Multiple sequence alignment - TraesCS1D01G218600

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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 TraesCS1D01G218600 chr1D 100.000 4171 0 0 1 4171 305580672 305584842 0.000000e+00 7703.0
1 TraesCS1D01G218600 chr1A 94.365 3070 115 25 770 3823 384324010 384327037 0.000000e+00 4658.0
2 TraesCS1D01G218600 chr1A 92.521 361 12 5 3817 4171 384328186 384328537 1.730000e-138 503.0
3 TraesCS1D01G218600 chr1B 93.671 2133 90 18 1 2113 412857567 412859674 0.000000e+00 3149.0
4 TraesCS1D01G218600 chr1B 94.598 1555 53 15 2108 3659 412870739 412872265 0.000000e+00 2377.0
5 TraesCS1D01G218600 chr1B 90.062 161 14 2 3698 3857 188452463 188452304 1.520000e-49 207.0
6 TraesCS1D01G218600 chr1B 81.132 212 14 6 3859 4066 412872282 412872471 3.360000e-31 147.0
7 TraesCS1D01G218600 chr4A 83.429 175 19 5 3691 3857 566298852 566299024 2.010000e-33 154.0
8 TraesCS1D01G218600 chr4A 100.000 28 0 0 4022 4049 30354668 30354641 8.000000e-03 52.8
9 TraesCS1D01G218600 chr5A 93.204 103 6 1 613 715 494977102 494977203 2.600000e-32 150.0
10 TraesCS1D01G218600 chr6B 97.297 37 0 1 4027 4063 683375514 683375479 1.250000e-05 62.1
11 TraesCS1D01G218600 chr2A 100.000 28 0 0 4023 4050 16861356 16861383 8.000000e-03 52.8


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 TraesCS1D01G218600 chr1D 305580672 305584842 4170 False 7703.0 7703 100.000 1 4171 1 chr1D.!!$F1 4170
1 TraesCS1D01G218600 chr1A 384324010 384328537 4527 False 2580.5 4658 93.443 770 4171 2 chr1A.!!$F1 3401
2 TraesCS1D01G218600 chr1B 412857567 412859674 2107 False 3149.0 3149 93.671 1 2113 1 chr1B.!!$F1 2112
3 TraesCS1D01G218600 chr1B 412870739 412872471 1732 False 1262.0 2377 87.865 2108 4066 2 chr1B.!!$F2 1958

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
670 681 0.603569 ACGAACGAGATGAGTTGGCT 59.396 50.000 0.14 0.00 31.82 4.75 F
793 804 0.678950 TCAATGTCAGACGTCCAGCA 59.321 50.000 13.01 8.93 0.00 4.41 F
1100 1114 0.685785 TGCCCGCTTCTCTCATCTCT 60.686 55.000 0.00 0.00 0.00 3.10 F
2490 2521 1.072173 ACTATGTCAGCTGTTGGTGCA 59.928 47.619 14.67 5.13 41.10 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 1960 2.105477 AGTGAGAATGGTGCTTGAGTGT 59.895 45.455 0.0 0.0 0.00 3.55 R
2530 2561 2.627699 TCTCATTCTTTGGGTTGTTGGC 59.372 45.455 0.0 0.0 0.00 4.52 R
2878 2912 0.107017 CCCCTTCAACGCAGGATGAT 60.107 55.000 0.0 0.0 39.69 2.45 R
3992 5197 0.103208 CGTATGAGGTGGCAGAGACC 59.897 60.000 0.0 0.0 0.00 3.85 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
