Multiple sequence alignment - TraesCS3B01G182300

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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 TraesCS3B01G182300 chr3B 100.000 3713 0 0 1 3713 191133560 191137272 0.000000e+00 6857
1 TraesCS3B01G182300 chr3B 87.266 1068 131 5 1 1066 714974304 714975368 0.000000e+00 1214
2 TraesCS3B01G182300 chr3B 83.065 124 15 3 3528 3646 764684524 764684646 1.410000e-19 108
3 TraesCS3B01G182300 chr2B 98.905 2740 28 2 1 2740 78076292 78079029 0.000000e+00 4892
4 TraesCS3B01G182300 chr2B 85.115 2600 377 9 4 2598 654522260 654519666 0.000000e+00 2649
5 TraesCS3B01G182300 chr5B 98.504 2740 40 1 1 2740 611691563 611688825 0.000000e+00 4831
6 TraesCS3B01G182300 chr5B 84.918 2745 401 13 4 2740 619918555 619915816 0.000000e+00 2763
7 TraesCS3B01G182300 chr5B 84.851 2746 401 12 4 2741 402729720 402726982 0.000000e+00 2752
8 TraesCS3B01G182300 chr1B 92.995 2741 186 3 5 2740 679605583 679602844 0.000000e+00 3993
9 TraesCS3B01G182300 chr3A 88.626 2743 301 7 1 2738 696291391 696294127 0.000000e+00 3326
10 TraesCS3B01G182300 chr3A 91.923 780 44 10 2740 3503 149564005 149564781 0.000000e+00 1074
11 TraesCS3B01G182300 chr1D 87.218 2746 335 14 4 2740 75887975 75885237 0.000000e+00 3112
12 TraesCS3B01G182300 chr2A 90.777 1854 166 4 892 2741 90583618 90581766 0.000000e+00 2471
13 TraesCS3B01G182300 chr4A 98.655 892 12 0 1849 2740 641392972 641393863 0.000000e+00 1581
14 TraesCS3B01G182300 chr3D 90.314 795 42 19 2740 3507 134830530 134831316 0.000000e+00 1009
15 TraesCS3B01G182300 chr6B 86.154 130 10 7 3517 3641 346625053 346625179 2.330000e-27 134
16 TraesCS3B01G182300 chr2D 84.328 134 17 4 3517 3648 537183528 537183659 1.080000e-25 128


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 TraesCS3B01G182300 chr3B 191133560 191137272 3712 False 6857 6857 100.000 1 3713 1 chr3B.!!$F1 3712
1 TraesCS3B01G182300 chr3B 714974304 714975368 1064 False 1214 1214 87.266 1 1066 1 chr3B.!!$F2 1065
2 TraesCS3B01G182300 chr2B 78076292 78079029 2737 False 4892 4892 98.905 1 2740 1 chr2B.!!$F1 2739
3 TraesCS3B01G182300 chr2B 654519666 654522260 2594 True 2649 2649 85.115 4 2598 1 chr2B.!!$R1 2594
4 TraesCS3B01G182300 chr5B 611688825 611691563 2738 True 4831 4831 98.504 1 2740 1 chr5B.!!$R2 2739
5 TraesCS3B01G182300 chr5B 619915816 619918555 2739 True 2763 2763 84.918 4 2740 1 chr5B.!!$R3 2736
6 TraesCS3B01G182300 chr5B 402726982 402729720 2738 True 2752 2752 84.851 4 2741 1 chr5B.!!$R1 2737
7 TraesCS3B01G182300 chr1B 679602844 679605583 2739 True 3993 3993 92.995 5 2740 1 chr1B.!!$R1 2735
8 TraesCS3B01G182300 chr3A 696291391 696294127 2736 False 3326 3326 88.626 1 2738 1 chr3A.!!$F2 2737
9 TraesCS3B01G182300 chr3A 149564005 149564781 776 False 1074 1074 91.923 2740 3503 1 chr3A.!!$F1 763
10 TraesCS3B01G182300 chr1D 75885237 75887975 2738 True 3112 3112 87.218 4 2740 1 chr1D.!!$R1 2736
11 TraesCS3B01G182300 chr2A 90581766 90583618 1852 True 2471 2471 90.777 892 2741 1 chr2A.!!$R1 1849
