Multiple sequence alignment - TraesCS3A01G208000

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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 TraesCS3A01G208000 chr3A 100.000 3761 0 0 1 3761 366880233 366876473 0.000000e+00 6946
1 TraesCS3A01G208000 chr3A 96.047 2555 97 4 771 3324 740089822 740087271 0.000000e+00 4156
2 TraesCS3A01G208000 chr3A 97.210 1828 49 1 771 2596 60827172 60825345 0.000000e+00 3092
3 TraesCS3A01G208000 chr3A 92.318 2187 126 13 1056 3234 443101632 443099480 0.000000e+00 3070
4 TraesCS3A01G208000 chr3A 97.419 775 17 2 1 773 60827975 60827202 0.000000e+00 1317
5 TraesCS3A01G208000 chr3A 97.368 190 5 0 3572 3761 740087148 740086959 1.300000e-84 324
6 TraesCS3A01G208000 chr7A 95.689 2969 110 6 771 3735 665978246 665981200 0.000000e+00 4758
7 TraesCS3A01G208000 chr7A 96.216 2616 93 3 771 3382 94445070 94442457 0.000000e+00 4277
8 TraesCS3A01G208000 chr7A 90.503 1232 82 7 2560 3761 620527674 620528900 0.000000e+00 1594
9 TraesCS3A01G208000 chr7A 97.545 774 13 4 1 773 665977448 665978216 0.000000e+00 1319
10 TraesCS3A01G208000 chr7A 96.061 787 16 2 1 773 546231726 546232511 0.000000e+00 1267
11 TraesCS3A01G208000 chr7A 93.423 745 47 2 2638 3381 492494304 492495047 0.000000e+00 1103
12 TraesCS3A01G208000 chr7A 87.858 593 41 3 3198 3761 94442754 94442164 0.000000e+00 667
13 TraesCS3A01G208000 chr7A 87.004 554 43 1 3237 3761 492494787 492495340 6.950000e-167 597
14 TraesCS3A01G208000 chr7A 88.787 437 48 1 2918 3354 546250402 546250837 5.530000e-148 534
15 TraesCS3A01G208000 chr7A 88.485 165 16 3 3335 3497 665980580 665980743 2.960000e-46 196
16 TraesCS3A01G208000 chr4A 95.724 2947 96 5 831 3761 534190190 534187258 0.000000e+00 4717
17 TraesCS3A01G208000 chr4A 95.076 2559 117 8 771 3324 311670415 311667861 0.000000e+00 4019
18 TraesCS3A01G208000 chr4A 97.416 774 18 2 1 773 534199661 534198889 0.000000e+00 1317
19 TraesCS3A01G208000 chr2A 96.825 2614 80 2 771 3382 690342761 690345373 0.000000e+00 4364
20 TraesCS3A01G208000 chr2A 97.671 773 17 1 1 773 690341960 690342731 0.000000e+00 1327
21 TraesCS3A01G208000 chr2A 94.690 565 26 4 3198 3761 690345076 690345637 0.000000e+00 874
22 TraesCS3A01G208000 chr5A 96.734 2266 72 2 771 3035 30144341 30146605 0.000000e+00 3773
23 TraesCS3A01G208000 chr5A 97.804 774 15 2 1 773 523619989 523620761 0.000000e+00 1334
24 TraesCS3A01G208000 chr5A 90.484 578 39 6 3198 3761 523622790 523623365 0.000000e+00 749
25 TraesCS3A01G208000 chr5A 96.154 442 15 2 1 441 612761054 612761494 0.000000e+00 721
26 TraesCS3A01G208000 chr5A 97.368 190 5 0 3572 3761 27605256 27605445 1.300000e-84 324
27 TraesCS3A01G208000 chr1A 94.522 2008 104 3 771 2776 72585422 72587425 0.000000e+00 3094
28 TraesCS3A01G208000 chr1A 88.384 594 38 7 3197 3761 49342320 49341729 0.000000e+00 686
29 TraesCS3A01G208000 chr3B 90.979 776 62 7 1 773 8358754 8359524 0.000000e+00 1038