32 33 6.968263 TTGTGGATTCCAAAAGTATTCACA 57.032 33.333 7.05 0.00 39.33 3.58
66 67 5.333299 TCTTCGGAGATTTAACGGATTCA 57.667 39.130 0.00 0.00 35.04 2.57
240 247 8.947055 AAGTTCAAGCATTAAAAATGTTCAGT 57.053 26.923 1.94 0.00 0.00 3.41
380 389 8.997621 AAAGAAAAGAGTAAACAAGGGAAAAC 57.002 30.769 0.00 0.00 0.00 2.43
381 390 7.712204 AGAAAAGAGTAAACAAGGGAAAACA 57.288 32.000 0.00 0.00 0.00 2.83
382 391 8.129496 AGAAAAGAGTAAACAAGGGAAAACAA 57.871 30.769 0.00 0.00 0.00 2.83
383 392 8.590204 AGAAAAGAGTAAACAAGGGAAAACAAA 58.410 29.630 0.00 0.00 0.00 2.83
384 393 8.542497 AAAAGAGTAAACAAGGGAAAACAAAC 57.458 30.769 0.00 0.00 0.00 2.93
385 394 6.844097 AGAGTAAACAAGGGAAAACAAACA 57.156 33.333 0.00 0.00 0.00 2.83
386 395 7.234661 AGAGTAAACAAGGGAAAACAAACAA 57.765 32.000 0.00 0.00 0.00 2.83
387 396 7.847096 AGAGTAAACAAGGGAAAACAAACAAT 58.153 30.769 0.00 0.00 0.00 2.71
388 397 8.973182 AGAGTAAACAAGGGAAAACAAACAATA 58.027 29.630 0.00 0.00 0.00 1.90
389 398 9.589111 GAGTAAACAAGGGAAAACAAACAATAA 57.411 29.630 0.00 0.00 0.00 1.40
390 399 9.945904 AGTAAACAAGGGAAAACAAACAATAAA 57.054 25.926 0.00 0.00 0.00 1.40
393 402 8.622948 AACAAGGGAAAACAAACAATAAAACA 57.377 26.923 0.00 0.00 0.00 2.83
394 403 8.262715 ACAAGGGAAAACAAACAATAAAACAG 57.737 30.769 0.00 0.00 0.00 3.16
443 452 8.471609 AGGAAAACTCAAAAATAGGAAAAACGA 58.528 29.630 0.00 0.00 0.00 3.85
510 520 2.702592 ACCGAACAAACTGGTGAAGA 57.297 45.000 0.00 0.00 33.91 2.87
565 575 1.423541 TGCACCCTGTACCATTTGTCT 59.576 47.619 0.00 0.00 0.00 3.41
566 576 2.084546 GCACCCTGTACCATTTGTCTC 58.915 52.381 0.00 0.00 0.00 3.36
567 577 2.552155 GCACCCTGTACCATTTGTCTCA 60.552 50.000 0.00 0.00 0.00 3.27
568 578 3.338249 CACCCTGTACCATTTGTCTCAG 58.662 50.000 0.00 0.00 0.00 3.35
571 581 2.002586 CTGTACCATTTGTCTCAGGCG 58.997 52.381 0.00 0.00 0.00 5.52
572 582 1.621317 TGTACCATTTGTCTCAGGCGA 59.379 47.619 0.00 0.00 0.00 5.54
580 591 2.672961 TGTCTCAGGCGACAAATAGG 57.327 50.000 0.00 0.00 40.69 2.57
589 600 2.618709 GGCGACAAATAGGAGGATTTGG 59.381 50.000 12.18 0.00 46.61 3.28
623 634 4.038402 GGCCATACAAAAGAGCAATGCTAT 59.962 41.667 8.12 0.49 39.88 2.97
637 648 7.608376 AGAGCAATGCTATATCTACGAAGAGTA 59.392 37.037 8.12 0.00 39.88 2.59
668 679 4.092771 TCTTACGAACGAGATGAGTTGG 57.907 45.455 0.14 0.00 34.26 3.77
670 681 0.603569 ACGAACGAGATGAGTTGGCT 59.396 50.000 0.14 0.00 31.82 4.75
681 692 5.717119 AGATGAGTTGGCTGCTTTTAATTG 58.283 37.500 0.00 0.00 0.00 2.32
