Multiple sequence alignment - TraesCS3B01G214000

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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 TraesCS3B01G214000 chr3B 100.000 4095 0 0 1 4095 253897591 253893497 0.000000e+00 7563
1 TraesCS3B01G214000 chr3D 96.580 3421 76 18 1 3398 174927310 174923908 0.000000e+00 5631
2 TraesCS3B01G214000 chr3A 95.940 3424 89 21 1 3398 214291315 214287916 0.000000e+00 5507
3 TraesCS3B01G214000 chr4D 92.100 481 37 1 3616 4095 394957037 394956557 0.000000e+00 676
4 TraesCS3B01G214000 chr4D 94.977 219 10 1 3399 3616 394957222 394957004 3.920000e-90 342
5 TraesCS3B01G214000 chr6B 88.358 481 54 2 3616 4095 646235507 646235028 9.870000e-161 577
6 TraesCS3B01G214000 chr6B 88.991 218 23 1 3400 3616 225199665 225199448 6.750000e-68 268
7 TraesCS3B01G214000 chr1A 88.494 478 54 1 3616 4092 257408751 257408274 9.870000e-161 577
8 TraesCS3B01G214000 chr1A 91.705 217 17 1 3401 3616 257408934 257408718 2.390000e-77 300
9 TraesCS3B01G214000 chr1A 88.938 226 22 3 3393 3616 19848258 19848482 4.030000e-70 276
10 TraesCS3B01G214000 chr1A 88.053 226 24 3 3393 3616 19817537 19817761 8.730000e-67 265
11 TraesCS3B01G214000 chr7D 88.715 319 35 1 3778 4095 179023770 179023452 4.960000e-104 388
12 TraesCS3B01G214000 chr7D 92.202 218 17 0 3399 3616 179119349 179119132 3.980000e-80 309
13 TraesCS3B01G214000 chr7D 94.410 161 9 0 3616 3776 179119165 179119005 8.790000e-62 248
14 TraesCS3B01G214000 chr4B 94.495 218 11 1 3400 3616 180562633 180562416 6.560000e-88 335
15 TraesCS3B01G214000 chr6D 90.909 220 19 1 3398 3616 443748179 443748398 1.110000e-75 294
16 TraesCS3B01G214000 chr2D 90.000 220 21 1 3398 3616 68622979 68622760 2.410000e-72 283


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 TraesCS3B01G214000 chr3B 253893497 253897591 4094 True 7563.0 7563 100.0000 1 4095 1 chr3B.!!$R1 4094
1 TraesCS3B01G214000 chr3D 174923908 174927310 3402 True 5631.0 5631 96.5800 1 3398 1 chr3D.!!$R1 3397
2 TraesCS3B01G214000 chr3A 214287916 214291315 3399 True 5507.0 5507 95.9400 1 3398 1 chr3A.!!$R1 3397
3 TraesCS3B01G214000 chr4D 394956557 394957222 665 True 509.0 676 93.5385 3399 4095 2 chr4D.!!$R1 696
4 TraesCS3B01G214000 chr1A 257408274 257408934 660 True 438.5 577 90.0995 3401 4092 2 chr1A.!!$R1 691

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
612 625 1.860676 TTTCTCGTGACACCCGAAAG 58.139 50.000 11.01 0.0 33.34 2.62 F
1015 1030 2.290577 ACAGAGATGGCTGGAAAAGGAC 60.291 50.000 0.00 0.0 40.20 3.85 F
