Multiple sequence alignment - TraesCS3A01G044700

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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 TraesCS3A01G044700 chr3A 100.000 3113 0 0 1 3113 24036088 24039200 0.000000e+00 5749.0
1 TraesCS3A01G044700 chr3A 77.545 334 67 6 1499 1828 660196052 660196381 9.620000e-46 195.0
2 TraesCS3A01G044700 chr3A 100.000 52 0 0 3347 3398 24039434 24039485 2.790000e-16 97.1
3 TraesCS3A01G044700 chr3B 92.137 3205 112 39 1 3113 18849013 18845857 0.000000e+00 4394.0
4 TraesCS3A01G044700 chr3D 91.998 2437 90 35 746 3113 13169311 13166911 0.000000e+00 3323.0
5 TraesCS3A01G044700 chr3D 95.269 761 10 10 1 744 13170032 13169281 0.000000e+00 1182.0
6 TraesCS3A01G044700 chr3D 77.982 327 63 8 1511 1834 525917673 525917353 2.670000e-46 196.0
7 TraesCS3A01G044700 chr1A 81.690 284 46 6 1511 1791 58946932 58947212 7.330000e-57 231.0
8 TraesCS3A01G044700 chr2D 85.577 208 28 2 1499 1705 48133243 48133449 2.050000e-52 217.0
9 TraesCS3A01G044700 chr2B 85.577 208 28 2 1499 1705 75847560 75847766 2.050000e-52 217.0
10 TraesCS3A01G044700 chr1D 80.634 284 49 6 1511 1791 60317518 60317798 7.380000e-52 215.0
11 TraesCS3A01G044700 chr2A 85.096 208 29 2 1499 1705 51008495 51008289 9.550000e-51 211.0
12 TraesCS3A01G044700 chr4D 79.264 299 56 6 1496 1791 315597320 315597615 1.600000e-48 204.0


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 TraesCS3A01G044700 chr3A 24036088 24039485 3397 False 2923.05 5749 100.0000 1 3398 2 chr3A.!!$F2 3397
1 TraesCS3A01G044700 chr3B 18845857 18849013 3156 True 4394.00 4394 92.1370 1 3113 1 chr3B.!!$R1 3112
2 TraesCS3A01G044700 chr3D 13166911 13170032 3121 True 2252.50 3323 93.6335 1 3113 2 chr3D.!!$R2 3112

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
564 593 0.968405 GGTGGTGGTTCACAATGCAT 59.032 50.000 0.00 0.0 39.27 3.96 F
1094 1143 1.135141 CACTCCAGCACTCTGAGCTAC 60.135 57.143 4.19 0.0 42.95 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 2225 0.538584 TGAGGTAGTCGAGGAGCGTA 59.461 55.0 0.0 0.0 41.80 4.42 R
2787 2919 0.038251 TCTGTCTCACACATCCACGC 60.038 55.0 0.0 0.0 33.23 5.34 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
280 305 2.094752 CCCAAATCGGCACAAAAGGTAG 60.095 50.000 0.00 0.00 0.00 3.18
343 368 7.359514 GCAAGCAAGGACAACAAAAGAATTATC 60.360 37.037 0.00 0.00 0.00 1.75
564 593 0.968405 GGTGGTGGTTCACAATGCAT 59.032 50.000 0.00 0.00 39.27 3.96
567 596 3.951037 GGTGGTGGTTCACAATGCATATA 59.049 43.478 0.00 0.00 39.27 0.86
568 597 4.584325 GGTGGTGGTTCACAATGCATATAT 59.416 41.667 0.00 0.00 39.27 0.86