12 TraesCS3B01G182300 chr4A 641392972 641393863 891 False 1581 1581 98.655 1849 2740 1 chr4A.!!$F1 891
13 TraesCS3B01G182300 chr3D 134830530 134831316 786 False 1009 1009 90.314 2740 3507 1 chr3D.!!$F1 767

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
87 88 2.616842 GGGTACATGCCGGAAGTTATTG 59.383 50.000 5.05 0.0 0.0 1.90 F
1578 1586 1.004745 GAGAGAACCTTCATTGCCCCA 59.995 52.381 0.00 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1846 1855 1.640917 TCCCCTATATGTCTTCGGCC 58.359 55.0 0.0 0.0 0.00 6.13 R
3547 3589 0.111061 AGCCACTGCCATTGAGACAA 59.889 50.0 0.0 0.0 38.69 3.18 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
87 88 2.616842 GGGTACATGCCGGAAGTTATTG 59.383 50.000 5.05 0.00 0.00 1.90
378 379 3.361053 GGATATGATGAAAGCGTACGACG 59.639 47.826 21.65 0.00 45.88 5.12
579 580 5.701224 ACTTGTTTCTTCTATGTGGGGAAA 58.299 37.500 0.00 0.00 0.00 3.13
1578 1586 1.004745 GAGAGAACCTTCATTGCCCCA 59.995 52.381 0.00 0.00 0.00 4.96
1846 1855 0.806492 GCCGGCGAAGGAAGAGTTAG 60.806 60.000 12.58 0.00 0.00 2.34
2024 2033 2.485122 GTCGCGGGATTTGCTTGG 59.515 61.111 6.13 0.00 0.00 3.61
2568 2580 6.325286 ACTTTCAGGGGTTGCAACTAAAATTA 59.675 34.615 27.64 9.34 0.00 1.40
2574 2586 5.340803 GGGTTGCAACTAAAATTAGCTAGC 58.659 41.667 27.64 6.62 34.09 3.42
2646 2658 8.950403 ATAGTGCTTCGATTGTAAACTTTTTC 57.050 30.769 0.00 0.00 0.00 2.29
2655 2667 9.291664 TCGATTGTAAACTTTTTCGATGTTTTT 57.708 25.926 10.14 0.25 37.03 1.94
2819 2836 4.601019 CCATTATAGGCTTTTGACTTGCG 58.399 43.478 0.00 0.00 39.50 4.85
2833 2850 3.127895 TGACTTGCGAAATTAAATCCCCG 59.872 43.478 0.00 0.00 0.00 5.73
2891 2918 1.006086 CAGTGAACGAGCACACACAA 58.994 50.000 13.19 0.00 41.19 3.33
2929 2956 1.949631 GGCATCGGTCGATCGGTTC 60.950 63.158 19.53 5.07 31.62 3.62
2936 2963 1.227002 GTCGATCGGTTCCTCCTGC 60.227 63.158 16.41 0.00 0.00 4.85
3127 3154 2.025727 CCATCGTCGGAGGTACGC 59.974 66.667 0.00 0.00 40.12 4.42
3147 3185 2.997897 AGTGCTCCTCCGTCCACC 60.998 66.667 0.00 0.00 0.00 4.61
3160 3199 0.179468 GTCCACCTAATGCCGGCTAA 59.821 55.000 29.70 8.87 0.00 3.09
3168 3207 3.632145 CCTAATGCCGGCTAAATCTGTTT 59.368 43.478 29.70 9.27 0.00 2.83
3203 3242 0.467844 TGCACACACCCTGAAGCAAT 60.468 50.000 0.00 0.00 33.52 3.56
3209 3248 1.072331 ACACCCTGAAGCAATCGTTCT 59.928 47.619 0.00 0.00 0.00 3.01
3213 3252 5.116180 CACCCTGAAGCAATCGTTCTATAA 58.884 41.667 0.00 0.00 0.00 0.98
3270 3312 0.889186 GGGCACACACACCTACCAAG 60.889 60.000 0.00 0.00 0.00 3.61
3276 3318 0.319405 ACACACCTACCAAGTACGGC 59.681 55.000 0.00 0.00 0.00 5.68
3298 3340 2.025441 CACGTGTGTTTTGCCCCG 59.975 61.111 7.58 0.00 0.00 5.73
3377 3419 1.469940 CGTCTGAGGAATCGGTTGAGG 60.470 57.143 0.00 0.00 0.00 3.86
3417 3459 0.608640 CCAGTAGGTTCTGAGCGGTT 59.391 55.000 0.00 0.00 37.61 4.44
3483 3525 7.403312 TGCTTGCATATATTACACTGGTTTT 57.597 32.000 0.00 0.00 0.00 2.43
3503 3545 1.954146 GAAGCTCGCACGTCACCAA 60.954 57.895 0.00 0.00 0.00 3.67
