Multiple sequence alignment - TraesCS2B01G340800

Loading Multiple Alignment...

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 TraesCS2B01G340800 chr2B 100.000 4126 0 0 1 4126 486580699 486584824 0.000000e+00 7620.0
1 TraesCS2B01G340800 chr2B 94.444 90 5 0 3711 3800 214532872 214532783 5.560000e-29 139.0
2 TraesCS2B01G340800 chr2B 97.619 42 1 0 131 172 115903460 115903419 5.720000e-09 73.1
3 TraesCS2B01G340800 chr2D 96.134 3725 108 10 1 3713 413259842 413263542 0.000000e+00 6048.0
4 TraesCS2B01G340800 chr2D 96.407 334 12 0 3793 4126 413263539 413263872 6.030000e-153 551.0
5 TraesCS2B01G340800 chr2D 97.015 67 1 1 3867 3932 413263551 413263617 1.210000e-20 111.0
6 TraesCS2B01G340800 chr2A 95.808 3602 106 18 154 3713 580248102 580251700 0.000000e+00 5773.0
7 TraesCS2B01G340800 chr2A 96.108 334 13 0 3793 4126 580251697 580252030 2.800000e-151 545.0
8 TraesCS2B01G340800 chr2A 93.895 344 17 3 7 350 413416065 413416404 2.200000e-142 516.0
9 TraesCS2B01G340800 chr2A 94.025 318 16 3 7 324 413452037 413452351 2.890000e-131 479.0
10 TraesCS2B01G340800 chr2A 91.473 129 10 1 1 128 580247974 580248102 4.240000e-40 176.0
11 TraesCS2B01G340800 chr2A 97.015 67 1 1 3867 3932 580251709 580251775 1.210000e-20 111.0
12 TraesCS2B01G340800 chr7A 95.143 350 16 1 1 350 39288239 39288587 6.030000e-153 551.0
13 TraesCS2B01G340800 chr7A 94.000 350 20 1 1 350 443987026 443987374 2.820000e-146 529.0
14 TraesCS2B01G340800 chr1A 93.484 353 22 1 1 353 67029158 67028807 1.310000e-144 523.0
15 TraesCS2B01G340800 chr6A 92.923 325 21 2 1 324 603716420 603716097 4.830000e-129 472.0
16 TraesCS2B01G340800 chr5B 98.837 86 1 0 3710 3795 711245669 711245584 1.990000e-33 154.0
17 TraesCS2B01G340800 chr4B 95.699 93 3 1 3710 3802 37193085 37192994 9.240000e-32 148.0
18 TraesCS2B01G340800 chr1B 95.455 88 4 0 3710 3797 628049899 628049812 1.550000e-29 141.0
19 TraesCS2B01G340800 chr1B 90.654 107 6 4 3697 3801 548535444 548535548 5.560000e-29 139.0
20 TraesCS2B01G340800 chr7B 95.402 87 4 0 3711 3797 747110257 747110343 5.560000e-29 139.0
21 TraesCS2B01G340800 chr6D 94.444 90 5 0 3709 3798 199210414 199210325 5.560000e-29 139.0
22 TraesCS2B01G340800 chr3A 95.402 87 4 0 3711 3797 99426185 99426271 5.560000e-29 139.0
23 TraesCS2B01G340800 chr3B 93.478 92 6 0 3710 3801 200860768 200860677 2.000000e-28 137.0
24 TraesCS2B01G340800 chr7D 92.222 90 6 1 87 175 574037631 574037720 4.330000e-25 126.0


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 TraesCS2B01G340800 chr2B 486580699 486584824 4125 False 7620.000000 7620 100.000000 1 4126 1 chr2B.!!$F1 4125
1 TraesCS2B01G340800 chr2D 413259842 413263872 4030 False 2236.666667 6048 96.518667 1 4126 3 chr2D.!!$F1 4125
