Multiple sequence alignment - TraesCS1D01G217200

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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 TraesCS1D01G217200 chr1D 100.000 4079 0 0 1 4079 302816445 302820523 0 7533
1 TraesCS1D01G217200 chr1B 93.829 4116 153 40 1 4077 409626912 409630965 0 6100
2 TraesCS1D01G217200 chr1A 93.508 4051 161 46 68 4077 377426618 377430607 0 5930


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 TraesCS1D01G217200 chr1D 302816445 302820523 4078 False 7533 7533 100.000 1 4079 1 chr1D.!!$F1 4078
1 TraesCS1D01G217200 chr1B 409626912 409630965 4053 False 6100 6100 93.829 1 4077 1 chr1B.!!$F1 4076
2 TraesCS1D01G217200 chr1A 377426618 377430607 3989 False 5930 5930 93.508 68 4077 1 chr1A.!!$F1 4009

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
472 495 0.179094 TTGTTGTCTTGGCTCGTCGT 60.179 50.000 0.0 0.0 0.0 4.34 F
474 497 0.232303 GTTGTCTTGGCTCGTCGTTG 59.768 55.000 0.0 0.0 0.0 4.10 F
516 539 0.465705 ATCCCTGCGTATGACCACTG 59.534 55.000 0.0 0.0 0.0 3.66 F
517 540 0.613572 TCCCTGCGTATGACCACTGA 60.614 55.000 0.0 0.0 0.0 3.41 F
518 541 0.465705 CCCTGCGTATGACCACTGAT 59.534 55.000 0.0 0.0 0.0 2.90 F
520 543 1.136891 CCTGCGTATGACCACTGATCA 59.863 52.381 0.0 0.0 0.0 2.92 F
1170 1194 1.327303 GATCCATCAGCCTCTCTCGT 58.673 55.000 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 1620 0.818296 TCTAGCCTCCGAGAAAGCAC 59.182 55.000 0.0 0.0 0.00 4.40 R
2457 2490 1.278985 TCAGGTGCTCCCAGTTACATG 59.721 52.381 0.0 0.0 34.66 3.21 R
2743 2776 1.202855 GCCAGTGATGCCATGATACCT 60.203 52.381 0.0 0.0 0.00 3.08 R
2873 2907 4.759693 TGCCATTAAGAACAGTTGTCGAAT 59.240 37.500 0.0 0.0 0.00 3.34 R
2977 3011 3.623510 GCATAGACAAAGGCTCTACCAAC 59.376 47.826 0.0 0.0 43.14 3.77 R
2985 3019 1.747709 CTGCAGCATAGACAAAGGCT 58.252 50.000 0.0 0.0 36.99 4.58 R
3093 3127 0.038801 GCCAAAGCCTTCAAGTCTGC 60.039 55.000 0.0 0.0 0.00 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
40 41 1.766143 GCATGGCTCGCGACCTTTAG 61.766 60.000 22.40 7.69 0.00 1.85
61 62 1.823295 GAGTAGAAGGATGCGCCCA 59.177 57.895 4.18 0.00 37.37 5.36
95 96 3.018840 GCGAAAAACGACCGGCGAT 62.019 57.895 22.10 9.85 45.77 4.58
99 100 3.894547 AAAACGACCGGCGATGGCT 62.895 57.895 22.10 0.00 44.57 4.75
313 314 0.534877 AGCAGACGCCACATGTTTCA 60.535 50.000 0.00 0.00 39.83 2.69
320 321 1.535028 CGCCACATGTTTCACTAAGCA 59.465 47.619 0.00 0.00 0.00 3.91
321 322 2.162208 CGCCACATGTTTCACTAAGCAT 59.838 45.455 0.00 0.00 37.04 3.79
342 343 1.200716 CGTGCTGATTGAAATGGTGCT 59.799 47.619 0.00 0.00 0.00 4.40
386 409 5.801531 TTCACTGGTTAGTTAGCTCTTCA 57.198 39.130 0.00 0.00 34.07 3.02
405 428 6.472887 TCTTCAGTTAAATTCTAGTGGTGGG 58.527 40.000 0.00 0.00 0.00 4.61
465 488 3.193267 TGATTGGCTATTGTTGTCTTGGC 59.807 43.478 0.00 0.00 0.00 4.52
