Multiple sequence alignment - TraesCS6B01G352100

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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 TraesCS6B01G352100 chr6B 100.000 3622 0 0 1 3622 617647484 617643863 0.000000e+00 6689
1 TraesCS6B01G352100 chr6D 87.597 3741 156 125 4 3615 410830112 410826551 0.000000e+00 4054
2 TraesCS6B01G352100 chr6A 89.122 2666 157 63 1022 3622 555753875 555751278 0.000000e+00 3193
3 TraesCS6B01G352100 chr6A 86.214 515 24 14 496 976 555754389 555753888 6.930000e-142 514
4 TraesCS6B01G352100 chr6A 84.735 321 5 13 75 390 555754701 555754420 7.660000e-72 281


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 TraesCS6B01G352100 chr6B 617643863 617647484 3621 True 6689.000000 6689 100.000000 1 3622 1 chr6B.!!$R1 3621
1 TraesCS6B01G352100 chr6D 410826551 410830112 3561 True 4054.000000 4054 87.597000 4 3615 1 chr6D.!!$R1 3611
2 TraesCS6B01G352100 chr6A 555751278 555754701 3423 True 1329.333333 3193 86.690333 75 3622 3 chr6A.!!$R1 3547


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
977 1058 0.227234 CAAATCCGAGCGTCGAATCG 59.773 55.0 11.89 11.89 43.74 3.34 F
1177 1267 0.393448 TGATCACGTTCCGTTTGGGA 59.607 50.0 0.00 0.00 45.40 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2466 2601 0.462759 GCTTTCATCGGCTGGCTAGT 60.463 55.0 0.00 0.00 0.0 2.57 R
2985 3152 0.111832 AGGCGGAATCATGCATGGAT 59.888 50.0 25.97 15.15 0.0 3.41 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
115 116 1.882625 CTGCGCGCAACTAGGCATA 60.883 57.895 35.50 7.85 34.49 3.14
116 117 1.224069 CTGCGCGCAACTAGGCATAT 61.224 55.000 35.50 0.00 34.49 1.78
117 118 1.205064 GCGCGCAACTAGGCATATG 59.795 57.895 29.10 0.00 0.00 1.78
118 119 1.205064 CGCGCAACTAGGCATATGC 59.795 57.895 19.79 19.79 41.14 3.14
138 139 0.253894 CAGCATCCATCCACCAGTCA 59.746 55.000 0.00 0.00 0.00 3.41
206 207 4.802051 ATCAACCAGCGGCGGCAT 62.802 61.111 19.21 0.23 43.41 4.40
264 265 1.754380 CTCCACCCACCGAACTCACA 61.754 60.000 0.00 0.00 0.00 3.58
265 266 1.597027 CCACCCACCGAACTCACAC 60.597 63.158 0.00 0.00 0.00 3.82
294 302 2.044806 CTGCCAAGGTAGATCCGGGG 62.045 65.000 0.00 0.00 41.99 5.73
295 303 2.819284 GCCAAGGTAGATCCGGGGG 61.819 68.421 0.00 0.00 41.99 5.40
296 304 2.819284 CCAAGGTAGATCCGGGGGC 61.819 68.421 0.00 0.00 41.99 5.80
407 425 3.118454 CGTTACACGGCTGGCCAG 61.118 66.667 29.34 29.34 38.08 4.85
410 428 1.078497 TTACACGGCTGGCCAGATG 60.078 57.895 37.21 29.03 35.37 2.90
411 429 1.836999 TTACACGGCTGGCCAGATGT 61.837 55.000 37.21 32.44 35.37 3.06
413 431 1.078497 CACGGCTGGCCAGATGTTA 60.078 57.895 37.21 0.00 35.37 2.41
415 433 1.128200 ACGGCTGGCCAGATGTTATA 58.872 50.000 37.21 0.00 35.37 0.98
417 435 2.092646 ACGGCTGGCCAGATGTTATAAA 60.093 45.455 37.21 0.00 35.37 1.40
419 437 3.569701 CGGCTGGCCAGATGTTATAAAAT 59.430 43.478 37.21 0.00 35.37 1.82