2161 2183 2.009042 GCCTTTCTGGATGTCGTCTGG 61.009 57.143 0.00 0.0 38.35 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 1808 0.177604 GCTCCAGTGAGATGTCAGGG 59.822 60.0 0.00 0.0 41.42 4.45 R
2297 2319 0.249398 AATGGACGTAGGACCAGCAC 59.751 55.0 11.98 0.0 40.68 4.40 R
3756 3789 0.319297 GCACTTCAAAGGCAAGCTGG 60.319 55.0 0.00 0.0 0.00 4.85 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
234 235 3.665745 TTGGATTTCTGCTTGCTTTCC 57.334 42.857 0.00 0.00 0.00 3.13
422 435 3.576118 CTCACGTCATCCCTGATAGGATT 59.424 47.826 0.00 0.00 44.61 3.01
453 466 2.502538 TGTTATAAGAGTTCCGTGGGGG 59.497 50.000 0.00 0.00 37.02 5.40
475 488 4.633126 GGTGTAACGGTAAGAAAGAATCCC 59.367 45.833 0.00 0.00 38.12 3.85
490 503 2.194201 ATCCCTTGTTACCGTTGTGG 57.806 50.000 0.00 0.00 46.41 4.17
544 557 7.792032 TCCATAATTCCGTTTCTATCTTGAGT 58.208 34.615 0.00 0.00 0.00 3.41
578 591 3.383185 ACACCGAATTGGAAAGCTTGAAA 59.617 39.130 0.00 0.00 42.00 2.69
612 625 1.860676 TTTCTCGTGACACCCGAAAG 58.139 50.000 11.01 0.00 33.34 2.62
622 635 2.465860 CACCCGAAAGTATGGTGTGA 57.534 50.000 0.00 0.00 43.62 3.58
705 719 2.539688 GCTTGTTTTTGCCAACTGCTAC 59.460 45.455 0.00 0.00 42.00 3.58
719 733 6.504398 CCAACTGCTACTGTTCTCGATTATA 58.496 40.000 0.00 0.00 0.00 0.98
758 772 4.459330 TCGGAATTATGACATGCCATCAA 58.541 39.130 0.00 0.00 0.00 2.57
767 781 4.338012 TGACATGCCATCAATTCAAGAGT 58.662 39.130 0.00 0.00 0.00 3.24
795 810 7.951591 ACTGGTAAACATGCATTTACTCTTTT 58.048 30.769 17.94 4.57 42.34 2.27
876 891 5.767816 ATCAAACACACCAGAAGTTTACC 57.232 39.130 0.00 0.00 34.03 2.85
920 935 3.599412 GGTCTCTGCACCGTGTTAA 57.401 52.632 0.00 0.00 0.00 2.01
943 958 3.364621 GCGGCACTGTTGAATGTTTTATG 59.635 43.478 0.00 0.00 0.00 1.90
984 999 6.040391 TGTGCTTTTATTTTACCAGAACTGCT 59.960 34.615 0.00 0.00 0.00 4.24
1015 1030 2.290577 ACAGAGATGGCTGGAAAAGGAC 60.291 50.000 0.00 0.00 40.20 3.85
1253 1268 5.163530 TGCTATTTGGTTGCATGATAGGTTG 60.164 40.000 0.00 0.00 33.63 3.77
1278 1293 9.179909 TGAAAAGTAAATCTTCAAACTGTACCA 57.820 29.630 0.00 0.00 35.02 3.25
1395 1417 4.373156 AGGAAGTAGGAACAAGTGCATT 57.627 40.909 0.00 0.00 0.00 3.56
1447 1469 6.120507 ACTTATGAGAGAAACTTCTTGCCT 57.879 37.500 0.00 0.00 37.73 4.75
1448 1470 6.538263 ACTTATGAGAGAAACTTCTTGCCTT 58.462 36.000 0.00 0.00 37.73 4.35
1449 1471 7.001073 ACTTATGAGAGAAACTTCTTGCCTTT 58.999 34.615 0.00 0.00 37.73 3.11
1450 1472 8.157476 ACTTATGAGAGAAACTTCTTGCCTTTA 58.843 33.333 0.00 0.00 37.73 1.85
1601 1623 4.672587 ATCTGGTCGAATGCTTAGCTAA 57.327 40.909 5.60 5.94 0.00 3.09
1772 1794 4.054780 ACTGTCTTGTTCAGCGTTCTAA 57.945 40.909 0.00 0.00 36.50 2.10
1786 1808 6.091713 TCAGCGTTCTAAGTGCTAAAATTACC 59.908 38.462 0.00 0.00 37.15 2.85