466 489 2.584835 TGGCTATTGTTGTCTTGGCT 57.415 45.000 0.00 0.00 0.00 4.75
467 490 2.436417 TGGCTATTGTTGTCTTGGCTC 58.564 47.619 0.00 0.00 0.00 4.70
468 491 1.398390 GGCTATTGTTGTCTTGGCTCG 59.602 52.381 0.00 0.00 0.00 5.03
470 493 2.094417 GCTATTGTTGTCTTGGCTCGTC 59.906 50.000 0.00 0.00 0.00 4.20
472 495 0.179094 TTGTTGTCTTGGCTCGTCGT 60.179 50.000 0.00 0.00 0.00 4.34
474 497 0.232303 GTTGTCTTGGCTCGTCGTTG 59.768 55.000 0.00 0.00 0.00 4.10
484 507 1.915965 GCTCGTCGTTGTTGCTTTCAC 60.916 52.381 0.00 0.00 0.00 3.18
485 508 1.593006 CTCGTCGTTGTTGCTTTCACT 59.407 47.619 0.00 0.00 0.00 3.41
487 510 2.417239 TCGTCGTTGTTGCTTTCACTTT 59.583 40.909 0.00 0.00 0.00 2.66
488 511 2.776225 CGTCGTTGTTGCTTTCACTTTC 59.224 45.455 0.00 0.00 0.00 2.62
489 512 3.726486 CGTCGTTGTTGCTTTCACTTTCA 60.726 43.478 0.00 0.00 0.00 2.69
511 534 1.339097 ACCCTATCCCTGCGTATGAC 58.661 55.000 0.00 0.00 0.00 3.06
516 539 0.465705 ATCCCTGCGTATGACCACTG 59.534 55.000 0.00 0.00 0.00 3.66
517 540 0.613572 TCCCTGCGTATGACCACTGA 60.614 55.000 0.00 0.00 0.00 3.41
518 541 0.465705 CCCTGCGTATGACCACTGAT 59.534 55.000 0.00 0.00 0.00 2.90
520 543 1.136891 CCTGCGTATGACCACTGATCA 59.863 52.381 0.00 0.00 0.00 2.92
522 545 1.824852 TGCGTATGACCACTGATCAGT 59.175 47.619 22.89 22.89 43.61 3.41
523 546 3.020984 TGCGTATGACCACTGATCAGTA 58.979 45.455 27.44 13.12 40.20 2.74
524 547 3.445805 TGCGTATGACCACTGATCAGTAA 59.554 43.478 27.44 13.97 40.20 2.24
525 548 4.099419 TGCGTATGACCACTGATCAGTAAT 59.901 41.667 27.44 18.19 40.20 1.89
526 549 5.050490 GCGTATGACCACTGATCAGTAATT 58.950 41.667 27.44 14.56 40.20 1.40
527 550 5.175856 GCGTATGACCACTGATCAGTAATTC 59.824 44.000 27.44 21.59 40.20 2.17
529 552 6.419116 CGTATGACCACTGATCAGTAATTCAG 59.581 42.308 27.44 14.04 43.97 3.02
575 598 3.025978 CCATGTGTATGTGCCAGGAATT 58.974 45.455 0.00 0.00 32.21 2.17
601 624 5.356882 TTTTCAGAGTTCTTTATGTGCCG 57.643 39.130 0.00 0.00 0.00 5.69
607 630 3.994392 GAGTTCTTTATGTGCCGTTCAGA 59.006 43.478 0.00 0.00 0.00 3.27
609 632 4.819630 AGTTCTTTATGTGCCGTTCAGAAA 59.180 37.500 0.00 0.00 0.00 2.52
610 633 4.742438 TCTTTATGTGCCGTTCAGAAAC 57.258 40.909 0.00 0.00 0.00 2.78
612 635 4.213270 TCTTTATGTGCCGTTCAGAAACTG 59.787 41.667 0.00 0.00 32.95 3.16
614 637 2.254546 TGTGCCGTTCAGAAACTGAT 57.745 45.000 2.30 0.00 40.39 2.90
615 638 2.143122 TGTGCCGTTCAGAAACTGATC 58.857 47.619 2.30 1.71 40.39 2.92
616 639 2.143122 GTGCCGTTCAGAAACTGATCA 58.857 47.619 0.00 0.00 40.39 2.92
617 640 2.158449 GTGCCGTTCAGAAACTGATCAG 59.842 50.000 21.37 21.37 40.39 2.90
618 641 2.224281 TGCCGTTCAGAAACTGATCAGT 60.224 45.455 22.89 22.89 40.39 3.41
619 642 3.006430 TGCCGTTCAGAAACTGATCAGTA 59.994 43.478 28.10 10.00 40.39 2.74
620 643 3.368236 GCCGTTCAGAAACTGATCAGTAC 59.632 47.826 28.10 22.79 40.39 2.73
621 644 4.556233 CCGTTCAGAAACTGATCAGTACA 58.444 43.478 28.10 8.22 40.39 2.90