699 710 4.696479 ATTGGACATTAGTAGAGGCTGG 57.304 45.455 0.00 0.00 0.00 4.85
725 736 3.689649 CCACCCTGAAAAGGAAGATTACG 59.310 47.826 0.00 0.00 0.00 3.18
793 804 0.678950 TCAATGTCAGACGTCCAGCA 59.321 50.000 13.01 8.93 0.00 4.41
941 953 1.186267 AACAGTCTCCTCACCGGTCC 61.186 60.000 2.59 0.00 0.00 4.46
1100 1114 0.685785 TGCCCGCTTCTCTCATCTCT 60.686 55.000 0.00 0.00 0.00 3.10
1142 1158 2.824936 CGCTCACATATCTCCCTGATCT 59.175 50.000 0.00 0.00 36.65 2.75
1359 1375 3.428452 CGCAATTGAGTTTCATCATGGCT 60.428 43.478 10.34 0.00 0.00 4.75
1360 1376 3.863424 GCAATTGAGTTTCATCATGGCTG 59.137 43.478 10.34 0.00 0.00 4.85
1389 1405 1.181741 TTGAGTCCTGCTGCGAGAGT 61.182 55.000 0.00 0.00 0.00 3.24
1480 1502 9.631257 TGGAGTAACAAATTCACATGATATGAT 57.369 29.630 0.00 0.00 0.00 2.45
1503 1525 5.968528 TTTGTTTTGGTAAGACCGCATAT 57.031 34.783 0.00 0.00 42.58 1.78
1525 1547 9.064706 CATATTGTGATAAGGCAAGAGAGATTT 57.935 33.333 0.00 0.00 0.00 2.17
1594 1616 6.648879 ATTCGGGGTCAATATTTTGTATGG 57.351 37.500 0.00 0.00 34.32 2.74
1619 1641 5.603170 ATTAAACATGATTCTGCTTGGGG 57.397 39.130 0.00 0.00 0.00 4.96
1800 1822 4.675190 CAAATAGGTTGCTCACAGACAG 57.325 45.455 0.00 0.00 0.00 3.51
1930 1960 4.871871 TGACCCCATTTGGCTAGAATTA 57.128 40.909 0.00 0.00 0.00 1.40
1951 1981 2.105477 ACACTCAAGCACCATTCTCACT 59.895 45.455 0.00 0.00 0.00 3.41
2079 2110 9.807649 ATCTTGGAAATGATAAAATGTTGCTAC 57.192 29.630 0.00 0.00 0.00 3.58
2080 2111 9.023962 TCTTGGAAATGATAAAATGTTGCTACT 57.976 29.630 0.00 0.00 0.00 2.57
2185 2216 5.772825 AAGCTTCATGCACACTTCTAAAA 57.227 34.783 0.00 0.00 45.94 1.52
2186 2217 5.772825 AGCTTCATGCACACTTCTAAAAA 57.227 34.783 0.00 0.00 45.94 1.94
2490 2521 1.072173 ACTATGTCAGCTGTTGGTGCA 59.928 47.619 14.67 5.13 41.10 4.57
2590 2621 7.402071 TGGGTGGTAGAAAGAGAAAGTATGTAT 59.598 37.037 0.00 0.00 0.00 2.29
2662 2693 9.685276 ATTATTTCTCCATGAAGTGTCATTACA 57.315 29.630 0.00 0.00 42.03 2.41
2752 2786 2.990066 ATTCGAGGGTGATCCAACTC 57.010 50.000 0.00 0.00 38.24 3.01
2759 2793 1.278127 GGGTGATCCAACTCGAAAGGA 59.722 52.381 3.01 3.01 35.59 3.36
2820 2854 9.442047 ACCTCTTCACTTATTCTGTAAAGATTG 57.558 33.333 0.00 0.00 0.00 2.67
2863 2897 6.793505 TCTTAGGAGAACTGAATTAGTCCC 57.206 41.667 0.00 0.00 39.18 4.46
2864 2898 5.360144 TCTTAGGAGAACTGAATTAGTCCCG 59.640 44.000 0.00 0.00 39.18 5.14
2865 2899 3.442076 AGGAGAACTGAATTAGTCCCGT 58.558 45.455 0.00 0.00 39.18 5.28
2866 2900 3.447944 AGGAGAACTGAATTAGTCCCGTC 59.552 47.826 0.00 0.00 39.18 4.79
2867 2901 3.430513 GGAGAACTGAATTAGTCCCGTCC 60.431 52.174 0.00 0.00 39.18 4.79