1788 1810 5.448225 GCGTTCTAAGTGCTAAAATTACCCC 60.448 44.000 0.00 0.00 0.00 4.95
1791 1813 6.630203 TCTAAGTGCTAAAATTACCCCTGA 57.370 37.500 0.00 0.00 0.00 3.86
1846 1868 6.692486 TGAGACAAACTGAGATCCTTAAGAC 58.308 40.000 3.36 0.00 0.00 3.01
1886 1908 8.292448 GTGATAATGTGCCAATTTATCGAGAAT 58.708 33.333 0.00 0.00 35.87 2.40
1914 1936 3.246403 GCTTTCTGCTGCCTTCTCT 57.754 52.632 0.00 0.00 38.95 3.10
2161 2183 2.009042 GCCTTTCTGGATGTCGTCTGG 61.009 57.143 0.00 0.00 38.35 3.86
2297 2319 5.048782 TGTTTAAGACACATTAAGCCTGCAG 60.049 40.000 6.78 6.78 32.00 4.41
2345 2372 7.659390 CCACCTCTTAATTCTGCTTCCTAATAG 59.341 40.741 0.00 0.00 0.00 1.73
2604 2631 0.879400 CTCTCGCTGGATCATGCACC 60.879 60.000 9.33 0.00 0.00 5.01
2607 2634 1.746239 CGCTGGATCATGCACCACA 60.746 57.895 6.60 0.00 32.44 4.17
2730 2757 0.949105 ACCGCCAAGCACTAAGAACG 60.949 55.000 0.00 0.00 0.00 3.95
2770 2797 2.032030 CGTAGTTTGAACTTGTGCCAGG 60.032 50.000 1.20 0.00 40.37 4.45
2775 2802 0.819259 TGAACTTGTGCCAGGCTGTC 60.819 55.000 14.15 0.00 0.00 3.51
2837 2864 6.038161 TGACATGTTATTAATCCTTTGGCTCG 59.962 38.462 0.00 0.00 0.00 5.03
2866 2893 4.435425 GCAATTGCCTTATCTTGCATTCA 58.565 39.130 20.06 0.00 42.66 2.57
2870 2897 5.664294 TTGCCTTATCTTGCATTCATGTT 57.336 34.783 0.00 0.00 37.33 2.71
2882 2909 6.528014 TGCATTCATGTTGTGATTTGTTTC 57.472 33.333 0.00 0.00 36.54 2.78
3033 3060 0.171455 ATCCGCGAGAGAACAGACAC 59.829 55.000 8.23 0.00 0.00 3.67
3088 3115 0.729116 CGGTGCAGACAATGGATGAC 59.271 55.000 0.00 0.00 0.00 3.06
3132 3164 5.677091 GCAAACATATCCTGACTCGCAAATT 60.677 40.000 0.00 0.00 0.00 1.82
3210 3242 3.245797 CCACAACTACGATGTCAGACTG 58.754 50.000 1.31 0.00 0.00 3.51
3235 3267 4.910458 ACAGCTGGTGTAAAGATAACCT 57.090 40.909 19.93 0.00 37.75 3.50
3286 3318 1.388547 ACCTGTTGTTGCACGATTGT 58.611 45.000 0.00 0.00 0.00 2.71
3392 3424 0.034896 GTGCCTATACACCCGGATGG 59.965 60.000 0.73 0.00 41.37 3.51
3446 3478 7.717875 AGCATACCGTATTTTTATAGAAGGCAA 59.282 33.333 0.00 0.00 0.00 4.52
3450 3482 7.255569 ACCGTATTTTTATAGAAGGCAAAAGC 58.744 34.615 0.00 0.00 0.00 3.51
3468 3500 3.828875 AGCTTATGTACAAGAGCCCTC 57.171 47.619 22.77 4.08 35.79 4.30
3486 3518 2.061773 CTCACGAGATGCGAACAAGTT 58.938 47.619 0.00 0.00 44.57 2.66
3571 3604 1.192146 AAGCACCAACTCCGCCTAGA 61.192 55.000 0.00 0.00 0.00 2.43
3602 3635 7.618907 CCTTCCTCCAATCATCTATCTCATCTA 59.381 40.741 0.00 0.00 0.00 1.98
3603 3636 8.592529 TTCCTCCAATCATCTATCTCATCTAG 57.407 38.462 0.00 0.00 0.00 2.43
3604 3637 7.124721 TCCTCCAATCATCTATCTCATCTAGG 58.875 42.308 0.00 0.00 0.00 3.02