622 645 5.171476 CCGTTCAGAAACTGATCAGTACAT 58.829 41.667 28.10 17.21 40.39 2.29
623 646 6.330278 CCGTTCAGAAACTGATCAGTACATA 58.670 40.000 28.10 13.81 40.39 2.29
624 647 6.811665 CCGTTCAGAAACTGATCAGTACATAA 59.188 38.462 28.10 17.86 40.39 1.90
625 648 7.201444 CCGTTCAGAAACTGATCAGTACATAAC 60.201 40.741 28.10 24.36 40.39 1.89
626 649 7.201444 CGTTCAGAAACTGATCAGTACATAACC 60.201 40.741 28.10 13.33 40.39 2.85
627 650 7.239763 TCAGAAACTGATCAGTACATAACCA 57.760 36.000 28.10 5.77 41.58 3.67
628 651 7.323420 TCAGAAACTGATCAGTACATAACCAG 58.677 38.462 28.10 11.44 41.58 4.00
631 654 5.420725 ACTGATCAGTACATAACCAGCAA 57.579 39.130 26.87 0.00 40.43 3.91
634 657 5.178061 TGATCAGTACATAACCAGCAACTG 58.822 41.667 0.00 0.00 36.52 3.16
667 690 6.045955 TCACCTTTTGTTAACATTTTGAGCC 58.954 36.000 9.56 0.00 0.00 4.70
673 696 6.656632 TTGTTAACATTTTGAGCCATGGTA 57.343 33.333 14.67 0.00 0.00 3.25
674 697 6.019779 TGTTAACATTTTGAGCCATGGTAC 57.980 37.500 14.67 8.43 0.00 3.34
725 748 5.733373 GCTGGGCACTACTAATATGTTTTGC 60.733 44.000 0.00 0.00 0.00 3.68
740 763 1.974265 TTTGCACTCGTTGGGATTGA 58.026 45.000 0.00 0.00 0.00 2.57
744 767 2.000447 GCACTCGTTGGGATTGACTAC 59.000 52.381 0.00 0.00 0.00 2.73
902 926 7.068593 TGGTTCCTATTGCTTCCTGATTTTATG 59.931 37.037 0.00 0.00 0.00 1.90
909 933 5.693961 TGCTTCCTGATTTTATGAGGCATA 58.306 37.500 0.00 0.00 35.29 3.14
910 934 6.128486 TGCTTCCTGATTTTATGAGGCATAA 58.872 36.000 0.00 0.00 35.29 1.90
920 944 2.228545 TGAGGCATAAATTGGTGGCA 57.771 45.000 16.00 0.00 42.73 4.92
924 948 4.122046 GAGGCATAAATTGGTGGCAATTC 58.878 43.478 16.00 4.92 42.73 2.17
1170 1194 1.327303 GATCCATCAGCCTCTCTCGT 58.673 55.000 0.00 0.00 0.00 4.18
1391 1415 1.407851 CCATGGCTACAGCTCACATGT 60.408 52.381 0.00 0.00 41.70 3.21
1459 1483 2.012673 GCTCATCAGGCAAGGTACAAG 58.987 52.381 0.00 0.00 0.00 3.16
1497 1521 5.886992 TGAGTGATTGCTTGCAATTATCAG 58.113 37.500 19.90 0.00 0.00 2.90
1596 1620 5.389859 TTTCCTGCAGGTTGAACAATATG 57.610 39.130 31.58 1.87 36.34 1.78
1738 1765 8.552034 GTGATCTTCCTTAGTGTACATAAATGC 58.448 37.037 0.00 0.00 0.00 3.56
1806 1837 6.014327 ACCCATGCATTCAGAAAACATTTACT 60.014 34.615 0.00 0.00 0.00 2.24
2029 2061 6.126911 TGGGCTATACTGACACATGTTAATGA 60.127 38.462 0.00 0.00 37.24 2.57
2093 2125 5.886609 TGGTTTGGGATCATCTTTAAGACA 58.113 37.500 0.00 0.00 0.00 3.41
2292 2324 8.136165 AGTGCTATTAGTCCAGAATTAGTTACG 58.864 37.037 0.00 0.00 0.00 3.18
2457 2490 7.631717 AGGAAAATAGTTCAATAGGAAGCAC 57.368 36.000 0.00 0.00 35.82 4.40
2743 2776 1.541147 GTAGCCAATGTTCTTGCTGCA 59.459 47.619 0.00 0.00 36.60 4.41
2873 2907 6.426937 GTCTTTCTGTAGGTGAATACAAAGCA 59.573 38.462 0.00 0.00 35.32 3.91
2985 3019 1.972198 CAGCGGACAGGTTGGTAGA 59.028 57.895 0.00 0.00 0.00 2.59
3093 3127 9.888878 CATTACCAATAGCTTCATGAAGTATTG 57.111 33.333 32.57 32.57 39.19 1.90
