1812 1856 1.000955 CTGACGTACCTCAACCTGCTT 59.999 52.381 0.00 0.00 0.00 3.91
1831 1875 1.227943 GGCAACAGACTGACAGGCA 60.228 57.895 11.83 0.00 0.00 4.75
1902 1946 3.136443 TGTCCAAGAACAACATCTCTGGT 59.864 43.478 0.00 0.00 33.28 4.00
2061 2105 0.261991 TAGAAGGAGGCATCGAGGGT 59.738 55.000 0.00 0.00 0.00 4.34
2166 2210 1.955778 TCGAACCTTGTCGACCTTGTA 59.044 47.619 14.12 0.00 44.76 2.41
2175 2219 2.224185 TGTCGACCTTGTACTGCACAAT 60.224 45.455 14.12 0.00 45.96 2.71
2208 2252 1.237285 GCGTTGTGCCACCTCAGATT 61.237 55.000 0.00 0.00 37.76 2.40
2209 2253 1.943968 GCGTTGTGCCACCTCAGATTA 60.944 52.381 0.00 0.00 37.76 1.75
2233 2277 1.701847 ACTTGAGCAACCTGGAGATGT 59.298 47.619 0.00 0.00 0.00 3.06
2250 2294 2.335316 TGTTGTCCCTGTACCACAAC 57.665 50.000 15.24 15.24 46.73 3.32
2394 2438 0.693049 AGGTGGACTTCTTCGGCAAT 59.307 50.000 0.00 0.00 0.00 3.56
2584 2628 0.603569 GTTCAGGCTTCTCACCGAGA 59.396 55.000 0.00 0.00 36.86 4.04
2586 2630 0.820226 TCAGGCTTCTCACCGAGATG 59.180 55.000 0.00 0.00 38.56 2.90
2745 2789 3.231889 CTCCGTGCTGGTGCTGACT 62.232 63.158 0.00 0.00 40.48 3.41
2970 3014 1.461127 CTGAACCTTGAGCGTAACAGC 59.539 52.381 0.00 0.00 37.41 4.40
2979 3023 1.741770 GCGTAACAGCCTGACAGGG 60.742 63.158 23.09 9.79 35.37 4.45
3051 3095 1.003851 CGTCGAATGCATTAACCGGT 58.996 50.000 12.97 0.00 0.00 5.28
3057 3101 3.546020 CGAATGCATTAACCGGTGTCATC 60.546 47.826 12.97 0.00 0.00 2.92
3060 3104 1.680555 GCATTAACCGGTGTCATCCCA 60.681 52.381 8.52 0.00 0.00 4.37
3469 3513 2.710724 GAACCGCCTCAACCTGTCGT 62.711 60.000 0.00 0.00 0.00 4.34
3486 3530 1.211212 TCGTACAATCTCCTCTCCGGA 59.789 52.381 2.93 2.93 40.30 5.14
3818 3862 2.890474 GGTTGTCGCGCCATCGAT 60.890 61.111 0.00 0.00 40.84 3.59
3876 3920 1.198094 TCCATGGGAAGCTCACGGAA 61.198 55.000 13.02 0.00 0.00 4.30
3979 4025 5.915196 GTGGCTGTTTCTTGTATCAAAGTTC 59.085 40.000 0.00 0.00 0.00 3.01
3992 4038 2.035237 AAAGTTCTCGGTCGCCACCA 62.035 55.000 0.16 0.00 44.02 4.17
4100 4147 9.561270 GCTTTTTCAATTATCAGAGGACTTTAC 57.439 33.333 0.00 0.00 0.00 2.01
4115 4162 8.586744 AGAGGACTTTACTGTAAACTAGGAAAG 58.413 37.037 8.84 7.89 46.72 2.62
4121 4168 5.827326 ACTGTAAACTAGGAAAGCCTTCT 57.173 39.130 0.00 0.00 43.90 2.85
4169 4216 2.371841 ACATGCACCCTGAAGACTACAA 59.628 45.455 0.00 0.00 0.00 2.41
4510 4557 7.549134 TCTGCAACAACGAAATGTTCTATAGAT 59.451 33.333 2.58 0.00 41.44 1.98
4538 4585 3.067461 GGATGCACACAACCTTACAACAA 59.933 43.478 0.00 0.00 35.88 2.83
4603 4657 0.173255 GCTGCAACACAAACCACTGT 59.827 50.000 0.00 0.00 0.00 3.55