3605 3638 7.036279 TCCTCCAATCATCTATCTCATCTAGGA 60.036 40.741 0.00 0.00 0.00 2.94
3606 3639 7.785985 CCTCCAATCATCTATCTCATCTAGGAT 59.214 40.741 0.00 0.00 0.00 3.24
3607 3640 8.765488 TCCAATCATCTATCTCATCTAGGATC 57.235 38.462 0.00 0.00 0.00 3.36
3608 3641 8.567851 TCCAATCATCTATCTCATCTAGGATCT 58.432 37.037 0.00 0.00 0.00 2.75
3609 3642 8.853126 CCAATCATCTATCTCATCTAGGATCTC 58.147 40.741 0.00 0.00 0.00 2.75
3610 3643 9.636789 CAATCATCTATCTCATCTAGGATCTCT 57.363 37.037 0.00 0.00 0.00 3.10
3611 3644 9.636789 AATCATCTATCTCATCTAGGATCTCTG 57.363 37.037 0.00 0.00 0.00 3.35
3612 3645 8.161640 TCATCTATCTCATCTAGGATCTCTGT 57.838 38.462 0.00 0.00 0.00 3.41
3613 3646 8.267183 TCATCTATCTCATCTAGGATCTCTGTC 58.733 40.741 0.00 0.00 0.00 3.51
3614 3647 7.813087 TCTATCTCATCTAGGATCTCTGTCT 57.187 40.000 0.00 0.00 0.00 3.41
3615 3648 8.218423 TCTATCTCATCTAGGATCTCTGTCTT 57.782 38.462 0.00 0.00 0.00 3.01
3616 3649 8.321353 TCTATCTCATCTAGGATCTCTGTCTTC 58.679 40.741 0.00 0.00 0.00 2.87
3617 3650 5.630121 TCTCATCTAGGATCTCTGTCTTCC 58.370 45.833 0.00 0.00 0.00 3.46
3618 3651 5.133491 TCTCATCTAGGATCTCTGTCTTCCA 59.867 44.000 0.00 0.00 31.65 3.53
3619 3652 5.770919 TCATCTAGGATCTCTGTCTTCCAA 58.229 41.667 0.00 0.00 31.65 3.53
3620 3653 6.380414 TCATCTAGGATCTCTGTCTTCCAAT 58.620 40.000 0.00 0.00 31.65 3.16
3621 3654 6.493115 TCATCTAGGATCTCTGTCTTCCAATC 59.507 42.308 0.00 0.00 31.65 2.67
3622 3655 5.770919 TCTAGGATCTCTGTCTTCCAATCA 58.229 41.667 0.00 0.00 31.65 2.57
3623 3656 6.380414 TCTAGGATCTCTGTCTTCCAATCAT 58.620 40.000 0.00 0.00 31.65 2.45
3624 3657 5.549742 AGGATCTCTGTCTTCCAATCATC 57.450 43.478 0.00 0.00 31.65 2.92
3625 3658 5.218179 AGGATCTCTGTCTTCCAATCATCT 58.782 41.667 0.00 0.00 31.65 2.90
3626 3659 6.380414 AGGATCTCTGTCTTCCAATCATCTA 58.620 40.000 0.00 0.00 31.65 1.98
3627 3660 7.018150 AGGATCTCTGTCTTCCAATCATCTAT 58.982 38.462 0.00 0.00 31.65 1.98
3628 3661 7.178983 AGGATCTCTGTCTTCCAATCATCTATC 59.821 40.741 0.00 0.00 31.65 2.08
3629 3662 7.178983 GGATCTCTGTCTTCCAATCATCTATCT 59.821 40.741 0.00 0.00 0.00 1.98
3630 3663 7.523293 TCTCTGTCTTCCAATCATCTATCTC 57.477 40.000 0.00 0.00 0.00 2.75
3631 3664 7.065504 TCTCTGTCTTCCAATCATCTATCTCA 58.934 38.462 0.00 0.00 0.00 3.27
3632 3665 7.729431 TCTCTGTCTTCCAATCATCTATCTCAT 59.271 37.037 0.00 0.00 0.00 2.90
3633 3666 7.894708 TCTGTCTTCCAATCATCTATCTCATC 58.105 38.462 0.00 0.00 0.00 2.92
3634 3667 7.729431 TCTGTCTTCCAATCATCTATCTCATCT 59.271 37.037 0.00 0.00 0.00 2.90
3667 3700 2.472695 TAAGTTGTGCAGCCGATCTT 57.527 45.000 0.00 0.00 0.00 2.40
3673 3706 1.303561 TGCAGCCGATCTTTGCCTT 60.304 52.632 9.52 0.00 37.03 4.35