3172 3206 6.642540 CGCAATTCTCAGCATACATAGTTAGA 59.357 38.462 0.00 0.00 0.00 2.10
3376 3417 7.806487 GCATATGAAATGAATGTATCACCTGTG 59.194 37.037 6.97 0.00 41.93 3.66
3423 3465 4.688879 TGTTTATGGAGTAGCTTTGTCACG 59.311 41.667 0.00 0.00 0.00 4.35
3430 3472 2.224079 AGTAGCTTTGTCACGCATGTTG 59.776 45.455 0.00 0.00 0.00 3.33
3438 3480 1.194547 GTCACGCATGTTGGTACACAG 59.805 52.381 0.00 0.00 39.29 3.66
3556 3598 4.968259 ACACAACTACATGCTAACCTGAA 58.032 39.130 0.00 0.00 0.00 3.02
3597 3640 6.169800 TGCTGTAATGCAAGTATCTGTACAA 58.830 36.000 0.00 0.00 40.29 2.41
3645 3688 7.677454 TGCAGATACAATATGGATGATGAAC 57.323 36.000 0.00 0.00 0.00 3.18
3661 3704 9.561069 GGATGATGAACTATTTGTACCTACAAT 57.439 33.333 0.00 0.00 44.72 2.71
3675 3718 9.743057 TTGTACCTACAATTTTTCAAGTGAATG 57.257 29.630 0.00 0.00 40.93 2.67
3676 3719 7.865385 TGTACCTACAATTTTTCAAGTGAATGC 59.135 33.333 0.00 0.00 32.13 3.56
3677 3720 6.815089 ACCTACAATTTTTCAAGTGAATGCA 58.185 32.000 0.00 0.00 32.13 3.96
3678 3721 6.925165 ACCTACAATTTTTCAAGTGAATGCAG 59.075 34.615 0.00 0.00 32.13 4.41
3679 3722 5.662211 ACAATTTTTCAAGTGAATGCAGC 57.338 34.783 0.00 0.00 32.13 5.25
3680 3723 5.117584 ACAATTTTTCAAGTGAATGCAGCA 58.882 33.333 0.00 0.00 32.13 4.41
3681 3724 5.585445 ACAATTTTTCAAGTGAATGCAGCAA 59.415 32.000 0.00 0.00 32.13 3.91
3682 3725 6.261381 ACAATTTTTCAAGTGAATGCAGCAAT 59.739 30.769 0.00 0.00 32.13 3.56
3683 3726 5.910637 TTTTTCAAGTGAATGCAGCAATC 57.089 34.783 0.00 0.00 33.54 2.67
3725 3771 2.035530 AGTAATGCTGAGCTTCCTGC 57.964 50.000 5.83 0.00 43.29 4.85
3767 3821 4.513318 TGTGACATGACAAAGCGATGTTTA 59.487 37.500 0.00 0.00 32.57 2.01
3773 3827 5.743026 TGACAAAGCGATGTTTACTTGAA 57.257 34.783 0.00 0.00 32.57 2.69
3800 3854 6.801539 ATTTGTGAAATCACTTCTTCGCTA 57.198 33.333 14.15 0.00 46.55 4.26
3825 3879 2.550487 TGGTATGCCAAGTCGCAAC 58.450 52.632 0.00 0.00 43.24 4.17
3864 3921 7.123355 AGAATATCTGTTCCTCTTCCTTCAG 57.877 40.000 0.00 0.00 0.00 3.02
3869 3926 4.022242 TCTGTTCCTCTTCCTTCAGTTACG 60.022 45.833 0.00 0.00 0.00 3.18
3895 3952 1.379044 CAGCAGAACCCCCATGTCC 60.379 63.158 0.00 0.00 0.00 4.02
3929 3986 3.627123 CACCACCGATTCTTTATGATGCA 59.373 43.478 0.00 0.00 0.00 3.96
3931 3988 4.889409 ACCACCGATTCTTTATGATGCAAT 59.111 37.500 0.00 0.00 0.00 3.56
3934 3991 6.267817 CACCGATTCTTTATGATGCAATTGT 58.732 36.000 7.40 0.00 0.00 2.71
3937 3994 8.632679 ACCGATTCTTTATGATGCAATTGTTAT 58.367 29.630 7.40 2.19 0.00 1.89
3941 3998 9.897744 ATTCTTTATGATGCAATTGTTATACCG 57.102 29.630 7.40 0.00 0.00 4.02
3943 4000 3.600717 TGATGCAATTGTTATACCGCG 57.399 42.857 7.40 0.00 0.00 6.46
3957 4014 1.153449 CCGCGCTTGTTCAGGGATA 60.153 57.895 5.56 0.00 37.67 2.59
3958 4015 0.532862 CCGCGCTTGTTCAGGGATAT 60.533 55.000 5.56 0.00 37.67 1.63
3959 4016 0.583438 CGCGCTTGTTCAGGGATATG 59.417 55.000 5.56 0.00 37.67 1.78