30 TraesCS3A01G208000 chr5B 87.179 780 85 10 1 773 113329163 113329934 0.000000e+00 872
31 TraesCS3A01G208000 chr5D 86.410 780 84 12 1 773 104114339 104115103 0.000000e+00 833
32 TraesCS3A01G208000 chr6D 98.571 70 1 0 771 840 448956014 448955945 1.420000e-24 124


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 TraesCS3A01G208000 chr3A 366876473 366880233 3760 True 6946.000000 6946 100.000000 1 3761 1 chr3A.!!$R1 3760
1 TraesCS3A01G208000 chr3A 443099480 443101632 2152 True 3070.000000 3070 92.318000 1056 3234 1 chr3A.!!$R2 2178
2 TraesCS3A01G208000 chr3A 740086959 740089822 2863 True 2240.000000 4156 96.707500 771 3761 2 chr3A.!!$R4 2990
3 TraesCS3A01G208000 chr3A 60825345 60827975 2630 True 2204.500000 3092 97.314500 1 2596 2 chr3A.!!$R3 2595
4 TraesCS3A01G208000 chr7A 94442164 94445070 2906 True 2472.000000 4277 92.037000 771 3761 2 chr7A.!!$R1 2990
5 TraesCS3A01G208000 chr7A 665977448 665981200 3752 False 2091.000000 4758 93.906333 1 3735 3 chr7A.!!$F5 3734
6 TraesCS3A01G208000 chr7A 620527674 620528900 1226 False 1594.000000 1594 90.503000 2560 3761 1 chr7A.!!$F3 1201
7 TraesCS3A01G208000 chr7A 546231726 546232511 785 False 1267.000000 1267 96.061000 1 773 1 chr7A.!!$F1 772
8 TraesCS3A01G208000 chr7A 492494304 492495340 1036 False 850.000000 1103 90.213500 2638 3761 2 chr7A.!!$F4 1123
9 TraesCS3A01G208000 chr4A 534187258 534190190 2932 True 4717.000000 4717 95.724000 831 3761 1 chr4A.!!$R2 2930
10 TraesCS3A01G208000 chr4A 311667861 311670415 2554 True 4019.000000 4019 95.076000 771 3324 1 chr4A.!!$R1 2553
11 TraesCS3A01G208000 chr4A 534198889 534199661 772 True 1317.000000 1317 97.416000 1 773 1 chr4A.!!$R3 772
12 TraesCS3A01G208000 chr2A 690341960 690345637 3677 False 2188.333333 4364 96.395333 1 3761 3 chr2A.!!$F1 3760
13 TraesCS3A01G208000 chr5A 30144341 30146605 2264 False 3773.000000 3773 96.734000 771 3035 1 chr5A.!!$F2 2264
14 TraesCS3A01G208000 chr5A 523619989 523623365 3376 False 1041.500000 1334 94.144000 1 3761 2 chr5A.!!$F4 3760
15 TraesCS3A01G208000 chr1A 72585422 72587425 2003 False 3094.000000 3094 94.522000 771 2776 1 chr1A.!!$F1 2005
16 TraesCS3A01G208000 chr1A 49341729 49342320 591 True 686.000000 686 88.384000 3197 3761 1 chr1A.!!$R1 564
17 TraesCS3A01G208000 chr3B 8358754 8359524 770 False 1038.000000 1038 90.979000 1 773 1 chr3B.!!$F1 772
18 TraesCS3A01G208000 chr5B 113329163 113329934 771 False 872.000000 872 87.179000 1 773 1 chr5B.!!$F1 772
19 TraesCS3A01G208000 chr5D 104114339 104115103 764 False 833.000000 833 86.410000 1 773 1 chr5D.!!$F1 772

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
965 1023 2.029020 GGAATCTTTTGACCCAAGTGGC 60.029 50.0 0.00 0.00 37.83 5.01 F
1285 1343 0.889186 TTGCTCCGGAAGAACCTTGC 60.889 55.0 5.23 2.94 36.31 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2713 2784 0.834687 TTCCCCCTGTTGACGTAGCT 60.835 55.0 0.00 0.00 0.00 3.32 R