4632 4686 3.840666 AGCACCTAGAGTCCAAATTCTCA 59.159 43.478 0.00 0.00 33.63 3.27
4703 4757 7.715657 ACTGATTAAATGTGATGTTTGTGTGT 58.284 30.769 0.00 0.00 0.00 3.72
4758 4812 4.148128 AGGTCTCATTATCAGGTTGCAG 57.852 45.455 0.00 0.00 0.00 4.41
4823 4880 5.475719 TGTAGATGGTTTGGTAGAGTTTCG 58.524 41.667 0.00 0.00 0.00 3.46
4877 4934 7.703621 AGCAATTTTGTCATATGCACAAGATAC 59.296 33.333 16.80 13.87 39.42 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
259 267 3.341823 ACCACGACGACATACTTCTAGT 58.658 45.455 0.00 0.00 0.00 2.57
283 291 0.175760 CTGTGCCTACTGCGTACCAT 59.824 55.000 0.00 0.00 45.60 3.55
285 293 1.810030 GCTGTGCCTACTGCGTACC 60.810 63.158 0.00 0.00 45.60 3.34
321 329 6.586082 CCATCTAACCGAAAACAAAGGAATTG 59.414 38.462 0.00 0.00 44.95 2.32
350 358 5.248477 GGCTATCAACTATTGGGGATACTGA 59.752 44.000 0.00 0.00 0.00 3.41
358 366 2.158623 TGGCAGGCTATCAACTATTGGG 60.159 50.000 0.00 0.00 0.00 4.12
384 392 6.384258 TTCTGACAATTCAACGGAAATTCA 57.616 33.333 0.00 0.00 36.43 2.57
419 446 8.627403 CGTACTTACATTGTCTCCTATAGGAAA 58.373 37.037 21.93 14.00 44.91 3.13
430 457 9.649167 AAACTAAATAGCGTACTTACATTGTCT 57.351 29.630 0.00 0.00 0.00 3.41
448 476 9.736023 CAGCTTTAGTGACAAGAAAAACTAAAT 57.264 29.630 7.17 0.00 41.67 1.40
450 478 8.500753 TCAGCTTTAGTGACAAGAAAAACTAA 57.499 30.769 0.00 0.00 34.24 2.24
452 480 6.458888 GCTCAGCTTTAGTGACAAGAAAAACT 60.459 38.462 0.00 0.00 0.00 2.66
453 481 5.683302 GCTCAGCTTTAGTGACAAGAAAAAC 59.317 40.000 0.00 0.00 0.00 2.43
454 482 5.356751 TGCTCAGCTTTAGTGACAAGAAAAA 59.643 36.000 0.00 0.00 0.00 1.94
459 487 4.060900 TCTTGCTCAGCTTTAGTGACAAG 58.939 43.478 0.00 0.00 36.01 3.16
462 491 3.809832 TGTTCTTGCTCAGCTTTAGTGAC 59.190 43.478 0.00 0.00 0.00 3.67
467 496 8.615878 TTAAATAGTGTTCTTGCTCAGCTTTA 57.384 30.769 0.00 0.00 0.00 1.85
471 500 7.076842 TGATTAAATAGTGTTCTTGCTCAGC 57.923 36.000 0.00 0.00 0.00 4.26
508 537 1.137086 AGCATAAGGACAGCTACGTGG 59.863 52.381 0.00 0.00 36.73 4.94
516 545 5.297776 CCTTGATTTGGTAGCATAAGGACAG 59.702 44.000 16.45 1.47 36.23 3.51
603 632 1.298157 TGACGAGCATGAAAAGGGCG 61.298 55.000 0.00 0.00 0.00 6.13
615 644 2.885266 TGGGTGATATCTAGTGACGAGC 59.115 50.000 3.98 0.00 0.00 5.03
649 678 4.993905 ACCTTGTTGCTTTGACTTGTTAC 58.006 39.130 0.00 0.00 0.00 2.50
688 717 8.187913 TCTGAATAATGCAGAGCTAGTTATCT 57.812 34.615 0.00 0.00 37.46 1.98
759 796 2.937433 GCCAAAGGAGAAGGTAGAGCAC 60.937 54.545 0.00 0.00 0.00 4.40
858 895 3.313791 CAAAAAGGGGGAAAAAGGAGGA 58.686 45.455 0.00 0.00 0.00 3.71