3960 4017 1.806247 CGCGCTTGTTCAGGGATATGA 60.806 52.381 5.56 0.00 37.67 2.15
3962 4019 2.225019 GCGCTTGTTCAGGGATATGATG 59.775 50.000 0.00 0.00 37.67 3.07
3963 4020 2.225019 CGCTTGTTCAGGGATATGATGC 59.775 50.000 0.00 0.00 37.67 3.91
3964 4021 3.216800 GCTTGTTCAGGGATATGATGCA 58.783 45.455 0.00 0.00 0.00 3.96
3965 4022 3.004106 GCTTGTTCAGGGATATGATGCAC 59.996 47.826 0.00 0.00 0.00 4.57
3966 4023 3.213206 TGTTCAGGGATATGATGCACC 57.787 47.619 0.00 0.00 0.00 5.01
3967 4024 2.779430 TGTTCAGGGATATGATGCACCT 59.221 45.455 0.00 0.00 0.00 4.00
3983 4040 1.967066 CACCTGTCCAGTCTCTGTTCT 59.033 52.381 0.00 0.00 0.00 3.01
4019 4076 3.111098 CTGTGCAAAGAACAAACAGCTC 58.889 45.455 0.00 0.00 32.61 4.09
4024 4081 3.065925 GCAAAGAACAAACAGCTCTCACT 59.934 43.478 0.00 0.00 0.00 3.41
4025 4082 4.595116 CAAAGAACAAACAGCTCTCACTG 58.405 43.478 0.00 0.00 43.59 3.66
4051 4109 9.813080 GTGACAAAGTTCTTATCACAAGTAATC 57.187 33.333 17.43 0.00 39.57 1.75
4077 4135 2.097825 GCCTGAGCATCCTTCAACATT 58.902 47.619 0.00 0.00 39.53 2.71
4078 4136 2.159282 GCCTGAGCATCCTTCAACATTG 60.159 50.000 0.00 0.00 39.53 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.270305 GCGAGCCATGCCTGTATCTTA 60.270 52.381 0.00 0.00 0.00 2.10
36 37 3.488721 GCGCATCCTTCTACTCGTCTAAA 60.489 47.826 0.30 0.00 0.00 1.85
40 41 0.595310 GGCGCATCCTTCTACTCGTC 60.595 60.000 10.83 0.00 0.00 4.20
320 321 2.159338 GCACCATTTCAATCAGCACGAT 60.159 45.455 0.00 0.00 35.12 3.73
321 322 1.199789 GCACCATTTCAATCAGCACGA 59.800 47.619 0.00 0.00 0.00 4.35
386 409 4.600111 TGGACCCACCACTAGAATTTAACT 59.400 41.667 0.00 0.00 44.64 2.24
465 488 1.593006 AGTGAAAGCAACAACGACGAG 59.407 47.619 0.00 0.00 0.00 4.18
466 489 1.647346 AGTGAAAGCAACAACGACGA 58.353 45.000 0.00 0.00 0.00 4.20
467 490 2.452006 AAGTGAAAGCAACAACGACG 57.548 45.000 0.00 0.00 0.00 5.12
468 491 3.753842 TGAAAGTGAAAGCAACAACGAC 58.246 40.909 0.00 0.00 0.00 4.34
484 507 2.224066 CGCAGGGATAGGGTACTGAAAG 60.224 54.545 0.00 0.00 42.29 2.62
485 508 1.760613 CGCAGGGATAGGGTACTGAAA 59.239 52.381 0.00 0.00 32.86 2.69
487 510 0.260816 ACGCAGGGATAGGGTACTGA 59.739 55.000 0.00 0.00 32.86 3.41
488 511 1.991121 TACGCAGGGATAGGGTACTG 58.009 55.000 0.00 0.00 33.89 2.74
489 512 2.109480 TCATACGCAGGGATAGGGTACT 59.891 50.000 0.00 0.00 37.25 2.73
529 552 9.809096 GGGGTACTGAACTAAAACTAACTATAC 57.191 37.037 0.00 0.00 0.00 1.47
530 553 9.545928 TGGGGTACTGAACTAAAACTAACTATA 57.454 33.333 0.00 0.00 0.00 1.31
531 554 8.439964 TGGGGTACTGAACTAAAACTAACTAT 57.560 34.615 0.00 0.00 0.00 2.12
532 555 7.854166 TGGGGTACTGAACTAAAACTAACTA 57.146 36.000 0.00 0.00 0.00 2.24
533 556 6.752285 TGGGGTACTGAACTAAAACTAACT 57.248 37.500 0.00 0.00 0.00 2.24
534 557 6.938596 ACATGGGGTACTGAACTAAAACTAAC 59.061 38.462 0.00 0.00 0.00 2.34
535 558 6.938030 CACATGGGGTACTGAACTAAAACTAA 59.062 38.462 0.00 0.00 0.00 2.24