2868 2902 3.442076 AGAACTGAATTAGTCCCGTCCT 58.558 45.455 0.00 0.00 39.18 3.85
2869 2903 4.607239 AGAACTGAATTAGTCCCGTCCTA 58.393 43.478 0.00 0.00 39.18 2.94
2870 2904 5.209659 AGAACTGAATTAGTCCCGTCCTAT 58.790 41.667 0.00 0.00 39.18 2.57
2871 2905 5.302313 AGAACTGAATTAGTCCCGTCCTATC 59.698 44.000 0.00 0.00 39.18 2.08
2872 2906 4.543689 ACTGAATTAGTCCCGTCCTATCA 58.456 43.478 0.00 0.00 33.17 2.15
2873 2907 5.148502 ACTGAATTAGTCCCGTCCTATCAT 58.851 41.667 0.00 0.00 33.17 2.45
2874 2908 6.312529 ACTGAATTAGTCCCGTCCTATCATA 58.687 40.000 0.00 0.00 33.17 2.15
2875 2909 6.434652 ACTGAATTAGTCCCGTCCTATCATAG 59.565 42.308 0.00 0.00 33.17 2.23
2876 2910 8.450924 ACTGAATTAGTCCCGTCCTATCATAGG 61.451 44.444 4.00 4.00 40.67 2.57
2895 2929 1.672881 GGAATCATCCTGCGTTGAAGG 59.327 52.381 0.00 0.00 42.93 3.46
2896 2930 1.672881 GAATCATCCTGCGTTGAAGGG 59.327 52.381 0.00 0.00 35.35 3.95
2903 2937 2.111999 CTGCGTTGAAGGGGTGGAGA 62.112 60.000 0.00 0.00 0.00 3.71
3047 3082 4.976116 GTGTGCATGGTAGTTTGAGTTTTC 59.024 41.667 0.00 0.00 0.00 2.29
3236 3271 1.850345 TGGAAACTCACCTCCCTGTTT 59.150 47.619 0.00 0.00 35.64 2.83
3367 3402 6.910191 TCATTTATCTTATCCTGGCCTTTGA 58.090 36.000 3.32 0.00 0.00 2.69
3709 3757 3.740832 GGAAAAACGCAAAGGATCTTTGG 59.259 43.478 18.33 12.28 0.00 3.28
3712 3760 0.251341 ACGCAAAGGATCTTTGGGCT 60.251 50.000 26.34 16.20 43.43 5.19
3719 3767 5.554070 CAAAGGATCTTTGGGCTTCATTTT 58.446 37.500 11.36 0.00 0.00 1.82
3736 3784 7.493645 GCTTCATTTTATTGAAAAGATGGGGAG 59.506 37.037 0.00 0.00 37.94 4.30
3871 5074 3.363341 TTGGCCACGAATTCACTTTTC 57.637 42.857 3.88 0.00 0.00 2.29
3875 5078 3.500680 GGCCACGAATTCACTTTTCTACA 59.499 43.478 6.22 0.00 0.00 2.74
4021 5226 6.704493 TCTGCCACCTCATACGAATAATAAAC 59.296 38.462 0.00 0.00 0.00 2.01
4075 5284 2.920490 CAAAAACGTATTTGCGGGATGG 59.080 45.455 0.00 0.00 33.90 3.51
4093 5302 7.525692 GCGGGATGGAGAGAGTAATTAAAGTAT 60.526 40.741 0.00 0.00 0.00 2.12
4132 5341 9.354544 GAAAATAACAAAGATACTTCGATACGC 57.645 33.333 0.00 0.00 0.00 4.42
4133 5342 6.670990 ATAACAAAGATACTTCGATACGCG 57.329 37.500 3.53 3.53 42.69 6.01
4134 5343 3.369385 ACAAAGATACTTCGATACGCGG 58.631 45.455 12.47 0.00 41.33 6.46
4135 5344 2.701073 AAGATACTTCGATACGCGGG 57.299 50.000 12.47 0.00 41.33 6.13
4136 5345 1.888215 AGATACTTCGATACGCGGGA 58.112 50.000 12.47 0.00 41.33 5.14
4137 5346 2.434428 AGATACTTCGATACGCGGGAT 58.566 47.619 12.47 2.56 41.33 3.85
4138 5347 2.161808 AGATACTTCGATACGCGGGATG 59.838 50.000 12.47 7.03 41.33 3.51