3504 3546 1.291877 GAAGCTCGCACGTCACCAAT 61.292 55.000 0.00 0.00 0.00 3.16
3505 3547 1.568612 AAGCTCGCACGTCACCAATG 61.569 55.000 0.00 0.00 0.00 2.82
3506 3548 2.476051 CTCGCACGTCACCAATGC 59.524 61.111 0.00 0.00 35.96 3.56
3507 3549 2.029288 CTCGCACGTCACCAATGCT 61.029 57.895 0.00 0.00 37.20 3.79
3508 3550 1.568612 CTCGCACGTCACCAATGCTT 61.569 55.000 0.00 0.00 37.20 3.91
3509 3551 1.440850 CGCACGTCACCAATGCTTG 60.441 57.895 0.00 0.00 37.20 4.01
3510 3552 1.730547 GCACGTCACCAATGCTTGC 60.731 57.895 0.00 0.00 36.40 4.01
3511 3553 1.653667 CACGTCACCAATGCTTGCA 59.346 52.632 0.00 0.00 0.00 4.08
3512 3554 0.241749 CACGTCACCAATGCTTGCAT 59.758 50.000 1.81 1.81 0.00 3.96
3513 3555 1.468127 CACGTCACCAATGCTTGCATA 59.532 47.619 8.61 0.00 0.00 3.14
3514 3556 2.097954 CACGTCACCAATGCTTGCATAT 59.902 45.455 8.61 0.00 0.00 1.78
3515 3557 3.312146 CACGTCACCAATGCTTGCATATA 59.688 43.478 8.61 0.00 0.00 0.86
3516 3558 4.023792 CACGTCACCAATGCTTGCATATAT 60.024 41.667 8.61 0.00 0.00 0.86
3517 3559 4.580167 ACGTCACCAATGCTTGCATATATT 59.420 37.500 8.61 0.00 0.00 1.28
3518 3560 5.067674 ACGTCACCAATGCTTGCATATATTT 59.932 36.000 8.61 0.00 0.00 1.40
3519 3561 6.262049 ACGTCACCAATGCTTGCATATATTTA 59.738 34.615 8.61 0.00 0.00 1.40
3520 3562 6.578545 CGTCACCAATGCTTGCATATATTTAC 59.421 38.462 8.61 3.43 0.00 2.01
3521 3563 7.424803 GTCACCAATGCTTGCATATATTTACA 58.575 34.615 8.61 0.00 0.00 2.41
3522 3564 7.920151 GTCACCAATGCTTGCATATATTTACAA 59.080 33.333 8.61 0.00 0.00 2.41
3523 3565 8.473219 TCACCAATGCTTGCATATATTTACAAA 58.527 29.630 8.61 0.00 0.00 2.83
3524 3566 8.757789 CACCAATGCTTGCATATATTTACAAAG 58.242 33.333 8.61 0.00 0.00 2.77
3525 3567 7.927629 ACCAATGCTTGCATATATTTACAAAGG 59.072 33.333 8.61 0.00 0.00 3.11
3526 3568 7.385752 CCAATGCTTGCATATATTTACAAAGGG 59.614 37.037 8.61 0.00 0.00 3.95
3527 3569 7.601705 ATGCTTGCATATATTTACAAAGGGT 57.398 32.000 6.28 0.00 0.00 4.34
3528 3570 7.416964 TGCTTGCATATATTTACAAAGGGTT 57.583 32.000 0.00 0.00 0.00 4.11
3529 3571 7.264221 TGCTTGCATATATTTACAAAGGGTTG 58.736 34.615 0.00 0.00 40.84 3.77
3530 3572 7.123397 TGCTTGCATATATTTACAAAGGGTTGA 59.877 33.333 0.00 0.00 38.20 3.18
3531 3573 8.143835 GCTTGCATATATTTACAAAGGGTTGAT 58.856 33.333 0.00 0.00 38.20 2.57
3532 3574 9.467258 CTTGCATATATTTACAAAGGGTTGATG 57.533 33.333 0.00 0.00 38.20 3.07
3533 3575 8.759481 TGCATATATTTACAAAGGGTTGATGA 57.241 30.769 0.00 0.00 38.20 2.92
3534 3576 9.365906 TGCATATATTTACAAAGGGTTGATGAT 57.634 29.630 0.00 0.00 38.20 2.45
3538 3580 8.947055 ATATTTACAAAGGGTTGATGATTTGC 57.053 30.769 0.00 0.00 38.20 3.68
3539 3581 3.683365 ACAAAGGGTTGATGATTTGCC 57.317 42.857 0.00 0.00 38.20 4.52
3540 3582 2.302733 ACAAAGGGTTGATGATTTGCCC 59.697 45.455 0.00 0.00 38.20 5.36
3541 3583 1.571955 AAGGGTTGATGATTTGCCCC 58.428 50.000 0.00 0.00 40.14 5.80
3542 3584 0.413037 AGGGTTGATGATTTGCCCCA 59.587 50.000 0.00 0.00 40.14 4.96
3543 3585 1.008693 AGGGTTGATGATTTGCCCCAT 59.991 47.619 0.00 0.00 40.14 4.00
3544 3586 1.139455 GGGTTGATGATTTGCCCCATG 59.861 52.381 0.00 0.00 33.40 3.66
