Multiple sequence alignment - TraesCS1A01G178500

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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 TraesCS1A01G178500 chr1A 100.000 3939 0 0 1 3939 323187610 323191548 0.000000e+00 7275
1 TraesCS1A01G178500 chr1D 92.114 3335 158 40 667 3939 252482018 252478727 0.000000e+00 4604
2 TraesCS1A01G178500 chr1B 93.286 2547 116 25 685 3204 361011785 361014303 0.000000e+00 3705
3 TraesCS1A01G178500 chr1B 95.418 742 32 2 3198 3939 361014462 361015201 0.000000e+00 1181
4 TraesCS1A01G178500 chr5D 89.759 664 56 4 1 653 394838043 394837381 0.000000e+00 839
5 TraesCS1A01G178500 chr4B 87.199 664 72 3 1 654 119387293 119386633 0.000000e+00 743
6 TraesCS1A01G178500 chrUn 86.076 395 50 4 209 602 27444758 27445148 1.690000e-113 420


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 TraesCS1A01G178500 chr1A 323187610 323191548 3938 False 7275 7275 100.000 1 3939 1 chr1A.!!$F1 3938
1 TraesCS1A01G178500 chr1D 252478727 252482018 3291 True 4604 4604 92.114 667 3939 1 chr1D.!!$R1 3272
2 TraesCS1A01G178500 chr1B 361011785 361015201 3416 False 2443 3705 94.352 685 3939 2 chr1B.!!$F1 3254
3 TraesCS1A01G178500 chr5D 394837381 394838043 662 True 839 839 89.759 1 653 1 chr5D.!!$R1 652
4 TraesCS1A01G178500 chr4B 119386633 119387293 660 True 743 743 87.199 1 654 1 chr4B.!!$R1 653

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
704 716 0.535335 TAGCTTACCGGGTCTTGCTG 59.465 55.0 22.96 4.81 32.72 4.41 F
821 833 0.600255 CGGACGCACCTCTGACTTTT 60.600 55.0 0.00 0.00 36.31 2.27 F
2407 2479 0.179000 ATCGCCTCCCTTCATGTCAC 59.821 55.0 0.00 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 1997 0.185901 ACCAACCTCTGCCACAATGT 59.814 50.000 0.00 0.00 0.00 2.71 R
2511 2583 2.435938 CGGGGTGTGATCGGGTTG 60.436 66.667 0.00 0.00 0.00 3.77 R
3878 4241 0.104120 GTGTTTGGCCCAACTTGGAC 59.896 55.000 19.58 6.69 40.96 4.02 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
48 49 4.871993 ACATGATGACGAATTTCAGAGC 57.128 40.909 0.00 0.00 0.00 4.09
52 53 2.099141 TGACGAATTTCAGAGCCCTG 57.901 50.000 0.00 0.00 41.74 4.45
75 76 5.163468 TGTGTCCACAATGTGCTTTGTAAAT 60.163 36.000 8.05 0.00 37.73 1.40
77 78 4.923281 GTCCACAATGTGCTTTGTAAATCC 59.077 41.667 8.05 0.00 37.73 3.01
93 94 2.972153 ATCCCTACTTGGAGGACCTT 57.028 50.000 0.00 0.00 39.15 3.50
132 133 3.186613 GGAAACCTGCAGCTAATATACGC 59.813 47.826 8.66 0.00 0.00 4.42
147 148 3.349006 CGCTTGCCTCAACAGCGT 61.349 61.111 4.65 0.00 43.00 5.07
150 151 1.205064 CTTGCCTCAACAGCGTTCG 59.795 57.895 0.00 0.00 0.00 3.95