420 438 4.557296 CGGCTGGCCAGATGTTATAAAATG 60.557 45.833 37.21 5.64 35.37 2.32
421 439 4.262164 GGCTGGCCAGATGTTATAAAATGG 60.262 45.833 37.21 4.89 35.81 3.16
423 441 5.278660 GCTGGCCAGATGTTATAAAATGGAG 60.279 44.000 37.21 4.07 0.00 3.86
424 442 4.584325 TGGCCAGATGTTATAAAATGGAGC 59.416 41.667 0.00 2.63 0.00 4.70
426 444 4.829492 GCCAGATGTTATAAAATGGAGCCT 59.171 41.667 9.53 0.00 0.00 4.58
428 446 6.736794 GCCAGATGTTATAAAATGGAGCCTTG 60.737 42.308 9.53 0.00 0.00 3.61
429 447 6.211515 CAGATGTTATAAAATGGAGCCTTGC 58.788 40.000 0.00 0.00 0.00 4.01
432 450 6.603940 TGTTATAAAATGGAGCCTTGCTTT 57.396 33.333 0.00 0.00 39.88 3.51
437 455 1.255667 ATGGAGCCTTGCTTTGCCAG 61.256 55.000 0.00 0.00 39.88 4.85
452 472 4.025401 CAGCCCGCCGTTTCACAC 62.025 66.667 0.00 0.00 0.00 3.82
462 482 0.240945 CGTTTCACACATTCCCTGGC 59.759 55.000 0.00 0.00 0.00 4.85
492 524 3.478857 TGTCACGTACATGTCCCTTTT 57.521 42.857 0.00 0.00 31.43 2.27
493 525 3.811083 TGTCACGTACATGTCCCTTTTT 58.189 40.909 0.00 0.00 31.43 1.94
562 605 0.895530 GCAGGTGCTGACACTACCTA 59.104 55.000 5.74 0.00 46.57 3.08
587 630 2.352001 CGGCGATCCTCGTACACG 60.352 66.667 0.00 0.00 42.81 4.49
591 634 2.416260 GATCCTCGTACACGGCCC 59.584 66.667 0.00 0.00 40.29 5.80
634 677 1.016130 CATCACGTGTGGAGTGGAGC 61.016 60.000 16.51 0.00 39.86 4.70
650 708 2.506217 GCGGATTGCAGACGACGA 60.506 61.111 0.00 0.00 45.45 4.20
662 720 3.132139 CGACGAGCTTCCCGAGGA 61.132 66.667 0.00 0.00 0.00 3.71
663 721 2.482333 CGACGAGCTTCCCGAGGAT 61.482 63.158 0.00 0.00 0.00 3.24
701 763 2.815647 TGCGCAACACACGTCACA 60.816 55.556 8.16 0.00 0.00 3.58
705 767 2.521771 GCAACACACGTCACAGCGA 61.522 57.895 0.00 0.00 35.59 4.93
706 768 1.559814 CAACACACGTCACAGCGAG 59.440 57.895 0.00 0.00 35.59 5.03
707 769 2.237751 AACACACGTCACAGCGAGC 61.238 57.895 0.00 0.00 35.59 5.03
708 770 3.406361 CACACGTCACAGCGAGCC 61.406 66.667 0.00 0.00 35.59 4.70
709 771 3.606662 ACACGTCACAGCGAGCCT 61.607 61.111 0.00 0.00 35.59 4.58
842 908 4.918360 ACCCACCCAGCACCCAGA 62.918 66.667 0.00 0.00 0.00 3.86
843 909 4.351054 CCCACCCAGCACCCAGAC 62.351 72.222 0.00 0.00 0.00 3.51
844 910 4.351054 CCACCCAGCACCCAGACC 62.351 72.222 0.00 0.00 0.00 3.85
845 911 4.351054 CACCCAGCACCCAGACCC 62.351 72.222 0.00 0.00 0.00 4.46
846 912 4.918360 ACCCAGCACCCAGACCCA 62.918 66.667 0.00 0.00 0.00 4.51
847 913 4.039092 CCCAGCACCCAGACCCAG 62.039 72.222 0.00 0.00 0.00 4.45
848 914 2.930019 CCAGCACCCAGACCCAGA 60.930 66.667 0.00 0.00 0.00 3.86
849 915 2.348998 CAGCACCCAGACCCAGAC 59.651 66.667 0.00 0.00 0.00 3.51
850 916 2.930562 AGCACCCAGACCCAGACC 60.931 66.667 0.00 0.00 0.00 3.85
851 917 4.035102 GCACCCAGACCCAGACCC 62.035 72.222 0.00 0.00 0.00 4.46
967 1048 1.147153 GGCCCTCTCCAAATCCGAG 59.853 63.158 0.00 0.00 0.00 4.63