569 598 5.507817 GGTGGTGGTTCACAATGCATATATG 60.508 44.000 8.45 8.45 39.27 1.78
570 599 4.037803 TGGTGGTTCACAATGCATATATGC 59.962 41.667 27.45 27.45 44.16 3.14
727 756 2.213499 CGAAGCCTCTCTCTCTCTCTC 58.787 57.143 0.00 0.00 0.00 3.20
728 757 2.158900 CGAAGCCTCTCTCTCTCTCTCT 60.159 54.545 0.00 0.00 0.00 3.10
729 758 3.471680 GAAGCCTCTCTCTCTCTCTCTC 58.528 54.545 0.00 0.00 0.00 3.20
730 759 2.769209 AGCCTCTCTCTCTCTCTCTCT 58.231 52.381 0.00 0.00 0.00 3.10
731 760 2.703007 AGCCTCTCTCTCTCTCTCTCTC 59.297 54.545 0.00 0.00 0.00 3.20
732 761 2.703007 GCCTCTCTCTCTCTCTCTCTCT 59.297 54.545 0.00 0.00 0.00 3.10
733 762 3.244044 GCCTCTCTCTCTCTCTCTCTCTC 60.244 56.522 0.00 0.00 0.00 3.20
734 763 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
735 764 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
736 765 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
737 766 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
738 767 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
739 768 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
740 769 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
741 770 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
742 771 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
743 772 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
744 773 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
745 774 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
746 775 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
865 894 2.368221 CCTGCTTCTATCTTCCTCCCAG 59.632 54.545 0.00 0.00 0.00 4.45
1023 1056 2.493099 AGGCCCTCTTCTCATCTCAT 57.507 50.000 0.00 0.00 0.00 2.90
1024 1057 2.328319 AGGCCCTCTTCTCATCTCATC 58.672 52.381 0.00 0.00 0.00 2.92
1025 1058 2.090606 AGGCCCTCTTCTCATCTCATCT 60.091 50.000 0.00 0.00 0.00 2.90
1026 1059 2.299867 GGCCCTCTTCTCATCTCATCTC 59.700 54.545 0.00 0.00 0.00 2.75
1027 1060 3.233507 GCCCTCTTCTCATCTCATCTCT 58.766 50.000 0.00 0.00 0.00 3.10
1028 1061 3.256631 GCCCTCTTCTCATCTCATCTCTC 59.743 52.174 0.00 0.00 0.00 3.20
1029 1062 3.828451 CCCTCTTCTCATCTCATCTCTCC 59.172 52.174 0.00 0.00 0.00 3.71
1030 1063 3.828451 CCTCTTCTCATCTCATCTCTCCC 59.172 52.174 0.00 0.00 0.00 4.30
1031 1064 4.472496 CTCTTCTCATCTCATCTCTCCCA 58.528 47.826 0.00 0.00 0.00 4.37
1032 1065 4.214310 TCTTCTCATCTCATCTCTCCCAC 58.786 47.826 0.00 0.00 0.00 4.61
1033 1066 3.969466 TCTCATCTCATCTCTCCCACT 57.031 47.619 0.00 0.00 0.00 4.00
1056 1105 7.071824 CACTTCTCCTTCCTCCTAAATCCTAAT 59.928 40.741 0.00 0.00 0.00 1.73