862 899 2.849942 CTGCAAAAAGGGGGAAAAAGG 58.150 47.619 0.00 0.00 0.00 3.11
863 900 2.158769 AGCTGCAAAAAGGGGGAAAAAG 60.159 45.455 1.02 0.00 0.00 2.27
864 901 1.843206 AGCTGCAAAAAGGGGGAAAAA 59.157 42.857 1.02 0.00 0.00 1.94
865 902 1.506025 AGCTGCAAAAAGGGGGAAAA 58.494 45.000 1.02 0.00 0.00 2.29
938 982 3.235200 CTTACAGGATAGCTGCTACCCT 58.765 50.000 17.22 17.22 27.83 4.34
1004 1048 1.952102 AAGCGGAATGGCCATTGCTG 61.952 55.000 37.23 31.10 37.05 4.41
1177 1221 0.039256 CATGAAACACCGTGCCAAGG 60.039 55.000 0.00 0.00 0.00 3.61
1179 1223 1.361993 GCATGAAACACCGTGCCAA 59.638 52.632 0.00 0.00 41.81 4.52
1374 1418 0.741915 CGAGGGAGTTGGAGTAGAGC 59.258 60.000 0.00 0.00 0.00 4.09
1425 1469 3.007614 TCCTGAGAACTTTTAGGTTCCCG 59.992 47.826 1.62 0.00 44.56 5.14
1459 1503 1.878522 GTATCTCACCGTGCAGCCG 60.879 63.158 0.00 0.00 0.00 5.52
1536 1580 0.679960 GGTAAGGAATGGCGCCACTT 60.680 55.000 35.50 30.60 0.00 3.16
1542 1586 1.949525 CCAATCTGGTAAGGAATGGCG 59.050 52.381 0.00 0.00 31.35 5.69
1552 1596 2.642311 TCTTCAGGTTGCCAATCTGGTA 59.358 45.455 17.29 5.69 40.46 3.25
1590 1634 3.214328 GGTGAGAGTGTTGTTGTCCAAT 58.786 45.455 0.00 0.00 35.02 3.16
1655 1699 2.783828 ATTATCAGACGCCGACAGAG 57.216 50.000 0.00 0.00 0.00 3.35
1662 1706 1.338200 CCCAGCCTATTATCAGACGCC 60.338 57.143 0.00 0.00 0.00 5.68
1664 1708 2.289072 CCACCCAGCCTATTATCAGACG 60.289 54.545 0.00 0.00 0.00 4.18
1713 1757 3.553922 GGTTGAGAGACTGGAGAACACTG 60.554 52.174 0.00 0.00 0.00 3.66
1760 1804 0.036164 CCCAATATCCGCCGGAATCA 59.964 55.000 11.19 0.00 34.34 2.57
1797 1841 0.250727 TGCCAAGCAGGTTGAGGTAC 60.251 55.000 14.16 0.00 38.60 3.34
1812 1856 1.227943 GCCTGTCAGTCTGTTGCCA 60.228 57.895 0.00 0.00 0.00 4.92
1831 1875 0.909610 TTCAGCTCTTCCGGGATGGT 60.910 55.000 0.00 0.00 39.52 3.55
1902 1946 2.502538 TGATGTGGAGATGCTGATCACA 59.497 45.455 0.00 0.00 41.64 3.58
2166 2210 3.081804 GGTAAGGCTGTTATTGTGCAGT 58.918 45.455 0.00 0.00 35.33 4.40
2194 2238 4.473477 AGTTACTAATCTGAGGTGGCAC 57.527 45.455 9.70 9.70 0.00 5.01
2203 2247 5.352569 CCAGGTTGCTCAAGTTACTAATCTG 59.647 44.000 0.00 0.00 0.00 2.90
2208 2252 4.157246 TCTCCAGGTTGCTCAAGTTACTA 58.843 43.478 0.00 0.00 0.00 1.82
2209 2253 2.972713 TCTCCAGGTTGCTCAAGTTACT 59.027 45.455 0.00 0.00 0.00 2.24
2233 2277 0.107081 CCGTTGTGGTACAGGGACAA 59.893 55.000 0.00 0.00 41.80 3.18
2417 2461 1.476891 TCTTGAGGTTCCCGATCTTCG 59.523 52.381 0.00 0.00 40.07 3.79
2584 2628 2.773661 TGTACAGGGTGATGATGCTCAT 59.226 45.455 0.00 0.00 40.34 2.90
2586 2630 2.988010 TGTACAGGGTGATGATGCTC 57.012 50.000 0.00 0.00 0.00 4.26