3271 3808 0.041663 ATGTTCACGAAACGTTGCCG 60.042 50.0 18.01 18.01 41.02 5.69 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
865 923 2.350772 CCATCTGGTGTTTTGTTCTCGC 60.351 50.000 0.00 0.00 0.00 5.03
965 1023 2.029020 GGAATCTTTTGACCCAAGTGGC 60.029 50.000 0.00 0.00 37.83 5.01
1160 1218 5.316327 TGTGTGTAAAAATGTGCAGTTGA 57.684 34.783 0.00 0.00 0.00 3.18
1285 1343 0.889186 TTGCTCCGGAAGAACCTTGC 60.889 55.000 5.23 2.94 36.31 4.01
1396 1461 5.112129 GGGGGTATAAGGCATACATAAGG 57.888 47.826 0.00 0.00 41.26 2.69
1645 1716 2.356382 TCGTGTTTCGAAGCAATTTGGT 59.644 40.909 16.65 0.00 45.98 3.67
1712 1783 6.127423 GGTGCTACATAGGTGAGAGTTTCTTA 60.127 42.308 0.00 0.00 0.00 2.10
1773 1844 7.216494 TGAAAATGATGCCGATACTTCTCATA 58.784 34.615 0.00 0.00 0.00 2.15
1860 1931 3.609853 GGTAGACATGTGGAATGCTCAA 58.390 45.455 1.15 0.00 0.00 3.02
1892 1963 4.633126 CCGAATTGAAGATGATCACACACT 59.367 41.667 0.00 0.00 0.00 3.55
1902 1973 3.727726 TGATCACACACTTGACAACGAT 58.272 40.909 0.00 0.00 0.00 3.73
2151 2222 5.029807 TCATGAGTGGTGTGTCACTTAAA 57.970 39.130 4.27 0.00 46.76 1.52
2163 2234 8.573035 GGTGTGTCACTTAAATTTTATTCAGGA 58.427 33.333 4.27 0.00 34.40 3.86
2234 2305 2.037251 GCACCTGGTAGAGAAACAGACA 59.963 50.000 0.00 0.00 34.21 3.41
2351 2422 3.405831 CTCTGCAGAAGGTTGTGAATCA 58.594 45.455 18.85 0.00 0.00 2.57
2467 2538 2.809665 GCTCATCCATCTTCGAGCCAAT 60.810 50.000 0.00 0.00 44.06 3.16
2498 2569 1.218047 CCGCTCGTCCATCTTCCAA 59.782 57.895 0.00 0.00 0.00 3.53
2541 2612 1.935873 CGAGCACGGATTGATGAACAT 59.064 47.619 0.00 0.00 35.72 2.71
2692 2763 1.475280 CAAGAACCATCCGACGTCCTA 59.525 52.381 10.58 0.00 0.00 2.94
2708 2779 2.763448 GTCCTAGATGGCAGAACACTCT 59.237 50.000 0.00 0.00 35.26 3.24
2713 2784 3.974719 AGATGGCAGAACACTCTAGAGA 58.025 45.455 26.57 0.31 0.00 3.10
3055 3129 1.076485 GGAATGGACATGGGCAGCT 60.076 57.895 0.00 0.00 0.00 4.24
3227 3764 2.593436 CCACGGAGGGCGTTTTGT 60.593 61.111 0.00 0.00 0.00 2.83
3228 3765 2.190841 CCACGGAGGGCGTTTTGTT 61.191 57.895 0.00 0.00 0.00 2.83
3229 3766 1.008995 CACGGAGGGCGTTTTGTTG 60.009 57.895 0.00 0.00 0.00 3.33
3230 3767 1.452470 ACGGAGGGCGTTTTGTTGT 60.452 52.632 0.00 0.00 0.00 3.32
3231 3768 0.179051 ACGGAGGGCGTTTTGTTGTA 60.179 50.000 0.00 0.00 0.00 2.41
3232 3769 0.515564 CGGAGGGCGTTTTGTTGTAG 59.484 55.000 0.00 0.00 0.00 2.74
3233 3770 0.879090 GGAGGGCGTTTTGTTGTAGG 59.121 55.000 0.00 0.00 0.00 3.18
3234 3771 0.879090 GAGGGCGTTTTGTTGTAGGG 59.121 55.000 0.00 0.00 0.00 3.53
3235 3772 0.184211 AGGGCGTTTTGTTGTAGGGT 59.816 50.000 0.00 0.00 0.00 4.34
3236 3773 0.312729 GGGCGTTTTGTTGTAGGGTG 59.687 55.000 0.00 0.00 0.00 4.61
3237 3774 0.312729 GGCGTTTTGTTGTAGGGTGG 59.687 55.000 0.00 0.00 0.00 4.61
3238 3775 1.310904 GCGTTTTGTTGTAGGGTGGA 58.689 50.000 0.00 0.00 0.00 4.02
3239 3776 1.677052 GCGTTTTGTTGTAGGGTGGAA 59.323 47.619 0.00 0.00 0.00 3.53