217 228 1.111277 TCGCGGAATGGAAGATCAGA 58.889 50.000 6.13 0.00 0.00 3.27
225 236 0.826062 TGGAAGATCAGATGCAGCGA 59.174 50.000 0.00 0.00 0.00 4.93
244 255 2.223971 CGACGGCTATTTGTAGGGACAT 60.224 50.000 0.00 0.00 34.86 3.06
251 262 1.354101 TTTGTAGGGACATGGACGGT 58.646 50.000 0.00 0.00 34.86 4.83
263 274 5.118729 ACATGGACGGTAATTATTTGGGA 57.881 39.130 0.00 0.00 0.00 4.37
309 320 1.300931 GTTGACGCTGCAGGTCTCA 60.301 57.895 25.75 15.39 35.45 3.27
314 325 2.684843 CGCTGCAGGTCTCAAAGCC 61.685 63.158 17.12 0.00 0.00 4.35
317 328 0.538057 CTGCAGGTCTCAAAGCCCAA 60.538 55.000 5.57 0.00 0.00 4.12
368 379 3.842820 AGATCTCAACATCTCACGTGTG 58.157 45.455 16.51 13.78 0.00 3.82
371 382 5.358160 AGATCTCAACATCTCACGTGTGATA 59.642 40.000 27.34 14.74 39.13 2.15
386 397 3.551890 GTGTGATAATCGCGTCTGATTGT 59.448 43.478 5.77 0.00 38.92 2.71
395 406 2.337583 GCGTCTGATTGTCTGCAAGTA 58.662 47.619 0.00 0.00 38.10 2.24
401 412 3.838120 TGATTGTCTGCAAGTAGTCTCG 58.162 45.455 0.00 0.00 38.10 4.04
416 427 6.002704 AGTAGTCTCGGATATTAATGGACGT 58.997 40.000 0.00 0.00 0.00 4.34
420 431 4.340097 TCTCGGATATTAATGGACGTGTGT 59.660 41.667 0.00 0.00 0.00 3.72
425 436 6.036735 CGGATATTAATGGACGTGTGTTTTCT 59.963 38.462 0.00 0.00 0.00 2.52
436 447 4.336993 ACGTGTGTTTTCTTTCTTATGCCA 59.663 37.500 0.00 0.00 0.00 4.92
437 448 4.675114 CGTGTGTTTTCTTTCTTATGCCAC 59.325 41.667 0.00 0.00 0.00 5.01
453 464 3.445008 TGCCACTGTCTTAGAGGAGATT 58.555 45.455 0.00 0.00 39.29 2.40
460 471 7.123547 CCACTGTCTTAGAGGAGATTAAAGAGT 59.876 40.741 0.00 0.00 39.29 3.24
470 481 7.944554 AGAGGAGATTAAAGAGTCTATGAGAGG 59.055 40.741 0.00 0.00 0.00 3.69
476 487 9.660180 GATTAAAGAGTCTATGAGAGGTTTTGT 57.340 33.333 0.00 0.00 0.00 2.83
482 493 6.635755 AGTCTATGAGAGGTTTTGTTAGAGC 58.364 40.000 0.00 0.00 0.00 4.09
484 495 7.616150 AGTCTATGAGAGGTTTTGTTAGAGCTA 59.384 37.037 0.00 0.00 0.00 3.32
535 546 0.815095 TGAAGCTCATGCCATTGCTG 59.185 50.000 3.14 0.00 40.80 4.41
584 595 0.911769 CACTTGTGGCTAGGGATCCA 59.088 55.000 15.23 0.00 0.00 3.41
604 615 5.180271 TCCAACCGGACATTACTTGTATTC 58.820 41.667 9.46 0.00 39.18 1.75
608 619 5.812286 ACCGGACATTACTTGTATTCCTTT 58.188 37.500 9.46 0.00 39.18 3.11
615 626 7.590279 ACATTACTTGTATTCCTTTTTCGGTG 58.410 34.615 0.00 0.00 36.57 4.94
693 705 4.160736 CAAGTGGTTTGCTTAGCTTACC 57.839 45.455 17.17 17.17 34.83 2.85
695 707 1.467342 GTGGTTTGCTTAGCTTACCGG 59.533 52.381 18.20 0.00 36.19 5.28
704 716 0.535335 TAGCTTACCGGGTCTTGCTG 59.465 55.000 22.96 4.81 32.72 4.41
740 752 5.867174 GCATTTTGTATTGTTCCCAACCTAC 59.133 40.000 0.00 0.00 32.26 3.18
765 777 2.159310 CGTTTCACAAGCCTGGTTTTGA 60.159 45.455 16.45 10.52 0.00 2.69