3676 3709 1.167851 CAGCCGATCTTTGCCTTGAA 58.832 50.000 0.00 0.00 0.00 2.69
3733 3766 2.601905 AGGGCCCATGCAATTAGAATC 58.398 47.619 27.56 0.00 40.13 2.52
3738 3771 3.254166 GCCCATGCAATTAGAATCGTGAT 59.746 43.478 0.00 0.00 37.47 3.06
3756 3789 2.695666 TGATGGAGTCGAATCCTCTTCC 59.304 50.000 30.04 15.47 40.29 3.46
3796 3829 0.339859 TCCTCTGGTCTAGCCACCAT 59.660 55.000 3.88 0.00 45.76 3.55
3805 3838 2.819608 GTCTAGCCACCATTGCAAGAAA 59.180 45.455 4.94 0.00 0.00 2.52
3836 3870 4.582869 TGTGGATGAGATTTGAGGTTGAG 58.417 43.478 0.00 0.00 0.00 3.02
3844 3878 5.013495 TGAGATTTGAGGTTGAGTCTCCATT 59.987 40.000 0.00 0.00 33.04 3.16
3873 3907 1.188219 ATGAGTGCCACACCTCTCGT 61.188 55.000 0.00 0.00 34.49 4.18
3887 3921 3.196901 ACCTCTCGTGCATAACCACAATA 59.803 43.478 0.00 0.00 35.47 1.90
3888 3922 3.555956 CCTCTCGTGCATAACCACAATAC 59.444 47.826 0.00 0.00 35.47 1.89
3910 3944 0.394352 AAGGATGTGGTCGGGATTGC 60.394 55.000 0.00 0.00 0.00 3.56
3930 3964 0.108186 CCTCATCTTGCAGGCACGTA 60.108 55.000 0.00 0.00 0.00 3.57
3960 3994 1.003580 GAAGGTGCATCTTGGAGACCA 59.996 52.381 19.03 0.00 0.00 4.02
4032 4066 5.929992 CCACATGAAGATTTTGCATTTGAGT 59.070 36.000 0.00 0.00 0.00 3.41
4080 4114 1.207791 CAGTGGGGGATCTAGCTTGT 58.792 55.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.387565 GAGCTTAGCTCGGGGAAGAG 59.612 60.000 18.89 0.00 45.85 2.85
120 121 0.767998 GGCAGATAAGAGGGAAGGGG 59.232 60.000 0.00 0.00 0.00 4.79
234 235 6.854892 GCGGATTACAGATTTCAATTGATCAG 59.145 38.462 9.40 4.53 0.00 2.90
279 280 2.654079 CCAGTCCAGGAGCGCTCTT 61.654 63.158 34.46 26.82 0.00 2.85
389 402 9.035890 TCAGGGATGACGTGAGATATATAAAAT 57.964 33.333 0.00 0.00 38.93 1.82
390 403 8.417273 TCAGGGATGACGTGAGATATATAAAA 57.583 34.615 0.00 0.00 38.93 1.52
405 418 7.918076 TGGTAAATAATCCTATCAGGGATGAC 58.082 38.462 0.00 0.00 44.50 3.06
446 459 0.390209 CTTACCGTTACACCCCCACG 60.390 60.000 0.00 0.00 0.00 4.94
453 466 5.485620 AGGGATTCTTTCTTACCGTTACAC 58.514 41.667 0.00 0.00 0.00 2.90
490 503 5.803020 AAGCTATCCACAAATCGAGAAAC 57.197 39.130 0.00 0.00 0.00 2.78
496 509 7.819415 TGGATCTAATAAGCTATCCACAAATCG 59.181 37.037 9.18 0.00 42.25 3.34
544 557 0.684535 TTCGGTGTCAGGCTCATGAA 59.315 50.000 0.00 0.00 0.00 2.57
578 591 8.082242 TGTCACGAGAAATACATCGATATGAAT 58.918 33.333 0.00 0.00 41.40 2.57
598 611 1.337447 ACCATACTTTCGGGTGTCACG 60.337 52.381 0.00 0.00 32.60 4.35
612 625 3.350219 ACCACCATCTTCACACCATAC 57.650 47.619 0.00 0.00 0.00 2.39
622 635 1.950484 GCATCACGGAACCACCATCTT 60.950 52.381 0.00 0.00 38.90 2.40
758 772 7.230510 TGCATGTTTACCAGTTAACTCTTGAAT 59.769 33.333 4.77 0.00 0.00 2.57