2637 2681 1.964223 AGGTTCTTGAGCTCGAACAGA 59.036 47.619 25.97 15.37 40.88 3.41
2745 2789 1.208535 ACACCGGAGAAGTTGTTGTCA 59.791 47.619 9.46 0.00 0.00 3.58
2935 2979 0.035725 TTCAGATGGGTGAGCTGCAG 60.036 55.000 10.11 10.11 38.04 4.41
3051 3095 1.607801 CGAGCTCCACTGGGATGACA 61.608 60.000 8.47 0.00 43.91 3.58
3057 3101 4.020617 TTGCCGAGCTCCACTGGG 62.021 66.667 8.47 4.02 46.68 4.45
3060 3104 2.345244 CAGTTGCCGAGCTCCACT 59.655 61.111 8.47 2.41 0.00 4.00
3303 3347 1.556911 CTTAGGTCCAGCATCACCTGT 59.443 52.381 10.04 0.00 43.30 4.00
3486 3530 2.028658 CGATAGCATGGCAGGTATCACT 60.029 50.000 23.25 8.49 44.93 3.41
3488 3532 2.232208 CTCGATAGCATGGCAGGTATCA 59.768 50.000 23.25 15.07 44.93 2.15
3567 3611 4.528039 CTCCCATTGGCCCCGCAT 62.528 66.667 0.00 0.00 0.00 4.73
3771 3815 1.263356 CGACCTTCCAGTACTTCCCA 58.737 55.000 0.00 0.00 0.00 4.37
3813 3857 2.625790 GCTGTACTTCTCCTCCATCGAT 59.374 50.000 0.00 0.00 0.00 3.59
3818 3862 1.464734 CGAGCTGTACTTCTCCTCCA 58.535 55.000 0.00 0.00 0.00 3.86
3876 3920 2.510238 GAGTTGATGGCGCTCGCT 60.510 61.111 7.64 0.00 41.60 4.93
3979 4025 1.429148 GCTTAATGGTGGCGACCGAG 61.429 60.000 13.67 9.29 46.62 4.63
3992 4038 7.875971 AGAGAAACGAGAACAAAATGCTTAAT 58.124 30.769 0.00 0.00 0.00 1.40
4037 4083 7.962934 TGAAGAACACACGAACAAAATTTAG 57.037 32.000 0.00 0.00 0.00 1.85
4100 4147 6.231211 TGAAGAAGGCTTTCCTAGTTTACAG 58.769 40.000 4.73 0.00 43.40 2.74
4115 4162 7.172190 TCGATCATTTAATCATCTGAAGAAGGC 59.828 37.037 0.00 0.00 0.00 4.35
4121 4168 8.387190 AGCAATCGATCATTTAATCATCTGAA 57.613 30.769 0.00 0.00 0.00 3.02
4169 4216 8.283708 AGGGAGTACTTTATTCTAGCTAAGAGT 58.716 37.037 0.00 0.00 35.05 3.24
4186 4233 1.939980 AAGAAAGCGGAGGGAGTACT 58.060 50.000 0.00 0.00 0.00 2.73
4443 4490 9.803315 GGTATCTTCACGATATTAGCATATTCA 57.197 33.333 0.00 0.00 36.99 2.57
4510 4557 3.620427 AGGTTGTGTGCATCCGTAATA 57.380 42.857 0.00 0.00 39.01 0.98
4616 4670 5.995282 TCGCTTTTTGAGAATTTGGACTCTA 59.005 36.000 0.00 0.00 34.65 2.43
4632 4686 0.321653 ATCTGGAGGCGTCGCTTTTT 60.322 50.000 18.11 0.31 0.00 1.94
4676 4730 9.117145 CACACAAACATCACATTTAATCAGTAC 57.883 33.333 0.00 0.00 0.00 2.73
4703 4757 1.486310 GTGGATCATCAGCACCACCTA 59.514 52.381 0.00 0.00 44.59 3.08
4758 4812 5.860716 CAGTACTACAAACCTTCGGAAGTAC 59.139 44.000 16.07 9.90 38.59 2.73
4823 4880 4.320608 TCCATTTTGGCTTTCTCAACAC 57.679 40.909 0.00 0.00 37.47 3.32
4877 4934 3.785486 TGCTCTCTTTCCACATGATACG 58.215 45.455 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.