783 795 0.784778 GACCGCACTTCTCGTGAAAG 59.215 55.000 1.12 0.00 46.81 2.62
821 833 0.600255 CGGACGCACCTCTGACTTTT 60.600 55.000 0.00 0.00 36.31 2.27
875 887 1.976132 GCCCAGACAGCCTGCTCATA 61.976 60.000 0.00 0.00 41.57 2.15
934 951 1.640069 CAGCGATTCGATGCCACAG 59.360 57.895 11.72 0.00 36.27 3.66
942 959 0.612744 TCGATGCCACAGGATTGACA 59.387 50.000 0.00 0.00 0.00 3.58
1000 1019 9.840427 ATACAAAGAGGTTATGAAATTTGAACG 57.160 29.630 0.00 0.00 33.14 3.95
1103 1131 6.045698 TCATCGTACTCATCTCGTTAGTTC 57.954 41.667 0.00 0.00 0.00 3.01
1119 1147 6.083925 GTTAGTTCAACGAGTTGCTGATAG 57.916 41.667 10.83 0.00 40.24 2.08
1306 1351 4.557690 TCTTTCGTATTTTCTTCGAGCGAG 59.442 41.667 0.00 0.00 35.13 5.03
1344 1389 1.231018 ACCATTTATAGGCTGCCCCA 58.769 50.000 16.57 3.70 35.39 4.96
1428 1474 1.973515 ACCAACAGAGAGCACTCATCA 59.026 47.619 13.86 0.00 44.79 3.07
1702 1755 3.747976 GCCGCCTGCGACCAAATT 61.748 61.111 13.94 0.00 42.83 1.82
1725 1778 1.676006 CGAAAGGTTCCTTGTGCTTGT 59.324 47.619 4.77 0.00 0.00 3.16
1772 1825 1.372251 CTCGTCACGCTCAAGCAGT 60.372 57.895 2.50 0.00 42.21 4.40
1823 1876 1.995066 AGGGACGGCATGATGGTCA 60.995 57.895 0.00 0.00 32.39 4.02
1873 1926 3.909086 GAAGGAGCTGTGCCGCCTT 62.909 63.158 12.10 12.10 43.27 4.35
1943 1996 2.038426 ACCACGAACAATGAGGTGATCA 59.962 45.455 0.00 0.00 43.70 2.92
1944 1997 3.073678 CCACGAACAATGAGGTGATCAA 58.926 45.455 0.00 0.00 42.53 2.57
1957 2010 2.163010 GGTGATCAACATTGTGGCAGAG 59.837 50.000 5.69 0.00 0.00 3.35
1960 2013 2.363306 TCAACATTGTGGCAGAGGTT 57.637 45.000 0.00 0.00 0.00 3.50
1962 2015 1.000060 CAACATTGTGGCAGAGGTTGG 60.000 52.381 17.73 5.44 33.77 3.77
2191 2244 2.287248 GGTTTTCAGAAGACTGCTGCAC 60.287 50.000 5.45 2.56 43.17 4.57
2264 2335 5.087323 ACAGTCAGGATGTTAGAAGAGGAA 58.913 41.667 0.00 0.00 37.40 3.36
2293 2364 1.336887 ACATGTAGTGGCAGTGACGAC 60.337 52.381 4.76 0.00 0.00 4.34
2309 2380 4.845060 GTGACGACAGTAGAAGAAACGTAG 59.155 45.833 0.00 0.00 32.88 3.51
2348 2419 7.119262 GTGGCATACTGTATGTAGTTTCAGTTT 59.881 37.037 24.32 0.00 40.77 2.66
2407 2479 0.179000 ATCGCCTCCCTTCATGTCAC 59.821 55.000 0.00 0.00 0.00 3.67
2462 2534 8.263940 TGCTACAAACTGGAGAATAATGTTAC 57.736 34.615 0.00 0.00 26.39 2.50
2484 2556 1.203287 GGCTGGTTGAATTCTTCCTGC 59.797 52.381 26.35 26.35 41.76 4.85
2485 2557 2.165998 GCTGGTTGAATTCTTCCTGCT 58.834 47.619 26.68 0.00 40.21 4.24
2620 2806 4.572389 ACTGACAACTGAAAACACAGCTAG 59.428 41.667 0.00 0.00 41.06 3.42
2694 2880 0.106819 CCCTCTCCAAAGCATCAGGG 60.107 60.000 0.00 0.00 34.83 4.45
2714 2900 2.665165 GATACCATGATTTGCACCCCA 58.335 47.619 0.00 0.00 0.00 4.96