977 1058 0.227234 CAAATCCGAGCGTCGAATCG 59.773 55.000 11.89 11.89 43.74 3.34
1005 1090 1.603306 CCCGTTCGAATTACCCCCA 59.397 57.895 0.00 0.00 0.00 4.96
1007 1092 1.589803 CCGTTCGAATTACCCCCATC 58.410 55.000 0.00 0.00 0.00 3.51
1008 1093 1.134340 CCGTTCGAATTACCCCCATCA 60.134 52.381 0.00 0.00 0.00 3.07
1009 1094 2.486548 CCGTTCGAATTACCCCCATCAT 60.487 50.000 0.00 0.00 0.00 2.45
1010 1095 2.806244 CGTTCGAATTACCCCCATCATC 59.194 50.000 0.00 0.00 0.00 2.92
1011 1096 3.742954 CGTTCGAATTACCCCCATCATCA 60.743 47.826 0.00 0.00 0.00 3.07
1012 1097 4.398319 GTTCGAATTACCCCCATCATCAT 58.602 43.478 0.00 0.00 0.00 2.45
1013 1098 4.286297 TCGAATTACCCCCATCATCATC 57.714 45.455 0.00 0.00 0.00 2.92
1014 1099 3.009033 TCGAATTACCCCCATCATCATCC 59.991 47.826 0.00 0.00 0.00 3.51
1015 1100 3.244875 CGAATTACCCCCATCATCATCCA 60.245 47.826 0.00 0.00 0.00 3.41
1016 1101 4.568380 CGAATTACCCCCATCATCATCCAT 60.568 45.833 0.00 0.00 0.00 3.41
1017 1102 4.598036 ATTACCCCCATCATCATCCATC 57.402 45.455 0.00 0.00 0.00 3.51
1018 1103 1.837252 ACCCCCATCATCATCCATCA 58.163 50.000 0.00 0.00 0.00 3.07
1019 1104 1.426598 ACCCCCATCATCATCCATCAC 59.573 52.381 0.00 0.00 0.00 3.06
1020 1105 1.709115 CCCCCATCATCATCCATCACT 59.291 52.381 0.00 0.00 0.00 3.41
1037 1122 5.448225 CCATCACTCATCAGTTTCAAATCCG 60.448 44.000 0.00 0.00 0.00 4.18
1105 1191 3.406361 CGTGTCACGCCTGCAGAC 61.406 66.667 17.39 1.25 33.65 3.51
1109 1195 2.661537 TCACGCCTGCAGACAACG 60.662 61.111 17.39 15.34 0.00 4.10
1177 1267 0.393448 TGATCACGTTCCGTTTGGGA 59.607 50.000 0.00 0.00 45.40 4.37
1377 1482 0.837691 AGCGGCATCATATCCCTCCA 60.838 55.000 1.45 0.00 0.00 3.86
1426 1531 3.681473 GGAAACGGCCAAAGGAGG 58.319 61.111 2.24 0.00 0.00 4.30
1582 1695 1.741770 CGTTTCCAAGAGGAGGCGG 60.742 63.158 0.00 0.00 46.74 6.13
1858 1980 0.972471 GCAAGGTGAGGGAATTGGGG 60.972 60.000 0.00 0.00 0.00 4.96
2049 2171 4.842531 TCTTGTGAATTATGCCTCCTGA 57.157 40.909 0.00 0.00 0.00 3.86
2375 2503 1.079875 TCGCCGGAATTCTAACGTGC 61.080 55.000 5.05 5.86 0.00 5.34
2385 2513 0.448197 TCTAACGTGCGAGCTCTCTG 59.552 55.000 12.85 3.61 0.00 3.35
2471 2606 3.479370 CGGTGAGCAGCAACTAGC 58.521 61.111 0.00 0.00 46.19 3.42
2609 2745 4.398319 AGATGCTCCGGAAAGAAGAAAAA 58.602 39.130 5.23 0.00 0.00 1.94
2674 2812 7.169158 TCAACCAACTTTTTCTTTCACTCAT 57.831 32.000 0.00 0.00 0.00 2.90
2677 2815 7.169158 ACCAACTTTTTCTTTCACTCATTCA 57.831 32.000 0.00 0.00 0.00 2.57
2709 2847 2.026356 CCCACCATTATCACCTCACACA 60.026 50.000 0.00 0.00 0.00 3.72
2713 2851 2.239654 CCATTATCACCTCACACACCCT 59.760 50.000 0.00 0.00 0.00 4.34
2714 2852 3.308402 CCATTATCACCTCACACACCCTT 60.308 47.826 0.00 0.00 0.00 3.95
2715 2853 4.080582 CCATTATCACCTCACACACCCTTA 60.081 45.833 0.00 0.00 0.00 2.69
2716 2854 5.397899 CCATTATCACCTCACACACCCTTAT 60.398 44.000 0.00 0.00 0.00 1.73