2 TraesCS2B01G340800 chr2A 580247974 580252030 4056 False 1651.250000 5773 95.101000 1 4126 4 chr2A.!!$F3 4125

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
728 754 0.890542 TTGCGCATGTTCCTGCTCTT 60.891 50.000 12.75 0.0 40.06 2.85 F
1312 1343 1.796151 CGCAGTTCGCATGGATTGT 59.204 52.632 0.00 0.0 42.60 2.71 F
1686 1720 0.037303 CTCTTTGCTCCCTGCTCCAA 59.963 55.000 0.00 0.0 43.37 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 1720 1.00243 TCTCGTTGGCAGCAGAAGAAT 59.998 47.619 1.39 0.0 0.00 2.40 R
2866 2900 0.82346 TGCCGTCACTATCTGATGCA 59.177 50.000 0.00 0.0 37.24 3.96 R
3572 3608 1.00358 ACGAAACATCTGCATGGGACT 59.996 47.619 0.00 0.0 33.82 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
39 40 2.832733 AGTCAACTAGTCTACCCTTGCC 59.167 50.000 0.00 0.00 0.00 4.52
54 55 3.165071 CCTTGCCCCTGTATTTTGAACT 58.835 45.455 0.00 0.00 0.00 3.01
106 108 4.536489 AGCTACTACCTCTGTCCCAAATTT 59.464 41.667 0.00 0.00 0.00 1.82
189 191 6.012858 AGGAAGTACCATTTAACATCTGACCA 60.013 38.462 0.00 0.00 42.04 4.02
218 221 5.049405 CACGATTAATTATGGGAGGTTCTGC 60.049 44.000 0.00 0.00 0.00 4.26
316 319 1.388547 TGTTTGACAGTGGTTGCCTC 58.611 50.000 0.00 0.00 0.00 4.70
441 453 5.975344 CCATGAGCAATTTGACATGACATAC 59.025 40.000 24.73 0.00 41.45 2.39
467 479 5.103982 TGGATGATGGTGTCCATTACATTCT 60.104 40.000 2.71 0.00 45.26 2.40
511 523 5.647658 TGCTAGTGGAATGTGTTTAGATTGG 59.352 40.000 0.00 0.00 0.00 3.16
524 536 7.174253 TGTGTTTAGATTGGATTGTAACTGGTC 59.826 37.037 0.00 0.00 0.00 4.02
559 571 2.933906 GTGGATGTACCGTAACATGGTG 59.066 50.000 4.74 0.00 40.17 4.17
665 678 1.542108 GCATCTGCTGGGGTATCAGTC 60.542 57.143 0.00 0.00 37.12 3.51
675 688 2.629051 GGGTATCAGTCGGTCAAAAGG 58.371 52.381 0.00 0.00 0.00 3.11
676 689 2.027469 GGGTATCAGTCGGTCAAAAGGT 60.027 50.000 0.00 0.00 0.00 3.50
677 690 3.558533 GGGTATCAGTCGGTCAAAAGGTT 60.559 47.826 0.00 0.00 0.00 3.50
678 691 4.322953 GGGTATCAGTCGGTCAAAAGGTTA 60.323 45.833 0.00 0.00 0.00 2.85
679 692 5.425630 GGTATCAGTCGGTCAAAAGGTTAT 58.574 41.667 0.00 0.00 0.00 1.89
680 693 5.293569 GGTATCAGTCGGTCAAAAGGTTATG 59.706 44.000 0.00 0.00 0.00 1.90
681 694 4.345859 TCAGTCGGTCAAAAGGTTATGT 57.654 40.909 0.00 0.00 0.00 2.29
682 695 5.471556 TCAGTCGGTCAAAAGGTTATGTA 57.528 39.130 0.00 0.00 0.00 2.29
683 696 5.856156 TCAGTCGGTCAAAAGGTTATGTAA 58.144 37.500 0.00 0.00 0.00 2.41
684 697 6.289834 TCAGTCGGTCAAAAGGTTATGTAAA 58.710 36.000 0.00 0.00 0.00 2.01
685 698 6.766944 TCAGTCGGTCAAAAGGTTATGTAAAA 59.233 34.615 0.00 0.00 0.00 1.52
686 699 7.282675 TCAGTCGGTCAAAAGGTTATGTAAAAA 59.717 33.333 0.00 0.00 0.00 1.94
687 700 8.079809 CAGTCGGTCAAAAGGTTATGTAAAAAT 58.920 33.333 0.00 0.00 0.00 1.82
728 754 0.890542 TTGCGCATGTTCCTGCTCTT 60.891 50.000 12.75 0.00 40.06 2.85
734 760 2.162408 GCATGTTCCTGCTCTTGGTTAC 59.838 50.000 0.00 0.00 39.12 2.50