3545 3587 2.109774 GGTTGATGATTTGCCCCATGA 58.890 47.619 0.00 0.00 0.00 3.07
3546 3588 2.701951 GGTTGATGATTTGCCCCATGAT 59.298 45.455 0.00 0.00 0.00 2.45
3547 3589 3.135167 GGTTGATGATTTGCCCCATGATT 59.865 43.478 0.00 0.00 0.00 2.57
3548 3590 4.384427 GGTTGATGATTTGCCCCATGATTT 60.384 41.667 0.00 0.00 0.00 2.17
3549 3591 4.409718 TGATGATTTGCCCCATGATTTG 57.590 40.909 0.00 0.00 0.00 2.32
3550 3592 3.775866 TGATGATTTGCCCCATGATTTGT 59.224 39.130 0.00 0.00 0.00 2.83
3551 3593 3.891422 TGATTTGCCCCATGATTTGTC 57.109 42.857 0.00 0.00 0.00 3.18
3552 3594 3.443052 TGATTTGCCCCATGATTTGTCT 58.557 40.909 0.00 0.00 0.00 3.41
3553 3595 3.448301 TGATTTGCCCCATGATTTGTCTC 59.552 43.478 0.00 0.00 0.00 3.36
3554 3596 2.601240 TTGCCCCATGATTTGTCTCA 57.399 45.000 0.00 0.00 0.00 3.27
3555 3597 2.601240 TGCCCCATGATTTGTCTCAA 57.399 45.000 0.00 0.00 0.00 3.02
3556 3598 3.104519 TGCCCCATGATTTGTCTCAAT 57.895 42.857 0.00 0.00 0.00 2.57
3557 3599 2.761767 TGCCCCATGATTTGTCTCAATG 59.238 45.455 0.00 0.00 0.00 2.82
3558 3600 2.101917 GCCCCATGATTTGTCTCAATGG 59.898 50.000 0.00 0.00 0.00 3.16
3559 3601 2.101917 CCCCATGATTTGTCTCAATGGC 59.898 50.000 0.00 0.00 0.00 4.40
3560 3602 2.761767 CCCATGATTTGTCTCAATGGCA 59.238 45.455 0.00 0.00 0.00 4.92
3561 3603 3.181479 CCCATGATTTGTCTCAATGGCAG 60.181 47.826 0.00 0.00 0.00 4.85
3562 3604 3.446161 CCATGATTTGTCTCAATGGCAGT 59.554 43.478 0.00 0.00 0.00 4.40
3563 3605 4.421058 CATGATTTGTCTCAATGGCAGTG 58.579 43.478 8.96 8.96 0.00 3.66
3564 3606 2.821378 TGATTTGTCTCAATGGCAGTGG 59.179 45.455 15.62 6.11 0.00 4.00
3565 3607 0.961019 TTTGTCTCAATGGCAGTGGC 59.039 50.000 15.62 10.30 40.13 5.01
3566 3608 0.111061 TTGTCTCAATGGCAGTGGCT 59.889 50.000 18.53 0.36 40.87 4.75
3567 3609 0.321919 TGTCTCAATGGCAGTGGCTC 60.322 55.000 18.53 6.21 40.87 4.70
3568 3610 1.028868 GTCTCAATGGCAGTGGCTCC 61.029 60.000 18.53 0.00 40.87 4.70
3569 3611 1.001764 CTCAATGGCAGTGGCTCCA 60.002 57.895 18.53 4.22 40.87 3.86
3570 3612 1.001764 TCAATGGCAGTGGCTCCAG 60.002 57.895 18.53 5.54 40.87 3.86
3571 3613 2.050350 CAATGGCAGTGGCTCCAGG 61.050 63.158 18.53 0.00 40.87 4.45
3572 3614 3.951769 AATGGCAGTGGCTCCAGGC 62.952 63.158 18.53 4.43 40.87 4.85
3590 3632 3.775654 CCCACCCGGCAGTCTCTC 61.776 72.222 0.00 0.00 0.00 3.20
3591 3633 2.997315 CCACCCGGCAGTCTCTCA 60.997 66.667 0.00 0.00 0.00 3.27
3592 3634 2.575993 CACCCGGCAGTCTCTCAG 59.424 66.667 0.00 0.00 0.00 3.35
3593 3635 2.681778 ACCCGGCAGTCTCTCAGG 60.682 66.667 0.00 0.00 0.00 3.86
3594 3636 3.465403 CCCGGCAGTCTCTCAGGG 61.465 72.222 0.00 0.00 0.00 4.45
3595 3637 3.465403 CCGGCAGTCTCTCAGGGG 61.465 72.222 0.00 0.00 0.00 4.79
3596 3638 2.363018 CGGCAGTCTCTCAGGGGA 60.363 66.667 0.00 0.00 0.00 4.81
3597 3639 2.422231 CGGCAGTCTCTCAGGGGAG 61.422 68.421 0.00 0.00 42.80 4.30
3610 3652 6.829985 TCTCAGGGGAGATAAATGATCAAA 57.170 37.500 0.00 0.00 45.12 2.69
3611 3653 7.398289 TCTCAGGGGAGATAAATGATCAAAT 57.602 36.000 0.00 0.00 45.12 2.32