2717 2855 6.183361 CCATTATCACCTCACACACCCTTATA 60.183 42.308 0.00 0.00 0.00 0.98
2743 2881 1.829222 CCTGATTTTTCCCAGCAGCAT 59.171 47.619 0.00 0.00 0.00 3.79
2784 2927 5.851418 ACTTCCCCTACTGGTACTTATCTT 58.149 41.667 0.00 0.00 0.00 2.40
2785 2928 5.898397 ACTTCCCCTACTGGTACTTATCTTC 59.102 44.000 0.00 0.00 0.00 2.87
2802 2959 0.109458 TTCGTTGACAGGACGGATCG 60.109 55.000 0.14 0.00 40.70 3.69
2845 3006 8.640063 TGTAATTGTCACCTAGTAGTAGTTGA 57.360 34.615 0.91 0.91 0.00 3.18
2846 3007 9.251440 TGTAATTGTCACCTAGTAGTAGTTGAT 57.749 33.333 7.96 0.00 31.03 2.57
2850 3011 7.636150 TGTCACCTAGTAGTAGTTGATTACC 57.364 40.000 7.96 0.00 31.03 2.85
2851 3012 7.408543 TGTCACCTAGTAGTAGTTGATTACCT 58.591 38.462 7.96 0.00 31.03 3.08
2853 3014 9.401058 GTCACCTAGTAGTAGTTGATTACCTTA 57.599 37.037 7.96 0.00 31.03 2.69
2854 3015 9.401058 TCACCTAGTAGTAGTTGATTACCTTAC 57.599 37.037 0.91 0.00 0.00 2.34
2855 3016 9.182214 CACCTAGTAGTAGTTGATTACCTTACA 57.818 37.037 3.91 0.00 0.00 2.41
2897 3064 1.848608 CTGTACATCGTCGTCAGCATG 59.151 52.381 0.00 0.00 37.54 4.06
2899 3066 2.420722 TGTACATCGTCGTCAGCATGTA 59.579 45.455 0.00 0.90 37.40 2.29
2901 3068 0.848942 CATCGTCGTCAGCATGTAGC 59.151 55.000 0.00 0.00 46.19 3.58
2985 3152 0.536460 GTCTCCCTTTGCCGTTTCCA 60.536 55.000 0.00 0.00 0.00 3.53
3054 3225 0.791422 TGCACACGTTATGCGGTTAC 59.209 50.000 14.98 0.00 46.49 2.50
3055 3226 0.095762 GCACACGTTATGCGGTTACC 59.904 55.000 5.84 0.00 46.52 2.85
3074 3245 2.510768 CCAGATCGTTGGGTAGCTAC 57.489 55.000 15.88 15.88 34.46 3.58
3075 3246 2.032620 CCAGATCGTTGGGTAGCTACT 58.967 52.381 22.74 1.33 34.46 2.57
3076 3247 2.034812 CCAGATCGTTGGGTAGCTACTC 59.965 54.545 22.74 20.19 34.46 2.59
3142 3313 2.251642 ACGGAAACAGCTTCGGCAC 61.252 57.895 0.00 0.00 44.74 5.01
3144 3315 2.626780 GGAAACAGCTTCGGCACCC 61.627 63.158 0.00 0.00 44.74 4.61
3145 3316 1.896660 GAAACAGCTTCGGCACCCA 60.897 57.895 0.00 0.00 44.74 4.51
3146 3317 1.228552 AAACAGCTTCGGCACCCAT 60.229 52.632 0.00 0.00 44.74 4.00
3269 3457 1.876664 GCCGTGGAAAGAAGGCTTC 59.123 57.895 19.53 19.53 45.67 3.86
3355 3548 1.153565 AGAAGGGGAGGGAAGTTACCA 59.846 52.381 6.96 0.00 0.00 3.25
3414 3607 2.772515 GGGGTTAGATAGAGCAAGTGGT 59.227 50.000 0.00 0.00 0.00 4.16
3444 3637 6.291377 ACCTATGCGTGAATGATTAGTGATT 58.709 36.000 0.00 0.00 0.00 2.57
3449 3642 5.463392 TGCGTGAATGATTAGTGATTAGAGC 59.537 40.000 0.00 0.00 0.00 4.09
3450 3643 5.387855 GCGTGAATGATTAGTGATTAGAGCG 60.388 44.000 0.00 0.00 0.00 5.03
3451 3644 5.117745 CGTGAATGATTAGTGATTAGAGCGG 59.882 44.000 0.00 0.00 0.00 5.52
3452 3645 4.991056 TGAATGATTAGTGATTAGAGCGGC 59.009 41.667 0.00 0.00 0.00 6.53
3455 3648 1.108776 TTAGTGATTAGAGCGGCCGT 58.891 50.000 28.70 13.92 0.00 5.68
3458 3651 0.872021 GTGATTAGAGCGGCCGTCTG 60.872 60.000 28.95 5.83 0.00 3.51