788 819 6.368791 TGGAAAGATACACAGATTCGTCTTTG 59.631 38.462 3.22 0.00 36.40 2.77
789 820 6.369065 GGAAAGATACACAGATTCGTCTTTGT 59.631 38.462 3.22 3.17 36.40 2.83
822 853 5.112686 TGGTTAAGTTCATGCCAAACAAAC 58.887 37.500 0.00 0.00 0.00 2.93
823 854 5.112686 GGTTAAGTTCATGCCAAACAAACA 58.887 37.500 12.16 0.00 31.60 2.83
824 855 5.582665 GGTTAAGTTCATGCCAAACAAACAA 59.417 36.000 12.16 0.00 31.60 2.83
1049 1080 2.028130 CAGTGGTGGTTGCTTTGGTAA 58.972 47.619 0.00 0.00 0.00 2.85
1195 1226 8.432013 TCATAGTGTTAAGCTGTGATGGATAAT 58.568 33.333 0.00 0.00 30.89 1.28
1312 1343 1.796151 CGCAGTTCGCATGGATTGT 59.204 52.632 0.00 0.00 42.60 2.71
1679 1713 2.122768 CATCCCTACTCTTTGCTCCCT 58.877 52.381 0.00 0.00 0.00 4.20
1686 1720 0.037303 CTCTTTGCTCCCTGCTCCAA 59.963 55.000 0.00 0.00 43.37 3.53
1702 1736 1.888512 TCCAATTCTTCTGCTGCCAAC 59.111 47.619 0.00 0.00 0.00 3.77
1709 1743 0.601046 TTCTGCTGCCAACGAGACAG 60.601 55.000 0.00 0.00 34.48 3.51
2230 2264 1.900351 CATTCGGAGTGCTGAGGGA 59.100 57.895 0.00 0.00 0.00 4.20
2293 2327 0.981183 AGTATCCGGACTGTGCCAAA 59.019 50.000 6.12 0.00 0.00 3.28
2728 2762 1.178534 CCGCACATGGAACCTTGGTT 61.179 55.000 4.52 4.52 0.00 3.67
2866 2900 1.145598 CTCATCGGGCATCAGCACT 59.854 57.895 0.00 0.00 43.86 4.40
2914 2948 0.106708 GCCAAGCGATGATACCTCCA 59.893 55.000 0.00 0.00 0.00 3.86
2970 3004 2.202623 GTCGGAGCCTACTGTGCG 60.203 66.667 0.00 0.00 0.00 5.34
2993 3027 2.039405 GGCAGAGAAGCAGGCTGTG 61.039 63.158 17.16 6.27 35.83 3.66
3103 3137 2.061028 GTTTTCTCCGCCTGCAAATTG 58.939 47.619 0.00 0.00 0.00 2.32
3262 3296 1.913262 ATGCCGGTCCAGTCAGTCA 60.913 57.895 1.90 0.00 0.00 3.41
3269 3303 3.637229 CCGGTCCAGTCAGTCATAGTTAT 59.363 47.826 0.00 0.00 0.00 1.89
3460 3496 5.743026 TTGCAGTTCTGTAACGATGAAAA 57.257 34.783 0.00 0.00 40.73 2.29
3546 3582 8.926710 GTTATATTACTCTTGATCCCAACATCG 58.073 37.037 0.00 0.00 0.00 3.84
3551 3587 4.256920 CTCTTGATCCCAACATCGACTTT 58.743 43.478 0.00 0.00 0.00 2.66
3554 3590 5.181245 TCTTGATCCCAACATCGACTTTTTC 59.819 40.000 0.00 0.00 0.00 2.29
3564 3600 5.961272 ACATCGACTTTTTCTTTTTGTGGT 58.039 33.333 0.00 0.00 0.00 4.16
3591 3636 1.742761 AGTCCCATGCAGATGTTTCG 58.257 50.000 0.00 0.00 0.00 3.46
3643 3698 5.064452 GTCTGATTGAACTTGATACCTGCTG 59.936 44.000 0.00 0.00 0.00 4.41
3715 3772 6.900568 CATCTCAGAAAAGATGTGTACTCC 57.099 41.667 5.86 0.00 45.01 3.85
3716 3773 5.407407 TCTCAGAAAAGATGTGTACTCCC 57.593 43.478 0.00 0.00 0.00 4.30
3717 3774 5.087323 TCTCAGAAAAGATGTGTACTCCCT 58.913 41.667 0.00 0.00 0.00 4.20
3718 3775 5.186021 TCTCAGAAAAGATGTGTACTCCCTC 59.814 44.000 0.00 0.00 0.00 4.30
3719 3776 4.223032 TCAGAAAAGATGTGTACTCCCTCC 59.777 45.833 0.00 0.00 0.00 4.30
3720 3777 3.195825 AGAAAAGATGTGTACTCCCTCCG 59.804 47.826 0.00 0.00 0.00 4.63
3721 3778 2.233305 AAGATGTGTACTCCCTCCGT 57.767 50.000 0.00 0.00 0.00 4.69