2870 3056 9.958180 TTTGACAATTCATATAAGAGTCAAGGA 57.042 29.630 9.69 0.00 42.95 3.36
2921 3108 4.178545 ACAGCATAAACCTGTTTGATGC 57.821 40.909 18.77 18.77 40.45 3.91
2996 3183 5.964477 TCAAGCTAGAAGGATAAGGGAAAGA 59.036 40.000 0.00 0.00 0.00 2.52
3100 3297 0.622665 AGCTAGATGCACCAGGCTTT 59.377 50.000 0.00 0.00 45.94 3.51
3113 3310 5.294552 GCACCAGGCTTTCTTAGTACAATAG 59.705 44.000 0.00 0.00 40.25 1.73
3138 3335 6.870965 GTGAATATTCTATCGGAGCACTTGAT 59.129 38.462 16.24 0.00 0.00 2.57
3140 3337 7.386025 TGAATATTCTATCGGAGCACTTGATTG 59.614 37.037 16.24 0.00 0.00 2.67
3141 3338 4.471904 TTCTATCGGAGCACTTGATTGT 57.528 40.909 0.00 0.00 0.00 2.71
3142 3339 5.592104 TTCTATCGGAGCACTTGATTGTA 57.408 39.130 0.00 0.00 0.00 2.41
3143 3340 4.933330 TCTATCGGAGCACTTGATTGTAC 58.067 43.478 0.00 0.00 0.00 2.90
3144 3341 3.895232 ATCGGAGCACTTGATTGTACT 57.105 42.857 0.00 0.00 0.00 2.73
3145 3342 3.232213 TCGGAGCACTTGATTGTACTC 57.768 47.619 0.00 0.00 31.40 2.59
3146 3343 2.094182 TCGGAGCACTTGATTGTACTCC 60.094 50.000 4.33 4.33 43.60 3.85
3317 3679 6.599638 GTGCCTATCAACTTAATCAGGACTTT 59.400 38.462 0.00 0.00 0.00 2.66
3357 3719 9.981114 AAACTAGGAAAAACATAAAGTGGATTG 57.019 29.630 0.00 0.00 0.00 2.67
3461 3823 8.970859 AAGAATAATCTGGTGGATAAACTGAG 57.029 34.615 0.00 0.00 35.59 3.35
3527 3889 2.158900 AGGTCCTTCATTAGGCATGTCG 60.159 50.000 0.00 0.00 44.37 4.35
3531 3893 2.223340 CCTTCATTAGGCATGTCGCAAC 60.223 50.000 0.00 0.00 45.17 4.17
3564 3926 4.278419 ACAATAAGCAACACCAAGGAACTC 59.722 41.667 0.00 0.00 38.49 3.01
3617 3979 2.839486 TCAACCAAGTGCTACTGAGG 57.161 50.000 0.00 0.00 32.38 3.86
3799 4161 7.875041 AGTTTTGAGTATACTGGCTAGCATATG 59.125 37.037 18.24 0.00 0.00 1.78
3867 4230 4.655649 TCATATGGATCTGCACCACTAACT 59.344 41.667 2.13 0.00 40.36 2.24
3871 4234 6.747414 ATGGATCTGCACCACTAACTTATA 57.253 37.500 0.00 0.00 40.36 0.98
3875 4238 4.368315 TCTGCACCACTAACTTATATGCG 58.632 43.478 0.00 0.00 34.32 4.73
3876 4239 2.869801 TGCACCACTAACTTATATGCGC 59.130 45.455 0.00 0.00 34.32 6.09
3877 4240 2.223377 GCACCACTAACTTATATGCGCC 59.777 50.000 4.18 0.00 0.00 6.53
3878 4241 2.475111 CACCACTAACTTATATGCGCCG 59.525 50.000 4.18 0.00 0.00 6.46
3924 4287 5.049886 GCTTAACAGGTTACGCTAAACAAGT 60.050 40.000 11.92 0.00 37.34 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.344535 TCATGTATTGCCCTCCTCCTA 57.655 47.619 0.00 0.00 0.00 2.94
48 49 0.538057 AGCACATTGTGGACACAGGG 60.538 55.000 18.05 4.83 42.94 4.45
52 53 2.869233 ACAAAGCACATTGTGGACAC 57.131 45.000 18.05 1.76 41.78 3.67
75 76 1.435563 TCAAGGTCCTCCAAGTAGGGA 59.564 52.381 0.00 0.00 37.24 4.20