767 781 8.630054 AGAGTAAATGCATGTTTACCAGTTAA 57.370 30.769 15.92 0.00 42.68 2.01
876 891 5.295292 AGCTTTAGTGATGACATTTCGGATG 59.705 40.000 0.00 0.00 0.00 3.51
914 929 0.941542 TCAACAGTGCCGCTTAACAC 59.058 50.000 0.00 0.00 37.05 3.32
915 930 1.669604 TTCAACAGTGCCGCTTAACA 58.330 45.000 0.00 0.00 0.00 2.41
920 935 1.032014 AAACATTCAACAGTGCCGCT 58.968 45.000 0.00 0.00 0.00 5.52
943 958 4.820284 AGCACAGCTTCACTAAGAAAAC 57.180 40.909 0.00 0.00 33.89 2.43
984 999 4.278170 CCAGCCATCTCTGTAACACAAAAA 59.722 41.667 0.00 0.00 32.32 1.94
1015 1030 2.947118 TACTGCGGCGGAACATAGCG 62.947 60.000 17.15 0.00 0.00 4.26
1434 1456 8.593492 ATTCACAAATAAAGGCAAGAAGTTTC 57.407 30.769 0.00 0.00 0.00 2.78
1447 1469 9.743057 CACCAACTACTGAAATTCACAAATAAA 57.257 29.630 0.00 0.00 0.00 1.40
1448 1470 8.356657 CCACCAACTACTGAAATTCACAAATAA 58.643 33.333 0.00 0.00 0.00 1.40
1449 1471 7.504238 ACCACCAACTACTGAAATTCACAAATA 59.496 33.333 0.00 0.00 0.00 1.40
1450 1472 6.323739 ACCACCAACTACTGAAATTCACAAAT 59.676 34.615 0.00 0.00 0.00 2.32
1732 1754 9.944376 AAGACAGTTGATTTTGCTACTCTTATA 57.056 29.630 0.00 0.00 0.00 0.98
1772 1794 4.650972 TGTCAGGGGTAATTTTAGCACT 57.349 40.909 0.00 0.00 45.07 4.40
1786 1808 0.177604 GCTCCAGTGAGATGTCAGGG 59.822 60.000 0.00 0.00 41.42 4.45
1788 1810 0.900421 TGGCTCCAGTGAGATGTCAG 59.100 55.000 0.00 0.00 41.42 3.51
1791 1813 1.701847 AGTTTGGCTCCAGTGAGATGT 59.298 47.619 0.00 0.00 41.42 3.06
1900 1922 4.039730 GTCCATATAAGAGAAGGCAGCAGA 59.960 45.833 0.00 0.00 0.00 4.26
1914 1936 6.068461 TGGCAGTAACCAAAGTCCATATAA 57.932 37.500 0.00 0.00 36.55 0.98
2073 2095 6.366877 GTGCTACTGAAACAGGTTACGAATAA 59.633 38.462 0.00 0.00 35.51 1.40
2161 2183 6.164176 ACTAAGCACCTTGTTACTGTGATAC 58.836 40.000 0.00 0.00 31.66 2.24
2297 2319 0.249398 AATGGACGTAGGACCAGCAC 59.751 55.000 11.98 0.00 40.68 4.40
2345 2372 9.124807 GCTACAATAGTCCACACAAAATTAAAC 57.875 33.333 0.00 0.00 0.00 2.01
2438 2465 5.869649 AAGGGTATTTTTATGCATGTCCC 57.130 39.130 10.16 9.92 0.00 4.46
2770 2797 5.593010 AGAACAATAGAGGATAACGACAGC 58.407 41.667 0.00 0.00 0.00 4.40
2799 2826 1.378250 ATGTCAGCAGGCAAGGAGC 60.378 57.895 0.00 0.00 44.65 4.70
2837 2864 5.207768 CAAGATAAGGCAATTGCGTATGAC 58.792 41.667 24.59 15.81 43.26 3.06
2866 2893 4.942761 AGCCTGAAACAAATCACAACAT 57.057 36.364 0.00 0.00 0.00 2.71
2870 2897 7.148086 GGAACATATAGCCTGAAACAAATCACA 60.148 37.037 0.00 0.00 0.00 3.58
2882 2909 4.103153 TCAAGGGAAGGAACATATAGCCTG 59.897 45.833 0.00 0.00 31.06 4.85
2956 2983 5.107104 GCAGAATAAGTGTGTCGTCAAATCA 60.107 40.000 0.00 0.00 0.00 2.57
3033 3060 1.078567 GGAGCTGAAGAGGTGCCAG 60.079 63.158 0.00 0.00 32.19 4.85