3722 3779 3.377253 AAGATGTGTACTCCCTCCGTA 57.623 47.619 0.00 0.00 0.00 4.02
3723 3780 3.377253 AGATGTGTACTCCCTCCGTAA 57.623 47.619 0.00 0.00 0.00 3.18
3724 3781 3.705051 AGATGTGTACTCCCTCCGTAAA 58.295 45.455 0.00 0.00 0.00 2.01
3725 3782 3.700038 AGATGTGTACTCCCTCCGTAAAG 59.300 47.826 0.00 0.00 0.00 1.85
3726 3783 3.159213 TGTGTACTCCCTCCGTAAAGA 57.841 47.619 0.00 0.00 0.00 2.52
3727 3784 3.499338 TGTGTACTCCCTCCGTAAAGAA 58.501 45.455 0.00 0.00 0.00 2.52
3728 3785 3.896888 TGTGTACTCCCTCCGTAAAGAAA 59.103 43.478 0.00 0.00 0.00 2.52
3729 3786 4.529377 TGTGTACTCCCTCCGTAAAGAAAT 59.471 41.667 0.00 0.00 0.00 2.17
3730 3787 5.716228 TGTGTACTCCCTCCGTAAAGAAATA 59.284 40.000 0.00 0.00 0.00 1.40
3731 3788 6.381994 TGTGTACTCCCTCCGTAAAGAAATAT 59.618 38.462 0.00 0.00 0.00 1.28
3732 3789 7.560991 TGTGTACTCCCTCCGTAAAGAAATATA 59.439 37.037 0.00 0.00 0.00 0.86
3733 3790 8.416329 GTGTACTCCCTCCGTAAAGAAATATAA 58.584 37.037 0.00 0.00 0.00 0.98
3734 3791 8.636213 TGTACTCCCTCCGTAAAGAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
3735 3792 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
3736 3793 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
3737 3794 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
3738 3795 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
3739 3796 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
3740 3797 7.365741 CCTCCGTAAAGAAATATAAGAGCGTA 58.634 38.462 0.00 0.00 0.00 4.42
3741 3798 8.027771 CCTCCGTAAAGAAATATAAGAGCGTAT 58.972 37.037 0.00 0.00 0.00 3.06
3759 3816 9.775854 AGAGCGTATAGATTACTAAAGTAGTGA 57.224 33.333 0.00 0.00 39.81 3.41
3769 3826 9.512435 GATTACTAAAGTAGTGATCTAAACGCA 57.488 33.333 11.11 0.00 44.10 5.24
3770 3827 8.679288 TTACTAAAGTAGTGATCTAAACGCAC 57.321 34.615 0.00 0.00 39.81 5.34
3771 3828 6.921914 ACTAAAGTAGTGATCTAAACGCACT 58.078 36.000 0.00 0.00 44.38 4.40
3772 3829 7.376615 ACTAAAGTAGTGATCTAAACGCACTT 58.623 34.615 0.00 0.00 42.40 3.16
3773 3830 8.517878 ACTAAAGTAGTGATCTAAACGCACTTA 58.482 33.333 0.00 0.00 42.40 2.24
3774 3831 7.578169 AAAGTAGTGATCTAAACGCACTTAC 57.422 36.000 0.00 0.00 42.40 2.34
3775 3832 6.263516 AGTAGTGATCTAAACGCACTTACA 57.736 37.500 0.00 0.00 42.40 2.41
3776 3833 6.864342 AGTAGTGATCTAAACGCACTTACAT 58.136 36.000 0.00 0.00 42.40 2.29
3777 3834 7.321153 AGTAGTGATCTAAACGCACTTACATT 58.679 34.615 0.00 0.00 42.40 2.71
3778 3835 7.817962 AGTAGTGATCTAAACGCACTTACATTT 59.182 33.333 0.00 0.00 42.40 2.32
3779 3836 6.831769 AGTGATCTAAACGCACTTACATTTG 58.168 36.000 0.00 0.00 39.69 2.32
3780 3837 6.426937 AGTGATCTAAACGCACTTACATTTGT 59.573 34.615 0.00 0.00 39.69 2.83
3781 3838 7.041372 AGTGATCTAAACGCACTTACATTTGTT 60.041 33.333 0.00 0.00 39.69 2.83
3782 3839 7.589954 GTGATCTAAACGCACTTACATTTGTTT 59.410 33.333 0.00 0.00 34.32 2.83