3612 3654 7.229308 TCTCAGGGGAGATAAATGATCAAATG 58.771 38.462 0.00 0.00 45.12 2.32
3613 3655 7.072834 TCTCAGGGGAGATAAATGATCAAATGA 59.927 37.037 0.00 0.00 45.12 2.57
3614 3656 7.585440 TCAGGGGAGATAAATGATCAAATGAA 58.415 34.615 0.00 0.00 36.98 2.57
3615 3657 7.722728 TCAGGGGAGATAAATGATCAAATGAAG 59.277 37.037 0.00 0.00 36.98 3.02
3616 3658 7.722728 CAGGGGAGATAAATGATCAAATGAAGA 59.277 37.037 0.00 0.00 36.98 2.87
3617 3659 8.284435 AGGGGAGATAAATGATCAAATGAAGAA 58.716 33.333 0.00 0.00 36.98 2.52
3618 3660 8.574737 GGGGAGATAAATGATCAAATGAAGAAG 58.425 37.037 0.00 0.00 36.98 2.85
3619 3661 9.129532 GGGAGATAAATGATCAAATGAAGAAGT 57.870 33.333 0.00 0.00 36.98 3.01
3627 3669 9.903682 AATGATCAAATGAAGAAGTAAAGTGTG 57.096 29.630 0.00 0.00 0.00 3.82
3628 3670 7.874940 TGATCAAATGAAGAAGTAAAGTGTGG 58.125 34.615 0.00 0.00 0.00 4.17
3629 3671 6.072112 TCAAATGAAGAAGTAAAGTGTGGC 57.928 37.500 0.00 0.00 0.00 5.01
3630 3672 5.592282 TCAAATGAAGAAGTAAAGTGTGGCA 59.408 36.000 0.00 0.00 0.00 4.92
3631 3673 6.096141 TCAAATGAAGAAGTAAAGTGTGGCAA 59.904 34.615 0.00 0.00 0.00 4.52
3632 3674 6.463995 AATGAAGAAGTAAAGTGTGGCAAA 57.536 33.333 0.00 0.00 0.00 3.68
3633 3675 5.906113 TGAAGAAGTAAAGTGTGGCAAAA 57.094 34.783 0.00 0.00 0.00 2.44
3634 3676 5.890334 TGAAGAAGTAAAGTGTGGCAAAAG 58.110 37.500 0.00 0.00 0.00 2.27
3635 3677 5.650266 TGAAGAAGTAAAGTGTGGCAAAAGA 59.350 36.000 0.00 0.00 0.00 2.52
3636 3678 6.321181 TGAAGAAGTAAAGTGTGGCAAAAGAT 59.679 34.615 0.00 0.00 0.00 2.40
3637 3679 6.319141 AGAAGTAAAGTGTGGCAAAAGATC 57.681 37.500 0.00 0.00 0.00 2.75
3638 3680 5.827797 AGAAGTAAAGTGTGGCAAAAGATCA 59.172 36.000 0.00 0.00 0.00 2.92
3639 3681 6.321181 AGAAGTAAAGTGTGGCAAAAGATCAA 59.679 34.615 0.00 0.00 0.00 2.57
3640 3682 6.655078 AGTAAAGTGTGGCAAAAGATCAAT 57.345 33.333 0.00 0.00 0.00 2.57
3641 3683 6.681777 AGTAAAGTGTGGCAAAAGATCAATC 58.318 36.000 0.00 0.00 0.00 2.67
3642 3684 5.796424 AAAGTGTGGCAAAAGATCAATCT 57.204 34.783 0.00 0.00 39.22 2.40
3711 3753 8.725405 TTTCATCAGTTAATAAAGTATCGGCA 57.275 30.769 0.00 0.00 0.00 5.69
3712 3754 8.902540 TTCATCAGTTAATAAAGTATCGGCAT 57.097 30.769 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 6.697892 GGTATAAGCACTATGACAGTTCTGTC 59.302 42.308 21.57 21.57 34.26 3.51
203 204 3.375699 GTCCAGAATCTCCCTCAACCTA 58.624 50.000 0.00 0.00 0.00 3.08
579 580 6.378280 AGTTTTTCAACAAACATGAGAGTCCT 59.622 34.615 0.00 0.00 38.86 3.85
1467 1475 5.360714 ACCCATATTGCATACAGGTTTGAAG 59.639 40.000 0.00 0.00 0.00 3.02
1578 1586 6.447162 CATGTTCATGATAGCATTTGCATCT 58.553 36.000 6.94 0.00 45.16 2.90
1620 1628 3.181463 CCCATGCCCAAAAATCAGGTATG 60.181 47.826 0.00 0.00 41.76 2.39
1846 1855 1.640917 TCCCCTATATGTCTTCGGCC 58.359 55.000 0.00 0.00 0.00 6.13
2024 2033 2.305927 TCTCTCCCAATGAAACTGGGAC 59.694 50.000 6.49 0.00 46.13 4.46
2574 2586 1.404391 GCAACCTCATTGGCATCTCTG 59.596 52.381 0.00 0.00 38.88 3.35
2646 2658 4.797471 TCAATGAAGCAGGAAAAACATCG 58.203 39.130 0.00 0.00 0.00 3.84