3088 3115 4.183865 TGCGTCATCTACTCAATCAAAGG 58.816 43.478 0.00 0.00 0.00 3.11
3132 3164 0.534652 GCATGCCAAGCCAACCAAAA 60.535 50.000 6.36 0.00 0.00 2.44
3167 3199 0.519175 GCAGTGCGCGATAACACAAG 60.519 55.000 12.10 6.50 39.30 3.16
3194 3226 5.007823 GCTGTATACAGTCTGACATCGTAGT 59.992 44.000 28.95 1.64 45.45 2.73
3210 3242 7.498443 AGGTTATCTTTACACCAGCTGTATAC 58.502 38.462 13.81 0.00 35.18 1.47
3235 3267 2.413796 CGCGCTGTCCATTAGTTTACAA 59.586 45.455 5.56 0.00 0.00 2.41
3338 3370 2.637382 TCCATGTGCAGGAGAACACTTA 59.363 45.455 0.00 0.00 35.69 2.24
3339 3371 1.421268 TCCATGTGCAGGAGAACACTT 59.579 47.619 0.00 0.00 35.69 3.16
3340 3372 1.059098 TCCATGTGCAGGAGAACACT 58.941 50.000 0.00 0.00 35.69 3.55
3341 3373 3.631453 TCCATGTGCAGGAGAACAC 57.369 52.632 0.00 0.00 35.69 3.32
3446 3478 4.019321 TGAGGGCTCTTGTACATAAGCTTT 60.019 41.667 22.20 14.18 35.12 3.51
3450 3482 3.130516 TCGTGAGGGCTCTTGTACATAAG 59.869 47.826 0.00 0.00 0.00 1.73
3468 3500 1.526887 ACAACTTGTTCGCATCTCGTG 59.473 47.619 0.00 0.00 39.67 4.35
3571 3604 1.639635 ATGATTGGAGGAAGGCCGCT 61.640 55.000 0.00 0.00 39.96 5.52
3602 3635 5.218179 AGATGATTGGAAGACAGAGATCCT 58.782 41.667 0.00 0.00 34.24 3.24
3603 3636 5.549742 AGATGATTGGAAGACAGAGATCC 57.450 43.478 0.00 0.00 0.00 3.36
3604 3637 8.125978 AGATAGATGATTGGAAGACAGAGATC 57.874 38.462 0.00 0.00 0.00 2.75
3605 3638 7.729431 TGAGATAGATGATTGGAAGACAGAGAT 59.271 37.037 0.00 0.00 0.00 2.75
3606 3639 7.065504 TGAGATAGATGATTGGAAGACAGAGA 58.934 38.462 0.00 0.00 0.00 3.10
3607 3640 7.287512 TGAGATAGATGATTGGAAGACAGAG 57.712 40.000 0.00 0.00 0.00 3.35
3608 3641 7.729431 AGATGAGATAGATGATTGGAAGACAGA 59.271 37.037 0.00 0.00 0.00 3.41
3609 3642 7.898918 AGATGAGATAGATGATTGGAAGACAG 58.101 38.462 0.00 0.00 0.00 3.51
3610 3643 7.852550 AGATGAGATAGATGATTGGAAGACA 57.147 36.000 0.00 0.00 0.00 3.41
3611 3644 8.469200 CCTAGATGAGATAGATGATTGGAAGAC 58.531 40.741 0.00 0.00 0.00 3.01
3612 3645 8.397172 TCCTAGATGAGATAGATGATTGGAAGA 58.603 37.037 0.00 0.00 0.00 2.87
3613 3646 8.592529 TCCTAGATGAGATAGATGATTGGAAG 57.407 38.462 0.00 0.00 0.00 3.46
3614 3647 9.199645 GATCCTAGATGAGATAGATGATTGGAA 57.800 37.037 0.00 0.00 0.00 3.53
3615 3648 8.567851 AGATCCTAGATGAGATAGATGATTGGA 58.432 37.037 0.00 0.00 0.00 3.53
3616 3649 8.771521 AGATCCTAGATGAGATAGATGATTGG 57.228 38.462 0.00 0.00 0.00 3.16
3617 3650 9.636789 AGAGATCCTAGATGAGATAGATGATTG 57.363 37.037 0.00 0.00 0.00 2.67
3618 3651 9.636789 CAGAGATCCTAGATGAGATAGATGATT 57.363 37.037 0.00 0.00 0.00 2.57
3619 3652 8.784880 ACAGAGATCCTAGATGAGATAGATGAT 58.215 37.037 0.00 0.00 0.00 2.45