3783 3840 8.775527 TGATCTAAACGCACTTACATTTGTTTA 58.224 29.630 0.00 0.00 32.41 2.01
3784 3841 8.944212 ATCTAAACGCACTTACATTTGTTTAC 57.056 30.769 0.00 0.00 32.41 2.01
3785 3842 7.917597 TCTAAACGCACTTACATTTGTTTACA 58.082 30.769 0.00 0.00 32.41 2.41
3786 3843 8.065407 TCTAAACGCACTTACATTTGTTTACAG 58.935 33.333 0.00 0.00 32.41 2.74
3787 3844 5.994887 ACGCACTTACATTTGTTTACAGA 57.005 34.783 0.00 0.00 0.00 3.41
3788 3845 5.985781 ACGCACTTACATTTGTTTACAGAG 58.014 37.500 0.00 0.00 0.00 3.35
3789 3846 5.049680 ACGCACTTACATTTGTTTACAGAGG 60.050 40.000 0.00 0.00 0.00 3.69
3790 3847 5.616866 CGCACTTACATTTGTTTACAGAGGG 60.617 44.000 0.00 0.00 0.00 4.30
3791 3848 5.472137 GCACTTACATTTGTTTACAGAGGGA 59.528 40.000 0.00 0.00 0.00 4.20
3792 3849 6.348540 GCACTTACATTTGTTTACAGAGGGAG 60.349 42.308 0.00 0.00 0.00 4.30
3793 3850 6.710744 CACTTACATTTGTTTACAGAGGGAGT 59.289 38.462 0.00 0.00 0.00 3.85
3794 3851 7.876068 CACTTACATTTGTTTACAGAGGGAGTA 59.124 37.037 0.00 0.00 0.00 2.59
3795 3852 7.876582 ACTTACATTTGTTTACAGAGGGAGTAC 59.123 37.037 0.00 0.00 0.00 2.73
3796 3853 6.435292 ACATTTGTTTACAGAGGGAGTACT 57.565 37.500 0.00 0.00 0.00 2.73
3811 3868 4.380339 GGGAGTACTAAAGACTGGACGAAC 60.380 50.000 0.00 0.00 0.00 3.95
3837 3894 5.529060 GGCATACAAGGAGAAAACTAGATGG 59.471 44.000 0.00 0.00 0.00 3.51
3859 3916 0.822164 TTGAGACTAGCCGCCCTAAC 59.178 55.000 0.00 0.00 0.00 2.34
3925 3982 3.306613 AGACTAGCCGCCCTAAACTAAT 58.693 45.455 0.00 0.00 0.00 1.73
3951 4008 0.881118 TGAAGCGAGCAATTTGGGAC 59.119 50.000 0.00 0.00 0.00 4.46
4094 4151 0.685785 TAGGAGCTGGCAGAGTGGAG 60.686 60.000 20.86 0.00 0.00 3.86
4104 4161 0.034476 CAGAGTGGAGCTCAGCACAA 59.966 55.000 20.74 0.00 46.47 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.065925 AGTTGACTTCAAACTTGCAGCTC 59.934 43.478 0.00 0.00 37.63 4.09
39 40 8.960591 AGATGACAAATAGTTCAAAATACAGGG 58.039 33.333 0.00 0.00 0.00 4.45
54 55 6.000246 TGGATGGCAGTAAGATGACAAATA 58.000 37.500 0.00 0.00 42.78 1.40
68 70 2.169352 AGTAGCTAACACTGGATGGCAG 59.831 50.000 0.00 0.00 0.00 4.85
159 161 8.258007 CAGATGTTAAATGGTACTTCCTCTGTA 58.742 37.037 0.00 0.00 37.07 2.74
189 191 5.833131 ACCTCCCATAATTAATCGTGCATTT 59.167 36.000 0.00 0.00 0.00 2.32
218 221 7.060600 TGACATATTTGAAGAGCGTTAACAG 57.939 36.000 6.39 0.00 0.00 3.16
460 472 2.661176 AGAACCCCCAGGAGAATGTA 57.339 50.000 0.00 0.00 36.73 2.29
511 523 4.160626 AGTCAGCTAGGACCAGTTACAATC 59.839 45.833 0.75 0.00 38.59 2.67
524 536 2.026822 ACATCCACCAAAGTCAGCTAGG 60.027 50.000 0.00 0.00 0.00 3.02
653 666 1.646912 TTTGACCGACTGATACCCCA 58.353 50.000 0.00 0.00 0.00 4.96
665 678 8.582433 AACATTTTTACATAACCTTTTGACCG 57.418 30.769 0.00 0.00 0.00 4.79
676 689 9.689501 CCCCTAAGTCCTAACATTTTTACATAA 57.310 33.333 0.00 0.00 0.00 1.90