1094 1143 1.135141 CACTCCAGCACTCTGAGCTAC 60.135 57.143 4.19 0.00 42.95 3.58
1127 1176 4.343231 ACTTGTGCATGGTCATATCCAAA 58.657 39.130 0.00 0.00 41.09 3.28
1128 1177 4.957954 ACTTGTGCATGGTCATATCCAAAT 59.042 37.500 0.00 0.00 41.09 2.32
1151 1205 9.432982 AAATCCATCTATCTATAAGGGAGCTAG 57.567 37.037 0.00 0.00 0.00 3.42
1166 1220 1.745264 CTAGCTAGCTGTGCCCTCC 59.255 63.158 27.68 0.00 0.00 4.30
1250 1304 2.820479 GAGCAGCAGCAGCAGGAG 60.820 66.667 12.92 0.00 45.49 3.69
1251 1305 4.411981 AGCAGCAGCAGCAGGAGG 62.412 66.667 12.92 0.00 45.49 4.30
1252 1306 4.405671 GCAGCAGCAGCAGGAGGA 62.406 66.667 4.63 0.00 45.49 3.71
1272 1326 4.765970 AGGAGCTGGGCCCATGGA 62.766 66.667 28.82 0.83 0.00 3.41
1294 1348 3.797353 GCGGCCATGGAGGAGGAA 61.797 66.667 18.40 0.00 41.22 3.36
1297 1351 2.381941 GGCCATGGAGGAGGAAGCT 61.382 63.158 18.40 0.00 41.22 3.74
1481 1539 8.213518 TCCATGAATATTTTCTTACTGCTGTC 57.786 34.615 0.00 0.00 32.78 3.51
1495 1557 3.181477 ACTGCTGTCTATCTCTGTCATGC 60.181 47.826 0.00 0.00 0.00 4.06
1899 1961 3.430862 GCAATCGGCAGCGACCAA 61.431 61.111 0.00 0.00 43.97 3.67
2157 2225 4.415150 TCGTACCTCCCGGACGCT 62.415 66.667 0.73 0.00 35.33 5.07
2193 2261 1.201181 CTCAACTACTCGAGCTGCACT 59.799 52.381 13.61 0.00 0.00 4.40
2287 2364 4.430765 ACGGCGATCACCACGACC 62.431 66.667 16.62 0.00 35.13 4.79
2419 2499 1.616921 AGCCAAGTGGATGGATGGG 59.383 57.895 0.18 0.00 43.54 4.00
2524 2608 3.314541 TGGAGCTCATCATCATCATCG 57.685 47.619 17.19 0.00 0.00 3.84
2554 2638 6.699204 CCATGTAGCTAGTAGTGATCAAAGTG 59.301 42.308 0.00 0.00 0.00 3.16
2582 2666 5.973899 TTGATCGAGATTGCTAGCTCTAT 57.026 39.130 17.23 6.03 34.63 1.98
2644 2730 3.795488 GCATGCATGATCAATGAGGTGTG 60.795 47.826 30.64 0.00 38.72 3.82
2665 2779 6.369065 GTGTGACCTTTTGGATCTAGTAACTG 59.631 42.308 0.00 0.00 44.07 3.16
2730 2862 1.201181 TGTTTGTTGGTGTGTGTGAGC 59.799 47.619 0.00 0.00 0.00 4.26
2770 2902 2.341846 ATCGTTTGTGTTGGTGAGGT 57.658 45.000 0.00 0.00 0.00 3.85
2787 2919 0.881118 GGTGGTGGTGCACTTACATG 59.119 55.000 17.98 0.00 34.40 3.21
2788 2920 0.240945 GTGGTGGTGCACTTACATGC 59.759 55.000 17.98 6.73 46.32 4.06
2805 2937 0.319813 TGCGTGGATGTGTGAGACAG 60.320 55.000 0.00 0.00 38.23 3.51
2810 2942 2.027745 GTGGATGTGTGAGACAGATGGT 60.028 50.000 0.00 0.00 38.23 3.55
2853 2985 6.095580 ACATATTGACAAGTCGCTCTAAGAGA 59.904 38.462 0.00 0.00 0.00 3.10
2900 3035 8.969260 ACTATTGCATGATCATAACAAGAGAA 57.031 30.769 31.69 16.92 33.38 2.87
2907 3042 7.148771 GCATGATCATAACAAGAGAAGATCGAG 60.149 40.741 8.15 0.00 35.77 4.04
2908 3043 6.743110 TGATCATAACAAGAGAAGATCGAGG 58.257 40.000 0.00 0.00 35.77 4.63