536 559 6.043474 ACACATGGGGTACTGAACTAAAACTA 59.957 38.462 0.00 0.00 0.00 2.24
537 560 5.163131 ACACATGGGGTACTGAACTAAAACT 60.163 40.000 0.00 0.00 0.00 2.66
538 561 5.067954 ACACATGGGGTACTGAACTAAAAC 58.932 41.667 0.00 0.00 0.00 2.43
539 562 5.313280 ACACATGGGGTACTGAACTAAAA 57.687 39.130 0.00 0.00 0.00 1.52
540 563 4.986054 ACACATGGGGTACTGAACTAAA 57.014 40.909 0.00 0.00 0.00 1.85
601 624 7.602644 TGGTTATGTACTGATCAGTTTCTGAAC 59.397 37.037 32.14 24.99 44.04 3.18
607 630 5.804639 TGCTGGTTATGTACTGATCAGTTT 58.195 37.500 32.14 19.35 42.54 2.66
609 632 5.046304 AGTTGCTGGTTATGTACTGATCAGT 60.046 40.000 30.11 30.11 45.02 3.41
610 633 5.292834 CAGTTGCTGGTTATGTACTGATCAG 59.707 44.000 21.37 21.37 36.07 2.90
612 635 5.063944 CACAGTTGCTGGTTATGTACTGATC 59.936 44.000 0.00 0.00 37.15 2.92
614 637 4.202315 ACACAGTTGCTGGTTATGTACTGA 60.202 41.667 0.00 0.00 37.15 3.41
615 638 4.065088 ACACAGTTGCTGGTTATGTACTG 58.935 43.478 0.00 0.00 39.03 2.74
616 639 4.351874 ACACAGTTGCTGGTTATGTACT 57.648 40.909 0.00 0.00 35.51 2.73
617 640 6.737254 ATAACACAGTTGCTGGTTATGTAC 57.263 37.500 15.44 0.00 36.95 2.90
618 641 7.753309 AAATAACACAGTTGCTGGTTATGTA 57.247 32.000 16.22 1.51 37.61 2.29
619 642 6.648879 AAATAACACAGTTGCTGGTTATGT 57.351 33.333 16.22 11.75 37.61 2.29
620 643 7.114811 GTGAAAATAACACAGTTGCTGGTTATG 59.885 37.037 16.22 4.38 37.61 1.90
621 644 7.145323 GTGAAAATAACACAGTTGCTGGTTAT 58.855 34.615 12.70 12.70 38.34 1.89
622 645 6.460399 GGTGAAAATAACACAGTTGCTGGTTA 60.460 38.462 0.00 6.82 39.65 2.85
623 646 5.348164 GTGAAAATAACACAGTTGCTGGTT 58.652 37.500 1.08 5.07 38.05 3.67
624 647 4.202111 GGTGAAAATAACACAGTTGCTGGT 60.202 41.667 0.00 0.00 39.65 4.00
625 648 4.037923 AGGTGAAAATAACACAGTTGCTGG 59.962 41.667 0.00 0.00 39.65 4.85
626 649 5.186996 AGGTGAAAATAACACAGTTGCTG 57.813 39.130 0.00 0.00 39.65 4.41
627 650 5.852282 AAGGTGAAAATAACACAGTTGCT 57.148 34.783 0.00 0.00 39.65 3.91
628 651 6.312672 ACAAAAGGTGAAAATAACACAGTTGC 59.687 34.615 0.00 0.00 39.65 4.17
631 654 9.361315 GTTAACAAAAGGTGAAAATAACACAGT 57.639 29.630 0.00 0.00 39.65 3.55
681 704 6.183360 CCCAGCAAAGTTCAGAAAGTAAGAAA 60.183 38.462 0.00 0.00 0.00 2.52
725 748 3.056821 TCTGTAGTCAATCCCAACGAGTG 60.057 47.826 0.00 0.00 37.93 3.51
740 763 9.750125 GAAAAATCACAAATTCCTTTCTGTAGT 57.250 29.630 0.00 0.00 0.00 2.73
809 833 4.132336 GCTGAAGCTGGATCAATCACATA 58.868 43.478 0.00 0.00 38.21 2.29
819 843 1.999648 TTTGTTGGCTGAAGCTGGAT 58.000 45.000 1.74 0.00 41.70 3.41
902 926 3.825143 ATTGCCACCAATTTATGCCTC 57.175 42.857 0.00 0.00 38.49 4.70
1170 1194 1.456196 GGATCGAGTCGCCCATCTCA 61.456 60.000 7.92 0.00 0.00 3.27
1391 1415 2.427320 GTGCTGGCAGACCTGTGA 59.573 61.111 20.86 0.00 37.23 3.58
1459 1483 6.798959 GCAATCACTCAACTCAAAGTACAATC 59.201 38.462 0.00 0.00 0.00 2.67
1596 1620 0.818296 TCTAGCCTCCGAGAAAGCAC 59.182 55.000 0.00 0.00 0.00 4.40