677 690 8.838741 ACCCCTAAGTCCTAACATTTTTACATA 58.161 33.333 0.00 0.00 0.00 2.29
678 691 7.705700 ACCCCTAAGTCCTAACATTTTTACAT 58.294 34.615 0.00 0.00 0.00 2.29
679 692 7.093965 ACCCCTAAGTCCTAACATTTTTACA 57.906 36.000 0.00 0.00 0.00 2.41
680 693 9.334947 GATACCCCTAAGTCCTAACATTTTTAC 57.665 37.037 0.00 0.00 0.00 2.01
681 694 9.060137 TGATACCCCTAAGTCCTAACATTTTTA 57.940 33.333 0.00 0.00 0.00 1.52
682 695 7.935405 TGATACCCCTAAGTCCTAACATTTTT 58.065 34.615 0.00 0.00 0.00 1.94
683 696 7.519347 TGATACCCCTAAGTCCTAACATTTT 57.481 36.000 0.00 0.00 0.00 1.82
684 697 7.707467 ATGATACCCCTAAGTCCTAACATTT 57.293 36.000 0.00 0.00 0.00 2.32
685 698 7.707467 AATGATACCCCTAAGTCCTAACATT 57.293 36.000 0.00 0.00 0.00 2.71
686 699 7.518188 CAAATGATACCCCTAAGTCCTAACAT 58.482 38.462 0.00 0.00 0.00 2.71
687 700 6.634039 GCAAATGATACCCCTAAGTCCTAACA 60.634 42.308 0.00 0.00 0.00 2.41
728 754 2.375174 ACAGAAATGCCTCCAGTAACCA 59.625 45.455 0.00 0.00 0.00 3.67
734 760 3.705043 GCATAACAGAAATGCCTCCAG 57.295 47.619 0.00 0.00 43.17 3.86
788 819 5.682943 TGAACTTAACCAGTTGTATGCAC 57.317 39.130 0.00 0.00 46.53 4.57
789 820 6.252967 CATGAACTTAACCAGTTGTATGCA 57.747 37.500 0.00 0.00 46.53 3.96
1110 1141 0.250901 GCTGAAGAAACAGGGGCTGA 60.251 55.000 0.00 0.00 38.22 4.26
1312 1343 2.747460 GCCATTGCTGAGCCGACA 60.747 61.111 0.23 0.00 33.53 4.35
1566 1600 6.108015 ACTGTTTCATTTTGTGTTTGCAGAT 58.892 32.000 0.00 0.00 0.00 2.90
1679 1713 1.171308 GCAGCAGAAGAATTGGAGCA 58.829 50.000 0.00 0.00 0.00 4.26
1686 1720 1.002430 TCTCGTTGGCAGCAGAAGAAT 59.998 47.619 1.39 0.00 0.00 2.40
1702 1736 5.164233 TCTCTGCTTTGTAATTCTGTCTCG 58.836 41.667 0.00 0.00 0.00 4.04
1709 1743 9.548208 GTTTAGTGAATCTCTGCTTTGTAATTC 57.452 33.333 0.00 0.00 0.00 2.17
2230 2264 2.165998 GAAATGCAGAGTCCAGCCTTT 58.834 47.619 7.74 7.74 32.54 3.11
2536 2570 2.591429 CAACAGTCAGTGCGGCCA 60.591 61.111 2.24 0.00 0.00 5.36
2728 2762 3.578968 ATGCTCTTGCTGCCTGGCA 62.579 57.895 21.96 21.96 40.74 4.92
2743 2777 1.747355 CCACTCTTCACCATTCCATGC 59.253 52.381 0.00 0.00 0.00 4.06
2866 2900 0.823460 TGCCGTCACTATCTGATGCA 59.177 50.000 0.00 0.00 37.24 3.96
2914 2948 2.667536 CGAGGCACAAGCAGCTGT 60.668 61.111 16.64 0.00 44.61 4.40
2970 3004 2.045536 CTGCTTCTCTGCCCCCAC 60.046 66.667 0.00 0.00 0.00 4.61
3028 3062 2.262915 CCACCGAGGAGTGACAGC 59.737 66.667 0.00 0.00 40.34 4.40
3103 3137 6.915843 CCTTTTATGTACAACCAAACTGACAC 59.084 38.462 0.00 0.00 0.00 3.67
3262 3296 5.008613 CACACGGCTTATTGGCAATAACTAT 59.991 40.000 24.83 10.79 41.89 2.12
3269 3303 2.186532 TACACACGGCTTATTGGCAA 57.813 45.000 0.68 0.68 41.89 4.52
3350 3384 5.303078 TCAATTTTACAAAACCTGCCTAGCA 59.697 36.000 0.00 0.00 36.92 3.49
3551 3587 8.252417 GGGACTAAAAAGTACCACAAAAAGAAA 58.748 33.333 1.75 0.00 42.38 2.52
3564 3600 5.815581 ACATCTGCATGGGACTAAAAAGTA 58.184 37.500 0.00 0.00 33.82 2.24