2655 2667 1.006281 AGGGCAATCAATGAAGCAGGA 59.994 47.619 11.98 0.00 0.00 3.86
2806 2823 6.401047 GGGATTTAATTTCGCAAGTCAAAAGC 60.401 38.462 0.00 0.00 39.48 3.51
2819 2836 5.816449 TTTCGTACCGGGGATTTAATTTC 57.184 39.130 6.32 0.00 0.00 2.17
2833 2850 0.250597 AGGCAGGGTGTTTTCGTACC 60.251 55.000 0.00 0.00 36.21 3.34
2891 2918 2.187599 GAGCGCGCTGGATGTTTGTT 62.188 55.000 41.82 10.17 0.00 2.83
2917 2944 1.437986 CAGGAGGAACCGATCGACC 59.562 63.158 18.66 16.21 44.74 4.79
2918 2945 1.227002 GCAGGAGGAACCGATCGAC 60.227 63.158 18.66 7.50 44.74 4.20
2929 2956 2.123982 GATGGCCAAGGCAGGAGG 60.124 66.667 10.96 0.00 42.43 4.30
2936 2963 2.825836 GTCAGCGGATGGCCAAGG 60.826 66.667 10.96 2.52 45.17 3.61
3142 3180 0.913205 TTTAGCCGGCATTAGGTGGA 59.087 50.000 31.54 0.12 0.00 4.02
3147 3185 4.096382 ACAAACAGATTTAGCCGGCATTAG 59.904 41.667 31.54 13.65 0.00 1.73
3160 3199 2.607771 GCATGCACGGAACAAACAGATT 60.608 45.455 14.21 0.00 0.00 2.40
3168 3207 3.342909 CACTGCATGCACGGAACA 58.657 55.556 18.46 0.00 0.00 3.18
3223 3262 7.387122 ACCTAGCTGTAACTAACTAAACAAAGC 59.613 37.037 0.00 0.00 0.00 3.51
3236 3278 0.546747 TGCCCCACCTAGCTGTAACT 60.547 55.000 0.00 0.00 0.00 2.24
3243 3285 2.359975 GTGTGTGCCCCACCTAGC 60.360 66.667 1.61 0.00 43.85 3.42
3298 3340 4.982295 GCACAGGTGTTTCCATTTTTCTAC 59.018 41.667 0.91 0.00 39.02 2.59
3377 3419 6.016108 ACTGGTTCTACTCTGTCACTTTCTAC 60.016 42.308 0.00 0.00 0.00 2.59
3408 3450 1.856265 GCAAGGAACCAACCGCTCAG 61.856 60.000 0.00 0.00 34.73 3.35
3417 3459 2.280524 CGACGTGGCAAGGAACCA 60.281 61.111 5.22 0.00 33.84 3.67
3470 3512 4.556699 GCGAGCTTCAAAAACCAGTGTAAT 60.557 41.667 0.00 0.00 0.00 1.89
3471 3513 3.242936 GCGAGCTTCAAAAACCAGTGTAA 60.243 43.478 0.00 0.00 0.00 2.41
3474 3516 1.065401 TGCGAGCTTCAAAAACCAGTG 59.935 47.619 0.00 0.00 0.00 3.66
3476 3518 1.758783 GTGCGAGCTTCAAAAACCAG 58.241 50.000 0.00 0.00 0.00 4.00
3483 3525 1.954146 GGTGACGTGCGAGCTTCAA 60.954 57.895 0.00 0.00 0.00 2.69
3503 3545 7.601705 ACCCTTTGTAAATATATGCAAGCAT 57.398 32.000 12.66 12.66 40.19 3.79
3504 3546 7.123397 TCAACCCTTTGTAAATATATGCAAGCA 59.877 33.333 0.00 0.00 34.02 3.91
3505 3547 7.488322 TCAACCCTTTGTAAATATATGCAAGC 58.512 34.615 0.00 0.00 34.02 4.01
3506 3548 9.467258 CATCAACCCTTTGTAAATATATGCAAG 57.533 33.333 0.00 0.00 34.02 4.01
3507 3549 9.194972 TCATCAACCCTTTGTAAATATATGCAA 57.805 29.630 0.00 0.00 34.02 4.08
3508 3550 8.759481 TCATCAACCCTTTGTAAATATATGCA 57.241 30.769 0.00 0.00 34.02 3.96
3513 3555 7.986889 GGCAAATCATCAACCCTTTGTAAATAT 59.013 33.333 0.00 0.00 34.02 1.28
3514 3556 7.327214 GGCAAATCATCAACCCTTTGTAAATA 58.673 34.615 0.00 0.00 34.02 1.40
3515 3557 6.172630 GGCAAATCATCAACCCTTTGTAAAT 58.827 36.000 0.00 0.00 34.02 1.40
3516 3558 5.512232 GGGCAAATCATCAACCCTTTGTAAA 60.512 40.000 0.00 0.00 37.59 2.01
3517 3559 4.020662 GGGCAAATCATCAACCCTTTGTAA 60.021 41.667 0.00 0.00 37.59 2.41
3518 3560 3.513515 GGGCAAATCATCAACCCTTTGTA 59.486 43.478 0.00 0.00 37.59 2.41
3519 3561 2.302733 GGGCAAATCATCAACCCTTTGT 59.697 45.455 0.00 0.00 37.59 2.83