1738 1765 2.544685 ACTTTCATCGATCTTCCGCTG 58.455 47.619 0.00 0.00 0.00 5.18
2029 2061 2.366266 AGCTGATGCACAAACATTTGGT 59.634 40.909 9.09 0.00 42.74 3.67
2093 2125 4.122776 GTTCAGATATGTGCCGAATGTCT 58.877 43.478 0.00 0.00 0.00 3.41
2292 2324 8.677148 TGATTTCCCTTGTGTCTATATTTAGC 57.323 34.615 0.00 0.00 0.00 3.09
2300 2333 7.723616 TCAAAAGAATGATTTCCCTTGTGTCTA 59.276 33.333 0.00 0.00 31.84 2.59
2347 2380 5.430886 TCATTGACGATGAACATTCCTGAT 58.569 37.500 2.65 0.00 41.73 2.90
2457 2490 1.278985 TCAGGTGCTCCCAGTTACATG 59.721 52.381 0.00 0.00 34.66 3.21
2743 2776 1.202855 GCCAGTGATGCCATGATACCT 60.203 52.381 0.00 0.00 0.00 3.08
2873 2907 4.759693 TGCCATTAAGAACAGTTGTCGAAT 59.240 37.500 0.00 0.00 0.00 3.34
2977 3011 3.623510 GCATAGACAAAGGCTCTACCAAC 59.376 47.826 0.00 0.00 43.14 3.77
2985 3019 1.747709 CTGCAGCATAGACAAAGGCT 58.252 50.000 0.00 0.00 36.99 4.58
3093 3127 0.038801 GCCAAAGCCTTCAAGTCTGC 60.039 55.000 0.00 0.00 0.00 4.26
3172 3206 8.885693 AAGCAGATAAAATTCCCTAGAAAAGT 57.114 30.769 0.00 0.00 35.09 2.66
3217 3251 1.952990 ACGCCATCATGTTCAACAACA 59.047 42.857 0.00 0.00 46.71 3.33
3376 3417 5.596845 TGGATGTTGTTTTCTTTTGCTACC 58.403 37.500 0.00 0.00 0.00 3.18
3410 3452 2.574322 CAACATGCGTGACAAAGCTAC 58.426 47.619 14.17 0.00 0.00 3.58
3423 3465 2.616376 TGTTGTCTGTGTACCAACATGC 59.384 45.455 9.66 0.00 42.41 4.06
3430 3472 3.904571 TCGTGTATGTTGTCTGTGTACC 58.095 45.455 0.00 0.00 0.00 3.34
3438 3480 5.163804 TGGTGCATAAATCGTGTATGTTGTC 60.164 40.000 0.00 0.00 32.51 3.18
3556 3598 5.280654 ACAGCAAGGAAATGTGATTTTGT 57.719 34.783 0.00 0.00 31.47 2.83
3597 3640 5.192927 TCTGTGTCCAGTTTCAGAAAATGT 58.807 37.500 19.32 0.00 39.82 2.71
3661 3704 5.603596 AGATTGCTGCATTCACTTGAAAAA 58.396 33.333 22.15 0.00 37.61 1.94
3662 3705 5.204409 AGATTGCTGCATTCACTTGAAAA 57.796 34.783 22.15 0.00 37.61 2.29
3665 3708 3.414269 TGAGATTGCTGCATTCACTTGA 58.586 40.909 22.15 0.00 0.00 3.02
3666 3709 3.842732 TGAGATTGCTGCATTCACTTG 57.157 42.857 22.15 0.00 0.00 3.16
3667 3710 4.077108 TCTTGAGATTGCTGCATTCACTT 58.923 39.130 22.15 6.02 0.00 3.16
3668 3711 3.682696 TCTTGAGATTGCTGCATTCACT 58.317 40.909 22.15 11.33 0.00 3.41
3669 3712 4.413087 CTTCTTGAGATTGCTGCATTCAC 58.587 43.478 22.15 17.47 0.00 3.18
3670 3713 3.442625 CCTTCTTGAGATTGCTGCATTCA 59.557 43.478 22.15 14.95 0.00 2.57
3671 3714 3.734293 GCCTTCTTGAGATTGCTGCATTC 60.734 47.826 14.85 14.85 0.00 2.67
3672 3715 2.165845 GCCTTCTTGAGATTGCTGCATT 59.834 45.455 1.84 0.00 0.00 3.56
3673 3716 1.749634 GCCTTCTTGAGATTGCTGCAT 59.250 47.619 1.84 0.00 0.00 3.96
3674 3717 1.171308 GCCTTCTTGAGATTGCTGCA 58.829 50.000 0.00 0.00 0.00 4.41
3675 3718 0.455005 GGCCTTCTTGAGATTGCTGC 59.545 55.000 0.00 0.00 0.00 5.25
3676 3719 1.743958 CTGGCCTTCTTGAGATTGCTG 59.256 52.381 3.32 0.00 0.00 4.41