2910 3045 5.201243 TCATAACAAGAGAAGATCGAGGGA 58.799 41.667 0.00 0.00 0.00 4.20
2916 3065 5.130145 ACAAGAGAAGATCGAGGGAATGATT 59.870 40.000 0.00 0.00 0.00 2.57
2935 3084 6.220726 TGATTCCTTCATCGTCATAAGTCA 57.779 37.500 0.00 0.00 0.00 3.41
2940 3089 3.145212 TCATCGTCATAAGTCACCACG 57.855 47.619 0.00 0.00 0.00 4.94
2944 3093 1.337447 CGTCATAAGTCACCACGGGTT 60.337 52.381 0.00 0.00 31.02 4.11
2947 3096 3.194116 GTCATAAGTCACCACGGGTTCTA 59.806 47.826 0.00 0.00 31.02 2.10
2962 3111 4.161102 GGGTTCTAGCTAGGTATGGACAT 58.839 47.826 20.58 0.00 0.00 3.06
2968 3117 3.669949 AGCTAGGTATGGACATTCCCTT 58.330 45.455 4.57 0.00 35.03 3.95
2969 3118 3.648545 AGCTAGGTATGGACATTCCCTTC 59.351 47.826 4.57 1.48 35.03 3.46
2990 3139 7.862873 CCCTTCAACAAATCTCTAAAAGTTGTC 59.137 37.037 0.00 0.00 37.97 3.18
3009 3158 6.377146 AGTTGTCACTTTGAACAATACTTGGT 59.623 34.615 0.00 0.00 34.12 3.67
3027 3176 4.399004 TGGTCATCAAACCCAACTTTTG 57.601 40.909 0.00 0.00 38.65 2.44
3028 3177 3.772025 TGGTCATCAAACCCAACTTTTGT 59.228 39.130 0.00 0.00 38.65 2.83
3032 3181 3.878160 TCAAACCCAACTTTTGTGTCC 57.122 42.857 0.00 0.00 35.75 4.02
3043 3192 1.257743 TTTGTGTCCCTCTCTCTCGG 58.742 55.000 0.00 0.00 0.00 4.63
3049 3198 2.364317 CCTCTCTCTCGGGGGCAA 60.364 66.667 0.00 0.00 0.00 4.52
3077 3228 0.104934 CTAGCCACCCACCCCTATCT 60.105 60.000 0.00 0.00 0.00 1.98
3088 3239 2.711009 CACCCCTATCTTCCTATTGCCA 59.289 50.000 0.00 0.00 0.00 4.92
3098 3251 0.390860 CCTATTGCCACCTCCGAGAG 59.609 60.000 0.00 0.00 0.00 3.20
3363 3516 3.403624 TGAAGGCAGCTAGGTGGG 58.596 61.111 22.69 0.00 0.00 4.61
3364 3517 1.538876 TGAAGGCAGCTAGGTGGGT 60.539 57.895 22.69 0.00 0.00 4.51
3365 3518 1.078143 GAAGGCAGCTAGGTGGGTG 60.078 63.158 22.69 0.00 37.71 4.61
3366 3519 1.842381 GAAGGCAGCTAGGTGGGTGT 61.842 60.000 22.69 0.00 37.09 4.16
3367 3520 2.045926 GGCAGCTAGGTGGGTGTG 60.046 66.667 22.69 0.00 37.09 3.82
3368 3521 2.045926 GCAGCTAGGTGGGTGTGG 60.046 66.667 22.69 0.00 37.09 4.17
3369 3522 2.895424 GCAGCTAGGTGGGTGTGGT 61.895 63.158 22.69 0.00 37.09 4.16
3370 3523 1.296715 CAGCTAGGTGGGTGTGGTC 59.703 63.158 14.29 0.00 0.00 4.02
3371 3524 1.918800 AGCTAGGTGGGTGTGGTCC 60.919 63.158 0.00 0.00 0.00 4.46
3372 3525 2.221299 GCTAGGTGGGTGTGGTCCA 61.221 63.158 0.00 0.00 0.00 4.02
3373 3526 1.983224 CTAGGTGGGTGTGGTCCAG 59.017 63.158 0.00 0.00 34.56 3.86
3374 3527 0.836400 CTAGGTGGGTGTGGTCCAGT 60.836 60.000 0.00 0.00 34.56 4.00
3375 3528 0.834687 TAGGTGGGTGTGGTCCAGTC 60.835 60.000 0.00 0.00 34.56 3.51
3376 3529 2.448582 GGTGGGTGTGGTCCAGTCA 61.449 63.158 0.00 0.00 34.56 3.41