3480 3673 2.527547 CTAAACAAAGCGCCGCTGGG 62.528 60.000 14.52 10.87 39.62 4.45
3615 3810 7.170489 GTCAGTCAGTAGGTTGGTAAAAACTAC 59.830 40.741 5.36 5.36 0.00 2.73
3616 3811 7.070322 TCAGTCAGTAGGTTGGTAAAAACTACT 59.930 37.037 9.48 9.48 30.70 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.366111 TTACCGCGCAAAGATCCAGC 61.366 55.000 8.75 0.00 0.00 4.85
2 3 0.373716 GTTACCGCGCAAAGATCCAG 59.626 55.000 8.75 0.00 0.00 3.86
15 16 3.634568 TTTGGATGCTTTGTGTTACCG 57.365 42.857 0.00 0.00 0.00 4.02
16 17 4.055360 GGTTTTGGATGCTTTGTGTTACC 58.945 43.478 0.00 0.00 0.00 2.85
58 59 2.865603 CACGAGCGACGACGACAG 60.866 66.667 12.29 3.21 45.77 3.51
73 74 2.380410 GGTCGTGTGCGTGATCCAC 61.380 63.158 0.00 0.00 39.49 4.02
115 116 1.152610 GGTGGATGGATGCTGGCAT 60.153 57.895 7.86 7.86 39.69 4.40
116 117 2.276409 GGTGGATGGATGCTGGCA 59.724 61.111 0.00 0.00 0.00 4.92
117 118 1.826921 CTGGTGGATGGATGCTGGC 60.827 63.158 0.00 0.00 0.00 4.85
118 119 0.465097 GACTGGTGGATGGATGCTGG 60.465 60.000 0.00 0.00 0.00 4.85
119 120 0.253894 TGACTGGTGGATGGATGCTG 59.746 55.000 0.00 0.00 0.00 4.41
120 121 1.142465 GATGACTGGTGGATGGATGCT 59.858 52.381 0.00 0.00 0.00 3.79
121 122 1.134007 TGATGACTGGTGGATGGATGC 60.134 52.381 0.00 0.00 0.00 3.91
122 123 2.172082 ACTGATGACTGGTGGATGGATG 59.828 50.000 0.00 0.00 0.00 3.51
123 124 2.485659 ACTGATGACTGGTGGATGGAT 58.514 47.619 0.00 0.00 0.00 3.41
124 125 1.956869 ACTGATGACTGGTGGATGGA 58.043 50.000 0.00 0.00 0.00 3.41
138 139 5.827797 ACGGTGATATTTTTGGCATACTGAT 59.172 36.000 0.00 0.00 0.00 2.90
180 181 3.554692 CTGGTTGATCGTCGCGGC 61.555 66.667 6.13 1.93 0.00 6.53
181 182 3.554692 GCTGGTTGATCGTCGCGG 61.555 66.667 6.13 0.00 0.00 6.46
182 183 3.902063 CGCTGGTTGATCGTCGCG 61.902 66.667 0.00 0.00 34.50 5.87
183 184 3.554692 CCGCTGGTTGATCGTCGC 61.555 66.667 0.00 0.00 0.00 5.19
184 185 3.554692 GCCGCTGGTTGATCGTCG 61.555 66.667 0.00 0.00 0.00 5.12
185 186 3.554692 CGCCGCTGGTTGATCGTC 61.555 66.667 0.00 0.00 0.00 4.20
243 244 0.178955 TGAGTTCGGTGGGTGGAGTA 60.179 55.000 0.00 0.00 0.00 2.59
407 425 6.396829 AGCAAGGCTCCATTTTATAACATC 57.603 37.500 0.00 0.00 30.62 3.06
410 428 5.291858 GCAAAGCAAGGCTCCATTTTATAAC 59.708 40.000 0.00 0.00 38.25 1.89
411 429 5.418676 GCAAAGCAAGGCTCCATTTTATAA 58.581 37.500 0.00 0.00 38.25 0.98
413 431 3.369787 GGCAAAGCAAGGCTCCATTTTAT 60.370 43.478 0.00 0.00 38.25 1.40
415 433 1.271001 GGCAAAGCAAGGCTCCATTTT 60.271 47.619 0.00 0.00 38.25 1.82
417 435 0.832983 TGGCAAAGCAAGGCTCCATT 60.833 50.000 0.00 0.00 38.25 3.16
419 437 1.904865 CTGGCAAAGCAAGGCTCCA 60.905 57.895 0.00 0.00 38.25 3.86
420 438 2.968206 CTGGCAAAGCAAGGCTCC 59.032 61.111 0.00 0.00 38.25 4.70
437 455 2.796245 GAATGTGTGAAACGGCGGGC 62.796 60.000 13.24 0.00 42.39 6.13
440 458 1.209127 GGGAATGTGTGAAACGGCG 59.791 57.895 4.80 4.80 42.39 6.46