3240 3777 2.099427 GCGTTTTGTTGTAGGGTGGAAA 59.901 45.455 0.00 0.00 0.00 3.13
3241 3778 3.697982 CGTTTTGTTGTAGGGTGGAAAC 58.302 45.455 0.00 0.00 0.00 2.78
3242 3779 3.697982 GTTTTGTTGTAGGGTGGAAACG 58.302 45.455 0.00 0.00 0.00 3.60
3243 3780 1.310904 TTGTTGTAGGGTGGAAACGC 58.689 50.000 0.00 0.00 41.20 4.84
3253 3790 3.355077 TGGAAACGCCATGGACATT 57.645 47.368 18.40 5.94 43.33 2.71
3254 3791 0.887247 TGGAAACGCCATGGACATTG 59.113 50.000 18.40 1.11 43.33 2.82
3255 3792 0.173255 GGAAACGCCATGGACATTGG 59.827 55.000 18.40 0.00 36.34 3.16
3256 3793 0.458370 GAAACGCCATGGACATTGGC 60.458 55.000 18.40 4.61 44.69 4.52
3259 3796 3.287445 GCCATGGACATTGGCGTT 58.713 55.556 18.40 0.00 39.06 4.84
3260 3797 1.591183 GCCATGGACATTGGCGTTT 59.409 52.632 18.40 0.00 39.06 3.60
3261 3798 0.458370 GCCATGGACATTGGCGTTTC 60.458 55.000 18.40 0.00 39.06 2.78
3262 3799 0.887247 CCATGGACATTGGCGTTTCA 59.113 50.000 5.56 0.00 0.00 2.69
3263 3800 1.135315 CCATGGACATTGGCGTTTCAG 60.135 52.381 5.56 0.00 0.00 3.02
3264 3801 1.135315 CATGGACATTGGCGTTTCAGG 60.135 52.381 0.00 0.00 0.00 3.86
3265 3802 0.179004 TGGACATTGGCGTTTCAGGT 60.179 50.000 0.00 0.00 0.00 4.00
3266 3803 0.240945 GGACATTGGCGTTTCAGGTG 59.759 55.000 0.00 0.00 0.00 4.00
3267 3804 0.951558 GACATTGGCGTTTCAGGTGT 59.048 50.000 0.00 0.00 0.00 4.16
3268 3805 0.667993 ACATTGGCGTTTCAGGTGTG 59.332 50.000 0.00 0.00 0.00 3.82
3269 3806 0.950836 CATTGGCGTTTCAGGTGTGA 59.049 50.000 0.00 0.00 0.00 3.58
3270 3807 1.069022 CATTGGCGTTTCAGGTGTGAG 60.069 52.381 0.00 0.00 32.98 3.51
3271 3808 1.444119 TTGGCGTTTCAGGTGTGAGC 61.444 55.000 0.00 0.00 32.98 4.26
3272 3809 2.551270 GCGTTTCAGGTGTGAGCG 59.449 61.111 0.00 0.00 36.55 5.03
3273 3810 2.954753 GCGTTTCAGGTGTGAGCGG 61.955 63.158 0.00 0.00 35.05 5.52
3274 3811 2.946762 GTTTCAGGTGTGAGCGGC 59.053 61.111 0.00 0.00 32.98 6.53
3275 3812 1.891919 GTTTCAGGTGTGAGCGGCA 60.892 57.895 1.45 0.00 32.98 5.69
3276 3813 1.153066 TTTCAGGTGTGAGCGGCAA 60.153 52.632 1.45 0.00 32.98 4.52
3277 3814 1.444119 TTTCAGGTGTGAGCGGCAAC 61.444 55.000 1.45 0.25 32.98 4.17
3290 3827 3.837669 GGCAACGTTTCGTGAACAT 57.162 47.368 0.00 0.00 39.99 2.71
3291 3828 1.394697 GGCAACGTTTCGTGAACATG 58.605 50.000 0.00 0.00 39.99 3.21
3292 3829 1.394697 GCAACGTTTCGTGAACATGG 58.605 50.000 0.00 0.00 39.99 3.66
3293 3830 1.394697 CAACGTTTCGTGAACATGGC 58.605 50.000 0.00 0.00 39.99 4.40
3294 3831 0.309612 AACGTTTCGTGAACATGGCC 59.690 50.000 0.00 0.00 39.99 5.36
3295 3832 1.209127 CGTTTCGTGAACATGGCCC 59.791 57.895 0.00 0.00 38.18 5.80
3296 3833 1.511318 CGTTTCGTGAACATGGCCCA 61.511 55.000 0.00 0.00 38.18 5.36
3297 3834 0.671251 GTTTCGTGAACATGGCCCAA 59.329 50.000 0.00 0.00 38.18 4.12
3298 3835 0.671251 TTTCGTGAACATGGCCCAAC 59.329 50.000 0.00 0.00 0.00 3.77
3299 3836 1.175983 TTCGTGAACATGGCCCAACC 61.176 55.000 0.00 0.00 39.84 3.77