77 78 2.821437 TCTCAAGGTCCTCCAAGTAGG 58.179 52.381 0.00 0.00 38.06 3.18
93 94 4.158025 GGTTTCCTAACAGAGACGATCTCA 59.842 45.833 14.62 0.00 45.73 3.27
132 133 1.205064 CGAACGCTGTTGAGGCAAG 59.795 57.895 0.00 0.00 0.00 4.01
147 148 1.768870 GGAGAAATCCATCCCCTCGAA 59.231 52.381 0.00 0.00 0.00 3.71
150 151 1.423161 CCTGGAGAAATCCATCCCCTC 59.577 57.143 0.00 0.00 39.34 4.30
209 220 0.529337 CCGTCGCTGCATCTGATCTT 60.529 55.000 0.00 0.00 0.00 2.40
225 236 2.158813 CCATGTCCCTACAAATAGCCGT 60.159 50.000 0.00 0.00 39.58 5.68
230 241 3.109151 ACCGTCCATGTCCCTACAAATA 58.891 45.455 0.00 0.00 39.58 1.40
236 247 6.292923 CAAATAATTACCGTCCATGTCCCTA 58.707 40.000 0.00 0.00 0.00 3.53
244 255 3.201266 AGCTCCCAAATAATTACCGTCCA 59.799 43.478 0.00 0.00 0.00 4.02
251 262 5.509498 ACTGCTGAAGCTCCCAAATAATTA 58.491 37.500 3.61 0.00 42.66 1.40
263 274 2.923121 TCAAAAGTGACTGCTGAAGCT 58.077 42.857 3.61 0.00 42.66 3.74
314 325 1.648467 GGGCTTCGCTACAAGCTTGG 61.648 60.000 29.18 14.26 46.89 3.61
317 328 1.078848 CAGGGCTTCGCTACAAGCT 60.079 57.895 10.61 0.00 46.89 3.74
320 331 2.046314 GCCAGGGCTTCGCTACAA 60.046 61.111 2.30 0.00 38.26 2.41
346 357 3.856521 CACACGTGAGATGTTGAGATCTC 59.143 47.826 25.01 16.21 46.00 2.75
365 376 3.780902 ACAATCAGACGCGATTATCACA 58.219 40.909 15.93 0.00 33.82 3.58
368 379 3.121194 GCAGACAATCAGACGCGATTATC 60.121 47.826 15.93 0.00 33.82 1.75
371 382 1.002366 GCAGACAATCAGACGCGATT 58.998 50.000 15.93 0.00 36.00 3.34
386 397 6.954487 TTAATATCCGAGACTACTTGCAGA 57.046 37.500 0.00 0.00 0.00 4.26
395 406 4.583489 ACACGTCCATTAATATCCGAGACT 59.417 41.667 6.77 0.00 0.00 3.24
401 412 7.316544 AGAAAACACACGTCCATTAATATCC 57.683 36.000 0.00 0.00 0.00 2.59
416 427 5.359576 ACAGTGGCATAAGAAAGAAAACACA 59.640 36.000 0.00 0.00 0.00 3.72
420 431 6.959639 AAGACAGTGGCATAAGAAAGAAAA 57.040 33.333 0.00 0.00 0.00 2.29
425 436 5.483937 TCCTCTAAGACAGTGGCATAAGAAA 59.516 40.000 0.00 0.00 37.75 2.52
436 447 8.113462 AGACTCTTTAATCTCCTCTAAGACAGT 58.887 37.037 0.00 0.00 0.00 3.55
437 448 8.519799 AGACTCTTTAATCTCCTCTAAGACAG 57.480 38.462 0.00 0.00 0.00 3.51
460 471 6.859112 AGCTCTAACAAAACCTCTCATAGA 57.141 37.500 0.00 0.00 0.00 1.98
484 495 7.125811 TGCTTCCCTACACTCAAATCTATAACT 59.874 37.037 0.00 0.00 0.00 2.24
494 505 4.761739 CAGAATTTGCTTCCCTACACTCAA 59.238 41.667 0.00 0.00 34.11 3.02
498 509 4.379918 GCTTCAGAATTTGCTTCCCTACAC 60.380 45.833 0.00 0.00 34.11 2.90
535 546 1.886777 GGAGCGATGAAGCAGCCTC 60.887 63.158 0.00 0.00 40.15 4.70
584 595 5.431179 AGGAATACAAGTAATGTCCGGTT 57.569 39.130 0.00 0.00 42.70 4.44