444 462 0.240945 CGCCAGGGAATGTGTGAAAC 59.759 55.000 0.00 0.00 37.35 2.78
445 463 1.523154 GCGCCAGGGAATGTGTGAAA 61.523 55.000 0.00 0.00 0.00 2.69
446 464 1.971167 GCGCCAGGGAATGTGTGAA 60.971 57.895 0.00 0.00 0.00 3.18
447 465 2.359850 GCGCCAGGGAATGTGTGA 60.360 61.111 0.00 0.00 0.00 3.58
448 466 3.803082 CGCGCCAGGGAATGTGTG 61.803 66.667 0.00 0.00 0.00 3.82
452 472 2.514592 ATCACGCGCCAGGGAATG 60.515 61.111 5.73 0.00 0.00 2.67
491 523 6.373774 AGTGAAATGGCAAATGTGTTCAAAAA 59.626 30.769 0.00 0.00 0.00 1.94
492 524 5.879223 AGTGAAATGGCAAATGTGTTCAAAA 59.121 32.000 0.00 0.00 0.00 2.44
493 525 5.426504 AGTGAAATGGCAAATGTGTTCAAA 58.573 33.333 0.00 0.00 0.00 2.69
494 526 5.021033 AGTGAAATGGCAAATGTGTTCAA 57.979 34.783 0.00 0.00 0.00 2.69
549 592 1.065251 GTAGCGGTAGGTAGTGTCAGC 59.935 57.143 0.00 0.00 0.00 4.26
587 630 2.747855 CGGTTGAAGCTGAGGGCC 60.748 66.667 0.00 0.00 43.05 5.80
591 634 3.793144 GCGGCGGTTGAAGCTGAG 61.793 66.667 9.78 0.00 43.29 3.35
634 677 2.508891 GCTCGTCGTCTGCAATCCG 61.509 63.158 0.00 0.00 0.00 4.18
650 708 0.970937 TTCGTCATCCTCGGGAAGCT 60.971 55.000 0.00 0.00 34.34 3.74
662 720 1.134280 CCCCTGATCTGCTTTCGTCAT 60.134 52.381 0.00 0.00 0.00 3.06
663 721 0.250234 CCCCTGATCTGCTTTCGTCA 59.750 55.000 0.00 0.00 0.00 4.35
842 908 4.354943 CCTCCCCTGGGTCTGGGT 62.355 72.222 12.71 0.00 42.80 4.51
1005 1090 5.827326 ACTGATGAGTGATGGATGATGAT 57.173 39.130 0.00 0.00 0.00 2.45
1007 1092 5.820947 TGAAACTGATGAGTGATGGATGATG 59.179 40.000 0.00 0.00 30.61 3.07
1008 1093 5.997843 TGAAACTGATGAGTGATGGATGAT 58.002 37.500 0.00 0.00 30.61 2.45
1009 1094 5.425196 TGAAACTGATGAGTGATGGATGA 57.575 39.130 0.00 0.00 30.61 2.92
1010 1095 6.505044 TTTGAAACTGATGAGTGATGGATG 57.495 37.500 0.00 0.00 30.61 3.51
1011 1096 6.320672 GGATTTGAAACTGATGAGTGATGGAT 59.679 38.462 0.00 0.00 30.61 3.41
1012 1097 5.649395 GGATTTGAAACTGATGAGTGATGGA 59.351 40.000 0.00 0.00 30.61 3.41
1013 1098 5.448225 CGGATTTGAAACTGATGAGTGATGG 60.448 44.000 0.00 0.00 30.61 3.51
1014 1099 5.122869 ACGGATTTGAAACTGATGAGTGATG 59.877 40.000 0.00 0.00 30.61 3.07
1015 1100 5.248640 ACGGATTTGAAACTGATGAGTGAT 58.751 37.500 0.00 0.00 30.61 3.06
1016 1101 4.641396 ACGGATTTGAAACTGATGAGTGA 58.359 39.130 0.00 0.00 30.61 3.41
1017 1102 4.692625 AGACGGATTTGAAACTGATGAGTG 59.307 41.667 0.00 0.00 30.61 3.51
1018 1103 4.899502 AGACGGATTTGAAACTGATGAGT 58.100 39.130 0.00 0.00 0.00 3.41
1019 1104 5.869753 AAGACGGATTTGAAACTGATGAG 57.130 39.130 0.00 0.00 0.00 2.90
1020 1105 6.148811 GGTTAAGACGGATTTGAAACTGATGA 59.851 38.462 0.00 0.00 0.00 2.92
1037 1122 2.271173 CCTGGGCGGGGTTAAGAC 59.729 66.667 0.00 0.00 0.00 3.01
1094 1180 2.356313 CTCGTTGTCTGCAGGCGT 60.356 61.111 14.71 0.00 0.00 5.68
1099 1185 2.410322 ATTGCCCCTCGTTGTCTGCA 62.410 55.000 0.00 0.00 0.00 4.41