3572 3608 1.003580 ACGAAACATCTGCATGGGACT 59.996 47.619 0.00 0.00 33.82 3.85
3591 3636 4.092821 GTGGTTTCTGCTTCCAAACAAAAC 59.907 41.667 0.00 0.00 34.68 2.43
3668 3724 6.210385 TGCAAGTATTTCCTTCAGGCAAAATA 59.790 34.615 0.00 0.00 34.44 1.40
3713 3770 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
3714 3771 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
3715 3772 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
3716 3773 8.967552 ATACGCTCTTATATTTCTTTACGGAG 57.032 34.615 0.00 0.00 0.00 4.63
3733 3790 9.775854 TCACTACTTTAGTAATCTATACGCTCT 57.224 33.333 0.00 0.00 37.23 4.09
3742 3799 9.733219 GCGTTTAGATCACTACTTTAGTAATCT 57.267 33.333 4.72 4.72 37.23 2.40
3743 3800 9.512435 TGCGTTTAGATCACTACTTTAGTAATC 57.488 33.333 0.00 0.00 37.23 1.75
3744 3801 9.298774 GTGCGTTTAGATCACTACTTTAGTAAT 57.701 33.333 0.00 0.00 37.23 1.89
3745 3802 8.517878 AGTGCGTTTAGATCACTACTTTAGTAA 58.482 33.333 0.00 0.00 39.08 2.24
3746 3803 8.048534 AGTGCGTTTAGATCACTACTTTAGTA 57.951 34.615 0.00 0.00 39.08 1.82
3747 3804 6.921914 AGTGCGTTTAGATCACTACTTTAGT 58.078 36.000 0.00 0.00 39.08 2.24
3748 3805 7.813852 AAGTGCGTTTAGATCACTACTTTAG 57.186 36.000 0.00 0.00 39.86 1.85
3749 3806 8.298854 TGTAAGTGCGTTTAGATCACTACTTTA 58.701 33.333 0.00 0.00 39.86 1.85
3750 3807 7.149973 TGTAAGTGCGTTTAGATCACTACTTT 58.850 34.615 0.00 0.00 39.86 2.66
3751 3808 6.684686 TGTAAGTGCGTTTAGATCACTACTT 58.315 36.000 0.00 0.00 39.86 2.24
3752 3809 6.263516 TGTAAGTGCGTTTAGATCACTACT 57.736 37.500 0.00 0.00 39.86 2.57
3753 3810 7.521509 AATGTAAGTGCGTTTAGATCACTAC 57.478 36.000 0.00 0.00 39.86 2.73
3754 3811 7.601130 ACAAATGTAAGTGCGTTTAGATCACTA 59.399 33.333 0.00 0.00 39.86 2.74
3755 3812 6.426937 ACAAATGTAAGTGCGTTTAGATCACT 59.573 34.615 0.00 0.00 42.28 3.41
3756 3813 6.599437 ACAAATGTAAGTGCGTTTAGATCAC 58.401 36.000 0.00 0.00 0.00 3.06
3757 3814 6.795098 ACAAATGTAAGTGCGTTTAGATCA 57.205 33.333 0.00 0.00 0.00 2.92
3758 3815 9.047871 GTAAACAAATGTAAGTGCGTTTAGATC 57.952 33.333 0.00 0.00 31.53 2.75
3759 3816 8.561212 TGTAAACAAATGTAAGTGCGTTTAGAT 58.439 29.630 0.00 0.00 31.53 1.98
3760 3817 7.917597 TGTAAACAAATGTAAGTGCGTTTAGA 58.082 30.769 0.00 0.00 31.53 2.10
3761 3818 8.065407 TCTGTAAACAAATGTAAGTGCGTTTAG 58.935 33.333 0.00 0.00 31.53 1.85
3762 3819 7.917597 TCTGTAAACAAATGTAAGTGCGTTTA 58.082 30.769 0.00 0.00 0.00 2.01
3763 3820 6.787225 TCTGTAAACAAATGTAAGTGCGTTT 58.213 32.000 0.00 0.00 0.00 3.60
3764 3821 6.366315 TCTGTAAACAAATGTAAGTGCGTT 57.634 33.333 0.00 0.00 0.00 4.84
3765 3822 5.049680 CCTCTGTAAACAAATGTAAGTGCGT 60.050 40.000 0.00 0.00 0.00 5.24
3766 3823 5.382303 CCTCTGTAAACAAATGTAAGTGCG 58.618 41.667 0.00 0.00 0.00 5.34
3767 3824 5.472137 TCCCTCTGTAAACAAATGTAAGTGC 59.528 40.000 0.00 0.00 0.00 4.40