3520 3562 2.355007 GGGGCAAATCATCAACCCTTTG 60.355 50.000 0.00 0.00 40.64 2.77
3521 3563 1.908619 GGGGCAAATCATCAACCCTTT 59.091 47.619 0.00 0.00 40.64 3.11
3522 3564 1.203288 TGGGGCAAATCATCAACCCTT 60.203 47.619 0.00 0.00 40.64 3.95
3523 3565 0.413037 TGGGGCAAATCATCAACCCT 59.587 50.000 0.00 0.00 40.64 4.34
3524 3566 1.139455 CATGGGGCAAATCATCAACCC 59.861 52.381 0.00 0.00 40.05 4.11
3525 3567 2.109774 TCATGGGGCAAATCATCAACC 58.890 47.619 0.00 0.00 0.00 3.77
3526 3568 4.411256 AATCATGGGGCAAATCATCAAC 57.589 40.909 0.00 0.00 0.00 3.18
3527 3569 4.225492 ACAAATCATGGGGCAAATCATCAA 59.775 37.500 0.00 0.00 0.00 2.57
3528 3570 3.775866 ACAAATCATGGGGCAAATCATCA 59.224 39.130 0.00 0.00 0.00 3.07
3529 3571 4.100498 AGACAAATCATGGGGCAAATCATC 59.900 41.667 0.00 0.00 0.00 2.92
3530 3572 4.035112 AGACAAATCATGGGGCAAATCAT 58.965 39.130 0.00 0.00 0.00 2.45
3531 3573 3.443052 AGACAAATCATGGGGCAAATCA 58.557 40.909 0.00 0.00 0.00 2.57
3532 3574 3.448301 TGAGACAAATCATGGGGCAAATC 59.552 43.478 0.00 0.00 0.00 2.17
3533 3575 3.443052 TGAGACAAATCATGGGGCAAAT 58.557 40.909 0.00 0.00 0.00 2.32
3534 3576 2.886913 TGAGACAAATCATGGGGCAAA 58.113 42.857 0.00 0.00 0.00 3.68
3535 3577 2.601240 TGAGACAAATCATGGGGCAA 57.399 45.000 0.00 0.00 0.00 4.52
3536 3578 2.601240 TTGAGACAAATCATGGGGCA 57.399 45.000 0.00 0.00 0.00 5.36
3537 3579 2.101917 CCATTGAGACAAATCATGGGGC 59.898 50.000 0.00 0.00 30.53 5.80
3538 3580 2.101917 GCCATTGAGACAAATCATGGGG 59.898 50.000 0.00 0.00 32.76 4.96
3539 3581 2.761767 TGCCATTGAGACAAATCATGGG 59.238 45.455 0.00 0.00 32.76 4.00
3540 3582 3.446161 ACTGCCATTGAGACAAATCATGG 59.554 43.478 0.00 0.00 34.06 3.66
3541 3583 4.421058 CACTGCCATTGAGACAAATCATG 58.579 43.478 0.00 0.00 0.00 3.07
3542 3584 3.446161 CCACTGCCATTGAGACAAATCAT 59.554 43.478 0.00 0.00 0.00 2.45
3543 3585 2.821378 CCACTGCCATTGAGACAAATCA 59.179 45.455 0.00 0.00 0.00 2.57
3544 3586 2.416431 GCCACTGCCATTGAGACAAATC 60.416 50.000 0.00 0.00 0.00 2.17
3545 3587 1.547372 GCCACTGCCATTGAGACAAAT 59.453 47.619 0.00 0.00 0.00 2.32
3546 3588 0.961019 GCCACTGCCATTGAGACAAA 59.039 50.000 0.00 0.00 0.00 2.83
3547 3589 0.111061 AGCCACTGCCATTGAGACAA 59.889 50.000 0.00 0.00 38.69 3.18
3548 3590 0.321919 GAGCCACTGCCATTGAGACA 60.322 55.000 0.00 0.00 38.69 3.41
3549 3591 1.028868 GGAGCCACTGCCATTGAGAC 61.029 60.000 0.00 0.00 38.69 3.36
3550 3592 1.300963 GGAGCCACTGCCATTGAGA 59.699 57.895 0.00 0.00 38.69 3.27
3551 3593 1.001764 TGGAGCCACTGCCATTGAG 60.002 57.895 0.00 0.00 38.69 3.02
3552 3594 1.001764 CTGGAGCCACTGCCATTGA 60.002 57.895 0.00 0.00 38.69 2.57
3553 3595 2.050350 CCTGGAGCCACTGCCATTG 61.050 63.158 0.00 0.00 38.69 2.82
3554 3596 2.357836 CCTGGAGCCACTGCCATT 59.642 61.111 0.00 0.00 38.69 3.16
3555 3597 4.437587 GCCTGGAGCCACTGCCAT 62.438 66.667 0.00 0.00 38.69 4.40
3573 3615 3.775654 GAGAGACTGCCGGGTGGG 61.776 72.222 2.18 0.00 39.58 4.61
3574 3616 2.997315 TGAGAGACTGCCGGGTGG 60.997 66.667 2.18 0.00 38.77 4.61