1102 1188 0.250513 GAGATTGCCCCTCGTTGTCT 59.749 55.000 0.00 0.00 0.00 3.41
1105 1191 3.799753 CGAGATTGCCCCTCGTTG 58.200 61.111 10.20 0.00 45.89 4.10
1109 1195 1.389609 TACGGACGAGATTGCCCCTC 61.390 60.000 0.00 0.00 0.00 4.30
1177 1267 1.445871 GGTAACGGCGTTCTGGAAAT 58.554 50.000 30.35 5.01 0.00 2.17
1278 1374 2.237643 ACACATATAACACGCCAAGGGA 59.762 45.455 0.00 0.00 0.00 4.20
1279 1375 2.639065 ACACATATAACACGCCAAGGG 58.361 47.619 0.00 0.00 0.00 3.95
1280 1376 3.244345 CGTACACATATAACACGCCAAGG 59.756 47.826 0.00 0.00 0.00 3.61
1446 1556 2.372074 TACTTCCCCATCGCCCCAC 61.372 63.158 0.00 0.00 0.00 4.61
1447 1557 2.041430 TACTTCCCCATCGCCCCA 59.959 61.111 0.00 0.00 0.00 4.96
1567 1680 3.717294 GGCCGCCTCCTCTTGGAA 61.717 66.667 0.71 0.00 42.66 3.53
1798 1920 3.449227 CACGACGGCAGGCTCCTA 61.449 66.667 0.00 0.00 0.00 2.94
1834 1956 2.629617 CAATTCCCTCACCTTGCTGTTT 59.370 45.455 0.00 0.00 0.00 2.83
1839 1961 0.972471 CCCCAATTCCCTCACCTTGC 60.972 60.000 0.00 0.00 0.00 4.01
1911 2033 0.963856 TAGAGCGGAGAAAGCCACGA 60.964 55.000 0.00 0.00 34.64 4.35
1954 2076 2.896801 CTCCGCGTTGTTGCTTGCT 61.897 57.895 4.92 0.00 0.00 3.91
1957 2079 2.607892 GCTCTCCGCGTTGTTGCTT 61.608 57.895 4.92 0.00 0.00 3.91
2075 2197 2.660490 CGCCTGAATTTTCAAAAGCGA 58.340 42.857 19.19 0.00 45.84 4.93
2385 2513 1.145803 GTCGAAGTTGTACCTGGCAC 58.854 55.000 0.00 0.00 0.00 5.01
2466 2601 0.462759 GCTTTCATCGGCTGGCTAGT 60.463 55.000 0.00 0.00 0.00 2.57
2471 2606 2.817423 GCTCGCTTTCATCGGCTGG 61.817 63.158 0.00 0.00 0.00 4.85
2475 2610 2.697425 CACGCTCGCTTTCATCGG 59.303 61.111 0.00 0.00 0.00 4.18
2479 2614 1.279539 CTTTGCACGCTCGCTTTCA 59.720 52.632 0.00 0.00 0.00 2.69
2511 2647 6.896021 ACAGTGAGTAACTTTCTAGCTACA 57.104 37.500 0.00 0.00 36.83 2.74
2609 2745 5.104109 TGGTTGGTTAGGCTATAATGCTTCT 60.104 40.000 0.00 0.00 0.00 2.85
2674 2812 4.860802 ATGGTGGGAATATGTGAGTGAA 57.139 40.909 0.00 0.00 0.00 3.18
2677 2815 6.299141 GTGATAATGGTGGGAATATGTGAGT 58.701 40.000 0.00 0.00 0.00 3.41
2709 2847 9.601810 GGGAAAAATCAGGATTAATATAAGGGT 57.398 33.333 0.00 0.00 0.00 4.34
2713 2851 9.653516 TGCTGGGAAAAATCAGGATTAATATAA 57.346 29.630 0.00 0.00 0.00 0.98
2714 2852 9.300681 CTGCTGGGAAAAATCAGGATTAATATA 57.699 33.333 0.00 0.00 31.25 0.86
2715 2853 7.256083 GCTGCTGGGAAAAATCAGGATTAATAT 60.256 37.037 0.00 0.00 31.25 1.28
2716 2854 6.040842 GCTGCTGGGAAAAATCAGGATTAATA 59.959 38.462 0.00 0.00 31.25 0.98
2717 2855 5.163374 GCTGCTGGGAAAAATCAGGATTAAT 60.163 40.000 0.00 0.00 31.25 1.40
2743 2881 3.126001 AGTAAAACTGCTACTGCTGCA 57.874 42.857 0.88 0.88 41.07 4.41
2784 2927 1.504900 CGATCCGTCCTGTCAACGA 59.495 57.895 0.00 0.00 42.62 3.85
2785 2928 2.158959 GCGATCCGTCCTGTCAACG 61.159 63.158 0.00 0.00 39.78 4.10
2845 3006 6.668645 TCCAGGCAAATACATGTAAGGTAAT 58.331 36.000 10.14 0.00 36.33 1.89