3309 3846 2.360475 GCCCAACCAGCCTCTGTC 60.360 66.667 0.00 0.00 0.00 3.51
3310 3847 2.900106 GCCCAACCAGCCTCTGTCT 61.900 63.158 0.00 0.00 0.00 3.41
3311 3848 1.763770 CCCAACCAGCCTCTGTCTT 59.236 57.895 0.00 0.00 0.00 3.01
3312 3849 0.984230 CCCAACCAGCCTCTGTCTTA 59.016 55.000 0.00 0.00 0.00 2.10
3313 3850 1.351017 CCCAACCAGCCTCTGTCTTAA 59.649 52.381 0.00 0.00 0.00 1.85
3314 3851 2.224769 CCCAACCAGCCTCTGTCTTAAA 60.225 50.000 0.00 0.00 0.00 1.52
3315 3852 3.077359 CCAACCAGCCTCTGTCTTAAAG 58.923 50.000 0.00 0.00 0.00 1.85
3316 3853 3.244561 CCAACCAGCCTCTGTCTTAAAGA 60.245 47.826 0.00 0.00 0.00 2.52
3317 3854 4.389374 CAACCAGCCTCTGTCTTAAAGAA 58.611 43.478 0.00 0.00 0.00 2.52
3318 3855 4.706842 ACCAGCCTCTGTCTTAAAGAAA 57.293 40.909 0.00 0.00 0.00 2.52
3319 3856 4.390264 ACCAGCCTCTGTCTTAAAGAAAC 58.610 43.478 0.00 0.00 0.00 2.78
3320 3857 3.433615 CCAGCCTCTGTCTTAAAGAAACG 59.566 47.826 0.00 0.00 0.00 3.60
3321 3858 3.067833 AGCCTCTGTCTTAAAGAAACGC 58.932 45.455 0.00 0.00 0.00 4.84
3322 3859 2.159824 GCCTCTGTCTTAAAGAAACGCC 59.840 50.000 0.00 0.00 0.00 5.68
3323 3860 3.399330 CCTCTGTCTTAAAGAAACGCCA 58.601 45.455 0.00 0.00 0.00 5.69
3324 3861 4.003648 CCTCTGTCTTAAAGAAACGCCAT 58.996 43.478 0.00 0.00 0.00 4.40
3325 3862 4.093556 CCTCTGTCTTAAAGAAACGCCATC 59.906 45.833 0.00 0.00 0.00 3.51
3326 3863 4.000988 TCTGTCTTAAAGAAACGCCATCC 58.999 43.478 0.00 0.00 0.00 3.51
3327 3864 3.078837 TGTCTTAAAGAAACGCCATCCC 58.921 45.455 0.00 0.00 0.00 3.85
3328 3865 3.078837 GTCTTAAAGAAACGCCATCCCA 58.921 45.455 0.00 0.00 0.00 4.37
3329 3866 3.078837 TCTTAAAGAAACGCCATCCCAC 58.921 45.455 0.00 0.00 0.00 4.61
3330 3867 1.444836 TAAAGAAACGCCATCCCACG 58.555 50.000 0.00 0.00 0.00 4.94
3331 3868 1.241315 AAAGAAACGCCATCCCACGG 61.241 55.000 0.00 0.00 0.00 4.94
3332 3869 2.046700 GAAACGCCATCCCACGGA 60.047 61.111 0.00 0.00 35.55 4.69
3333 3870 2.046314 AAACGCCATCCCACGGAG 60.046 61.111 0.00 0.00 34.05 4.63
3334 3871 3.622060 AAACGCCATCCCACGGAGG 62.622 63.158 0.00 0.00 34.05 4.30
3393 4046 2.424842 TTTCTGGGGTGAGCGGCAAT 62.425 55.000 1.45 0.00 0.00 3.56
3417 4070 0.700564 AGTGAACATGTCCCAGCCAT 59.299 50.000 0.00 0.00 0.00 4.40
3431 4084 1.280133 CAGCCATCCTCTGTCTTCCAA 59.720 52.381 0.00 0.00 0.00 3.53
3529 4182 0.531753 GCCCATTTGTTTGGCGTTGT 60.532 50.000 0.00 0.00 35.08 3.32
3740 4450 4.942944 TCACCACATAAAGGAGTCTAGGA 58.057 43.478 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 9.574516 AACACAAGGAGTATATGTCTTCTTTTT 57.425 29.630 1.93 0.00 29.27 1.94
70 71 9.574516 AAACACAAGGAGTATATGTCTTCTTTT 57.425 29.630 1.93 0.00 29.27 2.27
316 337 9.983024 TCCTACAAAATAAGGTCAATGGATTTA 57.017 29.630 0.00 0.00 34.30 1.40
685 711 1.949525 GAGCAAGGTGAAAAGAGTGCA 59.050 47.619 0.00 0.00 34.44 4.57
812 870 5.832595 TCCTTCTTTGTTTCATGAATCCACA 59.167 36.000 9.40 8.16 0.00 4.17
865 923 5.107220 ACTCGTAAAAATGTTCTTGTAGCCG 60.107 40.000 0.00 0.00 0.00 5.52