604 615 3.574284 TTCATGATGCACCGAAAAAGG 57.426 42.857 0.00 0.00 37.30 3.11
608 619 6.272318 GGATTTTATTCATGATGCACCGAAA 58.728 36.000 0.00 0.00 0.00 3.46
615 626 8.078596 GTGAACTAGGGATTTTATTCATGATGC 58.921 37.037 0.00 0.00 0.00 3.91
681 693 1.066430 CAAGACCCGGTAAGCTAAGCA 60.066 52.381 0.00 0.00 0.00 3.91
693 705 2.260869 CCACCAACAGCAAGACCCG 61.261 63.158 0.00 0.00 0.00 5.28
695 707 0.385390 CAACCACCAACAGCAAGACC 59.615 55.000 0.00 0.00 0.00 3.85
704 716 3.177997 ACAAAATGCTCAACCACCAAC 57.822 42.857 0.00 0.00 0.00 3.77
783 795 1.367471 GTTTTGTTGGGGCCTCTGC 59.633 57.895 3.07 0.00 0.00 4.26
821 833 2.304470 TCCAATGGTCGGAAAGATCACA 59.696 45.455 0.00 0.00 43.79 3.58
872 884 2.226437 AGGCTGTCTGCGTTTTTGTATG 59.774 45.455 0.00 0.00 44.05 2.39
875 887 0.381801 CAGGCTGTCTGCGTTTTTGT 59.618 50.000 6.28 0.00 44.05 2.83
896 913 1.471287 GGATTAACACCCTTTGCCGAC 59.529 52.381 0.00 0.00 0.00 4.79
897 914 1.074084 TGGATTAACACCCTTTGCCGA 59.926 47.619 0.00 0.00 0.00 5.54
898 915 1.472480 CTGGATTAACACCCTTTGCCG 59.528 52.381 0.00 0.00 0.00 5.69
901 918 2.432444 TCGCTGGATTAACACCCTTTG 58.568 47.619 0.00 0.00 0.00 2.77
902 919 2.871096 TCGCTGGATTAACACCCTTT 57.129 45.000 0.00 0.00 0.00 3.11
934 951 3.074412 ACAAATCGTGTCCTGTCAATCC 58.926 45.455 0.00 0.00 34.38 3.01
960 978 5.823045 CCTCTTTGTATGAACTGGGGAATAC 59.177 44.000 0.00 0.00 0.00 1.89
963 981 3.655777 ACCTCTTTGTATGAACTGGGGAA 59.344 43.478 0.00 0.00 0.00 3.97
1103 1131 2.345641 CGTTCCTATCAGCAACTCGTTG 59.654 50.000 5.45 5.45 43.14 4.10
1324 1369 1.573376 TGGGGCAGCCTATAAATGGTT 59.427 47.619 12.43 0.00 0.00 3.67
1412 1457 1.549620 CCTGTGATGAGTGCTCTCTGT 59.450 52.381 16.23 5.77 40.98 3.41
1448 1501 4.796231 CGTCTTCCCCGCTGGTCG 62.796 72.222 0.00 0.00 34.77 4.79
1666 1719 2.980233 GTGGCTGTGTGGAGTGCC 60.980 66.667 0.00 0.00 45.10 5.01
1702 1755 1.416401 AGCACAAGGAACCTTTCGAGA 59.584 47.619 3.10 0.00 33.42 4.04
1805 1858 1.995066 TGACCATCATGCCGTCCCT 60.995 57.895 0.00 0.00 0.00 4.20
1823 1876 2.357396 TGCACGAAGCGATGCAGT 60.357 55.556 11.08 0.00 46.63 4.40
1943 1996 1.331214 CCAACCTCTGCCACAATGTT 58.669 50.000 0.00 0.00 0.00 2.71
1944 1997 0.185901 ACCAACCTCTGCCACAATGT 59.814 50.000 0.00 0.00 0.00 2.71
1962 2015 3.357079 CTTCCACAGTGGCCGCAC 61.357 66.667 20.59 1.15 37.47 5.34
2161 2214 3.430556 GTCTTCTGAAAACCTTCTCGCTC 59.569 47.826 0.00 0.00 32.33 5.03
2164 2217 3.185391 GCAGTCTTCTGAAAACCTTCTCG 59.815 47.826 0.00 0.00 43.76 4.04
2252 2323 6.937436 TGTTTCCTGTTTTCCTCTTCTAAC 57.063 37.500 0.00 0.00 0.00 2.34
2264 2335 3.561143 TGCCACTACATGTTTCCTGTTT 58.439 40.909 2.30 0.00 0.00 2.83