3377 3530 1.761174 GTGGGTGTGGTCCAGTCAT 59.239 57.895 0.00 0.00 34.56 3.06
3378 3531 0.321653 GTGGGTGTGGTCCAGTCATC 60.322 60.000 0.00 0.00 34.56 2.92
3379 3532 0.766288 TGGGTGTGGTCCAGTCATCA 60.766 55.000 0.00 0.00 0.00 3.07
3380 3533 0.036010 GGGTGTGGTCCAGTCATCAG 60.036 60.000 0.00 0.00 0.00 2.90
3381 3534 0.674895 GGTGTGGTCCAGTCATCAGC 60.675 60.000 0.00 0.00 0.00 4.26
3382 3535 0.674895 GTGTGGTCCAGTCATCAGCC 60.675 60.000 0.00 0.00 0.00 4.85
3383 3536 1.126948 TGTGGTCCAGTCATCAGCCA 61.127 55.000 0.00 0.00 0.00 4.75
3384 3537 0.036732 GTGGTCCAGTCATCAGCCAA 59.963 55.000 0.00 0.00 0.00 4.52
3385 3538 0.770499 TGGTCCAGTCATCAGCCAAA 59.230 50.000 0.00 0.00 0.00 3.28
3386 3539 1.355381 TGGTCCAGTCATCAGCCAAAT 59.645 47.619 0.00 0.00 0.00 2.32
3387 3540 2.019984 GGTCCAGTCATCAGCCAAATC 58.980 52.381 0.00 0.00 0.00 2.17
3388 3541 2.019984 GTCCAGTCATCAGCCAAATCC 58.980 52.381 0.00 0.00 0.00 3.01
3389 3542 1.634973 TCCAGTCATCAGCCAAATCCA 59.365 47.619 0.00 0.00 0.00 3.41
3390 3543 2.022195 CCAGTCATCAGCCAAATCCAG 58.978 52.381 0.00 0.00 0.00 3.86
3391 3544 2.356432 CCAGTCATCAGCCAAATCCAGA 60.356 50.000 0.00 0.00 0.00 3.86
3392 3545 3.552875 CAGTCATCAGCCAAATCCAGAT 58.447 45.455 0.00 0.00 0.00 2.90
3393 3546 3.564644 CAGTCATCAGCCAAATCCAGATC 59.435 47.826 0.00 0.00 0.00 2.75
3394 3547 3.458857 AGTCATCAGCCAAATCCAGATCT 59.541 43.478 0.00 0.00 0.00 2.75
3395 3548 3.564644 GTCATCAGCCAAATCCAGATCTG 59.435 47.826 16.24 16.24 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
343 368 5.136105 AGCTAGCCTTTTTATTCCATCAGG 58.864 41.667 12.13 0.00 0.00 3.86
531 560 2.154462 CACCACCTCCTTTTGCACTAG 58.846 52.381 0.00 0.00 0.00 2.57
569 598 4.091800 GCAAATTGTTGGATGTACACATGC 59.908 41.667 0.00 6.89 43.79 4.06
570 599 4.626604 GGCAAATTGTTGGATGTACACATG 59.373 41.667 0.00 0.00 34.35 3.21
727 756 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
728 757 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
729 758 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
730 759 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
731 760 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
732 761 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
733 762 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
734 763 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
735 764 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
736 765 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
737 766 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
738 767 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