965 1023 3.411351 CCGTGCCGTCAGGAAACG 61.411 66.667 6.32 6.32 43.99 3.60
1146 1204 2.543653 GCTCCGTTCAACTGCACATTTT 60.544 45.455 0.00 0.00 0.00 1.82
1160 1218 2.111384 ACTCCTCATACATGCTCCGTT 58.889 47.619 0.00 0.00 0.00 4.44
1285 1343 2.325082 CCCGTCAAAAGGCCACTCG 61.325 63.158 5.01 0.40 0.00 4.18
1376 1441 5.629366 GCTCCCTTATGTATGCCTTATACCC 60.629 48.000 0.00 0.00 40.80 3.69
1396 1461 4.253685 TGTAAGTAAGCATGTCAAGCTCC 58.746 43.478 2.51 0.00 42.53 4.70
1645 1716 1.888172 CGGGGTGCGTTGTTGTACA 60.888 57.895 0.00 0.00 0.00 2.90
1712 1783 9.066892 GGTTACACATTGATCAACATATGGTAT 57.933 33.333 11.07 0.00 0.00 2.73
1773 1844 1.590147 CCGGCTCGTCCTACAAAGT 59.410 57.895 0.00 0.00 0.00 2.66
1860 1931 3.085952 TCTTCAATTCGGGCATTCCTT 57.914 42.857 0.00 0.00 0.00 3.36
1892 1963 1.002624 GCCCCCTCATCGTTGTCAA 60.003 57.895 0.00 0.00 0.00 3.18
1902 1973 1.856259 TGCCTTAAATATGCCCCCTCA 59.144 47.619 0.00 0.00 0.00 3.86
2123 2194 3.876914 TGACACACCACTCATGAAGAAAC 59.123 43.478 0.00 0.00 0.00 2.78
2151 2222 4.222124 AGCTCCGTGTCCTGAATAAAAT 57.778 40.909 0.00 0.00 0.00 1.82
2163 2234 1.781786 ACATCTCCATAGCTCCGTGT 58.218 50.000 0.00 0.00 0.00 4.49
2234 2305 7.588169 ACCTGTAGAGTACTCCTAATGAGAAT 58.412 38.462 19.38 0.00 44.42 2.40
2240 2311 7.519927 CCTCTAACCTGTAGAGTACTCCTAAT 58.480 42.308 19.38 3.39 39.42 1.73
2351 2422 2.106683 GCGGCTAGTGTTCGGCAAT 61.107 57.895 0.00 0.00 0.00 3.56
2467 2538 4.357947 AGCGGAAGAAGCGCGTGA 62.358 61.111 8.43 0.00 40.04 4.35
2541 2612 4.022603 CTGTCTCCTCCTCTTCATCTTCA 58.977 47.826 0.00 0.00 0.00 3.02
2692 2763 3.953612 CTCTCTAGAGTGTTCTGCCATCT 59.046 47.826 19.21 0.00 37.40 2.90
2708 2779 2.366533 CCCTGTTGACGTAGCTCTCTA 58.633 52.381 0.00 0.00 0.00 2.43
2713 2784 0.834687 TTCCCCCTGTTGACGTAGCT 60.835 55.000 0.00 0.00 0.00 3.32
3055 3129 0.682532 TGCAGAACACAGCAAACCCA 60.683 50.000 0.00 0.00 37.90 4.51
3090 3164 0.179051 TAAACGCCGTTGTCCTTGGT 60.179 50.000 1.95 0.00 0.00 3.67
3222 3759 2.099427 GCGTTTCCACCCTACAACAAAA 59.901 45.455 0.00 0.00 0.00 2.44
3223 3760 1.677052 GCGTTTCCACCCTACAACAAA 59.323 47.619 0.00 0.00 0.00 2.83
3224 3761 1.310904 GCGTTTCCACCCTACAACAA 58.689 50.000 0.00 0.00 0.00 2.83
3225 3762 0.535553 GGCGTTTCCACCCTACAACA 60.536 55.000 0.00 0.00 34.01 3.33
3226 3763 0.535553 TGGCGTTTCCACCCTACAAC 60.536 55.000 0.00 0.00 40.72 3.32
3227 3764 1.837789 TGGCGTTTCCACCCTACAA 59.162 52.632 0.00 0.00 40.72 2.41
3228 3765 3.564775 TGGCGTTTCCACCCTACA 58.435 55.556 0.00 0.00 40.72 2.74
3236 3773 0.173255 CCAATGTCCATGGCGTTTCC 59.827 55.000 6.96 0.00 0.00 3.13
3237 3774 3.719699 CCAATGTCCATGGCGTTTC 57.280 52.632 6.96 0.00 0.00 2.78
3243 3780 0.887247 TGAAACGCCAATGTCCATGG 59.113 50.000 4.97 4.97 41.08 3.66
3244 3781 1.135315 CCTGAAACGCCAATGTCCATG 60.135 52.381 0.00 0.00 0.00 3.66
3245 3782 1.176527 CCTGAAACGCCAATGTCCAT 58.823 50.000 0.00 0.00 0.00 3.41
3246 3783 0.179004 ACCTGAAACGCCAATGTCCA 60.179 50.000 0.00 0.00 0.00 4.02