2348 2419 9.463902 AGATAGTACTACTTTAGAAGTCTGCAA 57.536 33.333 4.31 0.00 41.77 4.08
2407 2479 4.599047 TTTTGGTGGCTCAAGGTTAATG 57.401 40.909 0.00 0.00 0.00 1.90
2439 2511 8.883731 CCTGTAACATTATTCTCCAGTTTGTAG 58.116 37.037 0.00 0.00 0.00 2.74
2511 2583 2.435938 CGGGGTGTGATCGGGTTG 60.436 66.667 0.00 0.00 0.00 3.77
2620 2806 6.364976 AGACAAAAGTTGTAGTTTTGCACAAC 59.635 34.615 7.67 7.67 46.89 3.32
2694 2880 2.624838 CTGGGGTGCAAATCATGGTATC 59.375 50.000 0.00 0.00 0.00 2.24
2760 2946 6.682861 GCCAGTTTACAGAAACCAATGAGTTT 60.683 38.462 0.65 0.65 45.21 2.66
2870 3056 8.041323 TCGAAGAAAAGCTTTAGATATGAAGGT 58.959 33.333 13.10 0.00 36.83 3.50
2965 3152 7.174599 CCCTTATCCTTCTAGCTTGATGATTTG 59.825 40.741 11.69 7.46 0.00 2.32
2996 3183 5.705609 ACACGAAAAAGTCCTTGCATATT 57.294 34.783 0.00 0.00 0.00 1.28
3113 3310 6.216569 TCAAGTGCTCCGATAGAATATTCAC 58.783 40.000 17.56 7.55 39.76 3.18
3125 3322 3.232213 GAGTACAATCAAGTGCTCCGA 57.768 47.619 0.00 0.00 42.96 4.55
3143 3340 3.842732 TGGCACGTATGATATACGGAG 57.157 47.619 21.05 15.17 44.38 4.63
3144 3341 3.570975 AGTTGGCACGTATGATATACGGA 59.429 43.478 21.05 4.25 44.38 4.69
3145 3342 3.909430 AGTTGGCACGTATGATATACGG 58.091 45.455 21.05 13.03 44.38 4.02
3146 3343 6.319399 TCATAGTTGGCACGTATGATATACG 58.681 40.000 17.01 17.01 45.44 3.06
3206 3568 2.412870 TGCATGTAGTTGGACGTCTTG 58.587 47.619 16.46 0.00 0.00 3.02
3357 3719 3.317603 TGCTTATTTGGGCTTTTCTGC 57.682 42.857 0.00 0.00 0.00 4.26
3461 3823 7.876582 ACCTAGACCAACAACTACAGTTAATTC 59.123 37.037 0.00 0.00 36.32 2.17
3527 3889 3.117346 GCTTATTGTTGTTTCGTCGTTGC 59.883 43.478 0.00 0.00 0.00 4.17
3531 3893 4.144051 GTGTTGCTTATTGTTGTTTCGTCG 59.856 41.667 0.00 0.00 0.00 5.12
3617 3979 4.329462 AGGTCAAGACTCAAGACTGAAC 57.671 45.455 0.00 0.00 32.98 3.18
3764 4126 7.764443 GCCAGTATACTCAAAACTCAGATTACA 59.236 37.037 1.26 0.00 0.00 2.41
3799 4161 1.410153 GGATGGTGGTCAATTGGCATC 59.590 52.381 12.93 5.99 0.00 3.91
3812 4174 3.019564 GGATGTTTCTTCAGGGATGGTG 58.980 50.000 0.00 0.00 0.00 4.17
3867 4230 1.937223 CAACTTGGACGGCGCATATAA 59.063 47.619 10.83 0.00 0.00 0.98
3871 4234 3.055719 CCAACTTGGACGGCGCAT 61.056 61.111 10.83 0.00 40.96 4.73
3875 4238 4.966787 TGGCCCAACTTGGACGGC 62.967 66.667 9.61 6.54 40.96 5.68
3876 4239 1.830408 TTTGGCCCAACTTGGACGG 60.830 57.895 9.61 0.00 40.96 4.79
3877 4240 1.362355 GTTTGGCCCAACTTGGACG 59.638 57.895 12.38 0.00 40.96 4.79
3878 4241 0.104120 GTGTTTGGCCCAACTTGGAC 59.896 55.000 19.58 6.69 40.96 4.02


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

AutoCloner maintained by Alex Coulton.