3575 3617 2.575993 CTGAGAGACTGCCGGGTG 59.424 66.667 2.18 0.00 0.00 4.61
3576 3618 2.681778 CCTGAGAGACTGCCGGGT 60.682 66.667 2.18 0.00 0.00 5.28
3577 3619 3.465403 CCCTGAGAGACTGCCGGG 61.465 72.222 2.18 0.00 0.00 5.73
3578 3620 3.465403 CCCCTGAGAGACTGCCGG 61.465 72.222 0.00 0.00 0.00 6.13
3579 3621 2.363018 TCCCCTGAGAGACTGCCG 60.363 66.667 0.00 0.00 0.00 5.69
3580 3622 1.000993 TCTCCCCTGAGAGACTGCC 59.999 63.158 0.00 0.00 42.73 4.85
3581 3623 4.774820 TCTCCCCTGAGAGACTGC 57.225 61.111 0.00 0.00 42.73 4.40
3588 3630 7.229308 TCATTTGATCATTTATCTCCCCTGAG 58.771 38.462 0.00 0.00 40.17 3.35
3589 3631 7.152942 TCATTTGATCATTTATCTCCCCTGA 57.847 36.000 0.00 0.00 35.45 3.86
3590 3632 7.722728 TCTTCATTTGATCATTTATCTCCCCTG 59.277 37.037 0.00 0.00 35.45 4.45
3591 3633 7.819500 TCTTCATTTGATCATTTATCTCCCCT 58.180 34.615 0.00 0.00 35.45 4.79
3592 3634 8.469309 TTCTTCATTTGATCATTTATCTCCCC 57.531 34.615 0.00 0.00 35.45 4.81
3593 3635 9.129532 ACTTCTTCATTTGATCATTTATCTCCC 57.870 33.333 0.00 0.00 35.45 4.30
3601 3643 9.903682 CACACTTTACTTCTTCATTTGATCATT 57.096 29.630 0.00 0.00 0.00 2.57
3602 3644 8.517878 CCACACTTTACTTCTTCATTTGATCAT 58.482 33.333 0.00 0.00 0.00 2.45
3603 3645 7.522073 GCCACACTTTACTTCTTCATTTGATCA 60.522 37.037 0.00 0.00 0.00 2.92
3604 3646 6.803807 GCCACACTTTACTTCTTCATTTGATC 59.196 38.462 0.00 0.00 0.00 2.92
3605 3647 6.265196 TGCCACACTTTACTTCTTCATTTGAT 59.735 34.615 0.00 0.00 0.00 2.57
3606 3648 5.592282 TGCCACACTTTACTTCTTCATTTGA 59.408 36.000 0.00 0.00 0.00 2.69
3607 3649 5.830912 TGCCACACTTTACTTCTTCATTTG 58.169 37.500 0.00 0.00 0.00 2.32
3608 3650 6.463995 TTGCCACACTTTACTTCTTCATTT 57.536 33.333 0.00 0.00 0.00 2.32
3609 3651 6.463995 TTTGCCACACTTTACTTCTTCATT 57.536 33.333 0.00 0.00 0.00 2.57
3610 3652 6.321181 TCTTTTGCCACACTTTACTTCTTCAT 59.679 34.615 0.00 0.00 0.00 2.57
3611 3653 5.650266 TCTTTTGCCACACTTTACTTCTTCA 59.350 36.000 0.00 0.00 0.00 3.02
3612 3654 6.131544 TCTTTTGCCACACTTTACTTCTTC 57.868 37.500 0.00 0.00 0.00 2.87
3613 3655 6.321181 TGATCTTTTGCCACACTTTACTTCTT 59.679 34.615 0.00 0.00 0.00 2.52
3614 3656 5.827797 TGATCTTTTGCCACACTTTACTTCT 59.172 36.000 0.00 0.00 0.00 2.85
3615 3657 6.072112 TGATCTTTTGCCACACTTTACTTC 57.928 37.500 0.00 0.00 0.00 3.01
3616 3658 6.463995 TTGATCTTTTGCCACACTTTACTT 57.536 33.333 0.00 0.00 0.00 2.24
3617 3659 6.491403 AGATTGATCTTTTGCCACACTTTACT 59.509 34.615 0.00 0.00 31.97 2.24
3618 3660 6.681777 AGATTGATCTTTTGCCACACTTTAC 58.318 36.000 0.00 0.00 31.97 2.01
3619 3661 6.899393 AGATTGATCTTTTGCCACACTTTA 57.101 33.333 0.00 0.00 31.97 1.85
3620 3662 5.796424 AGATTGATCTTTTGCCACACTTT 57.204 34.783 0.00 0.00 31.97 2.66
3621 3663 5.796424 AAGATTGATCTTTTGCCACACTT 57.204 34.783 0.44 0.00 44.28 3.16
3685 3727 9.337396 TGCCGATACTTTATTAACTGATGAAAT 57.663 29.630 0.00 0.00 0.00 2.17
3686 3728 8.725405 TGCCGATACTTTATTAACTGATGAAA 57.275 30.769 0.00 0.00 0.00 2.69
3687 3729 8.902540 ATGCCGATACTTTATTAACTGATGAA 57.097 30.769 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.