3247 3784 0.240945 CACCTGAAACGCCAATGTCC 59.759 55.000 0.00 0.00 0.00 4.02
3248 3785 0.951558 ACACCTGAAACGCCAATGTC 59.048 50.000 0.00 0.00 0.00 3.06
3249 3786 0.667993 CACACCTGAAACGCCAATGT 59.332 50.000 0.00 0.00 0.00 2.71
3250 3787 0.950836 TCACACCTGAAACGCCAATG 59.049 50.000 0.00 0.00 0.00 2.82
3251 3788 1.238439 CTCACACCTGAAACGCCAAT 58.762 50.000 0.00 0.00 0.00 3.16
3252 3789 1.444119 GCTCACACCTGAAACGCCAA 61.444 55.000 0.00 0.00 0.00 4.52
3253 3790 1.891919 GCTCACACCTGAAACGCCA 60.892 57.895 0.00 0.00 0.00 5.69
3254 3791 2.946762 GCTCACACCTGAAACGCC 59.053 61.111 0.00 0.00 0.00 5.68
3255 3792 2.551270 CGCTCACACCTGAAACGC 59.449 61.111 0.00 0.00 0.00 4.84
3256 3793 2.954753 GCCGCTCACACCTGAAACG 61.955 63.158 0.00 0.00 0.00 3.60
3257 3794 1.444119 TTGCCGCTCACACCTGAAAC 61.444 55.000 0.00 0.00 0.00 2.78
3258 3795 1.153066 TTGCCGCTCACACCTGAAA 60.153 52.632 0.00 0.00 0.00 2.69
3259 3796 1.891919 GTTGCCGCTCACACCTGAA 60.892 57.895 0.00 0.00 0.00 3.02
3260 3797 2.280797 GTTGCCGCTCACACCTGA 60.281 61.111 0.00 0.00 0.00 3.86
3261 3798 3.716006 CGTTGCCGCTCACACCTG 61.716 66.667 0.00 0.00 0.00 4.00
3262 3799 3.750373 AACGTTGCCGCTCACACCT 62.750 57.895 0.00 0.00 37.70 4.00
3263 3800 2.711185 GAAACGTTGCCGCTCACACC 62.711 60.000 0.00 0.00 37.70 4.16
3264 3801 1.368850 GAAACGTTGCCGCTCACAC 60.369 57.895 0.00 0.00 37.70 3.82
3265 3802 2.876879 CGAAACGTTGCCGCTCACA 61.877 57.895 0.00 0.00 37.70 3.58
3266 3803 2.127758 CGAAACGTTGCCGCTCAC 60.128 61.111 0.00 0.00 37.70 3.51
3267 3804 2.586635 ACGAAACGTTGCCGCTCA 60.587 55.556 19.09 0.00 36.35 4.26
3268 3805 2.096481 TTCACGAAACGTTGCCGCTC 62.096 55.000 19.09 5.25 38.32 5.03
3269 3806 2.174969 TTCACGAAACGTTGCCGCT 61.175 52.632 19.09 7.57 38.32 5.52
3270 3807 2.001880 GTTCACGAAACGTTGCCGC 61.002 57.895 19.09 2.73 38.32 6.53
3271 3808 0.041663 ATGTTCACGAAACGTTGCCG 60.042 50.000 18.01 18.01 41.02 5.69
3272 3809 1.394697 CATGTTCACGAAACGTTGCC 58.605 50.000 0.00 0.00 41.02 4.52
3273 3810 1.394697 CCATGTTCACGAAACGTTGC 58.605 50.000 0.00 0.00 41.02 4.17
3274 3811 1.394697 GCCATGTTCACGAAACGTTG 58.605 50.000 0.00 0.00 41.02 4.10
3275 3812 0.309612 GGCCATGTTCACGAAACGTT 59.690 50.000 0.00 0.00 41.02 3.99
3276 3813 1.512156 GGGCCATGTTCACGAAACGT 61.512 55.000 4.39 0.00 41.02 3.99
3277 3814 1.209127 GGGCCATGTTCACGAAACG 59.791 57.895 4.39 0.00 41.02 3.60
3278 3815 0.671251 TTGGGCCATGTTCACGAAAC 59.329 50.000 7.26 0.00 38.43 2.78
3279 3816 0.671251 GTTGGGCCATGTTCACGAAA 59.329 50.000 7.26 0.00 0.00 3.46
3280 3817 1.175983 GGTTGGGCCATGTTCACGAA 61.176 55.000 7.26 0.00 37.17 3.85
3281 3818 1.602323 GGTTGGGCCATGTTCACGA 60.602 57.895 7.26 0.00 37.17 4.35
3282 3819 1.900981 TGGTTGGGCCATGTTCACG 60.901 57.895 7.26 0.00 43.61 4.35
3283 3820 4.189539 TGGTTGGGCCATGTTCAC 57.810 55.556 7.26 0.86 43.61 3.18
3292 3829 2.360475 GACAGAGGCTGGTTGGGC 60.360 66.667 0.00 0.00 35.51 5.36