739 768 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
740 769 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
741 770 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
742 771 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
743 772 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
744 773 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
745 774 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
746 775 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
865 894 3.421567 ACTTTGGCAGTCTGGTTCC 57.578 52.632 1.14 0.00 0.00 3.62
929 962 4.096532 GGCAATCATATGGAGCATGATCTG 59.903 45.833 11.34 1.06 41.24 2.90
930 963 4.263771 TGGCAATCATATGGAGCATGATCT 60.264 41.667 11.34 0.00 41.24 2.75
1023 1056 1.719378 AGGAAGGAGAAGTGGGAGAGA 59.281 52.381 0.00 0.00 0.00 3.10
1024 1057 2.107366 GAGGAAGGAGAAGTGGGAGAG 58.893 57.143 0.00 0.00 0.00 3.20
1025 1058 1.273324 GGAGGAAGGAGAAGTGGGAGA 60.273 57.143 0.00 0.00 0.00 3.71
1026 1059 1.199615 GGAGGAAGGAGAAGTGGGAG 58.800 60.000 0.00 0.00 0.00 4.30
1027 1060 0.793617 AGGAGGAAGGAGAAGTGGGA 59.206 55.000 0.00 0.00 0.00 4.37
1028 1061 2.552093 TAGGAGGAAGGAGAAGTGGG 57.448 55.000 0.00 0.00 0.00 4.61
1029 1062 4.141597 GGATTTAGGAGGAAGGAGAAGTGG 60.142 50.000 0.00 0.00 0.00 4.00
1030 1063 4.719273 AGGATTTAGGAGGAAGGAGAAGTG 59.281 45.833 0.00 0.00 0.00 3.16
1031 1064 4.966611 AGGATTTAGGAGGAAGGAGAAGT 58.033 43.478 0.00 0.00 0.00 3.01
1032 1065 7.256511 GGATTAGGATTTAGGAGGAAGGAGAAG 60.257 44.444 0.00 0.00 0.00 2.85
1033 1066 6.559157 GGATTAGGATTTAGGAGGAAGGAGAA 59.441 42.308 0.00 0.00 0.00 2.87
1056 1105 1.965643 GTGTACTGTGTGTGTAGGGGA 59.034 52.381 0.00 0.00 0.00 4.81
1094 1143 6.095021 TGACCATGCACAAGTACTACTACTAG 59.905 42.308 0.00 0.00 32.46 2.57
1127 1176 7.010160 GCTAGCTCCCTTATAGATAGATGGAT 58.990 42.308 7.70 0.00 35.44 3.41
1128 1177 6.161348 AGCTAGCTCCCTTATAGATAGATGGA 59.839 42.308 12.68 0.00 35.44 3.41
1151 1205 3.438017 CTCGGAGGGCACAGCTAGC 62.438 68.421 6.62 6.62 0.00 3.42
1166 1220 2.558795 AGTATGATCGATGAACCCCTCG 59.441 50.000 0.54 0.00 36.25 4.63
1209 1263 1.142060 TCCTCCGTGACATTGTTGGTT 59.858 47.619 0.00 0.00 0.00 3.67
1252 1306 4.444957 ATGGGCCCAGCTCCTCCT 62.445 66.667 31.97 7.68 0.00 3.69
1272 1326 3.882326 CCTCCATGGCCGCCATCT 61.882 66.667 22.62 0.00 43.15 2.90
1297 1351 2.757508 CCTCTCCTCAGCTCGGCA 60.758 66.667 0.00 0.00 0.00 5.69
1402 1456 1.596934 GCGGGAGATCAACTCACCA 59.403 57.895 0.00 0.00 45.50 4.17
1456 1514 8.049117 AGACAGCAGTAAGAAAATATTCATGGA 58.951 33.333 0.00 0.00 38.06 3.41