4139 5348 0.039798 TACTTCGATACGCGGGATGC 60.040 55.000 12.47 0.00 41.33 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 6.417191 TTCTTTGAATCCGTTAAATCTCCG 57.583 37.500 0.00 0.00 0.00 4.63
57 58 6.996282 TCTAGGAACTTTTCTTTGAATCCGTT 59.004 34.615 0.00 0.00 41.75 4.44
217 223 9.986833 AAAACTGAACATTTTTAATGCTTGAAC 57.013 25.926 2.02 0.00 0.00 3.18
476 486 9.511144 AGTTTGTTCGGTTTTAATAGTTTCTTG 57.489 29.630 0.00 0.00 0.00 3.02
488 498 3.759618 TCTTCACCAGTTTGTTCGGTTTT 59.240 39.130 0.00 0.00 0.00 2.43
565 575 1.860641 TCCTCCTATTTGTCGCCTGA 58.139 50.000 0.00 0.00 0.00 3.86
566 576 2.918712 ATCCTCCTATTTGTCGCCTG 57.081 50.000 0.00 0.00 0.00 4.85
567 577 3.545703 CAAATCCTCCTATTTGTCGCCT 58.454 45.455 0.00 0.00 40.44 5.52
568 578 2.618709 CCAAATCCTCCTATTTGTCGCC 59.381 50.000 8.13 0.00 42.68 5.54
571 581 2.033424 GCGCCAAATCCTCCTATTTGTC 59.967 50.000 0.00 0.00 42.68 3.18
572 582 2.024414 GCGCCAAATCCTCCTATTTGT 58.976 47.619 0.00 0.00 42.68 2.83
580 591 1.429423 CTTTCGGCGCCAAATCCTC 59.571 57.895 28.98 0.00 0.00 3.71
652 663 0.994995 CAGCCAACTCATCTCGTTCG 59.005 55.000 0.00 0.00 0.00 3.95
656 667 1.446907 AAAGCAGCCAACTCATCTCG 58.553 50.000 0.00 0.00 0.00 4.04
659 670 4.866486 CCAATTAAAAGCAGCCAACTCATC 59.134 41.667 0.00 0.00 0.00 2.92
668 679 7.985476 TCTACTAATGTCCAATTAAAAGCAGC 58.015 34.615 0.00 0.00 0.00 5.25
670 681 7.067008 GCCTCTACTAATGTCCAATTAAAAGCA 59.933 37.037 0.00 0.00 0.00 3.91
681 692 1.694696 CCCCAGCCTCTACTAATGTCC 59.305 57.143 0.00 0.00 0.00 4.02
709 720 7.198390 CGTATCCTACGTAATCTTCCTTTTCA 58.802 38.462 0.00 0.00 46.41 2.69
725 736 4.531332 CGTAAGGCTGTTACGTATCCTAC 58.469 47.826 18.16 0.00 41.79 3.18
741 752 6.128391 TGCAAAAATGCTAGACTTACGTAAGG 60.128 38.462 32.63 19.11 37.41 2.69
745 756 5.880054 ATGCAAAAATGCTAGACTTACGT 57.120 34.783 0.00 0.00 35.49 3.57
793 804 0.690762 ACCGTGCAGGGTCTTATTGT 59.309 50.000 25.10 0.00 46.96 2.71
919 931 1.489230 ACCGGTGAGGAGACTGTTTTT 59.511 47.619 6.12 0.00 44.43 1.94
1086 1100 5.108517 CCTAAACACAGAGATGAGAGAAGC 58.891 45.833 0.00 0.00 0.00 3.86
1087 1101 6.071672 TGACCTAAACACAGAGATGAGAGAAG 60.072 42.308 0.00 0.00 0.00 2.85
1100 1114 0.104487 TTCCGCGTGACCTAAACACA 59.896 50.000 4.92 0.00 38.04 3.72
1142 1158 4.953868 CAACCGACACGACGCCCA 62.954 66.667 0.00 0.00 0.00 5.36
1359 1375 2.862541 CAGGACTCAACCCACAAATCA 58.137 47.619 0.00 0.00 0.00 2.57
1360 1376 1.541588 GCAGGACTCAACCCACAAATC 59.458 52.381 0.00 0.00 0.00 2.17
1409 1425 7.704472 ACGCAATCAACAACAAGAAAAATTCTA 59.296 29.630 0.00 0.00 39.61 2.10