3293 3830 0.984230 TAAGACAGAGGCTGGTTGGG 59.016 55.000 0.00 0.00 35.51 4.12
3294 3831 2.859165 TTAAGACAGAGGCTGGTTGG 57.141 50.000 0.00 0.00 35.51 3.77
3295 3832 4.008074 TCTTTAAGACAGAGGCTGGTTG 57.992 45.455 0.00 0.00 35.51 3.77
3296 3833 4.706842 TTCTTTAAGACAGAGGCTGGTT 57.293 40.909 0.00 0.00 35.51 3.67
3297 3834 4.390264 GTTTCTTTAAGACAGAGGCTGGT 58.610 43.478 0.00 0.00 35.51 4.00
3298 3835 3.433615 CGTTTCTTTAAGACAGAGGCTGG 59.566 47.826 0.00 0.00 35.51 4.85
3299 3836 3.120511 GCGTTTCTTTAAGACAGAGGCTG 60.121 47.826 0.00 0.00 37.52 4.85
3300 3837 3.067833 GCGTTTCTTTAAGACAGAGGCT 58.932 45.455 0.00 0.00 0.00 4.58
3301 3838 2.159824 GGCGTTTCTTTAAGACAGAGGC 59.840 50.000 0.00 1.78 0.00 4.70
3302 3839 3.399330 TGGCGTTTCTTTAAGACAGAGG 58.601 45.455 0.00 0.00 0.00 3.69
3303 3840 4.093556 GGATGGCGTTTCTTTAAGACAGAG 59.906 45.833 0.00 0.00 0.00 3.35
3304 3841 4.000988 GGATGGCGTTTCTTTAAGACAGA 58.999 43.478 0.00 0.00 0.00 3.41
3305 3842 3.127030 GGGATGGCGTTTCTTTAAGACAG 59.873 47.826 0.00 0.00 0.00 3.51
3306 3843 3.078837 GGGATGGCGTTTCTTTAAGACA 58.921 45.455 0.00 0.00 0.00 3.41
3307 3844 3.078837 TGGGATGGCGTTTCTTTAAGAC 58.921 45.455 0.00 0.00 0.00 3.01
3308 3845 3.078837 GTGGGATGGCGTTTCTTTAAGA 58.921 45.455 0.00 0.00 0.00 2.10
3309 3846 2.159572 CGTGGGATGGCGTTTCTTTAAG 60.160 50.000 0.00 0.00 0.00 1.85
3310 3847 1.807742 CGTGGGATGGCGTTTCTTTAA 59.192 47.619 0.00 0.00 0.00 1.52
3311 3848 1.444836 CGTGGGATGGCGTTTCTTTA 58.555 50.000 0.00 0.00 0.00 1.85
3312 3849 1.241315 CCGTGGGATGGCGTTTCTTT 61.241 55.000 0.00 0.00 0.00 2.52
3313 3850 1.674322 CCGTGGGATGGCGTTTCTT 60.674 57.895 0.00 0.00 0.00 2.52
3314 3851 2.046314 CCGTGGGATGGCGTTTCT 60.046 61.111 0.00 0.00 0.00 2.52
3315 3852 2.046700 TCCGTGGGATGGCGTTTC 60.047 61.111 0.00 0.00 0.00 2.78
3316 3853 2.046314 CTCCGTGGGATGGCGTTT 60.046 61.111 0.00 0.00 0.00 3.60
3317 3854 4.096003 CCTCCGTGGGATGGCGTT 62.096 66.667 0.00 0.00 0.00 4.84
3329 3866 0.515564 CTACAACAAAACGCCCTCCG 59.484 55.000 0.00 0.00 44.21 4.63
3330 3867 0.879090 CCTACAACAAAACGCCCTCC 59.121 55.000 0.00 0.00 0.00 4.30
3331 3868 0.879090 CCCTACAACAAAACGCCCTC 59.121 55.000 0.00 0.00 0.00 4.30
3332 3869 0.184211 ACCCTACAACAAAACGCCCT 59.816 50.000 0.00 0.00 0.00 5.19
3333 3870 0.312729 CACCCTACAACAAAACGCCC 59.687 55.000 0.00 0.00 0.00 6.13
3334 3871 0.312729 CCACCCTACAACAAAACGCC 59.687 55.000 0.00 0.00 0.00 5.68
3335 3872 1.310904 TCCACCCTACAACAAAACGC 58.689 50.000 0.00 0.00 0.00 4.84
3336 3873 3.697982 GTTTCCACCCTACAACAAAACG 58.302 45.455 0.00 0.00 0.00 3.60
3337 3874 3.697982 CGTTTCCACCCTACAACAAAAC 58.302 45.455 0.00 0.00 0.00 2.43
3417 4070 2.218603 GCGTTTTTGGAAGACAGAGGA 58.781 47.619 0.00 0.00 0.00 3.71
3529 4182 4.950475 TGTTTTGACACCCTGTTATGACAA 59.050 37.500 0.00 0.00 34.85 3.18


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

AutoCloner maintained by Alex Coulton.