3620 3653 8.161640 ACAGAGATCCTAGATGAGATAGATGA 57.838 38.462 0.00 0.00 0.00 2.92
3621 3654 8.270030 AGACAGAGATCCTAGATGAGATAGATG 58.730 40.741 0.00 0.00 0.00 2.90
3622 3655 8.397951 AGACAGAGATCCTAGATGAGATAGAT 57.602 38.462 0.00 0.00 0.00 1.98
3623 3656 7.813087 AGACAGAGATCCTAGATGAGATAGA 57.187 40.000 0.00 0.00 0.00 1.98
3624 3657 9.958180 TTAAGACAGAGATCCTAGATGAGATAG 57.042 37.037 0.00 0.00 0.00 2.08
3625 3658 9.958180 CTTAAGACAGAGATCCTAGATGAGATA 57.042 37.037 0.00 0.00 0.00 1.98
3626 3659 8.448008 ACTTAAGACAGAGATCCTAGATGAGAT 58.552 37.037 10.09 0.00 0.00 2.75
3627 3660 7.811282 ACTTAAGACAGAGATCCTAGATGAGA 58.189 38.462 10.09 0.00 0.00 3.27
3628 3661 8.352201 CAACTTAAGACAGAGATCCTAGATGAG 58.648 40.741 10.09 0.00 0.00 2.90
3629 3662 7.836685 ACAACTTAAGACAGAGATCCTAGATGA 59.163 37.037 10.09 0.00 0.00 2.92
3630 3663 7.920151 CACAACTTAAGACAGAGATCCTAGATG 59.080 40.741 10.09 0.00 0.00 2.90
3631 3664 7.417342 GCACAACTTAAGACAGAGATCCTAGAT 60.417 40.741 10.09 0.00 0.00 1.98
3632 3665 6.127591 GCACAACTTAAGACAGAGATCCTAGA 60.128 42.308 10.09 0.00 0.00 2.43
3633 3666 6.039616 GCACAACTTAAGACAGAGATCCTAG 58.960 44.000 10.09 0.00 0.00 3.02
3634 3667 5.480422 TGCACAACTTAAGACAGAGATCCTA 59.520 40.000 10.09 0.00 0.00 2.94
3667 3700 4.629200 GTGTTCAACAATGTTTCAAGGCAA 59.371 37.500 0.00 0.00 0.00 4.52
3673 3706 4.657055 CACGAGTGTTCAACAATGTTTCA 58.343 39.130 0.00 0.00 0.00 2.69
3676 3709 2.421775 TGCACGAGTGTTCAACAATGTT 59.578 40.909 0.00 0.00 0.00 2.71
3733 3766 1.678627 AGAGGATTCGACTCCATCACG 59.321 52.381 22.40 0.00 37.81 4.35
3738 3771 1.273041 TGGGAAGAGGATTCGACTCCA 60.273 52.381 22.40 0.98 37.81 3.86
3756 3789 0.319297 GCACTTCAAAGGCAAGCTGG 60.319 55.000 0.00 0.00 0.00 4.85
3796 3829 5.129634 TCCACAGATGTTACTTTCTTGCAA 58.870 37.500 0.00 0.00 0.00 4.08
3822 3855 5.511386 AATGGAGACTCAACCTCAAATCT 57.489 39.130 4.53 0.00 32.48 2.40
3836 3870 4.217118 ACTCATGCTTCAACAAATGGAGAC 59.783 41.667 0.00 0.00 36.68 3.36
3873 3907 2.421775 CCTTGCGTATTGTGGTTATGCA 59.578 45.455 0.00 0.00 39.24 3.96
3879 3913 2.083774 CACATCCTTGCGTATTGTGGT 58.916 47.619 0.00 0.00 35.25 4.16
3887 3921 2.047274 CCGACCACATCCTTGCGT 60.047 61.111 0.00 0.00 0.00 5.24
3888 3922 2.593468 ATCCCGACCACATCCTTGCG 62.593 60.000 0.00 0.00 0.00 4.85
3910 3944 2.110967 CGTGCCTGCAAGATGAGGG 61.111 63.158 0.00 0.00 34.07 4.30
3915 3949 1.138859 TGCTATACGTGCCTGCAAGAT 59.861 47.619 11.95 4.20 34.07 2.40
3930 3964 1.987807 ATGCACCTTCGGCCTGCTAT 61.988 55.000 14.32 4.71 0.00 2.97
4062 4096 1.501582 GACAAGCTAGATCCCCCACT 58.498 55.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.