1480 1502 4.657436 ATGCGGTCTTACCAAAACAAAA 57.343 36.364 0.00 0.00 38.47 2.44
1481 1503 5.968528 ATATGCGGTCTTACCAAAACAAA 57.031 34.783 0.00 0.00 38.47 2.83
1482 1504 5.241949 ACAATATGCGGTCTTACCAAAACAA 59.758 36.000 0.00 0.00 38.47 2.83
1483 1505 4.762765 ACAATATGCGGTCTTACCAAAACA 59.237 37.500 0.00 0.00 38.47 2.83
1484 1506 5.092781 CACAATATGCGGTCTTACCAAAAC 58.907 41.667 0.00 0.00 38.47 2.43
1485 1507 5.004448 TCACAATATGCGGTCTTACCAAAA 58.996 37.500 0.00 0.00 38.47 2.44
1503 1525 9.466497 AATTAAATCTCTCTTGCCTTATCACAA 57.534 29.630 0.00 0.00 0.00 3.33
1594 1616 6.461509 CCCCAAGCAGAATCATGTTTAATACC 60.462 42.308 0.00 0.00 0.00 2.73
1619 1641 7.971722 ACAAAACAAATACTATAAACGCCATCC 59.028 33.333 0.00 0.00 0.00 3.51
1800 1822 3.181483 CCTGTACCATAACAGTACGACCC 60.181 52.174 3.56 0.00 44.45 4.46
1930 1960 2.105477 AGTGAGAATGGTGCTTGAGTGT 59.895 45.455 0.00 0.00 0.00 3.55
1951 1981 9.783256 GAAAAAGAAGCTTGTAAACAGTAAAGA 57.217 29.630 2.10 0.00 0.00 2.52
2039 2070 5.779241 TTCCAAGATCCTTTATGTCCACT 57.221 39.130 0.00 0.00 0.00 4.00
2101 2132 5.012148 CCTCGGGAGATAAACATATCCACTT 59.988 44.000 0.00 0.00 38.80 3.16
2117 2148 2.683362 GCTTTAACCAATTCCTCGGGAG 59.317 50.000 0.00 0.00 31.21 4.30
2121 2152 3.751175 TGACTGCTTTAACCAATTCCTCG 59.249 43.478 0.00 0.00 0.00 4.63
2439 2470 2.985847 GGTGGTGCAGGAACAGGC 60.986 66.667 0.00 0.00 0.00 4.85
2530 2561 2.627699 TCTCATTCTTTGGGTTGTTGGC 59.372 45.455 0.00 0.00 0.00 4.52
2590 2621 5.635278 TGATTGATTGCAAGATAGGGAGA 57.365 39.130 4.94 0.00 37.45 3.71
2640 2671 7.502226 ACTTTGTAATGACACTTCATGGAGAAA 59.498 33.333 8.39 0.00 42.00 2.52
2712 2743 8.698210 TCGAATATAACACCTGTTAACTATGGT 58.302 33.333 7.22 9.52 42.93 3.55
2752 2786 3.313526 CAGAATGGCCATAACTCCTTTCG 59.686 47.826 21.15 5.12 39.85 3.46
2767 2801 7.664731 ACTTCATAATCTAGATTGGCAGAATGG 59.335 37.037 25.22 14.36 32.00 3.16
2805 2839 9.102757 GAGAGCATCAACAATCTTTACAGAATA 57.897 33.333 0.00 0.00 37.82 1.75
2810 2844 6.936335 TCTTGAGAGCATCAACAATCTTTACA 59.064 34.615 0.59 0.00 43.09 2.41
2820 2854 3.940221 AGAAGCATCTTGAGAGCATCAAC 59.060 43.478 0.59 0.00 43.09 3.18
2875 2909 1.672881 CCTTCAACGCAGGATGATTCC 59.327 52.381 0.00 0.00 39.69 3.01
2876 2910 1.672881 CCCTTCAACGCAGGATGATTC 59.327 52.381 0.00 0.00 39.69 2.52
2877 2911 1.683011 CCCCTTCAACGCAGGATGATT 60.683 52.381 0.00 0.00 39.69 2.57
2878 2912 0.107017 CCCCTTCAACGCAGGATGAT 60.107 55.000 0.00 0.00 39.69 2.45
2879 2913 1.299648 CCCCTTCAACGCAGGATGA 59.700 57.895 0.00 0.00 39.69 2.92