3768 3825 6.710744 ACTCCCTCTGTAAACAAATGTAAGTG 59.289 38.462 0.00 0.00 0.00 3.16
3769 3826 6.838382 ACTCCCTCTGTAAACAAATGTAAGT 58.162 36.000 0.00 0.00 0.00 2.24
3770 3827 8.095169 AGTACTCCCTCTGTAAACAAATGTAAG 58.905 37.037 0.00 0.00 0.00 2.34
3771 3828 7.970102 AGTACTCCCTCTGTAAACAAATGTAA 58.030 34.615 0.00 0.00 0.00 2.41
3772 3829 7.549147 AGTACTCCCTCTGTAAACAAATGTA 57.451 36.000 0.00 0.00 0.00 2.29
3773 3830 6.435292 AGTACTCCCTCTGTAAACAAATGT 57.565 37.500 0.00 0.00 0.00 2.71
3774 3831 8.842358 TTTAGTACTCCCTCTGTAAACAAATG 57.158 34.615 0.00 0.00 0.00 2.32
3775 3832 8.877195 TCTTTAGTACTCCCTCTGTAAACAAAT 58.123 33.333 0.00 0.00 0.00 2.32
3776 3833 8.146412 GTCTTTAGTACTCCCTCTGTAAACAAA 58.854 37.037 0.00 0.00 0.00 2.83
3777 3834 7.508296 AGTCTTTAGTACTCCCTCTGTAAACAA 59.492 37.037 0.00 0.00 0.00 2.83
3778 3835 7.008941 AGTCTTTAGTACTCCCTCTGTAAACA 58.991 38.462 0.00 0.00 0.00 2.83
3779 3836 7.314393 CAGTCTTTAGTACTCCCTCTGTAAAC 58.686 42.308 0.00 0.00 0.00 2.01
3780 3837 6.436532 CCAGTCTTTAGTACTCCCTCTGTAAA 59.563 42.308 0.00 0.00 0.00 2.01
3781 3838 5.950549 CCAGTCTTTAGTACTCCCTCTGTAA 59.049 44.000 0.00 0.00 0.00 2.41
3782 3839 5.252397 TCCAGTCTTTAGTACTCCCTCTGTA 59.748 44.000 0.00 0.00 0.00 2.74
3783 3840 4.044317 TCCAGTCTTTAGTACTCCCTCTGT 59.956 45.833 0.00 0.00 0.00 3.41
3784 3841 4.399934 GTCCAGTCTTTAGTACTCCCTCTG 59.600 50.000 0.00 3.57 0.00 3.35
3785 3842 4.602107 GTCCAGTCTTTAGTACTCCCTCT 58.398 47.826 0.00 0.00 0.00 3.69
3786 3843 3.377798 CGTCCAGTCTTTAGTACTCCCTC 59.622 52.174 0.00 0.00 0.00 4.30
3787 3844 3.009916 TCGTCCAGTCTTTAGTACTCCCT 59.990 47.826 0.00 0.00 0.00 4.20
3788 3845 3.350833 TCGTCCAGTCTTTAGTACTCCC 58.649 50.000 0.00 0.00 0.00 4.30
3789 3846 4.671250 CGTTCGTCCAGTCTTTAGTACTCC 60.671 50.000 0.00 0.00 0.00 3.85
3790 3847 4.401714 CGTTCGTCCAGTCTTTAGTACTC 58.598 47.826 0.00 0.00 0.00 2.59
3791 3848 3.190118 CCGTTCGTCCAGTCTTTAGTACT 59.810 47.826 0.00 0.00 0.00 2.73
3792 3849 3.496155 CCGTTCGTCCAGTCTTTAGTAC 58.504 50.000 0.00 0.00 0.00 2.73
3793 3850 2.489329 CCCGTTCGTCCAGTCTTTAGTA 59.511 50.000 0.00 0.00 0.00 1.82
3794 3851 1.271656 CCCGTTCGTCCAGTCTTTAGT 59.728 52.381 0.00 0.00 0.00 2.24
3795 3852 1.992170 CCCGTTCGTCCAGTCTTTAG 58.008 55.000 0.00 0.00 0.00 1.85
3796 3853 0.037975 GCCCGTTCGTCCAGTCTTTA 60.038 55.000 0.00 0.00 0.00 1.85
3811 3868 2.711542 AGTTTTCTCCTTGTATGCCCG 58.288 47.619 0.00 0.00 0.00 6.13
3837 3894 1.449778 GGGCGGCTAGTCTCAAACC 60.450 63.158 9.56 0.00 0.00 3.27
3859 3916 2.986534 ATGCCCATTCTCCCATTAGG 57.013 50.000 0.00 0.00 0.00 2.69
3902 3959 0.822164 GTTTAGGGCGGCTAGTCTCA 59.178 55.000 9.56 0.00 0.00 3.27
3925 3982 0.543277 ATTGCTCGCTTCATCTCCCA 59.457 50.000 0.00 0.00 0.00 4.37
4094 4151 1.818642 AAGGAGATGTTGTGCTGAGC 58.181 50.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.