1481 1539 2.045524 ACCCTGGCATGACAGAGATAG 58.954 52.381 30.79 12.43 40.97 2.08
1495 1557 1.296715 CCGTCCTCTTCAACCCTGG 59.703 63.158 0.00 0.00 0.00 4.45
1834 1896 2.747460 GCCGTGCTGCTCCATCAA 60.747 61.111 0.00 0.00 0.00 2.57
1854 1916 4.477975 GAGGAGGTCACGACGCCG 62.478 72.222 0.00 0.00 42.50 6.46
1861 1923 2.179517 CGACTGCGAGGAGGTCAC 59.820 66.667 0.00 0.00 40.82 3.67
1899 1961 1.687493 GGGAGGGTAGCAGCAGAGT 60.687 63.158 0.00 0.00 0.00 3.24
2157 2225 0.538584 TGAGGTAGTCGAGGAGCGTA 59.461 55.000 0.00 0.00 41.80 4.42
2193 2261 0.892814 TCATGTTCATGGCGTTGGCA 60.893 50.000 12.02 0.00 43.52 4.92
2268 2345 4.124351 TCGTGGTGATCGCCGTCC 62.124 66.667 20.16 9.70 0.00 4.79
2397 2477 2.765969 CCATCCACTTGGCTGGGT 59.234 61.111 9.93 0.00 45.38 4.51
2419 2499 2.303175 CTAGGAGTAGGAGAGTGCCAC 58.697 57.143 0.00 0.00 0.00 5.01
2524 2608 3.875727 TCACTACTAGCTACATGGTCGAC 59.124 47.826 7.13 7.13 0.00 4.20
2554 2638 4.084118 GCTAGCAATCTCGATCAATTGGTC 60.084 45.833 10.63 8.76 41.32 4.02
2582 2666 9.698309 CACTAGAATCAACAAGTAAAAGAGAGA 57.302 33.333 0.00 0.00 0.00 3.10
2644 2730 4.567159 CGCAGTTACTAGATCCAAAAGGTC 59.433 45.833 0.00 0.00 0.00 3.85
2665 2779 0.161024 GAAAGAGCACACACGTACGC 59.839 55.000 16.72 0.00 0.00 4.42
2770 2902 1.233950 CGCATGTAAGTGCACCACCA 61.234 55.000 14.63 7.84 45.30 4.17
2787 2919 0.038251 TCTGTCTCACACATCCACGC 60.038 55.000 0.00 0.00 33.23 5.34
2788 2920 2.265683 CATCTGTCTCACACATCCACG 58.734 52.381 0.00 0.00 33.23 4.94
2805 2937 1.466856 TGCCAAGCTGATCAACCATC 58.533 50.000 0.00 0.00 0.00 3.51
2810 2942 2.516906 TGTCATTGCCAAGCTGATCAA 58.483 42.857 0.00 0.00 0.00 2.57
2839 2971 0.257616 AGCCCTCTCTTAGAGCGACT 59.742 55.000 4.03 0.00 40.98 4.18
2853 2985 0.251519 CAAAAGCCCTGAGAAGCCCT 60.252 55.000 0.00 0.00 0.00 5.19
2916 3065 3.767131 TGGTGACTTATGACGATGAAGGA 59.233 43.478 0.00 0.00 0.00 3.36
2918 3067 3.547868 CGTGGTGACTTATGACGATGAAG 59.452 47.826 0.00 0.00 31.71 3.02
2935 3084 0.040794 ACCTAGCTAGAACCCGTGGT 59.959 55.000 22.70 6.77 37.65 4.16
2940 3089 3.573695 TGTCCATACCTAGCTAGAACCC 58.426 50.000 22.70 3.92 0.00 4.11
2944 3093 4.108124 AGGGAATGTCCATACCTAGCTAGA 59.892 45.833 22.70 3.20 38.64 2.43
2947 3096 3.352611 AGGGAATGTCCATACCTAGCT 57.647 47.619 0.00 0.00 38.64 3.32
2962 3111 8.413229 CAACTTTTAGAGATTTGTTGAAGGGAA 58.587 33.333 0.00 0.00 37.53 3.97
2968 3117 8.506168 AGTGACAACTTTTAGAGATTTGTTGA 57.494 30.769 10.06 0.00 38.36 3.18
2997 3146 5.144100 TGGGTTTGATGACCAAGTATTGTT 58.856 37.500 0.00 0.00 46.99 2.83
3004 3153 4.670896 AAAGTTGGGTTTGATGACCAAG 57.329 40.909 0.00 0.00 44.27 3.61