2846 3007 6.068461 TCCAGGCAAATACATGTAAGGTAA 57.932 37.500 10.14 0.00 36.33 2.85
2847 3008 5.702065 TCCAGGCAAATACATGTAAGGTA 57.298 39.130 10.14 0.00 37.57 3.08
2848 3009 4.584638 TCCAGGCAAATACATGTAAGGT 57.415 40.909 10.14 0.00 32.53 3.50
2849 3010 6.469782 AAATCCAGGCAAATACATGTAAGG 57.530 37.500 10.14 3.68 0.00 2.69
2985 3152 0.111832 AGGCGGAATCATGCATGGAT 59.888 50.000 25.97 15.15 0.00 3.41
3055 3226 2.032620 AGTAGCTACCCAACGATCTGG 58.967 52.381 20.31 0.00 36.10 3.86
3074 3245 3.764434 TCACTTGCAGAACTACCTAGGAG 59.236 47.826 17.98 11.09 0.00 3.69
3075 3246 3.764434 CTCACTTGCAGAACTACCTAGGA 59.236 47.826 17.98 0.00 0.00 2.94
3076 3247 3.677424 GCTCACTTGCAGAACTACCTAGG 60.677 52.174 7.41 7.41 0.00 3.02
3146 3317 1.468506 GCATCCATCCATGCCATGCA 61.469 55.000 0.00 0.00 43.03 3.96
3269 3457 3.866582 GTCCCCCATCTCCCAGCG 61.867 72.222 0.00 0.00 0.00 5.18
3327 3519 1.229984 CCTCCCCTTCTTCCCTGGT 60.230 63.158 0.00 0.00 0.00 4.00
3355 3548 0.324830 GGCAGAGGTAGGGAGACAGT 60.325 60.000 0.00 0.00 0.00 3.55
3414 3607 7.931407 ACTAATCATTCACGCATAGGTTAATCA 59.069 33.333 0.00 0.00 0.00 2.57
3424 3617 6.146837 GCTCTAATCACTAATCATTCACGCAT 59.853 38.462 0.00 0.00 0.00 4.73
3444 3637 0.393402 TAGTTCAGACGGCCGCTCTA 60.393 55.000 28.58 16.78 0.00 2.43
3449 3642 1.504359 TTGTTTAGTTCAGACGGCCG 58.496 50.000 26.86 26.86 0.00 6.13
3450 3643 2.350484 GCTTTGTTTAGTTCAGACGGCC 60.350 50.000 0.00 0.00 0.00 6.13
3451 3644 2.661979 CGCTTTGTTTAGTTCAGACGGC 60.662 50.000 0.00 0.00 0.00 5.68
3452 3645 2.661979 GCGCTTTGTTTAGTTCAGACGG 60.662 50.000 0.00 0.00 0.00 4.79
3455 3648 1.529438 CGGCGCTTTGTTTAGTTCAGA 59.471 47.619 7.64 0.00 0.00 3.27
3458 3651 0.237498 AGCGGCGCTTTGTTTAGTTC 59.763 50.000 31.35 0.00 33.89 3.01
3480 3673 3.086600 CAGACCCAGCTCCCCTCC 61.087 72.222 0.00 0.00 0.00 4.30
3481 3674 2.905676 ATCCAGACCCAGCTCCCCTC 62.906 65.000 0.00 0.00 0.00 4.30
3482 3675 2.905676 GATCCAGACCCAGCTCCCCT 62.906 65.000 0.00 0.00 0.00 4.79
3483 3676 2.367512 ATCCAGACCCAGCTCCCC 60.368 66.667 0.00 0.00 0.00 4.81
3484 3677 2.447714 GGATCCAGACCCAGCTCCC 61.448 68.421 6.95 0.00 0.00 4.30
3485 3678 1.059006 ATGGATCCAGACCCAGCTCC 61.059 60.000 21.33 0.00 35.67 4.70
3486 3679 0.108207 CATGGATCCAGACCCAGCTC 59.892 60.000 21.33 0.00 35.67 4.09
3487 3680 1.351080 CCATGGATCCAGACCCAGCT 61.351 60.000 21.33 0.00 35.67 4.24
3488 3681 1.150081 CCATGGATCCAGACCCAGC 59.850 63.158 21.33 0.00 35.67 4.85
3489 3682 1.150081 GCCATGGATCCAGACCCAG 59.850 63.158 21.33 5.90 35.67 4.45
3490 3683 1.619057 TGCCATGGATCCAGACCCA 60.619 57.895 21.33 11.35 36.79 4.51
3491 3684 1.152881 GTGCCATGGATCCAGACCC 60.153 63.158 21.33 8.86 0.00 4.46
3492 3685 0.184451 ATGTGCCATGGATCCAGACC 59.816 55.000 21.33 10.64 0.00 3.85



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

AutoCloner maintained by Alex Coulton.