3677 3720 1.954258 GCTGGCCTTCTTGAGATTGCT 60.954 52.381 3.32 0.00 0.00 3.91
3678 3721 0.455005 GCTGGCCTTCTTGAGATTGC 59.545 55.000 3.32 0.00 0.00 3.56
3679 3722 1.743958 CTGCTGGCCTTCTTGAGATTG 59.256 52.381 3.32 0.00 0.00 2.67
3680 3723 1.632409 TCTGCTGGCCTTCTTGAGATT 59.368 47.619 3.32 0.00 0.00 2.40
3681 3724 1.283347 TCTGCTGGCCTTCTTGAGAT 58.717 50.000 3.32 0.00 0.00 2.75
3682 3725 1.059098 TTCTGCTGGCCTTCTTGAGA 58.941 50.000 3.32 0.00 0.00 3.27
3683 3726 1.901591 TTTCTGCTGGCCTTCTTGAG 58.098 50.000 3.32 0.00 0.00 3.02
3725 3771 1.475280 CATGCCAATGGACACAGGAAG 59.525 52.381 2.05 0.00 0.00 3.46
3789 3843 6.258068 GCATACCAAGTAAATAGCGAAGAAGT 59.742 38.462 0.00 0.00 0.00 3.01
3793 3847 4.814234 TGGCATACCAAGTAAATAGCGAAG 59.186 41.667 0.00 0.00 45.37 3.79
3848 3904 3.554337 GCGTAACTGAAGGAAGAGGAACA 60.554 47.826 0.00 0.00 0.00 3.18
3886 3943 4.489771 GGACCTGCGGACATGGGG 62.490 72.222 0.00 0.00 0.00 4.96
3895 3952 2.358737 GTGGTGAAGGGACCTGCG 60.359 66.667 0.00 0.00 36.88 5.18
3929 3986 3.437395 TGAACAAGCGCGGTATAACAATT 59.563 39.130 12.91 0.00 0.00 2.32
3931 3988 2.413796 CTGAACAAGCGCGGTATAACAA 59.586 45.455 12.91 0.00 0.00 2.83
3934 3991 1.647346 CCTGAACAAGCGCGGTATAA 58.353 50.000 12.91 0.00 0.00 0.98
3937 3994 1.895020 ATCCCTGAACAAGCGCGGTA 61.895 55.000 12.91 0.00 0.00 4.02
3939 3996 0.532862 ATATCCCTGAACAAGCGCGG 60.533 55.000 8.83 0.00 0.00 6.46
3941 3998 1.953559 TCATATCCCTGAACAAGCGC 58.046 50.000 0.00 0.00 0.00 5.92
3943 4000 3.004106 GTGCATCATATCCCTGAACAAGC 59.996 47.826 0.00 0.00 0.00 4.01
3957 4014 1.209019 GAGACTGGACAGGTGCATCAT 59.791 52.381 0.00 0.00 0.00 2.45
3958 4015 0.610174 GAGACTGGACAGGTGCATCA 59.390 55.000 0.00 0.00 0.00 3.07
3959 4016 0.901124 AGAGACTGGACAGGTGCATC 59.099 55.000 4.14 0.00 0.00 3.91
3960 4017 0.612229 CAGAGACTGGACAGGTGCAT 59.388 55.000 4.14 0.00 0.00 3.96
3962 4019 0.394565 AACAGAGACTGGACAGGTGC 59.605 55.000 4.14 0.00 35.51 5.01
3963 4020 1.967066 AGAACAGAGACTGGACAGGTG 59.033 52.381 4.14 0.00 35.51 4.00
3964 4021 2.243810 GAGAACAGAGACTGGACAGGT 58.756 52.381 4.14 0.00 35.51 4.00
3965 4022 2.242926 TGAGAACAGAGACTGGACAGG 58.757 52.381 4.14 0.00 35.51 4.00
3966 4023 4.327982 TTTGAGAACAGAGACTGGACAG 57.672 45.455 0.00 0.00 35.51 3.51
3967 4024 4.405680 TCTTTTGAGAACAGAGACTGGACA 59.594 41.667 0.00 0.00 35.51 4.02
3968 4025 4.950050 TCTTTTGAGAACAGAGACTGGAC 58.050 43.478 0.00 0.00 35.51 4.02
3983 4040 3.819368 TGCACAGGAGACATTCTTTTGA 58.181 40.909 0.00 0.00 0.00 2.69
4019 4076 6.479990 TGTGATAAGAACTTTGTCACAGTGAG 59.520 38.462 20.52 0.00 39.63 3.51
4024 4081 8.725405 TTACTTGTGATAAGAACTTTGTCACA 57.275 30.769 20.52 20.52 41.15 3.58
4025 4082 9.813080 GATTACTTGTGATAAGAACTTTGTCAC 57.187 33.333 17.54 17.54 37.43 3.67
4028 4085 9.561069 ACAGATTACTTGTGATAAGAACTTTGT 57.439 29.630 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.