3032 3181 2.364317 TTGCCCCCGAGAGAGAGG 60.364 66.667 0.00 0.00 0.00 3.69
3043 3192 1.303282 CTAGGGTTCCAGTTGCCCC 59.697 63.158 0.00 0.00 43.32 5.80
3049 3198 1.923909 GGGTGGCTAGGGTTCCAGT 60.924 63.158 0.00 0.00 32.15 4.00
3077 3228 0.830648 CTCGGAGGTGGCAATAGGAA 59.169 55.000 0.00 0.00 0.00 3.36
3346 3499 1.538876 ACCCACCTAGCTGCCTTCA 60.539 57.895 0.00 0.00 0.00 3.02
3347 3500 1.078143 CACCCACCTAGCTGCCTTC 60.078 63.158 0.00 0.00 0.00 3.46
3348 3501 1.847968 ACACCCACCTAGCTGCCTT 60.848 57.895 0.00 0.00 0.00 4.35
3349 3502 2.203998 ACACCCACCTAGCTGCCT 60.204 61.111 0.00 0.00 0.00 4.75
3350 3503 2.045926 CACACCCACCTAGCTGCC 60.046 66.667 0.00 0.00 0.00 4.85
3351 3504 2.045926 CCACACCCACCTAGCTGC 60.046 66.667 0.00 0.00 0.00 5.25
3352 3505 1.296715 GACCACACCCACCTAGCTG 59.703 63.158 0.00 0.00 0.00 4.24
3353 3506 1.918800 GGACCACACCCACCTAGCT 60.919 63.158 0.00 0.00 0.00 3.32
3354 3507 2.185310 CTGGACCACACCCACCTAGC 62.185 65.000 0.00 0.00 0.00 3.42
3355 3508 0.836400 ACTGGACCACACCCACCTAG 60.836 60.000 0.00 0.00 0.00 3.02
3356 3509 0.834687 GACTGGACCACACCCACCTA 60.835 60.000 0.00 0.00 0.00 3.08
3357 3510 2.039831 ACTGGACCACACCCACCT 60.040 61.111 0.00 0.00 0.00 4.00
3358 3511 1.779061 ATGACTGGACCACACCCACC 61.779 60.000 0.00 0.00 0.00 4.61
3359 3512 0.321653 GATGACTGGACCACACCCAC 60.322 60.000 0.00 0.00 0.00 4.61
3360 3513 0.766288 TGATGACTGGACCACACCCA 60.766 55.000 0.00 0.00 0.00 4.51
3361 3514 0.036010 CTGATGACTGGACCACACCC 60.036 60.000 0.00 0.00 0.00 4.61
3362 3515 0.674895 GCTGATGACTGGACCACACC 60.675 60.000 0.00 0.00 0.00 4.16
3363 3516 0.674895 GGCTGATGACTGGACCACAC 60.675 60.000 0.00 0.00 0.00 3.82
3364 3517 1.126948 TGGCTGATGACTGGACCACA 61.127 55.000 0.00 0.00 0.00 4.17
3365 3518 0.036732 TTGGCTGATGACTGGACCAC 59.963 55.000 0.00 0.00 0.00 4.16
3366 3519 0.770499 TTTGGCTGATGACTGGACCA 59.230 50.000 0.00 0.00 0.00 4.02
3367 3520 2.019984 GATTTGGCTGATGACTGGACC 58.980 52.381 0.00 0.00 0.00 4.46
3368 3521 2.019984 GGATTTGGCTGATGACTGGAC 58.980 52.381 0.00 0.00 0.00 4.02
3369 3522 1.634973 TGGATTTGGCTGATGACTGGA 59.365 47.619 0.00 0.00 0.00 3.86
3370 3523 2.022195 CTGGATTTGGCTGATGACTGG 58.978 52.381 0.00 0.00 0.00 4.00
3371 3524 2.995283 TCTGGATTTGGCTGATGACTG 58.005 47.619 0.00 0.00 0.00 3.51
3372 3525 3.458857 AGATCTGGATTTGGCTGATGACT 59.541 43.478 0.00 0.00 0.00 3.41
3373 3526 3.564644 CAGATCTGGATTTGGCTGATGAC 59.435 47.826 15.38 0.00 0.00 3.06
3374 3527 3.816994 CAGATCTGGATTTGGCTGATGA 58.183 45.455 15.38 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.