2880 2914 1.002134 ACCCCTTCAACGCAGGATG 60.002 57.895 0.00 0.00 40.87 3.51
2881 2915 1.002134 CACCCCTTCAACGCAGGAT 60.002 57.895 0.00 0.00 32.41 3.24
2882 2916 2.429930 CACCCCTTCAACGCAGGA 59.570 61.111 0.00 0.00 32.41 3.86
2883 2917 2.672996 CCACCCCTTCAACGCAGG 60.673 66.667 0.00 0.00 0.00 4.85
2884 2918 1.672356 CTCCACCCCTTCAACGCAG 60.672 63.158 0.00 0.00 0.00 5.18
2888 2922 3.084786 CAGATTTCTCCACCCCTTCAAC 58.915 50.000 0.00 0.00 0.00 3.18
2889 2923 2.716424 ACAGATTTCTCCACCCCTTCAA 59.284 45.455 0.00 0.00 0.00 2.69
2895 2929 5.946377 ACAAATAGAACAGATTTCTCCACCC 59.054 40.000 0.00 0.00 0.00 4.61
2896 2930 7.362142 GGAACAAATAGAACAGATTTCTCCACC 60.362 40.741 0.00 0.00 31.39 4.61
2980 3015 4.152402 CACACAGGCATAACAACACTACTC 59.848 45.833 0.00 0.00 0.00 2.59
3047 3082 7.649306 CACAAGAGGAAAAAGAAATAACCTGTG 59.351 37.037 0.00 0.00 0.00 3.66
3236 3271 3.714798 ACTTCAAAGGTCTACCAACAGGA 59.285 43.478 1.26 0.00 38.89 3.86
3367 3402 8.462016 GCAAGTAAAGATTCCATTCAACTACAT 58.538 33.333 0.00 0.00 0.00 2.29
3684 3732 0.601057 ATCCTTTGCGTTTTTCCGGG 59.399 50.000 0.00 0.00 0.00 5.73
3685 3733 1.539827 AGATCCTTTGCGTTTTTCCGG 59.460 47.619 0.00 0.00 0.00 5.14
3686 3734 2.989422 AGATCCTTTGCGTTTTTCCG 57.011 45.000 0.00 0.00 0.00 4.30
3689 3737 3.727726 CCCAAAGATCCTTTGCGTTTTT 58.272 40.909 12.53 0.00 0.00 1.94
3709 3757 6.539826 CCCCATCTTTTCAATAAAATGAAGCC 59.460 38.462 0.00 0.00 40.21 4.35
3712 3760 8.663209 TCTCCCCATCTTTTCAATAAAATGAA 57.337 30.769 0.00 0.00 35.41 2.57
3719 3767 6.884472 TGTACTCTCCCCATCTTTTCAATA 57.116 37.500 0.00 0.00 0.00 1.90
3762 3810 1.067142 TGAGAGCGTGACCCATGTAAC 60.067 52.381 0.00 0.00 0.00 2.50
3763 3811 1.262417 TGAGAGCGTGACCCATGTAA 58.738 50.000 0.00 0.00 0.00 2.41
3764 3812 1.262417 TTGAGAGCGTGACCCATGTA 58.738 50.000 0.00 0.00 0.00 2.29
3810 3858 2.812613 GCACAGTGGCTTAGGGTTGTTA 60.813 50.000 1.84 0.00 0.00 2.41
3854 5057 4.742438 TGTAGAAAAGTGAATTCGTGGC 57.258 40.909 0.04 0.00 32.04 5.01
3871 5074 5.351465 AGTTTCAGGCGTGAACATATTGTAG 59.649 40.000 20.76 0.00 42.60 2.74
3875 5078 5.705609 AAAGTTTCAGGCGTGAACATATT 57.294 34.783 20.76 11.02 42.60 1.28
3984 5189 0.530288 GTGGCAGAGACCAGAGACTC 59.470 60.000 0.00 0.00 41.46 3.36
3992 5197 0.103208 CGTATGAGGTGGCAGAGACC 59.897 60.000 0.00 0.00 0.00 3.85
4021 5226 0.388294 GGGACGGAGGGAGTATTTCG 59.612 60.000 0.00 0.00 0.00 3.46
4106 5315 9.354544 GCGTATCGAAGTATCTTTGTTATTTTC 57.645 33.333 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.